Difference between revisions of "Julie Thompson"

Revision as of 11:19, 30 November 2016

Research director CNRS, at Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie, Université de Strasbourg, Unité Mixte de Recherche CNRS 7357.
Joint head of LBGI Bioinformatique et Génomique Intégratives.
Scientific leader of the bio-informatics and complex systems platform BICS and the bioinformatics platform BISTRO.

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 (with funding)

Partner, FRM project: 1000 exomes against myopathies: integrated identification and analysis of novel genes (2014-2017)
Partner, ANR infrastructure project: “ReNaBi-IFB : Structural bioinformatics" (2013-2020)
Task leader, ANR infrastructure project BIPBIP: ‘Bayesian inference paradigm: Biology in processors’ (2012-2017)
Bioinformatics development for INSTRUCT : European Strategy Forum for Research Infrastructures (ESFRI) (2011-2016)
Bioinformatics development for ‘French Infrastructure for Integrated Structural Biology’ (FRISBI) (2011-2016)
Task leader, ANR project: EvolHHuPro, “Definition of evolutionary histories for the human proteome” (2007-2010)
Task leader, AFM Décrypthon project: “Large-scale identification of transcriptional networks during myogenesis" (2007-2009)
Partner, FP7 project: SPINE2-Complexes (From Receptor to Gene: Structures of complexes from signalling pathways linking immunology, neurobiology and cancer) (2006-2009)

On-going Projects (without funding)

Contributions to UNESCO UniTwin Complex Systems Digital Campus
Evolutionary analyzes of protein sequences from NGS data, applied to Health in collaboration with the team Data Science and Knowledge and the theme SONIC: Stochastic Optimization and Native Inspired Complex Systems.
GREMSAP (GRid Evolutionary Multiple Sequence Alignment Platform), in collaboration with the theme SONIC: Stochastic Optimization and Native Inspired Complex Systems.
Social Network Clinical Database for Intellectual Disabilities : Implementation of a social network of patients with genetic disorders leading to intellectual disabilities, in collaboration with the theme SONIC: Stochastic Optimization and Native Inspired Complex Systems, the team Médecine translationnelle et neurogénétique, IGBMC andl’Université Cheikh Anta Diop, Senegal.
Big data infrastructure for the translational analysis of the mutations involved in human genetic diseases. SM2PH-central aims to integrate heterogeneous data (genomics, phenotypic, evolutionary, cellular networks, ...), with data mining methods (association rules, inductive logical programming, ...).

Other activities

French representative for Elixir European infrastructure, Programmes of Work : (i) ‘data interoperability strategy’ et (ii) ‘training’

Book editor “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, project expertise

Member of steering committee: FRM bioinformatics analysis, 2014

Member of committee, ‘Gravitation’ program, Netherlands Organisation for Scientific Research, 2012

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

Member of Comité National, CNRS (2007-2008)

Jury member for HDR defence : M Smail, 2014

Jury member for thesis defence : 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 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, 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)

Student supervision 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.

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)

Publications

Liste des publications

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

@@ Line 2: / Line 2: @@
 * Research director CNRS, at [http://icube.unistra.fr Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie], [http://www.unistra.fr Université de Strasbourg], Unité Mixte de Recherche CNRS 7357.
 * Joint head of [http://lbgi.fr LBGI Bioinformatique et Génomique Intégratives].
-* Scientific leader of bioinformatics platform [http://bioinfo-bistro.fr BISTRO].
+* Scientific leader of the bio-informatics and complex systems platform [http://plateforme.icube.unistra.fr/bics BICS] and the bioinformatics platform [http://bioinfo-bistro.fr BISTRO].
 ==Research==
@@ Line 9: / Line 9: @@
-==On-going Projects==
+==On-going Projects (with funding) ==
+* Partner, FRM project: 1000 exomes against myopathies: integrated identification and analysis of novel genes (2014-2017)
+* Partner, ANR infrastructure project: “ReNaBi-IFB : Structural bioinformatics" (2013-2020)
+* Task leader, ANR infrastructure project BIPBIP: ‘Bayesian inference paradigm: Biology in processors’ (2012-2017)
+* Bioinformatics development for INSTRUCT : European Strategy Forum for Research Infrastructures (ESFRI) (2011-2016)
+* Bioinformatics development for ‘French Infrastructure for Integrated Structural Biology’ (FRISBI) (2011-2016)
+* Task leader, ANR project: EvolHHuPro, “Definition of evolutionary histories for the human proteome” (2007-2010)
+* Task leader, AFM Décrypthon project: “Large-scale identification of transcriptional networks during myogenesis" (2007-2009)
+* Partner, FP7 project: SPINE2-Complexes (From Receptor to Gene: Structures of complexes from signalling pathways linking immunology, neurobiology and cancer) (2006-2009)
-* Implication in the European Infrastructures project: [www.structuralbiology.eu/ INSTRUCT]
+==On-going Projects (without funding) ==
-* Implication in the ANR Infrastructures project: BIPBIP: Paradigme d'Inference Bayesienne pour la Biologie Structurale in silico
+* Contributions to [http://unitwin-cs.org UNESCO UniTwin Complex Systems Digital Campus]
-* Implication in the [http://unitwin-cs.org UniTwin Complex Systems Digital Campus de l'UNESCO] project
+* Evolutionary analyzes of protein sequences from NGS data, applied to Health in collaboration with the team [[Data Science and Knowledge]] and the theme [[SONIC|SONIC: Stochastic Optimization and Native Inspired Complex Systems]].
-* Evolutionary analyses of protein sequences from NGS data, applied to human health in collaboration with [[Fouille_de_données|Data mining]] and [[Evolution_artificielle,_optimisation_et_apprentissage|stochastic optimisation]] themes.
+* GREMSAP (GRid Evolutionary Multiple Sequence Alignment Platform), in collaboration with the theme [[SONIC|SONIC: Stochastic Optimization and Native Inspired Complex Systems]].
-* GREMSAP (GRid Evolutionary Multiple Sequence Alignment Platform), in collaboration with the theme [[Evolution_artificielle,_optimisation_et_apprentissage|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 of patients with genetic disorders leading to intellectual disabilities, in collaboration with the theme [[SONIC|SONIC: Stochastic Optimization and Native Inspired Complex Systems]], the team [http://www.igbmc.fr/research/department/4/team/44/ Médecine translationnelle et neurogénétique, IGBMC] and[http://www.ucad.sn l’Université Cheikh Anta Diop, Senegal].
-* 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 [[Evolution_artificielle,_optimisation_et_apprentissage|stochastic optimisation]], the team [http://www.igbmc.fr/research/department/4/team/44/ Médecine translationnelle et neurogénétique, IGBMC] and [http://www.ucad.sn l’Université Cheikh Anta Diop, Senegal].
+* Big data infrastructure for the translational analysis of the mutations involved in human genetic diseases. SM2PH-central aims to integrate heterogeneous data (genomics, phenotypic, evolutionary, cellular networks, ...), with data mining methods (association rules, inductive logical programming, ...).
-* 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==
-* [http://icube-publis.unistra.fr/appli.php?author=Julie+Thompson&title=&team=toutes&annee1=&annee2=&nationalRank=toutes&project=tous Liste des publications]
 ==Other activities==
+French representative for Elixir European infrastructure, Programmes of Work : (i) ‘data interoperability strategy’ et (ii) ‘training’
 '''Book editor'''
@@ Line 29: / Line 34: @@
 '''Editorial board'''
-Current Bioinformatics, Molecular Biotechnology
+BMC Bioinformatics, Current Bioinformatics, PeerJ
 '''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
+'''Expertise'''
+HCERES (LBMC, Lyon; 2015)
+ANR, project expertise
+Member of steering committee: FRM bioinformatics analysis, 2014
+Member of committee, ‘Gravitation’ program, Netherlands Organisation for Scientific Research, 2012
+Evaluator, 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;
+Jury member for HDR defence : M Smail, 2014
+Jury member for thesis defence : 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 of conferences'''
@@ Line 44: / Line 63: @@
 '''Teaching'''
-Bioinformatics and comparative genomics course, Unioversité de la Réunion. (~20 H) (2013)
+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)
@@ Line 51: / Line 70: @@
 '''Student supervision'''
-Post-docs: Prosdocimi F 2008-2009; Ruano-Rubio V 2008-2009;
+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;
-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.
+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.
 '''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)
+==Publications==
+* [http://icube-publis.unistra.fr/appli.php?author=Julie+Thompson&title=&team=toutes&annee1=&annee2=&nationalRank=toutes&project=tous Liste des publications]
 ==Contact==