Pfam
Names
More detailed information about this field from each metasource.
Pfam
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
Pfam Protein Families
metasource: re3data.org
version: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
pfam
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
Names
More detailed information about this field from each metasource.
Pfam
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
Pfam Protein Families
metasource: re3data.orgversion: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
pfam
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:11.823842
Other names: Pfam Protein Families, pfam
Names
More detailed information about this field from each metasource.
Pfam
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
Pfam Protein Families
metasource: re3data.orgversion: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
pfam
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:11.823842
The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Pfam also generates higher-level groupings of related entries, known as clans. A clan is a collection of Pfam entries which are related by similarity of sequence, structure or profile-HMM.
Description
More detailed information about this field from each metasource.
The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Pfam also generates higher-level groupings of related entries, known as clans. A clan is a collection of Pfam entries which are related by similarity of sequence, structure or profile-HMM.
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Pfam database is a widely used resource for classifying protein sequences into families and domains. Since Pfam was last described in this journal, over 350 new families have been added in Pfam 33.1 and numerous improvements have been made to existing entries. To facilitate research on COVID-19, we have revised the Pfam entries that cover the SARS-CoV-2 proteome, and built new entries for regions that were not covered by Pfam. We have reintroduced Pfam-B which provides an automatically generated supplement to Pfam and contains 136 730 novel clusters of sequences that are not yet matched by a Pfam family. The new Pfam-B is based on a clustering by the MMseqs2 software. We have compared all of the regions in the RepeatsDB to those in Pfam and have started to use the results to build and refine Pfam repeat families. Pfam is freely available for browsing and download at http://pfam.xfam.org/.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). !!! Powering down the Pfam website On October 5th, redirecting the traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro) will start. The Pfam website will be available at legacy.pfam.xfam.org until January 2023, when it will be decommissioned. You can read more about the sunset period in the blog post (https://xfam.wordpress.com/2022/08/04/pfam-website-decommission/). !!!
metasource: re3data.orgversion: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
Database which contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:11.823842
Webpage:
http://pfam.xfam.org/Webpage
More detailed information about this field from each metasource.
http://pfam.xfam.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
Licence:
Name: Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain DedicationLicence name
More detailed information about this field from each metasource.
Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
CC0
metasource: re3data.orgversion: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
CC0-1.0
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:11.823842
Licence URL
More detailed information about this field from each metasource.
https://creativecommons.org/publicdomain/zero/1.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
https://creativecommons.org/
metasource: re3data.orgversion: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
Publications:
(10)
Publications
More detailed information about this field from each metasource.
Pfam: the protein families database
PMID: 24288371
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
The Pfam protein families database: towards a more sustainable future
PMID: 26673716
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
The Pfam protein families database
PMID: 22127870
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Pfam protein families database
PMID: 19920124
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Pfam protein families database in 2019
PMID: 30357350
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Pfam protein families database
PMID: 18039703
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Pfam: clans, web tools and services
PMID: 16381856
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Pfam: The protein families database in 2021
PMID: 33125078
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
Pfam: a comprehensive database of protein domain families based on seed alignments
PMID: 9223186
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
http://dx.doi.org/10.1093/nar/gkaa913
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Pfam: the protein families database
PMID: 24288371
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
The Pfam protein families database: towards a more sustainable future
PMID: 26673716
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
The Pfam protein families database
PMID: 22127870
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Pfam protein families database
PMID: 19920124
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Pfam protein families database in 2019
PMID: 30357350
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Pfam protein families database
PMID: 18039703
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Pfam: clans, web tools and services
PMID: 16381856
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Pfam: The protein families database in 2021
PMID: 33125078
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
Pfam: a comprehensive database of protein domain families based on seed alignments
PMID: 9223186
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
http://dx.doi.org/10.1093/nar/gkaa913
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
-
Pfam: the protein families database
PubMed citations: 2674.
2674 articles citing: Pfam: the protein families database
Genome-wide identification and expression analysis of phospholipase D gene in leaves of sorghum in response to abiotic stresses. PMID:35910446
Novel Microorganisms Contribute to Biosulfidogenesis in the Deep Layer of an Acidic Pit Lake. PMID:35910036
Genome-Wide Analysis of Anthocyanin Biosynthesis Regulatory WD40 Gene FcTTG1 and Related Family in Ficus carica L. PMID:35909733
Mutations in SORL1 and MTHFDL1 possibly contribute to the development of Alzheimer's disease in a multigenerational Colombian Family. PMID:35905044
Dynamic Transcriptomic Profiling During Liver Development in Schizothorax Prenanti. PMID:35899028
Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins. PMID:35891400
Integrated Analysis of Single-Molecule Real-Time Sequencing and Next-Generation Sequencing Eveals Insights into Drought Tolerance Mechanism of Lolium multiflorum. PMID:35887272
Identification of New Toxicity Mechanisms in Drug-Induced Liver Injury through Systems Pharmacology. PMID:35886075
Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage. PMID:35884206
Identification of sugar transporter (SWEET) genes involved in pomegranate seed coat sugar accumulation. PMID:35875178
Analysis of phylogenetic markers for classification of a hydrogen peroxide producing Streptococcus oralis isolated from saliva by a newly devised differential medium. PMID:35835959
Genomics analysis and degradation characteristics of lignin by Streptomyces thermocarboxydus strain DF3-3. PMID:35831866
Genome-Wide Identification of PLATZ Transcription Factors in Ginkgo biloba L. and Their Expression Characteristics During Seed Development. PMID:35812908
The Hidden Potential of High-Throughput RNA-Seq Re-Analysis, a Case Study for DHDPS, Key Enzyme of the Aspartate-Derived Lysine Biosynthesis Pathway and Its Role in Abiotic and Biotic Stress Responses in Soybean. PMID:35807714
Transcript Complexity and New Insights of Restorer Line in CMS-D8 Cotton Through Full-Length Transcriptomic Analysis. PMID:35800603
Biomimetic generation of the strongest known biomaterial found in limpet tooth. PMID:35798724
Meta-omics approaches reveal unique small RNAs exhibited by the uncultured microorganisms dwelling deep-sea hydrothermal sediment in Guaymas Basin. PMID:35792953
Integrated Metabolomics and Transcriptome Analyses Unveil Pathways Involved in Sugar Content and Rind Color of Two Sugarcane Varieties. PMID:35783968
Heterotrophic Sulfur Oxidation of Halomonas titanicae SOB56 and Its Habitat Adaptation to the Hydrothermal Environment. PMID:35774465
Genome-wide identification and characterization of long noncoding RNAs during peach (Prunus persica) fruit development and ripening. PMID:35773470
VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features. PMID:35761171
Metagenomic Screening for Lipolytic Genes Reveals an Ecology-Clustered Distribution Pattern. PMID:35756004
Whole-genome sequence analysis of Bipolaris sorokiniana infecting wheat in India and characterization of ToxA gene in different isolates as pathogenicity determinants. PMID:35747503
Assembly and Comparison of Ca. Neoehrlichia mikurensis Genomes. PMID:35744652
Identification and Regulatory Network Analysis of Genes Related to Reproductive Performance in the Hypothalamus and Pituitary of Angus Cattle. PMID:35741727
SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning. PMID:35725628
A Phage Receptor-Binding Protein as a Promising Tool for the Detection of Escherichia coli in Human Specimens. PMID:35722298
RIViT-seq enables systematic identification of regulons of transcriptional machineries. PMID:35715393
Prediction of Plant Resistance Proteins Based on Pairwise Energy Content and Stacking Framework. PMID:35712582
Efficient and specific DNA oligonucleotide rRNA probe-based rRNA removal in Talaromyces marneffei. PMID:35711330
Genome-wide identification of R2R3-MYB gene family and association with anthocyanin biosynthesis in Brassica species. PMID:35701743
Complete genome sequence of the Pogostemon cablin bacterial wilt pathogen Ralstonia solanacearum strain SY1. PMID:35670995
Widespread phages of endosymbionts: Phage WO genomics and the proposed taxonomic classification of Symbioviridae. PMID:35666732
Full-Length Transcriptional Analysis of the Same Soybean Genotype With Compatible and Incompatible Reactions to Heterodera glycines Reveals Nematode Infection Activating Plant Defense Response. PMID:35665156
Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum. PMID:35654976
A Standardized Framework for Better Understanding of Phenotypic Differences within Bacterial Phyla Based on Protein Domain. PMID:35652670
The GP-45 Protein, a Highly Variable Antigen from Babesia bigemina, Contains Conserved B-Cell Epitopes in Geographically Distant Isolates. PMID:35631112
Dynamic Changes in Ascorbic Acid Content during Fruit Development and Ripening of Actinidia latifolia (an Ascorbate-Rich Fruit Crop) and the Associated Molecular Mechanisms. PMID:35628618
Genome-Wide Identification, Characterization, and Expression Profiling Analysis of SPL Gene Family during the Inflorescence Development in Trifolium repens. PMID:35627286
Functional Characterization and Whole-Genome Analysis of an Aflatoxin-Degrading Rhodococcus pyridinivorans Strain. PMID:35625502
PepNN: a deep attention model for the identification of peptide binding sites. PMID:35618814
Profile of the in silico secretome of the palm dieback pathogen, Fusarium oxysporum f. sp. albedinis, a fungus that puts natural oases at risk. PMID:35617325
Genome-Wide Identification and Expression of FAR1 Gene Family Provide Insight Into Pod Development in Peanut (Arachis hypogaea). PMID:35592563
Physiological Effects and Transcriptomic Analysis of sbGnRH on the Liver in Pompano (Trachinotus ovatus). PMID:35586618
CFVisual: an interactive desktop platform for drawing gene structure and protein architecture. PMID:35562653
Transcriptomic profile of the predatory mite Amblyseius swirskii (Acari: Phytoseiidae) on different host plants. PMID:35534782
Long Noncoding RNA Expression Rofiles Elucidate the Potential Roles of lncRNA- XR_003496198 in Duck Hepatitis A Virus Type 1 Infection. PMID:35531338
Sugars dominate the seagrass rhizosphere. PMID:35501482
Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India. PMID:35495730
A Novel Efficient L-Lysine Exporter Identified by Functional Metagenomics. PMID:35495724
Research on lncRNA related to drought resistance of Shanlan upland rice. PMID:35490237
A periplasmic cinched protein is required for siderophore secretion and virulence of Mycobacterium tuberculosis. PMID:35474308
Integrative Analysis of Long- and Short-Read Transcriptomes Identify the Regulation of Terpenoids Biosynthesis Under Shading Cultivation in Oenanthe javanica. PMID:35464839
The Genome of Bacillus velezensis SC60 Provides Evidence for Its Plant Probiotic Effects. PMID:35456817
Complete genome sequence of pueraria virus A, a new member of the genus Caulimovirus. PMID:35451686
In-Silico Functional Annotation of Plasmodium falciparum Hypothetical Proteins to Identify Novel Drug Targets. PMID:35444689
Molecular characterization of matrix metalloproteinase gene family across primates. PMID:35444067
Integration of Aspergillus niger transcriptomic profile with metabolic model identifies potential targets to optimise citric acid production from lignocellulosic hydrolysate. PMID:35418297
Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics. PMID:35417463
Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors. PMID:35414589
SSGraphCPI: A Novel Model for Predicting Compound-Protein Interactions Based on Deep Learning. PMID:35409140
A New Ilarvirus Found in French Hydrangea. PMID:35406923
Pangenome Analysis of the Soilborne Fungal Phytopathogen Rhizoctonia solani and Development of a Comprehensive Web Resource: RsolaniDB. PMID:35401459
CsrD regulates amylovoran biosynthesis and virulence in Erwinia amylovora in a novel cyclic-di-GMP dependent manner. PMID:35396793
Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance. PMID:35379360
Investigating the Functional Role of Hypothetical Proteins From an Antarctic Bacterium Pseudomonas sp. Lz4W: Emphasis on Identifying Proteins Involved in Cold Adaptation. PMID:35360867
Tracing back variations in archaeal ESCRT-based cell division to protein domain architectures. PMID:35358274
Innovation and Emerging Roles of Populus trichocarpa TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR Transcription Factors in Abiotic Stresses by Whole-Genome Duplication. PMID:35356113
Multiple Profile Models Extract Features from Protein Sequence Data and Resolve Functional Diversity of Very Different Protein Families. PMID:35353898
In silico analysis of nitrilase-3 protein from Corynebacterium glutamicum for bioremediation of nitrile herbicides. PMID:35348933
Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics. PMID:35348662
De novo assembly of a fruit transcriptome set identifies AmMYB10 as a key regulator of anthocyanin biosynthesis in Aronia melanocarpa. PMID:35337270
Genomic Characterisation of UFJF_PfDIW6: A Novel Lytic Pseudomonas fluorescens-Phage with Potential for Biocontrol in the Dairy Industry. PMID:35337036
Donor Splice Site Variant in SLC9A6 Causes Christianson Syndrome in a Lithuanian Family: A Case Report. PMID:35334527
Systematic identification and expression profiles of the BAHD superfamily acyltransferases in barley (Hordeum vulgare). PMID:35332203
Functional Classification and Characterization of the Fungal Glycoside Hydrolase 28 Protein Family. PMID:35330219
Theoretical Studies of Cyanophycin Dipeptides as Inhibitors of Tyrosinases. PMID:35328756
The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success. PMID:35328000
Draft genomes assembly and annotation of Carex parvula and Carex kokanica reveals stress-specific genes. PMID:35322069
Metagenomic mining and structure-function studies of a hyper-thermostable cellobiohydrolase from hot spring sediment. PMID:35318423
A Novel and Ubiquitous Marine Methylophage Provides Insights into Viral-Host Coevolution and Possible Host-Range Expansion in Streamlined Marine Heterotrophic Bacteria. PMID:35311512
Transcriptome Analysis Revealed a Cold Stress-Responsive Transcription Factor, PaDREB1A, in Plumbago auriculata That Can Confer Cold Tolerance in Transgenic Arabidopsis thaliana. PMID:35310656
Detection and Analysis of Syntenic Quantitative Trait Loci Controlling Cell Wall Quality in Angiosperms. PMID:35310628
CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments. PMID:35310163
Genome-wide Identification, Expression, and Functional Analysis of MdMSI Genes in Apples (Malus domestica Borkh.). PMID:35309144
Comprehensive Transcriptome Analysis of Stem-Differentiating Xylem Upon Compression Stress in Cunninghamia Lanceolata. PMID:35309135
Identification and characterization of heat-responsive lncRNAs in maize inbred line CM1. PMID:35291949
Multi-Approach Analysis Reveals Pathways of Cold Tolerance Divergence in Camellia japonica. PMID:35283896
A near-chromosome level genome assembly of the European hoverfly, Sphaerophoria rueppellii (Diptera: Syrphidae), provides comparative insights into insecticide resistance-related gene family evolution. PMID:35279098
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
Complete Genome Sequence Analysis of Ralstonia solanacearum Strain PeaFJ1 Provides Insights Into Its Strong Virulence in Peanut Plants. PMID:35273586
The UV-B-Induced Transcription Factor HY5 Regulated Anthocyanin Biosynthesis in Zanthoxylum bungeanum. PMID:35269793
Deciphering the Host-Pathogen Interactome of the Wheat-Common Bunt System: A Step towards Enhanced Resilience in Next Generation Wheat. PMID:35269732
RNA-Seq reveals miRNA role in thermogenic regulation in brown adipose tissues of goats. PMID:35255830
Genome-wide identification and expression analysis of HAK/KUP/KT potassium transporter provides insights into genes involved in responding to potassium deficiency and salt stress in pepper (Capsicum annuum L.). PMID:35251880
A High-Quality, Chromosome-Level Genome Provides Insights Into Determinate Flowering Time and Color of Cotton Rose (Hibiscus mutabilis). PMID:35251086
Computational Systems Biology of Alfalfa - Bacterial Blight Host-Pathogen Interactions: Uncovering the Complex Molecular Networks for Developing Durable Disease Resistant Crop. PMID:35251063
Genomic Analysis of Molecular Bacterial Mechanisms of Resistance to Phage Infection. PMID:35250902
Mammary epithelial cell transcriptome reveals potential roles of lncRNAs in regulating milk synthesis pathways in Jersey and Kashmiri cattle. PMID:35246027
Genome-wide evolution and expression analysis of the MYB-CC gene family in Brassica spp. PMID:35237467
SMRT sequencing of full-length transcriptome and gene expression analysis in two chemical types of Pogostemon cablin (Blanco) Benth. PMID:35223208
Identification of Type VI Secretion Systems Effector Proteins That Contribute to Interbacterial Competition in Salmonella Dublin. PMID:35222335
Dynamic Gene Expression and Alternative Splicing Events Demonstrate Co-Regulation of Testicular Differentiation and Maturation by the Brain and Gonad in Common Carp. PMID:35222265
Genome-Wide Analysis of LBD Transcription Factor Genes in Dendrobiumcatenatum. PMID:35216201
Identification of Peanut Aux/IAA Genes and Functional Prediction during Seed Development and Maturation. PMID:35214804
Genome-Wide Association Study Reveals Genetic Architecture and Candidate Genes for Yield and Related Traits under Terminal Drought, Combined Heat and Drought in Tropical Maize Germplasm. PMID:35205393
IMA Genome - F16 : Draft genome assemblies of Fusarium marasasianum, Huntiella abstrusa, two Immersiporthe knoxdaviesiana isolates, Macrophomina pseudophaseolina, Macrophomina phaseolina, Naganishia randhawae, and Pseudocercospora cruenta. PMID:35197126
Insights into glucosinolate accumulation and metabolic pathways in Isatis indigotica Fort. PMID:35193497
Metabolic Diversity and Aero-Tolerance in Anammox Bacteria from Geochemically Distinct Aquifers. PMID:35191775
Identification, Molecular Characteristics, and Evolution of GRF Gene Family in Foxtail Millet (Setaria italica L.). PMID:35185998
Insight Into Pituitary lncRNA and mRNA at Two Estrous Stages in Small Tail Han Sheep With Different FecB Genotypes. PMID:35178025
Comparative transcriptome and weighted correlation network analyses reveal candidate genes involved in chlorogenic acid biosynthesis in sweet potato. PMID:35177832
Whole-transcriptome analysis and construction of an anther development-related ceRNA network in Chinese cabbage (Brassica campestris L. ssp. pekinensis). PMID:35177672
Active anaerobic methane oxidation and sulfur disproportionation in the deep terrestrial subsurface. PMID:35173296
METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. PMID:35172890
Impairment of a cyanobacterial glycosyltransferase that modifies a pilin results in biofilm development. PMID:35172394
Isolation and Characterization of Novel Lytic Phages Infecting Multidrug-Resistant Escherichia coli. PMID:35171030
Genome-wide analysis of the rose (Rosa chinensis) NAC family and characterization of RcNAC091. PMID:35169911
Genome-wide identification and expression profiling analysis of maize AP2/ERF superfamily genes reveal essential roles in abiotic stress tolerance. PMID:35151253
ProtPlat: an efficient pre-training platform for protein classification based on FastText. PMID:35148686
The dynamic trophic architecture of open-ocean protist communities revealed through machine-guided metatranscriptomics. PMID:35145022
Giant sponge grounds of Central Arctic seamounts are associated with extinct seep life. PMID:35136058
Ionotropic receptors in the turnip moth Agrotis segetum respond to repellent medium-chain fatty acids. PMID:35130883
Leaf color formation mechanisms in Alternanthera bettzickiana elucidated by metabolite and transcriptome analyses. PMID:35128619
EST-SSR Marker Development and Full-Length Transcriptome Sequence Analysis of Tiger Lily (Lilium lancifolium Thunb). PMID:35126662
Deeply conserved synteny and the evolution of metazoan chromosomes. PMID:35108053
Database of glutamate-gated chloride (GluCl) subunits across 125 nematode species: patterns of gene accretion and sequence diversification. PMID:35100348
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
Proteomics Uncovers Novel Components of an Interactive Protein Network Supporting RNA Export in Trypanosomes. PMID:35091090
A molecular map of long non-coding RNA expression, isoform switching and alternative splicing in osteoarthritis. PMID:35088088
A Peroxide-Responding sRNA Evolved from a Peroxidase mRNA. PMID:35084505
Nicotinamide Riboside-Conditioned Microbiota Deflects High-Fat Diet-Induced Weight Gain in Mice. PMID:35076278
Genome-Wide Identification and Co-Expression Analysis of ARF and IAA Family Genes in Euscaphis konishii: Potential Regulators of Triterpenoids and Anthocyanin Biosynthesis. PMID:35069676
Mobile Genetic Elements Drive Antimicrobial Resistance Gene Spread in Pasteurellaceae Species. PMID:35069478
CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation. PMID:35069469
Isolation, Classification, and Growth-Promoting Effects of Pantoea sp. YSD J2 from the Aboveground Leaves of Cyperus Esculentus L. var. sativus. PMID:35059843
Genetic and Comparative Genome Analysis of Exiguobacterium aurantiacum SW-20, a Petroleum-Degrading Bacteria with Salt Tolerance and Heavy Metal-Tolerance Isolated from Produced Water of Changqing Oilfield, China. PMID:35056515
Identification of an Amylomaltase from the Halophilic Archaeon Haloquadratum walsbyi by Functional Metagenomics: Structural and Functional Insights. PMID:35054477
A Large-Scale Multiple Genome Comparison of Acidophilic Archaea (pH ≤ 5.0) Extends Our Understanding of Oxidative Stress Responses in Polyextreme Environments. PMID:35052563
Chitinase Chi 2 Positively Regulates Cucumber Resistance against Fusarium oxysporum f. sp. cucumerinum. PMID:35052402
Actinoporin-like Proteins Are Widely Distributed in the Phylum Porifera. PMID:35049929
An Integrative Sialomic Analysis Reveals Molecules From Triatoma sordida (Hemiptera: Reduviidae). PMID:35047420
Proteome-scale mapping of binding sites in the unstructured regions of the human proteome. PMID:35044719
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
Universal gene co-expression network reveals receptor-like protein genes involved in broad-spectrum resistance in pepper (Capsicum annuum L.). PMID:35043174
Association between Arsenic Level, Gene Expression in Asian Population, and In Vitro Carcinogenic Bladder Tumor. PMID:35039759
Enrichment of phosphate-accumulating organisms (PAOs) in a microfluidic model biofilm system by mimicking a typical aerobic granular sludge feast/famine regime. PMID:35032186
Mining for novel cyclomaltodextrin glucanotransferases unravels the carbohydrate metabolism pathway via cyclodextrins in Thermoanaerobacterales. PMID:35031648
Heat shock transcription factor (Hsf) gene family in common bean (Phaseolus vulgaris): genome-wide identification, phylogeny, evolutionary expansion and expression analyses at the sprout stage under abiotic stress. PMID:35031009
Newly identified HMO-2011-type phages reveal genomic diversity and biogeographic distributions of this marine viral group. PMID:35022515
A scaffold-level genome assembly of a minute pirate bug, Orius laevigatus (Hemiptera: Anthocoridae), and a comparative analysis of insecticide resistance-related gene families with hemipteran crop pests. PMID:35012450
Genome-Wide Identification of Stress-Associated Proteins (SAPs) Encoding A20/AN1 Zinc Finger in Almond (Prunus dulcis) and Their Differential Expression during Fruit Development. PMID:35009120
Bidirectional lncRNA Transfer between Cuscuta Parasites and Their Host Plant. PMID:35008986
MYB transcription factor family in sweet cherry (Prunus avium L.): genome-wide investigation, evolution, structure, characterization and expression patterns. PMID:34979911
Insights into phosphatase-activated chemical defense in a marine sponge holobiont. PMID:34977575
Interference With ACSL1 Gene in Bovine Adipocytes: Transcriptome Profiling of mRNA and lncRNA Related to Unsaturated Fatty Acid Synthesis. PMID:34977220
Investigation and Computational Analysis of the Sulfotransferase (SOT) Gene Family in Potato (Solanum tuberosum): Insights into Sulfur Adjustment for Proper Development and Stimuli Responses. PMID:34961068
Functional Characterization of Cotton C-Repeat Binding Factor Genes Reveal Their Potential Role in Cold Stress Tolerance. PMID:34956264
Genome-Wide Analysis of the Soybean Calmodulin-Binding Protein 60 Family and Identification of GmCBP60A-1 Responses to Drought and Salt Stresses. PMID:34948302
Genome Mining of Pseudomonas Species: Diversity and Evolution of Metabolic and Biosynthetic Potential. PMID:34946606
Characterization of a Secretory YML079-like Cupin Protein That Contributes to Sclerotinia sclerotiorum Pathogenicity. PMID:34946121
Identification, Synthesis, Conformation and Activity of an Insulin-like Peptide from a Sea Anemone. PMID:34944429
Recombinant Production and Characterization of a New Toxin from Cryptops iheringi Centipede Venom Revealed by Proteome and Transcriptome Analysis. PMID:34941696
Amyloid-like aggregating proteins cause lysosomal defects in neurons via gain-of-function toxicity. PMID:34933920
BrCNGC gene family in field mustard: genome-wide identification, characterization, comparative synteny, evolution and expression profiling. PMID:34921218
Worldwide distribution and environmental origin of the Adelaide imipenemase (AIM-1), a potent carbapenemase in Pseudomonas aeruginosa. PMID:34919514
Genomic analysis of Elsinoë arachidis reveals its potential pathogenic mechanism and the biosynthesis pathway of elsinochrome toxin. PMID:34914789
Cryptosporidium felis differs from other Cryptosporidium spp. in codon usage. PMID:34907893
A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data. PMID:34900140
The genome of the zebra mussel, Dreissena polymorpha: a resource for comparative genomics, invasion genetics, and biocontrol. PMID:34897429
Deep Conservation of Histone Variants in Thermococcales Archaea. PMID:34894218
Structural Predictive Model of Presenilin-2 Protein and Analysis of Structural Effects of Familial Alzheimer's Disease Mutations. PMID:34881055
Circular RNA Expression and Regulation Profiling in Testicular Tissues of Immature and Mature Wandong Cattle (Bos taurus). PMID:34880896
RNA-Binding Protein Expression Alters Upon Differentiation of Human B Cells and T Cells. PMID:34867946
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
Identification of genes related to tipburn resistance in Chinese cabbage and preliminary exploration of its molecular mechanism. PMID:34861825
Structural dynamics in the evolution of a bilobed protein scaffold. PMID:34845009
Nanopore-Based Comparative Transcriptome Analysis Reveals the Potential Mechanism of High-Temperature Tolerance in Cotton (Gossypium hirsutum L.). PMID:34834881
Comprehensive Comparative Analysis of the GATA Transcription Factors in Four Rosaceae Species and Phytohormonal Response in Chinese Pear (Pyrus bretschneideri) Fruit. PMID:34830372
Infection Process and Genome Assembly Provide Insights into the Pathogenic Mechanism of Destructive Mycoparasite Calcarisporium cordycipiticola with Host Specificity. PMID:34829206
Selective Sweeps and Polygenic Adaptation Drive Local Adaptation along Moisture and Temperature Gradients in Natural Populations of Coast Redwood and Giant Sequoia. PMID:34828432
Genome-Wide Analysis of the Glutathione S-Transferase (GST) Genes and Functional Identification of MdGSTU12 Reveals the Involvement in the Regulation of Anthocyanin Accumulation in Apple. PMID:34828339
In Silico and Transcription Analysis of Trehalose-6-phosphate Phosphatase Gene Family of Wheat: Trehalose Synthesis Genes Contribute to Salinity, Drought Stress and Leaf Senescence. PMID:34828258
Integrated Analysis of lncRNA and mRNA Reveals Novel Insights into Wool Bending in Zhongwei Goat. PMID:34828057
De Novo Reconstruction of Transcriptome Identified Long Non-Coding RNA Regulator of Aging-Related Brown Adipose Tissue Whitening in Rabbits. PMID:34827171
First Report of OvoA Gene in Marine Arthropods: A New Candidate Stress Biomarker in Copepods. PMID:34822518
Single-cell RNA sequencing of the Strongylocentrotus purpuratus larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome. PMID:34821556
MicroRNA-222 Transferred From Semen Extracellular Vesicles Inhibits Sperm Apoptosis by Targeting BCL2L11. PMID:34820370
Genome-Wide Investigation of the NAC Transcription Factor Family in Miscanthus sinensis and Expression Analysis Under Various Abiotic Stress. PMID:34804100
Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus. PMID:34800971
Diversity, multifaceted evolution, and facultative saprotrophism in the European Batrachochytrium salamandrivorans epidemic. PMID:34795258
Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii. PMID:34789157
Unveiling Ecological and Genetic Novelty within Lytic and Lysogenic Viral Communities of Hot Spring Phototrophic Microbial Mats. PMID:34787442
Characterisation of a putative M23-domain containing protein in Mycobacterium tuberculosis. PMID:34784363
Neuroprotective effects of long noncoding RNAs involved in ischemic postconditioning after ischemic stroke. PMID:34782575
Whole-transcriptome sequencing reveals a vernalization-related ceRNA regulatory network in chinese cabbage (Brassica campestris L. ssp. pekinensis). PMID:34773977
Computationally Reconstructed Interactome of Bradyrhizobium diazoefficiens USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation. PMID:34769335
Current Approaches in Supersecondary Structures Investigation. PMID:34769310
Antimicrobial Peptides: An Update on Classifications and Databases. PMID:34769122
Transcriptome based identification and validation of heat stress transcription factors in wheat progenitor species Aegilops speltoides. PMID:34764387
Vibrio neptunius Produces Piscibactin and Amphibactin and Both Siderophores Contribute Significantly to Virulence for Clams. PMID:34760718
Verification of TRI3 Acetylation of Trichodermol to Trichodermin in the Plant Endophyte Trichoderma taxi. PMID:34759898
High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems. PMID:34758284
Genome-Wide Analysis of Major Facilitator Superfamily and Its Expression in Response of Poplar to Fusarium oxysporum. PMID:34745233
Genome-wide in silico analysis of long intergenic non-coding RNAs from rice peduncles at the heading stage. PMID:34744373
Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state. PMID:34743175
Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site. PMID:34737728
Recurrent mutations promote widespread structural and functional divergence of MULE-derived genes in plants. PMID:34725701
DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes. PMID:34724822
Integrating full-length transcriptomics and metabolomics reveals the regulatory mechanisms underlying yellow pigmentation in tree peony (Paeonia suffruticosa Andr.) flowers. PMID:34719694
Identification of defense related gene families and their response against powdery and downy mildew infections in Vitis vinifera. PMID:34717533
Genomic and Transcriptomic Insight of Giant Sclerotium Formation of Wood-Decay Fungi. PMID:34712214
In action-an early warning system for the detection of unexpected or novel pathogens. PMID:34703624
The GH19 Engineering Database: Sequence diversity, substrate scope, and evolution in glycoside hydrolase family 19. PMID:34699529
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
Characterization of Inducible HSP70 Genes in an Antarctic Yeast, Glaciozyma antarctica PI12, in Response to Thermal Stress. PMID:34683390
Genomic Characterization of Two Novel RCA Phages Reveals New Insights into the Diversity and Evolution of Marine Viruses. PMID:34668749
A histidine kinase and a response regulator provide phage resistance to Marinomonas mediterranea via CRISPR-Cas regulation. PMID:34663886
Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds. PMID:34659136
Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis. PMID:34656184
Thinopyrum intermedium TiAP1 interacts with a chitin deacetylase from Blumeria graminis f. sp. tritici and increases the resistance to Bgt in wheat. PMID:34651397
The Distinct Properties of the Consecutive Disordered Regions Inside or Outside Protein Domains and Their Functional Significance. PMID:34639018
Genome-Wide Analysis of the TCP Transcription Factor Genes in Dendrobium catenatum Lindl. PMID:34638610
Transcriptomics Reveals the Putative Mycoparasitic Strategy of the Mushroom Entoloma abortivum on Species of the Mushroom Genus Armillaria. PMID:34636668
The Biocontrol and Plant Growth-Promoting Properties of Streptomyces alfalfae XN-04 Revealed by Functional and Genomic Analysis. PMID:34630371
Distribution of bacteriocin genes in the lineages of Lactiplantibacillus plantarum. PMID:34625657
Whole Genome Sequence of Alternaria alternata, the Causal Agent of Black Spot of Kiwifruit. PMID:34616379
Identification of ABC transporter G subfamily in white lupin and functional characterization of L.albABGC29 in phosphorus use. PMID:34615466
An automated and combinative method for the predictive ranking of candidate effector proteins of fungal plant pathogens. PMID:34611252
Complete genome sequence of a putative novel ilarvirus isolated from Eleocharis dulcis. PMID:34608526
Comparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice. PMID:34608238
Transcriptome Analysis Revealed Potential Mechanisms of Resistance to Trichomoniasis gallinae Infection in Pigeon (Columba livia). PMID:34595226
Mining nematode protein secretomes to explain lifestyle and host specificity. PMID:34587193
Analysis of PRX Gene Family and Its Function on Cell Lignification in Pears (Pyrus bretschneideri). PMID:34579408
Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce's disease. PMID:34568917
Profiling of MicroRNAs in Midguts of Plutella xylostella Provides Novel Insights Into the Bacillus thuringiensis Resistance. PMID:34567090
StAR-Related Lipid Transfer (START) Domains Across the Rice Pangenome Reveal How Ontogeny Recapitulated Selection Pressures During Rice Domestication. PMID:34567086
Insights Into the Molecular Evolution of AT-Hook Motif Nuclear Localization Genes in Brassica napus. PMID:34567028
Marine Transcriptomics Analysis for the Identification of New Antimicrobial Peptides. PMID:34564152
Transcriptome-based analysis reveals that the biosynthesis of anthocyanins is more active than that of flavonols and proanthocyanins in the colorful flowers of Lagerstroemia indica. PMID:34554492
Proteomic Tools for the Analysis of Cytoskeleton Proteins. PMID:34542864
Improvement of the Catalytic Ability of a Thermostable and Acidophilic β-Mannanase Using a Consensus Sequence Design Strategy. PMID:34539615
Genome-wide identification, phylogeny, and expression analysis of the bHLH gene family in tobacco (Nicotiana tabacum). PMID:34539114
D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions. PMID:34536380
Identification and Expression Analyses of Invertase Genes in Moso Bamboo Reveal Their Potential Drought Stress Functions. PMID:34527019
PathFams: statistical detection of pathogen-associated protein domains. PMID:34521345
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. PMID:34520557
Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants. PMID:34518545
Full-length transcriptome analysis of Spodoptera frugiperda larval brain reveals detoxification genes. PMID:34513339
Complete genome sequence and identification of polyunsaturated fatty acid biosynthesis genes of the myxobacterium Minicystis rosea DSM 24000T. PMID:34511070
A highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest. PMID:34504275
A high-quality chromosome-level genome of wild Rosa rugosa. PMID:34499118
Genome-wide analysis of OSCA gene family members in Vigna radiata and their involvement in the osmotic response. PMID:34493199
Packpred: Predicting the Functional Effect of Missense Mutations. PMID:34490344
Comparative genomic analysis reveals metabolic flexibility of Woesearchaeota. PMID:34489402
Zanthoxylum-specific whole genome duplication and recent activity of transposable elements in the highly repetitive paleotetraploid Z. bungeanum genome. PMID:34480029
A high-quality chromosome-scale assembly of the centipedegrass [Eremochloa ophiuroides (Munro) Hack.] genome provides insights into chromosomal structural evolution and prostrate growth habit. PMID:34465733
ProteinEvolverABC: Coestimation of Recombination and Substitution Rates in Protein Sequences by approximate Bayesian computation. PMID:34450622
Moisture modulates soil reservoirs of active DNA and RNA viruses. PMID:34446837
Pan-transcriptome identifying master genes and regulation network in response to drought and salt stresses in Alfalfa (Medicago sativa L.). PMID:34446782
OTX2 Homeoprotein Functions in Adult Choroid Plexus. PMID:34445655
Metatranscriptomic Analysis of Bacterial Communities on Laundered Textiles: A Pilot Case Study. PMID:34442670
Comparative Transcriptomic Analysis Reveals the Effects of Drought on the Biosynthesis of Methyleugenol in Asarum sieboldii Miq. PMID:34439899
A Computational Approach to Evaluate the Combined Effect of SARS-CoV-2 RBD Mutations and ACE2 Receptor Genetic Variants on Infectivity: The COVID-19 Host-Pathogen Nexus. PMID:34434902
Identification of Oral Bacterial Biosynthetic Gene Clusters Associated with Caries. PMID:34410645
DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data. PMID:34408730
Comprehensive in silico Characterization of Universal Stress Proteins in Rice (Oryza sativa L.) With Insight Into Their Stress-Specific Transcriptional Modulation. PMID:34394169
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
Pseudomonas nanhaiensis sp. nov., a lipase-producing bacterium isolated from deep-sea sediment of the South China Sea. PMID:34392431
Comparative evolution of vegetative branching in sorghum. PMID:34388196
Antimicrobial Resistance Profiling and Phylogenetic Analysis of Neisseria gonorrhoeae Clinical Isolates From Kenya in a Resource-Limited Setting. PMID:34385981
Evolution and origin of sliding clamp in bacteria, archaea and eukarya. PMID:34379636
P2T2: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants. PMID:34377961
Insight into membraneless organelles and their associated proteins: Drivers, Clients and Regulators. PMID:34377363
De novo genome assembly of the potent medicinal plant Rehmannia glutinosa using nanopore technology. PMID:34377362
Conversion of dietary inositol into propionate and acetate by commensal Anaerostipes associates with host health. PMID:34376656
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
Integrated Analysis of Long Non-Coding RNA and mRNA Expression Profiles in Testes of Calves and Sexually Mature Wandong Bulls (Bos taurus). PMID:34359134
Male Differentiation in the Marine Copepod Oithona nana Reveals the Development of a New Nervous Ganglion and Lin12-Notch-Repeat Protein-Associated Proteolysis. PMID:34356512
Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger. PMID:34354050
An Ecological Basis for Dual Genetic Code Expansion in Marine Deltaproteobacteria. PMID:34335502
Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree. PMID:34325658
An astonishing wealth of new proteasome homologs. PMID:34323935
Targeted immune epitope prediction to HHLA2 and MAGEB5 protein variants as therapeutic approach to related viral diseases. PMID:34320928
Genome-wide identification of candidate aquaporins involved in water accumulation of pomegranate outer seed coat. PMID:34316414
Comparative genome and transcriptome analyses reveal innate differences in response to host plants by two color forms of the two-spotted spider mite Tetranychus urticae. PMID:34301178
Genome-Wide Identification of GRAS Gene Family and Their Responses to Abiotic Stress in Medicago sativa. PMID:34299352
Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri. PMID:34294116
The complete mitochondrial genome of Cycas debaoensis revealed unexpected static evolution in gymnosperm species. PMID:34293066
Single-Molecule Real-Time and Illumina-Based RNA Sequencing Data Identified Vernalization-Responsive Candidate Genes in Faba Bean (Vicia faba L.). PMID:34290734
Genetic association studies of alterations in protein function expose recessive effects on cancer predisposition. PMID:34290314
Evolution of Toll, Spatzle and MyD88 in insects: the problem of the Diptera bias. PMID:34289811
Co-evolutionary landscape at the interface and non-interface regions of protein-protein interaction complexes. PMID:34285778
Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato). PMID:34283859
Leri: A web-server for identifying protein functional networks from evolutionary couplings. PMID:34257835
The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts. PMID:34253727
High-quality genome assembly of Huazhan and Tianfeng, the parents of an elite rice hybrid Tian-you-hua-zhan. PMID:34251582
A Chromosome-Level Genome Assembly of the Mandarin Fish (Siniperca chuatsi). PMID:34249093
Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa). PMID:34243710
Transcriptome Profile Analysis of Strawberry Leaves Reveals Flowering Regulation under Blue Light Treatment. PMID:34235213
Genomic diversity, life strategies and ecology of marine HTVC010P-type pelagiphages. PMID:34227930
Cloning, expression analysis and In silico characterization of HSP101: a potential player conferring heat stress in Aegilops speltoides (Tausch) Gren. PMID:34220041
Microbiome diversity and host immune functions influence survivorship of sponge holobionts under future ocean conditions. PMID:34218251
Integrated Insight into the Molecular Mechanisms of Spontaneous Abortion during Early Pregnancy in Pigs. PMID:34205766
Nanopore-based full-length transcriptome sequencing of Muscovy duck (Cairina moschata) ovary. PMID:34198095
Multiple responses contribute to the enhanced drought tolerance of the autotetraploid Ziziphus jujuba Mill. var. spinosa. PMID:34193297
Development and Interrogation of a Transcriptomic Resource for the Giant Triton Snail (Charonia tritonis). PMID:34191212
LncRNA VEAL2 regulates PRKCB2 to modulate endothelial permeability in diabetic retinopathy. PMID:34180064
Characterization of a Hyaluronic Acid Utilization Locus and Identification of Two Hyaluronate Lyases in a Marine Bacterium Vibrio alginolyticus LWW-9. PMID:34177877
Identification, evolution, expression analysis of phospholipase D (PLD) gene family in tea (Camellia sinensis). PMID:34177145
Genome-wide characterization of LTR retrotransposons in the non-model deep-sea annelid Lamellibrachia luymesi. PMID:34157969
Duplication and Functional Divergence of Branched-Chain Amino Acid Biosynthesis Genes in Aspergillus nidulans. PMID:34154419
The extracellular contractile injection system is enriched in environmental microbes and associates with numerous toxins. PMID:34145238
A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics. PMID:34145222
COSMIC Cancer Gene Census 3D database: understanding the impacts of mutations on cancer targets. PMID:34137435
Differential responses of anthers of stress tolerant and sensitive wheat cultivars to high temperature stress. PMID:34131818
Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses. PMID:34117322
Genomic adaptations enabling Acidithiobacillus distribution across wide-ranging hot spring temperatures and pHs. PMID:34116726
Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils. PMID:34105010
Translation role of circRNAs in cancers. PMID:34097315
Genome-Wide Analysis of DA1-Like Genes in Gossypium and Functional Characterization of GhDA1-1A Controlling Seed Size. PMID:34093610
Genome-Wide Study of NOT2_3_5 Protein Subfamily in Cotton and Their Necessity in Resistance to Verticillium wilt. PMID:34073210
TILLING-by-Sequencing+ Reveals the Role of Novel Fatty Acid Desaturases (GmFAD2-2s) in Increasing Soybean Seed Oleic Acid Content. PMID:34069320
Avian Influenza H7N9 Virus Adaptation to Human Hosts. PMID:34068495
Homology and Modular Evolution of CATCHR at the Origin of the Eukaryotic Endomembrane System. PMID:34061181
Nutrient Loading and Viral Memory Drive Accumulation of Restriction Modification Systems in Bloom-Forming Cyanobacteria. PMID:34060332
Systematic screening of long intergenic noncoding RNAs expressed during chicken embryogenesis. PMID:34058566
Maize Endochitinase Expression in Response to Fall Armyworm Herbivory. PMID:34056671
Pretraining model for biological sequence data. PMID:34050350
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
Draft Genome Sequences of Five Fungal Strains Isolated from Kefir. PMID:34042484
Structure-based protein function prediction using graph convolutional networks. PMID:34039967
Gene Ontology Meta Annotator for Plants (GOMAP). PMID:34034755
De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn. PMID:34034673
MyCLADE: a multi-source domain annotation server for sequence functional exploration. PMID:34023906
Microbial sulfate reduction by Desulfovibrio is an important source of hydrogen sulfide from a large swine finishing facility. PMID:34021225
Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets. PMID:34011275
Characterization of a new bifunctional endo-1,4-β-xylanase/esterase found in the rumen metagenome. PMID:34001974
On the evolution of chaperones and cochaperones and the expansion of proteomes across the Tree of Life. PMID:34001607
Abundance Imparts Evolutionary Constraints of Similar Magnitude on the Buried, Surface, and Disordered Regions of Proteins. PMID:33996892
Genome-wide identification and characterization of NAC genes in Brassica juncea var. tumida. PMID:33996278
Genome-wide analysis of the serine carboxypeptidase-like protein family in Triticum aestivum reveals TaSCPL184-6D is involved in abiotic stress response. PMID:33992092
Adhesive Functions or Pseudogenization of Type Va Autotransporters in Brucella Species. PMID:33987105
Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts. PMID:33972727
Single-cell transcriptome profiling of buffelgrass (Cenchrus ciliaris) eggs unveils apomictic parthenogenesis signatures. PMID:33972603
Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets. PMID:33971924
The order of PDZ3 and TrpCage in fusion chimeras determines their properties-a biophysical characterization. PMID:33969912
Elucidating the Regulatory Elements for Transcription Termination and Posttranscriptional Processing in the Streptomyces clavuligerus Genome. PMID:33947798
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. PMID:33944776
Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides. PMID:33941076
Genome-wide characterization and expression and co-expression analysis suggested diverse functions of WOX genes in bread wheat. PMID:33937537
Comprehensive analysis of coding and non-coding RNA transcriptomes related to hypoxic adaptation in Tibetan chickens. PMID:33934713
How Quality Control Systems AID Sec-Dependent Protein Translocation. PMID:33928127
Genome-wide identification of superoxide dismutase gene families and their expression patterns under low-temperature, salt and osmotic stresses in watermelon and melon. PMID:33927985
Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum. PMID:33927397
Stepwise pathogenic evolution of Mycobacterium abscessus. PMID:33926925
Structural, Evolutionary, and Functional Analysis of the Protein O-Mannosyltransferase Family in Pathogenic Fungi. PMID:33922798
Deep Learning in Virtual Screening: Recent Applications and Developments. PMID:33922714
A First Insight into the Gonad Transcriptome of Hong Kong Catfish (Clarias fuscus). PMID:33920938
Novel Siphoviridae Bacteriophages Infecting Bacteroides uniformis Contain Diversity Generating Retroelement. PMID:33919474
Chromosome-scale assembly and analysis of biomass crop Miscanthus lutarioriparius genome. PMID:33911077
Molecular mechanism of lateral bud differentiation of Pinus massoniana based on high-throughput sequencing. PMID:33907200
Forecasting the dissemination of antibiotic resistance genes across bacterial genomes. PMID:33893312
Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences. PMID:33876751
Large-Scale Phylogenomic Analyses Reveal the Monophyly of Bryophytes and Neoproterozoic Origin of Land Plants. PMID:33871608
A pan-cancer transcriptome analysis of exitron splicing identifies novel cancer driver genes and neoepitopes. PMID:33861991
Structure-based phylogeny identifies avoralstat as a TMPRSS2 inhibitor that prevents SARS-CoV-2 infection in mice. PMID:33844653
LncRNA lnc_13814 promotes the cells apoptosis in granulosa cells of duck by acting as apla-miR-145-4 sponge. PMID:33843432
Gene and Transposable Element Expression Evolution Following Recent and Past Polyploidy Events in Spartina (Poaceae). PMID:33841492
Identification and evolution analysis of the JAZ gene family in maize. PMID:33838665
Evolutionary research on the expansin protein family during the plant transition to land provides new insights into the development of Tartary buckwheat fruit. PMID:33836656
Aspirin Modulation of the Colorectal Cancer-Associated Microbe Fusobacterium nucleatum. PMID:33824205
In silico identification of Capsicum type III polyketide synthase genes and expression patterns in Capsicum annuum. PMID:33817263
Characterization of Haemophilus Parasuis Serovar 2 CL120103, a Moderately Virulent Strain in China. PMID:33817086
Method for Essential Protein Prediction Based on a Novel Weighted Protein-Domain Interaction Network. PMID:33815480
Single individual structural variant detection uncovers widespread hemizygosity in molluscs. PMID:33813894
Genome-wide Identification and Characterization of FCS-Like Zinc Finger (FLZ) Family Genes in Maize (Zea mays) and Functional Analysis of ZmFLZ25 in Plant Abscisic Acid Response. PMID:33805388
The Mitochondrial Genome of a Plant Fungal Pathogen Pseudocercospora fijiensis (Mycosphaerellaceae), Comparative Analysis and Diversification Times of the Sigatoka Disease Complex Using Fossil Calibrated Phylogenies. PMID:33803147
Full-Length Transcriptome Sequencing Provides Insights into Flavonoid Biosynthesis in Fritillaria hupehensis. PMID:33800612
Genome Wide Analysis of U-Box E3 Ubiquitin Ligases in Wheat (Triticum aestivum L.). PMID:33800063
Bacterial cyclic diguanylate signaling networks sense temperature. PMID:33790266
Immunity proteins of dual nuclease T6SS effectors function as transcriptional repressors. PMID:33786997
Expansion and persistence of antibiotic-specific resistance genes following antibiotic treatment. PMID:33779498
Two-step functional screen on multiple proteinaceous substrates reveals temperature-robust proteases with a broad-substrate range. PMID:33770243
Comparative population genomic analyses of transporters within the Asgard archaeal superphylum. PMID:33770091
Full length sequencing reveals novel transcripts of detoxification genes along with related alternative splicing events and lncRNAs in Phyllotreta striolata. PMID:33760871
Molecular Evolution and Local Root Heterogeneous Expression of the Chenopodium quinoa ARF Genes Provide Insights into the Adaptive Domestication of Crops in Complex Environments. PMID:33755734
Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases. PMID:33750949
Dissemination of novel Tn7 family transposons carrying genes for synthesis and uptake of fimsbactin siderophores among Acinetobacter baumannii isolates. PMID:33749577
Insights into the genome and secretome of Fusarium metavorans DSM105788 by cultivation on agro-residual biomass and synthetic nutrient sources. PMID:33743779
Understanding and exploiting the fatty acid desaturation system in Rhodotorula toruloides. PMID:33741038
High-Fiber, Whole-Food Dietary Intervention Alters the Human Gut Microbiome but Not Fecal Short-Chain Fatty Acids. PMID:33727392
Genome-wide transcriptome profiling uncovers differential miRNAs and lncRNAs in ovaries of Hu sheep at different developmental stages. PMID:33712687
Genome-wide identification, characterization, and expression analysis of the NAC transcription factor family in orchardgrass (Dactylis glomerata L.). PMID:33711917
Adaptive Gene Content and Allele Distribution Variations in the Wild and Domesticated Populations of Saccharomyces cerevisiae. PMID:33679656
Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA. PMID:33660784
A novel family of secreted insect proteins linked to plant gall development. PMID:33657407
The soybean (Glycine max L.) cytokinin oxidase/dehydrogenase multigene family; Identification of natural variations for altered cytokinin content and seed yield. PMID:33644633
A gene expression atlas for kiwifruit (Actinidia chinensis) and network analysis of transcription factors. PMID:33639842
Transcriptome analysis of the role of autophagy in plant response to heat stress. PMID:33635879
Generating functional protein variants with variational autoencoders. PMID:33635868
Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume. PMID:33622244
Characteristic and evolution of HAT and HDAC genes in Gramineae genomes and their expression analysis under diverse stress in Oryza sativa. PMID:33606144
Draft Genome Sequences of Pelagimyophage Mosig EXVC030M and Pelagipodophage Lederberg EXVC029P, Isolated from Devil's Hole, Bermuda. PMID:33602731
DeepRTCP: Predicting ATP-Binding Cassette Transporters Based on 1-Dimensional Convolutional Network. PMID:33598454
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
High Quality Aspergillus aculeatus Genomes and Transcriptomes: A Platform for Cellulase Activity Optimization Toward Industrial Applications. PMID:33585410
Domain Unknown Function DUF1668-Containing Genes in Multiple Lineages Are Responsible for F1 Pollen Sterility in Rice. PMID:33574828
A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida). PMID:33570560
Genome-wide identification and characterization of long non-coding RNAs involved in flag leaf senescence of rice. PMID:33569692
Evolution, expression and functional analysis of cultivated allotetraploid cotton DIR genes. PMID:33568051
A Novel Trichomonas vaginalis Surface Protein Modulates Parasite Attachment via Protein:Host Cell Proteoglycan Interaction. PMID:33563826
Combined Metabolome and Transcriptome Profiling Reveal Optimal Harvest Strategy Model Based on Different Production Purposes in Olive. PMID:33562421
De novo genome assembly of the tobacco hornworm moth (Manduca sexta). PMID:33561252
Activity of bacteria isolated from bats against Pseudogymnoascus destructans in China. PMID:33559264
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
prPred: A Predictor to Identify Plant Resistance Proteins by Incorporating k-Spaced Amino Acid (Group) Pairs. PMID:33553134
Genome-wide identification, evolution, expression, and alternative splicing profiles of peroxiredoxin genes in cotton. PMID:33552724
Intrinsic disorder in protein domains contributes to both organism complexity and clade-specific functions. PMID:33542394
Four families of folate-independent methionine synthases. PMID:33534785
From genomes to molecular dynamics - A bottom up approach in extrication of SARS CoV-2 main protease inhibitors. PMID:33532671
Long-Term Waterlogging as Factor Contributing to Hypoxia Stress Tolerance Enhancement in Cucumber: Comparative Transcriptome Analysis of Waterlogging Sensitive and Tolerant Accessions. PMID:33525400
A Transcriptomic Approach to the Recruitment of Venom Proteins in a Marine Annelid. PMID:33525375
Insights into triterpene synthesis and unsaturated fatty-acid accumulation provided by chromosomal-level genome analysis of Akebia trifoliata subsp. australis. PMID:33518712
Impacts of fludioxonil resistance on global gene expression in the necrotrophic fungal plant pathogen Sclerotinia sclerotiorum. PMID:33516198
The rise and fall of the ancient northern pike master sex-determining gene. PMID:33506762
Bridging Themes: Short Protein Segments Found in Different Architectures. PMID:33502503
Genomic analysis of WD40 protein family in the mango reveals a TTG1 protein enhances root growth and abiotic tolerance in Arabidopsis. PMID:33500544
Comparative transcriptomics and host-specific parasite gene expression profiles inform on drivers of proliferative kidney disease. PMID:33495500
Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics. PMID:33489789
BSR-Seq analysis provides insights into the cold stress response of Actinidia arguta F1 populations. PMID:33482717
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
Comprehensive analysis of NAC transcription factor family uncovers drought and salinity stress response in pearl millet (Pennisetum glaucum). PMID:33478383
A genomic view of the microbiome of coral reef demosponges. PMID:33469166
Discovery of a hidden transient state in all bromodomain families. PMID:33468647
Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia. PMID:33462312
Investigation of circular RNAs in an ectoparasitic mite Varroa destructor (Acarina: Varroidae) of the honey bee. PMID:33452589
Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway. PMID:33452484
The pineapple MADS-box gene family and the evolution of early monocot flower. PMID:33441609
Genomic signatures of the evolution of defence against its natural enemies in the poisonous and medicinal plant Datura stramonium (Solanaceae). PMID:33441607
Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community. PMID:33436509
Transcriptomic analysis of early stages of intestinal regeneration in Holothuria glaberrima. PMID:33431961
Genome-wide identification of the histone acetyltransferase gene family in Triticum aestivum. PMID:33430760
Analysis of Apoptosis-Related Genes Reveals that Apoptosis Functions in Conidiation and Pathogenesis of Fusarium pseudograminearum. PMID:33408234
Transcriptional response of Asarum heterotropoides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. leaves grown under full and partial daylight conditions. PMID:33407099
Sequencing, de novo assembly and annotation of Digitalis ferruginea subsp. schischkinii transcriptome. PMID:33403559
Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean. PMID:33398100
The Complete Genome of Probiotic Lactobacillus sakei Derived from Plateau Yak Feces. PMID:33371298
RELT stains prominently in B-cell lymphomas and binds the hematopoietic transcription factor MDFIC. PMID:33367115
Functional metagenomics of the thioredoxin superfamily. PMID:33361108
Physiological and transcriptomic analyses of yellow horn (Xanthoceras sorbifolia) provide important insights into salt and saline-alkali stress tolerance. PMID:33351842
Functional and computational identification of a rescue mutation near the active site of an mRNA methyltransferase. PMID:33318548
Deciphering the functional role of hypothetical proteins from Chloroflexus aurantiacs J-10-f1 using bioinformatics approach. PMID:33313333
Identification of chalcone synthase genes and their expression patterns reveal pollen abortion in cotton. PMID:33304181
Chromosome-level draft genome of a diploid plum (Prunus salicina). PMID:33300949
Microbe-set enrichment analysis facilitates functional interpretation of microbiome profiling data. PMID:33293650
Multiple Sequence Alignment Computation Using the T-Coffee Regressive Algorithm Implementation. PMID:33289888
Genome-wide characterization, expression analyses, and functional prediction of the NPF family in Brassica napus. PMID:33287703
Comparative Genomics Analysis Provides New Strategies for Bacteriostatic Ability of Bacillus velezensis HAB-2. PMID:33281792
Long noncoding RNAs implicated in embryonic development in Ybx1 knockout zebrafish. PMID:33278865
NemChR-DB: a database of parasitic nematode chemosensory G-protein coupled receptors. PMID:33275943
CCDC66 frameshift variant associated with a new form of early-onset progressive retinal atrophy in Portuguese Water Dogs. PMID:33273526
Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses. PMID:33270651
Identification and functional characterization of ABCC transporters for Cd tolerance and accumulation in Sedum alfredii Hance. PMID:33262396
Genome-wide identification and characterization of long non-coding RNAs related to grain yield in foxtail millet [Setaria italica (L.) P. Beauv.]. PMID:33261549
The Two TpsB-Like Proteins in Anabaena sp. Strain PCC 7120 Are Involved in Secretion of Selected Substrates. PMID:33257527
Remote homology search with hidden Potts models. PMID:33253143
The Draft Genome of Red Lechwe, Kobus leche leche. PMID:33250921
Expression profiling of MADS-box gene family revealed its role in vegetative development and stem ripening in S. spontaneum. PMID:33239664
Genome-Wide Characterization of OFP Family Genes in Wheat (Triticum aestivum L.) Reveals That TaOPF29a-A Promotes Drought Tolerance. PMID:33224986
Prophages are associated with extensive CRISPR-Cas auto-immunity. PMID:33219687
The emergence and evolution of intron-poor and intronless genes in intron-rich plant gene families. PMID:33217085
Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment. PMID:33208892
Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease. PMID:33208745
Analysis and Screening of Reproductive Long Non-coding RNAs Through Genome-Wide Analyses of Goat Endometrium During the Pre-attachment Phase. PMID:33193661
Transcriptome analysis reveals mechanism of early ripening in Kyoho grape with hydrogen peroxide treatment. PMID:33176674
Identification, evolution, expression, and docking studies of fatty acid desaturase genes in wheat (Triticum aestivum L.). PMID:33167859
Genome-wide analysis of PHD finger gene family and identification of potential miRNA and their PHD finger gene specific targets in Oryza sativa indica. PMID:33163736
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
The Transcriptome of Cunninghamia lanceolata male/female cone reveal the association between MIKC MADS-box genes and reproductive organs development. PMID:33153428
Genome-wide analysis of acute traumatic spinal cord injury-related RNA expression profiles and uncovering of a regulatory axis in spinal fibrotic scars. PMID:33150698
In-depth transcriptome reveals the potential biotechnological application of Bothrops jararaca venom gland. PMID:33149734
(p)ppGpp-Dependent Regulation of the Nucleotide Hydrolase PpnN Confers Complement Resistance in Salmonella enterica Serovar Typhimurium. PMID:33139383
Opposing functions of Fng1 and the Rpd3 HDAC complex in H4 acetylation in Fusarium graminearum. PMID:33137093
Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species. PMID:33125363
Identification and Characterization of New Bacteriophages to Control Multidrug-Resistant Pseudomonas aeruginosa Biofilm on Endotracheal Tubes. PMID:33123112
Structure-Function Characterization of the Conserved Regulatory Mechanism of the Escherichia coli M48 Metalloprotease BepA. PMID:33106348
Pacific Biosciences assembly with Hi-C mapping generates an improved, chromosome-level goose genome. PMID:33099628
Sensing of autoinducer-2 by functionally distinct receptors in prokaryotes. PMID:33097715
Assessing the Genomic Variability of Gardnerella vaginalis through Comparative Genomic Analyses: Evolutionary and Ecological Implications. PMID:33097505
Genome-scale analyses and characteristics of putative pathogenicity genes of Stagonosporopsis cucurbitacearum, a pumpkin gummy stem blight fungus. PMID:33093634
In Silico Analyses of Autophagy-Related Genes in Rapeseed (Brassica napus L.) under Different Abiotic Stresses and in Various Tissues. PMID:33092180
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
A high-quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance. PMID:33073445
Chlorella vulgaris and Its Phycosphere in Wastewater: Microalgae-Bacteria Interactions During Nutrient Removal. PMID:33072721
Role of BgaA as a Pneumococcal Virulence Factor Elucidated by Molecular Evolutionary Analysis. PMID:33072054
Aspergillus sydowii: Genome Analysis and Characterization of Two Heterologous Expressed, Non-redundant Xylanases. PMID:33071998
PacBio Long-Read Sequencing Transcriptome Dataset of Adult Harmonia axyridis Under Diapause Inducing and Reproductive Inducing Photoperiod. PMID:33061940
Ancestral Reconstructions Decipher Major Adaptations of Ammonia-Oxidizing Archaea upon Radiation into Moderate Terrestrial and Marine Environments. PMID:33051370
Analysis of lncRNA Expression Profile during the Formation of Male Germ Cells in Chickens. PMID:33050652
Agasicles hygrophila attack increases nerolidol synthase gene expression in Alternanthera philoxeroides, facilitating host finding. PMID:33046727
Growth Performance and Transcriptomic Response of Warm-Acclimated Hybrid Abalone Haliotis rufescens (♀) × H. corrugata (♂). PMID:33040235
Identification of a hippocampal lncRNA-regulating network in cognitive dysfunction caused by chronic cerebral hypoperfusion. PMID:33040050
Terpenes and Terpenoids in Plants: Interactions with Environment and Insects. PMID:33036280
Identification and Characterization of lncRNAs Related to the Muscle Growth and Development of Japanese Flounder (Paralichthys olivaceus). PMID:33033494
In silico identification and validation of miRNA and their DIR specific targets in Oryza sativa Indica under abiotic stress. PMID:33024905
A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant. PMID:33024567
Molecular characterization and functional annotation of a hypothetical protein (SCO0618) of Streptomyces coelicolor A3(2). PMID:33017872
Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific mule and hinny hybrids fed ad libitum and overfed. PMID:33008290
F-Box Genes in the Wheat Genome and Expression Profiling in Wheat at Different Developmental Stages. PMID:33007852
Molecular Simulations and Network Modeling Reveal an Allosteric Signaling in the SARS-CoV-2 Spike Proteins. PMID:33006900
Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis. PMID:33004908
DeeplyEssential: a deep neural network for predicting essential genes in microbes. PMID:32998698
Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak. PMID:32998696
A Fluorescence Polarization-Based High-Throughput Screen to Identify the First Small-Molecule Modulators of the Human Adenylyltransferase HYPE/FICD. PMID:32992526
The evolution of TNF signaling in platyhelminths suggests the cooptation of TNF receptor in the host-parasite interplay. PMID:32977830
Metagenomic Insights into the Sewage RNA Virosphere of a Large City. PMID:32967111
Expanded genome-wide comparisons give novel insights into population structure and genetic heterogeneity of Leishmania tropica complex. PMID:32946436
Whole transcriptome approach to evaluate the effect of aluminium hydroxide in ovine encephalon. PMID:32943671
Potential Pathogenicity Determinants Identified from Structural Proteomics of SARS-CoV and SARS-CoV-2. PMID:32941612
Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma). PMID:32938378
Bioinformatic Characterization of Sulfotransferase Provides New Insights for the Exploitation of Sulfated Polysaccharides in Caulerpa. PMID:32932673
A large accessory protein interactome is rewired across environments. PMID:32924934
Chlamydial contribution to anaerobic metabolism during eukaryotic evolution. PMID:32923644
Distribution, evolution and expression of GATA-TFs provide new insights into their functions in light response and fruiting body development of Tolypocladium guangdongense. PMID:32923181
A case study of salivary microbiome in smokers and non-smokers in Hungary: analysis by shotgun metagenome sequencing. PMID:32922678
A flavin-dependent monooxygenase catalyzes the initial step in cyanogenic glycoside synthesis in ferns. PMID:32917937
Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing. PMID:32917720
In silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis. PMID:32913672
Increased resolution of African swine fever virus genome patterns based on profile HMMs of protein domains. PMID:32913663
Response of Downy Oak (Quercus pubescens Willd.) to Climate Change: Transcriptome Assembly, Differential Gene Analysis and Targeted Metabolomics. PMID:32899727
RNA-Seq Reveals the Expression Profiles of Long Non-Coding RNAs in Lactating Mammary Gland from Two Sheep Breeds with Divergent Milk Phenotype. PMID:32899158
Analysis of insect nuclear small heat shock proteins and interacting proteins. PMID:32888179
RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery. PMID:32873609
Genome-wide identification and analysis of GRAS transcription factors in the bottle gourd genome. PMID:32868844
Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress. PMID:32859149
The Phylogeny of Class B Flavoprotein Monooxygenases and the Origin of the YUCCA Protein Family. PMID:32854417
Determining the interaction status and evolutionary fate of duplicated homomeric proteins. PMID:32853212
Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis). PMID:32852039
Closed mitosis requires local disassembly of the nuclear envelope. PMID:32848252
In-Depth In Silico Search for Cuttlefish (Sepia officinalis) Antimicrobial Peptides Following Bacterial Challenge of Haemocytes. PMID:32847054
Acetylation of Surface Carbohydrates in Bacterial Pathogens Requires Coordinated Action of a Two-Domain Membrane-Bound Acyltransferase. PMID:32843546
In silico Functional Annotation and Characterization of Hypothetical Proteins from Serratia marcescens FGI94. PMID:32834707
Slr4, a newly identified S-layer protein from marine Gammaproteobacteria, is a major biofilm matrix component. PMID:32804439
TGF-β1-Mediated FDNCR1 Regulates Porcine Preadipocyte Differentiation via the TGF-β Signaling Pathway. PMID:32796679
Genomic Characteristics and Potential Metabolic Adaptations of Hadal Trench Roseobacter and Alteromonas Bacteria Based on Single-Cell Genomics Analyses. PMID:32793171
Identification of transcription factors controlling floral morphology in wild Petunia species with contrasting pollination syndromes. PMID:32780443
Terabase Metagenome Sequencing of Grassland Soil Microbiomes. PMID:32763940
Evaluating the effect of TLR4-overexpressing on the transcriptome profile in ovine peripheral blood mononuclear cells. PMID:32760682
Genome-Wide Analysis Reveals Changes in Long Noncoding RNAs in the Differentiation of Canine BMSCs into Insulin-Producing Cells. PMID:32756402
Whole-genome de novo assemblies reveal extensive structural variations and dynamic organelle-to-nucleus DNA transfers in African and Asian rice. PMID:32748498
Rational design and implementation of a chemically inducible heterotrimerization system. PMID:32747768
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
Identification and Bioinformatic Analysis of the GmDOG1-Like Family in Soybean and Investigation of Their Expression in Response to Gibberellic Acid and Abscisic Acid. PMID:32722147
Exploration of Long Non-coding RNAs and Circular RNAs in Porcine Milk Exosomes. PMID:32714373
Diazotroph Genomes and Their Seasonal Dynamics in a Stratified Humic Bog Lake. PMID:32714313
PertInInt: An Integrative, Analytical Approach to Rapidly Uncover Cancer Driver Genes with Perturbed Interactions and Functionalities. PMID:32711844
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. PMID:32706331
Identification and distribution of gene clusters required for synthesis of sphingolipid metabolism inhibitors in diverse species of the filamentous fungus Fusarium. PMID:32703172
An Easy Protocol for Evolutionary Analysis of Intrinsically Disordered Proteins. PMID:32696356
Analyzing the Sequences of Intrinsically Disordered Regions with CIDER and localCIDER. PMID:32696354
Diversity and evolution of cytochrome P450s of Jacobaea vulgaris and Jacobaea aquatica. PMID:32689941
Characterization of Novel Broad-Host-Range Bacteriophage DLP3 Specific to Stenotrophomonas maltophilia as a Potential Therapeutic Agent. PMID:32670234
RNA-sequencing based gene expression landscape of guava cv. Allahabad Safeda and comparative analysis to colored cultivars. PMID:32669108
Systematic Characterization of Recurrent Genomic Alterations in Cyclin-Dependent Kinases Reveals Potential Therapeutic Strategies for Cancer Treatment. PMID:32668240
PWAS: proteome-wide association study-linking genes and phenotypes by functional variation in proteins. PMID:32665031
Comparative Genomic Analysis Reveals the Metabolism and Evolution of the Thermophilic Archaeal Genus Metallosphaera. PMID:32655516
Phylogenomic Analysis of R2R3 MYB Transcription Factors in Sorghum and their Role in Conditioning Biofuel Syndrome. PMID:32655308
The regulatory landscape of early maize inflorescence development. PMID:32631399
Computational identification of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes. PMID:32620079
Genome-wide identification and expression profiling of the YUCCA gene family in Malus domestica. PMID:32616911
Discovery, identification, and functional characterization of long noncoding RNAs in Arachis hypogaea L. PMID:32615935
Influence of genetic diversity of seventeen Beauveria bassiana isolates from different hosts on virulence by comparative genomics. PMID:32605539
Coding and Non-coding RNAs: Molecular Basis of Forest-Insect Outbreaks. PMID:32596236
Comparative genomics of the genus Roseburia reveals divergent biosynthetic pathways that may influence colonic competition among species. PMID:32589566
Identification and characterization of long non-coding RNA (lncRNA) in the developing seeds of Jatropha curcas. PMID:32587349
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
Genome-wide characterization and expression analyses of the auxin/indole-3-acetic acid (Aux/IAA) gene family in barley (Hordeum vulgare L.). PMID:32581321
GapMind: Automated Annotation of Amino Acid Biosynthesis. PMID:32576650
Comparative Transcriptome Analysis of Two Contrasting Soybean Varieties in Response to Aluminum Toxicity. PMID:32560405
Analysis of lncRNAs Expression Profiles in Hair Follicle of Hu Sheep Lambskin. PMID:32549352
Plasmid-Encoded blaNDM-5 Gene That Confers High-Level Carbapenem Resistance in Salmonella Typhimurium of Pork Origin. PMID:32547117
Genome-wide identification and expression analysis of jasmonate ZIM domain gene family in tuber mustard (Brassica juncea var. tumida). PMID:32544205
Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome. PMID:32536962
Characterization of Burkholderia cepacia Complex Core Genome and the Underlying Recombination and Positive Selection. PMID:32528528
Genome sequence of Kobresia littledalei, the first chromosome-level genome in the family Cyperaceae. PMID:32528014
SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae). PMID:32509454
Transcriptome analysis of blood for the discovery of sex-related genes in ricefield eel Monopterus albus. PMID:32472467
Isolation and characterisation of novel phages infecting Lactobacillus plantarum and proposal of a new genus, "Silenusvirus". PMID:32472049
Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum. PMID:32471448
Questing functions and structures of hypothetical proteins from Campylobacter jejuni: a computer-aided approach. PMID:32458979
In silico Analyses of Core Proteins and Putative Effector and Immunity Proteins for T6SS in Enterohemorrhagic E. coli. PMID:32432054
Comparative genomic analysis of three intestinal species reveals reductions in secreted pathogenesis determinants in bovine-specific and non-pathogenic Cryptosporidium species. PMID:32416746
High-resolution profile of transcriptomes reveals a role of alternative splicing for modulating response to nitrogen in maize. PMID:32393171
A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type. PMID:32392251
Long-term outcomes and response to treatment in diacylglycerol kinase epsilon nephropathy. PMID:32386968
MetaGeneHunt for protein domain annotation in short-read metagenomes. PMID:32382098
A high-quality reference genome of wild Cannabis sativa. PMID:32377363
The Quest for Orthologs benchmark service and consensus calls in 2020. PMID:32374845
Casparian strip membrane domain proteins in Gossypium arboreum: genome-wide identification and negative regulation of lateral root growth. PMID:32366264
Genetic basis for virulence differences of various Cryptosporidium parvum carcinogenic isolates. PMID:32355272
Genetic Underpinnings of Host Manipulation by Ophiocordyceps as Revealed by Comparative Transcriptomics. PMID:32354705
Integrated Analysis of mRNA and microRNA Elucidates the Regulation of Glycyrrhizic Acid Biosynthesis in Glycyrrhiza uralensis Fisch. PMID:32353999
Identification and in silico structural and functional analysis of a trypsin-like protease from shrimp Macrobrachium carcinus. PMID:32351789
A draft genome assembly of spotted hyena, Crocuta crocuta. PMID:32345970
Repurposing a chemosensory macromolecular machine. PMID:32341341
Comparative Metatranscriptomics of Periodontitis Supports a Common Polymicrobial Shift in Metabolic Function and Identifies Novel Putative Disease-Associated ncRNAs. PMID:32328037
Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow. PMID:32327732
A comparative chemogenic analysis for predicting Drug-Target Pair via Machine Learning Approaches. PMID:32322011
Single-molecule long-read sequencing of the full-length transcriptome of Rhododendron lapponicum L. PMID:32317724
From conservation to structure, studies of magnetosome associated cation diffusion facilitators (CDF) proteins in Proteobacteria. PMID:32310978
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
Exploring dynamic protein-protein interactions in cassava through the integrative interactome network. PMID:32300157
Draft Genome Sequence of the Oomycete Globisporangium splendens Strain rgcb-1. PMID:32299889
Characterization of the Gh4CL gene family reveals a role of Gh4CL7 in drought tolerance. PMID:32293290
First de novo whole genome sequencing and assembly of the bar-headed goose. PMID:32292659
The hypertrophic cardiomyopathy mutations R403Q and R663H increase the number of myosin heads available to interact with actin. PMID:32284968
A novel flow cytometry assay based on bacteriophage-derived proteins for Staphylococcus detection in blood. PMID:32277078
Exploring Evolutionary Constraints in the Proteomes of Zika, Dengue, and Other Flaviviruses to Find Fitness-Critical Sites. PMID:32266427
Integrated Analysis of Long Non-coding RNAs (lncRNAs) and mRNAs Reveals the Regulatory Role of lncRNAs Associated With Salt Resistance in Camellia sinensis. PMID:32265948
Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus. PMID:32257234
Chromosome doubling mediates superior drought tolerance in Lycium ruthenicum via abscisic acid signaling. PMID:32257226
Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms. PMID:32245418
Iron is a ligand of SecA-like metal-binding domains in vivo. PMID:32241912
Draft Genome Sequence of the Yeast Rhodotorula sp. Strain CCFEE 5036, Isolated from McMurdo Dry Valleys, Antarctica. PMID:32241854
Genome wide characterization revealed MnMLO2 and MnMLO6A as candidate genes involved in powdery mildew susceptibility in mulberry. PMID:32239465
Interaction between the scaffold proteins CBP by IQGAP1 provides an interface between gene expression and cytoskeletal activity. PMID:32238831
A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries. PMID:32236097
Phylogeny and Functions of LOB Domain Proteins in Plants. PMID:32224847
Comparative Transcriptome Analysis Provides Insights Into Yellow Rind Formation and Preliminary Mapping of the Clyr (Yellow Rind) Gene in Watermelon. PMID:32218790
Sergentomyia schwetzi: Salivary gland transcriptome, proteome and enzymatic activities in two lineages adapted to different blood sources. PMID:32208452
A bacteriophage mimic of the bacterial nucleoid-associated protein Fis. PMID:32207815
Bi-allelic LoF NRROS Variants Impairing Active TGF-β1 Delivery Cause a Severe Infantile-Onset Neurodegenerative Condition with Intracranial Calcification. PMID:32197075
Comparative Genome Analysis of the Lignocellulose Degrading Bacteria Citrobacter freundii so4 and Sphingobacterium multivorum w15. PMID:32194522
Genome-wide investigation of WRKY transcription factors in Tartary buckwheat (Fagopyrum tataricum) and their potential roles in regulating growth and development. PMID:32185114
Whole transcriptome expression profiles in placenta samples from women with gestational diabetes mellitus. PMID:32174045
COST1 regulates autophagy to control plant drought tolerance. PMID:32170020
Digenic inheritance of mutations in EPHA2 and SLC26A4 in Pendred syndrome. PMID:32165640
Comprehensive transcriptome profiling of Taiwanese colorectal cancer implicates an ethnic basis for pathogenesis. PMID:32161294
Comparison of Viromes in Ticks from Different Domestic Animals in China. PMID:32157603
C2H2 Zinc Finger Proteins: Master Regulators of Abiotic Stress Responses in Plants. PMID:32153617
Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus. PMID:32150860
Evolution and roles of cytokinin genes in angiosperms 2: Do ancient CKXs play housekeeping roles while non-ancient CKXs play regulatory roles? PMID:32140238
Evolution and roles of cytokinin genes in angiosperms 1: Do ancient IPTs play housekeeping while non-ancient IPTs play regulatory roles? PMID:32140237
Preferential gene retention increases the robustness of cold regulation in Brassicaceae and other plants after polyploidization. PMID:32133148
The ankyrin repeat gene family in Capsicum spp: Genome-wide survey, characterization and gene expression profile. PMID:32132613
Lactosyl-sepharose binding proteins from pancreatic cancer cells show differential expression in primary and metastatic organs. PMID:32131629
Epistatic contributions promote the unification of incompatible models of neutral molecular evolution. PMID:32123092
Association of a Variant in VWA3A with Response to Anti-Vascular Endothelial Growth Factor Treatment in Neovascular AMD. PMID:32106291
The genome evolution and low-phosphorus adaptation in white lupin. PMID:32103018
Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of Burkholderia cenocepacia J2315 and Other Members of the B. cepacia Complex. PMID:32098200
Exploring Integrative Analysis Using the BioMedical Evidence Graph. PMID:32097025
Caldicellulosiruptor bescii Adheres to Polysaccharides via a Type IV Pilin-Dependent Mechanism. PMID:32086304
Systematic analysis of the Hippo pathway organization and oncogenic alteration in evolution. PMID:32081887
Genome of Tripterygium wilfordii and identification of cytochrome P450 involved in triptolide biosynthesis. PMID:32080175
Resequencing 93 accessions of coffee unveils independent and parallel selection during Coffea species divergence. PMID:32072392
Genome-Wide Profiling and Phylogenetic Analysis of the SWEET Sugar Transporter Gene Family in Walnut and Their Lack of Responsiveness to Xanthomonas arboricola pv. juglandis Infection. PMID:32070009
Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii. PMID:32066773
Computational Analysis of Crystallization Additives for the Identification of New Allosteric Sites. PMID:32064372
CEP44 ensures the formation of bona fide centriole wall, a requirement for the centriole-to-centrosome conversion. PMID:32060285
The Shb scaffold binds the Nck adaptor protein, p120 RasGAP, and Chimaerins and thereby facilitates heterotypic cell segregation by the receptor EphB2. PMID:32060095
Clades of huge phages from across Earth's ecosystems. PMID:32051592
Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs. PMID:32047225
Transcriptomic and Metabolomic Changes Triggered by Fusarium solani in Common Bean (Phaseolus vulgaris L.). PMID:32046085
The evolution of protein domain repertoires: Shedding light on the origins of the Herpesviridae family. PMID:32042448
The hornwort genome and early land plant evolution. PMID:32042158
Transcriptome-Wide Identification, Evolutionary Analysis, and GA Stress Response of the GRAS Gene Family in Panax ginseng C. A. Meyer. PMID:32033157
Complete Genome Sequence of Methylomonas koyamae LM6, a Potential Aerobic Methanotroph. PMID:32029563
Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass. PMID:32026320
Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization. PMID:32024005
Functional Analysis of Long Non-Coding RNAs Reveal Their Novel Roles in Biocontrol of Bacteria-Induced Tomato Resistance to Meloidogyne incognita. PMID:32019153
Tools for Analysis of the Microbiome. PMID:32002757
Global transcriptome analysis of alfalfa reveals six key biological processes of senescent leaves. PMID:32002335
Genomic Characterization of a Novel Gut Symbiont From the Hadal Snailfish. PMID:31998265
Novel Hyperthermophilic Crenarchaeon Thermofilum adornatum sp. nov. Uses GH1, GH3, and Two Novel Glycosidases for Cellulose Hydrolysis. PMID:31998263
Origin Recognition Complex (ORC) Evolution Is Influenced by Global Gene Duplication/Loss Patterns in Eukaryotic Genomes. PMID:31990293
Tentacle Transcriptomes of the Speckled Anemone (Actiniaria: Actiniidae: Oulactis sp.): Venom-Related Components and Their Domain Structure. PMID:31981004
Mechanism underlying autoinducer recognition in the Vibrio cholerae DPO-VqmA quorum-sensing pathway. PMID:31964715
Identification, functional prediction, and key lncRNA verification of cold stress-related lncRNAs in rats liver. PMID:31949263
Systematic Analysis of the Maize OSCA Genes Revealing ZmOSCA Family Members Involved in Osmotic Stress and ZmOSCA2.4 Confers Enhanced Drought Tolerance in Transgenic Arabidopsis. PMID:31948071
Characterization of the Soybean GmIREG Family Genes and the Function of GmIREG3 in Conferring Tolerance to Aluminum Stress. PMID:31941034
Domain-mediated interactions for protein subfamily identification. PMID:31937869
Continuous pre- and post-transplant exposure to a disease-associated gut microbiome promotes hyper-acute graft-versus-host disease in wild-type mice. PMID:31928131
Mesostigma viride Genome and Transcriptome Provide Insights into the Origin and Evolution of Streptophyta. PMID:31921561
Gene Expression Profiling of the Shoot Meristematic Tissues in Woodland Strawberry Fragaria vesca. PMID:31921266
Genome-Wide Identification and Characterization of the Mitochondrial Transcription Termination Factors (mTERFs) in Capsicum annuum L. PMID:31906076
Transcriptional Differences of Coding and Non-Coding Genes Related to the Absence of Melanocyte in Skins of Bama Pig. PMID:31905971
Dissection of Dynamic Transcriptome Landscape of Leaf, Bract, and Lupulin Gland in Hop (Humulus lupulus L.). PMID:31905722
Genome-Wide Analysis of the NAC Domain Transcription Factor Gene Family in Theobroma cacao. PMID:31905649
Genome-wide identification and functional analysis of JmjC domain-containing genes in flower development of Rosa chinensis. PMID:31898146
Deep analysis and optimization of CARD antibiotic resistance gene discovery models. PMID:31888459
Genome-Wide Analysis of Cyclophilin Proteins in 21 Oomycetes. PMID:31888032
PhoH2 proteins couple RNA helicase and RNAse activities. PMID:31886915
Local adaptation of a dominant coastal tree to freshwater availability and solar radiation suggested by genomic and ecophysiological approaches. PMID:31882752
Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line. PMID:31881839
Chromosome-Level Comprehensive Genome of Mangrove Sediment-Derived Fungus Penicillium variabile HXQ-H-1. PMID:31878043
Identification of highly conserved, serotype-specific dengue virus sequences: implications for vaccine design. PMID:31874646
JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants. PMID:31874631
Comparative transcriptomic analysis of the flower induction and development of the Lei bamboo (Phyllostachys violascens). PMID:31874613
Integrative transcriptome analysis discloses the molecular basis of a heterogeneous fungal phytopathogen complex, Rhizoctonia solani AG-1 subgroups. PMID:31873088
Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions. PMID:31873071
Genome-wide identification and expression profile of the MADS-box gene family in Erigeron breviscapus. PMID:31860684
Transcriptome landscape of Rafflesia cantleyi floral buds reveals insights into the roles of transcription factors and phytohormones in flower development. PMID:31851702
A Phylogenomic Analysis of the Floral Transcriptomes of Sexually Deceptive and Rewarding European Orchids, Ophrys and Gymnadenia. PMID:31850034
Current challenges and best-practice protocols for microbiome analysis. PMID:31848574
Combined De Novo Transcriptome and Metabolome Analysis of Common Bean Response to Fusarium oxysporum f. sp. phaseoli Infection. PMID:31842411
Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools. PMID:31830054
Sensitive Biomarker Analysis of Xue-Fu-Zhu-Yu Capsule for Patients with Qi Stagnation and Blood Stasis Pattern: A Nested Case-Control Study. PMID:31827557
Logomaker: beautiful sequence logos in Python. PMID:31821414
Mitochondrial genomes of the early land plant lineage liverworts (Marchantiophyta): conserved genome structure, and ongoing low frequency recombination. PMID:31818248
Results of multigene panel testing in familial cancer cases without genetic cause demonstrated by single gene testing. PMID:31811167
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
Full-Length Transcriptome Survey and Expression Analysis of Parasitoid Wasp Chouioia cunea upon Exposure to 1-Dodecene. PMID:31796851
Characterization and Functional Divergence of a Novel DUF668 Gene Family in Rice Based on Comprehensive Expression Patterns. PMID:31795257
Large multiple sequence alignments with a root-to-leaf regressive method. PMID:31792410
Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion. PMID:31791230
Analysis of glycoside hydrolases from oat (Avena sativa) seedling extract. PMID:31787817
RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants. PMID:31779641
Transcriptome profiling analysis reveals key genes of different coat color in sheep skin. PMID:31772839
Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages. PMID:31766550
Comparative analysis of differential proteome-wide protein-protein interaction network of Methanobrevibacter ruminantium M1. PMID:31763465
Identification, Evolution, and Expression Profiling of Histone Lysine Methylation Moderators in Brassica rapa. PMID:31756989
Screening and characterization of long noncoding RNAs involved in the albinism of Ananas comosus var. bracteatus leaves. PMID:31756232
Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere. PMID:31754206
The Driver of Extreme Human-Specific Olduvai Repeat Expansion Remains Highly Active in the Human Genome. PMID:31754017
Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader 'Candidatus Leucobacter sulfamidivorax' strain GP. PMID:31752666
Genome-wide identification and characterization of long non-coding RNAs during differentiation of visceral preadipocytes in rabbit. PMID:31745672
Intra-species recombination among strains of the ampelovirus Grapevine leafroll-associated virus 4. PMID:31744534
The evolution and genomic basis of beetle diversity. PMID:31740605
Integrated transcriptome and miRNA analysis uncovers molecular regulators of aerial stem-to-rhizome transition in the medical herb Gynostemma pentaphyllum. PMID:31730459
Genome-Wide Analysis of the DYW Subgroup PPR Gene Family and Identification of GmPPR4 Responses to Drought Stress. PMID:31726763
Annotation of a hypothetical protein coding gene PAS_chr2-2_0152 containing Lysine Methyl transferase SMYD domain from Komagataella phaffii GS115. PMID:31719763
A New Lineage of Cryptococcus gattii (VGV) Discovered in the Central Zambezian Miombo Woodlands. PMID:31719178
Exploring the Molecular Mechanism underlying the Stable Purple-Red Leaf Phenotype in Lagerstroemia indica cv. Ebony Embers. PMID:31718025
Improved Draft Genome Sequence of Microbacterium sp. Strain LKL04, a Bacterial Endophyte Associated with Switchgrass Plants. PMID:31699756
Transcriptome Analysis Implicates Involvement of Long Noncoding RNAs in Cytoplasmic Male Sterility and Fertility Restoration in Cotton. PMID:31698756
Transcriptome sequencing of Salvia miltiorrhiza after infection by its endophytic fungi and identification of genes related to tanshinone biosynthesis. PMID:31694427
Nanopore sequencing improves the draft genome of the human pathogenic amoeba Naegleria fowleri. PMID:31690847
Genome-wide identification and characterization, phylogenetic comparison and expression profiles of SPL transcription factor family in B. juncea (Cruciferae). PMID:31689304
Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus. PMID:31681953
New insights into the mycobacterial PE and PPE proteins provide a framework for future research. PMID:31661176
Domainoid: domain-oriented orthology inference. PMID:31660857
The spinal cord-gut-immune axis as a master regulator of health and neurological function after spinal cord injury. PMID:31654639
Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities. PMID:31653790
Uncovering and characterizing splice variants associated with survival in lung cancer patients. PMID:31652257
Identification and Analysis of Long Repeats of Proteins at the Domain Level. PMID:31649924
Draft genome sequence of cauliflower (Brassica oleracea L. var. botrytis) provides new insights into the C genome in Brassica species. PMID:31645943
The draft genome of Actinia tenebrosa reveals insights into toxin evolution. PMID:31641475
Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics. PMID:31630686
Search for Nutritional Fitness Traits in a Biological Pest Control Agent Harmonia axyridis Using Comparative Transcriptomics. PMID:31620008
Zinc uptake in the Basidiomycota: Characterization of zinc transporters in Ustilago maydis. PMID:31617434
Identification of keratinases from Fervidobacterium islandicum AW-1 using dynamic gene expression profiling. PMID:31613061
Aminoacyl tRNA synthetases as potential drug targets of the Panthera pathogen Babesia. PMID:31610802
TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes. PMID:31601838
Alternative Splicing in Heat Shock Protein Transcripts as a Mechanism of Cell Adaptation in Trichophyton rubrum. PMID:31590387
Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes. PMID:31587639
De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens. PMID:31586052
Protective Role of Leaf Variegation in Pittosporum tobira under Low Temperature: Insights into the Physio-Biochemical and Molecular Mechanisms. PMID:31574927
Targeted isolation and cultivation of uncultivated bacteria by reverse genomics. PMID:31570900
Global phosphoproteomic analysis of Ebola virions reveals a novel role for VP35 phosphorylation-dependent regulation of genome transcription. PMID:31562565
Reference gene and small RNA data from multiple tissues of Davidia involucrata Baill. PMID:31551451
Draft Genome and Complete Hox-Cluster Characterization of the Sterlet (Acipenser ruthenus). PMID:31543900
Evolutionary and functional patterns of shared gene neighbourhood in fungi. PMID:31527797
Zinc Finger-Homeodomain Genes: Evolution, Functional Differentiation, and Expression Profiling Under Flowering-Related Treatments and Abiotic Stresses in Plants. PMID:31523124
Large-Scale Molecular Evolutionary Analysis Uncovers a Variety of Polynucleotide Kinase Clp1 Family Proteins in the Three Domains of Life. PMID:31513263
Differential Regulation of Anthocyanins in Green and Purple Turnips Revealed by Combined De Novo Transcriptome and Metabolome Analysis. PMID:31500111
GhVTC1, the Key Gene for Ascorbate Biosynthesis in Gossypium hirsutum, Involves in Cell Elongation Under Control of Ethylene. PMID:31492030
Genome-Wide Identification and Characterization of the UBP Gene Family in Moso Bamboo (Phyllostachys edulis). PMID:31484390
The Fish Pathogen Vibrio ordalii Under Iron Deprivation Produces the Siderophore Piscibactin. PMID:31484388
Transcriptome Analysis Reveals Key Seed-Development Genes in Common Buckwheat (Fagopyrum esculentum). PMID:31484314
A Comparative Genome-Wide Analysis of the R2R3-MYB Gene Family Among Four Gossypium Species and Their Sequence Variation and Association With Fiber Quality Traits in an Interspecific G. hirsutum × G. barbadense Population. PMID:31475040
An in vitro characterisation of the Trichomonas vaginalis TATA box-binding proteins (TBPs). PMID:31473857
Whole Genome Sequencing of Chinese White Dolphin (Sousa chinensis) for High-Throughput Screening of Antihypertensive Peptides. PMID:31466310
Structural and biochemical studies of an NB-ARC domain from a plant NLR immune receptor. PMID:31461469
The RabGAP Gene Family in Tomato (Solanum lycopersicum) and Wild Relatives: Identification, Interaction Networks, and Transcriptional Analysis during Plant Development and in Response to Salt Stress. PMID:31450820
Collection of antimicrobial peptides database and its derivatives: Applications and beyond. PMID:31441165
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
Genome-wide analysis of sulfotransferase genes and their responses to abiotic stresses in Chinese cabbage (Brassica rapa L.). PMID:31425555
Atypical cyclins: the extended family portrait. PMID:31420702
Size and structure of the sequence space of repeat proteins. PMID:31415557
Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota. PMID:31409660
Transcriptomic analysis of Pacific white shrimp (Litopenaeus vannamei, Boone 1931) in response to acute hepatopancreatic necrosis disease caused by Vibrio parahaemolyticus. PMID:31408485
An improved genome assembly of the fluke Schistosoma japonicum. PMID:31390359
The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion. PMID:31387118
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
Genome-wide exploration and characterization of miR172/euAP2 genes in Brassica napus L. for likely role in flower organ development. PMID:31370790
Genomic detection and molecular characterization of two distinct isolates of cycas necrotic stunt virus from Paeonia suffruticosa and Daphne odora. PMID:31352619
Rad5 dysregulation drives hyperactive recombination at replication forks resulting in cisplatin sensitivity and genome instability. PMID:31350889
Melatonin enhances cotton immunity to Verticillium wilt via manipulating lignin and gossypol biosynthesis. PMID:31349367
Analysis of Long Non-Coding RNA and mRNA Expression Profiling in Immature and Mature Bovine (Bos taurus) Testes. PMID:31333723
Aberrant DNA methylation defines isoform usage in cancer, with functional implications. PMID:31329578
In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes. PMID:31316134
Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences. PMID:31316056
GeneHunt for rapid domain-specific annotation of glycoside hydrolases. PMID:31300677
Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata. PMID:31297970
A transcriptional and functional analysis of heat hardening in two invasive fruit fly species, Bactrocera dorsalis and Bactrocera correcta. PMID:31293628
Core transcriptional signatures of phase change in the migratory locust. PMID:31292921
Expanding the Diversity of Myoviridae Phages Infecting Lactobacillus plantarum-A Novel Lineage of Lactobacillus Phages Comprising Five New Members. PMID:31277436
Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass. PMID:31276273
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
Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta. PMID:31271506
Combining genome-wide and transcriptome-wide analyses reveal the evolutionary conservation and functional diversity of aquaporins in cotton. PMID:31262248
Population Genome Sequencing of the Scab Fungal Species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata. PMID:31253647
Ancient Hybridization and Adaptive Introgression of an Invadolysin Gene in Schistosome Parasites. PMID:31251352
De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication. PMID:31249862
Terpene Synthase Genes Originated from Bacteria through Horizontal Gene Transfer Contribute to Terpenoid Diversity in Fungi. PMID:31239482
A Novel PL9 Pectate Lyase from Paenibacillus polymyxa KF-1: Cloning, Expression, and Its Application in Pectin Degradation. PMID:31234557
Genome-wide analyses of the bHLH gene family reveals structural and functional characteristics in the aquatic plant Nelumbo nucifera. PMID:31231599
Comparative physiology and transcriptome analysis allows for identification of lncRNAs imparting tolerance to drought stress in autotetraploid cassava. PMID:31226927
Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers. PMID:31221760
CAPRI enables comparison of evolutionarily conserved RNA interacting regions. PMID:31213602
Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution. PMID:31206013
Genomic signatures of heterokaryosis in the oomycete pathogen Bremia lactucae. PMID:31201315
Comprehensive analysis of Ogura cytoplasmic male sterility-related genes in turnip (Brassica rapa ssp. rapifera) using RNA sequencing analysis and bioinformatics. PMID:31199816
DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences. PMID:31199797
Genome-Wide Analysis of TCP Family Genes in Zea mays L. Identified a Role for ZmTCP42 in Drought Tolerance. PMID:31195663
Arsenite Oxidation by a Newly Isolated Betaproteobacterium Possessing arx Genes and Diversity of the arx Gene Cluster in Bacterial Genomes. PMID:31191509
Genome-wide identification and characterization of R2R3-MYB genes in Medicago truncatula. PMID:31188936
Genome-Wide Analysis of Coding and Long Non-Coding RNAs Involved in Cuticular Wax Biosynthesis in Cabbage (Brassica oleracea L. var. capitata). PMID:31185589
Comparative analysis of B-BOX genes and their expression pattern analysis under various treatments in Dendrobium officinale. PMID:31182022
Dicyemida and Orthonectida: Two Stories of Body Plan Simplification. PMID:31178892
Comparative transcriptomic and proteomic analysis of yellow shell and black shell pearl oysters, Pinctada fucata martensii. PMID:31176356
MTR-Viewer: identifying regions within genes under purifying selection. PMID:31170280
Evolutionary Analyses Reveal Diverged Patterns of SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family in Oryza Genus. PMID:31139200
Back to the Salt Mines: Genome and Transcriptome Comparisons of the Halophilic Fungus Aspergillus salisburgensis and Its Halotolerant Relative Aspergillus sclerotialis. PMID:31137536
Dynamic Transcriptome Analysis Reveals Potential Long Non-coding RNAs Governing Postnatal Pineal Development in Pig. PMID:31130986
Mosaic origin of the eukaryotic kinetochore. PMID:31127038
Sequencing of a Wild Apple (Malus baccata) Genome Unravels the Differences Between Cultivated and Wild Apple Species Regarding Disease Resistance and Cold Tolerance. PMID:31126974
Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage. PMID:31126947
Comparative analysis reveals conservation in genome organization among intestinal Cryptosporidium species and sequence divergence in potential secreted pathogenesis determinants among major human-infecting species. PMID:31117941
EcRBPome: a comprehensive database of all known E. coli RNA-binding proteins. PMID:31117939
Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States. PMID:31114882
Methanogenesis marker protein 10 (Mmp10) from Methanosarcina acetivorans is a radical S-adenosylmethionine methylase that unexpectedly requires cobalamin. PMID:31113866
Mutplot: An easy-to-use online tool for plotting complex mutation data with flexibility. PMID:31091262
Comparative Genomics of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical Dysideidae Sponges. PMID:31088928
A Novel Cadherin-like Protein Mediates Adherence to and Killing of Host Cells by the Parasite Trichomonas vaginalis. PMID:31088924
Diversification of cytokinin phosphotransfer signaling genes in Medicago truncatula and other legume genomes. PMID:31088345
Divergently expressed RNA identification and interaction prediction of long non-coding RNA and mRNA involved in Hu sheep hair follicle. PMID:31086232
Transcriptome Analysis of Apple Leaves in Response to Powdery Mildew (Podosphaera leucotricha) Infection. PMID:31083412
Engineering proteins for allosteric control by light or ligands. PMID:31076662
Draft Genome Sequence of an Antarctic Isolate of the Black Yeast Fungus Exophiala mesophila. PMID:31072892
Ocean acidification at a coastal CO2 vent induces expression of stress-related transcripts and transposable elements in the sea anemone Anemonia viridis. PMID:31067218
Correlation in Expression between LTR Retrotransposons and Potential Host Cis-Targets during Infection of Antherea pernyi with ApNPV Baculovirus. PMID:31064084
Investigation of evolutionary and expressional relationships in the function of the leucine-rich repeat receptor-like protein kinase gene family (LRR-RLK) in the radish (Raphanus sativus L.). PMID:31061443
Evolutionary Conservation and Divergence of Genes Encoding 3-Hydroxy-3-methylglutaryl Coenzyme A Synthase in the Allotetraploid Cotton Species Gossypium hirsutum. PMID:31058869
A Novel lncRNA Regulates the Toll-Like Receptor Signaling Pathway and Related Immune Function by Stabilizing FOS mRNA as a Competitive Endogenous RNA. PMID:31057556
The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition. PMID:31049561
Genome-wide identification and gene expression pattern of ABC transporter gene family in Capsicum spp. PMID:31039176
Identification and functional prediction of cold-related long non-coding RNA (lncRNA) in grapevine. PMID:31036931
Computational Characterization of the mtORF of Pocilloporid Corals: Insights into Protein Structure and Function in Stylophora Lineages from Contrasting Environments. PMID:31035578
Deciphering the three-domain architecture in schlafens and the structures and roles of human schlafen12 and serpinB12 in transcriptional regulation. PMID:31026779
Whole genomes and transcriptomes reveal adaptation and domestication of pistachio. PMID:30999938
Genome-wide analysis of maize OSCA family members and their involvement in drought stress. PMID:30997296
De Novo Transcriptome Assembly and Functional Annotation in Five Species of Bats. PMID:30996290
Investigating the Role of BATF3 in Grass Carp (Ctenopharyngodon idella) Immune Modulation: A Fundamental Functional Analysis. PMID:30987332
Population Genetics of Paramecium Mitochondrial Genomes: Recombination, Mutation Spectrum, and Efficacy of Selection. PMID:30980669
HSP superfamily of genes in the malaria vector Anopheles sinensis: diversity, phylogenetics and association with pyrethroid resistance. PMID:30975215
Genome-wide identification and expression profiling of trihelix gene family under abiotic stresses in wheat. PMID:30975075
Molecular and bioinformatics analyses reveal two differentially expressed intracellular GH1 β-glucosidases from the rare alkalophilic fungus Stachybotrys microspora. PMID:30974199
croFGD: Catharanthus roseus Functional Genomics Database. PMID:30967897
Purification and biochemical characterization of FrsA protein from Vibrio vulnificus as an esterase. PMID:30951551
Cotrimoxazole reduces systemic inflammation in HIV infection by altering the gut microbiome and immune activation. PMID:30944164
Chromosome-scale genome assembly of kiwifruit Actinidia eriantha with single-molecule sequencing and chromatin interaction mapping. PMID:30942870
Structural and Computational Characterization of Disease-Related Mutations Involved in Protein-Protein Interfaces. PMID:30934865
Roles of the GA-mediated SPL Gene Family and miR156 in the Floral Development of Chinese Chestnut (Castanea mollissima). PMID:30934840
Molecular evolution of Pr1 proteases depicts ongoing diversification in Metarhizium spp. PMID:30923942
Genomic Analysis of Pseudomonas sp. Strain SCT, an Iodate-Reducing Bacterium Isolated from Marine Sediment, Reveals a Possible Use for Bioremediation. PMID:30910818
Multi-metal Restriction by Calprotectin Impacts De Novo Flavin Biosynthesis in Acinetobacter baumannii. PMID:30905682
Genome-Wide Analysis of Multiple Organellar RNA Editing Factor Family in Poplar Reveals Evolution and Roles in Drought Stress. PMID:30901839
Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations. PMID:30891195
Mining, analyzing, and integrating viral signals from metagenomic data. PMID:30890181
A novel transcriptome-derived SNPs array for tench (Tinca tinca L.). PMID:30889192
Identification of evolutionarily conserved virulence factor by selective pressure analysis of Streptococcus pneumoniae. PMID:30886906
Functional characterization of the rice root Germin-like protein gene-1 (OsRGLP1) promoter in Nicotiana tabacum. PMID:30863709
Genome-Wide Identification and Expression Profiling of Wnt Family Genes in the Silkworm, Bombyx mori. PMID:30862048
Learning protein constitutive motifs from sequence data. PMID:30857591
Temporal Splicing Switches in Elements of the TNF-Pathway Identified by Computational Analysis of Transcriptome Data for Human Cell Lines. PMID:30857150
Genome sequence of Xanthomonas fuscans subsp. fuscans strain Xff49: a new isolate obtained from common beans in Southern Brazil. PMID:30850979
Similarities, variations, and evolution of cytochrome P450s in Streptomyces versus Mycobacterium. PMID:30850694
Genome-Wide Identification, Sequence Variation, and Expression of the Glycerol-3-Phosphate Acyltransferase (GPAT) Gene Family in Gossypium. PMID:30842789
Comprehensive Analysis of Differentially Expressed mRNA, lncRNA and circRNA and Their ceRNA Networks in the Longissimus Dorsi Muscle of Two Different Pig Breeds. PMID:30836719
Characterisation of novel-cell-wall LysM-domain proteins LdpA and LdpB from the human pathogenic fungus Aspergillus fumigatus. PMID:30833675
MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches. PMID:30832740
In silico analysis of fungal small RNA accumulation reveals putative plant mRNA targets in the symbiosis between an arbuscular mycorrhizal fungus and its host plant. PMID:30832582
A Needle in A Haystack: Tracing Bivalve-Associated Viruses in High-Throughput Transcriptomic Data. PMID:30832203
Comprehensive Analysis of the Chitinase Family Genes in Tomato (Solanum lycopersicum). PMID:30823433
CAFU: a Galaxy framework for exploring unmapped RNA-Seq data. PMID:30815667
Evidence for Highly Variable, Region-Specific Patterns of T-Cell Epitope Mutations Accumulating in Mycobacterium tuberculosis Strains. PMID:30814998
Investigating the Biological Relevance of In Vitro-Identified Putative Packaging Signals at the 5' Terminus of Satellite Tobacco Necrosis Virus 1 Genomic RNA. PMID:30814279
Genome-Wide Analysis of the Zn(II)₂Cys₆ Zinc Cluster-Encoding Gene Family in Tolypocladium guangdongense and Its Light-Induced Expression. PMID:30813610
Genome analysis of Rubritalea profundi SAORIC-165T, the first deep-sea verrucomicrobial isolate, from the northwestern Pacific Ocean. PMID:30806980
Survival Mechanisms of Campylobacter hepaticus Identified by Genomic Analysis and Comparative Transcriptomic Analysis of in vivo and in vitro Derived Bacteria. PMID:30804905
Adaptive Strategies in a Poly-Extreme Environment: Differentiation of Vegetative Cells in Serratia ureilytica and Resistance to Extreme Conditions. PMID:30804904
Genome analysis of the rice coral Montipora capitata. PMID:30796282
Reticulate evolution in eukaryotes: Origin and evolution of the nitrate assimilation pathway. PMID:30789903
Comparative genomics sheds light on the predatory lifestyle of accipitrids and owls. PMID:30783131
Pituitary Transcriptomic Study Reveals the Differential Regulation of lncRNAs and mRNAs Related to Prolificacy in Different FecB Genotyping Sheep. PMID:30781725
A draft genome assembly of the solar-powered sea slug Elysia chlorotica. PMID:30778257
Comparative analysis of seven types of superoxide dismutases for their ability to respond to oxidative stress in Bombyx mori. PMID:30778096
MapB, the Brucella suis TamB homologue, is involved in cell envelope biogenesis, cell division and virulence. PMID:30770847
Genome-Wide Identification and Characterization of SQUAMOSA-Promoter-Binding Protein (SBP) Genes Involved in the Flowering Development of Citrus Clementina. PMID:30769909
Molecular Evolution of the Vacuolar Iron Transporter (VIT) Family Genes in 14 Plant Species. PMID:30769903
DeepAffinity: interpretable deep learning of compound-protein affinity through unified recurrent and convolutional neural networks. PMID:30768156
Enrichment of bacteria and alginate lyase genes potentially involved in brown alga degradation in the gut of marine gastropods. PMID:30765748
Circadian Regulation of Alternative Splicing of Drought-Associated CIPK Genes in Dendrobium catenatum (Orchidaceae). PMID:30764546
Evolutionary Origins of Pseudogenes and Their Association with Regulatory Sequences in Plants. PMID:30760562
The Importance of Conserved Serine for C-Terminally Encoded Peptides Function Exertion in Apple. PMID:30759748
A combined computational strategy of sequence and structural analysis predicts the existence of a functional eicosanoid pathway in Drosophila melanogaster. PMID:30753230
Unique Patterns and Biogeochemical Relevance of Two-Component Sensing in Marine Bacteria. PMID:30746496
Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism. PMID:30746495
SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline. PMID:30733714
An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community. PMID:30728080
Genome expansion of an obligate parthenogenesis-associated Wolbachia poses an exception to the symbiont reduction model. PMID:30727958
RepetDB: a unified resource for transposable element references. PMID:30719103
RNA-seq of HaHV-1-infected abalones reveals a common transcriptional signature of Malacoherpesviruses. PMID:30700734
In silico Identification of Novel Toxin Homologs and Associated Mobile Genetic Elements in Clostridium perfringens. PMID:30699957
Development of novel EST-SSR markers for Ephedra sinica (Ephedraceae) by transcriptome database mining. PMID:30693158
iVikodak-A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities. PMID:30692979
A GntR Family Transcription Factor in Streptococcus mutans Regulates Biofilm Formation and Expression of Multiple Sugar Transporter Genes. PMID:30692967
Expansion and Diversification of MFS Transporters in Kluyveromyces marxianus. PMID:30687296
Identification of differentially expressed non-coding RNAs and mRNAs involved in Qi stagnation and blood stasis syndrome. PMID:30679994
Identification of genes associated with ricinoleic acid accumulation in Hiptage benghalensis via transcriptome analysis. PMID:30679955
Virulence Characteristics and an Action Mode of Antibiotic Resistance in Multidrug-Resistant Pseudomonas aeruginosa. PMID:30679735
Identification and Characterization of Mitogen-Activated Protein Kinase (MAPK) Genes in Sunflower (Helianthus annuus L.). PMID:30678298
Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children. PMID:30671194
Target of Rapamycin (TOR) Regulates the Expression of lncRNAs in Response to Abiotic Stresses in Cotton. PMID:30671083
Domain cross-talk within a bifunctional enzyme provides catalytic and allosteric functionality in the biosynthesis of aromatic amino acids. PMID:30670586
A High-quality Draft Genome Assembly of Sinella curviseta: A Soil Model Organism (Collembola). PMID:30668671
Comparative transcriptomic analysis unveils interactions between the regulatory CarS protein and light response in Fusarium. PMID:30665350
Functional characterization and proteomic analysis of lolA in Xanthomonas campestris pv. campestris. PMID:30665348
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
A major isoform of mitochondrial trans-2-enoyl-CoA reductase is dispensable for wax ester production in Euglena gracilis under anaerobic conditions. PMID:30650145
The Evolutionary Traceability of a Protein. PMID:30649284
The crystal structure of the N-acetylglucosamine 2-epimerase from Nostoc sp. KVJ10 reveals the true dimer. PMID:30644848
Differential NOVA2-Mediated Splicing in Excitatory and Inhibitory Neurons Regulates Cortical Development and Cerebellar Function. PMID:30638744
Differential co-expression networks of long non-coding RNAs and mRNAs in Cleistogenes songorica under water stress and during recovery. PMID:30634906
Characterization of B-BOX gene family and their expression profiles under hormonal, abiotic and metal stresses in Poaceae plants. PMID:30626335
Powdery Mildews Are Characterized by Contracted Carbohydrate Metabolism and Diverse Effectors to Adapt to Obligate Biotrophic Lifestyle. PMID:30619222
MMseqs2 desktop and local web server app for fast, interactive sequence searches. PMID:30615063
Genome-wide identification and comparative analysis of alternative splicing across four legume species. PMID:30603789
UbiHub: a data hub for the explorers of ubiquitination pathways. PMID:30601939
Analysis of transcripts and splice isoforms in Medicago sativa L. by single-molecule long-read sequencing. PMID:30600412
Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses. PMID:30585382
Identification, Molecular Characterization, and Biology of a Novel Quadrivirus Infecting the Phytopathogenic Fungus Leptosphaeria biglobosa. PMID:30585188
Comparative analysis of deep sequenced methanogenic communities: identification of microorganisms responsible for methane production. PMID:30572955
Gut colonization by a novel Clostridium species is associated with the onset of epizootic rabbit enteropathy. PMID:30572930
Genome Assembly for a Yunnan-Guizhou Plateau "3E" Fish, Anabarilius grahami (Regan), and Its Evolutionary and Genetic Applications. PMID:30564274
SCAPER-associated nonsyndromic autosomal recessive retinitis pigmentosa. PMID:30561111
Genome survey sequencing for the characterization of genetic background of Dracaena cambodiana and its defense response during dragon's blood formation. PMID:30550595
A novel lncRNA-mediated trans-regulatory mechanism in the development of cleft palate in mouse. PMID:30548829
Daphnia galeata responds to the exposure to an ichthyosporean gut parasite by down-regulation of immunity and lipid metabolism. PMID:30547741
A Pipeline for Classifying Deleterious Coding Mutations in Agricultural Plants. PMID:30546376
RNA sequencing and anthocyanin synthesis-related genes expression analyses in white-fruited Vaccinium uliginosum. PMID:30545307
Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions. PMID:30535108
Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants. PMID:30531940
Insights Into Limnothrix sp. Metabolism Based on Comparative Genomics. PMID:30515147
Genomic identification and functional analysis of essential genes in Caenorhabditis elegans. PMID:30514206
High-quality-draft genome sequence of the heavy metal resistant and exopolysaccharides producing bacterium Mucilaginibacter pedocola TBZ30T. PMID:30505390
Microbial Organic Matter Degradation Potential in Baltic Sea Sediments Is Influenced by Depositional Conditions and In Situ Geochemistry. PMID:30504213
Molecular genotyping, diversity studies and high-resolution molecular markers unveiled by microsatellites in Giardia duodenalis. PMID:30500829
A scalable peptide-GPCR language for engineering multicellular communication. PMID:30498215
Genome and Transcriptome Sequencing of the Astaxanthin-Producing Green Microalga, Haematococcus pluvialis. PMID:30496415
A robust method for the estimation and visualization of IgE cross-reactivity likelihood between allergens belonging to the same protein family. PMID:30496313
Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue. PMID:30486837
Comparative genomics of downy mildews reveals potential adaptations to biotrophy. PMID:30486780
An Improved Genome-Scale Metabolic Model of Arthrospira platensis C1 (iAK888) and Its Application in Glycogen Overproduction. PMID:30486288
Butyrivibrio hungatei MB2003 Competes Effectively for Soluble Sugars Released by Butyrivibrio proteoclasticus B316T during Growth on Xylan or Pectin. PMID:30478228
Phylogenomics and the evolution of hemipteroid insects. PMID:30478043
Genome-wide analysis of RNAs associated with Populus euphratica Oliv. heterophyll morphogenesis. PMID:30467318
Computational discovery of direct associations between GO terms and protein domains. PMID:30453875
CAARS: comparative assembly and annotation of RNA-Seq data. PMID:30452539
Comparative genome-wide analysis of WRKY transcription factors in two Asian legume crops: Adzuki bean and Mung bean. PMID:30451872
Involvement of sweet pepper CaLOX2 in jasmonate-dependent induced defence against Western flower thrips. PMID:30450727
Genomes of trombidid mites reveal novel predicted allergens and laterally transferred genes associated with secondary metabolism. PMID:30445460
15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms. PMID:30445427
Large-Scale Analyses of Site-Specific Evolutionary Rates across Eukaryote Proteomes Reveal Confounding Interactions between Intrinsic Disorder, Secondary Structure, and Functional Domains. PMID:30441862
Transcriptome and Resistance-Related Genes Analysis of Botrytis cinerea B05.10 Strain to Different Selective Pressures of Cyprodinil and Fenhexamid. PMID:30425701
The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions. PMID:30418645
MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs). PMID:30418481
Organic Particles: Heterogeneous Hubs for Microbial Interactions in Aquatic Ecosystems. PMID:30416497
Species-Specific Functional Regions of the Green Alga Gamete Fusion Protein HAP2 Revealed by Structural Studies. PMID:30416037
Changes in long non-coding RNA expression profiles related to the antagonistic effects of Escherichia coli F17 on lamb spleens. PMID:30410073
New insights into the evolution and functional divergence of the SWEET family in Saccharum based on comparative genomics. PMID:30404601
Genome-wide identification and analysis of WD40 proteins in wheat (Triticum aestivum L.). PMID:30400808
Reviving Phage Therapy for the Treatment of Cholera. PMID:30395214
Comparative transcriptome analysis to elucidate the enhanced thermotolerance of tea plants (Camellia sinensis) treated with exogenous calcium. PMID:30392143
FOXRED1 silencing in mice: a possible animal model for Leigh syndrome. PMID:30392038
Genome-wide Identification, Classification, and Expression Pattern of Homeobox Gene Family in Brassica rapa under Various Stresses. PMID:30389998
Mining Late Embryogenesis Abundant (LEA) Family Genes in Cleistogenes songorica, a Xerophyte Perennial Desert Plant. PMID:30388835
A planarian nidovirus expands the limits of RNA genome size. PMID:30383829
Long-term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis. PMID:30381904
RNA-Seq analysis of Polyrhachis vicina Roger and insights into the heat shock protein 90 and 70 families. PMID:30377954
Genome sequence of the cauliflower mushroom Sparassis crispa (Hanabiratake) and its association with beneficial usage. PMID:30375506
Microbial activity response to hydrogen injection in thermophilic anaerobic digesters revealed by genome-centric metatranscriptomics. PMID:30368244
Genomic and Transcriptomic Basis of Hanseniaspora vineae's Impact on Flavor Diversity and Wine Quality. PMID:30366992
Isolation and Genome Sequence Characterization of Bacteriophage vB_SalM_PM10, a Cba120virus, Concurrently Infecting Salmonella enterica Serovars Typhimurium, Typhi, and Enteritidis. PMID:30361843
The cellular economy of the Saccharomyces cerevisiae zinc proteome. PMID:30358795
Zinc Finger-Homeodomain Transcriptional Factors (ZHDs) in Upland Cotton (Gossypium hirsutum): Genome-Wide Identification and Expression Analysis in Fiber Development. PMID:30356782
The yeast GRASP Grh1 displays a high polypeptide backbone mobility along with an amyloidogenic behavior. PMID:30356074
Highly Continuous Genome Assembly of Eurasian Perch (Perca fluviatilis) Using Linked-Read Sequencing. PMID:30355765
Translational genomics and multi-omics integrated approaches as a useful strategy for crop breeding. PMID:30353370
Identification of the Acinetobacter baumannii Ribonuclease P Catalytic Subunit: Cleavage of a Target mRNA in the Presence of an External Guide Sequence. PMID:30349524
The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales. PMID:30340631
In silico characterization of a novel putative aerotaxis chemosensory system in the myxobacterium, Corallococcus coralloides. PMID:30340510
A most wanted list of conserved microbial protein families with no known domains. PMID:30332487
Detection of virulence factors of South African Lactococcus garvieae isolated from rainbow trout, Oncorhynchus mykiss (Walbaum). PMID:30326716
Genome-Wide Identification and Transcriptional Regulation of Aquaporin Genes in Bread Wheat (Triticum aestivum L.) under Water Stress. PMID:30326657
Genome-wide identification of the fatty acid desaturases gene family in four Aspergillus species and their expression profile in Aspergillus oryzae. PMID:30324529
Landscape of alternative splicing in Capra_hircus. PMID:30310084
Domain architecture of BAF250a reveals the ARID and ARM-repeat domains with implication in function and assembly of the BAF remodeling complex. PMID:30307988
Genome-wide transcriptome profiling of transgenic hop (Humulus lupulus L.) constitutively overexpressing HlWRKY1 and HlWDR1 transcription factors. PMID:30305019
Transcriptomic analyses identify albino-associated genes of a novel albino tea germplasm 'Huabai 1'. PMID:30302258
The genome of the oyster Saccostrea offers insight into the environmental resilience of bivalves. PMID:30295708
Fire ant social chromosomes: Differences in number, sequence and expression of odorant binding proteins. PMID:30283649
A New Freshwater Cyanosiphovirus Harboring Integrase. PMID:30283423
FLIM-MAP: Gene Context Based Identification of Functional Modules in Bacterial Metabolic Pathways. PMID:30283416
A complete bioconversion cascade for dehalogenation and denitration by bacterial flavin-dependent enzymes. PMID:30282807
Computational design of chemogenetic and optogenetic split proteins. PMID:30279442
An Introduced Crop Plant Is Driving Diversification of the Virulent Bacterial Pathogen Erwinia tracheiphila. PMID:30279283
The Digestive System of the Two-Spotted Spider Mite, Tetranychus urticae Koch, in the Context of the Mite-Plant Interaction. PMID:30271412
The genome of common long-arm octopus Octopus minor. PMID:30256935
Genome-Wide Identification and Functional Analyses of the CRK Gene Family in Cotton Reveals GbCRK18 Confers Verticillium Wilt Resistance in Gossypium barbadense. PMID:30254650
Comparative Transcriptome Profiling of mRNA and lncRNA Related to Tail Adipose Tissues of Sheep. PMID:30250481
Genome-wide identification and characterization of CONSTANS-like gene family in radish (Raphanus sativus). PMID:30248137
Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales. PMID:30245936
Tick galactosyltransferases are involved in α-Gal synthesis and play a role during Anaplasma phagocytophilum infection and Ixodes scapularis tick vector development. PMID:30242261
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
Factors Influencing Gene Family Size Variation Among Related Species in a Plant Family, Solanaceae. PMID:30239695
Transcriptome Sequencing and Metabolism Analysis Reveals the role of Cyanidin Metabolism in Dark-red Onion (Allium cepa L.) Bulbs. PMID:30237461
Loss of the Spinocerebellar Ataxia type 3 disease protein ATXN3 alters transcription of multiple signal transduction pathways. PMID:30231063
Discovery of microRNA-like RNAs during early fruiting body development in the model mushroom Coprinopsis cinerea. PMID:30231028
Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. PMID:30227846
Identification of Missing Carbon Fixation Enzymes as Potential Drug Targets in Mycobacterium Tuberculosis. PMID:30218604
A comprehensive manually-curated compendium of bovine transcription factors. PMID:30213987
Successive Domain Rearrangements Underlie the Evolution of a Regulatory Module Controlled by a Small Interfering Peptide. PMID:30203071
Deciphering evolutionary dynamics of SWEET genes in diverse plant lineages. PMID:30194417
Global Long Noncoding RNA and mRNA Expression Changes between Prenatal and Neonatal Lung Tissue in Pigs. PMID:30189656
Distinct Genomic Features Characterize Two Clades of Corynebacterium diphtheriae: Proposal of Corynebacterium diphtheriae Subsp. diphtheriae Subsp. nov. and Corynebacterium diphtheriae Subsp. lausannense Subsp. nov. PMID:30174653
An F-type lectin domain directs the activity of Streptosporangium roseum alpha-l-fucosidase. PMID:30169639
Shared Transcriptional Control and Disparate Gain and Loss of Aphid Parasitism Genes. PMID:30165560
A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species. PMID:30158558
A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling. PMID:30153857
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. PMID:30148503
Assessing the partners of the RBP9-mRNP complex in Trypanosoma cruzi using shotgun proteomics and RNA-seq. PMID:30146924
Evolutionary, structural and expression analysis of core genes involved in starch synthesis. PMID:30143668
Transcriptomic Analysis of Aedes aegypti in Response to Mosquitocidal Bacillus thuringiensis LLP29 Toxin. PMID:30140020
Designing bacterial signaling interactions with coevolutionary landscapes. PMID:30125296
Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation. PMID:30116788
In Vivo Analysis of miR-34a Regulated Glucose Metabolism Related Genes in Megalobrama amblycephala. PMID:30115855
Polysaccharide utilization loci of North Sea Flavobacteriia as basis for using SusC/D-protein expression for predicting major phytoplankton glycans. PMID:30111868
Biology and genome of a newly discovered sibling species of Caenorhabditis elegans. PMID:30097582
Cyclic Enterobacterial Common Antigen Maintains the Outer Membrane Permeability Barrier of Escherichia coli in a Manner Controlled by YhdP. PMID:30087168
Conducting metagenomic studies in microbiology and clinical research. PMID:30078138
Diversity and Evolution of Myxobacterial Type IV Pilus Systems. PMID:30072980
Related Endogenous Retrovirus-K Elements Harbor Distinct Protease Active Site Motifs. PMID:30072963
Tangled history of a multigene family: The evolution of ISOPENTENYLTRANSFERASE genes. PMID:30070990
Lipase maturation factor 1 affects redox homeostasis in the endoplasmic reticulum. PMID:30068531
Gonadal transcriptome sequencing of the critically endangered Acipenser dabryanus to discover candidate sex-related genes. PMID:30065900
Pan-Cancer Analysis Reveals the Functional Importance of Protein Lysine Modification in Cancer Development. PMID:30065750
Comparative genomics and the nature of placozoan species. PMID:30063702
Genome-Wide Identification of NBS-Encoding Resistance Genes in Sunflower (Helianthus annuus L.). PMID:30061549
High resolution annotation of zebrafish transcriptome using long-read sequencing. PMID:30061115
Genome-wide analysis of ATP binding cassette (ABC) transporters in tomato. PMID:30048467
Evolutionary cell biology traces the rise of the exomer complex in Fungi from an ancient eukaryotic component. PMID:30042439
Full-length transcriptome sequences and the identification of putative genes for flavonoid biosynthesis in safflower. PMID:30041604
Anomalies in the valve morphogenesis of the centric diatom alga Aulacoseira islandica caused by microtubule inhibitors. PMID:30037970
Antennal transcriptome analysis of the chemosensory gene families in Carposina sasakii (Lepidoptera: Carposinidae). PMID:30029592
Genome-wide analysis of genes encoding core components of the ubiquitin system in soybean (Glycine max) reveals a potential role for ubiquitination in host immunity against soybean cyst nematode. PMID:30021519
Bacterial sensing: A putative amphipathic helix in RsiV is the switch for activating σV in response to lysozyme. PMID:30020925
Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints. PMID:30016953
Transcriptional profiling and genes involved in acquired thermotolerance in Banana: a non-model crop. PMID:30013168
Genome-Guided Characterization of Ochrobactrum sp. POC9 Enhancing Sewage Sludge Utilization-Biotechnological Potential and Biosafety Considerations. PMID:30013002
Spatial Distribution and Diverse Metabolic Functions of Lignocellulose-Degrading Uncultured Bacteria as Revealed by Genome-Centric Metagenomics. PMID:30006398
A Pathogen-Responsive Leucine Rich Receptor Like Kinase Contributes to Fusarium Resistance in Cereals. PMID:29997638
Independent losses of a xenobiotic receptor across teleost evolution. PMID:29991818
Analysis of the Coding and Non-Coding RNA Transcriptomes in Response to Bell Pepper Chilling. PMID:29987249
Genome Sequencing and analyses of Two Marine Fungi from the North Sea Unraveled a Plethora of Novel Biosynthetic Gene Clusters. PMID:29976990
Expansion and evolutionary patterns of GDSL-type esterases/lipases in Rosaceae genomes. PMID:29948460
Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus. PMID:29941016
Proteome-wide analysis of human motif-domain interactions mapped on influenza a virus. PMID:29940841
Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance. PMID:29940001
A subregion-based burden test for simultaneous identification of susceptibility loci and subregions within. PMID:29931698
MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis. PMID:29927748
Novel Fungal Pathogenicity and Leaf Defense Strategies Are Revealed by Simultaneous Transcriptome Analysis of Colletotrichum fructicola and Strawberry Infected by This Fungus. PMID:29922301
Identification and Characterization of Genes Involved in Benzylisoquinoline Alkaloid Biosynthesis in Coptis Species. PMID:29915609
Mycobacterium terramassiliense, Mycobacterium rhizamassiliense and Mycobacterium numidiamassiliense sp. nov., three new Mycobacterium simiae complex species cultured from plant roots. PMID:29915369
Oak genome reveals facets of long lifespan. PMID:29915331
Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. PMID:29909521
The Evolutionary Consequences of Transposon-Related Pericentromer Expansion in Melon. PMID:29901717
Whole-Transcriptome Sequence Analysis of Verbena bonariensis in Response to Drought Stress. PMID:29899256
BioSankey: Visualization of Microbial Communities Over Time. PMID:29897884
The Human Virome Protein Cluster Database (HVPC): A Human Viral Metagenomic Database for Diversity and Function Annotation. PMID:29896176
Comprehensive analysis of Verticillium nonalfalfae in silico secretome uncovers putative effector proteins expressed during hop invasion. PMID:29894496
SEVENS: a database for comprehensive GPCR genes obtained from genomes: -Update to 68 eukaryotes. PMID:29892516
Characterization of C-ring component assembly in flagellar motors from amino acid coevolution. PMID:29892378
Investigating the Molecular Genetic Basis of Cytoplasmic Sex Determination Caused by Wolbachia Endosymbionts in Terrestrial Isopods. PMID:29890648
Structural and Dynamic Properties of Allergen and Non-Allergen Forms of Tropomyosin. PMID:29887498
Wireless control of cellular function by activation of a novel protein responsive to electromagnetic fields. PMID:29884813
Reconstruction of the Bifidobacterial Pan-Secretome Reveals the Network of Extracellular Interactions between Bifidobacteria and the Infant Gut. PMID:29884754
Structural mechanism of AadA, a dual-specificity aminoglycoside adenylyltransferase from Salmonella enterica. PMID:29871922
Disbiome database: linking the microbiome to disease. PMID:29866037
Genome-Wide Investigation and Expression Profiling of HD-Zip Transcription Factors in Foxtail Millet (Setaria italica L.). PMID:29862293
Genome-Wide Identification and Expression Analysis of the UGlcAE Gene Family in Tomato. PMID:29861481
Biochemical Characterization of Isoniazid-resistant Mycobacterium tuberculosis: Can the Analysis of Clonal Strains Reveal Novel Targetable Pathways? PMID:29844232
The effects of repeated whole genome duplication events on the evolution of cytokinin signaling pathway. PMID:29843594
The Auxiliary Role of the Amidase Domain in Cell Wall Binding and Exolytic Activity of Staphylococcal Phage Endolysins. PMID:29799482
Dietary aquaculture by-product hydrolysates: impact on the transcriptomic response of the intestinal mucosa of European seabass (Dicentrarchus labrax) fed low fish meal diets. PMID:29793421
Genomic and ecological study of two distinctive freshwater bacteriophages infecting a Comamonadaceae bacterium. PMID:29789681
Loci under selection and markers associated with host plant and host-related strains shape the genetic structure of Brazilian populations of Spodoptera frugiperda (Lepidoptera, Noctuidae). PMID:29787608
Phylogenomic analysis of Apoidea sheds new light on the sister group of bees. PMID:29776336
The Late Embryogenesis Abundant Protein Family in Cassava (Manihot esculenta Crantz): Genome-Wide Characterization and Expression during Abiotic Stress. PMID:29772750
Mutant phenotypes for thousands of bacterial genes of unknown function. PMID:29769716
Genomic and functional characterisation of IncX3 plasmids encoding blaSHV-12 in Escherichia coli from human and animal origin. PMID:29769695
Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes. PMID:29761466
Benzoxaborole treatment perturbs S-adenosyl-L-methionine metabolism in Trypanosoma brucei. PMID:29758036
Comparative in Silico Analysis of Ferric Reduction Oxidase (FRO) Genes Expression Patterns in Response to Abiotic Stresses, Metal and Hormone Applications. PMID:29757203
The Sucrose Synthase Gene Family in Chinese Pear (Pyrus bretschneideri Rehd.): Structure, Expression, and Evolution. PMID:29751599
Whole genome and transcriptome analysis reveal adaptive strategies and pathogenesis of Calonectria pseudoreteaudii to Eucalyptus. PMID:29747580
Lessons from my undergraduate research students. PMID:29743235
Comprehensive analyses of the BES1 gene family in Brassica napus and examination of their evolutionary pattern in representative species. PMID:29743014
A bipartite periplasmic receptor-diguanylate cyclase pair (XAC2383-XAC2382) in the bacterium Xanthomonas citri. PMID:29728456
A Fungal P450 Enzyme from Thanatephorus cucumeris with Steroid Hydroxylation Capabilities. PMID:29728383
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
Dissecting Structure-Encoded Determinants of Allosteric Cross-Talk between Post-Translational Modification Sites in the Hsp90 Chaperones. PMID:29720613
Overexpressed HDAC8 in cervical cancer cells shows functional redundancy of tubulin deacetylation with HDAC6. PMID:29716651
Adaptations in energy metabolism and gene family expansions revealed by comparative transcriptomics of three Chagas disease triatomine vectors. PMID:29699489
Signatures of DNA Methylation across Insects Suggest Reduced DNA Methylation Levels in Holometabola. PMID:29697817
Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys. PMID:29696004
The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides. PMID:29695739
Ectopic Expression of the ydaS and ydaT Genes of the Cryptic Prophage Rac of Escherichia coli K-12 May Be Toxic but Do They Really Encode Toxins?: a Case for Using Genetic Context To Understand Function. PMID:29695625
Elucidation of the anti-hyperammonemic mechanism of Lactobacillus amylovorus JBD401 by comparative genomic analysis. PMID:29695242
De Novo Sequencing of a Sparassis latifolia Genome and Its Associated Comparative Analyses. PMID:29682127
Hypoxia enhances lignification and affects the anatomical structure in hydroponic cultivation of carrot taproot. PMID:29680943
The architecture of an empirical genotype-phenotype map. PMID:29676774
NIPS, a 3D network-integrated predictor of deleterious protein SAPs, and its application in cancer prognosis. PMID:29662108
Draft genome of the protandrous Chinese black porgy, Acanthopagrus schlegelii. PMID:29659813
Systematic reconstruction of autism biology from massive genetic mutation profiles. PMID:29651456
Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi. PMID:29651164
Cameroonian fruit bats harbor divergent viruses, including rotavirus H, bastroviruses, and picobirnaviruses using an alternative genetic code. PMID:29644096
Characterization of a New Staphylococcus aureus Kayvirus Harboring a Lysin Active against Biofilms. PMID:29642449
Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells. PMID:29634734
Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition. PMID:29632744
The Novel Secreted Meloidogyne incognita Effector MiISE6 Targets the Host Nucleus and Facilitates Parasitism in Arabidopsis. PMID:29628931
A novel method for improved accuracy of transcription factor binding site prediction. PMID:29617876
Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP riboswitches in fungi. PMID:29615754
Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes. PMID:29597290
Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris. PMID:29593275
HMMER Cut-off Threshold Tool (HMMERCTTER): Supervised classification of superfamily protein sequences with a reliable cut-off threshold. PMID:29579071
A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection. PMID:29564396
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
Genome-Wide Identification and Characterization of Long Non-Coding RNA in Wheat Roots in Response to Ca2+ Channel Blocker. PMID:29559983
Genome-Wide Analysis Characterization and Evolution of SBP Genes in Fragaria vesca, Pyrus bretschneideri, Prunus persica and Prunus mume. PMID:29552026
Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein. PMID:29551514
Transcriptomic analysis of transgressive segregants revealed the central role of photosynthetic capacity and efficiency in biomass accumulation in sugarcane. PMID:29535363
Genome-Wide Analysis of the PYL Gene Family and Identification of PYL Genes That Respond to Abiotic Stress in Brassica napus. PMID:29534558
TryTransDB: A web-based resource for transport proteins in Trypanosomatidae. PMID:29531295
Genome-wide identification and characterization of Dof transcription factors in eggplant (Solanum melongena L.). PMID:29527420
Heterologous expression of kiwifruit (Actinidia chinensis) GOLDEN2-LIKE homolog elevates chloroplast level and nutritional quality in tomato (Solanum lycopersicum). PMID:29520458
Dynamin-Like Proteins Are Potentially Involved in Membrane Dynamics within Chloroplasts and Cyanobacteria. PMID:29520287
Identification of proteins interacting with the mitochondrial small heat shock protein Hsp22 of Drosophila melanogaster: Implication in mitochondrial homeostasis. PMID:29509794
Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals. PMID:29500236
The genome sequence of 'Kurodagosun', a major carrot variety in Japan and China, reveals insights into biological research and carrot breeding. PMID:29497811
Improving eukaryotic genome annotation using single molecule mRNA sequencing. PMID:29495964
Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. PMID:29491419
Different Modes of Gene Duplication Show Divergent Evolutionary Patterns and Contribute Differently to the Expansion of Gene Families Involved in Important Fruit Traits in Pear (Pyrus bretschneideri). PMID:29487610
c-di-GMP Regulates Various Phenotypes and Insecticidal Activity of Gram-Positive Bacillus thuringiensis. PMID:29487570
Microbial effects of part-stream low-frequency ultrasonic pretreatment on sludge anaerobic digestion as revealed by high-throughput sequencing-based metagenomics and metatranscriptomics. PMID:29483940
A family of unconventional deubiquitinases with modular chain specificity determinants. PMID:29476094
Evolution, functional differentiation, and co-expression of the RLK gene family revealed in Jilin ginseng, Panax ginseng C.A. Meyer. PMID:29468273
Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. PMID:29467397
Whole-Genome Analysis Illustrates Global Clonal Population Structure of the Ubiquitous Dermatophyte Pathogen Trichophyton rubrum. PMID:29467168
Genes sharing the protein family domain decrease the performance of classification with RNA-seq genomic signatures. PMID:29467011
Involvement of an ABI-like protein and a Ca2+-ATPase in drought tolerance as revealed by transcript profiling of a sweetpotato somatic hybrid and its parents Ipomoea batatas (L.) Lam. and I. triloba L. PMID:29466419
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
Characterization of viral RNA splicing using whole-transcriptome datasets from host species. PMID:29459752
Identification of genetic variants for clinical management of familial colorectal tumors. PMID:29458332
pMEX01, a 70kb plasmid isolated from Escherichia coli that confers resistance to multiple β-lactam antibiotics. PMID:29449172
Genome-wide differential expression profiling of mRNAs and lncRNAs associated with prolificacy in Hu sheep. PMID:29439142
A putative RNA binding protein from Plasmodium vivax apicoplast. PMID:29435408
Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome. PMID:29434576
Giant fish-killing water bug reveals ancient and dynamic venom evolution in Heteroptera. PMID:29427076
Genome-Wide Identification and Characterization of WD40 Protein Genes in the Silkworm, Bombyx mori. PMID:29425159
Cladogenesis and Genomic Streamlining in Extracellular Endosymbionts of Tropical Stink Bugs. PMID:29420776
The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile. PMID:29403466
SMRT sequencing of full-length transcriptome of flea beetle Agasicles hygrophila (Selman and Vogt). PMID:29396453
Comparative transcriptome analysis reveals molecular response to salinity stress of salt-tolerant and sensitive genotypes of indica rice at seedling stage. PMID:29391416
A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). PMID:29386578
Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes. PMID:29385986
A presumed homologue of the regulatory subunits of eIF2B functions as ribose-1,5-bisphosphate isomerase in Pyrococcus horikoshii OT3. PMID:29382938
A statistical model for improved membrane protein expression using sequence-derived features. PMID:29378850
Transcriptomic characterization and potential marker development of contrasting sugarcane cultivars. PMID:29374206
mRNA export in the apicomplexan parasite Toxoplasma gondii: emerging divergent components of a crucial pathway. PMID:29370868
Functional metagenomics identifies novel genes ABCTPP, TMSRP1 and TLSRP1 among human gut enterotypes. PMID:29362424
Function, distribution, and annotation of characterized cellulases, xylanases, and chitinases from CAZy. PMID:29359269
Altered chemomechanical coupling causes impaired motility of the kinesin-4 motors KIF27 and KIF7. PMID:29351996
Expansion of cytochrome P450 and cathepsin genes in the generalist herbivore brown marmorated stink bug. PMID:29347977
Genomic Identification and Functional Characterization of Essential Genes in Caenorhabditis elegans. PMID:29339407
Genome-wide identification and characterization of SPL transcription factor family and their evolution and expression profiling analysis in cotton. PMID:29335584
A multi-omics study of the grapevine-downy mildew (Plasmopara viticola) pathosystem unveils a complex protein coding- and noncoding-based arms race during infection. PMID:29335535
Structure, function and evolution of the hemerythrin-like domain superfamily. PMID:29330894
A-GAME: improving the assembly of pooled functional metagenomics sequence data. PMID:29329522
Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments. PMID:29327410
Relationship between histone modifications and transcription factor binding is protein family specific. PMID:29326300
Listeria monocytogenes Induces a Virulence-Dependent microRNA Signature That Regulates the Immune Response in Galleria mellonella. PMID:29312175
Discovering viral genomes in human metagenomic data by predicting unknown protein families. PMID:29311716
Identification of regenerative roadblocks via repeat deployment of limb regeneration in axolotls. PMID:29302364
dBBQs: dataBase of Bacterial Quality scores. PMID:29297289
Genomics of Clostridium taeniosporum, an organism which forms endospores with ribbon-like appendages. PMID:29293521
Transcriptional Response to Lactic Acid Stress in the Hybrid Yeast Zygosaccharomyces parabailii. PMID:29269498
Roles of Staphylococcus aureus Mnh1 and Mnh2 Antiporters in Salt Tolerance, Alkali Tolerance, and Pathogenesis. PMID:29263099
Identification of long non-coding RNAs in the immature and mature rat anterior pituitary. PMID:29259254
Progressive loss of hybrid histidine kinase genes during the evolution of budding yeasts (Saccharomycotina). PMID:29249052
Prediction of cassava protein interactome based on interolog method. PMID:29222529
Tracking the Taxonomy of the Genus Bifidobacterium Based on a Phylogenomic Approach. PMID:29222102
A Molecular Portrait of De Novo Genes in Yeasts. PMID:29220506
AllerBase: a comprehensive allergen knowledgebase. PMID:29220458
A multi-network clustering method for detecting protein complexes from multiple heterogeneous networks. PMID:29219066
Genome-wide analysis of the Brachypodium distachyon (L.) P. Beauv. Hsp90 gene family reveals molecular evolution and expression profiling under drought and salt stresses. PMID:29216330
Characterization of a membrane-bound C-glucosyltransferase responsible for carminic acid biosynthesis in Dactylopius coccus Costa. PMID:29215010
Mountain hare transcriptome and diagnostic markers as resources to monitor hybridization with European hares. PMID:29206218
In Vitro Biosynthetic Studies of Bottromycin Expand the Enzymatic Capabilities of the YcaO Superfamily. PMID:29200283
Intrinsic Disorder in Proteins with Pathogenic Repeat Expansions. PMID:29186753
Integrating sequence and gene expression information predicts genome-wide DNA-binding proteins and suggests a cooperative mechanism. PMID:29186632
Diversity-generating retroelements: natural variation, classification and evolution inferred from a large-scale genomic survey. PMID:29186518
Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader. PMID:29186423
Clec16a, Nrdp1, and USP8 Form a Ubiquitin-Dependent Tripartite Complex That Regulates β-Cell Mitophagy. PMID:29180353
Whole transcriptome RNA-Seq analysis reveals extensive cell type-specific compartmentalization in Volvox carteri. PMID:29179763
A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition. PMID:29165679
Identification of MsHsp20 Gene Family in Malus sieversii and Functional Characterization of MsHsp16.9 in Heat Tolerance. PMID:29163556
In Silico Analysis of Putrefaction Pathways in Bacteria and Its Implication in Colorectal Cancer. PMID:29163445
Sugar Metabolism of the First Thermophilic Planctomycete Thermogutta terrifontis: Comparative Genomic and Transcriptomic Approaches. PMID:29163426
Cloning and Molecular Characterization of an Alpha-Glucosidase (MalH) from the Halophilic Archaeon Haloquadratum walsbyi. PMID:29160840
Comparative Genomics of Myxobacterial Chemosensory Systems. PMID:29158239
Genomic, Transcriptomic, and Phenotypic Analyses of Neisseria meningitidis Isolates from Disease Patients and Their Household Contacts. PMID:29152586
Interplay of neuronal and non-neuronal genes regulates intestinal DAF-16-mediated immune response during Fusarium infection of Caenorhabditis elegans. PMID:29152379
Differential regulation of mRNAs and lncRNAs related to lipid metabolism in two pig breeds. PMID:29152100
The Membrane Attack Complex/Perforin Superfamily. PMID:29145176
A high-resolution mRNA expression time course of embryonic development in zebrafish. PMID:29144233
Transcriptome profiling of claw muscle of the mud crab (Scylla paramamosain) at different fattening stages. PMID:29141033
Visualizing the GPCR Network: Classification and Evolution. PMID:29138525
Genome-wide analysis and functional prediction of long non-coding RNAs in mouse uterus during the implantation window. PMID:29137430
Assigning chemoreceptors to chemosensory pathways in Pseudomonas aeruginosa. PMID:29133402
Comprehensive genomic analysis of the CNGC gene family in Brassica oleracea: novel insights into synteny, structures, and transcript profiles. PMID:29132315
Automated visualization of rule-based models. PMID:29131816
Evolutionary Epigenomics of Retrotransposon-Mediated Methylation Spreading in Rice. PMID:29126199
Sequencing and De Novo Assembly of the Toxicodendron radicans (Poison Ivy) Transcriptome. PMID:29125533
Targeted Gene Sequencing of Gallbladder Carcinoma Identifies High-impact Somatic and Rare Germline Mutations. PMID:29109099
Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions. PMID:29104938
Identification of Trans-4-Hydroxy-L-Proline as a Compatible Solute and Its Biosynthesis and Molecular Characterization in Halobacillus halophilus. PMID:29104571
KIXBASE: A comprehensive web resource for identification and exploration of KIX domains. PMID:29097748
The MAPKKK gene family in cassava: Genome-wide identification and expression analysis against drought stress. PMID:29097722
Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and communication pathways in cyclin-dependent kinases: Differentiating kinase clients of the Hsp90-Cdc37 chaperone. PMID:29095844
Insertion sequence polymorphism and genomic rearrangements uncover hidden Wolbachia diversity in Drosophila suzukii and D. subpulchrella. PMID:29093474
Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins. PMID:29091028
Proton-solute coupling mechanism of the maltose transporter from Saccharomyces cerevisiae. PMID:29084970
Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti. PMID:29078296
The Role of Cytoplasmic mRNA Cap-Binding Protein Complexes in Trypanosoma brucei and Other Trypanosomatids. PMID:29077018
Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria. PMID:29073099
A sensitive short read homology search tool for paired-end read sequencing data. PMID:29072140
Fusing multiple protein-protein similarity networks to effectively predict lncRNA-protein interactions. PMID:29072138
Functional classification of protein toxins as a basis for bioinformatic screening. PMID:29066768
In silico methods for linking genes and secondary metabolites: The way forward. PMID:29062931
How to normalize metatranscriptomic count data for differential expression analysis. PMID:29062598
A genome-wide analysis of the small auxin-up RNA (SAUR) gene family in cotton. PMID:29061116
Metagenomic Analysis of Microbial Diversity in Landfill Lysimeter Soil of Ghazipur Landfill Site, New Delhi, India. PMID:29051248
An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae. PMID:29049350
High-quality-draft genomic sequence of Paenibacillus ferrarius CY1T with the potential to bioremediate Cd, Cr and Se contamination. PMID:29046739
Wax Ester Synthase/Diacylglycerol Acyltransferase Isoenzymes Play a Pivotal Role in Wax Ester Biosynthesis in Euglena gracilis. PMID:29044218
Global Identification, Classification, and Expression Analysis of MAPKKK genes: Functional Characterization of MdRaf5 Reveals Evolution and Drought-Responsive Profile in Apple. PMID:29044159
Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution. PMID:29041914
Transcriptomic Analysis of Long Non-Coding RNAs and Coding Genes Uncovers a Complex Regulatory Network That Is Involved in Maize Seed Development. PMID:29039813
Transcript expression plasticity as a response to alternative larval host plants in the speciation process of corn and rice strains of Spodoptera frugiperda. PMID:29037161
PixelDB: Protein-peptide complexes annotated with structural conservation of the peptide binding mode. PMID:29024246
Genome-wide characterization, evolution, and expression analysis of the leucine-rich repeat receptor-like protein kinase (LRR-RLK) gene family in Rosaceae genomes. PMID:29017442
Genetic variants affecting equivalent protein family positions reflect human diversity. PMID:28986545
Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop. PMID:28985356
Genome sequencing and comparative genomics reveal the potential pathogenic mechanism of Cercospora sojina Hara on soybean. PMID:28985305
RNA-Seq Analysis Provides the First Insights into the Phylogenetic Relationship and Interspecific Variation between Agropyron cristatum and Wheat. PMID:28983310
Metagenomic Sequencing of Microbial Communities from Brackish Water of Pangong Lake of the Northwest Indian Himalayas. PMID:28982995
An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus. PMID:28978920
Alignment-free sequence comparison: benefits, applications, and tools. PMID:28974235
Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species. PMID:28973974
Association Between Gut Microbiota and Bone Health: Potential Mechanisms and Prospective. PMID:28973392
Ant-infecting Ophiocordyceps genomes reveal a high diversity of potential behavioral manipulation genes and a possible major role for enterotoxins. PMID:28970504
HUMA: A platform for the analysis of genetic variation in humans. PMID:28967693
Genome-wide analysis of potential cross-reactive endogenous allergens in rice (Oryza sativa L.). PMID:28962466
Identification and expression of GRAS family genes in maize (Zea mays L.). PMID:28957440
Global Survey and Genome Exploration of Bacteriophages Infecting the Lactic Acid Bacterium Streptococcus thermophilus. PMID:28955321
Strains, functions and dynamics in the expanded Human Microbiome Project. PMID:28953883
Insights on Osmotic Tolerance Mechanisms in Escherichia coli Gained from an rpoC Mutation. PMID:28952540
Thiamine Acquisition Strategies Impact Metabolism and Competition in the Gut Microbe Bacteroides thetaiotaomicron. PMID:28951891
A single point mutation in a TssB/VipA homolog disrupts sheath formation in the type VI secretion system of Proteus mirabilis. PMID:28949977
Contribution of single amino acid and codon substitutions to the production and secretion of a lipase by Bacillus subtilis. PMID:28946879
Mycoviruses in Aspergilli: A Comprehensive Review. PMID:28932216
Genome sequence of the ectophytic fungus Ramichloridium luteum reveals unique evolutionary adaptations to plant surface niche. PMID:28915794
Tremblaya phenacola PPER: an evolutionary beta-gammaproteobacterium collage. PMID:28914880
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
Genomic and transcriptomic analysis of the toluene degrading black yeast Cladophialophora immunda. PMID:28900256
Long noncoding RNAs in the model species Brachypodium distachyon. PMID:28900227
De Novo Assembly and Analysis of Polygonatum sibiricum Transcriptome and Identification of Genes Involved in Polysaccharide Biosynthesis. PMID:28895881
A Preliminary List of Horizontally Transferred Genes in Prokaryotes Determined by Tree Reconstruction and Reconciliation. PMID:28894459
The dynamic landscape of gene regulation during Bombyx mori oogenesis. PMID:28893182
Oxidative cyclization of prodigiosin by an alkylglycerol monooxygenase-like enzyme. PMID:28892091
Structural analyses of the Haemophilus influenzae peptidoglycan synthase activator LpoA suggest multiple conformations in solution. PMID:28887305
Evidence-based gene models for structural and functional annotations of the oil palm genome. PMID:28886750
Clustal Omega for making accurate alignments of many protein sequences. PMID:28884485
Prokaryotic and Highly-Repetitive WD40 Proteins: A Systematic Study. PMID:28878378
FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation. PMID:28874813
Comparative secretome analysis of Rhizoctonia solani isolates with different host ranges reveals unique secretomes and cell death inducing effectors. PMID:28874693
Myosin repertoire expansion coincides with eukaryotic diversification in the Mesoproterozoic era. PMID:28870165
Potential Roles of Intrinsic Disorder in Maternal-Effect Proteins Involved in the Maintenance of DNA Methylation. PMID:28869544
Regulation of Noncoding Transcriptome in Developing Photoreceptors by Rod Differentiation Factor NRL. PMID:28863214
Ixodes scapularis Tick Cells Control Anaplasma phagocytophilum Infection by Increasing the Synthesis of Phosphoenolpyruvate from Tyrosine. PMID:28861402
Protein-Protein Interactions in Virus-Host Systems. PMID:28861068
Structural and Functional View of Polypharmacology. PMID:28860623
Phylogeny and expression pattern analysis of TCP transcription factors in cassava seedlings exposed to cold and/or drought stress. PMID:28855620
Functional Analogy in Human Metabolism: Enzymes with Different Biological Roles or Functional Redundancy? PMID:28854631
Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes. PMID:28851873
Alternaria Toxins: Potential Virulence Factors and Genes Related to Pathogenesis. PMID:28848500
Modelling of microbial polyhydroxyalkanoate surface binding protein PhaP for rational mutagenesis. PMID:28840964
An integrated bioinformatics platform for investigating the human E3 ubiquitin ligase-substrate interaction network. PMID:28839186
Draft genome sequence of the halophilic Halobacillus mangrovi KTB 131 isolated from Topan salt of the Jeon-nam in Korea. PMID:28831380
Identification of candidate genes involved in isoquinoline alkaloids biosynthesis in Dactylicapnos scandens by transcriptome analysis. PMID:28831066
Monte Carlo simulation of a statistical mechanical model of multiple protein sequence alignment. PMID:28828285
Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton. PMID:28827361
Cancerouspdomains: comprehensive analysis of cancer type-specific recurrent somatic mutations in proteins and domains. PMID:28814324
Screening drug-target interactions with positive-unlabeled learning. PMID:28808275
ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology. PMID:28808136
High resolution measurement of DUF1220 domain copy number from whole genome sequence data. PMID:28807002
Neurodevelopmental Disorders Caused by De Novo Variants in KCNB1 Genotypes and Phenotypes. PMID:28806457
Chemical dispersants enhance the activity of oil- and gas condensate-degrading marine bacteria. PMID:28800137
Polymorphism and structure of style-specific arabinogalactan proteins as determinants of pollen tube growth in Nicotiana. PMID:28797243
The genetic architecture of amylose biosynthesis in maize kernel. PMID:28796926
A clinician's guide to microbiome analysis. PMID:28790452
Co-evolution techniques are reshaping the way we do structural bioinformatics. PMID:28781768
Virome comparisons in wild-diseased and healthy captive giant pandas. PMID:28780905
First report of cherry virus A infecting Prunus mume in South Korea. PMID:28770251
Neisseria lactamica Y92-1009 complete genome sequence. PMID:28770026
Global Gene Expression Analysis Reveals Crosstalk between Response Mechanisms to Cold and Drought Stresses in Cassava Seedlings. PMID:28769962
Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family. PMID:28764658
PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection. PMID:28761071
The first phlebo-like virus infecting plants: a case study on the adaptation of negative-stranded RNA viruses to new hosts. PMID:28752569
BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation. PMID:28750104
Suppressing a Putative Sterol Carrier Gene Reduces Plasmodesmal Permeability and Activates Sucrose Transporter Genes during Cotton Fiber Elongation. PMID:28747422
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web. PMID:28745621
Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals. PMID:28743941
Genome-wide comparative analysis of putative Pth11-related G protein-coupled receptors in fungi belonging to Pezizomycotina. PMID:28743231
Acylation of Superoxide Dismutase 1 (SOD1) at K122 Governs SOD1-Mediated Inhibition of Mitochondrial Respiration. PMID:28739857
Community detection in sequence similarity networks based on attribute clustering. PMID:28738060
Complete Genome Sequence of Campylobacter concisus ATCC 33237T and Draft Genome Sequences for an Additional Eight Well-Characterized C. concisus Strains. PMID:28729281
Major Novel QTL for Resistance to Cassava Bacterial Blight Identified through a Multi-Environmental Analysis. PMID:28725234
Assessment of genome annotation using gene function similarity within the gene neighborhood. PMID:28724412
Genome analysis of E. coli isolated from Crohn's disease patients. PMID:28724357
Draft Transcriptome of Globodera ellingtonae. PMID:28706310
Draft whole genome sequence of groundnut stem rot fungus Athelia rolfsii revealing genetic architect of its pathogenicity and virulence. PMID:28706242
Identification of long non-coding RNAs in two anthozoan species and their possible implications for coral bleaching. PMID:28706206
Identification, classification and transcriptional profiles of dirigent domain-containing proteins in sugarcane. PMID:28699001
DprA from Neisseria meningitidis: properties and role in natural competence for transformation. PMID:28696187
Draft Genome Sequences of the Antarctic Endolithic Fungi Rachicladosporium antarcticum CCFEE 5527 and Rachicladosporium sp. CCFEE 5018. PMID:28684563
Genome-Wide Identification and Comparative Analysis of Albumin Family in Vertebrates. PMID:28680266
Disruption of key NADH-binding pocket residues of the Mycobacterium tuberculosis InhA affects DD-CoA binding ability. PMID:28680153
Comparative analysis of lincRNA in insect species. PMID:28673235
Characterization of Sinorhizobium sp. LM21 Prophages and Virus-Encoded DNA Methyltransferases in the Light of Comparative Genomic Analyses of the Sinorhizobial Virome. PMID:28672885
Characterization of the emerging zoonotic pathogen Arcobacter thereius by whole genome sequencing and comparative genomics. PMID:28671965
Spatiotemporal profile of postsynaptic interactomes integrates components of complex brain disorders. PMID:28671696
Type VI Secretion Effectors: Methodologies and Biology. PMID:28664151
Transcription Factor Repertoire of Necrotrophic Fungal Phytopathogen Ascochyta rabiei: Predominance of MYB Transcription Factors As Potential Regulators of Secretome. PMID:28659964
Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida. PMID:28659179
Exploring Components of the CO2-Concentrating Mechanism in Alkaliphilic Cyanobacteria Through Genome-Based Analysis. PMID:28652895
Genome-Wide Analysis of the PvHsp20 Family in Switchgrass: Motif, Genomic Organization, and Identification of Stress or Developmental-Related Hsp20s. PMID:28649264
Survey of High Throughput RNA-Seq Data Reveals Potential Roles for lncRNAs during Development and Stress Response in Bread Wheat. PMID:28649263
Genome analysis of Diploscapter coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction. PMID:28646875
A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against Leishmania major. PMID:28638238
Evolution of miRNA Tailing by 3' Terminal Uridylyl Transferases in Metazoa. PMID:28633361
Putative archaeal viruses from the mesopelagic ocean. PMID:28630803
The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization. PMID:28623667
Alkene hydrogenation activity of enoate reductases for an environmentally benign biosynthesis of adipic acid. PMID:28616142
Pseudogymnoascus destructans transcriptome changes during white-nose syndrome infections. PMID:28614673
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
Family-specific scaling laws in bacterial genomes. PMID:28605556
Plant cell wall glycosyltransferases: High-throughput recombinant expression screening and general requirements for these challenging enzymes. PMID:28598995
An Alcaligenes strain emulates Bacillus thuringiensis producing a binary protein that kills corn rootworm through a mechanism similar to Cry34Ab1/Cry35Ab1. PMID:28596570
Genome-wide survey of switchgrass NACs family provides new insights into motif and structure arrangements and reveals stress-related and tissue-specific NACs. PMID:28596552
Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes. PMID:28594822
Duplication and Loss of Function of Genes Encoding RNA Polymerase III Subunit C4 Causes Hybrid Incompatibility in Rice. PMID:28592558
A Primer on Infectious Disease Bacterial Genomics. PMID:28590251
Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces. PMID:28588130
Analysis of the lipid body proteome of the oleaginous alga Lobosphaera incisa. PMID:28587627
Proteases of Dermatophagoides pteronyssinus. PMID:28587273
Prediction of bioluminescent proteins by using sequence-derived features and lineage-specific scheme. PMID:28583090
Changes in the neuropeptide content of Biomphalaria ganglia nervous system following Schistosoma infection. PMID:28578678
Understanding the mechanisms of dormancy in an invasive alien Sycamore lace bug, Corythucha ciliata through transcript and metabolite profiling. PMID:28572631
De novo characterization of the pine aphid Cinara pinitabulaeformis Zhang et Zhang transcriptome and analysis of genes relevant to pesticides. PMID:28570707
A dual-strategy expression screen for candidate connectivity labels in the developing thalamus. PMID:28558017
Evolution of the Apicomplexan Sugar Transporter Gene Family Repertoire. PMID:28555190
Systems-wide Studies Uncover Commander, a Multiprotein Complex Essential to Human Development. PMID:28544880
SesameFG: an integrated database for the functional genomics of sesame. PMID:28539606
RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases. PMID:28537551
Characterization of TRPA channels in the starfish Patiria pectinifera: involvement of thermally activated TRPA1 in thermotaxis in marine planktonic larvae. PMID:28526851
Genome Analysis of Conserved Dehydrin Motifs in Vascular Plants. PMID:28523013
GeMSTONE: orchestrated prioritization of human germline mutations in the cloud. PMID:28521008
Characterization of a secretory hydrolase from Mycobacterium tuberculosis sheds critical insight into host lipid utilization by M. tuberculosis. PMID:28515317
Architecture of the human interactome defines protein communities and disease networks. PMID:28514442
Genome-Wide Identification and Expression Analysis of the Biotin Carboxyl Carrier Subunits of Heteromeric Acetyl-CoA Carboxylase in Gossypium. PMID:28507552
Genome-wide identification of lncRNAs associated with chlorantraniliprole resistance in diamondback moth Plutella xylostella (L.). PMID:28506253
Analysis of CFB, a cytokinin-responsive gene of Arabidopsis thaliana encoding a novel F-box protein regulating sterol biosynthesis. PMID:28505379
Dissecting physical structure of calreticulin, an intrinsically disordered Ca2+-buffering chaperone from endoplasmic reticulum. PMID:28504081
Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum. PMID:28499417
Transcriptome-wide analysis of alternative RNA splicing events in Epstein-Barr virus-associated gastric carcinomas. PMID:28493890
Comparative genomic study of ALDH gene superfamily in Gossypium: A focus on Gossypium hirsutum under salt stress. PMID:28489898
Using Tn-seq To Identify Pigmentation-Related Genes of Porphyromonas gingivalis: Characterization of the Role of a Putative Glycosyltransferase. PMID:28484050
Activity-based protein profiling as a robust method for enzyme identification and screening in extremophilic Archaea. PMID:28480883
Genome-wide analysis identifies chickpea (Cicer arietinum) heat stress transcription factors (Hsfs) responsive to heat stress at the pod development stage. PMID:28474118
InlL from Listeria monocytogenes Is Involved in Biofilm Formation and Adhesion to Mucin. PMID:28473809
Organ-specific transcriptome profiling of metabolic and pigment biosynthesis pathways in the floral ornamental progenitor species Anthurium amnicola Dressler. PMID:28473720
Draft Genome Sequence of Brevundimonas sp. Strain SH203, Producing Cellouronate (β-1,4-Linked Polyglucuronate) Lyase. PMID:28473379
Unique Phylogenetic Distributions of the Ska and Dam1 Complexes Support Functional Analogy and Suggest Multiple Parallel Displacements of Ska by Dam1. PMID:28472331
Transcriptome analysis of muskrat scented glands degeneration mechanism. PMID:28472080
Computational Analysis of Host-Pathogen Protein Interactions between Humans and Different Strains of Enterohemorrhagic Escherichia coli. PMID:28469995
PAIRS: Prediction of Activation/Inhibition Regulation Signaling Pathway. PMID:28469669
Comparative Transcriptomic Analysis of Race 1 and Race 4 of Fusarium oxysporum f. sp. cubense Induced with Different Carbon Sources. PMID:28468818
Novel transcription-induced fusion RNAs in prostate cancer. PMID:28467780
Molecular detection and characterization of a divergent isolate of Plantago asiatica mosaic virus in Plantago asiatica. PMID:28466044
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
Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling. PMID:28462022
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper. PMID:28460117
plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters. PMID:28453650
Draft genome of the lined seahorse, Hippocampus erectus. PMID:28444302
Evolution of the 3R-MYB Gene Family in Plants. PMID:28444194
Deletion of Lipoteichoic Acid Synthase Impacts Expression of Genes Encoding Cell Surface Proteins in Lactobacillus acidophilus. PMID:28443071
Progranulin, lysosomal regulation and neurodegenerative disease. PMID:28435163
Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5. PMID:28432541
Identification and Characterization of Differentially-Regulated Type IVb Pilin Genes Necessary for Predation in Obligate Bacterial Predators. PMID:28432347
Genome-wide identification, characterization of the MADS-box gene family in Chinese jujube and their involvement in flower development. PMID:28432294
HirBin: high-resolution identification of differentially abundant functions in metagenomes. PMID:28431529
Somatic transposition and meiotically driven elimination of an active helitron family in Pleurotus ostreatus. PMID:28431016
Genome sequencing and analysis of Ralstonia solanacearum phylotype I strains FJAT-91, FJAT-452 and FJAT-462 isolated from tomato, eggplant, and chili pepper in China. PMID:28428834
Identification of Candidate Genes and Biosynthesis Pathways Related to Fertility Conversion by Wheat KTM3315A Transcriptome Profiling. PMID:28428792
Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa. PMID:28427330
Exhaustive search of linear information encoding protein-peptide recognition. PMID:28426660
Genetic basis for soma is present in undifferentiated volvocine green algae. PMID:28425150
Inbreeding and selection shape genomic diversity in captive populations: Implications for the conservation of endangered species. PMID:28423000
Genome-Wide Analyses of the Soybean F-Box Gene Family in Response to Salt Stress. PMID:28417911
Distinct Domains of CheA Confer Unique Functions in Chemotaxis and Cell Length in Azospirillum brasilense Sp7. PMID:28416707
An in silico pan-genomic probe for the molecular traits behind Lactobacillus ruminis gut autochthony. PMID:28414739
Genomics and Comparative Genomic Analyses Provide Insight into the Taxonomy and Pathogenic Potential of Novel Emmonsia Pathogens. PMID:28409126
Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. PMID:28401891
Improving the 'tool box' for robust industrial enzymes. PMID:28401315
Comparative transcriptome profiling and morphology provide insights into endocarp cleaving of apricot cultivar (Prunus armeniaca L.). PMID:28399812
Prospecting Biotechnologically-Relevant Monooxygenases from Cold Sediment Metagenomes: An In Silico Approach. PMID:28397770
Inclusion of biological knowledge in a Bayesian shrinkage model for joint estimation of SNP effects. PMID:28393391
regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution. PMID:28391525
De novo RNA sequence assembly during in vivo inflammatory stress reveals hundreds of unannotated lincRNAs in human blood CD14+ monocytes and in adipose tissue. PMID:28389524
Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar. PMID:28388875
High number of kinome-mutations in non-small cell lung cancer is associated with reduced immune response and poor relapse-free survival. PMID:28387924
Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava. PMID:28387315
Transcriptome Analyses of Two Citrus Cultivars (Shiranuhi and Huangguogan) in Seedling Etiolation. PMID:28387303
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
SIRT4 Is a Lysine Deacylase that Controls Leucine Metabolism and Insulin Secretion. PMID:28380376
Unravelling the Complete Genome of Archangium gephyra DSM 2261T and Evolutionary Insights into Myxobacterial Chitinases. PMID:28379546
Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents. PMID:28375213
Genome-wide identification of membrane-bound fatty acid desaturase genes in Gossypium hirsutum and their expressions during abiotic stress. PMID:28374822
Genome-Wide Identification, Evolution, and Expression Analysis of the ATP-Binding Cassette Transporter Gene Family in Brassica rapa. PMID:28367152
Engineering Pak1 Allosteric Switches. PMID:28365983
Biocuration in the structure-function linkage database: the anatomy of a superfamily. PMID:28365730
PCPPI: a comprehensive database for the prediction of Penicillium-crop protein-protein interactions. PMID:28365721
Selecting high-quality negative samples for effectively predicting protein-RNA interactions. PMID:28361676
Transcriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver. PMID:28360091
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
Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. PMID:28350393
Epipodial Tentacle Gene Expression and Predetermined Resilience to Summer Mortality in the Commercially Important Greenlip Abalone, Haliotis laevigata. PMID:28349286
Comparative genomics and evolution of transcriptional regulons in Proteobacteria. PMID:28348857
Comparative genomics of pyridoxal 5'-phosphate-dependent transcription factor regulons in Bacteria. PMID:28348826
Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes. PMID:28347275
Gene Expression, Protein Function and Pathways of Arabidopsis thaliana Responding to Silver Nanoparticles in Comparison to Silver Ions, Cold, Salt, Drought, and Heat. PMID:28347022
Systematic identification of phosphorylation-mediated protein interaction switches. PMID:28346509
Genomic characterization of Nontuberculous Mycobacteria. PMID:28345639
In silico functional elucidation of uncharacterized proteins of Chlamydia abortus strain LLG. PMID:28344832
F-Box Protein FBX92 Affects Leaf Size in Arabidopsis thaliana. PMID:28340173
The evolutionary fate of the chloroplast and nuclear rps16 genes as revealed through the sequencing and comparative analyses of four novel legume chloroplast genomes from Lupinus. PMID:28338826
Populus trichocarpa encodes small, effector-like secreted proteins that are highly induced during mutualistic symbiosis. PMID:28336910
Highly diverse population of Picornaviridae and other members of the Picornavirales, in Cameroonian fruit bats. PMID:28335731
Transcription factors of Schizophyllum commune involved in mushroom formation and modulation of vegetative growth. PMID:28331193
Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius. PMID:28327943
Structure-based functional annotation of hypothetical proteins from Candida dubliniensis: a quest for potential drug targets. PMID:28324558
Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi. PMID:28322291
Genome-wide analysis of brain and gonad transcripts reveals changes of key sex reversal-related genes expression and signaling pathways in three stages of Monopterus albus. PMID:28319194
A Vibrio cholerae autoinducer-receptor pair that controls biofilm formation. PMID:28319101
Distribution and diversity of enzymes for polysaccharide degradation in fungi. PMID:28302998
Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites. PMID:28300228
The isolation and characterization of Stenotrophomonas maltophilia T4-like bacteriophage DLP6. PMID:28291834
Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition in Trypanosoma cruzi. PMID:28286708
Development of Gene-Based SSR Markers in Winged Bean (Psophocarpus tetragonolobus (L.) DC.) for Diversity Assessment. PMID:28282950
Draft Genome Sequence of Idiomarina sp. Strain 5.13, a Highly Stress-Resistant Bacterium Isolated from the Southwest Indian Ridge. PMID:28280030
Draft Genome Assembly of Colletotrichum chlorophyti, a Pathogen of Herbaceous Plants. PMID:28280027
Functional metagenomics reveals novel β-galactosidases not predictable from gene sequences. PMID:28273103
Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families. PMID:28272521
RXLR Effector AVR2 Up-Regulates a Brassinosteroid-Responsive bHLH Transcription Factor to Suppress Immunity. PMID:28270626
High quality draft genome sequence of an extremely halophilic archaeon Natrinema altunense strain AJ2T. PMID:28265340
A genome-wide analysis of the lysophosphatidate acyltransferase (LPAAT) gene family in cotton: organization, expression, sequence variation, and association with seed oil content and fiber quality. PMID:28249560
A Gradient of Sitewise Diversity Promotes Evolutionary Fitness for Binder Discovery in a Three-Helix Bundle Protein Scaffold. PMID:28248518
A new genome-mining tool redefines the lasso peptide biosynthetic landscape. PMID:28244986
Leaf transcriptome analysis of a subtropical evergreen broadleaf plant, wild oil-tea camellia (Camellia oleifera), revealing candidate genes for cold acclimation. PMID:28241790
A Novel Subfamily Esterase with a Homoserine Transacetylase-like Fold but No Transferase Activity. PMID:28235874
A New Reference Genome Assembly for the Microcrustacean Daphnia pulex. PMID:28235826
Genome-wide screening and characterization of long non-coding RNAs involved in flowering development of trifoliate orange (Poncirus trifoliata L. Raf.). PMID:28233798
In silico serine β-lactamases analysis reveals a huge potential resistome in environmental and pathogenic species. PMID:28233789
Understanding the roles of intrinsic disorder in subunits of hemoglobin and the disease process of sickle cell anemia. PMID:28232898
Quarterly intrinsic disorder digest (January-February-March, 2014). PMID:28232896
Anaplasma phagocytophilum Infection Subverts Carbohydrate Metabolic Pathways in the Tick Vector, Ixodes scapularis. PMID:28229048
The effects of shared information on semantic calculations in the gene ontology. PMID:28217262
HAPPI-2: a Comprehensive and High-quality Map of Human Annotated and Predicted Protein Interactions. PMID:28212602
Plasmodium falciparum CRK4 directs continuous rounds of DNA replication during schizogony. PMID:28211852
Syntrophic linkage between predatory Carpediemonas and specific prokaryotic populations. PMID:28211847
RNA-Seq of Guar (Cyamopsis tetragonoloba, L. Taub.) Leaves: De novo Transcriptome Assembly, Functional Annotation and Development of Genomic Resources. PMID:28210265
Structure, kinetic characterization and subcellular localization of the two ribulose 5-phosphate epimerase isoenzymes from Trypanosoma cruzi. PMID:28207833
Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel families. PMID:28204924
Error-prone DnaE2 Balances the Genome Mutation Rates in Myxococcus xanthus DK1622. PMID:28203231
Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. PMID:28200013
Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. PMID:28196534
ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains. PMID:28193156
HIPPI: highly accurate protein family classification with ensembles of HMMs. PMID:28185571
Conserved Fever Pathways across Vertebrates: A Herpesvirus Expressed Decoy TNF-α Receptor Delays Behavioral Fever in Fish. PMID:28182952
Sinorhizobium meliloti YbeY is an endoribonuclease with unprecedented catalytic features, acting as silencing enzyme in riboregulation. PMID:28180335
Variability among Cucurbitaceae species (melon, cucumber and watermelon) in a genomic region containing a cluster of NBS-LRR genes. PMID:28178932
Guidelines for the successful generation of protein-ligand complex crystals. PMID:28177304
Functional characterization of AGAMOUS-subfamily members from cotton during reproductive development and in response to plant hormones. PMID:28176007
Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression. PMID:28170390
A New Essential Cell Division Protein in Caulobacter crescentus. PMID:28167520
Improving protein-protein interaction prediction using evolutionary information from low-quality MSAs. PMID:28166227
Phylogenetic Diversity of NTT Nucleotide Transport Proteins in Free-Living and Parasitic Bacteria and Eukaryotes. PMID:28164241
Plasmodium vivax Cell Traversal Protein for Ookinetes and Sporozoites (PvCelTOS) gene sequence and potential epitopes are highly conserved among isolates from different regions of Brazilian Amazon. PMID:28158176
Protein Bioinformatics Databases and Resources. PMID:28150231
Phosphatidylserine synthase 2 and phosphatidylserine decarboxylase are essential for aminophospholipid synthesis in Trypanosoma brucei. PMID:28142188
2b or Not 2b: Experimental Evolution of Functional Exogenous Sequences in a Plant RNA Virus. PMID:28137747
Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics. PMID:28128549
A comparative in-silico analysis of autophagy proteins in ciliates. PMID:28123910
Tensor Factorization for Precision Medicine in Heart Failure with Preserved Ejection Fraction. PMID:28116551
Studies on the Virome of the Entomopathogenic Fungus Beauveria bassiana Reveal Novel dsRNA Elements and Mild Hypervirulence. PMID:28114361
SecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems. PMID:28112271
Programmed Ribosomal Frameshifting Generates a Copper Transporter and a Copper Chaperone from the Same Gene. PMID:28107647
ProClaT, a new bioinformatics tool for in silico protein reclassification: case study of DraB, a protein coded from the draTGB operon in Azospirillum brasilense. PMID:28105917
GPCRs from fusarium graminearum detection, modeling and virtual screening - the search for new routes to control head blight disease. PMID:28105916
Origin and Evolution of the Sponge Aggregation Factor Gene Family. PMID:28104746
A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors. PMID:28099853
IsomiR expression patterns in canonical and Dicer‑independent microRNAs. PMID:28098889
Nematophagous fungus Arthrobotrys oligospora mimics olfactory cues of sex and food to lure its nematode prey. PMID:28098555
Rpn (YhgA-Like) Proteins of Escherichia coli K-12 and Their Contribution to RecA-Independent Horizontal Transfer. PMID:28096446
Ancient bacteria of the Ötzi's microbiome: a genomic tale from the Copper Age. PMID:28095919
ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana. PMID:28095775
Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication. PMID:28095400
Protein multiple sequence alignment benchmarking through secondary structure prediction. PMID:28093407
Genome Analysis of a Zygomycete Fungus Choanephora cucurbitarum Elucidates Necrotrophic Features Including Bacterial Genes Related to Plant Colonization. PMID:28091548
Identification of functional enolase genes of the silkworm Bombyx mori from public databases with a combination of dry and wet bench processes. PMID:28086791
Genetic mechanisms of bone digestion and nutrient absorption in the bone-eating worm Osedax japonicus inferred from transcriptome and gene expression analyses. PMID:28086748
Genome Sequence of Christensenella minuta DSM 22607T. PMID:28082495
Draft Genome Sequence of Micromonospora sp. Strain WMMB235, a Marine Ascidian-Associated Bacterium. PMID:28082484
Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease. PMID:28081260
Comparative Genomics of H. pylori and Non-Pylori Helicobacter Species to Identify New Regions Associated with Its Pathogenicity and Adaptability. PMID:28078297
Identification of new members of the Escherichia coli K-12 MG1655 SlyA regulon. PMID:28073397
A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species Colletotrichum graminicola and Colletotrichum sublineola. PMID:28073340
Embryonic origin of adult stem cells required for tissue homeostasis and regeneration. PMID:28072387
Burkholderia contaminans Biofilm Regulating Operon and Its Distribution in Bacterial Genomes. PMID:28070515
From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer. PMID:28066816
Comparative Temporal Transcriptome Profiling of Wheat near Isogenic Line Carrying Lr57 under Compatible and Incompatible Interactions. PMID:28066494
Widespread Inter- and Intra-Domain Horizontal Gene Transfer of d-Amino Acid Metabolism Enzymes in Eukaryotes. PMID:28066338
Insertion Polymorphisms of Mobile Genetic Elements in Sexual and Asexual Populations of Daphnia pulex. PMID:28057730
Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis. PMID:28056815
Deciphering the Translation Initiation Factor 5A Modification Pathway in Halophilic Archaea. PMID:28053595
A meiosis-specific Spt5 homolog involved in non-coding transcription. PMID:28053118
Co-Option and De Novo Gene Evolution Underlie Molluscan Shell Diversity. PMID:28053006
Global Analysis of Protein Expression of Inner Ear Hair Cells. PMID:28039372
Evolution of Chemosensory Gene Families in Arthropods: Insight from the First Inclusive Comparative Transcriptome Analysis across Spider Appendages. PMID:28028122
CaspNeuroD: a knowledgebase of predicted caspase cleavage sites in human proteins related to neurodegenerative diseases. PMID:28025335
Alternative splicing in tomato pollen in response to heat stress. PMID:28025318
Identification and Analysis of NaHCO3 Stress Responsive Genes in Wild Soybean (Glycine soja) Roots by RNA-seq. PMID:28018382
Genome analysis of Hibiscus syriacus provides insights of polyploidization and indeterminate flowering in woody plants. PMID:28011721
Biochemical and structural characterization of a novel halotolerant cellulase from soil metagenome. PMID:28008971
An expressed, endogenous Nodavirus-like element captured by a retrotransposon in the genome of the plant parasitic nematode Bursaphelenchus xylophilus. PMID:28004836
Complete genome sequence of new bacteriophage phiE142, which causes simultaneously lysis of multidrug-resistant Escherichia coli O157:H7 and Salmonella enterica. PMID:27999624
Comparative In silico Analysis of Butyrate Production Pathways in Gut Commensals and Pathogens. PMID:27994578
Glycoside Hydrolases across Environmental Microbial Communities. PMID:27992426
Non-canonical Helitrons in Fusarium oxysporum. PMID:27990178
AhDGR2, an amaranth abiotic stress-induced DUF642 protein gene, modifies cell wall structure and composition and causes salt and ABA hyper-sensibility in transgenic Arabidopsis. PMID:27988887
The regulation of antimicrobial peptide resistance in the transition to insect symbiosis. PMID:27987256
Complete Genome Sequence of Rhodococcus sp. Strain WMMA185, a Marine Sponge-Associated Bacterium. PMID:27979952
COUSCOus: improved protein contact prediction using an empirical Bayes covariance estimator. PMID:27978812
Thrombotic Microangiopathy in Inverted Formin 2-Mediated Renal Disease. PMID:27974406
Structure and Mechanism of Staphylococcus aureus TarS, the Wall Teichoic Acid β-glycosyltransferase Involved in Methicillin Resistance. PMID:27973583
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
Characterization of a DUF820 family protein Alr3200 of the cyanobacterium Anabaena sp. strain PCC7120. PMID:27966482
Ca2+/Cation Antiporters (CaCA): Identification, Characterization and Expression Profiling in Bread Wheat (Triticum aestivum L.). PMID:27965686
Evaluation of Machine Learning and Rules-Based Approaches for Predicting Antimicrobial Resistance Profiles in Gram-negative Bacilli from Whole Genome Sequence Data. PMID:27965630
Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone. PMID:27965389
Thermoregulation of Biofilm Formation in Burkholderia pseudomallei Is Disrupted by Mutation of a Putative Diguanylate Cyclase. PMID:27956524
Subunit NDUFV3 is present in two distinct isoforms in mammalian complex I. PMID:27940020
The evolution of function within the Nudix homology clan. PMID:27936487
Functional and structural characterization of a novel putative cysteine protease cell wall-modifying multi-domain enzyme selected from a microbial metagenome. PMID:27934875
Evolution of mitosome metabolism and invasion-related proteins in Cryptosporidium. PMID:27931183
Analysis of Domain Architecture and Phylogenetics of Family 2 Glycoside Hydrolases (GH2). PMID:27930742
Electric-field-stimulated protein mechanics. PMID:27926732
A unified statistical model of protein multiple sequence alignment integrating direct coupling and insertions. PMID:27924257
Query-seeded iterative sequence similarity searching improves selectivity 5-20-fold. PMID:27923999
Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium. PMID:27920771
EvalMSA: A Program to Evaluate Multiple Sequence Alignments and Detect Outliers. PMID:27920488
A Novel Transcriptional Regulator Related to Thiamine Phosphate Synthase Controls Thiamine Metabolism Genes in Archaea. PMID:27920295
The Streptococcus gordonii Adhesin CshA Protein Binds Host Fibronectin via a Catch-Clamp Mechanism. PMID:27920201
The crystal structure of dihydrodipicolinate reductase from the human-pathogenic bacterium Bartonella henselae strain Houston-1 at 2.3 Å resolution. PMID:27917836
Ion Channel Activity of Vpu Proteins Is Conserved throughout Evolution of HIV-1 and SIV. PMID:27916968
Identification of enzymes responsible for extracellular alginate depolymerization and alginate metabolism in Vibrio algivorus. PMID:27915375
The phenylalanine ammonia-lyase gene family in Isatis indigotica Fort.: molecular cloning, characterization, and expression analysis. PMID:27914524
Differential variation patterns between hubs and bottlenecks in human protein-protein interaction networks. PMID:27903259
A chitin deacetylase from the endophytic fungus Pestalotiopsis sp. efficiently inactivates the elicitor activity of chitin oligomers in rice cells. PMID:27901067
Mining the Cicer arietinum genome for the mildew locus O (Mlo) gene family and comparative evolutionary analysis of the Mlo genes from Medicago truncatula and some other plant species. PMID:27900493
Diversity and Evolutionary Analysis of Iron-Containing (Type-III) Alcohol Dehydrogenases in Eukaryotes. PMID:27893862
Single Amino Acid Repeats in the Proteome World: Structural, Functional, and Evolutionary Insights. PMID:27893794
Improving landscape inference by integrating heterogeneous data in the inverse Ising problem. PMID:27886273
Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi. PMID:27881071
Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses. PMID:27875982
Accelerating Information Retrieval from Profile Hidden Markov Model Databases. PMID:27875548
Whole-genome de novo sequencing, combined with RNA-Seq analysis, reveals unique genome and physiological features of the amylolytic yeast Saccharomycopsis fibuligera and its interspecies hybrid. PMID:27872659
The ERF transcription factor family in cassava: genome-wide characterization and expression analyses against drought stress. PMID:27869212
On the importance of composite protein multiple ligand interactions in protein pockets. PMID:27864975
Numerous small hammerhead ribozyme variants associated with Penelope-like retrotransposons cleave RNA as dimers. PMID:27858507
Characterization of the Sucrose Phosphate Phosphatase (SPP) Isoforms from Arabidopsis thaliana and Role of the S6PPc Domain in Dimerization. PMID:27855180
Adaptive phenotypic response to climate enabled by epigenetics in a K-strategy species, the fish Leucoraja ocellata (Rajidae). PMID:27853546
Diversity, evolution and expression profiles of histone acetyltransferases and deacetylases in oomycetes. PMID:27852223
Feature-based classification of human transcription factors into hypothetical sub-classes related to regulatory function. PMID:27842491
Intrinsic disorder in proteins involved in amyotrophic lateral sclerosis. PMID:27838743
Tailor-made transcriptional biosensors for optimizing microbial cell factories. PMID:27837353
DASP3: identification of protein sequences belonging to functionally relevant groups. PMID:27835946
Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma. PMID:27829365
Genome-Wide Identification, Characterization, and Stress-Responsive Expression Profiling of Genes Encoding LEA (Late Embryogenesis Abundant) Proteins in Moso Bamboo (Phyllostachys edulis). PMID:27829056
The Transcriptome of Exophiala dermatitidis during Ex-vivo Skin Model Infection. PMID:27822460
Novel RpoS-Dependent Mechanisms Strengthen the Envelope Permeability Barrier during Stationary Phase. PMID:27821607
Comparative Analysis of DNA Methyltransferase Gene Family in Fungi: A Focus on Basidiomycota. PMID:27818666
Evaluating Functional Annotations of Enzymes Using the Gene Ontology. PMID:27812939
Genome Sequence of Pandoraea sp. ISTKB, a Lignin-Degrading Betaproteobacterium, Isolated from Rhizospheric Soil. PMID:27811115
Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects : Insect insulator proteins. PMID:27809783
Characterization of the starch-acting MaAmyB enzyme from Microbacterium aurum B8.A representing the novel subfamily GH13_42 with an unusual, multi-domain organization. PMID:27808246
Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants. PMID:27806710
Insights into the innate immunome of actiniarians using a comparative genomic approach. PMID:27806695
Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. PMID:27803309
Aquerium: A web application for comparative exploration of domain-based protein occurrences on the taxonomically clustered genome tree. PMID:27802571
A computationally simplistic poly-phasic approach to explore microbial communities from the Yucatan aquifer as a potential sources of novel natural products. PMID:27796931
Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling. PMID:27796326
Genome Sequence of Carbon Dioxide-Sequestering Serratia sp. Strain ISTD04 Isolated from Marble Mining Rocks. PMID:27795274
In-silico prediction and deep-DNA sequencing validation indicate phase variation in 115 Neisseria meningitidis genes. PMID:27793092
Transcriptome Analysis and Ultrastructure Observation Reveal that Hawthorn Fruit Softening Is due to Cellulose/Hemicellulose Degradation. PMID:27790234
Genome-Wide Investigation of Hsf Genes in Sesame Reveals Their Segmental Duplication Expansion and Their Active Role in Drought Stress Response. PMID:27790233
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. PMID:27789697
The C-terminal domain of TPX2 is made of alpha-helical tandem repeats. PMID:27782824
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. PMID:27774985
A Novel Astrovirus-Like RNA Virus Detected in Human Stool. PMID:27774298
De Novo Transcriptomes of Forsythia koreana Using a Novel Assembly Method: Insight into Tissue- and Species-Specific Expression of Lignan Biosynthesis-Related Gene. PMID:27768772
Screening for clusters of charge in human virus proteomes. PMID:27766959
Identification of internalin-A-like virulent proteins in Leishmania donovani. PMID:27765050
RAP2.4a Is Transported through the Phloem to Regulate Cold and Heat Tolerance in Papaya Tree (Carica papaya cv. Maradol): Implications for Protection Against Abiotic Stress. PMID:27764197
Gold Nanoparticle Reprograms Pancreatic Tumor Microenvironment and Inhibits Tumor Growth. PMID:27758098
The mechanism of force transmission at bacterial focal adhesion complexes. PMID:27749817
Sex Change in Clownfish: Molecular Insights from Transcriptome Analysis. PMID:27748421
Phylotype Dynamics of Bacterial P Utilization Genes in Microbialites and Bacterioplankton of a Monomictic Endorheic Lake. PMID:27726035
RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information. PMID:27717309
Genomic Dissection and Expression Profiling Revealed Functional Divergence in Triticum aestivum Leucine Rich Repeat Receptor Like Kinases (TaLRRKs). PMID:27713749
Classification and substrate head-group specificity of membrane fatty acid desaturases. PMID:27708750
Transcriptome and Metabolite analysis reveal candidate genes of the cardiac glycoside biosynthetic pathway from Calotropis procera. PMID:27703261
Genomic Survey of a Hyperparasitic Microsporidian Amphiamblys sp. (Metchnikovellidae). PMID:27694476
ASAP: a machine learning framework for local protein properties. PMID:27694209
Adhesion of the genome-sequenced Lactococcus lactis subsp. cremoris IBB477 strain is mediated by specific molecular determinants. PMID:27687992
SPATA5 mutations cause a distinct autosomal recessive phenotype of intellectual disability, hypotonia and hearing loss. PMID:27683084
A Bat-Derived Putative Cross-Family Recombinant Coronavirus with a Reovirus Gene. PMID:27676249
Data set for phylogenetic tree and RAMPAGE Ramachandran plot analysis of SODs in Gossypium raimondii and G. arboreum. PMID:27672674
Draft genome sequence of the extremely halophilic Halorubrum sp. SAH-A6 isolated from rock salts of the Danakil depression, Ethiopia. PMID:27668183
In silico structural characterization of protein targets for drug development against Trypanosoma cruzi. PMID:27665464
Phosphate uptake kinetics and tissue-specific transporter expression profiles in poplar (Populus × canescens) at different phosphorus availabilities. PMID:27663513
Genomewide analysis of the lateral organ boundaries domain gene family in Vitis vinifera. PMID:27659322
Crystal Structure of the Escherichia coli Fic Toxin-Like Protein in Complex with Its Cognate Antitoxin. PMID:27657533
Characterization of CIPK Family in Asian Pear (Pyrus bretschneideri Rehd) and Co-expression Analysis Related to Salt and Osmotic Stress Responses. PMID:27656193
The tubulin repertoire of C. elegans sensory neurons and its context-dependent role in process outgrowth. PMID:27654945
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. PMID:27654921
Head regeneration in hemichordates is not a strict recapitulation of development. PMID:27649280
Genetic Characterization of Plasmodium Putative Pantothenate Kinase Genes Reveals Their Essential Role in Malaria Parasite Transmission to the Mosquito. PMID:27644319
Selection of Amine-Oxidizing Dairy Lactic Acid Bacteria and Identification of the Enzyme and Gene Involved in the Decrease of Biogenic Amines. PMID:27637883
Genome-wide identification and characterization of GRAS transcription factors in sacred lotus (Nelumbo nucifera). PMID:27635351
Novel Methyltransferase Recognition Motif Identified in Chania multitudinisentens RB-25(T) gen. nov., sp. nov. PMID:27630623
Genome-wide analysis of long intergenic non-coding RNAs in chickpea and their potential role in flower development. PMID:27628568
BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori. PMID:27623959
Origin of a folded repeat protein from an intrinsically disordered ancestor. PMID:27623012
First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Née (Fagaceae). PMID:27621377
Xanthomonas campestris attenuates virulence by sensing light through a bacteriophytochrome photoreceptor. PMID:27621284
The long noncoding RNA Chaer defines an epigenetic checkpoint in cardiac hypertrophy. PMID:27618650
The small unicellular diazotrophic symbiont, UCYN-A, is a key player in the marine nitrogen cycle. PMID:27617976
Nitrogen Fixation and Molecular Oxygen: Comparative Genomic Reconstruction of Transcription Regulation in Alphaproteobacteria. PMID:27617010
Molecular evolutionary dynamics of cytochrome P450 monooxygenases across kingdoms: Special focus on mycobacterial P450s. PMID:27616185
Mutation screening of GRIN2B in schizophrenia and autism spectrum disorder in a Japanese population. PMID:27616045
Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae). PMID:27614235
Substitutions in the Glycogenin-1 Gene Are Associated with the Evolution of Endothermy in Sharks and Tunas. PMID:27614233
COME: a robust coding potential calculation tool for lncRNA identification and characterization based on multiple features. PMID:27608726
Genome-wide Identification of TCP Family Transcription Factors from Populus euphratica and Their Involvement in Leaf Shape Regulation. PMID:27605130
De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia galeata. PMID:27604882
Comparative Genomics of Campylobacter iguaniorum to Unravel Genetic Regions Associated with Reptilian Hosts. PMID:27604878
Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes. PMID:27604223
Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57. PMID:27602182
Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum. PMID:27601008
Global Profiling of the Cellular Alternative RNA Splicing Landscape during Virus-Host Interactions. PMID:27598998
Revisiting Myosin Families Through Large-scale Sequence Searches Leads to the Discovery of New Myosins. PMID:27597808
Genome-based insights into the resistome and mobilome of multidrug-resistant Aeromonas sp. ARM81 isolated from wastewater. PMID:27590015
Complete Genome Sequence of Cryobacterium arcticum Strain PAMC 27867, Isolated from a Sedimentary Rock Sample in Northern Victoria Land, Antarctica. PMID:27587812
Substrate prediction of Ixodes ricinus salivary lipocalins differentially expressed during Borrelia afzelii infection. PMID:27584086
A biologically informed method for detecting rare variant associations. PMID:27582876
Genomic and transcriptomic analyses of the tangerine pathotype of Alternaria alternata in response to oxidative stress. PMID:27582273
Fine mapping of the stem rust resistance gene SrTA10187. PMID:27581540
Genome-wide analysis of lectin receptor-like kinases in Populus. PMID:27580945
Tma108, a putative M1 aminopeptidase, is a specific nascent chain-associated protein in Saccharomyces cerevisiae. PMID:27580715
De novo Sequencing and Transcriptome Analysis of Pinellia ternata Identify the Candidate Genes Involved in the Biosynthesis of Benzoic Acid and Ephedrine. PMID:27579029
Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi. PMID:27572831
Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea. PMID:27572167
Origination, Expansion, Evolutionary Trajectory, and Expression Bias of AP2/ERF Superfamily in Brassica napus. PMID:27570529
Biosynthesis of Salmonella enterica [NiFe]-hydrogenase-5: probing the roles of system-specific accessory proteins. PMID:27566174
Global profiling of alternative RNA splicing events provides insights into molecular differences between various types of hepatocellular carcinoma. PMID:27565572
Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex. PMID:27565344
Classification of the treble clef zinc finger: noteworthy lessons for structure and function evolution. PMID:27562564
A genome-wide loss-of-function screening method for minimizing false-negatives caused by functional redundancy. PMID:27561817
A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome. PMID:27558918
Genomic data mining reveals a rich repertoire of transport proteins in Streptomyces. PMID:27557108
Virome characterisation from Guthrie cards in children who later developed acute lymphoblastic leukaemia. PMID:27552439
Genome-Wide Identification, Expression Diversication of Dehydrin Gene Family and Characterization of CaDHN3 in Pepper (Capsicum annuum L.). PMID:27551973
Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding. PMID:27549116
Genomes of Candidatus Wolbachia bourtzisii wDacA and Candidatus Wolbachia pipientis wDacB from the Cochineal Insect Dactylopius coccus (Hemiptera: Dactylopiidae). PMID:27543297
UAP56 is a conserved crucial component of a divergent mRNA export pathway in Toxoplasma gondii. PMID:27542978
Identification of Complete Repertoire of Apis florea Odorant Receptors Reveals Complex Orthologous Relationships with Apis mellifera. PMID:27540087
A calcium sensor - protein kinase signaling module diversified in plants and is retained in all lineages of Bikonta species. PMID:27538881
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
SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity. PMID:27525735
Exome sequencing in a consanguineous family clinically diagnosed with early-onset Alzheimer's disease identifies a homozygous CTSF mutation. PMID:27524508
Paralog-Specific Patterns of Structural Disorder and Phosphorylation in the Vertebrate SH3-SH2-Tyrosine Kinase Protein Family. PMID:27519537
FliW antagonizes CsrA RNA binding by a noncompetitive allosteric mechanism. PMID:27516547
Comparative Genomics of the Sigatoka Disease Complex on Banana Suggests a Link between Parallel Evolutionary Changes in Pseudocercospora fijiensis and Pseudocercospora eumusae and Increased Virulence on the Banana Host. PMID:27513322
Molecular Characterization of the 14-3-3 Gene Family in Brachypodium distachyon L. Reveals High Evolutionary Conservation and Diverse Responses to Abiotic Stresses. PMID:27507982
Flavoprotein-Mediated Tellurite Reduction: Structural Basis and Applications to the Synthesis of Tellurium-Containing Nanostructures. PMID:27507969
Characterization of Outer Membrane Proteome of Akkermansia muciniphila Reveals Sets of Novel Proteins Exposed to the Human Intestine. PMID:27507967
Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians. PMID:27502555
Draft genomic sequence of a chromate- and sulfate-reducing Alishewanella strain with the ability to bioremediate Cr and Cd contamination. PMID:27499827
N-Terminal Peptide Detection with Optimized Peptide-Spectrum Matching and Streamlined Sequence Libraries. PMID:27498768
Draft Genome Sequence of Planomonospora sphaerica JCM9374, a Rare Actinomycete. PMID:27492001
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
Structural Basis of the Disorder in the Tandem Zinc Finger Domain of the RNA-Binding Protein Tristetraprolin. PMID:27487322
SAR11 bacteria linked to ocean anoxia and nitrogen loss. PMID:27487207
Microbial Community Responses to Increased Water and Organic Matter in the Arid Soils of the McMurdo Dry Valleys, Antarctica. PMID:27486436
On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1. PMID:27480115
Putative extremely high rate of proteome innovation in lancelets might be explained by high rate of gene prediction errors. PMID:27476717
Insight into the AP2/ERF transcription factor superfamily in sesame and expression profiling of DREB subfamily under drought stress. PMID:27475988
FocalScan: Scanning for altered genes in cancer based on coordinated DNA and RNA change. PMID:27474725
Genome-wide identification and expression analysis of sulfate transporter (SULTR) genes in potato (Solanum tuberosum L.). PMID:27473680
CicerTransDB 1.0: a resource for expression and functional study of chickpea transcription factors. PMID:27472917
Rapid construction of metabolite biosensors using domain-insertion profiling. PMID:27470466
Validation of a multi-omics strategy for prioritizing personalized candidate driver genes. PMID:27469031
The Ditylenchus destructor genome provides new insights into the evolution of plant parasitic nematodes. PMID:27466450
Discovery of midgut genes for the RNA interference control of corn rootworm. PMID:27464714
Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem. PMID:27458440
Computational studies of human class V alcohol dehydrogenase - the odd sibling. PMID:27455956
Type II Toxin-Antitoxin Systems in the Unicellular Cyanobacterium Synechocystis sp. PCC 6803. PMID:27455323
Construction of Global Acyl Lipid Metabolic Map by Comparative Genomics and Subcellular Localization Analysis in the Red Alga Cyanidioschyzon merolae. PMID:27446184
MATH-Domain Family Shows Response toward Abiotic Stress in Arabidopsis and Rice. PMID:27446153
Development of a Phage Cocktail to Control Proteus mirabilis Catheter-associated Urinary Tract Infections. PMID:27446059
The Crystal Structure of the C-Terminal Domain of the Salmonella enterica PduO Protein: An Old Fold with a New Heme-Binding Mode. PMID:27446048
Complete Genome Sequence of Psychrobacter alimentarius PAMC 27889, a Psychrophile Isolated from an Antarctic Rock Sample. PMID:27445386
Novel mutation in the CHST6 gene causes macular corneal dystrophy in a black South African family. PMID:27439461
Origin and Functional Prediction of Pollen Allergens in Plants. PMID:27436829
Biophysical characterization of the honeybee DSC1 orthologue reveals a novel voltage-dependent Ca2+ channel subfamily: CaV4. PMID:27432995
Global Transcriptomic Analysis Reveals the Mechanism of Phelipanche aegyptiaca Seed Germination. PMID:27428962
Multiple Domain Associations within the Arabidopsis Immune Receptor RPP1 Regulate the Activation of Programmed Cell Death. PMID:27427964
Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination. PMID:27426948
Online interactive analysis of protein structure ensembles with Bio3D-web. PMID:27423893
AcmB Is an S-Layer-Associated β-N-Acetylglucosaminidase and Functional Autolysin in Lactobacillus acidophilus NCFM. PMID:27422832
A conserved OmpA-like protein in Legionella pneumophila required for efficient intracellular replication. PMID:27421957
The protein domains of the Dictyostelium microprocessor that are required for correct subcellular localization and for microRNA maturation. PMID:27416267
Permanent draft genome sequence of sulfoquinovose-degrading Pseudomonas putida strain SQ1. PMID:27408681
A systems-oriented analysis of the grapevine R2R3-MYB transcription factor family uncovers new insights into the regulation of stilbene accumulation. PMID:27407139
Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. PMID:27402745
Glycoside Hydrolase (GH) 45 and 5 Candidate Cellulases in Aphelenchoides besseyi Isolated from Bird's-Nest Fern. PMID:27391812
Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals. PMID:27388460
Superoxide dismutase 2 knockdown leads to defects in locomotor activity, sensitivity to paraquat, and increased cuticle pigmentation in Tribolium castaneum. PMID:27387523
Elucidating and mining the Tulipa and Lilium transcriptomes. PMID:27387304
Reannotation of Yersinia pestis Strain 91001 Based on Omics Data. PMID:27382076
Experimental Analysis of Functional Variation within Protein Families: Receiver Domain Autodephosphorylation Kinetics. PMID:27381915
The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum. PMID:27381095
Misannotation Awareness: A Tale of Two Gene-Groups. PMID:27379147
Natural diversity of cellulases, xylanases, and chitinases in bacteria. PMID:27366206
A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies. PMID:27363390
Discovery of a Natural Microsporidian Pathogen with a Broad Tissue Tropism in Caenorhabditis elegans. PMID:27362540
Phosphoryl Group Flow within the Pseudomonas aeruginosa Pil-Chp Chemosensory System: DIFFERENTIAL FUNCTION OF THE EIGHT PHOSPHOTRANSFERASE AND THREE RECEIVER DOMAINS. PMID:27354279
Discovery and identification of candidate genes from the chitinase gene family for Verticillium dahliae resistance in cotton. PMID:27354165
SorghumFDB: sorghum functional genomics database with multidimensional network analysis. PMID:27352859
Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering. PMID:27348631
Hypermethylation reduces the expression of PNPLA7 in hepatocellular carcinoma. PMID:27347198
Cyanobacterial ultrastructure in light of genomic sequence data. PMID:27344651
Uncovering Notch pathway in the parasitic flatworm Schistosoma mansoni. PMID:27344453
Complete Genome Sequence of Dyella thiooxydans ATSB10, a Thiosulfate-Oxidizing Bacterium Isolated from Sunflower Fields in South Korea. PMID:27340060
AraPPISite: a database of fine-grained protein-protein interaction site annotations for Arabidopsis thaliana. PMID:27338257
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
Molecular Evolution of the Oxygen-Binding Hemerythrin Domain. PMID:27336621
Crystal Structure of Human Leukocyte Cell-derived Chemotaxin 2 (LECT2) Reveals a Mechanistic Basis of Functional Evolution in a Mammalian Protein with an M23 Metalloendopeptidase Fold. PMID:27334921
Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci. PMID:27325438
Isolation and Characterization of NDM-Positive Escherichia coli from Municipal Wastewater in Jeddah, Saudi Arabia. PMID:27324770
Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families. PMID:27322404
Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors under Multiple Stresses in Brassica napus. PMID:27322342
Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways. PMID:27321668
A Numbering System for MFS Transporter Proteins. PMID:27314000
High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM 17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T). PMID:27313837
Whole-Genome Sequencing of a Haarlem Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate from Medellín, Colombia. PMID:27313305
Evolution of an intron-poor cluster of the CIPK gene family and expression in response to drought stress in soybean. PMID:27311690
Whole Genome Re-Sequencing and Characterization of Powdery Mildew Disease-Associated Allelic Variation in Melon. PMID:27311063
Defining the consequences of genetic variation on a proteome-wide scale. PMID:27309819
DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequences. PMID:27307636
Dbl2 Regulates Rad51 and DNA Joint Molecule Metabolism to Ensure Proper Meiotic Chromosome Segregation. PMID:27304859
Plant-specific DUF1110 protein from Oryza sativa: expression, purification and crystallization. PMID:27303902
Identification of Plasmodium falciparum Translation Initiation eIF2β Subunit: Direct Interaction with Protein Phosphatase Type 1. PMID:27303372
Gene Family Evolution Reflects Adaptation to Soil Environmental Stressors in the Genome of the Collembolan Orchesella cincta. PMID:27289101
OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes. PMID:27289099
Regulation of Pyrroloquinoline Quinone-Dependent Glucose Dehydrogenase Activity in the Model Rhizosphere-Dwelling Bacterium Pseudomonas putida KT2440. PMID:27287323
Multiple-Localization and Hub Proteins. PMID:27285823
The complete genome of a baculovirus isolated from an insect of medical interest: Lonomia obliqua (Lepidoptera: Saturniidae). PMID:27282807
The ESX-5 System of Pathogenic Mycobacteria Is Involved In Capsule Integrity and Virulence through Its Substrate PPE10. PMID:27280885
Integrated Analysis of the Roles of Long Noncoding RNA and Coding RNA Expression in Sheep (Ovis aries) Skin during Initiation of Secondary Hair Follicle. PMID:27276011
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
Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during human erythroid differentiation. PMID:27272188
GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm. PMID:27260514
Transcriptome sequences spanning key developmental states as a resource for the study of the cestode Schistocephalus solidus, a threespine stickleback parasite. PMID:27259971
Benchmarking the next generation of homology inference tools. PMID:27256311
A GCN2-Like eIF2α Kinase (LdeK1) of Leishmania donovani and Its Possible Role in Stress Response. PMID:27248816
Computational recognition and analysis of hitherto uncharacterized nucleotide cyclase-like proteins in bacteria. PMID:27246835
Candidate Genes Involved in the Biosynthesis of Triterpenoid Saponins in Platycodon grandiflorum Identified by Transcriptome Analysis. PMID:27242873
gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes. PMID:27242033
Comprehensive analyses of the annexin gene family in wheat. PMID:27236332
Coronary artery disease susceptibility gene ADTRP regulates cell cycle progression, proliferation, and apoptosis by global gene expression regulation. PMID:27235449
Structural, Functional, and Immunological Characterization of Profilin Panallergens Amb a 8, Art v 4, and Bet v 2. PMID:27231348
Expanding the spectrum of PEX10-related peroxisomal biogenesis disorders: slowly progressive recessive ataxia. PMID:27230853
Stage-specific Proteomes from Onchocerca ochengi, Sister Species of the Human River Blindness Parasite, Uncover Adaptations to a Nodular Lifestyle. PMID:27226403
Deciphering the Molecular Variations of Pine Wood Nematode Bursaphelenchus xylophilus with Different Virulence. PMID:27224277
Prediction and Quantification of Splice Events from RNA-Seq Data. PMID:27218464
Cobalamin's (Vitamin B12) Surprising Function as a Photoreceptor. PMID:27217104
Defining the SUMO System in Maize: SUMOylation Is Up-Regulated during Endosperm Development and Rapidly Induced by Stress. PMID:27208252
Genome Structure of the Symbiont Bifidobacterium pseudocatenulatum CECT 7765 and Gene Expression Profiling in Response to Lactulose-Derived Oligosaccharides. PMID:27199952
A High-resolution Typing Assay for Uropathogenic Escherichia coli Based on Fimbrial Diversity. PMID:27199951
Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity. PMID:27199933
BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins. PMID:27198220
The genome and transcriptome of Phalaenopsis yield insights into floral organ development and flowering regulation. PMID:27190718
"Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis. PMID:27190206
Conserved Features in the Structure, Mechanism, and Biogenesis of the Inverse Autotransporter Protein Family. PMID:27190006
Searching the Evolutionary Origin of Epithelial Mucus Protein Components-Mucins and FCGBP. PMID:27189557
Systems-level analysis of human aging genes shed new light on mechanisms of aging. PMID:27179790
An RNA-dependent RNA polymerase gene in bat genomes derived from an ancient negative-strand RNA virus. PMID:27174689
Patterns of Genome-Wide Variation in Glossina fuscipes fuscipes Tsetse Flies from Uganda. PMID:27172181
Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean? PMID:27171220
The repetitive DNA element BncDNA, enriched in the B chromosome of the cichlid fish Astatotilapia latifasciata, transcribes a potentially noncoding RNA. PMID:27169573
De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease. PMID:27168971
Diversity and Evolution of Disease Resistance Genes in Barley (Hordeum vulgare L.). PMID:27168720
Structural and biochemical characterisation of Archaeoglobus fulgidus esterase reveals a bound CoA molecule in the vicinity of the active site. PMID:27160974
Transcriptomic profile of tobacco in response to Alternaria longipes and Alternaria alternata infections. PMID:27157477
UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB. PMID:27153729
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
MOCAT2: a metagenomic assembly, annotation and profiling framework. PMID:27153620
Genome-scale prediction of moonlighting proteins using diverse protein association information. PMID:27153604
Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks. PMID:27153592
Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics. PMID:27153067
Systematic analysis of somatic mutations driving cancer: uncovering functional protein regions in disease development. PMID:27150584
SpinachDB: A Well-Characterized Genomic Database for Gene Family Classification and SNP Information of Spinach. PMID:27148975
K-shell Analysis Reveals Distinct Functional Parts in an Electron Transfer Network and Its Implications for Extracellular Electron Transfer. PMID:27148219
Characterization of DNA Binding Sites of RokB, a ROK-Family Regulator from Streptomyces coelicolor Reveals the RokB Regulon. PMID:27145180
Characterization of novel Bovine Leukemia Virus (BLV) antisense transcripts by deep sequencing reveals constitutive expression in tumors and transcriptional interaction with viral microRNAs. PMID:27141823
The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. PMID:27138043
ATXN7L3 and ENY2 Coordinate Activity of Multiple H2B Deubiquitinases Important for Cellular Proliferation and Tumor Growth. PMID:27132940
Comparative genomics reveals Cyclospora cayetanensis possesses coccidia-like metabolism and invasion components but unique surface antigens. PMID:27129308
Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics. PMID:27128991
KvLEA, a New Isolated Late Embryogenesis Abundant Protein Gene from Kosteletzkya virginica Responding to Multiabiotic Stresses. PMID:27123459
The AS-RBM15 lncRNA enhances RBM15 protein translation during megakaryocyte differentiation. PMID:27118388
Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system. PMID:27118214
Independent Regulation of Type VI Secretion in Vibrio cholerae by TfoX and TfoY. PMID:27117415
Endogenous growth factor stimulation of hemocyte proliferation induces resistance to Schistosoma mansoni challenge in the snail host. PMID:27114544
Tick receptor for outer surface protein A from Ixodes ricinus - the first intrinsically disordered protein involved in vector-microbe recognition. PMID:27112540
Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture. PMID:27111722
Molecular Characterization and Global Expression Analysis of Lectin Receptor Kinases in Bread Wheat (Triticum aestivum). PMID:27111449
Companion: a web server for annotation and analysis of parasite genomes. PMID:27105845
Evidence of a Mild Mutator Phenotype in Cambodian Plasmodium falciparum Malaria Parasites. PMID:27100094
iGEMS: an integrated model for identification of alternative exon usage events. PMID:27095197
A putative nitroreductase from the DosR regulon of Mycobacterium tuberculosis induces pro-inflammatory cytokine expression via TLR2 signaling pathway. PMID:27094446
Two Groups of Thellungiella salsuginea RAVs Exhibit Distinct Responses and Sensitivity to Salt and ABA in Transgenic Arabidopsis. PMID:27093611
Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources. PMID:27092246
Draft genome sequencing and secretome analysis of fungal phytopathogen Ascochyta rabiei provides insight into the necrotrophic effector repertoire. PMID:27091329
Evolutionary relationships between heme-binding ferredoxin α + β barrels. PMID:27089923
ProViz-a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. PMID:27085803
Ribosome reinitiation at leader peptides increases translation of bacterial proteins. PMID:27084079
Single-cell analysis of long non-coding RNAs in the developing human neocortex. PMID:27081004
Overcoming Enterotoxigenic Escherichia coli Pathogen Diversity: Translational Molecular Approaches to Inform Vaccine Design. PMID:27076141
Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity. PMID:27074145
Transcriptomic analysis of the stationary phase response regulator SpdR in Caulobacter crescentus. PMID:27072651
Identification of Targets and Interaction Partners of Arginyl-tRNA Protein Transferase in the Moss Physcomitrella patens. PMID:27067052
Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus. PMID:27065959
Chimeric Sex-Determining Chromosomal Regions and Dysregulation of Cell-Type Identity in a Sterile Zygosaccharomyces Allodiploid Yeast. PMID:27065237
Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore-Forming Proteins. PMID:27064789
A Novel Typing Method for Streptococcus pneumoniae Using Selected Surface Proteins. PMID:27064593
ATtRACT-a database of RNA-binding proteins and associated motifs. PMID:27055826
Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms. PMID:27054497
Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes. PMID:27049771
Campylobacter fetus Subspecies Contain Conserved Type IV Secretion Systems on Multiple Genomic Islands and Plasmids. PMID:27049518
The Genome and Methylome of a Subsocial Small Carpenter Bee, Ceratina calcarata. PMID:27048475
Conservation and divergence of the histone code in nucleomorphs. PMID:27048461
Identification and Partial Characterization of a Novel UDP-N-Acetylenolpyruvoylglucosamine Reductase/UDP-N-Acetylmuramate:l-Alanine Ligase Fusion Enzyme from Verrucomicrobium spinosum DSM 4136(T). PMID:27047475
Phylogenetic analysis of β-xylanase SRXL1 of Sporisorium reilianum and its relationship with families (GH10 and GH11) of Ascomycetes and Basidiomycetes. PMID:27040368
Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism. PMID:27032335
Topology based identification and comprehensive classification of four-transmembrane helix containing proteins (4TMs) in the human genome. PMID:27030248
The tangled bank of amino acids. PMID:27028523
Utilizing yeast chemogenomic profiles for the prediction of pharmacogenomic associations in humans. PMID:27025271
Molecular Characterization of MaCCS, a Novel Copper Chaperone Gene Involved in Abiotic and Hormonal Stress Responses in Musa acuminata cv. Tianbaojiao. PMID:27023517
Anaplasma phagocytophilum increases the levels of histone modifying enzymes to inhibit cell apoptosis and facilitate pathogen infection in the tick vector Ixodes scapularis. PMID:27019326
Transcriptome analyses of insect cells to facilitate baculovirus-insect expression. PMID:27017378
Completion of the mitochondrial genome sequence of onion (Allium cepa L.) containing the CMS-S male-sterile cytoplasm and identification of an independent event of the ccmF N gene split. PMID:27016941
CCProf: exploring conformational change profile of proteins. PMID:27016699
tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs. PMID:27016142
The Pokeweed Leaf mRNA Transcriptome and Its Regulation by Jasmonic Acid. PMID:27014307
Genomic Insight into the Host-Endosymbiont Relationship of Endozoicomonas montiporae CL-33(T) with its Coral Host. PMID:27014194
Draft Genome Sequence of an Endophytic Actinoplanes Species, Encoding Uncommon trans-Acyltransferase Polyketide Synthases. PMID:27013046
UmuDAb: An Error-Prone Polymerase Accessory Homolog Whose N-Terminal Domain Is Required for Repression of DNA Damage Inducible Gene Expression in Acinetobacter baylyi. PMID:27010837
Finding Protein and Nucleotide Similarities with FASTA. PMID:27010337
Genome-Wide Identification of R2R3-MYB Genes and Expression Analyses During Abiotic Stress in Gossypium raimondii. PMID:27009386
Differences in environmental stress response among yeasts is consistent with species-specific lifestyles. PMID:27009200
Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins. PMID:27007663
Inside the Pan-genome - Methods and Software Overview. PMID:27006628
Functional Diversification after Gene Duplication: Paralog Specific Regions of Structural Disorder and Phosphorylation in p53, p63, and p73. PMID:27003913
GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations. PMID:26994912
A Chemotaxis Receptor Modulates Nodulation during the Azorhizobium caulinodans-Sesbania rostrata Symbiosis. PMID:26994081
Horizontal Gene Acquisitions, Mobile Element Proliferation, and Genome Decay in the Host-Restricted Plant Pathogen Erwinia Tracheiphila. PMID:26992913
KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins. PMID:26989151
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
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
PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins. PMID:26980520
PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya. PMID:26980519
Proteome distribution between nucleoplasm and nucleolus and its relation to ribosome biogenesis in Arabidopsis thaliana. PMID:26980300
Linalool isomerase, a membrane-anchored enzyme in the anaerobic monoterpene degradation in Thauera linaloolentis 47Lol. PMID:26979141
The Escherichia coli Cryptic Prophage Protein YfdR Binds to DnaA and Initiation of Chromosomal Replication Is Inhibited by Overexpression of the Gene Cluster yfdQ-yfdR-yfdS-yfdT. PMID:26973617
Systems biology of the structural proteome. PMID:26969117
The proteome and phosphoproteome of maize pollen uncovers fertility candidate proteins. PMID:26969016
Genome-wide analysis of MATE transporters and expression patterns of a subgroup of MATE genes in response to aluminum toxicity in soybean. PMID:26968518
Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the Southern bluefin tuna (Thunnus maccoyii). PMID:26965070
Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula. PMID:26964738
The Structural Basis of Coenzyme A Recycling in a Bacterial Organelle. PMID:26959993
Human symbionts inject and neutralize antibacterial toxins to persist in the gut. PMID:26957597
CoeViz: a web-based tool for coevolution analysis of protein residues. PMID:26956673
Transcriptome Profiling of Two Asparagus Bean (Vigna unguiculata subsp. sesquipedalis) Cultivars Differing in Chilling Tolerance under Cold Stress. PMID:26954786
In depth analysis of the mechanism of action of metal-dependent sigma factors: characterization of CorE2 from Myxococcus xanthus. PMID:26951374
Whole-Genome Sequence of Corynebacterium pseudotuberculosis Strain 226, Isolated from the Abscess of a Goat in California. PMID:26950327
In silico dissection of Type VII Secretion System components across bacteria: New directions towards functional characterization. PMID:26949095
Genome-wide characterization and analysis of bZIP transcription factor gene family related to abiotic stress in cassava. PMID:26947924
Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors. PMID:26945779
Three reasons protein disorder analysis makes more sense in the light of collagen. PMID:26941008
Genome-wide identification and evolutionary analysis of leucine-rich repeat receptor-like protein kinase genes in soybean. PMID:26935840
Structural model of FeoB, the iron transporter from Pseudomonas aeruginosa, predicts a cysteine lined, GTP-gated pore. PMID:26934982
Expression Atlas of the Deubiquitinating Enzymes in the Adult Mouse Retina, Their Evolutionary Diversification and Phenotypic Roles. PMID:26934049
Balance between Coiled-Coil Stability and Dynamics Regulates Activity of BvgS Sensor Kinase in Bordetella. PMID:26933056
Functional and topological diversity of LOV domain photoreceptors. PMID:26929367
Towards the bridging of molecular genetics data across Xenopus species. PMID:26925848
Structures of EccB1 and EccD1 from the core complex of the mycobacterial ESX-1 type VII secretion system. PMID:26922638
A LEA 4 protein up-regulated by ABA is involved in drought response in maize roots. PMID:26922182
Mutations in Novel Lipopolysaccharide Biogenesis Genes Confer Resistance to Amoebal Grazing in Synechococcus elongatus. PMID:26921432
Methuselah/Methuselah-like G protein-coupled receptors constitute an ancient metazoan gene family. PMID:26915348
Unique Loss of the PYHIN Gene Family in Bats Amongst Mammals: Implications for Inflammasome Sensing. PMID:26906452
Glutathione S-Transferase Gene Family in Gossypium raimondii and G. arboreum: Comparative Genomic Study and their Expression under Salt Stress. PMID:26904090
Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis. PMID:26904004
Transcriptional Regulation of Carbohydrate Utilization Pathways in the Bifidobacterium Genus. PMID:26903998
Pooled screening for antiproliferative inhibitors of protein-protein interactions. PMID:26900867
Complete Genome Sequence and Comparative Genomics of a Novel Myxobacterium Myxococcus hansupus. PMID:26900859
Transcriptional profiling of epigenetic regulators in somatic embryos during temperature induced formation of an epigenetic memory in Norway spruce. PMID:26895338
The Type III Secretion System-Related CPn0809 from Chlamydia pneumoniae. PMID:26895250
An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom. PMID:26892257
Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens. PMID:26891798
An Insight into the Triabin Protein Family of American Hematophagous Reduviids: Functional, Structural and Phylogenetic Analysis. PMID:26891325
Establishing the precise evolutionary history of a gene improves prediction of disease-causing missense mutations. PMID:26890452
Functional and Structural Analysis of a β-Glucosidase Involved in β-1,2-Glucan Metabolism in Listeria innocua. PMID:26886583
Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon. PMID:26882169
Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection. PMID:26879532
Evolutionary Changes on the Way to Clathrin-Mediated Endocytosis in Animals. PMID:26872775
A Comparative Analysis of Mitochondrial Genomes in Eustigmatophyte Algae. PMID:26872774
Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. PMID:26871637
Evolution and Functional Insights of Different Ancestral Orthologous Clades of Chitin Synthase Genes in the Fungal Tree of Life. PMID:26870058
Gene Expression Variation Resolves Species and Individual Strains among Coral-Associated Dinoflagellates within the Genus Symbiodinium. PMID:26868597
ApoCanD: Database of human apoptotic proteins in the context of cancer. PMID:26861916
Metagenomic Analysis Indicates Epsilonproteobacteria as a Potential Cause of Microbial Corrosion in Pipelines Injected with Bisulfite. PMID:26858705
Multi-tissue transcriptomics for construction of a comprehensive gene resource for the terrestrial snail Theba pisana. PMID:26852673
Design Principles Involving Protein Disorder Facilitate Specific Substrate Selection and Degradation by the Ubiquitin-Proteasome System. PMID:26851277
Proteomics reveals major components of oogenesis in the reproductive tract of sugar-fed Anopheles aquasalis. PMID:26850722
Missense Mutations Allow a Sequence-Blind Mutant of SpoIIIE to Successfully Translocate Chromosomes during Sporulation. PMID:26849443
Dramatic Number Variation of R Genes in Solanaceae Species Accounted for by a Few R Gene Subfamilies. PMID:26849045
A betabaculovirus encoding a gp64 homolog. PMID:26847652
A review of the new HGNC gene family resource. PMID:26842383
De Novo Assembled Wheat Transcriptomes Delineate Differentially Expressed Host Genes in Response to Leaf Rust Infection. PMID:26840746
Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic Branch. PMID:26840333
Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics. PMID:26840125
Novel origin of lamin-derived cytoplasmic intermediate filaments in tardigrades. PMID:26840051
Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy. PMID:26839589
Genome-Wide Analysis of the AP2/ERF Superfamily Genes and their Responses to Abiotic Stress in Medicago truncatula. PMID:26834762
Classification of proteins with shared motifs and internal repeats in the ECOD database. PMID:26833690
Streptomyces thermoautotrophicus does not fix nitrogen. PMID:26833023
The diversification of the basic leucine zipper family in eukaryotes correlates with the evolution of multicellularity. PMID:26831906
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
Draft genome sequence for virulent and avirulent strains of Xanthomonas arboricola isolated from Prunus spp. in Spain. PMID:26823958
Draft Genome Sequences of Five Pseudomonas aeruginosa Clinical Strains Isolated from Sputum Samples from Cystic Fibrosis Patients. PMID:26823574
ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments. PMID:26819408
Inference of domain-disease associations from domain-protein, protein-disease and disease-disease relationships. PMID:26818594
Identification of Genes Relevant to Pesticides and Biology from Global Transcriptome Data of Monochamus alternatus Hope (Coleoptera: Cerambycidae) Larvae. PMID:26815657
A survey of best practices for RNA-seq data analysis. PMID:26813401
A structured interdomain linker directs self-polymerization of human uromodulin. PMID:26811476
The Chemical Biology of Human Metallo-β-Lactamase Fold Proteins. PMID:26805042
Global analysis of human duplicated genes reveals the relative importance of whole-genome duplicates originated in the early vertebrate evolution. PMID:26801093
EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms. PMID:26800861
The Role of the Exo-Xis Region in Oxidative Stress-Mediated Induction of Shiga Toxin-Converting Prophages. PMID:26798427
The identification of immune genes in the milk transcriptome of the Tasmanian devil (Sarcophilus harrisii). PMID:26793426
Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes. PMID:26793234
Proteomics analysis of global regulatory cascades involved in clavulanic acid production and morphological development in Streptomyces clavuligerus. PMID:26790415
Insight into the Salivary Gland Transcriptome of Lygus lineolaris (Palisot de Beauvois). PMID:26789269
In silico Identification and Validation of a Linear and Naturally Immunogenic B-Cell Epitope of the Plasmodium vivax Malaria Vaccine Candidate Merozoite Surface Protein-9. PMID:26788998
The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny. PMID:26786968
Selective integrin endocytosis is driven by interactions between the integrin α-chain and AP2. PMID:26779610
dbEM: A database of epigenetic modifiers curated from cancerous and normal genomes. PMID:26777304
3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling. PMID:26772592
Systematic Identification and Characterization of Long Non-Coding RNAs in the Silkworm, Bombyx mori. PMID:26771876
A Factor Graph Approach to Automated GO Annotation. PMID:26771463
Divergence of the bZIP Gene Family in Strawberry, Peach, and Apple Suggests Multiple Modes of Gene Evolution after Duplication. PMID:26770968
Transcriptome profiling of Kentucky bluegrass (Poa pratensis L.) accessions in response to salt stress. PMID:26758626
CASP 11 target classification. PMID:26756794
Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species. PMID:26754847
Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases. PMID:26754199
Determination of specificity influencing residues for key transcription factor families. PMID:26753103
Use of a Probabilistic Motif Search to Identify Histidine Phosphotransfer Domain-Containing Proteins. PMID:26751210
Characterization of Rv0888, a Novel Extracellular Nuclease from Mycobacterium tuberculosis. PMID:26742696
Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms. PMID:26741367
Homology-Based Prediction of Potential Protein-Protein Interactions between Human Erythrocytes and Plasmodium falciparum. PMID:26740742
Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry. PMID:26740739
Comparative transcriptome analysis reveals insights into the streamlined genomes of haplosclerid demosponges. PMID:26738846
Identification and classification of small molecule kinases: insights into substrate recognition and specificity. PMID:26738562
A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases. PMID:26735851
Similar Microbial Communities Found on Two Distant Seafloor Basalts. PMID:26733957
A Porphyromonas gingivalis Periplasmic Novel Exopeptidase, Acylpeptidyl Oligopeptidase, Releases N-Acylated Di- and Tripeptides from Oligopeptides. PMID:26733202
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
Synthetic and natural consensus design for engineering charge within an affibody targeting epidermal growth factor receptor. PMID:26724421
Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq. PMID:26719891
Bioinformatic landscapes for plant transcription factor system research. PMID:26719053
KIAA0556 is a novel ciliary basal body component mutated in Joubert syndrome. PMID:26714646
Identification of Thyroid Hormones and Functional Characterization of Thyroid Hormone Receptor in the Pacific Oyster Crassostrea gigas Provide Insight into Evolution of the Thyroid Hormone System. PMID:26710071
Human Gut-Commensalic Lactobacillus ruminis ATCC 25644 Displays Sortase-Assembled Surface Piliation: Phenotypic Characterization of Its Fimbrial Operon through In Silico Predictive Analysis and Recombinant Expression in Lactococcus lactis. PMID:26709916
HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species. PMID:26708988
Diverse roles of the nucleic acid-binding protein KHSRP in cell differentiation and disease. PMID:26708421
Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium. PMID:26692227
Genome-wide transcriptomic analyses provide insights into the lifestyle transition and effector repertoire of Leptosphaeria maculans during the colonization of Brassica napus seedlings. PMID:26679637
Draft Genome of the Arthrobacter sp. Strain Edens01. PMID:26679586
The Pfam protein families database: towards a more sustainable future. PMID:26673716
The European Bioinformatics Institute in 2016: Data growth and integration. PMID:26673705
Metagenome-assembled genomes uncover a global brackish microbiome. PMID:26667648
Complete genome sequence of the molybdenum-resistant bacterium Bacillus subtilis strain LM 4-2. PMID:26664656
Genome sequences of two closely related strains of Escherichia coli K-12 GM4792. PMID:26664654
Functional prediction of hypothetical proteins in human adenoviruses. PMID:26664031
The Draft Genome Sequence of Xanthomonas sp. Strain Mitacek01 Expands the Pangenome of a Genus of Plant Pathogens. PMID:26659686
Toxoplasma gondii Chitinase Induces Macrophage Activation. PMID:26659253
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics. PMID:26656885
Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome. PMID:26652261
Genome sequence of the clover symbiont Rhizobium leguminosarum bv. trifolii strain CC275e. PMID:26649149
In planta Identification of Putative Pathogenicity Factors from the Chickpea Pathogen Ascochyta rabiei by De novo Transcriptome Sequencing Using RNA-Seq and Massive Analysis of cDNA Ends. PMID:26648917
A simple feature construction method for predicting upstream/downstream signal flow in human protein-protein interaction networks. PMID:26648121
Diversity and Divergence of Dinoflagellate Histone Proteins. PMID:26646152
The complete genome sequencing of Prevotella intermedia strain OMA14 and a subsequent fine-scale, intra-species genomic comparison reveal an unusual amplification of conjugative and mobile transposons and identify a novel Prevotella-lineage-specific repeat. PMID:26645327
ALCOdb: Gene Coexpression Database for Microalgae. PMID:26644461
'Deadman' and 'Passcode' microbial kill switches for bacterial containment. PMID:26641934
Repairing oxidized proteins in the bacterial envelope using respiratory chain electrons. PMID:26641313
Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics. PMID:26639611
AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast. PMID:26635866
The Structure of a Novel Thermophilic Esterase from the Planctomycetes Species, Thermogutta terrifontis Reveals an Open Active Site Due to a Minimal 'Cap' Domain. PMID:26635762
COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps. PMID:26635392
An extracellular biochemical screen reveals that FLRTs and Unc5s mediate neuronal subtype recognition in the retina. PMID:26633812
Genome-Wide Identification and Analysis of the VQ Motif-Containing Protein Family in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis). PMID:26633387
A network medicine approach to quantify distance between hereditary disease modules on the interactome. PMID:26631976
Designer and natural peptide toxin blockers of the KcsA potassium channel identified by phage display. PMID:26627718
orthoFind Facilitates the Discovery of Homologous and Orthologous Proteins. PMID:26624019
Metagenome and Metatranscriptome Revealed a Highly Active and Intensive Sulfur Cycle in an Oil-Immersed Hydrothermal Chimney in Guaymas Basin. PMID:26617579
Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires. PMID:26617277
Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage. PMID:26615204
Whole genome sequencing provides possible explanations for the difference in phage susceptibility among two Salmonella Typhimurium phage types (DT8 and DT30) associated with a single foodborne outbreak. PMID:26613761
Functional testing of a PF02458 homologue of putative rice arabinoxylan feruloyl transferase genes in Brachypodium distachyon. PMID:26612070
Complete nitrification by Nitrospira bacteria. PMID:26610024
Genome Analysis of Staphylococcus agnetis, an Agent of Lameness in Broiler Chickens. PMID:26606420
Complete genome sequence of bacteriophage P26218 infecting Rhodoferax sp. strain IMCC26218. PMID:26605005
Identification of Pathogenicity-Related Genes in Biofilm-Defective Acidovorax citrulli by Transposon Tn5 Mutagenesis. PMID:26602922
Regulation of a Protein Acetyltransferase in Myxococcus xanthus by the Coenzyme NADP. PMID:26598367
Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. PMID:26598135
Type II toxin: antitoxin systems. More than small selfish entities? PMID:26597447
Comparative genomics and metabolic profiling of the genus Lysobacter. PMID:26597042
Annotation inconsistencies beyond sequence similarity-based function prediction - phylogeny and genome structure. PMID:26594309
Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. PMID:26590262
The UCSC Genome Browser database: 2016 update. PMID:26590259
deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data. PMID:26590255
The Utility of Genome Skimming for Phylogenomic Analyses as Demonstrated for Glycerid Relationships (Annelida, Glyceridae). PMID:26590213
Arabidopsis Rab Geranylgeranyltransferases Demonstrate Redundancy and Broad Substrate Specificity in Vitro. PMID:26589801
Draft genome sequence of Cellulomonas carbonis T26(T) and comparative analysis of six Cellulomonas genomes. PMID:26587181
Discovery of Novel Plant Interaction Determinants from the Genomes of 163 Root Nodule Bacteria. PMID:26584898
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. PMID:26582926
Genome-wide identification and evolutionary analyses of bZIP transcription factors in wheat and its relatives and expression profiles of anther development related TabZIP genes. PMID:26581444
Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. PMID:26581338
Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA. PMID:26581084
High Innate Immune Specificity through Diversified C-Type Lectin-Like Domain Proteins in Invertebrates. PMID:26580547
BioGPS: building your own mash-up of gene annotations and expression profiles. PMID:26578587
PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with PolyCystic Ovary Syndrome. PMID:26578565
SugarBindDB, a resource of glycan-mediated host-pathogen interactions. PMID:26578555
DiffLogo: a comparative visualization of sequence motifs. PMID:26577052
Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential. PMID:26576951
Identification of the Elusive Pyruvate Reductase of Chlamydomonas reinhardtii Chloroplasts. PMID:26574578
Automated protein motif generation in the structure-based protein function prediction tool ProMOL. PMID:26573864
A new network representation of the metabolism to detect chemical transformation modules. PMID:26573681
Comparative Genomics of NAC Transcriptional Factors in Angiosperms: Implications for the Adaptation and Diversification of Flowering Plants. PMID:26569117
Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments. PMID:26568625
MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins. PMID:26568329
Investigating the Roles of the C-Terminal Domain of Plasmodium falciparum GyrA. PMID:26566222
High quality draft genomic sequence of Flavobacterium enshiense DK69(T) and comparison among Flavobacterium genomes. PMID:26561515
Getting ready for host invasion: elevated expression and action of xyloglucan endotransglucosylases/hydrolases in developing haustoria of the holoparasitic angiosperm Cuscuta. PMID:26561437
RNA Sequencing Revealed Numerous Polyketide Synthase Genes in the Harmful Dinoflagellate Karenia mikimotoi. PMID:26561394
Mitochondrial targeting sequence variants of the CHCHD2 gene are a risk for Lewy body disorders. PMID:26561290
Dead enzymes in the aldehyde dehydrogenase gene family: role in drug metabolism and toxicology. PMID:26558415
A phylogenetic approach to study the origin and evolution of the CRINKLY4 family. PMID:26557128
Evolutionary Rate Heterogeneity of Primary and Secondary Metabolic Pathway Genes in Arabidopsis thaliana. PMID:26556590
σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough. PMID:26555820
Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics. PMID:26555596
Distribution of Plasmids in Distinct Leptospira Pathogenic Species. PMID:26555137
The WRKY transcription factor family and senescence in switchgrass. PMID:26552372
Three Residues Make an Evolutionary Switch for Folding and RNA-Destabilizing Activity in the TTP Family of Proteins. PMID:26551835
Revisiting the reference genomes of human pathogenic Cryptosporidium species: reannotation of C. parvum Iowa and a new C. hominis reference. PMID:26549794
The Transporter Classification Database (TCDB): recent advances. PMID:26546518
Draft Genome Sequence of Caedibacter varicaedens, a Kappa Killer Endosymbiont Bacterium of the Ciliate Paramecium biaurelia. PMID:26543129
MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes. PMID:26541816
Systematic discovery of linear binding motifs targeting an ancient protein interaction surface on MAP kinases. PMID:26538579
AIP1 is a novel Agenet/Tudor domain protein from Arabidopsis that interacts with regulators of DNA replication, transcription and chromatin remodeling. PMID:26538092
The Distant Siblings-A Phylogenomic Roadmap Illuminates the Origins of Extant Diversity in Fungal Aromatic Polyketide Biosynthesis. PMID:26537223
The Skeleton Forming Proteome of an Early Branching Metazoan: A Molecular Survey of the Biomineralization Components Employed by the Coralline Sponge Vaceletia Sp. PMID:26536128
Genome-Wide Annotation and Comparative Analysis of Cytochrome P450 Monooxygenases in Basidiomycete Biotrophic Plant Pathogens. PMID:26536121
Computational analysis of candidate prion-like proteins in bacteria and their role. PMID:26528269
A combined bioinformatics and functional metagenomics approach to discovering lipolytic biocatalysts. PMID:26528261
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. PMID:26527724
Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors. PMID:26527717
Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors. PMID:26527297
Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus. PMID:26524597
Evidence for a Nonendosomal Function of the Saccharomyces cerevisiae ESCRT-III-Like Protein Chm7. PMID:26510789
Identification of MltG as a potential terminase for peptidoglycan polymerization in bacteria. PMID:26507882
Systematic Identification of Cyclic-di-GMP Binding Proteins in Vibrio cholerae Reveals a Novel Class of Cyclic-di-GMP-Binding ATPases Associated with Type II Secretion Systems. PMID:26506097
De Novo Assembly and Genome Analyses of the Marine-Derived Scopulariopsis brevicaulis Strain LF580 Unravels Life-Style Traits and Anticancerous Scopularide Biosynthetic Gene Cluster. PMID:26505484
Genomic variants of genes associated with three horticultural traits in apple revealed by genome re-sequencing. PMID:26504548
Dynamics of Wolbachia pipientis Gene Expression Across the Drosophila melanogaster Life Cycle. PMID:26497146
A catalogue of novel bovine long noncoding RNA across 18 tissues. PMID:26496443
Characterizing novel endogenous retroviruses from genetic variation inferred from short sequence reads. PMID:26493184
Modulation of Ambient Temperature-Dependent Flowering in Arabidopsis thaliana by Natural Variation of FLOWERING LOCUS M. PMID:26492483
Structural basis for suppression of hypernegative DNA supercoiling by E. coli topoisomerase I. PMID:26490962
From residue coevolution to protein conformational ensembles and functional dynamics. PMID:26487681
Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response. PMID:26485378
Recovering full-length viral genomes from metagenomes. PMID:26483782
Evolutionary history of phosphatidylinositol- 3-kinases: ancestral origin in eukaryotes and complex duplication patterns. PMID:26482564
Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development. PMID:26481460
DIDA: A curated and annotated digenic diseases database. PMID:26481352
A comprehensive mapping of the structure and gene organisation in the sheep MHC class I region. PMID:26480943
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. PMID:26476444
Conserved S-Layer-Associated Proteins Revealed by Exoproteomic Survey of S-Layer-Forming Lactobacilli. PMID:26475115
Characterization of Cercospora nicotianae Hypothetical Proteins in Cercosporin Resistance. PMID:26474162
Genome-wide analysis on Chlamydomonas reinhardtii reveals the impact of hydrogen peroxide on protein stress responses and overlap with other stress transcriptomes. PMID:26473430
Gene expression profiling during adventitious root formation in carnation stem cuttings. PMID:26467528
CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides. PMID:26467475
A JAZ Protein in Astragalus sinicus Interacts with a Leghemoglobin through the TIFY Domain and Is Involved in Nodule Development and Nitrogen Fixation. PMID:26460857
Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone. PMID:26459762
Discovering neutralizing antibodies targeting the stem epitope of H1N1 influenza hemagglutinin with synthetic phage-displayed antibody libraries. PMID:26456860
Crystal structure of a conserved domain in the intermembrane space region of the plastid division protein ARC6. PMID:26452626
WaspAtlas: a Nasonia vitripennis gene database and analysis platform. PMID:26452372
Diversity in protein domain superfamilies. PMID:26451979
Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality. PMID:26451775
De novo transcriptome profiling of highly purified human lymphocytes primary cells. PMID:26451251
MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins. PMID:26450961
Identification and characterization of a minisatellite contained within a novel miniature inverted-repeat transposable element (MITE) of Porphyromonas gingivalis. PMID:26448788
Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1. PMID:26446903
DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment. PMID:26445311
General Stress Signaling in the Alphaproteobacteria. PMID:26442844
Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM). PMID:26442528
Genome-wide analysis and expression profiling under heat and drought treatments of HSP70 gene family in soybean (Glycine max L.). PMID:26442082
A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones. PMID:26442032
Physiological and genomic characterization of Arcobacter anaerophilus IR-1 reveals new metabolic features in Epsilonproteobacteria. PMID:26441916
Diversity of laccase-coding genes in Fusarium oxysporum genomes. PMID:26441870
A Naturally Occurring Repeat Protein with High Internal Sequence Identity Defines a New Class of TPR-like Proteins. PMID:26439765
Clocks do not tick in unison: isolation of Clock and vrille shed new light on the clockwork model of the sand fly Lutzomyia longipalpis. PMID:26438221
Limb body wall complex, amniotic band sequence, or new syndrome caused by mutation in IQ Motif containing K (IQCK)? PMID:26436108
Cheminformatics Research at the Unilever Centre for Molecular Science Informatics Cambridge. PMID:26435758
An assessment of the amount of untapped fold level novelty in under-sampled areas of the tree of life. PMID:26434770
Following the Footsteps of Chlamydial Gene Regulation. PMID:26424812
The Recognition of Identical Ligands by Unrelated Proteins. PMID:26421501
Development of 23 novel polymorphic EST-SSR markers for the endangered relict conifer Metasequoia glyptostroboides. PMID:26421250
Genome sequence of a native-feather degrading extremely thermophilic Eubacterium, Fervidobacterium islandicum AW-1. PMID:26421103
Escherichia coli O157:H7 strains harbor at least three distinct sequence types of Shiga toxin 2a-converting phages. PMID:26416807
Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO-like genes in plant kingdom. PMID:26416765
Evidence-Based Structural Model of the Staphylococcal Repressor Protein: Separation of Functions into Different Domains. PMID:26414067
Genome sequence of Anoxybacillus ayderensis AB04(T) isolated from the Ayder hot spring in Turkey. PMID:26413199
An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products. PMID:26412281
The long noncoding RNA landscape in hypoxic and inflammatory renal epithelial injury. PMID:26400545
High-Throughput Identification of Cis-Regulatory Rewiring Events in Yeast. PMID:26399482
Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity. PMID:26397464
De novo sequencing and assembly analysis of transcriptome in the Sodom apple (Calotropis gigantea). PMID:26395839
Identification of 4CL Genes in Desert Poplars and Their Changes in Expression in Response to Salt Stress. PMID:26393655
Systematic Prediction of Scaffold Proteins Reveals New Design Principles in Scaffold-Mediated Signal Transduction. PMID:26393507
Simulating the function of sodium/proton antiporters. PMID:26392528
Detoxification of Indole by an Indole-Induced Flavoprotein Oxygenase from Acinetobacter baumannii. PMID:26390211
FARE-CAFE: a database of functional and regulatory elements of cancer-associated fusion events. PMID:26384373
Draft Genome Sequence of the Environmental Isolate Chryseobacterium sp. Hurlbut01. PMID:26383650
High-Throughput Ligand Discovery Reveals a Sitewise Gradient of Diversity in Broadly Evolved Hydrophilic Fibronectin Domains. PMID:26383268
Genome sequence of the haloarchaeon Haloterrigena jeotgali type strain A29(T) isolated from salt-fermented food. PMID:26380637
High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes. PMID:26380634
Draft-genome sequence of Shewanella algae strain C6G3. PMID:26380631
The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches. PMID:26380077
Draft genome sequence of the extremely halophilic archaeon Haladaptatus cibarius type strain D43(T) isolated from fermented seafood. PMID:26380039
Acinetobacter baumannii Virulence Is Mediated by the Concerted Action of Three Phospholipases D. PMID:26379240
Evolution of Chemical Diversity in a Group of Non-Reduced Polyketide Gene Clusters: Using Phylogenetics to Inform the Search for Novel Fungal Natural Products. PMID:26378577
Biochemical Characterization of Putative Adenylate Dimethylallyltransferase and Cytokinin Dehydrogenase from Nostoc sp. PCC 7120. PMID:26376297
Structural Bridges through Fold Space. PMID:26372166
Codon-level information improves predictions of inter-residue contacts in proteins by correlated mutation analysis. PMID:26371555
Dissecting Leishmania infantum Energy Metabolism - A Systems Perspective. PMID:26367006
Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View. PMID:26366735
Evolution of a Novel Antiviral Immune-Signaling Interaction by Partial-Gene Duplication. PMID:26356745
A Fluorescent, Reagentless Biosensor for ATP, Based on Malonyl-Coenzyme A Synthetase. PMID:26355992
Insights into the Evolutionary Relationships of LytA Autolysin and Ply Pneumolysin-Like Genes in Streptococcus pneumoniae and Related Streptococci. PMID:26349755
The identification of an integral membrane, cytochrome c urate oxidase completes the catalytic repertoire of a therapeutic enzyme. PMID:26349049
Molecular insights into cold active polygalacturonase enzyme for its potential application in food processing. PMID:26344963
Evolution of the Selenoproteome in Helicobacter pylori and Epsilonproteobacteria. PMID:26342139
Mercury Reduction and Methyl Mercury Degradation by the Soil Bacterium Xanthobacter autotrophicus Py2. PMID:26341208
Common Amino Acid Subsequences in a Universal Proteome--Relevance for Food Science. PMID:26340620
A survey of HK, HPt, and RR domains and their organization in two-component systems and phosphorelay proteins of organisms with fully sequenced genomes. PMID:26339559
Modeling and structural analysis of human Guanine nucleotide-binding protein-like 3,nucleostemin. PMID:26339152
Triterpenoid profiling and functional characterization of the initial genes involved in isoprenoid biosynthesis in neem (Azadirachta indica). PMID:26335498
A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design. PMID:26335248
Experimental Evidence for a Revision in the Annotation of Putative Pyridoxamine 5'-Phosphate Oxidases P(N/M)P from Fungi. PMID:26327315
Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage. PMID:26325358
Arabidopsis ALIX is required for the endosomal localization of the deubiquitinating enzyme AMSH3. PMID:26324913
The Fur homologue BosR requires Arg39 to activate rpoS transcription in Borrelia burgdorferi and thereby direct spirochaete infection in mice. PMID:26318670
Genomic detection and characterization of a Korean isolate of Little cherry virus 1 sampled from a peach tree. PMID:26315329
Comparative Analysis and Distribution of Omega-3 lcPUFA Biosynthesis Genes in Marine Molluscs. PMID:26308548
Genome-Wide Identification and Expression Analyses of Aquaporin Gene Family during Development and Abiotic Stress in Banana. PMID:26307965
Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira. PMID:26305944
DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool. PMID:26304539
Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses. PMID:26304538
OD-seq: outlier detection in multiple sequence alignments. PMID:26303676
Phylogenetic characterization and promoter expression analysis of a novel hybrid protein disulfide isomerase/cargo receptor subfamily unique to plants and chromalveolates. PMID:26300531
Complete Genome Sequence of the Type Strain Corynebacterium epidermidicanis DSM 45586, Isolated from the Skin of a Dog Suffering from Pruritus. PMID:26294641
Trypanosomes Modify the Behavior of Their Insect Hosts: Effects on Locomotion and on the Expression of a Related Gene. PMID:26291723
Cold shock induction of recombinant Arctic environmental genes. PMID:26286037
Gene expression during zombie ant biting behavior reflects the complexity underlying fungal parasitic behavioral manipulation. PMID:26285697
Identification and expression profiling analysis of calmodulin-binding transcription activator genes in maize (Zea mays L.) under abiotic and biotic stresses. PMID:26284092
A PAS domain-containing regulator controls flagella-flagella interactions in Campylobacter jejuni. PMID:26284050
Hypoxia-Inducible Factor α and Hif-prolyl Hydroxylase Characterization and Gene Expression in Short-Time Air-Exposed Mytilus galloprovincialis. PMID:26277612
Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning. PMID:26275894
Identifying and characterising key alternative splicing events in Drosophila development. PMID:26275604
Intraspecies Genomic Diversity and Long-Term Persistence of Bifidobacterium longum. PMID:26275230
Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends. PMID:26275154
Demonstration of the Coexistence of Duplicated LH Receptors in Teleosts, and Their Origin in Ancestral Actinopterygians. PMID:26271038
Comparison of predicted and actual consequences of missense mutations. PMID:26269570
Translational genomics for plant breeding with the genome sequence explosion. PMID:26269219
Deep sequencing of the Mexican avocado transcriptome, an ancient angiosperm with a high content of fatty acids. PMID:26268848
The octopus genome and the evolution of cephalopod neural and morphological novelties. PMID:26268193
Independent Co-Option of a Tailed Bacteriophage into a Killing Complex in Pseudomonas. PMID:26265717
The pre-vertebrate origins of neurogenic placodes. PMID:26258298
Remote homology and the functions of metagenomic dark matter. PMID:26257768
The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. PMID:26257709
The history of the CATH structural classification of protein domains. PMID:26253692
Prophage lysin Ply30 protects mice from Streptococcus suis and Streptococcus equi subsp. zooepidemicus infections. PMID:26253669
Draft De Novo Transcriptome of the Rat Kangaroo Potorous tridactylus as a Tool for Cell Biology. PMID:26252667
Identification of MicroRNAs in Meloidogyne incognita Using Deep Sequencing. PMID:26241472
The tuberculosis necrotizing toxin kills macrophages by hydrolyzing NAD. PMID:26237511
Commentary: The absence of protein Y4yS affects negatively the abundance of T3SS Mesorhizobium loti secretin, RhcC2, in bacterial membranes. PMID:26236295
Energy coupling mechanisms of MFS transporters. PMID:26234418
Genome wide comprehensive analysis and web resource development on cell wall degrading enzymes from phyto-parasitic nematodes. PMID:26232118
Exploring Vertical Transmission of Bifidobacteria from Mother to Child. PMID:26231653
Phylogeny of the Vitamin K 2,3-Epoxide Reductase (VKOR) Family and Evolutionary Relationship to the Disulfide Bond Formation Protein B (DsbB) Family. PMID:26230708
De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods. PMID:26228684
Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei. PMID:26228545
How Do Genomes Create Novel Phenotypes? Insights from the Loss of the Worker Caste in Ant Social Parasites. PMID:26226984
Transcription factors, chromatin proteins and the diversification of Hemiptera. PMID:26226651
Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models. PMID:26225866
Constructing sequence-dependent protein models using coevolutionary information. PMID:26223372
Draft genomic sequence of a selenite-reducing bacterium, Paenirhodobacter enshiensis DW2-9(T). PMID:26221419
Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project. PMID:26216192
Identification of candidate genes associated with fertility restoration of cytoplasmic male-sterility in onion (Allium cepa L.) using a combination of bulked segregant analysis and RNA-seq. PMID:26215184
Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks. PMID:26215102
Database of RNA binding protein expression and disease dynamics (READ DB). PMID:26210853
Roles of Thermophiles and Fungi in Bitumen Degradation in Mostly Cold Oil Sands Outcrops. PMID:26209669
Ubiquitous distribution of helmchrome in phototactic swarmers of the stramenopiles. PMID:26202473
Genome Wide Re-Annotation of Caldicellulosiruptor saccharolyticus with New Insights into Genes Involved in Biomass Degradation and Hydrogen Production. PMID:26196387
RNA helicase HEL-1 promotes longevity by specifically activating DAF-16/FOXO transcription factor signaling in Caenorhabditis elegans. PMID:26195740
Binding of Cyclic Di-AMP to the Staphylococcus aureus Sensor Kinase KdpD Occurs via the Universal Stress Protein Domain and Downregulates the Expression of the Kdp Potassium Transporter. PMID:26195599
The BioPlex Network: A Systematic Exploration of the Human Interactome. PMID:26186194
The Borrelia afzelii outer membrane protein BAPKO_0422 binds human factor-H and is predicted to form a membrane-spanning β-barrel. PMID:26181365
The SARP Family Regulator Txn9 and Two-Component Response Regulator Txn11 are Key Activators for Trioxacarcin Biosynthesis in Streptomyces bottropensis. PMID:26178900
Cofactor-induced reversible folding of Flavodoxin-4 from Lactobacillus acidophilus. PMID:26177955
Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma. PMID:26177267
A large-scale crop protection bioassay data set. PMID:26175909
Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. PMID:26175406
De novo assembly and characterization of central nervous system transcriptome reveals neurotransmitter signaling systems in the rice striped stem borer, Chilo suppressalis. PMID:26173787
IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites. PMID:26173699
Expression of pre-selected TMEMs with predicted ER localization as potential classifiers of ccRCC tumors. PMID:26169495
The First Paenibacillus larvae Bacteriophage Endolysin (PlyPl23) with High Potential to Control American Foulbrood. PMID:26167894
THOC2 Mutations Implicate mRNA-Export Pathway in X-Linked Intellectual Disability. PMID:26166480
The RAS-Binding Domain of Human BRAF Protein Serine/Threonine Kinase Exhibits Allosteric Conformational Changes upon Binding HRAS. PMID:26165597
Calcium-induced conformational changes in the regulatory domain of the human mitochondrial ATP-Mg/Pi carrier. PMID:26164100
Novel recA-Independent Horizontal Gene Transfer in Escherichia coli K-12. PMID:26162088
A widespread role of the motif environment in transcription factor binding across diverse protein families. PMID:26160164
Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes. PMID:26159227
Electron transport phosphorylation in rumen butyrivibrios: unprecedented ATP yield for glucose fermentation to butyrate. PMID:26157432
The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales. PMID:26156036
Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation. PMID:26154892
Identification of divergent type VI secretion effectors using a conserved chaperone domain. PMID:26150500
Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli. PMID:26148715
The Mitochondrial Genomes of a Myxozoan Genus Kudoa Are Extremely Divergent in Metazoa. PMID:26148004
100 Years later: Celebrating the contributions of x-ray crystallography to allergy and clinical immunology. PMID:26145985
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. PMID:26139634
SmedGD 2.0: The Schmidtea mediterranea genome database. PMID:26138588
Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome. PMID:26137199
Capturing coevolutionary signals inrepeat proteins. PMID:26134293
Visualization and dissemination of multidimensional proteomics data comparing protein abundance during Caenorhabditis elegans development. PMID:26133526
Diversity and evolution of cytochrome P450 monooxygenases in Oomycetes. PMID:26129850
Defining the RNA-binding glycine-rich (RBG) gene superfamily: new insights into nomenclature, phylogeny, and evolutionary trends obtained by genome-wide comparative analysis of Arabidopsis, Chinese cabbage, rice and maize genomes. PMID:26123085
The Streptomyces leeuwenhoekii genome: de novo sequencing and assembly in single contigs of the chromosome, circular plasmid pSLE1 and linear plasmid pSLE2. PMID:26122045
BEAN 2.0: an integrated web resource for the identification and functional analysis of type III secreted effectors. PMID:26120140
Comparative Transcriptome Analysis of the Cosmopolitan Marine Fungus Corollospora maritima Under Two Physiological Conditions. PMID:26116293
Degradation of Bunker C Fuel Oil by White-Rot Fungi in Sawdust Cultures Suggests Potential Applications in Bioremediation. PMID:26111162
Computational methods and resources for the interpretation of genomic variants in cancer. PMID:26111056
NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases. PMID:26110971
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
Dividing and Conquering the Family of RNA Recognition Motifs: A Representative Case Based on hnRNP L. PMID:26101840
Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology. PMID:26097471
Expression study of the hunchback ortholog in embryos of the onychophoran Euperipatoides rowelli. PMID:26093940
Identification and Heterologous Expression of the Chaxamycin Biosynthesis Gene Cluster from Streptomyces leeuwenhoekii. PMID:26092459
Uncovering major genomic features of essential genes in Bacteria and a methanogenic Archaea. PMID:26084810
Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens. PMID:26084502
Unusual biology across a group comprising more than 15% of domain Bacteria. PMID:26083755
Bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions. PMID:26077867
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
Structural Organization of Enzymes of the Phenylacetate Catabolic Hybrid Pathway. PMID:26075354
Analysis of cytochrome b(5) reductase-mediated metabolism in the phytopathogenic fungus Zymoseptoria tritici reveals novel functionalities implicated in virulence. PMID:26074495
Molecular and functional characterization of the durum wheat TdRL1, a member of the conserved Poaceae RSS1-like family that exhibits features of intrinsically disordered proteins and confers stress tolerance in yeast. PMID:26071212
Tomato Sl3-MMP, a member of the Matrix metalloproteinase family, is required for disease resistance against Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000. PMID:26070456
Discovery of Chemosensory Genes in the Oriental Fruit Fly, Bactrocera dorsalis. PMID:26070069
Complete Genome Sequence of Sporisorium scitamineum and Biotrophic Interaction Transcriptome with Sugarcane. PMID:26065709
Computational Prediction of acyl-coA Binding Proteins Structure in Brassica napus. PMID:26065422
Comparative genomic and phenomic analysis of Clostridium difficile and Clostridium sordellii, two related pathogens with differing host tissue preference. PMID:26059449
Expansion and Functional Divergence of Jumonji C-Containing Histone Demethylases: Significance of Duplications in Ancestral Angiosperms and Vertebrates. PMID:26059336
Microbial DNA records historical delivery of anthropogenic mercury. PMID:26057844
Stem cells and fluid flow drive cyst formation in an invertebrate excretory organ. PMID:26057828
Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off. PMID:26055961
Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms. PMID:26055114
A Plasmid-Borne System To Assess the Excision and Integration of Staphylococcal Cassette Chromosome mec Mediated by CcrA and CcrB. PMID:26055110
An Ebola virus-centered knowledge base. PMID:26055098
Synergistic function of four novel thermostable glycoside hydrolases from a long-term enriched thermophilic methanogenic digester. PMID:26052323
Structural Studies of the HIV-1 Integrase Protein: Compound Screening and Characterization of a DNA-Binding Inhibitor. PMID:26046987
Xenorhabdus bovienii Strain Diversity Impacts Coevolution and Symbiotic Maintenance with Steinernema spp. Nematode Hosts. PMID:26045536
Horizontal gene transfer and genome evolution in Methanosarcina. PMID:26044078
Identification of genomic features in the classification of loss- and gain-of-function mutation. PMID:26043747
Arterivirus nsp12 versus the coronavirus nsp16 2'-O-methyltransferase: comparison of the C-terminal cleavage products of two nidovirus pp1ab polyproteins. PMID:26041874
Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host. PMID:26040701
In silico identification of AMPylating enzymes and study of their divergent evolution. PMID:26039278
Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus. PMID:26038723
Surface hydrolysis of sphingomyelin by the outer membrane protein Rv0888 supports replication of Mycobacterium tuberculosis in macrophages. PMID:26036301
Homologues of Genetic Transformation DNA Import Genes Are Required for Rhodobacter capsulatus Gene Transfer Agent Recipient Capability Regulated by the Response Regulator CtrA. PMID:26031909
Origin and evolution of lysyl oxidases. PMID:26024311
Calcium affinity of human α-actinin 1. PMID:26020004
The CASC15 Long Intergenic Noncoding RNA Locus Is Involved in Melanoma Progression and Phenotype Switching. PMID:26016895
De novo transcriptome characterization and gene expression profiling of the desiccation tolerant moss Bryum argenteum following rehydration. PMID:26016800
Databases for Microbiologists. PMID:26013493
Depsipeptide Intermediates Interrogate Proposed Biosynthesis of Cereulide, the Emetic Toxin of Bacillus cereus. PMID:26013201
Evolutionary divergence of the plant elicitor peptides (Peps) and their receptors: interfamily incompatibility of perception but compatibility of downstream signalling. PMID:26002971
Garlic (A. sativum L.) alliinase gene family polymorphism reflects bolting types and cysteine sulphoxides content. PMID:25997498
Genome-Wide Analysis in Three Fusarium Pathogens Identifies Rapidly Evolving Chromosomes and Genes Associated with Pathogenicity. PMID:25994930
APPRIS WebServer and WebServices. PMID:25990727
First Staphylococcal Cassette Chromosome mec Containing a mecB-Carrying Gene Complex Independent of Transposon Tn6045 in a Macrococcus canis Isolate from a Canine Infection. PMID:25987634
Partial protein domains: evolutionary insights and bioinformatics challenges. PMID:25986583
Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. PMID:25983555
SIFTER search: a web server for accurate phylogeny-based protein function prediction. PMID:25979264
Promotion of bone morphogenetic protein signaling by tetraspanins and glycosphingolipids. PMID:25978409
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. PMID:25977477
Draft Genome Sequence of Anaeromyxobacter sp. Strain PSR-1, an Arsenate-Respiring Bacterium Isolated from Arsenic-Contaminated Soil. PMID:25977440
The eukaryotic translation initiation regulator CDC123 defines a divergent clade of ATP-grasp enzymes with a predicted role in novel protein modifications. PMID:25976611
A de novo floral transcriptome reveals clues into Phalaenopsis orchid flower development. PMID:25970572
The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. PMID:25969446
Contrasting host-pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes. PMID:25968466
Polyglycine hydrolases: Fungal β-lactamase-like endoproteases that cleave polyglycine regions within plant class IV chitinases. PMID:25966977
CATH FunFHMMer web server: protein functional annotations using functional family assignments. PMID:25964299
Comparative transcriptome profiling approach to glean virulence and immunomodulation-related genes of Fasciola hepatica. PMID:25956885
ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling. PMID:25956654
An ace up their sleeve: a transcriptomic approach exposes the AceI efflux protein of Acinetobacter baumannii and reveals the drug efflux potential hidden in many microbial pathogens. PMID:25954261
Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees. PMID:25953738
MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse. PMID:25953081
Egfl6 is involved in zebrafish notochord development. PMID:25952972
Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea. PMID:25952370
SELPHI: correlation-based identification of kinase-associated networks from global phospho-proteomics data sets. PMID:25948583
antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. PMID:25948579
Identification and distribution of the NBS-LRR gene family in the Cassava genome. PMID:25948536
HMMER web server: 2015 update. PMID:25943547
RNA-Seq Based De Novo Transcriptome Assembly and Gene Discovery of Cistanche deserticola Fleshy Stem. PMID:25938435
Target activation by regulatory RNAs in bacteria. PMID:25934124
Chemical and Biological Reduction of the Radical SAM Enzyme 7-Carboxy-7-deazaguanine [corrected] Synthase. PMID:25933252
novPTMenzy: a database for enzymes involved in novel post-translational modifications. PMID:25931459
The effect of imipenem and diffusible signaling factors on the secretion of outer membrane vesicles and associated Ax21 proteins in Stenotrophomonas maltophilia. PMID:25926824
Structure of the K12 capsule containing 5,7-di-N-acetylacinetaminic acid from Acinetobacter baumannii isolate D36. PMID:25926563
Domain atrophy creates rare cases of functional partial protein domains. PMID:25924720
Metazoans evolved by taking domains from soluble proteins to expand intercellular communication network. PMID:25923201
An assemblage of divergent variants of a novel putative closterovirus from American persimmon. PMID:25921465
Manual classification strategies in the ECOD database. PMID:25917548
The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. PMID:25915022
Long non-coding RNA discovery across the genus anopheles reveals conserved secondary structures within and beyond the Gambiae complex. PMID:25903279
Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks. PMID:25900361
Genome-wide identification and evolution of HECT genes in soybean. PMID:25894222
Characterization of 19 Genes Encoding Membrane-Bound Fatty Acid Desaturases and their Expression Profiles in Gossypium raimondii Under Low Temperature. PMID:25894196
Genome-wide identification and characterization of Fox genes in the silkworm, Bombyx mori. PMID:25893708
A property-based analysis of human transcription factors. PMID:25890365
Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes. PMID:25888081
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
Distribution in microbial genomes of genes similar to lodA and goxA which encode a novel family of quinoproteins with amino acid oxidase activity. PMID:25886995
Comparative transcriptome analysis within the Lolium/Festuca species complex reveals high sequence conservation. PMID:25886302
Streptophyte phytochromes exhibit an N-terminus of cyanobacterial origin and a C-terminus of proteobacterial origin. PMID:25886068
A RNA-seq approach to identify putative toxins from acrorhagi in aggressive and non-aggressive Anthopleura elegantissima polyps. PMID:25886045
High-throughput identification of proteins with AMPylation using self-assembled human protein (NAPPA) microarrays. PMID:25881200
Heterologous surface display on lactic acid bacteria: non-GMO alternative? PMID:25880164
A comprehensive genomic, transcriptomic and proteomic analysis of a hyperosmotic stress sensitive α-proteobacterium. PMID:25879753
Solution structure of a soluble fragment derived from a membrane protein by shotgun proteolysis. PMID:25877662
Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features. PMID:25875305
Prediction of cancer proteins by integrating protein interaction, domain frequency, and domain interaction data using machine learning algorithms. PMID:25866773
A structure-based classification and analysis of protein domain family binding sites and their interactions. PMID:25860777
All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences. PMID:25858953
The two-component system CpxAR is essential for virulence in the phytopathogen bacteria Dickeya dadantii EC3937. PMID:25856505
Investigation of genes encoding calcineurin B-like protein family in legumes and their expression analyses in chickpea (Cicer arietinum L.). PMID:25853855
The composition of the global and feature specific cyanobacterial core-genomes. PMID:25852675
Cofactor specificity motifs and the induced fit mechanism in class I ketol-acid reductoisomerases. PMID:25849365
The EMBL-EBI bioinformatics web and programmatic tools framework. PMID:25845596
Crystal structure of a two-subunit TrkA octameric gating ring assembly. PMID:25826626
Regulation of coronafacoyl phytotoxin production by the PAS-LuxR family regulator CfaR in the common scab pathogen Streptomyces scabies. PMID:25826255
Key challenges for the creation and maintenance of specialist protein resources. PMID:25820941
Hidden relationships between metalloproteins unveiled by structural comparison of their metal sites. PMID:25820752
Genome-wide identification, evolutionary, and expression analyses of histone H3 variants in plants. PMID:25815311
A statistical physics perspective on alignment-independent protein sequence comparison. PMID:25810434
Complete genome sequence of Borrelia afzelii K78 and comparative genome analysis. PMID:25798594
Predicting protein interface residues using easily accessible on-line resources. PMID:25797794
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
Highly Iterated Palindromic Sequences (HIPs) and Their Relationship to DNA Methyltransferases. PMID:25789551
Ribosomal frameshifting and dual-target antiactivation restrict quorum-sensing-activated transfer of a mobile genetic element. PMID:25787256
RNA-binding proteins involved in post-transcriptional regulation in bacteria. PMID:25784899
Quality scores for 32,000 genomes. PMID:25780509
The carbon starvation response of the ectomycorrhizal fungus Paxillus involutus. PMID:25778509
Topological analysis of the Escherichia coli WcaJ protein reveals a new conserved configuration for the polyisoprenyl-phosphate hexose-1-phosphate transferase family. PMID:25776537
Identification of AGO3-associated miRNAs and computational prediction of their targets in the green alga Chlamydomonas reinhardtii. PMID:25769981
Improving the consistency of domain annotation within the Conserved Domain Database. PMID:25767294
Transcriptome analysis of Panax vietnamensis var. fuscidicus discovers putative ocotillol-type ginsenosides biosynthesis genes and genetic markers. PMID:25765814
Comprehensive analysis of CCCH-type zinc finger family genes facilitates functional gene discovery and reflects recent allopolyploidization event in tetraploid switchgrass. PMID:25765300
Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales. PMID:25764277
A unique, highly conserved secretory invertase is differentially expressed by promastigote developmental forms of all species of the human pathogen, Leishmania. PMID:25763714
Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST. PMID:25754993
Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing. PMID:25751143
Multiple mechanisms of MYCN dysregulation in Wilms tumour. PMID:25749049
Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights. PMID:25745418
Genome Sequences of the Lignin-Degrading Pseudomonas sp. Strain YS-1p and Rhizobium sp. Strain YS-1r Isolated from Decaying Wood. PMID:25744986
The genome of Shigella dysenteriae strain Sd1617 comparison to representative strains in evaluating pathogenesis. PMID:25743074
A conserved glutamate residue in the C-terminal deaminase domain of pentatricopeptide repeat proteins is required for RNA editing activity. PMID:25739442
Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals. PMID:25735770
FR database 1.0: a resource focused on fruit development and ripening. PMID:25725058
Mutations in MAB21L2 result in ocular Coloboma, microcornea and cataracts. PMID:25719200
Defining the gene repertoire and spatiotemporal expression profiles of adhesion G protein-coupled receptors in zebrafish. PMID:25715737
The ferrous iron-responsive BqsRS two-component system activates genes that promote cationic stress tolerance. PMID:25714721
Structural and enzymatic analysis of TarM glycosyltransferase from Staphylococcus aureus reveals an oligomeric protein specific for the glycosylation of wall teichoic acid. PMID:25697358
Ancient dynamin segments capture early stages of host-mitochondrial integration. PMID:25691734
Eukaryotic LYR Proteins Interact with Mitochondrial Protein Complexes. PMID:25686363
The UCSC Ebola Genome Portal. PMID:25685613
Genome-wide identification, sequence characterization, and protein-protein interaction properties of DDB1 (damaged DNA binding protein-1)-binding WD40-repeat family members in Solanum lycopersicum. PMID:25680350
STBase: one million species trees for comparative biology. PMID:25679219
A metaproteomics approach to elucidate host and pathogen protein expression during catheter-associated urinary tract infections (CAUTIs). PMID:25673765
Homologs of the Acinetobacter baumannii AceI transporter represent a new family of bacterial multidrug efflux systems. PMID:25670776
Two-tiered histidine kinase pathway involved in heat shock and salt sensing in the general stress response of Sphingomonas melonis Fr1. PMID:25666137
Cloning, refolding, purification and preliminary crystallographic analysis of the sensory domain of the Campylobacter chemoreceptor for multiple ligands (CcmL). PMID:25664798
Transport domain unlocking sets the uptake rate of an aspartate transporter. PMID:25652997
PON-P2: prediction method for fast and reliable identification of harmful variants. PMID:25647319
Visualization of LC-MS/MS proteomics data in MaxQuant. PMID:25644178
Two distinct domains of the UVR8 photoreceptor interact with COP1 to initiate UV-B signaling in Arabidopsis. PMID:25627067
Draft genome sequence of adzuki bean, Vigna angularis. PMID:25626881
Structure and mechanism of Staphylococcus aureus TarM, the wall teichoic acid α-glycosyltransferase. PMID:25624472
Using comparative genomics to drive new discoveries in microbiology. PMID:25617609
Identification of divergent WH2 motifs by HMM-HMM alignments. PMID:25616999
The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam. PMID:25614388
RNAi screening of developmental toolkit genes: a search for novel wing genes in the red flour beetle, Tribolium castaneum. PMID:25613748
RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information. PMID:25609700
Genome-wide identification and expression pattern of drought-responsive members of the NAC family in maize. PMID:25606426
Vaccinia virus protein A49 is an unexpected member of the B-cell Lymphoma (Bcl)-2 protein family. PMID:25605733
Metabolic fate of unsaturated glucuronic/iduronic acids from glycosaminoglycans: molecular identification and structure determination of streptococcal isomerase and dehydrogenase. PMID:25605731
Evidence that TP_0144 of Treponema pallidum is a thiamine-binding protein. PMID:25605310
Reconstructing genome-wide protein-protein interaction networks using multiple strategies with homologous mapping. PMID:25602759
The landscape of long noncoding RNAs in the human transcriptome. PMID:25599403
Identification and characterization of LFD-2, a predicted fringe protein required for membrane integrity during cell fusion in neurospora crassa. PMID:25595444
The 2015 Nucleic Acids Research Database Issue and molecular biology database collection. PMID:25593347
The Ordospora colligata genome: Evolution of extreme reduction in microsporidia and host-to-parasite horizontal gene transfer. PMID:25587016
Comparative genomic analysis of evolutionarily conserved but functionally uncharacterized membrane proteins in archaea: Prediction of novel components of secretion, membrane remodeling and glycosylation systems. PMID:25583072
The Lectin Frontier Database (LfDB), and data generation based on frontal affinity chromatography. PMID:25580689
Complete Genome Sequence of VpKK5, a Novel Vibrio parahaemolyticus Lytic Siphophage. PMID:25573936
Draft Genome Sequence of Acinetobacter sp. HR7, Isolated from Hanwoo, Korean Native Cattle. PMID:25573931
Draft Genome Sequence of Bordetella trematum Strain HR18. PMID:25573930
Robustness of birth-death and gain models for inferring evolutionary events. PMID:25572914
Genomewide analysis of TCP transcription factor gene family in Malus domestica. PMID:25572232
A new family of secreted toxins in pathogenic Neisseria species. PMID:25569427
Insights into the origin and evolution of the plant hormone signaling machinery. PMID:25560880
Genome-wide association study for endothelial growth factors. PMID:25552591
β-Helical architecture of cytoskeletal bactofilin filaments revealed by solid-state NMR. PMID:25550503
CopM is a novel copper-binding protein involved in copper resistance in Synechocystis sp. PCC 6803. PMID:25545960
The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis. PMID:25539682
Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota. PMID:25538694
Evolutionary dynamics of hAT DNA transposon families in Saccharomycetaceae. PMID:25532815
Use of mCherry Red fluorescent protein for studies of protein localization and gene expression in Clostridium difficile. PMID:25527559
Genomic potential for polysaccharide deconstruction in bacteria. PMID:25527556
TXNDC5, a newly discovered disulfide isomerase with a key role in cell physiology and pathology. PMID:25526565
TINAGL1 and B3GALNT1 are potential therapy target genes to suppress metastasis in non-small cell lung cancer. PMID:25521548
Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. PMID:25520706
Characterization of three active transposable elements recently inserted in three independent DFR-A alleles and one high-copy DNA transposon isolated from the Pink allele of the ANS gene in onion (Allium cepa L.). PMID:25515665
Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation. PMID:25514978
Cellulolytic potential under environmental changes in microbial communities from grassland litter. PMID:25505459
Contribution of anion-π interactions to the stability of Sm/LSm proteins. PMID:25502146
Genome-scale identification and characterization of moonlighting proteins. PMID:25497125
Genome-wide identification of mitogen-activated protein kinase gene family in Gossypium raimondii and the function of their corresponding orthologs in tetraploid cultivated cotton. PMID:25492847
chromoWIZ: a web tool to query and visualize chromosome-anchored genes from cereal and model genomes. PMID:25491094
Achievements and challenges in structural bioinformatics and computational biophysics. PMID:25488929
Role of Dickeya dadantii 3937 chemoreceptors in the entry to Arabidopsis leaves through wounds. PMID:25487519
Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom. PMID:25478683
Integrative workflows for metagenomic analysis. PMID:25478562
Genome update of the dimorphic human pathogenic fungi causing paracoccidioidomycosis. PMID:25474325
An ancient autoproteolytic domain found in GAIN, ZU5 and Nucleoporin98. PMID:25451782
Determining microbial products and identifying molecular targets in the human microbiome. PMID:25440055
Plant-PrAS: a database of physicochemical and structural properties and novel functional regions in plant proteomes. PMID:25435546
Computational prediction of protein interactions related to the invasion of erythrocytes by malarial parasites. PMID:25433733
Nemertean toxin genes revealed through transcriptome sequencing. PMID:25432940
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic. PMID:25429972
Internal sense of direction: sensing and signaling from cytoplasmic chemoreceptors. PMID:25428939
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
Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments. PMID:25426110
Genome-wide analysis of the WW domain-containing protein genes in silkworm and their expansion in eukaryotes. PMID:25424044
X-ray structure of the mature ectodomain of phogrin. PMID:25421040
CDD: NCBI's conserved domain database. PMID:25414356
GRASP: guided reference-based assembly of short peptides. PMID:25414351
CFam: a chemical families database based on iterative selection of functional seeds and seed-directed compound clustering. PMID:25414339
ProteomeScout: a repository and analysis resource for post-translational modifications and proteins. PMID:25414335
Comparative genomics of transcriptional regulation of methionine metabolism in Proteobacteria. PMID:25411846
Comparative genomics of DtxR family regulons for metal homeostasis in Archaea. PMID:25404694
Global discovery of colonization determinants in the squid symbiont Vibrio fischeri. PMID:25404340
Complex two-component signaling regulates the general stress response in Alphaproteobacteria. PMID:25404331
Diversity and variability of NOD-like receptors in fungi. PMID:25398782
Pdsg1 and Pdsg2, novel proteins involved in developmental genome remodelling in Paramecium. PMID:25397898
In the multi-domain protein adenylate kinase, domain insertion facilitates cooperative folding while accommodating function at domain interfaces. PMID:25393408
Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions. PMID:25392414
Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes. PMID:25384563
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities. PMID:25378329
The tmRNA website. PMID:25378311
BRENDA in 2015: exciting developments in its 25th year of existence. PMID:25378310
Whole genome sequence of the Treponema pallidum subsp. endemicum strain Bosnia A: the genome is related to yaws treponemes but contains few loci similar to syphilis treponemes. PMID:25375929
Characteristics of protein residue-residue contacts and their application in contact prediction. PMID:25374390
Analysis of COQ2 gene in multiple system atrophy. PMID:25373618
Expression, regulation and activity of a B2-type cyclin in mitotic and endoreduplicating maize endosperm. PMID:25368625
Protectome analysis: a new selective bioinformatics tool for bacterial vaccine candidate discovery. PMID:25368410
Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB. PMID:25363770
MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins. PMID:25361972
The multi-protein family of sulfotransferases in plants: composition, occurrence, substrate specificity, and functions. PMID:25360143
Quantitative trait locus mapping of melanization in the plant pathogenic fungus Zymoseptoria tritici. PMID:25360032
Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling. PMID:25357249
A series of PDB-related databanks for everyday needs. PMID:25352545
Genome3D: exploiting structure to help users understand their sequences. PMID:25348407
WDSPdb: a database for WD40-repeat proteins. PMID:25348404
Genomic Investigations unmask Mycoplasma amphoriforme, a new respiratory pathogen. PMID:25344534
Dissection of hexosyl- and sialyltransferase domains in the bifunctional capsule polymerases from Neisseria meningitidis W and Y defines a new sialyltransferase family. PMID:25342753
Protein profiles reveal diverse responsive signaling pathways in kernels of two maize inbred lines with contrasting drought sensitivity. PMID:25334062
The human DEPhOsphorylation database DEPOD: a 2015 update. PMID:25332398
Cog5-Cog7 crystal structure reveals interactions essential for the function of a multisubunit tethering complex. PMID:25331899
Caspase cleavage sites in the human proteome: CaspDB, a database of predicted substrates. PMID:25330111
P2CS: updates of the prokaryotic two-component systems database. PMID:25324303
Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology. PMID:25320677
SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes. PMID:25309735
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
Cytosine chemoreceptor McpC in Pseudomonas putida F1 also detects nicotinic acid. PMID:25294107
CLAP: a web-server for automatic classification of proteins with special reference to multi-domain proteins. PMID:25282152
Identification and molecular characterization of MYB Transcription Factor Superfamily in C4 model plant foxtail millet (Setaria italica L.). PMID:25279462
A Ras-like domain in the light intermediate chain bridges the dynein motor to a cargo-binding region. PMID:25272277
Genome-wide characterization and expression profiling of the AUXIN RESPONSE FACTOR (ARF) gene family in Eucalyptus grandis. PMID:25269088
A genetic screen in Myxococcus xanthus identifies mutants that uncouple outer membrane exchange from a downstream cellular response. PMID:25266387
Comparative genome analysis of entomopathogenic fungi reveals a complex set of secreted proteins. PMID:25263348
NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. PMID:25262355
Maize and millet transcription factors annotated using comparative genomic and transcriptomic data. PMID:25261191
Systematic phenotypic screen of Arabidopsis peroxisomal mutants identifies proteins involved in β-oxidation. PMID:25253886
Plant protein peptidase inhibitors: an evolutionary overview based on comparative genomics. PMID:25253557
Variation in the OC locus of Acinetobacter baumannii genomes predicts extensive structural diversity in the lipooligosaccharide. PMID:25247305
Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection. PMID:25220818
Exposing the secrets of two well-known Lactobacillus casei phages, J-1 and PL-1, by genomic and structural analysis. PMID:25217012
Neighbor preferences of amino acids and context-dependent effects of amino acid substitutions in human, mouse, and dog. PMID:25210846
Proteome-wide subcellular topologies of E. coli polypeptides database (STEPdb). PMID:25210196
Insilico analysis of hypothetical proteins unveils putative metabolic pathways and essential genes in Leishmania donovani. PMID:25206363
Molecular characterization of a novel temperate sinorhizobium bacteriophage, ФLM21, encoding DNA methyltransferase with CcrM-like specificity. PMID:25187538
Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities. PMID:25179155
Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys. PMID:25168586
Comprehensive analysis of alternative splicing in Digitalis purpurea by strand-specific RNA-Seq. PMID:25167195
Ku-mediated coupling of DNA cleavage and repair during programmed genome rearrangements in the ciliate Paramecium tetraurelia. PMID:25166013
Genetic analysis of vegetative branching in sorghum. PMID:25163936
Entropy-driven partitioning of the hierarchical protein space. PMID:25161256
Function and evolution of two forms of SecDF homologs in Streptomyces coelicolor. PMID:25140821
Expression pattern of glycoside hydrolase genes in Lutzomyia longipalpis reveals key enzymes involved in larval digestion. PMID:25140153
PlantCAZyme: a database for plant carbohydrate-active enzymes. PMID:25125445
Structural basis for the recruitment and activation of the Legionella phospholipase VipD by the host GTPase Rab5. PMID:25114243
Functional analysis of the Na+,K+/H+ antiporter PeNHX3 from the tree halophyte Populus euphratica in yeast by model-guided mutagenesis. PMID:25093858
The mitochondrion-located protein OsB12D1 enhances flooding tolerance during seed germination and early seedling growth in rice. PMID:25089878
Small RNA functions in carbon metabolism and virulence of enteric pathogens. PMID:25077072
Evolutionary analysis of the cystatin family in three Schistosoma species. PMID:25071834
Massive expansion of Ubiquitination-related gene families within the Chlamydiae. PMID:25069652
Screening of a Leptospira biflexa mutant library to identify genes involved in ethidium bromide tolerance. PMID:25063661
Discovery of the β-barrel-type RNA methyltransferase responsible for N6-methylation of N6-threonylcarbamoyladenosine in tRNAs. PMID:25063302
Genome-wide search for eliminylating domains reveals novel function for BLES03-like proteins. PMID:25062915
Evidence for loss of a partial flagellar glycolytic pathway during trypanosomatid evolution. PMID:25050549
Expansion of the APC superfamily of secondary carriers. PMID:25043943
Whole-genome sequencing reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals. PMID:25038069
A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress. PMID:25024436
Identification of TNF-α-responsive promoters and enhancers in the intestinal epithelial cell model Caco-2. PMID:24990076
The intraflagellar transport dynein complex of trypanosomes is made of a heterodimer of dynein heavy chains and of light and intermediate chains of distinct functions. PMID:24989795
An introduction to the analysis of shotgun metagenomic data. PMID:24982662
Comparative genomics and evolution of regulons of the LacI-family transcription factors. PMID:24966856
PubServer: literature searches by homology. PMID:24957597
Settling down: the genome of Serratia symbiotica from the aphid Cinara tujafilina zooms in on the process of accommodation to a cooperative intracellular life. PMID:24951564
AraC/XylS family stress response regulators Rob, SoxS, PliA, and OpiA in the fire blight pathogen Erwinia amylovora. PMID:24936054
Conserved evolutionary units in the heme-copper oxidase superfamily revealed by novel homologous protein families. PMID:24931479
Coverage of protein domain families with structural protein-protein interactions: current progress and future trends. PMID:24931138
Latex clearing protein-an oxygenase cleaving poly(cis-1,4-isoprene) rubber at the cis double bonds. PMID:24928880
Functional and Evolutionary Analysis of the CASPARIAN STRIP MEMBRANE DOMAIN PROTEIN Family. PMID:24920445
Identification and characterization of a halotolerant, cold-active marine endo-β-1,4-glucanase by using functional metagenomics of seaweed-associated microbiota. PMID:24907332
Apolipoprotein L2 contains a BH3-like domain but it does not behave as a BH3-only protein. PMID:24901046
From sequence to enzyme mechanism using multi-label machine learning. PMID:24885296
fPoxDB: fungal peroxidase database for comparative genomics. PMID:24885079
Complete genome sequences of nine mycobacteriophages. PMID:24874666
AIDA: ab initio domain assembly server. PMID:24831546
CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems. PMID:24817877
Alignment-Annotator web server: rendering and annotating sequence alignments. PMID:24813445
Simultaneous alignment and folding of protein sequences. PMID:24766258
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis. PMID:24646163
Paleo-evolutionary plasticity of plant disease resistance genes. PMID:24617999
Molecular cloning and yeast expression of cinnamate 4-hydroxylase from Ornithogalum saundersiae baker. PMID:24476601
Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals. PMID:24429298
Comparative analysis of the full genome of Helicobacter pylori isolate Sahul64 identifies genes of high divergence. PMID:24375107
A novel protein kinase-like domain in a selenoprotein, widespread in the tree of life. PMID:22359664
An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference. PMID:22046320
Analysis of gene order conservation in eukaryotes identifies transcriptionally and functionally linked genes. PMID:20498846 -
The Pfam protein families database: towards a more sustainable future
PubMed citations: 2308.
2308 articles citing: The Pfam protein families database: towards a more sustainable future
Systematic in silico discovery of novel solute carrier-like proteins from proteomes. PMID:35901096
Genome-wide identification and characterization of GATA family genes in wheat. PMID:35896980
FastANI, Mash and Dashing equally differentiate between Klebsiella species. PMID:35891643
Integrated Analysis of Single-Molecule Real-Time Sequencing and Next-Generation Sequencing Eveals Insights into Drought Tolerance Mechanism of Lolium multiflorum. PMID:35887272
ContactPFP: Protein function prediction using predicted contact information. PMID:35875419
Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members. PMID:35842574
Transcriptomics of the Rooibos (Aspalathus linearis) Species Complex. PMID:35822822
Genome-wide signatures of synergistic epistasis during parallel adaptation in a Baltic Sea copepod. PMID:35821220
Using a Hybrid Mapping Population to Identify Genomic Regions of Pyrenophora teres Associated With Virulence. PMID:35812984
Identification and Characterization of the Core Region of ZmDi19-5 Promoter Activity and Its Upstream Regulatory Proteins. PMID:35806396
Evolution of Epidermal Growth Factor (EGF)-like and Zona Pellucida Domains Containing Shell Matrix Proteins in Mollusks. PMID:35796746
Systematic Analysis of bHLH Transcription Factors in Cassava Uncovers Their Roles in Postharvest Physiological Deterioration and Cyanogenic Glycosides Biosynthesis. PMID:35789698
Comparative Genomic Analyses Provide Insight Into the Pathogenicity of Metschnikowia bicuspidata LNES0119. PMID:35770163
Transcriptional Basis for Haustorium Formation and Host Establishment in Hemiparasitic Psittacanthus schiedeanus Mistletoes. PMID:35769994
The zinc proteome of SARS-CoV-2. PMID:35767875
Orrella daihaiensis sp. nov., a bacterium isolated from Daihai Lake in Inner Mongolia. PMID:35751751
Whole-Transcriptome Analysis of Non-Coding RNA Alteration in Porcine Alveolar Macrophage Exposed to Aflatoxin B1. PMID:35737034
Identification of Pathogenicity-Related Effector Proteins and the Role of Piwsc1 in the Virulence of Penicillium italicum on Citrus Fruits. PMID:35736129
In vitro and in silico Studies Reveal Bacillus cereus AA-18 as a Potential Candidate for Bioremediation of Mercury-Contaminated Wastewater. PMID:35733958
The evolution of BDNF is defined by strict purifying selection and prodomain spatial coevolution, but what does it mean for human brain disease? PMID:35732627
Genome Sequences of Two New Pandoravirus Strains Isolated from Brazil and France. PMID:35731201
Draft Genome Sequences of Erysipelothrix sp. Strains Isolated from Stranded Septic Bottlenose Dolphins in Alabama, USA. PMID:35730954
Phototransduction in a marine sponge provides insights into the origin of animal vision. PMID:35707725
Highly Specialized Carbohydrate Metabolism Capability in Bifidobacterium Strains Associated with Intestinal Barrier Maturation in Early Preterm Infants. PMID:35695455
Potential Roles of 1-Aminocyclopropane-1-carboxylic Acid Synthase Genes in the Response of Gossypium Species to Abiotic Stress by Genome-Wide Identification and Expression Analysis. PMID:35684296
Subtilisin of Leishmania amazonensis as Potential Druggable Target: Subcellular Localization, In Vitro Leishmanicidal Activity and Molecular Docking of PF-429242, a Subtilisin Inhibitor. PMID:35678670
Bioinformatic Identification of ABC Transporters in Candida auris. PMID:35674958
Genome-wide analysis of PTR transporters in Candida species and their functional characterization in Candida auris. PMID:35648145
miR-29a-5p Inhibits Prenatal Hair Placode Formation Through Targeting EDAR by ceRNA Regulatory Network. PMID:35646897
Spontaneous Suppressors against Debilitating Transmembrane Mutants of CaMdr1 Disclose Novel Interdomain Communication via Signature Motifs of the Major Facilitator Superfamily. PMID:35628792
Molecular Characterization and Expression Analysis of Putative Class C (Glutamate Family) G Protein-Coupled Receptors in Ascidian Styela clava. PMID:35625509
Hybrid Sequencing Resolved Inverted Terminal Repeats in the Genome of Megavirus Baoshan. PMID:35620092
Identification of a Novel Metabolic Target for Bioactive Triterpenoids Biosynthesis in Ganoderma lucidum. PMID:35615508
Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica. PMID:35614434
Integrative Analysis of lncRNA-miRNA-mRNA Regulatory Network Reveals the Key lncRNAs Implicated Potentially in the Differentiation of Adipocyte in Goats. PMID:35600305
Biotechnological Combination for Co-contaminated Soil Remediation: Focus on Tripartite "Meta-Enzymatic" Activity. PMID:35599908
The assembled and annotated genome of the masked palm civet (Paguma larvata). PMID:35583674
Machine Learning and Its Applications for Protozoal Pathogens and Protozoal Infectious Diseases. PMID:35573796
Differential Long Non-Coding RNA Expression Analysis in Chronic Non-Atrophic Gastritis, Gastric Mucosal Intraepithelial Neoplasia, and Gastric Cancer Tissues. PMID:35571069
The Genome-Wide Identification of Long Non-Coding RNAs Involved in Floral Thermogenesis in Nelumbo nucifera Gaertn. PMID:35563291
Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter. PMID:35545619
In silico functional and tumor suppressor role of hypothetical protein PCNXL2 with regulation of the Notch signaling pathway. PMID:35539910
Metagenomic ene-reductases for the bioreduction of sterically challenging enones. PMID:35539044
Full-Length Transcriptome Sequencing Reveals Tissue-Specific Gene Expression Profile of Mangrove Clam Geloina erosa. PMID:35514334
Dual RNA-Seq of H5N1 Avian Influenza Virus and Host Cell Transcriptomes Reveals Novel Insights Into Host-Pathogen Cross Talk. PMID:35495687
Structure and DNA binding analysis of AT-rich interaction domain present in human BAF-B specific subunit BAF250b. PMID:35481652
Deletion and tandem duplications of biosynthetic genes drive the diversity of triterpenoids in Aralia elata. PMID:35468919
Plant Cell Wall Proteomes: The Core of Conserved Protein Families and the Case of Non-Canonical Proteins. PMID:35457091
IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella. PMID:35456751
Genome-wide identification, classification and expression analysis of the JmjC domain-containing histone demethylase gene family in Jatropha curcas L. PMID:35449230
Transcriptome Analysis of Otodectes cynotis in Different Developmental Stages. PMID:35444625
Metabolic Profiling of Interspecies Interactions During Sessile Bacterial Cultivation Reveals Growth and Sporulation Induction in Paenibacillus amylolyticus in Response to Xanthomonas retroflexus. PMID:35425721
Label-Free LC-MS/MS Analysis Reveals Different Proteomic Profiles between Egg Yolks of Silky Fowl and Ordinary Chickens. PMID:35407122
Genome-Wide Identification, Expression Pattern and Sequence Variation Analysis of SnRK Family Genes in Barley. PMID:35406955
Evaluation of Host Depletion and Extraction Methods for Shotgun Metagenomic Analysis of Bovine Vaginal Samples. PMID:35404108
Full-Length Transcriptome Sequences Provide Insight Into Hermaphroditism of Freshwater Pearl Mussel Hyriopsis schlegelii. PMID:35401664
Deciphering Genomes: Genetic Signatures of Plant-Associated Micromonospora. PMID:35401599
A Large-Scale Genome-Based Survey of Acidophilic Bacteria Suggests That Genome Streamlining Is an Adaption for Life at Low pH. PMID:35387071
Characterization of the Neospora caninum peroxiredoxin: a novel peroxidase and antioxidant enzyme. PMID:35362740
Unifying the known and unknown microbial coding sequence space. PMID:35356891
Insights Into the MYB-Related Transcription Factors Involved in Regulating Floral Aroma Synthesis in Sweet Osmanthus. PMID:35356120
Innovation and Emerging Roles of Populus trichocarpa TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR Transcription Factors in Abiotic Stresses by Whole-Genome Duplication. PMID:35356113
Genome-wide identification and characterization of PdbHLH transcription factors related to anthocyanin biosynthesis in colored-leaf poplar (Populus deltoids). PMID:35350981
Positive Selection during Niche Adaptation Results in Large-Scale and Irreversible Rearrangement of Chromosomal Gene Order in Bacteria. PMID:35348727
Systematic identification and expression profiles of the BAHD superfamily acyltransferases in barley (Hordeum vulgare). PMID:35332203
Comprehensive identification and expression analysis of CRY gene family in Gossypium. PMID:35331129
Tissue-Specific Expression of the Terpene Synthase Family Genes in Rosa chinensis and Effect of Abiotic Stress Conditions. PMID:35328100
Genome-Wide Identification of the Long Noncoding RNAs of Tribolium castaneum in Response to Terpinen-4-ol Fumigation. PMID:35323581
Genome-wide characterization and expression analysis of Erf gene family in cotton. PMID:35317739
Phylogeny-Aware Chemoinformatic Analysis of Chemical Diversity in Lamiaceae Enables Iridoid Pathway Assembly and Discovery of Aucubin Synthase. PMID:35298643
Developmental transcriptomics throughout the embryonic developmental process of Rhipicephalus turanicus reveals stage-specific gene expression profiles. PMID:35292089
Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. strugatskii. PMID:35287351
Full-length transcriptome analysis of Adiantum flabellulatum gametophyte. PMID:35287343
Identification and Functional Analysis of lncRNA by CRISPR/Cas9 During the Cotton Response to Sap-Sucking Insect Infestation. PMID:35283887
Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria. PMID:35264790
Long-Term Cellulose Enrichment Selects for Highly Cellulolytic Consortia and Competition for Public Goods. PMID:35258341
The fiber diameter traits of Tibetan cashmere goats are governed by the inherent differences in stress, hypoxic, and metabolic adaptations: an integrative study of proteome and transcriptome. PMID:35255833
Comprehensive Analysis of Long Non-coding RNA Modulates Axillary Bud Development in Tobacco (Nicotiana tabacum L.). PMID:35237286
Next-generation sequencing identified novel truncating mutations in BBS9 causing Bardet Biedl syndrome in two Iranian consanguineous families. PMID:35222663
SMRT sequencing of the full-length transcriptome of Gekko gecko. PMID:35213661
Whole Genome Sequence of an Edible Mushroom Stropharia rugosoannulata (Daqiugaigu). PMID:35205854
A Highly Specific Holin-Mediated Mechanism Facilitates the Secretion of Lethal Toxin TcsL in Paeniclostridiumsordellii. PMID:35202151
First Multi-Organ Full-Length Transcriptome of Tree Fern Alsophila spinulosa Highlights the Stress-Resistant and Light-Adapted Genes. PMID:35186007
Structural and functional insights into ABHD5, a ligand-regulated lipase co-activator. PMID:35173175
Haloterrigena gelatinilytica sp. nov., a new extremely halophilic archaeon isolated from salt-lake. PMID:35166931
Microbial Functional Diversity Correlates with Species Diversity along a Temperature Gradient. PMID:35166562
CRP-Like Transcriptional Regulator MrpC Curbs c-di-GMP and 3',3'-cGAMP Nucleotide Levels during Development in Myxococcus xanthus. PMID:35164555
Comparative Phosphoproteomic Analysis of Sporulated Oocysts and Tachyzoites of Toxoplasma gondii Reveals Stage-Specific Patterns. PMID:35164288
De Novo Assembly and Annotation of the Vaginal Metatranscriptome Associated with Bacterial Vaginosis. PMID:35163545
Genome-Wide Identification and Expression Analysis of the 14-3-3 Gene Family in Mango (Mangifera indica L.). PMID:35163516
Transcription Factor RrANT1 of Rosa rugosa Positively Regulates Flower Organ Size in Petunia hybrida. PMID:35163160
Differential gene expression associated with a floral scent polymorphism in the evening primrose Oenothera harringtonii (Onagraceae). PMID:35151274
Genome-wide identification of StU-box gene family and assessment of their expression in developmental stages of Solanum tuberosum. PMID:35147812
Insights Into the Molecular Mechanisms of Late Flowering in Prunus sibirica by Whole-Genome and Transcriptome Analyses. PMID:35145534
PSL-LCCL: a resource for subcellular protein localization in liver cancer cell line SK_HEP1. PMID:35134877
Genome-Wide Identification and Analysis of the Ascorbate Peroxidase (APX) Gene Family of Winter Rapeseed (Brassica rapa L.) Under Abiotic Stress. PMID:35126448
Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains. PMID:35120642
RNA-Seq with a novel glabrous-ZM24fl reveals some key lncRNAs and the associated targets in fiber initiation of cotton. PMID:35114937
Genome-Wide Identification of JRL Genes in Moso Bamboo and Their Expression Profiles in Response to Multiple Hormones and Abiotic Stresses. PMID:35095981
DNA Methylation in Ensifer Species during Free-Living Growth and during Nitrogen-Fixing Symbiosis with Medicago spp. PMID:35089065
Access to highly specialized growth substrates and production of epithelial immunomodulatory metabolites determine survival of Haemophilus influenzae in human airway epithelial cells. PMID:35085362
The genome of medicinal leech (Whitmania pigra) and comparative genomic study for exploration of bioactive ingredients. PMID:35073842
Diverse DNA modification in marine prokaryotic and viral communities. PMID:35051998
New Deoxyenhygrolides from Plesiocystis pacifica Provide Insights into Butenolide Core Biosynthesis. PMID:35049927
Genome-Wide Identification and Expression Profile Analysis of the SnRK2 Gene Family in Nicotiana tabacum. PMID:35048221
Characterization and regulation mechanism analysis of ubiquitin-conjugating family genes in strawberry reveals a potential role in fruit ripening. PMID:35045827
Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes. PMID:35039616
Lnc-HZ05 regulates BPDE-inhibited human trophoblast cell proliferation and affects the occurrence of miscarriage by directly binding with miR-hz05. PMID:35038060
Genome-wide identification and characterization of the CLASP_N gene family in upland cotton (Gossypium hirsutum L.). PMID:35036102
Comparative genomic analysis of expansin superfamily gene members in zucchini and cucumber and their expression profiles under different abiotic stresses. PMID:35035133
De novo transcriptome sequencing of the northern fowl mite, Ornithonyssus sylviarum, shed light on parasitiform poultry mites evolution and its chemoreceptor repertoires. PMID:35032220
TcTI, a Kunitz-type trypsin inhibitor from cocoa associated with defense against pathogens. PMID:35027639
Genome wide analysis of DWARF27 genes in soybean and functional characterization of GmD27c reveals eminent role of strigolactones in rhizobia interaction and nodulation in Glycine max. PMID:35025033
Mitochondrial RNA processing defect caused by a SUPV3L1 mutation in two siblings with a novel neurodegenerative syndrome. PMID:35023579
RAD gene family analysis in cotton provides some key genes for flowering and stress tolerance in upland cotton G. hirsutum. PMID:35012446
Pax-5 Protein Expression Is Regulated by Transcriptional 3'UTR Editing. PMID:35011638
Complete de novo assembly of Wolbachia endosymbiont of Diaphorina citri Kuwayama (Hemiptera: Liviidae) using long-read genome sequencing. PMID:34996906
Early transcriptomic response of the mycoparasite Sphaerodes mycoparasitica to the mycotoxigenic Fusarium graminearum 3-ADON, the cause of Fusarium head blight. PMID:34993050
Optimized splitting of mixed-species RNA sequencing data. PMID:34991436
Horizontally Acquired Cellulases Assist the Expansion of Dietary Range in Pristionchus Nematodes. PMID:34978575
Metabolite and Transcriptome Profiling Analysis Revealed That Melatonin Positively Regulates Floral Scent Production in Hedychium coronarium. PMID:34975998
Genome-Guided Discovery of the First Myxobacterial Biarylitide Myxarylin Reveals Distinct C-N Biaryl Crosslinking in RiPP Biosynthesis. PMID:34946566
Full-Length Transcriptome Sequencing of the Scleractinian Coral Montipora foliosa Reveals the Gene Expression Profile of Coral-Zooxanthellae Holobiont. PMID:34943189
BrCNGC gene family in field mustard: genome-wide identification, characterization, comparative synteny, evolution and expression profiling. PMID:34921218
Lack of transcriptional coordination between mitochondrial and nuclear oxidative phosphorylation genes in the presence of two divergent mitochondrial genomes. PMID:34904419
Genome-Wide Analysis of the Fatty Acid Desaturase Gene Family Reveals the Key Role of PfFAD3 in α-Linolenic Acid Biosynthesis in Perilla Seeds. PMID:34899834
NLR diversity and candidate fusiform rust resistance genes in loblolly pine. PMID:34897455
Tapetal 3-Ketoacyl-Coenzyme A Synthases Are Involved in Pollen Coat Lipid Accumulation for Pollen-Stigma Interaction in Arabidopsis. PMID:34887893
Contrasting Community Assembly Forces Drive Microbial Structural and Potential Functional Responses to Precipitation in an Incipient Soil System. PMID:34887842
PAAR Proteins Are Versatile Clips That Enrich the Antimicrobial Weapon Arsenals of Prokaryotes. PMID:34874775
A Regulatory Network of Heat Shock Modules-Photosynthesis-Redox Systems in Response to Cold Stress Across a Latitudinal Gradient in Bermudagrass. PMID:34868138
Identification of WRKY transcription factors responding to abiotic stresses in Brassica napus L. PMID:34837557
Chloranthus genome provides insights into the early diversification of angiosperms. PMID:34836973
Biochemical Characterization of Recombinant Isocitrate Dehydrogenase and Its Putative Role in the Physiology of an Acidophilic Micrarchaeon. PMID:34835444
In Leishmania major, the Homolog of the Oncogene PES1 May Play a Critical Role in Parasite Infectivity. PMID:34830469
Multi-Omics Analysis of Gene and Protein Candidates Possibly Related to Tetrodotoxin Accumulation in the Skin of Takifugu flavidus. PMID:34822510
Synthetic Biology Advanced Natural Product Discovery. PMID:34822443
Rapidly evolving genetic features for desert adaptations in Stipagrostis pennata. PMID:34814836
Evolutionary history and divergence times of Odonata (dragonflies and damselflies) revealed through transcriptomics. PMID:34805787
Genome-Wide Identification of Wheat ZIP Gene Family and Functional Characterization of the TaZIP13-B in Plants. PMID:34804090
Genome-wide identification and expression analysis of sucrose nonfermenting-1-related protein kinase (SnRK) genes in Triticum aestivum in response to abiotic stress. PMID:34795369
Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing. PMID:34791313
Isolation, phenotypic characterization and comparative genomic analysis of 2019SD1, a polyvalent enterobacteria phage. PMID:34772986
Leaf Apoplast of Field-Grown Potato Analyzed by Quantitative Proteomics and Activity-Based Protein Profiling. PMID:34769464
The SR Splicing Factors: Providing Perspectives on Their Evolution, Expression, Alternative Splicing, and Function in Populus trichocarpa. PMID:34768799
Dissection of full-length transcriptome and metabolome of Dichocarpum (Ranunculaceae): implications in evolution of specialized metabolism of Ranunculales medicinal plants. PMID:34760397
Alternative Splicing Landscape of Small Brown Planthopper and Different Response of JNK2 Isoforms to Rice Stripe Virus Infection. PMID:34757837
An Ebola, Neisseria and Trypanosoma human protein interaction census reveals a conserved human protein cluster targeted by various human pathogens. PMID:34745452
The role of JrLACs in the lignification of walnut endocarp. PMID:34732134
Proteogenomic discovery of sORF-encoded peptides associated with bacterial virulence in Yersinia pestis. PMID:34728737
Plant ecological genomics at the limits of life in the Atacama Desert. PMID:34725254
Genetic and Molecular Analysis of Root Hair Development in Arabis alpina. PMID:34721494
Isolation and Identification of Dengue Virus Interactome with Human Plasma Proteins by Affinity Purification-Mass Spectrometry. PMID:34709640
Structural and Evolutionary Insights Into the Binding of Host Receptors by the Rabies Virus Glycoprotein. PMID:34708003
Genome-Wide Identification of LRR-RLK Family in Saccharum and Expression Analysis in Response to Biotic and Abiotic Stress. PMID:34698114
Convergent adaptation of the genomes of woody plants at the land-sea interface. PMID:34692119
The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley. PMID:34686763
DAKS1, a Kunitz Scaffold Peptide from the Venom Gland of Deinagkistrodon acutus Prevents Carotid-Artery and Middle-Cerebral-Artery Thrombosis via Targeting Factor XIa. PMID:34681191
Genome-Wide Identification of LATERAL ORGAN BOUNDARIES DOMAIN (LBD) Transcription Factors and Screening of Salt Stress Candidates of Rosa rugosa Thunb. PMID:34681091
FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow. PMID:34681040
Convergent Loss of Chemoreceptors across Independent Origins of Slave-Making in Ants. PMID:34668533
High-Quality Genome of the Medicinal Plant Strobilanthes cusia Provides Insights Into the Biosynthesis of Indole Alkaloids. PMID:34659312
Full-Length Transcriptome: A Reliable Alternative for Single-Cell RNA-Seq Analysis in the Spleen of Teleost Without Reference Genome. PMID:34646272
Lipid biomarkers: molecular tools for illuminating the history of microbial life. PMID:34635851
Identification and expression analysis of PUB genes in tea plant exposed to anthracnose pathogen and drought stresses. PMID:34633911
Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris. PMID:34629769
Archaeal community dynamics in biogas fermentation at various temperatures assessed by mcrA amplicon sequencing using different primer pairs. PMID:34611812
Genome-Wide Transcriptional Changes of Rhodosporidium kratochvilovae at Low Temperature. PMID:34603256
A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology. PMID:34599334
A systematic bioinformatics approach for large-scale identification and characterization of host-pathogen shared sequences. PMID:34583643
Full-length transcriptome analysis and identification of transcript structures in Eimeria necatrix from different developmental stages by single-molecule real-time sequencing. PMID:34579769
Genome-Wide Identification and Characterization of the Abiotic-Stress-Responsive GRF Gene Family in Diploid Woodland Strawberry (Fragaria vesca). PMID:34579449
Genome-Wide Analysis of Four Pathotypes of Wheat Rust Pathogen (Puccinia graminis) Reveals Structural Variations and Diversifying Selection. PMID:34575739
Identification of Long Non-Coding RNAs Involved in Porcine Fat Deposition Using Two High-Throughput Sequencing Methods. PMID:34573356
Analyses of open-access multi-omics data sets reveal genetic and expression characteristics of maize ZmCCT family genes. PMID:34567492
Cotton CC-NBS-LRR Gene GbCNL130 Confers Resistance to Verticillium Wilt Across Different Species. PMID:34567025
The Role of Mfsd2a in Nervous System Diseases. PMID:34566571
New Cytoplasmic Virus-Like Elements (VLEs) in the Yeast Debaryomyces hansenii. PMID:34564619
Genome-wide analysis and expression profiles of PdeMYB transcription factors in colored-leaf poplar (Populus deltoids). PMID:34556053
Effect of food source availability in the salivary gland transcriptome of the unique burying beetle Nicrophorus pustulatus (Coleoptera: Silphidae). PMID:34555059
Transcriptome analysis and genetic diversity of Allium victorialis germplasms from the Changbai Mountains. PMID:34553046
Transcriptional profiling reveals changes in gene regulation and signaling transduction pathways during temperature stress in wucai (Brassica campestris L.). PMID:34551703
The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole. PMID:34531387
PacBio Single-Molecule Long-Read Sequencing Provides New Light on the Complexity of Full-Length Transcripts in Cattle. PMID:34527015
Genome-wide analysis of BpDof genes and the tolerance to drought stress in birch (Betula platyphylla). PMID:34513325
More Than Meets the Eye Regarding Cancer Metabolism. PMID:34502416
Genome-Wide Identification and Characterization of Short-Chain Dehydrogenase/Reductase (SDR) Gene Family in Medicago truncatula. PMID:34502406
Up-regulation of apoptotic- and cell survival-related gene pathways following exposures of western corn rootworm to B. thuringiensis crystalline pesticidal proteins in transgenic maize roots. PMID:34479486
A Comparison of Two Monoterpenoid Synthases Reveals Molecular Mechanisms Associated With the Difference of Bioactive Monoterpenoids Between Amomum villosum and Amomum longiligulare. PMID:34475877
Nesterenkonia ebinurensis sp. nov., a Novel Actinobacterium Isolated From Populus euphratica. PMID:34468853
The whole-genome and expression profile analysis of WRKY and RGAs in Dactylis glomerata showed that DG6C02319.1 and DgWRKYs may cooperate in the immunity against rust. PMID:34466285
The parasite Schistocephalus solidus secretes proteins with putative host manipulation functions. PMID:34454597
Isolation and Characterisation of the Bundooravirus Genus and Phylogenetic Investigation of the Salasmaviridae Bacteriophages. PMID:34452423
Insights into the Host Specificity of a New Oomycete Root Pathogen, Pythium brassicum P1: Whole Genome Sequencing and Comparative Analysis Reveals Contracted Regulation of Metabolism, Protein Families, and Distinct Pathogenicity Repertoire. PMID:34445718
Hepatic Proteomic Analysis of Selenoprotein T Knockout Mice by TMT: Implications for the Role of Selenoprotein T in Glucose and Lipid Metabolism. PMID:34445217
Identification and Characterization of the ERF Subfamily B3 Group Revealed GhERF13.12 Improves Salt Tolerance in Upland Cotton. PMID:34434208
Structural and mechanistic basis for protein glutamylation by the kinase fold. PMID:34407442
Proteorhodopsin Phototrophy in Antarctic Coastal Waters. PMID:34406852
Genome-wide analysis of R2R3-MYB transcription factors family in the autopolyploid Saccharum spontaneum: an exploration of dominance expression and stress response. PMID:34404342
Transcriptomic analysis to elucidate the effects of high stocking density on grass carp (Ctenopharyngodon idella). PMID:34399686
Evolution of the Insect PPK Gene Family. PMID:34390578
Genome-wide identification of serine acetyltransferase (SAT) gene family in rice (Oryza sativa) and their expressions under salt stress. PMID:34389920
Genome-wide identification and analysis of the heat shock transcription factor family in moso bamboo (Phyllostachys edulis). PMID:34389742
Global Survey of Alternative Splicing in Rice by Direct RNA Sequencing During Reproductive Development: Landscape and Genetic Regulation. PMID:34383135
PHROG: families of prokaryotic virus proteins clustered using remote homology. PMID:34377978
Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities. PMID:34376140
High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement. PMID:34373642
A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense. PMID:34367224
JA signal-mediated immunity of Dendrobium catenatum to necrotrophic Southern Blight pathogen. PMID:34362300
FLAME: A Web Tool for Functional and Literature Enrichment Analysis of Multiple Gene Lists. PMID:34356520
Genome Mining and Comparative Genome Analysis Revealed Niche-Specific Genome Expansion in Antibacterial Bacillus pumilus Strain SF-4. PMID:34356076
Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom. PMID:34341414
Genome-Wide Identification of the Early Flowering 4 (ELF4) Gene Family in Cotton and Silent GhELF4-1 and GhEFL3-6 Decreased Cotton Stress Resistance. PMID:34326861
Comparative transcriptome analysis reveals regulatory network and regulators associated with proanthocyanidin accumulation in persimmon. PMID:34325657
RNA polymerases in strict endosymbiont bacteria with extreme genome reduction show distinct erosions that might result in limited and differential promoter recognition. PMID:34324516
Genome Size Estimation and Full-Length Transcriptome of Sphingonotus tsinlingensis: Genetic Background of a Drought-Adapted Grasshopper. PMID:34322153
Genome-Wide Patterns of Bracovirus Chromosomal Integration into Multiple Host Tissues during Parasitism. PMID:34319152
Deciphering Symbiotic Interactions of "Candidatus Aenigmarchaeota" with Inferred Horizontal Gene Transfers and Co-occurrence Networks. PMID:34313464
Comprehensive analysis of formin gene family highlights candidate genes related to pollen cytoskeleton and male fertility in wheat (Triticum aestivum L.). PMID:34303338
Genome-wide survey and expression analysis of NIN-like Protein (NLP) genes reveals its potential roles in the response to nitrate signaling in tomato. PMID:34301191
Mutational Analysis of Redβ Single Strand Annealing Protein: Roles of the 14 Lysine Residues in DNA Binding and Recombination In Vivo. PMID:34299376
Genome-Wide Identification and Expression Analysis of Tomato ADK Gene Family during Development and Stress. PMID:34299327
Machine learning for enzyme engineering, selection and design. PMID:34296736
Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest. PMID:34295368
Comparative Genomics Reveals Thermal Adaptation and a High Metabolic Diversity in "Candidatus Bathyarchaeia". PMID:34282939
Full-length transcriptome assembly of andrias davidianus (amphibia: caudata) skin via hybrid sequencing. PMID:34282833
High-Quality Genome Assembly and Comprehensive Transcriptome of the Painted Lady Butterfly Vanessa cardui. PMID:34282459
Statistical approaches for differential expression analysis in metatranscriptomics. PMID:34252963
DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction. PMID:34252926
Whole Transcriptome Analysis Reveals a Potential Regulatory Mechanism of LncRNA-FNIP2/miR-24-3p/FNIP2 Axis in Chicken Adipogenesis. PMID:34249911
A Eukaryote-Wide Perspective on the Diversity and Evolution of the ARF GTPase Protein Family. PMID:34247240
DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data. PMID:34241589
Analysis of lncRNA, miRNA, and mRNA Expression Profiling in Type I IFN and Type II IFN Overexpressed in Porcine Alveolar Macrophages. PMID:34222462
Genome-wide profiling of long noncoding RNAs involved in wheat spike development. PMID:34210256
Evolution of Terpene Synthases in Orchidaceae. PMID:34203299
EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains. PMID:34196123
Genome-wide identification and expression analysis of LBD transcription factor genes in Moso bamboo (Phyllostachys edulis). PMID:34182934
The Genomic Impact of Mycoheterotrophy in Orchids. PMID:34177974
Putative Causal Variant on Vlgr1 for the Epileptic Phenotype in the Model Wistar Audiogenic Rat. PMID:34177758
Genome-wide identification of auxin response factor (ARF) family in kiwifruit (Actinidia chinensis) and analysis of their inducible involvements in abiotic stresses. PMID:34177147
Morphological changes and functional circRNAs screening of rabbit skeletal muscle development. PMID:34167469
Identification of Isoflavonoid Biosynthesis-Related R2R3-MYB Transcription Factors in Callerya speciosa (Champ. ex Benth.) Schot Using Transcriptome-Based Gene Coexpression Analysis. PMID:34136563
Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. PMID:34135888
Biosynthesis of a sulfated exopolysaccharide, synechan, and bloom formation in the model cyanobacterium Synechocystis sp. strain PCC 6803. PMID:34127188
Genome-Wide Identification and Bioinformatics Characterization of Superoxide Dismutases in the Desiccation-Tolerant Cyanobacterium Chroococcidiopsis sp. CCMEE 029. PMID:34122375
Genome-wide characterization, evolution, and expression profiling of FBA gene family in response to light treatments and abiotic stress in Nicotiana tabacum. PMID:34120568
Comprehensive identification and expression analysis of B-Box genes in cotton. PMID:34118883
Structural and functional characterization of a plant alpha-actinin. PMID:34110107
Genomic insights into body size evolution in Carnivora support Peto's paradox. PMID:34107880
Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara). PMID:34103003
G protein-coupled receptors as candidates for modulation and activation of the chemical senses in decapod crustaceans. PMID:34086685
Genome-Wide Identification of Tannase Genes and Their Function of Wound Response and Astringent Substances Accumulation in Juglandaceae. PMID:34079571
A proximity-dependent biotinylation map of a human cell. PMID:34079125
Genome-Wide Identification of PRP Genes in Apple Genome and the Role of MdPRP6 in Response to Heat Stress. PMID:34073055
A Novel DUF569 Gene Is a Positive Regulator of the Drought Stress Response in Arabidopsis. PMID:34070080
Comprehensive Transcriptome Analysis of Rare Carpinus putoensis Plants under NO2 stress. PMID:34067657
Integrated Signals of Jasmonates, Sugars, Cytokinins and Auxin Influence the Initial Growth of the Second Buds of Chrysanthemum after Decapitation. PMID:34065759
Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans. PMID:34061031
Transcriptional Regulation of Plant Biomass Degradation and Carbohydrate Utilization Genes in the Extreme Thermophile Caldicellulosiruptor bescii. PMID:34060910
Distinct microbial community along the chronic oil pollution continuum of the Persian Gulf converge with oil spill accidents. PMID:34059729
Distribution and Classification of Dehydrins in Selected Plant Species Using Bioinformatics Approach. PMID:34056027
A phylogenetic approach for weighting genetic sequences. PMID:34049487
Assessing the functional relevance of splice isoforms. PMID:34046593
FGF signalling plays similar roles in development and regeneration of the skeleton in the brittle star Amphiura filiformis. PMID:34042967
A human respiratory tract-associated bacterium with an extremely small genome. PMID:34040152
Genome-wide identification of the tea plant bHLH transcription factor family and discovery of candidate regulators of trichome formation. PMID:34031482
Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes. PMID:34018328
Analysis of diverse eukaryotes suggests the existence of an ancestral mitochondrial apparatus derived from the bacterial type II secretion system. PMID:34011950
Sesbanimide R, a Novel Cytotoxic Polyketide Produced by Magnetotactic Bacteria. PMID:34006654
DOE JGI Metagenome Workflow. PMID:34006627
Structure and biosynthesis of sorangipyranone - a new γ-dihydropyrone from the myxobacterial strain MSr12020. PMID:34003283
Identification of a PadR-type regulator essential for intracellular pathogenesis of Burkholderia pseudomallei. PMID:34001967
Whole genome sequencing of a snailfish from the Yap Trench (~7,000 m) clarifies the molecular mechanisms underlying adaptation to the deep sea. PMID:33983934
Comparative genomics and analysis of the mechanism of PQQ overproduction in Methylobacterium. PMID:33983497
The tepary bean genome provides insight into evolution and domestication under heat stress. PMID:33976152
Disentangling the aging gene expression network of termite queens. PMID:33975542
Myeloid lncRNA LOUP mediates opposing regulatory effects of RUNX1 and RUNX1-ETO in t(8;21) AML. PMID:33971010
Comparison and Functional Analysis of Chemosensory Protein Genes From Eucryptorrhynchus scrobiculatus Motschulsky and Eucryptorrhynchus brandti Harold. PMID:33959040
Sporulation is dispensable for the vegetable-associated life cycle of the human pathogen Bacillus cereus. PMID:33955675
Everything Is Everywhere: Physiological Responses of the Mediterranean Sea and Eastern Pacific Ocean Epiphyte Cobetia Sp. to Varying Nutrient Concentration. PMID:33954842
Molecular evidence of the avocado defense response to Fusarium kuroshium infection: a deep transcriptome analysis using RNA-Seq. PMID:33954045
Evolutionary history of the mediterranean Pinus halepensis-brutia species complex using gene-resequencing and transcriptomic approaches. PMID:33934278
Correlation of Key Physiological Properties of Methanosarcina Isolates with Environment of Origin. PMID:33931421
In Silico Analysis of the Molecular-Level Impact of SMPD1 Variants on Niemann-Pick Disease Severity. PMID:33925997
Isolation and Characterization of Strain Exiguobacterium sp. KRL4, a Producer of Bioactive Secondary Metabolites from a Tibetan Glacier. PMID:33919419
Genome-Wide Identification, Comparison, and Expression Analysis of Transcription Factors in Ascidian Styela clava. PMID:33919240
Regulatory role of non-coding RNA in ginseng rusty root symptom tissue. PMID:33911151
Pathogenic missense protein variants affect different functional pathways and proteomic features than healthy population variants. PMID:33909605
Anaerobic gut fungi are an untapped reservoir of natural products. PMID:33906945
Characterization of the ERP gene family in Arabidopsis thaliana. PMID:33906568
Genome sequence analysis of the beneficial Bacillus subtilis PTA-271 isolated from a Vitis vinifera (cv. Chardonnay) rhizospheric soil: assets for sustainable biocontrol. PMID:33902737
Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences. PMID:33902725
A long-term field experiment demonstrates the influence of tillage on the bacterial potential to produce soil structure-stabilizing agents such as exopolysaccharides and lipopolysaccharides. PMID:33902712
Biodiversity-based development and evolution: the emerging research systems in model and non-model organisms. PMID:33893979
PacBio Single-Molecule Long-Read Sequencing Reveals Genes Tolerating Manganese Stress in Schima superba Saplings. PMID:33889177
Isolation and genomic characterization of five novel strains of Erysipelotrichaceae from commercial pigs. PMID:33888068
Comprehensive analysis and identification of drought-responsive candidate NAC genes in three semi-arid tropics (SAT) legume crops. PMID:33882825
Use of RNA Sequencing to Perform Comprehensive Analysis of Long Noncoding RNA Expression Profiles in Macrophages Infected with Trichosporon asahii. PMID:33877524
Spatially interacting phosphorylation sites and mutations in cancer. PMID:33875650
Three PilZ Domain Proteins, PlpA, PixA, and PixB, Have Distinct Functions in Regulation of Motility and Development in Myxococcus xanthus. PMID:33875546
Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa. PMID:33874907
Predictive Models of Genetic Redundancy in Arabidopsis thaliana. PMID:33871641
Multi-omics analysis provides insights into lignocellulosic biomass degradation by Laetiporus sulphureus ATCC 52600. PMID:33865436
Lnc-HZ08 regulates BPDE-induced trophoblast cell dysfunctions by promoting PI3K ubiquitin degradation and is associated with miscarriage. PMID:33864160
Genome-wide identification and expression pattern of SnRK gene family under several hormone treatments and its role in floral scent emission in Hedychium coronarium. PMID:33854831
Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium. PMID:33849527
Origin and evolution of nonulosonic acid synthases and their relationship with bacterial pathogenicity revealed by a large-scale phylogenetic analysis. PMID:33848237
A multilayered cross-species analysis of GRAS transcription factors uncovered their functional networks in plant adaptation to the environment. PMID:33842016
A review on compound-protein interaction prediction methods: Data, format, representation and model. PMID:33841755
Balancing selection maintains hyper-divergent haplotypes in Caenorhabditis elegans. PMID:33820969
Functional divergence and adaptive selection of KNOX gene family in plants. PMID:33817223
Characterization of Haemophilus Parasuis Serovar 2 CL120103, a Moderately Virulent Strain in China. PMID:33817086
A Comparison of Differential Gene Expression in Response to the Onset of Water Stress Between Three Hybrid Brachiaria Genotypes. PMID:33815444
Phylogenomics of Plant-Associated Botryosphaeriaceae Species. PMID:33815343
Single-Molecule Long-Read Sequencing of Purslane (Portulaca oleracea) and Differential Gene Expression Related with Biosynthesis of Unsaturated Fatty Acids. PMID:33808162
Population-Predicted MHC Class II Epitope Presentation of SARS-CoV-2 Structural Proteins Correlates to the Case Fatality Rates of COVID-19 in Different Countries. PMID:33807854
Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in Rhododendronsimsii (Ericaceae). PMID:33805478
Genome Analysis of Endotrypanum and Porcisia spp., Closest Phylogenetic Relatives of Leishmania, Highlights the Role of Amastins in Shaping Pathogenicity. PMID:33804709
Genome-Wide Identification and Characterization of Long Noncoding RNAs Involved in Chinese Wheat Mosaic Virus Infection of Nicotiana benthamiana. PMID:33802832
Full-Length Transcriptome Sequencing Provides Insights into Flavonoid Biosynthesis in Fritillaria hupehensis. PMID:33800612
Soil Biogeochemical Cycle Couplings Inferred from a Function-Taxon Network. PMID:33796862
LmjF.36.3850, a novel hypothetical Leishmania major protein, contributes to the infection. PMID:33764520
Genome-wide identification of HSF family in peach and functional analysis of PpHSF5 involvement in root and aerial organ development. PMID:33763299
Genome-wide identification of GMP genes in Rosaceae and functional characterization of FaGMP4 in strawberry (Fragaria × ananassa). PMID:33755919
Characterization of cotton ARF factors and the role of GhARF2b in fiber development. PMID:33752589
The Transcriptomic and Bioinformatic Characterizations of Iron Acquisition and Heme Utilization in Avibacterium paragallinarum in Response to Iron-Starvation. PMID:33746913
Comparative transcriptomic analysis of the different developmental stages of ovary in red swamp crayfish Procambarus clarkii. PMID:33745451
In-silico structural analysis of Pseudomonas syringae effector HopZ3 reveals ligand binding activity and virulence function. PMID:33730245
Comparative transcriptome analysis of the newly discovered insect vector of the pine wood nematode in China, revealing putative genes related to host plant adaptation. PMID:33726671
The Major Intrinsic Protein Family and Their Function Under Salt-Stress in Peanut. PMID:33719349
Genome-wide identification and expression profiling of basic leucine zipper transcription factors following abiotic stresses in potato (Solanum tuberosum L.). PMID:33711039
Full-Length Transcriptome Analysis of Plasmodium falciparum by Single-Molecule Long-Read Sequencing. PMID:33708645
Divergent CPEB prion-like domains reveal different assembly mechanisms for a generic amyloid-like fold. PMID:33706787
Characterization of a pericentric inversion in plateau fence lizards (Sceloporus tristichus): evidence from chromosome-scale genomes. PMID:33693605
Adaptation and convergence in circadian-related genes in Iberian freshwater fish. PMID:33685402
The Mitragyna speciosa (Kratom) Genome: a resource for data-mining potent pharmaceuticals that impact human health. PMID:33677570
Comparative Analysis, Characterization and Evolutionary Study of Dirigent Gene Family in Cucurbitaceae and Expression of Novel Dirigent Peptide against Powdery Mildew Stress. PMID:33668231
Characterization of the GRAS gene family reveals their contribution to the high adaptability of wheat. PMID:33665016
Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome. PMID:33664286
Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA. PMID:33660784
Disruption of exon-bridging interactions between the minor and major spliceosomes results in alternative splicing around minor introns. PMID:33660780
Mining oomycete proteomes for metalloproteases leads to identification of candidate virulence factors in Phytophthora infestans. PMID:33657266
Structural and Functional Characterization of the ABA-Water Deficit Stress Domain from Wheat and Barley: An Intrinsically Disordered Domain behind the Versatile Functions of the Plant Abscissic Acid, Stress and Ripening Protein Family. PMID:33652546
RhoGAP19D inhibits Cdc42 laterally to control epithelial cell shape and prevent invasion. PMID:33646271
DbStRiPs: Database of structural repeats in proteins. PMID:33641184
Mitonuclear Coevolution, but not Nuclear Compensation, Drives Evolution of OXPHOS Complexes in Bivalves. PMID:33616640
Genome-Wide Integrated Analysis Revealed Functions of lncRNA-miRNA-mRNA Interaction in Growth of Intermuscular Bones in Megalobrama amblycephala. PMID:33614620
IAPs Gene Expansion in the Scallop Patinopecten yessoensis and Their Expression Profiles After Exposure to the Toxic Dinoflagellate. PMID:33613325
Molecular basis of tail-anchored integral membrane protein recognition by the cochaperone Sgt2. PMID:33610544
Two PAAR Proteins with Different C-Terminal Extended Domains Have Distinct Ecological Functions in Myxococcus xanthus. PMID:33608292
DTI-SNNFRA: Drug-target interaction prediction by shared nearest neighbors and fuzzy-rough approximation. PMID:33606741
Taxonomic, functional and expression analysis of viral communities associated with marine sponges. PMID:33604175
PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data. PMID:33597026
Rapid molecular evolution of Spiroplasma symbionts of Drosophila. PMID:33591248
Transcriptome and Secretome Analysis of Intra-Mammalian Life-Stages of Calicophoron daubneyi Reveals Adaptation to a Unique Host Environment. PMID:33581320
Family-specific analysis of variant pathogenicity prediction tools. PMID:33575576
Phenotypic Characterization and Whole-Genome Analysis of a Novel Bacteriophage HCF1 Infecting Citrobacter amalonaticus and C. freundii. PMID:33569047
Novel lnc-HZ03 and miR-hz03 promote BPDE-induced human trophoblastic cell apoptosis and induce miscarriage by upregulating p53/SAT1 pathway. PMID:33566220
Pangenome analysis reveals genetic isolation in Campylobacter hyointestinalis subspecies adapted to different mammalian hosts. PMID:33564053
A telomere-to-telomere assembly of Oscheius tipulae and the evolution of rhabditid nematode chromosomes. PMID:33561231
Comparative mRNA and LncRNA Analysis of the Molecular Mechanisms Associated With Low Silk Production in Bombyx mori. PMID:33552120
"The Good, the Bad and the Double-Sword" Effects of Microplastics and Their Organic Additives in Marine Bacteria. PMID:33552008
The in-silico characterization of the Caenorhabditis elegans matrisome and proposal of a novel collagen classification. PMID:33543001
Intrinsic disorder in protein domains contributes to both organism complexity and clade-specific functions. PMID:33542394
Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential. PMID:33541265
Transcriptomic Analysis of the Anthocyanin Biosynthetic Pathway Reveals the Molecular Mechanism Associated with Purple Color Formation in Dendrobium Nestor. PMID:33540822
Genome annotation of disease-causing microorganisms. PMID:33537706
The Genomes of Two Billfishes Provide Insights into the Evolution of Endothermy in Teleosts. PMID:33533895
The Origin and Evolution of Antistasin-like Proteins in Leeches (Hirudinida, Clitellata). PMID:33527140
Surface chemistry-mediated modulation of adsorbed albumin folding state specifies nanocarrier clearance by distinct macrophage subsets. PMID:33510170
Discovery of divided RdRp sequences and a hitherto unknown genomic complexity in fungal viruses. PMID:33505709
SUMO is a pervasive regulator of meiosis. PMID:33502312
Complete mitochondrial genome of the freshwater red alga Lympha mucosa (Rhodophyta). PMID:33490473
Pearl Sac Gene Expression Profiles Associated With Pearl Attributes in the Silver-Lip Pearl Oyster, Pinctada maxima. PMID:33488672
New amino acid substitution matrix brings sequence alignments into agreement with structure matches. PMID:33469973
Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates. PMID:33467086
Full-Length Transcriptome Analysis of Four Different Tissues of Cephalotaxus oliveri. PMID:33466772
Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts. PMID:33466489
InsectOR-Webserver for sensitive identification of insect olfactory receptor genes from non-model genomes. PMID:33465132
Characterization of CHARK, an unusual cytokinin receptor of rice. PMID:33462253
A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense. PMID:33459341
PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response. PMID:33446096
Large-scale survey and database of high affinity ligands for peptide recognition modules. PMID:33438817
Bioinformatic mapping of a more precise Aspergillus niger degradome. PMID:33436802
Integration of full-length transcriptomics and targeted metabolomics to identify benzylisoquinoline alkaloid biosynthetic genes in Corydalis yanhusuo. PMID:33423040
Machine learning based CRISPR gRNA design for therapeutic exon skipping. PMID:33417623
The iPPI-DB initiative: A Community-centered database of Protein-Protein Interaction modulators. PMID:33416858
The role of JrPPOs in the browning of walnut explants. PMID:33407138
Alignment-free method for functional annotation of amino acid substitutions: Application on epigenetic factors involved in hematologic malignancies. PMID:33395407
Origin and evolution of a gibberellin-deactivating enzyme GAMT. PMID:33376939
Genotype and transcriptome effects on somatic embryogenesis in Cryptomeria japonica. PMID:33373415
A New Phage Lysin Isolated from the Oral Microbiome Targeting Streptococcus pneumoniae. PMID:33352708
Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. PMID:33335035
A dynamic, ring-forming MucB / RseB-like protein influences spore shape in Bacillus subtilis. PMID:33315869
Identification of type VI secretion system toxic effectors using adaptors as markers. PMID:33304467
The PacBio Full-Length Transcriptome of the Tea Aphid as a Reference Resource. PMID:33304379
Alteration in the Culex pipiens transcriptome reveals diverse mechanisms of the mosquito immune system implicated upon Rift Valley fever phlebovirus exposure. PMID:33301456
Symbiotic and Nonsymbiotic Members of the Genus Ensifer (syn. Sinorhizobium) Are Separated into Two Clades Based on Comparative Genomics and High-Throughput Phenotyping. PMID:33283865
Non-adaptive Evolution of Trimeric Autotransporters in Brucellaceae. PMID:33281759
Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in Brassica napus. PMID:33276730
Occurrence of Ordered and Disordered Structural Elements in Postsynaptic Proteins Supports Optimization for Interaction Diversity. PMID:33267475
The Phosphoglycerate Kinase (PGK) Gene Family of Maize (Zea mays var. B73). PMID:33255472
Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences. PMID:33247171
Identification of L-asparaginases from Streptomyces strains with competitive activity and immunogenic profiles: a bioinformatic approach. PMID:33240625
Integrated analysis of lncRNA and mRNA reveals novel insights into cashmere fineness in Tibetan cashmere goats. PMID:33240606
Evolution of Biomineralization Genes in the Prismatic Layer of the Pen Shell Atrina pectinata. PMID:33236260
Repositioned Drugs for Chagas Disease Unveiled via Structure-Based Drug Repositioning. PMID:33233837
Identification of Anthocyanins-Related Glutathione S-Transferase (GST) Genes in the Genome of Cultivated Strawberry (Fragaria × ananassa). PMID:33218073
Mycobacterial STAND adenylyl cyclases: The HTH domain binds DNA to form biocrystallized nucleoids. PMID:33217386
GPCR-PEnDB: a database of protein sequences and derived features to facilitate prediction and classification of G protein-coupled receptors. PMID:33216895
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
Identification of scavenger receptors and thrombospondin-type-1 repeat proteins potentially relevant for plastid recognition in Sacoglossa. PMID:33209293
Characterization of MSlys, the endolysin of Streptococcus pneumoniae phage MS1. PMID:33204659
The Role of Brachypodium distachyon Wall-Associated Kinases (WAKs) in Cell Expansion and Stress Responses. PMID:33202612
Transcriptome-wide identification of MAPKKK genes in bermudagrass (Cynodon dactylon L.) and their potential roles in low temperature stress responses. PMID:33194398
The Cyclically Seasonal Drosophila subobscura Inversion O7 Originated From Fragile Genomic Sites and Relocated Immunity and Metabolic Genes. PMID:33193649
Inhibition of DNA Methylation in Picochlorum soloecismus Alters Algae Productivity. PMID:33193644
Full Transcriptome Analysis of Callus Suspension Culture System of Bletilla striata. PMID:33193583
Comprehensive Genome-Wide Analysis of Thaumatin-Like Gene Family in Four Cotton Species and Functional Identification of GhTLP19 Involved in Regulating Tolerance to Verticillium dahlia and Drought. PMID:33193513
Whole-Genome Transcriptome Analyses of Native Symbionts Reveal Host Coral Genomic Novelties for Establishing Coral-Algae Symbioses. PMID:33185681
Identification of Growth Inhibitors of the Fish Pathogen Saprolegnia parasitica Using in silico Subtractive Proteomics, Computational Modeling, and Biochemical Validation. PMID:33178154
Genome-wide identification, and phylogenetic and expression profiling analyses, of XTH gene families in Brassica rapa L. and Brassica oleracea L. PMID:33176678
Genome-Wide Analysis of Biosynthetic Gene Cluster Reveals Correlated Gene Loss with Absence of Usnic Acid in Lichen-Forming Fungi. PMID:33151307
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. PMID:33147627
Global mRNA and microRNA expression dynamics in response to anthracnose infection in sorghum. PMID:33143636
Cycling in degradation of organic polymers and uptake of nutrients by a litter-degrading fungus. PMID:33140552
Warming Climate Is Reducing the Diversity of Dominant Microbes in the Largest High Arctic Lake. PMID:33133035
Evolution of the Brassicaceae-specific MS5-Like family and neofunctionalization of the novel MALE STERILITY 5 gene essential for male fertility in Brassica napus. PMID:33128826
Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter. PMID:33126925
Pfam: The protein families database in 2021. PMID:33125078
Transcription termination and antitermination of bacterial CRISPR arrays. PMID:33124980
Phylogenetic and ion-response analyses reveal a relationship between gene expansion and functional divergence in the Ca2+/cation antiporter family in Angiosperms. PMID:33123851
Timing the origin of eukaryotic cellular complexity with ancient duplications. PMID:33106602
Genome-Wide Characterization and Expression of Two-Component System Genes in Cytokinin-Regulated Gall Formation in Zizania latifolia. PMID:33105697
Genome- and Transcriptome-Wide Identification of C3Hs in Common Bean (Phaseolus vulgaris L.) and Structural and Expression-Based Analyses of Their Functions During the Sprout Stage Under Salt-Stress Conditions. PMID:33101386
Long non-coding RNAs in plants: emerging modulators of gene activity in development and stress responses. PMID:33099688
Formation and diversification of a paradigm biosynthetic gene cluster in plants. PMID:33097700
Structural bioinformatics predicts that the Retinitis Pigmentosa-28 protein of unknown function FAM161A is a homologue of the microtubule nucleation factor Tpx2. PMID:33093951
Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition. PMID:33077930
mMGE: a database for human metagenomic extrachromosomal mobile genetic elements. PMID:33074335
Amino acid synthesis loss in parasitoid wasps and other hymenopterans. PMID:33074103
Alternative Splicing Enhances the Transcriptome Complexity of Liriodendron chinense. PMID:33072153
Funneled energy landscape unifies principles of protein binding and evolution. PMID:33067388
A Need for Improved Cellulase Identification from Metagenomic Sequence Data. PMID:33067195
Comparative Transcriptome Analysis of Two Root-Feeding Grape Phylloxera (D. vitifoliae) Lineages Feeding on a Rootstock and V. vinifera. PMID:33053741
The mechanism of potato resistance to Globodera rostochiensis: comparison of root transcriptomes of resistant and susceptible Solanum phureja genotypes. PMID:33050888
New Environment, New Invaders-Repeated Horizontal Transfer of LINEs to Sea Snakes. PMID:33022046
Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode. PMID:33020495
Overexpression of GmUBC9 Gene Enhances Plant Drought Resistance and Affects Flowering Time via Histone H2B Monoubiquitination. PMID:33013972
Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae. PMID:33013721
A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae. PMID:33009392
A Functional K+ Channel from Tetraselmis Virus 1, a Member of the Mimiviridae. PMID:33003637
High-quality nuclear genome for Sarcoptes scabiei-A critical resource for a neglected parasite. PMID:33001992
Glucosylation prevents plant defense activation in phloem-feeding insects. PMID:32989301
Polyphyletic origin, intracellular invasion, and meiotic genes in the putatively asexual agamococcidians (Apicomplexa incertae sedis). PMID:32985520
A chromosome-scale reference genome of trifoliate orange (Poncirus trifoliata) provides insights into disease resistance, cold tolerance and genome evolution in Citrus. PMID:32985030
The Cardiac Syndecan-2 Interactome. PMID:32984315
Characteristics and Expression Analyses of Trehalose-6-Phosphate Synthase Family in Prunus mume Reveal Genes Involved in Trehalose Biosynthesis and Drought Response. PMID:32977584
Genome-Wide Network of lncRNA-mRNA During Ovine Oocyte Development From Germinal Vesicle to Metaphase II in vitro. PMID:32973554
Design principles of gene evolution for niche adaptation through changes in protein-protein interaction networks. PMID:32973219
Single cell transcriptomes reveal expression patterns of chemoreceptor genes in olfactory sensory neurons of the Caribbean spiny lobster, Panulirus argus. PMID:32962631
Genome-Wide Identification of the PHD-Finger Family Genes and Their Responses to Environmental Stresses in Oryza sativa L. PMID:32961651
Protein Databases Related to Liquid-Liquid Phase Separation. PMID:32947964
Systematic analysis of bypass suppression of essential genes. PMID:32939983
Diversity of Conopeptides and Their Precursor Genes of Conus Litteratus. PMID:32937857
New developments in RiPP discovery, enzymology and engineering. PMID:32935693
Complex Evolution of Light-Dependent Protochlorophyllide Oxidoreductases in Aerobic Anoxygenic Phototrophs: Origin, Phylogeny, and Function. PMID:32931580
The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during development and in response to gray mold infection. PMID:32928117
The ranging of amino acids substitution matrices of various types in accordance with the alignment accuracy criterion. PMID:32921315
Single-molecule real-time sequencing of the full-length transcriptome of loquat under low-temperature stress. PMID:32915882
Increased resolution of African swine fever virus genome patterns based on profile HMMs of protein domains. PMID:32913663
Evolution of isoprenyl diphosphate synthase-like terpene synthases in fungi. PMID:32913319
Parallel analysis of miRNAs and mRNAs suggests distinct regulatory networks in Crassostrea gigas infected by Ostreid herpesvirus 1. PMID:32912133
Characterizing Phage-Host Interactions in a Simplified Human Intestinal Barrier Model. PMID:32906839
A Reference Genome from the Symbiotic Hydrozoan, Hydra viridissima. PMID:32900905
Exploring the Remarkable Diversity of Culturable Escherichia coli Phages in the Danish Wastewater Environment. PMID:32899836
Generation of a chromosome-scale genome assembly of the insect-repellent terpenoid-producing Lamiaceae species, Callicarpa americana. PMID:32893861
Telomere-to-telomere assembled and centromere annotated genomes of the two main subspecies of the button mushroom Agaricus bisporus reveal especially polymorphic chromosome ends. PMID:32887908
Genome-Wide Identification and Characterization of Lectin Receptor-Like Kinase Gene Family in Cucumber and Expression Profiling Analysis under Different Treatments. PMID:32887423
An Unexpectedly Complex Mitoribosome in Andalucia godoyi, a Protist with the Most Bacteria-like Mitochondrial Genome. PMID:32886790
A tree frog (Boana pugnax) dataset of skin transcriptome for the identification of biomolecules with potential antimicrobial activities. PMID:32875010
Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C. PMID:32873785
RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery. PMID:32873609
Growth retardation-responsive analysis of mRNAs and long noncoding RNAs in the liver tissue of Leiqiong cattle. PMID:32868811
Wheat Disease Resistance Genes and Their Diversification Through Integrated Domain Fusions. PMID:32849852
Transcriptome Dynamics of the Inflorescence in Reciprocally Formed Allopolyploid Tragopogon miscellus (Asteraceae). PMID:32849847
Differently Expression Analysis and Function Prediction of Long Non-coding RNAs in Duck Embryo Fibroblast Cells Infected by Duck Tembusu Virus. PMID:32849615
Mutant POLQ and POLZ/REV3L DNA polymerases may contribute to the favorable survival of patients with tumors with POLE mutations outside the exonuclease domain. PMID:32838755
Third-generation sequencing found LncRNA associated with heat shock protein response to heat stress in Populus qiongdaoensis seedlings. PMID:32831021
Genome-wide characterization of the GRF family and their roles in response to salt stress in Gossypium. PMID:32831017
Comparison of Poly-A+ Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq. PMID:32825772
The sugar transporter system of strawberry: genome-wide identification and expression correlation with fruit soluble sugar-related traits in a Fragaria × ananassa germplasm collection. PMID:32793356
Genome-wide identification and characterization of bHLH family genes from Ginkgo biloba. PMID:32792673
JAGN1, tetraspanins, and Erv proteins: is common topology indicative of common function in cargo sorting? PMID:32783652
Characterization of the Exopolysaccharide Biosynthesis Pathway in Myxococcus xanthus. PMID:32778557
Functional Insight of Nitric-Oxide Induced DUF Genes in Arabidopsis thaliana. PMID:32765550
Genome-wide identification and characterization of DCL, AGO and RDR gene families in Saccharum spontaneum. PMID:32764599
FLUTE: Fast and reliable knowledge retrieval from biomedical literature. PMID:32761077
Comprehensive Network Analysis Reveals Alternative Splicing-Related lncRNAs in Hepatocellular Carcinoma. PMID:32760422
Evolution of pogo, a separate superfamily of IS630-Tc1-mariner transposons, revealing recurrent domestication events in vertebrates. PMID:32742312
lncRNA_Mdeep: An Alignment-Free Predictor for Distinguishing Long Non-Coding RNAs from Protein-Coding Transcripts by Multimodal Deep Learning. PMID:32718000
Genome-Wide Characterization and Expression Analysis of NHX Gene Family under Salinity Stress in Gossypium barbadense and Its Comparison with Gossypium hirsutum. PMID:32708576
Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases. PMID:32707033
Amino acid sequence associated with bacteriophage recombination site helps to reveal genes potentially acquired through horizontal gene transfer. PMID:32703190
Discovery and engineering of colchicine alkaloid biosynthesis. PMID:32699417
The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest. PMID:32698880
An Easy Protocol for Evolutionary Analysis of Intrinsically Disordered Proteins. PMID:32696356
A comprehensive survey of integron-associated genes present in metagenomes. PMID:32689930
Simplification of Ribosomes in Bacteria with Tiny Genomes. PMID:32681797
A Study to Assess the Role of Gluten Encoded Genes and Their Regulatory Elements in Bread Making Quality of Wheat. PMID:32671123
Genome-Wide Identification and Functional Characterization of β-Agarases in Vibrio astriarenae Strain HN897. PMID:32670245
Transcriptomic Analysis of Extracellular RNA Governed by the Endocytic Adaptor Protein Cin1 of Cryptococcus deneoformans. PMID:32656093
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. PMID:32652120
Biological rhythms in the deep-sea hydrothermal mussel Bathymodiolus azoricus. PMID:32651383
Genome assembly of Chiococca alba uncovers key enzymes involved in the biosynthesis of unusual terpenoids. PMID:32642754
Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies in Gossypium arboreum. PMID:32640982
Type III Secretion 1 Effector Gene Diversity Among Vibrio Isolates From Coastal Areas in China. PMID:32637366
Architecture and functional dynamics of the pentafunctional AROM complex. PMID:32632294
Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity. PMID:32631445
RNA-Seq of three free-living flatworm species suggests rapid evolution of reproduction-related genes. PMID:32631219
Computational identification of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes. PMID:32620079
Interaction mapping of endoplasmic reticulum ubiquitin ligases identifies modulators of innate immune signalling. PMID:32614325
Glutantβase: a database for improving the rational design of glucose-tolerant β-glucosidases. PMID:32611314
Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family Methanoperedenaceae. PMID:32605988
Comparative analysis of full-length transcriptomes based on hybrid population reveals regulatory mechanisms of anthocyanin biosynthesis in sweet potato (Ipomoea batatas (L.) Lam). PMID:32600332
Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12). PMID:32600330
Evolutionary History of the Globin Gene Family in Annelids. PMID:32597988
Isoform Sequencing Provides Insight Into Freezing Response of Common Wheat (Triticum aestivum L.). PMID:32595694
Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence. PMID:32589737
Genome-wide characterization and expression analyses of the auxin/indole-3-acetic acid (Aux/IAA) gene family in barley (Hordeum vulgare L.). PMID:32581321
A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes. PMID:32576248
Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus. PMID:32575906
Genome-wide identification and characterization of SnRK family genes in Brassica napus. PMID:32571241
Genome-wide identification and expression analysis of the Dof gene family under drought stress in tea (Camellia sinensis). PMID:32566398
Advances in actinomycete research: an ActinoBase review of 2019. PMID:32558638
Survey for positively selected coding regions in the genome of the hematophagous tsetse fly Glossina morsitans identifies candidate genes associated with feeding habits and embryonic development. PMID:32555940
Metabolomics as an Emerging Tool in the Search for Astrobiologically Relevant Biomarkers. PMID:32551936
SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera. PMID:32551204
Genome-wide sequence identification and expression analysis of ARF family in sugar beet (Beta vulgaris L.) under salinity stresses. PMID:32547857
Genomic Survey of Tyrosine Kinases Repertoire in Electrophorus electricus With an Emphasis on Evolutionary Conservation and Diversification. PMID:32546936
Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean. PMID:32546674
Toxin-Antitoxin Systems: A Tool for Taxonomic Analysis of Human Intestinal Microbiota. PMID:32545455
Transcriptome sequencing reveals signatures of positive selection in the Spot-Tailed Earless Lizard. PMID:32542006
Genome-wide analysis of proline-rich extension-like receptor protein kinase (PERK) in Brassica rapa and its association with the pollen development. PMID:32539701
Genome-wide analysis of expression quantitative trait loci (eQTLs) reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato. PMID:32528702
Differentially Regulated Transcription Factors and ABC Transporters in a Mitochondrial Dynamics Mutant Can Alter Azole Susceptibility of Aspergillus fumigatus. PMID:32528443
2-Hydroxysorangiadenosine: Structure and Biosynthesis of a Myxobacterial Sesquiterpene-Nucleoside. PMID:32527018
Modulation of bacterial multicellularity via spatio-specific polysaccharide secretion. PMID:32516311
Comparative tRNA sequencing and RNA mass spectrometry for surveying tRNA modifications. PMID:32514182
Multilayered VBC score predicts sgRNAs that efficiently generate loss-of-function alleles. PMID:32514112
R269C variant of ESR1: high prevalence and differential function in a subset of pancreatic cancers. PMID:32513126
SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae). PMID:32509454
Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family. PMID:32493223
Analysis of Pigment-Dispersing Factor Neuropeptides and Their Receptor in a Velvet Worm. PMID:32477266
Establishment of a CALU, AURKA, and MCM2 gene panel for discrimination of metastasis from primary colon and lung cancers. PMID:32469983
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
Alzheimer's Disease: The Role of Mutations in Protein Folding. PMID:32468481
The World of Cyclic Dinucleotides in Bacterial Behavior. PMID:32466317
High-resolution annotation of the mouse preimplantation embryo transcriptome using long-read sequencing. PMID:32461551
Identification of soybean trans-factors associated with plastid RNA editing sites. PMID:32459826
Third-Generation Sequencing Reveals LncRNA-Regulated HSP Genes in the Populus x canadensis Moench Heat Stress Response. PMID:32457788
Whole-genome sequence of Phellinus gilvus (mulberry Sanghuang) reveals its unique medicinal values. PMID:32455007
Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera. PMID:32442304
A Decoy Library Uncovers U-Box E3 Ubiquitin Ligases That Regulate Flowering Time in Arabidopsis. PMID:32434795
MetaSanity: an integrated microbial genome evaluation and annotation pipeline. PMID:32426808
In silico Prediction of Virus-Host Interactions for Marine Bacteroidetes With the Use of Metagenome-Assembled Genomes. PMID:32411107
Escherichia coli YcaQ is a DNA glycosylase that unhooks DNA interstrand crosslinks. PMID:32409837
DNA Variant in the RPGRIP1L Gene Influences Alternative Splicing. PMID:32399473
Genome reconstruction of the non-culturable spinach downy mildew Peronospora effusa by metagenome filtering. PMID:32396560
Comparative Transcriptome Analysis Combining SMRT- and Illumina-Based RNA-Seq Identifies Potential Candidate Genes Involved in Betalain Biosynthesis in Pitaya Fruit. PMID:32384685
Self-analysis of repeat proteins reveals evolutionarily conserved patterns. PMID:32381046
AFB1 Induced Transcriptional Regulation Related to Apoptosis and Lipid Metabolism in Liver of Chicken. PMID:32375309
Degradation of the Repetitive Genomic Landscape in a Close Relative of Caenorhabditis elegans. PMID:32359146
Complete Structure of the Enterococcal Polysaccharide Antigen (EPA) of Vancomycin-Resistant Enterococcus faecalis V583 Reveals that EPA Decorations Are Teichoic Acids Covalently Linked to a Rhamnopolysaccharide Backbone. PMID:32345640
Molecular Recognition between Cadherins Studied by a Coarse-Grained Model Interacting with a Coevolutionary Potential. PMID:32336092
BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. PMID:32325033
Genome-wide identification and functional analysis of ARF transcription factors in Brassica juncea var. tumida. PMID:32320456
Expansion of the Transporter-Opsin-G protein-coupled receptor superfamily with five new protein families. PMID:32320418
Novel Target Exploration from Hypothetical Proteins of Klebsiella pneumoniae MGH 78578 Reveals a Protein Involved in Host-Pathogen Interaction. PMID:32318354
Site-Specific Conditions Change the Response of Bacterial Producers of Soil Structure-Stabilizing Agents Such as Exopolysaccharides and Lipopolysaccharides to Tillage Intensity. PMID:32318044
An autoinhibitory mechanism controls RNA-binding activity of the nitrate-sensing protein NasR. PMID:32314426
Dataset for the combined transcriptome assembly of M. oleifera and functional annotation. PMID:32309524
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
Genome-wide identification of the PEBP genes in pears and the putative role of PbFT in flower bud differentiation. PMID:32296611
Identification and analysis of the FAD gene family in walnuts (Juglans regia L.) based on transcriptome data. PMID:32293267
Stress-mediated convergence of splicing landscapes in male and female rock doves. PMID:32293250
Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats. PMID:32293242
Modulation of stress and immune response by Amblyomin-X results in tumor cell death in a horse melanoma model. PMID:32286411
A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder. PMID:32283633
Conserved nuclear hormone receptors controlling a novel plastic trait target fast-evolving genes expressed in a single cell. PMID:32282814
Insight into the Functional Diversification of Lipases in the Endoparasitoid Pteromalus puparum (Hymenoptera: Pteromalidae) by Genome-scale Annotation and Expression Analysis. PMID:32260574
Cauliflower Mosaic Virus TAV, a Plant Virus Protein That Functions like Ribonuclease H1 and is Cytotoxic to Glioma Cells. PMID:32258141
Crystal Structure of the Ergothioneine Sulfoxide Synthase from Candidatus Chloracidobacterium thermophilum and Structure-Guided Engineering To Modulate Its Substrate Selectivity. PMID:32257583
Genome-wide analysis of wheat DNA-binding with one finger (Dof) transcription factor genes: evolutionary characteristics and diverse abiotic stress responses. PMID:32245398
Cell-type diversity and regionalized gene expression in the planarian intestine. PMID:32240093
Molecular Drivers of Lymphocyte Organization in Vertebrate Mucosal Surfaces: Revisiting the TNF Superfamily Hypothesis. PMID:32238457
NONU-1 Encodes a Conserved Endonuclease Required for mRNA Translation Surveillance. PMID:32234470
Type II and type IV toxin-antitoxin systems show different evolutionary patterns in the global Klebsiella pneumoniae population. PMID:32232417
Transcriptome sequencing and analysis reveals the molecular response to selenium stimuli in Pueraria lobata (willd.) Ohwi. PMID:32231880
Comparative genome sequence analysis of several species in the genus Tepidimonas and the description of a novel species Tepidimonas charontis sp. nov. PMID:32228748
A single amino acid substitution uncouples catalysis and allostery in an essential biosynthetic enzyme in Mycobacterium tuberculosis. PMID:32217694
Viruses with different genome types adopt a similar strategy to pack nucleic acids based on positively charged protein domains. PMID:32214181
Accurate Representation of Protein-Ligand Structural Diversity in the Protein Data Bank (PDB). PMID:32213914
Functional Annotation and Curation of Hypothetical Proteins Present in A Newly Emerged Serotype 1c of Shigella flexneri: Emphasis on Selecting Targets for Virulence and Vaccine Design Studies. PMID:32210046
Genome-wide characterization and expression analysis of soybean trihelix gene family. PMID:32206450
Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions. PMID:32203420
Isopod holobionts as promising models for lignocellulose degradation. PMID:32190114
Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms. PMID:32188862
CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers. PMID:32183712
Leucine-rich repeat receptor-like kinase II phylogenetics reveals five main clades throughout the plant kingdom. PMID:32175641
Sjögren syndrome/scleroderma autoantigen 1 is a direct Tankyrase binding partner in cancer cells. PMID:32170109
COST1 regulates autophagy to control plant drought tolerance. PMID:32170020
Learning supervised embeddings for large scale sequence comparisons. PMID:32168338
Cloning and characterization of two chlorophyll A/B binding protein genes and analysis of their gene family in Camellia sinensis. PMID:32165676
Comparison of transcriptomes from two chemosensory organs in four decapod crustaceans reveals hundreds of candidate chemoreceptor proteins. PMID:32163507
Recycling and metabolic flexibility dictate life in the lower oceanic crust. PMID:32161389
Development and validation of a lipogenic genes panel for diagnosis and recurrence of colorectal cancer. PMID:32155177
Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice. PMID:32152589
Transcriptomic and metabolomic analyses of Lycium ruthenicum and Lycium barbarum fruits during ripening. PMID:32152358
Genome-wide identification and expression analysis of PUB genes in cotton. PMID:32143567
Mycoparasitism illuminated by genome and transcriptome sequencing of Coniothyrium minitans, an important biocontrol fungus of the plant pathogen Sclerotinia sclerotiorum. PMID:32141811
Exosomes Transmit Viral Genetic Information and Immune Signals may cause Immunosuppression and Immune Tolerance in ALV-J Infected HD11 cells. PMID:32140061
Longitudinal survey of microbiome associated with particulate matter in a megacity. PMID:32127018
An assessment of genome annotation coverage across the bacterial tree of life. PMID:32124724
A de novo reference transcriptome for Bolitoglossa vallecula, an Andean mountain salamander in Colombia. PMID:32123704
SRSF7 maintains its homeostasis through the expression of Split-ORFs and nuclear body assembly. PMID:32123389
Genome-wide discovery, and computational and transcriptional characterization of an AIG gene family in the freshwater snail Biomphalaria glabrata, a vector for Schistosoma mansoni. PMID:32122294
A Moraxella Virulence Factor Catalyzes an Essential Esterase Reaction of Biotin Biosynthesis. PMID:32117167
Copper and Melanin Play a Role in Myxococcus xanthus Predation on Sinorhizobium meliloti. PMID:32117124
Comparative Insights Into the Complete Genome Sequence of Highly Metal Resistant Cupriavidus metallidurans Strain BS1 Isolated From a Gold-Copper Mine. PMID:32117100
New insight into the molecular mechanism of colour differentiation among floral segments in orchids. PMID:32111943
Chromosome-Level Assembly of the Caenorhabditis remanei Genome Reveals Conserved Patterns of Nematode Genome Organization. PMID:32111628
Analysis of the Complete Genome of the Alkaliphilic and Phototrophic Firmicute Heliorestis convoluta Strain HHT. PMID:32106460
A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina. PMID:32103005
The Medicago truncatula DREPP Protein Triggers Microtubule Fragmentation in Membrane Nanodomains during Symbiotic Infections. PMID:32102845
Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity. PMID:32101166
SPD_1495 Contributes to Capsular Polysaccharide Synthesis and Virulence in Streptococcus pneumoniae. PMID:32098834
Proteogenomic analysis of pitaya reveals cold stress-related molecular signature. PMID:32095361
Thermostable Tannase from Aspergillus Niger and Its Application in the Enzymatic Extraction of Green Tea. PMID:32093395
Protein expression in the obligate hydrocarbon-degrading psychrophile Oleispira antarctica RB-8 during alkane degradation and cold tolerance. PMID:32090431
Novel routes towards bioplastics from plants: elucidation of the methylperillate biosynthesis pathway from Salvia dorisiana trichomes. PMID:32090266
FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies. PMID:32082281
On the evolution of protein-adenine binding. PMID:32079721
Genome-wide identification and characterization of the soybean SOD family during alkaline stress. PMID:32071807
Polysaccharide niche partitioning of distinct Polaribacter clades during North Sea spring algal blooms. PMID:32071394
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
Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes. PMID:32066524
The modular nature of protein evolution: domain rearrangement rates across eukaryotic life. PMID:32059645
Data on the genome analysis of the wood-rotting fungus Steccherinum ochraceum LE-BIN 3174. PMID:32055659
MicroRNAs regulate innate immunity against uropathogenic and commensal-like Escherichia coli infections in the surrogate insect model Galleria mellonella. PMID:32054914
Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis. PMID:32050897
Physicochemical characterization of Pseudomonas stutzeri UFV5 and analysis of its transcriptome under heterotrophic nitrification/aerobic denitrification pathway induction condition. PMID:32042029
Comparative genomics applied to Mucor species with different lifestyles. PMID:32039703
Classification of Trispanins: A Diverse Group of Proteins That Function in Membrane Synthesis and Transport Mechanisms. PMID:32039202
Genome Sequencing and Comparative Analysis of Three Hanseniaspora uvarum Indigenous Wine Strains Reveal Remarkable Biotechnological Potential. PMID:32038567
Genomic characterization of Parengyodontium americanum sp. nov. PMID:32028048
Computational prediction of active sites and ligands in different AHL quorum quenching lactonases and acylases. PMID:32020908
The whole transcriptome regulation as a function of mitochondrial polymorphisms and aging in Caenorhabditis elegans. PMID:32019902
Diversity and Host Interactions Among Virulent and Temperate Baltic Sea Flavobacterium Phages. PMID:32019073
Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium. PMID:32013859
Characterising avenin-like proteins (ALPs) from albumin/globulin fraction of wheat grains by RP-HPLC, SDS-PAGE, and MS/MS peptides sequencing. PMID:31996140
Comprehensive analysis of the Gossypium hirsutum L. respiratory burst oxidase homolog (Ghrboh) gene family. PMID:31996127
Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid. PMID:31996126
Characterization of a sponge microbiome using an integrative genome-centric approach. PMID:31992859
Structural evolution drives diversification of the large LRR-RLK gene family. PMID:31990988
Diversity and metabolism of Woeseiales bacteria, global members of marine sediment communities. PMID:31988474
Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae. PMID:31988473
Unusual genome expansion and transcription suppression in ectomycorrhizal Tricholoma matsutake by insertions of transposable elements. PMID:31978083
ISOGO: Functional annotation of protein-coding splice variants. PMID:31974522
Paenibacillus odorifer, the Predominant Paenibacillus Species Isolated from Milk in the United States, Demonstrates Genetic and Phenotypic Conservation of Psychrotolerance but Clade-Associated Differences in Nitrogen Metabolic Pathways. PMID:31969477
Gene content evolution in the arthropods. PMID:31969194
Giant virus diversity and host interactions through global metagenomics. PMID:31968354
The mirid bug Apolygus lucorum deploys a glutathione peroxidase as a candidate effector to enhance plant susceptibility. PMID:31950164
Human Colon Mucosal Biofilms and Murine Host Communicate via Altered mRNA and microRNA Expression during Cancer. PMID:31937674
Relative expression analysis of light-harvesting genes in the freshwater alga Lympha mucosa (Batrachospermales, Rhodophyta). PMID:31930498
Shifts in reclamation management strategies shape the role of exopolysaccharide and lipopolysaccharide-producing bacteria during soil formation. PMID:31920012
Activity Dependence of a Novel Lectin Family on Structure and Carbohydrate-Binding Properties. PMID:31905927
Genome-wide analysis of PYL-PP2C-SnRK2s family in Camellia sinensis. PMID:31903833
Neurobiology of BDNF in fear memory, sensitivity to stress, and stress-related disorders. PMID:31900428
Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses. PMID:31900112
A bifunctional ATPase drives tad pilus extension and retraction. PMID:31897429
Analysis of MADS-box genes revealed modified flowering gene network and diurnal expression in pineapple. PMID:31896347
Genomic identification and characterization of MYC family genes in wheat (Triticum aestivum L.). PMID:31888472
Genome- and Transcriptome-Wide Characterization of bZIP Gene Family Identifies Potential Members Involved in Abiotic Stress Response and Anthocyanin Biosynthesis in Radish (Raphanus sativus L.). PMID:31888167
PhoH2 proteins couple RNA helicase and RNAse activities. PMID:31886915
Decrypting tubby-like protein gene family of multiple functions in starch root crop cassava. PMID:31871614
Identification of pathogenic variant enriched regions across genes and gene families. PMID:31871067
PHI-Nets: A Network Resource for Ascomycete Fungal Pathogens to Annotate and Identify Putative Virulence Interacting Proteins and siRNA Targets. PMID:31866958
Knowledge Base Commons (KBCommons) v1.1: a universal framework for multi-omics data integration and biological discoveries. PMID:31856718
Novel findings to the biosynthetic pathway of magnoflorine and taspine through transcriptomic and metabolomic analysis of Croton draco (Euphorbiaceae). PMID:31852435
NCBI's Conserved Domain Database and Tools for Protein Domain Analysis. PMID:31851420
Genomewide and Enzymatic Analysis Reveals Efficient d-Galacturonic Acid Metabolism in the Basidiomycete Yeast Rhodosporidium toruloides. PMID:31848309
Host-Microbe Interactions in the Chemosynthetic Riftia pachyptila Symbiosis. PMID:31848270
High-density chemical cross-linking for modeling protein interactions. PMID:31848235
Repurposing human kinase inhibitors to create an antibiotic active against drug-resistant Staphylococcus aureus, persisters and biofilms. PMID:31844194
An Annotated Draft Genome of the Mountain Hare (Lepus timidus). PMID:31834364
Genomes and secretomes of Ascomycota fungi reveal diverse functions in plant biomass decomposition and pathogenesis. PMID:31830917
Deciphering protein evolution and fitness landscapes with latent space models. PMID:31822668
A Novel Genus of Actinobacterial Tectiviridae. PMID:31817897
An analysis of mutational signatures of synonymous mutations across 15 cancer types. PMID:31815613
Proliferating Transitory T Cells with an Effector-like Transcriptional Signature Emerge from PD-1+ Stem-like CD8+ T Cells during Chronic Infection. PMID:31810882
Determining the pathogenicity of CFTR missense variants: Multiple comparisons of in silico predictors and variant annotation databases. PMID:31808782
A Combined Mass Spectrometry and Data Integration Approach to Predict the Mitochondrial Poly(A) RNA Interacting Proteome. PMID:31803741
A common root for coevolution and substitution rate variability in protein sequence evolution. PMID:31792239
Non-Catalytic Subunits Facilitate Quaternary Organization of Plastidic Acetyl-CoA Carboxylase. PMID:31792149
Computational search for UV radiation resistance strategies in Deinococcus swuensis isolated from Paramo ecosystems. PMID:31790419
The Indispensable Role of Histone Methyltransferase PoDot1 in Extracellular Glycoside Hydrolase Biosynthesis of Penicillium oxalicum. PMID:31787956
Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. PMID:31782791
Cis-Acting Relaxases Guarantee Independent Mobilization of MOBQ 4 Plasmids. PMID:31781067
Novel redox-active enzymes for ligninolytic applications revealed from multiomics analyses of Peniophora sp. CBMAI 1063, a laccase hyper-producer strain. PMID:31772294
Evidence for densovirus integrations into tapeworm genomes. PMID:31771643
Drivers of metabolic diversification: how dynamic genomic neighbourhoods generate new biosynthetic pathways in the Brassicaceae. PMID:31769874
A universal transportin protein drives stochastic choice of olfactory neurons via specific nuclear import of a sox-2-activating factor. PMID:31767767
Integrative Analysis of the lncRNA and mRNA Transcriptome Revealed Genes and Pathways Potentially Involved in the Anther Abortion of Cotton (Gossypium hirsutum L.). PMID:31756984
MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems. PMID:31754718
Full-length transcriptome sequencing from multiple tissues of duck, Anas platyrhynchos. PMID:31754106
Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader 'Candidatus Leucobacter sulfamidivorax' strain GP. PMID:31752666
Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes. PMID:31749830
Genomic Signatures for Sedimentary Microbial Utilization of Phytoplankton Detritus in a Fast-Flowing Estuary. PMID:31749780
The ABA-induced soybean ERF transcription factor gene GmERF75 plays a role in enhancing osmotic stress tolerance in Arabidopsis and soybean. PMID:31747904
Genome-Wide Identification and Characterization of ABC Transporters in Nine Rosaceae Species Identifying MdABCG28 as a Possible Cytokinin Transporter linked to Dwarfing. PMID:31744249
LmxM.22.0250-Encoded Dual Specificity Protein/Lipid Phosphatase Impairs Leishmania mexicana Virulence In Vitro. PMID:31744234
Single-molecule real-time sequencing identifies massive full-length cDNAs and alternative-splicing events that facilitate comparative and functional genomics study in the hexaploid crop sweet potato. PMID:31741783
In-depth serum virome analysis in patients with acute liver failure with indeterminate etiology. PMID:31741097
Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology. PMID:31740763
Mutually Regulated AP2/ERF Gene Clusters Modulate Biosynthesis of Specialized Metabolites in Plants. PMID:31727678
Cell-Wall Hydrolases as Antimicrobials against Staphylococcus Species: Focus on Sle1. PMID:31726796
Injury-Triggered Blueing Reactions of Psilocybe "Magic" Mushrooms. PMID:31725937
An influential meal: host plant dependent transcriptional variation in the beet armyworm, Spodoptera exigua (Lepidoptera: Noctuidae). PMID:31722664
Genome-wide identification and characterization of the MADS-box gene family in Salix suchowensis. PMID:31720123
Systematic analysis of NAC transcription factors in Gossypium barbadense uncovers their roles in response to Verticillium wilt. PMID:31720116
The Novel Serine/Threonine Protein Kinase LmjF.22.0810 from Leishmania major may be Involved in the Resistance to Drugs such as Paromomycin. PMID:31718000
Genome-Wide Analysis of Basic Helix-Loop-Helix Superfamily Members Reveals Organization and Chilling-Responsive Patterns in Cabbage (Brassica oleracea var. capitata L.). PMID:31717469
d-Ribose Catabolism in Archaea: Discovery of a Novel Oxidative Pathway in Haloarcula Species. PMID:31712277
PdWND3A, a wood-associated NAC domain-containing protein, affects lignin biosynthesis and composition in Populus. PMID:31711424
Sequencing of the black rockfish chromosomal genome provides insight into sperm storage in the female ovary. PMID:31711192
Identification of lncRNAs by RNA Sequencing Analysis During in Vivo Pre-Implantation Developmental Transformation in the Goat. PMID:31708972
The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae). PMID:31702783
Comprehensive characterization of the alternative splicing landscape in head and neck squamous cell carcinoma reveals novel events associated with tumorigenesis and the immune microenvironment. PMID:31695792
AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. PMID:31695717
Fungal Adaptation to the Advanced Stages of Wood Decomposition: Insights from the Steccherinum ochraceum. PMID:31694151
Ensembl 2020. PMID:31691826
Structural characterization of the RH1-LZI tandem of JIP3/4 highlights RH1 domains as a cytoskeletal motor-binding motif. PMID:31690808
The mutational landscape of quinolone resistance in Escherichia coli. PMID:31689338
Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts. PMID:31684862
An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. PMID:31681429
Identification of candidate ATP-binding cassette transporter gene family members in Diaphorina citri (Hemiptera: Psyllidae) via adult tissues transcriptome analysis. PMID:31676883
Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families. PMID:31676016
Co-expression of synaptic genes in the sponge Amphimedon queenslandica uncovers ancient neural submodules. PMID:31673079
Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria. PMID:31662456
Diversity and Horizontal Transfer of Antarctic Pseudomonas spp. Plasmids. PMID:31661808
Domainoid: domain-oriented orthology inference. PMID:31660857
The use of PanDrugs to prioritize anticancer drug treatments in a case of T-ALL based on individual genomic data. PMID:31655559
Genome-Wide Identification and Functional Prediction of Long Non-coding RNAs Involved in the Heat Stress Response in Metarhizium robertsii. PMID:31649657
Bioinformatics analysis of Ras homologue enriched in the striatum, a potential target for Huntington's disease therapy. PMID:31638189
Long Read Single-Molecule Real-Time Sequencing Elucidates Transcriptome-Wide Heterogeneity and Complexity in Esophageal Squamous Cells. PMID:31636653
A multi-scale coevolutionary approach to predict interactions between protein domains. PMID:31634362
Adaptive laboratory evolution of Escherichia coli under acid stress. PMID:31625833
Draft Genome Sequences of 12 Monophasic Salmonella enterica subsp. enterica Serotype Typhimurium 1,4,[5],12:i:- Strains Isolated from Wild Griffon Vultures in Eastern Spain. PMID:31624159
Genome-Wide Identification and Characterization of the Vacuolar H+-ATPase Subunit H Gene Family in Crop Plants. PMID:31623139
Using Transcriptome Analysis to Screen for Key Genes and Pathways Related to Cytoplasmic Male Sterility in Cotton (Gossypium hirsutum L.). PMID:31623069
The C-Terminal Domains SnRK2 Box and ABA Box Have a Role in Sugarcane SnRK2s Auto-Activation and Activity. PMID:31620147
Identification and characterisation of capidermicin, a novel bacteriocin produced by Staphylococcus capitis. PMID:31618225
Ectopic Expression of Litsea cubeba LcMADS20 Modifies Silique Architecture. PMID:31615834
PhaSePro: the database of proteins driving liquid-liquid phase separation. PMID:31612960
Global ecotypes in the ubiquitous marine clade SAR86. PMID:31611653
Bioinformatic Exploration of Metal-Binding Proteome of Zoonotic Pathogen Orientia tsutsugamushi. PMID:31608099
VarSite: Disease variants and protein structure. PMID:31606900
Genetic variation regulates the activation and specificity of Restriction-Modification systems in Neisseria gonorrhoeae. PMID:31605008
Zinc binding proteome of a phytopathogen Xanthomonas translucens pv. undulosa. PMID:31598288
SWEET Transporters for the Nourishment of Embryonic Tissues during Maize Germination. PMID:31591342
The Evolutionary History of Ephs and Ephrins: Toward Multicellular Organisms. PMID:31589243
Field evaluation ratified by transcript and computational analyses unveils myco-protective role of SUGARWIN proteins in sugarcane. PMID:31588401
Bioremediation of a Common Product of Food Processing by a Human Gut Bacterium. PMID:31585844
A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana. PMID:31585525
PDBe-KB: a community-driven resource for structural and functional annotations. PMID:31584092
Genetic diversity, functional properties and expression analysis of NnSBE genes involved in starch synthesis of lotus (Nelumbo nucifera Gaertn.). PMID:31579617
Genome-wide identification of growth-regulating factors in moso bamboo (Phyllostachys edulis): in silico and experimental analyses. PMID:31579567
Genome-wide identification and expression analyses of the LEA protein gene family in tea plant reveal their involvement in seed development and abiotic stress responses. PMID:31575979
Genome-Wide Identification, Evolution, and Expression Analysis of RING Finger Gene Family in Solanum lycopersicum. PMID:31574992
Genome-Wide Identification and Characterization of Glycosyltransferase Family 47 in Cotton. PMID:31572442
Characterization and Expression Analysis of ERF Genes in Fragaria vesca Suggest Different Divergences of Tandem ERF Duplicates. PMID:31572436
Macroalga-Derived Alginate Oligosaccharide Alters Intestinal Bacteria of Atlantic Salmon. PMID:31572312
Characterizing rare and low-frequency height-associated variants in the Japanese population. PMID:31562340
De novo transcriptome assembly and analysis of the freshwater araphid diatom Fragilaria radians, Lake Baikal. PMID:31562323
Overexpression of a Novel Cytochrome P450 Promotes Flavonoid Biosynthesis and Osmotic Stress Tolerance in Transgenic Arabidopsis. PMID:31561549
A Quest of Great Importance-Developing a Broad Spectrum Escherichia coli Phage Collection. PMID:31561510
Phasin PhaP1 is involved in polyhydroxybutyrate granules morphology and in controlling early biopolymer accumulation in Azospirillum brasilense Sp7. PMID:31555910
Domain-based Comparative Analysis of Bacterial Proteomes: Uniqueness, Interactions, and the Dark Matter. PMID:31555062
Mining MYB transcription factors from the genomes of orchids (Phalaenopsis and Dendrobium) and characterization of an orchid R2R3-MYB gene involved in water-soluble polysaccharide biosynthesis. PMID:31554868
Vibrio Proteases for Biomedical Applications: Modulating the Proteolytic Secretome of V. alginolyticus and V. parahaemolyticus for Improved Enzymes Production. PMID:31554228
The Cellulosome Paradigm in An Extreme Alkaline Environment. PMID:31547347
Updated Genome Assembly and Annotation for Metrosideros polymorpha, an Emerging Model Tree Species of Ecological Divergence. PMID:31540972
Genome-Wide Analysis Reveals the Role of Mediator Complex in the Soybean-Phytophthora sojae Interaction. PMID:31540158
Seaweed natural products modify the host inflammatory response via Nrf2 signaling and alter colon microbiota composition and gene expression. PMID:31536771
RCSB Protein Data Bank: Enabling biomedical research and drug discovery. PMID:31531901
Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence. PMID:31529539
Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method. PMID:31527871
Genomic analysis of siderophore β-hydroxylases reveals divergent stereocontrol and expands the condensation domain family. PMID:31527229
βγ-Crystallination Endows a Novel Bacterial Glycoside Hydrolase 64 with Ca2+-Dependent Activity Modulation. PMID:31527113
Environmental and epigenetic regulation of Rider retrotransposons in tomato. PMID:31525177
A Bacterial Effector Mimics a Host HSP90 Client to Undermine Immunity. PMID:31522888
Systematic prediction of functionally linked genes in bacterial and archaeal genomes. PMID:31520072
Computational and experimental analysis of the glycophosphatidylinositol-anchored proteome of the human parasitic nematode Brugia malayi. PMID:31513600
Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. PMID:31510914
iTRAQ-Based Global Phosphoproteomics Reveals Novel Molecular Differences Between Toxoplasma gondii Strains of Different Genotypes. PMID:31508380
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
Transcriptome characterization and expression profiling in chestnut cultivars resistant or susceptible to the gall wasp Dryocosmus kuriphilus. PMID:31506717
Machine learning-based chemical binding similarity using evolutionary relationships of target genes. PMID:31504818
Evolutionary Dissection of the Dot/Icm System Based on Comparative Genomics of 58 Legionella Species. PMID:31504472
A comprehensive analysis of the B3 superfamily identifies tissue-specific and stress-responsive genes in chickpea (Cicer arietinum L.). PMID:31497464
Genome-wide identification and characterization of the Hsp70 gene family in allopolyploid rapeseed (Brassica napus L.) compared with its diploid progenitors. PMID:31497395
Metagenomic and chemical characterization of soil cobalamin production. PMID:31492962
Capability for arsenic mobilization in groundwater is distributed across broad phylogenetic lineages. PMID:31490939
New factors for protein transport identified by a genome-wide CRISPRi screen in mammalian cells. PMID:31488582
Computer aided analysis of disease linked protein networks. PMID:31485137
An electrostatic switching mechanism to control the lipid transfer activity of Osh6p. PMID:31477717
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
Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles. PMID:31464627
Structural and biochemical studies of an NB-ARC domain from a plant NLR immune receptor. PMID:31461469
Measuring the impact of gene prediction on gene loss estimates in Eukaryotes by quantifying falsely inferred absences. PMID:31461468
Comparison of α-Helix and β-Sheet Structure Adaptation to a Quantum Dot Geometry: Toward the Identification of an Optimal Motif for a Protein Nanoparticle Cover. PMID:31460436
Systematic Functional Analysis of Active-Site Residues in l-Threonine Dehydrogenase from Thermoplasma volcanium. PMID:31457655
Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes. PMID:31455637
Normal transcription of cellulolytic enzyme genes relies on the balance between the methylation of H3K36 and H3K4 in Penicillium oxalicum. PMID:31452679
Exon 3 of the NUMB Gene Emerged in the Chordate Lineage Coopting the NUMB Protein to the Regulation of MDM2. PMID:31451549
Ferlin Overview: From Membrane to Cancer Biology. PMID:31443490
Genome-wide identification and characterization of long non-coding RNAs involved in fruit ripening and the climacteric in Cucumis melo. PMID:31438855
A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). PMID:31437279
Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae. PMID:31431676
A Membrane-Bound Cytochrome Enables Methanosarcina acetivorans To Conserve Energy from Extracellular Electron Transfer. PMID:31431545
Improving ionic liquid tolerance in Saccharomyces cerevisiae through heterologous expression and directed evolution of an ILT1 homolog from Yarrowia lipolytica. PMID:31428944
Assessing the utility of seed coat-specific promoters to engineer cell wall polysaccharide composition of mucilage. PMID:31422517
The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis. PMID:31420548
Investigation into the underlying regulatory mechanisms shaping inflorescence architecture in Chenopodium quinoa. PMID:31419932
Evidence of Extensive Intraspecific Noncoding Reshuffling in a 169-kb Mitochondrial Genome of a Basidiomycetous Fungus. PMID:31418013
Carbon assimilation profiles of mucoralean fungi show their metabolic versatility. PMID:31413281
UNIPred-Web: a web tool for the integration and visualization of biomolecular networks for protein function prediction. PMID:31412768
Complete genome sequence analysis of a lytic Shigella flexneri vB-SflS-ISF001 bacteriophage. PMID:31410079
The catalytic core of DEMETER guides active DNA demethylation in Arabidopsis. PMID:31409710
Estimating statistical significance of local protein profile-profile alignments. PMID:31409275
Analysis of Vibrio cholerae genomes identifies new type VI secretion system gene clusters. PMID:31405375
A deep learning genome-mining strategy for biosynthetic gene cluster prediction. PMID:31400112
Cassava AGPase genes and their encoded proteins are different from those of other plants. PMID:31399791
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. PMID:31395883
Full annotation of serum virome in Chinese blood donors with elevated alanine aminotransferase levels. PMID:31393615
Engineering DNA recognition and allosteric response properties of TetR family proteins by using a module-swapping strategy. PMID:31392336
IslandCafe: Compositional Anomaly and Feature Enrichment Assessment for Delineation of Genomic Islands. PMID:31387857
ABC Transporter Genes Show Upregulated Expression in Drug-Resistant Clinical Isolates of Candida auris: A Genome-Wide Characterization of ATP-Binding Cassette (ABC) Transporter Genes. PMID:31379756
Genome-Wide Screening for Identification of Novel Toxin-Antitoxin Systems in Staphylococcus aureus. PMID:31375497
Biological Soil Crusts from Different Soil Substrates Harbor Distinct Bacterial Groups with the Potential to Produce Exopolysaccharides and Lipopolysaccharides. PMID:31372685
Endosome and Golgi-associated degradation (EGAD) of membrane proteins regulates sphingolipid metabolism. PMID:31368600
Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids. PMID:31366885
Antibacterial effects of sodium tripolyphosphate against Porphyromonas species associated with periodontitis of companion animals. PMID:31364318
Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne). PMID:31361773
Three glycoside hydrolase family 12 enzymes display diversity in substrate specificities and synergistic action between each other. PMID:31359382
Viruses as key reservoirs of antibiotic resistance genes in the environment. PMID:31358910
A new family of cell surface located purine transporters in Microsporidia and related fungal endoparasites. PMID:31355745
Molecular Evolution and Functional Analysis of Rubredoxin-Like Proteins in Plants. PMID:31355252
The Conservation of VIT1-Dependent Iron Distribution in Seeds. PMID:31354774
An expanded landscape of human long noncoding RNA. PMID:31350901
Dicyemid Mesozoans: A Unique Parasitic Lifestyle and a Reduced Genome. PMID:31347665
Stem cell differentiation trajectories in Hydra resolved at single-cell resolution. PMID:31346039
Genome and transcriptome evolve separately in recently hybridized Trichosporon fungi. PMID:31341962
Rare, functional, somatic variants in gene families linked to cancer genes: GPCR signaling as a paradigm. PMID:31337866
A-to-I editing of Malacoherpesviridae RNAs supports the antiviral role of ADAR1 in mollusks. PMID:31337330
Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes. PMID:31332386
Complete genome sequence of the Sulfodiicoccus acidiphilus strain HS-1T, the first crenarchaeon that lacks polB3, isolated from an acidic hot spring in Ohwaku-dani, Hakone, Japan. PMID:31331368
Why do eukaryotic proteins contain more intrinsically disordered regions? PMID:31329574
Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL341. PMID:31324626
Understanding the impacts of missense mutations on structures and functions of human cancer-related genes: A preliminary computational analysis of the COSMIC Cancer Gene Census. PMID:31323058
An essential bifunctional enzyme in Mycobacterium tuberculosis for itaconate dissimilation and leucine catabolism. PMID:31320588
Combined alignments of sequences and domains characterize unknown proteins with remotely related protein search PSISearch2D. PMID:31317184
The ER Lumenal Hsp70 Protein FpLhs1 Is Important for Conidiation and Plant Infection in Fusarium pseudograminearum. PMID:31316483
Proteogenomic Analysis of Protein Sequence Alterations in Breast Cancer Cells. PMID:31316139
Mechanism of catalysis and inhibition of Mycobacterium tuberculosis SapM, implications for the development of novel antivirulence drugs. PMID:31312014
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
A maize polygalacturonase functions as a suppressor of programmed cell death in plants. PMID:31307401
ParaDB: A manually curated database containing genomic annotation for the human pathogenic fungi Paracoccidioides spp. PMID:31306428
A Comprehensive Survey on the Terpene Synthase Gene Family Provides New Insight into Its Evolutionary Patterns. PMID:31304957
Intrinsically disordered domains: Sequence ➔ disorder ➔ function relationships. PMID:31299122
Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes. PMID:31295964
The Transcriptome Landscape of Walnut Interspecies Hybrid (Juglans hindsii × Juglans regia) and Regulation of Cambial Activity in Relation to Grafting. PMID:31293615
Genomic reconstruction of σ54 regulons in Clostridiales. PMID:31288763
Genetic interactions of G-quadruplexes in humans. PMID:31287417
Systematic identification of intergenic long-noncoding RNAs in mouse retinas using full-length isoform sequencing. PMID:31286854
Genome-wide identification and expression analysis of the BURP domain-containing genes in Gossypium hirsutum. PMID:31286851
Functional analysis of the heterotrimeric NF-Y transcription factor complex in cassava disease resistance. PMID:31282544
TxtH is a key component of the thaxtomin biosynthetic machinery in the potato common scab pathogen Streptomyces scabies. PMID:31282068
In Vitro Acquisition of Specific Small Interfering RNAs Inhibits the Expression of Some Target Genes in the Plant Ectoparasite Xiphinema index. PMID:31277202
Genome-wide identification and comparative analysis of drought-related microRNAs in two maize inbred lines with contrasting drought tolerance by deep sequencing. PMID:31276526
Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases. PMID:31274316
ProtDCal-Suite: A web server for the numerical codification and functional analysis of proteins. PMID:31271472
PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database. PMID:31267135
Ancient duplications and grass-specific transposition influenced the evolution of LEAFY transcription factor genes. PMID:31263781
The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole-genome sequencing. PMID:31258950
Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution. PMID:31255177
Fold combinations in multi-domain proteins. PMID:31249437
Many rice genes are differentially spliced between roots and shoots but cytokinin has minimal effect on splicing. PMID:31245776
Altered nucleosome positions in maize haplotypes and mutants of a subset of SWI/SNF-like proteins. PMID:31245667
Structural Analysis and Conformational Dynamics of STN1 Gene Mutations Involved in Coat Plus Syndrome. PMID:31245382
Developmental dynamics of lncRNAs across mammalian organs and species. PMID:31243368
Suppressor mutations in ribosomal proteins and FliY restore Bacillus subtilis swarming motility in the absence of EF-P. PMID:31237868
Metagenomic analysis of bile salt biotransformation in the human gut microbiome. PMID:31234773
Genome-Wide Identification, Expression Analysis, and Subcellular Localization of Carthamus tinctorius bHLH Transcription Factors. PMID:31234449
ECOD: identification of distant homology among multidomain and transmembrane domain proteins. PMID:31226926
In-silico Prediction of Synergistic Anti-Cancer Drug Combinations Using Multi-omics Data. PMID:31222109
Synchronous profiling and analysis of mRNAs and ncRNAs in the dermal papilla cells from cashmere goats. PMID:31221080
De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate. PMID:31217263
Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA. PMID:31215393
Diquat Determines a Deregulation of lncRNA and mRNA Expression in the Liver of Postweaned Piglets. PMID:31214284
Identification of Fatty Acid Desaturases in Maize and Their Differential Responses to Low and High Temperature. PMID:31210171
Inferring protein 3D structure from deep mutation scans. PMID:31209393
Laying the foundation for genomically-based risk assessment in chronic myeloid leukemia. PMID:31209280
A genome-wide scan for genes under balancing selection in the plant pathogen Ralstonia solanacearum. PMID:31208326
In silico genome-wide identification and comprehensive characterization of the BES1 gene family in soybean. PMID:31206092
Characterisation of HvVIP1 and expression profile analysis of stress response regulators in barley under Agrobacterium and Fusarium infections. PMID:31199821
Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny. PMID:31195978
RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification. PMID:31195970
Evolution and comparative genomics of the most common Trichoderma species. PMID:31189469
Rapid Evolution of Gained Essential Developmental Functions of a Young Gene via Interactions with Other Essential Genes. PMID:31187122
Orb-weaving spider Araneus ventricosus genome elucidates the spidroin gene catalogue. PMID:31182776
Dicyemida and Orthonectida: Two Stories of Body Plan Simplification. PMID:31178892
Switching the Post-translational Modification of Translation Elongation Factor EF-P. PMID:31178848
Lignocellulose degradation in isopods: new insights into the adaptation to terrestrial life. PMID:31174468
Comprehensive Analysis of SnRK Gene Family and their Responses to Salt Stress in Eucalyptus grandis. PMID:31174407
Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes. PMID:31163637
Engineering repressors with coevolutionary cues facilitates toggle switches with a master reset. PMID:31162606
Illuminating G-Protein-Coupling Selectivity of GPCRs. PMID:31160049
Genome-Wide Characterization and Expression Analysis of Soybean TGA Transcription Factors Identified a Novel TGA Gene Involved in Drought and Salt Tolerance. PMID:31156656
The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions. PMID:31149898
Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy. PMID:31147549
PRECOG: PREdicting COupling probabilities of G-protein coupled receptors. PMID:31143927
A Multi-omics Approach to Unraveling the Microbiome-Mediated Effects of Arabinoxylan Oligosaccharides in Overweight Humans. PMID:31138673
The melREDCA Operon Encodes a Utilization System for the Raffinose Family of Oligosaccharides in Bacillus subtilis. PMID:31138628
The structure of a GH149 β-(1 → 3) glucan phosphorylase reveals a new surface oligosaccharide binding site and additional domains that are absent in the disaccharide-specific GH94 glucose-β-(1 → 3)-glucose (laminaribiose) phosphorylase. PMID:31134667
Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage. PMID:31126947
Recompleting the Caenorhabditis elegans genome. PMID:31123080
Epigenetics and transcription regulation during eukaryotic diversification: the saga of TFIID. PMID:31123066
Heat Stress-Responsive Transcriptome Analysis in the Liver Tissue of Hu Sheep. PMID:31121974
A Brief History of Protein Sorting Prediction. PMID:31119599
MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains. PMID:31116477
Investigating function roles of hypothetical proteins encoded by the Mycobacterium tuberculosis H37Rv genome. PMID:31113361
ABC Transporters Required for Hexose Uptake by Clostridium phytofermentans. PMID:31109990
Genome-Wide Identification, Comprehensive Gene Feature, Evolution, and Expression Analysis of Plant Metal Tolerance Proteins in Tobacco Under Heavy Metal Toxicity. PMID:31105736
Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles. PMID:31101123
Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism. PMID:31098412
Five life stage-specific transcriptome assemblies for the reniform nematode, Rotylenchulus reniformis Linford & Oliveira. PMID:31094147
Oxidative opening of the aromatic ring: Tracing the natural history of a large superfamily of dioxygenase domains and their relatives. PMID:31092555
PathMe: merging and exploring mechanistic pathway knowledge. PMID:31092193
Genome-wide identification of genes encoding putative secreted E3 ubiquitin ligases and functional characterization of PbRING1 in the biotrophic protist Plasmodiophora brassicae. PMID:31087129
Genome-Wide Identification of WRKY Transcription Factors in Chinese jujube (Ziziphus jujuba Mill.) and Their Involvement in Fruit Developing, Ripening, and Abiotic Stress. PMID:31083435
AnnoTree: visualization and exploration of a functionally annotated microbial tree of life. PMID:31081040
Exploring the Potential Role of Moonlighting Function of the Surface-Associated Proteins From Mycobacterium bovis BCG Moreau and Pasteur by Comparative Proteomic. PMID:31080447
Genome Features and Secondary Metabolites Biosynthetic Potential of the Class Ktedonobacteria. PMID:31080444
Conserved juxtamembrane domains in the yeast golgin Coy1 drive assembly of a megadalton-sized complex and mediate binding to tethering and SNARE proteins. PMID:31073031
AlloDriver: a method for the identification and analysis of cancer driver targets. PMID:31069394
Modeling the Tertiary Structure of the Rift Valley Fever Virus L Protein. PMID:31067727
Nfat5 is involved in the hyperosmotic regulation of Tmem184b: a putative modulator of ibuprofen transport in renal MDCK I cells. PMID:31066233
Identification and expression profiling analysis of NBS-LRR genes involved in Fusarium oxysporum f.sp. conglutinans resistance in cabbage. PMID:31065502
The Enamel Phenotype in Homozygous Fam83h Truncation Mice. PMID:31060110
Bioinformatic Mapping of Radical S-Adenosylmethionine-Dependent Ribosomally Synthesized and Post-Translationally Modified Peptides Identifies New Cα, Cβ, and Cγ-Linked Thioether-Containing Peptides. PMID:31059252
Contrasting Effects of Wild Arachis Dehydrin Under Abiotic and Biotic Stresses. PMID:31057593
Characterization of an OrtT-like toxin of Salmonella enterica serovar Houten. PMID:31055774
Immunogenicity profiling of protein antigens from capsular group B Neisseria meningitidis. PMID:31048732
Plasmid detection and assembly in genomic and metagenomic data sets. PMID:31048319
Genomic analyses of aminoacyl tRNA synthetases from human-infecting helminths. PMID:31046663
SeqTailor: a user-friendly webserver for the extraction of DNA or protein sequences from next-generation sequencing data. PMID:31045209
The bagworm genome reveals a unique fibroin gene that provides high tensile strength. PMID:31044173
A core set of venom proteins is released by entomopathogenic nematodes in the genus Steinernema. PMID:31042778
First evidence of cholinesterase-like activity in Basidiomycota. PMID:31039204
Conserved phosphorylation hotspots in eukaryotic protein domain families. PMID:31036831
Classification of barley U-box E3 ligases and their expression patterns in response to drought and pathogen stresses. PMID:31035917
A Preliminary Metagenome Analysis Based on a Combination of Protein Domains. PMID:31035705
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. PMID:31032519
Shared Signature Dynamics Tempered by Local Fluctuations Enables Fold Adaptability and Specificity. PMID:31028708
Structural characterization and heterologous expression of a new cyt gene cloned from Bacillus thuringiensis. PMID:31028552
Cla4 PAK-like kinase is required for pathogenesis, asexual/sexual development and polarized growth in Bipolaris maydis. PMID:31028454
Structural and functional impact of non-synonymous SNPs in the CST complex subunit TEN1: structural genomics approach. PMID:31028137
Genome-wide identification and analysis of the WUSCHEL-related homeobox (WOX) gene family in allotetraploid Brassica napus reveals changes in WOX genes during polyploidization. PMID:31023229
The trihelix family of transcription factors: functional and evolutionary analysis in Moso bamboo (Phyllostachys edulis). PMID:31023225
Benefits and Drawbacks of Harboring Plasmid pP32BP2, Identified in Arctic Psychrophilic Bacterium Psychrobacter sp. DAB_AL32B. PMID:31022896
Bioinformatic and mutational studies of related toxin-antitoxin pairs in Mycobacterium tuberculosis predict and identify key functional residues. PMID:31018964
Infection mechanisms and putative effector repertoire of the mosquito pathogenic oomycete Pythium guiyangense uncovered by genomic analysis. PMID:31017897
Comparative transcriptome analysis reveals the genetic basis of coat color variation in Pashmina goat. PMID:31015528
Complete genome sequence of natural rubber-degrading, gram-negative bacterium, Rhizobacter gummiphilus strain NS21T. PMID:31011550
Evolution Analysis of the Fasciclin-Like Arabinogalactan Proteins in Plants Shows Variable Fasciclin-AGP Domain Constitutions. PMID:31010036
Identification and sequencing of the gene encoding DNA methyltransferase 3 (DNMT3) from sea cucumber, Apostichopus japonicus. PMID:31006102
Genome sequencing and CRISPR/Cas9 gene editing of an early flowering Mini-Citrus (Fortunella hindsii). PMID:31004551
Ligand-Binding-Site Structure Shapes Allosteric Signal Transduction and the Evolution of Allostery in Protein Complexes. PMID:31004156
Structure and mechanism of TagA, a novel membrane-associated glycosyltransferase that produces wall teichoic acids in pathogenic bacteria. PMID:31002736
AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. PMID:30997504
De Novo Transcriptome Assembly and Functional Annotation in Five Species of Bats. PMID:30996290
Brevibacterium from Austrian hard cheese harbor a putative histamine catabolism pathway and a plasmid for adaptation to the cheese environment. PMID:30992535
Experimental Evidence that Stochasticity Contributes to Bacterial Composition and Functioning in a Decomposer Community. PMID:30992354
Deep Transcriptome Analysis Reveals Reactive Oxygen Species (ROS) Network Evolution, Response to Abiotic Stress, and Regulation of Fiber Development in Cotton. PMID:30991750
Stage-specific transcriptome of Bursaphelenchus xylophilus reveals temporal regulation of effector genes and roles of the dauer-like stages in the lifecycle. PMID:30988401
Protein Structure-Guided Hidden Markov Models (HMMs) as A Powerful Method in the Detection of Ancestral Endogenous Viral Elements. PMID:30986983
The EIL transcription factor family in soybean: Genome-wide identification, expression profiling and genetic diversity analysis. PMID:30984538
Rapid identification of novel protein families using similarity searches. PMID:30984369
Genes Associated With Psychrotolerant Bacillus cereus Group Isolates. PMID:30984157
Bacteriophage φEf11 ORF28 Endolysin, a Multifunctional Lytic Enzyme with Properties Distinct from All Other Identified Enterococcus faecalis Phage Endolysins. PMID:30979842
The three dimensional structure of Bovine Salivary Protein 30b (BSP30b) and its interaction with specific rumen bacteria. PMID:30978191
Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain. PMID:30977723
To what extent may peptide receptor gene diversity/complement contribute to functional flexibility in a simple pattern-generating neural network? PMID:30974344
In silico Characterization of Human Prion-Like Proteins: Beyond Neurological Diseases. PMID:30971948
Genome-Wide Identification and Characterization of the PERK Gene Family in Gossypium hirsutum Reveals Gene Duplication and Functional Divergence. PMID:30970629
Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons. PMID:30970224
Comparative analysis of homologous aminopeptidase PepN from pathogenic and non-pathogenic mycobacteria reveals divergent traits. PMID:30969995
The cardiac syndecan-4 interactome reveals a role for syndecan-4 in nuclear translocation of muscle LIM protein (MLP). PMID:30967474
Unveiling the function and regulation control of the DUF3129 family proteins in fungal infection of hosts. PMID:30967021
Integrative analysis of long noncoding RNA and mRNA reveals candidate lncRNAs responsible for meat quality at different physiological stages in Gushi chicken. PMID:30964907
Functional crosstalk across IMD and Toll pathways: insight into the evolution of incomplete immune cascades. PMID:30963836
The complexity of the Fragaria x ananassa (octoploid) transcriptome by single-molecule long-read sequencing. PMID:30962939
Enzyme promiscuity shapes adaptation to novel growth substrates. PMID:30962359
The intrinsic dimension of protein sequence evolution. PMID:30958823
Differential protein expression during growth on linear versus branched alkanes in the obligate marine hydrocarbon-degrading bacterium Alcanivorax borkumensis SK2T. PMID:30951249
Decoys provide a scalable platform for the identification of plant E3 ubiquitin ligases that regulate circadian function. PMID:30950791
Kluyveromyces marxianus developing ethanol tolerance during adaptive evolution with significant improvements of multiple pathways. PMID:30949239
High-Quality Draft Genome Sequence of the Microcolonial Black Fungus Aeminium ludgeri DSM 106916. PMID:30948467
Genomic insights into HSFs as candidate genes for high-temperature stress adaptation and gene editing with minimal off-target effects in flax. PMID:30944362
Marine RNA Virus Quasispecies Are Distributed throughout the Oceans. PMID:30944212
A new approach for rare variation collapsing on functional protein domains implicates specific genic regions in ALS. PMID:30940688
Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species. PMID:30937174
Brucella Periplasmic Protein EipB Is a Molecular Determinant of Cell Envelope Integrity and Virulence. PMID:30936371
CRISPR screening using an expanded toolkit of autophagy reporters identifies TMEM41B as a novel autophagy factor. PMID:30933966
Estimating probabilistic context-free grammars for proteins using contact map constraints. PMID:30918754
Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep. PMID:30918404
New insights into the structures and interactions of bacterial Y-family DNA polymerases. PMID:30916324
Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool. PMID:30916321
Functional Replacement of the BioC and BioH Proteins of Escherichia coli Biotin Precursor Biosynthesis by Ehrlichia chaffeensis Novel Proteins. PMID:30915508
Context-dependent activity of A domains in the tyrocidine synthetase. PMID:30914767
Novel compound mutations in the mitochondrial translation elongation factor (TSFM) gene cause severe cardiomyopathy with myocardial fibro-adipose replacement. PMID:30911037
A TonB-dependent transporter is required for secretion of protease PopC across the bacterial outer membrane. PMID:30911012
Combining microfluidics and RNA-sequencing to assess the inducible defensome of a mushroom against nematodes. PMID:30909884
Structure and mechanism of the Red recombination system of bacteriophage λ. PMID:30904699
A comprehensive in silico analysis of sortase superfamily. PMID:30900148
Homology modeling and docking analysis of ßC1 protein encoded by Cotton leaf curl Multan betasatellite with different plant flavonoids. PMID:30899831
Nucleotide Second Messenger-Based Signaling in Extreme Acidophiles of the Acidithiobacillus Species Complex: Partition Between the Core and Variable Gene Complements. PMID:30899248
Characterization and Transcript Expression Analyses of Atlantic Cod Viperin. PMID:30894853
The Dual Prey-Inactivation Strategy of Spiders-In-Depth Venomic Analysis of Cupiennius salei. PMID:30893800
Genome-wide identification and expression analysis of HSP90 gene family in Nicotiana tabacum. PMID:30890142
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
PRISMA: Protein Interaction Screen on Peptide Matrix Reveals Interaction Footprints and Modifications- Dependent Interactome of Intrinsically Disordered C/EBPβ. PMID:30884312
Cell Wall Hydrolases in Bacteria: Insight on the Diversity of Cell Wall Amidases, Glycosidases and Peptidases Toward Peptidoglycan. PMID:30873139
The rsmS (ybaM) mutation causes bypass suppression of the RsmAB post-transcriptional virulence regulation system in enterobacterial phytopathogens. PMID:30872786
Transposable elements contribute to fungal genes and impact fungal lifestyle. PMID:30867521
Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication. PMID:30866803
DeepDom: Predicting protein domain boundary from sequence alone using stacked bidirectional LSTM. PMID:30864311
Angiosperm-Wide and Family-Level Analyses of AP2/ERF Genes Reveal Differential Retention and Sequence Divergence After Whole-Genome Duplication. PMID:30863419
Studies Into β-Glucan Recognition in Fish Suggests a Key Role for the C-Type Lectin Pathway. PMID:30863400
GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. PMID:30862647
Differential Gene Expression Supports a Resource-Intensive, Defensive Role for Colony Production in the Bloom-Forming Haptophyte, Phaeocystis globosa. PMID:30860641
The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle. PMID:30858591
MdGSTF6, activated by MdMYB1, plays an essential role in anthocyanin accumulation in apple. PMID:30854214
Molecular cloning, GTP recognition mechanism and tissue-specific expression profiling of myxovirus resistance (Mx) protein in Labeo rohita (Hamilton) after Poly I:C induction. PMID:30850653
Validation and Stabilization of a Prophage Lysin of Clostridium perfringens by Using Yeast Surface Display and Coevolutionary Models. PMID:30850429
Investigating the role of Osiris genes in Drosophila sechellia larval resistance to a host plant toxin. PMID:30847082
Global analysis of methionine oxidation provides a census of folding stabilities for the human proteome. PMID:30846556
Halloween genes in panarthropods and the evolution of the early moulting pathway in Ecdysozoa. PMID:30839709
Wnt Signaling Pathway Linked to Intestinal Regeneration via Evolutionary Patterns and Gene Expression in the Sea Cucumber Apostichopus japonicus. PMID:30838034
Anaerobic Degradation of Sulfated Polysaccharides by Two Novel Kiritimatiellales Strains Isolated From Black Sea Sediment. PMID:30833937
Further studies on sugar transporter (SWEET) genes in wheat (Triticum aestivum L.). PMID:30830588
The Draft Genome of an Octocoral, Dendronephthya gigantea. PMID:30825304
The genetic basis for adaptation of model-designed syntrophic co-cultures. PMID:30822347
The temporal profile of activity-dependent presynaptic phospho-signalling reveals long-lasting patterns of poststimulus regulation. PMID:30822303
Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism. PMID:30815000
Evolutionary Implications of the microRNA- and piRNA Complement of Lepidodermella squamata (Gastrotricha). PMID:30813358
The draft genome of strain cCpun from biting midges confirms insect Cardinium are not a monophyletic group and reveals a novel gene family expansion in a symbiont. PMID:30809447
PIRSitePredict for protein functional site prediction using position-specific rules. PMID:30805646
Origin and evolution of the octoploid strawberry genome. PMID:30804557
An alkaline active feruloyl-CoA synthetase from soil metagenome as a potential key enzyme for lignin valorization strategies. PMID:30802241
Molecular cloning and characterization of six defensin genes from lentil plant (Lens culinaris L.). PMID:30800615
Complete genome sequence of the abscisic acid-utilizing strain Novosphingobium sp. P6W. PMID:30800605
PamulDB: a comprehensive genomic resource for the study of human- and animal-pathogenic Pasteurella multocida. PMID:30799499
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
Proteomic Analysis of Histones H2A/H2B and Variant Hv1 in Tetrahymena thermophila Reveals an Ancient Network of Chaperones. PMID:30796450
Moraxella catarrhalis NucM is an entry nuclease involved in extracellular DNA and RNA degradation, cell competence and biofilm scaffolding. PMID:30796312
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
Genome sequence and characterization of the bcs clusters for the production of nanocellulose from the low pH resistant strain Komagataeibacter medellinensis ID13488. PMID:30793484
A Magnesium Transport Protein Related to Mammalian SLC41 and Bacterial MgtE Contributes to Circadian Timekeeping in a Unicellular Green Alga. PMID:30791470
Modular type I polyketide synthase acyl carrier protein domains share a common N-terminally extended fold. PMID:30787330
Antibody Biomarkers Associated with Sterile Protection Induced by Controlled Human Malaria Infection under Chloroquine Prophylaxis. PMID:30787114
Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors. PMID:30784590
The Molecular Mechanism of Nitrate Chemotaxis via Direct Ligand Binding to the PilJ Domain of McpN. PMID:30782655
Natural Strain Variation Reveals Diverse Biofilm Regulation in Squid-Colonizing Vibrio fischeri. PMID:30782630
In silico characterization of microRNAs-like sequences in the genome of Paracoccidioides brasiliensis. PMID:30776047
Mechanistic insights into the evolution of DUF26-containing proteins in land plants. PMID:30775457
Oral administration of antibiotics increased the potential mobility of bacterial resistance genes in the gut of the fish Piaractus mesopotamicus. PMID:30773139
Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide. PMID:30770726
In Silico Genome-Wide Analysis of the ATP-Binding Cassette Transporter Gene Family in Soybean (Glycine max L.) and Their Expression Profiling. PMID:30766888
MultiDomainBenchmark: a multi-domain query and subject database suite. PMID:30764761
Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members. PMID:30762363
Long live the queen, the king and the commoner? Transcript expression differences between old and young in the termite Cryptotermes secundus. PMID:30759161
Convergent perturbation of the human domain-resolved interactome by viruses and mutations inducing similar disease phenotypes. PMID:30759076
Whole-Genome Sequence of Multidrug-Resistant Bibersteinia trehalosi Strain OADDL-BT1. PMID:30746527
Identification of possible hypoxia sensor for behavioral responses in a marine annelid, Capitella teleta. PMID:30745436
CRISPR/Cas9-mediated endogenous gene tagging in Fusarium oxysporum. PMID:30738140
RNA-Seq Transcriptome Profiling of the Queen Scallop (Aequipecten opercularis) Digestive Gland after Exposure to Domoic Acid-Producing Pseudo-nitzschia. PMID:30736356
Identification of non-specific Lipid Transfer Protein gene family members in Solanum lycopersicum and insights into the features of Sola l 3 protein. PMID:30733555
Bioinformatic discovery of a toxin family in Chryseobacterium piperi with sequence similarity to botulinum neurotoxins. PMID:30733520
Characterization of a phospholipid-regulated β-galactosidase from Akkermansia muciniphila involved in mucin degradation. PMID:30729732
Antimicrobial peptides from Rana [Lithobates] catesbeiana: Gene structure and bioinformatic identification of novel forms from tadpoles. PMID:30728430
Protein analysis reveals differential accumulation of late embryogenesis abundant and storage proteins in seeds of wild and cultivated amaranth species. PMID:30727945
Evolution of the modular, disordered stress proteins known as dehydrins. PMID:30726271
mlDEEPre: Multi-Functional Enzyme Function Prediction With Hierarchical Multi-Label Deep Learning. PMID:30723495
n-3 PUFA biosynthesis by the copepod Apocyclops royi documented using fatty acid profile analysis and gene expression analysis. PMID:30723075
Mycobacterium tuberculosis Rv0366c-Rv0367c encodes a non-canonical PezAT-like toxin-antitoxin pair. PMID:30718534
Integration of Self and Non-self Recognition Modulates Asexual Cell-to-Cell Communication in Neurospora crassa. PMID:30718271
Complete Genome Sequence of the Wolbachia wAlbB Endosymbiont of Aedes albopictus. PMID:30715337
Pan-genome analyses of model fungal species. PMID:30714895
Genome-wide identification and characterization of Hsp70 gene family in Nicotiana tabacum. PMID:30710231
Structural and Phylogenetic Diversity of Anaerobic Carbon-Monoxide Dehydrogenases. PMID:30705673
Bioinformatics Analysis of Metabolism Pathways of Archaeal Energy Reserves. PMID:30705313
Marine biofilms constitute a bank of hidden microbial diversity and functional potential. PMID:30705275
Genome-wide association analysis of stalk biomass and anatomical traits in maize. PMID:30704393
HuVarBase: A human variant database with comprehensive information at gene and protein levels. PMID:30703169
Evolution of vertebrate nicotinic acetylcholine receptors. PMID:30700248
Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures. PMID:30699115
Genome-wide characterization and expression analyses of the MYB superfamily genes during developmental stages in Chinese jujube. PMID:30697496
Genome-wide characterization and expression profiling of SWEET genes in cabbage (Brassica oleracea var. capitata L.) reveal their roles in chilling and clubroot disease responses. PMID:30696401
Structure and Evolution of Glycogen Branching Enzyme N-Termini From Bacteria. PMID:30692986
Genome structure and evolution of Antirrhinum majus L. PMID:30692677
ensembldb: an R package to create and use Ensembl-based annotation resources. PMID:30689724
Clinical trials, progression-speed differentiating features and swiftness rule of the innovative targets of first-in-class drugs. PMID:30689717
Comparative transcriptomics in Leishmania braziliensis: disclosing differential gene expression of coding and putative noncoding RNAs across developmental stages. PMID:30689499
LMI1-like and KNOX1 genes coordinately regulate plant leaf development in dicotyledons. PMID:30689141
Metagenomic Evidence for a Methylocystis Species Capable of Bioremediation of Diverse Heavy Metals. PMID:30687279
Extent and Origins of Functional Diversity in a Subfamily of Glycoside Hydrolases. PMID:30685401
Potential for Heightened Sulfur-Metabolic Capacity in Coastal Subtropical Microalgae. PMID:30684492
Chromosome conformation capture resolved near complete genome assembly of broomcorn millet. PMID:30683940
The genome of broomcorn millet. PMID:30683860
Symbiont type and environmental factors affect transcriptome-wide gene expression in the coral Montipora capitata. PMID:30680121
Tissue-Specific Transcriptome Analysis Reveals Candidate Genes for Terpenoid and Phenylpropanoid Metabolism in the Medicinal Plant Ferula assafoetida. PMID:30679248
Ask1 and Akt act synergistically to promote ROS-dependent regeneration in Drosophila. PMID:30677014
Robust predictions of specialized metabolism genes through machine learning. PMID:30674669
Leaf rust (Puccinia triticina) mediated RNAi in wheat (Triticum aestivum L.) prompting host susceptibility. PMID:30671704
Newly Discovered Occurrences and Gene Tree of the Extracellular Globins and Linker Chains from the Giant Hexagonal Bilayer Hemoglobin in Metazoans. PMID:30668717
Defining novel plant polyamine oxidase subfamilies through molecular modeling and sequence analysis. PMID:30665356
Role of the highly conserved G68 residue in the yeast phosphorelay protein Ypd1: implications for interactions between histidine phosphotransfer (HPt) and response regulator proteins. PMID:30665347
An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis. PMID:30661980
Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO). PMID:30660046
Proteogenomics Reveals Novel Reductive Dehalogenases and Methyltransferases Expressed during Anaerobic Dichloromethane Metabolism. PMID:30658979
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
Building Bridges Between Structural and Network-Based Systems Biology. PMID:30656572
Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns. PMID:30655514
Engineering a conserved RNA regulatory protein repurposes its biological function in vivo. PMID:30652968
Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi. PMID:30651609
Re-analysis of the coral Acropora digitifera transcriptome reveals a complex lncRNAs-mRNAs interaction network implicated in Symbiodinium infection. PMID:30651068
Genome-Wide Identification and Transcriptional Expression of the PAL Gene Family in Common Walnut (Juglans Regia L.). PMID:30650597
The Evolutionary Traceability of a Protein. PMID:30649284
Genome-Wide Comparison of Carbohydrate-Active Enzymes (CAZymes) Repertoire of Flammulina ononidis. PMID:30637143
Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community. PMID:30635580
Electron and Proton Flux for Carbon Dioxide Reduction in Methanosarcina barkeri During Direct Interspecies Electron Transfer. PMID:30631315
Systematic analysis of NAC transcription factors' gene family and identification of post-flowering drought stress responsive members in sorghum. PMID:30627770
Analysis of the complete genome sequence of a marine-derived strain Streptomyces sp. S063 CGMCC 14582 reveals its biosynthetic potential to produce novel anti-complement agents and peptides. PMID:30627488
Evolution of the Natural Transformation Protein, ComEC, in Bacteria. PMID:30627116
Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing. PMID:30626323
Biosynthetic Gene Content of the 'Perfume Lichens' Evernia prunastri and Pseudevernia furfuracea. PMID:30626017
Prediction of deleterious mutations in coding regions of mammals with transfer learning. PMID:30622632
The use of next generation sequencing for improving food safety: Translation into practice. PMID:30621881
Insight Into the Diversity and Possible Role of Plasmids in the Adaptation of Psychrotolerant and Metalotolerant Arthrobacter spp. to Extreme Antarctic Environments. PMID:30619210
Differential Protein Expression During Growth on Medium Versus Long-Chain Alkanes in the Obligate Marine Hydrocarbon-Degrading Bacterium Thalassolituus oleivorans MIL-1. PMID:30619200
Genomic and Genetic Insights Into a Cosmopolitan Fungus, Paecilomyces variotii (Eurotiales). PMID:30619145
Hybrid sequencing-based personal full-length transcriptomic analysis implicates proteostatic stress in metastatic ovarian cancer. PMID:30617306
A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication. PMID:30616511
Sequence analysis and confirmation of the type IV pili-associated proteins PilY1, PilW and PilV in Acidithiobacillus thiooxidans. PMID:30615628
Activation of the Bile Acid Pathway and No Observed Antimicrobial Peptide Sequences in the Skin of a Poison Frog. PMID:30606754
Candidatus Dactylopiibacterium carminicum, a Nitrogen-Fixing Symbiont of Dactylopius Cochineal Insects (Hemiptera: Coccoidea: Dactylopiidae). PMID:30605507
Comparative metabolic profiling of Vitis amurensis and Vitis vinifera during cold acclimation. PMID:30603094
Unknown mutations and genotype/phenotype correlations of autosomal recessive congenital ichthyosis in patients from Saudi Arabia and Pakistan. PMID:30600594
Detection and genetic characterization of porcine pegivirus from pigs in China. PMID:30600430
Analysis of Dendrobium huoshanense transcriptome unveils putative genes associated with active ingredients synthesis. PMID:30594136
Genome wide characterization of barley NAC transcription factors enables the identification of grain-specific transcription factors exclusive for the Poaceae family of monocotyledonous plants. PMID:30592743
Insights into photoreceptor ciliogenesis revealed by animal models. PMID:30590118
Global transcriptome analysis of the aphelid Paraphelidium tribonemae supports the phagotrophic origin of fungi. PMID:30588510
Genomic Signals of Adaptation towards Mutualism and Sociality in Two Ambrosia Beetle Complexes. PMID:30583535
The ER membrane protein complex promotes biogenesis of sterol-related enzymes maintaining cholesterol homeostasis. PMID:30578317
Plant-specific ribosome biogenesis factors in Arabidopsis thaliana with essential function in rRNA processing. PMID:30576513
Sequence variation, evolutionary constraint, and selection at the CD163 gene in pigs. PMID:30572815
EspL is essential for virulence and stabilizes EspE, EspF and EspH levels in Mycobacterium tuberculosis. PMID:30571761
Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains. PMID:30568804
Comprehensive profiling of the fission yeast transcription start site activity during stress and media response. PMID:30566651
Characterization and Expression Profiling of Neuropeptides and G-Protein-Coupled Receptors (GPCRs) for Neuropeptides in the Asian Citrus Psyllid, Diaphorina citri (Hemiptera: Psyllidae). PMID:30563248
Predicted glycosyltransferases promote development and prevent spurious cell clumping in the choanoflagellate S. rosetta. PMID:30556809
PlantEAR: Functional Analysis Platform for Plant EAR Motif-Containing Proteins. PMID:30555515
Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments. PMID:30555444
Understanding the Mechanisms Behind the Response to Environmental Perturbation in Microbial Mats: A Metagenomic-Network Based Approach. PMID:30555424
The novel EHEC gene asa overlaps the TEGT transporter gene in antisense and is regulated by NaCl and growth phase. PMID:30552341
Vertebrate SLRP family evolution and the subfunctionalization of osteoglycin gene duplicates in teleost fish. PMID:30545285
Proteomics Analysis Reveals That Caspase-Like and Metacaspase-Like Activities Are Dispensable for Activation of Proteases Involved in Early Response to Biotic Stress in Triticum aestivum L. PMID:30544979
Effect of Aspergillus flavus Fungal Elicitor on the Production of Terpenoid Indole Alkaloids in Catharanthus roseus Cambial Meristematic Cells. PMID:30544939
Genome-Wide Identification and Analysis of HAK/KUP/KT Potassium Transporters Gene Family in Wheat (Triticum aestivum L.). PMID:30544665
Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes. PMID:30544207
Structural characterization and molecular dynamics simulations of the caprine and bovine solute carrier family 11 A1 (SLC11A1). PMID:30543052
An updated gene atlas for maize reveals organ-specific and stress-induced genes. PMID:30537259
Periplasmic protein EipA determines envelope stress resistance and virulence in Brucella abortus. PMID:30536925
Divergence between bread wheat and Triticum militinae in the powdery mildew resistance QPm.tut-4A locus and its implications for cloning of the resistance gene. PMID:30535646
Comparative Analysis of Oomycete Genome Evolution Using the Oomycete Gene Order Browser (OGOB). PMID:30535146
Complete genome of Rhizobium leguminosarum Norway, an ineffective Lotus micro-symbiont. PMID:30534351
High-Quality Draft Genome Sequences of Eight Bacteria Isolated from Fungus Gardens Grown by Trachymyrmex septentrionalis Ants. PMID:30533809
Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment. PMID:30531977
A map of constrained coding regions in the human genome. PMID:30531870
New insights into the evolution of wheat avenin-like proteins in wild emmer wheat (Triticum dicoccoides). PMID:30530679
Photoperiod response-related gene SiCOL1 contributes to flowering in sesame. PMID:30526484
Genome-wide identification, molecular evolution, and expression analysis of auxin response factor (ARF) gene family in Brachypodium distachyon L. PMID:30522432
Daily changes in phytoplankton lipidomes reveal mechanisms of energy storage in the open ocean. PMID:30518752
Reconstructing the evolutionary history of F420-dependent dehydrogenases. PMID:30514849
Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress. PMID:30514299
The evolution of ependymin-related proteins. PMID:30514200
X-ray crystallographic analysis of the catalytic domain of α-1,3-glucanase FH1 from Paenibacillus glycanilyticus overexpressed in Brevibacillus choshinensis. PMID:30511670
Genome mining reveals uncommon alkylpyrones as type III PKS products from myxobacteria. PMID:30506464
Oligopeptide Signaling through TbGPR89 Drives Trypanosome Quorum Sensing. PMID:30503212
Genome-Wide Analysis of LRR-RLK Gene Family in Four Gossypium Species and Expression Analysis during Cotton Development and Stress Responses. PMID:30501109
An auxin controls bacterial antibiotics production. PMID:30500953
SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database. PMID:30500919
Representativeness of variation benchmark datasets. PMID:30497376
CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise. PMID:30486838
Evolutionary diversity and novelty of DNA repair genes in asexual Bdelloid rotifers. PMID:30486781
Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing. PMID:30477428
ENPD - A Database of Eukaryotic Nucleic Acid Binding Proteins: Linking Gene Regulations to Proteins. PMID:30476229
Coevolution of hytrosaviruses and host immune responses. PMID:30470186
Enhancing the Production of the Fungal Pigment Aurofusarin in Fusarium graminearum. PMID:30469367
Pivotal role of bZIPs in amylose biosynthesis by genome survey and transcriptome analysis in wheat (Triticum aestivum L.) mutants. PMID:30467374
Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions. PMID:30464192
Draft genome sequence and detailed characterization of biofuel production by oleaginous microalga Scenedesmus quadricauda LWG002611. PMID:30455737
Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance. PMID:30454646
Metabolic functions of the human gut microbiota: the role of metalloenzymes. PMID:30452039
Large-scale in-silico statistical mutagenesis analysis sheds light on the deleteriousness landscape of the human proteome. PMID:30451933
Hidden diversity of soil giant viruses. PMID:30451857
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. PMID:30445541
Genome-wide detection of terpene synthase genes in holy basil (Ocimum sanctum L.). PMID:30444870
The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain. PMID:30443017
Genome-wide analysis of the soybean CRK-family and transcriptional regulation by biotic stress signals triggering plant immunity. PMID:30440039
Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics. PMID:30429574
Structural insights into the function of type VI secretion system TssA subunits. PMID:30420757
Comprehensive evaluation of RNA-seq analysis pipelines in diploid and polyploid species. PMID:30418578
Discovery of three RNA viruses using ant transcriptomic datasets. PMID:30415391
Exploring the rearrangement of sensory intelligence in proteobacteria: insight of Pho regulon. PMID:30413888
CRELD1 is an evolutionarily-conserved maturational enhancer of ionotropic acetylcholine receptors. PMID:30407909
Cancer3D 2.0: interactive analysis of 3D patterns of cancer mutations in cancer subsets. PMID:30407596
Structural analysis of fungal CENP-H/I/K homologs reveals a conserved assembly mechanism underlying proper chromosome alignment. PMID:30407575
Polypharmacology or Promiscuity? Structural Interactions of Resveratrol With Its Bandwagon of Targets. PMID:30405416
SLiM-Enrich: computational assessment of protein-protein interaction data as a source of domain-motif interactions. PMID:30402352
Exploring Seipin: From Biochemistry to Bioinformatics Predictions. PMID:30402103
Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour. PMID:30400813
InterPro in 2019: improving coverage, classification and access to protein sequence annotations. PMID:30398656
Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing. PMID:30397543
A de Novo EDA-Variant in a Litter of Shorthaired Standard Dachshunds with X-Linked Hypohidrotic Ectodermal Dysplasia. PMID:30397018
Unexpected Evolution of Lesion-Recognition Modules in Eukaryotic NER and Kinetoplast DNA Dynamics Proteins from Bacterial Mobile Elements. PMID:30396152
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
VFDB 2019: a comparative pathogenomic platform with an interactive web interface. PMID:30395255
Ferredoxins as interchangeable redox components in support of MiaB, a radical S-adenosylmethionine methylthiotransferase. PMID:30394621
Insights into the Evolution of Shells and Love Darts of Land Snails Revealed from Their Matrix Proteins. PMID:30388206
High-quality-draft genome sequence of the multiple heavy metal resistant bacterium Pseudaminobacter manganicus JH-7T. PMID:30386456
Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages. PMID:30384840
Comparative genomic and methylome analysis of non-virulent D74 and virulent Nagasaki Haemophilus parasuis isolates. PMID:30383795
Identification and characterization of a large family of superbinding bacterial SH2 domains. PMID:30382091
Silencing of retrotransposon-derived imprinted gene RTL1 is the main cause for postimplantational failures in mammalian cloning. PMID:30381455
iEKPD 2.0: an update with rich annotations for eukaryotic protein kinases, protein phosphatases and proteins containing phosphoprotein-binding domains. PMID:30380109
dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data. PMID:30380085
Genomic distribution of a novel Pyrenophora tritici-repentis ToxA insertion element. PMID:30379913
Species-level functional profiling of metagenomes and metatranscriptomes. PMID:30377376
New insights into tomato microRNAs. PMID:30375421
Immunotopological Analysis of the Treponema denticola Major Surface Protein (Msp). PMID:30373754
Adhesins of Yeasts: Protein Structure and Interactions. PMID:30373267
Genome-Wide Identification and Characterization of Pectin Methylesterase Inhibitor Genes in Brassica oleracea. PMID:30373125
PubChem 2019 update: improved access to chemical data. PMID:30371825
Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances. PMID:30371672
Phylogenetic and conservation analyses of MFS transporters. PMID:30370203
Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities. PMID:30370186
Application of Proteomics Technologies in Oil Palm Research. PMID:30367348
Phosphodiesterase Genes Regulate Amylovoran Production, Biofilm Formation, and Virulence in Erwinia amylovora. PMID:30366999
Co-Evolution of Intrinsically Disordered Proteins with Folded Partners Witnessed by Evolutionary Couplings. PMID:30366362
Database Resources of the BIG Data Center in 2019. PMID:30365034
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes. PMID:30364992
FlyBase 2.0: the next generation. PMID:30364959
Comparative Genomics of Aspergillus flavus S and L Morphotypes Yield Insights into Niche Adaptation. PMID:30361280
Desiccation Tolerance Evolved through Gene Duplication and Network Rewiring in Lindernia. PMID:30361236
Comparative De Novo transcriptome analysis of the Australian black-lip and Sydney rock oysters reveals expansion of repetitive elements in Saccostrea genomes. PMID:30359422
De novo assembly and transcriptome of Pfaffia glomerata uncovers the role of photoautotrophy and the P450 family genes in 20-hydroxyecdysone production. PMID:30357479
The Pfam protein families database in 2019. PMID:30357350
Overlapping Patterns of Gene Expression Between Gametophyte and Sporophyte Phases in the Fern Polypodium amorphum (Polypodiales). PMID:30356815
A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage. PMID:30352623
Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families. PMID:30351380
Discovery of Bacterial Deaminases That Convert 5-Fluoroisocytosine Into 5-Fluorouracil. PMID:30349513
Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes. PMID:30349087
Computationally-guided drug repurposing enables the discovery of kinase targets and inhibitors as new schistosomicidal agents. PMID:30346968
Suppressor mutations reveal an NtrC-like response regulator, NmpR, for modulation of Type-IV Pili-dependent motility in Myxococcus xanthus. PMID:30346960
Complete Genome Sequence of Bacillus cereus CC-1, A Novel Marine Selenate/Selenite Reducing Bacterium Producing Metallic Selenides Nanomaterials. PMID:30343326
Unveiling gibberellin-responsive coding and long noncoding RNAs in maize. PMID:30341662
Diversity and evolution of cytochromes P450 in stramenopiles. PMID:30341489
The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales. PMID:30340631
A Negative-Stranded RNA Virus Infecting Citrus Trees: The Second Member of a New Genus Within the Order Bunyavirales. PMID:30333811
Saccharomyces paradoxus K66 Killer System Evidences Expanded Assortment of Helper and Satellite Viruses. PMID:30332789
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
Firefly genomes illuminate parallel origins of bioluminescence in beetles. PMID:30324905
Unicellular Origin of the Animal MicroRNA Machinery. PMID:30318349
Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus. PMID:30314449
PQ, a new program for phylogeny reconstruction. PMID:30314446
Overexpression of a Novel ROP Gene from the Banana (MaROP5g) Confers Increased Salt Stress Tolerance. PMID:30314273
Domain architecture of BAF250a reveals the ARID and ARM-repeat domains with implication in function and assembly of the BAF remodeling complex. PMID:30307988
Genome-wide analysis of fitness data and its application to improve metabolic models. PMID:30305012
Towards region-specific propagation of protein functions. PMID:30304483
Order in Disorder as Observed by the "Hydrophobic Cluster Analysis" of Protein Sequences. PMID:30299594
Is the genetic variability of Cathepsin B important in the pathogenesis of Blastocystis spp.? PMID:30298236
Embryonic transcriptome sequencing of the ocellate spot skate Okamejei kenojei. PMID:30295675
Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles. PMID:30291328
Genome-wide analysis of the plant-specific PLATZ proteins in maize and identification of their general role in interaction with RNA polymerase III complex. PMID:30290770
A draft genome of the striped catfish, Pangasianodon hypophthalmus, for comparative analysis of genes relevant to development and a resource for aquaculture improvement. PMID:30290758
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. PMID:30289528
Evidence for Stabilizing Selection Driving Mutational Turnover of Short Motifs in the Eukaryotic Complementary Sex Determiner (Csd) Protein. PMID:30287489
Environmental pH modulates transcriptomic responses in the fungus Fusarium sp. associated with KSHB Euwallacea sp. near fornicatus. PMID:30285612
Crystal structure and functional analysis of human C1ORF123. PMID:30280012
Molecular characterization of putative neuropeptide, amine, diffusible gas and small molecule transmitter biosynthetic enzymes in the eyestalk ganglia of the American lobster, Homarus americanus. PMID:30276482
Protein AMPylation by an Evolutionarily Conserved Pseudokinase. PMID:30270044
'Democratized' genomic enzymology web tools for functional assignment. PMID:30268904
DNA Motif Recognition Modeling from Protein Sequences. PMID:30267681
The interplay between membrane lipids and phospholipase A family members in grapevine resistance against Plasmopara viticola. PMID:30266912
The Origin of Mitochondria-Specific Outer Membrane β-Barrels from an Ancestral Bacterial Fragment. PMID:30265295
Considerations for Optimization of High-Throughput Sequencing Bioinformatics Pipelines for Virus Detection. PMID:30262776
Identification of a novel zinc-binding protein, C1orf123, as an interactor with a heavy metal-associated domain. PMID:30260988
Identification of Moonlighting Proteins in Genomes Using Text Mining Techniques. PMID:30260564
Novel Class of Viral Ankyrin Proteins Targeting the Host E3 Ubiquitin Ligase Cullin-2. PMID:30258003
The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing. PMID:30252911
Genome-scale analysis of Acetobacterium bakii reveals the cold adaptation of psychrotolerant acetogens by post-transcriptional regulation. PMID:30249742
Novel Metabolic Pathways and Regulons for Hexuronate Utilization in Proteobacteria. PMID:30249705
Robustness by intrinsically disordered C-termini and translational readthrough. PMID:30247639
Differential expression of the adult specifier E93 in the strepsipteran Xenos vesparum Rossi suggests a role in female neoteny. PMID:30242215
ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature. PMID:30241466
Chemoreceptor proteins in the Caribbean spiny lobster, Panulirus argus: Expression of Ionotropic Receptors, Gustatory Receptors, and TRP channels in two chemosensory organs and brain. PMID:30240423
POSTAR2: deciphering the post-transcriptional regulatory logics. PMID:30239819
PalmXplore: oil palm gene database. PMID:30239681
Consensus design for improved thermostability of lipoxygenase from Anabaena sp. PCC 7120. PMID:30236091
Talaropeptides A-D: Structure and Biosynthesis of Extensively N-methylated Linear Peptides From an Australian Marine Tunicate-Derived Talaromyces sp. PMID:30234104
Comparative genomics of molybdenum utilization in prokaryotes and eukaryotes. PMID:30231876
Exploring transcription factors reveals crucial members and regulatory networks involved in different abiotic stresses in Brassica napus L. PMID:30231862
Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host. PMID:30231855
Cloning and Characterization of Limonoid Glucosyltransferase from Kinnow Mandarin (Citrus reticulata Blanco). PMID:30228797
Parallel Evolution of Genome Streamlining and Cellular Bioenergetics across the Marine Radiation of a Bacterial Phylum. PMID:30228235
The kinome of pineapple: catalog and insights into functions in crassulacean acid metabolism plants. PMID:30227850
Six domesticated PiggyBac transposases together carry out programmed DNA elimination in Paramecium. PMID:30223944
Maintaining Biological Cultures and Measuring Gene Expression in Aphis nerii: A Non-model System for Plant-insect Interactions. PMID:30222148
WaspBase: a genomic resource for the interactions among parasitic wasps, insect hosts and plants. PMID:30219838
Diversity of Active Viral Infections within the Sphagnum Microbiome. PMID:30217851
Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas. PMID:30217226
The MAP4 Kinase SIK1 Ensures Robust Extracellular ROS Burst and Antibacterial Immunity in Plants. PMID:30212650
A General Protein O-Glycosylation Gene Cluster Encodes the Species-Specific Glycan of the Oral Pathogen Tannerella forsythia: O-Glycan Biosynthesis and Immunological Implications. PMID:30210478
Functional Characterization of c-di-GMP Signaling-Related Genes in the Probiotic Lactobacillus acidophilus. PMID:30210464
Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation. PMID:30210232
Distribution, Diversity, and Evolution of Endogenous Retroviruses in Perissodactyl Genomes. PMID:30209175
AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors. PMID:30204897
Signaling specificity in the c-di-GMP-dependent network regulating antibiotic synthesis in Lysobacter. PMID:30202891
Sinorhizobium meliloti Chemoreceptor McpV Senses Short-Chain Carboxylates via Direct Binding. PMID:30201781
YraP Contributes to Cell Envelope Integrity and Virulence of Salmonella enterica Serovar Typhimurium. PMID:30201701
Comprehensive off-target analysis of dCas9-SAM-mediated HIV reactivation via long noncoding RNA and mRNA profiling. PMID:30200981
Genome-wide identification and expression analyses of the pectate lyase (PEL) gene family in cotton (Gossypium hirsutum L.). PMID:30200887
Pseudomonas aeruginosa utilizes host polyunsaturated phosphatidylethanolamines to trigger theft-ferroptosis in bronchial epithelium. PMID:30198910
TssA from Aeromonas hydrophila: expression, purification and crystallographic studies. PMID:30198891
Uncoiling CNLs: Structure/Function Approaches to Understanding CC Domain Function in Plant NLRs. PMID:30192967
Sequence-guided approach to genotyping plant clones and species using polymorphic NB-ARC-related genes. PMID:30191440
The Ly6/uPAR protein Bouncer is necessary and sufficient for species-specific fertilization. PMID:30190407
What bacteria want. PMID:30187651
In silico Study of Iron, Zinc and Copper Binding Proteins of Pseudomonas syringae pv. lapsa: Emphasis on Secreted Metalloproteins. PMID:30186242
Insights into autophagosome biogenesis from structural and biochemical analyses of the ATG2A-WIPI4 complex. PMID:30185561
The genome of Naegleria lovaniensis, the basis for a comparative approach to unravel pathogenicity factors of the human pathogenic amoeba N. fowleri. PMID:30185166
Identification and comparison of key RNA interference machinery from western corn rootworm, fall armyworm, and southern green stink bug. PMID:30183751
Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea. PMID:30175688
Widespread evolutionary crosstalk among protein domains in the context of multi-domain proteins. PMID:30169546
Respiratory chain Complex I of unparalleled divergence in diplonemids. PMID:30166340
A glutaredoxin domain fused to the radical-generating subunit of ribonucleotide reductase (RNR) functions as an efficient RNR reductant. PMID:30166338
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences. PMID:30165572
Circular RNAs in the cardiovascular system. PMID:30159434
The hemicellulose-degrading enzyme system of the thermophilic bacterium Clostridium stercorarium: comparative characterisation and addition of new hemicellulolytic glycoside hydrolases. PMID:30159029
A family of silicon transporter structural genes in a pennate diatom Synedra ulna subsp. danica (Kütz.) Skabitsch. PMID:30157241
Comparative analysis of whole flower transcriptomes in the Zingiberales. PMID:30155368
The Pseudomonas aeruginosa Orphan Quorum Sensing Signal Receptor QscR Regulates Global Quorum Sensing Gene Expression by Activating a Single Linked Operon. PMID:30154259
The copper-deprivation stimulon of Corynebacterium glutamicum comprises proteins for biogenesis of the actinobacterial cytochrome bc 1-aa 3 supercomplex. PMID:30154248
A miR172 target-deficient AP2-like gene correlates with the double flower phenotype in roses. PMID:30150746
Genome-wide Identification of PP2C Genes and Their Expression Profiling in Response to Drought and Cold Stresses in Medicago truncatula. PMID:30150630
Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation. PMID:30143032
Instant Clue: A Software Suite for Interactive Data Visualization and Analysis. PMID:30140043
Genomic analysis of the original Elberg Brucella melitensis Rev.1 vaccine strain reveals insights into virulence attenuation. PMID:30139304
Genomic and molecular analysis of conserved and unique features of soybean PIF4. PMID:30135599
Complete genome of streamlined marine actinobacterium Pontimonas salivibrio strain CL-TW6T adapted to coastal planktonic lifestyle. PMID:30134835
Genomic analysis of an Argentinean isolate of Spodoptera frugiperda granulovirus reveals that various baculoviruses code for Lef-7 proteins with three F-box domains. PMID:30133523
Discovering Putative Prion-Like Proteins in Plasmodium falciparum: A Computational and Experimental Analysis. PMID:30131778
mRNA-specific translation regulation by a ribosome-associated ncRNA in Haloferax volcanii. PMID:30131517
Draft genome of Glyptosternon maculatum, an endemic fish from Tibet Plateau. PMID:30124856
Early Diverging Insect-Pathogenic Fungi of the Order Entomophthorales Possess Diverse and Unique Subtilisin-Like Serine Proteases. PMID:30111619
Approaches to target tractability assessment - a practical perspective. PMID:30108951
Comprehensive evaluation of coding region point mutations in microsatellite-unstable colorectal cancer. PMID:30108113
Cloning and characterization of trehalase: a conserved glycosidase from oriental midge, Chironomus ramosus. PMID:30105177
Characterization of a L-Gulono-1,4-Lactone Oxidase Like Protein in the Floral Nectar of Mucuna sempervirens, Fabaceae. PMID:30105046
Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica. PMID:30104475
Multiple optic gland signaling pathways implicated in octopus maternal behaviors and death. PMID:30104305
Evolutionary diversification of the HAP2 membrane insertion motifs to drive gamete fusion across eukaryotes. PMID:30102690
Xenacoelomorpha Survey Reveals That All 11 Animal Homeobox Gene Classes Were Present in the First Bilaterians. PMID:30102357
Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. PMID:30097089
Genome-wide CRISPR screen identifies TMEM41B as a gene required for autophagosome formation. PMID:30093494
4-Hydroxy-tetrahydrodipicolinate reductase from Neisseria gonorrhoeae - structure and interactions with coenzymes and substrate analog. PMID:30093108
RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of fully mycoheterotrophic plants. PMID:30092758
Comparative transcriptomics of limb regeneration: Identification of conserved expression changes among three species of Ambystoma. PMID:30092345
Structural basis of cell wall anchoring by SLH domains in Paenibacillus alvei. PMID:30087354
A glutamine riboswitch is a key element for the regulation of glutamine synthetase in cyanobacteria. PMID:30085248
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. PMID:30084866
A metagenomic analysis of the camel rumen's microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation. PMID:30083229
Identification of a G2-like transcription factor, OsPHL3, functions as a negative regulator of flowering in rice by co-expression and reverse genetic analysis. PMID:30081823
Full-length transcriptome of Misgurnus anguillicaudatus provides insights into evolution of genus Misgurnus. PMID:30076392
Structure and nucleic acid binding properties of KOW domains 4 and 6-7 of human transcription elongation factor DSIF. PMID:30076330
Characterization of capsule genes in non-pathogenic Neisseria species. PMID:30074474
Alternatively spliced variants in Atlantic cod (Gadus morhua) support response to variable salinity environment. PMID:30072755
An Aspartate-Specific Solute-Binding Protein Regulates Protein Kinase G Activity To Control Glutamate Metabolism in Mycobacteria. PMID:30065086
BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea. PMID:30063227
Application of Transcriptomics to Compare the Carbohydrate Active Enzymes That Are Expressed by Diverse Genera of Anaerobic Fungi to Degrade Plant Cell Wall Carbohydrates. PMID:30061875
Biochemical and Phylogenetic Study of SltF, a Flagellar Lytic Transglycosylase from Rhodobacter sphaeroides. PMID:30061356
Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14. PMID:30060533
A Novel β-Glucuronidase from Talaromyces pinophilus Li-93 Precisely Hydrolyzes Glycyrrhizin into Glycyrrhetinic Acid 3-O-Mono-β-d-Glucuronide. PMID:30054355
FRETting about the affinity of bimolecular protein-protein interactions. PMID:30052312
Pectobacterium atrosepticum Phage vB_PatP_CB5: A Member of the Proposed Genus 'Phimunavirus'. PMID:30050020
Genetic correlation network prediction of forest soil microbial functional organization. PMID:30046166
Transposon Insertion Sequencing Elucidates Novel Gene Involvement in Susceptibility and Resistance to Phages T4 and T7 in Escherichia coli O157. PMID:30042196
Interaction of lipoprotein QseG with sensor kinase QseE in the periplasm controls the phosphorylation state of the two-component system QseE/QseF in Escherichia coli. PMID:30040820
Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome. PMID:30038309
Homology Inference Based on a Reconciliation Approach for the Comparative Genomics of Protozoa. PMID:30034216
Comparative proteomics of two Mycoplasma hyopneumoniae strains and Mycoplasma flocculare identified potential porcine enzootic pneumonia determinants. PMID:30027802
Coevolution-based inference of amino acid interactions underlying protein function. PMID:30024376
Assessing European Wheat Sensitivities to Parastagonospora nodorum Necrotrophic Effectors and Fine-Mapping the Snn3-B1 Locus Conferring Sensitivity to the Effector SnTox3. PMID:30022985
De novo profile generation based on sequence context specificity with the long short-term memory network. PMID:30021530
Highly active enzymes by automated combinatorial backbone assembly and sequence design. PMID:30018322
Morphological Stasis and Proteome Innovation in Cephalochordates. PMID:30013013
Studying Smaller and Neglected Organisms in Modern Evolutionary Venomics Implementing RNASeq (Transcriptomics)-A Critical Guide. PMID:30012955
Evolution and expression patterns of the trehalose-6-phosphate synthase gene family in drumstick tree (Moringa oleifera Lam.). PMID:30006657
A high-throughput method to identify trans-activation domains within transcription factor sequences. PMID:30006452
Transcriptome analysis of Cd-treated switchgrass root revealed novel transcripts and the importance of HSF/HSP network in switchgrass Cd tolerance. PMID:30003312
CRISPR-Cas systems in multicellular cyanobacteria. PMID:29995583
Shepherding DNA ends: Rif1 protects telomeres and chromosome breaks. PMID:29992129
Enoxacin extends lifespan of C. elegans by inhibiting miR-34-5p and promoting mitohormesis. PMID:29986212
Bioinformatic Expansion and Discovery of Thiopeptide Antibiotics. PMID:29983054
Members of the Arabidopsis FORKED1-LIKE gene family act to localize PIN1 in developing veins. PMID:29982821
Loose ends: almost one in five human genes still have unresolved coding status. PMID:29982784
Clinker: visualizing fusion genes detected in RNA-seq data. PMID:29982439
Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes. PMID:29980796
Identification of a New Antimicrobial Resistance Gene Provides Fresh Insights Into Pleuromutilin Resistance in Brachyspira hyodysenteriae, Aetiological Agent of Swine Dysentery. PMID:29971045
Plasmids of Psychrotolerant Polaromonas spp. Isolated From Arctic and Antarctic Glaciers - Diversity and Role in Adaptation to Polar Environments. PMID:29967598
Genome-Wide Association Analyses Reveal the Importance of Alternative Splicing in Diversifying Gene Function and Regulating Phenotypic Variation in Maize. PMID:29967286
Computational identification and evolutionary analysis of toxins in Mosquitocidal Bacillus thuringiensis strain S2160-1. PMID:29963353
A Bcl-2 Associated Athanogene (bagA) Modulates Sexual Development and Secondary Metabolism in the Filamentous Fungus Aspergillus nidulans. PMID:29963036
Microbial Community Structure-Function Relationships in Yaquina Bay Estuary Reveal Spatially Distinct Carbon and Nitrogen Cycling Capacities. PMID:29963029
Clustering huge protein sequence sets in linear time. PMID:29959318
Complete Genome Sequences of Two T4-Like Escherichia coli Bacteriophages. PMID:29954900
Draft Genome Sequence of the Antimicrobial-Producing Strain Paenibacillus elgii AC13. PMID:29954895
Uncovering the molecular mechanisms behind disease-associated leptin variants. PMID:29950524
Engineering Geobacillus thermodenitrificans to introduce cellulolytic activity; expression of native and heterologous cellulase genes. PMID:29945583
Wnt/β-catenin signalling is necessary for gut differentiation in a marine annelid, Platynereis dumerilii. PMID:29942461
Prediction of auxin response elements based on data fusion in Arabidopsis thaliana. PMID:29936576
Molecular characterization of a stress-induced NAC gene, GhSNAC3, from Gossypium hirsutum. PMID:29932074
RBPMetaDB: a comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins. PMID:29931156
Comprehensive in-silico prediction of damage associated SNPs in Human Prolidase gene. PMID:29930383
Arabidopsis response to the spider mite Tetranychus urticae depends on the regulation of reactive oxygen species homeostasis. PMID:29930298
Landscape of transcription and long non-coding RNAs reveals new insights into the inflammatory and fibrotic response following ventilator-induced lung injury. PMID:29929510
SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements. PMID:29928511
Genome-wide identification and classification of MYB superfamily genes in peach. PMID:29927971
Computational Methods for Predicting Protein-Protein Interactions Using Various Protein Features. PMID:29927082
Homeobox Gene Duplication and Divergence in Arachnids. PMID:29924328
The aggregation-promoting factor in Lactobacillus delbrueckii ssp. bulgaricus: confirmation of the presence and expression of the apf gene and in silico analysis of the corresponding protein. PMID:29923077
Annotation and profiling of barley GLYCOGEN SYNTHASE3/Shaggy-like genes indicated shift in organ-preferential expression. PMID:29920545
Gene Discovery of Characteristic Metabolic Pathways in the Tea Plant (Camellia sinensis) Using 'Omics'-Based Network Approaches: A Future Perspective. PMID:29915604
Thailandamide, a Fatty Acid Synthesis Antibiotic That Is Coexpressed with a Resistant Target Gene. PMID:29914944
Single-strand DNA processing: phylogenomics and sequence diversity of a superfamily of potential prokaryotic HuH endonucleases. PMID:29914351
Identification and Characterization of Flavonoid Biosynthetic Enzyme Genes in Salvia miltiorrhiza (Lamiaceae). PMID:29914175
HMMER web server: 2018 update. PMID:29905871
Improved genomic island predictions with IslandPath-DIMOB. PMID:29905770
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
Amino acid impact factor. PMID:29897971
Genome-wide identification and expression profile analysis of the NAC transcription factor family during abiotic and biotic stress in woodland strawberry. PMID:29897926
Comparative Transcriptomics in Two Bivalve Species Offers Different Perspectives on the Evolution of Sex-Biased Genes. PMID:29897459
Evidence of the Red-Queen Hypothesis from Accelerated Rates of Evolution of Genes Involved in Biotic Interactions in Pneumocystis. PMID:29893833
Genome-wide identification and characterization of the RIO atypical kinase family in plants. PMID:29892951
A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. PMID:29892093
An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. PMID:29892012
Horizontal Gene Transfer From Bacteria and Plants to the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis. PMID:29887874
Biophysical and structural characterization of the putative nickel chaperone CooT from Carboxydothermus hydrogenoformans. PMID:29882029
PTMscape: an open source tool to predict generic post-translational modifications and map modification crosstalk in protein domains and biological processes. PMID:29876573
Toxoplasma gondii GRA8 induces ATP5A1-SIRT3-mediated mitochondrial metabolic resuscitation: a potential therapy for sepsis. PMID:29869623
Group B Streptococcus Biofilm Regulatory Protein A Contributes to Bacterial Physiology and Innate Immune Resistance. PMID:29868829
Deletion of Endo-β-1,4-Xylanase VmXyl1 Impacts the Virulence of Valsa mali in Apple Tree. PMID:29868105
Identification of Putative Precursor Genes for the Biosynthesis of Cannabinoid-Like Compound in Radula marginata. PMID:29868043
Inducible promoters and functional genomic approaches for the genetic engineering of filamentous fungi. PMID:29860590
IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding. PMID:29860432
Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species. PMID:29859036
Genomic evidence for genes encoding leucine-rich repeat receptors linked to resistance against the eukaryotic extra- and intracellular Brassica napus pathogens Leptosphaeria maculans and Plasmodiophora brassicae. PMID:29856883
TPP riboswitch-dependent regulation of an ancient thiamin transporter in Candida. PMID:29852014
De novo assembly of English yew (Taxus baccata) transcriptome and its applications for intra- and inter-specific analyses. PMID:29850988
Atg9 establishes Atg2-dependent contact sites between the endoplasmic reticulum and phagophores. PMID:29848619
Metabolic co-dependence drives the evolutionarily ancient Hydra-Chlorella symbiosis. PMID:29848439
Evolution of oncogenic signatures of mutation hotspots in tyrosine kinases supports the atavistic hypothesis of cancer. PMID:29844492
Genome sequencing and protein domain annotations of Korean Hanwoo cattle identify Hanwoo-specific immunity-related and other novel genes. PMID:29843617
Comparative expression analysis identifies the respiratory transition-related miRNAs and their target genes in tissues of metamorphosing Chinese giant salamander (Andrias davidianus). PMID:29843595
Testing the Domino Theory of Gene Loss in Buchnera aphidicola: The Relevance of Epistatic Interactions. PMID:29843462
Sorting Five Human Tumor Types Reveals Specific Biomarkers and Background Classification Genes. PMID:29802335
Short-Term Transcriptional Response of Microbial Communities to Nitrogen Fertilization in a Pine Forest Soil. PMID:29802185
Metabolic reconstruction and experimental verification of glucose utilization in Desulfurococcus amylolyticus DSM 16532. PMID:29797222
An improved assembly and annotation of the melon (Cucumis melo L.) reference genome. PMID:29795526
Characterization of a newly isolated phage infecting pathogenic Escherichia coli and analysis of its mosaic structural genes. PMID:29795390
A High Quality Genome for Mus spicilegus, a Close Relative of House Mice with Unique Social and Ecological Adaptations. PMID:29794166
New genomic data and analyses challenge the traditional vision of animal epithelium evolution. PMID:29793430
Group I introns are widespread in archaea. PMID:29788499
The Evolution of Gene Expression Underlying Vision Loss in Cave Animals. PMID:29788330
A Computational Approach Using Bioinformatics to Screening Drug Targets for Leishmania infantum Species. PMID:29785196
Fungal-type carbohydrate binding modules from the coccolithophore Emiliania huxleyi show binding affinity to cellulose and chitin. PMID:29782536
Polymorphic sites preferentially avoid co-evolving residues in MHC class I proteins. PMID:29782520
Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8. PMID:29780371
Revised Phylogeny of the Cellulose Synthase Gene Superfamily: Insights into Cell Wall Evolution. PMID:29780036
Use of designed sequences in protein structure recognition. PMID:29776380
Phylogenomic analysis of Apoidea sheds new light on the sister group of bees. PMID:29776336
Complete genome sequence of "Thiodictyon syntrophicum" sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno. PMID:29774086
A Novel Enzyme Portfolio for Red Algal Polysaccharide Degradation in the Marine Bacterium Paraglaciecola hydrolytica S66T Encoded in a Sizeable Polysaccharide Utilization Locus. PMID:29774012
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
Function of a membrane-embedded domain evolutionarily multiplied in the GPI lipid anchor pathway proteins PIG-B, PIG-M, PIG-U, PIG-W, PIG-V, and PIG-Z. PMID:29764287
Using ZFIN: Data Types, Organization, and Retrieval. PMID:29761463
Short genome report of cellulose-producing commensal Escherichia coli 1094. PMID:29760866
The Transcriptional Regulator TFB-RF1 Activates Transcription of a Putative ABC Transporter in Pyrococcus furiosus. PMID:29760686
Novel N4-Like Bacteriophages of Pectobacterium atrosepticum. PMID:29757952
Structural biology data archiving - where we are and what lies ahead. PMID:29749603
RepeatsDB-lite: a web server for unit annotation of tandem repeat proteins. PMID:29746699
Metallopeptidases of Toxoplasma gondii: in silico identification and gene expression. PMID:29737275
Control of mitotic chromosome condensation by the fission yeast transcription factor Zas1. PMID:29735745
Longevity and transposon defense, the case of termite reproductives. PMID:29735660
The Disordered C-Terminus of Yeast Hsf1 Contains a Cryptic Low-Complexity Amyloidogenic Region. PMID:29734798
Microbial Diversity and Toxin Risk in Tropical Freshwater Reservoirs of Cape Verde. PMID:29734762
Characterization and Alternative Splicing Profiles of the Lipoxygenase Gene Family in Tea Plant (Camellia sinensis). PMID:29726968
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
Genome-Wide Identification, Molecular Evolution, and Expression Profiling Analysis of Pectin Methylesterase Inhibitor Genes in Brassica campestris ssp. chinensis. PMID:29724020
Functional and evolutionary analysis of viral proteins containing a Rossmann-like fold. PMID:29722076
Gene Unprediction with Spurio: A tool to identify spurious protein sequences. PMID:29721311
PhytoNet: comparative co-expression network analyses across phytoplankton and land plants. PMID:29718316
A genome-wide analysis of the flax (Linum usitatissimum L.) dirigent protein family: from gene identification and evolution to differential regulation. PMID:29713868
Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion. PMID:29713376
The Ustilago maydis repetitive effector Rsp3 blocks the antifungal activity of mannose-binding maize proteins. PMID:29703884
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
The Sequence of Two Bacteriophages with Hypermodified Bases Reveals Novel Phage-Host Interactions. PMID:29695085
Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome. PMID:29690875
Evolutionary novelty in gravity sensing through horizontal gene transfer and high-order protein assembly. PMID:29689046
Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa. PMID:29688451
GAN: a platform of genomics and genetics analysis and application in Nicotiana. PMID:29688356
FishTEDB: a collective database of transposable elements identified in the complete genomes of fish. PMID:29688350
YtfB, an OapA Domain-Containing Protein, Is a New Cell Division Protein in Escherichia coli. PMID:29686141
High quality draft genome sequence of Mycoplasma testudineum strain BH29T, isolated from the respiratory tract of a desert tortoise. PMID:29682170
Molecular identification of GAPDHs in cassava highlights the antagonism of MeGAPCs and MeATG8s in plant disease resistance against cassava bacterial blight. PMID:29679263
Genome-Wide Analyses of Calcium Sensors Reveal Their Involvement in Drought Stress Response and Storage Roots Deterioration after Harvest in Cassava. PMID:29671773
Discovery of Novel Bat Coronaviruses in South China That Use the Same Receptor as Middle East Respiratory Syndrome Coronavirus. PMID:29669833
Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation. PMID:29669603
Phosphoproteomic insights into processes influenced by the kinase-like protein DIA1/C3orf58. PMID:29666759
Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases. PMID:29666611
A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction. PMID:29662147
Heat shock transcription factor 3 regulates plant immune response through modulation of salicylic acid accumulation and signalling in cassava. PMID:29660238
Plant Lineage-Specific Amplification of Transcription Factor Binding Motifs by Miniature Inverted-Repeat Transposable Elements (MITEs). PMID:29659815
A sequence family database built on ECOD structural domains. PMID:29659718
Genome-wide analysis of basic helix-loop-helix superfamily members in peach. PMID:29659634
Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases. PMID:29659563
Bipartite graphs in systems biology and medicine: a survey of methods and applications. PMID:29648623
Genome-wide identification of hexokinase gene family in Brassica napus: structure, phylogenetic analysis, expression, and functional characterization. PMID:29644447
Identification of Morus notabilis MADS-box genes and elucidation of the roles of MnMADS33 during endodormancy. PMID:29643336
Identification of novel MITEs (miniature inverted-repeat transposable elements) in Coxiella burnetii: implications for protein and small RNA evolution. PMID:29642859
GROOLS: reactive graph reasoning for genome annotation through biological processes. PMID:29642842
Characterizing Phage Genomes for Therapeutic Applications. PMID:29642590
Molecular characterization and expression profiling of BMP 3 gene in broiler and layer chicken. PMID:29637489
Transcriptome-wide discovery of coding and noncoding RNA-binding proteins. PMID:29636419
Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats. PMID:29636006
The single berberine bridge enzyme homolog of Physcomitrella patens is a cellobiose oxidase. PMID:29633551
Highly parallel genome variant engineering with CRISPR-Cas9. PMID:29632376
Vms1 and ANKZF1 peptidyl-tRNA hydrolases release nascent chains from stalled ribosomes. PMID:29632312
Distinguishing allergens from non-allergenic homologues using Physical-Chemical Property (PCP) motifs. PMID:29627609
Genetic Loci Governing Androgenic Capacity in Perennial Ryegrass (Lolium perenne L.). PMID:29626084
Comprehensive Characterization of Cancer Driver Genes and Mutations. PMID:29625053
Sequence, genome organization, annotation and proteomics of the thermophilic, 47.7-kb Geobacillus stearothermophilus bacteriophage TP-84 and its classification in the new Tp84virus genus. PMID:29624616
Origin, Evolution, and Loss of Bacterial Small RNAs. PMID:29623872
New computational approaches to understanding molecular protein function. PMID:29621256
The grapevine kinome: annotation, classification and expression patterns in developmental processes and stress responses. PMID:29619230
Identification and Characterization of the MADS-Box Genes and Their Contribution to Flower Organ in Carnation (Dianthus caryophyllus L.). PMID:29617274
Technological and Genomic Analysis of Roles of the Cell-Envelope Protease PrtS in Yoghurt Starter Development. PMID:29614042
High-throughput interaction screens illuminate the role of c-di-AMP in cyanobacterial nighttime survival. PMID:29608558
Regulation of early endosomes across eukaryotes: Evolution and functional homology of Vps9 proteins. PMID:29603841
In Vitro Characteristics of Phages to Guide 'Real Life' Phage Therapy Suitability. PMID:29601536
luxR Homolog-Linked Biosynthetic Gene Clusters in Proteobacteria. PMID:29600287
Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes. PMID:29597290
Identification and Characterization of Wheat Yellow Striate Virus, a Novel Leafhopper-Transmitted Nucleorhabdovirus Infecting Wheat. PMID:29593700
Lignolytic-consortium omics analyses reveal novel genomes and pathways involved in lignin modification and valorization. PMID:29588660
Succinate-acetate permease from Citrobacter koseri is an anion channel that unidirectionally translocates acetate. PMID:29588525
Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPase. PMID:29588502
Identification of Wheat Inflorescence Development-Related Genes Using a Comparative Transcriptomics Approach. PMID:29581960
Integrating ChIP-seq with other functional genomics data. PMID:29579165
Bioinformatic characterization of the Anoctamin Superfamily of Ca2+-activated ion channels and lipid scramblases. PMID:29579047
Characterization of the basic helix-loop-helix gene family and its tissue-differential expression in response to salt stress in poplar. PMID:29576971
Systematic characterization of pan-cancer mutation clusters. PMID:29572294
Immunomolecular Characterization of MIC-1, a Novel Antigen in Babesia bigemina, Which Contains Conserved and Immunodominant B-Cell Epitopes that Induce Neutralizing Antibodies. PMID:29570654
Lipophosphoglycan 3 From Leishmania infantum chagasi Binds Heparin With Micromolar Affinity. PMID:29568220
Molecular control of gene expression by Brucella BaaR, an IclR-type transcriptional repressor. PMID:29567835
Old Yellow Enzyme from Trypanosoma cruzi Exhibits In Vivo Prostaglandin F2α Synthase Activity and Has a Key Role in Parasite Infection and Drug Susceptibility. PMID:29563916
Amino Acid Transporters and Glutamine Metabolism in Breast Cancer. PMID:29562706
Evaluation of variability in high-resolution protein structures by global distance scoring. PMID:29560428
Hitting with a BAM: Selective Killing by Lectin-Like Bacteriocins. PMID:29559575
TgTKL1 Is a Unique Plant-Like Nuclear Kinase That Plays an Essential Role in Acute Toxoplasmosis. PMID:29559568
Multiplex Fluorescent, Activity-Based Protein Profiling Identifies Active α-Glycosidases and Other Hydrolases in Plants. PMID:29555787
A Proposed Chaperone of the Bacterial Type VI Secretion System Functions To Constrain a Self-Identity Protein. PMID:29555703
CMV: visualization for RNA and protein family models and their comparisons. PMID:29554223
Microbial and Functional Biodiversity Patterns in Sponges that Accumulate Bromopyrrole Alkaloids Suggest Horizontal Gene Transfer of Halogenase Genes. PMID:29546438
Phosphorylation decelerates conformational dynamics in bacterial translation elongation factors. PMID:29546243
Comprehensive subcellular topologies of polypeptides in Streptomyces. PMID:29544487
The Ubiquitin-Conjugating Enzyme Gene Family in Longan (Dimocarpus longan Lour.): Genome-Wide Identification and Gene Expression during Flower Induction and Abiotic Stress Responses. PMID:29543725
The CLAVATA receptor FASCIATED EAR2 responds to distinct CLE peptides by signaling through two downstream effectors. PMID:29543153
Detection of Weakly Expressed Trypanosoma cruzi Membrane Proteins Using High-Performance Probes. PMID:29542839
Discovery and validation of a glioblastoma co-expressed gene module. PMID:29541392
A Flow Cytometry-Based Phenotypic Screen To Identify Novel Endocytic Factors in Saccharomyces cerevisiae. PMID:29540444
DNA-binding properties of MafR, a global regulator of Enterococcus faecalis. PMID:29537484
MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping. PMID:29534977
Characterization of a Novel Porin-Like Protein, ExtI, from Geobacter sulfurreducens and Its Implication in the Reduction of Selenite and Tellurite. PMID:29534491
Worldwide Protein Data Bank validation information: usage and trends. PMID:29533231
Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in AMPLE. PMID:29533226
Recent developments in MrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment. PMID:29533225
A High-Throughput Mutational Scan of an Intrinsically Disordered Acidic Transcriptional Activation Domain. PMID:29525204
The effect of auxin (indole-3-acetic acid) on the growth rate and tropism of the sporangiophore of Phycomyces blakesleeanus and identification of auxin-related genes. PMID:29523949
Proteasome Activity Is Influenced by the HECT_2 Protein Ipa1 in Budding Yeast. PMID:29519818
Spatiotemporal compartmentalization of hepatic NADH and NADPH metabolism. PMID:29514978
RecQ Helicases Function in Development, DNA Repair, and Gene Targeting in Physcomitrella patens. PMID:29514942
Exploring modular allostery via interchangeable regulatory domains. PMID:29507215
Alignment-free clustering of large data sets of unannotated protein conserved regions using minhashing. PMID:29506470
Landscape of the spliced leader trans-splicing mechanism in Schistosoma mansoni. PMID:29497070
UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. PMID:29492869
In silico structural and functional prediction of African swine fever virus protein-B263R reveals features of a TATA-binding protein. PMID:29492339
Surfaceome and Proteosurfaceome in Parietal Monoderm Bacteria: Focus on Protein Cell-Surface Display. PMID:29491848
Oenococcus oeni in Chilean Red Wines: Technological and Genomic Characterization. PMID:29491847
The Druggable Pocketome of Corynebacterium diphtheriae: A New Approach for in silico Putative Druggable Targets. PMID:29487617
Structure function relations in PDZ-domain-containing proteins: Implications for protein networks in cellular signalling. PMID:29485124
Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily. PMID:29478822
spe-43 is required for sperm activation in C. elegans. PMID:29477340
Bioinformatics for Prohormone and Neuropeptide Discovery. PMID:29476505
Diversity and evolution of four-domain voltage-gated cation channels of eukaryotes and their ancestral functional determinants. PMID:29476068
Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses. PMID:29475869
SUMO polymeric chains are involved in nuclear foci formation and chromatin organization in Trypanosoma brucei procyclic forms. PMID:29474435
Codominant grasses differ in gene expression under experimental climate extremes in native tallgrass prairie. PMID:29473008
Genetic Diversity and Functional Analysis of Sigma Factors in Enterobacter cloacae Complex Resourced From Various Niche. PMID:29472760
Genome-scale examination of NBS-encoding genes in blueberry. PMID:29467425
Biofilm Formation by the Acidophile Bacterium Acidithiobacillus thiooxidans Involves c-di-GMP Pathway and Pel exopolysaccharide. PMID:29466318
Genome-Wide Analysis of the GRF Family Reveals Their Involvement in Abiotic Stress Response in Cassava. PMID:29461467
Molecular, biochemical and kinetic analysis of a novel, thermostable lipase (LipSm) from Stenotrophomonas maltophilia Psi-1, the first member of a new bacterial lipase family (XVIII). PMID:29456971
The BioCyc collection of microbial genomes and metabolic pathways. PMID:29447345
Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes. PMID:29445826
Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level. PMID:29441050
Recognition of sites of functional specialisation in all known eukaryotic protein kinase families. PMID:29438395
Complete genome sequence of Pseudomonas alcaliphila JAB1 (=DSM 26533), a versatile degrader of organic pollutants. PMID:29435100
Host-induced gene silencing of a regulator of G protein signalling gene (VdRGS1) confers resistance to Verticillium wilt in cotton. PMID:29431919
Comparative genomics reveals new single-nucleotide polymorphisms that can assist in identification of adherent-invasive Escherichia coli. PMID:29426864
Dissection of the Mechanism for Compatible and Incompatible Graft Combinations of Citrus grandis (L.) Osbeck ('Hongmian Miyou'). PMID:29419732
Genome-Wide Identification and Expression Analysis of the KUP Family under Abiotic Stress in Cassava (Manihot esculenta Crantz). PMID:29416511
Pacing across the membrane: the novel PACE family of efflux pumps is widespread in Gram-negative pathogens. PMID:29409983
Hemimetabolous genomes reveal molecular basis of termite eusociality. PMID:29403074
The genomes of two Eutrema species provide insight into plant adaptation to high altitudes. PMID:29394339
A human gut phage catalog correlates the gut phageome with type 2 diabetes. PMID:29391057
The unique evolution of the carbohydrate-binding module CBM20 in laforin. PMID:29389008
DIBS: a repository of disordered binding sites mediating interactions with ordered proteins. PMID:29385418
Survey of Candidate Genes for Maize Resistance to Infection by Aspergillus flavus and/or Aflatoxin Contamination. PMID:29385107
Both positional and chemical variables control in vitro proteolytic cleavage of a presenilin ortholog. PMID:29382721
Prediction of enzymatic pathways by integrative pathway mapping. PMID:29377793
The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology. PMID:29376823
Identification of the Autochaperone Domain in the Type Va Secretion System (T5aSS): Prevalent Feature of Autotransporters with a β-Helical Passenger. PMID:29375499
Functional Classification and Experimental Dissection of Long Noncoding RNAs. PMID:29373828
Structure of aspartate β-semialdehyde dehydrogenase from Francisella tularensis. PMID:29372903
Alpha-actinin of the chlorarchiniophyte Bigelowiella natans. PMID:29372122
A global ocean atlas of eukaryotic genes. PMID:29371626
Diversity of Cell Wall Related Proteins in Human Pathogenic Fungi. PMID:29371499
Systematic discovery of antiphage defense systems in the microbial pangenome. PMID:29371424
Fungal Screening on Olive Oil for Extracellular Triacylglycerol Lipases: Selection of a Trichoderma harzianum Strain and Genome Wide Search for the Genes. PMID:29370083
De Novo characterization of transcriptomes from two North American Papaipema stem-borers (Lepidoptera: Noctuidae). PMID:29364900
Genome-Wide Identification and Comparative Analysis of the 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase (HMGR) Gene Family in Gossypium. PMID:29364830
ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes. PMID:29363425
Mapping HLA-A2, -A3 and -B7 supertype-restricted T-cell epitopes in the ebolavirus proteome. PMID:29363421
Genome-Wide Identification and Characterization of the Potato bHLH Transcription Factor Family. PMID:29361801
ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2. PMID:29360036
Structural Characterization and Function Prediction of Immunoglobulin-like Fold in Cell Adhesion and Cell Signaling. PMID:29356528
Functional Characteristics of the Flying Squirrel's Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling. PMID:29354108
Extension of the viral ecology in humans using viral profile hidden Markov models. PMID:29351302
Circular RNAs: Biogenesis, Function, and a Role as Possible Cancer Biomarkers. PMID:29349062
Uncovering Genomic Regions Associated with Trypanosoma Infections in Wild Populations of the Tsetse Fly Glossina fuscipes. PMID:29343494
Genome-wide identification, characterization and classification of ionotropic glutamate receptor genes (iGluRs) in the malaria vector Anopheles sinensis (Diptera: Culicidae). PMID:29334982
Global analysis of prokaryotic tRNA-derived cyclodipeptide biosynthesis. PMID:29334896
Transcriptome profiling with focus on potential key genes for wing development and evolution in Megaloprepus caerulatus, the damselfly species with the world's largest wings. PMID:29329292
Comparative Metagenomics of Cellulose- and Poplar Hydrolysate-Degrading Microcosms from Gut Microflora of the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus) after Long-Term Enrichment. PMID:29326667
Complete Genome Sequence of the Escherichia coli Phage Ayreon. PMID:29326205
Characterization of Translationally Controlled Tumour Protein from the Sea Anemone Anemonia viridis and Transcriptome Wide Identification of Cnidarian Homologues. PMID:29324689
The glutamine synthetase of Trypanosoma cruzi is required for its resistance to ammonium accumulation and evasion of the parasitophorous vacuole during host-cell infection. PMID:29320490
The 2018 Nucleic Acids Research database issue and the online molecular biology database collection. PMID:29316735
Assessing the Performances of Protein Function Prediction Algorithms from the Perspectives of Identification Accuracy and False Discovery Rate. PMID:29316706
Salicylic Acid Perturbs sRNA-Gibberellin Regulatory Network in Immune Response of Potato to Potato virus Y Infection. PMID:29312421
Simultaneous Silencing of Xylanase Genes in Botrytis cinerea. PMID:29312413
Power law tails in phylogenetic systems. PMID:29311320
Comparative genomics of chemosensory protein genes (CSPs) in twenty-two mosquito species (Diptera: Culicidae): Identification, characterization, and evolution. PMID:29304168
Pichia pastoris is a Suitable Host for the Heterologous Expression of Predicted Class I and Class II Hydrophobins for Discovery, Study, and Application in Biotechnology. PMID:29303996
A Dipteran's Novel Sucker Punch: Evolution of Arthropod Atypical Venom with a Neurotoxic Component in Robber Flies (Asilidae, Diptera). PMID:29303983
Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins. PMID:29302007
The Legionella pneumophila effector Ceg4 is a phosphotyrosine phosphatase that attenuates activation of eukaryotic MAPK pathways. PMID:29301934
Complete genome sequence of esterase-producing bacterium Croceicoccus marinus E4A9T. PMID:29299108
The gonadal transcriptome of the unisexual Amazon molly Poecilia formosa in comparison to its sexual ancestors, Poecilia mexicana and Poecilia latipinna. PMID:29298680
De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus. PMID:29297306
Suggested mechanisms for Zika virus causing microcephaly: what do the genomes tell us? PMID:29297281
Improving pairwise comparison of protein sequences with domain co-occurrence. PMID:29293498
About miRNAs, miRNA seeds, target genes and target pathways. PMID:29291020
Coordinated regulation of intracellular pH by two glucose-sensing pathways in yeast. PMID:29284676
RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis. PMID:29273740
Identification of potentially oncogenic alterations from tumor-only samples reveals Fanconi anemia pathway mutations in bladder carcinomas. PMID:29263839
Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems. PMID:29263101
Toward Understanding Phage:Host Interactions in the Rumen; Complete Genome Sequences of Lytic Phages Infecting Rumen Bacteria. PMID:29259581
Integrated transcriptomic analysis of Trichosporon Asahii uncovers the core genes and pathways of fluconazole resistance. PMID:29259317
Unravelling the specificity and mechanism of sialic acid recognition by the gut symbiont Ruminococcus gnavus. PMID:29259165
Homoacetogenesis in Deep-Sea Chloroflexi, as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes. PMID:29259088
Inferring defense-related gene families in Arabidopsis and wheat. PMID:29258426
Genomic features of bacterial adaptation to plants. PMID:29255260
Diversity and Functional Analysis of the FeMo-Cofactor Maturase NifB. PMID:29250084
3DCONS-DB: A Database of Position-Specific Scoring Matrices in Protein Structures. PMID:29244774
Novel linear motif filtering protocol reveals the role of the LC8 dynein light chain in the Hippo pathway. PMID:29240760
Genome Assembly and Annotation of the Medicinal Plant Calotropis gigantea, a Producer of Anticancer and Antimalarial Cardenolides. PMID:29237703
Evolution and Expansion of the Prokaryote-Like Lipoxygenase Family in the Brown Alga Saccharina japonica. PMID:29234336
Identification and characterization of a novel zebrafish (Danio rerio) pentraxin-carbonic anhydrase. PMID:29230365
Comparative analyses of putative toxin gene homologs from an Old World viper, Daboia russelii. PMID:29230357
Phylogenetic relationship and domain organisation of SET domain proteins of Archaeplastida. PMID:29228906
Transcriptional profiling of sugarcane leaves and roots under progressive osmotic stress reveals a regulated coordination of gene expression in a spatiotemporal manner. PMID:29228055
Draft genome sequence of Bacillus velezensis 2A-2B strain: a rhizospheric inhabitant of Sporobolus airoides (Torr.) Torr., with antifungal activity against root rot causing phytopathogens. PMID:29225729
Insights from the protein-protein interaction network analysis of Mycobacterium tuberculosis toxin-antitoxin systems. PMID:29225431
Conserved Gene Microsynteny Unveils Functional Interaction Between Protein Disulfide Isomerase and Rho Guanine-Dissociation Inhibitor Families. PMID:29222525
SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets. PMID:29220461
Expanding horizons: new roles for non-canonical RNA-binding proteins in cancer. PMID:29216518
Comprehensive Genome-Wide Classification Reveals That Many Plant-Specific Transcription Factors Evolved in Streptophyte Algae. PMID:29216360
Genome overview of eight Candida boidinii strains isolated from human activities and wild environments. PMID:29213357
Deletion of the hfsB gene increases ethanol production in Thermoanaerobacterium saccharolyticum and several other thermophilic anaerobic bacteria. PMID:29213322
Evolution of cytokinesis-related protein localization during the emergence of multicellularity in volvocine green algae. PMID:29212441
Proposed Role for KaiC-Like ATPases as Major Signal Transduction Hubs in Archaea. PMID:29208747
Novel Families of Archaeo-Eukaryotic Primases Associated with Mobile Genetic Elements of Bacteria and Archaea. PMID:29198957
Evolution of intron-poor clades and expression patterns of the glycosyltransferase family 47. PMID:29196940
The OncoPPi Portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery. PMID:29186335
A half-site multimeric enzyme achieves its cooperativity without conformational changes. PMID:29184087
A global view of structure-function relationships in the tautomerase superfamily. PMID:29184004
Transcriptome Sequencing Reveals Novel Candidate Genes for Cardinium hertigii-Caused Cytoplasmic Incompatibility and Host-Cell Interaction. PMID:29181449
Bactofilin-mediated organization of the ParABS chromosome segregation system in Myxococcus xanthus. PMID:29180656
Whole transcriptome RNA-Seq analysis reveals extensive cell type-specific compartmentalization in Volvox carteri. PMID:29179763
CrusTF: a comprehensive resource of transcriptomes for evolutionary and functional studies of crustacean transcription factors. PMID:29178828
A new parameter-rich structure-aware mechanistic model for amino acid substitution during evolution. PMID:29178386
The structure of the S-layer of Clostridium difficile. PMID:29170885
Structural insights into the committed step of bacterial phospholipid biosynthesis. PMID:29167463
COGNAT: a web server for comparative analysis of genomic neighborhoods. PMID:29166914
A compendium of transcription factor and Transcriptionally active protein coding gene families in cowpea (Vigna unguiculata L.). PMID:29166879
A Cell-Line-Specific Atlas of PARP-Mediated Protein Asp/Glu-ADP-Ribosylation in Breast Cancer. PMID:29166620
Computational Model of the Effect of a Surface-Binding Site on the Saccharomycopsis fibuligera R64 α-Amylase to the Substrate Adsorption. PMID:29162975
Modeling mutant/wild-type interactions to ascertain pathogenicity of PROKR2 missense variants in patients with isolated GnRH deficiency. PMID:29161432
Oxygen Activation by Cu LPMOs in Recalcitrant Carbohydrate Polysaccharide Conversion to Monomer Sugars. PMID:29155571
The dynamic evolution of Drosophila innubila Nudivirus. PMID:29155284
Comparative Transcriptome Analysis Provides Insights into Differentially Expressed Genes and Long Non-Coding RNAs between Ovary and Testis of the Mud Crab (Scylla paramamosain). PMID:29152671
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. PMID:29145643
Constraints on lateral gene transfer in promoting fimbrial usher protein diversity and function. PMID:29142104
An update on sORFs.org: a repository of small ORFs identified by ribosome profiling. PMID:29140531
Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits. PMID:29138307
Expanding the chondroitin glycoproteome of Caenorhabditis elegans. PMID:29138239
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
Structural basis of effector and operator recognition by the phenolic acid-responsive transcriptional regulator PadR. PMID:29136175
The immunophilin repertoire of Plasmodiophora brassicae and functional analysis of PbCYP3 cyclophilin. PMID:29128880
The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA. PMID:29127278
PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology. PMID:29126216
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. PMID:29126160
Exolysin Shapes the Virulence of Pseudomonas aeruginosa Clonal Outliers. PMID:29120408
fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks. PMID:29112720
RefSeq: an update on prokaryotic genome annotation and curation. PMID:29112715
Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters. PMID:29112695
A bacterial pioneer produces cellulase complexes that persist through community succession. PMID:29109478
Insights into the molecular evolution of peptidase inhibitors in arthropods. PMID:29108008
Target-Pathogen: a structural bioinformatic approach to prioritize drug targets in pathogens. PMID:29106651
iUUCD 2.0: an update with rich annotations for ubiquitin and ubiquitin-like conjugations. PMID:29106644
ASpedia: a comprehensive encyclopedia of human alternative splicing. PMID:29106599
Evolutionary Conservation of the Components in the TOR Signaling Pathways. PMID:29104218
Inter-residue, inter-protein and inter-family coevolution: bridging the scales. PMID:29101847
Cellular, ultrastructural and molecular analyses of epidermal cell development in the planarian Schmidtea mediterranea. PMID:29100657
Genome-wide analysis of the cellulose synthase-like (Csl) gene family in bread wheat (Triticum aestivum L.). PMID:29100539
Daily rhythms and enrichment patterns in the transcriptome of the behavior-manipulating parasite Ophiocordyceps kimflemingiae. PMID:29099875
PULDB: the expanded database of Polysaccharide Utilization Loci. PMID:29088389
The molecular structure of the glycoside hydrolase domain of Cwp19 from Clostridium difficile. PMID:29083543
Development of functional ectopic compound eyes in scarabaeid beetles by knockdown of orthodenticle. PMID:29078401
MetalPDB in 2018: a database of metal sites in biological macromolecular structures. PMID:29077942
The Role of Cytoplasmic mRNA Cap-Binding Protein Complexes in Trypanosoma brucei and Other Trypanosomatids. PMID:29077018
Prediction of protein disorder based on IUPred. PMID:29076577
Differences in the genetic control of early egg development and reproduction between C. elegans and its parthenogenetic relative D. coronatus. PMID:29075433
Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria. PMID:29073099
Sensory Repertoire of Bacterial Chemoreceptors. PMID:29070658
Biogenesis and iron-dependency of ribosomal RNA hydroxylation. PMID:29069499
APPRIS 2017: principal isoforms for multiple gene sets. PMID:29069475
DEEPre: sequence-based enzyme EC number prediction by deep learning. PMID:29069344
Functional classification of protein toxins as a basis for bioinformatic screening. PMID:29066768
The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes. PMID:29065523
A deep transcriptomic resource for the copepod crustacean Labidocera madurae: A potential indicator species for assessing near shore ecosystem health. PMID:29065152
Comparative transcriptome profile of the leaf elongation zone of wild barley (Hordeum spontaneum) eibi1 mutant and its isogenic wild type. PMID:29064514
Systematic Identification and Molecular Characteristics of Long Noncoding RNAs in Pig Tissues. PMID:29062838
Confronting the catalytic dark matter encoded by sequenced genomes. PMID:29059321
Prohibition of antibiotic growth promoters has affected the genomic profiles of Lactobacillus salivarius inhabiting the swine intestine. PMID:29059217
Genome-Wide Identification and Analysis of MAPK and MAPKK Gene Families in Bread Wheat (Triticum aestivum L.). PMID:29053643
High reactivity of deep biota under anthropogenic CO2 injection into basalt. PMID:29051484
Structural prediction of two novel human atypical SLC transporters, MFSD4A and MFSD9, and their neuroanatomical distribution in mice. PMID:29049335
Structural and functional characterization of the divergent Entamoeba Src using Src inhibitor-1. PMID:29047404
Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta). PMID:29040712
20 years of the SMART protein domain annotation resource. PMID:29040681
Systematic classification of the His-Me finger superfamily. PMID:29040665
CRISPR-UMI: single-cell lineage tracing of pooled CRISPR-Cas9 screens. PMID:29039415
Genomics alterations of metastatic and primary tissues across 15 cancer types. PMID:29038591
The major outer sheath protein forms distinct conformers and multimeric complexes in the outer membrane and periplasm of Treponema denticola. PMID:29038532
Forecasting residue-residue contact prediction accuracy. PMID:29036497
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. PMID:29035372
Predicting Amyloidogenic Proteins in the Proteomes of Plants. PMID:29035294
Plantaricyclin A, a Novel Circular Bacteriocin Produced by Lactobacillus plantarum NI326: Purification, Characterization, and Heterologous Production. PMID:29030449
Mevalonate 5-diphosphate mediates ATP binding to the mevalonate diphosphate decarboxylase from the bacterial pathogen Enterococcus faecalis. PMID:29025876
Carbohydrate-active enzymes in Trichoderma harzianum: a bioinformatic analysis bioprospecting for key enzymes for the biofuels industry. PMID:29025413
Dual Roles of Glutathione in Ecdysone Biosynthesis and Antioxidant Function During Larval Development in Drosophila. PMID:29021278
The molecular mechanism of N-acetylglucosamine side-chain attachment to the Lancefield group A carbohydrate in Streptococcus pyogenes. PMID:29021255
A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value. PMID:28994416
LAMTOR/Ragulator is a negative regulator of Arl8b- and BORC-dependent late endosomal positioning. PMID:28993467
Applications of sequence coevolution in membrane protein biochemistry. PMID:28993150
Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes. PMID:28992302
Expression of stem cell factors in the adult sea cucumber digestive tube. PMID:28986650
Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle. PMID:28985340
TM-Aligner: Multiple sequence alignment tool for transmembrane proteins with reduced time and improved accuracy. PMID:28970546
MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics. PMID:28969605
MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data. PMID:28968636
Microbial genome analysis: the COG approach. PMID:28968633
The Legionella pneumophila effector Lpg1137 is a homologue of mitochondrial SLC25 carrier proteins, not of known serine proteases. PMID:28966893
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
Highly diversified expansions shaped the evolution of membrane bound proteins in metazoans. PMID:28959054
The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves. PMID:28957460
Strains, functions and dynamics in the expanded Human Microbiome Project. PMID:28953883
The Plastid and Mitochondrial Peptidase Network in Arabidopsis thaliana: A Foundation for Testing Genetic Interactions and Functions in Organellar Proteostasis. PMID:28947489
The fused SnoaL_2 domain in the Mycobacterium tuberculosis sigma factor σJ modulates promoter recognition. PMID:28934483
Improving contig binning of metagenomic data using [Formula: see text] oligonucleotide frequency dissimilarity. PMID:28931373
Genome-Wide Analysis of the Biosynthesis and Deactivation of Gibberellin-Dioxygenases Gene Family in Camellia sinensis (L.) O. Kuntze. PMID:28925957
Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales. PMID:28923009
Investigation of Antimicrobial Peptide Genes Associated with Fungus and Insect Resistance in Maize. PMID:28914754
Integrative and conjugative elements and their hosts: composition, distribution and organization. PMID:28911112
The eBioKit, a stand-alone educational platform for bioinformatics. PMID:28910280
Evolution of polymer formation within the actin superfamily. PMID:28904122
Novel arsenic-transforming bacteria and the diversity of their arsenic-related genes and enzymes arising from arsenic-polluted freshwater sediment. PMID:28894204
Genomic Analysis of Terpene Synthase Family and Functional Characterization of Seven Sesquiterpene Synthases from Citrus sinensis. PMID:28883829
Computational genome-wide survey of odorant receptors from two solitary bees Dufourea novaeangliae (Hymenoptera: Halictidae) and Habropoda laboriosa (Hymenoptera: Apidae). PMID:28883425
Characteristics of 29 novel atypical solute carriers of major facilitator superfamily type: evolutionary conservation, predicted structure and neuronal co-expression. PMID:28878041
PDBsum: Structural summaries of PDB entries. PMID:28875543
The lysin motif-containing proteins, Lyp1, Lyk7 and LysMe3, play important roles in chitin perception and defense against Verticillium dahliae in cotton. PMID:28870172
MEGGASENSE - The Metagenome/Genome Annotated Sequence Natural Language Search Engine: A Platform for the Construction of Sequence Data Warehouses. PMID:28867956
Mating in the Closest Living Relatives of Animals Is Induced by a Bacterial Chondroitinase. PMID:28867285
Spatial Clustering of de Novo Missense Mutations Identifies Candidate Neurodevelopmental Disorder-Associated Genes. PMID:28867141
Genome Characterization of Oleaginous Aspergillus oryzae BCC7051: A Potential Fungal-Based Platform for Lipid Production. PMID:28865010
Polycipiviridae: a proposed new family of polycistronic picorna-like RNA viruses. PMID:28857036
Genomic Epidemiology of NDM-1-Encoding Plasmids in Latin American Clinical Isolates Reveals Insights into the Evolution of Multidrug Resistance. PMID:28854628
Decoding the similarities and differences among mycobacterial species. PMID:28854187
A widespread family of polymorphic toxins encoded by temperate phages. PMID:28851366
The core regulatory network of the abscisic acid pathway in banana: genome-wide identification and expression analyses during development, ripening, and abiotic stress. PMID:28851274
The Treponema pallidum Outer Membrane. PMID:28849315
Investigating the mechanisms of papillary thyroid carcinoma using transcriptome analysis. PMID:28849102
The complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus (Bivalvia, Veneridae). PMID:28848689
A Putative Type II Secretion System Is Involved in Cellulose Utilization in Cytophaga hutchisonii. PMID:28848505
A systematic analysis of the RNA-targeting potential of secreted bacterial effector proteins. PMID:28839189
Ancestor of land plants acquired the DNA-3-methyladenine glycosylase (MAG) gene from bacteria through horizontal gene transfer. PMID:28839126
Complete Genome Sequence of the Yogurt Isolate Lactobacillus delbrueckii subsp. bulgaricus ACA-DC 87. PMID:28839034
The Enigmatic Origin of Papillomavirus Protein Domains. PMID:28832519
Fungal lifestyle reflected in serine protease repertoire. PMID:28831173
Analyses of Long Non-Coding RNA and mRNA profiling using RNA sequencing in chicken testis with extreme sperm motility. PMID:28831078
GeNET: a web application to explore and share Gene Co-expression Network Analysis data. PMID:28828272
Eukaryotic transporters for hydroxyderivatives of benzoic acid. PMID:28827635
Genome-Wide Mapping of Transcriptional Regulation and Metabolism Describes Information-Processing Units in Escherichia coli. PMID:28824593
Evolutionary analysis of a novel zinc ribbon in the N-terminal region of threonine synthase. PMID:28820334
Small Alarmone Synthetases as novel bacterial RNA-binding proteins. PMID:28820325
Enzymes Involved in AMPylation and deAMPylation. PMID:28819965
Identification and characterization of tyrosine kinases in anole lizard indicate the conserved tyrosine kinase repertoire in vertebrates. PMID:28819830
Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato. PMID:28819320
MCE domain proteins: conserved inner membrane lipid-binding proteins required for outer membrane homeostasis. PMID:28819315
Sequential conformational transitions and α-helical supercoiling regulate a sensor histidine kinase. PMID:28819239
Discovering Condition-Specific Gene Co-Expression Patterns Using Gaussian Mixture Models: A Cancer Case Study. PMID:28819158
Association of coral algal symbionts with a diverse viral community responsive to heat shock. PMID:28818037
Aggregation of population-based genetic variation over protein domain homologues and its potential use in genetic diagnostics. PMID:28815929
New tools and functions in data-out activities at Protein Data Bank Japan (PDBj). PMID:28815765
Modeling of RAS complexes supports roles in cancer for less studied partners. PMID:28815022
A CRISPR Activation Screen Identifies a Pan-avian Influenza Virus Inhibitory Host Factor. PMID:28813663
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
Computational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence method. PMID:28811564
Differential epitope recognition in the immunodominant staphylococcal antigen A of Staphylococcus aureus by mouse versus human IgG antibodies. PMID:28811514
Structural characterization of CAS SH3 domain selectivity and regulation reveals new CAS interaction partners. PMID:28808245
Draft Genome Sequence of Dermatophagoides pteronyssinus, the European House Dust Mite. PMID:28798186
Sialotranscriptomics of Rhipicephalus zambeziensis reveals intricate expression profiles of secretory proteins and suggests tight temporal transcriptional regulation during blood-feeding. PMID:28797301
Comparative analysis of LytS/LytTR-type histidine kinase/response regulator systems in γ-proteobacteria. PMID:28796832
Development of novel genic microsatellite markers from transcriptome sequencing in sugar maple (Acer saccharum Marsh.). PMID:28789702
Carbonyl reduction by YmfI in Bacillus subtilis prevents accumulation of an inhibitory EF-P modification state. PMID:28787546
Spider Neurotoxins, Short Linear Cationic Peptides and Venom Protein Classification Improved by an Automated Competition between Exhaustive Profile HMM Classifiers. PMID:28786958
Whole genome comparative analysis of four Georgian grape cultivars. PMID:28785866
Distinctive Roles for Periplasmic Proteases in the Maintenance of Essential Outer Membrane Protein Assembly. PMID:28784813
Near-atomic resolution cryoelectron microscopy structure of the 30-fold homooligomeric SpoIIIAG channel essential to spore formation in Bacillus subtilis. PMID:28784753
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
A modular yeast biosensor for low-cost point-of-care pathogen detection. PMID:28782007
Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula. PMID:28778149
A glimpse into the genetic basis of symbiosis between Hydrogenophaga and their helper strains in the biodegradation of 4-aminobenzenesulfonate. PMID:28775791
Cell-Type-Specific Translation Profiling Reveals a Novel Strategy for Treating Fragile X Syndrome. PMID:28772121
An evolutionarily conserved glycine-tyrosine motif forms a folding core in outer membrane proteins. PMID:28771529
The role of core and accessory type IV pilus genes in natural transformation and twitching motility in the bacterium Acinetobacter baylyi. PMID:28771515
Isolation and Characterization of Metallosphaera Turreted Icosahedral Virus, a Founding Member of a New Family of Archaeal Viruses. PMID:28768871
De novo assembly and annotation of the retinal transcriptome for the Nile grass rat (Arvicanthis ansorgei). PMID:28759564
The first complete genomes of Metalmarks and the classification of butterfly families. PMID:28757157
Predicting Amino Acid Substitution Probabilities Using Single Nucleotide Polymorphisms. PMID:28754661
Genomic Reconstruction of Carbohydrate Utilization Capacities in Microbial-Mat Derived Consortia. PMID:28751880
Complete Genome Sequence of the Sourdough Isolate Lactobacillus zymae ACA-DC 3411. PMID:28751400
Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus. PMID:28749982
Predicting the functional consequences of non-synonymous single nucleotide polymorphisms in IL8 gene. PMID:28747718
The MalR type regulator AcrC is a transcriptional repressor of acarbose biosynthetic genes in Actinoplanes sp. SE50/110. PMID:28743243
Broad-range lytic bacteriophages that kill Staphylococcus aureus local field strains. PMID:28742812
Anion-selective Formate/nitrite transporters: taxonomic distribution, phylogenetic analysis and subfamily-specific conservation pattern in prokaryotes. PMID:28738779
Genetic Architecture of Flooding Tolerance in the Dry Bean Middle-American Diversity Panel. PMID:28729876
ProtozoaDB 2.0: A Trypanosoma Brucei Case Study. PMID:28726736
Computational design of a symmetrical β-trefoil lectin with cancer cell binding activity. PMID:28724971
Outer Membrane Proteome of Veillonella parvula: A Diderm Firmicute of the Human Microbiome. PMID:28713344
UCSF ChimeraX: Meeting modern challenges in visualization and analysis. PMID:28710774
Genome Sequences of New Faustovirus Strains ST1 and LC9, Isolated from the South of France. PMID:28705976
Complete Genome Sequence of Streptococcus pneumoniae Virulent Phage MS1. PMID:28705957
The yeast noncoding RNA interaction network. PMID:28701522
The putative polyketide cyclase MSMEG_0129 from Mycobacterium smegmatis: purification, crystallization and X-ray crystallographic analysis. PMID:28695854
Computational and Experimental Studies of ADP-Ribosylation. PMID:28695527
Diversification of HP1-like Chromo Domain Proteins in Tetrahymena thermophila. PMID:28692189
Lack of S-RNase-Based Gametophytic Self-Incompatibility in Orchids Suggests That This System Evolved after the Monocot-Eudicot Split. PMID:28690630
Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge. PMID:28690595
Genome-wide characterization of the aldehyde dehydrogenase gene superfamily in soybean and its potential role in drought stress response. PMID:28687067
Deconstruction of the Ras switching cycle through saturation mutagenesis. PMID:28686159
Structure of the WD40-domain of human ATG16L1. PMID:28685931
Sortase Transpeptidases: Structural Biology and Catalytic Mechanism. PMID:28683919
LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis. PMID:28678736
Identification of long non-coding RNA in the horse transcriptome. PMID:28676104
Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution. PMID:28673978
Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation. PMID:28673540
The PIN gene family in cotton (Gossypium hirsutum): genome-wide identification and gene expression analyses during root development and abiotic stress responses. PMID:28673242
Evolution and multiple roles of the Pancrustacea specific transcription factor zelda in insects. PMID:28671979
ATP prevents Woronin bodies from sealing septal pores in unwounded cells of the fungus Zymoseptoria tritici. PMID:28671740
Molecular Characterization, Gene Evolution, and Expression Analysis of the Fructose-1, 6-bisphosphate Aldolase (FBA) Gene Family in Wheat (Triticum aestivum L.). PMID:28659962
Physiological and Molecular Understanding of Bacterial Polysaccharide Monooxygenases. PMID:28659491
Probing the potential of CnaB-type domains for the design of tag/catcher systems. PMID:28654665
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
Helicobacter pylori gene silencing in vivo demonstrates urease is essential for chronic infection. PMID:28644872
Unexpected Dominance of Elusive Acidobacteria in Early Industrial Soft Coal Slags. PMID:28642744
A sorghum (Sorghum bicolor) mutant with altered carbon isotope ratio. PMID:28640841
The metagenomic data life-cycle: standards and best practices. PMID:28637310
Prediction and analysis of three gene families related to leaf rust (Puccinia triticina) resistance in wheat (Triticum aestivum L.). PMID:28633642
Toll-like receptor pathway evolution in deuterostomes. PMID:28630328
Truncating mutations in RBM12 are associated with psychosis. PMID:28628109
ELIXIR pilot action: Marine metagenomics - towards a domain specific set of sustainable services. PMID:28620454
Genome-Wide Identification of Glyoxalase Genes in Medicago truncatula and Their Expression Profiling in Response to Various Developmental and Environmental Stimuli. PMID:28620395
Streptococcus pyogenes quinolinate-salvage pathway-structural and functional studies of quinolinate phosphoribosyl transferase and NH3 -dependent NAD+ synthetase. PMID:28618168
Structure and Function of p97 and Pex1/6 Type II AAA+ Complexes. PMID:28611990
Adaptations to High Salt in a Halophilic Protist: Differential Expression and Gene Acquisitions through Duplications and Gene Transfers. PMID:28611746
Global proteomic analysis of advanced glycation end products in the Arabidopsis proteome provides evidence for age-related glycation hot spots. PMID:28611063
Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries. PMID:28610557
Genome-wide identification and characterization of SnRK2 gene family in cotton (Gossypium hirsutum L.). PMID:28606097
A genome-scale metabolic reconstruction of Lysinibacillus sphaericus unveils unexploited biotechnological potentials. PMID:28604819
Rif1 maintains telomeres and mediates DNA repair by encasing DNA ends. PMID:28604726
Amino Acids Are an Ineffective Fertilizer for Dunaliella spp. Growth. PMID:28603530
Molecular cloning, expression, and characterization of four novel thermo-alkaliphilic enzymes retrieved from a metagenomic library. PMID:28588643
Genome-Wide Characterization and Expression Profiling of Sugar Transporter Family in the Whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae). PMID:28588501
Proteases of Dermatophagoides pteronyssinus. PMID:28587273
Biochemical and Computational Insights on a Novel Acid-Resistant and Thermal-Stable Glucose 1-Dehydrogenase. PMID:28587256
Identification of Proteases and Protease Inhibitors in Allergenic and Non-Allergenic Pollen. PMID:28587253
PFASUM: a substitution matrix from Pfam structural alignments. PMID:28583067
An Atlas of β-Glucuronidases in the Human Intestinal Microbiome. PMID:28578872
Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance. PMID:28578660
Comprehensive classification of the PIN domain-like superfamily. PMID:28575517
Transcriptome analysis of Phytophthora litchii reveals pathogenicity arsenals and confirms taxonomic status. PMID:28570700
Properties of genes essential for mouse development. PMID:28562614
Plant Lectins and Lectin Receptor-Like Kinases: How Do They Sense the Outside? PMID:28561754
Metabolic network analysis reveals microbial community interactions in anammox granules. PMID:28561030
Genome-wide characterization of cellulases from the hemi-biotrophic plant pathogen, Bipolaris sorokiniana, reveals the presence of a highly stable GH7 endoglucanase. PMID:28559926
Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements. PMID:28559295
The UbiK protein is an accessory factor necessary for bacterial ubiquinone (UQ) biosynthesis and forms a complex with the UQ biogenesis factor UbiJ. PMID:28559279
AGeNNT: annotation of enzyme families by means of refined neighborhood networks. PMID:28545394
Genomic and transcriptomic analyses reveal adaptation mechanisms of an Acidithiobacillus ferrivorans strain YL15 to alpine acid mine drainage. PMID:28542527
Membrane protein contact and structure prediction using co-evolution in conjunction with machine learning. PMID:28542325
A bacterial negative transcription regulator binding on an inverted repeat in the promoter for epothilone biosynthesis. PMID:28535774
A comprehensive proteogenomic study of the human Brucella vaccine strain 104 M. PMID:28535754
The Evolutionary Basis of Translational Accuracy in Plants. PMID:28533334
Engineering protein stability with atomic precision in a monomeric miniprotein. PMID:28530710
Draft Genome Sequence of Roseovarius sp. A-2, an Iodide-Oxidizing Bacterium Isolated from Natural Gas Brine Water, Chiba, Japan. PMID:28529651
Recognition of a structural domain (RWDBD) in Gcn1 proteins that interacts with the RWD domain containing proteins. PMID:28526057
Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms. PMID:28518075
Experimental identification and computational characterization of a novel extracellular metalloproteinase produced by Clostridium sordellii. PMID:28515901
The Whole-Genome and Transcriptome of the Manila Clam (Ruditapes philippinarum). PMID:28505302
Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution. PMID:28500258
DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins. PMID:28498993
Molecular insights into Cassava brown streak virus susceptibility and resistance by profiling of the early host response. PMID:28494519
Genomic biomarkers of prenatal intrauterine inflammation in umbilical cord tissue predict later life neurological outcomes. PMID:28493900
Selectivity determinants of GPCR-G-protein binding. PMID:28489817
The PhytoClust tool for metabolic gene clusters discovery in plant genomes. PMID:28486689
Genome-wide analysis of WRKY transcription factors in wheat (Triticum aestivum L.) and differential expression under water deficit condition. PMID:28484671
Widespread adenine N6-methylation of active genes in fungi. PMID:28481340
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. PMID:28472432
Molecular identification of transmembrane protein 68 as an endoplasmic reticulum-anchored and brain-specific protein. PMID:28472192
Structural and functional mapping of Rtg2p determinants involved in retrograde signaling and aging of Saccharomyces cerevisiae. PMID:28472157
Performance of Hidden Markov Models in Recovering the Standard Classification of Glycoside Hydrolases. PMID:28469382
Comparative transcriptome analysis of venom glands from Cotesia vestalis and Diadromus collaris, two endoparasitoids of the host Plutella xylostella. PMID:28465546
SBSPKSv2: structure-based sequence analysis of polyketide synthases and non-ribosomal peptide synthetases. PMID:28460065
antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. PMID:28460038
SeMPI: a genome-based secondary metabolite prediction and identification web server. PMID:28453782
The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation. PMID:28453653
PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update. PMID:28453649
Genome-wide analysis of autophagy-related genes in banana highlights MaATG8s in cell death and autophagy in immune response to Fusarium wilt. PMID:28451821
The crystal structure of mammalian inositol 1,3,4,5,6-pentakisphosphate 2-kinase reveals a new zinc-binding site and key features for protein function. PMID:28450399
Small copy-number variations involving genes of the FGF pathway in differences in sex development. PMID:28446957
Genome Wide Identification and Characterization of Apple bHLH Transcription Factors and Expression Analysis in Response to Drought and Salt Stress. PMID:28443104
Insights on Structure and Function of a Late Embryogenesis Abundant Protein from Amaranthus cruentus: An Intrinsically Disordered Protein Involved in Protection against Desiccation, Oxidant Conditions, and Osmotic Stress. PMID:28439280
rAMPing Up Stress Signaling: Protein AMPylation in Metazoans. PMID:28433487
The Lon protease-like domain in the bacterial RecA paralog RadA is required for DNA binding and repair. PMID:28432121
Programmatic access to bioinformatics tools from EMBL-EBI update: 2017. PMID:28431173
Intracellular lipid binding protein family diversity from Oyster Crassostrea gigas: genomic and structural features of invertebrate lipid transporters. PMID:28429758
Noumeavirus replication relies on a transient remote control of the host nucleus. PMID:28429720
Draft Genome Sequence of Acinetobacter johnsonii C6, an Environmental Isolate Engaging in Interspecific Metabolic Interactions. PMID:28428290
Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa. PMID:28427330
Identification and analysis of mutational hotspots in oncogenes and tumour suppressors. PMID:28423505
RNA-Seq Validation of RNAi Identifies Additional Gene Connectivity in Tribolium castaneum (Coleoptera: Tenebrionidae). PMID:28423418
Genome-wide analysis of VQ motif-containing proteins in Moso bamboo (Phyllostachys edulis). PMID:28417193
An Extracellular Cell-Attached Pullulanase Confers Branched α-Glucan Utilization in Human Gut Lactobacillus acidophilus. PMID:28411221
Genome-wide identification and characterization of NB-ARC resistant genes in wheat (Triticum aestivum L.) and their expression during leaf rust infection. PMID:28401336
The human retinoblastoma susceptibility gene (RB1): an evolutionary story in primates. PMID:28401291
The Anti-helminthic Compound Mebendazole Has Multiple Antifungal Effects against Cryptococcus neoformans. PMID:28400768
Structure of a DNA glycosylase that unhooks interstrand cross-links. PMID:28396405
The SPOR Domain, a Widely Conserved Peptidoglycan Binding Domain That Targets Proteins to the Site of Cell Division. PMID:28396350
Characterization of a Basidiomycota hydrophobin reveals the structural basis for a high-similarity Class I subdivision. PMID:28393921
Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin. PMID:28390096
SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions. PMID:28387819
Genome-Wide Investigation of WRKY Transcription Factors Involved in Terminal Drought Stress Response in Common Bean. PMID:28386267
A Genome-Scale Model of Shewanella piezotolerans Simulates Mechanisms of Metabolic Diversity and Energy Conservation. PMID:28382331
The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest. PMID:28379940
The pathogenic development of Sclerotinia sclerotiorum in soybean requires specific host NADPH oxidases. PMID:28378935
Characterization and Expression Profiling Analysis of Calmodulin Genes in Response to Salt and Osmotic Stresses in Pear (Pyrus bretschneideri Rehd.) and in Comparison with Arabidopsis. PMID:28373986
Mechanisms for Pseudoalteromonas piscicida-Induced Killing of Vibrios and Other Bacterial Pathogens. PMID:28363962
Comparative Genomics of Four Isosphaeraceae Planctomycetes: A Common Pool of Plasmids and Glycoside Hydrolase Genes Shared by Paludisphaera borealis PX4T, Isosphaera pallida IS1BT, Singulisphaera acidiphila DSM 18658T, and Strain SH-PL62. PMID:28360896
The electrically conductive pili of Geobacter species are a recently evolved feature for extracellular electron transfer. PMID:28348867
Vibrio cholerae VciB Mediates Iron Reduction. PMID:28348025
Genomic Evidence for Bacterial Determinants Influencing Obesity Development. PMID:28346358
Overexpression of a Domain of Unknown Function 266-containing protein results in high cellulose content, reduced recalcitrance, and enhanced plant growth in the bioenergy crop Populus. PMID:28344649
EXPath tool-a system for comprehensively analyzing regulatory pathways and coexpression networks from high-throughput transcriptome data. PMID:28338930
Cross-Species Genome-Wide Identification of Evolutionary Conserved MicroProteins. PMID:28338802
APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins. PMID:28334975
Organismal and spatial partitioning of energy and macronutrient transformations within a hypersaline mat. PMID:28334407
Improving transcriptome de novo assembly by using a reference genome of a related species: Translational genomics from oil palm to coconut. PMID:28334050
De novo transcriptome sequencing in Monsonia burkeana revealed putative genes for key metabolic pathways involved in tea quality and medicinal value. PMID:28330322
Optogenetic Module for Dichromatic Control of c-di-GMP Signaling. PMID:28320886
Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum "Latescibacteria" (WS3). PMID:28314726
Comparative Investigation of Copper Tolerance and Identification of Putative Tolerance Related Genes in Tardigrades. PMID:28293195
Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis. PMID:28289198
Biochemical and structural analyses of a bacterial endo-β-1,2-glucanase reveal a new glycoside hydrolase family. PMID:28270506
An evolution-based strategy for engineering allosteric regulation. PMID:28266924
Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota. PMID:28265262
Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species. PMID:28261241
Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system. PMID:28259138
Growth condition dependency is the major cause of non-responsiveness upon genetic perturbation. PMID:28257504
Phosphotyrosine phosphatase R3 receptors: Origin, evolution and structural diversification. PMID:28257417
Prediction of GCRV virus-host protein interactome based on structural motif-domain interactions. PMID:28253857
Aberrant splicing in maize rough endosperm3 reveals a conserved role for U12 splicing in eukaryotic multicellular development. PMID:28242684
Prophage WO genes recapitulate and enhance Wolbachia-induced cytoplasmic incompatibility. PMID:28241146
The Ancient Gamete Fusogen HAP2 Is a Eukaryotic Class II Fusion Protein. PMID:28235200
Genome Sequence of Rhodoferax antarcticus ANT.BRT; A Psychrophilic Purple Nonsulfur Bacterium from an Antarctic Microbial Mat. PMID:28230808
Antibiotic Resistance Determinant-Focused Acinetobacter baumannii Vaccine Designed Using Reverse Vaccinology. PMID:28230771
A non-synonymous SNP with the allele frequency correlated with the altitude may contribute to the hypoxia adaptation of Tibetan chicken. PMID:28222154
Efficient gene targeting in non-homologous end-joining-deficient Lipomyces starkeyi strains. PMID:28220186
The Escherichia coli COG1738 Member YhhQ Is Involved in 7-Cyanodeazaguanine (preQ₀) Transport. PMID:28208705
Identification, classification, and transcription profiles of the B-type response regulator family in pear. PMID:28207822
The OncoPPi network of cancer-focused protein-protein interactions to inform biological insights and therapeutic strategies. PMID:28205554
Phylogenetic analysis of eukaryotic NEET proteins uncovers a link between a key gene duplication event and the evolution of vertebrates. PMID:28205535
Analysis of long noncoding RNA and mRNA using RNA sequencing during the differentiation of intramuscular preadipocytes in chicken. PMID:28199418
Comparative and functional triatomine genomics reveals reductions and expansions in insecticide resistance-related gene families. PMID:28199333
Global transcriptome analysis reveals extensive gene remodeling, alternative splicing and differential transcription profiles in non-seed vascular plant Selaginella moellendorffii. PMID:28198676
Structure and function of HWE/HisKA2-family sensor histidine kinases. PMID:28193573
An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PMID:28187133
A comprehensive software suite for protein family construction and functional site prediction. PMID:28182651
Structure of Methylobacterium extorquens malyl-CoA lyase: CoA-substrate binding correlates with domain shift. PMID:28177317
Red Algal Mitochondrial Genomes Are More Complete than Previously Reported. PMID:28175279
Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism. PMID:28174620
Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB. PMID:28174560
Origin and diversification of leucine-rich repeat receptor-like protein kinase (LRR-RLK) genes in plants. PMID:28173747
Decay of Sexual Trait Genes in an Asexual Parasitoid Wasp. PMID:28172869
The Carboxy Terminus of YCF1 Contains a Motif Conserved throughout >500 Myr of Streptophyte Evolution. PMID:28164224
The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2. PMID:28163827
From the research laboratory to the database: the Caenorhabditis elegans kinome in UniProtKB. PMID:28159896
Whole-Genome Sequence of the Cheese Isolate Lactobacillus rennini ACA-DC 565. PMID:28153908
Statoviruses, A novel taxon of RNA viruses present in the gastrointestinal tracts of diverse mammals. PMID:28152382
Transcriptomic investigation of wound healing and regeneration in the cnidarian Calliactis polypus. PMID:28150733
Tutorial on Protein Ontology Resources. PMID:28150233
Drosophila CG3303 is an essential endoribonuclease linked to TDP-43-mediated neurodegeneration. PMID:28139767
Exploring the dark foldable proteome by considering hydrophobic amino acids topology. PMID:28134276
Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics. PMID:28128549
Toxoplasma gondii GRA7-Targeted ASC and PLD1 Promote Antibacterial Host Defense via PKCα. PMID:28125719
Comparative Analysis of Mitochondrial N-Termini from Mouse, Human, and Yeast. PMID:28122942
TOMATOMICS: A Web Database for Integrated Omics Information in Tomato. PMID:28111364
Protein structure determination using metagenome sequence data. PMID:28104891
MarpoDB: An Open Registry for Marchantia Polymorpha Genetic Parts. PMID:28100647
Evolution and structural diversification of Nictaba-like lectin genes in food crops with a focus on soybean (Glycine max). PMID:28087663
Lysobacter PilR, the Regulator of Type IV Pilus Synthesis, Controls Antifungal Antibiotic Production via a Cyclic di-GMP Pathway. PMID:28087536
Draft Genome Sequence of Micromonospora sp. Strain WMMB235, a Marine Ascidian-Associated Bacterium. PMID:28082484
Determining the roles of the three alcohol dehydrogenases (AdhA, AdhB and AdhE) in Thermoanaerobacter ethanolicus during ethanol formation. PMID:28078513
Asgard archaea illuminate the origin of eukaryotic cellular complexity. PMID:28077874
Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study. PMID:28077566
Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces. PMID:28077065
Mispacking and the Fitness Landscape of the Green Fluorescent Protein Chromophore Milieu. PMID:28074648
Complete genome sequence of the heavy metal resistant bacterium Agromyces aureus AR33T and comparison with related Actinobacteria. PMID:28074120
Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes. PMID:28069893
Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis. PMID:28068432
Identification of microsporidia host-exposed proteins reveals a repertoire of rapidly evolving proteins. PMID:28067236
Characterization of Uncultured Genome Fragment from Soil Metagenomic Library Exposed Rare Mismatch of Internal Tetranucleotide Frequency. PMID:28066395
Plant genome and transcriptome annotations: from misconceptions to simple solutions. PMID:28062412
An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences. PMID:28054422
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges. PMID:28049838
The Pseudomonas putida T6SS is a plant warden against phytopathogens. PMID:28045455
viruSITE-integrated database for viral genomics. PMID:28025349
The Mutational Landscape of the Oncogenic MZF1 SCAN Domain in Cancer. PMID:28018905
Identification and characterization of tomato gibberellin 2-oxidases (GA2oxs) and effects of fruit-specific SlGA2ox1 overexpression on fruit and seed growth and development. PMID:28018605
Identification and Network-Enabled Characterization of Auxin Response Factor Genes in Medicago truncatula. PMID:28018393
Structural Insights on PHA Binding Protein PhaP from Aeromonas hydrophila. PMID:28009010
Structure and Function of the TIR Domain from the Grape NLR Protein RPV1. PMID:28008335
Biological Potential of Chitinolytic Marine Bacteria. PMID:27999269
Transcriptional signatures of somatic neoblasts and germline cells in Macrostomum lignano. PMID:27997336
Genome-Wide Analysis of Soybean JmjC Domain-Containing Proteins Suggests Evolutionary Conservation Following Whole-Genome Duplication. PMID:27994610
Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics. PMID:27980708
Cardiovascular proteomics in the era of big data: experimental and computational advances. PMID:27980500
Complete Genome Sequence of Rhodococcus sp. Strain WMMA185, a Marine Sponge-Associated Bacterium. PMID:27979952
Complete Genome Sequence of Type Strain Campylobacter fetus subsp. fetus ATCC 27374. PMID:27979934
Expansion of divergent SEA domains in cell surface proteins and nucleoporin 54. PMID:27977898
The Eucalyptus Tonoplast Intrinsic Protein (TIP) Gene Subfamily: Genomic Organization, Structural Features, and Expression Profiles. PMID:27965702
CozE is a member of the MreCD complex that directs cell elongation in Streptococcus pneumoniae. PMID:27941863
Molecular mechanism for sphingosine-induced Pseudomonas ceramidase expression through the transcriptional regulator SphR. PMID:27941831
The Toxin-Antitoxin System DarTG Catalyzes Reversible ADP-Ribosylation of DNA. PMID:27939941
Regulation of signaling directionality revealed by 3D snapshots of a kinase:regulator complex in action. PMID:27938660
Crystal Structure of the Streptomyces coelicolor Sortase E1 Transpeptidase Provides Insight into the Binding Mode of the Novel Class E Sorting Signal. PMID:27936128
Stable core virome despite variable microbiome after fecal transfer. PMID:27935413
Revisiting Vitis vinifera Subtilase Gene Family: A Possible Role in Grapevine Resistance against Plasmopara viticola. PMID:27933087
A diverse intrinsic antibiotic resistome from a cave bacterium. PMID:27929110
BRENDA in 2017: new perspectives and new tools in BRENDA. PMID:27924025
Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum. PMID:27917941
The unconventional kinetoplastid kinetochore: from discovery toward functional understanding. PMID:27911702
The plastid genome of some eustigmatophyte algae harbours a bacteria-derived six-gene cluster for biosynthesis of a novel secondary metabolite. PMID:27906133
IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes. PMID:27903896
TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life. PMID:27899676
CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. PMID:27899674
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
InterPro in 2017-beyond protein family and domain annotations. PMID:27899635
DisProt 7.0: a major update of the database of disordered proteins. PMID:27899601
ECOD: new developments in the evolutionary classification of domains. PMID:27899594
Uniclust databases of clustered and deeply annotated protein sequences and alignments. PMID:27899574
WormBase ParaSite - a comprehensive resource for helminth genomics. PMID:27899279
Evidence of functional divergence in MSP7 paralogous proteins: a molecular-evolutionary and phylogenetic analysis. PMID:27894257
Diversity and Evolutionary Analysis of Iron-Containing (Type-III) Alcohol Dehydrogenases in Eukaryotes. PMID:27893862
Disruption of the Gene Encoding Endo-β-1, 4-Xylanase Affects the Growth and Virulence of Sclerotinia sclerotiorum. PMID:27891117
Bioinformatic Identification of Rare Codon Clusters (RCCs) in HBV Genome and Evaluation of RCCs in Proteins Structure of Hepatitis B Virus. PMID:27882067
The Oxidosqualene Cyclase from the Oomycete Saprolegnia parasitica Synthesizes Lanosterol as a Single Product. PMID:27881978
Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi. PMID:27881071
Prediction of Protein-Protein Interactions by Evidence Combining Methods. PMID:27879651
Structures and Ribosomal Interaction of Ribosome-Inactivating Proteins. PMID:27879643
Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane Oxidizing Methylomirabilis Bioreactor Enrichment Culture. PMID:27877158
Loss-of-function of an Arabidopsis NADPH pyrophosphohydrolase, AtNUDX19, impacts on the pyridine nucleotides status and confers photooxidative stress tolerance. PMID:27874073
Multifunctional Thioredoxin-Like Protein from the Gastrointestinal Parasitic Nematodes Strongyloides ratti and Trichuris suis Affects Mucosal Homeostasis. PMID:27872753
Distribution of Type I Restriction-Modification Systems in Streptococcus suis: An Outlook. PMID:27869755
A Genome-Wide Identification and Analysis of the Basic Helix-Loop-Helix Transcription Factors in Brown Planthopper, Nilaparvata lugens. PMID:27869716
De-novo protein function prediction using DNA binding and RNA binding proteins as a test case. PMID:27869118
Heat shock transcription factors in banana: genome-wide characterization and expression profile analysis during development and stress response. PMID:27857174
Unmasking the U2AF homology motif family: a bona fide protein-protein interaction motif in disguise. PMID:27852923
Both adhE and a Separate NADPH-Dependent Alcohol Dehydrogenase Gene, adhA, Are Necessary for High Ethanol Production in Thermoanaerobacterium saccharolyticum. PMID:27849176
Insights into long noncoding RNAs of naked mole rat (Heterocephalus glaber) and their potential association with cancer resistance. PMID:27833660
Bioinformatic characterization of type-specific sequence and structural features in auxiliary activity family 9 proteins. PMID:27833654
The Human Kinome Targeted by FDA Approved Multi-Target Drugs and Combination Products: A Comparative Study from the Drug-Target Interaction Network Perspective. PMID:27828998
Beyond DNA: An Integrated and Functional Approach for Classifying Germline Variants in Breast Cancer Genes. PMID:27822389
Pyrimidine Salvage Enzymes Are Essential for De Novo Biosynthesis of Deoxypyrimidine Nucleotides in Trypanosoma brucei. PMID:27820863
Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse). PMID:27812417
Draft genome sequence of Streptomyces sp. TP-A0867, an alchivemycin producer. PMID:27800124
Genenames.org: the HGNC and VGNC resources in 2017. PMID:27799471
FlyBase at 25: looking to the future. PMID:27799470
Targeting Reactive Carbonyls for Identifying Natural Products and Their Biosynthetic Origins. PMID:27797509
Identification of candidate genes from the SAD gene family in cotton for determination of cottonseed oil composition. PMID:27796643
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
Genomic resources for a unique, low-virulence Babesia taxon from China. PMID:27784333
Acidithiobacillus ferrivorans SS3 presents little RNA transcript response related to cold stress during growth at 8 °C suggesting it is a eurypsychrophile. PMID:27783177
Genome sequences and annotation of two urinary isolates of E. coli. PMID:27777649
Bioinformatic Identification and Analysis of Hydroxyproline-Rich Glycoproteins in Populus trichocarpa. PMID:27769192
Draft genome sequence of Staphylococcus hominis strain Hudgins isolated from human skin implicates metabolic versatility and several virulence determinants. PMID:27766204
Evolution of the Tim17 protein family. PMID:27760563
Shedding light on the expansion and diversification of the Cdc48 protein family during the rise of the eukaryotic cell. PMID:27756227
MgaSpn and H-NS: Two Unrelated Global Regulators with Similar DNA-Binding Properties. PMID:27747214
PIECE 2.0: an update for the plant gene structure comparison and evolution database. PMID:27742820
IMG/M: integrated genome and metagenome comparative data analysis system. PMID:27738135
Draft Genome Sequence of Arenibacter sp. Strain C-21, an Iodine-Accumulating Bacterium Isolated from Surface Marine Sediment. PMID:27738047
Structural basis for ligand recognition by a Cache chemosensory domain that mediates carboxylate sensing in Pseudomonas syringae. PMID:27734909
Expression and chromatin structures of cellulolytic enzyme gene regulated by heterochromatin protein 1. PMID:27729944
Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes. PMID:27729905
Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis. PMID:27729520
Computational prediction shines light on type III secretion origins. PMID:27713481
Genome-Wide Characterization of the MADS-Box Gene Family in Radish (Raphanus sativus L.) and Assessment of Its Roles in Flowering and Floral Organogenesis. PMID:27703461
Role of Glycosyltransferases Modifying Type B Flagellin of Emerging Hypervirulent Clostridium difficile Lineages and Their Impact on Motility and Biofilm Formation. PMID:27703012
Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis. PMID:27699151
Draft genome sequence of Microbacterium oleivorans strain Wellendorf implicates heterotrophic versatility and bioremediation potential. PMID:27699150
Probing the diversity of healthy oral microbiome with bioinformatics approaches. PMID:27697111
Transcriptome Dynamics during Maize Endosperm Development. PMID:27695101
Dissecting the regulation rules of cancer-related miRNAs based on network analysis. PMID:27694936
Ferredoxin:NAD+ Oxidoreductase of Thermoanaerobacterium saccharolyticum and Its Role in Ethanol Formation. PMID:27694237
Listeria monocytogenes in Stone Fruits Linked to a Multistate Outbreak: Enumeration of Cells and Whole-Genome Sequencing. PMID:27694232
Insights into the Utility of the Focal Adhesion Scaffolding Proteins in the Anaerobic Fungus Orpinomyces sp. C1A. PMID:27685796
De novo transcriptome assembly databases for the butterfly orchid Phalaenopsis equestris. PMID:27673730
Inferring interaction partners from protein sequences. PMID:27663738
Structured States of Disordered Proteins from Genomic Sequences. PMID:27662088
Profiling of adhesive-related genes in the freshwater cnidarian Hydra magnipapillata by transcriptomics and proteomics. PMID:27661452
Simulating the Function of the MjNhaP1 Transporter. PMID:27654405
Zonula occludens toxins and their prophages in Campylobacter species. PMID:27651834
Origin of the plant Tm-1-like gene via two independent horizontal transfer events and one gene fusion event. PMID:27647002
Systematic Search for Evidence of Interdomain Horizontal Gene Transfer from Prokaryotes to Oomycete Lineages. PMID:27642638
Cloning, expression, and characterization of a peptidoglycan hydrolase from the Burkholderia pseudomallei phage ST79. PMID:27637947
Horizontal gene transfer drives adaptive colonization of apple trees by the fungal pathogen Valsa mali. PMID:27634406
Genome-wide identification and analysis of JHBP-domain family members in the silkworm Bombyx mori. PMID:27631967
The PorX Response Regulator of the Porphyromonas gingivalis PorXY Two-Component System Does Not Directly Regulate the Type IX Secretion Genes but Binds the PorL Subunit. PMID:27630829
Advances in Understanding Mating Type Gene Organization in the Mushroom-Forming Fungus Flammulina velutipes. PMID:27621376
A functional genomics screen in planarians reveals regulators of whole-brain regeneration. PMID:27612384
Draft genome sequence of Enterococcus faecium strain LMG 8148. PMID:27610213
Proteomic Identification of Immunodiagnostic Antigens for Trypanosoma vivax Infections in Cattle and Generation of a Proof-of-Concept Lateral Flow Test Diagnostic Device. PMID:27606593
Comprehensive analysis and discovery of drought-related NAC transcription factors in common bean. PMID:27604581
ExonImpact: Prioritizing Pathogenic Alternative Splicing Events. PMID:27604408
Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains. PMID:27601190
Draft genome sequence of Acinetobacter baumannii strain NCTC 13423, a multidrug-resistant clinical isolate. PMID:27594976
Biophysical Analysis of the N-Terminal Domain from the Human Protein Phosphatase 1 Nuclear Targeting Subunit PNUTS Suggests an Extended Transcription Factor TFIIS-Like Fold. PMID:27591855
Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest. PMID:27590805
The role of ADP-ribosylation in regulating DNA interstrand crosslink repair. PMID:27587838
Draft genome sequence of Pseudomonas moraviensis strain Devor implicates metabolic versatility and bioremediation potential. PMID:27583206
Draft genome sequence of Micrococcus luteus strain O'Kane implicates metabolic versatility and the potential to degrade polyhydroxybutyrates. PMID:27583205
Biochemical and Structural Characterisation of DNA Ligases from Bacteria and Archaea. PMID:27582505
Presence of a carboxy-terminal pseudorepeat and disease-like pseudohyperphosphorylation critically influence tau's interaction with microtubules in axon-like processes. PMID:27582388
Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes. PMID:27580370
Chemotaxis cluster 1 proteins form cytoplasmic arrays in Vibrio cholerae and are stabilized by a double signaling domain receptor DosM. PMID:27573843
Structure of the C-Terminal Helical Repeat Domain of Eukaryotic Elongation Factor 2 Kinase. PMID:27571275
Nectrisine Biosynthesis Genes in Thelonectria discophora SANK 18292: Identification and Functional Analysis. PMID:27565616
Genome Sequence of Jumbo Phage vB_AbaM_ME3 of Acinetobacter baumanni. PMID:27563033
The physiology and habitat of the last universal common ancestor. PMID:27562259
Baseplate assembly of phage Mu: Defining the conserved core components of contractile-tailed phages and related bacterial systems. PMID:27555589
An intact plastid genome is essential for the survival of colorless Euglena longa but not Euglena gracilis. PMID:27553633
A Fast Alignment-Free Approach for De Novo Detection of Protein Conserved Regions. PMID:27552220
Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank. PMID:27551105
Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat. PMID:27550073
Uncovering Earth's virome. PMID:27533034
Carboxylic ester hydrolases: Classification and database derived from their primary, secondary, and tertiary structures. PMID:27530203
Defining key roles for auxiliary proteins in an ABC transporter that maintains bacterial outer membrane lipid asymmetry. PMID:27529189
PoplarGene: poplar gene network and resource for mining functional information for genes from woody plants. PMID:27515999
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
Outer Membrane Proteins Derived from Non-cyanobacterial Lineage Cover the Peptidoglycan of Cyanophora paradoxa Cyanelles and Serve as a Cyanelle Diffusion Channel. PMID:27502278
The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response. PMID:27489856
Crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii. PMID:27487927
Reduction, alignment and visualisation of large diverse sequence families. PMID:27484804
A catalog of Xenopus tropicalis transcription factors and their regional expression in the early gastrula stage embryo. PMID:27475627
Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri. PMID:27474723
The Landscape of A-to-I RNA Editome Is Shaped by Both Positive and Purifying Selection. PMID:27467689
Type II Toxin-Antitoxin Systems in the Unicellular Cyanobacterium Synechocystis sp. PCC 6803. PMID:27455323
Population Genomics of Reduced Vancomycin Susceptibility in Staphylococcus aureus. PMID:27446992
Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks. PMID:27446025
Whole-Metagenome-Sequencing-Based Community Profiles of Vitis vinifera L. cv. Corvina Berries Withered in Two Post-harvest Conditions. PMID:27445999
Lokiarchaeota Marks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems. PMID:27413050
Toxin-Antitoxin Modules Are Pliable Switches Activated by Multiple Protease Pathways. PMID:27409636
On the Origin of De Novo Genes in Arabidopsis thaliana Populations. PMID:27401176
LEON-BIS: multiple alignment evaluation of sequence neighbours using a Bayesian inference system. PMID:27387560
Characterization of the Deep-Sea Streptomyces sp. SCSIO 02999 Derived VapC/VapB Toxin-Antitoxin System in Escherichia coli. PMID:27376329
Contributions of P2- and P22-like prophages to understanding the enormous diversity and abundance of tailed bacteriophages. PMID:27372181
Further insight into BRUTUS domain composition and functionality. PMID:27359166
Two propanediol utilization-like proteins of Moorella thermoacetica with phosphotransacetylase activity. PMID:27338272
Crystal structure of MytiLec, a galactose-binding lectin from the mussel Mytilus galloprovincialis with cytotoxicity against certain cancer cell types. PMID:27321048
Potential DNA binding and nuclease functions of ComEC domains characterized in silico. PMID:27318187
Characteristics of the Clostridium difficile cell envelope and its importance in therapeutics. PMID:27311697
Structure of an ABC transporter solute-binding protein specific for the amino sugars glucosamine and galactosamine. PMID:27303900
The Simple Chordate Ciona intestinalis Has a Reduced Complement of Genes Associated with Fanconi Anemia. PMID:27279728
Consensus protein design. PMID:27274091
Insights into the transcriptional and translational mechanisms of linear organellar chromosomes in the box jellyfish Alatina alata (Cnidaria: Medusozoa: Cubozoa). PMID:27267414
Integrative computational approach for genome-based study of microbial lipid-degrading enzymes. PMID:27263017
Development and clinical application of an integrative genomic approach to personalized cancer therapy. PMID:27245685
VESPUCCI: Exploring Patterns of Gene Expression in Grapevine. PMID:27242836
The Unicellular Ancestry of Groucho-Mediated Repression and the Origins of Metazoan Transcription Factors. PMID:27189982
NMR in structural genomics to increase structural coverage of the protein universe: Delivered by Prof. Kurt Wüthrich on 7 July 2013 at the 38th FEBS Congress in St. Petersburg, Russia. PMID:27154589
TOPDOM: database of conservatively located domains and motifs in proteins. PMID:27153630
Independent Evolution of Six Families of Halogenating Enzymes. PMID:27153321
The periplasmic sensing domain of Vibrio fischeri chemoreceptor protein A (VfcA): cloning, purification and crystallographic analysis. PMID:27139830
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. PMID:27131791
LassoProt: server to analyze biopolymers with lassos. PMID:27131383
The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. PMID:27131380
Impacts of somatic mutations on gene expression: an association perspective. PMID:27127206
Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P. PMID:27104580
Discovery Strategies of Bioactive Compounds Synthesized by Nonribosomal Peptide Synthetases and Type-I Polyketide Synthases Derived from Marine Microbiomes. PMID:27092515
Refined Pichia pastoris reference genome sequence. PMID:27084056
HPF1/C4orf27 Is a PARP-1-Interacting Protein that Regulates PARP-1 ADP-Ribosylation Activity. PMID:27067600
Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore-Forming Proteins. PMID:27064789
Characterization of a temperature-responsive two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii. PMID:27052690
Identification and Comparative Analysis of H2O2-Scavenging Enzymes (Ascorbate Peroxidase and Glutathione Peroxidase) in Selected Plants Employing Bioinformatics Approaches. PMID:27047498
Molecular docking of Glycine max and Medicago truncatula ureases with urea; bioinformatics approaches. PMID:26852122
The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. PMID:26740669 -
The Pfam protein families database
PubMed citations: 1992.
1992 articles citing: The Pfam protein families database
Development of a High Oleic Cardoon Cell Culture Platform by SAD Overexpression and RNAi-Mediated FAD2.2 Silencing. PMID:35845700
Comparative physiology and transcriptome analysis reveals that chloroplast development influences silver-white leaf color formation in Hydrangea macrophylla var. maculata. PMID:35842592
Genome-Wide Study of Hsp90 Gene Family in Cabbage (Brassica oleracea var. capitata L.) and Their Imperative Roles in Response to Cold Stress. PMID:35812899
New Mutations in cls Lead to Daptomycin Resistance in a Clinical Vancomycin- and Daptomycin-Resistant Enterococcus faecium Strain. PMID:35801099
Conserved and lineage-specific hypothetical proteins may have played a central role in the rise and diversification of major archaeal groups. PMID:35790962
Genome wide and evolutionary analysis of heat shock protein 70 proteins in tomato and their role in response to heat and drought stress. PMID:35788950
A consensus view of the proteome of the last universal common ancestor. PMID:35784055
Systematic Analysis of NB-ARC Gene Family in Rice and Functional Characterization of GNP12. PMID:35783267
Transcriptional Basis for Haustorium Formation and Host Establishment in Hemiparasitic Psittacanthus schiedeanus Mistletoes. PMID:35769994
The landscape of isoform switches in sepsis: a multicenter cohort study. PMID:35715539
Catching a Walker in the Act-DNA Partitioning by ParA Family of Proteins. PMID:35694299
The Long Read Transcriptome of Rice (Oryza sativa ssp. japonica var. Nipponbare) Reveals Novel Transcripts. PMID:35689714
A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution. PMID:35680998
Antioxidant potential of Pediococcus pentosaceus strains from the sow milk bacterial collection in weaned piglets. PMID:35650642
Whole-Transcriptome Analysis Reveals Long Noncoding RNAs Involved in Female Floral Development of Hickory (Carya cathayensis Sarg.). PMID:35646060
Plasmodium manipulates the expression of host long non-coding RNA during red blood cell intracellular infection. PMID:35643541
Genome Assembly and Evolutionary Analysis of the Mandarin Duck Aix galericulata Reveal Strong Genome Conservation among Ducks. PMID:35640266
Genome-Wide Screening of Transposable Elements in the Whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae), Revealed Insertions with Potential Insecticide Resistance Implications. PMID:35621732
In silico functional and tumor suppressor role of hypothetical protein PCNXL2 with regulation of the Notch signaling pathway. PMID:35539910
Genome-wide analysis of the B3 transcription factors reveals that RcABI3/VP1 subfamily plays important roles in seed development and oil storage in castor bean (Ricinus communis). PMID:35505987
Lentil allergens identification and quantification: An update from omics perspective. PMID:35495776
Functional dissection of human mitotic genes using CRISPR-Cas9 tiling screens. PMID:35483740
The genome of hibiscus hamabo reveals its adaptation to saline and waterlogged habitat. PMID:35480957
Distinctive signatures of pathogenic and antibiotic resistant potentials in the hadal microbiome. PMID:35468809
Integrated Analysis of the ceRNA Network and M-7474 Function in Testosterone-Mediated Fat Deposition in Pigs. PMID:35456474
Simple, efficient and thorough shotgun proteomic analysis with PatternLab V. PMID:35411045
A Systematic Phylogenomic Classification of the Multidrug and Toxic Compound Extrusion Transporter Gene Family in Plants. PMID:35371145
Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L. PMID:35328546
Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes. PMID:35323968
Chromosome-Level Genome Assembly for Acer pseudosieboldianum and Highlights to Mechanisms for Leaf Color and Shape Change. PMID:35310631
Transcriptome analysis of the bivalve Placuna placenta mantle reveals potential biomineralization-related genes. PMID:35304539
ATGPred-FL: sequence-based prediction of autophagy proteins with feature representation learning. PMID:35286461
Genome Analysis of the Broad Host Range Necrotroph Nalanthamala psidii Highlights Genes Associated With Virulence. PMID:35283890
Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnacle Pollicipes pollicipes. PMID:35277961
Genome-Wide Analyses of Aspartic Proteases on Potato Genome (Solanum tuberosum): Generating New Tools to Improve the Resistance of Plants to Abiotic Stress. PMID:35214878
Genome-wide analysis of sucrose synthase family in soybean and their expression in response to abiotic stress and seed development. PMID:35213642
Identification and regulatory network analysis of SPL family transcription factors in Populus euphratica Oliv. heteromorphic leaves. PMID:35190606
Genome‑wide identification of CAMTA gene family members in rice (Oryza sativa L.) and in silico study on their versatility in respect to gene expression and promoter structure. PMID:35169940
Identification of sodium homeostasis genes in Camelus bactrianus by whole transcriptome sequencing. PMID:35147292
Carbohydrate active enzymes (CAZy) regulate cellulolytic and pectinolytic enzymes in Colletotrichum falcatum causing red rot in sugarcane. PMID:35127303
Epigenomic and transcriptomic analyses reveal differences between low-grade inflammation and severe exhaustion in LPS-challenged murine monocytes. PMID:35091696
Comparative transcriptomics reveal tissue level specialization towards diet in prickleback fishes. PMID:35076747
Schistosoma mansoni α-N-acetylgalactosaminidase (SmNAGAL) regulates coordinated parasite movement and egg production. PMID:35025955
Chromosome-level genome assembly of the shuttles hoppfish, Periophthalmus modestus. PMID:35022698
Evolutionary Ecology of Natural Comammox Nitrospira Populations. PMID:35014874
Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes. PMID:35012468
Habitat Adaptation Drives Speciation of a Streptomyces Species with Distinct Habitats and Disparate Geographic Origins. PMID:35012331
Novel insights into water-deficit-responsive mRNAs and lncRNAs during fiber development in Gossypium hirsutum. PMID:34979912
High Molecular Weight Kininogen: A Review of the Structural Literature. PMID:34948166
An Exploration of Non-Coding RNAs in Extracellular Vesicles Delivered by Swine Anterior Pituitary. PMID:34912377
Two-Component System Genes in Sorghum bicolor: Genome-Wide Identification and Expression Profiling in Response to Environmental Stresses. PMID:34899869
Genome-wide characterization, evolution, structure, and expression analysis of the F-box genes in Caenorhabditis. PMID:34895149
Comparative Transcriptome Sequencing of Taro Corm Development With a Focus on the Starch and Sucrose Metabolism Pathway. PMID:34858484
Muribaculaceae Genomes Assembled from Metagenomes Suggest Genetic Drivers of Differential Response to Acarbose Treatment in Mice. PMID:34851167
Accurate expression quantification from nanopore direct RNA sequencing with NanoCount. PMID:34850115
Transcriptome Analysis of Testicular Aging in Mice. PMID:34831115
Genome-Wide Identification and Characterization of Soybean GmLOR Gene Family and Expression Analysis in Response to Abiotic Stresses. PMID:34830397
Comprehensive Comparative Analysis of the GATA Transcription Factors in Four Rosaceae Species and Phytohormonal Response in Chinese Pear (Pyrus bretschneideri) Fruit. PMID:34830372
Comparative RNA-Seq Analysis Reveals Potentially Resistance-Related Genes in Response to Bacterial Canker of Tomato. PMID:34828351
High Genomic Identity between Clinical and Environmental Strains of Herbaspirillum frisingense Suggests Pre-Adaptation to Different Hosts and Intrinsic Resistance to Multiple Drugs. PMID:34827347
Transcriptomic Profile of the Cockle Cerastoderma edule Exposed to Seasonal Diarrhetic Shellfish Toxin Contamination. PMID:34822568
Phenotypic Screening of Molecular Docking Enriched Chemical Libraries from Targets Identified in Ischemic Stroke Genome Data by Network-Based Method. PMID:34820079
Evolutionary history and divergence times of Odonata (dragonflies and damselflies) revealed through transcriptomics. PMID:34805787
Pneumococcal Extracellular Serine Proteases: Molecular Analysis and Impact on Colonization and Disease. PMID:34790590
The First De Novo Transcriptome Assembly and Transcriptomic Dynamics of the Mangrove Tree Rhizophora stylosa Griff. (Rhizophoraceae). PMID:34769393
Identification of discriminative gene-level and protein-level features associated with pathogenic gain-of-function and loss-of-function variants. PMID:34762822
The Subcellular Proteome of a Planctomycetes Bacterium Shows That Newly Evolved Proteins Have Distinct Fractionation Patterns. PMID:34745019
GFICLEE: ultrafast tree-based phylogenetic profile method inferring gene function at the genomic-wide level. PMID:34715785
Identification of GROWTH-REGULATING FACTOR transcription factors in lettuce (Lactuca sativa) genome and functional analysis of LsaGRF5 in leaf size regulation. PMID:34688264
Whole-Genome and Transcriptome Sequencing of Phlebopus portentosus Reveals Its Associated Ectomycorrhizal Niche and Conserved Pathways Involved in Fruiting Body Development. PMID:34659161
Sequence Engineering of an Aspergillus niger Tannase to Produce in Pichia pastoris a Single-Chain Enzyme with High Specific Activity. PMID:34655039
Transcriptome analysis of messenger RNA and long noncoding RNA related to different developmental stages of tail adipose tissues of sunite sheep. PMID:34646540
Chitinase Chit62J4 Essential for Chitin Processing by Human Microbiome Bacterium Clostridium paraputrificum J4. PMID:34641521
A Genomic Survey of Mayetiola destructor Mobilome Provides New Insights into the Evolutionary History of Transposable Elements in the Cecidomyiid Midges. PMID:34634072
Advances in the Regulation of Epidermal Cell Development by C2H2 Zinc Finger Proteins in Plants. PMID:34630497
The genome of the naturally evolved obesity-prone Ossabaw miniature pig. PMID:34585119
De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza). PMID:34576037
Genome sequencing and identification of cellulase genes in Bacillus paralicheniformis strains from the Red Sea. PMID:34548024
The GRAS gene family and its roles in seed development in litchi (Litchi chinensis Sonn). PMID:34535087
The genome sequence provides insights into salt tolerance of Achnatherum splendens (Gramineae), a constructive species of alkaline grassland. PMID:34487631
Integrative overview of IFITMs family based on Bioinformatics analysis. PMID:34466338
Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome. PMID:34465761
Comparison of mouse models reveals a molecular distinction between psychotic illness in PWS and schizophrenia. PMID:34417445
Comprehensive Analysis of the Expression Profiles of Hepatic lncRNAs in the Mouse Model of Alcoholic Liver Disease. PMID:34393788
Data on the first functionally-annotated de novo transcriptome assembly for North American flying squirrels (genus Glaucomys). PMID:34381854
Transcriptome profiling of Stevia rebaudiana MS007 revealed genes involved in flower development. PMID:34377055
Potential stress tolerance roles of barley germins and GLPs. PMID:34363524
Lactic Acid Bacteria Diversity and Characterization of Probiotic Candidates in Fermented Meats. PMID:34359389
Genome-wide identification and analysis of the YABBY gene family in Moso Bamboo (Phyllostachys edulis (Carrière) J. Houz). PMID:34327057
Reboot: a straightforward approach to identify genes and splicing isoforms associated with cancer patient prognosis. PMID:34316711
A Transcriptome-Wide Isoform Landscape of Melanocytic Nevi and Primary Melanomas Identifies Gene Isoforms Associated with Malignancy. PMID:34281234
Toxocara canis Infection Alters lncRNA and mRNA Expression Profiles of Dog Bone Marrow. PMID:34277631
Identification and Comparative Analysis of Long Non-coding RNAs in High- and Low-Fecundity Goat Ovaries During Estrus. PMID:34249080
Trajectories of Homoeolog-Specific Expression in Allotetraploid Tragopogon castellanus Populations of Independent Origins. PMID:34249049
Comparative genomic analysis of Escherichia coli isolates from cases of bovine clinical mastitis identifies nine specific pathotype marker genes. PMID:34227932
Zetaproteobacteria Pan-Genome Reveals Candidate Gene Cluster for Twisted Stalk Biosynthesis and Export. PMID:34220764
Enhanced mutualistic symbiosis between soil phages and bacteria with elevated chromium-induced environmental stress. PMID:34183048
Identification and Analysis of Long Non-coding RNAs in Leuciscus waleckii Adapted to Highly Alkaline Conditions. PMID:34177616
Network-based visualisation reveals new insights into transposable element diversity. PMID:34169647
Production of Glucose 6-Phosphate From a Cellulosic Feedstock in a One Pot Multi-Enzyme Synthesis. PMID:34150734
Protein Family Content Uncovers Lineage Relationships and Bacterial Pathway Maintenance Mechanisms in DPANN Archaea. PMID:34140936
Enterococcal PrgU Provides Additional Regulation of Pheromone-Inducible Conjugative Plasmids. PMID:34106752
Genomic analysis of the carboxylesterase family in the salmon louse (Lepeophtheirus salmonis). PMID:34098083
The landscape and biological relevance of aberrant alternative splicing events in esophageal squamous cell carcinoma. PMID:34079089
Genome Wide Analysis of Citrus sinensis Heat Shock Proteins. PMID:34056019
Trichoderma reesei ACE4, a Novel Transcriptional Activator Involved in the Regulation of Cellulase Genes during Growth on Cellulose. PMID:34047636
Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori. PMID:34022797
Draft Genome Sequence of Deefgea sp. Strain CFH1-16, Isolated from the Intestine of the Freshwater Fish Hypomesus nipponensis. PMID:33986104
Transcriptome analysis of the liver of Eospalax fontanierii under hypoxia. PMID:33981491
The microbiome of deep-sea fish reveals new microbial species and a sparsity of antibiotic resistance genes. PMID:33970781
Genome Recovery, Functional Profiling, and Taxonomic Classification from Metagenomes. PMID:33961223
Molecular evidence of the avocado defense response to Fusarium kuroshium infection: a deep transcriptome analysis using RNA-Seq. PMID:33954045
Structure and Expression Analysis of Sucrose Phosphate Synthase, Sucrose Synthase and Invertase Gene Families in Solanum lycopersicum. PMID:33946733
A stony coral cell atlas illuminates the molecular and cellular basis of coral symbiosis, calcification, and immunity. PMID:33945788
A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses. PMID:33920047
Intrinsically Disordered Proteins as Regulators of Transient Biological Processes and as Untapped Drug Targets. PMID:33917117
Tissue-specific regulatory mechanism of LncRNAs and methylation in sheep adipose and muscle induced by Allium mongolicum Regel extracts. PMID:33911127
Composition and function of ciliary inner-dynein-arm subunits studied in Chlamydomonas reinhardtii. PMID:33876572
An Overview of Antennal Esterases in Lepidoptera. PMID:33868009
Variation in Parasitoid Virulence of Tetrastichus brontispae during the Targeting of Two Host Beetles. PMID:33808261
A Roadmap for Genome-Based Phage Taxonomy. PMID:33803862
Rational Design of Adenylate Kinase Thermostability through Coevolution and Sequence Divergence Analysis. PMID:33803409
Characterization and Full Genome Sequence of Novel KPP-5 Lytic Phage against Klebsiella pneumoniae Responsible for Recalcitrant Infection. PMID:33800632
Genome-resolved metagenomics using environmental and clinical samples. PMID:33758906
Primary Metabolism co-Opted for Defensive Chemical Production in the Carabid Beetle, Harpalus pensylvanicus. PMID:33689113
Resequencing and SNP discovery of Amur ide (Leuciscus waleckii) provides insights into local adaptations to extreme environments. PMID:33658614
Identification, characterization and functional analysis of grape (Vitis vinifera L.) mitochondrial transcription termination factor (mTERF) genes in responding to biotic stress and exogenous phytohormone. PMID:33637035
Comparative genomics reveals broad genetic diversity, extensive recombination and nascent ecological adaptation in Micrococcus luteus. PMID:33602135
Brassica carinata genome characterization clarifies U's triangle model of evolution and polyploidy in Brassica. PMID:33599732
Evolution of frustrated and stabilising contacts in reconstructed ancient proteins. PMID:33569610
Contribution of horizontal gene transfer to the functionality of microbial biofilm on a macroalgae. PMID:33558686
Choanoflagellates and the ancestry of neurosecretory vesicles. PMID:33550951
Genome-Wide Identification and Comparative Analysis of ARF Family Genes in Three Apiaceae Species. PMID:33519895
The Draft Genome Sequence of a New Land-Hopper Platorchestia hallaensis. PMID:33505439
Integrated analysis of lncRNA and mRNA transcriptomes reveals the potential regulatory role of lncRNA in kiwifruit ripening and softening. PMID:33462344
AhR and Cancer: From Gene Profiling to Targeted Therapy. PMID:33451095
Transcriptome characterization and generation of marker resource for Himalayan vulnerable species, Ulmus wallichiana. PMID:33439411
Large-scale survey and database of high affinity ligands for peptide recognition modules. PMID:33438817
Topological Analysis for Sequence Variability: Case Study on more than 2K SARS-CoV-2 sequences of COVID-19 infected 54 countries in comparison with SARS-CoV-1 and MERS-CoV. PMID:33421654
Fluoxetine ameliorates depressive symptoms by regulating lncRNA expression in the mouse hippocampus. PMID:33420763
Classification and Computational Analysis of Arabidopsis thaliana Sperm Cell-Specific F-Box Protein Gene 3p.AtFBP113. PMID:33381153
Transcriptome Analysis Reveals the Potential Role of Long Non-coding RNAs in Mammary Gland of Yak During Lactation and Dry Period. PMID:33324637
Structure of dual BON-domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation. PMID:33315009
Understanding the relationship between viral infections and trace elements from a metallomics perspective: implications for COVID-19. PMID:33295922
Genome-wide characterization and expression analysis of HAK K+ transport family in Ipomoea. PMID:33269187
Major SCP/TAPS protein expansion in Lucilia cuprina is associated with novel tandem array organisation and domain architecture. PMID:33246493
Localized effect of treated wastewater effluent on the resistome of an urban watershed. PMID:33215210
Changing Expression Profiles of Messenger RNA, MicroRNA, Long Non-coding RNA, and Circular RNA Reveal the Key Regulators and Interaction Networks of Competing Endogenous RNA in Pulmonary Fibrosis. PMID:33193637
Omics approaches for conservation biology research on the bivalve Chamelea gallina. PMID:33154500
A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis. PMID:33146374
ABC-F translation factors: from antibiotic resistance to immune response. PMID:33135152
Genome-Wide Characterization and Expression of Two-Component System Genes in Cytokinin-Regulated Gall Formation in Zizania latifolia. PMID:33105697
Genomic and transcriptomic landscapes and evolutionary dynamics of molluscan glycoside hydrolase families with implications for algae-feeding biology. PMID:33101612
Transcriptomic and Epigenomic Dynamics of Honey Bees in Response to Lethal Viral Infection. PMID:33101388
Identification of Putative Non-Substrate-Based XT-I Inhibitors by Natural Product Library Screening. PMID:33096778
Systematic analysis of the OFP genes in six Rosaceae genomes and their roles in stress response in Chinese pear (Pyrus bretschneideri). PMID:33088052
Chorismate mutase and isochorismatase, two potential effectors of the migratory nematode Hirschmanniella oryzae, increase host susceptibility by manipulating secondary metabolite content of rice. PMID:33084136
Integrated omics unveil the secondary metabolic landscape of a basal dinoflagellate. PMID:33050904
Molecular evolutionary and structural analysis of human UCHL1 gene demonstrates the relevant role of intragenic epistasis in Parkinson's disease and other neurological disorders. PMID:33028204
Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts. PMID:32994284
Genome-Wide Identification and Characterization of Fusarium graminearum-Responsive lncRNAs in Triticum aestivum. PMID:32992604
High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae. PMID:32985109
Human SIRT1 Multispecificity Is Modulated by Active-Site Vicinity Substitutions during Natural Evolution. PMID:32956445
Transcriptomic data on the transgenerational exposure of the keystone amphipod Gammarus locusta to simvastatin. PMID:32944603
Structure of the bacterial ribosome at 2 Å resolution. PMID:32924932
Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate. PMID:32920602
Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network. PMID:32879328
The Infant-Derived Bifidobacterium bifidum Strain CNCM I-4319 Strengthens Gut Functionality. PMID:32872165
Diverse enzymatic activities mediate antiviral immunity in prokaryotes. PMID:32855333
"Mind the Gap": Hi-C Technology Boosts Contiguity of the Globe Artichoke Genome in Low-Recombination Regions. PMID:32817122
Large-scale tethered function assays identify factors that regulate mRNA stability and translation. PMID:32807991
HAK/KUP/KT family potassium transporter genes are involved in potassium deficiency and stress responses in tea plants (Camellia sinensis L.): expression and functional analysis. PMID:32791963
A Chinese White Pear (Pyrus bretschneideri) BZR Gene PbBZR1 Act as a Transcriptional Repressor of Lignin Biosynthetic Genes in Fruits. PMID:32765567
Functional Insight of Nitric-Oxide Induced DUF Genes in Arabidopsis thaliana. PMID:32765550
Evolutionary Remodeling of the Cell Envelope in Bacteria of the Planctomycetes Phylum. PMID:32761170
Genome-Wide Analysis Reveals Changes in Long Noncoding RNAs in the Differentiation of Canine BMSCs into Insulin-Producing Cells. PMID:32756402
Molecular Evolution and Characterization of Fish Stathmin Genes. PMID:32752168
Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog. PMID:32681159
Long noncoding RNA MARL regulates antiviral responses through suppression miR-122-dependent MAVS downregulation in lower vertebrates. PMID:32678830
The genetic factors of bilaterian evolution. PMID:32672535
To gel or not to gel: differential expression of carrageenan-related genes between the gametophyte and tetasporophyte life cycle stages of the red alga Chondrus crispus. PMID:32661246
Liver transcriptome resources of four commercially exploited teleost species. PMID:32636445
Computational identification of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes. PMID:32620079
Phospholipid ebb and flow makes mitochondria go. PMID:32614384
Shifting evolutionary sands: transcriptome characterization of the Aptostichus atomarius species complex. PMID:32539685
Isolation and transcriptomic analysis of Anopheles gambiae oenocytes enables the delineation of hydrocarbon biosynthesis. PMID:32538778
Evidence from ileum and liver transcriptomes of resistance to high-salt and water-deprivation conditions in camel. PMID:32518679
Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value. PMID:32514106
Genetic and functional diversification of chemosensory pathway receptors in mosquito-borne filarial nematodes. PMID:32511224
The N1-Methyladenosine Methylome of Petunia mRNA. PMID:32461301
The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenetic position of Lobotiformes and biological conservation. PMID:32424221
Insight into Evolution and Conservation Patterns of B1-Subfamily Members of GPCR. PMID:32421105
A Novel Computational Approach for Identifying Essential Proteins From Multiplex Biological Networks. PMID:32373163
Transcriptomic analysis of polyketide synthases in a highly ciguatoxic dinoflagellate, Gambierdiscus polynesiensis and low toxicity Gambierdiscus pacificus, from French Polynesia. PMID:32294110
Two-Level Protein Methylation Prediction using structure model-based features. PMID:32265459
De novo transcriptome assembly and data for the blue-winged teal (Spatula discors). PMID:32258268
Consistency of the Tools That Predict the Impact of Single Nucleotide Variants (SNVs) on Gene Functionality: The BRCA1 Gene. PMID:32244891
Identification and evolutionary analysis of the nucleolar proteome of Giardia lamblia. PMID:32228450
Targeted assemblies of cas1 suggest CRISPR-Cas's response to soil warming. PMID:32221408
The transcriptome of the newt Cynops orientalis provides new insights into evolution and function of sexual gene networks in sarcopterygians. PMID:32214214
First draft genome for the sand-hopper Trinorchestia longiramus. PMID:32152293
Genome-Wide Detection of Key Genes and Epigenetic Markers for Chicken Fatty Liver. PMID:32151087
Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus. PMID:32150860
Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing. PMID:32138663
The CRISPR-Cas systems were selectively inactivated during evolution of Bacillus cereus group for adaptation to diverse environments. PMID:32132663
Transcriptomics at Maize Embryo/Endosperm Interfaces Identifies a Transcriptionally Distinct Endosperm Subdomain Adjacent to the Embryo Scutellum. PMID:32086366
The first glimpse of the endometrial microbiota in early pregnancy. PMID:32057732
Evolutionary analysis of the most polymorphic gene family in falciparum malaria. PMID:32055709
Functional lncRNA-miRNA-mRNA networks in rabbit carotid atherosclerosis. PMID:32045883
Genome-wide identification and characterization of novel long non-coding RNA in Ruminal tissue affected with sub-acute Ruminal acidosis from Holstein cattle. PMID:32043213
Long noncoding RNA THAP9-AS1 is induced by Helicobacter pylori and promotes cell growth and migration of gastric cancer. PMID:32021238
A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference. PMID:32019526
Effects of Castration on miRNA, lncRNA, and mRNA Profiles in Mice Thymus. PMID:32019071
Draft Genome of the Asian Buffalo Leech Hirudinaria manillensis. PMID:32010187
MicroRNA and mRNA interactions coordinate the immune response in non-lethal heat stressed Litopenaeus vannamei against AHPND-causing Vibrio parahaemolyticus. PMID:31964916
Subchromosome-Scale Nuclear and Complete Mitochondrial Genome Characteristics of Morchella crassipes. PMID:31940908
Domain-mediated interactions for protein subfamily identification. PMID:31937869
Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses. PMID:31900112
Dataset on the formation of Thioredoxin interacting protein (Txnip) containing redox sensitive high molecular weight nucleoprotein complexes. PMID:31890777
The transcriptomic signature of low aggression in honey bees resembles a response to infection. PMID:31888487
PhoH2 proteins couple RNA helicase and RNAse activities. PMID:31886915
Hybrid de novo whole-genome assembly and annotation of the model tapeworm Hymenolepis diminuta. PMID:31796747
The Transcription Factor Aabzip9 Positively Regulates the Biosynthesis of Artemisinin in Artemisia annua. PMID:31787989
Dynamic Changes of DNA Methylation and Transcriptome Expression in Porcine Ovaries during Aging. PMID:31781648
A computational framework to explore large-scale biosynthetic diversity. PMID:31768033
Clinical Spectrum and Functional Consequences Associated with Bi-Allelic Pathogenic PNPT1 Variants. PMID:31752325
The Endophytic Fungus Chaetomium cupreum Regulates Expression of Genes Involved in the Tolerance to Metals and Plant Growth Promotion in Eucalyptus globulus Roots. PMID:31717780
Identification of lncRNAs by RNA Sequencing Analysis During in Vivo Pre-Implantation Developmental Transformation in the Goat. PMID:31708972
The mixed liver and heart transcriptome dataset of the New Zealand brushtail possum, Trichosurus vulpecula. PMID:31700950
A specific fungal transcription factor controls effector gene expression and orchestrates the establishment of the necrotrophic pathogen lifestyle on wheat. PMID:31685928
Transcriptome-Based Identification and Molecular Evolution of the Cytochrome P450 Genes and Expression Profiling under Dimethoate Treatment in Amur Stickleback (Pungitius sinensis). PMID:31661806
Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence. PMID:31649710
Genome-Wide Analysis of the YABBY Gene Family in Grapevine and Functional Characterization of VvYABBY4. PMID:31649691
The Genome Sequence of the Eastern Woodchuck (Marmota monax) - A Preclinical Animal Model for Chronic Hepatitis B. PMID:31645421
RFQAmodel: Random Forest Quality Assessment to identify a predicted protein structure in the correct fold. PMID:31634369
Hexa-Longin domain scaffolds for inter-Rab signalling. PMID:31562761
Small RNA inhibits infection by downy mildew pathogen Hyaloperonospora arabidopsidis. PMID:31557400
Integrative Analysis of the Core Fruit Lignification Toolbox in Pear Reveals Targets for Fruit Quality Bioengineering. PMID:31540505
The distinction of CPR bacteria from other bacteria based on protein family content. PMID:31519891
Complete Genome Sequence of Phreatobacter sp. Strain NMCR1094, a Formate-Utilizing Bacterium Isolated from a Freshwater Stream. PMID:31515346
Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max). PMID:31497394
Measuring the impact of gene prediction on gene loss estimates in Eukaryotes by quantifying falsely inferred absences. PMID:31461468
Transcriptome Landscape Variation in the Genus Thymus. PMID:31426352
Comprehensive Analysis of LncRNA Reveals the Temporal-Specific Module of Goat Skeletal Muscle Development. PMID:31416143
CasPDB: an integrated and annotated database for Cas proteins from bacteria and archaea. PMID:31411686
The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion. PMID:31387118
From the Amazon: A comprehensive liver transcriptome dataset of the teleost fish tambaqui, Colossoma macropomum. PMID:31372415
Proteomics and Docking Study Targeting Penicillin-Binding Protein and Penicillin-Binding Protein2a of Methicillin-Resistant Staphylococcus aureus Strain SO-1977 Isolated from Sudan. PMID:31360059
Lack of long-term acclimation in Antarctic encrusting species suggests vulnerability to warming. PMID:31358752
Hybrid Genome Assembly of a Neotropical Mutualistic Ant. PMID:31329228
Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value. PMID:31320697
De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China. PMID:31307060
Flowering plant immune repertoires expand under mycorrhizal symbiosis. PMID:31245768
Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family. PMID:31239280
Comparative physiology and transcriptome analysis allows for identification of lncRNAs imparting tolerance to drought stress in autotetraploid cassava. PMID:31226927
ECOD: identification of distant homology among multidomain and transmembrane domain proteins. PMID:31226926
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
Cyberbiosecurity Challenges of Pathogen Genome Databases. PMID:31157218
Comprehensive transcriptional profiling of aging porcine liver. PMID:31149403
Transcriptomics Analysis Reveals New Insights into the Roles of Notch1 Signaling on Macrophage Polarization. PMID:31142802
Comparative transcriptomic analysis of dermal wound healing reveals de novo skeletal muscle regeneration in Acomys cahirinus. PMID:31141508
Comprehensive Genomic Survey, Characterization and Expression Analysis of the HECT Gene Family in Brassica rapa L. and Brassica oleracea L. PMID:31137879
A genome-wide approach to the comprehensive analysis of GASA gene family in Glycine max. PMID:31123969
HOT or not: examining the basis of high-occupancy target regions. PMID:31114922
Integrative Analyses of Long Non-coding RNA and mRNA Involved in Piglet Ileum Immune Response to Clostridium perfringens Type C Infection. PMID:31114763
lncRNA profile of Apis mellifera and its possible role in behavioural transition from nurses to foragers. PMID:31113365
Whirly (Why) transcription factors in tomato (Solanum lycopersicum L.): genome-wide identification and transcriptional profiling under drought and salt stresses. PMID:31089915
Comparative Analysis of the aquaporin Gene Family in 12 Fish Species. PMID:31086002
Identification and characterization of pineapple leaf lncRNAs in crassulacean acid metabolism (CAM) photosynthesis pathway. PMID:31040312
An annual cycle of gene regulation in the red-legged salamander mental gland: from hypertrophy to expression of rapidly evolving pheromones. PMID:31029098
Prevalence and Diversity Analysis of Candidate Prophages to Provide An Understanding on Their Roles in Bacillus Thuringiensis. PMID:31027262
An Integrated Analysis of Cashmere Fineness lncRNAs in Cashmere Goats. PMID:30987022
Comparative analysis of the root and leaf transcriptomes in Chelidonium majus L. PMID:30986259
Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation. PMID:30976019
Key genes differential expressions and pathway involved in salt and water-deprivation stresses for renal cortex in camel. PMID:30961536
Closely related viruses of the marine picoeukaryotic alga Ostreococcus lucimarinus exhibit different ecological strategies. PMID:30924271
Aurora kinase protein family in Trypanosoma cruzi: Novel role of an AUK-B homologue in kinetoplast replication. PMID:30897087
Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton. PMID:30886425
Impact of a bathing tradition on shared gut microbe among Japanese families. PMID:30867524
Transcriptomic Analysis of Coding Genes and Non-Coding RNAs Reveals Complex Regulatory Networks Underlying the Black Back and White Belly Coat Phenotype in Chinese Wuzhishan Pigs. PMID:30866582
Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens. PMID:30814220
Flax (Linum usitatissimum L.) response to non-optimal soil acidity and zinc deficiency. PMID:30813909
Metacaspase gene family in Rosaceae genomes: Comparative genomic analysis and their expression during pear pollen tube and fruit development. PMID:30794567
Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE). PMID:30794542
Novel Insights reveal Anti-microbial Gene Regulation of Piglet Intestine Immune in response to Clostridium perfringens Infection. PMID:30760749
Thermostable Branched-Chain Amino Acid Transaminases From the Archaea Geoglobus acetivorans and Archaeoglobus fulgidus: Biochemical and Structural Characterization. PMID:30733943
Structure-function characterization of an insecticidal protein GNIP1Aa, a member of an MACPF and β-tripod families. PMID:30728296
Diversified secondary metabolite biosynthesis gene repertoire revealed in symbiotic dinoflagellates. PMID:30718591
A genome-wide analysis of coatomer protein (COP) subunits of apicomplexan parasites and their evolutionary relationships. PMID:30704415
Significant abundance of cis configurations of coding variants in diploid human genomes. PMID:30698752
Genome sequence of Malania oleifera, a tree with great value for nervonic acid production. PMID:30689848
The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.). PMID:30675191
The Genetic Structures of an Extensively Drug Resistant (XDR) Klebsiella pneumoniae and Its Plasmids. PMID:30662878
Gene expression changes elicited by a parasitic B chromosome in the grasshopper Eyprepocnemis plorans are consistent with its phenotypic effects. PMID:30617552
Bifunctional Chloroplastic DJ-1B from Arabidopsis thaliana is an Oxidation-Robust Holdase and a Glyoxalase Sensitive to H₂O₂. PMID:30609642
Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination. PMID:30592459
Genomic Signals of Adaptation towards Mutualism and Sociality in Two Ambrosia Beetle Complexes. PMID:30583535
Transcriptomic Characterization of the South American Freshwater Stingray Potamotrygon motoro Venom Apparatus. PMID:30567320
Draft Genome Sequence of Deinococcus koreensis SJW1-2T, a Gamma Radiation-Resistant Bacterium Isolated from River Water. PMID:30533895
Complete Genome Sequence of the Arcobacter suis Type Strain LMG 26152. PMID:30533764
Complete Genome Sequence of the Arcobacter skirrowii Type Strain LMG 6621. PMID:30533756
Complete Genome Sequence of the Arcobacter molluscorum Type Strain LMG 25693. PMID:30533749
Evolutionary Evidence of Algal Polysaccharide Degradation Acquisition by Pseudoalteromonas carrageenovora 9T to Adapt to Macroalgal Niches. PMID:30524390
Molecular Adaptations of Bacterial Mercuric Reductase to the Hypersaline Kebrit Deep in the Red Sea. PMID:30504211
Characterization of the Ubiquitin C-Terminal Hydrolase and Ubiquitin-Specific Protease Families in Rice (Oryza sativa). PMID:30498503
Comparative Analysis of the Nodule Transcriptomes of Ceanothus thyrsiflorus (Rhamnaceae, Rosales) and Datisca glomerata (Datiscaceae, Cucurbitales). PMID:30487804
Identification, Classification, and Functional Analysis of AP2/ERF Family Genes in the Desert Moss Bryum argenteum. PMID:30463185
A two-level model for the role of complex and young genes in the formation of organism complexity and new insights into the relationship between evolution and development. PMID:30455862
Combining bioinformatics, cheminformatics, functional genomics and whole organism approaches for identifying epigenetic drug targets in Schistosoma mansoni. PMID:30455056
Identification of O-acetylserine(thiol)lyase (OASTL) genes in sorghum (Sorghum bicolor) and gene expression analysis under cadmium stress. PMID:30443823
Isolation of A Novel Bacillus thuringiensis Phage Representing A New Phage Lineage and Characterization of Its Endolysin. PMID:30404215
In silico approach to identify non-synonymous SNPs with highest predicted deleterious effect on protein function in human obesity related gene, neuronal growth regulator 1 (NEGR1). PMID:30402368
Deciphering the structure of the condensin protein complex. PMID:30385633
Cross-strand disulfides in the hydrogen bonding site of antiparallel β-sheet (aCSDhs): Forbidden disulfides that are highly strained, easily broken. PMID:30383331
Genomic comparison of Trypanosoma conorhini and Trypanosoma rangeli to Trypanosoma cruzi strains of high and low virulence. PMID:30355302
Retraction: Site‐specific recombination of nitrogen‐fixation genes in cyanobacteria by XisF–XisH–XisI complex: Structures and models, William C. Hwang, James W. Golden, Jaime Pascual, Dong Xu, Anton Cheltsov, Adam Godzik. PMID:30338965
Genetic Evidence Supporting the Role of the Calcium Channel, CACNA1S, in Tooth Cusp and Root Patterning. PMID:30319441
DREB2 (dehydration-responsive element-binding protein 2) type transcription factor in sorghum (Sorghum bicolor): genome-wide identification, characterization and expression profiles under cadmium and salt stresses. PMID:30305995
Multiple paralogues of α-SNAP in Giardia lamblia exhibit independent subcellular localization and redistribution during encystation and stress. PMID:30286802
PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System. PMID:30266409
Using transcriptomics to enable a plethodontid salamander (Bolitoglossa ramosi) for limb regeneration research. PMID:30253734
Identifying Drivers of Parallel Evolution: A Regression Model Approach. PMID:30252076
Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638. PMID:30248960
Genome-Wide Analysis of Glycine soja Response Regulator GsRR Genes Under Alkali and Salt Stresses. PMID:30245700
A Robust Methodology for Assessing Differential Homeolog Contributions to the Transcriptomes of Allopolyploids. PMID:30213855
Flexibility and constraint: Evolutionary remodeling of the sporulation initiation pathway in Firmicutes. PMID:30212463
Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi. PMID:30181924
Comparative transcriptome analysis of TUCPs in Gossypium hirsutum Ligon-lintless-1 mutant and their proposed functions in cotton fiber development. PMID:30159616
Global Transcriptome Analyses Reveal Differentially Expressed Genes of Six Organs and Putative Genes Involved in (Iso)flavonoid Biosynthesis in Belamcanda chinensis. PMID:30154811
The Genome of a Thermo Tolerant, Pathogenic Albino Aspergillus fumigatus. PMID:30154766
A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling. PMID:30153857
Local and Systemic Effect of Cytokinins on Soybean Nodulation and Regulation of Their Isopentenyl Transferase (IPT) Biosynthesis Genes Following Rhizobia Inoculation. PMID:30135694
The genome sequence of the soft-rot fungus Penicillium purpurogenum reveals a high gene dosage for lignocellulolytic enzymes. PMID:30123662
Essential Gene Clusters Identified in Stenotrophomonas MB339 for Multiple Metal/Antibiotic Resistance and Xenobiotic Degradation. PMID:30109428
A new insight into the evolution and functional divergence of FRK genes in Pyrus bretschneideri. PMID:30109040
Transcriptome sequencing to detect the potential role of long non-coding RNAs in bovine mammary gland during the dry and lactation period. PMID:30103699
Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems. PMID:30103650
Effusion: prediction of protein function from sequence similarity networks. PMID:30084920
Tangled history of a multigene family: The evolution of ISOPENTENYLTRANSFERASE genes. PMID:30070990
Acquisition of MACPF domain-encoding genes is the main contributor to LPS glycan diversity in gut Bacteroides species. PMID:30065309
Functional Prediction of Hypothetical Transcription Factors of Escherichia coli K-12 Based on Expression Data. PMID:30050664
Insights into Avian Incomplete Dosage Compensation: Sex-Biased Gene Expression Coevolves with Sex Chromosome Degeneration in the Common Whitethroat. PMID:30049999
Identification of likely pathogenic and known variants in TSPEAR, LAMB3, BCOR, and WNT10A in four Turkish families with tooth agenesis. PMID:30046887
Characterization of esterase activity from an Acetomicrobium hydrogeniformans enzyme with high structural stability in extreme conditions. PMID:30014242
Comparative and Expression Analysis of Ubiquitin Conjugating Domain-Containing Genes in Two Pyrus Species. PMID:30012956
Genome-wide identification and characterization of mRNAs and lncRNAs involved in cold stress in the wild banana (Musa itinerans). PMID:29985922
Dicer-like and RNA-dependent RNA polymerase gene family identification and annotation in the cultivated Solanum tuberosum and its wild relative S. commersonii. PMID:29948127
Early metazoan cell type diversity and the evolution of multicellular gene regulation. PMID:29942020
Genome-Wide Identification and Functional Prediction of Novel Drought-Responsive lncRNAs in Pyrus betulifolia. PMID:29925818
Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families. PMID:29911924
A resource for sustainable management: De novo assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, Scomber colias. PMID:29896516
A novel chimaeric flocculation protein enhances flocculation in Saccharomyces cerevisiae. PMID:29896447
Cwp19 Is a Novel Lytic Transglycosylase Involved in Stationary-Phase Autolysis Resulting in Toxin Release in Clostridium difficile. PMID:29895635
Metagenomic Approaches to Investigate the Contribution of the Vineyard Environment to the Quality of Wine Fermentation: Potentials and Difficulties. PMID:29867889
Transcriptome Reveals Long Non-coding RNAs and mRNAs Involved in Primary Wool Follicle Induction in Carpet Sheep Fetal Skin. PMID:29867522
Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres. PMID:29862326
Gene family innovation, conservation and loss on the animal stem lineage. PMID:29848444
High pCO2-induced exopolysaccharide-rich ballasted aggregates of planktonic cyanobacteria could explain Paleoproterozoic carbon burial. PMID:29844378
Identification of transposons near predicted lncRNA and mRNA pools of Prunus mume using an integrative transposable element database constructed from Rosaceae plant genomes. PMID:29804262
Altered Expression of the Malate-Permeable Anion Channel OsALMT4 Reduces the Growth of Rice Under Low Radiance. PMID:29774038
Discovery and Sequence Analysis of Four Deltacoronaviruses from Birds in the Middle East Reveal Interspecies Jumping with Recombination as a Potential Mechanism for Avian-to-Avian and Avian-to-Mammalian Transmission. PMID:29769348
The aquatic animals' transcriptome resource for comparative functional analysis. PMID:29764375
Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs during Cryptosporidium baileyi infection. PMID:29747577
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
Molecular Mechanisms of Acclimatization to Phosphorus Starvation and Recovery Underlying Full-Length Transcriptome Profiling in Barley (Hordeum vulgare L.). PMID:29720989
Draft Genome Sequence of Paucibacter aquatile CR182T, a Strain with Antimicrobial Activity Isolated from Freshwater of Nakdong River in South Korea. PMID:29700134
The Gastrodia elata genome provides insights into plant adaptation to heterotrophy. PMID:29691383
Genome Wide Identification, Evolutionary, and Expression Analysis of VQ Genes from Two Pyrus Species. PMID:29690608
Systematic analysis and comparison of the PHD-Finger gene family in Chinese pear (Pyrus bretschneideri) and its role in fruit development. PMID:29675811
Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons. PMID:29632298
Profiling of Long Non-coding RNAs and mRNAs by RNA-Sequencing in the Hippocampi of Adult Mice Following Propofol Sedation. PMID:29628875
Deep Sequencing-Based Transcriptome Profiling Reveals Avian Interferon-Stimulated Genes and Provides Comprehensive Insight into Newcastle Disease Virus-Induced Host Responses. PMID:29601508
Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species. PMID:29563515
A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations. PMID:29560828
A Suppressor/Avirulence Gene Combination in Hyaloperonospora arabidopsidis Determines Race Specificity in Arabidopsis thaliana. PMID:29545818
Formation of chimeric genes with essential functions at the origin of eukaryotes. PMID:29534719
Genome-wide identification and expression analysis of GRAS family transcription factors in tea plant (Camellia sinensis). PMID:29500448
Comprehensive Redox Profiling of the Thiol Proteome of Clostridium difficile. PMID:29496906
Gene expression and ultrastructure of meso- and thermophilic methanotrophic consortia. PMID:29468803
Complete Genome Sequence of Mycobacterium sp. Strain 4858. PMID:29449406
A biallelic ANTXR1 variant expands the anthrax toxin receptor associated phenotype to tooth agenesis. PMID:29436111
Genome sequence and description of Haloferax massiliense sp. nov., a new halophilic archaeon isolated from the human gut. PMID:29435649
Comprehensive transcriptional landscape of porcine cardiac and skeletal muscles reveals differences of aging. PMID:29416711
PhcrTx2, a New Crab-Paralyzing Peptide Toxin from the Sea Anemone Phymanthus crucifer. PMID:29414882
Novel global effector mining from the transcriptome of early life stages of the soybean cyst nematode Heterodera glycines. PMID:29410430
Engineering yeast for the production of breviscapine by genomic analysis and synthetic biology approaches. PMID:29386648
Complete Genome Sequence of Mycobacterium sp. Strain 3519A. PMID:29371369
Function, distribution, and annotation of characterized cellulases, xylanases, and chitinases from CAZy. PMID:29359269
Interactome INSIDER: a structural interactome browser for genomic studies. PMID:29355848
Complete Genome Sequence of Bacillus methylotrophicus Strain NKG-1, Isolated from the Changbai Mountains, China. PMID:29348340
Draft Genome Sequence of Mycobacterium setense CSUR47. PMID:29348332
Novel Isoforms of N16 and N19 Families Implicated for the Nacreous Layer Formation in the Pearl Oyster Pinctada fucata. PMID:29340846
Transcriptome profiling with focus on potential key genes for wing development and evolution in Megaloprepus caerulatus, the damselfly species with the world's largest wings. PMID:29329292
Identification of a novel botulinum neurotoxin gene cluster in Enterococcus. PMID:29323697
Loss-of-function variants in ADCY3 increase risk of obesity and type 2 diabetes. PMID:29311636
Genomic diversity and distribution of Bifidobacterium longum subsp. longum across the human lifespan. PMID:29311585
A novel galactolipase from a green microalga Chlorella kessleri: purification, characterization, molecular cloning, and heterologous expression. PMID:29299622
Constructing an integrated gene similarity network for the identification of disease genes. PMID:29297379
Differential gene expression in response to Fusarium oxysporum infection in resistant and susceptible genotypes of flax (Linum usitatissimum L.). PMID:29297347
Acyl-CoA-binding protein family members in laticifers are possibly involved in lipid and latex metabolism of Hevea brasiliensis (the Para rubber tree). PMID:29295704
Comparative Analysis of 37 Acinetobacter Bacteriophages. PMID:29295549
CRISPR Screens Uncover Genes that Regulate Target Cell Sensitivity to the Morphogen Sonic Hedgehog. PMID:29290584
Genome-Wide Analysis of Long Non-Coding RNAs in Potato and Their Potential Role in Tuber Sprouting Process. PMID:29286332
Genome-wide characterization and expression profiling of NAC transcription factor genes under abiotic stresses in radish (Raphanus sativus L.). PMID:29259849
Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone. PMID:29259587
Characteristics of a PHD Finger Subtype. PMID:29253329
The Different Faces of Rolling-Circle Replication and Its Multifunctional Initiator Proteins. PMID:29250047
Functional characterization of a short peptidoglycan recognition protein from Chinese giant salamander (Andrias davidianus). PMID:29245904
A metagenome-derived thermostable β-glucanase with an unusual module architecture which defines the new glycoside hydrolase family GH148. PMID:29229913
LncRNA and mRNA profiling during activation of tilapia macrophages by HSP70 and Streptococcus agalactiae antigen. PMID:29228702
In silico characterization of tandem repeats in Trichophyton rubrum and related dermatophytes provides new insights into their role in pathogenesis. PMID:29220431
Long noncoding RNAs that respond to Fusarium oxysporum infection in 'Cavendish' banana (Musa acuminata). PMID:29209086
On the Early Evolution of Catabolic Pathways: A Comparative Genomics Approach. I. The Cases of Glucose, Ribose, and the Nucleobases Catabolic Routes. PMID:29189888
PlanNET: homology-based predicted interactome for multiple planarian transcriptomes. PMID:29186384
A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model. PMID:29183907
Whole transcriptome RNA-Seq analysis reveals extensive cell type-specific compartmentalization in Volvox carteri. PMID:29179763
Complete Genome Sequences of Seven Vibrio cholerae Phages Isolated in China. PMID:29167238
Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism. PMID:29162929
Sporulation capability and amylosome conservation among diverse human colonic and rumen isolates of the keystone starch-degrader Ruminococcus bromii. PMID:29159997
Complete Genome Sequences of Vibrio cholerae-Specific Bacteriophages 24 and X29. PMID:29146843
Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction. PMID:29136098
Identification of New Features from Known Bacterial Protective Vaccine Antigens Enhances Rational Vaccine Design. PMID:29123525
RNA-Seq de novo assembly and differential transcriptome analysis of the nematode Ascaridia galli in relation to in vivo exposure to flubendazole. PMID:29099835
Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and communication pathways in cyclin-dependent kinases: Differentiating kinase clients of the Hsp90-Cdc37 chaperone. PMID:29095844
Insight into cordycepin biosynthesis of Cordyceps militaris: Comparison between a liquid surface culture and a submerged culture through transcriptomic analysis. PMID:29091925
TMEM132: an ancient architecture of cohesin and immunoglobulin domains define a new family of neural adhesion molecules. PMID:29088312
PLATO software provides analytic framework for investigating complexity beyond genome-wide association studies. PMID:29079728
Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily. PMID:29078300
A sensitive short read homology search tool for paired-end read sequencing data. PMID:29072140
Comparative transcriptomics reveal developmental turning points during embryogenesis of a hemimetabolous insect, the damselfly Ischnura elegans. PMID:29051502
Genome-Based Analyses of Six Hexacorallian Species Reject the "Naked Coral" Hypothesis. PMID:29048525
Whole-genome comparison of urinary pathogenic Escherichia coli and faecal isolates of UTI patients and healthy controls. PMID:29031453
LiverWiki: a wiki-based database for human liver. PMID:29029599
Viral communities of the human gut: metagenomic analysis of composition and dynamics. PMID:29026445
Integrated analysis of coding genes and non-coding RNAs during hair follicle cycle of cashmere goat (Capra hircus). PMID:29020916
Integration of lncRNA-miRNA-mRNA reveals novel insights into oviposition regulation in honey bees. PMID:29018616
Hybrid Sequencing of Full-Length cDNA Transcripts of Stems and Leaves in Dendrobium officinale. PMID:28981454
Learning causal networks with latent variables from multivariate information in genomic data. PMID:28968390
Comparative Genomics of Ralstonia solanacearum Identifies Candidate Genes Associated with Cool Virulence. PMID:28955357
Both modular and single-domain Type I polyketide synthases are expressed in the brevetoxin-producing dinoflagellate, Karenia brevis (Dinophyceae). PMID:28949419
B-BOX genes: genome-wide identification, evolution and their contribution to pollen growth in pear (Pyrus bretschneideri Rehd.). PMID:28927374
Evolutionary history and functional divergence of the cytochrome P450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications. PMID:28923019
A Preliminary List of Horizontally Transferred Genes in Prokaryotes Determined by Tree Reconstruction and Reconciliation. PMID:28894459
De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read. PMID:28873963
Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids. PMID:28854624
Shear force-based genetic screen reveals negative regulators of cell adhesion and protrusive activity. PMID:28847951
A Bacterial Multidomain NAD-Independent d-Lactate Dehydrogenase Utilizes Flavin Adenine Dinucleotide and Fe-S Clusters as Cofactors and Quinone as an Electron Acceptor for d-Lactate Oxidization. PMID:28847921
Genome-wide identification and tissue-specific expression analysis of nucleotide binding site-leucine rich repeat gene family in Cicer arietinum (kabuli chickpea). PMID:28840100
Contrasting effects of copper limitation on the photosynthetic apparatus in two strains of the open ocean diatom Thalassiosira oceanica. PMID:28837661
Deciphering the tRNA-dependent lipid aminoacylation systems in bacteria: Novel components and structural advances. PMID:28816600
Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins. PMID:28793925
The Cyanobacteria-Dominated Sponge Dactylospongia elegans in the South China Sea: Prokaryotic Community and Metagenomic Insights. PMID:28790992
The purplish bifurcate mussel Mytilisepta virgata gene expression atlas reveals a remarkable tissue functional specialization. PMID:28789640
c-di-AMP: An Essential Molecule in the Signaling Pathways that Regulate the Viability and Virulence of Gram-Positive Bacteria. PMID:28783096
The role of core and accessory type IV pilus genes in natural transformation and twitching motility in the bacterium Acinetobacter baylyi. PMID:28771515
Genome-Wide Analysis Reveals Extensive Changes in LncRNAs during Skeletal Muscle Development in Hu Sheep. PMID:28763026
Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species. PMID:28756777
Evolution of Daily Gene Co-expression Patterns from Algae to Plants. PMID:28751903
Predicting the functional consequences of non-synonymous single nucleotide polymorphisms in IL8 gene. PMID:28747718
Using RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver. PMID:28743867
Tpc1 is an important Zn(II)2Cys6 transcriptional regulator required for polarized growth and virulence in the rice blast fungus. PMID:28742127
Dynamics of genomic innovation in the unicellular ancestry of animals. PMID:28726632
Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation. PMID:28717205
In vitro and in silico characterization of metagenomic soil-derived cellulases capable of hydrolyzing oil palm empty fruit bunch. PMID:28702370
Long noncoding RNA expression profile changes associated with dietary energy in the sheep testis during sexual maturation. PMID:28701734
Isolation and characterization of a novel endo-β-1,4-glucanase from a metagenomic library of the black-goat rumen. PMID:28689814
Characterisation of phospholipid: diacylglycerol acyltransferases (PDATs) from Camelina sativa and their roles in stress responses. PMID:28679505
Transcriptomic profiling of Melilotus albus near-isogenic lines contrasting for coumarin content. PMID:28676637
Genome-Wide Analysis Suggests the Relaxed Purifying Selection Affect the Evolution of WOX Genes in Pyrus bretschneideri, Prunus persica, Prunus mume, and Fragaria vesca. PMID:28663757
Insecticide resistance and resistance mechanisms in bed bugs, Cimex spp. (Hemiptera: Cimicidae). PMID:28662724
Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics. PMID:28656958
Comparative transcriptomic analysis of Gardnerella vaginalis biofilms vs. planktonic cultures using RNA-seq. PMID:28649404
Genome-wide analysis of UDP-glycosyltransferase super family in Brassica rapa and Brassica oleracea reveals its evolutionary history and functional characterization. PMID:28645261
Complete genome sequence and description of Lactococcus garvieae M14 isolated from Algerian fermented milk. PMID:28626583
A Transcriptomics and Comparative Genomics Analysis Reveals Gene Families with a Role in Body Plan Complexity. PMID:28611798
Genome-Wide Analyses Reveal Genes Subject to Positive Selection in Pasteurella multocida. PMID:28611758
Comparative genome and transcriptome analysis reveals distinctive surface characteristics and unique physiological potentials of Pseudomonas aeruginosa ATCC 27853. PMID:28606056
A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome. PMID:28594826
A Transcriptome Survey Spanning Life Stages and Sexes of the Harlequin Bug, Murgantia histrionica. PMID:28587099
Genome-wide analysis suggests high level of microsynteny and purifying selection affect the evolution of EIN3/EIL family in Rosaceae. PMID:28584725
In silico Prediction, in vitro Antibacterial Spectrum, and Physicochemical Properties of a Putative Bacteriocin Produced by Lactobacillus rhamnosus Strain L156.4. PMID:28579977
Massive expansion and differential evolution of small heat shock proteins with wheat (Triticum aestivum L.) polyploidization. PMID:28566710
In silico approach to designing rational metagenomic libraries for functional studies. PMID:28532384
On patterns and re-use in bioinformatics databases. PMID:28525546
Identification of factors required for m6 A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI. PMID:28503769
Genomewide analysis of the lateral organ boundaries domain gene family in Eucalyptus grandis reveals members that differentially impact secondary growth. PMID:28499078
ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly. PMID:28498994
Draft Genome Sequences of 25 Listeria monocytogenes Isolates Associated with Human Clinical Listeriosis in Ireland. PMID:28495762
Draft Genome Sequence of Mycobacterium boenickei CIP 107829. PMID:28473389
A Profile Hidden Markov Model to investigate the distribution and frequency of LanB-encoding lantibiotic modification genes in the human oral and gut microbiome. PMID:28462050
Genome-wide analysis and expression patterns of the NAC transcription factor family in Medicago truncatula. PMID:28461723
Genome-wide identification, characterization of the MADS-box gene family in Chinese jujube and their involvement in flower development. PMID:28432294
Novel interactions of the von Hippel-Lindau (pVHL) tumor suppressor with the CDKN1 family of cell cycle inhibitors. PMID:28425505
Domain prediction with probabilistic directional context. PMID:28407137
Transcriptome analyses of differential gene expression in the bursa of Fabricius between Silky Fowl and White Leghorn. PMID:28406147
Transcriptomic changes in an animal-bacterial symbiosis under modeled microgravity conditions. PMID:28393904
TbIRK is a signature sequence free potassium channel from Trypanosoma brucei locating to acidocalcisomes. PMID:28386071
Draft Genome Sequence of Mycobacterium colombiense. PMID:28385843
Testing for the Occurrence of Selective Episodes During the Divergence of Otophysan Fishes: Insights from Mitogenomics. PMID:28378191
Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis. PMID:28376709
Crystal structures of β-carboxysome shell protein CcmP: ligand binding correlates with the closed or open central pore. PMID:28369612
Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes. PMID:28348841
Metagenomic Analysis of a Complex Community Present in Pond Sediment. PMID:28348642
Structural insights into ligand binding of PGRP1 splice variants in Chinese giant salamander (Andrias davidianus) from molecular dynamics and free energy calculations. PMID:28341996
Structure-based function analysis of putative conserved proteins with isomerase activity from Haemophilus influenzae. PMID:28324524
Structure-based functional annotation of putative conserved proteins having lyase activity from Haemophilus influenzae. PMID:28324295
Transcriptome-Wide Identification, Classification, and Characterization of AP2/ERF Family Genes in the Desert Moss Syntrichia caninervis. PMID:28289426
Seasonal patterns in Arctic prasinophytes and inferred ecology of Bathycoccus unveiled in an Arctic winter metagenome. PMID:28267153
Identification and functional analysis of the ICK gene family in maize. PMID:28262730
Genomic Sequence of Campylobacter jejuni subsp. jejuni HS:19 Penner Serotype Reference Strain RM3420. PMID:28232429
Characterisation and genome sequence of the lytic Acinetobacter baumannii bacteriophage vB_AbaS_Loki. PMID:28207864
Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. PMID:28196534
Large-scale bioactivity analysis of the small-molecule assayed proteome. PMID:28178331
Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes. PMID:28168115
Complete genome sequence of Pseudoalteromonas phage vB_PspS-H40/1 (formerly H40/1) that infects Pseudoalteromonas sp. strain H40 and is used as biological tracer in hydrological transport studies. PMID:28168014
Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics. PMID:28148977
Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade. PMID:28145490
QuickProbs 2: Towards rapid construction of high-quality alignments of large protein families. PMID:28139687
Complete Annotated Genome Sequences of Three Campylobacter jejuni Strains Isolated from Naturally Colonized Farm-Raised Chickens. PMID:28126931
High quality draft genome sequence of Janthinobacterium psychrotolerans sp. nov., isolated from a frozen freshwater pond. PMID:28116042
Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis. PMID:28100699
OsSGL, a Novel DUF1645 Domain-Containing Protein, Confers Enhanced Drought Tolerance in Transgenic Rice and Arabidopsis. PMID:28083013
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
Nucleoplasmin-like domain of FKBP39 from Drosophila melanogaster forms a tetramer with partly disordered tentacle-like C-terminal segments. PMID:28074868
"Mycobacterium massilipolynesiensis" sp. nov., a rapidly-growing mycobacterium of medical interest related to Mycobacterium phlei. PMID:28074866
A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species Colletotrichum graminicola and Colletotrichum sublineola. PMID:28073340
De novo assembly, annotation, and characterization of the whole brain transcriptome of male and female Syrian hamsters. PMID:28071753
From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer. PMID:28066816
Glutathione S-transferases and UDP-glycosyltransferases Are Involved in Response to Aluminum Stress in Flax. PMID:28066475
Comparative Genomic Analysis of Bacillus amyloliquefaciens and Bacillus subtilis Reveals Evolutional Traits for Adaptation to Plant-Associated Habitats. PMID:28066362
Transcriptome Analysis of Taxillusi chinensis (DC.) Danser Seeds in Response to Water Loss. PMID:28046012
Draft genome sequence of a human-associated isolate of Haloferax alexandrinus strain Arc-hr, an extremely halophilic archaea. PMID:28018603
Structural, Evolutionary, and Functional Analysis of the Class III Peroxidase Gene Family in Chinese Pear (Pyrus bretschneideri). PMID:28018406
Genome analysis of Hibiscus syriacus provides insights of polyploidization and indeterminate flowering in woody plants. PMID:28011721
Toxin inhibition in C. crescentus VapBC1 is mediated by a flexible pseudo-palindromic protein motif and modulated by DNA binding. PMID:27998932
The evolution of function within the Nudix homology clan. PMID:27936487
Comparative Genomic Analysis of the GRF Genes in Chinese Pear (Pyrus bretschneideri Rehd), Poplar (Populous), Grape (Vitis vinifera), Arabidopsis and Rice (Oryza sativa). PMID:27933074
SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database. PMID:27914894
The s48/45 six-cysteine proteins: mediators of interaction throughout the Plasmodium life cycle. PMID:27899328
Isolation and characterization of a novel glycosyl hydrolase family 74 (GH74) cellulase from the black goat rumen metagenomic library. PMID:27866354
Diversity of the Germination Apparatus in Clostridium botulinum Groups I, II, III, and IV. PMID:27840626
Steric Clash in the SET Domain of Histone Methyltransferase NSD1 as a Cause of Sotos Syndrome and Its Genetic Heterogeneity in a Brazilian Cohort. PMID:27834868
Molecular cloning, heterologous expression, and enzymatic characterization of lysoplasmalogen-specific phospholipase D from Thermocrispum sp. PMID:27833852
Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass. PMID:27821048
Combining biophysical methods to analyze the disulfide bond in SH2 domain of C-terminal Src kinase. PMID:27819029
Draft genome sequence of pectic polysaccharide-degrading moderate thermophilic bacterium Geobacillus thermodenitrificans DSM 101594. PMID:27818089
Complete Genomic Sequence of Campylobacter jejuni subsp. jejuni HS:19 Strain RM1285 Isolated from Packaged Chicken. PMID:27795263
Overexpression of PSK1, a SKP1-like gene homologue, from Paeonia suffruticosa, confers salinity tolerance in Arabidopsis. PMID:27787596
Systematic Analysis of the 4-Coumarate:Coenzyme A Ligase (4CL) Related Genes and Expression Profiling during Fruit Development in the Chinese Pear. PMID:27775579
A direct-sensing galactose chemoreceptor recently evolved in invasive strains of Campylobacter jejuni. PMID:27762269
Identification of Aedes aegypti Long Intergenic Non-coding RNAs and Their Association with Wolbachia and Dengue Virus Infection. PMID:27760142
A Developmental Transcriptome Map for Allotetraploid Arachis hypogaea. PMID:27746793
Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance. PMID:27734962
Mammalian Fe-S proteins: definition of a consensus motif recognized by the co-chaperone HSC20. PMID:27714045
Characterisation of the immune compounds in koala milk using a combined transcriptomic and proteomic approach. PMID:27713568
Alternative Splicing May Not Be the Key to Proteome Complexity. PMID:27712956
A genome-wide analysis of the ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES (AS2/LOB) gene family in barley (Hordeum vulgare L.). PMID:27704746
Expansion and Functional Divergence of AP2 Group Genes in Spermatophytes Determined by Molecular Evolution and Arabidopsis Mutant Analysis. PMID:27703459
Survey of Genes Involved in Biosynthesis, Transport, and Signaling of Phytohormones with Focus on Solanum lycopersicum. PMID:27695302
LncRNA mediated regulation of aging pathways in Drosophila melanogaster during dietary restriction. PMID:27687893
Evolution of Protein Domain Repeats in Metazoa. PMID:27671125
FAMSA: Fast and accurate multiple sequence alignment of huge protein families. PMID:27670777
De novo transcriptome assembly of mangosteen (Garcinia mangostana L.) fruit. PMID:27668185
Genome Analysis and Characterisation of the Exopolysaccharide Produced by Bifidobacterium longum subsp. longum 35624™. PMID:27656878
Genome-wide identification and characterization of WRKY gene family in Salix suchowensis. PMID:27651997
Substrate specificity characterization for eight putative nudix hydrolases. Evaluation of criteria for substrate identification within the Nudix family. PMID:27618147
QuaBingo: A Prediction System for Protein Quaternary Structure Attributes Using Block Composition. PMID:27610389
Transcriptome analyses of the Dof-like gene family in grapevine reveal its involvement in berry, flower and seed development. PMID:27610237
Genome-Wide Analysis of APETALA2/Ethylene-Responsive Factor (AP2/ERF) Gene Family in Barley (Hordeum vulgare L.). PMID:27598245
Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils. PMID:27590813
Characterization of Toxin Complex Gene Clusters and Insect Toxicity of Bacteria Representing Four Subgroups of Pseudomonas fluorescens. PMID:27580176
A Multicomponent Animal Virus Isolated from Mosquitoes. PMID:27569558
Computational analysis of translational readthrough proteins in Drosophila and yeast reveals parallels to alternative splicing. PMID:27561673
Comparative Genomics of the Extreme Acidophile Acidithiobacillus thiooxidans Reveals Intraspecific Divergence and Niche Adaptation. PMID:27548157
The complete genome sequence of the rumen methanogen Methanobrevibacter millerae SM9. PMID:27536339
Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. PMID:27535938
High diversity of picornaviruses in rats from different continents revealed by deep sequencing. PMID:27530749
Improved glycerol to ethanol conversion by E. coli using a metagenomic fragment isolated from an anaerobic reactor. PMID:27522660
Draft Genome Sequence of Mycobacterium acapulcensis Strain CSURP1424. PMID:27516522
RNA-seq-based evaluation of bicolor tepal pigmentation in Asiatic hybrid lilies (Lilium spp.). PMID:27516339
LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects. PMID:27515968
First Comprehensive Proteome Analyses of Lysine Acetylation and Succinylation in Seedling Leaves of Brachypodium distachyon L. PMID:27515067
De novo assembly of the blunt snout bream (Megalobrama amblycephala) gill transcriptome to identify ammonia exposure associated microRNAs and their targets. PMID:27504260
A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes. PMID:27503221
Integrating metabolomics and transcriptomics data to discover a biocatalyst that can generate the amine precursors for alkamide biosynthesis. PMID:27497272
A transcriptional blueprint for a spiral-cleaving embryo. PMID:27496340
Computational Identification of Novel Genes: Current and Future Perspectives. PMID:27493475
Genomic identification, rapid evolution, and expression of Argonaute genes in the tilapia, Oreochromis niloticus. PMID:27491892
Implementation and comparison of kernel-based learning methods to predict metabolic networks. PMID:27471658
Characterization of long non-coding RNA transcriptome in high-energy diet induced nonalcoholic steatohepatitis minipigs. PMID:27466003
IGDD: a database of intronless genes in dicots. PMID:27465544
Genome-wide identification, characterisation and expression profiles of calcium-dependent protein kinase genes in barley (Hordeum vulgare L.). PMID:27447459
Identification and functional characterization of novel xylose transporters from the cell factories Aspergillus niger and Trichoderma reesei. PMID:27446237
Machine Learning of Protein Interactions in Fungal Secretory Pathways. PMID:27441920
The Evolution of Olfactory Gene Families in Drosophila and the Genomic Basis of chemical-Ecological Adaptation in Drosophila suzukii. PMID:27435796
Biochemical Characterization of a Family 15 Carbohydrate Esterase from a Bacterial Marine Arctic Metagenome. PMID:27433797
Enhanced antimicrobial peptide-induced activity in the mollusc Toll-2 family through evolution via tandem Toll/interleukin-1 receptor. PMID:27429771
Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment. PMID:27416027
Long Noncoding RNA and mRNA Expression Profiles in the Thyroid Gland of Two Phenotypically Extreme Pig Breeds Using Ribo-Zero RNA Sequencing. PMID:27409639
High quality genome sequence and description of Enterobacter mori strain 5-4, isolated from a mixture of formation water and crude-oil. PMID:27408680
Mutation Drivers of Immunological Responses to Cancer. PMID:27401919
Characterization of the Xylella fastidiosa PD1311 gene mutant and its suppression of Pierce's disease on grapevines. PMID:27388152
bioassayR: Cross-Target Analysis of Small Molecule Bioactivity. PMID:27367556
Draft Genomes of Anopheles cracens and Anopheles maculatus: Comparison of Simian Malaria and Human Malaria Vectors in Peninsular Malaysia. PMID:27347683
Investigating polymorphisms by bioinformatics is a potential cost-effective method to screen for germline mutations in Chinese familial adenomatous polyposis patients. PMID:27347161
Systematic identification and analysis of frequent gene fusion events in metabolic pathways. PMID:27342196
Salinity-induced changes in gene expression from anterior and posterior gills of Callinectes sapidus (Crustacea: Portunidae) with implications for crustacean ecological genomics. PMID:27337176
Genome-Wide Analysis of Long Noncoding RNAs and Their Responses to Drought Stress in Cotton (Gossypium hirsutum L.). PMID:27294517
Mechanisms of transcription factor evolution in Metazoa. PMID:27288445
Comparative genomic and transcriptomic analyses of the Fuzhuan brick tea-fermentation fungus Aspergillus cristatus. PMID:27267057
Computational recognition and analysis of hitherto uncharacterized nucleotide cyclase-like proteins in bacteria. PMID:27246835
Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology. PMID:27245738
Proteomic Analysis of a Novel Bacillus Jumbo Phage Revealing Glycoside Hydrolase As Structural Component. PMID:27242758
Draft Genome Sequence of Mycobacterium interjectum Strain ATCC 51457T. PMID:27231376
Draft Genome Sequence of Mycobacterium houstonense Strain ATCC 49403T. PMID:27231371
Dimerization and Transactivation Domains as Candidates for Functional Modulation and Diversity of Sox9. PMID:27196604
Genome sequence and comparative analysis of clavicipitaceous insect-pathogenic fungus Aschersonia badia with Metarhizium spp. PMID:27189621
Genome- wide characterization of Nuclear Factor Y (NF-Y) gene family of sorghum [Sorghum bicolor (L.) Moench]: a bioinformatics approach. PMID:27186017
Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer. PMID:27175787
An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. PMID:27173435
The Role of Complement in Cnidarian-Dinoflagellate Symbiosis and Immune Challenge in the Sea Anemone Aiptasia pallida. PMID:27148208
Enantioselective Utilization of D-Amino Acids by Deep-Sea Microorganisms. PMID:27148200
Pan-Cancer Analysis of Mutation Hotspots in Protein Domains. PMID:27135912
A common theme in extracellular fluids of beetles: extracellular superoxide dismutases crucial for balancing ROS in response to microbial challenge. PMID:27068683
Proteomic Identification of Putative MicroRNA394 Target Genes in Arabidopsis thaliana Identifies Major Latex Protein Family Members Critical for Normal Development. PMID:27067051
Transposons to toxins: the provenance, architecture and diversification of a widespread class of eukaryotic effectors. PMID:27060143
Draft Genome Sequence of the Rumen Methanogen Methanobrevibacter olleyae YLM1. PMID:27056228
Complete Genome Sequence of Methanogenic Archaeon ISO4-G1, a Member of the Methanomassiliicoccales, Isolated from a Sheep Rumen. PMID:27056226
Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms. PMID:27054497
PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies. PMID:27039071
A long noncoding RNA associated with susceptibility to celiac disease. PMID:27034373
Developmental Cycle and Genome Analysis of "Rubidus massiliensis," a New Vermamoeba vermiformis Pathogen. PMID:27014641
Identification and characterization of Lateral Organ Boundaries Domain genes in mulberry, Morus notabilis. PMID:27014591
Analysis of the Prefoldin Gene Family in 14 Plant Species. PMID:27014333
Genomic Insights into a New Citrobacter koseri Strain Revealed Gene Exchanges with the Virulence-Associated Yersinia pestis pPCP1 Plasmid. PMID:27014253
Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis. PMID:27003415
New features of desiccation tolerance in the lichen photobiont Trebouxia gelatinosa are revealed by a transcriptomic approach. PMID:26992400
An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry. PMID:26982336
PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya. PMID:26980519
Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage. PMID:26973616
ChlamyNET: a Chlamydomonas gene co-expression network reveals global properties of the transcriptome and the early setup of key co-expression patterns in the green lineage. PMID:26968660
Mte1 interacts with Mph1 and promotes crossover recombination and telomere maintenance. PMID:26966248
Transcriptome analysis reveals a ribosome constituents disorder involved in the RPL5 downregulated zebrafish model of Diamond-Blackfan anemia. PMID:26961822
Comparative analysis of genome-wide Mlo gene family in Cajanus cajan and Phaseolus vulgaris. PMID:26961357
The Structural Basis of Coenzyme A Recycling in a Bacterial Organelle. PMID:26959993
Delta-proteobacterial SAR324 group in hydrothermal plumes on the South Mid-Atlantic Ridge. PMID:26953077
Recovering complete and draft population genomes from metagenome datasets. PMID:26951112
De novo analysis of transcriptome reveals genes associated with leaf abscission in sugarcane (Saccharum officinarum L.). PMID:26946183
Transcriptome Analysis Identifies Candidate Genes Related to Triacylglycerol and Pigment Biosynthesis and Photoperiodic Flowering in the Ornamental and Oil-Producing Plant, Camellia reticulata (Theaceae). PMID:26941748
Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach. PMID:26929980
Comparative transcript profiling of resistant and susceptible peanut post-harvest seeds in response to aflatoxin production by Aspergillus flavus. PMID:26922489
Novel insights on ENTH domain-containing proteins in apicomplexan parasites. PMID:26922178
The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4). PMID:26918089
Methuselah/Methuselah-like G protein-coupled receptors constitute an ancient metazoan gene family. PMID:26915348
PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database. PMID:26903996
Systematic Analysis of Intracellular-targeting Antimicrobial Peptides, Bactenecin 7, Hybrid of Pleurocidin and Dermaseptin, Proline-Arginine-rich Peptide, and Lactoferricin B, by Using Escherichia coli Proteome Microarrays. PMID:26902206
Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat (Capra hircus). PMID:26892324
Genome-Based Selection and Characterization of Fusarium circinatum-Specific Sequences. PMID:26888868
The mid-developmental transition and the evolution of animal body plans. PMID:26886793
Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158. PMID:26875695
First structure of archaeal branched-chain amino acid aminotransferase from Thermoproteus uzoniensis specific for L-amino acids and R-amines. PMID:26872794
Red Sea Atlantis II brine pool nitrilase with unique thermostability profile and heavy metal tolerance. PMID:26868129
Identification of Novel Pathways in Plant Lectin-Induced Cancer Cell Apoptosis. PMID:26867193
Transcript Abundance of Putative Lipid Phosphate Phosphatases During Development of Trypanosoma brucei in the Tsetse Fly. PMID:26856918
Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems. PMID:26837824
Different evolutionary patterns of SNPs between domains and unassigned regions in human protein-coding sequences. PMID:26833483
Analyses of Long Non-Coding RNA and mRNA profiling using RNA sequencing during the pre-implantation phases in pig endometrium. PMID:26822553
Why reinvent the wheel? Building new proteins based on ready-made parts. PMID:26821641
Draft genome sequence of Paenibacillus sp. strain A2. PMID:26819653
Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome. PMID:26818233
Chamber Specific Gene Expression Landscape of the Zebrafish Heart. PMID:26815362
Multidomain, Surface Layer-associated Glycoside Hydrolases Contribute to Plant Polysaccharide Degradation by Caldicellulosiruptor Species. PMID:26814128
Knockdown of Five Genes Encoding Uncharacterized Proteins Inhibits Entamoeba histolytica Phagocytosis of Dead Host Cells. PMID:26810036
Orphan Crops Browser: a bridge between model and orphan crops. PMID:26798323
Genome Sequence of a Clostridium neonatale Strain Isolated in a Canadian Neonatal Intensive Care Unit. PMID:26798088
Vasohibins: new transglutaminase-like cysteine proteases possessing a non-canonical Cys-His-Ser catalytic triad. PMID:26794318
Structures of replication initiation proteins from staphylococcal antibiotic resistance plasmids reveal protein asymmetry and flexibility are necessary for replication. PMID:26792891
Genome-wide analysis of long non-coding RNAs at early stage of skin pigmentation in goats (Capra hircus). PMID:26785828
Evolutionary distinctiveness of fatty acid and polyketide synthesis in eukaryotes. PMID:26784357
Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria. PMID:26784354
An evaluation of the accuracy and speed of metagenome analysis tools. PMID:26778510
Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances. PMID:26773059
A Factor Graph Approach to Automated GO Annotation. PMID:26771463
Divergence of the bZIP Gene Family in Strawberry, Peach, and Apple Suggests Multiple Modes of Gene Evolution after Duplication. PMID:26770968
Draft Genome Sequence of Actinobaculum massiliense Strain FC3. PMID:26769930
Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements. PMID:26768901
Identification of family determining residues in Jumonji-C lysine demethylases: A sequence-based, family wide classification. PMID:26757344
The Pseudomonas aeruginosa PAO1 Two-Component Regulator CarSR Regulates Calcium Homeostasis and Calcium-Induced Virulence Factor Production through Its Regulatory Targets CarO and CarP. PMID:26755627
FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants. PMID:26754669
Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires. PMID:26752266
The Female Post-Mating Response Requires Genes Expressed in the Secondary Cells of the Male Accessory Gland in Drosophila melanogaster. PMID:26746709
Homology-Based Prediction of Potential Protein-Protein Interactions between Human Erythrocytes and Plasmodium falciparum. PMID:26740742
The role of the intestinal microbiota in type 1 diabetes mellitus. PMID:26729037
YcgC represents a new protein deacetylase family in prokaryotes. PMID:26716769
Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum. PMID:26702038
Late Embryogenesis Abundant (LEA) Constitutes a Large and Diverse Family of Proteins Involved in Development and Abiotic Stress Responses in Sweet Orange (Citrus sinensis L. Osb.). PMID:26700652
Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis. PMID:26699225
Many lncRNAs, 5'UTRs, and pseudogenes are translated and some are likely to express functional proteins. PMID:26687005
Metagenome from a Spirulina digesting biogas reactor: analysis via binning of contigs and classification of short reads. PMID:26680455
Exploring the repeat protein universe through computational protein design. PMID:26675729
The Pfam protein families database: towards a more sustainable future. PMID:26673716
A novel RING finger in the C-terminal domain of the coatomer protein α-COP. PMID:26666296
Parameterizing sequence alignment with an explicit evolutionary model. PMID:26652060
Noncontiguous finished genome sequence and description of Virgibacillus massiliensis sp. nov., a moderately halophilic bacterium isolated from human gut. PMID:26649181
Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases. PMID:26628682
The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract. PMID:26626322
ELM 2016--data update and new functionality of the eukaryotic linear motif resource. PMID:26615199
Antibacterial phage ORFans of Pseudomonas aeruginosa phage LUZ24 reveal a novel MvaT inhibiting protein. PMID:26594207
MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer. PMID:26590264
Draft Genome Sequence of Mycobacterium mucogenicum Strain CSUR P2099. PMID:26586900
HGTree: database of horizontally transferred genes determined by tree reconciliation. PMID:26578597
Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. PMID:26575353
Multifunctional polyketide synthase genes identified by genomic survey of the symbiotic dinoflagellate, Symbiodinium minutum. PMID:26573520
Complete genome sequence of bacteriophage P8625, the first lytic phage that infects Verrucomicrobia. PMID:26566421
Coevolved Mutations Reveal Distinct Architectures for Two Core Proteins in the Bacterial Flagellar Motor. PMID:26561852
COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets. PMID:26561344
Mutation screening of SCN2A in schizophrenia and identification of a novel loss-of-function mutation. PMID:26555645
PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features. PMID:26553811
Genome-wide analysis and expression patterns of ZF-HD transcription factors under different developmental tissues and abiotic stresses in Chinese cabbage. PMID:26546019
Draft Genome Sequence of Mycobacterium neworleansense Strain ATCC 49404T. PMID:26543131
Complete Genome Sequences of Campylobacter jejuni Strains RM3196 (233.94) and RM3197 (308.95) Isolated from Patients with Guillain-Barré Syndrome. PMID:26543130
Draft Genome Sequence of Mycobacterium peregrinum Strain CSUR P2098. PMID:26543113
Genomic survey and expression analysis of DNA repair genes in the genus Leptospira. PMID:26527082
Genome sequence of Oceanobacillus picturae strain S1, an halophilic bacterium first isolated in human gut. PMID:26523201
BioDB extractor: customized data extraction system for commonly used bioinformatics databases. PMID:26516349
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4). PMID:26512311
Extending Protein Domain Boundary Predictors to Detect Discontinuous Domains. PMID:26502173
The rumen microbial metagenome associated with high methane production in cattle. PMID:26494241
Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes. PMID:26493560
Sequence and Structure Analysis of Distantly-Related Viruses Reveals Extensive Gene Transfer between Viruses and Hosts and among Viruses. PMID:26492264
Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems. PMID:26489930
Characterization and annotation of Babesia orientalis apicoplast genome. PMID:26474853
Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals. PMID:26465111
De novo transcriptome profiling of highly purified human lymphocytes primary cells. PMID:26451251
Draft Genome Sequence of Streptomyces ahygroscopicus subsp. wuyiensis CK-15, Isolated from Soil in Fujian Province, China. PMID:26450721
Three-dimensional structure model and predicted ATP interaction rewiring of a deviant RNA ligase 2. PMID:26449279
Transmembrane START domain proteins: in silico identification, characterization and expression analysis under stress conditions in chickpea (Cicer arietinum L.). PMID:26445326
The heat shock factor gene family in Salix suchowensis: a genome-wide survey and expression profiling during development and abiotic stresses. PMID:26442061
Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins. PMID:26439842
Genome-Wide Detection and Analysis of Multifunctional Genes. PMID:26436655
Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot. PMID:26422147
The Prediction and Validation of Small CDSs Expand the Gene Repertoire of the Smallest Known Eukaryotic Genomes. PMID:26421846
Pan-genomic analysis to redefine species and subspecies based on quantum discontinuous variation: the Klebsiella paradigm. PMID:26420254
Genome-wide comparison of ferritin family from Archaea, Bacteria, Eukarya, and Viruses: its distribution, characteristic motif, and phylogenetic relationship. PMID:26411976
Genome wide discovery of long intergenic non-coding RNAs in Diamondback moth (Plutella xylostella) and their expression in insecticide resistant strains. PMID:26411386
PanFP: pangenome-based functional profiles for microbial communities. PMID:26409790
Genome-Wide Characterization and Expression Analysis of Major Intrinsic Proteins during Abiotic and Biotic Stresses in Sweet Orange (Citrus sinensis L. Osb.). PMID:26397813
Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores. PMID:26393325
Assessing sequence plasticity of a virus-like nanoparticle by evolution toward a versatile scaffold for vaccines and drug delivery. PMID:26392546
Aspergillus niger membrane-associated proteome analysis for the identification of glucose transporters. PMID:26388937
Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi. PMID:26374290
Comparative genome-based identification of a cell wall-anchored protein from Lactobacillus plantarum increases adhesion of Lactococcus lactis to human epithelial cells. PMID:26370773
Comparative genomics between human and animal associated subspecies of the Mycobacterium avium complex: a basis for pathogenicity. PMID:26370227
Perilipin-related protein regulates lipid metabolism in C. elegans. PMID:26357594
A Unique Set of the Burkholderia Collagen-Like Proteins Provides Insight into Pathogenesis, Genome Evolution and Niche Adaptation, and Infection Detection. PMID:26356298
Draft genome of Brugia pahangi: high similarity between B. pahangi and B. malayi. PMID:26350613
Computational approaches to study the effects of small genomic variations. PMID:26350246
Functional and structural properties of a novel cellulosome-like multienzyme complex: efficient glycoside hydrolysis of water-insoluble 7-xylosyl-10-deacetylpaclitaxel. PMID:26347949
Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates. PMID:26346121
Combinatorial DNA Rearrangement Facilitates the Origin of New Genes in Ciliates. PMID:26338187
Using THz Spectroscopy, Evolutionary Network Analysis Methods, and MD Simulation to Map the Evolution of Allosteric Communication Pathways in c-Type Lysozymes. PMID:26337549
Implications of ethylene biosynthesis and signaling in soybean drought stress tolerance. PMID:26335593
Selection of recombinant anti-SH3 domain antibodies by high-throughput phage display. PMID:26332758
The Phylogenetic Signature Underlying ATP Synthase c-Ring Compliance. PMID:26331255
Large scale transcriptome analysis reveals interplay between development of forest trees and a beneficial mycorrhiza helper bacterium. PMID:26328611
Inntags: small self-structured epitopes for innocuous protein tagging. PMID:26322837
Anatomy of protein disorder, flexibility and disease-related mutations. PMID:26322316
Functional Basis of Microorganism Classification. PMID:26317871
Phylogenetic Co-Occurrence of ExoR, ExoS, and ChvI, Components of the RSI Bacterial Invasion Switch, Suggests a Key Adaptive Mechanism Regulating the Transition between Free-Living and Host-Invading Phases in Rhizobiales. PMID:26309130
Fungal endophyte infection of ryegrass reprograms host metabolism and alters development. PMID:26305687
Structural modeling and in silico analysis of non-synonymous single nucleotide polymorphisms of human 3β-hydroxysteroid dehydrogenase type 2. PMID:26288759
Computational approaches to natural product discovery. PMID:26284671
Systematic analyses reveal uniqueness and origin of the CFEM domain in fungi. PMID:26255557
Interspecific Differential Expression Analysis of RNA-Seq Data Yields Insight into Life Cycle Variation in Hydractiniid Hydrozoans. PMID:26251524
Draft Genome Sequence of Mycobacterium bohemicum Strain DSM 44277T. PMID:26251499
In-depth analysis of the critical genes and pathways in colorectal cancer. PMID:26239303
RNA-seq for gene identification and transcript profiling in relation to root growth of bermudagrass (Cynodon dactylon) under salinity stress. PMID:26238595
KLF/SP Transcription Factor Family Evolution: Expansion, Diversification, and Innovation in Eukaryotes. PMID:26232396
Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia. PMID:26231545
Draft Genome Sequence of the Lactobacillus mucosae Strain Marseille. PMID:26227603
Draft Genome Sequence of the Lactobacillus agilis Strain Marseille. PMID:26227602
Comparative analysis of the phytocyanin gene family in 10 plant species: a focus on Zea mays. PMID:26217366
CovRS-Regulated Transcriptome Analysis of a Hypervirulent M23 Strain of Group A Streptococcus pyogenes Provides New Insights into Virulence Determinants. PMID:26216843
Whole transcriptome profiling of the vernalization process in Lilium longiflorum (cultivar White Heaven) bulbs. PMID:26216467
Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project. PMID:26216192
The conserved carboxyl domain of MorC, an inner membrane protein of Aggregatibacter actinomycetemcomitans, is essential for membrane function. PMID:26205976
Draft Genome Sequence of Mycobacterium lentiflavum CSUR P1491. PMID:26205866
Draft Genome Sequence of Mycobacterium europaeum Strain CSUR P1344. PMID:26205865
Unearthing the genomes of plant-beneficial Pseudomonas model strains WCS358, WCS374 and WCS417. PMID:26198432
Associations of SNPs located at candidate genes to bovine growth traits, prioritized with an interaction networks construction approach. PMID:26198337
Functional Screening of Hydrolytic Activities Reveals an Extremely Thermostable Cellulase from a Deep-Sea Archaeon. PMID:26191525
The UBR-box and its relationship to binuclear RING-like treble clef zinc fingers. PMID:26185100
Complete Genome Sequences of Four Novel Escherichia coli Bacteriophages Belonging to New Phage Groups. PMID:26184932
Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins. PMID:26184334
Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes. PMID:26181593
Evolutionary Influenced Interaction Pattern as Indicator for the Investigation of Natural Variants Causing Nephrogenic Diabetes Insipidus. PMID:26180540
Identification of genetic and environmental factors stimulating excision from Streptomyces scabiei chromosome of the toxicogenic region responsible for pathogenicity. PMID:26177341
Genome-wide characterisation and analysis of bHLH transcription factors related to tanshinone biosynthesis in Salvia miltiorrhiza. PMID:26174967
Combined transcriptome and metabolite profiling reveals that IiPLR1 plays an important role in lariciresinol accumulation in Isatis indigotica. PMID:26163698
Soybean (Glycine max) SWEET gene family: insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis. PMID:26162601
How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations. PMID:26158498
Relationships between predicted moonlighting proteins, human diseases, and comorbidities from a network perspective. PMID:26157390
Genome-wide identification of CAMTA gene family members in Medicago truncatula and their expression during root nodule symbiosis and hormone treatments. PMID:26150823
Human IgG1 Responses to Surface Localised Schistosoma mansoni Ly6 Family Members Drop following Praziquantel Treatment. PMID:26147973
EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A. PMID:26140928
Map-based cloning and characterization of BPH29, a B3 domain-containing recessive gene conferring brown planthopper resistance in rice. PMID:26136269
Contact- and Protein Transfer-Dependent Stimulation of Assembly of the Gliding Motility Machinery in Myxococcus xanthus. PMID:26132848
SInCRe-structural interactome computational resource for Mycobacterium tuberculosis. PMID:26130660
The Peptidoglycan-Binding Protein SjcF1 Influences Septal Junction Function and Channel Formation in the Filamentous Cyanobacterium Anabaena. PMID:26126850
TMFoldRec: a statistical potential-based transmembrane protein fold recognition tool. PMID:26123059
AguR, a Transmembrane Transcription Activator of the Putrescine Biosynthesis Operon in Lactococcus lactis, Acts in Response to the Agmatine Concentration. PMID:26116671
Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes. PMID:26114425
A Database of Plastid Protein Families from Red Algae and Apicomplexa and Expression Regulation of the moeB Gene. PMID:26114108
Comparative Analysis of Apicoplast-Targeted Protein Extension Lengths in Apicomplexan Parasites. PMID:26114107
A de novo Assembly of the Common Frog (Rana temporaria) Transcriptome and Comparison of Transcription Following Exposure to Ranavirus and Batrachochytrium dendrobatidis. PMID:26111016
Better prediction of functional effects for sequence variants. PMID:26110438
The Rise and Fall of TRP-N, an Ancient Family of Mechanogated Ion Channels, in Metazoa. PMID:26100409
Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane. PMID:26093024
By the company they keep: interaction networks define the binding ability of transcription factors. PMID:26089389
Functional and Structural Characterization of the Antiphagocytic Properties of a Novel Transglutaminase from Streptococcus suis. PMID:26085092
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
Improving compound-protein interaction prediction by building up highly credible negative samples. PMID:26072486
Structural insight into the TRIAP1/PRELI-like domain family of mitochondrial phospholipid transfer complexes. PMID:26071602
Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level. PMID:26061177
Evolutionary dynamics of rhomboid proteases in Streptomycetes. PMID:26054641
Draft Genome Sequence of Mycobacterium tuberculosis Strain MT43, a Representative of the Manu2 Genotype. PMID:26044427
Draft Genome Sequence of Mycobacterium tuberculosis Strain MT11, Which Represents a New Lineage. PMID:26044426
Genome-Wide Collation of the Plasmodium falciparum WDR Protein Superfamily Reveals Malarial Parasite-Specific Features. PMID:26043001
In silico identification of AMPylating enzymes and study of their divergent evolution. PMID:26039278
Novel HER3/MUC4 oncogenic signaling aggravates the tumorigenic phenotypes of pancreatic cancer cells. PMID:26035354
Comparative transcriptomic analysis revealed adaptation mechanism of Phrynocephalus erythrurus, the highest altitude Lizard living in the Qinghai-Tibet Plateau. PMID:26031664
Proteins Related to the Type I Secretion System Are Associated with Secondary SecA_DEAD Domain Proteins in Some Species of Planctomycetes, Verrucomicrobia, Proteobacteria, Nitrospirae and Chlorobi. PMID:26030905
Origin and evolution of lysyl oxidases. PMID:26024311
INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity. PMID:26019177
Unravelling the genome of Holy basil: an "incomparable" "elixir of life" of traditional Indian medicine. PMID:26017011
Polyketide synthesis genes associated with toxin production in two species of Gambierdiscus (Dinophyceae). PMID:26016672
A large-scale structural classification of antimicrobial peptides. PMID:26000295
Phylogenomic analysis reveals deep divergence and recombination in an economically important grapevine virus. PMID:25992606
Protein structure prediction guided by crosslinking restraints--A systematic evaluation of the impact of the crosslinking spacer length. PMID:25986934
Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum. PMID:25986905
The Classification and Evolution of Enzyme Function. PMID:25986631
Genome-Wide Analysis of the AP2/ERF Transcription Factors Family and the Expression Patterns of DREB Genes in Moso Bamboo (Phyllostachys edulis). PMID:25985202
Genomic Analysis of the Evolution and Global Spread of Hyper-invasive Meningococcal Lineage 5. PMID:25984558
Biology-Driven Gene-Gene Interaction Analysis of Age-Related Cataract in the eMERGE Network. PMID:25982363
Most partial domains in proteins are alignment and annotation artifacts. PMID:25976240
Est10: A Novel Alkaline Esterase Isolated from Bovine Rumen Belonging to the New Family XV of Lipolytic Enzymes. PMID:25973851
X-linked TEX11 mutations, meiotic arrest, and azoospermia in infertile men. PMID:25970010
Domain similarity based orthology detection. PMID:25968113
Comparative transcriptome profiling approach to glean virulence and immunomodulation-related genes of Fasciola hepatica. PMID:25956885
Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees. PMID:25953738
Transcriptome-wide identification of salt-responsive members of the WRKY gene family in Gossypium aridum. PMID:25951083
Mutations associated with reduced surotomycin susceptibility in Clostridium difficile and Enterococcus species. PMID:25941217
Novel Transcriptional Regulons for Autotrophic Cycle Genes in Crenarchaeota. PMID:25939834
Identification of SlpB, a Cytotoxic Protease from Serratia marcescens. PMID:25939509
The role of RNA conformation in RNA-protein recognition. PMID:25932908
Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. PMID:25915636
Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype. PMID:25909478
The genomes of two key bumblebee species with primitive eusocial organization. PMID:25908251
Identification of novel esterase-active enzymes from hot environments by use of the host bacterium Thermus thermophilus. PMID:25904908
Building a better fragment library for de novo protein structure prediction. PMID:25901595
Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite. PMID:25898829
The crystal structure and small-angle X-ray analysis of CsdL/TcdA reveal a new tRNA binding motif in the MoeB/E1 superfamily. PMID:25897750
Genome-wide identification and evolution of HECT genes in soybean. PMID:25894222
Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. PMID:25893781
DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe. PMID:25888481
Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs. PMID:25887594
The observation of evolutionary interaction pattern pairs in membrane proteins. PMID:25887048
REGULATOR: a database of metazoan transcription factors and maternal factors for developmental studies. PMID:25880930
The central nervous system transcriptome of the weakly electric brown ghost knifefish (Apteronotus leptorhynchus): de novo assembly, annotation, and proteomics validation. PMID:25879418
Solution structure of a soluble fragment derived from a membrane protein by shotgun proteolysis. PMID:25877662
Sensor-response regulator interactions in a cross-regulated signal transduction network. PMID:25873583
Computational prediction of protein-protein interactions. PMID:25859943
Personalized biochemistry and biophysics. PMID:25856502
Statistical approaches to detecting and analyzing tandem repeats in genomic sequences. PMID:25853125
Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages. PMID:25852662
Histone chaperones in Arabidopsis and rice: genome-wide identification, phylogeny, architecture and transcriptional regulation. PMID:25849155
A common tRNA modification at an unusual location: the discovery of wyosine biosynthesis in mitochondria. PMID:25845597
Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability. PMID:25837579
MadR1, a Mycobacterium tuberculosis cell cycle stress response protein that is a member of a widely conserved protein class of prokaryotic, eukaryotic and archeal origin. PMID:25829286
Insight into neutral and disease-associated human genetic variants through interpretable predictors. PMID:25826299
Non-coding RNA: a new frontier in regulatory biology. PMID:25821635
Pyrosequencing and de novo assembly of Antarctic krill (Euphausia superba) transcriptome to study the adaptability of krill to climate-induced environmental changes. PMID:25818178
Characterization of the Xylella fastidiosa PD1671 gene encoding degenerate c-di-GMP GGDEF/EAL domains, and its role in the development of Pierce's disease. PMID:25811864
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
Genome-wide identification of auxin response factor (ARF) genes and its tissue-specific prominent expression in Gossypium raimondii. PMID:25809690
Limited portability of G-patch domains in regulators of the Prp43 RNA helicase required for pre-mRNA splicing and ribosomal RNA maturation in Saccharomyces cerevisiae. PMID:25808954
Exome analysis reveals differentially mutated gene signatures of stage, grade and subtype in breast cancers. PMID:25803781
Analysis and prediction of the critical regions of antimicrobial peptides based on conditional random fields. PMID:25803302
Genetic diversity of Trichoderma atroviride strains collected in Poland and identification of loci useful in detection of within-species diversity. PMID:25791292
The complete genome sequence of the rumen methanogen Methanobacterium formicicum BRM9. PMID:25780506
A novel Schistosoma japonicum endonuclease homologous to DNase II. PMID:25766859
Species-specific duplications driving the recent expansion of NBS-LRR genes in five Rosaceae species. PMID:25759136
Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PMID:25748510
Genome Sequence of Clostridium acetobutylicum GXAS18-1, a Novel Biobutanol Production Strain. PMID:25744989
Studies on Deimmunization of Antileukaemic L-Asparaginase to have Reduced Clinical Immunogenicity--An in silico Approach. PMID:25740072
Most highly expressed protein-coding genes have a single dominant isoform. PMID:25732134
Structure and function of the bacterial root microbiota in wild and domesticated barley. PMID:25732064
The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families. PMID:25730766
MnTEdb, a collective resource for mulberry transposable elements. PMID:25725060
Evidence for suppression of immunity as a driver for genomic introgressions and host range expansion in races of Albugo candida, a generalist parasite. PMID:25723966
Genome sequence, comparative analysis, and evolutionary insights into chitinases of entomopathogenic fungus Hirsutella thompsonii. PMID:25716828
Loss of Drosophila pheromone reverses its role in sexual communication in Drosophila suzukii. PMID:25716789
Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference. PMID:25711833
Molecular evolution and phylogenetic analysis of eight COL superfamily genes in group I related to photoperiodic regulation of flowering time in wild and domesticated cotton (Gossypium) species. PMID:25710777
Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences. PMID:25704316
Quality control test for sequence-phenotype assignments. PMID:25700273
Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution. PMID:25697822
Arginine-rhamnosylation as new strategy to activate translation elongation factor P. PMID:25686373
Biosynthesis and genomic analysis of medium-chain hydrocarbon production by the endophytic fungal isolate Nigrograna mackinnonii E5202H. PMID:25672844
Mining the entire Protein DataBank for frequent spatially cohesive amino acid patterns. PMID:25657820
Analysis of Arabidopsis floral transcriptome: detection of new florally expressed genes and expansion of Brassicaceae-specific gene families. PMID:25653662
MBBC: an efficient approach for metagenomic binning based on clustering. PMID:25652152
Genome-wide analysis of bHLH transcription factor and involvement in the infection by yellow leaf curl virus in tomato (Solanum lycopersicum). PMID:25652024
The draft genome of Primula veris yields insights into the molecular basis of heterostyly. PMID:25651398
First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking. PMID:25650158
LiZIP3 is a cellular zinc transporter that mediates the tightly regulated import of zinc in Leishmania infantum parasites. PMID:25644708
Sequence composition of disordered regions fine-tunes protein half-life. PMID:25643324
Autophagy Regulatory Network - a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy. PMID:25635527
Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon. PMID:25634987
PAV markers in Sorghum bicolour: genome pattern, affected genes and pathways, and genetic linkage map construction. PMID:25634103
The origin of the ADAR gene family and animal RNA editing. PMID:25630791
MDAT- Aligning multiple domain arrangements. PMID:25626688
Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes. PMID:25620970
Whole-transcriptome survey of the putative ATP-binding cassette (ABC) transporter family genes in the latex-producing laticifers of Hevea brasiliensis. PMID:25615936
The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam. PMID:25614388
Genome-wide analysis of the R2R3-MYB transcription factor genes in Chinese cabbage (Brassica rapa ssp. pekinensis) reveals their stress and hormone responsive patterns. PMID:25613160
Computational analysis and low-scale constitutive expression of laccases synthetic genes GlLCC1 from Ganoderma lucidum and POXA 1B from Pleurotus ostreatus in Pichia pastoris. PMID:25611746
A toolkit for ARB to integrate custom databases and externally built phylogenies. PMID:25607539
Genetic and genomic analysis of RNases in model cyanobacteria. PMID:25595545
A hormone-responsive C1-domain-containing protein At5g17960 mediates stress response in Arabidopsis thaliana. PMID:25590629
Habitat visualization and genomic analysis of "Candidatus Pantoea carbekii," the primary symbiont of the brown marmorated stink bug. PMID:25587021
Genome-wide analysis of PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE (PDAT) genes in plants reveals the eudicot-wide PDAT gene expansion and altered selective pressures acting on the core eudicot PDAT paralogs. PMID:25585619
Evolutionary patterns in coiled-coils. PMID:25577198
A Hypothetical Protein of Alteromonas macleodii AltDE1 (amad1_06475) Predicted to be a Cold-Shock Protein with RNA Chaperone Activity. PMID:25574135
Terminal-repeat retrotransposons with GAG domain in plant genomes: a new testimony on the complex world of transposable elements. PMID:25573958
Tannase sequence from a xerophilic Aspergillus niger Strain and production of the enzyme in Pichia pastoris. PMID:25572938
TM6SF2 and MAC30, new enzyme homologs in sterol metabolism and common metabolic disease. PMID:25566323
Analysis of two domains with novel RNA-processing activities throws light on the complex evolution of ribosomal RNA biogenesis. PMID:25566315
Assembly of viral genomes from metagenomes. PMID:25566226
Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria. PMID:25566214
A Novel Mutation in the ROGDI Gene in a Patient with Kohlschütter-Tönz Syndrome. PMID:25565929
Structural insight into operator dre-sites recognition and effector binding in the GntR/HutC transcription regulator NagR. PMID:25564531
Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing. PMID:25553907
Patterns of evolutionary conservation of ascorbic acid-related genes following whole-genome triplication in Brassica rapa. PMID:25552535
Genome Sequence of Afipia felis Strain 76713, Isolated in Hospital Water Using an Amoeba Co-Culture Procedure. PMID:25540358
Sequence search and analysis of gene products containing RNA recognition motifs in the human genome. PMID:25534245
The GPCR repertoire in the demosponge Amphimedon queenslandica: insights into the GPCR system at the early divergence of animals. PMID:25528161
Genomic potential for polysaccharide deconstruction in bacteria. PMID:25527556
CDvist: a webserver for identification and visualization of conserved domains in protein sequences. PMID:25527097
The secreted proteins of Achlya hypogyna and Thraustotheca clavata identify the ancestral oomycete secretome and reveal gene acquisitions by horizontal gene transfer. PMID:25527045
The eukaryotic ancestor had a complex ubiquitin signaling system of archaeal origin. PMID:25525215
Unique features of apicoplast DNA gyrases from Toxoplasma gondii and Plasmodium falciparum. PMID:25523502
Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. PMID:25517485
The loose evolutionary relationships between transcription factors and other gene products across prokaryotes. PMID:25515977
Alkane hydroxylase genes in psychrophile genomes and the potential for cold active catalysis. PMID:25515036
PHOTOSYSTEM II PROTEIN33, a protein conserved in the plastid lineage, is associated with the chloroplast thylakoid membrane and provides stability to photosystem II supercomplexes in Arabidopsis. PMID:25511433
Identification of novel and conserved microRNAs in Coffea canephora and Coffea arabica. PMID:25505842
Molecular evolution of nitrogen assimilatory enzymes in marine prasinophytes. PMID:25504421
Genome Sequence of Bacillus simplex Strain P558, Isolated from a Human Fecal Sample. PMID:25502663
New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of “Candidatus methanoplasma termitum”. PMID:25501486
Metatranscriptomic analyses of plant cell wall polysaccharide degradation by microorganisms in the cow rumen. PMID:25501482
Identification and phylogenetic analysis of late embryogenesis abundant proteins family in tomato (Solanum lycopersicum). PMID:25491641
Structural basis and dynamics of multidrug recognition in a minimal bacterial multidrug resistance system. PMID:25489067
Metatranscriptome profiling of a harmful algal bloom. PMID:25484636
Dissemination of 6S RNA among bacteria. PMID:25483037
Evolution and diversity of the Ras superfamily of small GTPases in prokaryotes. PMID:25480683
Novel and unique domains in aminoacyl-tRNA synthetases from human fungal pathogens Aspergillus niger, Candida albicans and Cryptococcus neoformans. PMID:25479903
Computational and experimental analysis of the secretome of Methylococcus capsulatus (Bath). PMID:25479164
Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case. PMID:25476999
ECOD: an evolutionary classification of protein domains. PMID:25474468
Structure-guided functional characterization of DUF1460 reveals a highly specific NlpC/P60 amidase family. PMID:25465128
Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening. PMID:25464976
A general computational approach for repeat protein design. PMID:25451037
The YhhN protein of Legionella pneumophila is a Lysoplasmalogenase. PMID:25445671
Determining microbial products and identifying molecular targets in the human microbiome. PMID:25440055
CED-3 caspase acts with miRNAs to regulate non-apoptotic gene expression dynamics for robust development in C. elegans. PMID:25432023
Evolutionary and expression analysis of a MADS-box gene superfamily involved in ovule development of seeded and seedless grapevines. PMID:25429734
Toward computational cumulative biology by combining models of biological datasets. PMID:25427176
Structure of putrescine aminotransferase from Escherichia coli provides insights into the substrate specificity among class III aminotransferases. PMID:25423189
Transcript profiling reveals auxin and cytokinin signaling pathways and transcription regulation during in vitro organogenesis of Ramie (Boehmeria nivea L. Gaud). PMID:25415356
Kin-Driver: a database of driver mutations in protein kinases. PMID:25414382
Community structure detection for overlapping modules through mathematical programming in protein interaction networks. PMID:25412367
Genome-wide investigation and expression profiling of AP2/ERF transcription factor superfamily in foxtail millet (Setaria italica L.). PMID:25409524
Diversification of bacterial genome content through distinct mechanisms over different timescales. PMID:25407023
Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships. PMID:25400621
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. PMID:25398609
Cancer3D: understanding cancer mutations through protein structures. PMID:25392415
Genomic characterization of variable surface antigens reveals a telomere position effect as a prerequisite for RNA interference-mediated silencing in Paramecium tetraurelia. PMID:25389173
A DEK domain-containing protein modulates chromatin structure and function in Arabidopsis. PMID:25387881
The pCri System: a vector collection for recombinant protein expression and purification. PMID:25386923
Interspecific and host-related gene expression patterns in nematode-trapping fungi. PMID:25384908
Metagenomic insights into the RDX-degrading potential of the ovine rumen microbiome. PMID:25383623
Comparative genomics of the Campylobacter lari group. PMID:25381664
Genome Sequence of Rickettsia hoogstraalii, a Geographically Widely Distributed Tick-Associated Bacterium. PMID:25377719
Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus. PMID:25374784
Comparative analyses of nonpathogenic, opportunistic, and totally pathogenic mycobacteria reveal genomic and biochemical variabilities and highlight the survival attributes of Mycobacterium tuberculosis. PMID:25370496
Effect of copper treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis. PMID:25370493
A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. PMID:25369365
Loss and retention of resistance genes in five species of the Brassicaceae family. PMID:25365911
Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling. PMID:25357249
dcGOR: an R package for analysing ontologies and protein domain annotations. PMID:25356683
Prevalence, evolution, and cis-regulation of diel transcription in Chlamydomonas reinhardtii. PMID:25354782
Genomic characterization of a temperate phage of the psychrotolerant deep-sea bacterium Aurantimonas sp. PMID:25354565
The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data. PMID:25352556
PPDMs-a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains. PMID:25348214
Genome wide in silico characterization of Dof gene families of pigeonpea (Cajanus cajan (L) Millsp.). PMID:25344821
Effects of actin-like proteins encoded by two Bacillus pumilus phages on unstable lysogeny, revealed by genomic analysis. PMID:25344242
Dissemination of the transmissible quinolone-resistance gene qnrS1 by IncX plasmids in Nigeria. PMID:25340787
A taxonomy of bacterial microcompartment loci constructed by a novel scoring method. PMID:25340524
An antimicrobial protein of the gut symbiont Bacteroides fragilis with a MACPF domain of host immune proteins. PMID:25339613
Molecular evolution and functional divergence of tubulin superfamily in the fungal tree of life. PMID:25339375
Acanthamoeba castellanii STAT protein. PMID:25338074
The Comparative Genomics and Phylogenomics of Leishmania amazonensis Parasite. PMID:25336895
Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. PMID:25333462
Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis. PMID:25330991
Association mapping of brassinosteroid candidate genes and plant architecture in a diverse panel of Sorghum bicolor. PMID:25326721
The same or not the same: lineage-specific gene expansions and homology relationships in multigene families in nematodes. PMID:25323991
New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM. PMID:25323955
Genome Sequence of Legionella massiliensis, Isolated from a Cooling Tower Water Sample. PMID:25323728
Homology modeling and comparative profiling of superoxide dismutase among extremophiles: exiguobacterium as a model organism. PMID:25320445
Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation. PMID:25318651
A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors. PMID:25315994
RNA sequencing and de novo assembly of the digestive gland transcriptome in Mytilus galloprovincialis fed with toxinogenic and non-toxic strains of Alexandrium minutum. PMID:25314922
Two structural motifs within canonical EF-hand calcium-binding domains identify five different classes of calcium buffers and sensors. PMID:25313560
The protein Compromised Hydrolysis of Triacylglycerols 7 (CHT7) acts as a repressor of cellular quiescence in Chlamydomonas. PMID:25313078
Computational and experimental characterization of dVHL establish a Drosophila model of VHL syndrome. PMID:25310726
Molecular cloning and in-silico characterization of high temperature stress responsive pAPX gene isolated from heat tolerant Indian wheat cv. Raj 3765. PMID:25304397
Spotlite: web application and augmented algorithms for predicting co-complexed proteins from affinity purification--mass spectrometry data. PMID:25300367
Improving contact prediction along three dimensions. PMID:25299132
Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam. PMID:25293379
Genome-wide identification and tissue-specific expression analysis of UDP-glycosyltransferases genes confirm their abundance in Cicer arietinum (Chickpea) genome. PMID:25290312
A 3D cellular context for the macromolecular world. PMID:25289590
MetaProx: the database of metagenomic proximons. PMID:25288655
GmFLD, a soybean homolog of the autonomous pathway gene FLOWERING LOCUS D, promotes flowering in Arabidopsis thaliana. PMID:25287450
Systematic exploration of guide-tree topology effects for small protein alignments. PMID:25282640
New gene models and alternative splicing in the maize pathogen Colletotrichum graminicola revealed by RNA-Seq analysis. PMID:25281481
Sequence and annotation of the apicoplast genome of the human pathogen Babesia microti. PMID:25280009
Draft Genome Sequence of the Pathogenic Fungus Scedosporium apiospermum. PMID:25278533
Structural comparison, substrate specificity, and inhibitor binding of AGPase small subunit from monocot and dicot: present insight and future potential. PMID:25276800
Evidence of a bacterial receptor for lysozyme: binding of lysozyme to the anti-σ factor RsiV controls activation of the ecf σ factor σV. PMID:25275625
High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis. PMID:25271953
PIGD: a database for intronless genes in the Poaceae. PMID:25270086
New insights into chloramphenicol biosynthesis in Streptomyces venezuelae ATCC 10712. PMID:25267678
NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. PMID:25262355
Domain analyses of Usher syndrome causing Clarin-1 and GPR98 protein models. PMID:25258483
Characterizing protein interactions employing a genome-wide siRNA cellular phenotyping screen. PMID:25255318
Hybrid and rogue kinases encoded in the genomes of model eukaryotes. PMID:25255313
Local effect of enhancer of zeste-like reveals cooperation of epigenetic and cis-acting determinants for zygotic genome rearrangements. PMID:25254958
Rapid identification of novel antigens of Salmonella Enteritidis by microarray-based immunoscreening. PMID:25253911
Iron-sulfur cluster biogenesis in mammalian cells: New insights into the molecular mechanisms of cluster delivery. PMID:25245479
Combining structural modeling with ensemble machine learning to accurately predict protein fold stability and binding affinity effects upon mutation. PMID:25243403
Genomic insights into processes driving the infection of Alexandrium tamarense by the Parasitoid Amoebophrya sp. PMID:25239978
Predicting virus mutations through statistical relational learning. PMID:25238967
Understanding the sequence requirements of protein families: insights from the BioVis 2013 contests. PMID:25237388
Genome-scale metabolic network validation of Shewanella oneidensis using transposon insertion frequency analysis. PMID:25233219
A systems biology approach reveals a link between systemic cytokines and skeletal muscle energy metabolism in a rodent smoking model and human COPD. PMID:25228925
A root-expressed L-phenylalanine:4-hydroxyphenylpyruvate aminotransferase is required for tropane alkaloid biosynthesis in Atropa belladonna. PMID:25228340
Full-length enriched cDNA libraries and ORFeome analysis of sugarcane hybrid and ancestor genotypes. PMID:25222706
De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. PMID:25218520
Genome-wide analysis of the MADS-box gene family in Brassica rapa (Chinese cabbage). PMID:25216934
Knowledge-driven genomic interactions: an application in ovarian cancer. PMID:25214892
Bioinformatic characterisation of genes encoding cell wall degrading enzymes in the Phytophthora parasitica genome. PMID:25214042
cddApp: a Cytoscape app for accessing the NCBI conserved domain database. PMID:25212755
Functional characterisation of germinant receptors in Clostridium botulinum and Clostridium sporogenes presents novel insights into spore germination systems. PMID:25210747
New insights about enzyme evolution from large scale studies of sequence and structure relationships. PMID:25210038
LCK: a new biomarker candidate for the early diagnosis of acute myocardial infarction. PMID:25209966
Fast and accurate discovery of degenerate linear motifs in protein sequences. PMID:25207816
The landscape of kinase fusions in cancer. PMID:25204415
Structural insights into the recognition of phosphopeptide by the FHA domain of kanadaptin. PMID:25197798
Non-contiguous finished genome sequence and description of Sulfurimonas hongkongensis sp. nov., a strictly anaerobic denitrifying, hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from marine sediment. PMID:25197498
Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California. PMID:25197496
Non-contiguous finished genome sequence and description of Anaerococcus provenciensis sp. nov. PMID:25197492
Non-contiguous finished genome sequence and description of Bacteroides neonati sp. nov., a new species of anaerobic bacterium. PMID:25197464
High quality draft genome sequence of Staphylococcus cohnii subsp. cohnii strain hu-01. PMID:25197460
Analysis of the opsin repertoire in the tardigrade Hypsibius dujardini provides insights into the evolution of opsin genes in panarthropoda. PMID:25193307
Characterization of the surfaceome of the metal-reducing bacterium Desulfotomaculum reducens. PMID:25191310
Genome Sequence of Rickettsia tamurae, a Recently Detected Human Pathogen in Japan. PMID:25189579
Small non-coding RNA profiling and the role of piRNA pathway genes in the protection of chicken primordial germ cells. PMID:25185950
FSim: a novel functional similarity search algorithm and tool for discovering functionally related gene products. PMID:25184141
Microsporidian genomes harbor a diverse array of transposable elements that demonstrate an ancestry of horizontal exchange with metazoans. PMID:25172905
Structural organization of very small chromosomes: study on a single-celled evolutionary distant eukaryote Giardia intestinalis. PMID:25171919
Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. PMID:25171894
Biophysics of protein evolution and evolutionary protein biophysics. PMID:25165599
A systematic approach to identify novel cancer drug targets using machine learning, inhibitor design and high-throughput screening. PMID:25165489
Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides. PMID:25164283
Genetic analysis of vegetative branching in sorghum. PMID:25163936
Entropy-driven partitioning of the hierarchical protein space. PMID:25161256
CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. PMID:25161238
Identifying transcription factor complexes and their roles. PMID:25161228
Broad-Enrich: functional interpretation of large sets of broad genomic regions. PMID:25161225
Abundant and diverse clustered regularly interspaced short palindromic repeat spacers in Clostridium difficile strains and prophages target multiple phage types within this pathogen. PMID:25161187
Origin and evolution of European community-acquired methicillin-resistant Staphylococcus aureus. PMID:25161186
Unconventionally secreted effectors of two filamentous pathogens target plant salicylate biosynthesis. PMID:25156390
Molecular and evolutionary analysis of NEAr-iron Transporter (NEAT) domains. PMID:25153520
Asymmetric mRNA localization contributes to fidelity and sensitivity of spatially localized systems. PMID:25150862
Phylogenomic analysis of glycogen branching and debranching enzymatic duo. PMID:25148856
Comparative analysis of functional metagenomic annotation and the mappability of short reads. PMID:25148512
Phosphorylation site dynamics of early T-cell receptor signaling. PMID:25147952
Complete Genome Sequence and Annotation of a Campylobacter jejuni Strain, MTVDSCj20, Isolated from a Naturally Colonized Farm-Raised Chicken. PMID:25146148
Complete Genome Sequence of Campylobacter iguaniorum Strain 1485ET, Isolated from a Bearded Dragon (Pogona vitticeps). PMID:25146144
Defining the estimated core genome of bacterial populations using a Bayesian decision model. PMID:25144616
IRBIS: a systematic search for conserved complementarity. PMID:25142064
Current functional metagenomic approaches only expand the existing protease sequence space, but does not presently add any novelty to it. PMID:25141963
Transcriptomic analysis of tail regeneration in the lizard Anolis carolinensis reveals activation of conserved vertebrate developmental and repair mechanisms. PMID:25140675
Transcriptome analysis of the oil-rich tea plant, Camellia oleifera, reveals candidate genes related to lipid metabolism. PMID:25136805
Xylan utilization in human gut commensal bacteria is orchestrated by unique modular organization of polysaccharide-degrading enzymes. PMID:25136124
Contrasting metabolism in perenniating structures of upland and lowland switchgrass plants late in the growing season. PMID:25133804
De novo assembly of the perennial ryegrass transcriptome using an RNA-Seq strategy. PMID:25126744
Proteomic analysis of the Plasmodium male gamete reveals the key role for glycolysis in flagellar motility. PMID:25124718
A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data. PMID:25122209
Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina). PMID:25121733
An improved method for including upper size range plasmids in metamobilomes. PMID:25116381
Target network differences between western drugs and Chinese herbal ingredients in treating cardiovascular disease. PMID:25104437
Frequent loss and alteration of the MOXD2 gene in catarrhines and whales: a possible connection with the evolution of olfaction. PMID:25102179
Cyclic di-GMP-dependent signaling pathways in the pathogenic Firmicute Listeria monocytogenes. PMID:25101646
A comprehensive analysis of the Omp85/TpsB protein superfamily structural diversity, taxonomic occurrence, and evolution. PMID:25101071
Inspecting the potential physiological and biomedical value of 44 conserved uncharacterised proteins of Streptococcus pneumoniae. PMID:25096389
Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer. PMID:25096367
Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. PMID:25093637
De novo assembly and characterization of the transcriptome in the desiccation-tolerant moss Syntrichia caninervis. PMID:25086984
Phage ORF family recombinases: conservation of activities and involvement of the central channel in DNA binding. PMID:25083707
HMM-ModE: implementation, benchmarking and validation with HMMER3. PMID:25073805
Computational methods for analysis and inference of kinase/inhibitor relationships. PMID:25071826
Computational and experimental prediction of human C-type lectin receptor druggability. PMID:25071783
Genomes and transcriptomes of partners in plant-fungal-interactions between canola (Brassica napus) and two Leptosphaeria species. PMID:25068644
e-Driver: a novel method to identify protein regions driving cancer. PMID:25064568
Crystal structure of the lytic CHAP(K) domain of the endolysin LysK from Staphylococcus aureus bacteriophage K. PMID:25064136
The genome and occlusion bodies of marine Penaeus monodon nudivirus (PmNV, also known as MBV and PemoNPV) suggest that it should be assigned to a new nudivirus genus that is distinct from the terrestrial nudiviruses. PMID:25063321
Comparative genomics suggests that the human pathogenic fungus Pneumocystis jirovecii acquired obligate biotrophy through gene loss. PMID:25062922
Genome-wide search for eliminylating domains reveals novel function for BLES03-like proteins. PMID:25062915
A novel missense mutation in CCDC88C activates the JNK pathway and causes a dominant form of spinocerebellar ataxia. PMID:25062847
Redox proteomics changes in the fungal pathogen Trichosporon asahii on arsenic exposure: identification of protein responses to metal-induced oxidative stress in an environmentally-sampled isolate. PMID:25062082
Draft Genome Sequence of Rickettsia aeschlimannii, Associated with Hyalomma marginatum Ticks. PMID:25059861
Cyanobacteriochrome SesA is a diguanylate cyclase that induces cell aggregation in Thermosynechococcus. PMID:25059661
A novel fibroblast growth factor receptor family member promotes neuronal outgrowth and synaptic plasticity in aplysia. PMID:25059541
A sugar phosphatase regulates the methylerythritol phosphate (MEP) pathway in malaria parasites. PMID:25058848
Identification of Giardia lamblia DHHC proteins and the role of protein S-palmitoylation in the encystation process. PMID:25058047
Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer? PMID:25057855
Broad-range glycosidase activity profiling. PMID:25056938
Homogalacturonan-modifying enzymes: structure, expression, and roles in plants. PMID:25056773
The cell envelope proteome of Aggregatibacter actinomycetemcomitans. PMID:25055881
Structure of a membrane-embedded prenyltransferase homologous to UBIAD1. PMID:25051182
Genome duplication and gene loss affect the evolution of heat shock transcription factor genes in legumes. PMID:25047803
Whole exome sequencing identifies three novel mutations in ANTXR1 in families with GAPO syndrome. PMID:25045128
Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake. PMID:25044324
Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features. PMID:25042424
The structure and specificity of the type III secretion system effector NleC suggest a DNA mimicry mechanism of substrate recognition. PMID:25040221
The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles. PMID:25034814
Bioinformatic analysis of proteomics data. PMID:25033288
SFannotation: A Simple and Fast Protein Function Annotation System. PMID:25031571
Structural basis of lipid binding for the membrane-embedded tetraacyldisaccharide-1-phosphate 4'-kinase LpxK. PMID:25023290
Identification of conserved, centrosome-targeting ASH domains in TRAPPII complex subunits and TRAPPC8. PMID:25018876
Draft Genome Sequence of Mycobacterium neoaurum Strain DSM 44074T. PMID:25013147
Characterization and regulation of the resistance-nodulation-cell division-type multidrug efflux pumps MdtABC and MdtUVW from the fire blight pathogen Erwinia amylovora. PMID:25012600
A structural model of the active ribosome-bound membrane protein insertase YidC. PMID:25012291
Identification of an ideal-like fingerprint for a protein fold using overlapped conserved residues based approach. PMID:25008052
Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. PMID:25003965
Establishing an in vivo assay system to identify components involved in environmental RNA interference in the western corn rootworm. PMID:25003334
Structure of pneumococcal peptidoglycan hydrolase LytB reveals insights into the bacterial cell wall remodeling and pathogenesis. PMID:25002590
Leveraging structure for enzyme function prediction: methods, opportunities, and challenges. PMID:24998033
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. PMID:24997787
Genomic insights into the fungal lignocellulolytic system of Myceliophthora thermophila. PMID:24995002
Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species. PMID:24984952
Engineering adenylate cyclases regulated by near-infrared window light. PMID:24982160
CutProtFam-Pred: detection and classification of putative structural cuticular proteins from sequence alone, based on profile hidden Markov models. PMID:24978609
Adaptive evolution and divergent expression of heat stress transcription factors in grasses. PMID:24974883
Swine interferon-induced transmembrane protein, sIFITM3, inhibits foot-and-mouth disease virus infection in vitro and in vivo. PMID:24973762
Structure and function of the LmbE-like superfamily. PMID:24970229
Genome-wide analysis of the NADK gene family in plants. PMID:24968225
Genome-wide prediction and validation of peptides that bind human prosurvival Bcl-2 proteins. PMID:24967846
Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes. PMID:24967627
Identification and phylogenetic analyses of VASt, an uncharacterized protein domain associated with lipid-binding domains in Eukaryotes. PMID:24965341
Correlating information contents of gene ontology terms to infer semantic similarity of gene products. PMID:24963342
Genome-wide survey and expression analysis of the bHLH-PAS genes in the amphioxus Branchiostoma floridae reveal both conserved and diverged expression patterns between cephalochordates and vertebrates. PMID:24959341
Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana. PMID:24954583
Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators. PMID:24953126
The draft assembly of the radically organized Stylonychia lemnae macronuclear genome. PMID:24951568
Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum. PMID:24947485
GIL, a new c-di-GMP-binding protein domain involved in regulation of cellulose synthesis in enterobacteria. PMID:24942809
Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. PMID:24939910
Evidence of extensive DNA transfer between bacteroidales species within the human gut. PMID:24939888
Sex-determination system in the diploid yeast Zygosaccharomyces sapae. PMID:24939186
Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase. PMID:24938123
Nucleophilic 1,4-additions for natural product discovery. PMID:24937678
Transcriptome profiling to discover putative genes associated with paraquat resistance in goosegrass (Eleusine indica L.). PMID:24927422
Genome Sequence of the ε-Poly-l-Lysine-Producing Strain Streptomyces albulus NK660, Isolated from Soil in Gutian, Fujian Province, China. PMID:24926050
Quantitative phosphoproteomic profiling of fiber differentiation and initiation in a fiberless mutant of cotton. PMID:24923550
BioAssemblyModeler (BAM): user-friendly homology modeling of protein homo- and heterooligomers. PMID:24922057
Mapping B-cell epitopes for the peroxidoxin of Leishmania (Viannia) braziliensis and its potential for the clinical diagnosis of tegumentary and visceral leishmaniasis. PMID:24921246
Chitinase-like (CTL) and cellulose synthase (CESA) gene expression in gelatinous-type cellulosic walls of flax (Linum usitatissimum L.) bast fibers. PMID:24918577
Crystal structure of human CRMP-4: correction of intensities for lattice-translocation disorder. PMID:24914979
Profiling the orphan enzymes. PMID:24906382
Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction. PMID:24904632
Structural basis for a pH-sensitive calcium leak across membranes. PMID:24904158
Genome-wide analysis of regulatory proteases sequences identified through bioinformatics data mining in Taenia solium. PMID:24899069
A bioinformatic and computational study of myosin phosphatase subunit diversity. PMID:24898838
Unraveling patterns of site-to-site synonymous rates variation and associated gene properties of protein domains and families. PMID:24896293
Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice. PMID:24892750
Comparative Genomic Analysis of Two-Component Signal Transduction Systems in Probiotic Lactobacillus casei. PMID:24891736
Sustainable harvest: managing plasticity for resilient crops. PMID:24891039
Network-based identification of key proteins involved in apoptosis and cell cycle regulation. PMID:24889965
Genome-wide survey and expression analysis of calcium-dependent protein kinase in Gossypium raimondii. PMID:24887436
Tissue-specific transcript profiling for ABC transporters in the sequestering larvae of the phytophagous leaf beetle Chrysomela populi. PMID:24887102
Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community. PMID:24886150
Secretome analysis reveals effector candidates associated with broad host range necrotrophy in the fungal plant pathogen Sclerotinia sclerotiorum. PMID:24886033
Large-scale phosphoproteome analysis in seedling leaves of Brachypodium distachyon L. PMID:24885693
Identification of G protein-coupled receptors in Schistosoma haematobium and S. mansoni by comparative genomics. PMID:24884876
Differential gene expression between functionally specialized polyps of the colonial hydrozoan Hydractinia symbiolongicarpus (Phylum Cnidaria). PMID:24884766
A multilocus timescale for oomycete evolution estimated under three distinct molecular clock models. PMID:24884411
Protein-protein interaction network of the marine microalga Tetraselmis subcordiformis: prediction and application for starch metabolism analysis. PMID:24879479
Draft Genome Sequence of Mycobacterium farcinogenes NCTC 10955. PMID:24874688
Draft Genome Sequence of Mycobacterium triplex DSM 44626. PMID:24874681
Genome-wide analysis and identification of stress-responsive genes of the CCCH zinc finger family in Solanum lycopersicum. PMID:24870401
Computational prediction of protein function based on weighted mapping of domains and GO terms. PMID:24868539
Characterisation of the horse transcriptome from immunologically active tissues. PMID:24860704
HeatMapViewer: interactive display of 2D data in biology. PMID:24860644
A comprehensive phylogenetic and structural analysis of the carcinoembryonic antigen (CEA) gene family. PMID:24858421
Structure-based computational study of two disease resistance gene homologues (Hm1 and Hm2) in maize (Zea mays L.) with implications in plant-pathogen interactions. PMID:24847713
Conserved expression of lincRNA during human and macaque prefrontal cortex development and maturation. PMID:24847104
Rapid evolution of piRNA pathway in the teleost fish: implication for an adaptation to transposon diversity. PMID:24846630
Genomewide analysis of LATERAL ORGAN BOUNDARIES Domain gene family in Zea mays. PMID:24840825
Core structure of the U6 small nuclear ribonucleoprotein at 1.7-Å resolution. PMID:24837192
Exploiting a Reference Genome in Terms of Duplications: The Network of Paralogs and Single Copy Genes in Arabidopsis thaliana. PMID:24833233
Novel Cold-Adapted Esterase MHlip from an Antarctic Soil Metagenome. PMID:24832657
Genes that bias Mendelian segregation. PMID:24830502
A Proteome-wide Domain-centric Perspective on Protein Phosphorylation. PMID:24830415
Aggregation factor as an inhibitor of bacterial binding to gut mucosa. PMID:24823989
Analysis pipeline for the epistasis search - statistical versus biological filtering. PMID:24817878
Assembly and nuclear export of pre-ribosomal particles in budding yeast. PMID:24817020
Alginate-dependent gene expression mechanism in Sphingomonas sp. strain A1. PMID:24816607
Draft Genome Sequence of Mycobacterium vulneris DSM 45247T. PMID:24812218
SuSPect: enhanced prediction of single amino acid variant (SAV) phenotype using network features. PMID:24810707
Synonymous constraint elements show a tendency to encode intrinsically disordered protein segments. PMID:24809503
The bacterial septal ring protein RlpA is a lytic transglycosylase that contributes to rod shape and daughter cell separation in Pseudomonas aeruginosa. PMID:24806796
Calponin-like Chd64 is partly disordered. PMID:24805353
Evolution of mitochondria reconstructed from the energy metabolism of living bacteria. PMID:24804722
Virus induced gene silencing of three putative prolyl 4-hydroxylases enhances plant growth in tomato (Solanum lycopersicum). PMID:24803411
PredictProtein--an open resource for online prediction of protein structural and functional features. PMID:24799431
Transcription-independent functions of an RNA polymerase II subunit, Rpb2, during genome rearrangement in the ciliate, Oxytricha trifallax. PMID:24793090
Draft Genome Sequence of Mycobacterium mageritense DSM 44476T. PMID:24786954
Discovery and confirmation of ligand binding specificities of the Schistosoma japonicum polarity protein Scribble. PMID:24784152
The first mouse mutants of D14Abb1e (Fam208a) show that it is critical for early development. PMID:24781204
Classification of intrinsically disordered regions and proteins. PMID:24773235
The major cockroach allergen Bla g 4 binds tyramine and octopamine. PMID:24769496
Proteomic analysis of cattle tick Rhipicephalus (Boophilus) microplus saliva: a comparison between partially and fully engorged females. PMID:24762651
Elastic network models capture the motions apparent within ensembles of RNA structures. PMID:24759093
Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PMID:24756107
Crystal structure of Arabidopsis glutamyl-tRNA reductase in complex with its stimulator protein. PMID:24753615
High-throughput sequencing exclusively identified a novel Torque teno virus genotype in serum of a patient with fatal fever. PMID:24752764
Characterization of an archaeal two-component system that regulates methanogenesis in Methanosaeta harundinacea. PMID:24748383
Phylogenetic analysis of the endoribonuclease Dicer family. PMID:24748168
Transcriptome-wide identification of bread wheat WRKY transcription factors in response to drought stress. PMID:24748053
Diffusible gas transmitter signaling in the copepod crustacean Calanus finmarchicus: identification of the biosynthetic enzymes of nitric oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H2S) using a de novo assembled transcriptome. PMID:24747481
Draft Genome Sequence of Mycobacterium asiaticum Strain DSM 44297. PMID:24744338
Draft Genome Sequence of Mycobacterium austroafricanum DSM 44191. PMID:24744336
Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase. PMID:24742328
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
MP3: a software tool for the prediction of pathogenic proteins in genomic and metagenomic data. PMID:24736651
Diversity of the metal-transporting P1B-type ATPases. PMID:24729073
Analysis of expressed genes of the bacterium 'Candidatus phytoplasma Mali' highlights key features of virulence and metabolism. PMID:24728201
Redefining the PF06864 Pfam family based on Burkholderia pseudomallei PilO2(Bp) S-SAD crystal structure. PMID:24728008
Intrinsic disorder in the BK channel and its interactome. PMID:24727949
Evolved osmotolerant Escherichia coli mutants frequently exhibit defective N-acetylglucosamine catabolism and point mutations in cell shape-regulating protein MreB. PMID:24727267
Identification and characterization of a gene cluster required for proper rod shape, cell division, and pathogenesis in Clostridium difficile. PMID:24727226
Draft Genome Sequence of Mycobacterium cosmeticum DSM 44829. PMID:24723727
Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia. PMID:24721644
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
Formin' cellular structures: Physiological roles of Diaphanous (Dia) in actin dynamics. PMID:24719676
Genome-wide identification, evolution and expression analysis of mTERF gene family in maize. PMID:24718683
DoReMi: context-based prioritization of linear motif matches. PMID:24711967
HNH proteins are a widespread component of phage DNA packaging machines. PMID:24711378
Flexibility of the linker between the domains of DNA methyltransferase SsoII revealed by small-angle X-ray scattering: implications for transcription regulation in SsoII restriction-modification system. PMID:24710319
An expanded genomic representation of the phylum cyanobacteria. PMID:24709563
Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction. PMID:24708835
Crosstalk and the evolution of specificity in two-component signaling. PMID:24706803
The palmitoyl acyltransferase HIP14 shares a high proportion of interactors with huntingtin: implications for a role in the pathogenesis of Huntington's disease. PMID:24705354
Transcription of two adjacent carbohydrate utilization gene clusters in Bifidobacterium breve UCC2003 is controlled by LacI- and repressor open reading frame kinase (ROK)-type regulators. PMID:24705323
SysPTM 2.0: an updated systematic resource for post-translational modification. PMID:24705204
Gene expression of lactobacilli in murine forestomach biofilms. PMID:24702817
3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families. PMID:24700812
MetalS(3), a database-mining tool for the identification of structurally similar metal sites. PMID:24699831
Preliminary crystallographic analysis of a double mutant of the acetyl xylo-oligosaccharide esterase Axe2 in its dimeric form. PMID:24699743
Molecular and ultrastructural analysis of forisome subunits reveals the principles of forisome assembly. PMID:24694827
Exonic splicing signals impose constraints upon the evolution of enzymatic activity. PMID:24692663
Symbiotic adaptation drives genome streamlining of the cyanobacterial sponge symbiont "Candidatus Synechococcus spongiarum". PMID:24692632
Recent advances in functional region prediction by using structural and evolutionary information - Remaining problems and future extensions. PMID:24688747
Effect of Wnt3a on keratinocytes utilizing in vitro and bioinformatics analysis. PMID:24686518
An In Silico Approach for Characterization of an Aminoglycoside Antibiotic-Resistant Methyltransferase Protein from Pyrococcus furiosus (DSM 3638). PMID:24683305
Molecular characterization and evolution of a gene family encoding both female- and male-specific reproductive proteins in Drosophila. PMID:24682282
Comparative genomics of Taphrina fungi causing varying degrees of tumorous deformity in plants. PMID:24682155
Systematic detection of internal symmetry in proteins using CE-Symm. PMID:24681267
Obligate insect endosymbionts exhibit increased ortholog length variation and loss of large accessory proteins concurrent with genome shrinkage. PMID:24671745
A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE). PMID:24667251
Insights into the origin of nematode chemosensory GPCRs: putative orthologs of the Srw family are found across several phyla of protostomes. PMID:24663674
Arabidopsis ANGULATA10 is required for thylakoid biogenesis and mesophyll development. PMID:24663344
Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners. PMID:24663061
The Mi-2 homolog Mit1 actively positions nucleosomes within heterochromatin to suppress transcription. PMID:24662054
Comparative genomics for mycobacterial peptidoglycan remodelling enzymes reveals extensive genetic multiplicity. PMID:24661741
Antibacterial enzymes from the functional screening of metagenomic libraries hosted in Ralstonia metallidurans. PMID:24661178
Extensive microbial and functional diversity within the chicken cecal microbiome. PMID:24657972
spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. PMID:24655717
Genes associated with agronomic traits in non-heading Chinese cabbage identified by expression profiling. PMID:24655567
Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. PMID:24653211
Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. PMID:24647006
A highly conserved family of domains related to the DNA-glycosylase fold helps predict multiple novel pathways for RNA modifications. PMID:24646681
Metavir 2: new tools for viral metagenome comparison and assembled virome analysis. PMID:24646187
Comparative analysis of Salmonella genomes identifies a metabolic network for escalating growth in the inflamed gut. PMID:24643865
The endocytic activity of the flagellar pocket in Trypanosoma brucei is regulated by an adjacent phosphatidylinositol phosphate kinase. PMID:24639465
De novo structure prediction of globular proteins aided by sequence variation-derived contacts. PMID:24637808
High precision prediction of functional sites in protein structures. PMID:24632601
AlgaePath: comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae. PMID:24628857
An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts. PMID:24625832
A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach. PMID:24621177
Towards a comprehensive Plasmodium falciparum merozoite cell surface and secreted recombinant protein library. PMID:24620899
The substrate specificity, enantioselectivity and structure of the (R)-selective amine : pyruvate transaminase from Nectria haematococca. PMID:24618038
Chromosomal replication dynamics and interaction with the β sliding clamp determine orientation of bacterial transposable elements. PMID:24614824
Comparison of gene expression of Paramecium bursaria with and without Chlorella variabilis symbionts. PMID:24612690
Genome-wide identification, classification and expression analysis of the heat shock transcription factor family in Chinese cabbage. PMID:24609322
Hsp90-dependent assembly of the DBC2/RhoBTB2-Cullin3 E3-ligase complex. PMID:24608665
Draft Genome Sequence of Lactococcus lactis subsp. cremoris HPT, the First Defined-Strain Dairy Starter Culture Bacterium. PMID:24604643
Functional organization of a multimodular bacterial chemosensory apparatus. PMID:24603697
Analysis of the skin transcriptome in two oujiang color varieties of common carp. PMID:24603653
BambooGDB: a bamboo genome database with functional annotation and an analysis platform. PMID:24602877
Single cell genomic study of Dehalococcoidetes species from deep-sea sediments of the Peruvian Margin. PMID:24599070
Multi-PAS domain-mediated protein oligomerization of PpsR from Rhodobacter sphaeroides. PMID:24598755
A unique mutation in a MYB gene cosegregates with the nectarine phenotype in peach. PMID:24595269
Helminth Allergens, Parasite-Specific IgE, and Its Protective Role in Human Immunity. PMID:24592267
Carnitine metabolism to trimethylamine by an unusual Rieske-type oxygenase from human microbiota. PMID:24591617
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
Genetically distinct pathways guide effector export through the type VI secretion system. PMID:24589350
Identification of a fungi-specific lineage of protein kinases closely related to tyrosine kinases. PMID:24587055
Improved lanthipeptide detection and prediction for antiSMASH. PMID:24586765
Inferring domain-domain interactions from protein-protein interactions with formal concept analysis. PMID:24586450
Genome and transcriptome analysis of the basidiomycetous yeast Pseudozyma antarctica producing extracellular glycolipids, mannosylerythritol lipids. PMID:24586250
AvrBsT acetylates Arabidopsis ACIP1, a protein that associates with microtubules and is required for immunity. PMID:24586161
Genome-wide identification, phylogeny, duplication, and expression analyses of two-component system genes in Chinese cabbage (Brassica rapa ssp. pekinensis). PMID:24585003
Computational analysis of riboswitch-based regulation. PMID:24583554
Discovery of unconventional kinetochores in kinetoplastids. PMID:24582333
Alternative splicing during Arabidopsis flower development results in constitutive and stage-regulated isoforms. PMID:24575124
Benchmarking of methods for genomic taxonomy. PMID:24574292
Mutations enabling displacement of tryptophan by 4-fluorotryptophan as a canonical amino acid of the genetic code. PMID:24572018
High-throughput screening and whole genome sequencing identifies an antimicrobially active inhibitor of Vibrio cholerae. PMID:24568688
Functional genomics reveals that Clostridium difficile Spo0A coordinates sporulation, virulence and metabolism. PMID:24568651
Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative. PMID:24567391
The evolution of the GPCR signaling system in eukaryotes: modularity, conservation, and the transition to metazoan multicellularity. PMID:24567306
M-Finder: Uncovering functionally associated proteins from interactome data integrated with GO annotations. PMID:24565382
Investigation of anti-cancer mechanisms by comparative analysis of naked mole rat and rat. PMID:24565050
Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso. PMID:24564966
HMPAS: Human Membrane Protein Analysis System. PMID:24564858
Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi. PMID:24559402
TPX2: of spindle assembly, DNA damage response, and cancer. PMID:24556998
Land use type significantly affects microbial gene transcription in soil. PMID:24553913
Proteomics of a fuzzy organelle: interphase chromatin. PMID:24534090
Diversity of o-antigen repeat unit structures can account for the substantial sequence variation of wzx translocases. PMID:24532778
Function and localization dynamics of bifunctional penicillin-binding proteins in Caulobacter crescentus. PMID:24532768
CRISPR adaptive immune systems of Archaea. PMID:24531374
Long non-coding RNAs: modulators of nuclear structure and function. PMID:24529241
Functionally enigmatic genes: a case study of the brain ignorome. PMID:24523945
Integration of sequence data from a Consanguineous family with genetic data from an outbred population identifies PLB1 as a candidate rheumatoid arthritis risk gene. PMID:24520335
Evolutionary comparisons of miRNA regulation system in six model organisms. PMID:24515651
Biogenesis and functions of bacterial S-layers. PMID:24509785
Transcriptomics and identification of the chemoreceptor superfamily of the pupal parasitoid of the oriental fruit fly, Spalangia endius Walker (Hymenoptera: Pteromalidae). PMID:24505315
First Closed Genome Sequence of Campylobacter fetus subsp. venerealis bv. intermedius. PMID:24503995
Genome Sequence of Legionella anisa, Isolated from a Respiratory Sample, Using an Amoebal Coculture Procedure. PMID:24503989
Hundreds of circular novel plasmids and DNA elements identified in a rat cecum metamobilome. PMID:24503942
Non-contiguous finished genome sequence and description of Anaerococcus pacaensis sp. nov., a new species of anaerobic bacterium. PMID:24501638
In Candida albicans, phosphorylation of Exo84 by Cdk1-Hgc1 is necessary for efficient hyphal extension. PMID:24501427
Structural characterization of MepB from Staphylococcus aureus reveals homology to endonucleases. PMID:24501097
Global patterns of protein domain gain and loss in superkingdoms. PMID:24499935
ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa. PMID:24498971
Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development. PMID:24497530
Deep conservation of human protein tandem repeats within the eukaryotes. PMID:24497029
The Vibrio cholerae diguanylate cyclase VCA0965 has an AGDEF active site and synthesizes cyclic di-GMP. PMID:24490592
Functional characterization of WalRK: A two-component signal transduction system from Bacillus anthracis. PMID:24490131
Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome. PMID:24489955
Comparative genomic analysis reveals 2-oxoacid dehydrogenase complex lipoylation correlation with aerobiosis in archaea. PMID:24489835
The interplay of light and oxygen in the reactive oxygen stress response of Chlamydomonas reinhardtii dissected by quantitative mass spectrometry. PMID:24482124
Finding the missing honey bee genes: lessons learned from a genome upgrade. PMID:24479613
Molecular cloning and yeast expression of cinnamate 4-hydroxylase from Ornithogalum saundersiae baker. PMID:24476601
Comparative genomics of Cylindrospermopsis raciborskii strains with differential toxicities. PMID:24476316
Silencing motifs in the Clr2 protein from fission yeast, Schizosaccharomyces pombe. PMID:24475199
Non-redundant unique interface structures as templates for modeling protein interactions. PMID:24475173
ChEpiMod: a knowledgebase for chemical modulators of epigenome reader domains. PMID:24470572
Comparative phylogenetic analysis of genome-wide Mlo gene family members from Glycine max and Arabidopsis thaliana. PMID:24469270
Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data. PMID:24467687
Training set selection for the prediction of essential genes. PMID:24466248
RNA viral metagenome of whiteflies leads to the discovery and characterization of a whitefly-transmitted carlavirus in North America. PMID:24466220
Sequencing, De Novo assembly and annotation of the Colorado Potato Beetle, Leptinotarsa decemlineata, Transcriptome. PMID:24465841
The evolution of lncRNA repertoires and expression patterns in tetrapods. PMID:24463510
Bioinformatics analysis of bacterial annexins--putative ancestral relatives of eukaryotic annexins. PMID:24454864
Novel genes participating in the formation of prismatic and nacreous layers in the pearl oyster as revealed by their tissue distribution and RNA interference knockdown. PMID:24454739
Zinc finger transcription factors displaced SREBP proteins as the major Sterol regulators during Saccharomycotina evolution. PMID:24453983
BurrH: a new modular DNA binding protein for genome engineering. PMID:24452192
Interplay between phosphoinositide lipids and calcium signals at the leading edge of chemotaxing ameboid cells. PMID:24451847
InterProScan 5: genome-scale protein function classification. PMID:24451626
Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information. PMID:24449878
Analysis of the bovine rumen microbiome reveals a diversity of Sus-like polysaccharide utilization loci from the bacterial phylum Bacteroidetes. PMID:24448980
Evolution of a cellular immune response in Drosophila: a phenotypic and genomic comparative analysis. PMID:24443439
Evolution and classification of myosins, a paneukaryotic whole-genome approach. PMID:24443438
Crystal structures of the human Dysferlin inner DysF domain. PMID:24438169
Genomic comparison of sporeforming bacilli isolated from milk. PMID:24422886
A challenging interpretation of a hexagonally layered protein structure. PMID:24419393
Dependency of codon usage on protein sequence patterns: a statistical study. PMID:24410898
Evolutionary origins of sensation in metazoans: functional evidence for a new sensory organ in sponges. PMID:24410880
Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models. PMID:24410852
Identification of low-molecular-weight compounds inhibiting growth of corynebacteria: potential lead compounds for antibiotics. PMID:24403054
Chitin-induced activation of immune signaling by the rice receptor CEBiP relies on a unique sandwich-type dimerization. PMID:24395781
Putative sugar transporters of the mustard leaf beetle Phaedon cochleariae: their phylogeny and role for nutrient supply in larval defensive glands. PMID:24391959
Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20. PMID:24391926
MIDDAS-M: motif-independent de novo detection of secondary metabolite gene clusters through the integration of genome sequencing and transcriptome data. PMID:24391870
Tracking the origin and divergence of cholinesterases and neuroligins: the evolution of synaptic proteins. PMID:24390353
The ABC-F protein EttA gates ribosome entry into the translation elongation cycle. PMID:24389466
Genome-wide identification, phylogeny, evolution and expression patterns of AP2/ERF genes and cytokinin response factors in Brassica rapa ssp. pekinensis. PMID:24386201
Low frequency variants, collapsed based on biological knowledge, uncover complexity of population stratification in 1000 genomes project data. PMID:24385916
Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana. PMID:24383931
New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily. PMID:24383880
Systematic analysis of a wasp parasitism arsenal. PMID:24383716
Protein domains of unknown function are essential in bacteria. PMID:24381303
Identification of HilD-regulated genes in Salmonella enterica serovar Typhimurium. PMID:24375101
Identification of a broad family of lipid A late acyltransferases with non-canonical substrate specificity. PMID:24372821
On the origin and evolution of plant brassinosteroid receptor kinases. PMID:24370731
Structural insights into the unique single-stranded DNA-binding mode of Helicobacter pylori DprA. PMID:24369431
Genome-wide analysis of the cyclin gene family in tomato. PMID:24366066
Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. PMID:24364385
Genome-wide identification, splicing, and expression analysis of the myosin gene family in maize (Zea mays). PMID:24363426
C19orf12 mutation leads to a pallido-pyramidal syndrome. PMID:24361204
A new computational strategy for predicting essential genes. PMID:24359534
Draft Genome Sequences of Human Pathogenic Fungus Geomyces pannorum Sensu Lato and Bat White Nose Syndrome Pathogen Geomyces (Pseudogymnoascus) destructans. PMID:24356829
Two-component systems in Streptomyces: key regulators of antibiotic complex pathways. PMID:24354561
Probabilistic grammatical model for helix-helix contact site classification. PMID:24350601
Rbt1 protein domains analysis in Candida albicans brings insights into hyphal surface modifications and Rbt1 potential role during adhesion and biofilm formation. PMID:24349274
Feature-based classification of amino acid substitutions outside conserved functional protein domains. PMID:24348198
New insights into the phylogeny and molecular classification of nicotinamide mononucleotide deamidases. PMID:24340054
Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks. PMID:24339775
Evolutionary and structural analyses of mammalian haloacid dehalogenase-type phosphatases AUM and chronophin provide insight into the basis of their different substrate specificities. PMID:24338473
A special member of the rice SRO family, OsSRO1c, mediates responses to multiple abiotic stresses through interaction with various transcription factors. PMID:24337801
Complete Genome Sequence of Campylobacter fetus subsp. testudinum Strain 03-427T. PMID:24336365
A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors. PMID:24335957
Amyloplast-localized SUBSTANDARD STARCH GRAIN4 protein influences the size of starch grains in rice endosperm. PMID:24335509
Metagenomic frameworks for monitoring antibiotic resistance in aquatic environments. PMID:24334622
CLYBL is a polymorphic human enzyme with malate synthase and β-methylmalate synthase activity. PMID:24334609
PhaP phasins play a principal role in poly-β-hydroxybutyrate accumulation in free-living Bradyrhizobium japonicum. PMID:24330393
Novel roles of plant RETINOBLASTOMA-RELATED (RBR) protein in cell proliferation and asymmetric cell division. PMID:24323507
Expanding the catalog of cas genes with metagenomes. PMID:24319142
Identification of immunity-related genes in Arabidopsis and cassava using genomic data. PMID:24316329
The venom gland transcriptome of Latrodectus tredecimguttatus revealed by deep sequencing and cDNA library analysis. PMID:24312294
Homologs of the yeast Tvp38 vesicle-associated protein are conserved in chloroplasts and cyanobacteria. PMID:24312110
The structure of Rv3717 reveals a novel amidase from Mycobacterium tuberculosis. PMID:24311595
RepeatsDB: a database of tandem repeat protein structures. PMID:24311564
New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing. PMID:24311560
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
Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters. PMID:24299161
iPfam: a database of protein family and domain interactions found in the Protein Data Bank. PMID:24297255
MycoCosm portal: gearing up for 1000 fungal genomes. PMID:24297253
eggNOG v4.0: nested orthology inference across 3686 organisms. PMID:24297252
Evolution and dynamics of megaplasmids with genome sizes larger than 100 kb in the Bacillus cereus group. PMID:24295128
Graph representation of high-dimensional alpha-helical membrane protein data. PMID:24294896
SCOP2 prototype: a new approach to protein structure mining. PMID:24293656
A novel missense mutation in AFG3L2 associated with late onset and slow progression of spinocerebellar ataxia type 28. PMID:24293060
PDBe: Protein Data Bank in Europe. PMID:24288376
Pfam: the protein families database. PMID:24288371
Transferring functional annotations of membrane transporters on the basis of sequence similarity and sequence motifs. PMID:24283849
A proteomic investigation of soluble olfactory proteins in Anopheles gambiae. PMID:24282496
A novel mercuric reductase from the unique deep brine environment of Atlantis II in the Red Sea. PMID:24280218
Functional and genomic analyses of alpha-solenoid proteins. PMID:24278209
Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages. PMID:24277850
Transcriptomic and biochemical analyses identify a family of chlorhexidine efflux proteins. PMID:24277845
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. PMID:24275491
LUD, a new protein domain associated with lactate utilization. PMID:24274019
The Structure-Function Linkage Database. PMID:24271399
KBDOCK 2013: a spatial classification of 3D protein domain family interactions. PMID:24271397
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
The carbohydrate-active enzymes database (CAZy) in 2013. PMID:24270786
Minke whale genome and aquatic adaptation in cetaceans. PMID:24270359
CAMP: Collection of sequences and structures of antimicrobial peptides. PMID:24265220
Plasmids of carotenoid-producing Paracoccus spp. (Alphaproteobacteria) - structure, diversity and evolution. PMID:24260361
To tree or not to tree? Genome-wide quantification of recombination and reticulate evolution during the diversification of strict intracellular bacteria. PMID:24259310
Overlapping and distinct roles of Aspergillus fumigatus UDP-glucose 4-epimerases in galactose metabolism and the synthesis of galactose-containing cell wall polysaccharides. PMID:24257745
Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application). PMID:24256031
Amino-acid site variability among natural and designed proteins. PMID:24255821
A whole transcriptomal linkage analysis of gene co-regulation in insecticide resistant house flies, Musca domestica. PMID:24252181
Coxiella burnetii effector protein subverts clathrin-mediated vesicular trafficking for pathogen vacuole biogenesis. PMID:24248335
Overexpression of a new stress-repressive gene OsDSR2 encoding a protein with a DUF966 domain increases salt and simulated drought stress sensitivities and reduces ABA sensitivity in rice. PMID:24247850
Filling out the structural map of the NTF2-like superfamily. PMID:24246060
Structure-based function prediction of uncharacterized protein using binding sites comparison. PMID:24244144
Computational protein design quantifies structural constraints on amino acid covariation. PMID:24244128
P³DB 3.0: From plant phosphorylation sites to protein networks. PMID:24243849
Habitat-specific type I polyketide synthases in soils and street sediments. PMID:24241933
Deorphanizing the human transmembrane genome: A landscape of uncharacterized membrane proteins. PMID:24241348
Genome-wide analysis of the bHLH transcription factor family in Chinese cabbage (Brassica rapa ssp. pekinensis). PMID:24241166
A network of epigenetic regulators guides developmental haematopoiesis in vivo. PMID:24240475
The planarian regeneration transcriptome reveals a shared but temporally shifted regulatory program between opposing head and tail scenarios. PMID:24238224
The BtaF trimeric autotransporter of Brucella suis is involved in attachment to various surfaces, resistance to serum and virulence. PMID:24236157
The evolution of the ribosome biogenesis pathway from a yeast perspective. PMID:24234440
SeqDepot: streamlined database of biological sequences and precomputed features. PMID:24234005
Integrating in silico resources to map a signaling network. PMID:24233784
Discovery of a novel bottlenose dolphin coronavirus reveals a distinct species of marine mammal coronavirus in Gammacoronavirus. PMID:24227844
The transporter classification database. PMID:24225317
A comparative systems analysis of polysaccharide-elicited responses in Neurospora crassa reveals carbon source-specific cellular adaptations. PMID:24224966
Episodes of horizontal gene-transfer and gene-fusion led to co-existence of different metal-ion specific glyoxalase I. PMID:24220130
PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool. PMID:24219505
Isoform-selective oligomer formation of Saccharomyces cerevisiae p24 family proteins. PMID:24217251
EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases. PMID:24214991
UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks. PMID:24214987
Manually curated database of rice proteins. PMID:24214963
The eukaryotic linear motif resource ELM: 10 years and counting. PMID:24214962
The evolutionary origin of epithelial cell-cell adhesion mechanisms. PMID:24210433
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
A comparative study of lectin affinity based plant N-glycoproteome profiling using tomato fruit as a model. PMID:24198434
High-resolution network biology: connecting sequence with function. PMID:24197012
SIFT Indel: predictions for the functional effects of amino acid insertions/deletions in proteins. PMID:24194902
Inference of gene-phenotype associations via protein-protein interaction and orthology. PMID:24194887
TreeFam v9: a new website, more species and orthology-on-the-fly. PMID:24194607
Cloning, overexpression, purification and preliminary X-ray analysis of the catalytic domain of the ethylene receptor ETR1 from Arabidopsis thaliana. PMID:24192376
An estimated 5% of new protein structures solved today represent a new Pfam family. PMID:24189229
Mediation of clathrin-dependent trafficking during cytokinesis and cell expansion by Arabidopsis stomatal cytokinesis defective proteins. PMID:24179130
RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria. PMID:24175918
PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. PMID:24174544
Eukaryotic resistance to fluoride toxicity mediated by a widespread family of fluoride export proteins. PMID:24173035
Characterization and transcript profiling of the pectin methylesterase (PME) and pectin methylesterase inhibitor (PMEI) gene families in flax (Linum usitatissimum). PMID:24168262
IMG 4 version of the integrated microbial genomes comparative analysis system. PMID:24165883
EBI metagenomics--a new resource for the analysis and archiving of metagenomic data. PMID:24165880
Crystal structure and site-directed mutagenesis of 3-ketosteroid Δ1-dehydrogenase from Rhodococcus erythropolis SQ1 explain its catalytic mechanism. PMID:24165124
Toxicological evaluation of proteins introduced into food crops. PMID:24164515
A potential source for cellulolytic enzyme discovery and environmental aspects revealed through metagenomics of Brazilian mangroves. PMID:24160319
Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently "orphan" viral proteins. PMID:24155369
PDBsum additions. PMID:24153109
Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. PMID:24150943
Type I pyridoxal 5'-phosphate dependent enzymatic domains embedded within multimodular nonribosomal peptide synthetase and polyketide synthase assembly lines. PMID:24148833
Identification and developmental expression of the enzymes responsible for dopamine, histamine, octopamine and serotonin biosynthesis in the copepod crustacean Calanus finmarchicus. PMID:24148657
Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis. PMID:24147765
Turnerbactin, a novel triscatecholate siderophore from the shipworm endosymbiont Teredinibacter turnerae T7901. PMID:24146831
β-Propeller blades as ancestral peptides in protein evolution. PMID:24143202
Identification of genome-wide single nucleotide polymorphisms in allopolyploid crop Brassica napus. PMID:24138473
Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding. PMID:24136998
IMG/M 4 version of the integrated metagenome comparative analysis system. PMID:24136997
Bioinformatic analysis of the four transcription factors used to induce pluripotent stem cells. PMID:24129607
DNA assembly techniques for next-generation combinatorial biosynthesis of natural products. PMID:24127070
Analytical tools and databases for metagenomics in the next-generation sequencing era. PMID:24124405
DGIdb: mining the druggable genome. PMID:24122041
Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals. PMID:24119094
Identification of novel vaccine candidates against multidrug-resistant Acinetobacter baumannii. PMID:24116234
Mapping of genotype-phenotype diversity among clinical isolates of mycobacterium tuberculosis by sequence-based transcriptional profiling. PMID:24115728
Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes. PMID:24106089
FunGene: the functional gene pipeline and repository. PMID:24101916
Identification, characterization and preliminary X-ray diffraction analysis of the rolling-circle replication initiator protein from plasmid pSTK1. PMID:24100563
Crystal structure of c5321: a protective antigen present in uropathogenic Escherichia coli strains displaying an SLR fold. PMID:24099525
High-throughput RNA sequencing of pseudomonas-infected Arabidopsis reveals hidden transcriptome complexity and novel splice variants. PMID:24098335
ToPS: a framework to manipulate probabilistic models of sequence data. PMID:24098098
The mutational landscape of phosphorylation signaling in cancer. PMID:24089029
DIRS and Ngaro Retrotransposons in Fungi. PMID:24086727
3did: a catalog of domain-based interactions of known three-dimensional structure. PMID:24081580
The bilaterian roots of cordon-bleu. PMID:24079804
Bolbase: a comprehensive genomics database for Brassica oleracea. PMID:24079801
The RclR protein is a reactive chlorine-specific transcription factor in Escherichia coli. PMID:24078635
Cooperative degradation of chitin by extracellular and cell surface-expressed chitinases from Paenibacillus sp. strain FPU-7. PMID:24077704
Divergent evolution of protein conformational dynamics in dihydrofolate reductase. PMID:24077226
TRIAD1 and HHARI bind to and are activated by distinct neddylated Cullin-RING ligase complexes. PMID:24076655
Transcription regulation of plastid genes involved in sulfate transport in Viridiplantae. PMID:24073405
Presence-absence variation in A. thaliana is primarily associated with genomic signatures consistent with relaxed selective constraints. PMID:24072814
The clip-segment of the von Willebrand domain 1 of the BMP modulator protein Crossveinless 2 is preformed. PMID:24071977
Schistosoma mansoni Sirtuins: characterization and potential as chemotherapeutic targets. PMID:24069483
Automatic identification of highly conserved family regions and relationships in genome wide datasets including remote protein sequences. PMID:24069417
Cross-link guided molecular modeling with ROSETTA. PMID:24069194
Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries. PMID:24069019
Assessing the human gut microbiota in metabolic diseases. PMID:24065795
Evolution of the JAK-STAT pathway. PMID:24058787
Identification of SPOR domain amino acids important for septal localization, peptidoglycan binding, and a disulfide bond in the cell division protein FtsN. PMID:24056104
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
Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool. PMID:24045641
Protein similarity networks reveal relationships among sequence, structure, and function within the Cupin superfamily. PMID:24040257
Genome-wide discovery and information resource development of DNA polymorphisms in cassava. PMID:24040164
Control of RNA stability by NrrF, an iron-regulated small RNA in Neisseria gonorrhoeae. PMID:24039262
PainNetworks: a web-based resource for the visualisation of pain-related genes in the context of their network associations. PMID:24036287
Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: haloadaptations present and absent. PMID:24034603
The evolution of microRNA pathway protein components in Cnidaria. PMID:24030553
PPR proteins of green algae. PMID:24021981
Interaction between the genomes of Lactococcus lactis and phages of the P335 species. PMID:24009606
Overexpressed TPX2 causes ectopic formation of microtubular arrays in the nuclei of acentrosomal plant cells. PMID:24006426
Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila. PMID:24004689
Drift and conservation of differential exon usage across tissues in primate species. PMID:24003148
Structures of RNA polymerase II complexes with Bye1, a chromatin-binding PHF3/DIDO homologue. PMID:24003114
Identification, expression, and comparative genomic analysis of the IPT and CKX gene families in Chinese cabbage (Brassica rapa ssp. pekinensis). PMID:24001366
Web Apollo: a web-based genomic annotation editing platform. PMID:24000942
Computational analysis of virus-host interactomes. PMID:23996253
Adjusting scoring matrices to correct overextended alignments. PMID:23995390
Non-contiguous genome sequence of Mycobacterium simiae strain DSM 44165(T.). PMID:23991261
The Complete Genome Sequence of Methanobrevibacter sp. AbM4. PMID:23991254
Brittle Culm1, a COBRA-like protein, functions in cellulose assembly through binding cellulose microfibrils. PMID:23990797
The genome of Spraguea lophii and the basis of host-microsporidian interactions. PMID:23990793
From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction. PMID:23990764
The mycobacterial antibiotic resistance determinant WhiB7 acts as a transcriptional activator by binding the primary sigma factor SigA (RpoV). PMID:23990327
The other face of restriction: modification-dependent enzymes. PMID:23990325
The Tarenaya hassleriana genome provides insight into reproductive trait and genome evolution of crucifers. PMID:23983221
Experimental and computational analysis of the secretome of the hyperthermophilic archaeon Pyrococcus furiosus. PMID:23979514
Whole genome duplication and enrichment of metal cation transporters revealed by de novo genome sequencing of extremely halotolerant black yeast Hortaea werneckii. PMID:23977017
SHARP: genome-scale identification of gene-protein-reaction associations in cyanobacteria. PMID:23975204
Genome-wide analysis of the AP2/ERF transcription factor superfamily in Chinese cabbage (Brassica rapa ssp. pekinensis). PMID:23972083
Complete Genome Sequence of the Arcobacter butzleri Cattle Isolate 7h1h. PMID:23969057
MYRF is a membrane-associated transcription factor that autoproteolytically cleaves to directly activate myelin genes. PMID:23966833
Bacterial second messengers, cGMP and c-di-GMP, in a quest for regulatory dominance. PMID:23963313
Inherited mutations in the helicase RTEL1 cause telomere dysfunction and Hoyeraal-Hreidarsson syndrome. PMID:23959892
Improving the lethal effect of cpl-7, a pneumococcal phage lysozyme with broad bactericidal activity, by inverting the net charge of its cell wall-binding module. PMID:23959317
Different functions for the domains of the Arabidopsis thaliana RMI1 protein in DNA cross-link repair, somatic and meiotic recombination. PMID:23956219
Searching algorithm for type IV secretion system effectors 1.0: a tool for predicting type IV effectors and exploring their genomic context. PMID:23945940
Functional requirements driving the gene duplication in 12 Drosophila species. PMID:23945147
Metagenomic guilt by association: an operonic perspective. PMID:23940763
Systematic analysis and comparison of nucleotide-binding site disease resistance genes in a diploid cotton Gossypium raimondii. PMID:23936305
A contribution to the study of plant development evolution based on gene co-expression networks. PMID:23935602
Transposon domestication versus mutualism in ciliate genome rearrangements. PMID:23935529
A network of HMG-box transcription factors regulates sexual cycle in the fungus Podospora anserina. PMID:23935511
Mercury methylation by the methanogen Methanospirillum hungatei. PMID:23934484
Interactome map uncovers phosphatidylserine transport by oxysterol-binding proteins. PMID:23934110
Branched signal wiring of an essential bacterial cell-cycle phosphotransfer protein. PMID:23932593
Increments and duplication events of enzymes and transcription factors influence metabolic and regulatory diversity in prokaryotes. PMID:23922780
New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria. PMID:23913324
Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture-insights from genomics. PMID:23908658
Genetic determinants of swimming motility in the squid light-organ symbiont Vibrio fischeri. PMID:23907990
Functional profiling of the gut microbiome in disease-associated inflammation. PMID:23906180
Chemistry of the retinoid (visual) cycle. PMID:23905688
Plant F-box protein evolution is determined by lineage-specific timing of major gene family expansion waves. PMID:23904908
Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily. PMID:23904509
Analysis of periplasmic sensor domains from Anaeromyxobacter dehalogenans 2CP-C: structure of one sensor domain from a histidine kinase and another from a chemotaxis protein. PMID:23897711
Structure of allergens and structure based epitope predictions. PMID:23891546
The genome and transcriptome of the enteric parasite Entamoeba invadens, a model for encystation. PMID:23889909
Identification of G protein-coupled receptor signaling pathway proteins in marine diatoms using comparative genomics. PMID:23883327
Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline. PMID:23882027
Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. PMID:23879659
TCW: transcriptome computational workbench. PMID:23874959
Structural basis of the novel S. pneumoniae virulence factor, GHIP, a glycosyl hydrolase 25 participating in host-cell invasion. PMID:23874703
The Myxococcus xanthus two-component system CorSR regulates expression of a gene cluster involved in maintaining copper tolerance during growth and development. PMID:23874560
GEMINI: integrative exploration of genetic variation and genome annotations. PMID:23874191
Structural disorder provides increased adaptability for vesicle trafficking pathways. PMID:23874186
Utilization of heme as an iron source by marine Alphaproteobacteria in the Roseobacter clade. PMID:23872569
A novel function prediction approach using protein overlap networks. PMID:23866986
Enlarging cells initiating apomixis in Hieracium praealtum transition to an embryo sac program prior to entering mitosis. PMID:23864557
MisPred: a resource for identification of erroneous protein sequences in public databases. PMID:23864220
Crystal structure of a member of a novel family of dioxygenases (PF10014) reveals a conserved cupin fold and active site. PMID:23852666
Bioinformatics perspective on rhomboid intramembrane protease evolution and function. PMID:23845876
Identification of immunity related genes to study the Physalis peruviana--Fusarium oxysporum pathosystem. PMID:23844210
Lacto-N-biosidase encoded by a novel gene of Bifidobacterium longum subspecies longum shows unique substrate specificity and requires a designated chaperone for its active expression. PMID:23843461
Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. PMID:23842652
DBATE: database of alternative transcripts expression. PMID:23842462
KONAGAbase: a genomic and transcriptomic database for the diamondback moth, Plutella xylostella. PMID:23837716
Cytosine methylation is a conserved epigenetic feature found throughout the phylum Platyhelminthes. PMID:23837670
DNA-binding specificity changes in the evolution of forkhead transcription factors. PMID:23836653
Long noncoding RNA: a new player of heart failure? PMID:23835777
Evolutionary origins, molecular cloning and expression of carotenoid hydroxylases in eukaryotic photosynthetic algae. PMID:23834441
Complete Genome Sequence of the Thermophilic and Facultatively Chemolithoautotrophic Sulfate Reducer Archaeoglobus sulfaticallidus Strain PM70-1T. PMID:23833130
Integrating pathways of Parkinson's disease in a molecular interaction map. PMID:23832570
PUMA: a unified framework for penalized multiple regression analysis of GWAS data. PMID:23825936
Tracing evolutionary footprints to identify novel gene functional linkages. PMID:23825567
Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori. PMID:23825549
Assessment of computational methods for predicting the effects of missense mutations in human cancers. PMID:23819521
BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge. PMID:23819467
A protein domain-centric approach for the comparative analysis of human and yeast phenotypically relevant mutations. PMID:23819456
Analysis and consensus of currently available intrinsic protein disorder annotation sources in the MobiDB database. PMID:23815411
Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions. PMID:23815072
Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA. PMID:23814188
Cyclic di-AMP: another second messenger enters the fray. PMID:23812326
Novel Burkholderia mallei virulence factors linked to specific host-pathogen protein interactions. PMID:23800426
An unbiased approach to identifying tau kinases that phosphorylate tau at sites associated with Alzheimer disease. PMID:23798682
A conserved hydrolase responsible for the cleavage of aminoacylphosphatidylglycerol in the membrane of Enterococcus faecium. PMID:23793054
In silico prediction of a disease-associated STIL mutant and its affect on the recruitment of centromere protein J (CENPJ). PMID:23772360
Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation. PMID:23766293
Analysis of DNA repair and protection in the Tardigrade Ramazzottius varieornatus and Hypsibius dujardini after exposure to UVC radiation. PMID:23762256
Discovery of diversity in xylan biosynthetic genes by transcriptional profiling of a heteroxylan containing mucilaginous tissue. PMID:23761806
Gymnosperm B-sister genes may be involved in ovule/seed development and, in some species, in the growth of fleshy fruit-like structures. PMID:23761686
The architectural design of networks of protein domain architectures. PMID:23760167
Paleoproteomic study of the Iceman's brain tissue. PMID:23739949
webPDBinder: a server for the identification of ligand binding sites on protein structures. PMID:23737450
antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers. PMID:23737449
Transcriptomic analysis of Ustilago maydis infecting Arabidopsis reveals important aspects of the fungus pathogenic mechanisms. PMID:23733054
The pneumococcal MgaSpn virulence transcriptional regulator generates multimeric complexes on linear double-stranded DNA. PMID:23723245
Genome-wide characterization of endogenous retroviruses in the bat Myotis lucifugus reveals recent and diverse infections. PMID:23720713
Transcriptomic analysis of a tertiary relict plant, extreme xerophyte Reaumuria soongorica to identify genes related to drought adaptation. PMID:23717523
MISTIC: Mutual information server to infer coevolution. PMID:23716641
Metagenomic de novo assembly of an aquatic representative of the verrucomicrobial class Spartobacteria. PMID:23716574
IS-Dom: a dataset of independent structural domains automatically delineated from protein structures. PMID:23715893
The 216-bp marB gene of the marRAB operon in Escherichia coli encodes a periplasmic protein which reduces the transcription rate of marA. PMID:23710538
NRF2-ome: an integrated web resource to discover protein interaction and regulatory networks of NRF2. PMID:23710289
The genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader. PMID:23709508
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. PMID:23707974
Identification of novel arthropod vector G protein-coupled receptors. PMID:23705687
Genomic and expression analysis of the flax (Linum usitatissimum) family of glycosyl hydrolase 35 genes. PMID:23701735
DNA topoisomerase II is involved in regulation of cyst wall protein genes and differentiation in Giardia lamblia. PMID:23696909
Frequent loss of lineages and deficient duplications accounted for low copy number of disease resistance genes in Cucurbitaceae. PMID:23682795
Characterization of an M28 metalloprotease family member residing in the yeast vacuole. PMID:23679341
The first structure of a mycobacteriophage, the Mycobacterium abscessus subsp. bolletii phage Araucaria. PMID:23678183
Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. PMID:23676670
Differential transcript isoform usage pre- and post-zygotic genome activation in zebrafish. PMID:23676078
Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction. PMID:23675487
CLCAs - a family of metalloproteases of intriguing phylogenetic distribution and with cases of substituted catalytic sites. PMID:23671590
Computational meta'omics for microbial community studies. PMID:23670539
All or nothing: protein complexes flip essentiality between distantly related eukaryotes. PMID:23661563
Transcriptome of the Lymantria dispar (gypsy moth) larval midgut in response to infection by Bacillus thuringiensis. PMID:23658687
The CD225 domain of IFITM3 is required for both IFITM protein association and inhibition of influenza A virus and dengue virus replication. PMID:23658454
On the origin of large flexibility of P-glycoprotein in the inward-facing state. PMID:23658020
Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent. PMID:23657361
Using Bioinformatics to Develop and Test Hypotheses: E. coli-Specific Virulence Determinants. PMID:23653804
DNA marker applications to molecular genetics and genomics in tomato. PMID:23641178
Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint. PMID:23637705
The role of structural bioinformatics resources in the era of integrative structural biology. PMID:23633580
Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation. PMID:23630315
Collapsed abnormal pollen1 gene encoding the Arabinokinase-like protein is involved in pollen development in rice. PMID:23629836
Evidence for the widespread distribution of CRISPR-Cas system in the Phylum Cyanobacteria. PMID:23628889
Explaining microbial phenotypes on a genomic scale: GWAS for microbes. PMID:23625995
SNVDis: a proteome-wide analysis service for evaluating nsSNVs in protein functional sites and pathways. PMID:23618375
The challenge of increasing Pfam coverage of the human proteome. PMID:23603847
INstruct: a database of high-quality 3D structurally resolved protein interactome networks. PMID:23599502
Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. PMID:23598997
Transcriptional changes of the root-knot nematode Meloidogyne incognita in response to Arabidopsis thaliana root signals. PMID:23593446
Propeptides of eukaryotic proteases encode histidines to exploit organelle pH for regulation. PMID:23585398
The glove-like structure of the conserved membrane protein TatC provides insight into signal sequence recognition in twin-arginine translocation. PMID:23583035
A significant fraction of 21-nucleotide small RNA originates from phased degradation of resistance genes in several perennial species. PMID:23580593
Archaeal and eukaryotic homologs of Hfq: A structural and evolutionary perspective on Sm function. PMID:23579284
Structural mimicry between SLA/LP and Rickettsia surface antigens as a driver of autoimmune hepatitis: insights from an in silico study. PMID:23575112
New putative chloroplast vesicle transport components and cargo proteins revealed using a bioinformatics approach: an Arabidopsis model. PMID:23573218
Comprehensively identifying and characterizing the missing gene sequences in human reference genome with integrated analytic approaches. PMID:23572138
MS-desi, a desiccation-related protein in the floral nectar of the evergreen velvet bean (Mucuna sempervirens Hemsl): molecular identification and characterization. PMID:23568404
A genomic survey of HECT ubiquitin ligases in eukaryotes reveals independent expansions of the HECT system in several lineages. PMID:23563970
Functional and evolutionary analysis of the genome of an obligate fungal symbiont. PMID:23563967
Horizontal transfer and evolution of prokaryote transposable elements in eukaryotes. PMID:23563966
Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms. PMID:23557021
Multiple single-cell genomes provide insight into functions of uncultured Deltaproteobacteria in the human oral cavity. PMID:23555659
Horizontal transfer of a subtilisin gene from plants into an ancestor of the plant pathogenic fungal genus Colletotrichum. PMID:23554975
MGcV: the microbial genomic context viewer for comparative genome analysis. PMID:23547764
Structure of Neisseria meningitidis lipoprotein GNA1162. PMID:23545639
Identification of diverse full-length endogenous betaretroviruses in megabats and microbats. PMID:23537098
Predominant archaea in marine sediments degrade detrital proteins. PMID:23535597
A 1,681-locus consensus genetic map of cultivated cucumber including 67 NB-LRR resistance gene homolog and ten gene loci. PMID:23531125
Identification of triacylglycerol and steryl ester synthases of the methylotrophic yeast Pichia pastoris. PMID:23524242
Structural studies of Pseudomonas and Chromobacterium ω-aminotransferases provide insights into their differing substrate specificity. PMID:23519665
Missense substitutions reflecting regulatory control of transmitter phosphatase activity in two-component signalling. PMID:23517441
Ecogenomic perspectives on domains of unknown function: correlation-based exploration of marine metagenomes. PMID:23516388
Genome sequence of a novel deep-sea vent epsilonproteobacterial phage provides new insight into the co-evolution of Epsilonproteobacteria and their phages. PMID:23512119
Evolution of the ferric reductase domain (FRD) superfamily: modularity, functional diversification, and signature motifs. PMID:23505460
Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis. PMID:23504016
Deep sequencing for de novo construction of a marine fish (Sparus aurata) transcriptome database with a large coverage of protein-coding transcripts. PMID:23497320
phiBIOTICS: catalogue of therapeutic enzybiotics, relevant research studies and practical applications. PMID:23497033
Sequencing and annotation of the Ophiostoma ulmi genome. PMID:23496816
One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012. PMID:23494302
Evolution of Tre-2/Bub2/Cdc16 (TBC) Rab GTPase-activating proteins. PMID:23485563
Genome-wide SNP genotyping to infer the effects on gene functions in tomato. PMID:23482505
A continuous fluorescence assay for the characterization of Nudix hydrolases. PMID:23481913
Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. PMID:23471616
Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. PMID:23471540
A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium. PMID:23470992
Complete Genome Sequence of Anoxybacillus flavithermus TNO-09.006, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment. PMID:23469333
A genome-wide analysis of the LBD (LATERAL ORGAN BOUNDARIES domain) gene family in Malus domestica with a functional characterization of MdLBD11. PMID:23468909
Mechanistic characterization of the tetraacyldisaccharide-1-phosphate 4'-kinase LpxK involved in lipid A biosynthesis. PMID:23464738
A chemical proteomics approach to profiling the ATP-binding proteome of Mycobacterium tuberculosis. PMID:23462205
Exon-phase symmetry and intrinsic structural disorder promote modular evolution in the human genome. PMID:23460204
Increasing sequence search sensitivity with transitive alignments. PMID:23457449
The SHOCT domain: a widespread domain under-represented in model organisms. PMID:23451277
The genetic architecture of degenerin/epithelial sodium channels in Drosophila. PMID:23449991
CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models. PMID:23436912
Transcriptome analyses reveal protein and domain families that delineate stage-related development in the economically important parasitic nematodes, Ostertagia ostertagi and Cooperia oncophora. PMID:23432754
Complete mitochondrial genome of the aluminum-tolerant fungus Rhodotorula taiwanensis RS1 and comparative analysis of Basidiomycota mitochondrial genomes. PMID:23427135
A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration. PMID:23425577
Emergence of novel domains in proteins. PMID:23425224
Improving microbial genome annotations in an integrated database context. PMID:23424620
Using BioBin to explore rare variant population stratification. PMID:23424138
De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes. PMID:23414703
Massive-scale gene co-expression network construction and robustness testing using random matrix theory. PMID:23409071
Behavioural and genetic analyses of Nasonia shed light on the evolution of sex pheromones. PMID:23407492
Coupling mutagenesis and parallel deep sequencing to probe essential residues in a genome or gene. PMID:23401533
Interactome3D: adding structural details to protein networks. PMID:23399932
The repertoires of ubiquitinating and deubiquitinating enzymes in eukaryotic genomes. PMID:23393154
A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels. PMID:23390605
Genetic control and comparative genomic analysis of flowering time in Setaria (Poaceae). PMID:23390604
Association of candidate genes with drought tolerance traits in diverse perennial ryegrass accessions. PMID:23386684
Lack of RsmA-mediated control results in constant hypervirulence, cell elongation, and hyperflagellation in Pectobacterium wasabiae. PMID:23372695
Genome-wide identification, phylogeny and expression analysis of SUN, OFP and YABBY gene family in tomato. PMID:23371549
Inferring homologous protein-protein interactions through pair position specific scoring matrix. PMID:23367879
Staring at the cold sun: blue light regulation is distributed within the genus Acinetobacter. PMID:23358859
Identification and physiological characterization of phosphatidic acid phosphatase enzymes involved in triacylglycerol biosynthesis in Streptomyces coelicolor. PMID:23356794
A large-scale evaluation of computational protein function prediction. PMID:23353650
De novo transcriptome sequencing and analysis for Venturia inaequalis, the devastating apple scab pathogen. PMID:23349770
Integron gene cassettes: a repository of novel protein folds with distinct interaction sites. PMID:23349695
Mechanisms and dynamics of orphan gene emergence in insect genomes. PMID:23348040
Prediction of contact residue pairs based on co-substitution between sites in protein structures. PMID:23342110
Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome. PMID:23339658
Detection of African swine fever virus-like sequences in ponds in the Mississippi Delta through metagenomic sequencing. PMID:23338931
wksl3, a New biocontrol agent for Salmonella enterica serovars enteritidis and typhimurium in foods: characterization, application, sequence analysis, and oral acute toxicity study. PMID:23335772
Evolutionary acquisition and loss of saxitoxin biosynthesis in dinoflagellates: the second "core" gene, sxtG. PMID:23335767
Characterization of the yeast actin patch protein App1p phosphatidate phosphatase. PMID:23335564
Helix bundle loops determine whether histidine kinases autophosphorylate in cis or in trans. PMID:23333741
MAFFT multiple sequence alignment software version 7: improvements in performance and usability. PMID:23329690
Assembly of the type II secretion system such as found in Vibrio cholerae depends on the novel Pilotin AspS. PMID:23326233
Structural determinants of skeletal muscle ryanodine receptor gating. PMID:23319589
BtaE, an adhesin that belongs to the trimeric autotransporter family, is required for full virulence and defines a specific adhesive pole of Brucella suis. PMID:23319562
Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome. PMID:23303792
Development of transcriptomic resources for interrogating the biosynthesis of monoterpene indole alkaloids in medicinal plant species. PMID:23300689
Molecular and microscopic evidence of viruses in marine copepods. PMID:23297243
The AEROPATH project targeting Pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discovery. PMID:23295481
Identification of a mammalian-type phosphatidylglycerophosphate phosphatase in the Eubacterium Rhodopirellula baltica. PMID:23293031
FastAnnotator--an efficient transcript annotation web tool. PMID:23281853
Genes involved in host-parasite interactions can be revealed by their correlated expression. PMID:23275547
A conserved START domain coenzyme Q-binding polypeptide is required for efficient Q biosynthesis, respiratory electron transport, and antioxidant function in Saccharomyces cerevisiae. PMID:23270816
The methyltransferase NSD3 has chromatin-binding motifs, PHD5-C5HCH, that are distinct from other NSD (nuclear receptor SET domain) family members in their histone H3 recognition. PMID:23269674
Phylogenetic distribution of potential cellulases in bacteria. PMID:23263967
Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). PMID:23263233
Endonuclease V: an unusual enzyme for repair of DNA deamination. PMID:23263163
Multiple inter-kingdom horizontal gene transfers in the evolution of the phosphoenolpyruvate carboxylase gene family. PMID:23251445
Regulation of H2O2 stress-responsive genes through a novel transcription factor in the protozoan pathogen Entamoeba histolytica. PMID:23250742
A link between host plant adaptation and pesticide resistance in the polyphagous spider mite Tetranychus urticae. PMID:23248300
Functional identification of valerena-1,10-diene synthase, a terpene synthase catalyzing a unique chemical cascade in the biosynthesis of biologically active sesquiterpenes in Valeriana officinalis. PMID:23243312
Non-traditional antibacterial screening approaches for the identification of novel inhibitors of the glyoxylate shunt in gram-negative pathogens. PMID:23240059
A global comparison of the human and T. brucei degradomes gives insights about possible parasite drug targets. PMID:23236535
Calciomics: integrative studies of Ca2+-binding proteins and their interactomes in biological systems. PMID:23235533
Evaluation method for the potential functionome harbored in the genome and metagenome. PMID:23234305
Genome-wide characterization of the phosphate starvation response in Schizosaccharomyces pombe. PMID:23231582
Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey. PMID:23220349
Stage-specific expression of protease genes in the apicomplexan parasite, Eimeria tenella. PMID:23216867
The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes. PMID:23209799
TgpA, a protein with a eukaryotic-like transglutaminase domain, plays a critical role in the viability of Pseudomonas aeruginosa. PMID:23209712
Genome sequence of Afipia birgiae, a rare bacterium associated with Amoebae. PMID:23209256
Genomic analysis of Rickettsia japonica strain YHT. PMID:23209240
Draft genome sequence of Staphylococcus massiliensis strain 5402776T. PMID:23209235
Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum. PMID:23209028
PDBTM: Protein Data Bank of transmembrane proteins after 8 years. PMID:23203988
Dfam: a database of repetitive DNA based on profile hidden Markov models. PMID:23203985
MetaMicrobesOnline: phylogenomic analysis of microbial communities. PMID:23203984
OrysPSSP: a comparative platform for small secreted proteins from rice and other plants. PMID:23203890
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. PMID:23203869
Proteins of unknown function in the Protein Data Bank (PDB): an inventory of true uncharacterized proteins and computational tools for their analysis. PMID:23202924
The tomato RLK superfamily: phylogeny and functional predictions about the role of the LRRII-RLK subfamily in antiviral defense. PMID:23198823
Fife, a Drosophila Piccolo-RIM homolog, promotes active zone organization and neurotransmitter release. PMID:23197698
CDD: conserved domains and protein three-dimensional structure. PMID:23197659
TIGRFAMs and Genome Properties in 2013. PMID:23197656
LUCApedia: a database for the study of ancient life. PMID:23193296
NPIDB: Nucleic acid-Protein Interaction DataBase. PMID:23193292
GenColors-based comparative genome databases for small eukaryotic genomes. PMID:23193285
KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms. PMID:23193279
HAMAP in 2013, new developments in the protein family classification and annotation system. PMID:23193261
The RCSB Protein Data Bank: new resources for research and education. PMID:23193259
ESTHER, the database of the α/β-hydrolase fold superfamily of proteins: tools to explore diversity of functions. PMID:23193256
Molecular evolution of translin superfamily proteins within the genomes of eubacteria, archaea and eukaryotes. PMID:23188094
PIECE: a database for plant gene structure comparison and evolution. PMID:23180792
Evolution of animal and plant dicers: early parallel duplications and recurrent adaptation of antiviral RNA binding in plants. PMID:23180579
UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation. PMID:23172288
Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus. PMID:23171342
Genomic resources for a model in adaptation and speciation research: characterization of the Poecilia mexicana transcriptome. PMID:23170846
Heptahelical protein PQLC2 is a lysosomal cationic amino acid exporter underlying the action of cysteamine in cystinosis therapy. PMID:23169667
Counterbalance of ligand- and self-coupled motions characterizes multispecificity of ubiquitin. PMID:23169174
Differential expression of in vivo and in vitro protein profile of outer membrane of Acidovorax avenae subsp. avenae. PMID:23166741
Complete genome sequence of Serratia plymuthica bacteriophage ΦMAM1. PMID:23166269
Genome sequence of a new Streptomyces coelicolor generalized transducing bacteriophage, ΦCAM. PMID:23166260
Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. PMID:23165928
eProS--a database and toolbox for investigating protein sequence-structure-function relationships through energy profiles. PMID:23161695
DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. PMID:23161684
APPRIS: annotation of principal and alternative splice isoforms. PMID:23161672
Identification and characterization of a high-affinity choline uptake system of Brucella abortus. PMID:23161032
A toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.). PMID:23157543
Dynamics of domain coverage of the protein sequence universe. PMID:23157439
MetalPDB: a database of metal sites in biological macromolecular structures. PMID:23155064
RNApathwaysDB--a database of RNA maturation and decay pathways. PMID:23155061
Bioinformatic analysis of epigenetic and microRNA mediated regulation of drought responsive genes in rice. PMID:23145152
Metagenomic profiling of microbial composition and antibiotic resistance determinants in Puget Sound. PMID:23144718
Pseudomonas syringae pv. tomato DC3000 CmaL (PSPTO4723), a DUF1330 family member, is needed to produce L-allo-isoleucine, a precursor for the phytotoxin coronatine. PMID:23144243
Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction. PMID:23139845
ST proteins, a new family of plant tandem repeat proteins with a DUF2775 domain mainly found in Fabaceae and Asteraceae. PMID:23134664
Metagenomic analysis of the microbiota from the crop of an invasive snail reveals a rich reservoir of novel genes. PMID:23133637
Rfam 11.0: 10 years of RNA families. PMID:23125362
Insights into the evolutionary features of human neurodegenerative diseases. PMID:23118989
The rice B-box zinc finger gene family: genomic identification, characterization, expression profiling and diurnal analysis. PMID:23118960
Dynamic hubs show competitive and static hubs non-competitive regulation of their interaction partners. PMID:23118954
Identifying structural domains of proteins using clustering. PMID:23116496
Functional analysis of pneumococcal drug efflux pumps associates the MATE DinF transporter with quinolone susceptibility. PMID:23114782
Identification of essential genes of the periodontal pathogen Porphyromonas gingivalis. PMID:23114059
Bio-crude transcriptomics: gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa). PMID:23110428
Solution structure of Escherichia coli FeoA and its potential role in bacterial ferrous iron transport. PMID:23104801
Genomic approaches for interrogating the biochemistry of medicinal plant species. PMID:23084937
Putting the pieces together: high-performance LC-MS/MS provides network-, pathway-, and protein-level perspectives in Populus. PMID:23073815
The Saccharomyces cerevisiae actin patch protein App1p is a phosphatidate phosphatase enzyme. PMID:23071111
Structure Motivator: a tool for exploring small three-dimensional elements in proteins. PMID:23067391
Computational tools for viral metagenomics and their application in clinical research. PMID:23062738
Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. PMID:23061897
Extensive evolutionary and functional diversity among mammalian AIM2-like receptors. PMID:23045604
Genome sequence of Legionella tunisiensis strain LegM(T), a new Legionella species isolated from hypersaline lake water. PMID:23045493
Genomic comparison of Kingella kingae strains. PMID:23045489
LNCipedia: a database for annotated human lncRNA transcript sequences and structures. PMID:23042674
Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates. PMID:23035824
Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. PMID:23033316
MESSA: MEta-Server for protein Sequence Analysis. PMID:23031578
ThioFinder: a web-based tool for the identification of thiopeptide gene clusters in DNA sequences. PMID:23029291
A response regulator interfaces between the Frz chemosensory system and the MglA/MglB GTPase/GAP module to regulate polarity in Myxococcus xanthus. PMID:23028358
Adding unaligned sequences into an existing alignment using MAFFT and LAST. PMID:23023983
Bacterial biosynthetic gene clusters encoding the anti-cancer haterumalide class of molecules: biogenesis of the broad spectrum antifungal and anti-oomycete compound, oocydin A. PMID:23012376
Genome sequence of Reyranella massiliensis, a bacterium associated with amoebae. PMID:23012280
Proteome variation among Filifactor alocis strains. PMID:23008013
Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat. PMID:22989011
Prediction of protein domain boundaries from inverse covariances. PMID:22987736
Recent duplications drive rapid diversification of trypsin genes in 12 Drosophila. PMID:22987293
Effects of MACPF/CDC proteins on lipid membranes. PMID:22983385
Structure and location of the regulatory β subunits in the (αβγδ)4 phosphorylase kinase complex. PMID:22969083
Hydrophobic contributions to the membrane docking of synaptotagmin 7 C2A domain: mechanistic contrast between isoforms 1 and 7. PMID:22966849
Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective. PMID:22966151
SANS: high-throughput retrieval of protein sequences allowing 50% mismatches. PMID:22962464
Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding. PMID:22962462
DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders. PMID:22962312
Characterization of a viral synergism in the monocot Brachypodium distachyon reveals distinctly altered host molecular processes associated with disease. PMID:22961132
RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. PMID:22960373
Phylogenetic and functional metagenomic profiling for assessing microbial biodiversity in environmental monitoring. PMID:22952724
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
Draft genome sequence of Brevibacterium massiliense strain 541308T. PMID:22933772
Genome sequence of Rickettsia conorii subsp. israelensis, the agent of Israeli spotted fever. PMID:22933760
Draft genome sequence of Actinomyces massiliensis strain 4401292T. PMID:22933754
Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima. PMID:22925190
Characterization of novel phages isolated in coagulase-negative staphylococci reveals evolutionary relationships with Staphylococcus aureus phages. PMID:22923589
Identification of Cj1051c as a major determinant for the restriction barrier of Campylobacter jejuni strain NCTC11168. PMID:22923403
EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes. PMID:22923291
Evolution of the FGF Gene Family. PMID:22919541
Human more complex than mouse at cellular level. PMID:22911852
Multidomain Carbohydrate-binding Proteins Involved in Bacteroides thetaiotaomicron Starch Metabolism. PMID:22910908
Minireview: progress and challenges in proteomics data management, sharing, and integration. PMID:22902541
Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data. PMID:22891638
Genome sequence of Rickettsia conorii subsp. caspia, the agent of Astrakhan fever. PMID:22887666
Cardiac mitochondrial matrix and respiratory complex protein phosphorylation. PMID:22886415
Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes. PMID:22882546
Relating the disease mutation spectrum to the evolution of the cystic fibrosis transmembrane conductance regulator (CFTR). PMID:22879944
Alternative protein-protein interfaces are frequent exceptions. PMID:22876170
Autoinhibition of the formin Cappuccino in the absence of canonical autoinhibitory domains. PMID:22875983
Comparison of transcript profiles in different life stages of the nematode Globodera pallida under different host potato genotypes. PMID:22863280
Exploring metazoan evolution through dynamic and holistic changes in protein families and domains. PMID:22862991
Diversity in the protein N-glycosylation pathways within the Campylobacter genus. PMID:22859570
A BCAM0223 mutant of Burkholderia cenocepacia is deficient in hemagglutination, serum resistance, adhesion to epithelial cells and virulence. PMID:22848588
The Arabidopsis HEI10 is a new ZMM protein related to Zip3. PMID:22844245
Complete genome sequence of Croceibacter bacteriophage P2559S. PMID:22843867
Complete genome sequence of Marinomonas bacteriophage P12026. PMID:22843865
Activity of the osmotically regulated yqiHIK promoter from Bacillus subtilis is controlled at a distance. PMID:22843846
State of the art in silico tools for the study of signaling pathways in cancer. PMID:22837650
Cofactor binding protects flavodoxin against oxidative stress. PMID:22829943
Crystal structure of LpxK, the 4'-kinase of lipid A biosynthesis and atypical P-loop kinase functioning at the membrane interface. PMID:22826246
Genome reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids. PMID:22821013
Predictive sequence analysis of the Candidatus Liberibacter asiaticus proteome. PMID:22815919
Complete genome sequence of Geobacillus thermoglucosidans TNO-09.020, a thermophilic sporeformer associated with a dairy-processing environment. PMID:22815439
Template-based protein structure modeling using the RaptorX web server. PMID:22814390
The structure of the BfrB-Bfd complex reveals protein-protein interactions enabling iron release from bacterioferritin. PMID:22812654
Comparative genomic and transcriptional analyses of CRISPR systems across the genus Pyrobaculum. PMID:22811677
Endosomal crosstalk: meeting points for signaling pathways. PMID:22796207
Cysteine peptidases and their inhibitors in Tetranychus urticae: a comparative genomic approach. PMID:22784002
Functional assignment of metagenomic data: challenges and applications. PMID:22772835
ProteinHistorian: tools for the comparative analysis of eukaryote protein origin. PMID:22761559
Structure of the signal transduction protein TRAP (target of RNAIII-activating protein). PMID:22750855
Conserved rules govern genetic interaction degree across species. PMID:22747640
Cloning, expression and characterization of an aryl-alcohol dehydrogenase from the white-rot fungus Phanerochaete chrysosporium strain BKM-F-1767. PMID:22742413
General secretion signal for the mycobacterial type VII secretion pathway. PMID:22733768
Structure of the sensor domain of Mycobacterium tuberculosis PknH receptor kinase reveals a conserved binding cleft. PMID:22727744
Engineering ecosystems and synthetic ecologies. PMID:22722235
ChromoHub: a data hub for navigators of chromatin-mediated signalling. PMID:22718786
The immune gene repertoire of an important viral reservoir, the Australian black flying fox. PMID:22716473
N-acetylgalactosamine utilization pathway and regulon in proteobacteria: genomic reconstruction and experimental characterization in Shewanella. PMID:22711537
NMR structure of lipoprotein YxeF from Bacillus subtilis reveals a calycin fold and distant homology with the lipocalin Blc from Escherichia coli. PMID:22693626
MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates. PMID:22689643
CombFunc: predicting protein function using heterogeneous data sources. PMID:22641853
Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. PMID:22638584
Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass. PMID:22636774
Activation of the carbon concentrating mechanism by CO2 deprivation coincides with massive transcriptional restructuring in Chlamydomonas reinhardtii. PMID:22634764
The use of evolutionary patterns in protein annotation. PMID:22633559
Genome sequence of Rickettsia conorii subsp. indica, the agent of Indian tick typhus. PMID:22628514
Genome sequence of Diplorickettsia massiliensis, an emerging Ixodes ricinus-associated human pathogen. PMID:22628513
Structural genomics plucks high-hanging membrane proteins. PMID:22622032
Automated identification of binding sites for phosphorylated ligands in protein structures. PMID:22619105
Genome-wide identification and in silico analysis of poplar peptide deformylases. PMID:22606033
Bioinformatics opportunities for identification and study of medicinal plants. PMID:22589384
The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. PMID:22588877
Three-dimensional structures of membrane proteins from genomic sequencing. PMID:22579045
Complete genome sequence of the giant Pseudomonas phage Lu11. PMID:22570243
Structural study of MCPIP1 N-terminal conserved domain reveals a PIN-like RNase. PMID:22561375
Two-component signal transduction in Corynebacterium glutamicum and other corynebacteria: on the way towards stimuli and targets. PMID:22539022
Genomic comparison of Rickettsia helvetica and other Rickettsia species. PMID:22535934
Sequence fingerprints of enzyme specificities from the glycoside hydrolase family GH57. PMID:22527043
Abberent expression analysis of LMNA gene in hutchinson-gilford progeria syndrome. PMID:22493523
Structure of the Plasmodium 6-cysteine s48/45 domain. PMID:22493233
Genome sequence of "Rickettsia sibirica subsp. mongolitimonae". PMID:22493199
Sequence and annotation of Rickettsia sibirica sibirica genome. PMID:22493192
Sequence and structure relationships within von Willebrand factor. PMID:22490677
SS18 together with animal-specific factors defines human BAF-type SWI/SNF complexes. PMID:22442726
AntiFam: a tool to help identify spurious ORFs in protein annotation. PMID:22434837
Role of ATG8 and autophagy in programmed nuclear degradation in Tetrahymena thermophila. PMID:22366125
A classification scoring schema to validate protein interactors. PMID:22359432
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:22144685
Making your database available through Wikipedia: the pros and cons. PMID:22144683 -
The Pfam protein families database
PubMed citations: 1640.
1640 articles citing: The Pfam protein families database
Exploring the SiCCT Gene Family and Its Role in Heading Date in Foxtail Millet. PMID:35755676
Genome-Wide Identification and Expression Pattern Analysis of KNOX Gene Family in Orchidaceae. PMID:35712569
Comparative Transcriptomics and Metabolites Analysis of Two Closely Related Euphorbia Species Reveal Environmental Adaptation Mechanism and Active Ingredients Difference. PMID:35712557
HDACs Gene Family Analysis of Eight Rosaceae Genomes Reveals the Genomic Marker of Cold Stress in Prunus mume. PMID:35682633
Analysis of the β-Glucosidase Family Reveals Genes Involved in the Lignification of Stone Cells in Chinese White Pear (Pyrus bretschneideri Rehd.). PMID:35620693
Genome-wide identification, characterization of expansin gene family of banana and their expression pattern under various stresses. PMID:35463044
Snake Venomics: Fundamentals, Recent Updates, and a Look to the Next Decade. PMID:35448856
Genome-wide analysis and functional characterization of CHYR gene family associated with abiotic stress tolerance in bread wheat (Triticum aestivum L.). PMID:35443615
Cisplatin resistance-related multi-omics differences and the establishment of machine learning models. PMID:35410350
Mutations in PpAGO3 Lead to Enhanced Virulence of Phytophthora parasitica by Activation of 25-26 nt sRNA-Associated Effector Genes. PMID:35401482
Genome-Wide Analysis of Late Embryogenesis Abundant Protein Gene Family in Vigna Species and Expression of VrLEA Encoding Genes in Vigna glabrescens Reveal Its Role in Heat Tolerance. PMID:35392521
Characterizing the oral and distal gut microbiota of the threatened southern sea otter (Enhydra lutris nereis) to enhance conservation practice. PMID:35382031
Partially Resistant Avocado Rootstock Dusa® Shows Prolonged Upregulation of Nucleotide Binding-Leucine Rich Repeat Genes in Response to Phytophthora cinnamomi Infection. PMID:35360305
Bulinus truncatus transcriptome - a resource to enable molecular studies of snail and schistosome biology. PMID:35284899
Identification of TIFY gene family in walnut and analysis of its expression under abiotic stresses. PMID:35255828
Isolation, Characterization and Draft Genome Analysis of Bacteriophages Infecting Acidovorax citrulli. PMID:35185829
Transcription Factor RrANT1 of Rosa rugosa Positively Regulates Flower Organ Size in Petunia hybrida. PMID:35163160
AU-Rich Element RNA Binding Proteins: At the Crossroads of Post-Transcriptional Regulation and Genome Integrity. PMID:35008519
Physiological, Biochemical and Transcriptomic Analysis of the Aerial Parts (Leaf-Blade and Petiole) of Asarum sieboldii Responding to Drought Stress. PMID:34948197
High Molecular Weight Kininogen: A Review of the Structural Literature. PMID:34948166
Phylogenetic Analysis with Prediction of Cofactor or Ligand Binding for Pseudomonas aeruginosa PAS and Cache Domains. PMID:34937179
Unique roles of vaginal Megasphaera phylotypes in reproductive health. PMID:34898422
Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance. PMID:34880890
Recurrent expansions of B30.2-associated immune receptor families in fish. PMID:34850255
Integrative genome, transcriptome, microRNA, and degradome analysis of water dropwort (Oenanthe javanica) in response to water stress. PMID:34848704
Trends in the Application of "Omics" to Ecotoxicology and Stress Ecology. PMID:34680873
AtPGAP1 functions as a GPI inositol-deacylase required for efficient transport of GPI-anchored proteins. PMID:34618080
The genomic basis of army ant chemosensory adaptations. PMID:34582590
Full-length transcriptome analysis of Spodoptera frugiperda larval brain reveals detoxification genes. PMID:34513339
Multistep Signaling in Nature: A Close-Up of Geobacter Chemotaxis Sensing. PMID:34445739
Comparison of differential expression genes in ovaries and testes of Pearlscale angelfish Centropyge vrolikii based on RNA-Seq analysis. PMID:34415453
Genome-wide identification of alcohol dehydrogenase (ADH) gene family under waterlogging stress in wheat (Triticum aestivum). PMID:34386306
First Evidence of Function for Schistosoma japonicumriok-1 and RIOK-1. PMID:34358012
Evaluation of Indigenous Olive Biocontrol Rhizobacteria as Protectants against Drought and Salt Stress. PMID:34204989
catRAPID omics v2.0: going deeper and wider in the prediction of protein-RNA interactions. PMID:34086933
Genome-Wide Analysis of Potassium Channel Genes in Rice: Expression of the OsAKT and OsKAT Genes under Salt Stress. PMID:34065373
New Insights Into Structure and Function of TIFY Genes in Zea mays and Solanum lycopersicum: A Genome-Wide Comprehensive Analysis. PMID:34054921
The Sugar Transporter family in wheat (Triticum aestivum. L): genome-wide identification, classification, and expression profiling during stress in seedlings. PMID:33987032
The cytochrome P450 (CYP) superfamily in cnidarians. PMID:33972594
Anaerobic gut fungi are an untapped reservoir of natural products. PMID:33906945
A multi-omics approach to lignocellulolytic enzyme discovery reveals a new ligninase activity from Parascedosporium putredinis NO1. PMID:33903229
Activation mechanism of a small prototypic Rec-GGDEF diguanylate cyclase. PMID:33846343
Genome-wide comparative analysis of Mg transporter gene family between Triticum turgidum and Camelina sativa. PMID:33783656
Use of Mathematical Methods for the Biosafety Assessment of Agricultural Crops. PMID:33727728
Gene expression for secondary metabolite biosynthesis in hop (Humulus lupulus L.) leaf lupulin glands exposed to heat and low-water stress. PMID:33664420
Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika. PMID:33619328
ELIHKSIR Web Server: Evolutionary Links Inferred for Histidine Kinase Sensors Interacting with Response Regulators. PMID:33573110
Novel Two-Component System-Like Elements Reveal Functional Domains Associated with Restriction-Modification Systems and paraMORC ATPases in Bacteria. PMID:33565597
Genome-wide identification, evolution, expression, and alternative splicing profiles of peroxiredoxin genes in cotton. PMID:33552724
Genera specific distribution of DEAD-box RNA helicases in cyanobacteria. PMID:33539277
Genomic Insights Into the Lifestyles of Thaumarchaeota Inside Sponges. PMID:33537022
Complete Genome Sequencing of Acinetobacter baumannii AC1633 and Acinetobacter nosocomialis AC1530 Unveils a Large Multidrug-Resistant Plasmid Encoding the NDM-1 and OXA-58 Carbapenemases. PMID:33504662
Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics. PMID:33482715
Insights into structure and dynamics of extracellular domain of Toll-like receptor 5 in Cirrhinus mrigala (mrigala): A molecular dynamics simulation approach. PMID:33444377
The Dfam community resource of transposable element families, sequence models, and genome annotations. PMID:33436076
Origins and Stepwise Expansion of R2R3-MYB Transcription Factors for the Terrestrial Adaptation of Plants. PMID:33424877
An Educational Bioinformatics Project to Improve Genome Annotation. PMID:33365016
CheckV assesses the quality and completeness of metagenome-assembled viral genomes. PMID:33349699
Genome-Wide Analysis of the Cyclin Gene Family and Their Expression Profile in Medicago truncatula. PMID:33322339
Acinetobacter Plasmids: Diversity and Development of Classification Strategies. PMID:33304332
The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses. PMID:33297327
The hypothetical periplasmic protein PA1624 from Pseudomonas aeruginosa folds into a unique two-domain structure. PMID:33263573
Leaf shape in Populus tremula is a complex, omnigenic trait. PMID:33209260
HpeNet: Co-expression Network Database for de novo Transcriptome Assembly of Paeonia lactiflora Pall. PMID:33193666
Genome-enabled insights into the biology of thrips as crop pests. PMID:33070780
Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria. PMID:32974097
Genome-Wide Characterization, Evolution, and Expression Analysis of the Leucine-Rich Repeat Receptor-Like Protein Kinase (LRR-RLK) Gene Family in Medicago truncatula. PMID:32899802
Structural Characterization of the Essential Cell Division Protein FtsE and Its Interaction with FtsX in Streptococcus pneumoniae. PMID:32873757
PINCER: improved CRISPR/Cas9 screening by efficient cleavage at conserved residues. PMID:32821942
A high-quality sponge gourd (Luffa cylindrica) genome. PMID:32821411
Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs. PMID:32753684
Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont, Basidiobolus. PMID:32727924
Positive Selection and Gene Expression Analyses from Salivary Glands Reveal Discrete Adaptations within the Ecologically Diverse Bat Family Phyllostomidae. PMID:32697843
Genome-wide identification and transcript profiles of walnut heat stress transcription factor involved in abiotic stress. PMID:32650719
A redox-active switch in fructosamine-3-kinases expands the regulatory repertoire of the protein kinase superfamily. PMID:32636308
Transcriptome, Spliceosome and Editome Expression Patterns of the Porcine Endometrium in Response to a Single Subclinical Dose of Salmonella Enteritidis Lipopolysaccharide. PMID:32545766
Differential gene expression in response to water deficit in leaf and root tissues of soybean genotypes with contrasting tolerance profiles. PMID:32478791
Genome-wide identification and characterization of TCP family genes in Brassica juncea var. tumida. PMID:32461831
Chloroplast development at low temperature requires the pseudouridine synthase gene TCD3 in rice. PMID:32444695
Genetic and Clinical Heterogeneity in Thirteen New Cases with Aceruloplasminemia. Atypical Anemia as a Clue for an Early Diagnosis. PMID:32235485
Adjustment of photosynthetic activity to drought and fluctuating light in wheat. PMID:32176335
Genome-wide analysis of WRKY transcription factors in Aquilaria sinensis (Lour.) Gilg. PMID:32080225
Coevolutionary Analysis of Protein Subfamilies by Sequence Reweighting. PMID:32002010
Horizontally Acquired Quorum-Sensing Regulators Recruited by the PhoP Regulatory Network Expand the Host Adaptation Repertoire in the Phytopathogen Pectobacterium brasiliense. PMID:31992632
The round goby genome provides insights into mechanisms that may facilitate biological invasions. PMID:31992286
A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize. PMID:31891625
Hybrid histidine kinase activation by cyclic di-GMP-mediated domain liberation. PMID:31882446
Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis). PMID:31878322
A large self-transmissible resistance plasmid from Nigeria contains genes that ameliorate a carrying cost. PMID:31873110
A Depletion of Stop Codons in lincRNA is Owing to Transfer of Selective Constraint from Coding Sequences. PMID:31841162
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 Analysis of the YABBY Gene Family of Bienertia sinuspersici, a Single-Cell C4 Plant. PMID:31766767
O-antigen biosynthesis gene clusters of Escherichia albertii: their diversity and similarity to Escherichia coli gene clusters and the development of an O-genotyping method. PMID:31738701
Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.). PMID:31651257
Genome-wide identification of and functional insights into the late embryogenesis abundant (LEA) gene family in bread wheat (Triticum aestivum). PMID:31527624
Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes. PMID:31477173
Large-scale identification and functional analysis of NLR genes in blast resistance in the Tetep rice genome sequence. PMID:31451649
Regulation of phosphoribosyl ubiquitination by a calmodulin-dependent glutamylase. PMID:31330531
Gains and losses of metabolic function inferred from a phylotranscriptomic analysis of algae. PMID:31324835
Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment. PMID:31293610
Sharing Programming Resources Between Bio* Projects. PMID:31278684
Genome-wide identification and functional analysis of oleosin genes in Brassica napus L. PMID:31272381
Genome-Wide Identification and Expression Analyses of the bZIP Transcription Factor Genes in moso bamboo (Phyllostachys edulis). PMID:31060272
Adaptive dif Modules in Permafrost Strains of Acinetobacter lwoffii and Their Distribution and Abundance Among Present Day Acinetobacter Strains. PMID:30984151
Selection pressure causes differentiation of the SPL gene family in the Juglandaceae. PMID:30976906
Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. PMID:30935422
Isolation and Genomic Characterization of an Acinetobacter johnsonii Bacteriophage AJO2 From Bulking Activated Sludge. PMID:30873130
Temporal variability of diazotroph community composition in the upwelling region off NW Iberia. PMID:30842510
Grammar of protein domain architectures. PMID:30733291
Comparative transcriptome analysis reveals new molecular pathways for cucumber genes related to sex determination. PMID:30719568
Genome-Wide Analysis of Domain-Swap Predicted Products in the Genome of Anti-Stress Medicinal Plant: Ocimum tenuiflorum. PMID:30692846
Comparative transcriptomics in Leishmania braziliensis: disclosing differential gene expression of coding and putative noncoding RNAs across developmental stages. PMID:30689499
Complete Genome Sequence of Lactococcus lactis subsp. cremoris 3107, Host for the Model Lactococcal P335 Bacteriophage TP901-1. PMID:30687843
Genome-scale identification, classification, and tissue specific expression analysis of late embryogenesis abundant (LEA) genes under abiotic stress conditions in Sorghum bicolor L. PMID:30650107
Genetic basis for the establishment of endosymbiosis in Paramecium. PMID:30647459
Comparative Analysis of Genomic Island Prediction Tools. PMID:30631340
Secretome analysis of Strongyloides venezuelensis parasitic stages reveals that soluble and insoluble proteins are involved in its parasitism. PMID:30626426
Expansion and Divergence of Argonaute Genes in the Oomycete Genus Phytophthora. PMID:30555430
Computational genome-wide identification of heat shock protein genes in the bovine genome. PMID:30542619
The draft genomes of five agriculturally important African orphan crops. PMID:30535374
A map of constrained coding regions in the human genome. PMID:30531870
Transcriptome and Comparative Genomics Analyses Reveal New Functional Insights on Key Determinants of Pathogenesis and Interbacterial Competition in Pectobacterium and Dickeya spp. PMID:30413477
Comparative genomics of the major parasitic worms. PMID:30397333
Mining Late Embryogenesis Abundant (LEA) Family Genes in Cleistogenes songorica, a Xerophyte Perennial Desert Plant. PMID:30388835
Strategies for Pathway Analysis Using GWAS and WGS Data. PMID:30387919
Deciphering the structure of the condensin protein complex. PMID:30385633
TCP Transcription Factors in Moso Bamboo (Phyllostachys edulis): Genome-Wide Identification and Expression Analysis. PMID:30344527
Complete genome sequence of the halophile bacterium Kushneria konosiri X49T, isolated from salt-fermented Konosirus punctatus. PMID:30305867
Extremophiles as a Model of a Natural Ecosystem: Transcriptional Coordination of Genes Reveals Distinct Selective Responses of Plants Under Climate Change Scenarios. PMID:30283484
Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia. PMID:30177915
Phylogenomics Reveal the Dynamic Evolution of Fungal Nitric Oxide Reductases and Their Relationship to Secondary Metabolism. PMID:30165640
Effect of SrtA on Interspecies Adherence of Oral Bacteria. PMID:30074166
Identification of WRKY Gene Family from Dimocarpus longan and Its Expression Analysis during Flower Induction and Abiotic Stress Responses. PMID:30044387
Genome sequence and genetic transformation of a widely distributed and cultivated poplar. PMID:30044051
Protein moonlighting elucidates the essential human pathway catalyzing lipoic acid assembly on its cognate enzymes. PMID:29987032
Mutational analysis of the pro-peptide of a marine intracellular subtilisin protease supports its role in inhibition. PMID:29907987
Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes. PMID:29898658
Development of Versatile Vectors for Heterologous Expression in Bacillus. PMID:29875331
Transcriptome Analysis Reveals Dynamic Gene Expression Profiles in Porcine Alveolar Macrophages in Response to the Chinese Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus. PMID:29854728
Whole-Genome Sequencing and Comparative Genome Analysis Provided Insight into the Predatory Features and Genetic Diversity of Two Bdellovibrio Species Isolated from Soil. PMID:29850478
Assessment of an Organ-Specific de Novo Transcriptome of the Nematode Trap-Crop, Solanum sisymbriifolium. PMID:29769290
Distribution Patterns of Polyphosphate Metabolism Pathway and Its Relationships With Bacterial Durability and Virulence. PMID:29755430
Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant. PMID:29722814
Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups. PMID:29717207
A Possible Trifunctional β-Carotene Synthase Gene Identified in the Draft Genome of Aurantiochytrium sp. Strain KH105. PMID:29642531
Multispecies reconstructions uncover widespread conservation, and lineage-specific elaborations in eukaryotic mRNA metabolism. PMID:29561870
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
In silico comparative analysis of GGDEF and EAL domain signaling proteins from the Azospirillum genomes. PMID:29523074
Membrane Topology and Heme Binding of the Histidine Kinases HrrS and ChrS in Corynebacterium glutamicum. PMID:29479345
Reconstruction of the sialylation pathway in the ancestor of eukaryotes. PMID:29440651
Dynamics of venom composition across a complex life cycle. PMID:29424690
Novel ATP-cone-driven allosteric regulation of ribonucleotide reductase via the radical-generating subunit. PMID:29388911
Cancer-Associated Long Noncoding RNA SMRT-2 Controls Epidermal Differentiation. PMID:29360484
Identification and expression analyses of WRKY genes reveal their involvement in growth and abiotic stress response in watermelon (Citrullus lanatus). PMID:29338040
Genome Wide Mapping of Peptidases in Rhodnius prolixus: Identification of Protease Gene Duplications, Horizontally Transferred Proteases and Analysis of Peptidase A1 Structures, with Considerations on Their Role in the Evolution of Hematophagy in Triatominae. PMID:29326597
Cell-type-resolved alternative splicing patterns in mouse liver. PMID:29325017
Collagen-Induced Arthritis Analysis in Rhbdf2 Knockout Mouse. PMID:29223140
The Sit-and-Wait Hypothesis in Bacterial Pathogens: A Theoretical Study of Durability and Virulence. PMID:29209284
Clinical and molecular characterization of KCNT1-related severe early-onset epilepsy. PMID:29196579
Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate. PMID:29167704
Genome-wide identification and characterization of GRAS transcription factors in tomato (Solanum lycopersicum). PMID:29134140
Deep RNA Sequencing Uncovers a Repertoire of Human Macrophage Long Intergenic Noncoding RNAs Modulated by Macrophage Activation and Associated With Cardiometabolic Diseases. PMID:29133519
Mycobacterium tuberculosis Rv3651 is a triple sensor-domain protein. PMID:29119630
Assessment of vocation of rifabutin and rifapentine in replace of rifampcin in drug resistance leprosy patients: a molecular simulation study. PMID:29071280
Synbiological systems for complex natural products biosynthesis. PMID:29062947
The Conserved RNA Exonuclease Rexo5 Is Required for 3' End Maturation of 28S rRNA, 5S rRNA, and snoRNAs. PMID:29045842
Genome-wide identification and expression analyses of the homeobox transcription factor family during ovule development in seedless and seeded grapes. PMID:28974771
Relating protein functional diversity to cell type number identifies genes that determine dynamic aspects of chromatin organisation as potential contributors to organismal complexity. PMID:28945800
De novo Assembly of the Camellia nitidissima Transcriptome Reveals Key Genes of Flower Pigment Biosynthesis. PMID:28936220
Genome-wide identification of the MADS-box transcription factor family in pear (Pyrus bretschneideri) reveals evolution and functional divergence. PMID:28924499
Novel Organelles with Elements of Bacterial and Eukaryotic Secretion Systems Weaponize Parasites of Drosophila. PMID:28889977
Draft genome sequences of two opportunistic pathogenic strains of Staphylococcus cohnii isolated from human patients. PMID:28878860
Molecular characterization of transport lectin vesicular integral membrane protein 36 kDa (VIP36) in the life cycle of Schistosoma mansoni. PMID:28840376
A novel lipoate attachment enzyme is shared by Plasmodium and Chlamydia species. PMID:28836704
Genome-wide identification of CBL family and expression analysis of CBLs in response to potassium deficiency in cotton. PMID:28828254
Immunohistochemical null-phenotype for mismatch repair proteins in colonic carcinoma associated with concurrent MLH1 hypermethylation and MSH2 somatic mutations. PMID:28819720
The hnRNP Q-like gene is retroinserted into the B chromosomes of the cichlid fish Astatotilapia latifasciata. PMID:28776210
Conserved Transcriptional Responses to Nutrient Stress in Bloom-Forming Algae. PMID:28769884
Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept. PMID:28729861
WHITE STRIPE LEAF4 Encodes a Novel P-Type PPR Protein Required for Chloroplast Biogenesis during Early Leaf Development. PMID:28694820
Segmental duplications: evolution and impact among the current Lepidoptera genomes. PMID:28683762
Analysis of the grape (Vitis vinifera L.) thaumatin-like protein (TLP) gene family and demonstration that TLP29 contributes to disease resistance. PMID:28655869
YSK2 Type Dehydrin (SbDhn1) from Sorghum bicolor Showed Improved Protection under High Temperature and Osmotic Stress Condition. PMID:28611819
Identifying pathogenicity of human variants via paralog-based yeast complementation. PMID:28542158
Whole-Genome Identification and Expression Pattern of the Vicinal Oxygen Chelate Family in Rapeseed (Brassica napus L.). PMID:28536594
Characterization of Cytosine Methylation and the DNA Methyltransferases of Toxoplasma gondii. PMID:28529454
Distribution and cluster analysis of predicted intrinsically disordered protein Pfam domains. PMID:28516017
The Biomphalaria glabrata DNA methylation machinery displays spatial tissue expression, is differentially active in distinct snail populations and is modulated by interactions with Schistosoma mansoni. PMID:28510608
Structural conservation of the PIN domain active site across all domains of life. PMID:28508407
Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. PMID:28499419
Identification of a Novel Alternative Splicing Variant of VvPMA1 in Grape Root under Salinity. PMID:28484478
RNA-binding proteins and their role in the regulation of gene expression in Trypanosoma cruzi and Saccharomyces cerevisiae. PMID:28463381
The Nucleoporin Nup2 Contains a Meiotic-Autonomous Region that Promotes the Dynamic Chromosome Events of Meiosis. PMID:28455351
Bioinformatic and expression analyses on carotenoid dioxygenase genes in fruit development and abiotic stress responses in Fragaria vesca. PMID:28444444
Comparative genomic analysis of SET domain family reveals the origin, expansion, and putative function of the arthropod-specific SmydA genes as histone modifiers in insects. PMID:28444351
Oncodomains: A protein domain-centric framework for analyzing rare variants in tumor samples. PMID:28426665
Domain prediction with probabilistic directional context. PMID:28407137
Identification and expression analyses of the alanine aminotransferase (AlaAT) gene family in poplar seedlings. PMID:28378825
Exploring the genomic diversity of black yeasts and relatives (Chaetothyriales, Ascomycota). PMID:28348446
The Human CCHC-type Zinc Finger Nucleic Acid-Binding Protein Binds G-Rich Elements in Target mRNA Coding Sequences and Promotes Translation. PMID:28329689
Genome-wide identification of the TIFY gene family in three cultivated Gossypium species and the expression of JAZ genes. PMID:28186193
Red Algal Mitochondrial Genomes Are More Complete than Previously Reported. PMID:28175279
Identification and expression analysis of the apple (Malus × domestica) basic helix-loop-helix transcription factor family. PMID:28174429
Transcriptome analysis reveals rod/cone photoreceptor specific signatures across mammalian retinas. PMID:28172828
GExplore 1.4: An expanded web interface for queries on Caenorhabditis elegans protein and gene function. PMID:28090394
Bioactive Nutrients and Nutrigenomics in Age-Related Diseases. PMID:28075340
Trypanosome outer kinetochore proteins suggest conservation of chromosome segregation machinery across eukaryotes. PMID:28034897
Burkholderia pseudomallei type III secreted protein BipC: role in actin modulation and translocation activities required for the bacterial intracellular lifecycle. PMID:28028452
A Two-component NADPH Oxidase (NOX)-like System in Bacteria Is Involved in the Electron Transfer Chain to the Methionine Sulfoxide Reductase MsrP. PMID:28028176
Diazotroph Diversity in the Sea Ice, Melt Ponds, and Surface Waters of the Eurasian Basin of the Central Arctic Ocean. PMID:27933047
DHCR24 associates strongly with the endoplasmic reticulum beyond predicted membrane domains: implications for the activities of this multi-functional enzyme. PMID:27919032
xHMMER3x2: Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation. PMID:27894340
Bioinformatic Identification of Rare Codon Clusters (RCCs) in HBV Genome and Evaluation of RCCs in Proteins Structure of Hepatitis B Virus. PMID:27882067
NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors. PMID:27880916
DNA Barcodes for the Northern European Tachinid Flies (Diptera: Tachinidae). PMID:27814365
Genome-wide identification and characterization of TIFY family genes in Moso Bamboo (Phyllostachys edulis) and expression profiling analysis under dehydration and cold stresses. PMID:27812419
RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants. PMID:27806688
Complex Evolutionary Dynamics of Massively Expanded Chemosensory Receptor Families in an Extreme Generalist Chelicerate Herbivore. PMID:27797949
Resistance of Permafrost and Modern Acinetobacter lwoffii Strains to Heavy Metals and Arsenic Revealed by Genome Analysis. PMID:27795957
Biochemical pathways supporting beta-lactam biosynthesis in the springtail Folsomia candida. PMID:27793835
MET-activating Residues in the B-repeat of the Listeria monocytogenes Invasion Protein InlB. PMID:27789707
LINEs between Species: Evolutionary Dynamics of LINE-1 Retrotransposons across the Eukaryotic Tree of Life. PMID:27702814
Evolution of Protein Domain Repeats in Metazoa. PMID:27671125
Differential Communications between Fungi and Host Plants Revealed by Secretome Analysis of Phylogenetically Related Endophytic and Pathogenic Fungi. PMID:27658302
The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T). PMID:27651857
A Primary Sequence Analysis of the ARGONAUTE Protein Family in Plants. PMID:27635128
Comparative Genomics of Acetobacterpasteurianus Ab3, an Acetic Acid Producing Strain Isolated from Chinese Traditional Rice Vinegar Meiguichu. PMID:27611790
A Variable Active Site Residue Influences the Kinetics of Response Regulator Phosphorylation and Dephosphorylation. PMID:27589219
Repeated Duplication of Argonaute2 Is Associated with Strong Selection and Testis Specialization in Drosophila. PMID:27535930
Global transcriptional analysis suggests Lasiodiplodia theobromae pathogenicity factors involved in modulation of grapevine defensive response. PMID:27514986
Metazoan evolution of the armadillo repeat superfamily. PMID:27497926
GPU-Acceleration of Sequence Homology Searches with Database Subsequence Clustering. PMID:27482905
Counting animal species with DNA barcodes: Canadian insects. PMID:27481785
Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence. PMID:27472895
Genome-Wide Prediction and Analysis of 3D-Domain Swapped Proteins in the Human Genome from Sequence Information. PMID:27467780
Systematic Investigation of FLOWERING LOCUS T-Like Poaceae Gene Families Identifies the Short-Day Expressed Flowering Pathway Gene, TaFT3 in Wheat (Triticum aestivum L.). PMID:27458461
A Combined Pathway and Regional Heritability Analysis Indicates NETRIN1 Pathway Is Associated With Major Depressive Disorder. PMID:27422368
Complete Genome Sequence of Bacillus velezensis CBMB205, a Phosphate-Solubilizing Bacterium Isolated from the Rhizoplane of Rice in the Republic of Korea. PMID:27417835
Structural Determinants of Sleeping Beauty Transposase Activity. PMID:27401040
A Combined Computational and Genetic Approach Uncovers Network Interactions of the Cyanobacterial Circadian Clock. PMID:27381914
SARI inhibits angiogenesis and tumour growth of human colon cancer through directly targeting ceruloplasmin. PMID:27353863
The Gearbox of the Bacterial Flagellar Motor Switch. PMID:27345932
Complete Genome Sequence of Dyella thiooxydans ATSB10, a Thiosulfate-Oxidizing Bacterium Isolated from Sunflower Fields in South Korea. PMID:27340060
Cloning, molecular characterization, and expression analysis of the unc45 myosin chaperone b(unc45b)gene of grass carp (Ctenopharyngodon idellus). PMID:27334505
A Large and Phylogenetically Diverse Class of Type 1 Opsins Lacking a Canonical Retinal Binding Site. PMID:27327432
Long noncoding RNAs: Central to nervous system development. PMID:27296516
De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis. PMID:27292122
Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences. PMID:27289096
Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera. PMID:27288478
DUF3380 Domain from a Salmonella Phage Endolysin Shows Potent N-Acetylmuramidase Activity. PMID:27287318
Environmental Breviatea harbour mutualistic Arcobacter epibionts. PMID:27279223
Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements. PMID:27194050
Phosphorylation of spore coat proteins by a family of atypical protein kinases. PMID:27185916
Identification of a Non-Pentapeptide Region Associated with Rapid Mycobacterial Evolution. PMID:27149271
Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins. PMID:27131381
Positively charged residues within the MYO19 MyMOMA domain are essential for proper localization of MYO19 to the mitochondrial outer membrane. PMID:27126804
Next Generation Sequencing Identifies Five Major Classes of Potentially Therapeutic Enzymes Secreted by Lucilia sericata Medical Maggots. PMID:27119084
The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity. PMID:27102219
Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology. PMID:27096056
Crystal Structure of the GRAS Domain of SCARECROW-LIKE7 in Oryza sativa. PMID:27081181
Identification of VPS13C as a Galectin-12-Binding Protein That Regulates Galectin-12 Protein Stability and Adipogenesis. PMID:27073999
Genome-wide identification, structural analysis and new insights into late embryogenesis abundant (LEA) gene family formation pattern in Brassica napus. PMID:27072743
Identification and characterization of histone lysine methylation modifiers in Fragaria vesca. PMID:27049067
Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms. PMID:27017967
Diverse Evolutionary Trajectories for Small RNA Biogenesis Genes in the Oomycete Genus Phytophthora. PMID:27014308
The CopC Family: Structural and Bioinformatic Insights into a Diverse Group of Periplasmic Copper Binding Proteins. PMID:27010565
Characterization of multiple sequence alignment errors using complete-likelihood score and position-shift map. PMID:26992851
Systems biology of the structural proteome. PMID:26969117
Characterization of DNA methyltransferase and demethylase genes in Fragaria vesca. PMID:26956009
Complex Formed between Intramembrane Metalloprotease SpoIVFB and Its Substrate, Pro-σK. PMID:26953342
Hologenome analysis of two marine sponges with different microbiomes. PMID:26926518
Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates. PMID:26903979
iRhoms; Its Functions and Essential Roles. PMID:26869525
Duplication and Diversification of Dipteran Argonaute Genes, and the Evolutionary Divergence of Piwi and Aubergine. PMID:26868596
Comparative phylogenetic analysis and transcriptional profiling of MADS-box gene family identified DAM and FLC-like genes in apple (Malusx domestica). PMID:26856238
Three DUF1996 Proteins Localize in Vacuoles and Function in Fungal Responses to Multiple Stresses and Metal Ions. PMID:26839279
Genome-wide analysis of CrRLK1L gene family in Gossypium and identification of candidate CrRLK1L genes related to fiber development. PMID:26833484
DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions. PMID:26827237
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
Genome Sequence and Analysis of Escherichia coli MRE600, a Colicinogenic, Nonmotile Strain that Lacks RNase I and the Type I Methyltransferase, EcoKI. PMID:26802429
SeqTools: visual tools for manual analysis of sequence alignments. PMID:26801397
Identification and Validation of Selected Universal Stress Protein Domain Containing Drought-Responsive Genes in Pigeonpea (Cajanus cajan L.). PMID:26779199
Developing of the Computer Method for Annotation of Bacterial Genes. PMID:26770195
Rsite2: an efficient computational method to predict the functional sites of noncoding RNAs. PMID:26751501
Evolutionary Ancestry of Eukaryotic Protein Kinases and Choline Kinases. PMID:26742849
Mitochondrial metabolites extend lifespan. PMID:26729005
The Pfam protein families database: towards a more sustainable future. PMID:26673716
Complete genome sequence of Salinicoccus halodurans H3B36, isolated from the Qaidam Basin in China. PMID:26634017
Comparative Phylogenomics of Pathogenic and Nonpathogenic Species. PMID:26613950
The first draft genome of the aquatic model plant Lemna minor opens the route for future stress physiology research and biotechnological applications. PMID:26609323
Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities. PMID:26579098
De Novo Assembly and Characterization of the Invasive Northern Pacific Seastar Transcriptome. PMID:26529321
AnABlast: a new in silico strategy for the genome-wide search of novel genes and fossil regions. PMID:26494834
Identification of catalytically important residues of the carotenoid 1,2-hydratases from Rubrivivax gelatinosus and Thiocapsa roseopersicina. PMID:26481619
A multi-objective optimization approach accurately resolves protein domain architectures. PMID:26458889
Light-assisted small-molecule screening against protein kinases. PMID:26457372
The language of the protein universe. PMID:26451980
Event inference in multidomain families with phylogenetic reconciliation. PMID:26451642
Identification and characterization of TIFY family genes in Brachypodium distachyon. PMID:26423998
Exploring the rice dispensable genome using a metagenome-like assembly strategy. PMID:26403182
Virus proteins similar to human proteins as possible disturbance on human pathways. PMID:26396652
Complete genome and gene expression analyses of Asaia bogorensis reveal unique responses to culture with mammalian cells as a potential opportunistic human pathogen. PMID:26358298
Dimeric interactions and complex formation using direct coevolutionary couplings. PMID:26338201
Genome-Wide Identification and Expression of Xenopus F-Box Family of Proteins. PMID:26327321
Structure of the Bacillus anthracis Sortase A Enzyme Bound to Its Sorting Signal: A FLEXIBLE AMINO-TERMINAL APPENDAGE MODULATES SUBSTRATE ACCESS. PMID:26324714
Genome-wide Identification of WRKY Genes in the Desert Poplar Populus euphratica and Adaptive Evolution of the Genes in Response to Salt Stress. PMID:26309388
How Common Is Disorder? Occurrence of Disordered Residues in Four Domains of Life. PMID:26295225
Algorithms for modeling global and context-specific functional relationship networks. PMID:26254431
Trends in genome dynamics among major orders of insects revealed through variations in protein families. PMID:26251035
C-S bond cleavage by a polyketide synthase domain. PMID:26240335
dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarity. PMID:26228544
The Genome of Winter Moth (Operophtera brumata) Provides a Genomic Perspective on Sexual Dimorphism and Phenology. PMID:26227816
Draft genome sequence of Methylibium sp. strain T29, a novel fuel oxygenate-degrading bacterial isolate from Hungary. PMID:26221420
SpirPro: A Spirulina proteome database and web-based tools for the analysis of protein-protein interactions at the metabolic level in Spirulina (Arthrospira) platensis C1. PMID:26220682
Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. PMID:26202570
Scrutinizing the immune defence inventory of Camponotus floridanus applying total transcriptome sequencing. PMID:26198742
The Orphan Nuclear Receptor TLX Is an Enhancer of STAT1-Mediated Transcription and Immunity to Toxoplasma gondii. PMID:26196739
The Enterobacterium Trabulsiella odontotermitis Presents Novel Adaptations Related to Its Association with Fungus-Growing Termites. PMID:26162887
Changes in gene expression of Prymnesium parvum induced by nitrogen and phosphorus limitation. PMID:26157435
Structure and Assembly of TP901-1 Virion Unveiled by Mutagenesis. PMID:26147978
Contact- and Protein Transfer-Dependent Stimulation of Assembly of the Gliding Motility Machinery in Myxococcus xanthus. PMID:26132848
Nmf9 Encodes a Highly Conserved Protein Important to Neurological Function in Mice and Flies. PMID:26131556
Developmentally regulated HEART STOPPER, a mitochondrially targeted L18 ribosomal protein gene, is required for cell division, differentiation, and seed development in Arabidopsis. PMID:26105995
Characterization of epidemic IncI1-Iγ plasmids harboring ambler class A and C genes in Escherichia coli and Salmonella enterica from animals and humans. PMID:26100710
Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology. PMID:26097471
Computational Analysis of Missense Variants of G Protein-Coupled Receptors Involved in the Neuroendocrine Regulation of Reproduction. PMID:26088945
Discovery of Chemosensory Genes in the Oriental Fruit Fly, Bactrocera dorsalis. PMID:26070069
Evolution of the SH3 Domain Specificity Landscape in Yeasts. PMID:26068101
Insights into the evolution of enzyme substrate promiscuity after the discovery of (βα)₈ isomerase evolutionary intermediates from a diverse metagenome. PMID:26058375
Sequence and expression analysis of the AMT gene family in poplar. PMID:26052331
Regulation of transcription factors on sexual dimorphism of fig wasps. PMID:26031454
It's more than stamp collecting: how genome sequencing can unify biological research. PMID:26003218
Most partial domains in proteins are alignment and annotation artifacts. PMID:25976240
Biochemical and Kinetic Characterization of the Eukaryotic Phosphotransacetylase Class IIa Enzyme from Phytophthora ramorum. PMID:25956919
Influence of in situ progressive N-terminal is still controversial truncation of glycogen branching enzyme in Escherichia coli DH5α on glycogen structure, accumulation, and bacterial viability. PMID:25947105
Predicting peptide-mediated interactions on a genome-wide scale. PMID:25938916
Cyclic nucleotide binding and structural changes in the isolated GAF domain of Anabaena adenylyl cyclase, CyaB2. PMID:25922789
Convergent evolution toward an improved growth rate and a reduced resistance range in Prochlorococcus strains resistant to phage. PMID:25922520
A novel RNA binding surface of the TAM domain of TIP5/BAZ2A mediates epigenetic regulation of rRNA genes. PMID:25916849
ProtoBug: functional families from the complete proteomes of insects. PMID:25911153
Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. PMID:25905672
micropan: an R-package for microbial pan-genomics. PMID:25888166
Identification of three extra-chromosomal replicons in Leptospira pathogenic strain and development of new shuttle vectors. PMID:25887950
A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes. PMID:25887443
Expression of extra-cellular levansucrase in Pseudomonas syringae is controlled by the in planta fitness-promoting metabolic repressor HexR. PMID:25886911
Retained duplicate genes in green alga Chlamydomonas reinhardtii tend to be stress responsive and experience frequent response gains. PMID:25880851
The aspartate-less receiver (ALR) domains: distribution, structure and function. PMID:25875291
Genome-wide transcriptome and expression profile analysis of Phalaenopsis during explant browning. PMID:25874455
De novo transcriptome assembly and the putative biosynthetic pathway of steroidal sapogenins of Dioscorea composita. PMID:25860891
A structure-based classification and analysis of protein domain family binding sites and their interactions. PMID:25860777
Rapid turnover of antimicrobial-type cysteine-rich protein genes in closely related Oryza genomes. PMID:25842177
Computational tools for epitope vaccine design and evaluation. PMID:25837467
A functional role of Rv1738 in Mycobacterium tuberculosis persistence suggested by racemic protein crystallography. PMID:25831534
Diversity of the expression profiles of late embryogenesis abundant (LEA) protein encoding genes in the anhydrobiotic midge Polypedilum vanderplanki. PMID:25822798
In silico screening for novel inhibitors of DNA polymerase III alpha subunit of Mycobacterium tuberculosis (MtbDnaE2, H37Rv). PMID:25811866
Protein domain-level landscape of cancer-type-specific somatic mutations. PMID:25794154
Structure and functional annotation of hypothetical proteins having putative Rubisco activase function from Vitis vinifera. PMID:25780274
The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. PMID:25765701
Genome-wide survey and expression analysis of F-box genes in chickpea. PMID:25759239
The evolutionary and functional diversity of classical and lesser-known cytoplasmic and organellar translational GTPases across the tree of life. PMID:25756599
Protein topology determines cysteine oxidation fate: the case of sulfenyl amide formation among protein families. PMID:25741692
Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples. PMID:25734684
The origin and evolution of ribonucleotide reduction. PMID:25734234
Pinpointing disease genes through phenomic and genomic data fusion. PMID:25708473
Proteasome stress responses in Schistosoma mansoni. PMID:25663105
Reinforcing the egg-timer: recruitment of novel lophotrochozoa homeobox genes to early and late development in the pacific oyster. PMID:25631164
The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4. PMID:25621826
Soybean kinome: functional classification and gene expression patterns. PMID:25614662
Genome-wide identification and comparative analysis of the heat shock transcription factor family in Chinese white pear (Pyrus bretschneideri) and five other Rosaceae species. PMID:25604453
The phage growth limitation system in Streptomyces coelicolor A(3)2 is a toxin/antitoxin system, comprising enzymes with DNA methyltransferase, protein kinase and ATPase activity. PMID:25592393
The origin of CDR H3 structural diversity. PMID:25579815
Robustness of birth-death and gain models for inferring evolutionary events. PMID:25572914
RNA helicase A activity is inhibited by oncogenic transcription factor EWS-FLI1. PMID:25564528
Subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis. PMID:25551456
EvoTol: a protein-sequence based evolutionary intolerance framework for disease-gene prioritization. PMID:25550428
UProC: tools for ultra-fast protein domain classification. PMID:25540185
Terpene synthases are widely distributed in bacteria. PMID:25535391
Sequence search and analysis of gene products containing RNA recognition motifs in the human genome. PMID:25534245
Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes. PMID:25523484
Bhageerath-H: a homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins. PMID:25521245
Low frequency of paleoviral infiltration across the avian phylogeny. PMID:25496498
Adaptive genomic structural variation in the grape powdery mildew pathogen, Erysiphe necator. PMID:25487071
Kinase domain-targeted isolation of defense-related receptor-like kinases (RLK/Pelle) in Platanus×acerifolia: phylogenetic and structural analysis. PMID:25486898
Evolution and diversity of the Ras superfamily of small GTPases in prokaryotes. PMID:25480683
Discovering co-occurring patterns and their biological significance in protein families. PMID:25474736
A systematic computational analysis of biosynthetic gene cluster evolution: lessons for engineering biosynthesis. PMID:25474254
AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics. PMID:25468931
Batf3 deficiency is not critical for the generation of CD8α⁺ dendritic cells. PMID:25468565
Identifying pathogenicity islands in bacterial pathogenomics using computational approaches. PMID:25437607
Crystal structure of the human, FIC-domain containing protein HYPE and implications for its functions. PMID:25435325
Faster sequence homology searches by clustering subsequences. PMID:25432166
Inferring meaningful communities from topology-constrained correlation networks. PMID:25409022
Early chordate origin of the vertebrate integrin αI domains. PMID:25409021
Distribution, classification, domain architectures and evolution of prolyl oligopeptidases in prokaryotic lineages. PMID:25407321
The genome of a Mongolian individual reveals the genetic imprints of Mongolians on modern human populations. PMID:25377941
A census of human RNA-binding proteins. PMID:25365966
Identification of glycoproteins secreted by wild-type Botrytis cinerea and by protein O-mannosyltransferase mutants. PMID:25305780
The stability region of the Streptomyces lividans plasmid pIJ101 encodes a DNA-binding protein recognizing a highly conserved short palindromic sequence motif. PMID:25295034
Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics. PMID:25279954
AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors. PMID:25262351
FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus. PMID:25260589
Genome-wide analysis of the GRAS gene family in Prunus mume. PMID:25245166
Widespread genome reorganization of an obligate virus mutualist. PMID:25232843
Genome-wide identification and expression analysis of NBS-encoding genes in Malus x domestica and expansion of NBS genes family in Rosaceae. PMID:25232838
A root-expressed L-phenylalanine:4-hydroxyphenylpyruvate aminotransferase is required for tropane alkaloid biosynthesis in Atropa belladonna. PMID:25228340
Alfalfa snakin-1 prevents fungal colonization and probably coevolved with rhizobia. PMID:25227589
Determination and inference of eukaryotic transcription factor sequence specificity. PMID:25215497
Ball python nidovirus: a candidate etiologic agent for severe respiratory disease in Python regius. PMID:25205093
Expression patterns and protein structure of a lipid transfer protein END1 from Arabidopsis. PMID:25204629
Evolutionary conservation and expression of human RNA-binding proteins and their role in human genetic disease. PMID:25201102
Genome sequence of the chromate-resistant bacterium Leucobacter salsicius type strain M1-8(T.). PMID:25197435
Lactic acid bacterial symbionts in honeybees - an unknown key to honey's antimicrobial and therapeutic activities. PMID:25195876
Overexpression of p49/STRAP alters cellular cytoskeletal structure and gross anatomy in mice. PMID:25183317
Comparative expression profiling reveals gene functions in female meiosis and gametophyte development in Arabidopsis. PMID:25182975
Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities. PMID:25179155
Alternatives to vitamin B1 uptake revealed with discovery of riboswitches in multiple marine eukaryotic lineages. PMID:25171333
The genome of Paenibacillus sabinae T27 provides insight into evolution, organization and functional elucidation of nif and nif-like genes. PMID:25163544
Molecular and evolutionary analysis of NEAr-iron Transporter (NEAT) domains. PMID:25153520
Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PMID:25140992
High potential source for biomass degradation enzyme discovery and environmental aspects revealed through metagenomics of Indian buffalo rumen. PMID:25136572
A novel methyltransferase from the intracellular pathogen Plasmodiophora brassicae methylates salicylic acid. PMID:25135243
A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data. PMID:25122209
Transcriptome of American oysters, Crassostrea virginica, in response to bacterial challenge: insights into potential mechanisms of disease resistance. PMID:25122115
Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection. PMID:25114242
Novel mitochondrial mutations in the ATP6 and ATP8 genes in patients with breast cancer. PMID:25110199
NAC transcription factor genes: genome-wide identification, phylogenetic, motif and cis-regulatory element analysis in pigeonpea (Cajanus cajan (L.) Millsp.). PMID:25108674
Genome-wide screening of pathogenicity islands in Mycobacterium tuberculosis based on the genomic barcode visualization. PMID:25108673
Phenotypic profiling of ABC transporter coding genes in Myxococcus xanthus. PMID:25101061
Prediction of protein-protein interaction strength using domain features with supervised regression. PMID:25093200
Modular organization and reticulate evolution of the ORF1 of Jockey superfamily transposable elements. PMID:25093042
The reduced kinome of Ostreococcus tauri: core eukaryotic signalling components in a tractable model species. PMID:25085202
NMR solution structure of the terminal immunoglobulin-like domain from the leptospira host-interacting outer membrane protein, LigB. PMID:25068811
A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. PMID:25058116
Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets. PMID:25033262
The natural history of ADP-ribosyltransferases and the ADP-ribosylation system. PMID:25027823
Genome-wide analysis of the R2R3-MYB transcription factor gene family in sweet orange (Citrus sinensis). PMID:25008995
Promiscuous and adaptable enzymes fill "holes" in the tetrahydrofolate pathway in Chlamydia species. PMID:25006229
The ubiquitous distribution of late embryogenesis abundant proteins across cell compartments in Arabidopsis offers tailored protection against abiotic stress. PMID:25005920
Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM-type α-helical structure. PMID:24997568
The domain landscape of virus-host interactomes. PMID:24991570
Solution NMR structures of immunoglobulin-like domains 7 and 12 from obscurin-like protein 1 contribute to the structural coverage of the Human Cancer Protein Interaction Network. PMID:24989974
Conserved prosegment residues stabilize a late-stage folding transition state of pepsin independently of ground states. PMID:24983988
De novo transcriptomes of a mixotrophic and a heterotrophic ciliate from marine plankton. PMID:24983246
Genome-wide identification of transcription factors and transcription-factor binding sites in oleaginous microalgae Nannochloropsis. PMID:24965723
The structure and dynamics of BmR1 protein from Brugia malayi: in silico approaches. PMID:24950179
Draft Genome Sequence of Kitasatospora cheerisanensis KCTC 2395, Which Produces Plecomacrolide against Phytopathogenic Fungi. PMID:24948770
Solution NMR structures of homeodomains from human proteins ALX4, ZHX1, and CASP8AP2 contribute to the structural coverage of the Human Cancer Protein Interaction Network. PMID:24941917
Stenotrophomonas comparative genomics reveals genes and functions that differentiate beneficial and pathogenic bacteria. PMID:24939220
Molecular cloning and characterization of a lysozyme cDNA from the mole cricket Gryllotalpa orientalis (Orthoptera: Gryllotalpidae). PMID:24929538
Comparative transcriptome analysis of four prymnesiophyte algae. PMID:24926657
A homolog of lariat-debranching enzyme modulates turnover of branched RNA. PMID:24919400
A Pseudomonas aeruginosa EF-hand protein, EfhP (PA4107), modulates stress responses and virulence at high calcium concentration. PMID:24918783
Structural diversity in the dandelion (Taraxacum officinale) polyphenol oxidase family results in different responses to model substrates. PMID:24918587
Albino midrib 1, encoding a putative potassium efflux antiporter, affects chloroplast development and drought tolerance in rice. PMID:24917171
Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family. PMID:24911101
Characterization of the kidney transcriptome of the South American olive mouse Abrothrix olivacea. PMID:24909751
A reference genome for common bean and genome-wide analysis of dual domestications. PMID:24908249
Evolutionary insights into premetazoan functions of the neuronal protein homer. PMID:24899667
Genome-wide analysis of regulatory proteases sequences identified through bioinformatics data mining in Taenia solium. PMID:24899069
On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation. PMID:24890864
Comparative genomics of Bradyrhizobium japonicum CPAC 15 and Bradyrhizobium diazoefficiens CPAC 7: elite model strains for understanding symbiotic performance with soybean. PMID:24888481
A network-based approach to identify substrate classes of bacterial glycosyltransferases. PMID:24885406
Genome analysis and CRISPR typing of Salmonella enterica serovar Virchow. PMID:24885207
The nuclear receptor gene family in the Pacific oyster, Crassostrea gigas, contains a novel subfamily group. PMID:24885009
Massive gene transfer and extensive RNA editing of a symbiotic dinoflagellate plastid genome. PMID:24881086
Sequence comparison and phylogenetic analysis by the Maximum Likelihood method of ribosome-inactivating proteins from angiosperms. PMID:24880476
Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation. PMID:24865297
A roadmap for functional structural variants in the soybean genome. PMID:24855315
The complexity of vesicle transport factors in plants examined by orthology search. PMID:24844592
Cloning and in silico analysis of a cinnamyl alcohol dehydrogenase gene in Pennisetum purpureum. PMID:24840831
Mitochondrial genome of Phlebia radiata is the second largest (156 kbp) among fungi and features signs of genome flexibility and recent recombination events. PMID:24824642
The plasmid complement of Lactococcus lactis UC509.9 encodes multiple bacteriophage resistance systems. PMID:24814781
A customized Web portal for the genome of the ctenophore Mnemiopsis leidyi. PMID:24773765
PLIC: protein-ligand interaction clusters. PMID:24763918
High-resolution analysis of gene activity during the Xenopus mid-blastula transition. PMID:24757007
Genome sequence and transcriptome analyses of the thermophilic zygomycete fungus Rhizomucor miehei. PMID:24746234
Evolution of bacterial protein-tyrosine kinases and their relaxed specificity toward substrates. PMID:24728941
Histidine degradation via an aminotransferase increases the nutritional flexibility of Candida glabrata. PMID:24728193
Redefining the PF06864 Pfam family based on Burkholderia pseudomallei PilO2(Bp) S-SAD crystal structure. PMID:24728008
Conformational landscapes for KMSKS loop in tyrosyl-tRNA synthetases. PMID:24723074
Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest. PMID:24722629
A multicopy Y-chromosomal SGNH hydrolase gene expressed in the testis of the platyfish has been captured and mobilized by a Helitron transposon. PMID:24712907
The evolution of protein structures and structural ensembles under functional constraint. PMID:24710290
Reassessing domain architecture evolution of metazoan proteins: major impact of gene prediction errors. PMID:24710207
Molecular architecture and the structural basis for anion interaction in prestin and SLC26 transporters. PMID:24710176
Biochemical properties and atomic resolution structure of a proteolytically processed β-mannanase from cellulolytic Streptomyces sp. SirexAA-E. PMID:24710170
Expression of the pupal determinant broad during metamorphic and neotenic development of the strepsipteran Xenos vesparum Rossi. PMID:24709670
3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families. PMID:24700812
Copy number variations among silkworms. PMID:24684762
Genetic characterisation of Langerin gene in human immunodeficiency virus-1-infected women from Bahia, Brazil. PMID:24676666
Insights into the origin of nematode chemosensory GPCRs: putative orthologs of the Srw family are found across several phyla of protostomes. PMID:24663674
Linker mutations reveal the complexity of synaptotagmin 1 action during synaptic transmission. PMID:24657966
Exploring the biological and chemical complexity of the ligases. PMID:24657765
Prevalence of transcription factors in ascomycete and basidiomycete fungi. PMID:24650355
A pangenomic analysis of the Nannochloropsis organellar genomes reveals novel genetic variations in key metabolic genes. PMID:24646409
De novo structure prediction of globular proteins aided by sequence variation-derived contacts. PMID:24637808
Genomics and bioinformatics resources for translational science in Rosaceae. PMID:24634697
High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes. PMID:24624126
Strong genome-wide selection early in the evolution of Prochlorococcus resulted in a reduced genome through the loss of a large number of small effect genes. PMID:24594762
Phylogeny and molecular evolution analysis of PIN-FORMED 1 in angiosperm. PMID:24586663
A population-based evolutionary search approach to the multiple minima problem in de novo protein structure prediction. PMID:24565020
Ranking and compacting binding segments of protein families using aligned pattern clusters. PMID:24564874
An evolutionary ratchet leading to loss of elongation factors in eukaryotes. PMID:24564225
Genomic characteristics and comparative genomics analysis of Penicillium chrysogenum KF-25. PMID:24555742
Characterization of human papillomavirus type 154 and tissue tropism of gammapapillomaviruses. PMID:24551244
A subfamily of putative cytokinin receptors is revealed by an analysis of the evolution of the two-component signaling system of plants. PMID:24520157
The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments. PMID:24516394
Quantitative analysis of the mitochondrial and plastid proteomes of the moss Physcomitrella patens reveals protein macrocompartmentation and microcompartmentation. PMID:24515833
Evolution and expression analysis of the grape (Vitis vinifera L.) WRKY gene family. PMID:24510937
Edc3 function in yeast and mammals is modulated by interaction with NAD-related compounds. PMID:24504254
A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria. PMID:24501396
A comparative study of Whi5 and retinoblastoma proteins: from sequence and structure analysis to intracellular networks. PMID:24478706
C2orf62 and TTC17 are involved in actin organization and ciliogenesis in zebrafish and human. PMID:24475127
Selecting age-related functional characteristics in the human gut microbiome. PMID:24467949
Large scale identification and categorization of protein sequences using structured logistic regression. PMID:24465495
Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines. PMID:24427317
Strategies and molecular tools to fight antimicrobial resistance: resistome, transcriptome, and antimicrobial peptides. PMID:24427156
Lipoteichoic acids, phosphate-containing polymers in the envelope of gram-positive bacteria. PMID:24415723
Lineage-specific expansions of TET/JBP genes and a new class of DNA transposons shape fungal genomic and epigenetic landscapes. PMID:24398522
Cell-free translation of biofuel enzymes. PMID:24395410
Sequence analysis, structure and binding site prediction of Sigma 1 receptor protein by in silico method. PMID:24391355
EttA regulates translation by binding the ribosomal E site and restricting ribosome-tRNA dynamics. PMID:24389465
Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium. PMID:24386394
Genomic analyses with biofilter 2.0: knowledge driven filtering, annotation, and model development. PMID:24378202
Generalized Baum-Welch algorithm based on the similarity between sequences. PMID:24376498
A nodule-specific lipid transfer protein AsE246 participates in transport of plant-synthesized lipids to symbiosome membrane and is essential for nodule organogenesis in Chinese milk vetch. PMID:24367021
An assembly of proteins and lipid domains regulates transport of phosphatidylserine to phosphatidylserine decarboxylase 2 in Saccharomyces cerevisiae. PMID:24366873
Comparative analysis of genome sequences from four strains of the Buchnera aphidicola Mp endosymbion of the green peach aphid, Myzus persicae. PMID:24365332
Signaling regulates activity of DHCR24, the final enzyme in cholesterol synthesis. PMID:24363437
The solution structure of the regulatory domain of tyrosine hydroxylase. PMID:24361276
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
A versatile class of cell surface directional motors gives rise to gliding motility and sporulation in Myxococcus xanthus. PMID:24339744
Gene duplication, lineage-specific expansion, and subfunctionalization in the MADF-BESS family patterns the Drosophila wing hinge. PMID:24336749
Genome-wide mapping of DNA methylation in the human malaria parasite Plasmodium falciparum. PMID:24331467
New insights into histidine triad proteins: solution structure of a Streptococcus pneumoniae PhtD domain and zinc transfer to AdcAII. PMID:24312273
Snf2 family gene distribution in higher plant genomes reveals DRD1 expansion and diversification in the tomato genome. PMID:24312269
LigSearch: a knowledge-based web server to identify likely ligands for a protein target. PMID:24311580
Coevolutionary signals across protein lineages help capture multiple protein conformations. PMID:24297889
Pfam: the protein families database. PMID:24288371
Phylogenetic and transcriptional analysis of an expanded bZIP transcription factor family in Phytophthora sojae. PMID:24286285
Metabolic analysis of Chlorobium chlorochromatii CaD3 reveals clues of the symbiosis in 'Chlorochromatium aggregatum'. PMID:24285361
Functional analysis of light-harvesting-like protein 3 (LIL3) and its light-harvesting chlorophyll-binding motif in Arabidopsis. PMID:24275650
Population structure and domestication revealed by high-depth resequencing of Korean cultivated and wild soybean genomes. PMID:24271940
KBDOCK 2013: a spatial classification of 3D protein domain family interactions. PMID:24271397
A comparative analysis of trypanosomatid SNARE proteins. PMID:24269876
Transcriptome profiling of fruit development and maturation in Chinese white pear (Pyrus bretschneideri Rehd). PMID:24267665
Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. PMID:24259309
Genomic mechanisms accounting for the adaptation to parasitism in nematode-trapping fungi. PMID:24244185
Evolution of the cytosolic iron-sulfur cluster assembly machinery in Blastocystis species and other microbial eukaryotes. PMID:24243793
Revealing the hidden functional diversity of an enzyme family. PMID:24240508
Functional evaluation of the role of C-type lectin domain family 16A at the chromosome 16p13 locus. PMID:24237155
Classification of α-helical membrane proteins using predicted helix architectures. PMID:24204844
Elementary flux modes analysis of functional domain networks allows a better metabolic pathway interpretation. PMID:24204596
DisMeta: a meta server for construct design and optimization. PMID:24203321
Functional analysis of sporophytic transcripts repressed by the female gametophyte in the ovule of Arabidopsis thaliana. PMID:24194852
An estimated 5% of new protein structures solved today represent a new Pfam family. PMID:24189229
Yeast PPR proteins, watchdogs of mitochondrial gene expression. PMID:24184848
Bioinformatics tools for genome mining of polyketide and non-ribosomal peptides. PMID:24174214
Structural analysis and molecular dynamics simulations of novel δ-endotoxin Cry1Id from Bacillus thuringiensis to pave the way for development of novel fusion proteins against insect pests of crops. PMID:24154610
Proteins of novel lactic acid bacteria from Apis mellifera mellifera: an insight into the production of known extra-cellular proteins during microbial stress. PMID:24148670
Protein kinase C-dependent signaling controls the midgut epithelial barrier to malaria parasite infection in anopheline mosquitoes. PMID:24146884
A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity. PMID:24137537
Genomic and expression analysis of a solute carrier protein (CcSLC25a5) gene from Cyprinus carpio Linnaeus. PMID:24133640
Annotation extension through protein family annotation coherence metrics. PMID:24130572
Re-annotation of the Saccharopolyspora erythraea genome using a systems biology approach. PMID:24118942
OptZyme: computational enzyme redesign using transition state analogues. PMID:24116038
Ancient origins of vertebrate-specific innate antiviral immunity. PMID:24109602
Exploring mechanisms of human disease through structurally resolved protein interactome networks. PMID:24096645
GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. PMID:24096415
Characterization and phylogenetic analysis of the mitochondrial genome of Glarea lozoyensis indicates high diversity within the order Helotiales. PMID:24086376
Modeling the effect of APC truncation on destruction complex function in colorectal cancer cells. PMID:24086117
Phycobilisome: architecture of a light-harvesting supercomplex. PMID:24081814
Cooperative degradation of chitin by extracellular and cell surface-expressed chitinases from Paenibacillus sp. strain FPU-7. PMID:24077704
Carbohydrate-active enzymes in pythium and their role in plant cell wall and storage polysaccharide degradation. PMID:24069150
SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation. PMID:24065691
Whole genome duplication events in plant evolution reconstructed and predicted using myosin motor proteins. PMID:24053117
Solution NMR structure of CD1104B from pathogenic Clostridium difficile reveals a distinct α-helical architecture and provides first structural representative of protein domain family PF14203. PMID:24048810
Agrigenomics for microalgal biofuel production: an overview of various bioinformatics resources and recent studies to link OMICS to bioenergy and bioeconomy. PMID:24044362
Hydrogenosomes in the diplomonad Spironucleus salmonicida. PMID:24042146
Systematic mutational analysis of the putative hydrolase PqsE: toward a deeper molecular understanding of virulence acquisition in Pseudomonas aeruginosa. PMID:24040042
Insights into the loblolly pine genome: characterization of BAC and fosmid sequences. PMID:24023741
Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron. PMID:24019987
Structural and biochemical analyses of Mycobacterium tuberculosis N-acetylmuramyl-L-alanine amidase Rv3717 point to a role in peptidoglycan fragment recycling. PMID:24019530
Characterization of the AtsR hybrid sensor kinase phosphorelay pathway and identification of its response regulator in Burkholderia cenocepacia. PMID:24014026
A comparison of the molecular organization of genomic regions associated with resistance to common bacterial blight in two Phaseolus vulgaris genotypes. PMID:24009615
Protein interactions in the murine cytomegalovirus capsid revealed by cryoEM. PMID:24006185
Learning the language of post-transcriptional gene regulation. PMID:23998708
The Herbaspirillum seropedicae SmR1 Fnr orthologs controls the cytochrome composition of the electron transport chain. PMID:23996052
Genome sequence of the moderately halophilic bacterium Salinicoccus carnicancri type strain Crm(T) (= DSM 23852(T)). PMID:23991257
Giant hydrogen sulfide plume in the oxygen minimum zone off Peru supports chemolithoautotrophy. PMID:23990875
Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research. PMID:23986771
catRAPID omics: a web server for large-scale prediction of protein-RNA interactions. PMID:23975767
SHARP: genome-scale identification of gene-protein-reaction associations in cyanobacteria. PMID:23975204
Cloud prediction of protein structure and function with PredictProtein for Debian. PMID:23971032
Examining marginal sequence similarities between bacterial type III secretion system components and Trypanosoma cruzi surface proteins: horizontal gene transfer or convergent evolution? PMID:23967008
Solution NMR structures provide first structural coverage of the large protein domain family PF08369 and complementary structural coverage of dark operative protochlorophyllide oxidoreductase complexes. PMID:23963952
Transdifferentiation of MALME-3M and MCF-7 Cells toward Adipocyte-like Cells is Dependent on Clathrin-mediated Endocytosis. PMID:23961369
The root transcriptome for North American ginseng assembled and profiled across seasonal development. PMID:23957709
Uses of phage display in agriculture: sequence analysis and comparative modeling of late embryogenesis abundant client proteins suggest protein-nucleic acid binding functionality. PMID:23956788
Sarm1-mediated axon degeneration requires both SAM and TIR interactions. PMID:23946415
kClust: fast and sensitive clustering of large protein sequence databases. PMID:23945046
Novel autoproteolytic and DNA-damage sensing components in the bacterial SOS response and oxidized methylcytosine-induced eukaryotic DNA demethylation systems. PMID:23945014
Dirigent domain-containing protein is part of the machinery required for formation of the lignin-based Casparian strip in the root. PMID:23940370
Are cellulosome scaffolding protein CipC and CBM3-containing protein HycP, involved in adherence of Clostridium cellulolyticum to cellulose? PMID:23935995
Genome Sequence of Serratia plymuthica Strain S13, an Endophyte with Germination- and Plant-Growth-Promoting Activity from the Flower of Styrian Oil Pumpkin. PMID:23929484
PAAR-repeat proteins sharpen and diversify the type VI secretion system spike. PMID:23925114
Reductive evolution and the loss of PDC/PAS domains from the genus Staphylococcus. PMID:23902280
Segmental duplications in the silkworm genome. PMID:23901934
Immune response of the Caribbean sea fan, Gorgonia ventalina, exposed to an Aplanochytrium parasite as revealed by transcriptome sequencing. PMID:23898300
Analysis of periplasmic sensor domains from Anaeromyxobacter dehalogenans 2CP-C: structure of one sensor domain from a histidine kinase and another from a chemotaxis protein. PMID:23897711
Adaptation of the osmotolerant yeast Zygosaccharomyces rouxii to an osmotic environment through copy number amplification of FLO11D. PMID:23893487
IruO is a reductase for heme degradation by IsdI and IsdG proteins in Staphylococcus aureus. PMID:23893407
Recent recombination events in the core genome are associated with adaptive evolution in Enterococcus faecium. PMID:23882129
Putative osmosensor--OsHK3b--a histidine kinase protein from rice shows high structural conservation with its ortholog AtHK1 from Arabidopsis. PMID:23869567
A predicted functional gene network for the plant pathogen Phytophthora infestans as a framework for genomic biology. PMID:23865555
A DNA-based registry for all animal species: the barcode index number (BIN) system. PMID:23861743
An alignment-free domain architecture similarity search (ADASS) algorithm for inferring homology between multi-domain proteins. PMID:23861564
Comparative Genomics Reveal That Host-Innate Immune Responses Influence the Clinical Prevalence of Legionella pneumophila Serogroups. PMID:23826259
PFClust: a novel parameter free clustering algorithm. PMID:23819480
ThreaDom: extracting protein domain boundary information from multiple threading alignments. PMID:23812990
Variant surface antigens of malaria parasites: functional and evolutionary insights from comparative gene family classification and analysis. PMID:23805789
Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key. PMID:23805191
Separating homeologs by phasing in the tetraploid wheat transcriptome. PMID:23800085
Global transcriptome profiles of Camellia sinensis during cold acclimation. PMID:23799877
eFG: an electronic resource for Fusarium graminearum. PMID:23798489
Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. PMID:23795294
Specificity through cooperation: BATF-IRF interactions control immune-regulatory networks. PMID:23787991
Plasmidome-analysis of ESBL-producing escherichia coli using conventional typing and high-throughput sequencing. PMID:23785449
Charge asymmetry in the proteins of the outer membrane. PMID:23782617
Genome-wide survey of DNA-binding proteins in Arabidopsis thaliana: analysis of distribution and functions. PMID:23775796
Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon. PMID:23773438
Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum. PMID:23770896
Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. PMID:23768067
Analysis of complete genomes of Propionibacterium acnes reveals a novel plasmid and increased pseudogenes in an acne associated strain. PMID:23762865
Silicon era of carbon-based life: application of genomics and bioinformatics in crop stress research. PMID:23759993
A high molecular-mass Anoxybacillus sp. SK3-4 amylopullulanase: characterization and its relationship in carbohydrate utilization. PMID:23759984
Two novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in eukaryotes. PMID:23758928
Members of the Sinorhizobium meliloti ChvI regulon identified by a DNA binding screen. PMID:23758731
Molecular phylogeny, homology modeling, and molecular dynamics simulation of race-specific bacterial blight disease resistance protein (xa5) of rice: a comparative agriproteomics approach. PMID:23758479
Large linear plasmids of Borrelia species that cause relapsing fever. PMID:23749977
Molecular mechanism of membrane binding of the GRP1 PH domain. PMID:23747485
Characterizing protein domain associations by Small-molecule ligand binding. PMID:23745168
Identification of the YfgF MASE1 domain as a modulator of bacterial responses to aspartate. PMID:23740576
Transcriptome and proteome data reveal candidate genes for pollinator attraction in sexually deceptive orchids. PMID:23734209
Database citation in full text biomedical articles. PMID:23734176
A novel type of peptidoglycan-binding domain highly specific for amidated D-Asp cross-bridge, identified in Lactobacillus casei bacteriophage endolysins. PMID:23733182
Taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges. PMID:23728164
The nuclear F-actin interactome of Xenopus oocytes reveals an actin-bundling kinesin that is essential for meiotic cytokinesis. PMID:23727888
Profiling protein kinases and other ATP binding proteins in Arabidopsis using Acyl-ATP probes. PMID:23722185
The nucleic acid-binding domain and translational repression activity of a Xenopus terminal uridylyl transferase. PMID:23709223
Domain analysis of symbionts and hosts (DASH) in a genome-wide survey of pathogenic human viruses. PMID:23706066
Identification of novel arthropod vector G protein-coupled receptors. PMID:23705687
Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways. PMID:23695164
Partial venom gland transcriptome of a Drosophila parasitoid wasp, Leptopilina heterotoma, reveals novel and shared bioactive profiles with stinging Hymenoptera. PMID:23688557
A SAS-6-like protein suggests that the Toxoplasma conoid complex evolved from flagellar components. PMID:23687115
Structural representative of the protein family PF14466 has a new fold and establishes links with the C2 and PLAT domains from the widely distant Pfams PF00168 and PF01477. PMID:23681886
CLCAs - a family of metalloproteases of intriguing phylogenetic distribution and with cases of substituted catalytic sites. PMID:23671590
Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: recurrence of tyrosine aminotransferase activity in the Iα subfamily. PMID:23671031
Evolution of and horizontal gene transfer in the Endornavirus genus. PMID:23667703
Structural and population-based evaluations of TBC1D1 p.Arg125Trp. PMID:23667688
Proteolytic processing of the Yersinia pestis YapG autotransporter by the omptin protease Pla and the contribution of YapG to murine plague pathogenesis. PMID:23657527
Reconstituting protein interaction networks using parameter-dependent domain-domain interactions. PMID:23651452
CMCompare webserver: comparing RNA families via covariance models. PMID:23640335
Simultaneous transcriptome analysis of Sorghum and Bipolaris sorghicola by using RNA-seq in combination with de novo transcriptome assembly. PMID:23638091
Gene invasion in distant eukaryotic lineages: discovery of mutually exclusive genetic elements reveals marine biodiversity. PMID:23635865
RNA pentaloop structures as effective targets of regulators belonging to the RsmA/CsrA protein family. PMID:23635605
Chapter 15: disease gene prioritization. PMID:23633938
Tam41 is a CDP-diacylglycerol synthase required for cardiolipin biosynthesis in mitochondria. PMID:23623749
The challenge of increasing Pfam coverage of the human proteome. PMID:23603847
Deep sequencing of non-ribosomal peptide synthetases and polyketide synthases from the microbiomes of Australian marine sponges. PMID:23598791
Reductive evolution in Streptococcus agalactiae and the emergence of a host adapted lineage. PMID:23586779
Identification and prioritization of novel uncharacterized peptidases for biochemical characterization. PMID:23584835
Assembly of the yeast exoribonuclease Rrp6 with its associated cofactor Rrp47 occurs in the nucleus and is critical for the controlled expression of Rrp47. PMID:23580640
Function relaxation followed by diversifying selection after whole-genome duplication in flowering plants. PMID:23580595
Growth temperature and genome size in bacteria are negatively correlated, suggesting genomic streamlining during thermal adaptation. PMID:23563968
Extrapolating the effect of deleterious nsSNPs in the binding adaptability of flavopiridol with CDK7 protein: a molecular dynamics approach. PMID:23561625
The orphan protein bis-γ-glutamylcystine reductase joins the pyridine nucleotide disulfide reductase family. PMID:23560638
Genomic evaluation of Thermoanaerobacter spp. for the construction of designer co-cultures to improve lignocellulosic biofuel production. PMID:23555660
Identification of distant co-evolving residues in antigen 85C from Mycobacterium tuberculosis using statistical coupling analysis of the esterase family proteins. PMID:23554685
Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. PMID:23550210
The discovery of Foxl2 paralogs in chondrichthyan, coelacanth and tetrapod genomes reveals an ancient duplication in vertebrates. PMID:23549337
Crystallization and preliminary crystallographic analysis of Axe2, an acetylxylan esterase from Geobacillus stearothermophilus. PMID:23545652
Exploration of noncoding sequences in metagenomes. PMID:23536879
Fly cryptochrome and the visual system. PMID:23536301
RNAseq versus genome-predicted transcriptomes: a large population of novel transcripts identified in an Illumina-454 Hydra transcriptome. PMID:23530871
Genomic organization, phylogenetic comparison and differential expression of the SBP-box family genes in grape. PMID:23527172
Genome sequence of Lactobacillus pentosus KCA1: vaginal isolate from a healthy premenopausal woman. PMID:23527145
Sequencing and comparative analysis of the straw mushroom (Volvariella volvacea) genome. PMID:23526973
Intron retention and transcript chimerism conserved across mammals: Ly6g5b and Csnk2b-Ly6g5b as examples. PMID:23521802
Structure of the flavoprotein tryptophan 2-monooxygenase, a key enzyme in the formation of galls in plants. PMID:23521653
Ecogenomic perspectives on domains of unknown function: correlation-based exploration of marine metagenomes. PMID:23516388
Complete Genome Sequence of the Sugar Beet Endophyte Pseudomonas poae RE*1-1-14, a Disease-Suppressive Bacterium. PMID:23516179
Function prediction from networks of local evolutionary similarity in protein structure. PMID:23514548
How to inherit statistically validated annotation within BAR+ protein clusters. PMID:23514411
Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex. PMID:23514195
Integration of the second messenger c-di-GMP into the chemotactic signaling pathway. PMID:23512960
The protein translocation systems in plants - composition and variability on the example of Solanum lycopersicum. PMID:23506162
Evolution of the ferric reductase domain (FRD) superfamily: modularity, functional diversification, and signature motifs. PMID:23505460
Cyclic Di-GMP modulates the disease progression of Erwinia amylovora. PMID:23475975
Reciprocal influence of protein domains in the cold-adapted acyl aminoacyl peptidase from Sporosarcina psychrophila. PMID:23457536
The SHOCT domain: a widespread domain under-represented in model organisms. PMID:23451277
Genome mining for methanobactins. PMID:23442874
Carbohydrate-binding modules (CBMs) revisited: reduced amount of water counterbalances the need for CBMs. PMID:23442543
The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer. PMID:23439773
Atypical glycolysis in Clostridium thermocellum. PMID:23435896
The crystal structure of the DNA-binding domain of vIRF-1 from the oncogenic KSHV reveals a conserved fold for DNA binding and reinforces its role as a transcription factor. PMID:23435230
Predicting the binding patterns of hub proteins: a study using yeast protein interaction networks. PMID:23431393
Proteome-wide prediction of self-interacting proteins based on multiple properties. PMID:23422585
Protein signature-based estimation of metagenomic abundances including all domains of life and viruses. PMID:23418187
Prediction of contact matrix for protein-protein interaction. PMID:23418186
Understanding and identifying amino acid repeats. PMID:23418055
Complete Genome of Lactococcus lactis subsp. cremoris UC509.9, Host for a Model Lactococcal P335 Bacteriophage. PMID:23405300
Planarians as a model to assess in vivo the role of matrix metalloproteinase genes during homeostasis and regeneration. PMID:23405188
Common bean (Phaseolus vulgaris L.) PvTIFY orchestrates global changes in transcript profile response to jasmonate and phosphorus deficiency. PMID:23402340
Impact of whole-genome and tandem duplications in the expansion and functional diversification of the F-box family in legumes (Fabaceae). PMID:23390519
Defining the core proteome of the chloroplast envelope membranes. PMID:23390424
Genome sequence and analysis of a broad-host range lytic bacteriophage that infects the Bacillus cereus group. PMID:23388049
Crystallization and preliminary diffraction analysis of the catalytic domain of major extracellular endoglucanase from Xanthomonas campestris pv. campestris. PMID:23385754
Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework. PMID:23383610
Genomic and secretomic analyses reveal unique features of the lignocellulolytic enzyme system of Penicillium decumbens. PMID:23383313
Signal balancing by the CetABC and CetZ chemoreceptors controls energy taxis in Campylobacter jejuni. PMID:23382896
Computational modeling and experimental validation of the Legionella and Coxiella virulence-related type-IVB secretion signal. PMID:23382224
Evolutionary history of the TBP-domain superfamily. PMID:23376926
Genomic analysis of the regulatory elements and links with intrinsic DNA structural properties in the shrunken genome of Buchnera. PMID:23375088
FANTOM: Functional and taxonomic analysis of metagenomes. PMID:23375020
The structural model of Salmonella typhimurium ethanolamine ammonia-lyase directs a rational approach to the assembly of the functional [(EutB-EutC)₂]₃ oligomer from isolated subunits. PMID:23374068
Evolutionary, structural and functional interplay of the IκB family members. PMID:23372681
Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries. PMID:23361328
Evaluation of methods for modeling transcription factor sequence specificity. PMID:23354101
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
Mining of novel thermo-stable cellulolytic genes from a thermophilic cellulose-degrading consortium by metagenomics. PMID:23341999
Turning gold into 'junk': transposable elements utilize central proteins of cellular networks. PMID:23341038
Dynamic evolution of endogenous retrovirus-derived genes expressed in bovine conceptuses during the period of placentation. PMID:23335121
Orchidstra: an integrated orchid functional genomics database. PMID:23324169
Zinc biochemistry: from a single zinc enzyme to a key element of life. PMID:23319127
Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. PMID:23316438
Heuristic methods for finding pathogenic variants in gene coding sequences. PMID:23316295
Caffeate respiration in the acetogenic bacterium Acetobacterium woodii: a coenzyme A loop saves energy for caffeate activation. PMID:23315745
Importance of different types of prior knowledge in selecting genome-wide findings for follow-up. PMID:23307621
Inferring the Brassica rapa Interactome Using Protein-Protein Interaction Data from Arabidopsis thaliana. PMID:23293649
SpoIVA and SipL are Clostridium difficile spore morphogenetic proteins. PMID:23292781
Comparative genomics of odorant binding proteins in Anopheles gambiae, Aedes aegypti, and Culex quinquefasciatus. PMID:23292137
Nuclear magnetic resonance solution structure of the peptidoglycan-binding SPOR domain from Escherichia coli DamX: insights into septal localization. PMID:23290046
Marine microbial symbiosis heats up: the phylogenetic and functional response of a sponge holobiont to thermal stress. PMID:23283017
Bacteriophage cocktail significantly reduces Escherichia coli O157: H7 contamination of lettuce and beef, but does not protect against recontamination. PMID:23275869
Beyond BLASTing: tertiary and quaternary structure analysis helps identify major vault proteins. PMID:23275487
Genome-wide survey of pseudogenes in 80 fully re-sequenced Arabidopsis thaliana accessions. PMID:23272162
Biosynthetic multitasking facilitates thalassospiramide structural diversity in marine bacteria. PMID:23270364
The twilight zone of cis element alignments. PMID:23268451
Role of the guanine nucleotide exchange factor Rom2 in cell wall integrity maintenance of Aspergillus fumigatus. PMID:23264643
Identification of MDP (muramyl dipeptide)-binding key domains in NOD2 (nucleotide-binding and oligomerization domain-2) receptor of Labeo rohita. PMID:23255217
Computational prediction of protein-protein interactions in Leishmania predicted proteomes. PMID:23251492
TnpPred: A Web Service for the Robust Prediction of Prokaryotic Transposases. PMID:23251097
Discovery of Novel DENN Proteins: Implications for the Evolution of Eukaryotic Intracellular Membrane Structures and Human Disease. PMID:23248642
Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. PMID:23246775
Is chemically dispersed oil more toxic to Atlantic cod (Gadus morhua) larvae than mechanically dispersed oil? A transcriptional evaluation. PMID:23241080
Predicting permanent and transient protein-protein interfaces. PMID:23239312
Genetic and biochemical dissection of a HisKA domain identifies residues required exclusively for kinase and phosphatase activities. PMID:23226719
A novel dnaJ family gene, sflA, encodes an inhibitor of flagellation in marine Vibrio species. PMID:23222726
A transcriptomic analysis of Echinococcus granulosus larval stages: implications for parasite biology and host adaptation. PMID:23209850
Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity. PMID:23209685
Draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus sediminis" AR2, from Svalbard in the Arctic Circle. PMID:23209211
Draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus koreensis" AR1, from marine sediment. PMID:23209206
Meta-analysis of the expression of the mitosis-related gene Fam83D. PMID:23205133
Role of the CipA scaffoldin protein in cellulose solubilization, as determined by targeted gene deletion and complementation in Clostridium thermocellum. PMID:23204466
Regulon controlled by the GppX hybrid two component system in Porphyromonas gingivalis. PMID:23194602
Myosinome: a database of myosins from select eukaryotic genomes to facilitate analysis of sequence-structure-function relationships. PMID:23189029
Interactogeneous: disease gene prioritization using heterogeneous networks and full topology scores. PMID:23185389
Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation. PMID:23181723
Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum. PMID:23181666
Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB. PMID:23180575
The genetic architecture of biofilm formation in a clinical isolate of Saccharomyces cerevisiae. PMID:23172850
The protein interaction network of a taxis signal transduction system in a halophilic archaeon. PMID:23171228
The plant short-chain dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns. PMID:23167570
Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779. PMID:23166516
This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes. PMID:23166479
Identification of two novel endoplasmic reticulum body-specific integral membrane proteins. PMID:23166355
Dynamics of domain coverage of the protein sequence universe. PMID:23157439
Remarkable diversity in the enzymes catalyzing the last step in synthesis of the pimelate moiety of biotin. PMID:23152908
Unusual domain architecture of aminoacyl tRNA synthetases and their paralogs from Leishmania major. PMID:23151081
The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite's biology. PMID:23148687
ALOG domains: provenance of plant homeotic and developmental regulators from the DNA-binding domain of a novel class of DIRS1-type retroposons. PMID:23146749
Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity. PMID:23145189
Cloning, purification and preliminary X-ray data analysis of the human ID2 homodimer. PMID:23143248
Structure of the recombinant BPTI/Kunitz-type inhibitor rShPI-1A from the marine invertebrate Stichodactyla helianthus. PMID:23143234
DLocalMotif: a discriminative approach for discovering local motifs in protein sequences. PMID:23142965
Putative monofunctional type I polyketide synthase units: a dinoflagellate-specific feature? PMID:23139807
Protein structure prediction from sequence variation. PMID:23138306
In vitro site selection of a consensus binding site for the Drosophila melanogaster Tbx20 homolog midline. PMID:23133562
The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution. PMID:23133373
Bio-crude transcriptomics: gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa). PMID:23110428
Characterization of Erysiphe necator-responsive genes in Chinese Wild Vitis quinquangularis. PMID:23109867
Whole genome sequencing of phage resistant Bacillus anthracis mutants reveals an essential role for cell surface anchoring protein CsaB in phage AP50c adsorption. PMID:23098174
The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events. PMID:23093603
DFVF: database of fungal virulence factors. PMID:23092926
Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. PMID:23088596
Biochemical properties and crystal structure of a β-phenylalanine aminotransferase from Variovorax paradoxus. PMID:23087034
Genome-wide identification and analysis of late embryogenesis abundant (LEA) genes in Prunus mume. PMID:23086279
Genomic approaches for interrogating the biochemistry of medicinal plant species. PMID:23084937
The independent prokaryotic origins of eukaryotic fructose-1, 6-bisphosphatase and sedoheptulose-1, 7-bisphosphatase and the implications of their origins for the evolution of eukaryotic Calvin cycle. PMID:23083334
Evolutionarily consistent families in SCOP: sequence, structure and function. PMID:23078280
Analysis of the organic hydroperoxide response of Chromobacterium violaceum reveals that OhrR is a cys-based redox sensor regulated by thioredoxin. PMID:23071722
Predicting the accuracy of multiple sequence alignment algorithms by using computational intelligent techniques. PMID:23066102
SPLOOCE: a new portal for the analysis of human splicing variants. PMID:23064119
Solution NMR structure of yeast succinate dehydrogenase flavinylation factor Sdh5 reveals a putative Sdh1 binding site. PMID:23062074
Habitat-associated phylogenetic community patterns of microbial ammonia oxidizers. PMID:23056629
A walk into the LuxR regulators of Actinobacteria: phylogenomic distribution and functional diversity. PMID:23056438
Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining. PMID:23055974
Sequence, structure, and evolution of cellulases in glycoside hydrolase family 48. PMID:23055526
Additive multiple k-mer transcriptome of the keelworm Pomatoceros lamarckii (Annelida; Serpulidae) reveals annelid trochophore transcription factor cassette. PMID:23053624
Detailed transcriptome description of the neglected cestode Taenia multiceps. PMID:23049872
Functional biogeography of ocean microbes revealed through non-negative matrix factorization. PMID:23049741
Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization. PMID:23046301
Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing. PMID:23044854
Genome dynamics explain the evolution of flowering time CCT domain gene families in the Poaceae. PMID:23028921
System wide analysis of the evolution of innate immunity in the nematode model species Caenorhabditis elegans and Pristionchus pacificus. PMID:23028509
Massive expansion of the calpain gene family in unicellular eukaryotes. PMID:23020305
Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic. PMID:23019363
Modeling the Thermoproteaceae RNase P RNA. PMID:23018780
Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage. PMID:23013770
The crystal structure of the Rv0301-Rv0300 VapBC-3 toxin-antitoxin complex from M. tuberculosis reveals a Mg²⁺ ion in the active site and a putative RNA-binding site. PMID:23011806
Long-term and short-term evolutionary impacts of transposable elements on Drosophila. PMID:22997235
Charting the landscape of tandem BRCT domain-mediated protein interactions. PMID:22990118
The study of two barley type I-like MADS-box genes as potential targets of epigenetic regulation during seed development. PMID:22985436
Susceptibility towards enterotoxigenic Escherichia coli F4ac diarrhea is governed by the MUC13 gene in pigs. PMID:22984528
Genome-wide identification and analysis of the TIFY gene family in grape. PMID:22984514
Structure of a novel winged-helix like domain from human NFRKB protein. PMID:22984442
Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction. PMID:22978315
SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions. PMID:22977176
Evolutionary history and genome organization of DUF1220 protein domains. PMID:22973535
Identification of an additional protein involved in mannan biosynthesis. PMID:22966747
Metagenomic analysis reveals a functional signature for biomass degradation by cecal microbiota in the leaf-eating flying squirrel (Petaurista alborufus lena). PMID:22963241
Techniques to cope with missing data in host-pathogen protein interaction prediction. PMID:22962468
Metagenomic analysis: the challenge of the data bonanza. PMID:22962339
Structural, functional, and evolutionary analysis of the unusually large stilbene synthase gene family in grapevine. PMID:22961129
Homology modeling and functional annotation of bubaline pregnancy associated glycoprotein 2. PMID:22958467
On-line resources for Xenopus. PMID:22956109
GENCODE: the reference human genome annotation for The ENCODE Project. PMID:22955987
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
Subversion of cell signaling by pathogens. PMID:22952390
Adaptive immunity restricts replication of novel murine astroviruses. PMID:22951832
Molecular characterization and comparative sequence analysis of defense-related gene, Oryza rufipogon receptor-like protein kinase 1. PMID:22942769
Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. PMID:22942020
Identification of unknown protein function using metabolite cocktail screening. PMID:22940582
Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated lncRNAs and novel transcripts. PMID:22936659
Diversity of integrating conjugative elements in actinobacteria: Coexistence of two mechanistically different DNA-translocation systems. PMID:22934248
Revelation of a catalytic calcium-binding site elucidates unusual metal dependence of a human apyrase. PMID:22928549
Phosphoproteome of Pristionchus pacificus provides insights into architecture of signaling networks in nematode models. PMID:22923814
HSPIR: a manually annotated heat shock protein information resource. PMID:22923302
Positive-unlabeled learning for disease gene identification. PMID:22923290
Gene flow and biological conflict systems in the origin and evolution of eukaryotes. PMID:22919680
Deep sequencing of Porphyromonas gingivalis and comparative transcriptome analysis of a LuxS mutant. PMID:22919670
Trimeric autotransporter adhesins in members of the Burkholderia cepacia complex: a multifunctional family of proteins implicated in virulence. PMID:22919579
Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling. PMID:22913808
The landscape of the prion protein's structural response to mutation revealed by principal component analysis of multiple NMR ensembles. PMID:22912570
Intrinsic disorder in the human spliceosomal proteome. PMID:22912569
Novel insights into the transcriptome of Dirofilaria immitis. PMID:22911833
A bioinformatic strategy for the detection, classification and analysis of bacterial autotransporters. PMID:22905239
The chordate proteome history database. PMID:22904610
4-O-methylation of glucuronic acid in Arabidopsis glucuronoxylan is catalyzed by a domain of unknown function family 579 protein. PMID:22893684
Missense mutation in the ATPase, aminophospholipid transporter protein ATP8A2 is associated with cerebellar atrophy and quadrupedal locomotion. PMID:22892528
Diversity, classification and function of the plant protein kinase superfamily. PMID:22889912
A genome-wide RNAi screen for enhancers of par mutants reveals new contributors to early embryonic polarity in Caenorhabditis elegans. PMID:22887819
Identification of the dehydrin gene family from grapevine species and analysis of their responsiveness to various forms of abiotic and biotic stress. PMID:22882870
Genome-wide mapping of NBS-LRR genes and their association with disease resistance in soybean. PMID:22877146
Cloning and expression analysis of genes encoding lytic endopeptidases L1 and L5 from Lysobacter sp. strain XL1. PMID:22865082
Characterization of the interactions of mammalian RNA polymerase I associated proteins PAF53 and PAF49. PMID:22849406
Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. PMID:22848480
Prediction and analysis of the protein interactome in Pseudomonas aeruginosa to enable network-based drug target selection. PMID:22848443
Determinants of exon-level evolutionary rates in Arabidopsis species. PMID:22844194
Profiling lipid-protein interactions using nonquenched fluorescent liposomal nanovesicles and proteome microarrays. PMID:22843995
Genome sequence of Blattabacterium sp. strain BGIGA, endosymbiont of the Blaberus giganteus cockroach. PMID:22843586
Crystal structure of a catalytically active GG(D/E)EF diguanylate cyclase domain from Marinobacter aquaeolei with bound c-di-GMP product. PMID:22843345
Three structural representatives of the PF06855 protein domain family from Staphyloccocus aureus and Bacillus subtilis have SAM domain-like folds and different functions. PMID:22843344
Patterns and architecture of genomic islands in marine bacteria. PMID:22839777
Functional divergence of gene duplicates - a domain-centric view. PMID:22839301
Origin of metazoan cadherin diversity and the antiquity of the classical cadherin/β-catenin complex. PMID:22837400
Molecular evolution of A-kinase anchoring protein (AKAP)-7: implications in comparative PKA compartmentalization. PMID:22834419
The NsrR regulon in nitrosative stress resistance of Salmonella enterica serovar Typhimurium. PMID:22831173
A survey of putative secreted and transmembrane proteins encoded in the C. elegans genome. PMID:22823938
Cellulose degradation by Sulfolobus solfataricus requires a cell-anchored endo-β-1-4-glucanase. PMID:22821975
Predictive sequence analysis of the Candidatus Liberibacter asiaticus proteome. PMID:22815919
Identification of potential small molecule binding pockets on Rho family GTPases. PMID:22815826
Draft genome sequence of the sulfur-oxidizing bacterium "Candidatus Sulfurovum sediminum" AR, which belongs to the Epsilonproteobacteria. PMID:22815446
Template-based protein structure modeling using the RaptorX web server. PMID:22814390
Metagenomic insights into the fibrolytic microbiome in yak rumen. PMID:22808161
The ABC transporters in Candidatus Liberibacter asiaticus. PMID:22807026
The dengue vector Aedes aegypti contains a functional high mobility group box 1 (HMGB1) protein with a unique regulatory C-terminus. PMID:22802955
Subtractive libraries for prospecting differentially expressed genes in the soybean under water deficit. PMID:22802715
Evolution and virulence contributions of the autotransporter proteins YapJ and YapK of Yersinia pestis CO92 and their homologs in Y. pseudotuberculosis IP32953. PMID:22802344
Large-scale transcriptome analysis of retroelements in the migratory locust, Locusta migratoria. PMID:22792363
GmcA is a putative glucose-methanol-choline oxidoreductase required for the induction of asexual development in Aspergillus nidulans. PMID:22792266
IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project. PMID:22792232
GFam: a platform for automatic annotation of gene families. PMID:22790981
Expression of PaNAC01, a Picea abies CUP-SHAPED COTYLEDON orthologue, is regulated by polar auxin transport and associated with differentiation of the shoot apical meristem and formation of separated cotyledons. PMID:22778149
Comparative analysis of diguanylate cyclase and phosphodiesterase genes in Klebsiella pneumoniae. PMID:22776320
Assessment of the structural and functional impact of in-frame mutations of the DMD gene, using the tools included in the eDystrophin online database. PMID:22776072
Ultrafast clustering algorithms for metagenomic sequence analysis. PMID:22772836
Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes. PMID:22769602
Genes for the major structural components of Thermotogales species' togas revealed by proteomic and evolutionary analyses of OmpA and OmpB homologs. PMID:22768259
Independent evolution of striated muscles in cnidarians and bilaterians. PMID:22763458
HEMD: an integrated tool of human epigenetic enzymes and chemical modulators for therapeutics. PMID:22761927
MuSiC: identifying mutational significance in cancer genomes. PMID:22759861
Predict impact of single amino acid change upon protein structure. PMID:22759652
Prioritization of pathogenic mutations in the protein kinase superfamily. PMID:22759651
Structure of the surface layer of the methanogenic archaean Methanosarcina acetivorans. PMID:22753492
A novel phage element of Salmonella enterica serovar Enteritidis P125109 contributes to accelerated type III secretion system 2-dependent early inflammation kinetics in a mouse colitis model. PMID:22753379
Cyclic Di-GMP phosphodiesterases RmdA and RmdB are involved in regulating colony morphology and development in Streptomyces coelicolor. PMID:22753061
A minimal ligand binding pocket within a network of correlated mutations identified by multiple sequence and structural analysis of G protein coupled receptors. PMID:22748306
Genes2FANs: connecting genes through functional association networks. PMID:22748121
Novel enzymes for the degradation of cellulose. PMID:22747961
Comparative transcriptome analysis between planarian Dugesia japonica and other platyhelminth species. PMID:22747887
Fungal genome resources at NCBI. PMID:22737589
Large-scale collection and annotation of gene models for date palm (Phoenix dactylifera, L.). PMID:22736259
Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. PMID:22731697
A global characterization and identification of multifunctional enzymes. PMID:22723914
Detecting differential usage of exons from RNA-seq data. PMID:22722343
Vasa-Like DEAD-Box RNA Helicases of Schistosoma mansoni. PMID:22720105
How many protein-protein interactions types exist in nature? PMID:22719985
A SEL1L mutation links a canine progressive early-onset cerebellar ataxia to the endoplasmic reticulum-associated protein degradation (ERAD) machinery. PMID:22719266
Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans. PMID:22712530
Surface display of N-terminally anchored invasin by Lactobacillus plantarum activates NF-κB in monocytes. PMID:22706054
iAK692: a genome-scale metabolic model of Spirulina platensis C1. PMID:22703714
Collagen-like proteins in pathogenic E. coli strains. PMID:22701585
Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts. PMID:22699508
Variation of presence/absence genes among Arabidopsis populations. PMID:22697058
Structural variants in the soybean genome localize to clusters of biotic stress-response genes. PMID:22696021
NMR structure of lipoprotein YxeF from Bacillus subtilis reveals a calycin fold and distant homology with the lipocalin Blc from Escherichia coli. PMID:22693626
Cysteine-rich domains related to Frizzled receptors and Hedgehog-interacting proteins. PMID:22693159
The molecular basis of ubiquitin-like protein NEDD8 deamidation by the bacterial effector protein Cif. PMID:22691497
Ancient gene transfer from algae to animals: mechanisms and evolutionary significance. PMID:22690978
CD45-deficient severe combined immunodeficiency caused by uniparental disomy. PMID:22689986
Recognition models to predict DNA-binding specificities of homeodomain proteins. PMID:22689783
Comparative analysis of the 5S rRNA and its associated proteins reveals unique primitive rather than parasitic features in Giardia lamblia. PMID:22685540
Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis. PMID:22670053
Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity. PMID:22666442
Flexibility in MuA transposase family protein structures: functional mapping with scanning mutagenesis and sequence alignment of protein homologues. PMID:22666413
A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function. PMID:22651983
Genome and proteome analysis of 7-7-1, a flagellotropic phage infecting Agrobacterium sp H13-3. PMID:22650361
Comparative genome analysis of 19 Ureaplasma urealyticum and Ureaplasma parvum strains. PMID:22646228
MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments. PMID:22646090
Co-expression of cell-wall related genes: new tools and insights. PMID:22645599
TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes. PMID:22645565
Protein Phylogenetic Analysis of Ca(2+)/cation Antiporters and Insights into their Evolution in Plants. PMID:22645563
Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis. PMID:22645369
Large-scale co-expression approach to dissect secondary cell wall formation across plant species. PMID:22639584
Linear motifs confer functional diversity onto splice variants. PMID:22638587
iELM--a web server to explore short linear motif-mediated interactions. PMID:22638578
Analyzing large biological datasets with association networks. PMID:22638576
Predicting inter-species cross-talk in two-component signalling systems. PMID:22629451
Plant Glycosyltransferases Beyond CAZy: A Perspective on DUF Families. PMID:22629278
Characterization of modular bacteriophage endolysins from Myoviridae phages OBP, 201φ2-1 and PVP-SE1. PMID:22615864
SH3 domain tyrosine phosphorylation--sites, role and evolution. PMID:22615764
The YARHG domain: an extracellular domain in search of a function. PMID:22615736
The Bic-C family of developmental translational regulators. PMID:22611335
Genome-wide identification and in silico analysis of poplar peptide deformylases. PMID:22606033
Solution NMR structure of Alr2454 from Nostoc sp. PCC 7120, the first structural representative of Pfam domain family PF11267. PMID:22592539
Bacteriophages with the ability to degrade uropathogenic Escherichia coli biofilms. PMID:22590682
Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis interactomes. PMID:22589098
Metagenomics - a guide from sampling to data analysis. PMID:22587947
Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes. PMID:22587903
Characterization of the [2Fe-2S] cluster of Escherichia coli transcription factor IscR. PMID:22583201
A comparative evaluation of sequence classification programs. PMID:22574964
GHOSTM: a GPU-accelerated homology search tool for metagenomics. PMID:22574135
Structural bioinformatics of the human spliceosomal proteome. PMID:22573172
Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum. PMID:22570076
Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours. PMID:22569339
The Helicobacter pylori autotransporter ImaA (HP0289) modulates the immune response and contributes to host colonization. PMID:22566509
Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations. PMID:22563243
required to maintain repression2 is a novel protein that facilitates locus-specific paramutation in maize. PMID:22562610
CENP-T proteins are conserved centromere receptors of the Ndc80 complex. PMID:22561346
From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer. PMID:22553170
Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum. PMID:22548871
The dormancy regulator DosR controls ribosome stability in hypoxic mycobacteria. PMID:22544737
A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons. PMID:22544262
Fission yeast Lem2 and Man1 perform fundamental functions of the animal cell nuclear lamina. PMID:22540024
Determination of ribonuclease sequence-specificity using Pentaprobes and mass spectrometry. PMID:22539524
Nprl3 is required for normal development of the cardiovascular system. PMID:22538705
Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms. PMID:22536960
Scalable global alignment for multiple biological networks. PMID:22536895
Use of structural phylogenetic networks for classification of the ferritin-like superfamily. PMID:22535960
The α2 helix in the DNA ligase IV BRCT-1 domain is required for targeted degradation of ligase IV during adenovirus infection. PMID:22534089
Genome-wide identification and characterization of replication origins by deep sequencing. PMID:22531001
Computational analysis of cysteine and methionine metabolism and its regulation in dairy starter and related bacteria. PMID:22522891
A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses. PMID:22515485
A beginner's guide to eukaryotic genome annotation. PMID:22510764
Reduced polymorphism in domains involved in protein-protein interactions. PMID:22509312
Computer-based annotation of putative AraC/XylS-family transcription factors of known structure but unknown function. PMID:22505803
Pangenomic study of Corynebacterium diphtheriae that provides insights into the genomic diversity of pathogenic isolates from cases of classical diphtheria, endocarditis, and pneumonia. PMID:22505676
Crystallization of a novel metal-containing cupin from Acidobacterium sp. and preliminary diffraction data analysis. PMID:22505418
Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum. PMID:22505259
Structural disorder in eukaryotes. PMID:22496841
MSV3d: database of human MisSense Variants mapped to 3D protein structure. PMID:22491796
Cactin is essential for G1 progression in Toxoplasma gondii. PMID:22486860
Amylases without known homologues discovered in an acid mine drainage: significance and impact. PMID:22482035
The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity. PMID:22479523
Membrane docking geometry of GRP1 PH domain bound to a target lipid bilayer: an EPR site-directed spin-labeling and relaxation study. PMID:22479423
Identification and characterization of microcin S, a new antibacterial peptide produced by probiotic Escherichia coli G3/10. PMID:22479389
Intronic cis-regulatory modules mediate tissue-specific and microbial control of angptl4/fiaf transcription. PMID:22479192
A genome-wide study of two-component signal transduction systems in eight newly sequenced mutans streptococci strains. PMID:22475007
SdhE is a conserved protein required for flavinylation of succinate dehydrogenase in bacteria. PMID:22474332
Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome. PMID:22472218
Mycobacteriophage endolysins: diverse and modular enzymes with multiple catalytic activities. PMID:22470512
Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events. PMID:22467916
Histone recognition and large-scale structural analysis of the human bromodomain family. PMID:22464331
Fluoride enhances the activity of fungicides that destabilize cell membranes. PMID:22460034
Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS). PMID:22458863
Evolutionary and genetic analyses of mitochondrial translation initiation factors identify the missing mitochondrial IF3 in S. cerevisiae. PMID:22457064
MotViz: a tool for sequence motif prediction in parallel to structural visualization and analyses. PMID:22449399
High through-put sequencing of the Parhyale hawaiensis mRNAs and microRNAs to aid comparative developmental studies. PMID:22448274
Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function. PMID:22446687
Transcriptional analysis of the Arabidopsis ovule by massively parallel signature sequencing. PMID:22442422
The diversification of the LIM superclass at the base of the metazoa increased subcellular complexity and promoted multicellular specialization. PMID:22438907
Network evolution: rewiring and signatures of conservation in signaling. PMID:22438796
Functional characterization of residues required for the herpes simplex virus 1 E3 ubiquitin ligase ICP0 to interact with the cellular E2 ubiquitin-conjugating enzyme UBE2D1 (UbcH5a). PMID:22438555
Tetrahymena Genome Database Wiki: a community-maintained model organism database. PMID:22434841
AntiFam: a tool to help identify spurious ORFs in protein annotation. PMID:22434837
Membrane topology and predicted RNA-binding function of the 'early responsive to dehydration (ERD4)' plant protein. PMID:22431979
Solution NMR structure of the ribosomal protein RP-L35Ae from Pyrococcus furiosus. PMID:22422653
A survey of sRNA families in α-proteobacteria. PMID:22418845
Comparative analysis of benzoxazinoid biosynthesis in monocots and dicots: independent recruitment of stabilization and activation functions. PMID:22415274
Beyond the binding site: the role of the β₂-β₃ loop and extra-domain structures in PDZ domains. PMID:22412368
The zinc-ribbon domain of Helicobacter pylori HP0958: requirement for RpoN accumulation and possible roles of homologs in other bacteria. PMID:22408721
The automatic annotation of bacterial genomes. PMID:22408191
Mutations derived from the thermophilic polyhydroxyalkanoate synthase PhaC enhance the thermostability and activity of PhaC from Cupriavidus necator H16. PMID:22408158
Core site-moiety maps reveal inhibitors and binding mechanisms of orthologous proteins by screening compound libraries. PMID:22393385
Plasmid pP62BP1 isolated from an Arctic Psychrobacter sp. strain carries two highly homologous type II restriction-modification systems and a putative organic sulfate metabolism operon. PMID:22392282
Evolution of a large, conserved, and syntenic gene family in insects. PMID:22384409
Analysis of the peptidoglycan hydrolase complement of Lactobacillus casei and characterization of the major γ-D-glutamyl-L-lysyl-endopeptidase. PMID:22384208
Integrative analysis workflow for the structural and functional classification of C-type lectins. PMID:22372988
Subclassification and biochemical analysis of plant papain-like cysteine proteases displays subfamily-specific characteristics. PMID:22371507
Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns. PMID:22369665
DetoxiProt: an integrated database for detoxification proteins. PMID:22369658
Interrogation of alternative splicing events in duplicated genes during evolution. PMID:22369477
Characterization of species-specific repeats in 613 prokaryotic species. PMID:22368180
Genetic basis of destruxin production in the entomopathogen Metarhizium robertsii. PMID:22367459
A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria. PMID:22366418
Contribution of a genomic accessory region encoding a putative cellobiose phosphotransferase system to virulence of Streptococcus pneumoniae. PMID:22363821
The dispanins: a novel gene family of ancient origin that contains 14 human members. PMID:22363774
Cystinosin, MPDU1, SWEETs and KDELR belong to a well-defined protein family with putative function of cargo receptors involved in vesicle trafficking. PMID:22363504
PIPS: pathogenicity island prediction software. PMID:22355329
Homology modeling, comparative genomics and functional annotation of Mycoplasma genitalium hypothetical protein MG_237. PMID:22355225
Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus. PMID:22354958
Target selection for structural genomics based on combining fold recognition and crystallisation prediction methods: application to the human proteome. PMID:22354707
Chlapsin, a chloroplastidial aspartic proteinase from the green algae Chlamydomonas reinhardtii. PMID:22349731
The human cytomegalovirus-specific UL1 gene encodes a late-phase glycoprotein incorporated in the virion envelope. PMID:22345456
Functional cell surface display and controlled secretion of diverse Agarolytic enzymes by Escherichia coli with a novel ligation-independent cloning vector based on the autotransporter YfaL. PMID:22344647
Modular regulatory principles of large non-coding RNAs. PMID:22337053
Identification and localisation of the NB-LRR gene family within the potato genome. PMID:22336098
BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins. PMID:22335941
Molecular structure and function of the novel BrnT/BrnA toxin-antitoxin system of Brucella abortus. PMID:22334680
Involvement of peptidylprolyl cis/trans isomerases in Enterococcus faecalis virulence. PMID:22331431
The identification of short linear motif-mediated interfaces within the human interactome. PMID:22328783
Discrete cyclic di-GMP-dependent control of bacterial predation versus axenic growth in Bdellovibrio bacteriovorus. PMID:22319440
Viral proteins acquired from a host converge to simplified domain architectures. PMID:22319434
Abundance and distribution of the highly iterated palindrome 1 (HIP1) among prokaryotes. PMID:22312590
Lipid targeting domain with dual-membrane specificity that expands the diversity of intracellular targeting reactions. PMID:22308463
Molecular evolution of the non-coding eosinophil granule ontogeny transcript. PMID:22303364
Systematic analysis of plant-specific B3 domain-containing proteins based on the genome resources of 11 sequenced species. PMID:22302388
Overexpression of rice CBS domain containing protein improves salinity, oxidative, and heavy metal tolerance in transgenic tobacco. PMID:22302312
A novel extracellular metallopeptidase domain shared by animal host-associated mutualistic and pathogenic microbes. PMID:22299034
Metaproteogenomic analysis of a community of sponge symbionts. PMID:22297557
Transaminases for the synthesis of enantiopure beta-amino acids. PMID:22293122
Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing. PMID:22293108
Genome-wide identification and characterization of novel genes involved in terpenoid biosynthesis in Salvia miltiorrhiza. PMID:22291132
Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks. PMID:22287626
Molecular characterization of the EhaG and UpaG trimeric autotransporter proteins from pathogenic Escherichia coli. PMID:22286983
The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms. PMID:22284070
Discovery of Pyrobaculum small RNA families with atypical pseudouridine guide RNA features. PMID:22282340
The Caenorhabditis elegans D2-like dopamine receptor DOP-2 physically interacts with GPA-14, a Gαi subunit. PMID:22280843
Bisulfite sequencing reveals that Aspergillus flavus holds a hollow in DNA methylation. PMID:22276181
Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae. PMID:22272658
The Ras protein superfamily: evolutionary tree and role of conserved amino acids. PMID:22270915
Structure- and sequence-based function prediction for non-homologous proteins. PMID:22270458
KB-Rank: efficient protein structure and functional annotation identification via text query. PMID:22270457
EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data. PMID:22267905
Genome-based reconstruction of the protein import machinery in the secondary plastid of a chlorarachniophyte alga. PMID:22267775
Computational tools for the synthetic design of biochemical pathways. PMID:22266781
Lactobacillus adhesion to mucus. PMID:22254114
A dynamic view of domain-motif interactions. PMID:22253583
Global analysis of small molecule binding to related protein targets. PMID:22253582
Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution. PMID:22250127
Full-length structural model of RET3 and SEC21 in COPI: identification of binding sites on the appendage for accessory protein recruitment motifs. PMID:22246286
Evolution, expansion and expression of the Kunitz/BPTI gene family associated with long-term blood feeding in Ixodes Scapularis. PMID:22244187
Convergent evolution in structural elements of proteins investigated using cross profile analysis. PMID:22244085
LTR retrotransposons in fungi. PMID:22242120
Production of virus-derived ping-pong-dependent piRNA-like small RNAs in the mosquito soma. PMID:22241995
Molecular identification of hydroxylysine kinase and of ammoniophospholyases acting on 5-phosphohydroxy-L-lysine and phosphoethanolamine. PMID:22241472
Using hierarchical clustering of secreted protein families to classify and rank candidate effectors of rust fungi. PMID:22238666
The origin of GPCRs: identification of mammalian like Rhodopsin, Adhesion, Glutamate and Frizzled GPCRs in fungi. PMID:22238661
C7orf30 is necessary for biogenesis of the large subunit of the mitochondrial ribosome. PMID:22238376
Deep sequencing identifies viral and wasp genes with potential roles in replication of Microplitis demolitor Bracovirus. PMID:22238295
Genomic organization and comparative chromosome mapping of the U1 snRNA gene in cichlid fish, with an emphasis in Oreochromis niloticus. PMID:22234547
The novel sigma factor-like regulator RpoQ controls luminescence, chitinase activity, and motility in Vibrio fischeri. PMID:22233679
Protein docking prediction using predicted protein-protein interface. PMID:22233443
Transient infantile hypertriglyceridemia, fatty liver, and hepatic fibrosis caused by mutated GPD1, encoding glycerol-3-phosphate dehydrogenase 1. PMID:22226083
Genomic and functional analysis of Vibrio phage SIO-2 reveals novel insights into ecology and evolution of marine siphoviruses. PMID:22225728
Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771. PMID:22223187
Identification of two voltage-dependent anion channel-like protein sequences conserved in Kinetoplastida. PMID:22219392
Controversies in modern evolutionary biology: the imperative for error detection and quality control. PMID:22217008
Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. PMID:22216014
The FGGY carbohydrate kinase family: insights into the evolution of functional specificities. PMID:22215998
Comparative analysis of human and bovine protein kinases reveals unique relationship and functional diversity. PMID:22215962
Identification of RNA-protein interaction networks using PAR-CLIP. PMID:22213601
Insights from the architecture of the bacterial transcription apparatus. PMID:22210308
Conservation of ciliary proteins in plants with no cilia. PMID:22208660
Evolution of biological interaction networks: from models to real data. PMID:22204388
Quantitative proteomics in teleost fish: insights and challenges for neuroendocrine and neurotoxicology research. PMID:22202605
E3Net: a system for exploring E3-mediated regulatory networks of cellular functions. PMID:22199232
Two surfaces on the histone chaperone Rtt106 mediate histone binding, replication, and silencing. PMID:22198837
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. PMID:22198341
Selective overproduction of the proteasome inhibitor salinosporamide A via precursor pathway regulation. PMID:22195555
ProKinO: an ontology for integrative analysis of protein kinases in cancer. PMID:22194913
The discovery of putative urine markers for the specific detection of prostate tumor by integrative mining of public genomic profiles. PMID:22194848
IMG: the Integrated Microbial Genomes database and comparative analysis system. PMID:22194640
Output targets and transcriptional regulation by a cyclic dimeric GMP-responsive circuit in the Vibrio parahaemolyticus Scr network. PMID:22194449
Widespread genetic switches and toxicity resistance proteins for fluoride. PMID:22194412
The HARE-HTH and associated domains: novel modules in the coordination of epigenetic DNA and protein modifications. PMID:22186017
Nature and intensity of selection pressure on CRISPR-associated genes. PMID:22178975
Active site detection by spatial conformity and electrostatic analysis--unravelling a proteolytic function in shrimp alkaline phosphatase. PMID:22174814
BnMs3 is required for tapetal differentiation and degradation, microspore separation, and pollen-wall biosynthesis in Brassica napus. PMID:22174440
Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors. PMID:22174267
Biophysical and structural considerations for protein sequence evolution. PMID:22171550
Modulation of the multistate folding of designed TPR proteins through intrinsic and extrinsic factors. PMID:22170589
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. PMID:22170421
Comparative genomic and transcriptomic characterization of the toxigenic marine dinoflagellate Alexandrium ostenfeldii. PMID:22164224
The Lymantria dispar IPLB-Ld652Y cell line transcriptome comprises diverse virus-associated transcripts. PMID:22163348
Protein 3D structure computed from evolutionary sequence variation. PMID:22163331
Characterization and expression of attacin, an antibacterial protein-encoding gene, from the beet armyworm, Spodoptera exigua (Hübner) (Insecta: Lepidoptera: Noctuidae). PMID:22160467
A single ancient origin for prototypical serine/arginine-rich splicing factors. PMID:22158759
Complete genome sequence of Pelagibacterium halotolerans B2(T). PMID:22156395
Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome. PMID:22156394
Structural and functional analysis of the archaeal endonuclease Nob1. PMID:22156373
Phylogenetic analysis of mitochondrial outer membrane β-barrel channels. PMID:22155732
Functional bias of positively selected genes in Streptococcus genomes. PMID:22155358
Identification of Anaplasma marginale type IV secretion system effector proteins. PMID:22140462
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. PMID:22139938
MetaBase--the wiki-database of biological databases. PMID:22139927
SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes. PMID:22139920
Crystallization and X-ray data collection of HP0902 from Helicobacter pylori 26695. PMID:22139181
DOMMINO: a database of macromolecular interactions. PMID:22135305
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. PMID:22135298
The Pfam protein families database. PMID:22127870
Production of a reference transcriptome and transcriptomic database (PocilloporaBase) for the cauliflower coral, Pocillopora damicornis. PMID:22126435
Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis. PMID:22123943
Draft genome sequence of Streptomyces sp. strain Wigar10, isolated from a surface-sterilized garlic bulb. PMID:22123757
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. PMID:22121228
Unexpected diversity in Shisa-like proteins suggests the importance of their roles as transmembrane adaptors. PMID:22120523
Xanthusbase after five years expands to become Openmods. PMID:22116063
GeneDB--an annotation database for pathogens. PMID:22116062
A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships. PMID:22115330
Uncovering the prevalence and diversity of integrating conjugative elements in actinobacteria. PMID:22114709
NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels. PMID:22110502
Comparative interactomics with Funcoup 2.0. PMID:22110034
PDBe: Protein Data Bank in Europe. PMID:22110033
DAMPD: a manually curated antimicrobial peptide database. PMID:22110032
DNAtraffic--a new database for systems biology of DNA dynamics during the cell life. PMID:22110027
Phytozome: a comparative platform for green plant genomics. PMID:22110026
Direct-coupling analysis of residue coevolution captures native contacts across many protein families. PMID:22106262
UniPathway: a resource for the exploration and annotation of metabolic pathways. PMID:22102589
YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. PMID:22102575
Purification and crystallization of Bacillus subtilis NrnA, a novel enzyme involved in nanoRNA degradation. PMID:22102036
Crystallization and preliminary X-ray analysis of the Entamoeba histolytica α-actinin-2 rod domain. PMID:22102030
Differential expression of cysteine desulfurases in soybean. PMID:22099069
Origins and evolution of the HET-s prion-forming protein: searching for other amyloid-forming solenoids. PMID:22096554
Whole-genome comparison of two Campylobacter jejuni isolates of the same sequence type reveals multiple loci of different ancestral lineage. PMID:22096527
ProOpDB: Prokaryotic Operon DataBase. PMID:22096236
InterPro in 2011: new developments in the family and domain prediction database. PMID:22096229
Evolutionary and functional insights into Leishmania META1: evidence for lateral gene transfer and a role for META1 in secretion. PMID:22093578
Structure and Function of the Small MutS-Related Domain. PMID:22091410
Ensembl 2012. PMID:22086963
IMG/M: the integrated metagenome data management and comparative analysis system. PMID:22086953
Is the genetic landscape of the deep subsurface biosphere affected by viruses? PMID:22084639
A protocol for computer-based protein structure and function prediction. PMID:22082966
Correlated mutations via regularized multinomial regression. PMID:22082126
Genome sequences and phylogenetic analysis of K88- and F18-positive porcine enterotoxigenic Escherichia coli. PMID:22081385
AnimalTFDB: a comprehensive animal transcription factor database. PMID:22080564
CADRE: the Central Aspergillus Data REpository 2012. PMID:22080563
MIPModDB: a central resource for the superfamily of major intrinsic proteins. PMID:22080560
The UCSC Archaeal Genome Browser: 2012 update. PMID:22080555
Multifunctional proteins revealed by overlapping clustering in protein interaction network. PMID:22080466
Expression of Wnt9, TCTP, and Bmp1/Tll in sea cucumber visceral regeneration. PMID:22079950
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. PMID:22075996
Molecular determinants of modulation of CaV2.1 channels by visinin-like protein 2. PMID:22074920
Disordered patterns in clustered Protein Data Bank and in eukaryotic and bacterial proteomes. PMID:22073276
Genomic transition to pathogenicity in chytrid fungi. PMID:22072962
Expressed sequence tag analysis of the erythrocytic stage of Plasmodium berghei. PMID:22072821
Nuclear import of a lipid-modified transcription factor: mobilization of NFAT5 isoform a by osmotic stress. PMID:22071693
Putting into practice domain-linear motif interaction predictions for exploration of protein networks. PMID:22069443
Inference of functional properties from large-scale analysis of enzyme superfamilies. PMID:22069325
Divergence and convergence in enzyme evolution. PMID:22069324
IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature. PMID:22067451
VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. PMID:22067448
PINA v2.0: mining interactome modules. PMID:22067443
Exploring the gonad transcriptome of two extreme male pigs with RNA-seq. PMID:22067327
Nucleoid-enriched proteomes in developing plastids and chloroplasts from maize leaves: a new conceptual framework for nucleoid functions. PMID:22065420
EcoliWiki: a wiki-based community resource for Escherichia coli. PMID:22064863
Approaches to Fungal Genome Annotation. PMID:22059117
A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of an obligate intracellular lifestyle. PMID:22056929
Complete genome sequence of Corynebacterium variabile DSM 44702 isolated from the surface of smear-ripened cheeses and insights into cheese ripening and flavor generation. PMID:22053731
InterEvol database: exploring the structure and evolution of protein complex interfaces. PMID:22053089
SMART 7: recent updates to the protein domain annotation resource. PMID:22053084
Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis. PMID:22046142
Exploration and mining of the bacterial terpenome. PMID:22039990
Comparative genomics of Helicobacter pylori and the human-derived Helicobacter bizzozeronii CIII-1 strain reveal the molecular basis of the zoonotic nature of non-pylori gastric Helicobacter infections in humans. PMID:22039924
Accelerated Profile HMM Searches. PMID:22039361
Genome sequences and characterization of the related Gordonia phages GTE5 and GRU1 and their use as potential biocontrol agents. PMID:22038604
Molecular characterization and expression analysis of the putative interleukin 6 receptor (IL-6Rα and glycoprotein-130) in rainbow trout (Oncorhynchus mykiss): salmonid IL-6Rα possesses a polymorphic N-terminal Ig domain with variable numbers of two repeats. PMID:22033524
Rational and computational design of stabilized variants of cyanovirin-N that retain affinity and specificity for glycan ligands. PMID:22032696
Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing. PMID:22028928
Bioinformatic analysis of pathogenic missense mutations of activin receptor like kinase 1 ectodomain. PMID:22028876
Sortase enzymes in Gram-positive bacteria. PMID:22026821
Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins. PMID:22024092
Endophytic life strategies decoded by genome and transcriptome analyses of the mutualistic root symbiont Piriformospora indica. PMID:22022265
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
Genome shrinkage and loss of nutrient-providing potential in the obligate symbiont of the primitive termite Mastotermes darwiniensis. PMID:22020505
The dynamics and evolutionary potential of domain loss and emergence. PMID:22016574
canSAR: an integrated cancer public translational research and drug discovery resource. PMID:22013161
Small but sufficient: the Rhodococcus phage RRH1 has the smallest known Siphoviridae genome at 14.2 kilobases. PMID:22013058
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. PMID:22006843
Evidence of cellulose metabolism by the giant panda gut microbiome. PMID:22006317
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
Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis. PMID:21999571
Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts. PMID:21995386
A new family of carbohydrate esterases is represented by a GDSL hydrolase/acetylxylan esterase from Geobacillus stearothermophilus. PMID:21994937
Orthopoxvirus genome evolution: the role of gene loss. PMID:21994715
Evidence of abundant stop codon readthrough in Drosophila and other metazoa. PMID:21994247
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. PMID:21988835
Analysis of conditions affecting auto-phosphorylation of human kinases during expression in bacteria. PMID:21985771
Identification of Plasmodium vivax proteins with potential role in invasion using sequence redundancy reduction and profile hidden Markov models. PMID:21984903
In vivo, in vitro, and x-ray crystallographic analyses suggest the involvement of an uncharacterized triose-phosphate isomerase (TIM) barrel protein in protection against oxidative stress. PMID:21984829
ATP synthase complex of Plasmodium falciparum: dimeric assembly in mitochondrial membranes and resistance to genetic disruption. PMID:21984828
A mass spectrometry-guided genome mining approach for natural product peptidogenomics. PMID:21983601
RNA-binding proteins and gene regulation in myogenesis. PMID:21982546
The UCSC Genome Browser. PMID:21975940
Ortho2ExpressMatrix--a web server that interprets cross-species gene expression data by gene family information. PMID:21970648
Hydrophilic aromatic residue and in silico structure for carbohydrate binding module. PMID:21966371
3DSwap: curated knowledgebase of proteins involved in 3D domain swapping. PMID:21959866
The N-acylneuraminate cytidyltransferase gene, neuA, is heterogenous in Legionella pneumophila strains but can be used as a marker for epidemiological typing in the consensus sequence-based typing scheme. PMID:21956982
Association between seed dormancy and pericarp color is controlled by a pleiotropic gene that regulates abscisic acid and flavonoid synthesis in weedy red rice. PMID:21954164
Identification of nicotinamide mononucleotide deamidase of the bacterial pyridine nucleotide cycle reveals a novel broadly conserved amidohydrolase family. PMID:21953451
Role of Sphingomonas sp. strain Fr1 PhyR-NepR-σEcfG cascade in general stress response and identification of a negative regulator of PhyR. PMID:21949070
The evolution of function in strictosidine synthase-like proteins. PMID:21948213
A holistic phylogeny of the coronin gene family reveals an ancient origin of the tandem-coronin, defines a new subfamily, and predicts protein function. PMID:21943019
Evolutionary traces decode molecular mechanism behind fast pace of myosin XI. PMID:21942950
Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles. PMID:21936920
Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice. PMID:21936904
The overlapping host responses to bacterial cyclic dinucleotides. PMID:21933720
Human retinoblastoma binding protein 9, a serine hydrolase implicated in pancreatic cancers. PMID:21933118
The GRP1 PH domain, like the AKT1 PH domain, possesses a sentry glutamate residue essential for specific targeting to plasma membrane PI(3,4,5)P(3). PMID:21932773
Tm1: a mutator/foldback transposable element family in root-knot nematodes. PMID:21931741
Emergence and modular evolution of a novel motility machinery in bacteria. PMID:21931562
The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment. PMID:21925113
Genome sequence of the ruminal bacterium Megasphaera elsdenii. PMID:21914887
Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PMID:21909270
Structural and functional assays of AtTLP18.3 identify its novel acid phosphatase activity in thylakoid lumen. PMID:21908686
Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma). PMID:21908640
A GCN2-like eukaryotic initiation factor 2 kinase increases the viability of extracellular Toxoplasma gondii parasites. PMID:21908594
High-throughput protein purification and quality assessment for crystallization. PMID:21907284
Computational approaches to selecting and optimising targets for structural biology. PMID:21906678
Insight from the draft genome of Dietzia cinnamea P4 reveals mechanisms of survival in complex tropical soil habitats and biotechnology potential. PMID:21901521
The steroid catabolic pathway of the intracellular pathogen Rhodococcus equi is important for pathogenesis and a target for vaccine development. PMID:21901092
Negative control in two-component signal transduction by transmitter phosphatase activity. PMID:21895797
Atomic resolution insights into curli fiber biogenesis. PMID:21893289
Crystal structures of an archaeal class II DNA photolyase and its complex with UV-damaged duplex DNA. PMID:21892138
Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. PMID:21890906
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. PMID:21890647
A valid mouse model of AGRIN-associated congenital myasthenic syndrome. PMID:21890498
TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data. PMID:21886867
One carbon metabolism in SAR11 pelagic marine bacteria. PMID:21886845
Disjunctive shared information between ontology concepts: application to Gene Ontology. PMID:21884591
Genetic response to bacteriophage infection in Lactococcus lactis reveals a four-strand approach involving induction of membrane stress proteins, D-alanylation of the cell wall, maintenance of proton motive force, and energy conservation. PMID:21880765
A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity. PMID:21880595
Reassessment of the lineage fusion hypothesis for the origin of double membrane bacteria. PMID:21876769
Protein folding and quality control in the ER. PMID:21875985
Expression during host infection and localization of Yersinia pestis autotransporter proteins. PMID:21873491
Atg8: an autophagy-related ubiquitin-like protein family. PMID:21867568
Gypsy and the birth of the SCAN domain. PMID:21865395
HCF243 encodes a chloroplast-localized protein involved in the D1 protein stability of the arabidopsis photosystem II complex. PMID:21862668
Flowering time variation in oilseed rape (Brassica napus L.) is associated with allelic variation in the FRIGIDA homologue BnaA.FRI.a. PMID:21862478
N-termini of fungal CSL transcription factors are disordered, enriched in regulatory motifs and inhibit DNA binding in fission yeast. PMID:21858190
Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome. PMID:21858014
Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: utility and potential for the discovery of novel evolutionary patterns. PMID:21857902
Determinants of homodimerization specificity in histidine kinases. PMID:21854787
Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. PMID:21854559
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
Topology of 1-acyl-sn-glycerol-3-phosphate acyltransferases SLC1 and ALE1 and related membrane-bound O-acyltransferases (MBOATs) of Saccharomyces cerevisiae. PMID:21849510
Klebsiella pneumoniae yggG gene product: a zinc-dependent metalloprotease. PMID:21845088
Ferlins: regulators of vesicle fusion for auditory neurotransmission, receptor trafficking and membrane repair. PMID:21838746
Structural classification and properties of ketoacyl synthases. PMID:21830247
Global analysis of proline-rich tandem repeat proteins reveals broad phylogenetic diversity in plant secretomes. PMID:21829715
The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants. PMID:21829493
Molecular evolution of the LNX gene family. PMID:21827680
Overexpression, crystallization and preliminary X-ray crystallographic analysis of Pyrococcus furiosus PF2050, a member of the DUF2666 protein family. PMID:21821898
Evolutionary history and functional characterization of three large genes involved in sporulation in Bacillus cereus group bacteria. PMID:21821775
Domain architecture conservation in orthologs. PMID:21819573
A systematic analysis of the early transcribed membrane protein family throughout the life cycle of Plasmodium yoelii. PMID:21819513
The fat body transcriptomes of the yellow fever mosquito Aedes aegypti, pre- and post- blood meal. PMID:21818341
Proteins with complex architecture as potential targets for drug design: a case study of Mycobacterium tuberculosis. PMID:21814507
Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing. PMID:21813626
Alba-domain proteins of Trypanosoma brucei are cytoplasmic RNA-binding proteins that interact with the translation machinery. PMID:21811616
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. PMID:21810205
Synergistic use of plant-prokaryote comparative genomics for functional annotations. PMID:21810204
A bacterial process for selenium nanosphere assembly. PMID:21808043
Downregulation of OsPK1, a cytosolic pyruvate kinase, by T-DNA insertion causes dwarfism and panicle enclosure in rice. PMID:21805151
Plasmids of raw milk cheese isolate Lactococcus lactis subsp. lactis biovar diacetylactis DPC3901 suggest a plant-based origin for the strain. PMID:21803914
Fast side chain replacement in proteins using a coarse-grained approach for evaluating the effects of mutation during evolution. PMID:21800121
Exploiting publicly available biological and biochemical information for the discovery of novel short linear motifs. PMID:21799808
Comparative genomics of the mating-type loci of the mushroom Flammulina velutipes reveals widespread synteny and recent inversions. PMID:21799803
Lafora disease E3-ubiquitin ligase malin is related to TRIM32 at both the phylogenetic and functional level. PMID:21798009
Genome-wide identification, classification, and expression analysis of autophagy-associated gene homologues in rice (Oryza sativa L.). PMID:21795261
LRR conservation mapping to predict functional sites within protein leucine-rich repeat domains. PMID:21789174
Sequence-structural features and evolutionary relationships of family GH57 α-amylases and their putative α-amylase-like homologues. PMID:21786160
Solution NMR structure of MED25(391-543) comprising the activator-interacting domain (ACID) of human mediator subunit 25. PMID:21785987
Sulfolobus mutants, generated via PCR products, which lack putative enzymes of UV photoproduct repair. PMID:21785574
Using the Acropora digitifera genome to understand coral responses to environmental change. PMID:21785439
The InterPro BioMart: federated query and web service access to the InterPro Resource. PMID:21785143
Regulation of the virulence determinant OspC by bbd18 on linear plasmid lp17 of Borrelia burgdorferi. PMID:21784941
Genome-scale phylogenetic function annotation of large and diverse protein families. PMID:21784873
Cloning, expression, and characterization of a novel Opisthorchis viverrini calcium-binding EF-hand protein. PMID:21782972
Functional Diversity of the Schistosoma mansoni Tyrosine Kinases. PMID:21776387
Type VI secretion delivers bacteriolytic effectors to target cells. PMID:21776080
Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies. PMID:21771858
ZF21 protein, a regulator of the disassembly of focal adhesions and cancer metastasis, contains a novel noncanonical pleckstrin homology domain. PMID:21768110
A complex lipoate utilization pathway in Listeria monocytogenes. PMID:21768091
The molecular basis of the Caskin1 and Mint1 interaction with CASK. PMID:21763699
A new disease-specific machine learning approach for the prediction of cancer-causing missense variants. PMID:21763417
The atypical two-component sensor kinase Lpl0330 from Legionella pneumophila controls the bifunctional diguanylate cyclase-phosphodiesterase Lpl0329 to modulate bis-(3'-5')-cyclic dimeric GMP synthesis. PMID:21757706
Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data. PMID:21749710
Characterisation of a desmosterol reductase involved in phytosterol dealkylation in the silkworm, Bombyx mori. PMID:21738635
CREST--a large and diverse superfamily of putative transmembrane hydrolases. PMID:21733186
A functionally required unfoldome from the plant kingdom: intrinsically disordered N-terminal domains of GRAS proteins are involved in molecular recognition during plant development. PMID:21732203
Identification and characterization of a multidomain hyperthermophilic cellulase from an archaeal enrichment. PMID:21730956
A white spruce gene catalog for conifer genome analyses. PMID:21730200
Independent subtilases expansions in fungi associated with animals. PMID:21727238
Identification of a chemoreceptor zinc-binding domain common to cytoplasmic bacterial chemoreceptors. PMID:21725005
New structural and functional contexts of the Dx[DN]xDG linear motif: insights into evolution of calcium-binding proteins. PMID:21720552
FFAS server: novel features and applications. PMID:21715387
Discovery of a metagenome-derived enzyme that produces branched-chain acyl-(acyl-carrier-protein)s from branched-chain α-keto acids. PMID:21714057
Update on the aldehyde dehydrogenase gene (ALDH) superfamily. PMID:21712190
Outer membrane adhesion factor multivalent adhesion molecule 7 initiates host cell binding during infection by gram-negative pathogens. PMID:21709226
Genetic mechanisms involved in the evolution of the cephalopod camera eye revealed by transcriptomic and developmental studies. PMID:21702923
Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT. PMID:21702434
Homology modeling, molecular dynamics and QM/MM study of the regulatory protein PhoP from Corynebacterium pseudotuberculosis. PMID:21701810
A novel stress-associated protein 'AtSAP10' from Arabidopsis thaliana confers tolerance to nickel, manganese, zinc, and high temperature stress. PMID:21695274
Binary classification of protein molecules into intrinsically disordered and ordered segments. PMID:21693062
Burkholderia cenocepacia ShvR-regulated genes that influence colony morphology, biofilm formation, and virulence. PMID:21690240
Conditional random field approach to prediction of protein-protein interactions using domain information. PMID:21689483
Extending the aerolysin family: from bacteria to vertebrates. PMID:21687664
Global proteomic analysis of two tick-borne emerging zoonotic agents: anaplasma phagocytophilum and ehrlichia chaffeensis. PMID:21687416
Cocos: Constructing multi-domain protein phylogenies. PMID:21686311
Maize opaque5 encodes monogalactosyldiacylglycerol synthase and specifically affects galactolipids necessary for amyloplast and chloroplast function. PMID:21685260
2,3-butanediol production by acetogenic bacteria, an alternative route to chemical synthesis, using industrial waste gas. PMID:21685168
Cellulases: ambiguous nonhomologous enzymes in a genomic perspective. PMID:21683463
A reverse transcriptase-related protein mediates phage resistance and polymerizes untemplated DNA in vitro. PMID:21676997
A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment. PMID:21673094
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. PMID:21672958
A PLAC8-containing protein from an endomycorrhizal fungus confers cadmium resistance to yeast cells by interacting with Mlh3p. PMID:21672957
Internal organization of large protein families: relationship between the sequence, structure, and function-based clustering. PMID:21671455
Diversification, phylogeny and evolution of auxin response factor (ARF) family: insights gained from analyzing maize ARF genes. PMID:21667107
Ligand-binding PAS domains in a genomic, cellular, and structural context. PMID:21663441
Involvement of a Toxoplasma gondii chromatin remodeling complex ortholog in developmental regulation. PMID:21655329
CorE from Myxococcus xanthus is a copper-dependent RNA polymerase sigma factor. PMID:21655090
Interaction of the human prostacyclin receptor with the PDZ adapter protein PDZK1: role in endothelial cell migration and angiogenesis. PMID:21653824
AUXIN UP-REGULATED F-BOX PROTEIN1 regulates the cross talk between auxin transport and cytokinin signaling during plant root growth. PMID:21653785
FACIL: Fast and Accurate Genetic Code Inference and Logo. PMID:21653513
Analysis of a viral metagenomic library from 200 m depth in Monterey Bay, California constructed by direct shotgun cloning. PMID:21651822
Guidelines for visualizing and annotating rule-based models. PMID:21647530
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
Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome. PMID:21645357
GmFtsH9 expression correlates with in vivo photosystem II function: chlorophyll a fluorescence transient analysis and eQTL mapping in soybean. PMID:21638036
The impact of Ty3-gypsy group LTR retrotransposons Fatima on B-genome specificity of polyploid wheats. PMID:21635794
Binding site prediction for protein-protein interactions and novel motif discovery using re-occurring polypeptide sequences. PMID:21635751
Sequencing and comparative genome analysis of two pathogenic Streptococcus gallolyticus subspecies: genome plasticity, adaptation and virulence. PMID:21633709
Going deeper: metagenome of a hadopelagic microbial community. PMID:21629664
Evaluating the fidelity of de novo short read metagenomic assembly using simulated data. PMID:21625384
The riboswitch regulates a thiamine pyrophosphate ABC transporter of the oral spirochete Treponema denticola. PMID:21622748
CoMet--a web server for comparative functional profiling of metagenomes. PMID:21622656
Phosfinder: a web server for the identification of phosphate-binding sites on protein structures. PMID:21622655
SLiMSearch 2.0: biological context for short linear motifs in proteins. PMID:21622654
Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding. PMID:21619637
Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins. PMID:21612628
In silico survey of the mitochondrial protein uptake and maturation systems in the brown alga Ectocarpus siliculosus. PMID:21611166
PredUs: a web server for predicting protein interfaces using structural neighbors. PMID:21609948
AMPylation: Something Old is New Again. PMID:21607083
GProX, a user-friendly platform for bioinformatics analysis and visualization of quantitative proteomics data. PMID:21602510
Whole genome sequences of four Brucella strains. PMID:21602346
Complete genome sequence of Gallibacterium anatis strain UMN179, isolated from a laying hen with peritonitis. PMID:21602325
The aspartic proteinase family of three Phytophthora species. PMID:21599950
Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon. PMID:21599934
A Shigella boydii bacteriophage which resembles Salmonella phage ViI. PMID:21595934
Bacterial metallothioneins: past, present, and questions for the future. PMID:21594652
Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC). PMID:21593603
The eisosome core is composed of BAR domain proteins. PMID:21593205
HMMER web server: interactive sequence similarity searching. PMID:21593126
Genome of Herbaspirillum seropedicae strain SmR1, a specialized diazotrophic endophyte of tropical grasses. PMID:21589895
Taxonomic classification of metagenomic shotgun sequences with CARMA3. PMID:21586583
The SLH-domain protein BslO is a determinant of Bacillus anthracis chain length. PMID:21585566
The N-terminal nucleophile serine of cephalosporin acylase executes the second autoproteolytic cleavage and acylpeptide hydrolysis. PMID:21576250
Combinations of protein-chemical complex structures reveal new targets for established drugs. PMID:21573205
An expanded binding model for Cys2His2 zinc finger protein-DNA interfaces. PMID:21572177
Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes. PMID:21571812
Expansion of type II CAAX proteases reveals evolutionary origin of γ-secretase subunit APH-1. PMID:21570408
Functional specialization in nucleotide sugar transporters occurred through differentiation of the gene cluster EamA (DUF6) before the radiation of Viridiplantae. PMID:21569384
Differential control of Yersinia pestis biofilm formation in vitro and in the flea vector by two c-di-GMP diguanylate cyclases. PMID:21559445
LFR1 ferric iron reductase of Leishmania amazonensis is essential for the generation of infective parasite forms. PMID:21558274
NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity. PMID:21558170
Transcription factor effector domains. PMID:21557087
Unpredictability of metabolism--the key role of metabolomics science in combination with next-generation genome sequencing. PMID:21556754
Chromatin-modifying complex component Nurf55/p55 associates with histones H3 and H4 and polycomb repressive complex 2 subunit Su(z)12 through partially overlapping binding sites. PMID:21550984
Eukaryotic protein kinases (ePKs) of the helminth parasite Schistosoma mansoni. PMID:21548963
A mighty small heart: the cardiac proteome of adult Drosophila melanogaster. PMID:21541028
Domain movement within a gene: a novel evolutionary mechanism for protein diversification. PMID:21533192
Tandem BRCT Domains: DNA's Praetorian Guard. PMID:21533002
Unexpected complexity of the reef-building coral Acropora millepora transcription factor network. PMID:21526989
The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist. PMID:21526192
NMR structure of the Bordetella bronchiseptica protein NP_888769.1 establishes a new phage-related protein family PF13554. PMID:21520320
The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage. PMID:21515685
Early cardiac morphogenesis defects caused by loss of embryonic macrophage function in Xenopus. PMID:21515365
Ultra-fast sequence clustering from similarity networks with SiLiX. PMID:21513511
DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases. PMID:21504591
The human postsynaptic density shares conserved elements with proteomes of unicellular eukaryotes and prokaryotes. PMID:21503141
Genetic basis for daptomycin resistance in enterococci. PMID:21502617
Characterization of the genome of the polyvalent lytic bacteriophage GTE2, which has potential for biocontrol of Gordonia-, Rhodococcus-, and Nocardia-stabilized foams in activated sludge plants. PMID:21498753
Metagenomics and the protein universe. PMID:21497084
Binding constraints on the evolution of enzymes and signalling proteins: the important role of negative pleiotropy. PMID:21490020
TP0326, a Treponema pallidum β-barrel assembly machinery A (BamA) orthologue and rare outer membrane protein. PMID:21488980
c-di-GMP turn-over in Clostridium difficile is controlled by a plethora of diguanylate cyclases and phosphodiesterases. PMID:21483756
Computational bacterial genome-wide analysis of phylogenetic profiles reveals potential virulence genes of Streptococcus agalactiae. PMID:21483735
Whole-genome sequences of four Mycobacterium bovis BCG vaccine strains. PMID:21478353
Genome sequences of Salmonella enterica serovar typhimurium, Choleraesuis, Dublin, and Gallinarum strains of well- defined virulence in food-producing animals. PMID:21478351
Genome sequence of the Spinosyns-producing bacterium Saccharopolyspora spinosa NRRL 18395. PMID:21478350
Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA. PMID:21478163
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
Bacterial tubulin distinct loop sequences and primitive assembly properties support its origin from a eukaryotic tubulin ancestor. PMID:21467045
Prediction and analysis of paralogous proteins in Trichomonas vaginalis genome. PMID:21464842
The Protein Data Bank in Europe (PDBe): bringing structure to biology. PMID:21460450
PRR7 is a transmembrane adaptor protein expressed in activated T cells involved in regulation of T cell receptor signaling and apoptosis. PMID:21460222
"Fluctuograms" reveal the intermittent intra-protein communication in subtilisin Carlsberg and correlate mechanical coupling with co-evolution. PMID:21455286
Using context to improve protein domain identification. PMID:21453511
Exploration of plant genomes in the FLAGdb++ environment. PMID:21447150
A new approach to assess and predict the functional roles of proteins across all known structures. PMID:21445639
Positional cloning of ds1, the target leaf spot resistance gene against Bipolaris sorghicola in sorghum. PMID:21442410
Full-length de novo sequence of the Chlamydophila psittaci type strain, 6BC. PMID:21441521
Prp8, the pivotal protein of the spliceosomal catalytic center, evolved from a retroelement-encoded reverse transcriptase. PMID:21441348
Germline fitness-based scoring of cancer mutations. PMID:21441214
Evolution of apoptosis-like programmed cell death in unicellular protozoan parasites. PMID:21439063
Phylogenetic distribution and evolutionary history of bacterial DEAD-Box proteins. PMID:21437710
Metalloproteins and the pyrite-based origin of life: a critical assessment. PMID:21431891
HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition. PMID:21423752
Elucidation of functional markers from Aspergillus nidulans developmental regulator FlbB and their phylogenetic distribution. PMID:21423749
Assembling a protein-protein interaction map of the SSU processome from existing datasets. PMID:21423703
Towards a semen proteome of the dengue vector mosquito: protein identification and potential functions. PMID:21423647
Identification of drought-responsive universal stress proteins in viridiplantae. PMID:21423406
Structure-function analysis of the HrpB2-HrcU interaction in the Xanthomonas citri type III secretion system. PMID:21408079
Disease and phenotype data at Ensembl. PMID:21400687
Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper. PMID:21396108
Transcriptome characterization of the South African abalone Haliotis midae using sequencing-by-synthesis. PMID:21396099
Purification, crystallization and preliminary crystallographic analysis of the CBS-domain protein MJ1004 from Methanocaldococcus jannaschii. PMID:21393835
Missense SLC25A38 variations play an important role in autosomal recessive inherited sideroblastic anemia. PMID:21393332
Diversity in functional organization of class I and class II biotin protein ligase. PMID:21390227
Spliceosomal intron size expansion in domesticated grapevine (Vitis vinifera). PMID:21385391
Characterization of mutants deficient in the L,D-carboxypeptidase (DacB) and WalRK (VicRK) regulon, involved in peptidoglycan maturation of Streptococcus pneumoniae serotype 2 strain D39. PMID:21378199
The YaaA protein of the Escherichia coli OxyR regulon lessens hydrogen peroxide toxicity by diminishing the amount of intracellular unincorporated iron. PMID:21378183
A differential proteome screening system for post-translational modification-dependent transcription factor interactions. PMID:21372816
Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics. PMID:21368207
Identification of surface proteins in Enterococcus faecalis V583. PMID:21362161
Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. PMID:21356090
Fold and function of the InlB B-repeat. PMID:21345802
A novel amidotransferase required for lipoic acid cofactor assembly in Bacillus subtilis. PMID:21338421
A non-canonical start codon in the Drosophila fragile X gene yields two functional isoforms. PMID:21333716
RSpred, a set of Hidden Markov Models to detect and classify the RIFIN and STEVOR proteins of Plasmodium falciparum. PMID:21332983
Systems biology: the next frontier for bioinformatics. PMID:21331364
General transcription factors and subunits of RNA polymerase III: Paralogs for promoter- and cell type-specific transcription in multicellular eukaryotes. PMID:21326886
A survey of schistosome protein domain types: insights into unique biological properties. PMID:21315771
A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. PMID:21306995
Novel analysis of oceanic surface water metagenomes suggests importance of polyphosphate metabolism in oligotrophic environments. PMID:21305044
Accurate quantification of functional analogy among close homologs. PMID:21304936
Rad23 escapes degradation because it lacks a proteasome initiation region. PMID:21304521
Dr. PIAS: an integrative system for assessing the druggability of protein-protein interactions. PMID:21303559
In vitro studies indicate a high resistance potential for the lantibiotic nisin in Staphylococcus aureus and define a genetic basis for nisin resistance. PMID:21300840
Phylogenetic comparison of F-Box (FBX) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift. PMID:21297981
Eukaryote-wide sequence analysis of mitochondrial β-barrel outer membrane proteins. PMID:21272379
Genome-wide identification, classification and analysis of heat shock transcription factor family in maize. PMID:21272351
Augmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability. PMID:21270388
Massive genomic decay in Serratia symbiotica, a recently evolved symbiont of aphids. PMID:21266540
Evolution of linear chromosomes and multipartite genomes in yeast mitochondria. PMID:21266473
A three-dimensional RNA motif in Potato spindle tuber viroid mediates trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana. PMID:21258006
Genome (re-)annotation and open-source annotation pipelines. PMID:21255336
Coding potential of the products of alternative splicing in human. PMID:21251333
Crystal structure of the human N-Myc downstream-regulated gene 2 protein provides insight into its role as a tumor suppressor. PMID:21247902
Identification of a putative chaperone involved in stress resistance and virulence in Francisella tularensis. PMID:21245269
Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires. PMID:21241503
Nitrogen fixation and nitrogenase (nifH) expression in tropical waters of the eastern North Atlantic. PMID:21228888
ARTADE2DB: improved statistical inferences for Arabidopsis gene functions and structure predictions by dynamic structure-based dynamic expression (DSDE) analyses. PMID:21227933
Blueprint for a minimal photoautotrophic cell: conserved and variable genes in Synechococcus elongatus PCC 7942. PMID:21226929
1,000 structures and more from the MCSG. PMID:21219649
Identification of Escherichia coli ZapC (YcbW) as a component of the division apparatus that binds and bundles FtsZ polymers. PMID:21216997
The tib adherence locus of enterotoxigenic Escherichia coli is regulated by cyclic AMP receptor protein. PMID:21216994
Fic domain-catalyzed adenylylation: insight provided by the structural analysis of the type IV secretion system effector BepA. PMID:21213248
Identification and sequencing of a novel rodent gammaherpesvirus that establishes acute and latent infection in laboratory mice. PMID:21209105
Development and application of bovine and porcine oligonucleotide arrays with protein-based annotation. PMID:21197395
Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. PMID:21194434
Pseudomonas aeruginosa β-lactamase induction requires two permeases, AmpG and AmpP. PMID:21192796
The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence. PMID:21192786
The maize ALDH protein superfamily: linking structural features to functional specificities. PMID:21190582
Specificity of the E. coli LysR-type transcriptional regulators. PMID:21187915
Genome sequence and characterization of the Tsukamurella bacteriophage TPA2. PMID:21183635
Hydrophobins from Aspergillus species cannot be clearly divided into two classes. PMID:21182770
A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology. PMID:21179477
The steady-state repertoire of human SCF ubiquitin ligase complexes does not require ongoing Nedd8 conjugation. PMID:21169563
Metagenomic analyses: past and future trends. PMID:21169428
Structures of domains I and IV from YbbR are representative of a widely distributed protein family. PMID:21154411
Acyl-protein thioesterase 2 catalyzes the deacylation of peripheral membrane-associated GAP-43. PMID:21152083
Identification, activity and disulfide connectivity of C-di-GMP regulating proteins in Mycobacterium tuberculosis. PMID:21151497
Complete nucleomorph genome sequence of the nonphotosynthetic alga Cryptomonas paramecium reveals a core nucleomorph gene set. PMID:21147880
Thiol signalling network with an eye to diabetes. PMID:21135801
The C-terminal region of the exosome-associated protein Rrp47 is specifically required for box C/D small nucleolar RNA 3'-maturation. PMID:21135092
Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression. PMID:21127008
A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes. PMID:21124907
Sequence motifs in MADS transcription factors responsible for specificity and diversification of protein-protein interaction. PMID:21124869
CDD: a Conserved Domain Database for the functional annotation of proteins. PMID:21109532
Computational study of the Na+/H + antiporter from Vibrio parahaemolyticus. PMID:21107625
Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins. PMID:21106129
Evolution of the Kdo2-lipid A biosynthesis in bacteria. PMID:21106097
DIMA 3.0: Domain Interaction Map. PMID:21097782
PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. PMID:21097470
Laminin database: a tool to retrieve high-throughput and curated data for studies on laminins. PMID:21087995
Role of RecJ-like protein with 5'-3' exonuclease activity in oligo(deoxy)nucleotide degradation. PMID:21087930
Lytic enzyme discovery through multigenomic sequence analysis in Clostridium perfringens. PMID:21085950
PhEVER: a database for the global exploration of virus-host evolutionary relationships. PMID:21081560
Conserved mechanism for sensor phosphatase control of two-component signaling revealed in the nitrate sensor NarX. PMID:21078995
The N-terminal domain of the Flo1 flocculation protein from Saccharomyces cerevisiae binds specifically to mannose carbohydrates. PMID:21076009
Extracellular aldonolactonase from Myceliophthora thermophila. PMID:21075873
Effective--a database of predicted secreted bacterial proteins. PMID:21071416
Computer aided selection of candidate vaccine antigens. PMID:21067543
Identification of a severe acute respiratory syndrome coronavirus-like virus in a leaf-nosed bat in Nigeria. PMID:21063474
Characterization of the relationship between integrase, excisionase and antirepressor activities associated with a superinfecting Shiga toxin encoding bacteriophage. PMID:21062824
SUPERFAMILY 1.75 including a domain-centric gene ontology method. PMID:21062816
Whole genome co-expression analysis of soybean cytochrome P450 genes identifies nodulation-specific P450 monooxygenases. PMID:21062474
Cross-talk between the catalytic core and the regulatory domain in cystathionine β-synthase: study by differential covalent labeling and computational modeling. PMID:21062078
Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. PMID:21059887
PolyQ: a database describing the sequence and domain context of polyglutamine repeats in proteins. PMID:21059684
DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. PMID:21059682
P2CS: a database of prokaryotic two-component systems. PMID:21051349
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. PMID:21051348
In silico prediction of human pathogenicity in the γ-proteobacteria. PMID:21048922
Characterization of a glucose-, xylose-, sucrose-, and D-galactose-stimulated β-glucosidase from the alkalophilic bacterium Bacillus halodurans C-125. PMID:21046402
Structural analysis of Bacillus pumilus phenolic acid decarboxylase, a lipocalin-fold enzyme. PMID:21045284
ThYme: a database for thioester-active enzymes. PMID:21045059
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. PMID:21045053
Complete genome sequence of Bifidobacterium bifidum S17. PMID:21037011
The RCSB Protein Data Bank: redesigned web site and web services. PMID:21036868
RBPDB: a database of RNA-binding specificities. PMID:21036867
The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms. PMID:21036862
Natural and engineered photoactivated nucleotidyl cyclases for optogenetic applications. PMID:21030591
Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement. PMID:20979641
Ancient origin of animal U-box ubiquitin ligases. PMID:20979629
Of bits and bugs--on the use of bioinformatics and a bacterial crystal structure to solve a eukaryotic repeat-protein structure. PMID:20976240
Library of disordered patterns in 3D protein structures. PMID:20976197
Phosphate binding sites identification in protein structures. PMID:20974634
Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon. PMID:20973991
Machine learning methods for prediction of CDK-inhibitors. PMID:20967128
3did: identification and classification of domain-based interactions of known three-dimensional structure. PMID:20965963
A widespread peroxiredoxin-like domain present in tumor suppression- and progression-implicated proteins. PMID:20964819
Autophagy in protists. PMID:20962583
Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments. PMID:20961958
ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome. PMID:20955618
OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria. PMID:20952406
PAIR: the predicted Arabidopsis interactome resource. PMID:20952401
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
The systematic functional analysis of Plasmodium protein kinases identifies essential regulators of mosquito transmission. PMID:20951971
Tight regulation of the intS gene of the KplE1 prophage: a new paradigm for integrase gene regulation. PMID:20949106
Involvement of EupR, a response regulator of the NarL/FixJ family, in the control of the uptake of the compatible solutes ectoines by the halophilic bacterium Chromohalobacter salexigens. PMID:20942908
The impact of gene expression regulation on evolution of extracellular signaling pathways. PMID:20935258
The Protein Ontology: a structured representation of protein forms and complexes. PMID:20935045
Comparative genomics of marine mussels (Mytilus spp.) gender associated mtDNA: rapidly evolving atp8. PMID:20931184
Uncovering the human methyltransferasome. PMID:20930037
Lipoic acid synthesis: a new family of octanoyltransferases generally annotated as lipoate protein ligases. PMID:20882995
NMR spectroscopic and theoretical analysis of a spontaneously formed Lys-Asp isopeptide bond. PMID:20878961
DAnCER: disease-annotated chromatin epigenetics resource. PMID:20876685
The N-terminal domain of the arenavirus L protein is an RNA endonuclease essential in mRNA transcription. PMID:20862324
Identification and characterization of a serine protease inhibitor with two trypsin inhibitor-like domains from the human hookworm Ancylostoma duodenale. PMID:20852886
Elective affinities: a Tudor-Aubergine tale of germline partnership. PMID:20844011
Rapid calcium-dependent activation of Aurora-A kinase. PMID:20842194
FMN binding and photochemical properties of plant putative photoreceptors containing two LOV domains, LOV/LOV proteins. PMID:20826774
The distribution of GYR- and YLP-like motifs in Drosophila suggests a general role in cuticle assembly and other protein-protein interactions. PMID:20824096
The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics. PMID:20813266
Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes. PMID:20807838
Comparative analysis of the biochemical and functional properties of C-terminal domains of autotransporters. PMID:20802036
A mixed community of actinomycetes produce multiple antibiotics for the fungus farming ant Acromyrmex octospinosus. PMID:20796277
Identification of novel families and classification of the C2 domain superfamily elucidate the origin and evolution of membrane targeting activities in eukaryotes. PMID:20713135
Brochothrix thermosphacta bacteriophages feature heterogeneous and highly mosaic genomes and utilize unique prophage insertion sites. PMID:20709901
Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences. PMID:20705649
Superpose3D: a local structural comparison program that allows for user-defined structure representations. PMID:20700534
RefProtDom: a protein database with improved domain boundaries and homology relationships. PMID:20693322
Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept. PMID:20688752
Symbiotic Streptomyces sp. TN119 GH 11 xylanase: a new pH-stable, protease- and SDS-resistant xylanase. PMID:20686913
More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology. PMID:20686689
Genomic architecture of MHC-linked odorant receptor gene repertoires among 16 vertebrate species. PMID:20680261
The PpaA/AerR regulators of photosynthesis gene expression from anoxygenic phototrophic proteobacteria contain heme-binding SCHIC domains. PMID:20675482
Genomic repertoires of DNA-binding transcription factors across the tree of life. PMID:20675356
Lineage-specific expansion of DNA-binding transcription factor families. PMID:20675012
Identification of a hemerythrin-like domain in a P1B-type transport ATPase. PMID:20672819
Phylogenetic analysis of ferlin genes reveals ancient eukaryotic origins. PMID:20667140
Molecular identification of N-acetylaspartylglutamate synthase and beta-citrylglutamate synthase. PMID:20657015
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
Analysis of promoter activity of members of the PECTATE LYASE-LIKE (PLL) gene family in cell separation in Arabidopsis. PMID:20649977
From complete genome sequence to 'complete' understanding? PMID:20647113
Highly divergent mitochondrial ATP synthase complexes in Tetrahymena thermophila. PMID:20644710
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. PMID:20639539
Quantifying the mechanisms of domain gain in animal proteins. PMID:20633280
Genome sequence of the model mushroom Schizophyllum commune. PMID:20622885
Localization and cellular amounts of the WalRKJ (VicRKX) two-component regulatory system proteins in serotype 2 Streptococcus pneumoniae. PMID:20622066
Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1. PMID:20613791
Orthology confers intron position conservation. PMID:20598118
Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana. PMID:20594336
What lessons can be learned from studying the folding of homologous proteins? PMID:20570731
EntrezAJAX: direct web browser access to the Entrez Programming Utilities. PMID:20565938
Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families. PMID:20532204
AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis. PMID:20530533
Proteomic analysis of the fish pathogen Flavobacterium columnare. PMID:20525376
Thioesterases: a new perspective based on their primary and tertiary structures. PMID:20506386
WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data. PMID:20501601
Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family. PMID:20500830
Characterization of the N-ATPase, a distinct, laterally transferred Na+-translocating form of the bacterial F-type membrane ATPase. PMID:20472544
agriGO: a GO analysis toolkit for the agricultural community. PMID:20435677
Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase. PMID:20423905
Predicting conserved protein motifs with Sub-HMMs. PMID:20420695
Improved microarray-based decision support with graph encoded interactome data. PMID:20419106
Origin and fate of pseudogenes in Hemiascomycetes: a comparative analysis. PMID:20412590
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. PMID:20369061
Systematic analysis of human protein complexes identifies chromosome segregation proteins. PMID:20360068
Diversity of structure and function of response regulator output domains. PMID:20226724
The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. PMID:19965766
Protein databases on the internet. PMID:18265344 -
The Pfam protein families database in 2019
PubMed citations: 1442.
1442 articles citing: The Pfam protein families database in 2019
Black pepper and tarragon essential oils suppress the lipolytic potential and the type II secretion system of P. psychrophila KM02. PMID:35361821
Genome-wide characterization and expression of the TLP gene family associated with Colletotrichum gloeosporioides inoculation in Fragaria × ananassa. PMID:35356470
Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily. PMID:35352015
Newly discovered Staphylococcus aureus serine hydrolase probe and drug targets. PMID:35350120
Genomic and Transcriptomic Landscape and Evolutionary Dynamics of Heat Shock Proteins in Spotted Sea Bass (Lateolabrax maculatus) under Salinity Change and Alkalinity Stress. PMID:35336727
Non-Coding Transcriptome Provides Novel Insights into the Escherichia coli F17 Susceptibility of Sheep Lamb. PMID:35336723
The Role of Lysine Methyltransferase SET7/9 in Proliferation and Cell Stress Response. PMID:35330113
Long Non-Coding RNAs Might Regulate Phenotypic Switch of Vascular Smooth Muscle Cells Acting as ceRNA: Implications for In-Stent Restenosis. PMID:35328496
Discovery and Biotechnological Exploitation of Glycoside-Phosphorylases. PMID:35328479
In Silico Methods for the Identification of Viral-Derived Small Interfering RNAs (vsiRNAs) and Their Application in Plant Genomics. PMID:35325416
Genome-wide identification, phylogenetic and expression pattern analysis of MADS-box family genes in foxtail millet (Setaria italica). PMID:35322041
Genomic Fishing and Data Processing for Molecular Evolution Research. PMID:35314663
Systematic estimation of cystic fibrosis prevalence in Chinese and genetic spectrum comparison to Caucasians. PMID:35313924
Shinella oryzae sp. nov., a novel zearalenone-resistant bacterium isolated from rice paddy soil. PMID:35312873
LCOR mediates interferon-independent tumor immunogenicity and responsiveness to immune-checkpoint blockade in triple-negative breast cancer. PMID:35301507
Genome-Wide Characterization and Anthocyanin-Related Expression Analysis of the B-BOX Gene Family in Capsicum annuum L. PMID:35295945
EnsembleFam: towards more accurate protein family prediction in the twilight zone. PMID:35287576
Characterization and Evaluation of a Novel Conserved Membrane Antigen P35 of Mycoplasma synoviae. PMID:35280133
A Thermodynamic Model for Water Activity and Redox Potential in Evolution and Development. PMID:35279735
Nettle manure: an unsuspected source of bacteriophages active against various phytopathogenic bacteria. PMID:35277777
Deciphering the Potential Coding of Human Cytomegalovirus: New Predicted Transmembrane Proteome. PMID:35269907
Mammalian HEMK1 methylates glutamine residue of the GGQ motif of mitochondrial release factors. PMID:35260756
Constructing benchmark test sets for biological sequence analysis using independent set algorithms. PMID:35255082
Genome-Wide Identification and Expression Profiling of Germin-Like Proteins Reveal Their Role in Regulating Abiotic Stress Response in Potato. PMID:35251067
Characterization of pectin methylesterase gene family and its possible role in juice sac granulation in navel orange (Citrus sinensis Osbeck). PMID:35249536
The Role of Intestinal Microbiota in Regulating the Metabolism of Bile Acids Is Conserved Across Vertebrates. PMID:35242120
Phylogenetic analysis of forkhead transcription factors in the Panarthropoda. PMID:35230523
Genome-Wide Analysis of Serine Hydroxymethyltransferase Genes in Triticeae Species Reveals That TaSHMT3A-1 Regulates Fusarium Head Blight Resistance in Wheat. PMID:35222497
Forgotten Actors: Glycoside Hydrolases During Elongation Growth of Maize Primary Root. PMID:35222452
Phenotypic and Genetic Characterization of Aeromonas hydrophila Phage AhMtk13a and Evaluation of Its Therapeutic Potential on Simulated Aeromonas Infection in Danio rerio. PMID:35216005
Genome-Wide Identification and Gene Expression Analysis of the OTU DUB Family in Oryza sativa. PMID:35215984
Functional Characterization of Replication-Associated Proteins Encoded by Alphasatellites Identified in Yunnan Province, China. PMID:35215816
Experimental evaluation of ecological principles to understand and modulate the outcome of bacterial strain competition in gut microbiomes. PMID:35210551
New Genomic Signals Underlying the Emergence of Human Proto-Genes. PMID:35205330
A Comparative Evaluation of the Structural and Dynamic Properties of Insect Odorant Binding Proteins. PMID:35204784
Chemerin Impact on Alternative mRNA Transcription in the Porcine Luteal Cells. PMID:35203364
The Caspase Homologues in Scallop Chlamys farreri and Their Expression Responses to Toxic Dinoflagellates Exposure. PMID:35202135
Wei2GO: weighted sequence similarity-based protein function prediction. PMID:35186498
Microsecond molecular dynamics simulations revealed the inhibitory potency of amiloride analogs against SARS-CoV-2 E viroporin. PMID:35172476
Diverse methylotrophic methanogenic archaea cause high methane emissions from seagrass meadows. PMID:35165204
Homologous Cloning of Potassium Channel Genes From the Superior Apple Rootstock Line 12-2, Which is Tolerant to Apple Replant Disease. PMID:35154275
Genomic Insights Into Cadmium Resistance of a Newly Isolated, Plasmid-Free Cellulomonas sp. Strain Y8. PMID:35154027
Structural characterization of the ANTAR antiterminator domain bound to RNA. PMID:35150565
Chromosome-Level Genome Assembly of Anthidium xuezhongi Niu & Zhu, 2020 (Hymenoptera: Apoidea: Megachilidae: Anthidiini). PMID:35150256
The genome of the Paleogene relic tree Bretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs. PMID:35137004
RNA-dependent synthesis of ergosteryl-3β-O-glycine in Ascomycota expands the diversity of steryl-amino acids. PMID:35131263
GRAND: An Integrated Genome, Transcriptome Resources, and Gene Network Database for Gossypium. PMID:35126443
Phylogenetic Analysis of the SQUAMOSA Promoter-Binding Protein-Like Genes in Four Ipomoea Species and Expression Profiling of the IbSPLs During Storage Root Development in Sweet Potato (Ipomoea batatas). PMID:35126426
A hyperpromiscuous antitoxin protein domain for the neutralization of diverse toxin domains. PMID:35121656
Complete genome sequence of the kiwifruit bacterial canker pathogen Pseudomonas savastanoi strain MHT1. PMID:35120460
A Chromosome-Level Genome Assembly of the Parasitic Wasp Chelonus formosanus Sonan 1932 (Hymenoptera: Braconidae). PMID:35104339
Genomic insight into the scale specialization of the biological control agent Novius pumilus (Weise, 1892). PMID:35100986
TransDTI: Transformer-Based Language Models for Estimating DTIs and Building a Drug Recommendation Workflow. PMID:35097268
A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss). PMID:35094708
Evolution of DNA Methylation Across Ecdysozoa. PMID:35089376
Florigen and its homologs of FT/CETS/PEBP/RKIP/YbhB family may be the enzymes of small molecule metabolism: review of the evidence. PMID:35086479
Promiscuous Domains in Eukaryotes and HAT Proteins in FUNGI Have Followed Different Evolutionary Paths. PMID:35084521
Sequence Divergence and Functional Specializations of the Ancient Spliceosomal SF3b: Implications in Flexibility and Adaptations of the Multi-Protein Complex. PMID:35082828
Distribution, organization and expression of genes concerned with anaerobic lactate utilization in human intestinal bacteria. PMID:35077342
The genome of medicinal leech (Whitmania pigra) and comparative genomic study for exploration of bioactive ingredients. PMID:35073842
QSalignWeb: A Server to Predict and Analyze Protein Quaternary Structure. PMID:35071324
MrTPS3 and MrTPS20 Are Responsible for β-Caryophyllene and α-Pinene Production, Respectively, in Red Bayberry (Morella rubra). PMID:35069655
Quantitative Proteome and Transcriptome Dynamics Analysis Reveals Iron Deficiency Response Networks and Signature in Neuronal Cells. PMID:35056799
Towards an Ideal In Cell Hybridization-Based Strategy to Discover Protein Interactomes of Selected RNA Molecules. PMID:35055128
Characterization of the Chitinase Gene Family in Mulberry (Morus notabilis) and MnChi18 Involved in Resistance to Botrytis cinerea. PMID:35052438
Stingray Venom Proteins: Mechanisms of Action Revealed Using a Novel Network Pharmacology Approach. PMID:35049882
Identification of putative essential protein domains from high-density transposon insertion sequencing. PMID:35046497
Comparative transcriptome analysis of two contrasting resistant and susceptible Aegilops tauschii accessions to wheat leaf rust (Puccinia triticina) using RNA-sequencing. PMID:35039525
Genome-wide identification and characterization of SPX-domain-containing protein gene family in Solanum lycopersicum. PMID:35036163
Genomic characterization of ZIP genes in pigeonpea (CcZIP) and their expression analysis among the genotypes with contrasting host response to pod borer. PMID:35035136
A chromosome-scale genome assembly for the holly (Ilex polyneura) provides insights into genomic adaptations to elevation in Southwest China. PMID:35031793
Rewards of divergence in sequences, 3-D structures and dynamics of yeast and human spliceosome SF3b complexes. PMID:35028595
Genome-wide identification and expression analysis of NtbHLH gene family in tobacco (Nicotiana tabacum) and the role of NtbHLH86 in drought adaptation. PMID:35024520
Distribution and Evolutionary History of Sialic Acid Catabolism in the Phylum Actinobacteria. PMID:35019771
Protein Interactome Analysis of the Type IX Secretion System Identifies PorW as the Missing Link between the PorK/N Ring Complex and the Sov Translocon. PMID:35019767
Genome-wide identification and expression profiling analysis of Wnt family genes affecting adipocyte differentiation in cattle. PMID:35017603
Tissue specific expression of UMAMIT amino acid transporters in wheat. PMID:35013480
Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf. PMID:35013291
De Novo Transcriptome Analysis of the Venom of Latrodectus geometricus with the Discovery of an Insect-Selective Na Channel Modulator. PMID:35011282
The role of junctophilin proteins in cellular function. PMID:35001666
Characterization of non-specific lipid transfer protein (nsLtp) gene families in the Brassica napus pangenome reveals abundance variation. PMID:34996379
Expression, Localization, and Protein Interactions of the Partitioning Proteins in the Gonococcal Type IV Secretion System. PMID:34975804
Genome-wide analysis uncovers tomato leaf lncRNAs transcriptionally active upon Pseudomonas syringae pv. tomato challenge. PMID:34972834
Mobilization of vitamin B12 transporters alters competitive dynamics in a human gut microbe. PMID:34965410
Photosynthesis-related genes induce resistance against soybean mosaic virus: Evidence for involvement of the RNA silencing pathway. PMID:34962034
Genome-Wide Identification and Characterization of Melon bHLH Transcription Factors in Regulation of Fruit Development. PMID:34961193
High Molecular Weight Kininogen: A Review of the Structural Literature. PMID:34948166
Chromosome-Level Genome Assembly Provides New Insights into Genome Evolution and Tuberous Root Formation of Potentilla anserina. PMID:34946942
Genome-Wide Analysis of the MADS-Box Gene Family in Maize: Gene Structure, Evolution, and Relationships. PMID:34946905
Genome-Wide Identification of the Q-type C2H2 Transcription Factor Family in Alfalfa (Medicago sativa) and Expression Analysis under Different Abiotic Stresses. PMID:34946855
H-NOX proteins in the virulence of pathogenic bacteria. PMID:34939646
In-depth assembly of organ and development dissected Picrorhiza kurroa proteome map using mass spectrometry. PMID:34937558
Genome-Wide Identification and Gene Expression Analysis of Acyl-Activating Enzymes Superfamily in Tomato (Solanum lycopersicum) Under Aluminum Stress. PMID:34925406
Thioesterase enzyme families: Functions, structures, and mechanisms. PMID:34921469
Genome-wide identification of PIP5K in wheat and its relationship with anther male sterility induced by high temperature. PMID:34915841
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. PMID:34911965
The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers. PMID:34906246
Computational modelling of chromosomally clustering protein domains in bacteria. PMID:34906073
Identification and classification of reverse transcriptases in bacterial genomes and metagenomes. PMID:34904653
Genome-Wide Identification and Expression Analysis of Terpene Synthase Genes in Cymbidium faberi. PMID:34899778
Fungal cellulases: protein engineering and post-translational modifications. PMID:34889986
Acidovorax pan-genome reveals specific functional traits for plant beneficial and pathogenic plant-associations. PMID:34889729
Prediction of Protein-Protein Binding Affinities from Unbound Protein Structures. PMID:34888728
A Method for the Analysis of African Swine Fever by Viral Metagenomic Sequencing. PMID:34888376
Phylogenomic and Microsynteny Analysis Provides Evidence of Genome Arrangements of High-Affinity Nitrate Transporter Gene Families of Plants. PMID:34884876
The Facts and Family Secrets of Plasmids That Replicate via the Rolling-Circle Mechanism. PMID:34878299
Dynamic Expression and Regulatory Network of Circular RNA for Abdominal Preadipocytes Differentiation in Chicken (Gallus gallus). PMID:34869349
Phylogenetic Analysis of the Membrane Attack Complex/Perforin Domain-Containing Proteins in Gossypium and the Role of GhMACPF26 in Cotton Under Cold Stress. PMID:34868097
Genome-wide characterization of bZIP gene family identifies potential members involved in flavonoids biosynthesis in Ginkgo biloba L. PMID:34862430
Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases. PMID:34857024
A comprehensive in silico investigation into the nsSNPs of Drd2 gene predicts significant functional consequences in dopamine signaling and pharmacotherapy. PMID:34853389
Transcriptomic dataset for Sardina pilchardus: Assembly, annotation, and expression of nine tissues. PMID:34849383
Genome-wide unbalanced expression bias and expression level dominance toward Brassica oleracea in artificially synthesized intergeneric hybrids of Raphanobrassica. PMID:34848691
Global identification and integrated analysis of heat-responsive long non-coding RNAs in contrasting rice cultivars. PMID:34846546
Protein domain-based prediction of drug/compound-target interactions and experimental validation on LIM kinases. PMID:34843456
New Insights into Plant TPK Ion Channel Evolution. PMID:34834689
Genome-Wide Identification, Characterization and Expression Analysis of Soybean CHYR Gene Family. PMID:34830077
Genome-Wide Identification and Analysis of the MADS-Box Gene Family in Theobroma cacao. PMID:34828404
A Missense Variant in the Bardet-Biedl Syndrome 2 Gene (BBS2) Leads to a Novel Syndromic Retinal Degeneration in the Shetland Sheepdog. PMID:34828377
Genome-Wide Identification and Functional Exploration of SBP-Box Gene Family in Black Pepper (Piper nigrum L.). PMID:34828347
Genome-wide analysis of autophagy-related genes in Medicago truncatula highlights their roles in seed development and response to drought stress. PMID:34824334
A ubiquitous disordered protein interaction module orchestrates transcription elongation. PMID:34822292
Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution. PMID:34820204
De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins. PMID:34820176
Rare germline variants in the AXIN2 gene in families with colonic polyposis and colorectal cancer. PMID:34817745
Heliorhodopsin Evolution Is Driven by Photosensory Promiscuity in Monoderms. PMID:34817235
Machine learning approaches to predict the Plant-associated phenotype of Xanthomonas strains. PMID:34814827
Slowest-first protein translation scheme: Structural asymmetry and co-translational folding. PMID:34813729
Transcript-targeted analysis reveals isoform alterations and double-hop fusions in breast cancer. PMID:34811492
Genome sequencing of the multicellular alga Astrephomene provides insights into convergent evolution of germ-soma differentiation. PMID:34811380
Characterization of the Flagellar Collar Reveals Structural Plasticity Essential for Spirochete Motility. PMID:34809456
Rapid Divergence of Key Spermatogenesis Genes in nasuta-Subgroup of Drosophila. PMID:34807291
The Angiostrongylus vasorum Excretory/Secretory and Surface Proteome Contains Putative Modulators of the Host Coagulation. PMID:34796127
Hox genes regulate asexual reproductive behavior and tissue segmentation in adult animals. PMID:34795249
Genetic fusions favor tumorigenesis through degron loss in oncogenes. PMID:34795215
Schistosoma mansoni Larval Extracellular Vesicle protein 1 (SmLEV1) is an immunogenic antigen found in EVs released from pre-acetabular glands of invading cercariae. PMID:34793443
Flagellin lysine methyltransferase FliB catalyzes a [4Fe-4S] mediated methyl transfer reaction. PMID:34788341
A Superefficient Ochratoxin A Hydrolase with Promising Potential for Industrial Applications. PMID:34788069
The SR Splicing Factors: Providing Perspectives on Their Evolution, Expression, Alternative Splicing, and Function in Populus trichocarpa. PMID:34768799
Two TGA Transcription Factor Members from Hyper-Susceptible Soybean Exhibiting Significant Basal Resistance to Soybean mosaic virus. PMID:34768757
Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data. PMID:34762392
Evolution of the Cytokinin Dehydrogenase (CKX) Domain. PMID:34757471
Surface residues and nonadditive interactions stabilize a consensus homeodomain protein. PMID:34757081
A computational screen for alternative genetic codes in over 250,000 genomes. PMID:34751130
The transposable element-rich genome of the cereal pest Sitophilus oryzae. PMID:34749730
A genome-phenome association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA. PMID:34747693
Transcriptome-Based Identification and Functional Characterization of NAC Transcription Factors Responsive to Drought Stress in Capsicum annuum L. PMID:34745217
Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.). PMID:34742240
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. PMID:34739369
eIF3k Domain-Containing Protein Regulates Conidiogenesis, Appressorium Turgor, Virulence, Stress Tolerance, and Physiological and Pathogenic Development of Magnaporthe oryzae Oryzae. PMID:34733303
Sex without crossing over in the yeast Saccharomycodes ludwigii. PMID:34732243
Transcriptome profiling reveals the developmental regulation of NaCl-treated Forcipomyia taiwana eggs. PMID:34732124
The chitinolytic activity of the Curtobacterium sp. isolated from field-grown soybean and analysis of its genome sequence. PMID:34731210
Assessment of the plasmidome of an extremophilic microbial community from the Diamante Lake, Argentina. PMID:34728656
The generative capacity of probabilistic protein sequence models. PMID:34728624
The APETALA2 homolog CaFFN regulates flowering time in pepper. PMID:34719686
The leptospiral LipL21 and LipL41 proteins exhibit a broad spectrum of interactions with host cell components. PMID:34719356
Functional Annotation from Structural Homology. PMID:34718998
Centrality of drug targets in protein networks. PMID:34715787
A Proposed Framework to Identify Dispensable and Essential Functions in Bifidobacteria: Case Study of Bifidobacterium breve UCC2003 as a Prototype of Its Genus. PMID:34709622
Genomic analysis of SBP gene family in Saccharum spontaneum reveals their association with vegetative and reproductive development. PMID:34706643
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
Rid7C, a Member of the YjgF/YER057c/UK114 (Rid) Protein Family, Is a Novel Endoribonuclease That Regulates the Expression of a Specialist RNA Polymerase Involved in Differentiation in Nonomuraea gerenzanensis. PMID:34694905
Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family. PMID:34688653
TAGOPSIN: collating taxa-specific gene and protein functional and structural information. PMID:34688246
Identification of Potential Citrate Metabolism Pathways in Carnobacterium maltaromaticum. PMID:34683489
Alternative Splicing Mechanisms Underlying Opioid-Induced Hyperalgesia. PMID:34680965
Trends in the Application of "Omics" to Ecotoxicology and Stress Ecology. PMID:34680873
De Novo Genome Assembly of Chinese Plateau Honeybee Unravels Intraspecies Genetic Diversity in the Eastern Honeybee, Apis cerana. PMID:34680661
Chromosome-Level Genome Assembly of Nephotettix cincticeps (Uhler, 1896) (Hemiptera: Cicadellidae: Deltocephalinae). PMID:34677607
Early-life formula feeding is associated with infant gut microbiota alterations and an increased antibiotic resistance load. PMID:34677583
Genome-Wide Characterization and Expression Analysis of bZIP Gene Family Under Abiotic Stress in Glycyrrhiza uralensis. PMID:34675967
An improved deep learning model for hierarchical classification of protein families. PMID:34669708
RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family. PMID:34669691
Sulfur cycling and host-virus interactions in Aquificales-dominated biofilms from Yellowstone's hottest ecosystems. PMID:34650231
Genome-wide identification and expression profile analysis of trihelix transcription factor family genes in response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]. PMID:34649496
Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor. PMID:34648493
Identification of Rare LRP5 Variants in a Cohort of Males with Impaired Bone Mass. PMID:34639175
The Distinct Properties of the Consecutive Disordered Regions Inside or Outside Protein Domains and Their Functional Significance. PMID:34639018
Global Survey of the Full-Length Cabbage Transcriptome (Brassica oleracea Var. capitata L.) Reveals Key Alternative Splicing Events Involved in Growth and Disease Response. PMID:34638781
Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication. PMID:34635656
Evolutionary Implications of the RNA N6-Methyladenosine Methylome in Plants. PMID:34633447
Genome-wide identification and expression analysis of the 2OG-Fe(II) oxygenase gene family in upland cotton (Gossypium hirsutum L.). PMID:34629772
Manual Annotation Studio (MAS): a collaborative platform for manual functional annotation of viral and microbial genomes. PMID:34627149
Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition. PMID:34622230
caAtlas: An immunopeptidome atlas of human cancer. PMID:34622160
Morphological and Genomic Features of the New Klosneuvirinae Isolate Fadolivirus IHUMI-VV54. PMID:34621250
Navigating the amino acid sequence space between functional proteins using a deep learning framework. PMID:34616884
Efficient generative modeling of protein sequences using simple autoregressive models. PMID:34608136
Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. PMID:34606606
Identification of a Novel Pyruvyltransferase Using 13C Solid-State Nuclear Magnetic Resonance To Analyze Rhizobial Exopolysaccharides. PMID:34606371
Prediction and analysis of antifreeze proteins. PMID:34604556
Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity. PMID:34603269
Prophages encode phage-defense systems with cognate self-immunity. PMID:34597593
Genome-Wide Comparative Analysis of R2R3 MYB Gene Family in Populus and Salix and Identification of Male Flower Bud Development-Related Genes. PMID:34594352
ECNet is an evolutionary context-integrated deep learning framework for protein engineering. PMID:34593817
Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing. PMID:34581030
In Vitro and In Vivo Assessment of the Potential of Escherichia coli Phages to Treat Infections and Survive Gastric Conditions. PMID:34576765
Genome-Wide Identification and Analyses of Drought/Salt-Responsive Cytochrome P450 Genes in Medicago truncatula. PMID:34576120
Internally Symmetrical Stwintrons and Related Canonical Introns in Hypoxylaceae Species. PMID:34575748
Adaptation of Fig Wasps (Agaodinae) to Their Host Revealed by Large-Scale Transcriptomic Data. PMID:34564255
Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class. PMID:34555022
Transcriptome-based analysis reveals that the biosynthesis of anthocyanins is more active than that of flavonols and proanthocyanins in the colorful flowers of Lagerstroemia indica. PMID:34554492
Improved pathogenicity prediction for rare human missense variants. PMID:34551312
Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria. PMID:34546073
Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives. PMID:34540375
Molecular Characterization and Expression Analysis of the Na+/H+ Exchanger Gene Family in Capsicum annuum L. PMID:34539731
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. PMID:34537014
The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole. PMID:34531387
Engineering the substrate binding site of the hyperthermostable archaeal endo-β-1,4-galactanase from Ignisphaera aggregans. PMID:34530892
Alterations of mRNA and lncRNA profiles associated with the extracellular matrix and spermatogenesis in goats. PMID:34530511
Chromosome-Level Genome Sequence of Aspergillus chevalieri M1, Isolated from Katsuobushi. PMID:34528823
Characterization and engineering of Streptomyces griseofuscus DSM 40191 as a potential host for heterologous expression of biosynthetic gene clusters. PMID:34526549
PDB-wide identification of physiological hetero-oligomeric assemblies based on conserved quaternary structure geometry. PMID:34520740
TnCentral: a Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis. PMID:34517763
Novel Lytic Enzyme of Prophage Origin from Clostridium botulinum E3 Strain Alaska E43 with Bactericidal Activity against Clostridial Cells. PMID:34502443
Chromosome-Level Genome Sequence of Aspergillus puulaauensis MK2, a Fungus Isolated from a Dead Hard Tick. PMID:34498921
Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms. PMID:34493810
High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing. PMID:34488624
A Comprehensive Phylogenetic Analysis of the MAP4K Family in the Green Lineage. PMID:34484252
Arms race in a cell: genomic, transcriptomic, and proteomic insights into intracellular phage-bacteria interplay in deep-sea snail holobionts. PMID:34479645
Duo: A Signature Based Method to Batch-Analyze Functional Similarities of Proteins. PMID:34475860
Genome-Wide Phylogenetic Analysis, Expression Pattern, and Transcriptional Regulatory Network of the Pig C/EBP Gene Family. PMID:34471342
Chlamydomonas proteases: classification, phylogeny, and molecular mechanisms. PMID:34468747
Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution. PMID:34465765
Genome-wide identification, characterization and expression analysis of MATE family genes in apple (Malus × domestica Borkh). PMID:34461821
TIAMMAt: Leveraging Biodiversity to Revise Protein Domain Models, Evidence from Innate Immunity. PMID:34459919
Genome-Wide Identification and Functional Investigation of 1-Aminocyclopropane-1-carboxylic Acid Oxidase (ACO) Genes in Cotton. PMID:34451744
Genome Analysis of Phytophthora nicotianae JM01 Provides Insights into Its Pathogenicity Mechanisms. PMID:34451665
Genome-wide identification and characterization of the Lateral Organ Boundaries Domain (LBD) gene family in polyploid wheat and related species. PMID:34447619
Global phylogenomic analyses of Mycobacterium abscessus provide context for non cystic fibrosis infections and the evolution of antibiotic resistance. PMID:34446725
Genome-wide Analysis of Basic Helix-Loop-Helix Family Genes and Expression Analysis in Response to Drought and Salt Stresses in Hibiscus hamabo Sieb. et Zucc. PMID:34445454
Metatranscriptomic Analysis of Bacterial Communities on Laundered Textiles: A Pilot Case Study. PMID:34442670
The Genome Analysis of the Human Lung-Associated Streptomyces sp. TR1341 Revealed the Presence of Beneficial Genes for Opportunistic Colonization of Human Tissues. PMID:34442631
Bioinformatic Analysis of Two TOR (Target of Rapamycin)-Like Proteins Encoded by Entamoeba histolytica Revealed Structural Similarities with Functional Homologs. PMID:34440318
Next-Generation Sequencing Analysis of the Tineola bisselliella Larval Gut Transcriptome Reveals Candidate Enzymes for Keratin Digestion. PMID:34440287
Genome-Wide Analysis and Expression Profile of Superoxide Dismutase (SOD) Gene Family in Rapeseed (Brassica napus L.) under Different Hormones and Abiotic Stress Conditions. PMID:34439430
Systematic dissection of σ70 sequence diversity and function in bacteria. PMID:34433066
Ankyrin repeats in context with human population variation. PMID:34428215
Ecological Specialization and Evolutionary Reticulation in Extant Hyaenidae. PMID:34426844
Exploring the evolutionary process of alkannin/shikonin O-acyltransferases by a reliable Lithospermum erythrorhizon genome. PMID:34424327
Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis. PMID:34418961
Identification of Photoperiod-Induced LncRNAs and mRNAs in Pituitary Pars Tuberalis of Sheep. PMID:34414222
Discovery of New Carbonyl Reductases Using Functional Metagenomics and Applications in Biocatalysis. PMID:34413714
The Oldest Co-opted gag Gene of a Human Endogenous Retrovirus Shows Placenta-Specific Expression and Is Upregulated in Diffuse Large B-Cell Lymphomas. PMID:34410386
Functional Classification of Super-Large Families of Enzymes Based on Substrate Binding Pocket Residues for Biocatalysis and Enzyme Engineering Applications. PMID:34409021
New Trends in Bioremediation Technologies Toward Environment-Friendly Society: A Mini-Review. PMID:34409018
Haploid Genome Analysis Reveals a Tandem Cluster of Four HSP20 Genes Involved in the High-Temperature Adaptation of Coriolopsis trogii. PMID:34406871
Capabilities of bioinformatics tools for optimizing physicochemical features of proteins used in Nano biosensors: A short overview of the tools related to bioinformatics. PMID:34401530
A Widespread Bacterial Secretion System with Diverse Substrates. PMID:34399622
DeepSec: a deep learning framework for secreted protein discovery in human body fluids. PMID:34398224
An essential role for the piRNA pathway in regulating the ribosomal RNA pool in C. elegans. PMID:34388368
The impacts of past, present and future ocean chemistry on predatory planktonic snails. PMID:34386247
Genome-Wide Identification of Triticum aestivum Xylanase Inhibitor Gene Family and Inhibitory Effects of XI-2 Subfamily Proteins on Fusarium graminearum GH11 Xylanase. PMID:34381472
Global Pharmacopoeia Genome Database is an integrated and mineable genomic database for traditional medicines derived from eight international pharmacopoeias. PMID:34378141
De novo genome assembly of the potent medicinal plant Rehmannia glutinosa using nanopore technology. PMID:34377362
De novo transcriptome characterization of Iris atropurpurea (the Royal Iris) and phylogenetic analysis of MADS-box and R2R3-MYB gene families. PMID:34376711
The Resistome and Mobilome of Multidrug-Resistant Staphylococcus sciuri C2865 Unveil a Transferable Trimethoprim Resistance Gene, Designated dfrE, Spread Unnoticed. PMID:34374564
PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions. PMID:34370723
A novel framework integrating AI model and enzymological experiments promotes identification of SARS-CoV-2 3CL protease inhibitors and activity-based probe. PMID:34368837
Genome-Wide Identification and Evolutionary Analysis of Gossypium Tubby-Like Protein (TLP) Gene Family and Expression Analyses During Salt and Drought Stress. PMID:34367198
The structural basis of bacterial manganese import. PMID:34362732
HrpL Regulon of Bacterial Pathogen of Woody Host Pseudomonas savastanoi pv. savastanoi NCPPB 3335. PMID:34361883
BonMOLière: Small-Sized Libraries of Readily Purchasable Compounds, Optimized to Produce Genuine Hits in Biological Screens across the Protein Space. PMID:34360558
Genome-wide analysis of HECT E3 ubiquitin ligase gene family in Solanum lycopersicum. PMID:34354159
ACO2 clinicobiological dataset with extensive phenotype ontology annotation. PMID:34354088
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
CCD2: design constructs for protein expression, the easy way. PMID:34342272
Distinct mutations in importin-β family nucleocytoplasmic transport receptors transportin-SR and importin-13 affect specific cargo binding. PMID:34341383
Inhibitory Compounds Targeting Plasmodium falciparum Gyrase B. PMID:34339271
N-terminus-independent activation of c-Src via binding to a tetraspan(in) TM4SF5 in hepatocellular carcinoma is abolished by the TM4SF5 C-terminal peptide application. PMID:34335982
Comparisons within the Rice GA 2-Oxidase Gene Family Revealed Three Dominant Paralogs and a Functional Attenuated Gene that Led to the Identification of Four Amino Acid Variants Associated with GA Deactivation Capability. PMID:34322729
Insulin signaling regulates longevity through protein phosphorylation in Caenorhabditis elegans. PMID:34315882
Genome of the pincer wasp Gonatopus flavifemur reveals unique venom evolution and a dual adaptation to parasitism and predation. PMID:34315471
The enigmatic RNase MRP of kinetoplastids. PMID:34308760
The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns. PMID:34305969
Comparative Genomics Provide Insights Into Function and Evolution of Odorant Binding Proteins in Cydia pomonella. PMID:34305643
The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities. PMID:34304594
Aspergillus niger trehalase enzyme induced morphological and protein alterations on Acanthamoeba cyst and molecular docking studies. PMID:34295046
Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea). PMID:34294825
Fine dissection of limber pine resistance to Cronartium ribicola using targeted sequencing of the NLR family. PMID:34294045
Chromosome-Level Genome Sequence of the Black Koji Fungus Aspergillus luchuensis RIB2601. PMID:34292062
Evolution of Toll, Spatzle and MyD88 in insects: the problem of the Diptera bias. PMID:34289811
Identification of a diguanylate cyclase expressed in the presence of plants and its application for discovering candidate gene products involved in plant colonization by Pantoea sp. YR343. PMID:34288916
The MpsAB Bicarbonate Transporter Is Superior to Carbonic Anhydrase in Biofilm-Forming Bacteria with Limited CO2 Diffusion. PMID:34287032
Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling. PMID:34285211
Accurate prediction of protein structures and interactions using a three-track neural network. PMID:34282049
Bioinformatic Analysis of the Campylobacter jejuni Type VI Secretion System and Effector Prediction. PMID:34276628
The CaCA superfamily genes in Saccharum: comparative analysis and their functional implications in response to biotic and abiotic stress. PMID:34275454
Discovery of fibrillar adhesins across bacterial species. PMID:34275445
Genome-wide analysis and expression patterns of lipid phospholipid phospholipase gene family in Brassica napus L. PMID:34273948
Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups. PMID:34272286
Distinct Retrotransposon Evolution Profile in the Genome of Rabbit (Oryctolagus cuniculus). PMID:34270728
The DUB family in Populus: identification, characterization, evolution and expression patterns. PMID:34266381
Expression profiling of the Dof gene family under abiotic stresses in spinach. PMID:34257328
Genome sequence of Apostasia ramifera provides insights into the adaptive evolution in orchids. PMID:34256691
Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx. PMID:34254998
High Transcriptional Activity and Diverse Functional Repertoires of Hundreds of Giant Viruses in a Coastal Marine System. PMID:34254826
Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle. PMID:34253191
Caenorhabditis elegans RMI2 functional homolog-2 (RMIF-2) and RMI1 (RMH-1) have both overlapping and distinct meiotic functions within the BTR complex. PMID:34252074
A Novel Family of RNA-Binding Proteins Regulate Polysaccharide Metabolism in Bacteroides thetaiotaomicron. PMID:34251866
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
A Novel Cooperative Metallo-β-Lactamase Fold Metallohydrolase from Pathogen Vibrio vulnificus Exhibits β-Lactam Antibiotic-Degrading Activities. PMID:34228542
Comprehensive transcriptome analysis of peripheral blood unravels key lncRNAs implicated in ABPA and asthma. PMID:34221710
Genome-Wide Analysis of Myeloblastosis-Related Genes in Brassica napus L. and Positive Modulation of Osmotic Tolerance by BnMRD107. PMID:34220898
Comparison of Hyaluronic Acid Biosynthetic Genes From Different Strains of Pasteurella multocida. PMID:34220200
On the diversity of F420 -dependent oxidoreductases: A sequence- and structure-based classification. PMID:34216160
Comparative genomics of DNA-binding transcription factors in archaeal and bacterial organisms. PMID:34214112
Genome sequences and in silico effector mining of Corynespora cassiicola CC_29 and Corynespora olivacea CBS 114450. PMID:34213598
Increasing the Accuracy of Single Sequence Prediction Methods Using a Deep Semi-Supervised Learning Framework. PMID:34213528
nZVI Impacts Substrate Conversion and Microbiome Composition in Chain Elongation From D- and L-Lactate Substrates. PMID:34211964
Development of DNA Markers From Physically Mapped Loci in Aegilops comosa and Aegilops umbellulata Using Single-Gene FISH and Chromosome Sequences. PMID:34211490
Pathogen Moonlighting Proteins: From Ancestral Key Metabolic Enzymes to Virulence Factors. PMID:34203698
Insights into Autotrophic Activities and Carbon Flow in Iron-Rich Pelagic Aggregates (Iron Snow). PMID:34201891
Transcriptome-Wide Identification and Quantification of Caffeoylquinic Acid Biosynthesis Pathway and Prediction of Its Putative BAHDs Gene Complex in A. spathulifolius. PMID:34199260
Structural characterization of two solute-binding proteins for N,N'-diacetylchitobiose/N,N',N''-triacetylchitotoriose of the gram-positive bacterium, Paenibacillus sp. str. FPU-7. PMID:34195603
Genome-wide identification and phylogenetic relationships of the Hsp70 gene family of Aegilops tauschii, wild emmer wheat (Triticum dicoccoides) and bread wheat (Triticum aestivum). PMID:34194894
Structural and functional characterization of the receptor binding proteins of Escherichia coli O157 phages EP75 and EP335. PMID:34194667
Comparative Genomic Insights Into the Taxonomic Classification, Diversity, and Secondary Metabolic Potentials of Kitasatospora, a Genus Closely Related to Streptomyces. PMID:34194415
Crystal structure of an archaeal CorB magnesium transporter. PMID:34188059
Pangenomics reveals alternative environmental lifestyles among chlamydiae. PMID:34188040
Reconstruction of the full-length transcriptome of cigar tobacco without a reference genome and characterization of anion channel/transporter transcripts. PMID:34187357
Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance. PMID:34184913
Eukaryotic TYW1 Is a Radical SAM Flavoenzyme. PMID:34184886
Functional Characterization of the Cnidarian Antiviral Immune Response Reveals Ancestral Complexity. PMID:34180999
Application of machine learning in bacteriophage research. PMID:34174831
FINER: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks. PMID:34169280
Whole Genome Level Analysis of the Wnt and DIX Gene Families in Mice and Their Coordination Relationship in Regulating Cardiac Hypertrophy. PMID:34168671
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. PMID:34168315
Evolutionary analysis and functional characterization of SiBRI1 as a Brassinosteroid receptor gene in foxtail millet. PMID:34167462
Long noncoding RNAs are potentially involved in the degeneration of virulence in an aphid-obligate pathogen, Conidiobolus obscurus (Entomophthoromycotina). PMID:34167451
Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodeling superfamily. PMID:34166615
Discovery of Viral Myosin Genes With Complex Evolutionary History Within Plankton. PMID:34163457
The brain transcriptome of the wolf spider, Schizocosa ocreata. PMID:34162407
Network-based analysis of virulence factors for uncovering Aeromonas veronii pathogenesis. PMID:34162325
Identification, systematic evolution and expression analyses of the AAAP gene family in Capsicum annuum. PMID:34157978
Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics. PMID:34154658
The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome. PMID:34150671
Genome-Wide Identification of Wheat WRKY Gene Family Reveals That TaWRKY75-A Is Referred to Drought and Salt Resistances. PMID:34149760
Sequencing and Comparative Genomic Analysis of a Highly Metal-Tolerant Penicillium janthinellum P1 Provide Insights Into Its Metal Tolerance. PMID:34149650
Chromosome Fusion Affects Genetic Diversity and Evolutionary Turnover of Functional Loci but Consistently Depends on Chromosome Size. PMID:34146107
A spinach genome assembly with remarkable completeness, and its use for rapid identification of candidate genes for agronomic traits. PMID:34142133
Genome-wide identification and expression profiling of DREB genes in Saccharum spontaneum. PMID:34139993
Metatranscriptome Library Preparation Influences Analyses of Viral Community Activity During a Brown Tide Bloom. PMID:34135876
Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia. PMID:34130656
Unique phage-bacterium interplay in sponge holobionts from the southern Okinawa Trough hydrothermal vent. PMID:34128329
Population-scale peach genome analyses unravel selection patterns and biochemical basis underlying fruit flavor. PMID:34127667
Pathways of Iron and Sulfur Acquisition, Cofactor Assembly, Destination, and Storage in Diverse Archaeal Methanogens and Alkanotrophs. PMID:34124941
The GRAS gene family in watermelons: identification, characterization and expression analysis of different tissues and root-knot nematode infestations. PMID:34123598
Papain-Like Cysteine Protease Gene Family in Fig (Ficus carica L.): Genome-Wide Analysis and Expression Patterns. PMID:34122493
Identification and Analysis of bZIP Family Genes in Potato and Their Potential Roles in Stress Responses. PMID:34122468
Genetic Dissection of a Prevalent Plasmid-Encoded Conjugation System in Lactococcus lactis. PMID:34122391
A hierarchical deep learning based approach for multi-functional enzyme classification. PMID:34118089
Mining of Gram-Negative Surface-Active Enzybiotic Candidates by Sequence-Based Calculation of Physicochemical Properties. PMID:34113327
Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan. PMID:34108585
Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics. PMID:34100635
Co-occurrence of enzyme domains guides the discovery of an oxazolone synthetase. PMID:34099916
Two RmlC homologs catalyze dTDP-4-keto-6-deoxy-D-glucose epimerization in Pseudomonas putida KT2440. PMID:34099824
Genome-wide identification of the Capsicum bHLH transcription factor family: discovery of a candidate regulator involved in the regulation of species-specific bioactive metabolites. PMID:34098881
Comparative Genomics of Peroxisome Biogenesis Proteins: Making Sense of the PEX Proteins. PMID:34095119
Phylogenetic, functional and structural characterization of a GH10 xylanase active at extreme conditions of temperature and alkalinity. PMID:34093984
Effect of Temperature on Metronidazole Resistance in Helicobacter pylori. PMID:34093508
Identifying Genes Devoted to the Cell Death Process in the Gene Regulatory Network of Ustilago maydis. PMID:34093501
Liver Transcriptome Dynamics During Hibernation Are Shaped by a Shifting Balance Between Transcription and RNA Stability. PMID:34093224
Identifying viruses from metagenomic data using deep learning. PMID:34084563
MiMiC: a bioinformatic approach for generation of synthetic communities from metagenomes. PMID:34081399
Mantis: flexible and consensus-driven genome annotation. PMID:34076241
Periscope Proteins are variable-length regulators of bacterial cell surface interactions. PMID:34074781
Characterization of an Endolysin Targeting Clostridioides difficile That Affects Spore Outgrowth. PMID:34073633
A Novel Broad Host Range Phage Infecting Alteromonas. PMID:34073246
Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity. PMID:34072989
Mining Indonesian Microbial Biodiversity for Novel Natural Compounds by a Combined Genome Mining and Molecular Networking Approach. PMID:34071728
MicroRNA Profiles of Maternal and Neonatal Endothelial Progenitor Cells in Preeclampsia. PMID:34070163
Propionate Fermentative Genes of the Gut Microbiome Decrease in Inflammatory Bowel Disease. PMID:34070019
Fatty Acid Desaturases: Uncovering Their Involvement in Grapevine Defence against Downy Mildew. PMID:34067363
A Peek into the Plasmidome of Global Sewage. PMID:34061588
Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans. PMID:34061031
Genome-Scale Metabolic Model of Caldicellulosiruptor bescii Reveals Optimal Metabolic Engineering Strategies for Bio-based Chemical Production. PMID:34060912
Genome of the fatal tapeworm Sparganum proliferum uncovers mechanisms for cryptic life cycle and aberrant larval proliferation. PMID:34059788
Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants. PMID:34059664
Polysaccharide utilization loci-driven enzyme discovery reveals BD-FAE: a bifunctional feruloyl and acetyl xylan esterase active on complex natural xylans. PMID:34059129
Protein Structure Prediction: Conventional and Deep Learning Perspectives. PMID:34050498
Structural basis for zinc-induced activation of a zinc uptake transcriptional regulator. PMID:34048589
Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions. PMID:34046017
RNA interference of an orthologue of Dicer of Meloidogyne incognita alludes to the gene's importance in nematode development. PMID:34045504
Genome-wide identification of the DUF668 gene family in cotton and expression profiling analysis of GhDUF668 in Gossypium hirsutum under adverse stress. PMID:34044774
Ecology and molecular targets of hypermutation in the global microbiome. PMID:34031405
Rare Missense Functional Variants at COL4A1 and COL4A2 in Sporadic Intracerebral Hemorrhage. PMID:34031201
On the effect of phylogenetic correlations in coevolution-based contact prediction in proteins. PMID:34029316
Mapping OMIM Disease-Related Variations on Protein Domains Reveals an Association Among Variation Type, Pfam Models, and Disease Classes. PMID:34026820
Comprehensive analysis of the lysine acetylome and succinylome in the hippocampus of gut microbiota-dysbiosis mice. PMID:34026284
Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. PMID:34021239
digIS: towards detecting distant and putative novel insertion sequence elements in prokaryotic genomes. PMID:34016050
A Chromosome-Level Genome Assembly of Ephestia elutella (Hübner, 1796) (Lepidoptera: Pyralidae). PMID:34014321
Structural Profiling of Bacterial Effectors Reveals Enrichment of Host-Interacting Domains and Motifs. PMID:34012977
Agrobacterium tumefaciens Growth Pole Ring Protein: C Terminus and Internal Apolipoprotein Homologous Domains Are Essential for Function and Subcellular Localization. PMID:34006657
Genome-wide identification and expression analysis of the AT-hook Motif Nuclear Localized gene family in soybean. PMID:34006214
Biosynthesis and Heterologous Production of Mycosporine-Like Amino Acid Palythines. PMID:34006097
Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis. PMID:34002013
Characterization of a new bifunctional endo-1,4-β-xylanase/esterase found in the rumen metagenome. PMID:34001974
dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains. PMID:33999210
PredictProtein - Predicting Protein Structure and Function for 29 Years. PMID:33999203
Association of NOS3-c.894G>T transversion with susceptibility to metabolic syndrome in Azar-cohort population: A case-control study and in silico analysis of the SNP molecular effects. PMID:33995953
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
In Silico Characterization of a Hypothetical Protein from Shigella dysenteriae ATCC 12039 Reveals a Pathogenesis-Related Protein of the Type-VI Secretion System. PMID:33994781
Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts. PMID:33990699
The SARS-CoV-2 RNA interactome. PMID:33989516
DoChaP: the domain change presenter. PMID:33988713
Transcription factor allosteric regulation through substrate coordination to zinc. PMID:33987533
De novo transcriptome analysis for examination of the nutrition metabolic system related to the evolutionary process through which stick insects gain the ability of flight (Phasmatodea). PMID:33985569
TGIF-DB: terse genomics interface for developing botany. PMID:33985559
eCOMPASS: evaluative comparison of multiple protein alignments by statistical score. PMID:33983436
Insights on the Evolutionary Genomics of the Blautia Genus: Potential New Species and Genetic Content Among Lineages. PMID:33981291
PhosIDP: a web tool to visualize the location of phosphorylation sites in disordered regions. PMID:33976270
Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities. PMID:33975974
Tryptophan Operon Diversity Reveals Evolutionary Trends among Geographically Disparate Chlamydia trachomatis Ocular and Urogenital Strains Affecting Tryptophan Repressor and Synthase Function. PMID:33975934
Diversity and distribution of viruses inhabiting the deepest ocean on Earth. PMID:33972725
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. PMID:33961781
Accurate Annotation of Microbial Metagenomic Genes and Identification of Core Sets. PMID:33961221
Structure elements can be predicted using the contact volume among protein residues. PMID:33954082
Identification and Analysis of Aux/IAA Family in Acer rubrum. PMID:33953533
Isotopic tracing reveals single-cell assimilation of a macroalgal polysaccharide by a few marine Flavobacteria and Gammaproteobacteria. PMID:33953365
Insight into the function and evolution of the Wood-Ljungdahl pathway in Actinobacteria. PMID:33953361
Transcriptional profile of oil palm pathogen, Ganoderma boninense, reveals activation of lignin degradation machinery and possible evasion of host immune response. PMID:33952202
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. PMID:33944776
Microbial iron and carbon metabolism as revealed by taxonomy-specific functional diversity in the Southern Ocean. PMID:33941887
A cortex-specific penicillin-binding protein contributes to heat resistance in Clostridioides difficile spores. PMID:33940167
Molecular analysis of the replication functions of the bifidobacterial conjugative megaplasmid pMP7017. PMID:33939264
Clinical and Genetic Characterization of Craniosynostosis in Saudi Arabia. PMID:33937142
Ending a diagnostic odyssey-The first case of Takenouchi-Kosaki syndrome in an African patient. PMID:33936654
Cell Wall Layer Induced in Xylem Fibers of Flax Upon Gravistimulation Is Similar to Constitutively Formed Cell Walls of Bast Fibers. PMID:33936149
Quantifying the Mutational Robustness of Protein-Coding Genes. PMID:33934169
CmMLO17 and its partner CmKIC potentially support Alternaria alternata growth in Chrysanthemum morifolium. PMID:33931614
A New Pathway for Forming Acetate and Synthesizing ATP during Fermentation in Bacteria. PMID:33931420
Integrated Biophysical Modeling of the SARS-CoV-2 Spike Protein Binding and Allosteric Interactions with Antibodies. PMID:33929853
Genome-wide identification of superoxide dismutase gene families and their expression patterns under low-temperature, salt and osmotic stresses in watermelon and melon. PMID:33927985
Long Intergenic Non-Coding RNAs in the Mammary Parenchyma and Fat Pad of Pre-Weaning Heifer Calves: Identification and Functional Analysis. PMID:33924848
Sex-Biased lncRNA Signature in Fetal Growth Restriction (FGR). PMID:33923632
Tracing the Evolution of Plant Glyoxalase III Enzymes for Structural and Functional Divergence. PMID:33922426
What Is in a Cat Scratch? Growth of Bartonella henselae in a Biofilm. PMID:33919891
Extracytoplasmic Function σ Factors as Tools for Coordinating Stress Responses. PMID:33918849
Genome-Wide Analysis of Terpene Synthase Gene Family in Mentha longifolia and Catalytic Activity Analysis of a Single Terpene Synthase. PMID:33918244
Data-driven computational protein design. PMID:33910104
Draft genome of a biparental beetle species, Lethrus apterus. PMID:33902445
Complete genome sequence of a grapevine Roditis leaf discoloration-associated virus (GRLDaV) variant from South Africa. PMID:33900469
The role of solute binding proteins in signal transduction. PMID:33897981
Evolutionary and functional analysis of an NRPS condensation domain integrates β-lactam, ᴅ-amino acid, and dehydroamino acid synthesis. PMID:33893237
Phylogenetic and Selection Analysis of an Expanded Family of Putatively Pore-Forming Jellyfish Toxins (Cnidaria: Medusozoa). PMID:33892512
APICURON: a database to credit and acknowledge the work of biocurators. PMID:33882120
A conserved folding nucleus sculpts the free energy landscape of bacterial and archaeal orthologs from a divergent TIM barrel family. PMID:33875592
Caenorhabditis elegans junctophilin has tissue-specific functions and regulates neurotransmission with extended-synaptotagmin. PMID:33871019
Genetic basis of negative heterosis for growth traits in chickens revealed by genome-wide gene expression pattern analysis. PMID:33865443
The control of polycomb repressive complexes by long noncoding RNAs. PMID:33861025
A Vernalization Response in a Winter Safflower (Carthamus tinctorius) Involves the Upregulation of Homologs of FT, FUL, and MAF. PMID:33859660
Mix and match: Patchwork domain evolution of the land plant-specific Ca2+-permeable mechanosensitive channel MCA. PMID:33857196
Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families. PMID:33857128
A novel predicted ADP-ribosyltransferase-like family conserved in eukaryotic evolution. PMID:33854844
A Radical Reimagining of Fungal Two-Component Regulatory Systems. PMID:33853736
The gut virome of healthy children during the first year of life is diverse and dynamic. PMID:33852569
A combined RAD-Seq and WGS approach reveals the genomic basis of yellow color variation in bumble bee Bombus terrestris. PMID:33846496
Topological clustering of regulatory genes confers pathogenic tolerance to cassava brown streak virus (CBSV) in cassava. PMID:33846415
A review on compound-protein interaction prediction methods: Data, format, representation and model. PMID:33841755
Elucidating molecular mechanisms of acquired resistance to BRAF inhibitors in melanoma using a microfluidic device and deep sequencing. PMID:33840166
Vestiges of the Bacterial Signal Recognition Particle-Based Protein Targeting in Mitochondria. PMID:33837778
Improving protein domain classification for third-generation sequencing reads using deep learning. PMID:33836667
Toggle switch residues control allosteric transitions in bacterial adhesins by participating in a concerted repacking of the protein core. PMID:33826682
Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence. PMID:33824960
Biallelic variants in TMEM222 cause a new autosomal recessive neurodevelopmental disorder. PMID:33824500
An Alternative and Conserved Cell Wall Enzyme That Can Substitute for the Lipid II Synthase MurG. PMID:33824209
Effects of Simulated Microgravity on the Proteome and Secretome of the Polyextremotolerant Black Fungus Knufia chersonesos. PMID:33815472
The Richness and Diversity of Catalases in Bacteria. PMID:33815333
MolluscDB: a genome and transcriptome database for molluscs. PMID:33813885
Crystal Structure of a Phospholipase D from the Plant-Associated Bacteria Serratia plymuthica Strain AS9 Reveals a Unique Arrangement of Catalytic Pocket. PMID:33809980
Putative LysM Effectors Contribute to Fungal Lifestyle. PMID:33808705
Cyanide Hydratase Modification Using Computational Design and Docking Analysis for Improved Binding Affinity in Cyanide Detoxification. PMID:33806828
Acetan and Acetan-Like Polysaccharides: Genetics, Biosynthesis, Structure, and Viscoelasticity. PMID:33799945
Using high-abundance proteins as guides for fast and effective peptide/protein identification from human gut metaproteomic data. PMID:33795009
Building blocks and blueprints for bacterial autolysins. PMID:33793553
Roles of the 14-3-3 gene family in cotton flowering. PMID:33789593
Bacterial community structure alterations within the colorectal cancer gut microbiome. PMID:33789570
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches. PMID:33787851
The human virome: assembly, composition and host interactions. PMID:33785903
Representative Diatom and Coccolithophore Species Exhibit Divergent Responses throughout Simulated Upwelling Cycles. PMID:33785571
Genome-wide identification and expression analysis of the B-box transcription factor gene family in grapevine (Vitis vinifera L.). PMID:33781207
An atlas of the binding specificities of transcription factors in Pseudomonas aeruginosa directs prediction of novel regulators in virulence. PMID:33779544
Genome-wide identification and expression pattern analysis of the ribonuclease T2 family in Eucommia ulmoides. PMID:33767357
Extensive structural variation in the Bowman-Birk inhibitor family in common wheat (Triticum aestivum L.). PMID:33765923
Evolution and Functional Divergence of SUN Genes in Plants. PMID:33763102
MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization. PMID:33757283
Genome-wide identification of MIKC-type genes related to stamen and gynoecium development in Liriodendron. PMID:33753780
Interpreting Sequence Variation in PDAC-Predisposing Genes Using a Multi-Tier Annotation Approach Performed at the Gene, Patient, and Cohort Level. PMID:33747920
Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes. PMID:33747544
The Transcriptomic and Bioinformatic Characterizations of Iron Acquisition and Heme Utilization in Avibacterium paragallinarum in Response to Iron-Starvation. PMID:33746913
Structure and activation mechanism of the human liver-type glutaminase GLS2. PMID:33746066
Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens. PMID:33743832
RNA-seq analysis and gene expression dynamics in the salivary glands of the argasid tick Ornithodoros erraticus along the trophogonic cycle. PMID:33743776
A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event. PMID:33739402
The Extracellular Superoxide Dismutase Sod5 From Fusarium oxysporum Is Localized in Response to External Stimuli and Contributes to Fungal Pathogenicity. PMID:33737941
PomX, a ParA/MinD ATPase activating protein, is a triple regulator of cell division in Myxococcus xanthus. PMID:33734087
A towering genome: Experimentally validated adaptations to high blood pressure and extreme stature in the giraffe. PMID:33731352
Characterization of microbial antifreeze protein with intermediate activity suggests that a bound-water network is essential for hyperactivity. PMID:33727595
Novel CARMIL2 loss-of-function variants are associated with pediatric inflammatory bowel disease. PMID:33723309
A ProQ/FinO family protein involved in plasmid copy number control favours fitness of bacteria carrying mcr-1-bearing IncI2 plasmids. PMID:33721023
Machine learning predicts and provides insights into milk acidification rates of Lactococcus lactis. PMID:33720959
Rv3722c Promotes Mycobacterium tuberculosis Survival in Macrophages by Interacting With TRAF3. PMID:33718275
Comprehensive Quantitative Proteome Analysis of Aedes aegypti Identifies Proteins and Pathways Involved in Wolbachia pipientis and Zika Virus Interference Phenomenon. PMID:33716790
Identification of eight QTL controlling multiple yield components in a German multi-parental wheat population, including Rht24, WAPO-A1, WAPO-B1 and genetic loci on chromosomes 5A and 6A. PMID:33712876
Protein context shapes the specificity of SH3 domain-mediated interactions in vivo. PMID:33712617
Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation. PMID:33711918
Coordinated control of the type IV pili and c-di-GMP-dependent antifungal antibiotic production in Lysobacter by the response regulator PilR. PMID:33709522
Genome-wide identification and expression profiling of chitinase genes in tea (Camellia sinensis (L.) O. Kuntze) under biotic stress conditions. PMID:33707875
Functional elucidation of TfuA in peptide backbone thioamidation. PMID:33707784
Predicted Input of Uncultured Fungal Symbionts to a Lichen Symbiosis from Metagenome-Assembled Genomes. PMID:33693712
Comparative genome analyses suggest a hemibiotrophic lifestyle and virulence differences for the beech bark disease fungal pathogens Neonectria faginata and Neonectria coccinea. PMID:33693679
Unification and extensive diversification of M/Orf3-related ion channel proteins in coronaviruses and other nidoviruses. PMID:33692906
gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. PMID:33691770
Biodegradation of lignin monomers and bioconversion of ferulic acid to vanillic acid by Paraburkholderia aromaticivorans AR20-38 isolated from Alpine forest soil. PMID:33687503
Genomic insights into the host specific adaptation of the Pneumocystis genus. PMID:33686174
lncRNADetector: a bioinformatics pipeline for long non-coding RNA identification and MAPslnc: a repository of medicinal and aromatic plant lncRNAs. PMID:33685383
The very early evolution of protein translocation across membranes. PMID:33684113
A De Novo Transcriptome Assembly of Ceratopteris richardii Provides Insights into the Evolutionary Dynamics of Complex Gene Families in Land Plants. PMID:33681974
Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina. PMID:33679672
HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis. PMID:33677507
Whole genome de novo sequencing and comparative genomic analyses suggests that Chlamydia psittaci strain 84/2334 should be reclassified as Chlamydia abortus species. PMID:33676404
Hyperthermophilic methanogenic archaea act as high-pressure CH4 cell factories. PMID:33674723
Structural characterization and duplication modes of pseudogenes in plants. PMID:33674668
Whole Exome Sequencing Identifies APCDD1 and HDAC5 Genes as Potentially Cancer Predisposing in Familial Colorectal Cancer. PMID:33673279
De Novo Transcriptome Profiling of Brain Tissue from the Annual Killifish Nothobranchius guentheri. PMID:33670176
Genome-Wide Identification and Analysis of the MYB Transcription Factor Gene Family in Chili Pepper (Capsicum spp.). PMID:33668082
Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments. PMID:33657378
Identification and phylogenetic analysis of RNA binding domain abundant in apicomplexans or RAP proteins. PMID:33656416
TMSNP: a web server to predict pathogenesis of missense mutations in the transmembrane region of membrane proteins. PMID:33655207
Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences. PMID:33654096
RNA-Seq Implies Divergent Regulation Patterns of LincRNA on Spermatogenesis and Testis Growth in Goats. PMID:33653002
Distribution and preservation of the components of the engulfment. What is beyond representative genomes? PMID:33651833
Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom. PMID:33649555
Genome-wide analysis and expression profile of the bZIP gene family in poplar. PMID:33648455
PAS domains in bacterial signal transduction. PMID:33647528
Regulation of a Trehalose-Specific Facilitated Transporter (TRET) by Insulin and Adipokinetic Hormone in Rhodnius prolixus, a Vector of Chagas Disease. PMID:33643069
A novel D-xylose isomerase from the gut of the wood feeding beetle Odontotaenius disjunctus efficiently expressed in Saccharomyces cerevisiae. PMID:33637780
The Campylobacter jejuni CiaD effector co-opts the host cell protein IQGAP1 to promote cell entry. PMID:33637714
Evolution, structure and emerging roles of C1ORF112 in DNA replication, DNA damage responses, and cancer. PMID:33625522
The Chloroplastic Small Heat Shock Protein Gene KvHSP26 Is Induced by Various Abiotic Stresses in Kosteletzkya virginica. PMID:33623779
Insights into the diversification of subclade IVa bHLH transcription factors in Fabaceae. PMID:33622255
The STI1-domain is a flexible alpha-helical fold with a hydrophobic groove. PMID:33620121
Microbial single-strand annealing proteins enable CRISPR gene-editing tools with improved knock-in efficiencies and reduced off-target effects. PMID:33619540
QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution. PMID:33616668
Identifying molecular features that are associated with biological function of intrinsically disordered protein regions. PMID:33616531
A New Family of Bacteriolytic Proteins in Dictyostelium discoideum. PMID:33614529
Characterization of Mungbean CONSTANS-LIKE Genes and Functional Analysis of CONSTANS-LIKE 2 in the Regulation of Flowering Time in Arabidopsis. PMID:33613600
Hologenome analysis reveals dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis. PMID:33608555
Analysis of Tandem Repeat Protein Folding Using Nearest-Neighbor Models. PMID:33606943
The Polymycovirus-Mediated Growth Enhancement of the Entomopathogenic Fungus Beauveria bassiana Is Dependent on Carbon and Nitrogen Metabolism. PMID:33603722
The importance of the RET gene in thyroid cancer and therapeutic implications. PMID:33603219
Biochemical characterisation of a collagenase from Bacillus cereus strain Q1. PMID:33603127
Genome-wide association studies provide insights into the genetic determination of fruit traits of pear. PMID:33602909
Genome-wide characterization of 2-oxoglutarate and Fe(II)-dependent dioxygenase family genes in tomato during growth cycle and their roles in metabolism. PMID:33602133
Phospho-dependent signaling during the general stress response by the atypical response regulator and ClpXP adaptor RssB. PMID:33599047
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
A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins. PMID:33592170
Genomic rearrangements generate hypervariable mini-chromosomes in host-specific isolates of the blast fungus. PMID:33591993
Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway. PMID:33591270
Bacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires. PMID:33590101
Gene Annotation in High Schools: Successful Student Pipeline and Teacher Professional Development in Bioscience Using GENI-ACT. PMID:33584559
Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria. PMID:33582841
PanACoTA: a modular tool for massive microbial comparative genomics. PMID:33575648
TOUCAN: a framework for fungal biosynthetic gene cluster discovery. PMID:33575642
Family-specific analysis of variant pathogenicity prediction tools. PMID:33575576
Evolution of the extracytoplasmic function σ factor protein family. PMID:33575573
RNAsamba: neural network-based assessment of the protein-coding potential of RNA sequences. PMID:33575571
Rapid Peptides Generator: fast and efficient in silico protein digestion. PMID:33575558
Identification, Classification, and Expression Analysis of the Triacylglycerol Lipase (TGL) Gene Family Related to Abiotic Stresses in Tomato. PMID:33573234
ELIHKSIR Web Server: Evolutionary Links Inferred for Histidine Kinase Sensors Interacting with Response Regulators. PMID:33573110
A Pipeline towards the Biochemical Characterization of the Arabidopsis GT14 Family. PMID:33572987
Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa. PMID:33570565
Chromosome-level reference genome of the soursop (Annona muricata): A new resource for Magnoliid research and tropical pomology. PMID:33569882
Genome-wide identification of chitinase genes in Thalassiosira pseudonana and analysis of their expression under abiotic stresses. PMID:33568068
Cadherin 2-Related Arrhythmogenic Cardiomyopathy: Prevalence and Clinical Features. PMID:33566628
Structural modeling and analysis of the SARS-CoV-2 cell entry inhibitor camostat bound to the trypsin-like protease TMPRSS2. PMID:33564221
Comparative genomics of a novel clade shed light on the evolution of the genus Erysipelothrix and characterise an emerging species. PMID:33564084
A Grad-seq View of RNA and Protein Complexes in Pseudomonas aeruginosa under Standard and Bacteriophage Predation Conditions. PMID:33563827
The actin networks of chytrid fungi reveal evolutionary loss of cytoskeletal complexity in the fungal kingdom. PMID:33561386
Genome assembly and annotation of the California harvester ant Pogonomyrmex californicus. PMID:33561225
Diverse Eukaryotic CGG-Binding Proteins Produced by Independent Domestications of hAT Transposons. PMID:33561217
Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile. PMID:33561170
Cryo-EM structures of human RNA polymerase III in its unbound and transcribing states. PMID:33558764
Elevated gut microbiome abundance of Christensenellaceae, Porphyromonadaceae and Rikenellaceae is associated with reduced visceral adipose tissue and healthier metabolic profile in Italian elderly. PMID:33557667
Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes. PMID:33556078
In silico design of novel aptamers utilizing a hybrid method of machine learning and genetic algorithm. PMID:33554306
Genomic and transcriptomic resources for candidate gene discovery in the Ranunculids. PMID:33552749
Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities. PMID:33547239
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
Evolutionary dynamics of transposable elements in bdelloid rotifers. PMID:33543711
Intrinsic disorder in protein domains contributes to both organism complexity and clade-specific functions. PMID:33542394
Identification of a solo acylhomoserine lactone synthase from the myxobacterium Archangium gephyra. PMID:33542315
Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal. PMID:33536943
Analysis of Fox genes in Schmidtea mediterranea reveals new families and a conserved role of Smed-foxO in controlling cell death. PMID:33536473
A persistent giant algal virus, with a unique morphology, encodes an unprecedented number of genes involved in energy metabolism. PMID:33536167
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
GmDNJ1, a type-I heat shock protein 40 (HSP40), is responsible for both Growth and heat tolerance in soybean. PMID:33532690
A Highly Contiguous Genome Assembly of a Polyphagous Predatory Mite Stratiolaelaps scimitus (Womersley) (Acari: Laelapidae). PMID:33528489
Microbial production and consumption of hydrocarbons in the global ocean. PMID:33526885
Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes. PMID:33526884
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. PMID:33522966
In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b. PMID:33520197
Computational resources for identifying and describing proteins driving liquid-liquid phase separation. PMID:33517364
Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera. PMID:33514746
Surface chemistry-mediated modulation of adsorbed albumin folding state specifies nanocarrier clearance by distinct macrophage subsets. PMID:33510170
Whole-genome characterization of Rosa chinensis AP2/ERF transcription factors and analysis of negative regulator RcDREB2B in Arabidopsis. PMID:33509074
Analysis of Rice Transcriptome Reveals the LncRNA/CircRNA Regulation in Tissue Development. PMID:33507446
CE16 acetylesterases: in silico analysis, catalytic machinery prediction and comparison with related SGNH hydrolases. PMID:33505839
Cenote-Taker 2 democratizes virus discovery and sequence annotation. PMID:33505708
Genome-Wide Mining of MYB Transcription Factors in the Anthocyanin Biosynthesis Pathway of Gossypium Hirsutum. PMID:33502632
Missense3D-DB web catalogue: an atom-based analysis and repository of 4M human protein-coding genetic variants. PMID:33502607
A Draft Genome Assembly of Culex pipiens pallens (Diptera: Culicidae) Using PacBio Sequencing. PMID:33501937
The soluble glutathione transferase superfamily: role of Mu class in triclabendazole sulphoxide challenge in Fasciola hepatica. PMID:33501588
Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens. PMID:33500331
Evolution of Plant Na+-P-Type ATPases: From Saline Environments to Land Colonization. PMID:33498844
HIV-1 Gag-Pol Sequences from Ugandan Early Infections Reveal Sequence Variants Associated with Elevated Replication Capacity. PMID:33498793
ViralRecall-A Flexible Command-Line Tool for the Detection of Giant Virus Signatures in 'Omic Data. PMID:33498458
Leptospiral Immunoglobulin-Like Domain Proteins: Roles in Virulence and Immunity. PMID:33488581
Aminoglycerophospholipid flipping and P4-ATPases in Toxoplasma gondii. PMID:33485966
A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses. PMID:33482803
Genome-wide analysis of haloacid dehalogenase genes reveals their function in phosphate starvation responses in rice. PMID:33481906
Minimal genome-wide human CRISPR-Cas9 library. PMID:33478580
De Novo Profiling of Long Non-Coding RNAs Involved in MC-LR-Induced Liver Injury in Whitefish: Discovery and Perspectives. PMID:33477898
A Legionella effector ADP-ribosyltransferase inactivates glutamate dehydrogenase. PMID:33476647
A corset function of exoskeletal ECM promotes body elongation in Drosophila. PMID:33469125
Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion. PMID:33468697
Evolution of A bHLH Interaction Motif. PMID:33466276
The impact of genetic diversity on gene essentiality within the Escherichia coli species. PMID:33462433
Characterization of CHARK, an unusual cytokinin receptor of rice. PMID:33462253
RNAi gene knockdown in the poultry red mite, Dermanyssus gallinae (De Geer 1778), a tool for functional genomics. PMID:33461614
Genome-wide identification and characterization of NBS-encoding genes in Raphanus sativus L. and their roles related to Fusarium oxysporum resistance. PMID:33461498
Neisseria meningitidis IgA1-specific serine protease exhibits novel cleavage activity against IgG3. PMID:33459578
Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. PMID:33453123
Bodo saltans (Kinetoplastida) is dependent on a novel Paracaedibacter-like endosymbiont that possesses multiple putative toxin-antitoxin systems. PMID:33452479
Genome-wide identification and comprehensive analysis of NAC family genes involved in fruit development in kiwifruit (Actinidia). PMID:33451304
Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA. PMID:33450012
A systems-level gene regulatory network model for Plasmodium falciparum. PMID:33450011
rfaRm: An R client-side interface to facilitate the analysis of the Rfam database of RNA families. PMID:33449976
In-Depth Characterization of the Staphylococcus aureus Phosphoproteome Reveals New Targets of Stk1. PMID:33444734
Genome-wide identification, characterization and transcriptional profiling of NHX-type (Na+/H+) antiporters under salinity stress in soybean. PMID:33442515
Signatures of conserved and unique molecular features in Afrotheria. PMID:33441654
Accurate and efficient detection of gene fusions from RNA sequencing data. PMID:33441414
Cysteine-Rich Hydrophobin Gene Family: Genome Wide Analysis, Phylogeny and Transcript Profiling in Cordyceps militaris. PMID:33440688
Type II Binders Targeting the "GLR-Out" Conformation of the Pseudokinase STRADα. PMID:33440120
BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters. PMID:33438731
Streamlining data-intensive biology with workflow systems. PMID:33438730
Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications. PMID:33436497
Conserved sequence motifs in human TMTC1, TMTC2, TMTC3, and TMTC4, new O-mannosyltransferases from the GT-C/PMT clan, are rationalized as ligand binding sites. PMID:33436046
CHD2-Related CNS Pathologies. PMID:33435571
Overexpression of the Bacteriophage T4 motB Gene Alters H-NS Dependent Repression of Specific Host DNA. PMID:33435393
Transposable Elements and Teleost Migratory Behaviour. PMID:33435333
Phage Origin of Mitochondrion-Localized Family A DNA Polymerases in Kinetoplastids and Diplonemids. PMID:33432342
A cytochrome c is the natural electron acceptor for nicotine oxidoreductase. PMID:33432238
Role of Transportome in the Gills of Chinese Mitten Crabs in Response to Salinity Change: A Meta-Analysis of RNA-Seq Datasets. PMID:33430106
Genome-wide identification, evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo (Phyllostachys edulis) shoots. PMID:33423665
Combined whole cell wall analysis and streamlined in silico carbohydrate-active enzyme discovery to improve biocatalytic conversion of agricultural crop residues. PMID:33422151
Exploring the taxonomical and functional profile of As Burgas hot spring focusing on thermostable β-galactosidases. PMID:33420292
Universal and taxon-specific trends in protein sequences as a function of age. PMID:33416492
Genome-Wide Identification of Populus Malectin/Malectin-Like Domain-Containing Proteins and Expression Analyses Reveal Novel Candidates for Signaling and Regulation of Wood Development. PMID:33414796
Draft Genome Sequence of the Termite-Associated "Cuckoo Fungus," Athelia (Fibularhizoctonia) sp. TMB Strain TB5. PMID:33414338
Genome-Wide Identification and Capsaicinoid Biosynthesis-Related Expression Analysis of the R2R3-MYB Gene Family in Capsicum annuum L. PMID:33408738
Conversion of Rutin, a Prevalent Dietary Flavonol, by the Human Gut Microbiota. PMID:33408702
A metabolic and physiological design study of Pseudomonas putida KT2440 capable of anaerobic respiration. PMID:33407113
MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes. PMID:33407081
The Campylobacter jejuni chemoreceptor Tlp10 has a bimodal ligand-binding domain and specificity for multiple classes of chemoeffectors. PMID:33402336
The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation. PMID:33402093
Coastal Bacterial Community Response to Glacier Melting in the Western Antarctic Peninsula. PMID:33401391
Additional Role of Nicotinic Acid Hydroxylase for the Transformation of 3-Succinoyl-Pyridine by Pseudomonas sp. Strain JY-Q. PMID:33397698
Probiogenomics Analysis of 97 Lactobacillus crispatus Strains as a Tool for the Identification of Promising Next-Generation Probiotics. PMID:33396617
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
Description and genomic characterization of Streptococcus symci sp. nov., isolated from a child's oropharynx. PMID:33387140
A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt. PMID:33384459
Insight into the bZIP Gene Family in Solanum tuberosum: Genome and Transcriptome Analysis to Understand the Roles of Gene Diversification in Spatiotemporal Gene Expression and Function. PMID:33383823
SeMPI 2.0-A Web Server for PKS and NRPS Predictions Combined with Metabolite Screening in Natural Product Databases. PMID:33383692
Classification and Computational Analysis of Arabidopsis thaliana Sperm Cell-Specific F-Box Protein Gene 3p.AtFBP113. PMID:33381153
β-Galactosidases from a Sequence-Based Metagenome: Cloning, Expression, Purification and Characterization. PMID:33379234
In silico screening and experimental analysis of family GH11 xylanases for applications under conditions of alkaline pH and high temperature. PMID:33372612
DeepNOG: Fast and accurate protein orthologous group assignment. PMID:33367584
An Educational Bioinformatics Project to Improve Genome Annotation. PMID:33365016
A recent origin of Orf3a from M protein across the coronavirus lineage arising by sharp divergence. PMID:33363705
A Clinical Extensively-Drug Resistant (XDR) Escherichia coli and Role of Its β-Lactamase Genes. PMID:33362736
Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases. PMID:33362253
Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity. PMID:33361114
Frustration and Direct-Coupling Analyses to Predict Formation and Function of Adeno-Associated Virus. PMID:33359833
An RNA Repair Operon Regulated by Damaged tRNAs. PMID:33357439
Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi. PMID:33355923
Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides. PMID:33351797
CheckV assesses the quality and completeness of metagenome-assembled viral genomes. PMID:33349699
Genome-wide identification and evolution of HECT genes in wheat. PMID:33344088
The Integrator complex at the crossroad of coding and noncoding RNA. PMID:33340967
Structural Characterization of Glycerol Kinase from the Thermophilic Fungus Chaetomium thermophilum. PMID:33339113
Deep Learning in Protein Structural Modeling and Design. PMID:33336200
ProdMX: Rapid query and analysis of protein functional domain based on compressed sparse matrices. PMID:33335686
The protozoan parasite Toxoplasma gondii encodes a gamut of phosphodiesterases during its lytic cycle in human cells. PMID:33335684
Horizontal Gene Transfer and Tandem Duplication Shape the Unique CAZyme Complement of the Mycoparasitic Oomycetes Pythium oligandrum and Pythium periplocum. PMID:33329445
Transcriptional regulation of bark freezing tolerance in apple (Malus domestica Borkh.). PMID:33328456
High-Throughput Discovery and Characterization of Human Transcriptional Effectors. PMID:33326746
Cobalt Resistance via Detoxification and Mineralization in the Iron-Reducing Bacterium Geobacter sulfurreducens. PMID:33324382
Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity. PMID:33323129
Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome. PMID:33323122
A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity. PMID:33319778
Computational prediction method to decipher receptor-glycoligand interactions in plant immunity. PMID:33316845
PtmC Catalyzes the Final Step of Thioplatensimycin, Thioplatencin, and Thioplatensilin Biosynthesis and Expands the Scope of Arylamine N-Acetyltransferases. PMID:33314918
Genome-wide identification and expression analysis of the CLC gene family in pomegranate (Punica granatum) reveals its roles in salt resistance. PMID:33308157
Candidate Binding Sites for Allosteric Inhibition of the SARS-CoV-2 Main Protease from the Analysis of Large-Scale Molecular Dynamics Simulations. PMID:33306377
Genomic Analysis of Natural Rough Brucella melitensis Rev.1 Vaccine Strains: Identification and Characterization of Mutations in Key Genes Associated with Bacterial LPS Biosynthesis and Virulence. PMID:33302421
Comparative proteomics of common allergenic tree pollens of birch, alder, and hazel. PMID:33301602
A skipping rope translocation mechanism in a widespread family of DNA repair helicases. PMID:33300032
Structures of three MORN repeat proteins and a re-evaluation of the proposed lipid-binding properties of MORN repeats. PMID:33296386
Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes. PMID:33290720
Cyclic-di-GMP Regulates Autoaggregation Through the Putative Peptidoglycan Hydrolase, EagA, and Regulates Transcription of the znuABC Zinc Uptake Gene Cluster in Erwinia amylovora. PMID:33281804
Diversity and Distribution of a Novel Genus of Hyperthermophilic Aquificae Viruses Encoding a Proof-Reading Family-A DNA Polymerase. PMID:33281778
The extracellular juncture domains in the intimin passenger adopt a constitutively extended conformation inducing restraints to its sphere of action. PMID:33277518
Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems. PMID:33275130
CCDC66 frameshift variant associated with a new form of early-onset progressive retinal atrophy in Portuguese Water Dogs. PMID:33273526
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. PMID:33270901
Genes Identification, Molecular Docking and Dynamics Simulation Analysis of Laccases from Amylostereum areolatum Provides Molecular Basis of Laccase Bound to Lignin. PMID:33266512
Sequence Features of Mitochondrial Transporter Protein Families. PMID:33260588
Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2. PMID:33259812
Functional analysis of a novel cryptochrome gene (GbCRY1) from Ginkgo biloba. PMID:33258712
Toward Developing Intuitive Rules for Protein Variant Effect Prediction Using Deep Mutational Scanning Data. PMID:33251402
Reactivity-Based Screening for Citrulline-Containing Natural Products Reveals a Family of Bacterial Peptidyl Arginine Deiminases. PMID:33249828
Functional characterisation of the transcriptome from leaf tissue of the fluoroacetate-producing plant, Dichapetalum cymosum, in response to mechanical wounding. PMID:33239700
Genome-Wide Identification and Expression Profiling Analysis of the Trihelix Gene Family Under Abiotic Stresses in Medicago truncatula. PMID:33238556
MobiDB: intrinsically disordered proteins in 2021. PMID:33237329
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
Characterization and Stress Response of the JmjC Domain-Containing Histone Demethylase Gene Family in the Allotetraploid Cotton Species Gossypium hirsutum. PMID:33233854
Genome-Wide Identification and Characterization of the TCP Gene Family in Cucumber (Cucumis sativus L.) and Their Transcriptional Responses to Different Treatments. PMID:33233827
Structural and Functional Enrichment Analyses for Antimicrobial Peptides. PMID:33233636
Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning. PMID:33230264
Comparative analyses and structural insights of new class glutathione transferases in Cryptosporidium species. PMID:33230237
Chemosensory-Related Gene Family Members of the Horn Fly, Haematobia irritans irritans (Diptera: Muscidae), Identified by Transcriptome Analysis. PMID:33228086
Identification and Expression Analysis of Sugar Transporter Gene Family in Aspergillus oryzae. PMID:33224969
MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca. PMID:33219670
Identification and quantification of target metabolites combined with transcriptome of two rheum species focused on anthraquinone and flavonoids biosynthesis. PMID:33219248
Predicted rat interactome database and gene set linkage analysis. PMID:33216897
Localized effect of treated wastewater effluent on the resistome of an urban watershed. PMID:33215210
High-Quality Sequencing, Assembly, and Annotation of the Streptomyces griseofuscus DSM 40191 Genome. PMID:33214305
Proteome-Scale Detection of Differential Conservation Patterns at Protein and Subprotein Levels with BLUR. PMID:33211099
Mechanisms of Theta Plasmid Replication in Enterobacteria and Implications for Adaptation to Its Host. PMID:33210586
Widespread endogenization of giant viruses shapes genomes of green algae. PMID:33208937
Genome-enabled discovery of anthraquinone biosynthesis in Senna tora. PMID:33208749
CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats. PMID:33206958
Data on draft genome sequence of Caldanaerobacter sp. strain 1523vc, a thermophilic bacterium, isolated from a hot spring of Uzon Caldera, (Kamchatka, Russia). PMID:33204772
Cryo-EM structure of native human uromodulin, a zona pellucida module polymer. PMID:33196145
Engineering the Yeast Yarrowia lipolytica for Production of Polylactic Acid Homopolymer. PMID:33195110
Inhibition of DNA Methylation in Picochlorum soloecismus Alters Algae Productivity. PMID:33193644
GelFAP: Gene Functional Analysis Platform for Gastrodia elata. PMID:33193491
Gene Regulatory Networks of Penicillium echinulatum 2HH and Penicillium oxalicum 114-2 Inferred by a Computational Biology Approach. PMID:33193246
Physiological Processes Modulated by the Chloride-Sensitive WNK-SPAK/OSR1 Kinase Signaling Pathway and the Cation-Coupled Chloride Cotransporters. PMID:33192599
Organohalide-Respiring Bacteria at the Heart of Anaerobic Metabolism in Arctic Wet Tundra Soils. PMID:33187999
Evidence for Pentapeptide-Dependent and Independent CheB Methylesterases. PMID:33187094
Diversification of Fungal Chitinases and Their Functional Differentiation in Histoplasma capsulatum. PMID:33185664
Evolutionary History of Mitochondrial Genomes in Discoba, Including the Extreme Halophile Pleurostomum flabellatum (Heterolobosea). PMID:33185659
Quantitative Structure-Mutation-Activity Relationship Tests (QSMART) model for protein kinase inhibitor response prediction. PMID:33183223
A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain. PMID:33181823
Characterization of the Poplar R2R3-MYB Gene Family and Over-Expression of PsnMYB108 Confers Salt Tolerance in Transgenic Tobacco. PMID:33178243
Discovery and comparative genomic analysis of elk circovirus (ElkCV), a novel circovirus species and the first reported from a cervid host. PMID:33177604
A haplotype-phased genome of wheat stripe rust pathogen Puccinia striiformis f. sp. tritici, race PST-130 from the Western USA. PMID:33175843
LectomeXplore, an update of UniLectin for the discovery of carbohydrate-binding proteins based on a new lectin classification. PMID:33174598
In Silico Characterization and Phylogenetic Distribution of Extracellular Matrix Components in the Model Rhizobacteria Pseudomonas fluorescens F113 and Other Pseudomonads. PMID:33171989
A Genomic Survey of Signalling in the Myxococcaceae. PMID:33171896
Bioinformatic and Reactivity-Based Discovery of Linaridins. PMID:33170617
Genome Variation Map: a worldwide collection of genome variations across multiple species. PMID:33170268
The Transporter Classification Database (TCDB): 2021 update. PMID:33170213
Molecular signatures of the rediae, cercariae and adult stages in the complex life cycles of parasitic flatworms (Digenea: Psilostomatidae). PMID:33168070
COG database update: focus on microbial diversity, model organisms, and widespread pathogens. PMID:33167031
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
Comparative Genome Analysis of Scutellaria baicalensis and Scutellaria barbata Reveals the Evolution of Active Flavonoid Biosynthesis. PMID:33157301
The InterPro protein families and domains database: 20 years on. PMID:33156333
KMT2B-related disorders: expansion of the phenotypic spectrum and long-term efficacy of deep brain stimulation. PMID:33150406
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. PMID:33147627
The Protein-Protein Interaction Network Reveals a Novel Role of the Signal Transduction Protein PII in the Control of c-di-GMP Homeostasis in Azospirillum brasilense. PMID:33144311
Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L. PMID:33142722
Genomics and metatranscriptomics of biogeochemical cycling and degradation of lignin-derived aromatic compounds in thermal swamp sediment. PMID:33139871
Lysogenization of a Lactococcal Host with Three Distinct Temperate Phages Provides Homologous and Heterologous Phage Resistance. PMID:33138325
Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants. PMID:33137950
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses. PMID:33137183
Opposing functions of Fng1 and the Rpd3 HDAC complex in H4 acetylation in Fusarium graminearum. PMID:33137093
From sequence to information. PMID:33131436
Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. PMID:33127895
Heavy Metal Transporters-Associated Proteins in S. tuberosum: Genome-Wide Identification, Comprehensive Gene Feature, Evolution and Expression Analysis. PMID:33126505
Glutathione Restores Hg-Induced Morpho-Physiological Retardations by Inducing Phytochelatin and Oxidative Defense in Alfalfa. PMID:33126453
Pfam: The protein families database in 2021. PMID:33125078
Phylogenetic Diversity and Physiological Roles of Plant Monovalent Cation/H+ Antiporters. PMID:33123183
Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut. PMID:33121006
The MemMoRF database for recognizing disordered protein regions interacting with cellular membranes. PMID:33119751
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. PMID:33119741
Diversity of Light Sensing Molecules and Their Expression During the Embryogenesis of the Cuttlefish (Sepia officinalis). PMID:33117186
Origins and Molecular Evolution of the NusG Paralog RfaH. PMID:33109766
A physiologic overview of the organ-specific transcriptome of the cattle tick Rhipicephalus microplus. PMID:33106528
Diverse Horizontally-Acquired Gene Clusters Confer Sucrose Utilization to Different Lineages of the Marine Pathogen Photobacterium damselae subsp. damselae. PMID:33105683
SMART: recent updates, new developments and status in 2020. PMID:33104802
Computational Identification of Human Biological Processes and Protein Sequence Motifs Putatively Targeted by SARS-CoV-2 Proteins Using Protein-Protein Interaction Networks. PMID:33103435
Reaction mechanism of tetrathionate hydrolysis based on the crystal structure of tetrathionate hydrolase from Acidithiobacillus ferrooxidans. PMID:33103311
Transcriptional Profiles of Long Non-coding RNA and mRNA in Sheep Mammary Gland During Lactation Period. PMID:33101361
A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans. PMID:33096989
Identification, expression, and artificial selection of silkworm epigenetic modification enzymes. PMID:33096977
Arginine-Rich Small Proteins with a Domain of Unknown Function, DUF1127, Play a Role in Phosphate and Carbon Metabolism of Agrobacterium tumefaciens. PMID:33093235
SurA is a cryptically grooved chaperone that expands unfolded outer membrane proteins. PMID:33093201
De novo transcriptome assembly from the gonads of a scleractinian coral, Euphyllia ancora: molecular mechanisms underlying scleractinian gametogenesis. PMID:33087060
Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures. PMID:33086653
The genome of Chinese flowering cherry (Cerasus serrulata) provides new insights into Cerasus species. PMID:33082971
Reference transcriptomes and comparative analyses of six species in the threatened rosewood genus Dalbergia. PMID:33082403
Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes. PMID:33076954
Genome-wide identification of ATP binding cassette (ABC) transporter and heavy metal associated (HMA) gene families in flax (Linum usitatissimum L.). PMID:33076828
The relationship between protein domains and homopeptides in the Plasmodium falciparum proteome. PMID:33062426
The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic. PMID:33058468
Exploration into biomarker potential of region-specific brain gene co-expression networks. PMID:33051491
Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication. PMID:33051376
Identification of polycomb repressive complex 1 and 2 core components in hexaploid bread wheat. PMID:33050875
Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. PMID:33049387
The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes. PMID:33040418
Proteomic and transcriptomic profiling of aerial organ development in Arabidopsis. PMID:33037224
Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community. PMID:33036549
Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease. PMID:33035590
FilterDCA: Interpretable supervised contact prediction using inter-domain coevolution. PMID:33035205
Genome-wide analysis of PRR gene family uncovers their roles in circadian rhythmic changes and response to drought stress in Gossypium hirsutum L. PMID:33033660
CryoEM structure of the type IVa pilus secretin required for natural competence in Vibrio cholerae. PMID:33033258
LSD1 inhibition induces differentiation and cell death in Merkel cell carcinoma. PMID:33026191
Evolutionary aspects of the Viridiplantae nitroreductases. PMID:33025290
Genome-wide characterization and expression analysis suggested diverse functions of the mechanosensitive channel of small conductance-like (MSL) genes in cereal crops. PMID:33024170
A Novel Secreted Cysteine-Rich Anionic (Sca) Protein from the Citrus Postharvest Pathogen Penicillium digitatum Enhances Virulence and Modulates the Activity of the Antifungal Protein B (AfpB). PMID:33023232
Genome Mining of the Genus Streptacidiphilus for Biosynthetic and Biodegradation Potential. PMID:33022985
Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench. PMID:33022036
A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae. PMID:33009392
Molecular Simulations and Network Modeling Reveal an Allosteric Signaling in the SARS-CoV-2 Spike Proteins. PMID:33006900
Multiple Isolated Transcription Factors Act as Switches and Contribute to Species Uniqueness. PMID:33003522
Genetic Diversity of Serine Protease Inhibitors in Myxozoan (Cnidaria, Myxozoa) Fish Parasites. PMID:33003479
Genome-Wide Analysis of OPR Family Genes in Cotton Identified a Role for GhOPR9 in Verticillium dahliae Resistance. PMID:32992523
The E3 ubiquitin-protein ligase MDM2 is a novel interactor of the von Hippel-Lindau tumor suppressor. PMID:32985545
Expression of an Extracellular Protein (SMU.63) Is Regulated by SprV in Streptococcus mutans. PMID:32978138
Molecular Characterizations of Double-Stranded RNA Degrading Nuclease Genes from Ostrinia nubilalis. PMID:32977554
DIGGER: exploring the functional role of alternative splicing in protein interactions. PMID:32976589
Diversity and evolution of B-family DNA polymerases. PMID:32976577
Comparative Analysis of the Secretome and Interactome of Trypanosoma cruzi and Trypanosoma rangeli Reveals Species Specific Immune Response Modulating Proteins. PMID:32973747
Cell type specific gene expression profiling reveals a role for complement component C3 in neutrophil responses to tissue damage. PMID:32973200
Abiotic and past climatic conditions drive protein abundance variation among natural populations of the caddisfly Crunoecia irrorata. PMID:32968134
Genome-wide identification and expression analysis of bZIP gene family in Carthamus tinctorius L. PMID:32968100
Whitefly genomes contain ribotoxin coding genes acquired from plants. PMID:32968092
Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota. PMID:32968071
Construction of a chromosome-scale long-read reference genome assembly for potato. PMID:32964225
Genome-Wide Identification and Characterization of the SHI-Related Sequence Gene Family in Rice. PMID:32963469
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
Elucidation of the aberrant 3' splice site selection by cancer-associated mutations on the U2AF1. PMID:32958768
Mining and evolution analysis of lateral organ boundaries domain (LBD) genes in Chinese white pear (Pyrus bretschneideri). PMID:32957912
Extension of the taxonomic coverage of the family GH126 outside Firmicutes and in silico characterization of its non-catalytic terminal domains. PMID:32953382
Genome-wide identification and expression patterns analysis of the RPD3/HDA1 gene family in cotton. PMID:32948145
High-Temperature-Responsive Poplar lncRNAs Modulate Target Gene Expression via RNA Interference and Act as RNA Scaffolds to Enhance Heat Tolerance. PMID:32948072
Recombinant bacteriophage LysKB317 endolysin mitigates Lactobacillus infection of corn mash fermentations. PMID:32944073
Arrangement and symmetry of the fungal E3BP-containing core of the pyruvate dehydrogenase complex. PMID:32938938
Nanaerobic growth enables direct visualization of dynamic cellular processes in human gut symbionts. PMID:32938803
Larvae of the Clothing Moth Tineola bisselliella Maintain Gut Bacteria that Secrete Enzyme Cocktails to Facilitate the Digestion of Keratin. PMID:32937935
Genome-Wide Identification, Characterization, and Regulation of RWP-RK Gene Family in the Nitrogen-Fixing Clade. PMID:32932820
How to use the MEROPS database and website to help understand peptidase specificity. PMID:32920969
Advances in encapsulin nanocompartment biology and engineering. PMID:32918485
Trehalose Degradation by Cellvibrio japonicus Exhibits No Functional Redundancy and Is Solely Dependent on the Tre37A Enzyme. PMID:32917758
Mining and Statistical Modeling of Natural and Variant Class IIa Bacteriocins Elucidate Activity and Selectivity Profiles across Species. PMID:32917749
Increased resolution of African swine fever virus genome patterns based on profile HMMs of protein domains. PMID:32913663
Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC. PMID:32912302
A distinct lineage of Caudovirales that encodes a deeply branching multi-subunit RNA polymerase. PMID:32908149
DrpB (YedR) Is a Nonessential Cell Division Protein in Escherichia coli. PMID:32900831
Characterization of the Burkholderia cenocepacia J2315 Surface-Exposed Immunoproteome. PMID:32899969
An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice. PMID:32899740
The use of consensus sequence information to engineer stability and activity in proteins. PMID:32896279
An Unexpectedly Complex Mitoribosome in Andalucia godoyi, a Protist with the Most Bacteria-like Mitochondrial Genome. PMID:32886790
A phylogenetic view and functional annotation of the animal β1,3-glycosyltransferases of the GT31 CAZy family. PMID:32886776
The Association between Insertion Sequences and Antibiotic Resistance Genes. PMID:32878926
Reengineering biocatalysts: Computational redesign of chondroitinase ABC improves efficacy and stability. PMID:32875119
Promiscuous Enzyme Activity as a Driver of Allo and Iso Convergent Evolution, Lessons from the β-Lactamases. PMID:32872436
Vaccine design of coronavirus spike (S) glycoprotein in chicken: immunoinformatics and computational approaches. PMID:32869000
Identification of Uncharacterized Components of Prokaryotic Immune Systems and Their Diverse Eukaryotic Reformulations. PMID:32868406
Comparative genomic analysis of Vibrios yields insights into genes associated with virulence towards C. gigas larvae. PMID:32867668
Keep Calm and Survive: Adaptation Strategies to Energy Crisis in Fruit Trees under Root Hypoxia. PMID:32867316
Genome-wide analysis of the polyamine oxidase gene family in wheat (Triticum aestivum L.) reveals involvement in temperature stress response. PMID:32866160
Sequencing, assembly, annotation, and gene expression: novel insights into browning-resistant Luffa cylindrica. PMID:32864209
A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane. PMID:32859984
Diversity in the intrinsic apoptosis pathway of nematodes. PMID:32859965
Endosymbionts of Metazoans Dwelling in the PACManus Hydrothermal Vent: Diversity and Potential Adaptive Features Revealed by Genome Analysis. PMID:32859597
RNA-binding and prion domains: the Yin and Yang of phase separation. PMID:32857852
Circadian clock mechanism driving mammalian photoperiodism. PMID:32855407
A Novel Primer Mixture for GH48 Genes: Quantification and Identification of Truly Cellulolytic Bacteria in Biogas Fermenters. PMID:32854333
Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms. PMID:32850729
RIGD: A Database for Intronless Genes in the Rosaceae. PMID:32849839
Closed mitosis requires local disassembly of the nuclear envelope. PMID:32848252
Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems. PMID:32839535
A DUF4148 family protein produced inside RAW264.7 cells is a critical Burkholderia pseudomallei virulence factor. PMID:32835600
Atypical Membrane-Anchored Cytokine MIF in a Marine Dinoflagellate. PMID:32825358
The Absence of C-5 DNA Methylation in Leishmania donovani Allows DNA Enrichment from Complex Samples. PMID:32824654
Canthaxanthin, a Red-Hot Carotenoid: Applications, Synthesis, and Biosynthetic Evolution. PMID:32824217
FLAVi: An Enhanced Annotator for Viral Genomes of Flaviviridae. PMID:32824044
Spacer acquisition by Type III CRISPR-Cas system during bacteriophage infection of Thermus thermophilus. PMID:32821943
Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C sequencing. PMID:32821405
Age-dependent expression of cancer-related genes in a long-lived seabird. PMID:32821278
Crystal structure of GCN5 PCAF N-terminal domain reveals atypical ubiquitin ligase structure. PMID:32820047
Comparative genomic analysis of Flavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis. PMID:32819293
Genomic and transcriptomic insights into Raffaelea lauricola pathogenesis. PMID:32819276
Molecular causes of an evolutionary shift along the parasitism-mutualism continuum in a bacterial symbiont. PMID:32817434
Complete Genome Sequence of Sulfitobacter Phage ϕGT1, Isolated from a Tidal Flat. PMID:32817157
Alternative Splicing During the Chlamydomonas reinhardtii Cell Cycle. PMID:32817123
Autotransporters Drive Biofilm Formation and Autoaggregation in the Diderm Firmicute Veillonella parvula. PMID:32817093
Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli. PMID:32813020
Strong homology between SARS-CoV-2 envelope protein and a Mycobacterium sp. antigen allows rapid diagnosis of Mycobacterial infections and may provide specific anti-SARS-CoV-2 immunity via the BCG vaccine. PMID:32805515
Comparative Genomics Underlines Multiple Roles of Profftella, an Obligate Symbiont of Psyllids: Providing Toxins, Vitamins, and Carotenoids. PMID:32797185
The DUF328 family member YaaA is a DNA-binding protein with a novel fold. PMID:32796037
SQMtools: automated processing and visual analysis of 'omics data with R and anvi'o. PMID:32795263
Development and Application of SSR Markers Related to Genes Involved in Leaf Adaxial-Abaxial Polarity Establishment in Chinese Cabbage (Brassica rapa L. ssp. pekinensis). PMID:32793286
Abundant Taxa and Favorable Pathways in the Microbiome of Soda-Saline Lakes in Inner Mongolia. PMID:32793172
Amoeba Genome Reveals Dominant Host Contribution to Plastid Endosymbiosis. PMID:32790833
A LysM Domain-Containing Protein LtLysM1 Is Important for Vegetative Growth and Pathogenesis in Woody Plant Pathogen Lasiodiplodia theobromae. PMID:32788891
Structure and Multitasking of the c-di-GMP-Sensing Cellulose Secretion Regulator BcsE. PMID:32788377
The Ribbon-Helix-Helix Domain Protein CdrS Regulates the Tubulin Homolog ftsZ2 To Control Cell Division in Archaea. PMID:32788376
Spatial Transcriptomics of Nematodes Identifies Sperm Cells as a Source of Genomic Novelty and Rapid Evolution. PMID:32785688
JAGN1, tetraspanins, and Erv proteins: is common topology indicative of common function in cargo sorting? PMID:32783652
Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown. PMID:32782292
Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application. PMID:32778133
Allelic polymorphisms in a glycosyltransferase gene shape glycan repertoire in the O-linked protein glycosylation system of Neisseria. PMID:32776107
Chemoreceptors with C-terminal pentapeptides for CheR and CheB binding are abundant in bacteria that maintain host interactions. PMID:32774789
Sodium-coupled glucose transport, the SLC5 family, and therapeutically relevant inhibitors: from molecular discovery to clinical application. PMID:32767111
DRAM for distilling microbial metabolism to automate the curation of microbiome function. PMID:32766782
Functional Insight of Nitric-Oxide Induced DUF Genes in Arabidopsis thaliana. PMID:32765550
Transcriptomic Analysis of Four Cerianthid (Cnidaria, Ceriantharia) Venoms. PMID:32764303
[Quantitative determination and optimun extraction technique of nine compounds of Paeoniae Radix Alba]. PMID:32762162
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
Description of Komagataeibacter melaceti sp. nov. and Komagataeibacter melomenusus sp. nov. Isolated from Apple Cider Vinegar. PMID:32756518
Differential neuropeptide modulation of premotor and motor neurons in the lobster cardiac ganglion. PMID:32755328
Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs. PMID:32753684
Coevolutionary Analysis Reveals a Conserved Dual Binding Interface between Extracytoplasmic Function σ Factors and Class I Anti-σ Factors. PMID:32753504
A comprehensive rat transcriptome built from large scale RNA-seq-based annotation. PMID:32749457
Integration of the pSLT Plasmid into the Salmonella Chromosome Results in a Temperature-Sensitive Growth Defect Due to Aberrant DNA Replication. PMID:32747428
Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys. PMID:32745123
Genome-wide identification and expression profiles of ERF subfamily transcription factors in Zea mays. PMID:32742811
Genome sequencing of four culinary herbs reveals terpenoid genes underlying chemodiversity in the Nepetoideae. PMID:32735328
The Flavoproteome of the Model Plant Arabidopsis thaliana. PMID:32731628
Machine-learning approach expands the repertoire of anti-CRISPR protein families. PMID:32728052
The alcohol dehydrogenase gene family in sugarcane and its involvement in cold stress regulation. PMID:32727370
Chemical structure and genetic organization of the E. coli O6:K15 capsular polysaccharide. PMID:32724125
A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes. PMID:32723799
Transfer of endogenous small RNAs between branches of scions and rootstocks in grafted sweet cherry trees. PMID:32722723
Protein-Protein Interactions Mediated by Intrinsically Disordered Protein Regions Are Enriched in Missense Mutations. PMID:32722039
Structure and function of the juxtamembrane GAF domain of potassium biosensor KdpD. PMID:32713093
Improved Reference Genome for Cyclotella cryptica CCMP332, a Model for Cell Wall Morphogenesis, Salinity Adaptation, and Lipid Production in Diatoms (Bacillariophyta). PMID:32709619
Amino acid sequence associated with bacteriophage recombination site helps to reveal genes potentially acquired through horizontal gene transfer. PMID:32703190
Calmodulin-binding transcription activator (CAMTA) genes family: Genome-wide survey and phylogenetic analysis in flax (Linum usitatissimum). PMID:32702710
The transcriptome of Listeria monocytogenes during co-cultivation with cheese rind bacteria suggests adaptation by induction of ethanolamine and 1,2-propanediol catabolism pathway genes. PMID:32701964
Genome-Wide Identification and Functional Characterization of the Heat Shock Factor Family in Eggplant (Solanum melongena L.) under Abiotic Stress Conditions. PMID:32698415
Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras. PMID:32697992
An Easy Protocol for Evolutionary Analysis of Intrinsically Disordered Proteins. PMID:32696356
Exploring Protein Intrinsic Disorder with MobiDB. PMID:32696355
How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource. PMID:32696353
Family-Specific Gains and Losses of Protein Domains in the Legume and Grass Plant Families. PMID:32694909
Reference Genome for the Highly Transformable Setaria viridis ME034V. PMID:32694197
Machine Boss: rapid prototyping of bioinformatic automata. PMID:32683444
Two novel bacteriophage genera from a groundwater reservoir highlight subsurface environments as underexplored biotopes in bacteriophage ecology. PMID:32681144
Expansions and contractions in gene families of independently-evolved blood-feeding insects. PMID:32680460
In Silico Evaluation of Putative S100B Interacting Proteins in Healthy and IBD Gut Microbiota. PMID:32679810
A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron. PMID:32678091
Chain reactions: molecular mechanisms of RBR ubiquitin ligases. PMID:32677670
Genome-Wide Identification of the CrRLK1L Subfamily and Comparative Analysis of Its Role in the Legume-Rhizobia Symbiosis. PMID:32674446
Ancient co-option of an amino acid ABC transporter locus in Pseudomonas syringae for host signal-dependent virulence gene regulation. PMID:32673374
Computational approaches in viral ecology. PMID:32670501
Proteome-wide analysis of a malaria vaccine study reveals personalized humoral immune profiles in Tanzanian adults. PMID:32662772
Transcriptomic Analysis of Extracellular RNA Governed by the Endocytic Adaptor Protein Cin1 of Cryptococcus deneoformans. PMID:32656093
First Report on the Plasmidome From a High-Altitude Lake of the Andean Puna. PMID:32655530
The Genome of the Softshell Clam Mya arenaria and the Evolution of Apoptosis. PMID:32653903
Reconstruction of the Carbohydrate 6-O Sulfotransferase Gene Family Evolution in Vertebrates Reveals Novel Member, CHST16, Lost in Amniotes. PMID:32652010
Porin from Marine Bacterium Marinomonas primoryensis KMM 3633T: Isolation, Physico-Chemical Properties, and Functional Activity. PMID:32650591
Type I beta turns make a new twist in pentapeptide repeat proteins: Crystal structure of Alr5209 from Nostoc sp. PCC 7120 determined at 1.7 angström resolution. PMID:32647815
Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein. PMID:32646969
The Magnetic Receptor of Monascus ruber M7: Gene Clone and Its Heterologous Expression in Escherichia coli. PMID:32636810
Genome-Scale Metabolic Model Driven Design of a Defined Medium for Campylobacter jejuni M1cam. PMID:32636809
Descent of Bacteria and Eukarya From an Archaeal Root of Life. PMID:32636606
The Intrinsically Disordered Protein CARP9 Bridges HYL1 to AGO1 in the Nucleus to Promote MicroRNA Activity. PMID:32636339
The barley lectin, horcolin, binds high-mannose glycans in a multivalent fashion, enabling high-affinity, specific inhibition of cellular HIV infection. PMID:32636304
Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju. PMID:32633756
Peptides derived from Kex2-processed repeat proteins are widely distributed and highly diverse in the Fungi kingdom. PMID:32626593
Structure and Evolution of Acinetobacter baumannii Plasmids. PMID:32625185
ULK1 and ULK2 are less redundant than previously thought: computational analysis uncovers distinct regulation and functions of these autophagy induction proteins. PMID:32616830
Identification of novel genetic factors underlying the host-pathogen interaction between barley (Hordeum vulgare L.) and powdery mildew (Blumeria graminis f. sp. hordei). PMID:32614894
Using AnABlast for intergenic sORF prediction in the Caenorhabditis elegans genome. PMID:32614398
CHDGKB: a knowledgebase for systematic understanding of genetic variations associated with non-syndromic congenital heart disease. PMID:32608479
Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys. PMID:32605604
Gene Expression and Functional Analyses of Odorant Receptors in Small Hive Beetles (Aethina tumida). PMID:32605135
In Silico Comparison Shows that the Pan-Genome of a Dairy-Related Bacterial Culture Collection Covers Most Reactions Annotated to Human Microbiomes. PMID:32605102
Mass Spectrometry to Study Chromatin Compaction. PMID:32604817
Evaluating the Potential for Cross-Interactions of Antitoxins in Type II TA Systems. PMID:32604745
The bottromycin epimerase BotH defines a group of atypical α/β-hydrolase-fold enzymes. PMID:32601484
PelX is a UDP-N-acetylglucosamine C4-epimerase involved in Pel polysaccharide-dependent biofilm formation. PMID:32601062
Crystal structure of Oryza sativa TDC reveals the substrate specificity for TDC-mediated melatonin biosynthesis. PMID:32595985
Insights into the Evolution of Neoteny from the Genome of the Asian Icefish Protosalanx chinensis. PMID:32593955
Domain-centric database to uncover structure of minimally characterized viral genomes. PMID:32587259
Using Cellular Automata to Simulate Domain Evolution in Proteins. PMID:32582278
Immunoreactive Proteins in the Esophageal Gland Cells of Anisakis Simplex Sensu Stricto Detected by MALDI-TOF/TOF Analysis. PMID:32580523
Inducible aging in Hydra oligactis implicates sexual reproduction, loss of stem cells, and genome maintenance as major pathways. PMID:32578072
The bacterial copper resistance protein CopG contains a cysteine-bridged tetranuclear copper cluster. PMID:32571874
Mitochondrial CLPP2 Assists Coordination and Homeostasis of Respiratory Complexes. PMID:32571844
Genome-Wide Identification of RNA Silencing-Related Genes and Their Expressional Analysis in Response to Heat Stress in Barley (Hordeum vulgare L.). PMID:32570964
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
Genome-wide characterization of the Zn(II)2Cys6 zinc cluster-encoding gene family in Pleurotus ostreatus and expression analyses of this family during developmental stages and under heat stress. PMID:32566411
Pterocarpan synthase (PTS) structures suggest a common quinone methide-stabilizing function in dirigent proteins and proteins with dirigent-like domains. PMID:32565424
Understanding the Landscape of X-linked Variants Causing Intellectual Disability in Females Through Extreme X Chromosome Inactivation Skewing. PMID:32564284
Primordial emergence of a nucleic acid-binding protein via phase separation and statistical ornithine-to-arginine conversion. PMID:32561643
Shotgun proteomics reveals putative polyesterases in the secretome of the rock-inhabiting fungus Knufia chersonesos. PMID:32555357
The Scaffold Protein Axin Promotes Signaling Specificity within the Wnt Pathway by Suppressing Competing Kinase Reactions. PMID:32553184
Patterns of Sequence and Expression Diversification Associate Members of the PADRE Gene Family With Response to Fungal Pathogens. PMID:32547597
Initial Mapping of the New York City Wastewater Virome. PMID:32546676
Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type. PMID:32546614
A new mode of NPR1 action via an NB-ARC-NPR1 fusion protein negatively regulates the defence response in wheat to stem rust pathogen. PMID:32544264
β-Strand-mediated interactions of protein domains. PMID:32543729
GTDB: an integrated resource for glycosyltransferase sequences and annotations. PMID:32542364
ForageGrassBase: molecular resource for the forage grass meadow fescue (Festuca pratensis Huds.). PMID:32539086
Fatty acid bioconversion in harpacticoid copepods in a changing environment: a transcriptomic approach. PMID:32536309
Enhanced Triacylglycerol Metabolism Contributes to Efficient Oil Utilization and High-Level Production of Salinomycin in Streptomyces albus ZD11. PMID:32532869
Hybrid de novo genome assembly of red gromwell (Lithospermum erythrorhizon) reveals evolutionary insight into shikonin biosynthesis. PMID:32528694
Identifying a Molecular Mechanism That Imparts Species-Specific Toxicity to YoeB Toxins. PMID:32528435
Genome-wide analysis of the Saccharina japonica sulfotransferase genes and their transcriptional profiles during whole developmental periods and under abiotic stresses. PMID:32527219
Spt6 is a maintenance factor for centromeric CENP-A. PMID:32522980
VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. PMID:32522236
A Comprehensive Multi-Omic Approach Reveals a Relatively Simple Venom in a Diet Generalist, the Northern Short-Tailed Shrew, Blarina brevicauda. PMID:32520994
Host glycan utilization within the Bacteroidetes Sus-like paradigm. PMID:32518945
Alteromonas Myovirus V22 Represents a New Genus of Marine Bacteriophages Requiring a Tail Fiber Chaperone for Host Recognition. PMID:32518192
Depth-related variability in viral communities in highly stratified sulfidic mine tailings. PMID:32517753
PSIONplusm Server for Accurate Multi-Label Prediction of Ion Channels and Their Types. PMID:32517331
Comparative Genomics Determines Strain-Dependent Secondary Metabolite Production in Streptomyces venezuelae Strains. PMID:32516997
An ECF-type transporter scavenges heme to overcome iron-limitation in Staphylococcus lugdunensis. PMID:32515736
Gray whale transcriptome reveals longevity adaptations associated with DNA repair and ubiquitination. PMID:32515539
Animal biosynthesis of complex polyketides in a photosynthetic partnership. PMID:32513940
Novel Immunoglobulin Domain Proteins Provide Insights into Evolution and Pathogenesis Mechanisms of SARS-Related Coronaviruses. PMID:32511297
Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation. PMID:32511244
Diversity and Evolutionary Dynamics of Antiphage Defense Systems in Ralstonia solanacearum Species Complex. PMID:32508782
SMRT Sequencing of Paramecium Bursaria Chlorella Virus-1 Reveals Diverse Methylation Stability in Adenines Targeted by Restriction Modification Systems. PMID:32508769
Comparative Target Analysis of Chlorinated Biphenyl Antimicrobials Highlights MenG as a Molecular Target of Triclocarban. PMID:32503913
From the Argonauts Mythological Sailors to the Argonautes RNA-Silencing Navigators: Their Emerging Roles in Human-Cell Pathologies. PMID:32503341
DSCAM-AS1-Driven Proliferation of Breast Cancer Cells Involves Regulation of Alternative Exon Splicing and 3'-End Usage. PMID:32503257
Obtaining extremely large and accurate protein multiple sequence alignments from curated hierarchical alignments. PMID:32500917
The minimal meningococcal ProQ protein has an intrinsic capacity for structure-based global RNA recognition. PMID:32499480
Draft Genome Sequence of the Astaxanthin-Producing Microalga Haematococcus lacustris Strain NIES-144. PMID:32499361
Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation. PMID:32498246
The nuclear and mitochondrial genomes of Frieseomelitta varia - a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste. PMID:32493270
Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family. PMID:32493223
Coevolutionary data-based interaction networks approach highlighting key residues across protein families: The case of the G-protein coupled receptors. PMID:32489528
Crystal structure of β-L-arabinobiosidase belonging to glycoside hydrolase family 121. PMID:32479540
A decade of research on the second messenger c-di-AMP. PMID:32472931
Novel Immunoglobulin Domain Proteins Provide Insights into Evolution and Pathogenesis of SARS-CoV-2-Related Viruses. PMID:32471829
Genome-wide characterization of tea plant (Camellia sinensis) Hsf transcription factor family and role of CsHsfA2 in heat tolerance. PMID:32471355
Improved bacterial recombineering by parallelized protein discovery. PMID:32467157
Mining the Yucatan Coastal Microbiome for the Identification of Non-Ribosomal Peptides Synthetase (NRPS) Genes. PMID:32466531
The World of Cyclic Dinucleotides in Bacterial Behavior. PMID:32466317
Heavy Metal Stress-Associated Proteins in Rice and Arabidopsis: Genome-Wide Identification, Phylogenetics, Duplication, and Expression Profiles Analysis. PMID:32457808
MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome-Host Interactions. PMID:32455748
Genome-Wide Analysis, Characterization, and Expression Profile of the Basic Leucine Zipper Transcription Factor Family in Pineapple. PMID:32455125
A molecular filter for the cnidarian stinging response. PMID:32452384
Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan. PMID:32451471
Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure. PMID:32449750
A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. PMID:32449511
Discovery of new group I-D introns leads to creation of subtypes and link to an adaptive response of the mitochondrial genome in fungi. PMID:32449459
The intestinal virome in children with cystic fibrosis differs from healthy controls. PMID:32442222
Whole genome sequence and comparative genome analyses of multi-resistant Staphylococcus warneri GD01 isolated from a diseased pig in China. PMID:32442199
Phylogenomic analysis of the APETALA2 transcription factor subfamily across angiosperms reveals both deep conservation and lineage-specific patterns. PMID:32436321
Chromosomal-Level Genome Assembly of the Sea Urchin Lytechinus variegatus Substantially Improves Functional Genomic Analyses. PMID:32433766
The Biotechnological Potential of the Marine Diatom Skeletonema dohrnii to the Elevated Temperature and pCO2 Concentration. PMID:32429035
An Endolysin LysSE24 by Bacteriophage LPSE1 Confers Specific Bactericidal Activity against Multidrug-Resistant Salmonella Strains. PMID:32429030
Secretome-Based Screening in Target Discovery. PMID:32425085
Modulation of Response Regulator CheY Reaction Kinetics by Two Variable Residues That Affect Conformation. PMID:32424010
PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins. PMID:32421769
Large-scale network analysis captures biological features of bacterial plasmids. PMID:32415210
Dynamic Expansion and Functional Evolutionary Profiles of Plant Conservative Gene Family SBP-Box in Twenty Two Flowering Plants and the Origin of miR156. PMID:32414086
Mitochondrial genome sequence of Phytophthora sansomeana and comparative analysis of Phytophthora mitochondrial genomes. PMID:32407378
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
AcrFinder: genome mining anti-CRISPR operons in prokaryotes and their viruses. PMID:32402073
UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase. PMID:32399560
DNA Variant in the RPGRIP1L Gene Influences Alternative Splicing. PMID:32399473
Genome-wide association study leads to novel genetic insights into resistance to Aspergillus flavus in maize kernels. PMID:32393173
Oviz-Bio: a web-based platform for interactive cancer genomics data visualization. PMID:32392343
EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities. PMID:32392342
Identification of HMG-box family establishes the significance of SOX6 in the malignant progression of glioblastoma. PMID:32388501
Genomic Identification, Evolution, and Expression Analysis of Collagen Genes Family in Water Buffalo during Lactation. PMID:32384775
Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi. PMID:32382073
Genome-Wide Identification, Evolutionary Patterns, and Expression Analysis of bZIP Gene Family in Olive (Olea europaea L.). PMID:32380769
Discovery of Widespread Host Protein Interactions with the Pre-replicated Genome of CHIKV Using VIR-CLASP. PMID:32380061
Hypogonadotropic hypogonadism due to variants in RAB3GAP2: expanding the phenotypic and genotypic spectrum of Martsolf syndrome. PMID:32376645
The model cyanobacteria Anabaena sp. PCC 7120 possess an intact but partially degenerated gene cluster encoding gas vesicles. PMID:32375647
Identification and Comparative Analysis of Long Non-Coding RNA in the Skeletal Muscle of Two Dezhou Donkey Strains. PMID:32375413
GCN2-Like Kinase Modulates Stress Granule Formation During Nutritional Stress in Trypanosoma cruzi. PMID:32373547
Conserved Outer Tegument Component UL11 from Herpes Simplex Virus 1 Is an Intrinsically Disordered, RNA-Binding Protein. PMID:32371601
Antimicrobial resistance genes in raw milk for human consumption. PMID:32366826
Lanthanide-dependent alcohol dehydrogenases require an essential aspartate residue for metal coordination and enzymatic function. PMID:32366463
PRMT7 regulates RNA-binding capacity and protein stability in Leishmania parasites. PMID:32365184
Lysine Acetyltransferase p300/CBP Plays an Important Role in Reproduction, Embryogenesis and Longevity of the Pea Aphid Acyrthosiphon pisum. PMID:32357443
Independent Whole-Genome Duplications Define the Architecture of the Genomes of the Devastating West African Cacao Black Pod Pathogen Phytophthora megakarya and Its Close Relative Phytophthora palmivora. PMID:32354704
A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. PMID:32353859
Ambiguity Coding Allows Accurate Inference of Evolutionary Parameters from Alignments in an Aggregated State-Space. PMID:32353118
CRISPR-Cas13 Inhibitors Block RNA Editing in Bacteria and Mammalian Cells. PMID:32348779
Comparative transcriptomics characterized the distinct biosynthetic abilities of terpenoid and paeoniflorin biosynthesis in herbaceous peony strains. PMID:32341893
Deep conservation of prion-like composition in the eukaryotic prion-former Pub1/Tia1 family and its relatives. PMID:32337108
MiDaf16-like and MiSkn1-like gene families are reliable targets to develop biotechnological tools for the control and management of Meloidogyne incognita. PMID:32332904
Dominant Vibrio cholerae phage exhibits lysis inhibition sensitive to disruption by a defensive phage satellite. PMID:32329714
Aspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis. PMID:32327655
Genomic analysis of a riboflavin-overproducing Ashbya gossypii mutant isolated by disparity mutagenesis. PMID:32326906
Apcdd1 is a dual BMP/Wnt inhibitor in the developing nervous system and skin. PMID:32320685
The PRR14 heterochromatin tether encodes modular domains that mediate and regulate nuclear lamina targeting. PMID:32317397
Annotation and characterization of Babesia gibsoni apicoplast genome. PMID:32317011
Characterization of Regulatory and Transporter Genes in the Biosynthesis of Anti-Tuberculosis Ilamycins and Production in a Heterologous Host. PMID:32316457
Structural Characterization of Carbonic Anhydrase VIII and Effects of Missense Single Nucleotide Variations to Protein Structure and Function. PMID:32316137
The Interaction Between lncRNA SNHG6 and hnRNPA1 Contributes to the Growth of Colorectal Cancer by Enhancing Aerobic Glycolysis Through the Regulation of Alternative Splicing of PKM. PMID:32296635
The Versatility of Opportunistic Infections Caused by Gemella Isolates Is Supported by the Carriage of Virulence Factors From Multiple Origins. PMID:32296407
Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio). PMID:32293261
A Chromosome-Scale Assembly of the Asian Honeybee Apis cerana Genome. PMID:32292419
Specificity in PDZ-peptide interaction networks: Computational analysis and review. PMID:32289118
TREND: a platform for exploring protein function in prokaryotes based on phylogenetic, domain architecture and gene neighborhood analyses. PMID:32282909
Exploiting the Diversity of Saccharomycotina Yeasts To Engineer Biotin-Independent Growth of Saccharomyces cerevisiae. PMID:32276977
Investigation of sequence features of hinge-bending regions in proteins with domain movements using kernel logistic regression. PMID:32272894
Integrated Analysis of RNA-Binding Proteins in Glioma. PMID:32272554
Functional Characterization of Clinical Isolates of the Opportunistic Fungal Pathogen Aspergillus nidulans. PMID:32269156
Mob Family Proteins: Regulatory Partners in Hippo and Hippo-Like Intracellular Signaling Pathways. PMID:32266255
Genome-wide identification and expression analysis of the NAC transcription factor family in tomato (Solanum lycopersicum) during aluminum stress. PMID:32264854
Characterization of the AP2/ERF Transcription Factor Family and Expression Profiling of DREB Subfamily under Cold and Osmotic Stresses in Ammopiptanthus nanus. PMID:32260365
The Cell Wall PAC (Proline-Rich, Arabinogalactan Proteins, Conserved Cysteines) Domain-Proteins Are Conserved in the Green Lineage. PMID:32260156
CsWAKL08, a pathogen-induced wall-associated receptor-like kinase in sweet orange, confers resistance to citrus bacterial canker via ROS control and JA signaling. PMID:32257228
Molecular Topology of RNA Polymerase I Upstream Activation Factor. PMID:32253346
Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses. PMID:32249765
NLGenomeSweeper: A Tool for Genome-Wide NBS-LRR Resistance Gene Identification. PMID:32245073
Inventory and Evolution of Mitochondrion-localized Family A DNA Polymerases in Euglenozoa. PMID:32244644
Computation-Driven Analysis of Model Polyextremo-tolerant Fungus Exophiala dermatitidis: Defensive Pigment Metabolic Costs and Human Applications. PMID:32240950
Toxin-Antitoxin Gene Pairs Found in Tn3 Family Transposons Appear To Be an Integral Part of the Transposition Module. PMID:32234815
Integrated Informatics Analysis of Cancer-Related Variants. PMID:32228266
A single amino acid substitution uncouples catalysis and allostery in an essential biosynthetic enzyme in Mycobacterium tuberculosis. PMID:32217694
Assessment and comparison of putative amine receptor complement/diversity in the brain and eyestalk ganglia of the lobster, Homarus americanus. PMID:32215729
An atypical DYRK kinase connects quorum-sensing with posttranscriptional gene regulation in Trypanosoma brucei. PMID:32213288
No More Tears: Mining Sequencing Data for Novel Bt Cry Toxins with CryProcessor. PMID:32210056
Unraveling CAF-1 family in Plasmodium falciparum: comparative genome-wide identification and phylogenetic analysis among eukaryotes, expression profiling and protein-protein interaction studies. PMID:32206492
Expansion of the Major Facilitator Superfamily (MFS) to include novel transporters as well as transmembrane-acting enzymes. PMID:32205149
Developing and applying computational resources for biochemistry education. PMID:32203640
Bioinformatic Analysis of the Flavin-Dependent Amine Oxidase Superfamily: Adaptations for Substrate Specificity and Catalytic Diversity. PMID:32198115
Disinfection exhibits systematic impacts on the drinking water microbiome. PMID:32197656
Portal of Juglandaceae: A comprehensive platform for Juglandaceae study. PMID:32194971
Genome relationships and LTR-retrotransposon diversity in three cultivated Capsicum L. (Solanaceae) species. PMID:32183698
LRRpredictor-A New LRR Motif Detection Method for Irregular Motifs of Plant NLR Proteins Using an Ensemble of Classifiers. PMID:32182725
New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements. PMID:32182341
The Nature and Arrangement of Pentatricopeptide Domains and the Linker Sequences Between Them. PMID:32180683
Wikidata as a knowledge graph for the life sciences. PMID:32180547
Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 endoplasmic reticulum-plasma membrane contact site complexes in Arabidopsis. PMID:32179893
Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts. PMID:32170292
Neural networks for protein structure and function prediction and dynamic analysis. PMID:32166610
A Uniquely Complex Mitochondrial Proteome from Euglena gracilis. PMID:32159766
The extracellular thioredoxin Etrx3 is required for macrophage infection in Rhodococcus equi. PMID:32156317
Genome-Wide Analysis of the Lateral Organ Boundaries Domain Gene Family in Brassica Napus. PMID:32155746
Perspectives for Glyco-Engineering of Recombinant Biopharmaceuticals from Microalgae. PMID:32151094
TRPM7 activation potentiates SOCE in enamel cells but requires ORAI. PMID:32146159
Draft Genome Sequence of a New Zealand Isolate of Mycoplasma ovipneumoniae. PMID:32139576
Bacteria Boost Mammalian Host NAD Metabolism by Engaging the Deamidated Biosynthesis Pathway. PMID:32130883
Transcriptomic resources for evolutionary studies in flat periwinkles and related species. PMID:32127542
Recent advances in functional research in Giardia intestinalis. PMID:32122532
The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome. PMID:32122349
Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids. PMID:32122335
The structure, functional evolution, and evolutionary trajectories of the H+-PPase gene family in plants. PMID:32122295
Host Transcriptional Response of Sclerotinia sclerotiorum Induced by the Mycoparasite Coniothyrium minitans. PMID:32117180
RcLS2F - A Novel Fungal Class 1 KDAC Co-repressor Complex in Aspergillus nidulans. PMID:32117098
Corrigendum: Genotype-Phenotype Association Analysis Reveals New Pathogenic Factors for Osteogenesis Imperfecta Disease. PMID:32116662
Whole-Genome Sequencing of Lactobacillus helveticus D75 and D76 Confirms Safety and Probiotic Potential. PMID:32111071
Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study. PMID:32108239
Polymerization in the actin ATPase clan regulates hexokinase activity in yeast. PMID:32108112
Functions of Vertebrate Ferlins. PMID:32106631
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
Rhapsody: predicting the pathogenicity of human missense variants. PMID:32101277
Exploring Integrative Analysis Using the BioMedical Evidence Graph. PMID:32097025
Cyclic di-AMP, a second messenger of primary importance: tertiary structures and binding mechanisms. PMID:32095817
Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes. PMID:32093654
Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors. PMID:32092934
Genomewide analysis of the CIII peroxidase family in sweet orange (Citrus sinensis) and expression profiles induced by Xanthomonas citri subsp. citri and hormones. PMID:32089529
A New Family of Diverse Skin Peptides from the Microhylid Frog Genus Phrynomantis. PMID:32085597
Iron metabolic pathways in the processes of sponge plasticity. PMID:32084159
Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities. PMID:32075851
Current Trends in Diagnostics of Viral Infections of Unknown Etiology. PMID:32074965
Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution. PMID:32071806
Spectrum of EGFR aberrations and potential clinical implications: insights from integrative pan-cancer analysis. PMID:32067422
Phylogenomic analysis of novel Diaforarchaea is consistent with sulfite but not sulfate reduction in volcanic environments on early Earth. PMID:32066874
Wheat PP2C-a10 regulates seed germination and drought tolerance in transgenic Arabidopsis. PMID:32065246
"Candidatus Galacturonibacter soehngenii" Shows Acetogenic Catabolism of Galacturonic Acid but Lacks a Canonical Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase Complex. PMID:32063897
Translation and functional roles of circular RNAs in human cancer. PMID:32059672
The modular nature of protein evolution: domain rearrangement rates across eukaryotic life. PMID:32059645
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP). PMID:32055028
Probing Carbon Utilization of Cordyceps militaris by Sugar Transportome and Protein Structural Analysis. PMID:32050592
Identification of the molecular components of a putative Jasus edwardsii (Crustacea; Decapoda; Achelata) circadian signaling system. PMID:32048048
The Remarkable Dual-Level Diversity of Prokaryotic Flagellins. PMID:32047063
Physicochemical characterization of Pseudomonas stutzeri UFV5 and analysis of its transcriptome under heterotrophic nitrification/aerobic denitrification pathway induction condition. PMID:32042029
The Genome-Wide Analysis of RALF-Like Genes in Strawberry (Wild and Cultivated) and Five Other Plant Species (Rosaceae). PMID:32041308
Comprehensive Genomic Analysis and Expression Profiling of the C2H2 Zinc Finger Protein Family Under Abiotic Stresses in Cucumber (Cucumis sativus L.). PMID:32041281
Evolutionary Histories of Type III Polyketide Synthases in Fungi. PMID:32038517
The Genome Assembly and Annotation of the Southern Elephant Seal Mirounga leonina. PMID:32028680
ProtCID: a data resource for structural information on protein interactions. PMID:32024829
1RS arm of Secale cereanum 'Kriszta' confers resistance to stripe rust, improved yield components and high arabinoxylan content in wheat. PMID:32019962
A chromosome-scale reference genome for Giardia intestinalis WB. PMID:32019935
Genome-wide identification of BXL genes in Populus trichocarpa and their expression under different nitrogen treatments. PMID:32015953
Two-stage electro-mechanical coupling of a KV channel in voltage-dependent activation. PMID:32015334
Discovery of several thousand highly diverse circular DNA viruses. PMID:32014111
Draft Genome of a Blister Beetle Mylabris aulica. PMID:32010178
Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin. PMID:32004459
LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins. PMID:32003788
An integrated computational and experimental study to investigate Staphylococcus aureus metabolism. PMID:32001720
Genomic Sequencing of Phyllosticta citriasiana Provides Insight Into Its Conservation and Diversification With Two Closely Related Phyllosticta Species Associated With Citrus. PMID:31998266
hnRNPDL Phase Separation Is Regulated by Alternative Splicing and Disease-Causing Mutations Accelerate Its Aggregation. PMID:31995753
Genome-wide rare variant analysis for thousands of phenotypes in over 70,000 exomes from two cohorts. PMID:31992710
Structural evolution drives diversification of the large LRR-RLK gene family. PMID:31990988
Genome Sequence of the Euryhaline Javafish Medaka, Oryzias javanicus: A Small Aquarium Fish Model for Studies on Adaptation to Salinity. PMID:31988161
Identification of putative neuropeptidergic signaling systems in the spiny lobster, Panulirus argus. PMID:31980901
Biosynthesis of Nitrogenase Cofactors. PMID:31975585
The C. difficile toxin B membrane translocation machinery is an evolutionarily conserved protein delivery apparatus. PMID:31974369
Structure-function analyses of alkylhydroperoxidase D from Streptococcus pneumoniae reveal an unusual three-cysteine active site architecture. PMID:31974167
A protocol to automatically calculate homo-oligomeric protein structures through the integration of evolutionary constraints and NMR ambiguous contacts. PMID:31969972
Genome-Wide Investigation of Heat Shock Transcription Factor Family in Wheat (Triticum aestivum L.) and Possible Roles in Anther Development. PMID:31963482
Profile Comparer Extended: phylogeny of lytic polysaccharide monooxygenase families using profile hidden Markov model alignments. PMID:31956399
Fam151b, the mouse homologue of C.elegans menorin gene, is essential for retinal function. PMID:31949211
Annotated Genome Sequence of Aspergillus tanneri NIH1004. PMID:31948962
What do archaeal and eukaryotic histidine kinases sense? PMID:31942238
A protein-centric approach for exome variant aggregation enables sensitive association analysis with clinical outcomes. PMID:31930623
Transcriptome and Phytochemical Analyses Provide New Insights Into Long Non-Coding RNAs Modulating Characteristic Secondary Metabolites of Oolong Tea (Camellia sinensis) in Solar-Withering. PMID:31929782
In silico analysis of alternative splicing on drug-target gene interactions. PMID:31924844
Vanillin Production in Pseudomonas: Whole-Genome Sequencing of Pseudomonas sp. Strain 9.1 and Reannotation of Pseudomonas putida CalA as a Vanillin Reductase. PMID:31924622
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
Harvesting of Prebiotic Fructooligosaccharides by Nonbeneficial Human Gut Bacteria. PMID:31915220
UDSMProt: universal deep sequence models for protein classification. PMID:31913448
Whole genome sequencing of Borrelia miyamotoi isolate Izh-4: reference for a complex bacterial genome. PMID:31906865
Looking for the X Factor in Bacterial Pathogenesis: Association of orfX-p47 Gene Clusters with Toxin Genes in Clostridial and Non-Clostridial Bacterial Species. PMID:31906154
Conserved genomic neighborhood is a strong but no perfect indicator for a direct interaction of microbial gene products. PMID:31900122
Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses. PMID:31900112
Molecular mechanisms of vancomycin resistance. PMID:31899563
Structural characterization of aminoglycoside 4'-O-adenylyltransferase ANT(4')-IIb from Pseudomonas aeruginosa. PMID:31891426
Knockout of the S-acyltransferase Gene, PbPAT14, Confers the Dwarf Yellowing Phenotype in First Generation Pear by ABA Accumulation. PMID:31888281
Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement. PMID:31886770
Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation. PMID:31886458
Phosphatidylserine synthase regulates cellular homeostasis through distinct metabolic mechanisms. PMID:31869331
A novel de novo dominant mutation of NOTCH1 gene in an Iranian family with non-syndromic congenital heart disease. PMID:31867804
Comparative Pangenomics of the Mammalian Gut Commensal Bifidobacterium longum. PMID:31861401
Ecotin, a microbial inhibitor of serine proteases, blocks multiple complement dependent and independent microbicidal activities of human serum. PMID:31860690
Comparative analysis of ascorbate peroxidases (APXs) from selected plants with a special focus on Oryza sativa employing public databases. PMID:31856232
Whole Genome Re-sequencing Reveals Natural Variation and Adaptive Evolution of Phytophthora sojae. PMID:31849921
GenFam: A web application and database for gene family-based classification and functional enrichment analysis. PMID:31844835
Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria. PMID:31844663
ReVac: a reverse vaccinology computational pipeline for prioritization of prokaryotic protein vaccine candidates. PMID:31842745
Whole genome sequencing and novel candidate genes for CAKUT and altered nephrogenesis in the HSRA rat. PMID:31841396
Igh locus structure and evolution in Platyrrhines: new insights from a genomic perspective. PMID:31838542
The human DEPhOsphorylation Database DEPOD: 2019 update. PMID:31836896
Identification of Homeobox Genes Associated with Lignification and Their Expression Patterns in Bamboo Shoots. PMID:31835882
Thriving in Wetlands: Ecophysiology of the Spiral-Shaped Methanotroph Methylospira mobilis as Revealed by the Complete Genome Sequence. PMID:31835835
TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome. PMID:31831861
Identification of emerging viral genomes in transcriptomic datasets of alfalfa (Medicago sativa L.). PMID:31818304
Differential gene expression among three sex types reveals a MALE STERILITY 1 (CpMS1) for sex differentiation in papaya. PMID:31818257
The Chalcone Isomerase Family in Cotton: Whole-Genome Bioinformatic and Expression Analyses of the Gossypium barbadense L. Response to Fusarium Wilt Infection. PMID:31817162
Bioinformatics Analysis of the Lipoxygenase Gene Family in Radish (Raphanus sativus) and Functional Characterization in Response to Abiotic and Biotic Stresses. PMID:31816887
Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment. PMID:31811683
Phylogenomic Analyses of Members of the Widespread Marine Heterotrophic Genus Pseudovibrio Suggest Distinct Evolutionary Trajectories and a Novel Genus, Polycladidibacter gen. nov. PMID:31811036
Reactome and ORCID-fine-grained credit attribution for community curation. PMID:31802127
Epigenetic therapy of novel tumour suppressor ZAR1 and its cancer biomarker function. PMID:31801617
Type II-Metacaspases are involved in cell stress but not in cell death in the unicellular green alga Dunaliella tertiolecta. PMID:31799323
A global analysis of function and conservation of catalytic residues in enzymes. PMID:31796628
Detecting, Categorizing, and Correcting Coverage Anomalies of RNA-Seq Quantification. PMID:31786209
Repurposing the GNAT Fold in the Initiation of Polyketide Biosynthesis. PMID:31785925
CDD/SPARCLE: the conserved domain database in 2020. PMID:31777944
Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil. PMID:31772013
Transcriptional characterization and response to defense elicitors of mevalonate pathway genes in cotton (Gossypium arboreum L.). PMID:31768304
Myofibril diameter is set by a finely tuned mechanism of protein oligomerization in Drosophila. PMID:31746737
Functional Multigenomic Screening of Human-Associated Bacteria for NF-κB-Inducing Bioactive Effectors. PMID:31744921
Self-identity barcodes encoded by six expansive polymorphic toxin families discriminate kin in myxobacteria. PMID:31744876
Improved linking of motifs to their TFs using domain information. PMID:31742324
Structural Conservation and Diversity of PilZ-Related Domains. PMID:31740493
Comprehensive Analysis of the Chitinase Gene Family in Cucumber (Cucumis sativus L.): From Gene Identification and Evolution to Expression in Response to Fusarium oxysporum. PMID:31731414
DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples. PMID:31727957
The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures. PMID:31724711
In silico characterization of hypothetical proteins from Orientia tsutsugamushi str. Karp uncovers virulence genes. PMID:31720472
DisProt: intrinsic protein disorder annotation in 2020. PMID:31713636
New insights on Pseudoalteromonas haloplanktis TAC125 genome organization and benchmarks of genome assembly applications using next and third generation sequencing technologies. PMID:31712730
The Dundee Resource for Sequence Analysis and Structure Prediction. PMID:31710725
The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences. PMID:31701143
Transcriptional analysis of amino acid, metal ion, vitamin and carbohydrate uptake in butanol-producing Clostridium beijerinckii NRRL B-598. PMID:31697692
MGnify: the microbiome analysis resource in 2020. PMID:31696235
PDBe: improved findability of macromolecular structure data in the PDB. PMID:31691821
Cause and Effectors: Whole-Genome Comparisons Reveal Shared but Rapidly Evolving Effector Sets among Host-Specific Plant-Castrating Fungi. PMID:31690676
Genome-Wide Analysis of Known and Potential Tetraspanins in Entamoeba histolytica. PMID:31684194
Biochemical Characterization of a Novel α/β-Hydrolase/FSH from the White Shrimp Litopenaeus vannamei. PMID:31683580
Genotype-Phenotype Association Analysis Reveals New Pathogenic Factors for Osteogenesis Imperfecta Disease. PMID:31680973
Early Diverging Fungus Mucor circinelloides Lacks Centromeric Histone CENP-A and Displays a Mosaic of Point and Regional Centromeres. PMID:31679929
Cyanuric Acid Biodegradation via Biuret: Physiology, Taxonomy, and Geospatial Distribution. PMID:31676480
The long non-coding RNA lncRNA973 is involved in cotton response to salt stress. PMID:31666019
BacFITBase: a database to assess the relevance of bacterial genes during host infection. PMID:31665505
ChlamDB: a comparative genomics database of the phylum Chlamydiae and other members of the Planctomycetes-Verrucomicrobiae-Chlamydiae superphylum. PMID:31665454
MaGenDB: a functional genomics hub for Malvaceae plants. PMID:31665439
Spider Venom: Components, Modes of Action, and Novel Strategies in Transcriptomic and Proteomic Analyses. PMID:31652611
Terpene synthases in disguise: enzymology, structure, and opportunities of non-canonical terpene synthases. PMID:31650156
Prediction of protein architectures involved in the signaling-pathway initiating sporulation in Firmicutes. PMID:31647017
SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm. PMID:31642484
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
Implications of Gene Inheritance Patterns on the Heterosis of Abdominal Fat Deposition in Chickens. PMID:31635393
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
CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers. PMID:31624845
Archaeal nitrification is constrained by copper complexation with organic matter in municipal wastewater treatment plants. PMID:31624348
Characterization of Cronartium ribicola dsRNAs reveals novel members of the family Totiviridae and viral association with fungal virulence. PMID:31623644
PADS Arsenal: a database of prokaryotic defense systems related genes. PMID:31620779
Structural and biochemical characterisation of a novel alginate lyase from Paenibacillus sp. str. FPU-7. PMID:31619701
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. PMID:31614509
PhaSePro: the database of proteins driving liquid-liquid phase separation. PMID:31612960
Identification of a candidate gene underlying qKRN5b for kernel row number in Zea mays L. PMID:31612262
Systematic Analysis and Functional Validation of Citrus XTH Genes Reveal the Role of Csxth04 in Citrus Bacterial Canker Resistance and Tolerance. PMID:31611887
Density-dependent oxylipin production in natural diatom communities: possible implications for plankton dynamics. PMID:31611654
DALI and the persistence of protein shape. PMID:31606894
Structure and functional implications of WYL domain-containing bacterial DNA damage response regulator PafBC. PMID:31604936
Crystal structure of ErmE - 23S rRNA methyltransferase in macrolide resistance. PMID:31601908
Plasmodium kinesin-8X associates with mitotic spindles and is essential for oocyst development during parasite proliferation and transmission. PMID:31600347
EuRBPDB: a comprehensive resource for annotation, functional and oncological investigation of eukaryotic RNA binding proteins (RBPs). PMID:31598693
ProCarbDB: a database of carbohydrate-binding proteins. PMID:31598690
Phytovirome Analysis of Wild Plant Populations: Comparison of Double-Stranded RNA and Virion-Associated Nucleic Acid Metagenomic Approaches. PMID:31597769
A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana. PMID:31585525
Genus for biomolecules. PMID:31584078
MYB transcription factors in alfalfa (Medicago sativa): genome-wide identification and expression analysis under abiotic stresses. PMID:31576246
Genome Mining Coupled with OSMAC-Based Cultivation Reveal Differential Production of Surugamide A by the Marine Sponge Isolate Streptomyces sp. SM17 When Compared to Its Terrestrial Relative S. albidoflavus J1074. PMID:31561472
Whole-Genome Sequencing Redefines Shewanella Taxonomy. PMID:31555221
Genetic Modification of mfsT Gene Stimulating the Putative Penicillin Production in Monascus ruber M7 and Exhibiting the Sensitivity towards Precursor Amino Acids of Penicillin Pathway. PMID:31554331
Identification of putative amine receptor complement in the eyestalk of the crayfish, Procambarus clarkii. PMID:31549228
Genome-Wide Analysis of Cotton Auxin Early Response Gene Families and Their Roles in Somatic Embryogenesis. PMID:31547015
Characterization of LysBC17, a Lytic Endopeptidase from Bacillus cereus. PMID:31546935
Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs. PMID:31539080
Identification of the Coding-Complete Genome of Cycas Necrotic Stunt Virus in Transcriptomic Data Sets of Alfalfa (Medicago sativa). PMID:31537674
Proteomics and bioinformatics analysis reveal potential roles of cadmium-binding proteins in cadmium tolerance and accumulation of Enterobacter cloacae. PMID:31534833
Temporal changes in transcriptome profile provide insights of White Spot Syndrome Virus infection in Litopenaeus vannamei. PMID:31534145
Characterization of a Dehydratase and Methyltransferase in the Biosynthesis of Ribosomally Synthesized and Post-translationally Modified Peptides in Lachnospiraceae. PMID:31532570
NeuRiPP: Neural network identification of RiPP precursor peptides. PMID:31527713
Predicting Sequence Features, Function, and Structure of Proteins Using MESSA. PMID:31524991
Comparative study of excretory-secretory proteins released by Schistosoma mansoni-resistant, susceptible and naïve Biomphalaria glabrata. PMID:31521183
HH-suite3 for fast remote homology detection and deep protein annotation. PMID:31521110
SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences. PMID:31510679
Bioinformatics Identification of Anti-CRISPR Loci by Using Homology, Guilt-by-Association, and CRISPR Self-Targeting Spacer Approaches. PMID:31506266
Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning. PMID:31504150
The structure of bactofilin filaments reveals their mode of membrane binding and lack of polarity. PMID:31501539
Construction of pseudomolecule sequences of Brassica rapa ssp. pekinensis inbred line CT001 and analysis of spontaneous mutations derived via sexual propagation. PMID:31498838
The ubiquitin ligase adaptor SPOP in cancer. PMID:31495053
Hybrid Two-Component Sensors for Identification of Bacterial Chemoreceptor Function. PMID:31492670
Genome Sequence of Metarhizium rileyi, a Microbial Control Agent for Lepidoptera. PMID:31488537
Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints. PMID:31484923
An improved auxin-inducible degron system preserves native protein levels and enables rapid and specific protein depletion. PMID:31467088
Disruption of the OLE ribonucleoprotein complex causes magnesium toxicity in Bacillus halodurans. PMID:31461569
Novel Inhibitory Function of the Rhizomucor miehei Lipase Propeptide and Three-Dimensional Structures of Its Complexes with the Enzyme. PMID:31460089
Screening for New Surface Anchoring Domains for Lactococcus lactis. PMID:31456787
The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs. PMID:31454312
Niche differentiation among annually recurrent coastal Marine Group II Euryarchaeota. PMID:31447484
Genome-Wide Identification and Characterization of Long Noncoding RNAs of Brown to White Adipose Tissue Transformation in Goats. PMID:31443273
Protein Abundance Biases the Amino Acid Composition of Disordered Regions to Minimize Non-functional Interactions. PMID:31442477
Identification of new components of the RipC-FtsEX cell separation pathway of Corynebacterineae. PMID:31437147
Crystal structures of AztD provide mechanistic insights into direct zinc transfer between proteins. PMID:31428696
Identification and functional analysis of LecRLK genes in Taxodium 'Zhongshanshan'. PMID:31423364
Characteristics and Functions of the Yip1 Domain Family (YIPF), Multi-Span Transmembrane Proteins Mainly Localized to the Golgi Apparatus. PMID:31417902
Transcriptomic Analysis of Marine Gastropod Hemifusus tuba Provides Novel Insights into Conotoxin Genes. PMID:31405144
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
MpsAB is important for Staphylococcus aureus virulence and growth at atmospheric CO2 levels. PMID:31399577
Spatially conserved motifs in complement control protein domains determine functionality in regulators of complement activation-family proteins. PMID:31396570
An RNAi Screen for Genes Required for Growth of Drosophila Wing Tissue. PMID:31387856
Applications and Considerations of GToTree: A User-Friendly Workflow for Phylogenomics. PMID:31384124
The Kaposi's Sarcoma-Associated Herpesvirus Protein ORF42 Is Required for Efficient Virion Production and Expression of Viral Proteins. PMID:31382485
Genome-Wide Analysis of the WOX Gene Family and Function Exploration of GmWOX18 in Soybean. PMID:31373320
An engineered mutant of a host phospholipid synthesis gene inhibits viral replication without compromising host fitness. PMID:31362985
Quantitative Proteomic Analyses of a Pathogenic Strain and Its Highly Passaged Attenuated Strain of Mycoplasma hyopneumoniae. PMID:31355261
Genomic Identification and Expression Analysis of the Cathelicidin Gene Family of the Forest Musk Deer. PMID:31344924
Can We Still Trust Docking Results? An Extension of the Applicability of DockBench on PDBbind Database. PMID:31330841
Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility. PMID:31323028
Formin-2 drives polymerisation of actin filaments enabling segregation of apicoplasts and cytokinesis in Plasmodium falciparum. PMID:31322501
FunFam protein families improve residue level molecular function prediction. PMID:31319797
A novel CHD7 variant disrupting acceptor splice site in a patient with mild features of CHARGE syndrome: a case report. PMID:31315586
Genome-Wide Identification and Characterization of Xyloglucan Endotransglycosylase/Hydrolase in Ananas comosus during Development. PMID:31315260
Clinical Persistence of Chlamydia trachomatis Sexually Transmitted Strains Involves Novel Mutations in the Functional αββα Tetramer of the Tryptophan Synthase Operon. PMID:31311884
CASP13 target classification into tertiary structure prediction categories. PMID:31294862
Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C. PMID:31289832
Mycobacterium tuberculosis Rv2700 Contributes to Cell Envelope Integrity and Virulence. PMID:31285241
Conceptual Evolution of Cell Signaling. PMID:31277491
Proteome-wide signatures of function in highly diverged intrinsically disordered regions. PMID:31264965
Identification of putative amine biosynthetic enzymes in the nervous system of the crab, Cancer borealis. PMID:31263964
Genome-wide Transcript Structure Resolution Reveals Abundant Alternate Isoform Usage from Murine Gammaherpesvirus 68. PMID:31242428
Pollination Type Recognition from a Distance by the Ovary Is Revealed Through a Global Transcriptomic Analysis. PMID:31238522
The Pseudomonas syringae pv. tomato DC3000 PSPTO_0820 multidrug transporter is involved in resistance to plant antimicrobials and bacterial survival during tomato plant infection. PMID:31237890
Genome-Wide Identification and Expression Analyses of the Chitinases under Cold and Osmotic stress in Ammopiptanthus nanus. PMID:31234426
Trimerization of dopamine transporter triggered by AIM-100 binding: Molecular mechanism and effect of mutations. PMID:31228486
Phylogenomics Provides New Insights into Gains and Losses of Selenoproteins among Archaeplastida. PMID:31226841
What functional genomics has taught us about transcriptional regulation in malaria parasites. PMID:31220867
Sequencing, genome analysis and prevalence of a cytorhabdovirus discovered in Carica papaya. PMID:31220099
Gene Information eXtension (GIX): effortless retrieval of gene product information on any website. PMID:31217594
Insights into Klebsiella pneumoniae type VI secretion system transcriptional regulation. PMID:31215404
Considering B7-CD28 as a family through sequence and structure. PMID:31208204
VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations. PMID:31192369
Metal-responsive RNA polymerase extracytoplasmic function (ECF) sigma factors. PMID:31187912
First crystal structure of an endo-levanase - the BT1760 from a human gut commensal Bacteroides thetaiotaomicron. PMID:31186460
Characterization of a GDP-Fucose Transporter and a Fucosyltransferase Involved in the Fucosylation of Glycoproteins in the Diatom Phaeodactylum tricornutum. PMID:31164895
Bacteria-Killing Type IV Secretion Systems. PMID:31164878
Comprehensive transcriptome analysis reveals genes potentially involved in isoflavone biosynthesis in Pueraria thomsonii Benth. PMID:31163077
Deorphanizing NUDIX hydrolases from Trypanosoma: tantalizing links with metabolic regulation and stress tolerance. PMID:31160481
Proteomic and Metabolomic Characteristics of Extremophilic Fungi Under Simulated Mars Conditions. PMID:31156574
In Silico Genome-Wide Analysis of Respiratory Burst Oxidase Homolog (RBOH) Family Genes in Five Fruit-Producing Trees, and Potential Functional Analysis on Lignification of Stone Cells in Chinese White Pear. PMID:31146469
Dissecting the genetic control of root and leaf tissue-specific anthocyanin pigmentation in carrot (Daucus carota L.). PMID:31144001
Transcriptome Response of Female Culicoides sonorensis Biting Midges (Diptera: Ceratopogonidae) to Early Infection with Epizootic Hemorrhagic Disease Virus (EHDV-2). PMID:31137627
Primary transcriptome and translatome analysis determines transcriptional and translational regulatory elements encoded in the Streptomyces clavuligerus genome. PMID:31131406
Fine Mapping of the Wheat Leaf Rust Resistance Gene Lr42. PMID:31108903
Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning. PMID:31106379
Life at Home and on the Roam: Genomic Adaptions Reflect the Dual Lifestyle of an Intracellular, Facultative Symbiont. PMID:31086829
GROWTH POLE RING protein forms a 200-nm-diameter ring structure essential for polar growth and rod shape in Agrobacterium tumefaciens. PMID:31085632
De novo assembly of the Indian blue peacock (Pavo cristatus) genome using Oxford Nanopore technology and Illumina sequencing. PMID:31077316
DOGMA: a web server for proteome and transcriptome quality assessment. PMID:31076763
modEnrichr: a suite of gene set enrichment analysis tools for model organisms. PMID:31069376
Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2. PMID:31060509
A highly expressed intestinal cysteine protease of Ancylostoma ceylanicum protects vaccinated hamsters from hookworm infection. PMID:31009474
A Comprehensive Drosophila melanogaster Transcription Factor Interactome. PMID:30995488
Genome-Wide Analysis of Glycoside Hydrolase Family 1 β-glucosidase Genes in Brassica rapa and Their Potential Role in Pollen Development. PMID:30987159
Genome Organization of Canada Goose Coronavirus, A Novel Species Identified in a Mass Die-off of Canada Geese. PMID:30976080
Two forms of phosphomannomutase in gammaproteobacteria: The overlooked membrane-bound form of AlgC is required for twitching motility of Lysobacter enzymogenes. PMID:30938049
Extracytoplasmic Function σ Factors Can Be Implemented as Robust Heterologous Genetic Switches in Bacillus subtilis. PMID:30897511
Infection Strategies Deployed by Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer as a Function of Tomato Fruit Ripening Stage. PMID:30881367
GToTree: a user-friendly workflow for phylogenomics. PMID:30865266
Genomic Characteristics of Desulfonema ishimotonii Tokyo 01T Implying Horizontal Gene Transfer Among Phylogenetically Dispersed Filamentous Gliding Bacteria. PMID:30837965
Structural characterization of the Imm52 family protein TsiT in Pseudomonas aeruginosa. PMID:30834616
The anti-bacterial iron-restriction defence mechanisms of egg white; the potential role of three lipocalin-like proteins in resistance against Salmonella. PMID:30810876
Transcriptome, proteome and draft genome of Euglena gracilis. PMID:30732613
A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways. PMID:30698701
Novel pseudo-aspartic peptidase from the midgut of the tick Rhipicephalus microplus. PMID:30679545
Global Analysis of Genes Essential for Francisella tularensis Schu S4 Growth In Vitro and for Fitness during Competitive Infection of Fischer 344 Rats. PMID:30642993
Genome-Wide Characterization and Identification of Trihelix Transcription Factor and Expression Profiling in Response to Abiotic Stresses in Rice (Oryza sativa L.). PMID:30634597
The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection. PMID:30626175
Identification of Viral Taxon-Specific Genes (VTSG): Application to Caliciviridae. PMID:30602084
The European Bioinformatics Institute in 2018: tools, infrastructure and training. PMID:30445657 -
The Pfam protein families database
PubMed citations: 1165.
1165 articles citing: The Pfam protein families database
LARGE-SCALE MULTIPLE INFERENCE OF COLLECTIVE DEPENDENCE WITH APPLICATIONS TO PROTEIN FUNCTION. PMID:35910493
Effects of turning over intensity on fatty acid metabolites in postharvest leaves of Tieguanyin oolong tea (Camellia sinensis). PMID:35722255
Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment. PMID:35668508
Polyploid giant cancer cells are dependent on cholesterol for progeny formation through amitotic division. PMID:35624221
Identification and Characterization of the MIKC-Type MADS-Box Gene Family in Brassica napus and Its Role in Floral Transition. PMID:35457106
DUF1005 Family Identification, Evolution Analysis in Plants, and Primary Root Elongation Regulation of CiDUF1005 From Caragana intermedia. PMID:35422842
Systematic identification and characterization of long noncoding RNAs (lncRNAs) during Aedes albopictus development. PMID:35417446
PpePL1 and PpePL15 Are the Core Members of the Pectate Lyase Gene Family Involved in Peach Fruit Ripening and Softening. PMID:35401624
Genome-Wide Identification and Expression Profiling of Germin-Like Proteins Reveal Their Role in Regulating Abiotic Stress Response in Potato. PMID:35251067
Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean. PMID:35236926
Haplotype-Resolved Genome Analyses Reveal Genetically Distinct Nuclei within a Commercial Cultivar of Lentinula edodes. PMID:35205921
Hydroxyl Radical Overproduction in the Envelope: an Achilles' Heel in Peptidoglycan Synthesis. PMID:35170991
High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function. PMID:35112110
Differential Expression of lncRNAs and miRNAs Between Self-Rooting Juvenile and Donor Clones Unveils Novel Insight Into the Molecular Regulation of Rubber Biosynthesis in Hevea brasiliensis. PMID:35069613
Transcriptomic profiling suggests candidate molecular responses to waterlogging in cassava. PMID:35061680
Molecular Characterization and Functional Localization of a Novel SUMOylation Gene in Oryza sativa. PMID:35053052
High Molecular Weight Kininogen: A Review of the Structural Literature. PMID:34948166
Genome-Wide Identification, Characterization, and Expression Analysis of DDE_Tnp_4 Family Genes in Eriocheir sinensis. PMID:34943642
Artemisinin Binds and Inhibits the Activity of Plasmodium falciparum Ddi1, a Retroviral Aspartyl Protease. PMID:34832620
ElyC and Cyclic Enterobacterial Common Antigen Regulate Synthesis of Phosphoglyceride-Linked Enterobacterial Common Antigen. PMID:34809459
A Novel Spo11 Homologue Functions as a Positive Regulator in Cyst Differentiation in Giardia lamblia. PMID:34769330
Genome-Wide Identification and Expression Analysis of AP2/ERF Transcription Factor Related to Drought Stress in Cultivated Peanut (Arachis hypogaea L.). PMID:34721538
De novo transcriptome analysis provides insights into the salt tolerance of Podocarpus macrophyllus under salinity stress. PMID:34696735
Comparative transcriptome provides insights into the selection adaptation between wild and farmed foxes. PMID:34646484
Identification and Characterization of 24-Dehydrocholesterol Reductase (DHCR24) in the Two-Spotted Cricket, Gryllus bimaculatus. PMID:34564222
Integrated analysis of lncRNA and mRNA in liver of Megalobrama amblycephala post Aeromonas hydrophila infection. PMID:34511071
Metabolomics integrated with transcriptomics reveals the distribution of iridoid and crocin metabolic flux in Gardenia jasminoides Ellis. PMID:34506519
The DUF221 domain-containing (DDP) genes identification and expression analysis in tomato under abiotic and phytohormone stress. PMID:34379048
IDOPS, a Profile HMM-Based Tool to Detect Pesticidal Sequences and Compare Their Genetic Context. PMID:34276598
EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains. PMID:34196123
Genomic Island Prediction via Chi-Square Test and Random Forest Algorithm. PMID:34122622
Evolution of networks of protein domain organization. PMID:34103558
Genome-Wide Analysis of the DUF4228 Family in Soybean and Functional Identification of GmDUF4228 -70 in Response to Drought and Salt Stresses. PMID:34079564
Characterization of the pectin methylesterase inhibitor gene family in Rosaceae and role of PbrPMEI23/39/41 in methylesterified pectin distribution in pear pollen tube. PMID:33961146
Whole-genome resequencing of Osmanthus fragrans provides insights into flower color evolution. PMID:33931610
Genome-wide Analysis of the WRKY Gene Family and its Response to Abiotic Stress in Buckwheat (Fagopyrum Tataricum). PMID:33817140
Additional description and genome analyses of Caenorhabditis auriculariae representing the basal lineage of genus Caenorhabditis. PMID:33762598
High genomic diversity of novel phages infecting the plant pathogen Ralstonia solanacearum, isolated in Mauritius and Reunion islands. PMID:33686106
Transcriptional profiling of two contrasting genotypes uncovers molecular mechanisms underlying salt tolerance in alfalfa. PMID:33664362
The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids. PMID:33642574
Construction of a reference transcriptome for the analysis of male sterility in sugi (Cryptomeria japonica D. Don) focusing on MALE STERILITY 1 (MS1). PMID:33630910
Identifying Poly(ADP-ribose)-Binding Proteins with Photoaffinity-Based Proteomics. PMID:33596067
Histoplasma capsulatum Glycans From Distinct Genotypes Share Structural and Serological Similarities to Cryptococcus neoformans Glucuronoxylomannan. PMID:33585262
A Novel Multiprotein Bridging Factor 1-Like Protein Induces Cyst Wall Protein Gene Expression and Cyst Differentiation in Giardia lamblia. PMID:33573049
Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens. PMID:33500331
The identification of novel immunogenic antigens as potential Shigella vaccine components. PMID:33451348
An automated protocol for modelling peptide substrates to proteases. PMID:33375946
Quick and efficient approach to develop genomic resources in orphan species: Application in Lavandula angustifolia. PMID:33306734
Identification of CCCH Zinc Finger Proteins Family in Moso Bamboo (Phyllostachys edulis), and PeC3H74 Confers Drought Tolerance to Transgenic Plants. PMID:33240298
The expanding world of plant J-domain proteins. PMID:33223602
HpeNet: Co-expression Network Database for de novo Transcriptome Assembly of Paeonia lactiflora Pall. PMID:33193666
Plasmodium DEH is ER-localized and crucial for oocyst mitotic division during malaria transmission. PMID:33106323
Genome-Wide Identification of the Gossypium hirsutum NHX Genes Reveals that the Endosomal-Type GhNHX4A is Critical for the Salt Tolerance of Cotton. PMID:33081060
COVID-19 and iron dysregulation: distant sequence similarity between hepcidin and the novel coronavirus spike glycoprotein. PMID:33066821
Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.). PMID:33024641
Genome-Wide Identification of Barley ABC Genes and Their Expression in Response to Abiotic Stress Treatment. PMID:32998428
Transcriptome and Flavonoids Metabolomic Analysis Identifies Regulatory Networks and Hub Genes in Black and White Fruits of Lycium ruthenicum Murray. PMID:32922426
Genome-wide identification of lysin motif containing protein family genes in eight rosaceae species, and expression analysis in response to pathogenic fungus Botryosphaeria dothidea in Chinese white pear. PMID:32894061
Computational identification of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes. PMID:32620079
Long non-coding RNAs in the alkaline stress response in sugar beet (Beta vulgaris L.). PMID:32434543
The draft genome sequence of an upland wild rice species, Oryza granulata. PMID:32350267
2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome. PMID:32349677
LncRNA regulates tomato fruit cracking by coordinating gene expression via a hormone-redox-cell wall network. PMID:32293294
Functional Divergence of Microtubule-Associated TPX2 Family Members in Arabidopsis thaliana. PMID:32235723
Gill transcriptomes reveal expression changes of genes related with immune and ion transport under salinity stress in silvery pomfret (Pampus argenteus). PMID:32162151
Comparative Genomics of Actinobacillus pleuropneumoniae Serotype 8 Reveals the Importance of Prophages in the Genetic Variability of the Species. PMID:32149072
Identification of a molecular marker associated with lignotuber in Eucalyptus ssp. PMID:32107409
Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column. PMID:32060418
Genome-Wide Identification, Evolution and Expression of the Complete Set of Cytoplasmic Ribosomal Protein Genes in Nile Tilapia. PMID:32059409
DNA topoisomerase IIIβ promotes cyst generation by inducing cyst wall protein gene expression in Giardia lamblia. PMID:32019477
Genome and population sequencing of a chromosome-level genome assembly of the Chinese tapertail anchovy (Coilia nasus) provides novel insights into migratory adaptation. PMID:31895412
Structural and functional characterization of Tomato SUMO1 gene. PMID:31889857
Identifying protein-protein interface via a novel multi-scale local sequence and structural representation. PMID:31874604
Genome-Wide Characterization and Gene Expression Analyses of GATA Transcription Factors in Moso Bamboo (Phyllostachys edulis). PMID:31861396
Localization and enzyme kinetics of aminopeptidase N3 from Toxoplasma gondii. PMID:31836922
Transcriptomic Profile and Sexual Reproduction-Relevant Genes of Alexandrium minutum in Response to Nutritional Deficiency. PMID:31803162
De novo transcriptome analysis of stressed blood clam (Anadara broughtonii) and identification of genes associated with hemoglobin. PMID:31797313
Proteomics and bioinformatics analysis reveal potential roles of cadmium-binding proteins in cadmium tolerance and accumulation of Enterobacter cloacae. PMID:31534833
Chicken Meat-Associated Enterococci: Influence of Agricultural Antibiotic Use and Connection to the Clinic. PMID:31471308
Combining Mutations That Inhibit Two Distinct Steps of the ATP Hydrolysis Cycle Restores Wild-Type Function in the Lipopolysaccharide Transporter and Shows that ATP Binding Triggers Transport. PMID:31431556
Flavonoid Biosynthesis Is Likely More Susceptible to Elevation and Tree Age Than Other Branch Pathways Involved in Phenylpropanoid Biosynthesis in Ginkgo Leaves. PMID:31417595
Characteristics and Expression Pattern of MYC Genes in Triticum aestivum, Oryza sativa, and Brachypodium distachyon. PMID:31398900
Hybrid sequencing of the Gynostemma pentaphyllum transcriptome provides new insights into gypenoside biosynthesis. PMID:31382891
Shared Pathogenomic Patterns Characterize a New Phylotype, Revealing Transition toward Host-Adaptation Long before Speciation of Mycobacterium tuberculosis. PMID:31368488
An interplay of structure and intrinsic disorder in the functionality of peptidylarginine deiminases, a family of key autoimmunity-related enzymes. PMID:31342121
Molecular identification and expression of sesquiterpene pathway genes responsible for patchoulol biosynthesis and regulation in Pogostemon cablin. PMID:31267260
Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp. PMID:31226932
Isolation, cultivation, and genome analysis of proteorhodopsin-containing SAR116-clade strain Candidatus Puniceispirillum marinum IMCC1322. PMID:31201724
The Class III Peroxidase (POD) Gene Family in Cassava: Identification, Phylogeny, Duplication, and Expression. PMID:31163686
Transcriptomic analysis provides insight into the mechanism of salinity adjustment in swimming crab Portunus trituberculatus. PMID:31127502
Iso-Seq analysis of the Taxus cuspidata transcriptome reveals the complexity of Taxol biosynthesis. PMID:31113367
The Parallel Molecular Adaptations to the Antarctic Cold Environment in Two Psychrophilic Green Algae. PMID:31106822
Identification and comparative analysis of the CIPK gene family and characterization of the cold stress response in the woody plant Prunus mume. PMID:31106064
Geometric description of self-interaction potential in symmetric protein complexes. PMID:31101822
Superantigen SpeA attenuates the biofilm forming capacity of Streptococcus pyogenes. PMID:31054134
Transcriptome Profiles of Alternaria oxytropis Provides Insights into Swainsonine Biosynthesis. PMID:30988322
Impact of antibiotic treatment and host innate immune pressure on enterococcal adaptation in the human bloodstream. PMID:30971455
Network-based characterization of drug-protein interaction signatures with a space-efficient approach. PMID:30953486
Structural characterization of plasmodial aminopeptidase: a combined molecular docking and QSAR-based in silico approaches. PMID:30730017
Building Bridges Between Structural and Network-Based Systems Biology. PMID:30656572
LncRNA expression profile and ceRNA analysis in tomato during flowering. PMID:30653557
A benchmark study of sequence alignment methods for protein clustering. PMID:30598070
The crystal structure of Mycobacterium tuberculosis high-temperature requirement A protein reveals an autoregulatory mechanism. PMID:30511675
SynerClust: a highly scalable, synteny-aware orthologue clustering tool. PMID:30418868
Draft genome sequence of Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321, an endophyte microorganism from Vitis vinifera with biocontrol potential. PMID:30410642
Phytophthora methylomes are modulated by 6mA methyltransferases and associated with adaptive genome regions. PMID:30382931
Dissecting the functional domains of the Arabidopsis thaliana nonhost resistance 2B (AtNHR2B) protein. PMID:30325257
TMC1 Forms the Pore of Mechanosensory Transduction Channels in Vertebrate Inner Ear Hair Cells. PMID:30138589
Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake. PMID:30108167
Genome Wide Identification of Novel Long Non-coding RNAs and Their Potential Associations With Milk Proteins in Chinese Holstein Cows. PMID:30105049
The Chaperone Activities of DsbG and Spy Restore Peptidoglycan Biosynthesis in the elyC Mutant by Preventing Envelope Protein Aggregation. PMID:30012727
Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel. PMID:29971217
Transcriptome analysis of the typical freshwater rhodophytes Sheathia arcuata grown under different light intensities. PMID:29813098
Assessment of an Organ-Specific de Novo Transcriptome of the Nematode Trap-Crop, Solanum sisymbriifolium. PMID:29769290
A Statistical Approach to Correcting Cross-Annotations in a Metagenomic Functional Profile Generated by Short Reads. PMID:29710879
Structural Basis for the Initiation of Glycosaminoglycan Biosynthesis by Human Xylosyltransferase 1. PMID:29681470
Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome. PMID:29621340
Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes. PMID:29597290
Prediction of Disordered Regions and Their Roles in the Anti-Pathogenic and Immunomodulatory Functions of Butyrophilins. PMID:29401697
The Glaciozyma antarctica genome reveals an array of systems that provide sustained responses towards temperature variations in a persistently cold habitat. PMID:29385175
First insights into a type II toxin-antitoxin system from the clinical isolate Mycobacterium sp. MHSD3, similar to epsilon/zeta systems. PMID:29236773
Genomic features of "Candidatus Venteria ishoeyi", a new sulfur-oxidizing macrobacterium from the Humboldt Sulfuretum off Chile. PMID:29236755
Systematic CRISPR-Cas9-Mediated Modifications of Plasmodium yoelii ApiAP2 Genes Reveal Functional Insights into Parasite Development. PMID:29233900
KiPho: malaria parasite kinome and phosphatome portal. PMID:29220464
Ultra-low input transcriptomics reveal the spore functional content and phylogenetic affiliations of poorly studied arbuscular mycorrhizal fungi. PMID:29211832
Computational design of fully overlapping coding schemes for protein pairs and triplets. PMID:29158504
Identification of the PAK4 interactome reveals PAK4 phosphorylation of N-WASP and promotion of Arp2/3-dependent actin polymerization. PMID:29100370
MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle. PMID:29069412
Insights into Microalga and Bacteria Interactions of Selected Phycosphere Biofilms Using Metagenomic, Transcriptomic, and Proteomic Approaches. PMID:29067007
The chromosomal organization of horizontal gene transfer in bacteria. PMID:29018197
De Novo Assembly and Analysis of Tartary Buckwheat (Fagopyrum tataricum Garetn.) Transcriptome Discloses Key Regulators Involved in Salt-Stress Response. PMID:28972562
Interaction of Recombinant Gallus gallus SEPT5 and Brain Proteins of H5N1-Avian Influenza Virus-Infected Chickens. PMID:28895884
Comparative transcriptome analysis and identification of candidate effectors in two related rust species (Gymnosporangium yamadae and Gymnosporangium asiaticum). PMID:28830353
Coronafacoyl Phytotoxin Biosynthesis and Evolution in the Common Scab Pathogen Streptomyces scabiei. PMID:28754703
ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer. PMID:28549153
Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach. PMID:28545131
Comparative transcriptome analysis of Rimicaris sp. reveals novel molecular features associated with survival in deep-sea hydrothermal vent. PMID:28515421
Network and role analysis of autophagy in Phytophthora sojae. PMID:28500315
Responses of the Housefly, Musca domestica, to the Hytrosavirus Replication: Impacts on Host's Vitellogenesis and Immunity. PMID:28424677
Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species. PMID:28413161
In Entamoeba histolytica, a BspA family protein is required for chemotaxis toward tumour necrosis factor. PMID:28357299
Bacterial virulence phenotypes of Escherichia coli and host susceptibility determine risk for urinary tract infections. PMID:28330863
Transcriptomes of three species of Tipuloidea (Diptera, Tipulomorpha) and implications for phylogeny of Tipulomorpha. PMID:28264066
The Cytosolic Oligosaccharide-Degrading Proteome of Butyrivibrio Proteoclasticus. PMID:28248275
Intrinsic disorder in biomarkers of insulin resistance, hypoadiponectinemia, and endothelial dysfunction among the type 2 diabetic patients. PMID:28232897
Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression. PMID:28170390
Genome-Wide analysis of the AAAP gene family in moso bamboo (Phyllostachys edulis). PMID:28143411
Aberrant coordination geometries discovered in the most abundant metalloproteins. PMID:28142195
Pharmacological profile of the aerial parts of Rubus ulmifolius Schott. PMID:28103863
Genome Sequence of Christensenella minuta DSM 22607T. PMID:28082495
Evolution of protein N-glycosylation process in Golgi apparatus which shapes diversity of protein N-glycan structures in plants, animals and fungi. PMID:28074929
MTGIpick allows robust identification of genomic islands from a single genome. PMID:28025178
OsdR of Streptomyces coelicolor and the Dormancy Regulator DevR of Mycobacterium tuberculosis Control Overlapping Regulons. PMID:27822533
Cryptophyte farming by symbiotic ciliate host detected in situ. PMID:27791006
Metagenomic Insights into Effects of Chemical Pollutants on Microbial Community Composition and Function in Estuarine Sediments Receiving Polluted River Water. PMID:27744476
Genome Sequences of Nine Gram-Negative Vaginal Bacterial Isolates. PMID:27688330
Genome Sequences of 14 Firmicutes Strains Isolated from the Human Vagina. PMID:27688329
Genome Sequences of 12 Bacterial Isolates Obtained from the Urine of Pregnant Women. PMID:27688327
Genome-Wide Characterization and Expression Analysis of the Germin-Like Protein Family in Rice and Arabidopsis. PMID:27669230
SSH Analysis of Endosperm Transcripts and Characterization of Heat Stress Regulated Expressed Sequence Tags in Bread Wheat. PMID:27582756
Structure-guided selection of specificity determining positions in the human Kinome. PMID:27556159
Identification of differentially expressed genes implicated in peel color (red and green) of Dimocarpus confinis. PMID:27468388
Structure and dynamics of the multi-domain resuscitation promoting factor RpfB from Mycobacterium tuberculosis. PMID:27420638
Wider than Thought Phylogenetic Occurrence of Apicortin, A Characteristic Protein of Apicomplexan Parasites. PMID:27282556
Ionotropic Receptors Identified within the Tentacle of the Freshwater Snail Biomphalaria glabrata, an Intermediate Host of Schistosoma mansoni. PMID:27253696
Genomic Analysis Unravels Reduced Inorganic Sulfur Compound Oxidation of Heterotrophic Acidophilic Acidicaldus sp. Strain DX-1. PMID:27239474
De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species. PMID:27148320
Identification and analysis of integrons and cassette arrays in bacterial genomes. PMID:27130947
The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity. PMID:27102219
Trait changes induced by species interactions in two phenotypically distinct strains of a marine dinoflagellate. PMID:27093044
Genome-Wide Transcriptional Excavation of Dipsacus asperoides Unmasked both Cryptic Asperosaponin Biosynthetic Genes and SSR Markers. PMID:27066018
Cupincin: A Unique Protease Purified from Rice (Oryza sativa L.) Bran Is a New Member of the Cupin Superfamily. PMID:27064905
FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases. PMID:27060136
Genetic and life-history traits associated with the distribution of prophages in bacteria. PMID:27015004
ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures. PMID:26982818
Identification of protein secretion systems in bacterial genomes. PMID:26979785
Computational Identification Raises a Riddle for Distribution of Putative NACHT NTPases in the Genome of Early Green Plants. PMID:26930396
Glutathione S-Transferase Gene Family in Gossypium raimondii and G. arboreum: Comparative Genomic Study and their Expression under Salt Stress. PMID:26904090
High frequency of +1 programmed ribosomal frameshifting in Euplotes octocarinatus. PMID:26891713
Identification and Functional Prediction of Large Intergenic Noncoding RNAs (lincRNAs) in Rainbow Trout (Oncorhynchus mykiss). PMID:26864089
LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer. PMID:26860319
BLAST-based structural annotation of protein residues using Protein Data Bank. PMID:26810894
Comprehensive annotation of Glossina pallidipes salivary gland hypertrophy virus from Ethiopian tsetse flies: a proteogenomics approach. PMID:26801744
Global Regulation of Gene Expression by the MafR Protein of Enterococcus faecalis. PMID:26793169
Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction. PMID:26751217
The cytomegalovirus protein UL138 induces apoptosis of gastric cancer cells by binding to heat shock protein 70. PMID:26735338
The drug target genes show higher evolutionary conservation than non-target genes. PMID:26716901
SH3 Domains Differentially Stimulate Distinct Dynamin I Assembly Modes and G Domain Activity. PMID:26659814
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
Tracing the structural evolution of eukaryotic ATP binding cassette transporter superfamily. PMID:26577702
Three Residues Make an Evolutionary Switch for Folding and RNA-Destabilizing Activity in the TTP Family of Proteins. PMID:26551835
Complete genome sequences and analysis of the Fusobacterium nucleatum subspecies animalis 7-1 bacteriophage ɸFunu1 and ɸFunu2. PMID:26545740
Bacterial calpains and the evolution of the calpain (C2) family of peptidases. PMID:26527411
The conservation and signatures of lincRNAs in Marek's disease of chicken. PMID:26471251
Intrinsically disordered caldesmon binds calmodulin via the "buttons on a string" mechanism. PMID:26417545
De Novo Assembly of the Whole Transcriptome of the Wild Embryo, Preleptocephalus, Leptocephalus, and Glass Eel of Anguilla japonica and Deciphering the Digestive and Absorptive Capacities during Early Development. PMID:26406914
Lipopolysaccharide transport to the cell surface: periplasmic transport and assembly into the outer membrane. PMID:26370939
Citing a Data Repository: A Case Study of the Protein Data Bank. PMID:26317409
Clustering and Differential Alignment Algorithm: Identification of Early Stage Regulators in the Arabidopsis thaliana Iron Deficiency Response. PMID:26317202
Comparative Genomics Including the Early-Diverging Smut Fungus Ceraceosorus bombacis Reveals Signatures of Parallel Evolution within Plant and Animal Pathogens of Fungi and Oomycetes. PMID:26314305
De Novo Transcriptome Analysis of Warburgia ugandensis to Identify Genes Involved in Terpenoids and Unsaturated Fatty Acids Biosynthesis. PMID:26305373
MUCOSAL IMMUNOLOGY. Individual intestinal symbionts induce a distinct population of RORγ⁺ regulatory T cells. PMID:26272906
Structural Determinants for Substrate Binding and Catalysis in Triphosphate Tunnel Metalloenzymes. PMID:26221030
CGMD: An integrated database of cancer genes and markers. PMID:26160459
γ-PGA Hydrolases of Phage Origin in Bacillus subtilis and Other Microbial Genomes. PMID:26158264
Polymorphism Analysis Reveals Reduced Negative Selection and Elevated Rate of Insertions and Deletions in Intrinsically Disordered Protein Regions. PMID:26047845
Extreme Sensory Complexity Encoded in the 10-Megabase Draft Genome Sequence of the Chromatically Acclimating Cyanobacterium Tolypothrix sp. PCC 7601. PMID:25953173
Characterization of Novel Family IV Esterase and Family I.3 Lipase from an Oil-Polluted Mud Flat Metagenome. PMID:25943044
Hierarchical ensemble methods for protein function prediction. PMID:25937954
The genome of the basal agaricomycete Xanthophyllomyces dendrorhous provides insights into the organization of its acetyl-CoA derived pathways and the evolution of Agaricomycotina. PMID:25887949
Census of solo LuxR genes in prokaryotic genomes. PMID:25815274
Systems biology network-based discovery of a small molecule activator BL-AD008 targeting AMPK/ZIPK and inducing apoptosis in cervical cancer. PMID:25797270
Lytic activity of the staphylolytic Twort phage endolysin CHAP domain is enhanced by the SH3b cell wall binding domain. PMID:25790497
Efficient assembly of ribosomes is inhibited by deletion of bipA in Escherichia coli. PMID:25777676
Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment. PMID:25756680
A new method to improve network topological similarity search: applied to fold recognition. PMID:25717198
Physiological and proteomic analyses of leaves from the halophyte Tangut Nitraria reveals diverse response pathways critical for high salinity tolerance. PMID:25713577
MDAT- Aligning multiple domain arrangements. PMID:25626688
Genomic and transcriptomic analysis of the endophytic fungus Pestalotiopsis fici reveals its lifestyle and high potential for synthesis of natural products. PMID:25623211
mRNA secondary structure engineering of Thermobifida fusca endoglucanase (Cel6A) for enhanced expression in Escherichia coli. PMID:25617066
WallProtDB, a database resource for plant cell wall proteomics. PMID:25614757
Computational analysis and low-scale constitutive expression of laccases synthetic genes GlLCC1 from Ganoderma lucidum and POXA 1B from Pleurotus ostreatus in Pichia pastoris. PMID:25611746
Rare allele of a previously unidentified histone H4 acetyltransferase enhances grain weight, yield, and plant biomass in rice. PMID:25535376
The GPCR repertoire in the demosponge Amphimedon queenslandica: insights into the GPCR system at the early divergence of animals. PMID:25528161
A chemical proteomics approach for global analysis of lysine monomethylome profiling. PMID:25505155
Comparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis. PMID:25480015
Conservation analysis of the CydX protein yields insights into small protein identification and evolution. PMID:25475368
FGF8 promotes colorectal cancer growth and metastasis by activating YAP1. PMID:25473897
Genome wide in silico analysis of Plasmodium falciparum phosphatome. PMID:25425018
Convergent bacterial microbiotas in the fungal agricultural systems of insects. PMID:25406380
Text mining in cancer gene and pathway prioritization. PMID:25392685
Unencapsulated Streptococcus pneumoniae from conjunctivitis encode variant traits and belong to a distinct phylogenetic cluster. PMID:25388376
Genome-wide cloning, identification, classification and functional analysis of cotton heat shock transcription factors in cotton (Gossypium hirsutum). PMID:25378022
Transcriptomic analysis of the mussel Elliptio complanata identifies candidate stress-response genes and an abundance of novel or noncoding transcripts. PMID:25375103
Evolution of invasion in a diverse set of Fusobacterium species. PMID:25370491
Dynamic evolution of the GnRH receptor gene family in vertebrates. PMID:25344287
MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PMID:25330359
Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge. PMID:25216354
A comparative metagenome survey of the fecal microbiota of a breast- and a plant-fed Asian elephant reveals an unexpectedly high diversity of glycoside hydrolase family enzymes. PMID:25208077
Complete genome sequence of the Radiation-Resistant bacterium Rubrobacter radiotolerans RSPS-4. PMID:25197483
Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PMID:25140992
Physiological and genomic features of a novel sulfur-oxidizing gammaproteobacterium belonging to a previously uncultivated symbiotic lineage isolated from a hydrothermal vent. PMID:25133584
Transcriptome analysis of extant cotton progenitors revealed tetraploidization and identified genome-specific single nucleotide polymorphism in diploid and allotetraploid cotton. PMID:25099166
Prediction and functional analysis of the sweet orange protein-protein interaction network. PMID:25091279
LTR retroelements are intrinsic components of transcriptional networks in frogs. PMID:25056159
Leucine-Rich Repeat (LRR) Domains Containing Intervening Motifs in Plants. PMID:24970139
Identification of divergent protein domains by combining HMM-HMM comparisons and co-occurrence detection. PMID:24901648
DUF581 is plant specific FCS-like zinc finger involved in protein-protein interaction. PMID:24901469
Tissue-specific transcript profiling for ABC transporters in the sequestering larvae of the phytophagous leaf beetle Chrysomela populi. PMID:24887102
pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families. PMID:24852248
Coupled ion binding and structural transitions along the transport cycle of glutamate transporters. PMID:24842876
Aminopeptidase N1 (EtAPN1), an M1 metalloprotease of the apicomplexan parasite Eimeria tenella, participates in parasite development. PMID:24839124
DINIES: drug-target interaction network inference engine based on supervised analysis. PMID:24838565
ATPase subdomain IA is a mediator of interdomain allostery in Hsp70 molecular chaperones. PMID:24831085
Functional genomic analysis of human mitochondrial RNA processing. PMID:24746820
SET domain-containing Protein 4 (SETD4) is a Newly Identified Cytosolic and Nuclear Lysine Methyltransferase involved in Breast Cancer Cell Proliferation. PMID:24738023
Identification of functional modules by integration of multiple data sources using a Bayesian network classifier. PMID:24736851
A thermo-halo-tolerant and proteinase-resistant endoxylanase from Bacillus sp. HJ14. PMID:24728834
Molecular evolution of the vertebrate FK506 binding protein 25. PMID:24724077
Transcriptome sequencing and gene expression analysis of Trichoderma brevicompactum under different culture conditions. PMID:24710600
Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T. PMID:24710291
Correcting for differential transcript coverage reveals a strong relationship between alternative splicing and organism complexity. PMID:24682283
Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners. PMID:24663061
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the LRR domain of the LePRK1 receptor-like kinase from tomato. PMID:24637764
Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion. PMID:24623814
Trypanosoma brucei adenine-phosphoribosyltransferases mediate adenine salvage and aminopurinol susceptibility but not adenine toxicity. PMID:24596669
QuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors. PMID:24586435
Inferring protein domains associated with drug side effects based on drug-target interaction network. PMID:24565527
Scalable prediction of compound-protein interactions using minwise hashing. PMID:24564870
Residue correlation networks in nuclear receptors reflect functional specialization and the formation of the nematode-specific P-box. PMID:24564869
The lipopolysaccharide export pathway in Escherichia coli: structure, organization and regulated assembly of the Lpt machinery. PMID:24549203
Drechslerella stenobrocha genome illustrates the mechanism of constricting rings and the origin of nematode predation in fungi. PMID:24507587
Candidate disease gene prediction using Gentrepid: application to a genome-wide association study on coronary artery disease. PMID:24498628
Expression and in silico characterization of Phenylalanine ammonium lyase against karnal bunt (Tilletia indica) in wheat (Triticum aestivum). PMID:24497728
A Bayesian sampler for optimization of protein domain hierarchies. PMID:24494927
Gingipains from Porphyromonas gingivalis - Complex domain structures confer diverse functions. PMID:24466435
Helicobacter pylori RNA polymerase α-subunit C-terminal domain shows features unique to ɛ-proteobacteria and binds NikR/DNA complexes. PMID:24442709
Phylogenetic analysis of CDK and cyclin proteins in premetazoan lineages. PMID:24433236
Genome sequencing and comparative analysis of three Chlamydia pecorum strains associated with different pathogenic outcomes. PMID:24417976
Putative sugar transporters of the mustard leaf beetle Phaedon cochleariae: their phylogeny and role for nutrient supply in larval defensive glands. PMID:24391959
A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism. PMID:24391520
Mutations in the UQCC1-interacting protein, UQCC2, cause human complex III deficiency associated with perturbed cytochrome b protein expression. PMID:24385928
High-Quality Draft Genome Sequence of Vagococcus lutrae Strain LBD1, Isolated from the Largemouth Bass Micropterus salmoides. PMID:24371201
Identification and expression analysis of primary auxin-responsive Aux/IAA gene family in cucumber (Cucumis sativus). PMID:24371172
Sequencing and de novo assembly of the transcriptome of the glassy-winged sharpshooter (Homalodisca vitripennis). PMID:24339955
Cell growth inhibition upon deletion of four toxin-antitoxin loci from the megaplasmids of Sinorhizobium meliloti. PMID:24317400
Comparative genome analysis of Solanum lycopersicum and Solanum tuberosum. PMID:24307771
iPfam: a database of protein family and domain interactions found in the Protein Data Bank. PMID:24297255
Transferring functional annotations of membrane transporters on the basis of sequence similarity and sequence motifs. PMID:24283849
Conformational coupling between receptor and kinase binding sites through a conserved salt bridge in a signaling complex scaffold protein. PMID:24244143
Discovery of microorganisms and enzymes involved in high-solids decomposition of rice straw using metagenomic analyses. PMID:24205054
Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining. PMID:24204279
Identification of lysine succinylation substrates and the succinylation regulatory enzyme CobB in Escherichia coli. PMID:24176774
Crystal structure of a putative quorum sensing-regulated protein (PA3611) from the Pseudomonas-specific DUF4146 family. PMID:24174223
Gleaning evolutionary insights from the genome sequence of a probiotic yeast Saccharomyces boulardii. PMID:24148866
Structure and function of a novel LD-carboxypeptidase a involved in peptidoglycan recycling. PMID:24123814
Understanding the sequential activation of Type III and Type VI Secretion Systems in Salmonella typhimurium using Boolean modeling. PMID:24079299
The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution. PMID:24068976
Allosteric Modulation of G Protein Coupled Receptors by Cytoplasmic, Transmembrane and Extracellular Ligands. PMID:24009470
Endogenous retrovirus EAV-HP linked to blue egg phenotype in Mapuche fowl. PMID:23990950
Homology modeling of the CheW coupling protein of the chemotaxis signaling complex. PMID:23950985
Predicting a novel pathogenicity island in Helicobacter pylori by genomic barcoding. PMID:23946608
Identification of novel adhesins of M. tuberculosis H37Rv using integrated approach of multiple computational algorithms and experimental analysis. PMID:23922800
The shells of BMC-type microcompartment organelles in bacteria. PMID:23920492
Metagenome survey of a multispecies and alga-associated biofilm revealed key elements of bacterial-algal interactions in photobioreactors. PMID:23913425
PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions. PMID:23896518
Detecting and comparing non-coding RNAs in the high-throughput era. PMID:23887659
Short toxin-like proteins attack the defense line of innate immunity. PMID:23881252
A lover and a fighter: the genome sequence of an entomopathogenic nematode Heterorhabditis bacteriophora. PMID:23874975
Common and pathogen-specific virulence factors are different in function and structure. PMID:23863604
SVM based model generation for binding site prediction on helix turn helix motif type of transcription factors in eukaryotes. PMID:23861565
Genome-wide identification and expression profiling of ankyrin-repeat gene family in maize. PMID:23839078
Bcl2-associated athanogene 3 interactome analysis reveals a new role in modulating proteasome activity. PMID:23824909
Structure-function analysis of the LytM domain of EnvC, an activator of cell wall remodelling at the Escherichia coli division site. PMID:23796240
Alternative splicing tends to avoid partial removals of protein-protein interaction sites. PMID:23758645
Combinatorial clustering of residue position subsets predicts inhibitor affinity across the human kinome. PMID:23754939
Insight into the specific virulence related genes and toxin-antitoxin virulent pathogenicity islands in swine streptococcosis pathogen Streptococcus equi ssp. zooepidemicus strain ATCC35246. PMID:23742619
Computational identification of functional RNA homologs in metagenomic data. PMID:23722291
Crystallization and preliminary crystallographic analysis of an Escherichia coli-selected mutant of the nuclease domain of the metallonuclease colicin E7. PMID:23695575
Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen. PMID:23685541
Large-scale modelling of the divergent spectrin repeats in nesprins: giant modular proteins. PMID:23671687
Transcription profile of soybean-root-knot nematode interaction reveals a key role of phythormones in the resistance reaction. PMID:23663436
Genome-wide identification, characterization and expression analysis of populus leucine-rich repeat receptor-like protein kinase genes. PMID:23663326
DIALIGN at GOBICS--multiple sequence alignment using various sources of external information. PMID:23620293
P2RP: a Web-based framework for the identification and analysis of regulatory proteins in prokaryotic genomes. PMID:23601859
CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that is active in vivo. PMID:23590861
Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens. PMID:23584789
Structure and function of the DUF2233 domain in bacteria and in the human mannose 6-phosphate uncovering enzyme. PMID:23572527
ProtoNet: charting the expanding universe of protein sequences. PMID:23563419
SH3 interactome conserves general function over specific form. PMID:23549480
Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools. PMID:23547799
Identification and Characterisation CRN Effectors in Phytophthora capsici Shows Modularity and Functional Diversity. PMID:23536880
5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea. PMID:23514374
Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex. PMID:23514195
Mining for class-specific motifs in protein sequence classification. PMID:23496846
Global analysis of transcriptional regulators in Staphylococcus aureus. PMID:23442205
A human skeletal muscle interactome centered on proteins involved in muscular dystrophies: LGMD interactome. PMID:23414517
Draft Genome Sequence of Rhodococcus opacus Strain M213 Shows a Diverse Catabolic Potential. PMID:23409266
Eomesodermin of atlantic salmon: an important regulator of cytolytic gene and interferon gamma expression in spleen lymphocytes. PMID:23409078
The diversity and evolution of Wolbachia ankyrin repeat domain genes. PMID:23390535
A transcriptional regulator linking quorum sensing and chitin induction to render Vibrio cholerae naturally transformable. PMID:23382174
Genome-wide identification and analysis of the B3 superfamily of transcription factors in Brassicaceae and major crop plants. PMID:23377560
Sequencing and de novo assembly of the western tarnished plant bug (Lygus hesperus) transcriptome. PMID:23357950
The role of the N-terminal loop in the function of the colicin E7 nuclease domain. PMID:23334162
Phylogeny of Toll-like receptor signaling: adapting the innate response. PMID:23326591
Comparative genomic analysis of the microbiome [corrected] of herbivorous insects reveals eco-environmental adaptations: biotechnology applications. PMID:23326236
Draft genome sequence of the male-killing Wolbachia strain wBol1 reveals recent horizontal gene transfers from diverse sources. PMID:23324387
Comparative genomics of the lipid-body-membrane proteins oleosin, caleosin and steroleosin in magnoliophyte, lycophyte and bryophyte. PMID:23317702
Bacterial cell division regulation by Ser/Thr kinases: a structural perspective. PMID:23305362
Ecology of marine Bacteroidetes: a comparative genomics approach. PMID:23303374
Chapter 12: Human microbiome analysis. PMID:23300406
The Escherichia coli Lpt transenvelope protein complex for lipopolysaccharide export is assembled via conserved structurally homologous domains. PMID:23292770
Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study. PMID:23237380
Contribution of lateral gene transfers to the genome composition and parasitic ability of root-knot nematodes. PMID:23226415
The origins of the evolutionary signal used to predict protein-protein interactions. PMID:23217198
1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data. PMID:23176165
A new protein superfamily: TPPP-like proteins. PMID:23166627
Dynamics of domain coverage of the protein sequence universe. PMID:23157439
P2TF: a comprehensive resource for analysis of prokaryotic transcription factors. PMID:23153078
Genome-wide comparison of FGFRL1 with structurally related surface receptors. PMID:23136609
Comparative genomics suggests an independent origin of cytoplasmic incompatibility in Cardinium hertigii. PMID:23133394
Detection of dengue group viruses by fluorescence in situ hybridization. PMID:23110979
A non-linear deterministic model for regulation of diauxic lag on cellobiose by the pneumococcal multidomain transcriptional regulator CelR. PMID:23110070
The binding of Varp to VAMP7 traps VAMP7 in a closed, fusogenically inactive conformation. PMID:23104059
Tissue-specific transcriptome profiling of Plutella xylostella third instar larval midgut. PMID:23091412
Homepeptide repeats: implications for protein structure, function and evolution. PMID:23084777
Provirophages and transpovirons as the diverse mobilome of giant viruses. PMID:23071316
Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis. PMID:23050870
Inferring domain-domain interactions from protein-protein interactions in the complex network conformation. PMID:23046795
A Toll/IL-1R/resistance domain-containing thioredoxin regulates phagocytosis in Entamoeba histolytica. PMID:23043976
Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state. PMID:23029181
The Aspergillus fumigatus dihydroxyacid dehydratase Ilv3A/IlvC is required for full virulence. PMID:23028460
Combining laser microdissection and RNA-seq to chart the transcriptional landscape of fungal development. PMID:23016559
Mapping and candidate-gene screening of the novel Turnip mosaic virus resistance gene retr02 in Chinese cabbage (Brassica rapa L.). PMID:22996569
Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers. PMID:22962471
Genome-wide and molecular evolution analysis of the Poplar KT/HAK/KUP potassium transporter gene family. PMID:22957200
XatA, an AT-1 autotransporter important for the virulence of Xylella fastidiosa Temecula1. PMID:22950010
Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal. PMID:22948926
Evolutionary history of exon shuffling. PMID:22948334
Auxin response factor gene family in Brassica rapa: genomic organization, divergence, expression, and evolution. PMID:22915303
Constructing the angiome: a global angiogenesis protein interaction network. PMID:22911453
Discovering patterns in drug-protein interactions based on their fingerprints. PMID:22901089
Comparative analysis of the genomes of two field isolates of the rice blast fungus Magnaporthe oryzae. PMID:22876203
Mapping the mutual information network of enzymatic families in the protein structure to unveil functional features. PMID:22848494
Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma. PMID:22829753
Parasites, proteomes and systems: has Descartes' clock run out of time? PMID:22828391
Evolution of viral proteins originated de novo by overprinting. PMID:22821011
Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring. PMID:22793672
TolC-dependent secretion of an ankyrin repeat-containing protein of Rickettsia typhi. PMID:22773786
The crystal structure of the periplasmic domain of Vibrio parahaemolyticus CpxA. PMID:22760860
Domain landscapes of somatic mutations in cancer. PMID:22759657
A systematic comparison of genome-scale clustering algorithms. PMID:22759431
Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures. PMID:22726767
A conformational switch controls cell wall-remodelling enzymes required for bacterial cell division. PMID:22715947
An elm EST database for identifying leaf beetle egg-induced defense genes. PMID:22702658
Novel domain combinations in proteins encoded by chimeric transcripts. PMID:22689780
Interactions of an Arabidopsis RanBPM homologue with LisH-CTLH domain proteins revealed high conservation of CTLH complexes in eukaryotes. PMID:22676313
Regulated assembly of the transenvelope protein complex required for lipopolysaccharide export. PMID:22668317
Activator role of the pneumococcal Mga-like virulence transcriptional regulator. PMID:22661692
Structural and functional dissection of aminocoumarin antibiotic biosynthesis: a review. PMID:22644392
Mining disease-resistance genes in roses: functional and molecular characterization of the rdr1 locus. PMID:22639591
Profile-based short linear protein motif discovery. PMID:22607209
New cis-regulatory elements in the Rht-D1b locus region of wheat. PMID:22592657
Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset. PMID:22587810
The genome of Ganoderma lucidum provides insights into triterpenes biosynthesis and wood degradation [corrected]. PMID:22567134
Characterization of a novel ArsR-like regulator encoded by Rv2034 in Mycobacterium tuberculosis. PMID:22558408
Novel metagenome-derived, cold-adapted alkaline phospholipase with superior lipase activity as an intermediate between phospholipase and lipase. PMID:22544255
Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals. PMID:22529998
DICER-LIKE3 activity in Physcomitrella patens DICER-LIKE4 mutants causes severe developmental dysfunction and sterility. PMID:22511605
Expansion and diversification of the SET domain gene family following whole-genome duplications in Populus trichocarpa. PMID:22497662
Characterization of a novel bipartite double-stranded RNA mycovirus conferring hypovirulence in the phytopathogenic fungus Botrytis porri. PMID:22496220
The transcription factor encyclopedia. PMID:22458515
Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis. PMID:22452820
QTLs for agronomic and cell wall traits in a maize RIL progeny derived from a cross between an old Minnesota13 line and a modern Iodent line. PMID:22437492
A novel xylanase with tolerance to ethanol, salt, protease, SDS, heat, and alkali from actinomycete Lechevalieria sp. HJ3. PMID:22430498
Regular patterns for proteome-wide distribution of protein abundance across species. PMID:22427835
Sequence evolution correlates with structural dynamics. PMID:22427707
Zds1 regulates PP2A(Cdc55) activity and Cdc14 activation during mitotic exit through its Zds_C motif. PMID:22427694
A study on mutational dynamics of simple sequence repeats in relation to mismatch repair system in prokaryotic genomes. PMID:22415400
SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone. PMID:22408192
Characterization of the CRISPR/Cas subtype I-A system of the hyperthermophilic crenarchaeon Thermoproteus tenax. PMID:22408157
The gpsX gene encoding a glycosyltransferase is important for polysaccharide production and required for full virulence in Xanthomonas citri subsp. citri. PMID:22404966
Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides. PMID:22396667
Strain Variation in the Transcriptome of the Dengue Fever Vector, Aedes aegypti. PMID:22384387
Pleiotropic roles of a ribosomal protein in Dictyostelium discoideum. PMID:22363460
Characterization of protein glycosylation in Francisella tularensis subsp. holarctica: identification of a novel glycosylated lipoprotein required for virulence. PMID:22361235
Roles of major facilitator superfamily transporters in phosphate response in Drosophila. PMID:22359624
Computational prediction and molecular characterization of an oomycete effector and the cognate Arabidopsis resistance gene. PMID:22359513
Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase. PMID:22356826
Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms. PMID:22331370
Translating Mendelian and complex inheritance of Alzheimer's disease genes for predicting unique personal genome variants. PMID:22319180
Incorporating molecular and functional context into the analysis and prioritization of human variants associated with cancer. PMID:22319177
Aspartate-Derived Amino Acid Biosynthesis in Arabidopsis thaliana. PMID:22303247
ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. PMID:22268964
C7orf30 specifically associates with the large subunit of the mitochondrial ribosome and is involved in translation. PMID:22238375
Metagenomic evidence for h(2) oxidation and h(2) production by serpentinite-hosted subsurface microbial communities. PMID:22232619
Garvieacin Q, a novel class II bacteriocin from Lactococcus garvieae BCC 43578. PMID:22210221
Using amino acid correlation and community detection algorithms to identify functional determinants in protein families. PMID:22205928
Lysosomal protein trafficking in Giardia lamblia: common and distinct features. PMID:22202006
GlyGly-CTERM and rhombosortase: a C-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease. PMID:22194940
Analysis of yeast endocytic site formation and maturation through a regulatory transition point. PMID:22190733
Novel search method for the discovery of functional relationships. PMID:22180409
Experimental and analytical tools for studying the human microbiome. PMID:22179717
Expansion of genes encoding piRNA-associated argonaute proteins in the pea aphid: diversification of expression profiles in different plastic morphs. PMID:22162754
The SH2 domain-containing proteins in 21 species establish the provenance and scope of phosphotyrosine signaling in eukaryotes. PMID:22155787
The STARD9/Kif16a kinesin associates with mitotic microtubules and regulates spindle pole assembly. PMID:22153075
Regulation of phenotypic heterogeneity permits Salmonella evasion of the host caspase-1 inflammatory response. PMID:22143773
SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss. PMID:22120661
Sucrose synthase in unicellular cyanobacteria and its relationship with salt and hypoxic stress. PMID:22113826
Specific inhibition of bacterial RNase T2 by helix 41 of 16S ribosomal RNA. PMID:22109523
DBETH: a Database of Bacterial Exotoxins for Human. PMID:22102573
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. PMID:22096231
The H/ACA RNP assembly factor SHQ1 functions as an RNA mimic. PMID:22085966
Functional Annotation Analytics of Rhodopseudomonas palustris Genomes. PMID:22084572
Analysis of genome-wide association study data using the protein knowledge base. PMID:22077927
A novel cold-adapted lipase from Sorangium cellulosum strain So0157-2: gene cloning, expression, and enzymatic characterization. PMID:22072918
Protein Domain Analysis of C. botulinum Type A Neurotoxin and Its Relationship with Other Botulinum Serotypes. PMID:22069543
Evolution of the TOR pathway. PMID:22057117
Brr6 drives the Schizosaccharomyces pombe spindle pole body nuclear envelope insertion/extrusion cycle. PMID:22042620
Conservation of the human integrin-type beta-propeller domain in bacteria. PMID:22022374
Physiological and biochemical characterization of AnNitA, the Aspergillus nidulans high-affinity nitrite transporter. PMID:22021238
Comparative void-volume analysis of psychrophilic and mesophilic enzymes: Structural bioinformatics of psychrophilic enzymes reveals sources of core flexibility. PMID:22013889
The multiple functions of plant serine protease inhibitors: defense against herbivores and beyond. PMID:22004998
Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop. PMID:21994619
Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures. PMID:21979275
PROTS: a fragment based protein thermo-stability potential. PMID:21976375
Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome. PMID:21974828
Structural and biochemical characterization of the salicylyl-acyltranferase SsfX3 from a tetracycline biosynthetic pathway. PMID:21965680
Regulation of biofilm components in Salmonella enterica serovar Typhimurium by lytic transglycosylases involved in cell wall turnover. PMID:21965572
Spatial analysis of biomineralization associated gene expression from the mantle organ of the pearl oyster Pinctada maxima. PMID:21936921
Molecular characterization of 60 isolated wheat MYB genes and analysis of their expression during abiotic stress. PMID:21934119
Discovery of the first insect nidovirus, a missing evolutionary link in the emergence of the largest RNA virus genomes. PMID:21931546
Evidence for direct electron transfer by a gram-positive bacterium isolated from a microbial fuel cell. PMID:21908627
Conserved meiotic machinery in Glomus spp., a putatively ancient asexual fungal lineage. PMID:21876220
Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium. PMID:21867535
A novel E2F-like protein involved in transcriptional activation of cyst wall protein genes in Giardia lamblia. PMID:21835923
The Proteome Folding Project: proteome-scale prediction of structure and function. PMID:21824995
The Vein Patterning 1 (VEP1) gene family laterally spread through an ecological network. PMID:21818306
A shortest-path graph kernel for estimating gene product semantic similarity. PMID:21801410
Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database. PMID:21801404
Gene coexpression network analysis as a source of functional annotation for rice genes. PMID:21799793
Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions in proteins. PMID:21771306
Characterization of the deoxynucleotide triphosphate triphosphohydrolase (dNTPase) activity of the EF1143 protein from Enterococcus faecalis and crystal structure of the activator-substrate complex. PMID:21757692
Genome sequence of the ethanol-producing Zymomonas mobilis subsp. pomaceae lectotype strain ATCC 29192. PMID:21742897
Genome sequence of Idiomarina sp. strain A28L, isolated from Pangong Lake, India. PMID:21742887
Genome sequence of Rheinheimera sp. strain A13L, isolated from Pangong Lake, India. PMID:21742876
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
Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque. PMID:21733155
Genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis lectotype strain ATCC 10988. PMID:21725006
In search of Brucella abortus type IV secretion substrates: screening and identification of four proteins translocated into host cells through VirB system. PMID:21707904
Dynamics of gene duplication in the genomes of chlorophyll d-producing cyanobacteria: implications for the ecological niche. PMID:21697100
Sulfur metabolism in the extreme acidophile acidithiobacillus caldus. PMID:21687411
Evolution of the Ras-like small GTPases and their regulators. PMID:21686276
Novel family of carbohydrate-binding modules revealed by the genome sequence of Spirochaeta thermophila DSM 6192. PMID:21685171
Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning. PMID:21685095
Draft genome sequencing and comparative analysis of Aspergillus sojae NBRC4239. PMID:21659486
Structure collisions between interacting proteins. PMID:21655095
BEL/Pao retrotransposons in metazoan genomes. PMID:21639932
LinkinPath: from sequence to interconnected pathway. PMID:21636594
BlastR--fast and accurate database searches for non-coding RNAs. PMID:21624887
Analysis of the disintegrin-metalloproteinases family reveals ADAM29 and ADAM7 are often mutated in melanoma. PMID:21618342
Constructing de novo biosynthetic pathways for chemical synthesis inside living cells. PMID:21591680
Knowledge-driven multi-locus analysis reveals gene-gene interactions influencing HDL cholesterol level in two independent EMR-linked biobanks. PMID:21589926
Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks. PMID:21573011
A user-friendly web portal for T-Coffee on supercomputers. PMID:21569428
Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus. PMID:21569391
Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features. PMID:21559529
A bioinformatics classifier and database for heme-copper oxygen reductases. PMID:21559461
Evolution of the karyopherin-β family of nucleocytoplasmic transport factors; ancient origins and continued specialization. PMID:21556326
Genetic and epigenetic association studies suggest a role of microRNA biogenesis gene exportin-5 (XPO5) in breast tumorigenesis. PMID:21552306
EXORDIUM-LIKE1 promotes growth during low carbon availability in Arabidopsis. PMID:21543728
Methods and strategies for gene structure curation in WormBase. PMID:21543339
Molecular characterization of Cronobacter lipopolysaccharide O-antigen gene clusters and development of serotype-specific PCR assays. PMID:21531829
Structural features and chaperone activity of the NudC protein family. PMID:21530541
Computational prediction and experimental validation of novel markers for detection of STEC O157:H7. PMID:21528067
Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples. PMID:21498766
The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases. PMID:21498547
Characterization of metalloproteins by high-throughput X-ray absorption spectroscopy. PMID:21482623
Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus. PMID:21478372
Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification. PMID:21478363
Feed-forward regulation of microbisporicin biosynthesis in Microbispora corallina. PMID:21478362
Implications of the inability of Listeria monocytogenes EGD-e to grow anaerobically due to a deletion in the class III NrdD ribonucleotide reductase for its use as a model laboratory strain. PMID:21478338
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
Exploring the link between MORF4L1 and risk of breast cancer. PMID:21466675
AS160 phosphotyrosine-binding domain constructs inhibit insulin-stimulated GLUT4 vesicle fusion with the plasma membrane. PMID:21454690
A systems biology approach for the investigation of the heparin/heparan sulfate interactome. PMID:21454685
Baculovirus VP80 protein and the F-actin cytoskeleton interact and connect the viral replication factory with the nuclear periphery. PMID:21450830
Structure and function of the first full-length murein peptide ligase (Mpl) cell wall recycling protein. PMID:21445265
PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. PMID:21441431
HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition. PMID:21423752
How vaccinia virus has evolved to subvert the host immune response. PMID:21419849
Crystal structure of tarocystatin-papain complex: implications for the inhibition property of group-2 phytocystatins. PMID:21416241
Genome-wide identification, characterization and phylogenetic analysis of the rice LRR-kinases. PMID:21408199
Genome-wide identification of molecular mimicry candidates in parasites. PMID:21408160
Detection of selection utilizing molecular phylogenetics: a possible approach. PMID:21400220
Complete genome sequence of the commensal Enterococcus faecalis 62, isolated from a healthy Norwegian infant. PMID:21398545
Molecular basis for mycophenolic acid biosynthesis in Penicillium brevicompactum. PMID:21398490
The contribution of entropy, enthalpy, and hydrophobic desolvation to cooperativity in repeat-protein folding. PMID:21397186
The zebrafish maternal-effect gene mission impossible encodes the DEAH-box helicase Dhx16 and is essential for the expression of downstream endodermal genes. PMID:21396359
A tetrapyrrole-regulated ubiquitin ligase controls algal nuclear DNA replication. PMID:21378982
A negative effector of blue light-induced and gravitropic bending in Arabidopsis. PMID:21367967
A computational method for prediction of excretory proteins and application to identification of gastric cancer markers in urine. PMID:21365014
The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon. PMID:21356104
Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. PMID:21356102
Meet me halfway: when genomics meets structural bioinformatics. PMID:21350909
GARNET--gene set analysis with exploration of annotation relations. PMID:21342555
The DamX protein of Escherichia coli and Salmonella enterica. PMID:21327035
Complete genome sequence of Methanoculleus marisnigri Romesser et al. 1981 type strain JR1. PMID:21304656
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes. PMID:21304638
Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. PMID:21297863
RNA-seq analyses of blood-induced changes in gene expression in the mosquito vector species, Aedes aegypti. PMID:21276245
Bioinformatic identification of novel protein phosphatases in the dog genome. PMID:21240543
Discriminative motif finding for predicting protein subcellular localization. PMID:21233524
Insertion sequence-excision enhancer removes transposable elements from bacterial genomes and induces various genomic deletions. PMID:21224843
Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners. PMID:21223593
Selection patterns on restorer-like genes reveal a conflict between nuclear and mitochondrial genomes throughout angiosperm evolution. PMID:21220331
Unraveling the molecular mechanisms of nitrogenase conformational protection against oxygen in diazotrophic bacteria. PMID:21210973
Strain-specific activation of the NF-kappaB pathway by GRA15, a novel Toxoplasma gondii dense granule protein. PMID:21199955
Novel genes exhibit distinct patterns of function acquisition and network integration. PMID:21187012
The solute carrier families have a remarkably long evolutionary history with the majority of the human families present before divergence of Bilaterian species. PMID:21186191
Lipoprotein cofactors located in the outer membrane activate bacterial cell wall polymerases. PMID:21183074
Cholera- and anthrax-like toxins are among several new ADP-ribosyltransferases. PMID:21170356
Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments. PMID:21167037
An Integrated Database for Complex Protein Structure Modeling. PMID:21151784
Biological functions of the genes in the mammaprint breast cancer profile reflect the hallmarks of cancer. PMID:21151591
Efficient algorithms for training the parameters of hidden Markov models using stochastic expectation maximization (EM) training and Viterbi training. PMID:21143925
Discovery of a minimal form of RNase P in Pyrobaculum. PMID:21135215
Genome-wide analysis of BURP domain-containing genes in maize and sorghum. PMID:21127990
Evolution of domain promiscuity in eukaryotic genomes--a perspective from the inferred ancestral domain architectures. PMID:21127809
The Apicomplexan AP2 family: integral factors regulating Plasmodium development. PMID:21126543
A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae. PMID:21119626
Characterization of a nitric oxide synthase from the plant kingdom: NO generation from the green alga Ostreococcus tauri is light irradiance and growth phase dependent. PMID:21119059
A domain-centric analysis of oomycete plant pathogen genomes reveals unique protein organization. PMID:21119047
The KP4 killer protein gene family. PMID:21116630
Theoretical and experimental characterization of the scope of protein O-glycosylation in Bacteroides fragilis. PMID:21115495
Molecular characterization and mRNA expression of two key enzymes of hypoxia-sensing pathways in eastern oysters Crassostrea virginica (Gmelin): hypoxia-inducible factor α (HIF-α) and HIF-prolyl hydroxylase (PHD). PMID:21106446
DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection. PMID:21106128
Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. PMID:21092232
Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification. PMID:21079665
Identification of a family of effectors secreted by the type III secretion system that are conserved in pathogenic Chlamydiae. PMID:21078856
An atypical proprotein convertase in Giardia lamblia differentiation. PMID:21075147
Evolutionary history of tissue kallikreins. PMID:21072173
The LabelHash algorithm for substructure matching. PMID:21070651
Tissue-specific transcriptomics of the exotic invasive insect pest emerald ash borer (Agrilus planipennis). PMID:21060843
Identification and genome-wide prediction of DNA binding specificities for the ApiAP2 family of regulators from the malaria parasite. PMID:21060817
Identification of family-determining residues in PHD fingers. PMID:21059680
ARABIDILLO proteins have a novel and conserved domain structure important for the regulation of their stability. PMID:21052782
A recombination hotspot leads to sequence variability within a novel gene (AK005651) and contributes to type 1 diabetes susceptibility. PMID:21051460
ASD: a comprehensive database of allosteric proteins and modulators. PMID:21051350
Protein folds and protein folding. PMID:21051320
Genomic and functional adaptation in surface ocean planktonic prokaryotes. PMID:21048761
Ancestral centriole and flagella proteins identified by analysis of Naegleria differentiation. PMID:21045110
PDBe: Protein Data Bank in Europe. PMID:21045060
Monoamine neurotransmitters as substrates for novel tick sulfotransferases, homology modeling, molecular docking, and enzyme kinetics. PMID:21043483
An Allergen Portrait Gallery: Representative Structures and an Overview of IgE Binding Surfaces. PMID:20981266
Scaffolding a Caenorhabditis nematode genome with RNA-seq. PMID:20980554
Evolutionary mode and functional divergence of vertebrate NMDA receptor subunit 2 genes. PMID:20976280
Genome-wide comparative gene family classification. PMID:20976221
Infectivity acts as in vivo selection for maintenance of the chlamydial cryptic plasmid. PMID:20974819
Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera. PMID:20973996
Verification of alternative splicing variants based on domain integrity, truncation length and intrinsic protein disorder. PMID:20972208
Nucleotide parasitism by Simkania negevensis (Chlamydiae). PMID:20971898
The aconitate hydratase family from Citrus. PMID:20958971
Comparative genomic evidence for a complete nuclear pore complex in the last eukaryotic common ancestor. PMID:20949036
Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger. PMID:20944230
Ligands in PSI structures. PMID:20944227
The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function. PMID:20944221
Open and closed conformations of two SpoIIAA-like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding. PMID:20944218
Structure of LP2179, the first representative of Pfam family PF08866, suggests a new fold with a role in amino-acid metabolism. PMID:20944212
The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45 Å resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator. PMID:20944211
The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation. PMID:20944208
Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation. PMID:20944207
DUFs: families in search of function. PMID:20944204
Evolutionary history of the poly(ADP-ribose) polymerase gene family in eukaryotes. PMID:20942953
Laser microsurgery provides evidence for merotelic kinetochore attachments in fission yeast cells lacking Pcs1 or Clr4. PMID:20935472
Genome sequence of the polysaccharide-degrading, thermophilic anaerobe Spirochaeta thermophila DSM 6192. PMID:20935097
Molecular and phylogenetic characterization of the sieve element occlusion gene family in Fabaceae and non-Fabaceae plants. PMID:20932300
Structural basis for the dual RNA-recognition modes of human Tra2-β RRM. PMID:20926394
An insect herbivore microbiome with high plant biomass-degrading capacity. PMID:20885794
Finding the "dark matter" in human and yeast protein network prediction and modelling. PMID:20885791
ATHENA: A knowledge-based hybrid backpropagation-grammatical evolution neural network algorithm for discovering epistasis among quantitative trait Loci. PMID:20875103
Genomic characterization of Campylobacter jejuni strain M1. PMID:20865039
Tryptophanyl-tRNA synthetase Urzyme: a model to recapitulate molecular evolution and investigate intramolecular complementation. PMID:20864539
Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs. PMID:20862304
Plasmodium falciparum erythrocyte membrane protein 1 diversity in seven genomes--divide and conquer. PMID:20862303
Comparative genome analysis reveals an absence of leucine-rich repeat pattern-recognition receptor proteins in the kingdom Fungi. PMID:20856863
The ancient function of RB-E2F pathway: insights from its evolutionary history. PMID:20849664
Phylogenomics of ligand-gated ion channels predicts monepantel effect. PMID:20838602
The crystal structure of a bacterial Sufu-like protein defines a novel group of bacterial proteins that are similar to the N-terminal domain of human Sufu. PMID:20836087
Legionella pneumophila strain 130b possesses a unique combination of type IV secretion systems and novel Dot/Icm secretion system effector proteins. PMID:20833813
Mitochondria-specific transgenic overexpression of connexin-43 simulates preconditioning-induced cytoprotection of stem cells. PMID:20833648
Global regulator H-NS and lipoprotein NlpI influence production of extracellular DNA in Escherichia coli. PMID:20833130
The immunoregulatory properties of oncolytic myxoma virus and their implications in therapeutics. PMID:20832500
The role of cis dimerization of signal regulatory protein alpha (SIRPalpha) in binding to CD47. PMID:20826801
Genetic analysis of mobile tetQ elements in oral Prevotella species. PMID:20826220
Prediction and testing of biological networks underlying intestinal cancer. PMID:20824133
Glycoside hydrolases as components of putative carbohydrate biosensor proteins in Clostridium thermocellum. PMID:20820855
Solution structure and function of YndB, an AHSA1 protein from Bacillus subtilis. PMID:20818668
Insulin-like signaling determines survival during stress via posttranscriptional mechanisms in C. elegans. PMID:20816092
Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction. PMID:20808886
Genes and pathways for CO2 fixation in the obligate, chemolithoautotrophic acidophile, Acidithiobacillus ferrooxidans, carbon fixation in A. ferrooxidans. PMID:20799944
The crystal structure Escherichia coli Spy. PMID:20799348
CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation. PMID:20796320
Identification of a bacterial inhibitor against g-type lysozyme. PMID:20734102
Hidden Markov model speed heuristic and iterative HMM search procedure. PMID:20718988
TOPSAN: a collaborative annotation environment for structural genomics. PMID:20716366
A novel pax-like protein involved in transcriptional activation of cyst wall protein genes in Giardia lamblia. PMID:20699219
FACT: functional annotation transfer between proteins with similar feature architectures. PMID:20696036
GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques. PMID:20689020
Symbiotic Streptomyces sp. TN119 GH 11 xylanase: a new pH-stable, protease- and SDS-resistant xylanase. PMID:20686913
DMDM: domain mapping of disease mutations. PMID:20685956
Germin-like proteins (GLPs) in cereal genomes: gene clustering and dynamic roles in plant defence. PMID:20683632
A subtilisin-like protein from soybean contains an embedded, cryptic signal that activates defense-related genes. PMID:20679205
Novel Zn2+-binding sites in human transthyretin: implications for amyloidogenesis and retinol-binding protein recognition. PMID:20659897
The construction and use of log-odds substitution scores for multiple sequence alignment. PMID:20657661
Expression and physiological role of three Myxococcus xanthus copper-dependent P1B-type ATPases during bacterial growth and development. PMID:20656859
Prediction of mucin-type O-glycosylation sites by a two-staged strategy. PMID:20652405
Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. PMID:20644220
Identification of the gene encoding alkylglycerol monooxygenase defines a third class of tetrahydrobiopterin-dependent enzymes. PMID:20643956
RosR (Cg1324), a hydrogen peroxide-sensitive MarR-type transcriptional regulator of Corynebacterium glutamicum. PMID:20643656
The ABC transporter HrtAB confers resistance to hemin toxicity and is regulated in a hemin-dependent manner by the ChrAS two-component system in Corynebacterium diphtheriae. PMID:20639324
Dynamics of SecY translocons with translocation-defective mutations. PMID:20637421
Viruses in the faecal microbiota of monozygotic twins and their mothers. PMID:20631792
PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies. PMID:20631208
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. PMID:20626842
A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes. PMID:20626840
PROFESS: a PROtein function, evolution, structure and sequence database. PMID:20624718
Effective gene silencing in a microsporidian parasite associated with honeybee (Apis mellifera) colony declines. PMID:20622131
The Giardia lamblia vsp gene repertoire: characteristics, genomic organization, and evolution. PMID:20618957
Combining next-generation sequencing strategies for rapid molecular resource development from an invasive aphid species, Aphis glycines. PMID:20614011
Comparative proteomic analysis of extracellular proteins of Clostridium perfringens type A and type C strains. PMID:20605988
When simple sequence comparison fails: the cryptic case of the shared domains of the bacterial replication initiation proteins DnaB and DnaD. PMID:20587500
The role of lipid transfer proteins in allergic diseases. PMID:20582490
Bioinformatic Identification of Novel Methyltransferases. PMID:20582239
Modular composition predicts kinase/substrate interactions. PMID:20579376
An arthropod enzyme, Dfurin1, and a vertebrate furin homolog display distinct cleavage site sequence preferences for a shared viral proprotein substrate. PMID:20578951
A phylogenetic survey of myotubularin genes of eukaryotes: distribution, protein structure, evolution, and gene expression. PMID:20576132
The phosphatomes of the multicellular myxobacteria Myxococcus xanthus and Sorangium cellulosum in comparison with other prokaryotic genomes. PMID:20567509
Differential regulation of six heavy metal efflux systems in the response of Myxococcus xanthus to copper. PMID:20562277
Expansion of the target of rapamycin (TOR) kinase family and function in Leishmania shows that TOR3 is required for acidocalcisome biogenesis and animal infectivity. PMID:20551225
Prediction of prognostic biomarkers for interferon-based therapy to hepatitis C virus patients: a meta-analysis of the NS5A protein in subtypes 1a, 1b, and 3a. PMID:20550652
Cloning, overexpression, purification and preliminary characterization of human septin 8. PMID:20544379
Slip-sliding away: serial changes and homoplasy in repeat number in the Drosophila yakuba homolog of human cancer susceptibility gene BRCA2. PMID:20543987
High-throughput production of human proteins for crystallization: the SGC experience. PMID:20541610
Apicomplexan perforin-like proteins. PMID:20539776
CODA: accurate detection of functional associations between proteins in eukaryotic genomes using domain fusion. PMID:20532224
Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families. PMID:20532204
Validation of coevolving residue algorithms via pipeline sensitivity analysis: ELSC and OMES and ZNMI, oh my! PMID:20531955
Low-homology protein threading. PMID:20529920
Archaic chaos: intrinsically disordered proteins in Archaea. PMID:20522251
Robustness and evolvability in natural chemical resistance: identification of novel systems properties, biochemical mechanisms and regulatory interactions. PMID:20517567
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. PMID:20513647
Cell surface display of chimeric glycoproteins via the S-layer of Paenibacillus alvei. PMID:20513375
Evolutionary bases of carbohydrate recognition and substrate discrimination in the ROK protein family. PMID:20512568
PCFamily: a web server for searching homologous protein complexes. PMID:20511590
Domain distribution and intrinsic disorder in hubs in the human protein-protein interaction network. PMID:20509167
Signatures of RNA binding proteins globally coupled to effective microRNA target sites. PMID:20508147
Structural and enzymatic insights into the ATP binding and autophosphorylation mechanism of a sensor histidine kinase. PMID:20507988
Wheat beta-expansin (EXPB11) genes: Identification of the expressed gene on chromosome 3BS carrying a pollen allergen domain. PMID:20507562
A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block. PMID:20507561
Threshold Average Precision (TAP-k): a measure of retrieval designed for bioinformatics. PMID:20505002
POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations. PMID:20504857
Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures. PMID:20502673
Mutations in the Cc.rmt1 gene encoding a putative protein arginine methyltransferase alter developmental programs in the basidiomycete Coprinopsis cinerea. PMID:20495806
Comparative genomics of cyclic-di-GMP signalling in bacteria: post-translational regulation and catalytic activity. PMID:20483912
Hub promiscuity in protein-protein interaction networks. PMID:20480050
PhenoFam-gene set enrichment analysis through protein structural information. PMID:20478033
The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PMID:20463976
Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition. PMID:20463972
A database for human Y chromosome protein data. PMID:20461156
Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. PMID:20459833
Computational prediction of the osmoregulation network in Synechococcus sp. WH8102. PMID:20459751
The mixed lineage nature of nitrogen transport and assimilation in marine eukaryotic phytoplankton: a case study of micromonas. PMID:20457585
Molecular modeling studies of Fatty acyl-CoA synthetase (FadD13) from Mycobacterium tuberculosis--a potential target for the development of antitubercular drugs. PMID:20454815
Computing biological functions using BioPsi, a formal description of biological processes based on elementary bricks of actions. PMID:20448138
Proteins required for lipopolysaccharide assembly in Escherichia coli form a transenvelope complex. PMID:20446753
Crystallization and preliminary crystallographic analysis of nosiheptide-resistance methyltransferase from Streptomyces actuosus in complex with SAM. PMID:20445264
Crystallization and preliminary crystallographic analysis of the central domain of Drosophila Dribble, a protein that is essential for ribosome biogenesis. PMID:20445256
Genome-wide in silico screen for CCCH-type zinc finger proteins of Trypanosoma brucei, Trypanosoma cruzi and Leishmania major. PMID:20444260
A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling. PMID:20444259
Brittle Culm 12, a dual-targeting kinesin-4 protein, controls cell-cycle progression and wall properties in rice. PMID:20444225
The molecular evolution of PL10 homologs. PMID:20438638
Signal processing for metagenomics: extracting information from the soup. PMID:20436876
Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach. PMID:20433736
Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. PMID:20433725
Meeting report: a workshop on Best Practices in Genome Annotation. PMID:20428316
Semantic integration of data on transcriptional regulation. PMID:20427517
Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins. PMID:20420672
Lysozymes in the animal kingdom. PMID:20413917
Marine metagenomics: new tools for the study and exploitation of marine microbial metabolism. PMID:20411118
Identification of DIM-7, a protein required to target the DIM-5 H3 methyltransferase to chromatin. PMID:20404183
Detecting genomic islands using bioinformatics approaches. PMID:20395967
Protein kinase A phosphorylation activates Vpr-induced cell cycle arrest during human immunodeficiency virus type 1 infection. PMID:20392842
Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii. PMID:20388224
De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. PMID:20386741
High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics. PMID:20383749
Genome-wide analysis of helicase gene family from rice and Arabidopsis: a comparison with yeast and human. PMID:20383562
Detection and architecture of small heat shock protein monomers. PMID:20383329
SpoIID-mediated peptidoglycan degradation is required throughout engulfment during Bacillus subtilis sporulation. PMID:20382772
Protein sequences classification by means of feature extraction with substitution matrices. PMID:20377887
Detection of locally over-represented GO terms in protein-protein interaction networks. PMID:20377456
CdnL, a member of the large CarD-like family of bacterial proteins, is vital for Myxococcus xanthus and differs functionally from the global transcriptional regulator CarD. PMID:20371514
Getting started in gene orthology and functional analysis. PMID:20361041
Mutation@A Glance: an integrative web application for analysing mutations from human genetic diseases. PMID:20360267
Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery. PMID:20356358
Genome-wide computational identification of WG/GW Argonaute-binding proteins in Arabidopsis. PMID:20338883
Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. PMID:20333304
The essentials of protein import in the degenerate mitochondrion of Entamoeba histolytica. PMID:20333239
Lethal protein produced in response to competition between sibling bacterial colonies. PMID:20308591
Defective nucleolar localization and dominant interfering properties of a parafibromin L95P missense mutant causing the hyperparathyroidism-jaw tumor syndrome. PMID:20304979
The expression of ELK transcription factors in adult DRG: Novel isoforms, antisense transcripts and upregulation by nerve damage. PMID:20304071
Transcriptome profiling of a toxic dinoflagellate reveals a gene-rich protist and a potential impact on gene expression due to bacterial presence. PMID:20300646
Interplay of heritage and habitat in the distribution of bacterial signal transduction systems. PMID:20237650
A genetic determinant in Streptococcus gordonii Challis encodes a peptide with activity similar to that of enterococcal sex pheromone cAM373, which facilitates intergeneric DNA transfer. PMID:20233933
Genome-wide analysis of primary auxin-responsive Aux/IAA gene family in maize (Zea mays. L.). PMID:20232157
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
The structure of the dust mite allergen Der p 7 reveals similarities to innate immune proteins. PMID:20226507
The manganese/iron-carboxylate proteins: what is what, where are they, and what can the sequences tell us? PMID:20225400
Proteomic analysis of tardigrades: towards a better understanding of molecular mechanisms by anhydrobiotic organisms. PMID:20224743
Characterization of potential allergens in fenugreek (Trigonella foenum-graecum) using patient sera and MS-based proteomic analysis. PMID:20219717
Transposases are the most abundant, most ubiquitous genes in nature. PMID:20215432
Dual coding in alternative reading frames correlates with intrinsic protein disorder. PMID:20212158
The structure of DinB from Geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily. PMID:20208147
Genomics and bioinformatics resources for crop improvement. PMID:20208064
Characterization of the two-protein complex in Escherichia coli responsible for lipopolysaccharide assembly at the outer membrane. PMID:20203010
GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis systems. PMID:20202206
Protein tyrosine O-glycosylation--a rather unexplored prokaryotic glycosylation system. PMID:20200052
Conservation and divergence of known apicomplexan transcriptional regulons. PMID:20199665
Predicting highly-connected hubs in protein interaction networks by QSAR and biological data descriptors. PMID:20198194
HNHDb: a database on pattern based classification of HNH domains reveals functional relevance of sequence patterns and domain associations. PMID:20198175
A primer on metagenomics. PMID:20195499
Visualization of multiple alignments, phylogenies and gene family evolution. PMID:20195253
Hidden Markov Models and their Applications in Biological Sequence Analysis. PMID:20190955
Siderophores are not involved in Fe(III) solubilization during anaerobic Fe(III) respiration by Shewanella oneidensis MR-1. PMID:20190086
Use of the plant defense protein osmotin to identify Fusarium oxysporum genes that control cell wall properties. PMID:20190074
Bacterial lifestyle in a deep-sea hydrothermal vent chimney revealed by the genome sequence of the thermophilic bacterium Deferribacter desulfuricans SSM1. PMID:20189949
Arabidopsis AtSerpin1, crystal structure and in vivo interaction with its target protease RESPONSIVE TO DESICCATION-21 (RD21). PMID:20181955
Expansion of the miRNA pathway in the hemipteran insect Acyrthosiphon pisum. PMID:20179251
Comparative analysis of fungal protein kinases and associated domains. PMID:20178650
Human carboxymethylenebutenolidase as a bioactivating hydrolase of olmesartan medoxomil in liver and intestine. PMID:20177059
The porcelain crab transcriptome and PCAD, the porcelain crab microarray and sequence database. PMID:20174471
Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A. PMID:20170513
A highly coordinated cell wall degradation machine governs spore morphogenesis in Bacillus subtilis. PMID:20159959
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
Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs. PMID:20157482
The abi proteins and their involvement in bacteriocin self-immunity. PMID:20154137
Practical application of bioinformatics by the multidisciplinary VIZIER consortium. PMID:20153379
Analysis of high-throughput sequencing and annotation strategies for phage genomes. PMID:20140207
Bioinformatics as a tool for assessing the quality of sub-cellular proteomic strategies and inferring functions of proteins: plant cell wall proteomics as a test case. PMID:20140071
Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. PMID:20140026
The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PMID:20126622
Sequence alignment reveals possible MAPK docking motifs on HIV proteins. PMID:20126615
Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances. PMID:20126523
Crystal structure of the first eubacterial Mre11 nuclease reveals novel features that may discriminate substrates during DNA repair. PMID:20122942
Comparative genomics reveals selective distribution and domain organization of FYVE and PX domain proteins across eukaryotic lineages. PMID:20122178
Novel candidate cancer genes identified by a large-scale cross-species comparative oncogenomics approach. PMID:20103622
Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function. PMID:20102603
Cooperativity within proximal phosphorylation sites is revealed from large-scale proteomics data. PMID:20100358
A systematic investigation of multiheme c-type cytochromes in prokaryotes. PMID:20084531
TollML: a database of toll-like receptor structural motifs. PMID:20084417
Expanding small-molecule functional metagenomics through parallel screening of broad-host-range cosmid environmental DNA libraries in diverse proteobacteria. PMID:20081001
Amot recognizes a juxtanuclear endocytic recycling compartment via a novel lipid binding domain. PMID:20080965
The imprinted retrotransposon-like gene PEG11 (RTL1) is expressed as a full-length protein in skeletal muscle from Callipyge sheep. PMID:20072617
The crystal structure and activity of a putative trypanosomal nucleoside phosphorylase reveal it to be a homodimeric uridine phosphorylase. PMID:20070944
The WUS homeobox-containing (WOX) protein family. PMID:20067590
Homologous over-extension: a challenge for iterative similarity searches. PMID:20064877
Microarray data analysis of gene expression evolution. PMID:20054404
Model-guided mutagenesis drives functional studies of human NHA2, implicated in hypertension. PMID:20053353
Characterization of proteins with wide-angle X-ray solution scattering (WAXS). PMID:20049539
Mago Nashi, Tsunagi/Y14, and Ranshi form a complex that influences oocyte differentiation in Drosophila melanogaster. PMID:20045686
Bioinformatic mapping and production of recombinant N-terminal domains of human cardiac ryanodine receptor 2. PMID:20045464
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. PMID:20043185
The C-terminal repeat domain of Spt5 plays an important role in suppression of Rad26-independent transcription coupled repair. PMID:20042611
A conformational switch in the scaffolding protein NHERF1 controls autoinhibition and complex formation. PMID:20042604
Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs. PMID:20042087
Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions. PMID:20042074
The evolutionary history of protein domains viewed by species phylogeny. PMID:20041107
Large-scale identification of odorant-binding proteins and chemosensory proteins from expressed sequence tags in insects. PMID:20034407
The genome of the amoeba symbiont "Candidatus Amoebophilus asiaticus" reveals common mechanisms for host cell interaction among amoeba-associated bacteria. PMID:20023027
Discovery and characterization of cadherin domains in Saccharophagus degradans 2-40. PMID:20023015
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. PMID:20021646
Genetic tools for the investigation of Roseobacter clade bacteria. PMID:20021642
High-resolution protein complexes from integrating genomic information with molecular simulation. PMID:20018738
Short paths in protein structure space originate in graph structure. PMID:20018710
The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes. PMID:20017931
Biochemical networks: the evolution of gene annotation. PMID:20016491
Identification of novel aspartic proteases from Strongyloides ratti and characterisation of their evolutionary relationships, stage-specific expression and molecular structure. PMID:20015380
Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PMID:20011109
THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves. PMID:20010837
Expression of BfrH, a putative siderophore receptor of Bordetella bronchiseptica, is regulated by iron, Fur1, and the extracellular function sigma factor EcfI. PMID:20008538
No Nogo66- and NgR-mediated inhibition of regenerating axons in the zebrafish optic nerve. PMID:20007473
The impact of long-distance horizontal gene transfer on prokaryotic genome size. PMID:20007373
Prediction of calcium-binding sites by combining loop-modeling with machine learning. PMID:20003365
RNRdb, a curated database of the universal enzyme family ribonucleotide reductase, reveals a high level of misannotation in sequences deposited to Genbank. PMID:19995434
Asymmetric cross-regulation between the nitrate-responsive NarX-NarL and NarQ-NarP two-component regulatory systems from Escherichia coli K-12. PMID:19968795
A robust and extracellular heme-containing peroxidase from Thermobifida fusca as prototype of a bacterial peroxidase superfamily. PMID:19967355
The S helix mediates signal transmission as a HAMP domain coiled-coil extension in the NarX nitrate sensor from Escherichia coli K-12. PMID:19966007
Functional diversity of ankyrin repeats in microbial proteins. PMID:19962898
Bactofilins, a ubiquitous class of cytoskeletal proteins mediating polar localization of a cell wall synthase in Caulobacter crescentus. PMID:19959992
Protein comparison at the domain architecture level. PMID:19958515
DNA-binding residues and binding mode prediction with binding-mechanism concerned models. PMID:19958487
Comparative study of protein-protein interaction observed in PolyGalacturonase-Inhibiting Proteins from Phaseolus vulgaris and Glycine max and PolyGalacturonase from Fusarium moniliforme. PMID:19958482
Genome-wide analysis of alternative splicing in cow: implications in bovine as a model for human diseases. PMID:19958474
The UCSC Genome Browser. PMID:19957273
Gene context analysis in the Integrated Microbial Genomes (IMG) data management system. PMID:19956731
Identification of the Schistosoma mansoni TNF-alpha receptor gene and the effect of human TNF-alpha on the parasite gene expression profile. PMID:19956564
Inferring protein function by domain context similarities in protein-protein interaction networks. PMID:19954509
Variations at the semiconserved glycine in the IQ domain consensus sequence have a major impact on Ca2+-dependent switching in calmodulin-IQ domain complexes. PMID:19954189
Evolution, ecology and the engineered organism: lessons for synthetic biology. PMID:19941672
Unique sequence features of the Human adenovirus 31 complete genomic sequence are conserved in clinical isolates. PMID:19939241
Detailed analysis of a contiguous 22-Mb region of the maize genome. PMID:19936048
Fission yeast Iec1-ino80-mediated nucleosome eviction regulates nucleotide and phosphate metabolism. PMID:19933844
Structural mechanism of abscisic acid binding and signaling by dimeric PYR1. PMID:19933100
Transport mechanism of a bacterial homologue of glutamate transporters. PMID:19924125
Crystallization and preliminary X-ray crystallographic analysis of gamma-carboxymucolactone decarboxylase from Sulfolobus solfataricus. PMID:19923750
Large-scale phosphoprotein analysis in Medicago truncatula roots provides insight into in vivo kinase activity in legumes. PMID:19923235
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. PMID:19923231
Structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis. PMID:19923209
The pheV phenylalanine tRNA gene Klebsiella pneumoniae clinical isolates is an integration hotspot for possible niche-adaptation genomic islands. PMID:19921332
ELM: the status of the 2010 eukaryotic linear motif resource. PMID:19920119
Horizontal gene transfer and diverse functional constrains within a common replication-partitioning system in Alphaproteobacteria: the repABC operon. PMID:19919719
GExplore: a web server for integrated queries of protein domains, gene expression and mutant phenotypes. PMID:19917126
Structural determinants of DNA binding by a P. falciparum ApiAP2 transcriptional regulator. PMID:19913037
Arrestin-mediated endocytosis of yeast plasma membrane transporters. PMID:19912579
Thalidomide attenuates nitric oxide-driven angiogenesis by interacting with soluble guanylyl cyclase. PMID:19912234
A threading-based method for the prediction of DNA-binding proteins with application to the human genome. PMID:19911048
MeMotif: a database of linear motifs in alpha-helical transmembrane proteins. PMID:19910368
Biochemical analysis of the biosynthetic pathway of an anticancer tetracycline SF2575. PMID:19908837
GTP-dependent structural rearrangement of the eRF1:eRF3 complex and eRF3 sequence motifs essential for PABP binding. PMID:19906736
MicrobesOnline: an integrated portal for comparative and functional genomics. PMID:19906701
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
dbDEPC: a database of differentially expressed proteins in human cancers. PMID:19900968
The MiST2 database: a comprehensive genomics resource on microbial signal transduction. PMID:19900966
The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus. PMID:19895685
The comprehensive microbial resource. PMID:19892825
MEROPS: the peptidase database. PMID:19892822
Anti-schistosomal intervention targets identified by lifecycle transcriptomic analyses. PMID:19885392
Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster. PMID:19885390
Nitrogen recycling and nutritional provisioning by Blattabacterium, the cockroach endosymbiont. PMID:19880743
Discovery and characterization of three new Escherichia coli septal ring proteins that contain a SPOR domain: DamX, DedD, and RlpA. PMID:19880599
Identification and characterization of a novel deoxyhypusine synthase in Leishmania donovani. PMID:19880510
PepX: a structural database of non-redundant protein-peptide complexes. PMID:19880386
Topological analysis of a haloacid permease of a Burkholderia sp. bacterium with a PhoA-LacZ reporter. PMID:19878597
The integrated microbial genomes system: an expanding comparative analysis resource. PMID:19864254
Role of a novel disulfide bridge within the all-beta fold of soluble Rieske proteins. PMID:19862563
Structural genomics target selection for the New York consortium on membrane protein structure. PMID:19859826
PROSITE, a protein domain database for functional characterization and annotation. PMID:19858104
PlnTFDB: updated content and new features of the plant transcription factor database. PMID:19858103
PDBe: Protein Data Bank in Europe. PMID:19858099
Fungal PDR transporters: Phylogeny, topology, motifs and function. PMID:19857594
The crystal structure of the novobiocin biosynthetic enzyme NovP: the first representative structure for the TylF O-methyltransferase superfamily. PMID:19857499
SALAD database: a motif-based database of protein annotations for plant comparative genomics. PMID:19854933
Physical and genetic interactions of yeast Cwc21p, an ortholog of human SRm300/SRRM2, suggest a role at the catalytic center of the spliceosome. PMID:19854871
ProPhylER: a curated online resource for protein function and structure based on evolutionary constraint analyses. PMID:19846609
Predicting meiotic pathways in human fetal oogenesis. PMID:19846598
Transcriptome profiling defines a novel regulon modulated by the LysR-type transcriptional regulator MexT in Pseudomonas aeruginosa. PMID:19846594
REBASE--a database for DNA restriction and modification: enzymes, genes and genomes. PMID:19846593
Pathema: a clade-specific bioinformatics resource center for pathogen research. PMID:19843611
The evolution of RecD outside of the RecBCD complex. PMID:19841849
Genome-wide identification of NBS-encoding resistance genes in Brassica rapa. PMID:19838736
Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human. PMID:19833706
A novel bipartite double-stranded RNA Mycovirus from the white root rot Fungus Rosellinia necatrix: molecular and biological characterization, taxonomic considerations, and potential for biological control. PMID:19828620
Significant speedup of database searches with HMMs by search space reduction with PSSM family models. PMID:19828575
Reconstitution of human claspin-mediated phosphorylation of Chk1 by the ATR (ataxia telangiectasia-mutated and rad3-related) checkpoint kinase. PMID:19828454
XML-based approaches for the integration of heterogeneous bio-molecular data. PMID:19828083
Origin and evolution of the Notch signalling pathway: an overview from eukaryotic genomes. PMID:19825158
Human aldehyde dehydrogenase genes: alternatively spliced transcriptional variants and their suggested nomenclature. PMID:19823103
Plasmid-mediated quinolone resistance: a multifaceted threat. PMID:19822894
A thiolase of Mycobacterium tuberculosis is required for virulence and production of androstenedione and androstadienedione from cholesterol. PMID:19822655
Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades. PMID:19821996
TonB-dependent transporters and their occurrence in cyanobacteria. PMID:19821963
Plant MetGenMAP: an integrative analysis system for plant systems biology. PMID:19819981
The otubain YOD1 is a deubiquitinating enzyme that associates with p97 to facilitate protein dislocation from the ER. PMID:19818707
Different gene regulation strategies revealed by analysis of binding motifs. PMID:19815308
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
Bioinformatics construction of the human cell surfaceome. PMID:19805368
Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. PMID:19805315
Structural plasticity and catalysis regulation of a thermosensor histidine kinase. PMID:19805278
Universal architecture of bacterial chemoreceptor arrays. PMID:19805102
Bioinformatics and structural characterization of a hypothetical protein from Streptococcus mutans: implication of antibiotic resistance. PMID:19798411
Characterization and structure of the manganese-responsive transcriptional regulator ScaR. PMID:19795834
Exploration of uncharted regions of the protein universe. PMID:19787035
INTS3 controls the hSSB1-mediated DNA damage response. PMID:19786574
Fine-grained annotation and classification of de novo predicted LTR retrotransposons. PMID:19786494
Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment. PMID:19776767
Early-arriving Syp1p and Ede1p function in endocytic site placement and formation in budding yeast. PMID:19776351
Changes in reflectin protein phosphorylation are associated with dynamic iridescence in squid. PMID:19776150
Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5. PMID:19775431
HHsvm: fast and accurate classification of profile-profile matches identified by HHsearch. PMID:19773335
Solution structure and phylogenetics of Prod1, a member of the three-finger protein superfamily implicated in salamander limb regeneration. PMID:19771161
Reproducing the manual annotation of multiple sequence alignments using a SVM classifier. PMID:19770262
3D-footprint: a database for the structural analysis of protein-DNA complexes. PMID:19767616
Complete genome sequence of the ethanol producer Zymomonas mobilis NCIMB 11163. PMID:19767433
The novel polysaccharide deacetylase homologue Pdi contributes to virulence of the aquatic pathogen Streptococcus iniae. PMID:19762441
A potentially novel overlapping gene in the genomes of Israeli acute paralysis virus and its relatives. PMID:19761605
Phylogenetic analysis of the NEEP21/calcyon/P19 family of endocytic proteins: evidence for functional evolution in the vertebrate CNS. PMID:19760447
Something old, something new, something borrowed; how the thermoacidophilic archaeon Sulfolobus solfataricus responds to oxidative stress. PMID:19759909
Crystal structure of a mucus-binding protein repeat reveals an unexpected functional immunoglobulin binding activity. PMID:19758995
Extraction of human kinase mutations from literature, databases and genotyping studies. PMID:19758464
Structural and functional constraints in the evolution of protein families. PMID:19756040
A CAAX motif can compensate for the PH domain of Num1 for cortical dynein attachment. PMID:19755860
In planta mutagenesis determines the functional regions of the wheat puroindoline proteins. PMID:19752217
Cyclic-di-GMP-binding CRP-like protein: a spectacular new role for a veteran signal transduction actor. PMID:19749051
The amoebal MAP kinase response to Legionella pneumophila is regulated by DupA. PMID:19748467
HMMCONVERTER 1.0: a toolbox for hidden Markov models. PMID:19740770
Automated inference of molecular mechanisms of disease from amino acid substitutions. PMID:19734154
Legume transcription factor genes: what makes legumes so special? PMID:19726573
UFO: a web server for ultra-fast functional profiling of whole genome protein sequences. PMID:19725959
Template-based and free modeling by RAPTOR++ in CASP8. PMID:19722267
Comparative analyses of plant transcription factor databases. PMID:19721806
An energetic representation of protein architecture that is independent of primary and secondary structure. PMID:19720035
Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. PMID:19717792
The ArsR repressor mediates arsenite-dependent regulation of arsenate respiration and detoxification operons of Shewanella sp. strain ANA-3. PMID:19717602
Pushing structural information into the yeast interactome by high-throughput protein docking experiments. PMID:19714207
Gene mapping and phylogenetic analysis of the complete genome from 30 single-stranded RNA male-specific coliphages (family Leviviridae). PMID:19710143
Caenorhabditis elegans BAH-1 is a DUF23 protein expressed in seam cells and required for microbial biofilm binding to the cuticle. PMID:19707590
A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528. PMID:19703286
Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes. PMID:19689787
Self-enhanced accumulation of FtsN at Division Sites and Roles for Other Proteins with a SPOR domain (DamX, DedD, and RlpA) in Escherichia coli cell constriction. PMID:19684127
The Anabaena sensory rhodopsin transducer defines a novel superfamily of prokaryotic small-molecule binding domains. PMID:19682383
Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin. PMID:19678920
Generation and analysis of expressed sequence tags from leaf and root of Withania somnifera (Ashwgandha). PMID:19669665
5' and 3' end modifications of spliceosomal RNAs in Plasmodium falciparum. PMID:19669595
Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks. PMID:19667081
Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels. PMID:19656385
Structure and function of Bacillus subtilis YphP, a prokaryotic disulfide isomerase with a CXC catalytic motif. PMID:19653655
Local combinational variables: an approach used in DNA-binding helix-turn-helix motif prediction with sequence information. PMID:19651875
Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation. PMID:19640978
Cloning, expression, and characterization of a peculiar choline-binding beta-galactosidase from Streptococcus mitis. PMID:19633119
The paralogous genes RADICAL-INDUCED CELL DEATH1 and SIMILAR TO RCD ONE1 have partially redundant functions during Arabidopsis development. PMID:19625634
Diversity and dispersal of a ubiquitous protein family: acyl-CoA dehydrogenases. PMID:19625492
Molecular geometry of CsrA (RsmA) binding to RNA and its implications for regulated expression. PMID:19619561
The Schistosoma japonicum genome reveals features of host-parasite interplay. PMID:19606140
ProteinArchitect: protein evolution above the sequence level. PMID:19603068
Benefits of structural genomics for drug discovery research. PMID:19594422
Hmrbase: a database of hormones and their receptors. PMID:19589147
Exon 6 of human JAG1 encodes a conserved structural unit. PMID:19586525
KlAft, the Kluyveromyces lactis ortholog of Aft1 and Aft2, mediates activation of iron-responsive transcription through the PuCACCC Aft-type sequence. PMID:19581449
Molecular cloning and characterization of five genes encoding pentatricopeptide repeat proteins from Upland cotton (Gossypium hirsutum L.). PMID:19578975
Biological insights from structures of two-component proteins. PMID:19575571
Remote homology between Munc13 MUN domain and vesicle tethering complexes. PMID:19563813
FACS-assisted microarray profiling implicates novel genes and pathways in zebrafish gastrointestinal tract development. PMID:19563808
A membrane-bound matrix-metalloproteinase from Nicotiana tabacum cv. BY-2 is induced by bacterial pathogens. PMID:19563670
NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. PMID:19563654
Rodent and nonrodent malaria parasites differ in their phospholipid metabolic pathways. PMID:19561325
Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. PMID:19561200
Computational analysis of the interaction between transcription factors and the predicted secreted proteome of the yeast Kluyveromyces lactis. PMID:19555482
Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3. PMID:19553194
Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function. PMID:19546170
B7-H3 is a potent inhibitor of human T-cell activation: No evidence for B7-H3 and TREML2 interaction. PMID:19544488
FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci. PMID:19542150
7TMRmine: a Web server for hierarchical mining of 7TMR proteins. PMID:19538753
Visualising biological data: a semantic approach to tool and database integration. PMID:19534744
Proteins recruited by SH3 domains of Ruk/CIN85 adaptor identified by LC-MS/MS. PMID:19531213
LytM-domain factors are required for daughter cell separation and rapid ampicillin-induced lysis in Escherichia coli. PMID:19525345
PSI-2: structural genomics to cover protein domain family space. PMID:19523904
The Thermoplasma acidophilum LplA-LplB complex defines a new class of bipartite lipoate-protein ligases. PMID:19520844
The repertoire of G-protein-coupled receptors in Xenopus tropicalis. PMID:19508718
Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance. PMID:19506028
Rapid detection, classification and accurate alignment of up to a million or more related protein sequences. PMID:19505947
Fido, a novel AMPylation domain common to fic, doc, and AvrB. PMID:19503829
Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees. PMID:19503607
Proteome-wide prediction of signal flow direction in protein interaction networks based on interacting domains. PMID:19502588
DASMIweb: online integration, analysis and assessment of distributed protein interaction data. PMID:19502495
Generation and analysis of transcriptomic resources for a model system on the rise: the sea anemone Aiptasia pallida and its dinoflagellate endosymbiont. PMID:19500365
ProGMap: an integrated annotation resource for protein orthology. PMID:19494185
The evolution of nuclear auxin signalling. PMID:19493348
Plant lectins: the ties that bind in root symbiosis and plant defense. PMID:19488786
Structure-based phylogeny as a diagnostic for functional characterization of proteins with a cupin fold. PMID:19478949
Domain-oriented edge-based alignment of protein interaction networks. PMID:19477994
seeMotif: exploring and visualizing sequence motifs in 3D structures. PMID:19477961
Biases in Drosophila melanogaster protein trap screens. PMID:19476619
PLecDom: a program for identification and analysis of plant lectin domains. PMID:19474338
Genome sequence of the recombinant protein production host Pichia pastoris. PMID:19465926
spr1630 is responsible for the lethality of clpX mutations in Streptococcus pneumoniae. PMID:19465654
RHYTHM--a server to predict the orientation of transmembrane helices in channels and membrane-coils. PMID:19465378
Cytosolic phospholipase A2: a member of the signalling pathway of a new G protein alpha subunit in Sporothrix schenckii. PMID:19454031
In vitro nuclear interactome of the HIV-1 Tat protein. PMID:19454010
The High Throughput Sequence Annotation Service (HT-SAS) - the shortcut from sequence to true Medline words. PMID:19445703
PhyloPars: estimation of missing parameter values using phylogeny. PMID:19443453
A eukaryote-like cardiolipin synthase is present in Streptomyces coelicolor and in most actinobacteria. PMID:19439403
Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors. PMID:19436720
COMPASS server for homology detection: improved statistical accuracy, speed and functionality. PMID:19435884
The Rho GTPase inactivation domain in Vibrio cholerae MARTX toxin has a circularly permuted papain-like thiol protease fold. PMID:19434753
TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences. PMID:19429695
Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes. PMID:19429624
Insights into the evolution of the snail superfamily from metazoan wide molecular phylogenies and expression data in annelids. PMID:19426549
TGF-beta signaling proteins and the Protein Ontology. PMID:19426460
A novel WRKY-like protein involved in transcriptional activation of cyst wall protein genes in Giardia lamblia. PMID:19423705
varDB: common ground for a shifting landscape. PMID:19423393
DASMI: exchanging, annotating and assessing molecular interaction data. PMID:19420069
webPRC: the Profile Comparer for alignment-based searching of public domain databases. PMID:19420063
PPISearch: a web server for searching homologous protein-protein interactions across multiple species. PMID:19417070
ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii. PMID:19409111
Regulation of quinone oxidoreductase by the redox-sensing transcriptional regulator QorR in Corynebacterium glutamicum. PMID:19403527
Protein-protein interaction databases: keeping up with growing interactomes. PMID:19403463
Human ATP-binding cassette (ABC) transporter family. PMID:19403462
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
Exploiting structural classifications for function prediction: towards a domain grammar for protein function. PMID:19398323
Impact of pretreated Switchgrass and biomass carbohydrates on Clostridium thermocellum ATCC 27405 cellulosome composition: a quantitative proteomic analysis. PMID:19384422
Structure and mechanism of a eukaryotic FMN adenylyltransferase. PMID:19375431
A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. PMID:19373234
Conservation of core gene expression in vertebrate tissues. PMID:19371447
To investigate protein evolution by detecting suppressed epitope structures. PMID:19365646
dndDB: a database focused on phosphorothioation of the DNA backbone. PMID:19357771
ModLink+: improving fold recognition by using protein-protein interactions. PMID:19357100
Basal expression studies of cystatins during specific growth stages of wheat spikes for defining their possible role in differential and stage dependent immunity against Karnal bunt (Tilletia indica). PMID:19347606
The origin recognition complex protein family. PMID:19344485
Bves: ten years after. PMID:19337975
Phylogenetic analysis, subcellular localization, and expression patterns of RPD3/HDA1 family histone deacetylases in plants. PMID:19327164
A new genomic resource dedicated to wood formation in Eucalyptus. PMID:19327132
Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes. PMID:19321712
CPDadh: a new peptidase family homologous to the cysteine protease domain in bacterial MARTX toxins. PMID:19309740
Aegerolysins: structure, function, and putative biological role. PMID:19309687
The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases. PMID:19296857
Identification of Archaea-specific chemotaxis proteins which interact with the flagellar apparatus. PMID:19291314
Energetic profiling of protein folds. PMID:19289211
HHP1 is involved in osmotic stress sensitivity in Arabidopsis. PMID:19286917
The action of key factors in protein evolution at high temporal resolution. PMID:19279682
Rhomboid protease dynamics and lipid interactions. PMID:19278654
Identification of coevolving residues and coevolution potentials emphasizing structure, bond formation and catalytic coordination in protein evolution. PMID:19274093
An Ehrlichia chaffeensis tandem repeat protein interacts with multiple host targets involved in cell signaling, transcriptional regulation, and vesicle trafficking. PMID:19273555
A mouse chromosome 4 balancer ENU-mutagenesis screen isolates eleven lethal lines. PMID:19267930
Genome-wide analysis of Carica papaya reveals a small NBS resistance gene family. PMID:19263082
Protein structure prediction on the Web: a case study using the Phyre server. PMID:19247286
NMR structural analysis of DNA recognition by a novel Myb1 DNA-binding domain in the protozoan parasite Trichomonas vaginalis. PMID:19246540
Crystal structures of YkuI and its complex with second messenger cyclic Di-GMP suggest catalytic mechanism of phosphodiester bond cleavage by EAL domains. PMID:19244251
Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway. PMID:19232106
Protein function annotation by homology-based inference. PMID:19226439
Sequence-based feature prediction and annotation of proteins. PMID:19226438
TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. PMID:19210774
Biofilter: a knowledge-integration system for the multi-locus analysis of genome-wide association studies. PMID:19209715
GAIA: a gram-based interaction analysis tool--an approach for identifying interacting domains in yeast. PMID:19208164
Evolutionarily evolved discriminators in the 3-TPR domain of the Toc64 family involved in protein translocation at the outer membrane of chloroplasts and mitochondria. PMID:19198901
A comparative chemogenomics strategy to predict potential drug targets in the metazoan pathogen, Schistosoma mansoni. PMID:19198654
Rational stabilization of enzymes by computational redesign of surface charge-charge interactions. PMID:19196981
DETORQUEO, QUIRKY, and ZERZAUST represent novel components involved in organ development mediated by the receptor-like kinase STRUBBELIG in Arabidopsis thaliana. PMID:19180193
Genome-wide analysis of chimpanzee genes with premature termination codons. PMID:19178713
Temporal global expression data reveal known and novel salicylate-impacted processes and regulators mediating powdery mildew growth and reproduction on Arabidopsis. PMID:19176722
The Thermotoga maritima Trk potassium transporter--from frameshift to function. PMID:19168617
Single-molecule fluorescence studies of a PH domain: new insights into the membrane docking reaction. PMID:19167305
Generation and analysis of expressed sequence tags from six developing xylem libraries in Pinus radiata D. Don. PMID:19159482
Domain mobility in proteins: functional and evolutionary implications. PMID:19151098
Jalview Version 2--a multiple sequence alignment editor and analysis workbench. PMID:19151095
New genes of Xanthomonas citri subsp. citri involved in pathogenesis and adaptation revealed by a transposon-based mutant library. PMID:19149882
The 2008 update of the Aspergillus nidulans genome annotation: a community effort. PMID:19146970
Diversity of serine hydrolase activities of unchallenged and botrytis-infected Arabidopsis thaliana. PMID:19136719
Protein structure homology modeling using SWISS-MODEL workspace. PMID:19131951
Mesothelin, Stereocilin, and Otoancorin are predicted to have superhelical structures with ARM-type repeats. PMID:19128473
Identification of direct residue contacts in protein-protein interaction by message passing. PMID:19116270
Inferring selection on amino acid preference in protein domains. PMID:19095755
MucR, a novel membrane-associated regulator of alginate biosynthesis in Pseudomonas aeruginosa. PMID:19088322
The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program. PMID:19084081
Improved prediction of malaria degradomes by supervised learning with SVM and profile kernel. PMID:19057851
Evolutionary diversification of plant shikimate kinase gene duplicates. PMID:19057671
GeneDistiller--distilling candidate genes from linkage intervals. PMID:19057649
A bioinformatician's guide to metagenomics. PMID:19052320
Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PMID:19043537
The Protein Model Portal. PMID:19037750
RICD: a rice indica cDNA database resource for rice functional genomics. PMID:19036133
Evolutionary origin and genomic organisation of runt-domain containing genes in arthropods. PMID:19032778
The three fungal transmembrane nuclear pore complex proteins of Aspergillus nidulans are dispensable in the presence of an intact An-Nup84-120 complex. PMID:19019988
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
M148R and M149R are two virulence factors for myxoma virus pathogenesis in the European rabbit. PMID:19019281
A functional proteomics approach links the ubiquitin-related modifier Urm1 to a tRNA modification pathway. PMID:19017811
Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site. PMID:19014591
Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors. PMID:19010806
Genome pool strategy for structural coverage of protein families. PMID:19000818
A unique cell division machinery in the Archaea. PMID:18987308
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
Bionemo: molecular information on biodegradation metabolism. PMID:18986994
LRRML: a conformational database and an XML description of leucine-rich repeats (LRRs). PMID:18986514
ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes. PMID:18984624
CDD: specific functional annotation with the Conserved Domain Database. PMID:18984618
GtRNAdb: a database of transfer RNA genes detected in genomic sequence. PMID:18984615
SMART 6: recent updates and new developments. PMID:18978020
Identification of a 2 Mb human ortholog of Drosophila eyes shut/spacemaker that is mutated in patients with retinitis pigmentosa. PMID:18976725
Modifier effects between regulatory and protein-coding variation. PMID:18974877
SysZNF: the C2H2 zinc finger gene database. PMID:18974185
CentrosomeDB: a human centrosomal proteins database. PMID:18971254
3did Update: domain-domain and peptide-mediated interactions of known 3D structure. PMID:18953040
Fusion and fission of genes define a metric between fungal genomes. PMID:18949021
The National Center for Biotechnology Information's Protein Clusters Database. PMID:18940865
Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics. PMID:18940860
InterPro: the integrative protein signature database. PMID:18940856
Insights into corn genes derived from large-scale cDNA sequencing. PMID:18937034
The SWISS-MODEL Repository and associated resources. PMID:18931379
A novel class of modular transporters for vitamins in prokaryotes. PMID:18931129
The genome of the simian and human malaria parasite Plasmodium knowlesi. PMID:18843368
CC+: a relational database of coiled-coil structures. PMID:18842638
MetaSim: a sequencing simulator for genomics and metagenomics. PMID:18841204
JAIL: a structure-based interface library for macromolecules. PMID:18832369
Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes. PMID:18828897
Suppression of DeltabipA phenotypes in Escherichia coli by abolishment of pseudouridylation at specific sites on the 23S rRNA. PMID:18820021
Structure-guided comparative analysis of proteins: principles, tools, and applications for predicting function. PMID:18818720
GabiPD: the GABI primary database--a plant integrative 'omics' database. PMID:18812395
The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism. PMID:18806794
C2H2 zinc finger genes of the Gli, Zic, KLF, SP, Wilms' tumour, Huckebein, Snail, Ovo, Spalt, Odd, Blimp-1, Fez and related gene families from Branchiostoma floridae. PMID:18795322
The three adaptation systems of Bacillus subtilis chemotaxis. PMID:18774298
Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity. PMID:18769675
Integrating expression data with domain interaction networks. PMID:18710874
Vaccinia virus proteins A52 and B14 Share a Bcl-2-like fold but have evolved to inhibit NF-kappaB rather than apoptosis. PMID:18704168
A novel CHHC Zn-finger domain found in spliceosomal proteins and tRNA modifying enzymes. PMID:18703587
A protein domain-based interactome network for C. elegans early embryogenesis. PMID:18692475
Nucleus-specific importin alpha proteins and nucleoporins regulate protein import and nuclear division in the binucleate Tetrahymena thermophila. PMID:18676955
Integrating biological data--the Distributed Annotation System. PMID:18673527
Whole proteome identification of plant candidate G-protein coupled receptors in Arabidopsis, rice, and poplar: computational prediction and in-vivo protein coupling. PMID:18671868
Streptococcus iniae M-like protein contributes to virulence in fish and is a target for live attenuated vaccine development. PMID:18665241
Experience using web services for biological sequence analysis. PMID:18621748
Sequence analysis of GerM and SpoVS, uncharacterized bacterial 'sporulation' proteins with widespread phylogenetic distribution. PMID:18562273
Structures and functional implications of an AMP-binding cystathionine beta-synthase domain protein from a hyperthermophilic archaeon. PMID:18513746
GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways. PMID:18511460
cpRAS: a novel circularly permuted RAS-like GTPase domain with a highly scattered phylogenetic distribution. PMID:18510733
Life-cycle and genome of OtV5, a large DNA virus of the pelagic marine unicellular green alga Ostreococcus tauri. PMID:18509524
The small ubiquitin-like modifier (SUMO) and SUMO-conjugating system of Chlamydomonas reinhardtii. PMID:18493050
A novel pathway of intercellular signalling in Bacillus subtilis involves a protein with similarity to a component of type III secretion channels. PMID:18485064
Prediction of interacting single-stranded RNA bases by protein-binding patterns. PMID:18452949
DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture. PMID:18411203
Genome-wide detection of serpentine receptor-like proteins in malaria parasites. PMID:18365025
Orphan SelD proteins and selenium-dependent molybdenum hydroxylases. PMID:18289380
Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. PMID:18263724 -
Pfam: clans, web tools and services
PubMed citations: 1012.
1012 articles citing: Pfam: clans, web tools and services
Identification and Comprehensive Ggenome-Wide Analysis of Glutathione S-Transferase Gene Family in Sweet Cherry (Prunus avium) and Their Expression Profiling Reveals a Likely Role in Anthocyanin Accumulation. PMID:35903236
Systematic in silico discovery of novel solute carrier-like proteins from proteomes. PMID:35901096
Evolutionary and Integrative Analysis of Gibberellin-Dioxygenase Gene Family and Their Expression Profile in Three Rosaceae Genomes (F. vesca, P. mume, and P. avium) Under Phytohormone Stress. PMID:35874024
MRTF specifies a muscle-like contractile module in Porifera. PMID:35840552
Engineering and screening of novel β-1,3-xylanases with desired hydrolysate type by optimized ancestor sequence reconstruction and data mining. PMID:35832630
Loci underlying leaf agronomic traits identified by re-sequencing celery accessions based on an assembled genome. PMID:35784787
Identification and Defensive Characterization of PmCYP720B11v2 from Pinus massoniana. PMID:35743081
Integrative Analysis of the GRAS Genes From Chinese White Pear (Pyrus bretschneideri): A Critical Role in Leaf Regeneration. PMID:35734253
Chromosome-scale genome assembly of an important medicinal plant honeysuckle. PMID:35610245
Fine-tuning the transcriptional regulatory model of adaptation response to phosphate stress in maize (Zea mays L.). PMID:35592478
Transcriptome Profiles of IncRNA and mRNA Highlight the Role of Ferroptosis in Chronic Neuropathic Pain With Memory Impairment. PMID:35547819
RNA Sequencing of Cardiac in a Rat Model Uncovers Potential Target LncRNA of Diabetic Cardiomyopathy. PMID:35495145
Genome-Wide Identification and Functional Characterization of the Chloride Channel TaCLC Gene Family in Wheat (Triticum aestivum L.). PMID:35368658
Identification of the LOX Gene Family in Peanut and Functional Characterization of AhLOX29 in Drought Tolerance. PMID:35356112
Knowledge-Based Unfolded State Model for Protein Design. PMID:35298824
LncRNA-miRNA-mRNA Network Analysis Reveals the Potential Biomarkers in Crohn's Disease Rats Treated with Herb-Partitioned Moxibustion. PMID:35282268
Identification and expression analysis of the PtGATL genes under different nitrogen and carbon dioxide treatments in Populus trichocarpa. PMID:35223353
Unraveling the Genome Sequence of Plant Growth Promoting Aspergillus niger (CSR3) Provides Insight into the Synthesis of Secondary Metabolites and Its Comparative Genomics. PMID:35205861
Molecular characterization of the serotonergic transporter from the cestode Echinococcus granulosus: pharmacology and potential role in the nervous system. PMID:35169884
Differential microRNA expression profile in blood of children with Down syndrome suggests a role in immunological dysfunction. PMID:35060072
Genome-wide identification and expression analysis of calmodulin and calmodulin-like genes in wheat (Triticum aestivum L.). PMID:35034573
Chromosome-level genome assembly of Bactrocera dorsalis reveals its adaptation and invasion mechanisms. PMID:35017661
Resveratrol inhibits cell apoptosis by suppressing long noncoding RNA (lncRNA) XLOC_014869 during lipopolysaccharide-induced acute lung injury in rats. PMID:34992821
Novel Picornavirus Detected in Wild Deer: Identification, Genomic Characterisation, and Prevalence in Australia. PMID:34960681
High Molecular Weight Kininogen: A Review of the Structural Literature. PMID:34948166
Comprehensive Analysis of Arabinogalactan Protein-Encoding Genes Reveals the Involvement of Three BrFLA Genes in Pollen Germination in Brassica rapa. PMID:34884948
YhdP, TamB, and YdbH Are Redundant but Essential for Growth and Lipid Homeostasis of the Gram-Negative Outer Membrane. PMID:34781743
Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity. PMID:34773106
Characterization of a new type of neuronal 5-HT G- protein coupled receptor in the cestode nervous system. PMID:34762657
Genome-wide identification and expression analysis of the JAZ gene family in turnip. PMID:34716392
Genome-wide identification, classification, and expression analysis of the JmjC domain-containing histone demethylase gene family in birch. PMID:34711171
Global Transcriptome Characterization and Assembly of the Thermophilic Ascomycete Chaetomium thermophilum. PMID:34680944
Genome-wide identification of FRK genes in Populus trichocarpa and their expression under different nitrogen treatments. PMID:34616114
Genome-wide analysis of the maize superoxide dismutase (SOD) gene family reveals important roles in drought and salt responses. PMID:34606562
Sensory Perception in Bacterial Cyclic Diguanylate Signal Transduction. PMID:34606374
Complete Genomic Characterization and Identification of Saccharomycopsisphalluae sp. nov., a Novel Pathogen Causes Yellow Rot Disease on Phallus rubrovolvatus. PMID:34575745
Genome-wide identification and characterization of bZIP transcription factors and their expression profile under abiotic stresses in Chinese pear (Pyrus bretschneideri). PMID:34503442
Genome Identification and Expression Profiles in Response to Nitrogen Treatment Analysis of the Class I CCoAOMT Gene Family in Populus. PMID:34410559
The evolutionary history of topological variations in the CPA/AT transporters. PMID:34403419
Large-scale computational discovery and analysis of virus-derived microbial nanocompartments. PMID:34362927
Comparative transcriptome analysis reveals regulatory network and regulators associated with proanthocyanidin accumulation in persimmon. PMID:34325657
Bioinformatics analysis of PAE family in Populus trichocarpa and responsiveness to carbon and nitrogen treatment. PMID:34295610
Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling. PMID:34285211
Transcriptome profiling of the diaphragm in a controlled mechanical ventilation model reveals key genes involved in ventilator-induced diaphragmatic dysfunction. PMID:34172008
Genome-wide identification and analysis of class III peroxidases in Betula pendula. PMID:33932996
Fasciola gigantica-Derived Excretory-Secretory Products Alter the Expression of mRNAs, miRNAs, lncRNAs, and circRNAs Involved in the Immune Response and Metabolism in Goat Peripheral Blood Mononuclear Cells. PMID:33912180
Use of RNA Sequencing to Perform Comprehensive Analysis of Long Noncoding RNA Expression Profiles in Macrophages Infected with Trichosporon asahii. PMID:33877524
Computational characterizations of GDP-mannose 4,6-dehydratase (NoeL) Rhizobial proteins. PMID:33837815
Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis. PMID:33791429
Integrated microRNA and transcriptome profiling reveal key miRNA-mRNA interaction pairs associated with seed development in Tartary buckwheat (Fagopyrum tataricum). PMID:33750309
Genome-wide analysis of UGDH genes in Populus trichocarpa and responsiveness to nitrogen treatment. PMID:33732570
Genome-wide identification and expression analysis of ADP-ribosylation factors associated with biotic and abiotic stress in wheat (Triticum aestivum L.). PMID:33717696
Genome-Wide Identification and Characterization of Wheat 14-3-3 Genes Unravels the Role of TaGRF6-A in Salt Stress Tolerance by Binding MYB Transcription Factor. PMID:33673010
Biochemical characterisation of a collagenase from Bacillus cereus strain Q1. PMID:33603127
ProdMX: Rapid query and analysis of protein functional domain based on compressed sparse matrices. PMID:33335686
Genome-Wide Analysis of Heat Shock Transcription Factors in Ziziphus jujuba Identifies Potential Candidates for Crop Improvement Under Abiotic Stress. PMID:33244672
Evaluating the number of different genomes in a metagenome by means of the compositional spectra approach. PMID:33156862
Pfam: The protein families database in 2021. PMID:33125078
Identification and Expression of the Multidrug and Toxic Compound Extrusion (MATE) Gene Family in Capsicum annuum and Solanum tuberosum. PMID:33120967
De novo transcriptome assembly from the gonads of a scleractinian coral, Euphyllia ancora: molecular mechanisms underlying scleractinian gametogenesis. PMID:33087060
Identification and functional analysis of the CorA/MGT/MRS2-type magnesium transporter in banana. PMID:33001980
Increased c-di-GMP Levels Lead to the Production of Alginates of High Molecular Mass in Azotobacter vinelandii. PMID:32989088
Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) gene family in wheat (Triticum aestivum L.). PMID:32928120
Evolution and Expression of the Membrane Attack Complex and Perforin Gene Family in the Poaceae. PMID:32785137
Dual lysine and N-terminal acetyltransferases reveal the complexity underpinning protein acetylation. PMID:32633465
Comparative genomics of four strains of the edible brown alga, Cladosiphon okamuranus. PMID:32586267
Knock-out of TERMINAL FLOWER 1 genes altered flowering time and plant architecture in Brassica napus. PMID:32429836
A High-Quality Genome Sequence of Model Legume Lotus japonicus (MG-20) Provides Insights into the Evolution of Root Nodule Symbiosis. PMID:32365501
Characterization of DNA methylation variations during fruit development and ripening of Vitis vinifera (cv. 'Fujiminori'). PMID:32255927
Genomic Features of Cladobotryum dendroides, Which Causes Cobweb Disease in Edible Mushrooms, and Identification of Genes Related to Pathogenicity and Mycoparasitism. PMID:32245129
Comparison of Arachis monticola with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut. PMID:32099754
Analysis of Terpene Synthase Family Genes in Camellia sinensis with an Emphasis on Abiotic Stress Conditions. PMID:31969641
Characterization of Venom Components and Their Phylogenetic Properties in Some Aculeate Bumblebees and Wasps. PMID:31947554
ZFP628 Is a TAF4b-Interacting Transcription Factor Required for Mouse Spermiogenesis. PMID:31932482
GO2Vec: transforming GO terms and proteins to vector representations via graph embeddings. PMID:31874639
The persimmon (Diospyros oleifera Cheng) genome provides new insights into the inheritance of astringency and ancestral evolution. PMID:31871686
Emergence and Evolution of ERM Proteins and Merlin in Metazoans. PMID:31851361
Genome-wide identification and expression analysis of the StSWEET family genes in potato (Solanum tuberosum L.). PMID:31782074
Molecular cloning of Gibel carp (Carassius auratus gibelio) complement component C3 and its expression profile after Cyprinid herpesvirus 2 infection. PMID:31723065
A novel miRNA negatively regulates resistance to Glomerella leaf spot by suppressing expression of an NBS gene in apple. PMID:31645951
Genome-Wide Identification and Characterization of the UBP Gene Family in Moso Bamboo (Phyllostachys edulis). PMID:31484390
A blue light receptor that mediates RNA binding and translational regulation. PMID:31451761
Revisiting the Phylogenetic History of Helminths Through Genomics, the Case of the New Echinococcus oligarthrus Genome. PMID:31440275
Signal transduction in photoreceptor histidine kinases. PMID:31397927
Shared Pathogenomic Patterns Characterize a New Phylotype, Revealing Transition toward Host-Adaptation Long before Speciation of Mycobacterium tuberculosis. PMID:31368488
An interplay of structure and intrinsic disorder in the functionality of peptidylarginine deiminases, a family of key autoimmunity-related enzymes. PMID:31342121
Trait-based analysis of the human skin microbiome. PMID:31277701
Comparative genome analysis of the SPL gene family reveals novel evolutionary features in maize. PMID:31271590
N6-methyladenosine regulatory machinery in plants: composition, function and evolution. PMID:31070865
Genome-Wide Identification and Expression Analyses of the bZIP Transcription Factor Genes in moso bamboo (Phyllostachys edulis). PMID:31060272
PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and microRNAs across 32 cancers. PMID:31029062
The trihelix family of transcription factors: functional and evolutionary analysis in Moso bamboo (Phyllostachys edulis). PMID:31023225
An Open Science Approach to Artificial Intelligence in Healthcare. PMID:31022753
Genome-wide identification, classification and expression analysis of the JmjC domain-containing histone demethylase gene family in maize. PMID:30935385
Draft genome of the brown alga, Nemacystus decipiens, Onna-1 strain: Fusion of genes involved in the sulfated fucan biosynthesis pathway. PMID:30872679
Expression analysis of four pseudo-response regulator (PRR) genes in Chrysanthemum morifolium under different photoperiods. PMID:30809439
The Legionella effector LtpM is a new type of phosphoinositide-activated glucosyltransferase. PMID:30573678
SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database. PMID:30500919
Phylogenetic analysis of upland cotton MATE gene family reveals a conserved subfamily involved in transport of proanthocyanidins. PMID:30467666
Genome-wide analysis reveals the evolution and structural features of WRINKLED1 in plants. PMID:30446819
The Pfam protein families database in 2019. PMID:30357350
Genome-Wide Identification and Characterization of wALOG Family Genes Involved in Branch Meristem Development of Branching Head Wheat. PMID:30347757
TCP Transcription Factors in Moso Bamboo (Phyllostachys edulis): Genome-Wide Identification and Expression Analysis. PMID:30344527
GFDP: the gene family database in poplar. PMID:30339216
WRKY transcription factors in legumes. PMID:30332991
RNA-Seq Analysis for Assessing the Early Response to DSP Toxins in Mytilus galloprovincialis Digestive Gland and Gill. PMID:30332849
A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling. PMID:30153857
Genome-wide identification of lipoxygenase gene family in cotton and functional characterization in response to abiotic stresses. PMID:30092779
Tangled history of a multigene family: The evolution of ISOPENTENYLTRANSFERASE genes. PMID:30070990
Searching ECOD for Homologous Domains by Sequence and Structure. PMID:30040199
Homology Inference Based on a Reconciliation Approach for the Comparative Genomics of Protozoa. PMID:30034216
Blue-Light Receptors for Optogenetics. PMID:29984995
A 5-Enolpyruvylshikimate 3-Phosphate Synthase Functions as a Transcriptional Repressor in Populus. PMID:29891568
Comparative Analysis of V-Akt Murine Thymoma Viral Oncogene Homolog 3 (AKT3) Gene between Cow and Buffalo Reveals Substantial Differences for Mastitis. PMID:29862252
Ubiquitin Proteasome pathway proteins as potential drug targets in parasite Trypanosoma cruzi. PMID:29849031
Use of designed sequences in protein structure recognition. PMID:29776380
Genomic Comparison of the P-ATPase Gene Family in Four Cotton Species and Their Expression Patterns in Gossypium hirsutum. PMID:29734726
Unique pharmacological properties of serotoninergic G-protein coupled receptors from cestodes. PMID:29425245
Prediction of Disordered Regions and Their Roles in the Anti-Pathogenic and Immunomodulatory Functions of Butyrophilins. PMID:29401697
Genome-Wide Identification and Expression Analysis of the HD-Zip Gene Family in Wheat (Triticum aestivum L.). PMID:29389910
GO FEAT: a rapid web-based functional annotation tool for genomic and transcriptomic data. PMID:29379090
Comparative genomic analyses reveal the features for adaptation to nematodes in fungi. PMID:29315395
Overexpression of TaWRKY146 Increases Drought Tolerance through Inducing Stomatal Closure in Arabidopsis thaliana. PMID:29225611
Prediction of protein-ligand interactions from paired protein sequence motifs and ligand substructures. PMID:29218866
On the Early Evolution of Catabolic Pathways: A Comparative Genomics Approach. I. The Cases of Glucose, Ribose, and the Nucleobases Catabolic Routes. PMID:29189888
The crystal structure of the Yersinia pestis iron chaperone YiuA reveals a basic triad binding motif for the chelated metal. PMID:29095164
A sensitive short read homology search tool for paired-end read sequencing data. PMID:29072140
Identification of YfiH and the Catalase CatA As Polyphenol Oxidases of Aeromonas media and CatA as a Regulator of Pigmentation by Its Peroxyl Radical Scavenging Capacity. PMID:29051758
Membrane Trafficking Modulation during Entamoeba Encystation. PMID:28993644
A transcription network of interlocking positive feedback loops maintains intracellular iron balance in archaea. PMID:28973467
Systematic Discovery of Archaeal Transcription Factor Functions in Regulatory Networks through Quantitative Phenotyping Analysis. PMID:28951888
The phospholipase PNPLA7 functions as a lysophosphatidylcholine hydrolase and interacts with lipid droplets through its catalytic domain. PMID:28887301
Characterization and Functional Analysis of the Poplar Pectate Lyase-Like Gene PtPL1-18 Reveal Its Role in the Development of Vascular Tissues. PMID:28702042
Genome-wide identification and expression analysis of SBP-like transcription factor genes in Moso Bamboo (Phyllostachys edulis). PMID:28655295
Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta. PMID:28644839
Family-specific scaling laws in bacterial genomes. PMID:28605556
Plasmobase: a comparative database of predicted domain architectures for Plasmodium genomes. PMID:28592293
Genome-wide analysis suggests high level of microsynteny and purifying selection affect the evolution of EIN3/EIL family in Rosaceae. PMID:28584725
Identifying pathogenicity of human variants via paralog-based yeast complementation. PMID:28542158
The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae). PMID:28431014
Spicule formation in calcareous sponges: Coordinated expression of biomineralization genes and spicule-type specific genes. PMID:28406140
Characterization of TPP-binding proteins in Methanococci archaeal species. PMID:28275290
The essence of NAC gene family to the cultivation of drought-resistant soybean (Glycine max L. Merr.) cultivars. PMID:28241800
The Echinococcus canadensis (G7) genome: a key knowledge of parasitic platyhelminth human diseases. PMID:28241794
Intrinsic disorder in biomarkers of insulin resistance, hypoadiponectinemia, and endothelial dysfunction among the type 2 diabetic patients. PMID:28232897
Prediction driven functional annotation of hypothetical proteins in the major facilitator superfamily of S. aureus NCTC 8325. PMID:28197063
Genome-Wide analysis of the AAAP gene family in moso bamboo (Phyllostachys edulis). PMID:28143411
Evolution of protein N-glycosylation process in Golgi apparatus which shapes diversity of protein N-glycan structures in plants, animals and fungi. PMID:28074929
pHMM-tree: phylogeny of profile hidden Markov models. PMID:28062446
The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion. PMID:27849518
A network-pathway based module identification for predicting the prognosis of ovarian cancer patients. PMID:27806724
Comprehensive analysis of trihelix genes and their expression under biotic and abiotic stresses in Populus trichocarpa. PMID:27782188
Retention and Molecular Evolution of Lipoxygenase Genes in Modern Rosid Plants. PMID:27746812
A Novel FC116/BC10 Mutation Distinctively Causes Alteration in the Expression of the Genes for Cell Wall Polymer Synthesis in Rice. PMID:27708650
ProFold: Protein Fold Classification with Additional Structural Features and a Novel Ensemble Classifier. PMID:27660761
Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains. PMID:27601190
Identification of epigenetic factors regulating the mesenchyme to epithelium transition by RNA interference screening in breast cancer cells. PMID:27581651
Data Mining and Pattern Recognition Models for Identifying Inherited Diseases: Challenges and Implications. PMID:27559342
Draft Genome Sequence of a Multidrug-Resistant Klebsiella pneumoniae Carbapenemase-Producing Acinetobacter baumannii Sequence Type 2 Isolate from Puerto Rico. PMID:27540056
A draft genome of the brown alga, Cladosiphon okamuranus, S-strain: a platform for future studies of 'mozuku' biology. PMID:27501718
Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence. PMID:27472895
Comparative Analysis of the Chloroplast Genomic Information of Cunninghamia lanceolata (Lamb.) Hook with Sibling Species from the Genera Cryptomeria D. Don, Taiwania Hayata, and Calocedrus Kurz. PMID:27399686
A proposed integrated approach for the preclinical evaluation of phage therapy in Pseudomonas infections. PMID:27301427
sHSPdb: a database for the analysis of small Heat Shock Proteins. PMID:27297221
Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters in Aspergillus oryzae: A Representative Case Study. PMID:27274991
Bioinformatics resources for pollen. PMID:27271281
Black perithecial pigmentation in Fusarium species is due to the accumulation of 5-deoxybostrycoidin-based melanin. PMID:27193384
Identification and Expression Analysis of BURP Domain-Containing Genes in Medicago truncatula. PMID:27148311
Genome-wide identification and characterization of Glyceraldehyde-3-phosphate dehydrogenase genes family in wheat (Triticum aestivum). PMID:26984398
Molecular evolution and gene expression differences within the HD-Zip transcription factor family of Zea mays L. PMID:26979310
EBV noncoding RNA EBER2 interacts with host RNA-binding proteins to regulate viral gene expression. PMID:26951683
Methuselah/Methuselah-like G protein-coupled receptors constitute an ancient metazoan gene family. PMID:26915348
MGFD: the maize gene families database. PMID:26896848
Genome-Wide Identification, Characterization and Expression Analysis of the Chalcone Synthase Family in Maize. PMID:26828478
Ecological Genomics of the Uncultivated Marine Roseobacter Lineage CHAB-I-5. PMID:26826224
Focused Analysis of Exome Sequencing Data for Rare Germline Mutations in Familial and Sporadic Lung Cancer. PMID:26762739
Functional divergence of GhCFE5 homoeologs revealed in cotton fiber and Arabidopsis root cell development. PMID:26759310
FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants. PMID:26754669
High level of microsynteny and purifying selection affect the evolution of WRKY family in Gramineae. PMID:26754485
The Pfam protein families database: towards a more sustainable future. PMID:26673716
C-terminal domains of a histone demethylase interact with a pair of transcription factors and mediate specific chromatin association. PMID:26617990
Database resources of the National Center for Biotechnology Information. PMID:26615191
Significant Microsynteny with New Evolutionary Highlights Is Detected through Comparative Genomic Sequence Analysis of Maize CCCH IX Gene Subfamily. PMID:26539461
Genome-wide analysis of the IQD gene family in maize. PMID:26453258
Genomewide identification, classification and analysis of NAC type gene family in maize. PMID:26440076
Intrinsically disordered caldesmon binds calmodulin via the "buttons on a string" mechanism. PMID:26417545
Solute Carrier Family 26 Member a2 (slc26a2) Regulates Otic Development and Hair Cell Survival in Zebrafish. PMID:26375458
Common and rare variants associated with kidney stones and biochemical traits. PMID:26272126
Trends in genome dynamics among major orders of insects revealed through variations in protein families. PMID:26251035
Genome-Wide Analysis of C2H2 Zinc-Finger Family Transcription Factors and Their Responses to Abiotic Stresses in Poplar (Populus trichocarpa). PMID:26237514
De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods. PMID:26228684
Outer Membrane Vesicle-Mediated Export of Processed PrtV Protease from Vibrio cholerae. PMID:26222047
In Silico Structural and Functional Annotation of Hypothetical Proteins of Vibrio cholerae O139. PMID:26175663
The Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families in Populus trichocarpa: gene structure, gene expression, phylogenetic analysis and evolution. PMID:26174682
Bioinformatics and Moonlighting Proteins. PMID:26157797
TMFoldRec: a statistical potential-based transmembrane protein fold recognition tool. PMID:26123059
A cupin domain-containing protein with a quercetinase activity (VdQase) regulates Verticillium dahliae's pathogenicity and contributes to counteracting host defenses. PMID:26113857
Potential impact on kidney infection: a whole-genome analysis of Leptospira santarosai serovar Shermani. PMID:26038504
Cracking the nodule worm code advances knowledge of parasite biology and biotechnology to tackle major diseases of livestock. PMID:26026709
Characterization of the Newly Isolated Lytic Bacteriophages KTN6 and KT28 and Their Efficacy against Pseudomonas aeruginosa Biofilm. PMID:25996839
Most partial domains in proteins are alignment and annotation artifacts. PMID:25976240
A de novo floral transcriptome reveals clues into Phalaenopsis orchid flower development. PMID:25970572
The Lipoxygenase Gene Family in Poplar: Identification, Classification, and Expression in Response to MeJA Treatment. PMID:25928711
The central nervous system transcriptome of the weakly electric brown ghost knifefish (Apteronotus leptorhynchus): de novo assembly, annotation, and proteomics validation. PMID:25879418
Draft Genome Sequence of Klebsiella pneumoniae Carbapenemase-Producing Acinetobacter baumannii Strain M3AC9-7, Isolated from Puerto Rico. PMID:25858845
Features of two new proteins with OmpA-like domains identified in the genome sequences of Leptospira interrogans. PMID:25849456
Protein domain-level landscape of cancer-type-specific somatic mutations. PMID:25794154
A novel Schistosoma japonicum endonuclease homologous to DNase II. PMID:25766859
Biological databases for human research. PMID:25712261
Replicating phages in the epidermal mucosa of the eel (Anguilla anguilla). PMID:25688234
MDAT- Aligning multiple domain arrangements. PMID:25626688
Identification and characterization of the RCI2 gene family in maize (Zea mays). PMID:25572224
Exopolysaccharide production and ropy phenotype are determined by two gene clusters in putative probiotic strain Lactobacillus paraplantarum BGCG11. PMID:25527533
Genome re-sequencing and bioinformatics analysis of a nutraceutical rice. PMID:25492220
Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function. PMID:25480530
From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease. PMID:25426780
Genome-wide analysis of the WW domain-containing protein genes in silkworm and their expansion in eukaryotes. PMID:25424044
Calcareous sponge genomes reveal complex evolution of α-carbonic anhydrases and two key biomineralization enzymes. PMID:25421146
Genome-wide analysis of the Hsf family in soybean and functional identification of GmHsf-34 involvement in drought and heat stresses. PMID:25416131
Computational characterization of moonlighting proteins. PMID:25399606
Database resources of the National Center for Biotechnology Information. PMID:25398906
Genome-wide classification and evolutionary and expression analyses of citrus MYB transcription factor families in sweet orange. PMID:25375352
The IQD gene family in soybean: structure, phylogeny, evolution and expression. PMID:25343341
Comparison of amino acids physico-chemical properties and usage of late embryogenesis abundant proteins, hydrophilins and WHy domain. PMID:25296175
RADB: a database of rheumatoid arthritis-related polymorphisms. PMID:25228593
Molecular cloning and expression analysis of 13 NAC transcription factors in Miscanthus lutarioriparius. PMID:25224554
Genome-wide phylogenetic analysis of the pathogenic potential of Vibrio furnissii. PMID:25191313
Structural insights of the ssDNA binding site in the multifunctional endonuclease AtBFN2 from Arabidopsis thaliana. PMID:25157844
Transcriptional analysis of Volvox photoreceptors suggests the existence of different cell-type specific light-signaling pathways. PMID:25117716
Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets. PMID:25033262
Inferring non-synonymous single-nucleotide polymorphisms-disease associations via integration of multiple similarity networks. PMID:25014223
Genome-wide analysis of the NADK gene family in plants. PMID:24968225
Transposable element dynamics among asymbiotic and ectomycorrhizal Amanita fungi. PMID:24923322
Think globally and solve locally: secondary memory-based network learning for automated multi-species function prediction. PMID:24843788
Comprehensive analysis of CCCH-type zinc finger gene family in citrus (Clementine mandarin) by genome-wide characterization. PMID:24820208
The WRKY Transcription Factor Genes in Lotus japonicus. PMID:24745006
Evolution and quantitative comparison of genome-wide protein domain distributions. PMID:24710298
MetalS(3), a database-mining tool for the identification of structurally similar metal sites. PMID:24699831
Thumb-loops up for catalysis: a structure/function investigation of a functional loop movement in a GH11 xylanase. PMID:24688637
in silico identification of protein-protein interactions in Silkworm, Bombyx mori. PMID:24616555
Collective prediction of protein functions from protein-protein interaction networks. PMID:24564855
ProphNet: a generic prioritization method through propagation of information. PMID:24564336
Characterization of resistance gene analogues (RGAs) in apple (Malus × domestica Borkh.) and their evolutionary history of the Rosaceae family. PMID:24505246
Genome-wide analysis of soybean HD-Zip gene family and expression profiling under salinity and drought treatments. PMID:24498296
Genome-wide survey and expression analysis of the putative non-specific lipid transfer proteins in Brassica rapa L. PMID:24497919
In silico identification and characterization of N-Terminal acetyltransferase genes of poplar (Populus trichocarpa). PMID:24473137
A snapshot of a coral "holobiont": a transcriptome assembly of the scleractinian coral, porites, captures a wide variety of genes from both the host and symbiotic zooxanthellae. PMID:24454815
Identification and characterization of the SET domain gene family in maize. PMID:24390243
Genome-wide mapping of DNA methylation in the human malaria parasite Plasmodium falciparum. PMID:24331467
Pfam: the protein families database. PMID:24288371
KBDOCK 2013: a spatial classification of 3D protein domain family interactions. PMID:24271397
Identification of the type II cytochrome c maturation pathway in anammox bacteria by comparative genomics. PMID:24267221
Database resources of the National Center for Biotechnology Information. PMID:24259429
Industrial robustness: understanding the mechanism of tolerance for the Populus hydrolysate-tolerant mutant strain of Clostridium thermocellum. PMID:24205326
Decoding the ubiquitin-mediated pathway of arthropod disease vectors. PMID:24205097
Classification of α-helical membrane proteins using predicted helix architectures. PMID:24204844
An estimated 5% of new protein structures solved today represent a new Pfam family. PMID:24189229
Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently "orphan" viral proteins. PMID:24155369
A comparative proteomic analysis of Pinellia ternata leaves exposed to heat stress. PMID:24132150
Definition and classification of evaluation units for CASP10. PMID:24123179
Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics. PMID:24098807
An easy operating pathogen microarray (EOPM) platform for rapid screening of vertebrate pathogens. PMID:24053492
Adhesins of Leptospira interrogans mediate the interaction to fibrinogen and inhibit fibrin clot formation in vitro. PMID:24009788
Charting the signal trajectory in a light-oxygen-voltage photoreceptor by random mutagenesis and covariance analysis. PMID:24003219
Disruption of the rice plastid ribosomal protein s20 leads to chloroplast developmental defects and seedling lethality. PMID:23979931
Cloning and biochemical characterization of an endo-1,4-β-mannanase from the coffee berry borer Hypothenemus hampei. PMID:23965285
Characterization of three novel adhesins of Leptospira interrogans. PMID:23958908
Characterisation and analysis of the Aegilops sharonensis transcriptome, a wild relative of wheat in the Sitopsis section. PMID:23951332
Experimental characterization of the human non-sequence-specific nucleic acid interactome. PMID:23902751
Comparison of Listeria monocytogenes Exoproteomes from biofilm and planktonic state: Lmo2504, a protein associated with biofilms. PMID:23892746
Whole-genome sequencing reveals a link between β-lactam resistance and synthetases of the alarmone (p)ppGpp in Staphylococcus aureus. PMID:23659600
Gene expression analysis distinguishes tissue-specific and gender-related functions among adult Ascaris suum tissues. PMID:23572074
Genome-wide survey and expression analysis of the MADS-box gene family in soybean. PMID:23559340
Expression, purification, crystallization and preliminary X-ray crystallographic analysis of the L,D-transpeptidase LdtMt1 from Mycobacterium tuberculosis. PMID:23519798
In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment. PMID:23514353
SUN proteins belong to a novel family of β-(1,3)-glucan-modifying enzymes involved in fungal morphogenesis. PMID:23508952
Sequence mutations of the substrate binding pocket of stem cell factor and multidrug resistance protein ABCG2 in renal cell cancer: a possible link to treatment resistance. PMID:23467750
Probing a coral genome for components of the photoprotective scytonemin biosynthetic pathway and the 2-aminoethylphosphonate pathway. PMID:23434798
Draft genome sequence of the rubber tree Hevea brasiliensis. PMID:23375136
Unique secreted-surface protein complex of Lactobacillus rhamnosus, identified by phage display. PMID:23233310
The diverse applications of RNA-seq for functional genomic studies in Aspergillus fumigatus. PMID:23230834
Cloning, sequencing, and in silico characterization of Omp 28 of Salmonella Typhi (strain MTCC 733) to develop r-DNA vaccine for typhoid fever. PMID:23225974
In silico approach to predict candidate R proteins and to define their domain architecture. PMID:23216678
The putative phytocyanin genes in Chinese cabbage (Brassica rapa L.): genome-wide identification, classification and expression analysis. PMID:23212439
Database resources of the National Center for Biotechnology Information. PMID:23193264
Evaluation of function predictions by PFP, ESG,and PSI-BLAST for moonlighting proteins. PMID:23173871
Evaluation of immunoprotective activity of six leptospiral proteins in the hamster model of leptospirosis. PMID:23173023
This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes. PMID:23166479
Solution NMR structure of the helicase associated domain BVU_0683(627-691) from Bacteroides vulgatus provides first structural coverage for protein domain family PF03457 and indicates domain binding to DNA. PMID:23160728
Draft genome sequence of high-melanin-yielding Aeromonas media strain WS. PMID:23144426
Plasminogen binding proteins and plasmin generation on the surface of Leptospira spp.: the contribution to the bacteria-host interactions. PMID:23118516
Genome-wide identification, classification and expression analysis of genes encoding putative fasciclin-like arabinogalactan proteins in Chinese cabbage (Brassica rapa L.). PMID:23053954
Unusual and typical features of a novel restorer-of-fertility gene of sugar beet (Beta vulgaris L.). PMID:22997236
Tracing genomic variations in two highly virulent Yersinia enterocolitica strains with unequal ability to compete for host colonization. PMID:22963272
Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. PMID:22942020
The development and application of a multiple gene co-silencing system using endogenous URA3 as a reporter gene in Ganoderma lucidum. PMID:22937087
The complete genome sequence of Natrinema sp. J7-2, a haloarchaeon capable of growth on synthetic media without amino acid supplements. PMID:22911826
Exploring metazoan evolution through dynamic and holistic changes in protein families and domains. PMID:22862991
Prediction and analysis of the protein interactome in Pseudomonas aeruginosa to enable network-based drug target selection. PMID:22848443
CCCH-type zinc finger family in maize: genome-wide identification, classification and expression profiling under abscisic acid and drought treatments. PMID:22792223
Evidence for horizontally transferred genes involved in the biosynthesis of vitamin B(1), B(5), and B(7) in Heterodera glycines. PMID:22736827
Isolation and characterization of cold responsive NAC gene from Lepidium latifolium. PMID:22733493
Comprehensive analysis of CCCH zinc finger family in poplar (Populus trichocarpa). PMID:22708723
Conservation of complex knotting and slipknotting patterns in proteins. PMID:22685208
dbCAN: a web resource for automated carbohydrate-active enzyme annotation. PMID:22645317
A multi-faceted analysis of RutD reveals a novel family of α/β hydrolases. PMID:22641504
Computational and statistical analyses of amino acid usage and physico-chemical properties of the twelve late embryogenesis abundant protein classes. PMID:22615859
Different evolutionary modifications as a guide to rewire two-component systems. PMID:22586357
The hepatitis E virus polyproline region is involved in viral adaptation. PMID:22545153
Expansion and diversification of the SET domain gene family following whole-genome duplications in Populus trichocarpa. PMID:22497662
CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure. PMID:22480135
"Guilt by association" is the exception rather than the rule in gene networks. PMID:22479173
Cloning, in silico characterization and prediction of three dimensional structure of SbDof1, SbDof19, SbDof23 and SbDof24 proteins from Sorghum [Sorghum bicolor (L.) Moench]. PMID:22476870
Features of two proteins of Leptospira interrogans with potential role in host-pathogen interactions. PMID:22463075
Genetic analysis of the Cronobacter sakazakii O4 to O7 O-antigen gene clusters and development of a PCR assay for identification of all C. sakazakii O serotypes. PMID:22447597
Disruption of a rice pentatricopeptide repeat protein causes a seedling-specific albino phenotype and its utilization to enhance seed purity in hybrid rice production. PMID:22430843
System-wide studies of N-lysine acetylation in Rhodopseudomonas palustris reveal substrate specificity of protein acetyltransferases. PMID:22416131
The N-terminal region of acyl-CoA synthetase 3 is essential for both the localization on lipid droplets and the function in fatty acid uptake. PMID:22357706
d-Xylose concentration-dependent hydrolase expression profiles and the function of CreA and XlnR in Aspergillus niger. PMID:22344641
Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology. PMID:22315334
Characterizing ncRNAs in Human Pathogenic Protists Using High-Throughput Sequencing Technology. PMID:22303390
Predicting the impact of alternative splicing on plant MADS domain protein function. PMID:22295091
Deconstruction of the (paleo)polyploid grapevine genome based on the analysis of transposition events involving NBS resistance genes. PMID:22253773
Characterization and genetic analysis of an EIN4-like sequence (CaETR-1) located in QTL(AR1) implicated in ascochyta blight resistance in chickpea. PMID:22238063
Prediction and characterization of protein-protein interaction networks in swine. PMID:22230699
Solution NMR structures reveal a distinct architecture and provide first structures for protein domain family PF04536. PMID:22198206
Genome-wide comparative in silico analysis of calcium transporters of rice and sorghum. PMID:22196357
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. PMID:22192575
Genome characterization of the oleaginous fungus Mortierella alpina. PMID:22174787
Regulation of a Myb transcription factor by cyclin-dependent kinase 2 in Giardia lamblia. PMID:22167200
Systematic analysis of sequences and expression patterns of drought-responsive members of the HD-Zip gene family in maize. PMID:22164299
Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome. PMID:22156394
Database resources of the National Center for Biotechnology Information. PMID:22140104
Identification and localization of Myxococcus xanthus porins and lipoproteins. PMID:22132103
The Pfam protein families database. PMID:22127870
The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes. PMID:22120664
Horizontal gene transfer in Histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses. PMID:22111657
BYKdb: the Bacterial protein tYrosine Kinase database. PMID:22080550
Inducible ASABF-type antimicrobial peptide from the sponge Suberites domuncula: microbicidal and hemolytic activity in vitro and toxic effect on molluscs in vivo. PMID:22073005
Examination of triacylglycerol biosynthetic pathways via de novo transcriptomic and proteomic analyses in an unsequenced microalga. PMID:22043295
Deep sequencing of pyrethroid-resistant bed bugs reveals multiple mechanisms of resistance within a single population. PMID:22039447
Histatin 5 uptake by Candida albicans utilizes polyamine transporters Dur3 and Dur31 proteins. PMID:22033918
Identification of RNA binding motif proteins essential for cardiovascular development. PMID:22011202
DomPep--a general method for predicting modular domain-mediated protein-protein interactions. PMID:22003397
A novel bacteriophage Tail-Associated Muralytic Enzyme (TAME) from Phage K and its development into a potent antistaphylococcal protein. PMID:21985151
Identification of a conserved anti-apoptotic protein that modulates the mitochondrial apoptosis pathway. PMID:21980415
Structure-based characterization of the binding of peptide to the human endophilin-1 Src homology 3 domain using position-dependent noncovalent potential analysis. PMID:21947444
The phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes. PMID:21943402
Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development. PMID:21931557
Quantification of protein group coherence and pathway assignment using functional association. PMID:21929787
Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. PMID:21926223
An online conserved SSR discovery through cross-species comparison. PMID:21918613
CastorDB: a comprehensive knowledge base for Ricinus communis. PMID:21914200
Protein disulfide isomerase-2 of Arabidopsis mediates protein folding and localizes to both the secretory pathway and nucleus, where it interacts with maternal effect embryo arrest factor. PMID:21909944
Expression during host infection and localization of Yersinia pestis autotransporter proteins. PMID:21873491
The RelA/SpoT homolog (RSH) superfamily: distribution and functional evolution of ppGpp synthetases and hydrolases across the tree of life. PMID:21858139
Biochemical characterization of the tetrahydrobiopterin synthesis pathway in the oleaginous fungus Mortierella alpina. PMID:21852350
The novel leptospiral surface adhesin Lsa20 binds laminin and human plasminogen and is probably expressed during infection. PMID:21844229
Molecular cloning and copy number variation of a ferritin subunit (Fth1) and its association with growth in freshwater pearl mussel Hyriopsis cumingii. PMID:21818403
Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem. PMID:21764968
Domain-domain interactions underlying herpesvirus-human protein-protein interaction networks. PMID:21760902
Characterization of novel OmpA-like protein of Leptospira interrogans that binds extracellular matrix molecules and plasminogen. PMID:21755014
Genome-wide mutagenesis of Xanthomonas axonopodis pv. citri reveals novel genetic determinants and regulation mechanisms of biofilm formation. PMID:21750733
Calcium/calmodulin kinase1 and its relation to thermotolerance and HSP90 in Sporothrix schenckii: an RNAi and yeast two-hybrid study. PMID:21745372
Protein-protein complex structure predictions by multimeric threading and template recombination. PMID:21742262
Identification of Xanthomonas fragariae, Xanthomonas axonopodis pv. phaseoli, and Xanthomonas fuscans subsp. fuscans with novel markers and using a dot blot platform coupled with automatic data analysis. PMID:21705524
MarkUs: a server to navigate sequence-structure-function space. PMID:21672961
A network of SCOP hidden Markov models and its analysis. PMID:21635719
Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements. PMID:21622749
Interactions among Trypanosoma brucei RAD51 paralogues in DNA repair and antigenic variation. PMID:21615552
New methods to measure residues coevolution in proteins. PMID:21612664
Novel transposable elements from Anopheles gambiae. PMID:21605407
Shewanella oneidensis MR-1 sensory box protein involved in aerobic and anoxic growth. PMID:21602393
Characteristics and evolution of the PUF gene family in Bombyx mori and 27 other species. PMID:21598114
HMMER web server: interactive sequence similarity searching. PMID:21593126
New cell surface protein involved in biofilm formation by Streptococcus parasanguinis. PMID:21576336
Secretins: dynamic channels for protein transport across membranes. PMID:21565514
Expression patterns and miRNA regulation of DNA methyltransferases in chicken primordial germ cells. PMID:21559294
The anaerobe-specific orange protein complex of Desulfovibrio vulgaris hildenborough is encoded by two divergent operons coregulated by σ54 and a cognate transcriptional regulator. PMID:21531797
Comparative genomics of the odorant-binding and chemosensory protein gene families across the Arthropoda: origin and evolutionary history of the chemosensory system. PMID:21527792
Molecular modeling and in silico characterization of Mycobacterium tuberculosis TlyA: possible misannotation of this tubercle bacilli-hemolysin. PMID:21443791
Deletion of a cation transporter promotes lysis in Streptococcus pneumoniae. PMID:21422174
Molecular and virulence characteristics of an outer membrane-associated RTX exoprotein in Pasteurella pneumotropica. PMID:21410992
Evidence for involvement of TRPA1 in the detection of vibrations by hair bundle mechanoreceptors in sea anemones. PMID:21394510
Phylogenetics and evolution of Su(var)3-9 SET genes in land plants: rapid diversification in structure and function. PMID:21388541
A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. PMID:21385052
Bacillus thuringiensis: a genomics and proteomics perspective. PMID:21327125
Chemogenomic analysis of G-protein coupled receptors and their ligands deciphers locks and keys governing diverse aspects of signalling. PMID:21326864
Molecular analysis of a family of Arabidopsis genes related to galacturonosyltransferases. PMID:21300919
An atlas of altered expression of deubiquitinating enzymes in human cancer. PMID:21283576
Predicting functions of proteins in mouse based on weighted protein-protein interaction network and protein hybrid properties. PMID:21283518
Protein structure databases. PMID:21225378
The solute carrier families have a remarkably long evolutionary history with the majority of the human families present before divergence of Bilaterian species. PMID:21186191
Complete genome sequence of Algoriphagus sp. PR1, bacterial prey of a colony-forming choanoflagellate. PMID:21183675
Expansion mechanisms and functional divergence of the glutathione s-transferase family in sorghum and other higher plants. PMID:21169340
Some remarks on protein attribute prediction and pseudo amino acid composition. PMID:21168420
An essential Aurora-related kinase transiently associates with spindle pole bodies during Plasmodium falciparum erythrocytic schizogony. PMID:21166904
Metallothionein-like gene from Cicer microphyllum is regulated by multiple abiotic stresses. PMID:21161305
Phylogenomic analysis of the uracil-DNA glycosylase superfamily. PMID:21135150
GOAPhAR: An Integrative Discovery Tool for Annotation, Pathway Analysis. PMID:21132056
Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components. PMID:21124865
Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human. PMID:21124763
DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection. PMID:21106128
Database resources of the National Center for Biotechnology Information. PMID:21097890
LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria. PMID:21092245
In silico gene expression analysis in Codonopsis lanceolata root. PMID:21088900
A tutorial on protein ontology resources for proteomic studies. PMID:21082429
Prediction of a new class of RNA recognition motif. PMID:21082207
Insights into metazoan evolution from Alvinella pompejana cDNAs. PMID:21080938
Rfam: Wikipedia, clans and the "decimal" release. PMID:21062808
Classification of genomic islands using decision trees and their ensemble algorithms. PMID:21047376
Post-translational regulation by gustavus contributes to selective Vasa protein accumulation in multipotent cells during embryogenesis. PMID:21035437
Toward understanding the mechanism of action of the yeast multidrug resistance transporter Pdr5p: a molecular modeling study. PMID:21034832
Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines. PMID:21034480
Characterization of the functional domain of β2-microglobulin from the Asian seabass, Lates calcarifer. PMID:20949082
Structural basis for the dual RNA-recognition modes of human Tra2-β RRM. PMID:20926394
Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection. PMID:20875130
Structure of a Burkholderia pseudomallei trimeric autotransporter adhesin head. PMID:20862217
PeptideMine--a webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes. PMID:20858292
Structure of the cholera toxin secretion channel in its closed state. PMID:20852644
FACT: functional annotation transfer between proteins with similar feature architectures. PMID:20696036
Diverse somatic mutation patterns and pathway alterations in human cancers. PMID:20668451
Crystal structure of the GerBC component of a Bacillus subtilis spore germinant receptor. PMID:20654628
Metagenomics: Facts and Artifacts, and Computational Challenges*. PMID:20648230
Comprehensive analysis of NAC domain transcription factor gene family in Populus trichocarpa. PMID:20630103
Solution NMR structure of Lin0431 protein from Listeria innocua reveals high structural similarity with domain II of bacterial transcription antitermination protein NusG. PMID:20602357
Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization. PMID:20596258
Properties of the phage-shock-protein (Psp) regulatory complex that govern signal transduction and induction of the Psp response in Escherichia coli. PMID:20595257
Evidence for the heparin-binding ability of the ascidian Xlink domain and insight into the evolution of the Xlink domain in chordates. PMID:20582409
In vitro identification of novel plasminogen-binding receptors of the pathogen Leptospira interrogans. PMID:20582320
Unique gating properties of C. elegans ClC anion channel splice variants are determined by altered CBS domain conformation and the R-helix linker. PMID:20581474
The phosphatomes of the multicellular myxobacteria Myxococcus xanthus and Sorangium cellulosum in comparison with other prokaryotic genomes. PMID:20567509
CODA: accurate detection of functional associations between proteins in eukaryotic genomes using domain fusion. PMID:20532224
Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution. PMID:20529918
RTX proteins: a highly diverse family secreted by a common mechanism. PMID:20528947
Evolution and function of the plant cell wall synthesis-related glycosyltransferase family 8. PMID:20522722
The small heat shock protein 20 RSI2 interacts with and is required for stability and function of tomato resistance protein I-2. PMID:20497382
A human functional protein interaction network and its application to cancer data analysis. PMID:20482850
JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis. PMID:20478993
Sequence embedding for fast construction of guide trees for multiple sequence alignment. PMID:20470396
Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition. PMID:20463972
The transcriptome of the early life history stages of the California Sea Hare Aplysia californica. PMID:20434970
Enzymatic deconstruction of xylan for biofuel production. PMID:20431716
Predicting conserved protein motifs with Sub-HMMs. PMID:20420695
PRP-17 and the pre-mRNA splicing pathway are preferentially required for the proliferation versus meiotic development decision and germline sex determination in Caenorhabditis elegans. PMID:20419786
Knockdown of bicaudal C in zebrafish (Danio rerio) causes cystic kidneys: a nonmammalian model of polycystic kidney disease. PMID:20412683
Functional characterization of LcpA, a surface-exposed protein of Leptospira spp. that binds the human complement regulator C4BP. PMID:20404075
Systematic search for putative new domain families in Mycoplasma gallisepticum genome. PMID:20384986
A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0. PMID:20368981
Multiple interaction domains in FtsL, a protein component of the widely conserved bacterial FtsLBQ cell division complex. PMID:20363951
LEAPdb: a database for the late embryogenesis abundant proteins. PMID:20359361
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
Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium. PMID:20348266
Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity. PMID:20338066
High throughput genome-wide survey of small RNAs from the parasitic protists Giardia intestinalis and Trichomonas vaginalis. PMID:20333187
A Plasmodium falciparum transcriptional cyclin-dependent kinase-related kinase with a crucial role in parasite proliferation associates with histone deacetylase activity. PMID:20305001
Evolutionary history and stress regulation of the lectin superfamily in higher plants. PMID:20236552
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. PMID:20230605
DEAD-box helicases: posttranslational regulation and function. PMID:20206133
Automatic prediction of catalytic residues by modeling residue structural neighborhood. PMID:20199672
A comprehensive resource of interacting protein regions for refining human transcription factor networks. PMID:20195357
Functional diversity of four glycoside hydrolase family 3 enzymes from the rumen bacterium Prevotella bryantii B14. PMID:20190048
Large-scale analyses of glycosylation in cellulases. PMID:20172492
Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins. PMID:20162627
Quat-2L: a web-server for predicting protein quaternary structural attributes. PMID:20148364
Identification of the tirandamycin biosynthetic gene cluster from Streptomyces sp. 307-9. PMID:20127927
Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin. PMID:20123795
Role for CysJ flavin reductase in molybdenum cofactor-dependent resistance of Escherichia coli to 6-N-hydroxylaminopurine. PMID:20118259
Transcriptome analysis of the Cryptocaryon irritans tomont stage identifies potential genes for the detection and control of cryptocaryonosis. PMID:20113487
NMR structure of F-actin-binding domain of Arg/Abl2 from Homo sapiens. PMID:20077570
Combining structure and sequence information allows automated prediction of substrate specificities within enzyme families. PMID:20072606
Peptide vocabulary analysis reveals ultra-conservation and homonymity in protein sequences. PMID:20066129
Integrative approaches to the prediction of protein functions based on the feature selection. PMID:20043848
Identification of mammalian orthologs using local synteny. PMID:20030836
Genome-wide identification and evolutionary analysis of the animal specific ETS transcription factor family. PMID:20011068
Extracytoplasmic PAS-like domains are common in signal transduction proteins. PMID:20008068
Expansion of tandem repeats in sea anemone Nematostella vectensis proteome: A source for gene novelty? PMID:20003297
Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons. PMID:19969543
3PFDB--a database of best representative PSSM profiles (BRPs) of protein families generated using a novel data mining approach. PMID:19961575
The oligonucleotide frequency derived error gradient and its application to the binning of metagenome fragments. PMID:19958473
Generation and gene ontology based analysis of expressed sequence tags (EST) from a Panax ginseng C. A. Meyer roots. PMID:19943115
Purification, crystallization and preliminary X-ray analysis of beta-glucosidase from Kluyveromyces marxianus NBRC1777. PMID:19923748
The Negatome database: a reference set of non-interacting protein pairs. PMID:19920129
The Pfam protein families database. PMID:19920124
Database resources of the National Center for Biotechnology Information. PMID:19910364
Toward understanding allosteric signaling mechanisms in the ATPase domain of molecular chaperones. PMID:19908379
Phylogenetic analysis and homology modelling of Paracentrotus lividus nectin. PMID:19908157
Genome-scale identification method applied to find cryptic aminoglycoside resistance genes in Pseudomonas aeruginosa. PMID:19907650
TmpL, a transmembrane protein required for intracellular redox homeostasis and virulence in a plant and an animal fungal pathogen. PMID:19893627
Molecular diversity of the antimicrobial domain of beta-defensin 3 and homologous peptides. PMID:19888439
Edgetic perturbation models of human inherited disorders. PMID:19888216
Transcript-based cloning of RRP46, a regulator of rRNA processing and R gene-independent cell death in barley-powdery mildew interactions. PMID:19861556
Conservation of structure and protein-protein interactions mediated by the secreted mycobacterial proteins EsxA, EsxB, and EspA. PMID:19854905
A structure filter for the Eukaryotic Linear Motif Resource. PMID:19852836
Molecular characterization of a novel Staphylococcus aureus surface protein (SasC) involved in cell aggregation and biofilm accumulation. PMID:19851500
An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations. PMID:19851441
Analysis of regulatory protease sequences identified through bioinformatic data mining of the Schistosoma mansoni genome. PMID:19845954
Glutathione transferases are structural and functional outliers in the thioredoxin fold. PMID:19842715
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PMID:19841731
Post-transcriptional control of chloroplast gene expression. PMID:19838333
Structure and signaling mechanism of Per-ARNT-Sim domains. PMID:19836329
Significant speedup of database searches with HMMs by search space reduction with PSSM family models. PMID:19828575
Knowledge-based characterization of similarity relationships in the human protein-tyrosine phosphatase family for rational inhibitor design. PMID:19810703
Survey of large protein complexes in D. vulgaris reveals great structural diversity. PMID:19805340
Exploration of uncharted regions of the protein universe. PMID:19787035
TIR-NBS-LRR genes are rare in monocots: evidence from diverse monocot orders. PMID:19785756
Discovering cancer genes by integrating network and functional properties. PMID:19765316
Achievements and new knowledge unraveled by metagenomic approaches. PMID:19760178
A survey of integral alpha-helical membrane proteins. PMID:19760129
Repeat-associated plasticity in the Helicobacter pylori RD gene family. PMID:19749042
BRICHOS - a superfamily of multidomain proteins with diverse functions. PMID:19747390
HOPS interacts with Apl5 at the vacuole membrane and is required for consumption of AP-3 transport vesicles. PMID:19741093
Caenorhabditis elegans BAH-1 is a DUF23 protein expressed in seam cells and required for microbial biofilm binding to the cuticle. PMID:19707590
The functional domain grouping of microtubule associated proteins. PMID:19704789
Acetylsalicylic acid (aspirin) reduces damage to reconstituted human tissues infected with Candida species by inhibiting extracellular fungal lipases. PMID:19703582
Genome mining in Sorangium cellulosum So ce56: identification and characterization of the homologous electron transfer proteins of a myxobacterial cytochrome P450. PMID:19696019
Gastric Cancer (Biomarkers) Knowledgebase (GCBKB): A Curated and Fully Integrated Knowledgebase of Putative Biomarkers Related to Gastric Cancer. PMID:19690644
Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes. PMID:19689787
Unraveling the evolution of cytokinin signaling. PMID:19675156
The C-Ala domain brings together editing and aminoacylation functions on one tRNA. PMID:19661429
Early development of Moniliophthora perniciosa basidiomata and developmentally regulated genes. PMID:19653910
The cellulose synthase superfamily in fully sequenced plants and algae. PMID:19646250
Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation. PMID:19640978
Prediction of ligand binding sites using homologous structures and conservation at CASP8. PMID:19626715
Identification and expression profiling analysis of TIFY family genes involved in stress and phytohormone responses in rice. PMID:19618278
Functional analysis of 5' untranslated region of a TIR-NBS-encoding gene from triploid white poplar. PMID:19618215
Genomic resources of Magnaporthe oryzae (GROMO): a comprehensive and integrated database on rice blast fungus. PMID:19604367
Sequence and structural analysis of the Asp-box motif and Asp-box beta-propellers; a widespread propeller-type characteristic of the Vps10 domain family and several glycoside hydrolase families. PMID:19594936
HAPPI: an online database of comprehensive human annotated and predicted protein interactions. PMID:19594875
Essential role for Schizosaccharomyces pombe pik1 in septation. PMID:19587793
Crystal structure of the HEAT domain from the Pre-mRNA processing factor Symplekin. PMID:19576221
The putative cyclooctadepsipeptide receptor depsiphilin of the canine hookworm Ancylostoma caninum. PMID:19575230
Characterization of the repertoire diversity of the Plasmodium falciparum stevor multigene family in laboratory and field isolates. PMID:19558642
Identification of unusual E6 and E7 proteins within avian papillomaviruses: cellular localization, biophysical characterization, and phylogenetic analysis. PMID:19553340
Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3. PMID:19553194
Klassevirus 1, a previously undescribed member of the family Picornaviridae, is globally widespread. PMID:19552824
Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyre. PMID:19542347
Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase. PMID:19536266
Backup in gene regulatory networks explains differences between binding and knockout results. PMID:19536199
An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell. PMID:19536198
Expansion mechanisms and functional annotations of hypothetical genes in the rice genome. PMID:19535473
Identification and characterization of the doublesex gene of Nasonia. PMID:19523063
Combining specificity determining and conserved residues improves functional site prediction. PMID:19508719
Toxoplasma gondii proteomics. PMID:19489701
ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors. PMID:19483101
Iron-sulfur (Fe/S) protein biogenesis: phylogenomic and genetic studies of A-type carriers. PMID:19478995
Genomic analyses reveal a conserved glutathione homeostasis pathway in the invertebrate chordate Ciona intestinalis. PMID:19470804
CORAL: aligning conserved core regions across domain families. PMID:19470584
Hepatitis C virus NS4B carboxy terminal domain is a membrane binding domain. PMID:19467155
Borrelia burgdorferi bb0426 encodes a 2'-deoxyribosyltransferase that plays a central role in purine salvage. PMID:19460093
NMR structure of protein YvyC from Bacillus subtilis reveals unexpected structural similarity between two PFAM families. PMID:19455708
Outsourcing the nucleus: nuclear pore complex genes are no longer encoded in nucleomorph genomes. PMID:19455199
Improving protein structure similarity searches using domain boundaries based on conserved sequence information. PMID:19454035
Variation in host specificity and gene content in strains from genetically isolated lineages of the ectomycorrhizal fungus Paxillus involutus s. lat. PMID:19452174
Molecular characterisation and genetic mapping of candidate genes for qualitative disease resistance in perennial ryegrass (Lolium perenne L.). PMID:19450286
Domain shuffling and the evolution of vertebrates. PMID:19443856
Analytical methods for inferring functional effects of single base pair substitutions in human cancers. PMID:19434427
Molecular analyses of the rice glutamate dehydrogenase gene family and their response to nitrogen and phosphorous deprivation. PMID:19430792
Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs. PMID:19423640
webPRC: the Profile Comparer for alignment-based searching of public domain databases. PMID:19420063
Human ATP-binding cassette (ABC) transporter family. PMID:19403462
Genome wide expression analysis of CBS domain containing proteins in Arabidopsis thaliana (L.) Heynh and Oryza sativa L. reveals their developmental and stress regulation. PMID:19400948
Characterization of a putative endoxylanase in the migratory plant-parasitic nematode Radopholus similis. PMID:19400841
Functional genomics of HMGN3a and SMARCAL1 in early mammalian embryogenesis. PMID:19393058
Sequence-based prediction of type III secreted proteins. PMID:19390696
Augmented training of hidden Markov models to recognize remote homologs via simulated evolution. PMID:19389731
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. PMID:19377059
A transcriptomic analysis of superhybrid rice LYP9 and its parents. PMID:19372371
Analysis of the impact of solvent on contacts prediction in proteins. PMID:19368710
Genome-wide identification of BURP domain-containing genes in rice reveals a gene family with diverse structures and responses to abiotic stresses. PMID:19363683
The origins of apicomplexan sequence innovation. PMID:19363216
Structural and motional contributions of the Bacillus subtilis ClpC N-domain to adaptor protein interactions. PMID:19361434
Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome. PMID:19358722
The impact of cellular networks on disease comorbidity. PMID:19357641
A complex cell division machinery was present in the last common ancestor of eukaryotes. PMID:19352429
Identification of a Gene Cluster for the Biosynthesis of a Long, Galactose-Rich Exopolysaccharide in Lactobacillus rhamnosus GG and Functional Analysis of the Priming Glycosyltransferase. PMID:19346339
DEX-1 and DYF-7 establish sensory dendrite length by anchoring dendritic tips during cell migration. PMID:19344940
FINDSITE: a combined evolution/structure-based approach to protein function prediction. PMID:19324930
Biochemical analysis of a beta-D-xylosidase and a bifunctional xylanase-ferulic acid esterase from a xylanolytic gene cluster in Prevotella ruminicola 23. PMID:19304844
S. pombe btn1, the orthologue of the Batten disease gene CLN3, is required for vacuole protein sorting of Cpy1p and Golgi exit of Vps10p. PMID:19299465
The multi-AT-hook chromosomal protein of Drosophila melanogaster, D1, is dispensable for viability. PMID:19293138
Analyses of domains and domain fusions in human proto-oncogenes. PMID:19292927
Ancient diversification of eukaryotic MCM DNA replication proteins. PMID:19292915
Detection of alpha-rod protein repeats using a neural network and application to huntingtin. PMID:19282972
A novel polyketide biosynthesis gene cluster is involved in fruiting body morphogenesis in the filamentous fungi Sordaria macrospora and Neurospora crassa. PMID:19277664
Identification of coevolving residues and coevolution potentials emphasizing structure, bond formation and catalytic coordination in protein evolution. PMID:19274093
Diversity of polyproline recognition by EVH1 domains. PMID:19273103
Intergenic regions of Borrelia plasmids contain phylogenetically conserved RNA secondary structure motifs. PMID:19267927
Identification and analyses of candidate genes for rpp4-mediated resistance to Asian soybean rust in soybean. PMID:19251904
Exploring the human genome with functional maps. PMID:19246570
Identification of DNA-binding proteins using structural, electrostatic and evolutionary features. PMID:19233205
A HaemAtlas: characterizing gene expression in differentiated human blood cells. PMID:19228925
An Arabidopsis GPI-anchor plasmodesmal neck protein with callose binding activity and potential to regulate cell-to-cell trafficking. PMID:19223515
Isolation and characterization of metalloproteases with a novel domain structure by construction and screening of metagenomic libraries. PMID:19218412
Subunit interactions and composition of the fructose 6-phosphate catalytic site and the fructose 2,6-bisphosphate allosteric site of mammalian phosphofructokinase. PMID:19218242
Crystal structure of the N-terminal domain of the secretin GspD from ETEC determined with the assistance of a nanobody. PMID:19217396
Role of Acinetobacter baylyi Crc in catabolite repression of enzymes for aromatic compound catabolism. PMID:19201803
The core oligosaccharide and thioredoxin of Vibrio cholerae are necessary for binding and propagation of its typing phage VP3. PMID:19201789
Structural genomics reveals EVE as a new ASCH/PUA-related domain. PMID:19191354
Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PMID:19190775
Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide. PMID:19187283
A single regulatory gene is sufficient to alter bacterial host range. PMID:19182778
Novel thigmomorphogenetic responses in Carica papaya: touch decreases anthocyanin levels and stimulates petiole cork outgrowths. PMID:19182220
Complete genome of the broad-host-range Erwinia amylovora phage phiEa21-4 and its relationship to Salmonella phage felix O1. PMID:19181832
The organelle proteome of the DT40 lymphocyte cell line. PMID:19181659
Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance. PMID:19175938
Mycobacterium tuberculosis Rv3802c encodes a phospholipase/thioesterase and is inhibited by the antimycobacterial agent tetrahydrolipstatin. PMID:19169353
EPIC-DB: a proteomics database for studying Apicomplexan organisms. PMID:19159464
Prediction of nuclear proteins using SVM and HMM models. PMID:19152693
Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon. PMID:19146703
The Talpid3 gene (KIAA0586) encodes a centrosomal protein that is essential for primary cilia formation. PMID:19144723
Evolution of prokaryotic SPFH proteins. PMID:19138386
An atypical soybean leucine-rich repeat receptor-like kinase, GmLRK1, may be involved in the regulation of cell elongation. PMID:19115064
T-POP array identifies EcnR and PefI-SrgD as novel regulators of flagellar gene expression. PMID:19114490
Functional differentiation of Brassica napus guard cells and mesophyll cells revealed by comparative proteomics. PMID:19106087
Comparative kinomics of human and chimpanzee reveal unique kinship and functional diversity generated by new domain combinations. PMID:19105813
Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. PMID:19103665
Identification of a novel picornavirus related to cosaviruses in a child with acute diarrhea. PMID:19102772
A nitrile hydratase in the eukaryote Monosiga brevicollis. PMID:19096720
MucR, a novel membrane-associated regulator of alginate biosynthesis in Pseudomonas aeruginosa. PMID:19088322
Analysis of mammalian gene batteries reveals both stable ancestral cores and highly dynamic regulatory sequences. PMID:19087242
LRRCE: a leucine-rich repeat cysteine capping motif unique to the chordate lineage. PMID:19077264
Functional differentiation of tbf1 orthologues in fission and budding yeasts. PMID:19074598
Over-expression of the BRMS1 family member SUDS3 does not suppress metastasis of human cancer cells. PMID:19070953
Computational analysis and experimental validation of gene predictions in Toxoplasma gondii. PMID:19065262
A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. PMID:19061648
Prdm proto-oncogene transcription factor family expression and interaction with the Notch-Hes pathway in mouse neurogenesis. PMID:19050759
snoRNA, a novel precursor of microRNA in Giardia lamblia. PMID:19043559
The MYST histone acetyltransferases are essential for gametophyte development in Arabidopsis. PMID:19040736
Protein chaperones Q8ZP25_SALTY from Salmonella typhimurium and HYAE_ECOLI from Escherichia coli exhibit thioredoxin-like structures despite lack of canonical thioredoxin active site sequence motif. PMID:19039680
Aspergillus genomes and the Aspergillus cloud. PMID:19039001
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. PMID:19036790
Characterization of domain-peptide interaction interface: a generic structure-based model to decipher the binding specificity of SH3 domains. PMID:19023120
Genome-wide survey of prokaryotic serine proteases: analysis of distribution and domain architectures of five serine protease families in prokaryotes. PMID:19019219
Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum strain A neurotoxin gene cluster. PMID:19014598
Protein subfamily assignment using the Conserved Domain Database. PMID:19014584
Molecular basis for G-actin binding to RPEL motifs from the serum response factor coactivator MAL. PMID:19008859
The mechanism of transport by mitochondrial carriers based on analysis of symmetry. PMID:19001266
A structural basis for the regulatory inactivation of DnaA. PMID:19000695
Genome-wide analysis of MIKCC-type MADS box genes in grapevine. PMID:18997115
Bacteria possessing two RelA/SpoT-like proteins have evolved a specific stringent response involving the acyl carrier protein-SpoT interaction. PMID:18996989
PDBsum new things. PMID:18996896
Proteome-wide identification of poly(ADP-ribose) binding proteins and poly(ADP-ribose)-associated protein complexes. PMID:18981049
Michigan molecular interactions r2: from interacting proteins to pathways. PMID:18978014
The prediction of protein-protein interaction networks in rice blast fungus. PMID:18976500
FastBLAST: homology relationships for millions of proteins. PMID:18974889
In silico identification of specialized secretory-organelle proteins in apicomplexan parasites and in vivo validation in Toxoplasma gondii. PMID:18974850
Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PMID:18959479
Pseudofam: the pseudogene families database. PMID:18957444
MetaMine--a tool to detect and analyse gene patterns in their environmental context. PMID:18957118
Multiple unbiased prospective screens identify TRP channels and their conserved gating elements. PMID:18955590
A computational screen for type I polyketide synthases in metagenomics shotgun data. PMID:18953415
RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases. PMID:18953028
The GAF-like-domain-containing transcriptional regulator DfdR is a sensor protein for dibenzofuran and several hydrophobic aromatic compounds. PMID:18952799
Characteristic motifs for families of allergenic proteins. PMID:18951633
In silico analysis of methyltransferase domains involved in biosynthesis of secondary metabolites. PMID:18950525
Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence. PMID:18950507
Database resources of the National Center for Biotechnology Information. PMID:18940862
Predicting small ligand binding sites in proteins using backbone structure. PMID:18940825
A novel autotransporter adhesin is required for efficient colonization during bubonic plague. PMID:18936182
SDR: a database of predicted specificity-determining residues in proteins. PMID:18927118
Structural assembly of two-domain proteins by rigid-body docking. PMID:18925951
The Bet v 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands. PMID:18922149
Complete genome sequence of a highly divergent astrovirus isolated from a child with acute diarrhea. PMID:18854035
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
Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis. PMID:18852473
Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function. PMID:18844997
Origins and evolution of the formin multigene family that is involved in the formation of actin filaments. PMID:18840602
The interactome: predicting the protein-protein interactions in cells. PMID:18839074
Crystal structure of MutS2 endonuclease domain and the mechanism of homologous recombination suppression. PMID:18838375
Eukaryotic-like protein kinases in the prokaryotes and the myxobacterial kinome. PMID:18836084
TB database: an integrated platform for tuberculosis research. PMID:18835847
Bioinformatics identification of MurJ (MviN) as the peptidoglycan lipid II flippase in Escherichia coli. PMID:18832143
The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications. PMID:18831785
Unassigned MURF1 of kinetoplastids codes for NADH dehydrogenase subunit 2. PMID:18831753
Splice-mediated Variants of Proteins (SpliVaP) - data and characterization of changes in signatures among protein isoforms due to alternative splicing. PMID:18831736
A specificity map for the PDZ domain family. PMID:18828675
Regulatory hotspots in the malaria parasite genome dictate transcriptional variation. PMID:18828674
The genome of Rhodobacter sphaeroides strain 2.4.1 encodes functional cobinamide salvaging systems of archaeal and bacterial origins. PMID:18808385
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
Identification and characterization of PWWP domain residues critical for LEDGF/p75 chromatin binding and human immunodeficiency virus type 1 infectivity. PMID:18799576
The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks. PMID:18796161
The protein-phosphatome of the human malaria parasite Plasmodium falciparum. PMID:18793411
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks. PMID:18782832
Ethanolamine activates a sensor histidine kinase regulating its utilization in Enterococcus faecalis. PMID:18776017
Tracking the evolution of a cold stress associated gene family in cold tolerant grasses. PMID:18775065
Structure of Staphylococcus aureus EsxA suggests a contribution to virulence by action as a transport chaperone and/or adaptor protein. PMID:18773907
Linear motif atlas for phosphorylation-dependent signaling. PMID:18765831
Identification and functional characterization of NifA variants that are independent of GlnB activation in the photosynthetic bacterium Rhodospirillum rubrum. PMID:18757802
Identification and correction of abnormal, incomplete and mispredicted proteins in public databases. PMID:18752676
AMIN domains have a predicted role in localization of diverse periplasmic protein complexes. PMID:18723522
Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. PMID:18722006
Amplification of uncultured single-stranded DNA viruses from rice paddy soil. PMID:18708511
Mining the genomes of plant pathogenic bacteria: how not to drown in gigabases of sequence. PMID:18705888
The role of bZIP transcription factors in green plant evolution: adaptive features emerging from four founder genes. PMID:18698409
Bacterial species exhibit diversity in their mechanisms and capacity for protein disulfide bond formation. PMID:18695247
LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice. PMID:18691433
Powerful fusion: PSI-BLAST and consensus sequences. PMID:18678588
The RNA acetyltransferase driven by ATP hydrolysis synthesizes N4-acetylcytidine of tRNA anticodon. PMID:18668122
Meta-basic estimates the size of druggable human genome. PMID:18663489
Mutator genes giving rise to decreased antibiotic susceptibility in Pseudomonas aeruginosa. PMID:18663021
Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. PMID:18652504
The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation. PMID:18644147
MSDmotif: exploring protein sites and motifs. PMID:18637174
Host-derived oxidized phospholipids and HDL regulate innate immunity in human leprosy. PMID:18636118
Novel endo-alpha-N-acetylgalactosaminidases with broader substrate specificity. PMID:18635885
Comprehensive 3D-modeling of allergenic proteins and amino acid composition of potential conformational IgE epitopes. PMID:18621419
An en masse phenotype and function prediction system for Mus musculus. PMID:18613952
Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. PMID:18613951
Predicting gene function in a hierarchical context with an ensemble of classifiers. PMID:18613947
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. PMID:18613946
The actinome of Dictyostelium discoideum in comparison to actins and actin-related proteins from other organisms. PMID:18612387
Local function conservation in sequence and structure space. PMID:18604264
Taxonomic distribution of large DNA viruses in the sea. PMID:18598358
On the extent and origins of genic novelty in the phylum Nematoda. PMID:18596977
Contextual specificity in peptide-mediated protein interactions. PMID:18596940
CyclinPred: a SVM-based method for predicting cyclin protein sequences. PMID:18596929
MACHOS: Markov clusters of homologous subsequences. PMID:18586748
Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. PMID:18586742
The effectiveness of position- and composition-specific gap costs for protein similarity searches. PMID:18586708
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors. PMID:18586699
SjTPdb: integrated transcriptome and proteome database and analysis platform for Schistosoma japonicum. PMID:18578888
Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins. PMID:18578882
Biochemical and functional evidence of p53 homology is inconsistent with molecular phylogenetics for distant sequences. PMID:18560747
Sf29 gene of Spodoptera frugiperda multiple nucleopolyhedrovirus is a viral factor that determines the number of virions in occlusion bodies. PMID:18550678
Deciphering the ubiquitin-mediated pathway in apicomplexan parasites: a potential strategy to interfere with parasite virulence. PMID:18545708
Plant mitochondrial rhomboid, AtRBL12, has different substrate specificity from its yeast counterpart. PMID:18543065
Folding of a LysM domain: entropy-enthalpy compensation in the transition state of an ideal two-state folder. PMID:18538343
Malectin: a novel carbohydrate-binding protein of the endoplasmic reticulum and a candidate player in the early steps of protein N-glycosylation. PMID:18524852
Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis. PMID:18523684
Word correlation matrices for protein sequence analysis and remote homology detection. PMID:18522726
Polycomb group gene expression in the sea urchin. PMID:18521949
A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PMID:18516236
Whole genome identification of Mycobacterium tuberculosis vaccine candidates by comprehensive data mining and bioinformatic analyses. PMID:18505592
A staphylococcal GGDEF domain protein regulates biofilm formation independently of cyclic dimeric GMP. PMID:18502872
Xenorhabdus nematophila lrhA is necessary for motility, lipase activity, toxin expression, and virulence in Manduca sexta insects. PMID:18502863
Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites. PMID:18501020
Green transcription factors: a chlamydomonas overview. PMID:18493038
Targeting the human cancer pathway protein interaction network by structural genomics. PMID:18487680
The metalloprotease PrtV from Vibrio cholerae. PMID:18479458
Sequence similarity network reveals common ancestry of multidomain proteins. PMID:18475320
Bifidobacterium bifidum lacto-N-biosidase, a critical enzyme for the degradation of human milk oligosaccharides with a type 1 structure. PMID:18469123
FliZ Is a posttranslational activator of FlhD4C2-dependent flagellar gene expression. PMID:18469103
Protein interaction predictions from diverse sources. PMID:18468558
Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES293 (West Pacific) strains. PMID:18462506
Mechanistic insights into a novel exporter-importer system of Mycobacterium tuberculosis unravel its role in trafficking of iron. PMID:18461140
Structure of a putative acetyltransferase (PA1377) from Pseudomonas aeruginosa. PMID:18453699
Prediction of interacting single-stranded RNA bases by protein-binding patterns. PMID:18452949
Characterization and prediction of residues determining protein functional specificity. PMID:18450811
The crystal structure and dimerization interface of GADD45gamma. PMID:18445651
Lsa21, a novel leptospiral protein binding adhesive matrix molecules and present during human infection. PMID:18445272
Identification of outer membrane proteins of Mycobacterium tuberculosis. PMID:18439872
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
TOPDOM: database of domains and motifs with conservative location in transmembrane proteins. PMID:18434342
Roots of angiosperm formins: the evolutionary history of plant FH2 domain-containing proteins. PMID:18430232
Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach. PMID:18424801
Identification of soluble protein fragments by gene fragmentation and genetic selection. PMID:18420658
The probiotic Lactobacillus johnsonii NCC 533 produces high-molecular-mass inulin from sucrose by using an inulosucrase enzyme. PMID:18408060
The genome of the brown alga Ectocarpus siliculosus contains a series of viral DNA pieces, suggesting an ancient association with large dsDNA viruses. PMID:18405387
Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato. PMID:18405374
Data capture in bioinformatics: requirements and experiences with Pedro. PMID:18402673
PSAIA - protein structure and interaction analyzer. PMID:18400099
Nature of protein family signatures: insights from singular value analysis of position-specific scoring matrices. PMID:18398479
Domain annotation of trimeric autotransporter adhesins--daTAA. PMID:18397894
Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective. PMID:18397526
Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface? PMID:18395225
The MoVIN server for the analysis of protein interaction networks. PMID:18387199
TarO: a target optimisation system for structural biology. PMID:18385152
Identification of two inner-membrane proteins required for the transport of lipopolysaccharide to the outer membrane of Escherichia coli. PMID:18375759
A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1. PMID:18371204
Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: focus on point miscalls and artefactual expansions. PMID:18366731
BioSAVE: display of scored annotation within a sequence context. PMID:18366701
H2r: identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments. PMID:18366663
Identification of a novel coronavirus from a beluga whale by using a panviral microarray. PMID:18353961
Isolation and identification of rhizoxin analogs from Pseudomonas fluorescens Pf-5 by using a genomic mining strategy. PMID:18344330
The Crohn's disease susceptibility gene DLG5 as a member of the CARD interaction network. PMID:18335190
Extremely thermostable esterases from the thermoacidophilic euryarchaeon Picrophilus torridus. PMID:18330499
Genome-wide analysis for identification of salt-responsive genes in common wheat. PMID:18320247
ADCK3, an ancestral kinase, is mutated in a form of recessive ataxia associated with coenzyme Q10 deficiency. PMID:18319074
LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana. PMID:18318901
Complete nucleotide sequence of pGS18, a 62.8-kb plasmid from Geobacillus stearothermophilus strain 18. PMID:18305896
Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria. PMID:18305186
Developmentally regulated expression, alternative splicing and distinct sub-groupings in members of the Schistosoma mansoni venom allergen-like (SmVAL) gene family. PMID:18294395
The solution structure of ZNF593 from Homo sapiens reveals a zinc finger in a predominantly unstructured protein. PMID:18287285
Degradation of a polyadenylated rRNA maturation by-product involves one of the three RRP6-like proteins in Arabidopsis thaliana. PMID:18285452
Phylogenetic classification of short environmental DNA fragments. PMID:18285365
Accurate statistical model of comparison between multiple sequence alignments. PMID:18285364
Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon. PMID:18276644
De novo high-resolution protein structure determination from sparse spin-labeling EPR data. PMID:18275810
Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes. PMID:18257921
Evolution of insect proteomes: insights into synapse organization and synaptic vesicle life cycle. PMID:18257909
Genome-wide analysis of intergenic regions of Mycobacterium tuberculosis H37Rv using Affymetrix GeneChips. PMID:18253472
Identification of a novel Leucine-rich repeat protein and candidate PP1 regulatory subunit expressed in developing spermatids. PMID:18237440
Structural Insights into ribosome recycling factor interactions with the 70S ribosome. PMID:18234219
Subfamily specific conservation profiles for proteins based on n-gram patterns. PMID:18234090
Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes. PMID:18231586
Evolution of protein domain promiscuity in eukaryotes. PMID:18230802
Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding. PMID:18230180
The origin of a novel gene through overprinting in Escherichia coli. PMID:18226237
The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation. PMID:18221520
The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction. PMID:18221517
Comparative analysis of the Photorhabdus luminescens and the Yersinia enterocolitica genomes: uncovering candidate genes involved in insect pathogenicity. PMID:18221513
In silico characterization of proteins: UniProt, InterPro and Integr8. PMID:18219596
Evolution of NMDA receptor cytoplasmic interaction domains: implications for organisation of synaptic signalling complexes. PMID:18197970
Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family. PMID:18197962
Virulence factor rtx in Legionella pneumophila, evidence suggesting it is a modular multifunctional protein. PMID:18194518
Genetic dissection of tropodithietic acid biosynthesis by marine roseobacters. PMID:18192410
The animal in the genome: comparative genomics and evolution. PMID:18192189
Quantitative analysis on the characteristics of targets with FDA approved drugs. PMID:18167532
The Arabidopsis MUM2 gene encodes a beta-galactosidase required for the production of seed coat mucilage with correct hydration properties. PMID:18165329
Functions of flavin reductase and quinone reductase in 2,4,6-trichlorophenol degradation by Cupriavidus necator JMP134. PMID:18165297
Genetic determinants of Sindbis virus mosquito infection are associated with a highly conserved alphavirus and flavivirus envelope sequence. PMID:18160430
Determination of glycosyltransferase specificities for the Escherichia coli O111 O antigen by a generic approach. PMID:18156323
lfnA from Pseudomonas aeruginosa O12 and wbuX from Escherichia coli O145 encode membrane-associated proteins and are required for expression of 2,6-dideoxy-2-acetamidino-L-galactose in lipopolysaccharide O antigen. PMID:18156256
AlterORF: a database of alternate open reading frames. PMID:18096612
A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PMID:18094749
The canine hookworm genome: analysis and classification of Ancylostoma caninum survey sequences. PMID:18082904
Comprehensive viral oligonucleotide probe design using conserved protein regions. PMID:18079152
Two zinc-cluster transcription factors control induction of alternative oxidase in Neurospora crassa. PMID:18073419
DBD--taxonomically broad transcription factor predictions: new content and functionality. PMID:18073188
Secreted-protein response to sigmaU activity in Streptomyces coelicolor. PMID:18065550
Structure of [NiFe] hydrogenase maturation protein HypE from Escherichia coli and its interaction with HypF. PMID:18065529
Evolution of the chaperone/usher assembly pathway: fimbrial classification goes Greek. PMID:18063717
Towards completion of the Earth's proteome. PMID:18059312
Framework for a protein ontology. PMID:18047702
Functional, genetic and bioinformatic characterization of a calcium/calmodulin kinase gene in Sporothrix schenckii. PMID:18047672
Application of phage display to high throughput antibody generation and characterization. PMID:18047641
Database resources of the National Center for Biotechnology Information. PMID:18045790
Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PMID:18043742
Distinguishing protein-coding and noncoding genes in the human genome. PMID:18040051
Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche. PMID:18039825
The Pfam protein families database. PMID:18039703
Gene3D: comprehensive structural and functional annotation of genomes. PMID:18032434
e-Fungi: a data resource for comparative analysis of fungal genomes. PMID:18028535
RPEL motifs link the serum response factor cofactor MAL but not myocardin to Rho signaling via actin binding. PMID:18025109
Plasticity within the obligatory folding nucleus of an immunoglobulin-like domain. PMID:18022190
Determination and validation of principal gene products. PMID:18006548
The 20 years of PROSITE. PMID:18003654
Data growth and its impact on the SCOP database: new developments. PMID:18000004
Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria. PMID:17999997
DIMA 2.0--predicted and known domain interactions. PMID:17999995
Structural mapping of protein interactions reveals differences in evolutionary pressures correlated to mRNA level and protein abundance. PMID:17997970
Bioinformatics and experimental analysis of proteins of two-component systems in Myxococcus xanthus. PMID:17993514
MEROPS: the peptidase database. PMID:17991683
Metals in the "omics" world: copper homeostasis and cytochrome c oxidase assembly in a new light. PMID:17987327
PairsDB atlas of protein sequence space. PMID:17986464
HMMatch: peptide identification by spectral matching of tandem mass spectra using hidden Markov models. PMID:17985986
Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification in the fungi. PMID:17984228
Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis. PMID:17982171
Determinants for the subcellular localization and function of a nonessential SEDS protein. PMID:17981970
Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome. PMID:17980019
Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network. PMID:17967049
The Molecule Pages database. PMID:17965093
The origins and early evolution of DNA mismatch repair genes--multiple horizontal gene transfers and co-evolution. PMID:17965091
Repeat-protein folding: new insights into origins of cooperativity, stability, and topology. PMID:17963718
Contact rearrangements form coupled networks from local motions in allosteric proteins. PMID:17957766
AvrAC(Xcc8004), a type III effector with a leucine-rich repeat domain from Xanthomonas campestris pathovar campestris confers avirulence in vascular tissues of Arabidopsis thaliana ecotype Col-0. PMID:17951377
eggNOG: automated construction and annotation of orthologous groups of genes. PMID:17942413
Characterization of protein hubs by inferring interacting motifs from protein interactions. PMID:17941705
Improved human disease candidate gene prioritization using mouse phenotype. PMID:17939863
PlantTFDB: a comprehensive plant transcription factor database. PMID:17933783
ATDB: a uni-database platform for animal toxins. PMID:17933766
FunSimMat: a comprehensive functional similarity database. PMID:17932054
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. PMID:17916580
DOMINE: a database of protein domain interactions. PMID:17913741
Sensor complexes regulating two-component signal transduction. PMID:17913492
Expression, purification, crystallization and preliminary X-ray crystallographic analysis of a resuscitation-promoting factor from Mycobacterium tuberculosis. PMID:17909292
Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties. PMID:17888146
Prediction of potential drug targets based on simple sequence properties. PMID:17883836
Telomeric co-localization of the modified base J and contingency genes in the protozoan parasite Trypanosoma cruzi. PMID:17881368
Genome-wide investigation reveals pathogen-specific and shared signatures in the response of Caenorhabditis elegans to infection. PMID:17875205
Crystal structures of flax rust avirulence proteins AvrL567-A and -D reveal details of the structural basis for flax disease resistance specificity. PMID:17873095
InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale. PMID:17868464
FIST: a sensory domain for diverse signal transduction pathways in prokaryotes and ubiquitin signaling in eukaryotes. PMID:17855421
Integrating sequence and structural biology with DAS. PMID:17850653
New insights into the WalK/WalR (YycG/YycF) essential signal transduction pathway reveal a major role in controlling cell wall metabolism and biofilm formation in Staphylococcus aureus. PMID:17827301
Functional conservation of Rel binding sites in drosophilid genomes. PMID:17785540
The anatomy of microbial cell state transitions in response to oxygen. PMID:17785531
MELOGEN: an EST database for melon functional genomics. PMID:17767721
Predicted functions and linkage specificities of the products of the Streptococcus pneumoniae capsular biosynthetic loci. PMID:17766420
Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center. PMID:17764033
Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D. PMID:17727718
PROCOGNATE: a cognate ligand domain mapping for enzymes. PMID:17720712
Predicting prokaryotic ecological niches using genome sequence analysis. PMID:17710143
An integrative in silico approach for discovering candidates for drug-targetable protein-protein interactions in interactome data. PMID:17705877
Domain architectures of the Scm3p protein provide insights into centromere function and evolution. PMID:17704645
Bacterial sensor kinase TodS interacts with agonistic and antagonistic signals. PMID:17693554
Predicting active site residue annotations in the Pfam database. PMID:17688688
A downstream mediator in the growth repression limb of the jasmonate pathway. PMID:17675405
Complete genomic sequence and mass spectrometric analysis of highly diverse, atypical Bacillus thuringiensis phage 0305phi8-36. PMID:17673272
Identification of genes encoding tRNA modification enzymes by comparative genomics. PMID:17673083
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
TrED: the Trichophyton rubrum Expression Database. PMID:17650345
Reuse of structural domain-domain interactions in protein networks. PMID:17640363
Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. PMID:17636889
Fungal CSL transcription factors. PMID:17629904
Identification of sensory and signal-transducing domains in two-component signaling systems. PMID:17628134
Comparative genomic and protein sequence analyses of a complex system controlling bacterial chemotaxis. PMID:17628132
The Schistosoma mansoni transcriptome: an update. PMID:17624328
The bromodomain protein LEX-1 acts with TAM-1 to modulate gene expression in C. elegans. PMID:17618463
Probabilistic prediction and ranking of human protein-protein interactions. PMID:17615067
Reconstructing the evolution of the mitochondrial ribosomal proteome. PMID:17604309
Molecular evolution of hemojuvelin and the repulsive guidance molecule family. PMID:17593421
Evolutionary history and functional implications of protein domains and their combinations in eukaryotes. PMID:17588271
Structural genomics: keeping up with expanding knowledge of the protein universe. PMID:17587562
The 2006 automated function prediction meeting. PMID:17570143
Comprehensive analysis of co-occurring domain sets in yeast proteins. PMID:17562021
Scm3, an essential Saccharomyces cerevisiae centromere protein required for G2/M progression and Cse4 localization. PMID:17548816
Evaluation of NAD(+) -dependent DNA ligase of mycobacteria as a potential target for antibiotics. PMID:17548501
A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants. PMID:17547750
Chemogenomic approaches to rational drug design. PMID:17533416
A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database. PMID:17521420
COMPASS server for remote homology inference. PMID:17517780
Evolution of the iron-responsive element. PMID:17513696
Mutational analysis of endoxylanases XylA and XylB from the phytopathogen Fusarium graminearum reveals comprehensive insights into their inhibitor insensitivity. PMID:17513587
Identification of a single HNH active site in type IIS restriction endonuclease Eco31I. PMID:17499273
Characterization of the opossum immune genome provides insights into the evolution of the mammalian immune system. PMID:17495011
The Fusarium verticillioides FUM gene cluster encodes a Zn(II)2Cys6 protein that affects FUM gene expression and fumonisin production. PMID:17483290
RNA-binding proteins: modular design for efficient function. PMID:17473849
Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. PMID:17465672
Supervised multivariate analysis of sequence groups to identify specificity determining residues. PMID:17451607
cTFbase: a database for comparative genomics of transcription factors in cyanobacteria. PMID:17439663
Why are there still over 1000 uncharacterized yeast genes? PMID:17435240
Transcriptional regulation of chemical diversity in Aspergillus fumigatus by LaeA. PMID:17432932
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
Query-dependent banding (QDB) for faster RNA similarity searches. PMID:17397253
Probabilistic protein function prediction from heterogeneous genome-wide data. PMID:17396164
Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir. PMID:17372208
The implications of alternative splicing in the ENCODE protein complement. PMID:17372197
Panmicrobial oligonucleotide array for diagnosis of infectious diseases. PMID:17370518
Stable isotope probing with 15N2 reveals novel noncultivated diazotrophs in soil. PMID:17369332
Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments. PMID:17369271
Burkholderia Hep_Hag autotransporter (BuHA) proteins elicit a strong antibody response during experimental glanders but not human melioidosis. PMID:17362501
Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. PMID:17360515
Hierarchical classification of functionally equivalent genes in prokaryotes. PMID:17353185
Genome-wide identification of spliced introns using a tiling microarray. PMID:17351133
GOTax: investigating biological processes and biochemical activities along the taxonomic tree. PMID:17346342
PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins. PMID:17337525
False occurrences of functional motifs in protein sequences highlight evolutionary constraints. PMID:17331242
A phylogenomic analysis of the Actinomycetales mce operons. PMID:17324287
Basic helix-loop-helix transcription factor heterocomplex of Yas1p and Yas2p regulates cytochrome P450 expression in response to alkanes in the yeast Yarrowia lipolytica. PMID:17322346
Congenital syndactyly in cattle: four novel mutations in the low density lipoprotein receptor-related protein 4 gene (LRP4). PMID:17319939
Overexpression of Akt converts radial growth melanoma to vertical growth melanoma. PMID:17318262
Proteomic and immunoblot analyses of Bartonella quintana total membrane proteins identify antigens recognized by sera from infected patients. PMID:17307937
Ancient origin of the new developmental superfamily DANGER. PMID:17301879
Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module. PMID:17301237
Analysis of a set of Australian northern brown bandicoot expressed sequence tags with comparison to the genome sequence of the South American grey short tailed opossum. PMID:17298671
A conserved carboxylesterase is a SUPPRESSOR OF AVRBST-ELICITED RESISTANCE in Arabidopsis. PMID:17293566
PlnTFDB: an integrative plant transcription factor database. PMID:17286856
Identification of novel peptide hormones in the human proteome by hidden Markov model screening. PMID:17284679
SCOOP: a simple method for identification of novel protein superfamily relationships. PMID:17277330
Genome of the opportunistic pathogen Streptococcus sanguinis. PMID:17277061
Sequence and annotation of the 288-kb ATCV-1 virus that infects an endosymbiotic chlorella strain of the heliozoon Acanthocystis turfacea. PMID:17276475
Detection and avoidance of a natural product from the pathogenic bacterium Serratia marcescens by Caenorhabditis elegans. PMID:17267603
Functional overlap between conserved and diverged KH domains in Saccharomyces cerevisiae SCP160. PMID:17264125
The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum. PMID:17259312
Evaluation and comparison of mammalian subcellular localization prediction methods. PMID:17254308
A novel superfamily containing the beta-grasp fold involved in binding diverse soluble ligands. PMID:17250770
ProServer: a simple, extensible Perl DAS server. PMID:17237073
The mimivirus genome encodes a mitochondrial carrier that transports dATP and dTTP. PMID:17229695
The AAA+ protein ATAD3 has displacement loop binding properties and is involved in mitochondrial nucleoid organization. PMID:17210950
Genes required for glycolipid synthesis and lipoteichoic acid anchoring in Staphylococcus aureus. PMID:17209021
REBASE--enzymes and genes for DNA restriction and modification. PMID:17202163
New developments in the InterPro database. PMID:17202162
LigProf: a simple tool for in silico prediction of ligand-binding sites. PMID:17200839
Molecular cloning and expression of two new allergens from Anisakis simplex. PMID:17180690
Interactions of the sweet protein brazzein with the sweet taste receptor. PMID:17177550
Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria. PMID:17173478
The coactivator function of Arabidopsis NPR1 requires the core of its BTB/POZ domain and the oxidation of C-terminal cysteines. PMID:17172357
Loss of a universal tRNA feature. PMID:17172343
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
Structural analysis of the plakin domain of bullous pemphigoid antigen1 (BPAG1) suggests that plakins are members of the spectrin superfamily. PMID:17161423
Proteins of the glycine decarboxylase complex in the hydrogenosome of Trichomonas vaginalis. PMID:17158739
GeneTrees: a phylogenomics resource for prokaryotes. PMID:17151073
The Molecular Biology Database Collection: 2007 update. PMID:17148484
Characterization of an ATP-dependent DNA ligase from the acidophilic archaeon "Ferroplasma acidarmanus" Fer1. PMID:17136487
CDD: a conserved domain database for interactive domain family analysis. PMID:17135202
Snap: an integrated SNP annotation platform. PMID:17135198
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. PMID:17135193
MiST: a microbial signal transduction database. PMID:17135192
Pfarao: a web application for protein family analysis customized for cytoskeletal and motor proteins (CyMoBase). PMID:17134497
GeneSpeed: protein domain organization of the transcriptome. PMID:17132830
Sequence comparison by sequence harmony identifies subtype-specific functional sites. PMID:17130172
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. PMID:17130145
ForestTreeDB: a database dedicated to the mining of tree transcriptomes. PMID:17130142
EVEREST: a collection of evolutionary conserved protein domains. PMID:17099230
The SUPERFAMILY database in 2007: families and functions. PMID:17098927
MAIZEWALL. Database and developmental gene expression profiling of cell wall biosynthesis and assembly in maize. PMID:17098859
Xanthusbase: adapting wikipedia principles to a model organism database. PMID:17090585
Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level. PMID:17090320
The Sulfolobus database. PMID:17088281
Evolution and comparative analysis of the MHC Class III inflammatory region. PMID:17081307
PROTCOM: searchable database of protein complexes enhanced with domain-domain structures. PMID:17071962
Structure-function analysis of delta trafficking, receptor binding and signaling in Drosophila. PMID:17028337
Sequence and annotation of the 369-kb NY-2A and the 345-kb AR158 viruses that infect Chlorella NC64A. PMID:17027058
Sequence and annotation of the 314-kb MT325 and the 321-kb FR483 viruses that infect Chlorella Pbi. PMID:17023017
Bacterial postgenomics: the promise and peril of systems biology. PMID:16997947
Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy. PMID:16984653
Sequence analysis of the lactococcal plasmid pNP40: a mobile replicon for coping with environmental hazards. PMID:16952955
The echinoderm adhesome. PMID:16950242
Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic. PMID:16930487
A RecA-mediated exon profiling method. PMID:16896013
Taverna: a tool for building and running workflows of services. PMID:16845108
PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments. PMID:16845080
Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. PMID:16845078
DOUTfinder--identification of distant domain outliers using subsignificant sequence similarity. PMID:16844996
A new measure for functional similarity of gene products based on Gene Ontology. PMID:16776819
Protein family expansions and biological complexity. PMID:16733546 -
Pfam: The protein families database in 2021
PubMed citations: 559.
559 articles citing: Pfam: The protein families database in 2021
A novel, non-GMO surface display in Limosilactobacillus fermentum mediated by cell surface hydrolase without anchor motif. PMID:35922769
Structural and biophysical properties of FopA, a major outer membrane protein of Francisella tularensis. PMID:35913965
Single-base methylome analysis reveals dynamic changes of genome-wide DNA methylation associated with rapid stem growth of woody bamboos. PMID:35913571
Polycyclic Aromatic Hydrocarbon Degradation in the Sea-Surface Microlayer at Coastal Antarctica. PMID:35910648
The roles of WRKY transcription factors in Malus spp. and Pyrus spp. PMID:35906324
Assessing clinical utility of preconception expanded carrier screening regarding residual risk for neurodevelopmental disorders. PMID:35906228
A Selective Adenylyl Cyclase 1 Inhibitor Relieves Pain Without Causing Tolerance. PMID:35899113
Genome-wide identification and expression pattern analysis of lipoxygenase gene family in turnip (Brassica rapa L. subsp. rapa). PMID:35898937
Genome-Wide Analysis of DoSPX Genes and the Function of DoSPX4 in Low Phosphorus Response in Dendrobium officinale. PMID:35898219
Bioinformatics Study of Aux/IAA Family Genes and Their Expression in Response to Different Hormones Treatments during Japanese Apricot Fruit Development and Ripening. PMID:35893602
Three New Stigmatellin Derivatives Reveal Biosynthetic Insights of Its Side Chain Decoration. PMID:35889529
Corallococcus soli sp. Nov., a Soil Myxobacterium Isolated from Subtropical Climate, Chalus County, Iran, and Its Potential to Produce Secondary Metabolites. PMID:35888982
LSAP: A Machine Learning Method for Leaf-Senescence-Associated Genes Prediction. PMID:35888183
Characterization and Functional Implications of the Nonexpressor of Pathogenesis-Related Genes 1 (NPR1) in Saccharum. PMID:35887330
Molecular Characterization of a DNA Polymerase from Thermus thermophilus MAT72 Phage vB_Tt72: A Novel Type-A Family Enzyme with Strong Proofreading Activity. PMID:35887293
The Exploring Functional Role of Ammonium Transporters of Aspergillus oryzae in Nitrogen Metabolism: Challenges towards Cell Biomass Production. PMID:35886914
Transcriptome Analysis Reveals Early Hemocyte Responses upon In Vivo Stimulation with LPS in the Stick Insect Bacillus rossius (Rossi, 1788). PMID:35886821
Systematic Functional Annotation Workflow for Insects. PMID:35886762
Genome-Wide Evolutionary Analysis of Putative Non-Specific Herbicide Resistance Genes and Compilation of Core Promoters between Monocots and Dicots. PMID:35885954
The Fate of IgE Epitopes and Coeliac Toxic Motifs during Simulated Gastrointestinal Digestion of Pizza Base. PMID:35885243
Essential Conditions for the Full Synergy of Probability of Occurrence Distributions. PMID:35885216
Deep-Sea Sediments from the Southern Gulf of Mexico Harbor a Wide Diversity of PKS I Genes. PMID:35884142
Genome-Wide Classification and Evolutionary Analysis Reveal Diverged Patterns of Chalcone Isomerase in Plants. PMID:35883518
Insights into the Antimicrobial Activities and Metabolomes of Aquimarina (Flavobacteriaceae, Bacteroidetes) Species from the Rare Marine Biosphere. PMID:35877716
A Cocktail of Three Virulent Phages Controls Multidrug-Resistant Salmonella Enteritidis Infection in Poultry. PMID:35875532
ContactPFP: Protein function prediction using predicted contact information. PMID:35875419
Evolutionary and Integrative Analysis of Gibberellin-Dioxygenase Gene Family and Their Expression Profile in Three Rosaceae Genomes (F. vesca, P. mume, and P. avium) Under Phytohormone Stress. PMID:35874024
Genome-Wide Analysis of CqCrRLK1L and CqRALF Gene Families in Chenopodium quinoa and Their Roles in Salt Stress Response. PMID:35873972
Genome-wide analysis and identification of the PEBP genes of Brassica juncea var. Tumida. PMID:35870881
Identifying and characterising Thrap3, Bclaf1 and Erh interactions using cross-linking mass spectrometry. PMID:35865489
Deletion of the H108R Gene Reduces Virulence of the Pandemic Eurasia Strain of African Swine Fever Virus with Surviving Animals Being Protected against Virulent Challenge. PMID:35862691
Overexpression of TaSNAC4-3D in Common Wheat (Triticum aestivum L.) Negatively Regulates Drought Tolerance. PMID:35860542
Phylogenetic Classification and Functional Review of Autotransporters. PMID:35860281
Signal binding at both modules of its dCache domain enables the McpA chemoreceptor of Bacillus velezensis to sense different ligands. PMID:35858353
Specialization of the photoreceptor transcriptome by Srrm3-dependent microexons is required for outer segment maintenance and vision. PMID:35858306
The two-domain elevator-type mechanism of zinc-transporting ZIP proteins. PMID:35857505
Phylogenomic Comparison of Neisseria gonorrhoeae Causing Disseminated Gonococcal Infections and Uncomplicated Gonorrhea in Georgia, United States. PMID:35855008
Analysis of repeat elements in the Pristionchus pacificus genome reveals an ancient invasion by horizontally transferred transposons. PMID:35854227
Chloroplastic pentatricopeptide repeat proteins (PPR) in albino plantlets of Agave angustifolia Haw. reveal unexpected behavior. PMID:35850575
Bacterial Endophytes Contribute to Rice Seedling Establishment Under Submergence. PMID:35845658
Taxonomically Restricted Genes Are Associated With Responses to Biotic and Abiotic Stresses in Sugarcane (Saccharum spp.). PMID:35845637
Isolation, Identification, and Investigation of Pathogenic Bacteria From Common Carp (Cyprinus carpio) Naturally Infected With Plesiomonas shigelloides. PMID:35844551
Loss of immunity-related GTPase GM4951 leads to nonalcoholic fatty liver disease without obesity. PMID:35842425
Human cytosolic transaminases: side activities and patterns of discrimination towards physiologically available alternative substrates. PMID:35834009
The Big Picture of Neurodegeneration: A Meta Study to Extract the Essential Evidence on Neurodegenerative Diseases in a Network-Based Approach. PMID:35832065
Genome-wide identification and expression analysis of the ftsH protein family and its response to abiotic stress in Nicotiana tabacum L. PMID:35831784
Comparative phylogeny and evolutionary analysis of Dicer-like protein family in two plant monophyletic lineages. PMID:35821291
PclR is a transcriptional activator of the gene that encodes the pneumococcal collagen-like protein PclA. PMID:35821046
Deletion of the Loop Linking Two Domains of Exo-Inulinase InuAMN8 Diminished the Enzymatic Thermo-Halo-Alcohol Tolerance. PMID:35814689
Identification, Molecular Cloning, and Functional Characterization of a Coniferyl Alcohol Acyltransferase Involved in the Biosynthesis of Dibenzocyclooctadiene Lignans in Schisandra chinensis. PMID:35812978
Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions. PMID:35810309
The evolutionary history of cribellate orb-weaver capture thread spidroins. PMID:35810286
Genetic variation associated with condensate dysregulation in disease. PMID:35809564
Chromosome-level genome assembly of Plazaster borealis sheds light on the morphogenesis of multiarmed starfish and its regenerative capacity. PMID:35809048
Arabinoxylan and Pectin Metabolism in Crohn's Disease Microbiota: An In Silico Study. PMID:35806099
Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants. PMID:35806066
Comparative Genomic Analysis of SAUR Gene Family, Cloning and Functional Characterization of Two Genes (PbrSAUR13 and PbrSAUR52) in Pyrus bretschneideri. PMID:35806062
Genome-Wide Analysis of the Peptidase M24 Superfamily in Triticum aestivum Demonstrates That TaM24-9 Is Involved in Abiotic Stress Response. PMID:35805912
New Mutations in cls Lead to Daptomycin Resistance in a Clinical Vancomycin- and Daptomycin-Resistant Enterococcus faecium Strain. PMID:35801099
PtoNF-YC9-SRMT-PtoRD26 module regulates the high saline tolerance of a triploid poplar. PMID:35799188
Functional metagenomic screening identifies an unexpected β-glucuronidase. PMID:35799064
Structural and biochemical analyses of the flagellar expression regulator DegU from Listeria monocytogenes. PMID:35798759
A statistical, reference-free algorithm subsumes myriad problems in genome science and enables novel discovery. PMID:35794890
The XTH Gene Family in Schima superba: Genome-Wide Identification, Expression Profiles, and Functional Interaction Network Analysis. PMID:35783982
Genomic Insight Into Lacticaseibacillus paracasei SP5, Reveals Genes and Gene Clusters of Probiotic Interest and Biotechnological Potential. PMID:35783439
C16orf72/HAPSTR1 is a molecular rheostat in an integrated network of stress response pathways. PMID:35776542
Reference nodule transcriptomes for Melilotus officinalis and Medicago sativa cv. Algonquin. PMID:35774624
Transcriptional Basis for Haustorium Formation and Host Establishment in Hemiparasitic Psittacanthus schiedeanus Mistletoes. PMID:35769994
Functional Micropeptides Encoded by Long Non-Coding RNAs: A Comprehensive Review. PMID:35769907
S097: a single, peri-operative antibiotic can persistently alter the post-operative gut microbiome after Roux-en-Y gastric bypass. PMID:35768736
Identification of stress-related genes by co-expression network analysis based on the improved turbot genome. PMID:35768602
ABC transporters mined through comparative transcriptomics associate with organ-specific accumulation of picrosides in a medicinal herb, Picrorhiza kurroa. PMID:35767110
A novel hypoxic lncRNA, HRL-SC, promotes the proliferation and migration of human dental pulp stem cells through the PI3K/AKT signaling pathway. PMID:35765088
Unprecedented frequency of mitochondrial introns in colonial bilaterians. PMID:35764672
Role of an FNIP Repeat Domain-Containing Protein Encoded by Megavirus Baoshan during Viral Infection. PMID:35762756
What the protein data bank tells us about the evolutionary conservation of protein conformational diversity. PMID:35762711
Multiple Alr genes exhibit allorecognition-associated variation in the colonial cnidarian Hydractinia. PMID:35761101
Phage-host coevolution in natural populations. PMID:35760840
A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses. PMID:35760836
Simulating domain architecture evolution. PMID:35758772
Metagenomic and Microscopic Analysis of Magnetotactic Bacteria in Tangyin Hydrothermal Field of Okinawa Trough. PMID:35756025
SAPFIR: A webserver for the identification of alternative protein features. PMID:35751026
Identification of Phage Receptor-Binding Protein Sequences with Hidden Markov Models and an Extreme Gradient Boosting Classifier. PMID:35746800
In-Depth Temporal Transcriptome Profiling of an Alphaherpesvirus Using Nanopore Sequencing. PMID:35746760
Transcriptome-Guided Identification of Pectin Methyl-Esterase-Related Enzymes and Novel Molecular Processes Effectuating the Hard-to-Cook Defect in Common Bean (Phaseolus vulgaris L.). PMID:35741889
Genome-Wide Identification and Expression Analysis of Expansin Gene Family in the Storage Root Development of Diploid Wild Sweetpotato Ipomoea trifida. PMID:35741805
An Aux/IAA Family Member, RhIAA14, Involved in Ethylene-Inhibited Petal Expansion in Rose (Rosa hybrida). PMID:35741802
MAPK1 Is Regulated by LOC102188416/miR-143-3p Axis in Dairy Goat Mammary Epithelial Cells. PMID:35741775
Transcriptome analysis reveals regulation mechanism of methyl jasmonate-induced terpenes biosynthesis in Curcuma wenyujin. PMID:35737688
Characterization of the Largest Secretory Protein Family, Ricin B Lectin-like Protein, in Nosema bombycis: Insights into Microsporidian Adaptation to Host. PMID:35736035
Analysis of Effector and Immunity Proteins of the GA2 Type VI Secretion Systems of Gut Bacteroidales. PMID:35735993
Pangenome Evolution in Environmentally Transmitted Symbionts of Deep-Sea Mussels Is Governed by Vertical Inheritance. PMID:35731940
Old genes in new places: A taxon-rich analysis of interdomain lateral gene transfer events. PMID:35731825
Detecting Structural Variants and Associated Gene Presence-Absence Variation Phenomena in the Genomes of Marine Organisms. PMID:35727540
A colorimetric method to measure in vitro nitrogenase functionality for engineering nitrogen fixation. PMID:35725884
Deep embeddings to comprehend and visualize microbiome protein space. PMID:35725732
Comparative genomic analysis reveals contraction of gene families with putative roles in pathogenesis in the fungal boxwood pathogens Calonectria henricotiae and C. pseudonaviculata. PMID:35725368
New Insights into Evolution of the ABC Transporter Family in Mesostigma viride, a Unicellular Charophyte Algae. PMID:35723370
In Depth Exploration of the Alternative Proteome of Drosophila melanogaster. PMID:35721519
A de novo genome assembly of cultivated Prunus persica cv. 'Sovetskiy'. PMID:35714114
Decoding phage resistance by mpr and its role in survivability of Mycobacterium smegmatis. PMID:35713559
Candidate Chemosensory Genes Identified in the Adult Antennae of Sympiezomias velatus and Binding Property of Odorant-Binding Protein 15. PMID:35711318
To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131. PMID:35710371
Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach. PMID:35709304
Integrated bioinformatics, modelling, and gene expression analysis of the putative pentose transporter from Candida tropicalis during xylose fermentation with and without glucose addition. PMID:35708749
Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations. PMID:35705644
High sorbic acid resistance of Penicillium roqueforti is mediated by the SORBUS gene cluster. PMID:35704633
Cm28, a scorpion toxin having a unique primary structure, inhibits KV1.2 and KV1.3 with high affinity. PMID:35699659
Gene expression profiling and protein-protein interaction analysis reveals the dynamic role of MCM7 in Alzheimer's disorder and breast cancer. PMID:35698583
Insight into mechanisms of pig lncRNA FUT3-AS1 regulating E. coli F18-bacterial diarrhea. PMID:35696408
CView: A network based tool for enhanced alignment visualization. PMID:35696379
Health-Promoting Nature of Lactococcus lactis IBB109 and Lactococcus lactis IBB417 Strains Exhibiting Proliferation Inhibition and Stimulation of Interleukin-18 Expression in Colorectal Cancer Cells. PMID:35694291
Genome-wide identification and characterization of glutathione S-transferase gene family in Musa acuminata L. AAA group and gaining an insight to their role in banana fruit development. PMID:35689012
Interpretable Deep Learning Model Reveals Subsequences of Various Functions for Long Non-Coding RNA Identification. PMID:35685437
Genome-Wide Identification and Functional Differentiation of Fatty Acid Desaturase Genes in Olea europaea L. PMID:35684188
Genome-Wide Identification and Analysis of Ariadne Gene Family Reveal Its Genetic Effects on Agronomic Traits of Brassica napus. PMID:35682945
BIAPSS: A Comprehensive Physicochemical Analyzer of Proteins Undergoing Liquid-Liquid Phase Separation. PMID:35682883
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
The Dual Functions of a Bracovirus C-Type Lectin in Caterpillar Immune Response Manipulation. PMID:35663984
Evidence for an Independent Hydrogenosome-to-Mitosome Transition in the CL3 Lineage of Fornicates. PMID:35663895
Loss of PPR protein Ppr2 induces ferroptosis-like cell death in Schizosaccharomyces pombe. PMID:35657410
Evolution and functional diversification of catalase genes in the green lineage. PMID:35650553
Co-component signal transduction systems: Fast-evolving virulence regulation cassettes discovered in enteric bacteria. PMID:35648808
UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions. PMID:35648479
RpoN-Based stapled peptides with improved DNA binding suppress Pseudomonas aeruginosa virulence. PMID:35647551
Chromosome-Scale, Haplotype-Resolved Genome Assembly of Suaeda Glauca. PMID:35646071
Genome-Wide Identification and Transcript Analysis Reveal Potential Roles of Oligopeptide Transporter Genes in Iron Deficiency Induced Cadmium Accumulation in Peanut. PMID:35646039
Origin, Expansion, and Divergence of ETHYLENE-INSENSITIVE 3 (EIN3)/EIN3-LIKE Transcription Factors During Streptophytes Evolution. PMID:35645995
FUNAGE-Pro: comprehensive web server for gene set enrichment analysis of prokaryotes. PMID:35641095
GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective. PMID:35639770
PRECOGx: exploring GPCR signaling mechanisms with deep protein representations. PMID:35639758
Complete Genome Sequence of the N4-like Pseudomonas aeruginosa Bacteriophage vB_PaeP_CMS1. PMID:35638894
Conservation and Evolution of the Sporulation Gene Set in Diverse Members of the Firmicutes. PMID:35638784
ColabFold: making protein folding accessible to all. PMID:35637307
Coevolution-derived native and non-native contacts determine the emergence of a novel fold in a universally conserved family of transcription factors. PMID:35634768
Characterization of Three Novel Virulent Aeromonas Phages Provides Insights into the Diversity of the Autographiviridae Family. PMID:35632757
The International Virus Bioinformatics Meeting 2022. PMID:35632715
The Search for Cryptic L-Rhamnosyltransferases on the Sporothrix schenckii Genome. PMID:35628784
Genome-Wide Identification and Transcriptional Expression Profiles of PP2C in the Barley (Hordeum vulgare L.) Pan-Genome. PMID:35627219
Genome-Wide Identification and Expressional Profiling of the Metal Tolerance Protein Gene Family in Brassica napus. PMID:35627146
DEAD/H-Box Helicases in Immunity, Inflammation, Cell Differentiation, and Cell Death and Disease. PMID:35626643
Venomics of the Central European Myrmicine Ants Myrmica rubra and Myrmica ruginodis. PMID:35622604
Inducible Expression of Several Drosophila melanogaster Genes Encoding Juvenile Hormone Binding Proteins by a Plant Diterpene Secondary Metabolite, Methyl Lucidone. PMID:35621756
Multi-Omic Data Improve Prediction of Personalized Tumor Suppressors and Oncogenes. PMID:35620468
Comprehensive evolutionary analysis and nomenclature of plant G3BPs. PMID:35618429
GrainGenes: a data-rich repository for small grains genetics and genomics. PMID:35616118
Dali server: structural unification of protein families. PMID:35610055
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid-liquid phase separation and aggregation of proteins. PMID:35610022
Genome-wide characterization and identification of candidate ERF genes involved in various abiotic stress responses in sesame (Sesamum indicum L.). PMID:35606719
Ancient plant-like terpene biosynthesis in corals. PMID:35606558
Stabilization of swine faecal samples influences taxonomic and functional results in microbiome analyses. PMID:35601955
Transcriptome and Metabolome Analysis of the Synthesis Pathways of Allelochemicals in Eupatorium adenophorum. PMID:35601343
Dataset of De Novo hybrid berry transcriptome profiling and characterization of Piper species (Piper nigrum and Piper longum) using Illumina and Nanopore sequencing. PMID:35599816
Machine learning and comparative genomics approaches for the discovery of xylose transporters in yeast. PMID:35596177
Fbxw17 is dispensable for viability and fertility in mice. PMID:35585383
Metagenomic psychrohalophilic xylanase from camel rumen investigated for bioethanol production from wheat bran using Bacillus subtilis AP. PMID:35581279
Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria. PMID:35580059
IBS 2.0: an upgraded illustrator for the visualization of biological sequences. PMID:35580044
Comprehensive Genome-Wide Identification, Characterization, and Expression Analysis of CCHC-Type Zinc Finger Gene Family in Wheat (Triticum aestivum L.). PMID:35574096
The Mantle Transcriptome of Chamelea gallina (Mollusca: Bivalvia) and Shell Biomineralization. PMID:35565623
α-Arrestins and Their Functions: From Yeast to Human Health. PMID:35563378
Identification, In Silico Characterization, and Differential Expression Profiles of Carotenoid, Xanthophyll, Apocarotenoid Biosynthetic Pathways Genes, and Analysis of Carotenoid and Xanthophyll Accumulation in Heracleum moellendorffii Hance. PMID:35563233
Identification, Phylogenetic and Expression Analyses of the AAAP Gene Family in Liriodendron chinense Reveal Their Putative Functions in Response to Organ and Multiple Abiotic Stresses. PMID:35563155
Transitions of foliar mycobiota community and transcriptome in response to pathogenic conifer needle interactions. PMID:35551491
Comprehensive Profiling of Tubby-Like Proteins in Soybean and Roles of the GmTLP8 Gene in Abiotic Stress Responses. PMID:35548296
A High-Quality Haplotype-Resolved Genome of Common Bermudagrass (Cynodon dactylon L.) Provides Insights Into Polyploid Genome Stability and Prostrate Growth. PMID:35548270
Genome-wide scan for selection signatures and genes related to heat tolerance in domestic chickens in the tropical and temperate regions in Asia. PMID:35537342
DEPCOD: a tool to detect and visualize co-evolution of protein domains. PMID:35536332
Expanding the Database of Signal-Anchor-Release Domain Endolysins Through Metagenomics. PMID:35525881
GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs. PMID:35524575
Evaluating metagenomic assembly approaches for biome-specific gene catalogues. PMID:35524337
Flavobacterium hungaricum sp. nov. a novel soil inhabitant, cellulolytic bacterium isolated from plough field. PMID:35524012
Comparative optimization of combinatorial CRISPR screens. PMID:35513429
A De Novo Chromosome-Level Genome Assembly of the White-Tailed Deer, Odocoileus Virginianus. PMID:35511871
Optimizing the Parametrization of Homologue Classification in the Pan-Genome Computation for a Bacterial Species: Case Study Streptococcus pyogenes. PMID:35507269
MrParse: finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more. PMID:35503204
Microbiome "Inception": an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host. PMID:35502903
Genome-wide identification, evolutionary and functional analyses of KFB family members in potato. PMID:35501691
Chromosome-Level Genome Assembly of the Hemiparasitic Taxillus chinensis (DC.) Danser. PMID:35482027
Innovation and tinkering in the evolution of oxidases. PMID:35481655
The RNA Chaperone Protein Hfq Regulates the Characteristic Sporulation and Insecticidal Activity of Bacillus thuringiensis. PMID:35479624
Copper Metabolism in Naegleria gruberi and Its Deadly Relative Naegleria fowleri. PMID:35478954
Functional Insights of Salinity Stress-Related Pathways in Metagenome-Resolved Methanothrix Genomes. PMID:35477253
Large-scale discovery of novel neurodevelopmental disorder-related genes through a unified analysis of single-nucleotide and copy number variants. PMID:35468861
Genome-wide identification and expression analysis of the SWEET gene family in daylily (Hemerocallis fulva) and functional analysis of HfSWEET17 in response to cold stress. PMID:35468723
Genome-Wide Identification and Characterization of the WRKY Gene Family in Scutellaria baicalensis Georgi under Diverse Abiotic Stress. PMID:35457040
Beyond the ABCs-Discovery of Three New Plasmid Types in Rhodobacterales (RepQ, RepY, RepW). PMID:35456790
Methodologies for the De novo Discovery of Transposable Element Families. PMID:35456515
Transcriptome Analysis Revealed Long Non-Coding RNAs Associated with mRNAs in Sheep Thyroid Gland under Different Photoperiods. PMID:35456411
Genome-Wide Analysis of the Protein Phosphatase 2C Genes in Tomato. PMID:35456410
Identification of Intrinsically Disordered Proteins and Regions in a Non-Model Insect Species Ostrinia nubilalis (Hbn.). PMID:35454181
Developments in Algorithms for Sequence Alignment: A Review. PMID:35454135
Non-Heading Chinese Cabbage Database: An Open-Access Platform for the Genomics of Brassica campestris (syn. Brassica rapa) ssp. chinensis. PMID:35448733
Transcriptional Regulation of Reproductive Diapause in the Convergent Lady Beetle, Hippodamia convergens. PMID:35447785
Incomplete lineage sorting and phenotypic evolution in marsupials. PMID:35447073
An Extracytoplasmic Function Sigma Factor Required for Full Virulence in Xanthomonas citri pv. citri. PMID:35446118
Fungi hijack a ubiquitous plant apoplastic endoglucanase to release a ROS scavenging β-glucan decasaccharide to subvert immune responses. PMID:35441693
High-quality genome and methylomes illustrate features underlying evolutionary success of oaks. PMID:35440538
The Rad9-Rad1-Hus1 DNA repair clamp is found in Microsporidia. PMID:35439302
OvoAMtht from Methyloversatilis thermotolerans ovothiol biosynthesis is a bifunction enzyme: thiol oxygenase and sulfoxide synthase activities. PMID:35432880
A de Novo ZMIZ1 Pathogenic Variant for Neurodevelopmental Disorder With Dysmorphic Facies and Distal Skeletal Anomalies. PMID:35432459
Genome-wide Identification of Metal Tolerance Protein Genes in Peanut: Differential Expression in the Root of Two Contrasting Cultivars Under Metal Stresses. PMID:35432419
Characterization and Genomic Analysis of the First Podophage Infecting Shewanella, Representing a Novel Viral Cluster. PMID:35432264
The grapevine aspartic protease gene family: characterization and expression modulation in response to Plasmopara viticola. PMID:35426578
DUF1005 Family Identification, Evolution Analysis in Plants, and Primary Root Elongation Regulation of CiDUF1005 From Caragana intermedia. PMID:35422842
Structural and Evolutionary Adaptations of Nei-Like DNA Glycosylases Proteins Involved in Base Excision Repair of Oxidative DNA Damage in Vertebrates. PMID:35419164
Prediction of Prophages and Their Host Ranges in Pathogenic and Commensal Neisseria Species. PMID:35418239
Natural variation and improved genome annotation of the emerging biofuel crop field pennycress (Thlaspi arvense). PMID:35416986
Genome-wide analysis of the VQ motif-containing gene family and expression profiles during phytohormones and abiotic stresses in wheat (Triticum aestivum L.). PMID:35410124
Structural and Biophysical Insights into SPINK1 Bound to Human Cationic Trypsin. PMID:35408828
Molecular Characterization, Evolutionary Analysis, and Expression Profiling of BOR Genes in Important Cereals. PMID:35406892
Metal Tolerance Protein Encoding Gene Family in Fagopyrum tartaricum: Genome-Wide Identification, Characterization and Expression under Multiple Metal Stresses. PMID:35406830
Evolution of binding preferences among whole-genome duplicated transcription factors. PMID:35404235
A Proteome-Level Investigation Into Plasmodiophora brassicae Resistance in Brassica napus Canola. PMID:35401597
HLB induce changes in the tree physiology of citron (Citrus medica L. var. sarcodactylis Swingle). PMID:35400879
The structure of Synechococcus elongatus enolase reveals key aspects of phosphoenolpyruvate binding. PMID:35400670
A Large-Scale Genome-Based Survey of Acidophilic Bacteria Suggests That Genome Streamlining Is an Adaption for Life at Low pH. PMID:35387071
Improving ΔΔG Predictions with a Multitask Convolutional Siamese Network. PMID:35380443
Potential Role of the Host-Derived Cell-Wall Binding Domain of Endolysin CD16/50L as a Molecular Anchor in Preservation of Uninfected Clostridioides difficile for New Rounds of Phage Infection. PMID:35377223
The genomic basis of host and vector specificity in non-pathogenic trypanosomatids. PMID:35373253
Profiling hymenopteran venom toxins: Protein families, structural landscape, biological activities, and pharmacological benefits. PMID:35372826
Expanding the RNA virome of nematodes and other soil-inhabiting organisms. PMID:35371560
Transcriptome Sequencing Reveals the Antiviral Innate Immunity by IFN-γ in Chinese Sturgeon Macrophages. PMID:35371107
Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota. PMID:35365790
Current progress and open challenges for applying deep learning across the biosciences. PMID:35365602
Population genomics of the grapevine pathogen Eutypa lata reveals evidence for population expansion and intraspecific differences in secondary metabolite gene clusters. PMID:35363788
Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0. PMID:35362464
Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation. PMID:35359727
A beginner's guide to manual curation of transposable elements. PMID:35354491
Antimicrobial resistance patterns and genetic elements associated with the antibiotic resistance of Helicobacter pylori strains from Shanghai. PMID:35354484
A chromosome-scale genome assembly of the false clownfish, Amphiprion ocellaris. PMID:35353192
Correlational networking guides the discovery of unclustered lanthipeptide protease-encoding genes. PMID:35347143
Engineering selectivity of Cutibacterium acnes phages by epigenetic imprinting. PMID:35344565
De novo assembly of a fruit transcriptome set identifies AmMYB10 as a key regulator of anthocyanin biosynthesis in Aronia melanocarpa. PMID:35337270
Molecular Characteristics and Incidence of Apple Rubbery Wood Virus 2 and Citrus Virus A Infecting Pear Trees in China. PMID:35336983
Genome-Wide Identification and Expression Profile Reveal Potential Roles of Peanut ZIP Family Genes in Zinc/Iron-Deficiency Tolerance. PMID:35336668
Mining folded proteomes in the era of accurate structure prediction. PMID:35333855
AutoCoEv-A High-Throughput In Silico Pipeline for Predicting Inter-Protein Coevolution. PMID:35328772
Genome-Wide Identification of YABBY Gene Family in Cucurbitaceae and Expression Analysis in Cucumber (Cucumis sativus L.). PMID:35328021
In Silico Study of Superoxide Dismutase Gene Family in Potato and Effects of Elevated Temperature and Salicylic Acid on Gene Expression. PMID:35326138
Transcriptional control of Arabidopsis seed development. PMID:35318532
Genome wide study of cysteine rich receptor like proteins in Gossypium sp. PMID:35318409
Self-incompatibility requires GPI anchor remodeling by the poppy PGAP1 ortholog HLD1. PMID:35316654
Computational Tools for the Analysis of Uncultivated Phage Genomes. PMID:35311574
Comparative Genomics of Cyclic di-GMP Metabolism and Chemosensory Pathways in Shewanella algae Strains: Novel Bacterial Sensory Domains and Functional Insights into Lifestyle Regulation. PMID:35311563
Mining for New Sources of Resistance to Powdery Mildew in Genetic Resources of Winter Wheat. PMID:35300015
Venom system variation and the division of labor in the colonial hydrozoan Hydractinia symbiolongicarpus. PMID:35287376
A Metagenomic Approach for Characterizing Antibiotic Resistance Genes in Specific Bacterial Populations: Demonstration with Escherichia coli in Cattle Manure. PMID:35285243
Heterologous Expression and Biochemical Analysis Reveal a Schizokinen-Based Siderophore Pathway in Leptolyngbya (Cyanobacteria). PMID:35285240
Fine Mapping of a Vigor QTL in Chickpea (Cicer arietinum L.) Reveals a Potential Role for Ca4_TIFY4B in Regulating Leaf and Seed Size. PMID:35283931
Genome-wide investigation of maize RAD51 binding affinity through phage display. PMID:35279087
Biogenesis, conservation, and function of miRNA in liverworts. PMID:35275209
DeepREAL: A Deep Learning Powered Multi-scale Modeling Framework for Predicting Out-of-distribution Ligand-induced GPCR Activity. PMID:35274689
Evolutionary genomic relationships and coupling in MK-STYX and STYX pseudophosphatases. PMID:35264672
Infection strategy and biogeography distinguish cosmopolitan groups of marine jumbo bacteriophages. PMID:35260829
The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus. PMID:35255818
The long non-coding RNA LNC_000397 negatively regulates PRRSV replication through induction of interferon-stimulated genes. PMID:35248059
The molecular basis of FimT-mediated DNA uptake during bacterial natural transformation. PMID:35246533
The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains. PMID:35242291
Genome-Wide Association Study-Guided Exome Rare Variant Burden Analysis Identifies IL1R1 and CD3E as Potential Autoimmunity Risk Genes for Celiac Disease. PMID:35237542
Bacteriophage Lytic Enzyme P9ly as an Alternative Antibacterial Agent Against Antibiotic-Resistant Shigella dysenteriae and Staphylococcus aureus. PMID:35237249
The APAF1_C/WD40 repeat domain-encoding gene from the sea lettuce Ulva mutabilis sheds light on the evolution of NB-ARC domain-containing proteins in green plants. PMID:35235070
Small molecule targeting CELF1 RNA-binding activity to control HSC activation and liver fibrosis. PMID:35234905
Structural and functional analysis of the SET3 histone deacetylase complex. PMID:35234136
Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA. PMID:35229157
PubChem Protein, Gene, Pathway, and Taxonomy Data Collections: Bridging Biology and Chemistry through Target-Centric Views of PubChem Data. PMID:35227770
Usher syndrome type IV: clinically and molecularly confirmed by novel ARSG variants. PMID:35226187
Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Five Solanaceae Species and Identification of Members Regulating Carotenoid Biosynthesis in Wolfberry. PMID:35216373
Genome-Wide Evolution and Comparative Analysis of Superoxide Dismutase Gene Family in Cucurbitaceae and Expression Analysis of Lagenaria siceraria Under Multiple Abiotic Stresses. PMID:35211150
Changes in Gene Expression in Leaves of Cacao Genotypes Resistant and Susceptible to Phytophthora palmivora Infection. PMID:35211126
Antiparasitic Ovalicin Derivatives from Pseudallescheria boydii, a Mutualistic Fungus of French Guiana Termites. PMID:35208983
Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera. PMID:35208935
Genome Mining and Analysis of PKS Genes in Eurotium cristatum E1 Isolated from Fuzhuan Brick Tea. PMID:35205947
Identification of the CesA Subfamily and Functional Analysis of GhMCesA35 in Gossypium hirsutum L. PMID:35205337
Viral dUTPases: Modulators of Innate Immunity. PMID:35204728
Comprehensive Analysis of Imipenemase (IMP)-Type Metallo-β-Lactamase: A Global Distribution Threatening Asia. PMID:35203838
Persistence and Dissemination Capacities of a blaNDM-5-Harboring IncX-3 Plasmid in Escherichia coli Isolated from an Urban River in Montpellier, France. PMID:35203799
Combined use of Oxford Nanopore and Illumina sequencing yields insights into soybean structural variation biology. PMID:35197050
The structure of the Clostridium thermocellum RsgI9 ectodomain provides insight into the mechanism of biomass sensing. PMID:35194841
Parental folate deficiency induces birth defects in mice accompanied with increased de novo mutations. PMID:35190523
Independent Evolution of the MYB Family in Brown Algae. PMID:35186015
Large-scale analyses of heat shock transcription factors and database construction based on whole-genome genes in horticultural and representative plants. PMID:35184193
Within-host quantitation of anellovirus genome complexity from clinical samples. PMID:35176352
Secondary Structures of Proteins Follow Menzerath-Altmann Law. PMID:35163493
PIPENN: Protein Interface Prediction from sequence with an Ensemble of Neural Nets. PMID:35150231
DECIPHER: Supporting the interpretation and sharing of rare disease phenotype-linked variant data to advance diagnosis and research. PMID:35143074
De Novo Genome Assembly of Stinkhorn Mushroom Clathrus columnatus (Basidiomycota, Fungi) Using Illumina and Nanopore Sequencing Data. PMID:35142541
LncPep: A Resource of Translational Evidences for lncRNAs. PMID:35141219
RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data. PMID:35136930
MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences. PMID:35134858
A Similarity-Based Method for Predicting Enzymatic Functions in Yeast Uncovers a New AMP Hydrolase. PMID:35123996
Chitosan induces differential transcript usage of chitosanase 3 encoding gene (csn3) in the biocontrol fungus Pochonia chlamydosporia 123. PMID:35123406
Complete Genome Sequence of a Jumbo Bacteriophage, Escherichia Phage vB_EcoM_EC001. PMID:35112904
Improvement of the Stability and Activity of an LPMO Through Rational Disulfide Bonds Design. PMID:35111741
Integrated Analysis of Basic Helix Loop Helix Transcription Factor Family and Targeted Terpenoids Reveals Candidate AarbHLH Genes Involved in Terpenoid Biosynthesis in Artemisia argyi. PMID:35111184
MetaLogo: a heterogeneity-aware sequence logo generator and aligner. PMID:35108357
Databases for intrinsically disordered proteins. PMID:35102880
SlERF.F12 modulates the transition to ripening in tomato fruit by recruiting the co-repressor TOPLESS and histone deacetylases to repress key ripening genes. PMID:35099538
Complexome Profiling-Exploring Mitochondrial Protein Complexes in Health and Disease. PMID:35096826
The Ancient Origins of Death Domains Support the 'Original Sin' Hypothesis for the Evolution of Programmed Cell Death. PMID:35084524
Gene expression alterations from reversible to irreversible stages during coral metamorphosis. PMID:35078542
A simple guide to de novo transcriptome assembly and annotation. PMID:35076693
Ultrafast end-to-end protein structure prediction enables high-throughput exploration of uncharacterized proteins. PMID:35074909
The structural coverage of the human proteome before and after AlphaFold. PMID:35073311
Using metagenomic data to boost protein structure prediction and discovery. PMID:35070166
Genome-wide survey of the dehydrin genes in bread wheat (Triticum aestivum L.) and its relatives: identification, evolution and expression profiling under various abiotic stresses. PMID:35065618
Structural Identification of Metalloproteomes in Marine Diatoms, an Efficient Algae Model in Toxic Metals Bioremediation. PMID:35056698
Molecular Responses to Thermal and Osmotic Stress in Arctic Intertidal Mussels (Mytilus edulis): The Limits of Resilience. PMID:35052494
Methylphosphonate Degradation and Salt-Tolerance Genes of Two Novel Halophilic Marivita Metagenome-Assembled Genomes from Unrestored Solar Salterns. PMID:35052488
A Novel GEMIN4 Variant in a Consanguineous Family Leads to Neurodevelopmental Impairment with Severe Microcephaly, Spastic Quadriplegia, Epilepsy, and Cataracts. PMID:35052432
Genome-Wide Identification, Primary Functional Characterization of the NHX Gene Family in Canavalia rosea, and Their Possible Roles for Adaptation to Tropical Coral Reefs. PMID:35052375
Redefining the coenzyme A transferase superfamily with a large set of manually annotated proteins. PMID:35049101
Ins and outs of AlphaFold2 transmembrane protein structure predictions. PMID:35034173
Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer. PMID:35030025
Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes. PMID:35022216
A Micrarchaeon Isolate Is Covered by a Proteinaceous S-Layer. PMID:35020453
DeepLRR: An Online Webserver for Leucine-Rich-Repeat Containing Protein Characterization Based on Deep Learning. PMID:35009139
Genome-Wide Characterization and Expression Analysis of KH Family Genes Response to ABA and SA in Arabidopsis thaliana. PMID:35008936
Synthesis of Dolichols in Candida albicans Is Co-Regulated with Elongation of Fatty Acids. PMID:35008833
A Comparison between Enrichment Optimization Algorithm (EOA)-Based and Docking-Based Virtual Screening. PMID:35008467
Rel/NF-κB Transcription Factors Emerged at the Onset of Opisthokonts. PMID:34999783
The embryonic transcriptome of Parhyale hawaiensis reveals different dynamics of microRNAs and mRNAs during the maternal-zygotic transition. PMID:34996916
The lolB gene in Xanthomonas campestris pv. campestris is required for bacterial attachment, stress tolerance, and virulence. PMID:34996353
Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs). PMID:34987183
HIT 2.0: an enhanced platform for Herbal Ingredients' Targets. PMID:34986599
Characterization of a novel broad-spectrum endolysin PlyD4 encoded by a highly conserved prophage found in Aeromonas hydrophila ST251 strains. PMID:34985567
SignalP 6.0 predicts all five types of signal peptides using protein language models. PMID:34980915
Horizontally Acquired Cellulases Assist the Expansion of Dietary Range in Pristionchus Nematodes. PMID:34978575
The Nutritional Environment Is Sufficient To Select Coexisting Biofilm and Quorum Sensing Mutants of Pseudomonas aeruginosa. PMID:34978461
First Comparative Analysis of Clostridium septicum Genomes Provides Insights Into the Taxonomy, Species Genetic Diversity, and Virulence Related to Gas Gangrene. PMID:34956133
High Molecular Weight Kininogen: A Review of the Structural Literature. PMID:34948166
Phenotypic Characterization and Comparative Genomics of the Melanin-Producing Yeast Exophiala lecanii-corni Reveals a Distinct Stress Tolerance Profile and Reduced Ribosomal Genetic Content. PMID:34947060
Evolutionary Characterization of the Short Protein SPAAR. PMID:34946813
Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors. PMID:34946800
Finding Aquaporins in Annelids: An Evolutionary Analysis and a Case Study. PMID:34944070
Genome-Wide Identification and Expression Analysis of Potential Antiviral Tripartite Motif Proteins (TRIMs) in Grass Carp (Ctenopharyngodon idella). PMID:34943167
A novel C-terminal DxRSDxE motif in ceramide synthases involved in dimer formation. PMID:34942147
Extremophile enzyme optimization for low temperature and high salinity are fundamentally incompatible. PMID:34940913
Exploring the multifunctionality of SR proteins. PMID:34940860
PreBINDS: An Interactive Web Tool to Create Appropriate Datasets for Predicting Compound-Protein Interactions. PMID:34938773
Functional Analysis of H+-Pumping Membrane-Bound Pyrophosphatase, ADP-Glucose Synthase, and Pyruvate Phosphate Dikinase as Pyrophosphate Sources in Clostridium thermocellum. PMID:34936842
Sequence Conservation, Domain Architectures, and Phylogenetic Distribution of the HD-GYP Type c-di-GMP Phosphodiesterases. PMID:34928179
Transcriptomic Response to Perkinsus marinus in Two Crassostrea Oysters Reveals Evolutionary Dynamics of Host-Parasite Interactions. PMID:34925467
An unconventionally secreted effector from the root knot nematode Meloidogyne incognita, Mi-ISC-1, promotes parasitism by disrupting salicylic acid biosynthesis in host plants. PMID:34923729
De novo transcriptome assembly and annotation of parthenogenetic lizard Darevskia unisexualis and its parental ancestors Darevskia valentini and Darevskia raddei nairensis. PMID:34917712
Genome-Wide Identification and Expression Analysis of the Plant U-Box Protein Gene Family in Phyllostachys edulis. PMID:34917124
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
Comparative transcriptome and metabolome analysis reveal glutathione metabolic network and functional genes underlying blue and red-light mediation in maize seedling leaf. PMID:34906076
Evolutionary analysis of angiosperm dehydrin gene family reveals three orthologues groups associated to specific protein domains. PMID:34903751
First report of Raphanus sativus cryptic virus 2 on cabbage seeds (Brassica rapa subsp. pekinensis) imported from Italy. PMID:34901331
Case Report: A Novel De Novo Missense Mutation of the GRIA2 Gene in a Chinese Case of Neurodevelopmental Disorder With Language Impairment. PMID:34899870
Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates. PMID:34893091
Development of a Molecular Serotyping Scheme for Morganella morganii. PMID:34887844
Cryo-EM structures of human RNA polymerase I. PMID:34887565
Comprehensive Analysis of SRO Gene Family in Sesamum indicum (L.) Reveals Its Association with Abiotic Stress Responses. PMID:34884850
New Findings on LMO7 Transcripts, Proteins and Regulatory Regions in Human and Vertebrate Model Organisms and the Intracellular Distribution in Skeletal Muscle Cells. PMID:34884689
Whole-Genome Sequencing of Acer catalpifolium Reveals Evolutionary History of Endangered Species. PMID:34878129
Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology. PMID:34873596
Mcc1229, an Stx2a-Amplifying Microcin, Is Produced In Vivo and Requires CirA for Activity. PMID:34871041
Sabulicella rubraurantiaca gen. nov., sp. nov., a new member of the family Acetobacteraceae, isolated from desert soil. PMID:34870748
Stage-specific disruption of X chromosome expression during spermatogenesis in sterile house mouse hybrids. PMID:34864964
Compendium of human transcription factor effector domains. PMID:34863368
Polyphenol Utilization Proteins in the Human Gut Microbiome. PMID:34851722
SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning. PMID:34850923
PRGdb 4.0: an updated database dedicated to genes involved in plant disease resistance process. PMID:34850118
A class I histone deacetylase HDA-2 is essential for embryonic development and size regulation of fertilized eggs in Caenorhabditis elegans. PMID:34843089
Functional Characterisation of Bile Metagenome: Study of Metagenomic Dark Matter. PMID:34835325
The Methods of Digging for "Gold" within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools. PMID:34828362
Lipid-Binding Aegerolysin from Biocontrol Fungus Beauveria bassiana. PMID:34822604
Phylogenetic Distribution of WhiB- and Lsr2-Type Regulators in Actinobacteriophage Genomes. PMID:34817283
Discovery and initial characterization of YloC, a novel endoribonuclease in Bacillus subtilis. PMID:34815358
Bacterial Sirtuins Overview: An Open Niche to Explore. PMID:34803965
Three critical regions of the erythromycin resistance methyltransferase, ErmE, are required for function supporting a model for the interaction of Erm family enzymes with substrate rRNA. PMID:34795028
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. PMID:34791371
FuzDB: a new phase in understanding fuzzy interactions. PMID:34791357
Draft genome sequences of strains CBS6241 and CBS6242 of the basidiomycetous yeast Filobasidium floriforme. PMID:34791213
ATRX proximal protein associations boast roles beyond histone deposition. PMID:34780483
Glycoproteomic Characterization of FUT8 Knock-Out CHO Cells Reveals Roles of FUT8 in the Glycosylation. PMID:34778211
An Evolutionary Analysis of B-Box Transcription Factors in Strawberry Reveals the Role of FaBBx28c1 in the Regulation of Flowering Time. PMID:34769196
Genome-Wide Identification and Transcriptional Analysis of Arabidopsis DUF506 Gene Family. PMID:34768874
Synthaser: a CD-Search enabled Python toolkit for analysing domain architecture of fungal secondary metabolite megasynth(et)ases. PMID:34763725
fLPS 2.0: rapid annotation of compositionally-biased regions in biological sequences. PMID:34760378
The trRosetta server for fast and accurate protein structure prediction. PMID:34759384
APPRIS: selecting functionally important isoforms. PMID:34755885
BRAD V3.0: an upgraded Brassicaceae database. PMID:34755871
Modeling Sequence-Space Exploration and Emergence of Epistatic Signals in Protein Evolution. PMID:34751386
Mitochondrial "dysmorphology" in variant classification. PMID:34750646
Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis. PMID:34748609
Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses. PMID:34747465
Identification of GATA Transcription Factors in Brachypodium distachyon and Functional Characterization of BdGATA13 in Drought Tolerance and Response to Gibberellins. PMID:34745195
High-throughput imaging of ATG9A distribution as a diagnostic functional assay for adaptor protein complex 4-associated hereditary spastic paraplegia. PMID:34729478
PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies. PMID:34718760
CompoDynamics: a comprehensive database for characterizing sequence composition dynamics. PMID:34718745
The Eukaryotic Linear Motif resource: 2022 release. PMID:34718738
MetazExp: a database for gene expression and alternative splicing profiles and their analyses based on 53 615 public RNA-seq samples in 72 metazoan species. PMID:34718719
PANTHER: Making genome-scale phylogenetics accessible to all. PMID:34717010
adabmDCA: adaptive Boltzmann machine learning for biological sequences. PMID:34715775
A conserved Neurite Outgrowth and Guidance motif with biomimetic potential in neuronal Cell Adhesion Molecules. PMID:34712402
A phylogenomic framework for charting the diversity and evolution of giant viruses. PMID:34705818
Utilizing the VirIdAl Pipeline to Search for Viruses in the Metagenomic Data of Bat Samples. PMID:34696436
Ambient Air Pollution Shapes Bacterial and Fungal Ivy Leaf Communities. PMID:34683409
Expression Patterns of the Heat Shock Protein 90 (Hsp90) Gene Suggest Its Possible Involvement in Maintaining the Dormancy of Dinoflagellate Resting Cysts. PMID:34681714
Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern. PMID:34681003
Diversity in Sensing and Signaling of Bacterial Sensor Histidine Kinases. PMID:34680156
Hybrid Sequencing in Different Types of Goat Skeletal Muscles Reveals Genes Regulating Muscle Development and Meat Quality. PMID:34679927
UbiBrowser 2.0: a comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotic species. PMID:34669962
Deletion of E184L, a Putative DIVA Target from the Pandemic Strain of African Swine Fever Virus, Produces a Reduction in Virulence and Protection against Virulent Challenge. PMID:34668772
NPCDR: natural product-based drug combination and its disease-specific molecular regulation. PMID:34664659
Identification of novel translated small ORFs in Escherichia coli using complementary ribosome profiling approaches. PMID:34662240
Structure of Venezuelan equine encephalitis virus in complex with the LDLRAD3 receptor. PMID:34646020
Lethal variants in humans: lessons learned from a large molecular autopsy cohort. PMID:34645488
Genome and Ecology of a Novel Alteromonas Podovirus, ZP6, Representing a New Viral Genus, Mareflavirus. PMID:34643440
Structural and functional characterization of Mpp75Aa1.1, a putative beta-pore forming protein from Brevibacillus laterosporus active against the western corn rootworm. PMID:34634061
OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. PMID:34632381
Efficient and accurate identification of protein complexes from protein-protein interaction networks based on the clustering coefficient. PMID:34630943
Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes. PMID:34630938
Novel Hemizygous Mutations of TEX11 Cause Meiotic Arrest and Non-obstructive Azoospermia in Chinese Han Population. PMID:34621296
A chromosome-level genome sequence of Chrysanthemum seticuspe, a model species for hexaploid cultivated chrysanthemum. PMID:34620992
Rapid specialization of counter defenses enables two-spotted spider mite to adapt to novel plant hosts. PMID:34618096
CyanoOmicsDB: an integrated omics database for functional genomic analysis of cyanobacteria. PMID:34614159
Predicted Functional and Structural Diversity of Receiver Domains in Fungal Two-Component Regulatory Systems. PMID:34612676
Sensory Perception in Bacterial Cyclic Diguanylate Signal Transduction. PMID:34606374
Automatic Prediction and Annotation: There Are Strong Biases for Multigenic Families. PMID:34603370
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. PMID:34597405
The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases. PMID:34591643
Chromosome-Level Genome Assembly and Annotation of the Fiber Flax (Linum usitatissimum) Genome. PMID:34589116
Genome-Wide Characterization of the MLO Gene Family in Cannabis sativa Reveals Two Genes as Strong Candidates for Powdery Mildew Susceptibility. PMID:34589104
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
OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes. PMID:34580179
Genome-Wide Identification and Analysis of the MADS-Box Gene Family in American Beautyberry (Callicarpa americana). PMID:34579338
Comparative Genomic Analysis of Novel Bifidobacterium longum subsp. longum Strains Reveals Functional Divergence in the Human Gut Microbiota. PMID:34576801
Extracellular Vesicle Signatures and Post-Translational Protein Deimination in Purple Sea Urchin (Strongylocentrotus purpuratus) Coelomic Fluid-Novel Insights into Echinodermata Biology. PMID:34571743
Characterization of the β-tubulin gene family in Ascaris lumbricoides and Ascaris suum and its implication for the molecular detection of benzimidazole resistance. PMID:34570778
A biallelic SNIP1 Amish founder variant causes a recognizable neurodevelopmental disorder. PMID:34570759
The Pbo Cluster from Pseudomonas syringae pv. Phaseolicola NPS3121 Is Thermoregulated and Required for Phaseolotoxin Biosynthesis. PMID:34564632
PncsHub: a platform for annotating and analyzing non-classically secreted proteins in Gram-positive bacteria. PMID:34551435
Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome. PMID:34546072
The genomes of nucleocytoplasmic large DNA viruses: viral evolution writ large. PMID:34542398
Classification of protein domains based on their three-dimensional shapes (CPD3DS). PMID:34541344
Identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network. PMID:34529933
Secondary metabolite biosynthetic diversity in the fungal family Hypoxylaceae and Xylaria hypoxylon. PMID:34527085
Comparative Phylogenomic Analysis Reveals Evolutionary Genomic Changes and Novel Toxin Families in Endophytic Liberibacter Pathogens. PMID:34523996
Proteogenomic Analysis Provides Novel Insight into Genome Annotation and Nitrogen Metabolism in Nostoc sp. PCC 7120. PMID:34523988
Lactococcus lactis Resistance to Aureocin A53- and Enterocin L50-Like Bacteriocins and Membrane-Targeting Peptide Antibiotics Relies on the YsaCB-KinG-LlrG Four-Component System. PMID:34516250
Integrating perspectives in actinomycete research: an ActinoBase review of 2020-21. PMID:34515628
Characterization and Genomic Analysis of Marinobacter Phage vB_MalS-PS3, Representing a New Lambda-Like Temperate Siphoviral Genus Infecting Algae-Associated Bacteria. PMID:34512604
Identification and Characterization of Antimicrobial Peptides From Butterflies: An Integrated Bioinformatics and Experimental Study. PMID:34512599
Identification and Characterization of an Antennae-Specific Glutathione S-Transferase From the Indian Meal Moth. PMID:34512396
Phylogenetic analyses, protein modeling and active site prediction of two pathogenesis related (PR2 and PR3) genes from bread wheat. PMID:34506613
Genome-Wide Identification and Analysis of the Metallothionein Genes in Oryza Genus. PMID:34502554
Certain Listeria monocytogenes plasmids contribute to increased UVC ultraviolet light stress. PMID:34498664
PUResNet: prediction of protein-ligand binding sites using deep residual neural network. PMID:34496970
VPS38/UVRAG and ATG14, the variant regulatory subunits of the ATG6/Beclin1-PI3K complexes, are crucial for the biogenesis of the yolk organelles and are transcriptionally regulated in the oocytes of the vector Rhodnius prolixus. PMID:34492013
Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae. PMID:34489462
Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom. PMID:34482372
How do I get the most out of my protein sequence using bioinformatics tools? PMID:34473083
The investigation of nonsynonymous SNPs of human SLC6A4 gene associated with depression: An in silico approach. PMID:34466701
Introducing Thioredoxin-Related Transmembrane Proteins: Emerging Roles of Human TMX and Clinical Implications. PMID:34465218
Horizontal transfer and subsequent explosive expansion of a DNA transposon in sea kraits (Laticauda). PMID:34464541
TIAMMAt: Leveraging Biodiversity to Revise Protein Domain Models, Evidence from Innate Immunity. PMID:34459919
Molecular Characterization, Expression Analysis of Carotenoid, Xanthophyll, Apocarotenoid Pathway Genes, and Carotenoid and Xanthophyll Accumulation in Chelidonium majus L. PMID:34451798
Transcriptome Analysis Reveals Key Genes Involved in Weevil Resistance in the Hexaploid Sweetpotato. PMID:34451581
Modular and Molecular Optimization of a LOV (Light-Oxygen-Voltage)-Based Optogenetic Switch in Yeast. PMID:34445244
Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes. PMID:34442314
Identification of Novel lncRNA and Differentially Expressed Genes (DEGs) of Testicular Tissues among Cattle, Yak, and Cattle-Yak Associated with Male Infertility. PMID:34438876
Conserved oligomeric Golgi (COG) complex genes functioning in defense are expressed in root cells undergoing a defense response to a pathogenic infection and exhibit regulation my MAPKs. PMID:34437620
Fungal Pathogen Emergence: Investigations with an Ustilago maydis × Sporisorium reilianum Hybrid. PMID:34436211
PI3K Plays an Essential Role in Planarian Regeneration and Tissue Maintenance. PMID:34422792
The Hob proteins are novel and conserved lipid-binding proteins at ER-PM contact sites. PMID:34415038
Deletion of the A137R Gene from the Pandemic Strain of African Swine Fever Virus Attenuates the Strain and Offers Protection against the Virulent Pandemic Virus. PMID:34406865
North Sea spring bloom-associated Gammaproteobacteria fill diverse heterotrophic niches. PMID:34404489
Peroxiredoxin Asp f3 Is Essential for Aspergillus fumigatus To Overcome Iron Limitation during Infection. PMID:34399627
A Widespread Bacterial Secretion System with Diverse Substrates. PMID:34399622
CASPredict: a web service for identifying Cas proteins. PMID:34395100
Comprehensive in silico Characterization of Universal Stress Proteins in Rice (Oryza sativa L.) With Insight Into Their Stress-Specific Transcriptional Modulation. PMID:34394169
Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana. PMID:34381973
Predicting Protein-Protein Interactions Between Rice and Blast Fungus Using Structure-Based Approaches. PMID:34367213
Sphingobacterium pedocola sp. nov. a novel halotolerant bacterium isolated from agricultural soil. PMID:34363180
Large-scale computational discovery and analysis of virus-derived microbial nanocompartments. PMID:34362927
Cellular costs underpin micronutrient limitation in phytoplankton. PMID:34362734
Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2. PMID:34362430
BonMOLière: Small-Sized Libraries of Readily Purchasable Compounds, Optimized to Produce Genuine Hits in Biological Screens across the Protein Space. PMID:34360558
Evidence of Immune Modulators in the Secretome of the Equine Tapeworm Anoplocephala perfoliata. PMID:34358062
Signatures of Transcription Factor Evolution and the Secondary Gain of Red Algae Complexity. PMID:34356071
Efficacy of Plant Growth-Promoting Bacteria Bacillus cereus YN917 for Biocontrol of Rice Blast. PMID:34354684
Cryo-EM structure of the human MT1-Gi signaling complex. PMID:34354246
Predicting moisture content during maize nixtamalization using machine learning with NIR spectroscopy. PMID:34345971
Ancestral Physical Stress and Later Immune Gene Family Expansions Shaped Bivalve Mollusc Evolution. PMID:34343278
Insights into a Pyruvate Sensing and Uptake System in Vibrio campbellii and Its Importance for Virulence. PMID:34339295
Diversification of the calponin family proteins by gene amplification and repeat expansion of calponin-like motifs. PMID:34333878
Biallelic COA7-Variants Leading to Developmental Regression With Progressive Spasticity and Brain Atrophy in a Chinese Patient. PMID:34322155
An Ancient Clade of Penelope-Like Retroelements with Permuted Domains Is Present in the Green Lineage and Protists, and Dominates Many Invertebrate Genomes. PMID:34320655
Endogenous Hemoprotein-Dependent Signaling Pathways of Nitric Oxide and Nitrite. PMID:34313417
Malectin/Malectin-like domain-containing proteins: A repertoire of cell surface molecules with broad functional potential. PMID:34308005
Highly accurate protein structure prediction for the human proteome. PMID:34293799
Structural and Functional Annotation of Napin-Like Protein from Momordica charantia to Explore its Medicinal Importance. PMID:34282529
Comparative and phylogenetic analyses of the chloroplast genomes of species of Paeoniaceae. PMID:34282194
Insights Into the Phylogenetic Distribution, Diversity, Structural Attributes, and Substrate Specificity of Putative Cyanobacterial Orthocaspases. PMID:34276616
Redefining the specificity of phosphoinositide-binding by human PH domain-containing proteins. PMID:34267198
A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases. PMID:34253785
The fluoride permeation pathway and anion recognition in Fluc family fluoride channels. PMID:34250906
Human D-aspartate Oxidase: A Key Player in D-aspartate Metabolism. PMID:34250021
Recognition of Streptococcal Promoters by the Pneumococcal SigA Protein. PMID:34250014
Cnidarian Pattern Recognition Receptor Repertoires Reflect Both Phylogeny and Life History Traits. PMID:34248980
A phylogeny-aware approach reveals unexpected venom components in divergent lineages of cone snails. PMID:34229491
Genome-wide analysis, identification, evolution and genomic organization of dehydration responsive element-binding (DREB) gene family in Solanum tuberosum. PMID:34221730
Genome-Wide Identification, Structure Characterization, Expression Pattern Profiling, and Substrate Specificity of the Metal Tolerance Protein Family in Canavalia rosea (Sw.) DC. PMID:34209283
Histamine: A Bacterial Signal Molecule. PMID:34204625
Genome-Wide Identification and Genetic Variations of the Starch Synthase Gene Family in Rice. PMID:34204124
Assessment of Evolutionary Relationships for Prioritization of Myxobacteria for Natural Product Discovery. PMID:34202719
Cellular Chaperone Function of Intrinsically Disordered Dehydrin ERD14. PMID:34201246
Complete Genome Sequence and Function Gene Identify of Prometryne-Degrading Strain Pseudomonas sp. DY-1. PMID:34200754
Draft Genome Sequences of Two Cadophora Strains Isolated from Water and a Nonalcoholic Beverage Ingredient. PMID:34197206
Clues to the function of bacterial microcompartments from ancillary genes. PMID:34196367
ORFograph: search for novel insecticidal protein genes in genomic and metagenomic assembly graphs. PMID:34183047
Completeness and Consistency in Structural Domain Classifications. PMID:34179613
From Genome to Drugs: New Approaches in Antimicrobial Discovery. PMID:34177572
Sequencing and Comparative Genomic Analysis of a Highly Metal-Tolerant Penicillium janthinellum P1 Provide Insights Into Its Metal Tolerance. PMID:34149650
Diverse Trajectories Drive the Expression of a Giant Virus in the Oomycete Plant Pathogen Phytophthora parasitica. PMID:34140938
Extending the Horizon of Homology Detection with Coevolution-based Structure Prediction. PMID:34139218
Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. PMID:34135888
Matrix-screening reveals a vast potential for direct protein-protein interactions among RNA binding proteins. PMID:34133714
Uncovering of cytochrome P450 anatomy by SecStrAnnotator. PMID:34117311
Structural Design and Analysis of the RHOA-ARHGEF1 Binding Mode: Challenges and Applications for Protein-Protein Interface Prediction. PMID:34109211
Mechnetor: a web server for exploring protein mechanism and the functional context of genetic variants. PMID:34076240
The Endocannabinoid System in the Mediterranean Mussel Mytilus galloprovincialis: Possible Mediators of the Immune Activity? PMID:34066927
Genome-Wide Identification of Barley Long Noncoding RNAs and Analysis of Their Regulatory Interactions during Shoot and Grain Development. PMID:34064912
A Machine Learning Approach to Study Glycosidase Activities from Bifidobacterium. PMID:34064844
Structural Perspectives on the Mechanism of Soluble Guanylate Cyclase Activation. PMID:34064029
AniProtDB: A Collection of Consistently Generated Metazoan Proteomes for Comparative Genomics Studies. PMID:34048573
IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation. PMID:34048569
G2PDeep: a web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers. PMID:34037802
Post-translational flavinylation is associated with diverse extracytosolic redox functionalities throughout bacterial life. PMID:34032212
Hybrid Histidine Kinase BinK Represses Vibrio fischeri Biofilm Signaling at Multiple Developmental Stages. PMID:34031036
DomainViz: intuitive visualization of consensus domain distributions across groups of proteins. PMID:34023887
Protein Composition and Associated Material Properties of Cobweb Spiders' Gumfoot Glue Droplets. PMID:34003260
EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure. PMID:33988716
Draft Genome Sequence of Lignin-Degrading Agrobacterium sp. Strain S2, Isolated from a Decaying Oil Palm Empty Fruit Bunch. PMID:33986086
antiSMASH 6.0: improving cluster detection and comparison capabilities. PMID:33978755
Structural Modeling of the Treponema pallidum Outer Membrane Protein Repertoire: a Road Map for Deconvolution of Syphilis Pathogenesis and Development of a Syphilis Vaccine. PMID:33972353
BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation. PMID:33963861
Proteo3Dnet: a web server for the integration of structural information with interactomics data. PMID:33963857
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. PMID:33956157
Detecting Protein Communities in Native Cell Extracts by Machine Learning: A Structural Biologist's Perspective. PMID:33937337
Integrated Biophysical Modeling of the SARS-CoV-2 Spike Protein Binding and Allosteric Interactions with Antibodies. PMID:33929853
Ubiquitin and Ubiquitin-Like Proteins and Domains in Ribosome Production and Function: Chance or Necessity? PMID:33921964
Structural Basis for the C-Terminal Domain of Mycobacterium tuberculosis Ribosome Maturation Factor RimM to Bind Ribosomal Protein S19. PMID:33919647
Terpenoid Biosynthesis Dominates among Secondary Metabolite Clusters in Mucoromycotina Genomes. PMID:33918813
An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies. PMID:33918473
Master Blaster: an approach to sensitive identification of remotely related proteins. PMID:33888741
SWEET Transporters and the Potential Functions of These Sequences in Tea (Camellia sinensis). PMID:33868386
Draft Genome Sequence and Polyhydroxyalkanoate Biosynthetic Potential of Jeongeupia naejangsanensis Type Strain DSM 24253. PMID:33858927
A SARS-CoV-2 -human metalloproteome interaction map. PMID:33813307
Combined Proteotranscriptomic-Based Strategy to Discover Novel Antimicrobial Peptides from Cone Snails. PMID:33805497
Co-Transcriptional RNA Processing in Plants: Exploring from the Perspective of Polyadenylation. PMID:33804866
Foamy Viruses, Bet, and APOBEC3 Restriction. PMID:33803830
Herbidospora solisilvae sp. nov., a novel cellulose-degrading actinobacterium isolated from forest soil. PMID:33649883
Cold-Shock Domains-Abundance, Structure, Properties, and Nucleic-Acid Binding. PMID:33430354
The European Bioinformatics Institute: empowering cooperation in response to a global health crisis. PMID:33245775 -
Pfam: a comprehensive database of protein domain families based on seed alignments
PubMed citations: 425.
425 articles citing: Pfam: a comprehensive database of protein domain families based on seed alignments
The PH Domain and C-Terminal polyD Motif of Phafin2 Exhibit a Unique Concurrence in Animals. PMID:35877899
Evolutionary origin and functional diversification of aminotransferases. PMID:35697072
Scrutinizing Deleterious Nonsynonymous SNPs and Their Effect on Human POLD1 Gene. PMID:35620275
Comparative analysis of the kinomes of Plasmodium falciparum, Plasmodium vivax and their host Homo sapiens. PMID:35346035
Comparative Genomics of Clostridium baratii Reveals Strain-Level Diversity in Toxin Abundance. PMID:35208668
Biological factors in the synthetic construction of overlapping genes. PMID:34895142
Characterization of the Flagellar Collar Reveals Structural Plasticity Essential for Spirochete Motility. PMID:34809456
First report of mitochondrial COI in foraminifera and implications for DNA barcoding. PMID:34772985
Brussowvirus SW13 Requires a Cell Surface-Associated Polysaccharide To Recognize Its Streptococcus thermophilus Host. PMID:34669424
Genome-Wide Identification and Evolutionary Analysis of the SRO Gene Family in Tomato. PMID:34621298
D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions. PMID:34536380
TIAMMAt: Leveraging Biodiversity to Revise Protein Domain Models, Evidence from Innate Immunity. PMID:34459919
Transcriptome profiling of Stevia rebaudiana MS007 revealed genes involved in flower development. PMID:34377055
Predicting antifreeze proteins with weighted generalized dipeptide composition and multi-regression feature selection ensemble. PMID:34162327
Prophage Genomics and Ecology in the Family Rhodobacteraceae. PMID:34064105
DRAGoM: Classification and Quantification of Noncoding RNA in Metagenomic Data. PMID:34025724
Sucrose synthase gene family in Brassica juncea: genomic organization, evolutionary comparisons, and expression regulation. PMID:33854830
A critical assessment of gene catalogs for metagenomic analysis. PMID:33792639
The very early evolution of protein translocation across membranes. PMID:33684113
Comparative transcriptomics of ice-crawlers demonstrates cold specialization constrains niche evolution in a relict lineage. PMID:33664782
Surface chemistry-mediated modulation of adsorbed albumin folding state specifies nanocarrier clearance by distinct macrophage subsets. PMID:33510170
Identification and characterization of the LRR repeats in plant LRR-RLKs. PMID:33509084
iBLP: An XGBoost-Based Predictor for Identifying Bioluminescent Proteins. PMID:33505515
Unraveling the roles of the reductant and free copper ions in LPMO kinetics. PMID:33478537
Diverse Evolution in 111 Plant Genomes Reveals Purifying and Dosage Balancing Selection Models for F-Box Genes. PMID:33467195
InsectOR-Webserver for sensitive identification of insect olfactory receptor genes from non-model genomes. PMID:33465132
The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility. PMID:33407123
LPMO AfAA9_B and Cellobiohydrolase AfCel6A from A. fumigatus Boost Enzymatic Saccharification Activity of Cellulase Cocktail. PMID:33383972
Literature on Applied Machine Learning in Metagenomic Classification: A Scoping Review. PMID:33316921
Pfam: The protein families database in 2021. PMID:33125078
Transcription termination and antitermination of bacterial CRISPR arrays. PMID:33124980
Characterization of the Bacteriophage vB_EfaS-271 Infecting Enterococcus faecalis. PMID:32882938
Scalable Empirical Mixture Models That Account for Across-Site Compositional Heterogeneity. PMID:32877529
Comparison of Poly-A+ Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq. PMID:32825772
The PANoptosome: A Deadly Protein Complex Driving Pyroptosis, Apoptosis, and Necroptosis (PANoptosis). PMID:32582562
Analysis of Pigment-Dispersing Factor Neuropeptides and Their Receptor in a Velvet Worm. PMID:32477266
STARCH SYNTHASE5, a Noncanonical Starch Synthase-Like Protein, Promotes Starch Granule Initiation in Arabidopsis. PMID:32471861
Long Non-Coding RNA and mRNA Profiling in Early-Stage Bovine Embryos Treated with Glutathione. PMID:32397280
Structural basis for loading and inhibition of a bacterial T6SS phospholipase effector by the VgrG spike. PMID:32350888
Dominant Vibrio cholerae phage exhibits lysis inhibition sensitive to disruption by a defensive phage satellite. PMID:32329714
Single-molecule long-read sequencing of the full-length transcriptome of Rhododendron lapponicum L. PMID:32317724
Identifying Antifreeze Proteins Based on Key Evolutionary Information. PMID:32274383
Low Long Terminal Repeat (LTR)-Retrotransposon Expression in Leaves of the Marine Phanerogam Posidonia Oceanica L. PMID:32213979
Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study. PMID:32108239
Expanded complement of Niemann-Pick type C2-like protein genes in Clonorchis sinensis suggests functions beyond sterol binding and transport. PMID:31973758
Venom Diversity and Evolution in the Most Divergent Cone Snail Genus Profundiconus. PMID:31661832
Discovery of a functional, contracted heme-binding motif within a multiheme cytochrome. PMID:31582564
Identification and characterization of a hyperthermophilic GH9 cellulase from the Arctic Mid-Ocean Ridge vent field. PMID:31491027
Relevance of Class I α-Mannosidases to Cassava Postharvest Physiological Deterioration. PMID:31459963
The Single-molecule long-read sequencing of Scylla paramamosain. PMID:31455827
Metatranscriptomic and metabolite profiling reveals vertical heterogeneity within a Zygnema green algal mat from Svalbard (High Arctic). PMID:31454446
Identification of Novel Bacteriophages with Therapeutic Potential That Target Enterococcus faecalis. PMID:31451618
Cold Acclimation Improves the Desiccation Stress Resilience of Polar Strains of Klebsormidium (Streptophyta). PMID:31447802
Specialized structural and functional roles of residues selectively conserved in subfamilies of the pleckstrin homology domain family. PMID:31436855
Molecular Modelling and Evaluation of Hidden Information in ABCB11 Gene Mutations. PMID:31341876
FunFam protein families improve residue level molecular function prediction. PMID:31319797
Genome-wide identification and expression profiling of the C2H2-type zinc finger protein genes in the silkworm Bombyx mori. PMID:31316872
Intrinsically disordered domains: Sequence ➔ disorder ➔ function relationships. PMID:31299122
RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification. PMID:31195970
ANASTASIA: An Automated Metagenomic Analysis Pipeline for Novel Enzyme Discovery Exploiting Next Generation Sequencing Data. PMID:31178894
Updated annotation of the wild strawberry Fragaria vesca V4 genome. PMID:31069085
MyDGR: a server for identification and characterization of diversity-generating retroelements. PMID:31049585
A Preliminary Metagenome Analysis Based on a Combination of Protein Domains. PMID:31035705
Rapid identification of novel protein families using similarity searches. PMID:30984369
Simplified Intestinal Microbiota to Study Microbe-Diet-Host Interactions in a Mouse Model. PMID:30917328
In-silico Evaluation of Rare Codons and their Positions in the Structure of ATP8b1 Gene. PMID:30881940
Identification and characterization of core abscisic acid (ABA) signaling components and their gene expression profile in response to abiotic stresses in Setaria viridis. PMID:30858491
Insights into the evolution of extracellular leucine-rich repeats in metazoans with special reference to Toll-like receptor 4. PMID:30837369
PDZ Domains Across the Microbial World: Molecular Link to the Proteases, Stress Response, and Protein Synthesis. PMID:30698789
A CATH domain functional family based approach to identify putative cancer driver genes and driver mutations. PMID:30670742
Structural and functional insights into TRiC chaperonin from a psychrophilic yeast, Glaciozyma antarctica. PMID:30649671
Proteogenomic Analysis of Epibacterium Mobile BBCC367, a Relevant Marine Bacterium Isolated From the South Pacific Ocean. PMID:30622520
The Genetic Basis of Mutation Rate Variation in Yeast. PMID:30504363
Single-molecule long-read sequencing facilitates shrimp transcriptome research. PMID:30446694
Transcriptomic Insight into Terpenoid Biosynthesis and Functional Characterization of Three Diterpene Synthases in Scutellaria barbata. PMID:30424547
The Pfam protein families database in 2019. PMID:30357350
Large-scale comparative analysis of microbial pan-genomes using PanOCT. PMID:30165579
SLING: a tool to search for linked genes in bacterial datasets. PMID:30124998
Evolution and expression analyses of the MADS-box gene family in Brassica napus. PMID:30024950
Wnt/β-catenin signalling is necessary for gut differentiation in a marine annelid, Platynereis dumerilii. PMID:29942461
Single-strand DNA processing: phylogenomics and sequence diversity of a superfamily of potential prokaryotic HuH endonucleases. PMID:29914351
De novo transcriptome assembly of Pueraria montana var. lobata and Neustanthus phaseoloides for the development of eSSR and SNP markers: narrowing the US origin(s) of the invasive kudzu. PMID:29871589
In Silico Analysis of Natural Resistance-Associated Macrophage Protein (NRAMP) Family of Transporters in Rice. PMID:29785641
Identification of TOEFAZ1-interacting proteins reveals key regulators of Trypanosoma brucei cytokinesis. PMID:29781112
Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups. PMID:29717207
A sequence family database built on ECOD structural domains. PMID:29659718
Fanconi Anemia FANCM/FNCM-1 and FANCD2/FCD-2 Are Required for Maintaining Histone Methylation Levels and Interact with the Histone Demethylase LSD1/SPR-5 in Caenorhabditis elegans. PMID:29588287
Completing sparse and disconnected protein-protein network by deep learning. PMID:29566671
U-Index, a dataset and an impact metric for informatics tools and databases. PMID:29557976
Alignment-free clustering of large data sets of unannotated protein conserved regions using minhashing. PMID:29506470
A Gene Homologous to rRNA Methylase Genes Confers Erythromycin and Clindamycin Resistance in Bifidobacterium breve. PMID:29500262
Draft genome sequences of bacteria isolated from the Deschampsia antarctica phyllosphere. PMID:29492666
Surfaceome and Proteosurfaceome in Parietal Monoderm Bacteria: Focus on Protein Cell-Surface Display. PMID:29491848
Variations on a theme: evolution of the phage-shock-protein system in Actinobacteria. PMID:29488183
Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity. PMID:29482619
Draft genome sequence of Venturia carpophila, the causal agent of peach scab. PMID:29213355
Aeropyrum pernix membrane topology of protein VKOR promotes protein disulfide bond formation in two subcellular compartments. PMID:29139344
Cyclic di-GMP differentially tunes a bacterial flagellar motor through a novel class of CheY-like regulators. PMID:29091032
Genome-wide analysis and expression profiling of PP2C clade D under saline and alkali stresses in wild soybean and Arabidopsis. PMID:29052008
Whole-genome comparison of urinary pathogenic Escherichia coli and faecal isolates of UTI patients and healthy controls. PMID:29031453
Evidence-based gene models for structural and functional annotations of the oil palm genome. PMID:28886750
Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens. PMID:28742161
One ligand, two regulators and three binding sites: How KDPG controls primary carbon metabolism in Pseudomonas. PMID:28658302
Improved Annotations of 23 Differentially Expressed Hypothetical Proteins in Methicillin Resistant S.aureus. PMID:28539731
Thiol redox biochemistry: insights from computer simulations. PMID:28509962
ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly. PMID:28498994
An Insight Into Structure, Function, and Expression Analysis of 3-Hydroxy-3-Methylglutaryl-CoA Reductase of Cymbopogon winterianus. PMID:28469419
Insights into a key sulfite scavenger enzyme sulfite oxidase (SOX) gene in plants. PMID:28461726
Characterization of TPP-binding proteins in Methanococci archaeal species. PMID:28275290
Sequencing the genomic regions flanking S-linked PvGLO sequences confirms the presence of two GLO loci, one of which lies adjacent to the style-length determinant gene CYP734A50. PMID:28229234
Prediction driven functional annotation of hypothetical proteins in the major facilitator superfamily of S. aureus NCTC 8325. PMID:28197063
An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PMID:28187133
Predictive characterization of hypothetical proteins in Staphylococcus aureus NCTC 8325. PMID:28149057
Complete genome sequence and whole-genome phylogeny of Kosmotoga pacifica type strain SLHLJ1T from an East Pacific hydrothermal sediment. PMID:28074121
An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences. PMID:28054422
Complete genome sequence and transcriptomic analysis of a novel marine strain Bacillus weihaiensis reveals the mechanism of brown algae degradation. PMID:27901120
Bioinformatic Identification of Rare Codon Clusters (RCCs) in HBV Genome and Evaluation of RCCs in Proteins Structure of Hepatitis B Virus. PMID:27882067
Sequence analysis of the gliding protein Gli349 in Mycoplasma mobile. PMID:27857551
iAFP-Ense: An Ensemble Classifier for Identifying Antifreeze Protein by Incorporating Grey Model and PSSM into PseAAC. PMID:27812737
Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse). PMID:27812417
A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications. PMID:27580722
Analyses of Compact Trichinella Kinomes Reveal a MOS-Like Protein Kinase with a Unique N-Terminal Domain. PMID:27412987
Identification and Analysis of a Novel Group of Bacteriophages Infecting the Lactic Acid Bacterium Streptococcus thermophilus. PMID:27316953
High-quality draft genome sequence of Enterobacter sp. Bisph2, a glyphosate-degrading bacterium isolated from a sandy soil of Biskra, Algeria. PMID:27222800
Thermotolerance and molecular chaperone function of an SGT1-like protein from the psychrophilic yeast, Glaciozyma antarctica. PMID:27154490
Identification of a Non-Pentapeptide Region Associated with Rapid Mycobacterial Evolution. PMID:27149271
UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation. PMID:27114492
Sequencing and characterization of leaf transcriptomes of six diploid Nicotiana species. PMID:27096138
Isolation and Complete Genome Sequence of Algibacter alginolytica sp. nov., a Novel Seaweed-Degrading Bacteroidetes Bacterium with Diverse Putative Polysaccharide Utilization Loci. PMID:26969704
Inference of protein-protein interaction networks from multiple heterogeneous data. PMID:26941784
Bayesian prediction of microbial oxygen requirement. PMID:26913185
In silico analysis of Mn transporters (NRAMP1) in various plant species. PMID:26878855
A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases. PMID:26818115
Evolutionary Ancestry of Eukaryotic Protein Kinases and Choline Kinases. PMID:26742849
Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes. PMID:26738725
The Haemonchus contortus kinome--a resource for fundamental molecular investigations and drug discovery. PMID:26644012
Defining the Schistosoma haematobium kinome enables the prediction of essential kinases as anti-schistosome drug targets. PMID:26635209
Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. PMID:26575353
Characterization of the Vibrio fischeri Fatty Acid Chemoreceptors, VfcB and VfcB2. PMID:26567312
Extending Protein Domain Boundary Predictors to Detect Discontinuous Domains. PMID:26502173
Instability in progressive multiple sequence alignment algorithms. PMID:26457114
Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality. PMID:26451775
Pathogen-regulated genes in wheat isogenic lines differing in resistance to brown rust Puccinia triticina. PMID:26438375
High-Throughput Ligand Discovery Reveals a Sitewise Gradient of Diversity in Broadly Evolved Hydrophilic Fibronectin Domains. PMID:26383268
Ccq1-Tpz1TPP1 interaction facilitates telomerase and SHREC association with telomeres in fission yeast. PMID:26354422
The value of protein structure classification information-Surveying the scientific literature. PMID:26313554
De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods. PMID:26228684
In Silico Structural and Functional Annotation of Hypothetical Proteins of Vibrio cholerae O139. PMID:26175663
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. PMID:26139634
Ubiquitin-specific proteases are differentially expressed throughout the Schistosoma mansoni life cycle. PMID:26112833
TargetFreeze: Identifying Antifreeze Proteins via a Combination of Weights using Sequence Evolutionary Information and Pseudo Amino Acid Composition. PMID:26058944
Machine learning applications in genetics and genomics. PMID:25948244
The Psp system of Mycobacterium tuberculosis integrates envelope stress-sensing and envelope-preserving functions. PMID:25899163
New Insights into the Post-Translational Regulation of DNA Damage Response and Double-Strand Break Repair in Caenorhabditis elegans. PMID:25819793
Unity in diversity, a systems approach to regulating plant cell physiology by 2-oxoglutarate-dependent dioxygenases. PMID:25814993
The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity. PMID:25684150
Annotation of proteins of unknown function: initial enzyme results. PMID:25630330
Identifying tandem Ankyrin repeats in protein structures. PMID:25547411
The liverwort Pellia endiviifolia shares microtranscriptomic traits that are common to green algae and land plants. PMID:25530158
The Xylella fastidiosa PD1063 protein is secreted in association with outer membrane vesicles. PMID:25426629
CFam: a chemical families database based on iterative selection of functional seeds and seed-directed compound clustering. PMID:25414339
Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis. PMID:25351875
The characteristics of rare codon clusters in the genome and proteins of hepatitis C virus; a bioinformatics look. PMID:25349685
ZTF-8 interacts with the 9-1-1 complex and is required for DNA damage response and double-strand break repair in the C. elegans germline. PMID:25329393
Phylogenetic analysis of STK gene family and Usp domain in maize. PMID:25326719
Complete genome sequence of Thalassolituus oleivorans R6-15, an obligate hydrocarbonoclastic marine bacterium from the Arctic Ocean. PMID:25197471
Origin and evolution of European community-acquired methicillin-resistant Staphylococcus aureus. PMID:25161186
Transcriptome sequencing and analysis of the zoonotic parasite Spirometra erinacei spargana (plerocercoids). PMID:25128015
Incorporating amino acids composition and functional domains for identifying bacterial toxin proteins. PMID:25110714
Phenotypic profiling of ABC transporter coding genes in Myxococcus xanthus. PMID:25101061
The growth-defense pivot: crisis management in plants mediated by LRR-RK surface receptors. PMID:25089011
Exploring representations of protein structure for automated remote homology detection and mapping of protein structure space. PMID:25080993
Gene loss rather than gene gain is associated with a host jump from monocots to dicots in the Smut Fungus Melanopsichium pennsylvanicum. PMID:25062916
Simple chained guide trees give high-quality protein multiple sequence alignments. PMID:25002495
Writers and readers of histone acetylation: structure, mechanism, and inhibition. PMID:24984779
Ranking non-synonymous single nucleotide polymorphisms based on disease concepts. PMID:24980617
Isolation, structural analysis, and expression characteristics of the maize (Zea mays L.) hexokinase gene family. PMID:24962048
Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing. PMID:24948191
The INA complex facilitates assembly of the peripheral stalk of the mitochondrial F1Fo-ATP synthase. PMID:24942160
The crystal structure of pyrimidine/thiamin biosynthesis precursor-like domain-containing protein CAE31940 from proteobacterium Bordetella bronchiseptica RB50, and evolutionary insight into the NMT1/THI5 family. PMID:24908050
Propensity scores for prediction and characterization of bioluminescent proteins from sequences. PMID:24828431
X1-homologous genes family as central components in biotic and abiotic stresses response in maize (Zea mays L.). PMID:24676795
Towards an integrative model of C4 photosynthetic subtypes: insights from comparative transcriptome analysis of NAD-ME, NADP-ME, and PEP-CK C4 species. PMID:24642845
Ranking and compacting binding segments of protein families using aligned pattern clusters. PMID:24564874
Staphylococcus aureus subsp. anaerobius strain ST1464 genome sequence. PMID:24501641
The Xanthomonas Ax21 protein is processed by the general secretory system and is secreted in association with outer membrane vesicles. PMID:24482761
A comparative study of Whi5 and retinoblastoma proteins: from sequence and structure analysis to intracellular networks. PMID:24478706
The genome sequence of the fungal pathogen Fusarium virguliforme that causes sudden death syndrome in soybean. PMID:24454689
New insights into dissemination and variation of the health care-associated pathogen Acinetobacter baumannii from genomic analysis. PMID:24449752
Incorporating significant amino acid pairs and protein domains to predict RNA splicing-related proteins with functional roles. PMID:24442949
Genome Sequence of the Asiatic Species Borrelia persica. PMID:24407639
Characterization of SLCO5A1/OATP5A1, a solute carrier transport protein with non-classical function. PMID:24376674
Orchestration of enzymatic processing by thiazole/oxazole-modified microcin dehydrogenases. PMID:24364559
Holocarboxylase synthetase catalyzes biotinylation of heat shock protein 72, thereby inducing RANTES expression in HEK-293 cells. PMID:24133061
Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses. PMID:24108328
Cooperative degradation of chitin by extracellular and cell surface-expressed chitinases from Paenibacillus sp. strain FPU-7. PMID:24077704
Phylogenomic network and comparative genomics reveal a diverged member of the ΦKZ-related group, marine vibrio phage ΦJM-2012. PMID:24067958
The genome of the alga-associated marine flavobacterium Formosa agariphila KMM 3901T reveals a broad potential for degradation of algal polysaccharides. PMID:23995932
Genome-wide analysis of the CCCH zinc finger gene family in Medicago truncatula. PMID:23749175
Characterizing protein domain associations by Small-molecule ligand binding. PMID:23745168
Protein-Protein Interactions Inferred from Domain-Domain Interactions in Genogroup II Genotype 4 Norovirus Sequences. PMID:23738320
Genome-wide identification and evolutionary and expression analyses of MYB-related genes in land plants. PMID:23690543
Acetylation dynamics of human nuclear proteins during the ionizing radiation-induced DNA damage response. PMID:23656789
Predicting the functional consequences of cancer-associated amino acid substitutions. PMID:23620363
The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PMID:23555215
Protein function prediction using domain families. PMID:23514456
Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using Biofilter, and gene-environment interactions using the PhenX Toolkit. PMID:23424120
Chemoreceptor VfcA mediates amino acid chemotaxis in Vibrio fischeri. PMID:23315744
Methods of combinatorial optimization to reveal factors affecting gene length. PMID:23300345
Mapping small molecule binding data to structural domains. PMID:23282026
Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation. PMID:23273979
Tetratricopeptide repeat motifs in the world of bacterial pathogens: role in virulence mechanisms. PMID:23264049
Genome-wide characterization of the phosphate starvation response in Schizosaccharomyces pombe. PMID:23231582
DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. PMID:23193290
Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens. PMID:23051057
A novel neural response algorithm for protein function prediction. PMID:23046521
Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. PMID:23033316
Integrating genome annotation and QTL position to identify candidate genes for productivity, architecture and water-use efficiency in Populus spp. PMID:23013168
Structure of AMP-PNP-bound vitamin B12 transporter BtuCD-F. PMID:23000901
Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective. PMID:22966151
Protein domain recurrence and order can enhance prediction of protein functions. PMID:22962465
Genome-wide and molecular evolution analysis of the Poplar KT/HAK/KUP potassium transporter gene family. PMID:22957200
Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. PMID:22942020
Evolution of SH2 domains and phosphotyrosine signalling networks. PMID:22889907
Drug-drug relationship based on target information: application to drug target identification. PMID:22784569
Complete genome sequence of Borrelia crocidurae. PMID:22740657
Genome-wide analysis and identification of HAK potassium transporter gene family in maize (Zea mays L.). PMID:22711305
Semi-selective fatty acyl reductases from four heliothine moths influence the specific pheromone composition. PMID:22615947
Spectraplakins: master orchestrators of cytoskeletal dynamics. PMID:22584905
Reduced polymorphism in domains involved in protein-protein interactions. PMID:22509312
The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012. PMID:22508994
Investigation and identification of protein γ-glutamyl carboxylation sites. PMID:22372765
Evolutionary link between the mycobacterial plasmid pAL5000 replication protein RepB and the extracytoplasmic function family of σ factors. PMID:22247504
Identification of RNA-protein interaction networks using PAR-CLIP. PMID:22213601
Incorporating evolutionary information and functional domains for identifying RNA splicing factors in humans. PMID:22110674
RNA-Seq analysis of a soybean near-isogenic line carrying bacterial leaf pustule-resistant and -susceptible alleles. PMID:21987089
BLProt: prediction of bioluminescent proteins based on support vector machine and relieff feature selection. PMID:21849049
The novel leptospiral surface adhesin Lsa20 binds laminin and human plasminogen and is probably expressed during infection. PMID:21844229
Transcriptomic analysis of grain amaranth (Amaranthus hypochondriacus) using 454 pyrosequencing: comparison with A. tuberculatus, expression profiling in stems and in response to biotic and abiotic stress. PMID:21752295
Immunogenicity of autoantigens. PMID:21726451
Markov models of amino acid substitution to study proteins with intrinsically disordered regions. PMID:21647374
An analysis of single amino acid repeats as use case for application specific background models. PMID:21595908
Identification of Hyaloperonospora arabidopsidis transcript sequences expressed during infection reveals isolate-specific effectors. PMID:21573066
Uncharacterized conserved motifs outside the HD-Zip domain in HD-Zip subfamily I transcription factors; a potential source of functional diversity. PMID:21371298
Protein domain assignment from the recurrence of locally similar structures. PMID:21287617
Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples. PMID:21261984
Gcn1 and actin binding to Yih1: implications for activation of the eIF2 kinase GCN2. PMID:21239490
Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics. PMID:21160538
Structural basis of flocculin-mediated social behavior in yeast. PMID:21149680
Interaction of the heterotrimeric G protein alpha subunit SSG-1 of Sporothrix schenckii with proteins related to stress response and fungal pathogenicity using a yeast two-hybrid assay. PMID:21143936
On the mechanism of chloroquine resistance in Plasmodium falciparum. PMID:21124966
Molecular evolution and selection patterns of plant F-box proteins with C-terminal kelch repeats. PMID:21119043
DIMA 3.0: Domain Interaction Map. PMID:21097782
Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans. PMID:21080964
Trypanosoma cruzi MSH2: Functional analyses on different parasite strains provide evidences for a role on the oxidative stress response. PMID:21073906
Adaptive GDDA-BLAST: fast and efficient algorithm for protein sequence embedding. PMID:21042584
Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement. PMID:20979641
TOPSAN: use of a collaborative environment for annotating, analyzing and disseminating data on JCSG and PSI structures. PMID:20944203
Structural basis of poly(ADP-ribose) recognition by the multizinc binding domain of checkpoint with forkhead-associated and RING Domains (CHFR). PMID:20880844
CodonTest: modeling amino acid substitution preferences in coding sequences. PMID:20808876
Genetic analysis of the nitrogen assimilation control protein from Klebsiella pneumoniae. PMID:20693327
The construction and use of log-odds substitution scores for multiple sequence alignment. PMID:20657661
Properties of the NAC (nitrogen assimilation control protein)-binding site within the ureD promoter of Klebsiella pneumoniae. PMID:20622063
New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information. PMID:20559563
Mechanisms of lipase maturation. PMID:20543905
Synonymous codon usage influences the local protein structure observed. PMID:20530529
Ontologies in quantitative biology: a basis for comparison, integration, and discovery. PMID:20520843
Thioesterases: a new perspective based on their primary and tertiary structures. PMID:20506386
Sequence embedding for fast construction of guide trees for multiple sequence alignment. PMID:20470396
The annotation of full zinc proteomes. PMID:20443034
Predicting conserved protein motifs with Sub-HMMs. PMID:20420695
Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins. PMID:20162627
Transposon identification using profile HMMs. PMID:20158867
The abi proteins and their involvement in bacteriocin self-immunity. PMID:20154137
The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth. PMID:20154119
Biochemical profiling of histone binding selectivity of the yeast bromodomain family. PMID:20126658
Molecular modeling of the reductase domain to elucidate the reaction mechanism of reduction of peptidyl thioester into its corresponding alcohol in non-ribosomal peptide synthetases. PMID:20067617
Insights into the domain and repeat architecture of target of rapamycin. PMID:20060908
Mago Nashi, Tsunagi/Y14, and Ranshi form a complex that influences oocyte differentiation in Drosophila melanogaster. PMID:20045686
A phenotypic profile of the Candida albicans regulatory network. PMID:20041210
TransportTP: a two-phase classification approach for membrane transporter prediction and characterization. PMID:20003433
DescFold: a web server for protein fold recognition. PMID:20003426
TIM-Finder: a new method for identifying TIM-barrel proteins. PMID:20003393
Inferring protein function by domain context similarities in protein-protein interaction networks. PMID:19954509
Globally, unrelated protein sequences appear random. PMID:19948773
Phylogenetic Profiles Reveal Structural and Functional Determinants of Lipid-binding. PMID:19946567
Caenorhabditis elegans HIM-18/SLX-4 interacts with SLX-1 and XPF-1 and maintains genomic integrity in the germline by processing recombination intermediates. PMID:19936019
Knowledge-based characterization of similarity relationships in the human protein-tyrosine phosphatase family for rational inhibitor design. PMID:19810703
Lipase maturation factor LMF1, membrane topology and interaction with lipase proteins in the endoplasmic reticulum. PMID:19783858
Highly sensitive detection of individual HEAT and ARM repeats with HHpred and COACH. PMID:19777061
In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling. PMID:19770167
Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. PMID:19717629
Crystal structures of Streptococcus suis mannonate dehydratase (ManD) and its complex with substrate: genetic and biochemical evidence for a catalytic mechanism. PMID:19617363
A comprehensive bioinformatics analysis of the Nudix superfamily in Arabidopsis thaliana. PMID:19590748
Regulation of glucose metabolism in Pseudomonas: the phosphorylative branch and entner-doudoroff enzymes are regulated by a repressor containing a sugar isomerase domain. PMID:19506074
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
Molecular determinants archetypical to the phylum Nematoda. PMID:19296854
Genome-wide and expression analysis of protein phosphatase 2C in rice and Arabidopsis. PMID:19021904
Protein subfamily assignment using the Conserved Domain Database. PMID:19014584
Hidden Markov models incorporating fuzzy measures and integrals for protein sequence identification and alignment. PMID:18973866
Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences. PMID:18852105
Splice-mediated Variants of Proteins (SpliVaP) - data and characterization of changes in signatures among protein isoforms due to alternative splicing. PMID:18831736
CENP-V is required for centromere organization, chromosome alignment and cytokinesis. PMID:18772885
Phylogenetic profiles reveal evolutionary relationships within the "twilight zone" of sequence similarity. PMID:18765810
Testing gene set enrichment for subset of genes: Sub-GSE. PMID:18764941
Molecular evolution of the CPP-like gene family in plants: insights from comparative genomics of Arabidopsis and rice. PMID:18696028
Validating annotations for uncharacterized proteins in Shewanella oneidensis. PMID:18687039
Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis. PMID:18523684
DNA double-strand breaks, but not crossovers, are required for the reorganization of meiotic nuclei in Tetrahymena. PMID:18522989
Identification of outer membrane proteins of Mycobacterium tuberculosis. PMID:18439872
Disease mechanism for retinitis pigmentosa (RP11) caused by missense mutations in the splicing factor gene PRPF31. PMID:18431455
Predicting co-complexed protein pairs from heterogeneous data. PMID:18421371
Towards an automatic classification of protein structural domains based on structural similarity. PMID:18237410
Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice. PMID:18221561
The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction. PMID:18221517
An automated protein annotation filter for integrating web-based annotation tools. PMID:18188426
Functional-genomics-based identification and characterization of open reading frames encoding alpha-glucoside-processing enzymes in the hyperthermophilic archaeon Pyrococcus furiosus. PMID:18156337
Building an understanding of cystic fibrosis on the foundation of ABC transporter structures. PMID:18080175
Comprehensive viral oligonucleotide probe design using conserved protein regions. PMID:18079152
The Pfam protein families database. PMID:18039703
Evaluating the protein coding potential of exonized transposable element sequences. PMID:18036258
Genomic and biochemical studies demonstrating the absence of an alkane-producing phenotype in Vibrio furnissii M1. PMID:17921268
Horizontal gene transfer in chromalveolates. PMID:17894863
A machine learning approach for the identification of odorant binding proteins from sequence-derived properties. PMID:17880712
Predicting active site residue annotations in the Pfam database. PMID:17688688
Quantitative sequence-function relationships in proteins based on gene ontology. PMID:17686158
Identification of Aeromonas veronii genes required for colonization of the medicinal leech, Hirudo verbana. PMID:17616592
Pcons.net: protein structure prediction meta server. PMID:17584798
Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence. PMID:17565669
Mutant batten disease protein says "no" to unsaturated fats. PMID:17520082
A kingdom-specific protein domain HMM library for improved annotation of fungal genomes. PMID:17425790
Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii. PMID:17400776
A new inhibitor of apoptosis from vaccinia virus and eukaryotes. PMID:17319741
Chitinase gene diversity at a deep sea station of the east Pacific nodule province. PMID:17225927
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. PMID:17202171
TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences. PMID:17199898
Structure and dynamics of UDP-glucose pyrophosphorylase from Arabidopsis thaliana with bound UDP-glucose and UTP. PMID:17178129
Phylogenetic analysis of RhoGAP domain-containing proteins. PMID:17127216
Solution structure of Escherichia coli PapI, a key regulator of the pap pili phase variation. PMID:17109885
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. PMID:16970830
Expansion of protein domain repeats. PMID:16933986
jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1. PMID:16845050
What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? PMID:16780599
Classification of protein quaternary structure by functional domain composition. PMID:16584572
Towards genome-scale structure prediction for transmembrane proteins. PMID:16524835
Computer-aided NMR assay for detecting natively folded structural domains. PMID:16522794
Application of DETECTER, an evolutionary genomic tool to analyze genetic variation, to the cystic fibrosis gene family. PMID:16522197
Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes. PMID:16436801
A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. PMID:16420670
A systematic approach to infer biological relevance and biases of gene network structures. PMID:16407322
MulPSSM: a database of multiple position-specific scoring matrices of protein domain families. PMID:16381855
Inherited disorder phenotypes: controlled annotation and statistical analysis for knowledge mining from gene lists. PMID:16351744
The CRAL/TRIO and GOLD domain protein CGR-1 promotes induction of vulval cell fates in Caenorhabditis elegans and interacts genetically with the Ras signaling pathway. PMID:16219793
Sequence variation in ligand binding sites in proteins. PMID:16194281
Identification of the iron-responsive genes of Neisseria gonorrhoeae by microarray analysis in defined medium. PMID:15995201
Phenotype-genotype correlation in Hirschsprung disease is illuminated by comparative analysis of the RET protein sequence. PMID:15956201
Structural and functional characterization of CFE88: evidence that a conserved and essential bacterial protein is a methyltransferase. PMID:15929997
Investigation of the microbial ecology of intertidal hot springs by using diversity analysis of 16S rRNA and chitinase genes. PMID:15870372
Distribution and phylogenies of enzymes of the Embden-Meyerhof-Parnas pathway from archaea and hyperthermophilic bacteria support a gluconeogenic origin of metabolism. PMID:15803666
Common evolutionary origins of mechanosensitive ion channels in Archaea, Bacteria and cell-walled Eukarya. PMID:15803657
Evolutionary profiles from the QR factorization of multiple sequence alignments. PMID:15741270
Global mapping of the protein structure space and application in structure-based inference of protein function. PMID:15705717
Homology modeling, force field design, and free energy simulation studies to optimize the activities of histone deacetylase inhibitors. PMID:15662999
Descriptor-based protein remote homology identification. PMID:15632283
GenDiS: Genomic Distribution of protein structural domain Superfamilies. PMID:15608190
Enhanced functional and structural domain assignments using remote similarity detection procedures for proteins encoded in the genome of Mycobacterium tuberculosis H37Rv. PMID:15381846
A classification of disulfide patterns and its relationship to protein structure and function. PMID:15273305
GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining. PMID:15215397
Network analysis of metabolic enzyme evolution in Escherichia coli. PMID:15113413
SUPFAM: a database of sequence superfamilies of protein domains. PMID:15113407
Molecular analysis of muskelin identifies a conserved discoidin-like domain that contributes to protein self-association. PMID:15084145
Calcium regulates the expression of a Dictyostelium discoideum asparaginyl tRNA synthetase gene. PMID:14660869
Visualisation and graph-theoretic analysis of a large-scale protein structural interactome. PMID:14531933
Exploring the sequence-structure protein landscape in the glycosyltransferase family. PMID:14500887
Profile-profile comparisons by COMPASS predict intricate homologies between protein families. PMID:14500884
PANTHER: a library of protein families and subfamilies indexed by function. PMID:12952881
Homology modeling provides insights into the binding mode of the PAAD/DAPIN/pyrin domain, a fourth member of the CARD/DD/DED domain family. PMID:12930987
LOC3D: annotate sub-cellular localization for protein structures. PMID:12824321
A comparison of Pfam and MEROPS: two databases, one comprehensive, and one specialised. PMID:12740029
DAVID: Database for Annotation, Visualization, and Integrated Discovery. PMID:12734009
Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. PMID:12671079
PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. PMID:12520017
Autotracing of Escherichia coli acetate CoA-transferase alpha-subunit structure using 3.4 A MAD and 1.9 A native data. PMID:12454473
Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. PMID:12218036
Dictionary-driven protein annotation. PMID:12202776
Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. PMID:12202761
Genes for glycosylphosphatidylinositol toxin biosynthesis in Plasmodium falciparum. PMID:12117963
Plant receptor kinases: systemin receptor identified. PMID:12093928
Large-scale analysis of the human and mouse transcriptomes. PMID:11904358
Novel, thermostable family-13-like glycoside hydrolase from Methanococcus jannaschii. PMID:11898335
PASS2: a semi-automated database of protein alignments organised as structural superfamilies. PMID:11752316
The Pfam protein families database. PMID:11752314
Origin of fibronectin type II (FN2) modules: structural analyses of distantly-related members of the kringle family idey the kringle domain of neurotrypsin as a potential link between FN2 domains and kringles. PMID:11567102
Massive sequence comparisons as a help in annotating genomic sequences. PMID:11435413
Neuropeptides and neuropeptide receptors in the Drosophila melanogaster genome. PMID:11381038
Discovering common stem-loop motifs in unaligned RNA sequences. PMID:11353083
A human protein containing multiple types of protease-inhibitory modules. PMID:11274388
Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. PMID:11230166
Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics. PMID:11206052
TIGRFAMs: a protein family resource for the functional identification of proteins. PMID:11125044
DNA sequence and comparison of virulence plasmids from Rhodococcus equi ATCC 33701 and 103. PMID:11083803
Novel genes coding for lithotrophic sulfur oxidation of Paracoccus pantotrophus GB17. PMID:10940005
Visual management of large scale data mining projects. PMID:10902176
Genome annotation assessment in Drosophila melanogaster. PMID:10779488
The Pfam protein families database. PMID:10592242
d2_cluster: a validated method for clustering EST and full-length cDNAsequences. PMID:10568753
An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: the Adh region. PMID:10471707
Myotactin, a novel hypodermal protein involved in muscle-cell adhesion in Caenorhabditis elegans. PMID:10444073
High-frequency RecA-dependent and -independent mechanisms of Congo red binding mutations in Yersinia pestis. PMID:10438760
X-linked late-onset sensorineural deafness caused by a deletion involving OA1 and a novel gene containing WD-40 repeats. PMID:10330347
Myxoma virus encodes an alpha2,3-sialyltransferase that enhances virulence. PMID:9971821
Kaposi's sarcoma-associated herpesvirus encodes a bZIP protein with homology to BZLF1 of Epstein-Barr virus. PMID:9971770
Syndapin I, a synaptic dynamin-binding protein that associates with the neural Wiskott-Aldrich syndrome protein. PMID:9950691
A homology identification method that combines protein sequence and structure information. PMID:9865944
Cloning and molecular analysis of the Poly(3-hydroxybutyrate) and Poly(3-hydroxybutyrate-co-3-hydroxyalkanoate) biosynthesis genes in Pseudomonas sp. strain 61-3. PMID:9851987
Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. PMID:9811845
Structure of an XRCC1 BRCT domain: a new protein-protein interaction module. PMID:9799248
The UNI3 gene is required for assembly of basal bodies of Chlamydomonas and encodes delta-tubulin, a new member of the tubulin superfamily. PMID:9614175
Highly specific protein sequence motifs for genome analysis. PMID:9600885
SMART, a simple modular architecture research tool: identification of signaling domains. PMID:9600884
Alternative gene form discovery and candidate gene selection from gene indexing projects. PMID:9521931
PROMISE: a database of information on prosthetic centres and metal ions in protein active sites. PMID:9399878
Pfam: multiple sequence alignments and HMM-profiles of protein domains. PMID:9399864
Superior performance in protein homology detection with the Blocks Database servers. PMID:9399861
The PRINTS protein fingerprint database in its fifth year. PMID:9399860 - http://dx.doi.org/10.1093/nar/gkaa913
Tags:
Tags
More detailed information about this field from each metasource.
binding motif
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
biocuration
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
computational predictions
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
evolution
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
function analysis
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
functional domain
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
hidden markov model
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
multiple sequence alignment
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: re3data.org
version: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
protein domain
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
proteome
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequence alignment
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequence motif
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequence similarity
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
polypeptide_region
metasource: Fairsharing.org
version: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.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
protein domain databases; protein classification
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
clans
metasource: re3data.org
version: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
protein families
metasource: re3data.org
version: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
protein sequence
metasource: re3data.org
version: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
proteomes
metasource: re3data.org
version: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
proteins
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
gene and protein families
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
protein folds and structural domains
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
sequence sites, features and motifs
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
sequence composition, complexity and repeats
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
sequence analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:11.823842
Tags
More detailed information about this field from each metasource.
binding motif
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
biocuration
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
computational predictions
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
evolution
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
function analysis
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
functional domain
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
hidden markov model
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
multiple sequence alignment
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: re3data.org
version: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
protein domain
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
proteome
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequence alignment
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequence motif
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequence similarity
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
polypeptide_region
metasource: Fairsharing.orgversion: FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.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
protein domain databases; protein classification
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
clans
metasource: re3data.orgversion: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
protein families
metasource: re3data.orgversion: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
protein sequence
metasource: re3data.orgversion: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
proteomes
metasource: re3data.orgversion: re3data.org: Pfam Protein Families; editing status 2022-09-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QV4F last accessed: 2022-11-04
proteins
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:11.823842
gene and protein families
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:11.823842
protein folds and structural domains
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:11.823842
sequence sites, features and motifs
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:11.823842
sequence composition, complexity and repeats
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:11.823842
sequence analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:11.823842
binding motif biocuration computational predictions evolution function analysis functional domain hidden markov model multiple sequence alignment protein protein domain proteome sequence alignment sequence motif sequence similarity polypeptide region protein sequence protein domains and classification clans protein families protein sequence proteomes proteins gene and protein families protein folds and structural domains sequence sites, features and motifs sequence composition, complexity and repeats sequence analysis
Need help integrating and/or managing biomedical data?