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	400	632
The ABCD database: a repository for chemically defined antibodies	Nucleic Acids Research	2020	636	286
A high-stringency blueprint of the human proteome	Nature Communications	2020	362	307
Brain metastasis cell lines panel: a public resource of organotropic cell lines	Cancer Research	2020	271	0
The neXtProt knowledgebase in 2020: data, tools and usability improvements	Nucleic Acids Research	2020	509	331
The feature-viewer: a visualization tool for positional annotations on a sequence	Bioinformatics	2020	295	0
CLASTR : the cellosaurus STR similarity search tool ‐ A precious help for cell line authentication	International Journal of Cancer	2020	493	1,018
Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines	eLife	2019	400	80
Cell lines as biological models: practical steps for more reliable research	Chemical Research in Toxicology	2019	359	1
Exploring the Uncharacterized Human Proteome Using neXtProt	Journal of Proteome Research	2018	440	0
Large-Scale Reanalysis of Publicly Available HeLa Cell Proteomics Data in the Context of the Human Proteome Project	Journal of Proteome Research	2018	475	3
Kinases and Cancer	Cancers	2018	535	192
A new bioinformatics tool to help assess the significance of BRCA1 variants	Human Genomics	2018	533	224
The Cellosaurus, a Cell-Line Knowledge Resource	Journal of Biomolecular Techniques	2018	611	677
A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells	Stem Cell Reports	2018	574	322
The neXtProt knowledgebase on human proteins: 2017 update	Nucleic acids research	2017	547	358
Triage by ranking to support the curation of protein interactions	Database	2017	558	512
Annotation of functional impact of voltage-gated sodium channel mutations	Human mutation	2017	586	362
The missing protein landscape of human chromosomes 2 and 14: progress and current status	Journal of proteome research	2016	559	142
ICEPO: the ion channel electrophysiology ontology	Database	2016	591	230
Deep Question Answering for protein annotation	Database	2015	602	1,131
Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat	Database	2015	547	292
N-terminome analysis of the human mitochondrial proteome	Proteomics	2015	598	0
The neXtProt knowledgebase on human proteins: current status	Nucleic acids research	2015	710	217
Converting neXtProt into Linked Data and nanopublications	Semantic web	2015	593	782
C11orf83, a Mitochondrial Cardiolipin-Binding Protein Involved in bc₁ Complex Assembly and Supercomplex Stabilization	Molecular and cellular biology	2015	732	197
Key challenges for the creation and maintenance of specialist protein resources	Proteins	2015	543	71
Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins	Journal of proteome research	2014	749	889
Querying neXtProt nanopublications and their value for insights on sequence variants and tissue expression	Journal of web semantics	2014	625	0
Standards for Reporting Enzyme Data: The STRENDA Consortium: What it aims to do and why it should be helpful	Perspectives in science	2014	699	465
C2orf62 and TTC17 are involved in actin organization and ciliogenesis in zebrafish and human	PloS one	2014	730	378
DERA is the human deoxyribose phosphate aldolase and is involved in stress response	Biochimica et biophysica acta. Molecular cell research	2014	735	267
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support	Nucleic acids research	2014	922	59
A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17	Journal of proteome research	2013	666	0
A large-scale evaluation of computational protein function prediction	Nature methods	2013	729	1,215
neXtProt: organizing protein knowledge in the context of human proteome projects	Journal of proteome research	2013	726	0
Standard guidelines for the chromosome-centric human proteome project	Journal of proteome research	2012	653	0
The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome	Nature biotechnology	2012	646	0
UniPathway: a resource for the exploration and annotation of metabolic pathways	Nucleic acids research	2012	614	783
neXtProt: a knowledge platform for human proteins	Nucleic acids research	2012	713	452
Functional identification of APIP as human mtnB, a key enzyme in the methionine salvage pathway	PloS one	2012	624	425
Towards BioDBcore: a community-defined information specification for biological databases	Nucleic acids research	2011	551	359
ViralZone: a knowledge resource to understand virus diversity	Nucleic acids research	2011	812	605
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	499	0
The human proteome project: current state and future direction	Molecular & cellular proteomics	2011	715	718
PROSITE, a protein domain database for functional characterization and annotation	Nucleic acids research	2010	740	530
Animal Toxins: How is Complexity Represented in Databases?	Toxins	2010	548	384
Mass spectrometry in high-throughput proteomics: ready for the big time	Nature methods	2010	552	0
A large-scale protein-function database	Nature chemical biology	2010	626	287
OpenFluDB, a database for human and animal influenza virus	Database	2010	653	591
Infrastructure for the life sciences: design and implementation of the UniProt website	BMC bioinformatics	2009	1,029	2,646
Human aldehyde dehydrogenase genes: alternatively spliced transcriptional variants and their suggested nomenclature	Pharmacogenetics and genomics	2009	681	2
Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands	Proteomics	2009	626	0
InterPro: the integrative protein signature database	Nucleic acids research	2009	658	124
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot	Nucleic acids research	2009	677	520
UniProtKB/Swiss-Prot manual and automated annotation of complete proteomes: the Dictyostelium discoideum case study	Bioinformatics: a Swiss Perspective	2009	534	0
The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program	Journal of proteomics	2009	641	0
CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens	Nucleic acids research	2009	719	172
Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase	Database	2009	712	407
The impact of 3D structures on a protein knowledgebase: from proteins to systems	Structural Proteomics and its Impact on the Life Sciences	2008	594	0
Calling on a million minds for community annotation in WikiProteins	GenomeBiology.com	2008	640	1,037
The 20 years of PROSITE	Nucleic acids research	2008	603	454
Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase	Human mutation	2008	710	220
UniProtKB/Swiss-Prot: new and future developments	Data Integration in the Life Sciences, Proceedings of the 5th International Workshop, DILS 2008	2008	625	0
New developments in the InterPro database	Nucleic acids research	2007	716	1,256
UniProtKB/Swiss-Prot	Methods in molecular biology	2007	752	0
Data integration in Proteomics	Proteome research: concepts, technology and applications	2007	564	0
Protein variations: resources and tools	Biomedical application of proteomics	2006	613	0
The Universal Protein Resource (UniProt): an expanding universe of protein information	Nucleic acids research	2006	713	1,173
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins	Nucleic acids research	2006	920	535
Small can be beautiful, but it remains complex!	Complexus	2006	550	0
The PROSITE database	Nucleic acids research	2006	703	461
Functionally and structurally relevant residues in PROSITE motif descriptors	Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics	2005	506	1
Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase	Toxicon	2005	689	0
ProRule: a new database containing functional and structural information on PROSITE profiles	Bioinformatics	2005	718	264
Plant protein annotation in the UniProt Knowledgebase	Plant physiology	2005	546	349
InterPro, progress and status in 2005	Nucleic acids research	2005	706	31
Protein identification and analysis tools on the ExPASy server	The Proteomics Protocols Handbook	2005	1,618	0
The Universal Protein Resource (UniProt)	Nucleic acids research	2005	1,005	513
Protein variety and functional diversity: Swiss-Prot annotation in its biological context	Comptes rendus. Biologies	2005	639	0
The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants	Human mutation	2004	610	0
IntAct: an open source molecular interaction database	Nucleic acids research	2004	721	224
Annotation of post-translational modifications in the Swiss-Prot knowledge base	Proteomics	2004	613	0
Protein sequence databases	Current opinion in chemical biology	2004	472	0
The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools	Plant physiology and biochemistry	2004	625	0
Swiss-Prot: juggling between evolution and stability	Briefings in bioinformatics	2004	615	311
Industrial-scale proteomics: from liters of plasma to chemically synthesized proteins	Proteomics	2004	629	0
Post-translational modifications: a challenge for proteomics and bioinformatics	Proteomics	2004	582	97
IntEnz, the integrated relational enzyme database	Nucleic acids research	2004	738	151
UniProt: the Universal Protein knowledgebase	Nucleic acids research	2004	1,333	344
Recent improvements to the PROSITE database	Nucleic acids research	2004	606	291
ExPASy: The proteomics server for in-depth protein knowledge and analysis	Nucleic acids research	2003	1,247	283
Protein databases	Nature Encyclopedia of the Human Genome	2003	569	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	636	0
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003	Nucleic acids research	2003	992	468
NEWT, a new taxonomy portal	Nucleic acids research	2003	618	72
The InterPro Database, 2003 brings increased coverage and new features	Nucleic acids research	2003	703	493
Automated annotation of microbial proteomes in SWISS-PROT	Computational biology and chemistry	2003	487	0
FindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification	Proteomics	2002	685	0
The application of bioinformatics to mass spectrometry	Proteomics	2002	486	0
El nuevo servidor Latinoamericano de biologia molecular de la UCB: bo.expasy.org	Acta Nova	2002	303	225
The Sulfinator: predicting tyrosine sulfation sites in protein sequences	Bioinformatics	2002	722	286
High-quality protein knowledge resource: SWISS-PROT and TrEMBL	Briefings in bioinformatics	2002	662	1,226
The PROSITE database, its status in 2002	Nucleic acids research	2002	593	144
PROSITE: a documented database using patterns and profiles as motif descriptors	Briefings in bioinformatics	2002	668	601
ScanProsite: a reference implementation of a PROSITE scanning tool	Applied bioinformatics	2002	1,177	355
Annotation of glycoproteins in the SWISS-PROT database	Proteomics	2001	632	0
The human proteomics initiative (HPI)	Trends in biotechnology	2001	574	0
SWISS-PROT: connecting biomolecular knowledge via a protein database	Current issues in molecular biology	2001	840	229
Technical comment to "Database verification studies of SWISS-PROT and GenBank" by Karp et al	Bioinformatics	2001	663	64
The InterPro database, an integrated documentation resource for protein families, domains and functional sites	Nucleic acids research	2001	686	190
Quality control in databanks for molecular biology	BioEssays	2000	557	0
InterPro--an integrated documentation resource for protein families, domains and functional sites	Bioinformatics	2000	712	424
The ENZYME database in 2000	Nucleic acids research	2000	517	667
A comprehensive web resource on RNA helicases from the baker's yeast Saccharomyces cerevisiae	Yeast	2000	621	0
Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times!	Bioinformatics	2000	644	1,562
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000	Nucleic acids research	2000	705	988
The 1999 SWISS-2DPAGE database update	Nucleic acids research	2000	581	388
The PROSITE database, its status in 1999	Nucleic acids research	1999	569	467
Eukaryotic aldehyde dehydrogenase (ALDH) genes: human polymorphisms, and recommended nomenclature based on divergent evolution and chromosomal mapping	Pharmacogenetics	1999	507	0
Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection	Electrophoresis	1999	592	0
Internet resources for protein identification and characterization	Microcharacterization of proteins	1999	386	0
The SWISS-2DPAGE database: what has changed during the last year	Nucleic acids research	1999	587	369
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	657	0
High-throughput mass spectrometric discovery of protein post-translational modifications	Journal of Molecular Biology	1999	692	1,190
A molecular scanner to automate proteomic research and to display proteome images	Analytical chemistry	1999	636	693
The ENZYME data bank in 1999	Nucleic acids research	1999	502	591
Protein identification and analysis tools in the ExPASy server	Methods in Molecular Biology	1999	435	0
Representation of functional information in the SWISS-PROT data bank	Bioinformatics	1999	498	29
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999	Nucleic acids research	1999	652	1,093
Low molecular weight proteins: a challenge for post-genomic research	Electrophoresis	1998	520	0
Multiple parameter cross-species protein identification using MultiIdent - a world-wide web accessible tool	Electrophoresis	1998	523	0
GPCRDB: an information system for G protein-coupled receptors	Nucleic acids research	1998	659	316
'98 Escherichia coli SWISS-2DPAGE database update	Electrophoresis	1998	674	2
Two-dimensional gel electrophoresis for proteome projects: the effects of protein hydrophobicity and copy number	Electrophoresis	1998	509	0
A superfamily of metalloenzymes unifies phosphopentomutase and cofactor-independent phosphoglycerate mutase with alkaline phosphatases and sulfatases	Protein science	1998	549	318
Construction of the gyrB Database for the Identification and Classification of Bacteria	Genomics & Informatics	1998	577	367
Protein annotation: detective work for function prediction	Trends in genetics	1998	503	0
Protein identification with N and C-terminal sequence tags in proteome projects	Journal of Molecular Biology	1998	533	0
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998	Nucleic acids research	1998	567	460
New insulin-like proteins with atypical disulfide bond pattern characterized in Caenorhabditis elegans by comparative sequence analysis and homology modeling	Genome research	1998	456	96
Current status of the SWISS-2DPAGE database	Nucleic acids research	1998	556	69
Sequences and topology: Predicting evolution	Current opinion in structural biology	1997	496	0
Proteome Databases	Proteome research: new frontiers in functional genomics	1997	374	0
The PROSITE database, its status in 1997	Nucleic acids research	1997	546	30
The UDP glycosyltransferase gene superfamily: recommended nomenclature update based on evolutionary divergence	Pharmacogenetics	1997	589	0
The SWISS-PROT protein sequence database: its relevance to human molecular medical research	Journal of molecular medicine	1997	534	0
Detailed peptide characterization using PEPTIDEMASS : a World-Wide-Web-accessible tool	Electrophoresis	1997	715	0
Arac/XylS family of transcriptional regulators	Microbiology and molecular biology reviews	1997	587	859
Molecular basis of symbiosis between Rhizobium and legumes	Nature	1997	988	0
Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL	Proceedings	1997	653	1,042
The SWISS-PROT protein sequence data bank and its supplement TrEMBL	Nucleic acids research	1997	688	366
The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis, its status in 1995	Nucleic acids research	1996	686	117
The yeast SWISS-2DPAGE database	Electrophoresis	1996	631	0
The PROSITE database, its status in 1995	Nucleic acids research	1996	542	105
Federated two-dimensional electrophoresis database: a simple means of publishing two-dimensional electrophoresis data	Electrophoresis	1996	572	0
Updating the sequence-based classification of glycosyl hydrolases	Biochemical journal	1996	672	207
The ENZYME data bank in 1995	Nucleic acids research	1996	569	165
Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database	Electrophoresis	1996	656	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	605	40
Integrating two-dimensional gel databases using the Melanie II software	Trends in biochemical sciences	1996	743	0
The SWISS-PROT protein sequence data bank and its new supplement TREMBL	Nucleic acids research	1996	692	671
Go hunting in sequence databases but watch out for the traps	Trends in genetics	1996	618	0
Inside SWISS-2DPAGE database	Electrophoresis	1995	678	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	565	0
The SWISS-PROT protein sequence data bank: current status	Nucleic acids research	1994	706	197
A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server	Trends in biochemical sciences	1994	612	0
Proposals for the naming of chloroplast genes. III. Nomenclature for open reading frames encoded in chloroplast genomes	Plant molecular biology reporter	1994	608	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	601	29
The ENZYME data bank	Nucleic acids research	1994	649	112
PROSITE: recent developments	Nucleic acids research	1994	536	113
A novel zinc-binding motif found in two ubiquitous deaminase families	Protein science	1994	631	129
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	579	299
The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis	Nucleic acids research	1994	631	185
The SWISS-PROT protein sequence data bank, recent developments	Nucleic acids research	1993	664	183
ExPASy: un système expert pour l'analyse de séquences protéiques	Technologie et Santé	1993	406	88
A diverse transketolase family that includes the RecP protein of Streptococcus pneumoniae, a protein implicated in genetic recombination	Research in microbiology	1993	573	0
Snake proteins and nucleic acids	Toxicon	1993	607	0
Human liver protein map: update 1993	Electrophoresis	1993	698	0
The PROSITE dictionary of sites and patterns in proteins, its current status	Nucleic acids research	1993	587	330
New families in the classification of glycosyl hydrolases based on amino acid sequence similarities	Biochemical journal	1993	942	161
SWISS-2DPAGE: a database of two-dimensional gel electrophoresis images	Electrophoresis	1993	731	0
Complementation of the DNA repair defect in xeroderma pigmentosum group G cells by a human cDNA related to yeast RAD2	Nature	1993	666	0
A possible mechanism for metal-ion induced DNA-protein dissociation in a family of prokaryotic transcriptional regulators	Nucleic acids research	1993	631	84
The ENZYME data bank	Nucleic acids research	1993	600	254
Electrophorèse bidimensionnelle et informatique: un outil pour le diagnostic médical?	Labolife	1993	513	162
Plasma and red blood cell protein maps: update 1993	Electrophoresis	1993	625	0
The SWISS-PROT protein sequence data bank	Nucleic acids research	1992	690	140
PROSITE: a dictionary of sites and patterns in proteins	Nucleic acids research	1992	736	1,018
Human liver protein map: a reference database established by microsequencing and gel comparison	Electrophoresis	1992	656	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	567	0
Proto-vav and gene expression	Nature	1992	618	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	579	109
The SWISS-PROT protein sequence data bank	Nucleic acids research	1991	943	526
Nucleotide sequences of the Acinetobacter calcoaceticus benABC genes for benzoate 1,2-dioxygenase reveal evolutionary relationships among multicomponent oxygenases	Journal of bacteriology	1991	604	599
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	595	254
PROSITE: a dictionary of sites and patterns in proteins	Nucleic acids research	1991	768	516
SEQANALREF: a sequence analysis bibliographic reference databank	Computer applications in the biosciences	1991	641	258
EF-hand motifs in inositol phospholipid-specific phospholipase C	FEBS letters	1990	685	461
Calcium-binding affinity and calcium-enhanced activity of Clostridium thermocellum endoglucanase D	Biochemical journal	1990	649	562
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	461	121
A unique signature identifies a family of zinc-dependent metallopeptidases	FEBS letters	1989	630	179
Sequence similarities in calcium-binding proteins	Nature	1988	585	0
Sequence patterns in protein kinases	Nature	1988	542	0
Using PC/GENE for protein and nucleic acid analysis	BioTechniques	1988	545	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	674	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	635	0
Amino acid sequence determination by gas chromatography—mass spectrometry of permethylated peptides	Journal of chromatography	1983	719	0
Suggestion to research groups working on protein and peptide sequence	Biochemical journal	1982	633	306
Evidence for the existence of a mutated enkephalin sequence in preproenkephalin	FEBS letters	1982	629	156

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

Database

2021

400

632

The ABCD database: a repository for chemically defined antibodies

Nucleic Acids Research

2020

636

286

A high-stringency blueprint of the human proteome

Nature Communications

2020

362

307

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

Cancer Research

2020

271

0

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

Nucleic Acids Research

2020

509

331

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

Bioinformatics

2020

295

0

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

International Journal of Cancer

2020

493

1,018

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

eLife

2019

400

80

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

Chemical Research in Toxicology

2019

359

1

Exploring the Uncharacterized Human Proteome Using neXtProt

Journal of Proteome Research

2018

440

0

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

Journal of Proteome Research

2018

475

3

Kinases and Cancer

Cancers

2018

535

192

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

Human Genomics

2018

533

224

The Cellosaurus, a Cell-Line Knowledge Resource

Journal of Biomolecular Techniques

2018

611

677

A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells

Stem Cell Reports

2018

574

322

The neXtProt knowledgebase on human proteins: 2017 update

Nucleic acids research

2017

547

358

Triage by ranking to support the curation of protein interactions

Database

2017

558

512

Annotation of functional impact of voltage-gated sodium channel mutations

Human mutation

2017

586

362

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

Journal of proteome research

2016

559

142

ICEPO: the ion channel electrophysiology ontology

Database

2016

591

230

Deep Question Answering for protein annotation

Database

2015

602

1,131

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

Database

2015

547

292

N-terminome analysis of the human mitochondrial proteome

Proteomics

2015

598

0

The neXtProt knowledgebase on human proteins: current status

Nucleic acids research

2015

710

217

Converting neXtProt into Linked Data and nanopublications

Semantic web

2015

593

782

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

Molecular and cellular biology

2015

732

197

Key challenges for the creation and maintenance of specialist protein resources

Proteins

2015

543

71

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

Journal of proteome research

2014

749

889

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

Journal of web semantics

2014

625

0

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

Perspectives in science

2014

699

465

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

PloS one

2014

730

378

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

Biochimica et biophysica acta. Molecular cell research

2014

735

267

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

Nucleic acids research

2014

922

59

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

Journal of proteome research

2013

666

0

A large-scale evaluation of computational protein function prediction

Nature methods

2013

729

1,215

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

Journal of proteome research

2013

726

0

Standard guidelines for the chromosome-centric human proteome project

Journal of proteome research

2012

653

0

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

Nature biotechnology

2012

646

0

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

Nucleic acids research

2012

614

783

neXtProt: a knowledge platform for human proteins

Nucleic acids research

2012

713

452

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

PloS one

2012

624

425

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

Nucleic acids research

2011

551

359

ViralZone: a knowledge resource to understand virus diversity

Nucleic acids research

2011

812

605

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

499

0

The human proteome project: current state and future direction

Molecular & cellular proteomics

2011

715

718

PROSITE, a protein domain database for functional characterization and annotation

Nucleic acids research

2010

740

530

Animal Toxins: How is Complexity Represented in Databases?

Toxins

2010

548

384

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

Nature methods

2010

552

0

A large-scale protein-function database

Nature chemical biology

2010

626

287

OpenFluDB, a database for human and animal influenza virus

Database

2010

653

591

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

BMC bioinformatics

2009

1,029

2,646

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

Pharmacogenetics and genomics

2009

681

2

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

Proteomics

2009

626

0

InterPro: the integrative protein signature database

Nucleic acids research

2009

658

124

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

Nucleic acids research

2009

677

520

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

Bioinformatics: a Swiss Perspective

2009

534

0

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

Journal of proteomics

2009

641

0

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

Nucleic acids research

2009

719

172

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

Database

2009

712

407

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

Structural Proteomics and its Impact on the Life Sciences

2008

594

0

Calling on a million minds for community annotation in WikiProteins

GenomeBiology.com

2008

640

1,037

The 20 years of PROSITE

Nucleic acids research

2008

603

454

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

Human mutation

2008

710

220

UniProtKB/Swiss-Prot: new and future developments

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

2008

625

0

New developments in the InterPro database

Nucleic acids research

2007

716

1,256

UniProtKB/Swiss-Prot

Methods in molecular biology

2007

752

0

Data integration in Proteomics

Proteome research: concepts, technology and applications

2007

564

0

Protein variations: resources and tools

Biomedical application of proteomics

2006

613

0

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

Nucleic acids research

2006

713

1,173

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

Nucleic acids research

2006

920

535

Small can be beautiful, but it remains complex!

Complexus

2006

550

0

The PROSITE database

Nucleic acids research

2006

703

461

Functionally and structurally relevant residues in PROSITE motif descriptors

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

2005

506

1

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

Toxicon

2005

689

0

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

Bioinformatics

2005

718

264

Plant protein annotation in the UniProt Knowledgebase

Plant physiology

2005

546

349

InterPro, progress and status in 2005

Nucleic acids research

2005

706

31

Protein identification and analysis tools on the ExPASy server

The Proteomics Protocols Handbook

2005

1,618

0

The Universal Protein Resource (UniProt)

Nucleic acids research

2005

1,005

513

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

Comptes rendus. Biologies

2005

639

0

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

Human mutation

2004

610

0

IntAct: an open source molecular interaction database

Nucleic acids research

2004

721

224

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

Proteomics

2004

613

0

Protein sequence databases

Current opinion in chemical biology

2004

472

0

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

Plant physiology and biochemistry

2004

625

0

Swiss-Prot: juggling between evolution and stability

Briefings in bioinformatics

2004

615

311

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

Proteomics

2004

629

0

Post-translational modifications: a challenge for proteomics and bioinformatics

Proteomics

2004

582

97

IntEnz, the integrated relational enzyme database

Nucleic acids research

2004

738

151

UniProt: the Universal Protein knowledgebase

Nucleic acids research

2004

1,333

344

Recent improvements to the PROSITE database

Nucleic acids research

2004

606

291

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

Nucleic acids research

2003

1,247

283

Protein databases

Nature Encyclopedia of the Human Genome

2003

569

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

636

0

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

Nucleic acids research

2003

992

468

NEWT, a new taxonomy portal

Nucleic acids research

2003

618

72

The InterPro Database, 2003 brings increased coverage and new features

Nucleic acids research

2003

703

493

Automated annotation of microbial proteomes in SWISS-PROT

Computational biology and chemistry

2003

487

0

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

Proteomics

2002

685

0

The application of bioinformatics to mass spectrometry

Proteomics

2002

486

0

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

Acta Nova

2002

303

225

The Sulfinator: predicting tyrosine sulfation sites in protein sequences

Bioinformatics

2002

722

286

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

Briefings in bioinformatics

2002

662

1,226

The PROSITE database, its status in 2002

Nucleic acids research

2002

593

144

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

Briefings in bioinformatics

2002

668

601

ScanProsite: a reference implementation of a PROSITE scanning tool

Applied bioinformatics

2002

1,177

355

Annotation of glycoproteins in the SWISS-PROT database

Proteomics

2001

632

0

The human proteomics initiative (HPI)

Trends in biotechnology

2001

574

0

SWISS-PROT: connecting biomolecular knowledge via a protein database

Current issues in molecular biology

2001

840

229

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

Bioinformatics

2001

663

64

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

Nucleic acids research

2001

686

190

Quality control in databanks for molecular biology

BioEssays

2000

557

0

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

Bioinformatics

2000

712

424

The ENZYME database in 2000

Nucleic acids research

2000

517

667

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

Yeast

2000

621

0

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

Bioinformatics

2000

644

1,562

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

Nucleic acids research

2000

705

988

The 1999 SWISS-2DPAGE database update

Nucleic acids research

2000

581

388

The PROSITE database, its status in 1999

Nucleic acids research

1999

569

467

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

Pharmacogenetics

1999

507

0

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

Electrophoresis

1999

592

0

Internet resources for protein identification and characterization

Microcharacterization of proteins

1999

386

0

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

Nucleic acids research

1999

587

369

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

657

0

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

Journal of Molecular Biology

1999

692

1,190

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

Analytical chemistry

1999

636

693

The ENZYME data bank in 1999

Nucleic acids research

1999

502

591

Protein identification and analysis tools in the ExPASy server

Methods in Molecular Biology

1999

435

0

Representation of functional information in the SWISS-PROT data bank

Bioinformatics

1999

498

29

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

Nucleic acids research

1999

652

1,093

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

Electrophoresis

1998

520

0

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

Electrophoresis

1998

523

0

GPCRDB: an information system for G protein-coupled receptors

Nucleic acids research

1998

659

316

'98 Escherichia coli SWISS-2DPAGE database update

Electrophoresis

1998

674

2

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

Electrophoresis

1998

509

0

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

Protein science

1998

549

318

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

Genomics & Informatics

1998

577

367

Protein annotation: detective work for function prediction

Trends in genetics

1998

503

0

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

Journal of Molecular Biology

1998

533

0

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

Nucleic acids research

1998

567

460

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

Genome research

1998

456

96

Current status of the SWISS-2DPAGE database

Nucleic acids research

1998

556

69

Sequences and topology: Predicting evolution

Current opinion in structural biology

1997

496

0

Proteome Databases

Proteome research: new frontiers in functional genomics

1997

374

0

The PROSITE database, its status in 1997

Nucleic acids research

1997

546

30

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

Pharmacogenetics

1997

589

0

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

Journal of molecular medicine

1997

534

0

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

Electrophoresis

1997

715

0

Arac/XylS family of transcriptional regulators

Microbiology and molecular biology reviews

1997

587

859

Molecular basis of symbiosis between Rhizobium and legumes

Nature

1997

988

0

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

Proceedings

1997

653

1,042

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

Nucleic acids research

1997

688

366

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

Nucleic acids research

1996

686

117

The yeast SWISS-2DPAGE database

Electrophoresis

1996

631

0

The PROSITE database, its status in 1995

Nucleic acids research

1996

542

105

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

Electrophoresis

1996

572

0

Updating the sequence-based classification of glycosyl hydrolases

Biochemical journal

1996

672

207

The ENZYME data bank in 1995

Nucleic acids research

1996

569

165

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

Electrophoresis

1996

656

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

605

40

Integrating two-dimensional gel databases using the Melanie II software

Trends in biochemical sciences

1996

743

0

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

Nucleic acids research

1996

692

671

Go hunting in sequence databases but watch out for the traps

Trends in genetics

1996

618

0

Inside SWISS-2DPAGE database

Electrophoresis

1995

678

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

565

0

The SWISS-PROT protein sequence data bank: current status

Nucleic acids research

1994

706

197

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

Trends in biochemical sciences

1994

612

0

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

Plant molecular biology reporter

1994

608

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

601

29

The ENZYME data bank

Nucleic acids research

1994

649

112

PROSITE: recent developments

Nucleic acids research

1994

536

113

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

Protein science

1994

631

129

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

579

299

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

Nucleic acids research

1994

631

185

The SWISS-PROT protein sequence data bank, recent developments

Nucleic acids research

1993

664

183

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

Technologie et Santé

1993

406

88

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

Research in microbiology

1993

573

0

Snake proteins and nucleic acids

Toxicon

1993

607

0

Human liver protein map: update 1993

Electrophoresis

1993

698

0

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

Nucleic acids research

1993

587

330

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

Biochemical journal

1993

942

161

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

Electrophoresis

1993

731

0

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

Nature

1993

666

0

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

Nucleic acids research

1993

631

84

The ENZYME data bank

Nucleic acids research

1993

600

254

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

Labolife

1993

513

162

Plasma and red blood cell protein maps: update 1993

Electrophoresis

1993

625

0

The SWISS-PROT protein sequence data bank

Nucleic acids research

1992

690

140

PROSITE: a dictionary of sites and patterns in proteins

Nucleic acids research

1992

736

1,018

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

Electrophoresis

1992

656

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

567

0

Proto-vav and gene expression

Nature

1992

618

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

579

109

The SWISS-PROT protein sequence data bank

Nucleic acids research

1991

943

526

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

Journal of bacteriology

1991

604

599

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

595

254

PROSITE: a dictionary of sites and patterns in proteins

Nucleic acids research

1991

768

516

SEQANALREF: a sequence analysis bibliographic reference databank

Computer applications in the biosciences

1991

641

258

EF-hand motifs in inositol phospholipid-specific phospholipase C

FEBS letters

1990

685

461

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

Biochemical journal

1990

649

562

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

461

121

A unique signature identifies a family of zinc-dependent metallopeptidases

FEBS letters

1989

630

179

Sequence similarities in calcium-binding proteins

Nature

1988

585

0

Sequence patterns in protein kinases

Nature

1988

542

0

Using PC/GENE for protein and nucleic acid analysis

BioTechniques

1988

545

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

674

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

635

0

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

Journal of chromatography

1983

719

0

Suggestion to research groups working on protein and peptide sequence

Biochemical journal

1982

633

306

Evidence for the existence of a mutated enkephalin sequence in preproenkephalin

FEBS letters

1982

629

156

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