Published in Nucleic Acids Res on November 26, 2014
The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res (2015) 5.97
Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma. Cell (2016) 2.65
The EMBL-EBI bioinformatics web and programmatic tools framework. Nucleic Acids Res (2015) 2.46
The UCSC Genome Browser database: 2016 update. Nucleic Acids Res (2015) 2.18
Genome evolution in the allotetraploid frog Xenopus laevis. Nature (2016) 1.66
Ensembl Genomes 2016: more genomes, more complexity. Nucleic Acids Res (2015) 1.66
Nucleotide binding by the widespread high-affinity cyclic di-GMP receptor MshEN domain. Nat Commun (2016) 1.49
Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet (2016) 1.49
Caenorhabditis elegans PAQR-2 and IGLR-2 Protect against Glucose Toxicity by Modulating Membrane Lipid Composition. PLoS Genet (2016) 1.44
Unusually Situated Binding Sites for Bacterial Transcription Factors Can Have Hidden Functionality. PLoS One (2016) 1.39
Expression and methylation patterns partition luminal-A breast tumors into distinct prognostic subgroups. Breast Cancer Res (2016) 1.39
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PLoS Comput Biol (2016) 1.22
UniProt: the universal protein knowledgebase. Nucleic Acids Res (2016) 1.19
Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks. Biochim Biophys Acta (2015) 1.15
Structure of mammalian eIF3 in the context of the 43S preinitiation complex. Nature (2015) 1.14
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. Nucleic Acids Res (2015) 1.14
The 2015 Nucleic Acids Research Database Issue and molecular biology database collection. Nucleic Acids Res (2015) 1.13
ELM 2016-data update and new functionality of the eukaryotic linear motif resource. Nucleic Acids Res (2015) 1.09
The genomic basis of parasitism in the Strongyloides clade of nematodes. Nat Genet (2016) 1.09
The extracellular matrix: Tools and insights for the "omics" era. Matrix Biol (2015) 1.08
InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res (2016) 1.08
An Ancient Yeast for Young Geneticists: A Primer on the Schizosaccharomyces pombe Model System. Genetics (2015) 1.06
The Transporter Classification Database (TCDB): recent advances. Nucleic Acids Res (2015) 1.05
PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements. Nucleic Acids Res (2016) 1.04
Definition of a consensus integrin adhesome and its dynamics during adhesion complex assembly and disassembly. Nat Cell Biol (2015) 1.02
The European Bioinformatics Institute in 2016: Data growth and integration. Nucleic Acids Res (2015) 0.98
FlyBase at 25: looking to the future. Nucleic Acids Res (2016) 0.97
The Conservation of the Germline Multipotency Program, from Sponges to Vertebrates: A Stepping Stone to Understanding the Somatic and Germline Origins. Genome Biol Evol (2017) 0.97
Biological databases for human research. Genomics Proteomics Bioinformatics (2015) 0.96
Can the natural diversity of quorum-sensing advance synthetic biology? Front Bioeng Biotechnol (2015) 0.96
X-ray structure of a mammalian stearoyl-CoA desaturase. Nature (2015) 0.95
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database (Oxford) (2016) 0.95
MitoMiner v3.1, an update on the mitochondrial proteomics database. Nucleic Acids Res (2015) 0.94
Biochemical and Spectroscopic Characterization of a Radical S-Adenosyl-l-methionine Enzyme Involved in the Formation of a Peptide Thioether Cross-Link. Biochemistry (2016) 0.92
ANISEED 2015: a digital framework for the comparative developmental biology of ascidians. Nucleic Acids Res (2015) 0.92
Interrogating the Plasmodium Sporozoite Surface: Identification of Surface-Exposed Proteins and Demonstration of Glycosylation on CSP and TRAP by Mass Spectrometry-Based Proteomics. PLoS Pathog (2016) 0.91
CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides. Nucleic Acids Res (2015) 0.91
Homeodomain proteins: an update. Chromosoma (2015) 0.91
The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI. Nucleic Acids Res (2015) 0.91
EBI metagenomics in 2016 - an expanding and evolving resource for the analysis and archiving of metagenomic data. Nucleic Acids Res (2015) 0.91
DIDA: A curated and annotated digenic diseases database. Nucleic Acids Res (2015) 0.90
A review of the new HGNC gene family resource. Hum Genomics (2016) 0.89
Key challenges for the creation and maintenance of specialist protein resources. Proteins (2015) 0.88
RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource. J Biomed Semantics (2015) 0.88
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. Bioinformatics (2015) 0.87
Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proc Natl Acad Sci U S A (2016) 0.87
A proposed integrated approach for the preclinical evaluation of phage therapy in Pseudomonas infections. Sci Rep (2016) 0.87
Cell-Size Homeostasis and the Incremental Rule in a Bacterial Pathogen. Biophys J (2015) 0.87
Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA. PLoS One (2015) 0.86
Chaos of Rearrangements in the Mating-Type Chromosomes of the Anther-Smut Fungus Microbotryum lychnidis-dioicae. Genetics (2015) 0.86
Global phylogeography and evolutionary history of Shigella dysenteriae type 1. Nat Microbiol (2016) 0.86
The Radical S-Adenosyl-l-methionine Enzyme MftC Catalyzes an Oxidative Decarboxylation of the C-Terminus of the MftA Peptide. Biochemistry (2016) 0.85
Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family. Nucleic Acids Res (2015) 0.85
Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB. Front Microbiol (2017) 0.85
Expansion of the Gene Ontology knowledgebase and resources. Nucleic Acids Res (2016) 0.85
WormBase ParaSite - a comprehensive resource for helminth genomics. Mol Biochem Parasitol (2016) 0.85
Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics. F1000Res (2016) 0.84
Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts. BMC Bioinformatics (2016) 0.84
Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery. Brief Bioinform (2015) 0.84
Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. Nucleic Acids Res (2015) 0.84
High frequency of +1 programmed ribosomal frameshifting in Euplotes octocarinatus. Sci Rep (2016) 0.84
Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data. Microb Genom (2016) 0.84
Draft genome of the living fossil Ginkgo biloba. Gigascience (2016) 0.83
Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. Nat Commun (2016) 0.83
Candidate gene prioritization with Endeavour. Nucleic Acids Res (2016) 0.83
Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders. Int J Mol Sci (2015) 0.83
Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. Cell Commun Signal (2015) 0.83
Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms. R Soc Open Sci (2015) 0.83
Dynamics of Human Mitochondrial Complex I Assembly: Implications for Neurodegenerative Diseases. Front Mol Biosci (2016) 0.83
PhytoPath: an integrative resource for plant pathogen genomics. Nucleic Acids Res (2015) 0.83
Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. Nucleic Acids Res (2015) 0.82
Requirement of Fra proteins for communication channels between cells in the filamentous nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120. Proc Natl Acad Sci U S A (2015) 0.82
A New Chicken Genome Assembly Provides Insight into Avian Genome Structure. G3 (Bethesda) (2016) 0.82
Defining the gene repertoire and spatiotemporal expression profiles of adhesion G protein-coupled receptors in zebrafish. BMC Genomics (2015) 0.82
Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance. Genome Biol (2017) 0.82
The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. Microbiol Mol Biol Rev (2016) 0.82
Genome-wide analysis of tomato NF-Y factors and their role in fruit ripening. BMC Genomics (2016) 0.82
The Genetic Basis of Haploid Induction in Maize Identified with a Novel Genome-Wide Association Method. Genetics (2016) 0.82
Stenotrophomonas maltophilia responds to exogenous AHL signals through the LuxR solo SmoR (Smlt1839). Front Cell Infect Microbiol (2015) 0.81
Modulation of FAK and Src adhesion signaling occurs independently of adhesion complex composition. J Cell Biol (2016) 0.81
Transcriptional cellular responses in midgut tissue of Aedes aegypti larvae following intoxication with Cry11Aa toxin from Bacillus thuringiensis. BMC Genomics (2015) 0.81
Functional and topological diversity of LOV domain photoreceptors. Proc Natl Acad Sci U S A (2016) 0.81
Novel genetic causes for cerebral visual impairment. Eur J Hum Genet (2015) 0.81
Tentacle Transcriptome and Venom Proteome of the Pacific Sea Nettle, Chrysaora fuscescens (Cnidaria: Scyphozoa). Toxins (Basel) (2016) 0.81
A new look at the LTR retrotransposon content of the chicken genome. BMC Genomics (2016) 0.81
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. Nucleic Acids Res (2016) 0.81
The comparative landscape of duplications in Heliconius melpomene and Heliconius cydno. Heredity (Edinb) (2016) 0.81
Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life. PLoS One (2015) 0.81
Neuropeptidergic Signaling in the American Lobster Homarus americanus: New Insights from High-Throughput Nucleotide Sequencing. PLoS One (2015) 0.80
Evolutionary Transition of Promoter and Gene Body DNA Methylation across Invertebrate-Vertebrate Boundary. Mol Biol Evol (2015) 0.80
PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with PolyCystic Ovary Syndrome. Nucleic Acids Res (2015) 0.80
cis-Encoded Small RNAs, a Conserved Mechanism for Repression of Polysaccharide Utilization in Bacteroides. J Bacteriol (2016) 0.80
Mouse Genome Database: From sequence to phenotypes and disease models. Genesis (2015) 0.80
The green ash transcriptome and identification of genes responding to abiotic and biotic stresses. BMC Genomics (2016) 0.80
Understanding the Role of the Master Regulator XYR1 in Trichoderma reesei by Global Transcriptional Analysis. Front Microbiol (2016) 0.80
Global analyses of TetR family transcriptional regulators in mycobacteria indicates conservation across species and diversity in regulated functions. BMC Genomics (2015) 0.79
A Glimpse to Background and Characteristics of Major Molecular Biological Networks. Biomed Res Int (2015) 0.79
Diversity in Biosynthetic Pathways of Galactolipids in the Light of Endosymbiotic Origin of Chloroplasts. Front Plant Sci (2016) 0.79
Indexing a protein-protein interaction network expedites network alignment. BMC Bioinformatics (2015) 0.78
Discrete and structurally unique proteins (tāpirins) mediate attachment of extremely thermophilic Caldicellulosiruptor species to cellulose. J Biol Chem (2015) 0.78
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol (2001) 66.87
KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res (1999) 40.62
The ENZYME database in 2000. Nucleic Acids Res (2000) 23.85
Pfam: the protein families database. Nucleic Acids Res (2013) 22.48
A combined transmembrane topology and signal peptide prediction method. J Mol Biol (2004) 15.77
Accelerated Profile HMM Searches. PLoS Comput Biol (2011) 15.22
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res (2006) 13.44
Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res (2007) 13.44
Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res (2013) 11.67
SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res (2011) 9.15
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res (2009) 9.14
InterProScan 5: genome-scale protein function classification. Bioinformatics (2014) 8.52
The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res (2005) 7.66
A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Int J Neural Syst (1999) 7.40
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res (2012) 6.90
Large-scale gene function analysis with the PANTHER classification system. Nat Protoc (2013) 6.41
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res (2013) 5.13
New and continuing developments at PROSITE. Nucleic Acids Res (2012) 4.41
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res (2013) 4.39
TIGRFAMs and Genome Properties in 2013. Nucleic Acids Res (2012) 3.45
SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Res (2010) 3.34
PIRSF family classification system for protein functional and evolutionary analysis. Evol Bioinform Online (2007) 3.03
Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucleic Acids Res (2010) 2.93
Rhea--a manually curated resource of biochemical reactions. Nucleic Acids Res (2011) 2.87
UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res (2011) 2.45
HAMAP in 2013, new developments in the protein family classification and annotation system. Nucleic Acids Res (2012) 2.16
The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012. Database (Oxford) (2012) 1.80
EBI metagenomics--a new resource for the analysis and archiving of metagenomic data. Nucleic Acids Res (2013) 1.74
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Res (2012) 1.63
Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis. Nucleic Acids Res (2013) 1.23
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res (2016) 2.62
HMMER web server: 2015 update. Nucleic Acids Res (2015) 1.98
The SIDER database of drugs and side effects. Nucleic Acids Res (2015) 1.30
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. Nucleic Acids Res (2014) 1.01
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. Nucleic Acids Res (2016) 0.78
Prediction and analysis of intrinsically disordered proteins. Methods Mol Biol (2015) 0.77
GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations. Database (Oxford) (2016) 0.77