, 2025 — multistrap: boosting phylogenetic analyses with structural information. Nature Communications vol. 16, n° 1, p. 293
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2041-1723
, 2025 — Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to Evade (Over-)optimization. Systematic Biology , , syaf043
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1063-5157, 1076-836X
, July 2024 — Deep learning of SARS-CoV-2 outbreak phylodynamics with contact tracing data. Deep learning has emerged as a powerful tool for phylodynamic analysis, addressing common computational limitations affecting… , , Type: 10.1101/2024.06.10.24308687
, 2024 — Integrating contact tracing data to enhance outbreak phylodynamic inference: a deep learning approach. Molecular Biology and Evolution , , msae232
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0737-4038, 1537-1719
, 2024 — Accurate 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
, 2024 — « Measures of Branch Support in Phylogenetics » in Models and Methods for Biological Evolution.. , , p. 213-234
ISBN
978-1-78945-069-9
, 2024 — The Bayesian Phylogenetic Bootstrap, Application to Short Trees and Branches. Molecular Biology and Evolution , , msae238
ISSN
0737-4038, 1537-1719
, 2023 — Fast 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
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1063-5157, 1076-836X
, 2023 — Modeling 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
, 2023 — In-depth characterization of full-length archived viral genomes after nine years of posttreatment HIV control. MICROBIOLOGY SPECTRUM vol. 11, n° 1, 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
, 2023 — Robustness 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
, 2023 — A massively parallel branch-&-bound algorithm for the balanced minimum evolution problem. Computers & Operations Research vol. 158, , p. 106308
ISSN
03050548
, December 2022 — Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks. Nature Communications vol. 13, n° 1, p. 3896
ISSN
2041-1723
, July 2022 — A 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
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0377-2217
, 2022 — Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks. Nature Communications , n° 3896,
, 2022 — Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal. Virus Evolution vol. 8, n° 1, veac029
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2057-1577
, 2022 — Measuring 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
, 2022 — Deciphering RNA G-quadruplex function during the early steps of HIV-1 infection. Abstract G-quadruplexes (G4s) are four-stranded nucleic acid structures formed by the stacking of G-tetrads. Here we… Nucleic Acids Research vol. 50, n° 21, p. 12328-12343
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0305-1048, 1362-4962
, 2022 — < span style="font-variant:small-caps;">TiPS</span> : Rapidly simulating trajectories and phylogenies from compartmental models. Methods in Ecology and Evolution , , 2041–210X.14038
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2041-210X, 2041-210X
, November 2021 — Sensitive Detection of Site-wise Convergent Evolution in Large Protein Alignments with ConDor. Evolutionary convergences are observed at all levels, from phenotype to DNA and protein sequences, and the changes observed at… , , Type: 10.1101/2021.06.30.450558