, 2024 — « Measures of Branch Support in Phylogenetics » in Models and Methods for Biological Evolution.. , , p. 213-234
ISBN
978-1-78945-069-9
, janvier 2017 — Special Issue: Mathematical and Computational Evolutionary Biology-2015. Systematic Biology vol. 66, n° 1, p. 1-2
ISSN
1063-5157
, 2025 — multistrap: boosting phylogenetic analyses with structural information. Nature Communications vol. 16, n° 1, p. 293
ISSN
2041-1723
, juillet 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
ISSN
0737-4038, 1537-1719
, 2024 — The Bayesian Phylogenetic Bootstrap, Application to Short Trees and Branches. Molecular Biology and Evolution , , msae238
ISSN
0737-4038, 1537-1719
, 2025 — Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to Evade (Over-)optimization. Systematic Biology , , syaf043
ISSN
1063-5157, 1076-836X
, mai 2025 — Accounting for contact tracing in epidemiological birth-death models. Phylodynamics bridges the gap between classical epidemiology and pathogen genome sequence data by estimating epidemiological… PLoS Computational Biology vol. 21, n° 5, e1012461 Accession Number: 40440423 ISBN: 1553-734X Type: 10.1371/journal.pcbi.1012461
ISSN
1553-7358
, novembre 2025 — PhyloCNN: Improving tree representation and neural network architecture for deep learning from trees in phylodynamics and diversification studies. Abstract Phylodynamics and diversification studies using complex evolutionary models can be challenging, especially with… Systematic Biology , , syaf082
ISSN
1063-5157, 1076-836X
, 2021 — Using machine learning and big data to explore the drug resistance landscape in HIV. Plos Computational Biology vol. 17, n° 8, p. 1008873
, septembre 2021 — Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows.. NAR genomics and bioinformatics vol. 3, n° 3, lqab075–lqab075 MEDLINE:34396097
, août 2021 — Using machine learning and big data to explore the drug resistance landscape in HIV.. Plos Computational Biology vol. 17, n° 8, p. 1008873 MEDLINE:34437532
, août 2021 — Cuban history of CRF19 recombinant subtype of HIV-1. Plos Pathogens vol. 17, n° 8, e1009786 WOS:000685263600004
ISSN
1553-7366
, 2021 — COVID -Align: accurate online alignment of hCoV-19 genomes using a profile HMM. Bioinformatics (Oxford, England) vol. 37, n° 12, p. 1761-1762 MEDLINE:33045068
ISSN
1367-4803, 1460-2059
, 2021 — Origin, evolution and global spread of SARS-CoV-2. Comptes Rendus Biologies vol. 344, n° 1, p. 57-75 WOS:000667242200006
ISSN
1631-0691
, octobre 2020 — The seventh pandemic of cholera in Europe revisited by microbial genomics. Nature Communications vol. 11, n° 1, p. 5347 WOS:000617728200006
ISSN
2041-1723
, juin 2020 — Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable. Proceedings of the National Academy of Sciences of the United States of America vol. 117, n° 23, p. 12522-12523 WOS:000545947700008
ISSN
0027-8424
, mai 2020 — A Darwinian Uncertainty Principle. Systematic Biology vol. 69, n° 3, p. 521-529 WOS:000537435800007
ISSN
1063-5157
, septembre 2019 — A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios. Molecular Biology and Evolution vol. 36, n° 9, p. 2069-2085 WOS:000493043800018
ISSN
0737-4038
, août 2019 — PastView : a user-friendly interface to explore ancestral scenarios. Bmc Evolutionary Biology vol. 19, n° 1, p. 163 WOS:000479274100002
ISSN
1471-2148