About
Statistical and Mathematical Modeling in Biological Applications — SaMMBA
Seminars are currently accessible onsite (seminar + buffet lunch) and online (link provided by email).
[It is possible to contact any of the organisers to be included on the mailing list]
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 be pre-registered and get 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*: Romulus Breban, Vittoria Colizza, Lulla Opatowski, Raphaëlle Metras & Laura Temime. To arrange to meet with an invited speaker, contact the host of that speaker.
The SaMMBA seminars is funded by the Inception program, Institut Pasteur and the ANRS-MIE.
We received financial support in the past from the ANRS, the region Ile de France through the DIM Systèm es complexes and the DIM One health, from Inserm and the department MIA of INRA.
Former active organizers of the seminars: Virginie Supervie and Elisabeta Vergu.
Next Lecture
Georg K. Gerber, MD, PhD (Harvard Medical School) Title : Novel Machine Learning Methods for Dissecting the Microbiome to Improve Human Health Abstract:Our microbiota, or the trillions of micro-organisms living on and within us, constitute extremely rich ecosystems with critical functions for human health. Major perturbations of the microbiome, such as diet or therapeutic drugs (e.g., antibiotics) may result in dysbiosis, which has been associated with many human disorders, including infections, inflammatory bowel disease, neurological diseases, autoimmunity/allergies, diabetes, and malignancies. However, understanding our microbiota and ultimately harnessing its properties to improve human health is challenging, given the scale, complexity, temporal/multi-modal nature, and noisiness of microbiome datasets. In this talk I will describe novel computational approaches my lab is developing to tackle these challenges, including: (1) probabilistic machine learning models that learn dynamical systems from longitudinal microbiome data to support rational design of bacteriotherapies, e.g., for C. difficile and autoimmune diseases, (2) deep learning methods that use metabolomics and sequencing data to infer fully human-interpretable predictive rules for improved diagnostics, e.g., for C. difficile recurrence, (3) generative deep learning methods for discovering relationships between the microbiome, human immune system, and infections, e.g., tuberculosis. My talk will be geared toward a general audience, focusing on the biomedical implications of our work and intuitive descriptions of core computational innovations. Contact: Lulla Opatowski |
Tuesday, April 2nd, 2024 |
Full Schedule 2023-2024
| Amandine Veber | Modelling the dynamics of genetic diversity in a spatially structured population | Tuesday, Sept 5th, 2023 12noon -1pm Institut Pasteur / Online |
| Juan Vesga | Modelling CCHF spillover in high endemic settings and the potential impact of vaccines | Tuesday, Oct 4th, 2023 12noon -1pm Institut Pasteur / Online |
| Kris Parag (Imperial College London) | Ineffective reproduction numbers. What do conventional measures of infectious disease transmissibility fail to measure? |
Wednesday, Dec 13th, 2023 12noon -1pm Institut Pasteur / Online |
| Stefan Flashe (LSHTM) | Pathogen interactions: relevant for vaccine decision making? | Wednesday, Jan 17th, 2024 12noon -1pm Institut Pasteur / Online |
| James Hay (Oxford Big Data Institute, UK) | Using quantitative biomarkers to track infectious disease dynamics | Friday, Feb 2nd, 2024 12noon -1pm Institut Pasteur / Online |
| Kevin Foster (Univ of Oxford) | Competition and warfare in bacteria and the human microbiome | Tuesday, March 12th 12noon -1pm Institut Pasteur / Online |
| Georg Gerber (Harvard) | Novel Machine Learning Methods for Dissecting the Microbiome to Improve Human Health | Tuesday, April 2nd 12noon -1pm Institut Pasteur / Online |
| Sebastian Duchesnes (Institut Pasteur) | TBA | Tuesday, May 14 12noon -1pm Institut Pasteur / Online |
| Luis Almeida (Sorbonne Univ) | TBA | Tuesday, June 4 12noon -1pm Institut Pasteur / Online |
Full Schedule 2022-2023
| Eugenio Valdano | Non-selective distribution of infectious disease prevention may outperform risk-based targeting | Wednesday, Sept 14th, 2022 12 noon -1 pm Institut Pasteur |
| François Massol | Some uses of network methods to understand host-microbiota interactions | Oct 4th 2022 12 noon -1 pm Institut Pasteur |
| Aleksandra Walczak & Thierry Mora | Immune repertoires: dynamics and co-evolution with pathogens | Wednesday, Nov 16th 2022 12 noon -1 pm Institut Pasteur |
| Florence Debarre | Stochastic models of early epidemics, and their applications to Covid-19 | Wednesday, Dec 7th 2022 12 noon -1 pm Institut Pasteur |
| Samuel Alizon | How host heterogeneity impacts the way (co)infections spread | Wednesday, Jan 4th 2023 12 noon -1 pm Institut Pasteur |
| Niel Hens | On risk perception and contact behaviour during the COVID-19 pandemic | Wednesday, March 8th 2023 12 noon -1 pm Institut Pasteur |
| Florence Bansept | Evolution in biphasic life cycles | Tuesday, April 4th 2023 12 noon -1 pm Institut Pasteur |
| Marga Pons Salort | Emergence of enteroviruses as novel causes of diseases: opportunities to infer changes in their circulation dynamics from sero-epidemiology data | Wednesday, May 17th 2023 12 noon -1 pm Institut Pasteur |
| Warren Tennant | Tuesday, June 6th 2023 12 noon -1 pm Institut Pasteur |
Schedule 2021-2022
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Wednesday, Sept 8th 2021, 12 noon -1 pm |
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| Fabien Crauste | Mathematical and Computational Immunology: Differentiation, Heterogeneity, and Multiscale Descriptions of the CD8 T Cell Immune Response |
Tuesday, Oct 5th 2021, 12 noon -1 pm |
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| Joshua Weitz | Pandemic Theory and Pasteur’s Quadrant: On the Ongoing Need for Response and Mitigation Instruments |
Tuesday, Nov 9th 2021, 12 noon -1 pm |
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| Ben Cooper |
Determining appropriate antibiotic treatment duration and understanding its impact on antimicrobial resistance. |
Wed, Dec 15th 2021, |
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| Frederik Graw | Deciphering infection and immune processes within tissues |
Wed, Feb 16th 2022, 12noon -1pm |
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| Manlio De Domenico | Coupling human behavior with epidemic spreading: multilayer networks and the distorting lens of human mobility data | Tuesday March 8th 2022 12noon -1pm Online |
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| Claude Loverdo | Bacteria in the digestive tract : Evolution in a flow; and stochastic models of population dynamics for inferring colonization probability. | Tuesday April 19th 2022 12noon -1pm Institut Pasteur / Online |
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| Guillaume Fournié | Avian influenza transmission and control across live poultry trading networks | Wed June 8th 2022 12noon -1pm Institut Pasteur / Online |
Schedule 2020-2021
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Tuesday, March 16th 2021, 12 noon -1 pm |
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| Benoit Liquet | Sparse Group Models for leveraging Pleiotropy effect from genome-wide association studies |
Tuesday, April 13th 2021 10am-11am Online |
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| Andrea Wilson | Investigating and modelling the impact of vaccines and genetic selection on infectious disease transmission in farmed animals |
Wednesday, May 12th 12noon-1pm Online |
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| Michael White | Mathematical modelling of novel serological diagnostic tools for malaria and coronaviruses |
Wednesday, June 16th 12noon-1pm Online |
Full 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, 201912 noon -1 pm Institut Pasteur |
| 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, 201912 noon -1 pm Institut Pasteur |
| Gabriela Gomez | Unveiling the effects of individual variation in epidemiology, ecology and evolution |
Tuesday, Jan 14th, 2020 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, Feb 25th, 2020 12 noon -1 pm |
| Nicole Mideo | Unveiling the effects of individual variation in epidemiology, ecology and evolution |
Wednesday, Mar 11th, 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 | 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 |
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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. | 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 |
