The Helix research group
Research themes
Work in progress and results
Software and databases
News from Helix
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The Helix research group
  Context and situation
    Where are Rhône-Alpes, Grenoble, Lyon and Geneva ?
    Mountains all around...
    A short presentation of the french research system
  Research activities
    Comparative genomics
    Evolutionary biology
    String algorithmics
    Tree and graph algorithmics
    Data and knowledge modeling
    Sanofi-Synthélabo Recherche, Toulouse
    GenoStar consortium
    Swiss Institute of Bioinformatics (SIB)
    CEA/LCP, Grenoble
    Departamento de Ciência da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo, Brazil
    Université Joseph Fourier - CEA Grenoble - INRIA Rhône-Alpes
    Rhône-Alpes Genopole
    XRCE (Xerox Research Center Europe)
    ORIEL IST project
    CCSTI, Grenoble
    Laboratoire Adaptation et Pathogénie des Microorganismes, FRE 2620, CNRS/UJF
  Teaching activities
    Continuing education in bioinformatics
    The bioinformatics optional course of the master of computer science at university Joseph Fourier
    Group leader
      Viari, Alain
    Researchers and professors
      Daubin, Vincent
      De Jong, Hidde
      Duret, Laurent
      Gautier, Christian
      Genoud, Philippe
      Gouy, Manolo
      Gueguen, Laurent
      Kahn, Daniel
      Lobry, Jean
      Marais, Gabriel
      Mouchiroud, Dominique
      Mousset, Sylvain
      Page, Michel
      Perrière, Guy
      Rechenmann, François
      Ropers, Delphine
      Sagot, Marie-France
      Tannier, Eric
      Ziébelin, Danielle
    Software and system engineers
      Delmotte, Stéphane
      Iltis, Agnès
      Lépy, Nathalie
      Monte, Régis
      Ribes, Emma
      Spataro, Bruno
    Post-doctoral students
      Aouacheria, Abdel
      Baldazzi, Valentina
      Boyer, Frédéric
      Dufayard, Jean-François
      Penel, Simon
    PhD students
      Arigon, Anne-Muriel
      Batt, Grégory
      Calteau, Alexandra
      Descorps-Declère, Stéphane
      Drulhe, Samuel
      Khelifi, Adel
      Lacroix, Vincent
      Melo de Lima, Christelle
      Meunier, Julien
      Navratil, Vincent
      Palmeira, Leonor
      Semon, Marie
    External members
      Coissac, Eric
      Lachaize, Corinne
      Morgat, Anne
    Secretarial staff
      De Coninck, Françoise
      Pieri, Marie-Josèphe
  Former members
    Software engineers
      Bruley, Christophe
      Bruley, Stéphane
      Brun, Antoine
      Ciron, Pierre-Emmanuel
      Dupierris, Véronique
      Faroux, Gaël
      Faucherand, Gilles
      Hernandez, Céline
      Réguer, Erwan
      Silvestre, Thimothée
      Wessel, Erik
    Post-doctoral students
      Hughes, Sandrine
      Merienne, Stéphanie
      Pillet, Violaine
      Pisanti, Nadia
      Provencher, Sébastien
      Rivière-Rolland, Hélène
      Tavarès, Raquel
    PhD students
      Piganeau, Gwenaële
      Ponger, Loïc
      Proux, Denys
      Rizzon, Carène
      Thormarat, Fabienne
      Zelwer, Marina
    External members
      Dina, Jean
      Fanchon, Eric
      Métivier, Charles
      Nugues, Estelle
Research themes
  Evolution of species and gene families
    Reconciliation of species and gene trees
  Spatial organization of genomic information
  Syntaxic and functionnal genome annotation
    Markov models
    Mass spectometry (MS vs MS/MS)
    Peptide Sequence Tag (PST)
  Modeling and simulation of genetic regulatory networks
    Methods for modeling and simulation
    Aim of research
  Information extraction from texts
    Examples of sentences
Work in progress and results
  Evolution of gene and gene families
    Phylogenetic tree conciliation
  Spatial organization of genomic information
  Syntaxic and functionnal genome annotation
    From MS/MS spectra to PSTs
    From PSTs to protein identification
    From PSTs to gene localization
    Validation of PepLine
  Modeling and simulation of genetic regulatory networks
    Method for qualitative modeling and simulation
    Implementation and application of the method
    Mathematical problems in the analysis of genetic regulatory networks
    Validation of genetic regulatory networks
    Identification of genetic regulatory networks from experimental data
    Nutritional stress response of Escherichia coli and Synechocystis
  Information extraction from text
    The identification of names in a perfect world
    Identification of gene, proteins and species names
  Publications by year
  Publications by author
Software and databases
  The GenoStar integrated bioinformatics platform for exploratory genomics
  GEB: GenoExpertBacteria
  GNA: Genetic Network Analyzer
  PepLine: high throughput proteomics
  Herbs: checking the consistency of proteome annotations
  ISee: In Silico biology e-learning environment
  BOX: XML specifications of genomic data
  AROM: entity-relationship knowledge modeling
    Call for partnership
    Gene finding strategy in bacterial sequences
    How to get ISee?
    Interactive lessons
    Introducing the genetic code and the translation process
    ISee copyright notice
    Pattern matching algorithms
    Sequence alignment
    Statistical analysis of DNA sequences
    Differential features of GenoStar
    Hardware and software requirements
    How to get GenoStar?
    Overview of GNA
    Installing GNA
    Using GNA
    Copyright notice GNA
    Presentation of BOXml
    GEB Copyright notice
    GEB system requirements
    The graphical user interface
    The inference engine
    Examples of biological knowledge modeling
News from Helix
  Initiez-vous à la bioinformatique !
  Les défis de la biologie intégrative
  This website is outdated.
  Software and database releases
  Talks, seminars, poster presentations,...
  PhD and Master thesis defenses
    PhD thesis defense - Gregory Batt - February 24th - 2pm - INRIA Rhône-Alpes (Montbonnot, Grenoble, France)
    PhD thesis defense, Carène Rizzon, Université Claude Bernard (Lyon 1), September 19th, 2003
    PhD thesis defense, Frédéric Boyer, Université Joseph Fourier (Grenoble), July 9th, 2004
    PhD thesis defense, Jean-François Dufayard, Université Joseph Fourier (Grenoble), December 14th, 2004
    PhD thesis defense, Loïc Ponger, Université Claude Bernard (Lyon 1), September 16th, 2003
  Training and job opportunities
What is bioinformatics?
  A short introduction to bioinformatics
    The first genome projects
    Whole genome sequencing
    Genomic databases
    The problem of heterogeneous databases
    Searching for homology through similarity of sequences
    Finding genes in procaryotic genomes
    Finding genes in eucaryotic genomes
    Inferring gene functions from homology relationships
    The quest for gene fonction has not yet found an algorithmic solution
    Modeling and simulating gene interaction networks and metabolic pathways
    Biological data and knowlege need to be formalized
  Another, more recent, introduction to bioinformatics (in French)
    La bioinformatique, un dossier du site Interstices
  A series of five papers (in French) published by the Biofutur journal in March 2007
    Editorial of the March 2007 issue of Biofutur journal
    The abstracts of the papers
  A series of five pedagogical papers on bioinformatics
    In silico annotation of genomic sequences
    Biological data and knowledge modeling
    Modelling, analysis and simulation of gene networks
    Comparative genomic mapping in mammals
    Molecular phylogeny and evolution
  A series of nine papers published (in French) by the Biofutur journal in 2005
    Editorial of the January 2005 issue of the Biofutur journal
    The abstracts of the papers (in French)
  Interactive applets to discover some basic bioinformatics algorithms
    Recherche de gènes dans un génome bactérien
    Alignement optimal de deux séquences biologiques
  Some key terms of molecular biology and their definition (in French)
    Macro-molécules, ADN, ARN, protéine, acide aminé,...
    Gènes, génome, génomique,...
    Code génétique, traduction, ARNm, ARNt, ARNr,...
    Eucaryotes/procaryotes, exons/introns, épissage,...
    Transcription, transcriptome, puces à ADN,...
    Protéines, protéomique, structure, fonction,...
    Régulation, signaux, réseaux,...
  Bioinformatics as a research domain
    Genomic and post-genomic data and knowledge modeling
    The art of Genes - How organisms make themselves
    Gene regulation and metabolism : postgenomic computational approaches
    Error-tolerant identification of peptides in sequence databases by peptide sequence tags.
What's new in bioinformatics?
Related links
  PBIL - Pôle BioInformatique Lyonnais
  ExPASy proteomics server
  IBCP - Institute of Biology and Chemistry of Proteins
  ARTEB Rhône-Alpes - Agency for the development of medical technologies and biotechnology
  Société Française de BioInformatique (SFBI)
  EBI - European Bioinformatics Institute
  NCBI - National Center for Biotechnology Information
  NAR (Nucleic Acids Research) journal
  GIW - International Conference on Genome Informatics
  PSB - Pacific Symposium on Biocomputing
  S* Alliance - BioInformatics Education
  ISCB - International Society for Computational Biology
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