Congratulations to our new FdV Doctor Nicolas TCHITCHEK who presented his thesis defense on december 19th 2011 at the CRI.

Title : Novel statistical and geometrical methods for integrative genomics

details below

Abstract :

During the three years of my Ph.D. project, I developed several complementary methods and frameworks for the analysis of -omics data, such as: (i) a framework for integrative genomics in which every kind of information that can be obtained about the genomic processes and features are modeled in a common probabilistic manner, allowing then to analyze the correlations among the heterogeneous genome-wide information. (ii) a fold-change based statistical test for the identification of differentially and similarly expressed genes between two biological conditions, allowing also the determination of confidence intervals of specific confidence levels for the fold-change. (iii) novel dimensionality reduction methods that outperform other related existing methods and provide more interpretable geometrical representations in the context of large dataset of -omics data.
These methods have been applied to several biological analyses and studies as part of different scientific collaborations: (i) to identify functional Glucocorticoid Response Elements in the promoter regions of specific candidate genes involved in Type 1 Pseudohypoaldosteronism. (ii) to uncover the host transcriptional responses underlying differences between low- and high- pathogenic pulmonary viruses based on a compendium of host transcription responses of infected cells from mouse lungs. (iii) to study the progression of the hepatitis C virus in infected patients who underwent orthotopic liver transplantation, based on a cohort of transcriptome profiles for liver biopsy specimens. (iv) to analyze an Expression Sequence Tag library obtained from Peripheral Blood Mononuclear Cells of African green monkeys infected or not by the Simian Immunodeficiency Virus.

Keywords : systems biology, integrative genomics, differentially and simmiliary expressed genes, dimensionality reduction methods, geometrical representations, systems virology, pulmonary viruses, hepatitis C virus, EST library, SIV.

JURY :
Rapporteur: Marc-Thorsten Hutt, Jacobs University, Bremen, Germany
Rapporteur: Franck Molina CNRS, SysDiag, Montpellier, France
Examinateur : Emmanuel Barillot Institut Curie, Paris, France
Examinateur : Frédéric Martinon CEA, Fontenay-aux-Roses, France
Examinateur : Jean Krivine CNRS, PPS, Paris, France
Directeur de thèse : Annick Lesne CNRS, IHES, Bures-sur-Yvette, France
Directeur de thèse : Arndt Benecke CNRS, IHES, Bures-sur-Yvette, France