Primary and high school studies in Belgium, France, Canada, and
Switzerland from 1963 to 1977. High school graduation in 1977.
Studies at the University of Geneva in
Biochemistry, Chemistry and Mathematics from 1977 to 1983.
1981: Licence (B. Sc.) in Biochemistry.
1981: Licence (B. Sc.) in Chemistry.
1983: Diplome (M. Sc.) in Biochemistry.
1990: Ph.D. thesis in Biochemistry; "PC/Gene: a protein and nucleic acid sequence
analysis microcomputer package, PROSITE: a dictionary of sites and patterns
in proteins, and SWISS-PROT: a protein sequence data bank".
Posts held
October 1982 to October 1987: 'Assistant' at the Medical Biochemistry
department of the University of Geneva.
October 1987 to October 1989: 'Maitre-assistant' at the same department.
October 1989 to December 1994: 'Collaborateur scientifique' in charge of
Biocomputing for the 'Unité d'analyse moléculaire'
of the Faculty of Medicine at the University of Geneva.
From January 1995 to March 2001: 'Maitre d'Enseignement et de Recherche'
(MER) at the Medical Biochemistry department of the University of Geneva.
In 1979-1980: development of a radio-immunoassay analysis package
on a microcomputer for the Clinical Biochemistry Institute of
the University of Geneva.
In 1982-1983: development of mini-computer programs for the analysis
of mass spectra of peptides for the Medical Biochemistry Department
of the University of Geneva.
In 1982-1984: in charge of the support of microcomputer systems
in several departments of the universities of Geneva, Lausanne,
and Fribourg. Installation of commercial software packages, organization
of seminars, hardware and software evaluation.
Principally from 1984 to 1987: development of PC/Gene,
a microcomputer software package for the analysis of protein and
nucleotide sequences. PC/Gene was distributed worldwide by IntelliGenetics (later owned by Oxford Molecular).
More than 2500 laboratories in 45 different countries have used PC/Gene.
In parallel: development of new methods and algorithms for the analysis of protein
sequences.
Since 1986: development and maintenance of the Swiss-Prot
protein knowledgebase. Swiss-Prot is the best known and most widely used
protein sequence database. From 1987 to 1994 it has
been a collaborative project with the European Molecular Biology
Laboratory Data Library group (Heidelberg / Germany) and since
1994 with the European Bioinformatics Institute (EBI) (Hinxton
/ U.K.).
From 1986 to 1989: moderator of two bulletin boards on the BIOSCI
computer resource network.
Since 1988: work on PROSITE, a database of protein
families and domains. At least 10'000 copies of PROSITE
are distributed at each release. Many academic and commercial programs have
been written by other scientists that make use of the database.
Since 1990: work on ENZYME, a database of information
on the nomenclature of enzymes.
Since 1993; work in collaboration with the group of Ron Appel
on a World Wide Web server for molecular biologists (ExPASy).
In May 2007 this server was queried at the rate of about 32 million documents per
month and it had reached a cumulative total of
1 billion connections. Mirror sites of ExPASy have been established in different
countries over the world.
Awards/prices
Recipient of the 1993 Friedrich Miescher award from the Swiss Society of Biochemistry.
Recipient of the 1995 Helmut Horten Foundation Incentive award.
Recipient of the 2004 Pehr Edman award.
Recipient of the 2004 European Latsis prize.
Recipient of the 2007 George F. Jauber prize.
Committees memberships and honorific positions
Since 1987: 'honorary consultant' of the Data Library group of
the European Molecular Biology Laboratory (EMBL) in Heidelberg,
now the European Bioinformatics Institute
(EBI) in Hinxton near Cambridge (UK).
In 1993, member of the Advisory Committee for the European Bioinformatics Institute (ACEBI).
From 1995 to 1998, member of the scientific council of GIS INFOBIOGEN,
the French national infrastructure for bioinformatics.
from 1995 to 2001: member of the International Union of Biochemistry
and Molecular Biology Nomenclature Committee (IUBMB-NC) also known as
JCBN.
From 1999 to 2001, member of the "Bioinformatics search committee" of the University of Basel, Switzerland
(selection of two professors of bioinformatics).
From 1999 to 2003, member of the Scientific Advisory Committee of GenoPlante (INRA; Evry / France).
Since 1999, member of the Scientific Advisory Board of the Presage database for Structural Genomics (Stanford, USA).
Since 1999, member of the Data Center Committee of the Protein Data Bank (PDB), USA.
Since 1999, member of the Panel of experts of Action plan "Genomics" of the French Ministry of National Education, Research and Technology.
Since 1999, member of the International Advisory Committee for the Human Gene Nomenclature Committee.
Since 2000, member of the "Comité de pilotage", Génopole Rhône Alpes (Lyon, France).
From 2001 to 2005, member of the Scientific Advisory Board of GeneProt.
From 1982 to 1984: numerous courses on various aspects of microcomputing.
From 1989 to 1997: instructor for the yearly ICGEB/UNIDO workshop on Computer
Applications in Molecular Biology, in Trieste (Italy).
From 1990 to 1995: in charge of giving a two-hour lecture on sequence
analysis in the framework of the Biochemistry course for undergraduate
students at the University of Geneva.
From 1992 to 1999: participation (once per year) in form of a seminar to the Swiss
biological science 3rd cycle course on Micro-techniques in protein and
peptide chemistry organized by Prof. J.-C. Jaton at the University of
Geneva.
In October 1992: instructor for the Biocomputing course 1992;
organized by the Norwegian node of EMBnet in Oslo.
In June 1995: instructor for an EMBO molecular phylogeny course
organized by the Laboratoire de Biométrie, Génétique
et Biologie des Populations in Lyon.
In 1996: participation to a post-graduate course on Bioinformatics
(Informatique et biologie: du modèle à l'outil) at the
Swiss Federal Polytechnic of Lausanne.
From 1996 to 1998: co-organizer of a one year
Bioinformatics course
(3 hours per week) at the Computer Sciences department of the University of Geneva.
From 1992 to 2004: in charge of giving an annual one-semester course (two hours
per week) Computer analysis of protein sequences to post-graduate
students in biochemistry and biology at the University of Geneva.
From 1994 to 2002: participation in the training courses
(3 to 4 times per year) on two-dimensional polyacrylamide gel electrophoresis
organized by Prof. Denis F. Hochstrasser of the Clinical Chemistry Department
of the Geneva University Hospital.
From 1997 to 2002: participation (1 to 2 times per year) in the joint course of the
Swiss node of EMBnet
and the Swiss biological science 3rd cycle course on Sequence analysis
From 1999 to 2004: co-organizer of the
Diplôme d'études approfondies (DEA) plurifacultaire en bioinformatique.
This is a one-year curriculum leading to a Master's degree in bioinformatics.
It is organized by the SIB and the universites of Geneva and Lausanne.
I am in charge of 2 of the 8 modules: Introduction to bioinformatics and
Databases for the life sciences.
From 2001 to 2003: participation (2h00) in the Medical Biochemistry course for first
year medical students at the University of Geneva. The topic of my intervention
is to introduce bioinformatics and its usage in the context of human
medical genetic research.
From 2001 to 2002: participation (2h00) in a course (APP module "microbiologie de
demain") for third year medical students at the University of Geneva.
The topic of my intervention is the importance of Bioinformatics in studying
complete microbial genomes and proteomes.
Since 2004: co-organizer of the
Master's in Proteomics and Bioinformatics.
This is a one-year curriculum organized by the SIB and the Faculties of Medicine and Sciences of the
University of Geneva.
I am in charge of 1 of the 10 modules: 14F01: Elements of bioinformatics.
In 2006: instructor for the ICGEB/LNCCTheoretical and Practical Course in Bioinformatics Applied to Proteomics and Structural Bioinformatics, in Petropolis (Brazil).
Conferences and workshops: invited speaker/participant
February 1987 / EMBL-NIH workshop; Future Databases for Molecular Biology / EMBL; Heidelberg; Germany.
January 1988 / Annual meeting of the CODATA task group on biological macromolecules / Paris; France.
October 1989 / EMBO Conference; Patterns in Protein Sequence and Structure / EMBL; Heidelberg; Germany.
July 1990 / NCBI software and database developers conference / NIH; Bethesda; USA.
December 1990 / HUGO meeting; Genome analysis: from sequence to function / Frankfurt am Main; Germany.
March 1991 / British Crystallographic Association (BCA) spring meeting / Sheffield; UK.
October 1991 / The role of Biocomputing in the characterization of human genome sequences / Bari; Italy.
November 1991 / Workshop for creating an infrastructure for intelligent systems in molecular biology / NLM/NSF; Bethesda; USA.
December 1992 / BioInformatics and molecular evolution: prediction of gene function / National Institute of Genetics; Mishima; Japan.
December 1992 / Teijin second seminar in BioInformatics / Osaka; Japan.
March 1993 / Annual meeting of the CODATA task group on biological macromolecules / Ringberg; Germany.
May 1993 / First international conference of the Commission on Plant Gene Nomenclature / Bellagio; Italy.
August 1993 / Macromolecules, Genes, and Computers: chapter three (MGC-III) / Waterville Valley; USA.
May 1994 / IUBMB-IUPAC Nomenclature Committee Meeting / Kiliney; Ireland.
June 1994 / Forum Interdisciplinaire "Génome et Informatique" (FIDGI) / Aussois; France.
July 1994 / HUGO Bioinformatics Forum / Hinxton; UK.
September 1994 / 2D Electrophoresis: from protein maps to genomes / Siena; Italy.
September 1994 / International workshop on extracellular protein modules: sequence, structure, function and evolution / Margretetorp; Sweden.
November 1994 / Third international E.coli genome meeting / Marine Biological laboratory; Woods Hole; USA.
November 1994 / Septième entretiens du Centre Jacques Cartier: Computer Science and Molecular Biology / Lyon; France.
December 1994 / 17th annual meeting of the Molecular Biology Society of Japan / Kobe; Japan.
December 1994 / 5th Genome Informatic Workshop / Yokohama; Japan.
February 1995 / 7th European Congress of Biotechnology (ECB7) / Nice; France.
May 1995 / IUBMB-IUPAC Nomenclature Committee Meeting / Hinxton; UK.
May 1995 / First European Symposium of the Protein Society / Davos; Switzerland.
June 1995 / International working conference on the use of Internet and World-Wide Web for telematics in healthcare / Geneva; Switzerland.
March 1996 / Getting the most from your protein sequence / British Biophysical Society meeting / London; UK.
May 1996 / DOE Macromolecular database workshop / Argonne National Laboratory / USA.
September 1996 / XIth International Conference on Methods in Protein Structure Analysis (MPSA) / Annecy; France.
September 1996 / From Genome to Proteome; 2nd Siena 2D Electrophoresis Meeting / Siena; Italy.
November 1996 / 24th Aharon Katzir-Katchalsky Conference; BioInformatics - Structure / Jerusalem; Israel (Member of Organizing Committee).
February 1997 / Genes and Computer IV (GPC-4) / Daresbury; UK.
March 1997 / 11th International Conference on Mathematical and Computer Modelling and Scientific Computing / Washington DC; USA.
April 1997 / Journée thématique: Dévelopements récents en Microanalyse des Protéines / Grenoble; France.
May 1997 / IUBMB-IUPAC Nomenclature Committee Meeting / Washington DC; USA.
July 1997 / Perspectives on Protein Engineering 1997 (POPE 1997) / John Innes Institute / Norwich; UK.
October 1997 / Workshop on interconnection of organism specific databases / La Treille; France.
November 1997 / 1st annual Computational Genomic Conference / Washington DC; USA.
December 1997 / Symposium in Computational Sciences; Bioinformatics from Experiment to Biological Knowledge / Basel; Switzerland.
February 1998 / Miami 30th Winter Symposia: Molecular Biology in the Conquest of Disease / Miami; USA.
February 1998 / Zoologia et Botanica 98 / Geneva; Switzerland.
April 1998 / Harnessing Innovation to Develop Effective Bioinformatics Programmes / London; UK.
August 1998 / From Genome to Proteome; 3rd Siena 2D Electrophoresis Meeting / Siena; Italy.
September 1998 / EU/US Workshop on Database Interoperability / Hinxton; UK.
October 1998 / Integrative Bioinformatics: High throughput Interpretation of Genes and Proteins / Zurich; Switzerland (Keynote speaker).
February 1999 / European Science Foundation Strategic Workshop on Beyond the Human Genome Sequence: Proteome Analysis in Medical Research / Chamonix; France.
March 1999 / Colloque de l'Institut Jacques-Monod: Evolution moléculaire / Paris; France.
April 1999 / European Science Foundation Exploratory Workshop on Functional Genomics / Paris; France.
May 1999 / IUBMB-IUPAC Nomenclature Committee Meeting / Cambridge; UK.
June 1999 / 26th meeting of the Federation of European Biochemical Societies (FEBS) / Nice; France.
June 1999 / Genomics, functional genomics, proteomics and beyond; Institute Pasteur Euroconferences / Paris; France.
August 1999 / 7th International Conference on Intelligent Systems for Molecular Biology / Heidelberg; Germany (Keynote speaker).
October 1999 / Sino-Swiss Workshop on Bioinformatics / Peking; China.
January 2000 / VIIth DBMS/IBS Workshop: From the Structure and Function to the Design of Modular Proteins / Autrans; France.
February 2000 / The Genome Conference 2000 / 21st Annual Conference on the Organisation and Expression of the Genome / Lorne; Australia.
April 2000 / Genomes 2000: International Conference on Microbial and Model Genomes / Paris; France.
May 2000 / Proteomics: new experimental approaches to unravel biological processes / Inserm Atelier 115 / Jouy-en-Josas; France.
August 2000 / Arolla workshop 2000; Genes and development: signalling in health and disease / Arolla; Switzerland.
September 2000 / From Genome to Proteome: Knowledge Acquisition and Representation; 4th Siena Meeting / Siena; Italy.
October 2000 / Journée Thématique de l'Institut Albert Bonniot: les banques de données en Biologie: pourquoi, comment? / Grenoble; France.
November 2000 / Transcriptome 2000; From Functional Genomics to Systems Biology / Paris; France.
December 2000 / Analyse de l'expression des gènes et bioinformatique: Nouveaux développements, applications industrielles et biomédicales / Lyon; France.
March 2001 / XIV Course in Medical Genetics / Sestri Levante; Italy.
April 2001 / BBC 2001; 2nd Belgian Bioinformatics Conference / Ghent; Belgium.
June 2001 / Global Health Equity: Medical progress and Quality of Life in the XXIst century / UNESCO Paris; France.
June 2001 / 2nd PROSITE Workshop / Marseille; France.
July 2001 / 27th meeting of the Federation of European Biochemical Societies (FEBS) / Lisbon; Portugal.
September 2001 / Proteomic Forum 2001 - International meeting on Proteome Analysis / Munich; Germany.
October 2001 / European Science Foundation Workshop: Data Integration in Functional Genomics and Proteomics / Geneva; Switzerland.
November 2001 / Swiss Proteomics Society 2001 Congress: Functional Proteomics / Geneva; Switzerland.
March 2002 / Ecole de Printemps du 3'ème cycle Romand d'informatique 2002 / Les Diablerets; Switzerland.
June 2002 / JOBIM 2002; Journées ouvertes Biologie Informatique Mathématiques / St-Malo; France.
June 2002 / GPBM 2002; Genomics, Proteomics and Bioinformatics for Medicine / St. Petersburg; Russia.
September 2002 / From Genome to Proteome: Functional Proteomics; 5th Siena Meeting / Siena; Italy.
November 2002 / HUPO First World Congress / Versailles; France.
June 2003 / HAMAP 2003 workshop on microbial protein annotation / Geneva; Switzerland (Organizer).
September 2003 / A scientific day on systematics and evolution / National Natural History Museum / Paris; France.
September 2003 / European Science Foundation Workshop: Data integration in Functional Genomics and Proteomics II / Geneva; Switzerland.
September 2003 / Internationale Biometrische Gesellschaft Region Osterreich-Schweiz (ROeS) seminar 2003 / St. Gallen; Switzerland.
March 2004 / Second Basel computational biology conference: from information to simulation / Basel; Switzerland.
April 2004 / Genomes 2004 / Hinxton; UK.
June 2004 / ASBMB Annual Meeting and 8th IUBMB Conference / Boston; USA.
September 2004 / From Genome to Proteome: Biomarkers Discovery and Proteome Imaging; 6th Siena Meeting / Siena; Italy.
September 2004 / XVth International Conference on Methods in Protein Structure Analysis (MPSA) / Seattle; USA.
November 2004 / Environmental Genomics and Environmental Metagenomics / Grenada; Spain.
January 2005 / Forum Biotech Innovation "du Savoir à la Valeur" Proteines / Grenoble; France.
May 2005 / European Science Foundation Workshop: Sustainability and Governance of Web and GRID Resources in Functional Genomics / Fraunhofer Institute; Sankt Augustin; Germany.
September 2005 / MIE 2005 - XIXth International Congress of the European Federation for Medical Informatics / Geneva; Switzerland (Keynote speaker).
September 2005 / HUPO 4th Annual World Congress / Munich; Germany (Keynote speaker).
February 2006 / 38th Annual Meeting of the Union of Swiss Societies for Experimental Biology (USGEB/USSBE) / Geneva; Switzerland.
May 2006 / European Life Sciences Forum Meeting: Research Infrastructures for the life sciences in Europe / Vienna; Austria.
July 2006 / In-silico analysis of proteins: celebrating the 20th anniversary of Swiss-Prot / Fortaleza; Brazil (Keynote speaker; Organizer).
August 2006 / BOSC 2006 (Bioinformatics Open Source Conference) / Fortaleza; Brazil (Keynote speaker).
August 2006 / 14th International Conference on Intelligent Systems for Molecular Biology / Fortaleza; Brazil.
August 2006 / ASM/NCBI Workshop on Microbial Genome Annotation / Washington DC; USA.
September 2006 / From Genome to Proteome: Back to the Future; 7th Siena Meeting / Siena; Italy (Closing main lecture).
October 2006 / HUPO 5th Annual World Congress / Long Beach; USA.
February 2007 / ESAO winter school 2007 - "Teaching the teachers" / Gstaad; Switzerland.
May 2007 / International Conference on the Bioinformatics of African Pathogens and Disease Vectors / Nairobi; Kenya (Keynote speaker).
June 2007 / International Workshop of Collaborative Bioinformatics / Malaga; Spain.
September 2007 / 53th Congresso Brasileiro de Genetica / Aguas de Lindoia; Brazil.
September 2007 / 1st Marseille-Nice Genopole scientific meeting / Marseille; France.
October 2007 / 2nd International Biocuration Meeting / San Jose; USA.
November 2007 / International symposium celebrating a decade of GeneCards at the Weizmann Institute of Science / Rehovot; Israel.
April 2008 / Genomes 2008: Functional Genomics of Microorganisms / Paris; France.
May 2008 / KHUPO 8th annual international proteomics conference: Proteomics for Future Life Science and Medicine / Jeju; Korea.
June 2008 / DILS 5th international workshop - Data Integration in the Life Sciences / Evry; France (Program co-chairman).
Seminars/presentations
Many seminars in various departments of Geneva University;
ISREC (Lausanne) [twice];
Institut de Biologie at Lausanne University;
Biozentrum (Basel) [twice];
Friedrich Mischer Institute (Basel) [3 times];
Institute of Biochemistry and Molecular Biology at Bern University;
Organic Chemistry Department of Bern University;
Institute for Veterinary Bacteriology at Bern University [twice];
University of Fribourg;
Institute of Pathology of the University of Zurich;
IBM Zurich Research Laboratory;
Nestlé Research Center (Lausanne);
Serono Pharmacutical Research Institute SA;
CERMAV (Grenoble / France);
Grenoble University Hospital [twice];
Centre de Biophysique Moléculaire (Orléans / France);
Paris Sud University;
Pasteur Institute (Paris / France);
Centre Génétique Moléculaire du CNRS (Gif-sur-Yvette / France);
Strasbourg University;
Marseille (Lumigny) University [3 times];
EMBL (Heidelberg / Germany) [twice];
DKFZ (Heidelberg / Germany);
Dortmund Max Plank Institute (Germany);
Glaxo Research group on protein chemistry (Greenford / UK);
Sanger Genome Center (Hinxton / UK);
Vanbug - Vancouver Bioinformatics User Group (Vancouver / Canada);
NCBI (NLM / NIH; Bethesda / USA) [twice];
Stanford University School of Medicine (Palo Alto / USA);
UCSD Department of Biology (San Diego / USA);
Celera Genomics (Rockville / USA);
Laboratório Nacional de Computação Científica (Brazil) [twice];
Universidade Federal de Sao Paulo (Brazil);
Universidade Federal do Rio Grande do Sul (Brazil);
University of Campinas (Unicamp) (Brazil);
Fourth Military Medical University (Xian / China);
Indian Institute of Technology (New Dehli / India);
Institute of Bioinformatics and Applied Biotechnology (IBAB) (Bangalore / India);
Weizmann Institute of Science (Rehovot / Israel) [twice];
Hebrew University of Jerusalem (Israel);
Institute for Chemical Research (Kyoto University / Japan);
Marine Biotechnology Institute (Kamaichi / Japan);
University of Kobe (Japan);
International Livestock Research Institute (ILRI) (Nairobi / Kenya).
Ph.D students supervisation
Alexandre Gattiker; Ph.D in Sciences 'mention' bioinformatics in Mars 2005; Geneva University thesis 3616
Pavel Dobrokhotov; Ph.D in Sciences 'mention' interdisciplinary in September 2005; Geneva University thesis 3667
Fabrice David; Ph.D student in Sciences 'mention' bioinformatics
Ph.D and other thesis jury participation
February 1995: Laurent Duret; Université Claude Bernard - Lyon I / France
December 1996: Ivan Moszer; Université Paris VI / France
February 1997: Florence Horn; Université de la Méditerannée - Marseille II / France
July 1998: Frédéric Achard; Université Paris VII / France
October 1998: Nicolas Moeri; Ecole Polytechnique Fédérale de Lausanne / Switzerland
June 1999: Catherine Cooper; Macquarie University; Sidney / Australia
July 2000: Guy Perrière; HDR thesis; Université Claude Bernard - Lyon I / France
September 2000: Claudine Médigue-Rousseau; HDR thesis; Université de Versailles-Saint Quentin / France
June 2001: Christophe Combet; Université Paris VII / France
May 2004: Stéphanie Bocs; Université Paris VI / France
November 2005: Bozena Korczak; Bern University / Switzerland
June 2007: Bernhard Sonderegger; Geneva University / Switzerland
February 2008: Jean-Luc Falcone; Geneva University / Switzerland
Funding
From 1985 to 1995: the royalties from the sale of PC/Gene
have been used to pay for the salaries of 1.5 'assistants' as well as
for various computer equipment.
From 1987 to 1993: a part of the budget of the Data Library group at
the European Molecular Biology Laboratory was been allocated to
the maintenance, development, and distribution of Swiss-Prot.
From 1992 to 1997: the company IntelliGenetics has provided a bursary for
a programmer to work, in Geneva, under my supervision in the
development of PC/Gene.
From 1992 to 1994: Dr. Denis Hochstrasser of the Digital Imaging Group
at the Medical Informatic Center of the Geneva University Hospital
created a position for a Ph.D. student to work, under our
joint guidance, in the development of an expert system for protein
function analysis. He also provided computer equipment for this project.
In April 1993: a grant of Fr.S. 481,798.- was awarded by the Swiss National
Science Foundation [FNRS/SNSF] (31-36393.92) over a two year period for the
development of Swiss-Prot and PROSITE. This grant was extended for a third
year (Fr.S. 235.887.-).
In July 1993: a grant of Fr.S. 224,000.- was awarded by Glaxo Group Research
Ltd over a three year period for the development of Swiss-Prot.
From February 1995 to December 1996: the EMBL - EBI has awarded a full
position for a student annotator.
Starting in January 1996 and for a five year period, the Helmut Horten
Foundation contributed up to Fr.S. 420,000.- per year for salaries and
equipment to my research activities (Helmut Horten Incentive Award).
In December 1996: a grant of Fr.S. 600,000.- was awarded by the Swiss National
Science Foundation [FNRS/SNSF] (31-49990.96) over a three year period for
Core activities of the SWISS-PROT protein sequence database.
In December 1996: a grant of Fr.S. 47,450.- was awarded by the EU
Biotechnology research program and the FOES/OFES (BIO4-CT96-0030 / OFES 96.0441-2)
over a three year period for EMBnet ca: Europe's bioinformatics infrastructure
network.
In February 1998: a grant of Fr.S. 748,800.- was awarded by the EU
Biotechnology research program and the FOES/OFES (BIO4-CT97-2099 / OFES 96.0403)
over a 31 month period for Enhancement of the SWISS-PROT protein sequence data bank
activities.
In August 1998: a grant of Fr.S. 259,200.- was awarded by the EU
Biotechnology research program and the FOES/OFES (BIO4-98-0052 / OFES 98.0202-1)
over a two year period for InterPro: the creation of an integrated resource
of protein domains and functional sites and its application to accelerate protein
functional analysis.
In April 1999: a grant of Fr.S. 105,393.- was awarded by the Swiss National
Science Foundation [FNRS/SNSF] (2153-055546.98) over a two year period for
The Anataxis projects: reconstructing the Tree of Life with a new
computerized parallel approach.
In December 2000: a grant of Fr.S 139'500.- was awarded by the EU
Biotechnology research program and the FOES/OFES (QLRI-CT-2000-00517 / OFES 01.0071)
over a two year period for ProFuSe: Automation of large-scale protein
functional sequence analysis.
In July 2001: a grant of Fr.S 425,000.- was awarded by the Swiss National
Science Foundation [FNRS/SNSF] (3100-063879.00) over a three year period for
Characterization of biomolecular sequence motifs by generalised profiles.
In November 2001: a grant of Fr.S 627,800.- was awarded by the EU
Biotechnology research program and the FOES/OFES (QLRI-CT-2001-00981 / OFES 01.0155)
over a three year period for BioBabel: Enhanced interoperability of
biological databases by standardisation of biochemical terminology and
introduction of a shared ontology.
In January 2002: a grant of Fr.S 1,016,680.- was awarded by the EU
Biotechnology research program and the FOES/OFES (QLRI-CT-2001-00015 / OFES 01.0101)
over a three year period for Temblor: The European molecular biology
linked original resources.
From September 1998 to December 2004: the licensing of Swiss-Prot and PROSITE to
commercial users by GeneBio is
generating yearly revenues which have grown from Fr.S 3,200,000 to slightly
over Fr.S. 5,000,000.- About 50% of this sum went to the Swiss-Prot group at
EBI and the rest to the Swiss-Prot group at the SIB.
For the period 2000-2003: the Swiss Federal Government allocated about
Fr.S. 1,520,000.- per year for the maintenance of Swiss-Prot and PROSITE.
In September 2002: the National Institutes of Health (NIH) has awarded a
grant (1 U01 HG02712-01) over a three year period for The UniProt protein sequence and
function knowledgebase. Out of a total of $15 million, the Swiss-Prot
group at SIB has received $ 4,780,000.-
In January 2003: a grant of Fr.S 527,635.- was awarded by the EU
Biotechnology research program and the FOES/OFES (QLRI-CT-2002-02770 / OFES 02.0126)
over a three year period for BioMint: Biological text mining.
In January 2003: a grant of Euro 134,920.- was awarded by GenoPlante-Valor
(BI-2001-071) over a 1.5 year period for the Structural and functional
annotation of Arabidopsis protein and gene families.
In April 2003: a grant of Yen 10,000,000 (about Fr.S 120,000) was awarded
by the National Institute of Technology and Evaluation (NITE) of Japan
over a one year period for the Annotation of ORFs in the genomic data
of Rhodococcus erythropolis.
In January 2004: a grant of Fr.S 720,556.- was awarded by the EU Network of
Excellence program and the FOES/OFES (LSHG-CT-2003-503265 / OFES 03.0700)
over a five year period for BioSapiens: developing methods and resources
in bioinformatics to focus on the annotation of human and other genomes.
For the period 2004-2007, the Swiss Federal Government has allocated about
Fr.S. 2,730,000.- per year for the maintenance of Swiss-Prot and PROSITE.
In September 2005: the National Institutes of Health (NIH) has awarded a
grant (5 U01 HG02712-03S1) over a 8 months period for The UniProt protein sequence and
function knowledgebase. Out of a total of $5 million, the Swiss-Prot
group at SIB has received $ 1,875,000.-
In March 2006, a grant of Euro 2,756,340.- was awarded by the EU
Integrated Infrastructure Initiative over a three year period for FELICS: Free European Life-science
Information and Computational Services.
For the period 2008-2011, the Swiss Federal Government has allocated about
Fr.S. 3,600,000.- per year for the maintenance of Swiss-Prot and PROSITE.
Publications
1. Bairoch A.;
Suggestions to research groups working on protein and peptide sequence;
Biochem. J. 203:527-528(1982).
[82283886]
2. Bairoch A.;
Evidence for the existence of mutated enkephalin sequence in preproenkephalin;
FEBS Letters 145:121-122(1982).
[83027821]
3. Rose K., Bairoch A., Offord R.E.;
Amino acid sequence determination by gas chromatography-mass spectrometry of permethylated peptides. The application of capillary columns;
J. Chromatography 268:197-206(1983).
4. Mermod N., Ramos J.L., Bairoch A., Timmis K.N.;
The xylS gene positive regulator of TOL plasmid pWWO: identification, sequence analysis and overproduction leading to constitutive expression of meta cleavage operon;
Mol. Gen. Genet. 207:349-354(1987).
[87286379]
5. Harayama S., Rekik M., Wasserfallen A., Bairoch A.;
Evolutionary relationships between catabolic pathways for aromatics: conservation of gene order and nucleotide sequences of catechol oxidation genes of pWWO and NAH7 plasmids;
Mol. Gen. Genet. 210:241-247(1987).
[88142541]
6. Bairoch A., Claverie J.-M.; Sequence patterns in protein kinases;
Nature 331:22-22(1988).
[88122534]
8. Moore J., Engleberg A., Bairoch A.;
Using PC/Gene for protein and nucleic acid analysis;
Biotechniques 6:566-572(1988).
[90198187]
9. Jongeneel C.V., Bouvier J., Bairoch A.;
A unique signature identifies a family of zinc-dependent metallopeptidases;
FEBS Letters 242:211-214(1989).
[89121072]
10. Lesk A.M., Boswell D.R., Lesk V.I., Lesk V.E., Bairoch A.;
A cross-reference table between the protein data bank of macro-molecular structures and the National Biomedical Research Foundation Protein Identification Resource amino acid sequence data bank;
Protein Seq. Data Anal. 2:295-308(1989).
[89367260]
11. Chauvaux S., Béguin P., Aubert J.-P., Bhat K.M., Gow L.A., Wood T.M., Bairoch A.;
Calcium-binding affinity and calcium-enhanced activity of Clostridium thermocellum endoglucanase D;
Biochem. J. 265:261-265(1990).
[90147577]
12. Bairoch A., Cox J.A.;
EF-hand motifs in inositol phospholipid-specific phospholipase C;
FEBS Letters 269:454-456(1990).
[90382598]
13. Bairoch A.;
SEQANALREF: a bibliographic sequence data bank;
Comp. Appl. Biosci. 7:268-268(1991).
[91283906]
14. Bairoch A.;
PROSITE: a dictionary of sites and patterns in proteins;
Nucleic Acids Res. 19:2241-2245(1991).
[91252344]
15. Bairoch A., Boeckmann B.;
The SWISS-PROT protein sequence data bank;
Nucleic Acids Res. 19:2247-2249(1991).
[91252345]
16. Bairoch A., Boeckmann B.;
SWISS-PROT;
(In) Genome analysis: from sequence to function, Collins J., Driesel A.J., Eds., pp. 151-151, Huethig Buch Verlag, Heidelberg, (1991).
17. Neidle E.L., Hartnett C., Ornston L.N., Bairoch A., Rekik M., Harayama S.;
Nucleotide sequences of the Acinetobacter calcoaceticus benABC genes for benzoate 1,2-dioxygenase reveal evolutionary relationships among multicomponent oxygenases;
J. Bacteriol. 173:5385-5395(1991).
[91358314]
18. Harayama S., Rekik M., Bairoch A., Neidle E.L., Ornston L.N.;
Potential DNA slippage structures acquired during evolutionary divergence of Acinetobacter calcoaceticus chromosomal benABC and Pseudomonas putida TOL pWW0 plasmid xylXYZ, genes encoding benzoate dioxygenase;
J. Bacteriol. 173:7540-7548(1991).
[92041666]
19. Neidle E.L., Hartnett C., Ornston L.N., Bairoch A., Rekik M., Harayama S.;
Cis-diol dehydrogeneases encoded by the TOL pWW0 plasmid xylL gene and the Acinetobacter calcoaceticus chromosomal benD gene are members of the short-chain alcohol dehydrogenase family;
Eur. J. Biochem. 204:113-120(1992).
[92155191]
20. Bairoch A.; PROSITE: a dictionary of sites and patterns in proteins;
Nucleic Acids Res. 20:2013-2018(1992).
[92285161]
21. Bairoch A., Boeckmann B.;
The SWISS-PROT protein sequence data bank;
Nucleic Acids Res. 20:2019-2022(1992).
[92285162]
22. Boguski M.S., Bairoch A., Attwood T.K., Michaels G.S.;
Prot-vav and gene expression;
Nature 358:113-113(1992).
[92310585]
23. Hochstrasser D.F., Frutiger S., Paquet N., Bairoch A., Ravier F., Pasquali C., Sanchez J.-C., Tissot J.-D., Bjellqvist B., Vargas R., Appel R.D., Hughes G.J.;
Human liver protein map: a reference database established by microsequencing and gel comparison;
Electrophoresis 13:992-1001(1992).
[93162045]
24. Brevario F., d'Aniello E.M., Golay J., Peri G., Bottazi B., Bairoch A., Saccone S., Marzella R., Predazzi V., Rocchi M., Della Valle G., Dejana E., Mantovani A., Introna M.;
Interleukin-1-inducible genes in endothelial cells. Cloning of a new gene related to C-reactive protein and serum amyloid P component;
J. Biol. Chem. 267:22190-22197(1992).
[93054498]
25. Henrissat B., Bairoch A.;
New families in the classification of glycosyl hydrolases based on amino acid sequence similarities;
Biochem. J. 293:781-788(1993).
[93356744]
26. Scherly D., Nouspikel T., Corlet J., Ucla C., Bairoch A., Clarkson S.G.;
Complementation of xeroderma pigmentosum group G cells by a human cDNA related to the yeast DNA repair gene RAD2;
Nature 363:182-185(1993).
[93247645]
27. Stoecklin R., Golay P., Bairoch A.;
Snake proteins and nucleic acids;
Toxicon 31:498-499(1993).
28. Appel R.D., Hochstrasser D.F., Bairoch A.;
Electrophorèse bidimensionnelle et informatique: un outil pour le diagnostic médical?;
Labolife 3:7-8(1993).
29. Reizer J., Reizer A., Bairoch A., Saier M.H. Jr.;
A diverse transketolase family that includes the recP protein of Streptococcus pneumoniae, a protein implicated in genetic recombination;
Res. Microbiol. 144:341-347(1993).
[94069049]
30. Bairoch A.;
A possible mechanism for metal-ion induced DNA-protein dissociation in a family of prokaryotic transcriptional regulators;
Nucleic Acids Res. 21:2515-2515(1993).
[93281406]
31. Bairoch A., Boeckmann B.;
The SWISS-PROT protein sequence data bank, recent developments;
Nucleic Acids Res. 21:3093-3096(1993).
[93324414]
32. Bairoch A.;
The PROSITE dictionary of sites and patterns in proteins, its current status;
Nucleic Acids Res. 21:3097-3103(1993).
[93324415]
33. Bairoch A.;
The ENZYME data bank;
Nucleic Acids Res. 21:3155-3156(1993).
[93324422]
34. Langevin E., Bairoch A., Appel R.D., Rialle V., Scherrer J.-R., Hochstrasser D.F.;
ExPASy: un système expert pour l'analyse de séquences protéiques;
Technologie et Santé 14:72-81(1993).
35. Golaz O., Hughes G.J., Frutiger S., Paquet N., Bairoch A., Pasquali C., Sanchez J.-C., Tissot J.-D., Appel R.D., Walzer C., Balant L., Hochstrasser D.F.;
Plasma and red blood cell protein maps: the 1993 update;
Electrophoresis 14:1223-1231(1993).
[94147970]
36. Hughes G.J., Frutiger S., Paquet N., Pasquali C., Sanchez J.-C., Tissot J.-D., Bairoch A., Appel R.D., Hochstrasser D.F.;
Human liver protein map: the 1993 update;
Electrophoresis 14:1216-1222(1993).
[94147969]
37. Appel R.D., Sanchez J.-C., Bairoch A., Golaz O., Miu M., Pasquali C., Reynaldo Vargas J., Hughes G.J., Hochstrasser D.F.;
SWISS-2DPAGE: a database of two-dimensional gel electrophoresis images;
Electrophoresis 14:1232-1238(1993).
[94147971]
38. Reizer J., Buskirk S., Bairoch A., Reizer A., Saier M.H. Jr.;
A novel zinc-binding motif found in two ubiquitous deaminase families;
Protein Sci. 3:853-856(1994).
[94339846]
39. Appel R.D., Bairoch A., Hochstrasser D.F.;
A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server;
Trends Biochem. Sci. 19:258-260(1994).
[94353486]
40. Hallick R.B., Bairoch A.;
Proposals for the naming of chloroplast genes. III. Nomenclature for open reading frames encoded in chloroplast genomes;
Plant Mol. Biol. Report. 12:S29-S30(1994).
41. Bairoch A., Boeckmann B.;
The SWISS-PROT protein sequence data bank, current status;
Nucleic Acids Res. 22:3578-3580(1994).
[95023094]
42. Appel R.D., Sanchez J.-C., Bairoch A., Golaz O., Ravier O., Pasquali C., Hughes G.J., Hochstrasser D.F.;
The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis;
Nucleic Acids Res. 22:3581-3582(1994).
[95023095]
44. Bairoch A.;
The ENZYME data bank;
Nucleic Acids Res. 22:3626-3627(1994).
[95023104]
45. Doelz R., Mosse M.-O., Slonimski P.P., Bairoch A., Linder P.;
LISTA, LISTA-HOP and LISTA-HON: a comprehensive compilation of protein encoding sequences and its associated homology databases from the yeast Saccharomyces;
Nucleic Acids Res. 22:3459-3461(1994).
[95023072]
46. Bucher P., Bairoch A.;
A generalized profile syntax for biomolecular sequences motifs and its function in automatic sequence interpretation;
(In) ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology. Altman R., Brutlag D., Karp P., Lathrop R., Searls D., Eds., pp. 53-61, AAAI Press, Menlo Park, (1994).
[96039003]
47. Bork P., Bairoch A.;
Extracellular protein modules: a proposed nomenclature;
Trends Biochem. Sci. 20:Special poster supplement(1995).
48. Hochstrasser D.F., Appel R.D., Golaz O., Pasquali C., Sanchez J.-C., Bairoch A.;
Sharing of worldwide spread knowledge using hypermedia facilities and fast communication protocols (Mosaic and World Wide Web): the example of ExPASy;
Meth. Inform. Med. 34:75-78(1995).
[97227852]
50. Bairoch A., Apweiler R.;
The SWISS-PROT protein sequence data bank and its new supplement TrEMBL;
Nucleic Acids Res. 24:21-25(1996).
[96174589]
51. Bairoch A., Bucher P., Hofmann K.;
The PROSITE database, its status in 1995;
Nucleic Acids Res. 24:189-196(1996).
[96174628]
52. Bairoch A.;
The ENZYME data bank in 1995;
Nucleic Acids Res. 24:221-222(1996).
[96174636]
53. Appel R.D., Sanchez J.-C., Bairoch A., Golaz O., Ravier F., Pasquali C., Hughes G.J., Hochstrasser D.F.;
The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis, its status in 1995;
Nucleic Acids Res. 24:180-181(1996).
[96174626]
54. Doelz R., Mosse M.-O., Slonimski P.P., Bairoch A., Linder P.;
LISTA, LISTA-HOP and LISTA-HON: a comprehensive compilation of protein encoding sequences and its associated homology databases from the yeast Saccharomyces;
Nucleic Acids Res. 26:50-52(1996).
[96174596]
55. Appel R.D, Bairoch A., Sanchez J.-C., Vargas J.R., Golaz O., Pasquali C., Hochstrasser D.F.;
Federated two-dimensional database: a simple means of publishing two-dimensional electrophoresis data;
Electrophoresis 17:540-546(1996).
[96314058]
56. Pasquali C., Frutiger S., Wilkins M.R., Hughes G.J., Appel R.D., Bairoch A., Schaller D., Sanchez J.-C., Hochstrasser D.F.
Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database;
Electrophoresis 17:547-555(1996).
[96314059]
57. Sanchez J.-C., Golaz O., Frutiger S., Schaller D., Appel R.D., Bairoch A., Hughes G.J., Hochstrasser D.F.;
The yeast SWISS-2DPAGE database;
Electrophoresis 17:556-565(1996).
[96314060]
58. Henrissat B., Bairoch A.;
Updating the sequence-based classification of glycosyl hydrolases;
Biochem. J. 316:695-696(1996).
[96257770]
59. Bork P., Bairoch A.;
Go hunting in sequence databases, but watch out for the traps;
Trends Genet. 12:425-427(1996).
[97065647]
60. Wilkins M.R., Hochstrasser D.F., Sanchez J-.C., Bairoch A., Appel R.D.
Integrating two-dimensional gel databases using the Melanie II software;
Trends Biochem. Sci. 21:496-497(1996).
[97162990]
61. Bairoch A., Apweiler R.;
The SWISS-PROT protein sequence data bank and its supplement TrEMBL;
Nucleic Acids Res. 25:31-36(1997).
[97169356]
62. Bairoch A., Bucher P., Hofmann K.;
The PROSITE database, its status in 1997;
Nucleic Acids Res. 25:217-221(1997).
[97169396]
63. Wilkins M.R., Lindskog I., Gasteiger E., Bairoch A., Sanchez J.-C., Hochstrasser D.F., Appel R.D.;
Detailed peptide characterization using PEPTIDEMASS - a World-Wide-Web accessible tool;
Electrophoresis 18:403-408(1997).
[97295276]
64. Bairoch A., Apweiler R.;
The SWISS-PROT protein sequence database: its relevance to human molecular medical research;
J. Mol. Med. 75:312-316(1997).
[97325419]
65. Freiberg C., Fellay R., Bairoch A., Broughton W.J., Rosenthal A., Perret X.;
Molecular basis of symbiosis between Rhizobium and legumes;
Nature 387:394-401(1997).
[97305956]
66. Apweiler R., Gateau A., Contrino S., Martin M.J., Junker V., O'Donovan C., Lang F., Mitaritonna N., Kappus S., Bairoch A.;
Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT + TREMBL;
(In) ISMB-97; Proceedings 5th International Conference on Intelligent Systems for Molecular Biology, pp. 33-43, AAAI Press, Menlo Park, (1997).
[97463228]
67. Bairoch A.;
Proteome databases;
(In) Proteome research: new frontiers in functional genomics, Wilkins M.R., Williams K.L, Appel R.D., Hochstrasser D.F., Eds., pp. 93-132, Springer Verlag, Heidelberg, (1997).
[ISBN: 3-540-62775-8]
68. Bairoch A., Appel R.D., Peitsch M.C.;
The ExPASY WWW server - a tool for proteome research;
Protein Data Bank Quat. Newsletter 81:5-7(1997).
[Full text]
69. Mackenzie P.I., Owens I.S., Burchell B., Bock K.W., Bairoch A., Belanger A., Fournel-Gigleux S., Green M., Hum D.W., Iyanagi T., Lancet D., Louisot P., Magdalou J., Chowdhury J.R., Ritter J.K., Schachter H., Tephly T.R., Tipton K.F., Nebert D.W.;
The UDP glycosyltransferase gene superfamily: recommended nomenclature update based on evolutionary divergence;
Pharmacogenetics 7:255-269(1997).
[97439498]
70. Bairoch A., Murzin A.G. [Editorial];
Sequences and topology: predicting evolution;
Curr. Opin. Struct. Biol. 7:367-368(1997).
[PMID:9218409]
71. Gallegos M.T., Schleif R., Bairoch A., Hofmann K., Ramos J.L.;
AraC/XylS family of transcriptional regulators;
Microbiol. Mol. Biol. Rev. 61:393-410(1997).
[98073559]
73. Bairoch A., Apweiler R.;
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998;
Nucleic Acids Res. 26:38-42(1998).
[98062389]
74. Horn F., Weare J., Beukers M.W., Hoersch S., Bairoch A., Chen W., Edvardsen O., Campagne F., Vriend G.;
GPCRDB: an information system for G protein-coupled receptors;
Nucleic Acids Res. 26:277-281(1998).
[98062445]
75. Hoogland C., Sanchez J.-C., Tonella L., Bairoch A., Hochstrasser D.F., Appel R.D.;
Current status of the SWISS-2DPAGE database;
Nucleic Acids Res. 26:332-333(1998).
[98062460]
76. Duret L., Guex N., Peitsch M.C., Bairoch A.;
New insulin-like proteins with atypical disulfide bond pattern characterized in Caernorhabditis elegans by comparative sequence analysis and homology modelling;
Genome Res. 8:348-353(1998).
[98217375]
77. Rudd K.E., Humphery-Smith I., Wasinger V.C., Bairoch A.;
Low molecular weight proteins: a challenge for post-genomic research;
Electrophoresis 19:536-544(1998).
[98248213]
78. Doerks T., Bairoch A., Bork P.;
Protein annotation: detective work for function prediction;
Trends Genet. 14:248-250(1998).
[98299164]
79. Wilkins M.R., Gasteiger E., Tonella L., Ou K., Tyler M., Sanchez J.-C., Gooley A.A., Walsh B.J., Bairoch A., Appel R.D., Williams K.L., Hochstrasser D.F.;
Protein identification with N- and C-terminal sequence tags in proteome projects;
J. Mol. Biol. 278:599-608(1998).
[98263247]
80. Wilkins M.R., Gasteiger E., Sanchez J.-C., Bairoch A., Hochstrasser D.F.;
Two-dimensional gel electrophoresis for proteome projects: the effects of protein hydrophobicity and copy number;
Electrophoresis 19:1501-1505(1998).
[98357675]
81. Tonella L., Walsh B.J., Sanchez J.-C., Ou K., Wilkins M.R., Tyler M., Frutiger S., Gooley A.A., Pescaru I., Appel R.D., Yan J.X., Bairoch A., Hoogland C., Morch F.S., Hughes G.J., Williams K.L., Hochstrasser D.F.;
'98 Escherichia coli SWISS-2DPAGE database update;
Electrophoresis 19:1960-1971(1998).
[98410772]
82. Galperin M.Y., Bairoch A., Koonin E.V.;
A superfamily of metalloenzymes unifies phosphopentomutase and cofactor-independent phosphoglycerate mutase with alkaline phosphatases and sulfatases;
Protein Sci. 7:1829-1835(1998).
[99180418]
83. Appel R.D., Bairoch A., Hochstrasser D.F.;
2-D databases on the World Wide Web;
(In) 2-D Protein Proteome Analysis Protocols, Link A.J., Ed., pp. 383-392, Humana Press, Totowa, (1998).
[99151325]
84. Appel R.D., Hoogland C., Bairoch A., Hochstrasser D.F.;
Constructing a 2-D database for the World Wide Web;
(In) 2-D Protein Proteome Analysis Protocols, Link A.J., Ed., pp. 411-416, Humana Press, Totowa, (1998).
[99151327]
85. Wilkins M.R., Gasteiger E., Bairoch A., Sanchez J.C., Williams K.L., Appel R.D., Hochstrasser D.F.;
Protein identification and analysis tools in the ExPASy server;
(In) 2-D Protein Proteome Analysis Protocols, Link A.J., Ed., pp. 531-552, Humana Press, Totowa, (1998).
[99151337]
86. Wilkins M.R., Gasteiger E., Wheeler C., Lindskog I., Sanchez J.-C., Bairoch A., Appel R.D., Dunn M.D., Hochstrasser D.F.;
Multiple parameter cross-species protein identification using MultiIdent - a world-wide web accessible tool;
Electrophoresis 19:3199-3206(1998).
[99129595]
87. Kasai H., Watanabe K., Gasteiger E., Bairoch A., Isono K., Yamamoto S., Harayama S.;
Construction of the gyrB database for Identification and Classification of Bacteria;
(In) Genome Informatics 1998, Miyano S., Takagi T., Eds., pp. 13-21, Universal Academy Press Inc.. Tokyo (1998). [ISBN 4-946443-52-5]
[11072317]
88. Bairoch A., Apweiler R.;
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999;
Nucleic Acids Res. 27:49-54(1999).
[99063650]
89. Hofmann K., Bucher P., Falquet L., Bairoch A.;
The PROSITE database, its status in 1999;
Nucleic Acids Res. 27:215-219(1999).
[99063695]
90. Hoogland C., Sanchez J.-C., Tonella L., Bairoch A., Hochstrasser D.F., Appel R.D.;
The SWISS-2DPAGE database: what has changed during the last year;
Nucleic Acids Res. 27:289-291(1999).
[99063715]
91. Bairoch A.;
The ENZYME data bank in 1999;
Nucleic Acids Res. 27:310-311(1999).
[99063723]
92. Binz P.-A., Wilkins M.R., Gasteiger E., Bairoch A., Appel R.D., Hochstrasser D.F.;
Internet resources for protein identification and characterization;
(In) Microcharacterization of proteins (Second edition), Kellner R., Lottspeich F., Meyer H.E., Eds., pp.277-299, Wiley-VCH, (1999).
[ISBN: 3-527-30084-8]
93. Wilkins M.R., Gasteiger E., Gooley A.A., Herbert B.R., Molloy M.P., Binz P.-A., Ou K., Sanchez J.-C., Bairoch A., Williams K.L., Hochstrasser D.F.;
High-throughput mass spectrometric discovery of protein post-translational modifications;
J. Mol. Biol. 289:645-657(1999).
[99286293]
94. Binz P.-A., Mueller M., Walther D., Bienvenut W.V., Gras R., Hoogland C., Bouchet G., Gasteiger E., Fabbretti R., Gay S., Palagi P, Wilkins M.R.,
Rouge V, Tonella L., Paesano S., Rossellat G., Karmime A., Bairoch A., Sanchez J.-C., Appel R.D., Hochstrasser D.F.;
A molecular scanner to highly automate proteomic research and to display proteome images;
Anal. Chem. 71:4981-4988(1999).
[20030525]
95. Chen H., Rossier C., Morris M.A., Scott H.S., Gos A., Bairoch A., Antonarakis S.E.;
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;
Hum. Genet. 105:399-409(1999).
[20065863]
96. Gras R., Mueller M., Gasteiger E., Gay S., Binz P.-A., Bienvenut W., Hoogland C., Sanchez J.-C., Bairoch A., Hochstrasser D.F., Appel R.D.;
Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection;
Electrophoresis 20:3535-3550(1999).
[20077527]
97. Vasiliou V., Bairoch A., Tipton K.F., Nebert D.W.;
Eukaryotic aldehyde dehydrogenase (ALDH) genes: human polymorphisms, and recommended nomenclature based on divergent evolution and chromosomal mapping;
Pharmacogenetics 9:421-434(1999).
[20242562]
98. Junker V.L., Apweiler R., Bairoch A.;
Representation of functional information in the SWISS-PROT data bank;
Bioinformatics 15:1066-1067(1999).
[20210096]
99. Bairoch A., Apweiler R.;
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000;
Nucleic Acids Res. 28:45-48(2000).
[20063212]
100. Bairoch A.;
The ENZYME database in 2000;
Nucleic Acids Res. 28:304-305(2000).
[20063289]
102. Bairoch A.;
Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times!;
Bioinformatics 16:48-64(2000).
[20272357]
103. Linder P., Gasteiger E., Bairoch A.;
A comprehensive web resource on RNA helicases from the baker's yeast Saccharomyces cerevisiae;
Yeast 16:507-509(2000).
[20253515]
104. Abola E.E., Bairoch A., Barker W.C., Beck S., Benson D.A., Berman H., Cameron G., Cantor C., Doubet S., Hubbard T.J.P., Jones T.A.,
Kleywegt G.J., Kolaskar A.S., Van Kuik A., Lesk A.M., Mewes H.-W., Neuhaus D., Pfeiffer F., TenEyck L.F., Simpson R.J., Stoesser G.,
Sussman J.L., Tateno Y., Tsugita A., Ulrich E.L., Vliegenthart J.F.G.;
Quality control in databanks for molecular biology;
BioEssays 22:1024-1034(2000).
[11056479]
105. Apweiler R., Attwood T.K., Bairoch A., Bateman A., Birney E., Biswas M.,
Bucher P., Cerutti L., Corpet F., Croning M.D., Durbin R., Falquet L., Fleischmann W.,
Gouzy J., Hermjakob H., Hulo N., Jonassen I., Kahn D., Kanapin A., Karavidopoulou Y.,
Lopez R., Marx B., Mulder N.J., Oinn T.M., Pagni M., Servant F., Sigrist C.J.,
Zdobnov E.M.;
InterPro -- an integrated documentation resource for protein families, domains and functional sites;
Bioinformatics 16:1145-1150(2000).
[11159333]
106. Apweiler R., Attwood T.K., Bairoch A., Bateman A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M.D., Durbin R.,
Falquet L., Fleischmann W., Gouzy J., Hermjakob H., Hulo N., Jonassen I., Kahn D., Kanapin A., Karavidopoulou Y., Lopez R., Marx B.,
Mulder N.J., Oinn T.M., Pagni M., Servant F., Sigrist C.J., Zdobnov E.M.;
The InterPro database, an integrated documentation resource for protein families, domains and functional sites;
Nucleic Acids Res 29:37-40(2001).
[11125043]
107. Jung E., Veuthey A.-L., Gasteiger E., Bairoch A.;
Annotations of glycoproteins in the SWISS-PROT database;
Proteomics 1:262-268(2001).
[11680872]
108. O'Donovan C., Apweiler R., Bairoch A.;
The human proteomics initiative (HPI);
Trends Biotechnol. 19:178-181(2001).
[11301130]
109. Gasteiger E., Jung E., Bairoch A.;
SWISS-PROT: connecting biomolecular knowledge via a protein database;
Curr. Issues Mol. Biol. 3:47-55(2001).
[11488411]
110. Apweiler R., Kersey P., Junker V., Bairoch A.;
Technical comment to "database verification studies of SWISS-PROT and GenBank" by Karp et Al.
Bioinformatics 17:533-534(2001).
[11395430]
111. Falquet L., Pagni M., Bucher P., Hulo N., Sigrist C.J.A., Hofmann K., Bairoch A.;
The PROSITE database, its status in 2002;
Nucleic Acids Res. 30:235-238(2002).
[11752303]
112. Monigatti F., Gasteiger E., Bairoch A., Jung E.;
The Sulfinator: a novel tool to predict tyrosine sulfation sites in protein sequences;
Bioinformatics 18:769-770(2002).
[12050077]
113. Mulder N.J., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D.,
Biswas M., Bradley P., Bork P., Bucher P., Copley R., Courcelle E.,
Durbin R., Falquet L., Fleischmann W., Gouzy J., Griffith-Jones S., Haft D.,
Hermjakob H., Hulo N., Kahn D., Kanapin A., Krestyaninova M., Lopez R.,
Letunic I., Pagni M., Peyruc D., Ponting C.P., Servant F., Sigrist C.J.A.;
InterPro - an integrated documentation resource for protein families, domains and functional sites;
Briefings Bioinform. 3:225-235(2002).
[12230031]
114. Sigrist C.J.A. Cerutti L., Hulo N., Gattiker A., Falquet L., Pagni M., Bairoch A., Bucher P.;
PROSITE, a documented database using patterns and profiles as motif descriptors;
Briefings Bioinform. 3:265-274(2002).
[12230035]
115. O'Donovan C., Martin M.-J., Gattiker A., Gasteiger E., Bairoch A., Apweiler R.;
High quality protein knowledge resource, Swiss-Prot and TrEMBL;
Briefings Bioinform. 3:275-284(2002).
[12230036]
116. Gattiker A., Gasteiger E., Bairoch A.;
ScanProsite: a reference implementation of a PROSITE scanning tool;
Applied Bioinform. 1:107-108(2002).
[15130850]
117. Appel R.D., Bairoch A.;
The application of bioinformatics to mass spectrometry [Editorial];
Proteomics 2:1363-1364(2002).
[12422353]
118. Gattiker A., Bienvenut W.V., Bairoch A., Gasteiger E.;
FindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification;
Proteomics 2:1435-1444(2002).
[12422360]
119. Vargas Altamirano R., Balderrama J.R., Hoogland C., Gasteiger E., Ivanyi I., Bairoch A., Appel R.D., Hochstrasser D.F.;
El nuovo servidor Latinoamericano de biologia molecular de la UCB: bo.expasy.org;
Acta Nova 2:72-81(2002).
120. Boeckmann B., Bairoch A., Apweiler R., Blatter M.-C., Estreicher A., Gasteiger E., Martin M.J., Michoud K., O'Donovan C., Phan I., Pilbout S., Schneider M.;
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2003;
Nucleic Acids Res. 31:354-370(2003).
[12520024]
121. Mulder N.J., Apweiler R., Attwood T.K., Bairoch A., Barrell D.,
Bateman A., Binns D., Biswas M., Bradley P., Bork P., Bucher P., Copley R.R., Courcelle E., Das U., Durbin R., Falquet L.,
Fleischmann W., Griffiths-Jones S., Haft D., Harte N., Hulo N., Kahn D., Kanapin A., Krestyaninova M., Lopez R., Letunic I.,
Lonsdale D., Silventoinen V., Orchard S.E., Pagni M., Peyruc D., Ponting C.P., Selengut J.D., Servant F., Sigrist C.J.A., Vaughan R., Zdobnov E.M.;
The InterPro Database, 2003 brings increased coverage and new features;
Nucleic Acids Res. 31:315-318(2003).
[12520011]
122. Gattiker A., Michoud K., Rivoire C., Auchincloss A.H., Coudert E., Lima T., Kersey P., Pagni M., Sigrist C.J.A., Lachaize C., Veuthey A.-L., Bairoch A.;
Automatic annotation of microbial proteomes in Swiss-Prot;
Comput. Biol. Chem. 27:49-58(2003).
[12798039]
123. Peeters H., Debeer P., Bairoch A., Wilquet V., Huysmans C., Parthoens E., Fryns J.-P., Nakamura Y., Niikawa N., Van de Ven W., Devriendt K.;
PA26 is a candidate gene for heterotaxia in humans: identification of a novel PA26-related gene family in human and mouse;
Human Genet. 112:573-580(2003).
[12607115]
124. Gasteiger E., Gattiker A., Hoogland C., Ivanyi I., Appel R.D., Bairoch A.;
ExPASy - the proteomics server for in-depth protein knowledge and analysis;
Nucleic Acids Res. 31:3784-3788(2003).
[12824418]
125. Phan I.Q.H., Pilbout S.F., Fleischmann W., Bairoch A.;
Newt, a new taxonomy portal;
Nucleic Acids Res. 31:3822-3823(2003).
[12824428]
126. Baillie Gerritsen V., Bairoch A.;
Protein databases;
(In) Nature Encyclopedia of the Human Genome; pp4:785-791, Nature Publishing Group, London (2003).
127. Apweiler R., Bairoch A., Wu C.H., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., Martin M.J., Natale D.A., O'Donovan C., Redaschi N., Yeh L.S.;
UniProt: the Universal Protein knowledgebase;
Nucleic Acids Res. 32:D115-D119(2004).
[14681372]
128. Hulo N., Sigrist C.J., Le Saux V., Langendijk-Genevaux P.S., Bordoli L., Gattiker A., De Castro E., Bucher P., Bairoch A.;
Recent improvements to the PROSITE database;
Nucleic Acids Res. 32:D134-D137(2004).
[14681377]
129. Fleischmann A., Darsow M., Degtyarenko K., Fleischmann W., Boyce S., Axelsen K.B., Bairoch A., Schomburg D., Tipton K.F., Apweiler R.;
IntEnz, the integrated relational enzyme database;
Nucleic Acids Res. 32:D434-D437(2004).
[14681451]
130. Hermjakob H., Montecchi-Palazzi L., Lewington C., Mudali S., Kerrien S., Orchard S., Vingron M., Roechert B., Roepstorff P., Valencia A., Margalit H., Armstrong J., Bairoch A., Cesareni G., Sherman D., Apweiler R.;
IntAct: an open source molecular interaction database;
Nucleic Acids Res. 32:D452-D455(2004).
[14681455]
131. Yip L., Famiglietti L.M., Gasteiger E., Bairoch A.;
Protein variations: resources and tools;
(In) Biomedical application of proteomics, Hochstrasser D.F., Corthals G., Sanchez J.-C., Eds, pp.389-421, Wiley-VCH (2004).
132. Apweiler R., Bairoch A., Wu C.H.;
Protein sequence databases;
Curr. Opin. Chem. Biol. 8:76-80(2004).
[15036160]
133. Yip L., Scheib H., Diemand A.V., Gattiker A., Famiglietti L.M., Gasteiger E., Bairoch A.;
The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants;
Hum. Mutat. 23:464-470(2004).
[15108278]
134. Bairoch A., Boeckmann B., Ferro S., Gasteiger E.;
Swiss-Prot: juggling between evolution and stability;
Briefings Bioinform. 5:39-55(2004).
[15153305]
135. Appel R., Bairoch A.;
Post-translational modifications: a challenge for proteomics and bioinformatics [Editorial];
Proteomics 4:1525-1526(2004).
[15174121]
136. Farriol-Mathis N., Garavelli J.S., Boeckmann B., Duvaud S., Gasteiger E., Gateau A., Veuthey A.-L., Bairoch A.;
Annotation of post-translational modifications in the Swiss-Prot knowledgebase;
Proteomics 4:1537-1550(2004).
[15174124]
137. Rose K., Bougueleret L., Baussant T., Boehm G., Botti P., Colinge J., Cusin J., Gaertner H., Gleizes A., Heller M., Jimenez S., Johnson A., Kussmann M., Menin L., Menzel C., Ranno F., Rodriguez-Tome P., Rogers J., Saudrais C., Villain M., Wetmore D., Bairoch A., Hochstrasser D.F.;
Industrial-scale proteomics: from liters of plasma to chemically synthesized proteins;
Proteomics 4:2125-2150(2004).
[15221774]
138. Nakamura K., Aebersold R., Bairoch A., Dunn M., Celis J., Hanash S., Hochstrasser D.F., Humphrey-Smith I., James P., Klose J., LaBaer J., Langen H., Mann M., Parekh R., Patterson S., Pearce C., Roepstorff P., Simpson R.J., Tomlinson I., Tsugita A., Yates J.;
From genome to proteome - aim of human proteomics [In Japanese];
Seikagaku 76:1271-1274(2004).
[15580857]
139. Schneider M., Tognolli M., Bairoch A.;
The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools;
Plant Physiol. Biochem. 42:1013-1021(2004).
[15707838]
140. Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., Bairoch A.;
Protein identification and analysis tools on the ExPASy server;
(In) The Proteomics Protocols Handbook, Walker J.M., Eds, pp573-609, Humana Press Inc (2005).
141. Bairoch A., Apweiler R., Wu C.H., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., Martin M.J., Natale D.A., O'Donovan C., Redaschi N., Yeh L.-S.;
The Universal Protein Resource (UniProt);
Nucleic Acids Res. 33:D154-D159(2005).
[15608167]
142. Mulder N.J., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., Bradley P., Bork P., Bucher P., Cerutti L., Copley R., Courcelle E., Das U., Durbin R., Fleischmann W., Gough J., Haft D., Harte N., Hulo N., Kahn D., Kanapin A., Krestyaninova M., Lonsdale D., Lopez R., Letunic I., Madera M., Maslen J., McDowall J., Mitchell A., Nikolskaya A.N., Orchard S., Pagni M., Ponting C.P., Quevillon E., Selengut J., Sigrist C.J.A., Silventoinen V., Studholme D.J., Vaughan R., Wu C.H.;
InterPro, progress and status in 2005;
Nucleic Acids Res. 33:D201-D205(2005).
[15608177]
143. Jungo F., Bairoch A.;
Tox-Prot, the toxin protein annotation project of the Swiss-Prot protein knowledgebase;
Toxicon 45:293-301(2005).
[15683867]
144. Schneider M., Bairoch A., Wu C.H., Apweiler R.;
Plant protein annotation in the UniProt knowledgebase;
Plant Physiol. 138:59-66(2005).
[15888679]
145. Sigrist C.J., De Castro E., Langendijk-Genevaux P.S., Le Saux V., Bairoch A., Hulo N.;
ProRule: a new database containing functional and structural information on PROSITE profiles;
Bioinformatics 21:4060-4066(2005).
[16091411]
146. Boeckmann B., Blatter M.-C., Famiglietti L., Hinz U., Lane L., Roechert B., Bairoch A.;
Protein variety and functional diversity: Swiss-Prot annotation in its biological context;
C. R. Biologies 328:882-899(2005).
[16286078]
147. Sigrist C.J., De Castro E., Langendijk-Genevaux P.S., Le Saux V., Bairoch A., Hulo N.;
Functionally and structurally relevant residues in PROSITE motif descriptors;
(In) Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Wiley (2005).
148. Wu C.H., Apweiler R., Bairoch A., Natale D.A., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., Martin M.J., Mazumder R., O'Donovan C., Redaschi N., Suzek B.;
The Universal Protein Resource (UniProt): an expanding universe of protein information;
Nucleic Acids Res. 34:D187-D191(2006).
[16381842]
149. Hulo N., Bairoch A., Bulliard V., Cerutti L., De Castro E., Langendijk-Genevaux P.S., Pagni M., Sigrist C.J.;
The PROSITE database;
Nucleic Acids Res. 34:D227-D230(2006).
[16381852]
150. Bairoch A., Schrenzel J.;
Small can be beautiful, but it remains complex! [Editorial];
ComPlexUs 2:V-VI(2006).
151. de Castro E., Sigrist C.J., Gattiker A., Bulliard V., Langendijk-Genevaux P.S., Gasteiger E., Bairoch A., Hulo N.;
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins;
Nucleic Acids Res. 34:W362-W365(2006).
[16845026]
152. Lisacek F., Hoogland C., Bougueleret L., Bairoch A.;
Data integration in Proteomics;
(In) Proteome research: concepts, technology and applications, Wilkins M.R., Appel R.D., Williams K.L, Hochstrasser D.F., Eds., pp. 145-168, Springer Verlag, Heidelberg, (2007).
153. Mulder N.J., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., Bork P., Buillard V., Cerutti L., Copley R., Courcelle E., Das U., Daugherty L., Dibley M., Finn R., Fleischmann W., Gough J., Haft D., Hulo N., Hunter S., Kahn D., Kanapin A., Kejariwal A., Labarga A., Langendijk-Genevaux P.S., Lonsdale D., Lopez R., Letunic I., Madera M., Maslen J., McAnulla C., McDowall J., Mistry J., Mitchell A., Nikolskaya A.N., Orchard S., Orengo C., Petryszak R., Selengut J.D., Sigrist C.J., Thomas P.D., Valentin F., Wilson D., Wu C.H., Yeats C.;
New developments in the InterPro database;
Nucleic Acids Res. 35:D224-D228(2007).
[17202162]
154. Hulo N., Bairoch A., Bulliard V., Cerutti L., Cuche B.A., de Castro E., Lachaize C., Langendijk-Genevaux P.S., Sigrist C.J.;
The 20 years of PROSITE;
Nucleic Acids Res. 36:D245-D249(2008).
[18003654]
155. Yip Y.L., Famiglietti M., Gos A., Duek P.D., David F.P., Gateau A., Bairoch A.;
Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase;
Hum Mutat. 29:361-366(2008).
[18175334]
156. Mons B., Ashburner M., Chichester C., van Mulligen E., Weeber M., den Dunnen J., van Ommen G.J., Musen M., Cockerill M., Hermjakob H., Mons A., Packer A., Pacheco R., Lewis S., Berkeley A., Melton W., Barris N., Wales J., Meijssen G., Moeller E., Roes P.J., Borner K., Bairoch A.
Calling on a million minds for community annotation in WikiProteins;
Genome Biol. 9:R89-R89(2008).
[18507872]
157. Hinz U., Bairoch A.
The impact of 3D structures on a protein knowledgebase: from proteins to systems;
(In) Structural Proteomics and its Impact on the Life Sciences, Sussman J.L., Silman I., Eds., pp. 51-78, World Scientific Publishing, Singapore, (2008).
158. Bairoch A.
UniProtKB/Swiss-Prot: new and future developments;
(In) Data Integration in the Life Sciences, Proceedings of the 5th International Workshop, DILS 2008, Bairoch A., Cohen-Boulakia S., Froidevaux C., Eds., pp. 204-206, Springer Verlag, Heidelberg, (2008).
Other publications
156. Bairoch A., Apweiler R., Wu C.H.;
UniProt knowledgebase: Swiss-Prot and TrEMBL user manual;
Release 13.0 of February 2008;
Swiss Institute of Bioinformatics and European Bioinformatics Institute.
[Full text]
160. Bairoch A., Hulo N., Sigrist C.J.A.;
The PROSITE database of protein families and domains user manual;
Release 19, April 2005;
Swiss Institute of Bioinformatics.
[Full text]
161. Bairoch A., Axelsen K.;
The ENZYME nomenclature database user manual;
Release 39, February 2006;
Swiss Institute of Bioinformatics.
[Full text]
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