MAB: Méthodes et algorithmes pour la bio informatique

logo de l'equipe MAB

À la croisée de la biologie et de l’informatique, la bioinformatique cherche à résoudre des questions biologiques par le calcul. Celles-ci couvrent un large spectre, de la biologie fondamentale à l’agronomie en passant par la santé et l’environnement. L’équipe MAB poursuit des travaux méthodologiques (algorithmique du texte et des arbres, combinatoire, optimisation, modélisation probabiliste, apprentissage statistique) pour répondre à des questions biologiques essentielles (évolution, phylogénie, génomique comparative, annotation fonctionnelle des gènes et des protéines, paludisme, HIV, cancer).

Les thématiques de recherche sont organisées en trois axes : Algorithmique du texte et méthodes pour l'analyse du séquençage à haut débit, Méthodes pour l’inférence évolutive, et Outils pour l’annotation fonctionnelle. Les logiciels développés dans l'équipe sont disponibles sur la plateforme ATGC.

Membres

Permanents

Non permanents

Actualités

Novembre 2017 : Soutenance de le thèse d'Emma Saulnier : "Phylodynamique des pathogènes viraux par calcul bayésien approché". Félicitations Emma !

Novembre 2017 : Olivier Gascuel reçoit le "Grand Prix INRIA Académie des Sciences". Félicitations Olivier !

Publications depuis 2013 - Evaluation 2019

Articles de revues internationales

2018

  1. Finding local genome rearrangements
    Krister Swenson, Pijus Simonaitis
    Algorithms for Molecular Biology, BioMed Central, 2018, 13 (9). <10.1186/s13015-018-0127-2>
  2. Relationship between superstring and compression measures: New insights on the greedy conjecture
    Bastien Cazaux, Eric Rivals
    Discrete Applied Mathematics, Elsevier, 2018, 245, pp.59-64.
  3. Scaffolding Problems Revisited: Complexity, Approximation and Fixed Parameter Tractable Algorithms, and Some Special Cases
    Mathias Weller, Annie Château, Clément Dallard, Rodolphe Giroudeau
    Algorithmica, Springer Verlag, 2018, 80 (6), pp.1771 - 1803.
  4. RecPhyloXML - a format for reconciled gene trees
    Wandrille Duchemin, Guillaume Gence, Anne-Muriel Arigon Chifolleau, Lars Arvestad, Mukul Bansal, Vincent Berry, Bastien Boussau, François Chevenet, Nicolas Comte, Adrián Davín, Christophe Dessimoz, David Dylus, Damir Hasic, Diego Mallo, Rémi Planel, David Posada, Celine Scornavacca, Gergely Szöllősi, Louxin Zhang, Eric Tannier, Vincent Daubin
    Bioinformatics, Oxford University Press (OUP), 2018, pp.1-8.
  5. Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes
    Yoann Anselmetti, Wandrille Duchemin, Eric Tannier, Cedric Chauve, Sèverine Bérard
    BMC Genomics, BioMed Central, 2018, 19 (S2), pp.1-15.
  6. Gearing up to handle the mosaic nature of life in the quest for orthologs
    Kristoffer Forslund, Cécile Pereira, Salvador Capella-Gutiérrez, Alan Sousa Da Silva, Adrian Altenhoff, Jaime Huerta-Cepas, Matthieu Muffato, Mateus Patricio, Klaas Vandepoele, Ingo Ebersberger, Judith Blake, Jesualdo Tomás Fernández Breis, Brigitte Boeckmann, Toni Gabaldon, Erik Sonnhammer, Christophe Dessimoz, Suzanna Lewis, Carla Bello, Sébastien Briois, Edward Chalstrey, Hirokazu Chiba, Oscar Conchillo-Solé, Vincent Daubin, Todd Deluca, Jean-François Dufayard, Dannie Durand, Jesualdo Tomás Fernández-Breis, Natasha Glover, Alexander Hauser, Davide Heller, Mateus Kaduk, Jan Koch, Eugene Koonin, Evgenia Kriventseva, Shigehiro Kuraku, Odile Lecompte, Olivier Lespinet, Jeremy Levy, Benjamin Liebeskind, Benjamin Linard, Marc Marcet-Houben, Martin Martin, Claire Mcwhite, Sergei Mekhedov, Sebastien Moretti, Steven Müller, El-Mabrouk Nadia, Cedric Notredame, Simon Penel, Ivana Pilizota, Henning Redestig, Marc Robinson-Rechavi, Fabian Schreiber, Kimmen Sjölander, Nives Škunca, Martin Steinegger, Damian Szklarczyk, Paul Thomas, Ernst Thuer, Clément Train, Ikuo Uchiyama, Lucas Wittwer, Ioannis Xenarios, Bethan Yates, Evgeny Zdobnov, Robert Waterhouse
    Bioinformatics, Oxford University Press (OUP), 2018, 34 (2), pp.323 - 329.
  7. Improving pairwise comparison of protein sequences with domain co-occurrence
    Christophe Menichelli, Olivier Gascuel, Laurent Brehelin
    PLoS Computational Biology, Public Library of Science, 2018, 14 (1), pp.e1005889.
  8. Probing instructions for expression regulation in gene nucleotide compositions
    Chloé Bessière, May Taha, Florent Petitprez, Jimmy Vandel, Jean-Michel Marin, Laurent Brehelin, Sophie Lèbre, Charles-Henri Lecellier
    PLoS Computational Biology, Public Library of Science, 2018, 14 (1), pp.e1005921.
  9. Computational pan-genomics: status, promises and challenges
    Tobias Marschall, Manja Marz, Thomas Abeel, Louis Dijkstra, Bas E. Dutilh, Ali Ghaffaari, Paul Kersey, Wigard P. Kloosterman, Veli Makinen, Adam M. Novak, Benedict Paten, David Porubsky, Eric Rivals, Can Alkan, Jasmijn A. Baaijens, Paul I. W. De Bakker, Valentina Boeva, Raoul J. P. Bonnal, Francesca Chiaromonte, Rayan Chikhi, Francesca D. Ciccarelli, Robin Cijvat, Erwin Datema, Cornelia M. Van Duijn, Evan E. Eichler, Corinna Ernst, Eleazar Eskin, Erik Garrison, Mohammed El-Kebir, Gunnar W. Klau, Jan O. Korbel, Eric-Wubbo Lameijer, Benjamin Langmead, Marcel Martin, Paul Medvedev, John C. Mu, Pieter Neerincx, Klaasjan Ouwens, Pierre Peterlongo, Nadia Pisanti, Sven Rahmann, Ben Raphael, Knut Reinert, Dick De Ridder, Jeroen De Ridder, Matthias Schlesner, Ole Schulz-Trieglaff, Ashley D. Sanders, Siavash Sheikhizadeh, Carl Shneider, Sandra Smit, Daniel Valenzuela, Jiayin Wang, Lodewyk Wessels, Ying Zhang, Victor Guryev, Fabio Vandin, Kai Ye, Alexander Schönhuth
    Briefings in Bioinformatics, Oxford University Press (OUP), 2018, 19 (1), pp.118-135.
  10. Accounting for Calibration Uncertainty: Bayesian Molecular Dating as a “Doubly Intractable” Problem
    Stéphane Guindon
    Systematic Biology, Oxford University Press (OUP), In press. <10.1093/sysbio/syy003>

2017

  1. Functional analysis of Plasmodium falciparum subpopulations associated with artemisinin resistance in Cambodia
    Ankit Dwivedi, Christelle Reynes, Axel Kuehn, Daniel B. Roche, Nimol Khim, Maxim Hebrard, Sylvain Milanesi, Eric Rivals, Roger Frutos, Didier Menard, Choukri Ben Mamoun, Jacques Colinge, Emmanuel Cornillot
    Malaria Journal, BioMed Central, 2017, 16 (1), pp.493.
  2. HIV-1 Full-Genome Phylogenetics of Generalized Epidemics in Sub-Saharan Africa: Impact of Missing Nucleotide Characters in Next-Generation Sequences
    Oliver Ratmann, Chris Wymant, Caroline Colijn, Siva Danaviah, Max Essex, Simon Frost, Astrid Gall, Simani Gaseitsiwe, Mary Grabowski, Ronald Gray, Stephane Guindon, Arndt Von Haeseler, Pontiano Kaleebu, Michelle Kendall, Alexey Kozlov, Justen Manasa, Bui Quang Minh, Sikhulile Moyo, Vlad Novitsky, Rebecca Nsubuga, Sureshnee Pillay, Thomas Quinn, David Serwadda, Deogratius Ssemwanga, Alexandros Stamatakis, Jana Trifinopoulos, Maria Wawer, Andy Leigh Brown, Tulio De Oliveira, Deenan Pillay, Christophe Fraser
    AIDS Research and Human Retroviruses, Mary Ann Liebert, 2017, 33 (11), pp.1083-1098.
  3. SMS: Smart Model Selection in PhyML
    Vincent Lefort, Jean-Emmanuel Longueville, Olivier Gascuel
    Molecular Biology and Evolution, Oxford University Press (OUP), 2017, 34 (9), pp.2422 - 2424.
  4. Population genomics of picophytoplankton unveils novel chromosome hypervariability
    Romain Blanc-Mathieu, Marc Krasovec, Maxime Hebrard, Sheree Yau, Elodie Desgranges, Joel Martin, Wendy Schackwitz, Alan Kuo, Gerald Salin, Cecile Donnadieu, Yves Desdevises, Sophie Sanchez-Ferandin, Hervé Moreau, Eric Rivals, Igor Grigoriev, Nigel Grimsley, Adam Eyre-Walker, Gwenael Piganeau
    Science Advances , American Association for the Advancement of Science (AAAS), 2017, 3 (7). <10.1126/sciadv.1700239>
  5. Ribo-seq enlightens codon usage bias
    Damien Paulet, Alexandre David, Eric Rivals
    DNA Research, Oxford University Press (OUP), 2017, 24 (3), pp.303-210.
  6. Le dixième gène du VIH
    Elodie Cassan, Anne-Muriel Arigon Chifolleau, Jean-Michel Mesnard, Antoine Gros, Olivier Gascuel
    médecine/sciences, EDP Sciences, 2017, 33 (5), pp.484-485.
  7. Phylodynamique des infections virales
    Samuel Alizon, Emma Saulnier
    Virologie, John Libbey Eurotext 2017, 21 (3), pp.119-129.
  8. De novo assembly of viral quasispecies using overlap graphs
    Jasmijn Baaijens, Amal Zine El Aabidine, Eric Rivals, Alexander Schönhuth
    Genome Research, Cold Spring Harbor Laboratory Press, 2017, 27 (5), pp.835-848.
  9. Accurate self-correction of errors in long reads using de Bruijn graphs
    Leena Salmela, Riku Walve, Eric Rivals, Esko Ukkonen
    Bioinformatics, Oxford University Press (OUP), 2017, 33 (6), pp.799-806.
  10. The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies
    Xavier Argout, Guillaume Martin, Gaetan Droc, Olivier Fouet, Karine Labadie, Eric Rivals, Jean-Marc Aury, Claire Lanaud
    BMC Genomics, BioMed Central, 2017, 18 (1), pp.730-739.
  11. Relationship between superstring and compression measures: New insights on the greedy conjecture
    Eric Rivals, Bastien Cazaux
    Discrete Applied Mathematics, Elsevier, In press. <10.1016/j.dam.2017.04.017>
  12. Inferring epidemiological parameters from phylogenies using regression-ABC: a comparative study
    Emma Saulnier, Olivier Gascuel, Samuel Alizon
    PLoS Computational Biology, Public Library of Science, 2017, 13 (3), pp.e1005416.
  13. Rearrangement Moves on Rooted Phylogenetic Networks
    Philippe Gambette, Leo Van Iersel, Mark Jones, Manuel Lafond, Fabio Pardi, Celine Scornavacca
    PLoS Computational Biology, Public Library of Science, 2017, 13 (8), pp.e1005611.1-21.

2016

  1. Read mapping on de Bruijn graphs
    Antoine Limasset, Bastien Cazaux, Eric Rivals, Pierre Peterlongo
    BMC Bioinformatics, BioMed Central, 2016, 17 (1). <10.1186/s12859-016-1103-9>
  2. Models and algorithms for genome rearrangement with positional constraints
    Krister M. Swenson, Pijus Simonaitis, Mathieu Blanchette
    Algorithms for Molecular Biology, BioMed Central, 2016, 11 (1). <10.1186/s13015-016-0065-9>
  3. Demographic inference under the coalescent in a spatial continuum
    Stéphane Guindon, Hongbin Guo, David Welch
    Theoretical Population Biology, Elsevier, 2016, 111, pp.43-50.
  4. 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
    Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2016, 113 (41), pp.11537-11542.
  5. Linking indexing data structures to de Bruijn graphs: Construction and update
    Bastien Cazaux, Thierry Lecroq, Eric Rivals
    Journal of Computer and System Sciences, Elsevier, 2016, in press. <10.1016/j.jcss.2016.06.008>
  6. A linear time algorithm for Shortest Cyclic Cover of Strings
    Bastien Cazaux, Eric Rivals
    Journal of Discrete Algorithms, Elsevier, 2016, 37, pp.56 - 67.
  7. Phylodynamics of the major HIV-1 CRF02_AG African lineages and its global dissemination
    Daiana Mir, Matthieu Jung, Edson Delatorre, Nicole Vidal, Martine Peeters, Gonzalo Bello
    Infection, Genetics and Evolution, Elsevier, 2016, In press. <10.1016/j.meegid.2016.05.017>
  8. TRM6/61 connects PKCα with translational control through tRNAiMet stabilization: impact on tumorigenesis
    Francoise Macari, Y El-Houfi, G Boldina, Hao Xu, S Khoury-Hanna, J Ollier, L Yazdani, Gang Zheng, I Bièche, Noémie Legrand, Damien Paulet, S Durrieu, A Byström, Stéphane Delbecq, Bernard Lapeyre, L Bauchet, J Pannequin, F Hollande, T Pan, M Teichmann, S Vagner, A David, A Choquet, D Joubert
    Oncogene, Nature Publishing Group, 2016, 35 (14), pp.1785-1796.
  9. Parameterized certificate dispersal and its variants
    Valentin Garnero, Mathias Weller
    Theoretical Computer Science, Elsevier, 2016, 622, pp.66-78.
  10. A ‘Stochastic Safety Radius’ for Distance-Based Tree Reconstruction
    Olivier Gascuel, Mike Steel
    Algorithmica, Springer Verlag, 2016, 74 (4), pp.1386-1403.
  11. Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads
    Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Eric Rivals, Claire Lemaitre, Vincent Miele, Gustavo Sacomoto, Camille Marchet, Bastien Cazaux, Amal Zine El Aabidine, Leena Salmela, Susete Alves-Carvalho, Alexan Andrieux, Raluca Uricaru, Pierre Peterlongo
    GigaScience, BioMed Central, 2016, 5 (1). <10.1186/s13742-015-0105-2>
  12. Aligning the unalignable: bacteriophage whole genome alignments
    Sèverine Bérard, Annie Château, Nicolas Pompidor, Paul Guertin, Anne Bergeron, Krister M. Swenson
    BMC Bioinformatics, BioMed Central, 2016, 17 (1), pp.1-13.
  13. Do branch lengths help to locate a tree in a phylogenetic network?
    Philippe Gambette, Leo Van Iersel, Steven Kelk, Fabio Pardi, Celine Scornavacca
    Bulletin of Mathematical Biology, Springer Verlag, 2016, 78 (9), pp.1773-1795.
  14. Standardized benchmarking in the quest for orthologs
    Adrian Altenhoff, Brigitte Boeckmann, Salvador Capella-Gutiérrez, Daniel Dalquen, Todd Deluca, Kristoffer Forslund, Jaime Huerta-Cepas, Benjamin Linard, Cécile Pereira, Leszek Pryszcz, Fabian Schreiber, Alan Sousa da Silva, Damian Szklarczyk, Clément-Marie Train, Peer Bork, Odile Lecompte, Christian Von Mering, Ioannis Xenarios, Kimmen Sjölander, Lars Juhl Jensen, Maria J Martin, Matthieu Muffato, Toni Gabaldon, Suzanna E Lewis, Paul D Thomas, Erik Sonnhammer, Christophe Dessimoz
    Nature Methods, Nature Publishing Group, 2016, 13 (5), pp.425-430.
  15. Fast and accurate branch lengths estimation for phylogenomic trees
    Manuel Binet, Olivier Gascuel, Celine Scornavacca, Emmanuel J P Douzery, Fabio Pardi
    BMC Bioinformatics, BioMed Central, 2016, 17 (23). <10.1186/s12859-015-0821-8>
  16. Assisted transcriptome reconstruction and splicing orthology
    Samuel Blanquart, Jean-Stéphane Varré, Paul Guertin, Amandine Perrin, Anne Bergeron, Krister M. Swenson
    BMC Genomics, BioMed Central, 2016, 17 (786). <10.1186/s12864-016-3103-6>
  17. The power of greedy algorithms for approximating Max-ATSP, Cyclic Cover, and superstrings
    Bastien Cazaux, Eric Rivals
    Discrete Applied Mathematics, Elsevier, 2016. <10.1016/j.dam.2015.06.003>
  18. Fast Dating Using Least-Squares Criteria and Algorithms
    Thu-Hien To, Matthieu Jung, Samantha Lycett, Olivier Gascuel
    Systematic Biology, Oxford University Press (OUP), 2016, 65 (1), pp.82-97.
  19. In-depth analysis of HIV-1 drug resistance mutations in HIV-infected individuals failing first-line regimens in West and Central Africa
    C. J. Villabona-Arenas, N. Vidal, E. Guichet, L. Serrano, E. Delaporte, Olivier Gascuel, M. Peeters
    AIDS, Lippincott, Williams & Wilkins, 2016, 30 (17), pp.2577-2589.
  20. Uncovering Trophic Interactions in Arthropod Predators through DNA Shotgun-Sequencing of Gut Contents
    Benjamin Linard, Débora Paula, Alex Crampton-Platt, Amrita Srivathsan, Martijn Timmermans, Edison Sujii, Carmen Pires, Lucas Souza, David Andow, Alfried Vogler
    PLoS ONE, Public Library of Science, 2016, 11 (9), pp.e0161841.
  21. Phylogenetic incongruence through the lens of Monadic Second Order logic
    Steven Kelk, Leo Van Iersel, Celine Scornavacca, Mathias Weller
    Journal of Graph Algorithms and Applications (JGAA), Brown University, 2016, 20 (2), pp.189-215.
  22. Inferring gene duplications, transfers and losses can be done in a discrete framework
    Vincent Ranwez, Celine Scornavacca, Jean-Philippe Doyon, Vincent Berry
    Journal of Mathematical Biology, Springer Verlag (Germany), 2016, 72 (7), pp.1811-1844.
  23. On the fixed parameter tractability of agreement-based phylogenetic distances
    Magnus Bordewich, Celine Scornavacca, Nihan Tokac, Mathias Weller
    Journal of Mathematical Biology, Springer Verlag (Germany), 2016, In press. <10.1007/s00285-016-1023-3>
  24. The combinatorics of overlapping genes
    Sophie Lèbre, Olivier Gascuel
    Journal of Theoretical Biology, Elsevier, 2016, In press. <10.1016/j.jtbi.2016.09.018>

2015

  1. Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods
    Daniel Roche, Danielle Allison Brackenridge, Liam James Mcguffin
    International Journal of Molecular Sciences, MDPI, 2015, 16 (12), pp.29829-29842.
  2. Molecular Evolution of the TET Gene Family in Mammals
    Hiromichi Akahori, Stéphane Guindon, Sumio Yoshizaki, Yoshinori Muto
    International Journal of Molecular Sciences, MDPI, 2015, 16 (12), pp.28472-28485.
  3. Closed form modeling of evolutionary rates by exponential Brownian functionals
    Nicolas Privault, Stéphane Guindon
    Journal of Mathematical Biology, Springer Verlag (Germany), 2015, 71 (6), pp.1387-1409.
  4. Interval scheduling and colorful independent sets
    René Van Bevern, Matthias Mnich, Rolf Niedermeier, Mathias Weller
    Journal of Scheduling, Springer Verlag, 2015, 18 (5), pp.449-469.
  5. A complexity and approximation framework for the maximization scaffolding problem
    Annie Château, Rodolphe Giroudeau
    Theoretical Computer Science, Elsevier, 2015, 595, pp.92-106.
  6. Mutation in NDUFA13/GRIM19 leads to early onset hypotonia, dyskinesia and sensorial deficiencies, and mitochondrial complex I instability
    Claire Angebault, Majida Charif, Naig Guegen, Camille Piro-Megy, Bénédicte Mousson de Camaret, Vincent Procaccio, Pierre-Olivier Guichet, Maxime Hebrard, Gaël Manes, Nicolas Leboucq, Francois Rivier, Christian Hamel, Guy Lenaers, Agathe Roubertie
    Human Molecular Genetics, Oxford University Press (OUP), 2015, 24 (14), pp.3948 - 3955.
  7. IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences
    Liam J. Mcguffin, Jennifer D. Atkins, Bajuna R. Salehe, Ahmad N. Shuid, Daniel B. Roche
    Nucleic Acids Research, Oxford University Press, 2015, 43 (W1), pp.W169-W173.
  8. FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program
    Vincent Lefort, Richard Desper, Olivier Gascuel
    Molecular Biology and Evolution, Oxford University Press (OUP), 2015, 32 (10), pp.2798-2800.
  9. TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction
    Jia-Ming Chang, Paolo Di tommaso, Vincent Lefort, Olivier Gascuel, Cedric Notredame
    Nucleic Acids Research, Oxford University Press, 2015, 43 (W1). <10.1093/nar/gkv310>
  10. YOC, A new strategy for pairwise alignment of collinear genomes
    Raluca Uricaru, Célia Michotey, Hélène Chiapello, Eric Rivals
    BMC Bioinformatics, BioMed Central, 2015, 16, pp.16:111.
  11. The ancient Yakuts: a population genetic enigma
    Christine Keyser, Clemence Hollard, Angela Gonzalez, Jean-Luc Fausser, Eric Rivals, Anatoly Nikolayevich Alexeev, Alexandre Riberon, Eric Crubezy, Bertrand Ludes
    Philosophical Transactions of the Royal Society B: Biological Sciences, Royal Society, The, 2015, Discussion meeting issue ‘Ancient DNA: the first three decades’, 370 (1660), pp.20130385.
  12. An assessment of the amount of untapped fold level novelty in under-sampled areas of the tree of life
    Daniel Barry Roche, Thomas Brüls
    Scientific Reports, Nature Publishing Group, 2015, 5, pp.14717.
  13. Polynomial-Time Data Reduction for the Subset Interconnection Design Problem
    Jiehua Chen, Christian Komusiewicz, Rolf Niedermeier, Manuel Sorge, Mathias Weller
    Siam Journal on Discrete Mathematics, Society for Industrial and Applied Mathematics, 2015, 29 (1), pp.1-25.
  14. SylvX: a viewer for phylogenetic tree reconciliations
    François Chevenet, Jean-Philippe Doyon, Celine Scornavacca, Edwin Jacox, Emmanuelle Jousselin, Vincent Berry
    Bioinformatics, Oxford University Press (OUP), 2015. <10.1093/bioinformatics/btv625>
  15. Metagenome Skimming of Insect Specimen Pools: Potential for Comparative Genomics
    Benjamin Linard, Alex Crampton-Platt, Conrad Gillett, Martijn Timmermans, Alfried Vogler
    Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2015, 7 (6), pp.1474-1489.
  16. Exact approaches for scaffolding
    Mathias Weller, Annie Château, Rodolphe Giroudeau
    BMC Bioinformatics, BioMed Central, 2015, pp.S2.
  17. Ancestral gene synteny reconstruction improves extant species scaffolding
    Yoann Anselmetti, Vincent Berry, Cedric Chauve, Annie Château, Eric Tannier, Sèverine Bérard
    BMC Genomics, BioMed Central, 2015, 16 (Suppl 10), pp.S11.
  18. Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable
    Fabio Pardi, Celine Scornavacca
    PLoS Computational Biology, Public Library of Science, 2015, 11 (4), pp.e1004135.
  19. How well can the exponential-growth coalescent approximate constant-rate birth-death population dynamics?
    Tanja Stadler, Timothy G. Vaughan, Alex Gavryushkin, Stéphane Guindon, Denise Kühnert, Gabriel E. Leventhal, Alexei J. Drummond
    Proceedings of the Royal Society B: Biological Sciences, Royal Society, The, 2015, 282 (1806), pp.20150420.
  20. Mathematical and Computational Evolutionary Biology (2013)
    Olivier Gascuel, Tanja Stadler
    Systematic Biology, Oxford University Press (OUP), 2015, 64 (1), pp.1-2.
  21. 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, David Asboe, Olivier Gascuel, Stéphane Hue
    AIDS, Lippincott, Williams & Wilkins, 2015, 29 (15), pp.1917-1925.

2014

  1. LoRDEC: accurate and efficient long read error correction
    Leena Salmela, Eric Rivals
    Bioinformatics, Oxford University Press (OUP), 2014, 30 (24), pp.3506-3514.
  2. Reverse engineering of compact suffix trees and links: A novel algorithm
    Bastien Cazaux, Eric Rivals
    Journal of Discrete Algorithms, Elsevier, 2014, StringMasters 2012 & 2013 Special Issue (Volume 1), 28, pp.9-22.
  3. 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, Sadok Ben Yahia, Olivier Gascuel, Laurent Brehelin
    PLoS ONE, Public Library of Science, 2014, 9 (6), pp.e95275.
  4. Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome
    Nicolas Philippe, Elias Bou Samra, Anthony Boureux, Alban Mancheron, Florence Rufflé, Qiang Bai, John De Vos, Eric Rivals, Thérèse Commes
    Nucleic Acids Research, Oxford University Press, 2014, 42 (5), pp.2820-2832.
  5. Deep Conservation of Human Protein Tandem Repeats within the Eukaryotes
    Elke Schaper, Olivier Gascuel, Maria Anisimova
    Molecular Biology and Evolution, Oxford University Press (OUP), 2014, 31 (5), pp.1132-1148.
  6. Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus
    François Hubert, Guido W. Grimm, Emmanuelle Jousselin, Vincent Berry, Alain Franc, Antoine Kremer
    Systematics and Biodiversity, Taylor & Francis: STM, Behavioural Science and Public Health Titles, 2014, 12 (4), pp.405-423.
  7. An improved genome of the model marine alga [i]Ostreococcus tauri[/i] unfolds by assessing Illumina [i]de novo[/i] assemblies
    Romain Blanc Mathieu, Bram Verhelst, Evelyne Derelle, Stephane Rombauts, Francois-Yves Bouget, Isabelle Carré, Annie Château, Adam Eyre Walker, Nigel Grimsley, Hervé Moreau, Benoît Piégu, Eric Rivals, Wendy Schackwitz, Yves Van de Peer, Gwenaël Piganeau
    BMC Genomics, BioMed Central, 2014, 15, pp.1-11.
  8. CompPhy: a web-based collaborative platform for comparing phylogenies
    Nicolas Fiorini, Vincent Lefort, François Chevenet, Vincent Berry, Anne-Muriel Arigon Chifolleau
    BMC Evolutionary Biology, BioMed Central, 2014, 14 (1), pp.253-255.
  9. FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets
    Cuong Cao Dang, Vinh Sy Le, Olivier Gascuel, Bart Hazes, Quang Si Le
    BMC Bioinformatics, BioMed Central, 2014, 15 (1), pp.341-3.
  10. Predicting the Ancestral Character Changes in a Tree is Typically Easier than Predicting the Root State
    Olivier Gascuel, Mike Steel
    Systematic Biology, Oxford University Press (OUP), 2014, 63 (3), pp.421-435.
  11. Modelling Competition and Dispersal in a Statistical Phylogeographic Framework
    Louis Ranjard, David Welch, Marie Paturel, Stéphane Guindon
    Systematic Biology, Oxford University Press (OUP), 2014, 63 (5), pp.743-752.
  12. Diversity of Prdm9 Zinc Finger Array in Wild Mice Unravels New Facets of the Evolutionary Turnover of this Coding Minisatellite
    Jérôme Buard, Eric Rivals, Denis Dunoyer de Segonzac, Charlotte Garres, Pierre Caminade, Bernard De Massy, Pierre Boursot
    PLoS ONE, Public Library of Science, 2014, 9 (1), pp.e85021.

2013

  1. Genetic structure and evolution of the Leishmania genus in Africa and Eurasia: what does MLSA tell us
    Fouad El Baidouri, Sylvain Brisse, Vincent Berry, François Chevenet, Laure Diancourt, Francine Pratlong, Pierre Marty, Christophe Ravel
    PLoS Neglected Tropical Diseases, Public Library of Science, 2013, 7 (6), pp.e2255.
  2. Representing a set of reconciliations in a compact way
    Celine Scornavacca, Wojciech Paprotny, Vincent Berry, Vincent Ranwez
    Journal of Bioinformatics and Computational Biology, World Scientific Publishing, 2013, 11 (2), pp.1250025.
  3. CRAC: an integrated approach to the analysis of RNA-seq reads
    Nicolas Philippe, Mikaël Salson, Thérèse Commes, Eric Rivals
    Genome Biology, BioMed Central, 2013, 14 (3), pp.R30.
  4. Amalgamating Source Trees with Different Taxonomic Levels
    Vincent Berry, Olaf Bininda-Emonds, Charles Semple
    Systematic Biology, Oxford University Press (OUP), 2013, 62 (2), pp.231-249.
  5. Searching for Virus Phylotypes
    François Chevenet, Matthieu Jung, Martine Peeters, Tulio De Oliveira, Olivier Gascuel
    Bioinformatics, Oxford University Press (OUP), 2013, 29 (5), pp.561-570.
  6. Reconciliation and local gene tree rearrangement can be of mutual profit
    Thi Nguyen, Vincent Ranwez, Stéphanie Pointet, Anne-Muriel Arigon Chifolleau, Jean-Philippe Doyon, Vincent Berry
    Algorithms for Molecular Biology, BioMed Central, 2013, 8 (12). <10.1186/1748-7188-8-12>
  7. The behavior of admixed populations in neighbor-joining inference of population trees
    N. M. Kopelman, N. Stone, Olivier Gascuel, N. A. Rosenberg
    Pacific Symposium on Biocomputing, World Scientific, 2013, pp.273-284.
  8. From Trajectories to Averages: An Improved Description of the Heterogeneity of Substitution Rates Along Lineages
    Stéphane Guindon
    Systematic Biology, Oxford University Press (OUP), 2013, pp.22-34.
  9. Is ecological speciation a major trend in aphids? Insights from a molecular phylogeny of the conifer-feeding genus [i]Cinara[/i]
    Emmanuelle Jousselin, Astrid Cruaud, Guénaëlle Genson, François Chevenet, Robert G. Foottit, Armelle Coeur d'Acier
    Frontiers in Zoology, BioMed Central, 2013, 10 (56). <10.1186/1742-9994-10-56>
  10. On the (non-)existence of polynomial kernels for $P_l$-free edge modification problems
    Sylvain Guillemot, Frédéric Havet, Christophe Paul, Anthony Perez
    Algorithmica, Springer Verlag, 2013, 65 (4), pp.900-926.
  11. Support measures to estimate the reliability of evolutionary events predicted by reconciliation methods
    Thi-Hau Nguyen, Vincent Ranwez, Vincent Berry, Celine Scornavacca
    PLoS ONE, Public Library of Science, 2013, 8 (10), pp.e73667.
  12. Sexually-Transmitted/Founder HIV-1 Cannot Be Directly Predicted from Plasma or PBMC-Derived Viral Quasispecies in the Transmitting Partner
    Pierre Frange, Laurence Meyer, Matthieu Jung, Cécile Goujard, David Zucman, Sylvie Abel, Patrick Hochedez, Marine Gousset, Olivier Gascuel, Christine Rouzioux, Marie-Laure Chaix
    PLoS ONE, Public Library of Science, 2013, 8 (7), pp.e69144.

Communications internationales

2018

  1. Superstrings with multiplicities
    Eric Rivals, Bastien Cazaux
    Gonzalo Navarro; David Sankoff; Binhai Zhu. CPM: Combinatorial Pattern Matching, Jul 2018, Qingdao, China. Leibniz International Proceedings in Informatics (LIPIcs), 105 (21), pp.21:1-21:16, 2018, 29th Annual Symposium on Combinatorial Pattern Matching.

2017

  1. On the Linearization of Scaffolds Sharing Repeated Contigs
    Mathias Weller, Annie Chateau, Rodolphe Giroudeau
    COCOA: Combinatorial Optimization and Applications, Dec 2017, Shanghai, China. Springer, 11th International Conference on Combinatorial Optimization and Applications, LNCS (10628), 2017, Part II. <10.1007/978-3-319-71147-8_38>
  2. New Insights for Power Edge Set Problem
    Benoit Darties, Annie Chateau, Rodolphe Giroudeau, Mathias Weller
    X. Gao; H. Du; M. Han. COCOA: Combinatorial Optimization and Applications, Dec 2017, Shanghai, China. Springer, 11th International Conference on Combinatorial Optimization and Applications, LNCS (10627), pp.180-194, 2017, Part I.
  3. Measuring Differences To Compare Sets Of Models And Improve Diversity In MDE
    Adel Ferdjoukh, Florian Galinier, Eric Bourreau, Annie Chateau, Clémentine Nebut
    ICSEA: International Conference on Software Engineering Advances, Oct 2017, Athenes, Greece. International Conference on Software Engineering Advances, 2017. <https://www.iaria.org/conferences2017/CfPICSEA17.html>
  4. Rearrangement Scenarios Guided by Chromatin Structure
    Sylvain Pulicani, Pijus Simonaitis, Eric Rivals, Krister Swenson
    15th International Workshop, RECOMB CG 2017, Oct 2017, Barcelona, Spain. Springer, Cham, 10562, pp.141-155, 2017, Comparative Genomics.
  5. Finding Local Genome Rearrangements
    Krister Swenson, Pijus Simonaitis
    WABI: Workshop on Algorithms in Bioinformatics, Aug 2017, Boston, United States. 17th International Workshop on Algorithms in Bioinformatics, Leibniz International Proceedings in Informatics (LIPIcs) (88), pp.24:1--24:13, 2017.
  6. Improved Complexity for Power Edge Set Problem
    Benoit Darties, Annie Chateau, Rodolphe Giroudeau, Mathias Weller
    IWOCA: International Workshop on Combinatorial Algorithms, Jul 2017, Newcastle, Australia. 28th International Workshop on Combinatorial Algorithms, 2017. <https://carma.newcastle.edu.au/meetings/iwoca/>

2016

  1. Instance guaranteed ratio for the Scaffolding problem
    Rodolphe Giroudeau, Annie Château, Clément Dallard, Mathias Weller
    COCOA: Conference on Combinatorial Optimization and Applications, Dec 2016, Hong Kong, China. 10th Annual International Conference on Combinatorial Optimization and Applications, 2016. <https://conference.cs.cityu.edu.hk/cocoa2016/>
  2. On Complexity and Residual Approximation in Solution Extension Problems
    Rodolphe Giroudeau, Annie Château, Jean-Claude König, Mathias Weller, Valentin Pollet
    COCOA: Combinatorial Optimization and Applications, Dec 2016, Hong Kong, China. 10th Annual International Conference on Combinatorial Optimization and Applications, LNCS (10043), 2016, Combinatorial Optimization and Applications. <https://conference.cs.cityu.edu.hk/cocoa2016/>
  3. Hybrid and non hybrid error correction for long reads: LoRDEC and LoRMA
    Eric Rivals
    Colib’read workshop, Nov 2016, Paris, France. 0007. <http://gdr-bim.cnrs.fr/colibread/>
  4. Genetic Algorithm to Improve Diversity in MDE
    Florian Galinier, Eric Bourreau, Annie Château, Adel Ferdjoukh, Clémentine Nebut
    META: Metaheuristics and Nature Inspired Computing, Oct 2016, Marrakech, Morocco. 6th International Conference on Metaheuristics and Nature Inspired Computing, 2016. <https://meta2016.sciencesconf.org/>
  5. A Graph Constraints Formulation for Contigs Scaffolding
    Rodolphe Giroudeau, Annie Château, Clément Dallard, Eric Bourreau
    WCB: Workshop on Constraint-Based Methods for Bioinformatics, Sep 2016, Toulouse, France. 12th International Workshop on Constraint-Based Methods for Bioinformatics, pp.136-149, 2016.
  6. Superstring Graph: A New Approach for Genome Assembly
    Bastien Cazaux, Gustavo Sacomoto, Eric Rivals
    Riccardo Dondi, Guillaume Fertin, Giancarlo Mauri Eleventh International Conference on Algorithmic Aspects in Information and Management, Jul 2016, Bergamo, Italy. Springer International Publishing AG Switzerland, Lecture Notes in Computer Science, 9778, pp.39 - 52, 2016, Eleventh International Conference on Algorithmic Aspects in Information and Management.
  7. A new tool for non-hybrid correction of long noisy reads
    Eric Rivals
    NGS Symposium 2016, Jul 2016, Illkirch, France. 2016. <https://ngssymposium.sciencesconf.org/>
  8. A Model-Driven Approach to Generate Relevant and Realistic Datasets
    Adel Ferdjoukh, Eric Bourreau, Annie Château, Clémentine Nebut
    SEKE: Software Engineering and Knowledge Engineering, Jul 2016, Redwood City, San Francisco Bay, United States. 28th International Conference on Software Engineering and Knowledge Engineering, pp.105-109, 2016.
  9. Fast Dating using Least Squares
    Olivier Gascuel
    Mathematical Models for Epidemiology and Phylogenetics, May 2016, Lille, France. 2016. <http://math.univ-lille1.fr/~tran/journees_epidemio2016.html>
  10. Phylogeny-reconstruction methods
    Olivier Gascuel
    CoME: Course on Computational Molecular Evolution, May 2016, Heraklion, Greece. 8th EMBO Practical Course on Computational Molecular Evolution, 2016, CoME VIII. <http://events.embo.org/16-computational-evolution/>
  11. Shortest DNA cyclic cover in compressed space
    Bastien Cazaux, Rodrigo Cánovas, Eric Rivals
    Data Compression Conference, Mar 2016, Snowbird, United States.

2015

  1. On the Complexity of Scaffolding Problems: From Cliques to Sparse Graphs
    Mathias Weller, Annie Château, Rodolphe Giroudeau
    COCOA: Combinatorial Optimization and Applications, Dec 2015, Houston, United States. COCOA 2015 - The 9th Annual International Conference on Combinatorial Optimization and Applications 9486, pp.409-423, 2015, LNCS.
  2. Méthodes bioinformatiques pour la prédiction de la fonction des gènes : identification des domaines protéiques dans les génomes de pathogènes
    Laurent Brehelin
    JFMPM: Journées Franco-Maghrébines de Parasitologie-Mycologie, Oct 2015, Tunis, Tunisie. 2es Journées Franco-Maghrébines de Parasitologie-Mycologie, 2015. <http://www.pasteur.tn/index.php?option=com_content&view=article&id=531&Itemid=808>
  3. LoRDEC: a tool for correcting errors in long sequencing reads
    Eric Rivals
    Mosig A.; Rahnenführer J.; Rahmann S.; Eisenacher M. GCB: German Conference on Bioinformatics, Sep 2015, Dortmund, Germany. PeerJ, 2015, German Conference on Bioinformatics 2015 Collection. <http://gcb2015.cs.tu-dortmund.de>
  4. Fast dating using least squares
    Olivier Gascuel
    SMBE: Society for Molecular Biology and Evolution, Jul 2015, Vienna, Austria. 16th annual meeting of the Society for Molecular Biology and Evolution 2015. <http://smbe2015.at>
  5. Reconstructible phylogenetic networks: do not distinguish the indistinguishable
    Fabio Pardi, Celine Scornavacca
    Evolution, Jun 2015, Guarujà, Brazil. 1st joint annual meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB), and the American Society of Naturalists (ASN), 2015. <http://evolution2015.org/>
  6. Fast and accurate branch lengths estimation for phylogenomic trees
    Manuel Binet, Olivier Gascuel, Celine Scornavacca, Emmanuel J. P. Douzery, Fabio Pardi
    Evolution, Jun 2015, Guarujà, Brazil. 1st Joint Annual Meeting on Evolution, 2015. <http://evolution2015.org/>
  7. Distance-based methods in phylogenomics
    Fabio Pardi, Manuel Binet
    FILOFOCS: French-Israeli Workshop on Foundations of Computer Science, May 2015, Tel Aviv, Israel. 2015, 4th French-Israeli Workshop on Foundations of Computer Science Tel-Aviv University - May 25-27, 2015. <http://hyde.eng.tau.ac.il/FILOFOCS-2015/>
  8. Correction of long sequencing reads: a novel approach
    Eric Rivals
    Abstract for the keynote presentation at " From Nucleotides to Networks " Symposium, Ghent, Belgium.. Symposium "From Nucleotides to Networks", May 2015, Gand (Ghent), Belgium. 2015. <http://www.bign2n.ugent.be>
  9. Phylogeny Reconstruction Methods
    Olivier Gascuel
    CoME: Course on Molecular Evolution, Apr 2015, Hinxton, United Kingdom. 7th Trust-EMBL-EBI Advanced Course on Computational Molecular Evolution, 2015, CoME VII. <http://abacus.gene.ucl.ac.uk/CoME/>
  10. Instantiation of meta-models constrained with OCL: A CSP approach
    Adel Ferdjoukh, Anne-Elisabeth Baert, Eric Bourreau, Annie Château, Remi Coletta, Clémentine Nebut
    MODELSWARD: Model-Driven Engineering and Software Development, Feb 2015, Angers, France. Proceedings of the third International Conference on Model Driven Engineering and Software Development, pp.213-222, 2015.

2014

  1. Models and Algorithms in Phylogenetics
    Olivier Gascuel
    Molecular Phylogenies Courses, Dec 2014, Hanoi, Vietnam. Training course in Molecular Phylogeny, 2014.
  2. Approximation of Greedy Algorithms for Max-ATSP, Maximal Compression, Maximal Cycle Cover, and Shortest Cyclic Cover of Strings
    Bastien Cazaux, Eric Rivals
    Jan Holub; Jan Zd’arek. PSC'2014: Prague Stringology Conference, Sep 2014, Prague, Czech Republic. Czech Technical University in Prague, Czech Republic, ISBN 978-80-01-05547-2, pp.148-161, 2014, Proceedings of the Prague Stringology Conference 2014.
  3. Complexity and Polynomial-Time Approximation Algorithms around the Scaffolding Problem
    Annie Château, Rodolphe Giroudeau
    Dediu, Adrian-Horia; Martín-Vide, Carlos; Truthe, Bianca. AlCoB: Algorithms for Computational Biology, Jul 2014, Tarragona, Spain. Springer International Publishing, First International Conference, AlCoB 2014, Tarragona, Spain, July 1-3, 2014, Proceedigns, LNCS (8542), pp.47-58, 2014, Algorithms for Computational Biology.
  4. From Indexing Data Structures to de Bruijn Graphs
    Bastien Cazaux, Thierry Lecroq, Eric Rivals
    Kulikov, Alexander S.; Kuznetsov, Sergei O.; Pevzner, Pavel. CPM: Combinatorial Pattern Matching, Jun 2014, Moscow, Russia. Springer International Publishing, CPM'2014: 25th Annual Symposium on Combinatorial Pattern Matching, LNCS (8486), pp.89-99, 2014, Combinatorial Pattern Matching.
  5. Identifiability of phylogenetic networks
    Fabio Pardi, Celine Scornavacca
    MCEB: Mathematical and Computational Evolutionary Biology, Jun 2014, Hameau de l'Etoile, St Martin de Londres, France. 2014. <http://www.lirmm.fr/mceb2014/program.php>
  6. Phylogenetic reconstruction: models, methods, and algorithms
    Olivier Gascuel
    Bioinformatics in the Tropics Brazil, May 2014, Salvador, Brazil. 2nd International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology, 2014. <http://www.bioafrica.net/manuscripts/2ndInternationalWorkshopBrazil2014A4.pdf>
  7. Phylogeny Reconstruction Methods
    Olivier Gascuel
    CoME: Course on Computational Molecular Evolution, May 2014, Heraklion, Greece. 6th EMBO Course on Computational Molecular Evolution, 2014, CoME VI. <http://events.embo.org/14-computational-evolution/>
  8. Phylogenetic networks: what can we reconstruct?
    Fabio Pardi
    FILOFOCS: French-Israeli Workshop on Foundations of Computer Science, May 2014, Paris, France. 2014. <http://www.liafa.univ-paris-diderot.fr/~adiro/filofocs/filofocs2014/index.html>
  9. Reconstructible phylogenetic networks: no need to distinguish the indistinguishable
    Fabio Pardi, Celine Scornavacca
    Waiheke: The Interface of Mathematics and Biology - New Zealand Phylogenomics Meeting, Feb 2014, Waiheke, New Zealand. The Interface of Mathematics and Biology, The 18th Annual New Zealand Phylogenomics Meeting, Sunday 2nd - Friday 7th February, 2014, 2014. <http://www.math.canterbury.ac.nz/bio/events/waiheke2014/>

2013

  1. Building the Assembly De Bruijn Graph from an Implicit Suffix Tree
    Eric Rivals
    Jens Stoye and Roland Wittler. Mini-Workshop on the Storage, Search and Annotation of Multiple Similar Genomes, Dec 2013, Bielefeld, Germany. 2013. <http://wiki.techfak.uni-bielefeld.de/didy/workshopPangenomeStorageSearch>
  2. A CSP Approach for Metamodel Instantiation
    Adel Ferdjoukh, Anne-Elisabeth Baert, Annie Château, Remi Coletta, Clémentine Nebut
    ICTAI: International Conference on Tools with Artificial Intelligence, Nov 2013, Washington, United States. 25th IEEE International Conference on Tools with Artificial Intelligence, pp.1044-1051, 2013.
  3. Phylogeny Reconstruction Methods
    Olivier Gascuel
    Bioinformatics in the Tropics, Sep 2013, Durban, South Africa. 2nd Workshop of the Bioinformatics in the Tropics series, 2013.
  4. Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data
    Niko Välimäki, Eric Rivals
    Z. Cai et al. ISBRA'2013: International Symposium on Bioinformatics Research and Applications, May 2013, Charlotte, NC, United States. Spinger-Verlag, 7875 (7875), pp.237-248, 2013, Lecture Notes in Bioinformatics (LNBI).
  5. Phylogeny Reconstruction Methods
    Olivier Gascuel
    CoME: Course on Computational Molecular Evolution, Apr 2013, Hinxton, United Kingdom. 5th Trust-EMBL-EBI Advanced Course on Computational Molecular Evolution (session leader), 2013, CoME V. <http://abacus.gene.ucl.ac.uk/meetings/CoME/>
  6. Phylogeny Reconstruction Methods
    Olivier Gascuel
    ISCB Africa ASBCB Conference on Bioinformatics, Mar 2013, Casablanca, Morocco. ISCB-Africa - Bi-annual ISCB Africa Conference, 2013. <http://www.iscb.org/iscbafrica2013>

Mots-clés

Algorithmique du texte et des arbres, Combinatoire, Optimisation, Modélisation probabiliste et statistique, Classification, Phylogénie, Séquençage haut debit, Génomes, Transcriptomes, Protéomes, Cancer, Paludisme, VIH

Dernière mise à jour le 27/06/2018