Number of documents

99

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 articles41 documents

Conference papers49 documents

  • Bastien Cazaux, Rodrigo Cánovas, Eric Rivals. Shortest DNA cyclic cover in compressed space. Data Compression Conference, Mar 2016, Snowbird, United States. <lirmm-01314330>
  • Eric Rivals. LoRDEC: a tool for correcting errors in long sequencing reads. Mosig A.; Rahnenführer J.; Rahmann S.; Eisenacher M. GCB: German Conference on Bioinformatics, Sep 2015, Dortmund, Germany. PeerJ, 2015, German Conference on Bioinformatics 2015 Collection. <http://gcb2015.cs.tu-dortmund.de>. <lirmm-01224319>
  • Eric Rivals. Correction of long sequencing reads: a novel approach: Abstract for the keynote presentation at " From Nucleotides to Networks " Symposium, Ghent, Belgium.. Symposium "From Nucleotides to Networks", May 2015, Gand (Ghent), Belgium. 2015, <http://www.bign2n.ugent.be>. <lirmm-01185688>
  • Eric Rivals. Data Mining et Big Data. Jean-Paul SCULIER. Rencontres Eveline Markiewicz sur les Urgences et Complications Sévères chez Patient Cancéreux, Nov 2015, Bruxelles, Belgique. 2015, <http://www.elcwp.org/New/Fr/index.html>. <lirmm-01286788>
  • Bastien Cazaux, Thierry Lecroq, Eric Rivals. From Indexing Data Structures to de Bruijn Graphs. Kulikov, Alexander S.; Kuznetsov, Sergei O.; Pevzner, Pavel. CPM: Combinatorial Pattern Matching, Jun 2014, Moscow, Russia. Springer International Publishing, CPM'2014: 25th Annual Symposium on Combinatorial Pattern Matching, LNCS (8486), pp.89-99, 2014, Combinatorial Pattern Matching. <http://www.springer.com/computer/image+processing/book/978-3-319-07565-5>. <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. Jan Holub; Jan Zd’arek. PSC'2014: Prague Stringology Conference, Sep 2014, Prague, Czech Republic. Czech Technical University in Prague, Czech Republic, ISBN 978-80-01-05547-2, pp.148-161, 2014, Proceedings of the Prague Stringology Conference 2014. <http://www.stringology.org/event/2014/p14.html>. <lirmm-01100683>
  • Eric Rivals. Défis computationnels des séquençage et phénotypage haut débit en science de la vie. Pierre Gançarski. Journées Big Data - 2ème journées - Principaux Défis, Nov 2014, Strasbourg, France. 2014, <http://icube.unistra.fr>. <lirmm-01176768>
  • Niko Välimäki, Eric Rivals. Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data. Z. Cai et al. ISBRA'2013: International Symposium on Bioinformatics Research and Applications, May 2013, Charlotte, NC, United States. Spinger-Verlag, 7875 (7875), pp.237-248, 2013, Lecture Notes in Bioinformatics (LNBI). <http://www.cvent.com/events/isbra-2013>. <lirmm-00806103>
  • Eric Rivals. Building the Assembly De Bruijn Graph from an Implicit Suffix Tree. Jens Stoye and Roland Wittler. Mini-Workshop on the Storage, Search and Annotation of Multiple Similar Genomes, Dec 2013, Bielefeld, Germany. 2013, <http://wiki.techfak.uni-bielefeld.de/didy/workshopPangenomeStorageSearch>. <lirmm-00938959>
  • Eric Rivals. CRAC: A multi-purpose program to analyse large read collections. Martin Figeac and David Hot and Guillemette Marot and Hélène Touzet. Analyse bio-informatique des données NGS, Dec 2011, Institut Pasteur de Lille, France. 2011, <http://www.lifl.fr/bonsai/seqbio2011/ngs11.html>. <lirmm-00832549>
  • Eric Rivals. Analysis of genomic data from high throughput sequencing: concepts and basic methods. Eva-Maria GEIGL and Thierry GRANGE. Palaeogenomics Summer School, Oct 2011, Cargese, France. 2011, <https://sites.google.com/site/palaeogenomicssummerschool2011/>. <lirmm-00832551>
  • 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>
  • 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. Julie Bernauer and Yann Ponty and Mireille Régnier. LIX Bioinformatics Colloquium 2010, Nov 2010, Ecole Polytechnique, Palaiseau, France. 2010, <http://www.lix.polytechnique.fr/bioinfo/colloquium2010>. <lirmm-00832548>
  • Raluca Uricaru, Alban Mancheron, Eric Rivals. Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps. Eric Tannier. RECOMB'10: Comparative Genomics, Oct 2010, Ottawa, Canada. Springer-Verlag, 6398 (6398), pp.161-172, 2010, LNCS. <http://recombcg.uottawa.ca/recombcg2010/>. <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. Eric Rivals; Irena Rusu. JOBIM'09 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2009, Nantes, France. pp.31-36, 2009, <http://www.jobim2009.fr/>. <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. 2009, <http://www.iscb.org/iscbafrica2009>. <lirmm-00491362>
  • Eric Rivals. Investigating the transcriptomic repertoire based on High Throughput Sequencing data. A. Denise and E. Rocha and S. Schbath. Colloque 2009 du GDR de Bioinformatique Moléculaire, Nov 2009, Paris, France. 2009, <http://www.gdr-bim.u-psud.fr/journees-gdr.php>. <lirmm-00833124>
  • Eric Rivals, Leena Salmela, Petri Kalsi, Petteri Kiiskinen, Jorma Tarhio. MPSCAN: Fast Localisation of Multiple Reads in Genomes. S. Salzberg and T. Warnow. WABI'09: Workshop on Algorithms in Bioinformatics, Sep 2009, Philadelphie, Springer-Verlag, pp.246-260, 2009, Lecture Notes in BioInformatics (LNBI/LNCS). <http://www.wabi09.org/>. <lirmm-00407173>
  • 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, 2009, <http://www.math.univ-toulouse.fr/biostat/6-17723-SMPGD09.php>. <lirmm-00375005>
  • Eric Rivals. Estimation of Sequence Errors and Prediction Capacity in Transcriptomic and DNA-Protein Interaction Assays. P. Peterlongo. Journée Thématique : Nouveaux Séquenceurs (NGS), Apr 2009, Rennes, France. 2009, <http://www.irisa.fr/manifestations/seminaires/bioinfo/2008_09/journee-thematique-ngs-new-generation-sequencer>. <lirmm-00375010>
  • Sèverine Bérard, Eric Rivals. Comparaison de Minisatellites. JOBIM'02 : Journées Ouvertes Biologie, Informatique, Mathématiques, St Malo, France, pp.261-262, 2002. <lirmm-00268469>
  • José R. Hernández Mora, Eric Rivals, Hakim Mireau, Françoise Budar. Evolutionary Dynamics of a Locus of Fertility Restoration in Plants. Jacques Van Helden, Yves Moreau. JOBIM'08 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2008, Lille, France, France. pp.273-274, 2008, <http://www2.lifl.fr/jobim2008/>. <lirmm-00343902>
  • Eric Rivals, Anthony Boureux, Mireille Lejeune, Florence Ottones, Oscar Pecharromàn Pérez, et al.. Combining SAGE Tags to Predict Genomic Transcribed Regions. Jacques van Helden, Yves Moreau. JOBIM'08 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2008, Lille, France, pp.141-146, 2008, <http://www2.lifl.fr/jobim2008/>. <lirmm-00343895>
  • Eric Rivals, Zhaojun Shao, Patrick Berrebi, Bin Zhu, Na Zhao, et al.. Evolutionary Process of a Tetranucleotide Microsatellite Locus in Acipenseriforms. Olivier Gascuel. MIEP: Mathematics and Informatics in Evolution and Phylogeny, Jun 2008, St Martin de Londres, France. pp.20-21, 2008, <http://www.lirmm.fr/MIEP08>. <lirmm-00345813>
  • Raluca Uricaru, Laurent Brehelin, Eric Rivals. A new type of Hidden Markov Models to predict complex domain architecture in protein sequences. C. Brun; G Didier. JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jul 2007, Marseille, France. pp.97-102, 2007, <http://crfb.univ-mrs.fr/jobim2007/>. <lirmm-00195493>
  • Eric Rivals. Species Wide Distribution of Highly Polymorphic Minisatellite Markers Suggests Past and Present Genetic Exchanges Among House Mouse Subspecies. F. Molina. Fourth Indo-French Bioinformatics Meeting, Nov 2007, Port-Camargue, France. 2007, <http://bioinformatics.univ-reunion.fr/ifbm2007/>. <lirmm-00194062>
  • Eric Rivals. L'analyse de marqueurs minisatellites variables suggèrent de fréquents échanges génétiques entre sous-espèces de la souris commune. A. Denise, O. Gascuel. Bioinformatique, Modélisation des Systèmes Biologiques, Oct 2007, Paris, France. 2007, <http://impbio.lirmm.fr/poincare/>. <lirmm-00193841>
  • 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. C. Brun et G. Didier. JOBIM'07 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2007, Marseille, pp.123-124, 2007, <http://crfb.univ-mrs.fr/jobim2007/>. <lirmm-00195503>
  • Eric Rivals. Minisatellite Markers Reveals Frequent Genetic Exchanges among House Mouse Subspecies. L. Duret; N. Galtier. Rencontres ALPHY - Génomique Evolutive, Bioinformatique, Alignement et Phylogénie, Feb 2007, Montpellier, France. pp.1, 2007. <lirmm-00195524>
  • Eric Rivals. Tandem Repeats Analysis. Scott Hazelhurst and Michèle Ramsay. Southern African Bioinformatics Workshop, Jan 2007, Johannesburg, South Africa. pp.2, 2007, <http://www.bioinf.wits.ac.za/conference/>. <lirmm-00193478>
  • Eric Rivals, Ezekiel Adebiyi. On the Detection of Recombination in Minisatellite Data. S. Hazelhurst, M. Ramsay. First Southern African Bioinformatics Workshop, Jan 2007, Johannesburg, South-Africa, 1, pp.25-32, 2007, <http://www.bioinf.wits.ac.za/conference/>. <lirmm-00193849>
  • Eric Rivals. Combinatorics of Periods in Strings. Vesa Halava. Workshop on Algorithms on Words, Mar 2007, Turku, Finland. pp.43-44, 2007, <http://www.math.utu.fi/projects/waw/>. <lirmm-00193520>
  • Eric Rivals, Anthony Boureux, Mireille Lejeune, Florence Ottones, Oscar Pecharromàn Pérez, et al.. Transcriptome annotation using tandem SAGE tags. Guy Perriere. Réunion satellite "Transcriptome et bioinformatique", Jul 2007, Marseille, France. Société Française de BioInformatique (SFBI), pp.8, 2007, <http://crfb.univ-mrs.fr/jobim2007/index.php?l=fr&c=satell>. <lirmm-00203923>
  • José R. Hernández Mora, Eric Rivals, Hakim Mireau, Françoise Budar. Evolutionary Dynamics of the Restorer and a non-restorer Allelic Rfo Locus.. Société française de biologie végétale. SFBV'07: VIIe Colloque National de la Société Française de Biologie Végétale, Sep 2007, Versailles, France. pp.113, 2007. <lirmm-00203886>
  • 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, 2006. <lirmm-00120164>
  • 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, 2006. <lirmm-00120171>
  • Sebastien Leclercq, Eric Rivals, Philippe Jarne. Detecting microsatellites within genomes: no exact solution?. Integrative Post-Genomics, Nov 2006, Lyon, pp.27, 2006. <lirmm-00120181>
  • Olivier Bodini, Eric Rivals. Tiling an Interval of the Discrete Line. Springer. CPM: Combinatorial Pattern Matching, Jul 2006, Barcelona, Spain. Springer Verlag, 17th Annual Symposium on Combinatorial Pattern Matching, LNCS (4009), pp.117-128, 2006, <10.1007/11780441_12>. <lirmm-00120188>
  • O. Delgrange, Eric Rivals. Modular Data Compression to Optimally Locate Regular Segments in Sequences. Application to DNA Sequence Analysis. J. Cardinal, N. Cerf, O. Delgrange, O. Markowich. IT'05: 26th Symposium on Information Theory in the Benelux, May 2005, Bruxelles (Belgique), pp.105-112, 2005. <lirmm-00106467>
  • Eric Rivals. Analyse des génomes: Quels enjeux algorithmiques ?. Rencontres des ASTI : Sciences et Technologies de l'Information, Oct 2005, 2005. <lirmm-00106555>
  • C. Bruyere, Eric Rivals, A. Lecharny. Formation of the Arabidopsis Pentatricopeptide Repeat (PPR) Protein Family. G. Perrière; A. Guénoche; C. Geourjon. JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jul 2005, Lyon, France. 6e Journées Ouvertes Biologie, Informatique, Mathématiques, pp.291-298, 2005. <lirmm-00106048>
  • François Nicolas, Eric Rivals. Hardness of Optimal Spaced Seed Design. A. Apostolico; M. Crochemore; K. Park. CPM: Combinatorial Pattern Matching, Jun 2005, Jeju City, South Korea. Springer Verlag, 16th Annual Symposium on Combinatorial Pattern Matching, LNCS (3537), pp.144-155, 2005, <10.1007/11496656_13>. <lirmm-00106448>
  • 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, 2003. <lirmm-00269459>
  • François Nicolas, Eric Rivals. Complexities of the Centre and Median String Problems. BAEZA-YATES R.; CHAVEZ E.; CHAVEZ E.;CROCHEMORE M. CPM: Combinatorial Pattern Matching, Jun 2003, Morelia, Mexico. Springer Verlag, 14th Annual Symposium on Combinatorial Pattern Matching, LNCS (2676), pp.315-327, 2003. <lirmm-00269556>
  • Eric Rivals. Histoires de Duplication et Répétitions en Tandem. ALBIO, Montpellier (France), France. pp.P nd., 2002. <lirmm-00269427>
  • Sèverine Bérard, Eric Rivals. Comparaison de Minisatellites. Réunion Annuelle du Groupe de Génétique et Biologie des Populations, Aug 2002, Montpellier, France. pp.128, 2002. <lirmm-00269317>
  • Sèverine Bérard, Eric Rivals. Comparison of Minisatellites. ACM Press. RECOMB'02: International Conference on Computational Molecular Biology, Apr 2002, Whashington, DC (USA), pp.67-76, 2002. <lirmm-00090351>
  • Eric Rivals. Histoires de Duplication et Répétitions en Tandem. ALBIO, Montpellier, France. pp.P nd., 2002. <lirmm-00191527>

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>
  • O. 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. Algorithmic Aspects of Tandem Repeats Evolution. 03017, 2003, pp.P nd. <lirmm-00269557>
  • 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>