• 2023
  Trémeaux P, Lemoine F, Mélard A, Gousset M, Boufassa F, Orr S, Monceaux V, Gascuel O, Lambotte O, Hocqueloux L, Saez-Cirion A, Rouzioux C, Avettand-Fenoel V, , In-Depth Characterization of Full-Length Archived Viral Genomes after Nine Years of Posttreatment HIV Control., Microbiol Spectr 2023 Feb; 11(1): e0326722.
• 2022
  Voznica J, Zhukova A, Boskova V, Saulnier E, Lemoine F, Moslonka-Lefebvre M, Gascuel O, , Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks., Nat Commun 2022 Jul; 13(1): 3896.
• 2021
  Blassel* L, Zhukova* A, Villabona-Arenas CJ, Atkins KE, Hué S, Gascuel O, , Drug resistance mutations in HIV: new bioinformatics approaches and challenges., Curr Opin Virol 2021 Sep; 51(): 56-64.
• 2021
  Zhukova A, Voznica J, Dávila Felipe M, To TH, Pérez L, Martínez Y, Pintos Y, Méndez M, Gascuel O, Kouri V, Cuban history of CRF19 recombinant subtype of HIV-1., PLoS Pathog 2021 Aug; 17(8): e1009786.
• 2021
  Blassel L, Tostevin A, Villabona-Arenas CJ, Peeters M, Hué S, Gascuel O, , , Using machine learning and big data to explore the drug resistance landscape in HIV., PLoS Comput Biol 2021 Aug; 17(8): e1008873.
• 2020
  Zhukova A, Blassel L, Lemoine F, Morel M, Voznica J, Gascuel O, Origin, evolution and global spread of SARS-CoV-2, Comptes Rendus Biologies 2020; 20 p.
• 2020
  Oprea* M, Njamkepo* E, Cristea* D, Zhukova* A, Clark CG, Kravetz AN, Monakhova E, Ciontea AS, Cojocaru R, Rauzier J, Damian M, Gascuel O, Quilici ML, Weill FX, , The seventh pandemic of cholera in Europe revisited by microbial genomics., Nat Commun 2020 10; 11(1): 5347.
• 2020
  Lemoine F, Blassel L, Voznica J, Gascuel O, , COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM., Bioinformatics 2020 Oct; (): .
• 2019
  Ishikawa* SA, Zhukova* A, Iwasaki W, Gascuel O, A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios, Mol. Biol. Evol. 2019 Sep;36(9):2069-2085.
• 2019
  Gascuel O, Steel M, A Darwinian Uncertainty Principle, Syst. Biol. 2019 Aug;.
• 2019
  Chevenet F, Castel G, Jousselin E, Gascuel O, PastView: a user-friendly interface to explore ancestral scenarios, BMC Evol. Biol. 2019 08;19(1):163.
• 2019
  Lemoine F, Correia D, Lefort V, Doppelt-Azeroual O, Mareuil F, Cohen-Boulakia S, Gascuel O, NGPhylogeny.fr: new generation phylogenetic services for non-specialists, Nucleic Acids Res. 2019 Jul;47(W1):W260-W265.
• 2019
  Dávila Felipe M, Domelevo Entfellner JB, Lemoine F, Truszkowski J, Gascuel O, , Distribution and asymptotic behavior of the phylogenetic transfer distance., J Math Biol 2019 07; 79(2): 485-508.
• 2019
  Oliva A, Pulicani S, Lefort V, Bréhélin L, Gascuel O, Guindon S, Accounting for ambiguity in ancestral sequence reconstruction, Bioinformatics 2019 Apr;.
• 2019
  Chang JM, Floden EW, Herrero J, Gascuel O, Di Tommaso P, Notredame C, Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability, Bioinformatics 2019 Feb;.
• 2018
  Lemoine F, Domelevo Entfellner JB, Wilkinson E, Correia D, Dávila Felipe M, De Oliveira T, Gascuel O, Renewing Felsenstein’s phylogenetic bootstrap in the era of big data, Nature 2018 Apr;.
• 2018
  Chatzou M, Floden EW, Di Tommaso P, Gascuel O, Notredame C, Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty, Systematic Biology. 2018: syx096.
• 2018
  Menichelli C, Gascuel O, Bréhélin L, Improving pairwise comparison of protein sequences with domain co-occurrence, PLoS Comput. Biol. 2018 01;14(1):e1005889.
• 2017
  Zhukova A, Cutino-Moguel T, Gascuel O, Pillay D, The Role of Phylogenetics as a Tool to Predict the Spread of Resistance, J. Infect. Dis. 2017 12;216(suppl_9):S820-S823.
• 2017
  Lefort V, Longueville JE, Gascuel O, SMS: Smart Model Selection in PhyML, Mol. Biol. Evol. 2017 Sep;34(9):2422-2424.
• 2017
  Cassan É, Arigon-Chifolleau AM, Mesnard JM, Gros A, Gascuel O, [The tenth gene of HIV], Med Sci (Paris) 2017 May;33(5):484-485.
• 2017
  Saulnier E, Gascuel O, Alizon S, Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study, PLoS Comput. Biol. 2017 Mar;13(3):e1005416.
• 2017
  Bryant D, Gascuel O, Special Issue: Mathematical and Computational Evolutionary Biology-2015, Syst. Biol. 2017 01;66(1):1-2.
• 2016
  Lèbre S, Gascuel O, The combinatorics of overlapping genes, J. Theor. Biol. 2017 Feb;415:90-101.
• 2016
  Cassan E, Arigon-Chifolleau AM, Mesnard JM, Gross A, Gascuel O, Concomitant emergence of the antisense protein gene of HIV-1 and of the pandemic., Proc Natl Acad Sci U S A. 2016 Sep 28.
• 2016
  Villabona-Arenas CJ, Vidal N, Guichet E, Serrano L, Delaporte E, Gascuel O, Peeters M, In-depth analysis of HIV-1 drug resistance mutations in HIV-infected individuals failing first-line regimens in West and Central Africa, AIDS 2016 11;30(17):2577-2589.
• 2016
  Gascuel O, Steel M, A ‘stochastic safety radius’ for distance-based tree reconstruction, Algorithmica 74 (4), 1386-1403.
• 2016
  Binet M, Gascuel O, Scornavacca C, Douzery EJ, Pardi F, Fast and accurate branch lengths estimation for phylogenomic trees, BMC Bioinformatics 2016 Jan;17:23.
• 2015
  Lefort V, Desper R, Gascuel O, FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program, Molecular biology and evolution 32 (10), 2798-2800.
• 2015
  Mourad R, Chevennet F, Dunn DT, Fearnhill E, Delpech V, Asboe D, Gascuel O, Hue S; UK HIV Drug Resistance Database & the Collaborative HIV, Anti-HIV Drug Resistance Network, A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK, Aids 29 (15), 1917-1925.
• 2015
  To TH, Jung M, Lycett S, Gascuel O., Fast Dating Using Least-Squares Criteria and Algorithms, Syst Biol. 2016 Jan;65(1):82-97.
• 2015
  Chang JM, Di Tommaso P, Lefort V, Gascuel O, Notredame C., TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction, Nucleic Acids Res. 2015 Jul 1;43(W1):W3-6.
• 2014
  Dang CC, Le VS, Gascuel O, Hazes B, Le QS, FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets, BMC Bioinformatics. 2014 Oct 24;15:341.
• 2014
  Ghouila A, Florent I, Guerfali FZ, Terrapon N, Laouini D, Yahia SB, Gascuel O, Bréhélin L, Identification of Divergent Protein Domains by Combining HMM-HMM Comparisons and Co-Occurrence Detection, PLoS One. 2014 Jun 5;9(6):e95275.
• 2014
  Gascuel O, Steel M, Predicting the ancestral character changes in a tree is typically easier than predicting the root state, Syst Biol. 2014 May;63(3):421-35.
• 2014
  Schaper E, Gascuel O, Anisimova M., Deep conservation of human protein tandem repeats within the eukaryotes, Mol Biol Evol. 2014 May;31(5):1132-48.