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Domaines Scientifiques
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Date de Début
30
Aug 2015
Date de Fin
01
Jul 2020
Statut
Ongoing
Membres
2
Structures
4

Présentation

Statistical and Mathematical Modeling in Biological Applications — SaMMBA

The seminar series Statistical and Mathematical Modeling in Biological Applications (SaMMBA) features monthly lectures and discussions with leading modelers in biological sciences. Presentations are in English or French and target an interdisciplinary audience. Seminars are held on the campus of Institut Pasteur. Access is free. However, to enter the campus, one needs a badge that is obtained at the main gate in exchange of a piece of ID (passport, citizen card or driver licence). If you are planning to come from outside the campus, please contact Lulla Opatowski to have a badge ready when you arrive.

For additional information about the series, contact the organizers: Pierre-Yves BöelleRomulus BrebanVittoria ColizzaJudith LegrandLulla OpatowskiChiara Poletto, Virginie SupervieLaura Temime and Elisabeta Vergu. To arrange to meet with an invited speaker, contact the host of that speaker. 

The SaMMBA seminars received financial support from the ANRS, the region Ile de France through the DIM Systèmes complexes, from Inserm and the department MIA of INRA. It is now funded by the region Ile de France through the DIM One health, and the Inception program, Institut Pasteur.

Next Lecture

Samuel Soubeyrand (INRA – BioSP, Avignon, France)

Inferring epidemiological links from deep sequencing data with a statistical learning approach

Abstract: 
Pathogen sequence data have been exploited to infer who infected whom, by using empirical and model-based approaches. Most of these approaches exploit one pathogen sequence per infected host (e.g. individual, household, field). However, modern sequencing techniques can reveal the polymorphic nature of within-host populations of pathogens. Thus, these techniques provide a subsample of the pathogen variants that were present in the host at the sampling time. Such data are expected to give more insight on epidemiological links than a single sequence per host. Relying on this assumption, we have developed a statistical learning approach whose idea consists of (i) learning the structure of epidemiological links with a pseudo-evolutionary model applied to training data obtained from contact tracing, for example, and (ii) using this initial stage to infer links for the whole dataset. In this talk, we will present the approach and illustrate its application in different contexts from animal, human and plant epidemiology.

Contact : Elisabeta Vergu

Wednesday, Oct 16th, 2019
12 noon -1 pm
Institut Pasteur
 

 

Schedule 2019-2020

 

Marc Baguelin Mathematical modelling to inform public health policies: shorts stories on influenza vaccination in the UK and ebola epidemics
Wednesday, Sept 25th, 2019
12 noon -1 pm
Institut Pasteur
Samuel Soubeyrand Inferring epidemiological links from deep sequencing data with a statistical learning approach Wednesday, Oct 16th, 2019
12 noon -1 pm
Institut Pasteur
Eric Volz Hidden population structure in pathogen phylogenies Wednesday, Nov 13th, 2019
France Mentré TBA Tuesday, Dec 10th, 2019

Full Schedule 2018-2019

 

Alberto d’Onofrio Behavioural Epidemiology and its limitations: A talk based on very simple models Tuesday, Sept 11th, 2018
12 noon -1 pm
Institut Pasteur
Amphitheatre Monod
Michael Blum Polygenic risk score: is there room for improvement? Wednesday, Oct 3rd, 2018
12 noon -1 pm
Institut Pasteur
 Rowland Kao Modelling explorations in bovine Tuberculosis: Investigations in a unique natural laboratory Tuesday, Nov 20th, 2018
12 noon -1 pm
Institut Pasteur
 Marc Chadeau-Hyam Developing hidden Markov Models for lung cancer risk and dynamics Tuesday, Dec 4th, 2018
12 noon -1 pm
Institut Pasteur
 Béatrice Laroche Inférence de dynamiques écologiques du microbiote digestif et lien avec des modèles épidémiologiques Wednesday, Jan 9th, 2019
12 noon -1 pm
Institut Pasteur
 Anne Cori Statistical modelling for real-time outbreak response: Recent examples on Ebola and other pathogens Tuesday, Feb 5th, 2019
12 noon -1 pm
Institut Pasteur
 Nicola Perra Forecasting the spreading of diseases in the digital era Wednesday, March 27th, 2019
12 noon -1 pm
Institut Pasteur
Christian Althaus Causes and consequences of variation in human papillomavirus vaccination uptake in Switzerland Tuesday, April 16th, 2019
12 noon -1 pm
Institut Pasteur
Shweta Bansal From Social Behavior to Network Structure for Wildlife Disease Transmission Tuesday, May 7th, 2019
12 noon -1 pm
Institut Pasteur
Eugenio Valdano Predicting epidemic risk from contact and mobility data Tuesday, June 4th, 2019
12 noon -1 pm
Institut Pasteur

 

Full Schedule 2017-2018

Benoit Durand Analysis of the Spatial Organization of Pastures as a Contact Network, Implications for Potential Disease Spread and Biosecurity in Livestock, France, 2010

Tuesday, Sept 5th, 2017
12 noon -1 pm
Institut Pasteur
Room BIME 28-01-01A

Thibaut Jombart The R Epidemics Consortium: building the next generation of statistical tools for outbreak response using R Tuesday, Oct 4th, 2017
12 noon -1 pm
Institut Pasteur
Room BIME 28-01-01A
 David Paltiel  Do Less Harm: Evaluating HIV Programmatic Alternatives in Response to Cutbacks in Foreign Aid  Wednesday, Nov 14th, 2017
12 noon -1 pm
Institut Pasteur
Room auditorium François Jacob
 Thibaud Porphyre   Climbing the ladder to preparedness: modelling the spread of swine fevers in Great Britain  Wednesday, Dec 13th, 2017
12 noon -1 pm
Institut Pasteur
Room auditorium François Jacob
 François Blanquart   The epidemiology and evolution of HIV-1 virulence  Wednesday, Jan 10th, 2018
12 noon -1 pm
Institut Pasteur
Room TBA

Tini Garske

 The Vaccine Impact Modelling Consortium: Estimating the mortality and morbidity averted through childhood vaccination programmes in low and middle income countries  Wednesday, Feb 7th, 2018
12 noon -1 pm
Institut Pasteur
Room TBA

 Cécile Viboud

Spatial dynamics and forecasting of infectious diseases: application to influenza and Ebola  Tuesday, March 13th, 2018
12 noon -1 pm
Institut Pasteur
Room Jean-Paul Aubert

 Troy Day

Can we use mathematical modeling to design evolution-proof drugs?  Tuesday, April 17th, 2018
12 noon -1 pm
Institut Pasteur
Room Jean-Paul Aubert
 Matt Ferrari  Better with age: insights on measles persistence and control

 Wednesday May 2nd 2018
12 noon -1pm
Institut Pasteur

Marc Lipsitch Why haven’t antibiotic-resistant bacteria (pneumococci, at least) taken over the world? Tuesday, June 19th 2018
12 noon -1pm
Institut Pasteur
Room Jean-Paul Aubert

 

Full Schedule 2016-2017

Raphaëlle METRAS  Studying drivers for arboviral emergence: the case of Rift Valley fever in Mayotte Abstract Wednesday, Sept 7th, 2016
12 noon -1 pm
Room BIME 28-01-01A
Rebecca GRAIS A heat-stable rotavirus vaccine: a Phase III trial in Niger Abstract Friday, Oct 14th, 2016
12 noon -1 pm
Room BIME 28-01-01A
Christophe FRASER Tracking and tackling the HIV-1 pandemic: models, evolution, genomics

 

Abstract Wednesday, Nov 9th, 2016
12 noon -1 pm
Room Retrovirus
Niel HENS Using frailty models to quantify heterogeneity in acquisition of infectious diseases based on multivariate serological data Abstract Tuesday, Dec 6th, 2016
12 noon -1 pm
Room Jean Paul  Aubert
Kevin JEAN Modelling Yellow Fever burden in Africa: insights for short- and long-term control strategies.

 

Abstract Wednesday, Jan 4th, 2017
12 noon -1 pm
Room BIME 28-01-01A
Michele TIZZONI  Fast and accurate dynamic estimation of field effectiveness of meningococcal vaccines Thursday, Feb 2nd, 2017
12 noon -1 pm
Room Jean Paul  Aubert
Anne GOELZER Quantitative prediction of genome-wide resource allocation in bacteria Tuesday, March 7th, 2017
12 noon -1 pm
Room Jean Paul  Aubert
Viet Chi Tran Modèles mathématiques pour des épidémies se propageant sur des graphes aléatoires Wednesday, April 19th, 2017
12 noon -1 pm
Room Retrovirus
Karoline Faust  Modeling the dynamics of a synthetic gut community  Wednesday, May 3rd, 2017
12 noon -1 pm
Room Retrovirus
Romulus Breban  Diffusion within Populations: From Infectious Diseases and Market Sales to Fashion First Names Thursday, June 8th, 2017
12 noon -1 pm
Room Jean Paul  Aubert

Full Schedule 2015-2016

Henrik SALJE Use of mathematical modelling to reconstruct 60 years of chikungunya epidemiology in the Philippines Abstract Wed, Sep 9th, 2015
12 noon -1 pm
Room Jean-Paul Aubert
Anton CAMACHO  The impact of dynamical modelling on public-health decisions made during the 2013-2015 Ebola outbreak Abstract Tuesday, Oct 6th, 2015
  12 noon -1 pm
Room BIME 28-01-01A
Marc LAVIELLE Modeling and simulation of complex pharmacometric models: methods and tools Abstract Tue, Nov 3rd, 2015
  12 noon -1 pm
Room BIME 28-01-01A
David CLAESSEN Eco-evolutionary dynamics in spatially complex systems: from agro-ecology to the global ocean Abstract Tue, Dec 8th, 2015
12 noon -1 pm
Room Jean-Paul Aubert
Jean-Pierre NADAL Modeling the contagion dynamics of the 2005 French riots Abstract Tuesday, Jan 5th, 2016
  12 noon -1 pm
Room BIME 28-01-01A
Mathieu ANDRAUD Infectious diseases in pigs: from parameter estimation to dynamic models Abstract Tue, Feb 9th, 2016
  12 noon -1 pm
Room BIME 28-01-01A
Marcel SALATHé Digital Epidemiology: Opportunities & Challenges of an Evolving Field Abstract Wed, March 16th, 2016
  12 noon -1 pm
Room BIME 28-01-01A
Daniela DE ANGELIS Prediction of antibiotic resistance in Staphylcoccus aureus Abstract Tue, April 5th, 2016
  12 noon -1 pm
Room Jean-Paul Aubert
Philippe LEMEY  

Phylodynamic inference in viral outbreaks: power and limitations.

 

Abstract Tue, May 3rd, 2016
  12 noon -1 pm
Room BIME 28-01-01A
Hans BOGAARDS Second-guessing the clustering of multiple HPV types: prospects of type replacement following mass immunization Abstract Tue, June 14th, 2016
  12 noon -1 pm
Room BIME 28-01-01A

 

Full Schedule 2014-2015

 

Yamir MORENO Dynamics of Interacting Diseases Abstract Tue, Sep 9th, 2014
12 noon -1 pm
Room Jean-Paul Aubert
Chiara POLLETO Modelling disease spatial spread and real time assessment of emerging pathogen events Abstract Wed, Oct 8th, 2014
  12 noon -1 pm
Room BIME 28-01-01A
Gilles WAINRIB Integrative network inference of gene expression data and applications to inflammatory bowel disease Abstract Tue, Nov 4th, 2014
  12 noon -1 pm
Room Jean-Paul Aubert
Christian ROBERT ABC methods for Bayesian model choice Abstract Tue, Dec 2nd, 2014
12 noon -1 pm
Room DUCLAUX RDC HAUT
Guillaume ACHAZ The strange case of the Standard Neutral Model of molecular evolution: when, what and why Abstract Tue, Jan 13th, 2015
 12 noon -1 pm
Room DUCLAUX RDC HAUT
Nicolas BACAER Epidemic models and seasonality Abstract Tue, Feb 10th, 2015
12 noon -1 pm
Room BIME 28-01-01A
Benoit PERTHAME Kinetic models of chemotaxis and traveling pulses Abtract Tue, Mar 10th, 2015
  12 noon -1 pm
Room DUCLAUX RDC HAUT
Samuel ALIZON Why does HIV harm its host? Clinical and epidemiological applications of virus phylogenies Abstract Tue, Apr 14th, 2015
  12 noon -1 pm
Room BIME 28-01-01A
Alan PERELSON Mathematical modeling and the potential cure of HIV Abstract Wed, May 20th, 2015
  12 noon -1 pm
Room Retrovirus
Ron BROOKMEYER Tracking the AIDS Epidemic: Estimating HIV Incidence Abtract Tue, June 2nd, 2015 
12 noon -1 pm
Pitié Salpétrière hospital,
Ecologie Cellulaire bldg.

 

 

Full Schedule 2013-2014

 

Alun LLOYD Modeling novel strategies for controlling mosquito-borne diseases Abstract Tue, Sep 24th, 2013 
12 noon -1 pm
Room Jean-Paul Aubert
Joseph DUREAU  The Public Library of Models: an open source project towards social modeling Abstract Tue, Oct 8th, 2013 
12 noon -1 pm 

Room Jules Bordet
Julia GOG Capturing the spread and evolution of influenza A Abstract Tue, Nov 5th, 2013 
12 noon -1 pm
Room Jean-Paul Aubert
Véronique THOMAS-VASLIN Modélisation de la dynamique lymphocytaire T  Abstract Tue, Dec 10th, 2013 
12 noon -1 pm 

Room Jean-Paul Aubert
Bernard
 CAZELLES Wavelet analysis as a tool for considering non-stationarity in Epidemiology Abstract Tue, Jan 7th, 2014 
12 noon -1 pm 

Room Jean-Paul Aubert
Jeremie GUEDJ Modeling hepatitis C viral kinetic in the era of direct acting antiviral agents: review and perspectives Abstract Tue, Feb 11th, 2014
12 noon -1 pm 

Room Jean-Paul Aubert
Peter WHITE Tackling TB in the Age of Austerity: ensuring we use novel tools and approaches cost-effectively Abstract Tue, Mar 4th, 2014
12:30 noon -1:30 pm

Room Jean-Paul Aubert  
Aurélien LATOUCHE Regression modeling of the cumulative incidence function with missing causes of failure Abstract Tue, Apr 1st, 2014
12 noon -1 pm

Room Jean-Paul Aubert 
Aaron KING How to tell if the honeymoon is over: testing hypotheses about pertussis and its resurgence Abstract Tue, May 6th, 2014
12 noon -1 pm 

Room Jean-Paul Aubert 
Carlo Giovanni CAMARDA Modelling Social Contact Data: a smoothing constrained approach Abstract Tue, Jun 10h, 2014
12 noon -1 pm 

Room Jean-Paul Aubert 

 

Financements