Entité de rattachement
Biologie intégrative des populations, Evolution moléculaire (BIPEM)

Contact

Courriel
olivier.gascuel [at] mnhn.fr

Présentation

 

Phylogenetics

My main research interest is in the field of evolution and phylogeny. My focus is on the mathematical and computational tools and concepts, which form an essential basis of evolutionary studies (2005 book, 2007 book). I am working on algorithms for phylogenetic inference. I (co)authored several software programs, some widely diffused and well cited: BioNJ (Mol Biol Evol 1997), FastME (J Comp Biol 2002, Mol Biol Evol 2004, Mol Biol Evol 2015) , SDM (Syst Biol 2006), PhyD* (BMC Bioinformatics 2008), Phylogeny.fr and NG-Phylogeny.fr (NAR 2008, NAR 2019), SeaView (Mol Biol EVol 2010), and PhyML  (Syst Biol 2003, Syst Biol 2010, Bioinformatics 2019,  Highly Cited!). Beyond tree building, testing is essential. I coauthored fast tests for branch support (Syst Biol 2006, Syst Biol 2011). Recently, we revisited the famous phylogenetic bootstrap of Felsenstein (>40,000 citations) and proposed a new version, the transfer bootstrap expectation (TBE, Nature 2018, web site), resulting in higher branch supports.  Applications to large data sets and trees show that TBE reveals their phylogenetic signals, whereas Felsenstein’s bootstrap fails to do so. To build trees, estimate evolutionary distances and study sequence evolution, we need models. I coauthored probabilistic models to describe protein evolution (Phil Trans Roy Soc B 2008, Mol Biol Evol 2008, Syst Biol 2010, Mol Biol Evol 2012), and a new estimation method for amino acid replacement matrices, which was used to infer the the LG matrix (Mol Biol Evol 2008, Bioinformatics 2011). We also: designed a fast and simple web interface to select phylogenetic models in the PhyML environment (SMS, MBE 2017, web site); published a very fast dating method, implemented in the LSD software (Syst Biol 2015); proposed a fast maximum-likelihood method to infer and visualize ancestral scenarios, implemented in PastML (Mol Biol Evol 2019).  With Mike Steel and Fabio Pardi, we addressed several theoretical questions related to tree building from evolutionary distances (Mol Biol Evol 2006, Bull Math Biol 2010, PNAS 2012, Algorithmica 2015), and to reconstruct ancestral characters (Math Biosciences 2010, Syst Biol 2014, Syst Biol 2020).

Pathogens

During the last twelve years, I turned part of my activities toward pathogens, most notably Plasmodium falciparum, HIV and, recently, SARS-CoV-2. Regarding P. falciparum our main goal was to decipher the function of its genes, most of them being fully unknown. We used postgenomic data and machine learning approaches to propose functional predictions for a number of its genes (BMC Bioinformatics 2008, BMC Genomics 2010). We refined the annotation of its proteins in structural domains (Bioinformatics 2009, BMC Bioinformatics 2012) and designed the RED2 method and program to search for regulation motifs (Genome Biology 2012). We also studied the origin of P. falciparum (BMC Evol Biol 2011). Regarding HIV and other viruses, notably Influenza, we implemented the PhyloType web server to extract relevant clusters or “phylotypes” from a phylogeny combined with extrinsic characters. PhyloType was applied to the phylogeography of HIV epidemics (Bioinformatics 2013). PastML is a continuation of PhyloType. We studied the emergence and diffusion of drug resistance mutations in HIV, both in the UK (AIDS 2015) and Africa (AIDS 2016). Importantly, our evolutionary analyses of large data sets support the idea that asp is the 10th gene of HIV-1 group M and indicate a correlation with the spread of the pandemic (PNAS 2016). Regarding SARS-CoV-2, we studied its origin, diffusion and global spread (PNAS 2020, CR Biol 2020), and designed an HMM-based web server to align the genomes of its variants at a very large scale (Bioinformatics 2020).

My Google Scholar

 

Current and recent services

Distinctions

 

 

Olivier gascuel

 

 

Publications

2024
  • Morel Marie, Zhukova Anna, Lemoine Frédéric & Gascuel Olivier, 2024Accurate Detection of Convergent Mutations in Large Protein Alignments with ConDor. Abstract Evolutionary convergences are observed at all levels, from phenotype to DNA and protein sequences, and changes at… Genome Biology and Evolution vol. 16, n° 4, evae040
    ISSN
    1759-6653
  • Gascuel O. & Lemoine F., 2024« Measures of Branch Support in Phylogenetics » in Models and Methods for Biological Evolution.. , , p. 213-234
    ISBN
    978-1-78945-069-9
2023
  • Zhukova Anna, Dunn David & Gascuel Olivier, 2023Modeling Drug Resistance Emergence and Transmission in HIV-1 in the UK. A deeper understanding of HIV-1 transmission and drug resistance mechanisms can lead to improvements in current treatment… Viruses vol. 15, n° 6, p. 1244
    ISSN
    1999-4915
  • Catanzaro Daniele, Frohn Martin, Gascuel Olivier & Pesenti Raffaele, 2023A massively parallel branch-&-bound algorithm for the balanced minimum evolution problem. Computers & Operations Research vol. 158, , p. 106308
    ISSN
    03050548
  • Zhukova Anna, Hecht Frédéric, Maday Yvon & Gascuel Olivier, 2023Fast and Accurate Maximum-Likelihood Estimation of Multi-Type Birth-Death Epidemiological Models from Phylogenetic Trees. Abstract Multi-type birth-death (MTBD) models are phylodynamic analogies of compartmental models in classical epidemiology… Systematic Biology , , syad059
    ISSN
    1063-5157, 1076-836X
  • Tremeaux Pauline, Lemoine Frederic, Melard Adeline, Gousset Marine, Boufassa Faroudy, Orr Sylvie, Monceaux Valerie, Gascuel Olivier, Lambotte Olivier, Hocqueloux Laurent, Saez-Cirion Asier, Rouzioux Christine, Avettand-Fenoel Veronique & Cohort CODEX VISCONTI ANRS, 2023In-depth characterization of full-length archived viral genomes after nine years of posttreatment HIV control. MICROBIOLOGY SPECTRUM , , tex.earlyaccessdate: JAN 2023 tex.orcid-numbers: Saez-Cirion, Asier/0000-0003-2406-7536 Avettand-Fenoel, Veronique/0000-0002-7022-2990 TREMEAUX, Pauline/0000-0001-8783-9885 tex.researcherid-numbers: avettand-fenoel, veronique/A-4707-2012 Saez-Cirion, Asie
    ISSN
    2165-0497
  • Zaharias Paul, Lemoine Frédéric & Gascuel Olivier, 2023Robustness of Felsenstein’s versus Transfer Bootstrap Supports with respect to Taxon Sampling. Abstract The bootstrap method is based on resampling sequence alignments and re-estimating trees. Felsenstein’s bootstrap… Systematic Biology vol. 72, n° 6, syad052
    ISSN
    1063-5157, 1076-836X
2022
  • Voznica J., Zhukova A., Boskova V., Saulnier E., Lemoine F., Moslonka-Lefebvre M. & Gascuel O., décembre 2022Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks. Nature Communications vol. 13, n° 1, p. 3896
    ISSN
    2041-1723
  • Catanzaro Daniele, Frohn Martin, Gascuel Olivier & Pesenti Raffaele, juillet 2022A tutorial on the balanced minimum evolution problem. EUROPEAN JOURNAL OF OPERATIONAL RESEARCH vol. 300, n° 1, p. 1-19 tex.earlyaccessdate: FEB 2022 tex.eissn: 1872-6860 tex.orcid-numbers: Catanzaro, Daniele/0000-0001-9427-1562 Pesenti, Raffaele/0000-0001-5890-4238 GASCUEL, Olivier/0000-0002-9412-9723 Frohn, Martin/0000-0002-5002-4049 tex.researcherid-numbers: Frohn, Mart
    ISSN
    0377-2217
  • Seo Tae-Kun, Gascuel Olivier & Thorne Jeffrey L, 2022Measuring Phylogenetic Information of Incomplete Sequence Data. Abstract Widely used approaches for extracting phylogenetic information from aligned sets of molecular sequences rely upon… Systematic Biology vol. 71, n° 3, p. 630-648
    ISSN
    1063-5157, 1076-836X