, June 2026 — Simpler is not always better: Phylodynamic misspecification and deep-learning corrections. , , tex.hal_id: pasteur-05661618 tex.hal_version: v1
, May 2026 — Scalable deep-learning-based inference of time-varying transmission dynamics from outbreak phylogenies. , , tex.hal_id: hal-05661606 tex.hal_version: v1
, 2026 — Maternal-fetal detection of rabies virus in the vampire bat Desmodus rotundus , Brazil. EMI: Animal & Environment , , p. 1-31
ISSN
2998-6990
, 2026 — Improving the resolution and informativity of the majority-rule consensus tree using fine-grained dissimilarity measures. Abstract Phylogenetic analyses often require the summarization of multiple trees, e.g., in Bayesian analyses to obtain the… Systematic Biology , , syag078
ISSN
1063-5157, 1076-836X
, 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
, 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
ISSN
1553-7358
, 2025 — multistrap: boosting phylogenetic analyses with structural information. Nature Communications vol. 16, n° 1, p. 293
ISSN
2041-1723
, 2025 — Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to Evade (Over-)optimization. Systematic Biology , , syaf043
ISSN
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
, April 2024 — Accurate Detection of Convergent Mutations in Large Protein Alignments with ConDor. Evolutionary convergences are observed at all levels, from phenotype to DNA and protein sequences, and changes at these… Genome Biology and Evolution vol. 16, n° 4, evae040 Accession Number: 38451738 ISBN: 1759-6653 Type: 10.1093/gbe/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 — 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
, 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 — A massively parallel branch-&-bound algorithm for the balanced minimum evolution problem. Computers & Operations Research vol. 158, , p. 106308
ISSN
03050548
, 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 — 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
ISSN
1063-5157, 1076-836X
, 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
ISSN
0377-2217