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	401	680
The ABCD database: a repository for chemically defined antibodies	Nucleic Acids Research	2020	636	333
A high-stringency blueprint of the human proteome	Nature Communications	2020	362	395
Brain metastasis cell lines panel: a public resource of organotropic cell lines	Cancer Research	2020	272	0
The neXtProt knowledgebase in 2020: data, tools and usability improvements	Nucleic Acids Research	2020	509	382
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	1,184
Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines	eLife	2019	400	112
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	441	0
Large-Scale Reanalysis of Publicly Available HeLa Cell Proteomics Data in the Context of the Human Proteome Project	Journal of Proteome Research	2018	476	3
Kinases and Cancer	Cancers	2018	535	201
A new bioinformatics tool to help assess the significance of BRCA1 variants	Human Genomics	2018	533	226
The Cellosaurus, a Cell-Line Knowledge Resource	Journal of Biomolecular Techniques	2018	611	836
A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells	Stem Cell Reports	2018	574	328
The neXtProt knowledgebase on human proteins: 2017 update	Nucleic acids research	2017	547	363
Triage by ranking to support the curation of protein interactions	Database	2017	560	517
Annotation of functional impact of voltage-gated sodium channel mutations	Human mutation	2017	586	376
The missing protein landscape of human chromosomes 2 and 14: progress and current status	Journal of proteome research	2016	559	155
ICEPO: the ion channel electrophysiology ontology	Database	2016	591	236
Deep Question Answering for protein annotation	Database	2015	604	1,138
Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat	Database	2015	547	302
N-terminome analysis of the human mitochondrial proteome	Proteomics	2015	598	0
The neXtProt knowledgebase on human proteins: current status	Nucleic acids research	2015	711	245
Converting neXtProt into Linked Data and nanopublications	Semantic web	2015	593	825
C11orf83, a Mitochondrial Cardiolipin-Binding Protein Involved in bc₁ Complex Assembly and Supercomplex Stabilization	Molecular and cellular biology	2015	733	217
Key challenges for the creation and maintenance of specialist protein resources	Proteins	2015	544	81
Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins	Journal of proteome research	2014	750	913
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	581
C2orf62 and TTC17 are involved in actin organization and ciliogenesis in zebrafish and human	PloS one	2014	730	380
DERA is the human deoxyribose phosphate aldolase and is involved in stress response	Biochimica et biophysica acta. Molecular cell research	2014	735	280
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support	Nucleic acids research	2014	922	62
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	1,241
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	615	788
neXtProt: a knowledge platform for human proteins	Nucleic acids research	2012	714	459
Functional identification of APIP as human mtnB, a key enzyme in the methionine salvage pathway	PloS one	2012	625	432
Towards BioDBcore: a community-defined information specification for biological databases	Nucleic acids research	2011	551	361
ViralZone: a knowledge resource to understand virus diversity	Nucleic acids research	2011	812	668
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	727
PROSITE, a protein domain database for functional characterization and annotation	Nucleic acids research	2010	740	576
Animal Toxins: How is Complexity Represented in Databases?	Toxins	2010	549	422
Mass spectrometry in high-throughput proteomics: ready for the big time	Nature methods	2010	553	0
A large-scale protein-function database	Nature chemical biology	2010	626	290
OpenFluDB, a database for human and animal influenza virus	Database	2010	653	621
Infrastructure for the life sciences: design and implementation of the UniProt website	BMC bioinformatics	2009	1,030	2,648
Human aldehyde dehydrogenase genes: alternatively spliced transcriptional variants and their suggested nomenclature	Pharmacogenetics and genomics	2009	683	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	659	135
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot	Nucleic acids research	2009	677	525
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	642	0
CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens	Nucleic acids research	2009	719	182
Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase	Database	2009	712	433
The impact of 3D structures on a protein knowledgebase: from proteins to systems	Structural Proteomics and its Impact on the Life Sciences	2008	595	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	467
Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase	Human mutation	2008	710	268
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	1,277
UniProtKB/Swiss-Prot	Methods in molecular biology	2007	754	0
Data integration in Proteomics	Proteome research: concepts, technology and applications	2007	565	0
Protein variations: resources and tools	Biomedical application of proteomics	2006	614	0
The Universal Protein Resource (UniProt): an expanding universe of protein information	Nucleic acids research	2006	713	1,376
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins	Nucleic acids research	2006	921	574
Small can be beautiful, but it remains complex!	Complexus	2006	551	0
The PROSITE database	Nucleic acids research	2006	703	500
Functionally and structurally relevant residues in PROSITE motif descriptors	Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics	2005	507	1
Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase	Toxicon	2005	691	0
ProRule: a new database containing functional and structural information on PROSITE profiles	Bioinformatics	2005	718	292
Plant protein annotation in the UniProt Knowledgebase	Plant physiology	2005	547	434
InterPro, progress and status in 2005	Nucleic acids research	2005	707	31
Protein identification and analysis tools on the ExPASy server	The Proteomics Protocols Handbook	2005	1,622	0
The Universal Protein Resource (UniProt)	Nucleic acids research	2005	1,006	663
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	724	303
Annotation of post-translational modifications in the Swiss-Prot knowledge base	Proteomics	2004	613	0
Protein sequence databases	Current opinion in chemical biology	2004	474	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	379
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	111
IntEnz, the integrated relational enzyme database	Nucleic acids research	2004	739	161
UniProt: the Universal Protein knowledgebase	Nucleic acids research	2004	1,336	446
Recent improvements to the PROSITE database	Nucleic acids research	2004	606	303
ExPASy: The proteomics server for in-depth protein knowledge and analysis	Nucleic acids research	2003	1,249	331
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	487
NEWT, a new taxonomy portal	Nucleic acids research	2003	618	87
The InterPro Database, 2003 brings increased coverage and new features	Nucleic acids research	2003	705	502
Automated annotation of microbial proteomes in SWISS-PROT	Computational biology and chemistry	2003	489	0
FindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification	Proteomics	2002	687	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	254
The Sulfinator: predicting tyrosine sulfation sites in protein sequences	Bioinformatics	2002	722	308
High-quality protein knowledge resource: SWISS-PROT and TrEMBL	Briefings in bioinformatics	2002	662	1,396
The PROSITE database, its status in 2002	Nucleic acids research	2002	593	149
PROSITE: a documented database using patterns and profiles as motif descriptors	Briefings in bioinformatics	2002	668	723
ScanProsite: a reference implementation of a PROSITE scanning tool	Applied bioinformatics	2002	1,177	375
Annotation of glycoproteins in the SWISS-PROT database	Proteomics	2001	632	0
The human proteomics initiative (HPI)	Trends in biotechnology	2001	576	0
SWISS-PROT: connecting biomolecular knowledge via a protein database	Current issues in molecular biology	2001	841	251
Technical comment to "Database verification studies of SWISS-PROT and GenBank" by Karp et al	Bioinformatics	2001	663	73
The InterPro database, an integrated documentation resource for protein families, domains and functional sites	Nucleic acids research	2001	686	306
Quality control in databanks for molecular biology	BioEssays	2000	559	0
InterPro--an integrated documentation resource for protein families, domains and functional sites	Bioinformatics	2000	713	445
The ENZYME database in 2000	Nucleic acids research	2000	518	687
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	1,743
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000	Nucleic acids research	2000	708	1,023
The 1999 SWISS-2DPAGE database update	Nucleic acids research	2000	581	400
The PROSITE database, its status in 1999	Nucleic acids research	1999	570	511
Eukaryotic aldehyde dehydrogenase (ALDH) genes: human polymorphisms, and recommended nomenclature based on divergent evolution and chromosomal mapping	Pharmacogenetics	1999	509	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	388	0
The SWISS-2DPAGE database: what has changed during the last year	Nucleic acids research	1999	587	384
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	659	0
High-throughput mass spectrometric discovery of protein post-translational modifications	Journal of Molecular Biology	1999	693	1,251
A molecular scanner to automate proteomic research and to display proteome images	Analytical chemistry	1999	636	724
The ENZYME data bank in 1999	Nucleic acids research	1999	502	610
Protein identification and analysis tools in the ExPASy server	Methods in Molecular Biology	1999	436	0
Representation of functional information in the SWISS-PROT data bank	Bioinformatics	1999	498	32
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999	Nucleic acids research	1999	652	1,148
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	661	351
'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	331
Construction of the gyrB Database for the Identification and Classification of Bacteria	Genomics & Informatics	1998	582	387
Protein annotation: detective work for function prediction	Trends in genetics	1998	504	0
Protein identification with N and C-terminal sequence tags in proteome projects	Journal of Molecular Biology	1998	534	0
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998	Nucleic acids research	1998	567	468
New insulin-like proteins with atypical disulfide bond pattern characterized in Caenorhabditis elegans by comparative sequence analysis and homology modeling	Genome research	1998	456	103
Current status of the SWISS-2DPAGE database	Nucleic acids research	1998	556	78
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	33
The UDP glycosyltransferase gene superfamily: recommended nomenclature update based on evolutionary divergence	Pharmacogenetics	1997	591	0
The SWISS-PROT protein sequence database: its relevance to human molecular medical research	Journal of molecular medicine	1997	535	0
Detailed peptide characterization using PEPTIDEMASS : a World-Wide-Web-accessible tool	Electrophoresis	1997	717	0
Arac/XylS family of transcriptional regulators	Microbiology and molecular biology reviews	1997	588	977
Molecular basis of symbiosis between Rhizobium and legumes	Nature	1997	989	0
Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL	Proceedings	1997	653	1,227
The SWISS-PROT protein sequence data bank and its supplement TrEMBL	Nucleic acids research	1997	689	515
The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis, its status in 1995	Nucleic acids research	1996	686	128
The yeast SWISS-2DPAGE database	Electrophoresis	1996	631	0
The PROSITE database, its status in 1995	Nucleic acids research	1996	542	130
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	674	235
The ENZYME data bank in 1995	Nucleic acids research	1996	569	176
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	45
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	720
Go hunting in sequence databases but watch out for the traps	Trends in genetics	1996	619	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	207
A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server	Trends in biochemical sciences	1994	614	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	32
The ENZYME data bank	Nucleic acids research	1994	649	117
PROSITE: recent developments	Nucleic acids research	1994	536	142
A novel zinc-binding motif found in two ubiquitous deaminase families	Protein science	1994	631	136
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	580	312
The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis	Nucleic acids research	1994	632	201
The SWISS-PROT protein sequence data bank, recent developments	Nucleic acids research	1993	664	223
ExPASy: un système expert pour l'analyse de séquences protéiques	Technologie et Santé	1993	407	89
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	397
New families in the classification of glycosyl hydrolases based on amino acid sequence similarities	Biochemical journal	1993	943	185
SWISS-2DPAGE: a database of two-dimensional gel electrophoresis images	Electrophoresis	1993	732	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	632	87
The ENZYME data bank	Nucleic acids research	1993	601	276
Electrophorèse bidimensionnelle et informatique: un outil pour le diagnostic médical?	Labolife	1993	513	170
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	164
PROSITE: a dictionary of sites and patterns in proteins	Nucleic acids research	1992	736	1,173
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	580	117
The SWISS-PROT protein sequence data bank	Nucleic acids research	1991	943	551
Nucleotide sequences of the Acinetobacter calcoaceticus benABC genes for benzoate 1,2-dioxygenase reveal evolutionary relationships among multicomponent oxygenases	Journal of bacteriology	1991	605	605
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	596	261
PROSITE: a dictionary of sites and patterns in proteins	Nucleic acids research	1991	768	543
SEQANALREF: a sequence analysis bibliographic reference databank	Computer applications in the biosciences	1991	641	264
EF-hand motifs in inositol phospholipid-specific phospholipase C	FEBS letters	1990	686	465
Calcium-binding affinity and calcium-enhanced activity of Clostridium thermocellum endoglucanase D	Biochemical journal	1990	649	575
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	136
A unique signature identifies a family of zinc-dependent metallopeptidases	FEBS letters	1989	630	195
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	636	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	634	311
Evidence for the existence of a mutated enkephalin sequence in preproenkephalin	FEBS letters	1982	629	172

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

Database

2021

401

680

The ABCD database: a repository for chemically defined antibodies

Nucleic Acids Research

2020

636

333

A high-stringency blueprint of the human proteome

Nature Communications

2020

362

395

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

Cancer Research

2020

272

0

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

Nucleic Acids Research

2020

509

382

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

1,184

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

eLife

2019

400

112

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

441

0

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

Journal of Proteome Research

2018

476

3

Kinases and Cancer

Cancers

2018

535

201

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

Human Genomics

2018

533

226

The Cellosaurus, a Cell-Line Knowledge Resource

Journal of Biomolecular Techniques

2018

611

836

A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells

Stem Cell Reports

2018

574

328

The neXtProt knowledgebase on human proteins: 2017 update

Nucleic acids research

2017

547

363

Triage by ranking to support the curation of protein interactions

Database

2017

560

517

Annotation of functional impact of voltage-gated sodium channel mutations

Human mutation

2017

586

376

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

Journal of proteome research

2016

559

155

ICEPO: the ion channel electrophysiology ontology

Database

2016

591

236

Deep Question Answering for protein annotation

Database

2015

604

1,138

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

Database

2015

547

302

N-terminome analysis of the human mitochondrial proteome

Proteomics

2015

598

0

The neXtProt knowledgebase on human proteins: current status

Nucleic acids research

2015

711

245

Converting neXtProt into Linked Data and nanopublications

Semantic web

2015

593

825

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

Molecular and cellular biology

2015

733

217

Key challenges for the creation and maintenance of specialist protein resources

Proteins

2015

544

81

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

Journal of proteome research

2014

750

913

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

581

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

PloS one

2014

730

380

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

Biochimica et biophysica acta. Molecular cell research

2014

735

280

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

Nucleic acids research

2014

922

62

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

1,241

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

615

788

neXtProt: a knowledge platform for human proteins

Nucleic acids research

2012

714

459

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

PloS one

2012

625

432

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

Nucleic acids research

2011

551

361

ViralZone: a knowledge resource to understand virus diversity

Nucleic acids research

2011

812

668

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

727

PROSITE, a protein domain database for functional characterization and annotation

Nucleic acids research

2010

740

576

Animal Toxins: How is Complexity Represented in Databases?

Toxins

2010

549

422

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

Nature methods

2010

553

0

A large-scale protein-function database

Nature chemical biology

2010

626

290

OpenFluDB, a database for human and animal influenza virus

Database

2010

653

621

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

BMC bioinformatics

2009

1,030

2,648

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

Pharmacogenetics and genomics

2009

683

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

659

135

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

Nucleic acids research

2009

677

525

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

642

0

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

Nucleic acids research

2009

719

182

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

Database

2009

712

433

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

Structural Proteomics and its Impact on the Life Sciences

2008

595

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

467

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

Human mutation

2008

710

268

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

1,277

UniProtKB/Swiss-Prot

Methods in molecular biology

2007

754

0

Data integration in Proteomics

Proteome research: concepts, technology and applications

2007

565

0

Protein variations: resources and tools

Biomedical application of proteomics

2006

614

0

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

Nucleic acids research

2006

713

1,376

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

Nucleic acids research

2006

921

574

Small can be beautiful, but it remains complex!

Complexus

2006

551

0

The PROSITE database

Nucleic acids research

2006

703

500

Functionally and structurally relevant residues in PROSITE motif descriptors

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

2005

507

1

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

Toxicon

2005

691

0

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

Bioinformatics

2005

718

292

Plant protein annotation in the UniProt Knowledgebase

Plant physiology

2005

547

434

InterPro, progress and status in 2005

Nucleic acids research

2005

707

31

Protein identification and analysis tools on the ExPASy server

The Proteomics Protocols Handbook

2005

1,622

0

The Universal Protein Resource (UniProt)

Nucleic acids research

2005

1,006

663

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

724

303

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

Proteomics

2004

613

0

Protein sequence databases

Current opinion in chemical biology

2004

474

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

379

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

111

IntEnz, the integrated relational enzyme database

Nucleic acids research

2004

739

161

UniProt: the Universal Protein knowledgebase

Nucleic acids research

2004

1,336

446

Recent improvements to the PROSITE database

Nucleic acids research

2004

606

303

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

Nucleic acids research

2003

1,249

331

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

487

NEWT, a new taxonomy portal

Nucleic acids research

2003

618

87

The InterPro Database, 2003 brings increased coverage and new features

Nucleic acids research

2003

705

502

Automated annotation of microbial proteomes in SWISS-PROT

Computational biology and chemistry

2003

489

0

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

Proteomics

2002

687

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

254

The Sulfinator: predicting tyrosine sulfation sites in protein sequences

Bioinformatics

2002

722

308

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

Briefings in bioinformatics

2002

662

1,396

The PROSITE database, its status in 2002

Nucleic acids research

2002

593

149

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

Briefings in bioinformatics

2002

668

723

ScanProsite: a reference implementation of a PROSITE scanning tool

Applied bioinformatics

2002

1,177

375

Annotation of glycoproteins in the SWISS-PROT database

Proteomics

2001

632

0

The human proteomics initiative (HPI)

Trends in biotechnology

2001

576

0

SWISS-PROT: connecting biomolecular knowledge via a protein database

Current issues in molecular biology

2001

841

251

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

Bioinformatics

2001

663

73

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

Nucleic acids research

2001

686

306

Quality control in databanks for molecular biology

BioEssays

2000

559

0

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

Bioinformatics

2000

713

445

The ENZYME database in 2000

Nucleic acids research

2000

518

687

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

1,743

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

Nucleic acids research

2000

708

1,023

The 1999 SWISS-2DPAGE database update

Nucleic acids research

2000

581

400

The PROSITE database, its status in 1999

Nucleic acids research

1999

570

511

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

Pharmacogenetics

1999

509

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

388

0

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

Nucleic acids research

1999

587

384

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

659

0

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

Journal of Molecular Biology

1999

693

1,251

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

Analytical chemistry

1999

636

724

The ENZYME data bank in 1999

Nucleic acids research

1999

502

610

Protein identification and analysis tools in the ExPASy server

Methods in Molecular Biology

1999

436

0

Representation of functional information in the SWISS-PROT data bank

Bioinformatics

1999

498

32

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

Nucleic acids research

1999

652

1,148

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

661

351

'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

331

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

Genomics & Informatics

1998

582

387

Protein annotation: detective work for function prediction

Trends in genetics

1998

504

0

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

Journal of Molecular Biology

1998

534

0

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

Nucleic acids research

1998

567

468

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

Genome research

1998

456

103

Current status of the SWISS-2DPAGE database

Nucleic acids research

1998

556

78

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

33

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

Pharmacogenetics

1997

591

0

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

Journal of molecular medicine

1997

535

0

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

Electrophoresis

1997

717

0

Arac/XylS family of transcriptional regulators

Microbiology and molecular biology reviews

1997

588

977

Molecular basis of symbiosis between Rhizobium and legumes

Nature

1997

989

0

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

Proceedings

1997

653

1,227

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

Nucleic acids research

1997

689

515

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

Nucleic acids research

1996

686

128

The yeast SWISS-2DPAGE database

Electrophoresis

1996

631

0

The PROSITE database, its status in 1995

Nucleic acids research

1996

542

130

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

674

235

The ENZYME data bank in 1995

Nucleic acids research

1996

569

176

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

45

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

720

Go hunting in sequence databases but watch out for the traps

Trends in genetics

1996

619

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

207

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

Trends in biochemical sciences

1994

614

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

32

The ENZYME data bank

Nucleic acids research

1994

649

117

PROSITE: recent developments

Nucleic acids research

1994

536

142

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

Protein science

1994

631

136

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

580

312

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

Nucleic acids research

1994

632

201

The SWISS-PROT protein sequence data bank, recent developments

Nucleic acids research

1993

664

223

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

Technologie et Santé

1993

407

89

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

397

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

Biochemical journal

1993

943

185

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

Electrophoresis

1993

732

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

632

87

The ENZYME data bank

Nucleic acids research

1993

601

276

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

Labolife

1993

513

170

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

164

PROSITE: a dictionary of sites and patterns in proteins

Nucleic acids research

1992

736

1,173

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

580

117

The SWISS-PROT protein sequence data bank

Nucleic acids research

1991

943

551

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

Journal of bacteriology

1991

605

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

596

261

PROSITE: a dictionary of sites and patterns in proteins

Nucleic acids research

1991

768

543

SEQANALREF: a sequence analysis bibliographic reference databank

Computer applications in the biosciences

1991

641

264

EF-hand motifs in inositol phospholipid-specific phospholipase C

FEBS letters

1990

686

465

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

Biochemical journal

1990

649

575

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

136

A unique signature identifies a family of zinc-dependent metallopeptidases

FEBS letters

1989

630

195

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

636

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

634

311

Evidence for the existence of a mutated enkephalin sequence in preproenkephalin

FEBS letters

1982

629

172

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