Team CSTB : Complex Systems and Translational Bioinformatics

Collaborations

From Team CSTB : Complex Systems and Translational Bioinformatics
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LBGI group

Our projects, ranging from low level molecular studies to clinical applications, require close collaborations with computer scientists and theoretical bioinformaticians (including the BFO team), and close links with researchers in experimental and medical biology, notably at the IGBMC and the Strasbourg Faculty of Medicine, to develop or improve the algorithms in the context of translational medicine.

Bioinformatics software development:

  • French Bioinformatics Institute (IFB)
  • INSTRUCT European Consortium
  • FRISBI French Consortium
  • BIP:BIP (Bayesian inference paradigm: Biology in processors) Consortium
  • GJ. Barton; Univeristy of Dundee, Scotland
  • P. Collet, N. Lachiche, P. Gançarski; ICube, Strasbourg
  • A. Dejaegere; IGBMC, Strasbourg
  • MD. Devignes; LORIA, Nancy
  • TJ. Gibson; EMBL, Heidelberg, Germany
  • DG. Higgins; University College Dublin, Ireland
  • P. Jollivet; Station Biologique de Roscoff
  • B. Klaholz; IGBMC, Strasbourg
  • P. Koehl; UC Davis, USA
  • G. Labesse; CBS, Montpellier
  • C. Marino Buslje; Uni. Buenos Aires, Argentina
  • C. Mayer; Institut Pasteur, Paris
  • D. Moras; IGBMC, Strasbourg
  • P. Pontarotti; Marseille
  • E. Pontelli; University of New Mexico, USA
  • AK. Royyuru; IBM Watson, USA
  • P. Schultz; IGBMC, Strasbourg
  • P Sempé, X. Mary; IBM France
  • A. Stoltzfus; NIST, USA
  • A. Van Dorsselaer; IPHC, Strasbourg

Database development:

  • P. Bork; EMBL, Heidelberg, Germany
  • P. Dollé; IGBMC, Strasbourg
  • W. Krezel; IGBMC, Strasbourg
  • A. Pujol; Barcelona University, Spain

Ciliopathies:

  • H. Dollfus; LGM, Strasbourg
  • JL. Mandel ; IGBMC, Strasbourg

Myopathies/AFM Décrypthon:

  • J. Laporte; IGBMC, Strasbourg
  • C. Marcelle; Melbourne University, Australia
  • T. Toursel; AFM, Paris

Retinal disease:

  • AMD Consortium (7 worldwide teams)
  • EVI-Genoret Consortium (42 European teams)
  • I. Audo; Université Pierre et Marie Curie, Paris
  • S. Bhattacharya; Inst. Ophthalmology, London, UK
  • J. Demongeot; U. Joseph Fourier, Grenoble
  • C. Grimm; Zurich, Switzerland
  • T. Léveillard; Institut de la Vision, Paris
  • J. Sahel; Institut de la Vision, Paris
  • D. Zack; John Hopkins Hospital, Baltimore USA
  • C. Zeitz; Institut de la Vision, Paris

Prostate cancer:

  • J. Abecassis, IGBMC, Strasbourg
  • M. Cecchini; University of Bern, Switzerland
  • J. Schalken; NCMLS, Nijmegen, Netherland
  • B. Wazylick; IGBMC, Strasbourg

Functional genomics data analysis:

  • TF. Baumert; UdS, Strasbourg
  • B. Bihain; Genclis SAS, Nancy
  • A. Bloch-Zupan; IGBMC, Strasbourg
  • P. Carbon; IBMC, Strasbourg
  • C. da Silva; Génoscope ; Evry
  • E. Friedrich; University of Luxembourg
  • J. Laporte; IGBMC, Strasbourg
  • V Laudet; ENS, Lyon
  • A. Marchini; University of Heidelberg, Germany
  • R. Romand; IGBMC, Strasbourg
  • M. Roux; INIST, Nancy
  • M. Sissler; IBMC, Strasbourg
  • L. Tora; IGBMC, Strasbourg
  • L. Vallar; CRP-Santé, Luxembourg

SONIC group

Department of Computer Science, Memorial University of Newfoundland, St John, Canada 
Venue du Pr Wolfgang Banzhaf dans l'équipe pendant 6 mois (d'avril 2010 à septembre 2010) pour y développer la chimie artificielle sur carte GPGPU.
Instituto de Tecnologia Quimica , Universidad Politecnica de Valencia (Espagne) 
Collaboration sur la recherche de nouvelles zéolites, avec plusieurs articles de conférence et de journaux scientifiques soumis.
Indian Institute of Technology of Kharagpur (Inde) 
avec la venue du doctorant Arijit Biswas pendant 8 mois (d'avril 2009 à décembre 2009) dans l'équipe dans le cadre d'une bourse franco-indienne Sandwitch. Un article de journal international a été soumis.
Laboratoire d'InfoRmatique en Image et Système d'informations, Université de Lyon 
co-tutelle de la thèse d'Olvier Kuhn (cf. ci-dessus).
Société PROSTEP France et Allemagne 
Thèse CIFRE d'Olivier Kuhn.
Société POLYVIONICS 
Thèse de Stéphane Querry.
Equipe Image et Calcul Parallèle Scientifique (ICPS) du LSIIT, dirigée par Philippe Clauss 
Un papier a été accepté à EuroPar'09 (Ogier et al. 2009b).
Projet INRIA ALEA, Centre de Recherche Bordeaux Sud Ouest et Service ORL de l'Hôpital Avicenne 
plusieurs articles de journaux et chapitres de livre publiés.
Bristol Institute of Technology, University of the West of England 
collaboration avec l'équipe d'Andy Adamatzky, et plusieurs articles publiés.

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The use of evolutionary methods creates obvious links with the theme Theoretical Bioinformatics of the team, especially regarding the study of genetic operators intended to modify the genotype of the individuals that are being evolved. Up to now, artificial evolution has been inspired by natural evolution only in broad outlines. The collaboration with the theme Theoretical Bioinformatics gives computer scientists access to much more precise knowledge about biological genetic mechanisms, to refine the models they use, and vice versa, biologists can learn from the in silico experiments of researchers in artificial evolution.

The links are also very strong with the theme "Data mining and classification", because evolutionary methods also make it possible to create classifiers and extractors of knowledge (supervised or not) by genetic programming, for example (see theses of [ [Sébastien Derivaux]] and Jonathan Weber).