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Evolution, Phylogenetics, Molecular epidemiology, Methods, Models, Algorithms

Countries

France

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Employment (1)

CNRS: Paris, FR

Directeur de Recherche
Employment
Source: Self-asserted source
Olivier GASCUEL

Works (28)

multistrap: boosting phylogenetic analyses with structural information

Nature Communications
2025-01-15 | Journal article
DOI: 10.1038/s41467-024-55264-0
Contributors: Athanasios Baltzis; Luisa Santus; Björn E. Langer; Cedrik Magis; Damien M. de Vienne; Olivier Gascuel; Leila Mansouri; Cedric Notredame
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Crossref

PhyloCNN: Improving tree representation and neural network architecture for deep learning from trees in phylodynamics and diversification studies

2024-12-13 | Preprint
DOI: 10.1101/2024.12.13.628187
Contributors: Manolo Fernandez Perez; Olivier Gascuel
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Crossref

Integrating Contact Tracing Data to Enhance Outbreak Phylodynamic Inference: A Deep Learning Approach

Molecular Biology and Evolution
2024-11-01 | Journal article
DOI: 10.1093/molbev/msae232
Contributors: Ruopeng Xie; Dillon C Adam; Shu Hu; Benjamin J Cowling; Olivier Gascuel; Anna Zhukova; Vijaykrishna Dhanasekaran; Tal Pupko
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Crossref

The Bayesian Phylogenetic Bootstrap and its Application to Short Trees and Branches

Molecular Biology and Evolution
2024-11-01 | Journal article
DOI: 10.1093/molbev/msae238
Contributors: Frédéric Lemoine; Olivier Gascuel; Xuhua Xia
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Crossref

Accounting for contact tracing in epidemiological birth-death-models

2024-09-09 | Preprint
DOI: 10.1101/2024.09.09.24313296
Contributors: Anna ZHUKOVA; Olivier Gascuel
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Crossref

Much Ado About Nothing: Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to evade (Over-)optimization

2024-07-08 | Preprint
DOI: 10.1101/2024.07.04.602058
Contributors: Anastasis Togkousidis; Alexandros Stamatakis; Olivier Gascuel
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Crossref

The Bayesian Phylogenetic Bootstrap, Application to Short Trees and Branches

2024-06-28 | Preprint
DOI: 10.1101/2024.06.22.600199
Contributors: Frederic Lemoine; Olivier Gascuel
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Crossref

Accurate Detection of Convergent Mutations in Large Protein Alignments With ConDor

Genome Biology and Evolution
2024-04-02 | Journal article
DOI: 10.1093/gbe/evae040
Contributors: Marie Morel; Anna Zhukova; Frédéric Lemoine; Olivier Gascuel; Carolin Kosiol
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Crossref

Fast and Accurate Maximum-Likelihood Estimation of Multi-Type Birth–Death Epidemiological Models from Phylogenetic Trees

Systematic Biology
2023-12-30 | Journal article
DOI: 10.1093/sysbio/syad059
Contributors: Anna Zhukova; Frédéric Hecht; Yvon Maday; Olivier Gascuel
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Crossref

Robustness of Felsenstein’s Versus Transfer Bootstrap Supports With Respect to Taxon Sampling

Systematic Biology
2023-12-30 | Journal article
DOI: 10.1093/sysbio/syad052
Contributors: Paul Zaharias; Frédéric Lemoine; Olivier Gascuel; Siavash Mirarab
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Crossref

A massively parallel branch-&-bound algorithm for the balanced minimum evolution problem

Computers & Operations Research
2023-10 | Journal article
DOI: 10.1016/j.cor.2023.106308
Contributors: Daniele Catanzaro; Martin Frohn; Olivier Gascuel; Raffaele Pesenti
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Crossref

Modeling Drug Resistance Emergence and Transmission in HIV-1 in the UK

Viruses
2023-05-25 | Journal article
DOI: 10.3390/v15061244
Contributors: Anna Zhukova; David Dunn; Olivier Gascuel
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Crossref
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Preferred source (of 2)‎

Modelling drug resistance emergence and transmission in HIV-1 in the UK

2023-04-25 | Preprint
DOI: 10.1101/2023.04.24.23288580
Contributors: Anna Zhukova; David Dunn; Olivier Gascuel
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Crossref

TiPS: Rapidly simulating trajectories and phylogenies from compartmental models

Methods in Ecology and Evolution
2023-02 | Journal article
DOI: 10.1111/2041-210X.14038
Contributors: Gonché Danesh; Emma Saulnier; Olivier Gascuel; Marc Choisy; Samuel Alizon
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Crossref

Robustness of Felsenstein’s versus Transfer Bootstrap Supports with respect to Taxon Sampling

2023-02-28 | Preprint
DOI: 10.1101/2023.02.27.530178
Contributors: Paul Zaharias; Frédéric Lemoine; Olivier Gascuel
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Crossref

Fast and Accurate Maximum-Likelihood Estimation of Multi-Type Birth-Death Epidemiological Models from Phylogenetic Trees

2022-08-03 | Preprint
DOI: 10.1101/2022.08.02.22278328
Contributors: Anna Zhukova; Frédéric Hecht; Yvon Maday; Olivier Gascuel
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Crossref

A tutorial on the balanced minimum evolution problem

European Journal of Operational Research
2022-07 | Journal article
DOI: 10.1016/j.ejor.2021.08.004
Contributors: Daniele Catanzaro; Martin Frohn; Olivier Gascuel; Raffaele Pesenti
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Crossref

Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks

Nature Communications
2022-07-06 | Journal article
DOI: 10.1038/s41467-022-31511-0
Contributors: J. Voznica; A. Zhukova; V. Boskova; E. Saulnier; F. Lemoine; M. Moslonka-Lefebvre; O. Gascuel
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Crossref

Drug resistance mutations in HIV: new bioinformatics approaches and challenges

Current Opinion in Virology
2021-12 | Journal article
DOI: 10.1016/j.coviro.2021.09.009
Contributors: Luc Blassel; Anna Zhukova; Christian J Villabona-Arenas; Katherine E Atkins; Stéphane Hué; Olivier Gascuel
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Crossref

Using machine learning and big data to explore the drug resistance landscape in HIV

PLOS Computational Biology
2021-08-26 | Journal article
DOI: 10.1371/journal.pcbi.1008873
Contributors: Luc Blassel; Alison L. Hill; Anna Tostevin; Christian Julian Villabona-Arenas; Martine Peeters; Stéphane Hué; Olivier Gascuel
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Crossref

Accurate Detection of Convergent Mutations in Large Protein Alignments with ConDor

2021-07-01 | Preprint
DOI: 10.1101/2021.06.30.450558
Contributors: Marie Morel; Frédéric Lemoine; Anna Zhukova; Olivier Gascuel
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Crossref

Correction to ‘Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows’

NAR Genomics and Bioinformatics
2021-06-23 | Journal article
DOI: 10.1093/nargab/lqab083
Contributors: Frédéric Lemoine; Olivier Gascuel
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Crossref

Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows

NAR Genomics and Bioinformatics
2021-06-23 | Journal article
DOI: 10.1093/nargab/lqab075
Contributors: Frédéric Lemoine; Olivier Gascuel
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Crossref

Gotree/Goalign : Toolkit and Go API to facilitate the development of phylogenetic workflows

2021-06-10 | Other
DOI: 10.1101/2021.06.09.447704
Contributors: Frédéric Lemoine; Olivier Gascuel
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Crossref

Using machine learning and big data to explore the drug resistance landscape in HIV

2021-03-16 | Preprint
DOI: 10.1101/2021.03.15.435398
Contributors: Luc Blassel; Anna Tostevin; Christian Julian Villabona-Arenas; Martine Peeters; Stéphane Hué; Olivier Gascuel
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Crossref

Using machine learning and big data to explore the drug resistance landscape in HIV

2021-03-16 | Preprint
DOI: 10.1101/2021.03.16.435621
Contributors: Luc Blassel; Anna Tostevin; Christian Julian Villabona-Arenas; Martine Peeters; Stéphane Hué; Olivier Gascuel
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Crossref

Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks

2021-03-12 | Preprint
DOI: 10.1101/2021.03.11.435006
Contributors: J Voznica; A Zhukova; V Boskova; E Saulnier; F Lemoine; M Moslonka-Lefebvre; O Gascuel
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Crossref

Cuban history of CRF19 recombinant subtype of HIV-1

2021-02-16 | Preprint
DOI: 10.1101/2021.02.15.431210
Contributors: Anna Zhukova; Jakub Voznica; Miraine Dávila Felipe; Thu-Hien To; Lissette Pérez; Yenisleidys Martínez; Yanet Pintos; Melissa Méndez; Olivier Gascuel; Vivian Kouri
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Crossref
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