User:AntonyLeBechec

File:Antony pic.jpg

Antony Le Béchec, First Assistant

Antony Le Béchec studied biology, mathematics, computer science and bioinformatics at the University of Rennes in France, to finally obtain a master in information systems management engineering in 2002 and a master in Bioinformatics in 2003. He obtained is PhD at the INSERM health institute in 2007, in integrative biology and biomedicine (hepatocellular carcinoma). He worked at the CNRS research institute (2007-2008) to develop a multi-pattern-matching approach to automatically classify proteins into families (amyloïds and MIPs, neurodegeneratives diseases). Then, he worked at the University of Luxembourg (2008-2012) to develop a meta-regulation networks analysis approach and studying dynamics of gene regulatory networks (cell plasticity and cancer). He joined the Computational Biology Group in the Department of Medical Genetics at the University of Lausanne in May 2012 in collaboration with the Vital-IT group at the SIB (Swiss Institute of Bioinformatics) and the CHUV (Centre hospitalier universitaire vaudois) to work on the Exome project.

Contact

• UNIL - University of Lausanne
  • DGM - Departement of Medical Genetics
  • Computational Biology Group (026)
  • Rue du Bugnon 27, CH-1005 Lausanne - Switzerland
  • Phone: +41-21-692-5463
  • email: antony[dot]lebechec[at]unil[dot]ch

• SIB - Swiss Institute of Bioinformatics
  • Vital-IT - High Performance Computing Center
  • Génopode, Sorge Campus (2016.1)
  • UNIL - University of Lausanne
  • CH-1015 Lausanne, Switzerland
  • Phone: +41-21-692-4085
  • email: antony[dot]lebechec[at]isb-sib[dot]ch

• CHUV - Centre Hospitalier Universitaire Vaudois
  • Rue du Bugnon 21
  • CH-1011 Lausanne, Switzerland
  • email: antony[dot]lebechec[at]chuv[dot]ch

Work experience

Systems Biology | Bioinformatics | Biomedicine | Knowledge Management | Database & Web development

• 2010-2012: Assistant Researcher (3 year contract | Life Sciences Research Unit | University of Luxembourg)

Analysis of gene regulatory networks to identify biologically relevant sub-networks explaining transitions between cellular phenotypes. Development of a discrete logic modelling optimization approach guided by network dynamics [XPred project – maia.uni.lu/XPred] (LCSB collaboration, Luxembourg). Application in cancer processes such as metastasis, anoïkis resistance (ISB collaboration, Seattle), epithelial/mesenchymal transition (EMT/MET) as a dynamic system. (Systems Biology, Gene Regulatory Networks, Network modeling, topology and dynamics, Transcriptomics, Cancers).

• 2008-2010: Post-Doc Researcher (2 year contract | Life Sciences Research Unit | University of Luxembourg)

Construction and analysis of meta-regulation networks integrating transcription factors, microRNAs and targeted coding genes, in order to detect relevant network motifs, such as feedback and feed-forward loops [MIR@NT@N project – mironton.uni.lu]. Application in epithelial to mesenchymal transition (EMT) processes in breast cancer. (Integrative Biology, Meta-regulation Networks, Transcriptomic & Post-transcriptomic regulations, Cancer and EMT).

• 2007-2008: Post-Doc Researcher and Faculty member (1 year contract | CNRS – Research Institute | University of Rennes 1)

Analysis and integration of proteomic data related to amyloïd proteins, mainly involved in the most serious neurodegeneratives diseases such as Alzheimer, Huntington and Parkinson [AMYPdb Project – amypdb.univ-rennes1.fr]. Classification method using a multi-pattern-matching approach, applied to major intrinsic proteins [MIPdb project – mipdb.genouest.org]. (Sequence annotation, Protein pattern & motifs, Database conception, Knowledge repository, Amyloidosis).

• 2003-2007: PhD in Bioinformatics (4 year contract | INSERM – Health Institute | University of Rennes 1)

Management, analysis and integration of transcriptomic data in hepatocellular carcinoma. Environment dedicated to gene expression data annotation and analysis, integration of biological knowledge and interaction graph analysis [M@IA Project – maia.genouest.org]. (Integrative Biology, Interaction graphs analysis, Meta-analysis, Transcriptomic analysis).

Publications

• Zindy PJ, L'Helgoualc'h A, Bonnier D, Le Béchec A, Bourd-Boitin K, Zhang CX, Musso O, Glaise D, Berangere Troadec M, Loreal O, Turlin B, Leger J, Clement B, Theret N. (2006) Upregulation of the tumor suppressor gene menin in hepatocellular carcinomas and its significance in fibrogenesis. Hepatology, 44(5):1296-307.
• Le Béchec A and Théret N, by Service d’Activités Industrielles et Commerciales (SAIC), University of Rennes 1. (2006) Software M@IA. DDN.FR.001.090012.000.S.P.2006.000.31230. Agence pour la protection des Programmes (APP), France.
• Le Béchec A, Zindy PJ, Sierocinski T, Petritis D, Bihouée A, Le Meur N, Léger J, Théret N. (2008) M@IA: A modular application for microarray workflow and integrative datamining. In Silico Biology, 08:0007.
• Sierocinski T, Le Béchec A, Théret N, Petritis D. (2008) Semantic distillation: a method for clustering objects by their contextual specificity. Studies in Computational Intelligence, 129:431-442.
• Pawlicki S*, Le Béchec A, Delamarche C*. (2008) AMYPdb: a database dedicated to amyloid precursor proteins. BMC Bioinformatics, 9:273.
• Vetter G* and Le Béchec A*, Muller J, Muller A, Moes M, Yatskou M, Altanoury Z, Poch O, Vallar L, Friederich (2009) Time-resolved analysis of transcriptional events during SNAI1-triggered epithelial to mesenchymal transition. Biochem Biophys Res Commun., 385(4):485-91
• Le Béchec A, by Cytoskeleton and Cell Plasticity Laboratory, Life Sciences Research Unit. (2010) Software MIR@NT@N. Number 7224. Office Benelux de la Propriété intellectuelle (OBPI), Benelux (Belgium, The Netherlands, Luxembourg).
• Le Béchec A. Analyse Transcriptomique et Biologie Intégrative. Editions Universitaires Européennes, 978-613- 1-53427-0
• Le Béchec A, Portales-Casamar E, Vetter G, Moes M, Zindy PJ, Saumet A, Theillet C, Wasserman WW, Lecellier C, Friederich E. (2011) MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify subnetwork motifs in a meta-regulation network model. BMC Bioinformatics, 4;12:67.
• Moes M, Le Béchec A, Crespo I, Laurini C, Halavatyi A, Vetter G, del Sol A, Friederich E. (under revision) A novel network integrating a miRNA-203/SNAI1 feedback loop which regulates epithelial to mesenchymal transition. PLoS One. 2012;7(4):e35440.
• Crespo I, Krishna A, Le Béchec A, del Sol A. (under revision) Predicting missing expression values in gene regulatory networks using a discrete logic modeling optimization guided by network stable states: XPred tool. Manuscript submitted to NAR.