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 Böelle, Romulus Breban, Vittoria Colizza, Judith Legrand, Lulla Opatowski, Chiara Poletto, Virginie Supervie, Laura 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
| France Mentré (Université de Paris, IAME, INSERM, Paris, France)
Modelling the impact of gut exposure to moxifloxacin (MXF) on the temporal changes in gut microbiota diversity in healthy volunteers Abstract:
Although the global deleterious impact of antibiotics on the intestinal microbiota is well known, temporal changes in microbial diversity during and after an antibiotic treatment are still poorly characterized. To prevent antibiotic-induced perturbations on gut microbiota, DAV132, a novel colon-targeted adsorbent, which sequesters antibiotic residues in the lower gastrointestinal tract was developed.
We analysed data from two randomized clinical trials performed in healthy volunteers. In trial CL1002, healthy volunteers were assigned to a 5-day treatment by MXF (n=14) or to a control group (n=8). In trial CL1004, healthy volunteers were assigned to a 5-day treatment by MXF with eleven different DAV132 dosing regimens (n=12 per dosing regimen) or to a control group (n=12). Repeated MXF concentrations were measured in both plasma and feces. Repeated Shannon diversity index were measured from 16S rRNA gene metagenomics analysis of fecal microbiota. Specific dynamic models were developed to relate MXF concentrations in the gut and bacterial diversity over time. Data were analysed using nonlinear mixed effect models with the SAEM algorithm in the MONOLIX software.
Data from trial CL1002 was first modelled. MXF reduces bacterial diversity in a gut concentration-dependent manner which was quantified through a turn-over model with the Emax model. As a consequence of both the long fecal half-life of MXF and the susceptibility of the gut microbiota to MXF, bacterial diversity indices did not return to their pre-treatment levels until day 16. We then extended that model to analysed the data of trial CL1004. We modeled reduced fecal MXF concentrations using a transit model for DAV132 kinetics and a Michaelis-Menten model with an effect of amount of activated charcoal on adsorption efficacy. Change in MXF-induced perturbation on gut microbiota diversity was then quantified through the same turn-over model.
The proposed model can be used to simulate the effect of various duration of MXF treatment and the protective effect of DAV132 on gut microbiota.
Contact : Lulla Opatowski
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Tuesday, Dec 10th, 2019 |
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
12 noon -1 pm |
| France Mentré | Modelling the impact of gut exposure to moxifloxacin (MXF) on the temporal changes in gut microbiota diversity in healthy volunteers | Tuesday, Dec 10th, 2019
12 noon -1 pm |
| Gabriela Gomez | TBA |
Tuesday, Jan 14th, 2020 12 noon -1 pm |
| Oliver Ratman | Quantifying HIV transmission flow from cross-sectional viral phylogenetic deep sequence data: a population-based study in Rakai, Uganda |
Tuesday, May 5th 2020, 12 noon -1 pm |
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 |
| 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 |
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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 |
| 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 |
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| Can we use mathematical modeling to design evolution-proof drugs? | Tuesday, April 17th, 2018 12 noon -1 pm Institut Pasteur Room Jean-Paul Aubert |
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| Matt Ferrari | Better with age: insights on measles persistence and control |
Wednesday May 2nd 2018 |
| 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
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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.
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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 |
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| Anne GOELZER | Quantitative prediction of genome-wide resource allocation in bacteria | Tuesday, March 7th, 2017 12 noon -1 pm Room Jean Paul Aubert |
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| Viet Chi Tran | Modèles mathématiques pour des épidémies se propageant sur des graphes aléatoires | Wednesday, April 19th, 2017 12 noon -1 pm Room Retrovirus |
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| Karoline Faust | Modeling the dynamics of a synthetic gut community | Wednesday, May 3rd, 2017 12 noon -1 pm Room Retrovirus |
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| 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.
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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 |
