Eric Rivals
145
Documents
Presentation
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)
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)
Publications
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Convergence of the number of period sets in stringsICALP 2023 - 50th International Colloquium on Automata, Languages, and Programming, Jul 2023, Paderborn, Germany. pp.100:1-100:14, ⟨10.4230/LIPICS.ICALP.2023.100⟩
Conference papers
lirmm-03780386v1
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Analysis of epitranscriptome for grading of gliomaSymposium on Cancer genomics and epitranscriptomics: from the bench to the clinic, Comprehensive Cancer Center (CIC), University of Salamanca, Nov 2022, Salamanca, Spain
Conference papers
lirmm-04287393v1
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A Linear Time Algorithm for Constructing Hierarchical Overlap GraphsCPM 2021 - 32nd Annual Symposium on Combinatorial Pattern Matching, Institute of Computer Science of University of Wrocław, Poland., Jul 2021, Wrocław, Poland. pp.22:1--22:9, ⟨10.4230/LIPIcs.CPM.2021.22⟩
Conference papers
lirmm-03431830v1
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Efficient Construction of Hierarchical Overlap GraphsSPIRE 2020 - 27th International Symposium on String Processing and Information Retrieval, Oct 2020, Orlando, FL, United States. pp.277-290, ⟨10.1007/978-3-030-59212-7_20⟩
Conference papers
lirmm-03014336v1
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Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length EncodingCPM 2019 - 30th Annual Symposium on Combinatorial Pattern Matching, University of Pisa, Jun 2019, Pise, Italy. pp.24:1--24:20, ⟨10.4230/LIPIcs.CPM.2019.24⟩
Conference papers
lirmm-02382066v1
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Computational Pan-GenomicsPangénomique végétale, GIS Biotechnologies Vertes, INRA, Jul 2019, Paris, France
Conference papers
lirmm-02387894v1
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Perspectives and challenges of Computational Pan-GenomicsLifeTime UnConference, Centre de Regulació Genòmica (CRG); centro nacional de análisis genómico (CNAG), Jul 2019, Barelone, Spain
Conference papers
lirmm-02388116v1
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High performance text indexing and applications in life sciencesUK-France Bilateral International Meeting on High Performance Computing and Biomathematics, Feb 2019, Chicheley, United Kingdom
Conference papers
lirmm-02093450v1
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Données génomiques massives : applications, enjeux computationnels et perspectivesOpen Science, Open Access, Open Data et données, Jun 2018, Strasbourg, France
Conference papers
lirmm-01951492v1
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Practical lower and upper bounds for the Shortest Linear SuperstringSEA: Symposium on Experimental Algorithms, Jun 2018, L'Aquilla, Italy. pp.18:1--18:14, ⟨10.4230/LIPIcs.SEA.2018.18⟩
Conference papers
lirmm-01929399v1
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Fast and accurate genome-scale identification of DNA-binding sitesBIBM: Bioinformatics and Biomedicine, Dec 2018, Madrid, Spain. pp.201-205, ⟨10.1109/BIBM.2018.8621093⟩
Conference papers
lirmm-01967466v1
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Superstrings with multiplicities29th Annual Symposium on Combinatorial Pattern Matching (CPM), Qingdao University, Jul 2018, Qingdao, China. pp.21:1-21:16, ⟨10.4230/LIPIcs.CPM.2018.21⟩
Conference papers
lirmm-01843225v1
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Rearrangement Scenarios Guided by Chromatin StructureRECOMB-CG: Comparative Genomics, Oct 2017, Barcelona, Spain. pp.141-155, ⟨10.1007/978-3-319-67979-2_8⟩
Conference papers
hal-01791974v1
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Full Compressed Affix Tree RepresentationsDCC: Data Compression Conference, IEEE, Apr 2017, Snowbird, UT, United States. pp.102-111, ⟨10.1109/DCC.2017.39⟩
Conference papers
lirmm-02093302v1
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LoRDEC: a tool for correcting errors in long sequencing readsMontpellier Omics Days, Université de Montpellier, Master BCD, Feb 2016, Montpellier, France
Conference papers
lirmm-01446431v1
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Shortest DNA cyclic cover in compressed spaceDCC: Data Compression Conference, Mar 2016, Snowbird, UT, United States. pp.536-545, ⟨10.1109/DCC.2016.79⟩
Conference papers
lirmm-01314330v1
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A new tool for non-hybrid correction of long noisy readsNGS Symposium, Thomas Sexton, Jul 2016, Illkirch, France
Conference papers
lirmm-01445496v1
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Superstring Graph: A New Approach for Genome AssemblyAAIM: 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⟩
Conference papers
lirmm-01446428v1
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Hybrid and non hybrid error correction for long reads: LoRDEC and LoRMAColib’read workshop, ANR Colib'read, Nov 2016, Paris, France
Conference papers
lirmm-01446434v1
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Data Mining et Big Data15ème 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
Conference papers
lirmm-01286788v1
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Correction of long sequencing reads: a novel approachBIG N2N: Bioinformatics Institute Ghent "From Nucleotides to Networks", Ghent University, Bioinformatics Institute Ghent, May 2015, Gand, Ghent, Belgium
Conference papers
lirmm-01185688v1
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Construction of a de Bruijn Graph for Assembly from a Truncated Suffix TreeLATA: Language and Automata Theory and Applications, Mar 2015, Nice, France. pp.109-120, ⟨10.1007/978-3-319-15579-1_8⟩
Conference papers
hal-01955978v1
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LoRDEC: a tool for correcting errors in long sequencing readsGCB: German Conference on Bioinformatics, University Alliance Ruhr, Sep 2015, Dortmund, Germany
Conference papers
lirmm-01224319v1
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Approximation of Greedy Algorithms for Max-ATSP, Maximal Compression, Maximal Cycle Cover, and Shortest Cyclic Cover of StringsPSC: Prague Stringology Conference, Czech Technical University in Prague, Sep 2014, Prague, Czech Republic. pp.148-161
Conference papers
lirmm-01100683v1
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Défis computationnels des séquençage et phénotypage haut débit en science de la vieJournées Big Data - 2ème journées - Principaux Défis, Laboratoire ICube, Nov 2014, Strasbourg, France
Conference papers
lirmm-01176768v1
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From Indexing Data Structures to de Bruijn GraphsCPM: Combinatorial Pattern Matching, Moscow State University, Jun 2014, Moscow, Russia. pp.89-99, ⟨10.1007/978-3-319-07566-2_10⟩
Conference papers
lirmm-01081429v1
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Functional annotation of polymorphisms identified by NGS approaches in P.falciparumSeqBio, Nov 2014, Montpellier, France
Conference papers
lirmm-01397406v1
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Scalable and Versatile k-mer Indexing for High-Throughput Sequencing DataISBRA'2013: International Symposium on Bioinformatics Research and Applications, May 2013, Charlotte, NC, United States. pp.237-248
Conference papers
lirmm-00806103v1
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Building the Assembly De Bruijn Graph from an Implicit Suffix TreeMini-Workshop on the Storage, Search and Annotation of Multiple Similar Genomes, Dec 2013, Bielefeld, Germany
Conference papers
lirmm-00938959v1
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Analysis of genomic data from high throughput sequencing: concepts and basic methodsPalaeogenomics Summer School, Oct 2011, Cargese, France
Conference papers
lirmm-00832551v1
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Approximate Common Intervals in Multiple Genome ComparisonBIBM'11: Bioinformatics and Biomedicine, Nov 2011, Atlanta, United States. pp.131-134, ⟨10.1109/BIBM.2011.96⟩
Conference papers
lirmm-00659473v1
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A solution to index large set of short readsseqBi11 - Workshop Algorithmique, combinatoire du texte et applications en bio-informatique, 2011, Rennes, France
Conference papers
hal-00560731v1
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CRAC: A multi-purpose program to analyse large read collectionsAnalyse bio-informatique des données NGS, Dec 2011, Institut Pasteur de Lille, France
Conference papers
lirmm-00832549v1
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Novel Definition and Algorithm for Chaining Fragments with Proportional OverlapsRECOMB-CG: Comparative Genomics, Oct 2010, Ottawa, Canada. pp.161-172, ⟨10.1007/978-3-642-16181-0_14⟩
Conference papers
lirmm-00527915v1
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An integrated approach to read analysisLIX Bioinformatics Colloquium 2010, Nov 2010, Ecole Polytechnique, Palaiseau, France
Conference papers
lirmm-00832548v1
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Estimation of Sequence Errors and Prediction Capacity in Transcriptomic and DNA-Protein Interaction AssaysSMPGD'09: Statistical Methods for Post-genomic Data Workshop, Jan 2009, Paris, France. pp.3
Conference papers
lirmm-00375005v1
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Estimation of Sequence Errors and Prediction Capacity in Transcriptomic and DNA-Protein Interaction AssaysJournée Thématique : Nouveaux Séquenceurs (NGS), Apr 2009, Rennes, France
Conference papers
lirmm-00375010v1
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Investigating the transcriptomic repertoire based on High Throughput Sequencing dataColloque 2009 du GDR de Bioinformatique Moléculaire, Nov 2009, Paris, France
Conference papers
lirmm-00833124v1
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Ehrlichia Ruminantium Genome Segmentations Reveal Novel Homologous GenesISCB Africa ASBCB Joint Conference on Bioinformatics of Infectious Diseases, Nov 2009, Bamako, Mali
Conference papers
lirmm-00491362v1
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MPSCAN: Fast Localisation of Multiple Reads in GenomesWABI: Workshop on Algorithms in Bioinformatics, Sep 2009, Philadelphie, United States. pp.246-260, ⟨10.1007/978-3-642-04241-6_21⟩
Conference papers
lirmm-00407173v1
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Improved Sensitivity And Reliability Of Anchor Based Genome AlignmentJOBIM 2009 - 10es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2009, Nantes, France. pp.31-36
Conference papers
lirmm-00407215v1
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Improved sensitivity and reliability of anchor based genome alignmentJOBIM - Journées Ouvertes en Biologie Informatique Mathématiques2009 - Nantes :, Jun 2009, Nantes, France. 259 p
Conference papers
hal-02751358v1
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Combining SAGE Tags to Predict Genomic Transcribed RegionsJOBIM 2008 - 9es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2008, Lille, France. pp.141-146
Conference papers
lirmm-00343895v1
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Evolutionary Process of a Tetranucleotide Microsatellite Locus in AcipenseriformsMIEP: Mathematics and Informatics in Evolution and Phylogeny, Jun 2008, St Martin de Londres, France. pp.20-21
Conference papers
lirmm-00345813v1
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Evolutionary Dynamics of a Locus of Fertility Restoration in PlantsJOBIM 2008 - 9es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2008, Lille, France. pp.273-274
Conference papers
lirmm-00343902v1
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Species Wide Distribution of Highly Polymorphic Minisatellite Markers Suggests Past and Present Genetic Exchanges Among House Mouse SubspeciesFourth Indo-French Bioinformatics Meeting, Nov 2007, Port-Camargue, France
Conference papers
lirmm-00194062v1
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Analysis of four polymorphic minisatellites suggests frequent genetic exchanges among House Mouse subspeciesJOBIM 2007 - 8es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2007, Marseille, France. pp.123-124
Conference papers
lirmm-00195503v1
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Tandem Repeats AnalysisSouthern African Bioinformatics Workshop, Jan 2007, Johannesburg, South Africa. pp.2
Conference papers
lirmm-00193478v1
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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
Conference papers
lirmm-00203886v1
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A new type of Hidden Markov Models to predict complex domain architecture in protein sequencesJOBIM 2007 - 8es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2007, Marseille, France. pp.97-102
Conference papers
lirmm-00195493v1
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Minisatellite Markers Reveals Frequent Genetic Exchanges among House Mouse SubspeciesRencontres ALPHY - Génomique Evolutive, Bioinformatique, Alignement et Phylogénie, Feb 2007, Montpellier, France. pp.1
Conference papers
lirmm-00195524v1
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Distribution of very short microsatellites are not consistent with a neutral model of apparition by substitutionConférences Jacque-Monod: "Evolutionary Genomics", May 2007, Roscoff, France
Conference papers
hal-02756290v1
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On the Detection of Recombination in Minisatellite DataFirst Southern African Bioinformatics Workshop, Jan 2007, Johannesburg, South-Africa, pp.25-32
Conference papers
lirmm-00193849v1
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L'analyse de marqueurs minisatellites variables suggèrent de fréquents échanges génétiques entre sous-espèces de la souris communeBioinformatique, Modélisation des Systèmes Biologiques, Oct 2007, Paris, France
Conference papers
lirmm-00193841v1
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Transcriptome annotation using tandem SAGE tagsRéunion satellite "Transcriptome et bioinformatique", Jul 2007, Marseille, France. pp.8
Conference papers
lirmm-00203923v1
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Combinatorics of Periods in StringsWorkshop on Algorithms on Words, Mar 2007, Turku, Finland. pp.43-44
Conference papers
lirmm-00193520v1
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Detecting microsatellites within genomes: no exact solution?Integrative Post-Genomics, Nov 2006, Lyon, pp.27
Conference papers
lirmm-00120181v1
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Tiling an Interval of the Discrete LineCPM: Combinatorial Pattern Matching, Jul 2006, Barcelona, Spain. pp.117-128, ⟨10.1007/11780441_12⟩
Conference papers
lirmm-00120188v1
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A new type of Hidden Markov Models to predict complex motif organization in protein sequencesIntegrative Post-Genomics, 2006, Lyon, pp.43
Conference papers
lirmm-00120171v1
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Human Transcriptome Annotation using Tandem SAGE TagsIntegrative Post-Genomics, Nov 2006, Lyon, France. pp.39
Conference papers
lirmm-00120164v1
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Modular Data Compression to Optimally Locate Regular Segments in Sequences. Application to DNA Sequence AnalysisIT'05: 26th Symposium on Information Theory in the Benelux, May 2005, Bruxelles (Belgique), pp.105-112
Conference papers
lirmm-00106467v1
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Hardness of Optimal Spaced Seed DesignCPM: Combinatorial Pattern Matching, Jun 2005, Jeju City, South Korea. pp.144-155, ⟨10.1007/11496656_13⟩
Conference papers
lirmm-00106448v1
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Analyse des génomes: Quels enjeux algorithmiques ?Rencontres des ASTI : Sciences et Technologies de l'Information, Oct 2005
Conference papers
lirmm-00106555v1
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Formation of the Arabidopsis Pentatricopeptide Repeat (PPR) Protein FamilyJOBIM 2005 - 6es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2005, Lyon, France. pp.291-298
Conference papers
lirmm-00106048v1
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Comparaison de Séquences avec Amplifications et ContractionsROADEF 2003 - 4e Congrès de la Société Française de Recherche Opérationnelle et d'Aide à la Décision, 2003, Avignon, France. pp.169-170
Conference papers
lirmm-00269459v1
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Complexities of the Centre and Median String ProblemsCPM: Combinatorial Pattern Matching, Jun 2003, Morelia, Mexico. pp.315-327
Conference papers
lirmm-00269556v1
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Comparison of MinisatellitesRECOMB 2002 - 6th International Conference on Computational Molecular Biology, Apr 2002, Whashington, DC, United States. pp.67-76, ⟨10.1145/565196.565205⟩
Conference papers
lirmm-00090351v1
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Comparaison de MinisatellitesRéunion Annuelle du Groupe de Génétique et Biologie des Populations, Aug 2002, Montpellier, France. pp.128
Conference papers
lirmm-00269317v1
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Histoires de Duplication et Répétitions en TandemALBIO, Montpellier, France. pp.P nd
Conference papers
lirmm-00191527v1
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Histoires de Duplication et Répétitions en TandemALBIO, Montpellier (France), France. pp.P nd
Conference papers
lirmm-00269427v1
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Comparaison de MinisatellitesJOBIM 2002 - 3es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2002, St Malo, France. pp.261-262
Conference papers
lirmm-00268469v1
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Purification Process Of Nascent DNAUnited States, Patent n° : US 61/238 315 - WO2011023827 (A1). 2011, pp.N/A
Patents
lirmm-00832553v1
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Purification Process Of Nascent DNAUnited States, Patent n° : US 61/238 315 - WO2011023827 (A1). 2010
Patents
hal-03102676v1
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A linear time algorithm for Shortest Cyclic Cover of Strings[Research Report] IBC; LIRMM. 2015
Reports
lirmm-01240278v1
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3-Shortest Superstring is 2-approximable by a greedy algorithm[Research Report] RR-14009, LIRMM. 2014
Reports
lirmm-01070596v1
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From Indexing Data Structures to de Bruijn Graphs[Research Report] RR-14004, LIRMM. 2014
Reports
lirmm-00950983v2
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Approximation of greedy algorithms for Max-ATSP, Maximal Compression, and Shortest Cyclic Cover of StringsRR-14001, 2013, pp.12
Reports
lirmm-00932660v1
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Tiling an Interval of the Discrete Line05019, 2005, pp.10
Reports
lirmm-00106677v1
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Longest Common Subsequence Problem for Unoriented and Cyclic Strings[Research Report] 04003, LIRMM. 2004, pp.12
Reports
lirmm-00109196v1
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Actes de la Réunion des Actions Spécifiques "Algorithmes et Séquences" et Indexation de Texte et Découverte de Motifs"03032, 2003, pp.15
Reports
lirmm-00191958v1
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Algorithmic Aspects of Tandem Repeats Evolution03017, 2003, pp.P nd
Reports
lirmm-00269557v1
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