Équipe CSTB : Systèmes Complexes et Bioinformatique Translationnelle

Julie Thompson

De Équipe CSTB : Systèmes Complexes et Bioinformatique Translationnelle
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Recherche

Mes centres d'intérêt concernent essentiellement le développement d’approches in silico robustes, automatisées et intégrées (approches analytiques, statistiques, intégration et fouille de données, extraction et représentation des connaissances...) pour étudier l'évolution et le comportement des systèmes biologiques complexes (« hyperstructures », réseaux, etc.) chez l'homme et divers modèles animaux. Profitant de nos approches informatiques intégrées et dans le cadre de collaborations au niveau international, national et local, nous participons à l'analyse de systèmes complexes impliqués dans diverses maladies humaines, notamment l'étude des déficiences fonctionnelles liées aux maladies rétiniennes ou du cerveau, l'identification de variations génétiques liées aux ciliopathies et la caractérisation du contexte génomique et transcriptomique dans divers cancers.


Projets en cours (avec financement)

  • Partenaire, projet FRM : 1000 exomes contre les myopathies: identification et analyse intégrée de nouveaux gènes (2014-2017)
  • Partenaire, projet ANR infrastructure: “ReNaBi-IFB : Bioinformatique structurale" (2013-2020)
  • Task leader, projet ANR infrastructure BIPBIP: ‘Bayesian inference paradigm: Biology in processors’ (2012-2017)
  • Responsable développement bioinformatique pour INSTRUCT : European Strategy Forum for Research Infrastructures (ESFRI) (2011-2016)
  • Responsable développement bioinformatique pour le ‘French Infrastructure for Integrated Structural Biology’ (FRISBI) (2011-2016)
  • Task leader, projet ANR : EvolHHuPro, “Definition of evolutionary histories for the human proteome” (2007-2010)
  • Task leader, projet AFM Décrypthon: “Large-scale identification of transcriptional networks during myogenesis" (2007-2009)
  • Partenaire, projet FP7: SPINE2-Complexes (From Receptor to Gene: Structures of complexes from signalling pathways linking immunology, neurobiology and cancer) (2006-2009)

Projets en cours (sans financement)


Autres activités

Représentant français pour l’infrastructure européenne Elixir, Programmes of Work : (i) ‘data interoperability strategy’ et (ii) ‘training’

Membre suppléant du Comité de Pilotage de l’Institut Français de Bioinformatique (IFB)

Auteur de livre "Statistics for Bioinformatics : Methods for multiple sequence alignment", ISTE Science Publishing (en cours)

Editeur de livre “Functional proteomics: Methods and protocols”, Springer Humana Press, USA

Editorial board BMC Bioinformatics, Current Bioinformatics, PeerJ

Reviewing Bioinformatics, BMC Bioinformatics, BMC Evolutionary Biology, Nucleic Acids Research, Proteins: Structure, Function and Bioinformatics, Journal of Molecular Evolution

Expertise

HCERES (LBMC, Lyon; 2015)

ANR, expertise projets

Membre du comité pilotage: FRM Analyse Bioinformatique, 2014

Membre du committee, ‘Gravitation’ program, Netherlands Organisation for Scientific Research, 2012

Evaluator, Partnership Programme, PCCA 2011, Romanian National Council for Development and Innovation

Membre du Comité National, CNRS (2007-2008)

Membre du jury HDR : M Smail, 2014

Member du jury de thèse : Mokaddem A, Université de Tunis, 2014; E Bresso, Univeristé de Lorraine, 2013; C Kemena, CRG, Barcelona 2012, P Gouret Univ Provence 2010, France; M Vanhulsel Hasselt University, Belgium, 2009;

Organisation de manifestations / conférences European Conference Computational Biology (ECCB) 2014. Journées Ouvertes en Biologie, Informatique et Mathématiques JOBIM 2010-. ACS/IEEE International Conference on Computer Systems and Applications AICCSA'10.

Enseignement Bioinformatics and comparative genomics course, Université de la Réunion. (~20 H) (2013) Bioinformatics and comparative genomics course, Institut Pasteur Paris. (~20 H) (2010) Bioinformatics and comparative genomics course, organised by Institut Pasteur and EMBO. Brazil. (~20 H) (2008) Bioinformatics courses for IGBMC PhD program and Université de Strasbourg. (~10 H) (since 2007) Organisation of bioinformatics courses for IGBMC PhD programme and Université de Strasbourg (since 2007)

Supervision d'étudiants

PhD thesis: Aouled El Haj Mohamed S 2014-2017; Bermejo C 2013-2016; Vanhoutrève R 2013-2106; Linard B 2009-2012; Aniba MR 2007-2010;

Masters: Gass H 2016; Gilg M 2016; Bruxelles T 2015; Khenoussi W 2014; Bermejo C 2012; Schneider 2012; Lahure A 2011; Tankari A 2009; Karstens K 2008; Aniba MR 2007.

Prix ISI Web of Science, highly cited researcher in Biology and Biochemistry (isihighlycited.com, >75,000 citations); Prix Madeleine Lecoq de l’Académie des Sciences (2007); Prix Cristal du CNRS (2005)


Publications

Linard B, Allot A, Schneider R, Morel C, Ripp R, Bigler M, Thompson JD, Poch P, Lecompte O. OrthoInspector 2.0: software and database updates. Bioinformatics 2015 31:447-8.

Khenoussi W, Vanhoutrève R, Poch O, Thompson JD. SIBIS: a Bayesian model for inconsistent protein sequence estimation. Bioinformatics. 2014 30:2432-9.

Costa IR, Thompson JD, Ortega JM, Prosdocimi F. Metazoan Remaining Genes for Essential Amino Acid Biosynthesis: Sequence Conservation and Evolutionary Analyses Nutrients 2014 7:1-16.

Bermejo-Das-Neves C, Nguyen HN, Poch O, Thompson JD. A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i). BMC Bioinformatics. 2014 15:111.

Nguyen H, Luu TD, Poch O, Thompson JD. Knowledge discovery in variant databases using inductive logic programming. Bioinform Biol Insights. 2013 7:119-31.

Bedez F, Linard B, Brochet X, Ripp R, Thompson JD, Moras D, Lecompte O, Poch O. Functional insights into the core-TFIIH from a comparative survey. Genomics. 2013 101(3):178-86.

Levasseur A, Paganini J, Dainat J, Thompson JD, Poch O, Pontarotti P, Gouret P. The chordate proteome history database. Evol Bioinform Online. 2012;8:437-47.

De Craene JO, Ripp R, Lecompte O, Thompson JD, Poch O, Friant S. Evolutionary analysis of the ENTH/ANTH/VHS protein superfamily reveals a coevolution between membrane trafficking and metabolism. BMC Genomics. 2012 13:297.

Luu TD, Rusu A, Walter V, Linard B, Poidevin L, Ripp R, Moulinier L, Muller J, Raffelsberger W, Wicker N, Lecompte O, Thompson JD, Poch O, Nguyen H. KD4v: Comprehensible Knowledge Discovery System for Missense Variant. Nucleic Acids Res. 2012 40(Web Server issue):W71-5.

Luu TD, Rusu AM, Walter V, Ripp R, Moulinier L, Muller J, Toursel T, Thompson JD, Poch O, Nguyen H. MSV3d: database of human MisSense Variants mapped to 3D protein structure. Database (Oxford). 2012 2012:bas018.

Linard B, Nguyen NH, Prosdocimi F, Poch O, Thompson JD. EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data. Evol Bioinform Online. 2012;8:61-77.

Prosdocimi F, Linard B, Pontarotti P, Poch O, Thompson JD. Controversies in modern evolutionary biology: the imperative for error detection and quality control. BMC Genomics. 2012 13:5.

Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011 7:539.

Thompson JD, Linard B, Lecompte O, Poch O. A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives. PLoS One. 2011 6(3):e18093.

Linard B, Thompson JD, Poch O, Lecompte O (2011) OrthoInspector: comprehensive orthology analysis and visual exploration. BMC Bioinformatics 12:11.

Thompson JD, Linard B, Lecompte O, Poch O (2011) A Comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives. PLoS ONE 6:e18093

Aniba MR, Poch O, Marchler-Bauer A, Thompson JD (2010) AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis. Nucleic Acids Res 38(19): 6338-6349

Aniba MR, Poch O, Thompson JD (2010) Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Res 38(21): 7353-7363

Procter JB, Thompson JD, Letunic I, Creevey C, Jossinet F, Barton GJ (2010) Visualization of multiple alignments, phylogenies and gene family evolution. Nat Methods 7(3 Suppl):S16-25

Muller J, Creevey CJ, Thompson JD, Arendt D, Bork P (2010) AQUA: automated quality improvement for multiple sequence alignments. Bioinformatics. 26(2):263-5.

Aniba MR, Siguenza S, Friedrich A, Plewniak F, Poch O, Marchler-Bauer A, Thompson JD (2009) Knowledge-based expert systems and a proof-of-concept case study for multiple sequence alignment construction and analysis. Brief Bioinform 10(1): 11-23

Gouret P, Thompson JD, Pontarotti P (2009) PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees. BMC Bioinformatics. 10:298.

Ruano-Rubio V, Poch O, Thompson JD (2009) Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods. BMC Bioinformatics 10: 383

Prosdocimi F, Chisham B, Pontelli E, Thompson JD, Stoltzfus A (2009) Initial implementation of a comparative data analysis ontology. Evol Bioinform Online. 5:47-66.

Levasseur A, Pontarotti P, Poch O, Thompson JD (2008) Strategies for reliable exploitation of evolutionary concepts in high throughput biology. Evol Bioinform Online 4: 121-137

Perrodou E, Chica C, Poch O, Gibson TJ, Thompson JD (2008) A new protein linear motif benchmark for multiple sequence alignment software. BMC Bioinformatics 9(1): 213

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947-8.

Thompson JD, Muller A, Waterhouse A, Procter J, Barton GJ, Plewniak F, Poch O. MACSIMS: multiple alignment of complete sequences information management system. BMC Bioinformatics. 2006 7:318.

Bianchetti L, Thompson JD, Lecompte O, Plewniak F, Poch O. vALId: validation of protein sequence quality based on multiple alignment data. J Bioinform Comput Biol. 2005 3(4):929-47.

Thompson JD, Koehl P, Ripp R, Poch O. BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins. 2005 61(1):127-36.

Thompson JD, Holbrook SR, Katoh K, Koehl P, Moras D, Westhof E, Poch O. MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences. Nucleic Acids Res. 2005 33(13):4164-71.

Chalmel F, Lardenois A, Thompson JD, Muller J, Sahel JA, Léveillard T, Poch O. GOAnno: GO annotation based on multiple alignment. Bioinformatics. 2005 21(9):2095-6.

Thompson JD, Prigent V, Poch O. LEON: multiple aLignment Evaluation Of Neighbours. Nucleic Acids Res. 2004 32(4):1298-307.

Plewniak F, Bianchetti L, Brelivet Y, Carles A, Chalmel F, Lecompte O, Mochel T, Moulinier L, Muller A, Muller J, Prigent V, Ripp R, Thierry JC, Thompson JD, Wicker N, Poch O. PipeAlign: A new toolkit for protein family analysis. Nucleic Acids Res. 2003 31(13):3829-32.

Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 2003 31(13):3497-500.

Thompson JD, Thierry JC, Poch O. RASCAL: rapid scanning and correction of multiple sequence alignments. Bioinformatics. 2003 19(9):1155-61.

Thompson JD, Plewniak F, Ripp R, Thierry JC, Poch O. Towards a reliable objective function for multiple sequence alignments. J Mol Biol. 2001 314(4):937-51.

Lecompte O, Thompson JD, Plewniak F, Thierry J, Poch O. Multiple alignment of complete sequences (MACS) in the post-genomic era. Gene. 2001 270(1-2):17-30.

Bahr A, Thompson JD, Thierry JC, Poch O. BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. Nucleic Acids Res. 2001 29(1):323-6.

Thompson JD, Plewniak F, Thierry J, Poch O. DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches. Nucleic Acids Res. 2000 28(15):2919-26.

Plewniak F, Thompson JD, Poch O. Ballast: blast post-processing based on locally conserved segments. Bioinformatics. 2000 16(9):750-9.

Thompson JD, Plewniak F, Poch O. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res. 1999 27(13):2682-90.

Thompson JD, Plewniak F, Poch O. BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics. 1999 15(1):87-8.

Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ. Multiple sequence alignment with Clustal X. Trends Biochem Sci. 1998 23(10):403-5.

Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997 25(24):4876-82.

Higgins DG, Thompson JD, Gibson TJ. Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 1996;266:383-402.

Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 22(22):4673-80.

Thompson JD, Higgins DG, Gibson TJ. Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput Appl Biosci. 1994 10(1):19-29.


Contact

Dr. Julie Thompson
ICube, UMR CNRS 7357 
Faculté de Médecine
Bât. 3 5ième étage,
11 rue Humann
F-67000 Strasbourg

Mailing address:
Faculté de Médecine
ICube, UMR 7357
LBGI
4, rue Kirschleger
F- 67085 Strasbourg cedex



Tel : +33 (0)3 68 85 32 96 
courriel :  thompson@unistra.fr
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