PubRank

Rolf Apweiler

Author PubWeight™ 613.71‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003 52.80
2 InterPro: the integrative protein signature database. Nucleic Acids Res 2008 25.07
3 The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res 2003 24.72
4 The Universal Protein Resource (UniProt). Nucleic Acids Res 2005 23.66
5 The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res 2006 22.70
6 The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res 2004 18.75
7 InterPro, progress and status in 2005. Nucleic Acids Res 2005 17.53
8 The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol 2004 16.08
9 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
10 IntAct: an open source molecular interaction database. Nucleic Acids Res 2004 15.02
11 The International Protein Index: an integrated database for proteomics experiments. Proteomics 2004 14.67
12 InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res 2011 13.45
13 Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol 2008 12.96
14 The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res 2003 12.81
15 New developments in the InterPro database. Nucleic Acids Res 2007 12.49
16 Prepublication data sharing. Nature 2009 12.24
17 UniProt archive. Bioinformatics 2004 11.92
18 A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol 2004 11.42
19 The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol 2007 10.24
20 The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Res 2008 10.21
21 EMBL Nucleotide Sequence Database in 2006. Nucleic Acids Res 2006 9.72
22 The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics 2006 8.68
23 The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol 2007 8.24
24 Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol 2007 8.03
25 PRIDE: the proteomics identifications database. Proteomics 2005 7.52
26 The EMBL Nucleotide Sequence Database. Nucleic Acids Res 2005 7.18
27 Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol 2004 7.17
28 The EMBL Nucleotide Sequence Database. Nucleic Acids Res 2004 6.72
29 An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics 2005 6.58
30 The EBI SRS server-new features. Bioinformatics 2002 6.38
31 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
32 The UniProt-GO Annotation database in 2011. Nucleic Acids Res 2011 5.19
33 EMBL Nucleotide Sequence Database: developments in 2005. Nucleic Acids Res 2006 5.13
34 High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Brief Bioinform 2002 4.95
35 UniProtJAPI: a remote API for accessing UniProt data. Bioinformatics 2008 4.88
36 The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res 2008 4.73
37 IntEnz, the integrated relational enzyme database. Nucleic Acids Res 2004 4.65
38 The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res 2007 4.23
39 PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res 2006 4.19
40 Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res 2005 4.15
41 The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. BMC Bioinformatics 2007 3.97
42 Evidence standards in experimental and inferential INSDC Third Party Annotation data. OMICS 2006 3.97
43 The Gene Ontology Annotation (GOA) Database--an integrated resource of GO annotations to the UniProt Knowledgebase. In Silico Biol 2003 3.86
44 Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Res 2007 3.84
45 The proteomics standards initiative. Proteomics 2003 3.78
46 Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. J Proteome Res 2009 3.77
47 The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible. Expert Rev Proteomics 2006 3.74
48 The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol 2007 3.55
49 UniSave: the UniProtKB sequence/annotation version database. Bioinformatics 2006 3.38
50 QuickGO: a web-based tool for Gene Ontology searching. Bioinformatics 2009 3.36
51 The European Bioinformatics Institute's data resources. Nucleic Acids Res 2003 3.34
52 The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. Nucleic Acids Res 2003 3.29
53 Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res 2007 3.13
54 InterPro and InterProScan: tools for protein sequence classification and comparison. Methods Mol Biol 2007 3.05
55 The EBI SRS server--recent developments. Bioinformatics 2002 3.04
56 The Integr8 project--a resource for genomic and proteomic data. In Silico Biol 2005 3.03
57 Applications of InterPro in protein annotation and genome analysis. Brief Bioinform 2002 3.03
58 The predictive power of the CluSTr database. Bioinformatics 2005 2.85
59 Clinical proteomics: A need to define the field and to begin to set adequate standards. Proteomics Clin Appl 2007 2.84
60 Dasty and UniProt DAS: a perfect pair for protein feature visualization. Bioinformatics 2005 2.74
61 ASTD: The Alternative Splicing and Transcript Diversity database. Genomics 2008 2.72
62 InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform 2002 2.66
63 Increase of functional diversity by alternative splicing. Trends Genet 2003 2.59
64 The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI). OMICS 2006 2.38
65 The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments. Pac Symp Biocomput 2005 2.29
66 The Gene Ontology Annotation (GOA) Project--Application of GO in SWISS-PROT, TrEMBL and InterPro. Comp Funct Genomics 2003 1.93
67 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
68 Finding one's way in proteomics: a protein species nomenclature. Chem Cent J 2009 1.75
69 Cardiovascular GO annotation initiative year 1 report: why cardiovascular GO? Proteomics 2008 1.72
70 Common interchange standards for proteomics data: Public availability of tools and schema. Proteomics 2004 1.68
71 GOAnnotator: linking protein GO annotations to evidence text. J Biomed Discov Collab 2006 1.66
72 Recommendations for biomarker identification and qualification in clinical proteomics. Sci Transl Med 2010 1.59
73 Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004. Proteomics 2005 1.54
74 Systematic comparison of the human saliva and plasma proteomes. Proteomics Clin Appl 2009 1.51
75 Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria. Proteomics 2008 1.51
76 Use of Gene Ontology Annotation to understand the peroxisome proteome in humans. Database (Oxford) 2013 1.48
77 The InterPro database and tools for protein domain analysis. Curr Protoc Bioinformatics 2008 1.43
78 Phosphoproteome analysis reveals regulatory sites in major pathways of cardiac mitochondria. Mol Cell Proteomics 2010 1.41
79 Analyzing large-scale proteomics projects with latent semantic indexing. J Proteome Res 2007 1.39
80 Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets. Proteomics 2011 1.31
81 The importance of uniformity in reporting protein-function data. Trends Biochem Sci 2005 1.27
82 The speciation of the proteome. Chem Cent J 2008 1.21
83 Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005). Proteomics 2005 1.20
84 Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative. Comp Funct Genomics 2003 1.18
85 The European Bioinformatics Institute's data resources 2014. Nucleic Acids Res 2013 1.17
86 The EMBL Nucleotide Sequence and Genome Reviews Databases. Methods Mol Biol 2007 1.17
87 Altered proteome biology of cardiac mitochondria under stress conditions. J Proteome Res 2008 1.16
88 Plant protein annotation in the UniProt Knowledgebase. Plant Physiol 2005 1.15
89 Integration of cardiac proteome biology and medicine by a specialized knowledgebase. Circ Res 2013 1.15
90 Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets. Proteomics 2008 1.14
91 Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005. Proteomics 2006 1.11
92 Missing in action: enzyme functional annotations in biological databases. Nat Chem Biol 2009 1.11
93 The impact of focused Gene Ontology curation of specific mammalian systems. PLoS One 2011 1.11
94 In silico characterization of proteins: UniProt, InterPro and Integr8. Mol Biotechnol 2007 1.10
95 TEMBLOR - Perspectives of EBI Database Services. Comp Funct Genomics 2002 1.09
96 A posteriori quality control for the curation and reuse of public proteomics data. Proteomics 2011 1.07
97 Genome Reviews: standardizing content and representation of information about complete genomes. OMICS 2006 1.07
98 The Renal Gene Ontology Annotation Initiative. Organogenesis 2010 1.06
99 Further advances in the development of a data interchange standard for proteomics data. Proteomics 2003 1.04
100 HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy. Proteomics 2006 1.02
101 The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data. Comp Funct Genomics 2003 1.01
102 QuickGO: a user tutorial for the web-based Gene Ontology browser. Database (Oxford) 2009 1.01
103 LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics. PLoS One 2013 1.00
104 On the importance of comprehensible classification models for protein function prediction. IEEE/ACM Trans Comput Biol Bioinform 2010 0.99
105 Linking publication, gene and protein data. Nat Cell Biol 2006 0.99
106 Cellular resolution models for even skipped regulation in the entire Drosophila embryo. Elife 2013 0.98
107 Proteomic data exchange and storage: the need for common standards and public repositories. Methods Mol Biol 2007 0.96
108 Who tangos with GOA?-Use of Gene Ontology Annotation (GOA) for biological interpretation of '-omics' data and for validation of automatic annotation tools. In Silico Biol 2005 0.95
109 Second proteomics standards initiative spring workshop. Expert Rev Proteomics 2005 0.95
110 A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies. Proteomics 2006 0.94
111 Characterization, design, and function of the mitochondrial proteome: from organs to organisms. J Proteome Res 2013 0.94
112 A guide to UniProt for protein scientists. Methods Mol Biol 2011 0.94
113 Annotating the human proteome: beyond establishing a parts list. Biochim Biophys Acta 2006 0.93
114 Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase. Proteomics 2006 0.91
115 Annotating the human proteome. Mol Cell Proteomics 2005 0.90
116 Comparative proteomics profiling reveals role of smooth muscle progenitors in extracellular matrix production. Arterioscler Thromb Vasc Biol 2010 0.89
117 Current status of proteomic standards development. Expert Rev Proteomics 2004 0.88
118 A large-scale protein-function database. Nat Chem Biol 2010 0.86
119 Advances in the development of common interchange standards for proteomic data. Proteomics 2004 0.85
120 Tools and resources for identifying protein families, domains and motifs. Genome Biol 2001 0.82
121 The power of cooperative investigation: summary and comparison of the HUPO Brain Proteome Project pilot study results. Proteomics 2006 0.82
122 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
123 Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study. Proteomics 2006 0.81
124 Bioinformatics database infrastructure for biotechnology research. J Biotechnol 2006 0.80
125 Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data. Proteomics 2006 0.80
126 Know your limits: assumptions, constraints and interpretation in systems biology. Biochim Biophys Acta 2009 0.80
127 Bioinformatics Resources for In Silico Proteome Analysis. J Biomed Biotechnol 2003 0.79
128 The HUPO initiative on Model Organism Proteomes, iMOP. Proteomics 2012 0.78
129 Do you do text? Bioinformatics 2005 0.77
130 Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy. Mol Cell Proteomics 2007 0.77
131 Towards data management of the HUPO Human Brain Proteome Project pilot phase. Proteomics 2004 0.75
132 Human Proteome Organisation Proteomics Standards Initiative. Pre-Congress Initiative. Proteomics 2005 0.75
133 Wiley-VCH and HUPO: a global effort to advance proteomic science. Proteomics 2008 0.75
134 Proteomics data collection--4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands. Proteomics 2009 0.75
135 Building a biological space based on protein sequence similarities and biological ontologies. Comb Chem High Throughput Screen 2008 0.75
136 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame. Proteomics 2005 0.75
137 Algorithms and databases. Methods Mol Biol 2009 0.75
138 Wiley-VCH and HUPO: A Global Effort to Advance Proteomic Science. Proteomics Clin Appl 2008 0.75
139 Proteomics Data Collection - 3rd ProDaC workshop April 22nd 2008, Toledo, Spain. Proteomics 2008 0.75
140 Getting a grip on proteomics data - Proteomics Data Collection (ProDaC). Proteomics 2009 0.75
141 Proteomics Data Collection - 2nd ProDaC Workshop 5 October 2007, Seoul, Korea. Proteomics 2008 0.75
142 The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies. Proteomics 2006 0.75
143 Proteomics Data Collection - the 1st ProDaC workshop 26 April 2007 Ecole Normale Supérieur, Lyon, France. Proteomics 2007 0.75
144 "4D Biology for health and disease" workshop report. N Biotechnol 2010 0.75
145 Proteomics Data Collection - 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece. Proteomics 2009 0.75
146 Databases and resources for in silico proteome analysis. Methods Biochem Anal 2006 0.75
147 Protein sequence database methods. Genet Eng (N Y) 2004 0.75
148 High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7-9, 2007 Wellcome Trust Conference Centre, Hinxton, UK. Proteomics 2007 0.75