L. Bougueleret

发表

New and continuing developments at PROSITE

Alan Bridge, Lydie Bougueleret, Ioannis Xenarios, 2012, Nucleic Acids Res..

High‐performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics

A. Masselot, J. Colinge, L. Bougueleret, 2004, Proteomics.

Experiments in searching small proteins in unannotated large eukaryotic genomes.

J. Colinge, L. Bougueleret, Isabelle Cusin, 2005, Journal of proteome research.

Toward interoperable bioscience data

Anne E. Trefethen, Catherine A. Shang, Gully A. Burns, 2012, Nature Genetics.

In vitro and in silico processes to identify differentially expressed proteins

Patricia Rodriguez-Tomé, Eduardo Gonzalez-Couto, Catherine Jeandenans, 2004, Proteomics.

Bacterial Virus Ontology; Coordinating across Databases

I. Xenarios, S. Poux, L. Bougueleret, 2017, Viruses.

Continuum of overlapping clones spanning the entire human chromosome 21q

X. Estivill, D. Cox, J. Weissenbach, 1992, Nature.

Genetic and physiological data implicating the new human gene G72 and the gene for d-amino acid oxidase in schizophrenia

P. Sham, L. Cavarec, R. Straub, 2002, Proceedings of the National Academy of Sciences of the United States of America.

UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View.

I. Xenarios, S. Poux, A. Bridge, 2016, Methods in molecular biology.

The candidate gene for the X-linked Kallmann syndrome encodes a protein related to adhesion molecules

J. Weissenbach, D. Paslier, J. Claverie, 1991, Cell.

An Integrated Ontology Resource to Explore and Study Host-Virus Relationships

Alan Bridge, Ioannis Xenarios, Jane Lomax, 2014, PloS one.

Rhea—a manually curated resource of biochemical reactions

Christoph Steinbeck, Hong Cao, Anne Morgat, 2011, Nucleic Acids Res..

Updates in Rhea – an expert curated resource of biochemical reactions

Anne Morgat, Elisabeth Coudert, Kristian B. Axelsen, 2017, Nucleic Acids Res..

K-tuple frequency analysis: from intron/exon discrimination to T-cell epitope mapping.

I Sauvaget, J. Claverie, L. Bougueleret, 1990, Methods in enzymology.

Differential proteomics via probabilistic peptide identification scores.

Jacques Colinge, Lydie Bougueleret, J. Colinge, 2005, Analytical chemistry.

Genetic Variations and Diseases in UniProtKB/Swiss-Prot: The Ins and Outs of Expert Manual Curation

Jerven T. Bolleman, I. Xenarios, S. Poux, 2014, Human mutation.

Sequence comparison of five polymerases (L proteins) of unsegmented negative-strand RNA viruses: theoretical assignment of functional domains.

N. Tordo, L. Bougueleret, O. Poch, 1990, The Journal of general virology.

The Universal Protein Resource (UniProt) in 2010

María Martín, Peter B. McGarvey, Cathy H. Wu, 2010 .

Acceleration of the pfsearch program to search PROSITE generalized profiles

I. Xenarios, L. Cerutti, M. Pagni, 2012 .

Structure and expression of hcr, a locus rearranged with c-myc in a woodchuck hepatocellular carcinoma.

M. Buendia, T. Möröy, L. Bougueleret, 1989, Oncogene.

Rare sequence motifs are common constituents of hypervariable antibody regions.

J. Claverie, L. Bougueleret, P. Kourilsky, 1987, Annales de l'Institut Pasteur. Immunology.

UniProt: the Universal Protein knowledgebase

Cathy H. Wu, Jerven T. Bolleman, Béatrice A. Cuche, 2004, Nucleic Acids Res..

Molecular Cloning of a Lipolysis-stimulated Remnant Receptor Expressed in the Liver*

L. Bougueleret, B. Bihain, P. André, 1999, The Journal of Biological Chemistry.

CAG/CTG and CGG/GCC repeats in human brain reference cDNAs: outcome in searching for new dynamic mutations.

J. Weissenbach, H. Cann, S. Meier-Ewert, 1998, Genomics.

E-box- and MEF-2-independent muscle-specific expression, positive autoregulation, and cross-activation of the chicken MyoD (CMD1) promoter reveal an indirect regulatory pathway

L. Bougueleret, P. Millasseau, B. Paterson, 1994, Molecular and cellular biology.

Frequent activation of N-myc genes by hepadnavirus insertion in woodchuck liver tumours

G. Fourel, M. Buendia, L. Bougueleret, 1990, Nature.

UniProt: the universal protein knowledgebase

Cathy H. Wu, Christian J. A. Sigrist, Jerven T. Bolleman, 2016, Nucleic Acids Research.

The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection

I. Xenarios, S. Poux, J. Lomax, 2017, PloS one.

Animal Toxins: How is Complexity Represented in Databases?

A. Bairoch, I. Xenarios, L. Bougueleret, 2010, Toxins.

Data Integration in Proteomics

F. Lisacek, C. Hoogland, A. Bairoch, 2007 .

High-level, plasmid-borne resistance to gentamicin in Streptococcus faecalis subsp. zymogenes

L. Bougueleret, F. Delbos, T. Horodniceanu, 1979, Antimicrobial Agents and Chemotherapy.

Conjugative R plasmids in Streptococcus agalactiae (group B).

L. Bougueleret, D. Bouanchaud, Y. Chabbert, 1979, Plasmid.

Dense Alu clustering and a potential new member of the NFκB family within a 90 kilobase HLA Class III segment

Lydie Bougueleret, J. Claverie, J. Jurka, 1993, Nature Genetics.

Databases and ontologies The SwissLipids knowledgebase for lipid biology

I. Xenarios, A. Bridge, L. Bougueleret, 2015 .

Characterization of the genes coding for the Eco RV restriction and modification system of Escherichia coli.

A. Tsugita, L. Bougueleret, M. Zabeau, 1984, Nucleic acids research.

Rearrangement of a common cellular DNA domain on chromosome 4 in human primary liver tumors

K. Grzeschik, L. Bougueleret, C. Bréchot, 1988, Journal of virology.

T‐immunogenic peptides are constituted of rare sequence patterns. Use in the identification of T epitopes in the human immunodeficiency virus gag protein

J. Claverie, L. Bougueleret, F. Tekaia, 1988, European journal of immunology.

Genetic and physiological data implicating the new human gene G72 and the gene for D-amino acid oxidase in schizophrenia.

P. Sham, L. Cavarec, R. Straub, 2002, Nature Reviews Genetics.

OpenFluDB, a database for human and animal influenza virus

Amos Bairoch, Lydie Bougueleret, Ioannis Xenarios, 2010, Database J. Biol. Databases Curation.

Application of text-mining for updating protein post-translational modification annotation in UniProtKB

I. Xenarios, J. Mcentyre, A. Bridge, 2013, BMC Bioinformatics.

UniProt: A hub for protein information

María Martín, Peter B. McGarvey, Y Wang, 2015 .

Activities at the Universal Protein Resource (UniProt)

María Martín, Peter B. McGarvey, Y Wang, 2013, Nucleic Acids Res..

Ongoing and future developments at the Universal Protein Resource

María Martín, Peter B. McGarvey, Y Wang, 2010, Nucleic Acids Res..

The UniProt-GO Annotation database in 2011

Rachael P. Huntley, Emily Dimmer, Yasmin Alam-Faruque, 2011, Nucleic Acids Res..

Activation of the human homologue of the Drosophila sina gene in apoptosis and tumor suppression.

D. Le Paslier, D. Israeli, L. Cazes, 1996, Proceedings of the National Academy of Sciences of the United States of America.

Isolation of 10 differentially expressed cDNAs in p53-induced apoptosis: activation of the vertebrate homologue of the drosophila seven in absentia gene.

D. Israeli, L. Cazes, L. Piouffre, 1996, Proceedings of the National Academy of Sciences of the United States of America.

Survey of CAG/CTG repeats in human cDNAs representing new genes: candidates for inherited neurological disorders.

J. Weissenbach, H. Cann, S. Meier-Ewert, 1996, Human molecular genetics.

The Gene Ontology in 2010: extensions and refinements

Giorgio Valle, Juancarlos Chan, Paul W. Sternberg, 2009, Nucleic Acids Res..

Relevance of the lariat model to the splicing of the H-2 gene family.

J. Claverie, L. Bougueleret, L Bougueleret, 1986, European journal of biochemistry.

ViralZone: a knowledge resource to understand virus diversity

Amos Bairoch, Lydie Bougueleret, Ioannis Xenarios, 2010, Nucleic Acids Res..

Hepatitis B virus DNA integration in a sequence homologous to v-erb-A and steroid receptor genes in a hepatocellular carcinoma

K. Grzeschik, A. Dejean, L. Bougueleret, 1986, Nature.

Polycystic kidney disease: The complete structure of the PKD1 gene and its protein

P. Bork, L. Bougueleret, G. Duyk, 1995, Cell.

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

Michel Schneider, Elisabeth Coudert, Kristian B. Axelsen, 2009, Database J. Biol. Databases Curation.

Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree

Ioannis Xenarios, David Dylus, Christophe Dessimoz, 2017, bioRxiv.

Nucleotide sequence and evolution of ETn elements.

P. Brûlet, L. Bougueleret, S. Wain-Hobson, 1987, Proceedings of the National Academy of Sciences of the United States of America.

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

Elisabeth Coudert, Guillaume Keller, Amos Bairoch, 2008, Nucleic Acids Res..

HAMAP in 2015: updates to the protein family classification and annotation system

Elisabeth Coudert, Guillaume Keller, Alan Bridge, 2014, Nucleic Acids Res..

The Gene Ontology: enhancements for 2011

María Martín, Juancarlos Chan, Paul W. Sternberg, 2011, Nucleic Acids Res..

ViralZone: recent updates to the virus knowledge resource

Hans Bitter, Lydie Bougueleret, Ioannis Xenarios, 2012, Nucleic Acids Res..

Activities at the Universal Protein Resource (UniProt)

Cathy H. Wu, Tony Sawford, Michel Schneider, 2014, Nucleic Acids Research.

Implications of a Fab-like structure for the T-cell receptor.

J. Claverie, L. Bougueleret, A. Prochnicka-Chalufour, 1989, Immunology today.

Industrial‐scale proteomics: From liters of plasma to chemically synthesized proteins

D. Hochstrasser, A. Bairoch, J. Colinge, 2004, Proteomics.

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

Michel Schneider, Amos Bairoch, Damien Lieberherr, 2009, Journal of proteomics.

The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases

Oliver Horlacher, Damian Szklarczyk, Christian von Mering, 2015, Nucleic Acids Res..

Variability analysis of the human and mouse T-cell receptor β chains

J. Claverie, L. Bougueleret, 2004, Immunogenetics.

Effective depletion of albumin using a new peptide‐based affinity medium

L. Bougueleret, K. Rose, T. Baussant, 2005, Proteomics.

The SwissLipids knowledgebase for lipid biology

Alan Bridge, Lydie Bougueleret, Ioannis Xenarios, 2015, Bioinform..

The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data.

Ioannis Xenarios, Sylvain Poux, Lydie Bougueleret, 2012, Toxicon : official journal of the International Society on Toxinology.

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

Christian von Mering, Ron D. Appel, Evgeny M. Zdobnov, 2014, Nucleic Acids Res..

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

Anne Morgat, Eric Coissac, Elisabeth Coudert, 2011, Nucleic Acids Res..

HAMAP in 2013, new developments in the protein family classification and annotation system

Elisabeth Coudert, Guillaume Keller, Alan Bridge, 2012, Nucleic Acids Res..

Overproduction of the EcoR V endonuclease and methylase.

L. Bougueleret, M. Zabeau, J. Botterman, 1985, Nucleic acids research.

Conjugative transfer of multiple-antibiotic resistance markers in beta-hemolytic group A, B, F, and G streptococci in the absence of extrachromosomal deoxyribonucleic acid.

L. Bougueleret, T. Horodniceanu, G. Bieth, 1981, Plasmid.

Genetic and physiological data implicating the new human gene G72 and the gene for D-amino acid oxidase in schizophrenia (vol 99, pg 13675, 2002)

P. Sham, L. Cavarec, R. Straub, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Updates in Rhea—a manually curated resource of biochemical reactions

Christoph Steinbeck, Anne Morgat, Elisabeth Coudert, 2014, Nucleic Acids Res..

Objective comparison of exon and intron sequences by means of 2-dimensional data analysis methods.

I Sauvaget, J. Claverie, L. Bougueleret, 1988, Nucleic acids research.

Characterization and chromosomal assignment of a human cDNA encoding a protein related to the murine 102-kDa cadherin-associated protein (alpha-catenin).

J. Claverie, L. Bougueleret, C. Petit, 1993, Genomics.

Updates in Rhea – an expert curated resource of biochemical reactions

Anne Morgat, Elisabeth Coudert, Kristian B. Axelsen, 2016, Nucleic Acids Res..

method for selecting at least one screen for mutations, its application to a method for rapid identification of alleles of polymorphic systems and device for its implementation óoeuvre.

J. Dausset, L. Bougueleret, D. Cohen, 1991 .

Heuristic informational analysis of sequences

Jean-Michel Claverie, Lydie Bougueleret, J. Claverie, 1986, Nucleic Acids Res..

Cloning of several cDNA segments coding for human liver proteins.

F Costanzo, R. Cortese, L. Castagnoli, 1983, The EMBO journal.

The Metagenomic Pizza: a simple recipe to introduce bioinformatics to the layman

Vivienne Baillie Gerritsen, I. Xenarios, L. Bougueleret, 2016 .

Nucleic Acids Research

J. Claverie, L. Bougueleret, 2011, Nucleic Acids Research.

Rhea—a manually curated resource of biochemical reactions

I. Xenarios, C. Steinbeck, A. Bridge, 2011, Nucleic Acids Res..

The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases

Joshua L. Payne, Christian J. A. Sigrist, Brian J. Stevenson, 2015, Nucleic Acids Res..

The Universal Protein Resource (UniProt) in 2010

Baris E. Suzek, Christian J. A. Sigrist, Petra S. Langendijk-Genevaux, 2009, Nucleic Acids Res..

Conjugative R plasmids in group C and G streptococci

L. Bougueleret, T. Horodniceanu, G. Bieth, 1981, Journal of bacteriology.