Parcours Bioinformatique et modélisation Specialization in Bioinformatics and Modeling

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Photo Stephen Nagy

Master d'informatique Master of Computer science

Responsables Directors :
Alessandra Carbone et and Martin Weigt,
Professeurs, Département d'Informatique Professors, Computer science Department
Coordination : Emilie Auger
Secrétariat Pédagogique BIM, 24-25.216
Tel : +33 (0)1 44 27 53 80
Email : master.info.bim@upmc.fr

Master de Biologie Moléculaire et Cellulaire Master of molecular and Cellular Biology

Responsables Directors :
Stéphane Le Crom (M2) et and Philippe Lopez (M1)
Professeurs, Département de Biologie Professors, Biology Department
Coordination : Carine Joseph
Secrétariat Master BMC, 33-34.111
Tel : +33 (0)1 44 27 35 35
Email : carine.joseph@upmc.fr

BIM teachers

Alessandra Carbone Alessandra Carbone: Alessandra Carbone is Professor at the Department of Computer Science at the Université Pierre et Marie Curie. Her group works on various problems connected with the functioning and evolution of biological systems. Mathematical methods coming from statistics and combinatorics, as well as algorithmic tools are employed to study fundamental principles of the cellular functioning starting from genomic data. The projects developed by her group are all aimed at understanding the basic principles of evolution and co-evolution of molecular structures in the cell. They concern sequence evolution of entire genomes as well as protein evolution.
Martin Weigt Martin Weigt: Martin Weigt is Professor for Computational Biology at the Department of Computer Science of the Université Pierre et Marie Curie. Inspired by his original background in statistical physics, he develops novel multi-disciplinary algorithmic approaches for statistical inference of biological networks and efficient information extraction from large-scale biological data set. Current focus of his team "Statistical Genomics and Biological Physics" is the coevolutionary analysis of large families of homologous (i.e. evolutionarily related) biomolecules, and their usage for structural and functional prediction.
Stéphane Le Crom Stéphane Le Crom: Stéphane Le Crom is a Professor in functional genomics at the Paris-Seine Institute of Biology (IBPS) of Université Pierre et Marie Curie. He is the principal investigator of he team "High throughput data analysis for genomics » associated to the platform department of IBPS. He his also responsible for the genomic platform at the Ecole normale superieure Institut of Biology (IBENS). His group at IBPS is focusing on RNA-Seq data analysis using methodologies and approaches coming from the evolution field. He is also involved in tight collaboration with the IBENS genomic platform in data treatment automation and distributed computing through Hadoop models using grid and cloud computing infrastructures.
Philippe Lopez Philippe Lopez: Philippe Lopez is a Professor in the Department of Life Sciences at the Université Pierre et Marie Curie. He is interested in non tree-like processes in evolution, like recombination, gene fusion and lateral transfer and he is exploring the use of evolutionary networks in order to describe, structure and explain genetic diversity.
Guillaume Achaz Guillaume Achaz: Guillaume Achaz is an Assistant Professor at the Department of Life Sciences at Université Pierre et Marie Curie. His research interest centers around genomics and population genetics.
Angelo Arleo Angelo Arleo: Angelo Arleo is a Senior Researcher (DR, CNRS) at the "Institut de la Vision" at Université Pierre et Marie Curie - INSERM - CNRS. He is leading the Aging in Vision and Action group, which investigates the impact of (primarily healthy) aging on perceptual and cognitive vision-dependent functions. In particular, the consequences of normal aging in vision-based cognitive functions will be investigated within a spatial orientation framework. Probing age-related effects on spatial orientation functions has the potential to reveal overt autonomy loss markers, pertinent to the way the elderly interact with their environment through active sensing and behavioral exploration. The Aging in Vision and Action group promotes an interdisciplinary approach combining experimental neuroscience (electrophysiology and psychophysics) and computational modeling.
Martine Boccara Martine Boccara: Martine Boccara is a Professor at the Department of Life Sciences at the Université Pierre et Marie Curie. Her research interest centers in Plant genomics and small non coding RNAs.
Jean Cognet Jean Cognet: Jean Cognet is a Professor at the Department of Life Sciences at Université Pierre et Marie Curie. His research interest centers around the biophysics of biological molecules.
Mathieu Desroches Mathieu Desroches: Matthieu Desroches research is mainly focused on applications of multiple timescale dynamics in neuroscience. In particular, he is interested in complex oscillatory behaviours created by the interplay between different timescales, such as Mixed-Mode Oscillations (MMOs) and bursting oscillations. A closely related phenomenon is that of canard solutions, which allow to understand continuous yet very rapid transitions between vastly different dynamical regimes, in particular in the context of neuronal models. he uses a mix of analytical tools (singular perturbation theory, bifurcation theory) and computational methods (numerical continuation) to investigate these complex systems.
Frédéric Devaux Frédéric Devaux: Frédéric Devaux is a Professor at the Department of Life Sciences at the Université Pierre et Marie Curie. He is leading the Genetic Networks team (LGM) which studies the functioning and the evolution of genetic networks that control gene expression in yeast. They use transcriptomic approaches to understand the response of the genome expression to toxic environmental conditions in different yeast species, combined with gene expression imaging techniques to get real-time, quantitative information on the functioning of these networks. These global and quantitative data are then used to set up in silico models of the structure, the dynamics and the evolution of our favorite networks.
Dirk Drasdo Dirk Drasdo: Dirk Drasdo is a Senior researcher at INRIA (Paris-France) and Interdisciplinary Center for Bioinformatics (Leipzig-Germany). His research group focuses on the understanding of tissue formation on different time and length scales. It pursues projects on the development of models to permit realistic simulation of multicellular organization processes, and on the analysis of data that occur during this processes.
Bernard Dujon Bernard Dujon: Bernard Dujon is a Professor at Université Pierre et Marie Curie and at Pasteur Institute and is a member of the french academy of science. His laboratory, Molecular Genetics of Yeast, combines in silico and in vivo approaches towards the mechanisms of genome organization and evolution in yeast.
Gilles Fisher Gilles Fischer: Gilles Fisher is a senior researcher (DR, CNRS) leading the Genome Biology team (LGM), Université Pierre et Marie Curie. He is interested to understand the biology and the evolution of yeast genomes. His team is combining experimental approaches based on molecular genetics and functional genomics to an analytical dimension requiring bio-informatic skills and the development of new tools. His group studies genome dynamics through the characterization of the structural polymorphism of chromosomes at different scales, from cells to populations, and from strains and to different species. He is interested by the relationships between replication/recombination and the evolution of gene content and organization along chromosomes.
J-P Françoise Jean-Pierre Françoise: Jean-Pierre Françoise is professor of mathematics at UPMC, member of the Jacques-Louis Lions Laboratory and associate member of the team MYCENAE at INRIA. His research interests are on Differential Equations, Dynamical Systems, Bifurcation Theory and Complex Analysis. His collaboration with medical doctors and biologists focuses on oscillations in Biology, in relation with population dynamics, profile secretion of neuroendocrine cells, and metabolism of neurons and astrocytes.
M. Garcia Mathilde garcia: Mathilde Garcia is assistant professor of biology at UPMC, member of the LCQB laboratory. Her research focuces on post-transiptionnal controls of gene expression in the model yeast S. cerevisiae. Indeed, she investigates how mRNA molecules are targeted by specific controls that determine their unique fate within the cell (localisation, stability, translation efficiency).
D. Holcman David Holcman: David Holcman is a professor and a director of interdisciplinary research at CNRS. The main interests of his group are to study the function of microdomains in cellular biology and to develop physical modeling, mathematical analysis, numerical simulations and data analysis. The goal is to identify principles underlying cellular and network function. For that purpose, in collaboration with experimental groups, they focus on basic questions in cellular biology such as molecular trafficking in cells, synaptic transmission in neurons and principles of nuclear organization.
Hervé Isambert Hervé Isambert: Hervé Isambert is a Senior Researcher (DR, CNRS) at the biophysics laboratory, Curie Institute. He is leading the RNA dynamics and biomolecular systems team whose research concerns the properties and adaptation of biomolecular networksat different scales, from their simple local structures to their more complex global organization. Projects concern: Synthetic RNA regulatory networks and self-assembly of bacterial RNA and Evolution of large biomolecular networks.
Ingrid Lafontaine Ingrid Lafontaine: Ingrid Lafontaine Ingrid Lafontaine is an Assistant Professor in the Department of Life Sciences at the Université Pierre et Marie Curie. She is interested in the relationships between the evolution of the coding sequences and genome dynamics. She uses phylogenetic and statistical models to describe gene evolution both at the sequence level and at the gene content level. She also does methodological development for the analysis of high throughput data.
Elodie Laine Elodie Laine: Elodie Laine is an Assistant Professor at the Department of Life Sciences at the Université Pierre et Marie Curie. Her research interests concern the study of protein evolution, conformational dynamics, interactions and allosteric inhibition. She employs and develops methods for molecular modeling and docking, with the aim of understanding the fundamental mechanisms underlying protein functions and activity in physio-pathological contexts.
Yvon Maday Yvon Maday: Yvon Maday is a Professor at the Jacques-Louis Lions laboratory, Department of Mathematics at the Université Pierre et Marie Curie. His research interests are numerical analysis and finite elements methods.
Yann Ponty Yann Ponty: Yann Ponty is a CNRS research scientist at LIX, the computer science department at Ecole Polytechnique, and Inria Saclay. His main research interest lies in the foundations and development of structure-centric methods for RNA computational biology. To that purpose, he focuses on discrete representations, such as the secondary structure, and uses tools borrowed from the fields of discrete optimization, such as dynamic programming, and enumerative/analytic combinatorics.
Hugues Richard Hugues Richard: Hugues Richard is an Assistant Professor in Computational Biology at the Department of Computer Science at the Université Pierre et Marie Curie. Coming from a mathematical background, his interests are now the development of statistical methods for the functional analysis of high throughput sequencing data, with a special twist for transcriptome data. He is doing both methodological development and data analysis.
Denis Sheynikhovich Denis Sheynikhovich: is an assistant professor at the Department of Life Sciences at the Université Pierre et Marie Curie. His research field is computational neuroscience of learning and memory, primarily in relation to spatial cognition. His main scientific interests lie in the understanding of how neuronal networks of the brain can construct, through adaptation, internal models of the external environment.
Nataliya Sokolvska Nataliya Sokolovska: Nataliya Skolovska is an Assistant Professor at the Department of Life Sciences at the Université Pierre et Marie Curie in the Nutriomics team. Her research interests are: Machine Learning, Graphical Models and Probabilistic Inference, Semi-Supervised Learning, Reinforcement Learning and Game Theory.
Denis Thieffry Denis Thieffry: Professor at ENS, Denis Thieffry heads the Computational Systems Biology team at IBENS, which focuses on the development and the application of computational methods and software to analyze and model regulatory networks involved in cell fate decision.
Pierre-Henri Wuillemin Pierre-Henri Wuillemin: Pierre-Henri Wuillemin is an Assistant Professor in the DECISION team at the Department of Computer Science at the Université Pierre et Marie Curie. His research interests are computational methods for inference in bayesian networks, structural learning, bayes networks based diagnostics and reinforced learning.
Jean Daniel Zucker Jean Daniel Zucker:Jean Daniel Zucker is a Research Director at the IRD (Research Institute for Development) in the International Laboratory UMI UMMISCO (International Laboratory on Mathematical and Multi-Agent Based Modeling of ecological, biological and social Complex Systems) funded by both IRD and University Paris 6. His research focus is in Artificial Intelligence, on Machine Learning (predictive analysis) and Change of Scales (abstraction) for Modeling Complex Systems. He relies on Multi-agent Simulations and Machine Learning algorithms to address problems where multi-scale and data integration are key issues. Fields of application include Metagenomics, Nutrigenomics, Epidemiology, Decision-support Research for Environmental Applications and Models.

BIM invited teachers

2016-2017:
Alberto Policriti, Professor at the University di Udine, Italy.
Algorithms in sequence analysis.
2015-2016:
Marco Punta, Laboratory of Computational and Quantitative Biology, Pierre & Marie Curie University.
Protein annotation, Pfam, disordered proteins.
2014-2015:
Michele Ceccarelli, Professor at University of Sannio, Italy & Qatar Computing Research Institue, Qatar.
Pattern Recognition, data mining, and bioinformatics.
2013-2014:
Andrea Pagnani, Professor at Politecnico di Torino and Researcher, Human Genetic Foundation.
Statistical Physics and data analysis.
2012-2013:
Arcady Mushiegan, Professor at Stower Institute, Kansas, USA.
Comparative Genomics.
2011-2012:
Peter Arndt, Researcher at the Max-Planck Institute of Molecular Genetics, Berlin, Germany.
Population Genetics.
2009-2010:
Susan Holmes, Professor at Stanford University, USA.
Phylogeny.