Number of documents

123

Eric Rivals


CNRS Research Director & Head of GDR Bioinformatique Moléculaire
LIRMM - UMR 5506 CNRS & Université de Montpellier

http://www.lirmm.fr/~rivals/

Education

2005    Habilitation, University of Montpellier 2
    Algorithms for sequence analysis in bioinformatics. Periodicity and repeats.

1996-1999    Postdoctoral fellow at the Deutsches Krebsforschung Zentrum (Heidelberg)
    by Dr. Martin Vingron, group Theoretical BioInformatik
    Fast algorithms for similarity search, Development of a gene index

1993-1996    PhD in Computer Science, University of Lille I
    LIFL (Fundamental Computer Science Laboratory of Lille)       

 


Journal articles52 documents

  • Bastien Cazaux, Guillaume Castel, Eric Rivals. AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees. Bioinformatics, Oxford University Press (OUP), In press, ⟨10.1093/bioinformatics/btz011⟩. ⟨lirmm-01980994⟩
  • Bastien Cazaux, Thierry Lecroq, Eric Rivals. Linking indexing data structures to de Bruijn graphs: Construction and update. Journal of Computer and System Sciences, Elsevier, 2019, 104, pp.165-183. ⟨10.1016/j.jcss.2016.06.008⟩. ⟨lirmm-01617207⟩
  • Tobias Marschall, Manja Marz, Thomas Abeel, Louis Dijkstra, Bas E. Dutilh, et al.. Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics, Oxford University Press (OUP), 2018, 19 (1), pp.118-135. ⟨10.1093/bib/bbw089⟩. ⟨hal-01390478⟩
  • Bastien Cazaux, Eric Rivals. Relationship between superstring and compression measures: New insights on the greedy conjecture. Discrete Applied Mathematics, Elsevier, 2018, 245, pp.59-64. ⟨10.1016/j.dam.2017.04.017⟩. ⟨lirmm-01800340⟩
  • Leena Salmela, Riku Walve, Eric Rivals, Esko Ukkonen. Accurate self-correction of errors in long reads using de Bruijn graphs. Bioinformatics, Oxford University Press (OUP), 2017, 33 (6), pp.799-806. ⟨10.1093/bioinformatics/btw321⟩. ⟨lirmm-01385006⟩
  • Xavier Argout, Guillaume Martin, Gaetan Droc, Olivier Fouet, Karine Labadie, et al.. The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies. BMC Genomics, BioMed Central, 2017, 18 (1), pp.730-739. ⟨10.1186/s12864-017-4120-9⟩. ⟨lirmm-01612258⟩
  • Romain Blanc-Mathieu, Marc Krasovec, Maxime Hebrard, Sheree Yau, Elodie Desgranges, et al.. Population genomics of picophytoplankton unveils novel chromosome hypervariability. Science Advances , American Association for the Advancement of Science (AAAS), 2017, 3 (7), ⟨10.1126/sciadv.1700239⟩. ⟨lirmm-01842137⟩
  • Jasmijn Baaijens, Amal Zine El Aabidine, Eric Rivals, Alexander Schönhuth. De novo assembly of viral quasispecies using overlap graphs. Genome Research, Cold Spring Harbor Laboratory Press, 2017, 27 (5), pp.835-848. ⟨10.1101/gr.215038.116⟩. ⟨lirmm-01693168⟩
  • Damien Paulet, Alexandre David, Eric Rivals. Ribo-seq enlightens codon usage bias. DNA Research, Oxford University Press (OUP), 2017, 24 (3), pp.303-210. ⟨10.1093/dnares/dsw062⟩. ⟨lirmm-01610054⟩
  • Ankit Dwivedi, Christelle Reynes, Axel Kuehn, Daniel Roche, Nimol Khim, et al.. Functional analysis of Plasmodium falciparum subpopulations associated with artemisinin resistance in Cambodia. Malaria Journal, BioMed Central, 2017, 16 (1), pp.493. ⟨10.1186/s12936-017-2140-1⟩. ⟨inserm-01672315⟩
  • Bastien Cazaux, Eric Rivals. A linear time algorithm for Shortest Cyclic Cover of Strings. Journal of Discrete Algorithms, Elsevier, 2016, 37, pp.56-67. ⟨10.1016/j.jda.2016.05.001⟩. ⟨lirmm-01525995⟩
  • Antoine Limasset, Bastien Cazaux, Eric Rivals, Pierre Peterlongo. Read mapping on de Bruijn graphs. BMC Bioinformatics, BioMed Central, 2016, 17 (1), ⟨10.1186/s12859-016-1103-9⟩. ⟨hal-01349636⟩
  • Bastien Cazaux, Eric Rivals. The power of greedy algorithms for approximating Max-ATSP, Cyclic Cover, and superstrings. Discrete Applied Mathematics, Elsevier, 2016, 212, pp.48-60. ⟨10.1016/j.dam.2015.06.003⟩. ⟨lirmm-01286943⟩
  • Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Eric Rivals, et al.. Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads. GigaScience, BioMed Central, 2016, 5 (1), ⟨10.1186/s13742-015-0105-2⟩. ⟨hal-01280238⟩
  • Christine Keyser, Clemence Hollard, Angela Gonzalez, Jean-Luc Fausser, Eric Rivals, et al.. The ancient Yakuts: a population genetic enigma. 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. ⟨10.1098/rstb.2013.0385⟩. ⟨lirmm-01170676⟩
  • Raluca Uricaru, Célia Michotey, Hélène Chiapello, Eric Rivals. YOC, A new strategy for pairwise alignment of collinear genomes. BMC Bioinformatics, BioMed Central, 2015, 16, pp.16:111. ⟨10.1186/s12859-015-0530-3⟩. ⟨lirmm-01170968⟩
  • Leena Salmela, Eric Rivals. LoRDEC: accurate and efficient long read error correction. Bioinformatics, Oxford University Press (OUP), 2014, 30 (24), pp.3506-3514. ⟨10.1093/bioinformatics/btu538⟩. ⟨lirmm-01100451⟩
  • Romain Blanc Mathieu, Bram Verhelst, Evelyne Derelle, Stephane Rombauts, Francois-Yves Bouget, et al.. An improved genome of the model marine alga [i]Ostreococcus tauri[/i] unfolds by assessing Illumina [i]de novo[/i] assemblies. BMC Genomics, BioMed Central, 2014, 15, pp.1-11. ⟨10.1186/1471-2164-15-1103⟩. ⟨hal-01130514⟩
  • Bastien Cazaux, Eric Rivals. Reverse engineering of compact suffix trees and links: A novel algorithm. Journal of Discrete Algorithms, Elsevier, 2014, StringMasters 2012 & 2013 Special Issue (Volume 1), 28, pp.9-22. ⟨10.1016/j.jda.2014.07.002⟩. ⟨lirmm-01082098⟩
  • Nicolas Philippe, Elias Bou Samra, Anthony Boureux, Alban Mancheron, Florence Rufflé, et al.. Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome. Nucleic Acids Research, Oxford University Press, 2014, 42 (5), pp.2820-2832. ⟨10.1093/nar/gkt1300⟩. ⟨lirmm-01233107⟩
  • Jérôme Buard, Eric Rivals, Denis Dunoyer de Segonzac, Charlotte Garres, Pierre Caminade, et al.. Diversity of Prdm9 Zinc Finger Array in Wild Mice Unravels New Facets of the Evolutionary Turnover of this Coding Minisatellite. PLoS ONE, Public Library of Science, 2014, 9 (1), pp.e85021. ⟨10.1371/journal.pone.0085021⟩. ⟨hal-00937288⟩
  • Nicolas Philippe, Mikaël Salson, Thérèse Commes, Eric Rivals. CRAC: an integrated approach to the analysis of RNA-seq reads. Genome Biology, BioMed Central, 2013, 14 (3), pp.R30. ⟨10.1186/gb-2013-14-3-r30⟩. ⟨inserm-00850972⟩
  • Eric Rivals, Nicolas Philippe, Mikael Salson, Martine Léonard, Thérèse Commes, et al.. A Scalable Indexing Solution to Mine Huge Genomic Sequence Collections. ERCIM News, ERCIM, 2012, 2012 (89), pp.20-21. ⟨http://ercim-news.ercim.eu/en89/special/a-scalable-indexing-solution-to-mine-huge-genomic-sequence-collections⟩. ⟨lirmm-00712653⟩
  • Zhaojun Shao, Eric Rivals, Na Zhao, Sovan Lek, Jianbo Chang, et al.. Evolutionary Process of a Tetranucleotide Microsatellite Locus in Acipenseriformes. Journal of Genetics, Indian Academy of Sciences, 2011, 90 (2), pp.217-227. ⟨10.1007/s12041-011-0055-0⟩. ⟨lirmm-00618055⟩
  • Nicolas Philippe, Mikael Salson, Thérèse Commes, Eric Rivals. A combinatorial and integrated method to analyse RNA-seq reads. EMBnet.journal, EMBnet, 2011, 17 (Supplement B), pp.1. ⟨http://journal.embnet.org/index.php/embnetjournal/article/view/290⟩. ⟨lirmm-00757979⟩
  • Nicolas Philippe, Florence Ruffle, Elias Bou Samra, Anthony Boureux, Thérèse Commes, et al.. Digital gene expression data, cross-species conservation and noncoding RNA. EMBnet.journal, EMBnet, 2011, 17 (Supplement B), pp.1. ⟨http://journal.embnet.org/index.php/embnetjournal/article/view/288⟩. ⟨lirmm-00757989⟩
  • Nicolas Philippe, Mikael Salson, Thierry Lecroq, Martine Léonard, Thérèse Commes, et al.. Read indexing. EMBnet.journal, EMBnet, 2011, 17 (Supplement B), pp.1. ⟨http://journal.embnet.org/index.php/embnetjournal/article/view/289⟩. ⟨lirmm-00757983⟩
  • Christelle Cayrou, Philippe Coulombe, Alice Vigneron, Slavica Stanojcic, Olivier Ganier, et al.. Genome-Scale Analysis of Metazoan Replication Origins Reveals their Organization in Specific but Flexible Sites Defined by Conserved Features. Genome Research, Cold Spring Harbor Laboratory Press, 2011, 21 (9), pp.1438-1449. ⟨10.1101/gr.121830.111⟩. ⟨lirmm-00631491⟩
  • Nicolas Philippe, Mikael Salson, Thierry Lecroq, Martine Léonard, Thérèse Commes, et al.. Querying Large Read Collections in Main Memory: A Versatile data Structure. BMC Bioinformatics, BioMed Central, 2011, 12, pp.242-258. ⟨10.1186/1471-2105-12-242⟩. ⟨lirmm-00632958⟩
  • Raluca Uricaru, Alban Mancheron, Eric Rivals. Novel definition and algorithm for chaining fragments with proportional overlaps. Journal of Computational Biology, Mary Ann Liebert, 2011, 18 (9), pp.1141-1154. ⟨10.1089/cmb.2011.0126⟩. ⟨lirmm-00834143⟩
  • Alban Mancheron, Raluca Uricaru, Eric Rivals. An Alternative Approach to Multiple Genome Comparison. Nucleic Acids Research, Oxford University Press, 2011, 39 (15), pp.e101. ⟨10.1093/nar/gkr177⟩. ⟨lirmm-00620931⟩
  • Eric Rivals, Alban Mancheron, Raluca Uricaru. Reliable Bacterial Genome Comparison Tools. ERCIM News, ERCIM, 2010, 82, pp.017-018. ⟨http://ercim-news.ercim.eu/en82/special/reliable-bacterial-genome-comparison-tools⟩. ⟨lirmm-00511509⟩
  • José R. Hernández Mora, Eric Rivals, Hakim Mireau, Françoise Budar. Sequence Analysis of Two Alleles Reveals That Intra-and Intergenic Recombination Played a Role in the Evolution of the Radish Fertility Eestorer (Rfo). BMC Plant Biology, BioMed Central, 2010, 10, pp.35. ⟨10.1186/1471-2229-10-35⟩. ⟨lirmm-00490860⟩
  • Sébastien Leclercq, Eric Rivals, Philippe Jarne. DNA Slippage Occurs at Microsatellite Loci without Minimal Threshold Length in Humans: A Comparative Genomic Approach. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2010, 2, pp.325-335. ⟨10.1093/gbe/evq023⟩. ⟨hal-00493962⟩
  • Nicolas Philippe, Anthony Boureux, Laurent Brehelin, Jorma Tarhio, Thérèse Commes, et al.. Estimation of sequence errors and capacity of genomic annotation in transcriptomic and DNA-protein interaction assays based on next generation sequencers. Cellular Oncology, IOS Press, 2009, 31 (2), pp.145-146. ⟨lirmm-00416012⟩
  • Nicolas Philippe, Anthony Boureux, Laurent Brehelin, Jorma Tarhio, Thérèse Commes, et al.. Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity. Nucleic Acids Research, Oxford University Press, 2009, 37 (15 e104), pp.11. ⟨10.1093/nar/gkp492⟩. ⟨lirmm-00415899⟩
  • N. Philippe, A. Boureux, Laurent Brehelin, J. Tarhio, T. Commes, et al.. Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity. Nucleic Acids Research, Oxford University Press, 2009, 37 (15), pp.e104. ⟨hal-00452377⟩
  • François Nicolas, Eric Rivals. Hardness of Optimal Spaced Seed Design. Journal of Computer and System Sciences, Elsevier, 2008, 74 (5), pp.831-849. ⟨10.1016/j.jcss.2007.10.001⟩. ⟨lirmm-00194171⟩
  • François Bonhomme, Eric Rivals, Annie Orth, Gemma R Grant, Alec J Jeffreys, et al.. Species-wide distribution of highly polymorphic minisatellite markers suggests past and present genetic exchanges among House Mouse subspecies. Genome Biology, BioMed Central, 2007, 8, pp.R80. ⟨http://genomebiology.com/2007/8/5/R80⟩. ⟨10.1186/gb-2007-8-5-r80⟩. ⟨lirmm-00193283⟩
  • Sébastien Leclercq, Eric Rivals, Philippe Jarne. Detecting Microsatellites within Genomes: Significant Variation Among Algorithms. BMC Bioinformatics, BioMed Central, 2007, 8, pp.125. ⟨10.1186/1471-2105-8-125⟩. ⟨lirmm-00193269⟩
  • Ezekiel Adebiyi, Eric Rivals. Detection of Recombination in Variable Number Tandem Repeat Sequences. South African Computer Journal, Computer Society of South Africa, 2007, 39, pp.1-7. ⟨lirmm-00194110⟩
  • Eric Rivals, A. Boureux, Martine Lejeune, F. Ottones, O. Pecharroman-Perez, et al.. Transcriptome annotation using tandem SAGE tags. Nucleic Acids Research, Oxford University Press, 2007, 35 (17), pp.e108. ⟨hal-00179244⟩
  • Eric Rivals, Anthony Boureux, Mireille Lejeune, Florence Ottones, Oscar Pecharromàn Pérez, et al.. Transcriptome Annotation using Tandem SAGE Tags. Nucleic Acids Research, Oxford University Press, 2007, 35 (17), pp.e108. ⟨10.1093/nar/gkm495⟩. ⟨lirmm-00193291⟩
  • François Nicolas, Eric Rivals. Longest Common Subsequence Problem for Unoriented and Cyclic Strings. Theoretical Computer Science, Elsevier, 2007, 370 (1-3), pp.1-18. ⟨10.1016/j.tcs.2006.10.002⟩. ⟨lirmm-00120152⟩
  • Eric Rivals, Clémence Bruyère, Claire Toffano-Nioche, Alain Lecharny. Formation of the Arabidopsis Pentatricopeptide Repeat Family. Plant Physiology, American Society of Plant Biologists, 2006, 141, pp.825-839. ⟨10.1104/pp.106.077826⟩. ⟨lirmm-00109042⟩
  • Sèverine Bérard, François Nicolas, Jérome Buard, Olivier Gascuel, Eric Rivals. A Fast and Specific Alignment Method for Minisatellite Maps. Evolutionary Bioinformatics, Libertas Academica (New Zealand), 2006, 2, pp.327-344. ⟨lirmm-00120145⟩
  • François Nicolas, Eric Rivals. Hardness Results for the Center and Median String Problems under the Weighted and Unweighted Edit Distances. Journal of Discrete Algorithms, Elsevier, 2005, 3 (2-4), pp.390-415. ⟨lirmm-00105320⟩
  • Olivier Delgrange, Eric Rivals. STAR: An Algorithm to Search for Tandem Approximate Repeats. Bioinformatics, Oxford University Press (OUP), 2004, 20 (16), pp.2812-2820. ⟨lirmm-00108544⟩
  • Eric Rivals. A Survey on Algorithmic Aspects of Tandem Repeats Evolution. International Journal of Foundations of Computer Science, World Scientific Publishing, 2004, 15 (2), pp.225-257. ⟨lirmm-00108543⟩
  • Sven Rahmann, Eric Rivals. On the Distribution of the Number of Missing Words in Random Texts. Combinatorics, Probability and Computing, Cambridge University Press (CUP), 2003, 12 (1), pp.73-87. ⟨10.1017/S0963548302005473⟩. ⟨lirmm-00269581⟩
  • Eric Rivals, Sven Rahmann. Combinatorics of Periods in Strings. Journal of Combinatorial Theory, Series A, Elsevier, 2003, 104 (1), pp.95-113. ⟨10.1016/S0097-3165(03)00123-7⟩. ⟨lirmm-00269554⟩
  • Sèverine Bérard, Eric Rivals. Comparison of Minisatellites. Journal of Computational Biology, Mary Ann Liebert, 2003, 10 (3-4), pp. 357-372. ⟨lirmm-00269555⟩

Conference papers62 documents

  • Eric Rivals. High performance text indexing and applications in life sciences. UK-France Bilateral International Meeting on High Performance Computing and Biomathematics, Feb 2019, Chicheley, United Kingdom. ⟨lirmm-02093450⟩
  • Eric Rivals. Données génomiques massives : applications, enjeux computationnels et perspectives. Open Science, Open Access, Open Data et données, Jun 2018, Strasbourg, France. ⟨lirmm-01951492⟩
  • David Martin, Vincent Maillol, Eric Rivals. Fast and accurate genome-scale identification of DNA-binding sites. BIBM: Bioinformatics and Biomedicine, Dec 2018, Madrid, Spain. pp.201-205, ⟨10.1109/BIBM.2018.8621093⟩. ⟨lirmm-01967466⟩
  • Eric Rivals, Bastien Cazaux. Superstrings with multiplicities. CPM: Combinatorial Pattern Matching, Qingdao University, Jul 2018, Qingdao, China. pp.21:1-21:16, ⟨10.4230/LIPIcs.CPM.2018.21⟩. ⟨lirmm-01843225⟩
  • Bastien Cazaux, Samuel Juhel, Eric Rivals. Practical lower and upper bounds for the Shortest Linear Superstring. SEA: Symposium on Experimental Algorithms, Jun 2018, L'Aquilla, Italy. pp.18:1--18:14, ⟨10.4230/LIPIcs.SEA.2018.18⟩. ⟨lirmm-01929399⟩
  • Rodrigo Cánovas, Eric Rivals. Full Compressed Affix Tree Representations. DCC: Data Compression Conference, IEEE, Apr 2017, Snowbird, UT, United States. pp.102-111, ⟨10.1109/DCC.2017.39⟩. ⟨lirmm-02093302⟩
  • Sylvain Pulicani, Pijus Simonaitis, Eric Rivals, Krister Swenson. Rearrangement Scenarios Guided by Chromatin Structure. RECOMB-CG: Comparative Genomics, Oct 2017, Barcelona, Spain. pp.141-155, ⟨10.1007/978-3-319-67979-2_8⟩. ⟨hal-01791974⟩
  • Eric Rivals. A new tool for non-hybrid correction of long noisy reads. NGS Symposium, Thomas Sexton, Jul 2016, Illkirch, France. ⟨lirmm-01445496⟩
  • Eric Rivals. LoRDEC: a tool for correcting errors in long sequencing reads. Montpellier Omics Days, Université de Montpellier, Master BCD, Feb 2016, Montpellier, France. ⟨lirmm-01446431⟩
  • Eric Rivals. Hybrid and non hybrid error correction for long reads: LoRDEC and LoRMA. Colib’read workshop, ANR Colib'read, Nov 2016, Paris, France. ⟨lirmm-01446434⟩
  • Bastien Cazaux, Gustavo Sacomoto, Eric Rivals. Superstring Graph: A New Approach for Genome Assembly. AAIM: Algorithmic Aspects in Information and Management, Università degli Studi di Bergamo, Jul 2016, Bergamo, Italy. pp.39-52, ⟨10.1007/978-3-319-41168-2_4⟩. ⟨lirmm-01446428⟩
  • Bastien Cazaux, Rodrigo Cánovas, Eric Rivals. Shortest DNA cyclic cover in compressed space. DCC: Data Compression Conference, Mar 2016, Snowbird, UT, United States. pp.536-545, ⟨10.1109/DCC.2016.79⟩. ⟨lirmm-01314330⟩
  • Eric Rivals. Data Mining et Big Data. 15ème Rencontre Eveline Markiewicz sur les urgences et complications sévères chez le patient cancéreux, European Lung Cancer Working Party & Institut Jules Bordet, Nov 2015, Bruxelles, Belgique. ⟨lirmm-01286788⟩
  • Eric Rivals. Correction of long sequencing reads: a novel approach: 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. ⟨lirmm-01185688⟩
  • Eric Rivals. LoRDEC: a tool for correcting errors in long sequencing reads. GCB: German Conference on Bioinformatics, University Alliance Ruhr, Sep 2015, Dortmund, Germany. ⟨lirmm-01224319⟩
  • Bastien Cazaux, Thierry Lecroq, Eric Rivals. Construction of a de Bruijn Graph for Assembly from a Truncated Suffix Tree. LATA: Language and Automata Theory and Applications, Mar 2015, Nice, France. pp.109-120. ⟨hal-01955978⟩
  • Bastien Cazaux, Thierry Lecroq, Eric Rivals. From Indexing Data Structures to de Bruijn Graphs. CPM: Combinatorial Pattern Matching, Moscow State University, Jun 2014, Moscow, Russia. pp.89-99, ⟨10.1007/978-3-319-07566-2_10⟩. ⟨lirmm-01081429⟩
  • Bastien Cazaux, Eric Rivals. Approximation of Greedy Algorithms for Max-ATSP, Maximal Compression, Maximal Cycle Cover, and Shortest Cyclic Cover of Strings. PSC: Prague Stringology Conference, Czech Technical University in Prague, Sep 2014, Prague, Czech Republic. pp.148-161. ⟨lirmm-01100683⟩
  • Eric Rivals. Défis computationnels des séquençage et phénotypage haut débit en science de la vie. Journées Big Data - 2ème journées - Principaux Défis, Laboratoire ICube, Nov 2014, Strasbourg, France. ⟨lirmm-01176768⟩
  • Ankit Dwivedi, Emmanuel Cornillot, Christelle Reynes, Nimol Khim, Didier Menard, et al.. Functional annotation of polymorphisms identified by NGS approaches in P.falciparum. SeqBio, Nov 2014, Montpellier, France. ⟨lirmm-01397406⟩
  • Niko Välimäki, Eric Rivals. Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data. ISBRA'2013: International Symposium on Bioinformatics Research and Applications, May 2013, Charlotte, NC, United States. pp.237-248. ⟨lirmm-00806103⟩
  • Eric Rivals. Building the Assembly De Bruijn Graph from an Implicit Suffix Tree. Mini-Workshop on the Storage, Search and Annotation of Multiple Similar Genomes, Dec 2013, Bielefeld, Germany. ⟨lirmm-00938959⟩
  • Pierre Riou, Eric Rivals, Annie Chateau. Approximate Common Intervals in Multiple Genome Comparison. Fang-Xiang Wu and Mohammed Zaki and Shinichi Morishita. BIBM'11: Bioinformatics and Biomedicine, Nov 2011, Atlanta, United States. IEEE Computer Society, pp.131-134, 2011, 〈http://www.cs.gsu.edu/BIBM2011/〉. 〈10.1109/BIBM.2011.96〉. 〈lirmm-00659473〉
  • Eric Rivals. Analysis of genomic data from high throughput sequencing: concepts and basic methods. Palaeogenomics Summer School, Oct 2011, Cargese, France. ⟨lirmm-00832551⟩
  • Eric Rivals. CRAC: A multi-purpose program to analyse large read collections. Analyse bio-informatique des données NGS, Dec 2011, Institut Pasteur de Lille, France. ⟨lirmm-00832549⟩
  • Nicolas Philippe, Mikael Salson, Thierry Lecroq, Martine Léonard, Thérèse Commes, et al.. A solution to index large set of short reads. seqBi11 - Workshop Algorithmique, combinatoire du texte et applications en bio-informatique, 2011, Rennes, France. ⟨hal-00560731⟩
  • Eric Rivals. An integrated approach to read analysis. LIX Bioinformatics Colloquium 2010, Nov 2010, Ecole Polytechnique, Palaiseau, France. ⟨lirmm-00832548⟩
  • Raluca Uricaru, Alban Mancheron, Eric Rivals. Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps. RECOMB-CG: Comparative Genomics, Oct 2010, Ottawa, Canada. pp.161-172, ⟨10.1007/978-3-642-16181-0_14⟩. ⟨lirmm-00527915⟩
  • Raluca Uricaru, Célia Michotey, Laurent Noé, Hélène Chiapello, Eric Rivals. Improved Sensitivity And Reliability Of Anchor Based Genome Alignment. JOBIM'09 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2009, Nantes, France. pp.31-36. ⟨lirmm-00407215⟩
  • Alban Mancheron, Raluca Uricaru, Eric Rivals. Ehrlichia Ruminantium Genome Segmentations Reveal Novel Homologous Genes. ISCB Africa ASBCB Joint Conference on Bioinformatics of Infectious Diseases, Nov 2009, Bamako, Mali. ⟨lirmm-00491362⟩
  • Eric Rivals. Estimation of Sequence Errors and Prediction Capacity in Transcriptomic and DNA-Protein Interaction Assays. Journée Thématique : Nouveaux Séquenceurs (NGS), Apr 2009, Rennes, France. ⟨lirmm-00375010⟩
  • Nicolas Philippe, Anthony Boureux, Laurent Brehelin, Jorma Tarhio, Thérèse Commes, et al.. Estimation of Sequence Errors and Prediction Capacity in Transcriptomic and DNA-Protein Interaction Assays. SMPGD'09: Statistical Methods for Post-genomic Data Workshop, Jan 2009, Paris, France. pp.3. ⟨lirmm-00375005⟩
  • Eric Rivals. Investigating the transcriptomic repertoire based on High Throughput Sequencing data. Colloque 2009 du GDR de Bioinformatique Moléculaire, Nov 2009, Paris, France. ⟨lirmm-00833124⟩
  • Eric Rivals, Leena Salmela, Petri Kalsi, Petteri Kiiskinen, Jorma Tarhio. MPSCAN: Fast Localisation of Multiple Reads in Genomes. WABI: Workshop on Algorithms in Bioinformatics, Sep 2009, Philadelphie, United States. pp.246-260, ⟨10.1007/978-3-642-04241-6_21⟩. ⟨lirmm-00407173⟩
  • Sèverine Bérard, Eric Rivals. Comparaison de Minisatellites. JOBIM'02 : Journées Ouvertes Biologie, Informatique, Mathématiques, St Malo, France, pp.261-262. ⟨lirmm-00268469⟩
  • Eric Rivals, Anthony Boureux, Mireille Lejeune, Florence Ottones, Oscar Pecharromàn Pérez, et al.. Combining SAGE Tags to Predict Genomic Transcribed Regions. JOBIM'08 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2008, Lille, France, pp.141-146. ⟨lirmm-00343895⟩
  • José R. Hernández Mora, Eric Rivals, Hakim Mireau, Françoise Budar. Evolutionary Dynamics of a Locus of Fertility Restoration in Plants. JOBIM'08 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2008, Lille, France, France. pp.273-274. ⟨lirmm-00343902⟩
  • Eric Rivals, Zhaojun Shao, Patrick Berrebi, Bin Zhu, Na Zhao, et al.. Evolutionary Process of a Tetranucleotide Microsatellite Locus in Acipenseriforms. MIEP: Mathematics and Informatics in Evolution and Phylogeny, Jun 2008, St Martin de Londres, France. pp.20-21. ⟨lirmm-00345813⟩
  • Eric Rivals. Tandem Repeats Analysis. Southern African Bioinformatics Workshop, Jan 2007, Johannesburg, South Africa. pp.2. ⟨lirmm-00193478⟩
  • Eric Rivals. Species Wide Distribution of Highly Polymorphic Minisatellite Markers Suggests Past and Present Genetic Exchanges Among House Mouse Subspecies. Fourth Indo-French Bioinformatics Meeting, Nov 2007, Port-Camargue, France. ⟨lirmm-00194062⟩
  • Eric Rivals. L'analyse de marqueurs minisatellites variables suggèrent de fréquents échanges génétiques entre sous-espèces de la souris commune. Bioinformatique, Modélisation des Systèmes Biologiques, Oct 2007, Paris, France. ⟨lirmm-00193841⟩
  • José R. Hernández Mora, Eric Rivals, Hakim Mireau, Françoise Budar. Evolutionary Dynamics of the Restorer and a non-restorer Allelic Rfo Locus.. SFBV'07: VIIe Colloque National de la Société Française de Biologie Végétale, Sep 2007, Versailles, France. pp.113. ⟨lirmm-00203886⟩
  • Eric Rivals, Anthony Boureux, Mireille Lejeune, Florence Ottones, Oscar Pecharromàn Pérez, et al.. Transcriptome annotation using tandem SAGE tags. Réunion satellite "Transcriptome et bioinformatique", Jul 2007, Marseille, France. pp.8. ⟨lirmm-00203923⟩
  • Eric Rivals. Combinatorics of Periods in Strings. Workshop on Algorithms on Words, Mar 2007, Turku, Finland. pp.43-44. ⟨lirmm-00193520⟩
  • Raluca Uricaru, Laurent Brehelin, Eric Rivals. A new type of Hidden Markov Models to predict complex domain architecture in protein sequences. JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jul 2007, Marseille, France. pp.97-102. ⟨lirmm-00195493⟩
  • Eric Rivals. Minisatellite Markers Reveals Frequent Genetic Exchanges among House Mouse Subspecies. Rencontres ALPHY - Génomique Evolutive, Bioinformatique, Alignement et Phylogénie, Feb 2007, Montpellier, France. pp.1. ⟨lirmm-00195524⟩
  • Eric Rivals, François Bonhomme, Annie Orth, Gemma R Grant, Alec J Jeffreys, et al.. Analysis of four polymorphic minisatellites suggests frequent genetic exchanges among House Mouse subspecies. JOBIM'07 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2007, Marseille, pp.123-124. ⟨lirmm-00195503⟩
  • Eric Rivals, Ezekiel Adebiyi. On the Detection of Recombination in Minisatellite Data. First Southern African Bioinformatics Workshop, Jan 2007, Johannesburg, South-Africa, pp.25-32. ⟨lirmm-00193849⟩
  • Olivier Bodini, Eric Rivals. Tiling an Interval of the Discrete Line. CPM: Combinatorial Pattern Matching, Jul 2006, Barcelona, Spain. pp.117-128, ⟨10.1007/11780441_12⟩. ⟨lirmm-00120188⟩
  • Raluca Uricaru, Laurent Brehelin, Eric Rivals. A new type of Hidden Markov Models to predict complex motif organization in protein sequences. Integrative Post-Genomics, 2006, Lyon, pp.43. ⟨lirmm-00120171⟩
  • Eric Rivals, Anthony Boureux, Mireille Lejeune, Florence Ottones, Oscar Pecharromàn Pérez, et al.. Human Transcriptome Annotation using Tandem SAGE Tags. Integrative Post-Genomics, Nov 2006, Lyon, pp.39. ⟨lirmm-00120164⟩
  • Sébastien Leclercq, Eric Rivals, Philippe Jarne. Detecting microsatellites within genomes: no exact solution?. Integrative Post-Genomics, Nov 2006, Lyon, pp.27. ⟨lirmm-00120181⟩
  • François Nicolas, Eric Rivals. Hardness of Optimal Spaced Seed Design. CPM: Combinatorial Pattern Matching, Jun 2005, Jeju City, South Korea. pp.144-155, ⟨10.1007/11496656_13⟩. ⟨lirmm-00106448⟩
  • O. Delgrange, Eric Rivals. Modular Data Compression to Optimally Locate Regular Segments in Sequences. Application to DNA Sequence Analysis. IT'05: 26th Symposium on Information Theory in the Benelux, May 2005, Bruxelles (Belgique), pp.105-112. ⟨lirmm-00106467⟩
  • C. Bruyere, Eric Rivals, A. Lecharny. Formation of the Arabidopsis Pentatricopeptide Repeat (PPR) Protein Family. JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jul 2005, Lyon, France. pp.291-298. ⟨lirmm-00106048⟩
  • Eric Rivals. Analyse des génomes: Quels enjeux algorithmiques ?. Rencontres des ASTI : Sciences et Technologies de l'Information, Oct 2005. ⟨lirmm-00106555⟩
  • François Nicolas, Eric Rivals. Complexities of the Centre and Median String Problems. CPM: Combinatorial Pattern Matching, Jun 2003, Morelia, Mexico. pp.315-327. ⟨lirmm-00269556⟩
  • Sèverine Bérard, Eric Rivals. Comparaison de Séquences avec Amplifications et Contractions. ROADEF'03: Congrès de la Société Française de Recherche Opérationnelle et d'Aide à la Décision, 2003, Avignon, France. pp.169-170. ⟨lirmm-00269459⟩
  • Eric Rivals. Histoires de Duplication et Répétitions en Tandem. ALBIO, Montpellier, France. pp.P nd. ⟨lirmm-00191527⟩
  • Sèverine Bérard, Eric Rivals. Comparaison de Minisatellites. Réunion Annuelle du Groupe de Génétique et Biologie des Populations, Aug 2002, Montpellier, France. pp.128. ⟨lirmm-00269317⟩
  • Eric Rivals. Histoires de Duplication et Répétitions en Tandem. ALBIO, Montpellier (France), France. pp.P nd. ⟨lirmm-00269427⟩
  • Sèverine Bérard, Eric Rivals. Comparison of Minisatellites. RECOMB: Computational Molecular Biology, Apr 2002, Whashington, DC, United States. pp.67-76, ⟨10.1145/565196.565205⟩. ⟨lirmm-00090351⟩

Patents1 document

  • Marcel Méchali, Philippe Coulombe, Christelle Cayrou, Eric Rivals. Purification Process Of Nascent DNA. United States, Patent n° : US 61/238 315 - WO2011023827 (A1). 2011, pp.N/A. ⟨lirmm-00832553⟩

Reports8 documents

  • Bastien Cazaux, Eric Rivals. A linear time algorithm for Shortest Cyclic Cover of Strings. [Research Report] IBC; LIRMM. 2015. ⟨lirmm-01240278⟩
  • Bastien Cazaux, Eric Rivals. 3-Shortest Superstring is 2-approximable by a greedy algorithm. [Research Report] RR-14009, LIRMM. 2014. ⟨lirmm-01070596⟩
  • Bastien Cazaux, Thierry Lecroq, Eric Rivals. From Indexing Data Structures to de Bruijn Graphs. [Research Report] RR-14004, LIRMM. 2014. ⟨lirmm-00950983v2⟩
  • Bastien Cazaux, Eric Rivals. Approximation of greedy algorithms for Max-ATSP, Maximal Compression, and Shortest Cyclic Cover of Strings. RR-14001, 2013, pp.12. ⟨lirmm-00932660⟩
  • Olivier Bodini, Eric Rivals. Tiling an Interval of the Discrete Line. 05019, 2005, pp.10. ⟨lirmm-00106677⟩
  • François Nicolas, Eric Rivals. Longest Common Subsequence Problem for Unoriented and Cyclic Strings. [Research Report] 04003, LIRMM. 2004, pp.12. ⟨lirmm-00109196⟩
  • Eric Rivals, G. Kucherov, T. Lecroq. Actes de la Réunion des Actions Spécifiques "Algorithmes et Séquences" et Indexation de Texte et Découverte de Motifs". 03032, 2003, pp.15. ⟨lirmm-00191958⟩
  • Eric Rivals. Algorithmic Aspects of Tandem Repeats Evolution. 03017, 2003, pp.P nd. ⟨lirmm-00269557⟩