Massively parallel sequencing applied to single cells allows us to investigate new questions that were out of reach for classical bulk genomics. Cell-to-cell variability is central in gene regulation or cell differentiation, as it provides information on the underlying molecular networks. Consequently, single cell expression profiling has the promise of revolutionizing our understanding of genomes regulation.

Nevertheless, the specific characteristics of single cell data as well as their dimensionality calls for new mathematical models and computational tools. The goal of this project is to develop new methodologies to investigate cell identity and the dynamics of cell differentiation, by integrating single cell expression and epigenomic data. For that purpose, our consortium gathers unique combined expertises in statistics, machine learning, optimal transport and systems biology, and an extended network of collaborators on single-cell (medical) genomics in France and abroad.

Consortium

Researchers

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Alice Cleynen

Université de Montpellier

CR CNRS, Statistics

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Angélina Roche

Université Dauphine

MCF, Statistics

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Bertrand Michel

Central Nantes

Laboratoire de Mathématiques Jean Leray

PR, Statistics

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Fabien Crauste

Université de Paris

Researcher

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Filippo Santambrogio

Lyon 1

PR, Optimal Transport

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Franck Picard

ENS de Lyon/LBMC

PI, DR CNRS, Statistics

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Jean-Philippe Vert

Google Brain/Mines Paris-Tech

Senior Researcher, Machine Learning

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Joon Kwon

AgroParisTech/INRAE

Mathématiques & Informatique Appliquées Paris

CR INRAE, Machine Learning

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Julien Chiquet

AgroParisTech/INRAE

Mathématiques & Informatique Appliquées Paris

PI, DR INRAE, Statistical learning

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Laure Sansonnet

AgroParisTech/INRAE

Mathématiques & Informatique Appliquées Paris

MCF, Statistics

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Laurent Modolo

ENS de Lyon/LBBE

IR CNRS, Computational Biology

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Olivier Gandrillon

ENS de Lyon/LBMC

Laboratoire de Biologie de Modélisation de la Cellule

PI, DR CNRS, Systems Biology

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Philippe Veber

CNRS/Lyon 1

IR CNRS

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Stéphane Robin

AgroParisTech/INRAE

Mathématiques & Informatique Appliquées Paris

DR INRAE, Statistics

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Thibault Espinasse

Lyon 1

MCF, Statistics

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Thomas Lepoutre

Inria/Lyon 1

Dracula, INRIA

CR INRIA, EDP

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Vincent Calvez

ENS de Lyon

DR CNRS

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Vincent Rivoirard

Université Dauphine

PR? Statistics

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Yohann de Castro

Centrale Lyon

PR, Statistics

Students

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Anthony Ozier-Lafontaine

Central Nantes/ENS Lyon

PhD Student

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Elias Ventre

Inria/ENS de Lyon

Laboratoire de Biologie de Modélisation de la Cellule

Dracula, INRIA

PhD Student

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Félix Raimundo

Google Brain

PhD Student

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Hugues Van Assel

ENS de Lyon/LBMC

M2 Internship

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Vincent Marty

Inria/ENS de Lyon

Laboratoire de Biologie de Modélisation de la Cellule

Dracula, INRIA

M2 Internship

Recent Publications

Meetings