Bairoch, Amos Marc

Title	Published in	Year	Views	Downloads
Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students	Database	2021	404	699
The ABCD database: a repository for chemically defined antibodies	Nucleic Acids Research	2020	640	418
A high-stringency blueprint of the human proteome	Nature Communications	2020	365	550
Brain metastasis cell lines panel: a public resource of organotropic cell lines	Cancer Research	2020	274	0
The neXtProt knowledgebase in 2020: data, tools and usability improvements	Nucleic Acids Research	2020	514	543
The feature-viewer: a visualization tool for positional annotations on a sequence	Bioinformatics	2020	304	0
CLASTR : the cellosaurus STR similarity search tool ‐ A precious help for cell line authentication	International Journal of Cancer	2020	497	1,386
Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines	eLife	2019	410	141
Cell lines as biological models: practical steps for more reliable research	Chemical Research in Toxicology	2019	362	1
Exploring the Uncharacterized Human Proteome Using neXtProt	Journal of Proteome Research	2018	442	0
Large-Scale Reanalysis of Publicly Available HeLa Cell Proteomics Data in the Context of the Human Proteome Project	Journal of Proteome Research	2018	478	3
Kinases and Cancer	Cancers	2018	538	230
A new bioinformatics tool to help assess the significance of BRCA1 variants	Human Genomics	2018	536	237
The Cellosaurus, a Cell-Line Knowledge Resource	Journal of Biomolecular Techniques	2018	616	1,081
A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells	Stem Cell Reports	2018	582	344
The neXtProt knowledgebase on human proteins: 2017 update	Nucleic acids research	2017	551	399
Triage by ranking to support the curation of protein interactions	Database	2017	565	534
Annotation of functional impact of voltage-gated sodium channel mutations	Human mutation	2017	590	416
The missing protein landscape of human chromosomes 2 and 14: progress and current status	Journal of proteome research	2016	561	177
ICEPO: the ion channel electrophysiology ontology	Database	2016	594	247
Deep Question Answering for protein annotation	Database	2015	607	1,160
Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat	Database	2015	550	317
N-terminome analysis of the human mitochondrial proteome	Proteomics	2015	602	0
The neXtProt knowledgebase on human proteins: current status	Nucleic acids research	2015	715	308
Converting neXtProt into Linked Data and nanopublications	Semantic web	2015	598	864
C11orf83, a Mitochondrial Cardiolipin-Binding Protein Involved in bc₁ Complex Assembly and Supercomplex Stabilization	Molecular and cellular biology	2015	737	266
Key challenges for the creation and maintenance of specialist protein resources	Proteins	2015	546	107
Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins	Journal of proteome research	2014	752	944
Querying neXtProt nanopublications and their value for insights on sequence variants and tissue expression	Journal of web semantics	2014	631	0
Standards for Reporting Enzyme Data: The STRENDA Consortium: What it aims to do and why it should be helpful	Perspectives in science	2014	703	968
C2orf62 and TTC17 are involved in actin organization and ciliogenesis in zebrafish and human	PloS one	2014	732	386
DERA is the human deoxyribose phosphate aldolase and is involved in stress response	Biochimica et biophysica acta. Molecular cell research	2014	739	326
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support	Nucleic acids research	2014	925	73
A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17	Journal of proteome research	2013	672	0
A large-scale evaluation of computational protein function prediction	Nature methods	2013	735	1,296
neXtProt: organizing protein knowledge in the context of human proteome projects	Journal of proteome research	2013	732	0
Standard guidelines for the chromosome-centric human proteome project	Journal of proteome research	2012	660	0
The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome	Nature biotechnology	2012	650	0
UniPathway: a resource for the exploration and annotation of metabolic pathways	Nucleic acids research	2012	618	808
neXtProt: a knowledge platform for human proteins	Nucleic acids research	2012	719	475
Functional identification of APIP as human mtnB, a key enzyme in the methionine salvage pathway	PloS one	2012	627	440
Towards BioDBcore: a community-defined information specification for biological databases	Nucleic acids research	2011	554	374
ViralZone: a knowledge resource to understand virus diversity	Nucleic acids research	2011	818	822
A preliminary study on the prediction of human protein functions	Foundations on Natural and Artificial Computation: 4th International Work-conference on the Interplay Between Natural and Artificial Computation, IWINAC 2011	2011	504	0
The human proteome project: current state and future direction	Molecular & cellular proteomics	2011	720	761
PROSITE, a protein domain database for functional characterization and annotation	Nucleic acids research	2010	746	696
Animal Toxins: How is Complexity Represented in Databases?	Toxins	2010	553	470
Mass spectrometry in high-throughput proteomics: ready for the big time	Nature methods	2010	556	0
A large-scale protein-function database	Nature chemical biology	2010	628	298
OpenFluDB, a database for human and animal influenza virus	Database	2010	656	656
Infrastructure for the life sciences: design and implementation of the UniProt website	BMC bioinformatics	2009	1,039	2,664
Human aldehyde dehydrogenase genes: alternatively spliced transcriptional variants and their suggested nomenclature	Pharmacogenetics and genomics	2009	685	2
Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands	Proteomics	2009	629	0
InterPro: the integrative protein signature database	Nucleic acids research	2009	662	154
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot	Nucleic acids research	2009	683	529
UniProtKB/Swiss-Prot manual and automated annotation of complete proteomes: the Dictyostelium discoideum case study	Bioinformatics: a Swiss Perspective	2009	539	0
The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program	Journal of proteomics	2009	644	0
CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens	Nucleic acids research	2009	726	224
Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase	Database	2009	714	477
The impact of 3D structures on a protein knowledgebase: from proteins to systems	Structural Proteomics and its Impact on the Life Sciences	2008	598	0
Calling on a million minds for community annotation in WikiProteins	GenomeBiology.com	2008	644	1,040
The 20 years of PROSITE	Nucleic acids research	2008	606	483
Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase	Human mutation	2008	714	322
UniProtKB/Swiss-Prot: new and future developments	Data Integration in the Life Sciences, Proceedings of the 5th International Workshop, DILS 2008	2008	628	0
New developments in the InterPro database	Nucleic acids research	2007	721	1,306
UniProtKB/Swiss-Prot	Methods in molecular biology	2007	761	0
Data integration in Proteomics	Proteome research: concepts, technology and applications	2007	567	0
Protein variations: resources and tools	Biomedical application of proteomics	2006	616	0
The Universal Protein Resource (UniProt): an expanding universe of protein information	Nucleic acids research	2006	716	1,677
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins	Nucleic acids research	2006	935	667
Small can be beautiful, but it remains complex!	Complexus	2006	553	0
The PROSITE database	Nucleic acids research	2006	708	611
Functionally and structurally relevant residues in PROSITE motif descriptors	Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics	2005	512	1
Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase	Toxicon	2005	693	0
ProRule: a new database containing functional and structural information on PROSITE profiles	Bioinformatics	2005	723	335
Plant protein annotation in the UniProt Knowledgebase	Plant physiology	2005	551	510
InterPro, progress and status in 2005	Nucleic acids research	2005	711	36
Protein identification and analysis tools on the ExPASy server	The Proteomics Protocols Handbook	2005	1,627	0
The Universal Protein Resource (UniProt)	Nucleic acids research	2005	1,011	922
Protein variety and functional diversity: Swiss-Prot annotation in its biological context	Comptes rendus. Biologies	2005	642	0
The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants	Human mutation	2004	613	0
IntAct: an open source molecular interaction database	Nucleic acids research	2004	729	416
Annotation of post-translational modifications in the Swiss-Prot knowledge base	Proteomics	2004	616	0
Protein sequence databases	Current opinion in chemical biology	2004	476	0
The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools	Plant physiology and biochemistry	2004	628	0
Swiss-Prot: juggling between evolution and stability	Briefings in bioinformatics	2004	619	462
Industrial-scale proteomics: from liters of plasma to chemically synthesized proteins	Proteomics	2004	635	0
Post-translational modifications: a challenge for proteomics and bioinformatics	Proteomics	2004	585	121
IntEnz, the integrated relational enzyme database	Nucleic acids research	2004	741	178
UniProt: the Universal Protein knowledgebase	Nucleic acids research	2004	1,345	555
Recent improvements to the PROSITE database	Nucleic acids research	2004	608	328
ExPASy: The proteomics server for in-depth protein knowledge and analysis	Nucleic acids research	2003	1,253	420
Protein databases	Nature Encyclopedia of the Human Genome	2003	574	0
PA26 is a candidate gene for heterotaxia in humans: identification of a novel PA26-related gene family in human and mouse	Human genetics	2003	638	0
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003	Nucleic acids research	2003	997	538
NEWT, a new taxonomy portal	Nucleic acids research	2003	620	108
The InterPro Database, 2003 brings increased coverage and new features	Nucleic acids research	2003	708	521
Automated annotation of microbial proteomes in SWISS-PROT	Computational biology and chemistry	2003	493	0
FindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification	Proteomics	2002	689	0
The application of bioinformatics to mass spectrometry	Proteomics	2002	492	0
El nuevo servidor Latinoamericano de biologia molecular de la UCB: bo.expasy.org	Acta Nova	2002	305	297
The Sulfinator: predicting tyrosine sulfation sites in protein sequences	Bioinformatics	2002	729	361
High-quality protein knowledge resource: SWISS-PROT and TrEMBL	Briefings in bioinformatics	2002	664	1,560
The PROSITE database, its status in 2002	Nucleic acids research	2002	596	167
PROSITE: a documented database using patterns and profiles as motif descriptors	Briefings in bioinformatics	2002	673	929
ScanProsite: a reference implementation of a PROSITE scanning tool	Applied bioinformatics	2002	1,180	401
Annotation of glycoproteins in the SWISS-PROT database	Proteomics	2001	636	0
The human proteomics initiative (HPI)	Trends in biotechnology	2001	580	0
SWISS-PROT: connecting biomolecular knowledge via a protein database	Current issues in molecular biology	2001	846	302
Technical comment to "Database verification studies of SWISS-PROT and GenBank" by Karp et al	Bioinformatics	2001	665	90
The InterPro database, an integrated documentation resource for protein families, domains and functional sites	Nucleic acids research	2001	689	564
Quality control in databanks for molecular biology	BioEssays	2000	562	0
InterPro--an integrated documentation resource for protein families, domains and functional sites	Bioinformatics	2000	718	463
The ENZYME database in 2000	Nucleic acids research	2000	520	721
A comprehensive web resource on RNA helicases from the baker's yeast Saccharomyces cerevisiae	Yeast	2000	628	0
Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times!	Bioinformatics	2000	647	1,994
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000	Nucleic acids research	2000	712	1,092
The 1999 SWISS-2DPAGE database update	Nucleic acids research	2000	586	420
The PROSITE database, its status in 1999	Nucleic acids research	1999	574	556
Eukaryotic aldehyde dehydrogenase (ALDH) genes: human polymorphisms, and recommended nomenclature based on divergent evolution and chromosomal mapping	Pharmacogenetics	1999	513	0
Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection	Electrophoresis	1999	596	0
Internet resources for protein identification and characterization	Microcharacterization of proteins	1999	390	0
The SWISS-2DPAGE database: what has changed during the last year	Nucleic acids research	1999	589	409
A testis-specific gene, TPTE, encodes a putative transmembrane tyrosine phosphatase and maps to the pericentromeric region of human chromosomes 21 and 13, and to chromosomes 15, 22, and Y	Human genetics	1999	663	0
High-throughput mass spectrometric discovery of protein post-translational modifications	Journal of Molecular Biology	1999	696	1,339
A molecular scanner to automate proteomic research and to display proteome images	Analytical chemistry	1999	644	785
The ENZYME data bank in 1999	Nucleic acids research	1999	505	629
Protein identification and analysis tools in the ExPASy server	Methods in Molecular Biology	1999	443	0
Representation of functional information in the SWISS-PROT data bank	Bioinformatics	1999	500	57
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999	Nucleic acids research	1999	654	1,192
Low molecular weight proteins: a challenge for post-genomic research	Electrophoresis	1998	524	0
Multiple parameter cross-species protein identification using MultiIdent - a world-wide web accessible tool	Electrophoresis	1998	527	0
GPCRDB: an information system for G protein-coupled receptors	Nucleic acids research	1998	664	411
'98 Escherichia coli SWISS-2DPAGE database update	Electrophoresis	1998	678	2
Two-dimensional gel electrophoresis for proteome projects: the effects of protein hydrophobicity and copy number	Electrophoresis	1998	511	0
A superfamily of metalloenzymes unifies phosphopentomutase and cofactor-independent phosphoglycerate mutase with alkaline phosphatases and sulfatases	Protein science	1998	551	336
Construction of the gyrB Database for the Identification and Classification of Bacteria	Genomics & Informatics	1998	586	444
Protein annotation: detective work for function prediction	Trends in genetics	1998	508	0
Protein identification with N and C-terminal sequence tags in proteome projects	Journal of Molecular Biology	1998	538	0
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998	Nucleic acids research	1998	571	488
New insulin-like proteins with atypical disulfide bond pattern characterized in Caenorhabditis elegans by comparative sequence analysis and homology modeling	Genome research	1998	461	121
Current status of the SWISS-2DPAGE database	Nucleic acids research	1998	560	93
Sequences and topology: Predicting evolution	Current opinion in structural biology	1997	498	0
Proteome Databases	Proteome research: new frontiers in functional genomics	1997	378	0
The PROSITE database, its status in 1997	Nucleic acids research	1997	549	82
The UDP glycosyltransferase gene superfamily: recommended nomenclature update based on evolutionary divergence	Pharmacogenetics	1997	594	0
The SWISS-PROT protein sequence database: its relevance to human molecular medical research	Journal of molecular medicine	1997	537	0
Detailed peptide characterization using PEPTIDEMASS : a World-Wide-Web-accessible tool	Electrophoresis	1997	719	0
Arac/XylS family of transcriptional regulators	Microbiology and molecular biology reviews	1997	590	1,207
Molecular basis of symbiosis between Rhizobium and legumes	Nature	1997	991	0
Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL	Proceedings	1997	656	1,459
The SWISS-PROT protein sequence data bank and its supplement TrEMBL	Nucleic acids research	1997	691	608
The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis, its status in 1995	Nucleic acids research	1996	690	157
The yeast SWISS-2DPAGE database	Electrophoresis	1996	634	0
The PROSITE database, its status in 1995	Nucleic acids research	1996	546	202
Federated two-dimensional electrophoresis database: a simple means of publishing two-dimensional electrophoresis data	Electrophoresis	1996	575	0
Updating the sequence-based classification of glycosyl hydrolases	Biochemical journal	1996	677	271
The ENZYME data bank in 1995	Nucleic acids research	1996	571	200
Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database	Electrophoresis	1996	659	0
LISTA, LISTA-HOP and LISTA-HON: a comprehensive compilation of protein encoding sequences and its associated homology databases from the yeast Saccharomyces	Nucleic acids research	1996	608	54
Integrating two-dimensional gel databases using the Melanie II software	Trends in biochemical sciences	1996	748	0
The SWISS-PROT protein sequence data bank and its new supplement TREMBL	Nucleic acids research	1996	695	767
Go hunting in sequence databases but watch out for the traps	Trends in genetics	1996	625	0
Inside SWISS-2DPAGE database	Electrophoresis	1995	681	0
Sharing of worldwide spread knowledge using hypermedia facilities & fast communication protocols (Mosaic and World Wide Web): the example of ExPASy	Methods of information in medicine	1995	567	0
The SWISS-PROT protein sequence data bank: current status	Nucleic acids research	1994	708	248
A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server	Trends in biochemical sciences	1994	617	0
Proposals for the naming of chloroplast genes. III. Nomenclature for open reading frames encoded in chloroplast genomes	Plant molecular biology reporter	1994	611	0
LISTA, LISTA-HOP and LISTA-HON: a comprehensive compilation of protein encoding sequences and its associated homology databases from the yeast Saccharomyces	Nucleic acids research	1994	604	35
The ENZYME data bank	Nucleic acids research	1994	651	125
PROSITE: recent developments	Nucleic acids research	1994	540	221
A novel zinc-binding motif found in two ubiquitous deaminase families	Protein science	1994	634	148
A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation	ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology	1994	583	394
The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis	Nucleic acids research	1994	634	225
The SWISS-PROT protein sequence data bank, recent developments	Nucleic acids research	1993	672	255
ExPASy: un système expert pour l'analyse de séquences protéiques	Technologie et Santé	1993	408	91
A diverse transketolase family that includes the RecP protein of Streptococcus pneumoniae, a protein implicated in genetic recombination	Research in microbiology	1993	576	0
Snake proteins and nucleic acids	Toxicon	1993	613	0
Human liver protein map: update 1993	Electrophoresis	1993	708	0
The PROSITE dictionary of sites and patterns in proteins, its current status	Nucleic acids research	1993	591	840
New families in the classification of glycosyl hydrolases based on amino acid sequence similarities	Biochemical journal	1993	945	217
SWISS-2DPAGE: a database of two-dimensional gel electrophoresis images	Electrophoresis	1993	734	0
Complementation of the DNA repair defect in xeroderma pigmentosum group G cells by a human cDNA related to yeast RAD2	Nature	1993	669	0
A possible mechanism for metal-ion induced DNA-protein dissociation in a family of prokaryotic transcriptional regulators	Nucleic acids research	1993	635	101
The ENZYME data bank	Nucleic acids research	1993	604	331
Electrophorèse bidimensionnelle et informatique: un outil pour le diagnostic médical?	Labolife	1993	516	182
Plasma and red blood cell protein maps: update 1993	Electrophoresis	1993	628	0
The SWISS-PROT protein sequence data bank	Nucleic acids research	1992	694	201
PROSITE: a dictionary of sites and patterns in proteins	Nucleic acids research	1992	749	1,829
Human liver protein map: a reference database established by microsequencing and gel comparison	Electrophoresis	1992	659	0
cis-diol dehydrogenases encoded by the TOL pWW0 plasmid xylL gene and the Acinetobacter calcoaceticus chromosomal benD gene are members of the short-chain alcohol dehydrogenase superfamily	European journal of biochemistry	1992	571	0
Proto-vav and gene expression	Nature	1992	621	0
Interleukin-1-inducible genes in endothelial cells. Cloning of a new gene related to C-reactive protein and serum amyloid P component	The Journal of biological chemistry	1992	585	126
The SWISS-PROT protein sequence data bank	Nucleic acids research	1991	945	578
Nucleotide sequences of the Acinetobacter calcoaceticus benABC genes for benzoate 1,2-dioxygenase reveal evolutionary relationships among multicomponent oxygenases	Journal of bacteriology	1991	607	621
Potential DNA slippage structures acquired during evolutionary divergence of Acinetobacter calcoaceticus chromosomal benABC and Pseudomonas putida TOL pWW0 plasmid xylXYZ, genes encoding benzoate dioxygenases	Journal of bacteriology	1991	598	275
PROSITE: a dictionary of sites and patterns in proteins	Nucleic acids research	1991	780	719
SEQANALREF: a sequence analysis bibliographic reference databank	Computer applications in the biosciences	1991	646	282
EF-hand motifs in inositol phospholipid-specific phospholipase C	FEBS letters	1990	688	472
Calcium-binding affinity and calcium-enhanced activity of Clostridium thermocellum endoglucanase D	Biochemical journal	1990	653	587
A cross-reference table between the Protein Data Bank of macromolecular structures and the National Biomedical Research Foundation-Protein Identification Resource amino acid sequence data bank	Protein sequences & data analysis	1989	464	147
A unique signature identifies a family of zinc-dependent metallopeptidases	FEBS letters	1989	634	237
Sequence similarities in calcium-binding proteins	Nature	1988	590	0
Sequence patterns in protein kinases	Nature	1988	550	0
Using PC/GENE for protein and nucleic acid analysis	BioTechniques	1988	547	0
The xylS gene positive regulator of TOL plasmid pWWO: identification, sequence analysis and overproduction leading to constitutive expression of meta cleavage operon	MGG. Molecular & general genetics	1987	677	0
Evolutionary relationships between catabolic pathways for aromatics: conservation of gene order and nucleotide sequences of catechol oxidation genes of pWW0 and NAH7 plasmids	MGG. Molecular & general genetics	1987	642	0
Amino acid sequence determination by gas chromatography—mass spectrometry of permethylated peptides	Journal of chromatography	1983	722	0
Suggestion to research groups working on protein and peptide sequence	Biochemical journal	1982	638	318
Evidence for the existence of a mutated enkephalin sequence in preproenkephalin	FEBS letters	1982	632	201

Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students

Database

2021

404

699

The ABCD database: a repository for chemically defined antibodies

Nucleic Acids Research

2020

640

418

A high-stringency blueprint of the human proteome

Nature Communications

2020

365

550

Brain metastasis cell lines panel: a public resource of organotropic cell lines

Cancer Research

2020

274

0

The neXtProt knowledgebase in 2020: data, tools and usability improvements

Nucleic Acids Research

2020

514

543

The feature-viewer: a visualization tool for positional annotations on a sequence

Bioinformatics

2020

304

0

CLASTR : the cellosaurus STR similarity search tool ‐ A precious help for cell line authentication

International Journal of Cancer

2020

497

1,386

Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines

eLife

2019

410

141

Cell lines as biological models: practical steps for more reliable research

Chemical Research in Toxicology

2019

362

1

Exploring the Uncharacterized Human Proteome Using neXtProt

Journal of Proteome Research

2018

442

0

Large-Scale Reanalysis of Publicly Available HeLa Cell Proteomics Data in the Context of the Human Proteome Project

Journal of Proteome Research

2018

478

3

Kinases and Cancer

Cancers

2018

538

230

A new bioinformatics tool to help assess the significance of BRCA1 variants

Human Genomics

2018

536

237

The Cellosaurus, a Cell-Line Knowledge Resource

Journal of Biomolecular Techniques

2018

616

1,081

A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells

Stem Cell Reports

2018

582

344

The neXtProt knowledgebase on human proteins: 2017 update

Nucleic acids research

2017

551

399

Triage by ranking to support the curation of protein interactions

Database

2017

565

534

Annotation of functional impact of voltage-gated sodium channel mutations

Human mutation

2017

590

416

The missing protein landscape of human chromosomes 2 and 14: progress and current status

Journal of proteome research

2016

561

177

ICEPO: the ion channel electrophysiology ontology

Database

2016

594

247

Deep Question Answering for protein annotation

Database

2015

607

1,160

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

Database

2015

550

317

N-terminome analysis of the human mitochondrial proteome

Proteomics

2015

602

0

The neXtProt knowledgebase on human proteins: current status

Nucleic acids research

2015

715

308

Converting neXtProt into Linked Data and nanopublications

Semantic web

2015

598

864

C11orf83, a Mitochondrial Cardiolipin-Binding Protein Involved in bc₁ Complex Assembly and Supercomplex Stabilization

Molecular and cellular biology

2015

737

266

Key challenges for the creation and maintenance of specialist protein resources

Proteins

2015

546

107

Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins

Journal of proteome research

2014

752

944

Querying neXtProt nanopublications and their value for insights on sequence variants and tissue expression

Journal of web semantics

2014

631

0

Standards for Reporting Enzyme Data: The STRENDA Consortium: What it aims to do and why it should be helpful

Perspectives in science

2014

703

968

C2orf62 and TTC17 are involved in actin organization and ciliogenesis in zebrafish and human

PloS one

2014

732

386

DERA is the human deoxyribose phosphate aldolase and is involved in stress response

Biochimica et biophysica acta. Molecular cell research

2014

739

326

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support

Nucleic acids research

2014

925

73

A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17

Journal of proteome research

2013

672

0

A large-scale evaluation of computational protein function prediction

Nature methods

2013

735

1,296

neXtProt: organizing protein knowledge in the context of human proteome projects

Journal of proteome research

2013

732

0

Standard guidelines for the chromosome-centric human proteome project

Journal of proteome research

2012

660

0

The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome

Nature biotechnology

2012

650

0

UniPathway: a resource for the exploration and annotation of metabolic pathways

Nucleic acids research

2012

618

808

neXtProt: a knowledge platform for human proteins

Nucleic acids research

2012

719

475

Functional identification of APIP as human mtnB, a key enzyme in the methionine salvage pathway

PloS one

2012

627

440

Towards BioDBcore: a community-defined information specification for biological databases

Nucleic acids research

2011

554

374

ViralZone: a knowledge resource to understand virus diversity

Nucleic acids research

2011

818

822

A preliminary study on the prediction of human protein functions

Foundations on Natural and Artificial Computation: 4th International Work-conference on the Interplay Between Natural and Artificial Computation, IWINAC 2011

2011

504

0

The human proteome project: current state and future direction

Molecular & cellular proteomics

2011

720

761

PROSITE, a protein domain database for functional characterization and annotation

Nucleic acids research

2010

746

696

Animal Toxins: How is Complexity Represented in Databases?

Toxins

2010

553

470

Mass spectrometry in high-throughput proteomics: ready for the big time

Nature methods

2010

556

0

A large-scale protein-function database

Nature chemical biology

2010

628

298

OpenFluDB, a database for human and animal influenza virus

Database

2010

656

Infrastructure for the life sciences: design and implementation of the UniProt website

BMC bioinformatics

2009

1,039

2,664

Human aldehyde dehydrogenase genes: alternatively spliced transcriptional variants and their suggested nomenclature

Pharmacogenetics and genomics

2009

685

2

Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands

Proteomics

2009

629

0

InterPro: the integrative protein signature database

Nucleic acids research

2009

662

154

HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot

Nucleic acids research

2009

683

529

UniProtKB/Swiss-Prot manual and automated annotation of complete proteomes: the Dictyostelium discoideum case study

Bioinformatics: a Swiss Perspective

2009

539

0

The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program

Journal of proteomics

2009

644

0

CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens

Nucleic acids research

2009

726

224

Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase

Database

2009

714

477

The impact of 3D structures on a protein knowledgebase: from proteins to systems

Structural Proteomics and its Impact on the Life Sciences

2008

598

0

Calling on a million minds for community annotation in WikiProteins

GenomeBiology.com

2008

644

1,040

The 20 years of PROSITE

Nucleic acids research

2008

606

483

Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase

Human mutation

2008

714

322

UniProtKB/Swiss-Prot: new and future developments

Data Integration in the Life Sciences, Proceedings of the 5th International Workshop, DILS 2008

2008

628

0

New developments in the InterPro database

Nucleic acids research

2007

721

1,306

UniProtKB/Swiss-Prot

Methods in molecular biology

2007

761

0

Data integration in Proteomics

Proteome research: concepts, technology and applications

2007

567

0

Protein variations: resources and tools

Biomedical application of proteomics

2006

616

0

The Universal Protein Resource (UniProt): an expanding universe of protein information

Nucleic acids research

2006

716

1,677

ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins

Nucleic acids research

2006

935

667

Small can be beautiful, but it remains complex!

Complexus

2006

553

0

The PROSITE database

Nucleic acids research

2006

708

611

Functionally and structurally relevant residues in PROSITE motif descriptors

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

2005

512

1

Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase

Toxicon

2005

693

0

ProRule: a new database containing functional and structural information on PROSITE profiles

Bioinformatics

2005

723

335

Plant protein annotation in the UniProt Knowledgebase

Plant physiology

2005

551

510

InterPro, progress and status in 2005

Nucleic acids research

2005

711

36

Protein identification and analysis tools on the ExPASy server

The Proteomics Protocols Handbook

2005

1,627

0

The Universal Protein Resource (UniProt)

Nucleic acids research

2005

1,011

922

Protein variety and functional diversity: Swiss-Prot annotation in its biological context

Comptes rendus. Biologies

2005

642

0

The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants

Human mutation

2004

613

0

IntAct: an open source molecular interaction database

Nucleic acids research

2004

729

416

Annotation of post-translational modifications in the Swiss-Prot knowledge base

Proteomics

2004

616

0

Protein sequence databases

Current opinion in chemical biology

2004

476

0

The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools

Plant physiology and biochemistry

2004

628

0

Swiss-Prot: juggling between evolution and stability

Briefings in bioinformatics

2004

619

462

Industrial-scale proteomics: from liters of plasma to chemically synthesized proteins

Proteomics

2004

635

0

Post-translational modifications: a challenge for proteomics and bioinformatics

Proteomics

2004

585

121

IntEnz, the integrated relational enzyme database

Nucleic acids research

2004

741

178

UniProt: the Universal Protein knowledgebase

Nucleic acids research

2004

1,345

555

Recent improvements to the PROSITE database

Nucleic acids research

2004

608

328

ExPASy: The proteomics server for in-depth protein knowledge and analysis

Nucleic acids research

2003

1,253

420

Protein databases

Nature Encyclopedia of the Human Genome

2003

574

0

PA26 is a candidate gene for heterotaxia in humans: identification of a novel PA26-related gene family in human and mouse

Human genetics

2003

638

0

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

Nucleic acids research

2003

997

538

NEWT, a new taxonomy portal

Nucleic acids research

2003

620

108

The InterPro Database, 2003 brings increased coverage and new features

Nucleic acids research

2003

708

521

Automated annotation of microbial proteomes in SWISS-PROT

Computational biology and chemistry

2003

493

0

FindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification

Proteomics

2002

689

0

The application of bioinformatics to mass spectrometry

Proteomics

2002

492

0

El nuevo servidor Latinoamericano de biologia molecular de la UCB: bo.expasy.org

Acta Nova

2002

305

297

The Sulfinator: predicting tyrosine sulfation sites in protein sequences

Bioinformatics

2002

729

361

High-quality protein knowledge resource: SWISS-PROT and TrEMBL

Briefings in bioinformatics

2002

664

1,560

The PROSITE database, its status in 2002

Nucleic acids research

2002

596

167

PROSITE: a documented database using patterns and profiles as motif descriptors

Briefings in bioinformatics

2002

673

929

ScanProsite: a reference implementation of a PROSITE scanning tool

Applied bioinformatics

2002

1,180

401

Annotation of glycoproteins in the SWISS-PROT database

Proteomics

2001

636

0

The human proteomics initiative (HPI)

Trends in biotechnology

2001

580

0

SWISS-PROT: connecting biomolecular knowledge via a protein database

Current issues in molecular biology

2001

846

302

Technical comment to "Database verification studies of SWISS-PROT and GenBank" by Karp et al

Bioinformatics

2001

665

90

The InterPro database, an integrated documentation resource for protein families, domains and functional sites

Nucleic acids research

2001

689

564

Quality control in databanks for molecular biology

BioEssays

2000

562

0

InterPro--an integrated documentation resource for protein families, domains and functional sites

Bioinformatics

2000

718

463

The ENZYME database in 2000

Nucleic acids research

2000

520

721

A comprehensive web resource on RNA helicases from the baker's yeast Saccharomyces cerevisiae

Yeast

2000

628

0

Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times!

Bioinformatics

2000

647

1,994

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000

Nucleic acids research

2000

712

1,092

The 1999 SWISS-2DPAGE database update

Nucleic acids research

2000

586

420

The PROSITE database, its status in 1999

Nucleic acids research

1999

574

556

Eukaryotic aldehyde dehydrogenase (ALDH) genes: human polymorphisms, and recommended nomenclature based on divergent evolution and chromosomal mapping

Pharmacogenetics

1999

513

0

Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection

Electrophoresis

1999

596

0

Internet resources for protein identification and characterization

Microcharacterization of proteins

1999

390

0

The SWISS-2DPAGE database: what has changed during the last year

Nucleic acids research

1999

589

409

A testis-specific gene, TPTE, encodes a putative transmembrane tyrosine phosphatase and maps to the pericentromeric region of human chromosomes 21 and 13, and to chromosomes 15, 22, and Y

Human genetics

1999

663

0

High-throughput mass spectrometric discovery of protein post-translational modifications

Journal of Molecular Biology

1999

696

1,339

A molecular scanner to automate proteomic research and to display proteome images

Analytical chemistry

1999

644

785

The ENZYME data bank in 1999

Nucleic acids research

1999

505

629

Protein identification and analysis tools in the ExPASy server

Methods in Molecular Biology

1999

443

0

Representation of functional information in the SWISS-PROT data bank

Bioinformatics

1999

500

57

The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999

Nucleic acids research

1999

654

1,192

Low molecular weight proteins: a challenge for post-genomic research

Electrophoresis

1998

524

0

Multiple parameter cross-species protein identification using MultiIdent - a world-wide web accessible tool

Electrophoresis

1998

527

0

GPCRDB: an information system for G protein-coupled receptors

Nucleic acids research

1998

664

411

'98 Escherichia coli SWISS-2DPAGE database update

Electrophoresis

1998

678

2

Two-dimensional gel electrophoresis for proteome projects: the effects of protein hydrophobicity and copy number

Electrophoresis

1998

511

0

A superfamily of metalloenzymes unifies phosphopentomutase and cofactor-independent phosphoglycerate mutase with alkaline phosphatases and sulfatases

Protein science

1998

551

336

Construction of the gyrB Database for the Identification and Classification of Bacteria

Genomics & Informatics

1998

586

444

Protein annotation: detective work for function prediction

Trends in genetics

1998

508

0

Protein identification with N and C-terminal sequence tags in proteome projects

Journal of Molecular Biology

1998

538

0

The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998

Nucleic acids research

1998

571

488

New insulin-like proteins with atypical disulfide bond pattern characterized in Caenorhabditis elegans by comparative sequence analysis and homology modeling

Genome research

1998

461

121

Current status of the SWISS-2DPAGE database

Nucleic acids research

1998

560

93

Sequences and topology: Predicting evolution

Current opinion in structural biology

1997

498

0

Proteome Databases

Proteome research: new frontiers in functional genomics

1997

378

0

The PROSITE database, its status in 1997

Nucleic acids research

1997

549

82

The UDP glycosyltransferase gene superfamily: recommended nomenclature update based on evolutionary divergence

Pharmacogenetics

1997

594

0

The SWISS-PROT protein sequence database: its relevance to human molecular medical research

Journal of molecular medicine

1997

537

0

Detailed peptide characterization using PEPTIDEMASS : a World-Wide-Web-accessible tool

Electrophoresis

1997

719

0

Arac/XylS family of transcriptional regulators

Microbiology and molecular biology reviews

1997

590

1,207

Molecular basis of symbiosis between Rhizobium and legumes

Nature

1997

991

0

Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL

Proceedings

1997

656

1,459

The SWISS-PROT protein sequence data bank and its supplement TrEMBL

Nucleic acids research

1997

691

608

The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis, its status in 1995

Nucleic acids research

1996

690

157

The yeast SWISS-2DPAGE database

Electrophoresis

1996

634

0

The PROSITE database, its status in 1995

Nucleic acids research

1996

546

202

Federated two-dimensional electrophoresis database: a simple means of publishing two-dimensional electrophoresis data

Electrophoresis

1996

575

0

Updating the sequence-based classification of glycosyl hydrolases

Biochemical journal

1996

677

271

The ENZYME data bank in 1995

Nucleic acids research

1996

571

200

Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database

Electrophoresis

1996

659

0

LISTA, LISTA-HOP and LISTA-HON: a comprehensive compilation of protein encoding sequences and its associated homology databases from the yeast Saccharomyces

Nucleic acids research

1996

608

54

Integrating two-dimensional gel databases using the Melanie II software

Trends in biochemical sciences

1996

748

0

The SWISS-PROT protein sequence data bank and its new supplement TREMBL

Nucleic acids research

1996

695

767

Go hunting in sequence databases but watch out for the traps

Trends in genetics

1996

625

0

Inside SWISS-2DPAGE database

Electrophoresis

1995

681

0

Sharing of worldwide spread knowledge using hypermedia facilities & fast communication protocols (Mosaic and World Wide Web): the example of ExPASy

Methods of information in medicine

1995

567

0

The SWISS-PROT protein sequence data bank: current status

Nucleic acids research

1994

708

248

A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server

Trends in biochemical sciences

1994

617

0

Proposals for the naming of chloroplast genes. III. Nomenclature for open reading frames encoded in chloroplast genomes

Plant molecular biology reporter

1994

611

0

LISTA, LISTA-HOP and LISTA-HON: a comprehensive compilation of protein encoding sequences and its associated homology databases from the yeast Saccharomyces

Nucleic acids research

1994

604

35

The ENZYME data bank

Nucleic acids research

1994

651

125

PROSITE: recent developments

Nucleic acids research

1994

540

221

A novel zinc-binding motif found in two ubiquitous deaminase families

Protein science

1994

634

148

A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation

ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology

1994

583

394

The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis

Nucleic acids research

1994

634

225

The SWISS-PROT protein sequence data bank, recent developments

Nucleic acids research

1993

672

255

ExPASy: un système expert pour l'analyse de séquences protéiques

Technologie et Santé

1993

408

91

A diverse transketolase family that includes the RecP protein of Streptococcus pneumoniae, a protein implicated in genetic recombination

Research in microbiology

1993

576

0

Snake proteins and nucleic acids

Toxicon

1993

613

0

Human liver protein map: update 1993

Electrophoresis

1993

708

0

The PROSITE dictionary of sites and patterns in proteins, its current status

Nucleic acids research

1993

591

840

New families in the classification of glycosyl hydrolases based on amino acid sequence similarities

Biochemical journal

1993

945

217

SWISS-2DPAGE: a database of two-dimensional gel electrophoresis images

Electrophoresis

1993

734

0

Complementation of the DNA repair defect in xeroderma pigmentosum group G cells by a human cDNA related to yeast RAD2

Nature

1993

669

0

A possible mechanism for metal-ion induced DNA-protein dissociation in a family of prokaryotic transcriptional regulators

Nucleic acids research

1993

635

101

The ENZYME data bank

Nucleic acids research

1993

604

331

Electrophorèse bidimensionnelle et informatique: un outil pour le diagnostic médical?

Labolife

1993

516

182

Plasma and red blood cell protein maps: update 1993

Electrophoresis

1993

628

0

The SWISS-PROT protein sequence data bank

Nucleic acids research

1992

694

201

PROSITE: a dictionary of sites and patterns in proteins

Nucleic acids research

1992

749

1,829

Human liver protein map: a reference database established by microsequencing and gel comparison

Electrophoresis

1992

659

0

cis-diol dehydrogenases encoded by the TOL pWW0 plasmid xylL gene and the Acinetobacter calcoaceticus chromosomal benD gene are members of the short-chain alcohol dehydrogenase superfamily

European journal of biochemistry

1992

571

0

Proto-vav and gene expression

Nature

1992

621

0

Interleukin-1-inducible genes in endothelial cells. Cloning of a new gene related to C-reactive protein and serum amyloid P component

The Journal of biological chemistry

1992

585

126

The SWISS-PROT protein sequence data bank

Nucleic acids research

1991

945

578

Nucleotide sequences of the Acinetobacter calcoaceticus benABC genes for benzoate 1,2-dioxygenase reveal evolutionary relationships among multicomponent oxygenases

Journal of bacteriology

1991

607

621

Potential DNA slippage structures acquired during evolutionary divergence of Acinetobacter calcoaceticus chromosomal benABC and Pseudomonas putida TOL pWW0 plasmid xylXYZ, genes encoding benzoate dioxygenases

Journal of bacteriology

1991

598

275

PROSITE: a dictionary of sites and patterns in proteins

Nucleic acids research

1991

780

719

SEQANALREF: a sequence analysis bibliographic reference databank

Computer applications in the biosciences

1991

646

282

EF-hand motifs in inositol phospholipid-specific phospholipase C

FEBS letters

1990

688

472

Calcium-binding affinity and calcium-enhanced activity of Clostridium thermocellum endoglucanase D

Biochemical journal

1990

653

587

A cross-reference table between the Protein Data Bank of macromolecular structures and the National Biomedical Research Foundation-Protein Identification Resource amino acid sequence data bank

Protein sequences & data analysis

1989

464

147

A unique signature identifies a family of zinc-dependent metallopeptidases

FEBS letters

1989

634

237

Sequence similarities in calcium-binding proteins

Nature

1988

590

0

Sequence patterns in protein kinases

Nature

1988

550

0

Using PC/GENE for protein and nucleic acid analysis

BioTechniques

1988

547

0

The xylS gene positive regulator of TOL plasmid pWWO: identification, sequence analysis and overproduction leading to constitutive expression of meta cleavage operon

MGG. Molecular & general genetics

1987

677

0

Evolutionary relationships between catabolic pathways for aromatics: conservation of gene order and nucleotide sequences of catechol oxidation genes of pWW0 and NAH7 plasmids

MGG. Molecular & general genetics

1987

642

0

Amino acid sequence determination by gas chromatography—mass spectrometry of permethylated peptides

Journal of chromatography

1983

722

0

Suggestion to research groups working on protein and peptide sequence

Biochemical journal

1982

638

318

Evidence for the existence of a mutated enkephalin sequence in preproenkephalin

FEBS letters

1982

632

201

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