Integrated resource of protein families, domains and functional sites
Names
More detailed information about this field from each metasource.
Integrated resource of protein families, domains and functional sites
metasource: Fairsharing.org
version: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
InterPro
metasource: Fairsharing.org
version: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 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: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
protein sequence analysis & classification
metasource: re3data.org
version: re3data.org: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
interpro
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
Names
More detailed information about this field from each metasource.
Integrated resource of protein families, domains and functional sites
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
InterPro
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 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: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
protein sequence analysis & classification
metasource: re3data.orgversion: re3data.org: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
interpro
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:09.686544
Other names: InterPro, protein sequence analysis & classification, interpro
Names
More detailed information about this field from each metasource.
Integrated resource of protein families, domains and functional sites
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
InterPro
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 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: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
protein sequence analysis & classification
metasource: re3data.orgversion: re3data.org: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
interpro
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:09.686544
InterPro is a resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites. To classify proteins in this way, InterPro uses predictive models, known as signatures, provided by several different databases (referred to as member databases) that make up the InterPro consortium.
Description
More detailed information about this field from each metasource.
InterPro is a resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites. To classify proteins in this way, InterPro uses predictive models, known as signatures, provided by several different databases (referred to as member databases) that make up the InterPro consortium.
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. InterProScan is the underlying software that allows protein and nucleic acid sequences to be searched against InterPro's signatures. Signatures are predictive models which describe protein families, domains or sites, and are provided by multiple databases. InterPro combines signatures representing equivalent families, domains or sites, and provides additional information such as descriptions, literature references and Gene Ontology (GO) terms, to produce a comprehensive resource for protein classification. Founded in 1999, InterPro has become one of the most widely used resources for protein family annotation. Here, we report the status of InterPro (version 81.0) in its 20th year of operation, and its associated software, including updates to database content, the release of a new website and REST API, and performance improvements in InterProScan.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
InterPro collects information about protein sequence analysis and classification, providing access to a database of predictive protein signatures used for the classification and automatic annotation of proteins and genomes. Sequences in InterPro are classified at superfamily, family, and subfamily. InterPro predicts the occurrence of functional domains, repeats, and important sites, and adds in-depth annotation such as GO terms to the protein signatures.
metasource: re3data.orgversion: re3data.org: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
Protein families, domains, regions, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:09.686544
Webpage:
https://www.ebi.ac.uk/interproWebpage
More detailed information about this field from each metasource.
https://www.ebi.ac.uk/interpro
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://www.ebi.ac.uk/interpro
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://www.ebi.ac.uk/interpro/beta/
metasource: re3data.orgversion: re3data.org: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
http://www.ebi.ac.uk/interpro/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:09.686544
Licence:
Name: Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0Licence name
More detailed information about this field from each metasource.
Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Public Domain
metasource: re3data.orgversion: re3data.org: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
URL: http://opendatacommons.org/licenses/pddl/1.0/
Licence URL
More detailed information about this field from each metasource.
http://opendatacommons.org/licenses/pddl/1.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
https://www.ebi.ac.uk/about/terms-of-use
metasource: re3data.orgversion: re3data.org: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
Publications:
(13)
Publications
More detailed information about this field from each metasource.
InterPro: the integrative protein signature database
PMID: 18940856
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
InterPro in 2017-beyond protein family and domain annotations
PMID: 27899635
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
The InterPro protein families database: the classification resource after 15 years
PMID: 25428371
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
InterPro in 2019: improving coverage, classification and access to protein sequence annotations
PMID: 30398656
metasource: Fairsharing.org
version: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
InterPro in 2011: new developments in the family and domain prediction database
PMID: 22096229
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
The InterPro database, an integrated documentation resource for protein families, domains and functional sites
PMID: 11125043
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
The InterPro Database, 2003 brings increased coverage and new features
PMID: 12520011
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
InterPro, progress and status in 2005
PMID: 15608177
metasource: Fairsharing.org
version: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
New developments in the InterPro database
PMID: 17202162
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
The InterPro protein families and domains database: 20 years on
PMID: 33156333
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
InterPro: an integrated documentation resource for protein families, domains and functional sites
PMID: 12230031
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
InterPro protein classification
PMID: 21082426
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
http://dx.doi.org/10.1093/nar/gkaa977
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.
InterPro: the integrative protein signature database
PMID: 18940856
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
InterPro in 2017-beyond protein family and domain annotations
PMID: 27899635
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
The InterPro protein families database: the classification resource after 15 years
PMID: 25428371
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
InterPro in 2019: improving coverage, classification and access to protein sequence annotations
PMID: 30398656
metasource: Fairsharing.org
version: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
InterPro in 2011: new developments in the family and domain prediction database
PMID: 22096229
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
The InterPro database, an integrated documentation resource for protein families, domains and functional sites
PMID: 11125043
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
The InterPro Database, 2003 brings increased coverage and new features
PMID: 12520011
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
InterPro, progress and status in 2005
PMID: 15608177
metasource: Fairsharing.org
version: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
New developments in the InterPro database
PMID: 17202162
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
The InterPro protein families and domains database: 20 years on
PMID: 33156333
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
InterPro: an integrated documentation resource for protein families, domains and functional sites
PMID: 12230031
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
InterPro protein classification
PMID: 21082426
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
http://dx.doi.org/10.1093/nar/gkaa977
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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InterPro: the integrative protein signature database
PubMed citations: 952.
952 articles citing: InterPro: the integrative protein signature database
SIN-3 functions through multi-protein interaction to regulate apoptosis, autophagy, and longevity in Caenorhabditis elegans. PMID:35732652
Profiles of Natural and Designed Protein-Like Sequences Effectively Bridge Protein Sequence Gaps: Implications in Distant Homology Detection. PMID:35507261
Comprehensive in silico modeling of the rice plant PRR Xa21 and its interaction with RaxX21-sY and OsSERK2. PMID:35493652
Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans. PMID:35484634
Integrating Phenotypic and Gene Expression Linkage Mapping to Dissect Rust Resistance in Chickling Pea. PMID:35463408
PtncRNAdb: plant transfer RNA-derived non-coding RNAs (tncRNAs) database. PMID:35462956
Genomic evidence for homoploid hybrid speciation between ancestors of two different genera. PMID:35418567
The Gastrodia menghaiensis (Orchidaceae) genome provides new insights of orchid mycorrhizal interactions. PMID:35392808
In silico analysis of nitrilase-3 protein from Corynebacterium glutamicum for bioremediation of nitrile herbicides. PMID:35348933
Draft Sequencing Crested Wheatgrass Chromosomes Identified Evolutionary Structural Changes and Genes and Facilitated the Development of SSR Markers. PMID:35328613
Draft genomes assembly and annotation of Carex parvula and Carex kokanica reveals stress-specific genes. PMID:35322069
Genomic Fishing and Data Processing for Molecular Evolution Research. PMID:35314663
Chromosome-level genome assembly of a xerophytic plant, Haloxylon ammodendron. PMID:35266513
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
An investigation into the role of inherited CEACAM gene family variants and colorectal cancer risk. PMID:35115044
A Large-Scale Multiple Genome Comparison of Acidophilic Archaea (pH ≤ 5.0) Extends Our Understanding of Oxidative Stress Responses in Polyextreme Environments. PMID:35052563
Impaired catabolism of free oligosaccharides due to MAN2C1 variants causes a neurodevelopmental disorder. PMID:35045343
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
Analysis of NIA and GSNOR family genes and nitric oxide homeostasis in response to wheat-leaf rust interaction. PMID:35039546
A chromosome-scale genome assembly for the holly (Ilex polyneura) provides insights into genomic adaptations to elevation in Southwest China. PMID:35031793
Tissue specific expression of UMAMIT amino acid transporters in wheat. PMID:35013480
Benchmark Evaluation of Protein-Protein Interaction Prediction Algorithms. PMID:35011283
Two novel cyanobacterial α-dioxygenases for the biosynthesis of fatty aldehydes. PMID:34882252
High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice. PMID:34868173
A comprehensive in silico investigation into the nsSNPs of Drd2 gene predicts significant functional consequences in dopamine signaling and pharmacotherapy. PMID:34853389
The Cymbidium genome reveals the evolution of unique morphological traits. PMID:34848682
Comprehensive Characterization of the Coding and Non-Coding Single Nucleotide Polymorphisms in the Tumor Protein p63 (TP63) Gene Using In Silico Tools. PMID:34827731
Contribution of the mutation rs8193069 in TLR4 to mastitis resistance and performance in Holstein cows in southern China. PMID:34812595
Candidate Effectors of Plasmodiophora brassicae Pathotype 5X During Infection of Two Brassica napus Genotypes. PMID:34803960
Integrative COVID-19 biological network inference with probabilistic core decomposition. PMID:34791019
Novel Enzymes From the Red Sea Brine Pools: Current State and Potential. PMID:34777282
Antimicrobial Peptides: An Update on Classifications and Databases. PMID:34769122
High-throughput imaging of ATG9A distribution as a diagnostic functional assay for adaptor protein complex 4-associated hereditary spastic paraplegia. PMID:34729478
Parallel introgression, not recurrent emergence, explains apparent elevational ecotypes of polyploid Himalayan snowtrout. PMID:34729207
Plant ecological genomics at the limits of life in the Atacama Desert. PMID:34725254
Functional Annotation from Structural Homology. PMID:34718998
Genomic and Transcriptomic Insight of Giant Sclerotium Formation of Wood-Decay Fungi. PMID:34712214
Network-driven analysis of human-Plasmodium falciparum interactome: processes for malaria drug discovery and extracting in silico targets. PMID:34702263
Whole-Genome Sequencing of Sinocyclocheilus maitianheensis Reveals Phylogenetic Evolution and Immunological Variances in Various Sinocyclocheilus Fishes. PMID:34675964
High-quality genome assembly of an important biodiesel plant, Euphorbia lathyris L. PMID:34664644
Sulfur cycling and host-virus interactions in Aquificales-dominated biofilms from Yellowstone's hottest ecosystems. PMID:34650231
The selective degradation of sirtuins via macroautophagy in the MPP+ model of Parkinson's disease is promoted by conserved oxidation sites. PMID:34642296
AtPGAP1 functions as a GPI inositol-deacylase required for efficient transport of GPI-anchored proteins. PMID:34618080
Neofunctionalization of an ancient domain allows parasites to avoid intraspecific competition by manipulating host behaviour. PMID:34531391
PathFams: statistical detection of pathogen-associated protein domains. PMID:34521345
The genome sequence provides insights into salt tolerance of Achnatherum splendens (Gramineae), a constructive species of alkaline grassland. PMID:34487631
CEACAM Gene Family Mutations Associated With Inherited Breast Cancer Risk - A Comparative Oncology Approach to Discovery. PMID:34447411
The whale shark genome reveals patterns of vertebrate gene family evolution. PMID:34409936
ARG-SHINE: improve antibiotic resistance class prediction by integrating sequence homology, functional information and deep convolutional neural network. PMID:34377977
A fragment-based approach identifies an allosteric pocket that impacts malate dehydrogenase activity. PMID:34376783
Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation. PMID:34372938
A novel machine learning-based approach for the computational functional assessment of pharmacogenomic variants. PMID:34372920
Analyses of Virulence Genes of Clavibacter michiganensis subsp. michiganensis Strains Reveal Heterogeneity and Deletions That Correlate with Pathogenicity. PMID:34361965
Linking Inflammatory Bowel Disease Symptoms to Changes in the Gut Microbiome Structure and Function. PMID:34349736
A Global Approach to Estimating the Abundance and Duplication of Polyketide Synthase Domains in Dinoflagellates. PMID:34345159
A chromosome-level genome assembly of Cairina moschata and comparative genomic analyses. PMID:34330207
Comparative genomic analysis of obligately piezophilic Moritella yayanosii DB21MT-5 reveals bacterial adaptation to the Challenger Deep, Mariana Trench. PMID:34319226
Genome sequence of Apostasia ramifera provides insights into the adaptive evolution in orchids. PMID:34256691
A Chromosome-Level Genome Assembly of the Mandarin Fish (Siniperca chuatsi). PMID:34249093
Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea. PMID:34202810
Predicting Lifestyle from Positive Selection Data and Genome Properties in Oomycetes. PMID:34202069
RNAseq reveals different transcriptomic responses to GA3 in early and midseason varieties before ripening initiation in sweet cherry fruits. PMID:34158527
Isolation and characterization of a new cold-active protease from psychrotrophic bacteria of Western Himalayan glacial soil. PMID:34140593
Pathways of Iron and Sulfur Acquisition, Cofactor Assembly, Destination, and Storage in Diverse Archaeal Methanogens and Alkanotrophs. PMID:34124941
Wolfberry genomes and the evolution of Lycium (Solanaceae). PMID:34083720
Rootstock effects on scion gene expression in maritime pine. PMID:34078936
A high-quality genome assembly of Morinda officinalis, a famous native southern herb in the Lingnan region of southern China. PMID:34059651
Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa. PMID:34059118
Large-scale identification of protein histidine methylation in human cells. PMID:34046594
Introgressing the Aegilops tauschii genome into wheat as a basis for cereal improvement. PMID:34045708
DomainViz: intuitive visualization of consensus domain distributions across groups of proteins. PMID:34023887
Protein transfer learning improves identification of heat shock protein families. PMID:34003870
Adaptive evolution of Moniliophthora PR-1 proteins towards its pathogenic lifestyle. PMID:33990179
Chromosomal-Level Reference Genome of the Neotropical Tree Jacaranda mimosifolia D. Don. PMID:33944940
The Chinese mitten crab genome provides insights into adaptive plasticity and developmental regulation. PMID:33888695
Bacterial avidins are a widely distributed protein family in Actinobacteria, Proteobacteria and Bacteroidetes. PMID:33836663
Comparative genome analyses of four rice-infecting Rhizoctonia solani isolates reveal extensive enrichment of homogalacturonan modification genes. PMID:33827423
Identification of Decrease in TRiC Proteins as Novel Targets of Alpha-Amanitin-Derived Hepatotoxicity by Comparative Proteomic Analysis In Vitro. PMID:33803263
A landscape for drug-target interactions based on network analysis. PMID:33730052
Generating functional protein variants with variational autoencoders. PMID:33635868
Ubiquitin-related processes and innate immunity in C. elegans. PMID:33630111
The Genome of Banana Leaf Blight Pathogen Fusarium sacchari str. FS66 Harbors Widespread Gene Transfer From Fusarium oxysporum. PMID:33613610
Genome-Mining-Based Discovery of the Cyclic Peptide Tolypamide and TolF, a Ser/Thr Forward O-Prenyltransferase. PMID:33586286
Chromosome-level reference genome of the soursop (Annona muricata): A new resource for Magnoliid research and tropical pomology. PMID:33569882
Two 20-Residue-Long Peptides Derived from Plasmodium vivax Merozoite Surface Protein 10 EGF-Like Domains Are Involved in Binding to Human Reticulocytes. PMID:33562650
Insights into triterpene synthesis and unsaturated fatty-acid accumulation provided by chromosomal-level genome analysis of Akebia trifoliata subsp. australis. PMID:33518712
Sex steroids and steroidogenesis-related genes in the sea cucumber, Holothuria scabra and their potential role in gonad maturation. PMID:33500499
Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics. PMID:33489789
Identification and Downstream Analyses of Domains Amplified in Plant Genomes: The Case of StAR-Related Lipid Transfer (START) Domains in Rice. PMID:33471342
Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway. PMID:33452484
Conservation and Loss of a Putative Iron Utilization Gene Cluster among Genotypes of Aspergillus flavus. PMID:33435439
Two novel venom proteins underlie divergent parasitic strategies between a generalist and a specialist parasite. PMID:33431897
Induced defense response in red mango fruit against Colletotrichum gloeosporioides. PMID:33423039
Elucidating the network features and evolutionary attributes of intra- and interspecific protein-protein interactions between human and pathogenic bacteria. PMID:33420198
The Developmental Transcriptome of Bagworm, Metisa plana (Lepidoptera: Psychidae) and Insights into Chitin Biosynthesis Genes. PMID:33374651
Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B. PMID:33370413
A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance. PMID:33328471
Three Novel Clostridia Isolates Produce n-Caproate and iso-Butyrate from Lactate: Comparative Genomics of Chain-Elongating Bacteria. PMID:33322390
Bioinformatic analysis and functional predictions of selected regeneration-associated transcripts expressed by zebrafish microglia. PMID:33287696
Proteomics and Lipidomics Investigations to Decipher the Behavior of Willaertia magna C2c Maky According to Different Culture Modes. PMID:33207645
Diverse Enzymes With Industrial Applications in Four Thraustochytrid Genera. PMID:33193181
Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel. PMID:33168033
Cycling in degradation of organic polymers and uptake of nutrients by a litter-degrading fungus. PMID:33140552
Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation. PMID:33137082
Heterologous Expression of the Core Genes in the Complex Fusarubin Gene Cluster of Fusarium Solani. PMID:33066643
Tissue-Specific Transcriptome Analysis Reveals Candidate Transcripts Associated with the Process of Programmed B Chromosome Elimination in Aegilops speltoides. PMID:33066598
The elephant grass (Cenchrus purpureus) genome provides insights into anthocyanidin accumulation and fast growth. PMID:33040437
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
The evolution of TNF signaling in platyhelminths suggests the cooptation of TNF receptor in the host-parasite interplay. PMID:32977830
Characterization of PlyB221 and PlyP32, Two Novel Endolysins Encoded by Phages Preying on the Bacillus cereus Group. PMID:32967292
Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis. PMID:32914530
A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating machinery. PMID:32898505
Reply: Segregation of ATP10B variants in families with autosomal recessive Parkinsonism. PMID:32892228
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
Combined Genome and Transcriptome Analyses of the Ciliate Schmidingerella arcuata (Spirotrichea) Reveal Patterns of DNA Elimination, Scrambling, and Inversion. PMID:32870974
Phf21b imprints the spatiotemporal epigenetic switch essential for neural stem cell differentiation. PMID:32820037
Molecular insights into biochar-mediated plant growth promotion and systemic resistance in tomato against Fusarium crown and root rot disease. PMID:32811849
Impact of spatial proximity on territoriality among human skin bacteria. PMID:32764612
FLUTE: Fast and reliable knowledge retrieval from biomedical literature. PMID:32761077
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. PMID:32706331
Shared up-regulation and contrasting down-regulation of gene expression distinguish desiccation-tolerant from intolerant green algae. PMID:32636259
The bottromycin epimerase BotH defines a group of atypical α/β-hydrolase-fold enzymes. PMID:32601484
Determining the Genetic Characteristics of Resistance and Virulence of the "Epidermidis Cluster Group" Through Pan-Genome Analysis. PMID:32596166
Functional and Structural Analysis of Predicted Proteins Obtained from Homo sapiens' Minisatellite 33.15-Tagged Transcript pAKT-45 Variants. PMID:32566673
The genome sequence of star fruit (Averrhoa carambola). PMID:32528707
Genome sequence of Kobresia littledalei, the first chromosome-level genome in the family Cyperaceae. PMID:32528014
Alteromonas Myovirus V22 Represents a New Genus of Marine Bacteriophages Requiring a Tail Fiber Chaperone for Host Recognition. PMID:32518192
Supernumerary B chromosomes of Aegilops speltoides undergo precise elimination in roots early in embryo development. PMID:32488019
Computational Prediction of Ubiquitination Proteins Using Evolutionary Profiles and Functional Domain Annotation. PMID:32476995
The Concerted Action of Two B3-Like Prophage Genes Excludes Superinfecting Bacteriophages by Blocking DNA Entry into Pseudomonas aeruginosa. PMID:32461312
Insight into the Lifestyle of Amoeba Willaertia magna during Bioreactor Growth Using Transcriptomics and Proteomics. PMID:32455615
SDN2GO: An Integrated Deep Learning Model for Protein Function Prediction. PMID:32411695
Encystment Induces Down-Regulation of an Acetyltransferase-Like Gene in Acanthamoeba castellanii. PMID:32357498
Genetic Underpinnings of Host Manipulation by Ophiocordyceps as Revealed by Comparative Transcriptomics. PMID:32354705
Characterization of SETD1A haploinsufficiency in humans and Drosophila defines a novel neurodevelopmental syndrome. PMID:32346159
AFP-LSE: Antifreeze Proteins Prediction Using Latent Space Encoding of Composition of k-Spaced Amino Acid Pairs. PMID:32345989
Integrative functional genomics decodes herpes simplex virus 1. PMID:32341360
Tung Tree (Vernicia fordii) Genome Provides A Resource for Understanding Genome Evolution and Improved Oil Production. PMID:32224189
Chromosome-level genome assembly of Aldrichina grahami, a forensically important blowfly. PMID:32191812
Reveals of New Candidate Active Components in Hemerocallis Radix and Its Anti-Depression Action of Mechanism Based on Network Pharmacology Approach. PMID:32182911
Mutated ATP10B increases Parkinson's disease risk by compromising lysosomal glucosylceramide export. PMID:32172343
De Novo Truncating Variants in the Last Exon of SEMA6B Cause Progressive Myoclonic Epilepsy. PMID:32169168
von Willebrand factor D and EGF domains is an evolutionarily conserved and required feature of blastemas capable of multitissue appendage regeneration. PMID:32163674
Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family. PMID:32118265
The genome evolution and low-phosphorus adaptation in white lupin. PMID:32103018
A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina. PMID:32103005
Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of Burkholderia cenocepacia J2315 and Other Members of the B. cepacia Complex. PMID:32098200
Genome of Tripterygium wilfordii and identification of cytochrome P450 involved in triptolide biosynthesis. PMID:32080175
Data on the genome analysis of the wood-rotting fungus Steccherinum ochraceum LE-BIN 3174. PMID:32055659
Tools for Analysis of the Microbiome. PMID:32002757
ISOGO: Functional annotation of protein-coding splice variants. PMID:31974522
RNA-seq Analysis of Salt-Stressed Versus Non Salt-Stressed Transcriptomes of Chenopodium quinoa Landrace R49. PMID:31888133
Identifying Acetylation Protein by Fusing Its PseAAC and Functional Domain Annotation. PMID:31867311
Genome-Wide Analysis of Whole Human Glycoside Hydrolases by Data-Driven Analysis in Silico. PMID:31847093
Early Stage Adaptation of a Mesophilic Green Alga to Antarctica: Systematic Increases in Abundance of Enzymes and LEA Proteins. PMID:31794607
Is MYND Domain-Mediated Assembly of SMYD3 Complexes Involved in Calcium Dependent Signaling? PMID:31737645
The wax gourd genomes offer insights into the genetic diversity and ancestral cucurbit karyotype. PMID:31727887
Prediction of Deleterious Non-synonymous SNPs of Human STK11 Gene by Combining Algorithms, Molecular Docking, and Molecular Dynamics Simulation. PMID:31712642
Fungal Adaptation to the Advanced Stages of Wood Decomposition: Insights from the Steccherinum ochraceum. PMID:31694151
Acetylome analysis of lysine acetylation in the plant pathogenic bacterium Brenneria nigrifluens. PMID:31677250
A high-quality Actinidia chinensis (kiwifruit) genome. PMID:31645971
Draft genome sequence of cauliflower (Brassica oleracea L. var. botrytis) provides new insights into the C genome in Brassica species. PMID:31645943
Alternative Splicing in Heat Shock Protein Transcripts as a Mechanism of Cell Adaptation in Trichophyton rubrum. PMID:31590387
Genome-Wide Identification, Characterization and Expression Patterns of the Pectin Methylesterase Inhibitor Genes in Sorghum bicolor. PMID:31561536
Draft Genome and Complete Hox-Cluster Characterization of the Sterlet (Acipenser ruthenus). PMID:31543900
Role of Clathrin Assembly Protein-2 Beta Subunit during White Spot Syndrome Virus Infection in Black Tiger Shrimp Penaeus monodon. PMID:31530841
Whole Genome Sequencing of Chinese White Dolphin (Sousa chinensis) for High-Throughput Screening of Antihypertensive Peptides. PMID:31466310
Whole Genome Sequencing of the Giant Grouper (Epinephelus lanceolatus) and High-Throughput Screening of Putative Antimicrobial Peptide Genes. PMID:31466296
Enzymatic Degradation of Biofilm by Metalloprotease From Microbacterium sp. SKS10. PMID:31448272
Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics. PMID:31405015
Computational analysis of high-risk SNPs in human CHK2 gene responsible for hereditary breast cancer: A functional and structural impact. PMID:31398194
Transcriptome analysis of acerola fruit ripening: insights into ascorbate, ethylene, respiration, and softening metabolisms. PMID:31338671
Comparative structural and evolutionary analyses predict functional sites in the artemisinin resistance malaria protein K13. PMID:31337835
Genome Sequencing of the Japanese Eel (Anguilla japonica) for Comparative Genomic Studies on tbx4 and a tbx4 Gene Cluster in Teleost Fishes. PMID:31330852
Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT. PMID:31324144
Whole-Genome Sequencing of the Giant Devil Catfish, Bagarius yarrelli. PMID:31274158
Whole Genome Sequencing of the Blue Tilapia (Oreochromis aureus) Provides a Valuable Genetic Resource for Biomedical Research on Tilapias. PMID:31261751
Maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER). PMID:31245718
Guarani Virophage, a New Sputnik-Like Isolate From a Brazilian Lake. PMID:31130943
De novo gene birth. PMID:31120894
Comparative evaluation of structure and characteristic of peptidyl-prolyl cis-trans isomerase proteins and their function in Salmonella Typhimurium stress responses and virulence. PMID:31111418
High precision protein functional site detection using 3D convolutional neural networks. PMID:31051039
The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition. PMID:31049561
Genome-Wide Analysis of Multiple Organellar RNA Editing Factor Family in Poplar Reveals Evolution and Roles in Drought Stress. PMID:30901839
DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies. PMID:30878356
GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. PMID:30862647
Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP. PMID:30858367
Coexpression patterns define epigenetic regulators associated with neurological dysfunction. PMID:30858344
Transcriptome datasets from leaves and fruits of the sweet cherry cultivars 'Bing', 'Lapins' and 'Rainier'. PMID:30788404
Comparative genomics sheds light on the predatory lifestyle of accipitrids and owls. PMID:30783131
Bioinformatic discovery of a toxin family in Chryseobacterium piperi with sequence similarity to botulinum neurotoxins. PMID:30733520
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 Assembly for a Yunnan-Guizhou Plateau "3E" Fish, Anabarilius grahami (Regan), and Its Evolutionary and Genetic Applications. PMID:30564274
Whole-Genome Sequencing of Chinese Yellow Catfish Provides a Valuable Genetic Resource for High-Throughput Identification of Toxin Genes. PMID:30477130
Genome-wide analysis reveals the evolution and structural features of WRINKLED1 in plants. PMID:30446819
Assessment of coding region variants in Kuwaiti population: implications for medical genetics and population genomics. PMID:30409984
An Interleukin-23-Interleukin-22 Axis Regulates Intestinal Microbial Homeostasis to Protect from Diet-Induced Atherosclerosis. PMID:30389414
Glycinebetaine Biosynthesis in Response to Osmotic Stress Depends on Jasmonate Signaling in Watermelon Suspension Cells. PMID:30369936
Peanut Stunt Virus and Its Satellite RNA Trigger Changes in Phosphorylation in N. benthamiana Infected Plants at the Early Stage of the Infection. PMID:30340407
De novo genome and transcriptome analyses provide insights into the biology of the trematode human parasite Fasciolopsis buski. PMID:30325945
Complete genome sequence of the halophile bacterium Kushneria konosiri X49T, isolated from salt-fermented Konosirus punctatus. PMID:30305867
Environmental pH modulates transcriptomic responses in the fungus Fusarium sp. associated with KSHB Euwallacea sp. near fornicatus. PMID:30285612
C.el Phosphatome: A Catalogue of Actual and Pseudo Phosphatases Based on In-Silico Studies in Caenorhabditis elegans. PMID:30242660
A comprehensive catalogue of polyketide synthase gene clusters in lichenizing fungi. PMID:30206732
Genomic characterization of Trichoderma atrobrunneum (T. harzianum species complex) ITEM 908: insight into the genetic endowment of a multi-target biocontrol strain. PMID:30200883
Carcinogenic Pesticide Control via Hijacking Endosymbiosis; The Paradigm of DSB-A from Wolbachia pipientis for the Management of Otiorhynchus singularis. PMID:30150426
The Defense Response of Nicotiana benthamiana to Peanut Stunt Virus Infection in the Presence of Symptom Exacerbating Satellite RNA. PMID:30142955
Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns. PMID:30086708
Comparative Genome Analysis of 2 Mycobacterium Tuberculosis Strains from Pakistan: Insights Globally Into Drug Resistance, Virulence, and Niche Adaptation. PMID:30083049
Genome sequence and genetic transformation of a widely distributed and cultivated poplar. PMID:30044051
Transcriptome Assembly and Profiling of Candida auris Reveals Novel Insights into Biofilm-Mediated Resistance. PMID:29997121
Identification of Antifungal Targets Based on Computer Modeling. PMID:29973534
Genetic Analysis of Rare Human Variants of Regulators of G Protein Signaling Proteins and Their Role in Human Physiology and Disease. PMID:29871944
Genomic and functional characterisation of IncX3 plasmids encoding blaSHV-12 in Escherichia coli from human and animal origin. PMID:29769695
PVCbase: an integrated web resource for the PVC bacterial proteomes. PMID:29718141
Draft genome of the protandrous Chinese black porgy, Acanthopagrus schlegelii. PMID:29659813
Ginseng Genome Database: an open-access platform for genomics of Panax ginseng. PMID:29649979
The draft genome sequence of forest musk deer (Moschus berezovskii). PMID:29635287
The Draft Genome Sequence of a Novel High-Efficient Butanol-Producing Bacterium Clostridium Diolis Strain WST. PMID:29564548
Biochemical and structural characterization of a novel cold-active esterase-like protein from the psychrophilic yeast Glaciozyma antarctica. PMID:29556723
Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms. PMID:29556065
The transcriptomic signature of different sexes in two protogynous hermaphrodites: Insights into the molecular network underlying sex phenotype in fish. PMID:29476120
The Phosphate Fast-Responsive Genes PECP1 and PPsPase1 Affect Phosphocholine and Phosphoethanolamine Content. PMID:29475899
Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat. PMID:29459707
Structure, function, and mechanism of the core circadian clock in cyanobacteria. PMID:29440392
Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework. PMID:29385081
Endoplasmic reticulum acyltransferase with prokaryotic substrate preference contributes to triacylglycerol assembly in Chlamydomonas. PMID:29382746
A widely conserved bacterial cytoskeletal component influences unique helical shape and motility of the spirochete Leptospira biflexa. PMID:29363884
Characterization of a Novel Tectivirus Phage Toil and Its Potential as an Agent for Biolipid Extraction. PMID:29348539
Complete Genome Sequence of Hyperthermophilic Archaeon Thermococcus sp. EXT12c, Isolated from the East Pacific Rise 9°N. PMID:29242226
LAST, a c-Myc-inducible long noncoding RNA, cooperates with CNBP to promote CCND1 mRNA stability in human cells. PMID:29199958
Identification of key genes and pathways associated with neuropathic pain in uninjured dorsal root ganglion by using bioinformatic analysis. PMID:29180893
Chromosome level assembly and secondary metabolite potential of the parasitic fungus Cordyceps militaris. PMID:29178836
Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews. PMID:29166857
Structural analyses unravel the molecular mechanism of cyclic di-GMP regulation of bacterial chemotaxis via a PilZ adaptor protein. PMID:29146598
Genome sequence of the small brown planthopper, Laodelphax striatellus. PMID:29136191
KIXBASE: A comprehensive web resource for identification and exploration of KIX domains. PMID:29097748
Shaping the evolutionary tree of green plants: evidence from the GST family. PMID:29084977
Ant-infecting Ophiocordyceps genomes reveal a high diversity of potential behavioral manipulation genes and a possible major role for enterotoxins. PMID:28970504
The draft genome sequence of a desert tree Populus pruinosa. PMID:28938721
De novo Assembly of the Camellia nitidissima Transcriptome Reveals Key Genes of Flower Pigment Biosynthesis. PMID:28936220
Genome-Wide Analysis of the Biosynthesis and Deactivation of Gibberellin-Dioxygenases Gene Family in Camellia sinensis (L.) O. Kuntze. PMID:28925957
The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies. PMID:28915793
Evolution and genome specialization of Brucella suis biovar 2 Iberian lineages. PMID:28899413
Transcriptome analysis of the response of Burmese python to digestion. PMID:28873961
MCE domain proteins: conserved inner membrane lipid-binding proteins required for outer membrane homeostasis. PMID:28819315
A clinician's guide to microbiome analysis. PMID:28790452
Complete Genome Sequence of Citrobacter freundii Myophage Mijalis. PMID:28774966
Bradyrhizobium elkanii nod regulon: insights through genomic analysis. PMID:28767122
In silico analyses of conservational, functional and phylogenetic distribution of the LuxI and LuxR homologs in Gram-positive bacteria. PMID:28765541
An in silico strategy for identification of novel drug targets against Plasmodium falciparum. PMID:28755265
Prediction of presynaptic and postsynaptic neurotoxins by combining various Chou's pseudo components. PMID:28724993
Discovery of Lysine Hydroxylases in the Clavaminic Acid Synthase-Like Superfamily for Efficient Hydroxylysine Bioproduction. PMID:28667106
Genomic, proteomic and bioinformatic analysis of two temperate phages in Roseobacter clade bacteria isolated from the deep-sea water. PMID:28655355
Novel regulatory mechanism of serine biosynthesis associated with 3-phosphoglycerate dehydrogenase in Arabidopsis thaliana. PMID:28615699
Analysis of EF-Hand Proteins in Soybean Genome Suggests Their Potential Roles in Environmental and Nutritional Stress Signaling. PMID:28596783
Prostaglandin E2 glyceryl ester is an endogenous agonist of the nucleotide receptor P2Y6. PMID:28539604
Computational Exploration of Putative LuxR Solos in Archaea and Their Functional Implications in Quorum Sensing. PMID:28515720
Identification and comparative analysis of the ovarian microRNAs of prolific and non-prolific goats during the follicular phase using high-throughput sequencing. PMID:28507337
Transcriptomic and macroevolutionary evidence for phenotypic uncoupling between frog life history phases. PMID:28504275
Systematic analysis of the lysine acetylome reveals diverse functions of lysine acetylation in the oleaginous yeast Yarrowia lipolytica. PMID:28497289
QueryOR: a comprehensive web platform for genetic variant analysis and prioritization. PMID:28454514
Draft genome of the lined seahorse, Hippocampus erectus. PMID:28444302
Genome-Wide Analyses of the Soybean F-Box Gene Family in Response to Salt Stress. PMID:28417911
Evolution of the endomembrane systems of trypanosomatids - conservation and specialisation. PMID:28386020
Genome sequence of a rice pest, the white-backed planthopper (Sogatella furcifera). PMID:28369349
In Entamoeba histolytica, a BspA family protein is required for chemotaxis toward tumour necrosis factor. PMID:28357299
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
Transcriptional Responses of Chilean Quinoa (Chenopodium quinoa Willd.) Under Water Deficit Conditions Uncovers ABA-Independent Expression Patterns. PMID:28337209
Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius. PMID:28327943
Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota. PMID:28265262
Transcriptome profile of the human placenta. PMID:28251419
In-silico screening, identification and validation of a novel vaccine candidate in the fight against Plasmodium falciparum. PMID:28236172
Systematic analysis of non-structural protein features for the prediction of PTM function potential by artificial neural networks. PMID:28225828
Transcriptome analysis reveals a complex interplay between resistance and effector genes during the compatible lentil-Colletotrichum lentis interaction. PMID:28186158
Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis. PMID:28068432
Genes essential for the morphogenesis of the Shiga toxin 2-transducing phage from Escherichia coli O157:H7. PMID:27966628
Bursaphelenchus xylophilus and B. mucronatus secretomes: a comparative proteomic analysis. PMID:27941947
Genome scale identification, structural analysis, and classification of periplasmic binding proteins from Mycobacterium tuberculosis. PMID:27858159
Beyond DNA: An Integrated and Functional Approach for Classifying Germline Variants in Breast Cancer Genes. PMID:27822389
Transcriptome Dynamics in Mango Fruit Peel Reveals Mechanisms of Chilling Stress. PMID:27812364
Metagenomic Insights into Effects of Chemical Pollutants on Microbial Community Composition and Function in Estuarine Sediments Receiving Polluted River Water. PMID:27744476
Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology. PMID:27639274
PGD: a pangolin genome hub for the research community. PMID:27616775
De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia galeata. PMID:27604882
Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains. PMID:27601190
Transcriptome Characterization of Dendrolimus punctatus and Expression Profiles at Different Developmental Stages. PMID:27560151
Multipronged regulatory functions of a novel endonuclease (TieA) from Helicobacter pylori. PMID:27550181
Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii. PMID:27487948
Genome-wide characterization of non-reference transposons in crops suggests non-random insertion. PMID:27485608
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
Acetylome analysis reveals the involvement of lysine acetylation in diverse biological processes in Phytophthora sojae. PMID:27412925
Permanent draft genome sequence of sulfoquinovose-degrading Pseudomonas putida strain SQ1. PMID:27408681
Hypothetical granulin-like molecule from Fasciola hepatica identified by bioinformatics analysis. PMID:27386259
Misannotation Awareness: A Tale of Two Gene-Groups. PMID:27379147
sHSPdb: a database for the analysis of small Heat Shock Proteins. PMID:27297221
Genome Sequences of Multiresistant Staphylococcus capitis Pulsotype NRCS-A and Methicillin-Susceptible S. capitis Pulsotype NRCS-C. PMID:27284154
Wider than Thought Phylogenetic Occurrence of Apicortin, A Characteristic Protein of Apicomplexan Parasites. PMID:27282556
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
Stage-specific Proteomes from Onchocerca ochengi, Sister Species of the Human River Blindness Parasite, Uncover Adaptations to a Nodular Lifestyle. PMID:27226403
dbCPG: A web resource for cancer predisposition genes. PMID:27192119
Fungal and host transcriptome analysis of pH-regulated genes during colonization of apple fruits by Penicillium expansum. PMID:27146851
Two Groups of Thellungiella salsuginea RAVs Exhibit Distinct Responses and Sensitivity to Salt and ABA in Transgenic Arabidopsis. PMID:27093611
Characterization of a Plasmodium falciparum Orthologue of the Yeast Ubiquinone-Binding Protein, Coq10p. PMID:27015086
Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage. PMID:26973616
In silico Analysis Revealed High-risk Single Nucleotide Polymorphisms in Human Pentraxin-3 Gene and their Impact on Innate Immune Response against Microbial Pathogens. PMID:26941719
Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge. PMID:26905629
Ecological Genomics of the Uncultivated Marine Roseobacter Lineage CHAB-I-5. PMID:26826224
A comparative gene analysis with rice identified orthologous group II HKT genes and their association with Na(+) concentration in bread wheat. PMID:26786911
Complete Genome Sequence of Caulobacter crescentus Podophage Percy. PMID:26607888
Genome-Wide Identification, Phylogenetic and Expression Analyses of the Ubiquitin-Conjugating Enzyme Gene Family in Maize. PMID:26606743
Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. PMID:26598659
Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources. PMID:26589635
High Innate Immune Specificity through Diversified C-Type Lectin-Like Domain Proteins in Invertebrates. PMID:26580547
Transcription analysis of neonicotinoid resistance in Mediterranean (MED) populations of B. tabaci reveal novel cytochrome P450s, but no nAChR mutations associated with the phenotype. PMID:26573457
Nucleotide binding database NBDB--a collection of sequence motifs with specific protein-ligand interactions. PMID:26507856
Complete Genome Sequence of Citrobacter freundii Myophage Mordin. PMID:26472844
Evolution and Structural Analyses of Glossina morsitans (Diptera; Glossinidae) Tetraspanins. PMID:26462947
The Genome and Methylome of a Beetle with Complex Social Behavior, Nicrophorus vespilloides (Coleoptera: Silphidae). PMID:26454014
Complete Genome Sequence of Caulobacter crescentus Siphophage Sansa. PMID:26450723
Complete Genome Sequence of Bacillus megaterium Siphophage Silence. PMID:26450722
Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora. PMID:26438312
Complete Genome Sequence of Klebsiella pneumoniae Carbapenemase-Producing K. pneumoniae Myophage Miro. PMID:26430050
Complete Genome Sequence of Carbapenemase-Producing Klebsiella pneumoniae Myophage Matisse. PMID:26430049
Complete Genome Sequence of Enterotoxigenic Escherichia coli Myophage Murica. PMID:26430048
Complete Genome Sequence of Citrobacter freundii Myophage Michonne. PMID:26430047
Complete Genome Sequence of Citrobacter freundii Myophage Merlin. PMID:26430046
Complete Genome Sequence of Caulobacter crescentus Siphophage Seuss. PMID:26430045
Ascaris lumbricoides β carbonic anhydrase: a potential target enzyme for treatment of ascariasis. PMID:26385556
Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels. PMID:26371554
Bacteriophages of wastewater foaming-associated filamentous Gordonia reduce host levels in raw activated sludge. PMID:26349678
Bacteriophage application restores ethanol fermentation characteristics disrupted by Lactobacillus fermentum. PMID:26339290
Complete Genome Sequence of Klebsiella pneumoniae Carbapenemase-Producing K. pneumoniae Siphophage Sushi. PMID:26337889
Complete Genome Sequence of Bacillus megaterium Podophage Pavlov. PMID:26337888
How Common Is Disorder? Occurrence of Disordered Residues in Four Domains of Life. PMID:26295225
Deciphering common and specific transcriptional immune responses in pea towards the oomycete pathogens Aphanomyces euteiches and Phytophthora pisi. PMID:26293353
De novo analysis of the transcriptome of Pratylenchus zeae to identify transcripts for proteins required for structural integrity, sensation, locomotion and parasitism. PMID:26292651
Gene expression during zombie ant biting behavior reflects the complexity underlying fungal parasitic behavioral manipulation. PMID:26285697
Comparative Analysis of Transcriptional Profiles of Adult Schistosoma japonicum from Different Laboratory Animals and the Natural Host, Water Buffalo. PMID:26285138
Comparative Genomics of Environmental and Clinical Stenotrophomonas maltophilia Strains with Different Antibiotic Resistance Profiles. PMID:26276674
An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.). PMID:26259924
Remote homology and the functions of metagenomic dark matter. PMID:26257768
Complete Genome Sequence of Bacillus megaterium Siphophage Stahl. PMID:26251491
Genome Sequences of Four Staphylococcus capitis NRCS-A Isolates from Geographically Distant Neonatal Intensive Care Units. PMID:26251481
Ebolavirus comparative genomics. PMID:26175035
BGD: a database of bat genomes. PMID:26110276
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
New features of triacylglycerol biosynthetic pathways of peanut seeds in early developmental stages. PMID:26071211
Large-Scale Evolutionary Analysis of Genes and Supergene Clusters from Terpenoid Modular Pathways Provides Insights into Metabolic Diversification in Flowering Plants. PMID:26046541
A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis. PMID:26025923
INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity. PMID:26019177
Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. PMID:25983555
GraP: platform for functional genomics analysis of Gossypium raimondii. PMID:25982315
ProtoBug: functional families from the complete proteomes of insects. PMID:25911153
DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe. PMID:25888481
Computational prediction of protein-protein interactions. PMID:25859943
Analysis of genomic regions of Trichoderma harzianum IOC-3844 related to biomass degradation. PMID:25836973
Exome analysis reveals differentially mutated gene signatures of stage, grade and subtype in breast cancers. PMID:25803781
The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. PMID:25765701
Complete Genome of Citrobacter freundii Siphophage Stevie. PMID:25657269
A complex interplay of tandem- and whole-genome duplication drives expansion of the L-type lectin receptor kinase gene family in the brassicaceae. PMID:25635042
Complete Genome of Bacillus megaterium Podophage Pascal. PMID:25635028
ocsESTdb: a database of oil crop seed EST sequences for comparative analysis and investigation of a global metabolic network and oil accumulation metabolism. PMID:25604238
Complete Genome Sequence of Bacillus megaterium Myophage Moonbeam. PMID:25593264
Complete Genome Sequence of Citrobacter freundii Myophage Miller. PMID:25593263
Complete Genome Sequence of Bacillus megaterium Myophage Mater. PMID:25593262
Complete Genome Sequence of VpKK5, a Novel Vibrio parahaemolyticus Lytic Siphophage. PMID:25573936
INTEGRATING COMPUTATIONAL PROTEIN FUNCTION PREDICTION INTO DRUG DISCOVERY INITIATIVES. PMID:25530654
Core and accessory genome architecture in a group of Pseudomonas aeruginosa Mu-like phages. PMID:25527250
The identification and functional characterization of WxL proteins from Enterococcus faecium reveal surface proteins involved in extracellular matrix interactions. PMID:25512313
Transcriptome profiles of the protoscoleces of Echinococcus granulosus reveal that excretory-secretory products are essential to metabolic adaptation. PMID:25500817
Metatranscriptome profiling of a harmful algal bloom. PMID:25484636
Unique aspects of fiber degradation by the ruminal ethanologen Ruminococcus albus 7 revealed by physiological and transcriptomic analysis. PMID:25477200
The role of palmitoylation for protein recruitment to the inner membrane complex of the malaria parasite. PMID:25425642
Evolution of the insect desaturase gene family with an emphasis on social Hymenoptera. PMID:25425561
Comparative transcriptomic analysis of male and female flowers of monoecious Quercus suber. PMID:25414713
In silico prediction of physical protein interactions and characterization of interactome orphans. PMID:25402006
Computational characterization of moonlighting proteins. PMID:25399606
Comparative analysis of predicted plastid-targeted proteomes of sequenced higher plant genomes. PMID:25393533
De-novo assembly of mango fruit peel transcriptome reveals mechanisms of mango response to hot water treatment. PMID:25373421
New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM. PMID:25323955
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
Comparison of amino acids physico-chemical properties and usage of late embryogenesis abundant proteins, hydrophilins and WHy domain. PMID:25296175
Exploration of potential roles of a new LOXL2 splicing variant using network knowledge in esophageal squamous cell carcinoma. PMID:25254241
Draft genome sequence of eggplant (Solanum melongena L.): the representative solanum species indigenous to the old world. PMID:25233906
Genomic analysis of the Pacific oyster (Crassostrea gigas) reveals possible conservation of vertebrate sex determination in a mollusc. PMID:25213692
Proteome-wide subcellular topologies of E. coli polypeptides database (STEPdb). PMID:25210196
Non-contiguous finished genome sequence of Staphylococcus capitis CR01 (pulsetype NRCS-A). PMID:25197487
Compositions of fungal secretomes indicate a greater impact of phylogenetic history than lifestyle adaptation. PMID:25159997
Transcriptome sequencing and analysis of the zoonotic parasite Spirometra erinacei spargana (plerocercoids). PMID:25128015
PlantCAZyme: a database for plant carbohydrate-active enzymes. PMID:25125445
Incorporating amino acids composition and functional domains for identifying bacterial toxin proteins. PMID:25110714
Gene loss rather than gene gain is associated with a host jump from monocots to dicots in the Smut Fungus Melanopsichium pennsylvanicum. PMID:25062916
Draft sequencing and analysis of the genome of pufferfish Takifugu flavidus. PMID:25053628
Intronic and plasmid-derived regions contribute to the large mitochondrial genome sizes of Agaricomycetes. PMID:25011705
Novel host-related virulence factors are encoded by squirrelpox virus, the main causative agent of epidemic disease in red squirrels in the UK. PMID:24983354
Interaction networks of prion, prionogenic and prion-like proteins in budding yeast, and their role in gene regulation. PMID:24972093
Transcriptomic analysis of Prunus domestica undergoing hypersensitive response to plum pox virus infection. PMID:24959894
The genome of Eucalyptus grandis. PMID:24919147
Genomic analysis of the emergence of 20th century epidemic dysentery. PMID:24886041
A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing. PMID:24885229
Genome-wide analysis and identification of stress-responsive genes of the CCCH zinc finger family in Solanum lycopersicum. PMID:24870401
Characterisation of the horse transcriptome from immunologically active tissues. PMID:24860704
Evolutionary history of redox metal-binding domains across the tree of life. PMID:24778258
Complete Genome of Bacillus megaterium Podophage Page. PMID:24744341
Plant-bacteria association and symbiosis: are there common genomic traits in alphaproteobacteria? PMID:24710303
Characterization of the transcriptome and temperature-induced differential gene expression in QPX, the thraustochytrid parasite of hard clams. PMID:24678810
In silico characterization of an atypical MAPK phosphatase of Plasmodium falciparum as a suitable target for drug discovery. PMID:24605883
Draft Genome Sequence of a Novel Lactobacillus salivarius Strain Isolated from Piglet. PMID:24526652
Review of biological network data and its applications. PMID:24465231
Revised Genome Sequence of Staphylococcus aureus Bacteriophage K. PMID:24459260
Incorporating significant amino acid pairs and protein domains to predict RNA splicing-related proteins with functional roles. PMID:24442949
DBM-DB: the diamondback moth genome database. PMID:24434032
Integration of latex protein sequence data provides comprehensive functional overview of latex proteins. PMID:24395295
Pseudogenization in pathogenic fungi with different host plants and lifestyles might reflect their evolutionary past. PMID:24393451
Assessment of the geographic origins of pinewood nematode isolates via single nucleotide polymorphism in effector genes. PMID:24391785
Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium. PMID:24386394
Molecular characterization of pHRDV1, a new virus-like mobile genetic element closely related to pleomorphic viruses in haloarchaea. PMID:24374718
Molecular characteristics of the HSP70 gene and its differential expression in female and male golden apple snails (Pomacea canaliculata) under temperature stimulation. PMID:24368711
Complete Genome of Salmonella enterica Serovar Typhimurium Myophage Maynard. PMID:24356822
TFpredict and SABINE: sequence-based prediction of structural and functional characteristics of transcription factors. PMID:24349230
Integrating human omics data to prioritize candidate genes. PMID:24344781
Complete Genome of Bacillus megaterium Siphophage Slash. PMID:24336363
Cold-induced cysts of the photosynthetic dinoflagellate Lingulodinium polyedrum have an arrested circadian bioluminescence rhythm and lower levels of protein phosphorylation. PMID:24335505
INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles. PMID:24324765
New insights into histidine triad proteins: solution structure of a Streptococcus pneumoniae PhtD domain and zinc transfer to AdcAII. PMID:24312273
Complete Genome of Clavibacter michiganensis subsp. sepedonicusis Siphophage CN1A. PMID:24309731
Complete Genome of Bacillus megaterium Siphophage Staley. PMID:24309730
Complete Genome of Bacillus megaterium Podophage Pony. PMID:24309727
Complete Genome of Bacillus pumilus Siphophage Glittering. PMID:24309725
Complete Genome of Bacillus pumilus Siphophage Blastoid. PMID:24309724
MycoCosm portal: gearing up for 1000 fungal genomes. PMID:24297253
A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress. PMID:24280345
Development of reference transcriptomes for the major field insect pests of cowpea: a toolbox for insect pest management approaches in west Africa. PMID:24278221
ModBase, a database of annotated comparative protein structure models and associated resources. PMID:24271400
The European Bioinformatics Institute's data resources 2014. PMID:24271396
OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. PMID:24271386
Transcriptome profiling of fruit development and maturation in Chinese white pear (Pyrus bretschneideri Rehd). PMID:24267665
PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool. PMID:24219505
Potential for sexual conflict assessed via testosterone-mediated transcriptional changes in liver and muscle of a songbird. PMID:24198265
Signature protein of the PVC superphylum. PMID:24185849
Cellular growth and mitochondrial ultrastructure of leishmania (Viannia) braziliensis promastigotes are affected by the iron chelator 2,2-dipyridyl. PMID:24147167
Evaluation and cross-comparison of lexical entities of biological interest (LexEBI). PMID:24124474
Aberrant DNA methylation at genes associated with a stem cell-like phenotype in cholangiocarcinoma tumors. PMID:24089088
Schistosoma mansoni Sirtuins: characterization and potential as chemotherapeutic targets. PMID:24069483
Functional characterization of sucrose non-fermenting 1 protein kinase complex genes in the Ascomycete Fusarium graminearum. PMID:24057127
Agrigenomics for microalgal biofuel production: an overview of various bioinformatics resources and recent studies to link OMICS to bioenergy and bioeconomy. PMID:24044362
Identification of genes involved in wild crucifer Rorippa indica resistance response on mustard aphid Lipaphis erysimi challenge. PMID:24040008
The coming of age of phosphoproteomics--from large data sets to inference of protein functions. PMID:24037665
Daily rhythms in antennal protein and olfactory sensitivity in the malaria mosquito Anopheles gambiae. PMID:23986098
The Tarenaya hassleriana genome provides insight into reproductive trait and genome evolution of crucifers. PMID:23983221
Functional genomic analyses of two morphologically distinct classes of Drosophila sensory neurons: post-mitotic roles of transcription factors in dendritic patterning. PMID:23977298
bZIP transcription factors in the oomycete phytophthora infestans with novel DNA-binding domains are involved in defense against oxidative stress. PMID:23975888
Application of Cydia pomonella expressed sequence tags: Identification and expression of three general odorant binding proteins in codling moth. PMID:23956229
Systematic analysis and comparison of nucleotide-binding site disease resistance genes in a diploid cotton Gossypium raimondii. PMID:23936305
Genome-wide identification and characterisation of F-box family in maize. PMID:23928825
Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE. PMID:23875683
A systems-genetics approach and data mining tool to assist in the discovery of genes underlying complex traits in Oryza sativa. PMID:23874666
An alignment-free domain architecture similarity search (ADASS) algorithm for inferring homology between multi-domain proteins. PMID:23861564
LOC689986, a unique gene showing specific expression in restricted areas of the rodent neocortex. PMID:23844656
Genetic basis for phenotypic differences between different Toxoplasma gondii type I strains. PMID:23837824
LAMP: A Database Linking Antimicrobial Peptides. PMID:23825543
Discovery of diversity in xylan biosynthetic genes by transcriptional profiling of a heteroxylan containing mucilaginous tissue. PMID:23761806
Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study. PMID:23738693
Integrative approach reveals composition of endoparasitoid wasp venoms. PMID:23717546
PLANEX: the plant co-expression database. PMID:23688397
Characterizing PvARP, a novel Plasmodium vivax antigen. PMID:23688042
Sequence and structural investigation of a novel psychrophilic α-amylase from Glaciozyma antarctica PI12 for cold-adaptation analysis. PMID:23686283
Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos. PMID:23684812
Age-dependent expression of stress and antimicrobial genes in the hemocytes and siphon tissue of the Antarctic bivalve, Laternula elliptica, exposed to injury and starvation. PMID:23666709
Discovering RNA-protein interactome by using chemical context profiling of the RNA-protein interface. PMID:23665222
Reconstituting protein interaction networks using parameter-dependent domain-domain interactions. PMID:23651452
Chapter 15: disease gene prioritization. PMID:23633938
The role of structural bioinformatics resources in the era of integrative structural biology. PMID:23633580
The Protein Model Portal--a comprehensive resource for protein structure and model information. PMID:23624946
Testosterone affects neural gene expression differently in male and female juncos: a role for hormones in mediating sexual dimorphism and conflict. PMID:23613935
Functional classification of immune regulatory proteins. PMID:23583034
Shotgun proteomic analysis on the diapause and non-diapause eggs of domesticated silkworm Bombyx mori. PMID:23580252
Comparative transcriptomics of infectious spores from the fungal pathogen Histoplasma capsulatum reveals a core set of transcripts that specify infectious and pathogenic states. PMID:23563482
ProtoNet: charting the expanding universe of protein sequences. PMID:23563419
Genomic evaluation of Thermoanaerobacter spp. for the construction of designer co-cultures to improve lignocellulosic biofuel production. PMID:23555660
Extensive circadian and light regulation of the transcriptome in the malaria mosquito Anopheles gambiae. PMID:23552056
Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest. PMID:23537049
Transcriptome analysis of artificial hybrid pufferfish Jiyan-1 and its parental species: implications for pufferfish heterosis. PMID:23520511
Draft Genome of the Marine Gammaproteobacterium Halomonas titanicae. PMID:23516210
Protein function prediction using domain families. PMID:23514456
In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment. PMID:23514353
Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex. PMID:23514195
One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012. PMID:23494302
Using existing drugs as leads for broad spectrum anthelmintics targeting protein kinases. PMID:23459584
Ancient complexity, opisthokont plasticity, and discovery of the 11th subfamily of Arf GAP proteins. PMID:23433073
Comparative transcriptomics of early dipteran development. PMID:23432914
Drug target predictions based on heterogeneous graph inference. PMID:23424111
Proteome-wide prediction of self-interacting proteins based on multiple properties. PMID:23422585
Prediction of S-glutathionylation sites based on protein sequences. PMID:23418443
Massive-scale gene co-expression network construction and robustness testing using random matrix theory. PMID:23409071
A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels. PMID:23390605
Genome-wide identification and analysis of the B3 superfamily of transcription factors in Brassicaceae and major crop plants. PMID:23377560
Cloning and sequencing of the kedarcidin biosynthetic gene cluster from Streptoalloteichus sp. ATCC 53650 revealing new insights into biosynthesis of the enediyne family of antitumor antibiotics. PMID:23360970
DNA damage and transcriptional changes in the gills of mytilus galloprovincialis exposed to nanomolar doses of combined metal salts (Cd, Cu, Hg). PMID:23355883
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
A heterozygous moth genome provides insights into herbivory and detoxification. PMID:23313953
Ecology of marine Bacteroidetes: a comparative genomics approach. PMID:23303374
Development of transcriptomic resources for interrogating the biosynthesis of monoterpene indole alkaloids in medicinal plant species. PMID:23300689
Module-based subnetwork alignments reveal novel transcriptional regulators in malaria parasite Plasmodium falciparum. PMID:23282319
Mapping small molecule binding data to structural domains. PMID:23282026
TranSeqAnnotator: large-scale analysis of transcriptomic data. PMID:23282024
DB Dehydrogenase: an online integrated structural database on enzyme dehydrogenase. PMID:23275696
Gene family matters: expanding the HGNC resource. PMID:23245209
In silico approach to predict candidate R proteins and to define their domain architecture. PMID:23216678
Evolution of Bcl-2 homology motifs: homology versus homoplasy. PMID:23199982
Tips and tricks for the assembly of a Corynebacterium pseudotuberculosis genome using a semiconductor sequencer. PMID:23199210
Learning virulent proteins from integrated query networks. PMID:23198735
DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. PMID:23193290
CFGP 2.0: a versatile web-based platform for supporting comparative and evolutionary genomics of fungi and Oomycetes. PMID:23193288
KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms. PMID:23193279
A catalogue of putative unique transcripts from Douglas-fir (Pseudotsuga menziesii) based on 454 transcriptome sequencing of genetically diverse, drought stressed seedlings. PMID:23190494
Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria. PMID:23188745
DoBISCUIT: a database of secondary metabolite biosynthetic gene clusters. PMID:23185043
Evaluation of function predictions by PFP, ESG,and PSI-BLAST for moonlighting proteins. PMID:23173871
A new protein superfamily: TPPP-like proteins. PMID:23166627
Nucleolar protein trafficking in response to HIV-1 Tat: rewiring the nucleolus. PMID:23166591
PMRD: a curated database for genes and mutants involved in plant male reproduction. PMID:23153247
The unique architecture and function of cellulose-interacting proteins in oomycetes revealed by genomic and structural analyses. PMID:23140525
Searching for resistance genes to Bursaphelenchus xylophilus using high throughput screening. PMID:23134679
Bioenergy grass feedstock: current options and prospects for trait improvement using emerging genetic, genomic, and systems biology toolkits. PMID:23122416
Efficient heterologous transformation of Chlamydomonas reinhardtii npq2 mutant with the zeaxanthin epoxidase gene isolated and characterized from Chlorella zofingiensis. PMID:23118714
Identifying structural domains of proteins using clustering. PMID:23116496
Enzyme informatics. PMID:23116471
RNA interference of endochitinases in the sugarcane endophyte Trichoderma virens 223 reduces its fitness as a biocontrol agent of pineapple disease. PMID:23110120
Analysis of genome survey sequences and SSR marker development for Siamese Mud Carp, Henicorhynchus siamensis, using 454 pyrosequencing. PMID:23109823
IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis. PMID:23095257
Annotation of microsporidian genomes using transcriptional signals. PMID:23072807
Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii). PMID:23056606
The Caulobacter crescentus phage phiCbK: genomics of a canonical phage. PMID:23050599
Detailed transcriptome description of the neglected cestode Taenia multiceps. PMID:23049872
Inferring domain-domain interactions from protein-protein interactions in the complex network conformation. PMID:23046795
Gene expression and physiological changes of different populations of the long-lived bivalve Arctica islandica under low oxygen conditions. PMID:23028566
MyDas, an extensible Java DAS server. PMID:23028496
Sex peptide of Drosophila melanogaster males is a global regulator of reproductive processes in females. PMID:22977156
Comparative genomic analysis of Geobacter sulfurreducens KN400, a strain with enhanced capacity for extracellular electron transfer and electricity production. PMID:22967216
ReLiance: a machine learning and literature-based prioritization of receptor--ligand pairings. PMID:22962483
Metagenomic analysis: the challenge of the data bonanza. PMID:22962339
A small predatory core genome in the divergent marine Bacteriovorax marinus SJ and the terrestrial Bdellovibrio bacteriovorus. PMID:22955231
Increasing coverage of transcription factor position weight matrices through domain-level homology. PMID:22952610
Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection. PMID:22951933
Comparative genome analysis of three eukaryotic parasites with differing abilities to transform leukocytes reveals key mediators of Theileria-induced leukocyte transformation. PMID:22951932
Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. PMID:22942020
Gene isoform specificity through enhancer-associated antisense transcription. PMID:22937057
Genome sequence of Staphylococcus equorum subsp. equorum Mu2, isolated from a French smear-ripened cheese. PMID:22933766
HSPIR: a manually annotated heat shock protein information resource. PMID:22923302
Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites. PMID:22920570
Predicting disease-related subnetworks for type 1 diabetes using a new network activity score. PMID:22917479
Characterization of the ubiquitylating components of the human malaria parasite's protein degradation pathway. PMID:22912882
Novel insights into the transcriptome of Dirofilaria immitis. PMID:22911833
A deep exploration of the transcriptome and "excretory/secretory" proteome of adult Fascioloides magna. PMID:22899770
Mining GO annotations for improving annotation consistency. PMID:22848383
Deciphering a global network of functionally associated post-translational modifications. PMID:22806145
Inability to catabolize galactose leads to increased ability to compete for nodule occupancy in Sinorhizobium meliloti. PMID:22797764
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
Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton. PMID:22768919
Independent evolution of striated muscles in cnidarians and bilaterians. PMID:22763458
Genome sequence of temperate bacteriophage Psymv2 from Antarctic Dry Valley soil isolate Psychrobacter sp. MV2. PMID:22760730
Domain landscapes of somatic mutations in cancer. PMID:22759657
Genes2FANs: connecting genes through functional association networks. PMID:22748121
Regulation of alternative splicing by the circadian clock and food related cues. PMID:22721557
Collagen-like proteins in pathogenic E. coli strains. PMID:22701585
Quality of computationally inferred gene ontology annotations. PMID:22693439
Biomine: predicting links between biological entities using network models of heterogeneous databases. PMID:22672646
Human gene correlation analysis (HGCA): a tool for the identification of transcriptionally co-expressed genes. PMID:22672625
Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses. PMID:22672222
Widespread uncoupling between transcriptome and translatome variations after a stimulus in mammalian cells. PMID:22672192
Biomarker identification for prostate cancer and lymph node metastasis from microarray data and protein interaction network using gene prioritization method. PMID:22654636
Gene expression profiling of Mycobacterium avium subsp. paratuberculosis in simulated multi-stress conditions and within THP-1 cells reveals a new kind of interactive intramacrophage behaviour. PMID:22646160
dbCAN: a web resource for automated carbohydrate-active enzyme annotation. PMID:22645317
Ecophysiology of an ammonia-oxidizing archaeon adapted to low-salinity habitats. PMID:22644483
SLocX: Predicting Subcellular Localization of Arabidopsis Proteins Leveraging Gene Expression Data. PMID:22639594
Transcriptome sequencing of and microarray development for a Helicoverpa zea cell line to investigate in vitro insect cell-baculovirus interactions. PMID:22629315
Computational and statistical analyses of amino acid usage and physico-chemical properties of the twelve late embryogenesis abundant protein classes. PMID:22615859
Genetic variation and metabolic pathway intricacy govern the active compound content and quality of the Chinese medicinal plant Lonicera japonica thunb. PMID:22607188
IRView: a database and viewer for protein interacting regions. PMID:22592381
3D profile-based approach to proteome-wide discovery of novel human chemokines. PMID:22586462
Clusters of ancestrally related genes that show paralogy in whole or in part are a major feature of the genomes of humans and other species. PMID:22563380
Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations. PMID:22563243
Current view on phytoplasma genomes and encoded metabolism. PMID:22550465
Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum. PMID:22548871
EnzML: multi-label prediction of enzyme classes using InterPro signatures. PMID:22533924
A scissor blade-like closing mechanism implicated in transmembrane signaling in a Bacteroides hybrid two-component system. PMID:22532667
Identification and characterization of a novel diterpene gene cluster in Aspergillus nidulans. PMID:22506079
Computer-based annotation of putative AraC/XylS-family transcription factors of known structure but unknown function. PMID:22505803
Crystallization of a novel metal-containing cupin from Acidobacterium sp. and preliminary diffraction data analysis. PMID:22505418
EnzyBase: a novel database for enzybiotic studies. PMID:22489867
A genome-wide study of two-component signal transduction systems in eight newly sequenced mutans streptococci strains. PMID:22475007
Mycobacteriophage endolysins: diverse and modular enzymes with multiple catalytic activities. PMID:22470512
The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data. PMID:22465017
Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. PMID:22457617
MotViz: a tool for sequence motif prediction in parallel to structural visualization and analyses. PMID:22449399
Massively parallel RNA sequencing identifies a complex immune gene repertoire in the lophotrochozoan Mytilus edulis. PMID:22448234
CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. PMID:22434836
Specific versus non-specific immune responses in an invertebrate species evidenced by a comparative de novo sequencing study. PMID:22427848
A survey of sRNA families in α-proteobacteria. PMID:22418845
SpiroESTdb: a transcriptome database and online tool for sparganum expressed sequences tags. PMID:22397686
Related haloarchaeal pleomorphic viruses contain different genome types. PMID:22396526
Core site-moiety maps reveal inhibitors and binding mechanisms of orthologous proteins by screening compound libraries. PMID:22393385
Insights into SCP/TAPS proteins of liver flukes based on large-scale bioinformatic analyses of sequence datasets. PMID:22384000
Integrative analysis workflow for the structural and functional classification of C-type lectins. PMID:22372988
DetoxiProt: an integrated database for detoxification proteins. PMID:22369658
Protease-associated cellular networks in malaria parasite Plasmodium falciparum. PMID:22369208
Cystinosin, MPDU1, SWEETs and KDELR belong to a well-defined protein family with putative function of cargo receptors involved in vesicle trafficking. PMID:22363504
A protein short motif search tool using amino acid sequence and their secondary structure assignment. PMID:22355226
Proteomic analysis of Plasmodium in the mosquito: progress and pitfalls. PMID:22336136
BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins. PMID:22335941
Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal. PMID:22323219
Characterization of the intronic portion of cadherin superfamily members, common cancer orchestrators. PMID:22317972
Structural modeling and biochemical characterization of recombinant KPN_02809, a zinc-dependent metalloprotease from Klebsiella pneumoniae MGH 78578. PMID:22312293
Systematic analysis of plant-specific B3 domain-containing proteins based on the genome resources of 11 sequenced species. PMID:22302388
A novel extracellular metallopeptidase domain shared by animal host-associated mutualistic and pathogenic microbes. PMID:22299034
Proteome of Hydra nematocyst. PMID:22291027
Regulation of enteric vapBC transcription: induction by VapC toxin dimer-breaking. PMID:22287572
Genome sequence for "Candidatus Mycoplasma haemominutum," a low-pathogenicity hemoplasma species. PMID:22275103
dHPLC efficiency for semi-automated cDNA-AFLP analyses and fragment collection in the apple scab-resistance gene model. PMID:22270558
Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.). PMID:22260238
Genome sequence of Corynebacterium casei UCMA 3821, isolated from a smear-ripened cheese. PMID:22247534
Transient infantile hypertriglyceridemia, fatty liver, and hepatic fibrosis caused by mutated GPD1, encoding glycerol-3-phosphate dehydrogenase 1. PMID:22226083
Impact of acute stress on antimicrobial polypeptides mRNA copy number in several tissues of marine sea bass (Dicentrarchus labrax). PMID:22204309
Dissecting plant genomes with the PLAZA comparative genomics platform. PMID:22198273
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
Identification of cis-acting promoter elements in cold- and dehydration-induced transcriptional pathways in Arabidopsis, rice, and soybean. PMID:22184637
Solving the Problem: Genome Annotation Standards before the Data Deluge. PMID:22180819
Novel search method for the discovery of functional relationships. PMID:22180409
Mutations in EZH2 cause Weaver syndrome. PMID:22177091
Transcriptomics of a giant freshwater prawn (Macrobrachium rosenbergii): de novo assembly, annotation and marker discovery. PMID:22174756
The impact of focused Gene Ontology curation of specific mammalian systems. PMID:22174742
Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors. PMID:22174267
Expansion of genes encoding piRNA-associated argonaute proteins in the pea aphid: diversification of expression profiles in different plastic morphs. PMID:22162754
Requirement for RNA helicase CsdA for growth of Yersinia pseudotuberculosis IP32953 at low temperatures. PMID:22156424
Doubly uniparental inheritance of mitochondria as a model system for studying germ line formation. PMID:22140544
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. PMID:22139938
SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes. PMID:22139920
Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data. PMID:22139919
S-layer homology domain proteins Csac_0678 and Csac_2722 are implicated in plant polysaccharide deconstruction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus. PMID:22138994
Metals in biology: defining metalloproteomes. PMID:22138493
The Pfam protein families database. PMID:22127870
The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes. PMID:22125637
The UniProt-GO Annotation database in 2011. PMID:22123736
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. PMID:22121228
Phylogenetic analysis and classification of the fungal bHLH domain. PMID:22114358
Sucrose synthase in unicellular cyanobacteria and its relationship with salt and hypoxic stress. PMID:22113826
Incorporating evolutionary information and functional domains for identifying RNA splicing factors in humans. PMID:22110674
LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes. PMID:22110036
DAMPD: a manually curated antimicrobial peptide database. PMID:22110032
Phytozome: a comparative platform for green plant genomics. PMID:22110026
Reorganizing the protein space at the Universal Protein Resource (UniProt). PMID:22102590
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
Genome-wide detection of gene extinction in early mammalian evolution. PMID:22094861
Characterization of non-specific cytotoxic cell receptor protein 1: a new member of the lectin-type subfamily of F-box proteins. PMID:22087255
Ensembl 2012. PMID:22086963
IMG/M: the integrated metagenome data management and comparative analysis system. PMID:22086953
The H/ACA RNP assembly factor SHQ1 functions as an RNA mimic. PMID:22085966
Functional Annotation Analytics of Rhodopseudomonas palustris Genomes. PMID:22084572
E622, a miniature, virulence-associated mobile element. PMID:22081398
modMine: flexible access to modENCODE data. PMID:22080565
CADRE: the Central Aspergillus Data REpository 2012. PMID:22080563
Disordered patterns in clustered Protein Data Bank and in eukaryotic and bacterial proteomes. PMID:22073276
Divergence and convergence in enzyme evolution. PMID:22069324
The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata. PMID:22064862
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
Molecular cloning, expression and biochemical characterisation of a cold-adapted novel recombinant chitinase from Glaciozyma antarctica PI12. PMID:22050784
RNA-Seq improves annotation of protein-coding genes in the cucumber genome. PMID:22047402
Extensive recombination events and horizontal gene transfer shaped the Legionella pneumophila genomes. PMID:22044686
Proteomic analysis of excretory-secretory products of Heligmosomoides polygyrus assessed with next-generation sequencing transcriptomic information. PMID:22039562
Accelerated Profile HMM Searches. PMID:22039361
Accelerated recruitment of new brain development genes into the human genome. PMID:22028629
Identification, characterization and antigenicity of the Plasmodium vivax rhoptry neck protein 1 (PvRON1). PMID:22024312
Epigenetic virtues of chromodomains. PMID:22023491
Compaction of chromatin by diverse Polycomb group proteins requires localized regions of high charge. PMID:22012622
Murein and pseudomurein cell wall binding domains of bacteria and archaea--a comparative view. PMID:22012341
Identification of Plasmodium vivax proteins with potential role in invasion using sequence redundancy reduction and profile hidden Markov models. PMID:21984903
Structural bioinformatics of Neisseria meningitidis LD-carboxypeptidase: implications for substrate binding and specificity. PMID:21983752
A mass spectrometry-guided genome mining approach for natural product peptidogenomics. PMID:21983601
Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures. PMID:21979275
De Novo assembly of the Manila clam Ruditapes philippinarum transcriptome provides new insights into expression bias, mitochondrial doubly uniparental inheritance and sex determination. PMID:21976711
The UCSC Genome Browser. PMID:21975940
Similarities and differences in peripheral blood gene-expression signatures of individuals with schizophrenia and their first-degree biological relatives. PMID:21972136
Expression of signal transduction system encoding genes of Yersinia pseudotuberculosis IP32953 at 28°C and 3°C. PMID:21949852
RNAcentral: A vision for an international database of RNA sequences. PMID:21940779
A molecular insight into algal-oomycete warfare: cDNA analysis of Ectocarpus siliculosus infected with the basal oomycete Eurychasma dicksonii. PMID:21935414
Quantification of protein group coherence and pathway assignment using functional association. PMID:21929787
CastorDB: a comprehensive knowledge base for Ricinus communis. PMID:21914200
Integrating GPCR-specific information with full text articles. PMID:21910883
Evidence for direct electron transfer by a gram-positive bacterium isolated from a microbial fuel cell. PMID:21908627
Computational approaches to selecting and optimising targets for structural biology. PMID:21906678
Deep sequencing-based transcriptome analysis of Plutella xylostella larvae parasitized by Diadegma semiclausum. PMID:21906285
Using the Saccharomyces Genome Database (SGD) for analysis of genomic information. PMID:21901739
Evolution at the subgene level: domain rearrangements in the Drosophila phylogeny. PMID:21900599
A New Family of Biuret Hydrolases Involved in S-Triazine Ring Metabolism. PMID:21897878
The transcriptome of Trichuris suis--first molecular insights into a parasite with curative properties for key immune diseases of humans. PMID:21887281
Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network. PMID:21886106
GO-based functional dissimilarity of gene sets. PMID:21884611
The DEG/ENaC protein MEC-10 regulates the transduction channel complex in Caenorhabditis elegans touch receptor neurons. PMID:21880930
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
BLProt: prediction of bioluminescent proteins based on support vector machine and relieff feature selection. PMID:21849049
Long-chain N-acyl amino acid synthases are linked to the putative PEP-CTERM/exosortase protein-sorting system in Gram-negative bacteria. PMID:21840974
Predicting receptor-ligand pairs through kernel learning. PMID:21834994
Molecular evolution of the LNX gene family. PMID:21827680
Evolutionary history and functional characterization of three large genes involved in sporulation in Bacillus cereus group bacteria. PMID:21821775
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. PMID:21810205
Genomes and characterization of phages Bcep22 and BcepIL02, founders of a novel phage type in Burkholderia cenocepacia. PMID:21804006
A toolbox for developing bioinformatics software. PMID:21803787
Selection for translation efficiency on synonymous polymorphisms in recent human evolution. PMID:21803767
Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes. PMID:21794110
Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database. PMID:21791039
The InterPro BioMart: federated query and web service access to the InterPro Resource. PMID:21785143
Ensembl BioMarts: a hub for data retrieval across taxonomic space. PMID:21785142
Regulation of the virulence determinant OspC by bbd18 on linear plasmid lp17 of Borrelia burgdorferi. PMID:21784941
A genomic approach to study anthocyanin synthesis and flower pigmentation in passionflowers. PMID:21772993
Transcriptome profiling and insilico analysis of Gynostemma pentaphyllum using a next generation sequencer. PMID:21769605
The evolution of MDM2 family genes. PMID:21762762
HelmCoP: an online resource for helminth functional genomics and drug and vaccine targets prioritization. PMID:21760913
Transcriptome sequencing, and rapid development and application of SNP markers for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae). PMID:21754987
Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data. PMID:21749710
Biochemical characterization and relative expression levels of multiple carbohydrate esterases of the xylanolytic rumen bacterium Prevotella ruminicola 23 grown on an ester-enriched substrate. PMID:21742923
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
Independent subtilases expansions in fungi associated with animals. PMID:21727238
Genome-wide profiling of diel and circadian gene expression in the malaria vector Anopheles gambiae. PMID:21715657
RuleGO: a logical rules-based tool for description of gene groups by means of Gene Ontology. PMID:21715384
BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation. PMID:21696594
Unity in variety--the pan-genome of the Chlamydiae. PMID:21690563
Regulatory link mapping between organisms. PMID:21689479
Two phosphodiesterases from ustilago maydis share structural and biochemical properties with non-fungal phosphodiesterases. PMID:21687762
Extending the aerolysin family: from bacteria to vertebrates. PMID:21687664
Sorting the nuclear proteome. PMID:21685104
MarkUs: a server to navigate sequence-structure-function space. PMID:21672961
Diversification, phylogeny and evolution of auxin response factor (ARF) family: insights gained from analyzing maize ARF genes. PMID:21667107
RcnB is a periplasmic protein essential for maintaining intracellular Ni and Co concentrations in Escherichia coli. PMID:21665978
OrthoList: a compendium of C. elegans genes with human orthologs. PMID:21647448
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
Binding site prediction for protein-protein interactions and novel motif discovery using re-occurring polypeptide sequences. PMID:21635751
Genome sequence of the vertebrate gut symbiont Lactobacillus reuteri ATCC 53608. PMID:21622738
Data mining using the Catalogue of Somatic Mutations in Cancer BioMart. PMID:21609966
Bacterial metallothioneins: past, present, and questions for the future. PMID:21594652
HMMER web server: interactive sequence similarity searching. PMID:21593126
Signalogs: orthology-based identification of novel signaling pathway components in three metazoans. PMID:21559328
Targeting protein-protein interactions for parasite control. PMID:21556146
Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PMID:21556138
Fusing a lasting relationship between ER tubules. PMID:21550242
Eukaryotic protein kinases (ePKs) of the helminth parasite Schistosoma mansoni. PMID:21548963
Methods and strategies for gene structure curation in WormBase. PMID:21543339
The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist. PMID:21526192
Scoring protein relationships in functional interaction networks predicted from sequence data. PMID:21526183
Ultra-fast sequence clustering from similarity networks with SiLiX. PMID:21513511
Metagenomics and the protein universe. PMID:21497084
Major prospects for exploring canine vector borne diseases and novel intervention methods using 'omic technologies. PMID:21489242
Regulatory mechanisms underlying oil palm fruit mesocarp maturation, ripening, and functional specialization in lipid and carotenoid metabolism. PMID:21487046
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 Protein Data Bank in Europe (PDBe): bringing structure to biology. PMID:21460450
Global phosphoproteomics reveals crosstalk between Bcr-Abl and negative feedback mechanisms controlling Src signaling. PMID:21447799
UniProt Knowledgebase: a hub of integrated protein data. PMID:21447597
Molecular evolution of urea amidolyase and urea carboxylase in fungi. PMID:21447149
Transcriptome analysis of the desert locust central nervous system: production and annotation of a Schistocerca gregaria EST database. PMID:21445293
A link between impaired purine nucleotide synthesis and apoptosis in Drosophila melanogaster. PMID:21441212
Genomes of the most dangerous epidemic bacteria have a virulence repertoire characterized by fewer genes but more toxin-antitoxin modules. PMID:21437250
Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. PMID:21415278
Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. PMID:21411447
AGeS: a software system for microbial genome sequence annotation. PMID:21408217
TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery. PMID:21408081
Diversity in protein glycosylation among insect species. PMID:21373189
Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. PMID:21364937
A computational framework for proteome-wide pursuit and prediction of metalloproteins using ICP-MS and MS/MS data. PMID:21356119
Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. PMID:21356090
Protein function prediction: towards integration of similarity metrics. PMID:21353529
The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. PMID:21347285
Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana. PMID:21332978
The what, where, how and why of gene ontology--a primer for bioinformaticians. PMID:21330331
Complete genome sequence of Mycoplasma haemofelis, a hemotropic mycoplasma. PMID:21317334
GeneReporter--sequence-based document retrieval and annotation. PMID:21310745
Accurate quantification of functional analogy among close homologs. PMID:21304936
Complete genome sequence of Archaeoglobus profundus type strain (AV18). PMID:21304717
Complete genome sequence of Methanoculleus marisnigri Romesser et al. 1981 type strain JR1. PMID:21304656
Differential gene expression in liver and small intestine from lactating rats compared to age-matched virgin controls detects increased mRNA of cholesterol biosynthetic genes. PMID:21291544
Eukaryote-wide sequence analysis of mitochondrial β-barrel outer membrane proteins. PMID:21272379
Insights into the innate immunity of the Mediterranean mussel Mytilus galloprovincialis. PMID:21269501
Blue and red light modulates SigB-dependent gene transcription, swimming motility and invasiveness in Listeria monocytogenes. PMID:21264304
Genome (re-)annotation and open-source annotation pipelines. PMID:21255336
ePlant and the 3D data display initiative: integrative systems biology on the world wide web. PMID:21249219
A new principle of oligomerization of plant DEG7 protease based on interactions of degenerated protease domains. PMID:21247409
Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires. PMID:21241503
Global identification of multiple substrates for Plasmodium falciparum SUB1, an essential malarial processing protease. PMID:21220481
OrthoInspector: comprehensive orthology analysis and visual exploration. PMID:21219603
De novo analysis of transcriptome dynamics in the migratory locust during the development of phase traits. PMID:21209894
The 'PUCE CAFE' Project: the first 15K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits. PMID:21208403
Identification of genes required for neural-specific glycosylation using functional genomics. PMID:21203496
The genome of woodland strawberry (Fragaria vesca). PMID:21186353
RiceFOX: a database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function. PMID:21186176
Deep insights into Dictyocaulus viviparus transcriptomes provides unique prospects for new drug targets and disease intervention. PMID:21182926
The role of two f-box proteins, SLEEPY1 and SNEEZY, in Arabidopsis gibberellin signaling. PMID:21163960
Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. PMID:21149391
Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi. PMID:21148284
Refining orthologue groups at the transcript level. PMID:21143794
Nuclear receptor coactivators: structural and functional biochemistry. PMID:21141906
The arthrobacter arilaitensis Re117 genome sequence reveals its genetic adaptation to the surface of cheese. PMID:21124797
Identification and characterization of a bacterial glutamic peptidase. PMID:21122090
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
Unifying themes in microbial associations with animal and plant hosts described using the gene ontology. PMID:21119014
Two major archaeal pseudomurein endoisopeptidases: PeiW and PeiP. PMID:21113291
Evolution of the Kdo2-lipid A biosynthesis in bacteria. PMID:21106097
PCDB: a database of protein conformational diversity. PMID:21097895
ModBase, a database of annotated comparative protein structure models, and associated resources. PMID:21097780
Laminin database: a tool to retrieve high-throughput and curated data for studies on laminins. PMID:21087995
AgBase: supporting functional modeling in agricultural organisms. PMID:21075795
PRIDB: a Protein-RNA interface database. PMID:21071426
CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality. PMID:21071393
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
The mouse Gene Expression Database (GXD): 2011 update. PMID:21062809
SAHG, a comprehensive database of predicted structures of all human proteins. PMID:21051360
FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum. PMID:21051345
Ongoing and future developments at the Universal Protein Resource. PMID:21051339
PDBe: Protein Data Bank in Europe. PMID:21045060
Complete genome sequence of Bifidobacterium bifidum S17. PMID:21037011
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
Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon. PMID:20973991
Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita. PMID:20973953
Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. PMID:20973947
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. PMID:20972218
Phylogenetic, microbiological, and glycoside hydrolase diversities within the extremely thermophilic, plant biomass-degrading genus Caldicellulosiruptor. PMID:20971878
ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome. PMID:20955618
High-throughput sequencing and analysis of the gill tissue transcriptome from the deep-sea hydrothermal vent mussel Bathymodiolus azoricus. PMID:20937131
The Renal Gene Ontology Annotation Initiative. PMID:20885853
Insights into substrate specificity of geranylgeranyl reductases revealed by the structure of digeranylgeranylglycerophospholipid reductase, an essential enzyme in the biosynthesis of archaeal membrane lipids. PMID:20869368
Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential. PMID:20865041
GreenPhylDB v2.0: comparative and functional genomics in plants. PMID:20864446
Structure of a Burkholderia pseudomallei trimeric autotransporter adhesin head. PMID:20862217
The FLIGHT Drosophila RNAi database: 2010 update. PMID:20855970
Mutated genes, pathways and processes in tumours. PMID:20847737
Glycoside hydrolases as components of putative carbohydrate biosensor proteins in Clostridium thermocellum. PMID:20820855
A genomic glance at the components of the mRNA export machinery in Plasmodium falciparum. PMID:20798816
Expression of secreted Wnt pathway components reveals unexpected complexity of the planarian amputation response. PMID:20707997
Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences. PMID:20705649
RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae. PMID:20691054
Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept. PMID:20688752
A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing. PMID:20682560
Genomic architecture of MHC-linked odorant receptor gene repertoires among 16 vertebrate species. PMID:20680261
Identification of a hemerythrin-like domain in a P1B-type transport ATPase. PMID:20672819
A bird's-eye view of post-translational modifications in the spliceosome and their roles in spliceosome dynamics. PMID:20672149
Prediction of mucin-type O-glycosylation sites by a two-staged strategy. PMID:20652405
From complete genome sequence to 'complete' understanding? PMID:20647113
Microbial metalloproteomes are largely uncharacterized. PMID:20639861
A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes. PMID:20626840
Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity. PMID:20616063
Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research. PMID:20615486
The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. PMID:20609256
Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila. PMID:20601587
Genome-wide and molecular evolution analyses of the phospholipase D gene family in Poplar and Grape. PMID:20565843
Predicting genetic modifier loci using functional gene networks. PMID:20538624
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
A multilevel data integration resource for breast cancer study. PMID:20525248
Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition. PMID:20513238
Identification of a chemoreceptor for tricarboxylic acid cycle intermediates: differential chemotactic response towards receptor ligands. PMID:20498372
Massively parallel sequencing and analysis of the Necator americanus transcriptome. PMID:20485481
PhenoFam-gene set enrichment analysis through protein structural information. PMID:20478033
Characterization of the N-ATPase, a distinct, laterally transferred Na+-translocating form of the bacterial F-type membrane ATPase. PMID:20472544
Genome-wide in silico screen for CCCH-type zinc finger proteins of Trypanosoma brucei, Trypanosoma cruzi and Leishmania major. PMID:20444260
A new bioinformatics analysis tools framework at EMBL-EBI. PMID:20439314
Differences in transcription between free-living and CO2-activated third-stage larvae of Haemonchus contortus. PMID:20420710
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. PMID:20369061
LEAPdb: a database for the late embryogenesis abundant proteins. PMID:20359361
Genome-wide analysis of primary auxin-responsive Aux/IAA gene family in maize (Zea mays. L.). PMID:20232157
Genomics and bioinformatics resources for crop improvement. PMID:20208064
Genomic structure of an economically important cyanobacterium, Arthrospira (Spirulina) platensis NIES-39. PMID:20203057
Expansion of the miRNA pathway in the hemipteran insect Acyrthosiphon pisum. PMID:20179251
Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A. PMID:20170513
Transcriptomic changes arising during light-induced sporulation in Physarum polycephalum. PMID:20163733
A DNA damage-activated checkpoint kinase phosphorylates tau and enhances tau-induced neurodegeneration. PMID:20159774
MicroScope: a platform for microbial genome annotation and comparative genomics. PMID:20157493
Differential gene expression in the developing human macula: microarray analysis using rare tissue samples. PMID:20157359
Fast and efficient searching of biological data resources--using EB-eye. PMID:20150321
Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics. PMID:20144183
Genomics, evolution, and crystal structure of a new family of bacterial spore kinases. PMID:20077512
CORNET: a user-friendly tool for data mining and integration. PMID:20053712
Integrative approaches to the prediction of protein functions based on the feature selection. PMID:20043848
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. PMID:20043185
Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions. PMID:20042074
PLAZA: a comparative genomics resource to study gene and genome evolution in plants. PMID:20040540
The genome of the amoeba symbiont "Candidatus Amoebophilus asiaticus" reveals common mechanisms for host cell interaction among amoeba-associated bacteria. PMID:20023027
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. PMID:20015972
Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PMID:20011109
Comparative genomics and transduction potential of Enterococcus faecalis temperate bacteriophages. PMID:20008075
Glycogen synthase kinase 3beta interaction protein functions as an A-kinase anchoring protein. PMID:20007971
The biological coherence of human phenome databases. PMID:20004759
Functional diversity of ankyrin repeats in microbial proteins. PMID:19962898
The UCSC Genome Browser. PMID:19957273
Identification of the Schistosoma mansoni TNF-alpha receptor gene and the effect of human TNF-alpha on the parasite gene expression profile. PMID:19956564
TrichOME: a comparative omics database for plant trichomes. PMID:19939948
A galaxy of folds. PMID:19937658
The European Bioinformatics Institute's data resources. PMID:19934258
NBRP databases: databases of biological resources in Japan. PMID:19934255
H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. PMID:19933760
Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods. PMID:19930674
Calling International Rescue: knowledge lost in literature and data landslide! PMID:19929850
The Pfam protein families database. PMID:19920124
ELM: the status of the 2010 eukaryotic linear motif resource. PMID:19920119
MeMotif: a database of linear motifs in alpha-helical transmembrane proteins. PMID:19910368
SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters. PMID:19906725
The Proteomics Identifications database: 2010 update. PMID:19906717
PRGdb: a bioinformatics platform for plant resistance gene analysis. PMID:19906694
Gene3D: merging structure and function for a Thousand genomes. PMID:19906693
Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. PMID:19893621
CyanoBase: the cyanobacteria genome database update 2010. PMID:19880388
PROSITE, a protein domain database for functional characterization and annotation. PMID:19858104
PDBe: Protein Data Bank in Europe. PMID:19858099
SALAD database: a motif-based database of protein annotations for plant comparative genomics. PMID:19854933
The IntAct molecular interaction database in 2010. PMID:19850723
A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions. PMID:19844580
Significant speedup of database searches with HMMs by search space reduction with PSSM family models. PMID:19828575
Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells. PMID:19820112
Plant MetGenMAP: an integrative analysis system for plant systems biology. PMID:19819981
NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis. PMID:19818133
A granulin-like growth factor secreted by the carcinogenic liver fluke, Opisthorchis viverrini, promotes proliferation of host cells. PMID:19816559
Exploratory visual analysis of conserved domains on multiple sequence alignments. PMID:19811691
Amphioxus (Branchiostoma floridae) has orthologs of vertebrate odorant receptors. PMID:19804645
Francisella tularensis novicida proteomic and transcriptomic data integration and annotation based on semantic web technologies. PMID:19796400
SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology. PMID:19793867
Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5. PMID:19775431
Genome-wide Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules. PMID:19767456
Structural and functional constraints in the evolution of protein families. PMID:19756040
XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services. PMID:19732427
Legume transcription factor genes: what makes legumes so special? PMID:19726573
A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in a Planktothrix rubescens strain. PMID:19706155
A guide to the Proteomics Identifications Database proteomics data repository. PMID:19662629
Discovery: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria. PMID:19642978
The ankyrin repeat gene family in rice: genome-wide identification, classification and expression profiling. PMID:19609685
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
Crystal structure of the HEAT domain from the Pre-mRNA processing factor Symplekin. PMID:19576221
mGene: accurate SVM-based gene finding with an application to nematode genomes. PMID:19564452
Carboxylic ester hydrolases from hyperthermophiles. PMID:19544040
The first draft of the endostatin interaction network. PMID:19542224
The Mycoplasma conjunctivae genome sequencing, annotation and analysis. PMID:19534756
Visualising biological data: a semantic approach to tool and database integration. PMID:19534744
Web services at the European Bioinformatics Institute-2009. PMID:19435877
PPISearch: a web server for searching homologous protein-protein interactions across multiple species. PMID:19417070
ANNIE: integrated de novo protein sequence annotation. PMID:19389726
A census of human transcription factors: function, expression and evolution. PMID:19274049
Techniques for integrating -omics data. PMID:19255651 -
InterPro in 2017-beyond protein family and domain annotations
PubMed citations: 636.
636 articles citing: InterPro in 2017-beyond protein family and domain annotations
In silico identification of the rare-coding pathogenic mutations and structural modeling of human NNAT gene associated with anorexia nervosa. PMID:35655118
Genome-wide identification and characterization of mungbean CIRCADIAN CLOCK ASSOCIATED 1 like genes reveals an important role of VrCCA1L26 in flowering time regulation. PMID:35581536
Machine Learning and Its Applications for Protozoal Pathogens and Protozoal Infectious Diseases. PMID:35573796
Antifungal Effect of Copper Nanoparticles against Fusarium kuroshium, an Obligate Symbiont of Euwallacea kuroshio Ambrosia Beetle. PMID:35448578
Genome Sequence of Streptomyces sp. Strain GQFP Isolated from Soil Near the Roots of Pharmaceutical Plant Elaeagnus pungens. PMID:35377185
Effect of chronic and acute enterotoxigenic E. coli challenge on growth performance, intestinal inflammation, microbiome, and metabolome of weaned piglets. PMID:35323827
Hyperosmolality in CHO cell culture: effects on the proteome. PMID:35312825
Chromosomal-Level Genome Assembly of the Springtail Tomocerus qinae (Collembola: Tomoceridae). PMID:35298623
Conservation and Divergence of SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Family between Wheat and Rice. PMID:35216210
Novel protein from larval sponge cells, ilborin, is related to energy turnover and calcium binding and is conserved among marine invertebrates. PMID:35193395
Zebrafish information network, the knowledgebase for Danio rerio research. PMID:35166825
Chromosome-Level Genome Assembly of Anthidium xuezhongi Niu & Zhu, 2020 (Hymenoptera: Apoidea: Megachilidae: Anthidiini). PMID:35150256
A Chromosome-Level Genome Assembly of the Parasitic Wasp Chelonus formosanus Sonan 1932 (Hymenoptera: Braconidae). PMID:35104339
Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information. PMID:35062881
Quantitative Insights into the Contribution of Nematocysts to the Adaptive Success of Cnidarians Based on Proteomic Analysis. PMID:35053089
Deciphering the evolution of composite-type GSKIP in mitochondria and Wnt signaling pathways. PMID:35051222
STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families. PMID:34991452
Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PMID:34986141
In Tuber Biocontrol of Potato Late Blight by a Collection of Phenazine-1-Carboxylic Acid-Producing Pseudomonas spp. PMID:34946127
Characterization of the MYB Genes Reveals Insights Into Their Evolutionary Conservation, Structural Diversity, and Functional Roles in Magnaporthe oryzae. PMID:34899620
Building a reference transcriptome for Juniperus squamata (Cupressaceae) based on single-molecule real-time sequencing. PMID:34865616
In Leishmania major, the Homolog of the Oncogene PES1 May Play a Critical Role in Parasite Infectivity. PMID:34830469
Bioinformatic Analysis of Lytic Polysaccharide Monooxygenases Reveals the Pan-Families Occurrence of Intrinsically Disordered C-Terminal Extensions. PMID:34827630
Transcriptome profiling based on Illumina- and SMRT-based RNA-seq reveals circadian regulation of key pathways in flower bud development in walnut. PMID:34793486
A Histone Deacetylase, Magnaporthe oryzae RPD3, Regulates Reproduction and Pathogenic Development in the Rice Blast Fungus. PMID:34781734
Gene4HL: An Integrated Genetic Database for Hearing Loss. PMID:34733322
Evidence for Lignocellulose-Decomposing Enzymes in the Genome and Transcriptome of the Aquatic Hyphomycete Clavariopsis aquatica. PMID:34682274
Global Transcriptome Characterization and Assembly of the Thermophilic Ascomycete Chaetomium thermophilum. PMID:34680944
Chromosome-Level Genome Assembly of Nephotettix cincticeps (Uhler, 1896) (Hemiptera: Cicadellidae: Deltocephalinae). PMID:34677607
RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family. PMID:34669691
Mitochondrial phosphate transporter and methyltransferase genes contribute to Fusarium head blight Type II disease resistance and grain development in wheat. PMID:34648604
Resveratrol enhanced mitochondrial recovery from cryopreservation-induced damages in oocytes and embryos. PMID:34646069
Genome assembly of the popular Korean soybean cultivar Hwangkeum. PMID:34568925
De novo missense variants in FBXO11 alter its protein expression and subcellular localization. PMID:34505148
Proteorhodopsin Phototrophy in Antarctic Coastal Waters. PMID:34406852
Identification of Potential Kinase Inhibitors within the PI3K/AKT Pathway of Leishmania Species. PMID:34356660
Lytic archaeal viruses infect abundant primary producers in Earth's crust. PMID:34330907
Genetic mapping of renal glutathione suggests a novel regulatory locus on the murine X chromosome and overlap with hepatic glutathione regulation. PMID:34324982
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 mapping coupled with CRISPR gene editing reveals a P450 gene confers avermectin resistance in the beet armyworm. PMID:34252082
The report of anthocyanins in the betalain-pigmented genus Hylocereus is not well evidenced and is not a strong basis to refute the mutual exclusion paradigm. PMID:34187352
Completeness and Consistency in Structural Domain Classifications. PMID:34179613
Transcriptomic analysis of shell repair and biomineralization in the blue mussel, Mytilus edulis. PMID:34112105
Evolution of networks of protein domain organization. PMID:34103558
Uncovering biosynthetic relationships between antifungal nonadrides and octadrides. PMID:34094403
Composition and function of the C1b/C1f region in the ciliary central apparatus. PMID:34083607
Distribution and Classification of Dehydrins in Selected Plant Species Using Bioinformatics Approach. PMID:34056027
High-Quality Reference Genome Sequence for the Oomycete Vegetable Pathogen Phytophthora capsici Strain LT1534. PMID:34042486
A Chromosome-Level Genome Assembly of Ephestia elutella (Hübner, 1796) (Lepidoptera: Pyralidae). PMID:34014321
A Bivalve Biomineralization Toolbox. PMID:34014311
DEFECTIVE EMBRYO AND MERISTEMS genes are required for cell division and gamete viability in Arabidopsis. PMID:33999950
Gene4PD: A Comprehensive Genetic Database of Parkinson's Disease. PMID:33981200
Comparative Genomics and Transcriptomics of the Extreme Halophyte Puccinellia tenuiflora Provides Insights Into Salinity Tolerance Differentiation Between Halophytes and Glycophytes. PMID:33968105
The genomic basis of evolutionary differentiation among honey bees. PMID:33947700
Fic and non-Fic AMPylases: protein AMPylation in metazoans. PMID:33947243
De novo Sequencing of Novel Mycoviruses From Fusarium sambucinum: An Attempt on Direct RNA Sequencing of Viral dsRNAs. PMID:33927702
Proteomic Charting of Imipenem Adaptive Responses in a Highly Carbapenem Resistant Clinical Enterobacter roggenkampii Isolate. PMID:33924830
A pseudomolecule assembly of the Rocky Mountain elk genome. PMID:33909645
Genome sequence, transcriptome, and annotation of rodent malaria parasite Plasmodium yoelii nigeriensis N67. PMID:33902452
Characterization of Glycoside Hydrolase Families 13 and 31 Reveals Expansion and Diversification of α-Amylase Genes in the Phlebotomine Lutzomyia longipalpis and Modulation of Sandfly Glycosidase Activities by Leishmania Infection. PMID:33897451
GPCards: An integrated database of genotype-phenotype correlations in human genetic diseases. PMID:33868597
Origin and evolution of nonulosonic acid synthases and their relationship with bacterial pathogenicity revealed by a large-scale phylogenetic analysis. PMID:33848237
ActiveDriverDB: Interpreting Genetic Variation in Human and Cancer Genomes Using Post-translational Modification Sites and Signaling Networks (2021 Update). PMID:33834021
Comparative genome analyses of four rice-infecting Rhizoctonia solani isolates reveal extensive enrichment of homogalacturonan modification genes. PMID:33827423
In Silico Analysis of Huntingtin Homologs in Lower Eukaryotes. PMID:33809947
Cyanide Hydratase Modification Using Computational Design and Docking Analysis for Improved Binding Affinity in Cyanide Detoxification. PMID:33806828
Evolution of Matrix Gla and Bone Gla Protein Genes in Jawed Vertebrates. PMID:33790944
LmjF.36.3850, a novel hypothetical Leishmania major protein, contributes to the infection. PMID:33764520
Recent loss of the Dim2 DNA methyltransferase decreases mutation rate in repeats and changes evolutionary trajectory in a fungal pathogen. PMID:33750960
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 Roles of the LIM Domain Proteins in Drosophila Cardiac and Hematopoietic Morphogenesis. PMID:33681304
The pyruvate:ferredoxin oxidoreductase of the thermophilic acetogen, Thermoanaerobacter kivui. PMID:33660937
HoSeIn: A Workflow for Integrating Various Homology Search Results from Metagenomic and Metatranscriptomic Sequence Datasets. PMID:33659350
Evolution, structure and emerging roles of C1ORF112 in DNA replication, DNA damage responses, and cancer. PMID:33625522
Characterization of Mungbean CONSTANS-LIKE Genes and Functional Analysis of CONSTANS-LIKE 2 in the Regulation of Flowering Time in Arabidopsis. PMID:33613600
Spatially Resolved Tagging of Proteolytic Neo-N termini with Subtiligase-TM. PMID:33599828
Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis. PMID:33574331
Near-Chromosome-Level Genome Assembly of the Dark Septate Endophyte Laburnicola rhizohalophila: A Model for Investigating Root-Fungus Symbiosis. PMID:33570561
A Novel Trichomonas vaginalis Surface Protein Modulates Parasite Attachment via Protein:Host Cell Proteoglycan Interaction. PMID:33563826
Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut. PMID:33563787
Characterization of prostanoid pathway and the control of its activity by the eyestalk optic ganglion in the female giant freshwater prawn, Macrobrachium rosenbergii. PMID:33553720
Sialotranscriptomics of the argasid tick Ornithodoros moubata along the trophogonic cycle. PMID:33544727
The in-silico characterization of the Caenorhabditis elegans matrisome and proposal of a novel collagen classification. PMID:33543001
Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential. PMID:33541265
A Highly Contiguous Genome Assembly of a Polyphagous Predatory Mite Stratiolaelaps scimitus (Womersley) (Acari: Laelapidae). PMID:33528489
Molecular and Structural Characterizations of Lipases from Chlorella by Functional Genomics. PMID:33525674
SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences. PMID:33507271
A Draft Genome Assembly of Culex pipiens pallens (Diptera: Culicidae) Using PacBio Sequencing. PMID:33501937
The hard clam genome reveals massive expansion and diversification of inhibitors of apoptosis in Bivalvia. PMID:33487168
Integrative multiomics analysis of Premolis semirufa caterpillar venom in the search for molecules leading to a joint disease. PMID:33479267
Large-scale survey and database of high affinity ligands for peptide recognition modules. PMID:33438817
Visualizing the superfamily of metallo-β-lactamases through sequence similarity network neighborhood connectivity analysis. PMID:33426353
A multi-omic screening approach for the discovery of thermoactive glycoside hydrolases. PMID:33416984
Functional Prediction and Assignment of Methanobrevibacter ruminantium M1 Operome Using a Combined Bioinformatics Approach. PMID:33391347
COPD-associated miR-145-5p is downregulated in early-decline FEV1 trajectories in childhood asthma. PMID:33385444
Non-adaptive Evolution of Trimeric Autotransporters in Brucellaceae. PMID:33281759
Differences in the antibody response to adult Fasciola hepatica excretory/secretory products in experimentally and naturally infected cattle and sheep. PMID:33276290
Magnesium efflux from Drosophila Kenyon cells is critical for normal and diet-enhanced long-term memory. PMID:33242000
In silico modelling and characterization of eight blast resistance proteins in resistant and susceptible rice cultivars. PMID:33237489
Phosphoglycerate kinase: structural aspects and functions, with special emphasis on the enzyme from Kinetoplastea. PMID:33234025
Engineering the Yeast Yarrowia lipolytica for Production of Polylactic Acid Homopolymer. PMID:33195110
The Cyclically Seasonal Drosophila subobscura Inversion O7 Originated From Fragile Genomic Sites and Relocated Immunity and Metabolic Genes. PMID:33193649
A genome-wide screening for RNAi pathway proteins in Acari. PMID:33183236
Genomic Characterisation of Mushroom Pathogenic Pseudomonads and Their Interaction with Bacteriophages. PMID:33182769
The InterPro protein families and domains database: 20 years on. PMID:33156333
Two Distinct Modes of Lysis Regulation in Campylobacter Fletchervirus and Firehammervirus Phages. PMID:33142851
Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L. PMID:33142722
Identification and Characterization of New Bacteriophages to Control Multidrug-Resistant Pseudomonas aeruginosa Biofilm on Endotracheal Tubes. PMID:33123112
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
Methylome and transcriptome profiles in three yak tissues revealed that DNA methylation and the transcription factor ZGPAT co-regulate milk production. PMID:33081725
Chlorella vulgaris and Its Phycosphere in Wastewater: Microalgae-Bacteria Interactions During Nutrient Removal. PMID:33072721
Novel Synergistic Mechanism for Lignocellulose Degradation by a Thermophilic Filamentous Fungus and a Thermophilic Actinobacterium Based on Functional Proteomics. PMID:33042052
Knockout of the gene encoding the extracellular matrix protein SNED1 results in early neonatal lethality and craniofacial malformations. PMID:33012048
Visual mate preference evolution during butterfly speciation is linked to neural processing genes. PMID:32958765
Human SIRT1 Multispecificity Is Modulated by Active-Site Vicinity Substitutions during Natural Evolution. PMID:32956445
Isolation and characterisation of Leishmania donovani protein antigens from urine of visceral leishmaniasis patients. PMID:32925980
Chlamydial contribution to anaerobic metabolism during eukaryotic evolution. PMID:32923644
Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate. PMID:32920602
Exploring Protein Space: From Hydrolase to Ligase by Substitution. PMID:32870983
Genome-wide identification and analysis of GRAS transcription factors in the bottle gourd genome. PMID:32868844
A high-quality sponge gourd (Luffa cylindrica) genome. PMID:32821411
Metalloproteins and apolipoprotein C: candidate plasma biomarkers of T2DM screened by comparative proteomics and lipidomics in ZDF rats. PMID:32817751
The Neighboring Subunit Is Engaged to Stabilize the Substrate in the Active Site of Plant Arginases. PMID:32754173
Characterization and Function Analysis of the Beta-Carotene Oxygenase-like Genes in Carotenoids Metabolism of the Ridgetail White Prawn Exopalaemon carinicauda. PMID:32733270
Integrated Analyses of lncRNA and mRNA Profiles Reveal Characteristic and Functional Changes of Leukocytes in Qi-Deficiency Constitution and Pi-Qi-Deficiency Syndrome of Chronic Superficial Gastritis. PMID:32724329
Amino acid sequence associated with bacteriophage recombination site helps to reveal genes potentially acquired through horizontal gene transfer. PMID:32703190
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. PMID:32652120
Challenges and advances in genome mining of ribosomally synthesized and post-translationally modified peptides (RiPPs). PMID:32637669
A First Insight into North American Plant Pathogenic Fungi Armillaria Sinapina Transcriptome. PMID:32635577
Dark Proteome Database: Studies on Disorder. PMID:32629790
Isolation, identification, and whole genome sequence analysis of the alginate-degrading bacterium Cobetia sp. cqz5-12. PMID:32616809
A ferredoxin-dependent dihydropyrimidine dehydrogenase in Clostridium chromiireducens. PMID:32614053
How Crucial is the Functional Pit Organ for the Varroa Mite? PMID:32604887
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
A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology. PMID:32547856
Essential roles for deubiquitination in Leishmania life cycle progression. PMID:32544189
PvP01-DB: computational structural and functional characterization of soluble proteome of PvP01 strain of Plasmodium vivax. PMID:32542363
In silico vaccine design against Chlamydia trachomatis infection. PMID:32537381
In silico analysis on the functional and structural impact of Rad50 mutations involved in DNA strand break repair. PMID:32509463
Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms. PMID:32482169
Questing functions and structures of hypothetical proteins from Campylobacter jejuni: a computer-aided approach. PMID:32458979
Ontogeny of Expression and Activity of Digestive Enzymes and Establishment of gh/igf1 Axis in the Omnivorous Fish Chelon labrosus. PMID:32443440
A Reference Genome of Bursaphelenchus mucronatus Provides New Resources for Revealing Its Displacement by Pinewood Nematode. PMID:32438771
Prochlorococcus phage ferredoxin: structural characterization and electron transfer to cyanobacterial sulfite reductases. PMID:32434930
New perspectives on butyrate assimilation in Rhodospirillum rubrum S1H under photoheterotrophic conditions. PMID:32434546
PLANT NATRIURETIC PEPTIDE A and Its Putative Receptor PNP-R2 Antagonize Salicylic Acid-Mediated Signaling and Cell Death. PMID:32409317
The First Draft Genome of the Plasterer Bee Colletes gigas (Hymenoptera: Colletidae: Colletes). PMID:32386319
Chromosome-scale assembly of the Kandelia obovata genome. PMID:32377365
Genome sequencing and comparison of five Tilletia species to identify candidate genes for the detection of regulated species infecting wheat. PMID:32355611
Genetic Underpinnings of Host Manipulation by Ophiocordyceps as Revealed by Comparative Transcriptomics. PMID:32354705
Sensor Histidine Kinase NarQ Activates via Helical Rotation, Diagonal Scissoring, and Eventually Piston-Like Shifts. PMID:32354084
Actinobacterial Degradation of 2-Hydroxyisobutyric Acid Proceeds via Acetone and Formyl-CoA by Employing a Thiamine-Dependent Lyase Reaction. PMID:32351493
A soil bacterial catabolic pathway on the move: Transfer of nicotine catabolic genes between Arthrobacter genus megaplasmids and invasion by mobile elements. PMID:32345784
Offspring reverse transcriptome responses to maternal deprivation when reared with pathogens in an insect with facultative family life. PMID:32345162
Identification and Immobilization of an Invertase With High Specific Activity and Sucrose Tolerance Ability of Gongronella sp. w5 for High Fructose Syrup Preparation. PMID:32328053
Genome-wide analysis of CCHC-type zinc finger (ZCCHC) proteins in yeast, Arabidopsis, and humans. PMID:32303790
A Comparison of Co-expression Networks in Silk Gland Reveals the Causes of Silk Yield Increase During Silkworm Domestication. PMID:32292415
Chondroitin sulfate proteoglycan 4 regulates zebrafish body axis organization via Wnt/planar cell polarity pathway. PMID:32240230
Portal of Juglandaceae: A comprehensive platform for Juglandaceae study. PMID:32194971
A roadmap for research in octoploid strawberry. PMID:32194969
LEAP: Using machine learning to support variant classification in a clinical setting. PMID:32176384
A pair of esterases from a commensal gut bacterium remove acetylations from all positions on complex β-mannans. PMID:32170022
Comparison of transcriptomes from two chemosensory organs in four decapod crustaceans reveals hundreds of candidate chemoreceptor proteins. PMID:32163507
Gender differences in diet-induced steatotic disease in Cyp2b-null mice. PMID:32155178
Functional switching of NPR1 between chloroplast and nucleus for adaptive response to salt stress. PMID:32152424
Stem rust resistance in wheat is suppressed by a subunit of the mediator complex. PMID:32111840
A comparative genomics study of 23 Aspergillus species from section Flavi. PMID:32107379
Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers. PMID:32095484
First Draft Genome of the Sable, Martes zibellina. PMID:32058545
S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula. PMID:32057875
Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild. PMID:32055408
Probing Carbon Utilization of Cordyceps militaris by Sugar Transportome and Protein Structural Analysis. PMID:32050592
Comparative transcriptome profiling of selected osmotic regulatory proteins in the gill during seawater acclimation of chum salmon (Oncorhynchus keta) fry. PMID:32029805
Pathway and network analysis of more than 2500 whole cancer genomes. PMID:32024854
A Mapped Locus on LG A6 of Brassica juncea Line Tumida Conferring Resistance to White Rust Contains a CNL Type R Gene. PMID:31998351
The Identification and Conservation of Tunicaminyluracil-Related Biosynthetic Gene Clusters in Several Rathayibacter Species Collected From Australia, Africa, Eurasia, and North America. PMID:31998251
Discovery of two novel and adjacent QTLs on chromosome B02 controlling resistance against bacterial wilt in peanut variety Zhonghua 6. PMID:31980836
High-quality genome sequence of white lupin provides insight into soil exploration and seed quality. PMID:31980615
A Pathway for Degradation of Uracil to Acetyl Coenzyme A in Bacillus megaterium. PMID:31953335
The N-terminal domains of the paralogous HycE and NuoCD govern assembly of the respective formate hydrogenlyase and NADH dehydrogenase complexes. PMID:31925988
The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns. PMID:31915577
Symbiont population control by host-symbiont metabolic interaction in Symbiodiniaceae-cnidarian associations. PMID:31913264
Identification and characterization of genes frequently responsive to Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae infections in rice. PMID:31906847
Gingimaps: Protein Localization in the Oral Pathogen Porphyromonas gingivalis. PMID:31896547
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
Pingu virus: A new picornavirus in penguins from Antarctica. PMID:31850147
Global Screening of Genomic and Transcriptomic Factors Associated with Phenotype Differences between Multidrug-Resistant and -Susceptible Candida haemulonii Strains. PMID:31848301
Host-Microbe Interactions in the Chemosynthetic Riftia pachyptila Symbiosis. PMID:31848270
The CC' loop of IgV domains of the immune checkpoint receptors, plays a key role in receptor:ligand affinity modulation. PMID:31844079
New Insight into HPts as Hubs in Poplar Cytokinin and Osmosensing Multistep Phosphorelays: Cytokinin Pathway Uses Specific HPts. PMID:31835814
Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei. PMID:31799430
Overexpression of OsPUB41, a Rice E3 ubiquitin ligase induced by cell wall degrading enzymes, enhances immune responses in Rice and Arabidopsis. PMID:31783788
Evolution-guided engineering of small-molecule biosensors. PMID:31777933
Genome sequence of the model rice variety KitaakeX. PMID:31775618
Myofibril diameter is set by a finely tuned mechanism of protein oligomerization in Drosophila. PMID:31746737
Gene Regulation Shifts Shed Light on Fungal Adaption in Plant Biomass Decomposers. PMID:31744914
Rapid microevolution of biofilm cells in response to antibiotics. PMID:31728201
PCOSBase: a manually curated database of polycystic ovarian syndrome. PMID:31725861
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
The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae). PMID:31702783
Extracellular production of the engineered thermostable protease pernisine from Aeropyrum pernix K1 in Streptomyces rimosus. PMID:31699090
Structural characterization of the RH1-LZI tandem of JIP3/4 highlights RH1 domains as a cytoskeletal motor-binding motif. PMID:31690808
Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes. PMID:31665645
Characterization of Three Novel Viruses from the Families Nyamiviridae, Orthomyxoviridae, and Peribunyaviridae, Isolated from Dead Birds Collected during West Nile Virus Surveillance in Harris County, Texas. PMID:31658646
The use of PanDrugs to prioritize anticancer drug treatments in a case of T-ALL based on individual genomic data. PMID:31655559
Gene4Denovo: an integrated database and analytic platform for de novo mutations in humans. PMID:31642496
Comprehensive Analysis Reveals the Evolution and Pathogenicity of Aeromonas, Viewed from Both Single Isolated Species and Microbial Communities. PMID:31641046
Extensive Tandem Duplication Events Drive the Expansion of the C1q-Domain-Containing Gene Family in Bivalves. PMID:31615007
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. PMID:31614509
Complete Genome Sequence of an Enterohemorrhagic Escherichia coli O111:H8 Strain Recovered from a Large Outbreak in Japan Associated with Consumption of Raw Beef. PMID:31582455
Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known. PMID:31565552
Cross-Kingdom Analysis of Diversity, Evolutionary History, and Site Selection within the Eukaryotic Macrophage Migration Inhibitory Factor Superfamily. PMID:31554205
Sulfate Ester Detergent Degradation in Pseudomonas aeruginosa Is Subject to both Positive and Negative Regulation. PMID:31540990
The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe. PMID:31540274
Machine learning-based chemical binding similarity using evolutionary relationships of target genes. PMID:31504818
Structural and functional insight into the Mycobacterium tuberculosis protein PrpR reveals a novel type of transcription factor. PMID:31504787
Utilizing Whole Fusobacterium Genomes To Identify, Correct, and Characterize Potential Virulence Protein Families. PMID:31501282
Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome. PMID:31494266
SamPler - a novel method for selecting parameters for gene functional annotation routines. PMID:31488049
Computer aided analysis of disease linked protein networks. PMID:31485137
Whole genome sequencing and identification of host-interactive genes in the rice endophytic Leifsonia sp. ku-ls. PMID:31482368
An electrostatic switching mechanism to control the lipid transfer activity of Osh6p. PMID:31477717
Interaction of the Ankyrin H Core Effector of Legionella with the Host LARP7 Component of the 7SK snRNP Complex. PMID:31455655
Resources to Discover and Use Short Linear Motifs in Viral Proteins. PMID:31427097
Role of a patatin-like phospholipase in Plasmodium falciparum gametogenesis and malaria transmission. PMID:31413195
UNIPred-Web: a web tool for the integration and visualization of biomolecular networks for protein function prediction. PMID:31412768
The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion. PMID:31387118
Expression of calcification-related ion transporters during blue mussel larval development. PMID:31380040
Genome-wide exploration and characterization of miR172/euAP2 genes in Brassica napus L. for likely role in flower organ development. PMID:31370790
Differential homotypic and heterotypic interactions of antigen 43 (Ag43) variants in autotransporter-mediated bacterial autoaggregation. PMID:31367003
A MYST family histone acetyltransferase, MoSAS3, is required for development and pathogenicity in the rice blast fungus. PMID:31364260
Identification, characterization and benefits of an exclusion system in an integrative and conjugative element of Bacillus subtilis. PMID:31361051
Genetic mapping in Diversity Outbred mice identifies a Trpa1 variant influencing late-phase formalin response. PMID:31335644
Adhesive Interactions Between Lactic Acid Bacteria and β-Lactoglobulin: Specificity and Impact on Bacterial Location in Whey Protein Isolate. PMID:31333617
Combined alignments of sequences and domains characterize unknown proteins with remotely related protein search PSISearch2D. PMID:31317184
Proteogenomic Analysis of Protein Sequence Alterations in Breast Cancer Cells. PMID:31316139
Mechanism of catalysis and inhibition of Mycobacterium tuberculosis SapM, implications for the development of novel antivirulence drugs. PMID:31312014
A high-quality genome of Eragrostis curvula grass provides insights into Poaceae evolution and supports new strategies to enhance forage quality. PMID:31308395
ParaDB: A manually curated database containing genomic annotation for the human pathogenic fungi Paracoccidioides spp. PMID:31306428
The LsVe1L allele provides a molecular marker for resistance to Verticillium dahliae race 1 in lettuce. PMID:31291883
Identification of a crucial amino acid implicated in the hydroxylation/desaturation ratio of CpFAH12 bifunctional hydroxylase. PMID:31282998
Genome-wide functional association networks: background, data & state-of-the-art resources. PMID:31281921
A new flavor of entry exclusion in ICE elements provides a selective advantage for the element and its host. PMID:31278791
Diversity of tryptophan halogenases in sponges of the genus Aplysina. PMID:31276591
Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass. PMID:31276273
Skeletal Mineralization in Association with Type X Collagen Expression Is an Ancestral Feature for Jawed Vertebrates. PMID:31270539
Dual pathways of tRNA hydroxylation ensure efficient translation by expanding decoding capability. PMID:31253794
The PSIPRED Protein Analysis Workbench: 20 years on. PMID:31251384
Analysis of RNA Methylation by Phylogenetically Diverse Cfr Radical S-Adenosylmethionine Enzymes Reveals an Iron-Binding Accessory Domain in a Clostridial Enzyme. PMID:31246421
Many rice genes are differentially spliced between roots and shoots but cytokinin has minimal effect on splicing. PMID:31245776
Waterlogging affects plant morphology and the expression of key genes in tef (Eragrostis tef). PMID:31245721
Maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER). PMID:31245718
Advances and Applications in the Quest for Orthologs. PMID:31241141
RedoxiBase: A database for ROS homeostasis regulated proteins. PMID:31228650
Functional Metagenomics Reveals a New Catalytic Domain, the Metallo-β-Lactamase Superfamily Domain, Associated with Phytase Activity. PMID:31217298
FusionPro, a Versatile Proteogenomic Tool for Identification of Novel Fusion Transcripts and Their Potential Translation Products in Cancer Cells. PMID:31208993
Borrelia burgdorferi chemotaxis toward tick protein Salp12 contributes to acquisition. PMID:31204044
Cyp2b-null male mice are susceptible to diet-induced obesity and perturbations in lipid homeostasis. PMID:31202118
Evolution and comparative genomics of the most common Trichoderma species. PMID:31189469
Dicyemida and Orthonectida: Two Stories of Body Plan Simplification. PMID:31178892
Genome-Wide Identification and Expression Profiles of Myosin Genes in the Pacific White Shrimp, Litopenaeus vannamei. PMID:31178751
Plasmodium pseudo-Tyrosine Kinase-like binds PP1 and SERA5 and is exported to host erythrocytes. PMID:31148576
Recent advances in understanding the replication initiator protein of the ssDNA plant viruses of the family Nanoviridae. PMID:31143829
Back to the Salt Mines: Genome and Transcriptome Comparisons of the Halophilic Fungus Aspergillus salisburgensis and Its Halotolerant Relative Aspergillus sclerotialis. PMID:31137536
Transcriptome Profile Analysis Reveals that CsTCP14 Induces Susceptibility to Foliage Diseases in Cucumber. PMID:31130701
A Pathway for Isethionate Dissimilation in Bacillus krulwichiae. PMID:31126948
Network Integrative Genomic and Transcriptomic Analysis of Carbapenem-Resistant Klebsiella pneumoniae Strains Identifies Genes for Antibiotic Resistance and Virulence. PMID:31117026
MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains. PMID:31116477
A haplotype-resolved draft genome of the European sardine (Sardina pilchardus). PMID:31112613
The ion channel ppk301 controls freshwater egg-laying in the mosquito Aedes aegypti. PMID:31112133
Consensus sequence design as a general strategy to create hyperstable, biologically active proteins. PMID:31110018
Potential KPC-2 carbapenemase reservoir of environmental Aeromonas hydrophila and Aeromonas caviae isolates from the effluent of an urban wastewater treatment plant in Japan. PMID:31106978
Genome-Wide Identification, Comprehensive Gene Feature, Evolution, and Expression Analysis of Plant Metal Tolerance Proteins in Tobacco Under Heavy Metal Toxicity. PMID:31105736
Resistance Gene-Directed Genome Mining of 50 Aspergillus Species. PMID:31098395
The most abundant cyst wall proteins of Acanthamoeba castellanii are lectins that bind cellulose and localize to distinct structures in developing and mature cyst walls. PMID:31095564
A Novel Cadherin-like Protein Mediates Adherence to and Killing of Host Cells by the Parasite Trichomonas vaginalis. PMID:31088924
Next-generation sequencing identified genomic region and diagnostic markers for resistance to bacterial wilt on chromosome B02 in peanut (Arachis hypogaea L.). PMID:31087470
Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies. PMID:31060495
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
Genomic Characterization of Arcobacter butzleri Isolated From Shellfish: Novel Insight Into Antibiotic Resistance and Virulence Determinants. PMID:31057492
BCL6 corepressor contributes to Th17 cell formation by inhibiting Th17 fate suppressors. PMID:31053612
BjuWRR1, a CC-NB-LRR gene identified in Brassica juncea, confers resistance to white rust caused by Albugo candida. PMID:31049632
Classification of barley U-box E3 ligases and their expression patterns in response to drought and pathogen stresses. PMID:31035917
Marek's Disease Virus Regulates the Ubiquitylome of Chicken CD4+ T Cells to Promote Tumorigenesis. PMID:31035338
TASmania: A bacterial Toxin-Antitoxin Systems database. PMID:31022176
HECT E3 Ligases: A Tale With Multiple Facets. PMID:31001145
Revealing the dominant long noncoding RNAs responding to the infection with Colletotrichum gloeosporioides in Hevea brasiliensis. PMID:30987641
Structural Study of Agmatine Iminohydrolase From Medicago truncatula, the Second Enzyme of the Agmatine Route of Putrescine Biosynthesis in Plants. PMID:30984210
Ant behaviour and brain gene expression of defending hosts depend on the ecological success of the intruding social parasite. PMID:30967075
Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction. PMID:30963849
Apple whole genome sequences: recent advances and new prospects. PMID:30962944
Prunus genetics and applications after de novo genome sequencing: achievements and prospects. PMID:30962943
Comprehensive proteomic analysis of exoproteins expressed by ERIC I, II, III and IV Paenibacillus larvae genotypes reveals a wide range of virulence factors. PMID:30957692
Discovery of novel astrovirus and calicivirus identified in ruddy turnstones in Brazil. PMID:30944402
Genomic insights into HSFs as candidate genes for high-temperature stress adaptation and gene editing with minimal off-target effects in flax. PMID:30944362
Whole genome sequencing of canids reveals genomic regions under selection and variants influencing morphology. PMID:30940804
Hidden in plain sight: what remains to be discovered in the eukaryotic proteome? PMID:30938578
Monitoring structural modulation of redox-sensitive proteins in cells with MS-CETSA. PMID:30925293
Induction of the immunoprotective coat of Yersinia pestis at body temperature is mediated by the Caf1R transcription factor. PMID:30922226
A Novel Hepacivirus in Wild Rodents from South America. PMID:30909631
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
Sensitivity to the two peptide bacteriocin plantaricin EF is dependent on CorC, a membrane-bound, magnesium/cobalt efflux protein. PMID:30891921
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
Galactitol catabolism in Sinorhizobium meliloti is dependent on a chromosomally encoded sorbitol dehydrogenase and a pSymB-encoded operon necessary for tagatose catabolism. PMID:30879203
Endoplasmic reticulum-localized UBC34 interaction with lignin repressors MYB221 and MYB156 regulates the transactivity of the transcription factors in Populus tomentosa. PMID:30866808
Comparative genomics of plant pathogenic Botrytis species with distinct host specificity. PMID:30866801
TCR Affinity Biases Th Cell Differentiation by Regulating CD25, Eef1e1, and Gbp2. PMID:30858199
Identification of Novel Interaction Partners of Ets-1: Focus on DNA Repair. PMID:30857266
Energy conservation by a hydrogenase-dependent chemiosmotic mechanism in an ancient metabolic pathway. PMID:30850546
Metagenomic Analysis Reveals Three Novel and Prevalent Mosquito Viruses from a Single Pool of Aedes vexans nipponii Collected in the Republic of Korea. PMID:30841520
Cysteinyl-tRNA Synthetase Mutations Cause a Multi-System, Recessive Disease That Includes Microcephaly, Developmental Delay, and Brittle Hair and Nails. PMID:30824121
Map of physical interactions between extracellular domains of Arabidopsis leucine-rich repeat receptor kinases. PMID:30806640
PIRSitePredict for protein functional site prediction using position-specific rules. PMID:30805646
Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0). PMID:30804569
An NAD+ Phosphorylase Toxin Triggers Mycobacterium tuberculosis Cell Death. PMID:30792174
A mechanism for temporary bioadhesion. PMID:30782790
Genus-Wide Comparative Genomics Analysis of Neisseria to Identify New Genes Associated with Pathogenicity and Niche Adaptation of Neisseria Pathogens. PMID:30775379
A polyextremophilic alcohol dehydrogenase from the Atlantis II Deep Red Sea brine pool. PMID:30761247
A Recurrent Motif: Diversity and Evolution of ShKT Domain Containing Proteins in the Vampire Snail Cumia reticulata. PMID:30759797
Enhanced Growth of Pilin-Deficient Geobacter sulfurreducens Mutants in Carbon Poor and Electron Donor Limiting Conditions. PMID:30759269
Convergent perturbation of the human domain-resolved interactome by viruses and mutations inducing similar disease phenotypes. PMID:30759076
Hereditary xanthinuria in a goat. PMID:30758870
The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. PMID:30732586
First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.). PMID:30727959
Protein analysis reveals differential accumulation of late embryogenesis abundant and storage proteins in seeds of wild and cultivated amaranth species. PMID:30727945
The sequence and de novo assembly of Oxygymnocypris stewartii genome. PMID:30720802
Ulcerative colitis: functional analysis of the in-depth proteome. PMID:30718987
Cobaviruses - a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems. PMID:30718806
Cu Transport by the Extended Family of CcoA-like Transporters (CalT) in Proteobacteria. PMID:30718766
Decoding Calcium Signaling Dynamics during Drosophila Wing Disc Development. PMID:30704858
ACTN2 mutations cause "Multiple structured Core Disease" (MsCD). PMID:30701273
Study of the whole genome, methylome and transcriptome of Cordyceps militaris. PMID:30696919
Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. PMID:30692531
Evolution of the Drosophila melanogaster Chromatin Landscape and Its Associated Proteins. PMID:30689829
T6SS contributes to gut microbiome invasion and killing of an herbivorous pest insect by plant-beneficial Pseudomonas protegens. PMID:30683920
Genome Assembly and Annotation of the Trichoplusia ni Tni-FNL Insect Cell Line Enabled by Long-Read Technologies. PMID:30678108
Meta-analysis of expression and methylation signatures indicates a stress-related epigenetic mechanism in multiple neuropsychiatric disorders. PMID:30670680
A High-quality Draft Genome Assembly of Sinella curviseta: A Soil Model Organism (Collembola). PMID:30668671
The Genetics of Mating Song Evolution Underlying Rapid Speciation: Linking Quantitative Variation to Candidate Genes for Behavioral Isolation. PMID:30647070
Ubiquitin fusion proteins in algae: implications for cell biology and the spread of photosynthesis. PMID:30642248
Resveratrol and Its Human Metabolites-Effects on Metabolic Health and Obesity. PMID:30641865
Identification of a Novel Elastin-Degrading Enzyme from the Fish Pathogen Flavobacterium psychrophilum. PMID:30635380
Chromosome level comparative analysis of Brassica genomes. PMID:30632049
Systematic analysis of NAC transcription factors' gene family and identification of post-flowering drought stress responsive members in sorghum. PMID:30627770
Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution. PMID:30626928
In Silico Analysis of Pacific Oyster (Crassostrea gigas) Transcriptome over Developmental Stages Reveals Candidate Genes for Larval Settlement. PMID:30625986
The transcriptome landscape of the carcinogenic treatment response in the blind mole rat: insights into cancer resistance mechanisms. PMID:30621584
The sequence and de novo assembly of hog deer genome. PMID:30620341
Mitochondrial Sco proteins are involved in oxidative stress defense. PMID:30593977
Transposons and pathogenicity in Xanthomonas: acquisition of murein lytic transglycosylases by TnXax1 enhances Xanthomonas citri subsp. citri 306 virulence and fitness. PMID:30588403
Genomic Signals of Adaptation towards Mutualism and Sociality in Two Ambrosia Beetle Complexes. PMID:30583535
A Cryptic Non-Inducible Prophage Confers Phage-Immunity on the Streptococcus thermophilus M17PTZA496. PMID:30583530
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. PMID:30576488
PhytoTypeDB: a database of plant protein inter-cultivar variability and function. PMID:30576486
Role of oxidative stress in Retinitis pigmentosa: new involved pathways by an RNA-Seq analysis. PMID:30569795
High Throughput Identification of Novel Conotoxins from the Vermivorous Oak Cone Snail (Conus quercinus) by Transcriptome Sequencing. PMID:30563163
Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea. PMID:30559729
Predicted glycosyltransferases promote development and prevent spurious cell clumping in the choanoflagellate S. rosetta. PMID:30556809
Insights into the transcriptional and post-transcriptional regulation of the rice SUMOylation machinery and into the role of two rice SUMO proteases. PMID:30541427
The Protozoan Trichomonas vaginalis Targets Bacteria with Laterally Acquired NlpC/P60 Peptidoglycan Hydrolases. PMID:30538181
An updated gene atlas for maize reveals organ-specific and stress-induced genes. PMID:30537259
Comparative Analysis of Oomycete Genome Evolution Using the Oomycete Gene Order Browser (OGOB). PMID:30535146
High-Quality Draft Genome Sequences of Eight Bacteria Isolated from Fungus Gardens Grown by Trachymyrmex septentrionalis Ants. PMID:30533809
Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism. PMID:30526846
The Roles of E93 and Kr-h1 in Metamorphosis of Nilaparvata lugens. PMID:30524315
High-yield production of human Dicer by transfection of human HEK293-EBNA1 cells grown in suspension. PMID:30522464
Regulation of Yeast-to-Hyphae Transition in Yarrowia lipolytica. PMID:30518677
The Caenorhabditis elegans SMOC-1 Protein Acts Cell Nonautonomously To Promote Bone Morphogenetic Protein Signaling. PMID:30518528
Reconstructing the evolutionary history of F420-dependent dehydrogenases. PMID:30514849
Tissue-Specific cis-Regulatory Divergence Implicates eloF in Inhibiting Interspecies Mating in Drosophila. PMID:30503619
Nephromyces Encodes a Urate Metabolism Pathway and Predicted Peroxisomes, Demonstrating That These Are Not Ancient Losses of Apicomplexans. PMID:30500900
Analyzing Diguanylate Cyclase Activity In Vivo using a Heterologous Escherichia coli Host. PMID:30489040
Comparative genomics of HORMA domain-containing proteins in prokaryotes and eukaryotes. PMID:30488757
Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids. PMID:30482201
Enhancing the Production of the Fungal Pigment Aurofusarin in Fusarium graminearum. PMID:30469367
Molecular Factors of Hypochlorite Tolerance in the Hypersaline Archaeon Haloferax volcanii. PMID:30463375
Combining bioinformatics, cheminformatics, functional genomics and whole organism approaches for identifying epigenetic drug targets in Schistosoma mansoni. PMID:30455056
The European Bioinformatics Institute in 2018: tools, infrastructure and training. PMID:30445657
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. PMID:30445541
Genomes of trombidid mites reveal novel predicted allergens and laterally transferred genes associated with secondary metabolism. PMID:30445460
Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce. PMID:30424733
Vacuolar hydrolysis and efflux: current knowledge and unanswered questions. PMID:30422029
Gene cluster conservation identifies melanin and perylenequinone biosynthesis pathways in multiple plant pathogenic fungi. PMID:30421572
Exploring the rearrangement of sensory intelligence in proteobacteria: insight of Pho regulon. PMID:30413888
Unlocking conserved and diverged metabolic characteristics in cassava carbon assimilation via comparative genomics approach. PMID:30413726
Genome-wide identification, characterization, and expression analysis of the expansin gene family in Chinese jujube (Ziziphus jujuba Mill.). PMID:30411169
Complete Genome Sequence and Characterization of Linezolid-Resistant Enterococcus faecalis Clinical Isolate KUB3006 Carrying a cfr(B)-Transposon on Its Chromosome and optrA-Plasmid. PMID:30410481
Structural Studies based on two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity within the Clavaminate Synthase-Like Family. PMID:30410048
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. PMID:30407594
Evolution and functional characterization of pectate lyase PEL12, a member of a highly expanded Clonostachys rosea polysaccharide lyase 1 family. PMID:30404596
Transcriptomics of Haemophilus (Glässerella) parasuis serovar 5 subjected to culture conditions partially mimetic to natural infection for the search of new vaccine antigens. PMID:30400794
InterPro in 2019: improving coverage, classification and access to protein sequence annotations. PMID:30398656
Common ancestry of heterodimerizing TALE homeobox transcription factors across Metazoa and Archaeplastida. PMID:30396330
Comparative analysis of the Pocillopora damicornis genome highlights role of immune system in coral evolution. PMID:30382153
iEKPD 2.0: an update with rich annotations for eukaryotic protein kinases, protein phosphatases and proteins containing phosphoprotein-binding domains. PMID:30380109
OrthoInspector 3.0: open portal for comparative genomics. PMID:30380106
dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data. PMID:30380085
A vesicular Na+/Ca2+ exchanger in coral calcifying cells. PMID:30379874
Novel Mitoviruses and a Unique Tymo-Like Virus in Hypovirulent and Virulent Strains of the Fusarium Head Blight Fungus, Fusarium boothii. PMID:30373133
Evasion of phagotrophic predation by protist hosts and innate immunity of metazoan hosts by Legionella pneumophila. PMID:30370624
Application of Proteomics Technologies in Oil Palm Research. PMID:30367348
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes. PMID:30364992
The Pfam protein families database in 2019. PMID:30357350
15 years of GDR: New data and functionality in the Genome Database for Rosaceae. PMID:30357347
What is an archaeon and are the Archaea really unique? PMID:30357005
CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis. PMID:30340514
MGH: a genome hub for the medicinal plant maca (Lepidium meyenii). PMID:30339215
REBELOTE, a regulator of floral determinacy in Arabidopsis thaliana, interacts with both nucleolar and nucleoplasmic proteins. PMID:30338215
Identification of Glycoproteins Isolated from Extracellular Polymeric Substances of Full-Scale Anammox Granular Sludge. PMID:30335377
An RND transporter in the monoterpene metabolism of Castellaniella defragrans. PMID:30334144
Editorial: The Role of AAA+ Proteins in Protein Repair and Degradation. PMID:30333982
Dissecting the functional domains of the Arabidopsis thaliana nonhost resistance 2B (AtNHR2B) protein. PMID:30325257
PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information. PMID:30321395
The Planktonic Core Microbiome and Core Functions in the Cattle Rumen by Next Generation Sequencing. PMID:30319585
Unicellular Origin of the Animal MicroRNA Machinery. PMID:30318349
Indoleacetate decarboxylase is a glycyl radical enzyme catalysing the formation of malodorant skatole. PMID:30310076
Towards region-specific propagation of protein functions. PMID:30304483
OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes. PMID:30299502
Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics. PMID:30297752
Two Regulators, PA3898 and PA2100, Modulate the Pseudomonas aeruginosa Multidrug Resistance MexAB-OprM and EmrAB Efflux Pumps and Biofilm Formation. PMID:30297364
cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly. PMID:30295745
Evolutionary and functional analyses of the 2-oxoglutarate-dependent dioxygenase genes involved in the flavonoid biosynthesis pathway in tobacco. PMID:30293202
Environmental pH modulates transcriptomic responses in the fungus Fusarium sp. associated with KSHB Euwallacea sp. near fornicatus. PMID:30285612
Exhaustive non-synonymous variants functionality prediction enables high resolution characterization of the neurofibromin architecture. PMID:30274822
'Democratized' genomic enzymology web tools for functional assignment. PMID:30268904
Topological alternate centrality measure capturing drug targets in the network of MAPK pathways. PMID:30259868
Alternative Splicing Plays a Critical Role in Maintaining Mineral Nutrient Homeostasis in Rice (Oryza sativa). PMID:30254029
PGD: Pineapple Genomics Database. PMID:30245835
C.el Phosphatome: A Catalogue of Actual and Pseudo Phosphatases Based on In-Silico Studies in Caenorhabditis elegans. PMID:30242660
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
Deep taxon sampling reveals the evolutionary dynamics of novel gene families in Pristionchus nematodes. PMID:30232197
Calcium-sensitive pyruvate dehydrogenase phosphatase is required for energy metabolism, growth, differentiation, and infectivity of Trypanosoma cruzi. PMID:30232153
Diversity of Active Viral Infections within the Sphagnum Microbiome. PMID:30217851
A comprehensive manually-curated compendium of bovine transcription factors. PMID:30213987
Identification and expression analysis of genes with pathogen-inducible cis-regulatory elements in the promoter regions in Oryza sativa. PMID:30209707
Characterization of a novel member of the family Caulimoviridae infecting Dioscorea nummularia in the Pacific, which may represent a new genus of dsDNA plant viruses. PMID:30208072
Genomic characterization of Trichoderma atrobrunneum (T. harzianum species complex) ITEM 908: insight into the genetic endowment of a multi-target biocontrol strain. PMID:30200883
Prediction of protein group function by iterative classification on functional relevance network. PMID:30192921
The role of conserved proteins DrpA and DrpB in nitrate respiration of Thermus thermophilus. PMID:30187633
Phylogenetic analysis and expression profiling of the Klotho gene family in the short-lived African killifish Nothobranchius furzeri. PMID:30178389
Genome Wide Identification of Mutational Hotspots in the Apicomplexan Parasite Neospora caninum and the Implications for Virulence. PMID:30165699
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences. PMID:30165572
A miR172 target-deficient AP2-like gene correlates with the double flower phenotype in roses. PMID:30150746
Substrate Specificity and Chemical Mechanism for the Reaction Catalyzed by Glutamine Kinase. PMID:30142271
TMEM41B is a novel regulator of autophagy and lipid mobilization. PMID:30126924
Characterization of ExeM, an Extracellular Nuclease of Shewanella oneidensis MR-1. PMID:30123203
OrthoList 2: A New Comparative Genomic Analysis of Human and Caenorhabditis elegans Genes. PMID:30120140
Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides. PMID:30116038
INFERNO: inferring the molecular mechanisms of noncoding genetic variants. PMID:30113658
The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana). PMID:30101322
Piercing Fishes: Porin Expansion and Adaptation to Hematophagy in the Vampire Snail Cumia reticulata. PMID:30099551
Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. PMID:30097089
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. PMID:30084866
HPO2GO: prediction of human phenotype ontology term associations for proteins using cross ontology annotation co-occurrences. PMID:30083448
Natural Genetic Variation in a Multigenerational Phenotype in C. elegans. PMID:30078564
An Aspartate-Specific Solute-Binding Protein Regulates Protein Kinase G Activity To Control Glutamate Metabolism in Mycobacteria. PMID:30065086
De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder. PMID:30057029
Velvet domain protein VosA represses the zinc cluster transcription factor SclB regulatory network for Aspergillus nidulans asexual development, oxidative stress response and secondary metabolism. PMID:30044771
Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques. PMID:30035760
Structural Analysis of Phosphoserine Aminotransferase (Isoform 1) From Arabidopsis thaliana- the Enzyme Involved in the Phosphorylated Pathway of Serine Biosynthesis. PMID:30034403
High Quality de Novo Transcriptome Assembly of Croton tiglium. PMID:30027092
Pan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway. PMID:30026808
A comprehensive review of web-based resources of non-coding RNAs for plant science research. PMID:29989090
In-depth proteomic analyses of Haliotis laevigata (greenlip abalone) nacre and prismatic organic shell matrix. PMID:29983641
FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced Fusobacterium Genomes Improves Gene Identification and Characterization. PMID:29976644
Ribonucleotide discrimination by translesion synthesis DNA polymerases. PMID:29972306
SDADB: a functional annotation database of protein structural domains. PMID:29961821
Lipid transport required to make lipids of photosynthetic membranes. PMID:29961189
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
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
Uncovering global metabolic response to cordycepin production in Cordyceps militaris through transcriptome and genome-scale network-driven analysis. PMID:29915355
Thailandamide, a Fatty Acid Synthesis Antibiotic That Is Coexpressed with a Resistant Target Gene. PMID:29914944
Metagenomic insights into the roles of Proteobacteria in the gastrointestinal microbiomes of healthy dogs and cats. PMID:29911322
Murine leukemia virus p12 tethers the capsid-containing pre-integration complex to chromatin by binding directly to host nucleosomes in mitosis. PMID:29906285
HMMER web server: 2018 update. PMID:29905871
Draft genome sequence of Trametes villosa (Sw.) Kreisel CCMB561, a tropical white-rot Basidiomycota from the semiarid region of Brazil. PMID:29904660
In silico Phylogenetic Analysis of hAT Transposable Elements in Plants. PMID:29882803
Machine learning provides predictive analysis into silver nanoparticle protein corona formation from physicochemical properties. PMID:29881624
Analysis of tail-anchored protein translocation pathway in plants. PMID:29872748
Chloroplastic Serine Hydroxymethyltransferase From Medicago truncatula: A Structural Characterization. PMID:29868052
Identification of Putative Precursor Genes for the Biosynthesis of Cannabinoid-Like Compound in Radula marginata. PMID:29868043
Comparative Genomics Analysis of Plasmid pPV989-94 from a Clinical Isolate of Pantoea vagans PV989. PMID:29862249
IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding. PMID:29860432
Regulating the human HECT E3 ligases. PMID:29858610
Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. PMID:29855388
TPP riboswitch-dependent regulation of an ancient thiamin transporter in Candida. PMID:29852014
Genome sequencing and protein domain annotations of Korean Hanwoo cattle identify Hanwoo-specific immunity-related and other novel genes. PMID:29843617
Evidence for interaction between Hsp90 and the ER membrane complex. PMID:29808299
Sorting Five Human Tumor Types Reveals Specific Biomarkers and Background Classification Genes. PMID:29802335
Discovery of a new Pro-Pro endopeptidase, PPEP-2, provides mechanistic insights into the differences in substrate specificity within the PPEP family. PMID:29794027
The draft genome sequence of cork oak. PMID:29786699
Genetic Analyses of Elys Mutations in Drosophila Show Maternal-Effect Lethality and Interactions with Nucleoporin Genes. PMID:29773558
Evolutionary and genomic analysis of the caleosin/peroxygenase (CLO/PXG) gene/protein families in the Viridiplantae. PMID:29771926
Using FlyBase to Find Functionally Related Drosophila Genes. PMID:29761468
Using ZFIN: Data Types, Organization, and Retrieval. PMID:29761463
EuPathDB: The Eukaryotic Pathogen Genomics Database Resource. PMID:29761457
GLUCOSAMINE INOSITOLPHOSPHORYLCERAMIDE TRANSFERASE1 (GINT1) Is a GlcNAc-Containing Glycosylinositol Phosphorylceramide Glycosyltransferase. PMID:29760197
De Novo DNA Synthesis in Aedes aegypti Midgut Cells as a Complementary Strategy to Limit Dengue Viral Replication. PMID:29755433
Structural biology data archiving - where we are and what lies ahead. PMID:29749603
Control of mitotic chromosome condensation by the fission yeast transcription factor Zas1. PMID:29735745
Male-killing toxin in a bacterial symbiont of Drosophila. PMID:29720654
Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants. PMID:29713790
The Rosa genome provides new insights into the domestication of modern roses. PMID:29713014
Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species. PMID:29700415
Targeting of epigenetic regulators in neuroblastoma. PMID:29700278
REDIdb 3.0: A Comprehensive Collection of RNA Editing Events in Plant Organellar Genomes. PMID:29696033
PvaxDB: a comprehensive structural repository of Plasmodium vivax proteome. PMID:29688373
LaoABCR, a Novel System for Oxidation of Long-Chain Alcohols Derived from SDS and Alkane Degradation in Pseudomonas aeruginosa. PMID:29678916
KDiamend: a package for detecting key drivers in a molecular ecological network of disease. PMID:29671403
Genome-Wide Identification and Expression Analysis of the Cation Diffusion Facilitator Gene Family in Turnip Under Diverse Metal Ion Stresses. PMID:29670641
Discovery of Novel Bat Coronaviruses in South China That Use the Same Receptor as Middle East Respiratory Syndrome Coronavirus. PMID:29669833
Stonewall and Brickwall: Two Partially Redundant Determinants Required for the Maintenance of Female Germline in Drosophila. PMID:29669801
Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases. PMID:29666611
Genome-wide detection of conservative site-specific recombination in bacteria. PMID:29621238
Two Groups of Cocirculating, Epidemic Clostridiodes difficile Strains Microdiversify through Different Mechanisms. PMID:29617810
Improving the annotation of the Heterorhabditis bacteriophora genome. PMID:29617768
The complete mitochondrial genome of the hermaphroditic freshwater mussel Anodonta cygnea (Bivalvia: Unionidae): in silico analyses of sex-specific ORFs across order Unionoida. PMID:29587633
Characterization of the basic helix-loop-helix gene family and its tissue-differential expression in response to salt stress in poplar. PMID:29576971
A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. PMID:29572503
Comprehensive subcellular topologies of polypeptides in Streptomyces. PMID:29544487
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
MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping. PMID:29534977
Dynamin-Like Proteins Are Potentially Involved in Membrane Dynamics within Chloroplasts and Cyanobacteria. PMID:29520287
Spatiotemporal compartmentalization of hepatic NADH and NADPH metabolism. PMID:29514978
Comparative Genomic Analysis of a Clinical Isolate of Klebsiella quasipneumoniae subsp. similipneumoniae, a KPC-2 and OKP-B-6 Beta-Lactamases Producer Harboring Two Drug-Resistance Plasmids from Southeast Brazil. PMID:29503635
Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals. PMID:29500236
Surfaceome and Proteosurfaceome in Parietal Monoderm Bacteria: Focus on Protein Cell-Surface Display. PMID:29491848
Complete genome sequence of Lactobacillus rhamnosus Pen, a probiotic component of a medicine used in prevention of antibiotic-associated diarrhoea in children. PMID:29483943
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
Rice matrix metalloproteinase OsMMP1 plays pleiotropic roles in plant development and symplastic-apoplastic transport by modulating cellulose and callose depositions. PMID:29426868
Tissue expression pattern of ABCG transporter indicates functional roles in reproduction of Toxocara canis. PMID:29423531
Unravelling the immune signature of Plasmodium falciparum transmission-reducing immunity. PMID:29422648
Novel global effector mining from the transcriptome of early life stages of the soybean cyst nematode Heterodera glycines. PMID:29410430
The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile. PMID:29403466
A computationally driven analysis of the polyphenol-protein interactome. PMID:29396566
The activity of the C4-dicarboxylic acid chemoreceptor of Pseudomonas aeruginosa is controlled by chemoattractants and antagonists. PMID:29391435
Substrate Recognition and Specificity of Chitin Deacetylases and Related Family 4 Carbohydrate Esterases. PMID:29385775
GO FEAT: a rapid web-based functional annotation tool for genomic and transcriptomic data. PMID:29379090
Identification of the Autochaperone Domain in the Type Va Secretion System (T5aSS): Prevalent Feature of Autotransporters with a β-Helical Passenger. PMID:29375499
Fungal Screening on Olive Oil for Extracellular Triacylglycerol Lipases: Selection of a Trichoderma harzianum Strain and Genome Wide Search for the Genes. PMID:29370083
Crystal structure of thermospermine synthase from Medicago truncatula and substrate discriminatory features of plant aminopropyltransferases. PMID:29367265
Genome-Wide Identification and Comparative Analysis of the 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase (HMGR) Gene Family in Gossypium. PMID:29364830
Mapping HLA-A2, -A3 and -B7 supertype-restricted T-cell epitopes in the ebolavirus proteome. PMID:29363421
Structure, function and evolution of the hemerythrin-like domain superfamily. PMID:29330894
A Novel Corynebacterium glutamicum l-Glutamate Exporter. PMID:29330181
Genetic diversity of three surface protein genes in Plasmodium malariae from three Asian countries. PMID:29325573
Characterization of Translationally Controlled Tumour Protein from the Sea Anemone Anemonia viridis and Transcriptome Wide Identification of Cnidarian Homologues. PMID:29324689
Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium. PMID:29312205
Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins. PMID:29302007
Multiplexed gene synthesis in emulsions for exploring protein functional landscapes. PMID:29301959
Mining of the Uncharacterized Cytochrome P450 Genes Involved in Alkaloid Biosynthesis in California Poppy Using a Draft Genome Sequence. PMID:29301019
De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus. PMID:29297306
Crystal Structure of Bicc1 SAM Polymer and Mapping of Interactions between the Ciliopathy-Associated Proteins Bicc1, ANKS3, and ANKS6. PMID:29290488
Parallel evolution of the POQR prolyl oligo peptidase gene conferring plant quantitative disease resistance. PMID:29272270
Transcriptomic characterization of Caecomyces churrovis: a novel, non-rhizoid-forming lignocellulolytic anaerobic fungus. PMID:29270219
Identification of a precursor processing protease from the spider Cupiennius salei essential for venom neurotoxin maturation. PMID:29269415
Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems. PMID:29263101
Ca2+-Induced Two-Component System CvsSR Regulates the Type III Secretion System and the Extracytoplasmic Function Sigma Factor AlgU in Pseudomonas syringae pv. tomato DC3000. PMID:29263098
Draft Sequencing of the Heterozygous Diploid Genome of Satsuma (Citrus unshiu Marc.) Using a Hybrid Assembly Approach. PMID:29259619
Evolutionary transition from blood feeding to obligate nonbiting in a mosquito. PMID:29255013
Novel linear motif filtering protocol reveals the role of the LC8 dynein light chain in the Hippo pathway. PMID:29240760
The Enigmatic Role of GBA2 in Controlling Locomotor Function. PMID:29234271
Insights from the protein-protein interaction network analysis of Mycobacterium tuberculosis toxin-antitoxin systems. PMID:29225431
Annotating gene sets by mining large literature collections with protein networks. PMID:29218918
Subcellular Localization and Functional Characterization of GII.4 Norovirus-Encoded NTPase. PMID:29212938
PvdO is required for the oxidation of dihydropyoverdine as the last step of fluorophore formation in Pseudomonas fluorescens. PMID:29208656
Identification and characterization of the Streptococcus pneumoniae type 3 capsule-specific glycoside hydrolase of Paenibacillus species 32352. PMID:29190349
Actin genes and their expression in pacific white shrimp, Litopenaeus vannamei. PMID:29189957
The European Bioinformatics Institute in 2017: data coordination and integration. PMID:29186510
A global view of structure-function relationships in the tautomerase superfamily. PMID:29184004
Structural insights into the committed step of bacterial phospholipid biosynthesis. PMID:29167463
A compendium of transcription factor and Transcriptionally active protein coding gene families in cowpea (Vigna unguiculata L.). PMID:29166879
Functional divergence of paralogous transcription factors supported the evolution of biomineralization in echinoderms. PMID:29154754
Identification and characterization of regulatory network components for anthocyanin synthesis in barley aleurone. PMID:29143621
MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. PMID:29136219
ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins. PMID:29126202
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. PMID:29126160
VarCards: an integrated genetic and clinical database for coding variants in the human genome. PMID:29112736
iUUCD 2.0: an update with rich annotations for ubiquitin and ubiquitin-like conjugations. PMID:29106644
Dupuytren's and Ledderhose Diseases in a Family with LMNA-Related Cardiomyopathy and a Novel Variant in the ASTE1 Gene. PMID:29104234
Interdependence of Primary Metabolism and Xenobiotic Mitigation Characterizes the Proteome of Bjerkandera adusta during Wood Decomposition. PMID:29101201
Identification of a molecular pH sensor in coral. PMID:29093223
POTAGE: A Visualisation Tool for Speeding up Gene Discovery in Wheat. PMID:29085014
Prediction of protein disorder based on IUPred. PMID:29076577
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies. PMID:29069476
20 years of the SMART protein domain annotation resource. PMID:29040681
The FASTK family of proteins: emerging regulators of mitochondrial RNA biology. PMID:29036396
DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier. PMID:29028931
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
Microbial genome analysis: the COG approach. PMID:28968633
Biochemical and structural characterization of a novel arginine kinase from the spider Polybetes pythagoricus. PMID:28924503
The periplasmic transaminase PtaA of Pseudomonas fluorescens converts the glutamic acid residue at the pyoverdine fluorophore to α-ketoglutaric acid. PMID:28912270
Critical Roles of Dual-Specificity Phosphatases in Neuronal Proteostasis and Neurological Diseases. PMID:28902166
Transcriptomic profiling in muscle and adipose tissue identifies genes related to growth and lipid deposition. PMID:28877211
An Alternative STAT Signaling Pathway Acts in Viral Immunity in Caenorhabditis elegans. PMID:28874466
Development of an Efficient Protein Extraction Method Compatible with LC-MS/MS for Proteome Mapping in Two Australian Seagrasses Zostera muelleri and Posidonia australis. PMID:28861098
Gene expression profile data for mouse facial development. PMID:28856179
Pathogenic Leptospires Modulate Protein Expression and Post-translational Modifications in Response to Mammalian Host Signals. PMID:28848720
PaperBLAST: Text Mining Papers for Information about Homologs. PMID:28845458
Quantitative phosphoproteomic analysis of acquired cancer drug resistance to pazopanib and dasatinib. PMID:28842319
Fungal Hybrid B heme peroxidases - unique fusions of a heme peroxidase domain with a carbohydrate-binding domain. PMID:28839281
Bioinformatics Analysis of Phylogeny and Transcription of TAA/YUC Auxin Biosynthetic Genes. PMID:28820425
Discovering Condition-Specific Gene Co-Expression Patterns Using Gaussian Mixture Models: A Cancer Case Study. PMID:28819158
Aggregation of population-based genetic variation over protein domain homologues and its potential use in genetic diagnostics. PMID:28815929
Silencing of Repetitive DNA Is Controlled by a Member of an Unusual Caenorhabditis elegans Gene Family. PMID:28801529
Spider Neurotoxins, Short Linear Cationic Peptides and Venom Protein Classification Improved by an Automated Competition between Exhaustive Profile HMM Classifiers. PMID:28786958
An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences. PMID:28777078
Cytochromes P450 for natural product biosynthesis in Streptomyces: sequence, structure, and function. PMID:28758170
Dynamic scaffolds for neuronal signaling: in silico analysis of the TANC protein family. PMID:28754924
BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation. PMID:28750104
Deficient glutamate biosynthesis triggers a concerted upregulation of ribosomal protein genes in Arabidopsis. PMID:28733652
Outer Membrane Proteome of Veillonella parvula: A Diderm Firmicute of the Human Microbiome. PMID:28713344
Gene Regulatory Networks for the Haploid-to-Diploid Transition of Chlamydomonas reinhardtii. PMID:28710131
ABA signalling manipulation suppresses senescence of a leafy vegetable stored at room temperature. PMID:28703416
The Two Cryptochrome/Photolyase Family Proteins Fulfill Distinct Roles in DNA Photorepair and Regulation of Conidiation in the Gray Mold Fungus Botrytis cinerea. PMID:28667107
Transcription Factor Repertoire of Necrotrophic Fungal Phytopathogen Ascochyta rabiei: Predominance of MYB Transcription Factors As Potential Regulators of Secretome. PMID:28659964
The transcriptome of a "sleeping" invader: de novo assembly and annotation of the transcriptome of aestivating Cornu aspersum. PMID:28659170
Discovery of a Glutamine Kinase Required for the Biosynthesis of the O-Methyl Phosphoramidate Modifications Found in the Capsular Polysaccharides of Campylobacter jejuni. PMID:28650156
GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species. PMID:28605774
Flipping states: a few key residues decide the winning conformation of the only universally conserved transcription factor. PMID:28605514
CottonFGD: an integrated functional genomics database for cotton. PMID:28595571
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. PMID:28472432
The EBI search engine: EBI search as a service-making biological data accessible for all. PMID:28472374
rAMPing Up Stress Signaling: Protein AMPylation in Metazoans. PMID:28433487
Programmatic access to bioinformatics tools from EMBL-EBI update: 2017. PMID:28431173
Draft Genome Sequence of Acinetobacter johnsonii C6, an Environmental Isolate Engaging in Interspecific Metabolic Interactions. PMID:28428290
Novel interactions of the von Hippel-Lindau (pVHL) tumor suppressor with the CDKN1 family of cell cycle inhibitors. PMID:28425505
Transcriptome-based investigation of cirrus development and identifying microsatellite markers in rattan (Daemonorops jenkinsiana). PMID:28383053
Biocuration in the structure-function linkage database: the anatomy of a superfamily. PMID:28365730
CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. PMID:27899674 -
The InterPro protein families database: the classification resource after 15 years
PubMed citations: 628.
628 articles citing: The InterPro protein families database: the classification resource after 15 years
Enhancing the Discovery of Functional Post-Translational Modification Sites with Machine Learning Models - Development, Validation, and Interpretation. PMID:35696084
The genome of hibiscus hamabo reveals its adaptation to saline and waterlogged habitat. PMID:35480957
Integration of Aspergillus niger transcriptomic profile with metabolic model identifies potential targets to optimise citric acid production from lignocellulosic hydrolysate. PMID:35418297
Integration of Neighbor Topologies Based on Meta-Paths and Node Attributes for Predicting Drug-Related Diseases. PMID:35409235
Genome-wide evolution and expression analysis of the MYB-CC gene family in Brassica spp. PMID:35237467
Next-generation sequencing identified novel truncating mutations in BBS9 causing Bardet Biedl syndrome in two Iranian consanguineous families. PMID:35222663
Characterization of the Novel Phage vB_VpaP_FE11 and Its Potential Role in Controlling Vibrio parahaemolyticus Biofilms. PMID:35215857
Haplotype-Resolved Genome Analyses Reveal Genetically Distinct Nuclei within a Commercial Cultivar of Lentinula edodes. PMID:35205921
New Genomic Signals Underlying the Emergence of Human Proto-Genes. PMID:35205330
Base excision repair system targeting DNA adducts of trioxacarcin/LL-D49194 antibiotics for self-resistance. PMID:35191495
The crewed journey to Mars and its implications for the human microbiome. PMID:35125119
Structural and Evolutionary Insights Into the Binding of Host Receptors by the Rabies Virus Glycoprotein. PMID:34708003
Music of metagenomics-a review of its applications, analysis pipeline, and associated tools. PMID:34657989
First Dye-Decolorizing Peroxidase from an Ascomycetous Fungus Secreted by Xylaria grammica. PMID:34572604
Uncovering Diagnostic Value of Mitogenome for Identification of Cryptic Species Fusarium graminearum Sensu Stricto. PMID:34531839
Features of the Opportunistic Behaviour of the Marine Bacterium Marinobacter algicola in the Microalga Ostreococcus tauri Phycosphere. PMID:34442856
Pleiotropic roles of Ras GTPases in the nematode-trapping fungus Arthrobotrys oligospora identified through multi-omics analyses. PMID:34337364
Disease gene prediction with privileged information and heteroscedastic dropout. PMID:34252957
The molecular identity of the characean OH- transporter: a candidate related to the SLC4 family of animal pH regulators. PMID:34232395
Cloning, expression analysis and In silico characterization of HSP101: a potential player conferring heat stress in Aegilops speltoides (Tausch) Gren. PMID:34220041
Chromosome-Scale Genome Assembly of the Resurrection Plant Acanthochlamys bracteata (Velloziaceae). PMID:34165527
Proteomics-Based Data Integration of Wheat Cultivars Facing Fusarium graminearum Strains Revealed a Core-Responsive Pattern Controlling Fusarium Head Blight. PMID:34135919
Pathways of Iron and Sulfur Acquisition, Cofactor Assembly, Destination, and Storage in Diverse Archaeal Methanogens and Alkanotrophs. PMID:34124941
Carbamoyl Phosphate Synthase Subunit CgCPS1 Is Necessary for Virulence and to Regulate Stress Tolerance in Colletotrichum gloeosporioides. PMID:34111913
A Peek into the Plasmidome of Global Sewage. PMID:34061588
Predicting phosphorylation sites using machine learning by integrating the sequence, structure, and functional information of proteins. PMID:34030700
MyCLADE: a multi-source domain annotation server for sequence functional exploration. PMID:34023906
The order of PDZ3 and TrpCage in fusion chimeras determines their properties-a biophysical characterization. PMID:33969912
Gene Coexpression Network Reveals Highly Conserved, Well-Regulated Anti-Ageing Mechanisms in Old Ant Queens. PMID:33944936
Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides. PMID:33941076
Whole-genome resequencing of Osmanthus fragrans provides insights into flower color evolution. PMID:33931610
Identification of a Chlorovirus PBCV-1 Protein Involved in Degrading the Host Cell Wall during Virus Infection. PMID:33924931
Thiocyanate and Organic Carbon Inputs Drive Convergent Selection for Specific Autotrophic Afipia and Thiobacillus Strains Within Complex Microbiomes. PMID:33897653
The acylfulvene alkylating agent, LP-184, retains nanomolar potency in non-small cell lung cancer carrying otherwise therapy-refractory mutations. PMID:33889302
Reverse vaccinology and subtractive genomics approaches for identifying common therapeutics against Mycobacterium leprae and Mycobacterium lepromatosis. PMID:33889182
In Silico Analysis of Huntingtin Homologs in Lower Eukaryotes. PMID:33809947
Genome Sequence of the Bacteriophage CL31 and Interaction with the Host Strain Corynebacterium glutamicum ATCC 13032. PMID:33802915
Divergent CPEB prion-like domains reveal different assembly mechanisms for a generic amyloid-like fold. PMID:33706787
Protein domain identification methods and online resources. PMID:33680357
From Data Mining of Chitinophaga sp. Genome to Enzyme Discovery of a Hyperthermophilic Metallocarboxypeptidase. PMID:33673011
DbStRiPs: Database of structural repeats in proteins. PMID:33641184
Multiple Pathways to Homothallism in Closely Related Yeast Lineages in the Basidiomycota. PMID:33593979
Phenotypic Characterization and Whole-Genome Analysis of a Novel Bacteriophage HCF1 Infecting Citrobacter amalonaticus and C. freundii. PMID:33569047
Computational resources for identifying and describing proteins driving liquid-liquid phase separation. PMID:33517364
SNF-NN: computational method to predict drug-disease interactions using similarity network fusion and neural networks. PMID:33482713
Integrative multiomics analysis of Premolis semirufa caterpillar venom in the search for molecules leading to a joint disease. PMID:33479267
HN1L promotes invasion and metastasis of the esophagogastric junction adenocarcinoma. PMID:33471419
Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA. PMID:33450012
Learning important features from multi-view data to predict drug side effects. PMID:33430979
In silico screening and experimental analysis of family GH11 xylanases for applications under conditions of alkaline pH and high temperature. PMID:33372612
A New Phage Lysin Isolated from the Oral Microbiome Targeting Streptococcus pneumoniae. PMID:33352708
Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides. PMID:33351797
Mycobacterial STAND adenylyl cyclases: The HTH domain binds DNA to form biocrystallized nucleoids. PMID:33217386
An updated evolutionary study of the Notch family reveals a new ancient origin and novel invariable motifs as potential pharmacological targets. PMID:33194454
"Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)". PMID:33138770
The Untapped Australasian Diversity of Astaxanthin-Producing Yeasts with Biotechnological Potential-Phaffia australis sp. nov. and Phaffia tasmanica sp. nov. PMID:33114402
Preclinical validation of therapeutic targets predicted by tensor factorization on heterogeneous graphs. PMID:33106501
Expression, epitope prediction and IgE-binding of the Tyrophagus putrescentiae group 13 allergen. PMID:32934686
F-Box Family Genes, LTSF1 and LTSF2, Regulate Low-Temperature Stress Tolerance in Pepper (Capsicum chinense). PMID:32933000
Calcium Binding Protein Ncs1 Is Calcineurin Regulated in Cryptococcus neoformans and Essential for Cell Division and Virulence. PMID:32907953
Nanoparticle treatment of maize analyzed through the metatranscriptome: compromised nitrogen cycling, possible phytopathogen selection, and plant hormesis. PMID:32907632
Bacillus velezensis 83 a bacterial strain from mango phyllosphere, useful for biological control and plant growth promotion. PMID:32894363
Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns. PMID:32875947
Acetylation of Surface Carbohydrates in Bacterial Pathogens Requires Coordinated Action of a Two-Domain Membrane-Bound Acyltransferase. PMID:32843546
Whole-genome de novo assemblies reveal extensive structural variations and dynamic organelle-to-nucleus DNA transfers in African and Asian rice. PMID:32748498
PertInInt: An Integrative, Analytical Approach to Rapidly Uncover Cancer Driver Genes with Perturbed Interactions and Functionalities. PMID:32711844
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
Energetics and IC50 based epitope screening in SARS CoV-2 (COVID 19) spike protein by immunoinformatic analysis implicating for a suitable vaccine development. PMID:32650788
Plasmid gene for putative integral membrane protein affects formation of lipopolysaccharide and motility in Azospirillum brasilense Sp245. PMID:32607666
Detecting Introgression Between Members of the Fusarium fujikuroi and F. oxysporum Species Complexes by Comparative Mitogenomics. PMID:32582074
Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus. PMID:32575906
Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus. PMID:32531032
Diversity of Mobile Genetic Elements in the Mitogenomes of Closely Related Fusarium culmorum and F. graminearum sensu stricto Strains and Its Implication for Diagnostic Purposes. PMID:32528440
MYB Superfamily in Brassica napus: Evidence for Hormone-Mediated Expression Profiles, Large Expansion, and Functions in Root Hair Development. PMID:32517318
A transcriptome-based approach to identify functional modules within and across primary human immune cells. PMID:32469933
Ubiquitome analysis reveals the involvement of lysine ubiquitination in the spermatogenesis process of adult buffalo (Bubalus bubalis) testis. PMID:32469046
Population Genomic Analysis Reveals a Highly Conserved Mitochondrial Genome in Fusarium asiaticum. PMID:32431686
Deimination Protein Profiles in Alligator mississippiensis Reveal Plasma and Extracellular Vesicle-Specific Signatures Relating to Immunity, Metabolic Function, and Gene Regulation. PMID:32411128
Proteolysis of Gingival Keratinocyte Cell Surface Proteins by Gingipains Secreted From Porphyromonas gingivalis - Proteomic Insights Into Mechanisms Behind Tissue Damage in the Diseased Gingiva. PMID:32411104
An improved high-quality genome assembly and annotation of Tibetan hulless barley. PMID:32385314
Autographivirinae Bacteriophage Arno 160 Infects Pectobacterium carotovorum via Depolymerization of the Bacterial O-Polysaccharide. PMID:32365879
Impact of intestinal parasites on microbiota and cobalamin gene sequences: a pilot study. PMID:32306993
Gene silencing of Diaphorina citri candidate effectors promotes changes in feeding behaviors. PMID:32265528
The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution. PMID:32257231
Divergent Evolution of Legionella RCC1 Repeat Effectors Defines the Range of Ran GTPase Cycle Targets. PMID:32209684
De novo transcriptome of the diatom Cylindrotheca closterium identifies genes involved in the metabolism of anti-inflammatory compounds. PMID:32139778
The modular nature of protein evolution: domain rearrangement rates across eukaryotic life. PMID:32059645
The evolution of protein domain repertoires: Shedding light on the origins of the Herpesviridae family. PMID:32042448
Morphologically Different Pectobacterium brasiliense Bacteriophages PP99 and PP101: Deacetylation of O-Polysaccharide by the Tail Spike Protein of Phage PP99 Accompanies the Infection. PMID:32038580
Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization. PMID:32024005
Whole Genome Sequencing and Assembly of the Asian Honey Bee Apis dorsata. PMID:31860080
Systematic analysis of linker histone PTM hotspots reveals phosphorylation sites that modulate homologous recombination and DSB repair. PMID:31821952
HeteroDualNet: A Dual Convolutional Neural Network With Heterogeneous Layers for Drug-Disease Association Prediction via Chou's Five-Step Rule. PMID:31780934
TGFB1-Mediated Gliosis in Multiple Sclerosis Spinal Cords Is Favored by the Regionalized Expression of HOXA5 and the Age-Dependent Decline in Androgen Receptor Ligands. PMID:31779094
Proximal tubule cyclophilin D regulates fatty acid oxidation in cisplatin-induced acute kidney injury. PMID:31733829
Time-coursed transcriptome analysis identifies key expressional regulation in growth cessation and dormancy induced by short days in Paulownia. PMID:31719639
Armadillo-like helical domain containing-4 is dynamically expressed in both the first and second heart fields. PMID:31655130
Genomic Basis of Convergent Island Phenotypes in Boa Constrictors. PMID:31642474
Genomic Analyses Provide Insights Into the Evolutionary History and Genetic Diversity of Auricularia Species. PMID:31632371
Light-Regulation of Tryptophan Synthase by Combining Protein Design and Enzymology. PMID:31618845
A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae. PMID:31579586
Characterization of Vibrio cholerae's Extracellular Nuclease Xds. PMID:31551990
Reference gene and small RNA data from multiple tissues of Davidia involucrata Baill. PMID:31551451
Genome-wide identification and characterization of the Hsp70 gene family in allopolyploid rapeseed (Brassica napus L.) compared with its diploid progenitors. PMID:31497395
Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing of Spirodela. PMID:31484765
Bioinformatic and Molecular Analysis of Inverse Autotransporters from Escherichia coli. PMID:31462414
Identification of histone methylation modifiers and their expression patterns during somatic embryogenesis in Hevea brasiliensis. PMID:31441928
Collection of antimicrobial peptides database and its derivatives: Applications and beyond. PMID:31441165
Computational and experimental elucidation of Plasmodium falciparum phosphoethanolamine methyltransferase inhibitors: Pivotal drug target. PMID:31437171
Why do eukaryotic proteins contain more intrinsically disordered regions? PMID:31329574
Structural and Functional Characterization of YdjI, an Aldolase of Unknown Specificity in Escherichia coli K12. PMID:31322866
Functional Characterization of YdjH, a Sugar Kinase of Unknown Specificity in Escherichia coli K12. PMID:31314509
Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda. PMID:31220115
CAPRI enables comparison of evolutionarily conserved RNA interacting regions. PMID:31213602
SpinachBase: a central portal for spinach genomics. PMID:31211398
Laying the foundation for genomically-based risk assessment in chronic myeloid leukemia. PMID:31209280
Combining learning and constraints for genome-wide protein annotation. PMID:31208327
Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution. PMID:31206013
Modeling post-translational modifications and cancer-associated mutations that impact the heterochromatin protein 1α-importin α heterodimers. PMID:31152607
A novel thermostable and halophilic thioredoxin reductase from the Red Sea Atlantis II hot brine pool. PMID:31150456
Genome Analysis of Hypomyces perniciosus, the Causal Agent of Wet Bubble Disease of Button Mushroom (Agaricus bisporus). PMID:31146507
Genome-Wide Identification of the LAC Gene Family and Its Expression Analysis Under Stress in Brassica napus. PMID:31126120
Methanogenesis marker protein 10 (Mmp10) from Methanosarcina acetivorans is a radical S-adenosylmethionine methylase that unexpectedly requires cobalamin. PMID:31113866
Pathway-specific protein domains are predictive for human diseases. PMID:31075101
Characterization and Transcriptome Studies of Autoinducer Synthase Gene from Multidrug Resistant Acinetobacter baumannii Strain 863. PMID:30965610
Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch). PMID:30953568
Phytoplasma-induced Changes in the Acetylome and Succinylome of Paulownia tomentosa Provide Evidence for Involvement of Acetylated Proteins in Witches' Broom Disease. PMID:30936209
Local Diversification of Methicillin- Resistant Staphylococcus aureus ST239 in South America After Its Rapid Worldwide Dissemination. PMID:30873127
Transposable elements contribute to fungal genes and impact fungal lifestyle. PMID:30867521
Differential Gene Expression Supports a Resource-Intensive, Defensive Role for Colony Production in the Bloom-Forming Haptophyte, Phaeocystis globosa. PMID:30860641
Genome-Wide Associations of Chlorophyll Fluorescence OJIP Transient Parameters Connected With Soil Drought Response in Barley. PMID:30828338
Tetrahymena Comparative Genomics Database (TCGD): a community resource for Tetrahymena. PMID:30810209
PamulDB: a comprehensive genomic resource for the study of human- and animal-pathogenic Pasteurella multocida. PMID:30799499
Sphingolipid-dependent Dscam sorting regulates axon segregation. PMID:30778062
Plasmodium palmitoylation machinery engineered in E. coli for high-throughput screening of palmitoyl acyl-transferase inhibitors. PMID:30761251
Messages From the Past: New Insights in Plant Lectin Evolution. PMID:30761173
A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems. PMID:30759970
Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member. PMID:30755506
Genome Sequencing of Cladobotryum protrusum Provides Insights into the Evolution and Pathogenic Mechanisms of the Cobweb Disease Pathogen on Cultivated Mushroom. PMID:30744046
The toxic guardians - multiple toxin-antitoxin systems provide stability, avoid deletions and maintain virulence genes of Pseudomonas syringae virulence plasmids. PMID:30728866
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
Genetic and clinical markers for predicting treatment responsiveness in rheumatoid arthritis. PMID:30635780
Biochemical Characterization and Phylogenetic Analysis of the Virulence Factor Lysine Decarboxylase From Vibrio vulnificus. PMID:30619163
First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes. PMID:30588394
Vertebrate SLRP family evolution and the subfunctionalization of osteoglycin gene duplicates in teleost fish. PMID:30545285
A scalable peptide-GPCR language for engineering multicellular communication. PMID:30498215
Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine. PMID:30497367
From sequencing data to gene functions: co-functional network approaches. PMID:30460054
Computational discovery of direct associations between GO terms and protein domains. PMID:30453875
Genome-Wide Characterization of the sHsp Gene Family in Salix suchowensis Reveals Its Functions under Different Abiotic Stresses. PMID:30347736
REBELOTE, a regulator of floral determinacy in Arabidopsis thaliana, interacts with both nucleolar and nucleoplasmic proteins. PMID:30338215
Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. PMID:30321383
Network Analysis of RAD51 Proteins in Metazoa and the Evolutionary Relationships With Their Archaeal Homologs. PMID:30319685
The Duality of the MAPK Signaling Pathway in the Control of Metabolic Processes and Cellulase Production in Trichoderma reesei. PMID:30297963
Leukocyte Immunoglobulin-Like Receptors A2 and A6 are Expressed in Avian Macrophages and Modulate Cytokine Production by Activating Multiple Signaling Pathways. PMID:30208630
Genomic characterization of Trichoderma atrobrunneum (T. harzianum species complex) ITEM 908: insight into the genetic endowment of a multi-target biocontrol strain. PMID:30200883
BAMLET kills chemotherapy-resistant mesothelioma cells, holding oleic acid in an activated cytotoxic state. PMID:30157247
A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling. PMID:30153857
Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation. PMID:30143032
Approaches to target tractability assessment - a practical perspective. PMID:30108951
Assessing Human Genetic Variations in Glucose Transporter SLC2A10 and Their Role in Altering Structural and Functional Properties. PMID:30090112
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
Pectobacterium atrosepticum Phage vB_PatP_CB5: A Member of the Proposed Genus 'Phimunavirus'. PMID:30050020
Calcium-binding proteins that are type B″ regulatory subunits of phosphatase 2A in Giardia intestinalis. PMID:30043281
TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. PMID:30032202
Network-based genetic investigation of virulence-associated phenotypes in methicillin-resistant Staphylococcus aureus. PMID:30018396
Genome-Wide Characterization and Expression Analyses of Pleurotus ostreatus MYB Transcription Factors during Developmental Stages and under Heat Stress Based on de novo Sequenced Genome. PMID:30011913
A Pathogen-Responsive Leucine Rich Receptor Like Kinase Contributes to Fusarium Resistance in Cereals. PMID:29997638
Identification and Characterization of a Novel Palmitoyl Acyltransferase as a Druggable Rheostat of Dynamic Palmitoylome in L. donovani. PMID:29977865
Gene prioritization using Bayesian matrix factorization with genomic and phenotypic side information. PMID:29949967
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. PMID:29931155
Phylogeny of dermatophytes with genomic character evaluation of clinically distinct Trichophyton rubrum and T. violaceum. PMID:29910521
Calculating the statistical significance of rare variants causal for Mendelian and complex disorders. PMID:29898714
The Human Virome Protein Cluster Database (HVPC): A Human Viral Metagenomic Database for Diversity and Function Annotation. PMID:29896176
Microcystin-LR-Triggered Neuronal Toxicity in Whitefish Does Not Involve MiR124-3p. PMID:29882005
The evolution of genomic and epigenomic features in two Pleurotus fungi. PMID:29844491
Revalidation and genetic characterization of new members of Group C (Orthobunyavirus genus, Peribunyaviridae family) isolated in the Americas. PMID:29795585
FAM188B enhances cell survival via interaction with USP7. PMID:29795372
Putative vaccine candidates and drug targets identified by reverse vaccinology and subtractive genomics approaches to control Haemophilus ducreyi, the causative agent of chancroid. PMID:29792307
Molecular modularity and asymmetry of the molluscan mantle revealed by a gene expression atlas. PMID:29788257
Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes. PMID:29761466
Novel N4-Like Bacteriophages of Pectobacterium atrosepticum. PMID:29757952
Longevity and transposon defense, the case of termite reproductives. PMID:29735660
Comparison of Staphylococcus Phage K with Close Phage Relatives Commonly Employed in Phage Therapeutics. PMID:29693603
MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs. PMID:29678199
Whole Genome Sequence of an Edible and Potential Medicinal Fungus, Cordyceps guangdongensis. PMID:29666196
Classification and phylogenetic analyses of the Arabidopsis and tomato G-type lectin receptor kinases. PMID:29625550
The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites. PMID:29590215
Homology modeling and epitope prediction of Der f 33. PMID:29561952
Environmental Metagenomic Assemblies Reveal Seven New Highly Divergent Chlamydial Lineages and Hallmarks of a Conserved Intracellular Lifestyle. PMID:29515524
On Burkholderiales order microorganisms and cystic fibrosis in Russia. PMID:29504898
Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals. PMID:29500236
Mapping of a Major QTL for Ceratocystis Wilt Disease in an F1 Population of Theobroma cacao. PMID:29491879
The End of a 60-year Riddle: Identification and Genomic Characterization of an Iridovirus, the Causative Agent of White Fat Cell Disease in Zooplankton. PMID:29487186
Cooption of heat shock regulatory system for anhydrobiosis in the sleeping chironomid Polypedilum vanderplanki. PMID:29463761
A putative RNA binding protein from Plasmodium vivax apicoplast. PMID:29435408
Novel global effector mining from the transcriptome of early life stages of the soybean cyst nematode Heterodera glycines. PMID:29410430
In silico analysis of the EF-hand proteins in the genome of Giardia intestinalis assembly A. PMID:29404745
Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation. PMID:29390084
The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology. PMID:29376823
Comparative Genomics Reveals Accelerated Evolution in Conserved Pathways during the Diversification of Anole Lizards. PMID:29360978
EOGD: the Euplotes octocarinatus genome database. PMID:29351734
A chelicerate-specific burst of nonclassical Dscam diversity. PMID:29351731
Discovery of Culex pipiens associated tunisia virus: a new ssRNA(+) virus representing a new insect associated virus family. PMID:29340209
A-GAME: improving the assembly of pooled functional metagenomics sequence data. PMID:29329522
Integrative View of the Diversity and Evolution of SWEET and SemiSWEET Sugar Transporters. PMID:29326750
Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio. PMID:29319806
Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species. PMID:29317534
Genomics of Clostridium taeniosporum, an organism which forms endospores with ribbon-like appendages. PMID:29293521
The pomegranate (Punica granatum L.) genome provides insights into fruit quality and ovule developmental biology. PMID:29271050
HN1L Promotes Triple-Negative Breast Cancer Stem Cells through LEPR-STAT3 Pathway. PMID:29249663
Surface pH changes suggest a role for H+/OH- channels in salinity response of Chara australis. PMID:29247277
First steps in automatic summarization of transcription factor properties for RegulonDB: classification of sentences about structural domains and regulated processes. PMID:29220462
Characterization of Fusobacterium varium Fv113-g1 isolated from a patient with ulcerative colitis based on complete genome sequence and transcriptome analysis. PMID:29216329
Transcriptome Sequencing Reveals Novel Candidate Genes for Cardinium hertigii-Caused Cytoplasmic Incompatibility and Host-Cell Interaction. PMID:29181449
Rama: a machine learning approach for ribosomal protein prediction in plants. PMID:29176736
Identification and analysis of seven effector protein families with different adaptive and evolutionary histories in plant-associated members of the Xanthomonadaceae. PMID:29170530
Cloning and Molecular Characterization of an Alpha-Glucosidase (MalH) from the Halophilic Archaeon Haloquadratum walsbyi. PMID:29160840
The Swinholide Biosynthesis Gene Cluster from a Terrestrial Cyanobacterium, Nostoc sp. Strain UHCC 0450. PMID:29150506
GyrI-like proteins catalyze cyclopropanoid hydrolysis to confer cellular protection. PMID:29133784
Structural and functional analysis of coral Hypoxia Inducible Factor. PMID:29117182
Identification and characterization of LysM effectors in Penicillium expansum. PMID:29084256
Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins. PMID:29083303
A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters. PMID:29079755
Field Synopsis and Re-analysis of Systematic Meta-analyses of Genetic Association Studies in Multiple Sclerosis: a Bayesian Approach. PMID:29027112
Carbohydrate-active enzymes in Trichoderma harzianum: a bioinformatic analysis bioprospecting for key enzymes for the biofuels industry. PMID:29025413
Transcriptomic changes in Echinochloa colona in response to treatment with the herbicide imazamox. PMID:29022094
Finding the genetic mechanisms of folate deficiency and neural tube defects-Leaving no stone unturned. PMID:28944587
Proteomic Analysis of Phytophthora infestans Reveals the Importance of Cell Wall Proteins in Pathogenicity. PMID:28935716
Insights into DDT Resistance from the Drosophila melanogaster Genetic Reference Panel. PMID:28935691
Mitochondrial genomes reveal recombination in the presumed asexual Fusarium oxysporum species complex. PMID:28923029
YeeJ is an inverse autotransporter from Escherichia coli that binds to peptidoglycan and promotes biofilm formation. PMID:28900103
p190RhoGAP proteins contain pseudoGTPase domains. PMID:28894085
Evidence-based gene models for structural and functional annotations of the oil palm genome. PMID:28886750
Halotolerant aminopeptidase M29 from Mesorhizobium SEMIA 3007 with biotechnological potential and its impact on biofilm synthesis. PMID:28878230
Protein-Protein Interactions in Virus-Host Systems. PMID:28861068
Role of SH3b binding domain in a natural deletion mutant of Kayvirus endolysin LysF1 with a broad range of lytic activity. PMID:28852930
Complete Genome sequence of the nematicidal Bacillus thuringiensis MYBT18246. PMID:28852435
RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes. PMID:28850115
Taxonomically Restricted Genes with Essential Functions Frequently Play Roles in Chromosome Segregation in Caenorhabditis elegans and Saccharomyces cerevisiae. PMID:28839119
A mobile pathogenicity chromosome in Fusarium oxysporum for infection of multiple cucurbit species. PMID:28831051
Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato. PMID:28819320
Structure of a 1.5-MDa adhesin that binds its Antarctic bacterium to diatoms and ice. PMID:28808685
Reduction of Mosquito Survival in Mice Vaccinated with Anopheles stephensi Glucose Transporter. PMID:28804714
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
OsbZIP48, a HY5 Transcription Factor Ortholog, Exerts Pleiotropic Effects in Light-Regulated Development. PMID:28775143
Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea. PMID:28765215
PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection. PMID:28761071
Rapid evolution of female-biased genes among four species of Anopheles malaria mosquitoes. PMID:28747381
Oxidative Stress Response Tips the Balance in Aspergillus terreus Amphotericin B Resistance. PMID:28739793
Anion-selective Formate/nitrite transporters: taxonomic distribution, phylogenetic analysis and subfamily-specific conservation pattern in prokaryotes. PMID:28738779
Biological iron-sulfur storage in a thioferrate-protein nanoparticle. PMID:28726794
Dynamics of genomic innovation in the unicellular ancestry of animals. PMID:28726632
Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica. PMID:28725468
Random mutagenesis analysis and identification of a novel C2H2-type transcription factor from the nematode-trapping fungus Arthrobotrys oligospora. PMID:28717216
A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria. PMID:28696203
Molecular adaptation to high pressure in cytochrome P450 1A and aryl hydrocarbon receptor systems of the deep-sea fish Coryphaenoides armatus. PMID:28694077
Evolution, gene expression profiling and 3D modeling of CSLD proteins in cotton. PMID:28693426
Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum. PMID:28662642
A Quantitative Acetylomic Analysis of Early Seed Development in Rice (Oryza sativa L.). PMID:28654018
Evolution of immune chemoreceptors into sensors of the outside world. PMID:28652375
Analysis of the ZAR1 Immune Complex Reveals Determinants for Immunity and Molecular Interactions. PMID:28652264
Unexpected Dominance of Elusive Acidobacteria in Early Industrial Soft Coal Slags. PMID:28642744
Proteomic Analysis of Trichinella spiralis Adult Worm Excretory-Secretory Proteins Recognized by Sera of Patients with Early Trichinellosis. PMID:28620363
Novel regulatory mechanism of serine biosynthesis associated with 3-phosphoglycerate dehydrogenase in Arabidopsis thaliana. PMID:28615699
Global proteomic analysis of advanced glycation end products in the Arabidopsis proteome provides evidence for age-related glycation hot spots. PMID:28611063
CHOmine: an integrated data warehouse for CHO systems biology and modeling. PMID:28605771
Coupled Caspase and N-End Rule Ligase Activities Allow Recognition and Degradation of Pluripotency Factor LIN-28 during Non-Apoptotic Development. PMID:28602583
Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes. PMID:28594822
Loci Contributing to Boric Acid Toxicity in Two Reference Populations of Drosophila melanogaster. PMID:28592646
Plasmobase: a comparative database of predicted domain architectures for Plasmodium genomes. PMID:28592293
Evolutionary relationships and expression analysis of EUL domain proteins in rice (Oryza sativa). PMID:28560587
Comparative transcriptomic analysis indicates genes associated with local and systemic resistance to Colletotrichum graminicola in maize. PMID:28559543
Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study. PMID:28549454
AGeNNT: annotation of enzyme families by means of refined neighborhood networks. PMID:28545394
Malonate degradation in Acinetobacter baylyi ADP1: operon organization and regulation by MdcR. PMID:28537542
A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing. PMID:28532419
In silico approach to designing rational metagenomic libraries for functional studies. PMID:28532384
A widespread family of serine/threonine protein phosphatases shares a common regulatory switch with proteasomal proteases. PMID:28527238
The Whole-Genome and Transcriptome of the Manila Clam (Ruditapes philippinarum). PMID:28505302
Proteomic responses to elevated ocean temperature in ovaries of the ascidian Ciona intestinalis. PMID:28500033
Discovery of Novel Leptospirosis Vaccine Candidates Using Reverse and Structural Vaccinology. PMID:28496441
Bioinformatic and expression analysis of the Brassica napus L. cyclophilins. PMID:28473712
WebGIVI: a web-based gene enrichment analysis and visualization tool. PMID:28472919
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
Accumulation and expression of multiple antibiotic resistance genes in Arcobacter cryaerophilus that thrives in sewage. PMID:28462059
The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression. PMID:28459453
Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance. PMID:28454557
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
Identification of MicroRNA Targets of Capsicum spp. Using MiRTrans-a Trans-Omics Approach. PMID:28443105
The identification of protein domains that mediate functional interactions between Rab-GTPases and RabGAPs using 3D protein modeling. PMID:28435300
Comparative transcriptomics of mountain pine beetle pheromone-biosynthetic tissues and functional analysis of CYP6DE3. PMID:28427347
Mroh1, a lysosomal regulator localized by WASH-generated actin. PMID:28424231
Inbreeding and selection shape genomic diversity in captive populations: Implications for the conservation of endangered species. PMID:28423000
Identification of protein features encoded by alternative exons using Exon Ontology. PMID:28420690
Detection of COPB2 as a KRAS synthetic lethal partner through integration of functional genomics screens. PMID:28415695
Concurrent Haloalkanoate Degradation and Chlorate Reduction by Pseudomonas chloritidismutans AW-1T. PMID:28411224
The elusive MAESTRO gene: Its human reproductive tissue-specific expression pattern. PMID:28406912
Staphylococcus sciuri bacteriophages double-convert for staphylokinase and phospholipase, mediate interspecies plasmid transduction, and package mecA gene. PMID:28406168
Adaptation and evolution of deep-sea scale worms (Annelida: Polynoidae): insights from transcriptome comparison with a shallow-water species. PMID:28397791
Expression and function of ATP-dependent potassium channels in zebrafish islet β-cells. PMID:28386438
Comparative Genomics Analysis of a New Exiguobacterium Strain from Salar de Huasco Reveals a Repertoire of Stress-Related Genes and Arsenic Resistance. PMID:28377753
Biocuration in the structure-function linkage database: the anatomy of a superfamily. PMID:28365730
SilkPathDB: a comprehensive resource for the study of silkworm pathogens. PMID:28365723
Identification and evolution of a plant cell wall specific glycoprotein glycosyl transferase, ExAD. PMID:28358137
Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data. PMID:28348874
Exploring the genomic diversity of black yeasts and relatives (Chaetothyriales, Ascomycota). PMID:28348446
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
Transcriptome analysis of molecular mechanisms responsible for light-stress response in Mythimna separata (Walker). PMID:28345615
APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins. PMID:28334975
Single Cell Transcriptomics, Mega-Phylogeny, and the Genetic Basis of Morphological Innovations in Rhizaria. PMID:28333264
The Transcriptome of the Zebrafish Embryo After Chemical Exposure: A Meta-Analysis. PMID:28329862
Revised domain structure of ulvan lyase and characterization of the first ulvan binding domain. PMID:28327560
A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data. PMID:28321234
Recurrent rewiring and emergence of RNA regulatory networks. PMID:28320951
Toxoplasma gondii AP2IX-4 Regulates Gene Expression during Bradyzoite Development. PMID:28317026
Phylogenetic analysis of proteins involved in the stringent response in plant cells. PMID:28303404
Draft Genome Sequence of Endophytic Herbaspirillum sp. Strain WT00C, a Tea Plant Growth-Promoting Bacterium. PMID:28302787
Systematic protein-protein interaction mapping for clinically relevant human GPCRs. PMID:28298427
New insights into the operative network of FaEO, an enone oxidoreductase from Fragaria x ananassa Duch. PMID:28283921
Identification of constraints influencing the bacterial genomes evolution in the PVC super-phylum. PMID:28274202
Identifying protein kinase-specific effectors of the osmostress response in yeast. PMID:28270554
Prediction of GCRV virus-host protein interactome based on structural motif-domain interactions. PMID:28253857
Plasmid Replicons from Pseudomonas Are Natural Chimeras of Functional, Exchangeable Modules. PMID:28243228
A three-way approach for protein function classification. PMID:28234929
Characterization of Carbonic Anhydrase 9 in the Alimentary Canal of Aedes aegypti and Its Relationship to Homologous Mosquito Carbonic Anhydrases. PMID:28230813
The Escherichia coli Serogroup O1 and O2 Lipopolysaccharides Are Encoded by Multiple O-antigen Gene Clusters. PMID:28224115
An In Silico Identification of Common Putative Vaccine Candidates against Treponema pallidum: A Reverse Vaccinology and Subtractive Genomics Based Approach. PMID:28216574
Functional Characterization of a 28-Kilobase Catabolic Island from Pseudomonas sp. Strain M1 Involved in Biotransformation of β-Myrcene and Related Plant-Derived Volatiles. PMID:28213543
A familial study of azoospermic men identifies three novel causative mutations in three new human azoospermia genes. PMID:28206990
Integrated genomic analyses of de novo pathways underlying atypical meningiomas. PMID:28195122
ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains. PMID:28193156
Clathrin in Chara australis: Molecular Analysis and Involvement in Charasome Degradation and Constitutive Endocytosis. PMID:28184226
A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline. PMID:28183913
The complex evolutionary history of aminoacyl-tRNA synthetases. PMID:28180287
Genome-Wide Identification and Characterization of SPX Domain-Containing Members and Their Responses to Phosphate Deficiency in Brassica napus. PMID:28179909
Asparagine-Linked Glycans of Cryptosporidium parvum Contain a Single Long Arm, Are Barely Processed in the Endoplasmic Reticulum (ER) or Golgi, and Show a Strong Bias for Sites with Threonine. PMID:28179475
Large-scale bioactivity analysis of the small-molecule assayed proteome. PMID:28178331
Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB. PMID:28174560
From the research laboratory to the database: the Caenorhabditis elegans kinome in UniProtKB. PMID:28159896
Reverse Methanogenesis and Respiration in Methanotrophic Archaea. PMID:28154498
Protein Bioinformatics Databases and Resources. PMID:28150231
Bacillus thuringiensis and Bacillus weihenstephanensis Inhibit the Growth of Phytopathogenic Verticillium Species. PMID:28149292
Lausannevirus Encodes a Functional Dihydrofolate Reductase Susceptible to Proguanil. PMID:28137801
Exploring the dark foldable proteome by considering hydrophobic amino acids topology. PMID:28134276
Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads. PMID:28122610
Effects of temperature on transcriptome and cuticular hydrocarbon expression in ecologically differentiated populations of desert Drosophila. PMID:28116058
Independent active and thermodynamic processes govern the nucleolus assembly in vivo. PMID:28115706
Mosaic structure of Mycobacterium bovis BCG genomes as a representation of phage sequences' mobility. PMID:28105923
MarpoDB: An Open Registry for Marchantia Polymorpha Genetic Parts. PMID:28100647
The expression of hypoxia-inducible factor-1α gene is not affected by low-oxygen conditions in yellow perch (Perca flavescens) juveniles. PMID:28097495
Rpn (YhgA-Like) Proteins of Escherichia coli K-12 and Their Contribution to RecA-Independent Horizontal Transfer. PMID:28096446
Recognition of protein-linked glycans as a determinant of peptidase activity. PMID:28096352
Evolution and structural diversification of Nictaba-like lectin genes in food crops with a focus on soybean (Glycine max). PMID:28087663
155R is a novel structural protein of bovine adenovirus type 3, but it is not essential for virus replication. PMID:28086071
The Conservation of the Germline Multipotency Program, from Sponges to Vertebrates: A Stepping Stone to Understanding the Somatic and Germline Origins. PMID:28082608
Phylogenetic analysis of ionotropic L-glutamate receptor genes in the Bilateria, with special notes on Aplysia californica. PMID:28077092
Burkholderia contaminans Biofilm Regulating Operon and Its Distribution in Bacterial Genomes. PMID:28070515
Fuerstia marisgermanicae gen. nov., sp. nov., an Unusual Member of the Phylum Planctomycetes from the German Wadden Sea. PMID:28066393
Plant genome and transcriptome annotations: from misconceptions to simple solutions. PMID:28062412
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
PDLIM5 links kidney anion exchanger 1 (kAE1) to ILK and is required for membrane targeting of kAE1. PMID:28045035
Evolution of Chemosensory Gene Families in Arthropods: Insight from the First Inclusive Comparative Transcriptome Analysis across Spider Appendages. PMID:28028122
The Mutational Landscape of the Oncogenic MZF1 SCAN Domain in Cancer. PMID:28018905
Developing integrated crop knowledge networks to advance candidate gene discovery. PMID:28018846
Novel thermostable antibiotic resistance enzymes from the Atlantis II Deep Red Sea brine pool. PMID:28004885
A Data Fusion Approach to Enhance Association Study in Epilepsy. PMID:27984588
Disentangling the influence of earthworms in sugarcane rhizosphere. PMID:27976685
The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance. PMID:27974049
Modeling Rice Metabolism: From Elucidating Environmental Effects on Cellular Phenotype to Guiding Crop Improvement. PMID:27965696
The Use of Peptide Markers of Carp and Herring Allergens as an Example of Detection of Sequenced and Non-Sequenced Proteins. PMID:27956857
Insecticidal Activity of Melaleuca alternifolia Essential Oil and RNA-Seq Analysis of Sitophilus zeamais Transcriptome in Response to Oil Fumigation. PMID:27936192
Functional and structural characterization of a novel putative cysteine protease cell wall-modifying multi-domain enzyme selected from a microbial metagenome. PMID:27934875
Exploring FlyBase Data Using QuickSearch. PMID:27930807
Analysis of Domain Architecture and Phylogenetics of Family 2 Glycoside Hydrolases (GH2). PMID:27930742
The comparative landscape of duplications in Heliconius melpomene and Heliconius cydno. PMID:27925618
The Streptococcus gordonii Adhesin CshA Protein Binds Host Fibronectin via a Catch-Clamp Mechanism. PMID:27920201
Sponge Microbiota Are a Reservoir of Functional Antibiotic Resistance Genes. PMID:27909433
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
UniProt: the universal protein knowledgebase. PMID:27899622
PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements. PMID:27899595
Expansion of the Gene Ontology knowledgebase and resources. PMID:27899567
WormBase ParaSite - a comprehensive resource for helminth genomics. PMID:27899279
Multigene phylogenetic analysis redefines dung beetles relationships and classification (Coleoptera: Scarabaeidae: Scarabaeinae). PMID:27899070
Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction. PMID:27895706
Genome-Wide Identification and Expression Analysis of the Tubby-Like Protein Family in the Malus domestica Genome. PMID:27895653
Characterization of the Pathogenicity of Streptococcus intermedius TYG1620 Isolated from a Human Brain Abscess Based on the Complete Genome Sequence with Transcriptome Analysis and Transposon Mutagenesis in a Murine Subcutaneous Abscess Model. PMID:27895128
Rice Cellulose SynthaseA8 Plant-Conserved Region Is a Coiled-Coil at the Catalytic Core Entrance. PMID:27879387
Draft genome of the living fossil Ginkgo biloba. PMID:27871309
De-novo protein function prediction using DNA binding and RNA binding proteins as a test case. PMID:27869118
Draft Genome Sequence of Curtobacterium sp. Strain ER1/6, an Endophytic Strain Isolated from Citrus sinensis with Potential To Be Used as a Biocontrol Agent. PMID:27856581
A New Chicken Genome Assembly Provides Insight into Avian Genome Structure. PMID:27852011
Membrane Proteomic Insights into the Physiology and Taxonomy of an Oleaginous Green Microalga. PMID:27837088
DASP3: identification of protein sequences belonging to functionally relevant groups. PMID:27835946
Ten Simple Rules for Developing Public Biological Databases. PMID:27832061
Discovery and Partial Genomic Characterisation of a Novel Nidovirus Associated with Respiratory Disease in Wild Shingleback Lizards (Tiliqua rugosa). PMID:27828982
Evaluating Functional Annotations of Enzymes Using the Gene Ontology. PMID:27812939
Exploring Human Diseases and Biological Mechanisms by Protein Structure Prediction and Modeling. PMID:27807743
FlyBase at 25: looking to the future. PMID:27799470
Global Dynamic Proteome Study of a Pellicle-forming Acinetobacter baumannii Strain. PMID:27799293
Sequence-Based Prediction of RNA-Binding Residues in Proteins. PMID:27787829
Genomic skimming for identification of medium/highly abundant transposable elements in Arundo donax and Arundo plinii. PMID:27778102
Identification of Genes Involved in Indole-3-Acetic Acid Biosynthesis by Gluconacetobacter diazotrophicus PAL5 Strain Using Transposon Mutagenesis. PMID:27774087
Genome evolution in the allotetraploid frog Xenopus laevis. PMID:27762356
Metagenomic survey of methanesulfonic acid (MSA) catabolic genes in an Atlantic Ocean surface water sample and in a partial enrichment. PMID:27761315
Gold Nanoparticle Reprograms Pancreatic Tumor Microenvironment and Inhibits Tumor Growth. PMID:27758098
Matching the Diversity of Sulfated Biomolecules: Creation of a Classification Database for Sulfatases Reflecting Their Substrate Specificity. PMID:27749924
Ancient recombination events and the origins of hepatitis E virus. PMID:27733122
Phylotype Dynamics of Bacterial P Utilization Genes in Microbialites and Bacterioplankton of a Monomictic Endorheic Lake. PMID:27726035
PG1058 Is a Novel Multidomain Protein Component of the Bacterial Type IX Secretion System. PMID:27711252
In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites. PMID:27698666
Genomic Survey of a Hyperparasitic Microsporidian Amphiamblys sp. (Metchnikovellidae). PMID:27694476
ASAP: a machine learning framework for local protein properties. PMID:27694209
Comparative genomic, transcriptomic and secretomic profiling of Penicillium oxalicum HP7-1 and its cellulase and xylanase hyper-producing mutant EU2106, and identification of two novel regulatory genes of cellulase and xylanase gene expression. PMID:27688806
Global transcriptional regulator TrmB family members in prokaryotes. PMID:27687225
Genome-wide identification of multifunctional laccase gene family in cotton (Gossypium spp.); expression and biochemical analysis during fiber development. PMID:27679939
Sex-Biased Transcriptome of Schistosoma mansoni: Host-Parasite Interaction, Genetic Determinants and Epigenetic Regulators Are Associated with Sexual Differentiation. PMID:27677173
Unveiling the functional diversity of the alpha/beta hydrolase superfamily in the plant kingdom. PMID:27662376
Zonula occludens toxins and their prophages in Campylobacter species. PMID:27651834
Novel Methyltransferase Recognition Motif Identified in Chania multitudinisentens RB-25(T) gen. nov., sp. nov. PMID:27630623
Functional Annotations of Paralogs: A Blessing and a Curse. PMID:27618105
Structural basis of haem-iron acquisition by fungal pathogens. PMID:27617569
The genomes of three North American orthopoxviruses. PMID:27613417
Global Profiling of the Cellular Alternative RNA Splicing Landscape during Virus-Host Interactions. PMID:27598998
Dynamics of Human Mitochondrial Complex I Assembly: Implications for Neurodegenerative Diseases. PMID:27597947
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
The green ash transcriptome and identification of genes responding to abiotic and biotic stresses. PMID:27589953
SSH Analysis of Endosperm Transcripts and Characterization of Heat Stress Regulated Expressed Sequence Tags in Bread Wheat. PMID:27582756
Plasmodium Helical Interspersed Subtelomeric (PHIST) Proteins, at the Center of Host Cell Remodeling. PMID:27582258
Identification of Conidiogenesis-Associated Genes in Colletotrichum gloeosporioides by Agrobacterium tumefaciens-Mediated Transformation. PMID:27582094
Transcriptional Analysis of The Adaptive Digestive System of The Migratory Locust in Response to Plant Defensive Protease Inhibitors. PMID:27581362
Genome-wide analysis of lectin receptor-like kinases in Populus. PMID:27580945
Nucleotide binding by the widespread high-affinity cyclic di-GMP receptor MshEN domain. PMID:27578558
A new look at the LTR retrotransposon content of the chicken genome. PMID:27577548
Global phylogeography and evolutionary history of Shigella dysenteriae type 1. PMID:27572446
FFPred 3: feature-based function prediction for all Gene Ontology domains. PMID:27561554
An Eye on Trafficking Genes: Identification of Four Eye Color Mutations in Drosophila. PMID:27558665
Impact of LytR-CpsA-Psr Proteins on Cell Wall Biosynthesis in Corynebacterium glutamicum. PMID:27551018
Born blonde: a recessive loss-of-function mutation in the melanocortin 1 receptor is associated with cream coat coloration in Antarctic fur seals. PMID:27547348
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
Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. PMID:27535938
SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity. PMID:27525735
Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection. PMID:27515663
Transcriptomics of liver and muscle in Holstein cows genetically divergent for fertility highlight differences in nutrient partitioning and inflammation processes. PMID:27514375
Membranome: a database for proteome-wide analysis of single-pass membrane proteins. PMID:27510400
Flavoprotein-Mediated Tellurite Reduction: Structural Basis and Applications to the Synthesis of Tellurium-Containing Nanostructures. PMID:27507969
Cel5I, a SLH-Containing Glycoside Hydrolase: Characterization and Investigation on Its Role in Ruminiclostridium cellulolyticum. PMID:27501457
Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation. PMID:27500531
Metazoan evolution of the armadillo repeat superfamily. PMID:27497926
Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri. PMID:27474723
Validation of a multi-omics strategy for prioritizing personalized candidate driver genes. PMID:27469031
Gene-Environment Interactions in Stress Response Contribute Additively to a Genotype-Environment Interaction. PMID:27437938
Cdk3, a conjugation-specific cyclin-dependent kinase, is essential for the initiation of meiosis in Tetrahymena thermophila. PMID:27420775
Transcriptomics of Intralocus Sexual Conflict: Gene Expression Patterns in Females Change in Response to Selection on a Male Secondary Sexual Trait in the Bulb Mite. PMID:27401174
Expression and methylation patterns partition luminal-A breast tumors into distinct prognostic subgroups. PMID:27386846
Comparative expression study of sipa family members during early Xenopus laevis development. PMID:27384056
AcsF Catalyzes the ATP-dependent Insertion of Nickel into the Ni,Ni-[4Fe4S] Cluster of Acetyl-CoA Synthase. PMID:27382049
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
cis-Encoded Small RNAs, a Conserved Mechanism for Repression of Polysaccharide Utilization in Bacteroides. PMID:27353652
Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering. PMID:27348631
Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. PMID:27339440
Yeast two-hybrid screening identified WDR77 as a novel interacting partner of TSC22D2. PMID:27337956
Molecular Evolution of the Oxygen-Binding Hemerythrin Domain. PMID:27336621
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PMID:27327495
DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequences. PMID:27307636
Association of HLA class I and II genes with cutaneous leishmaniasis: a case control study from Sri Lanka and a systematic review. PMID:27301744
A proposed integrated approach for the preclinical evaluation of phage therapy in Pseudomonas infections. PMID:27301427
Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity. PMID:27272929
Analysis of the Microprocessor in Dictyostelium: The Role of RbdB, a dsRNA Binding Protein. PMID:27272207
Identification of differentially expressed genes from multipotent epithelia at the onset of an asexual development. PMID:27264734
Unusually Situated Binding Sites for Bacterial Transcription Factors Can Have Hidden Functionality. PMID:27258043
Benchmarking the next generation of homology inference tools. PMID:27256311
Computational recognition and analysis of hitherto uncharacterized nucleotide cyclase-like proteins in bacteria. PMID:27246835
EP300 Protects from Light-Induced Retinopathy in Zebrafish. PMID:27242532
Cloning, Expression and Biochemical Characterization of Endomannanases from Thermobifida Species Isolated from Different Niches. PMID:27223892
Weighted mutual information analysis substantially improves domain-based functional network models. PMID:27207946
Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities. PMID:27199908
Transcriptome-Wide Survey and Expression Profile Analysis of Putative Chrysanthemum HD-Zip I and II Genes. PMID:27196930
Heme pathway evolution in kinetoplastid protists. PMID:27193376
Cyc17, a meiosis-specific cyclin, is essential for anaphase initiation and chromosome segregation in Tetrahymena thermophila. PMID:27192402
Conserved Features in the Structure, Mechanism, and Biogenesis of the Inverse Autotransporter Protein Family. PMID:27190006
The Radical S-Adenosyl-l-methionine Enzyme MftC Catalyzes an Oxidative Decarboxylation of the C-Terminus of the MftA Peptide. PMID:27158836
UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB. PMID:27153729
TOPDOM: database of conservatively located domains and motifs in proteins. PMID:27153630
Complete genome sequence of an agr-dysfunctional variant of the ST239 lineage of the methicillin-resistant Staphylococcus aureus strain GV69 from Brazil. PMID:27152133
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. PMID:27131791
Candidate gene prioritization with Endeavour. PMID:27131783
Interrogating the Plasmodium Sporozoite Surface: Identification of Surface-Exposed Proteins and Demonstration of Glycosylation on CSP and TRAP by Mass Spectrometry-Based Proteomics. PMID:27128092
Role of Arabidopsis NHL family in ABA and stress response. PMID:27110948
AtWRKY22 promotes susceptibility to aphids and modulates salicylic acid and jasmonic acid signalling. PMID:27107291
Leveraging family-specific signatures for AMP discovery and high-throughput annotation. PMID:27089856
Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource. PMID:27087306
RhVI1 is a membrane-anchored vacuolar invertase highly expressed in Rosa hybrida L. petals. PMID:27083698
Caenorhabditis elegans PAQR-2 and IGLR-2 Protect against Glucose Toxicity by Modulating Membrane Lipid Composition. PMID:27082444
Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PMID:27082250
A large family of Dscam genes with tandemly arrayed 5' cassettes in Chelicerata. PMID:27080167
Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients. PMID:27068610
Tentacle Transcriptome and Venom Proteome of the Pacific Sea Nettle, Chrysaora fuscescens (Cnidaria: Scyphozoa). PMID:27058558
Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters. PMID:27058503
ATtRACT-a database of RNA-binding proteins and associated motifs. PMID:27055826
Topology based identification and comprehensive classification of four-transmembrane helix containing proteins (4TMs) in the human genome. PMID:27030248
Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms. PMID:27017967
Ligand-binding specificity and promiscuity of the main lignocellulolytic enzyme families as revealed by active-site architecture analysis. PMID:27009476
Biochemical and Spectroscopic Characterization of a Radical S-Adenosyl-L-methionine Enzyme Involved in the Formation of a Peptide Thioether Cross-Link. PMID:27007615
Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma. PMID:26997480
GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations. PMID:26994912
Application of a Mass Spectrometric Approach to Detect the Presence of Fatty Acid Biosynthetic Phosphopeptides. PMID:26993480
An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. PMID:26989145
Evolution of Pentameric Ligand-Gated Ion Channels: Pro-Loop Receptors. PMID:26986966
PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya. PMID:26980519
GenSeed-HMM: A Tool for Progressive Assembly Using Profile HMMs as Seeds and its Application in Alpavirinae Viral Discovery from Metagenomic Data. PMID:26973638
Isolation and Complete Genome Sequence of Algibacter alginolytica sp. nov., a Novel Seaweed-Degrading Bacteroidetes Bacterium with Diverse Putative Polysaccharide Utilization Loci. PMID:26969704
Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula. PMID:26964738
Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C4 grass. PMID:26953271
An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors. PMID:26938925
Functional and topological diversity of LOV domain photoreceptors. PMID:26929367
Venom gland transcriptome analyses of two freshwater stingrays (Myliobatiformes: Potamotrygonidae) from Brazil. PMID:26916342
Corrigendum: Can the Natural Diversity of Quorum-Sensing Advance Synthetic Biology? PMID:26913281
Structure-based Markov random field model for representing evolutionary constraints on functional sites. PMID:26911566
Understanding the Role of the Master Regulator XYR1 in Trichoderma reesei by Global Transcriptional Analysis. PMID:26909077
The handedness-associated PCSK6 locus spans an intronic promoter regulating novel transcripts. PMID:26908617
Diversity in Biosynthetic Pathways of Galactolipids in the Light of Endosymbiotic Origin of Chloroplasts. PMID:26904079
The Genetic Basis of Haploid Induction in Maize Identified with a Novel Genome-Wide Association Method. PMID:26896330
High frequency of +1 programmed ribosomal frameshifting in Euplotes octocarinatus. PMID:26891713
The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. PMID:26864432
In Silico Analysis of the Structural and Biochemical Features of the NMD Factor UPF1 in Ustilago maydis. PMID:26863136
Transcriptome-Wide Identification and Expression Profiling Analysis of Chrysanthemum Trihelix Transcription Factors. PMID:26848650
A review of the new HGNC gene family resource. PMID:26842383
Modulation of FAK and Src adhesion signaling occurs independently of adhesion complex composition. PMID:26833789
The genomic basis of parasitism in the Strongyloides clade of nematodes. PMID:26829753
Using the Gene Ontology to Annotate Key Players in Parkinson's Disease. PMID:26825309
Acylsugar Acylhydrolases: Carboxylesterase-Catalyzed Hydrolysis of Acylsugars in Tomato Trichomes. PMID:26811191
Effects of Halide Ions on the Carbamidocyclophane Biosynthesis in Nostoc sp. CAVN2. PMID:26805858
Comprehensive annotation of Glossina pallidipes salivary gland hypertrophy virus from Ethiopian tsetse flies: a proteogenomics approach. PMID:26801744
Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes. PMID:26793234
Circuits of cancer drivers revealed by convergent misregulation of transcription factor targets across tumor types. PMID:26792175
Dynamin-2 is a novel NOS1β interacting protein and negative regulator in the collecting duct. PMID:26791826
3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling. PMID:26772592
The LSH/DDM1 Homolog MUS-30 Is Required for Genome Stability, but Not for DNA Methylation in Neurospora crassa. PMID:26771905
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
Molecular cloning and expression analysis of KIN10 and cold-acclimation related genes in wild banana 'Huanxi' (Musa itinerans). PMID:26753116
Use of a Probabilistic Motif Search to Identify Histidine Phosphotransfer Domain-Containing Proteins. PMID:26751210
Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts. PMID:26746786
Genome-wide analysis of tomato NF-Y factors and their role in fruit ripening. PMID:26742635
Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry. PMID:26740739
Neuropeptidergic Signaling in the American Lobster Homarus americanus: New Insights from High-Throughput Nucleotide Sequencing. PMID:26716450
Evolutionary Transition of Promoter and Gene Body DNA Methylation across Invertebrate-Vertebrate Boundary. PMID:26715626
Proteomic profiling of maize opaque endosperm mutants reveals selective accumulation of lysine-enriched proteins. PMID:26712829
Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders. PMID:26690135
Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1. PMID:26689807
The Pfam protein families database: towards a more sustainable future. PMID:26673716
The European Bioinformatics Institute in 2016: Data growth and integration. PMID:26673705
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics. PMID:26656885
Genome-wide analysis of the basic leucine zipper (bZIP) transcription factor gene family in six legume genomes. PMID:26651343
Transcriptional cellular responses in midgut tissue of Aedes aegypti larvae following intoxication with Cry11Aa toxin from Bacillus thuringiensis. PMID:26645277
The Pangenome of the Anticarsia gemmatalis Multiple Nucleopolyhedrovirus (AgMNPV). PMID:26615220
ELM 2016--data update and new functionality of the eukaryotic linear motif resource. PMID:26615199
MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer. PMID:26590264
Lynx: a knowledge base and an analytical workbench for integrative medicine. PMID:26590263
The UCSC Genome Browser database: 2016 update. PMID:26590259
Arabidopsis Rab Geranylgeranyltransferases Demonstrate Redundancy and Broad Substrate Specificity in Vitro. PMID:26589801
EBI metagenomics in 2016--an expanding and evolving resource for the analysis and archiving of metagenomic data. PMID:26582919
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
Ensembl Genomes 2016: more genomes, more complexity. PMID:26578574
PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with PolyCystic Ovary Syndrome. PMID:26578565
Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. PMID:26578564
LegumeIP 2.0--a platform for the study of gene function and genome evolution in legumes. PMID:26578557
The Transporter Classification Database (TCDB): recent advances. PMID:26546518
Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family. PMID:26546515
Comparison of Xenorhabdus bovienii bacterial strain genomes reveals diversity in symbiotic functions. PMID:26525894
Structural Insights into Separase Architecture and Substrate Recognition through Computational Modelling of Caspase-Like and Death Domains. PMID:26513470
Genome-wide identification and characterization of the apple (Malus domestica) HECT ubiquitin-protein ligase family and expression analysis of their responsiveness to abiotic stresses. PMID:26510744
RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource. PMID:26500754
A Glimpse to Background and Characteristics of Major Molecular Biological Networks. PMID:26491677
Protein Analysis of Sapienic Acid-Treated Porphyromonas gingivalis Suggests Differential Regulation of Multiple Metabolic Pathways. PMID:26483519
Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. PMID:26481361
DIDA: A curated and annotated digenic diseases database. PMID:26481352
Definition of a consensus integrin adhesome and its dynamics during adhesion complex assembly and disassembly. PMID:26479319
PhytoPath: an integrative resource for plant pathogen genomics. PMID:26476449
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. PMID:26476444
CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides. PMID:26467475
Homeodomain proteins: an update. PMID:26464018
Indexing a protein-protein interaction network expedites network alignment. PMID:26453444
Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses. PMID:26452555
The language of the protein universe. PMID:26451980
An Ancient Yeast for Young Geneticists: A Primer on the Schizosaccharomyces pombe Model System. PMID:26447128
MitoMiner v3.1, an update on the mitochondrial proteomics database. PMID:26432830
ANISEED 2015: a digital framework for the comparative developmental biology of ascidians. PMID:26420834
Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery. PMID:26420781
Genome analysis of quorum sensing Cedecea neteri SSMD04 leads to identification of its novel signaling synthase (cneI), cognate receptor (cneR) and an orphan receptor. PMID:26355540
Novel genetic causes for cerebral visual impairment. PMID:26350515
Structure of mammalian eIF3 in the context of the 43S preinitiation complex. PMID:26344199
Common Amino Acid Subsequences in a Universal Proteome--Relevance for Food Science. PMID:26340620
The Cell Shape-determining Csd6 Protein from Helicobacter pylori Constitutes a New Family of L,D-Carboxypeptidase. PMID:26306031
Identifying and characterising key alternative splicing events in Drosophila development. PMID:26275604
The history of the CATH structural classification of protein domains. PMID:26253692
Cell-Size Homeostasis and the Incremental Rule in a Bacterial Pathogen. PMID:26244734
Setting the PAS, the role of circadian PAS domain proteins during environmental adaptation in plants. PMID:26217364
Requirement of Fra proteins for communication channels between cells in the filamentous nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120. PMID:26216997
A large-scale crop protection bioassay data set. PMID:26175909
The extracellular matrix: Tools and insights for the "omics" era. PMID:26163349
γ-PGA Hydrolases of Phage Origin in Bacillus subtilis and Other Microbial Genomes. PMID:26158264
Mouse Genome Database: From sequence to phenotypes and disease models. PMID:26150326
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. PMID:26139634
Global analyses of TetR family transcriptional regulators in mycobacteria indicates conservation across species and diversity in regulated functions. PMID:26115658
X-ray structure of a mammalian stearoyl-CoA desaturase. PMID:26098370
Proteomic Identification of Cysteine Cathepsin Substrates Shed from the Surface of Cancer Cells. PMID:26081835
Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life. PMID:26075903
The P5 disulfide switch: taming the aging unfolded protein response. PMID:26045202
Chaos of Rearrangements in the Mating-Type Chromosomes of the Anther-Smut Fungus Microbotryum lychnidis-dioicae. PMID:26044594
Stenotrophomonas maltophilia responds to exogenous AHL signals through the LuxR solo SmoR (Smlt1839). PMID:26029670
Databases for Microbiologists. PMID:26013493
Rv2031c of Mycobacterium tuberculosis: a master regulator of Rv2028-Rv2031 (HspX) operon. PMID:25964780
Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks. PMID:25900361
The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI. PMID:25855807
The EMBL-EBI bioinformatics web and programmatic tools framework. PMID:25845596
Cryptococcus strains with different pathogenic potentials have diverse protein secretomes. PMID:25841021
Key challenges for the creation and maintenance of specialist protein resources. PMID:25820941
Can the natural diversity of quorum-sensing advance synthetic biology? PMID:25806368
Efficient prediction of progesterone receptor interactome using a support vector machine model. PMID:25741764
Discrete and structurally unique proteins (tāpirins) mediate attachment of extremely thermophilic Caldicellulosiruptor species to cellulose. PMID:25720489
Defining the gene repertoire and spatiotemporal expression profiles of adhesion G protein-coupled receptors in zebrafish. PMID:25715737
Biological databases for human research. PMID:25712261
The 2015 Nucleic Acids Research Database Issue and molecular biology database collection. PMID:25593347 -
InterPro in 2019: improving coverage, classification and access to protein sequence annotations
PubMed citations: 621.
621 articles citing: InterPro in 2019: improving coverage, classification and access to protein sequence annotations
Full-length transcriptomic analysis in murine and human heart reveals diversity of PGC-1α promoters and isoforms regulated distinctly in myocardial ischemia and obesity. PMID:35907957
An accurate prediction model of digenic interaction for estimating pathogenic gene pairs of human diseases. PMID:35891796
Emerging Computational Approaches for Antimicrobial Peptide Discovery. PMID:35884190
Phylogenetic Classification and Functional Review of Autotransporters. PMID:35860281
Evolutionary analysis of globin domains from kinetoplastids. PMID:35841431
iPCD: A Comprehensive Data Resource of Regulatory Proteins in Programmed Cell Death. PMID:35805101
The evolutionary origin of host association in the Rickettsiales. PMID:35798888
Core cysteine residues in the Plasminogen-Apple-Nematode (PAN) domain are critical for HGF/c-MET signaling. PMID:35778602
Identification of stress-related genes by co-expression network analysis based on the improved turbot genome. PMID:35768602
Genomic and Biological Profile of a Novel Bacteriophage, Vibrio phage Virtus, Which Improves Survival of Sparus aurata Larvae Challenged with Vibrio harveyi. PMID:35745484
An Overview of the Importance and Value of Porcine Species in Sialic Acid Research. PMID:35741423
Curtobacterium spp. and Curtobacterium flaccumfaciens: Phylogeny, Genomics-Based Taxonomy, Pathogenicity, and Diagnostics. PMID:35723345
Spatial and temporal proteomics reveals the distinct distributions and dynamics of O-GlcNAcylated proteins. PMID:35705054
Developing a bioinformatics pipeline for comparative protein classification analysis. PMID:35668373
Simulating the restoration of normal gene expression from different thyroid cancer stages using deep learning. PMID:35659616
Small Molecule 20S Proteasome Enhancer Regulates MYC Protein Stability and Exhibits Antitumor Activity in Multiple Myeloma. PMID:35625675
Exploring Posttranslational Modifications with the Plant PTM Viewer. PMID:35583790
Drosophila nicotinic acetylcholine receptor subunits and their native interactions with insecticidal peptide toxins. PMID:35575460
Contrasting Health Effects of Bacteroidetes and Firmicutes Lies in Their Genomes: Analysis of P450s, Ferredoxins, and Secondary Metabolite Clusters. PMID:35563448
Comparative Genomic Analysis of Vibrio cincinnatiensis Provides Insights into Genetic Diversity, Evolutionary Dynamics, and Pathogenic Traits of the Species. PMID:35562911
Design and application of a knowledge network for automatic prioritization of drug mechanisms. PMID:35561182
CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation. PMID:35560159
Evidence of multiple genome duplication events in Mytilus evolution. PMID:35501689
In Silico Identification and Characterization of a Hypothetical Protein From Rhodobacter capsulatus Revealing S-Adenosylmethionine-Dependent Methyltransferase Activity. PMID:35478993
Endolysin Regulation in Phage Mu Lysis. PMID:35471081
A de Novo ZMIZ1 Pathogenic Variant for Neurodevelopmental Disorder With Dysmorphic Facies and Distal Skeletal Anomalies. PMID:35432459
Beta-Amylase and Phosphatidic Acid Involved in Recalcitrant Seed Germination of Chinese Chestnut. PMID:35401618
A Systematic Immuno-Informatic Approach to Design a Multiepitope-Based Vaccine Against Emerging Multiple Drug Resistant Serratia marcescens. PMID:35371033
Tracing back variations in archaeal ESCRT-based cell division to protein domain architectures. PMID:35358274
Large-scale fungal strain sequencing unravels the molecular diversity in mating loci maintained by long-term balancing selection. PMID:35358178
Proteomic Identification of a Gastric Tumor ECM Signature Associated With Cancer Progression. PMID:35340765
The virota and its transkingdom interactions in the healthy infant gut. PMID:35320047
Asymmetric peptidoglycan editing generates cell curvature in Bdellovibrio predatory bacteria. PMID:35314810
Alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infection. PMID:35311472
New spinocerebellar ataxia subtype caused by SAMD9L mutation triggering mitochondrial dysregulation (SCA49). PMID:35310830
Predicting exon criticality from protein sequence. PMID:35286381
Immune phenotype of the CD4+ T cells in the aged lymphoid organs and lacrimal glands. PMID:35279788
Naturally acquired antibody kinetics against Plasmodium vivax antigens in people from a low malaria transmission region in western Thailand. PMID:35260169
Quantifying and Cataloguing Unknown Sequences within Human Microbiomes. PMID:35258340
SUMOylation of Jun fine-tunes the Drosophila gut immune response. PMID:35255103
Characterization of pectin methylesterase gene family and its possible role in juice sac granulation in navel orange (Citrus sinensis Osbeck). PMID:35249536
Forgotten Actors: Glycoside Hydrolases During Elongation Growth of Maize Primary Root. PMID:35222452
Evolutionary Significance of NHX Family and NHX1 in Salinity Stress Adaptation in the Genus Oryza. PMID:35216206
Novel nitrite reductase domain structure suggests a chimeric denitrification repertoire in the phylum Chloroflexi. PMID:35212484
Student biocuration projects as a learning environment. PMID:35211294
Verticillium dahliae CFEM proteins manipulate host immunity and differentially contribute to virulence. PMID:35197059
Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis. PMID:35191776
Quantitative multiplexed proteomics analysis reveals reshaping of the lysine 2-hydroxyisobutyrylome in Fusarium graminearum by tebuconazole. PMID:35180840
Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation. PMID:35167626
Single-Cell Analysis Uncovers Osteoblast Factor Growth Differentiation Factor 10 as Mediator of Vascular Smooth Muscle Cell Phenotypic Modulation Associated with Plaque Rupture in Human Carotid Artery Disease. PMID:35163719
A New Jasmine Virus C Isolate Identified by Nanopore Sequencing Is Associated to Yellow Mosaic Symptoms of Jasminum officinale in Italy. PMID:35161290
Single-Cell RNA-Seq Reveals a Crosstalk between Hyaluronan Receptor LYVE-1-Expressing Macrophages and Vascular Smooth Muscle Cells. PMID:35159221
Loss of a pyridoxal-phosphate phosphatase rescues Arabidopsis lacking an endoplasmic reticulum ATP carrier. PMID:35139220
The genome of the Paleogene relic tree Bretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs. PMID:35137004
PlantGF: an analysis and annotation platform for plant gene families. PMID:35134149
dCas9-VPR-mediated transcriptional activation of functionally equivalent genes for gene therapy. PMID:35132255
Genomic insight into the scale specialization of the biological control agent Novius pumilus (Weise, 1892). PMID:35100986
Heinz-resistant tomato cultivars exhibit a lignin-based resistance to field dodder (Cuscuta campestris) parasitism. PMID:35099559
Latent TGFβ-binding proteins 1 and 3 protect the larval zebrafish outflow tract from aneurysmal dilatation. PMID:35098309
Genome-Wide Identification of JRL Genes in Moso Bamboo and Their Expression Profiles in Response to Multiple Hormones and Abiotic Stresses. PMID:35095981
An Overview of Transcriptional Responses of Schistosome-Susceptible (M line) or -Resistant (BS-90) Biomphalaria glabrata Exposed or Not to Schistosoma mansoni Infection. PMID:35095891
Adaptation of the periplasm to maintain spatial constraints essential for cell envelope processes and cell viability. PMID:35084330
ILeukin10Pred: A Computational Approach for Predicting IL-10-Inducing Immunosuppressive Peptides Using Combinations of Amino Acid Global Features. PMID:35053004
Identification of putative essential protein domains from high-density transposon insertion sequencing. PMID:35046497
Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. PMID:35037202
Scripting Analyses of Genomes in Ensembl Plants. PMID:35037199
A chromosome-scale genome assembly for the holly (Ilex polyneura) provides insights into genomic adaptations to elevation in Southwest China. PMID:35031793
Genome-wide in silico characterization and stress induced expression analysis of BcL-2 associated athanogene (BAG) family in Musa spp. PMID:35022483
The genome of oil-Camellia and population genomics analysis provide insights into seed oil domestication. PMID:35012630
Identification of Putative β-Galactosidase Genes in the Genome of Lactobacillus helveticus OSU-PECh-4A. PMID:34989615
Identification of Novel Phage Resistance Mechanisms in Campylobacter jejuni by Comparative Genomics. PMID:34970240
Junctional instability in neuroepithelium and network hyperexcitability in a focal cortical dysplasia human model. PMID:34957478
Exploring complex and heterogeneous correlations on hypergraph for the prediction of drug-target interactions. PMID:34950907
Differentiation of adipose-derived stem cells to chondrocytes using electrospraying. PMID:34934143
Structural and functional insights into the first Bacillus thuringiensis vegetative insecticidal protein of the Vpb4 fold, active against western corn rootworm. PMID:34928980
An atypical class of non-coding small RNAs is produced in rice leaves upon bacterial infection. PMID:34921170
A comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in Botrytis cinerea and Trichoderma atroviride. PMID:34900134
NLR diversity and candidate fusiform rust resistance genes in loblolly pine. PMID:34897455
Candida tropicalis Infection Modulates the Gut Microbiome and Confers Enhanced Susceptibility to Colitis in Mice. PMID:34890843
Accurate protein function prediction via graph attention networks with predicted structure information. PMID:34882195
Single cell sequencing analysis identifies genetics-modulated ORMDL3+ cholangiocytes having higher metabolic effects on primary biliary cholangitis. PMID:34872583
The FtcR-Like Protein ActR in Azorhizobium caulinodans ORS571 Is Involved in Bacterial Motility and Symbiosis With the Host Plant. PMID:34867860
The chromosome-level genome provides insight into the molecular mechanism underlying the tortuous-branch phenotype of Prunus mume. PMID:34861048
The FUR-like regulators PerRA and PerRB integrate a complex regulatory network that promotes mammalian host-adaptation and virulence of Leptospira interrogans. PMID:34855918
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
Transcriptomic Profile of the Cockle Cerastoderma edule Exposed to Seasonal Diarrhetic Shellfish Toxin Contamination. PMID:34822568
Heliorhodopsin Evolution Is Driven by Photosensory Promiscuity in Monoderms. PMID:34817235
Haemonchus contortus Transthyretin-Like Protein TTR-31 Plays Roles in Post-Embryonic Larval Development and Potentially Apoptosis of Germ Cells. PMID:34805162
Temperature-induced reorganisation of Schistocephalus solidus (Cestoda) proteome during the transition to the warm-blooded host. PMID:34787304
Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection. PMID:34784345
cis-prenyltransferase 3 and α/β-hydrolase are new determinants of dolichol accumulation in Arabidopsis. PMID:34778961
Bioinformatics-Guided Expansion and Discovery of Graspetides. PMID:34766760
Evolution of the Cytokinin Dehydrogenase (CKX) Domain. PMID:34757471
BRAD V3.0: an upgraded Brassicaceae database. PMID:34755871
Characterization of a P-glycoprotein drug transporter from Toxocara canis with a novel pharmacological profile. PMID:34753107
The transposable element-rich genome of the cereal pest Sitophilus oryzae. PMID:34749730
Transcriptome-Based Identification and Functional Characterization of NAC Transcription Factors Responsive to Drought Stress in Capsicum annuum L. PMID:34745217
CdgC, a Cyclic-di-GMP Diguanylate Cyclase of Azospirillum baldaniorum Is Involved in Internalization to Wheat Roots. PMID:34745182
Essential Genes of Vibrio anguillarum and Other Vibrio spp. Guide the Development of New Drugs and Vaccines. PMID:34745063
Transcriptomic analysis of the Myxococcus xanthus FruA regulon, and comparative developmental transcriptomic analysis of two fruiting body forming species, Myxococcus xanthus and Myxococcus stipitatus. PMID:34724903
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. PMID:34718728
Maternal methionine supplementation during gestation alters alternative splicing and DNA methylation in bovine skeletal muscle. PMID:34717556
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
Identification, expression, and functional analysis of Hsf and Hsp20 gene families in Brachypodium distachyon under heat stress. PMID:34703676
Diversification of Ferredoxins across Living Organisms. PMID:34698119
PIM1 phosphorylation of the androgen receptor and 14-3-3 ζ regulates gene transcription in prostate cancer. PMID:34697370
Genomic Characterization of a Novel Alphacoronavirus Isolated from Bats, Korea, 2020. PMID:34696471
FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow. PMID:34681040
Antibiotics accelerate growth at the expense of immunity. PMID:34666517
Thylakoid attachment to the plasma membrane in Synechocystis sp. PCC 6803 requires the AncM protein. PMID:34665262
Enzyme engineering and in vivo testing of a formate reduction pathway. PMID:34651085
Genome-Wide DNA Methylation and Hydroxymethylation Changes Revealed Epigenetic Regulation of Neuromodulation and Myelination in Yak Hypothalamus. PMID:34646294
Diverse phosphate and auxin transport loci distinguish phosphate tolerant from sensitive Arabidopsis accessions. PMID:34636851
Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication. PMID:34635656
Structural and functional characterization of Mpp75Aa1.1, a putative beta-pore forming protein from Brevibacillus laterosporus active against the western corn rootworm. PMID:34634061
A Novel Neuron-Specific Regulator of the V-ATPase in Drosophila. PMID:34620624
Genome of Ganoderma Species Provides Insights Into the Evolution, Conifers Substrate Utilization, and Terpene Synthesis for Ganoderma tsugae. PMID:34603250
A novel thermostable prokaryotic fucoidan active sulfatase PsFucS1 with an unusual quaternary hexameric structure. PMID:34593864
De novo genome assembly of the marine teleost, bluefin trevally (Caranx melampygus). PMID:34568914
Analyses of open-access multi-omics data sets reveal genetic and expression characteristics of maize ZmCCT family genes. PMID:34567492
Differentially expressed genes reflect disease-induced rather than disease-causing changes in the transcriptome. PMID:34561431
Proteomic Tools for the Analysis of Cytoskeleton Proteins. PMID:34542864
The Conserved Colletotrichum spp. Effector Candidate CEC3 Induces Nuclear Expansion and Cell Death in Plants. PMID:34539598
Genome-wide detection and classification of terpene synthase genes in Aquilaria agallochum. PMID:34539112
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. PMID:34537014
Dietary Polyphenol and Methylsulfonylmethane Supplementation Improves Immune, DAMP Signaling, and Inflammatory Responses During Recovery From All-Out Running Efforts. PMID:34531760
Diverse Host Immune Responses of Different Geographical Populations of the Coconut Rhinoceros Beetle to Oryctes Rhinoceros Nudivirus (OrNV) Infection. PMID:34523987
TnCentral: a Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis. PMID:34517763
Mutations in the gdpP gene are a clinically relevant mechanism for β-lactam resistance in meticillin-resistant Staphylococcus aureus lacking mec determinants. PMID:34486969
A chromosome-level genome of Antechinus flavipes provides a reference for an Australian marsupial genus with male death after mating. PMID:34486812
Identification of anti-horn fly vaccine antigen candidates using a reverse vaccinology approach. PMID:34479607
Duo: A Signature Based Method to Batch-Analyze Functional Similarities of Proteins. PMID:34475860
Comparative Analysis of Bile-Salt Degradation in Sphingobium sp. Strain Chol11 and Pseudomonas stutzeri Strain Chol1 Reveals Functional Diversity of Proteobacterial Steroid Degradation Enzymes and Suggests a Novel Pathway for Side Chain Degradation. PMID:34469190
Clandestinovirus: A Giant Virus With Chromatin Proteins and a Potential to Manipulate the Cell Cycle of Its Host Vermamoeba vermiformis. PMID:34447361
Programmed Cell Death in Developing Brachypodium distachyon Grain. PMID:34445790
Transcription Factors in the Fungus Aspergillus nidulans: Markers of Genetic Innovation, Network Rewiring and Conflict between Genomics and Transcriptomics. PMID:34436139
Ebola virus protein VP40 binding to Sec24c for transport to the plasma membrane. PMID:34431571
Kinetic studies and homology modeling of a dual-substrate linalool/nerolidol synthase from Plectranthus amboinicus. PMID:34429465
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PMID:34411100
Cocultivation of Anaerobic Fungi with Rumen Bacteria Establishes an Antagonistic Relationship. PMID:34399620
Calcium in the Backstage of Malaria Parasite Biology. PMID:34395314
A conserved strategy for structure change and energy transduction in Hsp104 and other AAA+ protein motors. PMID:34384781
Safety and feasibility of an in situ vaccination and immunomodulatory targeted radionuclide combination immuno-radiotherapy approach in a comparative (companion dog) setting. PMID:34383787
Analysis of Bacterial Communities on North Sea Macroalgae and Characterization of the Isolated Planctomycetes Adhaeretor mobilis gen. nov., sp. nov., Roseimaritima multifibrata sp. nov., Rosistilla ulvae sp. nov. and Rubripirellula lacrimiformis sp. nov. PMID:34361930
Exome sequencing of child-parent trios with bladder exstrophy: Findings in 26 children. PMID:34355505
ACO2 clinicobiological dataset with extensive phenotype ontology annotation. PMID:34354088
Differentially Expressed Gene Pathways in the Conjunctiva of Sjögren Syndrome Keratoconjunctivitis Sicca. PMID:34349764
Probing an Ixodes ricinus salivary gland yeast surface display with tick-exposed human sera to identify novel candidates for an anti-tick vaccine. PMID:34344917
Genomic insight for algicidal activity in Rhizobium strain AQ_MP. PMID:34341843
DNA methylation atlas and machinery in the developing and regenerating annelid Platynereis dumerilii. PMID:34340707
Combining Cell Fate Reprogramming and Protein Engineering to Study Transcription Factor Functions. PMID:34324190
Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students. PMID:34318869
"Protein" no longer means what it used to. PMID:34308370
Aspergillus niger trehalase enzyme induced morphological and protein alterations on Acanthamoeba cyst and molecular docking studies. PMID:34295046
Genome-Wide Comparative Analysis of Flowering-Time Genes; Insights on the Gene Family Expansion and Evolutionary Perspective. PMID:34290729
Improving Mobilization of Foreign DNA into Zymomonas mobilis Strain ZM4 by Removal of Multiple Restriction Systems. PMID:34288704
Non-coding RNAs in the interaction between rice and Meloidogyne graminicola. PMID:34284724
Bioinformatic Analysis of the Campylobacter jejuni Type VI Secretion System and Effector Prediction. PMID:34276628
The Taxus genome provides insights into paclitaxel biosynthesis. PMID:34267359
Proteome, Bioinformatic, and Functional Analyses Reveal a Distinct and Conserved Metabolic Pathway for Bile Salt Degradation in the Sphingomonadaceae. PMID:34260303
The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts. PMID:34253727
DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction. PMID:34252926
Chronic cerebral lipocalin 2 exposure elicits hippocampal neuronal dysfunction and cognitive impairment. PMID:34245812
Printing Microbial Dark Matter: Using Single Cell Dispensing and Genomics to Investigate the Patescibacteria/Candidate Phyla Radiation. PMID:34220732
Differential expression of genes associated with non-target site resistance in Poa annua with target site resistance to acetolactate synthase inhibitors. PMID:34218510
Parkinson's disease patient-specific neuronal networks carrying the LRRK2 G2019S mutation unveil early functional alterations that predate neurodegeneration. PMID:34215735
Functional Domains and Evolutionary History of the PMEL and GPNMB Family Proteins. PMID:34207849
Pathogen Moonlighting Proteins: From Ancestral Key Metabolic Enzymes to Virulence Factors. PMID:34203698
Genome reduction and relaxed selection is associated with the transition to symbiosis in the basidiomycete genus Podaxis. PMID:34189441
Whole Genome Level Analysis of the Wnt and DIX Gene Families in Mice and Their Coordination Relationship in Regulating Cardiac Hypertrophy. PMID:34168671
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
Is mRNA decapping by ApaH like phosphatases present in eukaryotes beyond the Kinetoplastida? PMID:34162332
Genome analysis of Pseudomonas sp. OF001 and Rubrivivax sp. A210 suggests multicopper oxidases catalyze manganese oxidation required for cylindrospermopsin transformation. PMID:34157973
Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. PMID:34135888
Wheat ATIs: Characteristics and Role in Human Disease. PMID:34124122
Pseudomonas Strains Induce Transcriptional and Morphological Changes and Reduce Root Colonization of Verticillium spp. PMID:34108946
PINIR: a comprehensive information resource for Pin-II type protease inhibitors. PMID:34107869
Genetic origin of homopyrones, a rare type of hybrid phenylpropanoid- and polyketide-derived yellow pigments from Aspergillus homomorphus. PMID:34106309
Pre-diagnostic DNA methylation patterns differ according to mammographic breast density amongst women who subsequently develop breast cancer: a case-only study in the EPIC-Florence cohort. PMID:34101077
Integrated Multi-omics Investigations Reveal the Key Role of Synergistic Microbial Networks in Removing Plasticizer Di-(2-Ethylhexyl) Phthalate from Estuarine Sediments. PMID:34100638
Composition and function of the C1b/C1f region in the ciliary central apparatus. PMID:34083607
High Carotenoid Mutants of Chlorella vulgaris Show Enhanced Biomass Yield under High Irradiance. PMID:34062906
Multi-Dimensional Transcriptome Analysis Reveals Modulation of Cholesterol Metabolism as Highly Integrated Response to Brain Injury. PMID:34054419
Dynamic methylation of histone H3K18 in differentiating Theileria parasites. PMID:34050145
Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions. PMID:34046017
TSPEAR variants are primarily associated with ectodermal dysplasia and tooth agenesis but not hearing loss: A novel cohort study. PMID:34042254
Structure-based protein function prediction using graph convolutional networks. PMID:34039967
The Rhododendron Plant Genome Database (RPGD): a comprehensive online omics database for Rhododendron. PMID:34022814
Structures and kinetics of Thermotoga maritima MetY reveal new insights into the predominant sulfurylation enzyme of bacterial methionine biosynthesis. PMID:34019879
Mutation of an Arabidopsis Golgi membrane protein ELMO1 reduces cell adhesion. PMID:34015094
Structural Profiling of Bacterial Effectors Reveals Enrichment of Host-Interacting Domains and Motifs. PMID:34012977
Gene Expression Patterns for Proteins With Lectin Domains in Flax Stem Tissues Are Related to Deposition of Distinct Cell Wall Types. PMID:33995436
DoChaP: the domain change presenter. PMID:33988713
Diversity and infectivity of the RNA virome among different cryptic species of an agriculturally important insect vector: whitefly Bemisia tabaci. PMID:33986295
Staphylococcus epidermidis Phages Transduce Antimicrobial Resistance Plasmids and Mobilize Chromosomal Islands. PMID:33980677
Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase. PMID:33974913
Updates to HCOP: the HGNC comparison of orthology predictions tool. PMID:33959747
Uncovering genetic mechanisms of hypertension through multi-omic analysis of the kidney. PMID:33958779
A 20-kb lineage-specific genomic region tames virulence in pathogenic amphidiploid Verticillium longisporum. PMID:33955130
The Beta vulgaris-derived resistance gene Rz2 confers broad-spectrum resistance against soilborne sugar beet-infecting viruses from different families by recognizing triple gene block protein 1. PMID:33951264
Fic and non-Fic AMPylases: protein AMPylation in metazoans. PMID:33947243
Protein structure-based gene expression signatures. PMID:33941686
Cell Wall Layer Induced in Xylem Fibers of Flax Upon Gravistimulation Is Similar to Constitutively Formed Cell Walls of Bast Fibers. PMID:33936149
Best practices on the differential expression analysis of multi-species RNA-seq. PMID:33926528
Microbial and Genetic Resources for Cobalamin (Vitamin B12) Biosynthesis: From Ecosystems to Industrial Biotechnology. PMID:33926061
A Duplicated Copy of the Meiotic Gene ZIP4 Preserves up to 50% Pollen Viability and Grain Number in Polyploid Wheat. PMID:33918149
Rapid exploration of the epitope coverage produced by an Ebola survivor to guide the discovery of therapeutic antibody cocktails. PMID:33912793
Anaerobic gut fungi are an untapped reservoir of natural products. PMID:33906945
Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA. PMID:33904405
The role of solute binding proteins in signal transduction. PMID:33897981
SLC22A14 is a mitochondrial riboflavin transporter required for sperm oxidative phosphorylation and male fertility. PMID:33882315
Critical assessment of protein intrinsic disorder prediction. PMID:33875885
Molecular characterization and transcriptional regulation of two types of H+-pyrophosphatases in the scuticociliate parasite Philasterides dicentrarchi. PMID:33875762
Comparative analysis of MAPK and MKK gene families reveals differential evolutionary patterns in Brachypodium distachyon inbred lines. PMID:33868831
Substrate Inhibition of 5β-Δ4-3-Ketosteroid Dehydrogenase in Sphingobium sp. Strain Chol11 Acts as Circuit Breaker During Growth With Toxic Bile Salts. PMID:33868213
Lytic Bacteriophage EFA1 Modulates HCT116 Colon Cancer Cell Growth and Upregulates ROS Production in an Enterococcus faecalis Co-culture System. PMID:33868210
Multi-omics analysis provides insights into lignocellulosic biomass degradation by Laetiporus sulphureus ATCC 52600. PMID:33865436
A Radical Reimagining of Fungal Two-Component Regulatory Systems. PMID:33853736
Population Genomics of the Maize Pathogen Ustilago maydis: Demographic History and Role of Virulence Clusters in Adaptation. PMID:33837781
Common low complexity regions for SARS-CoV-2 and human proteomes as potential multidirectional risk factor in vaccine development. PMID:33832440
Genotyping-by-Sequencing of the regional Pacific abalone (Haliotis discus) genomes reveals population structures and patterns of gene flow. PMID:33826655
Characterization of GMPP from Dendrobium huoshanense yielding GDP-D-mannose. PMID:33817303
Genomic Approaches Reveal Pleiotropic Effects in Crossbred Beef Cattle. PMID:33815465
The UDP-Glycosyltransferase Family in Drosophila melanogaster: Nomenclature Update, Gene Expression and Phylogenetic Analysis. PMID:33815151
Building blocks and blueprints for bacterial autolysins. PMID:33793553
Carbohydrate-controlled serine protease inhibitor (serpin) production in Bifidobacterium longum subsp. longum. PMID:33790385
Roles of the 14-3-3 gene family in cotton flowering. PMID:33789593
Quantitative acetylome analysis reveals histone modifications that may predict prognosis in hepatitis B-related hepatocellular carcinoma. PMID:33783990
Paracoccus binzhouensis sp. nov., isolated from activated sludge. PMID:33774710
Deleterious fibronectin type III-related gene variants may induce a spinal extradural arachnoid cyst: an exome sequencing study of identical twin cases. PMID:33772355
Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease. PMID:33769280
SVEP1 is a human coronary artery disease locus that promotes atherosclerosis. PMID:33762433
Identification of the PP2C gene family in paper mulberry (Broussonetia papyrifera) and its roles in the regulation mechanism of the response to cold stress. PMID:33751277
A first insight into the genome of Prototheca wickerhamii, a major causative agent of human protothecosis. PMID:33750287
Multi-Omics Analysis of Anlotinib in Pancreatic Cancer and Development of an Anlotinib-Related Prognostic Signature. PMID:33748143
The structure of a major surface antigen SAG19 from Eimeria tenella unifies the Eimeria SAG family. PMID:33742128
A light life together: photosensing in the plant microbiota. PMID:33721277
The velvet protein Vel1 controls initial plant root colonization and conidia formation for xylem distribution in Verticillium wilt. PMID:33720931
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
The small DUF1127 protein CcaF1 from Rhodobacter sphaeroides is an RNA-binding protein involved in sRNA maturation and RNA turnover. PMID:33706375
Reconstruction of the Origin of a Neo-Y Sex Chromosome and Its Evolution in the Spotted Knifejaw, Oplegnathus punctatus. PMID:33693787
Saccharomyces cerevisiae Requires CFF1 To Produce 4-Hydroxy-5-Methylfuran-3(2H)-One, a Mimic of the Bacterial Quorum-Sensing Autoinducer AI-2. PMID:33688008
Biochemical and Structural Characterization of a novel thermophilic esterase EstD11 provide catalytic insights for the HSL family. PMID:33680362
First complete genome sequence of carnation latent virus, the type member of the genus Carlavirus. PMID:33677680
The DBSAV Database: Predicting Deleteriousness of Single Amino Acid Variations in the Human Proteome. PMID:33676930
Whole Exome Sequencing Identifies APCDD1 and HDAC5 Genes as Potentially Cancer Predisposing in Familial Colorectal Cancer. PMID:33673279
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
An update of KAIKObase, the silkworm genome database. PMID:33645624
Chromatin information content landscapes inform transcription factor and DNA interactions. PMID:33637709
Intracellular pathways for lignin catabolism in white-rot fungi. PMID:33622792
Proteogenomic Insights into the Physiology of Marine, Sulfate-Reducing, Filamentous Desulfonema limicola and Desulfonema magnum. PMID:33611323
Biochemical characterisation of a collagenase from Bacillus cereus strain Q1. PMID:33603127
Comprehensive Succinylome Profiling Reveals the Pivotal Role of Lysine Succinylation in Energy Metabolism and Quorum Sensing of Staphylococcus epidermidis. PMID:33597936
The evolutionary history of manatees told by their mitogenomes. PMID:33574363
Hiltonol Cocktail Kills Lung Cancer Cells by Activating Cancer-Suppressors, PKR/OAS, and Restraining the Tumor Microenvironment. PMID:33562773
Diverse Eukaryotic CGG-Binding Proteins Produced by Independent Domestications of hAT Transposons. PMID:33561217
Superoxide Dismutase Multigene Family from a Primitive Chondrostean Sturgeon, Acipenser baerii: Molecular Characterization, Evolution, and Antioxidant Defense during Development and Pathogen Infection. PMID:33546486
In-silico definition of the Drosophila melanogaster matrisome. PMID:33543012
American lobster postlarvae alter gene regulation in response to ocean warming and acidification. PMID:33520168
Computational resources for identifying and describing proteins driving liquid-liquid phase separation. PMID:33517364
SRGAP1 Controls Small Rho GTPases To Regulate Podocyte Foot Process Maintenance. PMID:33514561
CE16 acetylesterases: in silico analysis, catalytic machinery prediction and comparison with related SGNH hydrolases. PMID:33505839
Genome-Wide Identification and Analysis of Chitinase GH18 Gene Family in Mycogone perniciosa. PMID:33505368
Evolution of Plant Na+-P-Type ATPases: From Saline Environments to Land Colonization. PMID:33498844
Porphyromonas gingivalis fimbrial protein Mfa5 contains a von Willebrand factor domain and an intramolecular isopeptide. PMID:33495563
Identification of Lead Compounds against Scm (fms10) in Enterococcus faecium Using Computer Aided Drug Designing. PMID:33494233
Computing Cellulase Kinetics with a Two-Domain Linear Interaction Energy Approach. PMID:33490814
Selective antisense oligonucleotide inhibition of human IRF4 prevents malignant myeloma regeneration via cell cycle disruption. PMID:33476575
The impact of genetic diversity on gene essentiality within the Escherichia coli species. PMID:33462433
Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications. PMID:33436497
Structural Insights into Ankyrin Repeat-Containing Proteins and Their Influence in Ubiquitylation. PMID:33435370
MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes. PMID:33418085
MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes. PMID:33407081
Escherichia ruysiae sp. nov., a novel Gram-stain-negative bacterium, isolated from a faecal sample of an international traveller. PMID:33406029
Improved metagenome binning and assembly using deep variational autoencoders. PMID:33398153
Efflux identification and engineering for ansamitocin P-3 production in Actinosynnema pretiosum. PMID:33394151
Mutation Frequency in Main Susceptibility Genes Among Patients With Head and Neck Paragangliomas. PMID:33391357
RNA-Seq used to identify ipsdienone reductase (IDONER): A novel monoterpene carbon-carbon double bond reductase central to Ips confusus pheromone production. PMID:33388375
De novo ZIC2 frameshift variant associated with frontonasal dysplasia in a Limousin calf. PMID:33388042
Zone of Interaction Between the Parasite and the Host: Protein Profile of the Body Cavity Fluid of Gasterosteus aculeatus L. Infected with the Cestode Schistocephalus solidus (Muller, 1776). PMID:33387269
Defining the 'HoneySweet' insertion event utilizing NextGen sequencing and a de novo genome assembly of plum (Prunus domestica). PMID:33384410
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
Genetic and genomic resources to study natural variation in Brassica rapa. PMID:33364543
αα-Hub domains and intrinsically disordered proteins: A decisive combo. PMID:33361159
Exploring the pH-Dependent Structure-Dynamics-Function Relationship of Human Renin. PMID:33356221
Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi. PMID:33355923
Heteroexpression of Aspergillus nidulans laeA in Marine-Derived Fungi Triggers Upregulation of Secondary Metabolite Biosynthetic Genes. PMID:33352941
Novel perspectives of target-binding by the evolutionarily conserved PP4 phosphatase. PMID:33352067
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. PMID:33348379
Dehydroquinate dehydratase/shikimate dehydrogenases involved in gallate biosynthesis of the aluminum-tolerant tree species Eucalyptus camaldulensis. PMID:33346890
Furin cleavage sites naturally occur in coronaviruses. PMID:33340798
Metabolic Contributions of an Alphaproteobacterial Endosymbiont in the Apicomplexan Cardiosporidium cionae. PMID:33335517
Serum amyloid A is a positive acute phase protein in Russian sturgeon challenged with Aeromonas hydrophila. PMID:33335147
Biological and Genomic Characterization of a Novel Jumbo Bacteriophage, vB_VhaM_pir03 with Broad Host Lytic Activity against Vibrio harveyi. PMID:33333990
Polymer Adhesin Domains in Gram-Positive Cell Surface Proteins. PMID:33324381
Computational prediction method to decipher receptor-glycoligand interactions in plant immunity. PMID:33316845
Deciphering the functional role of hypothetical proteins from Chloroflexus aurantiacs J-10-f1 using bioinformatics approach. PMID:33313333
PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins. PMID:33305318
Computational methods for detecting cancer hotspots. PMID:33304455
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
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. PMID:33290554
Histone variants in archaea and the evolution of combinatorial chromatin complexity. PMID:33288720
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
Towards a unified open access dataset of molecular interactions. PMID:33262342
New variants and in silico analyses in GRK1 associated Oguchi disease. PMID:33252155
The Draft Genome of Red Lechwe, Kobus leche leche. PMID:33250921
Population genomics and antimicrobial resistance in Corynebacterium diphtheriae. PMID:33246485
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
GreenPhylDB v5: a comparative pangenomic database for plant genomes. PMID:33237299
UniProt: the universal protein knowledgebase in 2021. PMID:33237286
Expression of Pro-Angiogenic Markers Is Enhanced by Blue Light in Human RPE Cells. PMID:33233546
Additions to the genus Gimesia: description of Gimesia alba sp. nov., Gimesia algae sp. nov., Gimesia aquarii sp. nov., Gimesia aquatilis sp. nov., Gimesia fumaroli sp. nov. and Gimesia panareensis sp. nov., isolated from aquatic habitats of the Northern Hemisphere. PMID:33231764
Comparative analyses and structural insights of new class glutathione transferases in Cryptosporidium species. PMID:33230237
GP4: an integrated Gram-Positive Protein Prediction Pipeline for subcellular localization mimicking bacterial sorting. PMID:33227814
BRENDA, the ELIXIR core data resource in 2021: new developments and updates. PMID:33211880
Proteome-Scale Detection of Differential Conservation Patterns at Protein and Subprotein Levels with BLUR. PMID:33211099
DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations. PMID:33209251
A combined transcriptomic approach to identify candidates for an anti-tick vaccine blocking B. afzelii transmission. PMID:33208766
Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters. PMID:33199808
E3 Ubiquitin Ligase TRIP12: Regulation, Structure, and Physiopathological Functions. PMID:33198194
OrthoDB in 2020: evolutionary and functional annotations of orthologs. PMID:33196836
Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification. PMID:33196781
Inhibition of DNA Methylation in Picochlorum soloecismus Alters Algae Productivity. PMID:33193644
MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database. PMID:33193550
Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation. PMID:33193240
Structure of the human core transcription-export complex reveals a hub for multivalent interactions. PMID:33191911
Evolutionary History of Mitochondrial Genomes in Discoba, Including the Extreme Halophile Pleurostomum flabellatum (Heterolobosea). PMID:33185659
Comparative Genomics Platform and Phylogenetic Analysis of Fungal Laccases and Multi-Copper Oxidases. PMID:33177916
Isolation and Characterization of Bacillus cereus Phage vB_BceP-DLc1 Reveals the Largest Member of the Φ29-Like Phages. PMID:33171789
COG database update: focus on microbial diversity, model organisms, and widespread pathogens. PMID:33167031
First draft genome assembly of the desert locust, Schistocerca gregaria. PMID:33163158
The InterPro protein families and domains database: 20 years on. PMID:33156333
Updates to the recently introduced family Lacipirellulaceae in the phylum Planctomycetes: isolation of strains belonging to the novel genera Aeoliella, Botrimarina, Pirellulimonas and Pseudobythopirellula and the novel species Bythopirellula polymerisocia and Posidoniimonas corsicana. PMID:33151460
Phylogenetic Analysis of Filifactor alocis Strains Isolated from Several Oral Infections Identified a Novel RTX Toxin, FtxA. PMID:33143036
Genome sequence of an uncharted halophilic bacterium Robertkochia marina with deciphering its phosphate-solubilizing ability. PMID:33141351
IHP-PING-generating integrated human protein-protein interaction networks on-the-fly. PMID:33129201
Pfam: The protein families database in 2021. PMID:33125078
Depletion of the mini-chromosome maintenance complex binding protein allows the progression of cytokinesis despite abnormal karyokinesis during the asexual development of Plasmodium falciparum. PMID:33124706
Bi-Allelic Novel Variants in CLIC5 Identified in a Cameroonian Multiplex Family with Non-Syndromic Hearing Impairment. PMID:33114113
Prometheus, an omics portal for interkingdom comparative genomic analyses. PMID:33112870
Spatiotemporal identification of druggable binding sites using deep learning. PMID:33110179
Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants. PMID:33106425
Uncovering the Cyclic AMP Signaling Pathway of the Protozoan Parasite Entamoeba histolytica and Understanding Its Role in Phagocytosis. PMID:33102254
Tools of the trade: studying actin in zebrafish. PMID:33095903
Arginine-Rich Small Proteins with a Domain of Unknown Function, DUF1127, Play a Role in Phosphate and Carbon Metabolism of Agrobacterium tumefaciens. PMID:33093235
Shrinking of repeating unit length in leucine-rich repeats from double-stranded DNA viruses. PMID:33052487
Exploration into biomarker potential of region-specific brain gene co-expression networks. PMID:33051491
The role of selection in the evolution of marine turtles mitogenomes. PMID:33046778
Relatives of rubella virus in diverse mammals. PMID:33029010
Evolutionary aspects of the Viridiplantae nitroreductases. PMID:33025290
The reuse of public datasets in the life sciences: potential risks and rewards. PMID:33024631
Coding transcriptome analyses reveal altered functions underlying immunotolerance of PEG-fused rat sciatic nerve allografts. PMID:33008419
Differential network analysis of bovine muscle reveals changes in gene coexpression patterns in response to changes in maternal nutrition. PMID:33008289
High-quality nuclear genome for Sarcoptes scabiei-A critical resource for a neglected parasite. PMID:33001992
Structure-Based Deep Mining Reveals First-Time Annotations for 46 Percent of the Dark Annotation Space of the 9,671-Member Superproteome of the Nucleocytoplasmic Large DNA Viruses. PMID:32999026
IDPology of the living cell: intrinsic disorder in the subcellular compartments of the human cell. PMID:32997198
Ectopic Expression of the Transcriptional Regulator silky3 Causes Pleiotropic Meristem and Sex Determination Defects in Maize Inflorescences. PMID:32989171
Characterization and engineering of a two-enzyme system for plastics depolymerization. PMID:32989159
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
Immunohistochemistry and Mutation Analysis of SDHx Genes in Carotid Paragangliomas. PMID:32971818
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora. PMID:32932872
Forensic genomics of a novel Klebsiella quasipneumoniae type from a neonatal intensive care unit in China reveals patterns of colonization, evolution and epidemiology. PMID:32931409
Multi-omic studies on missense PLG variants in families with otitis media. PMID:32929111
Selective Inhibition of Coxiella burnetii Replication by the Steroid Hormone Progesterone. PMID:32928965
Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression. PMID:32918444
Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC. PMID:32912302
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
Valproic acid treatment rescues injured tissues after traumatic brain injury. PMID:32890344
Transcription Profile and Genomic Variations of Oryctes Rhinoceros Nudivirus in Coconut Rhinoceros Beetles. PMID:32878889
Plant expression of NifD protein variants resistant to mitochondrial degradation. PMID:32868448
High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus. PMID:32859687
Establishment of Proximity-Dependent Biotinylation Approaches in Different Plant Model Systems. PMID:32843435
Short, Rich, and Powerful: a New Family of Arginine-Rich Small Proteins Have Outsized Impact in Agrobacterium tumefaciens. PMID:32839178
Integrative genomics analysis identifies five promising genes implicated in insomnia risk based on multiple omics datasets. PMID:32830860
FLAVi: An Enhanced Annotator for Viral Genomes of Flaviviridae. PMID:32824044
Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C sequencing. PMID:32821405
Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics. PMID:32821400
An autoregulatory switch in sex-specific phf7 transcription causes loss of sexual identity and tumors in the Drosophila female germline. PMID:32816970
FuSe: a tool to move RNA-Seq analyses from chromosomal/gene loci to functional grouping of mRNA transcripts. PMID:32814975
Characterization of the β-glucuronidase Pn3Pase as the founding member of glycoside hydrolase family GH169. PMID:32810871
Post-translational formation of strained cyclophanes in bacteria. PMID:32807886
S-layer associated proteins contribute to the adhesive and immunomodulatory properties of Lactobacillus acidophilus NCFM. PMID:32787778
Characterization of a SPM-1 metallo-beta-lactamase-producing Pseudomonas aeruginosa by comparative genomics and phenotypic analysis. PMID:32764694
[Comparative analysis of structural characteristics and epitopes in S proteins between SARS-CoV-2 and SARS-CoV]. PMID:32762171
[Quantitative determination and optimun extraction technique of nine compounds of Paeoniae Radix Alba]. PMID:32762162
The Arabidopsis RboHB Encoded by At1g09090 Is Important for Resistance against Nematodes. PMID:32756498
Integration of the pSLT Plasmid into the Salmonella Chromosome Results in a Temperature-Sensitive Growth Defect Due to Aberrant DNA Replication. PMID:32747428
Defining the transcriptional responses of Aspergillus nidulans to cation/alkaline pH stress and the role of the transcription factor SltA. PMID:32735212
Chemical structure and genetic organization of the E. coli O6:K15 capsular polysaccharide. PMID:32724125
Genome Analysis of Two Novel Synechococcus Phages That Lack Common Auxiliary Metabolic Genes: Possible Reasons and Ecological Insights by Comparative Analysis of Cyanomyoviruses. PMID:32722486
Lysin LysMK34 of Acinetobacter baumannii Bacteriophage PMK34 Has a Turgor Pressure-Dependent Intrinsic Antibacterial Activity and Reverts Colistin Resistance. PMID:32709718
Araport Lives: An Updated Framework for Arabidopsis Bioinformatics. PMID:32699173
How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource. PMID:32696353
Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism. PMID:32694731
Molecular characterization and gene expression modulation of the alternative oxidase in a scuticociliate parasite by hypoxia and mitochondrial respiration inhibitors. PMID:32681023
Expansions and contractions in gene families of independently-evolved blood-feeding insects. PMID:32680460
UXT in Sertoli cells is required for blood-testis barrier integrity†. PMID:32678429
Characterization of the Role of a Non-GPCR Membrane-Bound CFEM Protein in the Pathogenicity and Germination of Botrytis cinerea. PMID:32674341
Identification and sub-cellular localization of a NAD transporter in Leishmania braziliensis (LbNDT1). PMID:32671255
Biofilm and Pathogenesis-Related Proteins in the Foodborne P. fluorescens ITEM 17298 With Distinctive Phenotypes During Cold Storage. PMID:32670211
Prognostic alternative mRNA splicing signatures and associated splicing factors in acute myeloid leukemia. PMID:32653835
VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development. PMID:32646368
The Intrinsically Disordered Protein CARP9 Bridges HYL1 to AGO1 in the Nucleus to Promote MicroRNA Activity. PMID:32636339
Rosistilla oblonga gen. nov., sp. nov. and Rosistilla carotiformis sp. nov., isolated from biotic or abiotic surfaces in Northern Germany, Mallorca, Spain and California, USA. PMID:32623658
Butyrate producing colonic Clostridiales metabolise human milk oligosaccharides and cross feed on mucin via conserved pathways. PMID:32620774
The bottromycin epimerase BotH defines a group of atypical α/β-hydrolase-fold enzymes. PMID:32601484
Fulvic acid increases forage legume growth inducing preferential up-regulation of nodulation and signalling-related genes. PMID:32599619
Environmental Enrichment Improved Learning and Memory, Increased Telencephalic Cell Proliferation, and Induced Differential Gene Expression in Colossoma macropomum. PMID:32595498
The C962R ORF of African Swine Fever Strain Georgia Is Non-Essential and Not Required for Virulence in Swine. PMID:32585808
Maioricimonas rarisocia gen. nov., sp. nov., a novel planctomycete isolated from marine sediments close to Mallorca Island. PMID:32583192
Thalassoglobus polymorphus sp. nov., a novel Planctomycete isolated close to a public beach of Mallorca Island. PMID:32583191
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). PMID:32566135
Bioinformatics analysis of BBX family genes and its response to UV-B in Arabidopsis thaliana. PMID:32552524
Molecular insights into the powerful mucus-based adhesion of limpets (Patella vulgata L.). PMID:32543352
Involvement of Chromosomally Encoded Homologs of the RRNPP Protein Family in Enterococcus faecalis Biofilm Formation and Urinary Tract Infection Pathogenesis. PMID:32540933
Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome. PMID:32537769
Exploration of Two Pectate Lyases from Caldicellulosiruptor bescii Reveals that the CBM66 Module Has a Crucial Role in Pectic Biomass Degradation. PMID:32532871
Adaptive evolution among cytoplasmic piRNA proteins leads to decreased genomic auto-immunity. PMID:32525870
The Prediction of miRNAs in SARS-CoV-2 Genomes: hsa-miR Databases Identify 7 Key miRs Linked to Host Responses and Virus Pathogenicity-Related KEGG Pathways Significant for Comorbidities. PMID:32512929
Defining Critical Genes During Spherule Remodeling and Endospore Development in the Fungal Pathogen, Coccidioides posadasii. PMID:32499817
Structural studies of geranylgeranylglyceryl phosphate synthase, a prenyltransferase found in thermophilic Euryarchaeota. PMID:32496216
Comparative transcriptomics of an arctic foundation species, tussock cottongrass (Eriophorum vaginatum), during an extreme heat event. PMID:32488082
A Novel Inducible Prophage from Burkholderia Vietnamiensis G4 is Widely Distributed across the Species and Has Lytic Activity against Pathogenic Burkholderia. PMID:32486377
Characterization of the Porcine CLEC12A and Analysis of Its Expression on Blood Dendritic Cell Subsets. PMID:32477350
dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes. PMID:32472030
H3.3 Nucleosome Assembly Mutants Display a Late-Onset Maternal Effect. PMID:32470364
The DNA methylation landscape of giant viruses. PMID:32461636
Heavy Metal Stress-Associated Proteins in Rice and Arabidopsis: Genome-Wide Identification, Phylogenetics, Duplication, and Expression Profiles Analysis. PMID:32457808
The Whole-Genome Sequencing and Hybrid Assembly of Mytilus coruscus. PMID:32457802
The Pheromone Module SteC-MkkB-MpkB-SteD-HamE Regulates Development, Stress Responses and Secondary Metabolism in Aspergillus fumigatus. PMID:32457716
MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome-Host Interactions. PMID:32455748
A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. PMID:32449511
Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera. PMID:32442304
The Biotechnological Potential of the Marine Diatom Skeletonema dohrnii to the Elevated Temperature and pCO2 Concentration. PMID:32429035
Decoding the vital segments in human ATP-dependent RNA helicase. PMID:32405168
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
Functional Characterisation of the Autophagy ATG12~5/16 Complex in Dictyostelium discoideum. PMID:32397394
Genome-wide association study leads to novel genetic insights into resistance to Aspergillus flavus in maize kernels. PMID:32393173
Structural and Proteomic Characterization of the Initiation of Giant Virus Infection. PMID:32392465
The Protector within: Comparative Genomics of APSE Phages across Aphids Reveals Rampant Recombination and Diverse Toxin Arsenals. PMID:32386316
ECMPride: prediction of human extracellular matrix proteins based on the ideal dataset using hybrid features with domain evidence. PMID:32377454
Hypogonadotropic hypogonadism due to variants in RAB3GAP2: expanding the phenotypic and genotypic spectrum of Martsolf syndrome. PMID:32376645
Honey-bee-associated prokaryotic viral communities reveal wide viral diversity and a profound metabolic coding potential. PMID:32341166
Hyd ubiquitinates the NF-κB co-factor Akirin to operate an effective immune response in Drosophila. PMID:32339205
Deep conservation of prion-like composition in the eukaryotic prion-former Pub1/Tia1 family and its relatives. PMID:32337108
Aspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis. PMID:32327655
Novel Target Exploration from Hypothetical Proteins of Klebsiella pneumoniae MGH 78578 Reveals a Protein Involved in Host-Pathogen Interaction. PMID:32318354
Fold-Change-Specific Enrichment Analysis (FSEA): Quantification of Transcriptional Response Magnitude for Functional Gene Groups. PMID:32316383
Pathological, Morphological, Cytogenomic, Biochemical and Molecular Data Support the Distinction between Colletotrichum cigarro comb. et stat. nov. and Colletotrichum kahawae. PMID:32295225
Unraveling 1,4-Butanediol Metabolism in Pseudomonas putida KT2440. PMID:32256468
MaveQuest: a web resource for planning experimental tests of human variant effects. PMID:32251504
High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements. PMID:32236090
Type II and type IV toxin-antitoxin systems show different evolutionary patterns in the global Klebsiella pneumoniae population. PMID:32232417
Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control. PMID:32227509
Genome analysis of cellulose and hemicellulose degrading Micromonospora sp. CP22. PMID:32206494
High Resolution Mapping of a Hordeum bulbosum-Derived Powdery Mildew Resistance Locus in Barley Using Distinct Homologous Introgression Lines. PMID:32194602
Elevated pCO2 Level Affects the Extracellular Polymer Metabolism of Phaeodactylum tricornutum. PMID:32194534
Klebsiella pneumoniae type VI secretion system-mediated microbial competition is PhoPQ controlled and reactive oxygen species dependent. PMID:32191774
LRRpredictor-A New LRR Motif Detection Method for Irregular Motifs of Plant NLR Proteins Using an Ensemble of Classifiers. PMID:32182725
Wikidata as a knowledge graph for the life sciences. PMID:32180547
Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts. PMID:32170292
Draft genomes of female and male turbot Scophthalmus maximus. PMID:32165614
Phylogenetics Identifies Two Eumetazoan TRPM Clades and an Eighth TRP Family, TRP Soromelastatin (TRPS). PMID:32159767
A Uniquely Complex Mitochondrial Proteome from Euglena gracilis. PMID:32159766
Isolation and Characterization of the Novel Phages vB_VpS_BA3 and vB_VpS_CA8 for Lysing Vibrio parahaemolyticus. PMID:32153543
Comprehensive analyses of the annexin (ANN) gene family in Brassica rapa, Brassica oleracea and Brassica napus reveals their roles in stress response. PMID:32152363
Mechanism of cargo recognition by retromer-linked SNX-BAR proteins. PMID:32150533
BarleyNet: A Network-Based Functional Omics Analysis Server for Cultivated Barley, Hordeum vulgare L. PMID:32133024
Range-wide neutral and adaptive genetic structure of an endemic herb from Amazonian Savannas. PMID:32128104
Recent advances in functional research in Giardia intestinalis. PMID:32122532
Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids. PMID:32122335
Arabidopsis RanBP2-Type Zinc Finger Proteins Related to Chloroplast RNA Editing Factor OZ1. PMID:32121603
Whole-Genome Sequencing of Lactobacillus helveticus D75 and D76 Confirms Safety and Probiotic Potential. PMID:32111071
Two New Alginate Lyases of PL7 and PL6 Families from Polysaccharide-Degrading Bacterium Formosa algae KMM 3553T: Structure, Properties, and Products Analysis. PMID:32102373
Phenotypic expansion of KMT2D-related disorder: Beyond Kabuki syndrome. PMID:32083401
The tetrameric pheromone module SteC-MkkB-MpkB-SteD regulates asexual sporulation, sclerotia formation and aflatoxin production in Aspergillus flavus. PMID:32068947
Wheat PP2C-a10 regulates seed germination and drought tolerance in transgenic Arabidopsis. PMID:32065246
Parallel quorum-sensing system in Vibrio cholerae prevents signal interference inside the host. PMID:32059031
Antibiotics from Haloarchaea: What Can We Learn from Comparative Genomics? PMID:32048095
The identification of tick autophagy-related genes in Ixodes scapularis responding to amino acid starvation. PMID:32035896
HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. PMID:32034905
High-resolution structural insights into the heliorhodopsin family. PMID:32034096
Non-intrinsic ATP-binding cassette proteins ABCI19, ABCI20 and ABCI21 modulate cytokinin response at the endoplasmic reticulum in Arabidopsis thaliana. PMID:32016506
Insect Mouthpart Transcriptome Unveils Extension of Cuticular Protein Repertoire and Complex Organization. PMID:32000126
Symbiotic lifestyle triggers drastic changes in the gene expression of the algal endosymbiont Breviolum minutum (Symbiodiniaceae). PMID:31993121
Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords. PMID:31984130
Biosynthesis of Nitrogenase Cofactors. PMID:31975585
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. PMID:31950984
Annotated Genome Sequence of Aspergillus tanneri NIH1004. PMID:31948962
The Tip of the VgrG Spike Is Essential to Functional Type VI Secretion System Assembly in Acinetobacter baumannii. PMID:31937641
Antimicrobial Activity of Protein Fraction from Naja ashei Venom Against Staphylococcus epidermidis. PMID:31936872
Gene copy number and function of the APL1 immune factor changed during Anopheles evolution. PMID:31931885
Construction of asthma related competing endogenous RNA network revealed novel long non-coding RNAs and potential new drugs. PMID:31924195
Molecular and genomic characterization of a novel equine molluscum contagiosum-like virus. PMID:31922947
Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within "Nassophorea-Synhymenia-Phyllopharyngea" Assemblage. PMID:31921016
Conserved genomic neighborhood is a strong but no perfect indicator for a direct interaction of microbial gene products. PMID:31900122
A systems biology approach reveals neuronal and muscle developmental defects after chronic exposure to ionising radiation in zebrafish. PMID:31882844
Decrypting tubby-like protein gene family of multiple functions in starch root crop cassava. PMID:31871614
Genetic Determinants of Hydroxycinnamic Acid Metabolism in Heterofermentative Lactobacilli. PMID:31862715
NCBI's Conserved Domain Database and Tools for Protein Domain Analysis. PMID:31851420
Whole genome sequencing and novel candidate genes for CAKUT and altered nephrogenesis in the HSRA rat. PMID:31841396
The human DEPhOsphorylation Database DEPOD: 2019 update. PMID:31836896
New Genus Fibralongavirus in Siphoviridae Phages of Staphylococcus pseudintermedius. PMID:31835553
Organising the cell cycle in the absence of transcriptional control: Dynamic phosphorylation co-ordinates the Trypanosoma brucei cell cycle post-transcriptionally. PMID:31830130
Identification of emerging viral genomes in transcriptomic datasets of alfalfa (Medicago sativa L.). PMID:31818304
Metabolic and Genomic Traits of Phytobeneficial Phenazine-Producing Pseudomonas spp. Are Linked to Rhizosphere Colonization in Arabidopsis thaliana and Solanum tuberosum. PMID:31811040
Type II-Metacaspases are involved in cell stress but not in cell death in the unicellular green alga Dunaliella tertiolecta. PMID:31799323
A Conserved Regulatory Circuit Controls Large Adhesins in Vibrio cholerae. PMID:31796544
Molecular replacement using structure predictions from databases. PMID:31793899
Loss of Oxidation Resistance 1, OXR1, Is Associated with an Autosomal-Recessive Neurological Disease with Cerebellar Atrophy and Lysosomal Dysfunction. PMID:31785787
Identification and Characterization of Aspergillus nidulans Mutants Impaired in Asexual Development under Phosphate Stress. PMID:31779253
CDD/SPARCLE: the conserved domain database in 2020. PMID:31777944
Transcriptional characterization and response to defense elicitors of mevalonate pathway genes in cotton (Gossypium arboreum L.). PMID:31768304
The fenestrae-associated protein Plvap regulates the rate of blood-borne protein passage into the hypophysis. PMID:31740533
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. PMID:31733063
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
Cell-Wall Hydrolases as Antimicrobials against Staphylococcus Species: Focus on Sle1. PMID:31726796
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
Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome. PMID:31697235
MGnify: the microbiome analysis resource in 2020. PMID:31696235
Viromics Reveal a Number of Novel RNA Viruses in Swedish Mosquitoes. PMID:31694175
MitoRibo-Tag Mice Provide a Tool for In Vivo Studies of Mitoribosome Composition. PMID:31693908
PDBe: improved findability of macromolecular structure data in the PDB. PMID:31691821
Subcellular Targeting of the Euplotes raikovi Kinase Er-MAPK1, as Revealed by Expression in Different Cell Systems. PMID:31681773
Comparative Genomic and Transcriptomic Analysis Suggests the Evolutionary Dynamic of GH3 Genes in Gramineae Crops. PMID:31681387
TDR Targets 6: driving drug discovery for human pathogens through intensive chemogenomic data integration. PMID:31680154
The subcellular localization of bHLH transcription factor TCF4 is mediated by multiple nuclear localization and nuclear export signals. PMID:31666615
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
Biological plasticity rescues target activity in CRISPR knock outs. PMID:31659326
Crystal structure of the catalytic unit of GH 87-type α-1,3-glucanase Agl-KA from Bacillus circulans. PMID:31653959
Exploring the Phytochemical Landscape of the Early-Diverging Flowering Plant Amborella trichopoda Baill. PMID:31652707
Spider Venom: Components, Modes of Action, and Novel Strategies in Transcriptomic and Proteomic Analyses. PMID:31652611
Molecular characterization and In Vitro synthesis of infectious RNA of a Turnip vein-clearing virus isolated from Alliaria petiolata in Hungary. PMID:31648277
Bovine Genome Database: new annotation tools for a new reference genome. PMID:31647100
Draft genome sequences of two oriental melons, Cucumis melo L. var. makuwa. PMID:31641135
POLR3A-related spastic ataxia: new mutations and a look into the phenotype. PMID:31637490
A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock. PMID:31636702
Disease related single point mutations alter the global dynamics of a tetratricopeptide (TPR) α-solenoid domain. PMID:31628985
Determination of Ligand Profiles for Pseudomonas aeruginosa Solute Binding Proteins. PMID:31627455
Whole Genome Sequencing of Familial Non-Medullary Thyroid Cancer Identifies Germline Alterations in MAPK/ERK and PI3K/AKT Signaling Pathways. PMID:31614935
TetR-family transcription factors in Gram-negative bacteria: conservation, variation and implications for efflux-mediated antimicrobial resistance. PMID:31606035
PDBe-KB: a community-driven resource for structural and functional annotations. PMID:31584092
The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics. PMID:31579570
Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome. PMID:31574156
The cbb 3-type cytochrome oxidase assembly factor CcoG is a widely distributed cupric reductase. PMID:31570589
Hexa-Longin domain scaffolds for inter-Rab signalling. PMID:31562761
Characterization of Vibrio cholerae's Extracellular Nuclease Xds. PMID:31551990
A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance. PMID:31545786
Prospecting for microbial α-N-acetylgalactosaminidases yields a new class of GH31 O-glycanase. PMID:31530641
Identification and Molecular Characterization of Superoxide Dismutases Isolated From A Scuticociliate Parasite: Physiological Role in Oxidative Stress. PMID:31527617
Using MARRVEL v1.2 for Bioinformatics Analysis of Human Genes and Variant Pathogenicity. PMID:31524990
HH-suite3 for fast remote homology detection and deep protein annotation. PMID:31521110
Structural Insights into the Regulation Mechanism of Small GTPases by GEFs. PMID:31514408
A protein architecture guided screen for modification dependent restriction endonucleases. PMID:31504772
Microbiome as an Immunological Modifier. PMID:31502171
Interspecies comparison of sea star adhesive proteins. PMID:31495313
Genome Sequence of Metarhizium rileyi, a Microbial Control Agent for Lepidoptera. PMID:31488537
Hemimetabolous insects elucidate the origin of sexual development via alternative splicing. PMID:31478483
Combinatorial Avidity Selection of Mosaic Landscape Phages Targeted at Breast Cancer Cells-An Alternative Mechanism of Directed Molecular Evolution. PMID:31454976
A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). PMID:31437279
The draft genome sequence of the spider Dysdera silvatica (Araneae, Dysderidae): A valuable resource for functional and evolutionary genomic studies in chelicerates. PMID:31430368
Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis. PMID:31428125
Resources to Discover and Use Short Linear Motifs in Viral Proteins. PMID:31427097
Identity and functions of inorganic and inositol polyphosphates in plants. PMID:31423587
Phellem Cell-Wall Components Are Discriminants of Cork Quality in Quercus suber. PMID:31417580
The expanding spectrum of neurological disorders of phosphoinositide metabolism. PMID:31413155
The ABCD database: a repository for chemically defined antibodies. PMID:31410491
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
Omics Driven Understanding of the Intestines of Parasitic Nematodes. PMID:31402928
Cassava AGPase genes and their encoded proteins are different from those of other plants. PMID:31399791
Spatially conserved motifs in complement control protein domains determine functionality in regulators of complement activation-family proteins. PMID:31396570
The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis. PMID:31396450
Proteome-wide subtractive approach to prioritize a hypothetical protein of XDR-Mycobacterium tuberculosis as potential drug target. PMID:31388979
An RNAi Screen for Genes Required for Growth of Drosophila Wing Tissue. PMID:31387856
Identification of a noncanonical RNA binding domain in the U2 snRNP protein SF3A1. PMID:31383795
Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards. PMID:31358948
Discovery of Two New Sorbicillinoids by Overexpression of the Global Regulator LaeA in a Marine-Derived Fungus Penicillium dipodomyis YJ-11. PMID:31357680
Quantitative Proteomic Analyses of a Pathogenic Strain and Its Highly Passaged Attenuated Strain of Mycoplasma hyopneumoniae. PMID:31355261
FunFam protein families improve residue level molecular function prediction. PMID:31319797
Environmental conditions shape the nature of a minimal bacterial genome. PMID:31308405
Royal jelly-derived proteins enhance proliferation and migration of human epidermal keratinocytes in an in vitro scratch wound model. PMID:31299973
A critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation. PMID:31273374
Characterization of intellectual disability and autism comorbidity through gene panel sequencing. PMID:31209962
Crystal Structure of the YcjX Stress Protein Reveals a Ras-Like GTP-Binding Protein. PMID:31202886
Correlation between Disease Severity and the Intestinal Microbiome in Mycobacterium tuberculosis-Infected Rhesus Macaques. PMID:31164469
Map and model-moving from observation to prediction in toxicogenomics. PMID:31140561
Evolutionary Analyses Reveal Diverged Patterns of SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family in Oryza Genus. PMID:31139200
Comprehensive Genomic Survey, Characterization and Expression Analysis of the HECT Gene Family in Brassica rapa L. and Brassica oleracea L. PMID:31137879
Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace (Oryza sativa ssp. indica cv. Purpleputtu). PMID:31134103
NetGO: improving large-scale protein function prediction with massive network information. PMID:31106361
Targeting protein methylation: from chemical tools to precision medicines. PMID:31104094
Co-cultivation of the anaerobic fungus Anaeromyces robustus with Methanobacterium bryantii enhances transcription of carbohydrate active enzymes. PMID:31089985
Rhodanese-Like Domain Protein UbaC and Its Role in Ubiquitin-Like Protein Modification and Sulfur Mobilization in Archaea. PMID:31085691
INGA 2.0: improving protein function prediction for the dark proteome. PMID:31073595
Identification of a role for an E6-like 1 gene in early pollen-stigma interactions in Arabidopsis thaliana. PMID:31069543
modEnrichr: a suite of gene set enrichment analysis tools for model organisms. PMID:31069376
Developmental regulators FlbE/D orchestrate the polarity site-to-nucleus dynamics of the fungal bZIP transcription factor FlbB. PMID:31065746
Computational Characterization of the mtORF of Pocilloporid Corals: Insights into Protein Structure and Function in Stylophora Lineages from Contrasting Environments. PMID:31035578
A highly expressed intestinal cysteine protease of Ancylostoma ceylanicum protects vaccinated hamsters from hookworm infection. PMID:31009474
Rapid identification of novel protein families using similarity searches. PMID:30984369
The EMBL-EBI search and sequence analysis tools APIs in 2019. PMID:30976793
Two forms of phosphomannomutase in gammaproteobacteria: The overlooked membrane-bound form of AlgC is required for twitching motility of Lysobacter enzymogenes. PMID:30938049
Cell Wall Hydrolases in Bacteria: Insight on the Diversity of Cell Wall Amidases, Glycosidases and Peptidases Toward Peptidoglycan. PMID:30873139
Mutational load in carotid body tumor. PMID:30871634
The Draft Genome of an Octocoral, Dendronephthya gigantea. PMID:30825304
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
The European Bioinformatics Institute in 2018: tools, infrastructure and training. PMID:30445657 -
InterPro in 2011: new developments in the family and domain prediction database
PubMed citations: 576.
576 articles citing: InterPro in 2011: new developments in the family and domain prediction database
Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methods. PMID:35729277
Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain. PMID:35581640
iAcety-SmRF: Identification of Acetylation Protein by Using Statistical Moments and Random Forest. PMID:35323738
In silico analyses of maleidride biosynthetic gene clusters. PMID:35177129
CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research. PMID:34961276
Integrative genome, transcriptome, microRNA, and degradome analysis of water dropwort (Oenanthe javanica) in response to water stress. PMID:34848704
Identification of quantitative trait nucleotides and candidate genes for tuber yield and mosaic virus tolerance in an elite population of white guinea yam (Dioscorea rotundata) using genome-wide association scan. PMID:34809560
Genomic convergence between Akkermansia muciniphila in different mammalian hosts. PMID:34715771
Transcriptome Analysis of Environmental Pseudomonas Isolates Reveals Mechanisms of Biodegradation of Naphthenic Acid Fraction Compounds (NAFCs) in Oil Sands Tailings. PMID:34683445
Cotton CC-NBS-LRR Gene GbCNL130 Confers Resistance to Verticillium Wilt Across Different Species. PMID:34567025
Absence of MMF1 disrupts heme biosynthesis by targeting Hem1pin Saccharomyces cerevisiae. PMID:34559917
The search for molecular mimicry in proteins carried by extracellular vesicles secreted by cells infected with Plasmodium falciparum. PMID:34527168
Transcriptome Profiling of the Pacific Oyster Crassostrea gigas Visceral Ganglia over a Reproduction Cycle Identifies Novel Regulatory Peptides. PMID:34436291
Conversion of dietary inositol into propionate and acetate by commensal Anaerostipes associates with host health. PMID:34376656
Characterization of the MurT/GatD complex in Mycobacterium tuberculosis towards validating a novel anti-tubercular drug target. PMID:34223102
Carbamoyl Phosphate Synthase Subunit CgCPS1 Is Necessary for Virulence and to Regulate Stress Tolerance in Colletotrichum gloeosporioides. PMID:34111913
Maize Endochitinase Expression in Response to Fall Armyworm Herbivory. PMID:34056671
A novel cripavirus of an ectoparasitoid wasp increases pupal duration and fecundity of the wasp's Drosophila melanogaster host. PMID:34007060
Predicting the Structure and Dynamics of Membrane Protein GerAB from Bacillus subtilis. PMID:33917581
A Single-Nucleotide Mutation in a GLUTAMATE RECEPTOR-LIKE Gene Confers Resistance to Fusarium Wilt in Gossypium hirsutum. PMID:33854882
In Silico Analysis of Huntingtin Homologs in Lower Eukaryotes. PMID:33809947
A Roadmap for Genome-Based Phage Taxonomy. PMID:33803862
Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA. PMID:33450012
Genomics- and Metabolomics-Based Investigation of the Deep-Sea Sediment-Derived Yeast, Rhodotorula mucilaginosa 50-3-19/20B. PMID:33396687
Structure of dual BON-domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation. PMID:33315009
Siberian sturgeon multi-tissue reference transcriptome database. PMID:33238003
The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans. PMID:33037220
High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae. PMID:32985109
In silico analysis predicting effects of deleterious SNPs of human RASSF5 gene on its structure and functions. PMID:32884013
In silico Functional Annotation and Characterization of Hypothetical Proteins from Serratia marcescens FGI94. PMID:32834707
Genome-Wide Association Analysis for Tuber Dry Matter and Oxidative Browning in Water Yam (Dioscorea alata L.). PMID:32751829
PbMC1a/1b regulates lignification during stone cell development in pear (Pyrus bretschneideri) fruit. PMID:32377350
Draft Genome Sequence of Daldinia childiae JS-1345, an Endophytic Fungus Isolated from Stem Tissue of Korean Fir. PMID:32241861
Posttranscriptional modification of messenger RNAs in eukaryotes. PMID:32214475
De novo transcriptome analysis of halotolerant bacterium Staphylococcus sp. strain P-TSB-70 isolated from East coast of India: In search of salt stress tolerant genes. PMID:32040520
Communication within East Antarctic Soil Bacteria. PMID:31628145
PADS Arsenal: a database of prokaryotic defense systems related genes. PMID:31620779
Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence. PMID:31529539
An in silico survey of Clostridioides difficile extrachromosomal elements . PMID:31526450
Omics Driven Understanding of the Intestines of Parasitic Nematodes. PMID:31402928
Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes. PMID:31295964
Draft Genome Sequence of Amphirosellinia nigrospora JS-1675, an Endophytic Fungus from Pteris cretica. PMID:31097494
Quantitative Temporal Proteomic Analysis of Vaccinia Virus Infection Reveals Regulation of Histone Deacetylases by an Interferon Antagonist. PMID:31067474
Evolutionary Conservation and Divergence of Genes Encoding 3-Hydroxy-3-methylglutaryl Coenzyme A Synthase in the Allotetraploid Cotton Species Gossypium hirsutum. PMID:31058869
Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri). PMID:31023218
Molecular and bioinformatics analyses reveal two differentially expressed intracellular GH1 β-glucosidases from the rare alkalophilic fungus Stachybotrys microspora. PMID:30974199
Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton. PMID:30886425
Pan-genome analyses of model fungal species. PMID:30714895
Synthetic lethality guiding selection of drug combinations in ovarian cancer. PMID:30682083
Proteogenomic Analysis of Epibacterium Mobile BBCC367, a Relevant Marine Bacterium Isolated From the South Pacific Ocean. PMID:30622520
Synthetic lethal combinations of low-toxicity drugs for breast cancer identified in silico by genetic screens in yeast. PMID:30555636
Polyomic tools for an emerging livestock parasite, the rumen fluke Calicophoron daubneyi; identifying shifts in rumen functionality. PMID:30509301
Molecular Adaptations of Bacterial Mercuric Reductase to the Hypersaline Kebrit Deep in the Red Sea. PMID:30504211
Suppression of Drug Resistance Reveals a Genetic Mechanism of Metabolic Plasticity in Malaria Parasites. PMID:30425143
Comparative genomics of the major parasitic worms. PMID:30397333
Cross-strand disulfides in the hydrogen bonding site of antiparallel β-sheet (aCSDhs): Forbidden disulfides that are highly strained, easily broken. PMID:30383331
Analysis of the Trichuris suis excretory/secretory proteins as a function of life cycle stage and their immunomodulatory properties. PMID:30374177
Translational genomics and multi-omics integrated approaches as a useful strategy for crop breeding. PMID:30353370
Bioinformatics Analysis and Functional Prediction of Transmembrane Proteins in Entamoeba histolytica. PMID:30332795
Environmental pH modulates transcriptomic responses in the fungus Fusarium sp. associated with KSHB Euwallacea sp. near fornicatus. PMID:30285612
Genome-Wide Identification and Functional Analyses of the CRK Gene Family in Cotton Reveals GbCRK18 Confers Verticillium Wilt Resistance in Gossypium barbadense. PMID:30254650
Whole-transcriptome changes in gene expression accompany aging of sensory neurons in Aplysia californica. PMID:29996779
Genomes of two archaeal endosymbionts show convergent adaptations to an intracellular lifestyle. PMID:29991760
Genome Sequencing and analyses of Two Marine Fungi from the North Sea Unraveled a Plethora of Novel Biosynthetic Gene Clusters. PMID:29976990
Unique function words characterize genomic proteins. PMID:29895692
An in silico pipeline to filter the Toxoplasma gondii proteome for proteins that could traffic to the host cell nucleus and influence host cell epigenetic regulation. PMID:29846382
Inversion variants in human and primate genomes. PMID:29776991
A Multi-Omics Database for Parasitic Nematodes and Trematodes. PMID:29761465
Studying microbial functionality within the gut ecosystem by systems biology. PMID:29556373
A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways. PMID:29540736
Unexplored therapeutic opportunities in the human genome. PMID:29472638
Host-induced gene silencing of a regulator of G protein signalling gene (VdRGS1) confers resistance to Verticillium wilt in cotton. PMID:29431919
The Glaciozyma antarctica genome reveals an array of systems that provide sustained responses towards temperature variations in a persistently cold habitat. PMID:29385175
Evidence for a hierarchical transcriptional circuit in Drosophila male germline involving testis-specific TAF and two gene-specific transcription factors, Mod and Acj6. PMID:29235675
Characterization of sulfhydryl oxidase from Aspergillus tubingensis. PMID:29216817
Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi. PMID:29184190
Recessive VARS2 mutation underlies a novel syndrome with epilepsy, mental retardation, short stature, growth hormone deficiency, and hypogonadism. PMID:29137650
Comparative analysis of genome sequences of the conifer tree pathogen, Heterobasidion annosum s.s. PMID:29085779
Complete Genome Sequence of Eubacterium hallii Strain L2-7. PMID:29074659
Diverse type 2 diabetes genetic risk factors functionally converge in a phenotype-focused gene network. PMID:29059180
Genome Sequence of an Endophytic Fungus, Fusarium solani JS-169, Which Has Antifungal Activity. PMID:29051243
Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster. PMID:29045400
Draft Genome Sequence of Aspergillus persii NIBRFGC000004109, Which Has Antibacterial Activity against Plant-Pathogenic Bacteria. PMID:28935731
Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine. PMID:28924494
Prokaryotic and Highly-Repetitive WD40 Proteins: A Systematic Study. PMID:28878378
The lysin motif-containing proteins, Lyp1, Lyk7 and LysMe3, play important roles in chitin perception and defense against Verticillium dahliae in cotton. PMID:28870172
Alternaria Toxins: Potential Virulence Factors and Genes Related to Pathogenesis. PMID:28848500
A large scale Plasmodium vivax- Saimiri boliviensis trophozoite-schizont transition proteome. PMID:28829774
Draft Genome Sequence of an Endophytic Fungus, Gaeumannomyces sp. Strain JS-464, Isolated from a Reed Plant, Phragmites communis. PMID:28774982
Functional Profiling of Transcription Factor Genes in Neurospora crassa. PMID:28696922
On patterns and re-use in bioinformatics databases. PMID:28525546
Global gene expression analysis provides insight into local adaptation to geothermal streams in tadpoles of the Andean toad Rhinella spinulosa. PMID:28512324
InlL from Listeria monocytogenes Is Involved in Biofilm Formation and Adhesion to Mucin. PMID:28473809
Identification of molecular characteristics induced by radiotherapy in rectal cancer based on microarray data. PMID:28454466
Autozygosity reveals recessive mutations and novel mechanisms in dominant genes: implications in variant interpretation. PMID:28383543
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
Improving transcriptome de novo assembly by using a reference genome of a related species: Translational genomics from oil palm to coconut. PMID:28334050
An integrated Java tool for generating amino acid sequence alignments with mapped secondary structure elements. PMID:28324365
Structure-based functional annotation of putative conserved proteins having lyase activity from Haemophilus influenzae. PMID:28324295
A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data. PMID:28321234
Persistence of Functional Protein Domains in Mycoplasma Species and their Role in Host Specificity and Synthetic Minimal Life. PMID:28224116
Genome-wide identification of direct HBx genomic targets. PMID:28212627
Draft Genome Sequence of Actinomyces glycerinitolerans Strain G10T, Isolated from Sheep Rumen Fluid. PMID:28209819
InterVar: Clinical Interpretation of Genetic Variants by the 2015 ACMG-AMP Guidelines. PMID:28132688
Tensor Factorization for Precision Medicine in Heart Failure with Preserved Ejection Fraction. PMID:28116551
Phylogenetic analysis of ionotropic L-glutamate receptor genes in the Bilateria, with special notes on Aplysia californica. PMID:28077092
Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes. PMID:28069893
Complete Genome Sequence of Akkermansia glycaniphila Strain PytT, a Mucin-Degrading Specialist of the Reticulated Python Gut. PMID:28057747
Global repositioning of transcription start sites in a plant-fermenting bacterium. PMID:27982035
Deep Insight into the Phosphatomes of Parasitic Protozoa and a Web Resource ProtozPhosDB. PMID:27930683
Primer on the Gene Ontology. PMID:27812933
Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana). PMID:27799338
Genomic resources for a unique, low-virulence Babesia taxon from China. PMID:27784333
Convert your favorite protein modeling program into a mutation predictor: "MODICT". PMID:27760515
A Conserved Structural Signature of the Homeobox Coding DNA in HOX genes. PMID:27739488
Sulfur deficiency-induced repressor proteins optimize glucosinolate biosynthesis in plants. PMID:27730214
Systematic functional analysis of kinases in the fungal pathogen Cryptococcus neoformans. PMID:27677328
Comparative analysis of transcriptomes in aerial stems and roots of Ephedra sinica based on high-throughput mRNA sequencing. PMID:27625990
Genomic and Transcriptional Mapping of PaMx41, Archetype of a New Lineage of Bacteriophages Infecting Pseudomonas aeruginosa. PMID:27590812
Identification of Conidiogenesis-Associated Genes in Colletotrichum gloeosporioides by Agrobacterium tumefaciens-Mediated Transformation. PMID:27582094
Transcriptome analysis revealed that a quorum sensing system regulates the transfer of the pAt megaplasmid in Agrobacterium tumefaciens. PMID:27543103
Temperature Modulates the Secretome of the Phytopathogenic Fungus Lasiodiplodia theobromae. PMID:27536303
Transcriptomic analysis of the autophagy machinery in crustaceans. PMID:27506197
MicroRNA expression and gene regulation drive breast cancer progression and metastasis in PyMT mice. PMID:27449149
Endogenous Small-Noncoding RNAs and Potential Functions in Desiccation Tolerance in Physcomitrella Patens. PMID:27443635
Clinical genomics expands the morbid genome of intellectual disability and offers a high diagnostic yield. PMID:27431290
The Presence of Two Receptor-Binding Proteins Contributes to the Wide Host Range of Staphylococcal Twort-Like Phages. PMID:27422842
Discovery and identification of candidate genes from the chitinase gene family for Verticillium dahliae resistance in cotton. PMID:27354165
Cyanobacterial ultrastructure in light of genomic sequence data. PMID:27344651
Comparative Protein Structure Modeling Using MODELLER. PMID:27322406
Comparative genomic and transcriptomic analyses of the Fuzhuan brick tea-fermentation fungus Aspergillus cristatus. PMID:27267057
Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family. PMID:27229309
Characterization and Comparison of the CPK Gene Family in the Apple (Malus × domestica) and Other Rosaceae Species and Its Response to Alternaria alternata Infection. PMID:27186637
The arabidopsis cyclic nucleotide interactome. PMID:27170143
Practical Approaches for Mining Frequent Patterns in Molecular Datasets. PMID:27168722
Genome-scale prediction of moonlighting proteins using diverse protein association information. PMID:27153604
A pseudouridylation switch in rRNA is implicated in ribosome function during the life cycle of Trypanosoma brucei. PMID:27142987
The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. PMID:27138043
UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation. PMID:27114492
Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources. PMID:27092246
Compartmentalization of functions and predicted miRNA regulation among contiguous regions of the nematode intestine. PMID:27002534
Evolution of Pentameric Ligand-Gated Ion Channels: Pro-Loop Receptors. PMID:26986966
A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis. PMID:26977809
Hologenome analysis of two marine sponges with different microbiomes. PMID:26926518
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. PMID:26911872
Transcript Abundance of Putative Lipid Phosphate Phosphatases During Development of Trypanosoma brucei in the Tsetse Fly. PMID:26856918
Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention. PMID:26856411
Bridging semantics and syntax with graph algorithms-state-of-the-art of extracting biomedical relations. PMID:26851224
Enhancing Nonribosomal Peptide Biosynthesis in Filamentous Fungi. PMID:26831707
Long-Term Persistence of Bi-functionality Contributes to the Robustness of Microbial Life through Exaptation. PMID:26824644
SOHSite: incorporating evolutionary information and physicochemical properties to identify protein S-sulfenylation sites. PMID:26819243
A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases. PMID:26818115
A survey of best practices for RNA-seq data analysis. PMID:26813401
Molecular Basis for Resistance Against Phosphonate Antibiotics and Herbicides. PMID:26811741
An evaluation of the accuracy and speed of metagenome analysis tools. PMID:26778510
Developing of the Computer Method for Annotation of Bacterial Genes. PMID:26770195
267 Spanish Exomes Reveal Population-Specific Differences in Disease-Related Genetic Variation. PMID:26764160
Use of a Probabilistic Motif Search to Identify Histidine Phosphotransfer Domain-Containing Proteins. PMID:26751210
Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry. PMID:26740739
Characterization of a Recombinant Cathepsin B-Like Cysteine Peptidase from Diaphorina citri Kuwayama (Hemiptera: Liviidae): A Putative Target for Control of Citrus Huanglongbing. PMID:26717484
Essential Genome of the Metabolically Versatile Alphaproteobacterium Rhodopseudomonas palustris. PMID:26712940
Genome-wide analysis of WRKY transcription factors in white pear (Pyrus bretschneideri) reveals evolution and patterns under drought stress. PMID:26704366
Genome sequences of two closely related strains of Escherichia coli K-12 GM4792. PMID:26664654
The MG-RAST metagenomics database and portal in 2015. PMID:26656948
An extracellular biochemical screen reveals that FLRTs and Unc5s mediate neuronal subtype recognition in the retina. PMID:26633812
Targeted gene disruption in Candida parapsilosis demonstrates a role for CPAR2_404800 in adhesion to a biotic surface and in a murine model of ascending urinary tract infection. PMID:26632333
The calcified eggshell matrix proteome of a songbird, the zebra finch (Taeniopygia guttata). PMID:26628892
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188
Transcriptome profiling of a spirodiclofen susceptible and resistant strain of the European red mite Panonychus ulmi using strand-specific RNA-seq. PMID:26581334
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
Functional demonstrations of starch binding domains present in Ostreococcus tauri starch synthases isoforms. PMID:26510916
A Novel SLC27A4 Splice Acceptor Site Mutation in Great Danes with Ichthyosis. PMID:26506231
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
Complete genome sequence of Propionibacterium freudenreichii DSM 20271(T). PMID:26500719
An Integrated Multiomics Approach to Identify Candidate Antigens for Serodiagnosis of Human Onchocerciasis. PMID:26472727
The genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles. PMID:26462797
Solving a Bloody Mess: B-Vitamin Independent Metabolic Convergence among Gammaproteobacterial Obligate Endosymbionts from Blood-Feeding Arthropods and the Leech Haementeria officinalis. PMID:26454017
Diversity in protein domain superfamilies. PMID:26451979
Genome-Wide Comparative Analysis of Flowering-Related Genes in Arabidopsis, Wheat, and Barley. PMID:26435710
PatchSurfers: Two methods for local molecular property-based binding ligand prediction. PMID:26427548
Translational compensation of genomic instability in neuroblastoma. PMID:26399178
The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches. PMID:26380077
Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View. PMID:26366735
AntiAngioPred: A Server for Prediction of Anti-Angiogenic Peptides. PMID:26335203
Cap-domain closure enables diverse substrate recognition by the C2-type haloacid dehalogenase-like sugar phosphatase Plasmodium falciparum HAD1. PMID:26327372
Induction of the Sugar-Phosphate Stress Response Allows Saccharomyces cerevisiae 2-Methyl-4-Amino-5-Hydroxymethylpyrimidine Phosphate Synthase To Function in Salmonella enterica. PMID:26324451
ReprOlive: a database with linked data for the olive tree (Olea europaea L.) reproductive transcriptome. PMID:26322066
Streamlined Construction of the Cyanobacterial CO2-Fixing Organelle via Protein Domain Fusions for Use in Plant Synthetic Biology. PMID:26320224
Proteomic analysis of quail calcified eggshell matrix: a comparison to chicken and turkey eggshell proteomes. PMID:26312056
Translational genomics for plant breeding with the genome sequence explosion. PMID:26269219
deFUME: Dynamic exploration of functional metagenomic sequencing data. PMID:26227142
Representing virus-host interactions and other multi-organism processes in the Gene Ontology. PMID:26215368
Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley. PMID:26208213
High quality draft genome of Lactobacillus kunkeei EFB6, isolated from a German European foulbrood outbreak of honeybees. PMID:26203329
Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S. PMID:26203328
The serine/threonine kinase 33 is present and expressed in palaeognath birds but has become a unitary pseudogene in neognaths about 100 million years ago. PMID:26199010
Domain organization of DNase from Thioalkalivibrio sp. provides insights into retention of activity in high salt environments. PMID:26191053
Interaction networks for identifying coupled molecular processes in microbial communities. PMID:26180552
Bioinformatics and Moonlighting Proteins. PMID:26157797
Genetic profiles of cervical tumors by high-throughput sequencing for personalized medical care. PMID:26155992
Novel drug target identification for the treatment of dementia using multi-relational association mining. PMID:26154857
A systematic analysis of human lipocalin family and its expression in esophageal carcinoma. PMID:26131602
Pseudomonas aeruginosa MifS-MifR Two-Component System Is Specific for α-Ketoglutarate Utilization. PMID:26114434
An Interspecies Comparative Analysis of the Predicted Secretomes of the Necrotrophic Plant Pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PMID:26107498
Early origin and adaptive evolution of the GW182 protein family, the key component of RNA silencing in animals. PMID:26106978
Characterization of the Maize Chitinase Genes and Their Effect on Aspergillus flavus and Aflatoxin Accumulation Resistance. PMID:26090679
The Plasmodiophora brassicae genome reveals insights in its life cycle and ancestry of chitin synthases. PMID:26084520
Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. PMID:26075521
microProtein Prediction Program (miP3): A Software for Predicting microProteins and Their Target Transcription Factors. PMID:26060811
Genome-Wide Collation of the Plasmodium falciparum WDR Protein Superfamily Reveals Malarial Parasite-Specific Features. PMID:26043001
A manual curation strategy to improve genome annotation: application to a set of haloarchael genomes. PMID:26042526
Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels. PMID:26035711
Genome Anatomy of Streptococcus parasanguinis Strain C1A, Isolated from a Patient with Acute Exacerbation of Chronic Obstructive Pulmonary Disease, Reveals Unusual Genomic Features. PMID:26021924
Evolutionary Dynamics of the Cellulose Synthase Gene Superfamily in Grasses. PMID:25999407
Evolution of the Translocation and Assembly Module (TAM). PMID:25994932
Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum. PMID:25986905
Most partial domains in proteins are alignment and annotation artifacts. PMID:25976240
Comparative transcriptome profiling approach to glean virulence and immunomodulation-related genes of Fasciola hepatica. PMID:25956885
A method of searching for related literature on protein structure analysis by considering a user's intention. PMID:25952498
Gene expression profiling via bioinformatics analysis reveals biomarkers in laryngeal squamous cell carcinoma. PMID:25936657
PaPI: pseudo amino acid composition to score human protein-coding variants. PMID:25928477
Proteochemometric modelling coupled to in silico target prediction: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules. PMID:25926892
Longevity GWAS Using the Drosophila Genetic Reference Panel. PMID:25922346
RNA-seq-Based Gene Annotation and Comparative Genomics of Four Fungal Grass Pathogens in the Genus Zymoseptoria Identify Novel Orphan Genes and Species-Specific Invasions of Transposable Elements. PMID:25917918
The evolutionary dynamics of major regulators for sexual development among Hymenoptera species. PMID:25914717
The Magellania venosa Biomineralizing Proteome: A Window into Brachiopod Shell Evolution. PMID:25912046
Nitrate sensing by the maize root apex transition zone: a merged transcriptomic and proteomic survey. PMID:25911739
The genomes of two key bumblebee species with primitive eusocial organization. PMID:25908251
Giving structure to the biofilm matrix: an overview of individual strategies and emerging common themes. PMID:25907113
The Psp system of Mycobacterium tuberculosis integrates envelope stress-sensing and envelope-preserving functions. PMID:25899163
Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. PMID:25893781
Natural variation of gene models in Drosophila melanogaster. PMID:25888292
Chlamydia psittaci comparative genomics reveals intraspecies variations in the putative outer membrane and type III secretion system genes. PMID:25887617
Genomic factors related to tissue tropism in Chlamydia pneumoniae infection. PMID:25887605
Codon usage and codon context bias in Xanthophyllomyces dendrorhous. PMID:25887493
The Alternaria genomes database: a comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic species. PMID:25887485
Mason: a JavaScript web site widget for visualizing and comparing annotated features in nucleotide or protein sequences. PMID:25884379
ANDSystem: an Associative Network Discovery System for automated literature mining in the field of biology. PMID:25881313
Systematic functional profiling of transcription factor networks in Cryptococcus neoformans. PMID:25849373
Biochemical functional predictions for protein structures of unknown or uncertain function. PMID:25848497
Structural and evolutionary divergence of cyclic nucleotide binding domains in eukaryotic pathogens: Implications for drug design. PMID:25847873
RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing. PMID:25830017
LOTUS-DB: an integrative and interactive database for Nelumbo nucifera study. PMID:25819075
Editorial. PMID:25793962
Exceptionally widespread nanomachines composed of type IV pilins: the prokaryotic Swiss Army knives. PMID:25793961
Homozygous MED25 mutation implicated in eye-intellectual disability syndrome. PMID:25792360
AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae. PMID:25781462
Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces. PMID:25765346
A bioinformatic survey of distribution, conservation, and probable functions of LuxR solo regulators in bacteria. PMID:25759807
Integrated regulatory mechanisms of miRNAs and targeted genes involved in colorectal cancer. PMID:25755742
A conserved domain in the scc3 subunit of cohesin mediates the interaction with both mcd1 and the cohesin loader complex. PMID:25748820
Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PMID:25748510
De novo assembly and characterization of Oryza officinalis leaf transcriptome by using RNA-seq. PMID:25713814
X-domain of peptide synthetases recruits oxygenases crucial for glycopeptide biosynthesis. PMID:25686610
The C. elegans Crumbs family contains a CRB3 homolog and is not essential for viability. PMID:25661870
EcoliNet: a database of cofunctional gene network for Escherichia coli. PMID:25650278
Characterization of novel acyl coenzyme A dehydrogenases involved in bacterial steroid degradation. PMID:25645564
Genetic redundancy is prevalent within the 6.7 Mb Sinorhizobium meliloti genome. PMID:25638282
Aquaria: simplifying discovery and insight from protein structures. PMID:25633501
Annotation of proteins of unknown function: initial enzyme results. PMID:25630330
Identification of the differentially expressed genes associated with familial combined hyperlipidemia using bioinformatics analysis. PMID:25625967
Functional and phylogenetic characterization of proteins detected in various nematode intestinal compartments. PMID:25609831
C11orf83, a mitochondrial cardiolipin-binding protein involved in bc1 complex assembly and supercomplex stabilization. PMID:25605331
Identification and characterization of LFD-2, a predicted fringe protein required for membrane integrity during cell fusion in neurospora crassa. PMID:25595444
Next generation sequencing analysis of nine Corynebacterium ulcerans isolates reveals zoonotic transmission and a novel putative diphtheria toxin-encoding pathogenicity island. PMID:25587356
The Ordospora colligata genome: Evolution of extreme reduction in microsporidia and host-to-parasite horizontal gene transfer. PMID:25587016
Genome-wide Analysis of Mycoplasma hominis for the Identification of Putative Therapeutic Targets. PMID:25574133
A RESTful API for accessing microbial community data for MG-RAST. PMID:25569221
Plasmodium vivax trophozoite-stage proteomes. PMID:25545414
Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes. PMID:25540822
Selecting causal genes from genome-wide association studies via functionally coherent subnetworks. PMID:25532137
The draft genome of the pest tephritid fruit fly Bactrocera tryoni: resources for the genomic analysis of hybridising species. PMID:25527032
Transcriptional, posttranscriptional, and posttranslational regulation of SHOOT MERISTEMLESS gene expression in Arabidopsis determines gene function in the shoot apex. PMID:25524441
Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes. PMID:25523484
funRNA: a fungi-centered genomics platform for genes encoding key components of RNAi. PMID:25522231
MOROKOSHI: transcriptome database in Sorghum bicolor. PMID:25505007
Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. PMID:25503938
Genome-scale identification and characterization of moonlighting proteins. PMID:25497125
What helminth genomes have taught us about parasite evolution. PMID:25482650
Mechanistic diversity of radical S-adenosylmethionine (SAM)-dependent methylation. PMID:25477520
Structural insight into substrate recognition by the endoplasmic reticulum folding-sensor enzyme: crystal structure of third thioredoxin-like domain of UDP-glucose:glycoprotein glucosyltransferase. PMID:25471383
A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease. PMID:25437566
Plant-PrAS: a database of physicochemical and structural properties and novel functional regions in plant proteomes. PMID:25435546
CED-3 caspase acts with miRNAs to regulate non-apoptotic gene expression dynamics for robust development in C. elegans. PMID:25432023
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
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. PMID:25428351
CFam: a chemical families database based on iterative selection of functional seeds and seed-directed compound clustering. PMID:25414339
The draft genome of the large yellow croaker reveals well-developed innate immunity. PMID:25407894
dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation. PMID:25399423
MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data. PMID:25398900
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. PMID:25398609
Analysis of the Na+/Ca2+ exchanger gene family within the phylum Nematoda. PMID:25397810
Text mining in cancer gene and pathway prioritization. PMID:25392685
Helminth.net: expansions to Nematode.net and an introduction to Trematode.net. PMID:25392426
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities. PMID:25378329
Molecular profiling of the Phytophthora plurivora secretome: a step towards understanding the cross-talk between plant pathogenic oomycetes and their hosts. PMID:25372870
An expanding universe of mRNA modifications. PMID:25372308
Comparative analyses of nonpathogenic, opportunistic, and totally pathogenic mycobacteria reveal genomic and biochemical variabilities and highlight the survival attributes of Mycobacterium tuberculosis. PMID:25370496
K₂p channels in plants and animals. PMID:25369776
TFClass: a classification of human transcription factors and their rodent orthologs. PMID:25361979
Genenames.org: the HGNC resources in 2015. PMID:25361968
dcGOR: an R package for analysing ontologies and protein domain annotations. PMID:25356683
UniProt: a hub for protein information. PMID:25348405
HAMAP in 2015: updates to the protein family classification and annotation system. PMID:25348399
MitProNet: A knowledgebase and analysis platform of proteome, interactome and diseases for mammalian mitochondria. PMID:25347823
In silico sequence analysis reveals new characteristics of fungal NADPH oxidase genes. PMID:25346600
Comparative genome analysis of Wolbachia strain wAu. PMID:25341639
Genome-wide linkage and exome analyses identify variants of HMCN1 for splenic epidermoid cyst. PMID:25338956
Protein profiles reveal diverse responsive signaling pathways in kernels of two maize inbred lines with contrasting drought sensitivity. PMID:25334062
Systems biology studies of adult paragonimus lung flukes facilitate the identification of immunodominant parasite antigens. PMID:25329661
Divergent and conserved elements comprise the chemoreceptive repertoire of the nonblood-feeding mosquito Toxorhynchites amboinensis. PMID:25326137
PLAZA 3.0: an access point for plant comparative genomics. PMID:25324309
The complex portal--an encyclopaedia of macromolecular complexes. PMID:25313161
Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens. PMID:25306241
SMART: recent updates, new developments and status in 2015. PMID:25300481
Joint genetic analysis of hippocampal size in mouse and human identifies a novel gene linked to neurodegenerative disease. PMID:25280473
Computational biophysical, biochemical, and evolutionary signature of human R-spondin family proteins, the member of canonical Wnt/β-catenin signaling pathway. PMID:25276837
Contribution of the nos-pdt operon to virulence phenotypes in methicillin-sensitive Staphylococcus aureus. PMID:25275514
Histone deacetylase inhibition rescues structural and functional brain deficits in a mouse model of Kabuki syndrome. PMID:25273096
Anaerobic activation of p-cymene in denitrifying betaproteobacteria: methyl group hydroxylation versus addition to fumarate. PMID:25261521
Maize and millet transcription factors annotated using comparative genomic and transcriptomic data. PMID:25261191
Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi. PMID:25244985
WHIRLY1 is a major organizer of chloroplast nucleoids. PMID:25237316
Overlapping binding sites of the frataxin homologue assembly factor and the heat shock protein 70 transfer factor on the Isu iron-sulfur cluster scaffold protein. PMID:25228696
Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. PMID:25219674
Serine integrase chimeras with activity in E. coli and HeLa cells. PMID:25217617
Isoprenoid biosynthesis in Plasmodium falciparum. PMID:25217461
A unique hexokinase in Cryptosporidium parvum, an apicomplexan pathogen lacking the Krebs cycle and oxidative phosphorylation. PMID:25216472
Nitric oxide production by necrotrophic pathogen Macrophomina phaseolina and the host plant in charcoal rot disease of jute: complexity of the interplay between necrotroph-host plant interactions. PMID:25208092
The landscape of kinase fusions in cancer. PMID:25204415
Sequencing and de novo transcriptome assembly of Brachypodium sylvaticum (Poaceae). PMID:25202520
Pvr expression regulators in equilibrium signal control and maintenance of Drosophila blood progenitors. PMID:25201876
Overexpression of p49/STRAP alters cellular cytoskeletal structure and gross anatomy in mice. PMID:25183317
Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities. PMID:25179155
Unbiased functional clustering of gene variants with a phenotypic-linkage network. PMID:25166029
Identifying transcription factor complexes and their roles. PMID:25161228
Large-scale phylogenetic classification of fungal chitin synthases and identification of a putative cell-wall metabolism gene cluster in Aspergillus genomes. PMID:25148134
A novel method for functional annotation prediction based on combination of classification methods. PMID:25133242
Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis. PMID:25129028
Proteomic analysis of the Plasmodium male gamete reveals the key role for glycolysis in flagellar motility. PMID:25124718
A comprehensive analysis of the Omp85/TpsB protein superfamily structural diversity, taxonomic occurrence, and evolution. PMID:25101071
Prediction of protein-protein interaction strength using domain features with supervised regression. PMID:25093200
Sequence divergence and diversity suggests ongoing functional diversification of vertebrate NAD metabolism. PMID:25084685
A sugar phosphatase regulates the methylerythritol phosphate (MEP) pathway in malaria parasites. PMID:25058848
Analysis of stop-gain and frameshift variants in human innate immunity genes. PMID:25058640
Standardized description of scientific evidence using the Evidence Ontology (ECO). PMID:25052702
Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features. PMID:25042424
Bioinformatic analysis of proteomics data. PMID:25033288
Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets. PMID:25033262
Role of YpeB in cortex hydrolysis during germination of Bacillus anthracis spores. PMID:25022853
Duplications and losses in gene families of rust pathogens highlight putative effectors. PMID:25018762
The Lottia gigantea shell matrix proteome: re-analysis including MaxQuant iBAQ quantitation and phosphoproteome analysis. PMID:25018669
Oil accumulation mechanisms of the oleaginous microalga Chlorella protothecoides revealed through its genome, transcriptomes, and proteomes. PMID:25012212
Analysis of genome sequences from plant pathogenic Rhodococcus reveals genetic novelties in virulence loci. PMID:25010934
Identification of an ideal-like fingerprint for a protein fold using overlapped conserved residues based approach. PMID:25008052
Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef). PMID:25007843
Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. PMID:24980702
Genome-wide identification of transcription factors and transcription-factor binding sites in oleaginous microalgae Nannochloropsis. PMID:24965723
Examining the condition-specific antisense transcription in S. cerevisiae and S. paradoxus. PMID:24965678
AmiA is a penicillin target enzyme with dual activity in the intracellular pathogen Chlamydia pneumoniae. PMID:24953137
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
Draft Genome Sequence of Kitasatospora cheerisanensis KCTC 2395, Which Produces Plecomacrolide against Phytopathogenic Fungi. PMID:24948770
Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase. PMID:24938123
An alternative, arginase-independent pathway for arginine metabolism in Kluyveromyces lactis involves guanidinobutyrase as a key enzyme. PMID:24912400
Discovery of a new antiviral protein isolated Lonomia obliqua analysed by bioinformatics and real-time approaches. PMID:24908059
Quantitative temporal viromics: an approach to investigate host-pathogen interaction. PMID:24906157
Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction. PMID:24904632
DUF581 is plant specific FCS-like zinc finger involved in protein-protein interaction. PMID:24901469
Coiled-coil proteins facilitated the functional expansion of the centrosome. PMID:24901223
Proteomic analysis of adult Ascaris suum fluid compartments and secretory products. PMID:24901219
A bioinformatic and computational study of myosin phosphatase subunit diversity. PMID:24898838
BZcon1, a SANT/Myb-type gene involved in the conidiation of Cochliobolus carbonum. PMID:24898708
Comparative genomic characterization of a Thailand-Myanmar isolate, MS6, of Vibrio cholerae O1 El Tor, which is phylogenetically related to a "US Gulf Coast" clone. PMID:24887199
Exploring mechanisms of diet-colon cancer associations through candidate molecular interaction networks. PMID:24886433
Genome-wide expression profile of the response to spinal cord injury in Xenopus laevis reveals extensive differences between regenerative and non-regenerative stages. PMID:24885550
From sequence to enzyme mechanism using multi-label machine learning. PMID:24885296
fPoxDB: fungal peroxidase database for comparative genomics. PMID:24885079
Proteomic analysis of the Burkholderia pseudomallei type II secretome reveals hydrolytic enzymes, novel proteins, and the deubiquitinase TssM. PMID:24866793
A comprehensive phylogenetic and structural analysis of the carcinoembryonic antigen (CEA) gene family. PMID:24858421
Draft Genome Sequence of Endocarpon pusillum Strain KoLRILF000583. PMID:24855301
De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum. PMID:24821410
Draft Genome Sequence of Umbilicaria muehlenbergii KoLRILF000956, a Lichen-Forming Fungus Amenable to Genetic Manipulation. PMID:24762942
Community-based network study of protein-carbohydrate interactions in plant lectins using glycan array data. PMID:24755681
Draft Genome Sequence of the Growth-Promoting Endophyte Paenibacillus sp. P22, Isolated from Populus. PMID:24723717
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
Precise genetic mapping and integrative bioinformatics in Diversity Outbred mice reveals Hydin as a novel pain gene. PMID:24700285
PRDE-1 is a nuclear factor essential for the biogenesis of Ruby motif-dependent piRNAs in C. elegans. PMID:24696457
Exonic splicing signals impose constraints upon the evolution of enzymatic activity. PMID:24692663
Isopentenyltransferase-1 (IPT1) knockout in Physcomitrella together with phylogenetic analyses of IPTs provide insights into evolution of plant cytokinin biosynthesis. PMID:24692654
Identification and characterization of alternative splicing in parasitic nematode transcriptomes. PMID:24690220
Characterization of the pigmented shell-forming proteome of the common grove snail Cepaea nemoralis. PMID:24684722
Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. PMID:24653211
Ancient association between cation leak channels and Mid1 proteins is conserved in fungi and animals. PMID:24639627
Genomics and bioinformatics resources for translational science in Rosaceae. PMID:24634697
High precision prediction of functional sites in protein structures. PMID:24632601
A comprehensive analysis of microProteins reveals their potentially widespread mechanism of transcriptional regulation. PMID:24616380
RNA binding protein-mediated post-transcriptional gene regulation in medulloblastoma. PMID:24608801
STINGRAY: system for integrated genomic resources and analysis. PMID:24606808
Homer1 alternative splicing is regulated by gonadotropin-releasing hormone and modulates gonadotropin gene expression. PMID:24591653
Protein fold recognition using geometric kernel data fusion. PMID:24590441
The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. PMID:24580726
Stringent DDI-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. PMID:24564941
HMPAS: Human Membrane Protein Analysis System. PMID:24564858
Fungal plant cell wall-degrading enzyme database: a platform for comparative and evolutionary genomics in fungi and Oomycetes. PMID:24564786
Draft Genome Sequence of Lichen-Forming Fungus Cladonia metacorallifera Strain KoLRI002260. PMID:24526650
Genome-wide tissue-specific gene expression, co-expression and regulation of co-expressed genes in adult nematode Ascaris suum. PMID:24516681
Evolutionary comparisons of miRNA regulation system in six model organisms. PMID:24515651
Genes involved in the endoplasmic reticulum N-glycosylation pathway of the red microalga Porphyridium sp.: a bioinformatic study. PMID:24514561
Comparative transcriptome of wild type and selected strains of the microalgae Tisochrysis lutea provides insights into the genetic basis, lipid metabolism and the life cycle. PMID:24489800
Finding the missing honey bee genes: lessons learned from a genome upgrade. PMID:24479613
PFMFind: a system for discovery of peptide homology and function. PMID:24479118
Prioritizing disease-linked variants, genes, and pathways with an interactive whole-genome analysis pipeline. PMID:24478219
Screening of candidate regulators for cellulase and hemicellulase production in Trichoderma reesei and identification of a factor essential for cellulase production. PMID:24472375
BurrH: a new modular DNA binding protein for genome engineering. PMID:24452192
InterProScan 5: genome-scale protein function classification. PMID:24451626
Genome of the human hookworm Necator americanus. PMID:24441737
The transcriptome of the NZ endemic sea urchin Kina (Evechinus chloroticus). PMID:24438054
ISAAC - InterSpecies Analysing Application using Containers. PMID:24428905
Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models. PMID:24410852
Genome-wide expression analysis of reactive oxygen species gene network in Mizuna plants grown in long-term spaceflight. PMID:24393219
Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20. PMID:24391926
Protein domains of unknown function are essential in bacteria. PMID:24381303
Reconstruction of the lipid metabolism for the microalga Monoraphidium neglectum from its genome sequence reveals characteristics suitable for biofuel production. PMID:24373495
Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow. PMID:24369854
The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). PMID:24352233
A comprehensive phylogenetic analysis of deadenylases. PMID:24348009
POGs2: a web portal to facilitate cross-species inferences about protein architecture and function in plants. PMID:24340041
Gene duplication, lineage-specific expansion, and subfunctionalization in the MADF-BESS family patterns the Drosophila wing hinge. PMID:24336749
Amyloplast-localized SUBSTANDARD STARCH GRAIN4 protein influences the size of starch grains in rice endosperm. PMID:24335509
INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles. PMID:24324765
Genomic mining of prokaryotic repressors for orthogonal logic gates. PMID:24316737
topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins. PMID:24302577
PDBe: Protein Data Bank in Europe. PMID:24288376
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. PMID:24285306
A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress. PMID:24280345
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
The Structure-Function Linkage Database. PMID:24271399
The carbohydrate-active enzymes database (CAZy) in 2013. PMID:24270786
Representing annotation compositionality and provenance for the Semantic Web. PMID:24268021
CAMP: Collection of sequences and structures of antimicrobial peptides. PMID:24265220
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
MEGANTE: a web-based system for integrated plant genome annotation. PMID:24253915
Iron-binding haemerythrin RING ubiquitin ligases regulate plant iron responses and accumulation. PMID:24253678
Activities at the Universal Protein Resource (UniProt). PMID:24253303
De novo assembly and characterization of tissue specific transcriptomes in the emerald notothen, Trematomus bernacchii. PMID:24252228
Analysis of the Protein phosphotome of Entamoeba histolytica reveals an intricate phosphorylation network. PMID:24236039
SeqDepot: streamlined database of biological sequences and precomputed features. PMID:24234005
Integrating in silico resources to map a signaling network. PMID:24233784
The Genome Database for Rosaceae (GDR): year 10 update. PMID:24225320
Characterization of novel virulent broad-host-range phages of Xylella fastidiosa and Xanthomonas. PMID:24214944
DisMeta: a meta server for construct design and optimization. PMID:24203321
The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. PMID:24194595
PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. PMID:24174544
SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage. PMID:24165881
EBI metagenomics--a new resource for the analysis and archiving of metagenomic data. PMID:24165880
The mouse Gene Expression Database (GXD): 2014 update. PMID:24163257
The pancreatic expression database: recent extensions and updates. PMID:24163255
Ensembl Genomes 2013: scaling up access to genome-wide data. PMID:24163254
Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. PMID:24150943
The first venomous crustacean revealed by transcriptomics and functional morphology: remipede venom glands express a unique toxin cocktail dominated by enzymes and a neurotoxin. PMID:24132120
Proteome analysis of peroxisomes from etiolated Arabidopsis seedlings identifies a peroxisomal protease involved in β-oxidation and development. PMID:24130194
Two distinct sensing pathways allow recognition of Klebsiella pneumoniae by Dictyostelium amoebae. PMID:24128258
DGIdb: mining the druggable genome. PMID:24122041
Glycerophosphocholine utilization by Candida albicans: role of the Git3 transporter in virulence. PMID:24114876
Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PMID:24109552
Thermal adaptation of conformational dynamics in ribonuclease H. PMID:24098095
yApoptosis: yeast apoptosis database. PMID:24082050
Complete Genome Sequence of Vibrio anguillarum M3, a Serotype O1 Strain Isolated from Japanese Flounder in China. PMID:24072867
Automatic identification of highly conserved family regions and relationships in genome wide datasets including remote protein sequences. PMID:24069417
Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases. PMID:24038354
PainNetworks: a web-based resource for the visualisation of pain-related genes in the context of their network associations. PMID:24036287
The predicted secretome and transmembranome of the poultry red mite Dermanyssus gallinae. PMID:24020355
Draft Genome Sequence of Cladonia macilenta KoLRI003786, a Lichen-Forming Fungus Producing Biruloquinone. PMID:24009123
PPR-SMRs: ancient proteins with enigmatic functions. PMID:24004908
The genome of the alga-associated marine flavobacterium Formosa agariphila KMM 3901T reveals a broad potential for degradation of algal polysaccharides. PMID:23995932
Draft Genome Sequence of Lichen-Forming Fungus Caloplaca flavorubescens Strain KoLRI002931. PMID:23990579
The proteome of the calcified layer organic matrix of turkey (Meleagris gallopavo) eggshell. PMID:23981693
Protein domain definition should allow for conditional disorder. PMID:23963781
The Capsaspora genome reveals a complex unicellular prehistory of animals. PMID:23942320
In silico resurrection of the major vault protein suggests it is ancestral in modern eukaryotes. PMID:23887922
Structural characterization of the bacteriophage T7 tail machinery. PMID:23884409
TCW: transcriptome computational workbench. PMID:23874959
A novel function prediction approach using protein overlap networks. PMID:23866986
dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. PMID:23843252
Integrating pathways of Parkinson's disease in a molecular interaction map. PMID:23832570
Integrative relational machine-learning for understanding drug side-effect profiles. PMID:23802887
GeneMANIA prediction server 2013 update. PMID:23794635
A method for WD40 repeat detection and secondary structure prediction. PMID:23776530
Viral categorization and discovery in human circulation by transcriptome sequencing. PMID:23764402
The architectural design of networks of protein domain architectures. PMID:23760167
Silicon era of carbon-based life: application of genomics and bioinformatics in crop stress research. PMID:23759993
FIDEA: a server for the functional interpretation of differential expression analysis. PMID:23754850
TIMPs of parasitic helminths - a large-scale analysis of high-throughput sequence datasets. PMID:23721526
Evidence for adaptive evolution of low-temperature stress response genes in a Pooideae grass ancestor. PMID:23701123
Genomic and proteomic dissection of the ubiquitous plant pathogen, Armillaria mellea: toward a new infection model system. PMID:23656496
Simultaneous transcriptome analysis of Sorghum and Bipolaris sorghicola by using RNA-seq in combination with de novo transcriptome assembly. PMID:23638091
Genome sequencing of the plant pathogen Taphrina deformans, the causal agent of peach leaf curl. PMID:23631913
The challenge of increasing Pfam coverage of the human proteome. PMID:23603847
Discovery-2: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria. PMID:23537208
Long-term strain improvements accumulate mutations in regulatory elements responsible for hyper-production of cellulolytic enzymes. PMID:23535838
A domain-centric solution to functional genomics via dcGO Predictor. PMID:23514627
Protein function prediction by massive integration of evolutionary analyses and multiple data sources. PMID:23514099
Evolution of the ferric reductase domain (FRD) superfamily: modularity, functional diversification, and signature motifs. PMID:23505460
De-novo assembly and characterization of the transcriptome of Metschnikowia fructicola reveals differences in gene expression following interaction with Penicillium digitatum and grapefruit peel. PMID:23496978
Organic cofactors in the metabolism of Dehalococcoides mccartyi strains. PMID:23479751
PepT1 mRNA expression levels in sea bream (Sparus aurata) fed different plant protein sources. PMID:23449729
Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. PMID:23433480
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
Improving microbial genome annotations in an integrated database context. PMID:23424620
canEvolve: a web portal for integrative oncogenomics. PMID:23418540
Complete Genome Sequence of Listeria monocytogenes LL195, a Serotype 4b Strain from the 1983-1987 Listeriosis Epidemic in Switzerland. PMID:23405339
Genomic and secretomic analyses reveal unique features of the lignocellulolytic enzyme system of Penicillium decumbens. PMID:23383313
Global transcriptome profile of Cryptococcus neoformans during exposure to hydrogen peroxide induced oxidative stress. PMID:23383070
Cloning, annotation and developmental expression of the chicken intestinal MUC2 gene. PMID:23349743
Identification and functional characterization of a novel monotreme- specific antibacterial protein expressed during lactation. PMID:23326486
Identification of new protein interactions between dengue fever virus and its hosts, human and mosquito. PMID:23326450
Identification of the Hevea brasiliensis AP2/ERF superfamily by RNA sequencing. PMID:23324139
Single-particle EM reveals extensive conformational variability of the Ltn1 E3 ligase. PMID:23319619
An integrated in silico approach to design specific inhibitors targeting human poly(a)-specific ribonuclease. PMID:23236441
Calciomics: integrative studies of Ca2+-binding proteins and their interactomes in biological systems. PMID:23235533
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. PMID:23203882
OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis. PMID:23203876
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
H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery. PMID:23197657
TIGRFAMs and Genome Properties in 2013. PMID:23197656
The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. PMID:23193278
MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. PMID:23193269
HAMAP in 2013, new developments in the protein family classification and annotation system. PMID:23193261
ESTHER, the database of the α/β-hydrolase fold superfamily of proteins: tools to explore diversity of functions. PMID:23193256
OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica. PMID:23185044
TFClass: an expandable hierarchical classification of human transcription factors. PMID:23180794
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. PMID:23180791
UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation. PMID:23172288
Genenames.org: the HGNC resources in 2013. PMID:23161694
Update on activities at the Universal Protein Resource (UniProt) in 2013. PMID:23161681
New and continuing developments at PROSITE. PMID:23161676
RNApathwaysDB--a database of RNA maturation and decay pathways. PMID:23155061
Human ALKBH4 interacts with proteins associated with transcription. PMID:23145062
Draft genome sequence of Lactobacillus casei W56. PMID:23144392
MonarchBase: the monarch butterfly genome database. PMID:23143105
Identification of pOENI-1 and related plasmids in Oenococcus oeni strains performing the malolactic fermentation in wine. PMID:23139835
When a domain is not a domain, and why it is important to properly filter proteins in databases: conflicting definitions and fold classification systems for structural domains make filtering of such databases imperative. PMID:23108912
IUPHAR-DB: updated database content and new features. PMID:23087376
Hybrid sequencing approach applied to human fecal metagenomic clone libraries revealed clones with potential biotechnological applications. PMID:23082187
PRD: A protein-RNA interaction database. PMID:23055619
Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates. PMID:23035824
Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage. PMID:23013770
SWI/SNF complex in disorder: SWItching from malignancies to intellectual disability. PMID:23010866
RhesusBase: a knowledgebase for the monkey research community. PMID:22965133
DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders. PMID:22962312
Large scale of human duplicate genes divergence. PMID:22922908
Human more complex than mouse at cellular level. PMID:22911852
Minireview: progress and challenges in proteomics data management, sharing, and integration. PMID:22902541
CaPSID: a bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes. PMID:22901030
Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes. PMID:22882546
Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions. PMID:22792073
Functional assignment of metagenomic data: challenges and applications. PMID:22772835
Engineering ecosystems and synthetic ecologies. PMID:22722235
An evolutionarily conserved enhancer regulates Bmp4 expression in developing incisor and limb bud. PMID:22701669
CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. PMID:22693220
CombFunc: predicting protein function using heterogeneous data sources. PMID:22641853
The use of evolutionary patterns in protein annotation. PMID:22633559
How we feel: ion channel partnerships that detect mechanical inputs and give rise to touch and pain perception. PMID:22632719
The human phosphatase interactome: An intricate family portrait. PMID:22626554
GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics. PMID:22573175
GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development. PMID:22570409
The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012. PMID:22508994
SS18 together with animal-specific factors defines human BAF-type SWI/SNF complexes. PMID:22442726
Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. PMID:22301074
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:22144685
Comparative protein structure modeling using Modeller. PMID:18428767 -
The InterPro database, an integrated documentation resource for protein families, domains and functional sites
PubMed citations: 374.
374 articles citing: The InterPro database, an integrated documentation resource for protein families, domains and functional sites
Chromosome-Level Genome Assembly of the Hemiparasitic Taxillus chinensis (DC.) Danser. PMID:35482027
Structural and functional characterization of a hypothetical protein in the RD7 region in clinical isolates of Mycobacterium tuberculosis - an in silico approach to candidate vaccines. PMID:35394551
Identification, analysis of deleterious SNPs of the human GSR gene and their effects on the structure and functions of associated proteins and other diseases. PMID:35361806
In Silico Genome-Wide Characterisation of the Lipid Transfer Protein Multigenic Family in Sunflower (H. annuus L.). PMID:35270134
A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data. PMID:34900140
Two novel cyanobacterial α-dioxygenases for the biosynthesis of fatty aldehydes. PMID:34882252
iMPT-FDNPL: Identification of Membrane Protein Types with Functional Domains and a Natural Language Processing Approach. PMID:34671418
Repertoire analysis of γδ T cells in the chicken enables functional annotation of the genomic region revealing highly variable pan-tissue TCR gamma V gene usage as well as identifying public and private repertoires. PMID:34610803
High-quality reference genome of Fasciola gigantica: Insights into the genomic signatures of transposon-mediated evolution and specific parasitic adaption in tropical regions. PMID:34610021
The genome of the naturally evolved obesity-prone Ossabaw miniature pig. PMID:34585119
Clinical, Biochemical, and Genetic Heterogeneity in Glutaric Aciduria Type II Patients. PMID:34573316
Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity. PMID:33925458
Genetic and physical mapping of Melampsora rust resistance genes in Populus and characterization of linkage disequilibrium and flanking genomic sequence. PMID:33873470
Genomic Characterization and Expression Analysis of the SnRK Family Genes in Dendrobium officinale Kimura et Migo (Orchidaceae). PMID:33802577
UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase-substrate interactions. PMID:33693667
The Campylobacter jejuni CiaD effector co-opts the host cell protein IQGAP1 to promote cell entry. PMID:33637714
Genome-wide association study reveals a patatin-like lipase relating to the reduction of seed oil content in Brassica napus. PMID:33407143
Genome sequencing of deep-sea hydrothermal vent snails reveals adaptions to extreme environments. PMID:33319911
Eco-evolutionary Dynamics Set the Tempo and Trajectory of Metabolic Evolution in Multispecies Communities. PMID:33035481
In silico analysis predicting effects of deleterious SNPs of human RASSF5 gene on its structure and functions. PMID:32884013
Genomic Characterization and Expression Analysis of Basic Helix-Loop-Helix (bHLH) Family Genes in Traditional Chinese Herb Dendrobium officinale. PMID:32824436
Functional analyses of small secreted cysteine-rich proteins identified candidate effectors in Verticillium dahliae. PMID:32314529
Genome-wide survey of the bHLH super gene family in Brassica napus. PMID:32171243
Identification of a Novel Betacoronavirus (Merbecovirus) in Amur Hedgehogs from China. PMID:31653070
Genome-Wide Identification, Gene Structure and Expression Analysis of the MADS-Box Gene Family Indicate Their Function in the Development of Tobacco (Nicotiana tabacum L.). PMID:31614589
Genome-wide identification and expression analysis of citrus fruitlet abscission-related polygalacturonase genes. PMID:31218174
The genomic basis for colonizing the freezing Southern Ocean revealed by Antarctic toothfish and Patagonian robalo genomes. PMID:30715292
Reduced Activity of Nitrate Reductase Under Heavy Metal Cadmium Stress in Rice: An in silico Answer. PMID:30697220
Genomic resources for the Neotropical tree genus Cedrela (Meliaceae) and its relatives. PMID:30658593
NAC Family Transcription Factors in Tobacco and Their Potential Role in Regulating Leaf Senescence. PMID:30622549
Full genome characterization of two novel Alpha-coronavirus species from Italian bats. PMID:30447246
Identification of putative flowering genes and transcription factors from flower de novo transcriptome dataset of tuberose (Polianthes tuberosa L.). PMID:30302357
Genome-wide analysis of horizontally acquired genes in the genus Mycobacterium. PMID:30287860
Identification and comparison of key RNA interference machinery from western corn rootworm, fall armyworm, and southern green stink bug. PMID:30183751
Dysregulated genes targeted by microRNAs and metabolic pathways in bladder cancer revealed by bioinformatics methods. PMID:29928337
Loading of malonyl-CoA onto tandem acyl carrier protein domains of polyunsaturated fatty acid synthases. PMID:29921583
Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases. PMID:29666611
A Whole Genome Assembly of the Horn Fly, Haematobia irritans, and Prediction of Genes with Roles in Metabolism and Sex Determination. PMID:29602812
Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms. PMID:29471790
XPAT: a toolkit to conduct cross-platform association studies with heterogeneous sequencing datasets. PMID:29294048
Draft Genome Sequence of Leuconostoc citreum CW28 Isolated from Pozol, a Pre-Hispanic Fermented Corn Beverage. PMID:29192074
Control of Western Corn Rootworm (Diabrotica virgifera virgifera) Reproduction through Plant-Mediated RNA Interference. PMID:28974735
The bHLH transcription factor CgbHLH001 is a potential interaction partner of CDPK in halophyte Chenopodium glaucum. PMID:28814803
Identification of an operon involved in fluoride resistance in Enterobacter cloacae FRM. PMID:28754999
Complete Genome Sequences of Eight Rhizobium Symbionts Associated with Common Bean (Phaseolus vulgaris). PMID:28751391
Discovery of a Highly Divergent Coronavirus in the Asian House Shrew from China Illuminates the Origin of the Alphacoronaviruses. PMID:28637760
Structure-based functional annotation of hypothetical proteins from Candida dubliniensis: a quest for potential drug targets. PMID:28324558
Complete Genome Sequences of Three Rhizobium gallicum Symbionts Associated with Common Bean (Phaseolus vulgaris). PMID:28302777
AcsF Catalyzes the ATP-dependent Insertion of Nickel into the Ni,Ni-[4Fe4S] Cluster of Acetyl-CoA Synthase. PMID:27382049
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees. PMID:27359102
Genetic diversity of coronaviruses in Miniopterus fuliginosus bats. PMID:27125516
Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast. PMID:26861823
Neuropeptidergic Signaling in the American Lobster Homarus americanus: New Insights from High-Throughput Nucleotide Sequencing. PMID:26716450
Identification of putative phosphoproteins in wheat spikes induced by Fusarium graminearum. PMID:26669597
Draft genome sequence of Halopiger salifodinae KCY07-B2(T), an extremly halophilic archaeon isolated from a salt mine. PMID:26664653
Genome-wide analysis of the basic leucine zipper (bZIP) transcription factor gene family in six legume genomes. PMID:26651343
Unbiased high-throughput characterization of mussel transcriptomic responses to sublethal concentrations of the biotoxin okadaic acid. PMID:26618092
Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos. PMID:26572793
The YHS-Domain of an Adenylyl Cyclase from Mycobacterium phlei Is a Probable Copper-Sensor Module. PMID:26512893
Event inference in multidomain families with phylogenetic reconciliation. PMID:26451642
The bacterial pangenome as a new tool for analysing pathogenic bacteria. PMID:26442149
KnowEnG: a knowledge engine for genomics. PMID:26205246
Reagent and Data Resources for Investigation of RNA Binding Protein Functions in Drosophila melanogaster Cultured Cells. PMID:26199285
A draft network of ligand-receptor-mediated multicellular signalling in human. PMID:26198319
Soybean (Glycine max) SWEET gene family: insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis. PMID:26162601
GLAD: an Online Database of Gene List Annotation for Drosophila. PMID:26157507
Comprehensive analysis of SAUR gene family in citrus and its transcriptional correlation with fruitlet drop from abscission zone A. PMID:26115718
NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases. PMID:26110971
An Ebola virus-centered knowledge base. PMID:26055098
Large-Scale Evolutionary Analysis of Genes and Supergene Clusters from Terpenoid Modular Pathways Provides Insights into Metabolic Diversification in Flowering Plants. PMID:26046541
The ARF, AUX/IAA and GH3 gene families in citrus: genome-wide identification and expression analysis during fruitlet drop from abscission zone A. PMID:25982744
Bio301: A Web-Based EST Annotation Pipeline That Facilitates Functional Comparison Studies. PMID:25969743
Machine learning applications in genetics and genomics. PMID:25948244
Physiological and proteomic analyses of leaves from the halophyte Tangut Nitraria reveals diverse response pathways critical for high salinity tolerance. PMID:25713577
Genome sequence and description of the mosquitocidal and heavy metal tolerant strain Lysinibacillus sphaericus CBAM5. PMID:25685257
A complex interplay of tandem- and whole-genome duplication drives expansion of the L-type lectin receptor kinase gene family in the brassicaceae. PMID:25635042
Prioritizing causal disease genes using unbiased genomic features. PMID:25633252
Discovery of a novel coronavirus, China Rattus coronavirus HKU24, from Norway rats supports the murine origin of Betacoronavirus 1 and has implications for the ancestor of Betacoronavirus lineage A. PMID:25552712
Genome-wide analysis of citrus R2R3MYB genes and their spatiotemporal expression under stresses and hormone treatments. PMID:25473954
Discovery, diversity and evolution of novel coronaviruses sampled from rodents in China. PMID:25463600
Predicting the potential ankylosing spondylitis-related genes utilizing bioinformatics approaches. PMID:25432079
Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis. PMID:25351875
Protein profiles reveal diverse responsive signaling pathways in kernels of two maize inbred lines with contrasting drought sensitivity. PMID:25334062
Evolutionary conservation and expression of human RNA-binding proteins and their role in human genetic disease. PMID:25201102
A novel eliminase from a marine bacterium that degrades hyaluronan and chondroitin sulfate. PMID:25122756
Genomic basis of symbiovar mimosae in Rhizobium etli. PMID:25005495
Transcriptome dynamics of Arabidopsis thaliana root penetration by the oomycete pathogen Phytophthora parasitica. PMID:24974100
Proteomics analysis of the non-muscle myosin heavy chain IIa-enriched actin-myosin complex reveals multiple functions within the podocyte. PMID:24949636
Identification of G protein-coupled receptors in Schistosoma haematobium and S. mansoni by comparative genomics. PMID:24884876
Differences in lactococcal cell wall polysaccharide structure are major determining factors in bacteriophage sensitivity. PMID:24803515
PLIC: protein-ligand interaction clusters. PMID:24763918
Novel SNPs and INDEL polymorphisms in the 3'UTR of DGAT1 gene: in silico analyses and a possible association. PMID:24676595
Protein fold recognition using geometric kernel data fusion. PMID:24590441
Expression and bioinformatic analysis of lymphoma-associated novel gene KIAA0372. PMID:24557625
Genome Sequence of the Oleaginous Yeast Rhodotorula glutinis ATCC 204091. PMID:24526636
Genes involved in the endoplasmic reticulum N-glycosylation pathway of the red microalga Porphyridium sp.: a bioinformatic study. PMID:24514561
Genome sequence and description of the heavy metal tolerant bacterium Lysinibacillus sphaericus strain OT4b.31. PMID:24501644
Draft Genome Sequence of Amphibacillus jilinensis Y1(T), a Facultatively Anaerobic, Alkaliphilic and Halotolerant Bacterium. PMID:24501633
Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus. PMID:24415955
The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes. PMID:24359881
Parallel evolution of chordate cis-regulatory code for development. PMID:24282393
Alu mobile elements: from junk DNA to genomic gems. PMID:24278713
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
Functional clustering of immunoglobulin superfamily proteins with protein-protein interaction information calibrated hidden Markov model sequence profiles. PMID:24246499
Discovery of a novel bottlenose dolphin coronavirus reveals a distinct species of marine mammal coronavirus in Gammacoronavirus. PMID:24227844
Enzyme reaction annotation using cloud techniques. PMID:24222895
Can inferred provenance and its visualisation be used to detect erroneous annotation? A case study using UniProtKB. PMID:24143170
Deep brain stimulation modulates nonsense-mediated RNA decay in Parkinson's patients leukocytes. PMID:23865419
Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study. PMID:23738693
Protein-Protein Interactions Inferred from Domain-Domain Interactions in Genogroup II Genotype 4 Norovirus Sequences. PMID:23738320
Genetic characterization of Betacoronavirus lineage C viruses in bats reveals marked sequence divergence in the spike protein of pipistrellus bat coronavirus HKU5 in Japanese pipistrelle: implications for the origin of the novel Middle East respiratory syndrome coronavirus. PMID:23720729
Genome-wide identification and evolutionary and expression analyses of MYB-related genes in land plants. PMID:23690543
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. PMID:23586463
Transcriptome-wide identification of R2R3-MYB transcription factors in barley with their boron responsive expression analysis. PMID:23539153
New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis. PMID:23497205
Massive-scale gene co-expression network construction and robustness testing using random matrix theory. PMID:23409071
Genomic diversity and evolution of the head crest in the rock pigeon. PMID:23371554
Proteomic analysis of cell walls of two developmental stages of alfalfa stems. PMID:23248635
Genome-wide scans for candidate genes involved in the aquatic adaptation of dolphins. PMID:23246795
Structure and function of human xylulokinase, an enzyme with important roles in carbohydrate metabolism. PMID:23179721
Use of a repetitive seeding protocol to obtain diffraction-quality crystals of a putative human D-xylulokinase. PMID:23027762
EnrichNet: network-based gene set enrichment analysis. PMID:22962466
Protein domain recurrence and order can enhance prediction of protein functions. PMID:22962465
Recent transmission of a novel alphacoronavirus, bat coronavirus HKU10, from Leschenault's rousettes to pomona leaf-nosed bats: first evidence of interspecies transmission of coronavirus between bats of different suborders. PMID:22933277
SECOM: a novel hash seed and community detection based-approach for genome-scale protein domain identification. PMID:22761802
The R2R3-MYB transcription factor gene family in maize. PMID:22719841
Shrimp ATP synthase genes complement yeast null mutants for ATP hydrolysis but not synthesis activity. PMID:22718514
In silico prediction and analysis of Caenorhabditis EF-hand containing proteins. PMID:22701514
Genomic mining for novel FADH₂-dependent halogenases in marine sponge-associated microbial consortia. PMID:22562484
The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012. PMID:22508994
Role of Aspergillus niger acrA in arsenic resistance and its use as the basis for an arsenic biosensor. PMID:22467499
Isolation and characterization of a novel Betacoronavirus subgroup A coronavirus, rabbit coronavirus HKU14, from domestic rabbits. PMID:22398294
ArabidopsisChitinases: a Genomic Survey. PMID:22303199
Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. PMID:22278237
PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data. PMID:22123829
Genome sequence of Halobiforma lacisalsi AJ5, an extremely halophilic archaeon which harbors a bop gene. PMID:22123770
gViz, a novel tool for the visualization of co-expression networks. PMID:22032859
Tripal: a construction toolkit for online genome databases. PMID:21959868
Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma). PMID:21908640
Molecular epidemiology of human coronavirus OC43 reveals evolution of different genotypes over time and recent emergence of a novel genotype due to natural recombination. PMID:21849456
Role of plant-specific N-terminal domain of maize CK2β1 subunit in CK2β functions and holoenzyme regulation. PMID:21789193
EuroPineDB: a high-coverage web database for maritime pine transcriptome. PMID:21762488
The conjugative plasmid of a bean-nodulating Sinorhizobium fredii strain is assembled from sequences of two Rhizobium plasmids and the chromosome of a Sinorhizobium strain. PMID:21702991
PredUs: a web server for predicting protein interfaces using structural neighbors. PMID:21609948
Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice. PMID:21606319
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
Complete genome sequence of a Yersinia enterocolitica "Old World" (3/O:9) strain and comparison with the "New World" (1B/O:8) strain. PMID:21325549
Gene ontology based transfer learning for protein subcellular localization. PMID:21284890
RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts. PMID:21245033
Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement. PMID:20979641
Length constraints of multi-domain proteins in metazoans. PMID:20975906
Eimeria maxima phosphatidylinositol 4-phosphate 5-kinase: locus sequencing, characterization, and cross-phylum comparison. PMID:20938684
Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913. PMID:20703316
Inclusion membrane proteins of Protochlamydia amoebophila UWE25 reveal a conserved mechanism for host cell interaction among the Chlamydiae. PMID:20675479
The association of multiple interacting genes with specific phenotypes in rice using gene coexpression networks. PMID:20668062
Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. PMID:20627892
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. PMID:20626842
Modular composition predicts kinase/substrate interactions. PMID:20579376
A phylogenetic survey of myotubularin genes of eukaryotes: distribution, protein structure, evolution, and gene expression. PMID:20576132
Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences. PMID:20565830
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
Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae. PMID:20472752
The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation. PMID:20398413
The transcript repeat element: the human Alu sequence as a component of gene networks influencing cancer. PMID:20393868
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. PMID:20378718
TopoGSA: network topological gene set analysis. PMID:20335277
Genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order Rhizobiales. PMID:20144182
Armadillo motifs involved in vesicular transport. PMID:20126549
Use of comparative proteomics to identify key proteins related to hepatic lipid metabolism in broiler chickens: evidence accounting for differential fat deposition between strains. PMID:20049584
Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae. PMID:20040079
aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species. PMID:20040078
Aging mice show a decreasing correlation of gene expression within genetic modules. PMID:20019809
Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences. PMID:20003388
Thalidomide attenuates nitric oxide-driven angiogenesis by interacting with soluble guanylyl cyclase. PMID:19912234
A novel and efficient tool for locating and characterizing protein cavities and binding sites. PMID:19847777
AntigenDB: an immunoinformatics database of pathogen antigens. PMID:19820110
The novel polysaccharide deacetylase homologue Pdi contributes to virulence of the aquatic pathogen Streptococcus iniae. PMID:19762441
Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns. PMID:19534823
The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community. PMID:19534734
The transcriptomes of the cattle parasitic nematode Ostertagia ostartagi. PMID:19346077
Unusual armadillo fold in the human general vesicular transport factor p115. PMID:19247479
Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation. PMID:19116666
A systematic survey of mini-proteins in bacteria and archaea. PMID:19107199
Phylogenetic distribution and membrane topology of the LytR-CpsA-Psr protein family. PMID:19099556
Cloning and bioactivity analysis of a CXC ligand in black seabream Acanthopagrus schlegeli: the evolutionary clues of ELR+CXC chemokines. PMID:18990254
Minimotif miner 2nd release: a database and web system for motif search. PMID:18978024
Comparative analysis of complete genome sequences of three avian coronaviruses reveals a novel group 3c coronavirus. PMID:18971277
VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts. PMID:18953038
BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams. PMID:18925949
Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs. PMID:18838389
A method for probabilistic mapping between protein structure and function taxonomies through cross training. PMID:18834528
Bacteriophage 2851 is a prototype phage for dissemination of the Shiga toxin variant gene 2c in Escherichia coli O157:H7. PMID:18824528
Collection and comparative analysis of 1888 full-length cDNAs from wild rice Oryza rufipogon Griff. W1943. PMID:18687674
Validating annotations for uncharacterized proteins in Shewanella oneidensis. PMID:18687039
Streptococcus iniae M-like protein contributes to virulence in fish and is a target for live attenuated vaccine development. PMID:18665241
TEMBLOR - Perspectives of EBI Database Services. PMID:18628871
Website review: how to get the best from fission yeast genome data. PMID:18628858
De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features. PMID:18461181
ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data. PMID:18460543
Overview of protein structural and functional folds. PMID:18429251
Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3. PMID:18398463
Comparative genome analysis of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I; rp-A) and "Ca. Phytoplasma asteris" Strains OY-M and AY-WB. PMID:18359806
Complete genome sequence of the mosquitocidal bacterium Bacillus sphaericus C3-41 and comparison with those of closely related Bacillus species. PMID:18296527
The expression and bioinformatic analysis of a novel gene C20orf14 associated with lymphoma. PMID:18278469
Protein databases on the internet. PMID:18265344
Protein function assignment through mining cross-species protein-protein interactions. PMID:18253506
A screen for modifiers of hedgehog signaling in Drosophila melanogaster identifies swm and mts. PMID:18245841
The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota. PMID:18218977
The canine hookworm genome: analysis and classification of Ancylostoma caninum survey sequences. PMID:18082904
Evaluating the protein coding potential of exonized transposable element sequences. PMID:18036258
Patterns of genetic diversity and candidate genes for ecological divergence in a homoploid hybrid sunflower, Helianthus anomalus. PMID:17944850
A functional and regulatory map of asthma. PMID:17921359
A new O-antigen gene cluster has a key role in the virulence of the Escherichia coli meningitis clone O45:K1:H7. PMID:17905975
A multidimensional analysis of genes mutated in breast and colorectal cancers. PMID:17693572
Topology of AspT, the aspartate:alanine antiporter of Tetragenococcus halophilus, determined by site-directed fluorescence labeling. PMID:17660287
Complete genome sequence of bat coronavirus HKU2 from Chinese horseshoe bats revealed a much smaller spike gene with a different evolutionary lineage from the rest of the genome. PMID:17617433
A basal deuterostome genome viewed as a natural experiment. PMID:17550788
FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments. PMID:17537819
Comparative analysis of eubacterial DNA polymerase III alpha subunits. PMID:17531796
A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies. PMID:17522955
Nimbus (BgI): an active non-LTR retrotransposon of the Schistosoma mansoni snail host Biomphalaria glabrata. PMID:17521654
Structural and functional insights into Mimivirus ORFans. PMID:17490476
Occurrence of protein structure elements in conserved sequence regions. PMID:17210087
H-DBAS: alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational. PMID:17130147
Comparative analysis of twelve genomes of three novel group 2c and group 2d coronaviruses reveals unique group and subgroup features. PMID:17121802
DDBJ working on evaluation and classification of bacterial genes in INSDC. PMID:17108353
A Phytophthora infestans cystatin-like protein targets a novel tomato papain-like apoplastic protease. PMID:17085509
Molecular dissection of porcine reproductive and respiratory virus putative nonstructural protein 2. PMID:17037507
PLPD: reliable protein localization prediction from imbalanced and overlapped datasets. PMID:16966337
Cataloging the relationships between proteins: a review of interaction databases. PMID:16943573
Genomic scale sub-family assignment of protein domains. PMID:16877569
Tissue expression map of a large number of expressed sequence tags and its application to in silico screening of stress response genes in common wheat. PMID:16832693
Association algorithm to mine the rules that govern enzyme definition and to classify protein sequences. PMID:16776838
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PMID:16683036
The DNA-remodelling activity of DnaD is the sum of oligomerization and DNA-binding activities on separate domains. PMID:16677303
Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling. PMID:16672307
A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database. PMID:16608522
Whitefly (Bemisia tabaci) genome project: analysis of sequenced clones from egg, instar, and adult (viruliferous and non-viruliferous) cDNA libraries. PMID:16608516
Identification of transposons, retroelements, and a gene family predominantly expressed in floral tissues in chromosome 3DS of the hexaploid wheat progenitor Aegilops tauschii. PMID:16534632
EST2Prot: mapping EST sequences to proteins. PMID:16515706
The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons. PMID:16505379
BIOZON: a system for unification, management and analysis of heterogeneous biological data. PMID:16480510
RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits. PMID:16476165
EST analysis of the scaly green flagellate Mesostigma viride (Streptophyta): implications for the evolution of green plants (Viridiplantae). PMID:16476162
Reconstruction and regulation of the central catabolic pathway in the thermophilic propionate-oxidizing syntroph Pelotomaculum thermopropionicum. PMID:16352836
pTAC2, -6, and -12 are components of the transcriptionally active plastid chromosome that are required for plastid gene expression. PMID:16326926
Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts. PMID:16273343
Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks. PMID:16261196
A novel representation of protein sequences for prediction of subcellular location using support vector machines. PMID:16251364
Update on chloroplast proteomics. PMID:16245050
A hypervariable 130-kilobase genomic region of Magnetospirillum gryphiswaldense comprises a magnetosome island which undergoes frequent rearrangements during stationary growth. PMID:16237001
Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. PMID:16169905
Origin and evolution of new exons in rodents. PMID:16109974
DynGO: a tool for visualizing and mining of Gene Ontology and its associations. PMID:16091147
Expressed sequence tags from the oomycete fish pathogen Saprolegnia parasitica reveal putative virulence factors. PMID:16076392
BRIGEP--the BRIDGE-based genome-transcriptome-proteome browser. PMID:15980569
Catabolism of benzoate and phthalate in Rhodococcus sp. strain RHA1: redundancies and convergence. PMID:15937168
Structural and functional characterization of AtPTR3, a stress-induced peptide transporter of Arabidopsis. PMID:15889294
Investigating hookworm genomes by comparative analysis of two Ancylostoma species. PMID:15854223
Super paramagnetic clustering of protein sequences. PMID:15804359
Columba: an integrated database of proteins, structures, and annotations. PMID:15801979
Evolution of distinct EGF domains with specific functions. PMID:15772310
Protein interaction mapping: a Drosophila case study. PMID:15710747
Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. PMID:15613317
PartiGeneDB--collating partial genomes. PMID:15608203
InterPro, progress and status in 2005. PMID:15608177
PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization. PMID:15608166
Functional genomics of cell elongation in developing cotton fibers. PMID:15604659
PreSPI: a domain combination based prediction system for protein-protein interaction. PMID:15576357
Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria. PMID:15535866
Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1. PMID:15516593
Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. PMID:15514110
Predicting enzyme family class in a hybridization space. PMID:15498934
An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression. PMID:15489324
Isolation and characterization of an Arabidopsis mutant that overaccumulates O-Acetyl-L-Ser. PMID:15466229
Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. PMID:15461803
Crystal structure of a dodecameric FMN-dependent UbiX-like decarboxylase (Pad1) from Escherichia coli O157: H7. PMID:15459342
Comparative homology agreement search: an effective combination of homology-search methods. PMID:15367730
A comparative genomic analysis of ESTs from Ustilago maydis. PMID:15349794
A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans. PMID:15338281
Functional proteomics mapping of a human signaling pathway. PMID:15231748
The mouse homeobox gene Not is required for caudal notochord development and affected by the truncate mutation. PMID:15231714
Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations. PMID:15215412
Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. PMID:15215334
Comparison of ESTs from juvenile and adult phases of the giant unicellular green alga Acetabularia acetabulum. PMID:15070428
Molecular and comparative genetics of mental retardation. PMID:15020472
Functional prediction of a T-DNA tagged gene of Arabidopsis thaliana by in silico analysis. PMID:14767695
Comparative genomics of gene expression in the parasitic and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegans. PMID:14762059
Interaxonal Eph-ephrin signaling may mediate sorting of olfactory sensory axons in Manduca sexta. PMID:14684856
The mouse Gene Expression Database (GXD): updates and enhancements. PMID:14681482
NEMBASE: a resource for parasitic nematode ESTs. PMID:14681449
A large complement of the predicted Arabidopsis ARM repeat proteins are members of the U-box E3 ubiquitin ligase family. PMID:14657406
Generation, annotation, evolutionary analysis, and database integration of 20,000 unique sea urchin EST clusters. PMID:14656975
Bioinformatics Resources for In Silico Proteome Analysis. PMID:14615630
The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. PMID:14566062
The kinesin-associated protein UNC-76 is required for axonal transport in the Drosophila nervous system. PMID:12925768
A comparative proteomics resource: proteins of Arabidopsis thaliana. PMID:12914659
The DNA sequence of chromosome I of an African trypanosome: gene content, chromosome organisation, recombination and polymorphism. PMID:12907729
The sequence and analysis of Trypanosoma brucei chromosome II. PMID:12907728
Target selection and determination of function in structural genomics. PMID:12880206
Exploring the nonlinear geometry of protein homology. PMID:12876310
PepPat, a pattern-based oligopeptide homology search method and the identification of a novel tachykinin-like peptide. PMID:12856286
Retinoschisin, a photoreceptor-secreted protein, and its interaction with bipolar and muller cells. PMID:12853421
Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. PMID:12844361
EST mining and functional expression assays identify extracellular effector proteins from the plant pathogen Phytophthora. PMID:12840044
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. PMID:12824381
Development and evaluation of an automated annotation pipeline and cDNA annotation system. PMID:12819153
Phosphoregulators: protein kinases and protein phosphatases of mouse. PMID:12819143
Analysis of the mouse transcriptome for genes involved in the function of the nervous system. PMID:12819138
Exploration of the cell-cycle genes found within the RIKEN FANTOM2 data set. PMID:12819135
Comprehensive analysis of the mouse metabolome based on the transcriptome. PMID:12819132
Mouse proteome analysis. PMID:12819131
Cytokine-related genes identified from the RIKEN full-length mouse cDNA data set. PMID:12819128
Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution. PMID:12808149
New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. PMID:12799346
RRP20, a component of the 90S preribosome, is required for pre-18S rRNA processing in Saccharomyces cerevisiae. PMID:12736301
Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. PMID:12702207
GenDB--an open source genome annotation system for prokaryote genomes. PMID:12682369
Identification and characterisation of a melon genomic region containing a resistance gene cluster from a constructed BAC library. Microcolinearity between Cucumis melo and Arabidopsis thaliana. PMID:12678558
Cloning and heterologous expression of a beta-D-mannosidase (EC 3.2.1.25)-encoding gene from Thermobifida fusca TM51. PMID:12676668
What's in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence. PMID:12655011
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. PMID:12654719
Mapping the proteome of barrel medic (Medicago truncatula). PMID:12644662
New knowledge from old: in silico discovery of novel protein domains in Streptomyces coelicolor. PMID:12625841
Identification of pseudogenes in the Drosophila melanogaster genome. PMID:12560500
Conservation of structure and function among tyrosine recombinases: homology-based modeling of the lambda integrase core-binding domain. PMID:12560475
The repertoire of protein kinases encoded in the draft version of the human genome: atypical variations and uncommon domain combinations. PMID:12537555
E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. PMID:12520052
The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. PMID:12520037
PRINTS and its automatic supplement, prePRINTS. PMID:12520033
Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters. PMID:12520029
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. PMID:12520024
ProtoNet: hierarchical classification of the protein space. PMID:12520020
The Nuclear Protein Database (NPD): sub-nuclear localisation and functional annotation of the nuclear proteome. PMID:12520015
The InterPro Database, 2003 brings increased coverage and new features. PMID:12520011
The PEDANT genome database. PMID:12519983
The European Bioinformatics Institute's data resources. PMID:12519944
The EMBL Nucleotide Sequence Database: major new developments. PMID:12519939
Cynomolgus monkey testicular cDNAs for discovery of novel human genes in the human genome sequence. PMID:12498619
Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis. PMID:12490726
Random sequencing of Paramecium somatic DNA. PMID:12455983
The COBRA family of putative GPI-anchored proteins in Arabidopsis. A new fellowship in expansion. PMID:12376623
Genome-wide identification of nodule-specific transcripts in the model legume Medicago truncatula. PMID:12376622
Analysis of EF-hand-containing proteins in Arabidopsis. PMID:12372144
Genome sequence of the human malaria parasite Plasmodium falciparum. PMID:12368864
CDART: protein homology by domain architecture. PMID:12368255
Dictionary-driven protein annotation. PMID:12202776
The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties. PMID:12186647
Large-scale protein annotation through gene ontology. PMID:11997345
A complete sequence of the T. tengcongensis genome. PMID:11997336
Predicting gene ontology functions from ProDom and CDD protein domains. PMID:11932249
An efficient algorithm for large-scale detection of protein families. PMID:11917018
Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database. PMID:11875040
Surviving in a sea of data: a survey of plant genome data resources and issues in building data management systems. PMID:11860214
Functional control of the binuclear metal site in the metallo-beta-lactamase-like fold by subtle amino acid replacements. PMID:11847294
Limb-girdle muscular dystrophy type 2H associated with mutation in TRIM32, a putative E3-ubiquitin-ligase gene. PMID:11822024
Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model approach. PMID:11818024
Tools and resources for identifying protein families, domains and motifs. PMID:11806833
Prediction of unidentified human genes on the basis of sequence similarity to novel cDNAs from cynomolgus monkey brain. PMID:11806829
Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. PMID:11792869
A receptor tyrosine kinase from choanoflagellates: molecular insights into early animal evolution. PMID:11752452
The SBASE protein domain library, release 9.0: an online resource for protein domain identification. PMID:11752313
The IMB Jena Image Library of Biological Macromolecules: 2002 update. PMID:11752308
Recent improvements to the SMART domain-based sequence annotation resource. PMID:11752305
PRINTS and PRINTS-S shed light on protein ancestry. PMID:11752304
The PROSITE database, its status in 2002. PMID:11752303
The Ensembl genome database project. PMID:11752248
Structural and evolutionary relationships among protein tyrosine phosphatase domains. PMID:11585896
Application of InterPro for the functional classification of the proteins of fish origin in SWISS-PROT and TrEMBL. PMID:11426064
trEST, trGEN and Hits: access to databases of predicted protein sequences. PMID:11125074
Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes. PMID:11125045
CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins. PMID:11125042 -
The InterPro Database, 2003 brings increased coverage and new features
PubMed citations: 268.
268 articles citing: The InterPro Database, 2003 brings increased coverage and new features
In Silico Characterisation of the Late Embryogenesis Abundant (LEA) Protein Families and Their Role in Desiccation Tolerance in Ramonda serbica Panc. PMID:35408906
De novo transcriptome assembly of transgenic tobacco (Nicotiana tabacum NC89) with early senescence characteristic. PMID:33707866
EPIC: software toolkit for elution profile-based inference of protein complexes. PMID:31308550
Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri). PMID:31023218
Size scaling of nucleolus in Caenorhabditis elegans embryos. PMID:30580798
Toward Identifying Subnetworks from FBF Binding Landscapes in Caenorhabditis Spermatogenic or Oogenic Germlines. PMID:30459181
Adaptive Evolution under Extreme Genetic Drift in Oxidatively Stressed Caenorhabditis elegans. PMID:29069345
Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome. PMID:28951866
Genome-Wide Transcriptome Analysis Reveals Extensive Alternative Splicing Events in the Protoscoleces of Echinococcus granulosus and Echinococcus multilocularis. PMID:28588571
Dietary protein-induced hepatic IGF-1 secretion mediated by PPARγ activation. PMID:28257428
HINT: a database of annotated protein-protein interactions and their homologs. PMID:27857549
The Multivesicular Bodies (MVBs)-Localized AAA ATPase LRD6-6 Inhibits Immunity and Cell Death Likely through Regulating MVBs-Mediated Vesicular Trafficking in Rice. PMID:27618555
From Plant Infectivity to Growth Patterns: The Role of Blue-Light Sensing in the Prokaryotic World. PMID:27135492
Identification of Differentially Expressed Genes Related to Dehydration Resistance in a Highly Drought-Tolerant Pear, Pyrus betulaefolia, as through RNA-Seq. PMID:26900681
Genome-wide analysis of WRKY transcription factors in white pear (Pyrus bretschneideri) reveals evolution and patterns under drought stress. PMID:26704366
A Survey of the ATP-Binding Cassette (ABC) Gene Superfamily in the Salmon Louse (Lepeophtheirus salmonis). PMID:26418738
Non-immune immunoglobulins shield Schistosoma japonicum from host immunorecognition. PMID:26299686
Quantifying the displacement of mismatches in multiple sequence alignment benchmarks. PMID:25993129
Mongolian Almond (Prunus mongolica Maxim): The Morpho-Physiological, Biochemical and Transcriptomic Response to Drought Stress. PMID:25893685
Genome Sequence of Phytophthora fragariae var. fragariae, a Quarantine Plant-Pathogenic Fungus. PMID:25814589
The temporal transcriptomic response of Pinus massoniana seedlings to phosphorus deficiency. PMID:25165828
Genome-wide transcriptome analysis shows extensive alternative RNA splicing in the zoonotic parasite Schistosoma japonicum. PMID:25156522
RC1339/APRc from Rickettsia conorii is a novel aspartic protease with properties of retropepsin-like enzymes. PMID:25144529
Analysis of the transcriptome of Erigeron breviscapus uncovers putative scutellarin and chlorogenic acids biosynthetic genes and genetic markers. PMID:24956277
Discriminative motif discovery via simulated evolution and random under-sampling. PMID:24551063
Genome-wide transcriptome analysis of Chinese pollination-constant nonastringent persimmon fruit treated with ethanol. PMID:24507483
Discovery of genes related to witches broom disease in Paulownia tomentosa × Paulownia fortunei by a De Novo assembled transcriptome. PMID:24278262
Identifying the candidate genes involved in the calyx abscission process of 'Kuerlexiangli' (Pyrus sinkiangensis Yu) by digital transcript abundance measurements. PMID:24152304
Molecular cloning and homology modelling of a subtilisin-like serine protease from the marine fungus, Engyodontium album BTMFS10. PMID:24026932
A genomic-scale artificial microRNA library as a tool to investigate the functionally redundant gene space in Arabidopsis. PMID:23956262
De novo assembly, gene annotation and marker development using Illumina paired-end transcriptome sequences in celery (Apium graveolens L.). PMID:23469050
Inferring quantitative trait pathways associated with bull fertility from a genome-wide association study. PMID:23335935
Sex peptide of Drosophila melanogaster males is a global regulator of reproductive processes in females. PMID:22977156
On-line resources for Xenopus. PMID:22956109
Expressed sequence tags in cultivated peanut (Arachis hypogaea): discovery of genes in seed development and response to Ralstonia solanacearum challenge. PMID:22648474
Cardiomyopathy in patients with POMT1-related congenital and limb-girdle muscular dystrophy. PMID:22549409
Complete genome and transcriptomes of Streptococcus parasanguinis FW213: phylogenic relations and potential virulence mechanisms. PMID:22529932
Characterization of member of DUF1888 protein family, self-cleaving and self-assembling endopeptidase. PMID:22493430
Gene-centered regulatory network mapping. PMID:22118281
Expressed sequence-tag analysis of ovaries of Brachiaria brizantha reveals genes associated with the early steps of embryo sac differentiation of apomictic plants. PMID:22068439
Learning cellular sorting pathways using protein interactions and sequence motifs. PMID:21999284
Developmental transcriptomic features of the carcinogenic liver fluke, Clonorchis sinensis. PMID:21738807
Discriminative motif finding for predicting protein subcellular localization. PMID:21233524
Identification and analysis of function of a novel splicing variant of mouse receptor activator of NF-κB. PMID:21153864
Prediction of conformational changes by single mutation in the hepatitis B virus surface antigen (HBsAg) identified in HBsAg-negative blood donors. PMID:21087462
Comparative genome biology of a serogroup B carriage and disease strain supports a polygenic nature of meningococcal virulence. PMID:20709895
In silico analyses of proteomic data suggest a role for heat shock proteins in umbilical cord blood hematopoietic stem cells. PMID:20697978
Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds. PMID:20406431
Down-regulation of four putative arabinoxylan feruloyl transferase genes from family PF02458 reduces ester-linked ferulate content in rice cell walls. PMID:20012086
Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology. PMID:19921742
Accounting for redundancy when integrating gene interaction databases. PMID:19847299
Recombination and insertion events involving the botulinum neurotoxin complex genes in Clostridium botulinum types A, B, E and F and Clostridium butyricum type E strains. PMID:19804621
Expression of metallothionein and alpha-tubulin in heavy metal-tolerant Anopheles gambiae sensu stricto (Diptera: Culicidae). PMID:19735939
Structural and mutational analysis of band 7 proteins in the cyanobacterium Synechocystis sp. strain PCC 6803. PMID:19684140
Functional assessment of time course microarray data. PMID:19534758
PIRSF family classification system for protein functional and evolutionary analysis. PMID:19455212
Crystal structure of YfeU protein from Haemophilus influenzae: a predicted etherase involved in peptidoglycan recycling. PMID:19234762
NOPdb: Nucleolar Proteome Database--2008 update. PMID:18984612
Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity. PMID:18841247
Complete genome of Phenylobacterium zucineum--a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562. PMID:18700039
The molecule role ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature. PMID:18629146
Shaping biological knowledge: applications in proteomics. PMID:18629073
Identification and analysis of novel tandem repeats in the cell surface proteins of archaeal and bacterial genomes using computational tools. PMID:18629042
Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. PMID:18613949
Characterization of an amino acid permease from the endomycorrhizal fungus Glomus mosseae. PMID:18344417
Denoising inferred functional association networks obtained by gene fusion analysis. PMID:18081932
Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within plasmids. PMID:18060065
Structure-templated predictions of novel protein interactions from sequence information. PMID:17892321
Identification of Francisella tularensis Himar1-based transposon mutants defective for replication in macrophages. PMID:17682043
The Taenia saginata homologue of the major surface antigen of Echinococcus spp. is immunogenic and 97% identical to its Taenia solium homologue. PMID:17674048
Evolutionary conservation of regulated longevity assurance mechanisms. PMID:17612391
Dating the early evolution of plants: detection and molecular clock analyses of orthologs. PMID:17593393
Comprehensive analysis of co-occurring domain sets in yeast proteins. PMID:17562021
Characterization of an 18,166 EST dataset for cassava (Manihot esculenta Crantz) enriched for drought-responsive genes. PMID:17541599
Identification and analysis of novel amino-acid sequence repeats in Bacillus anthracis str. Ames proteome using computational tools. PMID:17538688
Discovery and characterization of 91 novel transcripts expressed in cattle placenta. PMID:17488528
Involvement of PLEKHM1 in osteoclastic vesicular transport and osteopetrosis in incisors absent rats and humans. PMID:17404618
Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. PMID:17307855
Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome. PMID:17254304
Mutator-like elements identified in melon, Arabidopsis and rice contain ULP1 protease domains. PMID:17136348
Sentra: a database of signal transduction proteins for comparative genome analysis. PMID:17135204
Structural modeling of protein interactions by analogy: application to PSD-95. PMID:17096593
Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways. PMID:17044931
Characterization and prediction of protein-protein interactions within and between complexes. PMID:17003128
Isolation and characterization of a novel v-SNARE family protein that interacts with a calcium-dependent protein kinase from the common ice plant, Mesembryanthemum crystallinum. PMID:16947054
Cataloging the relationships between proteins: a review of interaction databases. PMID:16943573
Genome comparison using Gene Ontology (GO) with statistical testing. PMID:16901353
sgTarget: a target selection resource for structural genomics. PMID:16844998
Prediction of RNA binding sites in proteins from amino acid sequence. PMID:16790841
A novel coiled-coil protein co-localizes and interacts with a calcium-dependent protein kinase in the common ice plant during low-humidity stress. PMID:16773372
Topology and weights in a protein domain interaction network--a novel way to predict protein interactions. PMID:16716232
Analysis of 10,000 ESTs from lymphocytes of the cynomolgus monkey to improve our understanding of its immune system. PMID:16618371
Benchmarking ortholog identification methods using functional genomics data. PMID:16613613
The IclR family of transcriptional activators and repressors can be defined by a single profile. PMID:16597823
Structure of phage protein BC1872 from Bacillus cereus, a singleton with new fold. PMID:16596646
Predicting the subcellular localization of viral proteins within a mammalian host cell. PMID:16595001
Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications. PMID:16566839
INTEGRATOR: interactive graphical search of large protein interactomes over the Web. PMID:16542421
NovelFam3000--uncharacterized human protein domains conserved across model organisms. PMID:16533400
Analyses of expressed sequence tags from apple. PMID:16531485
Exploiting protein structure data to explore the evolution of protein function and biological complexity. PMID:16524831
Tracking the evolution of alternatively spliced exons within the Dscam family. PMID:16483367
LocustDB: a relational database for the transcriptome and biology of the migratory locust (Locusta migratoria). PMID:16426458
GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins. PMID:16417636
Analysis of and function predictions for previously conserved hypothetical or putative proteins in Blochmannia floridanus. PMID:16401340
Phytome: a platform for plant comparative genomics. PMID:16381967
Phytophthora functional genomics database (PFGD): functional genomics of phytophthora-plant interactions. PMID:16381913
PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. PMID:16381879
E-MSD: improving data deposition and structure quality. PMID:16381867
NOPdb: Nucleolar Proteome Database. PMID:16381850
TCDB: the Transporter Classification Database for membrane transport protein analyses and information. PMID:16381841
Lectin receptor kinases participate in protein-protein interactions to mediate plasma membrane-cell wall adhesions in Arabidopsis. PMID:16361528
High performance workflow implementation for protein surface characterization using grid technology. PMID:16351745
GNARE: automated system for high-throughput genome analysis with grid computational backend. PMID:16328950
Refining protein subcellular localization. PMID:16322766
Structural basis of severe acute respiratory syndrome coronavirus ADP-ribose-1''-phosphate dephosphorylation by a conserved domain of nsP3. PMID:16271890
Update on chloroplast proteomics. PMID:16245050
Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. PMID:16237009
Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae. PMID:16204194
Pyruvate fermentation by Oenococcus oeni and Leuconostoc mesenteroides and role of pyruvate dehydrogenase in anaerobic fermentation. PMID:16151074
Dynamic covariation between gene expression and proteome characteristics. PMID:16131395
Transcribed Tc1-like transposons in salmonid fish. PMID:16095544
Identification of four fimbria-encoding genomic islands that are highly specific for verocytotoxin-producing Escherichia coli serotype O157 strains. PMID:16081921
Localization of protein-binding sites within families of proteins. PMID:16081657
The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond. PMID:16010005
Genome-wide detection and analysis of cell wall-bound proteins with LPxTG-like sorting motifs. PMID:15995208
ProFunc: a server for predicting protein function from 3D structure. PMID:15980588
GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. PMID:15980548
MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes. PMID:15980515
BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. PMID:15980512
SOAP-based services provided by the European Bioinformatics Institute. PMID:15980463
PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families. PMID:15980440
Distribution of immunodeficiency fact files with XML--from Web to WAP. PMID:15978138
An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. PMID:15960829
Constitutive signal transduction by mutant Ssy5p and Ptr3p components of the SPS amino acid sensor system in Saccharomyces cerevisiae. PMID:15947203
The TetR family of transcriptional repressors. PMID:15944459
Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii. PMID:15938755
1.6 A crystal structure of YteR protein from Bacillus subtilis, a predicted lyase. PMID:15906318
HinT proteins and their putative interaction partners in Mollicutes and Chlamydiaceae. PMID:15904496
AnoEST: toward A. gambiae functional genomics. PMID:15899967
Plant protein annotation in the UniProt Knowledgebase. PMID:15888679
The institute for genomic research Osa1 rice genome annotation database. PMID:15888674
Comparative mapping of sequence-based and structure-based protein domains. PMID:15790427
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. PMID:15784138
The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen. PMID:15781495
Speeding disease gene discovery by sequence based candidate prioritization. PMID:15766383
Identification and characterization of regions of the rice genome associated with broad-spectrum, quantitative disease resistance. PMID:15716503
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes. PMID:15716312
Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. PMID:15710748
Crystal structure of the hypothetical protein TA1238 from Thermoplasma acidophilum: a new type of helical super-bundle. PMID:15704011
The Genomes of Oryza sativa: a history of duplications. PMID:15685292
Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. PMID:15684069
Arabidopsis emb175 and other ppr knockout mutants reveal essential roles for pentatricopeptide repeat (PPR) proteins in plant embryogenesis. PMID:15647901
Memory consolidation and gene expression in Periplaneta americana. PMID:15647592
Cyclic nucleotide binding proteins in the Arabidopsis thaliana and Oryza sativa genomes. PMID:15644130
Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis. PMID:15642098
Highly conserved non-coding sequences are associated with vertebrate development. PMID:15630479
Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. PMID:15613238
SpliceInfo: an information repository for mRNA alternative splicing in human genome. PMID:15608290
ECgene: genome annotation for alternative splicing. PMID:15608289
The Legume Information System (LIS): an integrated information resource for comparative legume biology. PMID:15608283
Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics. PMID:15608281
openSputnik--a database to ESTablish comparative plant genomics using unsaturated sequence collections. PMID:15608275
ArrayExpress--a public repository for microarray gene expression data at the EBI. PMID:15608260
The European Bioinformatics Institute's data resources: towards systems biology. PMID:15608238
Ensembl 2005. PMID:15608235
ChickVD: a sequence variation database for the chicken genome. PMID:15608233
SilkDB: a knowledgebase for silkworm biology and genomics. PMID:15608225
BacMap: an interactive picture atlas of annotated bacterial genomes. PMID:15608206
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. PMID:15608201
The EMBL Nucleotide Sequence Database. PMID:15608199
The PANTHER database of protein families, subfamilies, functions and pathways. PMID:15608197
E-MSD: an integrated data resource for bioinformatics. PMID:15608192
The SYSTERS Protein Family Database in 2005. PMID:15608183
The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines. PMID:15608182
ProtoNet 4.0: a hierarchical classification of one million protein sequences. PMID:15608180
The ProDom database of protein domain families: more emphasis on 3D. PMID:15608179
FunShift: a database of function shift analysis on protein subfamilies. PMID:15608176
ADDA: a domain database with global coverage of the protein universe. PMID:15608174
eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity. PMID:15608172
The Universal Protein Resource (UniProt). PMID:15608167
UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. PMID:15608165
Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. PMID:15601538
Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags. PMID:15590942
prot4EST: translating expressed sequence tags from neglected genomes. PMID:15571632
Functional analysis of methylthioribose kinase genes in plants. PMID:15557090
The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet). PMID:15518589
Human MicroRNA targets. PMID:15502875
From ORFeome to biology: a functional genomics pipeline. PMID:15489336
A gateway-compatible yeast one-hybrid system. PMID:15489331
Predicting subcellular localization via protein motif co-occurrence. PMID:15466294
Isolation and characterization of an Arabidopsis mutant that overaccumulates O-Acetyl-L-Ser. PMID:15466229
A comprehensive transcript index of the human genome generated using microarrays and computational approaches. PMID:15461792
Automated prediction of protein function and detection of functional sites from structure. PMID:15456910
Genomic and proteomic analysis of thirty-nine structural proteins of shrimp white spot syndrome virus. PMID:15452257
Clustering of genes coding for DNA binding proteins in a region of atypical evolution of the human genome. PMID:15383909
A comparative genomic analysis of ESTs from Ustilago maydis. PMID:15349794
A first-draft human protein-interaction map. PMID:15345047
IdentiCS--identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence. PMID:15312235
YAPI, a new Yersinia pseudotuberculosis pathogenicity island. PMID:15271940
Computational identification and characterization of novel genes from legumes. PMID:15266052
Laboratory scale structural genomics. PMID:15263853
New challenges in gene expression data analysis and the extended GEPAS. PMID:15215434
NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases. PMID:15215420
MyHits: a new interactive resource for protein annotation and domain identification. PMID:15215405
PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level. PMID:15215388
3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment. PMID:15215345
BLAST Filter and GraphAlign: rule-based formation and analysis of sets of related DNA and protein sequences. PMID:15215343
Public web-based services from the European Bioinformatics Institute. PMID:15215339
Interaction profile-based protein classification of death domain. PMID:15189571
The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. PMID:15188009
Genome SEGE: a database for 'intronless' genes in eukaryotic genomes. PMID:15175116
Functional annotation of the Arabidopsis genome using controlled vocabularies. PMID:15173566
Bacterial signal transduction network in a genomic perspective. PMID:15142243
High-throughput fluorescent tagging of full-length Arabidopsis gene products in planta. PMID:15141064
Visualizing sequence similarity of protein families. PMID:15140831
Progress towards mapping the universe of protein folds. PMID:15128436
The Ensembl analysis pipeline. PMID:15123589
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PMID:15103394
Identification of differentially expressed cDNA sequences in ovaries of sexual and apomictic plants of Brachiaria brizantha. PMID:15082923
Similar active sites in lysostaphins and D-Ala-D-Ala metallopeptidases. PMID:15044722
Comparative analysis of protein domain organization. PMID:14993202
Gene content and density in banana ( Musa acuminata) as revealed by genomic sequencing of BAC clones. PMID:14985976
LEON: multiple aLignment Evaluation Of Neighbours. PMID:14982955
Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families. PMID:14739328
Analysis of the lambdoid prophage element e14 in the E. coli K-12 genome. PMID:14733619
Antisense transcripts with rice full-length cDNAs. PMID:14709177
The novel plant homeodomain protein rhinoceros antagonizes Ras signaling in the Drosophila eye. PMID:14704181
Digging with experimental pick and computational shovel: a new addition to the histidine kinase superfamily. PMID:14702293
Transcriptome analysis of mouse stem cells and early embryos. PMID:14691545
HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE. PMID:14681467
FREP: a database of functional repeats in mouse cDNAs. PMID:14681460
MitoProteome: mitochondrial protein sequence database and annotation system. PMID:14681458
The aMAZE LightBench: a web interface to a relational database of cellular processes. PMID:14681453
Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes. PMID:14681448
PHYTOPROT: a database of clusters of plant proteins. PMID:14681432
GeneDB: a resource for prokaryotic and eukaryotic organisms. PMID:14681429
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. PMID:14681408
Genew: the Human Gene Nomenclature Database, 2004 updates. PMID:14681406
3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes. PMID:14681404
The SUPERFAMILY database in 2004: additions and improvements. PMID:14681402
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. PMID:14681401
SCOP database in 2004: refinements integrate structure and sequence family data. PMID:14681400
E-MSD: an integrated data resource for bioinformatics. PMID:14681397
TrSDB: a proteome database of transcription factors. PMID:14681387
MEROPS: the peptidase database. PMID:14681384
ESTHER, the database of the alpha/beta-hydrolase fold superfamily of proteins. PMID:14681380
SMART 4.0: towards genomic data integration. PMID:14681379
Recent improvements to the PROSITE database. PMID:14681377
UniProt: the Universal Protein knowledgebase. PMID:14681372
PIRSF: family classification system at the Protein Information Resource. PMID:14681371
MIPS: analysis and annotation of proteins from whole genomes. PMID:14681354
The EMBL Nucleotide Sequence Database. PMID:14681351
The WD-repeat protein superfamily in Arabidopsis: conservation and divergence in structure and function. PMID:14672542
Chlamydomonas reinhardtii at the crossroads of genomics. PMID:14665449
A genome-wide survey of human pseudogenes. PMID:14656963
POCUS: mining genomic sequence annotation to predict disease genes. PMID:14611661
PCAS--a precomputed proteome annotation database resource. PMID:14594458
PANDORA: keyword-based analysis of protein sets by integration of annotation sources. PMID:14500825
Pilot survey of expressed sequence tags (ESTs) from the asexual blood stages of Plasmodium vivax in human patients. PMID:12914668
Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins. PMID:12904577
OntoBlast function: From sequence similarities directly to potential functional annotations by ontology terms. PMID:12824422
GlobPlot: Exploring protein sequences for globularity and disorder. PMID:12824398
Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments. PMID:12824354
Integrated databanks access and sequence/structure analysis services at the PBIL. PMID:12824334
SWISS-MODEL: An automated protein homology-modeling server. PMID:12824332
GeneSilico protein structure prediction meta-server. PMID:12824313
A comparison of Pfam and MEROPS: two databases, one comprehensive, and one specialised. PMID:12740029 -
InterPro, progress and status in 2005
PubMed citations: 239.
239 articles citing: InterPro, progress and status in 2005
CsPOM1, a DYRK Family Kinase, Plays Diverse Roles in Fungal Development, Virulence, and Stress Tolerance in the Anthracnose Pathogen Colletotrichum scovillei. PMID:35558103
Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease. PMID:33769280
Design principles of gene evolution for niche adaptation through changes in protein-protein interaction networks. PMID:32973219
A PAS-Containing Histidine Kinase is Required for Conidiation, Appressorium Formation, and Disease Development in the Rice Blast Fungus, Magnaporthe oryzae. PMID:32010469
Genome-Wide Identification, Expression Profile of the TIFY Gene Family in Brassica oleracea var. capitata, and Their Divergent Response to Various Pathogen Infections and Phytohormone Treatments. PMID:31991606
De novo genome assembly and comparative annotation reveals metabolic versatility in cellulolytic bacteria from cropland and forest soils. PMID:31378834
Characterization of a Protein Phosphatase Type-1 and a Kinase Anchoring Protein in Plasmodium falciparum. PMID:30429842
Distinct roles of the YPEL gene family in development and pathogenicity in the ascomycete fungus Magnaporthe oryzae. PMID:30262874
Antivirals for allosteric inhibition of Zika virus using a homology model and experimentally determined structure of envelope protein. PMID:28754167
An Approach for Zika Virus Inhibition Using Homology Structure of the Envelope Protein. PMID:27683255
Evidence of recent interspecies horizontal gene transfer regarding nucleopolyhedrovirus infection of Spodoptera frugiperda. PMID:26607569
Virus proteins similar to human proteins as possible disturbance on human pathways. PMID:26396652
An orthology-based analysis of pathogenic protozoa impacting global health: an improved comparative genomics approach with prokaryotes and model eukaryote orthologs. PMID:24960463
Species-specific expansion and molecular evolution of the 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) gene family in plants. PMID:24722776
A Novel Type III Endosome Transmembrane Protein, TEMP. PMID:24710541
Mouse model phenotypes provide information about human drug targets. PMID:24158600
The genus Pseudovibrio contains metabolically versatile bacteria adapted for symbiosis. PMID:23601235
Catalog of Erycina pusilla miRNA and categorization of reproductive phase-related miRNAs and their target gene families. PMID:23575662
Computational model for pathway reconstruction to unravel the evolutionary significance of melanin synthesis. PMID:23390353
Gene sets for utilization of primary and secondary nutrition supplies in the distal gut of endangered Iberian lynx. PMID:23251564
Expression of a finger millet transcription factor, EcNAC1, in tobacco confers abiotic stress-tolerance. PMID:22808152
Genome-wide analysis of the MYB transcription factor superfamily in soybean. PMID:22776508
Novel domain combinations in proteins encoded by chimeric transcripts. PMID:22689780
"Guilt by association" is the exception rather than the rule in gene networks. PMID:22479173
A Resource of Quantitative Functional Annotation for Homo sapiens Genes. PMID:22384401
Structure- and sequence-based function prediction for non-homologous proteins. PMID:22270458
Generation and Analysis of Large-Scale Data-Driven Mycobacterium tuberculosis Functional Networks for Drug Target Identification. PMID:22190924
Time-resolved transcriptomics and bioinformatic analyses reveal intrinsic stress responses during batch culture of Bacillus subtilis. PMID:22087258
Genomic basis of endosymbiont-conferred protection against an insect parasitoid. PMID:21948522
Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales. PMID:21829548
Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features. PMID:21559529
Alternatively Spliced Genes as Biomarkers for Schizophrenia, Bipolar Disorder and Psychosis: A Blood-Based Spliceome-Profiling Exploratory Study. PMID:21532980
Scoring protein relationships in functional interaction networks predicted from sequence data. PMID:21526183
The draft genome of the parasitic nematode Trichinella spiralis. PMID:21336279
Design, validation and annotation of transcriptome-wide oligonucleotide probes for the oligochaete annelid Eisenia fetida. PMID:21170345
Genome-wide computational function prediction of Arabidopsis proteins by integration of multiple data sources. PMID:21098674
Inference of surface membrane factors of HIV-1 infection through functional interaction networks. PMID:20967291
Automatic, context-specific generation of Gene Ontology slims. PMID:20929524
In silico identification of carboxylate clamp type tetratricopeptide repeat proteins in Arabidopsis and rice as putative co-chaperones of Hsp90/Hsp70. PMID:20856808
Detecting novel genes with sparse arrays. PMID:20691772
Real-time ligand binding pocket database search using local surface descriptors. PMID:20455259
Mining Cytochrome b561 proteins from plant genomes. PMID:20223741
Bayesian Markov Random Field analysis for protein function prediction based on network data. PMID:20195360
Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity. PMID:20158875
Predicting Type 1 Diabetes Candidate Genes using Human Protein-Protein Interaction Networks. PMID:20148193
The comprehensive microbial resource. PMID:19892825
The integrated microbial genomes system: an expanding comparative analysis resource. PMID:19864254
Cloning and molecular characterization of a novel rolling-circle replicating plasmid, pK1S-1, from Bacillus thuringiensis subsp. kurstaki K1. PMID:19763421
Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. PMID:19728866
The functional domain grouping of microtubule associated proteins. PMID:19704789
Run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting Bartonella grahamii. PMID:19578403
Mining the Arabidopsis and rice genomes for cyclophilin protein families. PMID:19525202
An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. PMID:19491311
A novel pathogenicity gene is required in the rice blast fungus to suppress the basal defenses of the host. PMID:19390617
Evidence of a tick RNAi pathway by comparative genomics and reverse genetics screen of targets with known loss-of-function phenotypes in Drosophila. PMID:19323841
Molecular determinants archetypical to the phylum Nematoda. PMID:19296854
TFCat: the curated catalog of mouse and human transcription factors. PMID:19284633
Structural genomics reveals EVE as a new ASCH/PUA-related domain. PMID:19191354
Michigan molecular interactions r2: from interacting proteins to pathways. PMID:18978014
PlasmoDB: a functional genomic database for malaria parasites. PMID:18957442
MODOMICS: a database of RNA modification pathways. 2008 update. PMID:18854352
Just how versatile are domains? PMID:18854028
The genome of the simian and human malaria parasite Plasmodium knowlesi. PMID:18843368
Mutations in CHD7, encoding a chromatin-remodeling protein, cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome. PMID:18834967
RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome. PMID:18820292
Development and use of genetic system to identify genes required for efficient low-temperature growth of Psychrobacter arcticus 273-4. PMID:18818866
Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice. PMID:18813954
NetGrep: fast network schema searches in interactomes. PMID:18801179
Access to immunology through the Gene Ontology. PMID:18798919
Fungal cytochrome P450 database. PMID:18755027
Impacts of protein-protein interaction domains on organism and network complexity. PMID:18687879
Intestinal transcriptomes of nematodes: comparison of the parasites Ascaris suum and Haemonchus contortus with the free-living Caenorhabditis elegans. PMID:18682827
Meta-basic estimates the size of druggable human genome. PMID:18663489
Challenges and solutions in proteomics. PMID:18645629
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
Sequence similarity network reveals common ancestry of multidomain proteins. PMID:18475320
Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants. PMID:18426584
Complete genome sequence of the soil actinomycete Kocuria rhizophila. PMID:18408034
Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. PMID:18407065
JCoast - a biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes. PMID:18380896
Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria. PMID:18348319
Defining functional distances over gene ontology. PMID:18221506
Genes and (common) pathways underlying drug addiction. PMID:18179280
The Arabidopsis MUM2 gene encodes a beta-galactosidase required for the production of seed coat mucilage with correct hydration properties. PMID:18165329
Evaluating deterministic motif significance measures in protein databases. PMID:18157916
Structure of [NiFe] hydrogenase maturation protein HypE from Escherichia coli and its interaction with HypF. PMID:18065529
A primer on python for life science researchers. PMID:18052533
Assessing and combining reliability of protein interaction sources. PMID:17990508
GreenPhylDB: a database for plant comparative genomics. PMID:17986457
Gene Ontology annotations at SGD: new data sources and annotation methods. PMID:17982175
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. PMID:17980028
CFGP: a web-based, comparative fungal genomics platform. PMID:17947331
Characterization of protein hubs by inferring interacting motifs from protein interactions. PMID:17941705
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. PMID:17933782
Structural and transcriptional analyses of a purine nucleotide-binding protein from Pyrococcus furiosus: a component of a novel, membrane-bound multiprotein complex unique to this hyperthermophilic archaeon. PMID:17932790
AutoPSI: a database for automatic structural classification of protein sequences and structures. PMID:17932066
SmedGD: the Schmidtea mediterranea genome database. PMID:17881371
Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina. PMID:17868481
Automatic generation of 3D motifs for classification of protein binding sites. PMID:17760982
Characterising alternate splicing and tissue specific expression in the chicken from ESTs. PMID:17675868
Identification of sensory and signal-transducing domains in two-component signaling systems. PMID:17628134
Probabilistic prediction and ranking of human protein-protein interactions. PMID:17615067
FlyMine: an integrated database for Drosophila and Anopheles genomics. PMID:17615057
A topological algorithm for identification of structural domains of proteins. PMID:17608939
WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches. PMID:17584794
Evolution of symbiotic bacteria in the distal human intestine. PMID:17579514
Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site. PMID:17578578
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. PMID:17570147
A domain-based approach to predict protein-protein interactions. PMID:17567909
Differentiation-dependent expression of Adhfe1 in adipogenesis. PMID:17559793
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
MyHits: improvements to an interactive resource for analyzing protein sequences. PMID:17545200
Molecular concepts analysis links tumors, pathways, mechanisms, and drugs. PMID:17534450
ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences. PMID:17526512
Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome. PMID:17511520
Identification of a single HNH active site in type IIS restriction endonuclease Eco31I. PMID:17499273
Patterns of selection and tissue-specific expression among maize domestication and crop improvement loci. PMID:17496114
DBAli tools: mining the protein structure space. PMID:17478513
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. PMID:17478504
The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. PMID:17460045
Homology modeling of major intrinsic proteins in rice, maize and Arabidopsis: comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters. PMID:17445256
Statistical analysis of genomic protein family and domain controlled annotations for functional investigation of classified gene lists. PMID:17430558
A kingdom-specific protein domain HMM library for improved annotation of fungal genomes. PMID:17425790
From genes to functional classes in the study of biological systems. PMID:17407596
Gene function in early mouse embryonic stem cell differentiation. PMID:17394647
HitKeeper, a generic software package for hit list management. PMID:17391514
Membrane protein prediction methods. PMID:17367718
Linear array of conserved sequence motifs to discriminate protein subfamilies: study on pyridine nucleotide-disulfide reductases. PMID:17367536
Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. PMID:17356713
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PMID:17355171
GOTax: investigating biological processes and biochemical activities along the taxonomic tree. PMID:17346342
A phylogenomic analysis of the Actinomycetales mce operons. PMID:17324287
Specificity and evolvability in eukaryotic protein interaction networks. PMID:17305419
Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans. PMID:17274809
Genome-wide identification and analyses of the rice calmodulin and related potential calcium sensor proteins. PMID:17263873
Motif kernel generated by genetic programming improves remote homology and fold detection. PMID:17254344
Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology. PMID:17254302
Genomic functional investigation through statistical analysis of protein families and domains. PMID:17238639
Plant Gene and Alternatively Spliced Variant Annotator. A plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species. PMID:17220363
DiscoverySpace: an interactive data analysis application. PMID:17210078
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. PMID:17202171
New developments in the InterPro database. PMID:17202162
Analysis and prediction of functionally important sites in proteins. PMID:17192586
Evolutionary conservation of domain-domain interactions. PMID:17184549
EMBL Nucleotide Sequence Database in 2006. PMID:17148479
IntAct--open source resource for molecular interaction data. PMID:17145710
Expanded protein information at SGD: new pages and proteome browser. PMID:17142221
MiST: a microbial signal transduction database. PMID:17135192
GeneSpeed: protein domain organization of the transcriptome. PMID:17132830
The mouse Gene Expression Database (GXD): 2007 update. PMID:17130151
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. PMID:17130145
PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. PMID:17130144
EVEREST: a collection of evolutionary conserved protein domains. PMID:17099230
SynDB: a Synapse protein DataBase based on synapse ontology. PMID:17098931
The SUPERFAMILY database in 2007: families and functions. PMID:17098927
Human-specific insertions and deletions inferred from mammalian genome sequences. PMID:17095709
CancerGenes: a gene selection resource for cancer genome projects. PMID:17088289
Proteolytic adaptor for transfer-messenger RNA-tagged proteins from alpha-proteobacteria. PMID:17085560
ProtoBee: hierarchical classification and annotation of the honey bee proteome. PMID:17065614
'Genome design' model and multicellular complexity: golden middle. PMID:17062620
Java GUI for InterProScan (JIPS): a tool to help process multiple InterProScans and perform ortholog analysis. PMID:17054794
Maintenance DNA methyltransferase (Met1) and silencing of CpG-methylated foreign DNA in Volvox carteri. PMID:17033890
Comparative proteomic analysis of high cell density cultivations with two recombinant Bacillus megaterium strains for the production of a heterologous dextransucrase. PMID:17022804
Analysis of protein sequence and interaction data for candidate disease gene prediction. PMID:17020920
The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes. PMID:16980466
Cataloging the relationships between proteins: a review of interaction databases. PMID:16943573
A RecA-mediated exon profiling method. PMID:16896013
Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice. PMID:16861571
Crystal structure of TDP-fucosamine acetyltransferase (WecD) from Escherichia coli, an enzyme required for enterobacterial common antigen synthesis. PMID:16855251
ProKware: integrated software for presenting protein structural properties in protein tertiary structures. PMID:16845116
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. PMID:16845052
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. PMID:16845026
TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB. PMID:16845023
MACSIMS: multiple alignment of complete sequences information management system. PMID:16792820
Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis. PMID:16789813
A new measure for functional similarity of gene products based on Gene Ontology. PMID:16776819
The Escherichia coli proteome: past, present, and future prospects. PMID:16760308
Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis. PMID:16751553
A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model. PMID:16737530
Protein family expansions and biological complexity. PMID:16733546
The gain and loss of genes during 600 million years of vertebrate evolution. PMID:16723033
The effects of multiple features of alternatively spliced exons on the K(A)/K(S) ratio test. PMID:16709259
Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. PMID:16685651
Functional annotation prediction: all for one and one for all. PMID:16672244
Conversion of MapMan to allow the analysis of transcript data from Solanaceous species: effects of genetic and environmental alterations in energy metabolism in the leaf. PMID:16649112
Phylogenomic analysis of the GIY-YIG nuclease superfamily. PMID:16646971
Phylogenomic analysis of vertebrate thrombospondins reveals fish-specific paralogues, ancestral gene relationships and a tetrapod innovation. PMID:16620379
The dictyostelium kinome--analysis of the protein kinases from a simple model organism. PMID:16596165
Update of the NAD(P)H:quinone oxidoreductase (NQO) gene family. PMID:16595077
L-tartaric acid synthesis from vitamin C in higher plants. PMID:16567629
Amplification of the Gene Ontology annotation of Affymetrix probe sets. PMID:16549014
Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds. PMID:16549009
Domain-based small molecule binding site annotation. PMID:16545112
ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms. PMID:16539733
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat. PMID:16536879
Towards genome-scale structure prediction for transmembrane proteins. PMID:16524835
The proteome: structure, function and evolution. PMID:16524832
Structure of the conserved hypothetical protein MAL13P1.257 from Plasmodium falciparum. PMID:16511296
A comprehensive software suite for the analysis of cDNAs. PMID:16487083
Transcriptional activators in yeast. PMID:16464826
A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. PMID:16420670
MaGe: a microbial genome annotation system supported by synteny results. PMID:16407324
A systematic approach to infer biological relevance and biases of gene network structures. PMID:16407322
Panzea: a database and resource for molecular and functional diversity in the maize genome. PMID:16381974
Phytome: a platform for plant comparative genomics. PMID:16381967
Gramene: a bird's eye view of cereal genomes. PMID:16381966
The UCSC Genome Browser Database: update 2006. PMID:16381938
The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context. PMID:16381934
TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations. PMID:16381929
pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. PMID:16381926
FLIGHT: database and tools for the integration and cross-correlation of large-scale RNAi phenotypic datasets. PMID:16381916
The UCSC Archaeal Genome Browser. PMID:16381898
VMD: a community annotation database for oomycetes and microbial genomes. PMID:16381891
INVHOGEN: a database of homologous invertebrate genes. PMID:16381884
The integrated microbial genomes (IMG) system. PMID:16381883
The SWISS-MODEL Repository: new features and functionalities. PMID:16381875
SCOPPI: a structural classification of protein-protein interfaces. PMID:16381874
SIMAP: the similarity matrix of proteins. PMID:16381858
ChimerDB--a knowledgebase for fusion sequences. PMID:16381848
The Universal Protein Resource (UniProt): an expanding universe of protein information. PMID:16381842
MODOMICS: a database of RNA modification pathways. PMID:16381833
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. PMID:16381825
EMBL Nucleotide Sequence Database: developments in 2005. PMID:16381823
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity. PMID:16351747
The EH1 motif in metazoan transcription factors. PMID:16309560
Discover protein sequence signatures from protein-protein interaction data. PMID:16305745
Channel formation by CarO, the carbapenem resistance-associated outer membrane protein of Acinetobacter baumannii. PMID:16304148
Sequence and structural analysis of BTB domain proteins. PMID:16207353
Recognition of unknown conserved alternatively spliced exons. PMID:16110330
Mating type loci of Sporisorium reilianum: novel pattern with three a and multiple b specificities. PMID:16087737
MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences. PMID:16043635
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function. PMID:16011798
The MicrobesOnline Web site for comparative genomics. PMID:15998914
Proteomic analysis of a eukaryotic cilium. PMID:15998802
Scooby-domain: prediction of globular domains in protein sequence. PMID:15980446
InterProScan: protein domains identifier. PMID:15980438 -
New developments in the InterPro database
PubMed citations: 229.
229 articles citing: New developments in the InterPro database
Chromosome-scale assembly and high-density genetic map of the yellow drum, Nibea albiflora. PMID:34654820
Genetic variants of small airways and interstitial pulmonary disease in children. PMID:33526882
Donkey genomes provide new insights into domestication and selection for coat color. PMID:33293529
Engineering and application of a biosensor with focused ligand specificity. PMID:32978386
Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia. PMID:32488117
The Grass Carp Genomic Visualization Database (GCGVD): an informational platform for genome biology of grass carp. PMID:31592084
Expansion and Functional Diversification of SKP1-Like Genes in Wheat (Triticum aestivum L.). PMID:31277523
Identifying differentially expressed proteins in sorghum cell cultures exposed to osmotic stress. PMID:29875393
Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01. PMID:29721151
Exoproteome Analysis of the Seaweed Pathogen Nautella italica R11 Reveals Temperature-Dependent Regulation of RTX-Like Proteins. PMID:28706511
The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding. PMID:28541388
Melanisation of Aspergillus terreus-Is Butyrolactone I Involved in the Regulation of Both DOPA and DHN Types of Pigments in Submerged Culture? PMID:28471414
Transcriptomic Complexity of Aspergillus terreus Velvet Gene Family under the Influence of Butyrolactone I. PMID:28335447
A three-way approach for protein function classification. PMID:28234929
Epigenetic map and genetic map basis of complex traits in cassava population. PMID:28120898
Retention and Molecular Evolution of Lipoxygenase Genes in Modern Rosid Plants. PMID:27746812
Draft genome sequence of subterranean clover, a reference for genus Trifolium. PMID:27545089
Comparative analysis of the human and zebrafish kinomes: focus on the development of kinase inhibitors. PMID:27011661
A Factor Graph Approach to Automated GO Annotation. PMID:26771463
Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method. PMID:26568785
Solute Carrier Family 26 Member a2 (slc26a2) Regulates Otic Development and Hair Cell Survival in Zebrafish. PMID:26375458
toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research. PMID:26130662
The resurrection genome of Boea hygrometrica: A blueprint for survival of dehydration. PMID:25902549
Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don. PMID:25805887
Differential retention and expansion of the ancestral genes associated with the paleopolyploidies in modern rosid plants, as revealed by analysis of the extensins super-gene family. PMID:25047956
Computational prediction of protein function based on weighted mapping of domains and GO terms. PMID:24868539
Draft sequences of the radish (Raphanus sativus L.) genome. PMID:24848699
Think globally and solve locally: secondary memory-based network learning for automated multi-species function prediction. PMID:24843788
H2rs: deducing evolutionary and functionally important residue positions by means of an entropy and similarity based analysis of multiple sequence alignments. PMID:24766829
A Novel Type III Endosome Transmembrane Protein, TEMP. PMID:24710541
Complete genome sequence of Ilumatobacter coccineum YM16-304(T.). PMID:24501628
Sma3s: a three-step modular annotator for large sequence datasets. PMID:24501397
Genome-wide characterization of microRNA in foxtail millet (Setaria italica). PMID:24330712
Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species. PMID:24282021
Genotypic and phenotypic versatility of Aspergillus flavus during maize exploitation. PMID:23894339
A human skeletal muscle interactome centered on proteins involved in muscular dystrophies: LGMD interactome. PMID:23414517
Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids. PMID:23410187
Complete genome sequence of Oscillibacter valericigenes Sjm18-20(T) (=NBRC 101213(T)). PMID:23408234
Intricate interplay between astrocytes and motor neurons in ALS. PMID:23388633
Genome-wide identification and analysis of the B3 superfamily of transcription factors in Brassicaceae and major crop plants. PMID:23377560
An analysis of the transcriptome of Teladorsagia circumcincta: its biological and biotechnological implications. PMID:23282110
Protein domain recurrence and order can enhance prediction of protein functions. PMID:22962465
Deciphering the genome of polyphosphate accumulating actinobacterium Microlunatus phosphovorus. PMID:22923697
Subcellular localization of extracytoplasmic proteins in monoderm bacteria: rational secretomics-based strategy for genomic and proteomic analyses. PMID:22912771
Characterization of microRNAs expression during maize seed development. PMID:22853295
First analysis of the secretome of the canine heartworm, Dirofilaria immitis. PMID:22781075
A systematic comparison of genome-scale clustering algorithms. PMID:22759431
The yak genome and adaptation to life at high altitude. PMID:22751099
LDGIdb: a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs. PMID:22551073
Proteomic analysis of Plasmodium in the mosquito: progress and pitfalls. PMID:22336136
Effects of doxycycline on gene expression in Wolbachia and Brugia malayi adult female worms in vivo. PMID:22321609
The Biofuel Feedstock Genomics Resource: a web-based portal and database to enable functional genomics of plant biofuel feedstock species. PMID:22250003
Generation and Analysis of Large-Scale Data-Driven Mycobacterium tuberculosis Functional Networks for Drug Target Identification. PMID:22190924
The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes. PMID:22120664
An online conserved SSR discovery through cross-species comparison. PMID:21918613
Genome-wide structural analysis reveals novel membrane binding properties of AP180 N-terminal homology (ANTH) domains. PMID:21828048
Domain architecture conservation in orthologs. PMID:21819573
NELL-1 binds to APR3 affecting human osteoblast proliferation and differentiation. PMID:21723284
Determinants of antigenicity and specificity in immune response for protein sequences. PMID:21693021
Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning. PMID:21685095
Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement. PMID:21572172
A novel integrase-containing element may interact with Laem-Singh virus (LSNV) to cause slow growth in giant tiger shrimp. PMID:21569542
Intracellular eukaryotic parasites have a distinct unfolded protein response. PMID:21559456
Temperature-induced protein secretion by Leishmania mexicana modulates macrophage signalling and function. PMID:21559274
Evolution of the karyopherin-β family of nucleocytoplasmic transport factors; ancient origins and continued specialization. PMID:21556326
Scoring protein relationships in functional interaction networks predicted from sequence data. PMID:21526183
Inferring physical protein contacts from large-scale purification data of protein complexes. PMID:21451165
HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition. PMID:21423752
Mapping the sequences of potential guanine quadruplex motifs. PMID:21357607
Mycoplasma mycoides, from "mycoides Small Colony" to "capri". A microevolutionary perspective. PMID:21324191
Proteomic temporal profile of human brain endothelium after oxidative stress. PMID:21164131
Genome sequence of Kitasatospora setae NBRC 14216T: an evolutionary snapshot of the family Streptomycetaceae. PMID:21059706
Conserved and variable correlated mutations in the plant MADS protein network. PMID:20979667
Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon. PMID:20973991
Novel venom gene discovery in the platypus. PMID:20920228
Digital expression profiling of novel diatom transcripts provides insight into their biological functions. PMID:20738856
Genomic repertoires of DNA-binding transcription factors across the tree of life. PMID:20675356
Comparative Membranome expression analysis in primary tumors and derived cell lines. PMID:20668533
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. PMID:20478823
Predicting conserved protein motifs with Sub-HMMs. PMID:20420695
Systems biology in heart diseases. PMID:20411053
Growth delay of human bladder cancer cells by Prostate Stem Cell Antigen downregulation is associated with activation of immune signaling pathways. PMID:20374648
Bioinformatic tools for identifying disease gene and SNP candidates. PMID:20238089
Highly punctuated patterns of population structure on the X chromosome and implications for African evolutionary history. PMID:20085712
Disentangling direct from indirect co-evolution of residues in protein alignments. PMID:20052271
The secreted and surface proteomes of the adult stage of the carcinogenic human liver fluke Opisthorchis viverrini. PMID:20049860
Complete genomic structure of the cultivated rice endophyte Azospirillum sp. B510. PMID:20047946
Identification of a novel ABC transporter required for desiccation tolerance, and biofilm formation in Rhizobium leguminosarum bv. viciae 3841. PMID:20030718
CalA, a cyanobacterial AbrB protein, interacts with the upstream region of hypC and acts as a repressor of its transcription in the cyanobacterium Nostoc sp. strain PCC 7120. PMID:20023111
Spatial and temporal analysis of gene expression during growth and fusion of the mouse facial prominences. PMID:20016822
RNRdb, a curated database of the universal enzyme family ribonucleotide reductase, reveals a high level of misannotation in sequences deposited to Genbank. PMID:19995434
A genome-wide characterization of microRNA genes in maize. PMID:19936050
XML-based approaches for the integration of heterogeneous bio-molecular data. PMID:19828083
A stochastic context free grammar based framework for analysis of protein sequences. PMID:19814800
Exploration of uncharted regions of the protein universe. PMID:19787035
FIGfams: yet another set of protein families. PMID:19762480
Something old, something new, something borrowed; how the thermoacidophilic archaeon Sulfolobus solfataricus responds to oxidative stress. PMID:19759909
UFO: a web server for ultra-fast functional profiling of whole genome protein sequences. PMID:19725959
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. PMID:19723330
Microbial NAD metabolism: lessons from comparative genomics. PMID:19721089
Advances in the Development and Application of Computational Methodologies for Structural Modeling of G-Protein Coupled Receptors. PMID:19672320
A comparative genomics, network-based approach to understanding virulence in Vibrio cholerae. PMID:19666715
Bioinformatics annotation of the hypothetical proteins found by omics techniques can help to disclose additional virulence factors. PMID:19636617
Comprehensive EST analysis of the symbiotic sea anemone, Anemonia viridis. PMID:19627569
Triangle network motifs predict complexes by complementing high-error interactomes with structural information. PMID:19558694
Visualising biological data: a semantic approach to tool and database integration. PMID:19534744
ProGMap: an integrated annotation resource for protein orthology. PMID:19494185
Candidate chemoreceptor subfamilies differentially expressed in the chemosensory organs of the mollusc Aplysia. PMID:19493360
Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins. PMID:19486509
The High Throughput Sequence Annotation Service (HT-SAS) - the shortcut from sequence to true Medline words. PMID:19445703
Candidate effector gene identification in the ascomycete fungal phytopathogen Venturia inaequalis by expressed sequence tag analysis. PMID:19400844
Sequence-based prediction of type III secreted proteins. PMID:19390696
Comparative expression pathway analysis of human and canine mammary tumors. PMID:19327144
CNVVdb: a database of copy number variations across vertebrate genomes. PMID:19321736
Analysis of tarantula skeletal muscle protein sequences and identification of transcriptional isoforms. PMID:19298669
Bioinformatic characterizations and prediction of K+ and Na+ ion channels effector toxins. PMID:19284552
Type VI secretion apparatus and phage tail-associated protein complexes share a common evolutionary origin. PMID:19251641
Identification of DNA-binding proteins using structural, electrostatic and evolutionary features. PMID:19233205
S-layer, surface-accessible, and concanavalin A binding proteins of Methanosarcina acetivorans and Methanosarcina mazei. PMID:19228054
Protein function annotation by homology-based inference. PMID:19226439
Somatic, germline and sex hierarchy regulated gene expression during Drosophila metamorphosis. PMID:19216785
Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology. PMID:19208187
Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies. PMID:19208173
A comparative chemogenomics strategy to predict potential drug targets in the metazoan pathogen, Schistosoma mansoni. PMID:19198654
Exploiting genomic patterns to discover new supramolecular protein assemblies. PMID:19177352
Domain mobility in proteins: functional and evolutionary implications. PMID:19151098
Protein structure homology modeling using SWISS-MODEL workspace. PMID:19131951
Fourmidable: a database for ant genomics. PMID:19126223
The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program. PMID:19084081
LRRCE: a leucine-rich repeat cysteine capping motif unique to the chordate lineage. PMID:19077264
GeneDistiller--distilling candidate genes from linkage intervals. PMID:19057649
SNUGB: a versatile genome browser supporting comparative and functional fungal genomics. PMID:19055845
Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations. PMID:19055775
KAGIANA: an excel-based tool for retrieving summary information on Arabidopsis genes. PMID:19043069
Aspergillus genomes and the Aspergillus cloud. PMID:19039001
OryGenesDB 2008 update: database interoperability for functional genomics of rice. PMID:19036791
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. PMID:19036790
The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative. PMID:19027726
Microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility. PMID:19025650
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse. PMID:19015123
Microarray analysis identifies candidate genes for key roles in coral development. PMID:19014561
Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila. PMID:19014467
PIPs: human protein-protein interaction prediction database. PMID:18988626
ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes. PMID:18984624
Proteome-wide identification of poly(ADP-ribose) binding proteins and poly(ADP-ribose)-associated protein complexes. PMID:18981049
SMART 6: recent updates and new developments. PMID:18978020
FastBLAST: homology relationships for millions of proteins. PMID:18974889
SysZNF: the C2H2 zinc finger gene database. PMID:18974185
dictyBase--a Dictyostelium bioinformatics resource update. PMID:18974179
Stage- and gender-specific proteomic analysis of Brugia malayi excretory-secretory products. PMID:18958170
The GOA database in 2009--an integrated Gene Ontology Annotation resource. PMID:18957448
FlyBase: enhancing Drosophila Gene Ontology annotations. PMID:18948289
The National Center for Biotechnology Information's Protein Clusters Database. PMID:18940865
InterPro: the integrative protein signature database. PMID:18940856
Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis. PMID:18852473
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. PMID:18845581
SchistoDB: a Schistosoma mansoni genome resource. PMID:18842636
MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data. PMID:18834496
Splice-mediated Variants of Proteins (SpliVaP) - data and characterization of changes in signatures among protein isoforms due to alternative splicing. PMID:18831736
Needles in the EST haystack: large-scale identification and analysis of excretory-secretory (ES) proteins in parasitic nematodes using expressed sequence tags (ESTs). PMID:18820748
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks. PMID:18782832
Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus. PMID:18776029
The F-box gene family is expanded in herbaceous annual plants relative to woody perennial plants. PMID:18775973
Protein structure search and local structure characterization. PMID:18721472
Prioritization of candidate cancer genes--an aid to oncogenomic studies. PMID:18710882
Comparative analysis of testis protein evolution in rodents. PMID:18689890
Predicting pathway membership via domain signatures. PMID:18676972
Meta-basic estimates the size of druggable human genome. PMID:18663489
Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening. PMID:18655731
The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation. PMID:18644147
Experience using web services for biological sequence analysis. PMID:18621748
Unraveling protein networks with power graph analysis. PMID:18617988
On the extent and origins of genic novelty in the phylum Nematoda. PMID:18596977
Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. PMID:18586742
Assessment and improvement of the Plasmodium yoelii yoelii genome annotation through comparative analysis. PMID:18586738
Investigation of Lpin1 as a candidate gene for fat deposition in pigs. PMID:18581256
SjTPdb: integrated transcriptome and proteome database and analysis platform for Schistosoma japonicum. PMID:18578888
The combination approach of SVM and ECOC for powerful identification and classification of transcription factor. PMID:18554421
Analysis of the genome sequence of Lactobacillus gasseri ATCC 33323 reveals the molecular basis of an autochthonous intestinal organism. PMID:18539810
Anaerobic degradation of p-ethylphenol by "Aromatoleum aromaticum" strain EbN1: pathway, regulation, and involved proteins. PMID:18539747
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments. PMID:18515841
Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex. PMID:18515835
Genome structure of the legume, Lotus japonicus. PMID:18511435
ENDEAVOUR update: a web resource for gene prioritization in multiple species. PMID:18508807
Whole genome identification of Mycobacterium tuberculosis vaccine candidates by comprehensive data mining and bioinformatic analyses. PMID:18505592
Preparation and analysis of an expressed sequence tag library from the toxic dinoflagellate Alexandrium catenella. PMID:18478293
In silico and in vivo evaluation of bacteriophage phiEF24C, a candidate for treatment of Enterococcus faecalis infections. PMID:18456848
High-throughput functional annotation and data mining with the Blast2GO suite. PMID:18445632
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
Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato. PMID:18405374
In vitro selection and characterization of ceftobiprole-resistant methicillin-resistant Staphylococcus aureus. PMID:18378703
Rapid classification of protein structure models using unassigned backbone RDCs and probability density profile analysis (PDPA). PMID:18321742
In silico characterization of proteins: UniProt, InterPro and Integr8. PMID:18219596
Gene characterization index: assessing the depth of gene annotation. PMID:18213364
The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation. PMID:18197987
Complete genomic structure of the bloom-forming toxic cyanobacterium Microcystis aeruginosa NIES-843. PMID:18192279
A first glimpse at the transcriptome of Physarum polycephalum. PMID:18179708
Extending pathways based on gene lists using InterPro domain signatures. PMID:18177498
A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PMID:18094749
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. PMID:18089548
The canine hookworm genome: analysis and classification of Ancylostoma caninum survey sequences. PMID:18082904
DBD--taxonomically broad transcription factor predictions: new content and functionality. PMID:18073188
Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PMID:18043742
SIMAP--structuring the network of protein similarities. PMID:18037617
CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data. PMID:18034885
Gene3D: comprehensive structural and functional annotation of genomes. PMID:18032434
GenoList: an integrated environment for comparative analysis of microbial genomes. PMID:18032431
ToxoDB: an integrated Toxoplasma gondii database resource. PMID:18003657
DIMA 2.0--predicted and known domain interactions. PMID:17999995
PairsDB atlas of protein sequence space. PMID:17986464
Gramene: a growing plant comparative genomics resource. PMID:17984077
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees. PMID:17982176
ProtozoaDB: dynamic visualization and exploration of protozoan genomes. PMID:17981844
The Molecule Pages database. PMID:17965093
Improved human disease candidate gene prioritization using mouse phenotype. PMID:17939863
ProSAS: a database for analyzing alternative splicing in the context of protein structures. PMID:17933774
GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. PMID:17932055
DOMINE: a database of protein domain interactions. PMID:17913741
The cytochrome P450 enzyme CYP96A15 is the midchain alkane hydroxylase responsible for formation of secondary alcohols and ketones in stem cuticular wax of Arabidopsis. PMID:17905869
Integrating sequence and structural biology with DAS. PMID:17850653
Predicting active site residue annotations in the Pfam database. PMID:17688688
Applying negative rule mining to improve genome annotation. PMID:17659089
Web services at the European bioinformatics institute. PMID:17576686
The 2006 automated function prediction meeting. PMID:17570143
Dissection of the Bradyrhizobium japonicum NifA+sigma54 regulon, and identification of a ferredoxin gene (fdxN) for symbiotic nitrogen fixation. PMID:17569992
ConiferEST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs). PMID:17535431
ImmTree: database of evolutionary relationships of genes and proteins in the human immune system. PMID:17376226 -
The InterPro protein families and domains database: 20 years on
PubMed citations: 198.
198 articles citing: The InterPro protein families and domains database: 20 years on
The vacuolar morphology protein VAC14 plays an important role in sexual development in the filamentous ascomycete Sordaria macrospora. PMID:35776170
Detecting Structural Variants and Associated Gene Presence-Absence Variation Phenomena in the Genomes of Marine Organisms. PMID:35727540
Investigating a putative transcriptional regulatory protein encoded by Rv1719 gene of Mycobacterium tuberculosis. PMID:35715720
Genome evolution and diversity of wild and cultivated potatoes. PMID:35676481
TCMPG: an integrative database for traditional Chinese medicine plant genomes. PMID:35591924
Interactome and Ubiquitinome Analyses Identify Functional Targets of Herpes Simplex Virus 1 Infected Cell Protein 0. PMID:35516420
Data Mining, Quality and Management in the Life Sciences. PMID:35507257
Genome-wide identification, evolutionary and functional analyses of KFB family members in potato. PMID:35501691
Root-Knot Nematode Resistance in Gossypium hirsutum Determined by a Constitutive Defense-Response Transcriptional Program Avoiding a Fitness Penalty. PMID:35498643
Synergistic activity and molecular modelling of fosfomycin combinations with some antibiotics against multidrug resistant Helicobacter pylori. PMID:35486219
Characterisation of ascocorynin biosynthesis in the purple jellydisc fungus Ascocoryne sarcoides. PMID:35477441
Bioprospecting of Ribosomally Synthesized and Post-translationally Modified Peptides Through Genome Characterization of a Novel Probiotic Lactiplantibacillus plantarum UTNGt21A Strain: A Promising Natural Antimicrobials Factory. PMID:35464932
A single point mutation in the Plasmodium falciparum 3'-5' exonuclease does not alter piperaquine susceptibility. PMID:35459163
Complete Genome Characterization of Reticuloendotheliosis Virus Detected in Chickens with Multiple Viral Coinfections. PMID:35458529
Plant Cell Wall Proteomes: The Core of Conserved Protein Families and the Case of Non-Canonical Proteins. PMID:35457091
Identification of Intrinsically Disordered Proteins and Regions in a Non-Model Insect Species Ostrinia nubilalis (Hbn.). PMID:35454181
Integrative Proteome and Ubiquitinome Analyses Reveal the Substrates of BTBD9 and Its Underlying Mechanism in Sleep Regulation. PMID:35449961
Boosting the acetol production in methanotrophic biocatalyst Methylomonas sp. DH-1 by the coupling activity of heteroexpressed novel protein PmoD with endogenous particulate methane monooxygenase. PMID:35418298
Integration of Aspergillus niger transcriptomic profile with metabolic model identifies potential targets to optimise citric acid production from lignocellulosic hydrolysate. PMID:35418297
Bioinformatic comparison of three Embleya species and description of steffimycins production by Embleya sp. NF3. PMID:35403858
Hypothetical protein predicted to be tumor suppressor: a protein functional analysis. PMID:35399005
Multiomic profiling of the acute stress response in the mouse hippocampus. PMID:35383160
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
Fusobacterium nucleatum Subspecies Differ in Biofilm Forming Ability in vitro. PMID:35368312
Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0. PMID:35362464
Investigating the Functional Role of Hypothetical Proteins From an Antarctic Bacterium Pseudomonas sp. Lz4W: Emphasis on Identifying Proteins Involved in Cold Adaptation. PMID:35360867
Structural and mechanistic basis for redox sensing by the cyanobacterial transcription regulator RexT. PMID:35347217
Proteomic Identification of a Gastric Tumor ECM Signature Associated With Cancer Progression. PMID:35340765
Transcriptional control of Arabidopsis seed development. PMID:35318532
In silico evaluation of a targeted metaproteomics strategy for broad screening of cellulolytic enzyme capacities in anaerobic microbiome bioreactors. PMID:35303956
Tinker, Tailor, Tumour Suppressor: The Many Functions of PRP4K. PMID:35281802
Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis. PMID:35279680
Characterization of intrinsically disordered regions in proteins informed by human genetic diversity. PMID:35275927
Identification and Quantitation of Bioactive and Taste-Related Dipeptides in Low-Salt Dry-Cured Ham. PMID:35269650
FlyBase: a guided tour of highlighted features. PMID:35266522
Impact of deleterious missense PRKCI variants on structural and functional dynamics of protein. PMID:35260606
The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus. PMID:35255818
The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains. PMID:35242291
Considerations for constructing a protein sequence database for metaproteomics. PMID:35242286
Bacteriophage Lytic Enzyme P9ly as an Alternative Antibacterial Agent Against Antibiotic-Resistant Shigella dysenteriae and Staphylococcus aureus. PMID:35237249
Identification and functional characterization of multiple inositol polyphosphate phosphatase1 (Minpp1) isoform-2 in exosomes with potential to modulate tumor microenvironment. PMID:35235602
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
Genome Analysis of Celeribacter sp. PS-C1 Isolated from Sekinchan Beach in Selangor, Malaysia, Reveals Its β-Glucosidase and Licheninase Activities. PMID:35208867
Role of MBL2 Polymorphisms in Sepsis and Survival: A Pilot Study and In Silico Analysis. PMID:35204551
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
Normal and Neoplastic Growth Suppression by the Extended Myc Network. PMID:35203395
Secondary Metabolite Gene Regulation in Mycotoxigenic Fusarium Species: A Focus on Chromatin. PMID:35202124
Protease activities of vaginal Porphyromonas species disrupt coagulation and extracellular matrix in the cervicovaginal niche. PMID:35190575
Wei2GO: weighted sequence similarity-based protein function prediction. PMID:35186498
Cdc42/Rac Interactive Binding Containing Effector Proteins in Unicellular Protozoans With Reference to Human Host: Locks of the Rho Signaling. PMID:35186026
Assembly and Annotation of Escherichia coli Bacteriophage U115. PMID:35175109
Zebrafish information network, the knowledgebase for Danio rerio research. PMID:35166825
Comparative Genomics of Three Colletotrichum scovillei Strains and Genetic Analysis Revealed Genes Involved in Fungal Growth and Virulence on Chili Pepper. PMID:35154058
Transcriptomic analysis reveals myometrial topologically associated domains linked to the onset of human term labour. PMID:35150271
Sequence Analysis and Comparison of TCTP Proteins from Human Protozoan Parasites. PMID:35138574
WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans. PMID:35134929
A chromosome-level genome assembly and annotation of the desert horned lizard, Phrynosoma platyrhinos, provides insight into chromosomal rearrangements among reptiles. PMID:35134927
A truncated CC-NB-ARC gene TaRPP13L1-3D positively regulates powdery mildew resistance in wheat via the RanGAP-WPP complex-mediated nucleocytoplasmic shuttle. PMID:35133503
RNAi Screen of RING/U-Box Domain Ubiquitin Ligases Identifies Critical Regulators of Tissue Regeneration in Planarians. PMID:35127720
Whole-Genome Sequences of Two Kazachstania barnettii Strains Isolated from Anthropic Environments. PMID:35106561
Crystal structure and initial characterization of a novel archaeal-like Holliday junction-resolving enzyme from Thermus thermophilus phage Tth15-6. PMID:35102887
Databases for intrinsically disordered proteins. PMID:35102880
Phage Annotation Guide: Guidelines for Assembly and High-Quality Annotation. PMID:35083439
Matrin3: Disorder and ALS Pathogenesis. PMID:35083279
Translation initiation landscape profiling reveals hidden open-reading frames required for the pathogenesis of tomato yellow leaf curl Thailand virus. PMID:35080617
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
A potential implication of UDP-glucuronosyltransferase 2B10 in the detoxification of drugs used in pediatric hematopoietic stem cell transplantation setting: an in silico investigation. PMID:35062878
A noncanonical chaperone interacts with drug efflux pumps during their assembly into bacterial outer membranes. PMID:35061668
Sequence and Structure-Based Analyses of Human Ankyrin Repeats. PMID:35056738
A Novel GEMIN4 Variant in a Consanguineous Family Leads to Neurodevelopmental Impairment with Severe Microcephaly, Spastic Quadriplegia, Epilepsy, and Cataracts. PMID:35052432
A Novel Gelatinase from Marine Flocculibacter collagenilyticus SM1988: Characterization and Potential Application in Collagen Oligopeptide-Rich Hydrolysate Preparation. PMID:35049903
Molecular characterization of myelin basic protein a (mbpa) gene from red-bellied pacu (Piaractus brachypomus). PMID:35024999
The Omics Hunt for Novel Molecular Markers of Resistance to Phytophthora infestans. PMID:35009065
Integrating Wheat Nucleolus Structure and Function: Variation in the Wheat Ribosomal RNA and Protein Genes. PMID:35003148
Evaluating the Genetic Capacity of Mycoplasmas for Coenzyme A Biosynthesis in a Search for New Anti-mycoplasma Targets. PMID:34987490
The 2022 Nucleic Acids Research database issue and the online molecular biology database collection. PMID:34986604
Convergent evolution of venom gland transcriptomes across Metazoa. PMID:34983844
Insights into phosphatase-activated chemical defense in a marine sponge holobiont. PMID:34977575
Genomic Analysis of the First European Bacteriophages with Depolymerase Activity and Biocontrol Efficacy against the Phytopathogen Ralstonia solanacearum. PMID:34960808
Investigating the Endo-Lysosomal System in Major Neurocognitive Disorders Due to Alzheimer's Disease, Frontotemporal Lobar Degeneration and Lewy Body Disease: Evidence for SORL1 as a Cross-Disease Gene. PMID:34948429
Finding Aquaporins in Annelids: An Evolutionary Analysis and a Case Study. PMID:34944070
Evolutionary Adaptation of the Thyroid Hormone Signaling Toolkit in Chordates. PMID:34943899
Genome placement of alpha-haemolysin cluster is associated with alpha-haemolysin sequence variation, adhesin and iron acquisition factor profile of Escherichia coli. PMID:34939560
Mechanisms underlying Clostridium pasteurianum's metabolic shift when grown with Geobacter sulfurreducens. PMID:34939136
Sequence Conservation, Domain Architectures, and Phylogenetic Distribution of the HD-GYP Type c-di-GMP Phosphodiesterases. PMID:34928179
Prevalence and antimicrobial resistance profiling of Staphylococcus aureus isolated from traditional cheese in Yunnan, China. PMID:34926114
Global Profiling of N-Glycoproteins and N-Glycans in the Diatom Phaeodactylum tricornutum. PMID:34925422
Abundance of Lipopolysaccharide Heptosyltransferase I in Human Gut Microbiome and Its Association With Cardiovascular Disease and Liver Cirrhosis. PMID:34917047
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
Rice stripe virus activates the bZIP17/28 branch of the unfolded protein response signalling pathway to promote viral infection. PMID:34897936
Comprehensive Analysis of SRO Gene Family in Sesamum indicum (L.) Reveals Its Association with Abiotic Stress Responses. PMID:34884850
INTS7-ABCD3 Interaction Stimulates the Proliferation and Osteoblastic Differentiation of Mouse Bone Marrow Mesenchymal Stem Cells by Suppressing Oxidative Stress. PMID:34880777
Pelizaeus-Merzbacher-Like Disease 1 Caused by a Novel Mutation in GJC2 Gene: A Case Report. PMID:34840390
A Monoallelic Variant in REST Is Associated with Non-Syndromic Autosomal Dominant Hearing Impairment in a South African Family. PMID:34828371
A computational in silico approach to predict high-risk coding and non-coding SNPs of human PLCG1 gene. PMID:34793541
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. PMID:34791415
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. PMID:34791371
Pneumococcal Extracellular Serine Proteases: Molecular Analysis and Impact on Colonization and Disease. PMID:34790590
The Hydractinia allorecognition system. PMID:34773127
In silico analysis and expression profiling of S-domain receptor-like kinases (SD-RLKs) under different abiotic stresses in Arabidopsis thaliana. PMID:34772363
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
Resolving the Microalgal Gene Landscape at the Strain Level: a Novel Hybrid Transcriptome of Emiliania huxleyi CCMP3266. PMID:34757817
Expression analysis of miRNAs and their putative target genes confirm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress. PMID:34749653
PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants. PMID:34747486
HumanNet v3: an improved database of human gene networks for disease research. PMID:34747468
Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses. PMID:34747465
The Eukaryotic Linear Motif resource: 2022 release. PMID:34718738
Determination of the two-component systems regulatory network reveals core and accessory regulations across Pseudomonas aeruginosa lineages. PMID:34718721
PANTHER: Making genome-scale phylogenetics accessible to all. PMID:34717010
Shedding Light on Microbial "Dark Matter": Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake. PMID:34707591
In Vitro Characterization and In Vivo Efficacy Assessment in Galleria mellonella Larvae of Newly Isolated Bacteriophages against Escherichia coli K1. PMID:34696434
Discovery and Evolution of a Divergent Coronavirus in the Plateau Pika From China That Extends the Host Range of Alphacoronaviruses. PMID:34691006
Adaptation and genomic erosion in fragmented Pseudomonas aeruginosa populations in the sinuses of people with cystic fibrosis. PMID:34686349
Transcriptome Analysis of Potato Infected with the Necrotrophic Pathogen Alternaria solani. PMID:34686023
Functional Genomic Analyses Reveal an Open Pan-genome for the Chloroviruses and a Potential for Genetic Innovation in New Isolates. PMID:34669449
Pleiotropic Effects of the P5-Type ATPase SpfA on Stress Response Networks Contribute to Virulence in the Pathogenic Mold Aspergillus fumigatus. PMID:34663092
Structural basis of cytokine-mediated activation of ALK family receptors. PMID:34646012
OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. PMID:34632381
A dedicated flavin-dependent monooxygenase catalyzes the hydroxylation of demethoxyubiquinone into ubiquinone (coenzyme Q) in Arabidopsis. PMID:34626646
Sensory Perception in Bacterial Cyclic Diguanylate Signal Transduction. PMID:34606374
The Role of Substrate Mediated Allostery in the Catalytic Competency of the Bacterial Oligosaccharyltransferase PglB. PMID:34604309
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. PMID:34597405
Genome-Wide Characterization of the MLO Gene Family in Cannabis sativa Reveals Two Genes as Strong Candidates for Powdery Mildew Susceptibility. PMID:34589104
Comparative Genomic Analysis of Novel Bifidobacterium longum subsp. longum Strains Reveals Functional Divergence in the Human Gut Microbiota. PMID:34576801
Genome Analysis of Streptomyces nojiriensis JCM 3382 and Distribution of Gene Clusters for Three Antibiotics and an Azasugar across the Genus Streptomyces. PMID:34576698
Analysis of the Putative Nucleoporin POM33 in the Filamentous Fungus Sordaria macrospora. PMID:34575720
Substitutions in SurA and BamA Lead to Reduced Susceptibility to Broad Range Antibiotics in Gonococci. PMID:34573293
Genome Assembly and Sex-Determining Region of Male and Female Populus × sibirica. PMID:34567016
Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome. PMID:34563133
PANNZER-A practical tool for protein function prediction. PMID:34562305
Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class. PMID:34555022
Phylogeographic Clustering Suggests that Distinct Clades of Salmonella enterica Serovar Mississippi Are Endemic in Australia, the United Kingdom, and the United States. PMID:34550008
Characterization and genomic analysis of the first Oceanospirillum phage, vB_OliS_GJ44, representing a novel siphoviral cluster. PMID:34544379
Optimized expression and purification of adipose triglyceride lipase improved hydrolytic and transacylation activities in vitro. PMID:34543623
Allele-specific assembly of a eukaryotic genome corrects apparent frameshifts and reveals a lack of nonsense-mediated mRNA decay. PMID:34541528
Genome Mining and Molecular Networking-Based Metabolomics of the Marine Facultative Aspergillus sp. MEXU 27854. PMID:34500798
CRISPR/SpCas9-mediated double knockout of barley Microrchidia MORC1 and MORC6a reveals their strong involvement in plant immunity, transcriptional gene silencing and plant growth. PMID:34487614
Zooming in on the WNT/CTNNB1 Destruction Complex: Functional Mechanistic Details with Implications for Therapeutic Targeting. PMID:34486095
Physiology of the Nitrite-Oxidizing Bacterium Candidatus Nitrotoga sp. CP45 Enriched From a Colorado River. PMID:34484146
Bacteriophage-Mediated Risk Pathways Underlying the Emergence of Antimicrobial Resistance via Intrageneric and Intergeneric Recombination of Antibiotic Efflux Genes Across Natural populations of Human Pathogenic Bacteria. PMID:34467445
Architecture Insight of Bifidobacterial α-L-Fucosidases. PMID:34445166
Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes. PMID:34442314
Bioinformatic Analysis of Two TOR (Target of Rapamycin)-Like Proteins Encoded by Entamoeba histolytica Revealed Structural Similarities with Functional Homologs. PMID:34440318
Characterization of New Allergens from the Venom of the European Paper Wasp Polistes dominula. PMID:34437431
Ankyrin repeats in context with human population variation. PMID:34428215
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
Can We Pharmacologically Target Dishevelled: The Key Signal Transducer in the Wnt Pathways? PMID:34382124
Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana. PMID:34381973
Evidence of Immune Modulators in the Secretome of the Equine Tapeworm Anoplocephala perfoliata. PMID:34358062
The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research. PMID:34357286
FLAME: A Web Tool for Functional and Literature Enrichment Analysis of Multiple Gene Lists. PMID:34356520
Signatures of Transcription Factor Evolution and the Secondary Gain of Red Algae Complexity. PMID:34356071
DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug-target interactions. PMID:34320178
IDOPS, a Profile HMM-Based Tool to Detect Pesticidal Sequences and Compare Their Genetic Context. PMID:34276598
Loss of MGA repression mediated by an atypical polycomb complex promotes tumor progression and invasiveness. PMID:34236315
Genome Wide Prediction, Mapping and Development of Genomic Resources of Mastitis Associated Genes in Water Buffalo. PMID:34222390
Increasing the Accuracy of Single Sequence Prediction Methods Using a Deep Semi-Supervised Learning Framework. PMID:34213528
PhaLP: A Database for the Study of Phage Lytic Proteins and Their Evolution. PMID:34206969
Inhibition of Carotenoid Biosynthesis by CRISPR/Cas9 Triggers Cell Wall Remodelling in Carrot. PMID:34204559
Identification and bioinformatic analysis of neprilysin and neprilysin-like metalloendopeptidases in Drosophila melanogaster. PMID:34189422
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
Comprehensive glycoproteomics shines new light on the complexity and extent of glycosylation in archaea. PMID:34138841
COSMIC Cancer Gene Census 3D database: understanding the impacts of mutations on cancer targets. PMID:34137435
Population-scale peach genome analyses unravel selection patterns and biochemical basis underlying fruit flavor. PMID:34127667
A deep-sea bacterium related to coastal marine pathogens. PMID:34097814
Positioning Diverse Type IV Structures and Functions Within Class 1 CRISPR-Cas Systems. PMID:34093491
Positive Selection in Gene Regulatory Factors Suggests Adaptive Pleiotropic Changes During Human Evolution. PMID:34079582
Mechnetor: a web server for exploring protein mechanism and the functional context of genetic variants. PMID:34076240
Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity. PMID:34072989
The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing. PMID:34048576
The carbon source-dependent pattern of antimicrobial activity and gene expression in Pseudomonas donghuensis P482. PMID:34040089
Hybrid Histidine Kinase BinK Represses Vibrio fischeri Biofilm Signaling at Multiple Developmental Stages. PMID:34031036
NLRP7: From inflammasome regulation to human disease. PMID:34021586
DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web. PMID:34019664
The Trypanosoma brucei subpellicular microtubule array is organized into functionally discrete subdomains defined by microtubule associated proteins. PMID:34010336
BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation. PMID:33963861
GIMAP5 maintains liver endothelial cell homeostasis and prevents portal hypertension. PMID:33956074
A Comparison Between Recombinant Listeria GAPDH Proteins and GAPDH Encoding mRNA Conjugated to Lipids as Cross-Reactive Vaccines for Listeria, Mycobacterium, and Streptococcus. PMID:33953709
Arabidopsis thaliana EARLY RESPONSIVE TO DEHYDRATION 7 Localizes to Lipid Droplets via Its Senescence Domain. PMID:33936146
Annotation and Molecular Characterisation of the TaIRO3 and TaHRZ Iron Homeostasis Genes in Bread Wheat (Triticum aestivum L.). PMID:33925484
Global Analysis of RNA-Dependent RNA Polymerase-Dependent Small RNAs Reveals New Substrates and Functions for These Proteins and SGS3 in Arabidopsis. PMID:33925339
Genome-Wide Analysis of PL7 Alginate Lyases in the Genus Zobellia. PMID:33924031
Diaphorina citri Genome Possesses a Complete Melatonin Biosynthesis Pathway Differentially Expressed under the Influence of the Phytopathogenic Bacterium, Candidatus Liberibacter asiaticus. PMID:33916117
The Landscape of the Genomic Distribution and the Expression of the F-Box Genes Unveil Genome Plasticity in Hexaploid Wheat during Grain Development and in Response to Heat and Drought Stress. PMID:33803701
Glyceraldehyde-3-phosphate Dehydrogenase Common Peptides of Listeria monocytogenes, Mycobacterium marinum and Streptococcus pneumoniae as Universal Vaccines. PMID:33802959
Transcriptional Regulatory Networks Associate with Early Stages of Potato Virus X Infection of Solanum tuberosum. PMID:33799566
Generic injuries are sufficient to induce ectopic Wnt organizers in Hydra. PMID:33779545
Tailored biosynthesis of gibberellin plant hormones in yeast. PMID:33746070
Comparative Genomics: Insights on the Pathogenicity and Lifestyle of Rhizoctonia solani. PMID:33671736
Structure-Function Relationship Study of a Secretory Amoebic Phosphatase: A Computational-Experimental Approach. PMID:33671604
Biosynthesis of 6-Hydroxymellein Requires a Collaborating Polyketide Synthase-like Enzyme. PMID:33661567
Identification of 37 Heterogeneous Drug Candidates for Treatment of COVID-19 via a Rational Transcriptomics-Based Drug Repurposing Approach. PMID:33504008
Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB. PMID:33445429
CHD2-Related CNS Pathologies. PMID:33435571
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 -
InterPro: an integrated documentation resource for protein families, domains and functional sites
PubMed citations: 75.
75 articles citing: InterPro: an integrated documentation resource for protein families, domains and functional sites
GXP: Analyze and Plot Plant Omics Data in Web Browsers. PMID:35336631
Current status of PTMs structural databases: applications, limitations and prospects. PMID:35020020
A systematic bioinformatics approach for large-scale identification and characterization of host-pathogen shared sequences. PMID:34583643
Functional characterization of Caenorhabditis elegans cbs-2 gene during meiosis. PMID:33262405
Heat Stress Triggers Differential Protein Accumulation in the Extracellular Matrix of Sorghum Cell Suspension Cultures. PMID:33105781
Comparative physiological and root proteome analyses of two sorghum varieties responding to water limitation. PMID:32678202
Genome-Wide Analysis of Domain-Swap Predicted Products in the Genome of Anti-Stress Medicinal Plant: Ocimum tenuiflorum. PMID:30692846
BioSankey: Visualization of Microbial Communities Over Time. PMID:29897884
The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. PMID:29358652
EOGD: the Euplotes octocarinatus genome database. PMID:29351734
LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. PMID:29220437
Comparative genomic analysis of Mycobacterium neoaurum MN2 and MN4 substrate and product tolerance. PMID:28664368
A dual-strategy expression screen for candidate connectivity labels in the developing thalamus. PMID:28558017
Structure-based function analysis of putative conserved proteins with isomerase activity from Haemophilus influenzae. PMID:28324524
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
Comprehensive molecular profiling of the B7 family of immune-regulatory ligands in breast cancer. PMID:27622076
Comparative Genomics of Acetobacterpasteurianus Ab3, an Acetic Acid Producing Strain Isolated from Chinese Traditional Rice Vinegar Meiguichu. PMID:27611790
Reciprocal genomic evolution in the ant-fungus agricultural symbiosis. PMID:27436133
Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining. PMID:27390860
A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies. PMID:27363390
Draft Genomes of Anopheles cracens and Anopheles maculatus: Comparison of Simian Malaria and Human Malaria Vectors in Peninsular Malaysia. PMID:27347683
Selection pressure on human STR loci and its relevance in repeat expansion disease. PMID:27290643
Axial Spondylometaphyseal Dysplasia Is Caused by C21orf2 Mutations. PMID:26974433
Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot. PMID:26422147
Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry. PMID:26202522
Under-detection of endospore-forming Firmicutes in metagenomic data. PMID:25973144
Predicting protein interface residues using easily accessible on-line resources. PMID:25797794
Genome sequence of mungbean and insights into evolution within Vigna species. PMID:25384727
Phenotypic profiling of ABC transporter coding genes in Myxococcus xanthus. PMID:25101061
Proteomic analysis of free-living Bradyrhizobium diazoefficiens: highlighting potential determinants of a successful symbiosis. PMID:25086822
CELLO2GO: a web server for protein subCELlular LOcalization prediction with functional gene ontology annotation. PMID:24911789
BambooGDB: a bamboo genome database with functional annotation and an analysis platform. PMID:24602877
Boosting probabilistic graphical model inference by incorporating prior knowledge from multiple sources. PMID:23826291
Database citation in full text biomedical articles. PMID:23734176
Comparative analysis of the genomes of two field isolates of the rice blast fungus Magnaporthe oryzae. PMID:22876203
Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement. PMID:20979641
A genome-wide gene function prediction resource for Drosophila melanogaster. PMID:20711346
GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques. PMID:20689020
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. PMID:20626842
The bridge-region of the Ku superfamily is an atypical zinc ribbon domain. PMID:20580930
SoyDB: a knowledge database of soybean transcription factors. PMID:20082720
Homeobox transcription factors are required for conidiation and appressorium development in the rice blast fungus Magnaporthe oryzae. PMID:19997500
GExplore: a web server for integrated queries of protein domains, gene expression and mutant phenotypes. PMID:19917126
Gastric Cancer (Biomarkers) Knowledgebase (GCBKB): A Curated and Fully Integrated Knowledgebase of Putative Biomarkers Related to Gastric Cancer. PMID:19690644
A knowledge-based method to predict the cooperative relationship between transcription factors. PMID:19590970
Molecular cloning and characterization of five genes encoding pentatricopeptide repeat proteins from Upland cotton (Gossypium hirsutum L.). PMID:19578975
A comprehensive resource for integrating and displaying protein post-translational modifications. PMID:19549291
Databases and QSAR for cancer research. PMID:19458762
VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts. PMID:18953038
The unfoldomics decade: an update on intrinsically disordered proteins. PMID:18831774
TreeGenes: A forest tree genome database. PMID:18725987
Genome-based analysis of Chlamydomonas reinhardtii exoribonucleases and poly(A) polymerases predicts unexpected organellar and exosomal features. PMID:18493045
The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation. PMID:18197987
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. PMID:17678529
The Schistosoma mansoni transcriptome: an update. PMID:17624328
A domain-based approach to predict protein-protein interactions. PMID:17567909
Comprehensive analysis of co-occurring domain sets in yeast proteins. PMID:17562021
RINGdb: an integrated database for G protein-coupled receptors and regulators of G protein signaling. PMID:17173697
PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. PMID:17130144
The TIGR Plant Transcript Assemblies database. PMID:17088284
Java GUI for InterProScan (JIPS): a tool to help process multiple InterProScans and perform ortholog analysis. PMID:17054794
Interrogating the druggable genome with structural informatics. PMID:17031532
Cataloging the relationships between proteins: a review of interaction databases. PMID:16943573
EVEREST: automatic identification and classification of protein domains in all protein sequences. PMID:16749920
Functional annotation prediction: all for one and one for all. PMID:16672244
A tale of two ferredoxins: sequence similarity and structural differences. PMID:16603087
Conservation of intrinsic disorder in protein domains and families: I. A database of conserved predicted disordered regions. PMID:16602695
Regions of extreme synonymous codon selection in mammalian genes. PMID:16556911
Tracking the evolution of alternatively spliced exons within the Dscam family. PMID:16483367
dbPTM: an information repository of protein post-translational modification. PMID:16381945
A functional hierarchical organization of the protein sequence space. PMID:15596019
High-throughput protein analysis integrating bioinformatics and experimental assays. PMID:14762202
The German cDNA network: cDNAs, functional genomics and proteomics. PMID:14649292
PipeAlign: A new toolkit for protein family analysis. PMID:12824430
The SBASE domain sequence library, release 10: domain architecture prediction. PMID:12520034 -
InterPro protein classification
PubMed citations: 28.
28 articles citing: InterPro protein classification
A conserved Neurite Outgrowth and Guidance motif with biomimetic potential in neuronal Cell Adhesion Molecules. PMID:34712402
Genome analysis of a halophilic bacterium Halomonas malpeensis YU-PRIM-29T reveals its exopolysaccharide and pigment producing capabilities. PMID:33462335
Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in the Phytopathogenic Fungus Botrytis cinerea. PMID:33329453
The Class III Peroxidase (POD) Gene Family in Cassava: Identification, Phylogeny, Duplication, and Expression. PMID:31163686
A highly expressed intestinal cysteine protease of Ancylostoma ceylanicum protects vaccinated hamsters from hookworm infection. PMID:31009474
Expression of putative circadian clock components in the arbuscular mycorrhizal fungus Rhizoglomus irregulare. PMID:29931403
Distinct mutations with different inheritance mode caused similar retinal dystrophies in one family: a demonstration of the importance of genetic annotations in complicated pedigrees. PMID:29843741
New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication. PMID:29089032
Safety assessment of Staphylococcus phages of the family Myoviridae based on complete genome sequences. PMID:28117392
Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation. PMID:26729541
DYNC2LI1 mutations broaden the clinical spectrum of dynein-2 defects. PMID:26130459
A bioinformatic survey of distribution, conservation, and probable functions of LuxR solo regulators in bacteria. PMID:25759807
The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families. PMID:25730766
Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty. PMID:25534030
Comparative analyses of nonpathogenic, opportunistic, and totally pathogenic mycobacteria reveal genomic and biochemical variabilities and highlight the survival attributes of Mycobacterium tuberculosis. PMID:25370496
AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors. PMID:25262351
Basis for substrate recognition and distinction by matrix metalloproteinases. PMID:25246591
Functional genomic analyses of two morphologically distinct classes of Drosophila sensory neurons: post-mitotic roles of transcription factors in dendritic patterning. PMID:23977298
Large-scale gene function analysis with the PANTHER classification system. PMID:23868073
Comparative transcriptomics of infectious spores from the fungal pathogen Histoplasma capsulatum reveals a core set of transcripts that specify infectious and pathogenic states. PMID:23563482
Evolutionary, structural and functional interplay of the IκB family members. PMID:23372681
Molecular evolution and structural features of IRAK family members. PMID:23166766
Genome-wide identification and analysis of late embryogenesis abundant (LEA) genes in Prunus mume. PMID:23086279
Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. PMID:23061897
Genomics and localization of the Arabidopsis DHHC-cysteine-rich domain S-acyltransferase protein family. PMID:22968831
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. PMID:21873635
Long-chain N-acyl amino acid synthases are linked to the putative PEP-CTERM/exosortase protein-sorting system in Gram-negative bacteria. PMID:21840974
Disease and phenotype data at Ensembl. PMID:21400687 - http://dx.doi.org/10.1093/nar/gkaa977
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More detailed information about this field from each metasource.
binding motif
metasource: Fairsharing.org
version: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
computational predictions
metasource: Fairsharing.org
version: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
conserved region
metasource: Fairsharing.org
version: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
function analysis
metasource: Fairsharing.org
version: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
functional domain
metasource: Fairsharing.org
version: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
genome
metasource: Fairsharing.org
version: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
molecular function
metasource: Fairsharing.org
version: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein domain
metasource: Fairsharing.org
version: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequencing
metasource: Fairsharing.org
version: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
polypeptide_region
metasource: Fairsharing.org
version: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 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 sequence motifs and active sites
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
amino acid sequence
metasource: re3data.org
version: re3data.org: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
amino acids
metasource: re3data.org
version: re3data.org: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
genomes
metasource: re3data.org
version: re3data.org: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
nucleic acids
metasource: re3data.org
version: re3data.org: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
proteins
metasource: re3data.org
version: re3data.org: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
gene and protein families
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
sequence composition, complexity and repeats
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
Tags
More detailed information about this field from each metasource.
binding motif
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
computational predictions
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
conserved region
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
function analysis
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
functional domain
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
molecular function
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein domain
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
sequencing
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
polypeptide_region
metasource: Fairsharing.orgversion: FAIRsharing.org: InterPro; Integrated resource of protein families, domains and functional sites; DOI: https://doi.org/10.25504/FAIRsharing.pda11d; Last edited: Feb. 11, 2020, 8:37 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 sequence motifs and active sites
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
amino acid sequence
metasource: re3data.orgversion: re3data.org: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
amino acids
metasource: re3data.orgversion: re3data.org: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
genomes
metasource: re3data.orgversion: re3data.org: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
nucleic acids
metasource: re3data.orgversion: re3data.org: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
proteins
metasource: re3data.orgversion: re3data.org: InterPro; editing status 2021-10-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3FS61 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:09.686544
gene and protein families
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:09.686544
sequence composition, complexity and repeats
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:09.686544
binding motif computational predictions conserved region function analysis functional domain genome molecular function protein protein domain sequencing polypeptide region protein sequence protein sequence motifs and active sites amino acid sequence amino acids genomes nucleic acids proteins gene and protein families sequence composition, complexity and repeats
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