CSTB team: Complex Systems and Translational Bioinformatics

Julie Thompson

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Research

My research interests are mainly focused on the development of robust, automated and integrated in silico approaches (analytical / statistical approaches, data integration and mining, extraction and representation of knowledge ...) to study the evolution and behavior of complex biological systems ("hyperstructures", networks) in humans and various animal models. Taking advantage of our integrated computational approaches and in the context of collaborations at the international, national and local level, we participate in the analysis of complex systems involved in various human diseases, including the study of functional impairments associated with retinal or brain diseases, identification of genetic variations related to ciliopathies and characterization of the genomic and transcriptomic context in various cancers.


On-going Projects

  • Implication in the European Infrastructures project: [www.structuralbiology.eu/ INSTRUCT]
  • Implication in the ANR Infrastructures project: BIPBIP: Paradigme d'Inference Bayesienne pour la Biologie Structurale in silico
  • Implication in the UniTwin Complex Systems Digital Campus de l'UNESCO project
  • Evolutionary analyses of protein sequences from NGS data, applied to human health in collaboration with Data mining and stochastic optimisation themes.
  • GREMSAP (GRid Evolutionary Multiple Sequence Alignment Platform), in collaboration with the theme stochastic optimisation, l’Institut des Systèmes Complexes Paris Île de France, l’Institut de Neurobiologie Albert Fressard.
  • Social Network Clinical Database for Intellectual Disabilities : Implementation of a social network for patients with genetic disorders leading to intelectual disabilities, in collaboration with the theme stochastic optimisation, the team Médecine translationnelle et neurogénétique, IGBMC and l’Université Cheikh Anta Diop, Senegal.
  • Big data infrastructure for the translational analysis of mutations involved in human genetic diseases. The goal of BIRD/SM2PH-central is the integration of heterogeneous data (genomic, phenotypic, evolution, cellular networks, …), with data mining methods (association rules, inductive logic programming, …), and includes the design of a semantic query language (BIRD-QL) and the development of novel graphical interfaces.


Publications

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

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.

Other activities

Book editor “Functional proteomics: Methods and protocols”, Springer Humana Press, USA

Editorial board Current Bioinformatics, Molecular Biotechnology

Reviewing Bioinformatics, BMC Bioinformatics, BMC Evolutionary Biology, Nucleic Acids Research, Proteins: Structure, Function and Bioinformatics, Journal of Molecular Evolution Grant reviews for ANR Membre du committee, ‘Gravitation’ program, Netherlands Organisation for Scientific Research, 2012Evaluator, Partnership Programme, PCCA 2011, Romanian National Council for Development and Innovation Member of Comité National, CNRS (2007-2008) Member of thesis Jury: E Bresso, Univeristé de Lorraine, 2013; C Kemena, CRG, Barcelona 2012, P Gouret Univ Provence 2010, France; M Vanhulsel Hasselt University, Belgium, 2009;

Organisation of conferences European Conference Computational Biology (ECCB) 2014. Journées Ouvertes en Biologie, Informatique et Mathématiques JOBIM 2010-2012. ACS/IEEE International Conference on Computer Systems and Applications AICCSA'10.

Teaching Bioinformatics and comparative genomics course, Unioversité 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)

Student supervision Post-docs: Prosdocimi F 2008-2009; Ruano-Rubio V 2008-2009;

PhD thesis: Bermejo C 2013-2016; Vanhoutrève 2013-2106; Linard B 2009-2012; Aniba MR 2007-2010; Masters: Lahure A 2011; Tankari A 2009; Karstens K 2008; Aniba MR 2007.

Prizes 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)

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

Mail : thompson@unistra.fr

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