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, 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
, November 2020 — Differing impacts of global and regional responses on SARS-CoV-2 transmission cluster dynamics.. bioRxiv : the preprint server for biology , , MEDLINE:33173870
, 2021 — Soft Selective Sweep on Chemosensory Genes Correlates with Ancestral Preference for Toxic Noni in a Specialist Drosophila Population. Understanding how organisms adapt to environmental changes is a major question in evolution and ecology. In particular, the… Genes vol. 12, n° 1, p. 32 ISBN: 2073-4425 Publisher: MDPI Type: 10.3390/genes12010032
, December 2022 — Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks. Nature Communications vol. 13, n° 1, p. 3896
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2041-1723
, 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
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1063-5157, 1076-836X
, 2022 — Draft genome of the lowland anoa (Bubalus depressicornis) and comparison with buffalo genome assemblies (Bovidae, Bubalina). G3-GENES GENOMES GENETICS vol. 12, n° 11, tex.earlyaccessdate: SEP 2022 tex.orcid-numbers: Ropiquet, Anne/0000-0003-3755-5467 Hassanin, Alexandre/0000-0002-4905-8540 Curaudeau, Manon/0000-0003-3356-0701 Porrelli, Stefano/0000-0003-3878-7745 tex.researcherid-numbers: Ropiquet, Anne/E-6154-2011 Has
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2160-1836
, 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 — 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
, 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
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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
, March 2023 — Resolving Between Novelty and Homology in the Rapidly Evolving Phallus of Drosophila. The genitalia present some of the most rapidly evolving anatomical structures in the animal kingdom, possessing a variety of… Journal of Experimental Zoology Part B: Molecular and Developmental Evolution vol. 340, n° 2, p. 182-196 ISBN: 1552-5007 Publisher: Wiley Type: 10.1002/jez.b.23113
, 2023 — A massively parallel branch-&-bound algorithm for the balanced minimum evolution problem. Computers & Operations Research vol. 158, , p. 106308
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03050548
, 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