MAB: Méthodes et algorithmes pour la bio informatique

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
- Anne-Muriel Arigon, Assistant Professor UM
- Vincent Berry, Professor UM
- Laurent Brehelin, Research Fellow CNRS
- Annie Chateau, Assistant Professor UM
- Stéphane Guindon, Research Fellow CNRS
- Vincent Lefort, Research Engineer CNRS
- Alban Mancheron, Assistant Professor UM
- Fabio Pardi, Research Fellow CNRS
- Eric Rivals, Research Director CNRS
- Krister Swenson, Research Fellow CNRS
Associates & Students
- Bastien Cazaux, Research associate CNRS
- Tom Davot, CDD Teaching Researcher UM
- Quentin Delorme, PhD student Société ADNiD
- Elisa Gueneau, PhD student UM
- Nadine Jacquet, Research associate CNRS
- Nastasija Mijovic, PhD student UM
- Julie Ripoll, Research associate CNRS
- Nikolai Romashchenko, PhD student UM
- Raphael Romero, PhD student UM
- Johannes Wirtz, Long-term Guest DFG
Regular Co-workers
- Charles Lecellier, Research Fellow CNRS
- Sophie Lèbre, UPV
- 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
- FTO-mediated cytoplasmic m6Am demethylation adjusts stem-like properties in colorectal cancer cellSébastien 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 DavidNature Communications, Nature Publishing Group, 2021, 12 (1), pp.1716.
- The SgLasso and its cousins for selective genotyping and extreme sampling: application to association studies and genomic selectionCharles-Elie Rabier, Céline DelmasStatistics, Taylor & Francis: STM, Behavioural Science and Public Health Titles, In press.
2020
- Rapid screening and detection of inter-type viral recombinants using phylo- $k$ -mersGuillaume Scholz, Benjamin Linard, Nikolai Romashchenko, Eric Rivals, Fabio PardiBioinformatics, Oxford University Press (OUP), 2020, pp.#btaa1020.
- iMOKA: k-mer based software to analyze large collections of sequencing dataClaudio Lorenzi, Sylvain Barriere, Jean-Philippe Villemin, Laureline Dejardin Bretones, Alban Mancheron, William RitchieGenome Biology, BioMed Central, 2020, 21 (1). <10.1186/s13059-020-02165-2>
- Rates and Rocks: Strengths and Weaknesses of Molecular Dating MethodsStéphane GuindonFrontiers in Genetics, Frontiers, 2020, 11, pp.#526.
- Hierarchical Overlap GraphBastien Cazaux, Eric RivalsInformation Processing Letters, Elsevier, 2020, 155, pp.#105862.
- Diversity of bacteriophages encoding Panton-Valentine leukocidin in temporally and geographically related Staphylococcus aureusGeoffrey Coombs, Sarah Baines, Benjamin Howden, Krister Swenson, Frances O'BrienPLoS ONE, Public Library of Science, 2020, 15 (2), pp.e0228676.
- Sampling bias and model choice in continuous phylogeography: getting lost on a random walkAntanas Kalkauskas, Umberto Perron, Yuxuan Sun, Nick Goldman, Guy Baele, Stéphane Guindon, Nicola de MaioPLoS Computational Biology, Public Library of Science, In press. <10.1101/2020.02.18.954057>
- PEWO: a collection of workflows to benchmark phylogenetic placementBenjamin Linard, Nikolai Romashchenko, Fabio Pardi, Eric RivalsBioinformatics, Oxford University Press (OUP), In press. <10.1093/bioinformatics/btaa657>
- Computing the probability of gene trees concordant with the species tree in the multispecies coalescentJakub Truszkowski, Celine Scornavacca, Fabio PardiTheoretical Population Biology, Elsevier, In press.
2019
- A general framework for genome rearrangement with biological constraintsPijus Simonaitis, Annie Chateau, Krister SwensonAlgorithms for Molecular Biology, BioMed Central, 2019, 14 (1). <10.1186/s13015-019-0149-4>
- Accounting for ambiguity in ancestral sequence reconstructionAdrien Oliva, Sylvain Pulicani, Vincent Lefort, Laurent Brehelin, Olivier Gascuel, Stéphane GuindonBioinformatics, Oxford University Press (OUP), 2019. <10.1093/bioinformatics/btz249>
- Mitochondrial metagenomics reveals the ancient origin and phylodiversity of soil mites and provides a phylogeny of the AcariPaula Arribas, Carmelo Andujar, Maria Lourdes Moraza, Benjamin Linard, Brent Emerson, Alfried VoglerMolecular Biology and Evolution, Oxford University Press (OUP), 2019. <10.1093/molbev/msz255>
- Rapid alignment-free phylogenetic identification of metagenomic sequencesBenjamin Linard, Krister Swenson, Fabio PardiBioinformatics, Oxford University Press (OUP), 2019, 35 (18), pp.3303-3312.
- Linking indexing data structures to de Bruijn graphs: Construction and updateBastien Cazaux, Thierry Lecroq, Eric RivalsJournal of Computer and System Sciences, Elsevier, 2019, 104, pp.165-183.
- Large-scale mammalian genome rearrangements coincide with chromatin interactionsKrister Swenson, Mathieu BlanchetteBioinformatics, Oxford University Press (OUP), 2019, 35 (14), pp.i117-i126.
- NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted regionAndrew Oldfield, Telmo Henriques, Dhirendra Kumar, Adam Burkholder, Senthilkumar Cinghu, Damien Paulet, Brian Bennett, Pengyi Yang, Benjamin Scruggs, Christopher Lavender, Eric Rivals, Karen Adelman, Raja JothiNature Communications, Nature Publishing Group, 2019, 10 (1), pp.3072.
- New mitochondrial genomes of 39 soil dwelling Coleoptera from metagenome sequencingCarmelo Andujar, Paula Arribas, Michal Motyka, Mathew Bocek, Ladislav Bocak, Benjamin Linard, Alfried VoglerMitochondrial DNA Part B Resources, Taylor & Francis Online, 2019, 4 (2), pp.2447-2450.
- NGPhylogeny.fr: new generation phylogenetic services for non-specialistsFrédéric Lemoine, Damien Correia, Vincent Lefort, Olivia Doppelt-Azeroual, Fabien Mareuil, Sarah Cohen-Boulakia, Olivier GascuelNucleic Acids Research, Oxford University Press, 2019, 47 (W1), pp.W260-W265.
- Distribution and asymptotic behavior of the phylogenetic transfer distanceMiraine Dávila Felipe, Jean-Baka Domelevo Entfellner, Frédéric Lemoine, Jakub Truszkowski, Olivier GascuelJournal of Mathematical Biology, Springer Verlag (Germany), 2019, 79 (2), pp.485-508.
- GECKO is a genetic algorithm to classify and explore high throughput sequencing dataAubin Thomas, Sylvain Barriere, Lucile Broseus, Julie Brooke, Claudio Lorenzi, Jean-Philippe Villemin, Gregory Beurier, Robert Sabatier, Christelle Reynes, Alban Mancheron, William RitchieCommunications Biology, Nature Publishing Group, 2019, 2 (1), pp.1-8.
- A Faster Algorithm for Computing the Kernel of Maximum Agreement SubtreesBiing-Feng Wang, Krister SwensonIEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, In press, pp.1-1.
- Correction: Reconstructible Phylogenetic Networks: Do Not Distinguish the IndistinguishableFabio Pardi, Celine ScornavaccaPLoS Computational Biology, Public Library of Science, 2019, 15 (6), pp.e1007137.
- On the accuracy in high dimensional linear models and its application to genomic selectionCharles-Elie Rabier, Brigitte Mangin, Simona GruseaScandinavian Journal of Statistics, Wiley, 2019, 46 (1), pp.289-313.
- Probing transcription factor combinatorics in different promoter classes and in enhancersJimmy Vandel, Océane Cassan, Sophie Lebre, Charles-Henri Lecellier, Laurent BrehelinBMC Genomics, BioMed Central, 2019, 20 (103). <10.1186/s12864-018-5408-0>
- AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic treesBastien Cazaux, Guillaume Castel, Eric RivalsBioinformatics, Oxford University Press (OUP), 2019, 35 (17), pp.3163-3165.
- Origin, tempo, and mode of the spread of DENV-4 Genotype IIB across the state of São Paulo, Brazil during the 2012-2013 outbreakAyda Susana Ortiz-Baez, Marielton dos Passos Cunha, Danila Vedovello, Tatiana Elias Colombo, Maurício Lacerda Nogueira, Christian Julián Villabona-Arenas, Paolo Marinho de Andrade ZanottoMemórias do Instituto Oswaldo Cruz., Instituto Oswaldo Cruz, Ministério da Saúde, 2019, 114, pp.e180251.
- WAVES: a web application for versatile enhanced bioinformatic servicesMarc Chakiachvili, Sylvain Milanesi, Anne-Muriel Arigon Chifolleau, Vincent LefortBioinformatics, Oxford University Press (OUP), 2019, 35 (11), pp.140-142.
- Machine learning meets genome assemblyKleber Padovani de Souza, João Carlos Setubal, André Carlos Ponce de Leon F. de Carvalho, Guilherme Oliveira, Annie Chateau, Ronnie AlvesBriefings in Bioinformatics, Oxford University Press (OUP), 2019, 20 (6), pp.2116-2129.
- Finding a most parsimonious or likely tree in a network with respect to an alignmentSteven Kelk, Fabio Pardi, Celine Scornavacca, Leo van IerselJournal of Mathematical Biology, Springer Verlag (Germany), 2019, 78 (1-2), pp.527-547.
2018
- Finding local genome rearrangementsKrister Swenson, Pijus SimonaitisAlgorithms for Molecular Biology, BioMed Central, 2018, 13, pp.9-23.
- On Residual Approximation in Solution Extension ProblemsMathias Weller, Annie Chateau, Rodolphe Giroudeau, Jean-Claude König, Valentin PolletJournal of Combinatorial Optimization, Springer Verlag, 2018, 36 (4), pp.1195-1220.
- Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment UncertaintyMaria Chatzou, Evan Floden, Paolo Di Tommaso, Olivier Gascuel, Cedric NotredameSystematic Biology, Oxford University Press (OUP), 2018, 67 (6), pp.997-1009.
- 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 MartinGenome Biology and Evolution, Society for Molecular Biology and Evolution, 2018, 10 (12), pp.3129-3140.
- Complexity and lowers bounds for Power Edge Set ProblemBenoit Darties, Nicolas Champseix, Annie Chateau, Rodolphe Giroudeau, Mathias WellerJournal of Discrete Algorithms, Elsevier, 2018, 52-53, pp.70-91.
- A geography-aware reconciliation method to investigate diversification patterns in host/parasite interactionsVincent Berry, François Chevenet, Jean-Philippe Doyon, Emmanuelle JousselinMolecular Ecology Resources, Wiley/Blackwell, 2018, 18 (5), pp.1173-1184.
- Evolutionary history and spatio-temporal dynamics of dengue virus serotypes in an endemic region of ColombiaCinthy Jiménez-Silva, María Fernanda Carreño, Ayda Susana Ortiz-Baez, Luz Aida Rey, Christian Julián Villabona-Arenas, Raquel OcazionezPLoS ONE, Public Library of Science, 2018, 13 (8), pp.e0203090.
- Relationship between superstring and compression measures: New insights on the greedy conjectureBastien Cazaux, Eric RivalsDiscrete Applied Mathematics, Elsevier, 2018, 245, pp.59-64.
- Scaffolding Problems Revisited: Complexity, Approximation and Fixed Parameter Tractable Algorithms, and Some Special CasesMathias Weller, Annie Chateau, Clément Dallard, Rodolphe GiroudeauAlgorithmica, Springer Verlag, 2018, 80 (6), pp.1771-1803.
- RecPhyloXML: a format for reconciled gene treesWandrille 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 DaubinBioinformatics, Oxford University Press (OUP), 2018, 34 (21), pp.3646-3652.
- Renewing Felsenstein’s phylogenetic bootstrap in the era of big dataFréderic Lemoine, Jean-Baka Domelevo Entfellner, Eduan Wilkinson, Damien Correia, Miraine Dávila Felipe, Tulio de Oliveira, Olivier GascuelNature, Nature Publishing Group, 2018, 556 (7702), pp.452-456.
- Accurate template-based modeling in CASP12 using the IntFOLD4-TS, ModFOLD6, and ReFOLD methodsLiam Mcguffin, Ahmad Shuid, Robert Kempster, Ali H.A. Maghrabi, John Nealon, Bajuna Salehe, Jennifer Atkins, Daniel RocheProteins: Structure, Function, and Genetics, Wiley, 2018, 86, pp.335-344.
- Gearing up to handle the mosaic nature of life in the quest for orthologsKristoffer 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 WaterhouseBioinformatics, Oxford University Press (OUP), 2018, 34 (2), pp.323-329.
- Probing instructions for expression regulation in gene nucleotide compositionsChloé Bessière, May Taha, Florent Petitprez, Jimmy Vandel, Jean-Michel Marin, Laurent Brehelin, Sophie Lèbre, Charles-Henri LecellierPLoS Computational Biology, Public Library of Science, 2018, 14 (1), pp.e1005921.
- Improving pairwise comparison of protein sequences with domain co-occurrenceChristophe Menichelli, Olivier Gascuel, Laurent BrehelinPLoS Computational Biology, Public Library of Science, 2018, 14 (1), pp.e1005889.
- Short Communication: Nucleoside Reverse Transcriptase Inhibitors with Reduced Predicted Activity Do Not Impair Second-Line Therapy with Lopinavir/Ritonavir or Darunavir/RitonavirChristian Julián Villabona-Arenas, Sabrina Eymard-Duvernay, Avelin Aghokeng, Emilande Guichet, Coumba Toure-Kane, Guillaume Bado, Sinata Koulla-Shiro, Eric Delaporte, Laura Ciaffi, Martine PeetersAIDS Research and Human Retroviruses, Mary Ann Liebert, 2018, 34 (6), pp.477-480.
- Computational pan-genomics: status, promises and challengesTobias 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 SchönhuthBriefings in Bioinformatics, Oxford University Press (OUP), 2018, 19 (1), pp.118-135.
- Accounting for Calibration Uncertainty: Bayesian Molecular Dating as a “Doubly Intractable” ProblemStéphane GuindonSystematic Biology, Oxford University Press (OUP), 2018, 67 (4), pp.651-661.
- Measurement and Generation of Diversity and Meaningfulness in Model Driven EngineeringAdel Ferdjoukh, Florian Galinier, Eric Bourreau, Annie Chateau, Clémentine NebutInternational Journal On Advances in Software, IARIA, 2018, 11 (1/2), pp.131-146.
- CompPhy2: a flexible and real time collaborative web platform for editing and comparing phylogeniesFloréal Cabanettes, Jean-François Dufayard, Vincent Berry, Vincent Lefort, Frederic de Lamotte Guéry, Anne-Muriel Arigon ChifolleauBioinformatics, Oxford University Press (OUP), In press, In Press, pp.1-3.
2017
- Functional analysis of Plasmodium falciparum subpopulations associated with artemisinin resistance in CambodiaAnkit 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 CornillotMalaria Journal, BioMed Central, 2017, 16 (1), pp.493.
- HIV-1 Full-Genome Phylogenetics of Generalized Epidemics in Sub-Saharan Africa: Impact of Missing Nucleotide Characters in Next-Generation SequencesOliver 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 FraserAIDS Research and Human Retroviruses, Mary Ann Liebert, 2017, 33 (11), pp.1083-1098.
- Human babesiosis: Indication of a molecular mimicry between thrombospondin domains from a novel Babesia microti BmP53 protein and host platelets moleculesAhmed 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 CornillotPLoS ONE, Public Library of Science, 2017, 12 (10). <10.1371/journal.pone.0185372>
- Epidemiological and ecological determinants of Zika virus transmission in an urban settingJosé 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 ReckereLife, eLife Sciences Publication, 2017, 6, pp.e29820.
- SMS: Smart Model Selection in PhyMLVincent Lefort, Jean-Emmanuel Longueville, Olivier GascuelMolecular Biology and Evolution, Oxford University Press (OUP), 2017, 34 (9), pp.2422-2424.
- Population genomics of picophytoplankton unveils novel chromosome hypervariabilityRomain 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 PiganeauScience Advances , American Association for the Advancement of Science (AAAS), 2017, 3 (7), Non paginé. <10.1126/sciadv.1700239>
- Ribo-seq enlightens codon usage biasDamien Paulet, Alexandre David, Eric RivalsDNA Research, Oxford University Press (OUP), 2017, 24 (3), pp.303-210.
- De novo assembly of viral quasispecies using overlap graphsJasmijn Baaijens, Amal Zine El Aabidine, Eric Rivals, Alexander SchönhuthGenome Research, Cold Spring Harbor Laboratory Press, 2017, 27 (5), pp.835-848.
- Le dixième gène du VIHElodie Cassan, Anne-Muriel Arigon Chifolleau, Jean-Michel Mesnard, Antoine Gros, Olivier Gascuelmédecine/sciences, EDP Sciences, 2017, 33 (5), pp.484-485.
- Phylodynamique des infections viralesSamuel Alizon, Emma SaulnierVirologie, John Libbey Eurotext 2017, 21 (3), pp.119-129.
- The combinatorics of overlapping genesSophie Lèbre, Olivier GascuelJournal of Theoretical Biology, Elsevier, 2017, 415, pp.90-101.
- Accurate self-correction of errors in long reads using de Bruijn graphsLeena Salmela, Riku Walve, Eric Rivals, Esko UkkonenBioinformatics, Oxford University Press (OUP), 2017, 33 (6), pp.799-806.
- On the fixed parameter tractability of agreement-based phylogenetic distancesMagnus Bordewich, Celine Scornavacca, Nihan Tokac, Mathias WellerJournal of Mathematical Biology, Springer Verlag (Germany), 2017, 74 (1-2), pp.239-257.
- The mitochondrial genome of Iberobaenia (Coleoptera: Iberobaeniidae): first rearrangement of protein-coding genes in the beetlesCarmelo Andujar, Paula Arribas, Benjamin Linard, Robin Kundrata, Ladislav Bocak, Alfried VoglerMitochondrial DNA Part A, Taylor and Francis, 2017, 28 (2), pp.156-158.
- Rearrangement Moves on Rooted Phylogenetic NetworksPhilippe Gambette, Leo van Iersel, Mark Jones, Manuel Lafond, Fabio Pardi, Celine ScornavaccaPLoS Computational Biology, Public Library of Science, 2017, 13 (8), pp.e1005611.
- Inferring epidemiological parameters from phylogenies using regression-ABC: a comparative studyEmma Saulnier, Olivier Gascuel, Samuel AlizonPLoS Computational Biology, Public Library of Science, 2017, 13 (3), pp.e1005416.
- The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studiesXavier Argout, Guillaume Martin, Gaetan Droc, Olivier Fouet, Karine Labadie, Eric Rivals, Jean-Marc Aury, Claire LanaudBMC Genomics, BioMed Central, 2017, 18 (1), pp.730-739.
- Resolution and reconciliation of non-binary gene trees with transfers, duplications and lossesEdwin Jacox, Mathias Weller, Eric Tannier, Celine ScornavaccaBioinformatics, Oxford University Press (OUP), 2017, 33 (7), pp.980-987.
2016
- CSAM: Compressed SAM formatRodrigo Cánovas, Alistair Moffat, Andrew TurpinBioinformatics, Oxford University Press (OUP), 2016, 32 (24), pp.3709-3716.
- Read mapping on de Bruijn graphsAntoine Limasset, Bastien Cazaux, Eric Rivals, Pierre PeterlongoBMC Bioinformatics, BioMed Central, 2016, 17 (1). <10.1186/s12859-016-1103-9>
- 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 AfricaEmilande Guichet, Avelin Aghokeng, Laetitia Serrano, Guillaume Bado, Coumba Touré-Kane, Sabrina Eymard-Duvernay, Christian Julián Villabona-Arenas, Eric Delaporte, Laura Ciaffi, Martine PeetersAIDS Research and Human Retroviruses, Mary Ann Liebert, 2016, 32 (12), pp.1159-1162.
- Models and algorithms for genome rearrangement with positional constraintsKrister Swenson, Pijus Simonaitis, Mathieu BlanchetteAlgorithms for Molecular Biology, BioMed Central, 2016, 11 (1), pp.13-24.
- The power of greedy algorithms for approximating Max-ATSP, Cyclic Cover, and superstringsBastien Cazaux, Eric RivalsDiscrete Applied Mathematics, Elsevier, 2016, 212, pp.48-60.
- Concomitant emergence of the antisense protein gene of HIV-1 and of the pandemicElodie Cassan, Anne-Muriel Arigon Chifolleau, Jean-Michel Mesnard, Antoine Gross, Olivier GascuelProceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2016, 113 (41), pp.11537-11542.
- Demographic inference under the coalescent in a spatial continuumStéphane Guindon, Hongbin Guo, David WelchTheoretical Population Biology, Elsevier, 2016, 111, pp.43-50.
- A linear time algorithm for Shortest Cyclic Cover of StringsBastien Cazaux, Eric RivalsJournal of Discrete Algorithms, Elsevier, 2016, 37, pp.56-67.
- Phylodynamics of the major HIV-1 CRF02_AG African lineages and its global disseminationDaiana Mir, Matthieu Jung, Edson Delatorre, Nicole Vidal, Martine Peeters, Gonzalo BelloInfection, Genetics and Evolution, Elsevier, 2016, 46, pp.190-199.
- A ‘Stochastic Safety Radius’ for Distance-Based Tree ReconstructionOlivier Gascuel, Mike SteelAlgorithmica, Springer Verlag, 2016, 74 (4), pp.1386-1403.
- Parameterized certificate dispersal and its variantsValentin Garnero, Mathias WellerTheoretical Computer Science, Elsevier, 2016, 622, pp.66-78.
- TRM6/61 connects PKCα with translational control through tRNAiMet stabilization: impact on tumorigenesisFrançoise 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 JoubertOncogene, Nature Publishing Group, 2016, 35 (14), pp.1785-1796.
- SylvX: a viewer for phylogenetic tree reconciliationsFrançois Chevenet, Jean-Philippe Doyon, Celine Scornavacca, Edwin Jacox, Emmanuelle Jousselin, Vincent BerryBioinformatics, Oxford University Press (OUP), 2016, 32 (4), pp.608-610.
- Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS readsYvan 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 PeterlongoGigaScience, BioMed Central, 2016, 5 (1). <10.1186/s13742-015-0105-2>
- Aligning the unalignable: bacteriophage whole genome alignmentsSèverine Bérard, Annie Chateau, Nicolas Pompidor, Paul Guertin, Anne Bergeron, Krister SwensonBMC Bioinformatics, BioMed Central, 2016, 17 (1), pp.30-43.
- Fast Dating Using Least-Squares Criteria and AlgorithmsThu-Hien To, Matthieu Jung, Samantha Lycett, Olivier GascuelSystematic Biology, Oxford University Press (OUP), 2016, 65 (1), pp.82-97.
- Do branch lengths help to locate a tree in a phylogenetic network?Philippe Gambette, Leo van Iersel, Steven Kelk, Fabio Pardi, Celine ScornavaccaBulletin of Mathematical Biology, Springer Verlag, 2016, 78 (9), pp.1773-1795.
- Inferring gene duplications, transfers and losses can be done in a discrete frameworkVincent Ranwez, Celine Scornavacca, Jean-Philippe Doyon, Vincent BerryJournal of Mathematical Biology, Springer Verlag (Germany), 2016, 72 (7), pp.1811-1844.
- 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 SentenacFrontiers in Plant Science, Frontiers, 2016, 7, pp.794.
- Phylogenetic incongruence through the lens of Monadic Second Order logicSteven Kelk, Leo van Iersel, Celine Scornavacca, Mathias WellerJournal of Graph Algorithms and Applications, Brown University, 2016, 20 (2), pp.189-215.
- Standardized benchmarking in the quest for orthologsAdrian 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 DessimozNature Methods, Nature Publishing Group, 2016, 13 (5), pp.425-430.
- Fast and accurate branch lengths estimation for phylogenomic treesManuel Binet, Olivier Gascuel, Celine Scornavacca, Emmanuel Douzery, Fabio PardiBMC Bioinformatics, BioMed Central, 2016, 17 (23). <10.1186/s12859-015-0821-8>
- In-depth analysis of HIV-1 drug resistance mutations in HIV-infected individuals failing first-line regimens in West and Central AfricaChristian Julián Villabona-Arenas, N. Vidal, E. Guichet, L. Serrano, E. Delaporte, Olivier Gascuel, M. PeetersAIDS, Lippincott, Williams & Wilkins, 2016, 30 (17), pp.2577-2589.
- Uncovering Trophic Interactions in Arthropod Predators through DNA Shotgun-Sequencing of Gut ContentsDébora Paula, Benjamin Linard, Alex Crampton-Platt, Amrita Srivathsan, Martijn Timmermans, Edison Sujii, Carmen Pires, Lucas Souza, David Andow, Alfried VoglerPLoS ONE, Public Library of Science, 2016, 11 (9), pp.e0161841.
2015
- Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction MethodsDaniel Roche, Danielle Allison Brackenridge, Liam James McguffinInternational Journal of Molecular Sciences, MDPI, 2015, 16 (12), pp.29829-29842.
- Molecular Evolution of the TET Gene Family in MammalsHiromichi Akahori, Stéphane Guindon, Sumio Yoshizaki, Yoshinori MutoInternational Journal of Molecular Sciences, MDPI, 2015, 16 (12), pp.28472-28485.
- Closed form modeling of evolutionary rates by exponential Brownian functionalsNicolas Privault, Stéphane GuindonJournal of Mathematical Biology, Springer Verlag (Germany), 2015, 71 (6), pp.1387-1409.
- Interval scheduling and colorful independent setsRené van Bevern, Matthias Mnich, Rolf Niedermeier, Mathias WellerJournal of Scheduling, Springer Verlag, 2015, 18 (5), pp.449-469.
- A complexity and approximation framework for the maximization scaffolding problemAnnie Chateau, Rodolphe GiroudeauTheoretical Computer Science, Elsevier, 2015, 595, pp.92-106.
- IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequencesLiam J. Mcguffin, Jennifer D. Atkins, Bajuna R. Salehe, Ahmad N. Shuid, Daniel RocheNucleic Acids Research, Oxford University Press, 2015, 43 (W1), pp.W169-W173.
- FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference ProgramVincent Lefort, Richard Desper, Olivier GascuelMolecular Biology and Evolution, Oxford University Press (OUP), 2015, 32 (10), pp.2798-2800.
- TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstructionJia-Ming Chang, Paolo Di tommaso, Vincent Lefort, Olivier Gascuel, Cedric NotredameNucleic Acids Research, Oxford University Press, 2015, 43 (W1), pp.W3-W6.
- YOC, A new strategy for pairwise alignment of collinear genomesRaluca Uricaru, Célia Michotey, Hélène Chiapello, Eric RivalsBMC Bioinformatics, BioMed Central, 2015, 16 (1), pp.16:111.
- The ancient Yakuts: a population genetic enigmaChristine Keyser, Clemence Hollard, Angela Gonzalez, Jean-Luc Fausser, Eric Rivals, Anatoly Nikolayevich Alexeev, Alexandre Riberon, Eric Crubezy, Bertrand LudesPhilosophical 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.
- Mathematical and Computational Evolutionary Biology (2013)Olivier Gascuel, Tanja StadlerSystematic Biology, Oxford University Press (OUP), 2015, 64 (1), pp.1-2.
- Metagenome Skimming of Insect Specimen Pools: Potential for Comparative GenomicsBenjamin Linard, Alex Crampton-Platt, Conrad Gillett, Martijn Timmermans, Alfried VoglerGenome Biology and Evolution, Society for Molecular Biology and Evolution, 2015, 7 (6), pp.1474-1489.
- A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UKRaphaël Mourad, François Chevennet, David T. Dunn, Esther Fearnhill, Valerie Delpech, David Asboe, Olivier Gascuel, Stéphane HueAIDS, Lippincott, Williams & Wilkins, 2015, 29 (15), pp.1917-1925.
- An assessment of the amount of untapped fold level novelty in under-sampled areas of the tree of lifeDaniel Roche, Thomas BrülsScientific Reports, Nature Publishing Group, 2015, 5, pp.14717.
- Polynomial-Time Data Reduction for the Subset Interconnection Design ProblemJiehua Chen, Christian Komusiewicz, Rolf Niedermeier, Manuel Sorge, Mathias WellerSIAM Journal on Discrete Mathematics, Society for Industrial and Applied Mathematics, 2015, 29 (1), pp.1-25.
- 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. DrummondProceedings of the Royal Society B: Biological Sciences, Royal Society, The, 2015, 282 (1806), pp.20150420.
- Ancestral gene synteny reconstruction improves extant species scaffoldingYoann Anselmetti, Vincent Berry, Cedric Chauve, Annie Chateau, Eric Tannier, Sèverine BérardBMC Genomics, BioMed Central, 2015, 16 (Suppl 10), pp.S11.
- Exact approaches for scaffoldingMathias Weller, Annie Chateau, Rodolphe GiroudeauBMC Bioinformatics, BioMed Central, 2015, 16 (Suppl 14), pp.S2.
2014
- LoRDEC: accurate and efficient long read error correctionLeena Salmela, Eric RivalsBioinformatics, Oxford University Press (OUP), 2014, 30 (24), pp.3506-3514.
- Reverse engineering of compact suffix trees and links: A novel algorithmBastien Cazaux, Eric RivalsJournal of Discrete Algorithms, Elsevier, 2014, StringMasters 2012 & 2013 Special Issue (Volume 1), 28, pp.9-22.
- Multiple nuclear genes stabilize the phylogenetic backbone of the genus QuercusFrançois Hubert, Guido W. Grimm, Emmanuelle Jousselin, Vincent Berry, Alain Franc, Antoine KremerSystematics and Biodiversity, Taylor & Francis: STM, Behavioural Science and Public Health Titles, 2014, 12 (4), pp.405-423.
- Identification of divergent protein domains by combining HMM-HMM comparisons and co-occurrence detectionAmel Ghouila, Isabelle Florent, Fatma Zahra Guerfali, Nicolas Terrapon, Dhafer Laouini, Sadok Ben Yahia, Olivier Gascuel, Laurent BrehelinPLoS ONE, Public Library of Science, 2014, 9 (6), pp.e95275.
- Deep Conservation of Human Protein Tandem Repeats within the EukaryotesElke Schaper, Olivier Gascuel, Maria AnisimovaMolecular Biology and Evolution, Oxford University Press (OUP), 2014, 31 (5), pp.1132-1148.
- CompPhy: a web-based collaborative platform for comparing phylogeniesNicolas Fiorini, Vincent Lefort, François Chevenet, Vincent Berry, Anne-Muriel Arigon ChifolleauBMC Evolutionary Biology, BioMed Central, 2014, 14 (1), pp.253-255.
- Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genomeNicolas Philippe, Elias Bou Samra, Anthony Boureux, Alban Mancheron, Florence Rufflé, Qiang Bai, John de Vos, Eric Rivals, Thérèse CommesNucleic Acids Research, Oxford University Press, 2014, 42 (5), pp.2820-2832.
- Predicting the Ancestral Character Changes in a Tree is Typically Easier than Predicting the Root StateOlivier Gascuel, Mike SteelSystematic Biology, Oxford University Press (OUP), 2014, 63 (3), pp.421-435.
- FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data setsCuong Cao Dang, Vinh Sy Le, Olivier Gascuel, Bart Hazes, Quang Si LeBMC Bioinformatics, BioMed Central, 2014, 15 (1), pp.341-343.
- Modelling Competition and Dispersal in a Statistical Phylogeographic FrameworkLouis Ranjard, David Welch, Marie Paturel, Stéphane GuindonSystematic Biology, Oxford University Press (OUP), 2014, 63 (5), pp.743-752.
- Diversity of Prdm9 Zinc Finger Array in Wild Mice Unravels New Facets of the Evolutionary Turnover of this Coding MinisatelliteJérôme Buard, Eric Rivals, Denis Dunoyer de Segonzac, Charlotte Garres, Pierre Caminade, Bernard de Massy, Pierre BoursotPLoS ONE, Public Library of Science, 2014, 9 (1), pp.e85021.
- An improved genome of the model marine alga [i]Ostreococcus tauri[/i] unfolds by assessing Illumina [i]de novo[/i] assembliesRomain 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 PiganeauBMC Genomics, BioMed Central, 2014, 15, pp.1-11.
International Communications
2020
- Efficient Construction of Hierarchical Overlap GraphsSung Park, Bastien Cazaux, Kunsoo Park, Eric Rivals27th International Symposium on String Processing and Information Retrieval (SPIRE), Oct 2020, Orlando, FL, United States. pp.277-290.
- Linearizing Genomes: Exact Methods and Local SearchTom Davot, Annie Chateau, Rodolphe Giroudeau, Mathias WellerSOFSEM, Jan 2020, Limassol, Cyprus. pp.505-518.
- Scanning Phylogenetic Networks is NP-hardVincent Berry, Celine Scornavacca, Mathias WellerSOFSEM, Jan 2020, Limassol, Cyprus. pp.519-530.
2019
- Rapidly computing the phylogenetic transfer indexJakub Truszkowski, Olivier Gascuel, Krister Swenson19th International Workshop on Algorithms in Bioinformatics (WABI), Sep 2019, Niagara Falls, NY, United States. pp.20:1--20:12.
- Weighted minimum-length rearrangement scenariosPijus Simonaitis, Annie Chateau, Krister Swenson19th International Workshop on Algorithms in Bioinformatics (WABI), Sep 2019, Niagara Falls, NY, United States. pp.13:1-13:17.
- Power Edge Set and Zero Forcing Set Remain Difficult in Cubic GraphsPierre Cazals, Benoit Darties, Annie Chateau, Rodolphe Giroudeau, Mathias Weller30th International Workshop on Combinatorial Algorithms (IWOCA), Jul 2019, Pisa, Italy. pp.122-135.
- Perspectives and challenges of Computational Pan-GenomicsEric RivalsLifeTime UnConference, Centre de Regulació Genòmica (CRG); centro nacional de análisis genómico (CNAG), Jul 2019, Barelone, Spain. <https://lifetime-fetflagship.eu/lifetime-unconference/>
- Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length EncodingBastien Cazaux, Eric Rivals30th Annual Symposium on Combinatorial Pattern Matching (CPM), University of Pisa, Jun 2019, Pise, Italy. pp.24:1--24:20.
- New Polynomial-Time Algorithm around the Scaffolding ProblemTom Davot, Annie Chateau, Rodolphe Giroudeau, Mathias WellerAlCoB: Algorithms for Computational Biology, May 2019, Berkeley, United States. pp.25-38.
- High performance text indexing and applications in life sciencesEric RivalsUK-France Bilateral International Meeting on High Performance Computing and Biomathematics, Feb 2019, Chicheley, United Kingdom. <https://royalsociety.org/>
2018
- Fast and accurate genome-scale identification of DNA-binding sitesDavid Martin, Vincent Maillol, Eric RivalsBIBM: Bioinformatics and Biomedicine, Dec 2018, Madrid, Spain. pp.201-205.
- On the hardness of approximating Linearization of Scaffolds sharing Repeated ContigsTom Davot, Annie Chateau, Rodolphe Giroudeau, Mathias WellerRECOMB-CG: Comparative Genomics, Oct 2018, Magog-Orford, QC, Canada. pp.91-107.
- A General Framework for Genome Rearrangement with Biological ConstraintsPijus Simonaitis, Annie Chateau, Krister SwensonRECOMB-CG: Comparative Genomics, Oct 2018, Magog-Orford, QC, Canada. pp.49-71.
- New Results About the Linearization of Scaffolds Sharing Repeated ContigsDorine Tabary, Tom Davot, Mathias Weller, Annie Chateau, Rodolphe GiroudeauCOCOA: Conference on Combinatorial Optimization and Applications, Sep 2018, Atlanta, GA, United States. pp.94-107.
- Superstrings with multiplicitiesEric Rivals, Bastien Cazaux29th Annual Symposium on Combinatorial Pattern Matching (CPM), Qingdao University, Jul 2018, Qingdao, China. pp.21:1-21:16.
- Practical lower and upper bounds for the Shortest Linear SuperstringBastien Cazaux, Samuel Juhel, Eric RivalsSEA: Symposium on Experimental Algorithms, Jun 2018, L'Aquilla, Italy. pp.18:1--18:14.
- Rapid alignment-free phylogenec placement via ancestral k-mersBenjamin Linard, Krister Swenson, Fabio PardiMCEB: Mathematical and Computational Evolutionary Biology, Jun 2018, St Martin de Londres, France. <http://www.lirmm.fr/mceb2018/>
- Données génomiques massives : applications, enjeux computationnels et perspectivesEric RivalsOpen Science, Open Access, Open Data et données, Jun 2018, Strasbourg, France. <http://www.misha.fr>
2017
- On the Linearization of Scaffolds Sharing Repeated ContigsMathias Weller, Annie Chateau, Rodolphe GiroudeauCOCOA: Conference on Combinatorial Optimization and Applications, Dec 2017, Shanghai, China. pp.509-517.
- New Insights for Power Edge Set ProblemBenoit Darties, Annie Chateau, Rodolphe Giroudeau, Mathias WellerCOCOA: Conference on Combinatorial Optimization and Applications, Dec 2017, Shanghai, China. pp.180-194.
- Measuring Differences To Compare Sets Of Models And Improve Diversity In MDEAdel Ferdjoukh, Florian Galinier, Eric Bourreau, Annie Chateau, Clémentine NebutICSEA: International Conference on Software Engineering Advances, Oct 2017, Athenes, Greece. <https://www.iaria.org/conferences2017/CfPICSEA17.html>
- Rearrangement Scenarios Guided by Chromatin StructureSylvain Pulicani, Pijus Simonaitis, Eric Rivals, Krister SwensonRECOMB-CG: Comparative Genomics, Oct 2017, Barcelona, Spain. pp.141-155.
- LZ78 Compression in Low Main Memory SpaceDiego Arroyuelo, Rodrigo Cánovas, Gonzalo Navarro, Rajeev RamanSPIRE: String Processing and Information Retrieval, Sep 2017, Palermo, Italy. pp.38-50.
- Finding Local Genome RearrangementsPijus Simonaitis, Krister Swenson17th International Workshop on Algorithms in Bioinformatics (WABI 2017), Aug 2017, Boston, United States. pp.24:1--24:13.
- Improved Complexity for Power Edge Set ProblemBenoit Darties, Annie Chateau, Rodolphe Giroudeau, Mathias WellerIWOCA: International Workshop on Combinatorial Algorithms, Jul 2017, Newcastle, Australia. pp.128-141.
- Full Compressed Affix Tree RepresentationsRodrigo Cánovas, Eric RivalsDCC: Data Compression Conference, IEEE, Apr 2017, Snowbird, UT, United States. pp.102-111.
2016
- On Residual Approximation in Solution Extension ProblemsMathias Weller, Annie Chateau, Rodolphe Giroudeau, Jean-Claude König, Valentin PolletCOCOA: Conference on Combinatorial Optimization and Applications, Dec 2016, Hong Kong, China. pp.463-476.
- Instance Guaranteed Ratio on Greedy Heuristic for Genome ScaffoldingClément Dallard, Mathias Weller, Annie Chateau, Rodolphe GiroudeauCOCOA: Conference on Combinatorial Optimization and Applications, Dec 2016, Hong Kong, China. pp.294-308.
- Hybrid and non hybrid error correction for long reads: LoRDEC and LoRMAEric RivalsColib’read workshop, ANR Colib'read, Nov 2016, Paris, France. <http://gdr-bim.cnrs.fr/colibread/>
- Genetic Algorithm to Improve Diversity in MDEFlorian Galinier, Eric Bourreau, Annie Chateau, Adel Ferdjoukh, Clémentine NebutMETA: Metaheuristics and Nature Inspired Computing, Oct 2016, Marrakech, Morocco. <https://meta2016.sciencesconf.org/>
- A Graph Constraints Formulation for Contigs ScaffoldingEric Bourreau, Annie Chateau, Clément Dallard, Rodolphe GiroudeauWCB: Workshop on Constraint-Based Methods for Bioinformatics, Sep 2016, Toulouse, France. pp.136-149.
- Superstring Graph: A New Approach for Genome AssemblyBastien Cazaux, Gustavo Sacomoto, Eric RivalsAAIM: Algorithmic Aspects in Information and Management, Università degli Studi di Bergamo, Jul 2016, Bergamo, Italy. pp.39-52.
- A new tool for non-hybrid correction of long noisy readsEric RivalsNGS Symposium, Thomas Sexton, Jul 2016, Illkirch, France. <https://ngssymposium.sciencesconf.org/>
- A Model-Driven Approach to Generate Relevant and Realistic DatasetsAdel Ferdjoukh, Eric Bourreau, Annie Chateau, Clémentine NebutSEKE: Software Engineering and Knowledge Engineering, Jul 2016, Redwood City, San Francisco Bay, United States. pp.105-109.
- Fast Dating using Least SquaresOlivier GascuelMathematical Models for Epidemiology and Phylogenetics, May 2016, Lille, France. <http://math.univ-lille1.fr/~tran/journees_epidemio2016.html>
- Phylogeny-reconstruction methodsOlivier GascuelCoME: Course on Computational Molecular Evolution, May 2016, Heraklion, Greece. <http://events.embo.org/16-computational-evolution/>
- Shortest DNA cyclic cover in compressed spaceBastien Cazaux, Rodrigo Cánovas, Eric RivalsDCC: Data Compression Conference, Mar 2016, Snowbird, UT, United States. pp.536-545.
2015
- On the Complexity of Scaffolding Problems: From Cliques to Sparse GraphsMathias Weller, Annie Chateau, Rodolphe GiroudeauCOCOA: Conference on Combinatorial Optimization and Applications, Dec 2015, Houston, United States. pp.409-423.
- Méthodes bioinformatiques pour la prédiction de la fonction des gènes : identification des domaines protéiques dans les génomes de pathogènesLaurent BrehelinJFMPM: 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>
- LoRDEC: a tool for correcting errors in long sequencing readsEric RivalsGCB: German Conference on Bioinformatics, University Alliance Ruhr, Sep 2015, Dortmund, Germany. <http://gcb2015.cs.tu-dortmund.de>
- Fast dating using least squaresOlivier GascuelSMBE: Society for Molecular Biology and Evolution, Jul 2015, Vienna, Austria. <http://smbe2015.at>
- Fast and accurate branch lengths estimation for phylogenomic treesManuel Binet, Olivier Gascuel, Celine Scornavacca, Emmanuel Douzery, Fabio PardiEvolution, Jun 2015, Guarujà, Brazil. <http://evolution2015.org/>
- Reconstructible phylogenetic networks: do not distinguish the indistinguishableFabio Pardi, Celine ScornavaccaEvolution, Jun 2015, Guarujà, Brazil. <http://evolution2015.org/>
- Distance-based methods in phylogenomicsFabio Pardi, Manuel BinetFILOFOCS: French-Israeli Workshop on Foundations of Computer Science, May 2015, Tel Aviv, Israel. <http://hyde.eng.tau.ac.il/FILOFOCS-2015/>
- Correction of long sequencing reads: a novel approachEric Rivalsat " 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>
- Phylogeny Reconstruction MethodsOlivier GascuelCoME: Course on Molecular Evolution, Apr 2015, Hinxton, United Kingdom. <http://abacus.gene.ucl.ac.uk/CoME/>
- Construction of a de Bruijn Graph for Assembly from a Truncated Suffix TreeBastien Cazaux, Thierry Lecroq, Eric RivalsLATA: Language and Automata Theory and Applications, Mar 2015, Nice, France. pp.109-120.
- Instantiation of meta-models constrained with OCL: A CSP approachAdel Ferdjoukh, Anne-Elisabeth Baert, Eric Bourreau, Annie Chateau, Remi Coletta, Clémentine NebutMODELSWARD: Model-Driven Engineering and Software Development, Feb 2015, Angers, France. pp.213-222.
2014
- Models and Algorithms in PhylogeneticsOlivier GascuelMolecular Phylogenies Courses, Dec 2014, Hanoi, Vietnam.
- Approximation of Greedy Algorithms for Max-ATSP, Maximal Compression, Maximal Cycle Cover, and Shortest Cyclic Cover of StringsBastien Cazaux, Eric RivalsPSC: Prague Stringology Conference, Czech Technical University in Prague, Sep 2014, Prague, Czech Republic. pp.148-161.
- Complexity and Polynomial-Time Approximation Algorithms around the Scaffolding ProblemAnnie Chateau, Rodolphe GiroudeauAlCoB: Algorithms for Computational Biology, Jul 2014, Tarragona, Spain. pp.47-58.
- From Indexing Data Structures to de Bruijn GraphsBastien Cazaux, Thierry Lecroq, Eric RivalsCPM: Combinatorial Pattern Matching, Moscow State University, Jun 2014, Moscow, Russia. pp.89-99.
- Identifiability of phylogenetic networksFabio Pardi, Celine ScornavaccaMCEB: Mathematical and Computational Evolutionary Biology, Jun 2014, Hameau de l'Etoile, St Martin de Londres, France. <http://www.lirmm.fr/mceb2014/program.php>
- Phylogenetic reconstruction: models, methods, and algorithmsOlivier GascuelBioinformatics in the Tropics Brazil, May 2014, Salvador, Brazil. <http://www.bioafrica.net/manuscripts/2ndInternationalWorkshopBrazil2014A4.pdf>
- Phylogeny Reconstruction MethodsOlivier GascuelCoME: Course on Computational Molecular Evolution, May 2014, Heraklion, Greece. <http://events.embo.org/14-computational-evolution/>
- Phylogenetic networks: what can we reconstruct?Fabio PardiFILOFOCS: French-Israeli Workshop on Foundations of Computer Science, May 2014, Paris, France. <http://www.liafa.univ-paris-diderot.fr/~adiro/filofocs/filofocs2014/index.html>
- Reconstructible phylogenetic networks: no need to distinguish the indistinguishableFabio Pardi, Celine ScornavaccaWaiheke, Feb 2014, Waiheke, New Zealand. <http://www.math.canterbury.ac.nz/bio/events/waiheke2014/>
Last update on 14/11/2019
Department : Informatique
Head : Laurent BREHELIN
Initiative
MAB est à l'origine de la création de l'Institut de Biologie Computationnelle (IBC).
IBC est un hôtel à projets pluridisciplinaires avec un large domaine d'intervention qui s’étend de l'algorithmique et la modélisation mathématique, à la génomique, au cancer ou à l'épidémiologie. C'est un lieu de rencontre privilégié pour les chercheurs de bioinformatique, au niveaux régional, national et international.