MAB: Méthodes et algorithmes pour la bio informatique

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The MAB team (Methods and Algorithms for Bioinformatics) proposes mathematical and algorithmic methods (text and tree algorithms, combinatorial algorithms and optimization, probabilistic modeling, statistical machine learning) to address biological  issues such as evolution, phylogeny, comparative genomics, functional annotation of genes and proteins, malaria, HIV, cancer. The software systems developed by MAB are available through the ATGC platform.

Research themes are organized in three main axes :

The software developed by the team are available on the ATGC platform.

Members

Staff

Associates & Students

Regular Co-workers

  • Charles Lecellier, Research Fellow CNRS
  • Sophie Lèbre, UPVM
  • Olivier Gascuel, Research Director CNRS

News

September 2019 - See in the INS2I news: Réordonner les textes pour optimiser la compression de leur index

Publications 2014 - 2019: Evaluation period

International Journals

2021

  1. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
    Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli, Miki Kojima-Ishiyama, Hiromi Nishiyori-Sueki, Imad Abugessaisa, Stuart Aitken, Bronwen Aken, Intikhab Alam, Tanvir Alam, Rami Alasiri, Ahmad Alhendi, Hamid Alinejad-Rokny, Mariano Alvarez, Robin Andersson, Takahiro Arakawa, Marito Araki, Taly Arbel, John Archer, Alan Archibald, Erik Arner, Peter Arner, Kiyoshi Asai, Haitham Ashoor, Gaby Astrom, Magda Babina, Kenneth Baillie, Vladimir Bajic, Archana Bajpai, Sarah Baker, Richard Baldarelli, Adam Balic, Mukesh Bansal, Arsen Batagov, Serafim Batzoglou, Anthony Beckhouse, Antonio Beltrami, Carlo Beltrami, Nicolas Bertin, Sharmodeep Bhattacharya, Peter Bickel, Judith Blake, Mathieu Blanchette, Beatrice Bodega, Alessandro Bonetti, Hidemasa Bono, Jette Bornholdt, Michael Bttcher, Salim Bougouffa, Mette Boyd, Jeremie Breda, Frank Brombacher, James Brown, Carol Bult, Maxwell Burroughs, Dave Burt, Annika Busch, Giulia Caglio, Andrea Califano, Christopher Cameron, Carlo Cannistraci, Alessandra Carbone, Ailsa Carlisle, Kim Carter, Daniela Cesselli, Jen-Chien Chang, Julie Chen, Yun Chen, Marco Chierici, John Christodoulou, Yari Ciani, Emily Clark, Mehmet Coskun, Maria Dalby, Emiliano Dalla, Carsten Daub, Carrie Davis, Derek de Rie, Elena Denisenko, Bart Deplancke, Michael Detmar, Ruslan Deviatiiarov, Diego Di Bernardo, Alexander Diehl, Lothar Dieterich, Emmanuel Dimont, Sarah Djebali, Taeko Dohi, Jose Dostie, Finn Drablos, Albert Edge, Matthias Edinger, Anna Ehrlund, Karl Ekwall, Arne Elofsson, Mitsuhiro Endoh, Hideki Enomoto, Saaya Enomoto, Mohammad Faghihi, Michela Fagiolini, Mary Farach-Carson, Geoffrey Faulkner, Alexander Favorov, Ana Miguel Fernandes, Carmelo Ferrai, Alistair Forrest, Lesley Forrester, Mattias Forsberg, Alexandre Fort, Margherita Francescatto, Tom Freeman, Martin Frith, Shinji Fukuda, Manabu Funayama, Cesare Furlanello, Masaaki Furuno, Chikara Furusawa, Hui Gao, Iveta Gazova, Claudia Gebhard, Florian Geier, Teunis Geijtenbeek, Samik Ghosh, Yanal Ghosheh, Thomas Gingeras, Takashi Gojobori, Tatyana Goldberg, Daniel Goldowitz, Julian Gough, Dario Greco, Andreas Gruber, Sven Guhl, Roderic Guigo, Reto Guler, Oleg Gusev, Stefano Gustincich, Thomas Ha, Vanja Haberle, Paul Hale, Bjrn Hallstrom, Michiaki Hamada, Lusy Handoko, Mitsuko Hara, Matthias Harbers, Jennifer Harrow, Jayson Harshbarger, Takeshi Hase, Akira Hasegawa, Kosuke Hashimoto, Taku Hatano, Nobutaka Hattori, Ryuhei Hayashi, Yoshihide Hayashizaki, Meenhard Herlyn, Kristina Hettne, Peter Heutink, Winston Hide, Kelly Hitchens, Shannon Ho Sui, Peter ’t Hoen, Chung Chau Hon, Fumi Hori, Masafumi Horie, Katsuhisa Horimoto, Paul Horton, Rui Hou, Edward Huang, Yi Huang, Richard Hugues, David Hume, Hans Ienasescu, Kei Iida, Tomokatsu Ikawa, Toshimichi Ikemura, Kazuho Ikeo, Norihiko Inoue, Yuri Ishizu, Yosuke Ito, Masayoshi Itoh, Anna Ivshina, Boris Jankovic, Piroon Jenjaroenpun, Rory Johnson, Mette Jorgensen, Hadi Jorjani, Anagha Joshi, Giuseppe Jurman, Bogumil Kaczkowski, Chieko Kai, Kaoru Kaida, Kazuhiro Kajiyama, Rajaram Kaliyaperumal, Eli Kaminuma, Takashi Kanaya, Hiroshi Kaneda, Philip Kapranov, Artem Kasianov, Takeya Kasukawa, Toshiaki Katayama, Sachi Kato, Shuji Kawaguchi, Jun Kawai, Hideya Kawaji, Hiroshi Kawamoto, Yuki Kawamura, Satoshi Kawasaki, Tsugumi Kawashima, Judith Kempfle, Tony Kenna, Juha Kere, Levon Khachigian, Hisanori Kiryu, Mami Kishima, Hiroyuki Kitajima, Toshio Kitamura, Hiroaki Kitano, Enio Klaric, Kjetil Klepper, Peter Klinken, Edda Kloppmann, Alan Knox, Yuichi Kodama, Yasushi Kogo, Miki Kojima, Soichi Kojima, Norio Komatsu, Hiromitsu Komiyama, Tsukasa Kono, Haruhiko Koseki, Shigeo Koyasu, Anton Kratz, Alexander Kukalev, Ivan Kulakovskiy, Anshul Kundaje, Hiroshi Kunikata, Richard Kuo, Tony Kuo, Shigehiro Kuraku, Vladimir Kuznetsov, Tae Jun Kwon, Matt Larouche, Timo Lassmann, Andy Law, Kim-Anh Lê Cao, Weonju Lee, Boris Lenhard, Andreas Lennartsson, Kang Li, Ruohan Li, Berit Lilje, Leonard Lipovich, Marina Lizio, Gonzalo Lopez, Shigeyuki Magi, Gloria Mak, Vsevolod Makeev, Riichiro Manabe, Michiko Mandai, Jessica Mar, Kazuichi Maruyama, Taeko Maruyama, Elizabeth Mason, Anthony Mathelier, Hideo Matsuda, Yulia Medvedeva, Terrence Meehan, Niklas Mejhert, Alison Meynert, Norihisa Mikami, Akiko Minoda, Hisashi Miura, Yohei Miyagi, Atsushi Miyawaki, Yosuke Mizuno, Hiromasa Morikawa, Mitsuru Morimoto, Masaki Morioka, Soji Morishita, Kazuyo Moro, Efthymios Motakis, Hozumi Motohashi, Abdul Kadir Mukarram, Christine Mummery, Christopher Mungall, Yasuhiro Murakawa, Masami Muramatsu, Mitsuyoshi Murata, Kazunori Nagasaka, Takahide Nagase, Yutaka Nakachi, Fumio Nakahara, Kenta Nakai, Kumi Nakamura, Yasukazu Nakamura, Yukio Nakamura, Toru Nakazawa, Guy Nason, Chirag Nepal, Quan Hoang Nguyen, Lars Nielsen, Kohji Nishida, Koji Nishiguchi, Hiromi Nishiyori, Kazuhiro Nitta, Shuhei Noguchi, Shohei Noma, Cedric Notredame, Soichi Ogishima, Naganari Ohkura, Hiroshi Ohno, Mitsuhiro Ohshima, Takashi Ohtsu, Yukinori Okada, Mariko Okada-Hatakeyama, Yasushi Okazaki, Per Oksvold, Valerio Orlando, Ghim Sion Ow, Mumin Ozturk, Mikhail Pachkov, Triantafyllos Paparountas, Suraj Parihar, Sung-Joon Park, Giovanni Pascarella, Robert Passier, Helena Persson, Ingrid Philippens, Silvano Piazza, Charles Plessy, Ana Pombo, Fredrik Ponten, Stéphane Poulain, Thomas Poulsen, Swati Pradhan, Carolina Prezioso, Clare Pridans, Xiang-Yang Qin, John Quackenbush, Owen Rackham, Jordan Ramilowski, Timothy Ravasi, Michael Rehli, Sarah Rennie, Tiago Rito, Patrizia Rizzu, Christelle Robert, Marco Roos, Burkhard Rost, Filip Roudnicky, Riti Roy, Morten Rye, Oxana Sachenkova, Pal Saetrom, Hyonmi Sai, Shinji Saiki, Mitsue Saito, Akira Saito, Shimon Sakaguchi, Mizuho Sakai, Saori Sakaue, Asako Sakaue-Sawano, Albin Sandelin, Hiromi Sano, Yuzuru Sasamoto, Hiroki Sato, Alka Saxena, Hideyuki Saya, Andrea Schafferhans, Sebastian Schmeier, Christian Schmidl, Daniel Schmocker, Claudio Schneider, Marcus Schueler, Erik Schultes, Gundula Schulze-Tanzil, Colin Semple, Shigeto Seno, Wooseok Seo, Jun Sese, Jessica Severin, Guojun Sheng, Jiantao Shi, Yishai Shimoni, Jay Shin, Javier Simonsanchez, Asa Sivertsson, Evelina Sjostedt, Cilla Soderhall, Georges St Laurent, Marcus Stoiber, Daisuke Sugiyama, Kim Summers, Ana Maria Suzuki, Harukazu Suzuki, Kenji Suzuki, Mikiko Suzuki, Naoko Suzuki, Takahiro Suzuki, Douglas Swanson, Rolf Swoboda, Michihira Tagami, Ayumi Taguchi, Hazuki Takahashi, Masayo Takahashi, Kazuya Takamochi, Satoru Takeda, Yoichi Takenaka, Kin Tung Tam, Hiroshi Tanaka, Rica Tanaka, Yuji Tanaka, Dave Tang, Ichiro Taniuchi, Andrea Tanzer, Hiroshi Tarui, Martin Taylor, Aika Terada, Yasuhisa Terao, Alison Testa, Mark Thomas, Supat Thongjuea, Kentaro Tomii, Elena Torlai Triglia, Hiroo Toyoda, Gwen Tsang, Motokazu Tsujikawa, Mathias Uhlén, Eivind Valen, Marc van de Wetering, Erik van Nimwegen, Dmitry Velmeshev, Roberto Verardo, Morana Vitezic, Kristoffer Vitting-Seerup, Kalle von Feilitzen, Christian Voolstra, Ilya Vorontsov, Claes Wahlestedt, Kazuhide Watanabe, Shoko Watanabe, Christine Wells, Louise Winteringham, Ernst Wolvetang, Haruka Yabukami, Ken Yagi, Takuji Yamada, Yoko Yamaguchi, Masayuki Yamamoto, Yasutomo Yamamoto, Yumiko Yamamoto, Yasunari Yamanaka, Kojiro Yano, Kayoko Yasuzawa, Yukiko Yatsuka, Masahiro Yo, Shunji Yokokura, Misako Yoneda, Emiko Yoshida, Yuki Yoshida, Masahito Yoshihara, Rachel Young, Robert Young, Nancy Yu, Noriko Yumoto, Susan Zabierowski, Peter Zhang, Silvia Zucchelli, Martin Zwahlen, Clément Chatelain, Piero Carninci, Michiel de Hoon, Wyeth Wasserman, Laurent Brehelin, Charles-Henri Lecellier
    Nature Communications, Nature Publishing Group, 2021, 12 (1). <10.1038/s41467-021-23143-7>
  2. Efficient assembly consensus algorithms for divergent contig sets
    Annie Chateau, Tom Davot, Manuel Lafond
    Computational Biology and Chemistry, Elsevier, 2021, 93, pp.#107516.
  3. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
    Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli, Jordan Ramilowski, Jessica Severin, Yoshihide Hayashizaki, Masayoshi Itoh, Michihira Tagami, Mitsuyoshi Murata, Miki Kojima-Ishiyama, Shohei Noma, Shuhei Noguchi, Takeya Kasukawa, Akira Hasegawa, Harukazu Suzuki, Hiromi Nishiyori-Sueki, Martin Frith, Fantom Consortium, Clément Chatelain, Piero Carninci, Michiel J. L. de Hoon, Wyeth Wasserman, Laurent Brehelin, Charles-Henri Lecellier
    Nature Communications, Nature Publishing Group, 2021, 12, pp.1-18.
  4. Producing Genomic Sequences after Genome Scaffolding with Ambiguous Paths: Complexity, Approximation and Lower Bounds
    Tom Davot, Annie Chateau, Rodolphe Giroudeau, Mathias Weller, Dorine Tabary
    Algorithmica, Springer Verlag, 2021. <10.1007/s00453-021-00819-6>
  5. Ten years of collaborative progress in the Quest for Orthologs
    Benjamin Linard, Ingo Ebersberger, Shawn Mcglynn, Natasha Glover, Tomohiro Mochizuki, Mateus Patricio, Odile Lecompte, Yannis Nevers, Paul Thomas, Toni Gabaldón, Erik Sonnhammer, Christophe Dessimoz, Ikuo Uchiyama
    Molecular Biology and Evolution, Oxford University Press (OUP), 2021, pp.msab098.
  6. FTO-mediated cytoplasmic m6Am demethylation adjusts stem-like properties in colorectal cancer cell
    Sébastien Relier, Julie Ripoll, Hélène Guillorit, Amandine Amalric, Cyrinne Achour, Florence Boissière, Jérôme Vialaret, Aurore Attina, Françoise Debart, Armelle Choquet, Françoise Macari, Virginie Marchand, Yuri Motorin, Emmanuelle Samalin, Jean-Jacques Vasseur, Julie Pannequin, Francesca Aguilo, Evelyne Lopez-Crapez, Christophe Hirtz, Eric Rivals, Amandine Bastide, Alexandre David
    Nature Communications, Nature Publishing Group, 2021, 12 (1), pp.1716.
  7. Computing the probability of gene trees concordant with the species tree in the multispecies coalescent
    Jakub Truszkowski, Celine Scornavacca, Fabio Pardi
    Theoretical Population Biology, Elsevier, 2021, 137, pp.22-31.
  8. On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo
    Charles-Elie Rabier, Vincent Berry, Marnus Stoltz, Joao D. Santos, Wensheng Wang, Jean-Christophe Glaszmann, Fabio Pardi, Celine Scornavacca
    PLoS Computational Biology, Public Library of Science, In press. <10.1371/journal.pcbi.1008380>
  9. The SgLasso and its cousins for selective genotyping and extreme sampling: application to association studies and genomic selection
    Charles-Elie Rabier, Céline Delmas
    Statistics, Taylor & Francis: STM, Behavioural Science and Public Health Titles, In press.
  10. Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes
    Christophe Menichelli, Vincent Guitard, Rafael Miyazawa Martins, Sophie Lèbre, José Juan Lopez-Rubio, Charles-Henri Lecellier, Laurent Brehelin
    PLoS Computational Biology, Public Library of Science, 2021, 17 (4), pp.e1008909.

2020

  1. Rapid screening and detection of inter-type viral recombinants using phylo- $k$ -mers
    Guillaume Scholz, Benjamin Linard, Nikolai Romashchenko, Eric Rivals, Fabio Pardi
    Bioinformatics, Oxford University Press (OUP), 2020, pp.#btaa1020.
  2. iMOKA: k-mer based software to analyze large collections of sequencing data
    Claudio Lorenzi, Sylvain Barriere, Jean-Philippe Villemin, Laureline Dejardin Bretones, Alban Mancheron, William Ritchie
    Genome Biology, BioMed Central, 2020, 21 (1). <10.1186/s13059-020-02165-2>
  3. Rates and Rocks: Strengths and Weaknesses of Molecular Dating Methods
    Stéphane Guindon
    Frontiers in Genetics, Frontiers, 2020, 11, pp.#526.
  4. Hierarchical Overlap Graph
    Bastien Cazaux, Eric Rivals
    Information Processing Letters, Elsevier, 2020, 155, pp.#105862.
  5. Diversity of bacteriophages encoding Panton-Valentine leukocidin in temporally and geographically related Staphylococcus aureus
    Geoffrey Coombs, Sarah Baines, Benjamin Howden, Krister Swenson, Frances O'Brien
    PLoS ONE, Public Library of Science, 2020, 15 (2), pp.e0228676.
  6. Sampling bias and model choice in continuous phylogeography: getting lost on a random walk
    Antanas Kalkauskas, Umberto Perron, Yuxuan Sun, Nick Goldman, Guy Baele, Stéphane Guindon, Nicola de Maio
    PLoS Computational Biology, Public Library of Science, In press. <10.1101/2020.02.18.954057>
  7. PEWO: a collection of workflows to benchmark phylogenetic placement
    Benjamin Linard, Nikolai Romashchenko, Fabio Pardi, Eric Rivals
    Bioinformatics, Oxford University Press (OUP), In press. <10.1093/bioinformatics/btaa657>

2019

  1. A general framework for genome rearrangement with biological constraints
    Pijus Simonaitis, Annie Chateau, Krister Swenson
    Algorithms for Molecular Biology, BioMed Central, 2019, 14 (1). <10.1186/s13015-019-0149-4>
  2. Accounting for ambiguity in ancestral sequence reconstruction
    Adrien Oliva, Sylvain Pulicani, Vincent Lefort, Laurent Brehelin, Olivier Gascuel, Stéphane Guindon
    Bioinformatics, Oxford University Press (OUP), 2019, 35 (21), pp.4290-4297.
  3. Mitochondrial metagenomics reveals the ancient origin and phylodiversity of soil mites and provides a phylogeny of the Acari
    Paula Arribas, Carmelo Andujar, Maria Lourdes Moraza, Benjamin Linard, Brent Emerson, Alfried Vogler
    Molecular Biology and Evolution, Oxford University Press (OUP), 2019. <10.1093/molbev/msz255>
  4. Rapid alignment-free phylogenetic identification of metagenomic sequences
    Benjamin Linard, Krister Swenson, Fabio Pardi
    Bioinformatics, Oxford University Press (OUP), 2019, 35 (18), pp.3303-3312.
  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, 2019, 104, pp.165-183.
  6. Large-scale mammalian genome rearrangements coincide with chromatin interactions
    Krister Swenson, Mathieu Blanchette
    Bioinformatics, Oxford University Press (OUP), 2019, 35 (14), pp.i117-i126.
  7. NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region
    Andrew Oldfield, Telmo Henriques, Dhirendra Kumar, Adam Burkholder, Senthilkumar Cinghu, Damien Paulet, Brian Bennett, Pengyi Yang, Benjamin Scruggs, Christopher Lavender, Eric Rivals, Karen Adelman, Raja Jothi
    Nature Communications, Nature Publishing Group, 2019, 10 (1), pp.3072.
  8. New mitochondrial genomes of 39 soil dwelling Coleoptera from metagenome sequencing
    Carmelo Andujar, Paula Arribas, Michal Motyka, Mathew Bocek, Ladislav Bocak, Benjamin Linard, Alfried Vogler
    Mitochondrial DNA Part B Resources, Taylor & Francis Online, 2019, 4 (2), pp.2447-2450.
  9. NGPhylogeny.fr: new generation phylogenetic services for non-specialists
    Frédéric Lemoine, Damien Correia, Vincent Lefort, Olivia Doppelt-Azeroual, Fabien Mareuil, Sarah Cohen-Boulakia, Olivier Gascuel
    Nucleic Acids Research, Oxford University Press, 2019, 47 (W1), pp.W260-W265.
  10. Distribution and asymptotic behavior of the phylogenetic transfer distance
    Miraine Dávila Felipe, Jean-Baka Domelevo Entfellner, Frédéric Lemoine, Jakub Truszkowski, Olivier Gascuel
    Journal of Mathematical Biology, Springer Verlag (Germany), 2019, 79 (2), pp.485-508.
  11. GECKO is a genetic algorithm to classify and explore high throughput sequencing data
    Aubin Thomas, Sylvain Barriere, Lucile Broseus, Julie Brooke, Claudio Lorenzi, Jean-Philippe Villemin, Gregory Beurier, Robert Sabatier, Christelle Reynes, Alban Mancheron, William Ritchie
    Communications Biology, Nature Publishing Group, 2019, 2 (1), pp.1-8.
  12. A Faster Algorithm for Computing the Kernel of Maximum Agreement Subtrees
    Biing-Feng Wang, Krister Swenson
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, In press, pp.1-1.
  13. Correction: Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable
    Fabio Pardi, Celine Scornavacca
    PLoS Computational Biology, Public Library of Science, 2019, 15 (6), pp.e1007137.
  14. On the accuracy in high dimensional linear models and its application to genomic selection
    Charles-Elie Rabier, Brigitte Mangin, Simona Grusea
    Scandinavian Journal of Statistics, Wiley, 2019, 46 (1), pp.289-313.
  15. Probing transcription factor combinatorics in different promoter classes and in enhancers
    Jimmy Vandel, Océane Cassan, Sophie Lebre, Charles-Henri Lecellier, Laurent Brehelin
    BMC Genomics, BioMed Central, 2019, 20 (103). <10.1186/s12864-018-5408-0>
  16. AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees
    Bastien Cazaux, Guillaume Castel, Eric Rivals
    Bioinformatics, Oxford University Press (OUP), 2019, 35 (17), pp.3163-3165.
  17. Origin, tempo, and mode of the spread of DENV-4 Genotype IIB across the state of São Paulo, Brazil during the 2012-2013 outbreak
    Ayda Susana Ortiz-Baez, Marielton dos Passos Cunha, Danila Vedovello, Tatiana Elias Colombo, Maurício Lacerda Nogueira, Christian Julián Villabona-Arenas, Paolo Marinho de Andrade Zanotto
    Memórias do Instituto Oswaldo Cruz, Instituto Oswaldo Cruz, Ministério da Saúde, 2019, 114, pp.e180251.
  18. Finding a most parsimonious or likely tree in a network with respect to an alignment
    Steven Kelk, Fabio Pardi, Celine Scornavacca, Leo van Iersel
    Journal of Mathematical Biology, Springer Verlag (Germany), 2019, 78 (1-2), pp.527-547.
  19. WAVES: a web application for versatile enhanced bioinformatic services
    Marc Chakiachvili, Sylvain Milanesi, Anne-Muriel Arigon Chifolleau, Vincent Lefort
    Bioinformatics, Oxford University Press (OUP), 2019, 35 (11), pp.140-142.
  20. Machine learning meets genome assembly
    Kleber Padovani de Souza, João Carlos Setubal, André Carlos Ponce de Leon F. de Carvalho, Guilherme Oliveira, Annie Chateau, Ronnie Alves
    Briefings in Bioinformatics, Oxford University Press (OUP), 2019, 20 (6), pp.2116-2129.

2018

  1. Finding local genome rearrangements
    Krister Swenson, Pijus Simonaitis
    Algorithms for Molecular Biology, BioMed Central, 2018, 13, pp.9-23.
  2. On Residual Approximation in Solution Extension Problems
    Mathias Weller, Annie Chateau, Rodolphe Giroudeau, Jean-Claude König, Valentin Pollet
    Journal of Combinatorial Optimization, Springer Verlag, 2018, 36 (4), pp.1195-1220.
  3. Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty
    Maria Chatzou, Evan Floden, Paolo Di Tommaso, Olivier Gascuel, Cedric Notredame
    Systematic Biology, Oxford University Press (OUP), 2018, 67 (6), pp.997-1009.
  4. Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana)
    Gaëtan Droc, Julie Sardos, Alberto Cenci, Björn Geigle, Mark Hibbins, Nabila Yahiaoui, Franc-Christophe Baurens, Vincent Berry, Matthew W. Hahn, Angélique d'Hont, Nicolas Roux, Yann Hueber, Valentin Guignon, Mathieu Rouard, Guillaume Martin
    Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2018, 10 (12), pp.3129-3140.
  5. Complexity and lowers bounds for Power Edge Set Problem
    Benoit Darties, Nicolas Champseix, Annie Chateau, Rodolphe Giroudeau, Mathias Weller
    Journal of Discrete Algorithms, Elsevier, 2018, 52-53, pp.70-91.
  6. Evolutionary history and spatio-temporal dynamics of dengue virus serotypes in an endemic region of Colombia
    Cinthy Jiménez-Silva, María Fernanda Carreño, Ayda Susana Ortiz-Baez, Luz Aida Rey, Christian Julián Villabona-Arenas, Raquel Ocazionez
    PLoS ONE, Public Library of Science, 2018, 13 (8), pp.e0203090.
  7. 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.
  8. Scaffolding Problems Revisited: Complexity, Approximation and Fixed Parameter Tractable Algorithms, and Some Special Cases
    Mathias Weller, Annie Chateau, Clément Dallard, Rodolphe Giroudeau
    Algorithmica, Springer Verlag, 2018, 80 (6), pp.1771-1803.
  9. 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, 34 (21), pp.3646-3652.
  10. Renewing Felsenstein’s phylogenetic bootstrap in the era of big data
    Fréderic Lemoine, Jean-Baka Domelevo Entfellner, Eduan Wilkinson, Damien Correia, Miraine Dávila Felipe, Tulio de Oliveira, Olivier Gascuel
    Nature, Nature Publishing Group, 2018, 556 (7702), pp.452-456.
  11. Accurate template-based modeling in CASP12 using the IntFOLD4-TS, ModFOLD6, and ReFOLD methods
    Liam Mcguffin, Ahmad Shuid, Robert Kempster, Ali H.A. Maghrabi, John Nealon, Bajuna Salehe, Jennifer Atkins, Daniel Roche
    Proteins: Structure, Function, and Genetics, Wiley, 2018, 86, pp.335-344.
  12. 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 Kauffmann, 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.
  13. 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.
  14. 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.
  15. Short Communication: Nucleoside Reverse Transcriptase Inhibitors with Reduced Predicted Activity Do Not Impair Second-Line Therapy with Lopinavir/Ritonavir or Darunavir/Ritonavir
    Christian Julián Villabona-Arenas, Sabrina Eymard-Duvernay, Avelin Aghokeng, Emilande Guichet, Coumba Toure-Kane, Guillaume Bado, Sinata Koulla-Shiro, Eric Delaporte, Laura Ciaffi, Martine Peeters
    AIDS Research and Human Retroviruses, Mary Ann Liebert, 2018, 34 (6), pp.477-480.
  16. 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 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.
  17. CompPhy2: a flexible and real time collaborative web platform for editing and comparing phylogenies
    Floréal Cabanettes, Jean-François Dufayard, Vincent Berry, Vincent Lefort, Frederic de Lamotte Guéry, Anne-Muriel Arigon Chifolleau
    Bioinformatics, Oxford University Press (OUP), In press, In Press, pp.1-3.
  18. Accounting for Calibration Uncertainty: Bayesian Molecular Dating as a “Doubly Intractable” Problem
    Stéphane Guindon
    Systematic Biology, Oxford University Press (OUP), 2018, 67 (4), pp.651-661.
  19. Measurement and Generation of Diversity and Meaningfulness in Model Driven Engineering
    Adel Ferdjoukh, Florian Galinier, Eric Bourreau, Annie Chateau, Clémentine Nebut
    International Journal On Advances in Software, IARIA, 2018, 11 (1/2), pp.131-146.

2017

  1. Functional analysis of Plasmodium falciparum subpopulations associated with artemisinin resistance in Cambodia
    Ankit Dwivedi, Christelle Reynes, Axel Kuehn, Daniel Roche, Nimol Khim, Maxime 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, Stéphane 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. Human babesiosis: Indication of a molecular mimicry between thrombospondin domains from a novel Babesia microti BmP53 protein and host platelets molecules
    Ahmed Abdelmoniem Mousa, Daniel Roche, Mohamad Alaa Terkawi, Kyohko Kameyama, Ketsarin Kamyingkird, Patrick Vudriko, Akram Salama, Shinuo Cao, Sahar Orabi, Hanem Khalifa, Mohamed Ahmed, Mabrouk Attia, Ahmed Elkirdasy, Yoshifumi Nishikawa, Xuenan Xuan, Emmanuel Cornillot
    PLoS ONE, Public Library of Science, 2017, 12 (10). <10.1371/journal.pone.0185372>
  4. Epidemiological and ecological determinants of Zika virus transmission in an urban setting
    José Lourenço, Maricelia Maia de Lima, Nuno Rodrigues Faria, Andrew Walker, Moritz Kraemer, Christian Julián Villabona-Arenas, Ben Lambert, Erenilde Marques de Cerqueira, Oliver Pybus, Luiz Alcantara, Mario Recker
    eLife, eLife Sciences Publication, 2017, 6, pp.e29820.
  5. 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.
  6. 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), Non paginé. <10.1126/sciadv.1700239>
  7. Ribo-seq enlightens codon usage bias
    Damien Paulet, Alexandre David, Eric Rivals
    DNA Research, Oxford University Press (OUP), 2017, 24 (3), pp.303-210.
  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. 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.
  10. Phylodynamique des infections virales
    Samuel Alizon, Emma Saulnier
    Virologie, John Libbey Eurotext 2017, 21 (3), pp.119-129.
  11. The combinatorics of overlapping genes
    Sophie Lèbre, Olivier Gascuel
    Journal of Theoretical Biology, Elsevier, 2017, 415, pp.90-101.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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), 2017, 74 (1-2), pp.239-257.
  17. The mitochondrial genome of Iberobaenia (Coleoptera: Iberobaeniidae): first rearrangement of protein-coding genes in the beetles
    Carmelo Andujar, Paula Arribas, Benjamin Linard, Robin Kundrata, Ladislav Bocak, Alfried Vogler
    Mitochondrial DNA Part A, Taylor and Francis, 2017, 28 (2), pp.156-158.
  18. Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses
    Edwin Jacox, Mathias Weller, Eric Tannier, Celine Scornavacca
    Bioinformatics, Oxford University Press (OUP), 2017, 33 (7), pp.980-987.

2016

  1. CSAM: Compressed SAM format
    Rodrigo Cánovas, Alistair Moffat, Andrew Turpin
    Bioinformatics, Oxford University Press (OUP), 2016, 32 (24), pp.3709-3716.
  2. 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>
  3. Short Communication: High Viral Load and Multidrug Resistance Due to Late Switch to Second-Line Regimens Could Be a Major Obstacle to Reach the 90-90-90 UNAIDS Objectives in Sub-Saharan Africa
    Emilande Guichet, Avelin Aghokeng, Laetitia Serrano, Guillaume Bado, Coumba Touré-Kane, Sabrina Eymard-Duvernay, Christian Julián Villabona-Arenas, Eric Delaporte, Laura Ciaffi, Martine Peeters
    AIDS Research and Human Retroviruses, Mary Ann Liebert, 2016, 32 (12), pp.1159-1162.
  4. Models and algorithms for genome rearrangement with positional constraints
    Krister Swenson, Pijus Simonaitis, Mathieu Blanchette
    Algorithms for Molecular Biology, BioMed Central, 2016, 11 (1), pp.13-24.
  5. The power of greedy algorithms for approximating Max-ATSP, Cyclic Cover, and superstrings
    Bastien Cazaux, Eric Rivals
    Discrete Applied Mathematics, Elsevier, 2016, 212, pp.48-60.
  6. Demographic inference under the coalescent in a spatial continuum
    Stéphane Guindon, Hongbin Guo, David Welch
    Theoretical Population Biology, Elsevier, 2016, 111, pp.43-50.
  7. 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.
  8. A linear time algorithm for Shortest Cyclic Cover of Strings
    Bastien Cazaux, Eric Rivals
    Journal of Discrete Algorithms, Elsevier, 2016, 37, pp.56-67.
  9. Nod Factor Effects on Root Hair-Specific Transcriptome of Medicago truncatula: Focus on Plasma Membrane Transport Systems and Reactive Oxygen Species Networks.
    Isabelle Damiani, Alice Drain, Marjorie Guichard, Sandrine Balzergue, Alexandre Boscari, Jean-Christophe Boyer, Véronique Brunaud, Sylvain Cottaz, Corinne Rancurel, Martine da Rocha, Cécile Fizames, Sébastien Fort, Isabelle Gaillard, Vincent Maillol, Etienne G J Danchin, Hatem Rouached, Eric Samain, Yan-Hua Su, Julien Thouin, Bruno Touraine, Alain Puppo, Jean-Marie Frachisse, Nicolas Pauly, Hervé Sentenac
    Frontiers in Plant Science, Frontiers, 2016, 7, pp.794.
  10. 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, 46, pp.190-199.
  11. TRM6/61 connects PKCα with translational control through tRNAiMet stabilization: impact on tumorigenesis
    Françoise Macari, Y El-Houfi, G Boldina, Hao Xu, S Khoury-Hanna, Jérémy Ollier, Laura Yazdani, Gang Zheng, I Bièche, Noémie Legrand, Damien Paulet, S Durrieu, A Byström, Stéphane Delbecq, Bernard Lapeyre, L Bauchet, Julie Pannequin, Frédéric Hollande, T Pan, M Teichmann, S Vagner, Alexandre David, Armelle Choquet, Dominique Joubert
    Oncogene, Nature Publishing Group, 2016, 35 (14), pp.1785-1796.
  12. A ‘Stochastic Safety Radius’ for Distance-Based Tree Reconstruction
    Olivier Gascuel, Mike Steel
    Algorithmica, Springer Verlag, 2016, 74 (4), pp.1386-1403.
  13. Parameterized certificate dispersal and its variants
    Valentin Garnero, Mathias Weller
    Theoretical Computer Science, Elsevier, 2016, 622, pp.66-78.
  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), 2016, 32 (4), pp.608-610.
  15. 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>
  16. Aligning the unalignable: bacteriophage whole genome alignments
    Sèverine Bérard, Annie Chateau, Nicolas Pompidor, Paul Guertin, Anne Bergeron, Krister Swenson
    BMC Bioinformatics, BioMed Central, 2016, 17 (1), pp.30-43.
  17. 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.
  18. 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.
  19. 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.
  20. 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, Brown University, 2016, 20 (2), pp.189-215.
  21. Fast and accurate branch lengths estimation for phylogenomic trees
    Manuel Binet, Olivier Gascuel, Celine Scornavacca, Emmanuel Douzery, Fabio Pardi
    BMC Bioinformatics, BioMed Central, 2016, 17 (23). <10.1186/s12859-015-0821-8>
  22. In-depth analysis of HIV-1 drug resistance mutations in HIV-infected individuals failing first-line regimens in West and Central Africa
    Christian Julián Villabona-Arenas, N. Vidal, E. Guichet, L. Serrano, E. Delaporte, Olivier Gascuel, M. Peeters
    AIDS, Lippincott, Williams & Wilkins, 2016, 30 (17), pp.2577-2589.
  23. Uncovering Trophic Interactions in Arthropod Predators through DNA Shotgun-Sequencing of Gut Contents
    Débora Paula, Benjamin Linard, 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.
  24. 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.

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 Chateau, Rodolphe Giroudeau
    Theoretical Computer Science, Elsevier, 2015, 595, pp.92-106.
  6. 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 Roche
    Nucleic Acids Research, Oxford University Press, 2015, 43 (W1), pp.W169-W173.
  7. 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.
  8. 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), pp.W3-W6.
  9. YOC, A new strategy for pairwise alignment of collinear genomes
    Raluca Uricaru, Célia Michotey, Hélène Chiapello, Eric Rivals
    BMC Bioinformatics, BioMed Central, 2015, 16 (1), pp.16:111.
  10. 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.
  11. Mathematical and Computational Evolutionary Biology (2013)
    Olivier Gascuel, Tanja Stadler
    Systematic Biology, Oxford University Press (OUP), 2015, 64 (1), pp.1-2.
  12. 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.
  13. 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.
  14. 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.
  15. An assessment of the amount of untapped fold level novelty in under-sampled areas of the tree of life
    Daniel Roche, Thomas Brüls
    Scientific Reports, Nature Publishing Group, 2015, 5, pp.14717.
  16. 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.
  17. Exact approaches for scaffolding
    Mathias Weller, Annie Chateau, Rodolphe Giroudeau
    BMC Bioinformatics, BioMed Central, 2015, 16 (Suppl 14), pp.S2.
  18. Ancestral gene synteny reconstruction improves extant species scaffolding
    Yoann Anselmetti, Vincent Berry, Cedric Chauve, Annie Chateau, Eric Tannier, Sèverine Bérard
    BMC Genomics, BioMed Central, 2015, 16 (Suppl 10), pp.S11.

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. 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 Chateau, Adam Eyre Walker, Nigel Grimsley, Hervé Moreau, Benoit Piegu, Eric Rivals, Wendy Schackwitz, Yves van de Peer, Gwenaël Piganeau
    BMC Genomics, BioMed Central, 2014, 15, pp.1-11.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.341-343.
  11. 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.
  12. 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.

International Communications

2020

  1. Efficient Construction of Hierarchical Overlap Graphs
    Sung Park, Bastien Cazaux, Kunsoo Park, Eric Rivals
    27th International Symposium on String Processing and Information Retrieval (SPIRE), Oct 2020, Orlando, FL, United States. pp.277-290.
  2. Linearizing Genomes: Exact Methods and Local Search
    Tom Davot, Annie Chateau, Rodolphe Giroudeau, Mathias Weller
    SOFSEM, Jan 2020, Limassol, Cyprus. pp.505-518.
  3. Scanning Phylogenetic Networks is NP-hard
    Vincent Berry, Celine Scornavacca, Mathias Weller
    SOFSEM, Jan 2020, Limassol, Cyprus. pp.519-530.

2019

  1. Rapidly computing the phylogenetic transfer index
    Jakub Truszkowski, Olivier Gascuel, Krister Swenson
    19th International Workshop on Algorithms in Bioinformatics (WABI), Sep 2019, Niagara Falls, NY, United States. pp.20:1--20:12.
  2. Weighted minimum-length rearrangement scenarios
    Pijus Simonaitis, Annie Chateau, Krister Swenson
    19th International Workshop on Algorithms in Bioinformatics (WABI), Sep 2019, Niagara Falls, NY, United States. pp.13:1-13:17.
  3. Power Edge Set and Zero Forcing Set Remain Difficult in Cubic Graphs
    Pierre Cazals, Benoit Darties, Annie Chateau, Rodolphe Giroudeau, Mathias Weller
    30th International Workshop on Combinatorial Algorithms (IWOCA), Jul 2019, Pisa, Italy. pp.122-135.
  4. Perspectives and challenges of Computational Pan-Genomics
    Eric Rivals
    LifeTime UnConference, Centre de Regulació Genòmica (CRG); centro nacional de análisis genómico (CNAG), Jul 2019, Barelone, Spain. <https://lifetime-fetflagship.eu/lifetime-unconference/>
  5. Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length Encoding
    Bastien Cazaux, Eric Rivals
    30th Annual Symposium on Combinatorial Pattern Matching (CPM), University of Pisa, Jun 2019, Pise, Italy. pp.24:1--24:20.
  6. New Polynomial-Time Algorithm around the Scaffolding Problem
    Tom Davot, Annie Chateau, Rodolphe Giroudeau, Mathias Weller
    AlCoB: Algorithms for Computational Biology, May 2019, Berkeley, United States. pp.25-38.
  7. High performance text indexing and applications in life sciences
    Eric Rivals
    UK-France Bilateral International Meeting on High Performance Computing and Biomathematics, Feb 2019, Chicheley, United Kingdom. <https://royalsociety.org/>

2018

  1. Fast and accurate genome-scale identification of DNA-binding sites
    David Martin, Vincent Maillol, Eric Rivals
    BIBM: Bioinformatics and Biomedicine, Dec 2018, Madrid, Spain. pp.201-205.
  2. On the hardness of approximating Linearization of Scaffolds sharing Repeated Contigs
    Tom Davot, Annie Chateau, Rodolphe Giroudeau, Mathias Weller
    RECOMB-CG: Comparative Genomics, Oct 2018, Magog-Orford, QC, Canada. pp.91-107.
  3. A General Framework for Genome Rearrangement with Biological Constraints
    Pijus Simonaitis, Annie Chateau, Krister Swenson
    RECOMB-CG: Comparative Genomics, Oct 2018, Magog-Orford, QC, Canada. pp.49-71.
  4. New Results About the Linearization of Scaffolds Sharing Repeated Contigs
    Dorine Tabary, Tom Davot, Mathias Weller, Annie Chateau, Rodolphe Giroudeau
    COCOA: Conference on Combinatorial Optimization and Applications, Sep 2018, Atlanta, GA, United States. pp.94-107.
  5. Superstrings with multiplicities
    Eric Rivals, Bastien Cazaux
    29th Annual Symposium on Combinatorial Pattern Matching (CPM), Qingdao University, Jul 2018, Qingdao, China. pp.21:1-21:16.
  6. Practical lower and upper bounds for the Shortest Linear Superstring
    Bastien Cazaux, Samuel Juhel, Eric Rivals
    SEA: Symposium on Experimental Algorithms, Jun 2018, L'Aquilla, Italy. pp.18:1--18:14.
  7. Rapid alignment-free phylogenec placement via ancestral k-mers
    Benjamin Linard, Krister Swenson, Fabio Pardi
    MCEB: Mathematical and Computational Evolutionary Biology, Jun 2018, St Martin de Londres, France. <http://www.lirmm.fr/mceb2018/>
  8. Données génomiques massives : applications, enjeux computationnels et perspectives
    Eric Rivals
    Open Science, Open Access, Open Data et données, Jun 2018, Strasbourg, France. <http://www.misha.fr>

2017

  1. On the Linearization of Scaffolds Sharing Repeated Contigs
    Mathias Weller, Annie Chateau, Rodolphe Giroudeau
    COCOA: Conference on Combinatorial Optimization and Applications, Dec 2017, Shanghai, China. pp.509-517.
  2. New Insights for Power Edge Set Problem
    Benoit Darties, Annie Chateau, Rodolphe Giroudeau, Mathias Weller
    COCOA: Conference on Combinatorial Optimization and Applications, Dec 2017, Shanghai, China. pp.180-194.
  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. <https://www.iaria.org/conferences2017/CfPICSEA17.html>
  4. Rearrangement Scenarios Guided by Chromatin Structure
    Sylvain Pulicani, Pijus Simonaitis, Eric Rivals, Krister Swenson
    RECOMB-CG: Comparative Genomics, Oct 2017, Barcelona, Spain. pp.141-155.
  5. LZ78 Compression in Low Main Memory Space
    Diego Arroyuelo, Rodrigo Cánovas, Gonzalo Navarro, Rajeev Raman
    SPIRE: String Processing and Information Retrieval, Sep 2017, Palermo, Italy. pp.38-50.
  6. Finding Local Genome Rearrangements
    Pijus Simonaitis, Krister Swenson
    17th International Workshop on Algorithms in Bioinformatics (WABI 2017), Aug 2017, Boston, United States. pp.24:1--24:13.
  7. 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. pp.128-141.
  8. Full Compressed Affix Tree Representations
    Rodrigo Cánovas, Eric Rivals
    DCC: Data Compression Conference, IEEE, Apr 2017, Snowbird, UT, United States. pp.102-111.

2016

  1. On Residual Approximation in Solution Extension Problems
    Mathias Weller, Annie Chateau, Rodolphe Giroudeau, Jean-Claude König, Valentin Pollet
    COCOA: Conference on Combinatorial Optimization and Applications, Dec 2016, Hong Kong, China. pp.463-476.
  2. Instance Guaranteed Ratio on Greedy Heuristic for Genome Scaffolding
    Clément Dallard, Mathias Weller, Annie Chateau, Rodolphe Giroudeau
    COCOA: Conference on Combinatorial Optimization and Applications, Dec 2016, Hong Kong, China. pp.294-308.
  3. Hybrid and non hybrid error correction for long reads: LoRDEC and LoRMA
    Eric Rivals
    Colib’read workshop, ANR Colib'read, Nov 2016, Paris, France. <http://gdr-bim.cnrs.fr/colibread/>
  4. Genetic Algorithm to Improve Diversity in MDE
    Florian Galinier, Eric Bourreau, Annie Chateau, Adel Ferdjoukh, Clémentine Nebut
    META: Metaheuristics and Nature Inspired Computing, Oct 2016, Marrakech, Morocco. <https://meta2016.sciencesconf.org/>
  5. A Graph Constraints Formulation for Contigs Scaffolding
    Eric Bourreau, Annie Chateau, Clément Dallard, Rodolphe Giroudeau
    WCB: Workshop on Constraint-Based Methods for Bioinformatics, Sep 2016, Toulouse, France. pp.136-149.
  6. Superstring Graph: A New Approach for Genome Assembly
    Bastien Cazaux, Gustavo Sacomoto, Eric Rivals
    AAIM: Algorithmic Aspects in Information and Management, Università degli Studi di Bergamo, Jul 2016, Bergamo, Italy. pp.39-52.
  7. A new tool for non-hybrid correction of long noisy reads
    Eric Rivals
    NGS Symposium, Thomas Sexton, Jul 2016, Illkirch, France. <https://ngssymposium.sciencesconf.org/>
  8. A Model-Driven Approach to Generate Relevant and Realistic Datasets
    Adel Ferdjoukh, Eric Bourreau, Annie Chateau, Clémentine Nebut
    SEKE: Software Engineering and Knowledge Engineering, Jul 2016, Redwood City, San Francisco Bay, United States. pp.105-109.
  9. Fast Dating using Least Squares
    Olivier Gascuel
    Mathematical Models for Epidemiology and Phylogenetics, May 2016, Lille, France. <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. <http://events.embo.org/16-computational-evolution/>
  11. Shortest DNA cyclic cover in compressed space
    Bastien Cazaux, Rodrigo Cánovas, Eric Rivals
    DCC: Data Compression Conference, Mar 2016, Snowbird, UT, United States. pp.536-545.

2015

  1. On the Complexity of Scaffolding Problems: From Cliques to Sparse Graphs
    Mathias Weller, Annie Chateau, Rodolphe Giroudeau
    COCOA: Conference on Combinatorial Optimization and Applications, Dec 2015, Houston, United States. pp.409-423.
  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. <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
    GCB: German Conference on Bioinformatics, University Alliance Ruhr, Sep 2015, Dortmund, Germany. <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. <http://smbe2015.at>
  5. Fast and accurate branch lengths estimation for phylogenomic trees
    Manuel Binet, Olivier Gascuel, Celine Scornavacca, Emmanuel Douzery, Fabio Pardi
    Evolution, Jun 2015, Guarujà, Brazil. <http://evolution2015.org/>
  6. Reconstructible phylogenetic networks: do not distinguish the indistinguishable
    Fabio Pardi, Celine Scornavacca
    Evolution, Jun 2015, Guarujà, Brazil. <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. <http://hyde.eng.tau.ac.il/FILOFOCS-2015/>
  8. Correction of long sequencing reads: a novel approach
    Eric Rivals
    at " From Nucleotides to Networks " Symposium, Ghent, Belgium.. BIG N2N: Bioinformatics Institute Ghent "From Nucleotides to Networks", Ghent University, Bioinformatics Institute Ghent, May 2015, Gand, Ghent, Belgium. <http://www.bign2n.ugent.be>
  9. Phylogeny Reconstruction Methods
    Olivier Gascuel
    CoME: Course on Molecular Evolution, Apr 2015, Hinxton, United Kingdom. <http://abacus.gene.ucl.ac.uk/CoME/>
  10. Construction of a de Bruijn Graph for Assembly from a Truncated Suffix Tree
    Bastien Cazaux, Thierry Lecroq, Eric Rivals
    LATA: Language and Automata Theory and Applications, Mar 2015, Nice, France. pp.109-120.
  11. Instantiation of meta-models constrained with OCL: A CSP approach
    Adel Ferdjoukh, Anne-Elisabeth Baert, Eric Bourreau, Annie Chateau, Remi Coletta, Clémentine Nebut
    MODELSWARD: Model-Driven Engineering and Software Development, Feb 2015, Angers, France. pp.213-222.

2014

  1. Models and Algorithms in Phylogenetics
    Olivier Gascuel
    Molecular Phylogenies Courses, Dec 2014, Hanoi, Vietnam.
  2. Approximation of Greedy Algorithms for Max-ATSP, Maximal Compression, Maximal Cycle Cover, and Shortest Cyclic Cover of Strings
    Bastien Cazaux, Eric Rivals
    PSC: Prague Stringology Conference, Czech Technical University in Prague, Sep 2014, Prague, Czech Republic. pp.148-161.
  3. Complexity and Polynomial-Time Approximation Algorithms around the Scaffolding Problem
    Annie Chateau, Rodolphe Giroudeau
    AlCoB: Algorithms for Computational Biology, Jul 2014, Tarragona, Spain. pp.47-58.
  4. From Indexing Data Structures to de Bruijn Graphs
    Bastien Cazaux, Thierry Lecroq, Eric Rivals
    CPM: Combinatorial Pattern Matching, Moscow State University, Jun 2014, Moscow, Russia. pp.89-99.
  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. <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. <http://www.bioafrica.net/manuscripts/2ndInternationalWorkshopBrazil2014A4.pdf>
  7. Phylogeny Reconstruction Methods
    Olivier Gascuel
    CoME: Course on Computational Molecular Evolution, May 2014, Heraklion, Greece. <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. <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, Feb 2014, Waiheke, New Zealand. <http://www.math.canterbury.ac.nz/bio/events/waiheke2014/>

Tags

Optimisation, Classification, Transcriptomes, Cancer, Algorithmic of text and trees, Combinatoric, Probabilistic and statistic modeling, Phylogeny, Hight speed sequencing, Genomes, HIV, Proteomes, Malaria

Last update on 29/04/2021