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The seventh pandemic of cholera in Europe revisited by microbial genomics

Mihaela Oprea , Elisabeth Njamkepo , Daniela Cristea , Anna Zhukova , Clifford Clark et al.
Nature Communications, 2020, 11 (1), pp.5347. ⟨10.1038/s41467-020-19185-y⟩
Journal articles pasteur-03036907v1

SpliceLauncher: a tool for detection, annotation and relative quantification of alternative junctions from RNAseq data

Raphaël Leman , Valentin Harter , Alexandre Atkinson , Grégoire Davy , Antoine Rousselin et al.
Bioinformatics, 2019, 36 (5), pp.1634-1636. ⟨10.1093/bioinformatics/btz784⟩
Journal articles pasteur-02862337v1
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Inferring epidemiological parameters from phylogenies using regression-ABC: a comparative study

Emma Saulnier , Olivier Gascuel , Samuel Alizon
PLoS Computational Biology, 2017, 13 (3), pp.e1005416. ⟨10.1371/journal.pcbi.1005416⟩
Journal articles hal-01567904v1
Image document new generation phylogenetic services for non-specialists

Frédéric Lemoine , Damien Correia , Vincent Lefort , Olivia Doppelt-Azeroual , Fabien Mareuil et al.
Nucleic Acids Research, 2019, 47 (W1), pp.W260-W265. ⟨10.1093/nar/gkz303⟩
Journal articles hal-02341225v1
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Close proximity interactions support transmission of ESBL-K. pneumoniae but not ESBL-E. coli in healthcare settings

Audrey Duval , Thomas Obadia , Pierre-Yves Boëlle , Eric Fleury , Jean-Louis Herrmann et al.
PLoS Computational Biology, 2019, 15 (5), pp.e1006496. ⟨10.1371/journal.pcbi.1006496⟩
Journal articles inserm-02153937v1

The dream of Darwin: reconstructing evolution from DNA

Olivier Gascuel
13th Aykut Kence Evolution Conference, Feb 2019, Ankara, Turkey
Conference papers pasteur-02405696v1

Numerical Optimization Techniques in Maximum Likelihood Tree Inference

Stéphane Guindon , Olivier Gascuel
Tandy Warnow. Bioinformatics and Phylogenetics: Seminal Contributions of Bernard Moret, 29, Springer, pp.21-38, 2019, Computational Biology (COBO), 978-3-030-10837-3. ⟨10.1007/978-3-030-10837-3_2⟩
Book sections pasteur-02405302v1
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Ratiometric quorum sensing governs the trade-off between bacterial vertical and horizontal antibiotic resistance propagation

Alvaro Banderas , Arthur Carcano , Elisa Sia , Shuang Li , Ariel B Lindner et al.
PLoS Biology, 2020, 18 (8), pp.e3000814. ⟨10.1371/journal.pbio.3000814⟩
Journal articles inserm-02965404v1
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Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

Carla Mavian , Sergei Kosakovsky Pond , Simone Marini , Brittany Rife Magalis , Anne-Mieke Vandamme et al.
Proceedings of the National Academy of Sciences of the United States of America, 2020, 117 (23), pp.12522-12523. ⟨10.1073/pnas.2007295117⟩
Journal articles pasteur-03037656v1
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Drug resistance mutations in HIV: new bioinformatics approaches and challenges

Luc Blassel , Anna Zhukova , Christian J Villabona-Arenas , Katherine E Atkins , Stéphane Hué et al.
Current Opinion in Virology, 2021, 51, pp.56 - 64. ⟨10.1016/j.coviro.2021.09.009⟩
Journal articles hal-03369954v1
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SBML Level 3: an extensible format for the exchange and reuse of biological models

Sarah Keating , Frank Bergmann , Tomáš Helikar , Rahuman Malik‐sheriff , Ion Moraru et al.
Molecular Systems Biology, 2020, 16 (8), pp.1-21. ⟨10.15252/msb.20199110⟩
Journal articles hal-02924909v1
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Gradients of Rac1 Nanoclusters Support Spatial Patterns of Rac1 Signaling

Amanda Remorino , Simon de Beco , Fanny Cayrac , Fahima Di Federico , Gaetan Cornilleau et al.
Cell Reports, 2017, 21 (7), pp.1922-1935. ⟨10.1016/j.celrep.2017.10.069⟩
Journal articles hal-01637091v1
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Rapidly computing the phylogenetic transfer index

Jakub Truszkowski , Olivier Gascuel , Krister M. Swenson
WABI 2019 - 19th International Workshop on Algorithms in Bioinformatics, Sep 2019, Niagara Falls, NY, United States. pp.20:1--20:12, ⟨10.4230/LIPIcs.WABI.2019.20⟩
Conference papers lirmm-02410461v1

Phylogenetic Models

Olivier Gascuel
Molecular Phylogenetics Workshop, Oct 2018, Hong Kong, China
Conference papers pasteur-02405706v1

Phylogenetic models and algorithms

Olivier Gascuel
Mathematical and Computational methods for Phylogenetics and Evolutionary Epidemiology Workshop, Oct 2019, La Havanne, Cuba
Conference papers pasteur-02405688v1
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Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows

Frédéric Lemoine , Olivier Gascuel
NAR Genomics and Bioinformatics, 2021, 3 (3), pp.lqab075. ⟨10.1093/nargab/lqab075⟩
Journal articles pasteur-03427582v1
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COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM

Frédéric Lemoine , Luc Blassel , Jakub Voznica , Olivier Gascuel
Bioinformatics, 2021, pp.btaa871. ⟨10.1093/bioinformatics/btaa871⟩
Journal articles pasteur-02995703v1
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The Role of Phylogenetics as a Tool to Predict the Spread of Resistance

Anna Zhukova , Teresa Cutino-Moguel , Olivier Gascuel , Deenan K Pillay
Journal of Infectious Diseases, 2017, 216 (suppl_9), pp.S820-S823. ⟨10.1093/infdis/jix411⟩
Journal articles lirmm-02078446v1
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SMS: Smart Model Selection in PhyML

Vincent Lefort , Jean-Emmanuel Longueville , Olivier Gascuel
Molecular Biology and Evolution, 2017, 34 (9), pp.2422-2424. ⟨10.1093/molbev/msx149⟩
Journal articles lirmm-01794206v1
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Cuban history of CRF19 recombinant subtype of HIV-1

Anna Zhukova , Jakub Voznica , Miraine Davila Felipe , Thu-Hien To , Lissette Pérez et al.
PLoS Pathogens, 2021, 17 (8), pp.e1009786. ⟨10.1371/journal.ppat.1009786⟩
Journal articles hal-03228076v1
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Origin, evolution and global spread of SARS-CoV-2

Anna Zhukova , Luc Blassel , Frédéric Lemoine , Marie Morel , Jakub Voznica et al.
Comptes Rendus Biologies, 2021, pp.1-19. ⟨10.5802/crbiol.29⟩
Journal articles pasteur-03038752v1
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Phylogénétique : quelles mesures de support pour les branches d'un arbre

Olivier Gascuel , Frédéric Lemoine
Gilles Didier; Stéphane Guindon. Modèles et méthodes pour l’évolution biologique, ISTE editions, pp.223-246, 2022, 978-1-78949-069-5 (ebook). ⟨10.51926/ISTE.9069.ch9⟩
Book sections hal-03861414v1
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J. Voznica , A. Zhukova , V. Boskova , E. Saulnier , F. Lemoine et al.
Nature Communications, 2022, 13 (1), pp.3896. ⟨10.1038/s41467-022-31511-0⟩
Journal articles hal-03861407v1
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PastView : a user-friendly interface to explore ancestral scenarios

François Chevenet , Guillaume Castel , Emmanuelle Jousselin , Olivier Gascuel
BMC Evolutionary Biology, 2019, 19 (1), pp.163. ⟨10.1186/s12862-019-1490-4⟩
Journal articles pasteur-02404219v1
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Distribution and asymptotic behavior of the phylogenetic transfer distance

Miraine Dávila Felipe , Jean-Baka Domelevo Entfellner , Frédéric Lemoine , Jakub Truszkowski , Olivier Gascuel et al.
Journal of Mathematical Biology, 2019, 79 (2), pp.485-508. ⟨10.1007/s00285-019-01365-0⟩
Journal articles pasteur-02404376v1
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Accounting for ambiguity in ancestral sequence reconstruction

Adrien Oliva , Sylvain Pulicani , Vincent Lefort , Laurent Brehelin , Olivier Gascuel et al.
Bioinformatics, 2019, 35 (21), pp.4290-4297. ⟨10.1093/bioinformatics/btz249⟩
Journal articles pasteur-02404399v1
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Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability

Jia-Ming Chang , Evan Floden , Javier Herrero , Olivier Gascuel , Paolo Di Tommaso et al.
Journal articles pasteur-02405101v1
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Deciphering RNA G-quadruplex function during the early steps of HIV-1 infection

Samir Amrane , Chloé Jaubert , Amina Bedrat , Tiffany Rundstadler , Patricia Recordon-Pinson et al.
Nucleic Acids Research, 2022, 50 (21), pp.12328-12343. ⟨10.1093/nar/gkac1030⟩
Journal articles hal-03874577v1
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Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities

Sarah Cohen-Boulakia , Khalid Belhajjame , Olivier Collin , Jérôme Chopard , Christine Froidevaux et al.
Future Generation Computer Systems, 2017, 75, pp.284-298. ⟨10.1016/j.future.2017.01.012⟩
Journal articles hal-01516082v1
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Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations

Jean-Michel Arbona , Sébastien Herbert , Emmanuelle Fabre , Christophe Zimmer
Genome Biology, 2016, 18 (1), pp.81. ⟨10.1186/s13059-017-1199-x⟩
Journal articles inserm-01517883v1