Timeline

24 Jan 2023

publication

In-Depth Characterization of Full-Length Archived Viral Genomes after Nine Years of Posttreatment HIV Control.

06 Jul 2022

publication

Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks.

28 Sep 2021

publication

Drug resistance mutations in HIV: new bioinformatics approaches and challenges.

09 Aug 2021

publication

Cuban history of CRF19 recombinant subtype of HIV-1.

01 Aug 2021

publication

Using machine learning and big data to explore the drug resistance landscape in HIV.

24 Nov 2020

publication

Origin, evolution and global spread of SARS-CoV-2

22 Oct 2020

publication

The seventh pandemic of cholera in Europe revisited by microbial genomics.

12 Oct 2020

publication

COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM.

03 Jun 2020

software

COVID-Align

26 Mar 2020

project

The dynamics of HIV-1 epidemics in Cuba (Campus France)

24 Mar 2020

project

Applying machine learning to sequence analysis (PhD project)

12 Mar 2020

project

Phylogeography

12 Mar 2020

course

Introduction to Molecular Phylogenetics – ENS Paris

12 Mar 2020

event

MCEB 2020

09 Nov 2019

course

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

09 Nov 2019

course

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

09 Nov 2019

course

Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation

01 Sep 2019

publication

A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios

20 Aug 2019

publication

A Darwinian Uncertainty Principle

02 Aug 2019

publication

PastView: a user-friendly interface to explore ancestral scenarios

02 Jul 2019

publication

NGPhylogeny.fr: new generation phylogenetic services for non-specialists

04 Jun 2019

event

MCEB 2019

04 Jun 2019

course

Introduction à la phylogénie moléculaire

29 Apr 2019

publication

Distribution and asymptotic behavior of the phylogenetic transfer distance.

12 Apr 2019

publication

Accounting for ambiguity in ancestral sequence reconstruction

06 Feb 2019

publication

Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability

19 Jul 2018

software

NGPhylogeny.fr

19 Jul 2018

software

PastML

19 Jul 2018

software

Booster

19 Jul 2018

project

The phylodynamics of partner notification and contact tracing in HIV epidemics

26 Jun 2018

course

C3BI Course: Introduction to Molecular Phylogenetics – Hong Kong 2018

15 Jun 2018

project

Renewing Felsenstein’s phylogenetic bootstrap.

01 Jun 2018

project

Ancestral Reconstruction

18 Apr 2018

publication

Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

11 Apr 2018

event

MCEB 2018

29 Mar 2018

publication

Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty

02 Jan 2018

publication

Improving pairwise comparison of protein sequences with domain co-occurrence

23 Oct 2017

course

INTRODUCTION À LA PHYLOGÉNIE MOLÉCULAIRE : CONCEPTS, METHODES ET OUTILS

06 Oct 2017

publication

The Role of Phylogenetics as a Tool to Predict the Spread of Resistance

01 Sep 2017

publication

SMS: Smart Model Selection in PhyML

14 Jun 2017

publication

[The tenth gene of HIV]

10 May 2017

event

MCEB 2017

06 Mar 2017

publication

Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study

27 Jan 2017

news

Inauguration du C3BI

01 Jan 2017

publication

Special Issue: Mathematical and Computational Evolutionary Biology-2015

14 Oct 2016

project

HIV-1 Drug Resistance Mutation analysis

14 Oct 2016

event

MCEB 2016

14 Oct 2016

project

Virogenesis

14 Oct 2016

project

NGPhylogeny.fr

11 Oct 2016

publication

The combinatorics of overlapping genes

26 Sep 2016

publication

Concomitant emergence of the antisense protein gene of HIV-1 and of the pandemic.

24 Sep 2016

publication

In-depth analysis of HIV-1 drug resistance mutations in HIV-infected individuals failing first-line regimens in West and Central Africa

01 Apr 2016

publication

A ‘stochastic safety radius’ for distance-based tree reconstruction

07 Jan 2016

publication

Fast and accurate branch lengths estimation for phylogenomic trees

15 Nov 2015

event

C3BI Mini Symposium – New Data, New Questions, New Methods

01 Oct 2015

publication

FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program

24 Sep 2015

publication

A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK

16 Sep 2015

publication

Fast Dating Using Least-Squares Criteria and Algorithms

08 Apr 2015

publication

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction

24 Oct 2014

publication

FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets

05 Jun 2014

publication

Identification of Divergent Protein Domains by Combining HMM-HMM Comparisons and Co-Occurrence Detection

01 May 2014

publication

Predicting the ancestral character changes in a tree is typically easier than predicting the root state

03 Feb 2014

publication

A little guide for advanced search:

In-Depth Characterization of Full-Length Archived Viral Genomes after Nine Years of Posttreatment HIV Control.

Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks.

Drug resistance mutations in HIV: new bioinformatics approaches and challenges.

Cuban history of CRF19 recombinant subtype of HIV-1.

Using machine learning and big data to explore the drug resistance landscape in HIV.

Origin, evolution and global spread of SARS-CoV-2

The seventh pandemic of cholera in Europe revisited by microbial genomics.

COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM.

COVID-Align

The dynamics of HIV-1 epidemics in Cuba (Campus France)

Applying machine learning to sequence analysis (PhD project)

Phylogeography

Introduction to Molecular Phylogenetics – ENS Paris

MCEB 2020

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

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

Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation

A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios

A Darwinian Uncertainty Principle

PastView: a user-friendly interface to explore ancestral scenarios

NGPhylogeny.fr: new generation phylogenetic services for non-specialists

MCEB 2019

Introduction à la phylogénie moléculaire

Distribution and asymptotic behavior of the phylogenetic transfer distance.

Accounting for ambiguity in ancestral sequence reconstruction

Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability

NGPhylogeny.fr

PastML

Booster

The phylodynamics of partner notification and contact tracing in HIV epidemics

C3BI Course: Introduction to Molecular Phylogenetics – Hong Kong 2018

Renewing Felsenstein’s phylogenetic bootstrap.

Ancestral Reconstruction

Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

MCEB 2018

Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty

Improving pairwise comparison of protein sequences with domain co-occurrence

INTRODUCTION À LA PHYLOGÉNIE MOLÉCULAIRE : CONCEPTS, METHODES ET OUTILS

The Role of Phylogenetics as a Tool to Predict the Spread of Resistance

SMS: Smart Model Selection in PhyML

[The tenth gene of HIV]

MCEB 2017

Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study

Inauguration du C3BI

Special Issue: Mathematical and Computational Evolutionary Biology-2015

HIV-1 Drug Resistance Mutation analysis

MCEB 2016

Virogenesis

NGPhylogeny.fr

The combinatorics of overlapping genes

Concomitant emergence of the antisense protein gene of HIV-1 and of the pandemic.

In-depth analysis of HIV-1 drug resistance mutations in HIV-infected individuals failing first-line regimens in West and Central Africa

A ‘stochastic safety radius’ for distance-based tree reconstruction

Fast and accurate branch lengths estimation for phylogenomic trees

C3BI Mini Symposium – New Data, New Questions, New Methods

FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program

A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK

Fast Dating Using Least-Squares Criteria and Algorithms

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction

FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets

Identification of Divergent Protein Domains by Combining HMM-HMM Comparisons and Co-Occurrence Detection

Predicting the ancestral character changes in a tree is typically easier than predicting the root state

Deep conservation of human protein tandem repeats within the eukaryotes