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authIdHal_s : olivier-gascuel
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Combinatorics of Distance-Based Tree Inference

Fabio Pardi , Olivier Gascuel
Proceedings of the National Academy of Sciences of the United States of America, 2012, 109 (41), pp.16443-16448. ⟨10.1073/pnas.1118368109⟩
Journal articles lirmm-00726361v2
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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

Reconstructing the Duplication History of Tandemly Repeated Sequences

Olivier Gascuel , Denis Bertrand , O. Elemento
O. Gascuel. Mathematics of Evolution and Phylogeny, Oxford University Press, pp.205-235, 2005, 0-19-856610-7
Book sections lirmm-00106580v1
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Computational discovery of regulatory elements in a continuous expression space

Mathieu Lajoie , Olivier Gascuel , Vincent Lefort , Laurent Brehelin
Genome Biology, 2012, 13 (11), pp.41. ⟨10.1186/gb-2012-13-11-r109⟩
Journal articles lirmm-00796453v1
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Fast Dating Using Least-Squares Criteria and Algorithms

Thu-Hien To , Matthieu Jung , Samantha Lycett , Olivier Gascuel
Systematic Biology, 2016, 65 (1), pp.82-97. ⟨10.1093/sysbio/syv068⟩
Journal articles lirmm-01348367v1

Phylogeny Reconstruction Methods

Olivier Gascuel
ISCB Africa ASBCB Conference on Bioinformatics, Mar 2013, Casablanca, Morocco
Conference papers lirmm-01397607v1

Phylogeny Reconstruction Methods

Olivier Gascuel
Bioinformatics in the Tropics, Sep 2013, Durban, South Africa
Conference papers lirmm-01397573v1

Fast Dating using Least Squares

Olivier Gascuel
Mathematical Models for Epidemiology and Phylogenetics, May 2016, Lille, France
Conference papers lirmm-01397427v1

Models and Algorithms in Phylogenetics

Olivier Gascuel
Molecular Phylogenies Courses, Dec 2014, Hanoi, Vietnam
Conference papers lirmm-01397646v1
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Concomitant emergence of the antisense protein gene of HIV-1 and of the pandemic

Elodie Cassan , Anne-Muriel Arigon Chifolleau , Jean-Michel Mesnard , Antoine Gross , Olivier Gascuel et al.
Proceedings of the National Academy of Sciences of the United States of America, 2016, 113 (41), pp.11537-11542. ⟨10.1073/pnas.1605739113⟩
Journal articles lirmm-01397005v1

Mathematics of Evolution and Phylogeny

Olivier Gascuel
Oxford University Press, pp.416, 2004
Books hal-00005857v1
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BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data

Olivier Gascuel
Molecular Biology and Evolution, 1997, 14 (7), pp.685-695. ⟨10.1093/oxfordjournals.molbev.a025808⟩
Journal articles lirmm-00730410v1

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

Accounting for exposition and secondary structure in protein evolution: models and gains

Quang Le Si , Olivier Gascuel
The Annual New Zealand Phylogenetics Meeting, Feb 2007, Mount Ruapehu, New Zealand, New Zealand
Conference papers lirmm-00195966v1

Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle

Richard Desper , Olivier Gascuel
WABI 2002 - International Workshop on Algorithms in Bioinformatics, Sep 2002, Roma, Italy. pp.357-374, ⟨10.1007/3-540-45784-4_27⟩
Conference papers lirmm-00269513v1
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Using Repeated Measurements to Validate Hierarchical Gene Clusters

Laurent Brehelin , Olivier Gascuel , Olivier C. Martin
Bioinformatics, 2008, 24 (5), pp.682-688. ⟨10.1093/bioinformatics/btn017⟩
Journal articles lirmm-00272116v1

On the consistency of the minimum evolution principle of phylogenetic inference

François Denis , Olivier Gascuel
Discrete Applied Mathematics, 2003, Special issue: Computational molecular biology - Issue IV, 127 (1), pp.63-77. ⟨10.1016/S0166-218X(02)00285-8⟩
Journal articles lirmm-00269579v1
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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

A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK

Raphaël Mourad , François Chevennet , David T. Dunn , Esther Fearnhill , Valerie Delpech et al.
AIDS. Official journal of the international AIDS Society, 2015, 29 (15), pp.1917-1925. ⟨10.1097/QAD.0000000000000768⟩
Journal articles lirmm-01348643v1
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Identification of divergent protein domains by combining HMM-HMM comparisons and co-occurrence detection

Amel Ghouila , Isabelle Florent , Fatma Zahra Guerfali , Nicolas Terrapon , Dhafer Laouini et al.
PLoS ONE, 2014, 9 (6), pp.e95275. ⟨10.1371/journal.pone.0095275⟩
Journal articles pasteur-01060276v1
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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An Exact and Polynomial Distance-Based Algorithm to Reconstruct Single Copy Tandem Duplication Trees

O. Elemento , Olivier Gascuel
Journal of Discrete Algorithms, 2005, 3, pp.362-374. ⟨10.1016/j.jda.2004.08.013⟩
Journal articles lirmm-00105291v1
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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
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Robustness of Phylogenetic Inference Based on Minimum Evolution

Fabio Pardi , Sylvain Guillemot , Olivier Gascuel
Bulletin of Mathematical Biology, 2010, 72 (7), pp.1820-1839. ⟨10.1007/s11538-010-9510-y⟩
Journal articles istex lirmm-00511779v2

Improving Amino-Acid Substitution Modelling

Olivier Gascuel
Computational Phylogenetics and Molecular Systematics, Nov 2007, Russia
Conference papers lirmm-00193167v1
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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

Fast dating using least squares

Olivier Gascuel
SMBE: Society for Molecular Biology and Evolution, Jul 2015, Vienna, Austria
Conference papers lirmm-01397443v1

A simple method to predict protein binding from aligned sequences - application to MHC superfamily and beta2-microglobulin

Elodie Duprat , Marie-Paule Lefranc , Olivier Gascuel
Bioinformatics, 2006, 22 (4), pp.453-459. ⟨10.1093/bioinformatics/bti826⟩
Journal articles lirmm-00136659v1