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978-1-78945-069-9
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1063-5157
, 2025 — multistrap: boosting phylogenetic analyses with structural information. Nature Communications vol. 16, n° 1, p. 293
ISSN
2041-1723
, 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 — The Bayesian Phylogenetic Bootstrap, Application to Short Trees and Branches. Molecular Biology and Evolution , , msae238
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0737-4038, 1537-1719
, 2025 — Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to Evade (Over-)optimization. Systematic Biology , , syaf043
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1063-5157, 1076-836X
, May 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
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1553-7358
, November 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
, September 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
, August 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
, August 2021 — Cuban history of CRF19 recombinant subtype of HIV-1. Plos Pathogens vol. 17, n° 8, e1009786 WOS:000685263600004
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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
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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
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1631-0691
, October 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
, June 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
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0027-8424
, May 2020 — A Darwinian Uncertainty Principle. Systematic Biology vol. 69, n° 3, p. 521-529 WOS:000537435800007
ISSN
1063-5157
, September 2019 — A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios. Molecular Biology and Evolution vol. 36, n° 9, p. 2069-2085 WOS:000493043800018
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0737-4038
, August 2019 — PastView : a user-friendly interface to explore ancestral scenarios. Bmc Evolutionary Biology vol. 19, n° 1, p. 163 WOS:000479274100002
ISSN
1471-2148