Eric Rivals
Présentation
CNRS Research Director & Head of GDR Bioinformatique Moléculaire Education 2005 Habilitation, University of Montpellier 2 1996-1999 Postdoctoral fellow at the Deutsches Krebsforschung Zentrum (Heidelberg) 1993-1996 PhD in Computer Science, University of Lille I
LIRMM - UMR 5506 CNRS & Université de Montpellier
Algorithms for sequence analysis in bioinformatics. Periodicity and repeats.
by Dr. Martin Vingron, group Theoretical BioInformatik
Fast algorithms for similarity search, Development of a gene index
LIFL (Fundamental Computer Science Laboratory of Lille)
Publications
Publications
|
|
Selection of test instances for string algorithmsJOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Université de Bordeaux; Société Française de BioInformatique (SFBI), Jul 2025, Bordeaux & online, France |
|
|
Algorithms for the enumeration of b-canonical wordsSeqBIM 2025 - Séquences en Bioinformatique, Informatique et Mathématiques, Université de Nantes, Nov 2025, Nantes, France |
|
|
Counting Overlapping Pairs of WordsCOCOON 2025 - 31st International Computing and Combinatorics Conference, University of Electronic Science and Technology of China, Aug 2025, Chengdu, China. pp.381-395, ⟨10.1007/978-981-95-0218-9_28⟩ |
|
|
Incremental Computation of the Set of Period SetsSOFSEM 2025 - 50th International Conference on Current Trends in Theory and Practice of Computer Science, Comenius University, Bratislava, Slovakia, Jan 2025, Bratislava, Slovakia. pp.254-268, ⟨10.1007/978-3-031-82697-9_19⟩ |
|
|
Counting overlapping pairs of stringsWorkshop SeqBIM 2025, IRISA, Univ Rennes, Nov 2024, Rennes, France |
|
|
Incremental computation of the set of period setsWorkshop SeqBIM 2025, IRISA, Nov 2024, Rennes, France |
|
|
Periodicity of Degenerate StringsPSC 2023 - 27th Prague Stringology Conference, Aug 2023, Prague, Czech Republic. pp.42-56 |
|
|
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⟩ |
|
|
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 |
|
|
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⟩ |
|
|
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⟩ |
|
|
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⟩ |
|
|
High performance text indexing and applications in life sciencesUK-France Bilateral International Meeting on High Performance Computing and Biomathematics, Feb 2019, Chicheley, United Kingdom |
Perspectives and challenges of Computational Pan-GenomicsLifeTime UnConference, Centre de Regulació Genòmica (CRG); centro nacional de análisis genómico (CNAG), Jul 2019, Barelone, Spain |
|
Computational Pan-GenomicsPangénomique végétale, GIS Biotechnologies Vertes, INRA, Jul 2019, Paris, France |
|
|
|
Fast and accurate genome-scale identification of DNA-binding sitesBIBM 2018 - 12th IEEE International Conference on Bioinformatics and Biomedicine, Dec 2018, Madrid, Spain. pp.201-205, ⟨10.1109/BIBM.2018.8621093⟩ |
|
|
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⟩ |
|
|
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⟩ |
|
|
Données génomiques massives : applications, enjeux computationnels et perspectivesOpen Science, Open Access, Open Data et données, Jun 2018, Strasbourg, France |
|
|
Full Compressed Affix Tree RepresentationsDCC: Data Compression Conference, IEEE, Apr 2017, Snowbird, UT, United States. pp.102-111, ⟨10.1109/DCC.2017.39⟩ |
|
|
Rearrangement Scenarios Guided by Chromatin StructureRECOMB-CG: Comparative Genomics, Oct 2017, Barcelona, Spain. pp.141-155, ⟨10.1007/978-3-319-67979-2_8⟩ |
|
|
Shortest DNA cyclic cover in compressed spaceDCC: Data Compression Conference, Mar 2016, Snowbird, UT, United States. pp.536-545, ⟨10.1109/DCC.2016.79⟩ |
A new tool for non-hybrid correction of long noisy readsNGS Symposium, Thomas Sexton, Jul 2016, Illkirch, France |
|
|
|
Hybrid and non hybrid error correction for long reads: LoRDEC and LoRMAColib’read workshop, ANR Colib'read, Nov 2016, Paris, France |
|
|
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⟩ |
|
|
LoRDEC: a tool for correcting errors in long sequencing readsMontpellier Omics Days, Université de Montpellier, Master BCD, Feb 2016, Montpellier, France |
|
|
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⟩ |
|
|
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 |
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 |
|
|
|
LoRDEC: a tool for correcting errors in long sequencing readsGCB: German Conference on Bioinformatics, University Alliance Ruhr, Sep 2015, Dortmund, Germany |
|
|
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⟩ |
|
|
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 |
|
|
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 |
Functional annotation of polymorphisms identified by NGS approaches in P.falciparumSeqBio, Nov 2014, Montpellier, France |
|
|
|
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 |
|
|
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 |
Analysis of genomic data from high throughput sequencing: concepts and basic methodsPalaeogenomics Summer School, Oct 2011, Cargese, France |
|
A solution to index large set of short readsseqBi11 - Workshop Algorithmique, combinatoire du texte et applications en bio-informatique, 2011, Rennes, France |
|
CRAC: A multi-purpose program to analyse large read collectionsAnalyse bio-informatique des données NGS, Dec 2011, Institut Pasteur de Lille, France |
|
|
|
Approximate Common Intervals in Multiple Genome ComparisonBIBM'11: Bioinformatics and Biomedicine, Nov 2011, Atlanta, United States. pp.131-134, ⟨10.1109/BIBM.2011.96⟩ |
|
|
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⟩ |
An integrated approach to read analysisLIX Bioinformatics Colloquium 2010, Nov 2010, Ecole Polytechnique, Palaiseau, France |
|
|
|
Improved sensitivity and reliability of anchor based genome alignmentJOBIM - Journées Ouvertes en Biologie Informatique Mathématiques2009 - Nantes :, Jun 2009, Nantes, France. 259 p |
|
|
Investigating the transcriptomic repertoire based on High Throughput Sequencing dataColloque 2009 du GDR de Bioinformatique Moléculaire, Nov 2009, Paris, France |
|
|
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 |
|
|
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⟩ |
Ehrlichia Ruminantium Genome Segmentations Reveal Novel Homologous GenesISCB Africa ASBCB Joint Conference on Bioinformatics of Infectious Diseases, Nov 2009, Bamako, Mali |
|
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 |
|
Estimation of Sequence Errors and Prediction Capacity in Transcriptomic and DNA-Protein Interaction AssaysJournée Thématique : Nouveaux Séquenceurs (NGS), Apr 2009, Rennes, France |
|
|
|
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 |
|
|
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 |
|
|
Combining SAGE Tags to Predict Genomic Transcribed RegionsJOBIM 2008 - 9es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2008, Lille, France. pp.141-146 |
|
|
Combinatorics of Periods in StringsWorkshop on Algorithms on Words, Mar 2007, Turku, Finland. pp.43-44 |
|
|
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 |
|
|
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 |
|
|
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 |
|
|
Minisatellite Markers Reveals Frequent Genetic Exchanges among House Mouse SubspeciesRencontres ALPHY - Génomique Evolutive, Bioinformatique, Alignement et Phylogénie, Feb 2007, Montpellier, France. pp.1 |
|
|
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 |
|
|
On the Detection of Recombination in Minisatellite DataFirst Southern African Bioinformatics Workshop, Jan 2007, Johannesburg, South-Africa, pp.25-32 |
|
|
Transcriptome annotation using tandem SAGE tagsRéunion satellite "Transcriptome et bioinformatique", Jul 2007, Marseille, France. pp.8 |
Distribution of very short microsatellites are not consistent with a neutral model of apparition by substitutionConférences Jacque-Monod: "Evolutionary Genomics", May 2007, Roscoff, France |
|
Tandem Repeats AnalysisSouthern African Bioinformatics Workshop, Jan 2007, Johannesburg, South Africa. pp.2 |
|
Human Transcriptome Annotation using Tandem SAGE TagsIntegrative Post-Genomics, Nov 2006, Lyon, France. pp.39 |
|
Detecting microsatellites within genomes: no exact solution?Integrative Post-Genomics, Nov 2006, Lyon, pp.27 |
|
A new type of Hidden Markov Models to predict complex motif organization in protein sequencesIntegrative Post-Genomics, 2006, Lyon, pp.43 |
|
|
|
Tiling an Interval of the Discrete LineCPM: Combinatorial Pattern Matching, Jul 2006, Barcelona, Spain. pp.117-128, ⟨10.1007/11780441_12⟩ |
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 |
|
|
|
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 |
|
|
Hardness of Optimal Spaced Seed DesignCPM: Combinatorial Pattern Matching, Jun 2005, Jeju City, South Korea. pp.144-155, ⟨10.1007/11496656_13⟩ |
Analyse des génomes: Quels enjeux algorithmiques ?Rencontres des ASTI : Sciences et Technologies de l'Information, Oct 2005 |
|
Complexities of the Centre and Median String ProblemsCPM: Combinatorial Pattern Matching, Jun 2003, Morelia, Mexico. pp.315-327 |
|
|
|
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 |
|
|
Histoires de Duplication et Répétitions en TandemALBIO, Montpellier (France), France. pp.P nd |
|
|
Comparison of MinisatellitesRECOMB 2002 - 6th International Conference on Computational Molecular Biology, Apr 2002, Whashington, DC, United States. pp.67-76, ⟨10.1145/565196.565205⟩ |
Comparaison de MinisatellitesJOBIM 2002 - 3es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2002, St Malo, France. pp.261-262 |
|
|
|
Histoires de Duplication et Répétitions en TandemALBIO, Montpellier, France. pp.P nd |
Comparaison de MinisatellitesRéunion Annuelle du Groupe de Génétique et Biologie des Populations, Aug 2002, Montpellier, France. pp.128 |
Purification Process Of Nascent DNAUnited States, Patent n° : US 61/238 315 - WO2011023827 (A1). 2011, pp.N/A |
|
Purification Process Of Nascent DNAUnited States, Patent n° : US 61/238 315 - WO2011023827 (A1). 2010 |