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	399	583
The ABCD database: a repository for chemically defined antibodies	Nucleic Acids Research	2020	633	248
A high-stringency blueprint of the human proteome	Nature Communications	2020	360	255
Brain metastasis cell lines panel: a public resource of organotropic cell lines	Cancer Research	2020	269	0
The neXtProt knowledgebase in 2020: data, tools and usability improvements	Nucleic Acids Research	2020	508	306
The feature-viewer: a visualization tool for positional annotations on a sequence	Bioinformatics	2020	294	0
CLASTR : the cellosaurus STR similarity search tool ‐ A precious help for cell line authentication	International Journal of Cancer	2020	492	900
Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines	eLife	2019	399	65
Cell lines as biological models: practical steps for more reliable research	Chemical Research in Toxicology	2019	358	1
Exploring the Uncharacterized Human Proteome Using neXtProt	Journal of Proteome Research	2018	439	0
Large-Scale Reanalysis of Publicly Available HeLa Cell Proteomics Data in the Context of the Human Proteome Project	Journal of Proteome Research	2018	473	3
Kinases and Cancer	Cancers	2018	534	183
A new bioinformatics tool to help assess the significance of BRCA1 variants	Human Genomics	2018	532	220
The Cellosaurus, a Cell-Line Knowledge Resource	Journal of Biomolecular Techniques	2018	608	563
A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells	Stem Cell Reports	2018	571	312
The neXtProt knowledgebase on human proteins: 2017 update	Nucleic acids research	2017	546	344
Triage by ranking to support the curation of protein interactions	Database	2017	557	500
Annotation of functional impact of voltage-gated sodium channel mutations	Human mutation	2017	583	340
The missing protein landscape of human chromosomes 2 and 14: progress and current status	Journal of proteome research	2016	558	135
ICEPO: the ion channel electrophysiology ontology	Database	2016	590	221
Deep Question Answering for protein annotation	Database	2015	601	1,120
Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat	Database	2015	546	283
N-terminome analysis of the human mitochondrial proteome	Proteomics	2015	597	0
The neXtProt knowledgebase on human proteins: current status	Nucleic acids research	2015	708	193
Converting neXtProt into Linked Data and nanopublications	Semantic web	2015	592	747
C11orf83, a Mitochondrial Cardiolipin-Binding Protein Involved in bc₁ Complex Assembly and Supercomplex Stabilization	Molecular and cellular biology	2015	731	162
Key challenges for the creation and maintenance of specialist protein resources	Proteins	2015	541	62
Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins	Journal of proteome research	2014	746	865
Querying neXtProt nanopublications and their value for insights on sequence variants and tissue expression	Journal of web semantics	2014	623	0
Standards for Reporting Enzyme Data: The STRENDA Consortium: What it aims to do and why it should be helpful	Perspectives in science	2014	693	401
C2orf62 and TTC17 are involved in actin organization and ciliogenesis in zebrafish and human	PloS one	2014	727	371
DERA is the human deoxyribose phosphate aldolase and is involved in stress response	Biochimica et biophysica acta. Molecular cell research	2014	731	250
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support	Nucleic acids research	2014	918	52
A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17	Journal of proteome research	2013	659	0
A large-scale evaluation of computational protein function prediction	Nature methods	2013	723	1,165
neXtProt: organizing protein knowledge in the context of human proteome projects	Journal of proteome research	2013	720	0
Standard guidelines for the chromosome-centric human proteome project	Journal of proteome research	2012	651	0
The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome	Nature biotechnology	2012	644	0
UniPathway: a resource for the exploration and annotation of metabolic pathways	Nucleic acids research	2012	611	772
neXtProt: a knowledge platform for human proteins	Nucleic acids research	2012	710	443
Functional identification of APIP as human mtnB, a key enzyme in the methionine salvage pathway	PloS one	2012	622	419
Towards BioDBcore: a community-defined information specification for biological databases	Nucleic acids research	2011	549	355
ViralZone: a knowledge resource to understand virus diversity	Nucleic acids research	2011	809	547
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	497	0
The human proteome project: current state and future direction	Molecular & cellular proteomics	2011	711	706
PROSITE, a protein domain database for functional characterization and annotation	Nucleic acids research	2010	736	482
Animal Toxins: How is Complexity Represented in Databases?	Toxins	2010	545	365
Mass spectrometry in high-throughput proteomics: ready for the big time	Nature methods	2010	550	0
A large-scale protein-function database	Nature chemical biology	2010	624	282
OpenFluDB, a database for human and animal influenza virus	Database	2010	651	581
Infrastructure for the life sciences: design and implementation of the UniProt website	BMC bioinformatics	2009	1,026	2,642
Human aldehyde dehydrogenase genes: alternatively spliced transcriptional variants and their suggested nomenclature	Pharmacogenetics and genomics	2009	676	2
Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands	Proteomics	2009	623	0
InterPro: the integrative protein signature database	Nucleic acids research	2009	655	110
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot	Nucleic acids research	2009	674	516
UniProtKB/Swiss-Prot manual and automated annotation of complete proteomes: the Dictyostelium discoideum case study	Bioinformatics: a Swiss Perspective	2009	532	0
The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program	Journal of proteomics	2009	637	0
CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens	Nucleic acids research	2009	713	157
Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase	Database	2009	710	381
The impact of 3D structures on a protein knowledgebase: from proteins to systems	Structural Proteomics and its Impact on the Life Sciences	2008	590	0
Calling on a million minds for community annotation in WikiProteins	GenomeBiology.com	2008	637	1,033
The 20 years of PROSITE	Nucleic acids research	2008	598	441
Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase	Human mutation	2008	702	186
UniProtKB/Swiss-Prot: new and future developments	Data Integration in the Life Sciences, Proceedings of the 5th International Workshop, DILS 2008	2008	622	0
New developments in the InterPro database	Nucleic acids research	2007	713	1,238
UniProtKB/Swiss-Prot	Methods in molecular biology	2007	744	0
Data integration in Proteomics	Proteome research: concepts, technology and applications	2007	562	0
Protein variations: resources and tools	Biomedical application of proteomics	2006	610	0
The Universal Protein Resource (UniProt): an expanding universe of protein information	Nucleic acids research	2006	710	999
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins	Nucleic acids research	2006	916	502
Small can be beautiful, but it remains complex!	Complexus	2006	548	0
The PROSITE database	Nucleic acids research	2006	700	419
Functionally and structurally relevant residues in PROSITE motif descriptors	Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics	2005	505	1
Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase	Toxicon	2005	681	0
ProRule: a new database containing functional and structural information on PROSITE profiles	Bioinformatics	2005	715	252
Plant protein annotation in the UniProt Knowledgebase	Plant physiology	2005	544	299
InterPro, progress and status in 2005	Nucleic acids research	2005	704	26
Protein identification and analysis tools on the ExPASy server	The Proteomics Protocols Handbook	2005	1,608	0
The Universal Protein Resource (UniProt)	Nucleic acids research	2005	1,003	401
Protein variety and functional diversity: Swiss-Prot annotation in its biological context	Comptes rendus. Biologies	2005	637	0
The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants	Human mutation	2004	608	0
IntAct: an open source molecular interaction database	Nucleic acids research	2004	718	167
Annotation of post-translational modifications in the Swiss-Prot knowledge base	Proteomics	2004	611	0
Protein sequence databases	Current opinion in chemical biology	2004	468	0
The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools	Plant physiology and biochemistry	2004	623	0
Swiss-Prot: juggling between evolution and stability	Briefings in bioinformatics	2004	610	281
Industrial-scale proteomics: from liters of plasma to chemically synthesized proteins	Proteomics	2004	627	0
Post-translational modifications: a challenge for proteomics and bioinformatics	Proteomics	2004	579	82
IntEnz, the integrated relational enzyme database	Nucleic acids research	2004	732	136
UniProt: the Universal Protein knowledgebase	Nucleic acids research	2004	1,331	280
Recent improvements to the PROSITE database	Nucleic acids research	2004	602	278
ExPASy: The proteomics server for in-depth protein knowledge and analysis	Nucleic acids research	2003	1,242	253
Protein databases	Nature Encyclopedia of the Human Genome	2003	566	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	634	0
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003	Nucleic acids research	2003	989	448
NEWT, a new taxonomy portal	Nucleic acids research	2003	615	61
The InterPro Database, 2003 brings increased coverage and new features	Nucleic acids research	2003	699	486
Automated annotation of microbial proteomes in SWISS-PROT	Computational biology and chemistry	2003	485	0
FindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification	Proteomics	2002	683	0
The application of bioinformatics to mass spectrometry	Proteomics	2002	485	0
El nuevo servidor Latinoamericano de biologia molecular de la UCB: bo.expasy.org	Acta Nova	2002	300	201
The Sulfinator: predicting tyrosine sulfation sites in protein sequences	Bioinformatics	2002	720	279
High-quality protein knowledge resource: SWISS-PROT and TrEMBL	Briefings in bioinformatics	2002	660	1,146
The PROSITE database, its status in 2002	Nucleic acids research	2002	590	133
PROSITE: a documented database using patterns and profiles as motif descriptors	Briefings in bioinformatics	2002	666	526
ScanProsite: a reference implementation of a PROSITE scanning tool	Applied bioinformatics	2002	1,175	329
Annotation of glycoproteins in the SWISS-PROT database	Proteomics	2001	630	0
The human proteomics initiative (HPI)	Trends in biotechnology	2001	570	0
SWISS-PROT: connecting biomolecular knowledge via a protein database	Current issues in molecular biology	2001	837	213
Technical comment to "Database verification studies of SWISS-PROT and GenBank" by Karp et al	Bioinformatics	2001	660	58
The InterPro database, an integrated documentation resource for protein families, domains and functional sites	Nucleic acids research	2001	683	175
Quality control in databanks for molecular biology	BioEssays	2000	554	0
InterPro--an integrated documentation resource for protein families, domains and functional sites	Bioinformatics	2000	710	408
The ENZYME database in 2000	Nucleic acids research	2000	516	646
A comprehensive web resource on RNA helicases from the baker's yeast Saccharomyces cerevisiae	Yeast	2000	619	0
Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times!	Bioinformatics	2000	642	1,424
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000	Nucleic acids research	2000	702	946
The 1999 SWISS-2DPAGE database update	Nucleic acids research	2000	578	372
The PROSITE database, its status in 1999	Nucleic acids research	1999	566	419
Eukaryotic aldehyde dehydrogenase (ALDH) genes: human polymorphisms, and recommended nomenclature based on divergent evolution and chromosomal mapping	Pharmacogenetics	1999	505	0
Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection	Electrophoresis	1999	591	0
Internet resources for protein identification and characterization	Microcharacterization of proteins	1999	385	0
The SWISS-2DPAGE database: what has changed during the last year	Nucleic acids research	1999	586	356
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	653	0
High-throughput mass spectrometric discovery of protein post-translational modifications	Journal of Molecular Biology	1999	690	1,145
A molecular scanner to automate proteomic research and to display proteome images	Analytical chemistry	1999	632	667
The ENZYME data bank in 1999	Nucleic acids research	1999	501	585
Protein identification and analysis tools in the ExPASy server	Methods in Molecular Biology	1999	433	0
Representation of functional information in the SWISS-PROT data bank	Bioinformatics	1999	496	25
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999	Nucleic acids research	1999	651	1,058
Low molecular weight proteins: a challenge for post-genomic research	Electrophoresis	1998	519	0
Multiple parameter cross-species protein identification using MultiIdent - a world-wide web accessible tool	Electrophoresis	1998	522	0
GPCRDB: an information system for G protein-coupled receptors	Nucleic acids research	1998	657	277
'98 Escherichia coli SWISS-2DPAGE database update	Electrophoresis	1998	671	2
Two-dimensional gel electrophoresis for proteome projects: the effects of protein hydrophobicity and copy number	Electrophoresis	1998	508	0
A superfamily of metalloenzymes unifies phosphopentomutase and cofactor-independent phosphoglycerate mutase with alkaline phosphatases and sulfatases	Protein science	1998	548	313
Construction of the gyrB Database for the Identification and Classification of Bacteria	Genomics & Informatics	1998	576	348
Protein annotation: detective work for function prediction	Trends in genetics	1998	502	0
Protein identification with N and C-terminal sequence tags in proteome projects	Journal of Molecular Biology	1998	530	0
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998	Nucleic acids research	1998	566	454
New insulin-like proteins with atypical disulfide bond pattern characterized in Caenorhabditis elegans by comparative sequence analysis and homology modeling	Genome research	1998	454	83
Current status of the SWISS-2DPAGE database	Nucleic acids research	1998	552	63
Sequences and topology: Predicting evolution	Current opinion in structural biology	1997	494	0
Proteome Databases	Proteome research: new frontiers in functional genomics	1997	372	0
The PROSITE database, its status in 1997	Nucleic acids research	1997	544	26
The UDP glycosyltransferase gene superfamily: recommended nomenclature update based on evolutionary divergence	Pharmacogenetics	1997	578	0
The SWISS-PROT protein sequence database: its relevance to human molecular medical research	Journal of molecular medicine	1997	532	0
Detailed peptide characterization using PEPTIDEMASS : a World-Wide-Web-accessible tool	Electrophoresis	1997	713	0
Arac/XylS family of transcriptional regulators	Microbiology and molecular biology reviews	1997	584	739
Molecular basis of symbiosis between Rhizobium and legumes	Nature	1997	983	0
Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL	Proceedings	1997	650	925
The SWISS-PROT protein sequence data bank and its supplement TrEMBL	Nucleic acids research	1997	686	324
The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis, its status in 1995	Nucleic acids research	1996	684	107
The yeast SWISS-2DPAGE database	Electrophoresis	1996	629	0
The PROSITE database, its status in 1995	Nucleic acids research	1996	540	98
Federated two-dimensional electrophoresis database: a simple means of publishing two-dimensional electrophoresis data	Electrophoresis	1996	570	0
Updating the sequence-based classification of glycosyl hydrolases	Biochemical journal	1996	670	184
The ENZYME data bank in 1995	Nucleic acids research	1996	567	144
Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database	Electrophoresis	1996	654	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	603	32
Integrating two-dimensional gel databases using the Melanie II software	Trends in biochemical sciences	1996	741	0
The SWISS-PROT protein sequence data bank and its new supplement TREMBL	Nucleic acids research	1996	690	593
Go hunting in sequence databases but watch out for the traps	Trends in genetics	1996	612	0
Inside SWISS-2DPAGE database	Electrophoresis	1995	676	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	560	0
The SWISS-PROT protein sequence data bank: current status	Nucleic acids research	1994	703	180
A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server	Trends in biochemical sciences	1994	610	0
Proposals for the naming of chloroplast genes. III. Nomenclature for open reading frames encoded in chloroplast genomes	Plant molecular biology reporter	1994	606	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	599	22
The ENZYME data bank	Nucleic acids research	1994	647	105
PROSITE: recent developments	Nucleic acids research	1994	532	92
A novel zinc-binding motif found in two ubiquitous deaminase families	Protein science	1994	629	117
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	574	270
The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis	Nucleic acids research	1994	629	175
The SWISS-PROT protein sequence data bank, recent developments	Nucleic acids research	1993	661	157
ExPASy: un système expert pour l'analyse de séquences protéiques	Technologie et Santé	1993	404	83
A diverse transketolase family that includes the RecP protein of Streptococcus pneumoniae, a protein implicated in genetic recombination	Research in microbiology	1993	570	0
Snake proteins and nucleic acids	Toxicon	1993	605	0
Human liver protein map: update 1993	Electrophoresis	1993	696	0
The PROSITE dictionary of sites and patterns in proteins, its current status	Nucleic acids research	1993	584	272
New families in the classification of glycosyl hydrolases based on amino acid sequence similarities	Biochemical journal	1993	939	135
SWISS-2DPAGE: a database of two-dimensional gel electrophoresis images	Electrophoresis	1993	728	0
Complementation of the DNA repair defect in xeroderma pigmentosum group G cells by a human cDNA related to yeast RAD2	Nature	1993	662	0
A possible mechanism for metal-ion induced DNA-protein dissociation in a family of prokaryotic transcriptional regulators	Nucleic acids research	1993	629	75
The ENZYME data bank	Nucleic acids research	1993	595	232
Electrophorèse bidimensionnelle et informatique: un outil pour le diagnostic médical?	Labolife	1993	510	153
Plasma and red blood cell protein maps: update 1993	Electrophoresis	1993	622	0
The SWISS-PROT protein sequence data bank	Nucleic acids research	1992	688	120
PROSITE: a dictionary of sites and patterns in proteins	Nucleic acids research	1992	734	935
Human liver protein map: a reference database established by microsequencing and gel comparison	Electrophoresis	1992	654	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	565	0
Proto-vav and gene expression	Nature	1992	616	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	577	101
The SWISS-PROT protein sequence data bank	Nucleic acids research	1991	940	512
Nucleotide sequences of the Acinetobacter calcoaceticus benABC genes for benzoate 1,2-dioxygenase reveal evolutionary relationships among multicomponent oxygenases	Journal of bacteriology	1991	601	596
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	593	249
PROSITE: a dictionary of sites and patterns in proteins	Nucleic acids research	1991	761	498
SEQANALREF: a sequence analysis bibliographic reference databank	Computer applications in the biosciences	1991	638	251
EF-hand motifs in inositol phospholipid-specific phospholipase C	FEBS letters	1990	683	455
Calcium-binding affinity and calcium-enhanced activity of Clostridium thermocellum endoglucanase D	Biochemical journal	1990	646	548
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	460	113
A unique signature identifies a family of zinc-dependent metallopeptidases	FEBS letters	1989	627	152
Sequence similarities in calcium-binding proteins	Nature	1988	583	0
Sequence patterns in protein kinases	Nature	1988	537	0
Using PC/GENE for protein and nucleic acid analysis	BioTechniques	1988	543	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	672	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	633	0
Amino acid sequence determination by gas chromatography—mass spectrometry of permethylated peptides	Journal of chromatography	1983	717	0
Suggestion to research groups working on protein and peptide sequence	Biochemical journal	1982	631	299
Evidence for the existence of a mutated enkephalin sequence in preproenkephalin	FEBS letters	1982	627	142

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

Database

2021

399

583

The ABCD database: a repository for chemically defined antibodies

Nucleic Acids Research

2020

633

248

A high-stringency blueprint of the human proteome

Nature Communications

2020

360

255

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

Cancer Research

2020

269

0

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

Nucleic Acids Research

2020

508

306

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

Bioinformatics

2020

294

0

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

International Journal of Cancer

2020

492

900

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

eLife

2019

399

65

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

Chemical Research in Toxicology

2019

358

1

Exploring the Uncharacterized Human Proteome Using neXtProt

Journal of Proteome Research

2018

439

0

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

Journal of Proteome Research

2018

473

3

Kinases and Cancer

Cancers

2018

534

183

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

Human Genomics

2018

532

220

The Cellosaurus, a Cell-Line Knowledge Resource

Journal of Biomolecular Techniques

2018

608

563

A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells

Stem Cell Reports

2018

571

312

The neXtProt knowledgebase on human proteins: 2017 update

Nucleic acids research

2017

546

344

Triage by ranking to support the curation of protein interactions

Database

2017

557

500

Annotation of functional impact of voltage-gated sodium channel mutations

Human mutation

2017

583

340

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

Journal of proteome research

2016

558

135

ICEPO: the ion channel electrophysiology ontology

Database

2016

590

221

Deep Question Answering for protein annotation

Database

2015

601

1,120

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

Database

2015

546

283

N-terminome analysis of the human mitochondrial proteome

Proteomics

2015

597

0

The neXtProt knowledgebase on human proteins: current status

Nucleic acids research

2015

708

193

Converting neXtProt into Linked Data and nanopublications

Semantic web

2015

592

747

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

Molecular and cellular biology

2015

731

162

Key challenges for the creation and maintenance of specialist protein resources

Proteins

2015

541

62

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

Journal of proteome research

2014

746

865

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

Journal of web semantics

2014

623

0

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

Perspectives in science

2014

693

401

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

PloS one

2014

727

371

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

Biochimica et biophysica acta. Molecular cell research

2014

731

250

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

Nucleic acids research

2014

918

52

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

Journal of proteome research

2013

659

0

A large-scale evaluation of computational protein function prediction

Nature methods

2013

723

1,165

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

Journal of proteome research

2013

720

0

Standard guidelines for the chromosome-centric human proteome project

Journal of proteome research

2012

651

0

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

Nature biotechnology

2012

644

0

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

Nucleic acids research

2012

611

772

neXtProt: a knowledge platform for human proteins

Nucleic acids research

2012

710

443

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

PloS one

2012

622

419

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

Nucleic acids research

2011

549

355

ViralZone: a knowledge resource to understand virus diversity

Nucleic acids research

2011

809

547

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

497

0

The human proteome project: current state and future direction

Molecular & cellular proteomics

2011

711

706

PROSITE, a protein domain database for functional characterization and annotation

Nucleic acids research

2010

736

482

Animal Toxins: How is Complexity Represented in Databases?

Toxins

2010

545

365

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

Nature methods

2010

550

0

A large-scale protein-function database

Nature chemical biology

2010

624

282

OpenFluDB, a database for human and animal influenza virus

Database

2010

651

581

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

BMC bioinformatics

2009

1,026

2,642

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

Pharmacogenetics and genomics

2009

676

2

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

Proteomics

2009

623

0

InterPro: the integrative protein signature database

Nucleic acids research

2009

655

110

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

Nucleic acids research

2009

674

516

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

Bioinformatics: a Swiss Perspective

2009

532

0

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

Journal of proteomics

2009

637

0

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

Nucleic acids research

2009

713

157

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

Database

2009

710

381

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

Structural Proteomics and its Impact on the Life Sciences

2008

590

0

Calling on a million minds for community annotation in WikiProteins

GenomeBiology.com

2008

637

1,033

The 20 years of PROSITE

Nucleic acids research

2008

598

441

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

Human mutation

2008

702

186

UniProtKB/Swiss-Prot: new and future developments

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

2008

622

0

New developments in the InterPro database

Nucleic acids research

2007

713

1,238

UniProtKB/Swiss-Prot

Methods in molecular biology

2007

744

0

Data integration in Proteomics

Proteome research: concepts, technology and applications

2007

562

0

Protein variations: resources and tools

Biomedical application of proteomics

2006

610

0

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

Nucleic acids research

2006

710

999

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

Nucleic acids research

2006

916

502

Small can be beautiful, but it remains complex!

Complexus

2006

548

0

The PROSITE database

Nucleic acids research

2006

700

419

Functionally and structurally relevant residues in PROSITE motif descriptors

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

2005

505

1

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

Toxicon

2005

681

0

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

Bioinformatics

2005

715

252

Plant protein annotation in the UniProt Knowledgebase

Plant physiology

2005

544

299

InterPro, progress and status in 2005

Nucleic acids research

2005

704

26

Protein identification and analysis tools on the ExPASy server

The Proteomics Protocols Handbook

2005

1,608

0

The Universal Protein Resource (UniProt)

Nucleic acids research

2005

1,003

401

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

Comptes rendus. Biologies

2005

637

0

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

Human mutation

2004

608

0

IntAct: an open source molecular interaction database

Nucleic acids research

2004

718

167

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

Proteomics

2004

611

0

Protein sequence databases

Current opinion in chemical biology

2004

468

0

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

Plant physiology and biochemistry

2004

623

0

Swiss-Prot: juggling between evolution and stability

Briefings in bioinformatics

2004

610

281

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

Proteomics

2004

627

0

Post-translational modifications: a challenge for proteomics and bioinformatics

Proteomics

2004

579

82

IntEnz, the integrated relational enzyme database

Nucleic acids research

2004

732

136

UniProt: the Universal Protein knowledgebase

Nucleic acids research

2004

1,331

280

Recent improvements to the PROSITE database

Nucleic acids research

2004

602

278

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

Nucleic acids research

2003

1,242

253

Protein databases

Nature Encyclopedia of the Human Genome

2003

566

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

634

0

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

Nucleic acids research

2003

989

448

NEWT, a new taxonomy portal

Nucleic acids research

2003

615

61

The InterPro Database, 2003 brings increased coverage and new features

Nucleic acids research

2003

699

486

Automated annotation of microbial proteomes in SWISS-PROT

Computational biology and chemistry

2003

485

0

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

Proteomics

2002

683

0

The application of bioinformatics to mass spectrometry

Proteomics

2002

485

0

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

Acta Nova

2002

300

201

The Sulfinator: predicting tyrosine sulfation sites in protein sequences

Bioinformatics

2002

720

279

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

Briefings in bioinformatics

2002

660

1,146

The PROSITE database, its status in 2002

Nucleic acids research

2002

590

133

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

Briefings in bioinformatics

2002

666

526

ScanProsite: a reference implementation of a PROSITE scanning tool

Applied bioinformatics

2002

1,175

329

Annotation of glycoproteins in the SWISS-PROT database

Proteomics

2001

630

0

The human proteomics initiative (HPI)

Trends in biotechnology

2001

570

0

SWISS-PROT: connecting biomolecular knowledge via a protein database

Current issues in molecular biology

2001

837

213

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

Bioinformatics

2001

660

58

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

Nucleic acids research

2001

683

175

Quality control in databanks for molecular biology

BioEssays

2000

554

0

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

Bioinformatics

2000

710

408

The ENZYME database in 2000

Nucleic acids research

2000

516

646

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

Yeast

2000

619

0

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

Bioinformatics

2000

642

1,424

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

Nucleic acids research

2000

702

946

The 1999 SWISS-2DPAGE database update

Nucleic acids research

2000

578

372

The PROSITE database, its status in 1999

Nucleic acids research

1999

566

419

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

Pharmacogenetics

1999

505

0

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

Electrophoresis

1999

591

0

Internet resources for protein identification and characterization

Microcharacterization of proteins

1999

385

0

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

Nucleic acids research

1999

586

356

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

653

0

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

Journal of Molecular Biology

1999

690

1,145

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

Analytical chemistry

1999

632

667

The ENZYME data bank in 1999

Nucleic acids research

1999

501

585

Protein identification and analysis tools in the ExPASy server

Methods in Molecular Biology

1999

433

0

Representation of functional information in the SWISS-PROT data bank

Bioinformatics

1999

496

25

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

Nucleic acids research

1999

651

1,058

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

Electrophoresis

1998

519

0

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

Electrophoresis

1998

522

0

GPCRDB: an information system for G protein-coupled receptors

Nucleic acids research

1998

657

277

'98 Escherichia coli SWISS-2DPAGE database update

Electrophoresis

1998

671

2

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

Electrophoresis

1998

508

0

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

Protein science

1998

548

313

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

Genomics & Informatics

1998

576

348

Protein annotation: detective work for function prediction

Trends in genetics

1998

502

0

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

Journal of Molecular Biology

1998

530

0

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

Nucleic acids research

1998

566

454

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

Genome research

1998

454

83

Current status of the SWISS-2DPAGE database

Nucleic acids research

1998

552

63

Sequences and topology: Predicting evolution

Current opinion in structural biology

1997

494

0

Proteome Databases

Proteome research: new frontiers in functional genomics

1997

372

0

The PROSITE database, its status in 1997

Nucleic acids research

1997

544

26

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

Pharmacogenetics

1997

578

0

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

Journal of molecular medicine

1997

532

0

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

Electrophoresis

1997

713

0

Arac/XylS family of transcriptional regulators

Microbiology and molecular biology reviews

1997

584

739

Molecular basis of symbiosis between Rhizobium and legumes

Nature

1997

983

0

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

Proceedings

1997

650

925

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

Nucleic acids research

1997

686

324

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

Nucleic acids research

1996

684

107

The yeast SWISS-2DPAGE database

Electrophoresis

1996

629

0

The PROSITE database, its status in 1995

Nucleic acids research

1996

540

98

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

Electrophoresis

1996

570

0

Updating the sequence-based classification of glycosyl hydrolases

Biochemical journal

1996

670

184

The ENZYME data bank in 1995

Nucleic acids research

1996

567

144

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

Electrophoresis

1996

654

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

603

32

Integrating two-dimensional gel databases using the Melanie II software

Trends in biochemical sciences

1996

741

0

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

Nucleic acids research

1996

690

593

Go hunting in sequence databases but watch out for the traps

Trends in genetics

1996

612

0

Inside SWISS-2DPAGE database

Electrophoresis

1995

676

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

560

0

The SWISS-PROT protein sequence data bank: current status

Nucleic acids research

1994

703

180

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

Trends in biochemical sciences

1994

610

0

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

Plant molecular biology reporter

1994

606

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

599

22

The ENZYME data bank

Nucleic acids research

1994

647

105

PROSITE: recent developments

Nucleic acids research

1994

532

92

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

Protein science

1994

629

117

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

574

270

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

Nucleic acids research

1994

629

175

The SWISS-PROT protein sequence data bank, recent developments

Nucleic acids research

1993

661

157

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

Technologie et Santé

1993

404

83

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

Research in microbiology

1993

570

0

Snake proteins and nucleic acids

Toxicon

1993

605

0

Human liver protein map: update 1993

Electrophoresis

1993

696

0

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

Nucleic acids research

1993

584

272

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

Biochemical journal

1993

939

135

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

Electrophoresis

1993

728

0

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

Nature

1993

662

0

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

Nucleic acids research

1993

629

75

The ENZYME data bank

Nucleic acids research

1993

595

232

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

Labolife

1993

510

153

Plasma and red blood cell protein maps: update 1993

Electrophoresis

1993

622

0

The SWISS-PROT protein sequence data bank

Nucleic acids research

1992

688

120

PROSITE: a dictionary of sites and patterns in proteins

Nucleic acids research

1992

734

935

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

Electrophoresis

1992

654

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

565

0

Proto-vav and gene expression

Nature

1992

616

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

577

101

The SWISS-PROT protein sequence data bank

Nucleic acids research

1991

940

512

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

Journal of bacteriology

1991

601

596

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

593

249

PROSITE: a dictionary of sites and patterns in proteins

Nucleic acids research

1991

761

498

SEQANALREF: a sequence analysis bibliographic reference databank

Computer applications in the biosciences

1991

638

251

EF-hand motifs in inositol phospholipid-specific phospholipase C

FEBS letters

1990

683

455

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

Biochemical journal

1990

646

548

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

460

113

A unique signature identifies a family of zinc-dependent metallopeptidases

FEBS letters

1989

627

152

Sequence similarities in calcium-binding proteins

Nature

1988

583

0

Sequence patterns in protein kinases

Nature

1988

537

0

Using PC/GENE for protein and nucleic acid analysis

BioTechniques

1988

543

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

672

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

633

0

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

Journal of chromatography

1983

717

0

Suggestion to research groups working on protein and peptide sequence

Biochemical journal

1982

631

299

Evidence for the existence of a mutated enkephalin sequence in preproenkephalin

FEBS letters

1982

627

142

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