Published in OMICS on January 01, 2006
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol (2008) 12.96
Development of FuGO: an ontology for functional genomics investigations. OMICS (2006) 3.59
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nat Biotechnol (2008) 3.43
Data standards for flow cytometry. OMICS (2006) 1.95
TraML--a standard format for exchange of selected reaction monitoring transition lists. Mol Cell Proteomics (2011) 1.65
Meeting Report: BioSharing at ISMB 2010. Stand Genomic Sci (2010) 1.47
Facilitating the development of controlled vocabularies for metabolomics technologies with text mining. BMC Bioinformatics (2008) 1.20
Minimum information about a protein affinity reagent (MIAPAR). Nat Biotechnol (2010) 1.10
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ. Proteome Sci (2007) 1.08
The MetaboLights repository: curation challenges in metabolomics. Database (Oxford) (2013) 1.08
ISPIDER Central: an integrated database web-server for proteomics. Nucleic Acids Res (2008) 1.03
Making a new technology work: the standardization and regulation of microarrays. Yale J Biol Med (2007) 0.97
Challenges, current status and future perspectives of proteomics in improving understanding, diagnosis and treatment of vascular disease. Eur J Vasc Endovasc Surg (2009) 0.86
Dissemination of metabolomics results: role of MetaboLights and COSMOS. Gigascience (2013) 0.84
Proteomics, lipidomics, metabolomics: a mass spectrometry tutorial from a computer scientist's point of view. BMC Bioinformatics (2014) 0.80
The human plasma membrane peripherome: visualization and analysis of interactions. Biomed Res Int (2014) 0.78
Standardization and omics science: technical and social dimensions are inseparable and demand symmetrical study. OMICS (2010) 0.77
Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry. PLoS One (2015) 0.76
Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal. BMC Bioinformatics (2015) 0.75
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res (2003) 52.80
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem (2002) 35.30
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem (2003) 29.58
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). Nucleic Acids Res (2005) 23.66
The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res (2006) 22.70
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res (2004) 18.75
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res (2008) 15.69
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics (2009) 15.08
IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02
The International Protein Index: an integrated database for proteomics experiments. Proteomics (2004) 14.67
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res (2012) 13.14
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol (2008) 12.96
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res (2003) 12.81
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
Prepublication data sharing. Nature (2009) 12.24
UniProt archive. Bioinformatics (2004) 11.92
A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol (2004) 11.42
Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res (2010) 11.23
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Res (2008) 10.21
A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol (2005) 9.81
EMBL Nucleotide Sequence Database in 2006. Nucleic Acids Res (2006) 9.72
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics (2006) 8.68
The Reactome pathway knowledgebase. Nucleic Acids Res (2013) 8.56
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Mass spectrometry and protein analysis. Science (2006) 8.05
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol (2007) 8.03
The PeptideAtlas project. Nucleic Acids Res (2006) 7.87
Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol (2006) 7.56
PRIDE: the proteomics identifications database. Proteomics (2005) 7.52
The IntAct molecular interaction database in 2012. Nucleic Acids Res (2011) 7.49
The EMBL Nucleotide Sequence Database. Nucleic Acids Res (2005) 7.18
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
Calling on a million minds for community annotation in WikiProteins. Genome Biol (2008) 7.11
Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol (2003) 6.86
The EMBL Nucleotide Sequence Database. Nucleic Acids Res (2004) 6.72
An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics (2005) 6.58
Integrating biological data--the Distributed Annotation System. BMC Bioinformatics (2008) 6.56
Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell (2009) 6.54
The EBI SRS server-new features. Bioinformatics (2002) 6.38
Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol (2008) 6.38
Interpretation of shotgun proteomic data: the protein inference problem. Mol Cell Proteomics (2005) 6.28
PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep (2008) 6.10
Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics (2012) 5.95
Crucial step in cholesterol homeostasis: sterols promote binding of SCAP to INSIG-1, a membrane protein that facilitates retention of SREBPs in ER. Cell (2002) 5.70
A guide to the Proteomics Identifications Database proteomics data repository. Proteomics (2009) 5.63
Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep (2013) 5.38
An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron (2007) 5.35
The UniProt-GO Annotation database in 2011. Nucleic Acids Res (2011) 5.19
EMBL Nucleotide Sequence Database: developments in 2005. Nucleic Acids Res (2006) 5.13
Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods (2007) 5.10
A guided tour of the Trans-Proteomic Pipeline. Proteomics (2010) 5.09
PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods (2011) 5.01
Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc Natl Acad Sci U S A (2002) 4.96
High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Brief Bioinform (2002) 4.95
Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods (2012) 4.93
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol (2004) 4.91
CTCF physically links cohesin to chromatin. Proc Natl Acad Sci U S A (2008) 4.89
UniProtJAPI: a remote API for accessing UniProt data. Bioinformatics (2008) 4.88
mzML--a community standard for mass spectrometry data. Mol Cell Proteomics (2010) 4.81
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res (2008) 4.73
Toward interoperable bioscience data. Nat Genet (2012) 4.72
High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomics (2007) 4.72
Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol (2007) 4.70
IntEnz, the integrated relational enzyme database. Nucleic Acids Res (2004) 4.65
Scoring proteomes with proteotypic peptide probes. Nat Rev Mol Cell Biol (2005) 4.63
The quantitative proteome of a human cell line. Mol Syst Biol (2011) 4.57
Human Plasma PeptideAtlas. Proteomics (2005) 4.52
The Proteomics Identifications database: 2010 update. Nucleic Acids Res (2009) 4.47
PRIDE: new developments and new datasets. Nucleic Acids Res (2007) 4.42
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res (2013) 4.39
The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34
The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res (2007) 4.23
PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res (2006) 4.19
High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat Methods (2009) 4.17
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res (2005) 4.15
The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol Cell Proteomics (2004) 4.15