Computational and Mathematical Biology team (BCM) Seminars

(OLD) NEWS! Starting 09/2018, Magali Richard will be organizing the BCM Seminars, thanks Mag for taking over!
Check out the new BCM Seminars webpage

General information

When: usually Fridays between 2:00 PM and 3:00 PM.
Where: usually in room R31 at Pavillon Taillefer (links to maps can be found in the contact information section of my home page).
Any changes in schedule or room will appear in red below.

BCM speakers: we have a talk every other week by a BCM team member, according to the rotation indicated in the program below. This is more a "lab-meeting" type slot, although non-BCM audience members are very welcome. The speaker presents her/his recent results or work in progress, or discusses an exceptional publication that (s)he thinks we should all know about.
External speakers: every other week is free for inviting external speakers, marked in orange below. If you invite a speaker, please send me his/her name, affiliation and a title for the talk (in english).

If you have a problem with your scheduled slot, try to switch with another speaker, and once you're set let me know so I can update the program.

If you wish to receive the announcements, drop me an email.

Contact: Nicolas Thierry-Mieg


Date Speaker Title
29/6/2018 Antoine Roland Conformation de la chromatine appliquée à la senescence.
22/6/2018 Clémentine Decamps Hétérogénéité et stochasticité cellulaire dans les tissus sains et tumoraux.
15/6/2018, R32 Eymerik Belmonte TBA
8/6/2018 Basile Jumentier The key role of choice of latent factor adjustment methods in association studies and mediation analysis.
13/4/2018 guest speaker:
Charlotte Maugard, EPSP/TIMC-IMAG
Big-data and occupational health surveillance: application to agricultural workers.
23/3/2018 Florian Privé Predicting complex diseases: performance and robustness
16/3/2018 Alan Downey-Wall Characterizing the role of DNA methylation in mediating Eastern oyster responses to ocean acidification.
9/3/2018, R32 Bastien Boussat Comité de Retour d'Expérience et culture de sécurité des soins.
9/2/2018, R32 Olivier Francois Confounder adjustment in genome and epigenome wide association studies.
1/12/2017, R32 Kevin Caye Méthodes de factorisation matricielle pour la génomique des populations et les tests d’association
17/11/2017 Thomas Karaouzène Bioinformatique et infertilité : analyse des données de séquençage haut-débit et caractérisation moléculaire du gène DPY19L2.
13/10/2017 Florian Privé Visualization with ggplot2.
Monday 4/9/2017 at 11:00 AM guest speaker:
Ben Murrell, University of California San Diego
Deeply sequencing entire genes from rapidly evolving viruses.

2017 summer break

Tuesday 04/07/2017 at 2:00 PM guest speaker:
Isak Gath, Technion Israel Institute of Technology, Haifa, Israel
Mating patterns and genealogical trees: assessment of carrier rates of Familial Mediterranean Fever in rural Israeli districts.
30/6/2017 (Keurcien Luu) POSTPONED
23/6/2017 (Helena Martins) POSTPONED
9/6/2017, R32 NO SEMINAR: data challenge in Aussois
2/6/2017, R32 Ingrid Roche Analyse globale de l’autocorrélation spatiale de données d'incidence en Isère.
26/5/2017 thursday is a holiday => no seminar
12/5/2017 Bastien Boussat - POSTPONED
5/5/2017, R32
28/4/2017 11:00 AM
21/4/2017 Florian Privé "bigstatsr" and "bigsnpr": two R packages for efficient analysis of SNP arrays.
14/4/2017 Keurcien Luu - POSTPONED
7/4/2017, R32 Alexandre Rocca Optimal control for Erythropoiesis and Hemoglobin production modelling.
31/3/2017 Thomas Dias-Alves Local genetic ancestry Inference using Local Clustering.
24/3/2017 Thomas Karaouzene MutaScript: filter and prioritize variants to improve exome data analysis.
17/3/2017 Ingrid Roche - POSTPONED
10/3/2017 10:45 AM Kevin Caye Testing for Associations Using Latent Factor Mixed Models.
3/3/2017, R32
17/2/2017 guest speaker:
Flora Jay, LRI Paris Sud
Reconstructing past history from whole-genomes: an ABC approach handling recombining data.
10/2/2017 [PAS DE SALLE]
3/2/2017, R32 Magali Richard Assigning function to natural allelic variation via dynamic modeling of the inducibility of a gene network.
20/1/2017 Thomas Karaouzene POSTPONED
16/12/2016, R32 guest speaker:
Patrick Valentin
Modèle extensif trilocus à six étapes avec recombinaison asymétrique, fécondité et viabilité.
Wednesday 14/12/2016 2:00 PM, R32 guest speaker:
Samuel Alizon, CNRS MIVEGEC, Montpellier
Clinical and epidemiological applications of virus phylogenies.
Wednesday 7/12/2016 1:30 PM, R31 Om Kulkarni Bioinformatics analyses of Next Generation Sequencing data for studying within-patient genetic heterogeneity of Hepatitis C Virus
2/12/2016, R32 Surya Ghosh Coarse-grained polymer model of chromosome.
25/11/2016 guest speaker:
Fabien Pierrel, TIMC-IMAG/GEM
An experimental evolution approach to bypass mitochondrial respiratory deficiency in Saccharomyces cerevisiae and linkage analysis through a multiple backcross strategy.
18/11/2016 [lyonSysBio -> no seminar]
Tuesday 08/11/2016 11:30 AM, R31 guest speaker:
Sean Robinson, CEA BIG (Biosciences and Biotechnology Institute of Grenoble)
Incorporating interaction networks into the determination of gene hits with Markov random fields.
4/11/2016 11:00 AM, R32 guest speaker:
Anna BONNET, AgroParisTech
Heritability estimation in high dimensional mixed models.
07/10/2016 1:00 PM, R32 Florian Privé Getting My Colleagues Hooked on R.
Wednesday 31/08/2016 2:00 PM guest speaker:
Michael Fuchs, National Chiao Tung University, Hsinchu, Taiwan
Limit laws for k-pronged nodes and more general patterns in phylogenetic trees.

2016 summer break

01/07/2016 Olivier François The geographic distribution of singletons in the allelic frequency spectrum.
17/06/2016 Florian Privé Proposing a Genetic risk score based on statistical learning (using R).
10/06/2016 Ghislain Durif Count Matrix Factorization for single cell data analysis.
13/05/2016 Helena Martins A new Genome-Scan Method to Identify Loci under Selection in Continuous Populations.
29/04/2016 Keurcien Luu pcadapt: an R package to perform genome scans for selection based on principal component analysis.
15/04/2016, R218 Om Kulkarni Bayesian evolutionary analysis of Hepatitis C Virus using BEAST.
01/04/2016, R32 Thomas Dias-Alves Jupyter: an open source tool for data science, computing and pedagogy.
25/03/2016, R32 Arnaud Seigneurin 8-year survival rates of lung cancer: a population-based study using data from french cancer registries.
18/03/2016 guest speaker:
Stephane Guindon, LIRMM, Montpellier
Demographic inference under the coalescent in a spatial continuum.
11/03/2016 Eric Fanchon Reflections on stochastic spatial simulations.
Tuesday 09/02/2016
2:00 PM, R32
Bastien Boussat Team strategies and tools to improve hospital patient safety : contribution of the Experience Feedback Committee.
22/01/2016 Ingrid Roche Contribution of selected various methods of spatial analysis of incidence data : Application to the Isere cancer registry data.
15/01/2016 Kevin Caye Méthodes d'apprentissage statistique pour les tests d'association écologique
08/01/2016, R32 Thomas Karaouzene (BCM / TIMC et GETI / IAB, Grenoble) MutaScript: a new tool for calculating a mutational score for each coding transcript.
11/12/2015 guest speaker:
Magali Richard, LBMC, ENS Lyon
Functional genetic diversity of the yeast galactose network.
Wednesday 02/12/2015
11:15 AM
, R31
guest speaker:
Surya Ghosh, Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, Palaiseau
Anomalous tracer diffusion in crowded medium.
2:00 PM -> 5:00 PM
BCM/DYCTIM joint seminar
Tuesday 17/11/2015
11:00 AM R32
guest speaker:
Annaël Brunet, Laboratoire de Physique Théorique, Toulouse
Study at the single molecule level of conformational changes of the DNA molecule: impact of local defects and of physicochemical conditions.
13/11/2015 guest speaker:
Jean-Charles Walter, Labo. C. Coulomb (L2C) Montpellier
Physical modeling of active bacterial DNA segregation.
1:15 PM, R218
Daniel Jost A hierarchical folding algorithm to partition chromosomes into interacting compartments.
15/10/2015 3:00 PM
Agnès Sjostrand (pré-soutenance de thèse) Origins and adaptation in humans: case study of taste and lifestyle.
09/10/2015, R32 guest speaker:
Baptiste Bedessem, DYCTIM / TIMC-IMAG
SMT or TOFT? How the two main theories of carcinogenesis are made (artificially) incompatible.
29/09/2015 11:15 AM guest speaker:
Thibaut Lepage, LAPM Grenoble (TBC)
Modeling and simulation of long supercoiled DNA molecules.
25/09/2015 Nicolas Mobilia (pré-soutenance de thèse) Méthodologie semi-formelle pour l’étude de systèmes biologiques : Application à l’homéostasie du fer.

2015 summer break

07/07/2015 Olivier François Arbitrariness in research evaluation: What Bayes can tell us.
30/06/2015 1:00 PM, R32 José Labarère Derivation and validation of clinical prediction models.
23/06/2015 Helena Martins A Genome-Scan Method to Identify Loci under Selection in Continuous Populations.
16/06/2015, R32 Sophie Lambert-Lacroix Modèle mixte fonctionnel.
09/06/2015 11:00 AM guest speaker:
Ivan Junier, LAPM Grenoble
What underlies transcriptional co-expression in bacteria? An evolutionary perspective.
02/06/2015, R32 guest speaker:
Laurent Guyon, iRTSV/BGE/Biomics, CEA Grenoble
Inferring microRNA function(s) with target-based network.
19/05/2015, R32 Thomas Dias-Alves Machine learning for haplotype phasing in genomics.
12/05/2015 Keurcien Luu Fast principal components analysis reveals independent evolution of ADH1B gene in Europe and East Asia - manuscript
05/05/2015, R32 Alexandre Rocca Application of Formal Methods to Biological System Modelling.
28/04/2015 Kevin Caye Spatially regularized NMF for population genetic applications.
07/04/2015, R32 guest speaker:
Christine Brun, TAGC, Marseille
Interactomes of Multifunctional proteins.
31/03/2015 No seminar (persyval / persyvact day)
24/03/2015 guest speaker:
Patrick Schiavone, ASELTA Nanographics, Grenoble
Joint seminar with TIMC-GMCAO: overview of Patrick Schiavone's research topics.
17/03/2015 Eric Fanchon Modeling network dynamics -- methods for time scale separation
10/03/2015, R32
guest speaker:
Emilie Neveu, NANO-D / INRIA Grenoble
Searching for the structures of complexes of proteins: combining machine learning and 3D protein geometry.
03/03/2015 BCM-only project discussion:
Benoît Polack, TIMC-TheREx Grenoble
Nanostructure du caillot de fibrine
24/02/2015, R32 Arnaud Seigneurin Modélisation des bénéfices et des risques d'un programme de dépistage du cancer du sein en population générale.
27/01/2015, R218 Michaël Blum Detection of local adaptation based on principal component analysis: application to the 1000 Genome data
13/01/2015 guest speaker:
Olivier Rivoire, LIPhy Grenoble
Heredity in evolution & evolution of heredity
06/01/2015 no seminar: AERES preparation

16/12/2014 no seminar: AERES preparation
9/12/2014 guest speaker:
Thomas Karaouzene, AGIM/GETI, Grenoble
DNAseq pipeline design, from reads alignment to variant selection
2/12/2014, R32 guest speaker:
Yves Rozenholc, MAP5: laboratoire de Mathématiques Appliquées à Paris V
A probabilistic GAP for tumoral mutation characterization.
25/11/2014, R32 guest speaker:
Luiz Antonio R. de Santana, Department of Mathematics, Federal University of Paraná, Brazil
An eco-epidemiologic model: selective predation
2:00 PM, R31
Daniel Jost Modeling biological systems: from biomolecules to gene regulation.
Tuesday 21/10/2014
2:00 PM, R32

guest speaker:
Katalin Csilléry, INRA Avignon UR 629, Ecologie des Forêts Méditerranéennes
Estimating local parameters of an eco-physiological model for silver fir along three altitudinal gradients in the Mediterranean pre-Alps using Approximate Bayesian Computation.
Tuesday 30/09/2014
1:30 PM, R32
Nicolas Duforet-Frebourg (pré-soutenance de thèse) Statistiques bayésiennes en génétique des populations: modèle à facteurs et processus gaussiens pour étudier la variation génétique neutre et adaptative.
11:00 AM
room R32
Eric Frichot (pré-soutenance de thèse) Modèles a facteurs latents pour les études d’association écologique en génétique des populations.
room R32
guest speaker:
Adeline Leclercq-Samson, LJK Grenoble
Estimation in stochastic neuronal model with particle filter and stochastic approximation methods

2014 summer break

26/06/2014 Om Kulkarni VirEst: eHive bioinformatics pipeline for viral diversity estimation.
19/06/2014 Laurent Trilling ASP(Answer Set Programming) for expressing general CTL temporal formulas and modelling defaults.
room R32
Timo Deist Inference of individual ancestry coefficients using genomic and geographic data.
05/06/2014 cancelled

22/05/2014 guest speaker:
Vincent Bonneterre, EPSP/TIMC Grenoble
Detection of new work related diseases within the French National network for Work Related Diseases and Prevention Network : test of safety data mining tools used in pharmacovigilance
15/05/2014 Alexandre Rocca Exploiting the Eigenstructure of Linear Systems to speed up Reachability Computations
room R32
Agnès Sjostrand Taste perception and lifestyle in Central Africa.
Monday 14/04/2014
2:00 PM
guest speaker:
Thomas Hindré, LAPM Grenoble
Long term evolution of genome expression in Escherichia coli
10/04/2014 Arnaud Seigneurin Overdiagnosis from non-progressive cancers and competitive causes of deaths associated with mammography screening: a simulation study with calibration to population based data.
room R32
guest speaker:
Larissa Viraphong, LAPM Grenoble
Experimental and theoretical evolution of mutation rates
27/03/2014 Nicolas Mobilia Search and Characterization of High-dimensional Valid Sub-space : Application to Iron Homeostasis Model
guest speaker:
Jimmy Garnier, LAMA, Université de Savoie
Propagation d'espèce et diversité génétique : une nouvelle approche mathématique.
Tuesday 18/03/2014
2:00 PM
room R218
guest speaker:
Dominique Schneider, LAPM Grenoble
Experimental evolution with bacteria.
27/02/2014 Sophie Lambert-Lacroix On the robustness of the generalized Fused Lasso to prior specifications
20/02/2014 [réunion AERES des permanents BCM, pas de séminaire]
room R32
guest speaker:
Thomas Burger, iRTSV / EDyP, Grenoble
SAGA: Sparse And Geometry-Aware non-negative matrix factorization through non-linear local embedding.
23/01/2014 [réunion AERES des permanents BCM, pas de séminaire]
Monday 20/01/2014
1:30 PM
guest speaker:
Jon Wakefield, University of Washington
Detecting signals in pharmacogenomic genome-wide association studies.
09/01/2014 Michaël Blum Estimation of False Discovery Rates.
12/12/2013 Laure Sambourg Deciphering omics data: on the importance of quality control. Application to ovarian cancer.
guest speaker:
Marc Bailly-Bechet, LBBE Lyon / détaché à Paris
Codon usage, host-virus interactions and the HIV vaccine.
Thomas Karaouzene Design and implementation of a method for predicting non-allelic homologous recombination (NAHR).
14/11/2013 12h00 guest speaker:
Laurent Jacob, LBBE, Lyon
Correcting gene expression data when neither the unwanted variation nor the factor of interest are observed.
room R32
Eric Frichot. Latent Factor Mixed Models: software & perspectives.
03/10/2013 Nicolas Duforet-Frebourg Bayesian principal component analysis to detect genomic regions involved in local adaptation.
Friday 06/09/2013
at 13h30
Om Kulkarni Estimation of genetic diversity in NS3-protease region of Hepatitis C virus using 454 pyrosequencing.

2013 summer break

04/07/2013 séminaire extérieur:
Alexandra Vatsiou, LECA, Grenoble
Comparison of Haplotype Methods to detect selection.
27/06/2013 Laurent Trilling ASP (Answer Set Programming) for expressing protein signaling models and time series in genetic networks.
20/06/2013 séminaire extérieur:
Romain Testylier, Verimag, Grenoble
Reachability analysis of nonlinear dynamical systems.
13/06/2013 Olivier François Super fast inference of ancestry coefficients using NMF algorithms.
06/06/2013 Eric Fanchon The results of the ENCODE project. A journal club on the ENCODE paper, and related papers including criticisms.
à 14h15
séminaire extérieur:
Geoffroy Andrieux, IRSET, Rennes
A guarded transition approach to integrate the human cell signaling pathways into a single unified dynamic model.
16/05/2013 séminaire extérieur:
Eugenio Cinquemani, INRIA, Grenoble
Mixed-effects modelling of biochemical reaction networks: Two applications on two systems.
18/04/2013 séminaire extérieur:
Farida Enikeeva, INRIA Grenoble
High-dimensional change-point detection under sparsity assumptions.
11/04/2013 séminaire extérieur:
Pierre de Villemereuil, LECA, Grenoble
Bayesian models for comparative analysis integrating phylogenetic uncertainty.
28/03/2013 Nicolas Mobilia Model of Biological Systems: Application to Iron Homeostasis Network.
21/03/2013 séminaire extérieur:
Mattias Jakobsson, Uppsala University
Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe.
14/03/2013 Laure Sambourg
Analysis of ovarian cancer sequencing data.
21/02/2013 Arnaud Seigneurin
Apport des modèles de simulation dans le cadre de l'évaluation des dépistages des cancers.
07/02/2013 Agnès Sjostrand
Perceptions gustatives de deux populations africaines et analyses de puces de SNPs.
~ 25/01 à 15h
Nicolas Thierry-Mieg
remplacé (?) par ma soutenance d'HDR, le 25/01 à 15h
10/01/2013 José Labarère Systematic review and meta-analysis of diagnostic accuracy test studies.
20/12/2012 Michaël Blum
 Fine-scale genetic structure of the north-western French  population.
6/12/2012 Sean Schoville
Source-sink dynamics, not adaptation, governs patterns of genetic variation in an urban butterfly.
22/11/2012 Sophie Lambert
Clustering for mixed-effects functional models.
15/11/2012 Johanna Bertl Approximate maximum likelihood estimation in the coalescent.
08/11/2012 François Mathieu
Méthodes d'apprentissage statistique pour l'analyse de données génétiques.
11/10/2012 Eric Frichot Correcting principal component maps for effects of spatial autocorrelation in population genetic data.
à 14h00
séminaire extérieur:
Yanis Bouchenak-Khelladi, Departement de Botanique, Universite de Seville, Espagne, et Department de Ressources Genetiques et Biotechnologie, Institut National d'Agronomie, Alger, Algerie
Reconstructions biogeogeographiques et paleo-ecologiques a l'aide d'arbres phylogenetiques: exemples africains
à 14h15
Nicolas Duforet
Non-stationary patterns of Isolation-by-distance: inferring measures of genetic friction.

pause estivale 2012

14/06/2012 séminaire extérieur:
Denis Laloe, INRA, Jouy en Josas
On the genetic interpretation of Between-Group PCA on SNP data.
07/06/2012 Samuel Chorlton
Efficient parameter search in a re-examination of the IRMA GRN.
24/05/2012 Yu Zhang
Inference of Population Genetic Structure and Natural Selection using Latent Variable Models.
10/05/2012 Eric Frichot
Landscape genomic tests for associations between loci and environmental gradients.
03/05/2012   Nicolas Thierry-Mieg Genomic imprinting and NGS.
séminaire extérieur:
Amandine Veber, Centre de Mathématiques
Appliquées, Ecole Polytechnique, Palaiseau
De l'utilité des arbres généalogiques dans l'étude de populations structurées spatialement.
05/04/2012 Nicolas Mobilia

Modélisation Continue et Exploration du Réseau du Fer.

29/03/2012 Igor Marin Novel mitochondrial mechanism in hypoxia induced ROS release :
discrete modelling of the dynamics of molecular networks to
explain COPD comorbidities.
22/03/2012 à 11h
salle R31
séminaire extérieur:
Goran Frehse, Verimag, Grenoble
Safety Analysis of Hybrid Systems with SpaceEx.
15/03/2012 Igor Marin
08/03/2012 séminaire extérieur:
Hans Geiselmann, Adaptation et Pathogénie des Microorganismes, La Tronche
Analysis of genetic regulatory networks in Escherichia coli.
01/03/2012 nada, journée des doctorants

16/02/2012 José Labarère Quantification de la valeur ajoutée d'un biomarqueur à un modèle de prédiction clinique : le NRI.
Laure Sambourg Analyse de données de séquençage next-generation du cancer de l'ovaire: à la recherche de gènes "drivers".
19/01/2012 Michaël Blum The main orientations of intracontinental human genetic differentiation.
05/01/2012 Fabien Corblin Intégration de données partielles et inférence automatique de propriétés pour les réseaux de régulations génétiques.
08/12/2011 Sean Schoville Evolutionary diversification of alpine insects in California.
Hervé Guiol Nouveaux modèles de misanthropes et d'exclusion.
10/11/2011 Flora Jay
Méthodes bayésiennes pour la génétique des populations :
relations entre structure génétique des populations et environnement.
27/10/2011 Nicolas Duforet Method and software using haplotypes to improve population structure inference.
13/10/2011 Sophie Lambert Estimateurs pénalisés et modèles à coefficients variables.
salle R32
séminaire extérieur:
Guillaume Bouchard
Xerox Research Centre Europe, Meylan
Non-Gaussian Factor Analysis using Variational Approximations.
séminaire extérieur:
Aluisio de Souza Pinheiro
IMECC-Unicamp, Brésil
Quasi U-statistics and Applications to Genetics.

pause estivale 2011

13h, salle R218
Laurent Trilling Réseaux logiques de régulation génique intégrant délais et accumulations.
13h, salle R218
Eric Frichot
Etude de la longueur des gènes le long d'une phylogénie.
Olivier François
salle R218
séminaire extérieur:
Franck Picard, LBBE, Lyon
Statistical mapping of replication origins in the human genome.
mercredi 1/06/2011
salle R218
Agnès Sjostrand
Ancestral Structure of African populations and the Out-of-Africa Event.
Nicolas Thierry-Mieg Production et analyse de données ChIP-seq.
Nicolas Mobilia Modélisation en ASP.
salle R218

séminaire extérieur:
Phillip Endicott, labo d'Eco-anthropologie et Ethnobiologie, Paris
'Denisovans' and the burgeoning tree of hominins; the devil in the detail.
Eric Fanchon Questions combinatoires liées à la modélisation de réseaux booléens.
José Labarère
Analyse par propensity score en épidémiologie clinique.
Flora Jay La structure génétique de populations de plantes alpines et ses potentielles modifications suite à un changement climatique.
bonnes vacances
séminaire extérieur:
Adrien Richard, I3S, U. Nice
Théorèmes de point fixe dans les réseaux Booléen.
Fabien Corblin Answer Set Programming pour la modélisation de réseaux biologiques : le point sur mes travaux.
séminaire extérieur:
Miguel Arenas, Université de Berne
Consequences of Range Contractions and Range Shifts on Molecular Diversity.
Hervé Guiol Un modèle d'évolution en temps continu.
Michaël Blum No evidence for a human bottleneck during the penultimate glacial period.
Per Sjodin et al
déplacée au
Laure Sambourg
Finding the "dark matter" in human and yeast protein network prediction and modelling.
Ranea et al. PLoS Comput Biol. 2010 Sep 23;6(9). pubmed. pdf.
le catalogue de King Jouet?
Sophie Lambert
Analyse de données de spectrométrie de masse.