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About

The huge amount of molecular data available nowadays can help addressing new and essential questions in evolution. However, reconstructing evolution requires models, algorithms, and statistical and computational methods of ever increasing complexity. Developing methods that scale with the “deluge” of data is a real challenge, in terms of algorithmics but also modeling. Out unit aims at developing new methodologies and algorithms that are able to tackle efficiently these challenges, in the field of evolution and molecular phylogeny.

Our second aim is to apply these methods and tools to pathogens, mostly viruses, and especially HIV. The goals are multiple: understand their evolution (e.g. the emergence and transmission of drug resistance mutations), decipher their genome (e.g. to confirm the existence of the 10th gene of HIV), design surveillance tools (e.g. to control outbreaks). Most of the current methods to tackle these questions are based on Bayesian approaches, which are computationally heavy and not able to process the large data sets available nowadays. To overcome these limitations we are working on new maximum-likelihood and approximate bayesian methods (ABC) applicable to very large data sets comprising several dozens of thousands of sequences. Recently we started combining advanced research in machine learning with evolutionary approaches to analyse very large pathogen sequence data sets and complex virus transmission scenarios.

Every year we co-organize the Mathematical and Computational Evolutionary Biology conference in the South of France, and teach Phylogenetics courses in Paris and the International Network of Institut Pasteur (see below). We regularly host researchers from all around the world (New Zealand, Australia, Brazil, Japan, Corea, Cambodia, Cuba, Uk and  Nederlands for the past few years).

We have several postdoc positions available; if you are highly motivated and interested in our research themes, with a PhD in computer science, statistics, mathematics, evolutionary biology or molecular epidemiology, please contact (olivier dot gascuel [at] pasteur dot fr).

Former Members

2000
2000
Name
Position
2016
2017
Johanna Escobar
Administrative Staff
2016
2018
Damien Correia
Engineer
2016
2018
Sohta Ishikawa
Post-doc
2017
2017
Kristof Theys
Visiting Scientist
2017
2018
Miraine Davila Felipe
Post-doc
2017
2018
Tomochika Fujisawa
Post-doc
2017
2018
Mathieu Moslonka-Lefebvre
Post-doc
2018
2018
Kary Ocaña
Visiting Scientist
2018
2019
Sebastian Duchene
Visiting Scientist
2018
2018
Tristan Dot
Undergraduate Student
2018
2019
Alfried Vogler
Visiting Scientist
2019
2019
Sokhoun Yann
Visiting Scientist
2019
2019
Nimol Khim
Visiting Scientist
Show all

Courses

Molecular evolution and phylogenetics module (IBT 2020 H3ABioNet)

The Molecular evolution and phylogenetics is a 4-session module of the Introduction to Bioinformatics  Training 2020 (IBT) organised by Pan African Bioinformatics Network for the Human Heredity and Health in Africa (H3ABioNet) consortium. It […]

2020-07-28 09:00:00 2020-08-06 17:00:00 Europe/Paris Molecular evolution and phylogenetics module (IBT 2020 H3ABioNet) The Molecular evolution and phylogenetics is a 4-session module of the Introduction to Bioinformatics  Training 2020 (IBT) organised by Pan African Bioinformatics Network for the Human Heredity and Health in Africa (H3ABioNet) consortium. It […] Africa

minicourse Introduction to Phylogenetics – CentraleSupélec

The ‘Introduction to Phylogenetics’ was taught as a part of a course on mathematical modeling for biology for CentraleSupélec students. It introduced the mathematics and algorithms used for phylogenetic tree inference (with distance and […]

2018-12-18 13:45:00 2018-12-18 17:00:00 Europe/Paris minicourse Introduction to Phylogenetics – CentraleSupélec The ‘Introduction to Phylogenetics’ was taught as a part of a course on mathematical modeling for biology for CentraleSupélec students. It introduced the mathematics and algorithms used for phylogenetic tree inference (with distance and […] Centralesupélec, Rue Joliot Curie, Gif-sur-Yvette, France

Evolution and Phylogenetics – Institut Pasteur Tunis

This introductory course aims to give the basic theoretical and practical concepts, best practices, and software necessary to start working on molecular phylogenetics and its applications to epidemiology. The course is a part of […]

2020-12-02 09:00:00 2020-11-06 18:00:00 Europe/Paris Evolution and Phylogenetics – Institut Pasteur Tunis This introductory course aims to give the basic theoretical and practical concepts, best practices, and software necessary to start working on molecular phylogenetics and its applications to epidemiology. The course is a part of […] Institut Pasteur، Tunis, Tunisia

Behind Evolutionary Trees: Mathematics and Algorithms in Phylogenetics – Montevideo 2019

Evolutionary trees are used in many domains, to reveal the function of genes, study the outbreak of epidemics, and set up inventories of biodiversity and its decline, among other things. Phylogenetic software programs for […]

2019-10-22 09:00:00 2019-10-24 17:00:00 Europe/Paris Behind Evolutionary Trees: Mathematics and Algorithms in Phylogenetics – Montevideo 2019 Evolutionary trees are used in many domains, to reveal the function of genes, study the outbreak of epidemics, and set up inventories of biodiversity and its decline, among other things. Phylogenetic software programs for […] Institut Pasteur de Montevideo, Mataojo, Montevideo Montevideo Department, Uruguay

Mathematical and Computational methods for Phylogenetics and Evolutionary Epidemiology – Havana 2019

Mathematical and Computational concepts and models are essentials in new developments of the evolutionary studies related to outbreaks of infectious diseases pandemics.  Predicting, assessing and controlling potential outbreaks are key aspects of the worldwide […]

2019-10-14 09:00:00 2019-10-18 16:00:00 Europe/Paris Mathematical and Computational methods for Phylogenetics and Evolutionary Epidemiology – Havana 2019 Mathematical and Computational concepts and models are essentials in new developments of the evolutionary studies related to outbreaks of infectious diseases pandemics.  Predicting, assessing and controlling potential outbreaks are key aspects of the worldwide […] Institute of Tropical Medicine “Pedro Kourí” (IPK), Havana, Cuba

Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation

Ce cours a pour objectif de donner les bases théoriques et pratiques, ainsi que les bonnes pratiques nécessaires au démarrage de travaux en phylogénie et épidémiologie moléculaires. Les sessions théoriques donneront les bases du […]

2019-10-07 09:30:00 2019-11-11 17:30:00 Europe/Paris Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation Ce cours a pour objectif de donner les bases théoriques et pratiques, ainsi que les bonnes pratiques nécessaires au démarrage de travaux en phylogénie et épidémiologie moléculaires. Les sessions théoriques donneront les bases du […] 28 Rue du Dr Roux, Paris, France

Introduction à l’analyse Bio-informatique de séquences

L’objectif de cette formation est de présenter, au travers de l’utilisation d’outils largement utilisés, quelques grands principes sur l’analyse de séquence. L’ensemble de la formation combine exposés théoriques (fondements méthodologiques des programmes) et applications […]

2019-09-23 09:00:00 2019-09-27 17:00:00 Europe/Paris Introduction à l’analyse Bio-informatique de séquences L’objectif de cette formation est de présenter, au travers de l’utilisation d’outils largement utilisés, quelques grands principes sur l’analyse de séquence. L’ensemble de la formation combine exposés théoriques (fondements méthodologiques des programmes) et applications […] Institut Pasteur, Rue du Docteur Roux, Paris, France

Introduction à la phylogénie moléculaire

Ce cours d’introduction à la phylogénie a pour objectif d’apporter les connaissances théoriques et les bonnes pratiques d’analyse de données par les logiciels de phylogénie. Il est ouvert aux formations doctorales et aux professionnels […]

2019-02-18 09:00:00 2019-02-22 17:00:00 Europe/Paris Introduction à la phylogénie moléculaire Ce cours d’introduction à la phylogénie a pour objectif d’apporter les connaissances théoriques et les bonnes pratiques d’analyse de données par les logiciels de phylogénie. Il est ouvert aux formations doctorales et aux professionnels […] 28 Rue du Dr Roux, Paris, France

Analyse de séquences

OBJECTIFS : Les biologistes sont régulièrement confrontés à des gènes (ou des protéines) de fonctions inconnues ou mal annotés. Dans ce contexte, maîtriser quelques techniques basiques d’analyse de séquences peut se révéler d’une aide […]

2018-03-19 09:30:00 2018-09-23 17:00:00 Europe/Paris Analyse de séquences OBJECTIFS : Les biologistes sont régulièrement confrontés à des gènes (ou des protéines) de fonctions inconnues ou mal annotés. Dans ce contexte, maîtriser quelques techniques basiques d’analyse de séquences peut se révéler d’une aide […] Institut Pasteur, Rue du Docteur Roux, Paris, France

C3BI Course: Introduction to Molecular Phylogenetics – Hong Kong 2018

General Information: This introductory course aims to give the basic theoretical and practical concepts, best practices, and software necessary to start working on molecular phylogenetics and its applications to epidemiology. The course will have […]

2018-10-22 08:00:00 2018-10-27 19:00:00 Europe/Paris C3BI Course: Introduction to Molecular Phylogenetics – Hong Kong 2018 General Information: This introductory course aims to give the basic theoretical and practical concepts, best practices, and software necessary to start working on molecular phylogenetics and its applications to epidemiology. The course will have […] HKU-Pasteur Research Pole HKJC Building for Interdisciplinary Research 5 Sassoon Road, Pokfulam, Hong Kong

INTRODUCTION À LA PHYLOGÉNIE MOLÉCULAIRE : CONCEPTS, METHODES ET OUTILS

Nous proposons une formation classique à la phylogénie moléculaire avec des cours théoriques portant sur les trois méthodes de construction d’arbres phylogénétiques : distance, parcimonie et maximum de vraisemblance. Nous expliquerons les concepts généraux […]

2017-12-18 09:30:00 2017-12-22 17:30:00 Europe/Paris INTRODUCTION À LA PHYLOGÉNIE MOLÉCULAIRE : CONCEPTS, METHODES ET OUTILS Nous proposons une formation classique à la phylogénie moléculaire avec des cours théoriques portant sur les trois méthodes de construction d’arbres phylogénétiques : distance, parcimonie et maximum de vraisemblance. Nous expliquerons les concepts généraux […] 25-28 Rue du Dr Roux, 75015 Paris, France

Projects

We head the INCEPTION project for the interdisciplinary studies of the emergence of pathologies through individuals and populations. This large scale project involves nine partners (CNRS, INSERM, INRA, CEA, PSL…) and is funded by the call “Investissements d’Avenir – Convergence” (12 M€ / 10 years). We hold a Chair in PRAIRIE (Paris Artificial Intelligence Research Institute) which brings together the main researchers and teams in AI of Paris. We collaborate with a number of teams at Pasteur and worlwide on several major pathogens, notably HIV, Zika, Influenza and Dengue.

Software

Our unit aims at developing user-friendly and open-source tools (command-line or web based). These tools are mostly available on our GitHub page, and also usually as Docker images on Docker Hub (along many other tools that we wrapped on Docker containers) and sometimes on Bioconda or pypi.

Fundings

Publications

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Pictures & Media

2020 Retreat, Lausanne, UNIL 2019 Retreat, Barcelona, CRG