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The Stochastics and Biology Group (SBG), is one of the six research teams of the Probability and Statistics Lab. (LPSM — UMR CNRS 8001) of Sorbonne Université. The French name of SBG is Modélisation Aléatoire du Vivant (MAV). The team was created in 2011 in the former LPMA. SBG is led by G. Nuel since 2018 (A. Lambert former head of SBG, 2011-2017).

SBG gathers probabilists and statisticians of the LPSM interested in mathematical problems inspired by biology and/or applying mathematics to biological problems.

SBG's main biological research themes are:

  • Population Biology — Ecology; Population Genetics; Evolution; see also homepage of the SMILE group.
  • Genomics and Genetics — Analysis of Sequences; Gene Networks; Genetic Epidemiology; Cancer Genetics.
  • Neuroscience — Single Neuron; Neural Networks.

Contact Information

Stochastics and Biology Group,
LPSM, UMR CNRS 8001

Campus Pierre et Marie Curie,
4 place Jussieu,
F-75005 Paris — France

Bâtiment Sophie-Germain,
avenue de France,
F-75013 Paris — France

Collège de France,
11 Place Marcelin Berthelot,
75005 Paris - France



Research

Inference of Life Evolution

The SMILE project (Stochastic Models for the Inference of Life Evolution) has been led by Amaury Lambert since 2012. It gathers probabilists, bio-informaticians and biologists forming an autonomous research group hosted by the CIRB (Center for Interdisciplinary Research in Biology) at Collège de France.

The main topics covered by the project are:

  • Macroevolution: modeling and inference of population- and individual-based processes controlling speciation and extinction;
  • Population genetics and evolutionary ecology: modeling the effects of selection/cooperation on genetic/phenotypic diversity (chromosome painting, evolutionary game theory, evolution of pathogen virulence);
  • Conservation: inference of extinction risk status of contemporary species from time series or multilocus data;
  • Somatic evolution: Darwinian evolution in the human body (cancer, immunology).

Main partners involved:

  • LPSM (CNRS 8001), Sorbonne Université: A. Lambert, E. Schertzer
  • ISYEB (CNRS 7205), MNHN, Sorbonne Université: G. Achaz
  • CIRB (CNRS 7241), Collège de France: F. Débarre, F. Blanquart

Main collaborators in Paris: H. Morlon (ENS), R. Ferrière (ENS), S. De Monte (ENS), P. Rainey (ESPCI), V. Courtier-Orgogozo (CNRS), O. Rivoire (CNRS), O. Tenaillon (INSERM), E. Rocha (Pasteur).

Grants: SMILE is supported by Collège de France and CNRS. Salaries of postdocs and PhD students are provided by ANR, LabEx MemoLife, the Ministry of Research via Ecole Normale Supérieure and the IPV doctoral programme of Sorbonne Université.

Genetic Predisposition and Cancer

This project is led by G. Nuel since 2013. The primary objective of this project is to study the genetic factors in important age-dependent diseases like cancer, diabetes or rare genetic diseases. The challenge is to combine state-of-art survival analysis methods in the context of genetic dependence in (possibly large) pedigrees through Bayesian networks.

Our project initially focused on breast and ovarian cancers and BRCA mutations in partnership with Institut Curie. Beside this ongoing collaboration, we work now with Saint-Antoine Hospital on MSI Cancer (Lynch syndrome). This theme of research is one of the two priority axis of the recently obtained SIRIC CURASMUS (Sorbonne Université). SIRIC (sites de recherche intégrée sur le cancer — 7 SIRIC in France) is an excellence from the National Cancer Institute (INCA) to acknowledge a cancer site highly involved in translational research.

In this context, we are are interested in:

  • belief propagation in pedigrees
  • detection and estimation of cohort-effects
  • development of cure models
  • clinical cancer genetics

Main partners involved:

  • LPSM (CNRS 8001), Sorbonne Université: G. Nuel, A. Lefebvre
  • Institut Curie: D. Stoppa-Lyonnet, A. de Pauw
  • MAP5 (CNRS 8145), Paris Descartes: F. Alarcon, O. Bouaziz, V. Goepp
  • MSI Cancers, Saint-Antoine Hospital: A. Duval, V. Jonchère

Grants: INSERM/IRESP DECURION (2013-2016, €120K), LNCC PhD grant (2013-2016, €100K), LNCC PhD grant (2018-2021, €100K), SATT IDF, SIRIC CURASMUS.

Stochastic Modeling in Neuroscience

Stochastic modeling in Neuroscience has experienced an important development since the last ten years. Our objective is to address this topic with the recent achievements of Probability Theory and Statistics in connexion with our colleagues in computational and/or experimental Neuroscience. We hope that the mathematical approach will help to build simplified but biologically relevant models, to identify small sets of determinant parameters or to single out generic mechanisms that may help practitioners. We use both theory and numerics.

In the team we are interested at the same time in a single neuron and in populations of neurons. At the cell level we have focused on the role of the ion channels on the excitability of the neuron. Ion channels may undergo mutations and a dysfunction in the ion channels may cause pathologies (called channelopathies). Rythmic behaviours are also fundamental, at the cell level as well as for populations. Indeed alteration of natural rythm or emergence of collective periodic behaviour (synchrony) can be associated to neurologic diseases (epilepsy, Parkinson's disease, Alzheimer's disease in particular).

A few mathematical key words relevant for us: Piecewise Deterministic Markov Processes in finite and infinite dimension, stochastic Kuramoto model, synchronization, coupled random oscillators, hypoelliptic diffusions, long time behavior of time dependent multidimensional diffusions, thinning method, parameter estimation, fast-slow systems.

Michèle Thieullen has supervised the PhD theses of Gilles Wainrib (co-direction with K. Pakdaman IMJ Univ. Paris-Diderot), Alexandre Genadot, Vincent Renault (co-directed with Emmanuel Trélat LJLL-UPMC), Alexis Vigot. Currently she is co-supervising together with Vincent Lemaire (LPSM) the PhD Thesis of Nicolas Thomas.

We have benefited from the support of the french National Research Agency (ANR): projet ANR blanc MANDy (2009-2012), coordinator Michèle Thieullen (SBG, LPSM), 23 members, 4 poles: LPSM-UPMC, Univ. of Orléans (around Nils Berglund), INRIA Sophia-Antipolis (around Etienne Tanré), IMJ (Institut Jacques Monod) Univ. Paris-Diderot (around Khashayar Pakdaman). This project MANDy gathered colleagues from Probability Theory, PDE, Dynamical Systems and Computational Neuroscience.



Members

Grégory Nuel (DR CNRS), HDR — co-head of group

GN is an expert in probabilistic graphical models (e.g. HMMs, Bayesian networks) and computational statistics (e.g. EM algorithm, penalized likelihood). He is interested in a wide range of biomedical applications: tropical disease, bioaccoustics, genetic epidemiology, bioinformatics, clinical research, systems biology, and cancer genetics. Co-head of group since 2018.

Julien Berestycki (MC Sorbonne Université), HDR — permanent member

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Anna Bonnet (MC Sorbonne Université) — permanent member

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Amaury Lambert (PR Sorbonne Université), HDR — head of group

AL is professor at Sorbonne Université and at the biology department of Ecole Normale Supérieure. He is a specialist of random trees and of stochastic modeling and statistical inference in population genetics and phylogenetics. He leads the SMILE group, one of the 20 research groups of the Center for Interdisciplinary Research in Biology (CIRB, Collège de France). Former head of the group 2011-2017.

Catherine Larédo (DR INRA), HDR — permanent member

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Catherine Matias (DR CNRS), HDR — permanent member

CM is a statistician working at the interface between statistical modeling and life sciences. In particular, she has worked on the statistical analysis of graphs with a focus on ecological networks. Starting 2018, she is partly on leave as deputy director of the national scientific institute of mathematics and their interactions.

Todd Parsons (CR CNRS) — permanent member

TP studies stochastic population models and associated methods of inference with diverse applications in evolutionary ecology, population genetics, game theory, epidemiology, and phylogenetics.

Emmanuel Schertzer (MC Sorbonne Université) — permanent member

ES is a probabilist with expertise in stochastic modeling for population genetics and theoretical ecology. ES is interested in applying results from probability theory (such as branching processes) to understand exchangeable population models, and also to investigate how spatial structure and recombination have shaped the genetic diversity and the ecological composition of extant populations.

Michèle Thieullen (MC Sorbonne Université), HDR — permanent member

MT is a probabilist with expertise in stochastic modeling for Neuroscience. Up to now her research has focused on the role of ion channels in neural excitability through Piecewise Deterministic Markov Processes in finite and infinite dimension. MT is also interested in numerics and estimation problems for these models.

François Bienvenu (PhD student) — member

PhD started in 2016 under the supervision of F. Débarre (CIRB, Collège de France) and A. Lambert (SBG, LPSM). FB is working on random graphs models of evolution.

Jean-Jil Duchamps (PhD student) — member

PhD started in spring 2017 under the supervision A. Lambert (SBG, LPSM). JJD is working on stochastic modeling of phylogenetic trees via fragmentation and coalescent processes.

Félix Foutel-Rodier (PhD student) — member

PhD starting Sep 2018, supervised by A. Lambert (SBG, LPSM) and E. Schertzer (SBG, LPSM). Currently doing a six-month internship at Oxford under the supervision of Prof. Alison Etheridge.

Alexandra Lefebvre (PhD student) — member

PhD started in 2018 under the supervision G. Nuel (SBG, LPSM) and A. Duval (INSERM, Saint-Antoine Hospital). With a dual biology-mathematics background, AL is working on Bayesian network and survival analysis with applications in cancer genetics. Funding: Ligue Nationale contre le Cancer.

Léa Longepierre (PhD student) — member

PhD started in October 2016 under the supervision of C. Matias (SBG, LPSM). LL is working on statistical analysis of dynamic random graphs.

Verónica Miró Pina (PhD student) — member

PhD started in September 2015 under the supervision A. Lambert (SBG, LPSM) and E. Schertzer (SBG, LPSM). VMP has a background in biology and mathematics and she is working in probabilistic models in Population Genetics.

Nicolas Thomas (PhD student) — member

PhD started in 2014 under the supervision M. Thieullen (SBG, LPSM) and V. Lemaire (LPSM). NT is working on probabilistic numerical methods with applications in Neurosciences.

Bastien Fernandez (DR CNRS), HDR — associated member

Originally a physicist, BF has strong interest for mathematical approaches to the dynamics of collective systems. His contributions to modeling in Biology deal with gene regulatory networks, VDJ recombination and allelic exclusion, and populations of synthetic genetic circuits.

Giambattista Giacomin (PR Paris Diderot), HDR — associated member

GG is a probabilist working in equilibrium and nonequilibrium statistical mechanics. His activity on synchronization models is at the boundary between nonequilibrium statistical mechanics and life sciences.

Svetlana Gribkova (MC Paris Diderot) — associated member

SG is a statistician and assistant professor at Paris Diderot University. After a PHD in the field of survival analysis, she had done a post-doctorate in statistical analysis of single cell RNA-Seq data with applications to cancer research. Her actual research mainly focuses on statistical analysis of high dimensional genomic data and applications in biology and medicine.

Fanny Villers (MC Sorbonne Université) — associated member

FV is a statistician and assistant professor at Sorbonne Université. During her PhD in INRA, she worked on statistical models usefull for analysing transcriptomics data. Her main research field is high dimensional statistics and in particular the analysis of network data.

Etienne Roquain (MC Sorbonne Université), HDR — associated member

ER has defended his PhD at INRA Jouy-en-Josas and Université Paris Sud in 2007 and is Maître de conférences since 2008 at Université Pierre et Marie Curie (now Sorbonne Université), where he defended his HdR in 2015. His main research field is multiple testing and high dimensional statistics.

Olivier Bouaziz (MC Paris Descartes) — visiting member

OB is an expert in survival analysis, with applications to the biomedical field. His research mainly focuses on new estimation methods for recurrent event data, competing risk/multi state models, interval censoring and new algorithms for detecting heterogeneity in survival analysis. Delegation CNRS (6 months): February-July, 2018.

Vivien Goepp (PhD student, Paris Descartes) — visiting member

VG has a background in engineering and statistics. He is currently interested in models of heterogeneity in survival analysis based on penalized likelihood methods. Visiting SBG from February to July, 2018.

Eric Adjakossa (PhD student) — member

PhD defense in 2017 under the supervision of G. Nuel (SBG, LPSM) and A. Garcia (IRD UMR 216, Paris Descartes).

Ikram Allam (PhD student) — member

PhD defense in 2018 under the supervision of G. Nuel (SBG, LPSM) and A.-C. Camproux (MTi, Paris Diderot).

Pierre-Antoine Corre (PhD student) — member

PhD in 2017.

Alexandre Genadot (PhD student) — member

PhD defense in 2013 under the supervision of M. Thieullen (SBG, LPSM). Funding ED386.

Alexander Hartmann (PR University of Oldenburg, Germany) — visiting member

Spring, 2016.

Sabin Lessard (PR Université de Montréal, Canada) — visiting member

Fall, 2015.

Gilles Monneret (PhD student) — member

PhD started in 2014 under the supervision G. Nuel (SBG, LPSM) and F. Jaffrézic (INRA, Jouy-en-Josas). Defense scheduled in February 2018. Funding: ED386.

Vincent Renault (PhD student) — member

PhD defense in 2016 under the supervision of E. Trélat (LJLL, UPMC) and M. Thieullen (SBG, LPSM). Funding ED386.

Alexis Vigot (PhD student) — member

PhD defense in 2016 under the supervision M. Thieullen (SBG, LPSM).


Events

SMPGD, January 10-12, 2018 (Montpellier, France) — international conference

Statistical Methods for Post Genomic Data. Deadline for abstract submission: December 1, 2017.

Assises de Génétique, January 24-26, 2018 (Nantes, France) — national conference

The 9th (biennial) Assises de Génétique Humaine et Médicale. Deadline for abstract submission: November 15, 2017.

Physique Cancer 2018 (Cancer ITMO, AVIESAN) — national AAP

Research projects in physics, mathematics or engineering sciences relating to Cancer. Deadline for submission: January 26, 2018.

PhD grant IPV (Sorbonne Université) — local AAP

Programme doctoral "Interface pour le Vivant" (IPV) L'ambition de ce programme est de générer des recherches innovantes aux interfaces avec les sciences du vivant. Deadline for submission: March 9, 2018.

PhD grant COFUND (FSMP) — local AAP

40 PhD grants for mathematicians who spent no more than one year in France (withing the last three years). Deadline for submission: April 1, 2018.

EMGM, April 18-20, 2018 (Cagliari, Italy) — international conference

European Mathematical Genetics Meeting 2018. Deadline for abstract submission: March 11, 2018.

EPICLIN, May 30 - June 1, 2018 (Nice, France) — national conference

EPIdémiologie CLInique et biostatistique: le congrès des chercheurs et professionnels francophones.. Deadline for abstract submission: December 30, 2017.

IWAP 2018, June 18-21 2018 (Budapest, Hungary) — international conference

The 9th (biennial) International Workshop on Applied Probability. Deadline for abstract submission: March 15, 2018.

Probability Evolutionary Biology 2018, June 25-29 2018 (CIRM, Luminy, France) — international conference

The European Society for Evolutionary Biology holds its 2018 annual meeting in France jointly with the Canadian and American societies. Deadline for abstract submission: January 15, 2018.

MCEB - Mathematical and Computational Evolutionary Biology, June 25-29 2018 (Montpellier, France) — international conference

The theme of this year's edition will be "Methods for evolutionary genomics”, including genome evolution, phylogenomics, population genomics, functional genomics, etc. Deadline for registration: March 3, 2018.

IBC 2018, July 8-13 2018 (Barcelona, Spain) — international conference

The 29th (biennal) International Biometric Conference. Deadline for abstract submission: January 19, 2018.

Populations: Interactions and Evolution, September 10-14 2018 (IHP, Paris, France) — international conference

The gathering theme of the conference is the modelling of systems of interacting individuals. Free registration. Program to be announced.

PGM 2018, September 11-14 2018 (Prague, Czech Republic) — international conference

The 9th (biennal) International Conference on Probabilistic Graphical Models. Deadline for abstract submission: May 22, 2018.

Enfants, Adolescents et Cancer 2019 (LNCC) — national AAP

Research projects on Cancer. Deadline for abstract submission (to confirm): February, 2019. Full application (to confirm): June, 2019.

Recherche en Epidémiologie 2019 (LNCC) — national AAP

Research projects on Cancer Epidemiology. Deadline for abstract submission (to confirm): February, 2019. Full application (to confirm): June, 2019.

SMPGD, January 31 - February 1, 2019 (Barcelona, Spain) — international conference

Statistical Methods for Post Genomic Data. The main topics are : Genome conformation, Analysis of biological images, and Causal inference. Deadline for abstract submission: November 30, 2018. Deadline for (free !) registration: January 14, 2019.

MMEE, July 16-19, 2019 (Lyon, France) — international conference

Mathematical Models in Ecology and Evolution. Deadline for minisymposia proposal: December 1st, 2018. Deadline for abstract submission: March 15, 2019.


2191

cups of coffee drunk

384

conference talks given

3860

article pages published

785268

Lines of code written