PubRank

Henning Hermjakob

Author PubWeight™ 385.67‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008 31.04
2 Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 2008 15.69
3 The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res 2012 13.14
4 Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol 2008 12.96
5 A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol 2004 11.42
6 Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 2010 11.23
7 The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol 2007 10.24
8 The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics 2006 8.68
9 The Reactome pathway knowledgebase. Nucleic Acids Res 2013 8.56
10 The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol 2007 8.24
11 Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol 2007 8.03
12 PRIDE: the proteomics identifications database. Proteomics 2005 7.52
13 The IntAct molecular interaction database in 2012. Nucleic Acids Res 2011 7.49
14 Calling on a million minds for community annotation in WikiProteins. Genome Biol 2008 7.11
15 Integrating biological data--the Distributed Annotation System. BMC Bioinformatics 2008 6.56
16 A guide to the Proteomics Identifications Database proteomics data repository. Proteomics 2009 5.63
17 Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 2005 5.42
18 PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods 2011 5.01
19 mzML--a community standard for mass spectrometry data. Mol Cell Proteomics 2010 4.81
20 The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res 2008 4.73
21 Toward interoperable bioscience data. Nat Genet 2012 4.72
22 The Proteomics Identifications database: 2010 update. Nucleic Acids Res 2009 4.47
23 PRIDE: new developments and new datasets. Nucleic Acids Res 2007 4.42
24 The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res 2013 4.39
25 PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res 2006 4.19
26 The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. BMC Bioinformatics 2007 3.97
27 The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A 2007 3.93
28 The proteomics standards initiative. Proteomics 2003 3.78
29 Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. J Proteome Res 2009 3.77
30 The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible. Expert Rev Proteomics 2006 3.74
31 Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France. Proteomics 2007 3.69
32 The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol 2007 3.55
33 Dasty2, an Ajax protein DAS client. Bioinformatics 2008 3.26
34 Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods 2012 3.17
35 Clinical proteomics: A need to define the field and to begin to set adequate standards. Proteomics Clin Appl 2007 2.84
36 The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Proteomics 2012 2.82
37 Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition. Proteomics 2007 2.74
38 Dasty and UniProt DAS: a perfect pair for protein feature visualization. Bioinformatics 2005 2.74
39 InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform 2002 2.66
40 BioJS: an open source JavaScript framework for biological data visualization. Bioinformatics 2013 2.53
41 The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI). OMICS 2006 2.38
42 Annotating cancer variants and anti-cancer therapeutics in reactome. Cancers (Basel) 2012 2.35
43 The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinformatics 2008 2.33
44 The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments. Pac Symp Biocomput 2005 2.29
45 The Ontology Lookup Service: bigger and better. Nucleic Acids Res 2010 2.27
46 The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Mol Cell Proteomics 2012 2.10
47 PRIDE Inspector: a tool to visualize and validate MS proteomics data. Nat Biotechnol 2012 2.10
48 ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nat Methods 2007 2.04
49 MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data. Genome Biol 2008 1.76
50 Common interchange standards for proteomics data: Public availability of tools and schema. Proteomics 2004 1.68
51 Dasty3, a WEB framework for DAS. Bioinformatics 2011 1.67
52 The Reactome BioMart. Database (Oxford) 2011 1.66
53 PRIDE: quality control in a proteomics data repository. Database (Oxford) 2012 1.63
54 The PSI semantic validator: a framework to check MIAPE compliance of proteomics data. Proteomics 2009 1.62
55 A reagent resource to identify proteins and peptides of interest for the cancer community: a workshop report. Mol Cell Proteomics 2006 1.60
56 Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004. Proteomics 2005 1.54
57 jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats. Proteomics 2012 1.49
58 implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada. Proteomics 2010 1.46
59 From Peptidome to PRIDE: public proteomics data migration at a large scale. Proteomics 2013 1.46
60 Minimum information about a bioactive entity (MIABE). Nat Rev Drug Discov 2011 1.44
61 jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data. Proteomics 2012 1.44
62 Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics 2015 1.44
63 Recurated protein interaction datasets. Nat Methods 2009 1.43
64 Analyzing large-scale proteomics projects with latent semantic indexing. J Proteome Res 2007 1.39
65 Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project. Proteomics 2005 1.37
66 Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop. Stand Genomic Sci 2010 1.35
67 PRIDE Cluster: building a consensus of proteomics data. Nat Methods 2013 1.34
68 Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations. Database (Oxford) 2011 1.32
69 Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets. Proteomics 2011 1.31
70 The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database (Oxford) 2013 1.31
71 Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst Biol 2013 1.29
72 Improvements in the Protein Identifier Cross-Reference service. Nucleic Acids Res 2012 1.29
73 Published and perished? The influence of the searched protein database on the long-term storage of proteomics data. Mol Cell Proteomics 2011 1.26
74 R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases. Nucleic Acids Res 2010 1.26
75 A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis. OMICS 2012 1.25
76 Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005). Proteomics 2005 1.20
77 The PSI formal document process and its implementation on the PSI website. Proteomics 2007 1.20
78 Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative. Comp Funct Genomics 2003 1.18
79 Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories. Proteomics 2005 1.17
80 Reactome pathway analysis to enrich biological discovery in proteomics data sets. Proteomics 2011 1.17
81 ENFIN--A European network for integrative systems biology. C R Biol 2009 1.17
82 Integration of cardiac proteome biology and medicine by a specialized knowledgebase. Circ Res 2013 1.15
83 Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets. Proteomics 2008 1.14
84 InteroPORC: automated inference of highly conserved protein interaction networks. Bioinformatics 2008 1.13
85 Organelle proteomics experimental designs and analysis. Proteomics 2010 1.12
86 Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005. Proteomics 2006 1.11
87 A new reference implementation of the PSICQUIC web service. Nucleic Acids Res 2013 1.11
88 A community standard format for the representation of protein affinity reagents. Mol Cell Proteomics 2009 1.11
89 Minimum information about a protein affinity reagent (MIAPAR). Nat Biotechnol 2010 1.10
90 The systematic annotation of the three main GPCR families in Reactome. Database (Oxford) 2010 1.09
91 The publication and database deposition of molecular interaction data. Curr Protoc Protein Sci 2010 1.09
92 The ESF Programme on Functional Genomics Workshop on 'Data Integration in Functional Genomics: Application to Biological Pathways'. Comp Funct Genomics 2004 1.07
93 The HUPO proteomics standards initiative--easing communication and minimizing data loss in a changing world. Brief Bioinform 2007 1.04
94 Further advances in the development of a data interchange standard for proteomics data. Proteomics 2003 1.04
95 ISPIDER Central: an integrated database web-server for proteomics. Nucleic Acids Res 2008 1.03
96 Rintact: enabling computational analysis of molecular interaction data from the IntAct repository. Bioinformatics 2007 1.02
97 The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data. Comp Funct Genomics 2003 1.01
98 Analyzing protein-protein interaction networks. J Proteome Res 2012 1.01
99 LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics. PLoS One 2013 1.00
100 Open source libraries and frameworks for biological data visualisation: a guide for developers. Proteomics 2015 1.00
101 Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective. Biochim Biophys Acta 2013 1.00
102 How to submit MS proteomics data to ProteomeXchange via the PRIDE database. Proteomics 2014 0.99
103 Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML. Mol Cell Proteomics 2013 0.97
104 A domain level interaction network of amyloid precursor protein and Abeta of Alzheimer's disease. Proteomics 2010 0.96
105 Proteomic data exchange and storage: the need for common standards and public repositories. Methods Mol Biol 2007 0.96
106 iAnn: an event sharing platform for the life sciences. Bioinformatics 2013 0.96
107 DAS writeback: a collaborative annotation system. BMC Bioinformatics 2011 0.95
108 Second proteomics standards initiative spring workshop. Expert Rev Proteomics 2005 0.95
109 Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). Mol Cell Proteomics 2011 0.94
110 Characterization, design, and function of the mitochondrial proteome: from organs to organisms. J Proteome Res 2013 0.94
111 Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets. Plant Cell 2010 0.92
112 Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework. BMC Bioinformatics 2012 0.92
113 jmzTab: a java interface to the mzTab data standard. Proteomics 2014 0.92
114 Data standardization by the HUPO-PSI: how has the community benefitted? Methods Mol Biol 2011 0.92
115 Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). J Proteome Res 2011 0.91
116 The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative. Proteomics 2010 0.91
117 Annotating the human proteome. Mol Cell Proteomics 2005 0.90
118 Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA. Proteomics 2012 0.89
119 Preparing molecular interaction data for publication. Methods Mol Biol 2011 0.89
120 Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report. J Proteomics 2013 0.89
121 Current status of proteomic standards development. Expert Rev Proteomics 2004 0.88
122 easyDAS: automatic creation of DAS servers. BMC Bioinformatics 2011 0.88
123 Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Proteomics 2011 0.87
124 Data standards and controlled vocabularies for proteomics. Methods Mol Biol 2008 0.87
125 Charting online OMICS resources: A navigational chart for clinical researchers. Proteomics Clin Appl 2008 0.86
126 The EBI enzyme portal. Nucleic Acids Res 2012 0.86
127 A public repository for mass spectrometry imaging data. Anal Bioanal Chem 2015 0.86
128 Annual spring meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain. Proteomics 2008 0.86
129 Capturing cooperative interactions with the PSI-MI format. Database (Oxford) 2013 0.86
130 Advances in the development of common interchange standards for proteomic data. Proteomics 2004 0.85
131 Tackling quantitation: a report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea. Proteomics 2010 0.84
132 HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions. Anal Chem 2013 0.84
133 Identifying novel biomarkers through data mining-a realistic scenario? Proteomics Clin Appl 2015 0.84
134 Controlled vocabularies and ontologies in proteomics: overview, principles and practice. Biochim Biophys Acta 2013 0.83
135 Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK. Proteomics 2013 0.82
136 A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology. Proteomics 2015 0.82
137 Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany. Proteomics 2011 0.81
138 Proteomics data validation: why all must provide data. Mol Biosyst 2007 0.81
139 Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA. Proteomics 2006 0.81
140 6th HUPO Annual World Congress - Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea. Proteomics 2008 0.80
141 From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland. Proteomics 2012 0.80
142 HUPO 2011: The new Cardiovascular Initiative - integrating proteomics and cardiovascular biology in health and disease. Proteomics 2012 0.80
143 Annual spring meeting of the Proteomics Standards Initiative. Proteomics 2009 0.80
144 Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany. Proteomics 2014 0.80
145 Towards the collaborative curation of the registry underlying Identifiers.org. Database (Oxford) 2013 0.78
146 The HUPO initiative on Model Organism Proteomes, iMOP. Proteomics 2012 0.78
147 Second Joint HUPO publication and Proteomics Standards Initiative workshop. Proteomics 2009 0.77
148 Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy. Mol Cell Proteomics 2007 0.77
149 Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA. Proteomics 2007 0.77
150 Expression data analysis with reactome. Curr Protoc Bioinformatics 2015 0.76
151 Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Proteomics Clin Appl 2011 0.75
152 OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology. BMC Bioinformatics 2008 0.75
153 MyDas, an extensible Java DAS server. PLoS One 2012 0.75
154 The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies. Proteomics 2006 0.75
155 Human Proteome Organisation Proteomics Standards Initiative. Pre-Congress Initiative. Proteomics 2005 0.75
156 Proteomics data visualisation. Proteomics 2015 0.75