UniProt Knowledgebase
Names
More detailed information about this field from each metasource.
UniProt Knowledgebase
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
UniProtKB
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:46.405831
UniProt
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: The Universal Protein Resource; editing status 2020-05-27; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BW2M last accessed: 2022-11-04
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The Universal Protein Resource
metasource: re3data.org
version: re3data.org: The Universal Protein Resource; editing status 2020-05-27; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BW2M last accessed: 2022-11-04
uniprotkb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:46.405831
Names
More detailed information about this field from each metasource.
UniProt Knowledgebase
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
UniProtKB
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:46.405831
UniProt
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: The Universal Protein Resource; editing status 2020-05-27; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BW2M last accessed: 2022-11-04
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The Universal Protein Resource
metasource: re3data.orgversion: re3data.org: The Universal Protein Resource; editing status 2020-05-27; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BW2M last accessed: 2022-11-04
uniprotkb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:46.405831
Other names: UniProtKB, UniProt, The Universal Protein Resource, uniprotkb
Names
More detailed information about this field from each metasource.
UniProt Knowledgebase
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
UniProtKB
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:46.405831
UniProt
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: The Universal Protein Resource; editing status 2020-05-27; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BW2M last accessed: 2022-11-04
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The Universal Protein Resource
metasource: re3data.orgversion: re3data.org: The Universal Protein Resource; editing status 2020-05-27; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BW2M last accessed: 2022-11-04
uniprotkb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:46.405831
Universal Protein resource. A database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. a central repository of protein data created by combining the Swiss-Prot, TrEMBL and PIR-PSD databases.
Description
More detailed information about this field from each metasource.
Universal Protein resource. A database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. a central repository of protein data created by combining the Swiss-Prot, TrEMBL and PIR-PSD databases.
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data. The UniProt Knowledgebase consists of two sections: a reviewed section containing manually-annotated records with information extracted from literature and curator-evaluated computational analysis (aka "UniProtKB/Swiss-Prot"), and an unreviewed section with computationally analyzed records that await full manual annotation (aka "UniProtKB/TrEMBL").
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). The UniProt Metagenomic and Environmental Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data.
metasource: re3data.orgversion: re3data.org: The Universal Protein Resource; editing status 2020-05-27; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BW2M last accessed: 2022-11-04
The central hub for the collection of functional information on proteins with accurate, consistent and rich annotation. It consists of: UniProtKB/Swiss-Prot (manually-annotated records and curator-evaluated computational analysis) and UniProtKB/TrEMBL (computationally analyzed records awaiting manual annotation).
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:46.405831
Webpage:
https://www.uniprot.orgWebpage
More detailed information about this field from each metasource.
https://www.uniprot.org
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
http://www.uniprot.org/uniprot/
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:46.405831
http://www.uniprot.org/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
https://www.uniprot.org/
metasource: re3data.orgversion: re3data.org: The Universal Protein Resource; editing status 2020-05-27; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BW2M last accessed: 2022-11-04
Licence:
Name: Creative Commons Attribution v4.0Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution v4.0
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
Creative Commons Attribution 4.0 International (CC BY 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
CC
metasource: re3data.orgversion: re3data.org: The Universal Protein Resource; editing status 2020-05-27; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BW2M last accessed: 2022-11-04
CC-BY-ND-3.0
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:46.405831
URL: https://www.uniprot.org/help/license
Licence URL
More detailed information about this field from each metasource.
https://www.uniprot.org/help/license
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
https://creativecommons.org/licenses/by/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: re3data.org
version: re3data.org: The Universal Protein Resource; editing status 2020-05-27; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BW2M last accessed: 2022-11-04
Publications:
(25)
Publications
More detailed information about this field from each metasource.
UniProt: a worldwide hub of protein knowledge
PMID: 30395287
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
UniProt: a hub for protein information
PMID: 25348405
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:46.405831
UniProt: the universal protein knowledgebase
PMID: 27899622
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
PMID: 12520024
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
UniProt: the Universal Protein knowledgebase
PMID: 14681372
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
UniProt Knowledgebase: a hub of integrated protein data
PMID: 21447597
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
UniProt: the universal protein knowledgebase
PMID: 29425356
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
Activities at the Universal Protein Resource (UniProt)
PMID: 24253303
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Universal Protein Resource (UniProt)
PMID: 15608167
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Universal Protein Resource (UniProt) in 2010
PMID: 19843607
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Universal Protein Resource (UniProt): an expanding universe of protein information
PMID: 16381842
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The universal protein resource (UniProt)
PMID: 18045787
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
Update on activities at the Universal Protein Resource (UniProt) in 2013
PMID: 23161681
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Universal Protein Resource (UniProt) 2009
PMID: 18836194
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Universal Protein Resource (UniProt)
PMID: 17142230
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
UniProtKB/Swiss-Prot
PMID: 18287689
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The UniProt-GO Annotation database in 2011
PMID: 22123736
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
Swiss-Prot: juggling between evolution and stability
PMID: 15153305
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
High-quality protein knowledge resource: SWISS-PROT and TrEMBL
PMID: 12230036
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
SWISS-PROT: connecting biomolecular knowledge via a protein database
PMID: 11488411
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
UniProt archive
PMID: 15044231
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The SWISS-PROT protein sequence database: its relevance to human molecular medical research
PMID: 9181472
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
UniProt Tools
PMID: 27010333
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gkaa1100
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkt1140
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:46.405831
Publications
More detailed information about this field from each metasource.
UniProt: a worldwide hub of protein knowledge
PMID: 30395287
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
UniProt: a hub for protein information
PMID: 25348405
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:46.405831
UniProt: the universal protein knowledgebase
PMID: 27899622
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
PMID: 12520024
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
UniProt: the Universal Protein knowledgebase
PMID: 14681372
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
UniProt Knowledgebase: a hub of integrated protein data
PMID: 21447597
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
UniProt: the universal protein knowledgebase
PMID: 29425356
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
Activities at the Universal Protein Resource (UniProt)
PMID: 24253303
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Universal Protein Resource (UniProt)
PMID: 15608167
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Universal Protein Resource (UniProt) in 2010
PMID: 19843607
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Universal Protein Resource (UniProt): an expanding universe of protein information
PMID: 16381842
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The universal protein resource (UniProt)
PMID: 18045787
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
Update on activities at the Universal Protein Resource (UniProt) in 2013
PMID: 23161681
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Universal Protein Resource (UniProt) 2009
PMID: 18836194
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Universal Protein Resource (UniProt)
PMID: 17142230
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
UniProtKB/Swiss-Prot
PMID: 18287689
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The UniProt-GO Annotation database in 2011
PMID: 22123736
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
Swiss-Prot: juggling between evolution and stability
PMID: 15153305
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
High-quality protein knowledge resource: SWISS-PROT and TrEMBL
PMID: 12230036
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
SWISS-PROT: connecting biomolecular knowledge via a protein database
PMID: 11488411
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
UniProt archive
PMID: 15044231
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
The SWISS-PROT protein sequence database: its relevance to human molecular medical research
PMID: 9181472
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
UniProt Tools
PMID: 27010333
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gkaa1100
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkt1140
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:46.405831
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UniProt: a worldwide hub of protein knowledge
PubMed citations: 2354.
2354 articles citing: UniProt: a worldwide hub of protein knowledge
Mapping the cell-membrane proteome of the SKBR3/HER2+ cell line to the cancer hallmarks. PMID:35913978
Purification and Characterization of a Novel Extracellular Haloprotease Vpr from Bacillus licheniformis Strain KB111. PMID:35910276
Identification of Vesicle Transport Proteins via Hypergraph Regularized K-Local Hyperplane Distance Nearest Neighbour Model. PMID:35910197
Mutations in SORL1 and MTHFDL1 possibly contribute to the development of Alzheimer's disease in a multigenerational Colombian Family. PMID:35905044
JAK2 Alterations in Acute Lymphoblastic Leukemia: Molecular Insights for Superior Precision Medicine Strategies. PMID:35903543
Systematic in silico discovery of novel solute carrier-like proteins from proteomes. PMID:35901096
An accurate prediction model of digenic interaction for estimating pathogenic gene pairs of human diseases. PMID:35891796
Development of a Novel Multi-Epitope Vaccine Candidate against Streptococcus Iniae Infection in Fish: An Immunoinformatics Study. PMID:35891737
In Silico Genomic and Metabolic Atlas of Limosilactobacillus reuteri DSM 20016: An Insight into Human Health. PMID:35889060
Novel Insights on Human Carbonic Anhydrase Inhibitors Based on Coumalic Acid: Design, Synthesis, Molecular Modeling Investigation, and Biological Studies. PMID:35887299
Identification of New Toxicity Mechanisms in Drug-Induced Liver Injury through Systems Pharmacology. PMID:35886075
The Fate of IgE Epitopes and Coeliac Toxic Motifs during Simulated Gastrointestinal Digestion of Pizza Base. PMID:35885243
Oxidative stress differentially impacts apical and basolateral secretion of angiogenic factors from human iPSC-derived retinal pigment epithelium cells. PMID:35882889
Structural signatures: a web server for exploring a database of and generating protein structural features from human cell lines and tissues. PMID:35881481
N- glycoproteomic profiling revealing novel coronavirus therapeutic targets potentially involved in Cepharanthine's intervention. PMID:35879945
KSTAR: An algorithm to predict patient-specific kinase activities from phosphoproteomic data. PMID:35879309
Dynamic changes in O-GlcNAcylation regulate osteoclast differentiation and bone loss via nucleoporin 153. PMID:35879285
Quantitative In Silico Evaluation of Allergenic Proteins from Anacardium occidentale, Carya illinoinensis, Juglans regia and Pistacia vera and Their Epitopes as Precursors of Bioactive Peptides. PMID:35877438
Combined Theoretical and Experimental Study to Unravel the Differences in Promiscuous Amidase Activity of Two Nonhomologous Enzymes. PMID:35875595
Mechanism of Action of Yin Nourishing and Heat Clearing Prescription in Treating Cough Variant Asthma Based on Network Pharmacology and Molecular Docking Verification. PMID:35866040
Mini-review: Recent advances in post-translational modification site prediction based on deep learning. PMID:35860402
Neuropilin 1 and its inhibitory ligand mini-tryptophanyl-tRNA synthetase inversely regulate VE-cadherin turnover and vascular permeability. PMID:35858913
JAK2-CHK2 signaling safeguards the integrity of the mitotic spindle assembly checkpoint and genome stability. PMID:35851582
Total Flavonoids of Drynariae Rhizoma Improve Glucocorticoid-Induced Osteoporosis of Rats: UHPLC-MS-Based Qualitative Analysis, Network Pharmacology Strategy and Pharmacodynamic Validation. PMID:35846330
The genome sequences of the male and female green-veined white, Pieris napi (Linnaeus, 1758). PMID:35846179
SARS-CoV-2-Induced Immunosuppression: A Molecular Mimicry Syndrome. PMID:35846107
DCBLD1 Overexpression Is Associated With a Poor Prognosis in Head and Neck Squamous Cell Carcinoma. PMID:35844572
Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members. PMID:35842574
Systematic prediction of degrons and E3 ubiquitin ligase binding via deep learning. PMID:35836176
Deep learning frameworks for protein-protein interaction prediction. PMID:35832624
In-silico screening and in-vitro assay show the antiviral effect of Indomethacin against SARS-CoV-2. PMID:35809412
Analyzing BMP2, FGFR, and TGF Beta Expressions in High-Grade Osteosarcoma Untreated and Treated Autografts Using Proteomic Analysis. PMID:35806417
iPCD: A Comprehensive Data Resource of Regulatory Proteins in Programmed Cell Death. PMID:35805101
Characterization of a novel thermophilic metagenomic GH5 endoglucanase heterologously expressed in Escherichia coli and Saccharomyces cerevisiae. PMID:35799200
Toward a base-resolution panorama of the in vivo impact of cytosine methylation on transcription factor binding. PMID:35799193
Biomimetic generation of the strongest known biomaterial found in limpet tooth. PMID:35798724
Biochemical characterization and peptide mass fingerprinting of two glutathione transferases from Biomphalaria alexandrina snails (Gastropoda: Planorbidae). PMID:35792934
Genomic and phenotypic comparison of Prevotella intermedia strains possessing different virulence in vivo. PMID:35791444
The Role of m6A RNA Methylation in Cancer: Implication for Nature Products Anti-Cancer Research. PMID:35784761
A consensus view of the proteome of the last universal common ancestor. PMID:35784055
PHILM2Web: A high-throughput database of macromolecular host-pathogen interactions on the Web. PMID:35776535
Repositioning of Anti-Inflammatory Drugs for the Treatment of Cervical Cancer Sub-Types. PMID:35770086
Deep generative models for peptide design. PMID:35769205
Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning. PMID:35767567
Biosynthesis of saponin defensive compounds in sea cucumbers. PMID:35761075
The SKBR3 cell-membrane proteome reveals telltales of aberrant cancer cell proliferation and targets for precision medicine applications. PMID:35760832
Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity. PMID:35760776
DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms. PMID:35758802
Structural Elucidation of Rift Valley Fever Virus L Protein towards the Discovery of Its Potential Inhibitors. PMID:35745579
Proteomic Analysis of Human Milk Reveals Nutritional and Immune Benefits in the Colostrum from Mothers with COVID-19. PMID:35745243
Novel Insight into the Potential Role of Acylglycerophosphate Acyltransferases Family Members on Triacylglycerols Synthesis in Buffalo. PMID:35743005
The Repeating, Modular Architecture of the HtrA Proteases. PMID:35740918
P Starvation in Roses Leads to Strongly Genotype-Dependent Induction of P-Transporter Genes during Black Spot Leaf Disease. PMID:35736032
Insight Into the Properties and Immunoregulatory Effect of Extracellular Vesicles Produced by Candida glabrata, Candida parapsilosis, and Candida tropicalis Biofilms. PMID:35734578
Transcriptomic and proteomic profiling of peptidase expression in Fasciola hepatica eggs developing at host's body temperature. PMID:35725898
Revealing the human mucinome. PMID:35725833
Towards the First Multiepitope Vaccine Candidate against Neospora caninum in Mouse Model: Immunoinformatic Standpoint. PMID:35722460
Proteome-Wide and Protein-Specific Multi-Epitope Vaccine Constructs Against the Rift Valley Fever Virus Outbreak Using Integrated Omics Approaches. PMID:35711778
Mass spectrometry-based draft of the mouse proteome. PMID:35710609
Genome-wide association study and selection for field resistance to cassava root rot disease and productive traits. PMID:35709238
Evaluation of the Mechanism of Jiedu Huazhuo Quyu Formula in Treating Wilson's Disease-Associated Liver Fibrosis by Network Pharmacology Analysis and Molecular Dynamics Simulation. PMID:35707473
Spatial and temporal proteomics reveals the distinct distributions and dynamics of O-GlcNAcylated proteins. PMID:35705054
Menthol carbonates as potent antiparasitic agents: synthesis and in vitro studies along with computer-aided approaches. PMID:35698116
merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models. PMID:35694833
SM-COLSARSPROT: Highly Immunogenic Supramutational Synthetic Peptides Covering the World's Population. PMID:35693819
Conserved coronavirus proteins as targets of broad-spectrum antivirals. PMID:35691424
SALARECON connects the Atlantic salmon genome to growth and feed efficiency. PMID:35687595
40S hnRNP particles are a novel class of nuclear biomolecular condensates. PMID:35687109
Metformin Prevents Key Mechanisms of Obesity-Related Complications in Visceral White Adipose Tissue of Obese Pregnant Mice. PMID:35684088
Variations in Blood Platelet Proteome and Transcriptome Revealed Altered Expression of Transgelin-2 in Acute Coronary Syndrome Patients. PMID:35683019
Isogenic GAA-KO Murine Muscle Cell Lines Mimicking Severe Pompe Mutations as Preclinical Models for the Screening of Potential Gene Therapy Strategies. PMID:35682977
Control of CRK-RAC1 activity by the miR-1/206/133 miRNA family is essential for neuromuscular junction function. PMID:35676269
The genome sequence of the grizzled skipper, Pyrgus malvae (Linnaeus, 1758). PMID:35673393
Integrative analysis and prediction of human R-loop binding proteins. PMID:35666183
In silico SARS-CoV-2 vaccine development for Omicron strain using reverse vaccinology. PMID:35665465
A Network Pharmacology Analysis of Cytotoxic Triterpenes Isolated from Euphorbia abyssinica Latex Supported by Drug-likeness and ADMET Studies. PMID:35664578
Protposer: The web server that readily proposes protein stabilizing mutations with high PPV. PMID:35664235
MIAOME: Human microbiome affect the host epigenome. PMID:35664224
Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein. PMID:35660160
Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases. PMID:35655887
Expediting knowledge acquisition by a web framework for Knowledge Graph Exploration and Visualization (KGEV): case studies on COVID-19 and Human Phenotype Ontology. PMID:35655307
The sanitary indoor environment-a potential source for intact human-associated anaerobes. PMID:35650275
Flexible protein database based on amino acid k-mers. PMID:35650262
Resveratrol Ameliorates Lipopolysaccharide-Induced Sudden Sensorineural Hearing Loss in In Vitro Model through Multitarget Antiapoptotic Mechanism Based on Network Pharmacology and Molecular Docking. PMID:35646137
Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation. PMID:35640593
mebipred: identifying metal binding potential in protein sequence. PMID:35639953
Conditional generative modeling for de novo protein design with hierarchical functions. PMID:35639661
ColabFold: making protein folding accessible to all. PMID:35637307
Subcellular localization of Type VI secretion system assembly in response to cell-cell contact. PMID:35634969
Prediction of the Medicinal Mechanisms of Pinellia ternata Breitenbach, a Traditional Medicine for Gastrointestinal Motility Disorders, through Network Pharmacology. PMID:35631773
Targeting Nuclear Receptors in Lung Cancer-Novel Therapeutic Prospects. PMID:35631448
Bioactive Phytoconstituents as Potent Inhibitors of Tyrosine-Protein Kinase Yes (YES1): Implications in Anticancer Therapeutics. PMID:35630545
Bioprospecting for Thermozymes and Characterization of a Novel Lipolytic Thermozyme Belonging to the SGNH/GDSL Family of Hydrolases. PMID:35628544
Venomics of the Central European Myrmicine Ants Myrmica rubra and Myrmica ruginodis. PMID:35622604
PepNN: a deep attention model for the identification of peptide binding sites. PMID:35618814
Yaobishu Regulates Inflammatory, Metabolic, Autophagic, and Apoptosis Pathways to Attenuate Lumbar Disc Herniation. PMID:35615578
The genome sequence of the European water vole, Arvicola amphibius Linnaeus 1758. PMID:35600244
An Electrostatically-steered Conformational Selection Mechanism Promotes SARS-CoV-2 Spike Protein Variation. PMID:35595165
Revealing the novel complexity of plant long non-coding RNA by strand-specific and whole transcriptome sequencing for evolutionarily representative plant species. PMID:35590257
Conformational spread drives the evolution of the calcium-calmodulin protein kinase II. PMID:35589775
Clinical Evidence and Potential Mechanisms of Complementary Treatment of Ling Gui Zhu Gan Formula for the Management of Serum Lipids and Obesity. PMID:35586687
SARS-CoV-2 in silico binding affinity to human leukocyte antigen (HLA) Class II molecules predicts vaccine effectiveness across variants of concern (VOC). PMID:35577837
Temperature and Geographic Location Impact the Distribution and Diversity of Photoautotrophic Gene Variants in Alkaline Yellowstone Hot Springs. PMID:35575591
Combination of Genome-Scale Models and Bioreactor Dynamics to Optimize the Production of Commodity Chemicals. PMID:35573743
Comparative proteomics analysis of Pichia pastoris cultivating in glucose and methanol. PMID:35572767
Apolipoprotein E4 Effects a Distinct Transcriptomic Profile and Dendritic Arbor Characteristics in Hippocampal Neurons Cultured in vitro. PMID:35572125
Transcriptome profiling and proteomic validation reveals targets of the androgen receptor signaling in the BT-474 breast cancer cell line. PMID:35568821
A haploid pseudo-chromosome genome assembly for a keystone sagebrush species of western North American rangelands. PMID:35567476
The Mantle Transcriptome of Chamelea gallina (Mollusca: Bivalvia) and Shell Biomineralization. PMID:35565623
Potential of Inflammatory Protein Signatures for Enhanced Selection of People for Lung Cancer Screening. PMID:35565275
Placental Transcription Profiling in 6-23 Weeks' Gestation Reveals Differential Transcript Usage in Early Development. PMID:35562897
CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation. PMID:35560159
Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter. PMID:35545619
Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation. PMID:35532924
Structure-Activity Predictions From Computational Mining of Protein Databases to Assist Modular Design of Antimicrobial Peptides. PMID:35531270
Earliest Photic Zone Niches Probed by Ancestral Microbial Rhodopsins. PMID:35524714
Rheumatoid arthritis T cell and muscle oxidative metabolism associate with exercise-induced changes in cardiorespiratory fitness. PMID:35523821
The first laminin G-like domain of protein S is essential for binding and activation of Tyro3 receptor and intracellular signalling. PMID:35518197
SPIN enables high throughput species identification of archaeological bone by proteomics. PMID:35513387
Functional and Structural Changes in the Membrane-Bound O-Acyltransferase Family Member 7 (MBOAT7) Protein: The Pathomechanism of a Novel MBOAT7 Variant in Patients With Intellectual Disability. PMID:35509994
Analysis of host-pathogen gene association networks reveals patient-specific response to streptococcal and polymicrobial necrotising soft tissue infections. PMID:35505341
Biotechnological formation of dairy flavor inducing δ-lactones from vegetable oil. PMID:35498959
Machine learning model for fast prediction of the natural frequencies of protein molecules. PMID:35498827
Metaproteomic Profile of the Colonic Luminal Microbiota From Patients With Colon Cancer. PMID:35495697
Comparative Analysis of the Chalcone-Flavanone Isomerase Genes in Six Citrus Species and Their Expression Analysis in Sweet Orange (Citrus sinensis). PMID:35495138
Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida. PMID:35486731
Altered abundances of human immunoglobulin M and immunoglobulin G subclasses in Alzheimer's disease frontal cortex. PMID:35484384
A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis. PMID:35484353
Evolution of the murine gut resistome following broad-spectrum antibiotic treatment. PMID:35484157
The return of the rings: Evolutionary convergence of aromatic residues in the intrinsically disordered regions of RNA-binding proteins for liquid-liquid phase separation. PMID:35481633
In Silico Identification and Characterization of a Hypothetical Protein From Rhodobacter capsulatus Revealing S-Adenosylmethionine-Dependent Methyltransferase Activity. PMID:35478993
GraPES: The Granule Protein Enrichment Server for prediction of biological condensate constituents. PMID:35474477
HORDB a comprehensive database of peptide hormones. PMID:35469024
Mechanism of Phellodendron and Anemarrhena Drug Pair on the Treatment of Liver Cancer Based on Network Pharmacology and Bioinformatics. PMID:35463358
Carbon Nanotube-Mediated Plasmid DNA Delivery in Rice Leaves and Seeds. PMID:35456898
Surfactin Shows Relatively Low Antimicrobial Activity against Bacillus subtilis and Other Bacterial Model Organisms in the Absence of Synergistic Metabolites. PMID:35456828
Molecular Evolutionary Rate Predicts Intraspecific Genetic Polymorphism and Species-Specific Selection. PMID:35456514
Deep Neural Network-Assisted Drug Recommendation Systems for Identifying Potential Drug-Target Interactions. PMID:35449922
Application of quantitative protein mass spectrometric data in the early predictive analysis of target engagement by monoclonal antibodies. PMID:35445800
Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle. PMID:35444262
Development of first linkage map for Silphium integrifolium (Asteraceae) enables identification of sporophytic self-incompatibility locus. PMID:35437327
SARS-CoV-2 3CLpro whole human proteome cleavage prediction and enrichment/depletion analysis. PMID:35429835
Expanding the clinical-pathological and genetic spectrum of RYR1-related congenital myopathies with cores and minicores: an Italian population study. PMID:35428369
Phenylalanyl tRNA synthetase (PheRS) substrate mimics: design, synthesis, molecular dynamics and antimicrobial evaluation. PMID:35425259
Identification of aldehyde oxidase 3 as a binding protein for squid ink polysaccharides using magnetic nanoparticles. PMID:35424304
The inhibition of Mpro, the primary protease of COVID-19, by Poria cocos and its active compounds: a network pharmacology and molecular docking study. PMID:35423770
A proteolytic nanobiocatalyst with built-in disulphide reducing properties. PMID:35423716
Analysis of human brain tissue derived from DBS surgery. PMID:35418104
Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics. PMID:35417463
REIA: A database for cancer A-to-I RNA editing with interactive analysis. PMID:35414795
Linnemannia elongata (Mortierellaceae) stimulates Arabidopsis thaliana aerial growth and responses to auxin, ethylene, and reactive oxygen species. PMID:35413060
Variants in mitochondrial amidoxime reducing component 1 and hydroxysteroid 17-beta dehydrogenase 13 reduce severity of nonalcoholic fatty liver disease in children and suppress fibrotic pathways through distinct mechanisms. PMID:35411667
Bioinformatics Screening of Potential Biomarkers from mRNA Expression Profiles to Discover Drug Targets and Agents for Cervical Cancer. PMID:35409328
Repurposing Multiple-Molecule Drugs for COVID-19-Associated Acute Respiratory Distress Syndrome and Non-Viral Acute Respiratory Distress Syndrome via a Systems Biology Approach and a DNN-DTI Model Based on Five Drug Design Specifications. PMID:35409008
Potential Immunogenic Activity of Computationally Designed mRNA- and Peptide-Based Prophylactic Vaccines against MERS, SARS-CoV, and SARS-CoV-2: A Reverse Vaccinology Approach. PMID:35408772
A high-quality genome assembly and annotation of the dark-eyed junco Junco hyemalis, a recently diversified songbird. PMID:35404451
SARS-CoV-2 spike protein-, main protease- and papain-like-protease-targeting peptides from seed proteins following gastrointestinal digestion: An in silico study. PMID:35403082
Learning meaningful representations of protein sequences. PMID:35395843
Assembly of a Hybrid Formica aquilonia × F. polyctena Ant Genome From a Haploid Male. PMID:35394540
Modification of BRCA1-associated breast cancer risk by HMMR overexpression. PMID:35393420
Predicted mouse interactome and network-based interpretation of differentially expressed genes. PMID:35390003
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
Effects of Astragalus Polysaccharides on CD8+ Tissue-Resident Memory T Cells in Mice with Herpes Simplex. PMID:35388305
Potential Therapeutic Targets of Rehmannia Formulations on Diabetic Nephropathy: A Comparative Network Pharmacology Analysis. PMID:35387335
Unsupervised Mining of HLA-I Peptidomes Reveals New Binding Motifs and Potential False Positives in the Community Database. PMID:35386688
SuperDendrix algorithm integrates genetic dependencies and genomic alterations across pathways and cancer types. PMID:35382456
Exome sequencing of individuals with Huntington's disease implicates FAN1 nuclease activity in slowing CAG expansion and disease onset. PMID:35379994
Investigation and Functional Enrichment Analysis of the Human Host Interaction Network with Common Gram-Negative Respiratory Pathogens Predicts Possible Association with Lung Adenocarcinoma. PMID:35366267
AF2Complex predicts direct physical interactions in multimeric proteins with deep learning. PMID:35365655
Current progress and open challenges for applying deep learning across the biosciences. PMID:35365602
A network biology approach to identify crucial host targets for COVID-19. PMID:35364279
The D2R-DISC1 protein complex and associated proteins are altered in schizophrenia and normalized with antipsychotic treatment. PMID:35361701
Kinase domain autophosphorylation rewires the activity and substrate specificity of CK1 enzymes. PMID:35353987
Comprehensive spectral libraries for various rabbit eye tissue proteomes. PMID:35351915
Computational mining of MHC class II epitopes for the development of universal immunogenic proteins. PMID:35349604
Transcriptomic changes during the establishment of long-term methyl jasmonate-induced resistance in Norway spruce. PMID:35348221
Mechanism of Zhen Wu Decoction in the Treatment of Heart Failure Based on Network Pharmacology and Molecular Docking. PMID:35341142
Structural analysis of M1AP variants associated with severely impaired spermatogenesis causing male infertility. PMID:35341049
Deciphering functional redundancy and energetics of malate oxidation in mycobacteria. PMID:35337802
Whole-Genome Sequencing and Comparative Genomic Analysis of Antimicrobial Producing Streptococcus lutetiensis from the Rumen. PMID:35336126
Whole Proteome-Based Therapeutic Targets Annotation and Designing of Multi-Epitope-Based Vaccines against the Gram-Negative XDR-Alcaligenes faecalis Bacterium. PMID:35335094
Donor Splice Site Variant in SLC9A6 Causes Christianson Syndrome in a Lithuanian Family: A Case Report. PMID:35334527
Machine learning-assisted identification of bioindicators predicts medium-chain carboxylate production performance of an anaerobic mixed culture. PMID:35331330
AutoCoEv-A High-Throughput In Silico Pipeline for Predicting Inter-Protein Coevolution. PMID:35328772
Draft Sequencing Crested Wheatgrass Chromosomes Identified Evolutionary Structural Changes and Genes and Facilitated the Development of SSR Markers. PMID:35328613
Whole-genome sequence and methylome profiling of the almond [Prunus dulcis (Mill.) D.A. Webb] cultivar 'Nonpareil'. PMID:35325123
Reconstruction of a generic genome-scale metabolic network for chicken: Investigating network connectivity and finding potential biomarkers. PMID:35316277
Genomic Fishing and Data Processing for Molecular Evolution Research. PMID:35314663
Computational Tools for the Analysis of Uncultivated Phage Genomes. PMID:35311574
(+)-Catharanthine potentiates the GABAA receptor by binding to a transmembrane site at the β(+)/α(-) interface near the TM2-TM3 loop. PMID:35304861
Predicting residues involved in anti-DNA autoantibodies with limited neural networks. PMID:35303216
Age-Related Differences in Structure and Function of Nasal Epithelial Cultures From Healthy Children and Elderly People. PMID:35296085
The AOP-DB RDF: Applying FAIR Principles to the Semantic Integration of AOP Data Using the Research Description Framework. PMID:35295213
Leukemia Inhibitory Factor Promotes Survival of Hematopoietic Progenitors Ex Vivo and Is Post-Translationally Regulated by DPP4. PMID:35293568
Large-scale design and refinement of stable proteins using sequence-only models. PMID:35286324
Network Analysis Reveals Different Cellulose Degradation Strategies Across Trichoderma harzianum Strains Associated With XYR1 and CRE1. PMID:35281818
Unravelling the Biology of EhActo as the First Cofilin From Entamoeba histolytica. PMID:35281106
The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge. PMID:35279090
Computational identification of host genomic biomarkers highlighting their functions, pathways and regulators that influence SARS-CoV-2 infections and drug repurposing. PMID:35277538
Molecular physiology of pumiliotoxin sequestration in a poison frog. PMID:35275922
Protein Expression of AEBP1, MCM4, and FABP4 Differentiate Osteogenic, Adipogenic, and Mesenchymal Stromal Stem Cells. PMID:35269711
Tryptophan depletion results in tryptophan-to-phenylalanine substitutants. PMID:35264796
Inhibition of the hexamerization of SARS-CoV-2 endoribonuclease and modeling of RNA structures bound to the hexamer. PMID:35264667
Genomic patterns of homozygosity and inbreeding depression in Murciano-Granadina goats. PMID:35264251
Glycosyltransferases: Mining, engineering and applications in biosynthesis of glycosylated plant natural products. PMID:35261926
SCORPION is a stacking-based ensemble learning framework for accurate prediction of phage virion proteins. PMID:35260777
Identification of the potential mechanism of Radix pueraria in colon cancer based on network pharmacology. PMID:35260672
Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks. PMID:35260071
Aberrant hippocampal transmission and behavior in mice with a stargazin mutation linked to intellectual disability. PMID:35256745
In-Depth Serum Proteomics by DIA-MS with In Silico Spectral Libraries Reveals Dynamics during the Active Phase of Systemic Juvenile Idiopathic Arthritis. PMID:35252692
The genome sequence of the peach blossom moth, Thyatira batis (Linnaeus, 1758). PMID:35252591
A comprehensive WGS-based pipeline for the identification of new candidate genes in inherited retinal dystrophies. PMID:35246562
Network pharmacology analysis and experimental study strategy reveals the potential mechanism of puerarin against rotavirus. PMID:35242859
The Role of Intestinal Microbiota in Regulating the Metabolism of Bile Acids Is Conserved Across Vertebrates. PMID:35242120
Network pharmacology-based predictions of active components and pharmacological mechanisms of Artemisia annua L. for the treatment of the novel Corona virus disease 2019 (COVID-19). PMID:35241045
An Integrated Pharmacology-Based Strategy to Investigate the Potential Mechanism of Xiebai San in Treating Pediatric Pneumonia. PMID:35237157
VPS29 Exerts Opposing Effects on Endocytic Viral Entry. PMID:35229640
Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA. PMID:35229157
DNA topoisomerase inhibition with the HIF inhibitor acriflavine promotes transcription of lncRNAs in endothelial cells. PMID:35228897
Genome-wide linkage analysis combined with genome sequencing in large families with intracranial aneurysms. PMID:35228681
PubChem Protein, Gene, Pathway, and Taxonomy Data Collections: Bridging Biology and Chemistry through Target-Centric Views of PubChem Data. PMID:35227770
Transcriptome changes in the developing sugarcane culm associated with high yield and early-season high sugar content. PMID:35224663
Inferring Retinal Degeneration-Related Genes Based on Xgboost. PMID:35223997
Antifungal activity of an artificial peptide aptamer SNP-D4 against Fusarium oxysporum. PMID:35223198
Forgotten Actors: Glycoside Hydrolases During Elongation Growth of Maize Primary Root. PMID:35222452
BEND4 as a Candidate Gene for an Infection-Induced Acute Encephalopathy Characterized by a Cyst and Calcification of the Pons and Cerebellar Atrophy. PMID:35221871
Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes. PMID:35217859
Scaling laws in enzyme function reveal a new kind of biochemical universality. PMID:35217602
Comparative proteomics profiling revealed the involvement of GRB2-ROCK2 axis in Lyme neuroborreliosis caused by Borrelia Burgdorferi. PMID:35212166
Identification of intrinsically disorder regions in non-structural proteins of SARS-CoV-2: New insights into drug and vaccine resistance. PMID:35211823
Student biocuration projects as a learning environment. PMID:35211294
Identification of distinct cytotoxic granules as the origin of supramolecular attack particles in T lymphocytes. PMID:35210420
Effect of Physical Exercise and Genetic Background on Glucose Homeostasis and Liver/Muscle Proteomes in Mice. PMID:35208192
Characterization of the pVHL Interactome in Human Testis Using High-Throughput Library Screening. PMID:35205757
DOTA: Deep Learning Optimal Transport Approach to Advance Drug Repositioning for Alzheimer's Disease. PMID:35204697
Evolutionary information helps understand distinctive features of the angiotensin II receptors AT1 and AT2 in amniota. PMID:35202400
Comparative Genomic Analysis Reveals Preserved Features in Organohalide-Respiring Sulfurospirillum Strains. PMID:35196120
Convergent consequences of parthenogenesis on stick insect genomes. PMID:35196080
Top-down stepwise refinement identifies coding and noncoding RNA-associated epigenetic regulatory maps in malignant glioma. PMID:35194922
Metaproteomic profiling of fungal gut colonization in gnotobiotic mice. PMID:35193703
Evaluation of the Whole Proteome of Achromobacter xylosoxidans to Identify Vaccine Targets for mRNA and Peptides-Based Vaccine Designing Against the Emerging Respiratory and Lung Cancer-Causing Bacteria. PMID:35186980
Wei2GO: weighted sequence similarity-based protein function prediction. PMID:35186498
Network Pharmacology-Based and Experimental Identification of the Effects of Paeoniflorin on Major Depressive Disorder. PMID:35185541
Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis. PMID:35185305
New insights on familial colorectal cancer type X syndrome. PMID:35181726
In silico Analysis of SARS-CoV-2 ORF8-Binding Proteins Reveals the Involvement of ORF8 in Acquired-Immune and Innate-Immune Systems. PMID:35178414
Peptide-Based Vaccines for Tuberculosis. PMID:35173740
METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. PMID:35172890
Identification of a New Cholesterol-Binding Site within the IFN-γ Receptor that is Required for Signal Transduction. PMID:35166455
Thyroid-Stimulating Hormone Favors Runx2-Mediated Matrix Mineralization in HOS and SaOS2 Cells: An In Vitro and In Silico Approach. PMID:35163879
Characterisation of Endogenous Peptides Present in Virgin Olive Oil. PMID:35163634
Whole-Genome Sequencing and RNA-Seq Reveal Differences in Genetic Mechanism for Flowering Response between Weedy Rice and Cultivated Rice. PMID:35163531
Whole-Exome Sequencing Identifies a Novel Germline Variant in PTK7 Gene in Familial Colorectal Cancer. PMID:35163215
Phylogenetic and Expression Analysis of CENH3 and APOLLO Genes in Sexual and Apomictic Boechera Species. PMID:35161368
Are Cell Junctions Implicated in the Regulation of Vitellogenin Uptake? Insights from an RNAseq-Based Study in Eel, Anguilla australis. PMID:35159359
Fabrication of a New, Low-Cost, and Environment-Friendly Laccase-Based Biosensor by Electrospray Immobilization with Unprecedented Reuse and Storage Performances. PMID:35154910
Network Pharmacology Analysis on the Mechanism of Huangqi Sijunzi Decoction in Treating Cancer-Related Fatigue. PMID:35154614
A System Bioinformatics Approach Predicts the Molecular Mechanism Underlying the Course of Action of Radix Salviae Reverses GBM Effects. PMID:35154340
Genomic Insights Into Cadmium Resistance of a Newly Isolated, Plasmid-Free Cellulomonas sp. Strain Y8. PMID:35154027
Integration of Network Pharmacology and Experimental Validation to Explore the Pharmacological Mechanisms of Zhuanggu Busui Formula Against Osteoporosis. PMID:35154014
PSTPIP1-LYP phosphatase interaction: structural basis and implications for autoinflammatory disorders. PMID:35152348
Multimodal reasoning based on knowledge graph embedding for specific diseases. PMID:35150235
Multi-insecticide resistant malaria vectors in the field remain susceptible to malathion, despite the presence of Ace1 point mutations. PMID:35143477
Diosgenin From Dioscorea Nipponica Rhizoma Against Graves' Disease-On Network Pharmacology and Experimental Evaluation. PMID:35140607
The genome of the Paleogene relic tree Bretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs. PMID:35137004
The genome sequence of the heath fritillary, Melitaea athalia (Rottemburg, 1775). PMID:35136843
Co-circulation of two SARS-CoV-2 variant strains within imported pet hamsters in Hong Kong. PMID:35135441
A chromosome-level genome assembly and annotation of the desert horned lizard, Phrynosoma platyrhinos, provides insight into chromosomal rearrangements among reptiles. PMID:35134927
Combined assessment of MHC binding and antigen abundance improves T cell epitope predictions. PMID:35128348
The aqueous humor proteome is intrinsically disordered. PMID:35128080
A Preliminary Inquiry Into the Potential Mechanism of Huang-Lian-Jie-Du Decoction in Treating Rheumatoid Arthritis via Network Pharmacology and Molecular Docking. PMID:35127697
Moths passing in the night: Phenological and genomic divergences within a forest pest complex. PMID:35126654
Mouse genomic and cellular annotations. PMID:35124726
SPSED: A Signal Peptide Secretion Efficiency Database. PMID:35118058
Agent-based models for detecting the driving forces of biomolecular interactions. PMID:35115584
Systems pharmacology-based drug discovery and active mechanism of natural products for coronavirus pneumonia (COVID-19): An example using flavonoids. PMID:35114443
High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function. PMID:35112110
Deep learning program to predict protein functions based on sequence information. PMID:35111575
Autism genes converge on asynchronous development of shared neuron classes. PMID:35110736
K-29 linked ubiquitination of Arrdc4 regulates its function in extracellular vesicle biogenesis. PMID:35106941
Amphioxus muscle transcriptomes reveal vertebrate-like myoblast fusion genes and a highly conserved role of insulin signalling in the metabolism of muscle. PMID:35105312
SEQUENCE SLIDER: integration of structural and genetic data to characterize isoforms from natural sources. PMID:35104880
Epidemiology of Mutations in the 65-kDa Retinal Pigment Epithelium (RPE65) Gene-Mediated Inherited Retinal Dystrophies: A Systematic Literature Review. PMID:35098484
Potential Clinical Value of Biomarker-Guided Emergency Triage for Thoracic Aortic Dissection. PMID:35096998
DisEnrich: Database of Enriched Regions in Human Dark Proteome. PMID:35094056
Integrin-linked kinase (ILK): the known vs. the unknown and perspectives. PMID:35089438
3'mRNA sequencing reveals pro-regenerative properties of c5ar1 during resolution of murine acetaminophen-induced liver injury. PMID:35087052
Bioactive peptides from broccoli stems strongly enhance regenerative keratinocytes by stimulating controlled proliferation. PMID:35086428
Matrin3: Disorder and ALS Pathogenesis. PMID:35083279
Identification of shared tumor epitopes from endogenous retroviruses inducing high-avidity cytotoxic T cells for cancer immunotherapy. PMID:35080970
AMPlify: attentive deep learning model for discovery of novel antimicrobial peptides effective against WHO priority pathogens. PMID:35078402
Distribution, organization and expression of genes concerned with anaerobic lactate utilization in human intestinal bacteria. PMID:35077342
Native proline-rich motifs exploit sequence context to target actin-remodeling Ena/VASP protein ENAH. PMID:35076015
Identification of Constituents and Exploring the Mechanism for Toutongning Capsule in the Treatment of Migraine. PMID:35075364
Metabolic signatures of regulation by phosphorylation and acetylation. PMID:35072016
Antioxidant Effects and Potential Molecular Mechanism of Action of Limonium aureum Extract Based on Systematic Network Pharmacology. PMID:35071383
Establishment and characterization of NCC-DMM1-C1, a novel patient-derived cell line of desmoplastic malignant pleural mesothelioma. PMID:35069873
Genome-wide association study of beef bull semen attributes. PMID:35065600
Extracellular vesicles produced by the human commensal gut bacterium Bacteroides thetaiotaomicron affect host immune pathways in a cell-type specific manner that are altered in inflammatory bowel disease. PMID:35064769
A noncanonical chaperone interacts with drug efflux pumps during their assembly into bacterial outer membranes. PMID:35061668
Regenerating zebrafish scales express a subset of evolutionary conserved genes involved in human skeletal disease. PMID:35057801
Towards an Ideal In Cell Hybridization-Based Strategy to Discover Protein Interactomes of Selected RNA Molecules. PMID:35055128
A Novel GEMIN4 Variant in a Consanguineous Family Leads to Neurodevelopmental Impairment with Severe Microcephaly, Spastic Quadriplegia, Epilepsy, and Cataracts. PMID:35052432
Deciphering the evolution of composite-type GSKIP in mitochondria and Wnt signaling pathways. PMID:35051222
Stingray Venom Proteins: Mechanisms of Action Revealed Using a Novel Network Pharmacology Approach. PMID:35049882
Differential target multiplexed spinal cord stimulation programming modulates proteins involved in ion regulation in an animal model of neuropathic pain. PMID:35048719
Identification of putative essential protein domains from high-density transposon insertion sequencing. PMID:35046497
Gut microbiome alterations and gut barrier dysfunction are associated with host immune homeostasis in COVID-19 patients. PMID:35045853
Impaired catabolism of free oligosaccharides due to MAN2C1 variants causes a neurodevelopmental disorder. PMID:35045343
Proteome-scale mapping of binding sites in the unstructured regions of the human proteome. PMID:35044719
Minimal Information about MHC Multimers (MIAMM). PMID:35042788
Association between Arsenic Level, Gene Expression in Asian Population, and In Vitro Carcinogenic Bladder Tumor. PMID:35039759
Epigenetic aging of the demographically non-aging naked mole-rat. PMID:35039495
RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria. PMID:35037022
Pharmacological Mechanisms of Tinglizi against Chronic Heart Failure Determined by Network Pharmacology and Molecular Docking. PMID:35035498
A chromosome-scale genome assembly for the holly (Ilex polyneura) provides insights into genomic adaptations to elevation in Southwest China. PMID:35031793
The genome sequence of the holly blue, Celastrina argiolus (Linnaeus, 1758). PMID:35028429
Study on the Mechanism of Compound Kidney-Invigorating Granule for Osteoporosis based on Network Pharmacology and Experimental Verification. PMID:35027934
Analysis of the transcriptome of the needles and bark of Pinus radiata induced by bark stripping and methyl jasmonate. PMID:35026979
During FeS cluster biogenesis, ferredoxin and frataxin use overlapping binding sites on yeast cysteine desulfurase Nfs1. PMID:35026224
Discovering potential interactions between rare diseases and COVID-19 by combining mechanistic models of viral infection with statistical modeling. PMID:35022696
Genome-wide in silico characterization and stress induced expression analysis of BcL-2 associated athanogene (BAG) family in Musa spp. PMID:35022483
The amniotic fluid proteome changes with gestational age in normal pregnancy: a cross-sectional study. PMID:35022423
Deciphering the Plasmodium falciparum malaria-specific CD4+ T-cell response: ex vivo detection of high frequencies of PD-1+TIGIT+ EXP1-specific CD4+ T cells using a novel HLA-DR11-restricted MHC class II tetramer. PMID:35020841
African Swine Fever Virus and Host Response: Transcriptome Profiling of the Georgia 2007/1 Strain and Porcine Macrophages. PMID:35019713
MicroRNA-365 regulates human cardiac action potential duration. PMID:35017523
Evolutionary Ecology of Natural Comammox Nitrospira Populations. PMID:35014874
Grainyhead 1 acts as a drug-inducible conserved transcriptional regulator linked to insulin signaling and lifespan. PMID:35013237
Natural variant frequencies across domains from different sarcomere proteins cross-correlate to identify inter-protein contacts associated with cardiac muscle function and disease. PMID:35006463
Computational identification of 4-carboxyglutamate sites to supplement physiological studies using deep learning. PMID:34996975
Evaluating the aerobic xylene-degrading potential of the intrinsic microbial community of a legacy BTEX-contaminated aquifer by enrichment culturing coupled with multi-omics analysis: uncovering the role of Hydrogenophaga strains in xylene degradation. PMID:34989990
Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT. PMID:34983371
The Candida albicans Cdk8-dependent phosphoproteome reveals repression of hyphal growth through a Flo8-dependent pathway. PMID:34982775
Deep Time Course Proteomics of SARS-CoV- and SARS-CoV-2-Infected Human Lung Epithelial Cells (Calu-3) Reveals Strong Induction of Interferon-Stimulated Gene Expression by SARS-CoV-2 in Contrast to SARS-CoV. PMID:34982558
SignalP 6.0 predicts all five types of signal peptides using protein language models. PMID:34980915
Network Pharmacology-Based Investigation and Experimental Exploration of the Antiapoptotic Mechanism of Colchicine on Myocardial Ischemia Reperfusion Injury. PMID:34975499
The role of Leishmania GP63 in the modulation of innate inflammatory response to Leishmania major infection. PMID:34972189
Network Pharmacology Study on Molecular Mechanisms of Zhishi Xiebai Guizhi Decoction in the Treatment of Coronary Heart Disease. PMID:34966435
Collagen VI Regulates Motor Circuit Plasticity and Motor Performance by Cannabinoid Modulation. PMID:34965974
Evolution of 14-3-3 Proteins in Angiosperm Plants: Recurring Gene Duplication and Loss. PMID:34961196
Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. PMID:34957216
Impact of Qi-Invigorating Traditional Chinese Medicines on Diffuse Large B Cell Lymphoma Based on Network Pharmacology and Experimental Validation. PMID:34955857
In Silico Design of a New Multi-Epitope Peptide-Based Vaccine Candidate Against Q Fever. PMID:34955559
Expanding the Menu: Are Polyphagy and Gene Family Expansions Linked across Lepidoptera? PMID:34951642
DeepSVP: Integration of genotype and phenotype for structural variant prioritization using deep learning. PMID:34951628
A high-resolution mass spectrometry based proteomic dataset of human regulatory T cells. PMID:34950757
In Silico Prediction and Bioactivity Evaluation of Chemical Ingredients Against Influenza A Virus From Isatis tinctoria L. PMID:34950027
NAPRT Expression Regulation Mechanisms: Novel Functions Predicted by a Bioinformatics Approach. PMID:34946971
An Uninvited Seat at the Dinner Table: How Apicomplexan Parasites Scavenge Nutrients from the Host. PMID:34946193
A longer isoform of Stim1 is a negative SOCE regulator but increases cAMP-modulated NFAT signaling. PMID:34942054
Characterization of Anti-Ana o 3 Monoclonal Antibodies and Their Application in Comparing Brazilian Cashew Cultivars. PMID:34939998
H-NOX proteins in the virulence of pathogenic bacteria. PMID:34939646
Anticancer Action of Xiaoxianxiong Tang in Non-Small Cell Lung Cancer by Pharmacological Analysis and Experimental Validation. PMID:34938346
Exploring the Potential Targets and Mechanisms of Huang Lian Jie Du Decoction in the Treatment of Coronavirus Disease 2019 Based on Network Pharmacology. PMID:34938107
NGS read classification using AI. PMID:34936673
Intellectual disability genomics: current state, pitfalls and future challenges. PMID:34930158
Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections. PMID:34928200
What Is Motion? Recent Advances in the Study of Molecular Movement Patterns of the Peptidoglycan Synthesis Machines. PMID:34928180
A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck). PMID:34927191
Genetic analysis of four consanguineous multiplex families with inflammatory bowel disease. PMID:34925849
Nicotinic receptors as SARS-CoV-2 spike co-receptors? PMID:34924680
Thioesterase enzyme families: Functions, structures, and mechanisms. PMID:34921469
EMC is required for biogenesis of Xport-A, an essential chaperone of Rhodopsin-1 and the TRP channel. PMID:34918864
Development of RIKEN Plant Metabolome MetaDatabase. PMID:34918130
Genome-wide promoter analysis, homology modeling and protein interaction network of Dehydration Responsive Element Binding (DREB) gene family in Solanum tuberosum. PMID:34914734
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. PMID:34911965
CNVs with adaptive potential in Rangifer tarandus: genome architecture and new annotated assembly. PMID:34911809
A unified evolutionary origin for the ubiquitous protein transporters SecY and YidC. PMID:34911545
Rationalizing the generation of broad spectrum antibiotics with the addition of a positive charge. PMID:34909143
Transcriptomic adaptation during skeletal muscle habituation to eccentric or concentric exercise training. PMID:34907264
Chromatin Accessibility Predetermines Odontoblast Terminal Differentiation. PMID:34901015
Profile of Basal Cell Carcinoma Mutations and Copy Number Alterations - Focus on Gene-Associated Noncoding Variants. PMID:34900699
Network Pharmacology-Based Study on the Mechanism of Aloe Vera for Treating Cancer. PMID:34899953
Exploration of the mechanism of luteolin against ischemic stroke based on network pharmacology, molecular docking and experimental verification. PMID:34898370
Identification and Functional Analysis of lncRNAs Responsive to Hypoxia in Eospalax fontanierii. PMID:34889903
Protein biomarkers in serum as a conservation tool to assess reproduction: a case study on brown bears (Ursus arctos). PMID:34888057
Palm Oil-Rich Diet Affects Murine Liver Proteome and S-Palmitoylome. PMID:34884899
IFPTML Mapping of Drug Graphs with Protein and Chromosome Structural Networks vs. Pre-Clinical Assay Information for Discovery of Antimalarial Compounds. PMID:34884870
Genes and Pathways Associated with Skeletal Sagittal Malocclusions: A Systematic Review. PMID:34884839
Interpretation of network-based integration from multi-omics longitudinal data. PMID:34883510
Identification of the key functional genes in salt-stress tolerance of Cyanobacterium Phormidium tenue using in silico analysis. PMID:34881166
Exploring the Mechanisms of Arsenic Trioxide (Pishuang) in Hepatocellular Carcinoma Based on Network Pharmacology. PMID:34880920
Analysis of Iron and Iron-Interacting Protein Dynamics During T-Cell Activation. PMID:34880854
Network Pharmacology and Experimental Validation to Reveal the Pharmacological Mechanisms of Liuwei Dihuang Decoction Against Intervertebral Disc Degeneration. PMID:34880601
From Anti-Severe Acute Respiratory Syndrome Coronavirus 2 Immune Response to Cancer Onset via Molecular Mimicry and Cross-Reactivity. PMID:34877576
Thromboses and Hemostasis Disorders Associated with COVID-19: The Possible Causal Role of Cross-Reactivity and Immunological Imprinting. PMID:34877574
Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution. PMID:34876567
Exploring the Antiglioma Mechanisms of Luteolin Based on Network Pharmacology and Experimental Verification. PMID:34873410
Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction. PMID:34873061
Whole transcriptome analysis of high and low IFN-α producers reveals differential response patterns following rhinovirus stimulation. PMID:34868584
Epstein-Barr Virus+ B Cells in Breast Cancer Immune Response: A Case Report. PMID:34868006
A Bioactive Extract Rich in Triterpenic Acid and Polyphenols from Olea europaea Promotes Systemic Immunity and Protects Atlantic Salmon Smolts Against Furunculosis. PMID:34867959
Hybridization Dynamics and Extensive Introgression in the Daphnia longispina Species Complex: New Insights from a High-Quality Daphnia galeata Reference Genome. PMID:34865004
Compound heterozygous c.598_612del and c.1746-20C > G CAPN3 genotype cause autosomal recessive limb-girdle muscular dystrophy-1: a case report. PMID:34863162
Myeloid-associated differentiation marker is a novel SP-A-associated transmembrane protein whose expression on airway epithelial cells correlates with asthma severity. PMID:34862427
LPI-EnEDT: an ensemble framework with extra tree and decision tree classifiers for imbalanced lncRNA-protein interaction data classification. PMID:34861891
An NK-like CAR T cell transition in CAR T cell dysfunction. PMID:34861191
FOXN1 forms higher-order nuclear condensates displaced by mutations causing immunodeficiency. PMID:34860543
A computational exploration of resilience and evolvability of protein-protein interaction networks. PMID:34857859
The FUR-like regulators PerRA and PerRB integrate a complex regulatory network that promotes mammalian host-adaptation and virulence of Leptospira interrogans. PMID:34855918
Identification of the Active Constituents and Significant Pathways of Shen-qi-Yi-zhu Decoction on Antigastric Cancer: A Network Pharmacology Research and Experimental Validation. PMID:34853601
Multiomics Analysis of Spatially Distinct Stromal Cells Reveals Tumor-Induced O-Glycosylation of the CDK4-pRB Axis in Fibroblasts at the Invasive Tumor Edge. PMID:34853070
Managing the life cycle of a portfolio of open data resources at the SIB Swiss Institute of Bioinformatics. PMID:34850820
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. PMID:34850135
Discovery of new vascular disrupting agents based on evolutionarily conserved drug action, pesticide resistance mutations, and humanized yeast. PMID:34849907
De novo whole-genome assembly of Chrysanthemum makinoi, a key wild chrysanthemum. PMID:34849775
Transcriptomic dataset for Sardina pilchardus: Assembly, annotation, and expression of nine tissues. PMID:34849383
A 3D structural SARS-CoV-2-human interactome to explore genetic and drug perturbations. PMID:34845387
Metagenomic discovery of CRISPR-associated transposons. PMID:34845024
Structural dynamics in the evolution of a bilobed protein scaffold. PMID:34845009
Protein domain-based prediction of drug/compound-target interactions and experimental validation on LIM kinases. PMID:34843456
A systematic review of GWAS identified SNPs associated with outcomes of medications for opioid use disorder. PMID:34838141
LPI-HyADBS: a hybrid framework for lncRNA-protein interaction prediction integrating feature selection and classification. PMID:34836494
Structural-Dynamics and Binding Analysis of RBD from SARS-CoV-2 Variants of Concern (VOCs) and GRP78 Receptor Revealed Basis for Higher Infectivity. PMID:34835456
Facilitating Antiviral Drug Discovery Using Genetic and Evolutionary Knowledge. PMID:34834924
Transcriptome Analysis of Lolium temulentum Exposed to a Combination of Drought and Heat Stress. PMID:34834610
On the Applicability of Electrophoresis for Protein Quantification. PMID:34833270
Multidimensional Single-Nuclei RNA-Seq Reconstruction of Adipose Tissue Reveals Adipocyte Plasticity Underlying Thermogenic Response. PMID:34831295
A Deep Learning Approach with Data Augmentation to Predict Novel Spider Neurotoxic Peptides. PMID:34830173
Genetic Variability of the Functional Domains of Chromodomains Helicase DNA-Binding (CHD) Proteins. PMID:34828433
Integration and Visualization of Regulatory Elements and Variations of the EPAS1 Gene in Human. PMID:34828399
Long Non-Coding RNAs Associated with Ribosomes in Human Adipose-Derived Stem Cells: From RNAs to Microproteins. PMID:34827671
In silico Methods for Identification of Potential Therapeutic Targets. PMID:34826045
Mechanism of quercetin therapeutic targets for Alzheimer disease and type 2 diabetes mellitus. PMID:34824300
Network medicine for disease module identification and drug repurposing with the NeDRex platform. PMID:34824199
Carbon fullerene and nanotube are probable binders to multiple targets of SARS-CoV-2: Insights from computational modeling and molecular dynamic simulation studies. PMID:34823028
Overview of Metabolomic Analysis and the Integration with Multi-Omics for Economic Traits in Cattle. PMID:34822411
A roadmap for metagenomic enzyme discovery. PMID:34821235
A multi-scale map of cell structure fusing protein images and interactions. PMID:34819669
Heliorhodopsin Evolution Is Driven by Photosensory Promiscuity in Monoderms. PMID:34817235
Slowest-first protein translation scheme: Structural asymmetry and co-translational folding. PMID:34813729
Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution. PMID:34810219
RDFizing the biosynthetic pathway of E.coli O-antigen to enable semantic sharing of microbiology data. PMID:34809564
DeepPhospho accelerates DIA phosphoproteome profiling through in silico library generation. PMID:34795227
Genetic fusions favor tumorigenesis through degron loss in oncogenes. PMID:34795215
A computational in silico approach to predict high-risk coding and non-coding SNPs of human PLCG1 gene. PMID:34793541
InsectBase 2.0: a comprehensive gene resource for insects. PMID:34792158
Between Interactions and Aggregates: The PolyQ Balance. PMID:34791220
Eye-Transcriptome and Genome-Wide Sequencing for Scolecophidia: Implications for Inferring the Visual System of the Ancestral Snake. PMID:34791190
CellPAINT: Turnkey Illustration of Molecular Cell Biology. PMID:34790910
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions. PMID:34788826
Limits and potential of combined folding and docking. PMID:34788800
AI4AMP: an Antimicrobial Peptide Predictor Using Physicochemical Property-Based Encoding Method and Deep Learning. PMID:34783578
COVID-19 Knowledge Extractor (COKE): A Curated Repository of Drug-Target Associations Extracted from the CORD-19 Corpus of Scientific Publications on COVID-19. PMID:34783553
CyFi-MAP: an interactive pathway-based resource for cystic fibrosis. PMID:34782688
Multiple acyl-CoA dehydrogenase deficiency kills Mycobacterium tuberculosis in vitro and during infection. PMID:34782606
Building Structural Models of a Whole Mycoplasma Cell. PMID:34774566
Current Approaches in Supersecondary Structures Investigation. PMID:34769310
An RNA-Seq-Based Framework for Characterizing Canine Prostate Cancer and Prioritizing Clinically Relevant Biomarker Candidate Genes. PMID:34768937
Comprehensive quantitative characterization of the human term amnion proteome. PMID:34765964
Computational methods for protein localization prediction. PMID:34765098
DeepREx-WS: A web server for characterising protein-solvent interaction starting from sequence. PMID:34765094
Developmental series of gene expression clarifies maternal mRNA provisioning and maternal-to-zygotic transition in a reef-building coral. PMID:34763678
Toward a Computational NMR Procedure for Modeling Dipeptide Side-Chain Conformation. PMID:34762416
Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data. PMID:34762392
Computational insights into differential interaction of mammalian angiotensin-converting enzyme 2 with the SARS-CoV-2 spike receptor binding domain. PMID:34758907
Constraint-based modeling of yeast mitochondria reveals the dynamics of protein import and iron-sulfur cluster biogenesis. PMID:34755100
Co-evolution based machine-learning for predicting functional interactions between human genes. PMID:34753957
GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction. PMID:34748537
Allosteric pockets and dynamic residue network hubs of falcipain 2 in mutations including those linked to artemisinin resistance. PMID:34745456
Identifying stress responsive genes using overlapping communities in co-expression networks. PMID:34743699
The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research. PMID:34741192
Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis. PMID:34741074
Coating of a Novel Antimicrobial Nanoparticle with a Macrophage Membrane for the Selective Entry into Infected Macrophages and Killing of Intracellular Staphylococci. PMID:34737689
Identification of heat responsive genes in pea stipules and anthers through transcriptional profiling. PMID:34735457
Comparative Genomic Analysis and a Novel Set of Missense Mutation of the Leptospira weilii Serogroup Mini From the Urine of Asymptomatic Dogs in Thailand. PMID:34733249
Myoclonic status epilepticus and cerebellar hypoplasia associated with a novel variant in the GRIA3 gene. PMID:34731330
MCDB: A comprehensive curated mitotic catastrophe database for retrieval, protein sequence alignment, and target prediction. PMID:34729303
The generative capacity of probabilistic protein sequence models. PMID:34728624
Fungal genomes: suffering with functional annotation errors. PMID:34724975
Plasmodium falciparum Calcium-Dependent Protein Kinase 4 is Critical for Male Gametogenesis and Transmission to the Mosquito Vector. PMID:34724830
ECM-LSE: Prediction of Extracellular Matrix Proteins Using Deep Latent Space Encoding of k-Spaced Amino Acid Pairs. PMID:34722479
Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. PMID:34721467
Predominant Biphenyl Dioxygenase From Legacy Polychlorinated Biphenyl (PCB)-Contaminated Soil Is a Part of Unusual Gene Cluster and Transforms Flavone and Flavanone. PMID:34721309
High-quality reference genome and annotation aids understanding of berry development for evergreen blueberry (Vaccinium darrowii). PMID:34719668
The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials. PMID:34718737
PANTHER: Making genome-scale phylogenetics accessible to all. PMID:34717010
Transcriptomic analysis of Rhodococcus opacus R7 grown on polyethylene by RNA-seq. PMID:34716360
Nanoencapsulation of sulforaphane in broccoli membrane vesicles and their in vitro antiproliferative activity. PMID:34714214
Design, computational studies, synthesis and in vitro antimicrobial evaluation of benzimidazole based thio-oxadiazole and thio-thiadiazole analogues. PMID:34711258
Identifying carbohydrate-active enzymes of Cutaneotrichosporon oleaginosus using systems biology. PMID:34711240
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO). PMID:34710081
Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins. PMID:34705499
The 20S as a stand-alone proteasome in cells can degrade the ubiquitin tag. PMID:34702852
MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes. PMID:34702846
KDM6A mutations promote acute cytoplasmic DNA release, DNA damage response and mitosis defects. PMID:34702163
On the optimality of the enzyme-substrate relationship in bacteria. PMID:34699521
The Dynamic Codon Biaser: calculating prokaryotic codon usage biases. PMID:34699346
Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure. PMID:34698547
AoP-LSE: Antioxidant Proteins Classification Using Deep Latent Space Encoding of Sequence Features. PMID:34698113
From Anti-SARS-CoV-2 Immune Response to the Cytokine Storm via Molecular Mimicry. PMID:34698069
Gene Ontology curation of the blood-brain barrier to improve the analysis of Alzheimer's and other neurological diseases. PMID:34697638
Identifying Protein Interactomes of Target RNAs Using HyPR-MS. PMID:34694612
DeepTrio: a ternary prediction system for protein-protein interaction using mask multiple parallel convolutional neural networks. PMID:34694333
Structural and functional insights of GSU0105, a unique multiheme cytochrome from G. sulfurreducens. PMID:34688593
TAGOPSIN: collating taxa-specific gene and protein functional and structural information. PMID:34688246
Differential regulation of transposable elements (TEs) during the murine submandibular gland development. PMID:34686213
Resolution of Two Steps in Botulinum Neurotoxin Serotype A1 Light Chain Localization to the Intracellular Plasma Membrane. PMID:34681775
FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow. PMID:34681040
Structural Protein Analysis of Driver Gene Mutations in Conjunctival Melanoma. PMID:34681018
Targeting PirAvp and PirBvp Toxins of Vibrio parahaemolyticus with Oilseed Peptides: An In Silico Approach. PMID:34680792
CK2 Regulation: Perspectives in 2021. PMID:34680478
Potential Roles of Sestrin2 in Alzheimer's Disease: Antioxidation, Autophagy Promotion, and Beyond. PMID:34680426
In silico Approach for Validating and Unveiling New Applications for Prognostic Biomarkers of Endometrial Cancer. PMID:34680205
Text Mining for Building Biomedical Networks Using Cancer as a Case Study. PMID:34680062
Mining drug-target and drug-adverse drug reaction databases to identify target-adverse drug reaction relationships. PMID:34679164
Performance Assessment of the Network Reconstruction Approaches on Various Interactomes. PMID:34676243
Proteomic profile of mesothelial exosomes isolated from peritoneal dialysis effluent of children with focal segmental glomerulosclerosis. PMID:34675284
PIC-Me: paralogs and isoforms classifier based on machine-learning approaches. PMID:34674638
Comparability of reference-based and reference-free transcriptome analysis approaches at the gene expression level. PMID:34674628
An improved deep learning model for hierarchical classification of protein families. PMID:34669708
Structural and functional analysis of Hydra Actinoporin-Like Toxin 1 (HALT-1). PMID:34667248
Global quantification exposes abundant low-level off-target activity by base editors. PMID:34667118
SYNBIP: synthetic binding proteins for research, diagnosis and therapy. PMID:34664670
Connecting MHC-I-binding motifs with HLA alleles via deep learning. PMID:34663927
Correction to: The recurrent missense mutation p.(Arg367Trp) in YARS1 causes a distinct neurodevelopmental phenotype. PMID:34661688
Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis. PMID:34656184
Photoactivatable ribonucleosides mark base-specific RNA-binding sites. PMID:34654832
A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation. PMID:34649616
The selective degradation of sirtuins via macroautophagy in the MPP+ model of Parkinson's disease is promoted by conserved oxidation sites. PMID:34642296
Licorice extract inhibits growth of non-small cell lung cancer by down-regulating CDK4-Cyclin D1 complex and increasing CD8+ T cell infiltration. PMID:34641869
Identification of Rare LRP5 Variants in a Cohort of Males with Impaired Bone Mass. PMID:34639175
OryzaGP 2021 update: a rice gene and protein dataset for named-entity recognition. PMID:34638174
Whole-exome sequencing identified first homozygous frameshift variant in the COLEC10 gene in an Iranian patient causing 3MC syndrome type 3. PMID:34636477
Protein music of enhanced musicality by music style guided exploration of diverse amino acid properties. PMID:34632134
The genome sequence of the brown trout, Salmo trutta Linnaeus 1758. PMID:34632087
Whole-exome sequencing reveals a role of HTRA1 and EGFL8 in brain white matter hyperintensities. PMID:34626176
Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation. PMID:34609518
Efficient generative modeling of protein sequences using simple autoregressive models. PMID:34608136
LPI-deepGBDT: a multiple-layer deep framework based on gradient boosting decision trees for lncRNA-protein interaction identification. PMID:34607567
CDKL5 kinase controls transcription-coupled responses to DNA damage. PMID:34605059
Dietary, Cultural, and Pathogens-Related Selective Pressures Shaped Differential Adaptive Evolution among Native Mexican Populations. PMID:34597392
COVIDrugNet: a network-based web tool to investigate the drugs currently in clinical trial to contrast COVID-19. PMID:34593915
ECNet is an evolutionary context-integrated deep learning framework for protein engineering. PMID:34593817
EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates. PMID:34587449
Isolation, characterization, and genome assembly of Barnettozyma botsteinii sp. nov. and novel strains of Kurtzmaniella quercitrusa isolated from the intestinal tract of the termite Macrotermes bellicosus. PMID:34586397
AlphaMap: an open-source python package for the visual annotation of proteomics data with sequence specific knowledge. PMID:34586352
A glutamic acid-based traceless linker to address challenging chemical protein syntheses. PMID:34585207
In vivo CRISPR screens identify the E3 ligase Cop1 as a modulator of macrophage infiltration and cancer immunotherapy target. PMID:34582788
CPLM 4.0: an updated database with rich annotations for protein lysine modifications. PMID:34581824
An enhanced variant effect predictor based on a deep generative model and the Born-Again Networks. PMID:34580383
Evolutionary Analysis of OAT Gene Family in River and Swamp Buffalo: Potential Role of SLCO3A1 Gene in Milk Performance. PMID:34573376
STARD3: A Prospective Target for Cancer Therapy. PMID:34572920
Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase. PMID:34572495
Full-Atom Model of the Agonist LPS-Bound Toll-like Receptor 4 Dimer in a Membrane Environment. PMID:34569111
De novo genome assembly of the marine teleost, bluefin trevally (Caranx melampygus). PMID:34568914
Immune Mechanism, Gene Module, and Molecular Subtype Identification of Astragalus Membranaceus in the Treatment of Dilated Cardiomyopathy: An Integrated Bioinformatics Study. PMID:34567206
Systems-Level Proteomics Evaluation of Microglia Response to Tumor-Supportive Anti-Inflammatory Cytokines. PMID:34566949
Maturation of Rhodobacter capsulatus Multicopper Oxidase CutO Depends on the CopA Copper Efflux Pathway and Requires the cutF Product. PMID:34566924
Integrating Network Pharmacology and RT-qPCR Analysis to Investigate the Mechanisms Underlying ZeXie Decoction-Mediated Treatment of Non-alcoholic Fatty Liver Disease. PMID:34566646
Odorant-binding proteins in canine anal sac glands indicate an evolutionarily conserved role in mammalian chemical communication. PMID:34565329
Adaptation of Fig Wasps (Agaodinae) to Their Host Revealed by Large-Scale Transcriptomic Data. PMID:34564255
A phosphatase-centric mechanism drives stress signaling response. PMID:34558777
Computational identification of multiple lysine PTM sites by analyzing the instance hardness and feature importance. PMID:34556767
A novel lncRNA-protein interaction prediction method based on deep forest with cascade forest structure. PMID:34556758
Path to improving the life cycle and quality of genome-scale models of metabolism. PMID:34555324
Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class. PMID:34555022
My Cancer Genome: Coevolution of Precision Oncology and a Molecular Oncology Knowledgebase. PMID:34554823
Molecular docking studies of Indian variants of pathophysiological proteins of SARS-CoV-2 with selected drug candidates. PMID:34553696
RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation. PMID:34551440
Subcellular proteomics. PMID:34549195
Integrated Multi-omics, Virtual Screening and Molecular Docking Analysis of Methicillin-Resistant Staphylococcus aureus USA300 for the Identification of Potential Therapeutic Targets: An In-Silico Approach. PMID:34548853
Using informative features in machine learning based method for COVID-19 drug repurposing. PMID:34544500
The Brachypodium distachyon cold-acclimated plasma membrane proteome is primed for stress resistance. PMID:34544140
Data Management and Modeling in Plant Biology. PMID:34539712
The First Chemically-Synthesised, Highly Immunogenic Anti-SARS-CoV-2 Peptides in DNA Genotyped Aotus Monkeys for Human Use. PMID:34539660
Reassembling protein complexes after controlled disassembly by top-down mass spectrometry in native mode. PMID:34539228
Genome-wide detection and classification of terpene synthase genes in Aquilaria agallochum. PMID:34539112
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. PMID:34537014
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling. PMID:34536568
The recurrent missense mutation p.(Arg367Trp) in YARS1 causes a distinct neurodevelopmental phenotype. PMID:34536092
Chromosome-scale reference genome assembly of a diploid potato clone derived from an elite variety. PMID:34534288
GRASP55 restricts early-stage autophagy and regulates spatial organization of the early secretory network. PMID:34533192
Blood biomarkers for mild traumatic brain injury: a selective review of unresolved issues. PMID:34530937
Potential mechanism of Ziyin Tongluo Formula in the treatment of postmenopausal osteoporosis: based on network pharmacology and ovariectomized rat model. PMID:34530875
Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders. PMID:34529671
RNA-binding proteins of COSMIC importance in cancer. PMID:34523614
Single-cell analyses of human pancreas: characteristics of two populations of acinar cells in chronic pancreatitis. PMID:34523348
MULocDeep: A deep-learning framework for protein subcellular and suborganellar localization prediction with residue-level interpretation. PMID:34522290
Trycycler: consensus long-read assemblies for bacterial genomes. PMID:34521459
SARS-CoV-2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms. PMID:34519429
SCISSOR™: a single-cell inferred site-specific omics resource for tumor microenvironment association study. PMID:34514416
In silico predictions of protein interactions between Zika virus and human host. PMID:34513323
Self-mediated positive selection of T cells sets an obstacle to the recognition of nonself. PMID:34507984
A functionally divergent intrinsically disordered region underlying the conservation of stochastic signaling. PMID:34506483
Characterization of Emerging Pathogens Carrying bla KPC-2 Gene in IncP-6 Plasmids Isolated From Urban Sewage in Argentina. PMID:34504809
Accelerating antibiotic discovery through artificial intelligence. PMID:34504303
Taxonomic bias in AMP prediction of invertebrate peptides. PMID:34504226
Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging. PMID:34503120
Systematical Screening of Intracellular Protein Targets of Polyphemusin-I Using Escherichia coli Proteome Microarrays. PMID:34502067
Recent Advances in In Silico Target Fishing. PMID:34500568
Protein kinase N2 mediates flow-induced endothelial NOS activation and vascular tone regulation. PMID:34499618
Influenza virus genotype to phenotype predictions through machine learning: a systematic review. PMID:34498543
A Network Pharmacology Approach to Explore the Mechanism of HuangZhi YiShen Capsule for Treatment of Diabetic Kidney Disease. PMID:34497749
A novel activating JAK1 mutation in chronic eosinophilic leukemia. PMID:34496019
A Genome-Scale Antibiotic Screen in Serratia marcescens Identifies YdgH as a Conserved Modifier of Cephalosporin and Detergent Susceptibility. PMID:34491801
Predicted pH-dependent stability of SARS-CoV-2 spike protein trimer from interfacial acidic groups. PMID:34490059
Structure of the native pyruvate dehydrogenase complex reveals the mechanism of substrate insertion. PMID:34489474
Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails. PMID:34489435
High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing. PMID:34488624
Potential of Variovorax paradoxus isolate BFB1_13 for bioremediation of BTEX contaminated sites. PMID:34487274
Discovery of a transdermally deliverable pentapeptide for activating AdipoR1 to promote hair growth. PMID:34486824
Identifying Active Compounds and Mechanism of Camellia nitidissima Chi on Anti-Colon Cancer by Network Pharmacology and Experimental Validation. PMID:34484402
Machine learning methods, databases and tools for drug combination prediction. PMID:34477201
Whole blood transcriptomics identifies gene expression associated with peanut allergy in infants at high risk. PMID:34473385
Prospects and challenges of cancer systems medicine: from genes to disease networks. PMID:34471925
FSL-Kla: A few-shot learning-based multi-feature hybrid system for lactylation site prediction. PMID:34471495
Revealing the molecular interplay of curcumin as Culex pipiens Acetylcholine esterase 1 (AChE1) inhibitor. PMID:34471175
Structure of the human marker of self 5-transmembrane receptor CD47. PMID:34471125
Polo-like kinase 1 (Plk1) regulates DNA replication origin firing and interacts with Rif1 in Xenopus. PMID:34469577
Exploring targets and signaling pathways of paeonol involved in relieving inflammation based on modern technology. PMID:34463943
TLX, an Orphan Nuclear Receptor With Emerging Roles in Physiology and Disease. PMID:34463725
Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion. PMID:34463614
TIAMMAt: Leveraging Biodiversity to Revise Protein Domain Models, Evidence from Innate Immunity. PMID:34459919
Identifying cysteine residues susceptible to oxidation by photoactivatable atomic oxygen precursors using a proteome-wide analysis. PMID:34458801
An Epitope Platform for Safe and Effective HTLV-1-Immunization: Potential Applications for mRNA and Peptide-Based Vaccines. PMID:34452327
Pan-transcriptome identifying master genes and regulation network in response to drought and salt stresses in Alfalfa (Medicago sativa L.). PMID:34446782
SecProCT: In Silico Prediction of Human Secretory Proteins Based on Capsule Network and Transformer. PMID:34445760
Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review. PMID:34445667
Metatranscriptomic Analysis of Bacterial Communities on Laundered Textiles: A Pilot Case Study. PMID:34442670
Possible Protective Effect of LOXL1 Variant in the Cohort of Chernobyl Catastrophe Clean-Up Workers. PMID:34440405
Next-Generation Sequencing Analysis of the Tineola bisselliella Larval Gut Transcriptome Reveals Candidate Enzymes for Keratin Digestion. PMID:34440287
A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis. PMID:34437539
Evolutionary Profile for (Host and Viral) MLKL Indicates Its Activities as a Battlefront for Extensive Counteradaptation. PMID:34436583
A global map of associations between types of protein posttranslational modifications and human genetic diseases. PMID:34430807
Integrative genetic, genomic and transcriptomic analysis of heat shock protein and nuclear hormone receptor gene associations with spontaneous preterm birth. PMID:34429451
Transcriptomic analysis of a wild and a cultivated varieties of Capsicum annuum over fruit development and ripening. PMID:34428253
Ankyrin repeats in context with human population variation. PMID:34428215
A Combination of Metagenomic and Cultivation Approaches Reveals Hypermutator Phenotypes within Vibrio cholerae-Infected Patients. PMID:34427503
Rapid Genomic Evolution Drives the Diversification of Male Reproductive Genes in Dung Beetles. PMID:34426833
Heterogeneous graph attention networks for drug virus association prediction. PMID:34419588
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PMID:34411100
Characterization of the ABC methionine transporter from Neisseria meningitidis reveals that lipidated MetQ is required for interaction. PMID:34409939
Functional Classification of Super-Large Families of Enzymes Based on Substrate Binding Pocket Residues for Biocatalysis and Enzyme Engineering Applications. PMID:34409021
PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data. PMID:34407837
Molecular mimicry between SARS-CoV-2 and the female reproductive system. PMID:34407240
Transovarial transmission of a core virome in the Chagas disease vector Rhodnius prolixus. PMID:34407148
Immunopeptidomics toolkit library (IPTK): a python-based modular toolbox for analyzing immunopeptidomics data. PMID:34404349
Identification of COVID-19 prognostic markers and therapeutic targets through meta-analysis and validation of Omics data from nasopharyngeal samples. PMID:34392148
Sequence-dependent mechanics of collagen reflect its structural and functional organization. PMID:34390685
Paracoccus onubensis sp. nov., a novel alphaproteobacterium isolated from the wall of a show cave. PMID:34388083
Angiogenic gene networks are dysregulated in opioid use disorder: evidence from multi-omics and imaging of postmortem human brain. PMID:34385598
Genetic basis of cannabis use: a systematic review. PMID:34384432
Fold Evolution before LUCA: Common Ancestry of SH3 Domains and OB Domains. PMID:34383917
Integration of chronological omics data reveals mitochondrial regulatory mechanisms during the development of hepatocellular carcinoma. PMID:34383828
A new comprehensive annotation of leucine-rich repeat-containing receptors in rice. PMID:34382706
Chaperonin Abundance Enhances Bacterial Fitness. PMID:34381811
P2T2: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants. PMID:34377961
Shiquan Yuzhen Decoction inhibits angiogenesis and tumor apoptosis caused by non-small cell lung cancer and promotes immune response. PMID:34377231
Urine peptidome analysis in cardiorenal syndrome reflects molecular processes. PMID:34376786
The molecular basis, genetic control and pleiotropic effects of local gene co-expression. PMID:34376650
Cellular Uptake and Intracellular Phosphorylation of GS-441524: Implications for Its Effectiveness against COVID-19. PMID:34372575
Systematic Bioinformatic Analyses of Nutrigenomic Modifications by Polyphenols Associated with Cardiometabolic Health in Humans-Evidence from Targeted Nutrigenomic Studies. PMID:34371836
Phosphoinositide Recognition Sites Are Blocked by Metabolite Attachment. PMID:34368138
Large-scale computational discovery and analysis of virus-derived microbial nanocompartments. PMID:34362927
Analysis of Bacterial Communities on North Sea Macroalgae and Characterization of the Isolated Planctomycetes Adhaeretor mobilis gen. nov., sp. nov., Roseimaritima multifibrata sp. nov., Rosistilla ulvae sp. nov. and Rubripirellula lacrimiformis sp. nov. PMID:34361930
The Histidine Biosynthetic Genes in the Superphylum Bacteroidota-Rhodothermota-Balneolota-Chlorobiota: Insights into the Evolution of Gene Structure and Organization. PMID:34361875
Characterization of the Heat-Stable Proteome during Seed Germination in Arabidopsis with Special Focus on LEA Proteins. PMID:34360938
Expanding the MECP2 network using comparative genomics reveals potential therapeutic targets for Rett syndrome. PMID:34355696
Using agricultural metadata: a novel investigation of trends in sowing date in on-farm research trials using the Online Farm Trials database. PMID:34354820
Genome-wide analysis of HECT E3 ubiquitin ligase gene family in Solanum lycopersicum. PMID:34354159
An extended reconstruction of human gut microbiota metabolism of dietary compounds. PMID:34354065
GTXplorer: A portal to navigate and visualize the evolutionary information encoded in fold A glycosyltransferases. PMID:34351427
A domain damage index to prioritizing the pathogenicity of missense variants. PMID:34350656
Characterization of Five Transmembrane Proteins: With Focus on the Tweety, Sideroflexin, and YIP1 Domain Families. PMID:34350187
Influence of HLA Class II Polymorphism on Predicted Cellular Immunity Against SARS-CoV-2 at the Population and Individual Level. PMID:34349756
Network Pharmacology Prediction and Molecular Docking-Based Strategy to Discover the Potential Pharmacological Mechanism of Huai Hua San Against Ulcerative Colitis. PMID:34349502
Expanding the KIF4A-associated phenotype. PMID:34346154
CanImmunother: a manually curated database for identification of cancer immunotherapies associating with biomarkers, targets, and clinical effects. PMID:34345532
Probing an Ixodes ricinus salivary gland yeast surface display with tick-exposed human sera to identify novel candidates for an anti-tick vaccine. PMID:34344917
Comprehensive Strain-Level Analysis of the Gut Microbe Faecalibacterium prausnitzii in Patients with Liver Cirrhosis. PMID:34342541
Time-Resolved Proteome Analysis of Listeria monocytogenes during Infection Reveals the Role of the AAA+ Chaperone ClpC for Host Cell Adaptation. PMID:34342529
CCD2: design constructs for protein expression, the easy way. PMID:34342272
A systems-level study reveals host-targeted repurposable drugs against SARS-CoV-2 infection. PMID:34339582
Plasma proteins, cognitive decline, and 20-year risk of dementia in the Whitehall II and Atherosclerosis Risk in Communities studies. PMID:34338426
In-silico study of peptide-protein interaction of antimicrobial peptides potentially targeting SARS and SARS-CoV-2 nucleocapsid protein. PMID:34336545
Chromosome-Scale Genome for a Red-Fruited, Perpetual Flowering and Runnerless Woodland Strawberry (Fragaria vesca). PMID:34335685
A Computational Exploration of the Molecular Network Associated to Neuroinflammation in Alzheimer's Disease. PMID:34335238
TMEM180 contributes to SW480 human colorectal cancer cell proliferation through intra-cellular metabolic pathways. PMID:34332338
Affinity Proteomics and Deglycoproteomics Uncover Novel EDEM2 Endogenous Substrates and an Integrative ERAD Network. PMID:34332121
The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern. PMID:34324748
Topological network based drug repurposing for coronavirus 2019. PMID:34324563
Protein oligomer modeling guided by predicted interchain contacts in CASP14. PMID:34324224
Proteomic analysis reveals dexamethasone rescues matrix breakdown but not anabolic dysregulation in a cartilage injury model. PMID:34322675
New Family Members of FG Repeat Proteins and Their Unexplored Roles During Phase Separation. PMID:34322491
Broad and Efficient Activation of Memory CD4+ T Cells by Novel HAdV- and HCMV-Derived Peptide Pools. PMID:34322126
Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms. PMID:34318308
A blood-based prognostic liver secretome signature and long-term hepatocellular carcinoma risk in advanced liver fibrosis. PMID:34318286
Mechanistic models of signaling pathways deconvolute the glioblastoma single-cell functional landscape. PMID:34316686
Putatively cancer-specific exon-exon junctions are shared across patients and present in developmental and other non-cancer cells. PMID:34316681
A new strategy to uncover fragile X proteomic biomarkers using the nascent proteome of peripheral blood mononuclear cells (PBMCs). PMID:34312401
Spironolactone Ameliorates Senescence and Calcification by Modulating Autophagy in Rat Tendon-Derived Stem Cells via the NF-κB/MAPK Pathway. PMID:34306308
Sequence variation in the β7-β8 loop of bacterial class A sortase enzymes alters substrate selectivity. PMID:34302812
In Silico Prediction of the Mechanism of Action of Pyriproxyfen and 4'-OH-Pyriproxyfen against A. mellifera and H. sapiens Receptors. PMID:34299368
Analysis of the Structural Mechanism of ATP Inhibition at the AAA1 Subunit of Cytoplasmic Dynein-1 Using a Chemical "Toolkit". PMID:34299323
CFTR Lifecycle Map-A Systems Medicine Model of CFTR Maturation to Predict Possible Active Compound Combinations. PMID:34299207
Knock-Out of ACBD3 Leads to Dispersed Golgi Structure, but Unaffected Mitochondrial Functions in HEK293 and HeLa Cells. PMID:34298889
The genome of the Pyrenean desman and the effects of bottlenecks and inbreeding on the genomic landscape of an endangered species. PMID:34295371
Genomic data support management of anadromous Arctic Char fisheries in Nunavik by highlighting neutral and putatively adaptive genetic variation. PMID:34295370
Invasion and rapid adaptation of guppies (Poecilia reticulata) across the Hawaiian Archipelago. PMID:34295361
Integrative Identification of Crucial Genes Associated With Plant Hormone-Mediated Bud Dormancy in Prunus mume. PMID:34295354
Myco-remediation of Chlorinated Pesticides: Insights Into Fungal Metabolic System. PMID:34294989
Comparison of transcriptome between high- and low-marbling fineness in longissimus thoracis muscle of Korean cattle. PMID:34293845
Spatially resolved analysis of Pseudomonas aeruginosa biofilm proteomes measured by laser ablation sample transfer. PMID:34292966
Exploring amino acid functions in a deep mutational landscape. PMID:34292650
Distinct Human Gut Microbial Taxonomic Signatures Uncovered With Different Sample Processing and Microbial Cell Disruption Methods for Metaproteomic Analysis. PMID:34290676
ResidueFinder: extracting individual residue mentions from protein literature. PMID:34289903
Testicular disposition of clofarabine in rats is dependent on equilibrative nucleoside transporters. PMID:34288585
Comparative Genomics of Three Novel Jumbo Bacteriophages Infecting Staphylococcus aureus. PMID:34287047
Co-evolutionary landscape at the interface and non-interface regions of protein-protein interaction complexes. PMID:34285778
Structural binding site comparisons reveal Crizotinib as a novel LRRK2 inhibitor. PMID:34285770
Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato). PMID:34283859
Ribosome heterogeneity in Drosophila melanogaster gonads through paralog-switching. PMID:34283226
Representing a Heterogeneous Pharmaceutical Knowledge-Graph with Textual Information. PMID:34278204
IDOPS, a Profile HMM-Based Tool to Detect Pesticidal Sequences and Compare Their Genetic Context. PMID:34276598
Discovery of fibrillar adhesins across bacterial species. PMID:34275445
Prediction of combination therapies based on topological modeling of the immune signaling network in multiple sclerosis. PMID:34271980
Localization, proteomics, and metabolite profiling reveal a putative vesicular transporter for UDP-glucose. PMID:34269178
Crk adaptor proteins are necessary for the development of the zebrafish retina. PMID:34268820
The conserved ASTN2/BRINP1 locus at 9q33.1-33.2 is associated with major psychiatric disorders in a large pedigree from Southern Spain. PMID:34267256
ColBuilder: A server to build collagen fibril models. PMID:34265261
The tweety Gene Family: From Embryo to Disease. PMID:34262434
Metagenomics: a path to understanding the gut microbiome. PMID:34259891
Effect of dapagliflozin on diabetic patients with cardiovascular disease via MAPK signalling pathway. PMID:34258872
Signatures of mitonuclear coevolution in a warbler species complex. PMID:34257313
Structural basis of the membrane intramolecular transacylase reaction responsible for lyso-form lipoprotein synthesis. PMID:34253723
DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction. PMID:34252926
Epigenetic rewiring of skeletal muscle enhancers after exercise training supports a role in whole-body function and human health. PMID:34252634
Genetic Context of optrA and poxtA in Florfenicol-Resistant Enterococci Isolated from Flowing Surface Water in Switzerland. PMID:34252296
Target enrichment improves phylogenetic resolution in the genus Zanthoxylum (Rutaceae) and indicates both incomplete lineage sorting and hybridization events. PMID:34250543
Barcode sequencing and a high-throughput assay for chronological lifespan uncover ageing-associated genes in fission yeast. PMID:34250083
Recognition of Streptococcal Promoters by the Pneumococcal SigA Protein. PMID:34250014
DTL-DephosSite: Deep Transfer Learning Based Approach to Predict Dephosphorylation Sites. PMID:34249915
A Peptide Vaccine Candidate Tailored to Individuals' Genetics Mimics the Multi-Targeted T Cell Immunity of COVID-19 Convalescent Subjects. PMID:34249101
A Chromosome-Level Genome Assembly of the Mandarin Fish (Siniperca chuatsi). PMID:34249093
Altered skeletal muscle metabolic pathways, age, systemic inflammation, and low cardiorespiratory fitness associate with improvements in disease activity following high-intensity interval training in persons with rheumatoid arthritis. PMID:34246305
High-throughput analysis of the interactions between viral proteins and host cell RNAs. PMID:34246161
Genomic atlas of the proteome from brain, CSF and plasma prioritizes proteins implicated in neurological disorders. PMID:34239129
Predicting synchronized gene coexpression patterns from fibration symmetries in gene regulatory networks in bacteria. PMID:34238210
The RAS GTPase RIT1 compromises mitotic fidelity through spindle assembly checkpoint suppression. PMID:34237269
Integrated Multi-Omics Analysis of Mechanisms Underlying Yeast Ethanol Tolerance. PMID:34236875
Burkholderia multivorans requires species-specific GltJK for entry of a contact-dependent growth inhibition system protein. PMID:34236112
Cyclohexyl-α maltoside as a highly efficient tool for membrane protein studies. PMID:34235488
Saccharomyces cerevisiae as a superior host for overproduction of prokaryotic integral membrane proteins. PMID:34235486
Diffusive protein interactions in human versus bacterial cells. PMID:34235470
Predicted structural mimicry of spike receptor-binding motifs from highly pathogenic human coronaviruses. PMID:34234921
A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation. PMID:34233164
In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology. PMID:34232610
Achromobacter spp. genetic adaptation in cystic fibrosis. PMID:34232117
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes. PMID:34230640
The mitochondrial genome of the grape powdery mildew pathogen Erysiphe necator is intron rich and exhibits a distinct gene organization. PMID:34230575
PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences. PMID:34228733
A global transcriptomic analysis of Staphylococcus aureus biofilm formation across diverse clonal lineages. PMID:34227933
Comparative genomic analysis of Escherichia coli isolates from cases of bovine clinical mastitis identifies nine specific pathotype marker genes. PMID:34227932
Random forest classification for predicting lifespan-extending chemical compounds. PMID:34226569
Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding. PMID:34226565
Plasticity in plastid redox networks: evolution of glutathione-dependent redox cascades and glutathionylation sites. PMID:34225654
Protocol for HSDFinder: Identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes. PMID:34223195
A comprehensive review of integrative pharmacology-based investigation: A paradigm shift in traditional Chinese medicine. PMID:34221858
Mapping Salivary Proteases in Sjögren's Syndrome Patients Reveals Overexpression of Dipeptidyl Peptidase-4/CD26. PMID:34220840
Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. PMID:34214467
Increasing the Accuracy of Single Sequence Prediction Methods Using a Deep Semi-Supervised Learning Framework. PMID:34213528
SidechainNet: An all-atom protein structure dataset for machine learning. PMID:34213059
Translational Proteomics Analysis of Anthracycline-Induced Cardiotoxicity From Cardiac Microtissues to Human Heart Biopsies. PMID:34211507
Improving the Utility of Polygenic Risk Scores as a Biomarker for Alzheimer's Disease. PMID:34209762
MDCAN-Lys: A Model for Predicting Succinylation Sites Based on Multilane Dense Convolutional Attention Network. PMID:34208298
PhaLP: A Database for the Study of Phage Lytic Proteins and Their Evolution. PMID:34206969
17β-Estradiol-Induced Conformational Changes of Human Microsomal Triglyceride Transfer Protein: A Computational Molecular Modelling Study. PMID:34206252
Pathogen Moonlighting Proteins: From Ancestral Key Metabolic Enzymes to Virulence Factors. PMID:34203698
Conversion of the Sensor Kinase DcuS to the Fumarate Sensitive State by Interaction of the Bifunctional Transporter DctA at the TM2/PASC-Linker Region. PMID:34203512
Secretome Analysis of Arabidopsis-Trichoderma atroviride Interaction Unveils New Roles for the Plant Glutamate:Glyoxylate Aminotransferase GGAT1 in Plant Growth Induced by the Fungus and Resistance against Botrytis cinerea. PMID:34202732
Hyperoxia Inhibits Proliferation of Retinal Endothelial Cells in a Myc-Dependent Manner. PMID:34202240
Insights into Autotrophic Activities and Carbon Flow in Iron-Rich Pelagic Aggregates (Iron Snow). PMID:34201891
Proteogenomics Reveals Orthologous Alternatively Spliced Proteoforms in the Same Human and Mouse Brain Regions with Differential Abundance in an Alzheimer's Disease Mouse Model. PMID:34201730
Machine Learning-Based Approach Highlights the Use of a Genomic Variant Profile for Precision Medicine in Ovarian Failure. PMID:34199109
Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms. PMID:34197603
Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl. PMID:34195226
Cytoplasmic long noncoding RNAs are differentially regulated and translated during human neuronal differentiation. PMID:34193551
Nanoscape, a data-driven 3D real-time interactive virtual cell environment. PMID:34191720
Stepwise target controllability identifies dysregulations of macrophage networks in multiple sclerosis. PMID:34189368
Leveraging network analysis to evaluate biomedical named entity recognition tools. PMID:34188248
NOD: a web server to predict New use of Old Drugs to facilitate drug repurposing. PMID:34188160
Genomic and Phenotypic Evolution of Achromobacter xylosoxidans during Chronic Airway Infections of Patients with Cystic Fibrosis. PMID:34184916
Chemical profiling of DNA G-quadruplex-interacting proteins in live cells. PMID:34183817
Mechanism of protective effect of xuan-bai-cheng-qi decoction on LPS-induced acute lung injury based on an integrated network pharmacology and RNA-sequencing approach. PMID:34183011
Mode of action evaluation for reduced reproduction in Daphnia pulex exposed to the insensitive munition, 1-methyl-3-nitro-1-nitroguanidine (MeNQ). PMID:34173910
Optimization of a human milk-directed quantitative sIgA ELISA method substantiated by mass spectrometry. PMID:34169348
A tailored phosphoaspartate probe unravels CprR as a response regulator in Pseudomonas aeruginosa interkingdom signaling. PMID:34168754
Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodeling superfamily. PMID:34166615
Unraveling the surface glycoprotein interaction network by integrating chemical crosslinking with MS-based proteomics. PMID:34163979
Revealing the Characteristics of the Antarctic Snow Alga Chlorominima collina gen. et sp. nov. Through Taxonomy, Physiology, and Transcriptomics. PMID:34163502
NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II. PMID:34162981
Is mRNA decapping by ApaH like phosphatases present in eukaryotes beyond the Kinetoplastida? PMID:34162332
Network-based analysis of virulence factors for uncovering Aeromonas veronii pathogenesis. PMID:34162325
Genome-wide association study of signature genetic alterations among pseudomonas aeruginosa cystic fibrosis isolates. PMID:34161396
Interplay between SARS-CoV-2-derived miRNAs, immune system, vitamin D pathway and respiratory system. PMID:34159729
Adipsin promotes bone marrow adiposity by priming mesenchymal stem cells. PMID:34155972
Analysis of Two SusE-Like Enzymes From Bacteroides thetaiotaomicron Reveals a Potential Degradative Capacity for This Protein Family. PMID:34149636
Peptides of H. sapiens and P. falciparum that are predicted to bind strongly to HLA-A*24:02 and homologous to a SARS-CoV-2 peptide. PMID:34146538
Chromosome Fusion Affects Genetic Diversity and Evolutionary Turnover of Functional Loci but Consistently Depends on Chromosome Size. PMID:34146107
Somatic mutation subtypes of lung adenocarcinoma in East Asian reveal divergent biological characteristics and therapeutic vulnerabilities. PMID:34142036
Computational study to discover potent phytochemical inhibitors against drug target, squalene synthase from Leishmania donovani. PMID:34141935
DCBLD1 is associated with the integrin signaling pathway and has prognostic value in non-small cell lung and invasive breast carcinoma. PMID:34140574
Evaluating the lettuce metatranscriptome with MinION sequencing for future spaceflight food production applications. PMID:34140518
Machine learning differentiates enzymatic and non-enzymatic metals in proteins. PMID:34140507
Learning the protein language: Evolution, structure, and function. PMID:34139171
Fundamentals to function: Quantitative and scalable approaches for measuring protein stability. PMID:34139165
COSMIC Cancer Gene Census 3D database: understanding the impacts of mutations on cancer targets. PMID:34137435
Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist. PMID:34134983
Prediction of unconventional protein secretion by exosomes. PMID:34134630
Tools and methods for circular dichroism spectroscopy of proteins: a tutorial review. PMID:34132259
Proteome-wide prediction of bacterial carbohydrate-binding proteins as a tool for understanding commensal and pathogen colonisation of the vaginal microbiome. PMID:34131152
Insights into the genomic evolution of insects from cricket genomes. PMID:34127782
Sphingomyelin and Medullary Sponge Kidney Disease: A Biological Link Identified by Omics Approach. PMID:34124100
Molecular basis of anticoagulant and anticomplement activity of the tick salivary protein Salp14 and its homologs. PMID:34118237
Elevated metallothionein expression in long-lived species mediates the influence of cadmium accumulation on aging. PMID:34117600
Integrating protein networks and machine learning for disease stratification in the Hereditary Spastic Paraplegias. PMID:34113825
Unique Pathogen Peptidomes Facilitate Pathogen-Specific Selection and Specialization of MHC Alleles. PMID:34110412
Thioesterase superfamily member 1 undergoes stimulus-coupled conformational reorganization to regulate metabolism in mice. PMID:34108467
PINIR: a comprehensive information resource for Pin-II type protease inhibitors. PMID:34107869
Human Urine Alters Methicillin-Resistant Staphylococcus aureus Virulence and Transcriptome. PMID:34105987
Effects of FUdR on gene expression in the C. elegans bacterial diet OP50. PMID:34103088
Evolutionary crossroads of cell signaling: PP1 and PP2A substrate sites in intrinsically disordered regions. PMID:34100859
Two RmlC homologs catalyze dTDP-4-keto-6-deoxy-D-glucose epimerization in Pseudomonas putida KT2440. PMID:34099824
Human tear proteome dataset in response to daily wear of water gradient contact lens using SWATH-MS approach. PMID:34095372
A Novel GH Family 20 β-N-acetylhexosaminidase With Both Chitosanase and Chitinase Activity From Aspergillus oryzae. PMID:34095233
A combined evolutionary and structural approach to disclose the primary structural determinants essential for proneurotrophins biological functions. PMID:34094000
β-Lactoglobulin and Glycodelin: Two Sides of the Same Coin? PMID:34093238
Molecular docking analysis of antimicrobial peptides with the CXCL1 protein target for colorectal cancer. PMID:34092958
Mapping of m6A and Its Regulatory Targets in Prostate Cancer Reveals a METTL3-Low Induction of Therapy Resistance. PMID:34088870
Annotation of snoRNA abundance across human tissues reveals complex snoRNA-host gene relationships. PMID:34088344
Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations. PMID:34087064
Proteomic Characterization of the Dynamics of Ischemic Stroke in Mice. PMID:34085531
Single-nucleotide conservation state annotation of the SARS-CoV-2 genome. PMID:34083758
MBD5 and MBD6 couple DNA methylation to gene silencing through the J-domain protein SILENZIO. PMID:34083448
Mice with dysfunctional TGF-β signaling develop altered intestinal microbiome and colorectal cancer resistant to 5FU. PMID:34082069
Kinetoplastid kinetochore proteins KKT2 and KKT3 have unique centromere localization domains. PMID:34081090
Positive Selection in Gene Regulatory Factors Suggests Adaptive Pleiotropic Changes During Human Evolution. PMID:34079582
Mantis: flexible and consensus-driven genome annotation. PMID:34076241
Mechnetor: a web server for exploring protein mechanism and the functional context of genetic variants. PMID:34076240
Structural insights and inhibition mechanism of TMPRSS2 by experimentally known inhibitors Camostat mesylate, Nafamostat and Bromhexine hydrochloride to control SARS-coronavirus-2: A molecular modeling approach. PMID:34075338
Periscope Proteins are variable-length regulators of bacterial cell surface interactions. PMID:34074781
Regulation of the Phosphoinositide Code by Phosphorylation of Membrane Readers. PMID:34069055
Differential Methylation Patterns in Apomictic vs. Sexual Genotypes of the Diplosporous Grass Eragrostis curvula. PMID:34068493
Physicochemical Features and Peculiarities of Interaction of AMP with the Membrane. PMID:34067510
PGRP-LB: An Inside View into the Mechanism of the Amidase Reaction. PMID:34066955
Evaluating Mechanisms of IDH1 Regulation through Site-Specific Acetylation Mimics. PMID:34065652
Lemur Tyrosine Kinases and Prostate Cancer: A Literature Review. PMID:34064250
Effects of Three-Month Administration of High-Saturated Fat Diet and High-Polyunsaturated Fat Diets with Different Linoleic Acid (LA, C18:2n-6) to α-Linolenic Acid (ALA, C18:3n-3) Ratio on the Mouse Liver Proteome. PMID:34063343
High Resistance of a Sludge Enriched with Nitrogen-Fixing Bacteria to Ammonium Salts and Its Potential as a Biofertilizer. PMID:34062837
VB12Path for Accurate Metagenomic Profiling of Microbially Driven Cobalamin Synthesis Pathways. PMID:34060913
Genome-Scale Metabolic Model of Caldicellulosiruptor bescii Reveals Optimal Metabolic Engineering Strategies for Bio-based Chemical Production. PMID:34060912
DrugComb update: a more comprehensive drug sensitivity data repository and analysis portal. PMID:34060634
Traumatic injury compromises nucleocytoplasmic transport and leads to TDP-43 pathology. PMID:34060470
Model-based analysis uncovers mutations altering autophagy selectivity in human cancer. PMID:34059679
Comparative analysis of de novo genomes reveals dynamic intra-species divergence of NLRs in pepper. PMID:34059006
Substrate Selectivity of Coumarin Derivatives by Human CYP1 Enzymes: In Vitro Enzyme Kinetics and In Silico Modeling. PMID:34056284
Dasatinib-SIK2 Binding Elucidated by Homology Modeling, Molecular Docking, and Dynamics Simulations. PMID:34056256
Systems Pharmacology and In Silico Docking Analysis Uncover Association of CA2, PPARG, RXRA, and VDR with the Mechanisms Underlying the Shi Zhen Tea Formula Effect on Eczema. PMID:34055023
Systemic Bioinformatic Analyses of Nuclear-Encoded Mitochondrial Genes in Hypertrophic Cardiomyopathy. PMID:34054926
Medicinal Plant Leaf Extract From Sage and Lemon Verbena Promotes Intestinal Immunity and Barrier Function in Gilthead Seabream (Sparus aurata). PMID:34054843
Investigation of the Multi-Target Mechanism of Guanxin-Shutong Capsule in Cerebrovascular Diseases: A Systems Pharmacology and Experimental Assessment. PMID:34054530
Multi-Dimensional Transcriptome Analysis Reveals Modulation of Cholesterol Metabolism as Highly Integrated Response to Brain Injury. PMID:34054419
ncFANs v2.0: an integrative platform for functional annotation of non-coding RNAs. PMID:34050762
Pretraining model for biological sequence data. PMID:34050350
Molecular mechanisms of metabotropic GABAB receptor function. PMID:34049877
The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing. PMID:34048576
Introducing the metacore concept for multi-target ligand design. PMID:34046634
Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading. PMID:34046429
Noncontiguous T cell epitopes in autoimmune diabetes: From mice to men and back again. PMID:34044020
High-Quality Reference Genome Sequence for the Oomycete Vegetable Pathogen Phytophthora capsici Strain LT1534. PMID:34042486
TSPEAR variants are primarily associated with ectodermal dysplasia and tooth agenesis but not hearing loss: A novel cohort study. PMID:34042254
Identification of prognostic and bone metastasis-related alternative splicing signatures in mesothelioma. PMID:34041868
Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds. PMID:34041266
NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information. PMID:34038555
Based on Network Pharmacology and Molecular Docking to Explore the Underlying Mechanism of Huangqi Gegen Decoction for Treating Diabetic Nephropathy. PMID:34035828
A 3D system to model human pancreas development and its reference single-cell transcriptome atlas identify signaling pathways required for progenitor expansion. PMID:34035279
The Human Salivary Proteome Wiki: A Community-Driven Research Platform. PMID:34032471
SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome. PMID:34031561
Distinct EH domains of the endocytic TPLATE complex confer lipid and protein binding. PMID:34031427
Analysis of aqueous humor total antioxidant capacity and its correlation with corneal endothelial health. PMID:34027088
A Strategy Based on Loop Analysis to Develop Peptide Epitopes: Application to SARS-CoV-2 Spike Protein. PMID:34026833
Mapping OMIM Disease-Related Variations on Protein Domains Reveals an Association Among Variation Type, Pfam Models, and Disease Classes. PMID:34026820
Prokaryotic communities from a lava tube cave in La Palma Island (Spain) are involved in the biogeochemical cycle of major elements. PMID:34026356
Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale. PMID:34022966
DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web. PMID:34019664
Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures. PMID:34019656
Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay. PMID:34019569
Molecularly imprinted polymers by epitope imprinting: a journey from molecular interactions to the available bioinformatics resources to scout for epitope templates. PMID:34018035
COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. PMID:34015823
New diarylsulfonamide inhibitors of Leishmania infantum amastigotes. PMID:34015753
Host pharmacogenetic factors that may affect liver neoplasm incidence upon using direct-acting antivirals for treating hepatitis C infection. PMID:34013078
Structural Profiling of Bacterial Effectors Reveals Enrichment of Host-Interacting Domains and Motifs. PMID:34012977
A PROSS-designed extensively mutated estrogen receptor α variant displays enhanced thermal stability while retaining native allosteric regulation and structure. PMID:34006920
Application of beta and gamma carbonic anhydrase sequences as tools for identification of bacterial contamination in the whole genome sequence of inbred Wuzhishan minipig (Sus scrofa) annotated in databases. PMID:34003248
Proline codon pair selection determines ribosome pausing strength and translation efficiency in bacteria. PMID:34002016
Primordial super-enhancers: heat shock-induced chromatin organization in yeast. PMID:34001402
The fructose-1,6-bisphosphatase deficiency and the p.(Lys204ArgfsTer72) variant. PMID:33999094
Computational generation of proteins with predetermined three-dimensional shapes using ProteinSolver. PMID:33997819
Abundance Imparts Evolutionary Constraints of Similar Magnitude on the Buried, Surface, and Disordered Regions of Proteins. PMID:33996892
Identification of the key target profiles underlying the drugs of narrow therapeutic index for treating cancer and cardiovascular disease. PMID:33995923
Structure and evolutionary trace-assisted screening of a residue swapping the substrate ambiguity and chiral specificity in an esterase. PMID:33995922
ExVe: The knowledge base of orthologous proteins identified in fungal extracellular vesicles. PMID:33995920
Structural modeling of a novel membrane-bound globin-coupled sensor in Geobacter sulfurreducens. PMID:33995893
Gene Expression Patterns for Proteins With Lectin Domains in Flax Stem Tissues Are Related to Deposition of Distinct Cell Wall Types. PMID:33995436
Distinguishing Signal From Noise in Immunopeptidome Studies of Limiting-Abundance Biological Samples: Peptides Presented by I-Ab in C57BL/6 Mouse Thymus. PMID:33995376
Myomedin scaffold variants targeted to 10E8 HIV-1 broadly neutralizing antibody mimic gp41 epitope and elicit HIV-1 virus-neutralizing sera in mice. PMID:33993840
Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries. PMID:33993214
The SARS-CoV-2 RNA interactome. PMID:33989516
Pathogenic potential assessment of the Shiga toxin-producing Escherichia coli by a source attribution-considered machine learning model. PMID:33986113
Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models? PMID:33983933
Insights on the Evolutionary Genomics of the Blautia Genus: Potential New Species and Genetic Content Among Lineages. PMID:33981291
Reconstruction of ancient microbial genomes from the human gut. PMID:33981035
Landscape of allele-specific transcription factor binding in the human genome. PMID:33980847
Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions. PMID:33979327
Clustering FunFams using sequence embeddings improves EC purity. PMID:33978744
Inhibition of hyaluronan secretion by novel coumarin compounds and chitin synthesis inhibitors. PMID:33978736
PhosIDP: a web tool to visualize the location of phosphorylation sites in disordered regions. PMID:33976270
SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. PMID:33976134
Recurrent NFIA K125E substitution represents a loss-of-function allele: Sensitive in vitro and in vivo assays for nontruncating alleles. PMID:33973697
Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes. PMID:33972587
Knowledge bases and software support for variant interpretation in precision oncology. PMID:33971666
Paired SARS-CoV-2 spike protein mutations observed during ongoing SARS-CoV-2 viral transfer from humans to minks and back to humans. PMID:33971305
Complete genome sequence of Photobacterium ganghwense C2.2: A new polyhydroxyalkanoate production candidate. PMID:33970538
Updates to HCOP: the HGNC comparison of orthology predictions tool. PMID:33959747
Structural and mechanistic insights into the bifunctional HISN2 enzyme catalyzing the second and third steps of histidine biosynthesis in plants. PMID:33958623
Evolutionary Dynamics of the OR Gene Repertoire in Teleost Fishes: Evidence of an Association with Changes in Olfactory Epithelium Shape. PMID:33950257
Transcriptome of different fruiting stages in the cultivated mushroom Cyclocybe aegerita suggests a complex regulation of fruiting and reveals enzymes putatively involved in fungal oxylipin biosynthesis. PMID:33947322
Characterization of Extracellular Vesicles Secreted in Lentiviral Producing HEK293SF Cell Cultures. PMID:33946875
Gene Coexpression Network Reveals Highly Conserved, Well-Regulated Anti-Ageing Mechanisms in Old Ant Queens. PMID:33944936
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. PMID:33944776
Detecting Protein Communities in Native Cell Extracts by Machine Learning: A Structural Biologist's Perspective. PMID:33937337
Strategies for Enhancing in vitro Degradation of Linuron by Variovorax sp. Strain SRS 16 Under the Guidance of Metabolic Modeling. PMID:33937210
Clinical and Genetic Characterization of Craniosynostosis in Saudi Arabia. PMID:33937142
Cell Wall Layer Induced in Xylem Fibers of Flax Upon Gravistimulation Is Similar to Constitutively Formed Cell Walls of Bast Fibers. PMID:33936149
LanCLs add glutathione to dehydroamino acids generated at phosphorylated sites in the proteome. PMID:33932340
A SARS-CoV-2 (COVID-19) biological network to find targets for drug repurposing. PMID:33931664
Sequencing, assembly and annotation of the whole-insect genome of Lymantria dispar dispar, the European gypsy moth. PMID:33930134
CladeOScope: functional interactions through the prism of clade-wise co-evolution. PMID:33928243
An Overview of Biological and Computational Methods for Designing Mechanism-Informed Anti-biofilm Agents. PMID:33927701
Stepwise pathogenic evolution of Mycobacterium abscessus. PMID:33926925
AC2: An Efficient Protein Sequence Compression Tool Using Artificial Neural Networks and Cache-Hash Models. PMID:33925812
Identification of a Chlorovirus PBCV-1 Protein Involved in Degrading the Host Cell Wall during Virus Infection. PMID:33924931
The Human 2-Cys Peroxiredoxins form Widespread, Cysteine-Dependent- and Isoform-Specific Protein-Protein Interactions. PMID:33923941
Allosteric Modulation of the CB1 Cannabinoid Receptor by Cannabidiol-A Molecular Modeling Study of the N-Terminal Domain and the Allosteric-Orthosteric Coupling. PMID:33922473
Functional Interfaces, Biological Pathways, and Regulations of Interferon-Related DNA Damage Resistance Signature (IRDS) Genes. PMID:33922087
Protective Role of a TMPRSS2 Variant on Severe COVID-19 Outcome in Young Males and Elderly Women. PMID:33921689
Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data. PMID:33920040
Conformation-Specific Inhibitory Anti-MMP-7 Monoclonal Antibody Sensitizes Pancreatic Ductal Adenocarcinoma Cells to Chemotherapeutic Cell Kill. PMID:33918254
Evaluation of Immunohistochemical Markers, CK17 and SOX2, as Adjuncts to p53 for the Diagnosis of Differentiated Vulvar Intraepithelial Neoplasia (dVIN). PMID:33918187
Transcriptomic Profiles of CD47 in Breast Tumors Predict Outcome and Are Associated with Immune Activation. PMID:33917174
DPP9: Comprehensive In Silico Analyses of Loss of Function Gene Variants and Associated Gene Expression Signatures in Human Hepatocellular Carcinoma. PMID:33915844
Structural characterization of KKT4, an unconventional microtubule-binding kinetochore protein. PMID:33915106
Proteome-Wide Analysis of Heat-Stress in Pinus radiata Somatic Embryos Reveals a Combined Response of Sugar Metabolism and Translational Regulation Mechanisms. PMID:33912202
Tissue-specific regulatory mechanism of LncRNAs and methylation in sheep adipose and muscle induced by Allium mongolicum Regel extracts. PMID:33911127
Cyanophage Diversity and Community Structure in Dead Zone Sediments. PMID:33910994
A pseudomolecule assembly of the Rocky Mountain elk genome. PMID:33909645
A multi-targeting drug design strategy for identifying potent anti-SARS-CoV-2 inhibitors. PMID:33907306
Draft genome of a biparental beetle species, Lethrus apterus. PMID:33902445
Computer-Aided Drug Discovery Identifies Alkaloid Inhibitors of Parkinson's Disease Associated Protein, Prolyl Oligopeptidase. PMID:33897801
Familial Psychosis Associated With a Missense Mutation at MACF1 Gene Combined With the Rare Duplications DUP3p26.3 and DUP16q23.3, Affecting the CNTN6 and CDH13 Genes. PMID:33897758
ZapG (YhcB/DUF1043), a novel cell division protein in gamma-proteobacteria linking the Z-ring to septal peptidoglycan synthesis. PMID:33895137
Copper mining bacteria: Converting toxic copper ions into a stable single-atom copper. PMID:33893098
Effect of HPV 16 E6 Oncoprotein Variants on the Alterations of the Proteome of C33A Cells. PMID:33893080
Phylogenetic and Selection Analysis of an Expanded Family of Putatively Pore-Forming Jellyfish Toxins (Cnidaria: Medusozoa). PMID:33892512
Web resources facilitate drug discovery in treatment of COVID-19. PMID:33892145
Drosophila female reproductive tract gene expression reveals coordinated mating responses and rapidly evolving tissue-specific genes. PMID:33890615
Master Blaster: an approach to sensitive identification of remotely related proteins. PMID:33888741
Differential profiles of HDAC1 substrates and associated proteins in breast cancer cells revealed by trapping. PMID:33885658
Type VI Secretion System and Its Effectors PdpC, PdpD, and OpiA Contribute to Francisella Virulence in Galleria mellonella Larvae. PMID:33875476
Urinary Metabolomic and Proteomic Analyses in a Mouse Model of Prostatic Inflammation. PMID:33870183
Retrospective Use of Whole-Genome Sequencing Expands the Multicountry Outbreak Cluster of Listeria monocytogenes ST1247. PMID:33869622
Major Histocompatibility Complex Class I-Related Chain A (MICA) Allelic Variants Associate With Susceptibility and Prognosis of Gastric Cancer. PMID:33868281
Non-Genomic AhR-Signaling Modulates the Immune Response in Endotoxin-Activated Macrophages After Activation by the Environmental Stressor BaP. PMID:33868237
ATP1A3-Related Disorders: An Ever-Expanding Clinical Spectrum. PMID:33868146
Cytochrome bd promotes Escherichia coli biofilm antibiotic tolerance by regulating accumulation of noxious chemicals. PMID:33863914
A draft transcriptome of a parasite Neocamacolaimus parasiticus (Camacolaimidae, Plectida). PMID:33860270
Multi-platform omics analysis reveals molecular signature for COVID-19 pathogenesis, prognosis and drug target discovery. PMID:33859163
Obesity alters the ovarian proteomic response to zearalenone exposure†. PMID:33855340
Traditional Chinese Formula Xiaoyaosan Alleviates Depressive-Like Behavior in CUMS Mice by Regulating PEBP1-GPX4-Mediated Ferroptosis in the Hippocampus. PMID:33854318
Phylogenetic analysis of Harmonin homology domains. PMID:33853521
Analysis of temporal gene regulation of Listeria monocytogenes revealed distinct regulatory response modes after exposure to high pressure processing. PMID:33853520
AlnC: An extensive database of long non-coding RNAs in angiosperms. PMID:33852582
Type IV Collagen Variants in CKD: Performance of Computational Predictions for Identifying Pathogenic Variants. PMID:33851121
The whole is greater than its parts: ensembling improves protein contact prediction. PMID:33850214
Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users. PMID:33849055
CREB stimulates GPX4 transcription to inhibit ferroptosis in lung adenocarcinoma. PMID:33846793
Whole-exome sequencing with targeted analysis and epilepsy after acute symptomatic neonatal seizures. PMID:33846556
A combined RAD-Seq and WGS approach reveals the genomic basis of yellow color variation in bumble bee Bombus terrestris. PMID:33846496
Comparative analysis of 13C chemical shifts of β-sheet amyloid proteins and outer membrane proteins. PMID:33844106
Serpins in cartilage and osteoarthritis: what do we know? PMID:33843993
A Multi-Omics Analysis of Metastatic Melanoma Identifies a Germinal Center-Like Tumor Microenvironment in HLA-DR-Positive Tumor Areas. PMID:33842341
A review on compound-protein interaction prediction methods: Data, format, representation and model. PMID:33841755
Computational evaluation of interactions between olfactory receptor OR2W1 and its ligands. PMID:33840173
Coding and non-coding roles of MOCCI (C15ORF48) coordinate to regulate host inflammation and immunity. PMID:33837217
Dual-process brain mitochondria isolation preserves function and clarifies protein composition. PMID:33836587
A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism. PMID:33836000
ActiveDriverDB: Interpreting Genetic Variation in Human and Cancer Genomes Using Post-translational Modification Sites and Signaling Networks (2021 Update). PMID:33834021
Reprogramming enriches for somatic cell clones with small-scale mutations in cancer-associated genes. PMID:33831558
Life-extended glycosylated IL-2 promotes Treg induction and suppression of autoimmunity. PMID:33828163
Learning the molecular grammar of protein condensates from sequence determinants and embeddings. PMID:33827920
Massive parallel sequencing in a family with rectal cancer. PMID:33827643
An extended catalogue of tandem alternative splice sites in human tissue transcriptomes. PMID:33826604
Biallelic variants in TMEM222 cause a new autosomal recessive neurodevelopmental disorder. PMID:33824500
A slowly cleaved viral signal peptide acts as a protein-integral immune evasion domain. PMID:33824318
In silico investigation of the viroporin E as a vaccine target against SARS-CoV-2. PMID:33822639
Machine learning-based investigation of the cancer protein secretory pathway. PMID:33819271
Improved sequence-based prediction of interaction sites in α-helical transmembrane proteins by deep learning. PMID:33815689
Targeted Quantification of Detergent-Insoluble RNA-Binding Proteins in Human Brain Reveals Stage and Disease Specific Co-aggregation in Alzheimer's Disease. PMID:33815056
MolluscDB: a genome and transcriptome database for molluscs. PMID:33813885
IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs. PMID:33813065
Therapeutic wavelengths of ultraviolet B radiation activate apoptotic, circadian rhythm, redox signalling and key canonical pathways in psoriatic epidermis. PMID:33812333
Resourcing, annotating, and analysing synthetic peptides of SARS-CoV-2 for immunopeptidomics and other immunological studies. PMID:33811468
Label-free quantitative proteomics of Sorghum bicolor reveals the proteins strengthening plant defense against insect pest Chilo partellus. PMID:33810819
Deep Learning for Novel Antimicrobial Peptide Design. PMID:33810011
The Conservation of Low Complexity Regions in Bacterial Proteins Depends on the Pathogenicity of the Strain and Subcellular Location of the Protein. PMID:33809982
A Holistic Evolutionary and 3D Pharmacophore Modelling Study Provides Insights into the Metabolism, Function, and Substrate Selectivity of the Human Monocarboxylate Transporter 4 (hMCT4). PMID:33805725
Combined Proteotranscriptomic-Based Strategy to Discover Novel Antimicrobial Peptides from Cone Snails. PMID:33805497
Adenovirus Terminal Protein Contains a Bipartite Nuclear Localisation Signal Essential for Its Import into the Nucleus. PMID:33804953
Co-Transcriptional RNA Processing in Plants: Exploring from the Perspective of Polyadenylation. PMID:33804866
QTL Analysis of Adult Plant Resistance to Stripe Rust in a Winter Wheat Recombinant Inbred Population. PMID:33803625
Rational Design of Adenylate Kinase Thermostability through Coevolution and Sequence Divergence Analysis. PMID:33803409
Predicting Proteolysis in Complex Proteomes Using Deep Learning. PMID:33803033
Proteomic Analyses of Fibroblast- and Serum-Derived Exosomes Identify QSOX1 as a Marker for Non-invasive Detection of Colorectal Cancer. PMID:33802764
Diosmin Mitigates Cyclophosphamide Induced Premature Ovarian Insufficiency in Rat Model. PMID:33802633
Bioinformatic Analysis of the Nicotinamide Binding Site in Poly(ADP-Ribose) Polymerase Family Proteins. PMID:33801950
Pan-Cancer Analysis of Human Kinome Gene Expression and Promoter DNA Methylation Identifies Dark Kinase Biomarkers in Multiple Cancers. PMID:33801837
Sofosbuvir Selects for Drug-Resistant Amino Acid Variants in the Zika Virus RNA-Dependent RNA-Polymerase Complex In Vitro. PMID:33800884
MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops. PMID:33800690
The Basolateral Polarity Module Promotes Slit Diaphragm Formation in Drosophila Nephrocytes, a Model of Vertebrate Podocytes. PMID:33795424
An integrative multi-omics approach reveals new central nervous system pathway alterations in Alzheimer's disease. PMID:33794997
predPhogly-Site: Predicting phosphoglycerylation sites by incorporating probabilistic sequence-coupling information into PseAAC and addressing data imbalance. PMID:33793659
Building blocks and blueprints for bacterial autolysins. PMID:33793553
Dooming Phagocyte Responses: Inflammatory Effects of Endogenous Oxidized Phospholipids. PMID:33790857
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches. PMID:33787851
AMPGAN v2: Machine Learning-Guided Design of Antimicrobial Peptides. PMID:33787250
A protocol combining breath testing and ex vivo fermentations to study the human gut microbiome. PMID:33786457
The human virome: assembly, composition and host interactions. PMID:33785903
Demographic History, Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia. PMID:33784744
Genome-wide RNAi screen for regulators of UPRmt in Caenorhabditis elegans mutants with defects in mitochondrial fusion. PMID:33784383
Uncovering a novel function of the CCR4-NOT complex in phytochrome A-mediated light signalling in plants. PMID:33783355
MCPdb: The bacterial microcompartment database. PMID:33780471
Balancing Data on Deep Learning-Based Proteochemometric Activity Classification. PMID:33779173
CUTie2: The Attack of the Cyclic Nucleotide Sensor Clones. PMID:33778003
Influence of Disease-Causing Mutations on Protein Structural Networks. PMID:33778000
Dystonia and Contractures are Potential Early Signs of CACNA1E-Related Epileptic Encephalopathy. PMID:33776624
In-silico screening for identification of potential inhibitors against SARS-CoV-2 transmembrane serine protease 2 (TMPRSS2). PMID:33775827
Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution. PMID:33774510
Proteomics characterization of mitochondrial-derived vesicles under oxidative stress. PMID:33769614
Structural and Drug Screening Analysis of the Non-structural Proteins of Severe Acute Respiratory Syndrome Coronavirus 2 Virus Extracted From Indian Coronavirus Disease 2019 Patients. PMID:33767730
Ultra-fast proteomics with Scanning SWATH. PMID:33767396
Comparative proteomic profiling of newly acquired, virulent and attenuated Neoparamoeba perurans proteins associated with amoebic gill disease. PMID:33767232
Functional analysis of SARS-CoV-2 proteins in Drosophila identifies Orf6-induced pathogenic effects with Selinexor as an effective treatment. PMID:33766136
Characterization of SARS-CoV-2 proteins reveals Orf6 pathogenicity, subcellular localization, host interactions and attenuation by Selinexor. PMID:33766124
Transcriptional profiling of identified neurons in leech. PMID:33765928
Evolutionary Constraint on Visual and Nonvisual Mammalian Opsins. PMID:33765865
Whole-genome analysis of probiotic product isolates reveals the presence of genes related to antimicrobial resistance, virulence factors, and toxic metabolites, posing potential health risks. PMID:33761872
Microglial identity and inflammatory responses are controlled by the combined effects of neurons and astrocytes. PMID:33761343
SH3BP4 promotes neuropilin-1 and α5-integrin endocytosis and is inhibited by Akt. PMID:33761321
Viscoelastic properties of wheat gluten in a molecular dynamics study. PMID:33760823
Integrated Redox Proteomic Analysis Highlights New Mechanisms of Sensitivity to Silver Nanoparticles. PMID:33757833
TALE: Transformer-based protein function Annotation with joint sequence-Label Embedding. PMID:33755048
Corneal proteome and differentially expressed corneal proteins in highly myopic chicks using a label-free SWATH-MS quantification approach. PMID:33750851
A first insight into the genome of Prototheca wickerhamii, a major causative agent of human protothecosis. PMID:33750287
Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. PMID:33749993
A small molecule compound berberine as an orally active therapeutic candidate against COVID-19 and SARS: A computational and mechanistic study. PMID:33749932
Lack of Molecular Mimicry between Nonhuman Primates and Infectious Pathogens: The Possible Genetic Bases. PMID:33748822
The Molecular Basis of Kale Domestication: Transcriptional Profiling of Developing Leaves Provides New Insights Into the Evolution of a Brassica oleracea Vegetative Morphotype. PMID:33747016
Introducing the ArsR-Regulated Arsenic Stimulon. PMID:33746923
Molecular Docking Reveals Ivermectin and Remdesivir as Potential Repurposed Drugs Against SARS-CoV-2. PMID:33746908
Elucidation of the Mechanism of Action of Ginseng Against Acute Lung Injury/Acute Respiratory Distress Syndrome by a Network Pharmacology-Based Strategy. PMID:33746744
RNA-seq analysis and gene expression dynamics in the salivary glands of the argasid tick Ornithodoros erraticus along the trophogonic cycle. PMID:33743776
A DNA repair disorder caused by de novo monoallelic DDB1 variants is associated with a neurodevelopmental syndrome. PMID:33743206
Curvature sensing amphipathic helix in the C-terminus of RTNLB13 is conserved in all endoplasmic reticulum shaping reticulons in Arabidopsis thaliana. PMID:33737685
Proteomic blood profiling in mild, severe and critical COVID-19 patients. PMID:33737684
Genome Sequence of Clostridium sp. Strain P21, a CO-Fermenting Acetogen Isolated from Old Hay. PMID:33737364
Fast and sensitive taxonomic assignment to metagenomic contigs. PMID:33734313
Host restriction, pathogenesis and chronic carriage of typhoidal Salmonella. PMID:33733659
Functional domain studies uncover novel roles for the ZTL Kelch repeat domain in clock function. PMID:33730063
Molecular storytelling for online structural biology outreach and education. PMID:33728361
Detection of horizontal gene transfer in the genome of the choanoflagellate Salpingoeca rosetta. PMID:33727612
Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha. PMID:33722219
Alternatively Splicing Interactomes Identify Novel Isoform-Specific Partners for NSD2. PMID:33718354
Prediction of lncRNA-Protein Interactions via the Multiple Information Integration. PMID:33718346
Comprehensive Quantitative Proteome Analysis of Aedes aegypti Identifies Proteins and Pathways Involved in Wolbachia pipientis and Zika Virus Interference Phenomenon. PMID:33716790
A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology. PMID:33712730
Protein context shapes the specificity of SH3 domain-mediated interactions in vivo. PMID:33712617
Novel and Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice Created by Physiological Coupling-Uncoupling and Network Rewiring Effects. PMID:33708229
Significant non-existence of sequences in genomes and proteomes. PMID:33693858
Personalized Profiling Reveals Donor- and Lactation-Specific Trends in the Human Milk Proteome and Peptidome. PMID:33693758
Predicted Input of Uncultured Fungal Symbionts to a Lichen Symbiosis from Metagenome-Assembled Genomes. PMID:33693712
Polystyrene Topography Sticker Array for Cell-Based Assays. PMID:33693439
Inferring the number and position of changes in selective regime in a non-equilibrium mutation-selection framework. PMID:33691618
Global analysis of shared T cell specificities in human non-small cell lung cancer enables HLA inference and antigen discovery. PMID:33691136
Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. PMID:33688646
Proteome Regulation Patterns Determine Escherichia coli Wild-Type and Mutant Phenotypes. PMID:33688016
High genomic diversity of novel phages infecting the plant pathogen Ralstonia solanacearum, isolated in Mauritius and Reunion islands. PMID:33686106
Biological Phase Separation and Biomolecular Condensates in Plants. PMID:33684296
DeepViral: prediction of novel virus-host interactions from protein sequences and infectious disease phenotypes. PMID:33682875
Melanoma-associated glycosyltransferase GCNT2 as an emerging biomarker and therapeutic target. PMID:33660254
Generation and Testing of Fluorescent Adaptable Simple Theranostic (FAST) Proteins. PMID:33659348
A novel family of secreted insect proteins linked to plant gall development. PMID:33657407
TMSNP: a web server to predict pathogenesis of missense mutations in the transmembrane region of membrane proteins. PMID:33655207
A comparative study of protein-ssDNA interactions. PMID:33655206
Sputum Proteome Signatures of Mechanically Ventilated Intensive Care Unit Patients Distinguish Samples with or without Anti-pneumococcal Activity. PMID:33653939
Massively parallel gene expression variation measurement of a synonymous codon library. PMID:33653272
Identification of Potential HCV Inhibitors Based on the Interaction of Epigallocatechin-3-Gallate with Viral Envelope Proteins. PMID:33652639
The Interplay of Cholesterol and Ligand Binding in hTSPO from Classical Molecular Dynamics Simulations. PMID:33652554
Biological impact of mutually exclusive exon switching. PMID:33651795
Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia. PMID:33649590
Genome-wide shifts in climate-related variation underpin responses to selective breeding in a widespread conifer. PMID:33649218
Methylacidimicrobium thermophilum AP8, a Novel Methane- and Hydrogen-Oxidizing Bacterium Isolated From Volcanic Soil on Pantelleria Island, Italy. PMID:33643272
Structural characterization of the self-association domain of swallow. PMID:33641207
CiliOPD: a ciliopathy-associated COPD endotype. PMID:33639936
Investigating BB0405 as a novel Borrelia afzelii vaccination candidate in Lyme borreliosis. PMID:33637813
Defects in the cytoplasmic assembly of axonemal dynein arms cause morphological abnormalities and dysmotility in sperm cells leading to male infertility. PMID:33635866
A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. PMID:33634309
Identification of Vibrio parahaemolyticus and Vibrio spp. Specific Outer Membrane Proteins by Reverse Vaccinology and Surface Proteome. PMID:33633699
Long chain acyl CoA synthetase 4 catalyzes the first step in peroxisomal indole-3-butyric acid to IAA conversion. PMID:33631795
Formation and characterization of biofilms formed by salt-tolerant yeast strains in seawater-based growth medium. PMID:33630153
Recent Advances in Predicting Protein S-Nitrosylation Sites. PMID:33628788
Glycine acylation and trafficking of a new class of bacterial lipoprotein by a composite secretion system. PMID:33625358
A multivalent T-antigen-based vaccine for Group A Streptococcus. PMID:33623073
Detection of Epithelial Cell Adhesion Molecule in Feline Normal and Tumor Cell Lines and Tissues With Selected Commercial Anti-human EpCAM Antibodies. PMID:33614766
Characterization and complete genome sequence of Privateer, a highly prolate Proteus mirabilis podophage. PMID:33614267
Skin Multi-Omics-Based Interactome Analysis: Integrating the Tissue and Mucus Exuded Layer for a Comprehensive Understanding of the Teleost Mucosa Functionality as Model of Study. PMID:33613538
Circadian time series proteomics reveals daily dynamics in cartilage physiology. PMID:33610821
Data set of competitive and allosteric protein kinase inhibitors confirmed by X-ray crystallography. PMID:33604432
BLVector: Fast BLAST-Like Algorithm for Manycore CPU With Vectorization. PMID:33603776
Enrichment analyses of diseases and pathways associated with precocious puberty using PrecocityDB. PMID:33602974
Draft Genome Sequences of Pelagimyophage Mosig EXVC030M and Pelagipodophage Lederberg EXVC029P, Isolated from Devil's Hole, Bermuda. PMID:33602731
Comparative transcriptomics of spotted seatrout (Cynoscion nebulosus) populations to cold and heat stress. PMID:33598136
Comprehensive Succinylome Profiling Reveals the Pivotal Role of Lysine Succinylation in Energy Metabolism and Quorum Sensing of Staphylococcus epidermidis. PMID:33597936
PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data. PMID:33597026
Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections. PMID:33596852
The analysis on the human protein domain targets and host-like interacting motifs for the MERS-CoV and SARS-CoV/CoV-2 infers the molecular mimicry of coronavirus. PMID:33596252
mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection. PMID:33596079
Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees. PMID:33595436
Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through analysis of Viral Genomics and Structure. PMID:33594340
Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus. PMID:33594000
Nybomycin inhibits both types of E. coli DNA gyrase - fluoroquinolone-sensitive and fluoroquinolone-resistant. PMID:33593838
Epitope mimicry analysis of SARS-COV-2 surface proteins and human lung proteins. PMID:33588349
High Quality Aspergillus aculeatus Genomes and Transcriptomes: A Platform for Cellulase Activity Optimization Toward Industrial Applications. PMID:33585410
The CLAIRE COVID-19 initiative: approach, experiences and recommendations. PMID:33584129
Protein Phosphorylation in Depolarized Synaptosomes: Dissecting Primary Effects of Calcium from Synaptic Vesicle Cycling. PMID:33582301
Effects of pH on an IDP conformational ensemble explored by molecular dynamics simulation. PMID:33581430
Mitovesicles are a novel population of extracellular vesicles of mitochondrial origin altered in Down syndrome. PMID:33579698
The leucine zipper EF-hand containing transmembrane protein-1 EF-hand is a tripartite calcium, temperature, and pH sensor. PMID:33576522
TOUCAN: a framework for fungal biosynthetic gene cluster discovery. PMID:33575642
On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF. PMID:33575598
Diversity and evolution of bacterial bioluminescence genes in the global ocean. PMID:33575578
Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis. PMID:33574331
ELIHKSIR Web Server: Evolutionary Links Inferred for Histidine Kinase Sensors Interacting with Response Regulators. PMID:33573110
Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using Biological and Chemical Codes. PMID:33573096
Effect of An 84-bp Deletion of the Receptor-Binding Domain on the ACE2 Binding Affinity of the SARS-CoV-2 Spike Protein: An In Silico Analysis. PMID:33572725
The Role of Low Complexity Regions in Protein Interaction Modes: An Illustration in Huntingtin. PMID:33572172
HCN Channel Phosphorylation Sites Mapped by Mass Spectrometry in Human Epilepsy Patients and in an Animal Model of Temporal Lobe Epilepsy. PMID:33571596
Genetic determinants of daytime napping and effects on cardiometabolic health. PMID:33568662
Transcription Profiles Associated with Inducible Adhesion in Candida parapsilosis. PMID:33568454
Phylogenomics Identifies a New Major Subgroup of Apicomplexans, Marosporida class nov., with Extreme Apicoplast Genome Reduction. PMID:33566096
CXCR7 ameliorates myocardial infarction as a β-arrestin-biased receptor. PMID:33564089
Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources. PMID:33564056
The methyltransferase METTL9 mediates pervasive 1-methylhistidine modification in mammalian proteomes. PMID:33563959
A Grad-seq View of RNA and Protein Complexes in Pseudomonas aeruginosa under Standard and Bacteriophage Predation Conditions. PMID:33563827
Modular Reorganization of Signaling Networks during the Development of Colon Adenoma and Carcinoma. PMID:33562960
Whole Exome Sequencing Reveals a Novel AUTS2 In-Frame Deletion in a Boy with Global Developmental Delay, Absent Speech, Dysmorphic Features, and Cerebral Anomalies. PMID:33562463
A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina. PMID:33561229
Cryo-EM structures of human RNA polymerase III in its unbound and transcribing states. PMID:33558764
Mechanisms of Congenital Heart Disease Caused by NAA15 Haploinsufficiency. PMID:33557580
Role of Pirin, an Oxidative Stress Sensor Protein, in Epithelial Carcinogenesis. PMID:33557375
KinPred: A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions. PMID:33556051
Understanding protein structural changes for oncogenic missense variants. PMID:33553733
Mitochondrial Enzymes of the Urea Cycle Cluster at the Inner Mitochondrial Membrane. PMID:33551825
Beyond history and "on a roll": The list of the most well-studied human protein structures and overall trends in the protein data bank. PMID:33550681
Distinct clonal lineages and within-host diversification shape invasive Staphylococcus epidermidis populations. PMID:33544760
Sialotranscriptomics of the argasid tick Ornithodoros moubata along the trophogonic cycle. PMID:33544727
Draft Genome Sequences of 27 Northern Maine Clinical Isolates. PMID:33541879
The PSY Peptide Family-Expression, Modification and Physiological Implications. PMID:33540946
Does C-C Motif Chemokine Ligand 2 (CCL2) Link Obesity to a Pro-Inflammatory State? PMID:33540898
Identification of a Five-Gene Prognostic Model and Its Potential Drug Repurposing in Colorectal Cancer Based on TCGA, GTEx and GEO Databases. PMID:33537062
Angiomotin Counteracts the Negative Regulatory Effect of Host WWOX on Viral PPxY-Mediated Egress. PMID:33536174
The In Silico Identification of Potential Members of the Ded1/DDX3 Subfamily of DEAD-Box RNA Helicases from the Protozoan Parasite Leishmania infantum and Their Analyses in Yeast. PMID:33535521
Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway. PMID:33535033
Genetic analysis of 39 erythrocytosis and hereditary hemochromatosis-associated genes in the Slovenian family with idiopathic erythrocytosis. PMID:33534944
ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways. PMID:33534793
Four families of folate-independent methionine synthases. PMID:33534785
Human MiniPromoters for ocular-rAAV expression in ON bipolar, cone, corneal, endothelial, Müller glial, and PAX6 cells. PMID:33531684
SPACEPro: A Software Tool for Analysis of Protein Sample Cleavage for Tandem Mass Spectrometry. PMID:33529024
Genetic variants of small airways and interstitial pulmonary disease in children. PMID:33526882
Palmitoylation Controls NMDA Receptor Function and Steroid Sensitivity. PMID:33526476
A Conserved Motif in Intracellular Loop 1 Stabilizes the Outward-Facing Conformation of TmrAB. PMID:33524413
Overlap of NatA and IAP substrates implicates N-terminal acetylation in protein stabilization. PMID:33523899
S100A8/S100A9 cytokine acts as a transcriptional coactivator during breast cellular transformation. PMID:33523865
Targeted brachyury degradation disrupts a highly specific autoregulatory program controlling chordoma cell identity. PMID:33521702
From fuzziness to precision medicine: on the rapidly evolving proteomics with implications in mitochondrial connectivity to rare human disease. PMID:33521598
Adaptation of a Microfluidic qPCR System for Enzyme Kinetic Studies. PMID:33521438
Analysis of Human Faecal Host Proteins: Responsiveness to 10-Week Dietary Intervention Modifying Dietary Protein Intake in Elderly Males. PMID:33521034
Tumor-intrinsic and -extrinsic (immune) gene signatures robustly predict overall survival and treatment response in high grade serous ovarian cancer patients. PMID:33520368
AtxA-Controlled Small RNAs of Bacillus anthracis Virulence Plasmid pXO1 Regulate Gene Expression in trans. PMID:33519762
Computational resources for identifying and describing proteins driving liquid-liquid phase separation. PMID:33517364
SRGAP1 Controls Small Rho GTPases To Regulate Podocyte Foot Process Maintenance. PMID:33514561
My personal mutanome: a computational genomic medicine platform for searching network perturbing alleles linking genotype to phenotype. PMID:33514395
HIF1A: A Putative Modifier of Hemochromatosis. PMID:33513852
Identifying virulence determinants of multidrug-resistant Klebsiella pneumoniae in Galleria mellonella. PMID:33512418
Selective Inhibition of 2-Oxoglutarate and 2-Oxoadipate Dehydrogenases by the Phosphonate Analogs of Their 2-Oxo Acid Substrates. PMID:33511099
Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers. PMID:33507915
InSexBase: an annotated genomic resource of sex chromosomes and sex-biased genes in insects. PMID:33507270
Structural similarity-based prediction of host factors associated with SARS-CoV-2 infection and pathogenesis. PMID:33506741
Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. PMID:33505029
Identification of 37 Heterogeneous Drug Candidates for Treatment of COVID-19 via a Rational Transcriptomics-Based Drug Repurposing Approach. PMID:33504008
The Role of PKM2 in Metabolic Reprogramming: Insights into the Regulatory Roles of Non-Coding RNAs. PMID:33503959
Missense3D-DB web catalogue: an atom-based analysis and repository of 4M human protein-coding genetic variants. PMID:33502607
Genomics Reveals the Origins of Historical Specimens. PMID:33502509
Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation. PMID:33499731
The Structural Properties of Odorants Modulate Their Association to Human Odorant Binding Protein. PMID:33499295
Identification of Sortilin Alternatively Spliced Variants in Mouse 3T3L1 Adipocytes. PMID:33498179
ExonSkipAD provides the functional genomic landscape of exon skipping events in Alzheimer's disease. PMID:33497435
A network pharmacology perspective for deciphering potential mechanisms of action of Solanum nigrum L. in bladder cancer. PMID:33494738
Overproduction of Human Zip (SLC39) Zinc Transporters in Saccharomyces cerevisiae for Biophysical Characterization. PMID:33494457
Identification of Lead Compounds against Scm (fms10) in Enterococcus faecium Using Computer Aided Drug Designing. PMID:33494233
Posttranslational Modifications: Regulation of Nitrogen Utilization and Signaling. PMID:33493288
In-depth and 3-dimensional exploration of the budding yeast phosphoproteome. PMID:33491328
Computing Cellulase Kinetics with a Two-Domain Linear Interaction Energy Approach. PMID:33490814
Network Pharmacology Analysis of the Therapeutic Mechanisms Underlying Beimu-Gualou Formula Activity against Bronchiectasis with In Silico Molecular Docking Validation. PMID:33488758
The Hunt for Ancient Prions: Archaeal Prion-Like Domains Form Amyloid-Based Epigenetic Elements. PMID:33480998
Biomolecular condensation of NUP98 fusion proteins drives leukemogenic gene expression. PMID:33479542
Analysis of ovarian transcriptomes reveals thousands of novel genes in the insect vector Rhodnius prolixus. PMID:33479356
Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals. PMID:33479023
Mechanistic modeling of the SARS-CoV-2 disease map. PMID:33478554
De Novo Profiling of Long Non-Coding RNAs Involved in MC-LR-Induced Liver Injury in Whitefish: Discovery and Perspectives. PMID:33477898
Systematic Identification of Protein Phosphorylation-Mediated Interactions. PMID:33476154
Homology modeling and molecular docking simulation of some novel imidazo[1,2-a]pyridine-3-carboxamide (IPA) series as inhibitors of Mycobacterium tuberculosis. PMID:33474593
Cellinker: a platform of ligand-receptor interactions for intercellular communication analysis. PMID:33471060
Synthetic Siglec-9 Agonists Inhibit Neutrophil Activation Associated with COVID-19. PMID:33469569
Potential biomarkers of childhood brain tumor identified by proteomics of cerebrospinal fluid from extraventricular drainage (EVD). PMID:33469081
A platform for curated products from novel open reading frames prompts reinterpretation of disease variants. PMID:33468550
Prediction and analysis of metagenomic operons via MetaRon: a pipeline for prediction of Metagenome and whole-genome opeRons. PMID:33468056
Extensive hybridization reveals multiple coloration genes underlying a complex plumage phenotype. PMID:33468000
Neuronal Dopamine D3 Receptors: Translational Implications for Preclinical Research and CNS Disorders. PMID:33466844
JAK3 Is Expressed in the Nucleus of Malignant T Cells in Cutaneous T Cell Lymphoma (CTCL). PMID:33466582
Rosetta design with co-evolutionary information retains protein function. PMID:33465067
A novel terpene synthase controls differences in anti-aphrodisiac pheromone production between closely related Heliconius butterflies. PMID:33465061
Anomalous Phylogenetic Behavior of Ribosomal Proteins in Metagenome-Assembled Asgard Archaea. PMID:33462601
Giant lungfish genome elucidates the conquest of land by vertebrates. PMID:33461212
The rapidly evolving view of lysosomal storage diseases. PMID:33459519
Post-translational control of the long and winding road to cholesterol. PMID:33453997
Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. PMID:33453123
Exploring the treatment of COVID-19 with Yinqiao powder based on network pharmacology. PMID:33452734
Comprehensive computational target fishing approach to identify Xanthorrhizol putative targets. PMID:33452398
Early infection-induced natural antibody response. PMID:33452341
Parasite Presence Induces Gene Expression Changes in an Ant Host Related to Immunity and Longevity. PMID:33451085
Babesia Bovis Ligand-Receptor Interaction: AMA-1 Contains Small Regions Governing Bovine Erythrocyte Binding. PMID:33450807
Proteome dynamics at broken replication forks reveal a distinct ATM-directed repair response suppressing DNA double-strand break ubiquitination. PMID:33450211
Identification of a conserved N-terminal domain in the first module of ACV synthetases. PMID:33449449
Plasma Proteomes Can Be Reidentifiable and Potentially Contain Personally Sensitive and Incidental Findings. PMID:33444735
Exploring the selenium-over-sulfur substrate specificity and kinetics of a bacterial selenocysteine lyase. PMID:33444662
Embeddings from deep learning transfer GO annotations beyond homology. PMID:33441905
A Novel N4-Like Bacteriophage Isolated from a Wastewater Source in South India with Activity against Several Multidrug-Resistant Clinical Pseudomonas aeruginosa Isolates. PMID:33441405
Cerebrospinal fluid metabolomics identifies 19 brain-related phenotype associations. PMID:33437055
Longitudinal saliva omics responses to immune perturbation: a case study. PMID:33436912
Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications. PMID:33436497
An ensemble learning approach for modeling the systems biology of drug-induced injury. PMID:33435983
Evolution and diversification of the nuclear envelope. PMID:33435791
Transcriptomic Analysis of Respiratory Tissue and Cell Line Models to Examine Glycosylation Machinery during SARS-CoV-2 Infection. PMID:33435561
Structural Insights into Ankyrin Repeat-Containing Proteins and Their Influence in Ubiquitylation. PMID:33435370
Transposable Elements and Teleost Migratory Behaviour. PMID:33435333
Molecular and Structural Evolution of Cytochrome P450 Aromatase. PMID:33435208
One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome. PMID:33431010
Role of Transportome in the Gills of Chinese Mitten Crabs in Response to Salinity Change: A Meta-Analysis of RNA-Seq Datasets. PMID:33430106
Cartilage Targets of Knee Osteoarthritis Shared by Both Genders. PMID:33430025
Recombinant antibody against Trypanosoma cruzi from patients with chronic Chagas heart disease recognizes mammalian nervous system. PMID:33429173
Visualizing the superfamily of metallo-β-lactamases through sequence similarity network neighborhood connectivity analysis. PMID:33426353
Exploring the Antitumor Mechanisms of Zingiberis Rhizoma Combined with Coptidis Rhizoma Using a Network Pharmacology Approach. PMID:33426081
Dinoflagellate Host Chloroplasts and Mitochondria Remain Functional During Amoebophrya Infection. PMID:33424803
Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities. PMID:33424787
Octenidine-based hydrogel shows anti-inflammatory and protease-inhibitory capacities in wounded human skin. PMID:33420112
Genome Sequences of Serratia Strains Revealed Common Genes in Both Serratomolides Gene Clusters. PMID:33419369
MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes. PMID:33418085
The iPPI-DB initiative: A Community-centered database of Protein-Protein Interaction modulators. PMID:33416858
SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets. PMID:33416848
H2V: a database of human genes and proteins that respond to SARS-CoV-2, SARS-CoV, and MERS-CoV infection. PMID:33413085
Evaluation of the potential of Pap test fluid and cervical swabs to serve as clinical diagnostic biospecimens for the detection of ovarian cancer by mass spectrometry-based proteomics. PMID:33413078
Platypus and echidna genomes reveal mammalian biology and evolution. PMID:33408411
Opinion: Standardizing gene product nomenclature-a call to action. PMID:33408252
Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp. PMID:33407428
MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes. PMID:33407081
Limited Proteolysis-Coupled Mass Spectrometry Identifies Phosphatidylinositol 4,5-Bisphosphate Effectors in Human Nuclear Proteome. PMID:33406800
A pan-cancer atlas of somatic mutations in miRNA biogenesis genes. PMID:33406242
Bioinformatics Analysis of Key Genes and Pathways of Cervical Cancer. PMID:33402836
The Campylobacter jejuni chemoreceptor Tlp10 has a bimodal ligand-binding domain and specificity for multiple classes of chemoeffectors. PMID:33402336
Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding. PMID:33402206
Norwegian Soils and Waters Contain Mesophilic, Plastic-Degrading Bacteria. PMID:33401570
Identification and Characterization of Plant-Interacting Targets of Tomato Spotted Wilt Virus Silencing Suppressor. PMID:33401462
TGFBR3L-An Uncharacterised Pituitary Specific Membrane Protein Detected in the Gonadotroph Cells in Non-Neoplastic and Tumour Tissue. PMID:33396509
PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference. PMID:33392435
Evaluating Protein Transfer Learning with TAPE. PMID:33390682
A Fifth of the Protein World: Rossmann-like Proteins as an Evolutionarily Successful Structural unit. PMID:33387532
Network machine learning maps phytochemically rich "Hyperfoods" to fight COVID-19. PMID:33386081
Three Decades of Advances in Arabinogalactan-Protein Biosynthesis. PMID:33384708
SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets. PMID:33416848
H2V: a database of human genes and proteins that respond to SARS-CoV-2, SARS-CoV, and MERS-CoV infection. PMID:33413085
Evaluation of the potential of Pap test fluid and cervical swabs to serve as clinical diagnostic biospecimens for the detection of ovarian cancer by mass spectrometry-based proteomics. PMID:33413078
Platypus and echidna genomes reveal mammalian biology and evolution. PMID:33408411
Opinion: Standardizing gene product nomenclature-a call to action. PMID:33408252
Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp. PMID:33407428
MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes. PMID:33407081
Limited Proteolysis-Coupled Mass Spectrometry Identifies Phosphatidylinositol 4,5-Bisphosphate Effectors in Human Nuclear Proteome. PMID:33406800
A pan-cancer atlas of somatic mutations in miRNA biogenesis genes. PMID:33406242
Bioinformatics Analysis of Key Genes and Pathways of Cervical Cancer. PMID:33402836
The Campylobacter jejuni chemoreceptor Tlp10 has a bimodal ligand-binding domain and specificity for multiple classes of chemoeffectors. PMID:33402336
Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding. PMID:33402206
Norwegian Soils and Waters Contain Mesophilic, Plastic-Degrading Bacteria. PMID:33401570
Identification and Characterization of Plant-Interacting Targets of Tomato Spotted Wilt Virus Silencing Suppressor. PMID:33401462
TGFBR3L-An Uncharacterised Pituitary Specific Membrane Protein Detected in the Gonadotroph Cells in Non-Neoplastic and Tumour Tissue. PMID:33396509
PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference. PMID:33392435
Evaluating Protein Transfer Learning with TAPE. PMID:33390682
A Fifth of the Protein World: Rossmann-like Proteins as an Evolutionarily Successful Structural unit. PMID:33387532
Network machine learning maps phytochemically rich "Hyperfoods" to fight COVID-19. PMID:33386081
Three Decades of Advances in Arabinogalactan-Protein Biosynthesis. PMID:33384708
Interactions between nascent proteins translated by adjacent ribosomes drive homomer assembly. PMID:33384371
The Interactome of Cancer-Related Lysyl Oxidase and Lysyl Oxidase-Like Proteins. PMID:33383846
SeMPI 2.0-A Web Server for PKS and NRPS Predictions Combined with Metabolite Screening in Natural Product Databases. PMID:33383692
A target-mediated drug disposition population pharmacokinetic model of GC1118, a novel anti-EGFR antibody, in patients with solid tumors. PMID:33382918
A Multi-Pronged Computational Pipeline for Prioritizing Drug Target Strategies for Latent Tuberculosis. PMID:33381491
The Underlying Mechanism of Paeonia lactiflora Pall. in Parkinson's Disease Based on a Network Pharmacology Approach. PMID:33381034
The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. PMID:33378765
Inducible Stem-Cell-Derived Embryos Capture Mouse Morphogenetic Events In Vitro. PMID:33378662
Comparative Transcriptomics Identifies Neuronal and Metabolic Adaptations to Hypergravity and Microgravity in Caenorhabditis elegans. PMID:33376968
Formation of Biomolecular Condensates in Bacteria by Tuning Protein Electrostatics. PMID:33376791
Comparative Proteomics of Marinobacter sp. TT1 Reveals Corexit Impacts on Hydrocarbon Metabolism, Chemotactic Motility, and Biofilm Formation. PMID:33374976
Larvicidal Activity of Cinnamic Acid Derivatives: Investigating Alternative Products for Aedes aegypti L. Control. PMID:33374484
In Silico and In Vitro Analysis of Major Cannabis-Derived Compounds as Fatty Acid Amide Hydrolase Inhibitors. PMID:33374180
DeepTFactor: A deep learning-based tool for the prediction of transcription factors. PMID:33372147
Computational Analysis of African Swine Fever Virus Protein Space for the Design of an Epitope-Based Vaccine Ensemble. PMID:33371523
Genome-wide association analysis of Russian wheat aphid (Diuraphis noxia) resistance in Dn4 derived wheat lines evaluated in South Africa. PMID:33370360
UniBioDicts: Unified access to biological dictionaries. PMID:33367853
Identification of Sub-Golgi protein localization by use of deep representation learning features. PMID:33367627
Virxicon: A Lexicon Of Viral Sequences. PMID:33367605
An Educational Bioinformatics Project to Improve Genome Annotation. PMID:33365016
Heterogeneity in combined immunodeficiencies with associated or syndromic features (Review). PMID:33363595
Expression, Purification and Initial Characterization of Functional α1-Microglobulin (A1M) in Nicotiana benthamiana. PMID:33363557
Acadesine suppresses TNF-α induced complement component 3 (C3), in retinal pigment epithelial (RPE) cells. PMID:33362238
The Two-Component System CopRS Maintains Subfemtomolar Levels of Free Copper in the Periplasm of Pseudomonas aeruginosa Using a Phosphatase-Based Mechanism. PMID:33361129
Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control. PMID:33361111
Design and in silico study of the novel coumarin derivatives against SARS-CoV-2 main enzymes. PMID:33357038
The involvement of the Candida glabrata trehalase enzymes in stress resistance and gut colonization. PMID:33356857
Generation of an Interactome for the Tetratricopeptide Repeat Domain of O-GlcNAc Transferase Indicates a Role for the Enzyme in Intellectual Disability. PMID:33356293
Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates. PMID:33355531
BUB-1 targets PP2A:B56 to regulate chromosome congression during meiosis I in C. elegans oocytes. PMID:33355089
Mal-Light: Enhancing Lysine Malonylation Sites Prediction Problem Using Evolutionary-based Features. PMID:33354488
The complexity of co-limitation: nutrigenomics reveal non-additive interactions of calcium and phosphorus on gene expression in Daphnia pulex. PMID:33352081
Novel perspectives of target-binding by the evolutionarily conserved PP4 phosphatase. PMID:33352067
hnRNPLL controls pluripotency exit of embryonic stem cells by modulating alternative splicing of Tbx3 and Bptf. PMID:33349972
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. PMID:33348379
Multi-omics data integration considerations and study design for biological systems and disease. PMID:33347526
Phospho-islands and the evolution of phosphorylated amino acids in mammals. PMID:33344082
Does tetanus vaccination contribute to reduced severity of the COVID-19 infection? PMID:33341328
Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon. PMID:33339886
S-adenosyl-l-homocysteine Hydrolase: A Structural Perspective on the Enzyme with Two Rossmann-Fold Domains. PMID:33339190
Investigation of Genetic Variations of IL6 and IL6R as Potential Prognostic and Pharmacogenetics Biomarkers: Implications for COVID-19 and Neuroinflammatory Disorders. PMID:33339153
RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles. PMID:33338400
Deep Learning in Protein Structural Modeling and Design. PMID:33336200
Antibody profiling of patients with prostate cancer reveals differences in antibody signatures among disease stages. PMID:33335027
A Critical Role for Fas-Mediated Off-Target Tumor Killing in T-cell Immunotherapy. PMID:33334730
A Comprehensive Transcriptional Profiling of Pepper Responses to Root-Knot Nematode. PMID:33333784
Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome. PMID:33330920
Frameshift Variant in Novel Adenosine-A1-Receptor Homolog Associated With Bovine Spastic Syndrome/Late-Onset Bovine Spastic Paresis in Holstein Sires. PMID:33329738
The Neoantigen Landscape of Mycosis Fungoides. PMID:33329522
The Biosynthesis of Enzymatically Oxidized Lipids. PMID:33329396
Oncology and Pharmacogenomics Insights in Polycystic Ovary Syndrome: An Integrative Analysis. PMID:33329391
Unusual allergen in a butcher with respiratory symptoms. PMID:33326509
Collecting and managing taxonomic data with NCBI-taxonomist. PMID:33326008
Tools for the Recognition of Sorting Signals and the Prediction of Subcellular Localization of Proteins From Their Amino Acid Sequences. PMID:33324450
Cobalt Resistance via Detoxification and Mineralization in the Iron-Reducing Bacterium Geobacter sulfurreducens. PMID:33324382
GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans. PMID:33322545
Three Novel Clostridia Isolates Produce n-Caproate and iso-Butyrate from Lactate: Comparative Genomics of Chain-Elongating Bacteria. PMID:33322390
A Novel Amino Acid Substitution, Fibrinogen Bβp.Pro234Leu, Associated with Hypofibrinogenemia Causing Impairment of Fibrinogen Assembly and Secretion. PMID:33322044
Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes in Arabidopsis thaliana. PMID:33322028
Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and Their Augmentation by Compact Peptide Sets. PMID:33321075
Transport mechanism of P4 ATPase phosphatidylcholine flippases. PMID:33320091
Genome sequencing of deep-sea hydrothermal vent snails reveals adaptions to extreme environments. PMID:33319911
Computational prediction method to decipher receptor-glycoligand interactions in plant immunity. PMID:33316845
VIPERdb v3.0: a structure-based data analytics platform for viral capsids. PMID:33313778
RCSB Protein Data Bank 1D Tools and Services. PMID:33313665
Comparative proteomic analysis highlights metabolic dysfunction in α-synucleinopathy. PMID:33311497
CEG 2.0: an updated database of clusters of essential genes including eukaryotic organisms. PMID:33306800
Applying graph database technology for analyzing perturbed co-expression networks in cancer. PMID:33306799
Integrin α11β1 is a receptor for collagen XIII. PMID:33306155
The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes. PMID:33305470
PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins. PMID:33305318
Exosomes for Wound Healing: Purification Optimization and Identification of Bioactive Components. PMID:33304765
A Multi-Strategy Sequencing Workflow in Inherited Retinal Dystrophies: Routine Diagnosis, Addressing Unsolved Cases and Candidate Genes Identification. PMID:33302505
Origin of a Giant Sex Chromosome. PMID:33300980
Short-term treatment with dabigatran alters protein expression patterns in a late-stage tau-based Alzheimer's disease mouse model. PMID:33294639
Clinical, metabolic, and molecular genetic characterization of hereditary methemoglobinemia caused by cytochrome b5 reductase deficiency in 30 dogs. PMID:33293645
Cytogenetic and genomic analysis of a patient with turner syndrome and t(2;12): a case report. PMID:33292387
Comparative Assessment of Intrinsic Disorder Predictions with a Focus on Protein and Nucleic Acid-Binding Proteins. PMID:33291838
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. PMID:33290554
Improving the informativeness of Mendelian disease-derived pathogenicity scores for common disease. PMID:33288751
Wide-ranging transcriptomic analysis of Poncirus trifoliata, Citrus sunki, Citrus sinensis and contrasting hybrids reveals HLB tolerance mechanisms. PMID:33257732
Deciphering the Role of Filamin B Calponin-Homology Domain in Causing the Larsen Syndrome, Boomerang Dysplasia, and Atelosteogenesis Type I Spectrum Disorders via a Computational Approach. PMID:33255942
Essential gene prediction using limited gene essentiality information-An integrative semi-supervised machine learning strategy. PMID:33253254
A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19. PMID:33250934
The Draft Genome of Red Lechwe, Kobus leche leche. PMID:33250921
PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies. PMID:33245774
Investigating the human protein-host protein interactome of SARS-CoV-2 infection in the small intestine. PMID:33244381
Excavating the functionally crucial active-site residues of the DXS protein of Bacillus subtilis by exploring its closest homologues. PMID:33242110
Adaptive divergence, neutral panmixia, and algal symbiont population structure in the temperate coral Astrangia poculata along the Mid-Atlantic United States. PMID:33240603
Functional characterisation guides classification of novel BAP1 germline variants. PMID:33240524
Identification of Novel BRCA1 and RAD50 Mutations Associated With Breast Cancer Predisposition in Tunisian Patients. PMID:33240314
MobiDB: intrinsically disordered proteins in 2021. PMID:33237329
CATH: increased structural coverage of functional space. PMID:33237325
RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures. PMID:33237313
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. PMID:33237311
UniProt: the universal protein knowledgebase in 2021. PMID:33237286
The Uniqueness of Tryptophan in Biology: Properties, Metabolism, Interactions and Localization in Proteins. PMID:33233627
Metagenomic Information Recovery from Human Stool Samples Is Influenced by Sequencing Depth and Profiling Method. PMID:33233349
Additions to the genus Gimesia: description of Gimesia alba sp. nov., Gimesia algae sp. nov., Gimesia aquarii sp. nov., Gimesia aquatilis sp. nov., Gimesia fumaroli sp. nov. and Gimesia panareensis sp. nov., isolated from aquatic habitats of the Northern Hemisphere. PMID:33231764
Top-Down Proteomics of Endogenous Membrane Proteins Enabled by Cloud Point Enrichment and Multidimensional Liquid Chromatography-Mass Spectrometry. PMID:33231430
Human rhinovirus-specific CD8 T cell responses target conserved and unusual epitopes. PMID:33230881
Comparative analyses and structural insights of new class glutathione transferases in Cryptosporidium species. PMID:33230237
Discovery of Amoebicidal Compounds by Combining Computational and Experimental Approaches. PMID:33229426
Efficient Confirmation of Plant Viral Proteins and Identification of Specific Viral Strains by nanoLC-ESI-Q-TOF Using Single-Leaf-Tissue Samples. PMID:33228257
Convergence of Plasma Metabolomics and Proteomics Analysis to Discover Signatures of High-Grade Serous Ovarian Cancer. PMID:33228226
Bornyl Derivatives of p-(Benzyloxy)Phenylpropionic Acid: In Vivo Evaluation of Antidiabetic Activity. PMID:33228030
In Silico Analysis and In Vitro Characterization of the Bioactive Profile of Three Novel Peptides Identified from 19 kDa α-Zein Sequences of Maize. PMID:33227894
GP4: an integrated Gram-Positive Protein Prediction Pipeline for subcellular localization mimicking bacterial sorting. PMID:33227814
Investigating the Multitarget Mechanism of Traditional Chinese Medicine Prescription for Cancer-Related Pain by Using Network Pharmacology and Molecular Docking Approach. PMID:33224254
The UCSC Genome Browser database: 2021 update. PMID:33221922
EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments. PMID:33221906
FlyBase: updates to the Drosophila melanogaster knowledge base. PMID:33219682
canSAR: update to the cancer translational research and drug discovery knowledgebase. PMID:33219674
MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca. PMID:33219670
Predicted rat interactome database and gene set linkage analysis. PMID:33216897
GPCR-PEnDB: a database of protein sequences and derived features to facilitate prediction and classification of G protein-coupled receptors. PMID:33216895
Moving targets in drug discovery. PMID:33214619
BRENDA, the ELIXIR core data resource in 2021: new developments and updates. PMID:33211880
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. PMID:33211854
Gene expression responses to Zika virus infection in peripheral blood mononuclear cells from pregnant and non-pregnant women. PMID:33211409
Angiogenesis related gene expression significantly associated with the prognostic role of an urothelial bladder carcinoma. PMID:33209684
Identification of scavenger receptors and thrombospondin-type-1 repeat proteins potentially relevant for plastid recognition in Sacoglossa. PMID:33209293
A combined transcriptomic approach to identify candidates for an anti-tick vaccine blocking B. afzelii transmission. PMID:33208766
Genome-enabled discovery of anthraquinone biosynthesis in Senna tora. PMID:33208749
Exploring the Proteomic Alterations from Untreated and Cryoablation and Irradiation Treated Giant Cell Tumors of Bone Using Liquid-Chromatography Tandem Mass Spectrometry. PMID:33207819
Changes in Membrane Protein Structural Biology. PMID:33207666
The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions. PMID:33206959
CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats. PMID:33206958
DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier. PMID:33206638
Protein identification by 3D OrbiSIMS to facilitate in situ imaging and depth profiling. PMID:33203841
IOX1 Suppresses Wnt Target Gene Transcription and Colorectal Cancer Tumorigenesis through Inhibition of KDM3 Histone Demethylases. PMID:33203729
In Silico Identification of SOX1 Post-Translational Modifications Highlights a Shared Protein Motif. PMID:33202879
In silico and in vitro studies reveal complement system drives coagulation cascade in SARS-CoV-2 pathogenesis. PMID:33200027
Structural insight into the novel iron-coordination and domain interactions of transferrin-1 from a model insect, Manduca sexta. PMID:33197096
Open Targets Platform: supporting systematic drug-target identification and prioritisation. PMID:33196847
ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years. PMID:33196841
OrthoDB in 2020: evolutionary and functional annotations of orthologs. PMID:33196836
RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions. PMID:33196814
Including residual contact information into replica-exchange MD simulations significantly enriches native-like conformations. PMID:33196676
A Fixed Cohort Field Study of Gene Expression in Circulating Leukocytes From Dairy Cows With and Without Mastitis. PMID:33195534
Tumor Suppressor LINC02487 Inhibits Oral Squamous Cell Carcinoma Cell Migration and Invasion Through the USP17-SNAI1 Axis. PMID:33194625
Silicon flow from root to shoot in pepper: a comprehensive in silico analysis reveals a potential linkage between gene expression and hormone signaling that stimulates plant growth and metabolism. PMID:33194376
DPPN-SVM: Computational Identification of Mis-Localized Proteins in Cancers by Integrating Differential Gene Expressions With Dynamic Protein-Protein Interaction Networks. PMID:33193746
Identification of Proteins of Tobacco Mosaic Virus by Using a Method of Feature Extraction. PMID:33193664
MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database. PMID:33193550
MCIC: Automated Identification of Cellulases From Metagenomic Data and Characterization Based on Temperature and pH Dependence. PMID:33193158
Structure, dynamics and lipid interactions of serotonin receptors: excitements and challenges. PMID:33188638
Virus Isoelectric Point Estimation: Theories and Methods. PMID:33188001
Virtual screening and network pharmacology-based synergistic mechanism identification of multiple components contained in Guanxin V against coronary artery disease. PMID:33187508
Trop2: Jack of All Trades, Master of None. PMID:33187148
A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS. PMID:33184295
Antimicrobial antidegradative dental adhesive preserves restoration-tooth bond. PMID:33183773
Europe PMC in 2020. PMID:33180112
Connecting Longitudinal and Transverse Relaxation Rates in Live-Cell NMR. PMID:33179918
OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. PMID:33179748
FunRes: resolving tissue-specific functional cell states based on a cell-cell communication network model. PMID:33179736
Avian Immunome DB: an example of a user-friendly interface for extracting genetic information. PMID:33176685
A haplotype-phased genome of wheat stripe rust pathogen Puccinia striiformis f. sp. tritici, race PST-130 from the Western USA. PMID:33175843
The European Nucleotide Archive in 2020. PMID:33175160
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more. PMID:33174605
Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior. PMID:33174603
LectomeXplore, an update of UniLectin for the discovery of carbohydrate-binding proteins based on a new lectin classification. PMID:33174598
MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations. PMID:33174596
Association of the DNASE1L3 rs35677470 polymorphism with systemic lupus erythematosus, rheumatoid arthritis and systemic sclerosis: Structural biological insights. PMID:33173951
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. PMID:33173863
Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes. PMID:33172385
Functional Expression of All Human Sulfotransferases in Fission Yeast, Assay Development, and Structural Models for Isoforms SULT4A1 and SULT6B1. PMID:33171978
Host behaviour alteration by its parasite: from brain gene expression to functional test. PMID:33171082
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. PMID:33170273
PARP Inhibitor Olaparib Causes No Potentiation of the Bleomycin Effect in VERO Cells, Even in the Presence of Pooled ATM, DNA-PK, and LigIV Inhibitors. PMID:33167404
Dual-Inhibitors of N-Myc and AURKA as Potential Therapy for Neuroendocrine Prostate Cancer. PMID:33167327
FireProtDB: database of manually curated protein stability data. PMID:33166383
CG4928 Is Vital for Renal Function in Fruit Flies and Membrane Potential in Cells: A First In-Depth Characterization of the Putative Solute Carrier UNC93A. PMID:33163493
First draft genome assembly of the desert locust, Schistocerca gregaria. PMID:33163158
TCRD and Pharos 2021: mining the human proteome for disease biology. PMID:33156327
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. PMID:33156326
ZNF354C is a transcriptional repressor that inhibits endothelial angiogenic sprouting. PMID:33154469
Genenames.org: the HGNC and VGNC resources in 2021. PMID:33152070
Single-cell analysis of transcriptome and DNA methylome in human oocyte maturation. PMID:33152014
Updates to the recently introduced family Lacipirellulaceae in the phylum Planctomycetes: isolation of strains belonging to the novel genera Aeoliella, Botrimarina, Pirellulimonas and Pseudobythopirellula and the novel species Bythopirellula polymerisocia and Posidoniimonas corsicana. PMID:33151460
PubChem in 2021: new data content and improved web interfaces. PMID:33151290
DrugCentral 2021 supports drug discovery and repositioning. PMID:33151287
DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics. PMID:33151284
Constitution of a comprehensive phytochemical profile and network pharmacology based investigation to decipher molecular mechanisms of Teucrium polium L. in the treatment of type 2 diabetes mellitus. PMID:33150068
Combinatorial expression of GPCR isoforms affects signalling and drug responses. PMID:33149304
Systems evaluation reveals novel transporter YohJK renders 3-hydroxypropionate tolerance in Escherichia coli. PMID:33149261
Identification and characterization of the proteolytic flagellin from the common freshwater bacterium Hylemonella gracilis. PMID:33149258
Loss of PHF6 leads to aberrant development of human neuron-like cells. PMID:33149206
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. PMID:33147627
Inhibiting Sialidase-Induced TGF-β1 Activation Attenuates Pulmonary Fibrosis in Mice. PMID:33144389
Putative Antimicrobial Peptides of the Posterior Salivary Glands from the Cephalopod Octopus vulgaris Revealed by Exploring a Composite Protein Database. PMID:33143020
Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L. PMID:33142722
Delineation of the 1q24.3 microdeletion syndrome provides further evidence for the potential role of non-coding RNAs in regulating the skeletal phenotype. PMID:33141070
β-Barrel proteins tether the outer membrane in many Gram-negative bacteria. PMID:33139883
Chlorovirus PBCV-1 protein A064R has three of the transferase activities necessary to synthesize its capsid protein N-linked glycans. PMID:33139538
KinaseMD: kinase mutations and drug response database. PMID:33137204
Ensembl 2021. PMID:33137190
ADPriboDB 2.0: an updated database of ADP-ribosylated proteins. PMID:33137182
Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation. PMID:33137082
Identification and characterization of the first fish parvalbumin-like protein data from a pathogenic fungal species, Trichophyton violaceum. PMID:33134447
SURF1 related Leigh syndrome: Clinical and molecular findings of 16 patients from Turkey. PMID:33134083
Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production. PMID:33134082
IHP-PING-generating integrated human protein-protein interaction networks on-the-fly. PMID:33129201
Plasma Proteomics Identify Biomarkers and Pathogenesis of COVID-19. PMID:33128875
The Dynamic Proteome of Oligodendrocyte Lineage Differentiation Features Planar Cell Polarity and Macroautophagy Pathways. PMID:33128372
Mass spectrometry-based abundance atlas of ABC transporters in human liver, gut, kidney, brain and skin. PMID:33128234
Network-based machine learning in colorectal and bladder organoid models predicts anti-cancer drug efficacy in patients. PMID:33127883
Molecular Evidence for an Active Microbial Methane Cycle in Subsurface Serpentinite-Hosted Groundwaters in the Samail Ophiolite, Oman. PMID:33127818
Pfam: The protein families database in 2021. PMID:33125078
Complete and Circularized Genome Assemblies of the Kroppenstedtia eburnea Genus Type Strain and the Kroppenstedtia pulmonis Species Type Strain with MiSeq and MinION Sequence Data. PMID:33122418
EBV-EBNA1 constructs an immunosuppressive microenvironment for nasopharyngeal carcinoma by promoting the chemoattraction of Treg cells. PMID:33122398
Virus-Host Protein-Protein Interactions between Human Papillomavirus 16 E6 A1 and D2/D3 Sub-Lineages: Variances and Similarities. PMID:33121134
Automatic Gene Function Prediction in the 2020's. PMID:33120976
The MemMoRF database for recognizing disordered protein regions interacting with cellular membranes. PMID:33119751
DescribePROT: database of amino acid-level protein structure and function predictions. PMID:33119734
Identification of Novel Therapeutic Molecular Targets in Inflammatory Bowel Disease by Using Genetic Databases. PMID:33116744
Hybridization of Curcumin Analogues with Cinnamic Acid Derivatives as Multi-Target Agents Against Alzheimer's Disease Targets. PMID:33114751
Transcriptome Analysis of Amyloodinium ocellatum Tomonts Revealed Basic Information on the Major Potential Virulence Factors. PMID:33114415
Advances on Plant Ubiquitylome-From Mechanism to Application. PMID:33114409
Meta-Analysis of Transcriptome Data Detected New Potential Players in Response to Dioxin Exposure in Humans. PMID:33113971
In Vivo Validation of Alternative FDXR Transcripts in Human Blood in Response to Ionizing Radiation. PMID:33113898
Pleiotropic roles of cold shock proteins with special emphasis on unexplored cold shock protein member of Plasmodium falciparum. PMID:33109193
Leishmania differentiation requires ubiquitin conjugation mediated by a UBC2-UEV1 E2 complex. PMID:33108402
O-Pair Search with MetaMorpheus for O-glycopeptide characterization. PMID:33106676
Preclinical validation of therapeutic targets predicted by tensor factorization on heterogeneous graphs. PMID:33106501
Systematic Investigation of Resistance Evolution to Common Antibiotics Reveals Conserved Collateral Responses across Common Human Pathogens. PMID:33106260
Heat Stress Triggers Differential Protein Accumulation in the Extracellular Matrix of Sorghum Cell Suspension Cultures. PMID:33105781
SMART: recent updates, new developments and status in 2020. PMID:33104802
Determinants of correlated expression of transcription factors and their target genes. PMID:33104784
Computational Identification of Human Biological Processes and Protein Sequence Motifs Putatively Targeted by SARS-CoV-2 Proteins Using Protein-Protein Interaction Networks. PMID:33103435
Applying computer simulations in battling with COVID-19, using pre-analyzed molecular and chemical data to face the pandemic. PMID:33102687
Probing the Structural Dynamics of the Plasmodium falciparum Tunneling-Fold Enzyme 6-Pyruvoyl Tetrahydropterin Synthase to Reveal Allosteric Drug Targeting Sites. PMID:33102524
Uncovering the Cyclic AMP Signaling Pathway of the Protozoan Parasite Entamoeba histolytica and Understanding Its Role in Phagocytosis. PMID:33102254
Genomic and transcriptomic landscapes and evolutionary dynamics of molluscan glycoside hydrolase families with implications for algae-feeding biology. PMID:33101612
Tools of the trade: studying actin in zebrafish. PMID:33095903
Virtual Double-System Single-Box: A Nonequilibrium Alchemical Technique for Absolute Binding Free Energy Calculations: Application to Ligands of the SARS-CoV-2 Main Protease. PMID:33090785
MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline. PMID:33087062
KLIFS: an overhaul after the first 5 years of supporting kinase research. PMID:33084889
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria. PMID:33084862
Reference transcriptomes and comparative analyses of six species in the threatened rosewood genus Dalbergia. PMID:33082403
Unveiling the effect of dietary essential oils supplementation in Sparus aurata gills and its efficiency against the infestation by Sparicotyle chrysophrii. PMID:33082387
Genomic Features of a Food-Derived Pseudomonas aeruginosa Strain PAEM and Biofilm-Associated Gene Expression under a Marine Bacterial α-Galactosidase. PMID:33081309
Three-Dimensional Structures of Carbohydrates and Where to Find Them. PMID:33081008
Detergent Resistant Membrane Domains in Broccoli Plasma Membrane Associated to the Response to Salinity Stress. PMID:33080920
Evolutionary and Comparative Analysis of Bacterial Nonhomologous End Joining Repair. PMID:33078828
Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes. PMID:33076954
Temporal proteomic profiling reveals insight into critical developmental processes and temperature-influenced physiological response differences in a bivalve mollusc. PMID:33076839
The Immune Response to Eastern Equine Encephalitis Virus Acquired Through Organ Transplantation. PMID:33072022
The Drosophila seminal proteome and its role in postcopulatory sexual selection. PMID:33070726
NCAM protein and SARS-COV-2 surface proteins: In-silico hypothetical evidence for the immunopathogenesis of Guillain-Barré syndrome. PMID:33069093
Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas. PMID:33068420
Mapping glycan-mediated galectin-3 interactions by live cell proximity labeling. PMID:33067390
Proteomic Characterization of Urinary Extracellular Vesicles from Kidney-Transplanted Patients Treated with Calcineurin Inhibitors. PMID:33066346
Distribution of disease-causing germline mutations in coiled-coils implies an important role of their N-terminal region. PMID:33060664
smORFunction: a tool for predicting functions of small open reading frames and microproteins. PMID:33054771
A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions. PMID:33053376
Differential expression of full-length and NH2 terminally truncated FAM134B isoforms in normal physiology and cancer. PMID:33052704
Human trans-editing enzyme displays tRNA acceptor-stem specificity and relaxed amino acid selectivity. PMID:33051185
Uveal Melanoma-Derived Extracellular Vesicles Display Transforming Potential and Carry Protein Cargo Involved in Metastatic Niche Preparation. PMID:33050649
Characterization of the Vaginal DNA Virome in Health and Dysbiosis. PMID:33050261
HybridMine: A Pipeline for Allele Inheritance and Gene Copy Number Prediction in Hybrid Genomes and Its Application to Industrial Yeasts. PMID:33050146
Stearoyl-CoA desaturase 5 (SCD5), a Δ-9 fatty acyl desaturase in search of a function. PMID:33049404
Semantic similarity and machine learning with ontologies. PMID:33049044
SWATH-MS based proteomic profiling of pancreatic ductal adenocarcinoma tumours reveals the interplay between the extracellular matrix and related intracellular pathways. PMID:33048956
Protein ontology on the semantic web for knowledge discovery. PMID:33046717
SilencerDB: a comprehensive database of silencers. PMID:33045745
INTEDE: interactome of drug-metabolizing enzymes. PMID:33045737
GIMICA: host genetic and immune factors shaping human microbiota. PMID:33045729
Multiresolution Imaging Using Bioluminescence Resonance Energy Transfer Identifies Distinct Biodistribution Profiles of Extracellular Vesicles and Exomeres with Redirected Tropism. PMID:33042758
DockCoV2: a drug database against SARS-CoV-2. PMID:33035337
Mitochondria under the spotlight: On the implications of mitochondrial dysfunction and its connectivity to neuropsychiatric disorders. PMID:33033576
The mole genome reveals regulatory rearrangements associated with adaptive intersexuality. PMID:33033216
Data mining of human plasma proteins generates a multitude of highly predictive aging clocks that reflect different aspects of aging. PMID:33031577
Investigating the mechanism of ShuFeng JieDu capsule for the treatment of novel Coronavirus pneumonia (COVID-19) based on network pharmacology. PMID:33029094
Multicompartment modeling of protein shedding kinetics during vascularized tumor growth. PMID:33028917
An intrinsically disordered motif regulates the interaction between the p47 adaptor and the p97 AAA+ ATPase. PMID:33028677
Protein Concentrations of Thrombospondin-1, MIP-1β, and S100A8 Suggest the Reflection of a Pregnancy Clock in Mid-Trimester Amniotic Fluid. PMID:33026626
A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways. PMID:33024710
The reuse of public datasets in the life sciences: potential risks and rewards. PMID:33024631
Benchmarking evolutionary tinkering underlying human-viral molecular mimicry shows multiple host pulmonary-arterial peptides mimicked by SARS-CoV-2. PMID:33024578
HybridMine: A Pipeline for Allele Inheritance and Gene Copy Number Prediction in Hybrid Genomes and Its Application to Industrial Yeasts. PMID:33050146
Stearoyl-CoA desaturase 5 (SCD5), a Δ-9 fatty acyl desaturase in search of a function. PMID:33049404
Semantic similarity and machine learning with ontologies. PMID:33049044
SWATH-MS based proteomic profiling of pancreatic ductal adenocarcinoma tumours reveals the interplay between the extracellular matrix and related intracellular pathways. PMID:33048956
Protein ontology on the semantic web for knowledge discovery. PMID:33046717
SilencerDB: a comprehensive database of silencers. PMID:33045745
INTEDE: interactome of drug-metabolizing enzymes. PMID:33045737
GIMICA: host genetic and immune factors shaping human microbiota. PMID:33045729
Multiresolution Imaging Using Bioluminescence Resonance Energy Transfer Identifies Distinct Biodistribution Profiles of Extracellular Vesicles and Exomeres with Redirected Tropism. PMID:33042758
DockCoV2: a drug database against SARS-CoV-2. PMID:33035337
Mitochondria under the spotlight: On the implications of mitochondrial dysfunction and its connectivity to neuropsychiatric disorders. PMID:33033576
The mole genome reveals regulatory rearrangements associated with adaptive intersexuality. PMID:33033216
Data mining of human plasma proteins generates a multitude of highly predictive aging clocks that reflect different aspects of aging. PMID:33031577
Investigating the mechanism of ShuFeng JieDu capsule for the treatment of novel Coronavirus pneumonia (COVID-19) based on network pharmacology. PMID:33029094
Multicompartment modeling of protein shedding kinetics during vascularized tumor growth. PMID:33028917
An intrinsically disordered motif regulates the interaction between the p47 adaptor and the p97 AAA+ ATPase. PMID:33028677
Protein Concentrations of Thrombospondin-1, MIP-1β, and S100A8 Suggest the Reflection of a Pregnancy Clock in Mid-Trimester Amniotic Fluid. PMID:33026626
A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways. PMID:33024710
The reuse of public datasets in the life sciences: potential risks and rewards. PMID:33024631
Benchmarking evolutionary tinkering underlying human-viral molecular mimicry shows multiple host pulmonary-arterial peptides mimicked by SARS-CoV-2. PMID:33024578
CaaX-Like Protease of Cyanobacterial Origin Is Required for Complex Plastid Biogenesis in Malaria Parasites. PMID:33024034
Aggregation and disaggregation features of the human proteome. PMID:33022891
Structure, Dynamics, and Interactions of GPI-Anchored Human Glypican-1 with Heparan Sulfates in a Membrane. PMID:33021626
Treatment with Commonly Used Antiretroviral Drugs Induces a Type I/III Interferon Signature in the Gut in the Absence of HIV Infection. PMID:33015651
Serum protein biomarkers for juvenile dermatomyositis: a pilot study. PMID:33015544
miRNAs Predicted to Regulate Host Anti-viral Gene Pathways in IPNV-Challenged Atlantic Salmon Fry Are Affected by Viral Load, and Associated With the Major IPN Resistance QTL Genotypes in Late Infection. PMID:33013890
Genomic Characteristics Distinguish Geographically Distributed Dehalococcoidia. PMID:33013780
Deep phylogeny of cancer drivers and compensatory mutations. PMID:33009502
Keratin 17 regulates nuclear morphology and chromatin organization. PMID:33008845
In silico Prediction of New Drug Candidates Against the Multidrug-Resistant and Potentially Zoonotic Fish Pathogen Serotype III Streptococcus agalactiae. PMID:33005185
Genetic Diversity of Serine Protease Inhibitors in Myxozoan (Cnidaria, Myxozoa) Fish Parasites. PMID:33003479
ADPriboDB v2.0: An Updated Database of ADP-ribosylated Proteins. PMID:32995784
In vitro resynthesis of lichenization reveals the genetic background of symbiosis-specific fungal-algal interaction in Usnea hakonensis. PMID:32993496
Finding New Molecular Targets of Familiar Natural Products Using In Silico Target Prediction. PMID:32993084
Focus on Human Monoamine Transporter Selectivity. New Human DAT and NET Models, Experimental Validation, and SERT Affinity Exploration. PMID:32991141
Herbal pair Huangqin-Baishao: mechanisms underlying inflammatory bowel disease by combined system pharmacology and cell experiment approach. PMID:32988394
Sericin-Induced Melanogenesis in Cultured Retinal Pigment Epithelial Cells Is Associated with Elevated Levels of Hydrogen Peroxide and Inflammatory Proteins. PMID:32987810
Reversal of diet-induced hepatic steatosis by peripheral CB1 receptor blockade in mice is p53/miRNA-22/SIRT1/PPARα dependent. PMID:32987186
Expression analysis of mammalian mitochondrial ribosomal protein genes. PMID:32987154
CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean. PMID:32986829
Genomic Features of Parthenogenetic Animals. PMID:32985658
The E3 ubiquitin-protein ligase MDM2 is a novel interactor of the von Hippel-Lindau tumor suppressor. PMID:32985545
Structural and functional modelling of SARS-CoV-2 entry in animal models. PMID:32985513
Global quantitative analysis of the human brain proteome and phosphoproteome in Alzheimer's disease. PMID:32985496
Cancer-associated fibroblasts of the prostate promote a compliant and more invasive phenotype in benign prostate epithelial cells. PMID:32984808
Molecular Characteristics and Zoonotic Potential of Salmonella Weltevreden From Cultured Shrimp and Tilapia in Vietnam and China. PMID:32983012
Improved Virus Isoelectric Point Estimation by Exclusion of Known and Predicted Genome-Binding Regions. PMID:32978129
Longitudinal Metatranscriptomic Analysis of a Meat Spoilage Microbiome Detects Abundant Continued Fermentation and Environmental Stress Responses during Shelf Life and Beyond. PMID:32978125
Phylogenetic and genomic analysis reveals high genomic openness and genetic diversity of Clostridium perfringens. PMID:32975504
Intermittent leucine pulses during continuous feeding alters novel components involved in skeletal muscle growth of neonatal pigs. PMID:32974749
Comparative Analysis of the Secretome and Interactome of Trypanosoma cruzi and Trypanosoma rangeli Reveals Species Specific Immune Response Modulating Proteins. PMID:32973747
Mus musculus populations in Western Australia lack VKORC1 mutations conferring resistance to first generation anticoagulant rodenticides: Implications for conservation and biosecurity. PMID:32970676
A Membrane-Tethered Ubiquitination Pathway Regulates Hedgehog Signaling and Heart Development. PMID:32966817
Unveiling molecular signatures of preeclampsia and gestational diabetes mellitus with multi-omics and innovative cheminformatics visualization tools. PMID:32966491
Structure, dynamics and functions of UBQLNs: at the crossroads of protein quality control machinery. PMID:32965492
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
Comprehensive Survey and Comparative Assessment of RNA-Binding Residue Predictions with Analysis by RNA Type. PMID:32961749
Thermodynamic insight into viral infections 2: empirical formulas, molecular compositions and thermodynamic properties of SARS, MERS and SARS-CoV-2 (COVID-19) viruses. PMID:32954038
GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis. PMID:32952729
A Reference Genome Sequence for Giant Sequoia. PMID:32948606
Protein Databases Related to Liquid-Liquid Phase Separation. PMID:32947964
Transcriptomic data on the transgenerational exposure of the keystone amphipod Gammarus locusta to simvastatin. PMID:32944603
Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production. PMID:32942174
IDDB: a comprehensive resource featuring genes, variants and characteristics associated with infertility. PMID:32941628
From Anti-EBV Immune Responses to the EBV Diseasome via Cross-reactivity. PMID:32939516
Structural models of human ACE2 variants with SARS-CoV-2 Spike protein for structure-based drug design. PMID:32938937
DELTEX2 C-terminal domain recognizes and recruits ADP-ribosylated proteins for ubiquitination. PMID:32937373
COVID-19 Biomarkers in research: Extension of the OncoMX cancer biomarker data model to capture biomarker data from other diseases. PMID:32935101
StoneMod: a database for kidney stone modulatory proteins with experimental evidence. PMID:32934277
Quantitative Protein Corona Composition and Dynamics on Carbon Nanotubes in Biological Environments. PMID:32931615
Leveraging orthogonal mass spectrometry based strategies for comprehensive sequencing and characterization of ribosomal antimicrobial peptide natural products. PMID:32929442
Molecular Modeling of Pathogenic Mutations in the Keratin 1B Domain. PMID:32927888
Chitinase Gene Positively Regulates Hypersensitive and Defense Responses of Pepper to Colletotrichum acutatum Infection. PMID:32927746
Targeting Phosphotyrosine in Native Proteins with Conditional, Bispecific Antibody Traps. PMID:32924468
Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate. PMID:32920602
Ontogeny of arterial macrophages defines their functions in homeostasis and inflammation. PMID:32917889
Label-free quantitative proteomic analysis of gingival crevicular fluid to identify potential early markers for root resorption. PMID:32917196
Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis. PMID:32914530
Effect of cysteine addition and heat treatment on the properties and microstructure of a calcium-induced whey protein cold-set gel. PMID:32914103
Annotated genome sequences of the carnivorous plant Roridula gorgonias and a non-carnivorous relative, Clethra arborea. PMID:32912303
Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC. PMID:32912302
The UCSC SARS-CoV-2 Genome Browser. PMID:32908258
ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. PMID:32907876
Metagenomic Profiling and Microbial Metabolic Potential of Perdido Fold Belt (NW) and Campeche Knolls (SE) in the Gulf of Mexico. PMID:32903729
Transcriptomic Analysis of Rhodococcus opacus R7 Grown on o-Xylene by RNA-Seq. PMID:32903390
CB1-receptor-mediated inhibitory LTD triggers presynaptic remodeling via protein synthesis and ubiquitination. PMID:32902378
Diagnostic yield and clinical utility of whole exome sequencing using an automated variant prioritization system, EVIDENCE. PMID:32901917
Genome-wide Study Identifies Association between HLA-B∗55:01 and Self-Reported Penicillin Allergy. PMID:32888428
Analysis of insect nuclear small heat shock proteins and interacting proteins. PMID:32888179
Cystathionine β-synthase is involved in cysteine biosynthesis and H2S generation in Toxoplasma gondii. PMID:32887901
Non-Coding RNA Databases in Cardiovascular Research. PMID:32887511
Oligopeptide Transporter-1 is Associated with Fluorescence Intensity of 5-Aminolevulinic Acid-Based Photodynamic Diagnosis in Pancreatic Cancer Cells. PMID:32884434
UCSF ChimeraX: Structure visualization for researchers, educators, and developers. PMID:32881101
A Phylogeny-Informed Proteomics Approach for Species Identification within the Burkholderia cepacia Complex. PMID:32878952
Secretome Proteomic Approaches for Biomarker Discovery: An Update on Colorectal Cancer. PMID:32878319
Investigating Core Signaling Pathways of Hepatitis B Virus Pathogenesis for Biomarkers Identification and Drug Discovery via Systems Biology and Deep Learning Method. PMID:32878239
Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns. PMID:32875947
Genomic resources and toolkits for developmental study of whip spiders (Amblypygi) provide insights into arachnid genome evolution and antenniform leg patterning. PMID:32874529
Exploring the Diversity of Cysteine-Rich Natural Product Peptides via MS/MS Fingerprint Ions. PMID:32872784
Proteomics and Metabolomics Approaches towards a Functional Insight onto AUTISM Spectrum Disorders: Phenotype Stratification and Biomarker Discovery. PMID:32872562
Merged Tacrine-Based, Multitarget-Directed Acetylcholinesterase Inhibitors 2015-Present: Synthesis and Biological Activity. PMID:32825138
FLAVi: An Enhanced Annotator for Viral Genomes of Flaviviridae. PMID:32824044
De Novo KAT5 Variants Cause a Syndrome with Recognizable Facial Dysmorphisms, Cerebellar Atrophy, Sleep Disturbance, and Epilepsy. PMID:32822602
A Human IgSF Cell-Surface Interactome Reveals a Complex Network of Protein-Protein Interactions. PMID:32822567
DataRemix: a universal data transformation for optimal inference from gene expression datasets. PMID:32821903
Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C sequencing. PMID:32821405
Germline variants in HEY2 functional domains lead to congenital heart defects and thoracic aortic aneurysms. PMID:32820247
Novel variant in NSDHL gene associated with CHILD syndrome and syndactyly- a case report. PMID:32819291
Interplay of Disorder and Sequence Specificity in the Formation of Stable Dynein-Dynactin Complexes. PMID:32814057
Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli. PMID:32813020
First insight into the whole-genome sequence variations in Mycobacterium bovis BCG-1 (Russia) vaccine seed lots and their progeny clinical isolates from children with BCG-induced adverse events. PMID:32811436
A guide to plasma membrane solute carrier proteins. PMID:32810346
Cellular and Extracellular Proteome of the Animal Pathogen Corynebacterium silvaticum, a Close Relative of Zoonotic Corynebacterium ulcerans and Corynebacterium pseudotuberculosis. PMID:32806579
Anti-rods/rings autoantibody and IMPDH filaments: an update after fifteen years of discovery. PMID:32805424
Using collections of structural models to predict changes of binding affinity caused by mutations in protein-protein interactions. PMID:32797645
Comparative Genomics Underlines Multiple Roles of Profftella, an Obligate Symbiont of Psyllids: Providing Toxins, Vitamins, and Carotenoids. PMID:32797185
Heterologous expression of a glycosyl hydrolase and cellular reprogramming enable Zymomonas mobilis growth on cellobiose. PMID:32797046
Cell Sorting in Hydra vulgaris Arises from Differing Capacities for Epithelialization between Cell Types. PMID:32795440
Expression of genes involved in drug metabolism differs between perfusable 3D liver tissue and conventional 2D-cultured hepatocellular carcinoma cells. PMID:32794647
First Evidence of Acyl-Hydrolase/Lipase Activity From Human Probiotic Bacteria: Lactobacillus rhamnosus GG and Bifidobacterium longum NCC 2705. PMID:32793131
Identification of modified peptides using localization-aware open search. PMID:32792501
Optimization of Acetazolamide-Based Scaffold as Potent Inhibitors of Vancomycin-Resistant Enterococcus. PMID:32787141
Cyanobacterial Dihydroxyacid Dehydratases Are a Promising Growth Inhibition Target. PMID:32786290
JAGN1, tetraspanins, and Erv proteins: is common topology indicative of common function in cargo sorting? PMID:32783652
Building the vertebrate codex using the gene breaking protein trap library. PMID:32779569
Characterization of the Exopolysaccharide Biosynthesis Pathway in Myxococcus xanthus. PMID:32778557
Chemoreceptors with C-terminal pentapeptides for CheR and CheB binding are abundant in bacteria that maintain host interactions. PMID:32774789
Transgelin interacts with PARP1 in human colon cancer cells. PMID:32774160
Modelling, docking and simulation analysis of Bisphenol A interaction with laccase from Trichoderma. PMID:32773992
PIM1 accelerates prostate cancer cell motility by phosphorylating actin capping proteins. PMID:32771000
Mutant p53 induces Golgi tubulo-vesiculation driving a prometastatic secretome. PMID:32770028
Sodium-coupled glucose transport, the SLC5 family, and therapeutically relevant inhibitors: from molecular discovery to clinical application. PMID:32767111
Mapping Coeliac Toxic Motifs in the Prolamin Seed Storage Proteins of Barley, Rye, and Oats Using a Curated Sequence Database. PMID:32766270
Machine learning: A powerful tool for gene function prediction in plants. PMID:32765975
Proteome Comparison Between Natural Desiccation-Tolerant Plants and Drought-Protected Caspicum annuum Plants by Microbacterium sp. 3J1. PMID:32765446
Transcriptomic Analysis of Four Cerianthid (Cnidaria, Ceriantharia) Venoms. PMID:32764303
16q24.3 Microduplication in a Patient With Developmental Delay, Intellectual Disability, Short Stature, and Nonspecific Dysmorphic Features: Case Report and Review of the Literature. PMID:32760686
Genomic Variation and Arsenic Tolerance Emerged as Niche Specific Adaptations by Different Exiguobacterium Strains Isolated From the Extreme Salar de Huasco Environment in Chilean - Altiplano. PMID:32760381
Tn-Seq Analysis Identifies Genes Important for Yersinia pestis Adherence during Primary Pneumonic Plague. PMID:32759339
Glycosaminoglycan-Protein Interactions: The First Draft of the Glycosaminoglycan Interactome. PMID:32757871
IDRMutPred: predicting disease-associated germline nonsynonymous single nucleotide variants (nsSNVs) in intrinsically disordered regions. PMID:32756939
A comprehensive rat transcriptome built from large scale RNA-seq-based annotation. PMID:32749457
Deep Transcriptomic Analysis Reveals the Dynamic Developmental Progression during Early Development of Channel Catfish (Ictalurus punctatus). PMID:32748829
HISTome2: a database of histone proteins, modifiers for multiple organisms and epidrugs. PMID:32746900
Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys. PMID:32745123
Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder. PMID:32744794
Gliome database: a comprehensive web-based tool to access and analyze glia secretome data. PMID:32743661
Identification of an α-MoRF in the Intrinsically Disordered Region of the Escargot Transcription Factor. PMID:32743208
Cytotoxic and anticancer properties of the Malaysian mangrove pit viper (Trimeresurus purpureomaculatus) venom and its disintegrin (purpureomaculin). PMID:32742279
Iron binding and release properties of transferrin-1 from Drosophila melanogaster and Manduca sexta: Implications for insect iron homeostasis. PMID:32735914
STRING data mining of GWAS data in canine hereditary pigment-associated deafness. PMID:32734119
Glucose Availability Alters Gene and Protein Expression of Several Newly Classified and Putative Solute Carriers in Mice Cortex Cell Culture and D. melanogaster. PMID:32733888
Extracellular Vesicles Produced by the Probiotic Propionibacterium freudenreichii CIRM-BIA 129 Mitigate Inflammation by Modulating the NF-κB Pathway. PMID:32733422
Strategies to enable large-scale proteomics for reproducible research. PMID:32732981
The Flavoproteome of the Model Plant Arabidopsis thaliana. PMID:32731628
Structure-based drug repositioning over the human TMPRSS2 protease domain: search for chemical probes able to repress SARS-CoV-2 Spike protein cleavages. PMID:32730844
An Activity-Guided Map of Electrophile-Cysteine Interactions in Primary Human T Cells. PMID:32730809
Cloning and functional complementation of ten Schistosoma mansoni phosphodiesterases expressed in the mammalian host stages. PMID:32730343
A convenient protein library for spectroscopic calibrations. PMID:32728409
Mitochondria and Peroxisome Remodeling across Cytomegalovirus Infection Time Viewed through the Lens of Inter-ViSTA. PMID:32726614
A defect in COPI-mediated transport of STING causes immune dysregulation in COPA syndrome. PMID:32725126
Comparison of spleen transcriptomes of two wild rodent species reveals differences in the immune response against Borrelia afzelii. PMID:32724523
A Pilot Study of Multi-Input Recurrent Neural Networks for Drug-Kinase Binding Prediction. PMID:32722290
Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions. PMID:32721383
Analysis of ACE2 Gene-Encoded Proteins Across Mammalian Species. PMID:32719819
Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes. PMID:32719664
Role of Mitochondrial Glycerol-3-Phosphate Dehydrogenase in Metabolic Adaptations of Prostate Cancer. PMID:32717855
A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets. PMID:32716361
Identification of Sulfenylated Cysteines in Arabidopsis thaliana Proteins Using a Disulfide-Linked Peptide Reporter. PMID:32714340
NAuRA: Genomic Tool to Identify Staphylococcal Enterotoxins in Staphylococcus aureus Strains Responsible for FoodBorne Outbreaks. PMID:32714310
PertInInt: An Integrative, Analytical Approach to Rapidly Uncover Cancer Driver Genes with Perturbed Interactions and Functionalities. PMID:32711844
Neotropical Rattlesnake (Crotalus simus) Venom Pharmacokinetics in Lymph and Blood Using an Ovine Model. PMID:32708875
Carbonic Anhydrase VI in Skin Wound Healing Study on Car6 Knockout Mice. PMID:32708518
Characteristics of Extracellular Vesicles Released by the Pathogenic Yeast-Like Fungi Candida glabrata, Candida parapsilosis and Candida tropicalis. PMID:32708393
Characteristics of Biopeptides Released In Silico from Collagens Using Quantitative Parameters. PMID:32708318
Identification of RNA-Binding Proteins as Targetable Putative Oncogenes in Neuroblastoma. PMID:32707690
Single-nucleotide conservation state annotation of the SARS-CoV-2 genome. PMID:32699851
Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras. PMID:32697992
Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism. PMID:32694731
Increased nuclear factor I/B expression in prostate cancer correlates with AR expression. PMID:32692871
A novel CACNA1A variant in a child with early stroke and intractable epilepsy. PMID:32692472
Expansions and contractions in gene families of independently-evolved blood-feeding insects. PMID:32680460
SARS-CoV-2 Main Protease: A Molecular Dynamics Study. PMID:32678588
Chain reactions: molecular mechanisms of RBR ubiquitin ligases. PMID:32677670
Experimental approaches to tracking mobile genetic elements in microbial communities. PMID:32672812
Molecular docking analyses of CYP450 monooxygenases of Tribolium castaneum (Herbst) reveal synergism of quercetin with paraoxon and tetraethyl pyrophosphate: in vivo and in silico studies. PMID:32670552
Computational approaches in viral ecology. PMID:32670501
Black Soldier Fly Larvae Adapt to Different Food Substrates through Morphological and Functional Responses of the Midgut. PMID:32668813
Targeting Endogenous K-RAS for Degradation through the Affinity-Directed Protein Missile System. PMID:32668202
Unified inference of missense variant effects and gene constraints in the human genome. PMID:32667917
Uncoupling sodium channel dimers restores the phenotype of a pain-linked Nav 1.7 channel mutation. PMID:32663327
First-Principles Collision Cross Section Measurements of Large Proteins and Protein Complexes. PMID:32662991
Characterization of glutathione proteome in CHO cells and its relationship with productivity and cholesterol synthesis. PMID:32662871
Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook. PMID:32662816
Adenovirus-mediated ubiquitination alters protein-RNA binding and aids viral RNA processing. PMID:32661314
Drosophila Glia: Models for Human Neurodevelopmental and Neurodegenerative Disorders. PMID:32660023
Benchmarking gene ontology function predictions using negative annotations. PMID:32657372
Detection and Independent Validation of Model-Based Quantitative Transcriptional Regulation Relationships Altered in Lung Cancers. PMID:32656193
Investigation of microbial community interactions between Lake Washington methanotrophs using -------genome-scale metabolic modeling. PMID:32655999
Different Proteins Mediate Step-Wise Chromosome Architectures in Thermoplasma acidophilum and Pyrobaculum calidifontis. PMID:32655523
Hepatoprotective effects of Hovenia dulcis seeds against alcoholic liver injury and related mechanisms investigated via network pharmacology. PMID:32655267
Human carbonic anhydrases and post-translational modifications: a hidden world possibly affecting protein properties and functions. PMID:32648529
Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein. PMID:32646969
Transcriptional responses in Parascaris univalens after in vitro exposure to ivermectin, pyrantel citrate and thiabendazole. PMID:32646465
Machine learning and AI-based approaches for bioactive ligand discovery and GPCR-ligand recognition. PMID:32645448
Human genes differ by their UV sensitivity estimated through analysis of UV-induced silent mutations in melanoma. PMID:32643855
CHEDDA syndrome: a case report and review of the literature for this newly described entity. PMID:32642015
Visualisation tools for dependent peptide searches to support the exploration of in vitro protein modifications. PMID:32639981
SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome. PMID:32637963
Analysis of ACE2 Genetic Variability among Populations Highlights a Possible Link with COVID-19-Related Neurological Complications. PMID:32635188
C5a impairs phagosomal maturation in the neutrophil through phosphoproteomic remodeling. PMID:32634128
Structures of mammalian GLD-2 proteins reveal molecular basis of their functional diversity in mRNA and microRNA processing. PMID:32633758
A Genomic and Transcriptomic Overview of MATE, ABC, and MFS Transporters in Citrus sinensis Interaction with Xanthomonas citri subsp. citri. PMID:32630416
An Economic Dilemma Between Molecular Weapon Systems May Explain an Arachno-atypical Venom in Wasp Spiders (Argiope bruennichi). PMID:32630016
Unravelling the proteomic signature of extracellular vesicles released by drug-resistant Leishmania infantum parasites. PMID:32628683
Sequence Compression Benchmark (SCB) database-A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences. PMID:32627830
Structural insight into mitochondrial β-barrel outer membrane protein biogenesis. PMID:32620929
Analysis of H3K4me3 and H3K27me3 bivalent promotors in HER2+ breast cancer cell lines reveals variations depending on estrogen receptor status and significantly correlates with gene expression. PMID:32620123
Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection. PMID:32619549
Prediction of Nephrotoxicity Associated With Cisplatin-Based Chemotherapy in Testicular Cancer Patients. PMID:32617516
Glutamyl-Prolyl-tRNA Synthetase Regulates Proline-Rich Pro-Fibrotic Protein Synthesis During Cardiac Fibrosis. PMID:32611237
Eukaryotic life without tQCUG: the role of Elongator-dependent tRNA modifications in Dictyostelium discoideum. PMID:32609816
RNAWRE: a resource of writers, readers and erasers of RNA modifications. PMID:32608478
Development and validation of protein biomarkers of health in grizzly bears. PMID:32607241
Germline Mutations in DNA Repair Genes in Patients With Metastatic Castration-resistant Prostate Cancer. PMID:32606146
Ultrastructural, Cytochemical, and Comparative Genomic Evidence of Peroxisomes in Three Genera of Pathogenic Free-Living Amoebae, Including the First Morphological Data for the Presence of This Organelle in Heteroloboseans. PMID:32602891
Computational Chemogenomics Drug Repositioning Strategy Enables the Discovery of Epirubicin as a New Repurposed Hit for Plasmodium falciparum and P. vivax. PMID:32601162
Experimentally Determined Long Intrinsically Disordered Protein Regions Are Now Abundant in the Protein Data Bank. PMID:32599863
Fulvic acid increases forage legume growth inducing preferential up-regulation of nodulation and signalling-related genes. PMID:32599619
Designing a novel mRNA vaccine against SARS-CoV-2: An immunoinformatics approach. PMID:32599237
Single-cell RNA sequencing reveals cell type- and artery type-specific vascular remodelling in male spontaneously hypertensive rats. PMID:32589721
The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions. PMID:32587962
Structure and Dynamics in the ATG8 Family From Experimental to Computational Techniques. PMID:32587856
Phloem Exudate Protein Profiles during Drought and Recovery Reveal Abiotic Stress Responses in Tomato Vasculature. PMID:32586033
CD2 Immunobiology. PMID:32582179
Transcriptome Analysis of Wounding in the Model Grass Lolium temulentum. PMID:32580425
Structure-Based Discovery of Dual-Target Hits for Acetylcholinesterase and the α7 Nicotinic Acetylcholine Receptors: In Silico Studies and In Vitro Confirmation. PMID:32580406
Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores. PMID:32579097
Whole-genome sequence association analysis of blood proteins in a longitudinal wellness cohort. PMID:32576278
Elucidation of cellular targets and exploitation of the receptor-binding domain of SARS-CoV-2 for vaccine and monoclonal antibody synthesis. PMID:32573788
Genome-Wide Identification of RNA Silencing-Related Genes and Their Expressional Analysis in Response to Heat Stress in Barley (Hordeum vulgare L.). PMID:32570964
Pontiella desulfatans gen. nov., sp. nov., and Pontiella sulfatireligans sp. nov., Two Marine Anaerobes of the Pontiellaceae fam. nov. Producing Sulfated Glycosaminoglycan-like Exopolymers. PMID:32570748
Venomics Approach Reveals a High Proportion of Lactrodectus-Like Toxins in the Venom of the Noble False Widow Spider Steatoda nobilis. PMID:32570718
Assessing predictors for new post translational modification sites: A case study on hydroxylation. PMID:32569263
Identification of Active Compounds of Mahuang Fuzi Xixin Decoction and Their Mechanisms of Action by LC-MS/MS and Network Pharmacology. PMID:32565854
Non-cooperative 4E-BP2 folding with exchange between eIF4E-binding and binding-incompatible states tunes cap-dependent translation inhibition. PMID:32561718
T-Cell Epitopes and Neo-epitopes in Type 1 Diabetes: A Comprehensive Update and Reappraisal. PMID:32561620
Prognostic Biomarkers in Endometrial Cancer: A Systematic Review and Meta-Analysis. PMID:32560580
The Chromatin Regulator ZMYM2 Restricts Human Pluripotent Stem Cell Growth and Is Essential for Teratoma Formation. PMID:32559458
DeepRMethylSite: a deep learning based approach for prediction of arginine methylation sites in proteins. PMID:32555810
Functional shell matrix proteins tentatively identified by asymmetric snail shell morphology. PMID:32555253
Phosphoregulated orthogonal signal transduction in mammalian cells. PMID:32555187
Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons. PMID:32553182
Patterns of Sequence and Expression Diversification Associate Members of the PADRE Gene Family With Response to Fungal Pathogens. PMID:32547597
Network Pharmacology and Experimental Evidence Reveal Dioscin Suppresses Proliferation, Invasion, and EMT via AKT/GSK3b/mTOR Signaling in Lung Adenocarcinoma. PMID:32546976
Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the genus Sodalis. PMID:32543366
GTDB: an integrated resource for glycosyltransferase sequences and annotations. PMID:32542364
Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome. PMID:32537769
Ionizing Radiation-induced Proteomic Oxidation in Escherichia coli. PMID:32536603
Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome. PMID:32531926
DDIEM: drug database for inborn errors of metabolism. PMID:32527280
mRNA Interferase Bacillus cereus BC0266 Shows MazF-Like Characteristics Through Structural and Functional Study. PMID:32521689
More Than One-to-Four via 2R: Evidence of an Independent Amphioxus Expansion and Two-Gene Ancestral Vertebrate State for MyoD-Related Myogenic Regulatory Factors (MRFs). PMID:32520990
ACE2 diversity in placental mammals reveals the evolutionary strategy of SARS-CoV-2. PMID:32520981
BacEffluxPred: A two-tier system to predict and categorize bacterial efflux mediated antibiotic resistance proteins. PMID:32518231
Amino acid encoding for deep learning applications. PMID:32517697
CapsNet-SSP: multilane capsule network for predicting human saliva-secretory proteins. PMID:32517646
PSIONplusm Server for Accurate Multi-Label Prediction of Ion Channels and Their Types. PMID:32517331
The effect of phytoglobin overexpression on the plant proteome during nonhost response of barley (Hordeum vulgare) to wheat powdery mildew (Blumeria graminis f. sp. tritici). PMID:32513937
Computational Models Identify Several FDA Approved or Experimental Drugs as Putative Agents Against SARS-CoV-2. PMID:32511287
Identifying temporal molecular signatures underlying cardiovascular diseases: A data science platform. PMID:32504647
An evolutionarily conserved motif is required for Plasmodesmata-located protein 5 to regulate cell-to-cell movement. PMID:32504045
Proteins and Molecular Pathways Relevant for the Malignant Properties of Tumor-Initiating Pancreatic Cancer Cells. PMID:32503348
The minimal meningococcal ProQ protein has an intrinsic capacity for structure-based global RNA recognition. PMID:32499480
Structural analysis of the PATZ1 BTB domain homodimer. PMID:32496219
Insulin-like Growth Factor-1 and IGF Binding Proteins Predict All-Cause Mortality and Morbidity in Older Adults. PMID:32492897
Effect of pore size and spacing on neovascularization of a biodegradble shape memory polymer perivascular wrap. PMID:32490564
Coevolutionary data-based interaction networks approach highlighting key residues across protein families: The case of the G-protein coupled receptors. PMID:32489528
Genetic architecture underlying changes in carotenoid accumulation during the evolution of the blind Mexican cavefish, Astyanax mexicanus. PMID:32488995
Protein signatures to identify the different genera within the Xanthomonadaceae family. PMID:32488841
Demonstration of In Vitro to In Vivo Translation of a TYK2 Inhibitor That Shows Cross Species Potency Differences. PMID:32488071
An expanded role for dipeptidyl peptidase 4 in cell regulation. PMID:32487805
Using Reactome to build an autophagy mechanism knowledgebase. PMID:32486891
Virulence Potential of a Multidrug-Resistant Escherichia coli Strain Belonging to the Emerging Clonal Group ST101-B1 Isolated from Bloodstream Infection. PMID:32486334
Resveratrol: Multi-Targets Mechanism on Neurodegenerative Diseases Based on Network Pharmacology. PMID:32477148
Phenotype expansion of heterozygous FOXC1 pathogenic variants toward involvement of congenital anomalies of the kidneys and urinary tract (CAKUT). PMID:32475988
Anti-Alzheimer's Disease Molecular Mechanism of Acori Tatarinowii Rhizoma Based on Network Pharmacology. PMID:32475979
Binding affinities of 438 HLA proteins to complete proteomes of seven pandemic viruses and distributions of strongest and weakest HLA peptide binders in populations worldwide. PMID:32475052
Molecular signature of eutopic endometrium in endometriosis based on the multi-omics integrative synthesis. PMID:32474803
Engineered triply orthogonal pyrrolysyl-tRNA synthetase/tRNA pairs enable the genetic encoding of three distinct non-canonical amino acids. PMID:32472101
dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes. PMID:32472030
Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons. PMID:32470107
piNET: a versatile web platform for downstream analysis and visualization of proteomics data. PMID:32469073
Draft Genome Sequences of Rhodococcus sp. Strains YH1 and T7, Isolated from Explosive-Contaminated Environments. PMID:32467261
The Mouse Heart Mitochondria N Terminome Provides Insights into ClpXP-Mediated Proteolysis. PMID:32467259
Mining the Yucatan Coastal Microbiome for the Identification of Non-Ribosomal Peptides Synthetase (NRPS) Genes. PMID:32466531
High-resolution annotation of the mouse preimplantation embryo transcriptome using long-read sequencing. PMID:32461551
Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of nonclassic domestication. PMID:32461376
Dual Independent Roles of the p24 Complex in Selectivity of Secretory Cargo Export from the Endoplasmic Reticulum. PMID:32456004
Unstructured Biology of Proteins from Ubiquitin-Proteasome System: Roles in Cancer and Neurodegenerative Diseases. PMID:32455657
Balance between asymmetry and abundance in multi-domain DNA-binding proteins may regulate the kinetics of their binding to DNA. PMID:32453726
A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. PMID:32449511
Phase-separated bacterial ribonucleoprotein bodies organize mRNA decay. PMID:32445438
Single-cell analysis of murine fibroblasts identifies neonatal to adult switching that regulates cardiomyocyte maturation. PMID:32444791
GPS-PBS: A Deep Learning Framework to Predict Phosphorylation Sites that Specifically Interact with Phosphoprotein-Binding Domains. PMID:32443803
Maternal Protein Restriction in Rats Alters the Expression of Genes Involved in Mitochondrial Metabolism and Epitranscriptomics in Fetal Hypothalamus. PMID:32438566
Gene network analyses support subfunctionalization hypothesis for duplicated hsp70 genes in the Antarctic clam. PMID:32436134
TASL is the SLC15A4-associated adaptor for IRF5 activation by TLR7-9. PMID:32433612
Ensembles of Hydrophobicity Scales as Potent Classifiers for Chimeric Virus-Like Particle Solubility - An Amino Acid Sequence-Based Machine Learning Approach. PMID:32432098
The NtrYX Two-Component System Regulates the Bacterial Cell Envelope. PMID:32430476
'Kinesinopathies': emerging role of the kinesin family member genes in birth defects. PMID:32430361
A novel proangiogenic B cell subset is increased in cancer and chronic inflammation. PMID:32426497
Secretome-Based Screening in Target Discovery. PMID:32425085
Live-cell protein engineering with an ultra-short split intein. PMID:32424098
PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins. PMID:32421769
Progress, Challenges, and Surprises in Annotating the Human Genome. PMID:32421357
Natural brominated phenoxyphenols kill persistent and biofilm-incorporated cells of MRSA and other pathogenic bacteria. PMID:32418125
Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data. PMID:32417785
COVID-19: CADD to the rescue. PMID:32417181
The Role of Gene Elongation in the Evolution of Histidine Biosynthetic Genes. PMID:32414216
Genotype-phenotype analysis of LMNA-related diseases predicts phenotype-selective alterations in lamin phosphorylation. PMID:32413188
Missense NR2F1 variant in monozygotic twins affected with the Bosch-Boonstra-Schaaf optic atrophy syndrome. PMID:32412696
SDN2GO: An Integrated Deep Learning Model for Protein Function Prediction. PMID:32411695
Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus. PMID:32411167
RNA-Binding Proteins in Acute Leukemias. PMID:32408494
Aberrant glycosylation in schizophrenia: a review of 25 years of post-mortem brain studies. PMID:32404945
Trefoil factors share a lectin activity that defines their role in mucus. PMID:32404934
Molecular determinants underlying functional innovations of TBP and their impact on transcription initiation. PMID:32404905
Search for ABCB1 Modulators Among 2-Amine-5-Arylideneimidazolones as a New Perspective to Overcome Cancer Multidrug Resistance. PMID:32403277
UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase. PMID:32399560
Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank. PMID:32398145
Biochemical Convergence of Mitochondrial Hsp70 System Specialized in Iron-Sulfur Cluster Biogenesis. PMID:32397253
Secretion of a low and high molecular weight β-glycosidase by Yarrowia lipolytica. PMID:32393258
EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities. PMID:32392342
Cysteines and Disulfide Bonds as Structure-Forming Units: Insights From Different Domains of Life and the Potential for Characterization by NMR. PMID:32391319
Identification of potential cervical cancer serum biomarkers in Thai patients. PMID:32391095
Applying knowledge-driven mechanistic inference to toxicogenomics. PMID:32387679
Atypical ALPK2 kinase is not essential for cardiac development and function. PMID:32383995
Network Pharmacology Study of Heat-Clearing and Detoxifying Traditional Chinese Medicine for Alzheimer's Disease. PMID:32382304
Self-analysis of repeat proteins reveals evolutionarily conserved patterns. PMID:32381046
The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma. PMID:32380953
Revisiting TNF Receptor-Associated Periodic Syndrome (TRAPS): Current Perspectives. PMID:32380704
Glycobiology and schizophrenia: a biological hypothesis emerging from genomic research. PMID:32377000
Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures. PMID:32375858
The Quest for Orthologs benchmark service and consensus calls in 2020. PMID:32374845
SARS-CoV-2 and ORF3a: Nonsynonymous Mutations, Functional Domains, and Viral Pathogenesis. PMID:32371472
Cryo-EM Structure of the Fork Protection Complex Bound to CMG at a Replication Fork. PMID:32369734
Synergistic and antagonistic drug interactions in the treatment of systemic fungal infections. PMID:32367801
UPCLASS: a deep learning-based classifier for UniProtKB entry publications. PMID:32367111
Exomes of Ductal Luminal Breast Cancer Patients from Southwest Colombia: Gene Mutational Profile and Related Expression Alterations. PMID:32365829
Protein markers for Candida albicans EVs include claudin-like Sur7 family proteins. PMID:32363014
Integrative Proteome and Acetylome Analyses of Murine Responses to Cryptococcus neoformans Infection. PMID:32362878
Recent hybrids recapitulate ancient hybrid outcomes. PMID:32358487
Extracellular Vesicles Secreted by Corneal Epithelial Cells Promote Myofibroblast Differentiation. PMID:32357574
Structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV and the phylogeny of the aminotransferase pathway. PMID:32356521
Potential Molecular Mechanisms of Zhibai Dihuang Wan in Systemic Lupus Erythematosus Based on Network Biology. PMID:32351603
Structural analysis of pathogenic missense mutations in GABRA2 and identification of a novel de novo variant in the desensitization gate. PMID:32347641
AFP-LSE: Antifreeze Proteins Prediction Using Latent Space Encoding of Composition of k-Spaced Amino Acid Pairs. PMID:32345989
T cell costimulation, checkpoint inhibitors and anti-tumor therapy. PMID:32345776
Uncovering the mechanism of the effects of Paeoniae Radix Alba on iron-deficiency anaemia through a network pharmacology-based strategy. PMID:32345291
Structure of the ALS Mutation Target Annexin A11 Reveals a Stabilising N-Terminal Segment. PMID:32344647
Light-Activatable, 2,5-Disubstituted Tetrazoles for the Proteome-wide Profiling of Aspartates and Glutamates in Living Bacteria. PMID:32342004
Drug Research Meets Network Science: Where Are We? PMID:32338900
Testis-specific serine kinase protein family in male fertility and as targets for non-hormonal male contraception†. PMID:32337545
Deep conservation of prion-like composition in the eukaryotic prion-former Pub1/Tia1 family and its relatives. PMID:32337108
Synthesis and structure-activity relationships of thieno[2,3-d]pyrimidines as atypical protein kinase C inhibitors to control retinal vascular permeability and cytokine-induced edema. PMID:32327351
Novel Apoptotic Mediators Identified by Conservation of Vertebrate Caspase Targets. PMID:32326640
Hitchhiking with Nature: Snake Venom Peptides to Fight Cancer and Superbugs. PMID:32326531
GlyGen data model and processing workflow. PMID:32324859
Quantitative SWATH-Based Proteomic Profiling for Identification of Mechanism-Driven Diagnostic Biomarkers Conferring in the Progression of Metastatic Prostate Cancer. PMID:32322560
Oculodentodigital Dysplasia: A Case Report and Major Review of the Eye and Ocular Adnexa Features of 295 Reported Cases. PMID:32318302
Binding of the Human 14-3-3 Isoforms to Distinct Sites in the Leucine-Rich Repeat Kinase 2. PMID:32317922
Novel monoclonal antibodies against thymidine kinase 1 and their potential use for the immunotargeting of lung, breast and colon cancer cells. PMID:32317865
Physicochemical Characterisation of KEIF-The Intrinsically Disordered N-Terminal Region of Magnesium Transporter A. PMID:32316569
A transcriptional regulatory network of Rsv3-mediated extreme resistance against Soybean mosaic virus. PMID:32315334
Zebra2: advanced and easy-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies. PMID:32313959
novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model. PMID:32313937
Perturbing proteomes at single residue resolution using base editing. PMID:32313011
On the molecular determinants of the SARS-CoV-2 attack. PMID:32311462
Ceramide launches an acute anti-adhesion pro-migration cell signaling program in response to chemotherapy. PMID:32307766
Cold-inducible RNA-binding protein Cirp, but not Rbm3, may regulate transcript processing and protection in tissues of the hibernating ground squirrel. PMID:32307648
Active constituents and mechanisms of Respiratory Detox Shot, a traditional Chinese medicine prescription, for COVID-19 control and prevention: Network-molecular docking-LC-MSE analysis. PMID:32307268
Cathepsin B in neurodegeneration of Alzheimer's disease, traumatic brain injury, and related brain disorders. PMID:32305689
Transcriptome profiling and protease inhibition experiments identify proteases that activate H3N2 influenza A and influenza B viruses in murine airways. PMID:32303635
Draft Genome Sequence of Gordonia sp. Strain YY1, Isolated from an Explosive-Contaminated Environment. PMID:32299869
Juvenile Paget's Disease From Heterozygous Mutation of SP7 Encoding Osterix (Specificity Protein 7, Transcription Factor SP7). PMID:32298837
Disruption of genes associated with Charcot-Marie-Tooth type 2 lead to common behavioural, cellular and molecular defects in Caenorhabditis elegans. PMID:32294113
Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio). PMID:32293261
Specificity in PDZ-peptide interaction networks: Computational analysis and review. PMID:32289118
Metabolomics Adaptation of Juvenile Pacific Abalone Haliotis discus hannai to Heat Stress. PMID:32286374
LARP1 isoform expression in human cancer cell lines. PMID:32286153
Structured reviews for data and knowledge-driven research. PMID:32283553
Opening up connectivity between documents, structures and bioactivity. PMID:32280387
Portable nanopore analytics: are we there yet? PMID:32277811
Genome-Wide Changes in Genetic Diversity in a Population of Myotis lucifugus Affected by White-Nose Syndrome. PMID:32276959
Network Systems Pharmacology-Based Mechanism Study on the Beneficial Effects of Vitamin D against Psychosis in Alzheimer's Disease. PMID:32273551
Quantitative phenotyping of shell suture strength in walnut (Juglans regia L.) enhances precision for detection of QTL and genome-wide association mapping. PMID:32271818
Pseudomonas putida KT2440 is naturally endowed to withstand industrial-scale stress conditions. PMID:32267616
PRESnovo: Prescreening Prior to de novo Sequencing to Improve Accuracy and Sensitivity of Neuropeptide Identification. PMID:32266812
Mob Family Proteins: Regulatory Partners in Hippo and Hippo-Like Intracellular Signaling Pathways. PMID:32266255
Patterns of gene evolution following duplications and speciations in vertebrates. PMID:32266119
Two-Level Protein Methylation Prediction using structure model-based features. PMID:32265459
CDH1 Mutation Distribution and Type Suggests Genetic Differences between the Etiology of Orofacial Clefting and Gastric Cancer. PMID:32260281
Peptidylarginine Deiminase of Porphyromonas gingivalis Modulates the Interactions between Candida albicans Biofilm and Human Plasminogen and High-Molecular-Mass Kininogen. PMID:32260245
Unraveling 1,4-Butanediol Metabolism in Pseudomonas putida KT2440. PMID:32256468
A novel compound heterozygous missense mutation in ASNS broadens the spectrum of asparagine synthetase deficiency. PMID:32255274
MaveQuest: a web resource for planning experimental tests of human variant effects. PMID:32251504
Entropy based analysis of vertebrate sperm protamines sequences: evidence of potential dityrosine and cysteine-tyrosine cross-linking in sperm protamines. PMID:32245406
Characteristics of Potential Protein Nutraceuticals of Plant Origin with Antioxidant Activity. PMID:32244766
Overexpression of antisense long non‑coding RNA ZNF710‑AS1‑202 promotes cell proliferation and inhibits apoptosis of clear cell renal cell carcinoma via regulation of ZNF710 expression. PMID:32236626
Systematic analysis of lysine acetylome and succinylome reveals the correlation between modification of H2A.X complexes and DNA damage response in breast cancer. PMID:32236595
Deep evolutionary analysis reveals the design principles of fold A glycosyltransferases. PMID:32234211
Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota. PMID:32234071
Centenarian Exomes as a Tool for Evaluating the Clinical Relevance of Germline Tumor Suppressor Mutations. PMID:32233832
Musashi-1: An Example of How Polyalanine Tracts Contribute to Self-Association in the Intrinsically Disordered Regions of RNA-Binding Proteins. PMID:32225071
Long-Read Genome Sequencing and Assembly of Leptopilina boulardi: A Specialist Drosophila Parasitoid. PMID:32217632
The transcriptome of the newt Cynops orientalis provides new insights into evolution and function of sexual gene networks in sarcopterygians. PMID:32214214
Metabolic factors contribute to T-cell inhibition in the ovarian cancer ascites. PMID:32208517
Bioinformatic Analysis of the Flavin-Dependent Amine Oxidase Superfamily: Adaptations for Substrate Specificity and Catalytic Diversity. PMID:32198115
Proteomic signatures of in vivo muscle oxidative capacity in healthy adults. PMID:32196924
A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies. PMID:32191846
Association of Peroxisome Proliferator-Activated Receptors (PPARs) with Diabetic Retinopathy in Human and Animal Models: Analysis of the Literature and Genome Browsers. PMID:32190036
Non‑invasive proteome‑wide quantification of skin barrier‑related proteins using label‑free LC‑MS/MS analysis. PMID:32186761
In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13C and 2H Tracers. PMID:32184362
Variant effect predictions capture some aspects of deep mutational scanning experiments. PMID:32183714
Cyclosporine a directly affects human and mouse b cell migration in vitro by disrupting a hIF-1 αdependent, o2 sensing, molecular switch. PMID:32183695
Inherited DNA Repair Gene Mutations in Men with Lethal Prostate Cancer. PMID:32183364
Genomic Landscape and Mutational Spectrum of ADAMTS Family Genes in Mendelian Disorders Based on Gene Evidence Review for Variant Interpretation. PMID:32183147
Wikidata as a knowledge graph for the life sciences. PMID:32180547
In-depth proteome analysis of more than 12,500 proteins in buffalo mammary epithelial cell line identifies protein signatures for active proliferation and lactation. PMID:32179766
Gene mutations distinguishing gastric from colorectal and esophageal adenocarcinomas. PMID:32175104
SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning. PMID:32173600
Enabling reusability of plant phenomic datasets with MIAPPE 1.1. PMID:32171029
Biochemical and Genetic Analysis Identify CSLD3 as a beta-1,4-Glucan Synthase That Functions during Plant Cell Wall Synthesis. PMID:32169960
Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity. PMID:32168319
Complexities in Genetics of Psoriatic Arthritis. PMID:32166449
Flavodoxins as Novel Therapeutic Targets against Helicobacter pylori and Other Gastric Pathogens. PMID:32164177
von Willebrand factor D and EGF domains is an evolutionarily conserved and required feature of blastemas capable of multitissue appendage regeneration. PMID:32163674
Mitochondrial peptide BRAWNIN is essential for vertebrate respiratory complex III assembly. PMID:32161263
A method for CRISPR/Cas9 mutation of genes in fathead minnow (Pimephales promelas). PMID:32160575
ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis. PMID:32150535
OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data. PMID:32142370
Structural insights into the mechanism of oxidative activation of heme-free H-NOX from Vibrio cholerae. PMID:32141496
Structural and biochemical characterization of mitochondrial citrate synthase 4 from Arabidopsis thaliana. PMID:32133996
Identification of Milk and Cheese Intake Biomarkers in Healthy Adults Reveals High Interindividual Variability of Lewis System-Related Oligosaccharides. PMID:32133503
Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005-2017. PMID:32131727
Transcriptomic resources for evolutionary studies in flat periwinkles and related species. PMID:32127542
Systematic Localization of Escherichia coli Membrane Proteins. PMID:32127419
Human Hepatocyte Nuclear Factor 4-α Encodes Isoforms with Distinct Transcriptional Functions. PMID:32123031
Arabidopsis RanBP2-Type Zinc Finger Proteins Related to Chloroplast RNA Editing Factor OZ1. PMID:32121603
Molecular Evolution and Diversification of Proteins Involved in miRNA Maturation Pathway. PMID:32121542
Differential Dorsolateral Prefrontal Cortex Proteomic Profiles of Suicide Victims with Mood Disorders. PMID:32120974
Dynamic Alternative Splicing During Mouse Preimplantation Embryo Development. PMID:32117919
Chronic Sublethal Aluminum Exposure and Avena fatua Caryopsis Colonization Influence Gene Expression of Fusarium avenaceum F.a.1. PMID:32117103
Spatial proteomics revealed a CX3CL1-dependent crosstalk between the urothelium and relocated macrophages through IL-6 during an acute bacterial infection in the urinary bladder. PMID:32112048
Mass spectrometry-based identification of a B-cell maturation antigen-derived T-cell epitope for antigen-specific immunotherapy of multiple myeloma. PMID:32111817
Metagenomics-Guided Discovery of Potential Bacterial Metallothionein Genes from the Soil Microbiome That Confer Cu and/or Cd Resistance. PMID:32111593
Whole-Genome Sequencing of Lactobacillus helveticus D75 and D76 Confirms Safety and Probiotic Potential. PMID:32111071
A Quantitative Tissue-Specific Landscape of Protein Redox Regulation during Aging. PMID:32109415
The Evolution History of Fe-S Cluster A-Type Assembly Protein Reveals Multiple Gene Duplication Events and Essential Protein Motifs. PMID:32108236
Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis Using the PSI Extended FASTA Format. PMID:32106352
Predicted Drosophila Interactome Resource and web tool for functional interpretation of differentially expressed genes. PMID:32103267
Computational Identification and Analysis of Ubiquinone-Binding Proteins. PMID:32102444
Rational Design of Photo-Electrochemical Hybrid Devices Based on Graphene and Chlamydomonas reinhardtii Light-Harvesting Proteins. PMID:32099058
Analysis of protein missense alterations by combining sequence- and structure-based methods. PMID:32096919
Extracellular loops matter - subcellular location and function of the lysine transporter Lyp1 from Saccharomyces cerevisiae. PMID:32096906
Simultaneous Immunoglobulin A and G Glycopeptide Profiling for High-Throughput Applications. PMID:32091889
Specific Conformational Dynamics and Expansion Underpin a Multi-Step Mechanism for Specific Binding of p27 with Cdk2/Cyclin A. PMID:32088186
Transcriptomics at Maize Embryo/Endosperm Interfaces Identifies a Transcriptionally Distinct Endosperm Subdomain Adjacent to the Embryo Scutellum. PMID:32086366
An α/β-Hydrolase Fold Subfamily Comprising Pseudomonas Quinolone Signal-Cleaving Dioxygenases. PMID:32086305
A New Family of Diverse Skin Peptides from the Microhylid Frog Genus Phrynomantis. PMID:32085597
Identification of a novel base J binding protein complex involved in RNA polymerase II transcription termination in trypanosomes. PMID:32084124
Changes in nucleus accumbens gene expression accompany sex-specific suppression of spontaneous physical activity in aromatase knockout mice. PMID:32081742
Altering the Neisseria gonorrhoeae pilE Guanine Quadruplex Loop Bases Affects Pilin Antigenic Variation. PMID:32078293
Current Trends in Diagnostics of Viral Infections of Unknown Etiology. PMID:32074965
Data on assessment of safety and tear proteome change in response to orthokeratology lens - Insight from integrating clinical data and next generation proteomics. PMID:32071970
Structural insights into the main S-layer unit of Deinococcus radiodurans reveal a massive protein complex with porin-like features. PMID:32071085
Identification and validation of reference genes for RT-qPCR normalization in wheat meiosis. PMID:32066846
The pan-cancer landscape of prognostic germline variants in 10,582 patients. PMID:32066500
Proteogenomic Characterization of Endometrial Carcinoma. PMID:32059776
Inference of Multisite Phosphorylation Rate Constants and Their Modulation by Pathogenic Mutations. PMID:32059766
Residues of Fluoroquinolone Antibiotics Induce Carbonylation and Reduce In Vitro Digestion of Sarcoplasmic and Myofibrillar Beef Proteins. PMID:32053976
Quantitative Proteomics to Identify Nuclear RNA-Binding Proteins of Malat1. PMID:32050583
A Review of Small Molecule Inhibitors and Functional Probes of Human Cathepsin L. PMID:32041276
Detection of EXP1-Specific CD4+ T Cell Responses Directed Against a Broad Range of Epitopes Including Two Promiscuous MHC Class II Binders During Acute Plasmodium falciparum Malaria. PMID:32038611
Candidate gene screen for potential interaction partners and regulatory targets of the Hox gene labial in the spider Parasteatoda tepidariorum. PMID:32036446
HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. PMID:32034905
Predicting Antimicrobial and Other Cysteine-Rich Peptides in 1267 Plant Transcriptomes. PMID:32032999
Cis- and Trans-Regulatory Variations in the Domestication of the Chili Pepper Fruit. PMID:32031611
Complete Genome Sequence of Salmonella enterica Siphophage Shemara. PMID:32029558
Discovery of several thousand highly diverse circular DNA viruses. PMID:32014111
Machine Learning Strategy That Leverages Large Data sets to Boost Statistical Power in Small-Scale Experiments. PMID:32009418
The Eupentacta fraudatrix transcriptome provides insights into regulation of cell transdifferentiation. PMID:32001787
PIPE4: Fast PPI Predictor for Comprehensive Inter- and Cross-Species Interactomes. PMID:31996697
The round goby genome provides insights into mechanisms that may facilitate biological invasions. PMID:31992286
Crowd-Sourced Chemistry: Considerations for Building a Standardized Database to Improve Omic Analyses. PMID:31984253
Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords. PMID:31984130
Assessing Structural Determinants of Zn2+ Binding to Human HV1 via Multiple MD Simulations. PMID:31972155
Biotin proximity tagging favours unfolded proteins and enables the study of intrinsically disordered regions. PMID:31969649
Plant based production of myoglobin - a novel source of the muscle heme-protein. PMID:31969582
Inference of Multisite Phosphorylation Rate Constants and Their Modulation by Pathogenic Mutations. PMID:32059766
Residues of Fluoroquinolone Antibiotics Induce Carbonylation and Reduce In Vitro Digestion of Sarcoplasmic and Myofibrillar Beef Proteins. PMID:32053976
Quantitative Proteomics to Identify Nuclear RNA-Binding Proteins of Malat1. PMID:32050583
A Review of Small Molecule Inhibitors and Functional Probes of Human Cathepsin L. PMID:32041276
Detection of EXP1-Specific CD4+ T Cell Responses Directed Against a Broad Range of Epitopes Including Two Promiscuous MHC Class II Binders During Acute Plasmodium falciparum Malaria. PMID:32038611
Candidate gene screen for potential interaction partners and regulatory targets of the Hox gene labial in the spider Parasteatoda tepidariorum. PMID:32036446
HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. PMID:32034905
Predicting Antimicrobial and Other Cysteine-Rich Peptides in 1267 Plant Transcriptomes. PMID:32032999
Cis- and Trans-Regulatory Variations in the Domestication of the Chili Pepper Fruit. PMID:32031611
Complete Genome Sequence of Salmonella enterica Siphophage Shemara. PMID:32029558
Discovery of several thousand highly diverse circular DNA viruses. PMID:32014111
Machine Learning Strategy That Leverages Large Data sets to Boost Statistical Power in Small-Scale Experiments. PMID:32009418
The Eupentacta fraudatrix transcriptome provides insights into regulation of cell transdifferentiation. PMID:32001787
PIPE4: Fast PPI Predictor for Comprehensive Inter- and Cross-Species Interactomes. PMID:31996697
The round goby genome provides insights into mechanisms that may facilitate biological invasions. PMID:31992286
Crowd-Sourced Chemistry: Considerations for Building a Standardized Database to Improve Omic Analyses. PMID:31984253
Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords. PMID:31984130
Assessing Structural Determinants of Zn2+ Binding to Human HV1 via Multiple MD Simulations. PMID:31972155
Biotin proximity tagging favours unfolded proteins and enables the study of intrinsically disordered regions. PMID:31969649
Plant based production of myoglobin - a novel source of the muscle heme-protein. PMID:31969582
Photobiomodulation does not influence maturation and mildly improves functional healing of mouse achilles tendons. PMID:31965620
Four high-quality draft genome assemblies of the marine heterotrophic nanoflagellate Cafeteria roenbergensis. PMID:31964893
Building a pipeline to solicit expert knowledge from the community to aid gene summary curation. PMID:31960022
Quantitative Characterization of the Neuropeptide Level Changes in Dorsal Horn and Dorsal Root Ganglia Regions of the Murine Itch Models. PMID:31957451
Computational Analysis of the Silver Nanoparticle-Human Serum Albumin Complex. PMID:31956763
Open Data for Differential Network Analysis in Glioma. PMID:31952211
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. PMID:31950984
Compound heterozygous mutations in FBN1 in a large family with Marfan syndrome. PMID:31950671
Aluminium-silicon interactions in higher plants: an update. PMID:31950161
From Translation to Protein Degradation as Mechanisms for Regulating Biological Functions: A Review on the SLRP Family in Skeletal Tissues. PMID:31947880
Isolation of an archaeon at the prokaryote-eukaryote interface. PMID:31942073
Deciphering the enzymatic target of a new family of antischistosomal agents bearing a quinazoline scaffold using complementary computational tools. PMID:31939312
Domain-mediated interactions for protein subfamily identification. PMID:31937869
Automatic construction of metabolic models with enzyme constraints. PMID:31937255
Preferential Coupling of Dopamine D2S and D2L Receptor Isoforms with Gi1 and Gi2 Proteins-In Silico Study. PMID:31936673
Uncovering the Pharmacological Mechanism of Stemazole in the Treatment of Neurodegenerative Diseases Based on a Network Pharmacology Approach. PMID:31936558
General and Genomic DNA-Binding Specificity for the Thermus thermophilus HB8 Transcription Factor TTHB023. PMID:31935968
The DNA polymerases of Drosophila melanogaster. PMID:31933406
Emerging patterns of tyrosine sulfation and O-glycosylation cross-talk and co-localization. PMID:31927217
Defining the TLT-1 interactome from resting and activated human platelets. PMID:31923473
Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within "Nassophorea-Synhymenia-Phyllopharyngea" Assemblage. PMID:31921016
Structural insight into T cell coinhibition by PD-1H (VISTA). PMID:31919279
The transcriptional correlates of divergent electric organ discharges in Paramormyrops electric fish. PMID:31918666
UDSMProt: universal deep sequence models for protein classification. PMID:31913448
De novo transcriptome assembly and annotation for gene discovery in avocado, macadamia and mango. PMID:31913298
Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance. PMID:31910889
Human Plasma Protein Corona of Aβ Amyloid and Its Impact on Islet Amyloid Polypeptide Cross-Seeding. PMID:31909987
Differential Expression in Testis and Liver Transcriptomes from Four Species of Peromyscus (Rodentia: Cricetidae). PMID:31909812
Identification of antigens presented by MHC for vaccines against tuberculosis. PMID:31908851
A tunable orthogonal coiled-coil interaction toolbox for engineering mammalian cells. PMID:31907374
LLPSDB: a database of proteins undergoing liquid-liquid phase separation in vitro. PMID:31906602
Rad51 paralogs and the risk of unselected breast cancer: A case-control study. PMID:31905201
Fidelity of translation initiation is required for coordinated respiratory complex assembly. PMID:31903419
Complete Genome Sequence of Serratia marcescens Siphophage Slocum. PMID:31896657
Complete Genome Sequence of Serratia marcescens Podophage Pila. PMID:31896656
Complete Genome Sequence of Serratia Phage Muldoon. PMID:31896655
Complete Genome Sequence of Stenotrophomonas Phage Mendera. PMID:31896654
Development of a Retinal-Based Probe for the Profiling of Retinaldehyde Dehydrogenases in Cancer Cells. PMID:31893226
Proceedings of the EuBIC Winter School 2019. PMID:31890545
Analysis of Soybean Long Non-Coding RNAs Reveals a Subset of Small Peptide-Coding Transcripts. PMID:31882456
The Role of E3, E4 Ubiquitin Ligase (UBE4B) in Human Pathologies. PMID:31878315
Pathogenicity Reclasssification of RPE65 Missense Variants Related to Leber Congenital Amaurosis and Early-Onset Retinal Dystrophy. PMID:31878136
Identification of highly conserved, serotype-specific dengue virus sequences: implications for vaccine design. PMID:31874646
The Emerging Role of Cytidine Deaminase in Human Diseases: A New Opportunity for Therapy? PMID:31870623
ODF1, sperm flagelar protein is expressed in kidney collecting ducts of rats. PMID:31867458
Characterization of Human Dosage-Sensitive Transcription Factor Genes. PMID:31867040
Comparison of the transcriptomes of two tardigrades with different hatching coordination. PMID:31864287
Japanese version of The Cancer Genome Atlas, JCGA, established using fresh frozen tumors obtained from 5143 cancer patients. PMID:31863614
Functionally Annotating Regulatory Elements in the Equine Genome Using Histone Mark ChIP-Seq. PMID:31861495
The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity. PMID:31861318
Dual action of amitriptyline on NMDA receptors: enhancement of Ca-dependent desensitization and trapping channel block. PMID:31857688
Structural diversity in the atomic resolution 3D fingerprint of the titin M-band segment. PMID:31856237
Comparative analysis of ascorbate peroxidases (APXs) from selected plants with a special focus on Oryza sativa employing public databases. PMID:31856232
Endoplasmic reticulum transmembrane protein TMTC3 contributes to O-mannosylation of E-cadherin, cellular adherence, and embryonic gastrulation. PMID:31851597
Linker Domains: Why ABC Transporters 'Live in Fragments no Longer'. PMID:31839525
Detection and analysis of stable and flexible genes towards a genome signature framework in cancer. PMID:31831960
Engineering G protein-coupled receptor signalling in yeast for biotechnological and medical purposes. PMID:31825496
An intrinsically disordered proteins community for ELIXIR. PMID:31824649
Whole Genome Assembly of the Snout Otter Clam, Lutraria rhynchaena, Using Nanopore and Illumina Data, Benchmarked Against Bivalve Genome Assemblies. PMID:31824566
Analysis of Secondary Structure Biases in Naturally Presented HLA-I Ligands. PMID:31824508
Common Neurodegeneration-Associated Proteins Are Physiologically Expressed by Human B Lymphocytes and Are Interconnected via the Inflammation/Autophagy-Related Proteins TRAF6 and SQSTM1. PMID:31824497
Identification of Novel Putative Bacterial Feruloyl Esterases From Anaerobic Ecosystems by Use of Whole-Genome Shotgun Metagenomics and Genome Binning. PMID:31824458
Crystal structure of phytochromobilin synthase in complex with biliverdin IXα, a key enzyme in the biosynthesis of phytochrome. PMID:31822504
A History of Molecular Chaperone Structures in the Protein Data Bank. PMID:31817979
The Emerging Role of Gβ Subunits in Human Genetic Diseases. PMID:31817184
Accessible and reproducible mass spectrometry imaging data analysis in Galaxy. PMID:31816088
Casimicrobium huifangae gen. nov., sp. nov., a Ubiquitous "Most-Wanted" Core Bacterial Taxon from Municipal Wastewater Treatment Plants. PMID:31811031
Draft Genome Sequence of Enterobacter hormaechei ENT5, a Component of the Symbiotic Community of Tephritid Flies. PMID:31806752
The activating transcription factor 2: an influencer of cancer progression. PMID:31799611
Genomic and proteomic biases inform metabolic engineering strategies for anaerobic fungi. PMID:31799118
A global analysis of function and conservation of catalytic residues in enzymes. PMID:31796628
The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. PMID:31796553
Identification of four unconventional kinetoplastid kinetochore proteins KKT22-25 in Trypanosoma brucei. PMID:31795916
Structural Features of Tight-Junction Proteins. PMID:31795346
Production and characterization of Aspergillus niger GH29 family α-fucosidase and production of a novel non-reducing 1-fucosyllactose. PMID:31792892
Isotopically Labeled Desthiobiotin Azide (isoDTB) Tags Enable Global Profiling of the Bacterial Cysteinome. PMID:31782878
Membrane-Specific Targeting of Tail-Anchored Proteins SECE1 and SECE2 Within Chloroplasts. PMID:31781139
Crim1C140S mutant mice reveal the importance of cysteine 140 in the internal region 1 of CRIM1 for its physiological functions. PMID:31776724
An omics perspective on drug target discovery platforms. PMID:31774113
A Genetic Screen for Genes That Impact Peroxisomes in Drosophila Identifies Candidate Genes for Human Disease. PMID:31767637
ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins. PMID:31702846
Yield of next-generation neuropathy gene panels in axonal neuropathies. PMID:31701603
JASPAR 2020: update of the open-access database of transcription factor binding profiles. PMID:31701148
The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences. PMID:31701143
PlantRegMap: charting functional regulatory maps in plants. PMID:31701126
Induction of Lysosome-associated Protein Transmembrane 4 Beta via Sulfatase 2 Enhances Autophagic Flux in Liver Cancer Cells. PMID:31701075
Draft Genome Sequence of Bacillus cereus ET31, Isolated from an Extreme Environment. PMID:31699761
Improved Draft Genome Sequence of Microbacterium sp. Strain LKL04, a Bacterial Endophyte Associated with Switchgrass Plants. PMID:31699756
Quantitative Proteomics Reveals Remodeling of Protein Repertoire Across Life Phases of Daphnia pulex. PMID:31697011
Changes to the TDP-43 and FUS Interactomes Induced by DNA Damage. PMID:31693373
Prediction of impacts of mutations on protein structure and interactions: SDM, a statistical approach, and mCSM, using machine learning. PMID:31693276
The IUPHAR/BPS Guide to PHARMACOLOGY in 2020: extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY. PMID:31691834
Ensembl 2020. PMID:31691826
DrLLPS: a data resource of liquid-liquid phase separation in eukaryotes. PMID:31691822
PDBe: improved findability of macromolecular structure data in the PDB. PMID:31691821
The Clinical Genome and Ancestry Report: An interactive web application for prioritizing clinically implicated variants from genome sequencing data with ancestry composition. PMID:31691385
Enzyme annotation in UniProtKB using Rhea. PMID:31688925
Diverse cell junctions with unique molecular composition in tissues of a sponge (Porifera). PMID:31687123
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. PMID:31686107
Sequence and Structure Properties Uncover the Natural Classification of Protein Complexes Formed by Intrinsically Disordered Proteins via Mutual Synergistic Folding. PMID:31683980
Discovery of High Abundances of Aster-Like Nanoparticles in Pelagic Environments: Characterization and Dynamics. PMID:31681233
The DisGeNET knowledge platform for disease genomics: 2019 update. PMID:31680165
ELM-the eukaryotic linear motif resource in 2020. PMID:31680160
Proteomics Profiling of Autologous Blood and Semen Exosomes from HIV-infected and Uninfected Individuals Reveals Compositional and Functional Variabilities. PMID:31676584
Spider Knottin Pharmacology at Voltage-Gated Sodium Channels and Their Potential to Modulate Pain Pathways. PMID:31671792
Expression of TNRC6 (GW182) Proteins Is Not Necessary for Gene Silencing by Fully Complementary RNA Duplexes. PMID:31670606
NPInter v4.0: an integrated database of ncRNA interactions. PMID:31670377
Reverse diauxie phenotype in Pseudomonas aeruginosa biofilm revealed by exometabolomics and label-free proteomics. PMID:31666981
SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update. PMID:31665520
BacFITBase: a database to assess the relevance of bacterial genes during host infection. PMID:31665505
ProteomicsDB: a multi-omics and multi-organism resource for life science research. PMID:31665479
ChlamDB: a comparative genomics database of the phylum Chlamydiae and other members of the Planctomycetes-Verrucomicrobiae-Chlamydiae superphylum. PMID:31665454
Unraveling allosteric landscapes of allosterome with ASD. PMID:31665428
Venom Diversity and Evolution in the Most Divergent Cone Snail Genus Profundiconus. PMID:31661832
Molecular Cloning and Exploration of the Biochemical and Functional Analysis of Recombinant Glucose-6-Phosphate Dehydrogenase from Gluconoacetobacter diazotrophicus PAL5. PMID:31652968
Phage integration alters the respiratory strategy of its host. PMID:31650957
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. PMID:31647104
Bovine Genome Database: new annotation tools for a new reference genome. PMID:31647100
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. PMID:31647099
Plasma membrane receptor-like kinases and transporters are associated with 2,4-D resistance in wild radish. PMID:31646341
Candidate genes expression profiling during wilting in chickpea caused by Fusarium oxysporum f. sp. ciceris race 5. PMID:31644597
ExonSkipDB: functional annotation of exon skipping event in human. PMID:31642488
Transcriptomic analysis of Macrobrachium rosenbergii (giant fresh water prawn) post-larvae in response to M. rosenbergii nodavirus (MrNV) infection: de novo assembly and functional annotation. PMID:31640560
A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock. PMID:31636702
Molecular Phenotyping and Genomic Characterization of a Novel Neuroactive Bacterium Strain, Lactobacillus murinus HU-1. PMID:31636567
Different Pathways Mediate Amphotericin-Lactoferrin Drug Synergy in Cryptococcus and Saccharomyces. PMID:31632362
Integrated Bioinformatic Analyses and Immune Characterization of New Neisseria gonorrhoeae Vaccine Antigens Expressed during Natural Mucosal Infection. PMID:31627489
Determination of Ligand Profiles for Pseudomonas aeruginosa Solute Binding Proteins. PMID:31627455
Complete Genome Sequence of Stenotrophomonas Phage Pokken. PMID:31624175
Complete Genome Sequence of Xanthomonas Siphophage Samson. PMID:31624152
Challenges in the annotation of pseudoenzymes in databases: the UniProtKB approach. PMID:31618524
Going Too Far Is the Same as Falling Short†: Kinesin-3 Family Members in Hereditary Spastic Paraplegia. PMID:31616253
DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes. PMID:31612957
Guanylin, Uroguanylin and Guanylate Cyclase-C Are Expressed in the Gastrointestinal Tract of Horses. PMID:31611814
Advances and Challenges in Metatranscriptomic Analysis. PMID:31608125
Primary human chondrocytes respond to compression with phosphoproteomic signatures that include microtubule activation. PMID:31607375
VarSite: Disease variants and protein structure. PMID:31606900
Complete Genome Sequence of Proteus mirabilis Siphophage Saba. PMID:31601673
Complete Genome Sequence of Escherichia coli Phage Paul. PMID:31601672
The variability of SMCHD1 gene in FSHD patients: evidence of new mutations. PMID:31600781
MotifAnalyzer-PDZ: A computational program to investigate the evolution of PDZ-binding target specificity. PMID:31599029
Ensembl Genomes 2020-enabling non-vertebrate genomic research. PMID:31598706
ProCarbDB: a database of carbohydrate-binding proteins. PMID:31598690
Global gene expression analysis of Escherichia coli K-12 DH5α after exposure to 2.4 GHz wireless fidelity radiation. PMID:31595026
Uncovering Thousands of New Peptides with Sequence-Mask-Search Hybrid De Novo Peptide Sequencing Framework. PMID:31591261
MatrisomeDB: the ECM-protein knowledge database. PMID:31586405
PDBe-KB: a community-driven resource for structural and functional annotations. PMID:31584092
Complete Genome Sequence of Vibrio natriegens Phage Phriendly. PMID:31582448
Mining for protein S-sulfenylation in Arabidopsis uncovers redox-sensitive sites. PMID:31578252
Genome of Spea multiplicata, a Rapidly Developing, Phenotypically Plastic, and Desert-Adapted Spadefoot Toad. PMID:31578218
SASBDB: Towards an automatically curated and validated repository for biological scattering data. PMID:31576635
Genome Assemblies of Two Rare Opportunistic Yeast Pathogens: Diutina rugosa (syn. Candida rugosa) and Trichomonascus ciferrii (syn. Candida ciferrii). PMID:31575637
Targeting of copper-trafficking chaperones causes gene-specific systemic pathology in Drosophila melanogaster: prospective expansion of mutational landscapes that regulate tumor resistance to cisplatin. PMID:31575544
The cbb 3-type cytochrome oxidase assembly factor CcoG is a widely distributed cupric reductase. PMID:31570589
Human Cysteine Cathepsins Degrade Immunoglobulin G In Vitro in a Predictable Manner. PMID:31569504
Hexa-Longin domain scaffolds for inter-Rab signalling. PMID:31562761
Rotator Cuff Tenocytes Differentiate into Hypertrophic Chondrocyte-Like Cells to Produce Calcium Deposits in an Alkaline Phosphatase-Dependent Manner. PMID:31561454
Paralog dependency indirectly affects the robustness of human cells. PMID:31556487
RNA editing in the forefront of epitranscriptomics and human health. PMID:31547885
In Silico Identification of Antimicrobial Peptides in the Proteomes of Goat and Sheep Milk and Feta Cheese. PMID:31546575
NODULE INCEPTION Recruits the Lateral Root Developmental Program for Symbiotic Nodule Organogenesis in Medicago truncatula. PMID:31543454
FAIR adoption, assessment and challenges at UniProt. PMID:31541106
Lysine Methylation Regulators Moonlighting outside the Epigenome. PMID:31539507
Complete Genome Sequence of Escherichia coli Myophage Mangalitsa. PMID:31537680
Complete Genome Sequence of Salmonella enterica Myophage Matapan. PMID:31537677
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci. PMID:31537640
Predicting Sequence Features, Function, and Structure of Proteins Using MESSA. PMID:31524991
BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows. PMID:31506435
WALTZ-DB 2.0: an updated database containing structural information of experimentally determined amyloid-forming peptides. PMID:31504823
VARIDT 1.0: variability of drug transporter database. PMID:31495872
Microbial chitinases: properties, current state and biotechnological applications. PMID:31493195
Genome Sequence of Metarhizium rileyi, a Microbial Control Agent for Lepidoptera. PMID:31488537
Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity. PMID:31486770
Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens. PMID:31481610
The finger loop of the SRA domain in the E3 ligase UHRF1 is a regulator of ubiquitin targeting and is required for the maintenance of DNA methylation. PMID:31481468
The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs. PMID:31454312
A survey of known immune epitopes in the enteroviruses strains associated with acute flaccid myelitis. PMID:31451291
Data on proteomic profiling of cells and extracellular vesicles of the melittin-resistant Acholeplasma laidlawii strain. PMID:31440540
Post-transcriptional Regulation of Colorectal Cancer: A Focus on RNA-Binding Proteins. PMID:31440515
Identification of Rumen Microbial Genes Involved in Pathways Linked to Appetite, Growth, and Feed Conversion Efficiency in Cattle. PMID:31440274
Specialized structural and functional roles of residues selectively conserved in subfamilies of the pleckstrin homology domain family. PMID:31436855
Mitofusins modulate the increase in mitochondrial length, bioenergetics and secretory phenotype in therapy-induced senescent melanoma cells. PMID:31431479
Crystal structures of AztD provide mechanistic insights into direct zinc transfer between proteins. PMID:31428696
A mechanistic evaluation of the angiogenic properties of a dehydrated amnion chorion membrane in vitro and in vivo. PMID:31425636
Phellem Cell-Wall Components Are Discriminants of Cork Quality in Quercus suber. PMID:31417580
Binding site characterization - similarity, promiscuity, and druggability. PMID:31391887
Homology Modelling and Molecular Docking Studies of Selected Substituted Benzo[d]imidazol-1-yl)methyl)benzimidamide Scaffolds on Plasmodium falciparum Adenylosuccinate Lyase Receptor. PMID:31391779
A seed-extended algorithm for detecting protein complexes based on density and modularity with topological structure and GO annotations. PMID:31390979
The Role of Protein Thermodynamics and Primary Structure in Fibrillogenesis of Variable Domains from Immunoglobulin Light Chains. PMID:31364359
A Web Tool for Ranking Candidate Drugs Against a Selected Disease Based on a Combination of Functional and Structural Criteria. PMID:31360332
Whole-Genome Sequencing and Annotation of Clostridium tyrobutyricum Strain Cirm BIA 2237, Isolated from Silage. PMID:31346011
The Role of Iron and Copper on the Oligomerization Dynamics of DR_2577, the Main S-Layer Protein of Deinococcus radiodurans. PMID:31333601
N-terminal β-strand underpins biochemical specialization of an ATG8 isoform. PMID:31329577
Alphabet Projection of Spectra. PMID:31318211
RAFTS3G: an efficient and versatile clustering software to analyses in large protein datasets. PMID:31307371
Sleeping beauty genetic screen identifies miR-23b::BTBD7 gene interaction as crucial for colorectal cancer metastasis. PMID:31303496
Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions. PMID:31301672
Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS. PMID:31296583
Identification and Characterization of Preferred DNA-Binding Sites for the Thermus thermophilus HB8 Transcriptional Regulator TTHA0973. PMID:31284644
HyperFoods: Machine intelligent mapping of cancer-beating molecules in foods. PMID:31270435
O2 Reduction to Water by High Potential Multicopper Oxidases: Contributions of the T1 Copper Site Potential and the Local Environment of the Trinuclear Copper Cluster. PMID:31260290
In silico analysis of missense mutations in exons 1-5 of the F9 gene that cause hemophilia B. PMID:31253089
A structural model of the human serotonin transporter in an outward-occluded state. PMID:31251747
Design, Synthesis and Biological Evaluation of 7-Chloro-9H-pyrimido[4,5-b]indole-based Glycogen Synthase Kinase-3β Inhibitors. PMID:31242571
Advances and Applications in the Quest for Orthologs. PMID:31241141
Tick saliva protein Evasin-3 modulates chemotaxis by disrupting CXCL8 interactions with glycosaminoglycans and CXCR2. PMID:31235521
Metagenomic analysis of bile salt biotransformation in the human gut microbiome. PMID:31234773
The Transcriptional Landscape of Microglial Genes in Aging and Neurodegenerative Disease. PMID:31214167
VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations. PMID:31192369
The Role of a Key Amino Acid Position in Species-Specific Proteinaceous dUTPase Inhibition. PMID:31174420
Population Genomic Signatures of Genetic Structure and Environmental Selection in the Catadromous Roughskin Sculpin Trachidermus fasciatus. PMID:31173074
SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse. PMID:31171447
MTR-Viewer: identifying regions within genes under purifying selection. PMID:31170280
AutoDock CrankPep: combining folding and docking to predict protein-peptide complexes. PMID:31161213
Transcriptome Response of Female Culicoides sonorensis Biting Midges (Diptera: Ceratopogonidae) to Early Infection with Epizootic Hemorrhagic Disease Virus (EHDV-2). PMID:31137627
The role of ubiquitin-specific peptidases in cancer progression. PMID:31133011
Optimizing de novo genome assembly from PCR-amplified metagenomes. PMID:31119088
PrankWeb: a web server for ligand binding site prediction and visualization. PMID:31114880
Sequence similarity searches for morphine biosynthesis enzymes in bacteria yield putative targets for understanding associations between infection and opiate administration. PMID:31107204
NetGO: improving large-scale protein function prediction with massive network information. PMID:31106361
Yosshi: a web-server for disulfide engineering by bioinformatic analysis of diverse protein families. PMID:31106356
Protein Melting Temperature Cannot Fully Assess Whether Protein Folding Free Energy Underlies the Universal Abundance-Evolutionary Rate Correlation Seen in Proteins. PMID:31093676
Using genetically incorporated unnatural amino acids to control protein functions in mammalian cells. PMID:31092687
An enzyme in the test tube, and a transcription factor in the cell: Moonlighting proteins and cellular factors that affect their behavior. PMID:31087733
Proteomics Standards Initiative Extended FASTA Format. PMID:31081335
Comparative transcriptome analysis of trout skin pigment cells. PMID:31072301
g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). PMID:31066453
Cryo-EM density map fitting driven in-silico structure of human soluble guanylate cyclase (hsGC) reveals functional aspects of inter-domain cross talk upon NO binding. PMID:31055154
IntFOLD: an integrated web resource for high performance protein structure and function prediction. PMID:31045208
Attenuation of Infectious Bronchitis Virus in Eggs Results in Different Patterns of Genomic Variation across Multiple Replicates. PMID:31043525
Promiscuous Targeting of Cellular Proteins by Vpr Drives Systems-Level Proteomic Remodeling in HIV-1 Infection. PMID:31042482
Titin mutations and muscle disease. PMID:30919088
3DBIONOTES v3.0: crossing molecular and structural biology data with genomic variations. PMID:30768147
The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection. PMID:30626175
The European Bioinformatics Institute in 2018: tools, infrastructure and training. PMID:30445657 -
UniProt: a hub for protein information
PubMed citations: 2005.
2005 articles citing: UniProt: a hub for protein information
Comprehensive Linear Epitope Prediction System for Host Specificity in Nodaviridae. PMID:35891339
Vietnamese Dalbergia tonkinensis: A Promising Source of Mono- and Bifunctional Vasodilators. PMID:35889386
SIPGCN: A Novel Deep Learning Model for Predicting Self-Interacting Proteins from Sequence Information Using Graph Convolutional Networks. PMID:35884848
Artificial Intelligence, Healthcare, Clinical Genomics, and Pharmacogenomics Approaches in Precision Medicine. PMID:35873469
Activity-based protein profiling identifies alternating activation of enzymes involved in the bifidobacterium shunt pathway or mucin degradation in the gut microbiome response to soluble dietary fiber. PMID:35858888
Comparative physiology and transcriptome analysis reveals that chloroplast development influences silver-white leaf color formation in Hydrangea macrophylla var. maculata. PMID:35842592
A review on computational approaches that support the researches on traditional Chinese medicines (TCM) against COVID-19. PMID:35841663
Immunoinformatics- and Bioinformatics-Assisted Computational Designing of a Novel Multiepitopes Vaccine Against Cancer-Causing Merkel Cell Polyomavirus. PMID:35836414
PR-1-Like Protein as a Potential Target for the Identification of Fusarium oxysporum: An In Silico Approach. PMID:35822818
Genome-wide Meta-analysis Reveals New Gene Signatures and Potential Drug Targets of Hypertension. PMID:35811894
Biological Role of the Intercellular Transfer of Glycosylphosphatidylinositol-Anchored Proteins: Stimulation of Lipid and Glycogen Synthesis. PMID:35806423
Scorpion Neurotoxin Syb-prII-1 Exerts Analgesic Effect through Nav1.8 Channel and MAPKs Pathway. PMID:35806068
Modeling Kaempferol as a Potential Pharmacological Agent for COVID-19/PF Co-Occurrence Based on Bioinformatics and System Pharmacological Tools. PMID:35754492
Palaeoproteomics guidelines to identify proteinaceous binders in artworks following the study of a 15th-century painting by Sandro Botticelli's workshop. PMID:35739140
Compilation of parasitic immunogenic proteins from 30 years of published research using machine learning and natural language processing. PMID:35725870
Exploring kinase family inhibitors and their moiety preferences using deep SHapley additive exPlanations. PMID:35725381
Growth rate determines prokaryote-provirus network modulated by temperature and host genetic traits. PMID:35701838
A highly conserved core bacterial microbiota with nitrogen-fixation capacity inhabits the xylem sap in maize plants. PMID:35688828
Random peptides rich in small and disorder-promoting amino acids are less likely to be harmful. PMID:35668555
Establishment of mouse model of inherited PIGO deficiency and therapeutic potential of AAV-based gene therapy. PMID:35661110
Genetics of early-life head circumference and genetic correlations with neurological, psychiatric and cognitive outcomes. PMID:35659227
RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins. PMID:35649392
The Visayan Warty Pig (Sus cebifrons) Genome Provides Insight Into Chromosome Evolution and Sensory Adaptation in Pigs. PMID:35642310
Whole-Genome Sequencing of 100 Genomes Identifies a Distinctive Genetic Susceptibility Profile of Qatari Patients with Hypertension. PMID:35629146
ProGeo-Neo v2.0: A One-Stop Software for Neoantigen Prediction and Filtering Based on the Proteogenomics Strategy. PMID:35627168
Ethanolamine-phosphate on the second mannose is a preferential bridge for some GPI-anchored proteins. PMID:35603428
Localization of EccA3 at the growing pole in Mycobacterium smegmatis. PMID:35590245
Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain. PMID:35581640
Biochemical Investigation of Inhibitory Activities of Plant-Derived Bioactive Compounds Against Carbohydrate and Glucagon-Like Peptide-1 Metabolizing Enzymes. PMID:35574252
Machine Learning and Its Applications for Protozoal Pathogens and Protozoal Infectious Diseases. PMID:35573796
Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment. PMID:35572582
Targeting Cell Death Mechanism Specifically in Triple Negative Breast Cancer Cell Lines. PMID:35563174
Evaluation of tea (Camellia sinensis L.) phytochemicals as multi-disease modulators, a multidimensional in silico strategy with the combinations of network pharmacology, pharmacophore analysis, statistics and molecular docking. PMID:35536529
Zinc transport via ZNT5-6 and ZNT7 is critical for cell surface glycosylphosphatidylinositol-anchored protein expression. PMID:35525268
Insights into the biosynthesis pathway of phenolic compounds in microalgae. PMID:35521550
Eclectic characterisation of chemically modified cell-derived matrices obtained by metabolic glycoengineering and re-assessment of commonly used methods. PMID:35515672
Evolution, Expression Patterns, and Distribution of Novel Ribbon Worm Predatory and Defensive Toxins. PMID:35512366
Systematic Elaboration of the Pharmacological Targets and Potential Mechanisms of ZhiKe GanCao Decoction for Preventing and Delaying Intervertebral Disc Degeneration. PMID:35497916
A Novel Efficient L-Lysine Exporter Identified by Functional Metagenomics. PMID:35495724
UPIMAPI, reCOGnizer and KEGGCharter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets. PMID:35495109
Insights into the structure and function of the human organic anion transporter 1 in lipid bilayer membranes. PMID:35488116
Tissue remodeling by an opportunistic pathogen triggers allergic inflammation. PMID:35483356
The Minimal Translation Machinery: What We Can Learn From Naturally and Experimentally Reduced Genomes. PMID:35479634
Probing the competitive inhibitor efficacy of frog-skin alpha helical AMPs identified against ACE2 binding to SARS-CoV-2 S1 spike protein as therapeutic scaffold to prevent COVID-19. PMID:35461388
Subtractive proteomics assisted therapeutic targets mining and designing ensemble vaccine against Candida auris for immune response induction. PMID:35427985
The COMPARE Database: A Public Resource for Allergen Identification, Adapted for Continuous Improvement. PMID:35386979
INPUT: An intelligent network pharmacology platform unique for traditional Chinese medicine. PMID:35356545
Aberrant SKP1 Expression: Diverse Mechanisms Impacting Genome and Chromosome Stability. PMID:35345853
In Silico Multi-Target Approach Revealed Potential Lead Compounds as Scaffold for the Synthesis of Chemical Analogues Targeting SARS-CoV-2. PMID:35336838
Ligand binding remodels protein side-chain conformational heterogeneity. PMID:35312477
PhosVarDeep: deep-learning based prediction of phospho-variants using sequence information. PMID:35310161
Identification and Characterization of Bacillus tequilensis GYUN-300: An Antagonistic Bacterium Against Red Pepper Anthracnose Caused by Colletotrichum acutatum in Korea. PMID:35308370
Shotgun and TMT-Labeled Proteomic Analysis of the Ovarian Proteins of an Insect Vector, Aedes aegypti (Diptera: Culicidae). PMID:35303100
ELECTRA-DTA: a new compound-protein binding affinity prediction model based on the contextualized sequence encoding. PMID:35292100
Independent Size Expansions and Intron Proliferation in Red Algal Plastid and Mitochondrial Genomes. PMID:35289373
Using Omics to Study Leprosy, Tuberculosis, and Other Mycobacterial Diseases. PMID:35281437
Profile of Myracrodruon urundeuva Volatile Compounds Ease of Extraction and Biodegradability and In Silico Evaluation of Their Interactions with COX-1 and iNOS. PMID:35268733
Effects and Mechanisms of Rhus chinensis Mill. Fruits on Suppressing RANKL-Induced Osteoclastogenesis by Network Pharmacology and Validation in RAW264.7 Cells. PMID:35267996
Transcriptome-wide identification and expression analysis of the KT/HAK/KUP family in Salicornia europaea L. under varied NaCl and KCl treatments. PMID:35261820
Whole-Genome Analysis of Escherichia Phage vB_EcoM-S1P5QW, Isolated from Manures Collected from Cattle Farms in Maine. PMID:35254108
In-Depth Serum Proteomics by DIA-MS with In Silico Spectral Libraries Reveals Dynamics during the Active Phase of Systemic Juvenile Idiopathic Arthritis. PMID:35252692
Computational Design of a Multi-Epitope Vaccine Against Porphyromonas gingivalis. PMID:35250977
[Identification of traditional Chinese drugs containing active ingredients for treating myocardial infarction and analysis of their therapeutic mechanisms by network pharmacology and molecular docking]. PMID:35249866
Identifying protein function and functional links based on large-scale co-occurrence patterns. PMID:35239724
Gut Commensal Bacteroidetes Encode a Novel Class of Vitamin B12-Binding Proteins. PMID:35227073
Evaluation of protein descriptors in computer-aided rational protein engineering tasks and its application in property prediction in SARS-CoV-2 spike glycoprotein. PMID:35222841
Network Pharmacology and Experimental Verification to Explore the Potential Mechanism of Yin-Huo-Tang for Lung Adenocarcinoma Recurrence. PMID:35210754
Analysing miRNA-Target Gene Networks in Inflammatory Bowel Disease and Other Complex Diseases Using Transcriptomic Data. PMID:35205414
Mechanisms of Vitamin C Regulating Immune and Inflammation Associated with Neonatal Hypoxic-Ischemic Encephalopathy Based on Network Pharmacology and Molecular Simulation Technology. PMID:35198034
The OxyR and SoxR transcriptional regulators are involved in a broad oxidative stress response in Paraburkholderia xenovorans LB400. PMID:35184754
Multiple Reaction Monitoring-Mass Spectrometry Enables Robust Quantitation of Plasma Proteins Regardless of Whole Blood Processing Delays That May Occur in the Clinic. PMID:35182769
Herbal Formula Modified Bu-Shen-Huo-Xue Decoction Attenuates Intervertebral Disc Degeneration via Regulating Inflammation and Oxidative Stress. PMID:35154344
SWI/SNF senses carbon starvation with a pH-sensitive low-complexity sequence. PMID:35129437
Identification of the Association Between Toll-Like Receptors and T-Cell Activation in Takayasu's Arteritis. PMID:35126357
Tilting the Balance: Therapeutic Prospects of CD83 as a Checkpoint Molecule Controlling Resolution of Inflammation. PMID:35054916
Deciphering the evolution of composite-type GSKIP in mitochondria and Wnt signaling pathways. PMID:35051222
Integrated bioinformatics based subtractive genomics approach to decipher the therapeutic function of hypothetical proteins from Salmonella typhi XDR H-58 strain. PMID:35037232
Accurate and Automated High-Coverage Identification of Chemically Cross-Linked Peptides with MaxLynx. PMID:35014260
KANPHOS: A Database of Kinase-Associated Neural Protein Phosphorylation in the Brain. PMID:35011609
In Silico Sperm Proteome Analysis to Investigate DNA Repair Mechanisms in Varicocele Patients. PMID:34975746
Genome Mining of Pseudomonas Species: Diversity and Evolution of Metabolic and Biosynthetic Potential. PMID:34946606
The effects of Tbx15 and Pax1 on facial and other physical morphology in mice. PMID:34938962
Machine learning prediction of antiviral-HPV protein interactions for anti-HPV pharmacotherapy. PMID:34934067
Structural insights into the activation of blood coagulation factor XI zymogen by thrombin: A computational molecular dynamics study. PMID:34923393
Molecular modelling and de novo fragment-based design of potential inhibitors of beta-tubulin gene of Necator americanus from natural products. PMID:34912942
Chromosomal Fusions Facilitate Adaptation to Divergent Environments in Threespine Stickleback. PMID:34908155
Precise Investigation of the Efficacy of Multicomponent Drugs Against Pneumonia Infected With Influenza Virus. PMID:34867309
Full Genome Sequence of a Methanomassiliicoccales Representative Enriched from Peat Soil. PMID:34854727
Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora. PMID:34849814
A multitask transfer learning framework for the prediction of virus-human protein-protein interactions. PMID:34837942
A Genome-Wide Association Study Identifies Novel Risk Loci for Sarcopenia in a Taiwanese Population. PMID:34815687
Pharmacological Mechanism of Danggui-Sini Formula for Intervertebral Disc Degeneration: A Network Pharmacology Study. PMID:34805401
Exploring the mechanism of Yixinyin for myocardial infarction by weighted co-expression network and molecular docking. PMID:34799616
Herpesviruses assimilate kinesin to produce motorized viral particles. PMID:34789877
Schizophrenia is defined by cell-specific neuropathology and multiple neurodevelopmental mechanisms in patient-derived cerebral organoids. PMID:34789849
Comparative transcriptomic profiling of susceptible and resistant cultivars of pigeonpea demonstrates early molecular responses during Fusarium udum infection. PMID:34785701
First report of mitochondrial COI in foraminifera and implications for DNA barcoding. PMID:34772985
In Silico Core Proteomics and Molecular Docking Approaches for the Identification of Novel Inhibitors against Streptococcus pyogenes. PMID:34769873
Network Pharmacology-Based Identification of Key Mechanisms of Xihuang Pill in the Treatment of Triple-Negative Breast Cancer Stem Cells. PMID:34737698
Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. PMID:34721467
Natural products for infectious microbes and diseases: an overview of sources, compounds, and chemical diversities. PMID:34705221
Temporal proteomics during neurogenesis reveals large-scale proteome and organelle remodeling via selective autophagy. PMID:34699746
Identification of Potential Citrate Metabolism Pathways in Carnobacterium maltaromaticum. PMID:34683489
Investigating single amino acid substitutions in PIM1 kinase: A structural genomics approach. PMID:34679086
Huanglianjiedu Decoction as an effective treatment for oral squamous cell carcinoma based on network pharmacology and experimental validation. PMID:34674717
Characterization of the First Cultured Psychrotolerant Representative of Legionella from Antarctica Reveals Its Unique Genome Structure. PMID:34668737
Altered protein O-GlcNAcylation in placentas from mothers with diabetes causes aberrant endocytosis in placental trophoblast cells. PMID:34667181
Draft genome sequence, annotation and SSR mining data of Oryctes rhinoceros Linn. (Coleoptera: Scarabaeidae), the coconut rhinoceros beetle. PMID:34660857
Genome sequencing of turmeric provides evolutionary insights into its medicinal properties. PMID:34654884
Application of Computational Methods in Understanding Mutations in Mycobacterium tuberculosis Drug Resistance. PMID:34651013
Predicting drug targets by homology modelling of Pseudomonas aeruginosa proteins of unknown function. PMID:34648550
Kincore: a web resource for structural classification of protein kinases and their inhibitors. PMID:34643709
HBFP: a new repository for human body fluid proteome. PMID:34642750
Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes. PMID:34630938
Rescue of Glycosylphosphatidylinositol-Anchored Protein Biosynthesis Using Synthetic Glycosylphosphatidylinositol Oligosaccharides. PMID:34618440
Evidence-based complementary and alternative medicine bioinformatics approach through network pharmacology and molecular docking to determine the molecular mechanisms of Erjing pill in Alzheimer's disease. PMID:34539848
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling. PMID:34536568
Phylogeographic reconstruction of the marbled crayfish origin. PMID:34535758
Homologs of the Tumor Suppressor Protein p53: A Bioinformatics Study for Drug Design. PMID:34532721
Differential Abundance of Brain Mitochondrial Proteins in Yak and Cattle: A Proteomics-Based Study. PMID:34532350
The Marine Gastropod Crepidula fornicata Remains Resilient to Ocean Acidification Across Two Life History Stages. PMID:34512378
Effects of NaCl Concentrations on Growth Patterns, Phenotypes Associated With Virulence, and Energy Metabolism in Escherichia coli BW25113. PMID:34484145
DeepLINK: Deep learning inference using knockoffs with applications to genomics. PMID:34480002
Peptipedia: a user-friendly web application and a comprehensive database for peptide research supported by Machine Learning approach. PMID:34478499
Personalized Proteomics for Precision Diagnostics in Hearing Loss: Disease-Specific Analysis of Human Perilymph by Mass Spectrometry. PMID:34471729
Comparative genomic analysis of a naturally born serpentized pig reveals putative mutations related to limb and bone development. PMID:34454433
Quercetin and/or Ascorbic Acid Modulatory Effect on Phenobarbital-Induced Sleeping Mice Possibly through GABAA and GABAB Receptor Interaction Pathway. PMID:34451819
Characterization of Martelella soudanensis sp. nov., Isolated from a Mine Sediment. PMID:34442814
Identification of Targeted Proteins by Jamu Formulas for Different Efficacies Using Machine Learning Approach. PMID:34440610
Impact of Different Durations of Fasting on Intestinal Autophagy and Serum Metabolome in Broiler Chicken. PMID:34438641
L-Type Calcium Channel: Predicting Pathogenic/Likely Pathogenic Status for Variants of Uncertain Clinical Significance. PMID:34436362
OFF-State-Specific Inhibition of the Proprotein Convertase Furin. PMID:34415722
Generation and Characterization of Torudokimab (LY3375880): A Monoclonal Antibody That Neutralizes Interleukin-33. PMID:34408465
Multiple Losses of MSH1, Gain of mtMutS, and Other Changes in the MutS Family of DNA Repair Proteins in Animals. PMID:34402879
CASPredict: a web service for identifying Cas proteins. PMID:34395100
Computational Analysis of Gly482Ser Single-Nucleotide Polymorphism in PPARGC1A Gene Associated with CAD, NAFLD, T2DM, Obesity, Hypertension, and Metabolic Diseases. PMID:34394332
Identification of Three Clf-Sdr Subfamily Proteins in Staphylococcus warneri, and Comparative Genomics Analysis of a Locus Encoding CWA Proteins in Staphylococcus Species. PMID:34394031
Proteomic analysis of ubiquitination substrates reveals a CTLH E3 ligase complex-dependent regulation of glycolysis. PMID:34383978
Predicting Protein Therapeutic Candidates for Bovine Babesiosis Using Secondary Structure Properties and Machine Learning. PMID:34367264
Male Infertility Knowledgebase: decoding the genetic and disease landscape. PMID:34363073
Computational Investigation of the pH Dependence of Stability of Melanosome Proteins: Implication for Melanosome formation and Disease. PMID:34361043
TCA Cycle Replenishing Pathways in Photosynthetic Purple Non-Sulfur Bacteria Growing with Acetate. PMID:34357087
Changthangi Pashmina Goat Genome: Sequencing, Assembly, and Annotation. PMID:34354739
Finding inhibitors for PCSK9 using computational methods. PMID:34351937
The biochemical basis of mitochondrial dysfunction in Zellweger Spectrum Disorder. PMID:34351705
Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. PMID:34346317
Advances in the computational landscape for repurposed drugs against COVID-19. PMID:34339864
Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree. PMID:34325658
Proteome difference among the salivary proteins adsorbed onto metallic orthodontic brackets and hydroxyapatite discs. PMID:34319997
CCT and CCT-Like Modular Protein Interaction Domains in WNK Signaling. PMID:34312216
Transcriptome Characterization and Identification of Molecular Markers (SNP, SSR, and Indels) in the Medicinal Plant Sarcandra glabra spp. PMID:34307686
The Structural Effect of FLT3 Mutations at 835th Position and Their Interaction with Acute Myeloid Leukemia Inhibitors: In Silico Approach. PMID:34299222
Genetic association studies of alterations in protein function expose recessive effects on cancer predisposition. PMID:34290314
Analysis of the Taxonomy and Pathogenic Factors of Pectobacterium aroidearum L6 Using Whole-Genome Sequencing and Comparative Genomics. PMID:34276610
An Investigation of the Antigastric Cancer Effect in Tumor Microenvironment of Radix Rhei Et Rhizome: A Network Pharmacology Study. PMID:34257692
Brain Acetyl-CoA Production and Phosphorylation of Cytoskeletal Proteins Are Targets of CYP46A1 Activity Modulation and Altered Sterol Flux. PMID:34235635
Application of Machine Learning for Drug-Target Interaction Prediction. PMID:34234813
ALKBH3 partner ASCC3 mediates P-body formation and selective clearance of MMS-induced 1-methyladenosine and 3-methylcytosine from mRNA. PMID:34217309
Transcriptome Reveals Roles of Lignin-Modifying Enzymes and Abscisic Acid in the Symbiosis of Mycena and Gastrodia elata. PMID:34207287
Genome-Wide Identification of Soybean ABC Transporters Relate to Aluminum Toxicity. PMID:34207256
Comparative Transcriptome Profiling of Kappaphycus alvarezii (Rhodophyta, Solieriaceae) in Response to Light of Different Wavelengths and Carbon Dioxide Enrichment. PMID:34204578
Order and disorder-An integrative structure of the full-length human growth hormone receptor. PMID:34193419
Reconstruction of the full-length transcriptome of cigar tobacco without a reference genome and characterization of anion channel/transporter transcripts. PMID:34187357
StrongestPath: a Cytoscape application for protein-protein interaction analysis. PMID:34187355
Mosaic Ends Tagmentation (METa) Assembly for Highly Efficient Construction of Functional Metagenomic Libraries. PMID:34184912
A computational model for GPCR-ligand interaction prediction. PMID:34171942
Probiotics: their action against pathogens can be turned around. PMID:34168166
Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data. PMID:34136096
The Gene Expression Profile of the Song Control Nucleus HVC Shows Sex Specificity, Hormone Responsiveness, and Species Specificity Among Songbirds. PMID:34135731
Prognostic implications of troponin T variations in inherited cardiomyopathies using systems biology. PMID:34127679
Identification of Altered Proteins in the Plasma of Rats With Chronic Prostatic Inflammation Induced by Estradiol Benzoate and Sex Hormones. PMID:34124458
Applying Machine Learning to Predict the Exportome of Bovine and Canine Babesia Species That Cause Babesiosis. PMID:34071992
Oral Microbiome in Relation to Periodontitis Severity and Systemic Inflammation. PMID:34070915
An Integrated Analysis of Network Pharmacology, Molecular Docking, and Experiment Validation to Explore the New Candidate Active Component and Mechanism of Cuscutae Semen-Mori Fructus Coupled-Herbs in Treating Oligoasthenozoospermia. PMID:34040346
PhenCards: a data resource linking human phenotype information to biomedical knowledge. PMID:34034817
Gene Ontology Meta Annotator for Plants (GOMAP). PMID:34034755
Predicting MHC I restricted T cell epitopes in mice with NAP-CNB, a novel online tool. PMID:34031450
An overview of graph databases and their applications in the biomedical domain. PMID:34003247
Characterization of the multidrug efflux transporter styMdtM from Salmonella enterica serovar Typhi. PMID:33983672
Bayesian neural network with pretrained protein embedding enhances prediction accuracy of drug-protein interaction. PMID:33978713
Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding. PMID:33964091
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. PMID:33961781
Development of Stable Chimeric IL-15 for Trans-Presentation by the Antigen Presenting Cells. PMID:33953717
Elephant Genomes Reveal Accelerated Evolution in Mechanisms Underlying Disease Defenses. PMID:33944920
Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides. PMID:33941076
The Underlying Molecular Mechanisms Involved in Traditional Chinese Medicine Smilax china L. for the Treatment of Pelvic Inflammatory Disease. PMID:33927774
Gene Expression Analysis of Microtubers of Potato Solanum tuberosum L. Induced in Cytokinin Containing Medium and Osmotic Stress. PMID:33925316
From Proteomic Mapping to Invasion-Metastasis-Cascade Systemic Biomarkering and Targeted Drugging of Mutant BRAF-Dependent Human Cutaneous Melanomagenesis. PMID:33922182
First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies. PMID:33918864
Comprehensive genomic analysis contrasting primary colorectal cancer and matched liver metastases. PMID:33907576
Thiocyanate and Organic Carbon Inputs Drive Convergent Selection for Specific Autotrophic Afipia and Thiobacillus Strains Within Complex Microbiomes. PMID:33897653
Online biophysical predictions for SARS-CoV-2 proteins. PMID:33892639
SARS-CoV-2 requires cholesterol for viral entry and pathological syncytia formation. PMID:33890572
Assessing the degradation of ancient milk proteins through site-specific deamidation patterns. PMID:33833277
Sex-differences in circulating biomarkers during acute myocardial infarction: An analysis from the SWEDEHEART registry. PMID:33831096
SNARE-CNN: a 2D convolutional neural network architecture to identify SNARE proteins from high-throughput sequencing data. PMID:33816830
A Molecular Modeling Approach to Identify Potential Antileishmanial Compounds Against the Cell Division Cycle (cdc)-2-Related Kinase 12 (CRK12) Receptor of Leishmania donovani. PMID:33803906
Uterine infusion of conceptus fragments changes the protein profile from cyclic mares. PMID:33791032
MED15 prion-like domain forms a coiled-coil responsible for its amyloid conversion and propagation. PMID:33772081
Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases. PMID:33750949
A Network Pharmacology-Based Approach to Investigating the Mechanisms of Fushen Granule Effects on Intestinal Barrier Injury in Chronic Renal Failure. PMID:33747100
A network pharmacology based approach for predicting active ingredients and potential mechanism of Lianhuaqingwen capsule in treating COVID-19. PMID:33746604
Comparative transcriptomic analysis of the different developmental stages of ovary in red swamp crayfish Procambarus clarkii. PMID:33745451
pCysMod: Prediction of Multiple Cysteine Modifications Based on Deep Learning Framework. PMID:33732693
isa4j: a scalable Java library for creating ISA-Tab metadata. PMID:33728038
Network Pharmacology and Molecular Docking Analysis on Molecular Targets and Mechanisms of Buyang Huanwu Decoction in the Treatment of Ischemic Stroke. PMID:33727944
Genomic Characterization of Two Shiga Toxin-Converting Bacteriophages Induced From Environmental Shiga Toxin-Producing Escherichia coli. PMID:33716997
Evidence for CAT gene being functionally involved in the susceptibility of COVID-19. PMID:33710662
Identification of conserved slow codons that are important for protein expression and function. PMID:33691590
Adaptation and convergence in circadian-related genes in Iberian freshwater fish. PMID:33685402
Decoding the Mechanism of Huanglian Jiedu Decoction in Treating Pneumonia Based on Network Pharmacology and Molecular Docking. PMID:33681222
From Data Mining of Chitinophaga sp. Genome to Enzyme Discovery of a Hyperthermophilic Metallocarboxypeptidase. PMID:33673011
Genetic Adaptations in Mudskipper and Tetrapod Give Insights into Their Convergent Water-to-Land Transition. PMID:33672418
Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome. PMID:33664286
DbStRiPs: Database of structural repeats in proteins. PMID:33641184
Interaction of Plasmodium falciparum apicortin with α- and β-tubulin is critical for parasite growth and survival. PMID:33633135
Chromosome-Level Genome Assembly of the Common Chaffinch (Aves: Fringilla coelebs): A Valuable Resource for Evolutionary Biology. PMID:33616654
Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria. PMID:33582841
UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network. PMID:33575553
HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes. PMID:33557954
Comparative Transcriptome Analysis During the Seven Developmental Stages of Channel Catfish (Ictalurus punctatus) and Tra Catfish (Pangasianodon hypophthalmus) Provides Novel Insights for Terrestrial Adaptation. PMID:33552125
GMO Genetic Elements Thesaurus (GMO-GET): a controlled vocabulary for the consensus designation of introduced or modified genetic elements in genetically modified organisms. PMID:33546585
Amynthas corticis genome reveals molecular mechanisms behind global distribution. PMID:33514865
iBLP: An XGBoost-Based Predictor for Identifying Bioluminescent Proteins. PMID:33505515
Network pharmacology integrated molecular docking reveals the bioactive components and potential targets of Morinda officinalis-Lycium barbarum coupled-herbs against oligoasthenozoospermia. PMID:33500463
NLPEI: A Novel Self-Interacting Protein Prediction Model Based on Natural Language Processing and Evolutionary Information. PMID:33488064
Estimating the accuracy of pharmacophore-based detection of cognate receptor-ligand pairs in the immunoglobulin superfamily. PMID:33483991
Polymorphism rs368234815 of interferon lambda 4 gene and spontaneous clearance of hepatitis C virus in haemodialysis patients: a case-control study. PMID:33482747
AtPiezo Plays an Important Role in Root Cap Mechanotransduction. PMID:33466520
SARS-CoV-2 infection susceptibility influenced by ACE2 genetic polymorphisms: insights from Tehran Cardio-Metabolic Genetic Study. PMID:33452303
A systems-level gene regulatory network model for Plasmodium falciparum. PMID:33450011
Network pharmacology modeling identifies synergistic interaction of therapeutic and toxicological mechanisms for Tripterygium hypoglaucum Hutch. PMID:33446184
Computational drug repurposing strategy predicted peptide-based drugs that can potentially inhibit the interaction of SARS-CoV-2 spike protein with its target (humanACE2). PMID:33417604
Prediction of hub genes of Alzheimer's disease using a protein interaction network and functional enrichment analysis. PMID:33412755
Atlas of ACE2 gene expression reveals novel insights into transmission of SARS-CoV-2. PMID:33392409
Effects of Co-culture on Improved Productivity and Bioresource for Microalgal Biomass Using the Floc-Forming Bacteria Melaminivora Jejuensis. PMID:33392165
Integrative analysis of long extracellular RNAs reveals a detection panel of noncoding RNAs for liver cancer. PMID:33391469
Two New Aristolochic Acid Analogues from the Roots of Aristolochia contorta with Significant Cytotoxic Activity. PMID:33374869
Male pseudohermaphroditism: A case study of 46,XY disorder of sexual development using whole-exome sequencing. PMID:33363845
Distinct Preflowering Drought Tolerance Strategies of Sorghum bicolor Genotype RTx430 Revealed by Subcellular Protein Profiling. PMID:33352693
Distinct ecotypes within a natural haloarchaeal population enable adaptation to changing environmental conditions without causing population sweeps. PMID:33342997
Pulse-Chase Proteomics of the App Knockin Mouse Models of Alzheimer's Disease Reveals that Synaptic Dysfunction Originates in Presynaptic Terminals. PMID:33326751
High-Throughput Discovery and Characterization of Human Transcriptional Effectors. PMID:33326746
Graph embeddings on gene ontology annotations for protein-protein interaction prediction. PMID:33323115
Sodium-bile acid co-transporter is crucial for survival of a carcinogenic liver fluke Clonorchis sinensis in the bile. PMID:33284789
Comparative Genomics Analysis Provides New Strategies for Bacteriostatic Ability of Bacillus velezensis HAB-2. PMID:33281792
Repurposing of FDA approved ring systems through bi-directional target-ring system dual screening. PMID:33273509
The intracellular bacterium Rickettsia rickettsii exerts an inhibitory effect on the apoptosis of tick cells. PMID:33261663
A multicomponent screen for feeding behaviour and nutritional status in Drosophila to interrogate mammalian appetite-related genes. PMID:33242659
Contributions of protein microenvironment in tannase industrial applicability: An in-silico comparative study of pathogenic and non-pathogenic bacterial tannase. PMID:33241136
A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis. PMID:33240303
Inferring the molecular and phenotypic impact of amino acid variants with MutPred2. PMID:33219223
Genome Sequence of Klebsiella pneumoniae YBQ, a Clinical Strain Isolated from the Sputum of a Patient with Severe Pneumonia. PMID:33214313
Targeting SMYD3 to Sensitize Homologous Recombination-Proficient Tumors to PARP-Mediated Synthetic Lethality. PMID:33205017
Towards a novel peptide vaccine for Middle East respiratory syndrome coronavirus and its possible use against pandemic COVID-19. PMID:33173250
Deciphering cell-cell interactions and communication from gene expression. PMID:33168968
In-depth transcriptome reveals the potential biotechnological application of Bothrops jararaca venom gland. PMID:33149734
Network pharmacology and molecular docking analyses on Lianhua Qingwen capsule indicate Akt1 is a potential target to treat and prevent COVID-19. PMID:33140889
Cholesterol-Rich Microdomains Contribute to PAR1 Signaling in Platelets Despite a Weak Localization of the Receptor in These Microdomains. PMID:33138025
Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter. PMID:33126925
Illuminating the dark side of the human transcriptome with long read transcript sequencing. PMID:33126848
Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study. PMID:33112851
Cp1/cathepsin L is required for autolysosomal clearance in Drosophila. PMID:33112206
Effects of Selenium- and Zinc-Enriched Lactobacillus plantarum SeZi on Antioxidant Capacities and Gut Microbiome in an ICR Mouse Model. PMID:33096847
Combined Transcriptome and Metabolome analysis of Pitaya fruit unveiled the mechanisms underlying Peel and pulp color formation. PMID:33092530
Data set of activity cliffs with single-atom modification and associated X-ray structure information for medicinal and computational chemistry applications. PMID:33088875
NAMS webserver: coding potential assessment and functional annotation of plant transcripts. PMID:33080021
PIMD: An Integrative Approach for Drug Repositioning Using Multiple Characterization Fusion. PMID:33075523
Novel loci for childhood body mass index and shared heritability with adult cardiometabolic traits. PMID:33045005
A fluoride-responsive genetic circuit enables in vivo biofluorination in engineered Pseudomonas putida. PMID:33028813
Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus. PMID:33012227
SC2disease: a manually curated database of single-cell transcriptome for human diseases. PMID:33010177
Viral ecogenomics across the Porifera. PMID:33008461
Characterization of Local and Systemic Impact of Whitefly (Bemisia tabaci) Feeding and Whitefly-Transmitted Tomato Mottle Virus Infection on Tomato Leaves by Comprehensive Proteomics. PMID:33008056
Transcriptomic signatures of cold adaptation and heat stress in the winter ant (Prenolepis imparis). PMID:33002025
PartCrafter: find, generate and analyze BioParts. PMID:32995539
Quantitative analysis of global protein stability rates in tissues. PMID:32994440
Spritz: A Proteogenomic Database Engine. PMID:32967423
New developments in RiPP discovery, enzymology and engineering. PMID:32935693
High-resolution analysis of differential gene expression during skeletal muscle atrophy and programmed cell death. PMID:32926651
Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage. PMID:32906802
Kinase inhibitor data set for systematic analysis of representative kinases across the human kinome. PMID:32904416
Exoproteomics for Better Understanding Pseudomonas aeruginosa Virulence. PMID:32899849
PCOSKBR2: a database of genes, diseases, pathways, and networks associated with polycystic ovary syndrome. PMID:32895427
DNSS2: Improved ab initio protein secondary structure prediction using advanced deep learning architectures. PMID:32893403
Molecular-Level Understanding of the Somatostatin Receptor 1 (SSTR1)-Ligand Binding: A Structural Biology Study Based on Computational Methods. PMID:32875251
RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery. PMID:32873609
Correlated expression analysis of genes implicated in schizophrenia: identification of putative disease-related pathways. PMID:32864408
Transcriptome Dynamics of the Inflorescence in Reciprocally Formed Allopolyploid Tragopogon miscellus (Asteraceae). PMID:32849847
Functional Genomics, Transcriptomics, and Proteomics Reveal Distinct Combat Strategies Between Lineages of Wood-Degrading Fungi With Redundant Wood Decay Mechanisms. PMID:32849338
Normal modes analysis and surface electrostatics of haemagglutinin proteins as fingerprints for high pathogenic type A influenza viruses. PMID:32838732
"Mind the Gap": Hi-C Technology Boosts Contiguity of the Globe Artichoke Genome in Low-Recombination Regions. PMID:32817122
Transcriptome analysis of neratinib treated HER2 positive cancer model vs untreated cancer unravels the molecular mechanism of action of neratinib. PMID:32792841
Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity. PMID:32782301
A novel strain of acetic acid bacteria Gluconobacter oxydans FBFS97 involved in riboflavin production. PMID:32782276
Modeling the metabolic interplay between a parasitic worm and its bacterial endosymbiont allows the identification of novel drug targets. PMID:32779567
Evolutionary Remodeling of the Cell Envelope in Bacteria of the Planctomycetes Phylum. PMID:32761170
SWATH-MS-based quantitative proteomics reveals a uniquely intricate defense response in Cnaphalocrocis medinalis-resistant rice. PMID:32759951
CerealsDB-new tools for the analysis of the wheat genome: update 2020. PMID:32754757
Linking metabolic phenotypes to pathogenic traits among "Candidatus Liberibacter asiaticus" and its hosts. PMID:32753656
Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases. PMID:32707033
BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint. PMID:32703160
The PPAR Ω Pocket: Renewed Opportunities for Drug Development. PMID:32695150
First Reports of Effects of Insulin, Human-like Insulin Receptors and Adapter Proteins in Acanthamoeba castellanii. PMID:32678116
Streptococcus pneumoniae metal homeostasis alters cellular metabolism. PMID:32676626
Exploring the structural basis of conformational heterogeneity and autoinhibition of human cGMP-specific protein kinase Iα through computational modelling and molecular dynamics simulations. PMID:32670503
Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context. PMID:32669370
PWAS: proteome-wide association study-linking genes and phenotypes by functional variation in proteins. PMID:32665031
Gold/alpha-lactalbumin nanoprobes for the imaging and treatment of breast cancer. PMID:32661307
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. PMID:32652120
Systematic Discovery of Short Linear Motifs Decodes Calcineurin Phosphatase Signaling. PMID:32645368
Mechanism of Astragalus membranaceus in the treatment of laryngeal cancer based on gene co-expression network and molecular docking. PMID:32636440
Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju. PMID:32633756
Full Rescue of F508del-CFTR Processing and Function by CFTR Modulators Can Be Achieved by Removal of Two Regulatory Regions. PMID:32630527
Deep learning methods in protein structure prediction. PMID:32612753
Mechanistic Models of Signaling Pathways Reveal the Drug Action Mechanisms behind Gender-Specific Gene Expression for Cancer Treatments. PMID:32610626
Identification of Human Enzymes Using Amino Acid Composition and the Composition of k-Spaced Amino Acid Pairs. PMID:32596396
Determining the Genetic Characteristics of Resistance and Virulence of the "Epidermidis Cluster Group" Through Pan-Genome Analysis. PMID:32596166
The PANoptosome: A Deadly Protein Complex Driving Pyroptosis, Apoptosis, and Necroptosis (PANoptosis). PMID:32582562
Use of Dual RNA-seq for Systems Biology Analysis of Zea mays and Aspergillus flavus Interaction. PMID:32582038
Detecting and correcting misclassified sequences in the large-scale public databases. PMID:32579213
An amphipathic peptide with antibiotic activity against multidrug-resistant Gram-negative bacteria. PMID:32576824
Prediction of the Secretome and the Surfaceome: A Strategy to Decipher the Crosstalk between Adipose Tissue and Muscle during Fetal Growth. PMID:32575512
Predicting Self-Interacting Proteins Using a Recurrent Neural Network and Protein Evolutionary Information. PMID:32550764
Integrated analysis of a compendium of RNA-Seq datasets for splicing factors. PMID:32546682
PINOT: an intuitive resource for integrating protein-protein interactions. PMID:32527260
GOcats: A tool for categorizing Gene Ontology into subgraphs of user-defined concepts. PMID:32525872
Proteome characteristics of liver tissue from patients with parenteral nutrition-associated liver disease. PMID:32518576
Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value. PMID:32514106
Network pharmacology to dissect the mechanisms of Yinlai Decoction for pneumonia. PMID:32493296
Identification of Selective Novel Hits against Plasmodium falciparum Prolyl tRNA Synthetase Active Site and a Predicted Allosteric Site Using in silico Approaches. PMID:32471245
Intrinsic Disorder in Tetratricopeptide Repeat Proteins. PMID:32466138
GTP-Dependent FlhF Homodimer Supports Secretion of a Hemolysin in Bacillus cereus. PMID:32435240
Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa. PMID:32427850
SDN2GO: An Integrated Deep Learning Model for Protein Function Prediction. PMID:32411695
Genome Subtraction and Comparison for the Identification of Novel Drug Targets against Mycobacterium avium subsp. hominissuis. PMID:32408506
From Genome to Field-Observation of the Multimodal Nematicidal and Plant Growth-Promoting Effects of Bacillus firmus I-1582 on Tomatoes Using Hyperspectral Remote Sensing. PMID:32384661
Towards the routine use of in silico screenings for drug discovery using metabolic modelling. PMID:32369553
Computational Investigations on the Binding Mode of Ligands for the Cannabinoid-Activated G Protein-Coupled Receptor GPR18. PMID:32365486
The CD83 Molecule - An Important Immune Checkpoint. PMID:32362900
Human adipose-derived mesenchymal stem cell-conditioned medium ameliorates polyneuropathy and foot ulceration in diabetic BKS db/db mice. PMID:32357914
Proteomic profiling and bioinformatics analysis identify key regulators during the process from fanconi anemia to acute myeloid leukemia. PMID:32355551
Proteomic analysis and interactions network in leaves of mycorrhizal and nonmycorrhizal sorghum plants under water deficit. PMID:32351787
TCMIO: A Comprehensive Database of Traditional Chinese Medicine on Immuno-Oncology. PMID:32351388
GrAPFI: predicting enzymatic function of proteins from domain similarity graphs. PMID:32349654
Dynamics of Global Gene Expression and Regulatory Elements in Growing Brachypodium Root System. PMID:32341392
Transcriptomic analysis of sea star development through metamorphosis to the highly derived pentameral body plan with a focus on neural transcription factors. PMID:32339242
Deciphering MET-dependent modulation of global cellular responses to DNA damage by quantitative phosphoproteomics. PMID:32336009
PyRod Enables Rational Homology Model-based Virtual Screening Against MCHR1. PMID:32329245
Target Identification Using Homopharma and Network-Based Methods for Predicting Compounds Against Dengue Virus-Infected Cells. PMID:32325755
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
Integrated querying and version control of context-specific biological networks. PMID:32294194
Identifying nucleic acid-associated proteins in Mycobacterium smegmatis by mass spectrometry-based proteomics. PMID:32293251
Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution. PMID:32284579
Detection of Protein Aggregation in Live Plasmodium Parasites. PMID:32284383
Gene silencing of Diaphorina citri candidate effectors promotes changes in feeding behaviors. PMID:32265528
Classification of VUS and unclassified variants in BRCA1 BRCT repeats by molecular dynamics simulation. PMID:32257056
Phenotypic Screening of Chemical Libraries Enriched by Molecular Docking to Multiple Targets Selected from Glioblastoma Genomic Data. PMID:32243127
ProGeo-neo: a customized proteogenomic workflow for neoantigen prediction and selection. PMID:32241270
Automated gene data integration with Databio. PMID:32238171
Relative Retention Time Estimation Improves N-Glycopeptide Identifications by LC-MS/MS. PMID:32223173
Proteomic mapping of Drosophila transgenic elav.L-GAL4/+ brain as a tool to illuminate neuropathology mechanisms. PMID:32214222
Developing and applying computational resources for biochemistry education. PMID:32203640
The role of semen and seminal plasma in inducing large-scale genomic changes in the female porcine peri-ovulatory tract. PMID:32193402
Mutations in disordered proteins as early indicators of nucleic acid changes triggering speciation. PMID:32161300
Biosynthesis and biology of mammalian GPI-anchored proteins. PMID:32156170
Does the Pre-Ovulatory Pig Oviduct Rule Sperm Capacitation In Vivo Mediating Transcriptomics of Catsper Channels? PMID:32155986
Neighborhood Preference of Amino Acids in Protein Structures and its Applications in Protein Structure Assessment. PMID:32152349
Tryp-N: A Thermostable Protease for the Production of N-terminal Argininyl and Lysinyl Peptides. PMID:32141294
Micromonospora zhangzhouensis sp. nov., a Novel Actinobacterium Isolated from Mangrove Soil, Exerts a Cytotoxic Activity in vitro. PMID:32127574
Recent advances in functional research in Giardia intestinalis. PMID:32122532
Two Highly Similar Chitinases from Marine Vibrio Species have Different Enzymatic Properties. PMID:32120805
Genomic Identification of RNA Editing Through Integrating Omics Datasets and the Clinical Relevance in Hepatocellular Carcinoma. PMID:32117713
The transpeptidase PBP2 governs initial localization and activity of the major cell-wall synthesis machinery in E. coli. PMID:32077853
Identification of proteins from the secretory/excretory products (SEPs) of the branchiuran ectoparasite Argulus foliaceus (Linnaeus, 1758) reveals unique secreted proteins amongst haematophagous ecdysozoa. PMID:32070416
Plasmodium-infected erythrocytes induce secretion of IGFBP7 to form type II rosettes and escape phagocytosis. PMID:32066522
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
Molecular bases for drought tolerance in common vetch: designing new molecular breeding tools. PMID:32054459
Probing Carbon Utilization of Cordyceps militaris by Sugar Transportome and Protein Structural Analysis. PMID:32050592
The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach. PMID:32047482
Proteomic insight of seminal plasma in spinal cord injured men submitted to oral probenecid treatment for improved motility. PMID:32043922
Classification of Trispanins: A Diverse Group of Proteins That Function in Membrane Synthesis and Transport Mechanisms. PMID:32039202
DeepCPI: A Deep Learning-based Framework for Large-scale in silico Drug Screening. PMID:32035227
Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S. PMID:32033425
Human body-fluid proteome: quantitative profiling and computational prediction. PMID:32020158
A Unique Regulation Region in the 3' UTR of HLA-G with a Promising Potential. PMID:32019184
Tools for Analysis of the Microbiome. PMID:32002757
Conservation of the OmpC Porin Among Typhoidal and Non-Typhoidal Salmonella Serovars. PMID:31998292
Resolving the genetic paradox of invasions: Preadapted genomes and postintroduction hybridization of bigheaded carps in the Mississippi River Basin. PMID:31993075
Characterization and diversity of the complete set of GH family 3 enzymes from Rhodothermus marinus DSM 4253. PMID:31992772
Molecular characterization and safety assessment of biofortified provitamin A rice. PMID:31992721
Comparative genomics of multidrug-resistant Enterococcus spp. isolated from wastewater treatment plants. PMID:31980014
Reconstruction of a regulated two-cell metabolic model to study biohydrogen production in a diazotrophic cyanobacterium Anabaena variabilis ATCC 29413. PMID:31978122
A possible role for autoimmunity through molecular mimicry in alphavirus mediated arthritis. PMID:31969581
Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets. PMID:31947823
Hup-Type Hydrogenases of Purple Bacteria: Homology Modeling and Computational Assessment of Biotechnological Potential. PMID:31935912
Future of Evidence Synthesis in Precision Oncology: Between Systematic Reviews and Biocuration. PMID:31930186
Computational identification of vesicular transport proteins from sequences using deep gated recurrent units architecture. PMID:31921391
Tissue-specific gene expression and protein abundance patterns are associated with fractionation bias in maize. PMID:31900107
Human protein-RNA interaction network is highly stable across mammals. PMID:31888461
Variants in Miro1 Cause Alterations of ER-Mitochondria Contact Sites in Fibroblasts from Parkinson's Disease Patients. PMID:31888276
Identification of infectious disease-associated host genes using machine learning techniques. PMID:31881961
A novel algorithm for alignment of multiple PPI networks based on simulated annealing. PMID:31881842
Identification of self-interacting proteins by integrating random projection classifier and finite impulse response filter. PMID:31881833
GO2Vec: transforming GO terms and proteins to vector representations via graph embeddings. PMID:31874639
Classification of adaptor proteins using recurrent neural networks and PSSM profiles. PMID:31874633
Overlap matrix completion for predicting drug-associated indications. PMID:31869322
Type 2 diabetes-associated single nucleotide polymorphism in Sorcs1 gene results in alternative processing of the Sorcs1 protein in INS1 β-cells. PMID:31857633
A network pharmacology approach to reveal the protective mechanism of Salvia miltiorrhiza-Dalbergia odorifera coupled-herbs on coronary heart disease. PMID:31852981
Evolutionary Forces and Codon Bias in Different Flavors of Intrinsic Disorder in the Human Proteome. PMID:31820049
StructureDistiller: Structural relevance scoring identifies the most informative entries of a contact map. PMID:31811259
Full-Length Transcriptome Survey and Expression Analysis of Parasitoid Wasp Chouioia cunea upon Exposure to 1-Dodecene. PMID:31796851
Hybrid de novo whole-genome assembly and annotation of the model tapeworm Hymenolepis diminuta. PMID:31796747
Multimodal Long Noncoding RNA Interaction Networks: Control Panels for Cell Fate Specification. PMID:31796550
A common root for coevolution and substitution rate variability in protein sequence evolution. PMID:31792239
HKPocket: human kinase pocket database for drug design. PMID:31783725
Integrating the Ribonucleic Acid Sequencing Data From Various Studies for Exploring the Multiple Sclerosis-Related Long Noncoding Ribonucleic Acids and Their Functions. PMID:31781177
Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer. PMID:31772206
SXGBsite: Prediction of Protein-Ligand Binding Sites Using Sequence Information and Extreme Gradient Boosting. PMID:31771119
Supersaturated proteins are enriched at synapses and underlie cell and tissue vulnerability in Alzheimer's disease. PMID:31768427
Identifying Alzheimer's disease-related proteins by LRRGD. PMID:31760934
Ontology-based prediction of cancer driver genes. PMID:31757986
MiRNA therapeutics based on logic circuits of biological pathways. PMID:31757209
Next-Generation Sequencing Reveals Novel Genetic Variants (SRY, DMRT1, NR5A1, DHH, DHX37) in Adults With 46,XY DSD. PMID:31745530
Structural Conservation and Diversity of PilZ-Related Domains. PMID:31740493
Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research. PMID:31738437
Cross-Talk Between circRNAs and mRNAs Modulates MiRNA-mediated Circuits and Affects Melanoma Plasticity. PMID:31734859
PCOSBase: a manually curated database of polycystic ovarian syndrome. PMID:31725861
Biomarker identification of hepatocellular carcinoma using a methodical literature mining strategy. PMID:31725857
Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community. PMID:31719174
Autologous Exosome Transfer: A New Personalised Treatment Concept to Prevent Colitis in a Murine Model. PMID:31710674
MiPepid: MicroPeptide identification tool using machine learning. PMID:31703551
Integrating proteomic, sociodemographic and clinical data to predict future depression diagnosis in subthreshold symptomatic individuals. PMID:31699963
Transcriptional analysis of amino acid, metal ion, vitamin and carbohydrate uptake in butanol-producing Clostridium beijerinckii NRRL B-598. PMID:31697692
A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome. PMID:31687752
Multivariate Genome-wide Association Analysis of a Cytokine Network Reveals Variants with Widespread Immune, Haematological, and Cardiometabolic Pleiotropy. PMID:31679650
Immune Suppressive Extracellular Vesicle Proteins of Leptopilina heterotoma Are Encoded in the Wasp Genome. PMID:31676506
Analysis of Arabidopsis thaliana Redox Gene Network Indicates Evolutionary Expansion of Class III Peroxidase in Plants. PMID:31673065
Proteome characterization of small extracellular vesicles from spared nerve injury model of neuropathic pain. PMID:31669360
Intrinsic Disorder of the BAF Complex: Roles in Chromatin Remodeling and Disease Development. PMID:31652801
Chromosome-level genome assembly of golden pompano (Trachinotus ovatus) in the family Carangidae. PMID:31641137
Closing the Gap Between Therapeutic Use and Mode of Action in Remedial Herbs. PMID:31632273
Communication within East Antarctic Soil Bacteria. PMID:31628145
Genome-wide association mapping of date palm fruit traits. PMID:31615981
Trafficking and Function of the Voltage-Gated Sodium Channel β2 Subunit. PMID:31614896
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. PMID:31614509
Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes. PMID:31587639
Bioremediation of a Common Product of Food Processing by a Human Gut Bacterium. PMID:31585844
A Consensus Binding Motif for the PP4 Protein Phosphatase. PMID:31585692
Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. PMID:31584084
Competitive Interactions between PIRT, the Cold Sensing Ion Channel TRPM8, and PIP2 Suggest a Mechanism for Regulation. PMID:31575973
Detecting sequence signals in targeting peptides using deep learning. PMID:31570514
Novel Genetic Markers for Early Detection of Elevated Breast Cancer Risk in Women. PMID:31569399
Identifying Crohn's disease signal from variome analysis. PMID:31564248
RiceRelativesGD: a genomic database of rice relatives for rice research. PMID:31560050
Genome Sequence of Lactobacillus futsaii Y97, a Potential Probiotic Strain Isolated from Futsai of Taiwan. PMID:31558628
A RAGE-Targeted Antibody-Drug Conjugate: Surface Plasmon Resonance as a Platform for Accelerating Effective ADC Design and Development. PMID:31544813
New Functional Ingredients Based on Microencapsulation of Aqueous Anthocyanin-Rich Extracts Derived from Black Rice (Oryza sativa L.). PMID:31540422
Distinct evolution of toll-like receptor signaling pathway genes in cetaceans. PMID:31535317
Molecular function limits divergent protein evolution on planetary timescales. PMID:31532392
Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster (Saccostrea echinata) reveals population subdivision and informs sustainable aquaculture development. PMID:31514727
N-Glycosylation of the voltage-gated sodium channel β2 subunit is required for efficient trafficking of NaV1.5/β2 to the plasma membrane. PMID:31511323
SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences. PMID:31510679
The Role of Iron in the P-Acquisition Mechanisms of the Unicellular N2-Fixing Cyanobacteria Halothece sp., Found in Association With the Mediterranean Seagrass Posidonia oceanica. PMID:31507547
Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved. PMID:31504783
Duplication history and molecular evolution of the rbcS multigene family in angiosperms. PMID:31498865
Mitochondrial protein enriched extracellular vesicles discovered in human melanoma tissues can be detected in patient plasma. PMID:31497264
Complete Genome Sequence of a Shiga Toxin-Converting Bacteriophage, Escherichia Phage Lys12581Vzw, Induced from an Outbreak Shiga Toxin-Producing Escherichia coli Strain. PMID:31488531
The Acetylation of Lysine-376 of G3BP1 Regulates RNA Binding and Stress Granule Dynamics. PMID:31481451
The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat. PMID:31471988
Biosynthesis of Hyaluronic acid polymer: Dissecting the role of sub structural elements of hyaluronan synthase. PMID:31467312
Insights to the Assembly of a Functionally Active Leptospiral ClpP1P2 Protease Complex along with Its ATPase Chaperone ClpX. PMID:31460415
Extensive Thioautotrophic Gill Endosymbiont Diversity within a Single Ctena orbiculata (Bivalvia: Lucinidae) Population and Implications for Defining Host-Symbiont Specificity and Species Recognition. PMID:31455638
Enzymatic Degradation of Biofilm by Metalloprotease From Microbacterium sp. SKS10. PMID:31448272
Metabolomic and transcriptomic profiling of three types of litchi pericarps reveals that changes in the hormone balance constitute the molecular basis of the fruit cracking susceptibility of Litchi chinensis cv. Baitangying. PMID:31440876
Precise Prediction of Calpain Cleavage Sites and Their Aberrance Caused by Mutations in Cancer. PMID:31440276
Prediction of deleterious single nucleotide polymorphisms and their effect on the sequence and structure of the human CCND1 gene. PMID:31435243
Computational classification of MocR transcriptional regulators into subgroups as a support for experimental and functional characterization. PMID:31435161
Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris. PMID:31427456
Nucleo-cytoplasmic Partitioning of ARF Proteins Controls Auxin Responses in Arabidopsis thaliana. PMID:31421981
Advances in gene ontology utilization improve statistical power of annotation enrichment. PMID:31415589
Dimerization and phosphorylation of Lutheran/basal cell adhesion molecule are critical for its function in cell migration on laminin. PMID:31413112
The liver proteome in a mouse model for Ascaris suum resistance and susceptibility: evidence for an altered innate immune response. PMID:31412915
CasPDB: an integrated and annotated database for Cas proteins from bacteria and archaea. PMID:31411686
Comparative Genomics of Marine Sponge-Derived Streptomyces spp. Isolates SM17 and SM18 With Their Closest Terrestrial Relatives Provides Novel Insights Into Environmental Niche Adaptations and Secondary Metabolite Biosynthesis Potential. PMID:31404169
β-Catenin/Tcf7l2-dependent transcriptional regulation of GLUT1 gene expression by Zic family proteins in colon cancer. PMID:31392276
Bioinformatics classification of mutations in patients with Mucopolysaccharidosis IIIA. PMID:31385193
Evaluation of the Common Molecular Basis in Alzheimer's and Parkinson's Diseases. PMID:31366155
Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne). PMID:31361773
An effective biomedical data migration tool from resource description framework to JSON. PMID:31343683
Pathogenic Protist Transmembranome database (PPTdb): a web-based platform for searching and analysis of protist transmembrane proteins. PMID:31337335
Disorder Atlas: Web-based software for the proteome-based interpretation of intrinsic disorder predictions. PMID:31326853
Structural and Functional Characterization of YdjI, an Aldolase of Unknown Specificity in Escherichia coli K12. PMID:31322866
Functional Characterization of YdjH, a Sugar Kinase of Unknown Specificity in Escherichia coli K12. PMID:31314509
glypy: An Open Source Glycoinformatics Library. PMID:31310539
EPIC: software toolkit for elution profile-based inference of protein complexes. PMID:31308550
Multi-channel PINN: investigating scalable and transferable neural networks for drug discovery. PMID:31289963
A systematic approach to orient the human protein-protein interaction network. PMID:31289271
Pathological changes are associated with shifts in the employment of synonymous codons at the transcriptome level. PMID:31288782
Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths. PMID:31285347
ET-GRU: using multi-layer gated recurrent units to identify electron transport proteins. PMID:31277574
Exploring the dark genome: implications for precision medicine. PMID:31270560
An anionic human protein mediates cationic liposome delivery of genome editing proteins into mammalian cells. PMID:31266953
Separating Golgi Proteins from Cis to Trans Reveals Underlying Properties of Cisternal Localization. PMID:31266899
Proteomics INTegrator (PINT): An Online Tool To Store, Query, and Visualize Large Proteomics Experiment Results. PMID:31260318
Mutations in PIGB Cause an Inherited GPI Biosynthesis Defect with an Axonal Neuropathy and Metabolic Abnormality in Severe Cases. PMID:31256876
Ridge regression estimated linear probability model predictions of O-glycosylation in proteins with structural and sequence data. PMID:31253080
Maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER). PMID:31245718
Ligand-guided homology modeling drives identification of novel histamine H3 receptor ligands. PMID:31237914
Variations in the Structure and Evolution of Rice WRKY Genes in Indica and Japonica Genotypes and their Co-expression Network in Mediating Disease Resistance. PMID:31236008
Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers. PMID:31221760
Active repurposing of drug candidates for melanoma based on GWAS, PheWAS and a wide range of omics data. PMID:31221082
Gradient Boosting Decision Tree-Based Method for Predicting Interactions Between Target Genes and Drugs. PMID:31214240
Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution. PMID:31206013
Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data. PMID:31196115
Functional Analysis of the PgCesA3 White Spruce Cellulose Synthase Gene Promoter in Secondary Xylem. PMID:31191566
Dicyemida and Orthonectida: Two Stories of Body Plan Simplification. PMID:31178892
Profiling of Multiphosphorylated Peptides in Kefir and Their Release During Simulated Gastrointestinal Digestion. PMID:31172034
Endometriosis Knowledgebase: a gene-based resource on endometriosis. PMID:31169291
Identification and functional analysis of missense mutations in the lecithin cholesterol acyltransferase gene in a Chilean patient with hypoalphalipoproteinemia. PMID:31164121
De Novo Design and In Vitro Testing of Antimicrobial Peptides against Gram-Negative Bacteria. PMID:31163671
Split4Blank: Maintaining consistency while improving efficiency of loading RDF data with blank nodes. PMID:31163073
Mutational burden and signatures in 4000 Japanese cancers provide insights into tumorigenesis and response to therapy. PMID:31152682
Drug repositioning of herbal compounds via a machine-learning approach. PMID:31138103
Subproteome of Lachesis muta rhombeata venom and preliminary studies on LmrSP-4, a novel snake venom serine proteinase. PMID:31131000
Dynamic Transcriptome Analysis Reveals Potential Long Non-coding RNAs Governing Postnatal Pineal Development in Pig. PMID:31130986
β-Aminopeptidases: Insight into Enzymes without a Known Natural Substrate. PMID:31126950
In silico and in vitro studies of lupeol and iso-orientin as potential antidiabetic agents in a rat model. PMID:31123393
EcRBPome: a comprehensive database of all known E. coli RNA-binding proteins. PMID:31117939
Fragment-Based Ligand-Protein Contact Statistics: Application to Docking Simulations. PMID:31117183
Methanogenesis marker protein 10 (Mmp10) from Methanosarcina acetivorans is a radical S-adenosylmethionine methylase that unexpectedly requires cobalamin. PMID:31113866
Investigating function roles of hypothetical proteins encoded by the Mycobacterium tuberculosis H37Rv genome. PMID:31113361
Three New Isoflavonoid Glycosides from the Mangrove-Derived Actinomycete Micromonospora aurantiaca 110B. PMID:31108876
The carboxy-terminus, a key regulator of protein function. PMID:31106589
Identification and comparative analysis of the CIPK gene family and characterization of the cold stress response in the woody plant Prunus mume. PMID:31106064
Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity. PMID:31080084
De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers. PMID:31077315
Pathway-specific protein domains are predictive for human diseases. PMID:31075101
A voting mechanism-based linear epitope prediction system for the host-specific Iridoviridae family. PMID:31074372
Prediction and characterisation of lantibiotic structures with molecular modelling and molecular dynamics simulations. PMID:31073133
Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae). PMID:31070747
Marine Natural Products from Microalgae: An -Omics Overview. PMID:31067655
Envisioning data sharing for the biocomputing community. PMID:31065349
Aspergillus niger citrate exporter revealed by comparison of two alternative citrate producing conditions. PMID:31062025
OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. PMID:31053848
High precision protein functional site detection using 3D convolutional neural networks. PMID:31051039
Identification and Quantification of Proteoforms by Mass Spectrometry. PMID:31050378
Linkage-based genome assembly improvement of oil palm (Elaeis guineensis). PMID:31036825
Conserved Secondary Structures in Viral mRNAs. PMID:31035717
Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants. PMID:31029164
SEanalysis: a web tool for super-enhancer associated regulatory analysis. PMID:31028388
Genomic and Physiological Traits of the Marine Bacterium Alcaligenes aquatilis QD168 Isolated From Quintero Bay, Central Chile, Reveal a Robust Adaptive Response to Environmental Stressors. PMID:31024465
Transcriptome Alterations in Liver Metastases of Colorectal Cancer After Acquired Resistance to Cetuximab. PMID:31018951
Tracing the origin and evolution of pseudokinases across the tree of life. PMID:31015289
Genome sequencing and CRISPR/Cas9 gene editing of an early flowering Mini-Citrus (Fortunella hindsii). PMID:31004551
Altered Expression and Localization of Tumor Suppressive E3 Ubiquitin Ligase SMURF2 in Human Prostate and Breast Cancer. PMID:31003445
INKA, an integrative data analysis pipeline for phosphoproteomic inference of active kinases. PMID:30979792
Drug-induced activation of integrin alpha IIb beta 3 leads to minor localized structural changes. PMID:30978226
In silico Characterization of Human Prion-Like Proteins: Beyond Neurological Diseases. PMID:30971948
Detection of BDNF-Related Proteins in Human Perilymph in Patients With Hearing Loss. PMID:30971872
A plasma protein derived TGFβ signature is a prognostic indicator in triple negative breast cancer. PMID:30963111
TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets. PMID:30936560
Repertoires of G protein-coupled receptors for Ciona-specific neuropeptides. PMID:30936317
Genome and Ontogenetic-Based Transcriptomic Analyses of the Flesh Fly, Sarcophaga bullata. PMID:30926723
Human gut resistome can be country-specific. PMID:30923648
Combined Genomic, Transcriptomic, Proteomic, and Physiological Characterization of the Growth of Pecoramyces sp. F1 in Monoculture and Co-culture With a Syntrophic Methanogen. PMID:30894845
AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution. PMID:30893420
An Improved Deep Forest Model for Predicting Self-Interacting Proteins From Protein Sequence Using Wavelet Transformation. PMID:30881376
Fragment Hits: What do They Look Like and How do They Bind? PMID:30875465
Molecular modeling simulation studies reveal new potential inhibitors against HPV E6 protein. PMID:30875378
Dynamic analysis of human tyrosinase intra-melanosomal domain and mutant variants to further understand oculocutaneous albinism type 1. PMID:30868138
Autophagy accounts for approximately one-third of mitochondrial protein turnover and is protein selective. PMID:30865561
GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. PMID:30862647
When one phenotype is not enough: divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species. PMID:30862287
Three additional patients with EED-associated overgrowth: potential mutation hotspots identified? PMID:30858506
Coexpression patterns define epigenetic regulators associated with neurological dysfunction. PMID:30858344
Protein structure prediction. PMID:30853739
How to Develop a Drug Target Ontology: KNowledge Acquisition and Representation Methodology (KNARM). PMID:30848456
Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon). PMID:30842908
Identifying Small Proteins by Ribosome Profiling with Stalled Initiation Complexes. PMID:30837344
A hybrid approach for automated mutation annotation of the extended human mutation landscape in scientific literature. PMID:30815103
BGFE: A Deep Learning Model for ncRNA-Protein Interaction Predictions Based on Improved Sequence Information. PMID:30813451
Novel SCN2A mutation in a family associated with juvenile-onset myoclonus: Case report. PMID:30813219
Identifying Windows of Susceptibility by Temporal Gene Analysis. PMID:30809014
Repurposing population genetics data to discern genomic architecture: A case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae). PMID:30805148
Survival Mechanisms of Campylobacter hepaticus Identified by Genomic Analysis and Comparative Transcriptomic Analysis of in vivo and in vitro Derived Bacteria. PMID:30804905
PamulDB: a comprehensive genomic resource for the study of human- and animal-pathogenic Pasteurella multocida. PMID:30799499
Discovery and Characterization of a Nitroreductase Capable of Conferring Bacterial Resistance to Chloramphenicol. PMID:30799223
Prediction of Self-Interacting Proteins from Protein Sequence Information Based on Random Projection Model and Fast Fourier Transform. PMID:30795499
Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms. PMID:30770768
MultiDomainBenchmark: a multi-domain query and subject database suite. PMID:30764761
Molecular Modeling and Functional Analysis of Exome Sequencing-Derived Variants of Unknown Significance Identify a Novel, Constitutively Active FGFR2 Mutant in Cholangiocarcinoma. PMID:30761385
Inhibition of acetylcholinesterase and butyrylcholinesterase with uracil derivatives: kinetic and computational studies. PMID:30734597
Free, unlinked glycosylphosphatidylinositols on mammalian cell surfaces revisited. PMID:30728244
Aminoacyl tRNA synthetases as malarial drug targets: a comparative bioinformatics study. PMID:30728021
Ranking Cancer Proteins by Integrating PPI Network and Protein Expression Profiles. PMID:30723737
Identification and analysis of structurally critical fragments in HopS2. PMID:30717655
Understanding the evolutionary trend of intrinsically structural disorders in cancer relevant proteins as probed by Shannon entropy scoring and structure network analysis. PMID:30717651
Diverse dynamics features of novel protein kinase C (PKC) isozymes determine the selectivity of a fluorinated balanol analogue for PKCε. PMID:30717648
The Gene Toolkit Implicated in Functional Sex in Sparidae Hermaphrodites: Inferences From Comparative Transcriptomics. PMID:30713551
The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function. PMID:30698741
Transcriptome Analysis Clarified Genes Involved in Betalain Biosynthesis in the Fruit of Red Pitayas (Hylocereus costaricensis). PMID:30691184
Expression of Immune Regulatory Genes in the Porcine Internal Genital Tract Is Differentially Triggered by Spermatozoa and Seminal Plasma. PMID:30691059
Characterization of the Sinorhizobium meliloti HslUV and ClpXP Protease Systems in Free-Living and Symbiotic States. PMID:30670545
De Novo Sequencing and Hybrid Assembly of the Biofuel Crop Jatropha curcas L.: Identification of Quantitative Trait Loci for Geminivirus Resistance. PMID:30669588
Identification of selective inhibitors of Helicobacter pylori IMPDH as a targeted therapy for the infection. PMID:30655593
AMYCO: evaluation of mutational impact on prion-like proteins aggregation propensity. PMID:30642249
A Markov Chain Monte Carlo Method for Estimating the Statistical Significance of Proteoform Identifications by Top-Down Mass Spectrometry. PMID:30638379
Grafting, Stripping and Stapling of Helical Peptides from the Dimerization Interface of ONFH-Related Bone Morphogenetic Protein-2. PMID:30604108
Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. PMID:30602777
Integrating node embeddings and biological annotations for genes to predict disease-gene associations. PMID:30598097
Evaluation of top-down mass spectral identification with homologous protein sequences. PMID:30591035
Comparative Transcriptome Analysis Reveals an Efficient Mechanism of α-Linolenic Acid in Tree Peony Seeds. PMID:30586917
MDAD: A Special Resource for Microbe-Drug Associations. PMID:30581775
Biodegradation of the Allelopathic Chemical Pterostilbene by a Sphingobium sp. Strain from the Peanut Rhizosphere. PMID:30578258
Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase. PMID:30577795
Prediction of protein self-interactions using stacked long short-term memory from protein sequences information. PMID:30577794
iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature. PMID:30576489
NBDC RDF portal: a comprehensive repository for semantic data in life sciences. PMID:30576482
psims - A Declarative Writer for mzML and mzIdentML for Python. PMID:30563850
Identifying mouse developmental essential genes using machine learning. PMID:30563825
Vertebrate SLRP family evolution and the subfunctionalization of osteoglycin gene duplicates in teleost fish. PMID:30545285
SYNGAP1 encephalopathy: A distinctive generalized developmental and epileptic encephalopathy. PMID:30541864
Development of Onchocerca volvulus in humanized NSG mice and detection of parasite biomarkers in urine and serum. PMID:30540742
Mitoproteomics: Tackling Mitochondrial Dysfunction in Human Disease. PMID:30533169
GABA-modulating bacteria of the human gut microbiota. PMID:30531975
Structural and functional characterization of an intradiol ring-cleavage dioxygenase from the polyphagous spider mite herbivore Tetranychus urticae Koch. PMID:30529144
Comparative analysis of interactions between aryl hydrocarbon receptor ligand binding domain with its ligands: a computational study. PMID:30522477
Taxonomic and functional heterogeneity of the gill microbiome in a symbiotic coastal mangrove lucinid species. PMID:30518817
Discovery of Novel Conotoxin Candidates Using Machine Learning. PMID:30513724
ARP3 Controls the Podocyte Architecture at the Kidney Filtration Barrier. PMID:30503751
Protein variability in cerebrospinal fluid and its possible implications for neurological protein biomarker research. PMID:30496192
The genome of an underwater architect, the caddisfly Stenopsyche tienmushanensis Hwang (Insecta: Trichoptera). PMID:30476205
Ethylene Receptors, CTRs and EIN2 Target Protein Identification and Quantification Through Parallel Reaction Monitoring During Tomato Fruit Ripening. PMID:30467512
Harmonizing semantic annotations for computational models in biology. PMID:30462164
Quantitative metaproteomics of medieval dental calculus reveals individual oral health status. PMID:30459334
BioGraph: a web application and a graph database for querying and analyzing bioinformatics resources. PMID:30458802
The predictive performance of short-linear motif features in the prediction of calmodulin-binding proteins. PMID:30453876
The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain. PMID:30443017
WebNetCoffee: a web-based application to identify functionally conserved proteins from Multiple PPI networks. PMID:30419809
NAT/NCS2-hound: a webserver for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. PMID:30418564
A fast-evolving X-linked duplicate of importin-α2 is overexpressed in sex-ratio drive in Drosophila neotestacea. PMID:30411843
Exploring Exercise- and Context-Induced Peptide Changes in Mice by Quantitative Mass Spectrometry. PMID:30411050
Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures. PMID:30400856
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. PMID:30395277
Genome sequencing of oomycete isolates from Chile supports the New Zealand origin of Phytophthora kernoviae and makes available the first Nothophytophthora sp. genome. PMID:30390404
The Bipartite Network Projection-Recommended Algorithm for Predicting Long Non-coding RNA-Protein Interactions. PMID:30388620
Identification of key differentially expressed MicroRNAs in cancer patients through pan-cancer analysis. PMID:30384176
A planarian nidovirus expands the limits of RNA genome size. PMID:30383829
Discovery Methodology of Novel Conotoxins from Conus Species. PMID:30380764
qPhos: a database of protein phosphorylation dynamics in humans. PMID:30380102
Species-level functional profiling of metagenomes and metatranscriptomes. PMID:30377376
The in silico human surfaceome. PMID:30373828
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification. PMID:30373669
SEdb: a comprehensive human super-enhancer database. PMID:30371817
A GPU-based algorithm for fast node label learning in large and unbalanced biomolecular networks. PMID:30367594
Multiple model species selection for transcriptomics analysis of non-model organisms. PMID:30367568
Repellency, Toxicity, Gene Expression Profiling and In Silico Studies to Explore Insecticidal Potential of Melaleuca alternifolia Essential Oil against Myzus persicae. PMID:30366370
Phylotranscriptomic Insights into the Diversification of Endothermic Thunnus Tunas. PMID:30364966
ConfeitoGUI: A toolkit for size-sensitive community detection from a correlation network. PMID:30352084
HSP90-incorporating chaperome networks as biosensor for disease-related pathways in patient-specific midbrain dopamine neurons. PMID:30341316
Whole Proteome Profiling of N-Myristoyltransferase Activity and Inhibition Using Sortase A. PMID:30341083
EBP1 nuclear accumulation negatively feeds back on FERONIA-mediated RALF1 signaling. PMID:30339663
A most wanted list of conserved microbial protein families with no known domains. PMID:30332487
De novo genome and transcriptome analyses provide insights into the biology of the trematode human parasite Fasciolopsis buski. PMID:30325945
Deep-RBPPred: Predicting RNA binding proteins in the proteome scale based on deep learning. PMID:30323214
Preassembled GPCR signaling complexes mediate distinct cellular responses to ultralow ligand concentrations. PMID:30301787
Comparative transcriptomic profile of tolerogenic dendritic cells differentiated with vitamin D3, dexamethasone and rapamycin. PMID:30297862
In silico characterization of the global Geobacillus and Parageobacillus secretome. PMID:30285747
Assessment of shared alleles in drought-associated candidate genes among southern California white oak species (Quercus sect. Quercus). PMID:30285631
Fire ant social chromosomes: Differences in number, sequence and expression of odorant binding proteins. PMID:30283649
Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics. PMID:30275399
Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000. PMID:30265449
SemGen: a tool for semantics-based annotation and composition of biosimulation models. PMID:30256901
Glucocerebrosidase deficiency promotes protein aggregation through dysregulation of extracellular vesicles. PMID:30256786
Novel Metabolic Pathways and Regulons for Hexuronate Utilization in Proteobacteria. PMID:30249705
Genome-wide diversity in temporal and regional populations of the betabaculovirus Erinnyis ello granulovirus (ErelGV). PMID:30249206
Viruses.STRING: A Virus-Host Protein-Protein Interaction Database. PMID:30249048
Evolutionary Pressure against MHC Class II Binding Cancer Mutations. PMID:30245014
The Grayling Genome Reveals Selection on Gene Expression Regulation after Whole-Genome Duplication. PMID:30239729
Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling. PMID:30239666
Transcriptomic response of female adult moths to host and non-host plants in two closely related species. PMID:30236059
Systematic identification of cancer-specific MHC-binding peptides with RAVEN. PMID:30228952
Functional classification of long non-coding RNAs by k-mer content. PMID:30224646
Exploring Selectivity of Multikinase Inhibitors across the Human Kinome. PMID:30221217
Differences in possible TCA cycle replenishing pathways in purple non-sulfur bacteria possessing glyoxylate pathway. PMID:30219941
Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses. PMID:30209043
Knockout of the Hmt1p Arginine Methyltransferase in Saccharomyces cerevisiae Leads to the Dysregulation of Phosphate-associated Genes and Processes. PMID:30206180
Computational systems pharmacology analysis of cannabidiol: a combination of chemogenomics-knowledgebase network analysis and integrated in silico modeling and simulation. PMID:30202014
Transcriptomic Analysis Reveals Sex-Dependent Expression Patterns in the Basolateral Amygdala of Dominant and Subordinate Animals After Acute Social Conflict. PMID:30196395
Phylogenomics Reveal the Dynamic Evolution of Fungal Nitric Oxide Reductases and Their Relationship to Secondary Metabolism. PMID:30165640
A potential central role of Thaumarchaeota in N-Cycling in a semi-arid environment, Fort Stanton Cave, Snowy River passage, New Mexico, USA. PMID:30165514
Comparative analysis of whole flower transcriptomes in the Zingiberales. PMID:30155368
Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome. PMID:30134948
Discovering Putative Prion-Like Proteins in Plasmodium falciparum: A Computational and Experimental Analysis. PMID:30131778
ACP Acylation Is an Acetyl-CoA-Dependent Modification Required for Electron Transport Chain Assembly. PMID:30118679
DPAGT1 Deficiency with Encephalopathy (DPAGT1-CDG): Clinical and Genetic Description of 11 New Patients. PMID:30117111
Proteomics for blood biomarker exploration of severe mental illness: pitfalls of the past and potential for the future. PMID:30115926
Approaches to target tractability assessment - a practical perspective. PMID:30108951
Identification of potent cholecystokinin-B receptor antagonists: synthesis, molecular modeling and anti-cancer activity against pancreatic cancer cells. PMID:30108868
Cooperativity in Plant Plasma Membrane Intrinsic Proteins (PIPs): Mechanism of Increased Water Transport in Maize PIP1 Channels in Hetero-tetramers. PMID:30104609
Computational resources associating diseases with genotypes, phenotypes and exposures. PMID:30102366
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. PMID:30084866
Quantitative Yeast Genetic Interaction Profiling of Bacterial Effector Proteins Uncovers a Role for the Human Retromer in Salmonella Infection. PMID:30077634
The scale-free nature of protein sequence space. PMID:30067815
OC-2-KB: integrating crowdsourcing into an obesity and cancer knowledge base curation system. PMID:30066655
BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea. PMID:30063227
Cotton rat lung transcriptome reveals host immune response to Respiratory Syncytial Virus infection. PMID:30054492
KampoDB, database of predicted targets and functional annotations of natural medicines. PMID:30046160
Novel 3D Structure Based Model for Activity Prediction and Design of Antimicrobial Peptides. PMID:30046138
A Genome-Scale Metabolic Reconstruction of Phytophthora infestans With the Integration of Transcriptional Data Reveals the Key Metabolic Patterns Involved in the Interaction of Its Host. PMID:30042788
Network Rewiring in Cancer: Applications to Melanoma Cell Lines and the Cancer Genome Atlas Patients. PMID:30042785
Exploring Structural Relationships between Bioactive and Commercial Chemical Space and Developing Target Hypotheses for Compound Acquisition. PMID:30023563
IRWNRLPI: Integrating Random Walk and Neighborhood Regularized Logistic Matrix Factorization for lncRNA-Protein Interaction Prediction. PMID:30023002
Leveraging prior knowledge for protein-protein interaction extraction with memory network. PMID:30010731
Structure and energy based quantitative missense variant effect analysis provides insights into drug resistance mechanisms of anaplastic lymphoma kinase mutations. PMID:30006516
Impact of Leishmania donovani infection on the HLA I self peptide repertoire of human macrophages. PMID:30001391
Improving Prediction of Self-interacting Proteins Using Stacked Sparse Auto-Encoder with PSSM profiles. PMID:29989064
Defining the Species Micromonospora saelicesensis and Micromonospora noduli Under the Framework of Genomics. PMID:29988535
Engineering orthogonal synthetic timer circuits based on extracytoplasmic function σ factors. PMID:29986061
Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism. PMID:29973148
Hypothesis on monochromatic vision in scorpionflies questioned by new transcriptomic data. PMID:29959337
Post-translational buffering leads to convergent protein expression levels between primates. PMID:29950183
The choice of sequence homologs included in multiple sequence alignments has a dramatic impact on evolutionary conservation analysis. PMID:29947739
Systems-Based Interactome Analysis for Hematopoiesis Effect of Angelicae sinensis Radix: Regulated Network of Cell Proliferation towards Hemopoiesis. PMID:29943236
2-[2-(4-(trifluoromethyl)phenylamino)thiazol-4-yl]acetic acid (Activator-3) is a potent activator of AMPK. PMID:29942003
A CAZyme-Rich Genome of a Taxonomically Novel Rhodophyte-Associated Carrageenolytic Marine Bacterium. PMID:29936557
Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology. PMID:29932108
RBPMetaDB: a comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins. PMID:29931156
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. PMID:29931155
Homeobox Gene Duplication and Divergence in Arachnids. PMID:29924328
Differential Proteomic Analysis of Lactic Acid Bacteria-Escherichia coli O157:H7 Interaction and Its Contribution to Bioprotection Strategies in Meat. PMID:29922248
Tissue-Specific Analysis of Pharmacological Pathways. PMID:29920991
Molecular Determinants of the Promiscuity of MexB and MexY Multidrug Transporters of Pseudomonas aeruginosa. PMID:29910784
Probiotic strains detect and suppress cholera in mice. PMID:29899022
iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites. PMID:29897410
Prion-like Domains in Eukaryotic Viruses. PMID:29895872
Blazing Signature Filter: a library for fast pairwise similarity comparisons. PMID:29890950
Molecular profiling and sequential somatic mutation shift in hypermutator tumours harbouring POLE mutations. PMID:29880869
Weibel-Palade Body Localized Syntaxin-3 Modulates Von Willebrand Factor Secretion From Endothelial Cells. PMID:29880488
Venom allergen-like protein 28 in Clonorchis sinensis: four epitopes on its surface and the potential role of Cys124 for its conformational stability. PMID:29876859
Predicting Adverse Drug Effects from Literature- and Database-Mined Assertions. PMID:29876834
PTMscape: an open source tool to predict generic post-translational modifications and map modification crosstalk in protein domains and biological processes. PMID:29876573
MU-LOC: A Machine-Learning Method for Predicting Mitochondrially Localized Proteins in Plants. PMID:29875778
Genomic atlas of the human plasma proteome. PMID:29875488
MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization. PMID:29871590
Protein Expression Profile of Twenty-Week-Old Diabetic db/db and Non-Diabetic Mice Livers: A Proteomic and Bioinformatic Analysis. PMID:29857581
PhosContext2vec: a distributed representation of residue-level sequence contexts and its application to general and kinase-specific phosphorylation site prediction. PMID:29844483
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. PMID:29807988
Taxon Richness of "Megaviridae" Exceeds those of Bacteria and Archaea in the Ocean. PMID:29806626
Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria. PMID:29784978
Estimates of genomic heritability and genome-wide association study for fatty acids profile in Santa Inês sheep. PMID:29783944
Chemokine C-C motif ligand 33 is a key regulator of teleost fish barbel development. PMID:29760055
Xpo7 is a broad-spectrum exportin and a nuclear import receptor. PMID:29748336
Identification and application of exogenous dsRNA confers plant protection against Sclerotinia sclerotiorum and Botrytis cinerea. PMID:29743510
PANNZER2: a rapid functional annotation web server. PMID:29741643
Overview of Virus Metagenomic Classification Methods and Their Biological Applications. PMID:29740407
Potential molecular mechanisms of overgrazing-induced dwarfism in sheepgrass (Leymus chinensis) analyzed using proteomic data. PMID:29739327
Control of mitotic chromosome condensation by the fission yeast transcription factor Zas1. PMID:29735745
The Disordered C-Terminus of Yeast Hsf1 Contains a Cryptic Low-Complexity Amyloidogenic Region. PMID:29734798
High quality draft genome sequences of Mycoplasma agassizii strains PS6T and 723 isolated from Gopherus tortoises with upper respiratory tract disease. PMID:29725499
Genome-wide expert annotation of the epigenetic machinery of the plant-parasitic nematodes Meloidogyne spp., with a focus on the asexually reproducing species. PMID:29724186
Brain gene expression analyses in virgin and mated queens of fire ants reveal mating-independent and socially regulated changes. PMID:29721300
A proteomic analysis of an in vitro knock-out of miR-200c. PMID:29720730
A Strategy for Discovery of Endocrine Interactions with Application to Whole-Body Metabolism. PMID:29719227
Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola. PMID:29718205
Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses. PMID:29717040
Sensing the cilium, digital capture of ciliary data for comparative genomics investigations. PMID:29713460
Shared strategies for β-lactam catabolism in the soil microbiome. PMID:29713061
Functional and structural characterization of osteocytic MLO-Y4 cell proteins encoded by genes differentially expressed in response to mechanical signals in vitro. PMID:29712973
Computational Characterization of Small Molecules Binding to the Human XPF Active Site and Virtual Screening to Identify Potential New DNA Repair Inhibitors Targeting the ERCC1-XPF Endonuclease. PMID:29710850
The Egyptian Rousette Genome Reveals Unexpected Features of Bat Antiviral Immunity. PMID:29706541
Characterization of a novel organic solute transporter homologue from Clonorchis sinensis. PMID:29702646
Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome: Where There Is a Will, There Is a Way. PMID:29700069
Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome. PMID:29690875
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. PMID:29688351
YAAM: Yeast Amino Acid Modifications Database. PMID:29688347
Collection of analog series-based scaffolds from public compound sources. PMID:29682322
High quality draft genome sequence of Mycoplasma testudineum strain BH29T, isolated from the respiratory tract of a desert tortoise. PMID:29682170
CD81 Receptor Regions outside the Large Extracellular Loop Determine Hepatitis C Virus Entry into Hepatoma Cells. PMID:29677132
The architecture of an empirical genotype-phenotype map. PMID:29676774
A Novel Method for Drug Screen to Regulate G Protein-Coupled Receptors in the Metabolic Network of Alzheimer's Disease. PMID:29675426
Computational Prediction and Analysis of Associations between Small Molecules and Binding-Associated S-Nitrosylation Sites. PMID:29671802
Genome-Wide Analyses of Calcium Sensors Reveal Their Involvement in Drought Stress Response and Storage Roots Deterioration after Harvest in Cassava. PMID:29671773
Larval transcriptomic response to host plants in two related phytophagous lepidopteran species: implications for host specialization and species divergence. PMID:29669517
The role of the Human Metabolome Database in inborn errors of metabolism. PMID:29663269
SPIDR: small-molecule peptide-influenced drug repurposing. PMID:29661129
Targeted next generation sequencing identifies functionally deleterious germline mutations in novel genes in early-onset/familial prostate cancer. PMID:29659569
Tracing the evolution of the heterotrimeric G protein α subunit in Metazoa. PMID:29642851
Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles. PMID:29636439
Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats. PMID:29636006
Conditional mouse models support the role of SLC39A14 (ZIP14) in Hyperostosis Cranialis Interna and in bone homeostasis. PMID:29621230
Integrating images from multiple microscopy screens reveals diverse patterns of change in the subcellular localization of proteins. PMID:29620521
Global gene regulation in tomato plant (Solanum lycopersicum) responding to vector (Bactericera cockerelli) feeding and pathogen ('Candidatus Liberibacter solanacearum') infection. PMID:29619663
A novel method for improved accuracy of transcription factor binding site prediction. PMID:29617876
De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution. PMID:29615780
Teleost Fish-Specific Preferential Retention of Pigmentation Gene-Containing Families After Whole Genome Duplications in Vertebrates. PMID:29599177
HLPI-Ensemble: Prediction of human lncRNA-protein interactions based on ensemble strategy. PMID:29583068
Systematic Characterization of Stress-Induced RNA Granulation. PMID:29576526
Association Between Serotonin Syndrome and Second-Generation Antipsychotics via Pharmacological Target-Adverse Event Analysis. PMID:29575568
The Catalytically Inactive Mutation of the Ubiquitin-Conjugating Enzyme CDC34 Affects its Stability and Cell Proliferation. PMID:29564676
The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature. PMID:29560829
Evaluation of variability in high-resolution protein structures by global distance scoring. PMID:29560428
Heterodimer Binding Scaffolds Recognition via the Analysis of Kinetically Hot Residues. PMID:29547506
Charge and Polarity Preferences for N-Glycosylation: A Genome-Wide In Silico Study and Its Implications Regarding Constitutive Proliferation and Adhesion of Carcinoma Cells. PMID:29541627
Molecular evolution and functional divergence of eukaryotic translation initiation factor 2-alpha kinases. PMID:29538447
Statistically derived asymmetric membrane potentials from α-helical and β-barrel membrane proteins. PMID:29535329
GATA3 zinc finger 2 mutations reprogram the breast cancer transcriptional network. PMID:29535312
MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping. PMID:29534977
Loss and gain of N-linked glycosylation sequons due to single-nucleotide variation in cancer. PMID:29531238
Molecular Modeling of Structures and Interaction of Human Corticotropin-Releasing Factor (CRF) Binding Protein and CRF Type-2 Receptor. PMID:29515519
On the Regularities of the Polar Profiles of Proteins Related to Ebola Virus Infection and their Functional Domains. PMID:29511990
Multi-chaperone function modulation and association with cytoskeletal proteins are key features of the function of AIP in the pituitary gland. PMID:29507682
STRENDA DB: enabling the validation and sharing of enzyme kinetics data. PMID:29498804
Computational de novo discovery of distinguishing genes for biological processes and cell types in complex tissues. PMID:29494600
Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online. PMID:29494574
The End of a 60-year Riddle: Identification and Genomic Characterization of an Iridovirus, the Causative Agent of White Fat Cell Disease in Zooplankton. PMID:29487186
Bioinformatics for Prohormone and Neuropeptide Discovery. PMID:29476505
The transcriptomic signature of different sexes in two protogynous hermaphrodites: Insights into the molecular network underlying sex phenotype in fish. PMID:29476120
Unexplored therapeutic opportunities in the human genome. PMID:29472638
Worlds Apart - Transcriptome Profiles of Key Oral Microbes in the Periodontal Pocket Compared to Single Laboratory Culture Reflect Synergistic Interactions. PMID:29467738
Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. PMID:29467397
Cooption of heat shock regulatory system for anhydrobiosis in the sleeping chironomid Polypedilum vanderplanki. PMID:29463761
Genome-Wide Analysis of the GRF Family Reveals Their Involvement in Abiotic Stress Response in Cassava. PMID:29461467
Comprehensive Analysis of Constraint on the Spatial Distribution of Missense Variants in Human Protein Structures. PMID:29455857
Exploring autophagy with Gene Ontology. PMID:29455577
AOP-DB: A database resource for the exploration of Adverse Outcome Pathways through integrated association networks. PMID:29454060
Structural and compositional diversity of fibrillin microfibrils in human tissues. PMID:29453284
A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts. PMID:29447159
Interacting-heads motif has been conserved as a mechanism of myosin II inhibition since before the origin of animals. PMID:29444861
Draft genomes of two blister beetles Hycleus cichorii and Hycleus phaleratus. PMID:29444297
Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology. PMID:29440116
Recognition of sites of functional specialisation in all known eukaryotic protein kinase families. PMID:29438395
Proteome-wide comparison between the amino acid composition of domains and linkers. PMID:29426365
Genome-Wide Identification and Expression Analysis of the KUP Family under Abiotic Stress in Cassava (Manihot esculenta Crantz). PMID:29416511
Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori. PMID:29414760
Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia. PMID:29410487
The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile. PMID:29403466
Prediction of Disordered Regions and Their Roles in the Anti-Pathogenic and Immunomodulatory Functions of Butyrophilins. PMID:29401697
The genomes of two Eutrema species provide insight into plant adaptation to high altitudes. PMID:29394339
SMARCA2-regulated host cell factors are required for MxA restriction of influenza A viruses. PMID:29391557
Evolutionary analysis of polyproline motifs in Escherichia coli reveals their regulatory role in translation. PMID:29389943
The unique evolution of the carbohydrate-binding module CBM20 in laforin. PMID:29389008
Survey of Candidate Genes for Maize Resistance to Infection by Aspergillus flavus and/or Aflatoxin Contamination. PMID:29385107
Structural Studies of Predicted Ligand Binding Sites and Molecular Docking Analysis of Slc2a4 as a Therapeutic Target for the Treatment of Cancer. PMID:29382080
Survival of Anaerobic Fe2+ Stress Requires the ClpXP Protease. PMID:29378887
The Xanthomonas euvesicatoria type III effector XopAU is an active protein kinase that manipulates plant MAP kinase signaling. PMID:29377937
ProtDataTherm: A database for thermostability analysis and engineering of proteins. PMID:29377907
Systematic Functional Characterization of Human 21st Chromosome Orthologs in Caenorhabditis elegans. PMID:29367452
Whole-exome sequencing identifies common and rare variant metabolic QTLs in a Middle Eastern population. PMID:29362361
Respiromics - An integrative analysis linking mitochondrial bioenergetics to molecular signatures. PMID:29361498
Comparative Genomics Reveals Accelerated Evolution in Conserved Pathways during the Diversification of Anole Lizards. PMID:29360978
Systematic Analysis of the Binding Surfaces between tRNAs and Their Respective Aminoacyl tRNA Synthetase Based on Structural and Evolutionary Data. PMID:29358943
Aminode: Identification of Evolutionary Constraints in the Human Proteome. PMID:29358731
Screening and Genomic Characterization of Filamentous Hemagglutinin-Deficient Bordetella pertussis. PMID:29358336
Interactome INSIDER: a structural interactome browser for genomic studies. PMID:29355848
Regeneration in distantly related species: common strategies and pathways. PMID:29354283
Computational study of HIV gp120 as a target for polyanionic entry inhibitors: Exploiting the V3 loop region. PMID:29346393
Structure, function and evolution of the hemerythrin-like domain superfamily. PMID:29330894
Systematic Evaluation of Protein Sequence Filtering Algorithms for Proteoform Identification Using Top-Down Mass Spectrometry. PMID:29327814
Revealing Alzheimer's disease genes spectrum in the whole-genome by machine learning. PMID:29320986
Molecular and Biochemical Characterization of Opisthorchis viverrini Calreticulin. PMID:29320819
Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies. PMID:29309127
A High-Resolution Proteomic Landscaping of Primary Human Dental Stem Cells: Identification of SHED- and PDLSC-Specific Biomarkers. PMID:29304003
A Dipteran's Novel Sucker Punch: Evolution of Arthropod Atypical Venom with a Neurotoxic Component in Robber Flies (Asilidae, Diptera). PMID:29303983
Computational Investigation of the Missense Mutations in DHCR7 Gene Associated with Smith-Lemli-Opitz Syndrome. PMID:29300326
De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus. PMID:29297306
Characterizing the O-glycosylation landscape of human plasma, platelets, and endothelial cells. PMID:29296958
Erythrogene: a database for in-depth analysis of the extensive variation in 36 blood group systems in the 1000 Genomes Project. PMID:29296939
Genomic study and Medical Subject Headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers. PMID:29293733
Improving pairwise comparison of protein sequences with domain co-occurrence. PMID:29293498
Affinity purification mass spectrometry analysis of PD-1 uncovers SAP as a new checkpoint inhibitor. PMID:29282323
Phenotype inference in an Escherichia coli strain panel. PMID:29280730
Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat. PMID:29272997
Computational Studies of Snake Venom Toxins. PMID:29271884
Mammalian display screening of diverse cystine-dense peptides for difficult to drug targets. PMID:29269835
Catecholamine-Modulated Novel Surface-Exposed Adhesin LIC20035 of Leptospira spp. Binds Host Extracellular Matrix Components and Is Recognized by the Host during Infection. PMID:29269501
Parental investment matters for maternal and offspring immune defense in the mouthbrooding cichlid Astatotilapia burtoni. PMID:29262789
LPI-NRLMF: lncRNA-protein interaction prediction by neighborhood regularized logistic matrix factorization. PMID:29262614
Percolation in protein sequence space. PMID:29261740
Large Scale Identification of Variant Proteins in Glioma Stem Cells. PMID:29254333
Transcriptomic pathway analysis of urokinase receptor silenced breast cancer cells: a microarray study. PMID:29254187
Genome assembly of the Pink Ipê (Handroanthus impetiginosus, Bignoniaceae), a highly valued, ecologically keystone Neotropical timber forest tree. PMID:29253216
Reconstruction of Oryza sativa indica Genome Scale Metabolic Model and Its Responses to Varying RuBisCO Activity, Light Intensity, and Enzymatic Cost Conditions. PMID:29250098
Proteome profiling of clear cell renal cell carcinoma in von Hippel-Lindau patients highlights upregulation of Xaa-Pro aminopeptidase-1, an anti-proliferative and anti-migratory exoprotease. PMID:29245961
The landscape of human mutually exclusive splicing. PMID:29242366
Conservation of Specificity in Two Low-Specificity Proteins. PMID:29240404
Unravelling Protein-Protein Interaction Networks Linked to Aliphatic and Indole Glucosinolate Biosynthetic Pathways in Arabidopsis. PMID:29238354
Dependence of prevalence of contiguous pathways in proteins on structural complexity. PMID:29232711
Prediction of cassava protein interactome based on interolog method. PMID:29222529
SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets. PMID:29220461
AllerBase: a comprehensive allergen knowledgebase. PMID:29220458
LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. PMID:29220437
Global computational mutagenesis provides a critical stability framework in protein structures. PMID:29216252
A comparative transcriptomic analysis of replicating and dormant liver stages of the relapsing malaria parasite Plasmodium cynomolgi. PMID:29215331
Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry. PMID:29208937
Contrasting patterns of evolutionary constraint and novelty revealed by comparative sperm proteomic analysis in Lepidoptera. PMID:29197336
Properties of human genes guided by their enrichment in rare and common variants. PMID:29197136
Contributions of Zea mays subspecies mexicana haplotypes to modern maize. PMID:29187731
Integrating sequence and gene expression information predicts genome-wide DNA-binding proteins and suggests a cooperative mechanism. PMID:29186632
Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome. PMID:29186486
From word models to executable models of signaling networks using automated assembly. PMID:29175850
COGNAT: a web server for comparative analysis of genomic neighborhoods. PMID:29166914
Angiotensin II Infusion Does Not Cause Abdominal Aortic Aneurysms in Apolipoprotein E-Deficient Rats. PMID:29166645
Comparative Pan-Genome Analysis of Piscirickettsia salmonis Reveals Genomic Divergences within Genogroups. PMID:29164068
Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism. PMID:29162929
Knowledge-based prediction of protein backbone conformation using a structural alphabet. PMID:29161266
Coral-associated viral communities show high levels of diversity and host auxiliary functions. PMID:29158985
Inducible cellulase production from an organic solvent tolerant Bacillus sp. SV1 and evolutionary divergence of endoglucanase in different species of the genus Bacillus. PMID:29157901
Multidrug resistance-associated protein 4 is a bile transporter of Clonorchis sinensis simulated by in silico docking. PMID:29157307
Genomic, Transcriptomic, and Phenotypic Analyses of Neisseria meningitidis Isolates from Disease Patients and Their Household Contacts. PMID:29152586
Mucoadhesive functionality of cell wall structures from fruits and grains: Electrostatic and polymer network interactions mediated by soluble dietary polysaccharides. PMID:29150632
iPTMnet: an integrated resource for protein post-translational modification network discovery. PMID:29145615
Constraints on lateral gene transfer in promoting fimbrial usher protein diversity and function. PMID:29142104
Therapeutic target database update 2018: enriched resource for facilitating bench-to-clinic research of targeted therapeutics. PMID:29140520
Recessive VARS2 mutation underlies a novel syndrome with epilepsy, mental retardation, short stature, growth hormone deficiency, and hypogonadism. PMID:29137650
Genome sequence of the small brown planthopper, Laodelphax striatellus. PMID:29136191
Transcriptional changes measured in rice roots after exposure to arsenite-contaminated sediments. PMID:29134529
JMJD8 is a novel endoplasmic reticulum protein with a JmjC domain. PMID:29133832
The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA. PMID:29127278
MHC-I Genotype Restricts the Oncogenic Mutational Landscape. PMID:29107334
Granzyme B Disrupts Central Metabolism and Protein Synthesis in Bacteria to Promote an Immune Cell Death Program. PMID:29107333
Inter-residue, inter-protein and inter-family coevolution: bridging the scales. PMID:29101847
Year-Round Shotgun Metagenomes Reveal Stable Microbial Communities in Agricultural Soils and Novel Ammonia Oxidizers Responding to Fertilization. PMID:29101194
Cellular, ultrastructural and molecular analyses of epidermal cell development in the planarian Schmidtea mediterranea. PMID:29100657
The MAPKKK gene family in cassava: Genome-wide identification and expression analysis against drought stress. PMID:29097722
Genome-scale single-cell mechanical phenotyping reveals disease-related genes involved in mitotic rounding. PMID:29097687
SABIO-RK: an updated resource for manually curated biochemical reaction kinetics. PMID:29092055
Cyclic di-GMP differentially tunes a bacterial flagellar motor through a novel class of CheY-like regulators. PMID:29091032
MARK3-mediated phosphorylation of ARHGEF2 couples microtubules to the actin cytoskeleton to establish cell polarity. PMID:29089450
Computational methods using weighed-extreme learning machine to predict protein self-interactions with protein evolutionary information. PMID:29086182
Comparative analysis of genome sequences of the conifer tree pathogen, Heterobasidion annosum s.s. PMID:29085779
A deeper mining on the protein composition of VA-MENGOC-BC®: An OMV-based vaccine against N. meningitidis serogroup B and C. PMID:29083947
Predicting Protein Submitochondrial Locations: The 10th Anniversary. PMID:29081687
Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism. PMID:29078384
Complete Genome Sequence of Mesorhizobium sophorae ICMP 19535T, a Highly Specific, Nitrogen-Fixing Symbiont of New Zealand Endemic Sophora spp. PMID:29074646
Remodeling of the Streptococcus mutans proteome in response to LrgAB and external stresses. PMID:29070798
The maternal-zygotic transition and zygotic activation of the Mnemiopsis leidyi genome occurs within the first three cleavage cycles. PMID:29068507
Can Inhibitors of Snake Venom Phospholipases A₂ Lead to New Insights into Anti-Inflammatory Therapy in Humans? A Theoretical Study. PMID:29068410
Molecular Affinity of Mabolo Extracts to an Octopamine Receptor of a Fruit Fly. PMID:29064449
Molecular docking and simulation studies of Phyllanthus amarus phytocompounds against structural and nucleocapsid proteins of white spot syndrome virus. PMID:29062674
Xenbase: a genomic, epigenomic and transcriptomic model organism database. PMID:29059324
Confronting the catalytic dark matter encoded by sequenced genomes. PMID:29059321
Unsupervised gene expression analyses identify IPF-severity correlated signatures, associated genes and biomarkers. PMID:29058630
Preliminary comparative genomics revealed pathogenic potential and international spread of Staphylococcus argenteus. PMID:29058585
Therapeutic Innovations: Tyrosine Kinase Inhibitors in Cancer. PMID:29056714
Triterpenoids from Aglaia abbreviata exert cytotoxicity and multidrug resistant reversal effect in MCF-7/ADM cells via reactive oxygen species induction and P-glycoprotein inhibition. PMID:29050217
Proteomics analysis of bladder cancer invasion: Targeting EIF3D for therapeutic intervention. PMID:29050215
Draft genome of the gayal, Bos frontalis. PMID:29048483
AmyPro: a database of proteins with validated amyloidogenic regions. PMID:29040693
Antibodies to biotin enable large-scale detection of biotinylation sites on proteins. PMID:29039416
In Silico Prediction Analysis of Idiotope-Driven T-B Cell Collaboration in Multiple Sclerosis. PMID:29038659
DISNOR: a disease network open resource. PMID:29036667
In silico analysis of putative drug and vaccine targets of the metabolic pathways of Actinobacillus pleuropneumoniae using a subtractive/comparative genomics approach. PMID:29032659
Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer. PMID:29032074
Affected pathways and transcriptional regulators in gene expression response to an ultra-marathon trail: Global and independent activity approaches. PMID:29028836
QTLs and Potential Candidate Genes for Heat Stress Tolerance Identified from the Mapping Populations Specifically Segregating for Fv/Fm in Wheat. PMID:29021798
Physical Exercise Modulates L-DOPA-Regulated Molecular Pathways in the MPTP Mouse Model of Parkinson's Disease. PMID:29019056
Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes. PMID:28992302
A potentially crucial role of the PKD1 C-terminal tail in renal prognosis. PMID:28983800
Population-Genomic Insights into Variation in Prevotella intermedia and Prevotella nigrescens Isolates and Its Association with Periodontal Disease. PMID:28983469
Hybrid approach to structure modeling of the histamine H3 receptor: Multi-level assessment as a tool for model verification. PMID:28982153
Identification of sapovirus GV.2, astrovirus VA3 and novel anelloviruses in serum from patients with acute hepatitis of unknown aetiology. PMID:28982120
Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates. PMID:28981708
Exome-wide association study reveals novel psoriasis susceptibility locus at TNFSF15 and rare protective alleles in genes contributing to type I IFN signalling. PMID:28973304
Folding Membrane Proteins by Deep Transfer Learning. PMID:28957654
Human hepatic gene expression signature of non-alcoholic fatty liver disease progression, a meta-analysis. PMID:28955037
Parallel habitat acclimatization is realized by the expression of different genes in two closely related salamander species (genus Salamandra). PMID:28953268
γ-Carboxymuconolactone decarboxylase: a novel cell cycle-related basal body protein in the early branching eukaryote Trichomonas vaginalis. PMID:28950916
Spatial distribution of disease-associated variants in three-dimensional structures of protein complexes. PMID:28945216
Novel transcriptome resources for three scleractinian coral species from the Indo-Pacific. PMID:28938722
Characterization of Soft Amyloid Cores in Human Prion-Like Proteins. PMID:28935930
Proteomic Analysis of Phytophthora infestans Reveals the Importance of Cell Wall Proteins in Pathogenicity. PMID:28935716
Blocking the RecA activity and SOS-response in bacteria with a short α-helical peptide. PMID:28934502
HLA-DR7 and HLA-DQ2: Transgenic mouse strains tested as a model system for ximelagatran hepatotoxicity. PMID:28934241
α-Glucosidase inhibition by flavonoids: an in vitro and in silico structure-activity relationship study. PMID:28933564
Nutrient and acetate amendment leads to acetoclastic methane production and microbial community change in a non-producing Australian coal well. PMID:28925579
Alternative splicing complexity contributes to genetic improvement of drought resistance in the rice maintainer HuHan2B. PMID:28916800
Genomic analysis of exceptional responder to regorafenib in treatment-refractory metastatic rectal cancer: a case report and review of the literature. PMID:28915719
Structure-based domain assignment in Leishmania infantum EndoG: characterization of a pH-dependent regulatory switch and a C-terminal extension that largely dictates DNA substrate preferences. PMID:28911117
Combinatorial ensemble miRNA target prediction of co-regulation networks with non-prediction data. PMID:28911111
The eBioKit, a stand-alone educational platform for bioinformatics. PMID:28910280
Regulation of Neisseria meningitidis cytochrome bc1 components by NrrF, a Fur-controlled small noncoding RNA. PMID:28904860
Identification and characterization of preferred DNA-binding sites for the Thermus thermophilus transcriptional regulator FadR. PMID:28902898
The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction. PMID:28901589
Molecular Connectivity Predefines Polypharmacology: Aliphatic Rings, Chirality, and sp3 Centers Enhance Target Selectivity. PMID:28894419
Molecular details of secretory phospholipase A2 from flax (Linum usitatissimum L.) provide insight into its structure and function. PMID:28894144
Involvement of DPP9 in gene fusions in serous ovarian carcinoma. PMID:28893231
Oxidative cyclization of prodigiosin by an alkylglycerol monooxygenase-like enzyme. PMID:28892091
Novel Organelles with Elements of Bacterial and Eukaryotic Secretion Systems Weaponize Parasites of Drosophila. PMID:28889977
Monitoring storage induced changes in the platelet proteome employing label free quantitative mass spectrometry. PMID:28887518
Characterisation of the biflavonoid hinokiflavone as a pre-mRNA splicing modulator that inhibits SENP. PMID:28884683
PP2A-B' holoenzyme substrate recognition, regulation and role in cytokinesis. PMID:28884018
Modulation of Zinc Homeostasis in Acanthamoeba castellanii as a Possible Antifungal Strategy against Cryptococcus gattii. PMID:28883816
Genetic correlations reveal the shared genetic architecture of transcription in human peripheral blood. PMID:28883458
Identification of 2-hydroxyisocaproic acid production in lactic acid bacteria and evaluation of microbial dynamics during kimchi ripening. PMID:28883404
TITER: predicting translation initiation sites by deep learning. PMID:28881981
A Stat6/Pten Axis Links Regulatory T Cells with Adipose Tissue Function. PMID:28877454
Transcriptome analysis of inflammation-related gene expression in endothelial cells activated by complement MASP-1. PMID:28874747
Structures of Medicago truncatula L-Histidinol Dehydrogenase Show Rearrangements Required for NAD+ Binding and the Cofactor Positioned to Accept a Hydride. PMID:28874718
Deep Phospho- and Phosphotyrosine Proteomics Identified Active Kinases and Phosphorylation Networks in Colorectal Cancer Cell Lines Resistant to Cetuximab. PMID:28874695
Identification and Characterization of the Major Porin of Desulfovibrio vulgaris Hildenborough. PMID:28874410
Controlling Directed Protein Interaction Networks in Cancer. PMID:28871116
Autoantibody Repertoire in APECED Patients Targets Two Distinct Subgroups of Proteins. PMID:28861084
Protein-Protein Interactions in Virus-Host Systems. PMID:28861068
Position Matters: Network Centrality Considerably Impacts Rates of Protein Evolution in the Human Protein-Protein Interaction Network. PMID:28854629
The Y chromosome: a blueprint for men's health? PMID:28853720
Complete Genome sequence of the nematicidal Bacillus thuringiensis MYBT18246. PMID:28852435
Bioinformatics comparisons of RNA-binding proteins of pathogenic and non-pathogenic Escherichia coli strains reveal novel virulence factors. PMID:28836963
T-cell Responses in Individuals Infected with Zika Virus and in Those Vaccinated Against Dengue Virus. PMID:28835931
Pervasive coexpression of spatially proximal genes is buffered at the protein level. PMID:28835372
A large scale Plasmodium vivax- Saimiri boliviensis trophozoite-schizont transition proteome. PMID:28829774
Reference miRNAs for colorectal cancer: analysis and verification of current data. PMID:28827728
Eukaryotic transporters for hydroxyderivatives of benzoic acid. PMID:28827635
Acidic C-terminal domains autoregulate the RNA chaperone Hfq. PMID:28826489
Evolutionary analysis of a novel zinc ribbon in the N-terminal region of threonine synthase. PMID:28820334
MCE domain proteins: conserved inner membrane lipid-binding proteins required for outer membrane homeostasis. PMID:28819315
Landscape of submitochondrial protein distribution. PMID:28819139
Effects of the vertically transmitted microsporidian Facilispora margolisi and the parasiticide emamectin benzoate on salmon lice (Lepeophtheirus salmonis). PMID:28818044
Circadian and Feeding Rhythms Orchestrate the Diurnal Liver Acetylome. PMID:28813682
eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes. PMID:28812536
Associating mutations causing cystinuria with disease severity with the aim of providing precision medicine. PMID:28812535
Nuclear matrix metalloproteinases: functions resemble the evolution from the intracellular to the extracellular compartment. PMID:28811933
Joint inflammation related citrullination of functional arginines in extracellular proteins. PMID:28811641
Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. PMID:28810145
Molecular Rationale behind the Differential Substrate Specificity of Bacterial RND Multi-Drug Transporters. PMID:28808284
Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics. PMID:28804480
Interchromosomal Transfer of Immune Regulation During Infection of Barley with the Powdery Mildew Pathogen. PMID:28790145
Proteome profiling of s-nitrosylated synaptosomal proteins by isobaric mass tags. PMID:28789995
The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription. PMID:28787591
Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors. PMID:28787438
Spider Neurotoxins, Short Linear Cationic Peptides and Venom Protein Classification Improved by an Automated Competition between Exhaustive Profile HMM Classifiers. PMID:28786958
Regulation of gene expression in roots of the pH-sensitive Vaccinium corymbosum and the pH-tolerant Vaccinium arboreum in response to near neutral pH stress using RNA-Seq. PMID:28784085
Molecular evolution of acetohydroxyacid synthase in bacteria. PMID:28782269
The Image Data Resource: A Bioimage Data Integration and Publication Platform. PMID:28775673
Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea. PMID:28765215
T2DiACoD: A Gene Atlas of Type 2 Diabetes Mellitus Associated Complex Disorders. PMID:28761062
De novo assembly and annotation of the retinal transcriptome for the Nile grass rat (Arvicanthis ansorgei). PMID:28759564
Dynamic scaffolds for neuronal signaling: in silico analysis of the TANC protein family. PMID:28754924
Predicting Amino Acid Substitution Probabilities Using Single Nucleotide Polymorphisms. PMID:28754661
Expression and Purification of Active Recombinant Human Alpha-1 Antitrypsin (AAT) from Escherichia coli. PMID:28752459
mRNA/protein sequence complementarity and its determinants: The impact of affinity scales. PMID:28750009
Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus. PMID:28749982
Conformation and dynamics of the C-terminal region in human phosphoglycerate mutase 1. PMID:28748916
Family History of Early Infant Death Correlates with Earlier Age at Diagnosis But Not Shorter Time to Diagnosis for Severe Combined Immunodeficiency. PMID:28747913
The Protein Interactome of Streptococcus pneumoniae and Bacterial Meta-interactomes Improve Function Predictions. PMID:28744484
The evolution of duplicate gene expression in mammalian organs. PMID:28743766
p38 MAPK signaling and phosphorylations in the BRCT1 domain regulate XRCC1 recruitment to sites of DNA damage. PMID:28740101
Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule". PMID:28738801
Anion-selective Formate/nitrite transporters: taxonomic distribution, phylogenetic analysis and subfamily-specific conservation pattern in prokaryotes. PMID:28738779
Novel chaperonins are prevalent in the virioplankton and demonstrate links to viral biology and ecology. PMID:28731469
Exposure to the Epstein-Barr Viral Antigen Latent Membrane Protein 1 Induces Myelin-Reactive Antibodies In Vivo. PMID:28729867
Comparison of the protein-coding genomes of three deep-sea, sulfur-oxidising bacteria: "Candidatus Ruthia magnifica", "Candidatus Vesicomyosocius okutanii" and Thiomicrospira crunogena. PMID:28728564
Comparative analysis of signature genes in PRRSV-infected porcine monocyte-derived cells to different stimuli. PMID:28727780
Ribosomes are optimized for autocatalytic production. PMID:28726822
Knowledge base and mini-expert platform for the diagnosis of inborn errors of metabolism. PMID:28726811
MINERVA-a platform for visualization and curation of molecular interaction networks. PMID:28725475
Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica. PMID:28725468
CrossCheck: an open-source web tool for high-throughput screen data analysis. PMID:28724888
Lack of AcrB Efflux Function Confers Loss of Virulence on Salmonella enterica Serovar Typhimurium. PMID:28720734
Taltirelin alleviates fatigue-like behavior in mouse models of cancer-related fatigue. PMID:28720519
Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation. PMID:28717205
Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size. PMID:28717047
A community proposal to integrate proteomics activities in ELIXIR. PMID:28713550
Potential and active functions in the gut microbiota of a healthy human cohort. PMID:28709472
Cross-recognition of a pit viper (Crotalinae) polyspecific antivenom explored through high-density peptide microarray epitope mapping. PMID:28708892
The yeast noncoding RNA interaction network. PMID:28701522
Genome-wide identification of gene expression in contrasting maize inbred lines under field drought conditions reveals the significance of transcription factors in drought tolerance. PMID:28700592
A proteomic analysis of LRRK2 binding partners reveals interactions with multiple signaling components of the WNT/PCP pathway. PMID:28697798
A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria. PMID:28696203
Identifying and Validating Tankyrase Binders and Substrates: A Candidate Approach. PMID:28695526
Integrating Next-Generation Genomic Sequencing and Mass Spectrometry To Estimate Allele-Specific Protein Abundance in Human Brain. PMID:28691493
Dynamic ubiquitin signaling in cell cycle regulation. PMID:28684425
Identification of long non-coding RNA in the horse transcriptome. PMID:28676104
Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum. PMID:28662642
Systematic bacterialization of yeast genes identifies a near-universally swappable pathway. PMID:28661399
Replications of Two Closely Related Groups of Jumbo Phages Show Different Level of Dependence on Host-encoded RNA Polymerase. PMID:28659872
Comparative proteome analysis between C . briggsae embryos and larvae reveals a role of chromatin modification proteins in embryonic cell division. PMID:28655887
Exploring Components of the CO2-Concentrating Mechanism in Alkaliphilic Cyanobacteria Through Genome-Based Analysis. PMID:28652895
Skeletal Dysplasia Mutations Effect on Human Filamins' Structure and Mechanosensing. PMID:28652603
Stand-Alone EAL Domain Proteins Form a Distinct Subclass of EAL Proteins Involved in Regulation of Cell Motility and Biofilm Formation in Enterobacteria. PMID:28652301
Ontological interpretation of biomedical database content. PMID:28651575
Integrated molecular landscape of Parkinson's disease. PMID:28649614
Management of enzyme diversity in high-performance cellulolytic cocktails. PMID:28649275
mTORC2 Regulates Amino Acid Metabolism in Cancer by Phosphorylation of the Cystine-Glutamate Antiporter xCT. PMID:28648777
Genome analysis of Diploscapter coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction. PMID:28646875
Src family kinase phosphorylation of the motor domain of the human kinesin-5, Eg5. PMID:28646493
Comparative transcriptomic analysis of the evolution and development of flower size in Saltugilia (Polemoniaceae). PMID:28645249
Mutational Signatures Are Critical for Proper Estimation of Purifying Selection Pressures in Cancer Somatic Mutation Data When Using the dN/dS Metric. PMID:28642787
Probing the Structural Dynamics of the NMDA Receptor Activation by Coarse-Grained Modeling. PMID:28636915
Development of a range of fluorescent reagentless biosensors for ATP, based on malonyl-coenzyme A synthetase. PMID:28636641
Toll-like receptor pathway evolution in deuterostomes. PMID:28630328
MyGeneFriends: A Social Network Linking Genes, Genetic Diseases, and Researchers. PMID:28623182
ELIXIR pilot action: Marine metagenomics - towards a domain specific set of sustainable services. PMID:28620454
Streptococcus pyogenes quinolinate-salvage pathway-structural and functional studies of quinolinate phosphoribosyl transferase and NH3 -dependent NAD+ synthetase. PMID:28618168
ATria: a novel centrality algorithm applied to biological networks. PMID:28617231
Drug repositioning for enzyme modulator based on human metabolite-likeness. PMID:28617219
Characterisation of the circulating acellular proteome of healthy sheep using LC-MS/MS-based proteomics analysis of serum. PMID:28615994
3D deep convolutional neural networks for amino acid environment similarity analysis. PMID:28615003
Proteomic Analysis of Lipid Droplets from Arabidopsis Aging Leaves Brings New Insight into Their Biogenesis and Functions. PMID:28611809
Network Analysis Reveals a Common Host-Pathogen Interaction Pattern in Arabidopsis Immune Responses. PMID:28611808
Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries. PMID:28610557
Cognitive Characterization of Schizophrenia Risk Variants Involved in Synaptic Transmission: Evidence of CACNA1C's Role in Working Memory. PMID:28607492
CHOmine: an integrated data warehouse for CHO systems biology and modeling. PMID:28605771
Workflow and web application for annotating NCBI BioProject transcriptome data. PMID:28605765
Neighbours of cancer-related proteins have key influence on pathogenesis and could increase the drug target space for anticancer therapies. PMID:28603644
Coupled Caspase and N-End Rule Ligase Activities Allow Recognition and Degradation of Pluripotency Factor LIN-28 during Non-Apoptotic Development. PMID:28602583
Computational analysis of multimorbidity between asthma, eczema and rhinitis. PMID:28598986
Plant pectin acetylesterase structure and function: new insights from bioinformatic analysis. PMID:28595570
Insights into Hunter syndrome from the structure of iduronate-2-sulfatase. PMID:28593992
The Hfq regulon of Neisseria meningitidis. PMID:28593133
Network Analysis Reveals the Recognition Mechanism for Dimer Formation of Bulb-type Lectins. PMID:28588265
Prediction of bioluminescent proteins by using sequence-derived features and lineage-specific scheme. PMID:28583090
GPCR-SSFE 2.0-a fragment-based molecular modeling web tool for Class A G-protein coupled receptors. PMID:28582569
Databases, Repositories, and Other Data Resources in Structural Biology. PMID:28573593
Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. PMID:28573592
Genomewide Mutational Diversity in Escherichia coli Population Evolving in Prolonged Stationary Phase. PMID:28567442
The Agassiz's desert tortoise genome provides a resource for the conservation of a threatened species. PMID:28562605
Antigenicity of Bovine Pericardium Determined by a Novel Immunoproteomic Approach. PMID:28550302
Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study. PMID:28549454
Bacterial Virus Ontology; Coordinating across Databases. PMID:28545254
Ensemble variant interpretation methods to predict enzyme activity and assign pathogenicity in the CAGI4 NAGLU (Human N-acetyl-glucosaminidase) and UBE2I (Human SUMO-ligase) challenges. PMID:28544272
Integration of Tmc1/2 into the mechanotransduction complex in zebrafish hair cells is regulated by Transmembrane O-methyltransferase (Tomt). PMID:28534737
Radiation induced pulmonary fibrosis as a model of progressive fibrosis: Contributions of DNA damage, inflammatory response and cellular senescence genes. PMID:28534660
Structure-based prediction of Wnt binding affinities for Frizzled-type cysteine-rich domains. PMID:28533339
In silico approach to designing rational metagenomic libraries for functional studies. PMID:28532384
Recognition of a structural domain (RWDBD) in Gcn1 proteins that interacts with the RWD domain containing proteins. PMID:28526057
Gene expression of Vibrio parahaemolyticus growing in laboratory isolation conditions compared to those common in its natural ocean environment. PMID:28525966
One Year Genome Evolution of Lausannevirus in Allopatric versus Sympatric Conditions. PMID:28525571
Histone deacetylase 10 structure and molecular function as a polyamine deacetylase. PMID:28516954
Comparative Analysis of Immune Checkpoint Molecules and Their Potential Role in the Transmissible Tasmanian Devil Facial Tumor Disease. PMID:28515726
Flavin-containing monooxygenases in aging and disease: Emerging roles for ancient enzymes. PMID:28515321
Applications of contact predictions to structural biology. PMID:28512576
De novo Transcriptome Profiling of Flowers, Flower Pedicels and Pods of Lupinus luteus (Yellow Lupine) Reveals Complex Expression Changes during Organ Abscission. PMID:28512462
The Whole-Genome and Transcriptome of the Manila Clam (Ruditapes philippinarum). PMID:28505302
APC/CCdh1 Enables Removal of Shugoshin-2 from the Arms of Bivalent Chromosomes by Moderating Cyclin-Dependent Kinase Activity. PMID:28502659
GenProBiS: web server for mapping of sequence variants to protein binding sites. PMID:28498966
compleXView: a server for the interpretation of protein abundance and connectivity information to identify protein complexes. PMID:28498958
Specific MicroRNA Pattern in Colon Tissue of Young Children with Eosinophilic Colitis. PMID:28498330
The mitochondrial SIR2 related protein 2 (SIR2RP2) impacts Leishmania donovani growth and infectivity. PMID:28493888
Selectivity determinants of GPCR-G-protein binding. PMID:28489817
PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants. PMID:28482034
Unbiased Protein Association Study on the Public Human Proteome Reveals Biological Connections between Co-Occurring Protein Pairs. PMID:28480704
The RNA Exosome Syncs IAV-RNAPII Transcription to Promote Viral Ribogenesis and Infectivity. PMID:28475896
Bioinformatic and expression analysis of the Brassica napus L. cyclophilins. PMID:28473712
WebGIVI: a web-based gene enrichment analysis and visualization tool. PMID:28472919
PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database. PMID:28472422
Using hyperLOPIT to perform high-resolution mapping of the spatial proteome. PMID:28471460
NLRP3 inflammasome assembly is regulated by phosphorylation of the pyrin domain. PMID:28465465
Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range. PMID:28464870
Crude oil impairs immune function and increases susceptibility to pathogenic bacteria in southern flounder. PMID:28464028
Sirtuin 2 mutations in human cancers impair its function in genome maintenance. PMID:28461331
Insights into Ciliary Genes and Evolution from Multi-Level Phylogenetic Profiling. PMID:28460059
The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression. PMID:28459453
Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development. PMID:28459448
Methods, Tools and Current Perspectives in Proteogenomics. PMID:28456751
A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra. PMID:28453668
The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation. PMID:28453653
Neuro-symbolic representation learning on biological knowledge graphs. PMID:28449114
Integrated analysis of individual codon contribution to protein biosynthesis reveals a new approach to improving the basis of rational gene design. PMID:28449100
Characterization and expression analysis of Galnts in developing Strongylocentrotus purpuratus embryos. PMID:28448610
Systems biology guided by XCMS Online metabolomics. PMID:28448069
Model-enabled gene search (MEGS) allows fast and direct discovery of enzymatic and transport gene functions in the marine bacterium Vibrio fischeri. PMID:28446608
ChloroKB: A Web Application for the Integration of Knowledge Related to Chloroplast Metabolic Network. PMID:28442501
Ancient genes establish stress-induced mutation as a hallmark of cancer. PMID:28441401
The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions. PMID:28439458
Distinct Conformational Dynamics of Three G Protein-Coupled Receptors Measured Using FlAsH-BRET Biosensors. PMID:28439254
Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human. PMID:28438136
N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana. PMID:28432195
Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut. PMID:28431252
DNAproDB: an interactive tool for structural analysis of DNA-protein complexes. PMID:28431131
The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae). PMID:28431014
The effects of DLEU1 gene expression in Burkitt lymphoma (BL): potential mechanism of chemoimmunotherapy resistance in BL. PMID:28427156
Oncodomains: A protein domain-centric framework for analyzing rare variants in tumor samples. PMID:28426665
Novel interactions of the von Hippel-Lindau (pVHL) tumor suppressor with the CDKN1 family of cell cycle inhibitors. PMID:28425505
Identification of protein features encoded by alternative exons using Exon Ontology. PMID:28420690
Membrane potential independent transport of NH3 in the absence of ammonium permeases in Saccharomyces cerevisiae. PMID:28412970
Opportunities for developing therapies for rare genetic diseases: focus on gain-of-function and allostery. PMID:28412959
Tspan2: a tetraspanin protein involved in oligodendrogenesis and cancer metastasis. PMID:28408487
A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. PMID:28402429
The human retinoblastoma susceptibility gene (RB1): an evolutionary story in primates. PMID:28401291
Modeling disordered protein interactions from biophysical principles. PMID:28394890
Next-generation approaches to understand and combat the antibiotic resistome. PMID:28392565
SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions. PMID:28387819
Common Polymorphisms in IFI16 and AIM2 Genes Are Associated With Periodontal Disease. PMID:28387608
Genome Sequence of Mannheimia haemolytica Serotype 1 Strain 16041065 BH. PMID:28385859
Genome Sequence of a Spontaneous Nonhemolytic Mutant of Mannheimia haemolytica 16041065 GH. PMID:28385858
A curated gluten protein sequence database to support development of proteomics methods for determination of gluten in gluten-free foods. PMID:28385663
Badger macrophages fail to produce nitric oxide, a key anti-mycobacterial effector molecule. PMID:28382943
DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins. PMID:28381244
Genomic and transcriptomic landscape of Escherichia coli BL21(DE3). PMID:28379538
Core Genes Evolve Rapidly in the Long-Term Evolution Experiment with Escherichia coli. PMID:28379360
Quantitative proteomics by SWATH-MS reveals sophisticated metabolic reprogramming in hepatocellular carcinoma tissues. PMID:28378759
Identification of autoreactive B cells with labeled nucleosomes. PMID:28377609
Origin and Evolutionary Alteration of the Mitochondrial Import System in Eukaryotic Lineages. PMID:28369657
Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants. PMID:28369350
Klinefelter syndrome comorbidities linked to increased X chromosome gene dosage and altered protein interactome activity. PMID:28369266
Loss of the Arp2/3 complex component ARPC1B causes platelet abnormalities and predisposes to inflammatory disease. PMID:28368018
Proteomic signature of muscle fibre hyperplasia in response to faba bean intake in grass carp. PMID:28367976
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation. PMID:28365736
Better living through ontologies at the Immune Epitope Database. PMID:28365732
Biocuration in the structure-function linkage database: the anatomy of a superfamily. PMID:28365730
SilkPathDB: a comprehensive resource for the study of silkworm pathogens. PMID:28365723
VerSeDa: vertebrate secretome database. PMID:28365718
SheddomeDB: the ectodomain shedding database for membrane-bound shed markers. PMID:28361715
Draft Genome Sequences of Three Cellulolytic Bacillus licheniformis Strains Isolated from Imperial Geyser, Amphitheater Springs, and Whiterock Springs inside Yellowstone National Park. PMID:28360181
Transcriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver. PMID:28360091
HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency. PMID:28358052
The druggable genome and support for target identification and validation in drug development. PMID:28356508
Evolutionary origin and function of NOX4-art, an arthropod specific NADPH oxidase. PMID:28356077
High GC content causes orphan proteins to be intrinsically disordered. PMID:28355220
DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome. PMID:28355180
Genomic profiling reveals mutational landscape in parathyroid carcinomas. PMID:28352668
Metaproteogenomics Reveals Taxonomic and Functional Changes between Cecal and Fecal Microbiota in Mouse. PMID:28352255
Modification of the Streptococcus mutans transcriptome by LrgAB and environmental stressors. PMID:28348880
Systematic identification of phosphorylation-mediated protein interaction switches. PMID:28346509
Genomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressure. PMID:28341699
Bivariate genomic analysis identifies a hidden locus associated with bacteria hypersensitive response in Arabidopsis thaliana. PMID:28338080
APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins. PMID:28334975
ProtVista: visualization of protein sequence annotations. PMID:28334231
Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity. PMID:28334201
Improving transcriptome de novo assembly by using a reference genome of a related species: Translational genomics from oil palm to coconut. PMID:28334050
On the potential of using peculiarities of the protein intrinsic disorder distribution in mitochondrial cytochrome b to identify the source of animal meats. PMID:28331777
Comprehensive Transcriptome Analyses Reveal that Potato Spindle Tuber Viroid Triggers Genome-Wide Changes in Alternative Splicing, Inducible trans-Acting Activity of Phased Secondary Small Interfering RNAs, and Immune Responses. PMID:28331096
Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration. PMID:28328943
Elevated fecal peptidase D at onset of colitis in Galphai2-/- mice, a mouse model of IBD. PMID:28323866
Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae). PMID:28320315
Proteomic data on enzyme secretion and activity in the bacterium Chitinophaga pinensis. PMID:28317006
Peptidomic and transcriptomic profiling of four distinct spider venoms. PMID:28306751
Covariation of Peptide Abundances Accurately Reflects Protein Concentration Differences. PMID:28302922
Development of Bioinformatics Infrastructure for Genomics Research. PMID:28302555
Whole exome sequencing in the Framingham Heart Study identifies rare variation in HYAL2 that influences platelet aggregation. PMID:28300864
Systems-level understanding of ethanol-induced stresses and adaptation in E. coli. PMID:28300180
Systematic protein-protein interaction mapping for clinically relevant human GPCRs. PMID:28298427
Systematic identification of an integrative network module during senescence from time-series gene expression. PMID:28298218
Network reconstruction of the mouse secretory pathway applied on CHO cell transcriptome data. PMID:28298216
Phosphorylation-Induced Mechanical Regulation of Intrinsically Disordered Neurofilament Proteins. PMID:28297648
A new group of glycoside hydrolase family 13 α-amylases with an aberrant catalytic triad. PMID:28287181
Structural basis of homo- and heterotrimerization of collagen I. PMID:28281531
Therapeutic Potential for Bone Morphogenetic Protein 4 in Human Malignant Glioma. PMID:28278424
Structural and functional characterization of a ubiquitin variant engineered for tight and specific binding to an alpha-helical ubiquitin interacting motif. PMID:28276594
Systemic QSAR and phenotypic virtual screening: chasing butterflies in drug discovery. PMID:28274840
Analysis of triglyceride synthesis unveils a green algal soluble diacylglycerol acyltransferase and provides clues to potential enzymatic components of the chloroplast pathway. PMID:28274201
Bioinformatics analysis of the proteins interacting with LASP-1 and their association with HBV-related hepatocellular carcinoma. PMID:28266596
Regulation of Cell Polarity by Exocyst-Mediated Trafficking. PMID:28264817
A temporal proteome dynamics study reveals the molecular basis of induced phenotypic resistance in Mycobacterium smegmatis at sub-lethal rifampicin concentrations. PMID:28262820
Inhibition of DNA and Histone Methylation by 5-Aza-2'-Deoxycytidine (Decitabine) and 3-Deazaneplanocin-A on Antineoplastic Action and Gene Expression in Myeloid Leukemic Cells. PMID:28261562
Reactome pathway analysis: a high-performance in-memory approach. PMID:28249561
The amyloid interactome: Exploring protein aggregation. PMID:28249044
Comparative "Golgi" Proteome Study of Lolium multiflorum and Populus trichocarpa. PMID:28248233
The ancestors of diatoms evolved a unique mitochondrial dehydrogenase to oxidize photorespiratory glycolate. PMID:28247236
String kernels for protein sequence comparisons: improved fold recognition. PMID:28245816
A new genome-mining tool redefines the lasso peptide biosynthetic landscape. PMID:28244986
A three-way approach for protein function classification. PMID:28234929
Semi-quantitative proteomics of mammalian cells upon short-term exposure to non-ionizing electromagnetic fields. PMID:28234898
Evolutionary, computational, and biochemical studies of the salicylaldehyde dehydrogenases in the naphthalene degradation pathway. PMID:28233868
CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor. PMID:28232751
Regulation of Na+ channel inactivation by the DIII and DIV voltage-sensing domains. PMID:28232510
Identification of Genes in Saccharomyces cerevisiae that Are Haploinsufficient for Overcoming Amino Acid Starvation. PMID:28209762
The Escherichia coli COG1738 Member YhhQ Is Involved in 7-Cyanodeazaguanine (preQ₀) Transport. PMID:28208705
The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection. PMID:28207819
Empirical comparison of web-based antimicrobial peptide prediction tools. PMID:28203715
nala: text mining natural language mutation mentions. PMID:28200120
Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. PMID:28200013
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. PMID:28190782
Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis. PMID:28189581
KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba). PMID:28187156
HIPPI: highly accurate protein family classification with ensembles of HMMs. PMID:28185571
Complete Amino Acid Sequence of a Copper/Zinc-Superoxide Dismutase from Ginger Rhizome. PMID:28185046
The complex evolutionary history of aminoacyl-tRNA synthetases. PMID:28180287
Epidermal Growth Factor Pathway Signaling in Drosophila Embryogenesis: Tools for Understanding Cancer. PMID:28178204
Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions. PMID:28176778
Dosage sensitivity is a major determinant of human copy number variant pathogenicity. PMID:28176757
SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments. PMID:28172591
Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression. PMID:28170390
A rapid method for selecting suitable animal species for studying pathogen interactions with plasma protein ligands in vivo. PMID:28168836
The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement. PMID:28167525
Whole-genome sequencing of a Plasmodium vivax clinical isolate exhibits geographical characteristics and high genetic variation in China-Myanmar border area. PMID:28166727
Diversity and functions of the sheep faecal microbiota: a multi-omic characterization. PMID:28165194
Expanding Proteome Coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) Combined with Broad Specificity Proteolysis. PMID:28164708
The Carboxy Terminus of YCF1 Contains a Motif Conserved throughout >500 Myr of Streptophyte Evolution. PMID:28164224
From the research laboratory to the database: the Caenorhabditis elegans kinome in UniProtKB. PMID:28159896
An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge. PMID:28158609
Deep-proteome mapping of WM-266-4 human metastatic melanoma cells: From oncogenic addiction to druggable targets. PMID:28158294
Identifying Functional Cysteine Residues in the Mitochondria. PMID:28157297
MORO: a Cytoscape app for relationship analysis between modularity and robustness in large-scale biological networks. PMID:28155725
Identifying the missing proteins in human proteome by biological language model. PMID:28155671
Theoretical analysis of somatostatin receptor 5 with antagonists and agonists for the treatment of neuroendocrine tumors. PMID:28155055
Transcriptomic investigation of wound healing and regeneration in the cnidarian Calliactis polypus. PMID:28150733
Investigation of PDE5/PDE6 and PDE5/PDE11 selective potent tadalafil-like PDE5 inhibitors using combination of molecular modeling approaches, molecular fingerprint-based virtual screening protocols and structure-based pharmacophore development. PMID:28150511
iPTMnet: Integrative Bioinformatics for Studying PTM Networks. PMID:28150246
Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature. PMID:28150240
UniProt Protein Knowledgebase. PMID:28150232
Protein Bioinformatics Databases and Resources. PMID:28150231
Evaluation of a hypothetical protein for serodiagnosis and as a potential marker for post-treatment serological evaluation of tegumentary leishmaniasis patients. PMID:28150041
Association of DPP-4 activity with BMD, body composition, and incident hip fracture: the Cardiovascular Health Study. PMID:28150034
Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy. PMID:28149702
Bacillus thuringiensis and Bacillus weihenstephanensis Inhibit the Growth of Phytopathogenic Verticillium Species. PMID:28149292
Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in Bacteroides coprocola. PMID:28143583
Skewing in Arabidopsis roots involves disparate environmental signaling pathways. PMID:28143395
Lausannevirus Encodes a Functional Dihydrofolate Reductase Susceptible to Proguanil. PMID:28137801
Genomic Features of the Damselfly Calopteryx splendens Representing a Sister Clade to Most Insect Orders. PMID:28137743
Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators. PMID:28135246
Computational predictors fail to identify amino acid substitution effects at rheostat positions. PMID:28134345
Exploring the dark foldable proteome by considering hydrophobic amino acids topology. PMID:28134276
Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function. PMID:28133437
Distinct Growth and Secretome Strategies for Two Taxonomically Divergent Brown Rot Fungi. PMID:28130302
Identification of Entry Factors Involved in Hepatitis C Virus Infection Based on Host-Mimicking Short Linear Motifs. PMID:28129350
Multivalency in Rab effector interactions. PMID:28129037
The Protein Structure Context of PolyQ Regions. PMID:28125688
Comparative Analysis of Mitochondrial N-Termini from Mouse, Human, and Yeast. PMID:28122942
A Golden Age for Working with Public Proteomics Data. PMID:28118949
3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets. PMID:28115009
Quantification by nano liquid chromatography parallel reaction monitoring mass spectrometry of human apolipoprotein A-I, apolipoprotein B, and hemoglobin A1c in dried blood spots. PMID:28112871
SecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems. PMID:28112271
TOMATOMICS: A Web Database for Integrated Omics Information in Tomato. PMID:28111364
The systematic analysis of coding and long non-coding RNAs in the sub-chronic and chronic stages of spinal cord injury. PMID:28106101
GDE2 is essential for neuronal survival in the postnatal mammalian spinal cord. PMID:28103900
Splenic CD4+ T Cells in Progressive Visceral Leishmaniasis Show a Mixed Effector-Regulatory Phenotype and Impair Macrophage Effector Function through Inhibitory Receptor Expression. PMID:28103263
MarpoDB: An Open Registry for Marchantia Polymorpha Genetic Parts. PMID:28100647
An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. PMID:28100185
Conserved gene expression in sperm reservoirs between birds and mammals in response to mating. PMID:28100167
A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors. PMID:28099853
Differential Contribution of Transmembrane Domains IV, V, VI, and VII to Human Angiotensin II Type 1 Receptor Homomer Formation. PMID:28096461
In situ structure of trypanosomal ATP synthase dimer reveals a unique arrangement of catalytic subunits. PMID:28096380
The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights. PMID:28095778
Unraveling the microbial processes of black band disease in corals through integrated genomics. PMID:28094312
Structural insights into the mechanism of the DEAH-box RNA helicase Prp43. PMID:28092261
Comprehensive proteome analysis of lysosomes reveals the diverse function of macrophages in immune responses. PMID:28088779
Evolution of the angiopoietin-like gene family in teleosts and their role in skin regeneration. PMID:28086749
Direct Heme Uptake by Phytoplankton-Associated Roseobacter Bacteria. PMID:28083564
Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease. PMID:28081260
Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD). PMID:28079125
Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study. PMID:28077566
CIDER: Resources to Analyze Sequence-Ensemble Relationships of Intrinsically Disordered Proteins. PMID:28076807
O-GlcNAcylation of STAT5 controls tyrosine phosphorylation and oncogenic transcription in STAT5-dependent malignancies. PMID:28074064
A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea. PMID:28073944
Reading the Evolution of Compartmentalization in the Ribosome Assembly Toolbox: The YRG Protein Family. PMID:28072865
Suppression of C9orf72 RNA repeat-induced neurotoxicity by the ALS-associated RNA-binding protein Zfp106. PMID:28072389
Embryonic origin of adult stem cells required for tissue homeostasis and regeneration. PMID:28072387
De novo assembly, annotation, and characterization of the whole brain transcriptome of male and female Syrian hamsters. PMID:28071753
Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes. PMID:28069893
The chaperonin TRiC forms an oligomeric complex in the malaria parasite cytosol. PMID:28067475
Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers. PMID:28067311
Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation. PMID:28067254
Toward the next step in G protein-coupled receptor research: a knowledge-driven analysis for the next potential targets in drug discovery. PMID:28063110
Plant genome and transcriptome annotations: from misconceptions to simple solutions. PMID:28062412
Molecular and structural characteristics of multidrug resistance-associated protein 7 in Chinese liver fluke Clonorchis sinensis. PMID:28058535
KinMap: a web-based tool for interactive navigation through human kinome data. PMID:28056780
Functional constraints on adaptive evolution of protein ubiquitination sites. PMID:28054638
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Functional analysis of Brassica napus phloem protein and ribonucleoprotein complexes. PMID:28052459
REST corepressors RCOR1 and RCOR2 and the repressor INSM1 regulate the proliferation-differentiation balance in the developing brain. PMID:28049845
Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges. PMID:28049838
High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes. PMID:28042959
GC Content Heterogeneity Transition of Conserved Noncoding Sequences Occurred at the Emergence of Vertebrates. PMID:28040773
Global Analysis of Protein Expression of Inner Ear Hair Cells. PMID:28039372
Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools. PMID:28035947
Integrated molecular landscape of amyotrophic lateral sclerosis provides insights into disease etiology. PMID:28035716
DTNI: a novel toxicogenomics data analysis tool for identifying the molecular mechanisms underlying the adverse effects of toxic compounds. PMID:28032149
Longitudinal Analysis of Serum Autoantibody-Reactivities in Patients with Primary Open Angle Glaucoma and Optic Disc Hemorrhage. PMID:28030545
viruSITE-integrated database for viral genomics. PMID:28025349
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges. PMID:28025348
On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase. PMID:28025337
Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow. PMID:28025336
Minimizing proteome redundancy in the UniProt Knowledgebase. PMID:28025334
Genetic Algorithm Managed Peptide Mutant Screening: Optimizing Peptide Ligands for Targeted Receptor Binding. PMID:28024403
Data on Rad51 amino acid sequences from higher and lower eukaryotic model organisms and parasites. PMID:28018950
Developing integrated crop knowledge networks to advance candidate gene discovery. PMID:28018846
Identification and Network-Enabled Characterization of Auxin Response Factor Genes in Medicago truncatula. PMID:28018393
Association of Cell Adhesion Molecules Contactin-6 and Latrophilin-1 Regulates Neuronal Apoptosis. PMID:28018171
VaProS: a database-integration approach for protein/genome information retrieval. PMID:28012137
Driver gene classification reveals a substantial overrepresentation of tumor suppressors among very large chromatin-regulating proteins. PMID:28008934
Structure and Function of the TIR Domain from the Grape NLR Protein RPV1. PMID:28008335
Secreted Proteins Defy the Expression Level-Evolutionary Rate Anticorrelation. PMID:28007979
Genomic Basis of Adaptive Evolution: The Survival of Amur Ide (Leuciscus waleckii) in an Extremely Alkaline Environment. PMID:28007977
New CRISPR-Cas systems from uncultivated microbes. PMID:28005056
GPS-PAIL: prediction of lysine acetyltransferase-specific modification sites from protein sequences. PMID:28004786
MMP19 expression in the human optic nerve. PMID:28003733
Proteomic Profiling of Serial Prediagnostic Serum Samples for Early Detection of Colon Cancer in the U.S. Military. PMID:28003179
Identification of DEP domain-containing proteins by a machine learning method and experimental analysis of their expression in human HCC tissues. PMID:28000796
Association of adipocyte enhancer-binding protein 1 with Alzheimer's disease pathology in human hippocampi. PMID:27997051
Toward amino acid typing for proteins in FFLUX. PMID:27991680
When Does Chemical Elaboration Induce a Ligand To Change Its Binding Mode? PMID:27982595
ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants. PMID:27980519
The BioGRID interaction database: 2017 update. PMID:27980099
Leigh map: A novel computational diagnostic resource for mitochondrial disease. PMID:27977873
The Complex Transcriptional Response of Acaryochloris marina to Different Oxygen Levels. PMID:27974439
The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance. PMID:27974049
PluriPred: AWeb server for predicting proteins involved in pluripotent network. PMID:27966493
A conserved bacterial protein induces pancreatic beta cell expansion during zebrafish development. PMID:27960075
Improved genome-scale multi-target virtual screening via a novel collaborative filtering approach to cold-start problem. PMID:27958331
The Use of Peptide Markers of Carp and Herring Allergens as an Example of Detection of Sequenced and Non-Sequenced Proteins. PMID:27956857
High fidelity visualization of cell-to-cell variation and temporal dynamics in nascent extracellular matrix formation. PMID:27941914
Genetic invalidation of Lp-PLA2 as a therapeutic target: Large-scale study of five functional Lp-PLA2-lowering alleles. PMID:27940953
An Optimized Chromatographic Strategy for Multiplexing In Parallel Reaction Monitoring Mass Spectrometry: Insights from Quantitation of Activated Kinases. PMID:27940637
Proteome-Scale Investigation of Protein Allosteric Regulation Perturbed by Somatic Mutations in 7,000 Cancer Genomes. PMID:27939638
Intensification: A Resource for Amplifying Population-Genetic Signals with Protein Repeats. PMID:27939289
Insecticidal Activity of Melaleuca alternifolia Essential Oil and RNA-Seq Analysis of Sitophilus zeamais Transcriptome in Response to Oil Fumigation. PMID:27936192
Structure-Based Scaffold Repurposing for G Protein-Coupled Receptors: Transformation of Adenosine Derivatives into 5HT2B/5HT2C Serotonin Receptor Antagonists. PMID:27933810
Exploring FlyBase Data Using QuickSearch. PMID:27930807
Analysis of Domain Architecture and Phylogenetics of Family 2 Glycoside Hydrolases (GH2). PMID:27930742
Deep Insight into the Phosphatomes of Parasitic Protozoa and a Web Resource ProtozPhosDB. PMID:27930683
Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules-Search Options and Applications in Food Science. PMID:27929431
Site-specific glycosylation of the Newcastle disease virus haemagglutinin-neuraminidase. PMID:27928741
Multiple selection filters ensure accurate tail-anchored membrane protein targeting. PMID:27925580
Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins. PMID:27924270
PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. PMID:27924042
FARNA: knowledgebase of inferred functions of non-coding RNA transcripts. PMID:27924038
BRENDA in 2017: new perspectives and new tools in BRENDA. PMID:27924025
DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. PMID:27924018
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. PMID:27924014
Identification of critical paralog groups with indispensable roles in the regulation of signaling flow. PMID:27922122
A Novel Transcriptional Regulator Related to Thiamine Phosphate Synthase Controls Thiamine Metabolism Genes in Archaea. PMID:27920295
Three-dimensional Modelling of the Voltage-gated Sodium Ion Channel from Anopheles gambiae Reveals Spatial Clustering of Evolutionarily Conserved Acidic Residues at the Extracellular Sites. PMID:27919210
The crystal structure of dihydrodipicolinate reductase from the human-pathogenic bacterium Bartonella henselae strain Houston-1 at 2.3 Å resolution. PMID:27917836
Novel PIGT Variant in Two Brothers: Expansion of the Multiple Congenital Anomalies-Hypotonia Seizures Syndrome 3 Phenotype. PMID:27916860
The orphan G protein-coupled receptor GPR139 is activated by the peptides: Adrenocorticotropic hormone (ACTH), α-, and β-melanocyte stimulating hormone (α-MSH, and β-MSH), and the conserved core motif HFRW. PMID:27916541
Assembling the Tat protein translocase. PMID:27914200
Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis. PMID:27911809
The genetic basis and fitness consequences of sperm midpiece size in deer mice. PMID:27910854
mutLBSgeneDB: mutated ligand binding site gene DataBase. PMID:27907895
Maximized Autotransporter-Mediated Expression (MATE) for Surface Display and Secretion of Recombinant Proteins in Escherichia coli. PMID:27904356
dbSAP: single amino-acid polymorphism database for protein variation detection. PMID:27903894
Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine. PMID:27902695
Glycosaminoglycanomics: where we are. PMID:27900575
A novel hypothesis for histone-to-protamine transition in Bos taurus spermatozoa. PMID:27899719
The SWISS-MODEL Repository-new features and functionality. PMID:27899672
RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures. PMID:27899671
Open Targets: a platform for therapeutic target identification and validation. PMID:27899665
KEGG: new perspectives on genomes, pathways, diseases and drugs. PMID:27899662
InterPro in 2017-beyond protein family and domain annotations. PMID:27899635
European Nucleotide Archive in 2016. PMID:27899630
UniProt: the universal protein knowledgebase. PMID:27899622
RAID v2.0: an updated resource of RNA-associated interactions across organisms. PMID:27899615
PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements. PMID:27899595
CATH: an expanded resource to predict protein function through structure and sequence. PMID:27899584
OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs. PMID:27899580
Ensembl 2017. PMID:27899575
Uniclust databases of clustered and deeply annotated protein sequences and alignments. PMID:27899574
WormBase ParaSite - a comprehensive resource for helminth genomics. PMID:27899279
The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize. PMID:27899149
Transcriptomic Analysis Implicates the p53 Signaling Pathway in the Establishment of HIV-1 Latency in Central Memory CD4 T Cells in an In Vitro Model. PMID:27898737
Biochemical Characterization of Glutamate Racemase-A New Candidate Drug Target against Burkholderia cenocepacia Infections. PMID:27898711
Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases. PMID:27898009
The Human Skeletal Muscle Proteome Project: a reappraisal of the current literature. PMID:27897395
A potential founder variant in CARMIL2/RLTPR in three Norwegian families with warts, molluscum contagiosum, and T-cell dysfunction. PMID:27896283
Single Amino Acid Repeats in the Proteome World: Structural, Functional, and Evolutionary Insights. PMID:27893794
Computational Discovery of Putative Leads for Drug Repositioning through Drug-Target Interaction Prediction. PMID:27893735
A scored human protein-protein interaction network to catalyze genomic interpretation. PMID:27892958
The Proline/Glycine-Rich Region of the Biofilm Adhesion Protein Aap Forms an Extended Stalk that Resists Compaction. PMID:27890783
Genome-wide transcriptome analysis revealed organelle specific responses to temperature variations in algae. PMID:27883062
MathIOmica: An Integrative Platform for Dynamic Omics. PMID:27883025
Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences. PMID:27881428
Pre- and post-weaning diet alters the faecal metagenome in the cat with differences in vitamin and carbohydrate metabolism gene abundances. PMID:27876765
Accelerating Information Retrieval from Profile Hidden Markov Model Databases. PMID:27875548
The genome of Onchocerca volvulus, agent of river blindness. PMID:27869790
The ERF transcription factor family in cassava: genome-wide characterization and expression analyses against drought stress. PMID:27869212
mRNA changes in nucleus accumbens related to methamphetamine addiction in mice. PMID:27869204
Caenorhabditis elegans as a model system to study post-translational modifications of human transthyretin. PMID:27869126
De-novo protein function prediction using DNA binding and RNA binding proteins as a test case. PMID:27869118
Establishing a reference array for the CS-αβ superfamily of defensive peptides. PMID:27863510
Observation selection bias in contact prediction and its implications for structural bioinformatics. PMID:27857150
Protein ligand-specific binding residue predictions by an ensemble classifier. PMID:27855637
Choosing panels of genomics assays using submodular optimization. PMID:27846892
EYS Is a Protein Associated with the Ciliary Axoneme in Rods and Cones. PMID:27846257
Membrane Proteomic Insights into the Physiology and Taxonomy of an Oleaginous Green Microalga. PMID:27837088
Extracellular Protein Phosphorylation, the Neglected Side of the Modification. PMID:27834735
GWAS analysis of QTL for enteric septicemia of catfish and their involved genes suggest evolutionary conservation of a molecular mechanism of disease resistance. PMID:27826737
RNA Sequencing-Based Genome Reannotation of the Dermatophyte Arthroderma benhamiae and Characterization of Its Secretome and Whole Gene Expression Profile during Infection. PMID:27822542
Local Action with Global Impact: Highly Similar Infection Patterns of Human Viruses and Bacteriophages. PMID:27822522
Pyrimidine Salvage Enzymes Are Essential for De Novo Biosynthesis of Deoxypyrimidine Nucleotides in Trypanosoma brucei. PMID:27820863
Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver. PMID:27818260
Transcription factor ZNF25 is associated with osteoblast differentiation of human skeletal stem cells. PMID:27814695
Evaluating Functional Annotations of Enzymes Using the Gene Ontology. PMID:27812939
The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand. PMID:27812150
Sequence Determinants of the Conformational Properties of an Intrinsically Disordered Protein Prior to and upon Multisite Phosphorylation. PMID:27807972
FlhF Is Required for Swarming Motility and Full Pathogenicity of Bacillus cereus. PMID:27807433
Genomic Analysis of Vulcanisaeta thermophila Type Strain CBA1501T Isolated from Solfataric Soil. PMID:27807432
Large-scale gene co-expression network as a source of functional annotation for cattle genes. PMID:27806696
Insights into the innate immunome of actiniarians using a comparative genomic approach. PMID:27806695
Recombinant oncolytic poliovirus, PVSRIPO, has potent cytotoxic and innate inflammatory effects, mediating therapy in human breast and prostate cancer xenograft models. PMID:27806313
Genenames.org: the HGNC and VGNC resources in 2017. PMID:27799471
FlyBase at 25: looking to the future. PMID:27799470
Plant Reactome: a resource for plant pathways and comparative analysis. PMID:27799469
yMap: an automated method to map yeast variants to protein modifications and functional regions. PMID:27797766
Identification of a New Lipoprotein Export Signal in Gram-Negative Bacteria. PMID:27795390
The RCSB protein data bank: integrative view of protein, gene and 3D structural information. PMID:27794042
Navigating the dynamic landscape of long noncoding RNA and protein-coding gene annotations in GENCODE. PMID:27793185
Rare Variants in Neurodegeneration Associated Genes Revealed by Targeted Panel Sequencing in a German ALS Cohort. PMID:27790088
CGDB: a database of circadian genes in eukaryotes. PMID:27789706
Proteome-pI: proteome isoelectric point database. PMID:27789699
WERAM: a database of writers, erasers and readers of histone acetylation and methylation in eukaryotes. PMID:27789692
TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions. PMID:27789689
Genetic Variants in Isolated Ebstein Anomaly Implicated in Myocardial Development Pathways. PMID:27788187
Flexible Data Analysis Pipeline for High-Confidence Proteogenomics. PMID:27786492
Draft genome of the leopard gecko, Eublepharis macularius. PMID:27784328
Genomic skimming for identification of medium/highly abundant transposable elements in Arundo donax and Arundo plinii. PMID:27778102
M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity. PMID:27776117
Synthesis, biological evaluation and molecular modeling studies on novel quinonoid inhibitors of CDC25 phosphatases. PMID:27774816
Metabolic Complementation in Bacterial Communities: Necessary Conditions and Optimality. PMID:27774085
SR-BI: Linking Cholesterol and Lipoprotein Metabolism with Breast and Prostate Cancer. PMID:27774064
Expanding the archaellum regulatory network - the eukaryotic protein kinases ArnC and ArnD influence motility of Sulfolobus acidocaldarius. PMID:27771939
IPC - Isoelectric Point Calculator. PMID:27769290
C9orf72 Dipeptide Repeats Impair the Assembly, Dynamics, and Function of Membrane-Less Organelles. PMID:27768896
High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells. PMID:27768875
PreTIS: A Tool to Predict Non-canonical 5' UTR Translational Initiation Sites in Human and Mouse. PMID:27768687
Identification of internalin-A-like virulent proteins in Leishmania donovani. PMID:27765050
Proteomic analysis reveals diverse proline hydroxylation-mediated oxygen-sensing cellular pathways in cancer cells. PMID:27764789
Comparative Analysis of Membrane Vesicles from Three Piscirickettsia salmonis Isolates Reveals Differences in Vesicle Characteristics. PMID:27764198
Single nucleotide variant discovery of highly inbred Leghorn and Fayoumi chicken breeds using pooled whole genome resequencing data reveals insights into phenotype differences. PMID:27760519
Convert your favorite protein modeling program into a mutation predictor: "MODICT". PMID:27760515
HieranoiDB: a database of orthologs inferred by Hieranoid. PMID:27742821
Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling. PMID:27735058
Charging of Proteins in Native Mass Spectrometry. PMID:27734326
Identification of self-interacting proteins by exploring evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix. PMID:27732957
KinView: a visual comparative sequence analysis tool for integrated kinome research. PMID:27731453
Transcriptome Sequencing of Diverse Peanut (Arachis) Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability. PMID:27729436
A Gene for Genetic Background in Zea mays: Fine-Mapping enhancer of teosinte branched1.2 to a YABBY Class Transcription Factor. PMID:27729422
FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies. PMID:27724866
Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing. PMID:27716836
Iron homeostasis in Arabidopsis thaliana: transcriptomic analyses reveal novel FIT-regulated genes, iron deficiency marker genes and functional gene networks. PMID:27716045
The epichaperome is an integrated chaperome network that facilitates tumour survival. PMID:27706135
Determining the Mitochondrial Methyl Proteome in Saccharomyces cerevisiae using Heavy Methyl SILAC. PMID:27696855
Genomic Survey of a Hyperparasitic Microsporidian Amphiamblys sp. (Metchnikovellidae). PMID:27694476
The emerging role of lysine methyltransferase SETD8 in human diseases. PMID:27688818
Thrombin Cleavage of Inter-α-inhibitor Heavy Chain 1 Regulates Leukocyte Binding to an Inflammatory Hyaluronan Matrix. PMID:27679489
Determination of local chromatin composition by CasID. PMID:27676121
Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls. PMID:27672500
Impact of Moderate Temperature Changes on Neisseria meningitidis Adhesion Phenotypes and Proteome. PMID:27672084
The impact of sequence database choice on metaproteomic results in gut microbiota studies. PMID:27671352
Structured States of Disordered Proteins from Genomic Sequences. PMID:27662088
modPDZpep: a web resource for structure based analysis of human PDZ-mediated interaction networks. PMID:27655048
Head regeneration in hemichordates is not a strict recapitulation of development. PMID:27649280
Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein. PMID:27649274
Genetic Characterization of Plasmodium Putative Pantothenate Kinase Genes Reveals Their Essential Role in Malaria Parasite Transmission to the Mosquito. PMID:27644319
In Vivo Analysis of NH4+ Transport and Central Nitrogen Metabolism in Saccharomyces cerevisiae during Aerobic Nitrogen-Limited Growth. PMID:27637876
Disease-Associated Mutations in the HSPD1 Gene Encoding the Large Subunit of the Mitochondrial HSP60/HSP10 Chaperonin Complex. PMID:27630992
Mitochondrial DNA Sequence and Lack of Response to Anoxia in the Annual Killifish Austrofundulus limnaeus. PMID:27630577
Cancer: Acidic shield puts a chink in p53's armour. PMID:27626387
Acetylation-regulated interaction between p53 and SET reveals a widespread regulatory mode. PMID:27626385
The Arabidopsis sickle Mutant Exhibits Altered Circadian Clock Responses to Cool Temperatures and Temperature-Dependent Alternative Splicing. PMID:27624757
Dataset of differentially regulated proteins in HUVECs challenged with wild type and UGM1 mutant Aspergillus fumigatus strains. PMID:27622208
First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Née (Fagaceae). PMID:27621377
Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.). PMID:27617034
Evolving serodiagnostics by rationally designed peptide arrays: the Burkholderia paradigm in Cystic Fibrosis. PMID:27615705
Substitutions in the Glycogenin-1 Gene Are Associated with the Evolution of Endothermy in Sharks and Tunas. PMID:27614233
PCDDB: new developments at the Protein Circular Dichroism Data Bank. PMID:27613420
Structural basis for the Zn2+ inhibition of the zymogen-like kallikrein-related peptidase 10. PMID:27611765
New Genomic Insights into "Entotheonella" Symbionts in Theonella swinhoei: Mixotrophy, Anaerobic Adaptation, Resilience, and Interaction. PMID:27610106
Sequence Assembly of Yarrowia lipolytica Strain W29/CLIB89 Shows Transposable Element Diversity. PMID:27603307
WD40 domain of Apc1 is critical for the coactivator-induced allosteric transition that stimulates APC/C catalytic activity. PMID:27601667
Discovery of parvovirus-related sequences in an unexpected broad range of animals. PMID:27600734
Lytic polysaccharide monooxygenases and other oxidative enzymes are abundantly secreted by Aspergillus nidulans grown on different starches. PMID:27588040
A theoretical study on predicted protein targets of apple polyphenols and possible mechanisms of chemoprevention in colorectal cancer. PMID:27587238
dRHP-PseRA: detecting remote homology proteins using profile-based pseudo protein sequence and rank aggregation. PMID:27581095
A Computational Model for Predicting RNase H Domain of Retrovirus. PMID:27574780
Identifying lineage effects when controlling for population structure improves power in bacterial association studies. PMID:27572646
TMSEG: Novel prediction of transmembrane helices. PMID:27566436
G23D: Online tool for mapping and visualization of genomic variants on 3D protein structures. PMID:27565432
FFPred 3: feature-based function prediction for all Gene Ontology domains. PMID:27561554
Narcolepsy Following Yellow Fever Vaccination: A Case Report. PMID:27559330
Systems-level effects of ectopic galectin-7 reconstitution in cervical cancer and its microenvironment. PMID:27558259
A large-scale analysis of alternative splicing reveals a key role of QKI in lung cancer. PMID:27555542
Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank. PMID:27551105
Antimicrobial Protein Candidates from the Thermophilic Geobacillus sp. Strain ZGt-1: Production, Proteomics, and Bioinformatics Analysis. PMID:27548162
Proteomic indicators of oxidation and hydration state in colorectal cancer. PMID:27547546
msBiodat analysis tool, big data analysis for high-throughput experiments. PMID:27547241
A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks. PMID:27542402
DEAH-RHA helicase•Znf cofactor systems in kinetoplastid RNA editing and evolutionarily distant RNA processes. PMID:27540585
Identification of Complete Repertoire of Apis florea Odorant Receptors Reveals Complex Orthologous Relationships with Apis mellifera. PMID:27540087
Proteomics for Allergy: from Proteins to the Patients. PMID:27534655
A protein homeostasis signature in healthy brains recapitulates tissue vulnerability to Alzheimer's disease. PMID:27532054
NLDB: a database for 3D protein-ligand interactions in enzymatic reactions. PMID:27530928
Carboxylic ester hydrolases: Classification and database derived from their primary, secondary, and tertiary structures. PMID:27530203
miR-625-3p regulates oxaliplatin resistance by targeting MAP2K6-p38 signalling in human colorectal adenocarcinoma cells. PMID:27526785
SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity. PMID:27525735
Venom Insulins of Cone Snails Diversify Rapidly and Track Prey Taxa. PMID:27524826
HOMCOS: an updated server to search and model complex 3D structures. PMID:27522608
VHLdb: A database of von Hippel-Lindau protein interactors and mutations. PMID:27511743
Membranome: a database for proteome-wide analysis of single-pass membrane proteins. PMID:27510400
DTMiner: identification of potential disease targets through biomedical literature mining. PMID:27506226
Using AberOWL for fast and scalable reasoning over BioPortal ontologies. PMID:27502585
Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians. PMID:27502555
Fast Photochemical Oxidation of Proteins Maps the Topology of Intrinsic Membrane Proteins: Light-Harvesting Complex 2 in a Nanodisc. PMID:27500903
A transcriptional blueprint for a spiral-cleaving embryo. PMID:27496340
Lollipops in the Clinic: Information Dense Mutation Plots for Precision Medicine. PMID:27490490
Prediction of scaffold proteins based on protein interaction and domain architectures. PMID:27490120
A Proteomic Investigation of Hepatic Resistance to Ascaris in a Murine Model. PMID:27490109
Supervised Learning for Detection of Duplicates in Genomic Sequence Databases. PMID:27489953
Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung. PMID:27486204
Predicting G protein-coupled receptor downstream signaling by tissue expression. PMID:27485444
Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015. PMID:27480696
Genetic variation in MHC proteins is associated with T cell receptor expression biases. PMID:27479906
The Effectors and Sensory Sites of Formaldehyde-responsive Regulator FrmR and Metal-sensing Variant. PMID:27474740
Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri. PMID:27474723
Assessment of Protein Binding of 5-Hydroxythalidomide Bioactivated in Humanized Mice with Human P450 3A-Chromosome or Hepatocytes by Two-Dimensional Electrophoresis/Accelerator Mass Spectrometry. PMID:27464947
Representing and querying disease networks using graph databases. PMID:27462371
Proteomic analysis of FUS interacting proteins provides insights into FUS function and its role in ALS. PMID:27460707
Three-Dimensional Model of Human Nicotinamide Nucleotide Transhydrogenase (NNT) and Sequence-Structure Analysis of its Disease-Causing Variations. PMID:27459240
Altered Co-Translational Processing Plays a Role in Huntington's Pathogenesis-A Hypothesis. PMID:27458341
Biotechnological Trends in Spider and Scorpion Antivenom Development. PMID:27455327
A Bioinformatics Analysis Reveals a Group of MocR Bacterial Transcriptional Regulators Linked to a Family of Genes Coding for Membrane Proteins. PMID:27446613
Identification and functional characterization of novel xylose transporters from the cell factories Aspergillus niger and Trichoderma reesei. PMID:27446237
Two-pore channels (TPCs): Novel voltage-gated ion channels with pleiotropic functions. PMID:27440385
Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds. PMID:27437113
Origin and Functional Prediction of Pollen Allergens in Plants. PMID:27436829
Identification of Preferred DNA-Binding Sites for the Thermus thermophilus Transcriptional Regulator SbtR by the Combinatorial Approach REPSA. PMID:27428627
Protein function in precision medicine: deep understanding with machine learning. PMID:27423136
Markers associated with heading and aftermath heading in perennial ryegrass full-sib families. PMID:27422157
Association mapping reveals novel serpentine adaptation gene clusters in a population of symbiotic Mesorhizobium. PMID:27420027
Challenges in identifying cancer genes by analysis of exome sequencing data. PMID:27417679
GP0.4 from bacteriophage T7: in silico characterisation of its structure and interaction with E. coli FtsZ. PMID:27411831
Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens. PMID:27403523
Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining. PMID:27390860
Elucidating and mining the Tulipa and Lilium transcriptomes. PMID:27387304
HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1. PMID:27384951
Zinc Resistance Mechanisms of P1B-type ATPases in Sinorhizobium meliloti CCNWSX0020. PMID:27378600
Sex-biased gene expression and sequence conservation in Atlantic and Pacific salmon lice (Lepeophtheirus salmonis). PMID:27377915
Identification, Characterization, and X-ray Crystallographic Analysis of a Novel Type of Mannose-Specific Lectin CGL1 from the Pacific Oyster Crassostrea gigas. PMID:27377186
Computational genomics tools for dissecting tumour-immune cell interactions. PMID:27376489
HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts. PMID:27375564
Comparative Transcriptome Analysis Identifies CCDC80 as a Novel Gene Associated with Pulmonary Arterial Hypertension. PMID:27375481
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions. PMID:27372244
Missense splice variant (g.20746A>G, p.Ile183Val) of interferon gamma receptor 1 (IFNGR1) coincidental with mycobacterial osteomyelitis - a screen of osteoarticular lesions. PMID:27356097
Integration of Breast Cancer Secretomes with Clinical Data Elucidates Potential Serum Markers for Disease Detection, Diagnosis, and Prognosis. PMID:27355404
A metagenomic-based survey of microbial (de)halogenation potential in a German forest soil. PMID:27353292
Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions. PMID:27349423
A theoretical estimate for nucleotide sugar demand towards Chinese Hamster Ovary cellular glycosylation. PMID:27345611
Inhibition of glucose metabolism prevents glycosylation of the glutamine transporter ASCT2 and promotes compensatory LAT1 upregulation in leukemia cells. PMID:27344174
CerealsDB 3.0: expansion of resources and data integration. PMID:27342803
Extent of pre-translational regulation for the control of nucleocytoplasmic protein localization. PMID:27342569
NCBI prokaryotic genome annotation pipeline. PMID:27342282
AraPPISite: a database of fine-grained protein-protein interaction site annotations for Arabidopsis thaliana. PMID:27338257
Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale. PMID:27337644
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PMID:27336457
PEP_scaffolder: using (homologous) proteins to scaffold genomes. PMID:27334475
Model organism databases: essential resources that need the support of both funders and users. PMID:27334346
Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases. PMID:27332861
Peptide de novo sequencing of mixture tandem mass spectra. PMID:27329701
A collection of intrinsic disorder characterizations from eukaryotic proteomes. PMID:27326998
Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution. PMID:27324845
Potential DNA binding and nuclease functions of ComEC domains characterized in silico. PMID:27318187
MAD2γ, a novel MAD2 isoform, reduces mitotic arrest and is associated with resistance in testicular germ cell tumors. PMID:27315568
Proteome-wide covalent ligand discovery in native biological systems. PMID:27309814
Inherited Disease Genetics Improves the Identification of Cancer-Associated Genes. PMID:27304678
ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data. PMID:27302480
Rational design and validation of a vanilloid-sensitive TRPV2 ion channel. PMID:27298359
Long noncoding RNAs: Central to nervous system development. PMID:27296516
Bone Morphogenetic Protein 4 Signalling in Neural Stem and Progenitor Cells during Development and after Injury. PMID:27293450
Differential proteomics profiling of the ova between healthy and Rice stripe virus-infected female insects of Laodelphax striatellus. PMID:27277140
Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing γ-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T)). PMID:27274784
A novel resistance mutation in eccC5 of the ESX-5 secretion system confers ofloxacin resistance in Mycobacterium tuberculosis. PMID:27261264
Transcriptome sequences spanning key developmental states as a resource for the study of the cestode Schistocephalus solidus, a threespine stickleback parasite. PMID:27259971
The Proteasix Ontology. PMID:27259807
Genomic resources and draft assemblies of the human and porcine varieties of scabies mites, Sarcoptes scabiei var. hominis and var. suis. PMID:27250856
Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow. PMID:27250503
Computational recognition and analysis of hitherto uncharacterized nucleotide cyclase-like proteins in bacteria. PMID:27246835
Mutational Studies of Putative Biosynthetic Genes for the Cyanobacterial Sunscreen Scytonemin in Nostoc punctiforme ATCC 29133. PMID:27242750
EP300 Protects from Light-Induced Retinopathy in Zebrafish. PMID:27242532
Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria. PMID:27242034
Current state of the art for enhancing urine biomarker discovery. PMID:27232439
Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array. PMID:27230772
X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism. PMID:27227414
Coevolution of RAC Small GTPases and their Regulators GEF Proteins. PMID:27226705
PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions. PMID:27224906
A Caenorhabditis elegans Genome-Scale Metabolic Network Model. PMID:27211857
Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies. PMID:27207956
Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health. PMID:27206485
Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem. PMID:27199914
Venus flytrap carnivorous lifestyle builds on herbivore defense strategies. PMID:27197216
Conserved Features in the Structure, Mechanism, and Biogenesis of the Inverse Autotransporter Protein Family. PMID:27190006
Characterization of the Cadherin-Catenin Complex of the Sea Anemone Nematostella vectensis and Implications for the Evolution of Metazoan Cell-Cell Adhesion. PMID:27189570
Searching the Evolutionary Origin of Epithelial Mucus Protein Components-Mucins and FCGBP. PMID:27189557
Putative virulence factors of Corynebacterium pseudotuberculosis FRC41: vaccine potential and protein expression. PMID:27184574
Visualizing ensembles in structural biology. PMID:27179343
Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics. PMID:27175778
HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering. PMID:27174934
A combined computational and structural model of the full-length human prolactin receptor. PMID:27174498
A homology-based pipeline for global prediction of post-translational modification sites. PMID:27174170
Brain Radiation Information Data Exchange (BRIDE): integration of experimental data from low-dose ionising radiation research for pathway discovery. PMID:27170263
The repetitive DNA element BncDNA, enriched in the B chromosome of the cichlid fish Astatotilapia latifasciata, transcribes a potentially noncoding RNA. PMID:27169573
Circular sequence comparison: algorithms and applications. PMID:27168761
Integrative analysis of extracellular and intracellular bladder cancer cell line proteome with transcriptome: improving coverage and validity of -omics findings. PMID:27167498
Computational approaches for predicting mutant protein stability. PMID:27160393
Remarkable evolutionary relatedness among the enzymes and proteins from the α-amylase family. PMID:27154042
UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB. PMID:27153729
Computational clustering for viral reference proteomes. PMID:27153712
PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks. PMID:27153707
TnT: a set of libraries for visualizing trees and track-based annotations for the web. PMID:27153646
TOPDOM: database of conservatively located domains and motifs in proteins. PMID:27153630
Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom. PMID:27152931
PHYPred: a tool for identifying bacteriophage enzymes and hydrolases. PMID:27151186
StructMAn: annotation of single-nucleotide polymorphisms in the structural context. PMID:27150811
Systematic analysis of somatic mutations driving cancer: uncovering functional protein regions in disease development. PMID:27150584
The Exocyst Complex in Health and Disease. PMID:27148529
Understanding Neuropsychiatric Diseases, Analyzing the Peptide Sharing between Infectious Agents and the Language-Associated NMDA 2A Protein. PMID:27148089
Dorsal root ganglia in Friedreich ataxia: satellite cell proliferation and inflammation. PMID:27142428
Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions. PMID:27126702
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. PMID:27126040
HepatoDyn: A Dynamic Model of Hepatocyte Metabolism That Integrates 13C Isotopomer Data. PMID:27124774
Genetics of PCOS: A systematic bioinformatics approach to unveil the proteins responsible for PCOS. PMID:27114910
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF. PMID:27114493
Tcf1 and Lef1 transcription factors establish CD8(+) T cell identity through intrinsic HDAC activity. PMID:27111144
PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases. PMID:27106060
Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources. PMID:27092246
Prioritizing functional phosphorylation sites based on multiple feature integration. PMID:27090940
Leveraging family-specific signatures for AMP discovery and high-throughput annotation. PMID:27089856
Prediction of Toxin Genes from Chinese Yellow Catfish Based on Transcriptomic and Proteomic Sequencing. PMID:27089325
The Atlantic salmon genome provides insights into rediploidization. PMID:27088604
NPInter v3.0: an upgraded database of noncoding RNA-associated interactions. PMID:27087310
Kalium: a database of potassium channel toxins from scorpion venom. PMID:27087309
ProViz-a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. PMID:27085803
Refined Pichia pastoris reference genome sequence. PMID:27084056
Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PMID:27082250
Cleavage and polyadenylation specificity factor 30: An RNA-binding zinc-finger protein with an unexpected 2Fe-2S cluster. PMID:27071088
Neurotrophin, p75, and Trk Signaling Module in the Developing Nervous System of the Marine Annelid Platynereis dumerilii. PMID:27069919
A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer. PMID:27067391
A Quantitative Approach to Analyzing Genome Reductive Evolution Using Protein-Protein Interaction Networks: A Case Study of Mycobacterium leprae. PMID:27066064
FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases. PMID:27060136
Global Proteomic Analysis Reveals an Exclusive Role of Thylakoid Membranes in Bioenergetics of a Model Cyanobacterium. PMID:27056914
Oral squamous cell carcinoma: microRNA expression profiling and integrative analyses for elucidation of tumourigenesis mechanism. PMID:27056547
ATtRACT-a database of RNA-binding proteins and associated motifs. PMID:27055826
The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. PMID:27051515
A physiome interoperability roadmap for personalized drug development. PMID:27051513
Surface energetics and protein-protein interactions: analysis and mechanistic implications. PMID:27050828
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. PMID:27050687
Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation. PMID:27049631
The new (dis)order in RNA regulation. PMID:27048167
Computational Analysis of the Predicted Evolutionary Conservation of Human Phosphorylation Sites. PMID:27046079
Transcriptomics resources of human tissues and organs. PMID:27044256
CPAD, Curated Protein Aggregation Database: A Repository of Manually Curated Experimental Data on Protein and Peptide Aggregation. PMID:27043825
GAMDB: a web resource to connect microRNAs with autophagy in gerontology. PMID:27037912
The C-Terminal Acidic Region of Calreticulin Mediates Phosphatidylserine Binding and Apoptotic Cell Phagocytosis. PMID:27036911
Gene Prioritization by Integrated Analysis of Protein Structural and Network Topological Properties for the Protein-Protein Interaction Network of Neurological Disorders. PMID:27034906
In Silico Approach for SAR Analysis of the Predicted Model of DEPDC1B: A Novel Target for Oral Cancer. PMID:27034663
Are There Rab GTPases in Archaea? PMID:27034425
Topology based identification and comprehensive classification of four-transmembrane helix containing proteins (4TMs) in the human genome. PMID:27030248
An evolutionary roadmap to the microtubule-associated protein MAP Tau. PMID:27030133
Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications. PMID:27028541
Human Cytomegalovirus Infection Upregulates the Mitochondrial Transcription and Translation Machineries. PMID:27025248
CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state. PMID:27022160
Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes. PMID:27022157
Transcriptome analyses of insect cells to facilitate baculovirus-insect expression. PMID:27017378
Survey of variation in human transcription factors reveals prevalent DNA binding changes. PMID:27013732
HNdb: an integrated database of gene and protein information on head and neck squamous cell carcinoma. PMID:27013077
SM-TF: A structural database of small molecule-transcription factor complexes. PMID:27010673
Finding Protein and Nucleotide Similarities with FASTA. PMID:27010337
UniProt Tools. PMID:27010333
dbPAF: an integrative database of protein phosphorylation in animals and fungi. PMID:27010073
Evolutionary Conserved Positions Define Protein Conformational Diversity. PMID:27008419
Integrated bioinformatics to decipher the ascorbic acid metabolic network in tomato. PMID:27007138
Biochemical and functional characterization of glycosylation-associated mutational landscapes in colon cancer. PMID:27004849
GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations. PMID:26994912
KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins. PMID:26989151
Characterization of Disease-Associated Mutations in Human Transmembrane Proteins. PMID:26986070
Protein S-Glutathionylation Mediates Macrophage Responses to Metabolic Cues from the Extracellular Environment. PMID:26984580
Pipeline for the identification and classification of ion channels in parasitic flatworms. PMID:26983991
Active site specificity profiling datasets of matrix metalloproteinases (MMPs) 1, 2, 3, 7, 8, 9, 12, 13 and 14. PMID:26981551
Mutation-based structural modification and dynamics study of amyloid beta peptide (1-42): An in-silico-based analysis to cognize the mechanism of aggregation. PMID:26981406
PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins. PMID:26980520
The FAIR Guiding Principles for scientific data management and stewardship. PMID:26978244
Rare loss-of-function variants in SETD1A are associated with schizophrenia and developmental disorders. PMID:26974950
Genome Sequences of Five Clinical Isolates of Klebsiella pneumoniae. PMID:26966211
Cancer Metabolomics and the Human Metabolome Database. PMID:26950159
Genome-wide characterization and analysis of bZIP transcription factor gene family related to abiotic stress in cassava. PMID:26947924
Genome-Wide Association Study to Identify Genes Related to Renal Mercury Concentrations in Mice. PMID:26942574
Draft Genome of Rhodococcus rhodochrous TRN7, Isolated from the Coast of Trindade Island, Brazil. PMID:26941155
Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress. PMID:26935041
libChEBI: an API for accessing the ChEBI database. PMID:26933452
Divergence in gene expression within and between two closely related flycatcher species. PMID:26928872
Towards the bridging of molecular genetics data across Xenopus species. PMID:26925848
Autoimmune Responses to Soluble Aggregates of Amyloidogenic Proteins Involved in Neurodegenerative Diseases: Overlapping Aggregation Prone and Autoimmunogenic regions. PMID:26924748
Statistical prediction of protein structural, localization and functional properties by the analysis of its fragment mass distributions after proteolytic cleavage. PMID:26924271
Comparative Transcriptomics Indicates a Role for SHORT VEGETATIVE PHASE (SVP) Genes in Mimulus guttatus Vernalization Response. PMID:26921300
Venom gland transcriptome analyses of two freshwater stingrays (Myliobatiformes: Potamotrygonidae) from Brazil. PMID:26916342
The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies. PMID:26913054
Transcriptional Regulation of Carbohydrate Utilization Pathways in the Bifidobacterium Genus. PMID:26903998
Chemoproteomic profiling of host and pathogen enzymes active in cholera. PMID:26900865
The UniProtKB guide to the human proteome. PMID:26896845
The Genetic Basis of Haploid Induction in Maize Identified with a Novel Genome-Wide Association Method. PMID:26896330
Antibiotic binding of STY3178, a yfdX protein from Salmonella Typhi. PMID:26892637
TRPC6 G757D Loss-of-Function Mutation Associates with FSGS. PMID:26892346
ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis. PMID:26882475
Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon. PMID:26882169
BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine. PMID:26879404
Data for the crystal structure of APRIL-BAFF-BAFF heterotrimer. PMID:26870754
Proteomic data on the nuclear interactome of human MCM9. PMID:26870752
Post-translational processing targets functionally diverse proteins in Mycoplasma hyopneumoniae. PMID:26865024
Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments. PMID:26864881
Distinct lymphocyte antigens 6 (Ly6) family members Ly6D, Ly6E, Ly6K and Ly6H drive tumorigenesis and clinical outcome. PMID:26862846
Leaf apoplastic proteome composition in UV-B treated Arabidopsis thaliana mutants impaired in extracellular glutathione degradation. PMID:26862584
Selectivity profiling of BCRP versus P-gp inhibition: from automated collection of polypharmacology data to multi-label learning. PMID:26855674
Conserved Intramolecular Interactions Maintain Myosin Interacting-Heads Motifs Explaining Tarantula Muscle Super-Relaxed State Structural Basis. PMID:26851071
On Nature's Strategy for Assigning Genetic Code Multiplicity. PMID:26849571
A review of the new HGNC gene family resource. PMID:26842383
High-Density Peptide Microarray Analysis of IgG Autoantibody Reactivities in Serum and Cerebrospinal Fluid of Multiple Sclerosis Patients. PMID:26831522
The genomic basis of parasitism in the Strongyloides clade of nematodes. PMID:26829753
The Chlamydia trachomatis Protease CPAF Contains a Cryptic PDZ-Like Domain with Similarity to Human Cell Polarity and Tight Junction PDZ-Containing Proteins. PMID:26829550
Detecting β-Casein Variation in Bovine Milk. PMID:26821001
Interfering with Bacterial Quorum Sensing. PMID:26819549
SOHSite: incorporating evolutionary information and physicochemical properties to identify protein S-sulfenylation sites. PMID:26819243
Proteomic approaches to uncovering virus-host protein interactions during the progression of viral infection. PMID:26817613
Impact of germline and somatic missense variations on drug binding sites. PMID:26810135
Coenzyme Q Biosynthesis: Evidence for a Substrate Access Channel in the FAD-Dependent Monooxygenase Coq6. PMID:26808124
BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers. PMID:26803163
T-cell recognition is shaped by epitope sequence conservation in the host proteome and microbiome. PMID:26789414
Insight into the Salivary Gland Transcriptome of Lygus lineolaris (Palisot de Beauvois). PMID:26789269
The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes. PMID:26781712
The Phenotypic and Genetic Underpinnings of Flower Size in Polemoniaceae. PMID:26779209
Epithelial sodium channel (ENaC) family: Phylogeny, structure-function, tissue distribution, and associated inherited diseases. PMID:26772908
Systematic Identification and Characterization of Long Non-Coding RNAs in the Silkworm, Bombyx mori. PMID:26771876
Kinetic analysis and molecular modeling of the inhibition mechanism of roneparstat (SST0001) on human heparanase. PMID:26762172
Revealing the Effects of Missense Mutations Causing Snyder-Robinson Syndrome on the Stability and Dimerization of Spermine Synthase. PMID:26761001
Proteomics Based Identification of Proteins with Deregulated Expression in B Cell Lymphomas. PMID:26752561
Use of a Probabilistic Motif Search to Identify Histidine Phosphotransfer Domain-Containing Proteins. PMID:26751210
Virtual Screening and Experimental Validation Identify Novel Inhibitors of the Plasmodium falciparum Atg8-Atg3 Protein-Protein Interaction. PMID:26748931
Association of Arrhythmia-Related Genetic Variants With Phenotypes Documented in Electronic Medical Records. PMID:26746457
Inhibition of signaling between human CXCR4 and zebrafish ligands by the small molecule IT1t impairs the formation of triple-negative breast cancer early metastases in a zebrafish xenograft model. PMID:26744352
Creation of chimeric human/rabbit APOBEC1 with HIV-1 restriction and DNA mutation activities. PMID:26738439
p38 Mitogen-Activated Protein Kinase Pathway Regulates Genes during Proliferation and Differentiation in Oligodendrocytes. PMID:26714323
HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species. PMID:26708988
The linker region of breast cancer resistance protein ABCG2 is critical for coupling of ATP-dependent drug transport. PMID:26708291
Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods. PMID:26694353
Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders. PMID:26690135
De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome. PMID:26688806
Horizontal acquisition of toxic alkaloid synthesis in a clade of plant associated fungi. PMID:26688468
A Multiplex Kindred with Hennekam Syndrome due to Homozygosity for a CCBE1 Mutation that does not Prevent Protein Expression. PMID:26686525
Systems Proteomics View of the Endogenous Human Claudin Protein Family. PMID:26680015
A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning. PMID:26673895
The Pfam protein families database: towards a more sustainable future. PMID:26673716
The European Bioinformatics Institute in 2016: Data growth and integration. PMID:26673705
Common errors in mass spectrometry-based analysis of post-translational modifications. PMID:26667783
Complete genome sequence of the molybdenum-resistant bacterium Bacillus subtilis strain LM 4-2. PMID:26664656
The GPSM2/LGN GoLoco motifs are essential for hearing. PMID:26662512
CANTATAdb: A Collection of Plant Long Non-Coding RNAs. PMID:26657895
The Proteomic Profile of Deleted in Breast Cancer 1 (DBC1) Interactions Points to a Multifaceted Regulation of Gene Expression. PMID:26657080
Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search. PMID:26656740
Exome Sequencing Identifies Pathogenic and Modifier Mutations in a Child With Sporadic Dilated Cardiomyopathy. PMID:26656454
Cross-species conservation of complementary amino acid-ribonucleobase interactions and their potential for ribosome-free encoding. PMID:26656258
Heterotrimeric G-proteins in Picea abies and their regulation in response to Heterobasidion annosum s.l. infection. PMID:26654722
Parameterizing sequence alignment with an explicit evolutionary model. PMID:26652060
Involvement of the Cohesin Cofactor PDS5 (SPO76) During Meiosis and DNA Repair in Arabidopsis thaliana. PMID:26648949
Mechanism of Folding and Activation of Subtilisin Kexin Isozyme-1 (SKI-1)/Site-1 Protease (S1P). PMID:26645686
COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps. PMID:26635392
Molecular Evolution of the TET Gene Family in Mammals. PMID:26633372
Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases. PMID:26628682
"Salivary gland cellular architecture in the Asian malaria vector mosquito Anopheles stephensi". PMID:26627194
orthoFind Facilitates the Discovery of Homologous and Orthologous Proteins. PMID:26624019
PPIM: A Protein-Protein Interaction Database for Maize. PMID:26620522
Mapping Soluble Guanylyl Cyclase and Protein Disulfide Isomerase Regions of Interaction. PMID:26618351
ELM 2016--data update and new functionality of the eukaryotic linear motif resource. PMID:26615199
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188
Large-scale transcriptome sequencing reveals novel expression patterns for key sex-related genes in a sex-changing fish. PMID:26613014
Network Analysis Identifies Mitochondrial Regulation of Epidermal Differentiation by MPZL3 and FDXR. PMID:26609959
The first draft genome of the aquatic model plant Lemna minor opens the route for future stress physiology research and biotechnological applications. PMID:26609323
Global Profiling of Huntingtin-associated protein E (HYPE)-Mediated AMPylation through a Chemical Proteomic Approach. PMID:26604261
PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures. PMID:26602691
Systematic Analysis and Prediction of In Situ Cross Talk of O-GlcNAcylation and Phosphorylation. PMID:26601103
An evolutionary perspective on signaling peptides: toxic peptides are selected to provide information regarding the processing of the propeptide, which represents the phenotypic state of the signaling cell. PMID:26594342
FunTree: advances in a resource for exploring and contextualising protein function evolution. PMID:26590404
The UCSC Genome Browser database: 2016 update. PMID:26590259
UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures. PMID:26590254
TAILS N-terminomic and proteomic datasets of healthy human dental pulp. PMID:26587561
Draft Genome Sequence of the Ant-Associated Fungus Phialophora attae (CBS 131958). PMID:26586868
Sensing Small Changes in Protein Abundance: Stimulation of Caco-2 Cells by Human Whey Proteins. PMID:26586228
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. PMID:26582926
Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability. PMID:26582925
GPCRdb: an information system for G protein-coupled receptors. PMID:26582914
Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. PMID:26581338
The structure of Medicago truncatula δ(1)-pyrroline-5-carboxylate reductase provides new insights into regulation of proline biosynthesis in plants. PMID:26579138
Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information. PMID:26578601
SEA: a super-enhancer archive. PMID:26578594
PANTHER version 10: expanded protein families and functions, and analysis tools. PMID:26578592
GREENC: a Wiki-based database of plant lncRNAs. PMID:26578586
DBAASP v.2: an enhanced database of structure and antimicrobial/cytotoxic activity of natural and synthetic peptides. PMID:26578581
Assembly: a resource for assembled genomes at NCBI. PMID:26578580
Ensembl Genomes 2016: more genomes, more complexity. PMID:26578574
dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. PMID:26578568
PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with PolyCystic Ovary Syndrome. PMID:26578565
Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. PMID:26578564
LegumeIP 2.0--a platform for the study of gene function and genome evolution in legumes. PMID:26578557
In silico discovery of significant pathways in colorectal cancer metastasis using a two-stage optimisation approach. PMID:26577164
A new network representation of the metabolism to detect chemical transformation modules. PMID:26573681
Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos. PMID:26572793
MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins. PMID:26568329
GEneSTATION 1.0: a synthetic resource of diverse evolutionary and functional genomic data for studying the evolution of pregnancy-associated tissues and phenotypes. PMID:26567549
Biosynthesis of GPI-anchored proteins: special emphasis on GPI lipid remodeling. PMID:26563290
Getting ready for host invasion: elevated expression and action of xyloglucan endotransglucosylases/hydrolases in developing haustoria of the holoparasitic angiosperm Cuscuta. PMID:26561437
Dead enzymes in the aldehyde dehydrogenase gene family: role in drug metabolism and toxicology. PMID:26558415
Extensive T-Cell Epitope Repertoire Sharing among Human Proteome, Gastrointestinal Microbiome, and Pathogenic Bacteria: Implications for the Definition of Self. PMID:26557118
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. PMID:26553804
Cell-free plasma hemoglobin removal by dialyzers with various permeability profiles. PMID:26553708
The Transporter Classification Database (TCDB): recent advances. PMID:26546518
Electrostatic Similarity Analysis of Human β-Defensin Binding in the Melanocortin System. PMID:26536271
Computational analysis of candidate prion-like proteins in bacteria and their role. PMID:26528269
2016 update of the PRIDE database and its related tools. PMID:26527722
MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. PMID:26527720
Application of Functional Genomics for Bovine Respiratory Disease Diagnostics. PMID:26526746
ccmGDB: a database for cancer cell metabolism genes. PMID:26519468
Information Commons for Rice (IC4R). PMID:26519466
Integrated interactions database: tissue-specific view of the human and model organism interactomes. PMID:26516188
SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets. PMID:26516187
Structure and Function of the N-Terminal Domain of the Vesicular Stomatitis Virus RNA Polymerase. PMID:26512087
Multiclassifier combinatorial proteomics of organelle shadows at the example of mitochondria in chromatin data. PMID:26510496
Bioinformatics Knowledge Map for Analysis of Beta-Catenin Function in Cancer. PMID:26509276
Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria. PMID:26506513
RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource. PMID:26500754
Whole exome sequencing of microdissected splenic marginal zone lymphoma: a study to discover novel tumor-specific mutations. PMID:26498442
The potential clinical impact of the release of two drafts of the human proteome. PMID:26496066
Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing. PMID:26496030
AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis. PMID:26493317
Backbone and side chain chemical shift assignments of apolipophorin III from Galleria mellonella. PMID:26493308
A Glimpse to Background and Characteristics of Major Molecular Biological Networks. PMID:26491677
Baculovirus Inhibitor-of-Apoptosis Op-IAP3 Blocks Apoptosis by Interaction with and Stabilization of a Host Insect Cellular IAP. PMID:26491164
Evolutionary history of phosphatidylinositol- 3-kinases: ancestral origin in eukaryotes and complex duplication patterns. PMID:26482564
Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture. PMID:26482235
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. PMID:26481362
Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. PMID:26481361
ZINC 15--Ligand Discovery for Everyone. PMID:26479676
KEGG as a reference resource for gene and protein annotation. PMID:26476454
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. PMID:26476450
FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana. PMID:26476447
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. PMID:26476444
CauloBrowser: A systems biology resource for Caulobacter crescentus. PMID:26476443
SIGNOR: a database of causal relationships between biological entities. PMID:26467481
ChEBI in 2016: Improved services and an expanding collection of metabolites. PMID:26467479
CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides. PMID:26467475
The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands. PMID:26464438
Comparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer. PMID:26462790
A functional genomics screen identifies an Importin-α homolog as a regulator of stem cell function and tissue patterning during planarian regeneration. PMID:26459857
Event inference in multidomain families with phylogenetic reconciliation. PMID:26451642
The Hox cluster microRNA miR-615: a case study of intronic microRNA evolution. PMID:26451238
MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins. PMID:26450961
Rapid Bioinformatic Identification of Thermostabilizing Mutations. PMID:26445442
dbSUPER: a database of super-enhancers in mouse and human genome. PMID:26438538
SubtiWiki 2.0--an integrated database for the model organism Bacillus subtilis. PMID:26433225
iPPI-DB: an online database of modulators of protein-protein interactions. PMID:26432833
MitoMiner v3.1, an update on the mitochondrial proteomics database. PMID:26432830
PyMine: a PyMOL plugin to integrate and visualize data for drug discovery. PMID:26429562
Structural features of conopeptide genes inferred from partial sequences of the Conus tribblei genome. PMID:26423067
Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery. PMID:26420781
Aspergillus niger membrane-associated proteome analysis for the identification of glucose transporters. PMID:26388937
Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats. PMID:26377088
Devising a Consensus Framework for Validation of Novel Human Coding Loci. PMID:26367542
ASD v3.0: unraveling allosteric regulation with structural mechanisms and biological networks. PMID:26365237
Comparative Genomics of a Plant-Parasitic Nematode Endosymbiont Suggest a Role in Nutritional Symbiosis. PMID:26362082
Computational approaches to study the effects of small genomic variations. PMID:26350246
Multiple Reaction Monitoring Enables Precise Quantification of 97 Proteins in Dried Blood Spots. PMID:26342038
Common Amino Acid Subsequences in a Universal Proteome--Relevance for Food Science. PMID:26340620
Identification of hyaluronidase and phospholipase B in Lachesis muta rhombeata venom. PMID:26335358
Comparative Analysis of Label-Free and 8-Plex iTRAQ Approach for Quantitative Tissue Proteomic Analysis. PMID:26331617
Genome-Wide Identification and Expression Analyses of Aquaporin Gene Family during Development and Abiotic Stress in Banana. PMID:26307965
Integrated inference and evaluation of host-fungi interaction networks. PMID:26300851
Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes. PMID:26286020
The Ying and Yang of STAT3 in Human Disease. PMID:26280891
Next-generation analysis of gene expression regulation--comparing the roles of synthesis and degradation. PMID:26259698
pGenN, a gene normalization tool for plant genes and proteins in scientific literature. PMID:26258475
Large-scale identification of membrane proteins with properties favorable for crystallization. PMID:26257393
Draft De Novo Transcriptome of the Rat Kangaroo Potorous tridactylus as a Tool for Cell Biology. PMID:26252667
Itch WW Domains Inhibit Its E3 Ubiquitin Ligase Activity by Blocking E2-E3 Ligase Trans-thiolation. PMID:26245901
High Resolution Prediction of Calcium-Binding Sites in 3D Protein Structures Using FEATURE. PMID:26226489
Constructing sequence-dependent protein models using coevolutionary information. PMID:26223372
Myristoylation profiling in human cells and zebrafish. PMID:26217820
Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites. PMID:26213149
Database of RNA binding protein expression and disease dynamics (READ DB). PMID:26210853
SHIELD: an integrative gene expression database for inner ear research. PMID:26209310
Extracting biomedical events from pairs of text entities. PMID:26201478
Activity, assay and target data curation and quality in the ChEMBL database. PMID:26201396
Genetic meta-analysis of 15,901 African Americans identifies variation in EXOC3L1 is associated with HDL concentration. PMID:26199122
The UBR-box and its relationship to binuclear RING-like treble clef zinc fingers. PMID:26185100
A large-scale crop protection bioassay data set. PMID:26175909
RNA editing differently affects protein-coding genes in D. melanogaster and H. sapiens. PMID:26169954
The extracellular matrix: Tools and insights for the "omics" era. PMID:26163349
Predictive and comparative analysis of Ebolavirus proteins. PMID:26158395
Anatomy of BioJS, an open source community for the life sciences. PMID:26153621
Known structure, unknown function: An inquiry-based undergraduate biochemistry laboratory course. PMID:26148241
SmedGD 2.0: The Schmidtea mediterranea genome database. PMID:26138588
Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution. PMID:26075886
Biallelic Mutations in NBAS Cause Recurrent Acute Liver Failure with Onset in Infancy. PMID:26073778
Comparison of the Venom Peptides and Their Expression in Closely Related Conus Species: Insights into Adaptive Post-speciation Evolution of Conus Exogenomes. PMID:26047846
The P5 disulfide switch: taming the aging unfolded protein response. PMID:26045202
Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal. PMID:26013488
A modular open platform for systematic functional studies under physiological conditions. PMID:26007658
Genetic variability in GLP-1 receptor is associated with inter-individual differences in weight lowering potential of liraglutide in obese women with PCOS: a pilot study. PMID:25991051
A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis. PMID:25977815
OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. PMID:25964301
Current strategies and findings in clinically relevant post-translational modification-specific proteomics. PMID:25955281
Evolutionary Analysis of the B56 Gene Family of PP2A Regulatory Subunits. PMID:25950761
SELPHI: correlation-based identification of kinase-associated networks from global phospho-proteomics data sets. PMID:25948583
HMMER web server: 2015 update. PMID:25943547
Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance. PMID:25943316
Linking gene expression to phenotypes via pathway information. PMID:25901272
Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks. PMID:25900361
SANSparallel: interactive homology search against Uniprot. PMID:25855811
The EMBL-EBI bioinformatics web and programmatic tools framework. PMID:25845596
dbPSP: a curated database for protein phosphorylation sites in prokaryotes. PMID:25841437
Improving a recombinant Zymomonas mobilis strain 8b through continuous adaptation on dilute acid pretreated corn stover hydrolysate. PMID:25834640
Shared resources, shared costs--leveraging biocuration resources. PMID:25776020
Improving the consistency of domain annotation within the Conserved Domain Database. PMID:25767294
NlpI-mediated modulation of outer membrane vesicle production through peptidoglycan dynamics in Escherichia coli. PMID:25755088
Multidomain human peroxidasin 1 is a highly glycosylated and stable homotrimeric high spin ferric peroxidase. PMID:25713063
Virus-host interactomics: new insights and opportunities for antiviral drug discovery. PMID:25593595
The 2015 Nucleic Acids Research Database Issue and molecular biology database collection. PMID:25593347 -
UniProt: the universal protein knowledgebase
PubMed citations: 1769.
1769 articles citing: UniProt: the universal protein knowledgebase
Functional Classification and Characterization of the Fungal Glycoside Hydrolase 28 Protein Family. PMID:35330219
High Resistance to Quinclorac in Multiple-Resistant Echinochloa colona Associated with Elevated Stress Tolerance Gene Expression and Enriched Xenobiotic Detoxification Pathway. PMID:35328069
Intrinsically disordered signaling proteins: Essential hub players in the control of stress responses in Saccharomyces cerevisiae. PMID:35290420
Prediction of the Active Components and Possible Targets of Xanthii Fructus Based on Network Pharmacology for Use in Chronic Rhinosinusitis. PMID:35287308
Proteome dataset of sea bass (Dicentrarchus labrax) skin-scales exposed to fluoxetine and estradiol. PMID:35252491
Proteome based mapping and molecular docking revealed DnaA as a potential drug target against Shigella sonnei. PMID:35241965
Identification and Validation of Ikaros (IKZF1) as a Cancer Driver Gene for Marek's Disease Virus-Induced Lymphomas. PMID:35208856
Kinetic and Stoichiometric Modeling-Based Analysis of Docosahexaenoic Acid (DHA) Production Potential by Crypthecodinium cohnii from Glycerol, Glucose and Ethanol. PMID:35200644
Cultivating Lentinula edodes on Substrate Containing Composted Sawdust Affects the Expression of Carbohydrate and Aromatic Amino Acid Metabolism-Related Genes. PMID:35191774
Predicting lncRNA-Protein Interactions by Heterogenous Network Embedding. PMID:35186016
Genome Nexus: A Comprehensive Resource for the Annotation and Interpretation of Genomic Variants in Cancer. PMID:35148171
Network Pharmacology- and Molecular Docking-Based Identification of Potential Phytocompounds from Argyreia capitiformis in the Treatment of Inflammation. PMID:35140801
Comparative Transcriptome Analysis in Taraxacum koksaghyz to Identify Genes that Determine Root Volume and Root Length. PMID:35140739
Tousled-like kinase 2 targets ASF1 histone chaperones through client mimicry. PMID:35136069
A common TMPRSS2 variant has a protective effect against severe COVID-19. PMID:35104687
Genome-Scale Modeling Specifies the Metabolic Capabilities of Rhizophagus irregularis. PMID:35076269
The crystal structure of the varicella-zoster Orf24-Orf27 nuclear egress complex spotlights multiple determinants of herpesvirus subfamily specificity. PMID:35074430
Prediction of the Mechanisms by Which Quercetin Enhances Cisplatin Action in Cervical Cancer: A Network Pharmacology Study and Experimental Validation. PMID:35070983
Using metagenomic data to boost protein structure prediction and discovery. PMID:35070166
The Bacteroidetes Aequorivita sp. and Kaistella jeonii Produce Promiscuous Esterases With PET-Hydrolyzing Activity. PMID:35069509
Recent Developments in Clinical Plasma Proteomics-Applied to Cardiovascular Research. PMID:35052841
Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life. PMID:35024091
Purification, Characterization, and Structural Studies of a Sulfatase from Pedobacter yulinensis. PMID:35011319
TF-Marker: a comprehensive manually curated database for transcription factors and related markers in specific cell and tissue types in human. PMID:34986601
Network Pharmacology Study on Molecular Mechanisms of Zhishi Xiebai Guizhi Decoction in the Treatment of Coronary Heart Disease. PMID:34966435
Long-term in vivo survival of 3D-bioprinted human lipoaspirate-derived adipose tissue: proteomic signature and cellular content. PMID:34957918
A Conserved Allosteric Site on Drug-Metabolizing CYPs: A Systematic Computational Assessment. PMID:34948012
Scalable Enrichment of Immunomodulatory Human Acute Myeloid Leukemia Cell Line-Derived Extracellular Vesicles. PMID:34943829
Common Features in lncRNA Annotation and Classification: A Survey. PMID:34940758
The effects of Tbx15 and Pax1 on facial and other physical morphology in mice. PMID:34938962
Spike Protein and the Various Cell-Surface Carbohydrates: An Interaction Study. PMID:34928574
Redirected Stress Responses in a Genome-Minimized 'midiBacillus' Strain with Enhanced Capacity for Protein Secretion. PMID:34904864
Computational modeling of human-nCoV protein-protein interaction network. PMID:34902553
Interaction between Rag genes results in a unique synergistic transcriptional response that enhances soybean resistance to soybean aphids. PMID:34895143
In-Silico Tool for Predicting, Scanning, and Designing Defensins. PMID:34880873
Systems biology and machine learning approaches identify drug targets in diabetic nephropathy. PMID:34873190
Designing of a Multi-epitope Vaccine against the Structural Proteins of Marburg Virus Exploiting the Immunoinformatics Approach. PMID:34870027
The Identification of the Biomarkers of Sheng-Ji Hua-Yu Formula Treated Diabetic Wound Healing Using Modular Pharmacology. PMID:34867329
The possible mechanism of Hippophae fructus oil applied in tympanic membrane repair identified based on network pharmacology and molecular docking. PMID:34859918
Potential Mechanism of Dingji Fumai Decoction Against Atrial Fibrillation Based on Network Pharmacology, Molecular Docking, and Experimental Verification Integration Strategy. PMID:34859062
A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation. PMID:34858137
The carbohydrate-active enzyme database: functions and literature. PMID:34850161
Identification of cerebrospinal fluid biomarkers for parkinsonism using a proteomics approach. PMID:34848724
Enantioselectivity of Chiral Derivatives of Xanthones in Virulence Effects of Resistant Bacteria. PMID:34832923
Proteomics Profiling with SWATH-MS Quantitative Analysis of Changes in the Human Brain with HIV Infection Reveals a Differential Impact on the Frontal and Temporal Lobes. PMID:34827437
High-resolution epitope mapping and characterization of SARS-CoV-2 antibodies in large cohorts of subjects with COVID-19. PMID:34811480
Ensemble of Template-Free and Template-Based Classifiers for Protein Secondary Structure Prediction. PMID:34768880
Inhibition of the renin-angiotensin system causes concentric hypertrophy of renal arterioles in mice and humans. PMID:34762601
scEnhancer: a single-cell enhancer resource with annotation across hundreds of tissue/cell types in three species. PMID:34761274
Genomic expansion of Aldh1a1 protects beavers against high metabolic aldehydes from lipid oxidation. PMID:34758328
An Ebola, Neisseria and Trypanosoma human protein interaction census reveals a conserved human protein cluster targeted by various human pathogens. PMID:34745452
MPS1 is involved in the HPV16-E7-mediated centrosomes amplification. PMID:34736484
Explainable machine learning predictions of dual-target compounds reveal characteristic structural features. PMID:34732806
New tale on LianHuaQingWen: IL6R/IL6/IL6ST complex is a potential target for COVID-19 treatment. PMID:34731090
Structure-Aware Mycobacterium tuberculosis Functional Annotation Uncloaks Resistance, Metabolic, and Virulence Genes. PMID:34726489
Comprehensive functional network analysis and screening of deleterious pathogenic variants in non-syndromic hearing loss causative genes. PMID:34714320
HPLC-MS identification and expression of Candida drug-resistance proteins from African HIV-infected patients. PMID:34708175
Capsicumicine, a New Bioinspired Peptide from Red Peppers Prevents Staphylococcal Biofilm In Vitro and In Vivo via a Matrix Anti-Assembly Mechanism of Action. PMID:34704807
Plastic-Degrading Potential across the Global Microbiome Correlates with Recent Pollution Trends. PMID:34700384
De novo transcriptome analysis provides insights into the salt tolerance of Podocarpus macrophyllus under salinity stress. PMID:34696735
MINTIA: a metagenomic INserT integrated assembly and annotation tool. PMID:34692239
Global Transcriptome Characterization and Assembly of the Thermophilic Ascomycete Chaetomium thermophilum. PMID:34680944
Design, synthesis, biological evaluation, and molecular modeling studies of pyrazole-benzofuran hybrids as new α-glucosidase inhibitor. PMID:34675367
Post-Translational Modifications of PCNA in Control of DNA Synthesis and DNA Damage Tolerance-the Implications in Carcinogenesis. PMID:34671219
Enolase 1, a Moonlighting Protein, as a Potential Target for Cancer Treatment. PMID:34671213
Transcriptomic and rRNA:rDNA Signatures of Environmental versus Enteric Enterococcus faecalis Isolates under Oligotrophic Freshwater Conditions. PMID:34668732
Network Pharmacology-Based and Molecular Docking-Based Analysis of Suanzaoren Decoction for the Treatment of Parkinson's Disease with Sleep Disorder. PMID:34660782
Network Pharmacology-Based Study of the Underlying Mechanisms of Huangqi Sijunzi Decoction for Alzheimer's Disease. PMID:34650613
Peptide Location Fingerprinting Reveals Tissue Region-Specific Differences in Protein Structures in an Ageing Human Organ. PMID:34638745
Predictive regulatory and metabolic network models for systems analysis of Clostridioides difficile. PMID:34637780
Diverse phosphate and auxin transport loci distinguish phosphate tolerant from sensitive Arabidopsis accessions. PMID:34636851
Distribution of bacteriocin genes in the lineages of Lactiplantibacillus plantarum. PMID:34625657
High-quality reference genome of Fasciola gigantica: Insights into the genomic signatures of transposon-mediated evolution and specific parasitic adaption in tropical regions. PMID:34610021
Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the THP-1 human leukaemia cell line. PMID:34599159
Mutational spectrum of BRAF gene in colorectal cancer patients in Saudi Arabia. PMID:34588906
In Silico Analysis of Fungal and Chloride-Dependent α-Amylases within the Family GH13 with Identification of Possible Secondary Surface-Binding Sites. PMID:34577174
Genome assembly of the popular Korean soybean cultivar Hwangkeum. PMID:34568925
Metabolites from Marine-Derived Fungi as Potential Antimicrobial Adjuvants. PMID:34564137
A New Subfamily of Glycoside Hydrolase Family 30 with Strict Xylobiohydrolase Function. PMID:34557520
The function of twister ribozyme variants in non-LTR retrotransposition in Schistosoma mansoni. PMID:34551436
Improved pathogenicity prediction for rare human missense variants. PMID:34551312
Neuroligin-3 and neuroligin-4X form nanoscopic clusters and regulate growth cone organization and size. PMID:34542148
Accurate annotation of protein coding sequences with IDTAXA. PMID:34541527
Hepatic Regulator of G Protein Signaling 6 (RGS6) drives non-alcoholic fatty liver disease by promoting oxidative stress and ATM-dependent cell death. PMID:34534913
Proteogenomic characterization of pancreatic ductal adenocarcinoma. PMID:34534465
Contraceptive and Infertility Target DataBase: a contraceptive drug development tool for targeting and analysis of human reproductive specific tissues†. PMID:34514504
Unique somatic variants in DNA from urine exosomes of individuals with bladder cancer. PMID:34514028
Proteogenomic analysis of pancreatic cancer subtypes. PMID:34506537
Immunogenic amino acid motifs and linear epitopes of COVID-19 mRNA vaccines. PMID:34499652
Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility. PMID:34499026
Mitochondria-localized AMPK responds to local energetics and contributes to exercise and energetic stress-induced mitophagy. PMID:34493662
Packpred: Predicting the Functional Effect of Missense Mutations. PMID:34490344
Distribution and diversity of dimetal-carboxylate halogenases in cyanobacteria. PMID:34461836
Comprehensive Analysis of the Systemic Transcriptomic Alternations and Inflammatory Response during the Occurrence and Progress of COVID-19. PMID:34457122
Drug repurposing for COVID-19 using computational screening: Is Fostamatinib/R406 a potential candidate? PMID:34455072
Novel Anti-Melanogenic Compounds, (Z)-5-(Substituted Benzylidene)-4-thioxothiazolidin-2-one Derivatives: In Vitro and In Silico Insights. PMID:34443550
Chironomus ramosus Larval Microbiome Composition Provides Evidence for the Presence of Detoxifying Enzymes. PMID:34442650
Non-Specific Binding and Cross-Reaction of ELISA: A Case Study of Porcine Hemoglobin Detection. PMID:34441486
The value of primary transcripts to the clinical and non-clinical genomics community: Survey results and roadmap for improvements. PMID:34435752
Potential Arabidopsis thaliana glucosinolate genes identified from the co-expression modules using graph clustering approach. PMID:34430080
Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo. PMID:34428301
Escherichia coli AraJ boosts utilization of arabinose in metabolically engineered cyanobacterium Synechocystis sp. PCC 6803. PMID:34387784
Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors. PMID:34387667
Data on the first functionally-annotated de novo transcriptome assembly for North American flying squirrels (genus Glaucomys). PMID:34381854
Insight into membraneless organelles and their associated proteins: Drivers, Clients and Regulators. PMID:34377363
Properties of peptides released from salmon and carp via simulated human-like gastrointestinal digestion described applying quantitative parameters. PMID:34375367
High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement. PMID:34373642
Allosteric regulation within the highly interconnected structural scaffold of AraC/XylS homologs tolerates a wide range of amino acid changes. PMID:34369028
A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense. PMID:34367224
Differential Domain Distribution of gnomAD- and Disease-Linked Connexin Missense Variants. PMID:34360596
ACO2 clinicobiological dataset with extensive phenotype ontology annotation. PMID:34354088
State-of-the-Art Biocatalysis. PMID:34345663
In vitro and in silico analysis reveals antifungal activity and potential targets of curcumin on Paracoccidioides spp. PMID:34324170
Discovering and Summarizing Relationships Between Chemicals, Genes, Proteins, and Diseases in PubChem. PMID:34322655
Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students. PMID:34318869
The clinical importance of tandem exon duplication-derived substitutions. PMID:34302486
Ranked Choice Voting for Representative Transcripts with TRaCE. PMID:34297055
GWAS-Top Polymorphisms Associated With Late-Onset Alzheimer Disease in Brazil: Pointing Out Possible New Culprits Among Non-Coding RNAs. PMID:34291080
Accurate prediction of protein structures and interactions using a three-track neural network. PMID:34282049
Automatization and self-maintenance of the O-GlcNAcome catalog: a smart scientific database. PMID:34279596
NANOS2 is a sequence-specific mRNA-binding protein that promotes transcript degradation in spermatogonial stem cells. PMID:34278268
Trehalose-Induced Remodelling of the Human Microbiota Affects Clostridioides difficile Infection Outcome in an In Vitro Colonic Model: A Pilot Study. PMID:34277467
Transfer learning via multi-scale convolutional neural layers for human-virus protein-protein interaction prediction. PMID:34273146
Innate-like self-reactive B cells infiltrate human renal allografts during transplant rejection. PMID:34272370
Genetic Control of Human Infection with SARS-CoV-2. PMID:34248311
Reciprocal interaction between SIRT6 and APC/C regulates genomic stability. PMID:34244565
Study on the Molecular Mechanism of the Herbal Couple Sparganii Rhizoma-Curcumae Rhizoma in the Treatment of Lung Cancer Based on Network Pharmacology. PMID:34239587
MaxDIA enables library-based and library-free data-independent acquisition proteomics. PMID:34239088
Immune Tolerance-Adjusted Personalized Immunogenicity Prediction for Pompe Disease. PMID:34220802
De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism. PMID:34215181
Protein Secondary Structure Prediction With a Reductive Deep Learning Method. PMID:34211967
Network Pharmacology-Based Approach to Investigate the Molecular Targets of Rhubarb for Treating Cancer. PMID:34211578
The origin and radiation of the phosphoprotein phosphatase (PPP) enzymes of Eukaryotes. PMID:34211082
Toward a Coronavirus Knowledge Graph. PMID:34209818
Analysis of High Molecular Mass Compounds from the Spider Pamphobeteus verdolaga Venom Gland. A Transcriptomic and MS ID Approach. PMID:34209760
A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. PMID:34207490
Chimera Spectrum Diagnostics for Peptides Using Two-Dimensional Partial Covariance Mass Spectrometry. PMID:34207274
Antimicrobial Activity of a Library of Thioxanthones and Their Potential as Efflux Pump Inhibitors. PMID:34203998
Spatially Enriched Paralog Rearrangements Argue Functionally Diverse Ribosomes Arise during Cold Acclimation in Arabidopsis. PMID:34200446
Mutagenic Analysis of the Putative ABCC6 Substrate-Binding Cavity Using a New Homology Model. PMID:34199119
UniBind: maps of high-confidence direct TF-DNA interactions across nine species. PMID:34174819
Genome-scale comparative analysis for host resistance against sea lice between Atlantic salmon and rainbow trout. PMID:34168167
LSTM-PHV: prediction of human-virus protein-protein interactions by LSTM with word2vec. PMID:34160596
Immunoinformatics prediction of potential B-cell and T-cell epitopes as effective vaccine candidates for eliciting immunogenic responses against Epstein-Barr virus. PMID:34154948
Exploring the Mechanism of Total Flavonoids of Drynariae Rhizoma to Improve Large Bone Defects by Network Pharmacology and Experimental Assessment. PMID:34149403
Making fundamental scientific discoveries by combining information from literature, databases, and computational tools - An example. PMID:34136100
Identification METTL18 as a Potential Prognosis Biomarker and Associated With Immune Infiltrates in Hepatocellular Carcinoma. PMID:34123827
Ayurveda botanicals in COVID-19 management: An in silico multi-target approach. PMID:34115763
Identification of sequence changes in myosin II that adjust muscle contraction velocity. PMID:34111116
Investigating the active compounds and mechanism of HuaShi XuanFei formula for prevention and treatment of COVID-19 based on network pharmacology and molecular docking analysis. PMID:34105049
Assessment of protein-protein interfaces in cryo-EM derived assemblies. PMID:34099703
Comparative Genomics of Peroxisome Biogenesis Proteins: Making Sense of the PEX Proteins. PMID:34095119
The proteome of the human endolymphatic sac endolymph. PMID:34088924
Identifying the molecular targets and mechanisms of xuebijing injection for the treatment of COVID-19 via network parmacology and molecular docking. PMID:34077310
Prospecting Biomarkers for Diagnostic and Therapeutic Approaches in Pythiosis. PMID:34071174
Urolithin and Reduced Urolithin Derivatives as Potent Inhibitors of Tyrosinase and Melanogenesis: Importance of the 4-Substituted Resorcinol Moiety. PMID:34070680
Xanthones Active against Multidrug Resistance and Virulence Mechanisms of Bacteria. PMID:34069329
Myeloid-derived growth factor regulates neutrophil motility in interstitial tissue damage. PMID:34047769
Assessing the functional relevance of splice isoforms. PMID:34046593
Structured data sets of compounds with multi-target and corresponding single-target activity from biological assays. PMID:34046190
Comparative study of His- and Non-His-tagged CLIC proteins, reveals changes in their enzymatic activity. PMID:34036185
ML-AdVInfect: A Machine-Learning Based Adenoviral Infection Predictor. PMID:34026828
Comprehensive analysis of the lysine acetylome and succinylome in the hippocampus of gut microbiota-dysbiosis mice. PMID:34026284
Genome sequence and transcriptome profiles of pathogenic fungus Paecilomyces penicillatus reveal its interactions with edible fungus Morchella importuna. PMID:34025947
Deciphering the architecture and interactome of hnRNP proteins and enigmRBPs. PMID:34017973
The symbiotic relationship between Caenorhabditis elegans and members of its microbiome contributes to worm fitness and lifespan extension. PMID:34011272
Agrobacterium tumefaciens Growth Pole Ring Protein: C Terminus and Internal Apolipoprotein Homologous Domains Are Essential for Function and Subcellular Localization. PMID:34006657
Neutrophil-to-lymphocyte ratio and outcomes in patients with new-onset or worsening heart failure with reduced and preserved ejection fraction. PMID:33998162
ARTEMIS: A Novel Mass-Spec Platform for HLA-Restricted Self and Disease-Associated Peptide Discovery. PMID:33986749
Protein-Based Immunome Wide Association Studies (PIWAS) for the Discovery of Significant Disease-Associated Antigens. PMID:33986742
Analysis of Zika virus capsid-Aedes aegypti mosquito interactome reveals pro-viral host factors critical for establishing infection. PMID:33986255
IDSM ChemWebRDF: SPARQLing small-molecule datasets. PMID:33980298
Complementing the pulp proteome via sampling with a picosecond infrared laser (PIRL). PMID:33977388
hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies. PMID:33973408
A putative novel starch-binding domain revealed by in silico analysis of the N-terminal domain in bacterial amylomaltases from the family GH77. PMID:33968573
Reactome and the Gene Ontology: Digital convergence of data resources. PMID:33964129
A zinc finger protein gene signature enables bladder cancer treatment stratification. PMID:33962398
Spatial Distribution of Private Gene Mutations in Clear Cell Renal Cell Carcinoma. PMID:33946379
The human cytomegalovirus protein UL147A downregulates the most prevalent MICA allele: MICA*008, to evade NK cell-mediated killing. PMID:33939764
The mammalian cholesterol synthesis enzyme squalene monooxygenase is proteasomally truncated to a constitutively active form. PMID:33933449
IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease. PMID:33929018
Behavior of Chemokine Receptor 6 (CXCR6) in Complex with CXCL16 Soluble form Chemokine by Molecular Dynamic Simulations: General Protein‒Ligand Interaction Model and 3D-QSAR Studies of Synthetic Antagonists. PMID:33920834
Screening of Twelve Pea (Pisum sativum L.) Cultivars and Their Isolates Focusing on the Protein Characterization, Functionality, and Sensory Profiles. PMID:33918162
Purification and quantitative proteomic analysis of cell bodies and protrusions. PMID:33912849
CAZymes in Maribacter dokdonensis 62-1 From the Patagonian Shelf: Genomics and Physiology Compared to Related Flavobacteria and a Co-occurring Alteromonas Strain. PMID:33912144
Erosion of human X chromosome inactivation causes major remodeling of the iPSC proteome. PMID:33910018
An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19. PMID:33895786
Increased expression of peptides from non-coding genes in cancer proteomics datasets suggests potential tumor neoantigens. PMID:33888849
Critical assessment of protein intrinsic disorder prediction. PMID:33875885
Phylogenetic analysis of Harmonin homology domains. PMID:33853521
iNetModels 2.0: an interactive visualization and database of multi-omics data. PMID:33849075
Origin and evolution of nonulosonic acid synthases and their relationship with bacterial pathogenicity revealed by a large-scale phylogenetic analysis. PMID:33848237
Machine learning reveals that structural features distinguishing promiscuous and non-promiscuous compounds depend on target combinations. PMID:33846469
Bacterial avidins are a widely distributed protein family in Actinobacteria, Proteobacteria and Bacteroidetes. PMID:33836663
Peptide location fingerprinting reveals modification-associated biomarker candidates of ageing in human tissue proteomes. PMID:33830638
Database limitations for studying the human gut microbiome. PMID:33816940
Initial Insights Into the Genetic Epidemiology of SARS-CoV-2 Isolates From Kerala Suggest Local Spread From Limited Introductions. PMID:33815467
A SARS-CoV-2 -human metalloproteome interaction map. PMID:33813307
Linear B-Cell Epitope Prediction for In Silico Vaccine Design: A Performance Review of Methods Available via Command-Line Interface. PMID:33809918
Integration of Data from Liquid-Liquid Phase Separation Databases Highlights Concentration and Dosage Sensitivity of LLPS Drivers. PMID:33809541
Ensemble of Multiple Classifiers for Multilabel Classification of Plant Protein Subcellular Localization. PMID:33808227
Approaches to Identify and Characterise the Post-Transcriptional Roles of lncRNAs in Cancer. PMID:33803328
PIM-induced phosphorylation of Notch3 promotes breast cancer tumorigenicity in a CSL-independent fashion. PMID:33775697
Hepatic steatosis and steatohepatitis: a functional meta-analysis of sex-based differences in transcriptomic studies. PMID:33766130
Improving integrative 3D modeling into low- to medium-resolution electron microscopy structures with evolutionary couplings. PMID:33759266
Dissemination of novel Tn7 family transposons carrying genes for synthesis and uptake of fimsbactin siderophores among Acinetobacter baumannii isolates. PMID:33749577
Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics. PMID:33749263
Functional and genomic characterization of Komagataeibacter uvaceti FXV3, a multiple stress resistant bacterium producing increased levels of cellulose. PMID:33747802
Evolution of mammalian longevity: age-related increase in autophagy in bats compared to other mammals. PMID:33744862
Swiss-PO: a new tool to analyze the impact of mutations on protein three-dimensional structures for precision oncology. PMID:33737716
Genomic signatures of drift and selection driven by predation and human pressure in an insular lizard. PMID:33731784
Hepatitis B virus X protein promotes vimentin expression via LIM and SH3 domain protein 1 to facilitate epithelial-mesenchymal transition and hepatocarcinogenesis. PMID:33722250
Discovery and engineering of small SlugCas9 with broad targeting range and high specificity and activity. PMID:33721016
Crystal structure of timothy grass allergen Phl p 12.0101 reveals an unusual profilin dimer. PMID:33720678
A Second Look at FAIR in Proteomic Investigations. PMID:33719446
A comprehensive molecular characterization of the 8q22.2 region reveals the prognostic relevance of OSR2 mRNA in muscle invasive bladder cancer. PMID:33711044
Evidence for CAT gene being functionally involved in the susceptibility of COVID-19. PMID:33710662
Short loop functional commonality identified in leukaemia proteome highlights crucial protein sub-networks. PMID:33709075
UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase-substrate interactions. PMID:33693667
Network pharmacology-based study to explore the mechanism of the Yiqi Gubiao pill in lung cancer treatment. PMID:33692853
Integrative network analyses of transcriptomics data reveal potential drug targets for acute radiation syndrome. PMID:33692493
gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. PMID:33691770
Identifying loci with different allele frequencies among cases of eight psychiatric disorders using CC-GWAS. PMID:33686288
Dihydrouridine synthesis in tRNAs is under reductive evolution in Mollicutes. PMID:33685366
The very early evolution of protein translocation across membranes. PMID:33684113
The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application. PMID:33677548
Polymorphism Detection of GDF9 Gene and Its Association with Litter Size in Luzhong Mutton Sheep (Ovis aries). PMID:33671790
Study of Endogen Substrates, Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics. PMID:33671368
Mayday sustains trans-synaptic BMP signaling required for synaptic maintenance with age. PMID:33667157
Transcription-translation error: In-silico investigation of the structural and functional impact of deleterious single nucleotide polymorphisms in GULP1 gene. PMID:33665355
Sequence Alignment Using Machine Learning for Accurate Template-based Protein Structure Prediction. PMID:33659566
The Interplay of Cholesterol and Ligand Binding in hTSPO from Classical Molecular Dynamics Simulations. PMID:33652554
Deciphering potential pharmacological mechanism of Sha-Shen-Mai-Dong decoction on primary Sjogren's syndrome. PMID:33648502
Crystal structures of adenylylated and unadenylylated PII protein GlnK from Corynebacterium glutamicum. PMID:33645536
Haplotype-resolved diverse human genomes and integrated analysis of structural variation. PMID:33632895
Comprehensive in silico analysis and molecular dynamics of the superoxide dismutase 1 (SOD1) variants related to amyotrophic lateral sclerosis. PMID:33630959
The STI1-domain is a flexible alpha-helical fold with a hydrophobic groove. PMID:33620121
Molecular basis of tail-anchored integral membrane protein recognition by the cochaperone Sgt2. PMID:33610544
A potential interaction between the SARS-CoV-2 spike protein and nicotinic acetylcholine receptors. PMID:33609494
Identification of novel lipid droplet factors that regulate lipophagy and cholesterol efflux in macrophage foam cells. PMID:33590792
Transcriptome analysis reveals major transcriptional changes during regrowth after mowing of red clover (Trifolium pratense). PMID:33588756
A Network Pharmacology Approach to Estimate Potential Targets of the Active Ingredients of Epimedium for Alleviating Mild Cognitive Impairment and Treating Alzheimer's Disease. PMID:33574879
A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida). PMID:33570560
Electric Blue: Molecular Evolution of Three-Finger Toxins in the Long-Glanded Coral Snake Species Calliophis bivirgatus. PMID:33567660
Novel Two-Component System-Like Elements Reveal Functional Domains Associated with Restriction-Modification Systems and paraMORC ATPases in Bacteria. PMID:33565597
Practical Considerations Relating to Routine Clinical Biomarker Testing for Non-small Cell Lung Cancer: Focus on Testing for RET Fusions. PMID:33553195
BioMaster: An Integrated Database and Analytic Platform to Provide Comprehensive Information About BioBrick Parts. PMID:33552037
CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator. PMID:33547799
Proteomic fingerprints of damage in extracellular matrix assemblies. PMID:33543016
In-silico definition of the Drosophila melanogaster matrisome. PMID:33543012
Genome annotation of disease-causing microorganisms. PMID:33537706
Mapping proteolytic neo-N termini at the surface of living cells. PMID:33536314
Genome-wide DNA methylation dynamics during epigenetic reprogramming in the porcine germline. PMID:33536045
Analyzing the potential therapeutic mechanism of Huashi Baidu Decoction on severe COVID-19 through integrating network pharmacological methods. PMID:33520684
Physiological and Proteomic Signatures Reveal Mechanisms of Superior Drought Resilience in Pearl Millet Compared to Wheat. PMID:33519854
Coxsackievirus B3 Infection of Human iPSC Lines and Derived Primary Germ-Layer Cells Regarding Receptor Expression. PMID:33513663
Network Pharmacology-Based Analysis on the Mechanism of Action of Ephedrae Herba-Cinnamomi Ramulus Couplet Medicines in the Treatment for Psoriasis. PMID:33513128
Pervasive duplication of tumor suppressors in Afrotherians during the evolution of large bodies and reduced cancer risk. PMID:33513090
Arabidopsis REI-LIKE proteins activate ribosome biogenesis during cold acclimation. PMID:33510206
CE16 acetylesterases: in silico analysis, catalytic machinery prediction and comparison with related SGNH hydrolases. PMID:33505839
Mesenchymal stem cells secretome: The cornerstone of cell-free regenerative medicine. PMID:33505599
Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems. PMID:33495623
Ensemble-AMPPred: Robust AMP Prediction and Recognition Using the Ensemble Learning Method with a New Hybrid Feature for Differentiating AMPs. PMID:33494403
Integrative computational approach identifies drug targets in CD4+ T-cell-mediated immune disorders. PMID:33483502
A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses. PMID:33482803
SNF-NN: computational method to predict drug-disease interactions using similarity network fusion and neural networks. PMID:33482713
Metagenomic analysis of the cow, sheep, reindeer and red deer rumen. PMID:33479378
Integrative multiomics analysis of Premolis semirufa caterpillar venom in the search for molecules leading to a joint disease. PMID:33479267
Investigating β-Lactam Drug Targets in Mycobacterium tuberculosis Using Chemical Probes. PMID:33470787
In silico T cell epitope identification for SARS-CoV-2: Progress and perspectives. PMID:33465451
Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins. PMID:33446856
CHD2-Related CNS Pathologies. PMID:33435571
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions. PMID:33431024
SmartGraph: a network pharmacology investigation platform. PMID:33430980
Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species. PMID:33428734
Challenge of post-COVID era: management of cardiovascular complications in asymptomatic carriers of SARS-CoV-2. PMID:33426593
Proteomic analysis of platelet-rich and platelet-poor plasma. PMID:33426223
Artificial Intelligence-Based Application to Explore Inhibitors of Neurodegenerative Diseases. PMID:33414713
Combination of lyophilized adipose-derived stem cell concentrated conditioned medium and polysaccharide hydrogel in the inhibition of hypertrophic scarring. PMID:33413617
MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes. PMID:33407081
Integrated molecular characterisation of the MAPK pathways in human cancers reveals pharmacologically vulnerable mutations and gene dependencies. PMID:33398072
ADP-ribose and analogues bound to the deMARylating macrodomain from the bat coronavirus HKU4. PMID:33397718
Identification of Critical Genes and Proteins for Stent Restenosis Induced by Esophageal Benign Hyperplasia in Esophageal Cancer. PMID:33391336
Alteration of Proteotranscriptomic Landscape Reveals the Transcriptional Regulatory Circuits Controlling Key-Signaling Pathways and Metabolic Reprogramming During Tumor Evolution. PMID:33384992
Genotype and transcriptome effects on somatic embryogenesis in Cryptomeria japonica. PMID:33373415
Multipath: An R Package to Generate Integrated Reproducible Pathway Models. PMID:33371258
Complete chloroplast genome comparisons for Pityopsis (Asteraceae). PMID:33370297
Crosstalk between Ubiquitination and Other Post-translational Protein Modifications in Plant Immunity. PMID:33367245
In silico and in vitro insights into tyrosinase inhibitors with a 2-thioxooxazoline-4-one template. PMID:33363708
Comparison of the central human and mouse platelet signaling cascade by systems biological analysis. PMID:33353544
The identification and characterisation of novel bioactive peptides derived from porcine liver. PMID:33336193
Maternal diet alters human milk oligosaccharide composition with implications for the milk metagenome. PMID:33328537
Genetic architecture of host proteins involved in SARS-CoV-2 infection. PMID:33328453
Whole-exome sequencing of non-BRCA1/BRCA2 mutation carrier cases at high-risk for hereditary breast/ovarian cancer. PMID:33326660
Discovery and Structure-Activity Relationships of Novel Template, Truncated 1'-Homologated Adenosine Derivatives as Pure Dual PPARγ/δ Modulators. PMID:33325691
Improved Protein Model Quality Assessment By Integrating Sequential And Pairwise Features Using Deep Learning. PMID:33325480
Computational Prediction of Antiangiogenesis Synergistic Mechanisms of Total Saponins of Panax japonicus Against Rheumatoid Arthritis. PMID:33324204
The transcription regulator and c-di-GMP phosphodiesterase PdeL represses motility in Escherichia coli. PMID:33318048
Mechanism of Action of Bu-Fei-Yi-Shen Formula in Treating Chronic Obstructive Pulmonary Disease Based on Network Pharmacology Analysis and Molecular Docking Validation. PMID:33313323
Alteration in the Culex pipiens transcriptome reveals diverse mechanisms of the mosquito immune system implicated upon Rift Valley fever phlebovirus exposure. PMID:33301456
New information of dopaminergic agents based on quantum chemistry calculations. PMID:33299000
AnOxPePred: using deep learning for the prediction of antioxidative properties of peptides. PMID:33293615
Parthenolide inhibits the growth of non-small cell lung cancer by targeting epidermal growth factor receptor. PMID:33292235
Modelling and Recognition of Protein Contact Networks by Multiple Kernel Learning and Dissimilarity Representations. PMID:33286565
Non-adaptive Evolution of Trimeric Autotransporters in Brucellaceae. PMID:33281759
A Network Pharmacology-Based Strategy for Unveiling the Mechanisms of Tripterygium Wilfordii Hook F against Diabetic Kidney Disease. PMID:33274236
The Nucleosome Remodeling and Deacetylase Complex Has an Asymmetric, Dynamic, and Modular Architecture. PMID:33264611
Mining potentially actionable kinase gene fusions in cancer cell lines with the KuNG FU database. PMID:33257674
Deciphering the Role of Filamin B Calponin-Homology Domain in Causing the Larsen Syndrome, Boomerang Dysplasia, and Atelosteogenesis Type I Spectrum Disorders via a Computational Approach. PMID:33255942
Identification of the anti-breast cancer targets of triterpenoids in Liquidambaris Fructus and the hints for its traditional applications. PMID:33246450
MoonProt 3.0: an update of the moonlighting proteins database. PMID:33245761
Excavating the functionally crucial active-site residues of the DXS protein of Bacillus subtilis by exploring its closest homologues. PMID:33242110
UniProt: the universal protein knowledgebase in 2021. PMID:33237286
Top-Down Proteomics of Endogenous Membrane Proteins Enabled by Cloud Point Enrichment and Multidimensional Liquid Chromatography-Mass Spectrometry. PMID:33231430
Succinylation Site Prediction Based on Protein Sequences Using the IFS-LightGBM (BO) Model. PMID:33224267
E3 Ubiquitin Ligase APC/CCdh1 Negatively Regulates FAH Protein Stability by Promoting Its Polyubiquitination. PMID:33218190
Spatiotemporal Proteomic Analysis of Stress Granule Disassembly Using APEX Reveals Regulation by SUMOylation and Links to ALS Pathogenesis. PMID:33217318
Comparative Genomics of Strictly Vertically Transmitted, Feminizing Microsporidia Endosymbionts of Amphipod Crustaceans. PMID:33216144
Network-based approach highlighting interplay among anti-hypertensives: target coding-genes: diseases. PMID:33214616
Proteome-Scale Detection of Differential Conservation Patterns at Protein and Subprotein Levels with BLUR. PMID:33211099
Repurposed drugs and nutraceuticals targeting envelope protein: A possible therapeutic strategy against COVID-19. PMID:33189776
Impact of Porcine Arterivirus, Influenza B, and Their Coinfection on Antiviral Response in the Porcine Lung. PMID:33187194
Assessing the Ability of Developmentally Precocious Estrogen Signaling to Recapitulate Ovarian Transcriptomes and Follicle Dynamics in Alligators from a Contaminated Lake. PMID:33186072
A human cell atlas of fetal gene expression. PMID:33184181
Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry. PMID:33183009
Comparative Genomics Platform and Phylogenetic Analysis of Fungal Laccases and Multi-Copper Oxidases. PMID:33177916
RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef. PMID:33175867
Molecular signatures of the rediae, cercariae and adult stages in the complex life cycles of parasitic flatworms (Digenea: Psilostomatidae). PMID:33168070
Triage of documents containing protein interactions affected by mutations using an NLP based machine learning approach. PMID:33167858
LegumeIP V3: from models to crops-an integrative gene discovery platform for translational genomics in legumes. PMID:33166388
Transcriptomics reveals specific molecular mechanisms underlying transgenerational immunity in Manduca sexta. PMID:33144962
Expression of a novel brain specific isoform of C3G is regulated during development. PMID:33139841
Phage Proteins Required for Tail Fiber Assembly Also Bind Specifically to the Surface of Host Bacterial Strains. PMID:33139482
Modelling of pathogen-host systems using deeper ORF annotations and transcriptomics to inform proteomics analyses. PMID:33133425
ConCysFind: a pipeline tool to predict conserved amino acids of protein sequences across the plant kingdom. PMID:33129266
The Dynamic Proteome of Oligodendrocyte Lineage Differentiation Features Planar Cell Polarity and Macroautophagy Pathways. PMID:33128372
p39-associated Cdk5 activity regulates dendritic morphogenesis. PMID:33127972
Trametinib Induces the Stabilization of a Dual GNAQ p.Gly48Leu- and FGFR4 p.Cys172Gly-Mutated Uveal Melanoma. The Role of Molecular Modelling in Personalized Oncology. PMID:33126538
Evaluation of gene expression and protein structural modeling involved in persister cell formation in Salmonella Typhimurium. PMID:33125683
Transcriptomes of Major Proximal Tubule Cell Culture Models. PMID:33122286
Potential novel proteomic biomarkers for diagnosis of vertebral osteomyelitis identified using an immunomics protein array technique: Two cases reports. PMID:33120821
Chromatin accessibility dynamics of Chlamydia-infected epithelial cells. PMID:33109274
Radiation of nitrogen-metabolizing enzymes across the tree of life tracks environmental transitions in Earth history. PMID:33108025
The adenoviral protein E4orf4: a probing tool to decipher mechanical stress-induced nuclear envelope remodeling in tumor cells. PMID:33103553
Long non-coding RNAs in plants: emerging modulators of gene activity in development and stress responses. PMID:33099688
Late first trimester circulating microparticle proteins predict the risk of preeclampsia < 35 weeks and suggest phenotypic differences among affected cases. PMID:33087742
Differential gene regulatory pattern in the human brain from schizophrenia using transcriptomic-causal network. PMID:33087039
Dendritic Cells and Microglia Have Non-redundant Functions in the Inflamed Brain with Protective Effects of Type 1 cDCs. PMID:33086061
Effects of Single-Nucleotide Polymorphisms in Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2): A Comprehensive Study. PMID:33082841
A Network Pharmacology Technique to Investigate the Synergistic Mechanisms of Salvia miltiorrhiza and Radix puerariae in Treatment of Cardio-Cerebral Vascular Diseases. PMID:33082828
Torin 2 Derivative, NCATS-SM3710, Has Potent Multistage Antimalarial Activity through Inhibition of P. falciparum Phosphatidylinositol 4-Kinase (Pf PI4KIIIβ). PMID:33073193
Alternative Splicing Enhances the Transcriptome Complexity of Liriodendron chinense. PMID:33072153
A systematic evaluation of bioinformatics tools for identification of long noncoding RNAs. PMID:33055239
Vulpeculin: a novel and abundant lipocalin in the urine of the common brushtail possum, Trichosurus vulpecula. PMID:33022194
Genome-scale metabolic models highlight stage-specific differences in essential metabolic pathways in Trypanosoma cruzi. PMID:33021977
SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features. PMID:33019775
Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN. PMID:33013724
Alternative Splicing of Opioid Receptor Genes Shows a Conserved Pattern for 6TM Receptor Variants. PMID:33010019
Genome Analysis of "Candidatus Regiella insecticola" Strain TUt, Facultative Bacterial Symbiont of the Pea Aphid Acyrthosiphon pisum. PMID:33004445
Structure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies. PMID:32994567
Identification of osteoporosis markers through bioinformatic functional analysis of serum proteome. PMID:32991410
Physico-chemical characterization and topological analysis of pathogenesis-related proteins from Arabidopsis thaliana and Oryza sativa using in-silico approaches. PMID:32986761
Polyphyletic origin, intracellular invasion, and meiotic genes in the putatively asexual agamococcidians (Apicomplexa incertae sedis). PMID:32985520
Single-nucleotide polymorphism of the DNA cytosine deaminase APOBEC3H haplotype I leads to enzyme destabilization and correlates with lung cancer. PMID:32984821
Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome. PMID:32974593
Single-Cell RNA Sequencing Analysis Reveals a Crucial Role for CTHRC1 (Collagen Triple Helix Repeat Containing 1) Cardiac Fibroblasts After Myocardial Infarction. PMID:32972203
Complete genome sequence of the biocontrol agent Serratia marcescens strain N4-5 uncovers an assembly artefact. PMID:32965626
Identification of destabilizing SNPs in SARS-CoV2-ACE2 protein and spike glycoprotein: implications for virus entry mechanisms. PMID:32964802
Pulmonary alveolar microlithiasis: no longer in the stone age. PMID:32964001
Vitamin D3 receptor polymorphisms regulate T cells and T cell-dependent inflammatory diseases. PMID:32958661
Extension of the taxonomic coverage of the family GH126 outside Firmicutes and in silico characterization of its non-catalytic terminal domains. PMID:32953382
Transcriptomic data on the transgenerational exposure of the keystone amphipod Gammarus locusta to simvastatin. PMID:32944603
On-chip protein separation with single-molecule resolution. PMID:32943759
Functional characterization of rare NRXN1 variants identified in autism spectrum disorders and schizophrenia. PMID:32942984
Mechanisms of indigo naturalis on treating ulcerative colitis explored by GEO gene chips combined with network pharmacology and molecular docking. PMID:32938944
BITS2019: the sixteenth annual meeting of the Italian society of bioinformatics. PMID:32938383
Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito. PMID:32938368
Exercise immunology: Future directions. PMID:32928447
Isolation and characterisation of Leishmania donovani protein antigens from urine of visceral leishmaniasis patients. PMID:32925980
ANDDigest: a new web-based module of ANDSystem for the search of knowledge in the scientific literature. PMID:32921303
How to use the MEROPS database and website to help understand peptidase specificity. PMID:32920969
Mining and Statistical Modeling of Natural and Variant Class IIa Bacteriocins Elucidate Activity and Selectivity Profiles across Species. PMID:32917749
Executable biochemical space for specification and analysis of biochemical systems. PMID:32915842
Long non‑coding RNA MEG3 suppresses epithelial‑to‑mesenchymal transition by inhibiting the PSAT1‑dependent GSK‑3β/Snail signaling pathway in esophageal squamous cell carcinoma. PMID:32901893
High-resolution proteomics reveals differences in the proteome of spelt and bread wheat flour representing targets for research on wheat sensitivities. PMID:32895444
Effect of sequence padding on the performance of deep learning models in archaeal protein functional prediction. PMID:32884053
1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding. PMID:32883364
TargetDB: A target information aggregation tool and tractability predictor. PMID:32877430
Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns. PMID:32875947
Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution. PMID:32873878
Simple Targeted Assays for Metabolic Pathways and Signaling: A Powerful Tool for Targeted Proteomics. PMID:32865986
RNA-binding and prion domains: the Yin and Yang of phase separation. PMID:32857852
Characterization of the F Locus Responsible for Floral Anthocyanin Production in Potato. PMID:32855168
Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis). PMID:32852039
Functionally uncoupled transcription-translation in Bacillus subtilis. PMID:32848247
PSCAN: Spatial scan tests guided by protein structures improve complex disease gene discovery and signal variant detection. PMID:32847609
SBML Level 3: an extensible format for the exchange and reuse of biological models. PMID:32845085
An allosteric site on MKP5 reveals a strategy for small-molecule inhibition. PMID:32843541
Identification and classification of differentially expressed genes reveal potential molecular signature associated with SARS-CoV-2 infection in lung adenocarcinomal cells. PMID:32835074
Sex differences in circulating proteins in heart failure with preserved ejection fraction. PMID:32831121
Immunoinformatics-guided design of an epitope-based vaccine against severe acute respiratory syndrome coronavirus 2 spike glycoprotein. PMID:32828069
PINCER: improved CRISPR/Cas9 screening by efficient cleavage at conserved residues. PMID:32821942
Pan-cancer proteogenomic analysis reveals long and circular noncoding RNAs encoding peptides. PMID:32803163
Transcriptome dataset for RNA-seq analysis of axolotl embryonic oropharyngeal endoderm explants. PMID:32802925
Sequence alignment generation using intermediate sequence search for homology modeling. PMID:32802276
Abundant Taxa and Favorable Pathways in the Microbiome of Soda-Saline Lakes in Inner Mongolia. PMID:32793172
S-layer associated proteins contribute to the adhesive and immunomodulatory properties of Lactobacillus acidophilus NCFM. PMID:32787778
Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site. PMID:32785287
JAGN1, tetraspanins, and Erv proteins: is common topology indicative of common function in cargo sorting? PMID:32783652
Allelic polymorphisms in a glycosyltransferase gene shape glycan repertoire in the O-linked protein glycosylation system of Neisseria. PMID:32776107
Sexually Dimorphic Crosstalk at the Maternal-Fetal Interface. PMID:32772088
The Potential Role of Preoperative Pain, Catastrophizing, and Differential Gene Expression on Pain Outcomes after Pediatric Spinal Fusion. PMID:32771349
DRAM for distilling microbial metabolism to automate the curation of microbiome function. PMID:32766782
Mapping Coeliac Toxic Motifs in the Prolamin Seed Storage Proteins of Barley, Rye, and Oats Using a Curated Sequence Database. PMID:32766270
Characterization of a SPM-1 metallo-beta-lactamase-producing Pseudomonas aeruginosa by comparative genomics and phenotypic analysis. PMID:32764694
FLUTE: Fast and reliable knowledge retrieval from biomedical literature. PMID:32761077
Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data. PMID:32746932
Transcriptomic profiling of the medicinal plant Clitoria ternatea: identification of potential genes in cyclotide biosynthesis. PMID:32728092
Contributions of de novo variants to systemic lupus erythematosus. PMID:32724065
TEX15 is an essential executor of MIWI2-directed transposon DNA methylation and silencing. PMID:32719317
Functions of Bacterial tRNA Modifications: From Ubiquity to Diversity. PMID:32718697
(Phospho)proteomic Profiling of Microsatellite Unstable CRC Cells Reveals Alterations in Nuclear Signaling and Cholesterol Metabolism Caused by Frameshift Mutation of NMD Regulator UPF3A. PMID:32718059
Phosphodiesterase Inhibitors for Alzheimer's Disease: A Systematic Review of Clinical Trials and Epidemiology with a Mechanistic Rationale. PMID:32715279
Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity. PMID:32711472
Shedding the Light on Litopenaeus vannamei Differential Muscle and Hepatopancreas Immune Responses in White Spot Syndrome Virus (WSSV) Exposure. PMID:32708590
Comparative genomics and transcriptomics of 4 Paragonimus species provide insights into lung fluke parasitism and pathogenesis. PMID:32687148
Heatr9 is an infection responsive gene that affects cytokine production in alveolar epithelial cells. PMID:32678841
Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources. PMID:32676006
The gain-of-function allele bamA E470K bypasses the essential requirement for BamD in β-barrel outer membrane protein assembly. PMID:32675245
SPOCD1 is an essential executor of piRNA-directed de novo DNA methylation. PMID:32674113
From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes. PMID:32670511
Benchmarking gene ontology function predictions using negative annotations. PMID:32657372
Investigation on the Mechanism of Qubi Formula in Treating Psoriasis Based on Network Pharmacology. PMID:32655662
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. PMID:32652120
Network pharmacology and molecular docking analysis on molecular targets and mechanisms of Huashi Baidu formula in the treatment of COVID-19. PMID:32643448
Protein Interactions of the Mechanosensory Proteins Wsc2 and Wsc3 for Stress Resistance in Saccharomyces cerevisiae. PMID:32641451
Using iCn3D and the World Wide Web for structure-based collaborative research: Analyzing molecular interactions at the root of COVID-19. PMID:32637961
Liver transcriptome resources of four commercially exploited teleost species. PMID:32636445
Genomic Analysis of Bovine Staphylococcus aureus Isolates from Milk To Elucidate Diversity and Determine the Distributions of Antimicrobial and Virulence Genes and Their Association with Mastitis. PMID:32636332
The barley lectin, horcolin, binds high-mannose glycans in a multivalent fashion, enabling high-affinity, specific inhibition of cellular HIV infection. PMID:32636304
Shared up-regulation and contrasting down-regulation of gene expression distinguish desiccation-tolerant from intolerant green algae. PMID:32636259
Survey and Validation of tRNA Modifications and Their Corresponding Genes in Bacillus subtilis sp Subtilis Strain 168. PMID:32629984
Identifying Protein Biomarkers in Blood for Alzheimer's Disease. PMID:32626709
SDS-PAGE fractionation to increase metaproteomic insight into the taxonomic and functional composition of microbial communities for biogas plant samples. PMID:32624931
Computational identification of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes. PMID:32620079
Using AnABlast for intergenic sORF prediction in the Caenorhabditis elegans genome. PMID:32614398
A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals. PMID:32614390
Site of Action of Brain Neurosteroid Pregnenolone Sulfate at the N-Methyl-D-Aspartate Receptor. PMID:32611707
Pharmacological inhibition of lysine-specific demethylase 1 (LSD1) induces global transcriptional deregulation and ultrastructural alterations that impair viability in Schistosoma mansoni. PMID:32609727
Tol-Pal System and Rgs Proteins Interact to Promote Unipolar Growth and Cell Division in Sinorhizobium meliloti. PMID:32605980
Data and Text Mining Help Identify Key Proteins Involved in the Molecular Mechanisms Shared by SARS-CoV-2 and HIV-1. PMID:32604797
Topological features of integrin adhesion complexes revealed by multiplexed proximity biotinylation. PMID:32585685
GapMind: Automated Annotation of Amino Acid Biosynthesis. PMID:32576650
Regulation of cellular senescence by eukaryotic members of the FAH superfamily - A role in calcium homeostasis? PMID:32574647
Results of targeted next-generation sequencing in children with cystic kidney diseases often change the clinical diagnosis. PMID:32574212
The genome, transcriptome, and proteome of the fish parasite Pomphorhynchus laevis (Acanthocephala). PMID:32574180
Assessing predictors for new post translational modification sites: A case study on hydroxylation. PMID:32569263
The Role of Bone Morphogenetic Protein Signaling in Non-Alcoholic Fatty Liver Disease. PMID:32561790
Metabolomics as an Emerging Tool in the Search for Astrobiologically Relevant Biomarkers. PMID:32551936
Analysis of Virus and Host Proteomes During Productive HSV-1 and VZV Infection in Human Epithelial Cells. PMID:32547533
Differential Urinary Proteome Analysis for Predicting Prognosis in Type 2 Diabetes Patients with and without Renal Dysfunction. PMID:32545899
The Arg/N-Degron Pathway-A Potential Running Back in Fine-Tuning the Inflammatory Response? PMID:32545869
A Proline Derivative-Enriched Fraction from Sideroxylon obtusifolium Protects the Hippocampus from Intracerebroventricular Pilocarpine-Induced Injury Associated with Status Epilepticus in Mice. PMID:32545390
Essential roles for deubiquitination in Leishmania life cycle progression. PMID:32544189
Molecular insights into the powerful mucus-based adhesion of limpets (Patella vulgata L.). PMID:32543352
In silico vaccine design against Chlamydia trachomatis infection. PMID:32537381
Bacteriophage genotyping using BOXA repetitive-PCR. PMID:32527227
The Human Body as a Super Network: Digital Methods to Analyze the Propagation of Aging. PMID:32523526
Dataset of transcriptome assembly of date palm embryogenic calli and functional annotation. PMID:32518810
Gray whale transcriptome reveals longevity adaptations associated with DNA repair and ubiquitination. PMID:32515539
Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. PMID:32513234
VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo. PMID:32509450
The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification. PMID:32507889
Characterization of imine reductases in reductive amination for the exploration of structure-activity relationships. PMID:32494734
LGR4 deficiency results in delayed puberty through impaired Wnt/β-catenin signaling. PMID:32493844
Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia. PMID:32488117
Pan-Proteomic Analysis and Elucidation of Protein Abundance among the Closely Related Brucella Species, Brucella abortus and Brucella melitensis. PMID:32486122
Time-Course Transcriptome of Parageobacillus thermoglucosidasius DSM 6285 Grown in the Presence of Carbon Monoxide and Air. PMID:32485888
The role of 3'UTR-protein complexes in the regulation of protein multifunctionality and subcellular localization. PMID:32484544
Integrated omics in Drosophila uncover a circadian kinome. PMID:32483184
Computational Prediction of Ubiquitination Proteins Using Evolutionary Profiles and Functional Domain Annotation. PMID:32476995
RNA-protein coevolution study of Gemin5 uncovers the role of the PXSS motif of RBS1 domain for RNA binding. PMID:32476560
X-ray Structure-Based Chemoinformatic Analysis Identifies Promiscuous Ligands Binding to Proteins from Different Classes with Varying Shapes. PMID:32471121
Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment. PMID:32469311
Principal component analysis on LC‑MS/MS and 2DE‑MALDI‑TOF in glioblastoma cell lines reveals that mitochondria act as organelle sensors of the metabolic state in glioblastoma. PMID:32468038
Insights into Substrate and Inhibitor Selectivity among Human GLUT Transporters through Comparative Modeling and Molecular Docking. PMID:32462103
Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes. PMID:32457940
In Silico Subtractive Proteomics Approach for Identification of Potential Drug Targets in Staphylococcus saprophyticus. PMID:32455889
ZNF139/circZNF139 promotes cell proliferation, migration and invasion via activation of PI3K/AKT pathway in bladder cancer. PMID:32454461
Comprehensive analysis of the secreted proteome of adult Necator americanus hookworms. PMID:32453752
A biochemically-interpretable machine learning classifier for microbial GWAS. PMID:32444610
TraPS-VarI: Identifying genetic variants altering phosphotyrosine based signalling motifs. PMID:32439998
Structural basis for membrane insertion by the human ER membrane protein complex. PMID:32439656
A Reference Genome of Bursaphelenchus mucronatus Provides New Resources for Revealing Its Displacement by Pinewood Nematode. PMID:32438771
A bacterial biosynthetic pathway for methylated furan fatty acids. PMID:32434926
A Rapid, Sensitive, Low-Cost Assay for Detecting Hydrogenotrophic Methanogens in Anaerobic Digesters Using Loop-Mediated Isothermal Amplification. PMID:32429197
Rhodoxanthin synthase from honeysuckle; a membrane diiron enzyme catalyzes the multistep conversation of β-carotene to rhodoxanthin. PMID:32426461
Anti-vimentin, anti-TUFM, anti-NAP1L1 and anti-DPYSL2 nanobodies display cytotoxic effect and reduce glioblastoma cell migration. PMID:32426045
Post-translational Modification Crosstalk and Hotspots in Sirtuin Interactors Implicated in Cardiovascular Diseases. PMID:32425973
BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. PMID:32423472
AimB Is a Small Protein Regulator of Cell Size and MreB Assembly. PMID:32416080
Reversal of Regioselectivity in Zinc-Dependent Medium-Chain Alcohol Dehydrogenase from Rhodococcus erythropolis toward Octanone Derivatives. PMID:32415803
Salivary proteome signatures in the early and middle stages of human pregnancy with term birth outcome. PMID:32415095
ABC Transporter DerAB of Lactobacillus casei Mediates Resistance against Insect-Derived Defensins. PMID:32414796
Mutation severity spectrum of rare alleles in the human genome is predictive of disease type. PMID:32413045
RESTful API for iPTMnet: a resource for protein post-translational modification network discovery. PMID:32395768
MyoMiner: explore gene co-expression in normal and pathological muscle. PMID:32393257
The Bioinformatic and In Vitro Studies of Clostridioides Difficile Aminopeptidase M24 Revealed the Immunoreactive KKGIK Peptide. PMID:32392707
The secreted inhibitor of invasive cell growth CREG1 is negatively regulated by cathepsin proteases. PMID:32385587
ECMPride: prediction of human extracellular matrix proteins based on the ideal dataset using hybrid features with domain evidence. PMID:32377454
The Quest for Orthologs benchmark service and consensus calls in 2020. PMID:32374845
Comprehensive analysis of Translationally Controlled Tumor Protein (TCTP) provides insights for lineage-specific evolution and functional divergence. PMID:32374732
The Role of Genetic Variation of BMI, Body Composition, and Fat Distribution for Mental Traits and Disorders: A Look-Up and Mendelian Randomization Study. PMID:32373164
DRUGPATH: The Drug Gene Pathway Meta-Database. PMID:32365960
Tyrosinase-Targeting Gallacetophenone Inhibits Melanogenesis in Melanocytes and Human Skin-Equivalents. PMID:32365630
SHOGUN: a modular, accurate and scalable framework for microbiome quantification. PMID:32365167
QSAR without borders. PMID:32356548
PredDBP-Stack: Prediction of DNA-Binding Proteins from HMM Profiles using a Stacked Ensemble Method. PMID:32352006
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. PMID:32349661
The Cellular Response to Lanthanum Is Substrate Specific and Reveals a Novel Route for Glycerol Metabolism in Pseudomonas putida KT2440. PMID:32345644
Comparative transcriptomics characterized the distinct biosynthetic abilities of terpenoid and paeoniflorin biosynthesis in herbaceous peony strains. PMID:32341893
Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis. PMID:32341162
BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. PMID:32325033
Integrative and quantitative view of the CtrA regulatory network in a stalked budding bacterium. PMID:32324740
Alternative proteins are functional regulators in cell reprogramming by PKA activation. PMID:32324228
Osteoking improves OP rat by enhancing HSP90‑β expression. PMID:32323753
Computational Investigation of APOBEC3H Substrate Orientation and Selectivity. PMID:32321250
Post-translational modifications and stress adaptation: the paradigm of FKBP51. PMID:32318709
Structural Characterization of Carbonic Anhydrase VIII and Effects of Missense Single Nucleotide Variations to Protein Structure and Function. PMID:32316137
Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. PMID:32313939
HMMPred: Accurate Prediction of DNA-Binding Proteins Based on HMM Profiles and XGBoost Feature Selection. PMID:32300371
Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines. PMID:32286271
A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder. PMID:32283633
Structure of the Native Muscle-type Nicotinic Receptor and Inhibition by Snake Venom Toxins. PMID:32275860
Novel application of normalized pointwise mutual information (NPMI) to mine biomedical literature for gene sets associated with disease: use case in breast carcinogenesis. PMID:32274464
A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms. PMID:32272892
Nuclear and Chloroplast Sequences Resolve the Enigmatic Origin of the Concord Grape. PMID:32256506
Deletion of S-Layer Associated Ig-Like Domain Protein Disrupts the Lactobacillus acidophilus Cell Surface. PMID:32256464
Attractor Concepts to Evaluate the Transcriptome-wide Dynamics Guiding Anaerobic to Aerobic State Transition in Escherichia coli. PMID:32246034
MetaEuk-sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics. PMID:32245390
Iron is a ligand of SecA-like metal-binding domains in vivo. PMID:32241912
An integrated approach to unravel a crucial structural property required for the function of the insect steroidogenic Halloween protein Noppera-bo. PMID:32241910
The Function of Tafazzin, a Mitochondrial Phospholipid-Lysophospholipid Acyltransferase. PMID:32234310
Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins. PMID:32218151
Design, Synthesis, and Biological Evaluation of Quinazolin-4-one-Based Hydroxamic Acids as Dual PI3K/HDAC Inhibitors. PMID:32212730
Identifying the drivers of computationally detected correlated evolution among sites under antibiotic selection. PMID:32211067
Design of bioactive peptides derived from CART sequence isolated from the toadfish Thalassophryne nattereri. PMID:32206496
Co-expression clustering across flower development identifies modules for diverse floral forms in Achimenes (Gesneriaceae). PMID:32201652
Pharmacological Mechanisms Underlying the Neuroprotective Effects of Alpinia oxyphylla Miq. on Alzheimer's Disease. PMID:32197305
Deciphering the Active Compounds and Mechanisms of Qixuehe Capsule on Qi Stagnation and Blood Stasis Syndrome: A Network Pharmacology Study. PMID:32190085
Paradoxical activation of the protein kinase-transcription factor ERK5 by ERK5 kinase inhibitors. PMID:32170057
Functional cooperation of the glycine synthase-reductase and Wood-Ljungdahl pathways for autotrophic growth of Clostridium drakei. PMID:32170009
Hepatic transcriptome of the freeze-tolerant Cope's gray treefrog, Dryophytes chrysoscelis: responses to cold acclimation and freezing. PMID:32164545
Fibroblast-specific genome-scale modelling predicts an imbalance in amino acid metabolism in Refsum disease. PMID:32160399
Edgetic perturbation signatures represent known and novel cancer biomarkers. PMID:32152446
Expression and distribution of CD151 as a partner of alpha6 integrin in male germ cells. PMID:32152440
Mechanism of cargo recognition by retromer-linked SNX-BAR proteins. PMID:32150533
Two small, cysteine-rich and cationic antifungal proteins from Penicillium chrysogenum: A comparative study of PAF and PAFB. PMID:32142818
Mycoparasitism illuminated by genome and transcriptome sequencing of Coniothyrium minitans, an important biocontrol fungus of the plant pathogen Sclerotinia sclerotiorum. PMID:32141811
Identification of region-specific astrocyte subtypes at single cell resolution. PMID:32139688
Automated recognition of functional compound-protein relationships in literature. PMID:32126064
PHARMIP: An insilico method to predict genetics that underpin adverse drug reactions. PMID:32123669
Genome sequencing of human in vitro fertilisation embryos for pathogenic variation screening. PMID:32123222
Successful aging: insights from proteome analyses of healthy centenarians. PMID:32100723
Repertoire of morphable proteins in an organism. PMID:32095378
Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads. PMID:32093762
A multi-omics investigation of the molecular characteristics and classification of six metabolic syndrome relevant diseases. PMID:32089734
A Hybrid Model for Predicting Pattern Recognition Receptors Using Evolutionary Information. PMID:32082326
FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies. PMID:32082281
What Could Go Wrong? A Practical Guide to Single-Particle Cryo-EM: From Biochemistry to Atomic Models. PMID:32078321
Impact of the Protein Data Bank on antineoplastic approvals. PMID:32068073
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
High-throughput quantification of protein structural change reveals potential mechanisms of temperature adaptation in Mytilus mussels. PMID:32054457
Modification of the head proteome of nurse honeybees (Apis mellifera) exposed to field-relevant doses of pesticides. PMID:32042077
Predicting lncRNA-Protein Interactions With miRNAs as Mediators in a Heterogeneous Network Model. PMID:32038709
Computational Identification of the Proteins Associated With Quorum Sensing and Biofilm Formation in Mycobacterium tuberculosis. PMID:32038515
Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S. PMID:32033425
Genome-wide CRISPR screening identifies new regulators of glycoprotein secretion. PMID:32030357
PlaPPISite: a comprehensive resource for plant protein-protein interaction sites. PMID:32028878
Identifying Synergistic Mechanisms of Multiple Ingredients in Shuangbai Tablets against Proteinuria by Virtual Screening and a Network Pharmacology Approach. PMID:32025234
Emerging role of tumor-related functional peptides encoded by lncRNA and circRNA. PMID:32019587
Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties. PMID:32012150
Global transcriptome analysis of alfalfa reveals six key biological processes of senescent leaves. PMID:32002335
Coevolutionary Analysis of Protein Subfamilies by Sequence Reweighting. PMID:32002010
Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei. PMID:31992756
High-resolution crystal structures of two prototypical β- and γ-herpesviral nuclear egress complexes unravel the determinants of subfamily specificity. PMID:31980459
Nucleoside-modified AdoMet analogues for differential methyltransferase targeting. PMID:31970375
Prediction of human-virus protein-protein interactions through a sequence embedding-based machine learning method. PMID:31969974
Is the E. coli Homolog of the Formate/Nitrite Transporter Family an Anion Channel? A Computational Study. PMID:31968229
Mining histone methyltransferases and demethylases from whole genome sequence. PMID:31965987
Allosteric Binding Sites On Nuclear Receptors: Focus On Drug Efficacy and Selectivity. PMID:31947677
Making sense out of missense mutations: Mechanistic dissection of Notch receptors through structure-function studies in Drosophila. PMID:31943162
Human Colon Mucosal Biofilms and Murine Host Communicate via Altered mRNA and microRNA Expression during Cancer. PMID:31937674
Hesperidin improves insulin resistance via down-regulation of inflammatory responses: Biochemical analysis and in silico validation. PMID:31929574
Diversity spectrum analysis identifies mutation-specific effects of cancer driver genes. PMID:31925297
Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations. PMID:31924621
Venomics of the ectoparasitoid wasp Bracon nigricans. PMID:31924169
Molecular and genomic characterization of a novel equine molluscum contagiosum-like virus. PMID:31922947
Concentration Determination of >200 Proteins in Dried Blood Spots for Biomarker Discovery and Validation. PMID:31896676
Gingimaps: Protein Localization in the Oral Pathogen Porphyromonas gingivalis. PMID:31896547
Transcriptional changes during hepatic ischemia-reperfusion in the rat. PMID:31891620
Heat-induced hyperthermia impacts the follicular fluid proteome of the periovulatory follicle in lactating dairy cows. PMID:31887207
Potential Therapeutic Approaches to Alzheimer's Disease By Bioinformatics, Cheminformatics And Predicted Adme-Tox Tools. PMID:31885353
Structural and Functional Analyses of Human ChaC2 in Glutathione Metabolism. PMID:31878259
Identification of highly conserved, serotype-specific dengue virus sequences: implications for vaccine design. PMID:31874646
Computational Modeling Explains the Multi Sterol Ligand Specificity of the N-Terminal Domain of Niemann-Pick C1-Like 1 Protein. PMID:31867479
Identifying Acetylation Protein by Fusing Its PseAAC and Functional Domain Annotation. PMID:31867311
OutCyte: a novel tool for predicting unconventional protein secretion. PMID:31857603
Common activation mechanism of class A GPCRs. PMID:31855179
Increased Adaptive Variation Despite Reduced Overall Genetic Diversity in a Rapidly Adapting Invader. PMID:31850072
Expression Quantitative Trait Loci in Equine Skeletal Muscle Reveals Heritable Variation in Metabolism and the Training Responsive Transcriptome. PMID:31850069
Host-Microbe Interactions in the Chemosynthetic Riftia pachyptila Symbiosis. PMID:31848270
Detection of ALDH3B2 in Human Placenta. PMID:31847104
MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity. PMID:31839598
A Network Pharmacology Approach to Reveal the Underlying Mechanisms of Paeonia lactiflora Pall. On the Treatment of Alzheimer's Disease. PMID:31827565
Comprehensive Identification and Characterization of Human Secretome Based on Integrative Proteomic and Transcriptomic Data. PMID:31824949
Investigation of the host transcriptional response to intracellular bacterial infection using Dictyostelium discoideum as a host model. PMID:31823727
Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319. PMID:31822710
The functional landscape of the human phosphoproteome. PMID:31819260
Association of polymorphism in heat shock protein 70 genes with type 2 diabetes in Bangladeshi population. PMID:31816668
Determining the pathogenicity of CFTR missense variants: Multiple comparisons of in silico predictors and variant annotation databases. PMID:31808782
The X chromosome of the German cockroach, Blattella germanica, is homologous to a fly X chromosome despite 400 million years divergence. PMID:31806031
The distributions of protein coding genes within chromatin domains in relation to human disease. PMID:31805995
Conjoint Analysis of SMRT- and Illumina-Based RNA-Sequencing Data of Fenneropenaeus chinensis Provides Insight Into Sex-Biased Expression Genes Involved in Sexual Dimorphism. PMID:31803244
Sequence-Derived Markers of Drug Targets and Potentially Druggable Human Proteins. PMID:31803227
Skeletal muscle alterations in tachycardia-induced heart failure are linked to deficient natriuretic peptide signalling and are attenuated by RAS-/NEP-inhibition. PMID:31800630
mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations. PMID:31799603
Modern Approaches in the Identification and Quantification of Immunogenic Peptides in Cereals by LC-MS/MS. PMID:31798614
Full-Length Transcriptome Survey and Expression Analysis of Parasitoid Wasp Chouioia cunea upon Exposure to 1-Dodecene. PMID:31796851
The KLDpT activation loop motif is critical for MARK kinase activity. PMID:31794565
Bacterial DNA induces the formation of heat-resistant disease-associated proteins in human plasma. PMID:31784694
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. PMID:31780431
Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts. PMID:31775622
Novel redox-active enzymes for ligninolytic applications revealed from multiomics analyses of Peniophora sp. CBMAI 1063, a laccase hyper-producer strain. PMID:31772294
Systematic exploration of predicted destabilizing nonsynonymous single nucleotide polymorphisms (nsSNPs) of human aldehyde oxidase: A Bio-informatics study. PMID:31768259
DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. PMID:31768060
Genomic landscape and genetic manipulation of the black soldier fly Hermetia illucens, a natural waste recycler. PMID:31767972
SCGid: a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries of uncultured eukaryotes. PMID:31764940
Estradiol and genistein effects on the sea bass (Dicentrarchus labrax) scales: Transcriptome dataset. PMID:31763380
A3 adenosine receptor activation mechanisms: molecular dynamics analysis of inactive, active, and fully active states. PMID:31758354
A novel framework for horizontal and vertical data integration in cancer studies with application to survival time prediction models. PMID:31752974
SIMLIN: a bioinformatics tool for prediction of S-sulphenylation in the human proteome based on multi-stage ensemble-learning models. PMID:31752668
Towards discovery of new leishmanicidal scaffolds able to inhibit Leishmania GSK-3. PMID:31752556
An exome-wide rare variant analysis of Korean men identifies three novel genes predisposing to prostate cancer. PMID:31748686
Characterization of antibiotic resistance genes in the species of the rumen microbiota. PMID:31748524
Identifying genetic variants underlying medication-induced osteonecrosis of the jaw in cancer and osteoporosis: a case control study. PMID:31747953
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. PMID:31744546
Exploring a New Natural Treating Agent for Primary Hypertension: Recent Findings and Forthcoming Perspectives. PMID:31744165
Improved linking of motifs to their TFs using domain information. PMID:31742324
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. PMID:31733063
Multiple antibodies targeting tumor-specific mutations redirect immune cells to inhibit tumor growth and increase survival in experimental animal models. PMID:31732916
Cell-Specific DNA Methylation Signatures in Asthma. PMID:31731604
Structural insights into heme binding to IL-36α proinflammatory cytokine. PMID:31729440
Identification of candidate cancer drivers by integrative Epi-DNA and Gene Expression (iEDGE) data analysis. PMID:31729402
mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation. PMID:31727118
Global Vectors Representation of Protein Sequences and Its Application for Predicting Self-Interacting Proteins with Multi-Grained Cascade Forest Model. PMID:31726752
The neXtProt knowledgebase in 2020: data, tools and usability improvements. PMID:31724716
Genetic Support for Longevity-Enhancing Drug Targets: Issues, Preliminary Data, and Future Directions. PMID:31724058
Engineered Stochastic Adhesion Between Microbes as a Protection Mechanism Against Environmental Stress. PMID:31719890
Transcriptome analysis identifies genes related to the waxy coating on blueberry fruit in two northern-adapted rabbiteye breeding populations. PMID:31711416
Autologous Exosome Transfer: A New Personalised Treatment Concept to Prevent Colitis in a Murine Model. PMID:31710674
The Cytoscape BioGateway App: explorative network building from the BioGateway triple store. PMID:31710663
Amino acid substitution scoring matrices specific to intrinsically disordered regions in proteins. PMID:31704957
The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae). PMID:31702783
Automatic annotation of protein residues in published papers. PMID:31702580
LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. PMID:31701147
Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale. PMID:31694533
MitoRibo-Tag Mice Provide a Tool for In Vivo Studies of Mitoribosome Composition. PMID:31693908
Understanding allergic multimorbidity within the non-eosinophilic interactome. PMID:31693680
Co-regulation map of the human proteome enables identification of protein functions. PMID:31690884
Mechanism of Action of Non-Synonymous Single Nucleotide Variations Associated with α-Carbonic Anhydrase II Deficiency. PMID:31690045
The mutational landscape of quinolone resistance in Escherichia coli. PMID:31689338
RareLSD: a manually curated database of lysosomal enzymes associated with rare diseases. PMID:31688938
CSF levels of apolipoprotein C1 and autotaxin found to associate with neuropathic pain and fibromyalgia. PMID:31686904
The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation. PMID:31685817
ProTstab - predictor for cellular protein stability. PMID:31684883
Genome-Wide Analysis of Known and Potential Tetraspanins in Entamoeba histolytica. PMID:31684194
'One DB to rule them all'-the RING: a Regulatory INteraction Graph combining TFs, genes/proteins, SNPs, diseases and drugs. PMID:31682269
Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus. PMID:31681953
Cysteine-Rich Antifungal Proteins from Filamentous Fungi are Promising Bioactive Natural Compounds in Anti-Candida Therapy. PMID:31680702
MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect. PMID:31679514
Clinical and genetic risk factors for aromatase inhibitor-associated arthralgia in breast cancer survivors. PMID:31678641
A Genocentric Approach to Discovery of Mendelian Disorders. PMID:31668702
Experimental data from flesh quality assessment and shelf life monitoring of high pressure processed European sea bass (Dicentrarchus labrax) fillets. PMID:31667223
Metabolic Modeling of Streptococcus mutans Reveals Complex Nutrient Requirements of an Oral Pathogen. PMID:31662430
RaGOO: fast and accurate reference-guided scaffolding of draft genomes. PMID:31661016
Network inference with ensembles of bi-clustering trees. PMID:31660848
Chlamydia psittaci-Infected Dendritic Cells Communicate with NK Cells via Exosomes To Activate Antibacterial Immunity. PMID:31658957
Identification and Analysis of Long Repeats of Proteins at the Domain Level. PMID:31649924
Genomic Basis of Convergent Island Phenotypes in Boa Constrictors. PMID:31642474
In Silico Genetics Revealing 5 Mutations in CEBPA Gene Associated With Acute Myeloid Leukemia. PMID:31621694
A structure-based approach towards the identification of novel antichagasic compounds: Trypanosoma cruzi carbonic anhydrase inhibitors. PMID:31619095
PhaSePro: the database of proteins driving liquid-liquid phase separation. PMID:31612960
Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration. PMID:31611808
Continuous salt stress-induced long non-coding RNAs and DNA methylation patterns in soybean roots. PMID:31606033
Structure and functional implications of WYL domain-containing bacterial DNA damage response regulator PafBC. PMID:31604936
Amino Acid and Sugar Catabolism in the Marine Bacterium Phaeobacter inhibens DSM 17395 from an Energetic Viewpoint. PMID:31604772
ModelBricks-modules for reproducible modeling improving model annotation and provenance. PMID:31602314
Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture. PMID:31592187
PDBe-KB: a community-driven resource for structural and functional annotations. PMID:31584092
funtrp: identifying protein positions for variation driven functional tuning. PMID:31584091
PhaSepDB: a database of liquid-liquid phase separation related proteins. PMID:31584089
Complete Genome Sequence of the Biocontrol Agent Bacillus velezensis UFLA258 and Its Comparison with Related Species: Diversity within the Commons. PMID:31580420
Conserved Central Intraviral Protein Interactome of the Herpesviridae Family. PMID:31575665
Conotoxin Diversity in the Venom Gland Transcriptome of the Magician's Cone, Pionoconus magus. PMID:31569823
Limitations of Deuterium-Labelled Substrates for Quantifying NADPH Metabolism in Heterotrophic Arabidopsis Cell Cultures. PMID:31569392
NMDA Receptor Opening and Closing-Transitions of a Molecular Machine Revealed by Molecular Dynamics. PMID:31569344
Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies. PMID:31565556
Domain-specific Quantification of Prion Protein in Cerebrospinal Fluid by Targeted Mass Spectrometry. PMID:31558565
Pathogenic APC Variants in Latvian Familial Adenomatous Polyposis Patients. PMID:31547110
Transcriptomic Signatures of Experimental Alkaloid Consumption in a Poison Frog. PMID:31546679
Updated Genome Assembly and Annotation for Metrosideros polymorpha, an Emerging Model Tree Species of Ecological Divergence. PMID:31540972
Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs. PMID:31539080
XMAn v2-a database of Homo sapiens mutated peptides. PMID:31539018
Seaweed natural products modify the host inflammatory response via Nrf2 signaling and alter colon microbiota composition and gene expression. PMID:31536771
Temporal changes in transcriptome profile provide insights of White Spot Syndrome Virus infection in Litopenaeus vannamei. PMID:31534145
Protein Engineering of Multi-Modular Transcription Factor Alcohol Dehydrogenase Repressor 1 (Adr1p), a Tool for Dissecting In Vitro Transcription Activation. PMID:31533362
RCSB Protein Data Bank: Enabling biomedical research and drug discovery. PMID:31531901
Hibernation induces widespread transcriptional remodeling in metabolic tissues of the grizzly bear. PMID:31531397
Structural and functional aspects of mannuronic acid-specific PL6 alginate lyase from the human gut microbe Bacteroides cellulosilyticus. PMID:31530640
Computational and experimental analysis of the glycophosphatidylinositol-anchored proteome of the human parasitic nematode Brugia malayi. PMID:31513600
Large-Scale Molecular Evolutionary Analysis Uncovers a Variety of Polynucleotide Kinase Clp1 Family Proteins in the Three Domains of Life. PMID:31513263
Fail-safe genetic codes designed to intrinsically contain engineered organisms. PMID:31511890
Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny. PMID:31511700
Statistical compression of protein sequences and inference of marginal probability landscapes over competing alignments using finite state models and Dirichlet priors. PMID:31510703
Baseline human gut microbiota profile in healthy people and standard reporting template. PMID:31509535
Metatranscriptomics yields new genomic resources and sensitive detection of infections for diverse blood parasites. PMID:31507097
Machine learning-based chemical binding similarity using evolutionary relationships of target genes. PMID:31504818
Butterfly Mimicry Polymorphisms Highlight Phylogenetic Limits of Gene Reuse in the Evolution of Diverse Adaptations. PMID:31504750
The Evolution of Reverse Gyrase Suggests a Nonhyperthermophilic Last Universal Common Ancestor. PMID:31504731
Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning. PMID:31504150
Adaptive Radiation of the Flukes of the Family Fasciolidae Inferred from Genome-Wide Comparisons of Key Species. PMID:31501870
OPA1: 516 unique variants and 831 patients registered in an updated centralized Variome database. PMID:31500643
Dataset of de novo assembly and functional annotation of the transcriptome of blueberry (Vaccinium spp.). PMID:31497632
Metaproteomics analysis of microbial diversity of human saliva and tongue dorsum in young healthy individuals. PMID:31497257
GLUT1 and TUBB4 in Glioblastoma Could be Efficacious Targets. PMID:31491891
SamPler - a novel method for selecting parameters for gene functional annotation routines. PMID:31488049
Association Between aquaporin-1 and Endurance Performance: A Systematic Review. PMID:31486928
Structure-function guided modeling of chemokine-GPCR specificity for the chemokine XCL1 and its receptor XCR1. PMID:31481523
A Novel Homozygous Missense Variant in the NAGA Gene with Extreme Intrafamilial Phenotypic Heterogeneity. PMID:31468281
Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles. PMID:31464627
Promiscuous Ligands from Experimentally Determined Structures, Binding Conformations, and Protein Family-Dependent Interaction Hotspots. PMID:31459430
Structural Modeling and in Silico Screening of Potential Small-Molecule Allosteric Agonists of a Glucagon-like Peptide 1 Receptor. PMID:31459371
SAR by Space: Enriching Hit Sets from the Chemical Space. PMID:31454992
Construction of complete Tupaia belangeri transcriptome database by whole-genome and comprehensive RNA sequencing. PMID:31451757
Deeper Profiles and Cascaded Recurrent and Convolutional Neural Networks for state-of-the-art Protein Secondary Structure Prediction. PMID:31451723
Hybrid genome assembly and annotation of Danionella translucida. PMID:31451709
HERCing: Structural and Functional Relevance of the Large HERC Ubiquitin Ligases. PMID:31447701
ComplexBrowser: A Tool for Identification and Quantification of Protein Complexes in Large-scale Proteomics Datasets. PMID:31447428
Molecular Evolution of Extensively Drug-Resistant (XDR) Pseudomonas aeruginosa Strains From Patients and Hospital Environment in a Prolonged Outbreak. PMID:31440214
Epistatic Analysis of the Contribution of Rabs and Kifs to CATCHR Family Dependent Golgi Organization. PMID:31428608
Differentially Expressed MiRNAs and tRNA Genes Affect Host Homeostasis During Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus Infections in Young Pigs. PMID:31428130
I-TASSER gateway: A protein structure and function prediction server powered by XSEDE. PMID:31427836
Resources to Discover and Use Short Linear Motifs in Viral Proteins. PMID:31427097
Intrinsically disordered proteins and structured proteins with intrinsically disordered regions have different functional roles in the cell. PMID:31425549
Comparative Genomic Characterization of the Multimammate Mouse Mastomys coucha. PMID:31424545
Size and structure of the sequence space of repeat proteins. PMID:31415557
The ABCD database: a repository for chemically defined antibodies. PMID:31410491
Transcriptome annotation and characterization of novel toxins in six scorpion species. PMID:31409288
Bioinformatics analysis of various signal peptides for periplasmic expression of parathyroid hormone in E.coli. PMID:31406522
Transcriptomic Analysis of Marine Gastropod Hemifusus tuba Provides Novel Insights into Conotoxin Genes. PMID:31405144
Secretome profiling of PC3/nKR cells, a novel highly migrating prostate cancer subline derived from PC3 cells. PMID:31404090
Nascent Polypeptide Domain Topology and Elongation Rate Direct the Cotranslational Hierarchy of Hsp70 and TRiC/CCT. PMID:31400849
Anti-Myelin Proteolipid Protein Peptide Monoclonal Antibodies Recognize Cell Surface Proteins on Developing Neurons and Inhibit Their Differentiation. PMID:31400116
Parallel Evolution of Complex Centipede Venoms Revealed by Comparative Proteotranscriptomic Analyses. PMID:31396628
In Silico Phylogenetic and Structural Analyses of Plant Endogenous Danger Signaling Molecules upon Stress. PMID:31396307
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. PMID:31395883
ALG9 Mutation Carriers Develop Kidney and Liver Cysts. PMID:31395617
Differential gene expression analysis of symbiotic and aposymbiotic Exaiptasia anemones under immune challenge with Vibrio coralliilyticus. PMID:31380089
Origins of peptidases. PMID:31377195
Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery. PMID:31375809
Unraveling the structural landscape of intra-chain domain interfaces: Implication in the evolution of domain-domain interactions. PMID:31374091
Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework. PMID:31372637
SALM1 controls synapse development by promoting F-actin/PIP2-dependent Neurexin clustering. PMID:31368584
Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers. PMID:31366361
PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping. PMID:31363752
Combination of gallium(iii) with acetate for combating antibiotic resistant Pseudomonas aeruginosa. PMID:31360415
Modulation of Toxin-Antitoxin System Rnl AB Type II in Phage-Resistant Gammaproteobacteria Surviving Photodynamic Treatment. PMID:31360364
Viruses as key reservoirs of antibiotic resistance genes in the environment. PMID:31358910
Systematic analysis of the intersection of disease mutations with protein modifications. PMID:31345222
Benchmark and integration of resources for the estimation of human transcription factor activities. PMID:31340985
Systems biology-based investigation of cooperating microRNAs as monotherapy or adjuvant therapy in cancer. PMID:31340025
Network analysis of hyphae forming proteins in Candida albicans identifies important proteins responsible for pathovirulence in the organism. PMID:31338453
Rare, functional, somatic variants in gene families linked to cancer genes: GPCR signaling as a paradigm. PMID:31337866
Tryptophan Oxidation in the UQCRC1 Subunit of Mitochondrial Complex III (Ubiquinol-Cytochrome C Reductase) in a Mouse Model of Myodegeneration Causes Large Structural Changes in the Complex: A Molecular Dynamics Simulation Study. PMID:31337785
Using deep maxout neural networks to improve the accuracy of function prediction from protein interaction networks. PMID:31335894
Liver Cancer Cell Lines Treated with Doxorubicin under Normoxia and Hypoxia: Cell Viability and Oncologic Protein Profile. PMID:31330834
The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112. PMID:31328227
De Novo Missense Variants in WDR37 Cause a Severe Multisystemic Syndrome. PMID:31327510
Large-scale Discovery of Substrates of the Human Kinome. PMID:31324866
Binding affinities of human IgG1 and chimerized pig and rabbit derivatives to human, pig and rabbit Fc gamma receptor IIIA. PMID:31323052
Combined alignments of sequences and domains characterize unknown proteins with remotely related protein search PSISearch2D. PMID:31317184
Proteogenomic Analysis of Protein Sequence Alterations in Breast Cancer Cells. PMID:31316139
A 4-cyano-3-methylisoquinoline inhibitor of Plasmodium falciparum growth targets the sodium efflux pump PfATP4. PMID:31311978
Membrane protein-regulated networks across human cancers. PMID:31311925
Global transcriptome and gene co-expression network analyses on the development of distyly in Primula oreodoxa. PMID:31308492
Environmental conditions shape the nature of a minimal bacterial genome. PMID:31308405
PhenPath: a tool for characterizing biological functions underlying different phenotypes. PMID:31307376
CDKN2B upregulation prevents teratoma formation in multipotent fibromodulin-reprogrammed cells. PMID:31305260
Acetaminophen Overdose as a Potential Risk Factor for Parkinson's Disease. PMID:31305025
Dependency Between Protein-Protein Interactions and Protein Variability and Evolutionary Rates in Vertebrates: Observed Relationships and Stochastic Modeling. PMID:31302723
Decoding the PTM-switchboard of Notch. PMID:31301363
Chromatin-dependent regulation of secondary metabolite biosynthesis in fungi: is the picture complete? PMID:31301226
High-throughput mass spectrometry and bioinformatics analysis of breast cancer proteomic data. PMID:31294064
The Transcriptome Landscape of Walnut Interspecies Hybrid (Juglans hindsii × Juglans regia) and Regulation of Cambial Activity in Relation to Grafting. PMID:31293615
Genetic interactions of G-quadruplexes in humans. PMID:31287417
Reference genome and comparative genome analysis for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine. PMID:31286858
Extracellular Vesicles and Their Potential Use in Monitoring Cancer Progression and Therapy: The Contribution of Proteomics. PMID:31281356
Diversity of tryptophan halogenases in sponges of the genus Aplysina. PMID:31276591
Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases. PMID:31274316
Selective Proteolysis of α-Lactalbumin by Endogenous Enzymes of Human Milk at Acidic pH. PMID:31271254
Biosynthetic homeostasis and resilience of the complement system in health and infectious disease. PMID:31262714
Performance of computational methods for the evaluation of pericentriolar material 1 missense variants in CAGI-5. PMID:31260570
Computational Systems Pharmacology-Target Mapping for Fentanyl-Laced Cocaine Overdose. PMID:31257858
Nrf2 Activation Promotes Lung Cancer Metastasis by Inhibiting the Degradation of Bach1. PMID:31257023
PRRDB 2.0: a comprehensive database of pattern-recognition receptors and their ligands. PMID:31250014
TYR Gene in Llamas: Polymorphisms and Expression Study in Different Color Phenotypes. PMID:31249599
The C-terminal tail of the bacterial translocation ATPase SecA modulates its activity. PMID:31246174
Genetic and physical interactions between the organellar mechanosensitive ion channel homologs MSL1, MSL2, and MSL3 reveal a role for inter-organellar communication in plant development. PMID:31245767
Waterlogging affects plant morphology and the expression of key genes in tef (Eragrostis tef). PMID:31245721
Development of Allosteric BRAF Peptide Inhibitors Targeting the Dimer Interface of BRAF. PMID:31243962
Comparative Genomics of Wild Bee and Flower Isolated Lactobacillus Reveals Potential Adaptation to the Bee Host. PMID:31243442
Developmental dynamics of lncRNAs across mammalian organs and species. PMID:31243368
Advances and Applications in the Quest for Orthologs. PMID:31241141
Transcriptome characterization and differentially expressed genes under flooding and drought stress in the biomass grasses Phalaris arundinacea and Dactylis glomerata. PMID:31241131
The CYPome of the model xenobiotic-biotransforming fungus Cunninghamella elegans. PMID:31239505
SeQuery: an interactive graph database for visualizing the GPCR superfamily. PMID:31236561
Immune and environment-driven gene expression during invasion: An eco-immunological application of RNA-Seq. PMID:31236254
Genetic variant pathogenicity prediction trained using disease-specific clinical sequencing data sets. PMID:31235655
Cell Wall Enzymes in Zygnema circumcarinatum UTEX 1559 Respond to Osmotic Stress in a Plant-Like Fashion. PMID:31231410
Conditional Deletion of Eaf1 Induces Murine Prostatic Intraepithelial Neoplasia in Mice. PMID:31229879
A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation. PMID:31225796
De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate. PMID:31217263
In silico analysis of PFN1 related to amyotrophic lateral sclerosis. PMID:31216283
Consequences of Y chromosome microdeletions beyond male infertility. PMID:31214882
Locally advanced rectal cancer transcriptomic-based secretome analysis reveals novel biomarkers useful to identify patients according to neoadjuvant chemoradiotherapy response. PMID:31213644
Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter. PMID:31212313
A genome-wide scan for genes under balancing selection in the plant pathogen Ralstonia solanacearum. PMID:31208326
Altered Levels of Proteins and Phosphoproteins, in the Absence of Early Causative Transcriptional Changes, Shape the Molecular Pathogenesis in the Brain of Young Presymptomatic Ki91 SCA3/MJD Mouse. PMID:31201651
Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships. PMID:31199794
Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability. PMID:31196969
Identification of Breast Cancer Stem Cell Related Genes Using Functional Cellular Assays Combined With Single-Cell RNA Sequencing in MDA-MB-231 Cells. PMID:31191614
Alteration of Proteomes in First-Generation Cultures of Bacillus pumilus Spores Exposed to Outer Space. PMID:31186338
Characterization of the pleiotropic LysR-type transcription regulator LeuO of Escherichia coli. PMID:31184713
Phosphorylation mapping of Laminin β1-chain: Kinases in association with active sites. PMID:31180068
The Impact of Pyroglutamate: Sulfolobus acidocaldarius Has a Growth Advantage over Saccharolobus solfataricus in Glutamate-Containing Media. PMID:31178666
Salmonella enterica subsp. enterica Serovar Heidelberg Food Isolates Associated with a Salmonellosis Outbreak Have Enhanced Stress Tolerance Capabilities. PMID:31175193
What determines host specificity in hyperspecialized plant parasitic nematodes? PMID:31170914
Combining next-generation sequencing and progeny testing for rapid identification of induced recessive and dominant mutations in maize M2 individuals. PMID:31169333
Exploring the overlapping binding sites of ifenprodil and EVT-101 in GluN2B-containing NMDA receptors using novel chicken embryo forebrain cultures and molecular modeling. PMID:31164987
WDSPdb: an updated resource for WD40 proteins. PMID:31161214
A case of Coffin-Siris syndrome with severe congenital heart disease and a novel SMARCA4 variant. PMID:31160358
Differential analysis of combinatorial protein complexes with CompleXChange. PMID:31159772
Analysis of hereditary cancer syndromes by using a panel of genes: novel and multiple pathogenic mutations. PMID:31159747
Sea Anemone Toxins: A Structural Overview. PMID:31159357
Circulating Levels of Interferon Regulatory Factor-5 Associates With Subgroups of Systemic Lupus Erythematosus Patients. PMID:31156624
Modeling post-translational modifications and cancer-associated mutations that impact the heterochromatin protein 1α-importin α heterodimers. PMID:31152607
Diverse spinal commissural neuron populations revealed by fate mapping and molecular profiling using a novel Robo3Cre mouse. PMID:31152445
Systematic Analysis of Metabolic Pathway Distributions of Bacterial Energy Reserves. PMID:31151997
In Silico Identification of Potential Inhibitor Against a Fungal Histone Deacetylase, RPD3 from Magnaporthe Oryzae. PMID:31151320
Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II. PMID:31150387
Plasmodium pseudo-Tyrosine Kinase-like binds PP1 and SERA5 and is exported to host erythrocytes. PMID:31148576
Molecular mechanisms involved in drug-induced liver injury caused by urate-lowering Chinese herbs: A network pharmacology study and biology experiments. PMID:31141540
Comparative transcriptomic analysis of dermal wound healing reveals de novo skeletal muscle regeneration in Acomys cahirinus. PMID:31141508
HNCDB: An Integrated Gene and Drug Database for Head and Neck Cancer. PMID:31139565
Global Proteome and Ubiquitinome Changes in the Soluble and Insoluble Fractions of Q175 Huntington Mice Brains. PMID:31138642
Transcriptome analysis of the model grass Lolium temulentum exposed to green leaf volatiles. PMID:31138172
MHCSeqNet: a deep neural network model for universal MHC binding prediction. PMID:31138107
Kalium 2.0, a comprehensive database of polypeptide ligands of potassium channels. PMID:31133708
Molecular mechanisms of temperature acclimation and adaptation in marine diatoms. PMID:31127177
Leveraging genetic interactions for adverse drug-drug interaction prediction. PMID:31125330
DP-BINDER: machine learning model for prediction of DNA-binding proteins by fusing evolutionary and physicochemical information. PMID:31123959
Exploiting orthology and de novo transcriptome assembly to refine target sequence information. PMID:31122257
Network Integrative Genomic and Transcriptomic Analysis of Carbapenem-Resistant Klebsiella pneumoniae Strains Identifies Genes for Antibiotic Resistance and Virulence. PMID:31117026
Targeted next generation sequencing screening of Lynch syndrome in Tunisian population. PMID:31114938
HOT or not: examining the basis of high-occupancy target regions. PMID:31114922
Simple ClinVar: an interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database. PMID:31114901
Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States. PMID:31114882
ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism. PMID:31114881
BRCA1- and BRCA2-specific in silico tools for variant interpretation in the CAGI 5 ENIGMA challenge. PMID:31112341
A Functional Agonist of Insect Olfactory Receptors: Behavior, Physiology and Structure. PMID:31110474
Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. PMID:31110364
Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface. PMID:31107587
Gi/o-Protein Coupled Receptors in the Aging Brain. PMID:31105551
The thermophilic biomass-degrading bacterium Caldicellulosiruptor bescii utilizes two enzymes to oxidize glyceraldehyde 3-phosphate during glycolysis. PMID:31097544
CE-MS-based urinary biomarkers to distinguish non-significant from significant prostate cancer. PMID:31092909
Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism. PMID:31088371
Genome-wide screen identifies novel genes required for Borrelia burgdorferi survival in its Ixodes tick vector. PMID:31086414
Cell Cycle Kinase Polo Is Controlled by a Widespread 3' Untranslated Region Regulatory Sequence in Drosophila melanogaster. PMID:31085682
GROWTH POLE RING protein forms a 200-nm-diameter ring structure essential for polar growth and rod shape in Agrobacterium tumefaciens. PMID:31085632
Optimized Cross-Linking Mass Spectrometry for in Situ Interaction Proteomics. PMID:31083951
Genotify: Fast, lightweight gene lookup and summarization. PMID:31080942
Detection of Tumor NTRK Gene Fusions to Identify Patients Who May Benefit from Tyrosine Kinase (TRK) Inhibitor Therapy. PMID:31075511
PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic Variants. PMID:31075275
Molecular modeling studies on the interactions of 7-methoxytacrine-4-pyridinealdoxime, 4-PA, 2-PAM, and obidoxime with VX-inhibited human acetylcholinesterase: a near attack conformation approach. PMID:31074292
INGA 2.0: improving protein function prediction for the dark proteome. PMID:31073595
Genome Sequence of "Candidatus Serratia symbiotica" Strain IS, a Facultative Bacterial Symbiont of the Pea Aphid Acyrthosiphon pisum. PMID:31072900
CRISPR/Cas9-mediated mutagenesis of phytoene desaturase in diploid and octoploid strawberry. PMID:31068975
Identification of a potential allosteric site of Golgi α-mannosidase II using computer-aided drug design. PMID:31067280
Human contamination in bacterial genomes has created thousands of spurious proteins. PMID:31064768
Plasma protein biomarkers and their association with mutually exclusive cardiovascular phenotypes: the FIBRO-TARGETS case-control analyses. PMID:31062082
Biosynthesis of Long Chain Alkyl Diols and Long Chain Alkenols in Nannochloropsis spp. (Eustigmatophyceae). PMID:31058972
Bacterial Community Succession, Transmigration, and Differential Gene Transcription in a Controlled Vertebrate Decomposition Model. PMID:31057499
Genomic Characterization of Arcobacter butzleri Isolated From Shellfish: Novel Insight Into Antibiotic Resistance and Virulence Determinants. PMID:31057492
Impacts of cellulase deactivation at the moving air-liquid interface on cellulose conversions at low enzyme loadings. PMID:31044009
PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms. PMID:31040227
Navigating in vitro bioactivity data by investigating available resources using model compounds. PMID:31036807
Automated assessment of biological database assertions using the scientific literature. PMID:31035936
PlantMP: a database for moonlighting plant proteins. PMID:31032837
Intrinsically Disordered Linkers Impart Processivity on Enzymes by Spatial Confinement of Binding Domains. PMID:31032817
Shared Signature Dynamics Tempered by Local Fluctuations Enables Fold Adaptability and Specificity. PMID:31028708
Extended Multitarget Pharmacology of Anticancer Drugs. PMID:31025863
Structural basis of ligand recognition at the human MT1 melatonin receptor. PMID:31019306
Bioinformatic and mutational studies of related toxin-antitoxin pairs in Mycobacterium tuberculosis predict and identify key functional residues. PMID:31018964
Sex-specific and pleiotropic effects underlying kidney function identified from GWAS meta-analysis. PMID:31015462
In silico analysis of the V66M variant of human BDNF in psychiatric disorders: An approach to precision medicine. PMID:30998730
tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities. PMID:30996049
Variation in pigmentation gene expression is associated with distinct aposematic color morphs in the poison frog Dendrobates auratus. PMID:30995908
Can Predicted Protein 3D Structures Provide Reliable Insights into whether Missense Variants Are Disease Associated? PMID:30995449
A Bayesian framework that integrates multi-omics data and gene networks predicts risk genes from schizophrenia GWAS data. PMID:30988527
Comparative Analysis of the Transcriptome and Proteome during Mouse Placental Development. PMID:30986076
ProteinExplorer: A Repository-Scale Resource for Exploration of Protein Detection in Public Mass Spectrometry Data Sets. PMID:30985146
Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells. PMID:30983154
Machine learning-assisted directed protein evolution with combinatorial libraries. PMID:30979809
A global map of the protein shape universe. PMID:30978181
Genome-wide association study of an unusual dolphin mortality event reveals candidate genes for susceptibility and resistance to cetacean morbillivirus. PMID:30976305
Comparative analysis of homologous aminopeptidase PepN from pathogenic and non-pathogenic mycobacteria reveals divergent traits. PMID:30969995
Ant behaviour and brain gene expression of defending hosts depend on the ecological success of the intruding social parasite. PMID:30967075
Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction. PMID:30963849
Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database. PMID:30963208
Large-scale proteomic analysis of human brain identifies proteins associated with cognitive trajectory in advanced age. PMID:30962425
Defining the RNA interactome by total RNA-associated protein purification. PMID:30962360
Network reconstruction from infection cascades. PMID:30958195
Increased versatility despite reduced molecular complexity: evolution, structure and function of metazoan splicing factor PRPF39. PMID:30949712
Comprehensive Review of Human Plasmodium falciparum-Specific CD8+ T Cell Epitopes. PMID:30949162
High-Quality Draft Genome Sequence of the Microcolonial Black Fungus Aeminium ludgeri DSM 106916. PMID:30948467
Curated BLAST for Genomes. PMID:30944879
Ca2+-dependent regulation of sodium channels NaV1.4 and NaV1.5 is controlled by the post-IQ motif. PMID:30944319
Methods for Systematic Identification of Membrane Proteins for Specific Capture of Cancer-Derived Extracellular Vesicles. PMID:30943406
Adaptations of Alteromonas sp. 76-1 to Polysaccharide Degradation: A CAZyme Plasmid for Ulvan Degradation and Two Alginolytic Systems. PMID:30936857
An Acid Up-Regulated Surface Protein of Lactobacillus paracasei Strain GCRL 46 is Phylogenetically Related to the Secreted Glucan- (GpbB) and Immunoglobulin-Binding (SibA) Protein of Pathogenic Streptococci. PMID:30935131
Structural and Computational Characterization of Disease-Related Mutations Involved in Protein-Protein Interfaces. PMID:30934865
The First Transcriptome Assembly of Yenyuan Stream Salamander (Batrachuperus yenyuanensis) Provides Novel Insights into Its Molecular Evolution. PMID:30934682
Sweet and Sour Ehrlichia: Glycoproteomics and Phosphoproteomics Reveal New Players in Ehrlichia ruminantium Physiology and Pathogenesis. PMID:30930869
Relationship between conformation shift and disease related variation sites in ATP-binding cassette transporter proteins. PMID:30923664
Differential Expression of mRNAs in the Brain Tissues of Patients with Alzheimer's Disease Based on GEO Expression Profile and Its Clinical Significance. PMID:30918899
Deciphering Within-Host Microevolution of Mycobacterium tuberculosis through Whole-Genome Sequencing: the Phenotypic Impact and Way Forward. PMID:30918049
Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay. PMID:30916337
Identification of genes involved in shea butter biosynthesis from Vitellaria paradoxa fruits through transcriptomics and functional heterologous expression. PMID:30915502
Plasma-sensitive Escherichia coli mutants reveal plasma resistance mechanisms. PMID:30913981
A TonB-dependent transporter is required for secretion of protease PopC across the bacterial outer membrane. PMID:30911012
Asymmetric distribution of glucose transporter mRNA provides a growth advantage in yeast. PMID:30910878
Homotypic and heterotypic trans-assembly of human Rab-family small GTPases in reconstituted membrane tethering. PMID:30910814
Targeted interplay between bacterial pathogens and host autophagy. PMID:30909843
Electrostatics of Tau Protein by Molecular Dynamics. PMID:30909607
Structural investigation of Rett-inducing MeCP2 mutations. PMID:30906830
A comprehensive in silico analysis of sortase superfamily. PMID:30900148
Chicken Organic Anion-Transporting Polypeptide 1A2, a Novel Avian Hepatitis E Virus (HEV) ORF2-Interacting Protein, Is Involved in Avian HEV Infection. PMID:30894478
The Patchy Distribution of Restriction⁻Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria. PMID:30893937
The Light and Dark Sides of Virtual Screening: What Is There to Know? PMID:30893780
Network Pharmacology Deciphering Mechanisms of Volatiles of Wendan Granule for the Treatment of Alzheimer's Disease. PMID:30891080
Dissecting FOXP2 Oligomerization and DNA Binding. PMID:30887622
The Balancing Act of Intrinsically Disordered Proteins: Enabling Functional Diversity while Minimizing Promiscuity. PMID:30878482
DPH1 syndrome: two novel variants and structural and functional analyses of seven missense variants identified in syndromic patients. PMID:30877278
Lysosomal targeting of the ABC transporter TAPL is determined by membrane-localized charged residues. PMID:30877195
A Molecular Modeling Approach to Identify Novel Inhibitors of the Major Facilitator Superfamily of Efflux Pump Transporters. PMID:30875968
In Silico Analysis of Homologous Heterodimers of Cruzipain-Chagasin from Structural Models Built by Homology. PMID:30875920
Fragment Hits: What do They Look Like and How do They Bind? PMID:30875465
Shotgun Proteomics of Human Dentin with Different Prefractionation Methods. PMID:30872775
Identification and analysis of genes associated with papillary thyroid carcinoma by bioinformatics methods. PMID:30872410
Lightweight data management with dtool. PMID:30867992
Automatic Human-like Mining and Constructing Reliable Genetic Association Database with Deep Reinforcement Learning. PMID:30864315
Comprehensive Virulence Gene Profiling of Bovine Non-aureus Staphylococci Based on Whole-Genome Sequencing Data. PMID:30863792
PTMselect: optimization of protein modifications discovery by mass spectrometry. PMID:30862887
Using Machine Learning to Measure Relatedness Between Genes: A Multi-Features Model. PMID:30862804
MorCVD: A Unified Database for Host-Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes. PMID:30858555
A bacterial display system for effective selection of protein-biotin ligase BirA variants with novel peptide specificity. PMID:30858523
Cell Shape and Population Migration Are Distinct Steps of Proteus mirabilis Swarming That Are Decoupled on High-Percentage Agar. PMID:30858303
Waardenburg Syndrome Expression and Penetrance. PMID:30854529
Validation and Stabilization of a Prophage Lysin of Clostridium perfringens by Using Yeast Surface Display and Coevolutionary Models. PMID:30850429
Functional protein representations from biological networks enable diverse cross-species inference. PMID:30847485
Automated exploration of gene ontology term and pathway networks with ClueGO-REST. PMID:30847467
Mammary Gland Transcriptome and Proteome Modifications by Nutrient Restriction in Early Lactation Holstein Cows Challenged with Intra-Mammary Lipopolysaccharide. PMID:30845783
Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen. PMID:30845144
Positive-unlabelled learning of glycosylation sites in the human proteome. PMID:30841845
Functional Segments on Intrinsically Disordered Regions in Disease-Related Proteins. PMID:30841624
A Systematic Investigation of the Malignant Functions and Diagnostic Potential of the Cancer Secretome. PMID:30840886
Significantly different effects of tetrahydroberberrubine enantiomers on dopamine D1/D2 receptors revealed by experimental study and integrated in silico simulation. PMID:30840169
A Comparative Study of Cluster Detection Algorithms in Protein-Protein Interaction for Drug Target Discovery and Drug Repurposing. PMID:30837876
Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX). PMID:30837494
Insights into the evolution of extracellular leucine-rich repeats in metazoans with special reference to Toll-like receptor 4. PMID:30837369
DAKB-GPCRs: An Integrated Computational Platform for Drug Abuse Related GPCRs. PMID:30835466
Snails In Silico: A Review of Computational Studies on the Conopeptides. PMID:30832207
Identification of the OXA-48 Carbapenemase Family by Use of Tryptic Peptides and Liquid Chromatography-Tandem Mass Spectrometry. PMID:30814261
Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy. PMID:30814064
ProtParCon: A Framework for Processing Molecular Data and Identifying Parallel and Convergent Amino Acid Replacements. PMID:30813627
Free Accessible Databases as a Source of Information about Food Components and Other Compounds with Anticancer Activity⁻Brief Review. PMID:30813234
Ontology based text mining of gene-phenotype associations: application to candidate gene prediction. PMID:30809638
PIRSitePredict for protein functional site prediction using position-specific rules. PMID:30805646
Establishing synthesis pathway-host compatibility via enzyme solubility. PMID:30802311
Insights into Body Size Evolution: A Comparative Transcriptome Study on Three Species of Asian Sisoridae Catfish. PMID:30795590
Secreted frizzled related protein is a target of PaxB and plays a role in aquiferous system development in the freshwater sponge, Ephydatia muelleri. PMID:30794564
SuCComBase: a manually curated repository of plant sulfur-containing compounds. PMID:30793170
AAV9-TAZ Gene Replacement Ameliorates Cardiac TMT Proteomic Profiles in a Mouse Model of Barth Syndrome. PMID:30788385
Integrative Gene Selection on Gene Expression Data: Providing Biological Context to Traditional Approaches. PMID:30785707
Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors. PMID:30784590
Comparative genomics sheds light on the predatory lifestyle of accipitrids and owls. PMID:30783131
Sequential Windowed Acquisition of Reporter Masses for Quantitation-First Proteomics. PMID:30781952
Discovery of Amantamide, a Selective CXCR7 Agonist from Marine Cyanobacteria. PMID:30779584
Molecular modeling of LDLR aids interpretation of genomic variants. PMID:30778614
Two subgroups in systemic lupus erythematosus with features of antiphospholipid or Sjögren's syndrome differ in molecular signatures and treatment perspectives. PMID:30777133
Genus-Wide Comparative Genomics Analysis of Neisseria to Identify New Genes Associated with Pathogenicity and Niche Adaptation of Neisseria Pathogens. PMID:30775379
Systems Biology Approaches Toward Understanding Primary Mitochondrial Diseases. PMID:30774647
BioVR: a platform for virtual reality assisted biological data integration and visualization. PMID:30767777
Conodipine-P1-3, the First Phospholipases A2 Characterized from Injected Cone Snail Venom. PMID:30765458
Plasmodium palmitoylation machinery engineered in E. coli for high-throughput screening of palmitoyl acyl-transferase inhibitors. PMID:30761251
NRF2 Activation in Cancer: From DNA to Protein. PMID:30760522
A galling insect activates plant reproductive programs during gall development. PMID:30755671
Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member. PMID:30755506
Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins. PMID:30747917
A new genomic blueprint of the human gut microbiota. PMID:30745586
Multimodel inference for biomarker development: an application to schizophrenia. PMID:30745560
How good are pathogenicity predictors in detecting benign variants? PMID:30742610
Grammar of protein domain architectures. PMID:30733291
The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. PMID:30732586
Imbalanced sphingolipid signaling is maintained as a core proponent of a cancerous phenotype in spite of metabolic pressure and epigenetic drift. PMID:30728898
Autophagy and Apoptosis Specific Knowledgebases-guided Systems Pharmacology Drug Research. PMID:30727895
Inferring pathogen-host interactions between Leptospira interrogans and Homo sapiens using network theory. PMID:30723266
The sequence and de novo assembly of Oxygymnocypris stewartii genome. PMID:30720802
Ulcerative colitis: functional analysis of the in-depth proteome. PMID:30718987
Cu Transport by the Extended Family of CcoA-like Transporters (CalT) in Proteobacteria. PMID:30718766
Functional homogeneity and specificity of topological modules in human proteome. PMID:30717667
Genetic association in female stress urinary incontinence based on proteomic findings: a case-control study. PMID:30715578
A specialized MreB-dependent cell wall biosynthetic complex mediates the formation of stalk-specific peptidoglycan in Caulobacter crescentus. PMID:30707707
Identification of human endogenous retrovirus transcripts in Hodgkin Lymphoma cells. PMID:30707417
De Novo Transcriptome Assembly of Agave H11648 by Illumina Sequencing and Identification of Cellulose Synthase Genes in Agave Species. PMID:30704153
Misprediction of Structural Disorder in Halophiles. PMID:30699990
Study of the whole genome, methylome and transcriptome of Cordyceps militaris. PMID:30696919
Caspase-4 disaggregates lipopolysaccharide micelles via LPS-CARD interaction. PMID:30696842
Structure and Evolution of Glycogen Branching Enzyme N-Termini From Bacteria. PMID:30692986
Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase. PMID:30689844
Identification, Functional Characterization, and Regulon Prediction of the Zinc Uptake Regulator (zur) of Bacillus anthracis - An Insight Into the Zinc Homeostasis of the Pathogen. PMID:30687290
Bi-allelic Mutations in ARMC2 Lead to Severe Astheno-Teratozoospermia Due to Sperm Flagellum Malformations in Humans and Mice. PMID:30686508
Tobramycin reduces key virulence determinants in the proteome of Pseudomonas aeruginosa outer membrane vesicles. PMID:30682135
Investigating Lactococcus lactis MG1363 Response to Phage p2 Infection at the Proteome Level. PMID:30679258
Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons. PMID:30678683
Ask1 and Akt act synergistically to promote ROS-dependent regeneration in Drosophila. PMID:30677014
Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium. PMID:30673782
TGF-beta signalling in bovine mammary gland involution and a comparative assessment of MAC-T and BME-UV1 cells as in vitro models for its study. PMID:30671288
Phloem Companion Cell-Specific Transcriptomic and Epigenomic Analyses Identify MRF1, a Regulator of Flowering. PMID:30670485
P-Mart: Interactive Analysis of Ion Abundance Global Proteomics Data. PMID:30667224
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. PMID:30661755
Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO). PMID:30660046
Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics. PMID:30659192
Structural insights into the tyrosine phosphorylation-mediated inhibition of SH3 domain-ligand interactions. PMID:30659095
Cysteine-Rich Receptor-Like Kinase Gene Family Identification in the Phaseolus Genome and Comparative Analysis of Their Expression Profiles Specific to Mycorrhizal and Rhizobial Symbiosis. PMID:30658517
An Annotated Genome for Haliotis rufescens (Red Abalone) and Resequenced Green, Pink, Pinto, Black, and White Abalone Species. PMID:30657886
Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation. PMID:30654561
Organic cation transporter 3 (Oct3) is a distinct catecholamines clearance route in adipocytes mediating the beiging of white adipose tissue. PMID:30653498
Re-analysis of the coral Acropora digitifera transcriptome reveals a complex lncRNAs-mRNAs interaction network implicated in Symbiodinium infection. PMID:30651068
Exploring the Papillomaviral Proteome to Identify Potential Candidates for a Chimeric Vaccine against Cervix Papilloma Using Immunomics and Computational Structural Vaccinology. PMID:30650527
A web application and service for imputing and visualizing missense variant effect maps. PMID:30649215
Accurate Estimation of Context-Dependent False Discovery Rates in Top-Down Proteomics. PMID:30647073
Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle. PMID:30642389
Using a Chemical Genetic Screen to Enhance Our Understanding of the Antimicrobial Properties of Gallium against Escherichia coli. PMID:30634525
Genome-wide DNA methylation and transcriptomic profiles in the lifestyle strategies and asexual development of the forest fungal pathogen Heterobasidion parviporum. PMID:30633603
Comparative Analysis of Genomic Island Prediction Tools. PMID:30631340
Bioinformatic analysis of long-lasting transcriptional and translational changes in the basolateral amygdala following acute stress. PMID:30629705
NommPred: Prediction of Mitochondrial and Mitochondrion-Related Organelle Proteins of Nonmodel Organisms. PMID:30626996
The (R)-enantiomer of the 6-chromanol derivate SUL-121 improves renal graft perfusion via antagonism of the α1-adrenoceptor. PMID:30626882
TogoGenome/TogoStanza: modularized Semantic Web genome database. PMID:30624651
Prediction of deleterious mutations in coding regions of mammals with transfer learning. PMID:30622632
The sequence and de novo assembly of hog deer genome. PMID:30620341
BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification. PMID:30612223
Mitogenic Signals Stimulate the CREB Coactivator CRTC3 through PP2A Recruitment. PMID:30611118
Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis. PMID:30608666
Molecular Dynamics Simulations of Substrate Release from Trypanosoma cruzi UDP-Galactopyranose Mutase. PMID:30608160
Activation of the Bile Acid Pathway and No Observed Antimicrobial Peptide Sequences in the Skin of a Poison Frog. PMID:30606754
Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. PMID:30602777
A partially function-to-topic model for protein function prediction. PMID:30598098
ABCF ATPases Involved in Protein Synthesis, Ribosome Assembly and Antibiotic Resistance: Structural and Functional Diversification across the Tree of Life. PMID:30597160
Diversification of DNA binding specificities enabled SREBP transcription regulators to expand the repertoire of cellular functions that they govern in fungi. PMID:30596634
Proteomics and multivariate modelling reveal sex-specific alterations in distinct regions of human carotid atheroma. PMID:30594242
Arabidopsis thaliana responds to colonisation of Piriformospora indica by secretion of symbiosis-specific proteins. PMID:30589877
Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants. PMID:30582689
Identifying Potential Ageing-Modulating Drugs In Silico. PMID:30581056
Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt. PMID:30576492
Where differences resemble: sequence-feature analysis in curated databases of intrinsically disordered proteins. PMID:30576490
PhytoTypeDB: a database of plant protein inter-cultivar variability and function. PMID:30576486
Ensembl variation resources. PMID:30576484
Cross-ID: Analysis and Visualization of Complex XL-MS-Driven Protein Interaction Networks. PMID:30575379
Role of oxidative stress in Retinitis pigmentosa: new involved pathways by an RNA-Seq analysis. PMID:30569795
Transcriptomic Characterization of the South American Freshwater Stingray Potamotrygon motoro Venom Apparatus. PMID:30567320
Proteome Map of Pea (Pisum sativum L.) Embryos Containing Different Amounts of Residual Chlorophylls. PMID:30558315
A Pipeline for Classifying Deleterious Coding Mutations in Agricultural Plants. PMID:30546376
Structural characterization and molecular dynamics simulations of the caprine and bovine solute carrier family 11 A1 (SLC11A1). PMID:30543052
Tamoxifen mechanically reprograms the tumor microenvironment via HIF-1A and reduces cancer cell survival. PMID:30538116
BASILIScan: a tool for high-throughput analysis of intrinsic disorder patterns in homologous proteins. PMID:30537929
PopViz: a webserver for visualizing minor allele frequencies and damage prediction scores of human genetic variations. PMID:30535305
Genome of the small hive beetle (Aethina tumida, Coleoptera: Nitidulidae), a worldwide parasite of social bee colonies, provides insights into detoxification and herbivory. PMID:30535280
High-Quality Draft Genome Sequences of Eight Bacteria Isolated from Fungus Gardens Grown by Trachymyrmex septentrionalis Ants. PMID:30533809
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models. PMID:30531987
Architectural Dynamics of CaMKII-Actin Networks. PMID:30527447
An efficient proteome-wide strategy for discovery and characterization of cellular nucleotide-protein interactions. PMID:30521565
NLRP3 lacking the leucine-rich repeat domain can be fully activated via the canonical inflammasome pathway. PMID:30518920
A Systematic Overview of Type II and III Toxin-Antitoxin Systems with a Focus on Druggability. PMID:30518070
Both Intrinsically Disordered Regions and Structural Domains Evolve Rapidly in Immune-Related Mammalian Proteins. PMID:30518031
Protein structure networks provide insight into active site flexibility in esterase/lipases from the carnivorous plant Drosera capensis. PMID:30516771
Genetic variations in human papillomavirus and cervical cancer outcomes. PMID:30515767
The evolution of ependymin-related proteins. PMID:30514200
Targeting phosphorylated p53 to elicit tumor-reactive T helper responses against head and neck squamous cell carcinoma. PMID:30510853
Giant tortoise genomes provide insights into longevity and age-related disease. PMID:30510174
SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database. PMID:30500919
Proteomic profiling of senescent human diploid fibroblasts treated with gamma-tocotrienol. PMID:30497457
Representativeness of variation benchmark datasets. PMID:30497376
Different effects of long noncoding RNA NDRG1-OT1 fragments on NDRG1 transcription in breast cancer cells under hypoxia. PMID:30497328
Comparative genomics of downy mildews reveals potential adaptations to biotrophy. PMID:30486780
Riluzole Attenuates L-DOPA-Induced Abnormal Involuntary Movements Through Decreasing CREB1 Activity: Insights from a Rat Model. PMID:30484112
Data-Independent Acquisition Mass Spectrometry To Quantify Protein Levels in FFPE Tumor Biopsies for Molecular Diagnostics. PMID:30481034
Selective agonist of TRPML2 reveals direct role in chemokine release from innate immune cells. PMID:30479274
In Vivo Applicability of Neosartorya fischeri Antifungal Protein 2 (NFAP2) in Treatment of Vulvovaginal Candidiasis. PMID:30478163
NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies. PMID:30477135
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. PMID:30476243
The BioGRID interaction database: 2019 update. PMID:30476227
Enhancing the Production of the Fungal Pigment Aurofusarin in Fusarium graminearum. PMID:30469367
Statistical-based database fingerprint: chemical space dependent representation of compound databases. PMID:30467740
Genomic Deoxyxylulose Phosphate Reductoisomerase (DXR) Mutations Conferring Resistance to the Antimalarial Drug Fosmidomycin in E. coli. PMID:30462485
Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay. PMID:30458008
Loss of the Mia40a oxidoreductase leads to hepato-pancreatic insufficiency in zebrafish. PMID:30457989
A reference set of curated biomedical data and metadata from clinical case reports. PMID:30457569
Genome sequence of the opportunistic human pathogen Magnusiomyces capitatus. PMID:30456648
Draft genome sequence and detailed characterization of biofuel production by oleaginous microalga Scenedesmus quadricauda LWG002611. PMID:30455737
Automated selection of homologs to track the evolutionary history of proteins. PMID:30453878
Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data. PMID:30450911
RNAct: Protein-RNA interaction predictions for model organisms with supporting experimental data. PMID:30445601
The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver. PMID:30445555
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. PMID:30445541
15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms. PMID:30445427
A Text Mining Pipeline Using Active and Deep Learning Aimed at Curating Information in Computational Neuroscience. PMID:30443819
Large-Scale Analyses of Site-Specific Evolutionary Rates across Eukaryote Proteomes Reveal Confounding Interactions between Intrinsic Disorder, Secondary Structure, and Functional Domains. PMID:30441862
Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. PMID:30425690
Nonsense mutation in PMEL is associated with yellowish plumage colour phenotype in Japanese quail. PMID:30425278
X-search: an open access interface for cross-cohort exploration of the National Sleep Research Resource. PMID:30424756
IRSOM, a reliable identifier of ncRNAs based on supervised self-organizing maps with rejection. PMID:30423081
Ontology-based validation and identification of regulatory phenotypes. PMID:30423068
Prioritising candidate genes causing QTL using hierarchical orthologous groups. PMID:30423067
Vacuolar hydrolysis and efflux: current knowledge and unanswered questions. PMID:30422029
Auxin Function in the Brown Alga Dictyota dichotoma. PMID:30420566
Inhibition of Protein Secretion in Escherichia coli and Sub-MIC Effects of Arylomycin Antibiotics. PMID:30420476
PPARγ maintains the metabolic heterogeneity and homeostasis of renal tubules. PMID:30420298
A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events. PMID:30419019
Organic Particles: Heterogeneous Hubs for Microbial Interactions in Aquatic Ecosystems. PMID:30416497
PCNT point mutations and familial intracranial aneurysms. PMID:30413633
WDFY4 is required for cross-presentation in response to viral and tumor antigens. PMID:30409884
IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. PMID:30407591
PreMedKB: an integrated precision medicine knowledgebase for interpreting relationships between diseases, genes, variants and drugs. PMID:30407536
Ensembl 2019. PMID:30407521
Clinical, Genetics, and Bioinformatic Characterization of Mutations Affecting an Essential Region of PLS3 in Patients with BMND18. PMID:30405713
Comparative Glycomics of Immunoglobulin A and G From Saliva and Plasma Reveals Biomarker Potential. PMID:30405629
SLiM-Enrich: computational assessment of protein-protein interaction data as a source of domain-motif interactions. PMID:30402352
A bacteria-derived tail anchor localizes to peroxisomes in yeast and mammalian cells. PMID:30401812
Transcriptomics of Haemophilus (Glässerella) parasuis serovar 5 subjected to culture conditions partially mimetic to natural infection for the search of new vaccine antigens. PMID:30400794
MitoMiner v4.0: an updated database of mitochondrial localization evidence, phenotypes and diseases. PMID:30398659
InterPro in 2019: improving coverage, classification and access to protein sequence annotations. PMID:30398656
Minimal PAM specificity of a highly similar SpCas9 ortholog. PMID:30397647
Comparative transcriptomics identifies genes differentially expressed in the intestine of a new fast-growing strain of common carp with higher unsaturated fatty acid content in muscle. PMID:30395585
The PRIDE database and related tools and resources in 2019: improving support for quantification data. PMID:30395289
UniProt: a worldwide hub of protein knowledge. PMID:30395287
A Conditional Dependency on MELK for the Proliferation of Triple-Negative Breast Cancer Cells. PMID:30391850
Design of metalloproteins and novel protein folds using variational autoencoders. PMID:30385875
Comparative analysis of the Pocillopora damicornis genome highlights role of immune system in coral evolution. PMID:30382153
Association of Cystathionine β-Synthase Gene Polymorphisms With Preeclampsia. PMID:30380942
Translocatome: a novel resource for the analysis of protein translocation between cellular organelles. PMID:30380112
iEKPD 2.0: an update with rich annotations for eukaryotic protein kinases, protein phosphatases and proteins containing phosphoprotein-binding domains. PMID:30380109
OrthoInspector 3.0: open portal for comparative genomics. PMID:30380106
Cell migration inhibition activity of a non-RGD disintegrin from Crotalus durissus collilineatus venom. PMID:30377432
VarSome: the human genomic variant search engine. PMID:30376034
iDog: an integrated resource for domestic dogs and wild canids. PMID:30371881
COSMIC: the Catalogue Of Somatic Mutations In Cancer. PMID:30371878
PubChem 2019 update: improved access to chemical data. PMID:30371825
Mycobacterium tuberculosis serine/threonine protein kinases: structural information for the design of their specific ATP-competitive inhibitors. PMID:30367309
De Novo Hepatic Transcriptome Assembly and Systems Level Analysis of Three Species of Dietary Fish, Sardinops sagax, Scomber japonicus, and Pleuronichthys verticalis. PMID:30366465
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes. PMID:30364992
Elevated Autoantibodies in Subacute Human Spinal Cord Injury Are Naturally Occurring Antibodies. PMID:30364218
Proteomic analysis of Lactobacillus casei GCRL163 cell-free extracts reveals a SecB homolog and other biomarkers of prolonged heat stress. PMID:30359441
Comparative De Novo transcriptome analysis of the Australian black-lip and Sydney rock oysters reveals expansion of repetitive elements in Saccostrea genomes. PMID:30359422
Proteomic changes in traumatic brain injury: experimental approaches. PMID:30358641
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. PMID:30357405
GENCODE reference annotation for the human and mouse genomes. PMID:30357393
BitterDB: taste ligands and receptors database in 2019. PMID:30357384
CMAUP: a database of collective molecular activities of useful plants. PMID:30357356
The Pfam protein families database in 2019. PMID:30357350
Network-Based Methods for Prediction of Drug-Target Interactions. PMID:30356768
The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. PMID:30356183
A combined computational and experimental approach reveals the structure of a C/EBPβ-Spi1 interaction required for IL1B gene transcription. PMID:30355733
Parasitic Nematodes Exert Antimicrobial Activity and Benefit From Microbiota-Driven Support for Host Immune Regulation. PMID:30349532
In Vitro Assembly of Diverse Bacterial Microcompartment Shell Architectures. PMID:30346795
Comparative Genomics of Lactobacillus brevis Reveals a Significant Plasmidome Overlap of Brewery and Insect Isolates. PMID:30341451
PopHumanScan: the online catalog of human genome adaptation. PMID:30335169
Evidence of Polygenic Adaptation to High Altitude from Tibetan and Sherpa Genomes. PMID:30335146
Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance. PMID:30333483
Genomic data integration systematically biases interactome mapping. PMID:30332399
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
Disrupted Synthesis of a Di-N-acetylated Sugar Perturbs Mature Glycoform Structure and Microheterogeneity in the O-Linked Protein Glycosylation System of Neisseria elongata subsp. glycolytica. PMID:30322851
Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community. PMID:30322445
RetroRules: a database of reaction rules for engineering biology. PMID:30321422
PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information. PMID:30321395
Large-scale docking predicts that sORF-encoded peptides may function through protein-peptide interactions in Arabidopsis thaliana. PMID:30321192
Broad phylogenetic analysis of cation/proton antiporters reveals transport determinants. PMID:30310075
DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield. PMID:30309336
Circular Permutation Obscures Universality of a Ribosomal Protein. PMID:30306205
A recessive lethal chondrodysplasia in a miniature zebu family results from an insertion affecting the chondroitin sulfat domain of aggrecan. PMID:30305023
Towards region-specific propagation of protein functions. PMID:30304483
Genenames.org: the HGNC and VGNC resources in 2019. PMID:30304474
The C-terminal D/E-rich domain of MBD3 is a putative Z-DNA mimic that competes for Zα DNA-binding activity. PMID:30304469
OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes. PMID:30299502
Haplosaurus computes protein haplotypes for use in precision drug design. PMID:30297836
The jPOST environment: an integrated proteomics data repository and database. PMID:30295851
A de novo transcriptome assembly of the zebra bullhead shark, Heterodontus zebra. PMID:30295671
ProteomeGenerator: A Framework for Comprehensive Proteomics Based on de Novo Transcriptome Assembly and High-Accuracy Peptide Mass Spectral Matching. PMID:30295032
Identification of the Bisabolol Synthase in the Endangered Candeia Tree (Eremanthus erythropappus (DC) McLeisch). PMID:30294334
Automatic Inference of Sequence from Low-Resolution Crystallographic Data. PMID:30293812
Exon Skipping in a Dysf-Missense Mutant Mouse Model. PMID:30292141
High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites. PMID:30287822
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites. PMID:30285084
Pathogenic variants in glutamyl-tRNAGln amidotransferase subunits cause a lethal mitochondrial cardiomyopathy disorder. PMID:30283131
Yersinia pseudotuberculosis BarA-UvrY Two-Component Regulatory System Represses Biofilms via CsrB. PMID:30280093
The intracellular proteome of African swine fever virus. PMID:30279544
Genetic conflicts with Plasmodium parasites and functional constraints shape the evolution of erythrocyte cytoskeletal proteins. PMID:30279439
New N-(oxazolylmethyl)-thiazolidinedione Active against Candida albicans Biofilm: Potential Als Proteins Inhibitors. PMID:30279343
Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase. PMID:30279311
CXCR5 overexpression in HL-60 cells enhances chemotaxis toward CXCL13 without anticipated interaction partners or enhanced MAPK signaling. PMID:30276608
A community-driven reconstruction of the Aspergillus niger metabolic network. PMID:30275963
Fyn Regulates Binding Partners of Cyclic-AMP Dependent Protein Kinase A. PMID:30274258
Updates in Rhea: SPARQLing biochemical reaction data. PMID:30272209
Molecular phenotyping of laboratory mouse strains using 500 multiple reaction monitoring mass spectrometry plasma assays. PMID:30271959
Progress of analytical tools and techniques for human gut microbiome research. PMID:30267313
Transcriptional and Functional Analysis of Bifidobacterium animalis subsp. lactis Exposure to Tetracycline. PMID:30266728
Prediction and validation of the structural features of Ov58GPCR, an immunogenic determinant of Onchocerca volvulus. PMID:30256790
A new tool for studying waterfowl immune and metabolic responses: Molecular level analysis using kinome profiling. PMID:30250721
Optimisation of a serum albumin removal protocol for use in a proteomic study to identify the protein biomarkers for silent gastric ulceration in horses. PMID:30250392
Identifying and validating blood mRNA biomarkers for acute and chronic insufficient sleep in humans: a machine learning approach. PMID:30247731
KAT6A Syndrome: genotype-phenotype correlation in 76 patients with pathogenic KAT6A variants. PMID:30245513
C.el Phosphatome: A Catalogue of Actual and Pseudo Phosphatases Based on In-Silico Studies in Caenorhabditis elegans. PMID:30242660
The genetic architecture of aniridia and Gillespie syndrome. PMID:30242502
Comprehensive Evolutionary Analysis of the Major RNA-Induced Silencing Complex Members. PMID:30242207
THE-DB: a threading model database for comparative protein structure analysis of the E. coli K12 and human proteomes. PMID:30239678
The Encyclopedia of Proteome Dynamics: the KinoViewer. PMID:30239567
Epigenome-Wide Analyses Identify Two Novel Associations With Recurrent Stroke in the Vitamin Intervention for Stroke Prevention Clinical Trial. PMID:30237808
In silico identification of lipid-binding α helices of uncoupling protein 1. PMID:30233783
Global Profiling of Lysine Acetylation in Borrelia burgdorferi B31 Reveals Its Role in Central Metabolism. PMID:30233522
Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome. PMID:30232199
Hydrogen Peroxide: Its Role in Plant Biology and Crosstalk with Signalling Networks. PMID:30231521
Maintaining Biological Cultures and Measuring Gene Expression in Aphis nerii: A Non-model System for Plant-insect Interactions. PMID:30222148
Receptor pharmacophore ensemble (REPHARMBLE): a probabilistic pharmacophore modeling approach using multiple protein-ligand complexes. PMID:30220049
Impact of nanoparticle surface functionalization on the protein corona and cellular adhesion, uptake and transport. PMID:30219059
The Thaumarchaeon N. gargensis carries functional bioABD genes and has a promiscuous E. coli ΔbioH-complementing esterase EstN1. PMID:30218044
Role of phosphate sensing in bone and mineral metabolism. PMID:30218014
The Amino Acid Composition of Quadruplex Binding Proteins Reveals a Shared Motif and Predicts New Potential Quadruplex Interactors. PMID:30216987
drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics. PMID:30210791
Characterization of ML-005, a Novel Metaproteomics-Derived Esterase. PMID:30210461
Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation. PMID:30210232
Three-Finger Toxin Diversification in the Venoms of Cat-Eye Snakes (Colubridae: Boiga). PMID:30206667
Structural Basis of Pan-Ebolavirus Neutralization by a Human Antibody against a Conserved, yet Cryptic Epitope. PMID:30206174
Single mutations in the ε subunit from thermophilic Bacillus PS3 generate a high binding affinity site for ATP. PMID:30202650
Proteomic Approaches for the Discovery of Biofluid Biomarkers of Neurodegenerative Dementias. PMID:30200280
Genome sequence analysis of Zooshikella ganghwensis strain VG4 and its potential for the synthesis of antimicrobial metabolites. PMID:30197874
A biochemical and genetic discovery pipeline identifies PLCδ4b as a nonreceptor activator of heterotrimeric G-proteins. PMID:30194280
What bacteria want. PMID:30187651
Genetic landscape of isolated pediatric cataracts: extreme heterogeneity and variable inheritance patterns within genes. PMID:30187164
The genome of Naegleria lovaniensis, the basis for a comparative approach to unravel pathogenicity factors of the human pathogenic amoeba N. fowleri. PMID:30185166
From Molecules to Mechanisms: Functional Proteomics and Its Application to Renal Tubule Physiology. PMID:30182799
The Protein Coded by a Short Open Reading Frame, Not by the Annotated Coding Sequence, Is the Main Gene Product of the Dual-Coding Gene MIEF1. PMID:30181344
PKCε contributes to lipid-induced insulin resistance through cross talk with p70S6K and through previously unknown regulators of insulin signaling. PMID:30181290
Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk. PMID:30177862
A Luminal Loop of Wilson Disease Protein Binds Copper and Is Required for Protein Activity. PMID:30173886
Widespread evolutionary crosstalk among protein domains in the context of multi-domain proteins. PMID:30169546
Optimised Desorption Electrospray Ionisation Mass Spectrometry Imaging (DESI-MSI) for the Analysis of Proteins/Peptides Directly from Tissue Sections on a Travelling Wave Ion Mobility Q-ToF. PMID:30168053
The role of solute carrier (SLC) transporters in actinomycin D pharmacokinetics in paediatric cancer patients. PMID:30167756
Silent Witness: Dual-Species Transcriptomics Reveals Epithelial Immunological Quiescence to Helminth Larval Encounter and Fostered Larval Development. PMID:30158930
COSMIC-3D provides structural perspectives on cancer genetics for drug discovery. PMID:30158682
Carcinogenic Pesticide Control via Hijacking Endosymbiosis; The Paradigm of DSB-A from Wolbachia pipientis for the Management of Otiorhynchus singularis. PMID:30150426
Synthesis versus degradation: directions of amino acid metabolism during Arabidopsis abiotic stress response. PMID:30143990
Development and characterization of a novel monoclonal antibody that recognizes an epitope in the central protein interaction domain of RapGEF1 (C3G). PMID:30143974
coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers. PMID:30142147
Dysregulation of the calcium handling protein, CCDC47, is associated with diabetic cardiomyopathy. PMID:30140426
Genetics of hearing loss in the Arab population of Northern Israel. PMID:30139988
Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. PMID:30137486
Functional diversity of TMPRSS6 isoforms and variants expressed in hepatocellular carcinoma cell lines. PMID:30135444
Membrane Active Peptides and Their Biophysical Characterization. PMID:30135402
p62-Dependent Phase Separation of Patient-Derived KEAP1 Mutations and NRF2. PMID:30126895
Efficient proximity labeling in living cells and organisms with TurboID. PMID:30125270
SLING: a tool to search for linked genes in bacterial datasets. PMID:30124998
Draft genome of Glyptosternon maculatum, an endemic fish from Tibet Plateau. PMID:30124856
Proteomics for blood biomarker exploration of severe mental illness: pitfalls of the past and potential for the future. PMID:30115926
Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles. PMID:30114370
Intron retention is a source of neoepitopes in cancer. PMID:30114007
Genome-wide mapping of plasma protein QTLs identifies putatively causal genes and pathways for cardiovascular disease. PMID:30111768
Edema Induced by a Crotalus durissus terrificus Venom Serine Protease (Cdtsp 2) Involves the PAR Pathway and PKC and PLC Activation. PMID:30111691
In silico identification of inhibitors against Plasmodium falciparum histone deacetylase 1 (PfHDAC-1). PMID:30109440
Insights from the Molecular modeling, docking analysis of illicit drugs and Bomb Compounds with Honey Bee Odorant Binding Proteins (OBPs). PMID:30108419
Human proteins that interact with RNA/DNA hybrids. PMID:30108179
BALCONY: an R package for MSA and functional compartments of protein variability analysis. PMID:30107777
Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39. PMID:30107613
Monitoring changes in the Gene Ontology and their impact on genomic data analysis. PMID:30107399
Proteomics: Clinical and research applications in respiratory diseases. PMID:30105802
Iron Inhibits the Secretion of Apolipoprotein E in Cultured Human Adipocytes. PMID:30105281
PMLPR: A novel method for predicting subcellular localization based on recommender systems. PMID:30104743
Scaling up data curation using deep learning: An application to literature triage in genomic variation resources. PMID:30102703
Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. PMID:30097089
The Human Centrosomal Protein CCDC146 Binds Chlamydia trachomatis Inclusion Membrane Protein CT288 and Is Recruited to the Periphery of the Chlamydia-Containing Vacuole. PMID:30094225
Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns. PMID:30086708
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. PMID:30084866
Alchemical Grid Dock (AlGDock) calculations in the D3R Grand Challenge 3 : Binding free energies between flexible ligands and rigid receptors. PMID:30084078
HPO2GO: prediction of human phenotype ontology term associations for proteins using cross ontology annotation co-occurrences. PMID:30083448
The Evolutionary Conserved γ-Core Motif Influences the Anti-Candida Activity of the Penicillium chrysogenum Antifungal Protein PAF. PMID:30079061
Modification of Crocodile Spermatozoa Refutes the Tenet That Post-testicular Sperm Maturation Is Restricted To Mammals. PMID:30072580
A High-Quality, Long-Read De Novo Genome Assembly to Aid Conservation of Hawaii's Last Remaining Crow Species. PMID:30071683
Structure of mouse protocadherin 15 of the stereocilia tip link in complex with LHFPL5. PMID:30070639
Quorum-Quenching Bacteria Isolated From Red Sea Sediments Reduce Biofilm Formation by Pseudomonas aeruginosa. PMID:30065702
Liberating links between datasets using lightweight data publishing: an example using plant names and the taxonomic literature. PMID:30065607
The OB-fold proteins of the Trypanosoma brucei editosome execute RNA-chaperone activity. PMID:30060205
Conotoxin Diversity in Chelyconus ermineus (Born, 1778) and the Convergent Origin of Piscivory in the Atlantic and Indo-Pacific Cones. PMID:30060147
Oncogenic activation of the STAT3 pathway drives PD-L1 expression in natural killer/T-cell lymphoma. PMID:30054295
Structural Analysis of Hippocampal Kinase Signal Transduction. PMID:30053369
ADReCS-Target: target profiles for aiding drug safety research and application. PMID:30053268
dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation. PMID:30053267
Evidence for a Unique DNA-Dependent RNA Polymerase in Cereal Crops. PMID:30053133
Characterization of FGD5 Expression in Primary Breast Cancers and Lymph Node Metastases. PMID:30052477
Automatic extraction of gene-disease associations from literature using joint ensemble learning. PMID:30048465
GPCR-SAS: A web application for statistical analyses on G protein-coupled receptors sequences. PMID:30044824
Serum protein electrophoresis in healthy and injured southern white rhinoceros (Ceratotherium simum simum). PMID:30044807
De novo transcriptome assembly of the lobster cockroach Nauphoeta cinerea (Blaberidae). PMID:30043835
Epigenetic Variability Confounds Transcriptome but Not Proteome Profiling for Coexpression-based Gene Function Prediction. PMID:30042154
Identification of Potential Nematicidal Compounds against the Pine Wood Nematode, Bursaphelenchus xylophilus through an In Silico Approach. PMID:30041426
Leveraging Experimental Details for an Improved Understanding of Host-Pathogen Interactome. PMID:30040202
Gating mechanisms during actin filament elongation by formins. PMID:30035712
High-throughput profiling of the circulating proteome suggests sexually dimorphic corticosteroid signaling following ischemic stroke. PMID:30029587
Engineering a Rugged Nanoscaffold To Enhance Plug-and-Display Vaccination. PMID:30028591
High Quality de Novo Transcriptome Assembly of Croton tiglium. PMID:30027092
Computational Analysis of LOX1 Inhibition Identifies Descriptors Responsible for Binding Selectivity. PMID:30023828
X-ray-Structure-Based Identification of Compounds with Activity against Targets from Different Families and Generation of Templates for Multitarget Ligand Design. PMID:30023769
Alzheimer disease pathology and the cerebrospinal fluid proteome. PMID:30021611
Structural Biology Helps Interpret Variants of Uncertain Significance in Genes Causing Endocrine and Metabolic Disorders. PMID:30019023
Structural and Functional Insights Into Lysostaphin-Substrate Interaction. PMID:30018958
Integrative landscape of dysregulated signaling pathways of clinically distinct pancreatic cancer subtypes. PMID:30018740
Deep mutational analysis reveals functional trade-offs in the sequences of EGFR autophosphorylation sites. PMID:30012625
PRP-19, a conserved pre-mRNA processing factor and E3 ubiquitin ligase, inhibits the nuclear accumulation of GLP-1/Notch intracellular domain. PMID:30012553
An Open Library of Human Kinase Domain Constructs for Automated Bacterial Expression. PMID:30004690
Peptide presentation by HLA-DQ molecules is associated with the development of immune tolerance. PMID:30002966
Dual localized kinesin-12 POK2 plays multiple roles during cell division and interacts with MAP65-3. PMID:30002118
LMDIPred: A web-server for prediction of linear peptide sequences binding to SH3, WW and PDZ domains. PMID:30001346
In silico analysis of the α-amylase family GH57: eventual subfamilies reflecting enzyme specificities. PMID:29998051
The Genetics of a Behavioral Speciation Phenotype in an Island System. PMID:29996514
A molecular model for LINC complex regulation: activation of SUN2 for KASH binding. PMID:29995584
Comparative Metagenomics Provides Insight Into the Ecosystem Functioning of the Shark Bay Stromatolites, Western Australia. PMID:29988640
Genome instability is a consequence of transcription deficiency in patients with bone marrow failure harboring biallelic ERCC6L2 variants. PMID:29987015
Loose ends: almost one in five human genes still have unresolved coding status. PMID:29982784
Gene Regulatory Variation in Drosophila melanogaster Renal Tissue. PMID:29976765
Comparative Secretome Profiling and Mutant Protein Identification in Metastatic Prostate Cancer Cells by Quantitative Mass Spectrometry-based Proteomics. PMID:29976633
Multifunctional Activity-Based Protein Profiling of the Developing Lung. PMID:29972024
A variant in LMX1A causes autosomal recessive severe-to-profound hearing impairment. PMID:29971487
Whole-Cell MALDI-TOF MS Versus 16S rRNA Gene Analysis for Identification and Dereplication of Recurrent Bacterial Isolates. PMID:29971049
SIMBAD: a sequence-independent molecular-replacement pipeline. PMID:29968670
Fern genomes elucidate land plant evolution and cyanobacterial symbioses. PMID:29967517
The transcription factor Rfx7 limits metabolism of NK cells and promotes their maintenance and immunity. PMID:29967452
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. PMID:29967418
Enrichment of extracellular vesicles from human synovial fluid using size exclusion chromatography. PMID:29963299
Enhanced proteasomal activity is essential for long term survival and recurrence of innately radiation resistant residual glioblastoma cells. PMID:29963228
Anti-Correlation between the Dynamics of the Active Site Loop and C-Terminal Tail in Relation to the Homodimer Asymmetry of the Mouse Erythroid 5-Aminolevulinate Synthase. PMID:29958424
Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer. PMID:29955178
HFSP: high speed homology-driven function annotation of proteins. PMID:29950013
PrimAlign: PageRank-inspired Markovian alignment for large biological networks. PMID:29949962
In silico approach in reveal traditional medicine plants pharmacological material basis. PMID:29946351
Site-specific characterization of endogenous SUMOylation across species and organs. PMID:29942033
Prediction of auxin response elements based on data fusion in Arabidopsis thaliana. PMID:29936576
High and Low Levels of an NTRK2-Driven Genetic Profile Affect Motor- and Cognition-Associated Frontal Gray Matter in Prodromal Huntington's Disease. PMID:29932126
3DPatch: fast 3D structure visualization with residue conservation. PMID:29931189
Idiopathic Scoliosis Families Highlight Actin-Based and Microtubule-Based Cellular Projections and Extracellular Matrix in Disease Etiology. PMID:29930198
Sequencing and Annotation of the Genome of Mycobacterium tuberculosis MYC004, a Strain Causing Meningitis in Mexico. PMID:29930042
Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity. PMID:29925878
The PGRS Domain of Mycobacterium tuberculosis PE_PGRS Protein Rv0297 Is Involved in Endoplasmic Reticulum Stress-Mediated Apoptosis through Toll-Like Receptor 4. PMID:29921671
Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. PMID:29917034
Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center. PMID:29917015
Two New Secreted Proteases Generate a Casein-Derived Antimicrobial Peptide in Bacillus cereus Food Born Isolate Leading to Bacterial Competition in Milk. PMID:29915567
The Solution Structure of CCL28 Reveals Structural Lability that Does Not Constrain Antifungal Activity. PMID:29913161
Mutational analysis of the pro-peptide of a marine intracellular subtilisin protease supports its role in inhibition. PMID:29907987
GFPT1 deficiency in muscle leads to myasthenia and myopathy in mice. PMID:29905857
Introduction of novel thermostable α-amylases from genus Anoxybacillus and proposing to group the Bacillaceae related α-amylases under five individual GH13 subfamilies. PMID:29904894
Draft genome sequence of Trametes villosa (Sw.) Kreisel CCMB561, a tropical white-rot Basidiomycota from the semiarid region of Brazil. PMID:29904660
Deducing the presence of proteins and proteoforms in quantitative proteomics. PMID:29899466
Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. PMID:29890970
Cytotoxic, Anti-Proliferative and Apoptosis Activity of l-Amino Acid Oxidase from Malaysian Cryptelytrops purpureomaculatus (CP-LAAO) Venom on Human Colon Cancer Cells. PMID:29890640
Predicting human protein function with multi-task deep neural networks. PMID:29889900
Bacterial denitrifying nitric oxide reductases and aerobic respiratory terminal oxidases use similar delivery pathways for their molecular substrates. PMID:29883591
Machine learning provides predictive analysis into silver nanoparticle protein corona formation from physicochemical properties. PMID:29881624
A conserved loop-wedge motif moderates reaction site search and recognition by FEN1. PMID:29878258
BASiNET-BiologicAl Sequences NETwork: a case study on coding and non-coding RNAs identification. PMID:29873784
Analysis of tail-anchored protein translocation pathway in plants. PMID:29872748
Expanding the horizons of microRNA bioinformatics. PMID:29871895
Meta-Analysis of Maternal and Fetal Transcriptomic Data Elucidates the Role of Adaptive and Innate Immunity in Preterm Birth. PMID:29867970
CASTp 3.0: computed atlas of surface topography of proteins. PMID:29860391
The proteome of perilymph in patients with vestibular schwannoma. A possibility to identify biomarkers for tumor associated hearing loss? PMID:29856847
Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. PMID:29855388
Predicting Interactions between Virus and Host Proteins Using Repeat Patterns and Composition of Amino Acids. PMID:29854357
A Novel Heterozygous Missense Mutation in GNAT1 Leads to Autosomal Dominant Riggs Type of Congenital Stationary Night Blindness. PMID:29850563
Valine biosynthesis in Saccharomyces cerevisiae is regulated by the mitochondrial branched-chain amino acid aminotransferase Bat1. PMID:29850466
Ubiquitin Proteasome pathway proteins as potential drug targets in parasite Trypanosoma cruzi. PMID:29849031
ProteomeTools: Systematic Characterization of 21 Post-translational Protein Modifications by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Using Synthetic Peptides. PMID:29848782
Gene family innovation, conservation and loss on the animal stem lineage. PMID:29848444
Cdc48-like protein of actinobacteria (Cpa) is a novel proteasome interactor in mycobacteria and related organisms. PMID:29809155
HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information. PMID:29796670
A High Quality Genome for Mus spicilegus, a Close Relative of House Mice with Unique Social and Ecological Adaptations. PMID:29794166
Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits. PMID:29793448
The way is the goal: how SecA transports proteins across the cytoplasmic membrane in bacteria. PMID:29790985
Molecular Mechanisms Preventing Senescence in Response to Prolonged Darkness in a Desiccation-Tolerant Plant. PMID:29789435
ezTag: tagging biomedical concepts via interactive learning. PMID:29788413
SWISS-MODEL: homology modelling of protein structures and complexes. PMID:29788355
BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. PMID:29788290
Carbonyl reduction of NNK by recombinant human lung enzymes: identification of HSD17β12 as the reductase important in (R)-NNAL formation in human lung. PMID:29788210
The draft genome sequence of cork oak. PMID:29786699
Differences between fast and slow muscles in scallops revealed through proteomics and transcriptomics. PMID:29783952
Identification of Cyclin-dependent Kinase 1 Specific Phosphorylation Sites by an In Vitro Kinase Assay. PMID:29782014
TelNet - a database for human and yeast genes involved in telomere maintenance. PMID:29776332
The Hydrophobin-Like OmSSP1 May Be an Effector in the Ericoid Mycorrhizal Symbiosis. PMID:29765384
Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis. PMID:29764946
VAReporter: variant reporter for cancer research of massive parallel sequencing. PMID:29764369
In vitro gentamicin exposure alters caveolae protein profile in cochlear spiral ligament pericytes. PMID:29760588
De novo nonsense mutation in WHSC1 (NSD2) in patient with intellectual disability and dysmorphic features. PMID:29760529
Thymoquinone increases the expression of neuroprotective proteins while decreasing the expression of pro-inflammatory cytokines and the gene expression NFκB pathway signaling targets in LPS/IFNγ -activated BV-2 microglia cells. PMID:29759145
Distribution Patterns of Polyphosphate Metabolism Pathway and Its Relationships With Bacterial Durability and Virulence. PMID:29755430
Identification and structural characterization of a histidinol phosphate phosphatase from Mycobacterium tuberculosis. PMID:29752410
Structural biology data archiving - where we are and what lies ahead. PMID:29749603
Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells. PMID:29747587
PPI network analyses of human WD40 protein family systematically reveal their tendency to assemble complexes and facilitate the complex predictions. PMID:29745845
ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes. PMID:29741573
Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization. PMID:29740413
From in silico to in vitro: a trip to reveal flavonoid binding on the Rattus norvegicus Kir6.1 ATP-sensitive inward rectifier potassium channel. PMID:29736333
Metabolic Reprogramming of Vibrio cholerae Impaired in Respiratory NADH Oxidation Is Accompanied by Increased Copper Sensitivity. PMID:29735761
Identification of neoepitopes recognized by tumor-infiltrating lymphocytes (TILs) from patients with glioma. PMID:29731959
An Escherichia coli Nitrogen Starvation Response Is Important for Mutualistic Coexistence with Rhodopseudomonas palustris. PMID:29728387
Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis. PMID:29722876
Structural principles of distinct assemblies of the human α4β2 nicotinic receptor. PMID:29720657
Quantifying the Evolutionary Conservation of Genes Encoding Multidrug Efflux Pumps in the ESKAPE Pathogens To Identify Antimicrobial Drug Targets. PMID:29719870
iPath3.0: interactive pathways explorer v3. PMID:29718427
Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge. PMID:29718405
The Rosa genome provides new insights into the domestication of modern roses. PMID:29713014
Diapause in a tropical oil-collecting bee: molecular basis unveiled by RNA-Seq. PMID:29703143
Positive and Negative Regulation of Angiogenesis by Soluble Vascular Endothelial Growth Factor Receptor-1. PMID:29702562
Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species. PMID:29700415
Targeting of epigenetic regulators in neuroblastoma. PMID:29700278
Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome: Where There Is a Will, There Is a Way. PMID:29700069
IMPACT web portal: oncology database integrating molecular profiles with actionable therapeutics. PMID:29697364
Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources. PMID:29695735
StraPep: a structure database of bioactive peptides. PMID:29688386
Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation. PMID:29688381
YummyData: providing high-quality open life science data. PMID:29688370
Identification of errors in the IEDB using ontologies. PMID:29688357
Whole-Genome Analysis of an Extensively Drug-Resistance Empedobacter falsenii Strain Reveals Distinct Features and the Presence of a Novel Metallo-ß-Lactamase (EBR-2). PMID:29687150
Proteome-wide analysis of cysteine oxidation reveals metabolic sensitivity to redox stress. PMID:29679077
Identification of residue pairing in interacting β-strands from a predicted residue contact map. PMID:29673311
CD9 and CD81 Interactions and Their Structural Modelling in Sperm Prior to Fertilization. PMID:29671763
Exploring the Sea Urchin Neuropeptide Landscape by Mass Spectrometry. PMID:29667164
Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases. PMID:29666611
Identification of human glycosyltransferase genes expressed in erythroid cells predicts potential carbohydrate blood group loci. PMID:29662110
A sequence family database built on ECOD structural domains. PMID:29659718
Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases. PMID:29659563
Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules. PMID:29657133
Comparative qualitative phosphoproteomics analysis identifies shared phosphorylation motifs and associated biological processes in evolutionary divergent plants. PMID:29654922
Cutting an NKG2D Ligand Short: Cellular Processing of the Peculiar Human NKG2D Ligand ULBP4. PMID:29651291
JAMI: a Java library for molecular interactions and data interoperability. PMID:29642846
GROOLS: reactive graph reasoning for genome annotation through biological processes. PMID:29642842
Soil Selenium (Se) Biofortification Changes the Physiological, Biochemical and Epigenetic Responses to Water Stress in Zea mays L. by Inducing a Higher Drought Tolerance. PMID:29636765
A plasmid borne, functionally novel glycoside hydrolase family 30 subfamily 8 endoxylanase from solventogenic Clostridium. PMID:29626157
Pathogenic Germline Variants in 10,389 Adult Cancers. PMID:29625052
Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome. PMID:29621340
How cyclophosphamide at environmentally relevant concentration influences Daphnia magna life history and its proteome. PMID:29621334
Identification and functional analysis of glycemic trait loci in the China Health and Nutrition Survey. PMID:29621232
The solution structure of monomeric CCL5 in complex with a doubly sulfated N-terminal segment of CCR5. PMID:29619777
DDX49 is an RNA helicase that affects translation by regulating mRNA export and the levels of pre-ribosomal RNA. PMID:29618122
Structural dynamics is a determinant of the functional significance of missense variants. PMID:29610305
Evolution of photosynthetic reaction centers: insights from the structure of the heliobacterial reaction center. PMID:29603081
Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes. PMID:29597328
PON-tstab: Protein Variant Stability Predictor. Importance of Training Data Quality. PMID:29597263
Ferritin from the haemolymph of adult ants: an extraction method for characterization and a ferromagnetic study. PMID:29594412
Structure of the peptidoglycan polymerase RodA resolved by evolutionary coupling analysis. PMID:29590088
Dopamine-mediated calcium channel regulation in synaptic suppression in L. stagnalis interneurons. PMID:29589519
STAT3, stem cells, cancer stem cells and p63. PMID:29588647
Urinary CE-MS peptide marker pattern for detection of solid tumors. PMID:29588543
Succinate-acetate permease from Citrobacter koseri is an anion channel that unidirectionally translocates acetate. PMID:29588525
In Silico Discovery of a Substituted 6-Methoxy-quinalidine with Leishmanicidal Activity in Leishmania infantum. PMID:29584709
HMMER Cut-off Threshold Tool (HMMERCTTER): Supervised classification of superfamily protein sequences with a reliable cut-off threshold. PMID:29579071
Proteomic Characterization of the Neural Ectoderm Fated Cell Clones in the Xenopus laevis Embryo by High-Resolution Mass Spectrometry. PMID:29578674
Differential 3' Processing of Specific Transcripts Expands Regulatory and Protein Diversity Across Neuronal Cell Types. PMID:29578408
ProtaBank: A repository for protein design and engineering data. PMID:29575358
Toward clinical and molecular understanding of pathogenic variants in the ZBTB18 gene. PMID:29573576
Systematic characterization of pan-cancer mutation clusters. PMID:29572294
Opportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic β Cell. PMID:29570991
Plant Glycine-Rich Proteins in Stress Response: An Emerging, Still Prospective Story. PMID:29568308
Human transbodies that interfere with the functions of Ebola virus VP35 protein in genome replication and transcription and innate immune antagonism. PMID:29568066
Transcriptomic characterization of MRI contrast with focus on the T1-w/T2-w ratio in the cerebral cortex. PMID:29567503
Early and late feathering in turkey and chicken: same gene but different mutations. PMID:29566646
Characterization of a novel thermotolerant NAD+-dependent formate dehydrogenase from hot climate plant cotton (Gossypium hirsutum L.). PMID:29556429
ADPredict: ADP-ribosylation site prediction based on physicochemical and structural descriptors. PMID:29554239
Protein S100-A8: A potential metastasis-associated protein for breast cancer determined via iTRAQ quantitative proteomic and clinicopathological analysis. PMID:29552168
Fine-tuning of substrate preferences of the Src-family kinase Lck revealed through a high-throughput specificity screen. PMID:29547119
The Bacteroidetes Q-Rule: Pyroglutamate in Signal Peptidase I Substrates. PMID:29545777
The use of whole exome sequencing and murine patient derived xenografts as a method of chemosensitivity testing in sarcoma. PMID:29541442
Molecular Insights into the Mechanisms of SUN1 Oligomerization in the Nuclear Envelope. PMID:29539404
Worldwide Protein Data Bank validation information: usage and trends. PMID:29533231
Refined ab initio gene predictions of Heterorhabditis bacteriophora using RNA-seq. PMID:29530648
Insulin resistance causes inflammation in adipose tissue. PMID:29528335
Fungal Cytochrome P450s and the P450 Complement (CYPome) of Fusarium graminearum. PMID:29518888
Neuropeptidomics of the Rat Habenular Nuclei. PMID:29518334
Spatiotemporal compartmentalization of hepatic NADH and NADPH metabolism. PMID:29514978
Cysteine peptidases of Eudiplozoon nipponicum: a broad repertoire of structurally assorted cathepsins L in contrast to the scarcity of cathepsins B in an invasive species of haematophagous monogenean of common carp. PMID:29510760
A recombinant Fasciola gigantica 14-3-3 epsilon protein (rFg14-3-3e) modulates various functions of goat peripheral blood mononuclear cells. PMID:29510740
Building protein-protein interaction networks for Leishmania species through protein structural information. PMID:29510668
Alignment-free clustering of large data sets of unannotated protein conserved regions using minhashing. PMID:29506470
TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA-binding protein association. PMID:29504902
Peptide identifications and false discovery rates using different mass spectrometry platforms. PMID:29501178
Genome-reconstruction for eukaryotes from complex natural microbial communities. PMID:29496730
True Lies: Using Proteomics to Assess the Accuracy of Transcriptome-Based Venomics in Centipedes Uncovers False Positives and Reveals Startling Intraspecific Variation in Scolopendra Subspinipes. PMID:29495554
Rapid and robust MALDI-TOF MS techniques for microbial identification: a brief overview of their diverse applications. PMID:29492868
Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. PMID:29491419
Screening, large-scale production and structure-based classification of cystine-dense peptides. PMID:29483648
A Draft Map of the Human Ovarian Proteome for Tissue Engineering and Clinical Applications. PMID:29475978
Unexplored therapeutic opportunities in the human genome. PMID:29472638
Structural principles that enable oligomeric small heat-shock protein paralogs to evolve distinct functions. PMID:29472485
The H-subunit of the restriction endonuclease CglI contains a prototype DEAD-Z1 helicase-like motor. PMID:29471489
Genomewide Transcriptional Responses of Iron-Starved Chlamydia trachomatis Reveal Prioritization of Metabolic Precursor Synthesis over Protein Translation. PMID:29468197
Biochemical Characterization of Two Clinically-Relevant Human Fumarase Variants Defective for Oligomerization. PMID:29456767
Alternative splicing of ALCAM enables tunable regulation of cell-cell adhesion through differential proteolysis. PMID:29453336
Time- and polarity-dependent proteomic changes associated with homeostatic scaling at central synapses. PMID:29447110
TEOSINTE BRANCHED1 Regulates Inflorescence Architecture and Development in Bread Wheat (Triticum aestivum). PMID:29444813
How many human proteoforms are there? PMID:29443976
Structural and functional characterization of the Vindoline biosynthesis pathway enzymes of Catharanthus roseus. PMID:29442186
Transcriptome analysis reveals TMPRSS6 isoforms with distinct functionalities. PMID:29441715
Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method. PMID:29441237
Atomic structures of low-complexity protein segments reveal kinked β sheets that assemble networks. PMID:29439243
Coarse-grained molecular dynamics simulations reveal lipid access pathways in P-glycoprotein. PMID:29437858
The unique fold and lability of the [2Fe-2S] clusters of NEET proteins mediate their key functions in health and disease. PMID:29435647
Complete genome sequence of Pseudomonas alcaliphila JAB1 (=DSM 26533), a versatile degrader of organic pollutants. PMID:29435100
A monoclonal antibody against SV40 large T antigen (PAb416) does not label Merkel cell carcinoma. PMID:29430700
New Insights into the Function and Global Distribution of Polyethylene Terephthalate (PET)-Degrading Bacteria and Enzymes in Marine and Terrestrial Metagenomes. PMID:29427431
Network Analysis of UBE3A/E6AP-Associated Proteins Provides Connections to Several Distinct Cellular Processes. PMID:29426014
Cladogenesis and Genomic Streamlining in Extracellular Endosymbionts of Tropical Stink Bugs. PMID:29420776
Single and multiple phenotype QTL analyses of downy mildew resistance in interspecific grapevines. PMID:29417162
Antibiotic resistance ABCF proteins reset the peptidyl transferase centre of the ribosome to counter translational arrest. PMID:29415157
Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori. PMID:29414760
Comparative analysis of Salivette® and paraffin gum preparations for establishment of a metaproteomics analysis pipeline for stimulated human saliva. PMID:29410770
ProForma: A Standard Proteoform Notation. PMID:29397739
Protein Tertiary Structure by Crosslinking/Mass Spectrometry. PMID:29395654
Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration. PMID:29390967
A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). PMID:29386578
G2S: a web-service for annotating genomic variants on 3D protein structures. PMID:29385402
Phosphoproteome profiling reveals critical role of JAK-STAT signaling in maintaining chemoresistance in breast cancer. PMID:29383118
A presumed homologue of the regulatory subunits of eIF2B functions as ribose-1,5-bisphosphate isomerase in Pyrococcus horikoshii OT3. PMID:29382938
Ancient Diversification of Three-Finger Toxins in Micrurus Coral Snakes. PMID:29379986
New Targets for Zika Virus Determined by Human-Viral Interactomic: A Bioinformatics Approach. PMID:29379794
A scalable approach to the computation of invariant measures for high-dimensional Markovian systems. PMID:29379123
GO FEAT: a rapid web-based functional annotation tool for genomic and transcriptomic data. PMID:29379090
Interleukins and their signaling pathways in the Reactome biological pathway database. PMID:29378288
SLALOM, a flexible method for the identification and statistical analysis of overlapping continuous sequence elements in sequence- and time-series data. PMID:29373955
Proteomic Analyses of the Unexplored Sea Anemone Bunodactis verrucosa. PMID:29364843
Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches. PMID:29363422
Deciphering the Link between Doubly Uniparental Inheritance of mtDNA and Sex Determination in Bivalves: Clues from Comparative Transcriptomics. PMID:29360964
Gene annotation bias impedes biomedical research. PMID:29358745
Structural Characterization and Function Prediction of Immunoglobulin-like Fold in Cell Adhesion and Cell Signaling. PMID:29356528
Remarkable similarity in Plasmodium falciparum and Plasmodium vivax geranylgeranyl diphosphate synthase dynamics and its implication for antimalarial drug design. PMID:29345110
LocText: relation extraction of protein localizations to assist database curation. PMID:29343218
Network-Based Methods for Identifying Key Active Proteins in the Extracellular Electron Transfer Process in Shewanella oneidensis MR-1. PMID:29337910
3D-e-Chem: Structural Cheminformatics Workflows for Computer-Aided Drug Discovery. PMID:29337438
Sex differences in the late first trimester human placenta transcriptome. PMID:29335024
Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding. PMID:29330519
Hypoxia-inducible lipid droplet-associated protein inhibits adipose triglyceride lipase. PMID:29326160
Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions. PMID:29322920
Muscle molecular adaptations to endurance exercise training are conditioned by glycogen availability: a proteomics-based analysis in the McArdle mouse model. PMID:29315579
Biotea: semantics for Pubmed Central. PMID:29312824
Prediction of Metal Ion Binding Sites in Proteins from Amino Acid Sequences by Using Simplified Amino Acid Alphabets and Random Forest Model. PMID:29307143
G Protein-Coupled Receptors as Targets for Approved Drugs: How Many Targets and How Many Drugs? PMID:29298813
The gonadal transcriptome of the unisexual Amazon molly Poecilia formosa in comparison to its sexual ancestors, Poecilia mexicana and Poecilia latipinna. PMID:29298680
Predicting drug-disease interactions by semi-supervised graph cut algorithm and three-layer data integration. PMID:29297383
Emerging whole-cell modeling principles and methods. PMID:29275251
Bioinformatics for precision oncology. PMID:29272324
HMMBinder: DNA-Binding Protein Prediction Using HMM Profile Based Features. PMID:29270430
Cell Cycle Model System for Advancing Cancer Biomarker Research. PMID:29269772
Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems. PMID:29263101
Ca2+-Induced Two-Component System CvsSR Regulates the Type III Secretion System and the Extracytoplasmic Function Sigma Factor AlgU in Pseudomonas syringae pv. tomato DC3000. PMID:29263098
TRANSPARENT TESTA GLABRA 1-Dependent Regulation of Flavonoid Biosynthesis. PMID:29261137
The Essential UPP Phosphatase Pair BcrC and UppP Connects Cell Wall Homeostasis during Growth and Sporulation with Cell Envelope Stress Response in Bacillus subtilis. PMID:29259598
Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions. PMID:29257115
Expression system for structural and functional studies of human glycosylation enzymes. PMID:29251719
Objective, Quantitative, Data-Driven Assessment of Chemical Probes. PMID:29249694
Rice Paddy Nitrospirae Carry and Express Genes Related to Sulfate Respiration: Proposal of the New Genus "Candidatus Sulfobium". PMID:29247059
A noncoding variant in GANAB explains isolated polycystic liver disease (PCLD) in a large family. PMID:29243290
Mapping X-Disease Phytoplasma Resistance in Prunus virginiana. PMID:29238359
eRepo-ORP: Exploring the Opportunity Space to Combat Orphan Diseases with Existing Drugs. PMID:29237557
Ubiquitin-conjugating enzyme E2T (UBE2T) and denticleless protein homolog (DTL) are linked to poor outcome in breast and lung cancers. PMID:29235520
Proteomic analyses identify ARH3 as a serine mono-ADP-ribosylhydrolase. PMID:29234005
Race Disparities in the Contribution of miRNA Isoforms and tRNA-Derived Fragments to Triple-Negative Breast Cancer. PMID:29229607
Conserved Gene Microsynteny Unveils Functional Interaction Between Protein Disulfide Isomerase and Rho Guanine-Dissociation Inhibitor Families. PMID:29222525
eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality. PMID:29220476
Interactome Mapping Uncovers a General Role for Numb in Protein Kinase Regulation. PMID:29217616
14-3-3 proteins mediate inhibitory effects of cAMP on salt-inducible kinases (SIKs). PMID:29211348
The Sit-and-Wait Hypothesis in Bacterial Pathogens: A Theoretical Study of Durability and Virulence. PMID:29209284
Approaches to ab initio molecular replacement of α-helical transmembrane proteins. PMID:29199978
Multiplex quantitative SILAC for analysis of archaeal proteomes: a case study of oxidative stress responses. PMID:29194950
Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing. PMID:29194487
Annotation of Peptide Structures Using SMILES and Other Chemical Codes-Practical Solutions. PMID:29186902
The European Bioinformatics Institute in 2017: data coordination and integration. PMID:29186510
The OncoPPi Portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery. PMID:29186335
Responsive Proteins in Wheat Cultivars with Contrasting Nitrogen Efficiencies under the Combined Stress of High Temperature and Low Nitrogen. PMID:29186028
Dynamics of Intact MexAB-OprM Efflux Pump: Focusing on the MexA-OprM Interface. PMID:29184094
A global view of structure-function relationships in the tautomerase superfamily. PMID:29184004
Proteomics of phosphorylation and protein dynamics during fertilization and meiotic exit in the Xenopus egg. PMID:29183978
Varieties of charge distributions in coat proteins of ssRNA+ viruses. PMID:29182522
FunCoup 4: new species, data, and visualization. PMID:29165593
Evolutionary Analysis of HIV-1 Pol Proteins Reveals Representative Residues for Viral Subtype Differentiation. PMID:29163435
The WD40-domain containing protein CORO2B is specifically enriched in glomerular podocytes and regulates the ventral actin cytoskeleton. PMID:29162887
Fast batch searching for protein homology based on compression and clustering. PMID:29162030
PRGdb 3.0: a comprehensive platform for prediction and analysis of plant disease resistance genes. PMID:29156057
Ensembl 2018. PMID:29155950
Engineering peptide ligase specificity by proteomic identification of ligation sites. PMID:29155430
Viral Short ORFs and Their Possible Functions. PMID:29150926
FMNH2-dependent monooxygenases initiate catabolism of sulfonamides in Microbacterium sp. strain BR1 subsisting on sulfonamide antibiotics. PMID:29150672
The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY. PMID:29149325
Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development. PMID:29149249
Chemical space guided discovery of antimicrobial bridged bicyclic peptides against Pseudomonas aeruginosa and its biofilms. PMID:29147502
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. PMID:29145643
iPTMnet: an integrated resource for protein post-translational modification network discovery. PMID:29145615
Cell Line Secretome and Tumor Tissue Proteome Markers for Early Detection of Colorectal Cancer: A Systematic Review. PMID:29144439
Genome-wide identification of miRNAs and lncRNAs in Cajanus cajan. PMID:29141604
ECOdrug: a database connecting drugs and conservation of their targets across species. PMID:29140522
Minimotif Miner 4: a million peptide minimotifs and counting. PMID:29140456
HMDB 4.0: the human metabolome database for 2018. PMID:29140435
MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. PMID:29136219
The eukaryotic linear motif resource - 2018 update. PMID:29136216
MultitaskProtDB-II: an update of a database of multitasking/moonlighting proteins. PMID:29136215
Transcriptomic and proteomic landscape of mitochondrial dysfunction reveals secondary coenzyme Q deficiency in mammals. PMID:29132502
Using semantics for representing experimental protocols. PMID:29132408
Comparison of histone-like HU protein DNA-binding properties and HU/IHF protein sequence alignment. PMID:29131864
Human primary liver cancer-derived organoid cultures for disease modeling and drug screening. PMID:29131160
MoonProt 2.0: an expansion and update of the moonlighting proteins database. PMID:29126295
DBTSS/DBKERO for integrated analysis of transcriptional regulation. PMID:29126224
ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins. PMID:29126202
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. PMID:29126160
PedAM: a database for Pediatric Disease Annotation and Medicine. PMID:29126123
Binding of mycotoxins to proteins involved in neuronal plasticity: a combined in silico/wet investigation. PMID:29123130
Transcriptomics, metabolomics and histology indicate that high-carbohydrate diet negatively affects the liver health of blunt snout bream (Megalobrama amblycephala). PMID:29121861
Identification of a novel HERV-K(HML10): comprehensive characterization and comparative analysis in non-human primates provide insights about HML10 proviruses structure and diffusion. PMID:29118853
Gene3D: Extensive prediction of globular domains in proteins. PMID:29112716
ProteomicsDB. PMID:29106664
iUUCD 2.0: an update with rich annotations for ubiquitin and ubiquitin-like conjugations. PMID:29106644
eRAM: encyclopedia of rare disease annotations for precision medicine. PMID:29106618
NLSdb-major update for database of nuclear localization signals and nuclear export signals. PMID:29106588
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. PMID:29106569
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. PMID:29106550
Daily rhythms and enrichment patterns in the transcriptome of the behavior-manipulating parasite Ophiocordyceps kimflemingiae. PMID:29099875
iDNAProt-ES: Identification of DNA-binding Proteins Using Evolutionary and Structural Features. PMID:29097781
"Personalized Cancer Therapy": A Publicly Available Precision Oncology Resource. PMID:29092956
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. PMID:29092050
Mutations of PTPN23 in developmental and epileptic encephalopathy. PMID:29090338
RNA sequencing and proteomics approaches reveal novel deficits in the cortex of Mecp2-deficient mice, a model for Rett syndrome. PMID:29090078
TFClass: expanding the classification of human transcription factors to their mammalian orthologs. PMID:29087517
POTAGE: A Visualisation Tool for Speeding up Gene Discovery in Wheat. PMID:29085014
Site-specific identification and quantitation of endogenous SUMO modifications under native conditions. PMID:29079793
TITINdb-a computational tool to assess titin's role as a disease gene. PMID:29077808
A potent small-molecule inhibitor of the DCN1-UBC12 interaction that selectively blocks cullin 3 neddylation. PMID:29074978
Biogenesis and iron-dependency of ribosomal RNA hydroxylation. PMID:29069499
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies. PMID:29069476
APPRIS 2017: principal isoforms for multiple gene sets. PMID:29069475
RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. PMID:29067736
A deep transcriptomic resource for the copepod crustacean Labidocera madurae: A potential indicator species for assessing near shore ecosystem health. PMID:29065152
BtsT, a Novel and Specific Pyruvate/H+ Symporter in Escherichia coli. PMID:29061664
The MetaCyc database of metabolic pathways and enzymes. PMID:29059334
Computational design of new protein kinase D 1 (PKD1) inhibitors: homology-based active site prediction, energy-optimized pharmacophore, docking and database screening. PMID:29058231
SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation. PMID:29057095
The transcriptome, extracellular proteome and active secretome of agroinfiltrated Nicotiana benthamiana uncover a large, diverse protease repertoire. PMID:29055088
BioPlex Display: An Interactive Suite for Large-Scale AP-MS Protein-Protein Interaction Data. PMID:29054129
Interpreting T-Cell Cross-reactivity through Structure: Implications for TCR-Based Cancer Immunotherapy. PMID:29046675
How Many Protein Sequences Fold to a Given Structure? A Coevolutionary Analysis. PMID:29045866
Friedreich Ataxia: Developmental Failure of the Dorsal Root Entry Zone. PMID:29044418
The online Tabloid Proteome: an annotated database of protein associations. PMID:29040688
20 years of the SMART protein domain annotation resource. PMID:29040681
On expert curation and scalability: UniProtKB/Swiss-Prot as a case study. PMID:29036270
Combination of Cα-H Hydrogen Bonds and van der Waals Packing Modulates the Stability of GxxxG-Mediated Dimers in Membranes. PMID:29028318
Applications of sequence coevolution in membrane protein biochemistry. PMID:28993150
Enhanced unbiased sampling of protein dynamics using evolutionary coupling information. PMID:28983093
The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics. PMID:28981707
Defective mitochondrial rRNA methyltransferase MRM2 causes MELAS-like clinical syndrome. PMID:28973171
HPV8-E6 Interferes with Syntenin-2 Expression through Deregulation of Differentiation, Methylation and Phosphatidylinositide-Kinase Dependent Mechanisms. PMID:28970821
MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data. PMID:28968784
Microbial genome analysis: the COG approach. PMID:28968633
Sequence composition predicts immunoglobulin superfamily members that could share the intrinsically disordered properties of antibody CH1 domains. PMID:28963509
SWI/SNF Infobase-An exclusive information portal for SWI/SNF remodeling complex subunits. PMID:28961249
Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life. PMID:28961181
Strains, functions and dynamics in the expanded Human Microbiome Project. PMID:28953883
Analysis of drug binding pockets and repurposing opportunities for twelve essential enzymes of ESKAPE pathogens. PMID:28948099
Neural Mechanisms Underlying the Disruption of Male Courtship Behavior by Adult Exposure to Di(2-ethylhexyl) Phthalate in Mice. PMID:28934723
Phosphoproteome-based kinase activity profiling reveals the critical role of MAP2K2 and PLK1 in neuronal autophagy. PMID:28933595
Survey of Predictors of Propensity for Protein Production and Crystallization with Application to Predict Resolution of Crystal Structures. PMID:28933304
Cancer immunotherapy with recombinant poliovirus induces IFN-dominant activation of dendritic cells and tumor antigen-specific CTLs. PMID:28931654
Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination. PMID:28927400
Near-atomic structure of jasplakinolide-stabilized malaria parasite F-actin reveals the structural basis of filament instability. PMID:28923924
Critical Roles of Dual-Specificity Phosphatases in Neuronal Proteostasis and Neurological Diseases. PMID:28902166
Molecular Connectivity Predefines Polypharmacology: Aliphatic Rings, Chirality, and sp3 Centers Enhance Target Selectivity. PMID:28894419
Identifying relationships between unrelated pharmaceutical target proteins on the basis of shared active compounds. PMID:28884009
A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models. PMID:28878200
Transcriptomic profiling in muscle and adipose tissue identifies genes related to growth and lipid deposition. PMID:28877211
PDBsum: Structural summaries of PDB entries. PMID:28875543
The TORC2-Dependent Signaling Network in the Yeast Saccharomyces cerevisiae. PMID:28872598
Potential Roles of Intrinsic Disorder in Maternal-Effect Proteins Involved in the Maintenance of DNA Methylation. PMID:28869544
Optimizing genomic medicine in epilepsy through a gene-customized approach to missense variant interpretation. PMID:28864458
The molecular basis for peptide repertoire selection in the human leucocyte antigen (HLA) C*06:02 molecule. PMID:28855257
Decoding the similarities and differences among mycobacterial species. PMID:28854187
PaperBLAST: Text Mining Papers for Information about Homologs. PMID:28845458
Human protein secretory pathway genes are expressed in a tissue-specific pattern to match processing demands of the secretome. PMID:28845240
Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse. PMID:28838066
IonchanPred 2.0: A Tool to Predict Ion Channels and Their Types. PMID:28837067
De novo transcriptome assembly for the spiny mouse (Acomys cahirinus). PMID:28827620
Bioinformatic Analyses of Whole-Genome Sequence Data in a Public Health Laboratory. PMID:28820135
Differential oxidation of protein-tyrosine phosphatases during zebrafish caudal fin regeneration. PMID:28814789
Discovery of Variants Underlying Host Susceptibility to Virus Infection Using Whole-Exome Sequencing. PMID:28808973
Microbial ecology-based engineering of Microbial Electrochemical Technologies. PMID:28805354
AOD: the antioxidant protein database. PMID:28784999
An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences. PMID:28777078
Multi-omics Analysis Sheds Light on the Evolution and the Intracellular Lifestyle Strategies of Spotted Fever Group Rickettsia spp. PMID:28775717
Genetic Evidence for Erythrocyte Receptor Glycophorin B Expression Levels Defining a Dominant Plasmodium falciparum Invasion Pathway into Human Erythrocytes. PMID:28760933
Methods for the Development of In Silico GPCR Models. PMID:28750813
Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify. PMID:28747380
Bacterial tail anchors can target to the mitochondrial outer membrane. PMID:28738827
Flexible small molecular anti-estrogens with N,N-dialkylated-2,5-diethoxy-4-morpholinoaniline scaffold targets multiple estrogen receptor conformations. PMID:28723234
The human cytoplasmic dynein interactome reveals novel activators of motility. PMID:28718761
Genomewide identification of genes involved in the potato response to drought indicates functional evolutionary conservation with Arabidopsis plants. PMID:28718511
UCSF ChimeraX: Meeting modern challenges in visualization and analysis. PMID:28710774
Dynamic regulation of lysine acetylation: the balance between acetyltransferase and deacetylase activities. PMID:28701313
Comparison of Protein Extracts from Various Unicellular Green Sources. PMID:28701042
Interferon γ induced compositional changes in human bone marrow derived mesenchymal stem/stromal cells. PMID:28694743
A new genome-scale metabolic model of Corynebacterium glutamicum and its application. PMID:28680478
Carbohydrate-mediated responses during zygotic and early somatic embryogenesis in the endangered conifer, Araucaria angustifolia. PMID:28678868
Recent Advances in Conotoxin Classification by Using Machine Learning Methods. PMID:28672838
Molecular mechanics of Staphylococcus aureus adhesin, CNA, and the inhibition of bacterial adhesion by stretching collagen. PMID:28665944
Glycosylation of KEAP1 links nutrient sensing to redox stress signaling. PMID:28663241
Evolutionary dynamics of the kinetochore network in eukaryotes as revealed by comparative genomics. PMID:28642229
Inferring repeat-protein energetics from evolutionary information. PMID:28617812
Sequence Analysis and Phylogenetic Studies of Hypoxia-Inducible Factor-1α. PMID:28615919
Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery. PMID:28602100
Cellular Consequences of Diminished Protein O-Mannosyltransferase Activity in Baker's Yeast. PMID:28598353
Cross-Kingdom Regulation of Putative miRNAs Derived from Happy Tree in Cancer Pathway: A Systems Biology Approach. PMID:28587194
Gene expression and adaptive noncoding changes during human evolution. PMID:28583075
Protein-Sol: a web tool for predicting protein solubility from sequence. PMID:28575391
Major hnRNP proteins act as general TDP-43 functional modifiers both in Drosophila and human neuronal cells. PMID:28575377
Crystal structure of the thioesterification conformation of Bacillus subtilis o-succinylbenzoyl-CoA synthetase reveals a distinct substrate-binding mode. PMID:28559280
Last rolls of the yoyo: Assessing the human canonical protein count. PMID:28529709
RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links. PMID:28499008
Protein composition of the hepatitis A virus quasi-envelope. PMID:28490497
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. PMID:28472432
RegulatorTrail: a web service for the identification of key transcriptional regulators. PMID:28472408
The EBI search engine: EBI search as a service-making biological data accessible for all. PMID:28472374
Fsr1, a striatin homologue, forms an endomembrane-associated complex that regulates virulence in the maize pathogen Fusarium verticillioides. PMID:28467007
PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update. PMID:28453649
Comparative genomic analysis between Corynebacterium pseudotuberculosis strains isolated from buffalo. PMID:28445543
Programmatic access to bioinformatics tools from EMBL-EBI update: 2017. PMID:28431173
Identification and analysis of mutational hotspots in oncogenes and tumour suppressors. PMID:28423505
The Proteins API: accessing key integrated protein and genome information. PMID:28383659
Transcriptome-based investigation of cirrus development and identifying microsatellite markers in rattan (Daemonorops jenkinsiana). PMID:28383053
Probing Medin Monomer Structure and its Amyloid Nucleation Using 13C-Direct Detection NMR in Combination with Structural Bioinformatics. PMID:28327552
Determining Cysteines Available for Covalent Inhibition Across the Human Kinome. PMID:28326775 -
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
PubMed citations: 1153.
1153 articles citing: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
A chromosome-level genome assembly of the jade perch (Scortum barcoo). PMID:35840598
Deep learning frameworks for protein-protein interaction prediction. PMID:35832624
Machine-designed biotherapeutics: opportunities, feasibility and advantages of deep learning in computational antibody discovery. PMID:35830864
Metabolome and transcriptome profiling reveal regulatory network and mechanism of flavonoid biosynthesis during color formation of Dioscorea cirrhosa L. PMID:35811818
Lilac (Syringa oblata) genome provides insights into its evolution and molecular mechanism of petal color change. PMID:35810211
Mechanism of fertilization-induced auxin synthesis in the endosperm for seed and fruit development. PMID:35810202
Loci underlying leaf agronomic traits identified by re-sequencing celery accessions based on an assembled genome. PMID:35784787
A genome and gene catalog of glacier microbiomes. PMID:35760913
The evolution of multi-gene families and metabolic pathways in the evening primroses (Oenothera: Onagraceae): A comparative transcriptomics approach. PMID:35749399
The chromosome-level genome for Toxicodendron vernicifluum provides crucial insights into Anacardiaceae evolution and urushiol biosynthesis. PMID:35733792
Integration of Transcriptomics Data and Metabolomic Data Using Biomedical Literature Mining and Pathway Analysis. PMID:35713871
A chromosome-level genome assembly of Artocarpus nanchuanensis (Moraceae), an extremely endangered fruit tree. PMID:35701376
UMGAP: the Unipept MetaGenomics Analysis Pipeline. PMID:35689184
Chromosome-Scale, Haplotype-Resolved Genome Assembly of Non-Sex-Reversal Females of Swamp Eel Using High-Fidelity Long Reads and Hi-C Data. PMID:35669182
Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum. PMID:35654976
RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins. PMID:35649392
Ustilago maydis Metabolic Characterization and Growth Quantification with a Genome-Scale Metabolic Model. PMID:35628779
Proteome-wide prediction and analysis of the Cryptosporidium parvum protein-protein interaction network through integrative methods. PMID:35615014
Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica. PMID:35614434
Chromosome-scale genome assembly of an important medicinal plant honeysuckle. PMID:35610245
Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis. PMID:35605198
Complete genome sequence of Pseudomonas stutzeri S116 owning bifunctional catalysis provides insights into affecting performance of microbial fuel cells. PMID:35590268
T-cell epitope-based vaccine prediction against Aspergillus fumigatus: a harmful causative agent of aspergillosis. PMID:35575941
Chromosome-level genome assembly of Asian yellow pond turtle (Mauremys mutica) with temperature-dependent sex determination system. PMID:35550586
Chromosome-Level Genome Assembly of the Hemiparasitic Taxillus chinensis (DC.) Danser. PMID:35482027
The genome of hibiscus hamabo reveals its adaptation to saline and waterlogged habitat. PMID:35480957
Deletion and tandem duplications of biosynthetic genes drive the diversity of triterpenoids in Aralia elata. PMID:35468919
Plant Source Derived Compound Exhibited In Silico Inhibition of Membrane Glycoprotein In SARS-CoV-2: Paving the Way to Discover a New Class of Compound For Treatment of COVID-19. PMID:35462888
Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy. PMID:35449401
Gene expression profiles provide insights into the survival strategies in deep-sea mussel (Bathymodiolus platifrons) of different developmental stages. PMID:35439939
Oogenesis and lipid metabolism in the deep-sea sponge Phakellia ventilabrum (Linnaeus, 1767). PMID:35428825
Physicochemical and Functional Properties of Membrane-Fractionated Heat-Induced Pea Protein Aggregates. PMID:35399668
Hypothetical protein predicted to be tumor suppressor: a protein functional analysis. PMID:35399005
Identifying Membrane Protein Types Based on Lifelong Learning With Dynamically Scalable Networks. PMID:35371189
The phyllosphere microbiome shifts toward combating melanose pathogen. PMID:35366955
Seventeen Ustilaginaceae High-Quality Genome Sequences Allow Phylogenomic Analysis and Provide Insights into Secondary Metabolite Synthesis. PMID:35330271
Chromosome-Scale Assembly of the Dendrobium nobile Genome Provides Insights Into the Molecular Mechanism of the Biosynthesis of the Medicinal Active Ingredient of Dendrobium. PMID:35299950
RNA-Seq reveals miRNA role in thermogenic regulation in brown adipose tissues of goats. PMID:35255830
Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA. PMID:35229157
Comparative Metabolic Pathways Analysis and Subtractive Genomics Profiling to Prioritize Potential Drug Targets Against Streptococcus pneumoniae. PMID:35222301
Leucine-Rich, Potent Anti-Bacterial Protein against Vibrio cholerae, Staphylococcus aureus from Solanum trilobatum Leaves. PMID:35208951
Haplotype-Resolved Genome Analyses Reveal Genetically Distinct Nuclei within a Commercial Cultivar of Lentinula edodes. PMID:35205921
Genome assembly of the JD17 soybean provides a new reference genome for comparative genomics. PMID:35188189
Chromosome-scale assembly and population diversity analyses provide insights into the evolution of Sapindus mukorossi. PMID:35178562
Genome-Wide Analysis Indicates a Complete Prostaglandin Pathway from Synthesis to Inactivation in Pacific White Shrimp, Litopenaeus vannamei. PMID:35163575
Chromosome-level genome assembly of Aristolochia contorta provides insights into the biosynthesis of benzylisoquinoline alkaloids and aristolochic acids. PMID:35147168
EST-SSR Marker Development and Full-Length Transcriptome Sequence Analysis of Tiger Lily (Lilium lancifolium Thunb). PMID:35126662
Chromosomal-level genome and multi-omics dataset of Pueraria lobata var. thomsonii provide new insights into legume family and the isoflavone and puerarin biosynthesis pathways. PMID:35043180
Chromosome-level genome assembly of Bactrocera dorsalis reveals its adaptation and invasion mechanisms. PMID:35017661
Chromosome-level genome assembly of Zizania latifolia provides insights into its seed shattering and phytocassane biosynthesis. PMID:35017643
The genome of oil-Camellia and population genomics analysis provide insights into seed oil domestication. PMID:35012630
A Chromosome-Level Genome Assembly of the Pygmy Mole Cricket Xya riparia. PMID:34999819
Unravelling Rubber Tree Growth by Integrating GWAS and Biological Network-Based Approaches. PMID:34992619
Inferring the genetic responses to acute drought stress across an ecological gradient. PMID:34983380
Chromosome Genome Assembly of Cromileptes altivelis Reveals Loss of Genome Fragment in Cromileptes Compared with Epinephelus Species. PMID:34946822
Chloranthus genome provides insights into the early diversification of angiosperms. PMID:34836973
A roadmap for metagenomic enzyme discovery. PMID:34821235
Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity. PMID:34773106
First report of mitochondrial COI in foraminifera and implications for DNA barcoding. PMID:34772985
fLPS 2.0: rapid annotation of compositionally-biased regions in biological sequences. PMID:34760378
Parallel introgression, not recurrent emergence, explains apparent elevational ecotypes of polyploid Himalayan snowtrout. PMID:34729207
Decipher the Helicobacter pylori Protein Targeting in the Nucleus of Host Cell and their Implications in Gallbladder Cancer: An insilico approach. PMID:34729122
Protocol for using NoBadWordsCombiner to merge and minimize "bad words" from BLAST hits against multiple eukaryotic gene annotation databases. PMID:34704076
Genomic insights into biocontrol potential of Bacillus stercoris LJBS06. PMID:34692367
Convergent adaptation of the genomes of woody plants at the land-sea interface. PMID:34692119
Whole-Genome Sequencing of Sinocyclocheilus maitianheensis Reveals Phylogenetic Evolution and Immunological Variances in Various Sinocyclocheilus Fishes. PMID:34675964
Whole-Genome Sequencing and Genome-Wide Studies of Spiny Head Croaker (Collichthys lucidus) Reveals Potential Insights for Well-Developed Otoliths in the Family Sciaenidae. PMID:34659355
Genome-Wide Transcriptional Changes of Rhodosporidium kratochvilovae at Low Temperature. PMID:34603256
Design of Monovalent and Chimeric Tetravalent Dengue Vaccine Using an Immunoinformatics Approach. PMID:34602919
The Euscaphis japonica genome and the evolution of malvids. PMID:34587334
Whole-genome assembly of Ganoderma leucocontextum (Ganodermataceae, Fungi) discovered from the Tibetan Plateau of China. PMID:34586388
The genome of the naturally evolved obesity-prone Ossabaw miniature pig. PMID:34585119
Secondary metabolite biosynthetic diversity in the fungal family Hypoxylaceae and Xylaria hypoxylon. PMID:34527085
Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map. PMID:34512084
The chromosome-scale genome of Magnolia officinalis provides insight into the evolutionary position of magnoliids. PMID:34505009
The genome sequence provides insights into salt tolerance of Achnatherum splendens (Gramineae), a constructive species of alkaline grassland. PMID:34487631
Zanthoxylum-specific whole genome duplication and recent activity of transposable elements in the highly repetitive paleotetraploid Z. bungeanum genome. PMID:34480029
Nesterenkonia ebinurensis sp. nov., a Novel Actinobacterium Isolated From Populus euphratica. PMID:34468853
Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution. PMID:34465765
The whale shark genome reveals patterns of vertebrate gene family evolution. PMID:34409936
Genome Mining and Comparative Genome Analysis Revealed Niche-Specific Genome Expansion in Antibacterial Bacillus pumilus Strain SF-4. PMID:34356076
The Genome of the Haptophyte Diacronema lutheri (Pavlova lutheri, Pavlovales): A Model for Lipid Biosynthesis in Eukaryotic Algae. PMID:34343248
A chromosome-level genome assembly of Cairina moschata and comparative genomic analyses. PMID:34330207
Comparative transcriptome analysis reveals regulatory network and regulators associated with proanthocyanidin accumulation in persimmon. PMID:34325657
Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea). PMID:34294825
A Chromosome-Level Genome Assembly of the Mandarin Fish (Siniperca chuatsi). PMID:34249093
Protocol for HSDFinder: Identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes. PMID:34223195
Assessment of Paroxetine Molecular Interactions with Selected Monoamine and γ-Aminobutyric Acid Transporters. PMID:34208199
FINER: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks. PMID:34169280
A Chromosome-Level Genome Assembly of the Spotted Scat (Scatophagus argus). PMID:34146395
A chromosome-level Camptotheca acuminata genome assembly provides insights into the evolutionary origin of camptothecin biosynthesis. PMID:34112794
Rooting the Animal Tree of Life. PMID:34097041
Chromosome-level genome assembly of the Chinese longsnout catfish Leiocassis longirostris. PMID:34075735
VB12Path for Accurate Metagenomic Profiling of Microbially Driven Cobalamin Synthesis Pathways. PMID:34060913
The chromosome-level Stevia genome provides insights into steviol glycoside biosynthesis. PMID:34059662
Pretraining model for biological sequence data. PMID:34050350
Chromosome-Level Reference Genome Assembly for the American Pika (Ochotona princeps). PMID:34036348
Chromosome-scale assembly of the Sparassis latifolia genome obtained using long-read and Hi-C sequencing. PMID:34021320
Protein transfer learning improves identification of heat shock protein families. PMID:34003870
Protein transfer learning improves identification of heat shock protein families. PMID:34003870
Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling. PMID:33981000
Homopeptide and homocodon levels across fungi are coupled to GC/AT-bias and intrinsic disorder, with unique behaviours for some amino acids. PMID:33976321
The genome of Nautilus pompilius illuminates eye evolution and biomineralization. PMID:33972735
Whole-genome resequencing of Osmanthus fragrans provides insights into flower color evolution. PMID:33931610
Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications. PMID:33926388
The Bacterial Genomic Context of Highly Trimethoprim-Resistant DfrB Dihydrofolate Reductases Highlights an Emerging Threat to Public Health. PMID:33924456
Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly. PMID:33919286
Chromosome-level genome assembly of the hard-shelled mussel Mytilus coruscus, a widely distributed species from the temperate areas of East Asia. PMID:33891010
A chromosome-level reference genome of the hazelnut, Corylus heterophylla Fisch. PMID:33871007
The chromosome-level Hemerocallis citrina Borani genome provides new insights into the rutin biosynthesis and the lack of colchicine. PMID:33828071
The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae). PMID:33827435
Synthesis, Molecular Docking Studies and In Silico ADMET Screening of New Heterocycles Linked Thiazole Conjugates as Potent Anti-Hepatic Cancer Agents. PMID:33803823
The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758). PMID:33755103
The Mitragyna speciosa (Kratom) Genome: a resource for data-mining potent pharmaceuticals that impact human health. PMID:33677570
The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids. PMID:33642574
Balrog: A universal protein model for prokaryotic gene prediction. PMID:33635857
Seascape genomics reveals candidate molecular targets of heat stress adaptation in three coral species. PMID:33619812
Cytochrome P450 monooxygenase genes in the wild silkworm, Bombyx mandarina. PMID:33604192
Draft genome of the herbaceous bamboo Raddia distichophylla. PMID:33585868
Chromosome-level reference genome of the soursop (Annona muricata): A new resource for Magnoliid research and tropical pomology. PMID:33569882
Analyses of transcriptomes and the first complete genome of Leucocalocybe mongolica provide new insights into phylogenetic relationships and conservation. PMID:33536487
Long-Term Waterlogging as Factor Contributing to Hypoxia Stress Tolerance Enhancement in Cucumber: Comparative Transcriptome Analysis of Waterlogging Sensitive and Tolerant Accessions. PMID:33525400
Combined genomic, transcriptomic, and metabolomic analyses provide insights into chayote (Sechium edule) evolution and fruit development. PMID:33517348
The Compact Macronuclear Genome of the Ciliate Halteria grandinella: A Transcriptome-Like Genome with 23,000 Nanochromosomes. PMID:33500338
A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense. PMID:33459341
HGFDB: a collective database of helmeted guinea fowl genomics. PMID:33417691
Genome survey sequencing and genetic diversity of cultivated Akebia trifoliata assessed via phenotypes and SSR markers. PMID:33400074
Chromosomal-Level Genome Assembly of Silver Sillago (Sillago sihama). PMID:33367716
A Clinical Extensively-Drug Resistant (XDR) Escherichia coli and Role of Its β-Lactamase Genes. PMID:33362736
SARS-Cov-2 Interactome with Human Ghost Proteome: A Neglected World Encompassing a Wealth of Biological Data. PMID:33352703
FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction. PMID:33346815
Comparative genomics of Klebsiella michiganensis BD177 and related members of Klebsiella sp. reveal the symbiotic relationship with Bactrocera dorsalis. PMID:33339499
The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening. PMID:33328440
Genome sequencing of deep-sea hydrothermal vent snails reveals adaptions to extreme environments. PMID:33319911
Comparative transcriptome profiling of pomegranate genotypes having resistance and susceptible reaction to Xanthomonas axonopodis pv. punicae. PMID:33304163
Chromosomal assembly of the Antarctic toothfish ( Dissostichus mawsoni) genome using third-generation DNA sequencing and Hi-C technology. PMID:33258338
Multi-omics integration in biomedical research - A metabolomics-centric review. PMID:33248648
Functional characterisation of the transcriptome from leaf tissue of the fluoroacetate-producing plant, Dichapetalum cymosum, in response to mechanical wounding. PMID:33239700
Chromosomal genome of Triplophysa bleekeri provides insights into its evolution and environmental adaptation. PMID:33231676
Draft Genome Sequences of Lactococcus lactis Strains MS22314, MS22333, MS22336, and MS22337, Isolated from Fermented Camel Milk in Ethiopia. PMID:33214295
Transcriptome Analysis Identifies SenZfp536, a Sense LncRNA that Suppresses Self-renewal of Cortical Neural Progenitors. PMID:33196962
The draft genome of the blood pheasant (Ithaginis cruentus): Phylogeny and high-altitude adaptation. PMID:33144976
Synthesis, Molecular Docking Screening and Anti-Proliferative Potency Evaluation of Some New Imidazo[2,1-b]Thiazole Linked Thiadiazole Conjugates. PMID:33126630
The genome of Chinese flowering cherry (Cerasus serrulata) provides new insights into Cerasus species. PMID:33082971
The relationship between protein domains and homopeptides in the Plasmodium falciparum proteome. PMID:33062426
Molecular characterization and functional annotation of a hypothetical protein (SCO0618) of Streptomyces coelicolor A3(2). PMID:33017872
Comparative Analysis of the Secretome and Interactome of Trypanosoma cruzi and Trypanosoma rangeli Reveals Species Specific Immune Response Modulating Proteins. PMID:32973747
The Molecular Machinery of Gametogenesis in Geodia Demosponges (Porifera): Evolutionary Origins of a Conserved Toolkit across Animals. PMID:32929503
The Phoebe genome sheds light on the evolution of magnoliids. PMID:32922818
Seascape genomics as a new tool to empower coral reef conservation strategies: An example on north-western Pacific Acropora digitifera. PMID:32908595
Sequencing, assembly, annotation, and gene expression: novel insights into browning-resistant Luffa cylindrica. PMID:32864209
Variable absorption of mutational trends by prion-forming domains during Saccharomycetes evolution. PMID:32844065
Predicting Gram-Positive Bacterial Protein Subcellular Location by Using Combined Features. PMID:32802888
Use Chou's 5-Step Rule to Predict DNA-Binding Proteins with Evolutionary Information. PMID:32775434
Identification of multiple potential viral diseases in a large urban center using wastewater surveillance. PMID:32738707
Modeling and simulation study to identify threonine synthase as possible drug target in Leishmania major. PMID:32737682
MAGPEL: an autoMated pipeline for inferring vAriant-driven Gene PanEls from the full-length biomedical literature. PMID:32703994
Analyzing IDPs in Interactomes. PMID:32696395
A Genome-Wide Association Study of Coleoptile Length in Different Chinese Wheat Landraces. PMID:32582239
Detecting and correcting misclassified sequences in the large-scale public databases. PMID:32579213
Draft Genome Sequence of the Astaxanthin-Producing Microalga Haematococcus lacustris Strain NIES-144. PMID:32499361
Whole-genome sequence of Phellinus gilvus (mulberry Sanghuang) reveals its unique medicinal values. PMID:32455007
Lactococcus lactis Diversity Revealed by Targeted Amplicon Sequencing of purR Gene, Metabolic Comparisons and Antimicrobial Properties in an Undefined Mixed Starter Culture Used for Soft-Cheese Manufacture. PMID:32414204
Genome Sequencing and Analysis of the Fungal Symbiont of Sirex noctilio, Amylostereum areolatum: Revealing the Biology of Fungus-Insect Mutualism. PMID:32404513
An improved high-quality genome assembly and annotation of Tibetan hulless barley. PMID:32385314
Chromosome-scale assembly of the Kandelia obovata genome. PMID:32377365
AFP-LSE: Antifreeze Proteins Prediction Using Latent Space Encoding of Composition of k-Spaced Amino Acid Pairs. PMID:32345989
Probabilistic analysis of the frequencies of amino acid pairs within characterized protein sequences. PMID:32288076
Computational Proteome-Wide Study for the Prediction of Escherichia coli Protein Targeting in Host Cell Organelles and Their Implication in Development of Colon Cancer. PMID:32280866
Homology Modeling and Virtual Screening Studies of Antigen MLAA-42 Protein: Identification of Novel Drug Candidates against Leukemia-An In Silico Approach. PMID:32256683
The First Genome Survey of the Antarctic Krill (Euphausia superba) Provides a Valuable Genetic Resource for Polar Biomedical Research. PMID:32244466
Transcriptome sequencing and analysis reveals the molecular response to selenium stimuli in Pueraria lobata (willd.) Ohwi. PMID:32231880
Comparative Transcriptome Analysis Provides Insights Into Yellow Rind Formation and Preliminary Mapping of the Clyr (Yellow Rind) Gene in Watermelon. PMID:32218790
Bioinformatical study on the proteomics and evolution of SARS-CoV. PMID:32214704
Transcriptomic and metabolomic analyses of Lycium ruthenicum and Lycium barbarum fruits during ripening. PMID:32152358
Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family. PMID:32118265
Draft Genome Assembly of Floccularia luteovirens, an Edible and Symbiotic Mushroom on Qinghai-Tibet Plateau. PMID:32098800
Transcriptome and Parasitome Analysis of Beet Cyst Nematode Heterodera schachtii. PMID:32094373
The hornwort genome and early land plant evolution. PMID:32042158
The Genome Assembly and Annotation of the Southern Elephant Seal Mirounga leonina. PMID:32028680
The Genomes of the Livebearing Fish Species Poeciliopsis retropinna and Poeciliopsis turrubarensis Reflect Their Different Reproductive Strategies. PMID:31960923
In silico unravelling pathogen-host signaling cross-talks via pathogen mimicry and human protein-protein interaction networks. PMID:31956393
A Novel RNA Virus in the Parasitoid Wasp Lysiphlebus fabarum: Genomic Structure, Prevalence, and Transmission. PMID:31947801
TranCEP: Predicting the substrate class of transmembrane transport proteins using compositional, evolutionary, and positional information. PMID:31935244
Molecular modelling and docking analysis of pleurocidin (an antimicrobial peptide) like peptides with enterotoxin H from Klebsilla pneumonia. PMID:31902985
The dark side of Alzheimer's disease: unstructured biology of proteins from the amyloid cascade signaling pathway. PMID:31894361
Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis). PMID:31878322
The persimmon (Diospyros oleifera Cheng) genome provides new insights into the inheritance of astringency and ancestral evolution. PMID:31871686
A Phylogenomic Analysis of the Floral Transcriptomes of Sexually Deceptive and Rewarding European Orchids, Ophrys and Gymnadenia. PMID:31850034
An evaluation of different classification algorithms for protein sequence-based reverse vaccinology prediction. PMID:31834914
Data enabled prediction analysis assigns folate/biopterin transporter (BT1) family to 36 hypothetical membrane proteins in Leishmania donovani. PMID:31831951
Genomic insights into mite phylogeny, fitness, development, and reproduction. PMID:31818245
A chromosome-level genome assembly of the Chinese tupelo Nyssa sinensis. PMID:31767848
A Computational Framework for Predicting Direct Contacts and Substructures within Protein Complexes. PMID:31717703
Neglog: Homology-Based Negative Data Sampling Method for Genome-Scale Reconstruction of Human Protein-Protein Interaction Networks. PMID:31614890
A super-SILAC based proteomics analysis of diffuse large B-cell lymphoma-NOS patient samples to identify new proteins that discriminate GCB and non-GCB lymphomas. PMID:31603917
Identification and characterization of jasmonic acid- and linolenic acid-mediated transcriptional regulation of secondary laticifer differentiation in Hevea brasiliensis. PMID:31586098
Complete Genome Sequence of the Plant Growth-Promoting Bacterium Hartmannibacter diazotrophicus Strain E19T. PMID:31583244
A genomic view of the reef-building coral Porites lutea and its microbial symbionts. PMID:31548681
High-coverage genomes to elucidate the evolution of penguins. PMID:31531675
Whole Genome Sequencing of Chinese White Dolphin (Sousa chinensis) for High-Throughput Screening of Antihypertensive Peptides. PMID:31466310
A chromosome-level draft genome of the grain aphid Sitobion miscanthi. PMID:31430367
A chromosomal-level genome assembly for the insect vector for Chagas disease, Triatoma rubrofasciata. PMID:31425588
Complete Genome Sequence of Azoarcus sp. Strain DD4, a Gram-Negative Propanotroph That Degrades 1,4-Dioxane and 1,1-Dichloroethylene. PMID:31416874
Genome-wide analysis sheds light on the high-altitude adaptation of the buff-throated partridge (Tetraophasis szechenyii). PMID:31414227
Computational Assessment of Bacterial Protein Structures Indicates a Selection Against Aggregation. PMID:31398930
An improved genome assembly of the fluke Schistosoma japonicum. PMID:31390359
Conservation of Prion-Like Composition and Sequence in Prion-Formers and Prion-Like Proteins of Saccharomyces cerevisiae. PMID:31355208
Chromosome assembly of Collichthys lucidus, a fish of Sciaenidae with a multiple sex chromosome system. PMID:31341172
The genome assembly of asparagus bean, Vigna unguiculata ssp. sesquipedialis. PMID:31316072
Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C. PMID:31289832
Extensive intraspecific gene order and gene structural variations in upland cotton cultivars. PMID:31278252
Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan Plateau using single-molecule long-read sequencing and RNA-seq. PMID:31274170
Sequencing and comparative analysis of three Chlorella genomes provide insights into strain-specific adaptation to wastewater. PMID:31267025
Biosynthetic Potential of a Novel Antarctic Actinobacterium Marisediminicola antarctica ZS314T Revealed by Genomic Data Mining and Pigment Characterization. PMID:31266176
Whole Genome Sequencing of the Blue Tilapia (Oreochromis aureus) Provides a Valuable Genetic Resource for Biomedical Research on Tilapias. PMID:31261751
The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole-genome sequencing. PMID:31258950
Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome. PMID:31241154
Transcriptome Analysis Provides Novel Insights into the Capacity of the Ectomycorrhizal Fungus Amanita pantherina To Weather K-Containing Feldspar and Apatite. PMID:31126945
Involvement of Salicylic Acid in Anthracnose Infection in Tea Plants Revealed by Transcriptome Profiling. PMID:31108845
The carboxy-terminus, a key regulator of protein function. PMID:31106589
The harmful algae, Cochlodinium polykrikoides and Aureococcus anophagefferens, elicit stronger transcriptomic and mortality response in larval bivalves (Argopecten irradians) than climate change stressors. PMID:31031955
Diversity and Distribution of Bacteria Producing Known Secondary Metabolites. PMID:31016338
Whole genomes and transcriptomes reveal adaptation and domestication of pistachio. PMID:30999938
De novo genome assembly of the white-spotted flower chafer (Protaetia brevitarsis). PMID:30949689
Transcriptional profiling of Auricularia cornea in selenium accumulation. PMID:30948778
High-Throughput Identification and Analysis of Novel Conotoxins from Three Vermivorous Cone Snails by Transcriptome Sequencing. PMID:30917600
A novel transcriptome-derived SNPs array for tench (Tinca tinca L.). PMID:30889192
PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome. PMID:30871454
Prediction of Protein Subcellular Localization Based on Fusion of Multi-view Features. PMID:30845684
Evolutionary behaviour of bacterial prion-like proteins. PMID:30835736
De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing. PMID:30816255
Comparative genomics sheds light on the predatory lifestyle of accipitrids and owls. PMID:30783131
Generation and characterization of expressed sequence tags (ESTs) from coralloid root cDNA library of Cycas debaoensis. PMID:30740571
Extensive Reduction of the Nuclear Pore Complex in Nucleomorphs. PMID:30715330
Physiological, epigenetic and genetic regulation in some olive cultivars under salt stress. PMID:30705308
The Genetic Structures of an Extensively Drug Resistant (XDR) Klebsiella pneumoniae and Its Plasmids. PMID:30662878
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. PMID:30625152
Genome Analysis of Haplotype D of Candidatus Liberibacter Solanacearum. PMID:30619106
Analysis of Dendrobium huoshanense transcriptome unveils putative genes associated with active ingredients synthesis. PMID:30594136
Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptation. PMID:30572844
Genome Assembly for a Yunnan-Guizhou Plateau "3E" Fish, Anabarilius grahami (Regan), and Its Evolutionary and Genetic Applications. PMID:30564274
High Throughput Identification of Novel Conotoxins from the Vermivorous Oak Cone Snail (Conus quercinus) by Transcriptome Sequencing. PMID:30563163
Transcriptome Analysis of Phycocyanin-Mediated Inhibitory Functions on Non-Small Cell Lung Cancer A549 Cell Growth. PMID:30558318
Genome survey sequencing for the characterization of genetic background of Dracaena cambodiana and its defense response during dragon's blood formation. PMID:30550595
Reconstruction and analysis of carbon metabolic pathway of Ketogulonicigenium vulgare SPU B805 by genome and transcriptome. PMID:30546118
Recent Trends in System-Scale Integrative Approaches for Discovering Protective Antigens Against Mycobacterial Pathogens. PMID:30538722
The draft genomes of five agriculturally important African orphan crops. PMID:30535374
Building an octaploid genome and transcriptome of the medicinal plant Pogostemon cablin from Lamiales. PMID:30532075
Secreted Cysteine-Rich Repeat Proteins "SCREPs": A Novel Multi-Domain Architecture. PMID:30524283
Genome and Transcriptome Sequencing of the Astaxanthin-Producing Green Microalga, Haematococcus pluvialis. PMID:30496415
Deciphering the evolutionary signatures of pinnipeds using novel genome sequences: The first genomes of Phoca largha, Callorhinus ursinus, and Eumetopias jubatus. PMID:30442995
RNA-Seq-based transcriptome analysis of reproduction- and growth-related genes in Lateolabrax japonicus ovaries at four different ages. PMID:30386972
Comparative Genomics of Aspergillus flavus S and L Morphotypes Yield Insights into Niche Adaptation. PMID:30361280
De novo genome assembly of Oryza granulata reveals rapid genome expansion and adaptive evolution. PMID:30271965
Pathway networks generated from human disease phenome. PMID:30255817
Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci. PMID:30227868
Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. PMID:30227846
Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. PMID:30218022
De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome. PMID:30202061
Comprehensive network map of interferon gamma signaling. PMID:30191398
Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies. PMID:30131865
Structure modeling to function prediction of Uncharacterized Human Protein C15orf41. PMID:30108417
A network map of netrin receptor UNC5B-mediated signaling. PMID:30084000
A Novel Eukaryotic Denitrification Pathway in Foraminifera. PMID:30078568
Genome sequence and genetic transformation of a widely distributed and cultivated poplar. PMID:30044051
Homology Inference Based on a Reconciliation Approach for the Comparative Genomics of Protozoa. PMID:30034216
A transcriptome study on Macrobrachium nipponense hepatopancreas experimentally challenged with white spot syndrome virus (WSSV). PMID:29979781
Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis. PMID:29954330
Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub. PMID:29917074
Subcellular stoichiogenomics reveal cell evolution and electrostatic interaction mechanisms in cytoskeleton. PMID:29914356
Assigning biological function using hidden signatures in cystine-stabilized peptide sequences. PMID:29899538
Complete genome sequence of the sesame pathogen Ralstonia solanacearum strain SEPPX 05. PMID:29892946
De novo assembly, characterization and annotation for the transcriptome of Sphaeroma terebrans and microsatellite marker discovery. PMID:29892920
Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features. PMID:29860277
WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update. PMID:29788377
Genome Sequence of the Self-Flocculating Strain Saccharomyces cerevisiae SPSC01. PMID:29773621
Potential molecular mechanisms of overgrazing-induced dwarfism in sheepgrass (Leymus chinensis) analyzed using proteomic data. PMID:29739327
Complete Genome Sequence of Multiple-Antibiotic-Resistant Streptococcus parauberis Strain SPOF3K, Isolated from Diseased Olive Flounder (Paralichthys olivaceus). PMID:29700142
PDZscape: a comprehensive PDZ-protein database. PMID:29699484
To Decipher the Mycoplasma hominis Proteins Targeting into the Endoplasmic Reticulum and Their Implications in Prostate Cancer Etiology Using Next-Generation Sequencing Data. PMID:29695086
Draft genome of the protandrous Chinese black porgy, Acanthopagrus schlegelii. PMID:29659813
Transcriptomic Analysis of Flower Bud Differentiation in Magnolia sinostellata. PMID:29659525
The draft genome sequence of forest musk deer (Moschus berezovskii). PMID:29635287
Identification of Streptococcus mitis321A vaccine antigens based on reverse vaccinology. PMID:29620181
Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies. PMID:29538441
Differential Protein Profiling of Cerebrospinal Fluid in Piglets with Severe Meningoencephalitis Caused by Streptococcus suis Type 2 Compared to Controls. PMID:29479521
Prediction of HIV-1 and HIV-2 proteins by using Chou's pseudo amino acid compositions and different classifiers. PMID:29402983
Striate palmoplantar keratoderma resulting from a missense mutation in DSG1. PMID:29315490
Zygosaccharomyces bailii Is a Potential Producer of Various Flavor Compounds in Chinese Maotai-Flavor Liquor Fermentation. PMID:29312273
The genome of an intranuclear parasite, Paramicrosporidium saccamoebae, reveals alternative adaptations to obligate intracellular parasitism. PMID:29171834
fLPS: Fast discovery of compositional biases for the protein universe. PMID:29132292
Sex differentiation in grayling (Salmonidae) goes through an all-male stage and is delayed in genetic males who instead grow faster. PMID:29101375
Enhancing the Thermostability of Rhizomucor miehei Lipase with a Limited Screening Library by Rational-Design Point Mutations and Disulfide Bonds. PMID:29101200
Review of computational methods for virus-host protein interaction prediction: a case study on novel Ebola-human interactions. PMID:29028879
Dynamic mRNA and miRNA expression analysis in response to hypoxia and reoxygenation in the blunt snout bream (Megalobrama amblycephala). PMID:28993687
Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome. PMID:28951866
Petri Net-Based Model of Helicobacter pylori Mediated Disruption of Tight Junction Proteins in Stomach Lining during Gastric Carcinoma. PMID:28932213
The Apostasia genome and the evolution of orchids. PMID:28902843
Molecular insights into photosynthesis and carbohydrate metabolism in Jatropha curcas grown under elevated CO2 using transcriptome sequencing and assembly. PMID:28894153
Genomic and transcriptomic analyses reveal differential regulation of diverse terpenoid and polyketides secondary metabolites in Hericium erinaceus. PMID:28860534
Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints. PMID:28779005
Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins. PMID:28775330
Comparative genomic analysis of Paenibacillus sp. SSG-1 and its closely related strains reveals the effect of glycometabolism on environmental adaptation. PMID:28720902
Non-Toxin-Producing Bacillus cereus Strains Belonging to the B. anthracis Clade Isolated from the International Space Station. PMID:28680972
Comparative genomic analysis of Mycobacterium neoaurum MN2 and MN4 substrate and product tolerance. PMID:28664368
Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta. PMID:28644839
Transcriptome analyses provide insights into the difference of alkaloids biosynthesis in the Chinese goldthread (Coptis chinensis Franch.) from different biotopes. PMID:28533961
A computational framework for distinguishing direct versus indirect interactions in human functional protein-protein interaction networks. PMID:28524201
Protein post-translational modifications: In silico prediction tools and molecular modeling. PMID:28458782
PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update. PMID:28453649
Draft genome of the lined seahorse, Hippocampus erectus. PMID:28444302
The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae). PMID:28431014
Oncodomains: A protein domain-centric framework for analyzing rare variants in tumor samples. PMID:28426665
The genome of the Antarctic-endemic copepod, Tigriopus kingsejongensis. PMID:28369352
C9ORF135 encodes a membrane protein whose expression is related to pluripotency in human embryonic stem cells. PMID:28345668
Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius. PMID:28327943
Enabling comparative modeling of closely related genomes: example genus Brucella. PMID:28324362
Transcriptomic responses to environmental temperature by turtles with temperature-dependent and genotypic sex determination assessed by RNAseq inform the genetic architecture of embryonic gonadal development. PMID:28296881
High quality draft genome sequence of an extremely halophilic archaeon Natrinema altunense strain AJ2T. PMID:28265340
A Broad-Host-Range Tailocin from Burkholderia cenocepacia. PMID:28258146
In vitro anti-cancer activity of doxorubicin against human RNA helicase, DDX3. PMID:28246464
Leaf transcriptome analysis of a subtropical evergreen broadleaf plant, wild oil-tea camellia (Camellia oleifera), revealing candidate genes for cold acclimation. PMID:28241790
In-silico screening, identification and validation of a novel vaccine candidate in the fight against Plasmodium falciparum. PMID:28236172
VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology. PMID:28193166
An Atlas of annotations of Hydra vulgaris transcriptome. PMID:28185543
Incorporating efficient radial basis function networks and significant amino acid pairs for predicting GTP binding sites in transport proteins. PMID:28155651
Global inference of disease-causing single nucleotide variants from exome sequencing data. PMID:28155632
An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance. PMID:28111887
Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis. PMID:28056815
Toward amino acid typing for proteins in FFLUX. PMID:27991680
Sequence analysis of the gliding protein Gli349 in Mycoplasma mobile. PMID:27857551
Multi-label ℓ2-regularized logistic regression for predicting activation/inhibition relationships in human protein-protein interaction networks. PMID:27819359
Analysis of the genomic sequences and metabolites of Serratia surfactantfaciens sp. nov. YD25T that simultaneously produces prodigiosin and serrawettin W2. PMID:27809759
Computational workflow for the fine-grained analysis of metagenomic samples. PMID:27801291
Transcriptome analyses provide insights into the phylogeny and adaptive evolution of the mangrove fern genus Acrostichum. PMID:27782130
SARAH Domain-Mediated MST2-RASSF Dimeric Interactions. PMID:27716844
Comparative Genomics of Acetobacterpasteurianus Ab3, an Acetic Acid Producing Strain Isolated from Chinese Traditional Rice Vinegar Meiguichu. PMID:27611790
AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields. PMID:27587688
Draft genome sequence of pathogenic bacteria Vibrio parahaemolyticus strain Ba94C2, associated with acute hepatopancreatic necrosis disease isolate from South America. PMID:27570736
Whole genome sequencing of a banana wild relative Musa itinerans provides insights into lineage-specific diversification of the Musa genus. PMID:27531320
RNA-seq-based evaluation of bicolor tepal pigmentation in Asiatic hybrid lilies (Lilium spp.). PMID:27516339
De novo assembly of the blunt snout bream (Megalobrama amblycephala) gill transcriptome to identify ammonia exposure associated microRNAs and their targets. PMID:27504260
A transcriptional blueprint for a spiral-cleaving embryo. PMID:27496340
Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs. PMID:27475771
Computational discovery of Epstein-Barr virus targeted human genes and signalling pathways. PMID:27470517
Signaling network map of the aryl hydrocarbon receptor. PMID:27465749
PredPhos: an ensemble framework for structure-based prediction of phosphorylation sites. PMID:27437197
Reciprocal genomic evolution in the ant-fungus agricultural symbiosis. PMID:27436133
The Genome of the Self-Fertilizing Mangrove Rivulus Fish, Kryptolebias marmoratus: A Model for Studying Phenotypic Plasticity and Adaptations to Extreme Environments. PMID:27324916
Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile "Ferrovum". PMID:27303384
Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation. PMID:27270698
Survey of the genome of Pogostemon cablin provides insights into its evolutionary history and sesquiterpenoid biosynthesis. PMID:27198881
Comparative Genomics of Pathogens Causing Brown Spot Disease of Tobacco: Alternaria longipes and Alternaria alternata. PMID:27159564
An integrated signal transduction network of macrophage migration inhibitory factor. PMID:27139435
Text mining for precision medicine: automating disease-mutation relationship extraction from biomedical literature. PMID:27121612
UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation. PMID:27114492
Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. PMID:27074285
Prediction of mycoplasma hominis proteins targeting in mitochondria and cytoplasm of host cells and their implication in prostate cancer etiology. PMID:27027344
Genome analysis of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB revealed high numbers in secreted proteins and cell wall degrading enzymes. PMID:26988094
RNA-seq analysis for plant carnivory gene discovery in Nepenthes × ventrata. PMID:26981352
RNA-seq analysis for secondary metabolite pathway gene discovery in Polygonum minus. PMID:26981350
Systems biology of the structural proteome. PMID:26969117
Computational prediction of Mycoplasma hominis proteins targeting in nucleus of host cell and their implication in prostate cancer etiology. PMID:26874727
Short-Stalked Prosthecomicrobium hirschii Cells Have a Caulobacter-Like Cell Cycle. PMID:26833409
A Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes. PMID:26818838
A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases. PMID:26818115
Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus "Ferrovum". PMID:26808278
The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution. PMID:26754549
Pleurochrysome: A Web Database of Pleurochrysis Transcripts and Orthologs Among Heterogeneous Algae. PMID:26746174
Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome. PMID:26731733
Multi-label multi-instance transfer learning for simultaneous reconstruction and cross-talk modeling of multiple human signaling pathways. PMID:26718335
Opening a SWATH Window on Posttranslational Modifications: Automated Pursuit of Modified Peptides. PMID:26704149
Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium. PMID:26692227
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics. PMID:26656885
De novo assembly and characterization of the leaf, bud, and fruit transcriptome from the vulnerable tree Juglans mandshurica for the development of 20 new microsatellite markers using Illumina sequencing. PMID:26614514
Gekko japonicus genome reveals evolution of adhesive toe pads and tail regeneration. PMID:26598231
Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources. PMID:26589635
Comparative Genomics of an Emerging Amphibian Virus. PMID:26530419
Prioritization Of Nonsynonymous Single Nucleotide Variants For Exome Sequencing Studies Via Integrative Learning On Multiple Genomic Data. PMID:26459872
Comparative genome analysis of the candidate functional starter culture strains Lactobacillus fermentum 222 and Lactobacillus plantarum 80 for controlled cocoa bean fermentation processes. PMID:26459565
MST2-RASSF protein-protein interactions through SARAH domains. PMID:26443615
Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1. PMID:26441909
FARE-CAFE: a database of functional and regulatory elements of cancer-associated fusion events. PMID:26384373
Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi. PMID:26374290
Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels. PMID:26371554
Draft genome of Brugia pahangi: high similarity between B. pahangi and B. malayi. PMID:26350613
Deep Sequencing of the Scutellaria baicalensis Georgi Transcriptome Reveals Flavonoid Biosynthetic Profiling and Organ-Specific Gene Expression. PMID:26317778
Citing a Data Repository: A Case Study of the Protein Data Bank. PMID:26317409
Characterization and mapping of LanrBo: a locus conferring anthracnose resistance in narrow-leafed lupin (Lupinus angustifolius L.). PMID:26169875
State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet. PMID:26139527
Draft Genome Sequence of Gluconobacter oxydans NL71, a Strain That Efficiently Biocatalyzes Xylose to Xylonic Acid at a High Concentration. PMID:26089417
iSuc-PseAAC: predicting lysine succinylation in proteins by incorporating peptide position-specific propensity. PMID:26084794
Cracking the nodule worm code advances knowledge of parasite biology and biotechnology to tackle major diseases of livestock. PMID:26026709
Draft Genome Sequences of Six Different Staphylococcus epidermidis Clones, Isolated Individually from Preterm Neonates Presenting with Sepsis at Edinburgh's Royal Infirmary. PMID:25977439
RNA-seq analysis of Macrobrachium rosenbergii hepatopancreas in response to Vibrio parahaemolyticus infection. PMID:25922623
N-terminal modifications of cellular proteins: The enzymes involved, their substrate specificities and biological effects. PMID:25914051
Maximum-Likelihood Tree Estimation Using Codon Substitution Models with Multiple Partitions. PMID:25911229
Genome Sequence of Acidovorax citrulli Group 1 Strain pslb65 Causing Bacterial Fruit Blotch of Melons. PMID:25908136
Genome Sequence of a Copper-Resistant Strain of Acidovorax citrulli Causing Bacterial Fruit Blotch of Melons. PMID:25908132
From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data. PMID:25902288
Excessive antigen reactivity may underlie the clinical aggressiveness of chronic lymphocytic leukemia stereotyped subset #8. PMID:25900981
A RNA-seq approach to identify putative toxins from acrorhagi in aggressive and non-aggressive Anthopleura elegantissima polyps. PMID:25886045
Computational prediction of protein-protein interactions. PMID:25859943
The WRKY transcription factor genes in eggplant (Solanum melongena L.) and Turkey Berry (Solanum torvum Sw.). PMID:25853261
Genome-wide comparative analysis reveals similar types of NBS genes in hybrid Citrus sinensis genome and original Citrus clementine genome and provides new insights into non-TIR NBS genes. PMID:25811466
Protein topology determines cysteine oxidation fate: the case of sulfenyl amide formation among protein families. PMID:25741692
Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities. PMID:25707307
Comparison of sister species identifies factors underpinning plastid compatibility in green sea slugs. PMID:25652835
A novel one-class SVM based negative data sampling method for reconstructing proteome-wide HTLV-human protein interaction networks. PMID:25620466
A survey of computational intelligence techniques in protein function prediction. PMID:25574395
A Hypothetical Protein of Alteromonas macleodii AltDE1 (amad1_06475) Predicted to be a Cold-Shock Protein with RNA Chaperone Activity. PMID:25574135
Structural basis for heterogeneous phenotype of ERG11 dependent Azole resistance in C.albicans clinical isolates. PMID:25512882
Draft Genome Sequence of a Xylanase-Producing Bacterial Strain, Cellvibrio mixtus J3-8. PMID:25502674
Contribution of anion-π interactions to the stability of Sm/LSm proteins. PMID:25502146
Using EMBL-EBI Services via Web Interface and Programmatically via Web Services. PMID:25501941
Genomic insights into intrinsic and acquired drug resistance mechanisms in Achromobacter xylosoxidans. PMID:25487802
Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel. PMID:25474149
De novo assembly of the grass carp Ctenopharyngodon idella transcriptome to identify miRNA targets associated with motile aeromonad septicemia. PMID:25409340
Contribution of cation-π interactions to the stability of Sm/LSm oligomeric assemblies. PMID:25408427
The draft genome of the large yellow croaker reveals well-developed innate immunity. PMID:25407894
A human CCT5 gene mutation causing distal neuropathy impairs hexadecamer assembly in an archaeal model. PMID:25345891
AdaBoost based multi-instance transfer learning for predicting proteome-wide interactions between Salmonella and human proteins. PMID:25330226
Transcriptome analysis of the Trachinotus ovatus: identification of reproduction, growth and immune-related genes and microsatellite markers. PMID:25303650
De novo transcriptome of the Hemimetabolous German cockroach (Blattella germanica). PMID:25265537
Identification of biomarkers for radiation-induced acute intestinal symptoms (RIAISs) in cervical cancer patients by serum protein profiling. PMID:25256248
Complementary symbiont contributions to plant decomposition in a fungus-farming termite. PMID:25246537
Draft Genome Sequence of a Serratia marcescens Strain Isolated from a Preterm Neonatal Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom. PMID:25212627
Draft Genome Sequence of an Enterococcus faecalis Strain Isolated from a Neonatal Blood Sepsis Patient. PMID:25212626
Draft Genome Sequence of a Staphylococcus aureus Isolate Taken from the Blood of a Preterm Neonatal Blood Sepsis Patient. PMID:25212625
Fast and accurate discovery of degenerate linear motifs in protein sequences. PMID:25207816
Draft Genome Sequence of a Staphylococcus warneri Strain Isolated from a Preterm Neonate Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland. PMID:25189586
Draft Genome Sequence of a Streptococcus agalactiae Strain Isolated from a Preterm Neonate Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland. PMID:25189584
A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites. PMID:25156699
A multi-label classifier for prediction membrane protein functional types in animal. PMID:25107302
sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments. PMID:25053745
Developing hypothetical inhibition mechanism of novel urea transporter B inhibitor. PMID:25047372
Computational reconstruction of proteome-wide protein interaction networks between HTLV retroviruses and Homo sapiens. PMID:25037487
Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss? PMID:25013894
Draft Genome Sequence of Polaromonas glacialis Strain R3-9, a Psychrotolerant Bacterium Isolated from Arctic Glacial Foreland. PMID:25013146
Draft Genome Sequence of Vibrio fortis Dalian14 Isolated from Diseased Sea Urchin (Strongylocentrotus intermedius). PMID:24994792
Flavonoids with M1 muscarinic acetylcholine receptor binding activity. PMID:24979399
Prediction of membrane transport proteins and their substrate specificities using primary sequence information. PMID:24968309
An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases. PMID:24966208
IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools. PMID:24949626
Genome and transcriptome of the porcine whipworm Trichuris suis. PMID:24929829
Transcriptome profiling to discover putative genes associated with paraquat resistance in goosegrass (Eleusine indica L.). PMID:24927422
Draft Genome Sequences of Two Clinical Isolates of Streptococcus mutans. PMID:24926045
Comparative transcriptome analysis of eggplant (Solanum melongena L.) and turkey berry (Solanum torvum Sw.): phylogenomics and disease resistance analysis. PMID:24885385
Draft Genome Sequence of Bacillus thuringiensis Strain LM1212, Isolated from the Cadaver of an Oryctes gigas Larva in Madagascar. PMID:24874686
Pancreatic Cancer Database: an integrative resource for pancreatic cancer. PMID:24839966
Error removal in microchip-synthesized DNA using immobilized MutS. PMID:24829454
Evaluation of global differential gene and protein expression in primary Pterygium: S100A8 and S100A9 as possible drivers of a signaling network. PMID:24825356
Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PMID:24756107
New insights into Dehalococcoides mccartyi metabolism from a reconstructed metabolic network-based systems-level analysis of D. mccartyi transcriptomes. PMID:24733489
Draft Genome Sequence of the Growth-Promoting Endophyte Paenibacillus sp. P22, Isolated from Populus. PMID:24723717
Draft Genome Sequence of Nafulsella turpanensis ZLM-10T, a Novel Member of the Family Flammeovirgaceae. PMID:24699960
Towards decrypting cryptobiosis--analyzing anhydrobiosis in the tardigrade Milnesium tardigradum using transcriptome sequencing. PMID:24651535
Elapid snake venom analyses show the specificity of the peptide composition at the level of genera Naja and Notechis. PMID:24590383
PalmPred: an SVM based palmitoylation prediction method using sequence profile information. PMID:24586628
A network map of the gastrin signaling pathway. PMID:24584707
Genome sequencing of high-penicillin producing industrial strain of Penicillium chrysogenum. PMID:24564352
Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome. PMID:24489955
Multi-algorithm and multi-model based drug target prediction and web server. PMID:24487966
NitroDIGE analysis reveals inhibition of protein S-nitrosylation by epigallocatechin gallates in lipopolysaccharide-stimulated microglial cells. PMID:24472655
TrigNER: automatically optimized biomedical event trigger recognition on scientific documents. PMID:24401704
Putative sugar transporters of the mustard leaf beetle Phaedon cochleariae: their phylogeny and role for nutrient supply in larval defensive glands. PMID:24391959
A multi-omic analysis of an Enterococcus faecium mutant reveals specific genetic mutations and dramatic changes in mRNA and protein expression. PMID:24373636
Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing. PMID:24373163
Draft genome sequence of pseudomonas strain p818, isolated from glyphosate-polluted soil. PMID:24356842
The pattern and distribution of deleterious mutations in maize. PMID:24281428
In-silico screening of cancer associated mutation on PLK1 protein and its structural consequences. PMID:24271645
Probability weighted ensemble transfer learning for predicting interactions between HIV-1 and human proteins. PMID:24260261
Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations. PMID:24169659
Identification of B-cell epitopes in an antigen for inducing specific class of antibodies. PMID:24168386
Probabilistic Prediction of Protein Phosphorylation Sites Using Classification Relevance Units Machines. PMID:24163645
Updates of the HbVar database of human hemoglobin variants and thalassemia mutations. PMID:24137000
Complete Genome Sequence of Encapsulated Haemophilus influenzae Type f KR494, an Invasive Isolate That Caused Necrotizing Myositis. PMID:24092777
The relationship between gene isoform multiplicity, number of exons and protein divergence. PMID:24023641
Regression Modeling and Meta-Analysis of Diagnostic Accuracy of SNP-Based Pathogenicity Detection Tools for UGT1A1 Gene Mutation. PMID:23997956
The Tarenaya hassleriana genome provides insight into reproductive trait and genome evolution of crucifers. PMID:23983221
Towards precision medicine: advances in computational approaches for the analysis of human variants. PMID:23962656
SNP discovery in European anchovy (Engraulis encrasicolus, L) by high-throughput transcriptome and genome sequencing. PMID:23936375
Complete genome sequence and comparative analysis of Acetobacter pasteurianus 386B, a strain well-adapted to the cocoa bean fermentation ecosystem. PMID:23902333
Meta-analysis diagnostic accuracy of SNP-based pathogenicity detection tools: a case of UTG1A1 gene mutations. PMID:23875061
In silico screening and molecular dynamics simulation of disease-associated nsSNP in TYRP1 gene and its structural consequences in OCA3. PMID:23862152
A protein domain-centric approach for the comparative analysis of human and yeast phenotypically relevant mutations. PMID:23819456
The transition from a phytopathogenic smut ancestor to an anamorphic biocontrol agent deciphered by comparative whole-genome analysis. PMID:23800965
General approach to reversing ketol-acid reductoisomerase cofactor dependence from NADPH to NADH. PMID:23776225
Side pockets provide the basis for a new mechanism of Kv channel-specific inhibition. PMID:23728494
Phosphoproteome dynamics reveal novel ERK1/2 MAP kinase substrates with broad spectrum of functions. PMID:23712012
Investigation of specificity determinants in bacterial tRNA-guanine transglycosylase reveals queuine, the substrate of its eucaryotic counterpart, as inhibitor. PMID:23704982
Comprehensive database of Chorismate synthase enzyme from shikimate pathway in pathogenic bacteria. PMID:23697663
Complete Genome Sequence of Marinobacter sp. BSs20148. PMID:23682144
Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: recurrence of tyrosine aminotransferase activity in the Iα subfamily. PMID:23671031
Complete Genome Sequence of Glaciecola psychrophila Strain 170T. PMID:23640379
Simultaneous transcriptome analysis of Sorghum and Bipolaris sorghicola by using RNA-seq in combination with de novo transcriptome assembly. PMID:23638091
Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing. PMID:23575249
Drosophila signal peptidase complex member Spase12 is required for development and cell differentiation. PMID:23573290
Three-level prediction of protein function by combining profile-sequence search, profile-profile search, and domain co-occurrence networks. PMID:23514381
Combining heterogeneous data sources for accurate functional annotation of proteins. PMID:23514123
An integrated map of corticotropin-releasing hormone signaling pathway. PMID:23504413
The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels. PMID:23496936
Complete Genome Sequence of the Industrial Strain Gluconobacter oxydans H24. PMID:23472221
Draft genome sequence of the rubber tree Hevea brasiliensis. PMID:23375136
Genome sequencing of the important oilseed crop Sesamum indicum L. PMID:23369264
Signaling network of Oncostatin M pathway. PMID:23255051
TnpPred: A Web Service for the Robust Prediction of Prokaryotic Transposases. PMID:23251097
The origins of the evolutionary signal used to predict protein-protein interactions. PMID:23217198
The state of the human proteome in 2012 as viewed through PeptideAtlas. PMID:23215161
Draft genome sequence of the flocculating Zymomonas mobilis strain ZM401 (ATCC 31822). PMID:23209250
Proteins of unknown function in the Protein Data Bank (PDB): an inventory of true uncharacterized proteins and computational tools for their analysis. PMID:23202924
Exploring Pandora's box: potential and pitfalls of low coverage genome surveys for evolutionary biology. PMID:23185309
A multicellular signal transduction network of AGE/RAGE signaling. PMID:23161412
Draft genome sequence of Lactobacillus casei W56. PMID:23144392
Arginine and Lysine interactions with π residues in metalloproteins. PMID:23139592
A next-generation sequencing approach to study the transcriptomic changes during the differentiation of physarum at the single-cell level. PMID:23071390
Towards the improved discovery and design of functional peptides: common features of diverse classes permit generalized prediction of bioactivity. PMID:23056189
Comparative Genome Sequence Analysis Reveals the Extent of Diversity and Conservation for Glycan-Associated Proteins in Burkholderia spp. PMID:22991502
An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB. PMID:22962482
Global probabilistic annotation of metabolic networks enables enzyme discovery. PMID:22960854
HSPIR: a manually annotated heat shock protein information resource. PMID:22923302
Comparative genomics analysis of Mycobacterium ulcerans for the identification of putative essential genes and therapeutic candidates. PMID:22912793
Integrating external biological knowledge in the construction of regulatory networks from time-series expression data. PMID:22898396
Draft genome sequence of Gluconobacter oxydans WSH-003, a strain that is extremely tolerant of saccharides and alditols. PMID:22843589
Transcriptome analysis of head kidney in grass carp and discovery of immune-related genes. PMID:22776770
Disease-related mutations predicted to impact protein function. PMID:22759649
Multi-label multi-kernel transfer learning for human protein subcellular localization. PMID:22719847
A method to find longevity-selected positions in the mammalian proteome. PMID:22701678
Computational methods to work as first-pass filter in deleterious SNP analysis of alkaptonuria. PMID:22606059
Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals. PMID:22529998
An analysis of substitution, deletion and insertion mutations in cancer genes. PMID:22492711
Computational identification and modeling of crosstalk between phosphorylation, O-β-glycosylation and methylation of FoxO3 and implications for cancer therapeutics. PMID:22489133
The transcription factor encyclopedia. PMID:22458515
MotViz: a tool for sequence motif prediction in parallel to structural visualization and analyses. PMID:22449399
Congenital nephrogenic diabetes insipidus: the current state of affairs. PMID:22427315
In silico investigation of interactions between human cannabinoid receptor-1 and its antagonists. PMID:22402754
Homology modeling, comparative genomics and functional annotation of Mycoplasma genitalium hypothetical protein MG_237. PMID:22355225
Draft genome sequence of Mesorhizobium alhagi CCNWXJ12-2T, a novel salt-resistant species isolated from the desert of northwestern China. PMID:22328758
Incorporating molecular and functional context into the analysis and prioritization of human variants associated with cancer. PMID:22319177
Prediction of lysine ubiquitylation with ensemble classifier and feature selection. PMID:22272076
The human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer. PMID:22194470
Active site detection by spatial conformity and electrostatic analysis--unravelling a proteolytic function in shrimp alkaline phosphatase. PMID:22174814
Identification of protein-RNA interaction sites using the information of spatial adjacent residues. PMID:22165911
Scaffold hopping for identification of novel D(2) antagonist based on 3D pharmacophore modelling of illoperidone analogs. PMID:22161148
Mannose 6 dephosphorylation of lysosomal proteins mediated by acid phosphatases Acp2 and Acp5. PMID:22158965
A machine learning approach to identify hydrogenosomal proteins in Trichomonas vaginalis. PMID:22140228
IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. PMID:22102591
Comparative genomics study of polyhydroxyalkanoates (PHA) and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships. PMID:22040376
gViz, a novel tool for the visualization of co-expression networks. PMID:22032859
Ascaris suum draft genome. PMID:22031327
The Mediator complex in plants: structure, phylogeny, and expression profiling of representative genes in a dicot (Arabidopsis) and a monocot (rice) during reproduction and abiotic stress. PMID:22021418
O-GlcNAc modification of the anti-malarial vaccine candidate PfAMA1: in silico-defined structural changes and potential to generate a better vaccine. PMID:22020851
The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota. PMID:22003381
The energy landscape analysis of cancer mutations in protein kinases. PMID:21998754
A comprehensive curated resource for follicle stimulating hormone signaling. PMID:21996254
Red and problematic green phylogenetic signals among thousands of nuclear genes from the photosynthetic and apicomplexa-related Chromera velia. PMID:21965651
Complete genome sequence of the dog commensal and human pathogen Capnocytophaga canimorsus strain 5. PMID:21914877
A computational approach to finding novel targets for existing drugs. PMID:21909252
SSPred: A prediction server based on SVM for the identification and classification of proteins involved in bacterial secretion systems. PMID:21904425
Prediction of B-cell linear epitopes with a combination of support vector machine classification and amino acid propensity identification. PMID:21876642
Whole-genome sequencing of multiple Arabidopsis thaliana populations. PMID:21874002
Immunome database for marsupials and monotremes. PMID:21854560
Molecular characterization of Tob1 in muscle development in pigs. PMID:21845080
Prediction of body fluids where proteins are secreted into based on protein interaction network. PMID:21829572
Chemoenzymatic labeling of protein C-termini for positive selection of C-terminal peptides. PMID:21812462
A new disease-specific machine learning approach for the prediction of cancer-causing missense variants. PMID:21763417
Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma. PMID:21750257
Human linker histones: interplay between phosphorylation and O-β-GlcNAc to mediate chromatin structural modifications. PMID:21749719
Genome sequence of the ethanol-producing Zymomonas mobilis subsp. pomaceae lectotype strain ATCC 29192. PMID:21742897
Genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis lectotype strain ATCC 10988. PMID:21725006
A new drug design targeting the adenosinergic system for Huntington's disease. PMID:21713039
Whole-genome sequencing for optimized patient management. PMID:21677200
Identification of robust hypoxia biomarker candidates from fin of medaka (Oryzias latipes). PMID:21664487
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. PMID:21632744
Role of post translational modifications and novel crosstalk between phosphorylation and O-beta-GlcNAc modifications in human claudin-1, -3 and -4. PMID:21617949
OEP61 is a chaperone receptor at the plastid outer envelope. PMID:21612577
Deciphering enzyme function using peptide arrays. PMID:21604200
Structural determinants of the alpha2 adrenoceptor subtype selectivity. PMID:21602069
Prediction of peptides binding to the PKA RIIalpha subunit using a hierarchical strategy. PMID:21586518
Claudin-1 required for HCV virus entry has high potential for phosphorylation and O-glycosylation. PMID:21569618
Topography of tyrosine residues and their involvement in peroxidation of polyunsaturated cardiolipin in cytochrome c/cardiolipin peroxidase complexes. PMID:21550335
Serine 204 phosphorylation and O-β-GlcNAC interplay of IGFBP-6 as therapeutic indicator to regulate IGF-II functions in viral mediated hepatocellular carcinoma. PMID:21548981
Regulatory mechanisms underlying oil palm fruit mesocarp maturation, ripening, and functional specialization in lipid and carotenoid metabolism. PMID:21487046
A computational model of the LGI1 protein suggests a common binding site for ADAM proteins. PMID:21479274
Comparing phylogeny and the predicted pathogenicity of protein variations reveals equal purifying selection across the global human mtDNA diversity. PMID:21457906
Incorporating distant sequence features and radial basis function networks to identify ubiquitin conjugation sites. PMID:21408064
Evolutionary approach to predicting the binding site residues of a protein from its primary sequence. PMID:21402946
A bioinformatics workflow for variant peptide detection in shotgun proteomics. PMID:21389108
Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics. PMID:21368207
Sequence analysis and homology modeling of laccase from Pycnoporus cinnabarinus. PMID:21364777
Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception. PMID:21342548
Structure-function relationships of the competence lipoprotein ComL and SSB in meningococcal transformation. PMID:21330432
Eukaryote-wide sequence analysis of mitochondrial β-barrel outer membrane proteins. PMID:21272379
Coding potential of the products of alternative splicing in human. PMID:21251333
Discriminative motif finding for predicting protein subcellular localization. PMID:21233524
Stereotypical chronic lymphocytic leukemia B-cell receptors recognize survival promoting antigens on stromal cells. PMID:21209908
Prediction and analysis of protein hydroxyproline and hydroxylysine. PMID:21209839
Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction. PMID:21171995
Identification, activity and disulfide connectivity of C-di-GMP regulating proteins in Mycobacterium tuberculosis. PMID:21151497
Algorithms and semantic infrastructure for mutation impact extraction and grounding. PMID:21143808
Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature. PMID:21138947
Database resources of the National Center for Biotechnology Information. PMID:21097890
ModBase, a database of annotated comparative protein structure models, and associated resources. PMID:21097780
Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. PMID:21092232
LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana. PMID:21071420
N-CLAP: global profiling of N-termini by chemoselective labeling of the alpha-amine of proteins. PMID:21041401
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. PMID:21037261
ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures. PMID:21036864
Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database. PMID:21030493
Structural stability studies in adhesion molecules--role of cation-π interactions. PMID:20978808
PathEx: a novel multi factors based datasets selector web tool. PMID:20969778
FOXRED1, encoding an FAD-dependent oxidoreductase complex-I-specific molecular chaperone, is mutated in infantile-onset mitochondrial encephalopathy. PMID:20858599
Utopia documents: linking scholarly literature with research data. PMID:20823323
Investigation of an anomalously accelerating substitution in the folding of a prototypical two-state protein. PMID:20816985
Characterizing the metabolism of Dehalococcoides with a constraint-based model. PMID:20811585
A novel tissue-specific meta-analysis approach for gene expression predictions, initiated with a mammalian gene expression testis database. PMID:20699007
DMDM: domain mapping of disease mutations. PMID:20685956
The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. PMID:20624719
Proteome-wide analysis of protein carboxy termini: C terminomics. PMID:20526347
A computational genomics pipeline for prokaryotic sequencing projects. PMID:20519285
Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information. PMID:20492656
In-silico prediction of blood-secretory human proteins using a ranking algorithm. PMID:20465853
Targeted investigation of the Neandertal genome by array-based sequence capture. PMID:20448179
ConPlex: a server for the evolutionary conservation analysis of protein complex structures. PMID:20435678
Comprehensive characterization of methicillin-resistant Staphylococcus aureus subsp. aureus COL secretome by two-dimensional liquid chromatography and mass spectrometry. PMID:20418541
Investigation of cation-π interactions in sugar-binding proteins. PMID:20379838
Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithm. PMID:20333233
miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature. PMID:20233441
Mining Cytochrome b561 proteins from plant genomes. PMID:20223741
Deleterious amino acid polymorphisms in Arabidopsis thaliana and rice. PMID:20198468
Protein aggregation profile of the bacterial cytosol. PMID:20195530
HLA class I restriction as a possible driving force for Chikungunya evolution. PMID:20195467
Walk-weighted subsequence kernels for protein-protein interaction extraction. PMID:20184736
Evolution of spliceosomal introns following endosymbiotic gene transfer. PMID:20178587
Transcriptomic changes arising during light-induced sporulation in Physarum polycephalum. PMID:20163733
Genomic approaches in the identification of hypoxia biomarkers in model fish species. PMID:20161383
The molecular determinants of the increased reduction potential of the rubredoxin domain of rubrerythrin relative to rubredoxin. PMID:20159152
Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs. PMID:20157482
The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth. PMID:20154119
Systems metabolic engineering: genome-scale models and beyond. PMID:20151446
Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique. PMID:20122235
Amino acid classification based spectrum kernel fusion for protein subnuclear localization. PMID:20122188
SoyDB: a knowledge database of soybean transcription factors. PMID:20082720
In silico functional profiling of human disease-associated and polymorphic amino acid substitutions. PMID:20052762
CanProVar: a human cancer proteome variation database. PMID:20052754
Genomic inventory and transcriptional analysis of Medicago truncatula transporters. PMID:20023147
Advances in translational bioinformatics: computational approaches for the hunting of disease genes. PMID:20007728
A multi-species comparative structural bioinformatics analysis of inherited mutations in alpha-D-mannosidase reveals strong genotype-phenotype correlation. PMID:19958498
An electrostatic switch displaces phosphatidylinositol phosphate kinases from the membrane during phagocytosis. PMID:19951917
A cytogenetic abnormality and rare coding variants identify ABCA13 as a candidate gene in schizophrenia, bipolar disorder, and depression. PMID:19944402
Calling International Rescue: knowledge lost in literature and data landslide! PMID:19929850
Global profiling of protease cleavage sites by chemoselective labeling of protein N-termini. PMID:19892738
Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins. PMID:19888473
PIP(2)-binding site in Kir channels: definition by multiscale biomolecular simulations. PMID:19839652
Sequence and structure signatures of cancer mutation hotspots in protein kinases. PMID:19834613
AntigenDB: an immunoinformatics database of pathogen antigens. PMID:19820110
Recombination and insertion events involving the botulinum neurotoxin complex genes in Clostridium botulinum types A, B, E and F and Clostridium butyricum type E strains. PMID:19804621
PIE-efficient filters and coarse grained potentials for unbound protein-protein docking. PMID:19768784
Complete genome sequence of the ethanol producer Zymomonas mobilis NCIMB 11163. PMID:19767433
Automated inference of molecular mechanisms of disease from amino acid substitutions. PMID:19734154
The response of the tandem pore potassium channel TASK-3 (K(2P)9.1) to voltage: gating at the cytoplasmic mouth. PMID:19703964
Accurate prediction of DnaK-peptide binding via homology modelling and experimental data. PMID:19696878
ArachnoServer: a database of protein toxins from spiders. PMID:19674480
Local combinational variables: an approach used in DNA-binding helix-turn-helix motif prediction with sequence information. PMID:19651875
Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4. PMID:19640295
Calculation of the relative metastabilities of proteins in subcellular compartments of Saccharomyces cerevisiae. PMID:19615086
Alternative splicing of transcription factors' genes: beyond the increase of proteome diversity. PMID:19609452
Differences in duplication age distributions between human GPCRs and their downstream genes from a network prospective. PMID:19594873
Multiple horizontal gene transfer events and domain fusions have created novel regulatory and metabolic networks in the oomycete genome. PMID:19582169
A comprehensive resource for integrating and displaying protein post-translational modifications. PMID:19549291
Generation of a 3D model for human GABA transporter hGAT-1 using molecular modeling and investigation of the binding of GABA. PMID:19506924
Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins. PMID:19486509
Transmembrane protein topology prediction using support vector machines. PMID:19470175
Outsourcing the nucleus: nuclear pore complex genes are no longer encoded in nucleomorph genomes. PMID:19455199
An integrative multi-platform analysis for discovering biomarkers of osteosarcoma. PMID:19445706
BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology. PMID:19426462
Efficient use of unlabeled data for protein sequence classification: a comparative study. PMID:19426450
In silico mutagenesis: a case study of the melanocortin 4 receptor. PMID:19417090
Improving classification in protein structure databases using text mining. PMID:19416501
Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins. PMID:19383128
Hydrodynamic multibead modeling: problems, pitfalls, and solutions. 2. Proteins. PMID:19308400
Computational identification of protein methylation sites through bi-profile Bayes feature extraction. PMID:19290060
TFCat: the curated catalog of mouse and human transcription factors. PMID:19284633
MCAM: a database to accelerate the identification of functional cell adhesion molecules. PMID:19259402
Functional insights by comparison of modeled structures of 18kDa small heat shock protein and its mutant in Mycobacterium leprae. PMID:19255639
Identification of neisserial DNA binding components. PMID:19246756
A new prediction strategy for long local protein structures using an original description. PMID:19241475
Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information. PMID:19213741
Phosphorylation of p53 by IkappaB kinase 2 promotes its degradation by beta-TrCP. PMID:19196987
Jalview Version 2--a multiple sequence alignment editor and analysis workbench. PMID:19151095
Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases. PMID:19139070
Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation. PMID:19116666
The value of position-specific scoring matrices for assessment of protein allegenicity. PMID:19091021
Flanking signal and mature peptide residues influence signal peptide cleavage. PMID:19091014
PSI-BLAST pseudocounts and the minimum description length principle. PMID:19088134
GeneDistiller--distilling candidate genes from linkage intervals. PMID:19057649
Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome. PMID:19054114
An interrupted beta-propeller and protein disorder: structural bioinformatics insights into the N-terminus of alsin. PMID:19023603
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
SMART 6: recent updates and new developments. PMID:18978020
SysZNF: the C2H2 zinc finger gene database. PMID:18974185
Hidden Markov models incorporating fuzzy measures and integrals for protein sequence identification and alignment. PMID:18973866
SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2. PMID:18959793
The National Center for Biotechnology Information's Protein Clusters Database. PMID:18940865
Prediction of kinase-specific phosphorylation sites using conditional random fields. PMID:18940828
CC+: a relational database of coiled-coil structures. PMID:18842638
RAPID: Resource of Asian Primary Immunodeficiency Diseases. PMID:18842635
Calculation of the relative metastabilities of proteins using the CHNOSZ software package. PMID:18834534
A method for probabilistic mapping between protein structure and function taxonomies through cross training. PMID:18834528
Mining physical protein-protein interactions from the literature. PMID:18834490
Physical protein-protein interactions predicted from microarrays. PMID:18829707
Bacteriophage 2851 is a prototype phage for dissemination of the Shiga toxin variant gene 2c in Escherichia coli O157:H7. PMID:18824528
A resource for transcriptomic analysis in the mouse brain. PMID:18714383
Atomic resolution structures of Escherichia coli and Bacillus anthracis malate synthase A: comparison with isoform G and implications for structure-based drug discovery. PMID:18714089
Cell cycle kinases predicted from conserved biophysical properties. PMID:18704950
Crystal structures of C4-dicarboxylate ligand complexes with sensor domains of histidine kinases DcuS and DctB. PMID:18701447
Gain and loss of phosphorylation sites in human cancer. PMID:18689832
Integrating protein-protein interactions and text mining for protein function prediction. PMID:18673526
Challenges and solutions in proteomics. PMID:18645629
Comparative analysis of the testis and ovary transcriptomes in zebrafish by combining experimental and computational tools. PMID:18629171
Investigation into the use of C- and N-terminal GFP fusion proteins for subcellular localization studies using reverse transfection microarrays. PMID:18629169
The molecule role ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature. PMID:18629146
In silico identification of functional protein interfaces. PMID:18629079
Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan. PMID:18604266
Immunological hotspots analyzed by docking simulations: evidence for a general mechanism in pemphigus vulgaris pathology and transformation. PMID:18564435
The hidden universal distribution of amino acid biosynthetic networks: a genomic perspective on their origins and evolution. PMID:18541022
Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis. PMID:18523684
Genome-wide survey of allele-specific splicing in humans. PMID:18518984
SODa: an Mn/Fe superoxide dismutase prediction and design server. PMID:18518943
Identification of guanylate cyclases and related signaling proteins in sperm tail from sea stars by mass spectrometry. PMID:18461395
AMMO-Prot: amine system project 3D-model finder. PMID:18460178
Challenges in translating plasma proteomics from bench to bedside: update from the NHLBI Clinical Proteomics Programs. PMID:18456800
Functional classification analysis of somatically mutated genes in human breast and colorectal cancers. PMID:18434084
Multipattern consensus regions in multiple aligned protein sequences and their segmentation. PMID:18427583
Genome-wide subcellular localization of putative outer membrane and extracellular proteins in Leptospira interrogans serovar Lai genome using bioinformatics approaches. PMID:18423054
A comparison of sugar indicators enables a universal high-throughput sugar-1-phosphate nucleotidyltransferase assay. PMID:18387352
Annotating genes of known and unknown function by large-scale coexpression analysis. PMID:18354039
Antarctic marine molluscs do have an HSP70 heat shock response. PMID:18347940
Epidermal growth factor receptors: function modulation by phosphorylation and glycosylation interplay. PMID:18340549
Dynamics of Recognition between tRNA and elongation factor Tu. PMID:18336835
Predicting proteolytic sites in extracellular proteins: only halfway there. PMID:18321887
Towards ontology-driven navigation of the lipid bibliosphere. PMID:18315858
Nonspecific base recognition mediated by water bridges and hydrophobic stacking in ribonuclease I from Escherichia coli. PMID:18305191
DBMLoc: a Database of proteins with multiple subcellular localizations. PMID:18304364
Protein abundance profiling of the Escherichia coli cytosol. PMID:18304323
SciDBMaker: new software for computer-aided design of specialized biological databases. PMID:18298861
MeInfoText: associated gene methylation and cancer information from text mining. PMID:18194557
An automated protein annotation filter for integrating web-based annotation tools. PMID:18188426
Quantitative analysis on the characteristics of targets with FDA approved drugs. PMID:18167532
Homology modeling of hemagglutinin/protease [HA/P (vibriolysin)] from Vibrio cholerae: sequence comparision, residue interactions and molecular mechanism. PMID:18074211
Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses. PMID:18070355
Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within plasmids. PMID:18060065
Evaluating the protein coding potential of exonized transposable element sequences. PMID:18036258
Computational study on mechanism of G-quartet oligonucleotide T40214 selectively targeting Stat3. PMID:18034310
A comprehensive analysis of non-sequential alignments between all protein structures. PMID:18005453
Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines. PMID:18005451
SERpredict: detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements. PMID:17986331
AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology. PMID:17962307
Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family. PMID:17941992
ProSAS: a database for analyzing alternative splicing in the context of protein structures. PMID:17933774
ATDB: a uni-database platform for animal toxins. PMID:17933766
MetaCrop: a detailed database of crop plant metabolism. PMID:17933764
Homology modeling and examination of the effect of the D92E mutation on the H5N1 nonstructural protein NS1 effector domain. PMID:17917748
Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. PMID:17916244
Analysis of gene order data supports vertical inheritance of the leukotoxin operon and genome rearrangements in the 5' flanking region in genus Mannheimia. PMID:17915007
Characterization of oligopeptide patterns in large protein sets. PMID:17908308
X-ray structures of two proteins belonging to Pfam DUF178 revealed unexpected structural similarity to the DUF191 Pfam family. PMID:17908300
M-TASSER: an algorithm for protein quaternary structure prediction. PMID:17905848
SmedGD: the Schmidtea mediterranea genome database. PMID:17881371
MutDB: update on development of tools for the biochemical analysis of genetic variation. PMID:17827212
NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PMID:17726526
Efficacy of different protein descriptors in predicting protein functional families. PMID:17705863
Crystal structure and putative function of small Toprim domain-containing protein from Bacillus stearothermophilus. PMID:17705269
Complexity, connectivity, and duplicability as barriers to lateral gene transfer. PMID:17678544
The Taenia saginata homologue of the major surface antigen of Echinococcus spp. is immunogenic and 97% identical to its Taenia solium homologue. PMID:17674048
The functional modulation of epigenetic regulators by alternative splicing. PMID:17651478
Manual curation is not sufficient for annotation of genomic databases. PMID:17646325
A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds. PMID:17630830
Precise protein quantification based on peptide quantification using iTRAQ. PMID:17584939
firestar--prediction of functionally important residues using structural templates and alignment reliability. PMID:17584799
Anti-calmodulins and tricyclic adjuvants in pain therapy block the TRPV1 channel. PMID:17579717
DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities. PMID:17567620
Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. PMID:17563368
Comprehensive analysis of co-occurring domain sets in yeast proteins. PMID:17562021
ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ. PMID:17526514
A novel motif identified in dependence receptors. PMID:17520022
M4T: a comparative protein structure modeling server. PMID:17517764
3D-partner: a web server to infer interacting partners and binding models. PMID:17517763
Modeling and analysis of ligand-receptor interactions in the GABAc receptor. PMID:17506348
Spectroscopic and structural study of proton and halide ion cooperative binding to gfp. PMID:17434942
A computational approach for detecting peptidases and their specific inhibitors at the genome level. PMID:17430570
IDR knowledge base for primary immunodeficiencies. PMID:17394641
Molecular basis for repression of liver X receptor-mediated gene transcription by receptor-interacting protein 140. PMID:17391100
Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins. PMID:17391016
Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions. PMID:17391015
Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. PMID:17391014
The Arabidopsis thaliana AT PRP39-1 gene, encoding a tetratricopeptide repeat protein with similarity to the yeast pre-mRNA processing protein PRP39, affects flowering time. PMID:17380304
Membrane protein prediction methods. PMID:17367718
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PMID:17355171
The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C. PMID:17350933
Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database. PMID:17335583
AP endonuclease paralogues with distinct activities in DNA repair and bacterial pathogenesis. PMID:17318183
Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. PMID:17307855
Functional impact of missense variants in BRCA1 predicted by supervised learning. PMID:17305420
Automatic extraction of protein point mutations using a graph bigram association. PMID:17274683
DiscoverySpace: an interactive data analysis application. PMID:17210078
Towards alignment independent quantitative assessment of homology detection. PMID:17205117
A top-down/bottom-up study of the ribosomal proteins of Caulobacter crescentus. PMID:17203977
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. PMID:17202171
REBASE--enzymes and genes for DNA restriction and modification. PMID:17202163
LigProf: a simple tool for in silico prediction of ligand-binding sites. PMID:17200839
Molecular identification of microsomal acyl-CoA:glycerol-3-phosphate acyltransferase, a key enzyme in de novo triacylglycerol synthesis. PMID:17170135
Database resources of the National Center for Biotechnology Information. PMID:17170002
The Molecular Biology Database Collection: 2007 update. PMID:17148484
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. PMID:17145713
Snap: an integrated SNP annotation platform. PMID:17135198
Organelle DB: an updated resource of eukaryotic protein localization and function. PMID:17130152
The mouse Gene Expression Database (GXD): 2007 update. PMID:17130151
DWARF--a data warehouse system for analyzing protein families. PMID:17094801
Janus model of the Na,K-ATPase beta-subunit transmembrane domain: distinct faces mediate alpha/beta assembly and beta-beta homo-oligomerization. PMID:17078968
Modeling and active site refinement for G protein-coupled receptors: application to the beta-2 adrenergic receptor. PMID:17054017
Comparative genomics of fungal allergens and epitopes shows widespread distribution of closely related allergen and epitope orthologues. PMID:17029625
A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A, a selective kappa opioid receptor agonist. PMID:17009091
Serine hydrolase KIAA1363: toxicological and structural features with emphasis on organophosphate interactions. PMID:16978018
Computational detection of allergenic proteins attains a new level of accuracy with in silico variable-length peptide extraction and machine learning. PMID:16977698
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. PMID:16970830
Systematic identification of pseudogenes through whole genome expression evidence profiling. PMID:16945953
Homology modeling of tubulin: influence predictions for microtubule's biophysical properties. PMID:16941085
A combinatorial optimization approach for diverse motif finding applications. PMID:16916460
The distinctive signatures of promoter regions and operon junctions across prokaryotes. PMID:16914446
MultiSeq: unifying sequence and structure data for evolutionary analysis. PMID:16914055
Modeling the open and closed forms of GABAA receptor: analysis of ligand-receptor interactions for the GABA-binding site. PMID:16913422
Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information. PMID:16845118
ProKware: integrated software for presenting protein structural properties in protein tertiary structures. PMID:16845116
FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. PMID:16845089
New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate. PMID:16845086
TFBScluster web server for the identification of mammalian composite regulatory elements. PMID:16845063
DILIMOT: discovery of linear motifs in proteins. PMID:16845024
MeMo: a web tool for prediction of protein methylation modifications. PMID:16845004
AlgPred: prediction of allergenic proteins and mapping of IgE epitopes. PMID:16844994
SVMHC: a server for prediction of MHC-binding peptides. PMID:16844990
BBP: Brucella genome annotation with literature mining and curation. PMID:16842628
Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits. PMID:16835308
Saturating representation of loop conformational fragments in structure databanks. PMID:16820050
PROMPT: a protein mapping and comparison tool. PMID:16817977
Identification of a novel NADH-specific aldo-keto reductase using sequence and structural homologies. PMID:16813561
Large nucleotide-dependent movement of the N-terminal domain of the ClpX chaperone. PMID:16810315
The Autoimmune Disease Database: a dynamically compiled literature-derived database. PMID:16803617
Predicting protein subcellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chains. PMID:16774677
EVEREST: automatic identification and classification of protein domains in all protein sequences. PMID:16749920
Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. PMID:16738128
A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model. PMID:16737530
Intrinsic disorder in transcription factors. PMID:16734424
Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. PMID:16717195
Prediction of mitochondrial proteins using discrete wavelet transform. PMID:16703470
Distinguishing protein-coding from non-coding RNAs through support vector machines. PMID:16683024
Pseudo-messenger RNA: phantoms of the transcriptome. PMID:16683022
Predicting deleterious nsSNPs: an analysis of sequence and structural attributes. PMID:16630345
Benchmarking ortholog identification methods using functional genomics data. PMID:16613613
Whitefly (Bemisia tabaci) genome project: analysis of sequenced clones from egg, instar, and adult (viruliferous and non-viruliferous) cDNA libraries. PMID:16608516
Graph theoretical insights into evolution of multidomain proteins. PMID:16597245
Classification of protein quaternary structure by functional domain composition. PMID:16584572
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. PMID:16553966
Comparative genomic analysis of three strains of Ehrlichia ruminantium reveals an active process of genome size plasticity. PMID:16547041
Deciphering cellular states of innate tumor drug responses. PMID:16542501
The 3of5 web application for complex and comprehensive pattern matching in protein sequences. PMID:16542452
The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons. PMID:16505379
Integrating protein structures and precomputed genealogies in the Magnum database: examples with cellular retinoid binding proteins. PMID:16504077
Common features and interesting differences in transcriptional responses to secretion stress in the fungi Trichoderma reesei and Saccharomyces cerevisiae. PMID:16504068
Tracking the evolution of alternatively spliced exons within the Dscam family. PMID:16483367
Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space. PMID:16481312
Protein kinases associated with the yeast phosphoproteome. PMID:16445868
Oct-2 DNA binding transcription factor: functional consequences of phosphorylation and glycosylation. PMID:16431844
Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration. PMID:16426464
Modeling the bound conformation of Pemphigus vulgaris-associated peptides to MHC Class II DR and DQ alleles. PMID:16426456
A theoretical model of Aquifex pyrophilus flagellin: implications for its thermostability. PMID:16411078
Automatic discovery of cross-family sequence features associated with protein function. PMID:16409628
A systematic approach to infer biological relevance and biases of gene network structures. PMID:16407322
Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. PMID:16397293
The evolutionary relationship of the domain architectures in the RhoGEF-containing proteins. PMID:16393146
Pentapeptide repeat proteins. PMID:16388575
MitoP2: the mitochondrial proteome database--now including mouse data. PMID:16381964
dbPTM: an information repository of protein post-translational modification. PMID:16381945
MetaCyc: a multiorganism database of metabolic pathways and enzymes. PMID:16381923
LMPD: LIPID MAPS proteome database. PMID:16381922
Human protein reference database--2006 update. PMID:16381900
INVHOGEN: a database of homologous invertebrate genes. PMID:16381884
The HUGO Gene Nomenclature Database, 2006 updates. PMID:16381876
The PMDB Protein Model Database. PMID:16381873
The EROP-Moscow oligopeptide database. PMID:16381860
SMART 5: domains in the context of genomes and networks. PMID:16381859
ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. PMID:16381846
PPD v1.0--an integrated, web-accessible database of experimentally determined protein pKa values. PMID:16381845
PINT: Protein-protein Interactions Thermodynamic Database. PMID:16381844
TCDB: the Transporter Classification Database for membrane transport protein analyses and information. PMID:16381841
RNAi Codex: a portal/database for short-hairpin RNA (shRNA) gene-silencing constructs. PMID:16381835
NPInter: the noncoding RNAs and protein related biomacromolecules interaction database. PMID:16381834
The Gene Set Builder: collation, curation, and distribution of sets of genes. PMID:16371163
The Gene Set Builder: collation, curation, and distribution of sets of genes. PMID:16371163
MachineProse: an ontological framework for scientific assertions. PMID:16357355
Probabilistic annotation of protein sequences based on functional classifications. PMID:16354297
Reconstruction and regulation of the central catabolic pathway in the thermophilic propionate-oxidizing syntroph Pelotomaculum thermopropionicum. PMID:16352836
SNEP: SNP-derived epitope prediction program for minor H antigens. PMID:16341860
Structure and architecture of the maize genome. PMID:16339807
Biochemical characterization of the recombinant human Drosophila homologues Timekeeper and Andante involved in the Drosophila circadian oscillator. PMID:16335535
Glycolytic enzyme interactions with yeast and skeletal muscle F-actin. PMID:16326908
DSD--an integrated, web-accessible database of Dehydrogenase Enzyme Stereospecificities. PMID:16318635
AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. PMID:16305757
Systematic discovery of new recognition peptides mediating protein interaction networks. PMID:16279839
Gene and genome duplication in Acanthamoeba polyphaga Mimivirus. PMID:16254344
Dual targeting is the rule for organellar aminoacyl-tRNA synthetases in Arabidopsis thaliana. PMID:16251277
Endosperm-preferred expression of maize genes as revealed by transcriptome-wide analysis of expressed sequence tags. PMID:16247562
Structural evolution of the protein kinase-like superfamily. PMID:16244704
Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. PMID:16237009
Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs). PMID:16221976
An inquiry into protein structure and genetic disease: introducing undergraduates to bioinformatics in a large introductory course. PMID:16220142
Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural networks. PMID:16202129
GeneSeer: a sage for gene names and genomic resources. PMID:16176584
PubNet: a flexible system for visualizing literature derived networks. PMID:16168087
Expression and characterization of a histidine-rich protein, Hpn: potential for Ni2+ storage in Helicobacter pylori. PMID:16164421
Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different. PMID:16105176
FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform. PMID:16083500
Functional annotation by identification of local surface similarities: a novel tool for structural genomics. PMID:16076399
Variations in plant metallothioneins: the heavy metal hyperaccumulator Thlaspi caerulescens as a study case. PMID:16052319
Effective function annotation through catalytic residue conservation. PMID:16037208
Signs of ancient and modern exon-shuffling are correlated to the distribution of ancient and modern domains along proteins. PMID:16034650
Detection and preliminary analysis of motifs in promoters of anaerobically induced genes of different plant species. PMID:16027132
Plant genome resources at the national center for biotechnology information. PMID:16010002
The MicrobesOnline Web site for comparative genomics. PMID:15998914
The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota. PMID:15995215
The effect of long-range interactions on the secondary structure formation of proteins. PMID:15987894
Theme discovery from gene lists for identification and viewing of multiple functional groups. PMID:15987504
Expressed sequence tags (ESTs) and simple sequence repeat (SSR) markers from octoploid strawberry (Fragaria x ananassa). PMID:15985176
Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea. PMID:15983865
Recent additions and improvements to the Onto-Tools. PMID:15980579
The bioinformatics resource for oral pathogens. PMID:15980574
GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists. PMID:15980570
MutDB services: interactive structural analysis of mutation data. PMID:15980479
SRide: a server for identifying stabilizing residues in proteins. PMID:15980477
QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns. PMID:15980465
KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. PMID:15980458
SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites. PMID:15980457
PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families. PMID:15980440
Differential gene expression in benznidazole-resistant Trypanosoma cruzi parasites. PMID:15980339
Distribution of immunodeficiency fact files with XML--from Web to WAP. PMID:15978138
Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora. PMID:15968079
Gene/protein name recognition based on support vector machine using dictionary as features. PMID:15960842
A sentence sliding window approach to extract protein annotations from biomedical articles. PMID:15960831
A simple approach for protein name identification: prospects and limits. PMID:15960827
Refinement and prediction of protein prenylation motifs. PMID:15960807
The role of alternative translation start sites in the generation of human protein diversity. PMID:15959805
FPC Web tools for rice, maize, and distribution. PMID:15888684
Plant protein annotation in the UniProt Knowledgebase. PMID:15888679
Detecting remotely related proteins by their interactions and sequence similarity. PMID:15883372
Precise and parallel characterization of coding polymorphisms, alternative splicing, and modifications in human proteins by mass spectrometry. PMID:15863400
Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals. PMID:15860772
Evidence of selection for low cognate amino acid bias in amino acid biosynthetic enzymes. PMID:15853887
Detailed protein sequence alignment based on Spectral Similarity Score (SSS). PMID:15850477
Super paramagnetic clustering of protein sequences. PMID:15804359
Columba: an integrated database of proteins, structures, and annotations. PMID:15801979
Comparative mapping of sequence-based and structure-based protein domains. PMID:15790427
Tyrosine phosphorylation of myosin heavy chain during skeletal muscle differentiation: an integrated bioinformatics approach. PMID:15790426
Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms. PMID:15784611
Evolution of distinct EGF domains with specific functions. PMID:15772310
Go molecular function terms are predictive of subcellular localization. PMID:15759622
Automatic detection of false annotations via binary property clustering. PMID:15755318
Protein structure and evolutionary history determine sequence space topology. PMID:15741509
Evolutionary profiles from the QR factorization of multiple sequence alignments. PMID:15741270
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes. PMID:15716312
A new example of viral intein in Mimivirus. PMID:15707490
Clustering the annotation space of proteins. PMID:15703069
Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. PMID:15684069
Large scale hierarchical clustering of protein sequences. PMID:15663796
A7DB: a relational database for mutational, physiological and pharmacological data related to the alpha7 nicotinic acetylcholine receptor. PMID:15661073
Computational prediction of human metabolic pathways from the complete human genome. PMID:15642094
EST pipeline system: detailed and automated EST data processing and mining. PMID:15629036
A database for G proteins and their interaction with GPCRs. PMID:15619328
ECgene: genome annotation for alternative splicing. PMID:15608289
Brassica ASTRA: an integrated database for Brassica genomic research. PMID:15608282
GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. PMID:15608279
openSputnik--a database to ESTablish comparative plant genomics using unsaturated sequence collections. PMID:15608275
AMPDB: the Arabidopsis Mitochondrial Protein Database. PMID:15608271
Organelle DB: a cross-species database of protein localization and function. PMID:15608270
HOPPSIGEN: a database of human and mouse processed pseudogenes. PMID:15608268
MetaRouter: bioinformatics for bioremediation. PMID:15608267
DynaProt 2D: an advanced proteomic database for dynamic online access to proteomes and two-dimensional electrophoresis gels. PMID:15608266
Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues. PMID:15608255
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. PMID:15608254
Inparanoid: a comprehensive database of eukaryotic orthologs. PMID:15608241
The European Bioinformatics Institute's data resources: towards systems biology. PMID:15608238
The UCSC Proteome Browser. PMID:15608236
Database resources of the National Center for Biotechnology Information. PMID:15608222
The Ashbya Genome Database (AGD)--a tool for the yeast community and genome biologists. PMID:15608214
The PEDANT genome database in 2005. PMID:15608204
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. PMID:15608195
REBASE--restriction enzymes and DNA methyltransferases. PMID:15608184
The SYSTERS Protein Family Database in 2005. PMID:15608183
ProtoNet 4.0: a hierarchical classification of one million protein sequences. PMID:15608180
SPD--a web-based secreted protein database. PMID:15608170
PSORTdb: a protein subcellular localization database for bacteria. PMID:15608169
The Universal Protein Resource (UniProt). PMID:15608167
Production of soluble mammalian proteins in Escherichia coli: identification of protein features that correlate with successful expression. PMID:15598350
Modeling the helicase domain of Brome mosaic virus 1a replicase. PMID:15597207
A functional hierarchical organization of the protein sequence space. PMID:15596019
Predicting functional family of novel enzymes irrespective of sequence similarity: a statistical learning approach. PMID:15585667
Prediction of functional class of novel viral proteins by a statistical learning method irrespective of sequence similarity. PMID:15582660
Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. PMID:15576358
Hidden localization motifs: naturally occurring peroxisomal targeting signals in non-peroxisomal proteins. PMID:15575971
prot4EST: translating expressed sequence tags from neglected genomes. PMID:15571632
A novel method for multiple alignment of sequences with repeated and shuffled elements. PMID:15520295
Lrg1p Is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. PMID:15514049
Implications for domain fusion protein-protein interactions based on structural information. PMID:15504241
Protein thiol modifications visualized in vivo. PMID:15502869
High-throughput computational and experimental techniques in structural genomics. PMID:15489337
Phylogenetic analysis of proteins associated in the four major energy metabolism systems: photosynthesis, aerobic respiration, denitrification, and sulfur respiration. PMID:15486691
'Conserved hypothetical' proteins: prioritization of targets for experimental study. PMID:15479782
Plasticity of influenza haemagglutinin fusion peptides and their interaction with lipid bilayers. PMID:15475582
Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease. PMID:15471992
Predicting subcellular localization via protein motif co-occurrence. PMID:15466294
PhyloGenie: automated phylome generation and analysis. PMID:15459293
Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant. PMID:15453914
Structural and functional anatomy of the globular domain of complement protein C1q. PMID:15388251
Profiling of generic anti-phosphopeptide antibodies and kinases with peptide microarrays using radioactive and fluorescence-based assays. PMID:15384422
Allermatch, a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines. PMID:15373946
SMARCA2 and THAP11: potential candidates for polyglutamine disorders as evidenced from polymorphism and protein-folding simulation studies. PMID:15368101
GASP: Gapped Ancestral Sequence Prediction for proteins. PMID:15350199
Positive selection in MAOA gene is human exclusive: determination of the putative amino acid change selected in the human lineage. PMID:15349769
A first-draft human protein-interaction map. PMID:15345047
EGPred: prediction of eukaryotic genes using ab initio methods after combining with sequence similarity approaches. PMID:15342559
On the modeling of snake venom serine proteinase interactions with benzamidine-based thrombin inhibitors. PMID:15322279
Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae. PMID:15317790
The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases. PMID:15307895
Call for an enzyme genomics initiative. PMID:15287973
Proteome-wide functional classification and identification of prokaryotic transmembrane proteins by transmembrane topology similarity comparison. PMID:15273311
A classification of disulfide patterns and its relationship to protein structure and function. PMID:15273305
Computational identification and characterization of novel genes from legumes. PMID:15266052
Electron capture dissociation distinguishes a single D-amino acid in a protein and probes the tertiary structure. PMID:15234367
Determinants of quaternary association in legume lectins. PMID:15215518
CHOP: parsing proteins into structural domains. PMID:15215452
LOCnet and LOCtarget: sub-cellular localization for structural genomics targets. PMID:15215440
iMolTalk: an interactive, internet-based protein structure analysis server. PMID:15215439
BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria. PMID:15215418
PRED-GPCR: GPCR recognition and family classification server. PMID:15215415
PrediSi: prediction of signal peptides and their cleavage positions. PMID:15215414
CysView: protein classification based on cysteine pairing patterns. PMID:15215409
MyHits: a new interactive resource for protein annotation and domain identification. PMID:15215405
The PredictProtein server. PMID:15215403
GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining. PMID:15215397
ADVICE: Automated Detection and Validation of Interaction by Co-Evolution. PMID:15215353
The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update. PMID:15215340
SMART amplification combined with cDNA size fractionation in order to obtain large full-length clones. PMID:15198809
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. PMID:15189570
Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome? PMID:15186489
Computational approaches to protein-protein interaction. PMID:15185965
Genome-wide identification of genes likely to be involved in human genetic disease. PMID:15181176
Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology. PMID:15180906
Effects of antidepressant drug imipramine on gene expression in rat prefrontal cortex. PMID:15176480
Glycogen synthase kinase-3beta mediates convergence of protection signaling to inhibit the mitochondrial permeability transition pore. PMID:15173880
A Fugu-Human Genome Synteny Viewer: web software for graphical display and annotation reports of synteny between Fugu genomic sequence and human genes. PMID:15141032
Progress towards mapping the universe of protein folds. PMID:15128436
ESTGenes: alternative splicing from ESTs in Ensembl. PMID:15123595
The Ensembl automatic gene annotation system. PMID:15123590
Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. PMID:15121896
A structural study for the optimisation of functional motifs encoded in protein sequences. PMID:15119965
Frequent occurrence of recognition site-like sequences in the restriction endonucleases. PMID:15113406
MolTalk--a programming library for protein structures and structure analysis. PMID:15096277
Functional classification of proteins and protein variants. PMID:15087495
The DNA sequence and analysis of human chromosome 13. PMID:15057823
A guide to building image-centric databases. PMID:15043221
Theoretical model of the three-dimensional structure of a sugar-binding protein from Pyrococcus horikoshii: structural analysis and sugar-binding simulations. PMID:15015939
MYRbase: analysis of genome-wide glycine myristoylation enlarges the functional spectrum of eukaryotic myristoylated proteins. PMID:15003124
LEON: multiple aLignment Evaluation Of Neighbours. PMID:14982955
Definition of supertypes for HLA molecules using clustering of specificity matrices. PMID:14963618
Mining core histone sequences from public protein databases. PMID:14870656
The Yersinia adhesin YadA collagen-binding domain structure is a novel left-handed parallel beta-roll. PMID:14765110
High-throughput protein analysis integrating bioinformatics and experimental assays. PMID:14762202
An unappreciated role for RNA surveillance. PMID:14759258
Gene indexing: characterization and analysis of NLM's GeneRIFs. PMID:14728215
VKCDB: voltage-gated potassium channel database. PMID:14715090
Restricted changes in major surface protein-2 (msp2) transcription after prolonged in vitro passage of Anaplasma phagocytophilum. PMID:14713314
Evolutionary families of peptidase inhibitors. PMID:14705960
The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols. PMID:14681489
ANTIMIC: a database of antimicrobial sequences. PMID:14681487
The mouse Gene Expression Database (GXD): updates and enhancements. PMID:14681482
GermOnline, a cross-species community knowledgebase on germ cell differentiation. PMID:14681481
LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system. PMID:14681468
FREP: a database of functional repeats in mouse cDNAs. PMID:14681460
MitoProteome: mitochondrial protein sequence database and annotation system. PMID:14681458
MitoP2, an integrated database on mitochondrial proteins in yeast and man. PMID:14681457
IntAct: an open source molecular interaction database. PMID:14681455
The aMAZE LightBench: a web interface to a relational database of cellular processes. PMID:14681453
MetaCyc: a multiorganism database of metabolic pathways and enzymes. PMID:14681452
BRENDA, the enzyme database: updates and major new developments. PMID:14681450
CADRE: the Central Aspergillus Data REpository. PMID:14681443
PHYTOPROT: a database of clusters of plant proteins. PMID:14681432
GeneDB: a resource for prokaryotic and eukaryotic organisms. PMID:14681429
VirGen: a comprehensive viral genome resource. PMID:14681415
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. PMID:14681408
Genew: the Human Gene Nomenclature Database, 2004 updates. PMID:14681406
3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes. PMID:14681404
SURFACE: a database of protein surface regions for functional annotation. PMID:14681403
The SUPERFAMILY database in 2004: additions and improvements. PMID:14681402
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. PMID:14681401
The distribution and query systems of the RCSB Protein Data Bank. PMID:14681399
MODBASE, a database of annotated comparative protein structure models, and associated resources. PMID:14681398
HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database. PMID:14681395
ArchDB: automated protein loop classification as a tool for structural genomics. PMID:14681390
The KNOTTIN website and database: a new information system dedicated to the knottin scaffold. PMID:14681383
EyeSite: a semi-automated database of protein families in the eye. PMID:14681381
The Pfam protein families database. PMID:14681378
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. PMID:14681376
DBSubLoc: database of protein subcellular localization. PMID:14681374
ProTherm, version 4.0: thermodynamic database for proteins and mutants. PMID:14681373
UniProt: the Universal Protein knowledgebase. PMID:14681372
ASD: the Alternative Splicing Database. PMID:14681360
Xpro: database of eukaryotic protein-encoding genes. PMID:14681359
ACLAME: a CLAssification of Mobile genetic Elements. PMID:14681355
Database resources of the National Center for Biotechnology Information: update. PMID:14681353
The EMBL Nucleotide Sequence Database. PMID:14681351
Genome evolution reveals biochemical networks and functional modules. PMID:14673105
Mutations in and near the second calcium-binding domain of integrin alphaIIb affect the structure and function of integrin alphaIIbbeta3. PMID:14670082
Organismal complexity, protein complexity, and gene duplicability. PMID:14660792
ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research. PMID:14630514
Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. PMID:14627742
The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PMID:14624247
POCUS: mining genomic sequence annotation to predict disease genes. PMID:14611661
GeneViTo: visualizing gene-product functional and structural features in genomic datasets. PMID:14594459
Development of human protein reference database as an initial platform for approaching systems biology in humans. PMID:14525934
PANDORA: keyword-based analysis of protein sets by integration of annotation sources. PMID:14500825
Evidence that rice and other cereals are ancient aneuploids. PMID:12953120
Molecular modeling of the membrane targeting of phospholipase C pleckstrin homology domains. PMID:12930993
Tropheryma whipplei Twist: a human pathogenic Actinobacteria with a reduced genome. PMID:12902375
Comparative protein structure modeling by iterative alignment, model building and model assessment. PMID:12853614
A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). PMID:12826619
Update on XplorMed: A web server for exploring scientific literature. PMID:12824439
JVirGel: Calculation of virtual two-dimensional protein gels. PMID:12824438
PARSESNP: A tool for the analysis of nucleotide polymorphisms. PMID:12824424
OntoBlast function: From sequence similarities directly to potential functional annotations by ontology terms. PMID:12824422
WU-Blast2 server at the European Bioinformatics Institute. PMID:12824421
ExPASy: The proteomics server for in-depth protein knowledge and analysis. PMID:12824418
SIRW: A web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches. PMID:12824415
EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences. PMID:12824408
iSPOT: A web tool to infer the interaction specificity of families of protein modules. PMID:12824399
BPROMPT: A consensus server for membrane protein prediction. PMID:12824397
SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence. PMID:12824396
Integrated databanks access and sequence/structure analysis services at the PBIL. PMID:12824334
SWISS-MODEL: An automated protein homology-modeling server. PMID:12824332
Tools for comparative protein structure modeling and analysis. PMID:12824331
SPINE 2: a system for collaborative structural proteomics within a federated database framework. PMID:12771210
A comparison of Pfam and MEROPS: two databases, one comprehensive, and one specialised. PMID:12740029
PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine. PMID:12689350
The RESID Database of Protein Modifications: 2003 developments. PMID:12520062 -
UniProt: the Universal Protein knowledgebase
PubMed citations: 1122.
1122 articles citing: UniProt: the Universal Protein knowledgebase
Next-Generation Molecular Discovery: From Bottom-Up In Vivo and In Vitro Approaches to In Silico Top-Down Approaches for Therapeutics Neogenesis. PMID:35330114
Proteomic Studies of Psoriasis. PMID:35327421
Transcriptome Analysis Revealed a Cold Stress-Responsive Transcription Factor, PaDREB1A, in Plumbago auriculata That Can Confer Cold Tolerance in Transgenic Arabidopsis thaliana. PMID:35310656
Comprehensive Transcriptome Analysis of Stem-Differentiating Xylem Upon Compression Stress in Cunninghamia Lanceolata. PMID:35309135
Affinity2Vec: drug-target binding affinity prediction through representation learning, graph mining, and machine learning. PMID:35306525
CerealESTDb: A Comprehensive Resource for Abiotic Stress-Responsive Annotated ESTs With Predicted Genes, Gene Ontology, and Metabolic Pathways in Major Cereal Crops. PMID:35281847
Combined Transcriptomic and Proteomic Profiling of E. coli under Microaerobic versus Aerobic Conditions: The Multifaceted Roles of Noncoding Small RNAs and Oxygen-Dependent Sensing in Global Gene Expression Control. PMID:35269716
PSnpBind: a database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow. PMID:35227289
Comparative transcriptomes of three different skin sites for the Asiatic toad (Bufo gargarizans). PMID:35223212
Investigating the Mechanism of Unilateral Cross Incompatibility in Longan (Dimocarpus longan Lour.) Cultivars (Yiduo × Shixia). PMID:35222456
Comparative Venomics of the Cryptic Cone Snail Species Virroconus ebraeus and Virroconus judaeus. PMID:35200678
Physiological and transcriptome analysis reveals the differences in nitrate content between lamina and midrib of flue-cured tobacco. PMID:35190651
Comparative transcriptome and weighted correlation network analyses reveal candidate genes involved in chlorogenic acid biosynthesis in sweet potato. PMID:35177832
Differential Transcriptome Analysis Reveals Genes Related to Low- and High-Temperature Stress in the Fall Armyworm, Spodoptera frugiperda. PMID:35173626
ProtPlat: an efficient pre-training platform for protein classification based on FastText. PMID:35148686
Leaf color formation mechanisms in Alternanthera bettzickiana elucidated by metabolite and transcriptome analyses. PMID:35128619
PANDA2: protein function prediction using graph neural networks. PMID:35118378
Systems scale characterization of circadian rhythm pathway in Camellia sinensis. PMID:35116135
In vitro and in silico studies on clinically important enzymes inhibitory activities of flavonoids isolated from Euphorbia pulcherrima. PMID:35112936
Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin. PMID:35100403
ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs. PMID:35073170
Transcriptomic profiling suggests candidate molecular responses to waterlogging in cassava. PMID:35061680
Microbial enzymes induce colitis by reactivating triclosan in the mouse gastrointestinal tract. PMID:35013263
Comparative Analysis of Neuropeptides in Homologous Interneurons and Prohormone Annotation in Nudipleuran Sea Slugs. PMID:35002782
Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases. PMID:35001887
Early transcriptomic response of the mycoparasite Sphaerodes mycoparasitica to the mycotoxigenic Fusarium graminearum 3-ADON, the cause of Fusarium head blight. PMID:34993050
Effects of Qinghuang Powder on Acute Myeloid Leukemia Based on Network Pharmacology, Molecular Docking, and In Vitro Experiments. PMID:34992668
Insight Into the Multiple Branches Traits of a Mutant in Larix olgensis by Morphological, Cytological, and Transcriptional Analyses. PMID:34992622
The cold adaption profiles of Pseudoalteromonas shioyasakiensis D1497 from Yap trench to cope with cold. PMID:34987981
The Tongue Squamous Carcinoma Cell Line Cal27 Primarily Employs Integrin α6β4-Containing Type II Hemidesmosomes for Adhesion Which Contribute to Anticancer Drug Sensitivity. PMID:34977030
Binding mode analysis of ABCA7 for the prediction of novel Alzheimer's disease therapeutics. PMID:34976306
Effect of polyethylene glycol 20 000 on protein extraction efficiency of formalin-fixed paraffin-embedded tissues in South Africa. PMID:34966662
Semi-Supervised Pipeline for Autonomous Annotation of SARS-CoV-2 Genomes. PMID:34960694
In Vitro Study of Licorice on IL-1β-Induced Chondrocytes and In Silico Approach for Osteoarthritis. PMID:34959737
Exploring complex and heterogeneous correlations on hypergraph for the prediction of drug-target interactions. PMID:34950907
Physiological, Biochemical and Transcriptomic Analysis of the Aerial Parts (Leaf-Blade and Petiole) of Asarum sieboldii Responding to Drought Stress. PMID:34948197
Comparative Transcriptomics and Gene Knockout Reveal Virulence Factors of Arthrinium phaeospermum in Bambusa pervariabilis × Dendrocalamopsis grandis. PMID:34946984
Comparative Transcriptomic Analysis of Regenerated Skins Provides Insights into Cutaneous Air-Breathing Formation in Fish. PMID:34943209
Functional conservation and divergence of the helix-turn-helix motif of E2 ubiquitin-conjugating enzymes. PMID:34942047
Revealing the Mechanism of Astragali Radix against Cancer-Related Fatigue by Network Pharmacology and Molecular Docking. PMID:34925533
CCR5 and Biological Complexity: The Need for Data Integration and Educational Materials to Address Genetic/Biological Reductionism at the Interface of Ethical, Legal, and Social Implications. PMID:34925370
Identification of Enzymes-specific Protein Domain Based on DDE, and Convolutional Neural Network. PMID:34917128
Mechanism and Therapeutic Opportunities of Histone Modifications in Chronic Liver Disease. PMID:34887768
Whole-Genome Sequencing of Acer catalpifolium Reveals Evolutionary History of Endangered Species. PMID:34878129
Identification of genes related to tipburn resistance in Chinese cabbage and preliminary exploration of its molecular mechanism. PMID:34861825
Comparative Transcriptome Sequencing of Taro Corm Development With a Focus on the Starch and Sucrose Metabolism Pathway. PMID:34858484
Phosphoproteomic Comparison of Four Eimeria tenella Life Cycle Stages. PMID:34829991
lncRNAfunc: a knowledgebase of lncRNA function in human cancer. PMID:34791419
Transcriptomic responses to drought stress in Polygonatum kingianum tuber. PMID:34781887
Comparing Early Transcriptomic Responses of 18 Soybean (Glycine max) Genotypes to Iron Stress. PMID:34769077
Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. PMID:34720581
A drug repositioning algorithm based on a deep autoencoder and adaptive fusion. PMID:34717542
Centrality of drug targets in protein networks. PMID:34715787
Transcriptome Analysis of Zygophyllum xanthoxylum Adaptation Strategies to Phosphate Stress. PMID:34712251
Bacterial phospholipases C with dual activity: phosphatidylcholinesterase and sphingomyelinase. PMID:34709730
Network-driven analysis of human-Plasmodium falciparum interactome: processes for malaria drug discovery and extracting in silico targets. PMID:34702263
Comparative genomics reveals molecular mechanisms underlying health and reproduction in cryptorchid mammals. PMID:34702182
Transcriptome Analysis Reveals the Complex Molecular Mechanisms of Brassica napus-Sclerotinia sclerotiorum Interactions. PMID:34691098
Arabidopsis MED18 Interaction With RNA Pol IV and V Subunit NRPD2a in Transcriptional Regulation of Plant Immune Responses. PMID:34691090
Comparative RNA-Seq Analyses of Solenopsis japonica (Hymenoptera: Formicidae) Reveal Gene in Response to Cold Stress. PMID:34681004
Single-molecule mechanical fingerprinting with DNA nanoswitch calipers. PMID:34675411
NCATS Inxight Drugs: a comprehensive and curated portal for translational research. PMID:34648031
Myofilament Phosphorylation in Stem Cell Treated Diastolic Heart Failure. PMID:34641704
The Biocontrol and Plant Growth-Promoting Properties of Streptomyces alfalfae XN-04 Revealed by Functional and Genomic Analysis. PMID:34630371
PTEN mutations in autism spectrum disorder and congenital hydrocephalus: developmental pleiotropy and therapeutic targets. PMID:34625286
Exploring the Potential Mechanism of Shennao Fuyuan Tang for Ischemic Stroke Based on Network Pharmacology and Molecular Docking. PMID:34603472
Genome-wide association study and transcriptome of olecranon-type traits in peach (Prunus persica L.) germplasm. PMID:34583632
Gene Mining for Conserved, Non-Annotated Proteins of Podosphaera xanthii Identifies Novel Target Candidates for Controlling Powdery Mildews by Spray-Induced Gene Silencing. PMID:34575773
Profiling of MicroRNAs in Midguts of Plutella xylostella Provides Novel Insights Into the Bacillus thuringiensis Resistance. PMID:34567090
VicPred: A Vibrio cholerae Genotype Prediction Tool. PMID:34566903
SSMFN: a fused spatial and sequential deep learning model for methylation site prediction. PMID:34541311
Compendium of causative genes and their encoded proteins for common monogenic disorders. PMID:34515378
Epigenetic Regulation of the Vascular Endothelium by Angiogenic LncRNAs. PMID:34512715
Characterization and Application of a Lytic Phage D10 against Multidrug-Resistant Salmonella. PMID:34452490
Investigation of Bemethyl Biotransformation Pathways by Combination of LC-MS/HRMS and In Silico Methods. PMID:34445727
Comparative Transcriptomic Analysis Reveals the Effects of Drought on the Biosynthesis of Methyleugenol in Asarum sieboldii Miq. PMID:34439899
IdentPMP: identification of moonlighting proteins in plants using sequence-based learning models. PMID:34434652
Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution. PMID:34433494
CANVS: an easy-to-use application for the analysis and visualization of mass spectrometry-based protein-protein interaction/association data. PMID:34432510
RNA-Seq, physiological, and biochemical analysis of burley tobacco response to nitrogen deficiency. PMID:34413327
A Chromosome-Scale Assembly of the Wheat Leaf Rust Pathogen Puccinia triticina Provides Insights Into Structural Variations and Genetic Relationships With Haplotype Resolution. PMID:34394053
Comparison of gene expression in the red imported fire ant (Solenopsis invicta) under different temperature conditions. PMID:34389756
Closely related Lak megaphages replicate in the microbiomes of diverse animals. PMID:34386733
Transcriptome and Small RNA Combined Sequencing Analysis of Cold Tolerance in Non-heading Chinese Cabbage. PMID:34367230
Transcriptome analysis of differentially expressed genes in chrysanthemum MET1 RNA interference lines. PMID:34366589
High-Quality Genome Assembly and Comprehensive Transcriptome of the Painted Lady Butterfly Vanessa cardui. PMID:34282459
Analysis of the Taxonomy and Pathogenic Factors of Pectobacterium aroidearum L6 Using Whole-Genome Sequencing and Comparative Genomics. PMID:34276610
Evaluation of Protein Purification Techniques and Effects of Storage Duration on LC-MS/MS Analysis of Archived FFPE Human CRC Tissues. PMID:34257588
Intrinsically disordered electronegative clusters improve stability and binding specificity of RNA-binding proteins. PMID:34246632
Full-Length Transcriptome Analysis Reveals Candidate Genes Involved in Terpenoid Biosynthesis in Artemisia argyi. PMID:34239538
Zetaproteobacteria Pan-Genome Reveals Candidate Gene Cluster for Twisted Stalk Biosynthesis and Export. PMID:34220764
Nanopore-based full-length transcriptome sequencing of Muscovy duck (Cairina moschata) ovary. PMID:34198095
MHCVision: estimation of global and local false discovery rate for MHC class I peptide binding prediction. PMID:34196671
Genome of the Single Human Chromosome 18 as a "Gold Standard" for Its Transcriptome. PMID:34194472
Multiple responses contribute to the enhanced drought tolerance of the autotetraploid Ziziphus jujuba Mill. var. spinosa. PMID:34193297
Tyr-Asp inhibition of glyceraldehyde 3-phosphate dehydrogenase affects plant redox metabolism. PMID:34156108
Analysis of Antimicrobial Peptide Metabolome of Bacterial Endophyte Isolated From Traditionally Used Medicinal Plant Millettia pachycarpa Benth. PMID:34149644
Predicting MHC class I binder: existing approaches and a novel recurrent neural network solution. PMID:34131696
A methyl esterase 1 (PvMES1) promotes the salicylic acid pathway and enhances Fusarium wilt resistance in common beans. PMID:34128089
Target identification among known drugs by deep learning from heterogeneous networks. PMID:34123272
Cabozantinib and dasatinib synergize to induce tumor regression in non-clear cell renal cell carcinoma. PMID:34095877
Protective Effects of Swertiamarin against Methylglyoxal-Induced Epithelial-Mesenchymal Transition by Improving Oxidative Stress in Rat Kidney Epithelial (NRK-52E) Cells. PMID:34067107
Network Pharmacology Prediction and Pharmacological Verification Mechanism of Yeju Jiangya Decoction on Hypertension. PMID:34055010
Comparative proteomic analysis to annotate the structural and functional association of the hypothetical proteins of S. maltophilia k279a and predict potential T and B cell targets for vaccination. PMID:34043709
De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn. PMID:34034673
Identification of phytochemicals from North African plants for treating Alzheimer's diseases and of their molecular targets by in silico network pharmacology approach. PMID:34012873
Potential role of chimeric genes in pathway-related gene co-expression modules. PMID:33980272
Antarctic Rahnella inusitata: A Producer of Cold-Stable β-Galactosidase Enzymes. PMID:33923711
A First Insight into the Gonad Transcriptome of Hong Kong Catfish (Clarias fuscus). PMID:33920938
Computational and In Vitro Analysis of Plumbagin's Molecular Mechanism for the Treatment of Hepatocellular Carcinoma. PMID:33912033
Extracellular Vesicles from Human Adipose-Derived Mesenchymal Stem Cells: A Review of Common Cargos. PMID:33904115
In-depth Site-specific Analysis of N-glycoproteome in Human Cerebrospinal Fluid and Glycosylation Landscape Changes in Alzheimer's Disease. PMID:33862227
The landscape of molecular chaperones across human tissues reveals a layered architecture of core and variable chaperones. PMID:33846299
Genes Encoding Microbial Acyl Coenzyme A Binding Protein/Diazepam-Binding Inhibitor Orthologs Are Rare in the Human Gut Microbiome and Show No Links to Obesity. PMID:33837018
Genome-resolved metagenomics using environmental and clinical samples. PMID:33758906
Genome-wide identification of MIKC-type genes related to stamen and gynoecium development in Liriodendron. PMID:33753780
A haustorial-expressed lytic polysaccharide monooxygenase from the cucurbit powdery mildew pathogen Podosphaera xanthii contributes to the suppression of chitin-triggered immunity. PMID:33742545
DisCoVering potential candidates of RNAi-based therapy for COVID-19 using computational methods. PMID:33680575
Protein domain identification methods and online resources. PMID:33680357
Human Antibody Responses Following Vaccinia Immunization Using Protein Microarrays and Correlation With Cell-Mediated Immunity and Antibody-Dependent Cellular Cytotoxicity Responses. PMID:33675226
Effect of Syringopicroside Extracted from Syringa oblata Lindl on the Biofilm Formation of Streptococcus suis. PMID:33673668
Mayday sustains trans-synaptic BMP signaling required for synaptic maintenance with age. PMID:33667157
Borrelia burgdorferi infection modifies protein content in saliva of Ixodes scapularis nymphs. PMID:33663385
In silico screening and analysis of nonsynonymous SNPs in human CYP1A2 to assess possible associations with pathogenicity and cancer susceptibility. PMID:33654112
Ca2+-saturated calmodulin binds tightly to the N-terminal domain of A-type fibroblast growth factor homologous factors. PMID:33639159
Transcriptome analysis of the role of autophagy in plant response to heat stress. PMID:33635879
Prediction of drug-target binding affinity using similarity-based convolutional neural network. PMID:33627791
An Introduction to Whole-Metagenome Shotgun Sequencing Studies. PMID:33606255
Identification of differentially expressed genes involved in amino acid and lipid accumulation of winter turnip rape (Brassica rapa L.) in response to cold stress. PMID:33556109
Differential expression analysis and identification of sex-related genes by gonad transcriptome sequencing in estradiol-treated and non-treated Ussuri catfish Pseudobagrus ussuriensis. PMID:33523351
In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b. PMID:33520197
Study on mechanism of matrine in treatment of COVID-19 combined with liver injury by network pharmacology and molecular docking technology. PMID:33517789
Amynthas corticis genome reveals molecular mechanisms behind global distribution. PMID:33514865
Exploring the mechanism of aidi injection for lung cancer by network pharmacology approach and molecular docking validation. PMID:33506873
A candidate gene association analysis identifies SNPs potentially involved in drought tolerance in European beech (Fagus sylvatica L.). PMID:33504857
The hard clam genome reveals massive expansion and diversification of inhibitors of apoptosis in Bivalvia. PMID:33487168
BSR-Seq analysis provides insights into the cold stress response of Actinidia arguta F1 populations. PMID:33482717
Current cancer driver variant predictors learn to recognize driver genes instead of functional variants. PMID:33441128
Industry-scale application and evaluation of deep learning for drug target prediction. PMID:33430964
Proteomic identification and validation of novel interactions of the putative tumor suppressor PRELP with membrane proteins including IGFI-R and p75NTR. PMID:33428936
Transcriptomic landscaping of core genes and pathways of mild and severe psoriasis vulgaris. PMID:33416099
Transcriptional response of Asarum heterotropoides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. leaves grown under full and partial daylight conditions. PMID:33407099
Application of a Novel Lytic Podoviridae Phage Pu20 for Biological Control of Drug-Resistant Salmonella in Liquid Eggs. PMID:33406779
Differentiating Two Closely Related Alexandrium Species Using Comparative Quantitative Proteomics. PMID:33374829
RELT stains prominently in B-cell lymphomas and binds the hematopoietic transcription factor MDFIC. PMID:33367115
ProdMX: Rapid query and analysis of protein functional domain based on compressed sparse matrices. PMID:33335686
Mutational survivorship bias: The case of PNKP. PMID:33332469
Structural insights and evaluation of the potential impact of missense variants on the interactions of SLIT2 with ROBO1/4 in cancer progression. PMID:33318575
Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07. PMID:33316871
Deciphering the functional role of hypothetical proteins from Chloroflexus aurantiacs J-10-f1 using bioinformatics approach. PMID:33313333
Integrated Physiological and Transcriptomic Analyses Reveal a Regulatory Network of Anthocyanin Metabolism Contributing to the Ornamental Value in a Novel Hybrid Cultivar of Camellia Japonica. PMID:33297392
Bioinformatic analysis and functional predictions of selected regeneration-associated transcripts expressed by zebrafish microglia. PMID:33287696
Study on Medication Rules of Traditional Chinese Medicine against Antineoplastic Drug-Induced Cardiotoxicity Based on Network Pharmacology and Data Mining. PMID:33281914
Mobilization of Iron Stored in Bacterioferritin Is Required for Metabolic Homeostasis in Pseudomonas aeruginosa. PMID:33255203
Dataset of full-length transcriptome assembly and annotation of apocynum venetum using pacbio sequel II. PMID:33251304
Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance. PMID:33240317
Genome-wide identification of Argonautes in Solanaceae with emphasis on potato. PMID:33239724
The urgent need for pan-antiviral agents: from multitarget discovery to multiscale design. PMID:33225723
Identification and Characterization of the Heat-Induced Plastidial Stress Granules Reveal New Insight Into Arabidopsis Stress Response. PMID:33224174
HumDLoc: Human Protein Subcellular Localization Prediction Using Deep Neural Network. PMID:33214771
The Cyclically Seasonal Drosophila subobscura Inversion O7 Originated From Fragile Genomic Sites and Relocated Immunity and Metabolic Genes. PMID:33193649
Transcriptome analysis reveals mechanism of early ripening in Kyoho grape with hydrogen peroxide treatment. PMID:33176674
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. PMID:33173863
Computational drug re-purposing targeting the spike glycoprotein of SARS-CoV-2 as an effective strategy to neutralize COVID-19. PMID:33160938
The Transcriptome of Cunninghamia lanceolata male/female cone reveal the association between MIKC MADS-box genes and reproductive organs development. PMID:33153428
Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants. PMID:33106425
Systems pharmacology in combination with proteomics reveals underlying mechanisms of Xihuang pill against triple-negative breast cancer. PMID:33092442
The on-premise data sharing infrastructure e!DAL: Foster FAIR data for faster data acquisition. PMID:33090199
TNFPred: identifying tumor necrosis factors using hybrid features based on word embeddings. PMID:33087125
mRNA and miRNA expression profile reveals the role of miR-31 overexpression in neural stem cell. PMID:33067542
m6A RNA Methylation in Marine Plants: First Insights and Relevance for Biological Rhythms. PMID:33053767
A Sweep of Earth's Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease. PMID:33053371
Agasicles hygrophila attack increases nerolidol synthase gene expression in Alternanthera philoxeroides, facilitating host finding. PMID:33046727
The first versatile human iPSC-based model of ectopic virus induction allows new insights in RNA-virus disease. PMID:33033381
Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities. PMID:33028186
Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis. PMID:33004908
Tailor-made exopolysaccharides-CRISPR-Cas9 mediated genome editing in Paenibacillus polymyxa. PMID:32995508
Investigating the structural impacts of a novel missense variant identified with whole exome sequencing in an Egyptian patient with propionic acidemia. PMID:32995289
Extracellular vesicles in patients in the acute phase of psychosis and after clinical improvement: an explorative study. PMID:32995075
A Review of Prostanoid Receptors: Expression, Characterization, Regulation, and Mechanism of Action. PMID:32970276
Identification of destabilizing SNPs in SARS-CoV2-ACE2 protein and spike glycoprotein: implications for virus entry mechanisms. PMID:32964802
Development of robust targeted proteomics assays for cerebrospinal fluid biomarkers in multiple sclerosis. PMID:32963504
Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era. PMID:32952397
Diversity of Conopeptides and Their Precursor Genes of Conus Litteratus. PMID:32937857
Single-molecule real-time sequencing of the full-length transcriptome of loquat under low-temperature stress. PMID:32915882
Repertoire-scale determination of class II MHC peptide binding via yeast display improves antigen prediction. PMID:32887877
Identification of most influential co-occurring gene suites for gastrointestinal cancer using biomedical literature mining and graph-based influence maximization. PMID:32883271
Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State. PMID:32879348
Simple Targeted Assays for Metabolic Pathways and Signaling: A Powerful Tool for Targeted Proteomics. PMID:32865986
Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress. PMID:32859149
New Plasmodium vivax Genomes From the China-Myanmar Border. PMID:32849480
Identification of olfactory genes of a forensically important blow fly, Aldrichina grahami (Diptera: Calliphoridae). PMID:32844056
Screening and identification of miRNAs related to sexual differentiation of strobili in Ginkgo biloba by integration analysis of small RNA, RNA, and degradome sequencing. PMID:32842951
Large freshwater phages with the potential to augment aerobic methane oxidation. PMID:32839536
Proteome reallocation from amino acid biosynthesis to ribosomes enables yeast to grow faster in rich media. PMID:32817546
Potential Role of Photosynthesis in the Regulation of Reactive Oxygen Species and Defence Responses to Blumeria graminis f. sp. tritici in Wheat. PMID:32796723
Analysis of Salmonella typhimurium Protein-Targeting in the Nucleus of Host Cells and the Implications in Colon Cancer: An in-silico Approach. PMID:32765017
A Novel Network Pharmacology Strategy to Decode Metabolic Biomarkers and Targets Interactions for Depression. PMID:32760300
Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation. PMID:32747737
Genomic, transcriptomic, and protein landscape profile of CFTR and cystic fibrosis. PMID:32734384
A convenient protein library for spectroscopic calibrations. PMID:32728409
De novo assembly and Transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics. PMID:32727354
Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed. PMID:32727352
Mass-Spectrometry Based Proteome Comparison of Extracellular Vesicle Isolation Methods: Comparison of ME-kit, Size-Exclusion Chromatography, and High-Speed Centrifugation. PMID:32722497
Integrated transcriptomic and metabolomic analyses of yellow horn (Xanthoceras sorbifolia) in response to cold stress. PMID:32706804
Transcriptomic differences between male and female Trachycarpus fortunei. PMID:32704095
Biotin Synthesis in Ralstonia eutropha H16 Utilizes Pimeloyl Coenzyme A and Can Be Regulated by the Amount of Acceptor Protein. PMID:32680858
De novo sequencing of Bletilla striata (Orchidaceae) transcriptome and identification of genes involved in polysaccharide biosynthesis. PMID:32609279
Identification of vital candidate microRNA/mRNA pairs regulating ovule development using high-throughput sequencing in hazel. PMID:32605594
Long-Read-Based de novo Genome Assembly and Comparative Genomics of the Wheat Leaf Rust Pathogen Puccinia triticina Identifies Candidates for Three Avirulence Genes. PMID:32582280
Cellular polyamines condense hyperphosphorylated Tau, triggering Alzheimer's disease. PMID:32572101
Are synthetic biology standards applicable in everyday research practice? PMID:32567248
Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type. PMID:32546614
Data of de novo assembly and annotation of transcriptome from Aspidistra fenghuangensis (Asparagaceae: Nolinoideae). PMID:32529008
Gray whale transcriptome reveals longevity adaptations associated with DNA repair and ubiquitination. PMID:32515539
OsCpn60β1 is Essential for Chloroplast Development in Rice (Oryza sativa L.). PMID:32512821
SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae). PMID:32509454
Mutational bias and the protein code shape the evolution of splicing enhancers. PMID:32504065
Evidence of Echolocation in the Common Shrew from Molecular Convergence with Other Echolocating Mammals. PMID:32494297
Excessive Homeostatic Gain in Spinal Motoneurons in a Mouse Model of Amyotrophic Lateral Sclerosis. PMID:32493926
Transcriptome Analysis Identifies Candidate Target Genes Involved in Glyphosate-Resistance Mechanism in Lolium multiflorum. PMID:32481698
Microwave supported hydrolysis prepares Bacillus spores for proteomic analysis. PMID:32476986
HyperQuant-A Computational Pipeline for Higher Order Multiplexed Quantitative Proteomics. PMID:32455206
TASL is the SLC15A4-associated adaptor for IRF5 activation by TLR7-9. PMID:32433612
Comprehensive germline genomic profiles of children, adolescents and young adults with solid tumors. PMID:32371905
Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1. PMID:32356891
The crystal structure of the TonB-dependent transporter YncD reveals a positively charged substrate-binding site. PMID:32355044
Integrated Analysis of mRNA and microRNA Elucidates the Regulation of Glycyrrhizic Acid Biosynthesis in Glycyrrhiza uralensis Fisch. PMID:32353999
Single-molecule long-read sequencing of the full-length transcriptome of Rhododendron lapponicum L. PMID:32317724
Characterization of RNP Networks of PUM1 and PUM2 Post-Transcriptional Regulators in TCam-2 Cells, a Human Male Germ Cell Model. PMID:32316190
Computational Modeling and Analysis to Predict Intracellular Parasite Epitope Characteristics Using Random Forest Technique. PMID:32309231
Full-length transcriptome sequencing and comparative transcriptomic analysis to uncover genes involved in early gametogenesis in the gonads of Amur sturgeon (Acipenser schrenckii). PMID:32308726
ASFVdb: an integrative resource for genomic and proteomic analyses of African swine fever virus. PMID:32294195
Bacterial colonization reprograms the neonatal gut metabolome. PMID:32284564
New mutation of the ceruloplasmin gene in the case of a neurologically asymptomatic patient with microcytic anaemia, obesity and supposed Wilson's disease. PMID:32264837
Chromosome doubling mediates superior drought tolerance in Lycium ruthenicum via abscisic acid signaling. PMID:32257226
Transcriptome analysis of the response provided by Lasiopodomys mandarinus to severe hypoxia includes enhancing DNA repair and damage prevention. PMID:32256671
Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. PMID:32194980
First transcriptome of the Neotropical pest Euschistus heros (Hemiptera: Pentatomidae) with dissection of its siRNA machinery. PMID:32184426
Gene Expression Profiling Indicated Diverse Functions and Characteristics of Core Genes in Pea Aphid. PMID:32183501
Long-range replica exchange molecular dynamics guided drug repurposing against tyrosine kinase PtkA of Mycobacterium tuberculosis. PMID:32157138
Structural Biology in the Multi-Omics Era. PMID:32129623
User guide for the discovery of potential drugs via protein structure prediction and ligand docking simulation. PMID:32108318
OmixLitMiner: A Bioinformatics Tool for Prioritizing Biological Leads from 'Omics Data Using Literature Retrieval and Data Mining. PMID:32092871
Comparative in-silico proteomic analysis discerns potential granuloma proteins of Yersinia pseudotuberculosis. PMID:32080254
Genome-scale metabolic reconstruction and in silico analysis of the rice leaf blight pathogen, Xanthomonas oryzae. PMID:32068953
3D mapping of native extracellular matrix reveals cellular responses to the microenvironment. PMID:32055794
Designing minimal genomes using whole-cell models. PMID:32047145
Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates. PMID:32046633
Transcriptomic and Metabolomic Changes Triggered by Fusarium solani in Common Bean (Phaseolus vulgaris L.). PMID:32046085
CRISPR-Cas12a Possesses Unconventional DNase Activity that Can Be Inactivated by Synthetic Oligonucleotides. PMID:32045875
Transcriptome analysis of terpenoid biosynthetic genes and simple sequence repeat marker screening in Eucommia ulmoides. PMID:32040708
Text-mining in cancer research may help identify effective treatments. PMID:32038938
Comparative RNA-Seq Analysis of Differentially Expressed Genes in the Epididymides of Yak and Cattleyak. PMID:32030088
Investigation of hub genes and their nonsynonymous single nucleotide polymorphism analysis in Plasmodium falciparum for designing therapeutic methodologies using next-generation sequencing approach. PMID:32029961
Pentatricopeptide repeat protein MID1 modulates nad2 intron 1 splicing and Arabidopsis development. PMID:32029763
The developmental dynamics of the sweet sorghum root transcriptome elucidate the differentiation of apoplastic barriers. PMID:32024414
Knowledge-enhanced biomedical named entity recognition and normalization: application to proteins and genes. PMID:32000677
Network-based prediction of drug-target interactions using an arbitrary-order proximity embedded deep forest. PMID:31971579
Accumulation of genetic variants associated with immunity in the selective breeding of broilers. PMID:31952471
Defining the TLT-1 interactome from resting and activated human platelets. PMID:31923473
How to Illuminate the Druggable Genome Using Pharos. PMID:31898878
Serum coiled-coil domain containing 25 protein as a potential screening/diagnostic biomarker for cholangiocarcinoma. PMID:31897206
Immunity-related genes and signaling pathways under hypoxic stresses in Haliotis diversicolor: a transcriptome analysis. PMID:31874975
Metabolic Modeling Elucidates the Transactions in the Rumen Microbiome and the Shifts Upon Virome Interactions. PMID:31866953
Proteomics Analysis of Early Developmental Stages of Zebrafish Embryos. PMID:31861170
Combined De Novo Transcriptome and Metabolome Analysis of Common Bean Response to Fusarium oxysporum f. sp. phaseoli Infection. PMID:31842411
Electrostatic Surface Potential of Macrophages Correlates with Their Functional Phenotype. PMID:31838662
A Perspective on the Confident Comparison of Glycoprotein Site-Specific Glycosylation in Sample Cohorts. PMID:31833756
Dynamics, nanomechanics and signal transduction in reelin repeats. PMID:31831824
Integrative Multi-Kinase Approach for the Identification of Potent Antiplasmodial Hits. PMID:31824917
Rapamycin persistently improves cardiac function in aged, male and female mice, even following cessation of treatment. PMID:31823466
Molecular Analysis of UV-C Induced Resveratrol Accumulation in Polygonum cuspidatum Leaves. PMID:31817915
Results of multigene panel testing in familial cancer cases without genetic cause demonstrated by single gene testing. PMID:31811167
Identification of Key Genes Involved in Embryo Development and Differential Oil Accumulation in Two Contrasting Maize Genotypes. PMID:31805727
Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion. PMID:31791230
Comparative Analysis of Transcriptome Responses to Cold Stress in Galeruca daurica (Coleoptera: Chrysomelidae). PMID:31752020
Phosphorylation-dependent activity-based conformational changes in P21-activated kinase family members and screening of novel ATP competitive inhibitors. PMID:31738805
Arabidopsis ZINC FINGER PROTEIN1 Acts Downstream of GL2 to Repress Root Hair Initiation and Elongation by Directly Suppressing bHLH Genes. PMID:31732703
Integrated transcriptome and miRNA analysis uncovers molecular regulators of aerial stem-to-rhizome transition in the medical herb Gynostemma pentaphyllum. PMID:31730459
Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response. PMID:31729949
Leveraging word embeddings and medical entity extraction for biomedical dataset retrieval using unstructured texts. PMID:31725862
An influential meal: host plant dependent transcriptional variation in the beet armyworm, Spodoptera exigua (Lepidoptera: Noctuidae). PMID:31722664
Exploring the Molecular Mechanism underlying the Stable Purple-Red Leaf Phenotype in Lagerstroemia indica cv. Ebony Embers. PMID:31718025
ConSurf-DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins. PMID:31702846
Transcriptome sequencing of Salvia miltiorrhiza after infection by its endophytic fungi and identification of genes related to tanshinone biosynthesis. PMID:31694427
Melittin inhibits proliferation, migration and invasion of bladder cancer cells by regulating key genes based on bioinformatics and experimental assays. PMID:31691530
Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts. PMID:31684862
Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species. PMID:31675926
Pilot data of serum proteins from children with autism spectrum disorders. PMID:31673578
Evolutionary coupling saturation mutagenesis: Coevolution-guided identification of distant sites influencing Bacillus naganoensis pullulanase activity. PMID:31665817
Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes. PMID:31665645
NaCl treatment markedly enhanced pollen viability and pollen preservation time of euhalophyte Suaeda salsa via up regulation of pollen development-related genes. PMID:31654246
Protein secretion in wild-type and Othac1 mutant strains of thermotolerant methylotrophic yeast Ogataea thermomethanolica TBRC656. PMID:31654213
PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics. PMID:31647547
An integrated epigenome and transcriptome analysis identifies PAX2 as a master regulator of drug resistance in high grade pancreatic ductal adenocarcinoma. PMID:31622355
Search for Nutritional Fitness Traits in a Biological Pest Control Agent Harmonia axyridis Using Comparative Transcriptomics. PMID:31620008
Protease-associated import systems are widespread in Gram-negative bacteria. PMID:31613892
Analysis of a fully infectious bio-orthogonally modified human virus reveals novel features of virus cell entry. PMID:31589653
Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate. PMID:31583016
Protective Role of Leaf Variegation in Pittosporum tobira under Low Temperature: Insights into the Physio-Biochemical and Molecular Mechanisms. PMID:31574927
De novo transcriptome assembly and analysis of the freshwater araphid diatom Fragilaria radians, Lake Baikal. PMID:31562323
Chalcones as a basis for computer-aided drug design: innovative approaches to tackle malaria. PMID:31556721
Domain-based Comparative Analysis of Bacterial Proteomes: Uniqueness, Interactions, and the Dark Matter. PMID:31555062
Temporal analysis of vaginal proteome reveals developmental changes in lower reproductive tract of gilts across the first two weeks postnatal. PMID:31519940
Comparative Genomic and Phylogenomic Analyses Clarify Relationships Within and Between Bacillus cereus and Bacillus thuringiensis: Proposal for the Recognition of Two Bacillus thuringiensis Genomovars. PMID:31507580
Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans. PMID:31504044
Differential Regulation of Anthocyanins in Green and Purple Turnips Revealed by Combined De Novo Transcriptome and Metabolome Analysis. PMID:31500111
Data-Driven Construction of Antitumor Agents with Controlled Polypharmacology. PMID:31497954
Transcriptome Analysis Reveals Key Seed-Development Genes in Common Buckwheat (Fagopyrum esculentum). PMID:31484314
A Structure-Informed Atlas of Human-Virus Interactions. PMID:31474372
De novo transcriptome assembly for four species of crustose coralline algae and analysis of unique orthologous genes. PMID:31471551
The Reason for Growth Inhibition of Ulmus pumila 'Jinye': Lower Resistance and Abnormal Development of Chloroplasts Slow Down the Accumulation of Energy. PMID:31470529
Neuron-generated thrombin induces a protective astrocyte response via protease activated receptors. PMID:31453648
Retained Acetylated Histone Four in Bull Sperm Associated With Fertility. PMID:31417913
Identification of Wolbachia-Responsive miRNAs in the Small Brown Planthopper, Laodelphax striatellus. PMID:31396100
A genome-wide positioning systems network algorithm for in silico drug repurposing. PMID:31375661
Multigene Biomarkers of Pyrethroid Exposure: Exploratory Experiments. PMID:31365144
Genetic basis of functional variability in adhesion G protein-coupled receptors. PMID:31363148
Humanized yeast genetic interaction mapping predicts synthetic lethal interactions of FBXW7 in breast cancer. PMID:31351478
Natural and non-toxic products from Fabaceae Brazilian plants as a replacement for traditional antifouling biocides: an inhibition potential against initial biofouling. PMID:31317435
VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases. PMID:31317185
Defective HNF4alpha-dependent gene expression as a driver of hepatocellular failure in alcoholic hepatitis. PMID:31311938
RAFTS3G: an efficient and versatile clustering software to analyses in large protein datasets. PMID:31307371
In situ imaging of the bacterial flagellar motor disassembly and assembly processes. PMID:31304634
Delineating the Plausible Molecular Vaccine Candidates and Drug Targets of Multidrug-Resistant Acinetobacter baumannii. PMID:31281799
Whole-Genome Sequencing of the Giant Devil Catfish, Bagarius yarrelli. PMID:31274158
Interoperable chemical structure search service. PMID:31254167
Metagenomic analysis of bile salt biotransformation in the human gut microbiome. PMID:31234773
BCScreen: A gene panel to test for breast carcinogenesis in chemical safety screening. PMID:31218268
Analysis of the TP53 Deleterious Single Nucleotide Polymorphisms Impact on Estrogen Receptor Alpha-p53 Interaction: A Machine Learning Approach. PMID:31216622
Chemosensory Gene Families in the Oligophagous Pear Pest Cacopsylla chinensis (Hemiptera: Psyllidae). PMID:31212973
Characterization of intellectual disability and autism comorbidity through gene panel sequencing. PMID:31209962
Transcriptome analysis of finger millet (Eleusine coracana (L.) Gaertn.) reveals unique drought responsive genes. PMID:31204698
FunPred 3.0: improved protein function prediction using protein interaction network. PMID:31198622
Construction and analysis of an interologous protein-protein interaction network of Camellia sinensis leaf (TeaLIPIN) from RNA-Seq data sets. PMID:31197449
Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data. PMID:31196115
Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species. PMID:31188829
Identification of miRNAs and their target genes in Larix olgensis and verified of differential expression miRNAs. PMID:31185902
Exploring the tissue tropism of pseudorabies virus based on miRNA level analysis. PMID:31185898
Purple: A Computational Workflow for Strategic Selection of Peptides for Viral Diagnostics Using MS-Based Targeted Proteomics. PMID:31181768
Transcriptomic Analysis Identifies New Non-Target Site Glyphosate-Resistance Genes in Conyza bonariensis. PMID:31181629
ANASTASIA: An Automated Metagenomic Analysis Pipeline for Novel Enzyme Discovery Exploiting Next Generation Sequencing Data. PMID:31178894
Comparative transcriptomic and proteomic analysis of yellow shell and black shell pearl oysters, Pinctada fucata martensii. PMID:31176356
A survey of transcriptome complexity using PacBio single-molecule real-time analysis combined with Illumina RNA sequencing for a better understanding of ricinoleic acid biosynthesis in Ricinus communis. PMID:31170917
Comprehensive transcriptome analysis reveals genes potentially involved in isoflavone biosynthesis in Pueraria thomsonii Benth. PMID:31163077
Integrative Analysis of Somatic Mutations in Non-coding Regions Altering RNA Secondary Structures in Cancer Genomes. PMID:31160636
Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification. PMID:31145734
A haplotype-resolved draft genome of the European sardine (Sardina pilchardus). PMID:31112613
6mA-DNA-binding factor Jumu controls maternal-to-zygotic transition upstream of Zelda. PMID:31101825
Geometric description of self-interaction potential in symmetric protein complexes. PMID:31101822
PathMe: merging and exploring mechanistic pathway knowledge. PMID:31092193
Effects of 12 Weeks of Hypertrophy Resistance Exercise Training Combined with Collagen Peptide Supplementation on the Skeletal Muscle Proteome in Recreationally Active Men. PMID:31091754
Mutplot: An easy-to-use online tool for plotting complex mutation data with flexibility. PMID:31091262
What lies beneath? Molecular evolution during the radiation of caecilian amphibians. PMID:31072350
Genomewide Profiling of the Enterococcus faecalis Transcriptional Response to Teixobactin Reveals CroRS as an Essential Regulator of Antimicrobial Tolerance. PMID:31068434
Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus). PMID:31060501
Effect of triploidy on liver gene expression in coho salmon (Oncorhynchus kisutch) under different metabolic states. PMID:31053056
Anti-human Interleukin(IL)-4 Clone 8D4-8 Cross-Reacts With Myosin-9 Associated With Apoptotic Cells and Should Not Be Used for Flow Cytometry Applications Querying IL-4 Expression. PMID:31024909
Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements. PMID:31020842
The first draft genomes of the ant Formica exsecta, and its Wolbachia endosymbiont reveal extensive gene transfer from endosymbiont to host. PMID:30991952
A photocleavable surfactant for top-down proteomics. PMID:30988469
Quantitative Proteomic Analysis of Human Seminal Plasma from Normozoospermic and Asthenozoospermic Individuals. PMID:30984777
Salt-Enhanced Reproductive Development of Suaeda salsa L. Coincided With Ion Transporter Gene Upregulation in Flowers and Increased Pollen K+ Content. PMID:30984214
Identification of Phage Viral Proteins With Hybrid Sequence Features. PMID:30972038
Comparative transcriptome analyses revealed different heat stress responses in high- and low-GS Brassica alboglabra sprouts. PMID:30947685
GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamilies. PMID:30943284
MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps. PMID:30941409
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. PMID:30936548
Bioinformatic analysis of Chinese hamster ovary host cell protein lipases. PMID:30911190
Measuring the importance of vertices in the weighted human disease network. PMID:30901770
Role of the L-PGDS-PGD2-DP1 receptor axis in sleep regulation and neurologic outcomes. PMID:30893431
Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects. PMID:30885123
Predicting MicroRNA Target Genes and Identifying Hub Genes in IIA Stage Colon Cancer Patients Using Bioinformatics Analysis. PMID:30881993
Network-based prediction of drug combinations. PMID:30867426
LC‑MS/MS proteomic analysis revealed novel associations of 37 proteins with T2DM and notable upregulation of immunoglobulins. PMID:30864687
Transcriptomic Analysis for Indica and Japonica Rice Varieties under Aluminum Toxicity. PMID:30823582
The golden death bacillus Chryseobacterium nematophagum is a novel matrix digesting pathogen of nematodes. PMID:30813925
Reticulate evolution in eukaryotes: Origin and evolution of the nitrate assimilation pathway. PMID:30789903
Endopeptidase Regulation as a Novel Function of the Zur-Dependent Zinc Starvation Response. PMID:30782657
Interferon-stimulated gene 15 modulates cell migration by interacting with Rac1 and contributes to lymph node metastasis of oral squamous cell carcinoma cells. PMID:30765861
A polyextremophilic alcohol dehydrogenase from the Atlantis II Deep Red Sea brine pool. PMID:30761247
In silico prediction of prolactin molecules as a tool for equine genomics reproduction. PMID:30740642
In silico structural homology modeling of nif A protein of rhizobial strains in selective legume plants. PMID:30733794
Computational Investigation on Electrostatic Loop Mutants Instigating Destabilization and Aggregation on Human SOD1 Protein Causing Amyotrophic Lateral Sclerosis. PMID:30701485
Genome-Wide Analysis of Domain-Swap Predicted Products in the Genome of Anti-Stress Medicinal Plant: Ocimum tenuiflorum. PMID:30692846
Identification of differentially expressed non-coding RNAs and mRNAs involved in Qi stagnation and blood stasis syndrome. PMID:30679994
Virulence Characteristics and an Action Mode of Antibiotic Resistance in Multidrug-Resistant Pseudomonas aeruginosa. PMID:30679735
Genomic sequencing, genome-scale metabolic network reconstruction, and in silico flux analysis of the grape endophytic fungus Alternaria sp. MG1. PMID:30678677
Molecular Mechanism of Cancer Susceptibility Associated with Fok1 Single Nucleotide Polymorphism of VDR in Relation to Breast Cancer. PMID:30678432
De Novo Sequencing and Hybrid Assembly of the Biofuel Crop Jatropha curcas L.: Identification of Quantitative Trait Loci for Geminivirus Resistance. PMID:30669588
The Genetics of Mating Song Evolution Underlying Rapid Speciation: Linking Quantitative Variation to Candidate Genes for Behavioral Isolation. PMID:30647070
Interfering PLD1-PED/PEA15 interaction using self-inhibitory peptides: An in silico study to discover novel therapeutic candidates against type 2 diabetes. PMID:30622421
Recent Advances on the Machine Learning Methods in Identifying DNA Replication Origins in Eukaryotic Genomics. PMID:30619452
Androgen and Oestrogen Affect the Expression of Long Non-Coding RNAs During Phallus Development in a Marsupial. PMID:30598023
Mitochondrial Sco proteins are involved in oxidative stress defense. PMID:30593977
A resource of variant effect predictions of single nucleotide variants in model organisms. PMID:30573687
A novel deletion in KRT75L4 mediates the frizzle trait in a Chinese indigenous chicken. PMID:30572816
Using Transcriptome Analysis to Identify Genes Involved in Switchgrass Flower Reversion. PMID:30564266
RNA sequencing and anthocyanin synthesis-related genes expression analyses in white-fruited Vaccinium uliginosum. PMID:30545307
Search of Allosteric Inhibitors and Associated Proteins of an AKT-like Kinase from Trypanosoma cruzi. PMID:30544836
Archaeal NSUN6 catalyzes m5C72 modification on a wide-range of specific tRNAs. PMID:30541086
Differential responses of Lasiopodomys mandarinus and Lasiopodomys brandtii to chronic hypoxia: a cross-species brain transcriptome analysis. PMID:30537924
Complete Genome Sequence of Vitreoscilla sp. Strain C1, Source of the First Bacterial Hemoglobin. PMID:30533886
Gut microbiome structure and metabolic activity in inflammatory bowel disease. PMID:30531976
Platelet factor 4 promotes rapid replication and propagation of Dengue and Japanese encephalitis viruses. PMID:30527622
Enzymatic Phosphorylation of Ser in a Type I Collagen Peptide. PMID:30527445
GOnet: a tool for interactive Gene Ontology analysis. PMID:30526489
A new sequence logo plot to highlight enrichment and depletion. PMID:30526486
Secreted Cysteine-Rich Repeat Proteins "SCREPs": A Novel Multi-Domain Architecture. PMID:30524283
Gene ontology improves template selection in comparative protein docking. PMID:30520123
The Chinese herbal formula Fuzheng Quxie Decoction attenuates cognitive impairment and protects cerebrovascular function in SAMP8 mice. PMID:30519025
Analysis of the transcriptome data in Litopenaeus vannamei reveals the immune basis and predicts the hub regulation-genes in response to high-pH stress. PMID:30517152
Optimization of a 1,3,4-oxadiazole series for inhibition of Ca2+/calmodulin-stimulated activity of adenylyl cyclases 1 and 8 for the treatment of chronic pain. PMID:30472604
Genetic effects and gene-by-education interactions on episodic memory performance and decline in an aging population. PMID:30449520
De novo assembly and comparative transcriptome analysis: novel insights into terpenoid biosynthesis in Chamaemelum nobile L. PMID:30430213
Transcriptome and Resistance-Related Genes Analysis of Botrytis cinerea B05.10 Strain to Different Selective Pressures of Cyprodinil and Fenhexamid. PMID:30425701
DeepDTA: deep drug-target binding affinity prediction. PMID:30423097
C/VDdb: A multi-omics expression profiling database for a knowledge-driven approach in cardiovascular disease (CVD). PMID:30419069
Identifying antimicrobial peptides using word embedding with deep recurrent neural networks. PMID:30418485
Phosphorylation of Parkin at serine 65 is essential for its activation in vivo. PMID:30404819
Exploring Seipin: From Biochemistry to Bioinformatics Predictions. PMID:30402103
Comparative transcriptomics identifies genes differentially expressed in the intestine of a new fast-growing strain of common carp with higher unsaturated fatty acid content in muscle. PMID:30395585
Comparative transcriptome analysis to elucidate the enhanced thermotolerance of tea plants (Camellia sinensis) treated with exogenous calcium. PMID:30392143
Co-Evolution of Intrinsically Disordered Proteins with Folded Partners Witnessed by Evolutionary Couplings. PMID:30366362
Molecular mechanism of the extended oil accumulation phase contributing to the high seed oil content for the genotype of tung tree (Vernicia fordii). PMID:30340540
Small RNA and degradome profiling involved in seed development and oil synthesis of Brassica napus. PMID:30332454
GOGO: An improved algorithm to measure the semantic similarity between gene ontology terms. PMID:30305653
Transcriptomic analyses identify albino-associated genes of a novel albino tea germplasm 'Huabai 1'. PMID:30302258
Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions. PMID:30291327
Proteome and transcriptome profiling of equine myofibrillar myopathy identifies diminished peroxiredoxin 6 and altered cysteine metabolic pathways. PMID:30289745
CellMarker: a manually curated resource of cell markers in human and mouse. PMID:30289549
Characterization of novel glycosyl hydrolases discovered by cell wall glycan directed monoclonal antibody screening and metagenome analysis of maize aerial root mucilage. PMID:30256843
Crystal structure of rhodopsin in complex with a mini-Go sheds light on the principles of G protein selectivity. PMID:30255144
Network analysis of membranous glomerulonephritis based on metabolomics data. PMID:30221719
Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae. PMID:30202022
Metabolome and molecular basis for carbohydrate increase and nitrate reduction in burley tobacco seedlings by glycerol through upregulating carbon and nitrogen metabolism. PMID:30185870
From Molecules to Mechanisms: Functional Proteomics and Its Application to Renal Tubule Physiology. PMID:30182799
FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. PMID:30152809
Transcriptomic Analysis of Aedes aegypti in Response to Mosquitocidal Bacillus thuringiensis LLP29 Toxin. PMID:30140020
Structural analysis of human NHLRC2, mutations of which are associated with FINCA disease. PMID:30138417
Comparative Transcriptomic Analysis of Streptococcus thermophilus TH1436 and TH1477 Showing Different Capability in the Use of Galactose. PMID:30131781
In Vivo Analysis of miR-34a Regulated Glucose Metabolism Related Genes in Megalobrama amblycephala. PMID:30115855
Snake Venom Extracellular vesicles (SVEVs) reveal wide molecular and functional proteome diversity. PMID:30104604
Draft genome assembly of the invasive cane toad, Rhinella marina. PMID:30101298
Reconstruction of the Protein-Protein Interaction Network for Protein Complexes Identification by Walking on the Protein Pair Fingerprints Similarity Network. PMID:30087694
In silico analysis of SLC3A1 and SLC7A9 mutations in Iranian patients with Cystinuria. PMID:30069816
Hac1 function revealed by the protein expression profile of a OtHAC1 mutant of thermotolerant methylotrophic yeast Ogataea thermomethanolica. PMID:30066298
Gonadal transcriptome sequencing of the critically endangered Acipenser dabryanus to discover candidate sex-related genes. PMID:30065900
Comparative genomics and the nature of placozoan species. PMID:30063702
The Immune Protection Induced by a Serine Protease Inhibitor From the Foodborne Parasite Trichinella spiralis. PMID:30050521
Full-length transcriptome sequences and the identification of putative genes for flavonoid biosynthesis in safflower. PMID:30041604
Lateral Gene Transfer Between Protozoa-Related Giant Viruses of Family Mimiviridae and Chlamydiae. PMID:30038484
An Immunopharmacoinformatics Approach in Development of Vaccine and Drug Candidates for West Nile Virus. PMID:30035107
Genome-Wide Characterization and Expression Analyses of Pleurotus ostreatus MYB Transcription Factors during Developmental Stages and under Heat Stress Based on de novo Sequenced Genome. PMID:30011913
Network-based approach to prediction and population-based validation of in silico drug repurposing. PMID:30002366
Comparative transcriptome profiling of Blumeria graminis f. sp. tritici during compatible and incompatible interactions with sister wheat lines carrying and lacking Pm40. PMID:29975700
Transcriptome analysis of alternative splicing in peanut (Arachis hypogaea L.). PMID:29973157
DeepFam: deep learning based alignment-free method for protein family modeling and prediction. PMID:29949966
Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes. PMID:29931111
Synthesis and molecular modelling studies of pyrimidinones and pyrrolo[3,4-d]-pyrimidinodiones as new antiplasmodial compounds. PMID:29924131
Proteomic Architecture of Human Coronary and Aortic Atherosclerosis. PMID:29915101
Glutamine 89 is a key residue in the allosteric modulation of human serine racemase activity by ATP. PMID:29899358
Molecular Insights into Variable Electron Transfer in Amphibian Cryptochrome. PMID:29874607
Allosteric binding sites in Rab11 for potential drug candidates. PMID:29874286
Knowledge-Based Neuroendocrine Immunomodulation (NIM) Molecular Network Construction and Its Application. PMID:29848990
Evolution of oncogenic signatures of mutation hotspots in tyrosine kinases supports the atavistic hypothesis of cancer. PMID:29844492
Computational-based structural, functional and phylogenetic analysis of Enterobacter phytases. PMID:29805952
Towards a complete map of the human long non-coding RNA transcriptome. PMID:29795125
Network-Based Disease Module Discovery by a Novel Seed Connector Algorithm with Pathobiological Implications. PMID:29791871
Genomic and ecological study of two distinctive freshwater bacteriophages infecting a Comamonadaceae bacterium. PMID:29789681
Effects of flexibility of the α2 chain of type I collagen on collagenase cleavage. PMID:29763735
Phylogeny Trumps Chemotaxonomy: A Case Study Involving Turicella otitidis. PMID:29760685
Collagen Gly missense mutations: Effect of residue identity on collagen structure and integrin binding. PMID:29758270
Transcriptome sequencing and analysis during seed growth and development in Euryale ferox Salisb. PMID:29743016
An Integrated Study on the Antitumor Effect and Mechanism of Triphala Against Gynecological Cancers Based on Network Pharmacological Prediction and In Vitro Experimental Validation. PMID:29742928
Alpha-linolenic acid and linoleic acid differentially regulate the skeletal muscle secretome of obese Zucker rats. PMID:29727591
Functional and structural characterization of osteocytic MLO-Y4 cell proteins encoded by genes differentially expressed in response to mechanical signals in vitro. PMID:29712973
Transcriptome profiling provides insights into dormancy release during cold storage of Lilium pumilum. PMID:29703130
Transcriptomic analysis between self- and cross-pollinated pistils of tea plants (Camellia sinensis). PMID:29695246
To Decipher the Mycoplasma hominis Proteins Targeting into the Endoplasmic Reticulum and Their Implications in Prostate Cancer Etiology Using Next-Generation Sequencing Data. PMID:29695086
Identification of a cold-tolerant locus in rice (Oryza sativa L.) using bulked segregant analysis with a next-generation sequencing strategy. PMID:29671148
Clostridium sordellii outer spore proteins maintain spore structural integrity and promote bacterial clearance from the gastrointestinal tract. PMID:29668758
Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature. PMID:29650041
NCX-DB: a unified resource for integrative analysis of the sodium calcium exchanger super-family. PMID:29649983
An m6A-YTH Module Controls Developmental Timing and Morphogenesis in Arabidopsis. PMID:29643069
A two-tiered unsupervised clustering approach for drug repositioning through heterogeneous data integration. PMID:29642848
Screening of Genes Related to Early and Late Flowering in Tree Peony Based on Bulked Segregant RNA Sequencing and Verification by Quantitative Real-Time PCR. PMID:29562683
Transcriptome Analysis of Epithelioma Papulosum Cyprini Cells Infected by Reovirus Isolated from Allogynogenetic Silver Crucian Carp. PMID:29562634
Transcriptomic Profiles of Brain Provide Insights into Molecular Mechanism of Feed Conversion Efficiency in Crucian Carp (Carassius auratus). PMID:29538345
Genome-Wide Analysis of the PYL Gene Family and Identification of PYL Genes That Respond to Abiotic Stress in Brassica napus. PMID:29534558
Prediction and characterization of human ageing-related proteins by using machine learning. PMID:29511309
Relative Abundance of Proteins in Blood Plasma Samples from Patients with Chronic Cerebral Ischemia. PMID:29508191
The dynamic life of the glycogen granule. PMID:29483195
Codominant grasses differ in gene expression under experimental climate extremes in native tallgrass prairie. PMID:29473008
De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust. PMID:29463655
Identification of genetic variants for clinical management of familial colorectal tumors. PMID:29458332
StructureMapper: a high-throughput algorithm for analyzing protein sequence locations in structural data. PMID:29452363
Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains. PMID:29432415
Dissection of the Mechanism for Compatible and Incompatible Graft Combinations of Citrus grandis (L.) Osbeck ('Hongmian Miyou'). PMID:29419732
Transcriptomic and Physiological Evidence for the Relationship between Unsaturated Fatty Acid and Salt Stress in Peanut. PMID:29403517
SMRT sequencing of full-length transcriptome of flea beetle Agasicles hygrophila (Selman and Vogt). PMID:29396453
Molecular Profile of Priapism Associated with Low Nitric Oxide Bioavailability. PMID:29394072
DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data. PMID:29391044
High-throughput sequencing analysis revealed the regulation patterns of small RNAs on the development of A. comosus var. bracteatus leaves. PMID:29386560
Comparative Transcriptome Analyses Uncover Key Candidate Genes Mediating Flight Capacity in Bactrocera dorsalis (Hendel) and Bactrocera correcta (Bezzi) (Diptera: Tephritidae). PMID:29385681
Coordination of olfactory receptor choice with guidance receptor expression and function in olfactory sensory neurons. PMID:29385124
RNA-seq transcriptome analysis of the immature seeds of two Brassica napus lines with extremely different thousand-seed weight to identify the candidate genes related to seed weight. PMID:29381708
Proteomic Analyses of the Unexplored Sea Anemone Bunodactis verrucosa. PMID:29364843
Apelinergic System Structure and Function. PMID:29357134
Analysis of viral diversity for vaccine target discovery. PMID:29322922
The variome of pneumococcal virulence factors and regulators. PMID:29298677
Biological Implications of Differential Expression of Mitochondrial-Shaping Proteins in Parkinson's Disease. PMID:29267236
Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone. PMID:29259587
Genome of Leptospira borgpetersenii strain 4E, a highly virulent isolate obtained from Mus musculus in southern Brazil. PMID:29236926
Integrated analysis of motif activity and gene expression changes of transcription factors. PMID:29233921
The genomic study of an environmental isolate of Scedosporium apiospermum shows its metabolic potential to degrade hydrocarbons. PMID:29225727
In-Cardiome: integrated knowledgebase for coronary artery disease enabling translational research. PMID:29220465
MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go. PMID:29215871
Biochemical, Physiological and Transcriptomic Comparison between Burley and Flue-Cured Tobacco Seedlings in Relation to Carbohydrates and Nitrate Content. PMID:29207483
Intrinsic Disorder in Proteins with Pathogenic Repeat Expansions. PMID:29186753
Template-based quaternary structure prediction of proteins using enhanced profile-profile alignments. PMID:29178285
Identification of MsHsp20 Gene Family in Malus sieversii and Functional Characterization of MsHsp16.9 in Heat Tolerance. PMID:29163556
Metabolic reprogramming ensures cancer cell survival despite oncogenic signaling blockade. PMID:29138276
Random protein sequences can form defined secondary structures and are well-tolerated in vivo. PMID:29133927
Differential transcriptome analysis reveals genes related to cold tolerance in seabuckthorn carpenter moth, Eogystia hippophaecolus. PMID:29131867
A Chemoproteomic Approach to Query the Degradable Kinome Using a Multi-kinase Degrader. PMID:29129717
Identification and Characterization of MicroRNAs in the Goat (Capra hircus) Rumen during Embryonic Development. PMID:29123545
miPepBase: A Database of Experimentally Verified Peptides Involved in Molecular Mimicry. PMID:29109711
Production of Hypoallergenic Antibacterial Peptides from Defatted Soybean Meal in Membrane Bioreactor: A Bioprocess Engineering Study with Comprehensive Product Characterization. PMID:29089846
Physiological and transcriptome response to cadmium in cosmos (Cosmos bipinnatus Cav.) seedlings. PMID:29089633
Shaping the evolutionary tree of green plants: evidence from the GST family. PMID:29084977
Panax ginseng genome examination for ginsenoside biosynthesis. PMID:29048480
ProLanGO: Protein Function Prediction Using Neural Machine Translation Based on a Recurrent Neural Network. PMID:29039790
The major outer sheath protein forms distinct conformers and multimeric complexes in the outer membrane and periplasm of Treponema denticola. PMID:29038532
Native KCC2 interactome reveals PACSIN1 as a critical regulator of synaptic inhibition. PMID:29028184
PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology. PMID:29023571
Protein-protein interactions in paralogues: Electrostatics modulates specificity on a conserved steric scaffold. PMID:29016650
Achieving better-than-3-Å resolution by single-particle cryo-EM at 200 keV. PMID:28991891
Computational characterization of chromatin domain boundary-associated genomic elements. PMID:28977568
HUMA: A platform for the analysis of genetic variation in humans. PMID:28967693
MuMADS1 and MaOFP1 regulate fruit quality in a tomato ovate mutant. PMID:28944538
Survey of Predictors of Propensity for Protein Production and Crystallization with Application to Predict Resolution of Crystal Structures. PMID:28933304
Large-scale cross-species chemogenomic platform proposes a new drug discovery strategy of veterinary drug from herbal medicines. PMID:28915268
Transcriptomic profiling of genes in matured dimorphic seeds of euhalophyte Suaeda salsa. PMID:28903734
De Novo Assembly and Analysis of Polygonatum sibiricum Transcriptome and Identification of Genes Involved in Polysaccharide Biosynthesis. PMID:28895881
PRmePRed: A protein arginine methylation prediction tool. PMID:28813517
T-Time: A data repository of T cell and calcium release-activated calcium channel activation imagery. PMID:28807036
Novel atherogenic pathways from the differential transcriptome analysis of diabetic epicardial adipose tissue. PMID:28739185
An Update on Jacalin-Like Lectins and Their Role in Plant Defense. PMID:28737678
Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)-Enabled Intact Glycopeptide/Glycoproteome Characterization. PMID:28695533
Characterization of Sinorhizobium sp. LM21 Prophages and Virus-Encoded DNA Methyltransferases in the Light of Comparative Genomic Analyses of the Sinorhizobial Virome. PMID:28672885
EPSILON-CP: using deep learning to combine information from multiple sources for protein contact prediction. PMID:28623886
To be disordered or not to be disordered: is that still a question for proteins in the cell? PMID:28612216
Potentially pathogenic germline CHEK2 c.319+2T>A among multiple early-onset cancer families. PMID:28608266
De novo transcriptome assembly and quantification reveal differentially expressed genes between soft-seed and hard-seed pomegranate (Punica granatum L.). PMID:28594931
Plasmobase: a comparative database of predicted domain architectures for Plasmodium genomes. PMID:28592293
Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation. PMID:28582576
De novo characterization of the pine aphid Cinara pinitabulaeformis Zhang et Zhang transcriptome and analysis of genes relevant to pesticides. PMID:28570707
Dissecting physical structure of calreticulin, an intrinsically disordered Ca2+-buffering chaperone from endoplasmic reticulum. PMID:28504081
In silico target network analysis of de novo-discovered, tick saliva-specific microRNAs reveals important combinatorial effects in their interference with vertebrate host physiology. PMID:28473453
Transcriptome analysis of muskrat scented glands degeneration mechanism. PMID:28472080
Gene ORGANizer: linking genes to the organs they affect. PMID:28444223
HirBin: high-resolution identification of differentially abundant functions in metagenomes. PMID:28431529
Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa. PMID:28427330
Azathioprine, Mercaptopurine, and 5-Aminosalicylic Acid Affect the Growth of IBD-Associated Campylobacter Species and Other Enteric Microbes. PMID:28424670
Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics. PMID:28420677
Predicting neurological Adverse Drug Reactions based on biological, chemical and phenotypic properties of drugs using machine learning models. PMID:28408735
Comparative transcriptome profiling and morphology provide insights into endocarp cleaving of apricot cultivar (Prunus armeniaca L.). PMID:28399812
High number of kinome-mutations in non-small cell lung cancer is associated with reduced immune response and poor relapse-free survival. PMID:28387924
Transcriptome Analyses of Two Citrus Cultivars (Shiranuhi and Huangguogan) in Seedling Etiolation. PMID:28387303
Genome Sequences of Cyberlindnera fabianii 65, Pichia kudriavzevii 129, and Saccharomyces cerevisiae 131 Isolated from Fermented Masau Fruits in Zimbabwe. PMID:28385833
BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences. PMID:28365720
Using the entrapment sequence method as a standard to evaluate key steps of proteomics data analysis process. PMID:28361671
In silico-based vaccine design against Ebola virus glycoprotein. PMID:28356762
Sequence-based approach for rapid identification of cross-clade CD8+ T-cell vaccine candidates from all high-risk HPV strains. PMID:28330110
PSSMHCpan: a novel PSSM-based software for predicting class I peptide-HLA binding affinity. PMID:28327987
Ligand-guided homology modelling of the GABAB2 subunit of the GABAB receptor. PMID:28323850
GEAR: A database of Genomic Elements Associated with drug Resistance. PMID:28294141
Influence of DPH1 and DPH5 Protein Variants on the Synthesis of Diphthamide, the Target of ADPRibosylating Toxins. PMID:28245596
Understanding the roles of intrinsic disorder in subunits of hemoglobin and the disease process of sickle cell anemia. PMID:28232898
Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism. PMID:28174620
Global inference of disease-causing single nucleotide variants from exome sequencing data. PMID:28155632
Hydrogel scaffolds promote neural gene expression and structural reorganization in human astrocyte cultures. PMID:28097054
Expression and Secretion of Cyan Fluorescent Protein (CFP) in B. subtilis using the Chitinase Promoter from Bacillus pumilus SG2. PMID:28088132
Identification and Analysis of NaHCO3 Stress Responsive Genes in Wild Soybean (Glycine soja) Roots by RNA-seq. PMID:28018382
Identification of Development-Related Genes in the Ovaries of Adult Harmonia axyridis (Pallas) Lady Beetles Using a Time- Series Analysis by RNA-seq. PMID:27966611
PROPER: global protein interaction network alignment through percolation matching. PMID:27955623
Intrinsic disorder in proteins involved in amyotrophic lateral sclerosis. PMID:27838743
Evaluating Functional Annotations of Enzymes Using the Gene Ontology. PMID:27812939
Transcriptome Analysis and Ultrastructure Observation Reveal that Hawthorn Fruit Softening Is due to Cellulose/Hemicellulose Degradation. PMID:27790234
Cryo-EM structure of the large subunit of the spinach chloroplast ribosome. PMID:27762343
HCMV Displays a Unique Transcriptome of Immunomodulatory Genes in Primary Monocyte-Derived Cell Types. PMID:27760232
Integrating network, sequence and functional features using machine learning approaches towards identification of novel Alzheimer genes. PMID:27756223
Notions of similarity for systems biology models. PMID:27742665
SARAH Domain-Mediated MST2-RASSF Dimeric Interactions. PMID:27716844
Transcriptome Analysis of Sucrose Metabolism during Bulb Swelling and Development in Onion (Allium cepa L.). PMID:27713754
Identification of Genes Potentially Associated with the Fertility Instability of S-Type Cytoplasmic Male Sterility in Maize via Bulked Segregant RNA-Seq. PMID:27669430
Smyd2 is a Myc-regulated gene critical for MLL-AF9 induced leukemogenesis. PMID:27655694
In silico prediction of chemical mechanism of action via an improved network-based inference method. PMID:27646592
Pharmacophore-based virtual screening, biological evaluation and binding mode analysis of a novel protease-activated receptor 2 antagonist. PMID:27600555
High-Quality Genome Assembly and Annotation for Plasmodium coatneyi, Generated Using Single-Molecule Real-Time PacBio Technology. PMID:27587810
Differential expression of genes in the alate and apterous morphs of the brown citrus aphid, Toxoptera citricida. PMID:27577531
Gene Duplication and Gene Expression Changes Play a Role in the Evolution of Candidate Pollen Feeding Genes in Heliconius Butterflies. PMID:27553646
Comparative Transcriptome Analysis Identifies Candidate Genes Related to Skin Color Differentiation in Red Tilapia. PMID:27511178
From ZikV genome to vaccine: in silico approach for the epitope-based peptide vaccine against Zika virus envelope glycoprotein. PMID:27485738
Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence. PMID:27472895
Transcriptomic Analysis of Compromise Between Air-Breathing and Nutrient Uptake of Posterior Intestine in Loach (Misgurnus anguillicaudatus), an Air-Breathing Fish. PMID:27457889
Unfoldomics of prostate cancer: on the abundance and roles of intrinsically disordered proteins in prostate cancer. PMID:27453073
Genome-Wide Sequence Variation Identification and Floral-Associated Trait Comparisons Based on the Re-sequencing of the 'Nagafu No. 2' and 'Qinguan' Varieties of Apple (Malus domestica Borkh.). PMID:27446138
Therapeutics Insight with Inclusive Immunopharmacology Explication of Human Rotavirus A for the Treatment of Diarrhea. PMID:27445802
Transcriptomic Analysis of Multipurpose Timber Yielding Tree Neolamarckia cadamba during Xylogenesis Using RNA-Seq. PMID:27438485
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Evolution of the Calcium-Based Intracellular Signaling System. PMID:27358427
High-throughput sequencing reveals differential regulation of miRNAs in fenoxaprop-P-ethyl-resistant Beckmannia syzigachne. PMID:27353151
Transcriptome analysis of immature xylem in the Chinese fir at different developmental phases. PMID:27330860
The Size of the Human Proteome: The Width and Depth. PMID:27298622
Crystal structure of NOD2 and its implications in human disease. PMID:27283905
Protein kinase A-dependent phosphorylation stimulates the transcriptional activity of hypoxia-inducible factor 1. PMID:27245613
Genome Sequence of Madurella mycetomatis mm55, Isolated from a Human Mycetoma Case in Sudan. PMID:27231361
Coagulation Biomarkers in Healthy Chinese-Origin Rhesus Macaques (Macaca mulatta). PMID:27177557
Possible relationship between common genetic variation and white matter development in a pilot study of preterm infants. PMID:27110435
Analyzing the effect of peptide-HLA-binding ability on the immunogenicity of potential CD8+ and CD4+ T cell epitopes in a large dataset. PMID:27094547
Predicting cancer-relevant proteins using an improved molecular similarity ensemble approach. PMID:27083051
Draft genome of the Leptospira interrogans strains, Acegua, RCA, Prea, and Capivara, obtained from wildlife maintenance hosts and infected domestic animals. PMID:27074260
Transcriptome Analysis of Differentially Expressed Genes Provides Insight into Stolon Formation in Tulipa edulis. PMID:27064558
Molecular Basis of the Ligand Binding Specificity of αvβ8 Integrin. PMID:27033701
Prediction of mycoplasma hominis proteins targeting in mitochondria and cytoplasm of host cells and their implication in prostate cancer etiology. PMID:27027344
A Quantitative Glycomics and Proteomics Combined Purification Strategy. PMID:27023253
CCProf: exploring conformational change profile of proteins. PMID:27016699
Transcriptome Profiling of Two Asparagus Bean (Vigna unguiculata subsp. sesquipedalis) Cultivars Differing in Chilling Tolerance under Cold Stress. PMID:26954786
Chameleon sequences in neurodegenerative diseases. PMID:26920059
Genome-Wide Comparative Analysis of Chemosensory Gene Families in Five Tsetse Fly Species. PMID:26886411
Computational prediction of Mycoplasma hominis proteins targeting in nucleus of host cell and their implication in prostate cancer etiology. PMID:26874727
Rapid Identification of Candidate Genes for Seed Weight Using the SLAF-Seq Method in Brassica napus. PMID:26824525
Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach. PMID:26820892
Identification of Genes Relevant to Pesticides and Biology from Global Transcriptome Data of Monochamus alternatus Hope (Coleoptera: Cerambycidae) Larvae. PMID:26815657
A study of bias and increasing organismal complexity from their post-translational modifications and reaction site interplays. PMID:26764274
A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils. PMID:26754844
Predicting target proteins for drug candidate compounds based on drug-induced gene expression data in a chemical structure-independent manner. PMID:26684652
A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs. PMID:26680539
Genome sequences of two closely related strains of Escherichia coli K-12 GM4792. PMID:26664654
The quantitative and condition-dependent Escherichia coli proteome. PMID:26641532
Evolution of disorder in Mediator complex and its functional relevance. PMID:26590257
Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA. PMID:26581084
Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities. PMID:26579098
Molecular profiling of cetuximab and bevacizumab treatment of colorectal tumours reveals perturbations in metabolic and hypoxic response pathways. PMID:26517691
Complete Genome Sequence of Thermus aquaticus Y51MC23. PMID:26465632
Transcriptomic comparison of the self-pollinated and cross-pollinated flowers of Erigeron breviscapus to analyze candidate self-incompatibility-associated genes. PMID:26463824
Prioritization Of Nonsynonymous Single Nucleotide Variants For Exome Sequencing Studies Via Integrative Learning On Multiple Genomic Data. PMID:26459872
Indexing a protein-protein interaction network expedites network alignment. PMID:26453444
MST2-RASSF protein-protein interactions through SARAH domains. PMID:26443615
Tandem Repeats in Proteins: Prediction Algorithms and Biological Role. PMID:26442257
reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra. PMID:26419769
De novo sequencing and assembly analysis of transcriptome in the Sodom apple (Calotropis gigantea). PMID:26395839
New Elements To Consider When Modeling the Hazards Associated with Botulinum Neurotoxin in Food. PMID:26350137
Data integration in biological research: an overview. PMID:26336651
Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties. PMID:26315624
Curation of the Mammalian Palmitoylome Indicates a Pivotal Role for Palmitoylation in Diseases and Disorders of the Nervous System and Cancers. PMID:26275289
Systems Analysis of Protein Fatty Acylation in Herpes Simplex Virus-Infected Cells Using Chemical Proteomics. PMID:26256475
Trends in genome dynamics among major orders of insects revealed through variations in protein families. PMID:26251035
Prediction of O-glycosylation Sites Using Random Forest and GA-Tuned PSO Technique. PMID:26244014
The Genome of Winter Moth (Operophtera brumata) Provides a Genomic Perspective on Sexual Dimorphism and Phenology. PMID:26227816
BioModels: Content, Features, Functionality, and Use. PMID:26225232
Reagent and Data Resources for Investigation of RNA Binding Protein Functions in Drosophila melanogaster Cultured Cells. PMID:26199285
Identification and transcriptomic profiling of genes involved in increasing sugar content during salt stress in sweet sorghum leaves. PMID:26186930
Sulforaphane Reverses the Expression of Various Tumor Suppressor Genes by Targeting DNMT3B and HDAC1 in Human Cervical Cancer Cells. PMID:26161119
GenomePeek-an online tool for prokaryotic genome and metagenome analysis. PMID:26157610
State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet. PMID:26139527
Honey Bee Infecting Lake Sinai Viruses. PMID:26110586
Stress-induced DNA damage biomarkers: applications and limitations. PMID:26082923
Towards New Drug Targets? Function Prediction of Putative Proteins of Neisseria meningitidis MC58 and Their Virulence Characterization. PMID:26076386
Multi-instance multilabel learning with weak-label for predicting protein function in electricigens. PMID:26075251
Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals. PMID:26074880
Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature. PMID:26047637
De Novo Assembly of Bitter Gourd Transcriptomes: Gene Expression and Sequence Variations in Gynoecious and Monoecious Lines. PMID:26047102
Detection and analysis of disease-associated single nucleotide polymorphism influencing post-translational modification. PMID:26043787
Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies. PMID:26029180
Ab initio coordination chemistry for nickel chelation motifs. PMID:25985439
Whole-Genome Sequence and Annotation of Octopine-Utilizing Pseudomonas kilonensis (Previously P. fluorescens) Strain 1855-344. PMID:25977435
Comprehensive analysis of transcriptome response to salinity stress in the halophytic turf grass Sporobolus virginicus. PMID:25954282
De Novo Assembly and Transcriptome Analysis of Wheat with Male Sterility Induced by the Chemical Hybridizing Agent SQ-1. PMID:25898130
A mass spectrometric-derived cell surface protein atlas. PMID:25894527
Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. PMID:25888350
LOTUS-DB: an integrative and interactive database for Nelumbo nucifera study. PMID:25819075
The carbon starvation response of the ectomycorrhizal fungus Paxillus involutus. PMID:25778509
Comparative genome analysis of non-toxigenic non-O1 versus toxigenic O1 Vibrio cholerae. PMID:25722857
A new method to improve network topological similarity search: applied to fold recognition. PMID:25717198
A comprehensive immunoinformatics and target site study revealed the corner-stone toward Chikungunya virus treatment. PMID:25682054
Splice variants and seasonal expression of buffalo HSF genes. PMID:25655489
MBBC: an efficient approach for metagenomic binning based on clustering. PMID:25652152
Comparative modeling and benchmarking data sets for human histone deacetylases and sirtuin families. PMID:25633490
Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. PMID:25631240
Draft Genome Sequence and Gene Annotation of the Entomopathogenic Fungus Verticillium hemipterigenum. PMID:25614560
Identification of highly conserved regions in L-segment of Crimean-Congo hemorrhagic fever virus and immunoinformatic prediction about potential novel vaccine. PMID:25609983
Genome-wide association study of antibody level response to NDV and IBV in Jinghai yellow chicken based on SLAF-seq technology. PMID:25588649
Reconstruction and analysis of a genome-scale metabolic model of the oleaginous fungus Mortierella alpina. PMID:25582171
In silico repositioning-chemogenomics strategy identifies new drugs with potential activity against multiple life stages of Schistosoma mansoni. PMID:25569258
Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling. PMID:25540776
The application of the open pharmacological concepts triple store (open PHACTS) to support drug discovery research. PMID:25522365
Characterization and identification of protein O-GlcNAcylation sites with substrate specificity. PMID:25521204
Integrative workflows for metagenomic analysis. PMID:25478562
A-WINGS: an integrated genome database for Pleurocybella porrigens (Angel's wing oyster mushroom, Sugihiratake). PMID:25465051
Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. PMID:25431329
STRAP PTM: Software Tool for Rapid Annotation and Differential Comparison of Protein Post-Translational Modifications. PMID:25422678
Pre-metazoan origins and evolution of the cadherin adhesome. PMID:25395670
Interspecific and host-related gene expression patterns in nematode-trapping fungi. PMID:25384908
Influence of the hinge region and its adjacent domains on binding and signaling patterns of the thyrotropin and follitropin receptor. PMID:25340405
Combining physicochemical and evolutionary information for protein contact prediction. PMID:25338092
Exploring the human plasma proteome for humoral mediators of remote ischemic preconditioning--a word of caution. PMID:25333471
DEOP: a database on osmoprotectants and associated pathways. PMID:25326239
Molecular dissection of Mycobacterium tuberculosis integration host factor reveals novel insights into the mode of DNA binding and nucleoid compaction. PMID:25324543
Structure-based inhibition of protein-protein interactions. PMID:25253637
Single nucleotide variations: biological impact and theoretical interpretation. PMID:25234433
Global analysis of protein structural changes in complex proteomes. PMID:25218519
De Novo Whole-Genome Sequence and Genome Annotation of Lichtheimia ramosa. PMID:25212617
Design of an epitope-based peptide vaccine against spike protein of human coronavirus: an in silico approach. PMID:25187696
Molecular characterization of a novel temperate sinorhizobium bacteriophage, ФLM21, encoding DNA methyltransferase with CcrM-like specificity. PMID:25187538
Functional genomic analysis of constitutive and inducible defense responses to Fusarium verticillioides infection in maize genotypes with contrasting ear rot resistance. PMID:25155950
Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves. PMID:25149281
SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases. PMID:25127889
Incorporating amino acids composition and functional domains for identifying bacterial toxin proteins. PMID:25110714
Systematic analysis of gene properties influencing organ system phenotypes in mammalian perturbations. PMID:25061072
Efficient feature selection and classification of protein sequence data in bioinformatics. PMID:25045727
Multi-tissue computational modeling analyzes pathophysiology of type 2 diabetes in MKR mice. PMID:25029527
Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities. PMID:25028422
WDR72 models of structure and function: a stage-specific regulator of enamel mineralization. PMID:25008349
Two-layer modular analysis of gene and protein networks in breast cancer. PMID:24997799
Ranking non-synonymous single nucleotide polymorphisms based on disease concepts. PMID:24980617
MorusDB: a resource for mulberry genomics and genome biology. PMID:24923822
De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification. PMID:24912738
Profiling the orphan enzymes. PMID:24906382
Functional annotation of human cytomegalovirus gene products: an update. PMID:24904534
A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing. PMID:24885229
OWL reasoning framework over big biological knowledge network. PMID:24877076
Complete Genome Sequence of Pandoraea pnomenusa 3kgm, a Quorum-Sensing Strain Isolated from a Former Landfill Site. PMID:24812228
Label-free quantitative proteomics and N-terminal analysis of human metastatic lung cancer cells. PMID:24805778
GeneGenie: optimized oligomer design for directed evolution. PMID:24782527
PLIC: protein-ligand interaction clusters. PMID:24763918
Draft Genome Sequence of Quorum-Sensing and Quorum-Quenching Pseudomonas aeruginosa Strain MW3a. PMID:24744329
Study of query expansion techniques and their application in the biomedical information retrieval. PMID:24723793
Computational tools for rational protein engineering of aldolases. PMID:24688657
Identification of the novel interacting partners of the mammalian target of rapamycin complex 1 in human CCRF-CEM and HEK293 cells. PMID:24646917
STINGRAY: system for integrated genomic resources and analysis. PMID:24606808
ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins. PMID:24564381
Proteomic analysis of arginine methylation sites in human cells reveals dynamic regulation during transcriptional arrest. PMID:24563534
Exploring the relationship between drug side-effects and therapeutic indications. PMID:24551427
Expression and properties of the highly alkalophilic phenylalanine ammonia-lyase of thermophilic Rubrobacter xylanophilus. PMID:24475062
Incorporating significant amino acid pairs and protein domains to predict RNA splicing-related proteins with functional roles. PMID:24442949
Multi-omic network signatures of disease. PMID:24432028
A computational framework to infer human disease-associated long noncoding RNAs. PMID:24392133
Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20. PMID:24391926
Protein complex identification by integrating protein-protein interaction evidence from multiple sources. PMID:24386289
Three Dimensional Structure Prediction of Fatty Acid Binding Site on Human Transmembrane Receptor CD36. PMID:24348024
The haustorial transcriptomes of Uromyces appendiculatus and Phakopsora pachyrhizi and their candidate effector families. PMID:24341524
Prediction of Intrinsic Disorder in MERS-CoV/HCoV-EMC Supports a High Oral-Fecal Transmission. PMID:24270586
Transcriptome analysis of Nautilus and pygmy squid developing eye provides insights in lens and eye evolution. PMID:24205087
On the role of aggregation prone regions in protein evolution, stability, and enzymatic catalysis: insights from diverse analyses. PMID:24146608
Can inferred provenance and its visualisation be used to detect erroneous annotation? A case study using UniProtKB. PMID:24143170
Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources. PMID:24112383
Structural analysis of peptide-analogues of human Zona Pellucida ZP1 protein with amyloidogenic properties: insights into mammalian Zona Pellucida formation. PMID:24069181
DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures. PMID:24067102
Homology modeling and ligand docking of Mitogen-activated protein kinase-activated protein kinase 5 (MK5). PMID:24034446
An approach for identifying cytokines based on a novel ensemble classifier. PMID:24027761
PPR-SMRs: ancient proteins with enigmatic functions. PMID:24004908
M2SG: mapping human disease-related genetic variants to protein sequences and genomic loci. PMID:24002112
kClust: fast and sensitive clustering of large protein sequence databases. PMID:23945046
Tuning of thioredoxin redox properties by intramolecular hydrogen bonds. PMID:23936007
DNA damage-induced ubiquitylation of proteasome controls its proteolytic activity. PMID:23907514
3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data. PMID:23875761
Intraclonal genome diversity of Pseudomonas aeruginosa clones CHA and TB. PMID:23799896
eFG: an electronic resource for Fusarium graminearum. PMID:23798489
Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum. PMID:23770896
Homology modeling of human γ-butyric acid transporters and the binding of pro-drugs 5-aminolevulinic acid and methyl aminolevulinic acid used in photodynamic therapy. PMID:23762315
Structure, function, and behaviour of computational models in systems biology. PMID:23721297
Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates. PMID:23699412
Predicting the functional consequences of cancer-associated amino acid substitutions. PMID:23620363
Identification and analysis of red sea mangrove (Avicennia marina) microRNAs by high-throughput sequencing and their association with stress responses. PMID:23593307
Bioanalysis of eukaryotic organelles. PMID:23570618
Identification and characterization of potential therapeutic candidates in emerging human pathogen Mycobacterium abscessus: a novel hierarchical in silico approach. PMID:23527108
Mass spectrometry identification of granins and other proteins secreted by neuroblastoma cells. PMID:23519838
A novel multi-modal drug repurposing approach for identification of potent ACK1 inhibitors. PMID:23424109
Linking genome-scale metabolic modeling and genome annotation. PMID:23417799
XLink-DB: database and software tools for storing and visualizing protein interaction topology data. PMID:23413830
STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. PMID:23409969
Genomic diversity and evolution of the head crest in the rock pigeon. PMID:23371554
Visualization of protein interaction networks: problems and solutions. PMID:23368786
In silico study of human aquaporin AQP11 and AQP12 channels. PMID:23359558
De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity. PMID:23331995
A heterozygous moth genome provides insights into herbivory and detoxification. PMID:23313953
Disruption of the S41 peptidase gene in mycoplasma mycoides capri impacts proteome profile, H(2)O(2) production, and sensitivity to heat shock. PMID:23300541
Yeast protein phosphatase 2A-Cdc55 regulates the transcriptional response to hyperosmolarity stress by regulating Msn2 and Msn4 chromatin recruitment. PMID:23275436
UniProtKB amid the turmoil of plant proteomics research. PMID:23230445
Two distinct populations of exosomes are released from LIM1863 colon carcinoma cell-derived organoids. PMID:23230278
The origins of the evolutionary signal used to predict protein-protein interactions. PMID:23217198
Molecular modeling study on tunnel behavior in different histone deacetylase isoforms. PMID:23209570
Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function. PMID:23209562
TCMID: Traditional Chinese Medicine integrative database for herb molecular mechanism analysis. PMID:23203875
Using the unfolded state as the reference state improves the performance of statistical potentials. PMID:23199923
DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. PMID:23193290
Genome sequence of Roseomonas sp. strain B5, a quorum-quenching N-acylhomoserine lactone-degrading bacterium isolated from Malaysian tropical soil. PMID:23144419
Functional analyses of endometriosis-related polymorphisms in the estrogen synthesis and metabolism-related genes. PMID:23139742
mGOASVM: Multi-label protein subcellular localization based on gene ontology and support vector machines. PMID:23130999
SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models. PMID:23110173
Genome sequence of Dyella japonica strain A8, a quorum-quenching bacterium that degrades N-acylhomoserine lactones, isolated from Malaysian tropical soil. PMID:23105069
Understanding Viral Transmission Behavior via Protein Intrinsic Disorder Prediction: Coronaviruses. PMID:23097708
Predicting the accuracy of multiple sequence alignment algorithms by using computational intelligent techniques. PMID:23066102
Improving the thermostability of alpha-amylase by combinatorial coevolving-site saturation mutagenesis. PMID:23057711
Literature mining of protein-residue associations with graph rules learned through distant supervision. PMID:23046792
Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. PMID:23033316
Structure of β-1,4-mannanase from the common sea hare Aplysia kurodai at 1.05 Å resolution. PMID:23027740
Structure-based prediction of protein-protein interactions on a genome-wide scale. PMID:23023127
The enzymatic and metabolic capabilities of early life. PMID:22970111
Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective. PMID:22966151
Prediction of phenotypes of missense mutations in human proteins from biological assemblies. PMID:22965855
File formats commonly used in mass spectrometry proteomics. PMID:22956731
Deciphering the molecular nature of ovarian cancer biomarker CA125. PMID:22949880
Strategic protein target analysis for developing drugs to stop dental caries. PMID:22899687
Supervised protein family classification and new family construction. PMID:22876787
The Cell Collective: toward an open and collaborative approach to systems biology. PMID:22871178
Identifying protein phosphorylation sites with kinase substrate specificity on human viruses. PMID:22844408
Function prediction and analysis of mycobacterium tuberculosis hypothetical proteins. PMID:22837694
A strategy based on protein-protein interface motifs may help in identifying drug off-targets. PMID:22817115
SyStemCell: a database populated with multiple levels of experimental data from stem cell differentiation research. PMID:22807998
Computational prediction of N-linked glycosylation incorporating structural properties and patterns. PMID:22782545
Using semantic web technologies for cohort identification from electronic health records for clinical research. PMID:22779040
High performance transcription factor-DNA docking with GPU computing. PMID:22759575
Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. PMID:22716043
A topology-based metric for measuring term similarity in the gene ontology. PMID:22666244
Different evolutionary modifications as a guide to rewire two-component systems. PMID:22586357
Cardiomyopathy in patients with POMT1-related congenital and limb-girdle muscular dystrophy. PMID:22549409
Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature. PMID:22493694
Multidimensional plasma protein separation technique for identification of potential Alzheimer's disease plasma biomarkers: a pilot study. PMID:22415063
SpiroESTdb: a transcriptome database and online tool for sparganum expressed sequences tags. PMID:22397686
Shotgun proteomic monitoring of Clostridium acetobutylicum during stationary phase of butanol fermentation using xylose and comparison with the exponential phase. PMID:22395897
Investigation and identification of protein γ-glutamyl carboxylation sites. PMID:22372765
Viral proteins acquired from a host converge to simplified domain architectures. PMID:22319434
Synthesis, in vitro binding studies and docking of long-chain arylpiperazine nitroquipazine analogues, as potential serotonin transporter inhibitors. PMID:22309909
When one and one gives more than two: challenges and opportunities of integrative omics. PMID:22303399
IMID: integrated molecular interaction database. PMID:22238258
Advanced stoichiometric analysis of metabolic networks of mammalian systems. PMID:22196224
Generation and Analysis of Large-Scale Data-Driven Mycobacterium tuberculosis Functional Networks for Drug Target Identification. PMID:22190924
Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. PMID:22189060
Overview of biological database mapping services for interoperation between different 'omics' datasets. PMID:22155608
Crystal structure of human β-galactosidase: structural basis of Gm1 gangliosidosis and morquio B diseases. PMID:22128166
Incorporating evolutionary information and functional domains for identifying RNA splicing factors in humans. PMID:22110674
Structural annotation of Mycobacterium tuberculosis proteome. PMID:22073123
Molecular mechanism of serotonin transporter inhibition elucidated by a new flexible docking protocol. PMID:22071255
Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites. PMID:22038416
Comparative shotgun proteomic analysis of Clostridium acetobutylicum from butanol fermentation using glucose and xylose. PMID:22008648
Snat: a SNP annotation tool for bovine by integrating various sources of genomic information. PMID:21982513
Similarities and differences in peripheral blood gene-expression signatures of individuals with schizophrenia and their first-degree biological relatives. PMID:21972136
Bioinformatics and systems biology of the lipidome. PMID:21939287
Homology modeling and consensus protein disorder prediction of human filamin. PMID:21904422
Soybean homologs of MPK4 negatively regulate defense responses and positively regulate growth and development. PMID:21878550
Ferlins: regulators of vesicle fusion for auditory neurotransmission, receptor trafficking and membrane repair. PMID:21838746
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. PMID:21806842
Biphasic gene expression changes elicited by Phakopsora pachyrhizi in soybean correlate with fungal penetration and haustoria formation. PMID:21791600
Integrated bio-entity network: a system for biological knowledge discovery. PMID:21738677
Substrate binding and translocation of the serotonin transporter studied by docking and molecular dynamics simulations. PMID:21670993
The orphan disease networks. PMID:21664998
HIVToolbox, an integrated web application for investigating HIV. PMID:21647445
Prediction of binding hot spot residues by using structural and evolutionary parameters. PMID:21637529
Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus. PMID:21569391
ModEnzA: Accurate Identification of Metabolic Enzymes Using Function Specific Profile HMMs with Optimised Discrimination Threshold and Modified Emission Probabilities. PMID:21541071
Linking NCBI to Wikipedia: a wiki-based approach. PMID:21516242
Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells. PMID:21483477
miTALOS: analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs. PMID:21441347
Knowledge management for systems biology a general and visually driven framework applied to translational medicine. PMID:21375767
Omics-based molecular target and biomarker identification. PMID:21370102
Protein sequence redundancy reduction: comparison of various method. PMID:21364823
Virus interactions with human signal transduction pathways. PMID:21330695
XANNpred: neural nets that predict the propensity of a protein to yield diffraction-quality crystals. PMID:21246630
LPS-annotate: complete annotation of compositionally biased regions in the protein knowledgebase. PMID:21216786
Integrative bioinformatics analysis of proteins associated with the cardiorenal syndrome. PMID:21188212
Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. PMID:21118823
The identification of novel cyclic AMP-dependent protein kinase anchoring proteins using bioinformatic filters and peptide arrays. PMID:21115539
Genome annotation and intraviral interactome for the Streptococcus pneumoniae virulent phage Dp-1. PMID:21097633
Concept and application of a computational vaccinology workflow. PMID:21067549
Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins. PMID:21034461
Model of the complex of Parathyroid hormone-2 receptor and Tuberoinfundibular peptide of 39 residues. PMID:20979597
FAIR: A server for internal sequence repeats. PMID:20978598
A transcriptomic analysis of gene expression in the venom gland of the snake Bothrops alternatus (urutu). PMID:20977763
PEPPI: a peptidomic database of human protein isoforms for proteomics experiments. PMID:20946618
TOPSAN: use of a collaborative environment for annotating, analyzing and disseminating data on JCSG and PSI structures. PMID:20944203
In silico models of cancer. PMID:20836040
A predictor for toxin-like proteins exposes cell modulator candidates within viral genomes. PMID:20823311
GolgiP: prediction of Golgi-resident proteins in plants. PMID:20733061
Identification and structural characterization of FYVE domain-containing proteins of Arabidopsis thaliana. PMID:20678208
Re-annotation is an essential step in systems biology modeling of functional genomics data. PMID:20498845
Analysis of Transcripts Expressed in One-Day-Old Larvae and Fifth Instar Silk Glands of Tasar Silkworm, Antheraea mylitta. PMID:20454581
Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium. PMID:20441586
The Scottish Structural Proteomics Facility: targets, methods and outputs. PMID:20419351
The physiological importance of photosynthetic ferredoxin NADP+ oxidoreductase (FNR) isoforms in wheat. PMID:20410318
Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean. PMID:20199683
Protein aggregation profile of the bacterial cytosol. PMID:20195530
A large and accurate collection of peptidase cleavages in the MEROPS database. PMID:20157488
Systems metabolic engineering: genome-scale models and beyond. PMID:20151446
Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity. PMID:20147624
A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics. PMID:20087442
SoyDB: a knowledge database of soybean transcription factors. PMID:20082720
Active site prediction using evolutionary and structural information. PMID:20080507
Trade-off between positive and negative design of protein stability: from lattice models to real proteins. PMID:20011105
Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175. PMID:19927321
Automated quantitative assessment of proteins' biological function in protein knowledge bases. PMID:19920991
MEROPS: the peptidase database. PMID:19892822
Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences. PMID:19888206
(PS)2-v2: template-based protein structure prediction server. PMID:19878598
Structural genomics target selection for the New York consortium on membrane protein structure. PMID:19859826
An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations. PMID:19851441
Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae. PMID:19843335
Glutathione transferases are structural and functional outliers in the thioredoxin fold. PMID:19842715
Software tool for researching annotations of proteins: open-source protein annotation software with data visualization. PMID:19839595
Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions. PMID:19807911
Differential secreted proteome approach in murine model for candidate biomarker discovery in colon cancer. PMID:19769411
Comparative analyses of plant transcription factor databases. PMID:19721806
FLORA: a novel method to predict protein function from structure in diverse superfamilies. PMID:19714201
SNAD: Sequence Name Annotation-based Designer. PMID:19682364
Metabolic network analysis integrated with transcript verification for sequenced genomes. PMID:19597503
ResBoost: characterizing and predicting catalytic residues in enzymes. PMID:19558703
In silico studies on DARC. PMID:19519483
HotSpot Wizard: a web server for identification of hot spots in protein engineering. PMID:19465397
Variation in host specificity and gene content in strains from genetically isolated lineages of the ectomycorrhizal fungus Paxillus involutus s. lat. PMID:19452174
Solution structure of factor I-like modules from complement C7 reveals a pair of follistatin domains in compact pseudosymmetric arrangement. PMID:19419965
ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii. PMID:19409111
Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PMID:19402753
The origins of apicomplexan sequence innovation. PMID:19363216
EFICAz2: enzyme function inference by a combined approach enhanced by machine learning. PMID:19361344
Transcription and splicing regulation in human umbilical vein endothelial cells under hypoxic stress conditions by exon array. PMID:19320972
Identification and analyses of candidate genes for rpp4-mediated resistance to Asian soybean rust in soybean. PMID:19251904
Stable isotope dilution multidimensional liquid chromatography-tandem mass spectrometry for pancreatic cancer serum biomarker discovery. PMID:19199705
Structural genomics is the largest contributor of novel structural leverage. PMID:19194785
Structural genomics reveals EVE as a new ASCH/PUA-related domain. PMID:19191354
Reconstruction of biochemical networks in microorganisms. PMID:19116616
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
Arena3D: visualization of biological networks in 3D. PMID:19040715
The mechanism of transport by mitochondrial carriers based on analysis of symmetry. PMID:19001266
Defrosting the digital library: bibliographic tools for the next generation web. PMID:18974831
PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. PMID:18927104
Probing metagenomics by rapid cluster analysis of very large datasets. PMID:18846219
PMAP: databases for analyzing proteolytic events and pathways. PMID:18842634
Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity. PMID:18841247
DAVID gene ID conversion tool. PMID:18841237
Mining physical protein-protein interactions from the literature. PMID:18834490
Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures. PMID:18833291
How well can the accuracy of comparative protein structure models be predicted? PMID:18832340
The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle. PMID:18812508
Large-scale identification of polymorphic microsatellites using an in silico approach. PMID:18793407
INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification. PMID:18776193
Powerful fusion: PSI-BLAST and consensus sequences. PMID:18678588
The cadherin superfamily in Anopheles gambiae: a comparative study with Drosophila melanogaster. PMID:18629193
The molecule role ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature. PMID:18629146
On the extent and origins of genic novelty in the phylum Nematoda. PMID:18596977
Computational methods for protein identification from mass spectrometry data. PMID:18463710
FFPred: an integrated feature-based function prediction server for vertebrate proteomes. PMID:18463141
Complete genome sequence of the soil actinomycete Kocuria rhizophila. PMID:18408034
TarO: a target optimisation system for structural biology. PMID:18385152
Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence. PMID:18321373
PDTD: a web-accessible protein database for drug target identification. PMID:18282303
Construction of a fosmid library of cucumber (Cucumis sativus) and comparative analyses of the eIF4E and eIF(iso)4E regions from cucumber and melon (Cucumis melo). PMID:18273646
ProLoc-GO: utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization. PMID:18241343
Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm. PMID:18234819
Protein interactions in human genetic diseases. PMID:18199329
Analysis and prediction of protective continuous B-cell epitopes on pathogen proteins. PMID:18179690
Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines. PMID:18154662
Sequence alignment for molecular replacement. PMID:18094464
Differential expression of duplicated VAL-opsin genes in the developing zebrafish. PMID:18036148
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. PMID:17980028
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. PMID:17947321
On the detection of functionally coherent groups of protein domains with an extension to protein annotation. PMID:17937820
Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures. PMID:17937804
TOPDB: topology data bank of transmembrane proteins. PMID:17921502
Lateral gene transfer between obligate intracellular bacteria: evidence from the Rickettsia massiliae genome. PMID:17916642
Orthologous transcription factors in bacteria have different functions and regulate different genes. PMID:17845071
Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion. PMID:17785536
MELOGEN: an EST database for melon functional genomics. PMID:17767721
Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D. PMID:17727718
Automated protein subfamily identification and classification. PMID:17708678
Automating document classification for the Immune Epitope Database. PMID:17655769
WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches. PMID:17584794
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. PMID:17576678
Genome sequencing and genome resources in model legumes. PMID:17556522
SNAP: predict effect of non-synonymous polymorphisms on function. PMID:17526529
Comparative analysis of differentially expressed genes in normal and white spot syndrome virus infected Penaeus monodon. PMID:17506900
Phosphorus stress in common bean: root transcript and metabolic responses. PMID:17449651
Novel peptide identification from tandem mass spectra using ESTs and sequence database compression. PMID:17437027
Gene models from ESTs (GeneModelEST): an application on the Solanum lycopersicum genome. PMID:17430576
The BioPrompt-box: an ontology-based clustering tool for searching in biological databases. PMID:17430575
Structure-dependent relationships between growth temperature of prokaryotes and the amino acid frequency in their proteins. PMID:17429573
Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments. PMID:17369271
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PMID:17355171
Predicting mostly disordered proteins by using structure-unknown protein data. PMID:17338828
A network perspective on the evolution of metabolism by gene duplication. PMID:17326820
Blast sampling for structural and functional analyses. PMID:17319945
Using web ontology language to integrate heterogeneous databases in the neurosciences. PMID:17238384
Reductive genome evolution from the mother of Rickettsia. PMID:17238289
pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model. PMID:17222345
MaizeGDB's new data types, resources and activities. PMID:17202174
TBestDB: a taxonomically broad database of expressed sequence tags (ESTs). PMID:17202165
Conserved determinants for membrane association of nonstructural protein 5A from hepatitis C virus and related viruses. PMID:17192310
GOAnnotator: linking protein GO annotations to evidence text. PMID:17181854
IntAct--open source resource for molecular interaction data. PMID:17145710
CutDB: a proteolytic event database. PMID:17142225
Analysis of the wheat endosperm transcriptome. PMID:17132893
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. PMID:17099229
SynDB: a Synapse protein DataBase based on synapse ontology. PMID:17098931
Sensitivity of secondary structure propensities to sequence differences between alpha- and gamma-synuclein: implications for fibrillation. PMID:17088319
Testing statistical significance scores of sequence comparison methods with structure similarity. PMID:17038163
QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species. PMID:17029635
A path or a new road in laboratory diagnostics? Biological mass spectrometry: facts and perspectives. PMID:16998599
Serine hydrolase KIAA1363: toxicological and structural features with emphasis on organophosphate interactions. PMID:16978018
Genome comparison using Gene Ontology (GO) with statistical testing. PMID:16901353
Protein-protein interactions more conserved within species than across species. PMID:16854211
HubMed: a web-based biomedical literature search interface. PMID:16845111
The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis. PMID:16844980
Curation of complex, context-dependent immunological data. PMID:16836764
SPODOBASE: an EST database for the lepidopteran crop pest Spodoptera. PMID:16796757
A composite score for predicting errors in protein structure models. PMID:16751606
Protein fragment domains identified using 2D gel electrophoresis/MALDI-TOF. PMID:16741242
Soret spectral and bioinformatic approaches provide evidence for a critical role of the alpha -subunit in assembly of tetrameric hemoglobin. PMID:16721660
Topology and weights in a protein domain interaction network--a novel way to predict protein interactions. PMID:16716232
Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens. PMID:16703114
Domain-based small molecule binding site annotation. PMID:16545112
Exploiting protein structure data to explore the evolution of protein function and biological complexity. PMID:16524831
Predicting genes for orphan metabolic activities using phylogenetic profiles. PMID:16507154
Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation. PMID:16489136
Sex-dependent gene expression in early brain development of chicken embryos. PMID:16480516
A global assembly of cotton ESTs. PMID:16478941
Simple fold composition and modular architecture of the nuclear pore complex. PMID:16461911
On single and multiple models of protein families for the detection of remote sequence relationships. PMID:16448555
MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa. PMID:16433928
A theoretical model of Aquifex pyrophilus flagellin: implications for its thermostability. PMID:16411078
PRIDE: a public repository of protein and peptide identifications for the proteomics community. PMID:16381953
LMPD: LIPID MAPS proteome database. PMID:16381922
Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research. PMID:16381920
The PMDB Protein Model Database. PMID:16381873
The Molecular Biology Database Collection: 2006 update. PMID:16381871
E-MSD: improving data deposition and structure quality. PMID:16381867
MulPSSM: a database of multiple position-specific scoring matrices of protein domain families. PMID:16381855
The REFOLD database: a tool for the optimization of protein expression and refolding. PMID:16381847
Gene expression and metabolite profiling of Populus euphratica growing in the Negev desert. PMID:16356264
ParPEST: a pipeline for EST data analysis based on parallel computing. PMID:16351758
Inherited disorder phenotypes: controlled annotation and statistical analysis for knowledge mining from gene lists. PMID:16351744
SNEP: SNP-derived epitope prediction program for minor H antigens. PMID:16341860
MLH1 and MSH2 mutations in Colombian families with hereditary nonpolyposis colorectal cancer (Lynch syndrome)--description of four novel mutations. PMID:16341804
GNARE: automated system for high-throughput genome analysis with grid computational backend. PMID:16328950
Automated methods of predicting the function of biological sequences using GO and BLAST. PMID:16288652
KDE Bioscience: platform for bioinformatics analysis workflows. PMID:16260186
Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs). PMID:16221976
Comparative plant genomics resources at PlantGDB. PMID:16219921
Automatic classification and pattern discovery in high-throughput protein crystallization trials. PMID:16211519
Cycloheximide treatment of cotton ovules alters the abundance of specific classes of mRNAs and generates novel ESTs for microarray expression profiling. PMID:16208490
Adding some SPICE to DAS. PMID:16204122
XenDB: full length cDNA prediction and cross species mapping in Xenopus laevis. PMID:16162280
Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana. PMID:16102170
DynGO: a tool for visualizing and mining of Gene Ontology and its associations. PMID:16091147
Predicting specificity-determining residues in two large eukaryotic transcription factor families. PMID:16085755
Analysis of expressed sequence tags and the identification of associated short tandem repeats in switchgrass. PMID:16049706
Structural and functional analysis of a novel mutation of CYP21B in a heterozygote carrier of 21-hydroxylase deficiency. PMID:16028060
Genome-wide detection and analysis of cell wall-bound proteins with LPxTG-like sorting motifs. PMID:15995208
Theme discovery from gene lists for identification and viewing of multiple functional groups. PMID:15987504
The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite. PMID:15984913
ProFunc: a server for predicting protein function from 3D structure. PMID:15980588
GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases. PMID:15980578
MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes. PMID:15980515
BASys: a web server for automated bacterial genome annotation. PMID:15980511
SOAP-based services provided by the European Bioinformatics Institute. PMID:15980463
AutoFACT: an automatic functional annotation and classification tool. PMID:15960857
An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. PMID:15960829
Refinement and prediction of protein prenylation motifs. PMID:15960807
Genome organization of more than 300 defensin-like genes in Arabidopsis. PMID:15955924
A novel method for N-terminal acetylation prediction. PMID:15901254
AnoEST: toward A. gambiae functional genomics. PMID:15899967
Plant protein annotation in the UniProt Knowledgebase. PMID:15888679
Databases and information integration for the Medicago truncatula genome and transcriptome. PMID:15888676
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. PMID:15860774
A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models. PMID:15847681
The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation. PMID:15837807
Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. PMID:15824284
Sequencing the genespaces of Medicago truncatula and Lotus japonicus. PMID:15824279
The majority of human genes have regions repeated in other human genes. PMID:15802472
A Helicobacter pylori TolC efflux pump confers resistance to metronidazole. PMID:15793129
BioAfrica's HIV-1 proteomics resource: combining protein data with bioinformatics tools. PMID:15757512
Atlas - a data warehouse for integrative bioinformatics. PMID:15723693
Protein domains and architectural innovation in plant-associated Proteobacteria. PMID:15715905
A bipartite signal mediates the transfer of type IV secretion substrates of Bartonella henselae into human cells. PMID:15642951
Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis. PMID:15642098
A database for G proteins and their interaction with GPCRs. PMID:15619328
FunnyBase: a systems level functional annotation of Fundulus ESTs for the analysis of gene expression. PMID:15610557
GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. PMID:15608279
PlantMarkers--a database of predicted molecular markers from plants. PMID:15608276
openSputnik--a database to ESTablish comparative plant genomics using unsaturated sequence collections. PMID:15608275
Inparanoid: a comprehensive database of eukaryotic orthologs. PMID:15608241
Reactome: a knowledgebase of biological pathways. PMID:15608231
FlyBase: genes and gene models. PMID:15608223
CandidaDB: a genome database for Candida albicans pathogenomics. PMID:15608215
BacMap: an interactive picture atlas of annotated bacterial genomes. PMID:15608206
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. PMID:15608201
E-MSD: an integrated data resource for bioinformatics. PMID:15608192
The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines. PMID:15608182
InterPro, progress and status in 2005. PMID:15608177
ADDA: a domain database with global coverage of the protein universe. PMID:15608174
PSORTdb: a protein subcellular localization database for bacteria. PMID:15608169
NMPdb: Database of Nuclear Matrix Proteins. PMID:15608168
The Universal Protein Resource (UniProt). PMID:15608167
Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags. PMID:15590942
Update on genome completion and annotations: Protein Information Resource. PMID:15588483
CLOE: identification of putative functional relationships among genes by comparison of expression profiles between two species. PMID:15550177
Components of coated vesicles and nuclear pore complexes share a common molecular architecture. PMID:15523559
Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. PMID:15514110
Development of an expressed sequence tag (EST) resource for wheat (Triticum aestivum L.): EST generation, unigene analysis, probe selection and bioinformatics for a 16,000-locus bin-delineated map. PMID:15514037
The Cell Wall Navigator database. A systems-based approach to organism-unrestricted mining of protein families involved in cell wall metabolism. PMID:15489283
cuticleDB: a relational database of Arthropod cuticular proteins. PMID:15453918
PEDRo: a database for storing, searching and disseminating experimental proteomics data. PMID:15377392
Retrieving sequences of enzymes experimentally characterized but erroneously annotated : the case of the putrescine carbamoyltransferase. PMID:15287962
NLProt: extracting protein names and sequences from papers. PMID:15215466
Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments. PMID:15215428
Public web-based services from the European Bioinformatics Institute. PMID:15215339
Functions for S. cerevisiae Swd2p in 3' end formation of specific mRNAs and snoRNAs and global histone 3 lysine 4 methylation. PMID:15146080
Recent improvements to the PROSITE database. PMID:14681377
PIRSF: family classification system at the Protein Information Resource. PMID:14681371
The EMBL Nucleotide Sequence Database. PMID:14681351 -
UniProt Knowledgebase: a hub of integrated protein data
PubMed citations: 751.
751 articles citing: UniProt Knowledgebase: a hub of integrated protein data
Bromodomain and BET family proteins as epigenetic targets in cancer therapy: their degradation, present drugs, and possible PROTACs. PMID:35746919
Computational Investigations of Traditional Chinese Medicinal Compounds against the Omicron Variant of SARS-CoV-2 to Rescue the Host Immune System. PMID:35745660
Molecular Targets and Mechanisms of Hedyotis diffusa-Scutellaria barbata Herb Pair for the Treatment of Colorectal Cancer Based on Network Pharmacology and Molecular Docking. PMID:35707465
UMGAP: the Unipept MetaGenomics Analysis Pipeline. PMID:35689184
Predicting epitopes for vaccine development using bioinformatics tools. PMID:35647486
Investigation of the binding and dynamic features of A.30 variant revealed higher binding of RBD for hACE2 and escapes the neutralizing antibody: A molecular simulation approach. PMID:35533461
Sugars dominate the seagrass rhizosphere. PMID:35501482
A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae. PMID:35488861
Blocking key mutated hotspot residues in the RBD of the omicron variant (B.1.1.529) with medicinal compounds to disrupt the RBD-hACE2 complex using molecular screening and simulation approaches. PMID:35424688
Engineering an enthesis-like graft for rotator cuff repair: An approach to fabricate highly biomimetic scaffold capable of zone-specifically releasing stem cell differentiation inducers. PMID:35386315
Genomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas. PMID:35332281
Chromosome-scale Echinococcus granulosus (genotype G1) genome reveals the Eg95 gene family and conservation of the EG95-vaccine molecule. PMID:35241789
Nuclear genome of Bulinus truncatus, an intermediate host of the carcinogenic human blood fluke Schistosoma haematobium. PMID:35190553
The Omicron (B.1.1.529) variant of SARS-CoV-2 binds to the hACE2 receptor more strongly and escapes the antibody response: Insights from structural and simulation data. PMID:35063482
Core-Proteomics-Based Annotation of Antigenic Targets and Reverse-Vaccinology-Assisted Design of Ensemble Immunogen against the Emerging Nosocomial Infection-Causing Bacterium Elizabethkingia meningoseptica. PMID:35010455
Genome Characteristics Reveal the Biocontrol Potential of Actinobacteria Isolated From Sugarcane Rhizosphere. PMID:35003029
Epitope-Based Vaccine of a Brucella abortus Putative Small RNA Target Induces Protection and Less Tissue Damage in Mice. PMID:34992597
Mechanism of Elian granules in the treatment of precancerous lesions of gastric cancer in rats through the MAPK signalling pathway based on network pharmacology. PMID:34962453
Structural and biochemical analyses of selectivity determinants in chimeric Streptococcus Class A sortase enzymes. PMID:34939250
Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. PMID:34925297
Annotation of Potential Vaccine Targets and Design of a Multi-Epitope Subunit Vaccine against Yersinia pestis through Reverse Vaccinology and Validation through an Agent-Based Modeling Approach. PMID:34835260
Escherichia coli O127 group 4 capsule proteins assemble at the outer membrane. PMID:34780538
Genome-wide in silico analysis of long intergenic non-coding RNAs from rice peduncles at the heading stage. PMID:34744373
Antarctic Polyester Hydrolases Degrade Aliphatic and Aromatic Polyesters at Moderate Temperatures. PMID:34705547
MMV-db: vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses. PMID:34679165
Data-independent acquisition mass spectrometry for site-specific glycoproteomics characterization of SARS-CoV-2 spike protein. PMID:34635934
Quantitative phosphoproteomics reveals GSK3A substrate network is involved in the cryodamage of sperm motility. PMID:34596222
DTi2Vec: Drug-target interaction prediction using network embedding and ensemble learning. PMID:34551818
Carotenoid-Enriched Fractions From Spondias mombin Demonstrate HER2 ATP Kinase Domain Inhibition: Computational and In Vivo Animal Model of Breast Carcinoma Studies. PMID:34532287
Comparative analysis of the complete mitochondrial genome sequences and anther development cytology between maintainer and Ogura-type cytoplasm male-sterile cabbage (B. oleracea Var. capitata). PMID:34493212
Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil. PMID:34468166
VEGFR-2 kinase domain inhibition as a scaffold for anti-angiogenesis: Validation of the anti-angiogenic effects of carotenoids from Spondias mombin in DMBA model of breast carcinoma in Wistar rats. PMID:34408968
Single nucleotide polymorphisms in microRNA binding sites on the HOX genes regulate carcinogenesis: An in-silico approach. PMID:34368470
Genomic Analysis of the Mycoparasite Pestalotiopsis sp. PG52. PMID:34349810
Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. PMID:34335535
Analysis of microbial differences in amniotic fluid between advanced and normal age pregnant women. PMID:34315502
Sequence variation in the β7-β8 loop of bacterial class A sortase enzymes alters substrate selectivity. PMID:34302812
Bioinformatic Analysis of Temporal and Spatial Proteome Alternations During Infections. PMID:34276775
Mutational Landscape of Pirin and Elucidation of the Impact of Most Detrimental Missense Variants That Accelerate the Breast Cancer Pathways: A Computational Modelling Study. PMID:34262943
Repurposing proteases: An in-silico analysis of the binding potential of extracellular fungal proteases with selected viral proteins. PMID:34226889
Preliminary Structural Data Revealed That the SARS-CoV-2 B.1.617 Variant's RBD Binds to ACE2 Receptor Stronger Than the Wild Type to Enhance the Infectivity. PMID:34160124
Integrated analysis of three newly sequenced fern chloroplast genomes: Genome structure and comparative analysis. PMID:33976830
Complete chloroplast genome sequencing of Job's tears (Coix L.): genome structure, comparative analysis, and phylogenetic relationships. PMID:33948493
SWATH Based Quantitative Proteomics Reveals Significant Lipid Metabolism in Early Myopic Guinea Pig Retina. PMID:33946922
Immunogenomics guided design of immunomodulatory multi-epitope subunit vaccine against the SARS-CoV-2 new variants, and its validation through in silico cloning and immune simulation. PMID:33930764
BC-TFdb: a database of transcription factor drivers in breast cancer. PMID:33882119
Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins. PMID:33808029
A Molecular Modeling Approach to Identify Potential Antileishmanial Compounds Against the Cell Division Cycle (cdc)-2-Related Kinase 12 (CRK12) Receptor of Leishmania donovani. PMID:33803906
CODON-Software to manual curation of prokaryotic genomes. PMID:33788829
The first complete mitochondrial genome of eggplant (Solanum melongena). PMID:33763537
Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. PMID:33755190
Comparative analysis of chloroplast genomes of kenaf cytoplasmic male sterile line and its maintainer line. PMID:33674697
Genomic Comparison of Lactobacillus casei AP and Lactobacillus plantarum DR131 with Emphasis on the Butyric Acid Biosynthetic Pathways. PMID:33669502
Inheritance of Solanum chloroplast genomic DNA in interspecific hybrids. PMID:33659675
The complete mitochondrial genome of sponge Tethya sp. (Demospongiae, Tethyida, Tethyidae). PMID:33473525
Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway. PMID:33452484
Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community. PMID:33436509
Protein phosphorylation associated with drought priming-enhanced heat tolerance in a temperate grass species. PMID:33328446
GreenPhylDB v5: a comparative pangenomic database for plant genomes. PMID:33237299
Simultaneous RNAi Knockdown of Three FMRFamide-Like Peptide Genes, Mi-flp1, Mi-flp12, and Mi-flp18 Provides Resistance to Root-Knot Nematode, Meloidogyne incognita. PMID:33193182
First draft genome assembly of the desert locust, Schistocerca gregaria. PMID:33163158
A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis. PMID:33146374
Glycosylation of Serum Clusterin in Wild-Type Transthyretin-Associated (ATTRwt) Amyloidosis: A Study of Disease-Associated Compositional Features Using Mass Spectrometry Analyses. PMID:33141553
Characteristic and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Medicinal Plants of Schisandraceae. PMID:33123569
Model-driven design allows growth of Mycoplasma pneumoniae on serum-free media. PMID:33097709
Integrated omics unveil the secondary metabolic landscape of a basal dinoflagellate. PMID:33050904
High-quality nuclear genome for Sarcoptes scabiei-A critical resource for a neglected parasite. PMID:33001992
Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts. PMID:32994284
The Genetic Architecture of Emerging Fungicide Resistance in Populations of a Global Wheat Pathogen. PMID:32986802
Reconstruction of the birth of a male sex chromosome present in Atlantic herring. PMID:32938798
Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis. PMID:32914530
Complete Genome Sequence of Pseudomonas aeruginosa XN-1, Isolated from the Sputum of a Severe Pneumonia Patient. PMID:32883796
ACEP: improving antimicrobial peptides recognition through automatic feature fusion and amino acid embedding. PMID:32859150
Localization of the Interaction Site of Herpes Simplex Virus Glycoprotein D (gD) on the Membrane Fusion Regulator, gH/gL. PMID:32759318
SARS-CoV-2 and Guillain-Barré syndrome: molecular mimicry with human heat shock proteins as potential pathogenic mechanism. PMID:32729001
Protein-Protein Interactions Mediated by Intrinsically Disordered Protein Regions Are Enriched in Missense Mutations. PMID:32722039
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. PMID:32652120
Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion. PMID:32605573
Measuring Site-specific Glycosylation Similarity between Influenza a Virus Variants with Statistical Certainty. PMID:32601173
Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Six Almond Species (Prunus spp. L.). PMID:32576920
Leishmanicidal Potential of Hardwickiic Acid Isolated From Croton sylvaticus. PMID:32523532
Comparative Analyses of Five Complete Chloroplast Genomes from the Genus Pterocarpus (Fabacaeae). PMID:32466556
A Peptide Link Between Human Cytomegalovirus Infection, Neuronal Migration, and Psychosis. PMID:32457660
An Analysis of the Anti-Neuropathic Effects of Qi She Pill Based on Network Pharmacology. PMID:32454869
Complexity and ultrastructure of infectious extracellular vesicles from cells infected by non-enveloped virus. PMID:32409751
Identification and functional characterization of a β-glucosidase from Bacillus tequelensis BD69 expressed in bacterial and yeast heterologous systems. PMID:32266116
A genome-wide identification, characterization and functional analysis of salt-related long non-coding RNAs in non-model plant Pistacia vera L. using transcriptome high throughput sequencing. PMID:32221354
Metadata Analysis of mcr-1-Bearing Plasmids Inspired by the Sequencing Evidence for Horizontal Transfer of Antibiotic Resistance Genes Between Polluted River and Wild Birds. PMID:32210943
Complete genome sequences of two Enterococcus faecium strains and comparative genomic analysis. PMID:32104261
Draft Genome Assembly of Floccularia luteovirens, an Edible and Symbiotic Mushroom on Qinghai-Tibet Plateau. PMID:32098800
Characterization and whole genome sequencing of a novel strain of Bergeyella cardium related to infective endocarditis. PMID:32050896
The Genome of the Medicinal Macrofungus Sanghuang Provides Insights Into the Synthesis of Diverse Secondary Metabolites. PMID:31993039
The complete chloroplast genome of Microcycas calocoma (Miq.) A. DC. (Zamiaceae, Cycadales) and evolution in Cycadales. PMID:31976174
Scenarios of Genes-to-Terpenoids Network Led to the Identification of a Novel α/β-Farnesene/β-Ocimene Synthase in Camellia sinensis. PMID:31963919
A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains. PMID:31875044
Antimicrobial peptide identification using multi-scale convolutional network. PMID:31870282
Genome Sequencing of Mesonia algae K4-1 Reveals Its Adaptation to the Arctic Ocean. PMID:31866978
Comparative analysis of the complete chloroplast genome sequences of six species of Pulsatilla Miller, Ranunculaceae. PMID:31798674
Quantitative Proteomics of Uukuniemi Virus-host Cell Interactions Reveals GBF1 as Proviral Host Factor for Phleboviruses. PMID:31570497
A Diverse Benchmark Based on 3D Matched Molecular Pairs for Validating Scoring Functions. PMID:31458770
Characterizing the Binding Interactions between DNA-Binding Proteins, XPA and XPE: A Molecular Dynamics Approach. PMID:31458200
Exploration in the Mechanism of Action of Licorice by Network Pharmacology. PMID:31443210
Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome. PMID:31333721
Genome Sequencing of Pleurozium schreberi: The Assembled and Annotated Draft Genome of a Pleurocarpous Feather Moss. PMID:31285273
Sulfur-Oxidizing Symbionts without Canonical Genes for Autotrophic CO2 Fixation. PMID:31239380
The heparin-binding proteome in normal pancreas and murine experimental acute pancreatitis. PMID:31211768
Genome Analysis of Hypomyces perniciosus, the Causal Agent of Wet Bubble Disease of Button Mushroom (Agaricus bisporus). PMID:31146507
Genomic insights into a robust gamma-aminobutyric acid-producer Lactobacillus brevis CD0817. PMID:31127390
Computational prediction and in vitro validation of VEGFR1 as a novel protein target for 2,3,7,8-tetrachlorodibenzo-p-dioxin. PMID:31048752
Genome of 'Charleston Gray', the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection. PMID:31022325
Systematic Affiliation and Genome Analysis of Subtercola vilae DB165T with Particular Emphasis on Cold Adaptation of an Isolate from a High-Altitude Cold Volcano Lake. PMID:31018526
The first draft genomes of the ant Formica exsecta, and its Wolbachia endosymbiont reveal extensive gene transfer from endosymbiont to host. PMID:30991952
Genomic characterization of Kerstersia gyiorum SWMUKG01, an isolate from a patient with respiratory infection in China. PMID:30978196
Plastid genome and composition analysis of two medical ferns: Dryopteris crassirhizoma Nakai and Osmunda japonica Thunb. PMID:30911328
Comparative Genome and Transcriptome Study of the Gene Expression Difference Between Pathogenic and Environmental Strains of Prototheca zopfii. PMID:30899253
Matrix Metalloprotease Generated Fragments of Type VI Collagen Have Serum Biomarker Potential in Cancer - A Proof of Concept Study. PMID:30856553
Leptospiral phosphatidylinositol-specific phospholipase C: a novel conserved antigen for the definitive diagnosis of Leptospirosis. PMID:30848449
CSgator: an integrated web platform for compound set analysis. PMID:30830479
Genome-Wide Associations of Chlorophyll Fluorescence OJIP Transient Parameters Connected With Soil Drought Response in Barley. PMID:30828338
Design, antimicrobial activity and mechanism of action of Arg-rich ultra-short cationic lipopeptides. PMID:30789942
Genome Sequencing of Cladobotryum protrusum Provides Insights into the Evolution and Pathogenic Mechanisms of the Cobweb Disease Pathogen on Cultivated Mushroom. PMID:30744046
GRID-independent molecular descriptor analysis and molecular docking studies to mimic the binding hypothesis of γ-aminobutyric acid transporter 1 (GAT1) inhibitors. PMID:30723616
Molecular evidence for distinct modes of nutrient acquisition between visceral and neurotropic schistosomes of birds. PMID:30718911
Integration of Two In-depth Quantitative Proteomics Approaches Determines the Kallikrein-related Peptidase 7 (KLK7) Degradome in Ovarian Cancer Cell Secretome. PMID:30705123
Candidate Gene Selection for Cytoplasmic Male Sterility in Pepper (Capsicum annuum L.) through Whole Mitochondrial Genome Sequencing. PMID:30699994
Draft Genome Analysis Offers Insights Into the Mechanism by Which Streptomyces chartreusis WZS021 Increases Drought Tolerance in Sugarcane. PMID:30687260
Tolerance and dose-response assessment of subchronic dietary ethoxyquin exposure in Atlantic salmon (Salmo salar L.). PMID:30682099
Co-localization of genomic regions associated with seed morphology and composition in a desi chickpea (Cicer arietinum L.) population varying in seed protein concentration. PMID:30661107
Identification of selective inhibitors of Helicobacter pylori IMPDH as a targeted therapy for the infection. PMID:30655593
Expression Analysis of PIN Genes in Root Tips and Nodules of Lotus japonicus. PMID:30634426
Identification of potential drug targets and inhibitor of the pathogenic bacteria Shigella flexneri 2a through the subtractive genomic approach. PMID:30607324
Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses. PMID:30585382
VarQ: A Tool for the Structural and Functional Analysis of Human Protein Variants. PMID:30574164
Antimicrobial peptide similarity and classification through rough set theory using physicochemical boundaries. PMID:30522443
Genome Wide Analysis of WD40 Proteins in Saccharomyces cerevisiae and Their Orthologs in Candida albicans. PMID:30511317
Data on differentially expressed proteins in retinal emmetropization process in guinea pig using integrated SWATH-based and targeted-based proteomics. PMID:30505911
Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy. PMID:30500839
Large-scale in-silico statistical mutagenesis analysis sheds light on the deleteriousness landscape of the human proteome. PMID:30451933
Gene's hubs in retinal diseases: A retinal disease network. PMID:30417144
Three New Genome Assemblies Support a Rapid Radiation in Musa acuminata (Wild Banana). PMID:30321324
Neisseria gonorrhoeae Exposed to Sublethal Levels of Hydrogen Peroxide Mounts a Complex Transcriptional Response. PMID:30320218
Complete genome sequence of the Robinia pseudoacacia L. symbiont Mesorhizobium amorphae CCNWGS0123. PMID:30250634
Drug Repurposing of Metabolic Agents in Malignant Glioma. PMID:30223473
ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes. PMID:30169674
Assessing Human Genetic Variations in Glucose Transporter SLC2A10 and Their Role in Altering Structural and Functional Properties. PMID:30090112
The molecular genetic basis of herbivory between butterflies and their host plants. PMID:30076351
Role of CysI-CysIII Disulfide Bond on the Structure and Activity of α-Conotoxins at Human Neuronal Nicotinic Acetylcholine Receptors. PMID:30023726
Role of genetic and electrolyte abnormalities in prolonged QTc interval and sudden cardiac death in end-stage renal disease patients. PMID:30020974
A molecular model for LINC complex regulation: activation of SUN2 for KASH binding. PMID:29995584
Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon. PMID:29970182
Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population. PMID:29945935
Identification of Bacteriophage Virion Proteins Using Multinomial Naïve Bayes with g-Gap Feature Tree. PMID:29914091
The intrinsically disordered E-domains regulate the IGF-1 prohormones stability, subcellular localisation and secretion. PMID:29891966
Research Techniques Made Simple: Mass Spectrometry for Analysis of Proteins in Dermatological Research. PMID:29793618
Loss of TIGAR Induces Oxidative Stress and Meiotic Defects in Oocytes from Obese Mice. PMID:29776966
Determination of the μ-Conotoxin PIIIA Specificity Against Voltage-Gated Sodium Channels from Binding Energy Calculations. PMID:29735899
Computational Prediction and Analysis of Associations between Small Molecules and Binding-Associated S-Nitrosylation Sites. PMID:29671802
Whole Genome Sequence of an Edible and Potential Medicinal Fungus, Cordyceps guangdongensis. PMID:29666196
Genome Annotation Generator: a simple tool for generating and correcting WGS annotation tables for NCBI submission. PMID:29635297
Distinguishing allergens from non-allergenic homologues using Physical-Chemical Property (PCP) motifs. PMID:29627609
Invertebrate Iridoviruses: A Glance over the Last Decade. PMID:29601483
Deep learning improves antimicrobial peptide recognition. PMID:29590297
Functional annotation of genomic variants in studies of late-onset Alzheimer's disease. PMID:29590295
Long Non-Coding RNAs Responsive to Salt and Boron Stress in the Hyper-Arid Lluteño Maize from Atacama Desert. PMID:29558449
Defining the Transcriptional Targets of Leptin Reveals a Role for Atf3 in Leptin Action. PMID:29535089
Loss and gain of N-linked glycosylation sequons due to single-nucleotide variation in cancer. PMID:29531238
Essential Role for Hypothalamic Calcitonin Receptor‒Expressing Neurons in the Control of Food Intake by Leptin. PMID:29522093
In silico structural and functional prediction of African swine fever virus protein-B263R reveals features of a TATA-binding protein. PMID:29492339
The Druggable Pocketome of Corynebacterium diphtheriae: A New Approach for in silico Putative Druggable Targets. PMID:29487617
Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection. PMID:29475453
Pi-Pi contacts are an overlooked protein feature relevant to phase separation. PMID:29424691
Novel global effector mining from the transcriptome of early life stages of the soybean cyst nematode Heterodera glycines. PMID:29410430
Comparative transcriptomics uncovers differences in photoautotrophic versus photoheterotrophic modes of nutrition in relation to secondary metabolites biosynthesis in Swertia chirayita. PMID:29349608
Domain retention in transcription factor fusion genes and its biological and clinical implications: a pan-cancer study. PMID:29299133
The genomic study of an environmental isolate of Scedosporium apiospermum shows its metabolic potential to degrade hydrocarbons. PMID:29225727
Complete genome sequence of the Vibrio vulnificus strain VV2014DJH, a human-pathogenic bacterium isolated from a death case in China. PMID:29201149
On the Early Evolution of Catabolic Pathways: A Comparative Genomics Approach. I. The Cases of Glucose, Ribose, and the Nucleobases Catabolic Routes. PMID:29189888
Predicting CK2 beta-dependent substrates using linear patterns. PMID:29124183
Computer-Aided Design of an Epitope-Based Vaccine against Epstein-Barr Virus. PMID:29119120
eRAM: encyclopedia of rare disease annotations for precision medicine. PMID:29106618
KIXBASE: A comprehensive web resource for identification and exploration of KIX domains. PMID:29097748
De novo-based transcriptome profiling of male-sterile and fertile watermelon lines. PMID:29095876
MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle. PMID:29069412
An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae. PMID:29049350
TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms. PMID:29037173
A novel function of N-linked glycoproteins, alpha-2-HS-glycoprotein and hemopexin: Implications for small molecule compound-mediated neuroprotection. PMID:29016670
Isolation and complete genome sequence of Halorientalis hydrocarbonoclasticus sp. nov., a hydrocarbon-degrading haloarchaeon. PMID:28994006
Comparative proteomic analysis of growth hormone secretagogue A233 treatment of murine macrophage cells J774A.2 indicates it has a role in antiviral innate response. PMID:28955845
Metabolic control by sirtuins and other enzymes that sense NAD+, NADH, or their ratio. PMID:28947253
Establishing multiple omics baselines for three Southeast Asian populations in the Singapore Integrative Omics Study. PMID:28935855
CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components. PMID:28929969
Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides. PMID:28912798
More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis. PMID:28893308
Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment. PMID:28885627
PP2A-B' holoenzyme substrate recognition, regulation and role in cytokinesis. PMID:28884018
Large-scale structure prediction by improved contact predictions and model quality assessment. PMID:28881974
Prokaryotic and Highly-Repetitive WD40 Proteins: A Systematic Study. PMID:28878378
Simultaneous saccharification and viscosity reduction of cassava pulp using a multi-component starch- and cell-wall degrading enzyme for bioethanol production. PMID:28868217
Whole-Genome Sequence of the 1,4-Dioxane-Degrading Bacterium Mycobacterium dioxanotrophicus PH-06. PMID:28860235
Investigation of host-pathogen interaction between Burkholderia pseudomallei and autophagy-related protein LC3 using hydrophobic chromatography-based technique. PMID:28852470
Development of novel genic microsatellite markers from transcriptome sequencing in sugar maple (Acer saccharum Marsh.). PMID:28789702
Origins of coevolution between residues distant in protein 3D structures. PMID:28784799
Bradyrhizobium elkanii nod regulon: insights through genomic analysis. PMID:28767122
Analysis of Large-Scale Mutagenesis Data To Assess the Impact of Single Amino Acid Substitutions. PMID:28751422
Bacillus sp. JR3 esterase LipJ: A new mesophilic enzyme showing traces of a thermophilic past. PMID:28742841
The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks. PMID:28723946
Genome Sequence of Pseudomonas stutzeri 273 and Identification of the Exopolysaccharide EPS273 Biosynthesis Locus. PMID:28698510
Boronic Acid-Modified Magnetic Fe3O4@mTiO2 Microspheres for Highly Sensitive and Selective Enrichment of N-Glycopeptides in Amniotic Fluid. PMID:28676633
Characterization of the emerging zoonotic pathogen Arcobacter thereius by whole genome sequencing and comparative genomics. PMID:28671965
Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment. PMID:28667104
RGIFE: a ranked guided iterative feature elimination heuristic for the identification of biomarkers. PMID:28666416
In silico re-identification of properties of drug target proteins. PMID:28617227
Characterisation of the circulating acellular proteome of healthy sheep using LC-MS/MS-based proteomics analysis of serum. PMID:28615994
Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS. PMID:28604659
CorNet: Assigning function to networks of co-evolving residues by automated literature mining. PMID:28545124
Architecture of the human interactome defines protein communities and disease networks. PMID:28514442
Disease-associated mitochondrial mutations and the evolution of primate mitogenomes. PMID:28510580
Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects. PMID:28449705
Characterization and expression analysis of Galnts in developing Strongylocentrotus purpuratus embryos. PMID:28448610
A rare variant in the FHL1 gene associated with X-linked recessive hypoparathyroidism. PMID:28444561
Model-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism. PMID:28444480
Genome Sequencing Reveals the Complex Polysaccharide-Degrading Ability of Novel Deep-Sea Bacterium Flammeovirga pacifica WPAGA1. PMID:28443080
Draft Genome Sequence of Methylocaldum sp. Strain 14B, an Obligate Hydrogen Sulfide-Tolerant Methanotrophic Strain That Can Convert Biogas to Methanol. PMID:28428289
The Glial Cell-Derived Neurotrophic Factor (GDNF)-responsive Phosphoprotein Landscape Identifies Raptor Phosphorylation Required for Spermatogonial Progenitor Cell Proliferation. PMID:28408662
Correlated Mutation in the Evolution of Catalysis in Uracil DNA Glycosylase Superfamily. PMID:28397787
Comparative transcriptomics of Entelegyne spiders (Araneae, Entelegynae), with emphasis on molecular evolution of orphan genes. PMID:28379977
Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents. PMID:28375213
Distribution of Secretion Systems in the Genus Legionella and Its Correlation with Pathogenicity. PMID:28352254
Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. PMID:28350393
ADH1B: From alcoholism, natural selection, and cancer to the human phenome. PMID:28349588
Comparative genomics of pyridoxal 5'-phosphate-dependent transcription factor regulons in Bacteria. PMID:28348826
APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins. PMID:28334975
Comparative genomics reveals contraction in olfactory receptor genes in bats. PMID:28325942
Complete genome sequencing and antibiotics biosynthesis pathways analysis of Streptomyces lydicus 103. PMID:28317865
Delineating functional principles of the bow tie structure of a kinase-phosphatase network in the budding yeast. PMID:28298210
Exploring biomedical ontology mappings with graph theory methods. PMID:28265499
Social network architecture of human immune cells unveiled by quantitative proteomics. PMID:28263321
Proteomic Analysis of Matched Formalin-Fixed, Paraffin-Embedded Specimens in Patients with Advanced Serous Ovarian Carcinoma. PMID:28250404
Red-legged partridge (Alectoris rufa) de-novo transcriptome assembly and identification of gene-related markers. PMID:28239549
Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants. PMID:28228535
Differential Gene Expression Analysis in Polygonum minus Leaf upon 24 h of Methyl Jasmonate Elicitation. PMID:28220135
Molecular modeling and molecular dynamic simulation of the effects of variants in the TGFBR2 kinase domain as a paradigm for interpretation of variants obtained by next generation sequencing. PMID:28182693
Characterization of Leaf Transcriptome in Banksia hookeriana. PMID:28161492
From the research laboratory to the database: the Caenorhabditis elegans kinome in UniProtKB. PMID:28159896
The molecular basis of talin2's high affinity toward β1-integrin. PMID:28155884
UniProt Protein Knowledgebase. PMID:28150232
Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide. PMID:28145450
Characterization of Early-Phase Neutrophil Extracellular Traps in Urinary Tract Infections. PMID:28129394
A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements. PMID:28117833
HPV and systemic lupus erythematosus: a mosaic of potential crossreactions. PMID:28111707
Blind prediction of deleterious amino acid variations with SNPs&GO. PMID:28102005
Whole-Genome Sequence of Streptococcus parauberis Strain SP-llh, Isolated from Cows with Mastitis in Western China. PMID:28082485
Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis. PMID:28068432
A 2D-QSAR and Grid-Independent Molecular Descriptor (GRIND) Analysis of Quinoline-Type Inhibitors of Akt2: Exploration of the Binding Mode in the Pleckstrin Homology (PH) Domain. PMID:28036396
Brain transcriptomes of harbor seals demonstrate gene expression patterns of animals undergoing a metabolic disease and a viral infection. PMID:28028481
CaspNeuroD: a knowledgebase of predicted caspase cleavage sites in human proteins related to neurodegenerative diseases. PMID:28025335
Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study. PMID:28013235
Genome-wide Analysis of WD40 Protein Family in Human. PMID:27991561
Arsenic resistance strategy in Pantoea sp. IMH: Organization, function and evolution of ars genes. PMID:27966630
Systematic Identification of Oncogenic EGFR Interaction Partners. PMID:27956147
Complete genome sequence and transcriptomic analysis of a novel marine strain Bacillus weihaiensis reveals the mechanism of brown algae degradation. PMID:27901120
ChiTaRS-3.1-the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions. PMID:27899596
A Comprehensively Curated Genome-Scale Two-Cell Model for the Heterocystous Cyanobacterium Anabaena sp. PCC 7120. PMID:27899536
Biochemical characterization and synergism of cellulolytic enzyme system from Chaetomium globosum on rice straw saccharification. PMID:27871321
Observation selection bias in contact prediction and its implications for structural bioinformatics. PMID:27857150
Draft Genome Sequence of Lactobacillus plantarum XJ25 Isolated from Chinese Red Wine. PMID:27856576
Leaf transcriptome of two highly divergent genotypes of Urochloa humidicola (Poaceae), a tropical polyploid forage grass adapted to acidic soils and temporary flooding areas. PMID:27835957
Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface. PMID:27832824
Beyond DNA: An Integrated and Functional Approach for Classifying Germline Variants in Breast Cancer Genes. PMID:27822389
Large-scale gene co-expression network as a source of functional annotation for cattle genes. PMID:27806696
Path2enet: generation of human pathway-derived networks in an expression specific context. PMID:27801297
Complete Genome Sequence of Bacillus pumilus PDSLzg-1, a Hydrocarbon-Degrading Bacterium Isolated from Oil-Contaminated Soil in China. PMID:27795249
Draft Genome Sequence of Botryosphaeria dothidea, the Pathogen of Apple Ring Rot. PMID:27789635
Genomic resources for a unique, low-virulence Babesia taxon from China. PMID:27784333
The Chloroplast Genome of Utricularia reniformis Sheds Light on the Evolution of the ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family. PMID:27764252
3D structure prediction of histone acetyltransferase proteins of the MYST family and their interactome in Arabidopsis thaliana. PMID:27709438
Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining. PMID:27698135
Whole genome shotgun sequence of Bacillus amyloliquefaciens TF28, a biocontrol entophytic bacterium. PMID:27688836
REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. PMID:27666373
Sequence Based Prediction of Antioxidant Proteins Using a Classifier Selection Strategy. PMID:27662651
Functional characterization of a GFAP variant of uncertain significance in an Alexander disease case within the setting of an individualized medicine clinic. PMID:27648269
Key Structural Determinants in the Agonist Binding Loops of Human β2 and β4 Nicotinic Acetylcholine Receptor Subunits Contribute to α3β4 Subtype Selectivity of α-Conotoxins. PMID:27646000
Identifying the Types of Ion Channel-Targeted Conotoxins by Incorporating New Properties of Residues into Pseudo Amino Acid Composition. PMID:27631006
Genome-wide analysis of long intergenic non-coding RNAs in chickpea and their potential role in flower development. PMID:27628568
New HSP27 inhibitors efficiently suppress drug resistance development in cancer cells. PMID:27626687
Nitrogen Fixation and Molecular Oxygen: Comparative Genomic Reconstruction of Transcription Regulation in Alphaproteobacteria. PMID:27617010
Functional networks inference from rule-based machine learning models. PMID:27597880
The green ash transcriptome and identification of genes responding to abiotic and biotic stresses. PMID:27589953
Predicting essential proteins based on subcellular localization, orthology and PPI networks. PMID:27586883
Inferring metabolic pathway activity levels from RNA-Seq data. PMID:27585456
Computational Analysis of the Ligand Binding Site of the Extracellular ATP Receptor, DORN1. PMID:27583834
A Computational Model for Predicting RNase H Domain of Retrovirus. PMID:27574780
Computing energy landscape maps and structural excursions of proteins. PMID:27535545
Genes Expressed Differentially in Hessian Fly Larvae Feeding in Resistant and Susceptible Plants. PMID:27529231
Defining key roles for auxiliary proteins in an ABC transporter that maintains bacterial outer membrane lipid asymmetry. PMID:27529189
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. PMID:27504778
Structural mutation analysis of PTEN and its genotype-phenotype correlations in endometriosis and cancer. PMID:27481051
The Genome of Undifilum oxytropis Provides Insights into Swainsonine Biosynthesis and Locoism. PMID:27477109
In-silico discovery of cancer-specific peptide-HLA complexes for targeted therapy. PMID:27439771
In silico approach to explore the disruption in the molecular mechanism of human hyaluronidase 1 by mutant E268K that directs Natowicz syndrome. PMID:27424109
A membrane-bound esterase PA2949 from Pseudomonas aeruginosa is expressed and purified from Escherichia coli. PMID:27419054
Permanent draft genome sequence of sulfoquinovose-degrading Pseudomonas putida strain SQ1. PMID:27408681
Nuclear import sequence identification in hOAS3 protein. PMID:27379722
Coordination of Metabolism and Virulence Factors Expression of Extraintestinal Pathogenic Escherichia coli Purified from Blood Cultures of Patients with Sepsis. PMID:27364158
Proteome analysis of the Mycobacterium tuberculosis Beijing B0/W148 cluster. PMID:27356881
Comparative genomics analysis of the companion mechanisms of Bacillus thuringiensis Bc601 and Bacillus endophyticus Hbe603 in bacterial consortium. PMID:27353048
Reconstruction and Application of Protein-Protein Interaction Network. PMID:27338356
Different Endosymbiotic Interactions in Two Hydra Species Reflect the Evolutionary History of Endosymbiosis. PMID:27324918
Standardization for natural product synthetic biology. PMID:27313083
Defining the consequences of genetic variation on a proteome-wide scale. PMID:27309819
DREMECELS: A Curated Database for Base Excision and Mismatch Repair Mechanisms Associated Human Malignancies. PMID:27276067
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors. PMID:27270715
Metagenomic Reconstruction of Key Anaerobic Digestion Pathways in Municipal Sludge and Industrial Wastewater Biogas-Producing Systems. PMID:27252693
Analysis of tigecycline resistance development in clinical Acinetobacter baumannii isolates through a combined genomic and transcriptomic approach. PMID:27240484
Phenylphthalazines as small-molecule inhibitors of urea transporter UT-B and their binding model. PMID:27238209
Diverse, Biologically Relevant, and Targetable Gene Rearrangements in Triple-Negative Breast Cancer and Other Malignancies. PMID:27231203
A Plasma Membrane Association Module in Yeast Amino Acid Transporters. PMID:27226538
Massive Shift in Gene Expression during Transitions between Developmental Stages of the Gall Midge, Mayetiola Destructor. PMID:27224654
Biological function derived from predicted structures in CASP11. PMID:27181425
The arabidopsis cyclic nucleotide interactome. PMID:27170143
Genome-wide variant analysis of simplex autism families with an integrative clinical-bioinformatics pipeline. PMID:27148569
The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. PMID:27138043
Cell Wall Composition, Biosynthesis and Remodeling during Pollen Tube Growth. PMID:27137369
GCGene: a gene resource for gastric cancer with literature evidence. PMID:27127885
CoReCG: a comprehensive database of genes associated with colon-rectal cancer. PMID:27114494
Nanonets Collect Cancer Secretome from Pericellular Space. PMID:27100780
A new molecular signature method for prediction of driver cancer pathways from transcriptional data. PMID:27098033
Curcumin Reduces the Motility of Salmonella enterica Serovar Typhimurium by Binding to the Flagella, Thereby Leading to Flagellar Fragility and Shedding. PMID:27091154
RhVI1 is a membrane-anchored vacuolar invertase highly expressed in Rosa hybrida L. petals. PMID:27083698
Requirements for the formal representation of pathophysiology mechanisms by clinicians. PMID:27051514
GAMDB: a web resource to connect microRNAs with autophagy in gerontology. PMID:27037912
Oligomerization as a strategy for cold adaptation: Structure and dynamics of the GH1 β-glucosidase from Exiguobacterium antarcticum B7. PMID:27029646
Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga Porphyra umbilicalis. PMID:27015628
MaxReport: An Enhanced Proteomic Result Reporting Tool for MaxQuant. PMID:27003708
Genes with high penetrance for syndromic and non-syndromic autism typically function within the nucleus and regulate gene expression. PMID:26985359
Integrated Omics and Computational Glycobiology Reveal Structural Basis for Influenza A Virus Glycan Microheterogeneity and Host Interactions. PMID:26984886
A large dataset of protein dynamics in the mammalian heart proteome. PMID:26977904
PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data. PMID:26966684
Genome and network visualization facilitates the analyses of the effects of drugs and mutations on protein-protein and drug-protein networks. PMID:26961139
De novo Transcriptome Assembly of Floral Buds of Pineapple and Identification of Differentially Expressed Genes in Response to Ethephon Induction. PMID:26955375
Comparing Alzheimer's and Parkinson's diseases networks using graph communities structure. PMID:26935435
A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica. PMID:26931371
Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis. PMID:26904004
Featured Article: Genotation: Actionable knowledge for the scientific reader. PMID:26900164
Population structure and minimum core genome typing of Legionella pneumophila. PMID:26888563
Uncovering the pathways underlying whole body regeneration in a chordate model, Botrylloides leachi using de novo transcriptome analysis. PMID:26879048
miRNA Repertoires of Demosponges Stylissa carteri and Xestospongia testudinaria. PMID:26871907
Comparative Transcriptomic Exploration Reveals Unique Molecular Adaptations of Neuropathogenic Trichobilharzia to Invade and Parasitize Its Avian Definitive Host. PMID:26863542
A Novel Feature Extraction Method with Feature Selection to Identify Golgi-Resident Protein Types from Imbalanced Data. PMID:26861308
Multi-tissue transcriptomics for construction of a comprehensive gene resource for the terrestrial snail Theba pisana. PMID:26852673
Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses. PMID:26843925
Assembly and clustering of natural antibiotics guides target identification. PMID:26829473
In silico study of subtilisin-like protease 1 (SUB1) from different Plasmodium species in complex with peptidyl-difluorostatones and characterization of potent pan-SUB1 inhibitors. PMID:26826801
Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress. PMID:26792871
CSGene: a literature-based database for cell senescence genes and its application to identify critical cell aging pathways and associated diseases. PMID:26775705
267 Spanish Exomes Reveal Population-Specific Differences in Disease-Related Genetic Variation. PMID:26764160
Determination of specificity influencing residues for key transcription factor families. PMID:26753103
VIRALpro: a tool to identify viral capsid and tail sequences. PMID:26733451
Using host-pathogen protein interactions to identify and characterize Francisella tularensis virulence factors. PMID:26714771
Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing. PMID:26698853
Fundamentals of protein interaction network mapping. PMID:26681426
Identification of potential drug targets by subtractive genome analysis of Escherichia coli O157:H7: an in silico approach. PMID:26677339
Unraveling the distinctive features of hemorrhagic and non-hemorrhagic snake venom metalloproteinases using molecular simulations. PMID:26676823
Genomic Targets and Features of BarA-UvrY (-SirA) Signal Transduction Systems. PMID:26673755
Deletion of GSTA4-4 results in increased mitochondrial post-translational modification of proteins by reactive aldehydes following chronic ethanol consumption in mice. PMID:26654979
Structural features determining thermal adaptation of esterases. PMID:26647400
Complete genome sequence of Salinicoccus halodurans H3B36, isolated from the Qaidam Basin in China. PMID:26634017
The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract. PMID:26626322
Exploring molecular variation in Schistosoma japonicum in China. PMID:26621075
∆F508 CFTR interactome remodelling promotes rescue of cystic fibrosis. PMID:26618866
Database resources of the National Center for Biotechnology Information. PMID:26615191
Characterization of Burkholderia pseudomallei protein BPSL1375 validates the Putative hemolytic activity of the COG3176 N-Acyltransferase family. PMID:26597807
Leishmania donovani Encodes a Functional Selenocysteinyl-tRNA Synthase. PMID:26586914
Death of a dogma: eukaryotic mRNAs can code for more than one protein. PMID:26578573
Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. PMID:26559508
WITHDRAWN--a resource for withdrawn and discontinued drugs. PMID:26553801
Automatic generation of bioinformatics tools for predicting protein-ligand binding sites. PMID:26545824
Whole Genome Sequencing of the Symbiont Pseudovibrio sp. from the Intertidal Marine Sponge Polymastia penicillus Revealed a Gene Repertoire for Host-Switching Permissive Lifestyle. PMID:26519859
Increased hepatocellular protein carbonylation in human end-stage alcoholic cirrhosis. PMID:26518673
Bioengineering Human Myocardium on Native Extracellular Matrix. PMID:26503464
Extending Protein Domain Boundary Predictors to Detect Discontinuous Domains. PMID:26502173
CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area. PMID:26502070
An Exploration of the Universe of Polyglutamine Structures. PMID:26495838
Nonsynonymous Single-Nucleotide Variations on Some Posttranslational Modifications of Human Proteins and the Association with Diseases. PMID:26495027
An evidence-based knowledgebase of metastasis suppressors to identify key pathways relevant to cancer metastasis. PMID:26486520
An update of the macaque testis proteome. PMID:26484360
Recovering full-length viral genomes from metagenomes. PMID:26483782
Characterization of the Cardiac Overexpression of HSPB2 Reveals Mitochondrial and Myogenic Roles Supported by a Cardiac HspB2 Interactome. PMID:26465331
Functional Analyses of Transcription Factor Binding Sites that Differ between Present-Day and Archaic Humans. PMID:26454764
Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM). PMID:26442528
Actionable clinical decisions based on comprehensive genomic evaluation in asymptomatic adults. PMID:26436109
PATBox: A Toolbox for Classification and Analysis of P-Type ATPases. PMID:26422234
Genome sequence of Anoxybacillus ayderensis AB04(T) isolated from the Ayder hot spring in Turkey. PMID:26413199
PanFP: pangenome-based functional profiles for microbial communities. PMID:26409790
Semantic Assembly and Annotation of Draft RNAseq Transcripts without a Reference Genome. PMID:26393794
Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor. PMID:26384938
Identification of B6T173 (ZmPrx35) as the prevailing peroxidase in highly insect-resistant maize (Zea mays, p84C3) kernels by activity-directed purification. PMID:26379694
Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats. PMID:26377088
An Ensemble Method to Distinguish Bacteriophage Virion from Non-Virion Proteins Based on Protein Sequence Characteristics. PMID:26370987
An Ensemble Method to Distinguish Bacteriophage Virion from Non-Virion Proteins Based on Protein Sequence Characteristics. PMID:26370987
Different combinations of atomic interactions predict protein-small molecule and protein-DNA/RNA affinities with similar accuracy. PMID:26370248
Mating induces the expression of immune- and pH-regulatory genes in the utero-vaginal junction containing mucosal sperm-storage tubuli of hens. PMID:26370241
A user-friendly web portal for analyzing conformational changes in structures of Mycobacterium tuberculosis. PMID:26361768
Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm. PMID:26325505
Binding Interactions of Keratin-Based Hair Fiber Extract to Gold, Keratin, and BMP-2. PMID:26317522
Network Topologies Decoding Cervical Cancer. PMID:26308848
DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool. PMID:26304539
CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea. PMID:26289427
PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications. PMID:26283093
Detection and Quantitation of Circulating Human Irisin by Tandem Mass Spectrometry. PMID:26278051
OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization. PMID:26272982
Biosynthesis of Squalene from Farnesyl Diphosphate in Bacteria: Three Steps Catalyzed by Three Enzymes. PMID:26258173
A Disulfide Bond Is Required for the Transmission of Forces through SUN-KASH Complexes. PMID:26244732
Abnormal subcellular localization of GABAA receptor subunits in schizophrenia brain. PMID:26241350
Similar Neutrophil-Driven Inflammatory and Antibacterial Responses in Elderly Patients with Symptomatic and Asymptomatic Bacteriuria. PMID:26238715
De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods. PMID:26228684
Expression and Subcellular Distribution of GFP-Tagged Human Tetraspanin Proteins in Saccharomyces cerevisiae. PMID:26218426
The MI bundle: enabling network and structural biology in genome visualization tools. PMID:26209801
Draft genome sequences for the obligate bacterial predators Bacteriovorax spp. of four phylogenetic clusters. PMID:26203326
The BioPlex Network: A Systematic Exploration of the Human Interactome. PMID:26186194
Absence of catalytic domain in a putative protein kinase C (PkcA) suppresses tip dominance in Dictyostelium discoideum. PMID:26183108
Relationships between predicted moonlighting proteins, human diseases, and comorbidities from a network perspective. PMID:26157390
Novel drug target identification for the treatment of dementia using multi-relational association mining. PMID:26154857
In Silico/In Vivo Insights into the Functional and Evolutionary Pathway of Pseudomonas aeruginosa Oleate-Diol Synthase. Discovery of a New Bacterial Di-Heme Cytochrome C Peroxidase Subfamily. PMID:26154497
Transcriptome analysis of the biofilm formed by methicillin-susceptible Staphylococcus aureus. PMID:26149474
The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies. PMID:26149169
CB2 cannabinoid receptor agonist enantiomers HU-433 and HU-308: An inverse relationship between binding affinity and biological potency. PMID:26124120
De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes. PMID:26114291
Application of a hierarchical enzyme classification method reveals the role of gut microbiome in human metabolism. PMID:26099921
dbEMT: an epithelial-mesenchymal transition associated gene resource. PMID:26099468
Analysis of Low Frequency Protein Truncating Stop-Codon Variants and Fasting Concentration of Growth Hormone. PMID:26086970
HCSD: the human cancer secretome database. PMID:26078477
Lysoplex: An efficient toolkit to detect DNA sequence variations in the autophagy-lysosomal pathway. PMID:26075876
Pedican: an online gene resource for pediatric cancers with literature evidence. PMID:26073932
The Complexity of Posttranscriptional Small RNA Regulatory Networks Revealed by In Silico Analysis of Gossypium arboreum L. Leaf, Flower and Boll Small Regulatory RNAs. PMID:26070200
Genome-wide association study identifies novel genetic variants contributing to variation in blood metabolite levels. PMID:26068415
kpath: integration of metabolic pathway linked data. PMID:26055101
An integrated structural proteomics approach along the druggable genome of Corynebacterium pseudotuberculosis species for putative druggable targets. PMID:26041381
Structure Based Modeling of Small Molecules Binding to the TLR7 by Atomistic Level Simulations. PMID:26007168
ProteINSIDE to Easily Investigate Proteomics Data from Ruminants: Application to Mine Proteome of Adipose and Muscle Tissues in Bovine Foetuses. PMID:26000831
CleavPredict: A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events. PMID:25996941
Autocatalytic sets in E. coli metabolism. PMID:25995773
Evolution of the Translocation and Assembly Module (TAM). PMID:25994932
A repository of assays to quantify 10,000 human proteins by SWATH-MS. PMID:25977788
CARDIO-PRED: an in silico tool for predicting cardiovascular-disorder associated proteins. PMID:25972989
GLASS: a comprehensive database for experimentally validated GPCR-ligand associations. PMID:25971743
Sharing and Specificity of Co-expression Networks across 35 Human Tissues. PMID:25970446
ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling. PMID:25956654
Dissecting the calcium-induced differentiation of human primary keratinocytes stem cells by integrative and structural network analyses. PMID:25946651
MIMP: predicting the impact of mutations on kinase-substrate phosphorylation. PMID:25938373
Community challenges in biomedical text mining over 10 years: success, failure and the future. PMID:25935162
Pathways with PathWhiz. PMID:25934797
Metazoans evolved by taking domains from soluble proteins to expand intercellular communication network. PMID:25923201
ProtoBug: functional families from the complete proteomes of insects. PMID:25911153
Plasmodium vivax inhibits erythroid cell growth through altered phosphorylation of the cytoskeletal protein ezrin. PMID:25889165
Standard flow liquid chromatography for shotgun proteomics in bioenergy research. PMID:25883932
Solution structure of a soluble fragment derived from a membrane protein by shotgun proteolysis. PMID:25877662
Computational prediction of protein-protein interactions. PMID:25859943
Epitope-based peptide vaccine design and target site depiction against Ebola viruses: an immunoinformatics study. PMID:25857850
Global genome and transcriptome analyses of Magnaporthe oryzae epidemic isolate 98-06 uncover novel effectors and pathogenicity-related genes, revealing gene gain and lose dynamics in genome evolution. PMID:25837042
TRAP-seq defines markers for novel populations of hypothalamic and brainstem LepRb neurons. PMID:25830093
Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics. PMID:25814448
Potential role of glutathione in evolution of thiol-based redox signaling sites in proteins. PMID:25805991
The juxtamembrane regions of human receptor tyrosine kinases exhibit conserved interaction sites with anionic lipids. PMID:25779975
Shared resources, shared costs--leveraging biocuration resources. PMID:25776020
The NDST gene family in zebrafish: role of NDST1B in pharyngeal arch formation. PMID:25767878
The evolutionary and functional diversity of classical and lesser-known cytoplasmic and organellar translational GTPases across the tree of life. PMID:25756599
Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2-dehydrogenase. PMID:25752240
Mining host-pathogen protein interactions to characterize Burkholderia mallei infectivity mechanisms. PMID:25738731
PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples. PMID:25725063
Lysosomal calcium signalling regulates autophagy through calcineurin and TFEB. PMID:25720963
Computational polypharmacology analysis of the heat shock protein 90 interactome. PMID:25686391
The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity. PMID:25684150
Combining natural sequence variation with high throughput mutational data to reveal protein interaction sites. PMID:25671604
DBC1/CCAR2 and CCAR1 Are Largely Disordered Proteins that Have Evolved from One Common Ancestor. PMID:25610865
Evaluation of de novo transcriptome assemblies from RNA-Seq data. PMID:25608678
Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions. PMID:25592227
Proteome scale comparative modeling for conserved drug and vaccine targets identification in Corynebacterium pseudotuberculosis. PMID:25573232
Insight in genome-wide association of metabolite quantitative traits by exome sequence analyses. PMID:25569235
The enzymatic nature of an anonymous protein sequence cannot reliably be inferred from superfamily level structural information alone. PMID:25559918
Evolutionary genomics and adaptive evolution of the Hedgehog gene family (Shh, Ihh and Dhh) in vertebrates. PMID:25549322
FLAVIdB: A data mining system for knowledge discovery in flaviviruses with direct applications in immunology and vaccinology. PMID:25544857
DCDB 2.0: a major update of the drug combination database. PMID:25539768
Overview of computational vaccinology: vaccine development through information technology. PMID:25534541
Rapid evolution of virus sequences in intrinsically disordered protein regions. PMID:25502394
Evolutionary link between metazoan RHIM motif and prion-forming domain of fungal heterokaryon incompatibility factor HET-s/HET-s. PMID:25500536
Finding gene regulatory network candidates using the gene expression knowledge base. PMID:25490885
Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors. PMID:25478866
Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case. PMID:25476999
The role of palmitoylation for protein recruitment to the inner membrane complex of the malaria parasite. PMID:25425642
Proteomics-Based Identification of Differentially Abundant Proteins from Human Keratinocytes Exposed to Arsenic Trioxide. PMID:25419056
ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts. PMID:25414346
Structure-biological function relationship extended to mitotic arrest-deficient 2-like protein Mad2 native and mutants-new opportunity for genetic disorder control. PMID:25411801
Identification of rare alternative splicing events in MS/MS data reveals a significant fraction of alternative translation initiation sites. PMID:25405079
Database resources of the National Center for Biotechnology Information. PMID:25398906
Human cancer databases (review). PMID:25369839
Detection of atypical genes in virus families using a one-class SVM. PMID:25336138
Expression profiling of mitochondrial voltage-dependent anion channel-1 associated genes predicts recurrence-free survival in human carcinomas. PMID:25333947
Caspase cleavage sites in the human proteome: CaspDB, a database of predicted substrates. PMID:25330111
Draft Genome Sequence of the Pathogenic Fungus Scedosporium apiospermum. PMID:25278533
Virtual screening of phytochemicals to novel targets in Haemophilus ducreyi towards the treatment of Chancroid. PMID:25258485
Sequence-motif detection of NAD(P)-binding proteins: discovery of a unique antibacterial drug target. PMID:25253464
Single nucleotide variations: biological impact and theoretical interpretation. PMID:25234433
PeptideManager: a peptide selection tool for targeted proteomic studies involving mixed samples from different species. PMID:25228907
Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population. PMID:25215496
Genomic analysis of the Pacific oyster (Crassostrea gigas) reveals possible conservation of vertebrate sex determination in a mollusc. PMID:25213692
Cleavage specificity analysis of six type II transmembrane serine proteases (TTSPs) using PICS with proteome-derived peptide libraries. PMID:25211023
Deep proteomic evaluation of primary and cell line motoneuron disease models delineates major differences in neuronal characteristics. PMID:25193168
A systematic approach to identify novel cancer drug targets using machine learning, inhibitor design and high-throughput screening. PMID:25165489
Whole genome sequencing and analysis of plant growth promoting bacteria isolated from the rhizosphere of plantation crops coconut, cocoa and arecanut. PMID:25162593
PconsFold: improved contact predictions improve protein models. PMID:25161237
Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. PMID:25124552
Target network differences between western drugs and Chinese herbal ingredients in treating cardiovascular disease. PMID:25104437
A comprehensive analysis of the Omp85/TpsB protein superfamily structural diversity, taxonomic occurrence, and evolution. PMID:25101071
From genotype to functional phenotype: unraveling the metabolomic features of colorectal cancer. PMID:25055199
A dedicated database system for handling multi-level data in systems biology. PMID:25053973
Gene discovery through transcriptome sequencing for the invasive mussel Limnoperna fortunei. PMID:25047650
Dermal wound transcriptomic responses to Infection with Pseudomonas aeruginosa versus Klebsiella pneumoniae in a rabbit ear wound model. PMID:25035691
Modelling the structure of full-length Epstein-Barr virus nuclear antigen 1. PMID:25011696
Analysis of genome sequences from plant pathogenic Rhodococcus reveals genetic novelties in virulence loci. PMID:25010934
Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations. PMID:24980186
Induced fit docking, pharmacophore modeling, and molecular dynamic simulations on thiazolidinedione derivatives to explore key interactions with Tyr48 in polyol pathway. PMID:24974084
Structure and function of the LmbE-like superfamily. PMID:24970229
Comparative genomics and evolution of regulons of the LacI-family transcription factors. PMID:24966856
Chondroitin sulfate proteoglycans: structure-function relationship with implication in neural development and brain disorders. PMID:24955366
IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools. PMID:24949626
Comparative genomics of Riemerella anatipestifer reveals genetic diversity. PMID:24935762
BioAssemblyModeler (BAM): user-friendly homology modeling of protein homo- and heterooligomers. PMID:24922057
Transcriptional and biochemical responses of monoacylglycerol acyltransferase-mediated oil synthesis and associated senescence-like responses in Nicotiana benthamiana. PMID:24904604
Cryptosporidium parvum has an active hypusine biosynthesis pathway. PMID:24893338
Genome-wide expression profile of the response to spinal cord injury in Xenopus laevis reveals extensive differences between regenerative and non-regenerative stages. PMID:24885550
Biophysical constraints on the evolution of tissue structure and function. PMID:24882821
Identification of two poorly prognosed ovarian carcinoma subtypes associated with CHEK2 germ-line mutation and non-CHEK2 somatic mutation gene signatures. PMID:24879340
DDI-CPI, a server that predicts drug-drug interactions through implementing the chemical-protein interactome. PMID:24875476
Quantitative proteomics to characterize specific histone H2A proteolysis in chronic lymphocytic leukemia and the myeloid THP-1 cell line. PMID:24871368
A comprehensive phylogenetic and structural analysis of the carcinoembryonic antigen (CEA) gene family. PMID:24858421
PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins. PMID:24857970
OncoSearch: cancer gene search engine with literature evidence. PMID:24813447
De novo transcriptome sequencing and analysis of the cereal cyst nematode, Heterodera avenae. PMID:24802510
PredictProtein--an open resource for online prediction of protein structural and functional features. PMID:24799431
Molecular dynamics, dynamic site mapping, and highthroughput virtual screening on leptin and the Ob receptor as anti-obesity target. PMID:24797089
Substrate deconstruction and the nonadditivity of enzyme recognition. PMID:24791931
Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures. PMID:24780077
Effects of silver nitrate and silver nanoparticles on a planktonic community: general trends after short-term exposure. PMID:24755991
Proton channel models filling the gap between experimental data and the structural rationale. PMID:24755912
The membrane proteome of sensory cilia to the depth of olfactory receptors. PMID:24748648
Prediction and prioritization of rare oncogenic mutations in the cancer Kinome using novel features and multiple classifiers. PMID:24743239
Large scale analysis of co-existing post-translational modifications in histone tails reveals global fine structure of cross-talk. PMID:24741113
A meta analysis of pancreatic microarray datasets yields new targets as cancer genes and biomarkers. PMID:24740004
The haloarchaeal MCM proteins: bioinformatic analysis and targeted mutagenesis of the β7-β8 and β9-β10 hairpin loops and conserved zinc binding domain cysteines. PMID:24723920
Genome Sequence of the Aerobic Arsenate-Reducing Bacterium Pantoea sp. Strain IMH. PMID:24723713
The interaction of CRM1 and the nuclear pore protein Tpr. PMID:24722547
The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes. PMID:24710217
The bromodomain: from epigenome reader to druggable target. PMID:24686119
FreeContact: fast and free software for protein contact prediction from residue co-evolution. PMID:24669753
GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks. PMID:24667292
Identification of microRNAs in the coral Stylophora pistillata. PMID:24658574
Comparative analysis of Salmonella genomes identifies a metabolic network for escalating growth in the inflamed gut. PMID:24643865
Genome profiling of sterol synthesis shows convergent evolution in parasites and guides chemotherapeutic attack. PMID:24627128
Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. PMID:24622611
BambooGDB: a bamboo genome database with functional annotation and an analysis platform. PMID:24602877
Interactive exploration of integrated biological datasets using context-sensitive workflows. PMID:24600467
Sequence complexity of amyloidogenic regions in intrinsically disordered human proteins. PMID:24594841
Comprehensive analysis of HPV16 integration in OSCC reveals no significant impact of physical status on viral oncogene and virally disrupted human gene expression. PMID:24586376
COMPARTMENTS: unification and visualization of protein subcellular localization evidence. PMID:24573882
Prediction of protein interaction types based on sequence and network features. PMID:24564924
Identification of gene fusions from human lung cancer mass spectrometry data. PMID:24564548
Cluster based prediction of PDZ-peptide interactions. PMID:24564547
Literature classification for semi-automated updating of biological knowledgebases. PMID:24564403
LC-MS proteomics analysis of the insulin/IGF-1-deficient Caenorhabditis elegans daf-2(e1370) mutant reveals extensive restructuring of intermediary metabolism. PMID:24555535
The Arabidopsis cytosolic proteome: the metabolic heart of the cell. PMID:24550929
In silico prediction of antimalarial drug target candidates. PMID:24533280
Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes 'Gramella forsetii' KT0803. PMID:24522261
Structure to function prediction of hypothetical protein KPN_00953 (Ycbk) from Klebsiella pneumoniae MGH 78578 highlights possible role in cell wall metabolism. PMID:24499172
Characterization of the membrane proteome and N-glycoproteome in BV-2 mouse microglia by liquid chromatography-tandem mass spectrometry. PMID:24495382
3D modeling and characterization of the human CD115 monoclonal antibody H27K15 epitope and design of a chimeric CD115 target. PMID:24492308
Genetics of proteasome diseases. PMID:24490108
Analysis of the transcriptome of adult Dictyocaulus filaria and comparison with Dictyocaulus viviparus, with a focus on molecules involved in host-parasite interactions. PMID:24487001
Genome wide association and linkage analyses identified three loci-4q25, 17q23.2, and 10q11.21-associated with variation in leukocyte telomere length: the Long Life Family Study. PMID:24478790
The MoxR ATPase RavA and its cofactor ViaA interact with the NADH:ubiquinone oxidoreductase I in Escherichia coli. PMID:24454883
Deriving a mutation index of carcinogenicity using protein structure and protein interfaces. PMID:24454733
An Overview of the Challenges in Designing, Integrating, and Delivering BARD: A Public Chemical-Biology Resource and Query Portal for Multiple Organizations, Locations, and Disciplines. PMID:24441647
Multi-omic network signatures of disease. PMID:24432028
Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus. PMID:24415955
Allerdictor: fast allergen prediction using text classification techniques. PMID:24403538
bex-db: Bioinformatics workbench for comprehensive analysis of barley-expressed genes. PMID:24399916
Protein complex identification by integrating protein-protein interaction evidence from multiple sources. PMID:24386289
Cytoplasmic protein methylation is essential for neural crest migration. PMID:24379414
TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes. PMID:24373374
A comprehensive phylogenetic analysis of deadenylases. PMID:24348009
The HBM domain: introducing bimodularity to bacterial sensing. PMID:24347303
Assessment of ligand binding site predictions in CASP10. PMID:24339001
Gene duplication, lineage-specific expansion, and subfunctionalization in the MADF-BESS family patterns the Drosophila wing hinge. PMID:24336749
Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks. PMID:24330590
Molecular evolution of threonine dehydratase in bacteria. PMID:24324624
The venom gland transcriptome of Latrodectus tredecimguttatus revealed by deep sequencing and cDNA library analysis. PMID:24312294
Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. PMID:24309898
Conserved-residue mutations in Wzy affect O-antigen polymerization and Wzz-mediated chain-length regulation in Pseudomonas aeruginosa PAO1. PMID:24309320
Analysis of banana transcriptome and global gene expression profiles in banana roots in response to infection by race 1 and tropical race 4 of Fusarium oxysporum f. sp. cubense. PMID:24304681
Analysis of banana transcriptome and global gene expression profiles in banana roots in response to infection by race 1 and tropical race 4 of Fusarium oxysporum f. sp. cubense. PMID:24304681
Single nucleotide polymorphisms in microRNA binding sites of oncogenes: implications in cancer and pharmacogenomics. PMID:24286505
Functional and genomic analyses of alpha-solenoid proteins. PMID:24278209
Database resources of the National Center for Biotechnology Information. PMID:24259429
MEGANTE: a web-based system for integrated plant genome annotation. PMID:24253915
P³DB 3.0: From plant phosphorylation sites to protein networks. PMID:24243849
Revealing the hidden functional diversity of an enzyme family. PMID:24240508
CoMAGC: a corpus with multi-faceted annotations of gene-cancer relations. PMID:24225062
Enzyme reaction annotation using cloud techniques. PMID:24222895
Integrative pathway-based approach for genome-wide association studies: identification of new pathways for rheumatoid arthritis and type 1 diabetes. PMID:24205270
Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs. PMID:24204767
Regulation of OSR1 and the sodium, potassium, two chloride cotransporter by convergent signals. PMID:24191005
Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. PMID:24150943
Can inferred provenance and its visualisation be used to detect erroneous annotation? A case study using UniProtKB. PMID:24143170
Quantification of the impact of PSI:Biology according to the annotations of the determined structures. PMID:24139526
Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals. PMID:24119094
Ureidoglycolate hydrolase, amidohydrolase, lyase: how errors in biological databases are incorporated in scientific papers and vice versa. PMID:24107613
Complete Genome Sequence of Vibrio anguillarum M3, a Serotype O1 Strain Isolated from Japanese Flounder in China. PMID:24072867
Characterization, design, and function of the mitochondrial proteome: from organs to organisms. PMID:24070373
Assessment and reconstruction of novel HSP90 genes: duplications, gains and losses in fungal and animal lineages. PMID:24066039
BCov: a method for predicting β-sheet topology using sparse inverse covariance estimation and integer programming. PMID:24064422
Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. PMID:24060102
In silico ionomics segregates parasitic from free-living eukaryotes. PMID:24048281
Meta4: a web application for sharing and annotating metagenomic gene predictions using web services. PMID:24046776
IQdb: an intelligence quotient score-associated gene resource for human intelligence. PMID:24030781
Unraveling sterol-dependent membrane phenotypes by analysis of protein abundance-ratio distributions in different membrane fractions under biochemical and endogenous sterol depletion. PMID:24030099
Proton-dependent gating and proton uptake by Wzx support O-antigen-subunit antiport across the bacterial inner membrane. PMID:24023388
The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus. PMID:23985341
Cloud prediction of protein structure and function with PredictProtein for Debian. PMID:23971032
A viral-human interactome based on structural motif-domain interactions captures the human infectome. PMID:23951184
Assessment of protein disorder region predictions in CASP10. PMID:23946100
Exhaustive comparison and classification of ligand-binding surfaces in proteins. PMID:23934772
NetMHCstab - predicting stability of peptide-MHC-I complexes; impacts for cytotoxic T lymphocyte epitope discovery. PMID:23927693
Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels. PMID:23912596
The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites. PMID:23895374
The role of balanced training and testing data sets for binary classifiers in bioinformatics. PMID:23874456
Bioinformatics for spermatogenesis: annotation of male reproduction based on proteomics. PMID:23852026
Integrating pathways of Parkinson's disease in a molecular interaction map. PMID:23832570
A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains. PMID:23813002
Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis. PMID:23799973
DigSee: Disease gene search engine with evidence sentences (version cancer). PMID:23761452
Combinatorial clustering of residue position subsets predicts inhibitor affinity across the human kinome. PMID:23754939
Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint. PMID:23749465
A phylomedicine approach to understanding the evolution of auditory sensory perception and disease in mammals. PMID:23745134
Protein-Protein Interactions Inferred from Domain-Domain Interactions in Genogroup II Genotype 4 Norovirus Sequences. PMID:23738320
Ontology-Based Querying with Bio2RDF's Linked Open Data. PMID:23735196
Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data. PMID:23734622
Quantitative Proteomics via High Resolution MS Quantification: Capabilities and Limitations. PMID:23710359
Protein composition of bronchoalveolar lavage fluid and airway surface liquid from newborn pigs. PMID:23709621
Combined sequence-based and genetic mapping analysis of complex traits in outbred rats. PMID:23708188
Semi-supervised prediction of SH2-peptide interactions from imbalanced high-throughput data. PMID:23690949
Partial venom gland transcriptome of a Drosophila parasitoid wasp, Leptopilina heterotoma, reveals novel and shared bioactive profiles with stinging Hymenoptera. PMID:23688557
Genome-scale modeling of the protein secretory machinery in yeast. PMID:23667601
LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics. PMID:23667450
Bioinformatics analysis identify novel OB fold protein coding genes in C. elegans. PMID:23638006
Human protein cluster analysis using amino acid frequencies. PMID:23593177
The structure of yeast glutaminyl-tRNA synthetase and modeling of its interaction with tRNA. PMID:23583912
MGcV: the microbial genomic context viewer for comparative genome analysis. PMID:23547764
Discovery-2: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria. PMID:23537208
PI2PE: A Suite of Web Servers for Predictions Ranging From Protein Structure to Binding Kinetics. PMID:23526172
Application of text-mining for updating protein post-translational modification annotation in UniProtKB. PMID:23517090
The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics. PMID:23514033
Evolution of the ferric reductase domain (FRD) superfamily: modularity, functional diversification, and signature motifs. PMID:23505460
phiBIOTICS: catalogue of therapeutic enzybiotics, relevant research studies and practical applications. PMID:23497033
One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012. PMID:23494302
De Novo transcriptome assembly (NGS) of Curcuma longa L. rhizome reveals novel transcripts related to anticancer and antimalarial terpenoids. PMID:23468859
PASmiR: a literature-curated database for miRNA molecular regulation in plant response to abiotic stress. PMID:23448274
A uniquely adaptable pore is consistent with NALCN being an ion sensor. PMID:23442378
Non-catalytic participation of the Pin1 peptidyl-prolyl isomerase domain in target binding. PMID:23407864
Complete Genome Sequence of Listeria monocytogenes LL195, a Serotype 4b Strain from the 1983-1987 Listeriosis Epidemic in Switzerland. PMID:23405339
Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria. PMID:23398941
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. PMID:23398680
Computational model for pathway reconstruction to unravel the evolutionary significance of melanin synthesis. PMID:23390353
Exoproteome and secretome derived broad spectrum novel drug and vaccine candidates in Vibrio cholerae targeted by Piper betel derived compounds. PMID:23382822
Metabolic hormone FGF21 is induced in ground squirrels during hibernation but its overexpression is not sufficient to cause torpor. PMID:23301087
Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PMID:23300433
Large-scale reverse docking profiles and their applications. PMID:23282219
Meta-analytical biomarker search of EST expression data reveals three differentially expressed candidates. PMID:23282184
Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets. PMID:23281852
CYPSI: a structure-based interface for cytochrome P450s and ligands in Arabidopsis thaliana. PMID:23256889
Multiple inter-kingdom horizontal gene transfers in the evolution of the phosphoenolpyruvate carboxylase gene family. PMID:23251445
An integrated in silico approach to design specific inhibitors targeting human poly(a)-specific ribonuclease. PMID:23236441
Draft genome sequence of Staphylococcus massiliensis strain 5402776T. PMID:23209235
KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms. PMID:23193279
Database resources of the National Center for Biotechnology Information. PMID:23193264
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. PMID:23180789
Complex evolutionary relationships among four classes of modular RNA-binding splicing regulators in eukaryotes: the hnRNP, SR, ELAV-like and CELF proteins. PMID:23179353
Next generation sequencing and de novo transcriptome analysis of Costus pictus D. Don, a non-model plant with potent anti-diabetic properties. PMID:23176672
A broad specificity nucleoside kinase from Thermoplasma acidophilum. PMID:23161756
Chlorobaculum tepidum TLS displays a complex transcriptional response to sulfide addition. PMID:23161024
Draft genome sequences of Actinomyces timonensis strain 7400942T and its prophage. PMID:23144376
MODOMICS: a database of RNA modification pathways--2013 update. PMID:23118484
Spliceosome database: a tool for tracking components of the spliceosome. PMID:23118483
The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential. PMID:23083487
MK4MDD: a multi-level knowledge base and analysis platform for major depressive disorder. PMID:23071556
Type-IVC secretion system: a novel subclass of type IV secretion system (T4SS) common existing in gram-positive genus Streptococcus. PMID:23056296
Transcriptional analysis of prebiotic uptake and catabolism by Lactobacillus acidophilus NCFM. PMID:23028535
Development of an undergraduate bioinformatics degree program at a liberal arts college. PMID:23012579
AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities. PMID:22967011
Prediction of phenotypes of missense mutations in human proteins from biological assemblies. PMID:22965855
Draft genome sequence of Tsukamurella sp. strain 1534. PMID:22965100
An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB. PMID:22962482
Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal. PMID:22948926
Draft genome sequence of Brevibacterium massiliense strain 541308T. PMID:22933772
Draft genome sequence of Actinomyces massiliensis strain 4401292T. PMID:22933754
EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes. PMID:22923291
Intrinsic disorder in the human spliceosomal proteome. PMID:22912569
Metal dealing at the origin of the Chordata phylum: the metallothionein system and metal overload response in amphioxus. PMID:22905252
Post-translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding. PMID:22899623
Sequencing the genome of Marssonina brunnea reveals fungus-poplar co-evolution. PMID:22876864
The Cell Collective: toward an open and collaborative approach to systems biology. PMID:22871178
Functional annotation from the genome sequence of the giant panda. PMID:22865348
A strategy based on protein-protein interface motifs may help in identifying drug off-targets. PMID:22817115
SynProt: A Database for Proteins of Detergent-Resistant Synaptic Protein Preparations. PMID:22737123
A global characterization and identification of multifunctional enzymes. PMID:22723914
Short term evolution of a highly transmissible methicillin-resistant Staphylococcus aureus clone (ST228) in a tertiary care hospital. PMID:22720005
DEFOG: discrete enrichment of functionally organized genes. PMID:22706384
The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes. PMID:22693442
Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations. PMID:22685075
Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis. PMID:22645369
Analyzing large biological datasets with association networks. PMID:22638576
The YARHG domain: an extracellular domain in search of a function. PMID:22615736
MGEx-Udb: a mammalian uterus database for expression-based cataloguing of genes across conditions, including endometriosis and cervical cancer. PMID:22606288
Bioinformatics opportunities for identification and study of medicinal plants. PMID:22589384
Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. PMID:22588898
Structural bioinformatics of the human spliceosomal proteome. PMID:22573172
OREMPdb: a semantic dictionary of computational pathway models. PMID:22536973
Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events. PMID:22467916
The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data. PMID:22465017
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. PMID:22438567
PRIDE: quality control in a proteomics data repository. PMID:22434838
AntiFam: a tool to help identify spurious ORFs in protein annotation. PMID:22434837
CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. PMID:22434836
Annotation of functional sites with the Conserved Domain Database. PMID:22434827
PupDB: a database of pupylated proteins. PMID:22424087
Online electrospray ionization mass spectrometric monitoring of protease-catalyzed reactions in real time. PMID:22314937
Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. PMID:22301074
Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks. PMID:22287626
KB-Rank: efficient protein structure and functional annotation identification via text query. PMID:22270457
Roundup 2.0: enabling comparative genomics for over 1800 genomes. PMID:22247275
E3Net: a system for exploring E3-mediated regulatory networks of cellular functions. PMID:22199232
Network systems biology for targeted cancer therapies. PMID:22176777
Phosphorylation in protein-protein binding: effect on stability and function. PMID:22153503
Database resources of the National Center for Biotechnology Information. PMID:22140104
A computational analysis of the binding mode of closantel as inhibitor of the Onchocerca volvulus chitinase: insights on macrofilaricidal drug design. PMID:22101363
dbDEPC 2.0: updated database of differentially expressed proteins in human cancers. PMID:22096234
CADRE: the Central Aspergillus Data REpository 2012. PMID:22080563
Deep sequencing the transcriptome reveals seasonal adaptive mechanisms in a hibernating mammal. PMID:22046435
Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations. PMID:22025670
BitterDB: a database of bitter compounds. PMID:21940398
The representation of protein complexes in the Protein Ontology (PRO). PMID:21929785
SSPred: A prediction server based on SVM for the identification and classification of proteins involved in bacterial secretion systems. PMID:21904425 -
UniProt: the universal protein knowledgebase
PubMed citations: 677.
677 articles citing: UniProt: the universal protein knowledgebase
Network Pharmacology and Experimental Validation to Explore the Mechanism of Qing-Jin-Hua-Tan-Decoction Against Acute Lung Injury. PMID:35873580
NTD-DR: Nonnegative tensor decomposition for drug repositioning. PMID:35862409
Metformin and Gegen Qinlian Decoction boost islet α-cell proliferation of the STZ induced diabetic rats. PMID:35858880
Molecular Mechanisms of AMH Signaling. PMID:35813657
Heat Shock Alters the Proteomic Profile of Equine Mesenchymal Stem Cells. PMID:35806237
Gene function prediction in five model eukaryotes exclusively based on gene relative location through machine learning. PMID:35803984
The Allelic Variant A391T of Metal Ion Transporter ZIP8 (SLC39A8) Leads to Hypotension and Enhanced Insulin Resistance. PMID:35784893
Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy. PMID:35773283
The zinc proteome of SARS-CoV-2. PMID:35767875
Molecular Pathogenesis and New Therapeutic Dimensions for Spinal Muscular Atrophy. PMID:35741415
Network pharmacology integrated molecular dynamics reveals the bioactive compounds and potential targets of Tinospora crispa Linn. as insulin sensitizer. PMID:35737707
mGWAS-Explorer: Linking SNPs, Genes, Metabolites, and Diseases for Functional Insights. PMID:35736459
The chemistry of snake venom and its medicinal potential. PMID:35702592
Network pharmacology and molecular docking approach to elucidate the mechanisms of Liuwei Dihuang pill in diabetic osteoporosis. PMID:35701780
Systematic Characterization of Lysine Post-translational Modification Sites Using MUscADEL. PMID:35696083
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis. PMID:35689204
Network pharmacology and in vivo experiments reveal the pharmacological effects and molecular mechanisms of Simiao Powder in prevention and treatment for gout. PMID:35672755
Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment. PMID:35668508
Molecular Mechanism of the Effect of Zhizhu Pill on Gastroesophageal Reflux Disease Based on Network Pharmacology and Molecular Docking. PMID:35646148
Identifying amyloid-related diseases by mapping mutations in low-complexity protein domains to pathologies. PMID:35637421
A novel low temperature active maltooligosaccharides-forming amylase from Bacillus koreensis HL12 as biocatalyst for maltooligosaccharide production. PMID:35615748
Evolution of tunnels in α/β-hydrolase fold proteins-What can we learn from studying epoxide hydrolases? PMID:35580137
Understanding the interactability of chikungunya virus proteins via molecular recognition feature analysis. PMID:35539973
Rare and potential pathogenic mutations of LMNA and LAMA4 associated with familial arrhythmogenic right ventricular cardiomyopathy/dysplasia with right ventricular heart failure, cerebral thromboembolism and hereditary electrocardiogram abnormality. PMID:35526016
Bioinformatic approach for the discovery of cis-eQTL signals during fruit ripening of a woody species as grape (Vitis vinifera L.). PMID:35523985
Danggui Buxue Decoction Ameliorates Idiopathic Pulmonary Fibrosis through MicroRNA and Messenger RNA Regulatory Network. PMID:35518349
Complete Genome Sequence of Stenotrophomonas maltophilia Phage Philippe. PMID:35510862
Complete Genome Sequence of Stenotrophomonas maltophilia Siphophage Siara. PMID:35499340
Integrated analysis of microbe-host interactions in Crohn's disease reveals potential mechanisms of microbial proteins on host gene expression. PMID:35479407
Complete Genome Sequence of Stenotrophomonas maltophilia Podophage Pepon. PMID:35467385
Potential therapeutic targets and molecular details of anthocyan-treated inflammatory bowel disease: a systematic bioinformatics analysis of network pharmacology. PMID:35423341
Chromosome evolution and the genetic basis of agronomically important traits in greater yam. PMID:35422045
Hidden Relationships between N-Glycosylation and Disulfide Bonds in Individual Proteins. PMID:35409101
Theoretical Investigation of the Coronavirus SARS-CoV-2 (COVID-19) Infection Mechanism and Selectivity. PMID:35408482
Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications. PMID:35402106
Salvia miltiorrhiza Bunge (Danshen) and Bioactive Compound Tanshinone IIA Alleviates Cisplatin-Induced Acute Kidney Injury Through Regulating PXR/NF-κB Signaling. PMID:35401224
Exploring Active Compounds and Mechanisms of Angong Niuhuang Wan on Ischemic Stroke Based on Network Pharmacology and Molecular Docking. PMID:35388303
Panel of Engineered Ubiquitin Variants Targeting the Family of Human Ubiquitin Interacting Motifs. PMID:35385646
Complete Genome Sequence of Stenotrophomonas maltophilia Podophage Paxi. PMID:35377170
Unifying the known and unknown microbial coding sequence space. PMID:35356891
Mucins Inhibit Coronavirus Infection in a Glycan-Dependent Manner. PMID:35345395
Complete Genome Sequence of Enterococcus faecalis Siphophage Sigurd. PMID:35343805
Complete Genome Sequence of Burkholderia cenocepacia Phage Paku. PMID:35343779
Functional Similarities of Protein-Coding Genes in Topologically Associating Domains and Spatially-Proximate Genomic Regions. PMID:35328034
Draft genomes assembly and annotation of Carex parvula and Carex kokanica reveals stress-specific genes. PMID:35322069
Complete Genome Sequence of Stenotrophomonas maltophilia Podophage Piffle. PMID:35319268
Complete Genome Sequence of Stenotrophomonas maltophilia Siphophage Sonora. PMID:35319245
Detection and Analysis of Syntenic Quantitative Trait Loci Controlling Cell Wall Quality in Angiosperms. PMID:35310628
Phylogeny-Aware Chemoinformatic Analysis of Chemical Diversity in Lamiaceae Enables Iridoid Pathway Assembly and Discovery of Aucubin Synthase. PMID:35298643
A novel series of putative Brugia malayi histone demethylase inhibitors as potential anti-filarial drugs. PMID:35294431
Complete Genome Sequence of Alcaligenes faecalis Phage Piluca. PMID:35289650
Complete Genome Sequence of Stenotrophomonas maltophilia Podophage Ptah. PMID:35286172
Complete Genome Sequence of Stenotrophomonas maltophilia Siphophage Suso. PMID:35285692
Characterization of intrinsically disordered regions in proteins informed by human genetic diversity. PMID:35275927
An in silico and in vitro integrated analysis method to reveal the curative mechanisms and pharmacodynamic substances of Bufei granule on chronic obstructive pulmonary disease. PMID:35266101
Complete Genome Sequence of Stenotrophomonas maltophilia Siphophage Suzuki. PMID:35258338
Complete Genome Sequence of Stenotrophomonas maltophilia Siphophage Summit. PMID:35254110
Complete Genome Sequence of Stenotrophomonas maltophilia Myophage Marzo. PMID:35225674
Complete Genome Sequence of Stenotrophomonas maltophilia Siphophage Silvanus. PMID:35225669
Analysis of the Factors Affecting Static In Vitro Pepsinolysis of Food Proteins. PMID:35209049
Metabolic Diversity and Aero-Tolerance in Anammox Bacteria from Geochemically Distinct Aquifers. PMID:35191775
Protease activities of vaginal Porphyromonas species disrupt coagulation and extracellular matrix in the cervicovaginal niche. PMID:35190575
Identification of a New Cholesterol-Binding Site within the IFN-γ Receptor that is Required for Signal Transduction. PMID:35166455
Theta-Defensins to Counter COVID-19 as Furin Inhibitors: In Silico Efficiency Prediction and Novel Compound Design. PMID:35154362
The gut microbiome and antibiotic resistome of chronic diarrhea rhesus macaques (Macaca mulatta) and its similarity to the human gut microbiome. PMID:35139923
Network Pharmacology-Based Analysis on Lonicera japonica for Chronic Osteomyelitis Treatment. PMID:35111224
A knowledge graph to interpret clinical proteomics data. PMID:35102292
The genome of medicinal leech (Whitmania pigra) and comparative genomic study for exploration of bioactive ingredients. PMID:35073842
Three Microbial Musketeers of the Seas: Shewanella baltica, Aliivibrio fischeri and Vibrio harveyi, and Their Adaptation to Different Salinity Probed by a Proteomic Approach. PMID:35054801
Zn2+ and Cu2+ Binding to the Extramembrane Loop of Zrt2, a Zinc Transporter of Candida albicans. PMID:35053269
Mechanistic insights into the use of rhubarb in diabetic kidney disease treatment using network pharmacology. PMID:35029893
Identification, functional characterization, assembly and structure of ToxIN type III toxin-antitoxin complex from E. coli. PMID:35018473
Arabidopsis thaliana Plant Natriuretic Peptide Active Domain Forms Amyloid-like Fibrils in a pH-Dependent Manner. PMID:35009013
Analysis of the Efficacy and Pharmacological Mechanisms of Action of Zhenren Yangzang Decoction on Ulcerative Colitis Using Meta-Analysis and Network Pharmacology. PMID:34992665
AHSA1 is a promising therapeutic target for cellular proliferation and proteasome inhibitor resistance in multiple myeloma. PMID:34991674
Identification of COPA as a potential prognostic biomarker and pharmacological intervention target of cervical cancer by quantitative proteomics and experimental verification. PMID:34991628
Interaction with mammalian enteric viruses alters outer membrane vesicle production and content by commensal bacteria. PMID:34981901
Based on Network Pharmacology Tools to Investigate the Mechanism of Tripterygium wilfordii Against IgA Nephropathy. PMID:34977095
Exploration of the Potential Mechanisms of Wumei Pill for the Treatment of Ulcerative Colitis by Network Pharmacology. PMID:34970312
Age-Related Changes of Gene Expression Profiles in Drosophila. PMID:34946931
IFPTML Mapping of Drug Graphs with Protein and Chromosome Structural Networks vs. Pre-Clinical Assay Information for Discovery of Antimalarial Compounds. PMID:34884870
Accurate protein function prediction via graph attention networks with predicted structure information. PMID:34882195
In-Silico Tool for Predicting, Scanning, and Designing Defensins. PMID:34880873
Hotspots for mutations in the SARS-CoV-2 spike glycoprotein: a correspondence analysis. PMID:34880279
Whole-Genome Sequencing Highlights Conservative Genomic Strategies of a Stress-Tolerant, Long-Lived Scleractinian Coral, Porites australiensis Vaughan, 1918. PMID:34878117
Network Pharmacology Exploration Reveals Anti-Apoptosis as a Common Therapeutic Mechanism for Non-Alcoholic Fatty Liver Disease Treated with Blueberry Leaf Polyphenols. PMID:34836315
LGFC-CNN: Prediction of lncRNA-Protein Interactions by Using Multiple Types of Features through Deep Learning. PMID:34828296
Mono- and Biallelic Protein-Truncating Variants in Alpha-Actinin 2 Cause Cardiomyopathy Through Distinct Mechanisms. PMID:34802252
Individualized Proteogenomics Reveals the Mutational Landscape of Melanoma Patients in Response to Immunotherapy. PMID:34771574
FusionGDB 2.0: fusion gene annotation updates aided by deep learning. PMID:34755868
Digenic heterozygous mutations of KCNH2 and SCN5A induced young and early-onset long QT syndrome and sinoatrial node dysfunction. PMID:34755423
Gene4HL: An Integrated Genetic Database for Hearing Loss. PMID:34733322
High-quality chromosome-level genome assembly of redlip mullet ( Planiliza haematocheila). PMID:34704426
Recent innovations and in-depth aspects of post-genome wide association study (Post-GWAS) to understand the genetic basis of complex phenotypes. PMID:34689168
The Effect of Impaired Polyamine Transport on Pneumococcal Transcriptome. PMID:34684271
Proteogenomics Reveals Perturbed Signaling Networks in Malignant Melanoma Cells Resistant to BRAF Inhibition. PMID:34673281
Fur colour in the Arctic fox: genetic architecture and consequences for fitness. PMID:34583587
Topological and Structural Plasticity of the Single Ig Fold and the Double Ig Fold Present in CD19. PMID:34572502
Exploring the Molecular Mechanism of Liuwei Dihuang Pills for Treating Diabetic Nephropathy by Combined Network Pharmacology and Molecular Docking. PMID:34552655
Discovery of bladder cancer biomarkers in paired pre- and postoperative urine samples. PMID:34532265
PDB-wide identification of physiological hetero-oligomeric assemblies based on conserved quaternary structure geometry. PMID:34520740
Enhanced Recovery of Microbial Genes and Genomes From a Marine Water Column Using Long-Read Metagenomics. PMID:34512586
Longitudinal peripheral tissue RNA-Seq transcriptomic profiling, hyperalgesia, and wound healing in the rat plantar surgical incision model. PMID:34499774
Icariin, an Up-and-Coming Bioactive Compound Against Neurological Diseases: Network Pharmacology-Based Study and Literature Review. PMID:34447243
The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference? PMID:34440517
The mechanisms of Chuanxiong Rhizoma in treating spinal cord injury based on network pharmacology and experimental verification. PMID:34430586
Feasibility and Mechanism Analysis of Shenfu Injection in the Treatment of Idiopathic Pulmonary Fibrosis. PMID:34393772
RNA-Seq analysis reveals potential regulators of programmed cell death and leaf remodelling in lace plant (Aponogeton madagascariensis). PMID:34388962
Insight into the Phylogenetic Relationships among Three Subfamilies within Heptageniidae (Insecta: Ephemeroptera) along with Low-Temperature Selection Pressure Analyses Using Mitogenomes. PMID:34357316
FLAME: A Web Tool for Functional and Literature Enrichment Analysis of Multiple Gene Lists. PMID:34356520
Identification of Novel Rotihibin Analogues in Streptomyces scabies, Including Discovery of Its Biosynthetic Gene Cluster. PMID:34346752
Transcriptome features of striated muscle aging and predictability of protein level changes. PMID:34328155
Therapeutic manipulation of IKBKAP mis-splicing with a small molecule to cure familial dysautonomia. PMID:34301951
Differential Packaging Into Outer Membrane Vesicles Upon Oxidative Stress Reveals a General Mechanism for Cargo Selectivity. PMID:34276573
SERPINA11 Inhibits Metastasis in Hepatocellular Carcinoma by Suppressing MEK/ERK Signaling Pathway. PMID:34268259
DNA methylation analyses identify an intronic ZDHHC6 locus associated with time to recurrent stroke in the Vitamin Intervention for Stroke Prevention (VISP) clinical trial. PMID:34252155
Intrinsically disordered electronegative clusters improve stability and binding specificity of RNA-binding proteins. PMID:34246632
High-resolution serum proteome trajectories in COVID-19 reveal patient-specific seroconversion. PMID:34232570
Integrated in silico MS-based phosphoproteomics and network enrichment analysis of RASopathy proteins. PMID:34229750
Comprehensive transcriptome analysis of peripheral blood unravels key lncRNAs implicated in ABPA and asthma. PMID:34221710
Protein Secondary Structure Prediction With a Reductive Deep Learning Method. PMID:34211967
Modular Evolution of Coronavirus Genomes. PMID:34209881
Aberrant MCM10 SUMOylation induces genomic instability mediated by a genetic variant associated with survival of esophageal squamous cell carcinoma. PMID:34185429
Analysis of the dark proteome of Chandipura virus reveals maximum propensity for intrinsic disorder in phosphoprotein. PMID:34168211
Neural tube patterning: from a minimal model for rostrocaudal patterning toward an integrated 3D model. PMID:34142058
Regulatory properties of vitronectin and its glycosylation in collagen fibril formation and collagen-degrading enzyme cathepsin K activity. PMID:34103584
Co-occurrence of enzyme domains guides the discovery of an oxazolone synthetase. PMID:34099916
Responses to chemical cross-talk between the Mycobacterium ulcerans toxin, mycolactone, and Staphylococcus aureus. PMID:34083568
Pepscan Approach for the Identification of Protein-Protein Interfaces: Lessons from Experiment. PMID:34063976
Deep conservation of ribosome stall sites across RNA processing genes. PMID:34056595
DDX3X Links NLRP11 to the Regulation of Type I Interferon Responses and NLRP3 Inflammasome Activation. PMID:34054816
Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions. PMID:34046017
Complete Genome Sequence of Klebsiella pneumoniae Podophage Pone. PMID:34042488
Phylogenetic analysis of mutational robustness based on codon usage supports that the standard genetic code does not prefer extreme environments. PMID:34040064
Complete Genome Sequence of Burkholderia gladioli Myophage Mana. PMID:34016684
Investigation of the Mechanism of Traditional Chinese Medicines in Angiogenesis through Network Pharmacology and Data Mining. PMID:34007289
Deciphering Pharmacological Mechanism of Buyang Huanwu Decoction for Spinal Cord Injury by Network Pharmacology Approach. PMID:33976706
The RNA landscape of the human placenta in health and disease. PMID:33976128
Proteomic and Transcriptomic Analysis of Microviridae φX174 Infection Reveals Broad Upregulation of Host Escherichia coli Membrane Damage and Heat Shock Responses. PMID:33975962
Genoppi is an open-source software for robust and standardized integration of proteomic and genetic data. PMID:33972534
A Transfer Learning-Based Approach for Lysine Propionylation Prediction. PMID:33967828
Accurate Annotation of Microbial Metagenomic Genes and Identification of Core Sets. PMID:33961221
Reenacting the Birth of a Function: Functional Divergence of HIUases and Transthyretins as Inferred by Evolutionary and Biophysical Studies. PMID:33956179
In Silico Analysis of the Molecular-Level Impact of SMPD1 Variants on Niemann-Pick Disease Severity. PMID:33925997
Predicting the Structure and Dynamics of Membrane Protein GerAB from Bacillus subtilis. PMID:33917581
In silico annotation of unreviewed acetylcholinesterase (AChE) in some lepidopteran insect pest species reveals the causes of insecticide resistance. PMID:33911936
Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5' ends. PMID:33903630
Endosperm-based incompatibilities in hybrid monkeyflowers. PMID:33895820
Exploring the Pharmacological Mechanism of Duhuo Jisheng Decoction in Treating Osteoporosis Based on Network Pharmacology. PMID:33880122
GPCards: An integrated database of genotype-phenotype correlations in human genetic diseases. PMID:33868597
The Use of Traditional Chinese Medicine in Relieving EGFR-TKI-Associated Diarrhea Based on Network Pharmacology and Data Mining. PMID:33868436
Common low complexity regions for SARS-CoV-2 and human proteomes as potential multidirectional risk factor in vaccine development. PMID:33832440
Discovering the landscape of protein modifications. PMID:33798408
Representative Diatom and Coccolithophore Species Exhibit Divergent Responses throughout Simulated Upwelling Cycles. PMID:33785571
Quantitative acetylome analysis reveals histone modifications that may predict prognosis in hepatitis B-related hepatocellular carcinoma. PMID:33783990
Improving the clinical interpretation of missense variants in X linked genes using structural analysis. PMID:33766936
Differential expression of protein disulfide-isomerase A3 isoforms, PDIA3 and PDIA3N, in human prostate cancer cell lines representing different stages of prostate cancer. PMID:33761087
Network Pharmacology and Pharmacological Evaluation Reveals the Mechanism of the Sanguisorba Officinalis in Suppressing Hepatocellular Carcinoma. PMID:33746755
Computational analysis of 10,860 phenotypic annotations in individuals with SCN2A-related disorders. PMID:33731876
Atg9-centered multi-omics integration reveals new autophagy regulators in Saccharomyces cerevisiae. PMID:33722159
Quantitative Proteomics Reveals that the OGT Interactome Is Remodeled in Response to Oxidative Stress. PMID:33716169
Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future. PMID:33711481
Functional elucidation of TfuA in peptide backbone thioamidation. PMID:33707784
Mapping Gene-by-Gene Single-Nucleotide Variation in 8,535 Mycobacterium tuberculosis Genomes: a Resource To Support Potential Vaccine and Drug Development. PMID:33692198
Genomic insights into the host specific adaptation of the Pneumocystis genus. PMID:33686174
The DBSAV Database: Predicting Deleteriousness of Single Amino Acid Variations in the Human Proteome. PMID:33676930
A Network Pharmacology Study of the Molecular Mechanisms of Hypericum japonicum in the Treatment of Cholestatic Hepatitis with Validation in an Alpha-Naphthylisothiocyanate (ANIT) Hepatotoxicity Rat Model. PMID:33657087
Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences. PMID:33654096
A novel missense TGFBI variant p.(Ser591Phe) in a Finnish family with variant lattice corneal dystrophy. PMID:33645289
Chromosome-Level Genome Assembly of the American Cranberry (Vaccinium macrocarpon Ait.) and Its Wild Relative Vaccinium microcarpum. PMID:33643360
Biomedical articles share annotations with their citation neighbors. PMID:33637047
PFP-WGAN: Protein function prediction by discovering Gene Ontology term correlations with generative adversarial networks. PMID:33630862
Evolution, structure and emerging roles of C1ORF112 in DNA replication, DNA damage responses, and cancer. PMID:33625522
Converting disease maps into heavyweight ontologies: general methodology and application to Alzheimer's disease. PMID:33590873
A Review of Genetic and Physiological Disease Mechanisms Associated With Cav1 Channels: Implications for Incomplete Congenital Stationary Night Blindness Treatment. PMID:33584831
UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network. PMID:33575553
Complete Genome Sequence of Burkholderia cenocepacia Phage Magia. PMID:33574112
Complete Genome Sequence of Burkholderia cenocepacia Phage Mica. PMID:33574111
Interaction between Parkin and α-Synuclein in PARK2-Mediated Parkinson's Disease. PMID:33572534
The role of striated muscle Pik3r1 in glucose and protein metabolism following chronic glucocorticoid exposure. PMID:33567340
The in-silico characterization of the Caenorhabditis elegans matrisome and proposal of a novel collagen classification. PMID:33543001
Complete Genome Sequence of Bradyrhizobium japonicum Podophage Paso. PMID:33541886
Complete Genome Sequence of Burkholderia gladioli Phage Maja. PMID:33541882
Complete Genome Sequence of Klebsiella aerogenes Myophage Metamorpho. PMID:33541880
Identifying daily changes in circRNAs and circRNA-associated-ceRNA networks in the rat pineal gland. PMID:33526984
Potential effect of Maxing Shigan decoction against coronavirus disease 2019 (COVID-19) revealed by network pharmacology and experimental verification. PMID:33513419
Complete Genome Sequence of Rhizobium phaseoli Podophage Palo. PMID:33509996
Complete Genome Sequence of Klebsiella pneumoniae Jumbo Phage Miami. PMID:33509994
A biallelic variant in CLRN2 causes non-syndromic hearing loss in humans. PMID:33496845
Machine learning applications in drug development. PMID:33489002
Extracellular Vesicles Derived From Talaromyces marneffei Yeasts Mediate Inflammatory Response in Macrophage Cells by Bioactive Protein Components. PMID:33488545
Serum Amyloid P inhibits single stranded RNA-induced lung inflammation, lung damage, and cytokine storm in mice. PMID:33481950
Complete Genome Sequence of Rhizobium japonicum Podophage Pasto. PMID:33478994
Complete Genome Sequence of Klebsiella aerogenes Siphophage Solomon. PMID:33478993
Complete Genome Sequence of Klebsiella pneumoniae Myophage Muenster. PMID:33478992
Post-translational control of the long and winding road to cholesterol. PMID:33453997
Complete Genome Sequence of Achromobacter xylosoxidans Myophage Mano. PMID:33446599
Network pharmacology modeling identifies synergistic interaction of therapeutic and toxicological mechanisms for Tripterygium hypoglaucum Hutch. PMID:33446184
Quercetin as a potential treatment for COVID-19-induced acute kidney injury: Based on network pharmacology and molecular docking study. PMID:33444408
De novo transcriptomic analysis and identification of EST-SSR markers in Stephanandra incisa. PMID:33441871
Accurate and efficient detection of gene fusions from RNA sequencing data. PMID:33441414
The evolution and genetics of sexually dimorphic 'dual' mimicry in the butterfly Elymnias hypermnestra. PMID:33434461
Review on natural products databases: where to find data in 2020. PMID:33431011
Complete Genome Sequence of Streptomyces Phage Spernnie. PMID:33414328
Complete Genome Sequence of Streptomyces Siphophage Sycamore. PMID:33414327
Complete Genome Sequence of Streptomyces Phage Sentinel. PMID:33414325
Complete Genome Sequence of Streptomyces Phage Shaeky. PMID:33414324
Complete Genome Sequence of Streptomyces Siphophage Sitrop. PMID:33414323
Complete Genome Sequence of Streptomyces Phage Shady. PMID:33414322
Complete Genome Sequence of Streptomyces Phage Salutena. PMID:33414317
A multi-omic study for uncovering molecular mechanisms associated with hyperammonemia-induced cerebellar function impairment in rats. PMID:33404927
Alignment-free method for functional annotation of amino acid substitutions: Application on epigenetic factors involved in hematologic malignancies. PMID:33395407
Chromosome Segregation and Peptidoglycan Remodeling Are Coordinated at a Highly Stabilized Septal Pore to Maintain Bacterial Spore Development. PMID:33383000
Assessing the Anti-inflammatory Mechanism of Reduning Injection by Network Pharmacology. PMID:33381562
A chromosome-level reference genome of non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis]. PMID:33372175
Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi. PMID:33355923
Comment on 'Hayai-Annotation plants: an ultra-fast and comprehensive functional gene annotation system in plants'. The importance of taking the GO graph structure into account. PMID:33346790
Neuropeptide S receptor gene Asn107 polymorphism in obese male individuals in Pakistan. PMID:33332443
A semantic relationship mining method among disorders, genes, and drugs from different biomedical datasets. PMID:33317518
Poly(ADP-ribose) polymerase 1 in genome-wide expression control in Drosophila. PMID:33273587
Occurrence of Ordered and Disordered Structural Elements in Postsynaptic Proteins Supports Optimization for Interaction Diversity. PMID:33267475
Comparative Analysis of ROS Network Genes in Extremophile Eukaryotes. PMID:33266251
Deciphering the Role of Filamin B Calponin-Homology Domain in Causing the Larsen Syndrome, Boomerang Dysplasia, and Atelosteogenesis Type I Spectrum Disorders via a Computational Approach. PMID:33255942
The European Bioinformatics Institute: empowering cooperation in response to a global health crisis. PMID:33245775
Machine Learning Analysis of the Cerebrovascular Thrombi Proteome in Human Ischemic Stroke: An Exploratory Study. PMID:33240201
Phosphoglycerate kinase: structural aspects and functions, with special emphasis on the enzyme from Kinetoplastea. PMID:33234025
Expression of Pro-Angiogenic Markers Is Enhanced by Blue Light in Human RPE Cells. PMID:33233546
Longitudinal Transcriptomic Profiling in Carrageenan-Induced Rat Hind Paw Peripheral Inflammation and Hyperalgesia Reveals Progressive Recruitment of Innate Immune System Components. PMID:33227508
The Role of Small Extracellular Vesicles in Viral-Protozoan Symbiosis: Lessons From Trichomonasvirus in an Isogenic Host Parasite Model. PMID:33224901
Investigation of the Potential Mechanism Governing the Effect of the Shen Zhu San on COVID-19 by Network Pharmacology. PMID:33224256
Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment. PMID:33208892
Network Pharmacology Analysis to Identify Phytochemicals in Traditional Chinese Medicines That May Regulate ACE2 for the Treatment of COVID-19. PMID:33204291
The Anti-Inflammatory Protein TNIP1 Is Intrinsically Disordered with Structural Flexibility Contributed by Its AHD1-UBAN Domain. PMID:33182596
Molecular docking simulation reveals ACE2 polymorphisms that may increase the affinity of ACE2 with the SARS-CoV-2 Spike protein. PMID:33181224
A Study on the Mechanism of Milkvetch Root in the Treatment of Diabetic Nephropathy Based on Network Pharmacology. PMID:33178322
Genome Variation Map: a worldwide collection of genome variations across multiple species. PMID:33170268
Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data. PMID:33168813
Identification of Dominant Transcripts in Oxidative Stress Response by a Full-Length Transcriptome Analysis. PMID:33168698
Individuating Possibly Repurposable Drugs and Drug Targets for COVID-19 Treatment Through Hypothesis-Driven Systems Medicine Using CoVex. PMID:33164550
Network pharmacology for the identification of phytochemicals in traditional Chinese medicine for COVID-19 that may regulate interleukin-6. PMID:33146673
Baicalin inhibits inflammation caused by coinfection of Mycoplasma gallisepticum and Escherichia coli involving IL-17 signaling pathway. PMID:33142464
TOR Complex 2- independent mutations in the regulatory PIF pocket of Gad8AKT1/SGK1 define separate branches of the stress response mechanisms in fission yeast. PMID:33137119
Proteomic signatures of acute oxidative stress response to paraquat in the mouse heart. PMID:33116222
Human Histone Interaction Networks: An Old Concept, New Trends. PMID:33098859
Discover novel disease-associated genes based on regulatory networks of long-range chromatin interactions. PMID:33096239
Perspective on Proteomics for Virus Detection in Clinical Samples. PMID:33090795
The Onset of Tacrolimus Biosynthesis in Streptomyces tsukubaensis Is Dependent on the Intracellular Redox Status. PMID:33076498
Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage. PMID:33073387
CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors. PMID:33068433
RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing. PMID:33050530
COVID-19: molecular targets, drug repurposing and new avenues for drug discovery. PMID:33027420
A Novel Proteomic Method Reveals NLS Tagging of T-DM1 Contravenes Classical Nuclear Transport in a Model of HER2-Positive Breast Cancer. PMID:33024794
Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode. PMID:33020495
Protein kinase A catalytic-α and catalytic-β proteins have nonredundant regulatory functions. PMID:33017189
Secretion of pro-oncogenic AGR2 protein in cancer. PMID:33005802
A New Synuclein-Transgenic Mouse Model for Early Parkinson's Reveals Molecular Features of Preclinical Disease. PMID:32997293
An optimized quantitative proteomics method establishes the cell type-resolved mouse brain secretome. PMID:32954517
Transcriptomics predicts compound synergy in drug and natural product treated glioblastoma cells. PMID:32946518
Skeletal muscle and cardiac transcriptomics of a regionally endothermic fish, the Pacific bluefin tuna, Thunnus orientalis. PMID:32942994
Revealing the full-length transcriptome of caucasian clover rhizome development. PMID:32938399
Research on the potential mechanism of Chuanxiong Rhizoma on treating Diabetic Nephropathy based on network pharmacology. PMID:32922187
Comparative host-pathogen protein-protein interaction analysis of recent coronavirus outbreaks and important host targets identification. PMID:32914167
Genome Sequence of Salmonella enterica Serovar Typhimurium Bacteriophage MG40. PMID:32912919
Homozygous expression of the myofibrillar myopathy-associated p.W2710X filamin C variant reveals major pathomechanisms of sarcomeric lesion formation. PMID:32887649
Cancer cell line-specific protein profiles in extracellular vesicles identified by proteomics. PMID:32886718
Prediction of Promiscuity Cliffs Using Machine Learning. PMID:32881355
Eighteen Coral Genomes Reveal the Evolutionary Origin of Acropora Strategies to Accommodate Environmental Changes. PMID:32877528
Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology. PMID:32850764
An intramembrane chaperone complex facilitates membrane protein biogenesis. PMID:32814900
Network Pharmacology-Based Strategy for Predicting Active Ingredients and Potential Targets of Gegen Qinlian Decoction for Rotavirus Enteritis. PMID:32802121
Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site. PMID:32785287
Mapping Coeliac Toxic Motifs in the Prolamin Seed Storage Proteins of Barley, Rye, and Oats Using a Curated Sequence Database. PMID:32766270
Inducers of the endothelial cell barrier identified through chemogenomic screening in genome-edited hPSC-endothelial cells. PMID:32759214
GSK3 Inhibits Macropinocytosis and Lysosomal Activity through the Wnt Destruction Complex Machinery. PMID:32726636
A novel TIMP3 mutation associated with a retinitis pigmentosa-like phenotype. PMID:32715858
Virus-CKB: an integrated bioinformatics platform and analysis resource for COVID-19 research. PMID:32715315
Improved Reference Genome for Cyclotella cryptica CCMP332, a Model for Cell Wall Morphogenesis, Salinity Adaptation, and Lipid Production in Diatoms (Bacillariophyta). PMID:32709619
Polyvalent therapeutic vaccine for type 2 diabetes mellitus: Immunoinformatics approach to study co-stimulation of cytokines and GLUT1 receptors. PMID:32703184
MicroRNAs in ascending thoracic aortic aneurysms. PMID:32678444
The regulation of glucose and lipid homeostasis via PLTP as a mediator of BAT-liver communication. PMID:32672883
Brainstem Organoids From Human Pluripotent Stem Cells. PMID:32670003
Integrative pharmacological mechanism of vitamin C combined with glycyrrhizic acid against COVID-19: findings of bioinformatics analyses. PMID:32662814
The Salmonella enterica Plasmidome as a Reservoir of Antibiotic Resistance. PMID:32650601
A redox-active switch in fructosamine-3-kinases expands the regulatory repertoire of the protein kinase superfamily. PMID:32636308
Differential Dynamics of the Ruminal Microbiome of Jersey Cows in a Heat Stress Environment. PMID:32630754
ULK1 and ULK2 are less redundant than previously thought: computational analysis uncovers distinct regulation and functions of these autophagy induction proteins. PMID:32616830
A ferredoxin-dependent dihydropyrimidine dehydrogenase in Clostridium chromiireducens. PMID:32614053
Protein profile of well-differentiated versus un-differentiated human bronchial/tracheal epithelial cells. PMID:32613119
Alteration in Lysophospholipids and Converting Enzymes in Glaucomatous Optic Nerves. PMID:32602905
A Comprehensive Network Pharmacology-Based Strategy to Investigate Multiple Mechanisms of HeChan Tablet on Lung Cancer. PMID:32595734
Environmental Enrichment Improved Learning and Memory, Increased Telencephalic Cell Proliferation, and Induced Differential Gene Expression in Colossoma macropomum. PMID:32595498
Multiple Forms of Multifunctional Proteins in Health and Disease. PMID:32587857
Inducible aging in Hydra oligactis implicates sexual reproduction, loss of stem cells, and genome maintenance as major pathways. PMID:32578072
Predicting Functions of Uncharacterized Human Proteins: From Canonical to Proteoforms. PMID:32575886
Chromosome-level genome assembly of Tarim red deer, Cervus elaphus yarkandensis. PMID:32561793
Proteomic Screening for Prediction and Design of Antimicrobial Peptides with AmpGram. PMID:32560350
Activity-based protein profiling guided identification of urine proteinase 3 activity in subclinical rejection after renal transplantation. PMID:32549867
Semantic text mining in early drug discovery for type 2 diabetes. PMID:32542027
Dynamic rewiring of the human interactome by interferon signaling. PMID:32539747
A flexible network-based imputing-and-fusing approach towards the identification of cell types from single-cell RNA-seq data. PMID:32527285
Spt6 is a maintenance factor for centromeric CENP-A. PMID:32522980
Structure and Electron-Transfer Pathway of the Human Methionine Sulfoxide Reductase MsrB3. PMID:32517586
Landscape of drug-resistance mutations in kinase regulatory hotspots. PMID:32510566
Genomic consequences of dietary diversification and parallel evolution due to nectarivory in leaf-nosed bats. PMID:32510151
Can network pharmacology identify the anti-virus and anti- inflammatory activities of Shuanghuanglian oral liquid used in Chinese medicine for respiratory tract infection? PMID:32501408
Genome mining of the citrus pathogen Elsinoë fawcettii; prediction and prioritisation of candidate effectors, cell wall degrading enzymes and secondary metabolite gene clusters. PMID:32469865
Identification of Inhibitors to Trypanosoma cruzi Sirtuins Based on Compounds Developed to Human Enzymes. PMID:32455951
Changes in the Oligodendrocyte Progenitor Cell Proteome with Ageing. PMID:32434922
Chemokine CCL28 Is a Potent Therapeutic Agent for Oropharyngeal Candidiasis. PMID:32423961
FGviewer: an online visualization tool for functional features of human fusion genes. PMID:32421816
Genomes of the Venus Flytrap and Close Relatives Unveil the Roots of Plant Carnivory. PMID:32413308
Mutation severity spectrum of rare alleles in the human genome is predictive of disease type. PMID:32413045
MISCAST: MIssense variant to protein StruCture Analysis web SuiTe. PMID:32402084
An integrative multi-omics approach uncovers the regulatory role of CDK7 and CDK4 in autophagy activation induced by silica nanoparticles. PMID:32397800
ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms. PMID:32393825
Global ocean resistome revealed: Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples. PMID:32391909
Genome-Scale Metabolic Modeling of Glioblastoma Reveals Promising Targets for Drug Development. PMID:32362913
Mimicry diversification in Papilio dardanus via a genomic inversion in the regulatory region of engrailed-invected. PMID:32345166
Entropy, Fluctuations, and Disordered Proteins. PMID:32336912
Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow. PMID:32327732
PDZ Domains as Drug Targets. PMID:32313833
Pathological, Morphological, Cytogenomic, Biochemical and Molecular Data Support the Distinction between Colletotrichum cigarro comb. et stat. nov. and Colletotrichum kahawae. PMID:32295225
The effect of extrinsic Wnt/β-catenin signaling in Muller glia on retinal ganglion cell neurite growth. PMID:32267608
Cell-type diversity and regionalized gene expression in the planarian intestine. PMID:32240093
Autonomous aggregation suppression by acidic residues explains why chaperones favour basic residues. PMID:32237079
Phylogenetic Analyses of Sites in Different Protein Structural Environments Result in Distinct Placements of the Metazoan Root. PMID:32231097
Ellagic Acid, Kaempferol, and Quercetin from Acacia nilotica: Promising Combined Drug With Multiple Mechanisms of Action. PMID:32226726
COQ11 deletion mitigates respiratory deficiency caused by mutations in the gene encoding the coenzyme Q chaperone protein Coq10. PMID:32205446
Sperm Cohort-Specific Zinc Signature Acquisition and Capacitation-Induced Zinc Flux Regulate Sperm-Oviduct and Sperm-Zona Pellucida Interactions. PMID:32204514
Fibroblast Growth Factor 2-Mediated Regulation of Neuronal Exosome Release Depends on VAMP3/Cellubrevin in Hippocampal Neurons. PMID:32195080
Pseudo-Symmetric Assembly of Protodomains as a Common Denominator in the Evolution of Polytopic Helical Membrane Proteins. PMID:32189026
Molecular docking and network connections of active compounds from the classical herbal formula Ding Chuan Tang. PMID:32185106
CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers. PMID:32183712
Mapping of the chicken cleft primary palate mutation on chromosome 11 and sequencing of the 4.9 Mb linked region. PMID:32162363
Biochemical features of the novel Tail Tubular Protein A of Yersinia phage phiYeO3-12. PMID:32144374
Frameshifting preserves key physicochemical properties of proteins. PMID:32127487
Integrative proteomic and glycoproteomic profiling of Mycobacterium tuberculosis culture filtrate. PMID:32126063
Integrated structural and evolutionary analysis reveals common mechanisms underlying adaptive evolution in mammals. PMID:32123117
At the Crossroads of Apoptosis and Autophagy: Multiple Roles of the Co-Chaperone BAG3 in Stress and Therapy Resistance of Cancer. PMID:32121220
An Information Entropy-Based Approach for Computationally Identifying Histone Lysine Butyrylation. PMID:32117407
An Investigation of the Mechanism of Rapid Relief of Ulcerative Colitis Induced by Five-flavor Sophora Flavescens Enteric-coated Capsules Based on Network Pharmacology. PMID:32116186
Network Pharmacology-Based Investigation of the System-Level Molecular Mechanisms of the Hematopoietic Activity of Samul-Tang, a Traditional Korean Herbal Formula. PMID:32104198
Probing lncRNA-Protein Interactions: Data Repositories, Models, and Algorithms. PMID:32082358
Dimer Interface Organization is a Main Determinant of Intermonomeric Interactions and Correlates with Evolutionary Relationships of Retroviral and Retroviral-Like Ddi1 and Ddi2 Proteases. PMID:32079302
More than a Corepressor: The Role of CoREST Proteins in Neurodevelopment. PMID:32075869
Structural and functional comparison of fumarylacetoacetate domain containing protein 1 in human and mouse. PMID:32068790
Biological Activity Profiles of Multitarget Ligands from X-ray Structures. PMID:32059498
First Draft Genome of the Sable, Martes zibellina. PMID:32058545
NCBP2 modulates neurodevelopmental defects of the 3q29 deletion in Drosophila and Xenopus laevis models. PMID:32053595
Mechanical regulation of glycolysis via cytoskeleton architecture. PMID:32051585
Proteomic profiling and identification of significant markers from high-grade osteosarcoma after cryotherapy and irradiation. PMID:32034162
Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria. PMID:32029728
Accurate and Sensitive Quantitation of the Dynamic Heat Shock Proteome Using Tandem Mass Tags. PMID:32027144
Structure-Guided Design and In-Cell Target Profiling of a Cell-Active Target Engagement Probe for PARP Inhibitors. PMID:32017532
Function and regulation annotation of up-regulated long non-coding RNA LINC01234 in gastric cancer. PMID:32011780
In silico approach to predict pancreatic β-cells classically secreted proteins. PMID:32003782
Preclinical evaluation of an affinity-enhanced MAGE-A4-specific T-cell receptor for adoptive T-cell therapy. PMID:32002290
Compartment and hub definitions tune metabolic networks for metabolomic interpretations. PMID:31972021
A Pathway for Degradation of Uracil to Acetyl Coenzyme A in Bacillus megaterium. PMID:31953335
Pharmacological Chaperones: A Therapeutic Approach for Diseases Caused by Destabilizing Missense Mutations. PMID:31940970
Mesostigma viride Genome and Transcriptome Provide Insights into the Origin and Evolution of Streptophyta. PMID:31921561
Symbiont population control by host-symbiont metabolic interaction in Symbiodiniaceae-cnidarian associations. PMID:31913264
Complete Genome Sequence of Stenotrophomonas maltophilia Myophage Moby. PMID:31896658
PSO-LocBact: A Consensus Method for Optimizing Multiple Classifier Results for Predicting the Subcellular Localization of Bacterial Proteins. PMID:31886228
An improved catalogue of putative synaptic genes defined exclusively by temporal transcription profiles through an ensemble machine learning approach. PMID:31870293
Secretome profiling identifies neuron-derived neurotrophic factor as a tumor-suppressive factor in lung cancer. PMID:31852841
Proteomics: a powerful tool to study plant responses to biotic stress. PMID:31832077
Complete Genome Sequence of Citrobacter freundii Siphophage Sazh. PMID:31831614
Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome. PMID:31825849
Analysis of Secondary Structure Biases in Naturally Presented HLA-I Ligands. PMID:31824508
Deciphering protein evolution and fitness landscapes with latent space models. PMID:31822668
Comparative analysis of corrected tiger genome provides clues to its neuronal evolution. PMID:31804567
A Combined Mass Spectrometry and Data Integration Approach to Predict the Mitochondrial Poly(A) RNA Interacting Proteome. PMID:31803741
A metastable subproteome underlies inclusion formation in muscle proteinopathies. PMID:31796104
Electronic Cigarette (E-Cigarette) Vapor Exposure Alters the Streptococcus pneumoniae Transcriptome in a Nicotine-Dependent Manner without Affecting Pneumococcal Virulence. PMID:31791951
Specificity of a rodent alpha(α)6 nicotinic acetylcholine receptor subunit antibody. PMID:31786649
NNTox: Gene Ontology-Based Protein Toxicity Prediction Using Neural Network. PMID:31784686
TGFB1-Mediated Gliosis in Multiple Sclerosis Spinal Cords Is Favored by the Regionalized Expression of HOXA5 and the Age-Dependent Decline in Androgen Receptor Ligands. PMID:31779094
Dramatic increase in gene mutational burden after transformation of follicular lymphoma into TdT+ B-lymphoblastic leukemia/lymphoma. PMID:31776129
The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook. PMID:31761977
Coding-Complete Genome Sequence of Staphylococcus aureus Podophage Portland. PMID:31753959
Complete Genome Sequence of Proteus mirabilis Phage Myduc. PMID:31753957
Complete Genome Sequence of Proteus mirabilis Phage Mydo. PMID:31753956
Identifying Promiscuous Compounds with Activity against Different Target Classes. PMID:31752252
ADAPTABLE: a comprehensive web platform of antimicrobial peptides tailored to the user's research. PMID:31740563
PMBD: a Comprehensive Plastics Microbial Biodegradation Database. PMID:31738435
A Novel Prokaryote-Type ECF/ABC Transporter Module in Chloroplast Metal Homeostasis. PMID:31736987
Novel Compound Heterozygous Mutations in IL-7 Receptor α Gene in a 15-Month-Old Girl Presenting With Thrombocytopenia, Normal T Cell Count and Maternal Engraftment. PMID:31736942
Semi-rational design and molecular dynamics simulations study of the thermostability enhancement of cellobiose 2-epimerases. PMID:31733243
The Resurgence of Dirigent Story: Time for a Bacterial Chapter. PMID:31728698
TTC5 mediates autoregulation of tubulin via mRNA degradation. PMID:31727855
Complete Genome Sequence of Klebsiella pneumoniae Myophage Mulock. PMID:31727723
Complete Genome Sequence of Klebsiella pneumoniae Siphophage Seifer. PMID:31727722
Complete Genome Sequence of Klebsiella pneumoniae Podophage Pylas. PMID:31727721
Transcriptomic Signatures Predict Regulators of Drug Synergy and Clinical Regimen Efficacy against Tuberculosis. PMID:31719182
Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation. PMID:31699975
Enabling semantic queries across federated bioinformatics databases. PMID:31697362
Discovery of Human Signaling Systems: Pairing Peptides to G Protein-Coupled Receptors. PMID:31675498
Complete Genome Sequence of Klebsiella pneumoniae Siphophage Sanco. PMID:31672751
Nuclear Genome Assembly of the Microalga Nannochloropsis salina CCMP1776. PMID:31672738
Single-cell proteomics in complex tissues using microprobe capillary electrophoresis mass spectrometry. PMID:31668233
Development of a high-productivity, halophilic, thermotolerant microalga Picochlorum renovo. PMID:31667362
Suppression of the Peripheral Immune System Limits the Central Immune Response Following Cuprizone-Feeding: Relevance to Modelling Multiple Sclerosis. PMID:31653054
Complete Genome Sequence of Proteus mirabilis Siphophage Stubb. PMID:31649089
Complete Genome Sequence of Salmonella enterica Serovar Enteritidis Siphophage Seafire. PMID:31649087
Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Siphophage Seabear. PMID:31649086
Complete Genome Sequence of Citrobacter freundii Myophage Maroon. PMID:31649085
PACAP and Other Neuropeptide Targets Link Chronic Migraine and Opioid-induced Hyperalgesia in Mouse Models. PMID:31649062
Gene4Denovo: an integrated database and analytic platform for de novo mutations in humans. PMID:31642496
Insights revealed by the co-crystal structure of the Saccharomyces cerevisiae histidine phosphotransfer protein Ypd1 and the receiver domain of its downstream response regulator Ssk1. PMID:31642125
Phosphorylation of Histone Deacetylase 8: Structural and Mechanistic Analysis of the Phosphomimetic S39E Mutant. PMID:31633931
Complete Genome Sequence of Citrobacter freundii Myophage Maleficent. PMID:31624155
Genome-Wide Distribution of Nascent Transcripts in Sperm DNA, Products of a Late Wave of General Transcription. PMID:31623338
The Mechanistic Differences in HLA-Associated Carbamazepine Hypersensitivity. PMID:31618895
Zinc uptake in the Basidiomycota: Characterization of zinc transporters in Ustilago maydis. PMID:31617434
Predicting HLA class II antigen presentation through integrated deep learning. PMID:31611695
CancerGeneNet: linking driver genes to cancer hallmarks. PMID:31598703
Reporting on the future of integrative structural biology ORAU workshop. PMID:31585877
Complete Genome Sequence of Escherichia coli Siphophage Snoke. PMID:31582444
Complete Genome Sequence of Staphylococcus aureus Myophage Maine. PMID:31582443
Complete Genome Sequence of Escherichia coli Siphophage Shashou. PMID:31582440
Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome. PMID:31574156
Introducing "best single template" models as reference baseline for the Continuous Automated Model Evaluation (CAMEO). PMID:31571280
DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites. PMID:31566664
Complete Genome Sequence of Escherichia coli Podophage Peacock. PMID:31558648
Complete Genome Sequence of Escherichia coli Phage Pisces. PMID:31558647
Complete Genome Sequence of Escherichia coli Siphophage Schulenberg. PMID:31558646
Complete Genome Sequence of Klebsiella pneumoniae Myophage Magnus. PMID:31558645
Complete Genome Sequence of Sin4, a Siphophage Infecting Carbapenemase-Producing Klebsiella pneumoniae. PMID:31558644
Complete Genome Sequence of Klebsiella pneumoniae Phage Sweeny. PMID:31558643
Complete Genome Sequence of Klebsiella pneumoniae Siphophage Skenny. PMID:31558642
Complete Genome Sequence of Salmonella enterica Siphophage Shelanagig. PMID:31558641
Complete Genome Sequence of Stenotrophomonas maltophilia Podophage Ponderosa. PMID:31558640
Complete Genome Sequence of Xanthomonas Phage Pagan. PMID:31558639
Polyamine Synthesis Effects Capsule Expression by Reduction of Precursors in Streptococcus pneumoniae. PMID:31555234
Association study identified biologically relevant receptor genes with synergistic functions in celiac disease. PMID:31554915
Quantitative comparative analysis of human erythrocyte surface proteins between individuals from two genetically distinct populations. PMID:31552303
RNA ligation precedes the retrotransposition of U6/LINE-1 chimeric RNA. PMID:31548405
Complete Genome Sequence of Escherichia coli Siphophage Sciku. PMID:31537682
Complete Genome Sequence of Serratia marcescens Myophage MyoSmar. PMID:31537681
Complete Genome Sequence of Escherichia coli Myophage Mansfield. PMID:31537679
Complete Genome Sequence of Shelby, a Siphophage Infecting Carbapenemase-Producing Klebsiella pneumoniae. PMID:31537678
3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients. PMID:31527881
Molecular Profiling of the Drosophila Antenna Reveals Conserved Genes Underlying Olfaction in Insects. PMID:31527046
Distal hereditary motor neuronopathy of the Jerash type is caused by a novel SIGMAR1 c.500A>T missense mutation. PMID:31511340
Multifaceted protein-protein interaction prediction based on Siamese residual RCNN. PMID:31510705
Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning. PMID:31504150
Agonist Selectivity and Ion Permeation in the α3β4 Ganglionic Nicotinic Receptor. PMID:31488329
Challenges in the construction of knowledge bases for human microbiome-disease associations. PMID:31488215
Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints. PMID:31484923
Intestinal proteomic analysis of a novel non-human primate model of experimental colitis reveals signatures of mitochondrial and metabolic dysfunction. PMID:31481749
Systematical Analysis of the Protein Targets of Lactoferricin B and Histatin-5 Using Yeast Proteome Microarrays. PMID:31466342
Differential processing of high-molecular-weight kininogen during normal pregnancy. PMID:31412146
Complete Genome Sequence of Enterotoxigenic Escherichia coli Podophage LL11. PMID:31395642
Quantifying the impact of public omics data. PMID:31383865
Identification of potential drug targets and vaccine candidates in Clostridium botulinum using subtractive genomics approach. PMID:31359994
Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms. PMID:31353404
Haploinsufficiency of the Notch Ligand DLL1 Causes Variable Neurodevelopmental Disorders. PMID:31353024
Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis. PMID:31348891
Complete Genome Sequence of Salmonella enterica Serovar Heidelberg Siphophage Sepoy. PMID:31346029
Predicting functional long non-coding RNAs validated by low throughput experiments. PMID:31345106
Proteomic Analysis of Plasmodium Merosomes: The Link between Liver and Blood Stages in Malaria. PMID:31335145
FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria. PMID:31333719
Predictive models of protease specificity based on quantitative protease-activity profiling data. PMID:31330204
Tubulin response to intense nanosecond-scale electric field in molecular dynamics simulation. PMID:31324834
Complete Genome Sequence of Staphylococcus aureus Siphophage Sebago. PMID:31320442
Complete Genome Sequence of the Novel Klebsiella pneumoniae Phage Marfa. PMID:31320440
Complete Genome Sequence of Serratia marcescens Myophage Moabite. PMID:31320439
Salivary proteomics of canine oral tumors using MALDI-TOF mass spectrometry and LC-tandem mass spectrometry. PMID:31318878
Mechanism of catalysis and inhibition of Mycobacterium tuberculosis SapM, implications for the development of novel antivirulence drugs. PMID:31312014
Biophysical characterization and molecular phylogeny of human KIN protein. PMID:31309277
Benchmarking subcellular localization and variant tolerance predictors on membrane proteins. PMID:31307390
ParaDB: A manually curated database containing genomic annotation for the human pathogenic fungi Paracoccidioides spp. PMID:31306428
Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development. PMID:31302154
Multi-channel PINN: investigating scalable and transferable neural networks for drug discovery. PMID:31289963
β-amyloid and tau pathology in the aging feline brain. PMID:31273784
Complete Genome Sequence of Staphylococcus aureus Siphophage Lorac. PMID:31270202
Complete Genome Sequence of Serratia marcescens Podophage Parlo. PMID:31270199
What went wrong with variant effect predictor performance for the PCM1 challenge. PMID:31268618
A comparative analysis of secreted protein disulfide isomerases from the tropical co-endemic parasites Schistosoma mansoni and Leishmania major. PMID:31267027
Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean. PMID:31264806
The Liberfarb syndrome, a multisystem disorder affecting eye, ear, bone, and brain development, is caused by a founder pathogenic variant in thePISD gene. PMID:31263216
Functional characterization of SMN evolution in mouse models of SMA. PMID:31263170
Complete Genome Sequences of Staphylococcus epidermidis Myophages Quidividi, Terranova, and Twillingate. PMID:31248994
Post-Translational Modification-Dependent Activity of Matrix Metalloproteinases. PMID:31238509
Glycosylphosphatidylinositol biosynthesis and remodeling are required for neural tube closure, heart development, and cranial neural crest cell survival. PMID:31232685
Mr.Vc: a database of microarray and RNA-seq of Vibrio cholerae. PMID:31231774
Complete Genome Sequence of Agrobacterium tumefaciens Myophage Milano. PMID:31221656
Complete Genome Sequence of Serratia marcescens Phage MTx. PMID:31221655
Gene Information eXtension (GIX): effortless retrieval of gene product information on any website. PMID:31217594
A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.): A Community-Generated Genomic Resource. PMID:31217262
Multi omics analysis of fibrotic kidneys in two mouse models. PMID:31201317
Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability. PMID:31196969
First crystal structure of an endo-levanase - the BT1760 from a human gut commensal Bacteroides thetaiotaomicron. PMID:31186460
ProteinNet: a standardized data set for machine learning of protein structure. PMID:31185886
Improved peptide-MHC class II interaction prediction through integration of eluted ligand and peptide affinity data. PMID:31183519
Morph-specific protein patterns in the femoral gland secretions of a colour polymorphic lizard. PMID:31182789
Orb-weaving spider Araneus ventricosus genome elucidates the spidroin gene catalogue. PMID:31182776
Switching the Post-translational Modification of Translation Elongation Factor EF-P. PMID:31178848
Complete Genome Sequence of Escherichia coli Myophage Minorna. PMID:31171610
SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse. PMID:31171447
Arabidopsis thaliana organelles mimic the T7 phage DNA replisome with specific interactions between Twinkle protein and DNA polymerases Pol1A and Pol1B. PMID:31170927
Engineering repressors with coevolutionary cues facilitates toggle switches with a master reset. PMID:31162606
PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact. PMID:31161204
Horizontal transfer of a retrotransposon between parasitic nematodes and the common shrew. PMID:31160924
Cross-Reactivity as a Mechanism Linking Infections to Stroke. PMID:31156531
The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions. PMID:31149898
ORVAL: a novel platform for the prediction and exploration of disease-causing oligogenic variant combinations. PMID:31147699
Analysing Point Mutations in Protein Cleavage Sites by Using Enzyme Specificity Matrices. PMID:31130917
Follicle-Stimulating Hormone Glycobiology. PMID:31127275
Proteomic Analysis of the Breast Cancer Brain Metastasis Microenvironment. PMID:31121957
Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport. PMID:31114897
VOLPES: an interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences. PMID:31114895
Yvis: antibody high-density alignment visualization and analysis platform with an integrated database. PMID:31106372
Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration. PMID:31101000
Misfolded GPI-anchored proteins are escorted through the secretory pathway by ER-derived factors. PMID:31094677
Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants. PMID:31093654
Tissue-specific genes as an underutilized resource in drug discovery. PMID:31076736
Comparative analyses of the variation of the transcriptome and proteome of Rhodobacter sphaeroides throughout growth. PMID:31072330
Structural and Proteomic Changes in Viable but Non-culturable Vibrio cholerae. PMID:31057510
Exploring the Potential of Spherical Harmonics and PCVM for Compounds Activity Prediction. PMID:31052500
Human COQ10A and COQ10B are distinct lipid-binding START domain proteins required for coenzyme Q function. PMID:31048406
The bagworm genome reveals a unique fibroin gene that provides high tensile strength. PMID:31044173
Conserved phosphorylation hotspots in eukaryotic protein domain families. PMID:31036831
The Promoter Regions of Intellectual Disability-Associated Genes Are Uniquely Enriched in LTR Sequences of the MER41 Primate-Specific Endogenous Retrovirus: An Evolutionary Connection Between Immunity and Cognition. PMID:31031802
An Open Science Approach to Artificial Intelligence in Healthcare. PMID:31022753
Novel CSF biomarkers in genetic frontotemporal dementia identified by proteomics. PMID:31019994
Pathway-Based Analysis of the Liver Response to Intravenous Methylprednisolone Administration in Rats: Acute Versus Chronic Dosing. PMID:31019365
XFEL structures of the human MT2 melatonin receptor reveal the basis of subtype selectivity. PMID:31019305
A Bioinformatics View of Glycan⁻Virus Interactions. PMID:31018588
Profiling of Seed Proteome in Pea (Pisum sativum L.) Lines Characterized with High and Low Responsivity to Combined Inoculation with Nodule Bacteria and Arbuscular Mycorrhizal Fungi. PMID:31018578
Two Sides of the Coin: Ezrin/Radixin/Moesin and Merlin Control Membrane Structure and Contact Inhibition. PMID:31018575
Molecular architecture, polar targeting and biogenesis of the Legionella Dot/Icm T4SS. PMID:31011165
CesH Represses Cereulide Synthesis as an Alpha/Beta Fold Hydrolase in Bacillus cereus. PMID:31010094
Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community. PMID:31003499
Can Predicted Protein 3D Structures Provide Reliable Insights into whether Missense Variants Are Disease Associated? PMID:30995449
Brevibacterium from Austrian hard cheese harbor a putative histamine catabolism pathway and a plasmid for adaptation to the cheese environment. PMID:30992535
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. PMID:30944313
A hybrid de novo assembly of the sea pansy (Renilla muelleri) genome. PMID:30942866
An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar. PMID:30937429
Heterologous Machine Learning for the Identification of Antimicrobial Activity in Human-Targeted Drugs. PMID:30935109
Cellular and Animal Models of Striated Muscle Laminopathies. PMID:30934932
Netrin Family: Role for Protein Isoforms in Cancer. PMID:30923634
PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources. PMID:30922213
Multi-metal Restriction by Calprotectin Impacts De Novo Flavin Biosynthesis in Acinetobacter baumannii. PMID:30905682
Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population. PMID:30894435
Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects. PMID:30885123
Back to the future: Why we need enzymology to build a synthetic metabolism of the future. PMID:30873239
DeepDom: Predicting protein domain boundary from sequence alone using stacked bidirectional LSTM. PMID:30864311
Characterization of the Rosa roxburghii Tratt transcriptome and analysis of MYB genes. PMID:30860996
Unsupervised classification of multi-omics data during cardiac remodeling using deep learning. PMID:30853547
Physiological Expression of Ion Channel Receptors in Human Periodontal Ligament Stem Cells. PMID:30845727
Comparison of Open-Source Reverse Vaccinology Programs for Bacterial Vaccine Antigen Discovery. PMID:30837982
Multiple Genome Sequences of Lactobacillus pentosus Strains Isolated from Biofilms on the Skin of Fermented Green Table Olives. PMID:30834370
Insights into the complex role of GRAS transcription factors in the arbuscular mycorrhiza symbiosis. PMID:30833646
Protein Solubility Predictions Using the CamSol Method in the Study of Protein Homeostasis. PMID:30833455
Recognition and Degradation of Mislocalized Proteins in Health and Disease. PMID:30833453
Promiscuous Coxiella burnetii CD4 Epitope Clusters Associated With Human Recall Responses Are Candidates for a Novel T-Cell Targeted Multi-Epitope Q Fever Vaccine. PMID:30828331
The genetic basis for adaptation of model-designed syntrophic co-cultures. PMID:30822347
Comparative Phosphoproteomic Profiling of Type III Adenylyl Cyclase Knockout and Control, Male, and Female Mice. PMID:30814930
SERPINs-From Trap to Treatment. PMID:30809526
Phosphorylation Changes in Response to Kinase Inhibitor H89 in PKA-Null Cells. PMID:30808967
Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0). PMID:30804569
A Model Information Management Plan for Molecular Pathology Sequence Data Using Standards: From Sequencer to Electronic Health Record. PMID:30797065
LINC00116 codes for a mitochondrial peptide linking respiration and lipid metabolism. PMID:30796188
Targeting the Viral Polymerase of Diarrhea-Causing Viruses as a Strategy to Develop a Single Broad-Spectrum Antiviral Therapy. PMID:30791582
Sequential Windowed Acquisition of Reporter Masses for Quantitation-First Proteomics. PMID:30781952
A draft genome assembly of the solar-powered sea slug Elysia chlorotica. PMID:30778257
Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1. PMID:30773399
Small Molecule Docking of DNA Repair Proteins Associated with Cancer Survival Following PCNA Metagene Adjustment: A Potential Novel Class of Repair Inhibitors. PMID:30759820
Reproduction of contagious caprine pleuropneumonia reveals the ability of convalescent sera to reduce hydrogen peroxide production in vitro. PMID:30736863
Systematically Characterizing Chemical Profile and Potential Mechanisms of Qingre Lidan Decoction Acting on Cholelithiasis by Integrating UHPLC-QTOF-MS and Network Target Analysis. PMID:30719056
Quantitative insights into the cyanobacterial cell economy. PMID:30714903
Bioinformatics Analysis of Metabolism Pathways of Archaeal Energy Reserves. PMID:30705313
Pathogen diversity drives the evolution of generalist MHC-II alleles in human populations. PMID:30703088
S-Like-Phase Cyclin-Dependent Kinases Stabilize the Epstein-Barr Virus BDLF4 Protein To Temporally Control Late Gene Transcription. PMID:30700607
Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview. PMID:30695998
White Matter is the Predilection Site of Late-Delayed Radiation-Induced Brain Injury in Non-Human Primates. PMID:30694733
A conserved CAF40-binding motif in metazoan NOT4 mediates association with the CCR4-NOT complex. PMID:30692204
Clinical trials, progression-speed differentiating features and swiftness rule of the innovative targets of first-in-class drugs. PMID:30689717
Near-atomic structure of a giant virus. PMID:30674888
Computational characterization of the peptidome in transporter associated with antigen processing (TAP)-deficient cells. PMID:30645615
Discovery of a Thermostable GH10 Xylanase with Broad Substrate Specificity from the Arctic Mid-Ocean Ridge Vent System. PMID:30635385
Chromosome level comparative analysis of Brassica genomes. PMID:30632049
Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci. PMID:30611298
Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS). PMID:30607034
UbiHub: a data hub for the explorers of ubiquitination pathways. PMID:30601939
Clinically Relevant Post-Translational Modification Analyses-Maturing Workflows and Bioinformatics Tools. PMID:30577541
A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer. PMID:30568637
The 40S ribosomal protein uS5 (RPS2) assembles into an extraribosomal complex with human ZNF277 that competes with the PRMT3-uS5 interaction. PMID:30530495
Characterisation of the British honey bee metagenome. PMID:30478343
Plasma proteome correlates of lipid and lipoprotein: biomarkers of metabolic diversity and inflammation in children of rural Nepal. PMID:30473544
Proteomics of nucleocytoplasmic partitioning. PMID:30472625
An integrated approach towards the development of novel antifungal agents containing thiadiazole: synthesis and a combined similarity search, homology modelling, molecular dynamics and molecular docking study. PMID:30470928
Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO). PMID:30459171
Large-scale protein function prediction using heterogeneous ensembles. PMID:30450194
Determining the Balance Between Drug Efficacy and Safety by the Network and Biological System Profile of Its Therapeutic Target. PMID:30429792
MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs). PMID:30418481
EMC Is Required to Initiate Accurate Membrane Protein Topogenesis. PMID:30415835
Determining the Balance Between Drug Efficacy and Safety by the Network and Biological System Profile of Its Therapeutic Target. PMID:30429792
MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs). PMID:30418481
EMC Is Required to Initiate Accurate Membrane Protein Topogenesis. PMID:30415835
Critical observations that shaped our understanding of the function(s) of intracellular glycosylation (O-GlcNAc). PMID:30414174
Epithelial Shaping by Diverse Apical Extracellular Matrices Requires the Nidogen Domain Protein DEX-1 in Caenorhabditis elegans. PMID:30409789
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. PMID:30407594
ECO, the Evidence & Conclusion Ontology: community standard for evidence information. PMID:30407590
FusionGDB: fusion gene annotation DataBase. PMID:30407583
Identification of a 2'-O-Methyluridine Nucleoside Hydrolase Using the Metagenomic Libraries. PMID:30405065
CATH: expanding the horizons of structure-based functional annotations for genome sequences. PMID:30398663
ChEMBL: towards direct deposition of bioassay data. PMID:30398643
BRENDA in 2019: a European ELIXIR core data resource. PMID:30395242
Murine Oviductosomes (OVS) microRNA profiling during the estrous cycle: Delivery of OVS-borne microRNAs to sperm where miR-34c-5p localizes at the centrosome. PMID:30382141
dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data. PMID:30380085
Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life. PMID:30371900
MatrixDB: integration of new data with a focus on glycosaminoglycan interactions. PMID:30371822
MoonDB 2.0: an updated database of extreme multifunctional and moonlighting proteins. PMID:30371819
The cellular economy of the Saccharomyces cerevisiae zinc proteome. PMID:30358795
Editome Disease Knowledgebase (EDK): a curated knowledgebase of editome-disease associations in human. PMID:30357418
The Immune Epitope Database (IEDB): 2018 update. PMID:30357391
CORUM: the comprehensive resource of mammalian protein complexes-2019. PMID:30357367
RaftProt V2: understanding membrane microdomain function through lipid raft proteomes. PMID:30329070
Designing of CD8+ and CD8+-overlapped CD4+ epitope vaccine by targeting late and early proteins of human papillomavirus. PMID:30323556
Potential Effects of MSC-Derived Exosomes in Neuroplasticity in Alzheimer's Disease. PMID:30319358
Embryonic transcriptome sequencing of the ocellate spot skate Okamejei kenojei. PMID:30295675
Approximating Isotope Distributions of Biomolecule Fragments. PMID:30288463
Multiple paralogues of α-SNAP in Giardia lamblia exhibit independent subcellular localization and redistribution during encystation and stress. PMID:30286802
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites. PMID:30285084
'Democratized' genomic enzymology web tools for functional assignment. PMID:30268904
Meta-analysis of data from spaceflight transcriptome experiments does not support the idea of a common bacterial "spaceflight response". PMID:30258082
RNA editing derived epitopes function as cancer antigens to elicit immune responses. PMID:30254248
ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature. PMID:30241466
Nicotinamide-N-methyltransferase controls behavior, neurodegeneration and lifespan by regulating neuronal autophagy. PMID:30192747
LY6E mediates an evolutionarily conserved enhancement of virus infection by targeting a late entry step. PMID:30190477
Calmodulin Enhances Cryptochrome Binding to INAD in Drosophila Photoreceptors. PMID:30177872
Structures of the ligand-binding domain of Helicobacter pylori chemoreceptor TlpA. PMID:30171638
Bacterial Lipoproteins Constitute the TLR2-Stimulating Activity of Serum Amyloid A. PMID:30158125
Homology Modeling Informs Ligand Discovery for the Glutamine Transporter ASCT2. PMID:30137742
Endogenous HIF2A reporter systems for high-throughput functional screening. PMID:30104738
Glycomics@ExPASy: Bridging the Gap. PMID:30097532
Quality Control of Orphaned Proteins. PMID:30075143
Meeting Report of the International Life Science Integration Workshop 2018. PMID:29982395
HMMER web server: 2018 update. PMID:29905871
Epigenetic Mechanisms of Alcohol Neuroadaptation: Insights from Drosophila. PMID:29899666
Future Prospects of Spectral Clustering Approaches in Proteomics. PMID:29882266
How electrostatic networks modulate specificity and stability of collagen. PMID:29844169
Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z. PMID:29843739
Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction. PMID:29813047
No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects. PMID:29806194
The Cellosaurus, a Cell-Line Knowledge Resource. PMID:29805321
Structural Basis for Mutations of Human Aquaporins Associated to Genetic Diseases. PMID:29799470
Fluorogenic Peptide Substrate for Quantification of Bacterial Enzyme Activities. PMID:28287171
Identification of Differently Regulated Proteins after Fusarium graminearum Infection of Emmer (Triticum dicoccum) at Several Grain Ripening Stages. PMID:27904357
Differentially charged isoforms of apolipoprotein E from human blood are potential biomarkers of Alzheimer's disease. PMID:25478016
Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening. PMID:25464976
Allergenius, an expert system for the interpretation of allergen microarray results. PMID:24995073
Comparing the Chemical Structure and Protein Content of ChEMBL, DrugBank, Human Metabolome Database and the Therapeutic Target Database. PMID:24533037
Influence of developmental stage and genotype on liver mRNA levels among wild, domesticated, and hybrid rainbow trout (Oncorhynchus mykiss). PMID:24088438
A novel type of light-harvesting antenna protein of red algal origin in algae with secondary plastids. PMID:23899289
The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. PMID:23731509
VIROME: a standard operating procedure for analysis of viral metagenome sequences. PMID:23407591
Computational identification of transcriptionally co-regulated genes, validation with the four ANT isoform genes. PMID:22978616
Current status and emerging role of glutathione in food grade lactic acid bacteria. PMID:22920585
Developing a kidney and urinary pathway knowledge base. PMID:21624162
Immunologically reactive M. leprae antigens with relevance to diagnosis and vaccine development. PMID:21269435
The adsorption of biomolecules to multi-walled carbon nanotubes is influenced by both pulmonary surfactant lipids and surface chemistry. PMID:21159192
Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire. PMID:20923558
Pharmacoproteomic study of the effects of chondroitin and glucosamine sulfate on human articular chondrocytes. PMID:20626852
Quantitative assessment of the expanding complementarity between public and commercial databases of bioactive compounds. PMID:20298516
Automatic prediction of catalytic residues by modeling residue structural neighborhood. PMID:20199672
GIFtS: annotation landscape analysis with GeneCards. PMID:19852797
Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches. PMID:19014603
Subfamily specific conservation profiles for proteins based on n-gram patterns. PMID:18234090
MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. PMID:17640358
Fungal CSL transcription factors. PMID:17629904
FlyMine: an integrated database for Drosophila and Anopheles genomics. PMID:17615057
Genetic polymorphisms of human flavin-containing monooxygenase 3: implications for drug metabolism and clinical perspectives. PMID:17559352
Identification and comparative analysis of sixteen fungal peptidyl-prolyl cis/trans isomerase repertoires. PMID:16995943 -
Activities at the Universal Protein Resource (UniProt)
PubMed citations: 677.
677 articles citing: Activities at the Universal Protein Resource (UniProt)
Systematic prediction of EMS-induced mutations in a sorghum mutant population. PMID:35647479
Effect of Thrombin on the Metabolism and Function of Murine Macrophages. PMID:35626753
DBSCAN-SWA: An Integrated Tool for Rapid Prophage Detection and Annotation. PMID:35518360
Are transient protein-protein interactions more dispensable? PMID:35404956
Acetate Degradation at Low pH by the Moderately Acidophilic Sulfate Reducer Acididesulfobacillus acetoxydans gen. nov. sp. nov. PMID:35391737
Gel-Based Proteomic Identification of Suprabasin as a Potential New Candidate Biomarker in Endometrial Cancer. PMID:35216190
The Influence of Coronary Artery Disease in the Development of Aortic Stenosis and the Importance of the Albumin Redox State. PMID:35204200
Solution structure and dynamics of the mitochondrial-targeted GTPase-activating protein (GAP) VopE by an integrated NMR/SAXS approach. PMID:35137487
Structural Predictive Model of Presenilin-2 Protein and Analysis of Structural Effects of Familial Alzheimer's Disease Mutations. PMID:34881055
Discovering the Ultimate Limits of Protein Secondary Structure Prediction. PMID:34827624
A ubiquitous disordered protein interaction module orchestrates transcription elongation. PMID:34822292
Metal utilization in genome-reduced bacteria: Do human mycoplasmas rely on iron? PMID:34765092
Genetic and Functional Analysis of Glycosyltransferase 8 Domain-Containing Protein 1 in Taiwanese Patients With Amyotrophic Lateral Sclerosis. PMID:34746377
Coffea arabica L. Resistant to Coffee Berry Borer (Hypothenemus hampei) Mediated by Expression of the Bacillus thuringiensis Cry10Aa Protein. PMID:34745196
Decipher the Helicobacter pylori Protein Targeting in the Nucleus of Host Cell and their Implications in Gallbladder Cancer: An insilico approach. PMID:34729122
Clinical and genetic characterization of adult-onset leukoencephalopathy caused by CSF1R mutations. PMID:34652888
Nardosinone Alleviates Parkinson's Disease Symptoms in Mice by Regulating Dopamine D2 Receptor. PMID:34426745
The Application of High-Throughput Technologies for the Study of Microbiome and Cancer. PMID:34394190
A secondary structure-based position-specific scoring matrix applied to the improvement in protein secondary structure prediction. PMID:34320027
The influence of dataset homology and a rigorous evaluation strategy on protein secondary structure prediction. PMID:34260641
Drug Repurposing for the Treatment of COVID-19: A Knowledge Graph Approach. PMID:34179346
The tepary bean genome provides insight into evolution and domestication under heat stress. PMID:33976152
Behavior of Chemokine Receptor 6 (CXCR6) in Complex with CXCL16 Soluble form Chemokine by Molecular Dynamic Simulations: General Protein‒Ligand Interaction Model and 3D-QSAR Studies of Synthetic Antagonists. PMID:33920834
Multi-omics analysis provides insights into lignocellulosic biomass degradation by Laetiporus sulphureus ATCC 52600. PMID:33865436
De novo Prediction of Moonlighting Proteins Using Multimodal Deep Ensemble Learning. PMID:33828582
Protein domain identification methods and online resources. PMID:33680357
Study of Endogen Substrates, Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics. PMID:33671368
In Silico Analysis of Common Long Noncoding RNAs in Schistosoma mansoni and Schistosoma haematobium. PMID:33628277
Tracking changes in adaptation to suspension growth for MDCK cells: cell growth correlates with levels of metabolites, enzymes and proteins. PMID:33582836
Suprabasin-A Review. PMID:33477529
Interferon Regulatory Factor 9 Promotes Lung Cancer Progression via Regulation of Versican. PMID:33430083
Alkaloids with Anti-Onchocercal Activity from Voacanga africana Stapf (Apocynaceae): Identification and Molecular Modeling. PMID:33375687
Inter-protein residue covariation information unravels physically interacting protein dimers. PMID:33334319
ZNF354C is a transcriptional repressor that inhibits endothelial angiogenic sprouting. PMID:33154469
Actin R256 Mono-methylation Is a Conserved Post-translational Modification Involved in Transcription. PMID:32997990
Computational Study of C-X-C Chemokine Receptor (CXCR)3 Binding with Its Natural Agonists Chemokine (C-X-C Motif) Ligand (CXCL)9, 10 and 11 and with Synthetic Antagonists: Insights of Receptor Activation towards Drug Design for Vitiligo. PMID:32992956
Substitution scoring matrices for proteins - An overview. PMID:32954566
The Orphan G-Protein Coupled Receptor 182 Is a Negative Regulator of Definitive Hematopoiesis through Leukotriene B4 Signaling. PMID:32832870
JAGN1, tetraspanins, and Erv proteins: is common topology indicative of common function in cargo sorting? PMID:32783652
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. PMID:32652120
A systematic strategy for the investigation of vaccines and drugs targeting bacteria. PMID:32637049
A simple strategy to enhance the speed of protein secondary structure prediction without sacrificing accuracy. PMID:32603341
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. PMID:32427907
Total Protein Staining is Superior to Classical or Tissue-Specific Protein Staining for Standardization of Protein Biomarkers in Heterogeneous Tissue Samples. PMID:32377595
Prediction of cardiovascular risk in preterm neonates through urinary proteomics: An exploratory study. PMID:32258784
SubmitoLoc: Identification of mitochondrial sub cellular locations of proteins using support vector machine. PMID:32256006
Comparative functional genomic analysis of Alzheimer's affected and naturally aging brains. PMID:32219020
DISNET: a framework for extracting phenotypic disease information from public sources. PMID:32110491
Flavones Produced by Mulberry Flavone Synthase Type I Constitute a Defense Line against the Ultraviolet-B Stress. PMID:32045991
Differential tissue-specific damage caused by bacterial epididymo-orchitis in the mouse. PMID:32011693
Systematic analysis of lncRNA and microRNA dynamic features reveals diagnostic and prognostic biomarkers of myocardial infarction. PMID:31927529
High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets. PMID:31871119
Data enabled prediction analysis assigns folate/biopterin transporter (BT1) family to 36 hypothetical membrane proteins in Leishmania donovani. PMID:31831951
Using mechanistic models for the clinical interpretation of complex genomic variation. PMID:31831811
Styrene maleic acid recovers proteins from mammalian cells and tissues while avoiding significant cell death. PMID:31767876
Mapping the perturbome network of cellular perturbations. PMID:31723137
Investigating the Cellular Transcriptomic Response Induced by the Makona Variant of Ebola Virus in Differentiated THP-1 Cells. PMID:31689981
Bioinformatics analysis of Ras homologue enriched in the striatum, a potential target for Huntington's disease therapy. PMID:31638189
The functional repertoire contained within the native microbiota of the model nematode Caenorhabditis elegans. PMID:31484996
Estimating dispensable content in the human interactome. PMID:31324802
Compensated pathogenic variants in coagulation factors VIII and IX present complex mapping between molecular impact and hemophilia severity. PMID:31267011
Mutation spectrum of Charcot-Marie-Tooth disease among the Han Chinese in Taiwan. PMID:31211173
In Vivo Proteome of Pseudomonas aeruginosa in Airways of Cystic Fibrosis Patients. PMID:31060355
The bacteriocin from the prophylactic candidate Streptococcus suis 90-1330 is widely distributed across S. suis isolates and appears encoded in an integrative and conjugative element. PMID:31039174
The Proteome of Tetrasphaera elongata is adapted to Changing Conditions in Wastewater Treatment Plants. PMID:31027192
Dark Proteome Database: Studies on Dark Proteins. PMID:30934744
Novel compound mutations in the mitochondrial translation elongation factor (TSFM) gene cause severe cardiomyopathy with myocardial fibro-adipose replacement. PMID:30911037
Diet Induced Obesity Alters Intestinal Cytoplasmic Lipid Droplet Morphology and Proteome in the Postprandial Response to Dietary Fat. PMID:30890954
Domain cross-talk within a bifunctional enzyme provides catalytic and allosteric functionality in the biosynthesis of aromatic amino acids. PMID:30670586
Exploiting locational and topological overlap model to identify modules in protein interaction networks. PMID:30642247
Gene expression changes elicited by a parasitic B chromosome in the grasshopper Eyprepocnemis plorans are consistent with its phenotypic effects. PMID:30617552
Prediction of Horizontally and Widely Transferred Genes in Prokaryotes. PMID:30546254
Screening for insulin-independent pathways that modulate glucose homeostasis identifies androgen receptor antagonists. PMID:30520733
Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA. PMID:30498193
Comparative analysis of nucleus-encoded plastid-targeting proteins in Rafflesia cantleyi against photosynthetic and non-photosynthetic representatives reveals orthologous systems with potentially divergent functions. PMID:30467394
Genome-wide prediction of bacterial effector candidates across six secretion system types using a feature-based statistical framework. PMID:30464223
Structural disorder in the proteome and interactome of Alkhurma virus (ALKV). PMID:30443749
Reciprocal negative regulation between the tumor suppressor protein p53 and B cell CLL/lymphoma 6 (BCL6) via control of caspase-1 expression. PMID:30409904
Role of the Fractalkine Receptor in CNS Autoimmune Inflammation: New Approach Utilizing a Mouse Model Expressing the Human CX3CR1I249/M280 Variant. PMID:30386211
Prediction of high anti-angiogenic activity peptides in silico using a generalized linear model and feature selection. PMID:30356060
Systematic identification and analysis of dysregulated miRNA and transcription factor feed-forward loops in hypertrophic cardiomyopathy. PMID:30338905
The Bear Giant-Skipper genome suggests genetic adaptations to living inside yucca roots. PMID:30293092
The clinical spectrum of CASQ1-related myopathy. PMID:30258016
Structural and functional characterisation of the entry point to pyocyanin biosynthesis in Pseudomonas aeruginosa defines a new 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase subclass. PMID:30242059
Comparative transcriptome analysis to identify putative genes involved in thymol biosynthesis pathway in medicinal plant Trachyspermum ammi L. PMID:30194320
---A web resource for nutrient use efficiency-related genes, quantitative trait loci and microRNAs in important cereals and model plants. PMID:30135718
The genome sequence of the soft-rot fungus Penicillium purpurogenum reveals a high gene dosage for lignocellulolytic enzymes. PMID:30123662
An Immunopharmacoinformatics Approach in Development of Vaccine and Drug Candidates for West Nile Virus. PMID:30035107
Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment. PMID:29924794
Comprehensive identification of Vibrio vulnificus genes required for growth in human serum. PMID:29697309
To Decipher the Mycoplasma hominis Proteins Targeting into the Endoplasmic Reticulum and Their Implications in Prostate Cancer Etiology Using Next-Generation Sequencing Data. PMID:29695086
dbDEPC 3.0: the database of differentially expressed proteins in human cancer with multi-level annotation and drug indication. PMID:29688359
Computational Prediction and Analysis of Associations between Small Molecules and Binding-Associated S-Nitrosylation Sites. PMID:29671802
Genetic Loci Governing Androgenic Capacity in Perennial Ryegrass (Lolium perenne L.). PMID:29626084
Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship. PMID:29626081
TISSUES 2.0: an integrative web resource on mammalian tissue expression. PMID:29617745
The intracellular distribution of inorganic carbon fixing enzymes does not support the presence of a C4 pathway in the diatom Phaeodactylum tricornutum. PMID:29572588
BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform. PMID:29547394
Survivin Monoclonal Antibodies Detect Survivin Cell Surface Expression and Inhibit Tumor Growth In Vivo. PMID:29540489
Analysis of a gene panel for targeted sequencing of colorectal cancer samples. PMID:29507673
Effect of the sequence data deluge on the performance of methods for detecting protein functional residues. PMID:29482506
Whole-Genome Sequence Accuracy Is Improved by Replication in a Population of Mutagenized Sorghum. PMID:29378822
PhenoRank: reducing study bias in gene prioritization through simulation. PMID:29360927
Assessing the Performances of Protein Function Prediction Algorithms from the Perspectives of Identification Accuracy and False Discovery Rate. PMID:29316706
Precision Medicine for Acute Kidney Injury (AKI): Redefining AKI by Agnostic Kidney Tissue Interrogation and Genetics. PMID:29291761
eGARD: Extracting associations between genomic anomalies and drug responses from text. PMID:29261751
First insights into a type II toxin-antitoxin system from the clinical isolate Mycobacterium sp. MHSD3, similar to epsilon/zeta systems. PMID:29236773
On the Early Evolution of Catabolic Pathways: A Comparative Genomics Approach. I. The Cases of Glucose, Ribose, and the Nucleobases Catabolic Routes. PMID:29189888
Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi. PMID:29184190
Dynamical Binding Modes Determine Agonistic and Antagonistic Ligand Effects in the Prostate-Specific G-Protein Coupled Receptor (PSGR). PMID:29167480
THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy. PMID:29157087
Clinical and Molecular Characterization of PMP22 point mutations in Taiwanese patients with Inherited Neuropathy. PMID:29127354
Comprehensive analysis of the dynamic structure of nuclear localization signals. PMID:29124229
Glypre: In Silico Prediction of Protein Glycation Sites by Fusing Multiple Features and Support Vector Machine. PMID:29099805
Proteomic Analysis of Thiol Modifications and Assessment of Structural Changes in Hemoglobin Induced by the Aniline Metabolites N-Phenylhydroxylamine and Nitrosobenzene. PMID:29093547
Multi-omics Comparative Analysis Reveals Multiple Layers of Host Signaling Pathway Regulation by the Gut Microbiota. PMID:29085914
Complete Genome of Achalarus lyciades, The First Representative of the Eudaminae Subfamily of Skippers. PMID:29081692
A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters. PMID:29079755
Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti. PMID:29078296
Electrophilic probes for deciphering substrate recognition by O-GlcNAc transferase. PMID:29058723
Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts. PMID:28977405
Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine. PMID:28924494
Shotgun metagenomics, from sampling to analysis. PMID:28898207
DextMP: deep dive into text for predicting moonlighting proteins. PMID:28881966
A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models. PMID:28878200
Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing. PMID:28846689
Fungal Hybrid B heme peroxidases - unique fusions of a heme peroxidase domain with a carbohydrate-binding domain. PMID:28839281
Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton. PMID:28827361
Development of pathogenicity predictors specific for variants that do not comply with clinical guidelines for the use of computational evidence. PMID:28812538
Screening drug-target interactions with positive-unlabeled learning. PMID:28808275
A diacidic motif determines unconventional secretion of wild-type and ALS-linked mutant SOD1. PMID:28794127
The first complete genomes of Metalmarks and the classification of butterfly families. PMID:28757157
The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. PMID:28756775
Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals. PMID:28743941
Analysis of somatic mutations across the kinome reveals loss-of-function mutations in multiple cancer types. PMID:28743916
Anion-selective Formate/nitrite transporters: taxonomic distribution, phylogenetic analysis and subfamily-specific conservation pattern in prokaryotes. PMID:28738779
The Dark Proteome Database. PMID:28736578
Direct binding to GABARAP family members is essential for HIV-1 Nef plasma membrane localization. PMID:28729737
biochem4j: Integrated and extensible biochemical knowledge through graph databases. PMID:28708831
Integrated analysis of zone-specific protein and metabolite profiles within nitrogen-fixing Medicago truncatula-Sinorhizobium medicae nodules. PMID:28700717
Enriching plausible new hypothesis generation in PubMed. PMID:28678852
Predicting growth of the healthy infant using a genome scale metabolic model. PMID:28649430
A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against Leishmania major. PMID:28638238
Drug repurposing for aging research using model organisms. PMID:28620943
Supporting inter-topic entity search for biomedical Linked Data based on heterogeneous relationships. PMID:28601712
All atom NMDA receptor transmembrane domain model development and simulations in lipid bilayers and water. PMID:28582391
Comparative de novo transcriptome profiles in Asparagus officinalis and A. kiusianus during the early stage of Phomopsis asparagi infection. PMID:28572584
A knowledge-based framework for the discovery of cancer-predisposing variants using large-scale sequencing breast cancer data. PMID:28569218
Assessing protein-ligand binding modes with computational tools: the case of PDE4B. PMID:28534194
Draft Genome Sequence of Roseovarius sp. A-2, an Iodide-Oxidizing Bacterium Isolated from Natural Gas Brine Water, Chiba, Japan. PMID:28529651
Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data. PMID:28472398
Transcriptome analysis of creeping bentgrass exposed to drought stress and polyamine treatment. PMID:28445484
Transcriptome of interstitial cells of Cajal reveals unique and selective gene signatures. PMID:28426719
SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter. PMID:28420738
Use of Graph Database for the Integration of Heterogeneous Biological Data. PMID:28416946
Genome sequencing and comparative analysis of an NDM-1-producing Klebsiella pneumoniae ST15 isolated from a refugee patient. PMID:28395597
Exploring the differences in metabolic behavior of astrocyte and glioblastoma: a flux balance analysis approach. PMID:28392849
IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models. PMID:28389638
DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. PMID:28387604
Protein-coding genes in B chromosomes of the grasshopper Eyprepocnemis plorans. PMID:28367986
From Marine Venoms to Drugs: Efficiently Supported by a Combination of Transcriptomics and Proteomics. PMID:28358320
Comparative genomics and evolution of transcriptional regulons in Proteobacteria. PMID:28348857
The autophagy interaction network of the aging model Podospora anserina. PMID:28347269
NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology. PMID:28320317
Analysis of Pelagia noctiluca proteome Reveals a Red Fluorescent Protein, a Zinc Metalloproteinase and a Peroxiredoxin. PMID:28258523
A Comprehensive Gene Expression Meta-analysis Identifies Novel Immune Signatures in Rheumatoid Arthritis Patients. PMID:28210261
TB-IRIS: Proteomic analysis of in vitro PBMC responses to Mycobacterium tuberculosis and response modulation by dexamethasone. PMID:28209523
Evolutionary and functional implications of hypervariable loci within the skin virome. PMID:28194314
SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases. PMID:28178937
Complete genome of Pieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins. PMID:28163896
PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms. PMID:28155708
Tutorial on Protein Ontology Resources. PMID:28150233
Neurovirulent Murine Coronavirus JHM.SD Uses Cellular Zinc Metalloproteases for Virus Entry and Cell-Cell Fusion. PMID:28148786
Drosophila CG3303 is an essential endoribonuclease linked to TDP-43-mediated neurodegeneration. PMID:28139767
DRNApred, fast sequence-based method that accurately predicts and discriminates DNA- and RNA-binding residues. PMID:28132027
Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. PMID:28092920
Non-interacting proteins may resemble interacting proteins: prevalence and implications. PMID:28084410
Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation. PMID:28082953
Widespread Inter- and Intra-Domain Horizontal Gene Transfer of d-Amino Acid Metabolism Enzymes in Eukaryotes. PMID:28066338
Complete Genome Sequence of Akkermansia glycaniphila Strain PytT, a Mucin-Degrading Specialist of the Reticulated Python Gut. PMID:28057747
The use of novel selectivity metrics in kinase research. PMID:28056771
Proteome alterations associated with transformation of multiple myeloma to secondary plasma cell leukemia. PMID:28038447
Comparison of commercial nanoliquid chromatography columns for fast, targeted mass spectrometry-based proteomics. PMID:28031966
Transcriptomic comparison of invasive bigheaded carps (Hypophthalmichthys nobilis and Hypophthalmichthys molitrix) and their hybrids. PMID:28031797
Unique Transcriptional Programs Identify Subtypes of AKI. PMID:28028135
Disentangling genetic and environmental risk factors for individual diseases from multiplex comorbidity networks. PMID:28008973
iCAGES: integrated CAncer GEnome Score for comprehensively prioritizing driver genes in personal cancer genomes. PMID:28007024
Expansion and diversification of the MSDIN family of cyclic peptide genes in the poisonous agarics Amanita phalloides and A. bisporigera. PMID:27978833
Functional Genomics Identifies Tis21-Dependent Mechanisms and Putative Cancer Drug Targets Underlying Medulloblastoma Shh-Type Development. PMID:27965576
Evaluating the quality of Marfan genotype-phenotype correlations in existing FBN1 databases. PMID:27906200
Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23. PMID:27881076
In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075. PMID:27834373
The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations. PMID:27812948
Primer on the Gene Ontology. PMID:27812933
Physicochemical properties that control protein aggregation also determine whether a protein is retained or released from necrotic cells. PMID:27810968
Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. PMID:27803309
Molecular mechanisms underlying COPD-muscle dysfunction unveiled through a systems medicine approach. PMID:27794560
Draft Genome Sequence of Arenibacter sp. Strain C-21, an Iodine-Accumulating Bacterium Isolated from Surface Marine Sediment. PMID:27738047
Inhibition of Polo-like kinase 1 during the DNA damage response is mediated through loss of Aurora A recruitment by Bora. PMID:27721411
Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli. PMID:27713404
PRDM1/BLIMP1 is widely distributed to the nascent fetal-placental interface in the mouse gastrula. PMID:27696611
Transcriptome Profiling of Petal Abscission Zone and Functional Analysis of an Aux/IAA Family Gene RhIAA16 Involved in Petal Shedding in Rose. PMID:27695465
Domain Organization in the 54-kDa Subunit of the Chloroplast Signal Recognition Particle. PMID:27653474
Intra-molecular lysine-arginine derived advanced glycation end-product cross-linking in Type I collagen: A molecular dynamics simulation study. PMID:27648753
Ultra-deep tyrosine phosphoproteomics enabled by a phosphotyrosine superbinder. PMID:27642862
Large-scale analysis of intrinsic disorder flavors and associated functions in the protein sequence universe. PMID:27636733
The Bacterial Mobile Resistome Transfer Network Connecting the Animal and Human Microbiomes. PMID:27613679
Structure and variation of the mitochondrial genome of fishes. PMID:27604148
Circulating Memory CD4+ T Cells Target Conserved Epitopes of Rhinovirus Capsid Proteins and Respond Rapidly to Experimental Infection in Humans. PMID:27591323
Discrepancies between human DNA, mRNA and protein reference sequences and their relation to single nucleotide variants in the human population. PMID:27589963
aPPRove: An HMM-Based Method for Accurate Prediction of RNA-Pentatricopeptide Repeat Protein Binding Events. PMID:27560805
A machine learning strategy for predicting localization of post-translational modification sites in protein-protein interacting regions. PMID:27534850
Supervised Learning for Detection of Duplicates in Genomic Sequence Databases. PMID:27489953
Evolutionary and functional analysis of mulberry type III polyketide synthases. PMID:27487946
Determinants of Macromolecular Specificity from Proteomics-Derived Peptide Substrate Data. PMID:27455965
Therapeutics Insight with Inclusive Immunopharmacology Explication of Human Rotavirus A for the Treatment of Diarrhea. PMID:27445802
Multi-OMICs and Genome Editing Perspectives on Liver Cancer Signaling Networks. PMID:27403431
RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis. PMID:27379752
Identification, Characterization, and X-ray Crystallographic Analysis of a Novel Type of Mannose-Specific Lectin CGL1 from the Pacific Oyster Crassostrea gigas. PMID:27377186
KinMutRF: a random forest classifier of sequence variants in the human protein kinase superfamily. PMID:27357839
The Ensembl gene annotation system. PMID:27337980
Crystal Structures of the Global Regulator DasR from Streptomyces coelicolor: Implications for the Allosteric Regulation of GntR/HutC Repressors. PMID:27337024
Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases. PMID:27332861
Sequence- and Structure-Based Analysis of Tissue-Specific Phosphorylation Sites. PMID:27332813
An integer programming framework for inferring disease complexes from network data. PMID:27307626
An Adaptive Hybrid Algorithm for Global Network Alignment. PMID:27295633
Selection pressure on human STR loci and its relevance in repeat expansion disease. PMID:27290643
Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters in Aspergillus oryzae: A Representative Case Study. PMID:27274991
Identification of a small-molecule ligand that activates the neuropeptide receptor GPR171 and increases food intake. PMID:27245612
Multiple sclerosis: Molecular mimicry of an antimyelin HLA class I restricted T-cell receptor. PMID:27231714
Computational Framework for Prediction of Peptide Sequences That May Mediate Multiple Protein Interactions in Cancer-Associated Hub Proteins. PMID:27218803
Research Resources for Nuclear Receptor Signaling Pathways. PMID:27216565
Gene overlapping and size constraints in the viral world. PMID:27209091
An Integrated Data Driven Approach to Drug Repositioning Using Gene-Disease Associations. PMID:27196054
Argo: enabling the development of bespoke workflows and services for disease annotation. PMID:27189607
High-performance web services for querying gene and variant annotation. PMID:27154141
Genome-scale prediction of moonlighting proteins using diverse protein association information. PMID:27153604
DrugGenEx-Net: a novel computational platform for systems pharmacology and gene expression-based drug repurposing. PMID:27151405
Uncovering a Dual Regulatory Role for Caspases During Endoplasmic Reticulum Stress-induced Cell Death. PMID:27125827
PTIR: Predicted Tomato Interactome Resource. PMID:27121261
Complete genomes of Hairstreak butterflies, their speciation, and nucleo-mitochondrial incongruence. PMID:27120974
Integrating text mining, data mining, and network analysis for identifying genetic breast cancer trends. PMID:27112211
Characterization of piRNAs across postnatal development in mouse brain. PMID:27112104
Uncovering disease mechanisms through network biology in the era of Next Generation Sequencing. PMID:27080396
DiMeX: A Text Mining System for Mutation-Disease Association Extraction. PMID:27073839
Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters. PMID:27058503
Genic insights from integrated human proteomics in GeneCards. PMID:27048349
General intelligence is associated with subclinical inflammation in Nepalese children: A population-based plasma proteomics study. PMID:27039242
Systems psychopharmacology: A network approach to developing novel therapies. PMID:27014599
Conserved differences in protein sequence determine the human pathogenicity of Ebolaviruses. PMID:27009368
DephosSite: a machine learning approach for discovering phosphotase-specific dephosphorylation sites. PMID:27002216
Urine Proteome Biomarkers in Kidney Diseases. I. Limits, Perspectives, and First Focus on Normal Urine. PMID:26997865
Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome. PMID:26992093
Global Mapping of Traditional Chinese Medicine into Bioactivity Space and Pathways Annotation Improves Mechanistic Understanding and Discovers Relationships between Therapeutic Action (Sub)classes. PMID:26989424
Characterization of Disease-Associated Mutations in Human Transmembrane Proteins. PMID:26986070
Pipeline for the identification and classification of ion channels in parasitic flatworms. PMID:26983991
ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures. PMID:26982818
A Human "eFP" Browser for Generating Gene Expression Anatograms. PMID:26954504
Speciation in Cloudless Sulphurs Gleaned from Complete Genomes. PMID:26951782
In silico Analysis Revealed High-risk Single Nucleotide Polymorphisms in Human Pentraxin-3 Gene and their Impact on Innate Immune Response against Microbial Pathogens. PMID:26941719
Enhancement of DNaseI Salt Tolerance by Mimicking the Domain Structure of DNase from an Extremely Halotolerant Bacterium Thioalkalivibrio sp. K90mix. PMID:26939122
Linking Virus Genomes with Host Taxonomy. PMID:26938550
Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase. PMID:26928598
Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing. PMID:26922242
Linocin and OmpW Are Involved in Attachment of the Cystic Fibrosis-Associated Pathogen Burkholderia cepacia Complex to Lung Epithelial Cells and Protect Mice against Infection. PMID:26902727
Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. PMID:26898226
Ensembl comparative genomics resources. PMID:26896847
Conserved properties of individual Ca2+-binding sites in calmodulin. PMID:26884197
GMOL: An Interactive Tool for 3D Genome Structure Visualization. PMID:26868282
Data from comprehensive analysis of nuclear localization signals. PMID:26862559
Lambda Interferon Restructures the Nasal Microbiome and Increases Susceptibility to Staphylococcus aureus Superinfection. PMID:26861017
LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer. PMID:26860319
Effects of Oxygen Limitation on the Biosynthesis of Photo Pigments in the Red Microalgae Galdieria sulphuraria Strain 074G. PMID:26859750
Cell type-specific properties and environment shape tissue specificity of cancer genes. PMID:26856619
An integrated molecular landscape implicates the regulation of dendritic spine formation through insulin-related signalling in obsessive-compulsive disorder. PMID:26854754
UMD-Predictor: A High-Throughput Sequencing Compliant System for Pathogenicity Prediction of any Human cDNA Substitution. PMID:26842889
Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA. PMID:26836305
Streptomyces thermoautotrophicus does not fix nitrogen. PMID:26833023
Inhibiting Helicobacter pylori HtrA protease by addressing a computationally predicted allosteric ligand binding site. PMID:26819700
Clinical and Molecular Characterization of BSCL2 Mutations in a Taiwanese Cohort with Hereditary Neuropathy. PMID:26815532
Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles. PMID:26814845
Prominent scapulae mimicking an inherited myopathy expands the phenotype of CHD7-related disease. PMID:26813943
Hedgehog Signaling Strength Is Orchestrated by the mir-310 Cluster of MicroRNAs in Response to Diet. PMID:26801178
Gnaq(M1J): An ENU-Induced Mutant Allele Affecting Pigmentation in the Mouse. PMID:26763459
Homology-Based Prediction of Potential Protein-Protein Interactions between Human Erythrocytes and Plasmodium falciparum. PMID:26740742
Tripartite degrons confer diversity and specificity on regulated protein degradation in the ubiquitin-proteasome system. PMID:26732515
dEMBF: A Comprehensive Database of Enzymes of Microalgal Biofuel Feedstock. PMID:26727469
Origins of De Novo Genes in Human and Chimpanzee. PMID:26720152
Prediction of Intra-Species Protein-Protein Interactions in Enteropathogens Facilitating Systems Biology Study. PMID:26717407
Two Predicted Transmembrane Domains Exclude Very Long Chain Fatty acyl-CoAs from the Active Site of Mouse Wax Synthase. PMID:26714272
Compartmentalization and Functionality of Nuclear Disorder: Intrinsic Disorder and Protein-Protein Interactions in Intra-Nuclear Compartments. PMID:26712748
Identifying Predictors of Taxane-Induced Peripheral Neuropathy Using Mass Spectrometry-Based Proteomics Technology. PMID:26710119
Candida albicans Shaving to Profile Human Serum Proteins on Hyphal Surface. PMID:26696967
Ensembl 2016. PMID:26687719
Resolving the ambiguity: Making sense of intrinsic disorder when PDB structures disagree. PMID:26683124
Prediction of neddylation sites from protein sequences and sequence-derived properties. PMID:26679222
Taking Bioinformatics to Systems Medicine. PMID:26677177
Proteogenomics from a bioinformatics angle: A growing field. PMID:26670565
A Comparison of the Chicken and Turkey Proteomes and Phosphoproteomes in the Development of Poultry-Specific Immuno-Metabolism Kinome Peptide Arrays. PMID:26664921
Reproducible Analysis of Post-Translational Modifications in Proteomes--Application to Human Mutations. PMID:26659599
Fatty acid binding proteins have the potential to channel dietary fatty acids into enterocyte nuclei. PMID:26658423
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics. PMID:26656885
Text Mining for Protein Docking. PMID:26650466
Plasma Proteome Biomarkers of Inflammation in School Aged Children in Nepal. PMID:26636573
De novo and comparative transcriptome analysis of cultivated and wild spinach. PMID:26635144
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
Conserved mRNA-binding proteomes in eukaryotic organisms. PMID:26595419
FunTree: advances in a resource for exploring and contextualising protein function evolution. PMID:26590404
Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies. PMID:26585402
EBI metagenomics in 2016--an expanding and evolving resource for the analysis and archiving of metagenomic data. PMID:26582919
Coevolution Analysis of HIV-1 Envelope Glycoprotein Complex. PMID:26579711
Unexpected features of the dark proteome. PMID:26578815
Gene3D: expanding the utility of domain assignments. PMID:26578585
SugarBindDB, a resource of glycan-mediated host-pathogen interactions. PMID:26578555
Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides. PMID:26574429
KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins. PMID:26568635
pubmed.mineR: an R package with text-mining algorithms to analyse PubMed abstracts. PMID:26564970
Sexually dimorphic gene expression in the lateral eyes of Euphilomedes carcharodonta (Ostracoda, Pancrustacea). PMID:26561519
Identification of the nicotinamide mononucleotide adenylyltransferase of Trypanosoma cruzi. PMID:26560979
Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes. PMID:26560341
Gene Network Rewiring to Study Melanoma Stage Progression and Elements Essential for Driving Melanoma. PMID:26558755
Draft Genome Sequence of Caedibacter varicaedens, a Kappa Killer Endosymbiont Bacterium of the Ciliate Paramecium biaurelia. PMID:26543129
Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin. PMID:26539826
TIMP1, TIMP2, and TIMP4 are increased in aqueous humor from primary open angle glaucoma patients. PMID:26539028
Tools and data services registry: a community effort to document bioinformatics resources. PMID:26538599
The Distant Siblings-A Phylogenomic Roadmap Illuminates the Origins of Extant Diversity in Fungal Aromatic Polyketide Biosynthesis. PMID:26537223
Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity. PMID:26513360
Identification of the Streptococcus pyogenes surface antigens recognised by pooled human immunoglobulin. PMID:26508447
The LasB Elastase of Pseudomonas aeruginosa Acts in Concert with Alkaline Protease AprA To Prevent Flagellin-Mediated Immune Recognition. PMID:26502908
Asparagine deprivation mediated by Salmonella asparaginase causes suppression of activation-induced T cell metabolic reprogramming. PMID:26497246
KLIFS: a structural kinase-ligand interaction database. PMID:26496949
Overexpression of mitochondrial uncoupling protein 1 (UCP1) induces a hypoxic response in Nicotiana tabacum leaves. PMID:26494730
Sequence and Structure Analysis of Distantly-Related Viruses Reveals Extensive Gene Transfer between Viruses and Hosts and among Viruses. PMID:26492264
The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. PMID:26489866
Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response. PMID:26485378
ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. PMID:26481353
Using exposomics to assess cumulative risks and promote health. PMID:26475350
Complete Genome Sequence of Thermus aquaticus Y51MC23. PMID:26465632
G protein-coupled receptors directly bind filamin A with high affinity and promote filamin phosphorylation. PMID:26460884
Ribosome binding induces repositioning of the signal recognition particle receptor on the translocon. PMID:26459600
Next-generation-based targeted sequencing as an efficient tool for the study of the genetic background in Hirschsprung patients. PMID:26437850
Cheminformatics Research at the Unilever Centre for Molecular Science Informatics Cambridge. PMID:26435758
Loss of the Drosophila melanogaster DEAD box protein Ddx1 leads to reduced size and aberrant gametogenesis. PMID:26433063
Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search. PMID:26418581
Search for Allergens from the Pollen Proteome of Sunflower (Helianthus annuus L.): A Major Sensitizer for Respiratory Allergy Patients. PMID:26418046
Quantitative analysis of the murine lipid droplet-associated proteome during diet-induced hepatic steatosis. PMID:26416795
miRTex: A Text Mining System for miRNA-Gene Relation Extraction. PMID:26407127
htsint: a Python library for sequencing pipelines that combines data through gene set generation. PMID:26399714
Assessing sequence plasticity of a virus-like nanoparticle by evolution toward a versatile scaffold for vaccines and drug delivery. PMID:26392546
The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches. PMID:26380077
Integrated protein function prediction by mining function associations, sequences, and protein-protein and gene-gene interaction networks. PMID:26370280
Dissecting Leishmania infantum Energy Metabolism - A Systems Perspective. PMID:26367006
The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption. PMID:26366880
Cervicovaginal microbiome dysbiosis is associated with proteome changes related to alterations of the cervicovaginal mucosal barrier. PMID:26349657
Tyrosine Kinase Ligand-Receptor Pair Prediction by Using Support Vector Machine. PMID:26347773
Draft Genome Sequence of the Fungus Penicillium brasilianum MG11. PMID:26337871
Age-related obesity and type 2 diabetes dysregulate neuronal associated genes and proteins in humans. PMID:26337083
Large-scale determination of previously unsolved protein structures using evolutionary information. PMID:26335199
Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits. PMID:26334613
Integrated visual analysis of protein structures, sequences, and feature data. PMID:26329268
Kin of IRRE-like Protein 2 Is a Phosphorylated Glycoprotein That Regulates Basal Insulin Secretion. PMID:26324709
Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants. PMID:26317212
Skipper genome sheds light on unique phenotypic traits and phylogeny. PMID:26311350
Cardiolipin Interactions with Proteins. PMID:26300339
TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins. PMID:26289158
PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications. PMID:26283093
Blood-based lung cancer biomarkers identified through proteomic discovery in cancer tissues, cell lines and conditioned medium. PMID:26279647
Distilling a Visual Network of Retinitis Pigmentosa Gene-Protein Interactions to Uncover New Disease Candidates. PMID:26267445
MicroRNA and transcription factor mediated regulatory network analysis reveals critical regulators and regulatory modules in myocardial infarction. PMID:26258537
MetazSecKB: the human and animal secretome and subcellular proteome knowledgebase. PMID:26255309
Two Novel De Novo GARS Mutations Cause Early-Onset Axonal Charcot-Marie-Tooth Disease. PMID:26244500
Whole-genome sequencing identifies a novel ABCB7 gene mutation for X-linked congenital cerebellar ataxia in a large family of Mongolian ancestry. PMID:26242992
TMEM165 Deficiency: Postnatal Changes in Glycosylation. PMID:26238249
Cyanate as an energy source for nitrifiers. PMID:26222031
Representing virus-host interactions and other multi-organism processes in the Gene Ontology. PMID:26215368
Isoform-specific interactions of the von Hippel-Lindau tumor suppressor protein. PMID:26211615
Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S. PMID:26203328
Targeted Proteomics-Driven Computational Modeling of Macrophage S1P Chemosensing. PMID:26199343
A draft network of ligand-receptor-mediated multicellular signalling in human. PMID:26198319
Domain organization of DNase from Thioalkalivibrio sp. provides insights into retention of activity in high salt environments. PMID:26191053
p53-Regulated Networks of Protein, mRNA, miRNA, and lncRNA Expression Revealed by Integrated Pulsed Stable Isotope Labeling With Amino Acids in Cell Culture (pSILAC) and Next Generation Sequencing (NGS) Analyses. PMID:26183718
The Contribution of Missense Mutations in Core and Rim Residues of Protein-Protein Interfaces to Human Disease. PMID:26173036
Redox Activation of the Universally Conserved ATPase YchF by Thioredoxin 1. PMID:26160547
Comprehensive comparison of large-scale tissue expression datasets. PMID:26157623
Multi-level machine learning prediction of protein-protein interactions in Saccharomyces cerevisiae. PMID:26157620
Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification. PMID:26155816
Two high-mobility group box domains act together to underwind and kink DNA. PMID:26143914
EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A. PMID:26140928
State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet. PMID:26139527
Galectin-3 Binding Protein Secreted by Breast Cancer Cells Inhibits Monocyte-Derived Fibrocyte Differentiation. PMID:26136428
GPCRtm: An amino acid substitution matrix for the transmembrane region of class A G Protein-Coupled Receptors. PMID:26134144
A Simple Predictive Enhancer Syntax for Hindbrain Patterning Is Conserved in Vertebrate Genomes. PMID:26131856
Comparative Transcriptome Analysis of the Cosmopolitan Marine Fungus Corollospora maritima Under Two Physiological Conditions. PMID:26116293
Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction. PMID:26110515
Bioinformatics-Aided Venomics. PMID:26110505
Competition-cooperation relationship networks characterize the competition and cooperation between proteins. PMID:26108281
Early origin and adaptive evolution of the GW182 protein family, the key component of RNA silencing in animals. PMID:26106978
Prediction of protein targets of kinetin using in silico and in vitro methods: a case study on spinach seed germination mechanism. PMID:26101551
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. PMID:26100720
A novel role for peptidylarginine deiminases in microvesicle release reveals therapeutic potential of PAD inhibition in sensitizing prostate cancer cells to chemotherapy. PMID:26095379
Characterization of the Maize Chitinase Genes and Their Effect on Aspergillus flavus and Aflatoxin Accumulation Resistance. PMID:26090679
A Three-protein Charge Zipper Stabilizes a Complex Modulating Bacterial Gene Silencing. PMID:26085102
Identification of amino acids involved in histamine potentiation of GABA A receptors. PMID:26074818
The Complexity of Posttranscriptional Small RNA Regulatory Networks Revealed by In Silico Analysis of Gossypium arboreum L. Leaf, Flower and Boll Small Regulatory RNAs. PMID:26070200
dbHiMo: a web-based epigenomics platform for histone-modifying enzymes. PMID:26055100
Preferential sites for intramolecular glucosepane cross-link formation in type I collagen: A thermodynamic study. PMID:26049074
Implications of Genome-Based Discrimination between Clostridium botulinum Group I and Clostridium sporogenes Strains for Bacterial Taxonomy. PMID:26048939
Polymorphism Analysis Reveals Reduced Negative Selection and Elevated Rate of Insertions and Deletions in Intrinsically Disordered Protein Regions. PMID:26047845
Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism. PMID:26047810
Viral immunology. Comprehensive serological profiling of human populations using a synthetic human virome. PMID:26045439
Identification of genomic features in the classification of loss- and gain-of-function mutation. PMID:26043747
The Proteome of the Isolated Chlamydia trachomatis Containing Vacuole Reveals a Complex Trafficking Platform Enriched for Retromer Components. PMID:26042774
A manual curation strategy to improve genome annotation: application to a set of haloarchael genomes. PMID:26042526
Single-residue posttranslational modification sites at the N-terminus, C-terminus or in-between: To be or not to be exposed for enzyme access. PMID:26038108
Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies. PMID:26029180
Identification of an Auxiliary Leader Peptide-Binding Protein Required for Azoline Formation in Ribosomal Natural Products. PMID:26024319
INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity. PMID:26019177
PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. PMID:26013810
Databases for Microbiologists. PMID:26013493
From raw data to biological discoveries: a computational analysis pipeline for mass spectrometry-based proteomics. PMID:26002791
Characterization of the proteome of cytoplasmic lipid droplets in mouse enterocytes after a dietary fat challenge. PMID:25992653
A Combined Omics Approach to Generate the Surface Atlas of Human Naive CD4+ T Cells during Early T-Cell Receptor Activation. PMID:25991687
ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins. PMID:25982853
Insights into the Interactions of Fasciola hepatica Cathepsin L3 with a Substrate and Potential Novel Inhibitors through In Silico Approaches. PMID:25978322
Genome Sequence of Bacillus thuringiensis Strain Btm27, an Egyptian Isolate Highly Toxic to Cotton Leafworm. PMID:25977430
Most partial domains in proteins are alignment and annotation artifacts. PMID:25976240
CEMTDD: The database for elucidating the relationships among herbs, compounds, targets and related diseases for Chinese ethnic minority traditional drugs. PMID:25970778
The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. PMID:25969446
DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder. PMID:25968230
Quantification of histone deacetylase isoforms in human frontal cortex, human retina, and mouse brain. PMID:25962138
The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. PMID:25957950
Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins. PMID:25954868
Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees. PMID:25953738
The SwissLipids knowledgebase for lipid biology. PMID:25943471
Predicting peptide-mediated interactions on a genome-wide scale. PMID:25938916
Identification of novel transaminases from a 12-aminododecanoic acid-metabolizing Pseudomonas strain. PMID:25912724
PEIMAN 1.0: Post-translational modification Enrichment, Integration and Matching ANalysis. PMID:25911152
Co-regulation of translation in protein complexes. PMID:25909184
The ABC of Phytohormone Translocation. PMID:25905596
Predicting a double mutant in the twilight zone of low homology modeling for the skeletal muscle voltage-gated sodium channel subunit beta-1 (Nav1.4 β1). PMID:25904995
Hippocampal Pruning as a New Theory of Schizophrenia Etiopathogenesis. PMID:25902861
The BioMart community portal: an innovative alternative to large, centralized data repositories. PMID:25897122
Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework. PMID:25894391
A property-based analysis of human transcription factors. PMID:25890365
Mimoza: web-based semantic zooming and navigation in metabolic networks. PMID:25889977
DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe. PMID:25888481
GeneDig: a web application for accessing genomic and bioinformatics knowledge. PMID:25888373
Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data. PMID:25887857
Identifying named entities from PubMed for enriching semantic categories. PMID:25887671
CellWhere: graphical display of interaction networks organized on subcellular localizations. PMID:25883154
JPred4: a protein secondary structure prediction server. PMID:25883141
Sequence, structure and ligand binding evolution of rhodopsin-like G protein-coupled receptors: a crystal structure-based phylogenetic analysis. PMID:25881057
DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. PMID:25877637
Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data. PMID:25875762
Draft Genome Sequence of Klebsiella pneumoniae Carbapenemase-Producing Acinetobacter baumannii Strain M3AC9-7, Isolated from Puerto Rico. PMID:25858845
Epitope-based peptide vaccine design and target site depiction against Ebola viruses: an immunoinformatics study. PMID:25857850
The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI. PMID:25855807
Inbreeding Affects Gene Expression Differently in Two Self-Incompatible Arabidopsis lyrata Populations with Similar Levels of Inbreeding Depression. PMID:25855783
Transcript and protein expression decoupling reveals RNA binding proteins and miRNAs as potential modulators of human aging. PMID:25853883
Statistical approaches to detecting and analyzing tandem repeats in genomic sequences. PMID:25853125
Biochemical functional predictions for protein structures of unknown or uncertain function. PMID:25848497
Structural and evolutionary divergence of cyclic nucleotide binding domains in eukaryotic pathogens: Implications for drug design. PMID:25847873
Quantitative proteomics of heat-treated human cells show an across-the-board mild depletion of housekeeping proteins to massively accumulate few HSPs. PMID:25847399
Role of cysteine residues in the structure, stability, and alkane producing activity of cyanobacterial aldehyde deformylating oxygenase. PMID:25837679
The biochemical properties of the Arabidopsis ecto-nucleoside triphosphate diphosphohydrolase AtAPY1 contradict a direct role in purinergic signaling. PMID:25822168
Key challenges for the creation and maintenance of specialist protein resources. PMID:25820941
Complete Genome Sequences of Escherichia coli Strains 1303 and ECC-1470 Isolated from Bovine Mastitis. PMID:25814601
Thermal Stability of Dopamine Transporters. PMID:25812533
Difficulties in diagnosing Marfan syndrome using current FBN1 databases. PMID:25812041
New insights on the mechanism of the K(+-) independent activity of crenarchaeota pyruvate kinases. PMID:25811853
Can the natural diversity of quorum-sensing advance synthetic biology? PMID:25806368
Post-polymerization photografting on methacrylate-based monoliths for separation of intact proteins and protein digests with comprehensive two-dimensional liquid chromatography hyphenated with high-resolution mass spectrometry. PMID:25801383
BRAF V600E mutation in early-stage multiple myeloma: good response to broad acting drugs and no relation to prognosis. PMID:25794135
Homozygous MED25 mutation implicated in eye-intellectual disability syndrome. PMID:25792360
A method for multiplex gene synthesis employing error correction based on expression. PMID:25790188
Proteome-wide lysine acetylation in cortical astrocytes and alterations that occur during infection with brain parasite Toxoplasma gondii. PMID:25786129
Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology. PMID:25765281
Strong nonadditivity as a key structure-activity relationship feature: distinguishing structural changes from assay artifacts. PMID:25760829
Adaptive Evolution as a Predictor of Species-Specific Innate Immune Response. PMID:25758009
Exome sequencing and array-based comparative genomic hybridisation analysis of preferential 6-methylmercaptopurine producers. PMID:25752523
Analysis of the Candida albicans Phosphoproteome. PMID:25750214
Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights. PMID:25745418
Mango (Mangifera indica L.) cv. Kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening. PMID:25741352
The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families. PMID:25730766
LocSigDB: a database of protein localization signals. PMID:25725059
Genetic diversity of disease-associated loci in Turkish population. PMID:25716910
Molecular Characterization of Legionellosis Drug Target Candidate Enzyme Phosphoglucosamine Mutase from Legionella pneumophila (strain Paris): An In Silico Approach. PMID:25705169
Techniques for transferring host-pathogen protein interactions knowledge to new tasks. PMID:25699028
Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution. PMID:25697822
The roles of post-translational modifications in the context of protein interaction networks. PMID:25692714
Ancient dynamin segments capture early stages of host-mitochondrial integration. PMID:25691734
Replicating phages in the epidermal mucosa of the eel (Anguilla anguilla). PMID:25688234
The UCSC Ebola Genome Portal. PMID:25685613
Tiger Swallowtail Genome Reveals Mechanisms for Speciation and Caterpillar Chemical Defense. PMID:25683714
A comprehensive immunoinformatics and target site study revealed the corner-stone toward Chikungunya virus treatment. PMID:25682054
Valproic acid as a potential inhibitor of Plasmodium falciparum histone deacetylase 1 (PfHDAC1): an in silico approach. PMID:25679451
Validity of the MPTP-Treated Mouse as a Model for Parkinson's Disease. PMID:25676140
ABCE1 is a highly conserved RNA silencing suppressor. PMID:25659154
Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines. PMID:25656970
Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines. PMID:25656970
[FeFe]-hydrogenase maturation: insights into the role HydE plays in dithiomethylamine biosynthesis. PMID:25654171
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. PMID:25652942
Modeling and protein engineering studies of active and inactive states of human dopamine D2 receptor (D2R) and investigation of drug/receptor interactions. PMID:25652238
The conundrum of the high-affinity NGF binding site formation unveiled? PMID:25650935
Visualization of LC-MS/MS proteomics data in MaxQuant. PMID:25644178
The Putative mevalonate diphosphate decarboxylase from Picrophilus torridus is in reality a mevalonate-3-kinase with high potential for bioproduction of isobutene. PMID:25636853
Aquaria: simplifying discovery and insight from protein structures. PMID:25633501
Reinforcing the egg-timer: recruitment of novel lophotrochozoa homeobox genes to early and late development in the pacific oyster. PMID:25631164
Identification of Coq11, a new coenzyme Q biosynthetic protein in the CoQ-synthome in Saccharomyces cerevisiae. PMID:25631044
Enhanced stability and polyadenylation of select mRNAs support rapid thermogenesis in the brown fat of a hibernator. PMID:25626169
Data to knowledge: how to get meaning from your result. PMID:25610627
Distinguishing proteins from arbitrary amino acid sequences. PMID:25609314
Genome sequence of Coxiella burnetii strain Namibia. PMID:25593636
The neXtProt knowledgebase on human proteins: current status. PMID:25593349
The Ordospora colligata genome: Evolution of extreme reduction in microsporidia and host-to-parasite horizontal gene transfer. PMID:25587016
A proton relay enhances H2O2 sensitivity of GAPDH to facilitate metabolic adaptation. PMID:25580853
The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing. PMID:25569156
On the modularity of the intrinsic flexibility of the µ opioid receptor: a computational study. PMID:25549261
Allele Workbench: transcriptome pipeline and interactive graphics for allele-specific expression. PMID:25541944
Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling. PMID:25540776
Interrogation of the Burkholderia pseudomallei genome to address differential virulence among isolates. PMID:25536074
dbPPT: a comprehensive database of protein phosphorylation in plants. PMID:25534750
Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells--a benchmarking study. PMID:25521637
A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization. PMID:25512524
Temporal dynamics of the ABC transporter response to insecticide treatment: insights from the malaria vector Anopheles stephensi. PMID:25504146
Protein structure annotation resources. PMID:25502191
Genome-scale identification and characterization of moonlighting proteins. PMID:25497125
Purification of α-synuclein from human brain reveals an instability of endogenous multimers as the protein approaches purity. PMID:25490121
LAILAPS: the plant science search engine. PMID:25480116
Novel and unique domains in aminoacyl-tRNA synthetases from human fungal pathogens Aspergillus niger, Candida albicans and Cryptococcus neoformans. PMID:25479903
Discovering co-occurring patterns and their biological significance in protein families. PMID:25474736
Leishmania donovani infection enhances lateral mobility of macrophage membrane protein which is reversed by liposomal cholesterol. PMID:25474261
The HIV mutation browser: a resource for human immunodeficiency virus mutagenesis and polymorphism data. PMID:25474213
Computational approaches to interpreting genomic sequence variation. PMID:25473426
Molecular characterization of WDCP, a novel fusion partner for the anaplastic lymphoma tyrosine kinase ALK. PMID:25469238
Plant-PrAS: a database of physicochemical and structural properties and novel functional regions in plant proteomes. PMID:25435546
Triticeae resources in Ensembl Plants. PMID:25432969
Nemertean toxin genes revealed through transcriptome sequencing. PMID:25432940
PAS kinase is activated by direct SNF1-dependent phosphorylation and mediates inhibition of TORC1 through the phosphorylation and activation of Pbp1. PMID:25428989
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. PMID:25428375
The InterPro protein families database: the classification resource after 15 years. PMID:25428371
Expanded microbial genome coverage and improved protein family annotation in the COG database. PMID:25428365
The BioGRID interaction database: 2015 update. PMID:25428363
GRASP v2.0: an update on the Genome-Wide Repository of Associations between SNPs and phenotypes. PMID:25428361
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. PMID:25428351
Proteomics-Based Identification of Differentially Abundant Proteins from Human Keratinocytes Exposed to Arsenic Trioxide. PMID:25419056
Porphyromonas gingivalis RagB is a proinflammatory signal transducer and activator of transcription 4 agonist. PMID:25418117
BioModels: ten-year anniversary. PMID:25414348
ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts. PMID:25414346
The SUPERFAMILY 1.75 database in 2014: a doubling of data. PMID:25414345
The Pathogen-Host Interactions database (PHI-base): additions and future developments. PMID:25414340
ProteomeScout: a repository and analysis resource for post-translational modifications and proteins. PMID:25414335
Araport: the Arabidopsis information portal. PMID:25414324
Comparative genomics of transcriptional regulation of methionine metabolism in Proteobacteria. PMID:25411846
Characterization of age signatures of DNA methylation in normal and cancer tissues from multiple studies. PMID:25406591
Alternative splicing of MEF2C pre-mRNA controls its activity in normal myogenesis and promotes tumorigenicity in rhabdomyosarcoma cells. PMID:25404735
Comparative genomics of DtxR family regulons for metal homeostasis in Archaea. PMID:25404694
PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. PMID:25404129
Beyond protein expression, MOPED goes multi-omics. PMID:25404128
RNA-sequencing reveals early, dynamic transcriptome changes in the corollas of pollinated petunias. PMID:25403317
A recurrent de novo mutation in KCNC1 causes progressive myoclonus epilepsy. PMID:25401298
Computational characterization of moonlighting proteins. PMID:25399606
Fine mapping and candidate gene search of quantitative trait loci for growth and obesity using mouse intersubspecific subcongenic intercrosses and exome sequencing. PMID:25398139
Role of MTA2 in human cancer. PMID:25394532
Co-expression Network Analysis of Human lncRNAs and Cancer Genes. PMID:25392693
MiCroKiTS 4.0: a database of midbody, centrosome, kinetochore, telomere and spindle. PMID:25392421
PubAngioGen: a database and knowledge for angiogenesis and related diseases. PMID:25392416
VirHostNet 2.0: surfing on the web of virus/host molecular interactions data. PMID:25392406
DISOPRED3: precise disordered region predictions with annotated protein-binding activity. PMID:25391399
Distinct profiling of antimicrobial peptide families. PMID:25388148
Acetylome profiling reveals overlap in the regulation of diverse processes by sirtuins, gcn5, and esa1. PMID:25381059
Proteomics for systems toxicology. PMID:25379146
Europe PMC: a full-text literature database for the life sciences and platform for innovation. PMID:25378340
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities. PMID:25378329
MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae. PMID:25378328
Lessons from yeast on emerging roles of the ATAD2 protein family in gene regulation and genome organization. PMID:25377252
Characteristics of protein residue-residue contacts and their application in contact prediction. PMID:25374390
Development of a univariate membrane-based mid-infrared method for protein quantitation and total lipid content analysis of biological samples. PMID:25371845
Human cancer databases (review). PMID:25369839
Protectome analysis: a new selective bioinformatics tool for bacterial vaccine candidate discovery. PMID:25368410
Genome-wide analyses and functional classification of proline repeat-rich proteins: potential role of eIF5A in eukaryotic evolution. PMID:25364902
TFClass: a classification of human transcription factors and their rodent orthologs. PMID:25361979
MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins. PMID:25361972
Genenames.org: the HGNC resources in 2015. PMID:25361968
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. PMID:25361965
Participation of the Salmonella OmpD porin in the infection of RAW264.7 macrophages and BALB/c mice. PMID:25360745
The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data. PMID:25352556
SASBDB, a repository for biological small-angle scattering data. PMID:25352555
STRING v10: protein-protein interaction networks, integrated over the tree of life. PMID:25352553
Ensembl 2015. PMID:25352552
Integrating phosphoproteomics in systems biology. PMID:25349677
CATH: comprehensive structural and functional annotations for genome sequences. PMID:25348408
ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis. PMID:25348397
ToxDBScan: Large-scale similarity screening of toxicological databases for drug candidates. PMID:25338045
Expression profiling of mitochondrial voltage-dependent anion channel-1 associated genes predicts recurrence-free survival in human carcinomas. PMID:25333947
Dissecting domain-specific evolutionary pressure profiles of transient receptor potential vanilloid subfamily members 1 to 4. PMID:25333484
Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events. PMID:25332401
The human DEPhOsphorylation database DEPOD: a 2015 update. PMID:25332398
Updates in Rhea--a manually curated resource of biochemical reactions. PMID:25332395
EzCatDB: the enzyme reaction database, 2015 update. PMID:25324316
PLAZA 3.0: an access point for plant comparative genomics. PMID:25324309
Transcriptomic analysis reveals tomato genes whose expression is induced specifically during effector-triggered immunity and identifies the Epk1 protein kinase which is required for the host response to three bacterial effector proteins. PMID:25323444
The complex portal--an encyclopaedia of macromolecular complexes. PMID:25313161
Organ system heterogeneity DB: a database for the visualization of phenotypes at the organ system level. PMID:25313158
Structural elucidation of the DFG-Asp in and DFG-Asp out states of TAM kinases and insight into the selectivity of their inhibitors. PMID:25310149
SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes. PMID:25309735
sc-PDB: a 3D-database of ligandable binding sites--10 years on. PMID:25300483
The immune epitope database (IEDB) 3.0. PMID:25300482
SMART: recent updates, new developments and status in 2015. PMID:25300481
Linear motif-mediated interactions have contributed to the evolution of modularity in complex protein interaction networks. PMID:25299147
High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis. PMID:25271953
The role of the interactome in the maintenance of deleterious variability in human populations. PMID:25261458
Sequence co-evolution gives 3D contacts and structures of protein complexes. PMID:25255213
Integrative visual analysis of protein sequence mutations. PMID:25237389
Long non-coding RNAs as a source of new peptides. PMID:25233276
WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. PMID:25231498
PeptideManager: a peptide selection tool for targeted proteomic studies involving mixed samples from different species. PMID:25228907
Conserved and host-specific features of influenza virion architecture. PMID:25226414
VirusMentha: a new resource for virus-host protein interactions. PMID:25217587
New insights about enzyme evolution from large scale studies of sequence and structure relationships. PMID:25210038
Insilico analysis of hypothetical proteins unveils putative metabolic pathways and essential genes in Leishmania donovani. PMID:25206363
Functional characterization of chemosensory proteins in the scarab beetle, Holotrichia oblita Faldermann (Coleoptera: Scarabaeida). PMID:25188038
Reprogramming the specificity of sortase enzymes. PMID:25187567
A genome-wide identification of genes undergoing recombination and positive selection in Neisseria. PMID:25180194
Common variants near ABCA1, AFAP1 and GMDS confer risk of primary open-angle glaucoma. PMID:25173105
Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys. PMID:25168586
Whole genome sequencing and analysis of plant growth promoting bacteria isolated from the rhizosphere of plantation crops coconut, cocoa and arecanut. PMID:25162593
Identifying transcription factor complexes and their roles. PMID:25161228
Making proteomics data accessible and reusable: current state of proteomics databases and repositories. PMID:25158685
Morquio A syndrome-associated mutations: a review of alterations in the GALNS gene and a new locus-specific database. PMID:25137622
Purifying selection against gene conversions between the polyamine transport (TPO) genes of Saccharomyces species. PMID:25135753
RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information. PMID:25122463
Evolution of a genome-encoded bias in amino acid biosynthetic pathways is a potential indicator of amino acid dynamics in the environment. PMID:25118252
New subfamilies of major intrinsic proteins in fungi suggest novel transport properties in fungal channels: implications for the host-fungal interactions. PMID:25112373
Protein localization analysis of essential genes in prokaryotes. PMID:25105358
Heterogeneity of glycolysis in cancers and therapeutic opportunities. PMID:25093285
Cellular and Developmental Biology of TRPM7 Channel-Kinase: Implicated Roles in Cancer. PMID:25079291
BioJS: an open source standard for biological visualisation - its status in 2014. PMID:25075290
ABC transporters are involved in defense against permethrin insecticide in the malaria vector Anopheles stephensi. PMID:25073980
Evolutionary analysis of the cystatin family in three Schistosoma species. PMID:25071834
Massive expansion of Ubiquitination-related gene families within the Chlamydiae. PMID:25069652
The histidine-rich glycoprotein A1042G polymorphism and recurrent miscarriage: a pilot study. PMID:25064236
Starvation-response may not involve Atg1-dependent autophagy induction in non-unikont parasites. PMID:25059978
IthaGenes: an interactive database for haemoglobin variations and epidemiology. PMID:25058394
In silico comparative characterization of pharmacogenomic missense variants. PMID:25057096
Text-mining-assisted biocuration workflows in Argo. PMID:25037308
Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations. PMID:25015645
Draft Genome Sequence of Rhodosporidium toruloides CECT1137, an Oleaginous Yeast of Biotechnological Interest. PMID:25013136
Processing biological literature with customizable Web services supporting interoperable formats. PMID:25006225
In silico analysis of functional single nucleotide polymorphisms in the human TRIM22 gene. PMID:24983760
Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations. PMID:24980186
Desmosterolosis: an illustration of diagnostic ambiguity of cholesterol synthesis disorders. PMID:24961299
PubServer: literature searches by homology. PMID:24957597
Whole-Genome Sequence of Burkholderia sp. Strain RPE67, a Bacterial Gut Symbiont of the Bean Bug Riptortus pedestris. PMID:24948758
Epigenetic regulation of persistent pain. PMID:24948399
Structures of bacterial kynurenine formamidase reveal a crowded binuclear zinc catalytic site primed to generate a potent nucleophile. PMID:24942958
Representing kidney development using the gene ontology. PMID:24941002
MIRA: mutual information-based reporter algorithm for metabolic networks. PMID:24931981
MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data. PMID:24910945
A method for increasing expressivity of Gene Ontology annotations using a compositional approach. PMID:24885854
Enhancing UCSF Chimera through web services. PMID:24861624
MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network. PMID:24861622
Comparison of prokaryotic community structure from Mediterranean and Atlantic saltern concentrator ponds by a metagenomic approach. PMID:24847316
Survey of phosphorylation near drug binding sites in the Protein Data Bank (PDB) and their effects. PMID:24833420
TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model. PMID:24829452
Alignment-Annotator web server: rendering and annotating sequence alignments. PMID:24813445
A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. PMID:24803668
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. PMID:24792157
An Interaction Library for the FcεRI Signaling Network. PMID:24782869
The DynaMine webserver: predicting protein dynamics from sequence. PMID:24728994
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
Mechanistic and bioinformatic investigation of a conserved active site helix in α-isopropylmalate synthase from Mycobacterium tuberculosis, a member of the DRE-TIM metallolyase superfamily. PMID:24720347
3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families. PMID:24700812
Intratumoral decorin gene delivery by AAV vector inhibits brain glioblastomas and prolongs survival of animals by inducing cell differentiation. PMID:24625664
Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. PMID:24622611
Minimal model of self-assembly: emergence of diversity and complexity. PMID:24571643
DFLAT: functional annotation for human development. PMID:24507166 -
The Universal Protein Resource (UniProt)
PubMed citations: 661.
661 articles citing: The Universal Protein Resource (UniProt)
Mini-review: Recent advances in post-translational modification site prediction based on deep learning. PMID:35860402
Mass spectrometry-based draft of the mouse proteome. PMID:35710609
BepFAMN: A Method for Linear B-Cell Epitope Predictions Based on Fuzzy-ARTMAP Artificial Neural Network. PMID:35684648
The microbiome of cryospheric ecosystems. PMID:35655063
Machine learning aided construction of the quorum sensing communication network for human gut microbiota. PMID:35654892
Molecular docking analysis reveals the functional inhibitory effect of Genistein and Quercetin on TMPRSS2: SARS-COV-2 cell entry facilitator spike protein. PMID:35578172
An Immunoinformatic Strategy to Develop New Mycobacterium tuberculosis Multi-epitope Vaccine. PMID:35573911
Protein secondary structure prediction with context convolutional neural network. PMID:35540205
A Genome-Scale Metabolic Model of Methanoperedens nitroreducens: Assessing Bioenergetics and Thermodynamic Feasibility. PMID:35448501
LPInsider: a webserver for lncRNA-protein interaction extraction from the literature. PMID:35428172
Genome-wide analysis of JAZ family genes expression patterns during fig (Ficus carica L.) fruit development and in response to hormone treatment. PMID:35236292
Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera. PMID:35208935
The aqueous humor proteome is intrinsically disordered. PMID:35128080
Polymeric biocompatible iron oxide nanoparticles labeled with peptides for imaging in ovarian cancer. PMID:35103283
A New Prospect for the Treatment of Nephrotic Syndrome Based on Network Pharmacology Analysis. PMID:35098155
Design of a Novel Recombinant Multi-Epitope Vaccine against Triple-Negative Breast Cancer. PMID:35090304
On the Applicability of Electrophoresis for Protein Quantification. PMID:34833270
Exposing structural variations in SARS-CoV-2 evolution. PMID:34764391
Characterization and prognostic value of LXR splice variants in triple-negative breast cancer. PMID:34755086
Opioid Addiction and Opioid Receptor Dimerization: Structural Modeling of the OPRD1 and OPRM1 Heterodimer and Its Signaling Pathways. PMID:34638633
RFCM-PALM: In-Silico Prediction of S-Palmitoylation Sites in the Synaptic Proteins for Male/Female Mouse Data. PMID:34576064
Exposing Structural Variations in SARS-CoV-2 Evolution. PMID:34545355
Review on COVID-19 diagnosis models based on machine learning and deep learning approaches. PMID:34511689
Draft Genome of the Mirrorwing Flyingfish (Hirundichthys speculiger). PMID:34306036
Toward the solution of the protein structure prediction problem. PMID:34119522
Inwardly rectifying potassium channel 5.1: Structure, function, and possible roles in diseases. PMID:33997174
Systematic in silico Evaluation of Leishmania spp. Proteomes for Drug Discovery. PMID:33987166
Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics. PMID:33916464
A Molecular Modeling Approach to Identify Potential Antileishmanial Compounds Against the Cell Division Cycle (cdc)-2-Related Kinase 12 (CRK12) Receptor of Leishmania donovani. PMID:33803906
Soluble ACE2-mediated cell entry of SARS-CoV-2 via interaction with proteins related to the renin-angiotensin system. PMID:33713620
Reconstruction of the Origin of a Neo-Y Sex Chromosome and Its Evolution in the Spotted Knifejaw, Oplegnathus punctatus. PMID:33693787
The evolutionary conserved iron-sulfur protein TCR controls P700 oxidation in photosystem I. PMID:33554065
Emodin Inhibits the Proliferation of MCF-7 Human Breast Cancer Cells Through Activation of Aryl Hydrocarbon Receptor (AhR). PMID:33542691
Improving the Identification and Coverage of Plant Transmembrane Proteins in Medicago Using Bottom-Up Proteomics. PMID:33391307
New mixture models for decoy-free false discovery rate estimation in mass spectrometry proteomics. PMID:33381824
An automated protocol for modelling peptide substrates to proteases. PMID:33375946
Bioinformatic Analysis and Biophysical Characterization Reveal Structural Disorder in G0S2 Protein. PMID:33073109
PI3K-Akt pathway mediated antiviral mechanism in silkworm Antheraea mylitta. PMID:32904810
Completion of draft bacterial genomes by long-read sequencing of synthetic genomic pools. PMID:32727443
A transcriptome-based approach to identify functional modules within and across primary human immune cells. PMID:32469933
Protein Interaction Network Reconstruction Through Ensemble Deep Learning With Attention Mechanism. PMID:32432096
Identification and Modeling of a GT-A Fold in the α-Dystroglycan Glycosylating Enzyme LARGE1. PMID:32356985
Chromosome-level genome assembly of Aldrichina grahami, a forensically important blowfly. PMID:32191812
The C-terminal domain of M. tuberculosis ECF sigma factor I (SigI) interferes in SigI-RNAP interaction. PMID:32180013
FibroAtlas: A Database for the Exploration of Fibrotic Diseases and Their Genes. PMID:32082621
Characterizing Membrane Association and Periplasmic Transfer of Bacterial Lipoproteins through Molecular Dynamics Simulations. PMID:32053772
DeepKinZero: zero-shot learning for predicting kinase-phosphosite associations involving understudied kinases. PMID:32044914
Finding the Keys to the CAR: Identifying Novel Target Antigens for T Cell Redirection Immunotherapies. PMID:31947597
Druggable exosites of the human kino-pocketome. PMID:31925639
A network analysis revealed the essential and common downstream proteins related to inguinal hernia. PMID:31910207
Systematic analysis of linker histone PTM hotspots reveals phosphorylation sites that modulate homologous recombination and DSB repair. PMID:31821952
Analysis of glycoside hydrolases from oat (Avena sativa) seedling extract. PMID:31787817
DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning. PMID:31510699
ABCD: Alzheimer's disease Biomarkers Comprehensive Database. PMID:31501752
A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). PMID:31437279
Lack of long-term acclimation in Antarctic encrusting species suggests vulnerability to warming. PMID:31358752
A transcriptional and functional analysis of heat hardening in two invasive fruit fly species, Bactrocera dorsalis and Bactrocera correcta. PMID:31293628
Sharing Programming Resources Between Bio* Projects. PMID:31278684
Prediction of bacterial E3 ubiquitin ligase effectors using reduced amino acid peptide fingerprinting. PMID:31211016
Three New Isoflavonoid Glycosides from the Mangrove-Derived Actinomycete Micromonospora aurantiaca 110B. PMID:31108876
OsteoporosAtlas: a human osteoporosis-related gene database. PMID:31086734
The atypical thiol-disulfide exchange protein α-DsbA2 from Wolbachia pipientis is a homotrimeric disulfide isomerase. PMID:30950399
In silico design of a triple-negative breast cancer vaccine by targeting cancer testis antigens. PMID:30788259
Development and validation of whole genome-wide and genic microsatellite markers in oil palm (Elaeis guineensis Jacq.): First microsatellite database (OpSatdb). PMID:30760842
Predicting protein functions by applying predicate logic to biomedical literature. PMID:30736739
The genomic basis for colonizing the freezing Southern Ocean revealed by Antarctic toothfish and Patagonian robalo genomes. PMID:30715292
Antimicrobial peptide similarity and classification through rough set theory using physicochemical boundaries. PMID:30522443
Capsule network for protein post-translational modification site prediction. PMID:30520972
Pharmacoinformatic Approach to Explore the Antidote Potential of Phytochemicals on Bungarotoxin from Indian Krait, Bungarus caeruleus. PMID:30455855
The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions. PMID:30418645
Motif-Aware PRALINE: Improving the alignment of motif regions. PMID:30383764
The GIS2 Gene Is Repressed by a Zinc-Regulated Bicistronic RNA in Saccharomyces cerevisiae. PMID:30235899
Structure modeling to function prediction of Uncharacterized Human Protein C15orf41. PMID:30108417
afpCOOL: A tool for antifreeze protein prediction. PMID:30094375
Comparative analysis reveals unexpected genome features of newly isolated Thraustochytrids strains: on ecological function and PUFAs biosynthesis. PMID:30016947
Identification of Antifungal Targets Based on Computer Modeling. PMID:29973534
Combining Targeted Metabolites Analysis and Transcriptomics to Reveal Chemical Composition Difference and Underlying Transcriptional Regulation in Maca (Lepidium Meyenii Walp.) Ecotypes. PMID:29970867
Clustering huge protein sequence sets in linear time. PMID:29959318
Public proteomics data: How the field has evolved from sceptical inquiry to the promise of in silico proteomics. PMID:29900110
Polypharmacology Within the Full Kinome: a Machine Learning Approach. PMID:29888050
Genetic Analysis of Rare Human Variants of Regulators of G Protein Signaling Proteins and Their Role in Human Physiology and Disease. PMID:29871944
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
AllerGAtlas 1.0: a human allergy-related genes database. PMID:29688358
Mycobacterium tuberculosis H37Rv LpqG Protein Peptides Can Inhibit Mycobacterial Entry through Specific Interactions. PMID:29495456
Two inhibitors of yeast plasma membrane ATPase 1 (ScPma1p): toward the development of novel antifungal therapies. PMID:29464421
Genetic Separation of Listeria monocytogenes Causing Central Nervous System Infections in Animals. PMID:29459888
Draft Sequencing of the Heterozygous Diploid Genome of Satsuma (Citrus unshiu Marc.) Using a Hybrid Assembly Approach. PMID:29259619
Complete Genome Sequence of Hyperthermophilic Archaeon Thermococcus sp. EXT12c, Isolated from the East Pacific Rise 9°N. PMID:29242226
Poisson Model To Generate Isotope Distribution for Biomolecules. PMID:29202576
A Systematic Review of Computational Drug Discovery, Development, and Repurposing for Ebola Virus Disease Treatment. PMID:29053626
MusiteDeep: a deep-learning framework for general and kinase-specific phosphorylation site prediction. PMID:29036382
iTRAQ protein profile analysis of developmental dynamics in soybean [Glycine max (L.) Merr.] leaves. PMID:28953898
Interacting amino acid replacements allow poison frogs to evolve epibatidine resistance. PMID:28935799
PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasets. PMID:28931422
Genome analysis of E. coli isolated from Crohn's disease patients. PMID:28724357
Complete genome sequence of Microbulbifer sp. CCB-MM1, a halophile isolated from Matang Mangrove Forest, Malaysia. PMID:28694917
Predicting human protein subcellular localization by heterogeneous and comprehensive approaches. PMID:28658305
Accurate prediction of functional effects for variants by combining gradient tree boosting with optimal neighborhood properties. PMID:28614374
The alphabet of intrinsic disorder: II. Various roles of glutamic acid in ordered and intrinsically disordered proteins. PMID:28516010
The alphabet of intrinsic disorder: I. Act like a Pro: On the abundance and roles of proline residues in intrinsically disordered proteins. PMID:28516008
Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods. PMID:28388405
Predicting Presynaptic and Postsynaptic Neurotoxins by Developing Feature Selection Technique. PMID:28303250
The essential and downstream common proteins of amyotrophic lateral sclerosis: A protein-protein interaction network analysis. PMID:28282387
The intrinsic disorder alphabet. III. Dual personality of serine. PMID:28232888
Bioinformatic prediction of G protein-coupled receptor encoding sequences from the transcriptome of the foreleg, including the Haller's organ, of the cattle tick, Rhipicephalus australis. PMID:28231302
Systematic analysis of non-structural protein features for the prediction of PTM function potential by artificial neural networks. PMID:28225828
SCALEUS: Semantic Web Services Integration for Biomedical Applications. PMID:28214993
Making life difficult for Clostridium difficile: augmenting the pathogen's metabolic model with transcriptomic and codon usage data for better therapeutic target characterization. PMID:28209199
Dynamic changes in the transcriptome of Populus hopeiensis in response to abscisic acid. PMID:28198429
An improved method for functional similarity analysis of genes based on Gene Ontology. PMID:28155727
Incorporating efficient radial basis function networks and significant amino acid pairs for predicting GTP binding sites in transport proteins. PMID:28155651
Bioinformatics Analysis of Top-Down Mass Spectrometry Data with ProSight Lite. PMID:28150248
MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota. PMID:28077565
Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine. PMID:27902695
A Graph Approach to Mining Biological Patterns in the Binding Interfaces. PMID:27892693
Harnessing Big Data for Systems Pharmacology. PMID:27814027
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. PMID:27789697
A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti. PMID:27748755
Prediction of phosphothreonine sites in human proteins by fusing different features. PMID:27698459
Intrinsic Disorder of the C-Terminal Domain of Drosophila Methoprene-Tolerant Protein. PMID:27657508
An expanded evaluation of protein function prediction methods shows an improvement in accuracy. PMID:27604469
Identification of Secretory Proteins in Mycobacterium tuberculosis Using Pseudo Amino Acid Composition. PMID:27597968
Proton currents constrain structural models of voltage sensor activation. PMID:27572256
The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease. PMID:27564311
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. PMID:27504778
Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs. PMID:27475771
Identification of Bacterial Cell Wall Lyases via Pseudo Amino Acid Composition. PMID:27437396
Comparative Protein Structure Modeling Using MODELLER. PMID:27322406
Comparative chemical genomics reveal that the spiroindolone antimalarial KAE609 (Cipargamin) is a P-type ATPase inhibitor. PMID:27291296
Ebolavirus Database: Gene and Protein Information Resource for Ebolaviruses. PMID:27190508
DnaK-Dependent Accelerated Evolutionary Rate in Prokaryotes. PMID:27189986
Elucidation of the Mode of Action of a New Antibacterial Compound Active against Staphylococcus aureus and Pseudomonas aeruginosa. PMID:27167126
Evolutionary constraints over microsatellite abundance in larger mammals as a potential mechanism against carcinogenic burden. PMID:27125812
XLSearch: a Probabilistic Database Search Algorithm for Identifying Cross-Linked Peptides. PMID:27068484
Regulation of Receptor for Advanced Glycation End Products (RAGE) Ectodomain Shedding and Its Role in Cell Function. PMID:27022018
Modeling of babesipain-1 and identification of natural and synthetic leads for bovine babesiosis drug development. PMID:26969677
Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula. PMID:26964738
Robust classification of protein variation using structural modelling and large-scale data integration. PMID:26926108
Prediction of G protein-coupled receptor encoding sequences from the synganglion transcriptome of the cattle tick, Rhipicephalus microplus. PMID:26922323
Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network. PMID:26860696
Cytochrome P450 20A1 in zebrafish: Cloning, regulation and potential involvement in hyperactivity disorders. PMID:26853319
Broadly targeted CD8⁺ T cell responses restricted by major histocompatibility complex E. PMID:26797147
Predicting the functions of a protein from its ability to associate with other molecules. PMID:26767846
Control of TSC2-Rheb signaling axis by arginine regulates mTORC1 activity. PMID:26742086
Detection of secondary binding sites in proteins using fragment screening. PMID:26655740
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
eIF5A1/RhoGDIα pathway: a novel therapeutic target for treatment of spinal cord injury identified by a proteomics approach. PMID:26593060
Carbohydrate-Aromatic Interactions in Proteins. PMID:26561965
Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling. PMID:26549015
Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation. PMID:26473045
Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins. PMID:26439842
Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME. PMID:26384374
Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory. PMID:26370961
Citing a Data Repository: A Case Study of the Protein Data Bank. PMID:26317409
Trypanosomes Modify the Behavior of Their Insect Hosts: Effects on Locomotion and on the Expression of a Related Gene. PMID:26291723
Comparison of predicted and actual consequences of missense mutations. PMID:26269570
Using SEQUEST with theoretically complete sequence databases. PMID:26238326
GESPA: classifying nsSNPs to predict disease association. PMID:26206375
Scrutinizing the immune defence inventory of Camponotus floridanus applying total transcriptome sequencing. PMID:26198742
Function of a p24 Heterodimer in Morphogenesis and Protein Transport in Penicillium oxalicum. PMID:26149342
SInCRe-structural interactome computational resource for Mycobacterium tuberculosis. PMID:26130660
An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum. PMID:25990474
Implementation of linked data in the life sciences at BioHackathon 2011. PMID:25973165
Determining minimum set of driver nodes in protein-protein interaction networks. PMID:25947063
Pathways with PathWhiz. PMID:25934797
Capturing domain knowledge from multiple sources: the rare bone disorders use case. PMID:25926964
Molecular dynamics study of naturally existing cavity couplings in proteins. PMID:25816327
Protein topology determines cysteine oxidation fate: the case of sulfenyl amide formation among protein families. PMID:25741692
Automated training for algorithms that learn from genomic data. PMID:25695053
Genomic and transcriptomic analysis of the endophytic fungus Pestalotiopsis fici reveals its lifestyle and high potential for synthesis of natural products. PMID:25623211
Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells--a benchmarking study. PMID:25521637
Intrinsically disordered and pliable Starmaker-like protein from medaka (Oryzias latipes) controls the formation of calcium carbonate crystals. PMID:25490041
Identifying pathogenicity islands in bacterial pathogenomics using computational approaches. PMID:25437607
Gene expression microarray analysis of the sciatic nerve of mice with diabetic neuropathy. PMID:25435094
Computational and experimental characterization of dVHL establish a Drosophila model of VHL syndrome. PMID:25310726
Celastrol inhibits Plasmodium falciparum enoyl-acyl carrier protein reductase. PMID:25284249
Lactobacillus rossiae, a vitamin B12 producer, represents a metabolically versatile species within the Genus Lactobacillus. PMID:25264826
Amino acid sequence and structural comparison of BACE1 and BACE2 using evolutionary trace method. PMID:25254246
Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection. PMID:25220818
Randomness and preserved patterns in cancer network. PMID:25220184
A sentinel protein assay for simultaneously quantifying cellular processes. PMID:25194849
Biochemical characterization and crystal structures of a fungal family 3 β-glucosidase, Cel3A from Hypocrea jecorina. PMID:25164811
A novel eliminase from a marine bacterium that degrades hyaluronan and chondroitin sulfate. PMID:25122756
Predicting disease-related proteins based on clique backbone in protein-protein interaction network. PMID:25013377
Integrative analysis of longitudinal metabolomics data from a personal multi-omics profile. PMID:24958148
Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research. PMID:24932210
Membrane protein profiling of human colon reveals distinct regional differences. PMID:24889196
Genome-wide identification of heat shock proteins (Hsps) and Hsp interactors in rice: Hsp70s as a case study. PMID:24884676
TuberQ: a Mycobacterium tuberculosis protein druggability database. PMID:24816183
Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity. PMID:24794930
Community-based network study of protein-carbohydrate interactions in plant lectins using glycan array data. PMID:24755681
Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria. PMID:24678308
Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies. PMID:24651380
Identification of genes differentially expressed in myogenin knock-down bovine muscle satellite cells during differentiation through RNA sequencing analysis. PMID:24647404
Protein (multi-)location prediction: using location inter-dependencies in a probabilistic framework. PMID:24646119
BD SIMULATIONS OF THE IONIC STRENGTH DEPENDENCE OF THE INTERACTIONS BETWEEN TRIOSE PHOSPHATE ISOMERASE AND F-ACTIN. PMID:24639622
Cancer stem cell markers correlate with early recurrence and survival in hepatocellular carcinoma. PMID:24616575
Network analysis of neurodegenerative disease highlights a role of Toll-like receptor signaling. PMID:24551850
Discriminative motif discovery via simulated evolution and random under-sampling. PMID:24551063
Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra. PMID:24493012
Multi-algorithm and multi-model based drug target prediction and web server. PMID:24487966
PFMFind: a system for discovery of peptide homology and function. PMID:24479118
Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches. PMID:24432138
Joint probabilistic-logical refinement of multiple protein feature predictors. PMID:24428894
Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus. PMID:24415955
MOPED enables discoveries through consistently processed proteomics data. PMID:24350770
Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. PMID:24335146
Domain wise docking analyses of the modular chitin binding protein CBP50 from Bacillus thuringiensis serovar konkukian S4. PMID:24307767
Soluble expression of proteins correlates with a lack of positively-charged surface. PMID:24276756
ModBase, a database of annotated comparative protein structure models and associated resources. PMID:24271400
Exploring fold space preferences of new-born and ancient protein superfamilies. PMID:24244135
Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences. PMID:24175627
Can inferred provenance and its visualisation be used to detect erroneous annotation? A case study using UniProtKB. PMID:24143170
Quantification of the impact of PSI:Biology according to the annotations of the determined structures. PMID:24139526
A conserved sequence in calmodulin regulated spectrin-associated protein 1 links its interaction with spectrin and calmodulin to neurite outgrowth. PMID:24117850
Neutron-encoded signatures enable product ion annotation from tandem mass spectra. PMID:24043425
An approach for identifying cytokines based on a novel ensemble classifier. PMID:24027761
Analyzing LC/MS metabolic profiling data in the context of existing metabolic networks. PMID:24010053
Three dimensional (3D) structure prediction and substrate-protein interaction study of the chitin binding protein CBP24 from B. thuringiensis. PMID:23976829
Functional coding variants in SLC6A15, a possible risk gene for major depression. PMID:23874702
Acceleration of sequence clustering using longest common subsequence filtering. PMID:23815271
Identification of salt treated proteins in sorghum using gene ontology linkage. PMID:23814435
A daily-updated tree of (sequenced) life as a reference for genome research. PMID:23778980
Gut transcriptome of replete adult female cattle ticks, Rhipicephalus (Boophilus) microplus, feeding upon a Babesia bovis-infected bovine host. PMID:23749091
Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction. PMID:23704901
Top-down clustering for protein subfamily identification. PMID:23700359
Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction. PMID:23675487
Molecular evolution of peptidergic signaling systems in bilaterians. PMID:23671109
Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: recurrence of tyrosine aminotransferase activity in the Iα subfamily. PMID:23671031
A multi-platform draft de novo genome assembly and comparative analysis for the Scarlet Macaw (Ara macao). PMID:23667475
Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq. PMID:23629695
Explaining microbial phenotypes on a genomic scale: GWAS for microbes. PMID:23625995
Functional classification of immune regulatory proteins. PMID:23583034
Tyrosine pathway regulation is host-mediated in the pea aphid symbiosis during late embryonic and early larval development. PMID:23575215
Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms. PMID:23527883
Protein function prediction using text-based features extracted from the biomedical literature: the CAFA challenge. PMID:23514326
Evolution of the ferric reductase domain (FRD) superfamily: modularity, functional diversification, and signature motifs. PMID:23505460
New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis. PMID:23497205
Cross-species analysis of nicotine-induced proteomic alterations in pancreatic cells. PMID:23456891
A novel algorithm for validating peptide identification from a shotgun proteomics search engine. PMID:23402659
A large-scale evaluation of computational protein function prediction. PMID:23353650
Subcellular fractionation enhances proteome coverage of pancreatic duct cells. PMID:23352835
A consensus method for the prediction of 'aggregation-prone' peptides in globular proteins. PMID:23326595
Identification of MFS proteins in sorghum using semantic similarity. PMID:23299296
Functional characterization of AlgL, an alginate lyase from Pseudomonas aeruginosa. PMID:23215237
DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. PMID:23193290
Exploring Pandora's box: potential and pitfalls of low coverage genome surveys for evolutionary biology. PMID:23185309
DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. PMID:23161684
Draft genome sequence of the novel enteric bacterium Galloisinimonas intestini B14T KCTC 32180, isolated from the gut of a Galloisiana species (Notoptera: Grylloblattidae) fossil insect. PMID:23144398
A docking-based receptor library of antibiotics and its novel application in predicting chronic mixture toxicity for environmental risk assessment. PMID:23143826
NanoUPLC-MSE proteomic data assessment of soybean seeds using the Uniprot database. PMID:23126227
Genome sequence of the thermophile Bacillus coagulans Hammer, the type strain of the species. PMID:23105047
Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining. PMID:23055974
Finding biomedical categories in Medline®. PMID:23046816
Genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin. PMID:23043000
Endemic bacteriophages: a cautionary tale for evaluation of bacteriophage therapy and other interventions for infection control in animals. PMID:22985539
Draft genome sequence of Lactobacillus rossiae DSM 15814(T). PMID:22965087
Updating annotations with the distributed annotation system and the automated sequence annotation pipeline. PMID:22945787
Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. PMID:22942020
FunSAV: predicting the functional effect of single amino acid variants using a two-stage random forest model. PMID:22937107
A computational study on thiourea analogs as potent MK-2 inhibitors. PMID:22837679
The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. PMID:22801500
Predict impact of single amino acid change upon protein structure. PMID:22759652
Genome sequence of the unclassified marine Gammaproteobacterium BDW918. PMID:22740675
A dominant negative heterozygous G87R mutation in the zinc transporter, ZnT-2 (SLC30A2), results in transient neonatal zinc deficiency. PMID:22733820
Public domain databases for medicinal chemistry. PMID:22731701
The immune gene repertoire of an important viral reservoir, the Australian black flying fox. PMID:22716473
Detecting mutually exclusive interactions in protein-protein interaction maps. PMID:22715412
Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici. PMID:22712506
Scaffoldin conformation and dynamics revealed by a ternary complex from the Clostridium thermocellum cellulosome. PMID:22707718
An elm EST database for identifying leaf beetle egg-induced defense genes. PMID:22702658
CD45-deficient severe combined immunodeficiency caused by uniparental disomy. PMID:22689986
A conditional neural fields model for protein threading. PMID:22689779
The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation. PMID:22630137
Facile backbone structure determination of human membrane proteins by NMR spectroscopy. PMID:22609626
Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms. PMID:22536960
The molecular dynamics of Trypanosoma brucei UDP-galactose 4'-epimerase: a drug target for African sleeping sickness. PMID:22487100
Genome sequence of Lactobacillus fructivorans KCTC 3543. PMID:22461550
The Bone Dysplasia Ontology: integrating genotype and phenotype information in the skeletal dysplasia domain. PMID:22449239
Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio). PMID:22424280
Composite structural motifs of binding sites for delineating biological functions of proteins. PMID:22347478
Synthesis, docking studies and biological evaluation of benzo[b]thiophen-2-yl-3-(4-arylpiperazin-1-yl)-propan-1-one derivatives on 5-HT1A serotonin receptors. PMID:22306829
A dynamic view of domain-motif interactions. PMID:22253583
Proteomic analysis (GeLC-MS/MS) of ePFT-collected pancreatic fluid in chronic pancreatitis. PMID:22243521
SNPdbe: constructing an nsSNP functional impacts database. PMID:22210871
Methods, challenges, and promise of next-generation sequencing in cancer biology. PMID:22180681
Network systems biology for targeted cancer therapies. PMID:22176777
Overview of biological database mapping services for interoperation between different 'omics' datasets. PMID:22155608
Model-based clustering reveals vitamin D dependent multi-centrality hubs in a network of vitamin-related proteins. PMID:22136443
PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. PMID:22070195
YMDB: the Yeast Metabolome Database. PMID:22064855
An integrated transcriptomic and meta-analysis of hepatoma cells reveals factors that influence susceptibility to HCV infection. PMID:22046242
Protein-x of hepatitis B virus in interaction with CCAAT/enhancer-binding protein α (C/EBPα)--an in silico analysis approach. PMID:22035036
Proteomic analysis of formalin-fixed paraffin-embedded pancreatic tissue using liquid chromatography tandem mass spectrometry. PMID:22015969
Learning cellular sorting pathways using protein interactions and sequence motifs. PMID:21999284
Genome sequence of Leuconostoc carnosum KCTC 3525. PMID:21994929
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. PMID:21976737
Proteomic analysis of a rat pancreatic stellate cell line using liquid chromatography tandem mass spectrometry (LC-MS/MS). PMID:21968429
Genome sequence of Lactobacillus suebicus KCTC 3549. PMID:21914862
Deep brain stimulation induces rapidly reversible transcript changes in Parkinson's leucocytes. PMID:21910823
Ionic strength dependence of F-actin and glycolytic enzyme associations: a Brownian dynamics simulations approach. PMID:21905108
A face in the crowd: recognizing peptides through database search. PMID:21876205
Proteomic analysis of an immortalized mouse pancreatic stellate cell line identifies differentially-expressed proteins in activated vs nonproliferating cell states. PMID:21838295
Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales. PMID:21829548
Difference gel electrophoresis identifies differentially expressed proteins in endoscopically collected pancreatic fluid. PMID:21792986
Ortholog identification in the presence of domain architecture rearrangement. PMID:21712343
Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs. PMID:21689388
Genome sequence of Lactococcus garvieae 8831, isolated from rainbow trout lactococcosis outbreaks in Spain. PMID:21685280
Noise reduction in protein-protein interaction graphs by the implementation of a novel weighting scheme. PMID:21679454
Transcriptional regulatory programs underlying barley germination and regulatory functions of Gibberellin and abscisic acid. PMID:21668981
Predicting the functionally distinct residues in the heme, cation, and substrate-binding sites of peroxidase from stress-tolerant mangrove specie, Avicennia marina. PMID:21660646
Genome sequence of Lactococcus garvieae 21881, isolated in a case of human septicemia. PMID:21622739
Identification of the sequence motif of glycoside hydrolase 13 family members. PMID:21544166
WildSpan: mining structured motifs from protein sequences. PMID:21453542
Joint analysis of transcriptional and post- transcriptional brain tumor data: searching for emergent properties of cellular systems. PMID:21450054
Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite. PMID:21439036
Evolutionary transients in the rice transcriptome. PMID:21382590
Supervised learning and prediction of physical interactions between human and HIV proteins. PMID:21382517
Visualize: a free and open source multifunction tool for proteomics data analysis. PMID:21365761
Analysis of AML Genes in Dysregulated Molecular Networks. PMID:21347161
Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans. PMID:21324125
Interaction of diverse voltage sensor homologs with lipid bilayers revealed by self-assembly simulations. PMID:21320431
Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling. PMID:21291566
FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level. PMID:21287609
Genome-wide polymorphism and comparative analyses in the white-tailed deer (Odocoileus virginianus): a model for conservation genomics. PMID:21283515
Genome sequence of Lactobacillus farciminis KCTC 3681. PMID:21257766
Production of heterologous polygalacturonase I from Aspergillus kawachii in Saccharomyces cerevisiae in batch and fed-batch cultures. PMID:21188612
Genome sequence of Lactobacillus animalis KCTC 3501. PMID:21183665
Literature curation of protein interactions: measuring agreement across major public databases. PMID:21183497
On the accuracy and limits of peptide fragmentation spectrum prediction. PMID:21175207
Using bioinformatics to predict the functional impact of SNVs. PMID:21159622
Genome sequence of Lactobacillus coryniformis subsp. coryniformis KCTC 3167. PMID:21148735
PathLocdb: a comprehensive database for the subcellular localization of metabolic pathways and its application to multiple localization analysis. PMID:21143796
Proteomic analysis of endoscopically (endoscopic pancreatic function test) collected gastroduodenal fluid using in-gel tryptic digestion followed by LC-MS/MS. PMID:21137089
Toward the estimation of the absolute quality of individual protein structure models. PMID:21134891
Recognition of sulfonylurea receptor (ABCC8/9) ligands by the multidrug resistance transporter P-glycoprotein (ABCB1): functional similarities based on common structural features between two multispecific ABC proteins. PMID:21098040
ModBase, a database of annotated comparative protein structure models, and associated resources. PMID:21097780
Structural relationships in the lysozyme superfamily: significant evidence for glycoside hydrolase signature motifs. PMID:21085702
First investigation of the microbiology of the deepest layer of ocean crust. PMID:21079766
Genome sequence of Leuconostoc fallax KCTC 3537. PMID:21075921
Evolutionary history of tissue kallikreins. PMID:21072173
Analysis of Codon Usage Patterns in Toxic Dinoflagellate Alexandrium tamarense through Expressed Sequence Tag Data. PMID:21052492
Evolution of a signaling nexus constrained by protein interfaces and conformational States. PMID:20976244
Phosphate binding sites identification in protein structures. PMID:20974634
Follow the leader: preference for specific amino acids directly following the initial methionine in proteins of different organisms. PMID:20970746
OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria. PMID:20952406
Architecture of y-family DNA polymerases relevant to translesion DNA synthesis as revealed in structural and molecular modeling studies. PMID:20936174
Genomic characterization of Campylobacter jejuni strain M1. PMID:20865039
GOPred: GO molecular function prediction by combined classifiers. PMID:20824206
M-ORBIS: mapping of molecular binding sites and surfaces. PMID:20813758
Molecular insight into human platelet antigens: structural and evolutionary conservation analyses offer new perspective to immunogenic disorders. PMID:20804530
Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains. PMID:20799350
PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan. PMID:20798081
Identification and structural characterization of FYVE domain-containing proteins of Arabidopsis thaliana. PMID:20678208
A quantitative approach to study indirect effects among disease proteins in the human protein interaction network. PMID:20670417
Deletions and mutations in the acidic lipid-binding region of the plasma membrane Ca2+ pump: a study on different splicing variants of isoform 2. PMID:20643655
Deep-coverage rhesus red blood cell proteome: a first comparison with the human and mouse red blood cell. PMID:20606743
Antibodies as a model system for comparative model refinement. PMID:20602354
SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs. PMID:20497999
Computational identification of uncharacterized cruzain binding sites. PMID:20485483
Touring Ensembl: a practical guide to genome browsing. PMID:20459808
Detection of gene orthology from gene co-expression and protein interaction networks. PMID:20438654
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. PMID:20426874
Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins. PMID:20420672
Annular tautomerism: experimental observations and quantum mechanics calculations. PMID:20364360
Aphid feeding activates expression of a transcriptome of oxylipin-based defense signals in wheat involved in resistance to herbivory. PMID:20229216
Protein aggregation profile of the bacterial cytosol. PMID:20195530
Visualization of macromolecular structures. PMID:20195256
Bacterial lifestyle in a deep-sea hydrothermal vent chimney revealed by the genome sequence of the thermophilic bacterium Deferribacter desulfuricans SSM1. PMID:20189949
Walk-weighted subsequence kernels for protein-protein interaction extraction. PMID:20184736
Evolutionary dynamics of U12-type spliceosomal introns. PMID:20163699
Exit strategies for charged tRNA from GluRS. PMID:20156451
Decoding HMMs using the k best paths: algorithms and applications. PMID:20122200
Cooperativity within proximal phosphorylation sites is revealed from large-scale proteomics data. PMID:20100358
Xylose reductase from the thermophilic fungus Talaromyces emersonii: cloning and heterologous expression of the native gene (Texr) and a double mutant (TexrK271R + N273D) with altered coenzyme specificity. PMID:20093741
iDBPs: a web server for the identification of DNA binding proteins. PMID:20089514
Graphlet kernels for prediction of functional residues in protein structures. PMID:20078397
Combining structure and sequence information allows automated prediction of substrate specificities within enzyme families. PMID:20072606
Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB). PMID:20066127
The urine proteome for radiation biodosimetry: effect of total body vs. local kidney irradiation. PMID:20065682
The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. PMID:20064371
Insights into the domain and repeat architecture of target of rapamycin. PMID:20060908
Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins. PMID:20055997
Model-guided mutagenesis drives functional studies of human NHA2, implicated in hypertension. PMID:20053353
Next generation transcriptomes for next generation genomes using est2assembly. PMID:20034392
The structure of the KlcA and ArdB proteins reveals a novel fold and antirestriction activity against Type I DNA restriction systems in vivo but not in vitro. PMID:20007596
Network-based Identification of novel cancer genes. PMID:19959820
A comprehensive assessment of N-terminal signal peptides prediction methods. PMID:19958512
Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs. PMID:19936069
Automatic policing of biochemical annotations using genomic correlations. PMID:19935659
Automated quantitative assessment of proteins' biological function in protein knowledge bases. PMID:19920991
Loss of post-translational modification sites in disease. PMID:19908386
Elucidation of functional consequences of signalling pathway interactions. PMID:19895694
The comprehensive microbial resource. PMID:19892825
Structural genomics target selection for the New York consortium on membrane protein structure. PMID:19859826
Pathema: a clade-specific bioinformatics resource center for pathogen research. PMID:19843611
Proteomics data repositories. PMID:19795424
Analysis of AML genes in dysregulated molecular networks. PMID:19761572
The flexible pocketome engine for structural chemogenomics. PMID:19727619
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. PMID:19723330
Gastric Cancer (Biomarkers) Knowledgebase (GCBKB): A Curated and Fully Integrated Knowledgebase of Putative Biomarkers Related to Gastric Cancer. PMID:19690644
Structural and mutational analysis of band 7 proteins in the cyanobacterium Synechocystis sp. strain PCC 6803. PMID:19684140
Super paramagnetic clustering of DNA sequences. PMID:19669432
Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation. PMID:19640978
Quaternary benzyltriethylammonium ion binding to the Na,K-ATPase: a tool to investigate extracellular K+ binding reactions. PMID:19621894
The Mycoplasma conjunctivae genome sequencing, annotation and analysis. PMID:19534756
Prediction of type III secretion signals in genomes of gram-negative bacteria. PMID:19526054
Correlated mutation analysis on the catalytic domains of serine/threonine protein kinases. PMID:19526051
An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. PMID:19491311
Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools. PMID:19458756
Cross-platform analysis of cancer biomarkers: a Bayesian network approach to incorporating mass spectrometry and microarray data. PMID:19455243
ESG: extended similarity group method for automated protein function prediction. PMID:19435743
Efficient use of unlabeled data for protein sequence classification: a comparative study. PMID:19426450
Protinfo PPC: a web server for atomic level prediction of protein complexes. PMID:19420059
Improving classification in protein structure databases using text mining. PMID:19416501
Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction. PMID:19379498
IGF-I and IGFBP-3 polymorphisms in relation to circulating levels among African American and Caucasian women. PMID:19240240
Identification of DNA-binding proteins using structural, electrostatic and evolutionary features. PMID:19233205
Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays. PMID:19208186
An unusually small dimer interface is observed in all available crystal structures of cytosolic sulfotransferases. PMID:19173308
MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. PMID:19147664
The proteome of seed development in the model legume Lotus japonicus. PMID:19129418
ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family. PMID:19102758
Phylogenetic distribution and membrane topology of the LytR-CpsA-Psr protein family. PMID:19099556
SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms. PMID:19098027
Towards a semi-automatic functional annotation tool based on decision-tree techniques. PMID:19091050
Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. PMID:19090659
Data deposition and annotation at the worldwide protein data bank. PMID:19082769
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. PMID:19074493
BioTagger-GM: a gene/protein name recognition system. PMID:19074302
Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification. PMID:19072539
Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. PMID:19053777
The Protein Model Portal. PMID:19037750
The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative. PMID:19027726
Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes. PMID:19015150
Medium- and short-chain dehydrogenase/reductase gene and protein families : the MDR superfamily. PMID:19011751
Characterization of calcium- and integrin-binding protein 1 (CIB1) knockout platelets: potential compensation by CIB family members. PMID:18989529
PIG--the pathogen interaction gateway. PMID:18984614
Human Proteinpedia: a unified discovery resource for proteomics research. PMID:18948298
MODBASE, a database of annotated comparative protein structure models and associated resources. PMID:18948282
Prediction of extracellular proteases of the human pathogen Helicobacter pylori reveals proteolytic activity of the Hp1018/19 protein HtrA. PMID:18946507
The SWISS-MODEL Repository and associated resources. PMID:18931379
Discovery and validation of novel peptide agonists for G-protein-coupled receptors. PMID:18854305
A Myo6 mutation destroys coordination between the myosin heads, revealing new functions of myosin VI in the stereocilia of mammalian inner ear hair cells. PMID:18833301
PredGPI: a GPI-anchor predictor. PMID:18811934
SSMap: a new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase. PMID:18811932
Built-in loops allow versatility in domain-domain interactions: lessons from self-interacting domains. PMID:18757736
Epstein-barr virus encodes three bona fide ubiquitin-specific proteases. PMID:18715931
Characterization of expressed sequence tags from a full-length enriched cDNA library of Cryptomeria japonica male strobili. PMID:18691438
Comprehensive in silico mutagenesis highlights functionally important residues in proteins. PMID:18689826
Positional cloning of "Lisch-Like", a candidate modifier of susceptibility to type 2 diabetes in mice. PMID:18654634
Tissue-specific splicing factor gene expression signatures. PMID:18653532
Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase. PMID:18645234
Molecular modeling of the axial and circumferential elastic moduli of tubulin. PMID:18621829
Molecular motions of human HIV-1 gp120 envelope glycoproteins. PMID:18594881
GenoQuery: a new querying module for functional annotation in a genomic warehouse. PMID:18586731
Biochemical and functional evidence of p53 homology is inconsistent with molecular phylogenetics for distant sequences. PMID:18560747
Comparative genomics of enzymes in flavor-forming pathways from amino acids in lactic acid bacteria. PMID:18539796
Prediction of enzyme function by combining sequence similarity and protein interactions. PMID:18505562
Structural evidence for lack of inhibition of fish goose-type lysozymes by a bacterial inhibitor of lysozyme. PMID:18491152
E3Miner: a text mining tool for ubiquitin-protein ligases. PMID:18483079
Sequence similarity network reveals common ancestry of multidomain proteins. PMID:18475320
RDFScape: Semantic Web meets systems biology. PMID:18460179
Clinical uses of microarrays in cancer research. PMID:18453086
Characterization and prediction of residues determining protein functional specificity. PMID:18450811
GenoWatch: a disease gene mining browser for association study. PMID:18440974
Discovering sequence motifs with arbitrary insertions and deletions. PMID:18437229
TOPDOM: database of domains and motifs with conservative location in transmembrane proteins. PMID:18434342
Comparative protein structure modeling using Modeller. PMID:18428767
LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana. PMID:18318901
SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803. PMID:18315852
An integrated approach to inferring gene-disease associations in humans. PMID:18300252
Protein structure fitting and refinement guided by cryo-EM density. PMID:18275820
Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations. PMID:18197968
PARPs database: a LIMS systems for protein-protein interaction data mining or laboratory information management system. PMID:18093328
Homology modeling of hemagglutinin/protease [HA/P (vibriolysin)] from Vibrio cholerae: sequence comparision, residue interactions and molecular mechanism. PMID:18074211
The evolutionary conserved BER1 gene is involved in microtubule stability in yeast. PMID:18064466
Identifying foldable regions in protein sequence from the hydrophobic signal. PMID:18056079
A comparison study on algorithms of detecting long forms for short forms in biomedical text. PMID:18047706
Human papillomavirus E1 helicase interacts with the WD repeat protein p80 to promote maintenance of the viral genome in keratinocytes. PMID:18032488
Discovery of protein interaction networks shared by diseases. PMID:17992746
LOCATE: a mammalian protein subcellular localization database. PMID:17986452
Identification of HLA-DR-bound peptides presented by human bronchoalveolar lavage cells in sarcoidosis. PMID:17975675
Recombinant expression of twelve evolutionarily diverse subfamily Ialpha aminotransferases. PMID:17964807
Systematic analysis of alternative first exons in plant genomes. PMID:17941993
TOPDB: topology data bank of transmembrane proteins. PMID:17921502
SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. PMID:17912346
Evolutionary conservation of P-selectin glycoprotein ligand-1 primary structure and function. PMID:17868453
How to decide which are the most pertinent overly-represented features during gene set enrichment analysis. PMID:17848190
Genomic location of the human RNA polymerase II general machinery: evidence for a role of TFIIF and Rpb7 at both early and late stages of transcription. PMID:17848138
A systematic strategy for large-scale analysis of genotype phenotype correlations: identification of candidate genes involved in African trypanosomiasis. PMID:17709344
Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach. PMID:17683567
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. PMID:17678529
Novel metrics for evaluating the functional coherence of protein groups via protein semantic network. PMID:17672896
A survey of orphan enzyme activities. PMID:17623104
Defining nicotinic agonist binding surfaces through photoaffinity labeling. PMID:17614369
Recruitment of rare 3-grams at functional sites: is this a mechanism for increasing enzyme specificity? PMID:17598909
High-throughput identification of interacting protein-protein binding sites. PMID:17594507
PathExpress: a web-based tool to identify relevant pathways in gene expression data. PMID:17586825
Composition Profiler: a tool for discovery and visualization of amino acid composition differences. PMID:17578581
Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site. PMID:17578578
The SLiMDisc server: short, linear motif discovery in proteins. PMID:17576682
Identification of hot regions in protein-protein interactions by sequential pattern mining. PMID:17570867
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. PMID:17568002
RCPdb: An evolutionary classification and codon usage database for repeat-containing proteins. PMID:17567984
SNAP: predict effect of non-synonymous polymorphisms on function. PMID:17526529
Estimating the annotation error rate of curated GO database sequence annotations. PMID:17519041
WoLF PSORT: protein localization predictor. PMID:17517783
LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics. PMID:17493288
Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis. PMID:17488835
Relating destabilizing regions to known functional sites in proteins. PMID:17470296
Semantic classification of biomedical concepts using distributional similarity. PMID:17460124
A kingdom-specific protein domain HMM library for improved annotation of fungal genomes. PMID:17425790
Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. PMID:17407547
Non-empirical study of the phosphorylation reaction catalyzed by 4-methyl-5-beta-hydroxyethylthiazole kinase: relevance of the theory of intermolecular interactions. PMID:17384969
GeneBins: a database for classifying gene expression data, with application to plant genome arrays. PMID:17349060
False occurrences of functional motifs in protein sequences highlight evolutionary constraints. PMID:17331242
Directed mutagenesis identifies amino acid residues involved in elongation factor Tu binding to yeast Phe-tRNAPhe. PMID:17328911
Towards fully automated structure-based function prediction in structural genomics: a case study. PMID:17316683
Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance. PMID:17254327
Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology. PMID:17254302
SemCat: semantically categorized entities for genomics. PMID:17238442
pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model. PMID:17222345
Occurrence of protein structure elements in conserved sequence regions. PMID:17210087
DiscoverySpace: an interactive data analysis application. PMID:17210078
HMDB: the Human Metabolome Database. PMID:17202168
Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal center. PMID:17187687
Fast sequence evolution of Hox and Hox-derived genes in the genus Drosophila. PMID:17163987
Intrinsic disorder and functional proteomics. PMID:17158572
PEDANT genome database: 10 years online. PMID:17148486
TomatEST database: in silico exploitation of EST data to explore expression patterns in tomato species. PMID:17142232
Metalloprotein and metallo-DNA/RNAzyme design: current approaches, success measures, and future challenges. PMID:17140190
Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles. PMID:17136344
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. PMID:17135200
Analysis of the wheat endosperm transcriptome. PMID:17132893
FireDB--a database of functionally important residues from proteins of known structure. PMID:17132832
Dynamic domains and geometrical properties of HIV-1 gp120 during conformational changes induced by CD4 binding. PMID:17131136
Link test--A statistical method for finding prostate cancer biomarkers. PMID:17126079
Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space? PMID:17112376
Structural modeling of protein interactions by analogy: application to PSD-95. PMID:17096593
The TIGR Plant Transcript Assemblies database. PMID:17088284
TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences. PMID:17088282
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. PMID:17082206
Babel's tower revisited: a universal resource for cross-referencing across annotation databases. PMID:17068090
SISYPHUS--structural alignments for proteins with non-trivial relationships. PMID:17068077
ProtoBee: hierarchical classification and annotation of the honey bee proteome. PMID:17065614
Mining the Arabidopsis thaliana genome for highly-divergent seven transmembrane receptors. PMID:17064408
Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation. PMID:17059607
ORENZA: a web resource for studying ORphan ENZyme activities. PMID:17026747
Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. PMID:17003129
Analytical model of peptide mass cluster centres with applications. PMID:16995952
Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy. PMID:16984653
CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks. PMID:16952323
The Comparative Toxicogenomics Database (CTD): a resource for comparative toxicological studies. PMID:16902965
Gene and protein nomenclature in public databases. PMID:16899134
Bio-Ontology and text: bridging the modeling gap. PMID:16870928
SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. PMID:16855291
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. PMID:16855290
ProKware: integrated software for presenting protein structural properties in protein tertiary structures. PMID:16845116
New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate. PMID:16845086
TFBScluster web server for the identification of mammalian composite regulatory elements. PMID:16845063
APID: Agile Protein Interaction DataAnalyzer. PMID:16845013
The plug domain of yeast Sec61p is important for efficient protein translocation, but is not essential for cell viability. PMID:16822836
Dry work in a wet world: computation in systems biology. PMID:16820781
Saturating representation of loop conformational fragments in structure databanks. PMID:16820050
PROMPT: a protein mapping and comparison tool. PMID:16817977
Identification of a novel NADH-specific aldo-keto reductase using sequence and structural homologies. PMID:16813561
Unraveling the nature of the segmentation clock: Intrinsic disorder of clock proteins and their interaction map. PMID:16798096
The Escherichia coli proteome: past, present, and future prospects. PMID:16760308
A composite score for predicting errors in protein structure models. PMID:16751606
Structural classification of bacterial response regulators: diversity of output domains and domain combinations. PMID:16740923
Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. PMID:16738128
On the maximal cliques in c-max-tolerance graphs and their application in clustering molecular sequences. PMID:16737529
Discrete profile comparison using information bottleneck. PMID:16723011
Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier. PMID:16704727
PredSL: a tool for the N-terminal sequence-based prediction of protein subcellular localization. PMID:16689702
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PMID:16683036
The abundance of short proteins in the mammalian proteome. PMID:16683031
The comparative toxicogenomics database: a cross-species resource for building chemical-gene interaction networks. PMID:16675512
Functional annotation prediction: all for one and one for all. PMID:16672244
Organic anion transporting polypeptides of the OATP/SLCO superfamily: identification of new members in nonmammalian species, comparative modeling and a potential transport mode. PMID:16648940
Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. PMID:16646984
A FERM-adjacent (FA) region defines a subset of the 4.1 superfamily and is a potential regulator of FERM domain function. PMID:16626485
Length-dependent prediction of protein intrinsic disorder. PMID:16618368
A supersecondary structure library and search algorithm for modeling loops in protein structures. PMID:16617149
Integrating membrane transport with male gametophyte development and function through transcriptomics. PMID:16607029
Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins. PMID:16597327
Predicting the subcellular localization of viral proteins within a mammalian host cell. PMID:16595001
AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation. PMID:16556303
Amplification of the Gene Ontology annotation of Affymetrix probe sets. PMID:16549014
Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds. PMID:16549009
Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera). PMID:16542494
ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms. PMID:16539733
NovelFam3000--uncharacterized human protein domains conserved across model organisms. PMID:16533400
Protein protein interactions, evolutionary rate, abundance and age. PMID:16533385
EST2Prot: mapping EST sequences to proteins. PMID:16515706
Structure at 1.6 A resolution of the protein from gene locus At3g22680 from Arabidopsis thaliana. PMID:16511118
A gold standard set of mechanistically diverse enzyme superfamilies. PMID:16507141
Taxonomic colouring of phylogenetic trees of protein sequences. PMID:16503967
A comprehensive software suite for the analysis of cDNAs. PMID:16487083
Tracking the evolution of alternatively spliced exons within the Dscam family. PMID:16483367
Identifying biological concepts from a protein-related corpus with a probabilistic topic model. PMID:16466569
Comparison of human (and other) genome browsers. PMID:16460652
Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration. PMID:16426464
A theoretical model of Aquifex pyrophilus flagellin: implications for its thermostability. PMID:16411078
MaGe: a microbial genome annotation system supported by synteny results. PMID:16407324
Panzea: a database and resource for molecular and functional diversity in the maize genome. PMID:16381974
DBD: a transcription factor prediction database. PMID:16381970
DrugBank: a comprehensive resource for in silico drug discovery and exploration. PMID:16381955
HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma. PMID:16381942
The UCSC Genome Browser Database: update 2006. PMID:16381938
TreeFam: a curated database of phylogenetic trees of animal gene families. PMID:16381935
The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context. PMID:16381934
TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations. PMID:16381929
pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. PMID:16381926
FLIGHT: database and tools for the integration and cross-correlation of large-scale RNAi phenotypic datasets. PMID:16381916
ASD: a bioinformatics resource on alternative splicing. PMID:16381912
Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts. PMID:16381905
PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways. PMID:16381888
INVHOGEN: a database of homologous invertebrate genes. PMID:16381884
PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. PMID:16381879
The SWISS-MODEL Repository: new features and functionalities. PMID:16381875
MODBASE: a database of annotated comparative protein structure models and associated resources. PMID:16381869
Gene3D: modelling protein structure, function and evolution. PMID:16381865
LGICdb: a manually curated sequence database after the genomes. PMID:16381861
SIMAP: the similarity matrix of proteins. PMID:16381858
Pfam: clans, web tools and services. PMID:16381856
MulPSSM: a database of multiple position-specific scoring matrices of protein domain families. PMID:16381855
LOCATE: a mouse protein subcellular localization database. PMID:16381849
The evolutionary history of Cys-tRNACys formation. PMID:16380427
The Gene Set Builder: collation, curation, and distribution of sets of genes. PMID:16371163
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity. PMID:16351747
An investigation into the ability to define transmembrane protein spans using the biophysical properties of amino acid residues. PMID:16335798
Glycolytic enzyme interactions with yeast and skeletal muscle F-actin. PMID:16326908
Refining protein subcellular localization. PMID:16322766
A Chronic Fatigue Syndrome - related proteome in human cerebrospinal fluid. PMID:16321154
The EH1 motif in metazoan transcription factors. PMID:16309560
Computational identification of strain-, species- and genus-specific proteins. PMID:16305751
A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish. PMID:16271140
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. PMID:16246909
Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters. PMID:16236172
SPdb--a signal peptide database. PMID:16221310
Sequence and comparative genomic analysis of actin-related proteins. PMID:16195354
Functional genomics and expression analysis of the Corynebacterium glutamicum fpr2-cysIXHDNYZ gene cluster involved in assimilatory sulphate reduction. PMID:16159395
The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. PMID:16140995
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PMID:16118666
Tools and strategies for physiological genomics: the Rat Genome Database. PMID:16106031
Crystal structure of the bacterial YhcH protein indicates a role in sialic acid catabolism. PMID:16077096
Structure, function, and evolution of transient and obligate protein-protein interactions. PMID:16043700
MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences. PMID:16043635
Effective function annotation through catalytic residue conservation. PMID:16037208
The MicrobesOnline Web site for comparative genomics. PMID:15998914
MRS: a fast and compact retrieval system for biological data. PMID:15980580
Recent additions and improvements to the Onto-Tools. PMID:15980579
Integrating protein annotation resources through the Distributed Annotation System. PMID:15980514
TMB-Hunt: a web server to screen sequence sets for transmembrane beta-barrel proteins. PMID:15980452
Plant protein annotation in the UniProt Knowledgebase. PMID:15888679
TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins. PMID:15769290
The Rat Genome Database (RGD): developments towards a phenome database. PMID:15608243
The European Bioinformatics Institute's data resources: towards systems biology. PMID:15608238
The EMBL Nucleotide Sequence Database. PMID:15608199 -
The Universal Protein Resource (UniProt) in 2010
PubMed citations: 588.
588 articles citing: The Universal Protein Resource (UniProt) in 2010
Many dissimilar NusG protein domains switch between α-helix and β-sheet folds. PMID:35778397
A reverse vaccinology approach on transmembrane carbonic anhydrases from Plasmodium species as vaccine candidates for malaria prevention. PMID:35706028
MASTL is enriched in cancerous and pluripotent stem cells and influences OCT1/OCT4 levels. PMID:35677646
Novel Disease-Associated Missense Single-Nucleotide Polymorphisms Variants Predication by Algorithms Tools and Molecular Dynamics Simulation of Human TCIRG1 Gene Causing Congenital Neutropenia and Osteopetrosis. PMID:35573728
Cupressus sempervirens Essential Oil: Exploring the Antibacterial Multitarget Mechanisms, Chemcomputational Toxicity Prediction, and Safety Assessment in Zebrafish Embryos. PMID:35565980
Integration of Neighbor Topologies Based on Meta-Paths and Node Attributes for Predicting Drug-Related Diseases. PMID:35409235
Identification of a 3-Gene Prognostic Index for Papillary Thyroid Carcinoma. PMID:35372518
MonaGO: a novel gene ontology enrichment analysis visualisation system. PMID:35164667
Schistosoma mansoni α-N-acetylgalactosaminidase (SmNAGAL) regulates coordinated parasite movement and egg production. PMID:35025955
THEM6-mediated reprogramming of lipid metabolism supports treatment resistance in prostate cancer. PMID:35014179
In silico evaluation of naturally isolated triterpene glycosides (TG) from Gymnema sylvestre towards diabetic treatment. PMID:34917786
Nuclear-capture of endosomes depletes nuclear G-actin to promote SRF/MRTF activation and cancer cell invasion. PMID:34819513
Integrative COVID-19 biological network inference with probabilistic core decomposition. PMID:34791019
Computational and structural based approach to identify malignant nonsynonymous single nucleotide polymorphisms associated with CDK4 gene. PMID:34735543
Network-driven analysis of human-Plasmodium falciparum interactome: processes for malaria drug discovery and extracting in silico targets. PMID:34702263
Network Pharmacology to Explore the Molecular Mechanisms of Prunella vulgaris for Treating Hashimoto's Thyroiditis. PMID:34690752
Protein Persulfidation in Plants: Function and Mechanism. PMID:34679765
iMPT-FDNPL: Identification of Membrane Protein Types with Functional Domains and a Natural Language Processing Approach. PMID:34671418
Identification of potent inhibitors against transmembrane serine protease 2 for developing therapeutics against SARS-CoV-2. PMID:34590967
Comparative genomic analysis of obligately piezophilic Moritella yayanosii DB21MT-5 reveals bacterial adaptation to the Challenger Deep, Mariana Trench. PMID:34319226
A Quantitative Comparison of Inhibitory Interneuron Size and Distribution between Mouse and Macaque V1, Using Calcium-Binding Proteins. PMID:34296129
Eleven genomic loci affect plasma levels of chronic inflammation marker soluble urokinase-type plasminogen activator receptor. PMID:34079037
Microbial Hotspots in Lithic Microhabitats Inferred from DNA Fractionation and Metagenomics in the Atacama Desert. PMID:34065975
Predictable fold switching by the SARS-CoV-2 protein ORF9b. PMID:33934422
Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond. PMID:33902740
An ARF GTPase module promoting invasion and metastasis through regulating phosphoinositide metabolism. PMID:33712589
Recent Advances in Predicting Protein S-Nitrosylation Sites. PMID:33628788
Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism. PMID:33469028
Learning important features from multi-view data to predict drug side effects. PMID:33430979
Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria. PMID:33397904
Urinary vitronectin identifies patients with high levels of fibrosis in kidney grafts. PMID:33275196
Implementation of homology based and non-homology based computational methods for the identification and annotation of orphan enzymes: using Mycobacterium tuberculosis H37Rv as a case study. PMID:33076816
mMGE: a database for human metagenomic extrachromosomal mobile genetic elements. PMID:33074335
SUMO conjugation regulates immune signalling. PMID:32777975
Alteromonas Myovirus V22 Represents a New Genus of Marine Bacteriophages Requiring a Tail Fiber Chaperone for Host Recognition. PMID:32518192
2,4-dienoyl-CoA reductase regulates lipid homeostasis in treatment-resistant prostate cancer. PMID:32427840
Redox signaling modulates Rho activity and tissue contractility in the Caenorhabditis elegans spermatheca. PMID:32374641
Formate induces a metabolic switch in nucleotide and energy metabolism. PMID:32366892
MASTL promotes cell contractility and motility through kinase-independent signaling. PMID:32311005
Broad and thematic remodeling of the surfaceome and glycoproteome on isogenic cells transformed with driving proliferative oncogenes. PMID:32205440
The mammalian cytosolic thioredoxin reductase pathway acts via a membrane protein to reduce ER-localised proteins. PMID:32184267
Draft Genome of a Blister Beetle Mylabris aulica. PMID:32010178
Tissue-infiltrating macrophages mediate an exosome-based metabolic reprogramming upon DNA damage. PMID:31896748
SigUNet: signal peptide recognition based on semantic segmentation. PMID:31861981
Predicting and designing therapeutics against the Nipah virus. PMID:31830030
HeteroDualNet: A Dual Convolutional Neural Network With Heterogeneous Layers for Drug-Disease Association Prediction via Chou's Five-Step Rule. PMID:31780934
Systematic exploration of predicted destabilizing nonsynonymous single nucleotide polymorphisms (nsSNPs) of human aldehyde oxidase: A Bio-informatics study. PMID:31768259
In Silico Study of Rett Syndrome Treatment-Related Genes, MECP2, CDKL5, and FOXG1, by Evolutionary Classification and Disordered Region Assessment. PMID:31717404
Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar (Cyamopsis tetragonoloba (L.) Taub.): An Important Industrial and Forage Crop. PMID:31687376
Development of an Efficient Strategy to Improve Extracellular Polysaccharide Production of Ganoderma lucidum Using L-Phenylalanine as an Enhancer. PMID:31681192
Computational Methods for Identifying Similar Diseases. PMID:31678735
N-WASP Control of LPAR1 Trafficking Establishes Response to Self-Generated LPA Gradients to Promote Pancreatic Cancer Cell Metastasis. PMID:31668663
Targeting amphiregulin (AREG) derived from senescent stromal cells diminishes cancer resistance and averts programmed cell death 1 ligand (PD-L1)-mediated immunosuppression. PMID:31493351
mTORC1 Activation Requires DRAM-1 by Facilitating Lysosomal Amino Acid Efflux. PMID:31492633
Dietary Oligosaccharides Attenuate Stress-Induced Disruptions in Immune Reactivity and Microbial B-Vitamin Metabolism. PMID:31417554
CYRI/ Fam49 Proteins Represent a New Class of Rac1 Interactors. PMID:31413787
Why do eukaryotic proteins contain more intrinsically disordered regions? PMID:31329574
iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6. PMID:31293525
Superantigen SpeA attenuates the biofilm forming capacity of Streptococcus pyogenes. PMID:31054134
PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome. PMID:30871454
Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. PMID:30859819
DAMpred: Recognizing Disease-Associated nsSNPs through Bayes-Guided Neural-Network Model Built on Low-Resolution Structure Prediction of Proteins and Protein-Protein Interactions. PMID:30796987
Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations. PMID:30715293
The CDC42 effector protein MRCKβ autophosphorylates on Threonine 1108. PMID:30667325
Exploiting locational and topological overlap model to identify modules in protein interaction networks. PMID:30642247
Reconstruction and Analysis of a Genome-Scale Metabolic Model of Ganoderma lucidum for Improved Extracellular Polysaccharide Production. PMID:30619160
Design, Synthesis, and Evaluation of a Diazirine Photoaffinity Probe for Ligand-Based Receptor Capture Targeting G Protein-Coupled Receptors. PMID:30514721
Computational discovery of direct associations between GO terms and protein domains. PMID:30453875
ConnectedAlign: a PPI network alignment method for identifying conserved protein complexes across multiple species. PMID:30367584
Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem. PMID:30356154
Targeting SPINK1 in the damaged tumour microenvironment alleviates therapeutic resistance. PMID:30333494
BioPS: System for screening and assessment of biofuel-production potential of cyanobacteria. PMID:30096176
Investigation of recombination-intense viral groups and their genes in the Earth's virome. PMID:30065291
Migration of Type III Secretion System Transcriptional Regulators Links Gene Expression to Secretion. PMID:30065089
Harnessing the evolutionary information on oxygen binding proteins through Support Vector Machines based modules. PMID:29751818
An improved approach to infer protein-protein interaction based on a hierarchical vector space model. PMID:29699476
Computational Prediction and Analysis of Associations between Small Molecules and Binding-Associated S-Nitrosylation Sites. PMID:29671802
Identification of the Differential Expression Profiles of Serum and Tissue Proteins During Rat Hepatocarcinogenesis. PMID:29478368
Cancer Associated Fibroblasts: The Architects of Stroma Remodeling. PMID:29280568
Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches. PMID:29186295
Modelling pyruvate dehydrogenase under hypoxia and its role in cancer metabolism. PMID:29134060
AKT overactivation can suppress DNA repair via p70S6 kinase-dependent downregulation of MRE11. PMID:28967905
PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection. PMID:28761071
Tumor matrix stiffness promotes metastatic cancer cell interaction with the endothelium. PMID:28694244
Entering the 'big data' era in medicinal chemistry: molecular promiscuity analysis revisited. PMID:28670471
Remodeling adipose tissue through in silico modulation of fat storage for the prevention of type 2 diabetes. PMID:28606124
Comprehensive review of methods for prediction of intrinsic disorder and its molecular functions. PMID:28589442
DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins. PMID:28498993
Co-occurring protein phosphorylation are functionally associated. PMID:28459814
Antagonizing effects of membrane-acting androgens on the eicosanoid receptor OXER1 in prostate cancer. PMID:28290516
Structure-Promiscuity Relationship Puzzles-Extensively Assayed Analogs with Large Differences in Target Annotations. PMID:28265982
Secreted CLIC3 drives cancer progression through its glutathione-dependent oxidoreductase activity. PMID:28198360
ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains. PMID:28193156
The use of gene interaction networks to improve the identification of cancer driver genes. PMID:28149674
An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts. PMID:28135269
Derivative of Extremophilic 50S Ribosomal Protein L35Ae as an Alternative Protein Scaffold. PMID:28103321
Stable Isotope Labeling with Amino Acids (SILAC)-Based Proteomics of Primary Human Kidney Cells Reveals a Novel Link between Male Sex Hormones and Impaired Energy Metabolism in Diabetic Kidney Disease. PMID:28062795
In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria. PMID:28056772
Posttranslational Modifications of Lipid-Activated Nuclear Receptors: Focus on Metabolism. PMID:27925773
Posttranslational Modifications of Lipid-Activated Nuclear Receptors: Focus on Metabolism. PMID:27925773
Transcriptome and long noncoding RNA sequencing of three extracellular vesicle subtypes released from the human colon cancer LIM1863 cell line. PMID:27917920
Draft Genome Sequence of the Bacterium Comamonas aquatica CJG. PMID:27811093
Hepatitis B Virus Protein X Induces Degradation of Talin-1. PMID:27775586
A computational interactome and functional annotation for the human proteome. PMID:27770567
IPC - Isoelectric Point Calculator. PMID:27769290
Predicting essential proteins based on subcellular localization, orthology and PPI networks. PMID:27586883
Data Mining and Pattern Recognition Models for Identifying Inherited Diseases: Challenges and Implications. PMID:27559342
Comparative genomics reveals convergent rates of evolution in ant-plant mutualisms. PMID:27557866
Gene family expansions and contractions are associated with host range in plant pathogens of the genus Colletotrichum. PMID:27496087
The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus. PMID:27442123
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Comparative genomic and transcriptomic analyses of the Fuzhuan brick tea-fermentation fungus Aspergillus cristatus. PMID:27267057
Benchmarking the next generation of homology inference tools. PMID:27256311
The right motifs for plant cell adhesion: what makes an adhesive site? PMID:27091341
Evolutionary evidence on suitability of SecD as a target for development of antibacterial agents against Staphylococcus aureus. PMID:27087922
Integrated analysis of proteome and transcriptome changes in the mucopolysaccharidosis type VII mouse hippocampus. PMID:27053151
A Multifeatures Fusion and Discrete Firefly Optimization Method for Prediction of Protein Tyrosine Sulfation Residues. PMID:27034949
Progerin impairs chromosome maintenance by depleting CENP-F from metaphase kinetochores in Hutchinson-Gilford progeria fibroblasts. PMID:27015553
dbWGFP: a database and web server of human whole-genome single nucleotide variants and their functional predictions. PMID:26989155
Challenges in horizontal model integration. PMID:26968798
The Implicitome: A Resource for Rationalizing Gene-Disease Associations. PMID:26919047
Complete genome sequence and characterization of avian pathogenic Escherichia coli field isolate ACN001. PMID:26823959
COPD subtypes identified by network-based clustering of blood gene expression. PMID:26773458
Metaviromics of Namib Desert Salt Pans: A Novel Lineage of Haloarchaeal Salterproviruses and a Rich Source of ssDNA Viruses. PMID:26761024
Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality. PMID:26757703
Analysis on evolutionary relationship of amylases from archaea, bacteria and eukaryota. PMID:26745984
Reads meet rotamers: structural biology in the age of deep sequencing. PMID:26658741
Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. PMID:26598659
Novel myristoylation of the sperm-specific hexokinase 1 isoform regulates its atypical localization. PMID:26581589
Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method. PMID:26568785
METSP: a maximum-entropy classifier based text mining tool for transporter-substrate identification with semistructured text. PMID:26495291
Prioritization Of Nonsynonymous Single Nucleotide Variants For Exome Sequencing Studies Via Integrative Learning On Multiple Genomic Data. PMID:26459872
Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening. PMID:26444490
Design of chemical space networks using a Tanimoto similarity variant based upon maximum common substructures. PMID:26419860
Plasmodium Apicoplast Gln-tRNAGln Biosynthesis Utilizes a Unique GatAB Amidotransferase Essential for Erythrocytic Stage Parasites. PMID:26318454
Trends in genome dynamics among major orders of insects revealed through variations in protein families. PMID:26251035
Burkholderia Diffusible Signal Factor Signals to Francisella novicida To Disperse Biofilm and Increase Siderophore Production. PMID:26231649
iSuc-PseAAC: predicting lysine succinylation in proteins by incorporating peptide position-specific propensity. PMID:26084794
Tools for visualization and analysis of molecular networks, pathways, and -omics data. PMID:26082651
Accessible surface area from NMR chemical shifts. PMID:26078090
Identifying diabetes-related important protein targets with few interacting partners with the PageRank algorithm. PMID:26064627
The role of markup for enabling interoperability in health informatics. PMID:26042043
BOWS (bioinformatics open web services) to centralize bioinformatics tools in web services. PMID:26032494
N-terminal region of the catalytic domain of human N-myristoyltransferase 1 acts as an inhibitory module. PMID:26000639
Predict and Analyze Protein Glycation Sites with the mRMR and IFS Methods. PMID:25961025
Comparative proteomic analysis of hypertrophic chondrocytes in osteoarthritis. PMID:25945082
ProtoBug: functional families from the complete proteomes of insects. PMID:25911153
The iceLogo web server and SOAP service for determining protein consensus sequences. PMID:25897125
Properties of protein drug target classes. PMID:25822509
Large-scale evolutionary analyses on SecB subunits of bacterial sec system. PMID:25775430
De novo assembly and characterization of transcriptomes of early-stage fruit from two genotypes of Annona squamosa L. with contrast in seed number. PMID:25766098
Pinpointing disease genes through phenomic and genomic data fusion. PMID:25708473
Structural and Activity Profile Relationships Between Drug Scaffolds. PMID:25697829
The roles of post-translational modifications in the context of protein interaction networks. PMID:25692714
Identifying tandem Ankyrin repeats in protein structures. PMID:25547411
Whole-Genome Analysis of Aeromonas hydrophila Strain 187, Exhibiting Quorum-Sensing Activity. PMID:25540357
INTEGRATING COMPUTATIONAL PROTEIN FUNCTION PREDICTION INTO DRUG DISCOVERY INITIATIVES. PMID:25530654
Proteomic analysis and identification of cellular interactors of the giant ubiquitin ligase HERC2. PMID:25476789
Systematic analysis of the in situ crosstalk of tyrosine modifications reveals no additional natural selection on multiply modified residues. PMID:25476580
Information content-based Gene Ontology functional similarity measures: which one to use for a given biological data type? PMID:25474538
OntoGene web services for biomedical text mining. PMID:25472638
E-cadherin interactome complexity and robustness resolved by quantitative proteomics. PMID:25468996
NCBI viral genomes resource. PMID:25428358
Multi-omic landscape of rheumatoid arthritis: re-evaluation of drug adverse effects. PMID:25414848
Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation. PMID:25411636
De Novo sequencing and transcriptome analysis for Tetramorium bicarinatum: a comprehensive venom gland transcriptome analysis from an ant species. PMID:25407482
In silico prediction of physical protein interactions and characterization of interactome orphans. PMID:25402006
Identification of best indicators of peptide-spectrum match using a permutation resampling approach. PMID:25362838
Accurate assignment of significance to neuropeptide identifications using Monte Carlo k-permuted decoy databases. PMID:25329667
Application of a Bioinformatics-Based Approach to Identify Novel Putative in vivo BACE1 Substrates. PMID:25288897
Computational biophysical, biochemical, and evolutionary signature of human R-spondin family proteins, the member of canonical Wnt/β-catenin signaling pathway. PMID:25276837
CSI 2.0: a significantly improved version of the Chemical Shift Index. PMID:25273503
Prediction of S-nitrosylation modification sites based on kernel sparse representation classification and mRMR algorithm. PMID:25184139
The use of semantic similarity measures for optimally integrating heterogeneous Gene Ontology data from large scale annotation pipelines. PMID:25147557
Supergenomic network compression and the discovery of EXP1 as a glutathione transferase inhibited by artesunate. PMID:25126794
Composition and applications of focus libraries to phenotypic assays. PMID:25104937
The metagenomic telescope. PMID:25054802
Inferring non-synonymous single-nucleotide polymorphisms-disease associations via integration of multiple similarity networks. PMID:25014223
Prediction of membrane transport proteins and their substrate specificities using primary sequence information. PMID:24968309
CELLO2GO: a web server for protein subCELlular LOcalization prediction with functional gene ontology annotation. PMID:24911789
Event-based text mining for biology and functional genomics. PMID:24907365
Molecular characterization of novel pyridoxal-5'-phosphate-dependent enzymes from the human microbiome. PMID:24888348
ANP32B is a nuclear target of henipavirus M proteins. PMID:24823948
Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome. PMID:24792350
Inhibitory interneuron classes express complementary AMPA-receptor patterns in macaque primary visual cortex. PMID:24790201
Protein identification problem from a Bayesian point of view. PMID:24761189
The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. PMID:24755649
Reassessing domain architecture evolution of metazoan proteins: major impact of errors caused by confusing paralogs and epaktologs. PMID:24710209
Reassessing domain architecture evolution of metazoan proteins: major impact of gene prediction errors. PMID:24710207
HPVdb: a data mining system for knowledge discovery in human papillomavirus with applications in T cell immunology and vaccinology. PMID:24705205
The evolution of human cells in terms of protein innovation. PMID:24692656
Prediction of multi-type membrane proteins in human by an integrated approach. PMID:24676214
Molecular recognition in complexes of TRF proteins with telomeric DNA. PMID:24586793
Inferring protein domains associated with drug side effects based on drug-target interaction network. PMID:24565527
PREAL: prediction of allergenic protein by maximum Relevance Minimum Redundancy (mRMR) feature selection. PMID:24565053
Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso. PMID:24564966
Scalable prediction of compound-protein interactions using minwise hashing. PMID:24564870
Genome-wide structural modelling of TCR-pMHC interactions. PMID:24564684
Human transporter database: comprehensive knowledge and discovery tools in the human transporter genes. PMID:24558441
BiNA: a visual analytics tool for biological network data. PMID:24551056
Genome-wide identification and functional annotation of Plasmodium falciparum long noncoding RNAs from RNA-seq data. PMID:24522451
Complete genome sequence of Ilumatobacter coccineum YM16-304(T.). PMID:24501628
Large scale identification and categorization of protein sequences using structured logistic regression. PMID:24465495
Therapeutic targeting of cancers with loss of PTEN function. PMID:24387334
Early transcriptional response of soybean contrasting accessions to root dehydration. PMID:24349513
Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset. PMID:24348229
Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation. PMID:24341328
Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks. PMID:24339775
Secretory pathway of cellulase: a mini-review. PMID:24295495
Cigarette smoke induces distinct histone modifications in lung cells: implications for the pathogenesis of COPD and lung cancer. PMID:24283195
Generic information can retrieve known biological associations: implications for biomedical knowledge discovery. PMID:24260124
Analysis of bortezomib inhibitor docked within the catalytic subunits of the Plasmodium falciparum 20S proteasome. PMID:24255860
Analysis of Cdk5-related phosphoproteomics in growth cones. PMID:24234032
Current status and new features of the Consensus Coding Sequence database. PMID:24217909
Prediction and experimental validation of enzyme substrate specificity in protein structures. PMID:24145433
Profiling of the mammalian mitotic spindle proteome reveals an ER protein, OSTD-1, as being necessary for cell division and ER morphology. PMID:24130834
A nondiscriminating glutamyl-tRNA synthetase in the plasmodium apicoplast: the first enzyme in an indirect aminoacylation pathway. PMID:24072705
DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures. PMID:24067102
The relationship between gene isoform multiplicity, number of exons and protein divergence. PMID:24023641
Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome. PMID:24003029
Mutations in DNA binding and transactivation domains affect the dynamics of parvovirus NS1 protein. PMID:23986577
SILAC-based proteomics of human primary endothelial cell morphogenesis unveils tumor angiogenic markers. PMID:23979707
Automated extraction of precise protein expression patterns in lymphoma by text mining abstracts of immunohistochemical studies. PMID:23967385
A viral-human interactome based on structural motif-domain interactions captures the human infectome. PMID:23951184
Different effects of progesterone and estradiol on chimeric and wild type aldosterone synthase in vitro. PMID:23938178
PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions. PMID:23896518
Identification of methyllysine peptides binding to chromobox protein homolog 6 chromodomain in the human proteome. PMID:23842000
Double deficiency of cathepsins B and L results in massive secretome alterations and suggests a degradative cathepsin-MMP axis. PMID:23811845
Prediction and Analysis of Post-Translational Pyruvoyl Residue Modification Sites from Internal Serines in Proteins. PMID:23805260
PIMiner: a web tool for extraction of protein interactions from biomedical literature. PMID:23798227
Analysis and prediction of pathways in HeLa cells by integrating biological levels of organization with systems-biology approaches. PMID:23785426
SLC classification: an update. PMID:23778706
Genome Maps, a new generation genome browser. PMID:23748955
Discovering putative prion sequences in complete proteomes using probabilistic representations of Q/N-rich domains. PMID:23663289
Generation and analysis of the expressed sequence tags from the mycelium of Ganoderma lucidum. PMID:23658685
The ChEMBL database as linked open data. PMID:23657106
Chapter 15: disease gene prioritization. PMID:23633938
Structural and functional role of INI1 and LEDGF in the HIV-1 preintegration complex. PMID:23593299
Identification and prioritization of novel uncharacterized peptidases for biochemical characterization. PMID:23584835
Structure and function of the DUF2233 domain in bacteria and in the human mannose 6-phosphate uncovering enzyme. PMID:23572527
Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1. PMID:23509259
Comparative annotation of functional regions in the human genome using epigenomic data. PMID:23482391
Using weakly conserved motifs hidden in secretion signals to identify type-III effectors from bacterial pathogen genomes. PMID:23437191
Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. PMID:23435085
Prediction of deleterious nonsynonymous single-nucleotide polymorphism for human diseases. PMID:23431257
Human 14-3-3 paralogs differences uncovered by cross-talk of phosphorylation and lysine acetylation. PMID:23418452
ETMB-RBF: discrimination of metal-binding sites in electron transporters based on RBF networks with PSSM profiles and significant amino acid pairs. PMID:23405059
The repertoires of ubiquitinating and deubiquitinating enzymes in eukaryotic genomes. PMID:23393154
Genomic and secretomic analyses reveal unique features of the lignocellulolytic enzyme system of Penicillium decumbens. PMID:23383313
Coordinating the impact of structural genomics on the human α-helical transmembrane proteome. PMID:23381628
Discovery and analysis of consistent active sub-networks in cancers. PMID:23368093
Seq2Ref: a web server to facilitate functional interpretation. PMID:23356573
The genome sequences of Cellulomonas fimi and "Cellvibrio gilvus" reveal the cellulolytic strategies of two facultative anaerobes, transfer of "Cellvibrio gilvus" to the genus Cellulomonas, and proposal of Cellulomonas gilvus sp. nov. PMID:23342046
Recognition of methylated peptides by Drosophila melanogaster polycomb chromodomain. PMID:23320494
MycoProtease-DB: Useful resource for Mycobacterium tuberculosis complex and nontuberculous mycobacterial proteases. PMID:23275726
DB Dehydrogenase: an online integrated structural database on enzyme dehydrogenase. PMID:23275696
Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). PMID:23263233
Gene family matters: expanding the HGNC resource. PMID:23245209
Deletion of cysteine cathepsins B or L yields differential impacts on murine skin proteome and degradome. PMID:23233448
The Escherichia coli peripheral inner membrane proteome. PMID:23230279
Molecular changes in Opisthorchis viverrini (Southeast Asian liver fluke) during the transition from the juvenile to the adult stage. PMID:23209858
A transcriptomic analysis of Echinococcus granulosus larval stages: implications for parasite biology and host adaptation. PMID:23209850
ViralZone: recent updates to the virus knowledge resource. PMID:23193299
The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency. PMID:23193275
1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data. PMID:23176165
Interactome-wide prediction of protein-protein binding sites reveals effects of protein sequence variation in Arabidopsis thaliana. PMID:23077539
Prediction of protein cleavage site with feature selection by random forest. PMID:23029276
Multi-edge gene set networks reveal novel insights into global relationships between biological themes. PMID:23028852
The use of glycoinformatics in glycochemistry. PMID:23015842
An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB. PMID:22962482
Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers. PMID:22962471
Structures of human DPP7 reveal the molecular basis of specific inhibition and the architectural diversity of proline-specific peptidases. PMID:22952628
Increasing coverage of transcription factor position weight matrices through domain-level homology. PMID:22952610
Identifying the hotspots on the top faces of WD40-repeat proteins from their primary sequences by β-bulges and DHSW tetrads. PMID:22916195
The UCSC genome browser and associated tools. PMID:22908213
Discovering patterns in drug-protein interactions based on their fingerprints. PMID:22901089
Mapping the mutual information network of enzymatic families in the protein structure to unveil functional features. PMID:22848494
Mining GO annotations for improving annotation consistency. PMID:22848383
Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. PMID:22844098
Function prediction and analysis of mycobacterium tuberculosis hypothetical proteins. PMID:22837694
Sequencing of the smallest Apicomplexan genome from the human pathogen Babesia microti. PMID:22833609
Mapping between databases of compounds and protein targets. PMID:22821596
Deciphering a global network of functionally associated post-translational modifications. PMID:22806145
Incorporating RNA-seq data into the zebrafish Ensembl genebuild. PMID:22798491
SigCS base: an integrated genetic information resource for human cerebral stroke. PMID:22784567
Comparative transcriptome analysis between planarian Dugesia japonica and other platyhelminth species. PMID:22747887
Transcriptome analysis of the honey bee fungal pathogen, Ascosphaera apis: implications for host pathogenesis. PMID:22747707
SynProt: A Database for Proteins of Detergent-Resistant Synaptic Protein Preparations. PMID:22737123
Prediction of protein domain with mRMR feature selection and analysis. PMID:22720092
NMR structure of lipoprotein YxeF from Bacillus subtilis reveals a calycin fold and distant homology with the lipocalin Blc from Escherichia coli. PMID:22693626
Quality of computationally inferred gene ontology annotations. PMID:22693439
Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes. PMID:22672776
Biomine: predicting links between biological entities using network models of heterogeneous databases. PMID:22672646
A topology-based metric for measuring term similarity in the gene ontology. PMID:22666244
Linear motifs confer functional diversity onto splice variants. PMID:22638587
iELM--a web server to explore short linear motif-mediated interactions. PMID:22638578
NetAligner--a network alignment server to compare complexes, pathways and whole interactomes. PMID:22618871
Profile-based short linear protein motif discovery. PMID:22607209
Proteomic analysis of HIV-1 Nef cellular binding partners reveals a role for exocyst complex proteins in mediating enhancement of intercellular nanotube formation. PMID:22534017
Tachyon search speeds up retrieval of similar sequences by several orders of magnitude. PMID:22531216
Tandem mass spectrometry identifies many mouse brain O-GlcNAcylated proteins including EGF domain-specific O-GlcNAc transferase targets. PMID:22517741
The transcription factor encyclopedia. PMID:22458515
A pathologist-in-the-loop IHC antibody test selection using the entropy-based probabilistic method. PMID:22439121
QServer: a biclustering server for prediction and assessment of co-expressed gene clusters. PMID:22403692
The role of structural disorder in the rewiring of protein interactions through evolution. PMID:22389433
GrameneMart: the BioMart data portal for the Gramene project. PMID:22374386
Changes in predicted protein disorder tendency may contribute to disease risk. PMID:22369681
Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns. PMID:22369665
Amino acids biosynthesis and nitrogen assimilation pathways: a great genomic deletion during eukaryotes evolution. PMID:22369087
Exploring and challenging the network of angiogenesis. PMID:22355580
Identification of prostate-enriched proteins by in-depth proteomic analyses of expressed prostatic secretions in urine. PMID:22339264
Regulation of expression and catalytic activity of Escherichia coli RsmG methyltransferase. PMID:22337945
The identification of short linear motif-mediated interfaces within the human interactome. PMID:22328783
Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering. PMID:22328160
Whole-exome sequencing identifies mutations in GPR179 leading to autosomal-recessive complete congenital stationary night blindness. PMID:22325361
In silico insights into the symbiotic nitrogen fixation in Sinorhizobium meliloti via metabolic reconstruction. PMID:22319621
Predicting target DNA sequences of DNA-binding proteins based on unbound structures. PMID:22312425
Associating Drugs, Targets and Clinical Outcomes into an Integrated Network Affords a New Platform for Computer-Aided Drug Repurposing. PMID:22287994
Structure- and sequence-based function prediction for non-homologous proteins. PMID:22270458
Mutations in KAT6B, encoding a histone acetyltransferase, cause Genitopatellar syndrome. PMID:22265014
Mapping yeast N-glycosites with isotopically recoded glycans. PMID:22261724
Lactobacillus adhesion to mucus. PMID:22254114
S100A9 is a biliary protein marker of disease activity in primary sclerosing cholangitis. PMID:22253789
Ceramide synthases at the centre of sphingolipid metabolism and biology. PMID:22248339
Candidate serum biomarkers for prostate adenocarcinoma identified by mRNA differences in prostate tissue and verified with protein measurements in tissue and blood. PMID:22247499
Protein docking prediction using predicted protein-protein interface. PMID:22233443
Physical properties of biological entities: an introduction to the ontology of physics for biology. PMID:22216106
Identifying elemental genomic track types and representing them uniformly. PMID:22208806
Genomics of adaptation and speciation in cichlid fishes: recent advances and analyses in African and Neotropical lineages. PMID:22201168
Generation and Analysis of Large-Scale Data-Driven Mycobacterium tuberculosis Functional Networks for Drug Target Identification. PMID:22190924
Novel search method for the discovery of functional relationships. PMID:22180409
Prediction of protein modification sites of pyrrolidone carboxylic acid using mRMR feature selection and analysis. PMID:22174779
Protective effects of Commiphora erythraea resin constituents against cellular oxidative damage. PMID:22169939
Bioinformatic analysis and post-translational modification crosstalk prediction of lysine acetylation. PMID:22164248
BioCreative III interactive task: an overview. PMID:22151968
Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences. PMID:22146221
Making your database available through Wikipedia: the pros and cons. PMID:22144683
HIstome--a relational knowledgebase of human histone proteins and histone modifying enzymes. PMID:22140112
Genome-scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A. PMID:22139506
A comprehensive manually curated protein-protein interaction database for the Death Domain superfamily. PMID:22135292
The Pfam protein families database. PMID:22127870
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. PMID:22121228
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. PMID:22121212
Time-resolved transcriptomics and bioinformatic analyses reveal intrinsic stress responses during batch culture of Bacillus subtilis. PMID:22087258
Ensembl 2012. PMID:22086963
Predicting phenotypic variation in yeast from individual genome sequences. PMID:22081227
modMine: flexible access to modENCODE data. PMID:22080565
ENCODE whole-genome data in the UCSC Genome Browser: update 2012. PMID:22075998
ClubSub-P: Cluster-Based Subcellular Localization Prediction for Gram-Negative Bacteria and Archaea. PMID:22073040
Predicting flexible loop regions that interact with ligands: the challenge of accurate scoring. PMID:22072600
Putting into practice domain-linear motif interaction predictions for exploration of protein networks. PMID:22069443
SuperTarget goes quantitative: update on drug-target interactions. PMID:22067455
IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature. PMID:22067451
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. PMID:22067447
SMART 7: recent updates to the protein domain annotation resource. PMID:22053084
Quantitative proteomics reveals cellular targets of celastrol. PMID:22046318
Antibody-based protein profiling of the human chromosome 21. PMID:22042635
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. PMID:22041191
Novel proteomic tools reveal essential roles of SRP and importance of proper membrane protein biogenesis. PMID:22030350
Proteome-wide detection of Abl1 SH3-binding peptides by integrating computational prediction and peptide microarray. PMID:22023807
Endophytic life strategies decoded by genome and transcriptome analyses of the mutualistic root symbiont Piriformospora indica. PMID:22022265
Thousands of rab GTPases for the cell biologist. PMID:22022256
canSAR: an integrated cancer public translational research and drug discovery resource. PMID:22013161
Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control. PMID:22004680
Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site. PMID:21998155
Polbase: a repository of biochemical, genetic and structural information about DNA polymerases. PMID:21993301
Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers. PMID:21992066
The BioLexicon: a large-scale terminological resource for biomedical text mining. PMID:21992002
A novel method for protein-protein interaction site prediction using phylogenetic substitution models. PMID:21989996
An α/β hydrolase and associated Per-ARNT-Sim domain comprise a bipartite sensing module coupled with diverse output domains. PMID:21980452
Ortho2ExpressMatrix--a web server that interprets cross-species gene expression data by gene family information. PMID:21970648
Functional analysis beyond enrichment: non-redundant reciprocal linkage of genes and biological terms. PMID:21949701
The evolution of function in strictosidine synthase-like proteins. PMID:21948213
The UlaG protein family defines novel structural and functional motifs grafted on an ancient RNase fold. PMID:21943130
Computational Design of a DNA- and Fc-Binding Fusion Protein. PMID:21941539
BioMart Central Portal: an open database network for the biological community. PMID:21930507
BioMart: a data federation framework for large collaborative projects. PMID:21930506
Neisseria Base: a comparative genomics database for Neisseria meningitidis. PMID:21930505
Integrating GPCR-specific information with full text articles. PMID:21910883
A computational approach to finding novel targets for existing drugs. PMID:21909252
Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in Streptomyces coelicolor. PMID:21899768
Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids. PMID:21899737
OPM database and PPM web server: resources for positioning of proteins in membranes. PMID:21890895
Predicting the physiological role of circadian metabolic regulation in the green alga Chlamydomonas reinhardtii. PMID:21887226
Prediction of B-cell linear epitopes with a combination of support vector machine classification and amino acid propensity identification. PMID:21876642
ppiTrim: constructing non-redundant and up-to-date interactomes. PMID:21873645
Genome-enabled determination of amino acid biosynthesis in Xanthomonas campestris pv. campestris and identification of biosynthetic pathways for alanine, glycine, and isoleucine by 13C-isotopologue profiling. PMID:21853248
Three periods of regulatory innovation during vertebrate evolution. PMID:21852499
High-throughput identification of potential minor histocompatibility antigens by MHC tetramer-based screening: feasibility and limitations. PMID:21850230
Bacteriocyte-associated gammaproteobacterial symbionts of the Adelges nordmannianae/piceae complex (Hemiptera: Adelgidae). PMID:21833037
Phylogenetic and experimental characterization of an acyl-ACP thioesterase family reveals significant diversity in enzymatic specificity and activity. PMID:21831316
ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs. PMID:21831265
A newly described bovine type 2 scurs syndrome segregates with a frame-shift mutation in TWIST1. PMID:21814570
Proteins with complex architecture as potential targets for drug design: a case study of Mycobacterium tuberculosis. PMID:21814507
Comparative analyses imply that the enigmatic Sigma factor 54 is a central controller of the bacterial exterior. PMID:21806785
Trimethylaurintricarboxylic acid inhibits human DNA methyltransferase 1: insights from enzymatic and molecular modeling studies. PMID:21805123
A shortest-path graph kernel for estimating gene product semantic similarity. PMID:21801410
Exploiting publicly available biological and biochemical information for the discovery of novel short linear motifs. PMID:21799808
Small open reading frames: current prediction techniques and future prospect. PMID:21787300
Small open reading frames: current prediction techniques and future prospect. PMID:21787300
Sequence-structural features and evolutionary relationships of family GH57 α-amylases and their putative α-amylase-like homologues. PMID:21786160
Genome-scale phylogenetic function annotation of large and diverse protein families. PMID:21784873
Searching for an effective, safe and universal anti-HIV vaccine: Finding the answer in just one short peptide. PMID:21776335
Domain-domain interactions underlying herpesvirus-human protein-protein interaction networks. PMID:21760902
Spinning gland transcriptomics from two main clades of spiders (order: Araneae)--insights on their molecular, anatomical and behavioral evolution. PMID:21738742
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. PMID:21737420
New structural and functional contexts of the Dx[DN]xDG linear motif: insights into evolution of calcium-binding proteins. PMID:21720552
InterMitoBase: an annotated database and analysis platform of protein-protein interactions for human mitochondria. PMID:21718467
RuleGO: a logical rules-based tool for description of gene groups by means of Gene Ontology. PMID:21715384
A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle. PMID:21714867
Pathway annotation and analysis with Reactome: the solute carrier class of membrane transporters. PMID:21712192
Gene-disease network analysis reveals functional modules in mendelian, complex and environmental diseases. PMID:21695124
Binary classification of protein molecules into intrinsically disordered and ordered segments. PMID:21693062
Conditional random field approach to prediction of protein-protein interactions using domain information. PMID:21689483
Structural principles within the human-virus protein-protein interaction network. PMID:21680884
MarkUs: a server to navigate sequence-structure-function space. PMID:21672961
Testis-specific glyceraldehyde-3-phosphate dehydrogenase: origin and evolution. PMID:21663662
Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase. PMID:21660514
Identification of antifreeze proteins and their functional residues by support vector machine and genetic algorithms based on n-peptide compositions. PMID:21655262
Mitotic spindle proteomics in Chinese hamster ovary cells. PMID:21647379
Common peptides study of aminoacyl-tRNA synthetases. PMID:21647378
The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences. PMID:21646335
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation. PMID:21631914
PCR-based identification of Klebsiella pneumoniae subsp. rhinoscleromatis, the agent of rhinoscleroma. PMID:21629720
deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PMID:21625565
Analysis of the disintegrin-metalloproteinases family reveals ADAM29 and ADAM7 are often mutated in melanoma. PMID:21618342
Mitochondrial function and energy metabolism in umbilical cord blood- and bone marrow-derived mesenchymal stem cells. PMID:21615273
Computational prediction of O-linked glycosylation sites that preferentially map on intrinsically disordered regions of extracellular proteins. PMID:21614187
Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis. PMID:21612636
Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins. PMID:21612628
Data mining using the Catalogue of Somatic Mutations in Cancer BioMart. PMID:21609966
GPCR-SSFE: a comprehensive database of G-protein-coupled receptor template predictions and homology models. PMID:21605354
GProX, a user-friendly platform for bioinformatics analysis and visualization of quantitative proteomics data. PMID:21602510
Bacterial metallothioneins: past, present, and questions for the future. PMID:21594652
HMMER web server: interactive sequence similarity searching. PMID:21593126
The structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors. PMID:21575214
Linked open drug data for pharmaceutical research and development. PMID:21575203
N-Glycosylation profiling of recombinant mouse extracellular superoxide dismutase produced in Chinese hamster ovary cells. PMID:21573946
Comparative genomics of cell envelope components in mycobacteria. PMID:21573108
DAS writeback: a collaborative annotation system. PMID:21569281
Crystal structures of a halophilic archaeal malate synthase from Haloferax volcanii and comparisons with isoforms A and G. PMID:21569248
NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity. PMID:21558170
Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PMID:21556138
Directed evolution reveals the binding motif preference of the LC8/DYNLL hub protein and predicts large numbers of novel binders in the human proteome. PMID:21533121
Arabidopsis plasmodesmal proteome. PMID:21533090
Proteinortho: detection of (co-)orthologs in large-scale analysis. PMID:21526987
DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases. PMID:21504591
Metagenomics and the protein universe. PMID:21497084
The characterization of Thermotoga maritima ferritin reveals an unusual subunit dissociation behavior and efficient DNA protection from iron-mediated oxidative stress. PMID:21487935
Exploring off-targets and off-systems for adverse drug reactions via chemical-protein interactome--clozapine-induced agranulocytosis as a case study. PMID:21483481
Remote thioredoxin recognition using evolutionary conservation and structural dynamics. PMID:21481770
dbOGAP - an integrated bioinformatics resource for protein O-GlcNAcylation. PMID:21466708
A systems biology approach for the investigation of the heparin/heparan sulfate interactome. PMID:21454685
Discordant and chameleon sequences: their distribution and implications for amyloidogenicity. PMID:21432934
Cross-sample validation provides enhanced proteome coverage in rat vocal fold mucosa. PMID:21423617
Identification of drought-responsive universal stress proteins in viridiplantae. PMID:21423406
Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PMID:21408204
TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery. PMID:21408081
Proteomic and electron microscopy survey of large assemblies in macrophage cytoplasm. PMID:21406389
Disease and phenotype data at Ensembl. PMID:21400687
A unique iron-sulfur cluster is crucial for oxygen tolerance of a [NiFe]-hydrogenase. PMID:21390036
Study of protein complexes via homology modeling, applied to cysteine proteases and their protein inhibitors. PMID:21365221
RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. PMID:21357752
Protein function prediction: towards integration of similarity metrics. PMID:21353529
The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. PMID:21347285
Vimentin organization modulates the formation of lamellipodia. PMID:21346197
Unique spectrum of activity of prosimian TRIM5alpha against exogenous and endogenous retroviruses. PMID:21345948
RSpred, a set of Hidden Markov Models to detect and classify the RIFIN and STEVOR proteins of Plasmodium falciparum. PMID:21332983
Unusual outer membrane lipid composition of the gram-negative, lipopolysaccharide-lacking myxobacterium Sorangium cellulosum So ce56. PMID:21321121
Structure of the periplasmic stress response protein CpxP. PMID:21317318
GeneReporter--sequence-based document retrieval and annotation. PMID:21310745
Integrative features of the yeast phosphoproteome and protein-protein interaction map. PMID:21298081
Differential gene expression in liver and small intestine from lactating rats compared to age-matched virgin controls detects increased mRNA of cholesterol biosynthetic genes. PMID:21291544
MEMOSys: Bioinformatics platform for genome-scale metabolic models. PMID:21276275
Eukaryote-wide sequence analysis of mitochondrial β-barrel outer membrane proteins. PMID:21272379
PNAC: a protein nucleolar association classifier. PMID:21272300
The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus. PMID:21266083
Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment. PMID:21248859
The Biomolecular Interaction Network Database in PSI-MI 2.5. PMID:21233089
A bioinformatics approach for biomarker identification in radiation-induced lung inflammation from limited proteomics data. PMID:21226504
1,000 structures and more from the MCSG. PMID:21219649
The annotation of the asparagine N-linked glycosylation pathway in the Reactome database. PMID:21199820
Characterization of the Dictyostelium homolog of chromatin binding protein DET1 suggests a conserved pathway regulating cell type specification and developmental plasticity. PMID:21193547
The annotation and the usage of scientific databases could be improved with public issue tracker software. PMID:21186182
Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities. PMID:21179190
Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli. PMID:21173244
Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication. PMID:21173032
Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi. PMID:21148284
Towards a knowledge-based Human Protein Atlas. PMID:21139605
Structural basis of tumor suppressor in lung cancer 1 (TSLC1) binding to differentially expressed in adenocarcinoma of the lung (DAL-1/4.1B). PMID:21131357
A computational approach to analyze the mechanism of action of the kinase inhibitor bafetinib. PMID:21124949
Structure-function analyses point to a polynucleotide-accommodating groove essential for APOBEC3A restriction activities. PMID:21123384
T3SEdb: data warehousing of virulence effectors secreted by the bacterial Type III Secretion System. PMID:21106126
Comparative functional genomic analysis of Solanum glandular trichome types. PMID:21098679
PCDB: a database of protein conformational diversity. PMID:21097895
COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. PMID:21097892
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. PMID:21097781
Extending CATH: increasing coverage of the protein structure universe and linking structure with function. PMID:21097779
Laminin database: a tool to retrieve high-throughput and curated data for studies on laminins. PMID:21087995
N-glycosylation efficiency is determined by the distance to the C-terminus and the amino acid preceding an Asn-Ser-Thr sequon. PMID:21082725
A tutorial on protein ontology resources for proteomic studies. PMID:21082429
PHOSIDA 2011: the posttranslational modification database. PMID:21081558
Influence of histatin 5 on Candida albicans mitochondrial protein expression assessed by quantitative mass spectrometry. PMID:21080726
Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification. PMID:21079665
MimoDB: a new repository for mimotope data derived from phage display technology. PMID:21079566
An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology. PMID:21078182
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. PMID:21075798
AgBase: supporting functional modeling in agricultural organisms. PMID:21075795
ConsensusPathDB: toward a more complete picture of cell biology. PMID:21071422
PROMISCUOUS: a database for network-based drug-repositioning. PMID:21071407
Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera. PMID:21071397
Practical 4'-phosphopantetheine active site discovery from proteomic samples. PMID:21067235
BRENDA, the enzyme information system in 2011. PMID:21062828
SUPERFAMILY 1.75 including a domain-centric gene ontology method. PMID:21062816
Phospho.ELM: a database of phosphorylation sites--update 2011. PMID:21062810
The mouse Gene Expression Database (GXD): 2011 update. PMID:21062809
CPLA 1.0: an integrated database of protein lysine acetylation. PMID:21059677
Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. PMID:21059217
Human and chicken TLR pathways: manual curation and computer-based orthology analysis. PMID:21052677
SAHG, a comprehensive database of predicted structures of all human proteins. PMID:21051360
ThYme: a database for thioester-active enzymes. PMID:21045059
Ensembl 2011. PMID:21045057
GPCRDB: information system for G protein-coupled receptors. PMID:21045054
The RCSB Protein Data Bank: redesigned web site and web services. PMID:21036868
PREX: PeroxiRedoxin classification indEX, a database of subfamily assignments across the diverse peroxiredoxin family. PMID:21036863
Genotator: a disease-agnostic tool for genetic annotation of disease. PMID:21034472
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. PMID:21030441
Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. PMID:20973947
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. PMID:20972218
Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites. PMID:20965970
TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. PMID:20965969
The Pancreatic Expression database: 2011 update. PMID:20959292
KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions. PMID:20952400
CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge. PMID:20952398
HitPredict: a database of quality assessed protein-protein interactions in nine species. PMID:20947562
PICMI: mapping point mutations on genomes. PMID:20940168
The S-layer glycoprotein of the crenarchaeote Sulfolobus acidocaldarius is glycosylated at multiple sites with chitobiose-linked N-glycans. PMID:20936123
The Protein Ontology: a structured representation of protein forms and complexes. PMID:20935045
Uncovering the human methyltransferasome. PMID:20930037
genenames.org: the HGNC resources in 2011. PMID:20929869
DDPC: Dragon Database of Genes associated with Prostate Cancer. PMID:20880996
Accumulation of driver and passenger mutations during tumor progression. PMID:20876136
The Comparative Toxicogenomics Database: update 2011. PMID:20864448
Impact of the mitochondrial genetic background in complex III deficiency. PMID:20862300
Receptor cleavage reduces the fluid shear response in neutrophils of the spontaneously hypertensive rat. PMID:20861466
The FLIGHT Drosophila RNAi database: 2010 update. PMID:20855970
MatrixDB, the extracellular matrix interaction database. PMID:20852260
TRIP Database: a manually curated database of protein-protein interactions for mammalian TRP channels. PMID:20851834
Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. PMID:20847220
sRNATarBase: a comprehensive database of bacterial sRNA targets verified by experiments. PMID:20843985
Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions. PMID:20843356
Rapid calcium-dependent activation of Aurora-A kinase. PMID:20842194
Challenges and opportunities for discovery of disease biomarkers using urine proteomics. PMID:20840485
Exploring zebrafish genomic, functional and phenotypic data using ZFIN. PMID:20836073
Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network. PMID:20823846
BioXSD: the common data-exchange format for everyday bioinformatics web services. PMID:20823319
Co-regulation of alternative splicing by diverse splicing factors in Caenorhabditis elegans. PMID:20805248
Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution. PMID:20737437
RefProtDom: a protein database with improved domain boundaries and homology relationships. PMID:20693322
Characterization and prediction of protein nucleolar localization sequences. PMID:20663773
Update of human and mouse forkhead box (FOX) gene families. PMID:20650821
The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand. PMID:20646284
Gene promoter evolution targets the center of the human protein interaction network. PMID:20628608
BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks. PMID:20628073
Proteogenomics to discover the full coding content of genomes: a computational perspective. PMID:20620248
The metabolic network of Synechocystis sp. PCC 6803: systemic properties of autotrophic growth. PMID:20616194
Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity. PMID:20616063
Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research. PMID:20615486
Multiple ontologies in action: composite annotations for biosimulation models. PMID:20601121
MetaBar - a tool for consistent contextual data acquisition and standards compliant submission. PMID:20591175
Systematizing the generation of missing metabolic knowledge. PMID:20589842
Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. PMID:20589078
Communicating subcellular distributions. PMID:20552685
MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. PMID:20542913
SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study. PMID:20529875
A quick guide to large-scale genomic data mining. PMID:20523745
Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. PMID:20522724
Discovering causal signaling pathways through gene-expression patterns. PMID:20494976
The EMBRACE web service collection. PMID:20462862
Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. PMID:20459641
A new bioinformatics analysis tools framework at EMBL-EBI. PMID:20439314
A human-specific de novo protein-coding gene associated with human brain functions. PMID:20376170
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. PMID:20369061
An expanded Oct4 interaction network: implications for stem cell biology, development, and disease. PMID:20362542
A MOD(ern) perspective on literature curation. PMID:20221640
Homologous over-extension: a challenge for iterative similarity searches. PMID:20064877
The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. PMID:19965766
The European Bioinformatics Institute's data resources. PMID:19934258 -
The Universal Protein Resource (UniProt): an expanding universe of protein information
PubMed citations: 464.
464 articles citing: The Universal Protein Resource (UniProt): an expanding universe of protein information
Analysis of phylogenetic markers for classification of a hydrogen peroxide producing Streptococcus oralis isolated from saliva by a newly devised differential medium. PMID:35835959
Physiological, Agronomical, and Proteomic Studies Reveal Crucial Players in Rice Nitrogen Use Efficiency under Low Nitrogen Supply. PMID:35742855
In silico approaches to develop herbal acaricides against R. (Boophilus) Microplus and In vitro Anti-Tick activities of selected medicinal plants. PMID:35602870
Genomic features of the polyphagous cotton leafworm Spodoptera littoralis. PMID:35525948
Genome interpretation using in silico predictors of variant impact. PMID:35488922
AF2Complex predicts direct physical interactions in multimeric proteins with deep learning. PMID:35365655
MISF2 Encodes an Essential Mitochondrial Splicing Cofactor Required for nad2 mRNA Processing and Embryo Development in Arabidopsis thaliana. PMID:35269810
The evolution and competitive strategies of Akkermansia muciniphila in gut. PMID:35263215
Slipknot or Crystallographic Error: A Computational Analysis of the Plasmodium falciparum DHFR Structural Folds. PMID:35163439
Refining the domain architecture model of the replication origin firing factor Treslin/TICRR. PMID:35091422
An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer's disease. PMID:34953465
The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host. PMID:34911987
Revealing the Molecular Mechanisms of Alzheimer's Disease Based on Network Analysis. PMID:34768988
The importance of age in compositional and functional profiling of the human intestinal microbiome. PMID:34662347
A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology. PMID:34599334
Chromosome-Level Genome Sequence of Aspergillus chevalieri M1, Isolated from Katsuobushi. PMID:34528823
Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom. PMID:34499567
Chromosome-Level Genome Sequence of Aspergillus puulaauensis MK2, a Fungus Isolated from a Dead Hard Tick. PMID:34498921
Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids. PMID:34413505
First Insight into the Diversity and Antibacterial Potential of Psychrophilic and Psychotrophic Microbial Communities of Abandoned Amber Quarry. PMID:34361956
Identification of Potential Kinase Inhibitors within the PI3K/AKT Pathway of Leishmania Species. PMID:34356660
"Protein" no longer means what it used to. PMID:34308370
Chromosome-Level Genome Sequence of the Black Koji Fungus Aspergillus luchuensis RIB2601. PMID:34292062
Comparative Transcriptome Analyses of the Developmental Stages of Taenia multiceps. PMID:34291101
Dynamic landscape of protein occupancy across the Escherichia coli chromosome. PMID:34170902
Genomic adaptations enabling Acidithiobacillus distribution across wide-ranging hot spring temperatures and pHs. PMID:34116726
Draft Genome Sequence of Deefgea sp. Strain CFH1-16, Isolated from the Intestine of the Freshwater Fish Hypomesus nipponensis. PMID:33986104
Integrated Biophysical Modeling of the SARS-CoV-2 Spike Protein Binding and Allosteric Interactions with Antibodies. PMID:33929853
Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador. PMID:33872206
Type IV Collagen Variants in CKD: Performance of Computational Predictions for Identifying Pathogenic Variants. PMID:33851121
Bacteremic cholangitis due to Raoultella planticola complicating intrahepatic bile duct stricture 5 years post-laparoscopic cholecystectomy: a case report. PMID:33823908
Immunoinformatics and Molecular Docking Studies Predicted Potential Multiepitope-Based Peptide Vaccine and Novel Compounds against Novel SARS-CoV-2 through Virtual Screening. PMID:33728324
Understanding protein structural changes for oncogenic missense variants. PMID:33553733
Structure analysis of the proteins associated with polyA repeat expansion disorders. PMID:33459170
The Reliability of Metagenome-Assembled Genomes (MAGs) in Representing Natural Populations: Insights from Comparing MAGs against Isolate Genomes Derived from the Same Fecal Sample. PMID:33452027
ACID: a free tool for drug repurposing using consensus inverse docking strategy. PMID:33430982
Coevolution, Dynamics and Allostery Conspire in Shaping Cooperative Binding and Signal Transmission of the SARS-CoV-2 Spike Protein with Human Angiotensin-Converting Enzyme 2. PMID:33158276
Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. PMID:33006605
A novel sequence alignment algorithm based on deep learning of the protein folding code. PMID:32960943
Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity. PMID:32887943
lncRNA_Mdeep: An Alignment-Free Predictor for Distinguishing Long Non-Coding RNAs from Protein-Coding Transcripts by Multimodal Deep Learning. PMID:32718000
Systems Pharmacology-Dissection of the Molecular Mechanisms of Dragon's Blood in Improving Ischemic Stroke Prognosis. PMID:32508949
Revenant: a database of resurrected proteins. PMID:32400867
A Novel Combination of Vitamin C, Curcumin and Glycyrrhizic Acid Potentially Regulates Immune and Inflammatory Response Associated with Coronavirus Infections: A Perspective from System Biology Analysis. PMID:32344708
SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics. PMID:32196115
Comparative Genomics of Actinobacillus pleuropneumoniae Serotype 8 Reveals the Importance of Prophages in the Genetic Variability of the Species. PMID:32149072
PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data. PMID:32108861
A Systematic Approach to Bacterial Phylogeny Using Order Level Sampling and Identification of HGT Using Network Science. PMID:32102454
Gene coexpression network analysis reveals the role of SRS genes in senescence leaf of maize (Zea mays L.). PMID:32089522
Complete Genome Sequence of Methylomonas koyamae LM6, a Potential Aerobic Methanotroph. PMID:32029563
Network-Based Metabolism-Centered Screening of Potential Drug Targets in Klebsiella pneumoniae at Genome Scale. PMID:31993376
Mikania micrantha genome provides insights into the molecular mechanism of rapid growth. PMID:31953413
Synergistic Effect of Network-Based Multicomponent Drugs: An Investigation on the Treatment of Non-Small-Cell Lung Cancer with Compound Liuju Formula. PMID:31949474
Network-Based Prediction of Novel CRISPR-Associated Genes in Metagenomes. PMID:31937679
Insights into evolutionary interaction patterns of the 'Phosphorylation Activation Segment' in kinase. PMID:31787816
Deciphering Molecular Mechanism of the Neuropharmacological Action of Fucosterol through Integrated System Pharmacology and In Silico Analysis. PMID:31766220
Retinal artery occlusion is associated with compositional and functional shifts in the gut microbiome and altered trimethylamine-N-oxide levels. PMID:31653902
Complete Genome Sequence of Phreatobacter sp. Strain NMCR1094, a Formate-Utilizing Bacterium Isolated from a Freshwater Stream. PMID:31515346
Modeling the Interplay between Photosynthesis, CO2 Fixation, and the Quinone Pool in a Purple Non-Sulfur Bacterium. PMID:31477760
Evolutionary coupling analysis identifies the impact of disease-associated variants at less-conserved sites. PMID:31199866
PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome. PMID:30871454
DESTINI: A deep-learning approach to contact-driven protein structure prediction. PMID:30837676
Computational screening of medicinal plant phytochemicals to discover potent pan-serotype inhibitors against dengue virus. PMID:30723263
The Cdk8/19-cyclin C transcription regulator functions in genome replication through metazoan Sld7. PMID:30695077
An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis. PMID:30661980
Draft Genome Sequence of Deinococcus koreensis SJW1-2T, a Gamma Radiation-Resistant Bacterium Isolated from River Water. PMID:30533895
Effects of Phenothiazines on Aldehyde Oxidase Activity Towards Aldehydes and N-Heterocycles: an In Vitro and In Silico Study. PMID:30382490
Substrate Profile of the Phosphotriesterase Homology Protein from Escherichia coli. PMID:30277746
psichomics: graphical application for alternative splicing quantification and analysis. PMID:30277515
A graph-based filtering method for top-down mass spectral identification. PMID:30255788
Comprehensive Transcriptome Profiling and Identification of Potential Genes Responsible for Salt Tolerance in Tall Fescue Leaves under Salinity Stress. PMID:30248970
DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins. PMID:30209260
DES-Mutation: System for Exploring Links of Mutations and Diseases. PMID:30190574
Systems Pharmacological Approach to Investigate the Mechanism of Acori Tatarinowii Rhizoma for Alzheimer's Disease. PMID:30050590
Identification of transcribed protein coding sequence remnants within lincRNAs. PMID:29986053
Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community. PMID:29976643
The genome of tapeworm Taenia multiceps sheds light on understanding parasitic mechanism and control of coenurosis disease. PMID:29947776
Molecular and biochemical characterization of a novel isoprene synthase from Metrosideros polymorpha. PMID:29902970
SAMSA2: a standalone metatranscriptome analysis pipeline. PMID:29783945
Draft Genome Sequence of Paucibacter aquatile CR182T, a Strain with Antimicrobial Activity Isolated from Freshwater of Nakdong River in South Korea. PMID:29700134
A c-di-GMP-Modulating Protein Regulates Swimming Motility of Burkholderia cenocepacia in Response to Arginine and Glutamate. PMID:29541628
Prediction and interpretation of deleterious coding variants in terms of protein structural stability. PMID:29540703
A Spectrum Graph-Based Protein Sequence Filtering Algorithm for Proteoform Identification by Top-Down Mass Spectrometry. PMID:29503761
Whole-Genome Analysis Illustrates Global Clonal Population Structure of the Ubiquitous Dermatophyte Pathogen Trichophyton rubrum. PMID:29467168
Spherical: an iterative workflow for assembling metagenomic datasets. PMID:29361904
Effect of salt-stress on gene expression in citrus roots revealed by RNA-seq. PMID:29264749
Draft Sequencing of the Heterozygous Diploid Genome of Satsuma (Citrus unshiu Marc.) Using a Hybrid Assembly Approach. PMID:29259619
Systems Pharmacological Approach to the Effect of Bulsu-san Promoting Parturition. PMID:29234425
Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. PMID:29140462
TMEM132: an ancient architecture of cohesin and immunoglobulin domains define a new family of neural adhesion molecules. PMID:29088312
Molecular mechanisms and structural features of cardiomyopathy-causing troponin T mutants in the tropomyosin overlap region. PMID:28973951
Genome Architecture and Evolution of a Unichromosomal Asexual Nematode. PMID:28943090
Genetic and functional characterization of disease associations explains comorbidity. PMID:28740175
Systems Pharmacological Approach of Pulsatillae Radix on Treating Crohn's Disease. PMID:28659988
Variant effect prediction tools assessed using independent, functional assay-based datasets: implications for discovery and diagnostics. PMID:28511696
APC/CCdh1 Enables Removal of Shugoshin-2 from the Arms of Bivalent Chromosomes by Moderating Cyclin-Dependent Kinase Activity. PMID:28502659
Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae. PMID:28376722
Impact of genetic variation on three dimensional structure and function of proteins. PMID:28296894
Machine learning classifier for identification of damaging missense mutations exclusive to human mitochondrial DNA-encoded polypeptides. PMID:28270093
Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem. PMID:28258138
Identifying Functional Cysteine Residues in the Mitochondria. PMID:28157297
Understanding cancer complexome using networks, spectral graph theory and multilayer framework. PMID:28155908
Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication. PMID:28095400
Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration. PMID:28094305
iCAGES: integrated CAncer GEnome Score for comprehensively prioritizing driver genes in personal cancer genomes. PMID:28007024
Single-cell exome sequencing identifies mutations in KCP, LOC440040, and LOC440563 as drivers in renal cell carcinoma stem cells. PMID:27981968
The novel homozygous KCNJ10 c.986T>C (p.(Leu329Pro)) variant is pathogenic for the SeSAME/EAST homologue in Malinois dogs. PMID:27966545
Prediction of interacting proteins from homology-modeled complex structures using sequence and structure scores. PMID:27857563
Systems pharmacology exploration of botanic drug pairs reveals the mechanism for treating different diseases. PMID:27841365
Classification and substrate head-group specificity of membrane fatty acid desaturases. PMID:27708750
MetaStorm: A Public Resource for Customizable Metagenomics Annotation. PMID:27632579
The role of ADP-ribosylation in regulating DNA interstrand crosslink repair. PMID:27587838
Complete Genome Sequence of Cryobacterium arcticum Strain PAMC 27867, Isolated from a Sedimentary Rock Sample in Northern Victoria Land, Antarctica. PMID:27587812
Complete Genome Sequence of Psychrobacter alimentarius PAMC 27889, a Psychrophile Isolated from an Antarctic Rock Sample. PMID:27445386
Systems Pharmacology Uncovers the Multiple Mechanisms of Xijiao Dihuang Decoction for the Treatment of Viral Hemorrhagic Fever. PMID:27239215
Prediction of peptidoglycan hydrolases- a new class of antibacterial proteins. PMID:27229861
Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.). PMID:27169379
Activation of Shikimate, Phenylpropanoid, Oxylipins, and Auxin Pathways in Pectobacterium carotovorum Elicitors-Treated Moss. PMID:27047509
Identification of E-cadherin signature motifs functioning as cleavage sites for Helicobacter pylori HtrA. PMID:26983597
GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data. PMID:26983021
Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections. PMID:26969701
SNP2Structure: A Public and Versatile Resource for Mapping and Three-Dimensional Modeling of Missense SNPs on Human Protein Structures. PMID:26949480
Vasohibins: new transglutaminase-like cysteine proteases possessing a non-canonical Cys-His-Ser catalytic triad. PMID:26794318
Prediction of Protein Submitochondrial Locations by Incorporating Dipeptide Composition into Chou's General Pseudo Amino Acid Composition. PMID:26746980
Identification and characterization of a novel stress-responsive outer membrane protein Lip40 from Actinobacillus pleuropneumoniae. PMID:26608465
From Single Variants to Protein Cascades: MULTISCALE MODELING OF SINGLE NUCLEOTIDE VARIANT SETS IN GENETIC DISORDERS. PMID:26601959
Annotation inconsistencies beyond sequence similarity-based function prediction - phylogeny and genome structure. PMID:26594309
MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins. PMID:26450961
Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms. PMID:26437714
An integrated structure- and system-based framework to identify new targets of metabolites and known drugs. PMID:26286808
Software Analysis of Uncorrelated MS1 Peaks for Discovery of Post-Translational Modifications. PMID:26265041
RNA-seq for gene identification and transcript profiling in relation to root growth of bermudagrass (Cynodon dactylon) under salinity stress. PMID:26238595
BALL-SNP: combining genetic and structural information to identify candidate non-synonymous single nucleotide polymorphisms. PMID:26191084
HCSD: the human cancer secretome database. PMID:26078477
Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution. PMID:26075886
Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis. PMID:26027735
The human transmembrane proteome. PMID:26018427
A density-based clustering approach for identifying overlapping protein complexes with functional preferences. PMID:26013799
Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4. PMID:25971965
Transcriptome profiling identifies p53 as a key player during calreticulin deficiency: Implications in lipid accumulation. PMID:25946468
Identification of CTLA2A, DEFB29, WFDC15B, SERPINA1F and MUP19 as Novel Tissue-Specific Secretory Factors in Mouse. PMID:25946105
The transcriptome of equine peripheral blood mononuclear cells. PMID:25790166
Efficient prediction of progesterone receptor interactome using a support vector machine model. PMID:25741764
Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation. PMID:25708928
Analysis of the Campylobacter jejuni genome by SMRT DNA sequencing identifies restriction-modification motifs. PMID:25695747
Alternate Phosphorylation/O-GlcNAc Modification on Human Insulin IRSs: A Road towards Impaired Insulin Signaling in Alzheimer and Diabetes. PMID:25580119
TM6SF2 and MAC30, new enzyme homologs in sterol metabolism and common metabolic disease. PMID:25566323
Improved methods for classification, prediction, and design of antimicrobial peptides. PMID:25555720
Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. PMID:25552646
INTEGRATING COMPUTATIONAL PROTEIN FUNCTION PREDICTION INTO DRUG DISCOVERY INITIATIVES. PMID:25530654
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. PMID:25514926
Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions. PMID:25392414
Transcriptomic analysis of the mussel Elliptio complanata identifies candidate stress-response genes and an abundance of novel or noncoding transcripts. PMID:25375103
Structural basis for the recognition of human cytomegalovirus glycoprotein B by a neutralizing human antibody. PMID:25299639
A weighted multipath measurement based on gene ontology for estimating gene products similarity. PMID:25229994
The structural basis of ATP as an allosteric modulator. PMID:25211773
Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway. PMID:25210598
Insight derived from molecular dynamics simulations into molecular motions, thermodynamics and kinetics of HIV-1 gp120. PMID:25105502
Transcriptome analysis of extant cotton progenitors revealed tetraploidization and identified genome-specific single nucleotide polymorphism in diploid and allotetraploid cotton. PMID:25099166
GMEnzy: a genetically modified enzybiotic database. PMID:25084271
Genome and transcriptome of the porcine whipworm Trichuris suis. PMID:24929829
A word of caution about biological inference - Revisiting cysteine covalent state predictions. PMID:24918043
Transcriptomic and metabolomic analysis of copper stress acclimation in Ectocarpus siliculosus highlights signaling and tolerance mechanisms in brown algae. PMID:24885189
Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. PMID:24842992
Building and exploring an integrated human kinase network: global organization and medical entry points. PMID:24704859
Genomic convergence and network analysis approach to identify candidate genes in Alzheimer's disease. PMID:24628925
Spectral probabilities of top-down tandem mass spectra. PMID:24564718
geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. PMID:24475928
Mapping genetic variants underlying differences in the central nitrogen metabolism in fermenter yeasts. PMID:24466135
PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations. PMID:24453961
Multi-omic network signatures of disease. PMID:24432028
Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection. PMID:24318998
ModBase, a database of annotated comparative protein structure models and associated resources. PMID:24271400
SASD: the Synthetic Alternative Splicing Database for identifying novel isoform from proteomics. PMID:24267658
The microcephaly protein Asp regulates neuroepithelium morphogenesis by controlling the spatial distribution of myosin II. PMID:24142104
Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota. PMID:24108330
Physical motif clustering within intrinsically disordered nucleoporin sequences reveals universal functional features. PMID:24066078
An approach for identifying cytokines based on a novel ensemble classifier. PMID:24027761
Integration of cardiac proteome biology and medicine by a specialized knowledgebase. PMID:23965338
A viral-human interactome based on structural motif-domain interactions captures the human infectome. PMID:23951184
Experimental characterization of the human non-sequence-specific nucleic acid interactome. PMID:23902751
Utilization of heme as an iron source by marine Alphaproteobacteria in the Roseobacter clade. PMID:23872569
Comparison of ultra-fast 2D and 3D ligand and target descriptors for side effect prediction and network analysis in polypharmacology. PMID:23826885
Global transcriptome profiles of Camellia sinensis during cold acclimation. PMID:23799877
Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex. PMID:23514195
MISP is a novel Plk1 substrate required for proper spindle orientation and mitotic progression. PMID:23509069
Role of the phenylalanine-hydroxylating system in aromatic substance degradation and lipid metabolism in the oleaginous fungus Mortierella alpina. PMID:23503309
Organic cofactors in the metabolism of Dehalococcoides mccartyi strains. PMID:23479751
Structural Variations of Human Glucokinase Glu256Lys in MODY2 Condition Using Molecular Dynamics Study. PMID:23476789
Isobar(PTM): a software tool for the quantitative analysis of post-translationally modified proteins. PMID:23470796
Immunogenicity of recombinant Mycobacterium bovis bacille Calmette-Guèrin clones expressing T and B cell epitopes of Mycobacterium tuberculosis antigens. PMID:23458635
Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence. PMID:23402223
Discovery of glycoside hydrolase enzymes in an avicel-adapted forest soil fungal community by a metatranscriptomic approach. PMID:23393585
Phylogenetic analysis of cubilin (CUBN) gene. PMID:23390341
Software for automated interpretation of mass spectrometry data from glycans and glycopeptides. PMID:23293784
Phylogenetic analysis of uroporphyrinogen III synthase (UROS) gene. PMID:23275732
Expression of Paracoccidioides brasiliensis AMY1 in a Histoplasma capsulatum amy1 mutant, relates an α-(1,4)-amylase to cell wall α-(1,3)-glucan synthesis. PMID:23185578
C²Maps: a network pharmacology database with comprehensive disease-gene-drug connectivity relationships. PMID:23134618
In vivo modification of tyrosine residues in recombinant mussel adhesive protein by tyrosinase co-expression in Escherichia coli. PMID:23095646
A novel missense-mutation-related feature extraction scheme for 'driver' mutation identification. PMID:23044540
Protein domain recurrence and order can enhance prediction of protein functions. PMID:22962465
Correlation between protein sequence similarity and crystallization reagents in the biological macromolecule crystallization database. PMID:22949812
TFinDit: transcription factor-DNA interaction data depository. PMID:22943312
Subcellular localization of extracytoplasmic proteins in monoderm bacteria: rational secretomics-based strategy for genomic and proteomic analyses. PMID:22912771
In silico method for modelling metabolism and gene product expression at genome scale. PMID:22760628
Detecting mutually exclusive interactions in protein-protein interaction maps. PMID:22715412
A Phylogenetic analysis of Heparanase (HPSE) gene. PMID:22715311
3D profile-based approach to proteome-wide discovery of novel human chemokines. PMID:22586462
Nprl3 is required for normal development of the cardiovascular system. PMID:22538705
FUSE: a profit maximization approach for functional summarization of biological networks. PMID:22536894
Computational comparative study of tuberculosis proteomes using a model learned from signal peptide structures. PMID:22496884
EnzyBase: a novel database for enzybiotic studies. PMID:22489867
Core site-moiety maps reveal inhibitors and binding mechanisms of orthologous proteins by screening compound libraries. PMID:22393385
Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. PMID:22373417
Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal. PMID:22323219
Structure-based function discovery of an enzyme for the hydrolysis of phosphorylated sugar lactones. PMID:22313111
IntegromeDB: an integrated system and biological search engine. PMID:22260095
Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure. PMID:22210869
Accelerated protein evolution analysis reveals genes and pathways associated with the evolution of mammalian longevity. PMID:22205409
Genome characterization of the oleaginous fungus Mortierella alpina. PMID:22174787
Approaches to Fungal Genome Annotation. PMID:22059117
Ascaris suum draft genome. PMID:22031327
Crystal structure-based virtual screening for fragment-like ligands of the human histamine H(1) receptor. PMID:22007643
Impact of Fgd1 and ddn diversity in Mycobacterium tuberculosis complex on in vitro susceptibility to PA-824. PMID:21930879
Biochemical characterization of the tetrahydrobiopterin synthesis pathway in the oleaginous fungus Mortierella alpina. PMID:21852350
IFIT1 is an antiviral protein that recognizes 5'-triphosphate RNA. PMID:21642987
Full-length transcriptome assembly from RNA-Seq data without a reference genome. PMID:21572440
Identification of a myeloid-derived suppressor cell cystatin-like protein that inhibits metastasis. PMID:21518852
Systems analysis of endothelial cell plasma membrane proteome of rat lung microvasculature. PMID:21447187
Evolutionary approach to predicting the binding site residues of a protein from its primary sequence. PMID:21402946
Omics-based molecular target and biomarker identification. PMID:21370102
FunSecKB: the Fungal Secretome KnowledgeBase. PMID:21300622
Initial characterization of the human central proteome. PMID:21269460
Homology-based identification of capsid determinants that protect HIV1 from human TRIM5α restriction. PMID:21169362
3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes. PMID:21143789
ModBase, a database of annotated comparative protein structure models, and associated resources. PMID:21097780
PCRPi-DB: a database of computationally annotated hot spots in protein interfaces. PMID:21097468
Influence of histatin 5 on Candida albicans mitochondrial protein expression assessed by quantitative mass spectrometry. PMID:21080726
Pathway Commons, a web resource for biological pathway data. PMID:21071392
PEPPI: a peptidomic database of human protein isoforms for proteomics experiments. PMID:20946618
MEDELLER: homology-based coordinate generation for membrane proteins. PMID:20926421
Neisseria meningitidis rifampicin resistant strains: analysis of protein differentially expressed. PMID:20868485
Insights into the binding of Phenyltiocarbamide (PTC) agonist to its target human TAS2R38 bitter receptor. PMID:20811630
Characterizing the metabolism of Dehalococcoides with a constraint-based model. PMID:20811585
Molecular basis for the resistance of an insect chymotrypsin to a potato type II proteinase inhibitor. PMID:20696921
Identification and structural characterization of FYVE domain-containing proteins of Arabidopsis thaliana. PMID:20678208
PROCARB: A Database of Known and Modelled Carbohydrate-Binding Protein Structures with Sequence-Based Prediction Tools. PMID:20671979
GeneBrowser 2: an application to explore and identify common biological traits in a set of genes. PMID:20663121
Functional identification and structure determination of two novel prolidases from cog1228 in the amidohydrolase superfamily. PMID:20604542
A mutation in the mitochondrial fission gene Dnm1l leads to cardiomyopathy. PMID:20585624
Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM). PMID:20581473
Optimal selection of epitopes for TXP-immunoaffinity mass spectrometry. PMID:20579369
BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features. PMID:20522253
Dimerization of the hepatitis C virus nonstructural protein 4B depends on the integrity of an aminoterminal basic leucine zipper. PMID:20506268
Re-annotation is an essential step in systems biology modeling of functional genomics data. PMID:20498845
Phosphoproteome analysis reveals regulatory sites in major pathways of cardiac mitochondria. PMID:20495213
Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP. PMID:20482861
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. PMID:20472543
Mutations and variants in the cohesion factor genes NIPBL, SMC1A, and SMC3 in a cohort of 30 unrelated patients with Cornelia de Lange syndrome. PMID:20358602
HTAPP: high-throughput autonomous proteomic pipeline. PMID:20336676
Increasing alternative promoter repertories is positively associated with differential expression and disease susceptibility. PMID:20208995
Contribution of charged and polar residues for the formation of the E1-E2 heterodimer from Hepatitis C Virus. PMID:20195665
Large-scale analyses of glycosylation in cellulases. PMID:20172492
BisoGenet: a new tool for gene network building, visualization and analysis. PMID:20163717
Ontology engineering. PMID:20139945
Automatic assignment of EC numbers. PMID:20126531
Cooperativity within proximal phosphorylation sites is revealed from large-scale proteomics data. PMID:20100358
TollML: a database of toll-like receptor structural motifs. PMID:20084417
Domain organization of long autotransporter signal sequences. PMID:20072671
Microarray data analysis of gene expression evolution. PMID:20054404
Expansion of tandem repeats in sea anemone Nematostella vectensis proteome: A source for gene novelty? PMID:20003297
The Pfam protein families database. PMID:19920124
A threading-based method for the prediction of DNA-binding proteins with application to the human genome. PMID:19911048
Significant speedup of database searches with HMMs by search space reduction with PSSM family models. PMID:19828575
HPD: an online integrated human pathway database enabling systems biology studies. PMID:19811689
Francisella tularensis novicida proteomic and transcriptomic data integration and annotation based on semantic web technologies. PMID:19796400
Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb. PMID:19758468
A new set of ESTs and cDNA clones from full-length and normalized libraries for gene discovery and functional characterization in citrus. PMID:19747386
ZifBASE: a database of zinc finger proteins and associated resources. PMID:19737425
Context-driven discovery of gene cassettes in mobile integrons using a computational grammar. PMID:19735578
Comparison of structure-based and threading-based approaches to protein functional annotation. PMID:19731377
Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. PMID:19654296
Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis. PMID:19653905
A tool for calculating binding-site residues on proteins from PDB structures. PMID:19650927
HAPPI: an online database of comprehensive human annotated and predicted protein interactions. PMID:19594875
Prediction of DNA-binding residues from protein sequence information using random forests. PMID:19594868
Run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting Bartonella grahamii. PMID:19578403
mGene: accurate SVM-based gene finding with an application to nematode genomes. PMID:19564452
Common ancestry of the CENP-A chaperones Scm3 and HJURP. PMID:19563746
Structural implication of splicing stochastics. PMID:19528068
Genomic analyses reveal a conserved glutathione homeostasis pathway in the invertebrate chordate Ciona intestinalis. PMID:19470804
Public databases and software for the pathway analysis of cancer genomes. PMID:19455256
Connecting protein interaction data, mutations, and disease using bioinformatics. PMID:19381537
A kernel for open source drug discovery in tropical diseases. PMID:19381286
LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. PMID:19369493
Functional annotation of two new carboxypeptidases from the amidohydrolase superfamily of enzymes. PMID:19358546
Partitioning clustering algorithms for protein sequence data sets. PMID:19341454
SCGPred: a score-based method for gene structure prediction by combining multiple sources of evidence. PMID:19329068
Phylogenetic analysis, subcellular localization, and expression patterns of RPD3/HDA1 family histone deacetylases in plants. PMID:19327164
FINDSITE: a combined evolution/structure-based approach to protein function prediction. PMID:19324930
Integrating T-cell epitope annotations with sequence and structural information using DAS. PMID:19238238
Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. PMID:19219566
HistoneHits: a database for histone mutations and their phenotypes. PMID:19218532
Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information. PMID:19213741
Prediction of interactions between HIV-1 and human proteins by information integration. PMID:19209727
MitoMiner, an integrated database for the storage and analysis of mitochondrial proteomics data. PMID:19208617
Metadata mapping and reuse in caBIG. PMID:19208192
A comparative chemogenomics strategy to predict potential drug targets in the metazoan pathogen, Schistosoma mansoni. PMID:19198654
Next generation tools for the annotation of human SNPs. PMID:19181721
Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance. PMID:19175938
Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology. PMID:19154573
Protein structure homology modeling using SWISS-MODEL workspace. PMID:19131951
OxyGene: an innovative platform for investigating oxidative-response genes in whole prokaryotic genomes. PMID:19117520
POLAR MAPPER: a computational tool for integrated visualization of protein interaction networks and mRNA expression data. PMID:19091689
Classifying Variants of Undetermined Significance in BRCA2 with protein likelihood ratios. PMID:19043619
LRRML: a conformational database and an XML description of leucine-rich repeats (LRRs). PMID:18986514
In silico identification of specialized secretory-organelle proteins in apicomplexan parasites and in vivo validation in Toxoplasma gondii. PMID:18974850
The database of experimentally supported targets: a functional update of TarBase. PMID:18957447
MODBASE, a database of annotated comparative protein structure models and associated resources. PMID:18948282
TMFunction: database for functional residues in membrane proteins. PMID:18842639
Mutations in CHD7, encoding a chromatin-remodeling protein, cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome. PMID:18834967
Overview of BioCreative II gene normalization. PMID:18834494
PharmGKB: an integrated resource of pharmacogenomic data and knowledge. PMID:18819074
Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information. PMID:18818722
MAP20, a microtubule-associated protein in the secondary cell walls of hybrid aspen, is a target of the cellulose synthesis inhibitor 2,6-dichlorobenzonitrile. PMID:18805954
Integrating protein-protein interactions and text mining for protein function prediction. PMID:18673526
Domain organization of long signal peptides of single-pass integral membrane proteins reveals multiple functional capacity. PMID:18648515
MSDmotif: exploring protein sites and motifs. PMID:18637174
Taxonomic distribution of large DNA viruses in the sea. PMID:18598358
RAWUL: a new ubiquitin-like domain in PRC1 ring finger proteins that unveils putative plant and worm PRC1 orthologs. PMID:18588675
AMYPdb: a database dedicated to amyloid precursor proteins. PMID:18544157
X-ray structure of ILL2, an auxin-conjugate amidohydrolase from Arabidopsis thaliana. PMID:18543330
Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus. PMID:18522720
Calling on a million minds for community annotation in WikiProteins. PMID:18507872
PROMALS3D web server for accurate multiple protein sequence and structure alignments. PMID:18503087
Targeting the human cancer pathway protein interaction network by structural genomics. PMID:18487680
Identification of guanylate cyclases and related signaling proteins in sperm tail from sea stars by mass spectrometry. PMID:18461395
A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences. PMID:18460207
Metrics for GO based protein semantic similarity: a systematic evaluation. PMID:18460186
Expression patterns in soybean resistant to Phakopsora pachyrhizi reveal the importance of peroxidases and lipoxygenases. PMID:18414911
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. PMID:18414481
DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture. PMID:18411203
Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface? PMID:18395225
Annotating genes of known and unknown function by large-scale coexpression analysis. PMID:18354039
Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria. PMID:18348319
Antarctic marine molluscs do have an HSP70 heat shock response. PMID:18347940
Bioinformatics prediction of overlapping frameshifted translation products in mammalian transcripts. PMID:18325113
Isoelectric points of multi-domain proteins. PMID:18292801
PROMALS3D: a tool for multiple protein sequence and structure alignments. PMID:18287115
Analysis of the human kinome using methods including fold recognition reveals two novel kinases. PMID:18270584
Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction. PMID:18267018
A genomic view of the NOD-like receptor family in teleost fish: identification of a novel NLR subfamily in zebrafish. PMID:18254971
Universal seeds for cDNA-to-genome comparison. PMID:18215286
Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus. PMID:18215275
Marine mimivirus relatives are probably large algal viruses. PMID:18215256
Gene characterization index: assessing the depth of gene annotation. PMID:18213364
Protein interactions in human genetic diseases. PMID:18199329
Broad and Gag-biased HIV-1 epitope repertoires are associated with lower viral loads. PMID:18183304
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. PMID:18165317
Estimating the length of transmembrane helices using Z-coordinate predictions. PMID:18096645
TreeFam: 2008 Update. PMID:18056084
Alternative splicing and protein structure evolution. PMID:18055499
EndoNet: an information resource about regulatory networks of cell-to-cell communication. PMID:18045786
SIMAP--structuring the network of protein similarities. PMID:18037617
Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome. PMID:18021451
MEROPS: the peptidase database. PMID:17991683
An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data. PMID:17984082
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. PMID:17980028
Search of the human proteome for endomorphin-1 and endomorphin-2 precursor proteins. PMID:17964607
Identifying the subproteome of kinetically stable proteins via diagonal 2D SDS/PAGE. PMID:17956990
Multidimensional annotation of the Escherichia coli K-12 genome. PMID:17940092
AutoPSI: a database for automatic structural classification of protein sequences and structures. PMID:17932066
GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. PMID:17932055
FunSimMat: a comprehensive functional similarity database. PMID:17932054
PFAAT version 2.0: a tool for editing, annotating, and analyzing multiple sequence alignments. PMID:17931421
An EST database from saffron stigmas. PMID:17925031
PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation. PMID:17916232
BNDB - the Biochemical Network Database. PMID:17910766
The Edinburgh human metabolic network reconstruction and its functional analysis. PMID:17882155
Rod-derived Cone Viability Factor-2 is a novel bifunctional-thioredoxin-like protein with therapeutic potential. PMID:17764561
Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton. PMID:17727702
Quantitative assessment of protein function prediction from metagenomics shotgun sequences. PMID:17717083
Predicting active site residue annotations in the Pfam database. PMID:17688688
PepBank--a database of peptides based on sequence text mining and public peptide data sources. PMID:17678535
Introduction to computational proteomics. PMID:17676979
Unique genes in giant viruses: regular substitution pattern and anomalously short size. PMID:17652424
Reuse of structural domain-domain interactions in protein networks. PMID:17640363
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. PMID:17631615
HoxPred: automated classification of Hox proteins using combinations of generalised profiles. PMID:17626621
The Schistosoma mansoni transcriptome: an update. PMID:17624328
Probabilistic prediction and ranking of human protein-protein interactions. PMID:17615067
FlyMine: an integrated database for Drosophila and Anopheles genomics. PMID:17615057
Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate. PMID:17592630
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. PMID:17576678
CORRIE: enzyme sequence annotation with confidence estimates. PMID:17570146
MyHits: improvements to an interactive resource for analyzing protein sequences. PMID:17545200
A novel view of the transcriptome revealed from gene trapping in mouse embryonic stem cells. PMID:17540781
Chemogenomic approaches to rational drug design. PMID:17533416
SNAP: predict effect of non-synonymous polymorphisms on function. PMID:17526529
A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database. PMID:17521420
3D-partner: a web server to infer interacting partners and binding models. PMID:17517763
Plant SET domain-containing proteins: structure, function and regulation. PMID:17512990
caCORE version 3: Implementation of a model driven, service-oriented architecture for semantic interoperability. PMID:17512259
Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccines. PMID:17508277
Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution. PMID:17506888
Advancing translational research with the Semantic Web. PMID:17493285
Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins. PMID:17480235
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. PMID:17478504
PROMALS web server for accurate multiple protein sequence alignments. PMID:17452345
cTFbase: a database for comparative genomics of transcription factors in cyanobacteria. PMID:17439663
Statistical analysis of genomic protein family and domain controlled annotations for functional investigation of classified gene lists. PMID:17430558
A kingdom-specific protein domain HMM library for improved annotation of fungal genomes. PMID:17425790
From genes to functional classes in the study of biological systems. PMID:17407596
Gene function in early mouse embryonic stem cell differentiation. PMID:17394647
HitKeeper, a generic software package for hit list management. PMID:17391514
Comparative Bioinformatics Analyses and Profiling of Lysosome-Related Organelle Proteomes. PMID:17375895
The implications of alternative splicing in the ENCODE protein complement. PMID:17372197
The folding mechanics of a knotted protein. PMID:17368671
Reactome: a knowledge base of biologic pathways and processes. PMID:17367534
Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint. PMID:17349043
GOTax: investigating biological processes and biochemical activities along the taxonomic tree. PMID:17346342
A phylogenomic analysis of the Actinomycetales mce operons. PMID:17324287
Blast sampling for structural and functional analyses. PMID:17319945
Functional impact of missense variants in BRCA1 predicted by supervised learning. PMID:17305420
SCOOP: a simple method for identification of novel protein superfamily relationships. PMID:17277330
Evaluation and comparison of mammalian subcellular localization prediction methods. PMID:17254308
Mouse SNP Miner: an annotated database of mouse functional single nucleotide polymorphisms. PMID:17239255
BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. PMID:17202167
New developments in the InterPro database. PMID:17202162
Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium. PMID:17170010
The Molecular Biology Database Collection: 2007 update. PMID:17148484
EMBL Nucleotide Sequence Database in 2006. PMID:17148479
Ensembl 2007. PMID:17148474
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. PMID:17145713
PATRIC: the VBI PathoSystems Resource Integration Center. PMID:17142235
euHCVdb: the European hepatitis C virus database. PMID:17142229
The UCSC genome browser database: update 2007. PMID:17142222
AgBase: a unified resource for functional analysis in agriculture. PMID:17135208
Snap: an integrated SNP annotation platform. PMID:17135198
Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence. PMID:17134515
ArrayExpress--a public database of microarray experiments and gene expression profiles. PMID:17132828
The mouse Gene Expression Database (GXD): 2007 update. PMID:17130151
PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. PMID:17130144
EVEREST: a collection of evolutionary conserved protein domains. PMID:17099230
The SUPERFAMILY database in 2007: families and functions. PMID:17098927
MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes. PMID:17090601
The Sulfolobus database. PMID:17088281
PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification. PMID:16973001
Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors. PMID:16972168
Localization of binding sites in protein structures by optimization of a composite scoring function. PMID:16963645
Incorporating background frequency improves entropy-based residue conservation measures. PMID:16916457
ProSAT2--Protein Structure Annotation Server. PMID:16845114
JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information. PMID:16845060
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. PMID:16845052
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. PMID:16845026
YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms. PMID:16845020
DOUTfinder--identification of distant domain outliers using subsignificant sequence similarity. PMID:16844996
Cluster analysis of protein array results via similarity of Gene Ontology annotation. PMID:16836750
Quantitative assessment of dictionary-based protein named entity tagging. PMID:16799122
MACSIMS: multiple alignment of complete sequences information management system. PMID:16792820
A new measure for functional similarity of gene products based on Gene Ontology. PMID:16776819
High throughput profile-profile based fold recognition for the entire human proteome. PMID:16759376
EVEREST: automatic identification and classification of protein domains in all protein sequences. PMID:16749920
EMBL Nucleotide Sequence Database: developments in 2005. PMID:16381823 -
The universal protein resource (UniProt)
PubMed citations: 430.
430 articles citing: The universal protein resource (UniProt)
Deciphering Isoniazid Drug Resistance Mechanisms on Dimeric Mycobacterium tuberculosis KatG via Post-molecular Dynamics Analyses Including Combined Dynamic Residue Network Metrics. PMID:35474779
Lipid Peroxidation Induced ApoE Receptor-Ligand Disruption as a Unifying Hypothesis Underlying Sporadic Alzheimer's Disease in Humans. PMID:35466940
Cytotoxic Bioxanthracene and Macrocyclic Polyester from Endolichenic Fungus Talaromyces pinophilus: In-Vitro and In-Silico Analysis. PMID:35462704
A Web Application for Biomedical Text Mining of Scientific Literature Associated with Coronavirus-Related Syndromes: Coronavirus Finder. PMID:35453935
Simulation Testbed for Evaluating Distributed Querying and Searching of Mass Spectrometry Big Data in a Network-based Infrastructure. PMID:35425943
Machine learning to navigate fitness landscapes for protein engineering. PMID:35413604
Protein design via deep learning. PMID:35348602
Genetic alteration of human MYH6 is mimicked by SARS-CoV-2 polyprotein: mapping viral variants of cardiac interest. PMID:35314694
Experimental evaluation of ecological principles to understand and modulate the outcome of bacterial strain competition in gut microbiomes. PMID:35210551
Heterotypic Amyloid β interactions facilitate amyloid assembly and modify amyloid structure. PMID:34842295
Regulation of ER Composition and Extent, and Putative Action in Protein Networks by ER/NE Protein TMEM147. PMID:34638576
The Gossypium anomalum genome as a resource for cotton improvement and evolutionary analysis of hybrid incompatibility. PMID:34549783
Differential expression gene/protein contribute to heat stress-responsive in Tetraena propinqua in Saudi Arabia. PMID:34466077
A computational study on hydroxychloroquine binding to target proteins related to SARS-COV-2 infection. PMID:34458558
Functional meta-omics provide critical insights into long- and short-read assemblies. PMID:34453168
Genome Analysis of Phytophthora nicotianae JM01 Provides Insights into Its Pathogenicity Mechanisms. PMID:34451665
The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns. PMID:34305969
Evaluation of Indigenous Olive Biocontrol Rhizobacteria as Protectants against Drought and Salt Stress. PMID:34204989
Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry. PMID:34201152
Identification of Somatic Gene Signatures in Circulating Cell-Free DNA Associated with Disease Progression in Metastatic Prostate Cancer by a Novel Machine Learning Platform. PMID:34157173
Toward the solution of the protein structure prediction problem. PMID:34119522
Force Field Parameters for Fe2+4S2-4 Clusters of Dihydropyrimidine Dehydrogenase, the 5-Fluorouracil Cancer Drug Deactivation Protein: A Step towards In Silico Pharmacogenomics Studies. PMID:34069161
Draft genome sequence of the pulse crop blackgram [Vigna mungo (L.) Hepper] reveals potential R-genes. PMID:34045617
Computational modeling and bioinformatic analyses of functional mutations in drug target genes in Mycobacterium tuberculosis. PMID:34025934
Thousands of protein linear motif classes may still be undiscovered. PMID:33939703
In Silico Study of Mutational Stability of SARS-CoV-2 Proteins. PMID:33890205
Reverse vaccinology and subtractive genomics approaches for identifying common therapeutics against Mycobacterium leprae and Mycobacterium lepromatosis. PMID:33889182
Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences. PMID:33876751
The Gossypium stocksii genome as a novel resource for cotton improvement. PMID:33871013
Potential combination therapy using twenty phytochemicals from twenty plants to prevent SARS- CoV-2 infection: An in silico Approach. PMID:33842675
Computational approach to decipher cellular interactors and drug targets during co-infection of SARS-CoV-2, Dengue, and Chikungunya virus. PMID:33723515
Decoding the Molecular Effects of Atovaquone Linked Resistant Mutations on Plasmodium falciparum Cytb-ISP Complex in the Phospholipid Bilayer Membrane. PMID:33670016
Homologies between SARS-CoV-2 and allergen proteins may direct T cell-mediated heterologous immune responses. PMID:33637823
An empirical meta-analysis of the life sciences linked open data on the web. PMID:33479214
Essential interpretations of bioinformatics in COVID-19 pandemic. PMID:33349792
Identifying diseases that cause psychological trauma and social avoidance by GCN-Xgboost. PMID:33323103
Structural insights and evaluation of the potential impact of missense variants on the interactions of SLIT2 with ROBO1/4 in cancer progression. PMID:33318575
Differential expression between drought-tolerant and drought-sensitive sugarcane under mild and moderate water stress as revealed by a comparative analysis of leaf transcriptome. PMID:33240580
Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery. PMID:33206037
Homologies between SARS-CoV-2 and allergen proteins may direct T cell-mediated heterologous immune responses. PMID:33052330
The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering. PMID:33015004
Binding Modes and Selectivity of Cannabinoid 1 (CB1) and Cannabinoid 2 (CB2) Receptor Ligands. PMID:32997485
Genome-wide association study identifies 48 common genetic variants associated with handedness. PMID:32989287
Integrated Metabolic Modeling, Culturing, and Transcriptomics Explain Enhanced Virulence of Vibrio cholerae during Coinfection with Enterotoxigenic Escherichia coli. PMID:32900868
Dorsoventral inversion of the air-filled organ (lungs, gas bladder) in vertebrates: RNAsequencing of laser capture microdissected embryonic tissue. PMID:32864827
Application of the UHPLC-DIA-HRMS Method for Determination of Cheese Peptides. PMID:32718013
Prediction of Transcription Factors and Their Involvement in Regulating Rifamycin Production in Amycolatopsis mediterranei S699. PMID:32655198
Incorporating hybrid models into lysine malonylation sites prediction on mammalian and plant proteins. PMID:32601280
An Integrated Proteomic and Transcriptomic Analysis Reveals the Venom Complexity of the Bullet Ant Paraponera clavata. PMID:32422990
NEK10 interactome and depletion reveal new roles in mitochondria. PMID:32368190
Computational Modeling and Analysis to Predict Intracellular Parasite Epitope Characteristics Using Random Forest Technique. PMID:32309231
Thermodynamic and Evolutionary Coupling between the Native and Amyloid State of Globular Proteins. PMID:32294448
Bi-allelic LoF NRROS Variants Impairing Active TGF-β1 Delivery Cause a Severe Infantile-Onset Neurodegenerative Condition with Intracranial Calcification. PMID:32197075
Genome Sequences of vB_RleM_RL38JI and vB_RleM_RL2RES, Two Virulent Rhizobium leguminosarum Transducing Phages. PMID:32165392
pH-responsive high stability polymeric nanoparticles for targeted delivery of anticancer therapeutics. PMID:32127636
The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution. PMID:32122962
Current challenges and best-practice protocols for microbiome analysis. PMID:31848574
Identification of B Cell Epitopes of Blo t 13 Allergen and Cross-Reactivity with Human Adipocytes and Heart Fatty Acid Binding Proteins. PMID:31817065
Cell-Wall Hydrolases as Antimicrobials against Staphylococcus Species: Focus on Sle1. PMID:31726796
Short-Term Low Temperature Induces Nitro-Oxidative Stress that Deregulates the NADP-Malic Enzyme Function by Tyrosine Nitration in Arabidopsis thaliana. PMID:31581524
Enabling Web-scale data integration in biomedicine through Linked Open Data. PMID:31531395
A Metabolomics-Inspired Strategy for the Identification of Protein Covalent Modifications. PMID:31417895
Reverse vaccinology and subtractive genomics reveal new therapeutic targets against Mycoplasma pneumoniae: a causative agent of pneumonia. PMID:31417766
Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis). PMID:31357931
Comparative genomics identifies potential virulence factors in Clostridium tertium and C. paraputrificum. PMID:31304854
Novel de novo frameshift variant in the ASXL3 gene in a child with microcephaly and global developmental delay. PMID:31180560
Vitellogenin Receptor as a Target for Tick Control: A Mini-Review. PMID:31178755
DiVenn: An Interactive and Integrated Web-Based Visualization Tool for Comparing Gene Lists. PMID:31130993
ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism. PMID:31114881
Remodeling of ER-plasma membrane contact sites but not STIM1 phosphorylation inhibits Ca2+ influx in mitosis. PMID:31064875
Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model. PMID:31060515
Targeted, High-Resolution RNA Sequencing of Non-coding Genomic Regions Associated With Neuropsychiatric Functions. PMID:31031799
Genome sequence analysis of the fairy ring-forming fungus Lepista sordida and gene candidates for interaction with plants. PMID:30971747
TriPepSVM: de novo prediction of RNA-binding proteins based on short amino acid motifs. PMID:30923827
Differential proteostatic regulation of insoluble and abundant proteins. PMID:30903148
OGER++: hybrid multi-type entity recognition. PMID:30666476
TogoGenome/TogoStanza: modularized Semantic Web genome database. PMID:30624651
The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain. PMID:30443017
A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference. PMID:30408409
Precisely measured protein lifetimes in the mouse brain reveal differences across tissues and subcellular fractions. PMID:30315172
Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging. PMID:30309375
Genome-scale analysis of Acetobacterium bakii reveals the cold adaptation of psychrotolerant acetogens by post-transcriptional regulation. PMID:30249742
Development of sequence-based markers for seed protein content in pigeonpea. PMID:30173295
The NAD+ Salvage Pathway Supports PHGDH-Driven Serine Biosynthesis. PMID:30157431
A molecular simulation analysis of vitamin D targets interleukin 13 (IL13) as an alternative to mometasone in asthma. PMID:30105198
Consistent prediction of GO protein localization. PMID:29773825
Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. PMID:29684165
IreA Controls Endoplasmic Reticulum Stress-Induced Autophagy and Survival through Homeostasis Recovery. PMID:29632077
Computational modeling suggests impaired interactions between NKX2.5 and GATA4 in individuals carrying a novel pathogenic D16N NKX2.5 mutation. PMID:29568389
Indigenous Pseudomonas spp. Strains from the Olive (Olea europaea L.) Rhizosphere as Effective Biocontrol Agents against Verticillium dahliae: From the Host Roots to the Bacterial Genomes. PMID:29527195
Aggregating sequences that occur in many proteins constitute weak spots of bacterial proteostasis. PMID:29491361
Ligand-induced perturbation of the HIF-2α:ARNT dimer dynamics. PMID:29489822
Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat. PMID:29459707
Constructing an integrated gene similarity network for the identification of disease genes. PMID:29297379
Structural and functional annotation of hypothetical proteins of human adenovirus: prioritizing the novel drug targets. PMID:29212526
Interplay of neuronal and non-neuronal genes regulates intestinal DAF-16-mediated immune response during Fusarium infection of Caenorhabditis elegans. PMID:29152379
Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction. PMID:29145825
High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds. PMID:29115919
Early emergence of negative regulation of the tyrosine kinase Src by the C-terminal Src kinase. PMID:28939764
Molecular Resources from Transcriptomes in the Brassicaceae Family. PMID:28900436
Docking-based modeling of protein-protein interfaces for extensive structural and functional characterization of missense mutations. PMID:28841721
Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems. PMID:28821820
BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation. PMID:28750104
Metabolic modeling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification. PMID:28691262
Disease-associated mitochondrial mutations and the evolution of primate mitogenomes. PMID:28510580
Substitutional Analysis of Orthologous Protein Families Using BLOCKS. PMID:28479743
Analysis of Ebola virus polymerase domains to find strain-specific differences and to gain insight on their pathogenicity. PMID:28466035
Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5. PMID:28432541
Deep mining heterogeneous networks of biomedical linked data to predict novel drug-target associations. PMID:28430977
Structural characterization of core-bradavidin in complex with biotin. PMID:28426764
HopBase: a unified resource for Humulus genomics. PMID:28415075
Superoxide dismutase 1 is positively selected to minimize protein aggregation in great apes. PMID:28389720
VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology. PMID:28193166
Cancer Stem Cells Therapeutic Target Database: The First Comprehensive Database for Therapeutic Targets of Cancer Stem Cells. PMID:28191780
Genomic analysis of four strains of Corynebacterium pseudotuberculosis bv. Equi isolated from horses showing distinct signs of infection. PMID:28163825
Pretata: predicting TATA binding proteins with novel features and dimensionality reduction strategy. PMID:28155714
Aberrant coordination geometries discovered in the most abundant metalloproteins. PMID:28142195
Molecular and Proteomic Analysis of Levofloxacin and Metronidazole Resistant Helicobacter pylori. PMID:28018334
Recent Progress in Machine Learning-Based Methods for Protein Fold Recognition. PMID:27999256
Versatile, sensitive liquid chromatography mass spectrometry - Implementation of 10 μm OT columns suitable for small molecules, peptides and proteins. PMID:27897190
Text mining resources for the life sciences. PMID:27888231
Chemogenomics knowledgebase and systems pharmacology for hallucinogen target identification-Salvinorin A as a case study. PMID:27810775
Protein Translation Enzyme lysyl-tRNA Synthetase Presents a New Target for Drug Development against Causative Agents of Loiasis and Schistosomiasis. PMID:27806050
Associations of the calcium-sensing receptor gene CASR rs7652589 SNP with nephrolithiasis and secondary hyperparathyroidism in haemodialysis patients. PMID:27739473
Transcriptome and Metabolite analysis reveal candidate genes of the cardiac glycoside biosynthetic pathway from Calotropis procera. PMID:27703261
Interaction Analysis of T7 RNA Polymerase with Heparin and Its Low Molecular Weight Derivatives - An In Silico Approach. PMID:27594785
Phage display and structural studies reveal plasticity in substrate specificity of caspase-3a from zebrafish. PMID:27577093
A Gram-Negative Bacterial Secreted Protein Types Prediction Method Based on PSI-BLAST Profile. PMID:27563663
Characterization and Expression Analysis of PtAGL24, a SHORT VEGETATIVE PHASE/AGAMOUS-LIKE 24 (SVP/AGL24)-Type MADS-Box Gene from Trifoliate Orange (Poncirus trifoliata L. Raf.). PMID:27375669
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles. PMID:27319297
STRUM: structure-based prediction of protein stability changes upon single-point mutation. PMID:27318206
Structure-based prediction of transcription factor binding specificity using an integrative energy function. PMID:27307632
Consensus protein design. PMID:27274091
Horizontal gene transfer events reshape the global landscape of arm race between viruses and homo sapiens. PMID:27270140
Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities. PMID:27199908
Enteroviral proteases: structure, host interactions and pathogenicity. PMID:27145174
Inhibitor Discovery for the Human GLUT1 from Homology Modeling and Virtual Screening. PMID:27128978
RaptorX-Property: a web server for protein structure property prediction. PMID:27112573
Proteomic Responses of Switchgrass and Prairie Cordgrass to Senescence. PMID:27014316
Transcriptomic Analysis Using Olive Varieties and Breeding Progenies Identifies Candidate Genes Involved in Plant Architecture. PMID:26973682
Bridging semantics and syntax with graph algorithms-state-of-the-art of extracting biomedical relations. PMID:26851224
Amino acids in the cultivation of mammalian cells. PMID:26832172
The mechanism of the effect of U18666a on blocking the activity of 3β-hydroxysterol Δ-24-reductase (DHCR24): molecular dynamics simulation study and free energy analysis. PMID:26815033
Systems-Pharmacology Dissection of Traditional Chinese Medicine Compound Saffron Formula Reveals Multi-scale Treatment Strategy for Cardiovascular Diseases. PMID:26813334
Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields. PMID:26752681
Purification and Characterization of Suicin 65, a Novel Class I Type B Lantibiotic Produced by Streptococcus suis. PMID:26709705
Improving Protein Fold Recognition by Deep Learning Networks. PMID:26634993
Differential roles of the hemerythrin-like proteins of Mycobacterium smegmatis in hydrogen peroxide and erythromycin susceptibility. PMID:26607739
Cross-omics comparison of stress responses in mesothelial cells exposed to heat- versus filter-sterilized peritoneal dialysis fluids. PMID:26495307
DIDA: A curated and annotated digenic diseases database. PMID:26481352
Predicting the Functional Types of Singleplex and Multiplex Eukaryotic Membrane Proteins via Different Models of Chou's Pseudo Amino Acid Compositions. PMID:26458844
Exploring the potential of public proteomics data. PMID:26449181
NhaA antiporter functions using 10 helices, and an additional 2 contribute to assembly/stability. PMID:26417087
An eigenvalue transformation technique for predicting drug-target interaction. PMID:26350590
Computational approaches to study the effects of small genomic variations. PMID:26350246
Functional and Structural Consequences of Damaging Single Nucleotide Polymorphisms in Human Prostate Cancer Predisposition Gene RNASEL. PMID:26236721
Curcumin Resource Database. PMID:26220923
Insights into Protein Structure and Dynamics by Ultraviolet and Visible Resonance Raman Spectroscopy. PMID:26219819
Identification of genomic regions involved in tolerance to drought stress and drought stress induced leaf senescence in juvenile barley. PMID:25998066
Rv2031c of Mycobacterium tuberculosis: a master regulator of Rv2028-Rv2031 (HspX) operon. PMID:25964780
BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ. PMID:25960870
CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis. PMID:25833954
Active site and laminarin binding in glycoside hydrolase family 55. PMID:25752603
Suicin 3908, a new lantibiotic produced by a strain of Streptococcus suis serotype 2 isolated from a healthy carrier pig. PMID:25659110
Annotation of proteins of unknown function: initial enzyme results. PMID:25630330
Systematic characterization and prediction of post-translational modification cross-talk. PMID:25605461
Toxicoproteomic analysis of pulmonary carbon nanotube exposure using LC-MS/MS. PMID:25598225
Analysis of signaling networks distributed over intracellular compartments based on protein-protein interactions. PMID:25564293
The ins and outs of metal homeostasis by the root nodule actinobacterium Frankia. PMID:25495525
Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors. PMID:25478866
A new multi-label classifier in identifying the functional types of human membrane proteins. PMID:25433431
Text mining in cancer gene and pathway prioritization. PMID:25392685
The influence of selection for protein stability on dN/dS estimations. PMID:25355808
FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus. PMID:25260589
Neighbor preferences of amino acids and context-dependent effects of amino acid substitutions in human, mouse, and dog. PMID:25210846
PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data. PMID:25177766
Suicin 90-1330 from a nonvirulent strain of Streptococcus suis: a nisin-related lantibiotic active on gram-positive swine pathogens. PMID:24973067
The molecular mechanisms of Tanshinone IIA on the apoptosis and arrest of human esophageal carcinoma cells. PMID:24829906
Transcriptome analysis of differentially expressed genes relevant to variegation in peach flowers. PMID:24603808
The natural diyne-furan fatty acid EV-086 is an inhibitor of fungal delta-9 fatty acid desaturation with efficacy in a model of skin dermatophytosis. PMID:24189258
Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank. PMID:24173824
Proteomic profiling of sea bass muscle by two-dimensional gel electrophoresis and tandem mass spectrometry. PMID:24057758
Decreased transcriptional activity of calcium-sensing receptor gene promoter 1 is associated with calcium nephrolithiasis. PMID:23864702
Approaching the 5-HT₃ receptor heterogeneity by computational studies of the transmembrane and intracellular domains. PMID:23771549
Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach. PMID:23617634
N-glycoprotein SRMAtlas: a resource of mass spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications. PMID:23408683
Complete genome sequence of Oscillibacter valericigenes Sjm18-20(T) (=NBRC 101213(T)). PMID:23408234
Analysis of Expressed Sequence Tags from Chinese Bayberry Fruit (Myrica rubra Sieb. and Zucc.) at Different Ripening Stages and Their Association with Fruit Quality Development. PMID:23377019
EuLoc: a web-server for accurately predict protein subcellular localization in eukaryotes by incorporating various features of sequence segments into the general form of Chou's PseAAC. PMID:23283513
C-mii: a tool for plant miRNA and target identification. PMID:23281648
Genome-wide comparison of FGFRL1 with structurally related surface receptors. PMID:23136609
Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. PMID:23061897
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High selectivity of the γ-aminobutyric acid transporter 2 (GAT-2, SLC6A13) revealed by structure-based approach. PMID:22932902
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Rational engineering of enzyme allosteric regulation through sequence evolution analysis. PMID:22807670
GFam: a platform for automatic annotation of gene families. PMID:22790981
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Gene expression and proteomic analysis of the formation of Phakopsora pachyrhizi appressoria. PMID:22727213
New insights into Escherichia coli metabolism: carbon scavenging, acetate metabolism and carbon recycling responses during growth on glycerol. PMID:22513097
Potential T cell epitopes of Mycobacterium tuberculosis that can instigate molecular mimicry against host: implications in autoimmune pathogenesis. PMID:22435930
Acyl carrier protein structural classification and normal mode analysis. PMID:22374859
BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins. PMID:22335941
Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data. PMID:22276131
An NMR-based scoring function improves the accuracy of binding pose predictions by docking by two orders of magnitude. PMID:22167466
Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes. PMID:22166143
In-silico human genomics with GeneCards. PMID:22155609
Prediction of protein tertiary structures using MUFOLD. PMID:22130979
SProtP: a web server to recognize those short-lived proteins based on sequence-derived features in human cells. PMID:22114707
NNAlign: a web-based prediction method allowing non-expert end-user discovery of sequence motifs in quantitative peptide data. PMID:22073191
SMART 7: recent updates to the protein domain annotation resource. PMID:22053084
Conjugating effects of symbionts and environmental factors on gene expression in deep-sea hydrothermal vent mussels. PMID:22034982
The energy landscape analysis of cancer mutations in protein kinases. PMID:21998754
BSP-SLIM: a blind low-resolution ligand-protein docking approach using predicted protein structures. PMID:21971880
Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction. PMID:21955494
Structural classification and properties of ketoacyl synthases. PMID:21830247
A comparative proteome analysis links tyrosine kinase 2 (Tyk2) to the regulation of cellular glucose and lipid metabolism in response to poly(I:C). PMID:21787891
Effects of Elevated Atmospheric CO(2) on Rhizosphere Soil Microbial Communities in a Mojave Desert Ecosystem. PMID:21779135
RASOnD-a comprehensive resource and search tool for RAS superfamily oncogenes from various species. PMID:21729256
Homology modeling, molecular dynamics and QM/MM study of the regulatory protein PhoP from Corynebacterium pseudotuberculosis. PMID:21701810
Proteomic patterns of cervical cancer cell lines, a network perspective. PMID:21696634
Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction. PMID:21609491
An analysis of single amino acid repeats as use case for application specific background models. PMID:21595908
Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement. PMID:21572172
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MAISTAS: a tool for automatic structural evaluation of alternative splicing products. PMID:21498402
Structural models of CFTR-AMPK and CFTR-PKA interactions: R-domain flexibility is a key factor in CFTR regulation. PMID:21455600
New insights into the GABA(A) receptor structure and orthosteric ligand binding: receptor modeling guided by experimental data. PMID:21365676
Mapping protein interactions between Dengue virus and its human and insect hosts. PMID:21358811
A proteomics approach to decipher the molecular nature of planarian stem cells. PMID:21356107
Ontology-based instance data validation for high-quality curated biological pathways. PMID:21342591
Investigating the effect of paralogs on microarray gene-set analysis. PMID:21261946
Calcium oxalate monohydrate aggregation induced by aggregation of desialylated Tamm-Horsfall protein. PMID:21229239
Structural properties of MHC class II ligands, implications for the prediction of MHC class II epitopes. PMID:21209859
SVM-based prediction of linear B-cell epitopes using Bayes Feature Extraction. PMID:21143805
HSPVdb--the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands. PMID:21125265
Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium. PMID:21083885
Insights into metazoan evolution from Alvinella pompejana cDNAs. PMID:21080938
A series of PDB related databases for everyday needs. PMID:21071423
Predicted sub-populations in a marine shrimp proteome as revealed by combined EST and cDNA data from multiple Penaeus species. PMID:21067619
Genome sequence of Kitasatospora setae NBRC 14216T: an evolutionary snapshot of the family Streptomycetaceae. PMID:21059706
Ubiquitin accumulation in autophagy-deficient mice is dependent on the Nrf2-mediated stress response pathway: a potential role for protein aggregation in autophagic substrate selection. PMID:21041446
Verification of alternative splicing variants based on domain integrity, truncation length and intrinsic protein disorder. PMID:20972208
Shotgun proteomic analysis of Emiliania huxleyi, a marine phytoplankton species of major biogeochemical importance. PMID:20924652
Correlated mutations: a hallmark of phenotypic amino acid substitutions. PMID:20862353
HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. PMID:20823849
The genome of the domesticated apple (Malus × domestica Borkh.). PMID:20802477
Comparing interfacial dynamics in protein-protein complexes: an elastic network approach. PMID:20691107
GeneCards Version 3: the human gene integrator. PMID:20689021
The CoFactor database: organic cofactors in enzyme catalysis. PMID:20679331
Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information. PMID:20667087
Plus- and minus-end directed microtubule motors bind simultaneously to herpes simplex virus capsids using different inner tegument structures. PMID:20628567
Annotation of SBML models through rule-based semantic integration. PMID:20626923
Comparative analysis of secreted protein evolution using expressed sequence tags from four poplar leaf rusts (Melampsora spp.). PMID:20615251
Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks. PMID:20585543
F-BAR domain proteins: Families and function. PMID:20585502
A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. PMID:20537162
Thioesterases: a new perspective based on their primary and tertiary structures. PMID:20506386
Analysis of gene order conservation in eukaryotes identifies transcriptionally and functionally linked genes. PMID:20498846
Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network. PMID:20498836
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. PMID:20478830
The transcriptome of the early life history stages of the California Sea Hare Aplysia californica. PMID:20434970
Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens. PMID:20426868
The physiological importance of photosynthetic ferredoxin NADP+ oxidoreductase (FNR) isoforms in wheat. PMID:20410318
A review of the major penaeid shrimp EST studies and the construction of a shrimp transcriptome database based on the ESTs from four penaeid shrimp. PMID:20401624
The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression. PMID:20388198
Low-complexity regions within protein sequences have position-dependent roles. PMID:20385029
Discovery of Phytophthora infestans genes expressed in planta through mining of cDNA libraries. PMID:20352100
Interruptions in the collagen repeating tripeptide pattern can promote supramolecular association. PMID:20340134
Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production. PMID:20307315
Bioinformatic tools for identifying disease gene and SNP candidates. PMID:20238089
A non-tree-based comprehensive study of metazoan Hox and ParaHox genes prompts new insights into their origin and evolution. PMID:20222951
A rapid method for characterization of protein relatedness using feature vectors. PMID:20221427
GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis systems. PMID:20202206
The power of protein interaction networks for associating genes with diseases. PMID:20185403
Identification of 28 novel mutations in the Bardet-Biedl syndrome genes: the burden of private mutations in an extensively heterogeneous disease. PMID:20177705
The porcelain crab transcriptome and PCAD, the porcelain crab microarray and sequence database. PMID:20174471
In situ trans ligands of CD22 identified by glycan-protein photocross-linking-enabled proteomics. PMID:20172905
MIClique: An algorithm to identify differentially coexpressed disease gene subset from microarray data. PMID:20169000
Bioinformatic search of plant microtubule-and cell cycle related serine-threonine protein kinases. PMID:20158871
QuickGO: a user tutorial for the web-based Gene Ontology browser. PMID:20157483
FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology. PMID:20122162
Ginkgolide X is a potent antagonist of anionic Cys-loop receptors with a unique selectivity profile at glycine receptors. PMID:20106969
The quorum-quenching N-acyl homoserine lactone acylase PvdQ is an Ntn-hydrolase with an unusual substrate-binding pocket. PMID:20080736
The proteolytic system of lactic acid bacteria revisited: a genomic comparison. PMID:20078865
Comparison of human solute carriers. PMID:20052679
Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae. PMID:20040079
Large-scale identification of odorant-binding proteins and chemosensory proteins from expressed sequence tags in insects. PMID:20034407
DDIT3/CHOP and the sarcoma fusion oncoprotein FUS-DDIT3/TLS-CHOP bind cyclin-dependent kinase 2. PMID:20017906
Target-decoy search strategy for mass spectrometry-based proteomics. PMID:20013364
Bi-directional SIFT predicts a subset of activating mutations. PMID:20011534
Multiple genetic mechanisms lead to loss of functional TbAT1 expression in drug-resistant trypanosomes. PMID:19966032
3PFDB--a database of best representative PSSM profiles (BRPs) of protein families generated using a novel data mining approach. PMID:19961575
Network-based Identification of novel cancer genes. PMID:19959820
Multifunctional basic motif in the glycine receptor intracellular domain induces subunit-specific sorting. PMID:19959465
A multi-factor model for caspase degradome prediction. PMID:19958504
PDbase: a database of Parkinson's disease-related genes and genetic variation using substantia nigra ESTs. PMID:19958497
454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involved in biosynthesis of cyanogenic glucosides. PMID:19954531
Regulation of Dauer formation by O-GlcNAcylation in Caenorhabditis elegans. PMID:19940149
MUFOLD: A new solution for protein 3D structure prediction. PMID:19927325
Toward a quantitative theory of intrinsically disordered proteins and their function. PMID:19903882
CUCU modification of mRNA promotes decapping and transcript degradation in Aspergillus nidulans. PMID:19901075
Mapping of disulfide bonds within the amino-terminal extracellular domain of the inhibitory glycine receptor. PMID:19861413
Structure and signaling mechanism of Per-ARNT-Sim domains. PMID:19836329
Sequence and structure signatures of cancer mutation hotspots in protein kinases. PMID:19834613
Coevolution between a family of parasite virulence effectors and a class of LINE-1 retrotransposons. PMID:19829700
Systematic characterisation of cellular localisation and expression profiles of proteins containing MHC ligands. PMID:19826487
Hydrogen bonding and solvent polarity markers in the uv resonance raman spectrum of tryptophan: application to membrane proteins. PMID:19817473
Exploratory visual analysis of conserved domains on multiple sequence alignments. PMID:19811691
KA-SB: from data integration to large scale reasoning. PMID:19796402
BioGateway: a semantic systems biology tool for the life sciences. PMID:19796395
The interwinding nature of protein-protein interfaces and its implication for protein complex formation. PMID:19789269
Comparative characterization of a temperature responsive gene (lactate dehydrogenase-B, ldh-b) in two congeneric tropical fish, Lates calcarifer and Lates niloticus. PMID:19787021
Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets. PMID:19779614
Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5. PMID:19775431
From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways. PMID:19758470
Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models. PMID:19756152
Global changes in the transcript and metabolic profiles during symbiotic nitrogen fixation in phosphorus-stressed common bean plants. PMID:19755543
Saint: a lightweight integration environment for model annotation. PMID:19734151
Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development. PMID:19709400
A comparative genomics, network-based approach to understanding virulence in Vibrio cholerae. PMID:19666715
MicroPC (microPC): A comprehensive resource for predicting and comparing plant microRNAs. PMID:19660144
The cellulose synthase superfamily in fully sequenced plants and algae. PMID:19646250
Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing. PMID:19646242
Pathway databases and tools for their exploitation: benefits, current limitations and challenges. PMID:19638971
Comparative genomic sequence analysis of novel Helicoverpa armigera nucleopolyhedrovirus (NPV) isolated from Kenya and three other previously sequenced Helicoverpa spp. NPVs. PMID:19634008
Modern homology modeling of G-protein coupled receptors: which structural template to use? PMID:19627087
Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome. PMID:19625614
The transcriptional response of Pasteurella multocida to three classes of antibiotics. PMID:19607655
The Schistosoma japonicum genome reveals features of host-parasite interplay. PMID:19606140
GALT protein database, a bioinformatics resource for the management and analysis of structural features of a galactosemia-related protein and its mutants. PMID:19591794
DDEC: Dragon database of genes implicated in esophageal cancer. PMID:19580656
libAnnotationSBML: a library for exploiting SBML annotations. PMID:19561017
Kank proteins: structure, functions and diseases. PMID:19554261
7TMRmine: a Web server for hierarchical mining of 7TMR proteins. PMID:19538753
A chemogenomics view on protein-ligand spaces. PMID:19534738
The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti. PMID:19531251
Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits. PMID:19527659
PSI-2: structural genomics to cover protein domain family space. PMID:19523904
Generation and analysis of transcriptomic resources for a model system on the rise: the sea anemone Aiptasia pallida and its dinoflagellate endosymbiont. PMID:19500365
Structure of the ternary complex of phosphomevalonate kinase: the enzyme and its family. PMID:19485344
The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process. PMID:19480664
PathExpress update: the enzyme neighbourhood method of associating gene-expression data with metabolic pathways. PMID:19474337
A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism. PMID:19454033
Two distinct pathways for metabolism of theophylline and caffeine are coexpressed in Pseudomonas putida CBB5. PMID:19447909
Characterization of the prohormone complement in cattle using genomic libraries and cleavage prediction approaches. PMID:19445702
Infrastructure for the life sciences: design and implementation of the UniProt website. PMID:19426475
TGF-beta signaling proteins and the Protein Ontology. PMID:19426460
BioMart Central Portal--unified access to biological data. PMID:19420058
Protein-protein interaction databases: keeping up with growing interactomes. PMID:19403463
Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors. PMID:19402914
The bovine lactation genome: insights into the evolution of mammalian milk. PMID:19393040
ESTPiper--a web-based analysis pipeline for expressed sequence tags. PMID:19383159
A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. PMID:19373234
Evolution based on domain combinations: the case of glutaredoxins. PMID:19321008
Sequence signatures in envelope protein may determine whether flaviviruses produce hemorrhagic or encephalitic syndromes. PMID:19283462
Identification and quantification of preterm birth biomarkers in human cervicovaginal fluid by liquid chromatography/tandem mass spectrometry. PMID:19271751
Fate of the H-NS-repressed bgl operon in evolution of Escherichia coli. PMID:19266030
Characterization of a beta-glucoside operon (bgc) prevalent in septicemic and uropathogenic Escherichia coli strains. PMID:19233952
Protein function annotation by homology-based inference. PMID:19226439
Somatic, germline and sex hierarchy regulated gene expression during Drosophila metamorphosis. PMID:19216785
Evolutionary history of Na,K-ATPases and their osmoregulatory role. PMID:19214758
Low contents of carbon and nitrogen in highly abundant proteins: evidence of selection for the economy of atomic composition. PMID:19209379
Prediction of protein-protein interaction sites in sequences and 3D structures by random forests. PMID:19180183
A python analytical pipeline to identify prohormone precursors and predict prohormone cleavage sites. PMID:19169350
Genome Projector: zoomable genome map with multiple views. PMID:19166610
Crystallization and preliminary crystallographic analysis of cgHle, a homoserine acetyltransferase homologue, from Corynebacterium glutamicum. PMID:19153452
Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis. PMID:19152684
In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution. PMID:19136663
Adaptive evolution in zinc finger transcription factors. PMID:19119423
Metabolic pathway alignment between species using a comprehensive and flexible similarity measure. PMID:19108747
Prediction of protein-protein binding site by using core interface residue and support vector machine. PMID:19102736
Integrated Bioinformatics for Radiation-Induced Pathway Analysis from Proteomics and Microarray Data. PMID:19088860
Annotating genomes with massive-scale RNA sequencing. PMID:19087247
The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program. PMID:19084081
LRRCE: a leucine-rich repeat cysteine capping motif unique to the chordate lineage. PMID:19077264
Genome-scale models of bacterial metabolism: reconstruction and applications. PMID:19067749
A survey of visualization tools for biological network analysis. PMID:19040716
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. PMID:19033363
Ensembl 2009. PMID:19033362
KEPE--a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors. PMID:19033273
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse. PMID:19015123
CRONOS: the cross-reference navigation server. PMID:19010804
SuperToxic: a comprehensive database of toxic compounds. PMID:19004875
NetMHCpan, a method for MHC class I binding prediction beyond humans. PMID:19002680
Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods. PMID:18996943
PDBsum new things. PMID:18996896
The UCSC Genome Browser Database: update 2009. PMID:18996895
INTERFEROME: the database of interferon regulated genes. PMID:18996892
The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions. PMID:18987007
MoKCa database--mutations of kinases in cancer. PMID:18986996
G2Cdb: the Genes to Cognition database. PMID:18984621
Specificity and reactivity in menaquinone biosynthesis: the structure of Escherichia coli MenD (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase). PMID:18983854
SMART 6: recent updates and new developments. PMID:18978020
Petabyte-scale innovations at the European Nucleotide Archive. PMID:18978013
The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function. PMID:18974821
VirusMINT: a viral protein interaction database. PMID:18974184
Predicting protein post-translational modifications using meta-analysis of proteome scale data sets. PMID:18974045
The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. PMID:18971256
The GOA database in 2009--an integrated Gene Ontology Annotation resource. PMID:18957448
MAPU 2.0: high-accuracy proteomes mapped to genomes. PMID:18948283
ConsensusPathDB--a database for integrating human functional interaction networks. PMID:18940869
InterPro: the integrative protein signature database. PMID:18940856
Strepto-DB, a database for comparative genomics of group A (GAS) and B (GBS) streptococci, implemented with the novel database platform 'Open Genome Resource' (OGeR). PMID:18854354
The dual transcriptional regulator CysR in Corynebacterium glutamicum ATCC 13032 controls a subset of genes of the McbR regulon in response to the availability of sulphide acceptor molecules. PMID:18854009
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. PMID:18849571
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. PMID:18846089
UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. PMID:18842628
The IMGT/HLA database. PMID:18838392
CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens. PMID:18838390
PiSite: a database of protein interaction sites using multiple binding states in the PDB. PMID:18836195
ARDB--Antibiotic Resistance Genes Database. PMID:18832362
Amino acid contacts in proteins adapted to different temperatures: hydrophobic interactions and surface charges play a key role. PMID:18825305
iRefIndex: a consolidated protein interaction database with provenance. PMID:18823568
Structure-guided comparative analysis of proteins: principles, tools, and applications for predicting function. PMID:18818720
MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions. PMID:18786976
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks. PMID:18782832
InnateDB: facilitating systems-level analyses of the mammalian innate immune response. PMID:18766178
Single amino acid substitution in important hemoglobinopathies does not disturb molecular function and biological process. PMID:18686781
Local function conservation in sequence and structure space. PMID:18604264
MPIDB: the microbial protein interaction database. PMID:18556668
Word correlation matrices for protein sequence analysis and remote homology detection. PMID:18522726
GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways. PMID:18511460
Proteome of monocyte priming by lipopolysaccharide, including changes in interleukin-1beta and leukocyte elastase inhibitor. PMID:18492268
VisANT: an integrative framework for networks in systems biology. PMID:18463131
ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks. PMID:18440972
annot8r: GO, EC and KEGG annotation of EST datasets. PMID:18400082
Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. PMID:18039715 -
Update on activities at the Universal Protein Resource (UniProt) in 2013
PubMed citations: 385.
385 articles citing: Update on activities at the Universal Protein Resource (UniProt) in 2013
Pharmacological Effect of GABA Analogues on GABA-ϱ2 Receptors and Their Subtype Selectivity. PMID:35054520
Development of an experiment-split method for benchmarking the generalization of a PTM site predictor: Lysine methylome as an example. PMID:34879076
Decipher the Helicobacter pylori Protein Targeting in the Nucleus of Host Cell and their Implications in Gallbladder Cancer: An insilico approach. PMID:34729122
Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation. PMID:34372938
Heterologous expression of MlcE in Saccharomyces cerevisiae provides resistance to natural and semi-synthetic statins. PMID:34150514
Predicting Protein-Protein Interactions via Gated Graph Attention Signed Network. PMID:34071437
Analysis of human total antibody repertoires in TIF1γ autoantibody positive dermatomyositis. PMID:33772100
Large-scale survey and database of high affinity ligands for peptide recognition modules. PMID:33438817
Quantifying the distribution of protein oligomerization degree reflects cellular information capacity. PMID:33077848
Human SIRT1 Multispecificity Is Modulated by Active-Site Vicinity Substitutions during Natural Evolution. PMID:32956445
HAPPENN is a novel tool for hemolytic activity prediction for therapeutic peptides which employs neural networks. PMID:32616760
Proteomics pinpoints alterations in grade I meningiomas of male versus female patients. PMID:32587372
Computational Proteome-Wide Study for the Prediction of Escherichia coli Protein Targeting in Host Cell Organelles and Their Implication in Development of Colon Cancer. PMID:32280866
HDACi mediate UNG2 depletion, dysregulated genomic uracil and altered expression of oncoproteins and tumor suppressors in B- and T-cell lines. PMID:32264925
Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of Burkholderia cenocepacia J2315 and Other Members of the B. cepacia Complex. PMID:32098200
The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development. PMID:31560649
Collection of antimicrobial peptides database and its derivatives: Applications and beyond. PMID:31441165
Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance. PMID:31311848
A novel mitochondrial micropeptide MPM enhances mitochondrial respiratory activity and promotes myogenic differentiation. PMID:31296841
Shortcomings of Phylogenetic Studies on Recent Radiated Insular Groups: A Meta-Analysis Using Cabo Verde Biodiversity. PMID:31174340
Environmental contaminants modulate the transcriptional activity of polar bear (Ursus maritimus) and human peroxisome proliferator-activated receptor alpha (PPARA). PMID:31061404
Identification of pharmacodynamic biomarker hypotheses through literature analysis with IBM Watson. PMID:30958864
Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE). PMID:30794542
Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community. PMID:30635580
Predicting protein-protein interactions using high-quality non-interacting pairs. PMID:30598096
Synthesis and Biological Evaluation of Novel Triple-Modified Colchicine Derivatives as Potent Tubulin-Targeting Anticancer Agents. PMID:30463236
The EcoCyc Database. PMID:30406744
Kororamides, Convolutamines, and Indole Derivatives as Possible Tau and Dual-Specificity Kinase Inhibitors for Alzheimer's Disease: A Computational Study. PMID:30332805
Production of extracellular lysophosphatidic acid in the regulation of adipocyte functions and liver fibrosis. PMID:30271079
Comparative analysis of prokaryotic and eukaryotic transcription factors using machine-learning techniques. PMID:30237677
Multifunctional Proteins: Involvement in Human Diseases and Targets of Current Drugs. PMID:30123928
Identifying Phage Virion Proteins by Using Two-Step Feature Selection Methods. PMID:30103458
DeCoST: A New Approach in Drug Repurposing From Control System Theory. PMID:29922160
xiSPEC: web-based visualization, analysis and sharing of proteomics data. PMID:29741719
The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution. PMID:29700227
Computational Prediction and Analysis of Associations between Small Molecules and Binding-Associated S-Nitrosylation Sites. PMID:29671802
The BioCyc collection of microbial genomes and metabolic pathways. PMID:29447345
A reverse vaccinology approach to the identification and characterization of Ctenocephalides felis candidate protective antigens for the control of cat flea infestations. PMID:29347954
Computer-Aided Drug Design Applied to Marine Drug Discovery: Meridianins as Alzheimer's Disease Therapeutic Agents. PMID:29186912
Fusing multiple protein-protein similarity networks to effectively predict lncRNA-protein interactions. PMID:29072138
NDFIP allows NEDD4/NEDD4L-induced AQP2 ubiquitination and degradation. PMID:28931009
The PWWP domain of the human oncogene WHSC1L1/NSD3 induces a metabolic shift toward fermentation. PMID:28903324
The Role of Kinase Modulators in Cellular Senescence for Use in Cancer Treatment. PMID:28841181
CD24 induces changes to the surface receptors of B cell microvesicles with variable effects on their RNA and protein cargo. PMID:28819186
Comparative Genome Analysis of Rathayibacter tritici NCPPB 1953 with Rathayibacter toxicus Strains Can Facilitate Studies on Mechanisms of Nematode Association and Host Infection. PMID:28811754
Modeling the Colchicum autumnale Tubulin and a Comparison of Its Interaction with Colchicine to Human Tubulin. PMID:28767055
Schwann cells secrete extracellular vesicles to promote and maintain the proliferation and multipotency of hDPCs. PMID:28714175
Scalable Text Mining Assisted Curation of Post-Translationally Modified Proteoforms in the Protein Ontology. PMID:28706471
Crosstalk and the evolvability of intracellular communication. PMID:28691706
Building bridges between cellular and molecular structural biology. PMID:28682240
Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments. PMID:28652936
The myosin mesa and the basis of hypercontractility caused by hypertrophic cardiomyopathy mutations. PMID:28481356
Mining Exosomal Genes for Pancreatic Cancer Targets. PMID:28446531
An integrated method for the identification of novel genes related to oral cancer. PMID:28384236
Prediction of reversible disulfide based on features from local structural signatures. PMID:28376774
Selecting high-quality negative samples for effectively predicting protein-RNA interactions. PMID:28361676
GABA-ρ receptors: distinctive functions and molecular pharmacology. PMID:28258627
Prediction of GCRV virus-host protein interactome based on structural motif-domain interactions. PMID:28253857
Biophysical properties of human β-cardiac myosin with converter mutations that cause hypertrophic cardiomyopathy. PMID:28246639
A combination of mutational and computational scanning guides the design of an artificial ligand-binding controlled lipase. PMID:28218303
HAPPI-2: a Comprehensive and High-quality Map of Human Annotated and Predicted Protein Interactions. PMID:28212602
Distribution bias analysis of germline and somatic single-nucleotide variations that impact protein functional site and neighboring amino acids. PMID:28176830
Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. PMID:28106881
The Role of BAR Domain Proteins in the Regulation of Membrane Dynamics. PMID:28050267
Genome analysis of Hibiscus syriacus provides insights of polyploidization and indeterminate flowering in woody plants. PMID:28011721
Modeling Rice Metabolism: From Elucidating Environmental Effects on Cellular Phenotype to Guiding Crop Improvement. PMID:27965696
The genome of Onchocerca volvulus, agent of river blindness. PMID:27869790
Comparison of Substrate Specificity of Escherichia Coli p-Aminobenzoyl-Glutamate Hydrolase with Pseudomonas Carboxypeptidase G. PMID:27795973
A transcriptomic resource for Douglas-fir seed development and analysis of transcription during late megagametophyte development. PMID:27699505
Comparative analysis of Cucurbita pepo metabolism throughout fruit development in acorn squash and oilseed pumpkin. PMID:27688889
DBSecSys 2.0: a database of Burkholderia mallei and Burkholderia pseudomallei secretion systems. PMID:27650316
Comparative proteomic analysis reveals alterations in development and photosynthesis-related proteins in diploid and triploid rice. PMID:27619227
Substrate specificity characterization for eight putative nudix hydrolases. Evaluation of criteria for substrate identification within the Nudix family. PMID:27618147
A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant-microbe interactions and legume evolution. PMID:27557478
Investigation of glycan evolution based on a comprehensive analysis of glycosyltransferases using phylogenetic profiling. PMID:27493855
On the study of microbial transcriptomes using second- and third-generation sequencing technologies. PMID:27480632
Developing an Acidic Residue Reactive and Sulfoxide-Containing MS-Cleavable Homobifunctional Cross-Linker for Probing Protein-Protein Interactions. PMID:27417384
The genome and transcriptome of Trichormus sp. NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau. PMID:27381465
HPIDB 2.0: a curated database for host-pathogen interactions. PMID:27374121
A Concentration-Dependent Liquid Phase Separation Can Cause Toxicity upon Increased Protein Expression. PMID:27320918
PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq. PMID:27316337
FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. PMID:27296299
Complete genome sequence of Streptococcus agalactiae strain GBS85147 serotype of type Ia isolated from human oropharynx. PMID:27274785
Multidimensional structure-function relationships in human β-cardiac myosin from population-scale genetic variation. PMID:27247418
Investigating the Role of Loop C Hydrophilic Residue 'T244' in the Binding Site of ρ1 GABAC Receptors via Site Mutation and Partial Agonism. PMID:27244450
Practical Approaches for Mining Frequent Patterns in Molecular Datasets. PMID:27168722
systemsDock: a web server for network pharmacology-based prediction and analysis. PMID:27131384
A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of Mycobacterium tuberculosis. PMID:27096425
Prediction of mycoplasma hominis proteins targeting in mitochondria and cytoplasm of host cells and their implication in prostate cancer etiology. PMID:27027344
CSCdb: a cancer stem cells portal for markers, related genes and functional information. PMID:26989154
A Web Server and Mobile App for Computing Hemolytic Potency of Peptides. PMID:26953092
Investigation of the cause of geographic disparities in IDEXX ELISA sensitivity in serum samples from Mycobacterium bovis-infected cattle. PMID:26949166
Structure-Activity Relationship Studies of N- and C-Terminally Modified Secretin Analogs for the Human Secretin Receptor. PMID:26930505
Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach. PMID:26929980
LaGomiCs-Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order. PMID:26921276
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. PMID:26911872
Computational prediction of Mycoplasma hominis proteins targeting in nucleus of host cell and their implication in prostate cancer etiology. PMID:26874727
Gene Expression Variation Resolves Species and Individual Strains among Coral-Associated Dinoflagellates within the Genus Symbiodinium. PMID:26868597
Mining integrated semantic networks for drug repositioning opportunities. PMID:26844016
Characterising Complex Enzyme Reaction Data. PMID:26840640
AURA 2: Empowering discovery of post-transcriptional networks. PMID:26779400
A network analysis of cofactor-protein interactions for analyzing associations between human nutrition and diseases. PMID:26777674
Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami. PMID:26764021
Exploring the complete mutational space of the LDL receptor LA5 domain using molecular dynamics: linking SNPs with disease phenotypes in familial hypercholesterolemia. PMID:26755827
Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry. PMID:26740739
Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0. PMID:26658470
Identification of Small-Molecule Inhibitors against Meso-2, 6-Diaminopimelate Dehydrogenase from Porphyromonas gingivalis. PMID:26544875
An acorn squash (Cucurbita pepo ssp. ovifera) fruit and seed transcriptome as a resource for the study of fruit traits in Cucurbita. PMID:26504561
Identifying New Candidate Genes and Chemicals Related to Prostate Cancer Using a Hybrid Network and Shortest Path Approach. PMID:26504486
The EcoCyc Database. PMID:26442933
The Nuclear Proteome of a Vertebrate. PMID:26441354
Comprehensive Analysis of the Naturally Processed Peptide Repertoire: Differences between HLA-A and B in the Immunopeptidome. PMID:26375851
Computational evaluation of phytocompounds for combating drug resistant tuberculosis by multi-targeted therapy. PMID:26323856
Fibroblast activation protein-α, a stromal cell surface protease, shapes key features of cancer associated fibroblasts through proteome and degradome alterations. PMID:26304112
Differential Proteomic Analysis Using iTRAQ Reveals Alterations in Hull Development in Rice (Oryza sativa L.). PMID:26230730
Human metabolic atlas: an online resource for human metabolism. PMID:26209309
Implementation of a Molecular Tumor Board: The Impact on Treatment Decisions for 35 Patients Evaluated at Dartmouth-Hitchcock Medical Center. PMID:26205736
Adaptation of a Bioinformatics Microarray Analysis Workflow for a Toxicogenomic Study in Rainbow Trout. PMID:26186543
Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins. PMID:26184334
RefSeq curation and annotation of antizyme and antizyme inhibitor genes in vertebrates. PMID:26170238
Inhibition of Ebola virus glycoprotein-mediated cytotoxicity by targeting its transmembrane domain and cholesterol. PMID:26158910
Physical Features of Intracellular Proteins that Moonlight on the Cell Surface. PMID:26110848
Bioinformatics analysis of thousands of TCGA tumors to determine the involvement of epigenetic regulators in human cancer. PMID:26110843
Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling. PMID:26106450
Phenotypic Characterisation of Shewanella oneidensis MR-1 Exposed to X-Radiation. PMID:26098880
Neutral red-mediated microbial electrosynthesis by Escherichia coli, Klebsiella pneumoniae, and Zymomonas mobilis. PMID:26096579
PAGER: constructing PAGs and new PAG-PAG relationships for network biology. PMID:26072489
Comparative genomic and phenomic analysis of Clostridium difficile and Clostridium sordellii, two related pathogens with differing host tissue preference. PMID:26059449
Identification of New Candidate Genes and Chemicals Related to Esophageal Cancer Using a Hybrid Interaction Network of Chemicals and Proteins. PMID:26058041
Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies. PMID:26029180
The Classification and Evolution of Enzyme Function. PMID:25986631
Briefing in application of machine learning methods in ion channel prediction. PMID:25961077
novPTMenzy: a database for enzymes involved in novel post-translational modifications. PMID:25931459
Proteochemometric modelling coupled to in silico target prediction: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules. PMID:25926892
The genomes of two key bumblebee species with primitive eusocial organization. PMID:25908251
Transcriptomic characterization of the enzymatic antioxidants FeSOD, MnSOD, APX and KatG in the dinoflagellate genus Symbiodinium. PMID:25887897
Global gene expression profiling of brown to white adipose tissue transformation in sheep reveals novel transcriptional components linked to adipose remodeling. PMID:25887780
CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts. PMID:25887563
The Alternaria genomes database: a comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic species. PMID:25887485
Exploring triacylglycerol biosynthetic pathway in developing seeds of Chia (Salvia hispanica L.): a transcriptomic approach. PMID:25875809
Identification of novel thyroid cancer-related genes and chemicals using shortest path algorithm. PMID:25874234
Cryptococcus strains with different pathogenic potentials have diverse protein secretomes. PMID:25841021
Insight into neutral and disease-associated human genetic variants through interpretable predictors. PMID:25826299
Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces. PMID:25765346
mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support. PMID:25754864
New potential eukaryotic substrates of the mycobacterial protein tyrosine phosphatase PtpA: hints of a bacterial modulation of macrophage bioenergetics state. PMID:25743628
Algorithmic approaches to protein-protein interaction site prediction. PMID:25713596
cisPath: an R/Bioconductor package for cloud users for visualization and management of functional protein interaction networks. PMID:25708840
Quantitative phosphoproteomics analysis reveals a key role of insulin growth factor 1 receptor (IGF1R) tyrosine kinase in human sperm capacitation. PMID:25693802
Phosphatase specificity and pathway insulation in signaling networks. PMID:25692603
Known Allergen Structures Predict Schistosoma mansoni IgE-Binding Antigens in Human Infection. PMID:25691884
Spatial features for Escherichia coli genome organization. PMID:25652224
Bayesian models for syndrome- and gene-specific probabilities of novel variant pathogenicity. PMID:25649125
xiNET: cross-link network maps with residue resolution. PMID:25648531
Analysis of the complete mitochondrial genome of Pochonia chlamydosporia suggests a close relationship to the invertebrate-pathogenic fungi in Hypocreales. PMID:25636983
Transcription level analysis of intracellular Burkholderia pseudomallei illustrates the role of BPSL1502 during bacterial interaction with human lung epithelial cells. PMID:25626369
The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam. PMID:25614388
Biocontainment of genetically modified organisms by synthetic protein design. PMID:25607366
Reconstructing genome-wide protein-protein interaction networks using multiple strategies with homologous mapping. PMID:25602759
Effects of copy number variable regions on local gene expression in white blood cells of Mexican Americans. PMID:25585699
The transcriptomic and proteomic landscapes of bone marrow and secondary lymphoid tissues. PMID:25541736
ReNE: a cytoscape plugin for regulatory network enhancement. PMID:25541727
Comprehensive reconstruction and visualization of non-coding regulatory networks in human. PMID:25540777
Bioinformatic identification of connective tissue growth factor as an osteogenic protein within skeletal muscle. PMID:25539834
Investigation of protein secretion and secretion stress in Ashbya gossypii. PMID:25523110
SCMHBP: prediction and analysis of heme binding proteins using propensity scores of dipeptides. PMID:25522279
Tumor antigens as proteogenomic biomarkers in invasive ductal carcinomas. PMID:25521819
Bimodal signatures of germline methylation are linked with gene expression plasticity in the coral Acropora millepora. PMID:25511458
In silico analysis of autoimmune diseases and genetic relationships to vaccination against infectious diseases. PMID:25486901
Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel. PMID:25474149
MapZ marks the division sites and positions FtsZ rings in Streptococcus pneumoniae. PMID:25470041
Integration of genomic data enables selective discovery of breast cancer drivers. PMID:25433701
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic. PMID:25429972
Assessing variation in the potential susceptibility of fish to pharmaceuticals, considering evolutionary differences in their physiology and ecology. PMID:25405965
The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease. PMID:25402615
CMPD: cancer mutant proteome database. PMID:25398898
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. PMID:25398609
Transcriptome of the invasive brown marmorated stink bug, Halyomorpha halys (Stål) (Heteroptera: Pentatomidae). PMID:25386688
Current advances in systems and integrative biology. PMID:25379142
BRENDA in 2015: exciting developments in its 25th year of existence. PMID:25378310
Prediction of interactions between viral and host proteins using supervised machine learning methods. PMID:25375323
Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.). PMID:25362073
Computational analysis of amino acids and their sidechain analogs in crowded solutions of RNA nucleobases with implications for the mRNA-protein complementarity hypothesis. PMID:25361976
Quantitative and functional characterization of the hyper-conserved protein of Prochlorococcus and marine Synechococcus. PMID:25360678
WDSPdb: a database for WD40-repeat proteins. PMID:25348404
CRISPR-Cas systems in the marine actinomycete Salinispora: linkages with phage defense, microdiversity and biogeography. PMID:25344663
Comparative genome analysis of Wolbachia strain wAu. PMID:25341639
Dissecting domain-specific evolutionary pressure profiles of transient receptor potential vanilloid subfamily members 1 to 4. PMID:25333484
A PDB-wide, evolution-based assessment of protein-protein interfaces. PMID:25326082
MoonProt: a database for proteins that are known to moonlight. PMID:25324305
P2CS: updates of the prokaryotic two-component systems database. PMID:25324303
Analysis of the tryptic search space in UniProt databases. PMID:25307260
TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. PMID:25300491
Improving contact prediction along three dimensions. PMID:25299132
Systematic analysis of the phosphoproteome and kinase-substrate networks in the mouse testis. PMID:25293948
A 3D cellular context for the macromolecular world. PMID:25289590
Structure of the large ribosomal subunit from human mitochondria. PMID:25278503
Computational biophysical, biochemical, and evolutionary signature of human R-spondin family proteins, the member of canonical Wnt/β-catenin signaling pathway. PMID:25276837
Transcriptional diversity during lineage commitment of human blood progenitors. PMID:25258084
Combining structural modeling with ensemble machine learning to accurately predict protein fold stability and binding affinity effects upon mutation. PMID:25243403
Expanding the Halohydrin Dehalogenase Enzyme Family: Identification of Novel Enzymes by Database Mining. PMID:25239895
FixingTIM: interactive exploration of sequence and structural data to identify functional mutations in protein families. PMID:25237390
Human germline and pan-cancer variomes and their distinct functional profiles. PMID:25232094
Estimating overannotation across prokaryotic genomes using BLAST+, UBLAST, LAST and BLAT. PMID:25228073
Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. PMID:25227965
A Gly-zipper motif mediates homodimerization of the transmembrane domain of the mitochondrial kinase ADCK3. PMID:25216398
A sentinel protein assay for simultaneously quantifying cellular processes. PMID:25194849
A novel fatty acid-binding protein-like carotenoid-binding protein from the gonad of the New Zealand sea urchin Evechinus chloroticus. PMID:25192378
One origin for metallo-β-lactamase activity, or two? An investigation assessing a diverse set of reconstructed ancestral sequences based on a sample of phylogenetic trees. PMID:25185655
FSim: a novel functional similarity search algorithm and tool for discovering functionally related gene products. PMID:25184141
Cell separation in Vibrio cholerae is mediated by a single amidase whose action is modulated by two nonredundant activators. PMID:25182499
Insights into the mechanism of C5aR inhibition by PMX53 via implicit solvent molecular dynamics simulations and docking. PMID:25170421
Making proteomics data accessible and reusable: current state of proteomics databases and repositories. PMID:25158685
A phosphohistidine proteomics strategy based on elucidation of a unique gas-phase phosphopeptide fragmentation mechanism. PMID:25156620
Large-scale phylogenetic classification of fungal chitin synthases and identification of a putative cell-wall metabolism gene cluster in Aspergillus genomes. PMID:25148134
A comprehensive survey of non-canonical splice sites in the human transcriptome. PMID:25123659
Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca. PMID:25115351
KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems. PMID:25115331
BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data. PMID:25089180
Amino Acid metabolism conflicts with protein diversity. PMID:25086000
Probing SH2-domains using Inhibitor Affinity Purification (IAP). PMID:25067910
Analysis of stop-gain and frameshift variants in human innate immunity genes. PMID:25058640
A novel agarolytic β-galactosidase acts on agarooligosaccharides for complete hydrolysis of agarose into monomers. PMID:25038102
Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets. PMID:25033262
DBSecSys: a database of Burkholderia mallei secretion systems. PMID:25030112
Multi-tissue computational modeling analyzes pathophysiology of type 2 diabetes in MKR mice. PMID:25029527
Evolutionary and sequence-based relationships in bacterial AdoMet-dependent non-coding RNA methyltransferases. PMID:25012753
The structure of the catalytic domain of a plant cellulose synthase and its assembly into dimers. PMID:25012190
The evolution of enzyme function in the isomerases. PMID:25000289
Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing. PMID:24992012
Homology modeling and protein engineering of alkane monooxygenase in Burkholderia thailandensis MSMB121: in silico insights. PMID:24990796
Systems biology in the context of big data and networks. PMID:24982882
CutProtFam-Pred: detection and classification of putative structural cuticular proteins from sequence alone, based on profile hidden Markov models. PMID:24978609
ChIPseek, a web-based analysis tool for ChIP data. PMID:24974934
Evaluation of the Schistosoma mansoni Y-box-binding protein (SMYB1) potential as a vaccine candidate against schistosomiasis. PMID:24966869
An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases. PMID:24966208
A controlled vocabulary for pathway entities and events. PMID:24951798
Automated peptide mapping and protein-topographical annotation of proteomics data. PMID:24946880
Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. PMID:24939910
Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes. PMID:24938783
Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome. PMID:24932600
Improving functional annotation for industrial microbes: a case study with Pichia pastoris. PMID:24929579
Mutation G805R in the transmembrane domain of the LDL receptor gene causes familial hypercholesterolemia by inducing ectodomain cleavage of the LDL receptor in the endoplasmic reticulum. PMID:24918045
Mapping-by-sequencing accelerates forward genetics in barley. PMID:24917130
De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification. PMID:24912738
Negative feedback in genetic circuits confers evolutionary resilience and capacitance. PMID:24910431
MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra. PMID:24909410
The structural and functional signatures of proteins that undergo multiple events of post-translational modification. PMID:24888500
Overexpression of UCP1 in tobacco induces mitochondrial biogenesis and amplifies a broad stress response. PMID:24886177
From sequence to enzyme mechanism using multi-label machine learning. PMID:24885296
Mass-spectrometry-based draft of the human proteome. PMID:24870543
Network analyses reveal pervasive functional regulation between proteases in the human protease web. PMID:24865846
PIQMIe: a web server for semi-quantitative proteomics data management and analysis. PMID:24861615
HeatMapViewer: interactive display of 2D data in biology. PMID:24860644
Degradation of the deubiquitinating enzyme USP33 is mediated by p97 and the ubiquitin ligase HERC2. PMID:24855649
Reduced ribosomes of the apicoplast and mitochondrion of Plasmodium spp. and predicted interactions with antibiotics. PMID:24850912
Supervised learning classification models for prediction of plant virus encoded RNA silencing suppressors. PMID:24828116
Finding sequences for over 270 orphan enzymes. PMID:24826896
dbCRY: a Web-based comparative and evolutionary genomics platform for blue-light receptors. PMID:24816342
SuSPect: enhanced prediction of single amino acid variant (SAV) phenotype using network features. PMID:24810707
Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production. PMID:24808102
SwissTargetPrediction: a web server for target prediction of bioactive small molecules. PMID:24792161
H2rs: deducing evolutionary and functionally important residue positions by means of an entropy and similarity based analysis of multiple sequence alignments. PMID:24766829
TMTC1 and TMTC2 are novel endoplasmic reticulum tetratricopeptide repeat-containing adapter proteins involved in calcium homeostasis. PMID:24764305
Odorant and gustatory receptors in the tsetse fly Glossina morsitans morsitans. PMID:24763191
Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. PMID:24759411
Effects of cations on protein and peptide charging in electrospray ionization from aqueous solutions. PMID:24729190
Redefining the PF06864 Pfam family based on Burkholderia pseudomallei PilO2(Bp) S-SAD crystal structure. PMID:24728008
Sizing up models of heart failure: Proteomics from flies to humans. PMID:24723306
Mechanistic and bioinformatic investigation of a conserved active site helix in α-isopropylmalate synthase from Mycobacterium tuberculosis, a member of the DRE-TIM metallolyase superfamily. PMID:24720347
Molecular evolution of glycoside hydrolase genes in the Western corn rootworm (Diabrotica virgifera virgifera). PMID:24718603
Zearalenone lactonohydrolase activity in Hypocreales and its evolutionary relationships within the epoxide hydrolase subset of a/b-hydrolases. PMID:24708405
Interactions outside the proteinase-binding loop contribute significantly to the inhibition of activated coagulation factor XII by its canonical inhibitor from corn. PMID:24706752
FixPred: a resource for correction of erroneous protein sequences. PMID:24705206
SysPTM 2.0: an updated systematic resource for post-translational modification. PMID:24705204
De novo loss-of-function mutations in SETD5, encoding a methyltransferase in a 3p25 microdeletion syndrome critical region, cause intellectual disability. PMID:24680889
Genetic variation of the whole ICAM4 gene in Caucasians and African Americans. PMID:24673173
Structural and kinetic characterization of guinea pig L-asparaginase type III. PMID:24669941
Effects of cytosine methylation on transcription factor binding sites. PMID:24669864
Exploring the biological and chemical complexity of the ligases. PMID:24657765
Helix kinks are equally prevalent in soluble and membrane proteins. PMID:24638929
Rich annotation of DNA sequencing variants by leveraging the Ensembl Variant Effect Predictor with plugins. PMID:24626529
Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant Nicotiana benthamiana. PMID:24614631
Comparison of gene expression of Paramecium bursaria with and without Chlorella variabilis symbionts. PMID:24612690
BCL2DB: database of BCL-2 family members and BH3-only proteins. PMID:24608034
The bitter barricading of prostaglandin biosynthesis pathway: understanding the molecular mechanism of selective cyclooxygenase-2 inhibition by amarogentin, a secoiridoid glycoside from Swertia chirayita. PMID:24603686
Lysophospholipid receptor nomenclature review: IUPHAR Review 8. PMID:24602016
The automated function prediction SIG looks back at 2013 and prepares for 2014. PMID:24590444
iLIR: A web resource for prediction of Atg8-family interacting proteins. PMID:24589857
Variation ontology: annotator guide. PMID:24533660
A temporal examination of the planktonic and biofilm proteome of whole cell Pseudomonas aeruginosa PAO1 using quantitative mass spectrometry. PMID:24532839
ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome. PMID:24501395
PrionScan: an online database of predicted prion domains in complete proteomes. PMID:24498877
Finding the missing honey bee genes: lessons learned from a genome upgrade. PMID:24479613
Temperature-responsive release of thyroxine and its environmental adaptation in Australians. PMID:24478298
Genomic tools in acute myeloid leukemia: From the bench to the bedside. PMID:24474533
ChEpiMod: a knowledgebase for chemical modulators of epigenome reader domains. PMID:24470572
Predicting human protein subcellular locations by the ensemble of multiple predictors via protein-protein interaction network with edge clustering coefficients. PMID:24466278
Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information. PMID:24449878
Improved pan-specific MHC class I peptide-binding predictions using a novel representation of the MHC-binding cleft environment. PMID:24447175
Systems toxicology: from basic research to risk assessment. PMID:24446777
Protein interaction network for Alzheimer's disease using computational approach. PMID:24391359
Draft Genome Sequences of Human Pathogenic Fungus Geomyces pannorum Sensu Lato and Bat White Nose Syndrome Pathogen Geomyces (Pseudogymnoascus) destructans. PMID:24356829
TFpredict and SABINE: sequence-based prediction of structural and functional characteristics of transcription factors. PMID:24349230
Feature-based classification of amino acid substitutions outside conserved functional protein domains. PMID:24348198
Biotin ligase tagging identifies proteins proximal to E-cadherin, including lipoma preferred partner, a regulator of epithelial cell-cell and cell-substrate adhesion. PMID:24338363
Transcriptional regulation by BglJ-RcsB, a pleiotropic heteromeric activator in Escherichia coli. PMID:24335284
Generating NMR chemical shift assignments of intrinsically disordered proteins using carbon-detected NMR methods. PMID:24333248
The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. PMID:24319146
Ensembl 2014. PMID:24316576
Structural and functional analysis of human SOD1 in amyotrophic lateral sclerosis. PMID:24312616
Plasma Proteome Database as a resource for proteomics research: 2014 update. PMID:24304897
BacMet: antibacterial biocide and metal resistance genes database. PMID:24304895
canSAR: updated cancer research and drug discovery knowledgebase. PMID:24304894
topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins. PMID:24302577
NECTAR: a database of codon-centric missense variant annotations. PMID:24297257
MycoCosm portal: gearing up for 1000 fungal genomes. PMID:24297253
eggNOG v4.0: nested orthology inference across 3686 organisms. PMID:24297252
PDBe: Protein Data Bank in Europe. PMID:24288376
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. PMID:24285306
Transferring functional annotations of membrane transporters on the basis of sequence similarity and sequence motifs. PMID:24283849
Introducing glycomics data into the Semantic Web. PMID:24280648
Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer. PMID:24278371
The Structure-Function Linkage Database. PMID:24271399
The European Bioinformatics Institute's data resources 2014. PMID:24271396
Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis. PMID:24270792
CentrosomeDB: a new generation of the centrosomal proteins database for Human and Drosophila melanogaster. PMID:24270791
Protein Ontology: a controlled structured network of protein entities. PMID:24270789
Lynx: a database and knowledge extraction engine for integrative medicine. PMID:24270788
The UCSC Genome Browser database: 2014 update. PMID:24270787
Exploring drug-target interaction networks of illicit drugs. PMID:24268016
PAV ontology: provenance, authoring and versioning. PMID:24267948
Mutation of nonessential cysteines shows that the NF-κB essential modulator forms a constitutive noncovalent dimer that binds IκB kinase-β with high affinity. PMID:24266532
CAMP: Collection of sequences and structures of antimicrobial peptides. PMID:24265220
RefSeq: an update on mammalian reference sequences. PMID:24259432
MultitaskProtDB: a database of multitasking proteins. PMID:24253302
CNVannotator: a comprehensive annotation server for copy number variation in the human genome. PMID:24244640
P³DB 3.0: From plant phosphorylation sites to protein networks. PMID:24243849
miRNEST 2.0: a database of plant and animal microRNAs. PMID:24243848
FireDB: a compendium of biological and pharmacologically relevant ligands. PMID:24243844
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. PMID:24234451
The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands. PMID:24234439
The Genome Database for Rosaceae (GDR): year 10 update. PMID:24225320
DNASU plasmid and PSI:Biology-Materials repositories: resources to accelerate biological research. PMID:24225319
The transporter classification database. PMID:24225317
Highly homologous eEF1A1 and eEF1A2 exhibit differential post-translational modification with significant enrichment around localised sites of sequence variation. PMID:24220286
RNA Bricks--a database of RNA 3D motifs and their interactions. PMID:24220091
NPInter v2.0: an updated database of ncRNA interactions. PMID:24217916
CPLM: a database of protein lysine modifications. PMID:24214993
The ChEMBL bioactivity database: an update. PMID:24214965
DrugBank 4.0: shedding new light on drug metabolism. PMID:24203711
SMPDB 2.0: big improvements to the Small Molecule Pathway Database. PMID:24203708
CottonGen: a genomics, genetics and breeding database for cotton research. PMID:24203703
Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress. PMID:24196194
An estimated 5% of new protein structures solved today represent a new Pfam family. PMID:24189229
FunCoup 3.0: database of genome-wide functional coupling networks. PMID:24185702
IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners. PMID:24178034
The functional therapeutic chemical classification system. PMID:24177719
PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. PMID:24174544
Hemolytik: a database of experimentally determined hemolytic and non-hemolytic peptides. PMID:24174543
pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins. PMID:24174539
EBI metagenomics--a new resource for the analysis and archiving of metagenomic data. PMID:24165880
The mouse Gene Expression Database (GXD): 2014 update. PMID:24163257
The pancreatic expression database: recent extensions and updates. PMID:24163255
Ensembl Genomes 2013: scaling up access to genome-wide data. PMID:24163254
PDBsum additions. PMID:24153109
Type I pyridoxal 5'-phosphate dependent enzymatic domains embedded within multimodular nonribosomal peptide synthetase and polyketide synthase assembly lines. PMID:24148833
Can inferred provenance and its visualisation be used to detect erroneous annotation? A case study using UniProtKB. PMID:24143170
Systematic interrogation of the Conus marmoreus venom duct transcriptome with ConoSorter reveals 158 novel conotoxins and 13 new gene superfamilies. PMID:24131469
Synergetic regulatory networks mediated by oncogene-driven microRNAs and transcription factors in serous ovarian cancer. PMID:24129674
Secretome and degradome profiling shows that Kallikrein-related peptidases 4, 5, 6, and 7 induce TGFβ-1 signaling in ovarian cancer cells. PMID:24120346
pLogo: a probabilistic approach to visualizing sequence motifs. PMID:24097270
Interferon-induced transmembrane protein 3 is a type II transmembrane protein. PMID:24067232
Characterization of native protein complexes and protein isoform variation using size-fractionation-based quantitative proteomics. PMID:24043423
Protein modeling: what happened to the "protein structure gap"? PMID:24010712
Transcriptome analysis of Litopenaeus vannamei in response to white spot syndrome virus infection. PMID:23991181
A fast Peptide Match service for UniProt Knowledgebase. PMID:23958731
Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree. PMID:23940838
Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance. PMID:23935056
α-Amylase: an enzyme specificity found in various families of glycoside hydrolases. PMID:23807207
Transcriptomic analysis of Ustilago maydis infecting Arabidopsis reveals important aspects of the fungus pathogenic mechanisms. PMID:23733054
PlantLoc: an accurate web server for predicting plant protein subcellular localization by substantiality motif. PMID:23729470
Analysis Tool Web Services from the EMBL-EBI. PMID:23671338
The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud. PMID:23640334
The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection. PMID:23203983 -
The Universal Protein Resource (UniProt) 2009
PubMed citations: 279.
279 articles citing: The Universal Protein Resource (UniProt) 2009
Activation of Xist by an evolutionarily conserved function of KDM5C demethylase. PMID:35545632
Transcriptomic Analysis Revealed Reactive Oxygen Species Scavenging Mechanisms Associated With Ferrous Iron Toxicity in Aromatic Keteki Joha Rice. PMID:35283928
Limits and potential of combined folding and docking. PMID:34788800
Human Cystathionine γ-Lyase Is Inhibited by s-Nitrosation: A New Crosstalk Mechanism between NO and H2S. PMID:34573023
DeepRTCP: Predicting ATP-Binding Cassette Transporters Based on 1-Dimensional Convolutional Network. PMID:33598454
Schistosoma mansoni venom allergen-like protein 6 (SmVAL6) maintains tegumental barrier function. PMID:33253697
Bacterial contribution to genesis of the novel germ line determinant oskar. PMID:32091394
Physicochemical characterization of Pseudomonas stutzeri UFV5 and analysis of its transcriptome under heterotrophic nitrification/aerobic denitrification pathway induction condition. PMID:32042029
The repositioning of epigenetic probes/inhibitors identifies new anti-schistosomal lead compounds and chemotherapeutic targets. PMID:31730617
Identification of Ixodid Tick-Specific Aquaporin-1 Potential Anti-tick Vaccine Epitopes: An in-silico Analysis. PMID:31612130
Genome Wide Phosphoproteome Analysis of Zymomonas mobilis Under Anaerobic, Aerobic, and N2-Fixing Conditions. PMID:31551951
Comparative Transcriptomic Studies on a Cadmium Hyperaccumulator Viola baoshanensis and Its Non-Tolerant Counterpart V. inconspicua. PMID:30999673
Foundry: a message-oriented, horizontally scalable ETL system for scientific data integration and enhancement. PMID:30576493
Combining bioinformatics, cheminformatics, functional genomics and whole organism approaches for identifying epigenetic drug targets in Schistosoma mansoni. PMID:30455056
Molecular dynamics simulation reveals the possible druggable hot-spots of USP7. PMID:30344943
Computational Studies of Snake Venom Toxins. PMID:29271884
Protein-mRNA interactome capture: cartography of the mRNP landscape. PMID:29098073
Prediction of HBF-0259 interactions with hepatitis B Virus receptors and surface antigen secretory factors. PMID:28466034
Toward a Metagenomic Understanding on the Bacterial Composition and Resistome in Hong Kong Banknotes. PMID:28450856
Structural Insight into Anaphase Promoting Complex 3 Structure and Docking with a Natural Inhibitory Compound. PMID:28401073
From Toxoplasmosis to Schizophrenia via NMDA Dysfunction: Peptide Overlap between Toxoplasma gondii and N-Methyl-d-Aspartate Receptors As a Potential Mechanistic Link. PMID:28360866
Genome and transcriptome sequencing characterises the gene space of Macadamia integrifolia (Proteaceae). PMID:27855648
Exploring Human Diseases and Biological Mechanisms by Protein Structure Prediction and Modeling. PMID:27807743
Effects of Tocotrienols on Insulin Secretion-Associated Genes Expression of Rat Pancreatic Islets in a Dynamic Culture. PMID:27625609
Genome Sequences of Multiresistant Staphylococcus capitis Pulsotype NRCS-A and Methicillin-Susceptible S. capitis Pulsotype NRCS-C. PMID:27284154
ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods. PMID:27242037
HerDing: herb recommendation system to treat diseases using genes and chemicals. PMID:26980517
A review of methods for interpretation of glycopeptide tandem mass spectral data. PMID:26612686
Evolution and Structural Analyses of Glossina morsitans (Diptera; Glossinidae) Tetraspanins. PMID:26462947
Genome Sequences of Four Staphylococcus capitis NRCS-A Isolates from Geographically Distant Neonatal Intensive Care Units. PMID:26251481
Protein functional features are reflected in the patterns of mRNA translation speed. PMID:26155933
The genomes of closely related Pantoea ananatis maize seed endophytes having different effects on the host plant differ in secretion system genes and mobile genetic elements. PMID:26029184
Genomic factors related to tissue tropism in Chlamydia pneumoniae infection. PMID:25887605
INTEGRATING COMPUTATIONAL PROTEIN FUNCTION PREDICTION INTO DRUG DISCOVERY INITIATIVES. PMID:25530654
PeptideManager: a peptide selection tool for targeted proteomic studies involving mixed samples from different species. PMID:25228907
Non-contiguous finished genome sequence of Staphylococcus capitis CR01 (pulsetype NRCS-A). PMID:25197487
miR-2909-mediated regulation of KLF4: a novel molecular mechanism for differentiating between B-cell and T-cell pediatric acute lymphoblastic leukemias. PMID:25037230
Increasing the precision of orthology-based complex prediction through network alignment. PMID:24918034
Distinct evolutionary strategies in the GGPPS family from plants. PMID:24904625
Differential proteomic analysis of the pancreas of diabetic db/db mice reveals the proteins involved in the development of complications of diabetes mellitus. PMID:24886809
Mass spectrometry based biomarker discovery, verification, and validation--quality assurance and control of protein biomarker assays. PMID:24713096
The eGenVar data management system--cataloguing and sharing sensitive data and metadata for the life sciences. PMID:24682735
Improving predictions of protein-protein interfaces by combining amino acid-specific classifiers based on structural and physicochemical descriptors with their weighted neighbor averages. PMID:24489849
BurrH: a new modular DNA binding protein for genome engineering. PMID:24452192
antibacTR: dynamic antibacterial-drug-target ranking integrating comparative genomics, structural analysis and experimental annotation. PMID:24438389
The autodepalmitoylating activity of APT maintains the spatial organization of palmitoylated membrane proteins. PMID:24411241
Response of the calcifying coccolithophore Emiliania huxleyi to low pH/high pCO2: from physiology to molecular level. PMID:24391258
SASD: the Synthetic Alternative Splicing Database for identifying novel isoform from proteomics. PMID:24267658
RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation. PMID:24079885
Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila. PMID:24004689
Information exploration system for sickle cell disease and repurposing of hydroxyfasudil. PMID:23762313
Three infectious viral species lying in wait in the banana genome. PMID:23720724
Molecular evolution of peptidergic signaling systems in bilaterians. PMID:23671109
Identification and distribution of projections from monoaminergic and cholinergic nuclei to functionally differentiated subregions of prefrontal cortex. PMID:23665053
Genetic characterization of a core collection of flax (Linum usitatissimum L.) suitable for association mapping studies and evidence of divergent selection between fiber and linseed types. PMID:23647851
Complete Genome Sequence of Geobacillus sp. Strain GHH01, a Thermophilic Lipase-Secreting Bacterium. PMID:23618712
A systematic comparison of the MetaCyc and KEGG pathway databases. PMID:23530693
An amphipathic alpha-helix in the prodomain of cocaine and amphetamine regulated transcript peptide precursor serves as its sorting signal to the regulated secretory pathway. PMID:23527253
A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels. PMID:23390605
Peptide sharing between influenza A H1N1 hemagglutinin and human axon guidance proteins. PMID:23378012
SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS. PMID:23369106
Identification of small molecule inhibitors against UBE2C by using docking studies. PMID:23275705
Glycoproteomics enabled by tagging sialic acid- or galactose-terminated glycans. PMID:23070960
The importance of TM3-4 loop subdomains for functional reconstitution of glycine receptors by independent domains. PMID:22995908
Global secretome characterization of herpes simplex virus 1-infected human primary macrophages. PMID:22973042
In silico prediction of exposure amino acid sequences of outer inflammatory protein A of Helicobacter pylori for surface display on Eschierchia coli. PMID:22754227
The evolutionary landscape of cytosolic microbial sensors in humans. PMID:22748209
Personalized medicine: hope or hype? PMID:22659199
IMGT-ONTOLOGY 2012. PMID:22654892
The use of evolutionary patterns in protein annotation. PMID:22633559
Semantic text mining support for lignocellulose research. PMID:22595090
New cis-regulatory elements in the Rht-D1b locus region of wheat. PMID:22592657
Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. PMID:22580950
Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum. PMID:22548871
Comparative modeling of DszC, an enzyme in biodesulfurization, and performing in silico point mutation for increasing tendency to oil. PMID:22493530
Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies. PMID:22396634
DetoxiProt: an integrated database for detoxification proteins. PMID:22369658
A novel framework for the comparative analysis of biological networks. PMID:22363585
RIPPLY3 is a retinoic acid-inducible repressor required for setting the borders of the pre-placodal ectoderm. PMID:22354841
Regulation of blood-testis barrier dynamics by desmosome, gap junction, hemidesmosome and polarity proteins: An unexpected turn of events. PMID:22319658
Comparative modeling of PON2 and analysis of its substrate binding interactions using computational methods. PMID:22319641
BS-KNN: An Effective Algorithm for Predicting Protein Subchloroplast Localization. PMID:22267906
Solving the Problem: Genome Annotation Standards before the Data Deluge. PMID:22180819
Assessment of NER solutions against the first and second CALBC Silver Standard Corpus. PMID:22166494
neXtProt: a knowledge platform for human proteins. PMID:22139911
Molecular evolution of the transmembrane domains of G protein-coupled receptors. PMID:22132149
GONUTS: the Gene Ontology Normal Usage Tracking System. PMID:22110029
Analysis of genome-wide association study data using the protein knowledge base. PMID:22077927
Benchmarks for flexible and rigid transcription factor-DNA docking. PMID:22044637
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. PMID:22006843
Identification of a novel class of farnesylation targets by structure-based modeling of binding specificity. PMID:21998565
Genome-wide polymorphisms show unexpected targets of natural selection. PMID:21993504
Quantification of protein group coherence and pathway assignment using functional association. PMID:21929787
Molecular modeling of Trypanosoma cruzi glutamate cysteine ligase and investigation of its interactions with glutathione. PMID:21894564
A tool for biomarker discovery in the urinary proteome: a manually curated human and animal urine protein biomarker database. PMID:21876203
Predicting protein kinase specificity: Predikin update and performance in the DREAM4 challenge. PMID:21829434
Computational reverse-engineering of a spider-venom derived peptide active against Plasmodium falciparum SUB1. PMID:21818266
Ancestral genes can control the ability of horizontally acquired loci to confer new traits. PMID:21811415
Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database. PMID:21801404
Integrated genomics and proteomics of the Torpedo californica electric organ: concordance with the mammalian neuromuscular junction. PMID:21798097
BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation. PMID:21696594
Cocos: Constructing multi-domain protein phylogenies. PMID:21686311
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. PMID:21632744
Curation of characterized glycoside hydrolases of fungal origin. PMID:21622642
Transcriptome instability in colorectal cancer identified by exon microarray analyses: Associations with splicing factor expression levels and patient survival. PMID:21619627
Combinations of protein-chemical complex structures reveal new targets for established drugs. PMID:21573205
Extraction of consensus protein patterns in regions containing non-proline cis peptide bonds and their functional assessment. PMID:21569261
Evolution of the karyopherin-β family of nucleocytoplasmic transport factors; ancient origins and continued specialization. PMID:21556326
Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome. PMID:21554714
Methods and strategies for gene structure curation in WormBase. PMID:21543339
Molecular dynamics simulations of pro-apoptotic BH3 peptide helices in aqueous medium: relationship between helix stability and their binding affinities to the anti-apoptotic protein Bcl-X(L). PMID:21523491
Gene ontology function prediction in mollicutes using protein-protein association networks. PMID:21486441
A comprehensive protein-centric ID mapping service for molecular data integration. PMID:21478197
Revisiting gap locations in amino acid sequence alignments and a proposal for a method to improve them by introducing solvent accessibility. PMID:21465562
The Protein Data Bank in Europe (PDBe): bringing structure to biology. PMID:21460450
Using context to improve protein domain identification. PMID:21453511
Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. PMID:21415278
Omics-based molecular target and biomarker identification. PMID:21370102
Discovery and annotation of small proteins using genomics, proteomics, and computational approaches. PMID:21367939
Automated ontological gene annotation for computing disease similarity. PMID:21347137
The G protein-coupled receptors in the pufferfish Takifugu rubripes. PMID:21342560
Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis. PMID:21323774
Complete genome sequence of Methanoculleus marisnigri Romesser et al. 1981 type strain JR1. PMID:21304656
Bioinformatic identification of novel protein phosphatases in the dog genome. PMID:21240543
NClassG+: A classifier for non-classically secreted Gram-positive bacterial proteins. PMID:21235786
TMPad: an integrated structural database for helix-packing folds in transmembrane proteins. PMID:21177659
Evolutionary innovations and the organization of protein functions in genotype space. PMID:21152394
Large scale phosphoproteome profiles comprehensive features of mouse embryonic stem cells. PMID:21149613
BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation. PMID:21122127
Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome. PMID:21092105
BISC: binary subcomplexes in proteins database. PMID:21081561
PhEVER: a database for the global exploration of virus-host evolutionary relationships. PMID:21081560
LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana. PMID:21071420
PCDDB: the Protein Circular Dichroism Data Bank, a repository for circular dichroism spectral and metadata. PMID:21071417
Detailed analysis of function divergence in a large and diverse domain superfamily: toward a refined protocol of function classification. PMID:21070951
DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. PMID:21059682
ASD: a comprehensive database of allosteric proteins and modulators. PMID:21051350
PDBe: Protein Data Bank in Europe. PMID:21045060
Complete genome sequence of Cronobacter turicensis LMG 23827, a food-borne pathogen causing deaths in neonates. PMID:21037008
hnRNP L regulates the tumorigenic capacity of lung cancer xenografts in mice via caspase-9 pre-mRNA processing. PMID:20972334
Verification of alternative splicing variants based on domain integrity, truncation length and intrinsic protein disorder. PMID:20972208
Inference of surface membrane factors of HIV-1 infection through functional interaction networks. PMID:20967291
Molecular characterization of the evolution of phagosomes. PMID:20959821
Evolutionary history of the poly(ADP-ribose) polymerase gene family in eukaryotes. PMID:20942953
Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. PMID:20929876
Evolution of dopamine-related systems: biosynthesis, degradation and receptors. PMID:20890594
A Brassica exon array for whole-transcript gene expression profiling. PMID:20862292
FGsub: Fusarium graminearum protein subcellular localizations predicted from primary structures. PMID:20840726
Phylogenomics of ligand-gated ion channels predicts monepantel effect. PMID:20838602
Utopia documents: linking scholarly literature with research data. PMID:20823323
Improving disease gene prioritization using the semantic similarity of Gene Ontology terms. PMID:20823322
Comparing interfacial dynamics in protein-protein complexes: an elastic network approach. PMID:20691107
GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques. PMID:20689020
Systematic analysis of short internal indels and their impact on protein folding. PMID:20684774
Protein kinase-inhibitor database: structural variability of and inhibitor interactions with the protein kinase P-loop. PMID:20681595
The systematic annotation of the three main GPCR families in Reactome. PMID:20671204
Efficient plant gene identification based on interspecies mapping of full-length cDNAs. PMID:20668003
Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the secondary endosymbiont of tsetse flies. PMID:20649993
From complete genome sequence to 'complete' understanding? PMID:20647113
The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand. PMID:20646284
Mechanisms of haplotype divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana). PMID:20637079
PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies. PMID:20631208
RKB: a Semantic Web knowledge base for RNA. PMID:20626922
PROFESS: a PROtein function, evolution, structure and sequence database. PMID:20624718
PDBWiki: added value through community annotation of the Protein Data Bank. PMID:20624717
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. PMID:20587024
GPS-SNO: computational prediction of protein S-nitrosylation sites with a modified GPS algorithm. PMID:20585580
Localization and function of the membrane-bound riboflavin in the Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) from Vibrio cholerae. PMID:20558724
Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PMID:20532046
Synonymous codon usage influences the local protein structure observed. PMID:20530529
Cerebral malaria: insights from host-parasite protein-protein interactions. PMID:20529383
A multilevel data integration resource for breast cancer study. PMID:20525248
A computational genomics pipeline for prokaryotic sequencing projects. PMID:20519285
3DLigandSite: predicting ligand-binding sites using similar structures. PMID:20513649
Pathway signature and cellular differentiation in clear cell renal cell carcinoma. PMID:20502531
Real-time ligand binding pocket database search using local surface descriptors. PMID:20455259
Tissue localization and solubilities of αA-crystallin and its numerous C-terminal truncation products in pre- and postcataractous ICR/f rat lenses. PMID:20435586
Clinical assessment incorporating a personal genome. PMID:20435227
Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. PMID:20433725
AP2/EREBP transcription factors are part of gene regulatory networks and integrate metabolic, hormonal and environmental signals in stress acclimation and retrograde signalling. PMID:20411284
Contrasts between adaptive coding and noncoding changes during human evolution. PMID:20385805
Detection and architecture of small heat shock protein monomers. PMID:20383329
NetCTLpan: pan-specific MHC class I pathway epitope predictions. PMID:20379710
Proteomic analysis of osteogenic sarcoma: association of tumour necrosis factor with poor prognosis. PMID:20353421
Support vector machine-based mucin-type o-linked glycosylation site prediction using enhanced sequence feature encoding. PMID:20351933
Moara: a Java library for extracting and normalizing gene and protein mentions. PMID:20346105
Comparative analysis of the extracellular proteomes of two Clostridium sordellii strains exhibiting contrasting virulence. PMID:20338254
Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. PMID:20333304
A poxvirus Bcl-2-like gene family involved in regulation of host immune response: sequence similarity and evolutionary history. PMID:20230632
Missing genes in the annotation of prokaryotic genomes. PMID:20230630
Crystal structure of an eIF4G-like protein from Danio rerio. PMID:20229607
Characterization of potential allergens in fenugreek (Trigonella foenum-graecum) using patient sera and MS-based proteomic analysis. PMID:20219717
Genomic structure of an economically important cyanobacterium, Arthrospira (Spirulina) platensis NIES-39. PMID:20203057
Auxin metabolism and function in the multicellular brown alga Ectocarpus siliculosus. PMID:20200071
Predicting highly-connected hubs in protein interaction networks by QSAR and biological data descriptors. PMID:20198194
Visualization of multiple alignments, phylogenies and gene family evolution. PMID:20195253
Structural and functional restraints on the occurrence of single amino acid variations in human proteins. PMID:20169194
Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase. PMID:20157489
A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki. PMID:20157485
Fast and efficient searching of biological data resources--using EB-eye. PMID:20150321
LINNAEUS: a species name identification system for biomedical literature. PMID:20149233
Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications. PMID:20137074
Protein interactions and ligand binding: from protein subfamilies to functional specificity. PMID:20133844
A gene-centric human proteome project: HUPO--the Human Proteome organization. PMID:20124355
Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues. PMID:20122268
JNK contributes to Hif-1alpha regulation in hypoxic neurons. PMID:20110876
Easy retrieval of single amino-acid polymorphisms and phenotype information using SwissVar. PMID:20106818
PSiFR: an integrated resource for prediction of protein structure and function. PMID:20080513
Investigating protein isoforms via proteomics: a feasibility study. PMID:20077415
Simulation of spontaneous substrate binding revealing the binding pathway and mechanism and initial conformational response of GlpT. PMID:20058936
SKPDB: a structural database of shikimate pathway enzymes. PMID:20055992
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. PMID:20043185
Evolutionary trace annotation of protein function in the structural proteome. PMID:20036248
Peripheral facial nerve axotomy in mice causes sprouting of motor axons into perineuronal central white matter: time course and molecular characterization. PMID:20034058
Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PMID:20011109
The Protein Naming Utility: a rules database for protein nomenclature. PMID:20007151
The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species. PMID:20003425
The UCSC Genome Browser. PMID:19957273
SMPDB: The Small Molecule Pathway Database. PMID:19948758
NBRP databases: databases of biological resources in Japan. PMID:19934255
ACLAME: a CLAssification of Mobile genetic Elements, update 2010. PMID:19933762
H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. PMID:19933760
Calling International Rescue: knowledge lost in literature and data landslide! PMID:19929850
FunSimMat update: new features for exploring functional similarity. PMID:19923227
The Negatome database: a reference set of non-interacting protein pairs. PMID:19920129
ELM: the status of the 2010 eukaryotic linear motif resource. PMID:19920119
MeMotif: a database of linear motifs in alpha-helical transmembrane proteins. PMID:19910368
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. PMID:19907644
The UCSC Genome Browser database: update 2010. PMID:19906737
Gene expression atlas at the European bioinformatics institute. PMID:19906730
The Proteomics Identifications database: 2010 update. PMID:19906717
MicrobesOnline: an integrated portal for comparative and functional genomics. PMID:19906701
Ensembl's 10th year. PMID:19906699
Gene3D: merging structure and function for a Thousand genomes. PMID:19906693
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. PMID:19900971
phiSITE: database of gene regulation in bacteriophages. PMID:19900969
The MiST2 database: a comprehensive genomics resource on microbial signal transduction. PMID:19900966
MINT, the molecular interaction database: 2009 update. PMID:19897547
Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. PMID:19893621
Ensembl Genomes: extending Ensembl across the taxonomic space. PMID:19884133
PepX: a structural database of non-redundant protein-peptide complexes. PMID:19880386
KEGG for representation and analysis of molecular networks involving diseases and drugs. PMID:19880382
Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens. PMID:19874620
Structural genomics target selection for the New York consortium on membrane protein structure. PMID:19859826
PDBe: Protein Data Bank in Europe. PMID:19858099
The NCBI BioSystems database. PMID:19854944
The IntAct molecular interaction database in 2010. PMID:19850723
REBASE--a database for DNA restriction and modification: enzymes, genes and genomes. PMID:19846593
Mycobacterial cytochrome p450 125 (cyp125) catalyzes the terminal hydroxylation of c27 steroids. PMID:19846551
Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell. PMID:19832986
Clustering of protein domains for functional and evolutionary studies. PMID:19832975
Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells. PMID:19820112
MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore. PMID:19783819
Functional analysis and structural modeling of human APOBEC3G reveal the role of evolutionarily conserved elements in the inhibition of human immunodeficiency virus type 1 infection and Alu transposition. PMID:19776130
A family of diverse Kunitz inhibitors from Echinococcus granulosus potentially involved in host-parasite cross-talk. PMID:19759914
High-level chromate resistance in Arthrobacter sp. strain FB24 requires previously uncharacterized accessory genes. PMID:19758450
QuickGO: a web-based tool for Gene Ontology searching. PMID:19744993
Finding one's way in proteomics: a protein species nomenclature. PMID:19740416
XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services. PMID:19732427
Legume transcription factor genes: what makes legumes so special? PMID:19726573
PAVE: program for assembling and viewing ESTs. PMID:19709403
NASCENT: an automatic protein interaction network generation tool for non-model organisms. PMID:19707301
Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold. PMID:19670211
A guide to the Proteomics Identifications Database proteomics data repository. PMID:19662629
Missing in action: enzyme functional annotations in biological databases. PMID:19620987
ProteinArchitect: protein evolution above the sequence level. PMID:19603068
aGEM: an integrative system for analyzing spatial-temporal gene-expression information. PMID:19592395
Analysis of expressed sequence tags from the four main developmental stages of Trypanosoma congolense. PMID:19559733
The first draft of the endostatin interaction network. PMID:19542224
Databases of homologous gene families for comparative genomics. PMID:19534752
PosMed-plus: an intelligent search engine that inferentially integrates cross-species information resources for molecular breeding of plants. PMID:19528193
DASMIweb: online integration, analysis and assessment of distributed protein interaction data. PMID:19502495
ProGMap: an integrated annotation resource for protein orthology. PMID:19494185
Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases. PMID:19454601
An integrative multi-platform analysis for discovering biomarkers of osteosarcoma. PMID:19445706
Web services at the European Bioinformatics Institute-2009. PMID:19435877
SePreSA: a server for the prediction of populations susceptible to serious adverse drug reactions implementing the methodology of a chemical-protein interactome. PMID:19417066
The Microbe browser for comparative genomics. PMID:19406928
ModLink+: improving fold recognition by using protein-protein interactions. PMID:19357100 -
The Universal Protein Resource (UniProt)
PubMed citations: 223.
223 articles citing: The Universal Protein Resource (UniProt)
Reconstruction of a Genome-Scale Metabolic Network for Shewanella oneidensis MR-1 and Analysis of its Metabolic Potential for Bioelectrochemical Systems. PMID:35646853
Comparative analysis of web-based programs for single amino acid substitutions in proteins. PMID:35507592
Characterization of a T4-like Bacteriophage vB_EcoM-Sa45lw as a Potential Biocontrol Agent for Shiga Toxin-Producing Escherichia coli O45 Contaminated on Mung Bean Seeds. PMID:35107386
Structural Predictive Model of Presenilin-2 Protein and Analysis of Structural Effects of Familial Alzheimer's Disease Mutations. PMID:34881055
De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance. PMID:34118890
Coevolutionary and Phylogenetic Analysis of Mimiviral Replication Machinery Suggest the Cellular Origin of Mimiviruses. PMID:33570580
Computational design of SARS-CoV-2 spike glycoproteins to increase immunogenicity by T cell epitope engineering. PMID:33398234
Protocol for Biochemical Analysis and Structure Determination of the ZZ Domain of the E3 Ubiquitin Ligase HERC2. PMID:33377049
The elephant grass (Cenchrus purpureus) genome provides insights into anthocyanidin accumulation and fast growth. PMID:33040437
Whole Mitochondrial Genome Analysis in Serbian Cases of Leber's Hereditary Optic Neuropathy. PMID:32887465
Rational Design of SARS-CoV-2 Spike Glycoproteins To Increase Immunogenicity By T Cell Epitope Engineering. PMID:32817949
COVID-19 Coronavirus Vaccine Design Using Reverse Vaccinology and Machine Learning. PMID:32719684
Araport Lives: An Updated Framework for Arabidopsis Bioinformatics. PMID:32699173
IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data. PMID:32683045
COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning. PMID:32511333
tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing. PMID:32423416
Identifying Sialylation Linkages at the Glycopeptide Level by Glycosyltransferase Labeling Assisted Mass Spectrometry (GLAMS). PMID:32271005
Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens. PMID:32096826
An integrated computational and experimental study to investigate Staphylococcus aureus metabolism. PMID:32001720
Metabolic Modeling Elucidates the Transactions in the Rumen Microbiome and the Shifts Upon Virome Interactions. PMID:31866953
Genome Sequence of a T4-like Phage, Escherichia Phage vB_EcoM-Sa45lw, Infecting Shiga Toxin-Producing Escherichia coli Strains. PMID:31395650
Stems cells, big data and compendium-based analyses for identifying cell types, signalling pathways and gene regulatory networks. PMID:30684132
Transcriptomic analysis of male and female Schistosoma mekongi adult worms. PMID:30201055
Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia). PMID:29519939
The conserved basic residues and the charged amino acid residues at the α-helix of the zinc finger motif regulate the nuclear transport activity of triple C2H2 zinc finger proteins. PMID:29381770
Identification of New Features from Known Bacterial Protective Vaccine Antigens Enhances Rational Vaccine Design. PMID:29123525
Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling. PMID:29035697
Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins. PMID:28775330
Distribution and cluster analysis of predicted intrinsically disordered protein Pfam domains. PMID:28516017
Functional proteomic analysis of corticosteroid pharmacodynamics in rat liver: Relationship to hepatic stress, signaling, energy regulation, and drug metabolism. PMID:28315483
In silico designing of a new cysteine analogue of hirudin variant 3 for site specific PEGylation. PMID:28255315
YMDB 2.0: a significantly expanded version of the yeast metabolome database. PMID:27899612
Optimizing sgRNA position markedly improves the efficiency of CRISPR/dCas9-mediated transcriptional repression. PMID:27353328
Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals. PMID:27329977
A Querying Method over RDF-ized Health Level Seven v2.5 Messages Using Life Science Knowledge Resources. PMID:27050304
Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium. PMID:26692227
Molecular Cloning and Functional Expression of the Equine K+ Channel KV11.1 (Ether à Go-Go-Related/KCNH2 Gene) and the Regulatory Subunit KCNE2 from Equine Myocardium. PMID:26376488
Age-related thermal response: the cellular resilience of juveniles. PMID:26364303
Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease. PMID:26342919
Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry. PMID:26202522
toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research. PMID:26130662
iCataly-PseAAC: Identification of Enzymes Catalytic Sites Using Sequence Evolution Information with Grey Model GM (2,1). PMID:26077845
A knowledge base for Vitis vinifera functional analysis. PMID:26050794
Genome-wide analysis of phosphorylated PhoP binding to chromosomal DNA reveals several novel features of the PhoPR-mediated phosphate limitation response in Bacillus subtilis. PMID:25666134
Aber-OWL: a framework for ontology-based data access in biology. PMID:25627673
Genome-wide metabolic re-annotation of Ashbya gossypii: new insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis. PMID:25253284
Local packing density is the main structural determinant of the rate of protein sequence evolution at site level. PMID:25121105
Functional evolution of PLP-dependent enzymes based on active-site structural similarities. PMID:24920327
Herpes B virus gD interaction with its human receptor--an in silico analysis approach. PMID:24902525
RRHGE: a novel approach to classify the estrogen receptor based breast cancer subtypes. PMID:24563630
Sma3s: a three-step modular annotator for large sequence datasets. PMID:24501397
Charge segregation and low hydrophobicity are key features of ribosomal proteins from different organisms. PMID:24398678
Exploring the "dark matter" of a mammalian proteome by protein structure and function modeling. PMID:24321360
The semantic web in translational medicine: current applications and future directions. PMID:24197933
Characterization of bacteriophages Cp1 and Cp2, the strain-typing agents for Xanthomonas axonopodis pv. citri. PMID:24123743
Archaeal ubiquitin-like SAMP3 is isopeptide-linked to proteins via a UbaA-dependent mechanism. PMID:24097257
Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE. PMID:23875683
Equivalent indels--ambiguous functional classes and redundancy in databases. PMID:23658777
Toll-like receptor 9 interaction with CpG ODN--an in silico analysis approach. PMID:23497207
Further characterization of Cys-type and Ser-type anaerobic sulfatase maturating enzymes suggests a commonality in the mechanism of catalysis. PMID:23477283
Using the OntoGene pipeline for the triage task of BioCreative 2012. PMID:23396322
Catalytic contribution of threonine 244 in human ALDH2. PMID:23295226
Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining. PMID:23055974
Ranking relations between diseases, drugs and genes for a curation task. PMID:23046495
Growth-dependent release of carbohydrate metabolism-related and antioxidant enzymes from Staphylococcus aureus strain 6 as determined by proteomic analysis. PMID:22977644
Evaluation of research in biomedical ontologies. PMID:22962340
HINT: High-quality protein interactomes and their applications in understanding human disease. PMID:22846459
Probing the Xenopus laevis inner ear transcriptome for biological function. PMID:22676585
Functional analyses of mycobacterial lipoprotein diacylglyceryl transferase and comparative secretome analysis of a mycobacterial lgt mutant. PMID:22609911
Detection of interaction articles and experimental methods in biomedical literature. PMID:22151872
Sequence-based classification using discriminatory motif feature selection. PMID:22102890
The Histone Database: an integrated resource for histones and histone fold-containing proteins. PMID:22025671
Cfr and RlmN contain a single [4Fe-4S] cluster, which directs two distinct reactivities for S-adenosylmethionine: methyl transfer by SN2 displacement and radical generation. PMID:21916495
Discovery of novel selective serotonin reuptake inhibitors through development of a protein-based pharmacophore. PMID:21834587
Participation of protein sequence termini in crystal contacts. PMID:21739502
Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses. PMID:21658583
Activity control of the ClpC adaptor McsB in Bacillus subtilis. PMID:21622759
Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis. PMID:21605342
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
Meet me halfway: when genomics meets structural bioinformatics. PMID:21350909
B2G-FAR, a species-centered GO annotation repository. PMID:21335611
Modeling single nucleotide polymorphisms in the human AKR1C1 and AKR1C2 genes: implications for functional and genotyping analyses. PMID:21217827
Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction. PMID:21104192
Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement. PMID:20979641
Prediction of carbohydrate-binding proteins from sequences using support vector machines. PMID:20936154
High-throughput prediction of protein antigenicity using protein microarray data. PMID:20934990
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. PMID:20626842
Synonymous codon usage influences the local protein structure observed. PMID:20530529
Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing. PMID:20529341
The annotation of full zinc proteomes. PMID:20443034
PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach. PMID:20430828
Systems biology in heart diseases. PMID:20411053
Strategies for enhanced annotation of a microarray probe set. PMID:20223738
Complete-proteome mapping of human influenza A adaptive mutations: implications for human transmissibility of zoonotic strains. PMID:20140252
Biana: a software framework for compiling biological interactions and analyzing networks. PMID:20105306
A comprehensive proteomics and transcriptomics analysis of Bacillus subtilis salt stress adaptation. PMID:19948795
EST and microarray analysis of horn development in Onthophagus beetles. PMID:19878565
13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose. PMID:19874611
Inferring branching pathways in genome-scale metabolic networks. PMID:19874610
A stochastic context free grammar based framework for analysis of protein sequences. PMID:19814800
Knowledge-based variable selection for learning rules from proteomic data. PMID:19761570
A survey of integral alpha-helical membrane proteins. PMID:19760129
Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations. PMID:19758473
An integrated approach to the interpretation of single amino acid polymorphisms within the framework of CATH and Gene3D. PMID:19758469
BRICHOS - a superfamily of multidomain proteins with diverse functions. PMID:19747390
Bacillus subtilis SpoIIIJ and YqjG function in membrane protein biogenesis. PMID:19717609
Prediction of ligand binding sites using homologous structures and conservation at CASP8. PMID:19626715
Amyloidogenic determinants are usually not buried. PMID:19589171
Characterization of a multimeric, eukaryotic prolyl aminopeptidase: an inducible and highly specific intracellular peptidase from the non-pathogenic fungus Talaromyces emersonii. PMID:19556294
Cu(II) bis(thiosemicarbazone) radiopharmaceutical binding to serum albumin: further definition of species dependence and associated substituent effects. PMID:19520290
Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi. PMID:19445715
The High Throughput Sequence Annotation Service (HT-SAS) - the shortcut from sequence to true Medline words. PMID:19445703
A functional analysis of the pyrimidine catabolic pathway in Arabidopsis. PMID:19413687
Inferring stabilizing mutations from protein phylogenies: application to influenza hemagglutinin. PMID:19381264
Prediction of disease-related mutations affecting protein localization. PMID:19309509
Biopython: freely available Python tools for computational molecular biology and bioinformatics. PMID:19304878
Analyses of domains and domain fusions in human proto-oncogenes. PMID:19292927
Discovering genes associated with dormancy in the monogonont rotifer Brachionus plicatilis. PMID:19284654
Reconstruction of metabolic pathways for the cattle genome. PMID:19284618
Using triplet periodicity of nucleotide sequences for finding potential reading frame shifts in genes. PMID:19261626
Highly diversified molecular evolution of downstream transcription start sites in rice and Arabidopsis. PMID:19118127
An evolutionary and structural characterization of mammalian protein complex organization. PMID:19108706
nGASP--the nematode genome annotation assessment project. PMID:19099578
Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics. PMID:19073703
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence. PMID:19043579
The protein structure initiative structural genomics knowledgebase. PMID:19010965
dictyBase--a Dictyostelium bioinformatics resource update. PMID:18974179
Matching curated genome databases: a non trivial task. PMID:18950477
PhytAMP: a database dedicated to antimicrobial plant peptides. PMID:18836196
MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data. PMID:18834496
OntoGene in BioCreative II. PMID:18834491
Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks. PMID:18834489
Splice-mediated Variants of Proteins (SpliVaP) - data and characterization of changes in signatures among protein isoforms due to alternative splicing. PMID:18831736
Advanced genomic data mining. PMID:18818719
Characterization of quinolinate synthases from Escherichia coli, Mycobacterium tuberculosis, and Pyrococcus horikoshii indicates that [4Fe-4S] clusters are common cofactors throughout this class of enzymes. PMID:18803397
Interspecies data mining to predict novel ING-protein interactions in human. PMID:18801192
Genetic variation underlying protein expression in eggs of the marine mussel Mytilus edulis. PMID:18794572
Amino acid composition and protein dimension. PMID:18780815
Identification and correction of abnormal, incomplete and mispredicted proteins in public databases. PMID:18752676
Validating annotations for uncharacterized proteins in Shewanella oneidensis. PMID:18687039
Experience using web services for biological sequence analysis. PMID:18621748
MACHOS: Markov clusters of homologous subsequences. PMID:18586748
Predicting transcriptional regulatory interactions with artificial neural networks applied to E. coli multidrug resistance efflux pumps. PMID:18565227
In vitro characterization of AtsB, a radical SAM formylglycine-generating enzyme that contains three [4Fe-4S] clusters. PMID:18558715
The combination approach of SVM and ECOC for powerful identification and classification of transcription factor. PMID:18554421
Arabidopsis nuclear-encoded plastid transit peptides contain multiple sequence subgroups with distinctive chloroplast-targeting sequence motifs. PMID:18552198
Onto-CC: a web server for identifying Gene Ontology conceptual clusters. PMID:18544607
Relative quantitative comparisons of the extracellular protein profiles of Staphylococcus aureus UAMS-1 and its sarA, agr, and sarA agr regulatory mutants using one-dimensional polyacrylamide gel electrophoresis and nanocapillary liquid chromatography coupled with tandem mass spectrometry. PMID:18539737
Key interactions in integrin ectodomain responsible for global conformational change detected by elastic network normal-mode analysis. PMID:18515366
Genome structure of the legume, Lotus japonicus. PMID:18511435
Gene discovery in an invasive tephritid model pest species, the Mediterranean fruit fly, Ceratitis capitata. PMID:18500975
Prediction of membrane-protein topology from first principles. PMID:18477697
Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces. PMID:18474114
The Jpred 3 secondary structure prediction server. PMID:18463136
OREST: the online resource for EST analysis. PMID:18463135
De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features. PMID:18461181
Mapping proteins to disease terminologies: from UniProt to MeSH. PMID:18460185
Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology. PMID:18460183
What everybody should know about the rat genome and its online resources. PMID:18443589
EpiToolKit--a web server for computational immunomics. PMID:18440979
A new protein linear motif benchmark for multiple sequence alignment software. PMID:18439277
The annotation of both human and mouse kinomes in UniProtKB/Swiss-Prot: one small step in manual annotation, one giant leap for full comprehension of genomes. PMID:18436524
Protein robustness promotes evolutionary innovations on large evolutionary time-scales. PMID:18430649
Normalizing biomedical terms by minimizing ambiguity and variability. PMID:18426547
Computational studies reveal phosphorylation-dependent changes in the unstructured R domain of CFTR. PMID:18423665
EPO-KB: a searchable knowledge base of biomarker to protein links. PMID:18400772
Predicting cancer involvement of genes from heterogeneous data. PMID:18371197
Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: focus on point miscalls and artefactual expansions. PMID:18366731
ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts. PMID:18325116
Exploration of human ORFeome: high-throughput preparation of ORF clones and efficient characterization of their protein products. PMID:18316326
Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis. PMID:18315849
SciDBMaker: new software for computer-aided design of specialized biological databases. PMID:18298861
In silico characterization of proteins: UniProt, InterPro and Integr8. PMID:18219596
Comparative analysis of neuropeptide cleavage sites in human, mouse, rat, and cattle. PMID:18213482
SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements. PMID:18174224
Surviving extreme polar winters by desiccation: clues from Arctic springtail (Onychiurus arcticus) EST libraries. PMID:18154659
AlterORF: a database of alternate open reading frames. PMID:18096612
The UCSC Genome Browser Database: 2008 update. PMID:18086701
Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. PMID:18086700
Remediation of the protein data bank archive. PMID:18073189
Ma-LMM01 infecting toxic Microcystis aeruginosa illuminates diverse cyanophage genome strategies. PMID:18065537
PlantGDB: a resource for comparative plant genomics. PMID:18063570
Towards completion of the Earth's proteome. PMID:18059312
Discrimination of class I cyclobutane pyrimidine dimer photolyase from blue light photoreceptors by single methionine residue. PMID:18055535
Framework for a protein ontology. PMID:18047702
Gene regulatory networks in lactation: identification of global principles using bioinformatics. PMID:18039394
Gene3D: comprehensive structural and functional annotation of genomes. PMID:18032434
GenoList: an integrated environment for comparative analysis of microbial genomes. PMID:18032431
KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007. PMID:18025039
Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome. PMID:18021451
Determination and validation of principal gene products. PMID:18006548
Data growth and its impact on the SCOP database: new developments. PMID:18000004
DIMA 2.0--predicted and known domain interactions. PMID:17999995
GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update. PMID:17986454
The HGNC Database in 2008: a resource for the human genome. PMID:17984084
The Molecule Pages database. PMID:17965093
CORUM: the comprehensive resource of mammalian protein complexes. PMID:17965090
OrthoDB: the hierarchical catalog of eukaryotic orthologs. PMID:17947323
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. PMID:17945017
SuperTarget and Matador: resources for exploring drug-target relationships. PMID:17942422
BACTIBASE: a new web-accessible database for bacteriocin characterization. PMID:17941971
Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments. PMID:17940094
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. PMID:17933782
The Generation Challenge Programme comparative plant stress-responsive gene catalogue. PMID:17933772
ChEBI: a database and ontology for chemical entities of biological interest. PMID:17932057
Detailed estimation of bioinformatics prediction reliability through the Fragmented Prediction Performance Plots. PMID:17931407
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. PMID:17925023
NORINE: a database of nonribosomal peptides. PMID:17913739
Antibody-protein interactions: benchmark datasets and prediction tools evaluation. PMID:17910770
PROCOGNATE: a cognate ligand domain mapping for enzymes. PMID:17720712
An integrative in silico approach for discovering candidates for drug-targetable protein-protein interactions in interactome data. PMID:17705877
In silico characterization of immunogenic epitopes presented by HLA-Cw*0401. PMID:17705876
Sequence-based prioritization of nonsynonymous single-nucleotide polymorphisms for the study of disease mutations. PMID:17668383
Applying negative rule mining to improve genome annotation. PMID:17659089
Global analysis of patterns of gene expression during Drosophila embryogenesis. PMID:17645804
Web services at the European bioinformatics institute. PMID:17576686
Restauro-G: a rapid genome re-annotation system for comparative genomics. PMID:17572364
The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms. PMID:17565672
siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins. PMID:17553829
Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome. PMID:17511520
Transcriptome analysis of the venom gland of the Mexican scorpion Hadrurus gertschi (Arachnida: Scorpiones). PMID:17506894
ImmTree: database of evolutionary relationships of genes and proteins in the human immune system. PMID:17376226 -
UniProtKB/Swiss-Prot
PubMed citations: 217.
217 articles citing: UniProtKB/Swiss-Prot
Structure and biosynthesis of carotenoids produced by a novel Planococcus sp. isolated from South Africa. PMID:35305628
Full-length transcriptome analysis of Adiantum flabellulatum gametophyte. PMID:35287343
Comparative genomics and evolutionary analysis of Lactococcus garvieae isolated from human endocarditis. PMID:35196218
Slipknot or Crystallographic Error: A Computational Analysis of the Plasmodium falciparum DHFR Structural Folds. PMID:35163439
Computational analysis and prediction of PE_PGRS proteins using machine learning. PMID:35140886
The highly continuous reference genome of a leaf-chimeric red pineapple (Ananas comosus var. bracteatus f. tricolor) provides insights into elaboration of leaf color. PMID:35100332
CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research. PMID:34961276
Exploration and augmentation of pharmacological space via adversarial auto-encoder model for facilitating kinase-centric drug development. PMID:34872613
Daily rhythms in gene expression of the human parasite Schistosoma mansoni. PMID:34852797
The carbohydrate-active enzyme database: functions and literature. PMID:34850161
The CRISPR-associated Cas4 protein from Leptospira interrogans demonstrate versatile nuclease activity. PMID:34841331
Phenotypic Screening of Molecular Docking Enriched Chemical Libraries from Targets Identified in Ischemic Stroke Genome Data by Network-Based Method. PMID:34820079
A Superefficient Ochratoxin A Hydrolase with Promising Potential for Industrial Applications. PMID:34788069
Chalcones identify cTXNPx as a potential antileishmanial drug target. PMID:34780470
Transcriptomic and Metabolomic Analyses Reveals That Exogenous Methyl Jasmonate Regulates Galanthamine Biosynthesis in Lycoris longituba Seedlings. PMID:34659286
Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing. PMID:34581030
Effect of food source availability in the salivary gland transcriptome of the unique burying beetle Nicrophorus pustulatus (Coleoptera: Silphidae). PMID:34555059
A deep-learning framework for multi-level peptide-protein interaction prediction. PMID:34526500
Arabidopsis-Based Dual-Layered Biological Network Analysis Elucidates Fully Modulated Pathways Related to Sugarcane Resistance on Biotrophic Pathogen Infection. PMID:34490009
On the Need to Tell Apart Fraternal Twins eEF1A1 and eEF1A2, and Their Respective Outfits. PMID:34203525
Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds. PMID:34145392
Structure-based Method for Predicting Deleterious Missense SNPs. PMID:34136829
Structure-based protein function prediction using graph convolutional networks. PMID:34039967
digIS: towards detecting distant and putative novel insertion sequence elements in prokaryotic genomes. PMID:34016050
bla OXA-48-like genome architecture among carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the Netherlands. PMID:33961543
The language of proteins: NLP, machine learning & protein sequences. PMID:33897979
Effects of Simulated Microgravity on the Proteome and Secretome of the Polyextremotolerant Black Fungus Knufia chersonesos. PMID:33815472
Transcriptome analysis reveals major transcriptional changes during regrowth after mowing of red clover (Trifolium pratense). PMID:33588756
Querying knowledge graphs in natural language. PMID:33489717
Embeddings from deep learning transfer GO annotations beyond homology. PMID:33441905
Reconstruction and analysis of a genome-scale metabolic model for Agrobacterium tumefaciens. PMID:33433944
PTMsnp: A Web Server for the Identification of Driver Mutations That Affect Protein Post-translational Modification. PMID:33240890
GasPhos: Protein Phosphorylation Site Prediction Using a New Feature Selection Approach with a GA-Aided Ant Colony System. PMID:33114312
Side chain similarity comparisons for integrated drug repositioning and potential toxicity assessments in epidemic response scenarios: The case for COVID-19. PMID:33101604
MolTrans: Molecular Interaction Transformer for drug-target interaction prediction. PMID:33070179
IDPology of the living cell: intrinsic disorder in the subcellular compartments of the human cell. PMID:32997198
Hidden dynamic signatures drive substrate selectivity in the disordered phosphoproteome. PMID:32900925
High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus. PMID:32859687
Chromosome-Level Assembly of the Common Lizard (Zootoca vivipara) Genome. PMID:32835354
Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature. PMID:32770181
Hybrid phenotype mining method for investigating off-target protein and underlying side effects of anti-tumor immunotherapy. PMID:32646421
Large Ankyrin repeat proteins are formed with similar and energetically favorable units. PMID:32579546
Brain-related genes are specifically enriched with long phase 1 introns. PMID:32470086
Three Novel Variants identified in FBN1 and TGFBR2 in seven Iranian families with suspected Marfan syndrome. PMID:32431097
Independent evolution of ancestral and novel defenses in a genus of toxic plants (Erysimum, Brassicaceae). PMID:32252891
The genome evolution and low-phosphorus adaptation in white lupin. PMID:32103018
Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes. PMID:32093654
Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff. PMID:32060277
Isolation of an archaeon at the prokaryote-eukaryote interface. PMID:31942073
Predicting and designing therapeutics against the Nipah virus. PMID:31830030
Secretome analysis of patient-derived GBM tumor spheres identifies midkine as a potent therapeutic target. PMID:31811117
Complete Genome Sequence of the Plant Growth-Promoting Bacterium Hartmannibacter diazotrophicus Strain E19T. PMID:31583244
Reference gene and small RNA data from multiple tissues of Davidia involucrata Baill. PMID:31551451
Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets. PMID:31462646
Using distant supervision to augment manually annotated data for relation extraction. PMID:31361753
CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis. PMID:31282937
CELF2 suppresses non-small cell lung carcinoma growth by inhibiting the PREX2-PTEN interaction. PMID:31241130
Proteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic Alphaproteobacterium. PMID:31239395
Structural, functional, and stability change predictions in human telomerase upon specific point mutations. PMID:31213647
Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album. PMID:31199791
VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations. PMID:31192369
Hair Proteome Variation at Different Body Locations on Genetically Variant Peptide Detection for Protein-Based Human Identification. PMID:31113963
Proteomic characterisation of leech microglia extracellular vesicles (EVs): comparison between differential ultracentrifugation and Optiprep™ density gradient isolation. PMID:31069026
Cross-species alcohol dependence-associated gene networks: Co-analysis of mouse brain gene expression and human genome-wide association data. PMID:31017905
Computational Prediction of MoRFs, Short Disorder-to-order Transitioning Protein Binding Regions. PMID:31007871
Thermal selection as a driver of marine ecological speciation. PMID:30963923
How to design potent and selective DYRK1B inhibitors? Molecular modeling study. PMID:30673861
Draft Genome Sequence of an Onion Basal Rot Isolate of Fusarium proliferatum. PMID:30637390
Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex. PMID:30606234
Impact of Rearing Conditions on the Ambrosia Beetle's Microbiome. PMID:30551580
Protein-protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique. PMID:30520961
A differential k-mer analysis pipeline for comparing RNA-Seq transcriptome and meta-transcriptome datasets without a reference. PMID:30483906
Interactive online application for the prediction, ranking and prioritisation of drug targets in Schistosoma haematobium. PMID:30482220
WebNetCoffee: a web-based application to identify functionally conserved proteins from Multiple PPI networks. PMID:30419809
Marginal protein stability drives subcellular proteome isoelectric point. PMID:30385634
Desiccation Tolerance Evolved through Gene Duplication and Network Rewiring in Lindernia. PMID:30361236
Leishmania donovani Parasites Are Inhibited by the Benzoxaborole AN2690 Targeting Leucyl-tRNA Synthetase. PMID:29941647
Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome. PMID:29690875
Identification of Metabolites and Transcripts Involved in Salt Stress and Recovery in Peanut. PMID:29520289
Improving eukaryotic genome annotation using single molecule mRNA sequencing. PMID:29495964
Genetic variation in P2RX7 and pain tolerance. PMID:29470314
The Glaciozyma antarctica genome reveals an array of systems that provide sustained responses towards temperature variations in a persistently cold habitat. PMID:29385175
Listeria monocytogenes Induces a Virulence-Dependent microRNA Signature That Regulates the Immune Response in Galleria mellonella. PMID:29312175
Computational Studies of Snake Venom Toxins. PMID:29271884
Continuous Elution Proteoform Identification of Myelin Basic Protein by Superficially Porous Reversed-Phase Liquid Chromatography and Fourier Transform Mass Spectrometry. PMID:29016107
O2 sensing-associated glycosylation exposes the F-box-combining site of the Dictyostelium Skp1 subunit in E3 ubiquitin ligases. PMID:28928219
The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies. PMID:28915793
Genetic Validation of Leishmania donovani Lysyl-tRNA Synthetase Shows that It Is Indispensable for Parasite Growth and Infectivity. PMID:28875178
Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries. PMID:28610557
The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae). PMID:28431014
Drug-drug interaction discovery and demystification using Semantic Web technologies. PMID:28031284
Large-scale identification of human protein function using topological features of interaction network. PMID:27849060
EphA2 proteomics in human keratinocytes reveals a novel association with afadin and epidermal tight junctions. PMID:27815408
ASAP: a machine learning framework for local protein properties. PMID:27694209
Evaluating the accuracy of protein design using native secondary sub-structures. PMID:27597167
Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1. PMID:27595565
Prediction of redox-sensitive cysteines using sequential distance and other sequence-based features. PMID:27553667
Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome. PMID:27453469
A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies. PMID:27363390
DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank. PMID:27307615
Comparative genomics explains the evolutionary success of reef-forming corals. PMID:27218454
Hologenome analysis of two marine sponges with different microbiomes. PMID:26926518
Hydrophobic Core Variations Provide a Structural Framework for Tyrosine Kinase Evolution and Functional Specialization. PMID:26925779
Cytochrome P450 2C9 (CYP2C9) polymorphisms in Chinese Li population. PMID:26885033
Defining the Schistosoma haematobium kinome enables the prediction of essential kinases as anti-schistosome drug targets. PMID:26635209
sORFs.org: a repository of small ORFs identified by ribosome profiling. PMID:26527729
Transcriptomic Changes in Coral Holobionts Provide Insights into Physiological Challenges of Future Climate and Ocean Change. PMID:26510159
Prenatal notch1 receptor blockade by protein delta homolog 1 (DLK1) modulates adipocyte size in vivo. PMID:26499442
Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel). PMID:26442818
reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra. PMID:26419769
Identification of Circulating Biomarker Candidates for Hepatocellular Carcinoma (HCC): An Integrated Prioritization Approach. PMID:26414287
Molecular Simulations of Solved Co-crystallized X-Ray Structures Identify Action Mechanisms of PDEδ Inhibitors. PMID:26340817
Data for comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells. PMID:26306321
Maternal and zygotic transcriptomes in the appendicularian, Oikopleura dioica: novel protein-encoding genes, intra-species sequence variations, and trans-spliced RNA leader. PMID:26032664
APPRIS WebServer and WebServices. PMID:25990727
ChSeq: A database of chameleon sequences. PMID:25970262
SUMOhunt: Combining Spatial Staging between Lysine and SUMO with Random Forests to Predict SUMOylation. PMID:25937950
MitoFates: improved prediction of mitochondrial targeting sequences and their cleavage sites. PMID:25670805
Draft Genome Sequence of a Xylanase-Producing Bacterial Strain, Cellvibrio mixtus J3-8. PMID:25502674
Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress. PMID:25467196
Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton. PMID:25461969
A new multi-label classifier in identifying the functional types of human membrane proteins. PMID:25433431
FRET detection of lymphocyte function-associated antigen-1 conformational extension. PMID:25378583
Identifying common components across biological network graphs using a bipartite data model. PMID:25374613
Draft Genome Sequence of the Iron-Oxidizing, Acidophilic, and Halotolerant "Thiobacillus prosperus" Type Strain DSM 5130. PMID:25342676
Caspase cleavage sites in the human proteome: CaspDB, a database of predicted substrates. PMID:25330111
nDNA-Prot: identification of DNA-binding proteins based on unbalanced classification. PMID:25196432
FSim: a novel functional similarity search algorithm and tool for discovering functionally related gene products. PMID:25184141
Compositions of fungal secretomes indicate a greater impact of phylogenetic history than lifestyle adaptation. PMID:25159997
Functional annotation of human cytomegalovirus gene products: an update. PMID:24904534
NeuroPID: a classifier of neuropeptide precursors. PMID:24792159
qcML: an exchange format for quality control metrics from mass spectrometry experiments. PMID:24760958
A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i). PMID:24742296
Computational redesign of bacterial biotin carboxylase inhibitors using structure-based virtual screening of combinatorial libraries. PMID:24699146
Herceptin resistance database for understanding mechanism of resistance in breast cancer patients. PMID:24670875
Antimicrobial peptides in the centipede Scolopendra subspinipes mutilans. PMID:24652097
Plus ça change - evolutionary sequence divergence predicts protein subcellular localization signals. PMID:24438075
SIDD: a semantically integrated database towards a global view of human disease. PMID:24146757
In silico approach for predicting toxicity of peptides and proteins. PMID:24058508
eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures. PMID:23902875
Short toxin-like proteins attack the defense line of innate immunity. PMID:23881252
Mining Proteins with Non-Experimental Annotations Based on an Active Sample Selection Strategy for Predicting Protein Subcellular Localization. PMID:23840667
Insight into pleiotropic drug resistance ATP-binding cassette pump drug transport through mutagenesis of Cdr1p transmembrane domains. PMID:23824183
A study on the distribution of 37 well conserved families of C2H2 zinc finger genes in eukaryotes. PMID:23800006
NRF2-ome: an integrated web resource to discover protein interaction and regulatory networks of NRF2. PMID:23710289
Large-scale global identification of protein lysine methylation in vivo. PMID:23644510
Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA). PMID:23630983
Network characteristic analysis of ADR-related proteins and identification of ADR-ADR associations. PMID:23625301
Draft genome sequence of the rubber tree Hevea brasiliensis. PMID:23375136
Chapter 3: Small molecules and disease. PMID:23300405
The state of the human proteome in 2012 as viewed through PeptideAtlas. PMID:23215161
Short toxin-like proteins abound in Cnidaria genomes. PMID:23202321
PMRD: a curated database for genes and mutants involved in plant male reproduction. PMID:23153247
Microbial virus genome annotation-mustering the troops to fight the sequence onslaught. PMID:23084289
Draft genome sequence of butanol-acetone-producing Clostridium beijerinckii strain G117. PMID:22965093
Genetic characterization of Erve virus, a European Nairovirus distantly related to Crimean-Congo hemorrhagic fever virus. PMID:22864548
Getting personalized cancer genome analysis into the clinic: the challenges in bioinformatics. PMID:22839973
In silico prediction and analysis of Caenorhabditis EF-hand containing proteins. PMID:22701514
Linking proteins to signaling pathways for experiment design and evaluation. PMID:22558382
Iron sulfur cluster proteins and microbial regulation: implications for understanding tuberculosis. PMID:22483328
Pleiotropic roles of a ribosomal protein in Dictyostelium discoideum. PMID:22363460
Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data. PMID:22276131
EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data. PMID:22267905
The relationship between proteome size, structural disorder and organism complexity. PMID:22182830
Bioinformatic analysis and post-translational modification crosstalk prediction of lysine acetylation. PMID:22164248
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. PMID:22139938
Insulin-like growth factor-I receptor (IGF-IR) translocates to nucleus and autoregulates IGF-IR gene expression in breast cancer cells. PMID:22128190
The energy landscape analysis of cancer mutations in protein kinases. PMID:21998754
Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop. PMID:21994619
VPDB: Viral Protein Structural Database. PMID:21769196
Immunogenicity of autoantigens. PMID:21726451
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. PMID:21632744
BioProfiling.de: analytical web portal for high-throughput cell biology. PMID:21609949
Structural determinants of the alpha2 adrenoceptor subtype selectivity. PMID:21602069
Insights of interaction between small and large subunits of ADP-glucose pyrophosphorylase from bread wheat (Triticum aestivum L.). PMID:21572880
Signalogs: orthology-based identification of novel signaling pathway components in three metazoans. PMID:21559328
Cost-effective cloud computing: a case study using the comparative genomics tool, roundup. PMID:21258651
OrthoInspector: comprehensive orthology analysis and visual exploration. PMID:21219603
Predicting DNA-binding specificities of eukaryotic transcription factors. PMID:21152420
Arabidopsis lox3 lox4 double mutants are male sterile and defective in global proliferative arrest. PMID:21052784
VnD: a structure-centric database of disease-related SNPs and drugs. PMID:21051351
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. PMID:21051348
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. PMID:21037261
Verification of alternative splicing variants based on domain integrity, truncation length and intrinsic protein disorder. PMID:20972208
Microarray-based analysis of cell-cycle gene expression during spermatogenesis in the mouse. PMID:20631398
R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases. PMID:20519200
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. PMID:20478830
Bioinformatics and molecular modeling in glycobiology. PMID:20364395
Mutation@A Glance: an integrative web application for analysing mutations from human genetic diseases. PMID:20360267
Word add-in for ontology recognition: semantic enrichment of scientific literature. PMID:20181245
Large-scale analyses of glycosylation in cellulases. PMID:20172492
Identification of novel aspartic proteases from Strongyloides ratti and characterisation of their evolutionary relationships, stage-specific expression and molecular structure. PMID:20015380
The association of virulence factors with genomic islands. PMID:19956607
Novel protein-protein interactions inferred from literature context. PMID:19924298
The Negatome database: a reference set of non-interacting protein pairs. PMID:19920129
Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences. PMID:19888206
Predicting meiotic pathways in human fetal oogenesis. PMID:19846598
Sequence and structure signatures of cancer mutation hotspots in protein kinases. PMID:19834613
Correlating protein function and stability through the analysis of single amino acid substitutions. PMID:19758472
ZifBASE: a database of zinc finger proteins and associated resources. PMID:19737425
Allergen databases: current status and perspectives. PMID:19671381
Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens. PMID:19515247
Structural features of mammalian histidine decarboxylase reveal the basis for specific inhibition. PMID:19413567
FMM: a web server for metabolic pathway reconstruction and comparative analysis. PMID:19401437
Sequence-based prediction of type III secreted proteins. PMID:19390696
ANNIE: integrated de novo protein sequence annotation. PMID:19389726
The Human Gene Mutation Database: 2008 update. PMID:19348700
Global networks of functional coupling in eukaryotes from comprehensive data integration. PMID:19246318
An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases. PMID:19091018
Genome-scale models of bacterial metabolism: reconstruction and applications. PMID:19067749
Bionemo: molecular information on biodegradation metabolism. PMID:18986994
ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes. PMID:18984624
BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. PMID:18984617
The GOA database in 2009--an integrated Gene Ontology Annotation resource. PMID:18957448
FlyBase: enhancing Drosophila Gene Ontology annotations. PMID:18948289
MDPD: an integrated genetic information resource for Parkinson's disease. PMID:18948286
The SWISS-MODEL Repository and associated resources. PMID:18931379 -
The UniProt-GO Annotation database in 2011
PubMed citations: 193.
193 articles citing: The UniProt-GO Annotation database in 2011
Loci underlying leaf agronomic traits identified by re-sequencing celery accessions based on an assembled genome. PMID:35784787
A chromosome-level genome assembly of Artocarpus nanchuanensis (Moraceae), an extremely endangered fruit tree. PMID:35701376
Chromosome-scale genome assembly of an important medicinal plant honeysuckle. PMID:35610245
Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis. PMID:35605198
Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment. PMID:35572582
Qualitative Proteome-Wide Analysis Reveals the Diverse Functions of Lysine Crotonylation in Dendrobium huoshanense. PMID:35251091
Zebrafish information network, the knowledgebase for Danio rerio research. PMID:35166825
Transcriptome analysis of gibberellins and abscisic acid during the flooding response in Fokienia hodginsii. PMID:35148337
Chromosome-level genome assembly of the fully mycoheterotrophic orchid Gastrodia elata. PMID:35100375
Chromosome-level genome assembly of Bactrocera dorsalis reveals its adaptation and invasion mechanisms. PMID:35017661
Chromosome-level genome assembly of Zizania latifolia provides insights into its seed shattering and phytocassane biosynthesis. PMID:35017643
A Chromosome-Level Genome Assembly of the Pygmy Mole Cricket Xya riparia. PMID:34999819
Chromosome Genome Assembly of Cromileptes altivelis Reveals Loss of Genome Fragment in Cromileptes Compared with Epinephelus Species. PMID:34946822
Chromosome-Level Genome Assembly of the Burbot (Lota lota) Using Nanopore and Hi-C Technologies. PMID:34887901
Morus alba L. Leaves - Integration of Their Transcriptome and Metabolomics Dataset: Investigating Potential Genes Involved in Flavonoid Biosynthesis at Different Harvest Times. PMID:34868120
The Genetic Relatedness and Antimicrobial Resistance Patterns of Mastitis-Causing Staphylococcus aureus Strains Isolated from New Zealand Dairy Cattle. PMID:34822660
Genome and systems biology of Melilotus albus provides insights into coumarins biosynthesis. PMID:34717292
Global analysis of lysine acetylation in soybean leaves. PMID:34504199
Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia. PMID:34130656
nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning. PMID:34002774
Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications. PMID:33926388
The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae). PMID:33827435
Comparative analysis of drought-responsive and -adaptive genes in Chinese wingnut (Pterocarya stenoptera C. DC). PMID:33663380
Genome survey sequencing and genetic diversity of cultivated Akebia trifoliata assessed via phenotypes and SSR markers. PMID:33400074
System, Method and Software for Calculation of a Cannabis Drug Efficiency Index for the Reduction of Inflammation. PMID:33396562
Chromosomal-Level Genome Assembly of Silver Sillago (Sillago sihama). PMID:33367716
Genome sequencing and phylogenetic analysis of allotetraploid Salix matsudana Koidz. PMID:33328474
The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening. PMID:33328440
Chromosomal assembly of the Antarctic toothfish ( Dissostichus mawsoni) genome using third-generation DNA sequencing and Hi-C technology. PMID:33258338
Epigenetic Studies Revealed a Ghost Proteome in PC1/3 KD Macrophages under Antitumoral Resistance Induced by IL-10. PMID:33163760
The genome of Chinese flowering cherry (Cerasus serrulata) provides new insights into Cerasus species. PMID:33082971
Significant reductions in apoptosis-related proteins (HSPA6, HSPA8, ITGB3, YWHAH, and PRDX6) are involved in immune thrombocytopenia. PMID:33047245
High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae. PMID:32985109
A mini foxtail millet with an Arabidopsis-like life cycle as a C4 model system. PMID:32868891
Positive Selection and Gene Expression Analyses from Salivary Glands Reveal Discrete Adaptations within the Ecologically Diverse Bat Family Phyllostomidae. PMID:32697843
SuccSite: Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites. PMID:32592791
The New Biomarker for Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (CESC) Based on Public Database Mining. PMID:32351997
The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution. PMID:32257231
iMarmot: an integrative platform for comparative and functional genomics of marmots. PMID:32228437
SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics. PMID:32196115
Proteomic Analysis of Salmonella-modified Membranes Reveals Adaptations to Macrophage Hosts. PMID:32102972
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. PMID:31950972
The pomegranate (Punica granatum L.) draft genome dissects genetic divergence between soft- and hard-seeded cultivars. PMID:31549477
A chromosome-level draft genome of the grain aphid Sitobion miscanthi. PMID:31430367
Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C. PMID:31289832
Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome. PMID:31241154
Evaluating measures of association for single-cell transcriptomics. PMID:30962620
Long Noncoding RNA and Protein Interactions: From Experimental Results to Computational Models Based on Network Methods. PMID:30875752
Genomic data integration systematically biases interactome mapping. PMID:30332399
Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury. PMID:30277459
Protein lysine acetylation plays a regulatory role in Bacillus subtilis multicellularity. PMID:30265683
SDADB: a functional annotation database of protein structural domains. PMID:29961821
Comparative transcriptome analysis of Haematococcus pluvialis on astaxanthin biosynthesis in response to irradiation with red or blue LED wavelength. PMID:29916185
Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology. PMID:29440116
Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals. PMID:29242500
Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium. PMID:29220487
MatureP: prediction of secreted proteins with exclusive information from their mature regions. PMID:28607462
The effects of DLEU1 gene expression in Burkitt lymphoma (BL): potential mechanism of chemoimmunotherapy resistance in BL. PMID:28427156
Transcriptome Analysis Reveals Candidate Genes Related to Color Fading of 'Red Bartlett' (Pyrus communis L.). PMID:28408914
Preprotein mature domains contain translocase targeting signals that are essential for secretion. PMID:28404644
Drug-screening and genomic analyses of HER2-positive breast cancer cell lines reveal predictors for treatment response. PMID:28356768
Systematic protein-protein interaction mapping for clinically relevant human GPCRs. PMID:28298427
Using predictive specificity to determine when gene set analysis is biologically meaningful. PMID:28204549
Global Lysine Acetylome Analysis of Desiccated Somatic Embryos of Picea asperata. PMID:28066480
Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle. PMID:28004835
The evolution of function within the Nudix homology clan. PMID:27936487
Expansion of the Gene Ontology knowledgebase and resources. PMID:27899567
The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations. PMID:27812948
Silencing of Profilin-1 suppresses cell adhesion and tumor growth via predicted alterations in integrin and Ca2+ signaling in T24M-based bladder cancer models. PMID:27683119
Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development. PMID:27660483
Increased Intestinal Microbial Diversity Following Fecal Microbiota Transplant for Active Crohn's Disease. PMID:27542133
Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. PMID:27535938
Twenty-six circulating antigens and two novel diagnostic candidate molecules identified in the serum of canines with experimental acute toxoplasmosis. PMID:27357215
Network motif-based method for identifying coronary artery disease. PMID:27347046
Integrative analysis of extracellular and intracellular bladder cancer cell line proteome with transcriptome: improving coverage and validity of -omics findings. PMID:27167498
UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB. PMID:27153729
Generation and gene expression profiling of 48 transcription-factor-inducible mouse embryonic stem cell lines. PMID:27150017
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. PMID:27126040
Standardized benchmarking in the quest for orthologs. PMID:27043882
Genome and network visualization facilitates the analyses of the effects of drugs and mutations on protein-protein and drug-protein networks. PMID:26961139
Protein functional analysis data in support of comparative proteomics of the pathogenic black yeast Exophiala dermatitidis under different temperature conditions. PMID:26958594
Ensembl comparative genomics resources. PMID:26896847
ChemProt-3.0: a global chemical biology diseases mapping. PMID:26876982
Gene Expression Variation Resolves Species and Individual Strains among Coral-Associated Dinoflagellates within the Genus Symbiodinium. PMID:26868597
KNOWLEDGE DRIVEN BINNING AND PHEWAS ANALYSIS IN MARSHFIELD PERSONALIZED MEDICINE RESEARCH PROJECT USING BIOBIN. PMID:26776191
Integration of a Decrescent Transcriptome and Metabolomics Dataset of Peucedanum praeruptorum to Investigate the CYP450 and MDR Genes Involved in Coumarins Biosynthesis and Transport. PMID:26697023
Finding New Order in Biological Functions from the Network Structure of Gene Annotations. PMID:26588252
The effect of microbial colonization on the host proteome varies by gastrointestinal location. PMID:26574685
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. PMID:26476444
Global analysis of lysine acetylation in strawberry leaves. PMID:26442052
Quantitative analysis of the murine lipid droplet-associated proteome during diet-induced hepatic steatosis. PMID:26416795
ExAtlas: An interactive online tool for meta-analysis of gene expression data. PMID:26223199
Direct Estimates of the Genomic Contributions to Blood Pressure Heritability within a Population-Based Cohort (ARIC). PMID:26162070
Better prediction of functional effects for sequence variants. PMID:26110438
Functional Operons in Secondary Metabolic Gene Clusters in Glarea lozoyensis (Fungi, Ascomycota, Leotiomycetes). PMID:26081635
Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea. PMID:25952370
MicroRNA Expression Profile of Neural Progenitor-Like Cells Derived from Rat Bone Marrow Mesenchymal Stem Cells under the Influence of IGF-1, bFGF and EGF. PMID:25938966
NeuroPep: a comprehensive resource of neuropeptides. PMID:25931458
Fasting induces anti-Warburg effect that increases respiration but reduces ATP-synthesis to promote apoptosis in colon cancer models. PMID:25909219
Fasting induces anti-Warburg effect that increases respiration but reduces ATP-synthesis to promote apoptosis in colon cancer models. PMID:25909219
ANDSystem: an Associative Network Discovery System for automated literature mining in the field of biology. PMID:25881313
Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data. PMID:25875762
Exosomes released from breast cancer carcinomas stimulate cell movement. PMID:25798887
Malleable nature of mRNA-protein compositional complementarity and its functional significance. PMID:25753660
Network-assisted genetic dissection of pathogenicity and drug resistance in the opportunistic human pathogenic fungus Cryptococcus neoformans. PMID:25739925
The roles of post-translational modifications in the context of protein interaction networks. PMID:25692714
PhenomeExpress: a refined network analysis of expression datasets by inclusion of known disease phenotypes. PMID:25631385
The neXtProt knowledgebase on human proteins: current status. PMID:25593349
Global coordination in adaptation to gene rewiring. PMID:25564530
Transcriptome sequencing reveals the virulence and environmental genetic programs of Vibrio vulnificus exposed to host and estuarine conditions. PMID:25489854
Genomic characterisation of an endometrial pathogenic Escherichia coli strain reveals the acquisition of genetic elements associated with extra-intestinal pathogenicity. PMID:25481482
A chemical proteomics approach for the search of pharmacological targets of the antimalarial clinical candidate albitiazolium in Plasmodium falciparum using photocrosslinking and click chemistry. PMID:25470252
Gene Ontology Consortium: going forward. PMID:25428369
Community structure detection for overlapping modules through mathematical programming in protein interaction networks. PMID:25412367
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. PMID:25399418
Whole Genome Sequencing Reveals a Chromosome 9p Deletion Causing DOCK8 Deficiency in an Adult Diagnosed with Hyper IgE Syndrome Who Developed Progressive Multifocal Leukoencephalopathy. PMID:25388448
The GOA database: gene Ontology annotation updates for 2015. PMID:25378336
RNA-seq analysis and de novo transcriptome assembly of Jerusalem artichoke (Helianthus tuberosus Linne). PMID:25375764
AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species. PMID:25355510
Proteomes of host cell membranes modified by intracellular activities of Salmonella enterica. PMID:25348832
UniProt: a hub for protein information. PMID:25348405
Genetic resources for advanced biofuel production described with the Gene Ontology. PMID:25346727
A 3D cellular context for the macromolecular world. PMID:25289590
Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis. PMID:25279447
A high-resolution network model for global gene regulation in Mycobacterium tuberculosis. PMID:25232098
Proteome-wide subcellular topologies of E. coli polypeptides database (STEPdb). PMID:25210196
FSim: a novel functional similarity search algorithm and tool for discovering functionally related gene products. PMID:25184141
The use of semantic similarity measures for optimally integrating heterogeneous Gene Ontology data from large scale annotation pipelines. PMID:25147557
Protein localization analysis of essential genes in prokaryotes. PMID:25105358
A PWWP domain-containing protein targets the NuA3 acetyltransferase complex via histone H3 lysine 36 trimethylation to coordinate transcriptional elongation at coding regions. PMID:25104842
In vivo mRNA profiling of uropathogenic Escherichia coli from diverse phylogroups reveals common and group-specific gene expression profiles. PMID:25096872
Standardized description of scientific evidence using the Evidence Ontology (ECO). PMID:25052702
Hijacking of host cellular functions by an intracellular parasite, the microsporidian Anncaliia algerae. PMID:24967735
Insights into pathophysiology of dystropy through the analysis of gene networks: an example of bronchial asthma and tuberculosis. PMID:24954693
Improving functional annotation for industrial microbes: a case study with Pichia pastoris. PMID:24929579
A method for increasing expressivity of Gene Ontology annotations using a compositional approach. PMID:24885854
BioCreative-IV virtual issue. PMID:24852177
LocTree3 prediction of localization. PMID:24848019
Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PMID:24756107
Identification of microRNAs in the coral Stylophora pistillata. PMID:24658574
Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt. PMID:24641996
A second-generation protein-protein interaction network of Helicobacter pylori. PMID:24627523
Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. PMID:24622611
From the environment to the host: re-wiring of the transcriptome of Pseudomonas aeruginosa from 22°C to 37°C. PMID:24587139
Analysis of the transcriptome of adult Dictyocaulus filaria and comparison with Dictyocaulus viviparus, with a focus on molecules involved in host-parasite interactions. PMID:24487001
Predicting human protein subcellular locations by the ensemble of multiple predictors via protein-protein interaction network with edge clustering coefficients. PMID:24466278
Low frequency variants, collapsed based on biological knowledge, uncover complexity of population stratification in 1000 genomes project data. PMID:24385916
PDBe: Protein Data Bank in Europe. PMID:24288376
Proteomic analysis of membrane proteins of vero cells: exploration of potential proteins responsible for virus entry. PMID:24286161
Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis. PMID:24270792
PANADA: protein association network annotation, determination and analysis. PMID:24265686
Growth rate-coordinated transcriptome reorganization in bacteria. PMID:24252326
COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. PMID:24214998
The functional therapeutic chemical classification system. PMID:24177719
Quantification of the impact of PSI:Biology according to the annotations of the determined structures. PMID:24139526
Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals. PMID:24119094
Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data. PMID:23967161
BGDB: a database of bivalent genes. PMID:23894186
TCW: transcriptome computational workbench. PMID:23874959
Structural disorder provides increased adaptability for vesicle trafficking pathways. PMID:23874186
A novel function prediction approach using protein overlap networks. PMID:23866986
Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution. PMID:23829427
BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge. PMID:23819467
Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. PMID:23737737
A task-based approach for Gene Ontology evaluation. PMID:23734599
PlantLoc: an accurate web server for predicting plant protein subcellular localization by substantiality motif. PMID:23729470
Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA). PMID:23630983
The challenge of increasing Pfam coverage of the human proteome. PMID:23603847
Identification and analysis of red sea mangrove (Avicennia marina) microRNAs by high-throughput sequencing and their association with stress responses. PMID:23593307
Discovery-2: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria. PMID:23537208
Protein function prediction using domain families. PMID:23514456
hTERT extends the life of human fibroblasts without compromising type I interferon signaling. PMID:23472163
Expression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles. PMID:23427276
Using BioBin to explore rare variant population stratification. PMID:23424138
Identification and analysis of a novel dimerization domain shared by various members of c-Jun N-terminal kinase (JNK) scaffold proteins. PMID:23341463
Disruption of the S41 peptidase gene in mycoplasma mycoides capri impacts proteome profile, H(2)O(2) production, and sensitivity to heat shock. PMID:23300541
Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PMID:23300433
The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes. PMID:23209799
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. PMID:23203869
EcoGene 3.0. PMID:23197660
HAMAP in 2013, new developments in the protein family classification and annotation system. PMID:23193261
ChemProt-2.0: visual navigation in a disease chemical biology database. PMID:23185041
The draft genome of sweet orange (Citrus sinensis). PMID:23179022
The mouse genome database: genotypes, phenotypes, and models of human disease. PMID:23175610
Update on activities at the Universal Protein Resource (UniProt) in 2013. PMID:23161681
Genome reduction promotes increase in protein functional complexity in bacteria. PMID:23114380
SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models. PMID:23110173
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. PMID:23087378
Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii). PMID:23056606
The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. PMID:22961259
Endosomal crosstalk: meeting points for signaling pathways. PMID:22796207
CombFunc: predicting protein function using heterogeneous data sources. PMID:22641853
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:22144685 -
Swiss-Prot: juggling between evolution and stability
PubMed citations: 129.
129 articles citing: Swiss-Prot: juggling between evolution and stability
A chromosome-level genome assembly of the pollinating fig wasp Valisia javana. PMID:35595238
Origin and Evolution of Enzymes with MIO Prosthetic Group: Microbial Coevolution After the Mass Extinction Event. PMID:35422843
Multiomics study of a heterotardigrade, Echinisicus testudo, suggests the possibility of convergent evolution of abundant heat-soluble proteins in Tardigrada. PMID:34763673
Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp (Penaeus monodon) in the Indo-Pacific Region. PMID:32906759
Docking analysis of importin-11 homology model with the phyto compounds towards colorectal cancer treatment. PMID:32405167
A Network Pharmacology Study of the Multi-Targeting Profile of an Antiarrhythmic Chinese Medicine Xin Su Ning. PMID:31607935
Draft Genome Assembly and Population Genetics of an Agricultural Pollinator, the Solitary Alkali Bee (Halictidae: Nomia melanderi). PMID:30642875
Genome sequence of the cauliflower mushroom Sparassis crispa (Hanabiratake) and its association with beneficial usage. PMID:30375506
Cloning and Functional Analysis of SaCLCc1, a Gene Belonging to the Chloride Channel Family (CLC), from the Halophyte Suaeda altissima (L.) Pall. PMID:30168055
Defining the architecture of KPC-2 Carbapenemase: identifying allosteric networks to fight antibiotics resistance. PMID:30150677
Gene Expression Response to Sea Lice in Atlantic Salmon Skin: RNA Sequencing Comparison Between Resistant and Susceptible Animals. PMID:30123239
Mechanism of premature translation termination on a sense codon. PMID:29941456
No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects. PMID:29806194
Genome Sequence of the Self-Flocculating Strain Saccharomyces cerevisiae SPSC01. PMID:29773621
PVCbase: an integrated web resource for the PVC bacterial proteomes. PMID:29718141
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads. PMID:29499650
Landscape of the spliced leader trans-splicing mechanism in Schistosoma mansoni. PMID:29497070
Functional sequencing read annotation for high precision microbiome analysis. PMID:29194524
A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model. PMID:29183907
Functional classification of protein toxins as a basis for bioinformatic screening. PMID:29066768
Ensemble cryo-EM elucidates the mechanism of translation fidelity. PMID:28538735
Mechanism of ribosome rescue by ArfA and RF2. PMID:28300532
Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum. PMID:28245292
Genomic Features of the Damselfly Calopteryx splendens Representing a Sister Clade to Most Insect Orders. PMID:28137743
Legionella pneumophila OxyR Is a Redundant Transcriptional Regulator That Contributes to Expression Control of the Two-Component CpxRA System. PMID:27994017
Complete Genome Sequence of Pontibacter akesuensis Strain AKS 1T, Which Exhibits Robust Nutrient Metabolism in Harsh Environments. PMID:27795233
Metagenomic Insights into Effects of Chemical Pollutants on Microbial Community Composition and Function in Estuarine Sediments Receiving Polluted River Water. PMID:27744476
Draft genome sequences of three Xanthomonas translucens pathovar reference strains (pv. arrhenatheri, pv. poae and pv. phlei) with different specificities for forage grasses. PMID:27536340
Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation. PMID:27500531
Genome-wide characterization of non-reference transposons in crops suggests non-random insertion. PMID:27485608
Ribosome•RelA structures reveal the mechanism of stringent response activation. PMID:27434674
Design and Stereochemical Research (DFT, ECD and Crystal Structure) of Novel Bedaquiline Analogs as Potent Antituberculosis Agents. PMID:27384553
Characterization of Proteoforms with Unknown Post-translational Modifications Using the MIScore. PMID:27291504
Leveraging family-specific signatures for AMP discovery and high-throughput annotation. PMID:27089856
Draft Genome Sequence of Zymomonas mobilis ZM481 (ATCC 31823). PMID:27056218
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model. PMID:26989150
A survey of best practices for RNA-seq data analysis. PMID:26813401
Identification of potential cargo proteins of transportin protein AtTRN1 in Arabidopsis thaliana. PMID:26650834
Identification of Putative Nuclear Receptors and Steroidogenic Enzymes in Murray-Darling Rainbowfish (Melanotaenia fluviatilis) Using RNA-Seq and De Novo Transcriptome Assembly. PMID:26599404
Semantic Assembly and Annotation of Draft RNAseq Transcripts without a Reference Genome. PMID:26393794
Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics. PMID:26156868
Insights from the metagenome of an acid salt lake: the role of biology in an extreme depositional environment. PMID:25923206
HbAHP-25, an In-Silico Designed Peptide, Inhibits HIV-1 Entry by Blocking gp120 Binding to CD4 Receptor. PMID:25915507
The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. PMID:25765701
Draft Genome Sequence of Polaromonas glacialis Strain R3-9, a Psychrotolerant Bacterium Isolated from Arctic Glacial Foreland. PMID:25013146
Oil accumulation mechanisms of the oleaginous microalga Chlorella protothecoides revealed through its genome, transcriptomes, and proteomes. PMID:25012212
Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary. PMID:24835588
An In silico Based Comparison of Drug Interactions in Wild and Mutant Human β-tubulin through Docking Studies. PMID:24834310
PredictProtein--an open resource for online prediction of protein structural and functional features. PMID:24799431
Computational design of binding proteins to EGFR domain II. PMID:24710267
Draft Genome Sequence of Nafulsella turpanensis ZLM-10T, a Novel Member of the Family Flammeovirgaceae. PMID:24699960
Ramachandran analysis of conserved glycyl residues in homologous proteins of known structure. PMID:24687432
A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE). PMID:24667251
Integrated analysis of transcriptomic and proteomic data. PMID:24082820
Cloud prediction of protein structure and function with PredictProtein for Debian. PMID:23971032
Guanidination of tryptic peptides without desalting for matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry analysis. PMID:23964694
Computational identification and analysis of arsenate reductase protein in Cronobacter sakazakii ATCC BAA-894 suggests potential microorganism for reducing arsenate. PMID:23666632
Seq2Ref: a web server to facilitate functional interpretation. PMID:23356573
Draft genome sequence of the flocculating Zymomonas mobilis strain ZM401 (ATCC 31822). PMID:23209250
In silico design of targeted SRM-based experiments. PMID:23176520
Prioritization of pathogenic mutations in the protein kinase superfamily. PMID:22759651
A Novel ESRRB Deletion Is a Rare Cause of Autosomal Recessive Nonsyndromic Hearing Impairment among Pakistani Families. PMID:22567352
A beginner's guide to eukaryotic genome annotation. PMID:22510764
Genetic analysis of the upper phenylacetate catabolic pathway in the production of tropodithietic acid by Phaeobacter gallaeciensis. PMID:22407685
Novel CLDN14 mutations in Pakistani families with autosomal recessive non-syndromic hearing loss. PMID:22246673
SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss. PMID:22120661
GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution. PMID:21914205
Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment. PMID:21862625
Structural mass spectrometry of proteins using hydroxyl radical based protein footprinting. PMID:21770468
Taxonomic and functional metagenomic profiling of the microbial community in the anoxic sediment of a sub-saline shallow lake (Laguna de Carrizo, Central Spain). PMID:21735153
Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome. PMID:21645357
Conotoxin protein classification using free scores of words and support vector machines. PMID:21619696
MAISTAS: a tool for automatic structural evaluation of alternative splicing products. PMID:21498402
Homology modeling, molecular dynamics, e-pharmacophore mapping and docking study of Chikungunya virus nsP2 protease. PMID:21445710
When a module is not a domain: the case of the REJ module and the redefinition of the architecture of polycystin-1. PMID:21314639
NClassG+: A classifier for non-classically secreted Gram-positive bacterial proteins. PMID:21235786
Structural modelling and comparative analysis of homologous, analogous and specific proteins from Trypanosoma cruzi versus Homo sapiens: putative drug targets for chagas' disease treatment. PMID:21034488
Crystal structure of human interferon-λ1 in complex with its high-affinity receptor interferon-λR1. PMID:20934432
Correlated mutations: a hallmark of phenotypic amino acid substitutions. PMID:20862353
Sustainable digital infrastructure. Although databases and other online resources have become a central tool for biological research, their long-term support and maintenance is far from secure. PMID:20847740
Diverse somatic mutation patterns and pathway alterations in human cancers. PMID:20668451
Driving forces for transmembrane alpha-helix oligomerization. PMID:20655851
Computational prediction and experimental assessment of secreted/surface proteins from Mycobacterium tuberculosis H37Rv. PMID:20585611
Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins. PMID:20162627
DIGA--a database of improved gene annotation for phytopathogens. PMID:20089203
A comprehensive assessment of N-terminal signal peptides prediction methods. PMID:19958512
Arsenic (+ 3 oxidation state) methyltransferase and the methylation of arsenicals in the invertebrate chordate Ciona intestinalis. PMID:19833739
BRICHOS - a superfamily of multidomain proteins with diverse functions. PMID:19747390
OnEX: Exploring changes in life science ontologies. PMID:19678926
Network Features and Pathway Analyses of a Signal Transduction Cascade. PMID:19543432
Massive non-natural proteins structure prediction using grid technologies. PMID:19534748
The structural basis for the difference in absorbance spectra for the FMO antenna protein from various green sulfur bacteria. PMID:19437128
Infrastructure for the life sciences: design and implementation of the UniProt website. PMID:19426475
Dynamic alpha-helix structure of micelle-bound human amylin. PMID:19244249
Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information. PMID:19213741
Exploration of Csp genes from temperate and glacier soils of the Indian Himalayas and in silico analysis of encoding proteins. PMID:19159976
PDBalert: automatic, recurrent remote homology tracking and protein structure prediction. PMID:19025670
CyclinPred: a SVM-based method for predicting cyclin protein sequences. PMID:18596929
A blackberry (Rubus L.) expressed sequence tag library for the development of simple sequence repeat markers. PMID:18570660
Modular organization and combinatorial energetics of proline-tyrosine nuclear localization signals. PMID:18532879
JCoast - a biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes. PMID:18380896
Three dimensional modeling of N-terminal region of galanin and its interaction with the galanin receptor. PMID:18288336
Discrimination of outer membrane proteins with improved performance. PMID:18218108
A primer on python for life science researchers. PMID:18052533
Determination and validation of principal gene products. PMID:18006548
Genome analysis of Minibacterium massiliensis highlights the convergent evolution of water-living bacteria. PMID:17722982
Quantitative sequence-function relationships in proteins based on gene ontology. PMID:17686158
Identification of a common subnuclear localization signal. PMID:17652456
DrugMetZ DB: an anthology of human drug metabolizing Chytochrome P450 enzymes. PMID:17597900
PIR pairwise alignment - a slip up for signal peptides. PMID:17597886
Binding site prediction of galanin peptide using evolutionary trace method. PMID:17597884
Formal TCA cycle description based on elementary actions. PMID:17426387
"Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence. PMID:17426380
Editing modifies the GABA(A) receptor subunit alpha3. PMID:17369310
SUBA: the Arabidopsis Subcellular Database. PMID:17071959
Cataloging the relationships between proteins: a review of interaction databases. PMID:16943573
Rules for nuclear localization sequence recognition by karyopherin beta 2. PMID:16901787
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. PMID:16845026
An analysis of the Sargasso Sea resource and the consequences for database composition. PMID:16623953
Classification of protein quaternary structure by functional domain composition. PMID:16584572
2DDB - a bioinformatics solution for analysis of quantitative proteomics data. PMID:16549013
A theoretical model of Aquifex pyrophilus flagellin: implications for its thermostability. PMID:16411078
SPdb--a signal peptide database. PMID:16221310
Combining experimental and predicted datasets for determination of the subcellular location of proteins in Arabidopsis. PMID:16219920
Transmembrane glycine zippers: physiological and pathological roles in membrane proteins. PMID:16179394
Plant protein annotation in the UniProt Knowledgebase. PMID:15888679
Exploring relationships and mining data with the UCSC Gene Sorter. PMID:15867434
Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals. PMID:15860772
EzCatDB: the Enzyme Catalytic-mechanism Database. PMID:15608227 -
High-quality protein knowledge resource: SWISS-PROT and TrEMBL
PubMed citations: 82.
82 articles citing: High-quality protein knowledge resource: SWISS-PROT and TrEMBL
A consensus view of the proteome of the last universal common ancestor. PMID:35784055
Actinoporin-like Proteins Are Widely Distributed in the Phylum Porifera. PMID:35049929
VicPred: A Vibrio cholerae Genotype Prediction Tool. PMID:34566903
A chromosome-level genome of Antechinus flavipes provides a reference for an Australian marsupial genus with male death after mating. PMID:34486812
Reconstruction of the full-length transcriptome of cigar tobacco without a reference genome and characterization of anion channel/transporter transcripts. PMID:34187357
Sinbase 2.0: An Updated Database to Study Multi-Omics in Sesamum indicum. PMID:33573226
BioMaster: An Integrated Database and Analytic Platform to Provide Comprehensive Information About BioBrick Parts. PMID:33552037
Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya. PMID:33395690
Whole-Genome Sequencing of Bradyrhizobium diazoefficiens 113-2 and Comparative Genomic Analysis Provide Molecular Insights Into Species Specificity and Host Specificity. PMID:33329441
Genome-wide association study of turnip mosaic virus resistance in non-heading Chinese cabbage. PMID:32832324
The genome evolution and low-phosphorus adaptation in white lupin. PMID:32103018
Draft Genome Assembly of Floccularia luteovirens, an Edible and Symbiotic Mushroom on Qinghai-Tibet Plateau. PMID:32098800
Chromosomal level assembly and population sequencing of the Chinese tree shrew genome. PMID:31418539
Extracellular Vesicles and Their Potential Use in Monitoring Cancer Progression and Therapy: The Contribution of Proteomics. PMID:31281356
TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets. PMID:30936560
Understanding carbon utilization routes between high and low starch-producing cultivars of cassava through Flux Balance Analysis. PMID:30814632
Insight into the evolution and functional characteristics of the pan-genome assembly from sesame landraces and modern cultivars. PMID:30315621
Comparative Genomics and Description of Putative Virulence Factors of Melissococcus plutonius, the Causative Agent of European Foulbrood Disease in Honey Bees. PMID:30127293
Whole Genome Sequence of an Edible and Potential Medicinal Fungus, Cordyceps guangdongensis. PMID:29666196
Oxidative cross-linking of proteins to DNA following ischemia-reperfusion injury. PMID:29540307
Differential Protein Profiling of Cerebrospinal Fluid in Piglets with Severe Meningoencephalitis Caused by Streptococcus suis Type 2 Compared to Controls. PMID:29479521
The genomes of Crithidia bombi and C. expoeki, common parasites of bumblebees. PMID:29304093
MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data. PMID:29280960
Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction. PMID:29145825
Genome-wide identification of miRNAs and lncRNAs in Cajanus cajan. PMID:29141604
Proteomics analysis of bladder cancer invasion: Targeting EIF3D for therapeutic intervention. PMID:29050215
PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice and chickpea. PMID:29036354
A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins. PMID:28564540
Genome sequence of a rice pest, the white-backed planthopper (Sogatella furcifera). PMID:28369349
In search of genome annotation consistency: solid gene clusters and how to use them. PMID:28324432
From Plant Infectivity to Growth Patterns: The Role of Blue-Light Sensing in the Prokaryotic World. PMID:27135492
Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. PMID:27074285
The impact of structural genomics: the first quindecennial. PMID:26935210
A phylogenomic data-driven exploration of viral origins and evolution. PMID:26601271
Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. PMID:26598659
High quality draft genome of Lactobacillus kunkeei EFB6, isolated from a German European foulbrood outbreak of honeybees. PMID:26203329
Ab initio coordination chemistry for nickel chelation motifs. PMID:25985439
Tree shrew database (TreeshrewDB): a genomic knowledge base for the Chinese tree shrew. PMID:25413576
De novo assembly and transcriptome characterization: novel insights into catechins biosynthesis in Camellia sinensis. PMID:25316555
Operon for biosynthesis of lipstatin, the Beta-lactone inhibitor of human pancreatic lipase. PMID:25239907
Identification of G protein-coupled receptors in Schistosoma haematobium and S. mansoni by comparative genomics. PMID:24884876
Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PMID:24756107
Genes associated with agronomic traits in non-heading Chinese cabbage identified by expression profiling. PMID:24655567
Characterisation of divergent flavivirus NS3 and NS5 protein sequences detected in Rhipicephalus microplus ticks from Brazil. PMID:24626302
Genome sequencing of high-penicillin producing industrial strain of Penicillium chrysogenum. PMID:24564352
Putative sugar transporters of the mustard leaf beetle Phaedon cochleariae: their phylogeny and role for nutrient supply in larval defensive glands. PMID:24391959
Can inferred provenance and its visualisation be used to detect erroneous annotation? A case study using UniProtKB. PMID:24143170
Bolbase: a comprehensive genomics database for Brassica oleracea. PMID:24079801
BiDaS: a web-based Monte Carlo BioData Simulator based on sequence/feature characteristics. PMID:23716644
Increasing sequence search sensitivity with transitive alignments. PMID:23457449
A global comparison of the human and T. brucei degradomes gives insights about possible parasite drug targets. PMID:23236535
EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes. PMID:22923291
Logic minimization and rule extraction for identification of functional sites in molecular sequences. PMID:22897894
DNA-energetics-based analyses suggest additional genes in prokaryotes. PMID:22750981
LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes. PMID:22110036
GOmotif: A web server for investigating the biological role of protein sequence motifs. PMID:21943350
Protein profiling of human nonpigmented ciliary epithelium cell secretome: the differentiation factors characterization for retinal ganglion cell line. PMID:21860587
Membrane vesicles, current state-of-the-art: emerging role of extracellular vesicles. PMID:21560073
In silico studies of polyaromatic hydrocarbon inhibitors of cytochrome P450 enzymes 1A1, 1A2, 2A6, and 2B1. PMID:20078084
Critical role of glycosylation in determining the length and structure of T cell epitopes. PMID:19778434
AllerHunter: a SVM-pairwise system for assessment of allergenicity and allergic cross-reactivity in proteins. PMID:19516900
Conservation and variability of West Nile virus proteins. PMID:19401763
Targeting the human cancer pathway protein interaction network by structural genomics. PMID:18487680
Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray. PMID:18088402
PPT-DB: the protein property prediction and testing database. PMID:17916570
Structural genomics: keeping up with expanding knowledge of the protein universe. PMID:17587562
A limited universe of membrane protein families and folds. PMID:16815920
Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs. PMID:16111488
Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms. PMID:15784611
Components of coated vesicles and nuclear pore complexes share a common molecular architecture. PMID:15523559
The identification of Pcl1-interacting proteins that genetically interact with Cla4 may indicate a link between G1 progression and mitotic exit. PMID:15082539
The bioinformatics challenges in comparative analysis of cereal genomes-an overview. PMID:14770300
From phenotype to genotype: issues in navigating the available information resources. PMID:14654891
The German cDNA network: cDNAs, functional genomics and proteomics. PMID:14649292
Why is carbonic anhydrase essential to Escherichia coli? PMID:14563877
A multimeric model for murine anti-apoptotic protein Bcl-2 and structural insights for its regulation by post-translational modification. PMID:14517609
LumenP--a neural network predictor for protein localization in the thylakoid lumen. PMID:14500894
ExPASy: The proteomics server for in-depth protein knowledge and analysis. PMID:12824418
GeneLynx mouse: integrated portal to the mouse genome. PMID:12819149
The Comparative Toxicogenomics Database (CTD). PMID:12760826
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. PMID:12520024
NetAffx: Affymetrix probesets and annotations. PMID:12519953 -
SWISS-PROT: connecting biomolecular knowledge via a protein database
PubMed citations: 72.
72 articles citing: SWISS-PROT: connecting biomolecular knowledge via a protein database
Transcript Complexity and New Insights of Restorer Line in CMS-D8 Cotton Through Full-Length Transcriptomic Analysis. PMID:35800603
Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat. PMID:34760406
Hybrid Sequencing in Different Types of Goat Skeletal Muscles Reveals Genes Regulating Muscle Development and Meat Quality. PMID:34679927
Comparative proteomic analysis to annotate the structural and functional association of the hypothetical proteins of S. maltophilia k279a and predict potential T and B cell targets for vaccination. PMID:34043709
Sodium-bile acid co-transporter is crucial for survival of a carcinogenic liver fluke Clonorchis sinensis in the bile. PMID:33284789
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. PMID:32652120
In Silico Comparison Shows that the Pan-Genome of a Dairy-Related Bacterial Culture Collection Covers Most Reactions Annotated to Human Microbiomes. PMID:32605102
In-depth Understanding of Camellia oleifera Self-incompatibility by Comparative Transcriptome, Proteome and Metabolome. PMID:32111089
Single-molecule real-time sequencing facilitates the analysis of transcripts and splice isoforms of anthers in Chinese cabbage (Brassica rapa L. ssp. pekinensis). PMID:31771515
Comparative transcriptome analysis reveals the genetic basis underlying the biosynthesis of polysaccharides in Hericium erinaceus. PMID:31363932
De novo male gonad transcriptome draft for the marine mussel Perumytilus purpuratus with a focus on its reproductive-related proteins. PMID:30510598
Comparative Genomics and Description of Putative Virulence Factors of Melissococcus plutonius, the Causative Agent of European Foulbrood Disease in Honey Bees. PMID:30127293
The draft genome of Brucella abortus strain Ba col-B012, isolated from a dairy farm in Nariño, Colombia, bring new insights into the epidemiology of biovar 4 strains. PMID:29299109
Transcriptomic Response of Chinese Yew (Taxus chinensis) to Cold Stress. PMID:28503178
Transcriptome analysis illuminates the nature of the intracellular interaction in a vertebrate-algal symbiosis. PMID:28462779
Range expansion underlies historical introgressive hybridization in the Iberian hare. PMID:28120863
Comparative Genomics of a Bacterivorous Green Alga Reveals Evolutionary Causalities and Consequences of Phago-Mixotrophic Mode of Nutrition. PMID:26224703
High quality draft genome of Lactobacillus kunkeei EFB6, isolated from a German European foulbrood outbreak of honeybees. PMID:26203329
Towards New Drug Targets? Function Prediction of Putative Proteins of Neisseria meningitidis MC58 and Their Virulence Characterization. PMID:26076386
Critical role of the SPAK protein kinase CCT domain in controlling blood pressure. PMID:25994507
PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more. PMID:25925572
Identification of biomarkers for radiation-induced acute intestinal symptoms (RIAISs) in cervical cancer patients by serum protein profiling. PMID:25256248
Structural and biochemical characterization of the KLHL3-WNK kinase interaction important in blood pressure regulation. PMID:24641320
Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20. PMID:24391926
Metagenomic and biochemical characterizations of sulfur oxidation metabolism in uncultured large sausage-shaped bacterium in hot spring microbial mats. PMID:23185438
Complete genomic sequence of Salmonella enterica serovar Enteritidis phage SE2. PMID:22733878
Complete genome sequence of Pseudomonas aeruginosa lytic bacteriophage PA1O which resembles temperate bacteriophage D3112. PMID:22354942
Expressed sequence-tag analysis of ovaries of Brachiaria brizantha reveals genes associated with the early steps of embryo sac differentiation of apomictic plants. PMID:22068439
DomPep--a general method for predicting modular domain-mediated protein-protein interactions. PMID:22003397
Structural variation in bacterial glyoxalase I enzymes: investigation of the metalloenzyme glyoxalase I from Clostridium acetobutylicum. PMID:21914803
UniProt Knowledgebase: a hub of integrated protein data. PMID:21447597
DDPC: Dragon Database of Genes associated with Prostate Cancer. PMID:20880996
Testing computational prediction of missense mutation phenotypes: functional characterization of 204 mutations of human cystathionine beta synthase. PMID:20455263
Human cancer protein-protein interaction network: a structural perspective. PMID:20011507
DDEC: Dragon database of genes implicated in esophageal cancer. PMID:19580656
An integrative multi-platform analysis for discovering biomarkers of osteosarcoma. PMID:19445706
Identification of semaphorin 5A interacting protein by applying apriori knowledge and peptide complementarity related to protein evolution and structure. PMID:19329067
Search for inhibitors of aminoacyl-tRNA synthases by virtual click chemistry. PMID:19048310
Structural studies of shikimate dehydrogenase from Bacillus anthracis complexed with cofactor NADP. PMID:19043750
Bridging the synaptic gap: neuroligins and neurexin I in Apis mellifera. PMID:18974885
PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. PMID:18487273
Proteomic analysis of Haloferax volcanii reveals salinity-mediated regulation of the stress response protein PspA. PMID:18451052
TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates. PMID:17986453
Gene analogue finder: a GRID solution for finding functionally analogous gene products. PMID:17767718
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PMID:17355171
Visualizing the proteome of Escherichia coli: an efficient and versatile method for labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes. PMID:17272300
Minimal determinants for binding activated G alpha from the structure of a G alpha(i1)-peptide dimer. PMID:16981699
Antimutator role of the DNA glycosylase mutY gene in Helicobacter pylori. PMID:16923889
Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease. PMID:16762065
Genome-scale identification of membrane-associated human mRNAs. PMID:16415983
The Diamond STING server. PMID:15980473
Structural and functional divergence of MutS2 from bacterial MutS1 and eukaryotic MSH4-MSH5 homologs. PMID:15866941
Analysis of the cytoplasmic domains of Salmonella FlhA and interactions with components of the flagellar export machinery. PMID:15516571
Characterization of SLAC: a small laccase from Streptomyces coelicolor with unprecedented activity. PMID:15295117
Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing. PMID:15060008
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. PMID:14681401
Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization. PMID:14536023
Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. PMID:13129938
ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations. PMID:12952559
Natural selection of more designable folds: a mechanism for thermophilic adaptation. PMID:12843403
A model of the human M2 muscarinic acetylcholine receptor. PMID:12825791
ExPASy: The proteomics server for in-depth protein knowledge and analysis. PMID:12824418
Connecting sequence and biology in the laboratory mouse. PMID:12819150
Fishing new proteins in the twilight zone of genomes: the test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative bacteria. PMID:12761386
Genome informatics: current status and future prospects. PMID:12750305
DAVID: Database for Annotation, Visualization, and Integrated Discovery. PMID:12734009
Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. PMID:12552088
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. PMID:12520024
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. PMID:12519986
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. PMID:12477932
Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. PMID:12403464
Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). PMID:11752257 -
UniProt archive
PubMed citations: 62.
62 articles citing: UniProt archive
Unveiling the Possible Oryzalin-Binding Site in the α-Tubulin of Toxoplasma gondii. PMID:35694483
Designing, docking and molecular dynamics simulation studies of novel cloperastine analogues as anti-allergic agents: homology modeling and active site prediction for the human histamine H1 receptor. PMID:35495246
A GDPase/UDPase bifunctional enzyme from Candida albicans: purification and biochemical characterization. PMID:35175437
Finding inhibitors for PCSK9 using computational methods. PMID:34351937
Genome-Wide Identification and Bioinformatics Characterization of Superoxide Dismutases in the Desiccation-Tolerant Cyanobacterium Chroococcidiopsis sp. CCMEE 029. PMID:34122375
Protein Structure Prediction: Conventional and Deep Learning Perspectives. PMID:34050498
Immunoinformatics and Molecular Docking Studies Predicted Potential Multiepitope-Based Peptide Vaccine and Novel Compounds against Novel SARS-CoV-2 through Virtual Screening. PMID:33728324
Linking Biochemical and Structural States of SERCA: Achievements, Challenges, and New Opportunities. PMID:32532023
Identification of enzymatic genes with the potential to reduce biomass recalcitrance through lignin manipulation in Arabidopsis. PMID:32514309
Functional Site Discovery From Incomplete Training Data: A Case Study With Nucleic Acid-Binding Proteins. PMID:31543893
Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition. PMID:31147889
Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine. PMID:30295672
Glutamine 89 is a key residue in the allosteric modulation of human serine racemase activity by ATP. PMID:29899358
Functional association prediction by community profiling. PMID:28454776
Role of Structural Bioinformatics in Drug Discovery by Computational SNP Analysis: Analyzing Variation at the Protein Level. PMID:28302551
Protein Bioinformatics Databases and Resources. PMID:28150231
Evaluation of Long-Term Cryostorage of Brain Tissue Sections for Quantitative Histochemistry. PMID:28080173
UniProt: the universal protein knowledgebase. PMID:27899622
Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants. PMID:27258951
Towards the Physics of Calcium Signalling in Plants. PMID:27137393
A multi-objective optimization approach accurately resolves protein domain architectures. PMID:26458889
Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development. PMID:25735037
Div-BLAST: diversification of sequence search results. PMID:25531115
Grouping of large populations into few CTL immune 'response-types' from influenza H1N1 genome analysis. PMID:25505972
RNAcentral: an international database of ncRNA sequences. PMID:25352543
UniProt: a hub for protein information. PMID:25348405
TSpred: a web server for the rational design of temperature-sensitive mutants. PMID:24782523
Activities at the Universal Protein Resource (UniProt). PMID:24253303
On the role of aggregation prone regions in protein evolution, stability, and enzymatic catalysis: insights from diverse analyses. PMID:24146608
Amino acid composition of proteins reduces deleterious impact of mutations. PMID:24108121
hLGDB: a database of human lysosomal genes and their regulation. PMID:23584836
Update on activities at the Universal Protein Resource (UniProt) in 2013. PMID:23161681
NanoUPLC-MSE proteomic data assessment of soybean seeds using the Uniprot database. PMID:23126227
Improvements in the Protein Identifier Cross-Reference service. PMID:22544604
Reorganizing the protein space at the Universal Protein Resource (UniProt). PMID:22102590
Development of immune-specific interaction potentials and their application in the multi-agent-system VaccImm. PMID:21858048
Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PMID:21556138
UniProt Knowledgebase: a hub of integrated protein data. PMID:21447597
The PluriNetWork: an electronic representation of the network underlying pluripotency in mouse, and its applications. PMID:21179244
Ongoing and future developments at the Universal Protein Resource. PMID:21051339
CCRXP: exploring clusters of conserved residues in protein structures. PMID:20457748
The annotation of full zinc proteomes. PMID:20443034
Covariation of branch lengths in phylogenies of functionally related genes. PMID:20041191
The Universal Protein Resource (UniProt) in 2010. PMID:19843607
Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets. PMID:19779614
Yeast Ste23p shares functional similarities with mammalian insulin-degrading enzymes. PMID:19750477
Re-refinement from deposited X-ray data can deliver improved models for most PDB entries. PMID:19171973
InterPro: the integrative protein signature database. PMID:18940856
The Universal Protein Resource (UniProt) 2009. PMID:18836194
Progress in the PRIDE technique for rapidly comparing protein three-dimensional structures. PMID:18710497
Annotating genes of known and unknown function by large-scale coexpression analysis. PMID:18354039
In silico characterization of proteins: UniProt, InterPro and Integr8. PMID:18219596
The universal protein resource (UniProt). PMID:18045787
PRIDE: new developments and new datasets. PMID:18033805
An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data. PMID:17984082
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. PMID:17945017
An evolutionary method for learning HMM structure: prediction of protein secondary structure. PMID:17888163
pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model. PMID:17222345
The Universal Protein Resource (UniProt). PMID:17142230
Genomic scale sub-family assignment of protein domains. PMID:16877569
Genome cluster database. A sequence family analysis platform for Arabidopsis and rice. PMID:15888677
The Universal Protein Resource (UniProt). PMID:15608167 -
The SWISS-PROT protein sequence database: its relevance to human molecular medical research
PubMed citations: 29.
29 articles citing: The SWISS-PROT protein sequence database: its relevance to human molecular medical research
The Full Model of the pMHC-TCR-CD3 Complex: A Structural and Dynamical Characterization of Bound and Unbound States. PMID:35203317
ODiNPred: comprehensive prediction of protein order and disorder. PMID:32901090
Molecular Dynamics Simulations Reveal Canonical Conformations in Different pMHC/TCR Interactions. PMID:32290289
Evaluation of a Set of C9 N-acyl Neu5Ac2en Mimetics as Viral Sialidase Selective Inhibitors. PMID:27525119
Prestin at year 14: progress and prospect. PMID:24361298
Membrane protein orientation and refinement using a knowledge-based statistical potential. PMID:24047460
Integration of proteomics, bioinformatics, and systems biology in traumatic brain injury biomarker discovery. PMID:23750150
Integrative Approach for Computationally Inferring Interactions between the Alpha and Beta Subunits of the Calcium-Activated Potassium Channel (BK): a Docking Study. PMID:23492851
Homology modeling of the structure of acyl coA:isopenicillin N-acyltransferase (IAT) from Penicillium chrysogenum. IAT interaction studies with isopenicillin-N, combining molecular dynamics simulations and docking. PMID:21695507
Structure-based design of novel small-molecule inhibitors of Plasmodium falciparum. PMID:20426475
Genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order Rhizobiales. PMID:20144182
Candidate List of yoUr Biomarker (CLUB): A Web-based Platform to Aid Cancer Biomarker Research. PMID:19578495
Clique-based data mining for related genes in a biomedical database. PMID:19566964
An integrative multi-platform analysis for discovering biomarkers of osteosarcoma. PMID:19445706
Structural studies of shikimate dehydrogenase from Bacillus anthracis complexed with cofactor NADP. PMID:19043750
Structural descriptor database: a new tool for sequence-based functional site prediction. PMID:19032768
HoxPred: automated classification of Hox proteins using combinations of generalised profiles. PMID:17626621
Functional effects of coxsackievirus and adenovirus receptor glycosylation on homophilic adhesion and adenoviral infection. PMID:17376928
Multiple gene duplication and rapid evolution in the groEL gene: functional implications. PMID:17103057
Development and application of hybrid structure based method for efficient screening of ligands binding to G-protein coupled receptors. PMID:17054015
Energetics of aliphatic deletions in protein cores. PMID:16877708
Domain-based homology modeling and mapping of the conformational epitopes of envelope glycoprotein of west nile virus. PMID:15868152
Effects of cyclic nucleotides on the function of prestin. PMID:15649974
Structure prediction of membrane proteins. PMID:15629037
Bioinformatics Resources for In Silico Proteome Analysis. PMID:14615630
SIRW: A web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches. PMID:12824415
Automated Gene Ontology annotation for anonymous sequence data. PMID:12824400
Phosphorylation of the 24p3 protein secreted from mouse uterus in vitro and in vivo. PMID:11838544
The Genexpress IMAGE knowledge base of the human brain transcriptome: a prototype integrated resource for functional and computational genomics. PMID:10022985 -
UniProt Tools
PubMed citations: 28.
28 articles citing: UniProt Tools
Experimental Study of Potential CD8+ Trivalent Synthetic Peptides for Liver Cancer Vaccine Development Using Sprague Dawley Rat Models. PMID:35686237
Zinc and Copper Ions Induce Aggregation of Human β-Crystallins. PMID:35566320
Genome sequencing of Inonotus obliquus reveals insights into candidate genes involved in secondary metabolite biosynthesis. PMID:35443619
Proteomic Identification of a Gastric Tumor ECM Signature Associated With Cancer Progression. PMID:35340765
In vitro discovery of novel prokaryotic ion channel candidates for antiarrhythmic gene therapy. PMID:34120724
Diversity of Conopeptides and Conoenzymes from the Venom Duct of the Marine Cone Snail Conus bayani as Determined from Transcriptomic and Proteomic Analyses. PMID:33916793
Synergistic Network Pharmacology for Traditional Chinese Medicine Liangxue Tongyu Formula in Acute Intracerebral Hemorrhagic Stroke. PMID:33727915
Carboxylesterase Activities and Protein Expression in Rabbit and Pig Ocular Tissues. PMID:33595329
Antimicrobial Peptide Induced-Stress Renders Staphylococcus aureus Susceptible to Toxic Nucleoside Analogs. PMID:33133056
In Silico Prediction of Protein Adsorption Energy on Titanium Dioxide and Gold Nanoparticles. PMID:33020391
Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae. PMID:33013721
Characterization of Kinase Expression Related to Increased Migration of PC-3M Cells Using Global Comparative Phosphoproteome Analysis. PMID:32859632
Overexpression of the NMig1 Gene Encoding a NudC Domain Protein Enhances Root Growth and Abiotic Stress Tolerance in Arabidopsis thaliana. PMID:32595686
A flexible network-based imputing-and-fusing approach towards the identification of cell types from single-cell RNA-seq data. PMID:32527285
Inferring Virus-Host relationship between HPV and its host Homo sapiens using protein interaction network. PMID:32457456
Single-nucleotide variants in human CD81 influence hepatitis C virus infection of hepatoma cells. PMID:32322956
Pharmacological Mechanisms Underlying the Neuroprotective Effects of Alpinia oxyphylla Miq. on Alzheimer's Disease. PMID:32197305
Variant effect predictions capture some aspects of deep mutational scanning experiments. PMID:32183714
High-throughput metabolomic and transcriptomic analyses vet the potential route of cerpegin biosynthesis in two varieties of Ceropegia bulbosa Roxb. PMID:31802261
HELZ directly interacts with CCR4-NOT and causes decay of bound mRNAs. PMID:31570513
Fecal Metaproteomic Analysis Reveals Unique Changes of the Gut Microbiome Functions After Consumption of Sourdough Carasau Bread. PMID:31417524
Autoantigens PLA2R and THSD7A in membranous nephropathy share a common epitope motif in the N-terminal domain. PMID:31395435
Transcriptomics-based validation of the relatedness of heterogeneous nuclear ribonucleoproteins to chronic lymphocytic leukemia as potential biomarkers of the disease aggressiveness. PMID:30957125
The Bipartite Network Projection-Recommended Algorithm for Predicting Long Non-coding RNA-Protein Interactions. PMID:30388620
Computationally-guided drug repurposing enables the discovery of kinase targets and inhibitors as new schistosomicidal agents. PMID:30346968
IRWNRLPI: Integrating Random Walk and Neighborhood Regularized Logistic Matrix Factorization for lncRNA-Protein Interaction Prediction. PMID:30023002
Multi-Omic Biogeography of the Gastrointestinal Microbiota of a Pre-Weaned Lamb. PMID:29258228
Diversity and Evolutionary Analysis of Iron-Containing (Type-III) Alcohol Dehydrogenases in Eukaryotes. PMID:27893862 - http://dx.doi.org/10.1093/nar/gkaa1100
- http://dx.doi.org/10.1093/nar/gkt1140
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annotation
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
binding motif
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
biocuration
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
cellular component
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
function analysis
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene expression data
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene functional annotation
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
literature curation
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
molecular structure
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
proteome
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequence annotation
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequence similarity
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
structure
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
polypeptide_region
metasource: Fairsharing.org
version: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
general sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein function
metasource: re3data.org
version: re3data.org: The Universal Protein Resource; editing status 2020-05-27; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BW2M last accessed: 2022-11-04
protein information
metasource: re3data.org
version: re3data.org: The Universal Protein Resource; editing status 2020-05-27; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BW2M last accessed: 2022-11-04
proteomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:46.405831
proteins
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:46.405831
enzymes
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:46.405831
Tags
More detailed information about this field from each metasource.
annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
binding motif
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
biocuration
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
cellular component
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
function analysis
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene expression data
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
gene functional annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
literature curation
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
molecular structure
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
proteome
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequence annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequence similarity
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
structure
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
polypeptide_region
metasource: Fairsharing.orgversion: FAIRsharing.org: UniProtKB; UniProt Knowledgebase; DOI: https://doi.org/10.25504/FAIRsharing.s1ne3g; Last edited: March 19, 2021, 11:50 a.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
general sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein function
metasource: re3data.orgversion: re3data.org: The Universal Protein Resource; editing status 2020-05-27; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BW2M last accessed: 2022-11-04
protein information
metasource: re3data.orgversion: re3data.org: The Universal Protein Resource; editing status 2020-05-27; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BW2M last accessed: 2022-11-04
proteomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:46.405831
proteins
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:46.405831
enzymes
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:46.405831
binding motif biocuration cellular component function analysis gene expression gene functional annotation literature curation molecular structure protein proteome sequence annotation sequence similarity structure polypeptide region protein sequence general sequence protein function protein information proteomics proteins enzyme
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