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

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⟩
  • Sylvain Pulicani, Pijus Simonaitis, Eric Rivals, Krister Swenson. Rearrangement Scenarios Guided by Chromatin Structure. RECOMB-CG, Oct 2017, Barcelona, Spain. pp.141-155, ⟨10.1007/978-3-319-67979-2_8⟩. ⟨hal-01791974⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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'10: 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⟩
  • Eric Rivals, Leena Salmela, Petri Kalsi, Petteri Kiiskinen, Jorma Tarhio. MPSCAN: Fast Localisation of Multiple Reads in Genomes. WABI'09: Workshop on Algorithms in Bioinformatics, Sep 2009, Philadelphie, pp.246-260. ⟨lirmm-00407173⟩
  • 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⟩
  • 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⟩
  • Sébastien Leclercq, Eric Rivals, Philippe Jarne. Detecting microsatellites within genomes: no exact solution?. Integrative Post-Genomics, Nov 2006, Lyon, pp.27. ⟨lirmm-00120181⟩
  • 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⟩
  • 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⟩
  • Sèverine Bérard, Eric Rivals. Comparison of Minisatellites. RECOMB'02: International Conference on Computational Molecular Biology, Apr 2002, Whashington, DC (USA), pp.67-76. ⟨lirmm-00090351⟩
  • 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⟩

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⟩