Published in Nucleic Acids Res on December 01, 2011
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res (2012) 13.14
Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol Cell Proteomics (2013) 2.53
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. Nucleic Acids Res (2011) 2.16
The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics. BMC Bioinformatics (2013) 2.14
The WAVE regulatory complex links diverse receptors to the actin cytoskeleton. Cell (2014) 1.60
The neXtProt knowledgebase on human proteins: current status. Nucleic Acids Res (2015) 1.42
The TissueNet database of human tissue protein-protein interactions. Nucleic Acids Res (2012) 1.07
MALAT1 long non-coding RNA is overexpressed in multiple myeloma and may serve as a marker to predict disease progression. BMC Cancer (2014) 1.06
A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17. J Proteome Res (2012) 1.03
Network analyses reveal pervasive functional regulation between proteases in the human protease web. PLoS Biol (2014) 1.02
Protein domains of unknown function are essential in bacteria. MBio (2013) 0.99
Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. Curr Protoc Bioinformatics (2014) 0.96
Evidence classification of high-throughput protocols and confidence integration in RegulonDB. Database (Oxford) (2013) 0.90
Exploring the potential of public proteomics data. Proteomics (2015) 0.90
Key challenges for the creation and maintenance of specialist protein resources. Proteins (2015) 0.88
Cross-talking noncoding RNAs contribute to cell-specific neurodegeneration in SCA7. Nat Struct Mol Biol (2014) 0.86
The role of quantitative mass spectrometry in the discovery of pancreatic cancer biomarkers for translational science. J Transl Med (2014) 0.84
Recombinant renewable polyclonal antibodies. MAbs (2015) 0.83
Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow. Nat Commun (2016) 0.81
The neXtProt knowledgebase on human proteins: 2017 update. Nucleic Acids Res (2016) 0.81
Structural Bioinformatics Inspection of neXtProt PE5 Proteins in the Human Proteome. J Proteome Res (2015) 0.80
Identification of HYPK-interacting proteins reveals involvement of HYPK in regulating cell growth, cell cycle, unfolded protein response and cell death. PLoS One (2012) 0.80
Proteomics for systems toxicology. Comput Struct Biotechnol J (2014) 0.79
Can inferred provenance and its visualisation be used to detect erroneous annotation? A case study using UniProtKB. PLoS One (2013) 0.79
Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry. J Proteome Res (2015) 0.78
The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. Database (Oxford) (2015) 0.77
A community proposal to integrate proteomics activities in ELIXIR. F1000Res (2017) 0.76
Minireview: progress and challenges in proteomics data management, sharing, and integration. Mol Endocrinol (2012) 0.76
Isobar(PTM): a software tool for the quantitative analysis of post-translationally modified proteins. J Proteomics (2013) 0.76
Integrating omics technologies to study pulmonary physiology and pathology at the systems level. Cell Physiol Biochem (2014) 0.76
Accelerating the search for the missing proteins in the human proteome. Nat Commun (2017) 0.75
Identifying the missing proteins in human proteome by biological language model. BMC Syst Biol (2016) 0.75
The Human Skeletal Muscle Proteome Project: a reappraisal of the current literature. J Cachexia Sarcopenia Muscle (2016) 0.75
Lysine deacetylase (KDAC) regulatory pathways: an alternative approach to selective modulation. ChemMedChem (2014) 0.75
C2orf62 and TTC17 are involved in actin organization and ciliogenesis in zebrafish and human. PLoS One (2014) 0.75
neXtA5: accelerating annotation of articles via automated approaches in neXtProt. Database (Oxford) (2016) 0.75
The Size of the Human Proteome: The Width and Depth. Int J Anal Chem (2016) 0.75
Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS. Nat Biotechnol (2017) 0.75
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Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76
The ENZYME database in 2000. Nucleic Acids Res (2000) 23.85
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res (2010) 18.73
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res (2009) 14.90
The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res (2008) 14.82
Ensembl 2011. Nucleic Acids Res (2010) 14.68
The SWISS-MODEL Repository and associated resources. Nucleic Acids Res (2008) 11.61
The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res (2009) 11.49
Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res (2010) 11.32
Towards a knowledge-based Human Protein Atlas. Nat Biotechnol (2010) 11.05
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2010) 10.97
The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Res (2008) 10.21
The IntAct molecular interaction database in 2010. Nucleic Acids Res (2009) 9.85
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The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res (2010) 7.68
ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res (2010) 7.67
PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res (2009) 7.47
MINT, the molecular interaction database: 2009 update. Nucleic Acids Res (2009) 7.19
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Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. EMBO Rep (2000) 5.06
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol Cell Proteomics (2011) 3.37
UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res (2011) 2.45
The human proteome project: current state and future direction. Mol Cell Proteomics (2011) 2.34
A microscope-based screening platform for large-scale functional protein analysis in intact cells. FEBS Lett (2003) 2.04
Representing complexity in part-whole relationships within the Foundational Model of Anatomy. AMIA Annu Symp Proc (2003) 1.98
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. Nucleic Acids Res (2010) 1.71
The PeptideAtlas Project. Methods Mol Biol (2010) 1.46
Generation of a fluorescently labeled endogenous protein library in living human cells. Nat Protoc (2007) 1.36
Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. Mol Biotechnol (2011) 1.31
The publication and database deposition of molecular interaction data. Curr Protoc Protein Sci (2010) 1.09
Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands. Proteomics (2009) 1.04
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res (2003) 52.80
UniProt: the Universal Protein knowledgebase. Nucleic Acids Res (2004) 29.05
InterPro: the integrative protein signature database. Nucleic Acids Res (2008) 25.07
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72
The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res (2006) 22.70
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res (2003) 17.39
IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02
The PROSITE database, its status in 2002. Nucleic Acids Res (2002) 14.71
Automated annotation of microbial proteomes in SWISS-PROT. Comput Biol Chem (2003) 13.44
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
Recent improvements to the PROSITE database. Nucleic Acids Res (2004) 11.89
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res (2009) 9.14
Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics (2009) 8.87
PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform (2002) 8.77
The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools. Plant Physiol Biochem (2004) 8.59
The PROSITE database. Nucleic Acids Res (2006) 8.11
PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res (2009) 7.47
Calling on a million minds for community annotation in WikiProteins. Genome Biol (2008) 7.11
UniProtKB/Swiss-Prot. Methods Mol Biol (2007) 7.05
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res (2006) 6.13
The 20 years of PROSITE. Nucleic Acids Res (2007) 6.06
Rhythmic growth explained by coincidence between internal and external cues. Nature (2007) 6.05
ScanProsite: a reference implementation of a PROSITE scanning tool. Appl Bioinformatics (2002) 5.81
The UniProt-GO Annotation database in 2011. Nucleic Acids Res (2011) 5.19
High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Brief Bioinform (2002) 4.95
Toward interoperable bioscience data. Nat Genet (2012) 4.72
IntEnz, the integrated relational enzyme database. Nucleic Acids Res (2004) 4.65
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
Phytochrome-mediated inhibition of shade avoidance involves degradation of growth-promoting bHLH transcription factors. Plant J (2007) 3.54
ProRule: a new database containing functional and structural information on PROSITE profiles. Bioinformatics (2005) 3.41
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic Acids Res (2008) 3.29
Mass spectrometry in high-throughput proteomics: ready for the big time. Nat Methods (2010) 2.91
dictyBase--a Dictyostelium bioinformatics resource update. Nucleic Acids Res (2008) 2.75
OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics (2003) 2.73
InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform (2002) 2.66
The Sulfinator: predicting tyrosine sulfation sites in protein sequences. Bioinformatics (2002) 2.51
dictyBase, the model organism database for Dictyostelium discoideum. Nucleic Acids Res (2006) 2.45
UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res (2011) 2.45
Protein sequence databases. Curr Opin Chem Biol (2004) 2.43
A positive feedback loop stabilizes the guanine-nucleotide exchange factor Cdc24 at sites of polarization. EMBO J (2002) 2.39
The human proteome project: current state and future direction. Mol Cell Proteomics (2011) 2.34
BioCreative III interactive task: an overview. BMC Bioinformatics (2011) 2.16
The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat Biotechnol (2012) 2.14
CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens. Nucleic Acids Res (2008) 2.14
The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants. Hum Mutat (2004) 1.97
Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res (2010) 1.97
FindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification. Proteomics (2002) 1.83
neXtProt: organizing protein knowledge in the context of human proteome projects. J Proteome Res (2012) 1.80
Involvement of microRNAs in the cytotoxic effects exerted by proinflammatory cytokines on pancreatic beta-cells. Diabetes (2010) 1.80
Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. J Proteome Res (2013) 1.76
Annotation of post-translational modifications in the Swiss-Prot knowledge base. Proteomics (2004) 1.76
Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biol (2011) 1.72
Protocols for growth and development of Dictyostelium discoideum. Nat Protoc (2007) 1.68
ViralZone: a knowledge resource to understand virus diversity. Nucleic Acids Res (2010) 1.66
Protein variety and functional diversity: Swiss-Prot annotation in its biological context. C R Biol (2005) 1.54
Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase. Hum Mutat (2008) 1.50
Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase. Toxicon (2004) 1.47
Meeting Report: BioSharing at ISMB 2010. Stand Genomic Sci (2010) 1.47
Biocurators and biocuration: surveying the 21st century challenges. Database (Oxford) (2012) 1.46
Exploring glycopeptide-resistance in Staphylococcus aureus: a combined proteomics and transcriptomics approach for the identification of resistance-related markers. BMC Genomics (2006) 1.45
dictyBase: a new Dictyostelium discoideum genome database. Nucleic Acids Res (2004) 1.42
The X-ray structure of RANTES: heparin-derived disaccharides allows the rational design of chemokine inhibitors. Structure (2004) 1.42
The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program. J Proteomics (2008) 1.38
Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop. Stand Genomic Sci (2010) 1.35
Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford) (2011) 1.24
OpenFluDB, a database for human and animal influenza virus. Database (Oxford) (2010) 1.20
X-Rank: a robust algorithm for small molecule identification using tandem mass spectrometry. Anal Chem (2009) 1.20
Standard guidelines for the chromosome-centric human proteome project. J Proteome Res (2012) 1.20
Plant protein annotation in the UniProt Knowledgebase. Plant Physiol (2005) 1.15
InSilicoSpectro: an open-source proteomics library. J Proteome Res (2006) 1.12
Connexins protect mouse pancreatic β cells against apoptosis. J Clin Invest (2011) 1.08
Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands. Proteomics (2009) 1.04
A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17. J Proteome Res (2012) 1.03
Generation, annotation, and analysis of an extensive Aspergillus niger EST collection. BMC Microbiol (2006) 1.01
High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics. Proteomics (2004) 0.98
Industrial-scale proteomics: from liters of plasma to chemically synthesized proteins. Proteomics (2004) 0.96
The human proteome project: Current state and future direction. Mol Cell Proteomics (2011) 0.96
dictyBase and the Dicty Stock Center. Methods Mol Biol (2006) 0.96
Human aldehyde dehydrogenase genes: alternatively spliced transcriptional variants and their suggested nomenclature. Pharmacogenet Genomics (2009) 0.95