The seventh pandemic of cholera in Europe revisited by microbial genomics
Mihaela Oprea
,
Elisabeth Njamkepo
,
Daniela Cristea
,
Anna Zhukova
,
Clifford Clark
et al.
Journal articles
pasteur-03036907v1
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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.
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
Journal articles
hal-01567904v1
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NGPhylogeny.fr: new generation phylogenetic services for non-specialists
Frédéric Lemoine
,
Damien Correia
,
Vincent Lefort
,
Olivia Doppelt-Azeroual
,
Fabien Mareuil
et al.
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.
Journal articles
inserm-02153937v1
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The dream of Darwin: reconstructing evolution from DNA
Olivier Gascuel
13th Aykut Kence Evolution Conference , Feb 2019, Ankara, Turkey
Conference papers
pasteur-02405696v1
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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.
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.
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.
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.
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
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Phylogenetic Models
Olivier Gascuel
Molecular Phylogenetics Workshop , Oct 2018, Hong Kong, China
Conference papers
pasteur-02405706v1
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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
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
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 articles
lirmm-02078446v1
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SMS: Smart Model Selection in PhyML
Vincent Lefort
,
Jean-Emmanuel Longueville
,
Olivier Gascuel
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.
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.
Journal articles
pasteur-03038752v1
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Phylogénétique : quelles mesures de support pour les branches d'un arbre
Olivier Gascuel
,
Frédéric Lemoine
Book sections
hal-03861414v1
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DEEP LEARNING FROM PHYLOGENIES TO UNCOVER THE EPIDEMIOLOGICAL DYNAMICS OF OUTBREAKS
J. Voznica
,
A. Zhukova
,
V. Boskova
,
E. Saulnier
,
F. Lemoine
et al.
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
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 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.
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.
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.
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
Journal articles
inserm-01517883v1
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