Eric Rivals

154
Documents

Présentation

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

Publications

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Algorithms to reconstruct past indels: the deletion-only parsimony problem

Jordan Moutet , Eric Rivals , Fabio Pardi

PLoS Computational Biology, 2025, 21 (7), pp.e1012585. ⟨10.1371/journal.pcbi.1012585⟩

Article dans une revue lirmm-05212128v1
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Convergence of the Number of Period sets in Strings

Eric Rivals , Michelle Sweering , Pengfei Wang

Algorithmica, 2025, 87 (5), pp.690-711. ⟨10.1007/s00453-025-01295-y⟩

Article dans une revue lirmm-05393312v1
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Targeting transcription-replication conflicts using G-quadruplexes stabilizers in multiple myeloma

Laure Dutrieux , Sara Ovejero , Antoine Guillemin , Miss Leriem Zellagui , Elke de Bruyne et al.

Blood Neoplasia, 2025, 2 (2), pp.100072. ⟨10.1016/j.bneo.2025.100072⟩

Article dans une revue hal-05343640v1
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Mass Spectrometry-Based Pipeline for Identifying RNA Modifications Involved in a Functional Process: Application to Cancer Cell Adaptation

Amandine Amalric , Aurore Attina , Amandine Bastide , Marion Buffard , Stéphanie Mateus et al.

Analytical Chemistry, 2024, 96 (5), pp.1825-1833. ⟨10.1021/acs.analchem.3c02635⟩

Article dans une revue hal-04430022v1
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Computing Phylo-k-mers

Nikolai Romashchenko , Benjamin Linard , Eric Rivals , Fabio Pardi

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023, 20 (5), pp.2889-2897. ⟨10.1109/TCBB.2023.3278049⟩

Article dans une revue lirmm-03778953v2
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FT-GPI, a highly sensitive and accurate predictor of GPI-anchored proteins, reveals the composition and evolution of the GPI proteome in Plasmodium species

Lena M. Sauer , Rodrigo Cánovas , Daniel Barry Roche , Hosam Shams-Eldin , Patrice Ravel et al.

Malaria Journal, 2023, 22 (1), pp.27-46. ⟨10.1186/s12936-022-04430-0⟩

Article dans une revue lirmm-03962752v1
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Physical modeling of ribosomes along messenger RNA: estimating kinetic rates from ribosome profiling experiments with a ballistic model

Carole Chevalier , Jerome Dorignac , Yahaya Ibrahim , Armelle Choquet , Alexandre David et al.

PLoS Computational Biology, 2023, 19 (10), pp.e1011522. ⟨10.1371/journal.pcbi.1011522⟩

Article dans une revue hal-03832368v1
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EPIK: Precise and scalable evolutionary placement with informative k-mers

Nikolai Romashchenko , Benjamin Linard , Fabio Pardi , Eric Rivals

Bioinformatics, 2023, 39 (12), pp. btad692. ⟨10.1093/bioinformatics/btad692⟩

Article dans une revue lirmm-04308461v1
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dipwmsearch: a python package for searching di-PWM motifs

Marie Mille , Julie Ripoll , Bastien Cazaux , Eric Rivals

Bioinformatics, 2023, 39 (4), pp.btad141. ⟨10.1093/bioinformatics/btad141⟩

Article dans une revue lirmm-03834008v1
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The multifaceted functions of the Fat mass and Obesity-associated protein (FTO) in normal and cancer cells

Sébastien Relier , Eric Rivals , Alexandre David

RNA Biology, 2022, 19 (1), pp.132-142. ⟨10.1080/15476286.2021.2016203⟩

Article dans une revue hal-03545725v1
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Alteration of ribosome function upon 5-fluorouracil treatment favors cancer cell drug-tolerance

Gabriel Therizols , Zeina Bash-Imam , Baptiste Panthu , Christelle Machon , Anne Vincent et al.

Nature Communications, 2022, 13 (1), pp.173-187. ⟨10.1038/s41467-021-27847-8⟩

Article dans une revue hal-03523177v2
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Multivariate Analysis of RNA Chemistry Marks Uncovers Epitranscriptomics-Based Biomarker Signature for Adult Diffuse Glioma Diagnostics

Sébastien Relier , Amandine Amalric , Aurore Attina , Izoudine Blaise Koumare , Valérie Rigau et al.

Analytical Chemistry, 2022, 94 (35), pp.11967-11972. ⟨10.1021/acs.analchem.2c01526⟩

Article dans une revue lirmm-03761119v1
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FTO-mediated cytoplasmic m6Am demethylation adjusts stem-like properties in colorectal cancer cell

Sébastien Relier , Julie Ripoll , Hélène Guillorit , Amandine Amalric , Cyrinne Achour et al.

Nature Communications, 2021, 12 (1), pp.1716. ⟨10.1038/s41467-021-21758-4⟩

Article dans une revue hal-03178788v2
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Rapid screening and detection of inter-type viral recombinants using phylo- $k$ -mers

Guillaume E. Scholz , Benjamin Linard , Nikolai Romashchenko , Eric Rivals , Fabio Pardi

Bioinformatics, 2020, pp.#btaa1020. ⟨10.1093/bioinformatics/btaa1020⟩

Article dans une revue hal-03094833v1
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PEWO: a collection of workflows to benchmark phylogenetic placement

Benjamin Linard , Nikolai Romashchenko , Fabio Pardi , Eric Rivals

Bioinformatics, 2020, 36 (21), pp.5264-5266. ⟨10.1093/bioinformatics/btaa657⟩

Article dans une revue hal-02905244v1
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Hierarchical Overlap Graph

Bastien Cazaux , Eric Rivals

Information Processing Letters, 2020, 155, pp.#105862. ⟨10.1016/j.ipl.2019.105862⟩

Article dans une revue lirmm-01674319v2
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AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees

Bastien Cazaux , Guillaume Castel , Eric Rivals

Bioinformatics, 2019, 35 (17), pp.3163-3165. ⟨10.1093/bioinformatics/btz011⟩

Article dans une revue lirmm-01980994v1
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Linking indexing data structures to de Bruijn graphs: Construction and update

Bastien Cazaux , Thierry Lecroq , Eric Rivals

Journal of Computer and System Sciences, 2019, 104, pp.165-183. ⟨10.1016/j.jcss.2016.06.008⟩

Article dans une revue lirmm-01617207v1
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NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region

Andrew Oldfield , Telmo Henriques , Dhirendra Kumar , Adam B Burkholder , Senthilkumar Cinghu et al.

Nature Communications, 2019, 10 (1), pp.3072. ⟨10.1038/s41467-019-10905-7⟩

Article dans une revue lirmm-02383488v1
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Computational pan-genomics: status, promises and challenges

Tobias Marschall , Manja Marz , Thomas Abeel , Louis Dijkstra , Bas E. Dutilh et al.

Briefings in Bioinformatics, 2018, 19 (1), pp.118-135. ⟨10.1093/bib/bbw089⟩

Article dans une revue hal-01390478v1
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Relationship between superstring and compression measures: New insights on the greedy conjecture

Bastien Cazaux , Eric Rivals

Discrete Applied Mathematics, 2018, 245, pp.59-64. ⟨10.1016/j.dam.2017.04.017⟩

Article dans une revue lirmm-01800340v1
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The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies

Xavier Argout , Guillaume Martin , Gaetan Droc , Olivier Fouet , Karine Labadie et al.

BMC Genomics, 2017, 18 (1), pp.730-739. ⟨10.1186/s12864-017-4120-9⟩

Article dans une revue lirmm-01612258v1
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Population genomics of picophytoplankton unveils novel chromosome hypervariability

Romain Blanc-Mathieu , Marc Krasovec , Maxime Hebrard , Sheree Yau , Elodie Desgranges et al.

Science Advances , 2017, 3 (7), pp.e1700239. ⟨10.1126/sciadv.1700239⟩

Article dans une revue lirmm-01842137v1
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Accurate self-correction of errors in long reads using de Bruijn graphs

Leena Salmela , Riku Walve , Eric Rivals , Esko Ukkonen

Bioinformatics, 2017, 33 (6), pp.799-806. ⟨10.1093/bioinformatics/btw321⟩

Article dans une revue lirmm-01385006v1
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Ribo-seq enlightens codon usage bias

Damien Paulet , Alexandre David , Eric Rivals

DNA Research, 2017, 24 (3), pp.303-210. ⟨10.1093/dnares/dsw062⟩

Article dans une revue lirmm-01610054v1
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Functional analysis of Plasmodium falciparum subpopulations associated with artemisinin resistance in Cambodia

Ankit Dwivedi , Christelle Reynes , Axel Kuehn , Daniel Barry Roche , Nimol Khim et al.

Malaria Journal, 2017, 16 (1), pp.493. ⟨10.1186/s12936-017-2140-1⟩

Article dans une revue inserm-01672315v1
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De novo assembly of viral quasispecies using overlap graphs

Jasmijn A Baaijens , Amal Zine El Aabidine , Eric Rivals , Alexander Schönhuth

Genome Research, 2017, 27 (5), pp.835-848. ⟨10.1101/gr.215038.116⟩

Article dans une revue lirmm-01693168v1
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A linear time algorithm for Shortest Cyclic Cover of Strings

Bastien Cazaux , Eric Rivals

Journal of Discrete Algorithms, 2016, 37, pp.56-67. ⟨10.1016/j.jda.2016.05.001⟩

Article dans une revue lirmm-01525995v1

The power of greedy algorithms for approximating Max-ATSP, Cyclic Cover, and superstrings

Bastien Cazaux , Eric Rivals

Discrete Applied Mathematics, 2016, 212, pp.48-60. ⟨10.1016/j.dam.2015.06.003⟩

Article dans une revue lirmm-01286943v1
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Read mapping on de Bruijn graphs

Antoine Limasset , Bastien Cazaux , Eric Rivals , Pierre Peterlongo

BMC Bioinformatics, 2016, 17 (1), ⟨10.1186/s12859-016-1103-9⟩

Article dans une revue hal-01349636v1
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Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

Yvan Le Bras , Olivier Collin , Cyril Monjeaud , Vincent Lacroix , Eric Rivals et al.

GigaScience, 2016, 5 (1), ⟨10.1186/s13742-015-0105-2⟩

Article dans une revue hal-01280238v1
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YOC, A new strategy for pairwise alignment of collinear genomes

Raluca Uricaru , Célia Michotey , Hélène Chiapello , Eric Rivals

BMC Bioinformatics, 2015, 16 (1), pp.16:111. ⟨10.1186/s12859-015-0530-3⟩

Article dans une revue lirmm-01170968v1
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The ancient Yakuts: a population genetic enigma

Christine Keyser , Clemence Hollard , Angela Gonzalez , Jean-Luc Fausser , Eric Rivals et al.

Philosophical Transactions of the Royal Society B: Biological Sciences, 2015, Discussion meeting issue ‘Ancient DNA: the first three decades’, 370 (1660), pp.20130385. ⟨10.1098/rstb.2013.0385⟩

Article dans une revue lirmm-01170676v1
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Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome

Nicolas Philippe , Elias Bou Samra , Anthony Boureux , Alban Mancheron , Florence Rufflé et al.

Nucleic Acids Research, 2014, 42 (5), pp.2820-2832. ⟨10.1093/nar/gkt1300⟩

Article dans une revue lirmm-01233107v1
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An improved genome of the model marine alga [i]Ostreococcus tauri[/i] unfolds by assessing Illumina [i]de novo[/i] assemblies

Romain Blanc Mathieu , Bram Verhelst , Evelyne Derelle , Stephane Rombauts , Francois-Yves Bouget et al.

BMC Genomics, 2014, 15, pp.1-11. ⟨10.1186/1471-2164-15-1103⟩

Article dans une revue hal-01130514v1
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Reverse engineering of compact suffix trees and links: A novel algorithm

Bastien Cazaux , Eric Rivals

Journal of Discrete Algorithms, 2014, StringMasters 2012 & 2013 Special Issue (Volume 1), 28, pp.9-22. ⟨10.1016/j.jda.2014.07.002⟩

Article dans une revue lirmm-01082098v1
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Diversity of Prdm9 Zinc Finger Array in Wild Mice Unravels New Facets of the Evolutionary Turnover of this Coding Minisatellite

Jérôme Buard , Eric Rivals , Denis Dunoyer de Segonzac , Charlotte Garres , Pierre Caminade et al.

PLoS ONE, 2014, 9 (1), pp.e85021. ⟨10.1371/journal.pone.0085021⟩

Article dans une revue hal-00937288v1
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LoRDEC: accurate and efficient long read error correction

Leena Salmela , Eric Rivals

Bioinformatics, 2014, 30 (24), pp.3506-3514. ⟨10.1093/bioinformatics/btu538⟩

Article dans une revue lirmm-01100451v1
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CRAC: an integrated approach to the analysis of RNA-seq reads

Nicolas Philippe , Mikaël Salson , Thérèse Commes , Eric Rivals

Genome Biology, 2013, 14 (3), pp.R30. ⟨10.1186/gb-2013-14-3-r30⟩

Article dans une revue inserm-00850972v1
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A Scalable Indexing Solution to Mine Huge Genomic Sequence Collections

Eric Rivals , Nicolas Philippe , Mikael Salson , Martine Léonard , Thérèse Commes et al.

ERCIM News, 2012, 2012 (89), pp.20-21

Article dans une revue lirmm-00712653v1
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A combinatorial and integrated method to analyse RNA-seq reads

Nicolas Philippe , Mikael Salson , Thérèse Commes , Eric Rivals

EMBnet.journal, 2011, 17 (Supplement B), pp.1. ⟨10.14806/ej.17.B.290⟩

Article dans une revue lirmm-00757979v1
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Novel definition and algorithm for chaining fragments with proportional overlaps

Raluca Uricaru , Alban Mancheron , Eric Rivals

Journal of Computational Biology, 2011, 18 (9), pp.1141-1154. ⟨10.1089/cmb.2011.0126⟩

Article dans une revue lirmm-00834143v1
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Genome-Scale Analysis of Metazoan Replication Origins Reveals their Organization in Specific but Flexible Sites Defined by Conserved Features

Christelle Cayrou , Philippe Coulombe , Alice Vigneron , Slavica Stanojcic , Olivier Ganier et al.

Genome Research, 2011, 21 (9), pp.1438-1449. ⟨10.1101/gr.121830.111⟩

Article dans une revue lirmm-00631491v1
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Digital gene expression data, cross-species conservation and noncoding RNA

Nicolas Philippe , Florence Ruffle , Elias Bou Samra , Anthony Boureux , Thérèse Commes et al.

EMBnet.journal, 2011, 17 (Supplement B), pp.1. ⟨10.14806/ej.17.B.288⟩

Article dans une revue lirmm-00757989v1
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Evolutionary Process of a Tetranucleotide Microsatellite Locus in Acipenseriformes

Zhaojun Shao , Eric Rivals , Na Zhao , Sovan Lek , Jianbo Chang et al.

Journal of Genetics, 2011, 90 (2), pp.217-227. ⟨10.1007/s12041-011-0055-0⟩

Article dans une revue istex lirmm-00618055v1
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Read indexing

Nicolas Philippe , Mikael Salson , Thérèse Commes , Thierry Lecroq , Martine Léonard et al.

EMBnet.journal, 2011, 17 (Supplement B), pp.1. ⟨10.14806/ej.17.B.289⟩

Article dans une revue lirmm-00757983v1
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An Alternative Approach to Multiple Genome Comparison

Alban Mancheron , Raluca Uricaru , Eric Rivals

Nucleic Acids Research, 2011, 39 (15), pp.e101. ⟨10.1093/nar/gkr177⟩

Article dans une revue lirmm-00620931v1
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Querying Large Read Collections in Main Memory: A Versatile data Structure

Nicolas Philippe , Mikael Salson , Thierry Lecroq , Martine Léonard , Thérèse Commes et al.

BMC Bioinformatics, 2011, 12, pp.242-258. ⟨10.1186/1471-2105-12-242⟩

Article dans une revue lirmm-00632958v1
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Sequence Analysis of Two Alleles Reveals That Intra-and Intergenic Recombination Played a Role in the Evolution of the Radish Fertility Eestorer (Rfo)

José R. Hernández Mora , Eric Rivals , Hakim Mireau , Françoise Budar

BMC Plant Biology, 2010, 10 (n° article:35), pp.35. ⟨10.1186/1471-2229-10-35⟩

Article dans une revue lirmm-00490860v1
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DNA Slippage Occurs at Microsatellite Loci without Minimal Threshold Length in Humans: A Comparative Genomic Approach

Sébastien Leclercq , Eric Rivals , Philippe Jarne

Genome Biology and Evolution, 2010, 2, pp.325-335. ⟨10.1093/gbe/evq023⟩

Article dans une revue hal-00493962v1
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Reliable Bacterial Genome Comparison Tools

Eric Rivals , Alban Mancheron , Raluca Uricaru

ERCIM News, 2010, 82, pp.017-018

Article dans une revue lirmm-00511509v1

Estimation of sequence errors and capacity of genomic annotation in transcriptomic and DNA-protein interaction assays based on next generation sequencers

Nicolas Philippe , Anthony Boureux , Laurent Brehelin , Jorma Tarhio , Thérèse Commes et al.

Cellular Oncology, 2009, 31 (2), pp.145-146

Article dans une revue lirmm-00416012v1
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Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity

Nicolas Philippe , Anthony Boureux , Laurent Brehelin , Jorma Tarhio , Thérèse Commes et al.

Nucleic Acids Research, 2009, 37 (15 e104), pp.11. ⟨10.1093/nar/gkp492⟩

Article dans une revue lirmm-00415899v1
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Hardness of Optimal Spaced Seed Design

François Nicolas , Eric Rivals

Journal of Computer and System Sciences, 2008, 74 (5), pp.831-849. ⟨10.1016/j.jcss.2007.10.001⟩

Article dans une revue lirmm-00194171v1
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Longest Common Subsequence Problem for Unoriented and Cyclic Strings

François Nicolas , Eric Rivals

Theoretical Computer Science, 2007, 370 (1-3), pp.1-18. ⟨10.1016/j.tcs.2006.10.002⟩

Article dans une revue lirmm-00120152v1
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Species-wide distribution of highly polymorphic minisatellite markers suggests past and present genetic exchanges among House Mouse subspecies

François Bonhomme , Eric Rivals , Annie Orth , Gemma R Grant , Alec J Jeffreys et al.

Genome Biology, 2007, 8, pp.R80. ⟨10.1186/gb-2007-8-5-r80⟩

Article dans une revue lirmm-00193283v1
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Detection of Recombination in Variable Number Tandem Repeat Sequences

Ezekiel Adebiyi , Eric Rivals

South African Computer Journal, 2007, 39, pp.1-7

Article dans une revue lirmm-00194110v1
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Transcriptome Annotation using Tandem SAGE Tags

Eric Rivals , Anthony Boureux , Mireille Lejeune , Florence Ottones , Oscar Pecharromàn Pérez et al.

Nucleic Acids Research, 2007, 35 (17), pp.e108. ⟨10.1093/nar/gkm495⟩

Article dans une revue lirmm-00193291v1
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Detecting Microsatellites within Genomes: Significant Variation Among Algorithms

Sébastien Leclercq , Eric Rivals , Philippe Jarne

BMC Bioinformatics, 2007, 8 (1), pp.125. ⟨10.1186/1471-2105-8-125⟩

Article dans une revue lirmm-00193269v1

Formation of the Arabidopsis Pentatricopeptide Repeat Family

Eric Rivals , Clémence Bruyère , Claire Toffano-Nioche , Alain Lecharny

Plant Physiology, 2006, 141, pp.825-839. ⟨10.1104/pp.106.077826⟩

Article dans une revue lirmm-00109042v1
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A Fast and Specific Alignment Method for Minisatellite Maps

Sèverine Bérard , François Nicolas , Jérome Buard , Olivier Gascuel , Eric Rivals

Evolutionary Bioinformatics, 2006, 2, pp.327-344. ⟨10.1177/117693430600200025⟩

Article dans une revue lirmm-00120145v1

Hardness Results for the Center and Median String Problems under the Weighted and Unweighted Edit Distances

François Nicolas , Eric Rivals

Journal of Discrete Algorithms, 2005, 3 (2-4), pp.390-415. ⟨10.1016/j.jda.2004.08.015⟩

Article dans une revue lirmm-00105320v1
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A Survey on Algorithmic Aspects of Tandem Repeats Evolution

Eric Rivals

International Journal of Foundations of Computer Science, 2004, 15 (2), pp.225-257. ⟨10.1142/S012905410400239X⟩

Article dans une revue lirmm-00108543v1
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STAR: An Algorithm to Search for Tandem Approximate Repeats

Olivier Delgrange , Eric Rivals

Bioinformatics, 2004, 20 (16), pp.2812-2820. ⟨10.1093/bioinformatics/bth335⟩

Article dans une revue lirmm-00108544v1

Combinatorics of Periods in Strings

Eric Rivals , Sven Rahmann

Journal of Combinatorial Theory, Series A, 2003, 104 (1), pp.95-113. ⟨10.1016/S0097-3165(03)00123-7⟩

Article dans une revue istex lirmm-00269554v1

Comparison of Minisatellites

Sèverine Bérard , Eric Rivals

Journal of Computational Biology, 2003, 10 (3-4), pp. 357-372. ⟨10.1145/565196.565205⟩

Article dans une revue lirmm-00269555v1

On the Distribution of the Number of Missing Words in Random Texts

Sven Rahmann , Eric Rivals

Combinatorics, Probability and Computing, 2003, 12 (1), pp.73-87. ⟨10.1017/S0963548302005473⟩

Article dans une revue istex lirmm-00269581v1
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Selection of test instances for string algorithms

Eric Rivals

JOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Université de Bordeaux; Société Française de BioInformatique (SFBI), Jul 2025, Bordeaux & online, France

Communication dans un congrès lirmm-05234210v1
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Algorithms for the enumeration of b-canonical words

Tristan Dubois , Eric Rivals

SeqBIM 2025 - Séquences en Bioinformatique, Informatique et Mathématiques, Université de Nantes, Nov 2025, Nantes, France

Communication dans un congrès lirmm-05392211v1
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Counting Overlapping Pairs of Words

Eric Rivals , Pengfei Wang

COCOON 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⟩

Communication dans un congrès lirmm-05236172v1
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Incremental Computation of the Set of Period Sets

Eric Rivals

SOFSEM 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⟩

Communication dans un congrès lirmm-05388107v1
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Counting overlapping pairs of strings

Eric Rivals , Pengfei Wang

Workshop SeqBIM 2025, IRISA, Univ Rennes, Nov 2024, Rennes, France

Communication dans un congrès lirmm-04831119v1
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Incremental computation of the set of period sets

Eric Rivals

Workshop SeqBIM 2025, IRISA, Nov 2024, Rennes, France

Communication dans un congrès lirmm-04829668v1
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Periodicity of Degenerate Strings

Estéban Gabory , Eric Rivals , Michelle Sweering , Hilde Verbeek , Pengfei Wang

PSC 2023 - 27th Prague Stringology Conference, Aug 2023, Prague, Czech Republic. pp.42-56

Communication dans un congrès lirmm-04777487v1
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Convergence of the number of period sets in strings

Eric Rivals , Michelle Sweering , Pengfei Wang

ICALP 2023 - 50th International Colloquium on Automata, Languages, and Programming, Jul 2023, Paderborn, Germany. pp.100:1-100:14, ⟨10.4230/LIPICS.ICALP.2023.100⟩

Communication dans un congrès lirmm-03780386v1
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Analysis of epitranscriptome for grading of glioma

Eric Rivals

Symposium on Cancer genomics and epitranscriptomics: from the bench to the clinic, Comprehensive Cancer Center (CIC), University of Salamanca, Nov 2022, Salamanca, Spain

Communication dans un congrès lirmm-04287393v1
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A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs

Sangsoo Park , Sung Gwan Park , Bastien Cazaux , Kunsoo Park , Eric Rivals

CPM 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⟩

Communication dans un congrès lirmm-03431830v1
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Efficient Construction of Hierarchical Overlap Graphs

Sung Gwan Park , Bastien Cazaux , Kunsoo Park , Eric Rivals

SPIRE 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⟩

Communication dans un congrès lirmm-03014336v1
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Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length Encoding

Bastien Cazaux , Eric Rivals

CPM 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⟩

Communication dans un congrès lirmm-02382066v1
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High performance text indexing and applications in life sciences

Eric Rivals

UK-France Bilateral International Meeting on High Performance Computing and Biomathematics, Feb 2019, Chicheley, United Kingdom

Communication dans un congrès lirmm-02093450v1

Perspectives and challenges of Computational Pan-Genomics

Eric Rivals

LifeTime UnConference, Centre de Regulació Genòmica (CRG); centro nacional de análisis genómico (CNAG), Jul 2019, Barelone, Spain

Communication dans un congrès lirmm-02388116v1

Computational Pan-Genomics

Eric Rivals

Pangénomique végétale, GIS Biotechnologies Vertes, INRA, Jul 2019, Paris, France

Communication dans un congrès lirmm-02387894v1
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Fast and accurate genome-scale identification of DNA-binding sites

David Martin , Vincent Maillol , Eric Rivals

BIBM 2018 - 12th IEEE International Conference on Bioinformatics and Biomedicine, Dec 2018, Madrid, Spain. pp.201-205, ⟨10.1109/BIBM.2018.8621093⟩

Communication dans un congrès lirmm-01967466v1
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Practical lower and upper bounds for the Shortest Linear Superstring

Bastien Cazaux , Samuel Juhel , Eric Rivals

SEA: Symposium on Experimental Algorithms, Jun 2018, L'Aquilla, Italy. pp.18:1--18:14, ⟨10.4230/LIPIcs.SEA.2018.18⟩

Communication dans un congrès lirmm-01929399v1
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Superstrings with multiplicities

Eric Rivals , Bastien Cazaux

29th Annual Symposium on Combinatorial Pattern Matching (CPM), Qingdao University, Jul 2018, Qingdao, China. pp.21:1-21:16, ⟨10.4230/LIPIcs.CPM.2018.21⟩

Communication dans un congrès lirmm-01843225v1
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Données génomiques massives : applications, enjeux computationnels et perspectives

Eric Rivals

Open Science, Open Access, Open Data et données, Jun 2018, Strasbourg, France

Communication dans un congrès lirmm-01951492v1
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Full Compressed Affix Tree Representations

Rodrigo Cánovas , Eric Rivals

DCC: Data Compression Conference, IEEE, Apr 2017, Snowbird, UT, United States. pp.102-111, ⟨10.1109/DCC.2017.39⟩

Communication dans un congrès lirmm-02093302v1
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Rearrangement Scenarios Guided by Chromatin Structure

Sylvain Pulicani , Pijus Simonaitis , Eric Rivals , Krister M. Swenson

RECOMB-CG: Comparative Genomics, Oct 2017, Barcelona, Spain. pp.141-155, ⟨10.1007/978-3-319-67979-2_8⟩

Communication dans un congrès hal-01791974v1
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Shortest DNA cyclic cover in compressed space

Bastien Cazaux , Rodrigo Cánovas , Eric Rivals

DCC: Data Compression Conference, Mar 2016, Snowbird, UT, United States. pp.536-545, ⟨10.1109/DCC.2016.79⟩

Communication dans un congrès lirmm-01314330v1

A new tool for non-hybrid correction of long noisy reads

Eric Rivals

NGS Symposium, Thomas Sexton, Jul 2016, Illkirch, France

Communication dans un congrès lirmm-01445496v1
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Hybrid and non hybrid error correction for long reads: LoRDEC and LoRMA

Eric Rivals

Colib’read workshop, ANR Colib'read, Nov 2016, Paris, France

Communication dans un congrès lirmm-01446434v1
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Superstring Graph: A New Approach for Genome Assembly

Bastien Cazaux , Gustavo Sacomoto , Eric Rivals

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⟩

Communication dans un congrès lirmm-01446428v1
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LoRDEC: a tool for correcting errors in long sequencing reads

Eric Rivals

Montpellier Omics Days, Université de Montpellier, Master BCD, Feb 2016, Montpellier, France

Communication dans un congrès lirmm-01446431v1
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Construction of a de Bruijn Graph for Assembly from a Truncated Suffix Tree

Bastien Cazaux , Thierry Lecroq , Eric Rivals

LATA: Language and Automata Theory and Applications, Mar 2015, Nice, France. pp.109-120, ⟨10.1007/978-3-319-15579-1_8⟩

Communication dans un congrès hal-01955978v1
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Data Mining et Big Data

Eric Rivals

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

Communication dans un congrès lirmm-01286788v1

Correction of long sequencing reads: a novel approach

Eric Rivals

BIG N2N: Bioinformatics Institute Ghent "From Nucleotides to Networks", Ghent University, Bioinformatics Institute Ghent, May 2015, Gand, Ghent, Belgium

Communication dans un congrès lirmm-01185688v1
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LoRDEC: a tool for correcting errors in long sequencing reads

Eric Rivals

GCB: German Conference on Bioinformatics, University Alliance Ruhr, Sep 2015, Dortmund, Germany

Communication dans un congrès lirmm-01224319v1
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From Indexing Data Structures to de Bruijn Graphs

Bastien Cazaux , Thierry Lecroq , Eric Rivals

CPM: Combinatorial Pattern Matching, Moscow State University, Jun 2014, Moscow, Russia. pp.89-99, ⟨10.1007/978-3-319-07566-2_10⟩

Communication dans un congrès lirmm-01081429v1
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Défis computationnels des séquençage et phénotypage haut débit en science de la vie

Eric Rivals

Journées Big Data - 2ème journées - Principaux Défis, Laboratoire ICube, Nov 2014, Strasbourg, France

Communication dans un congrès lirmm-01176768v1
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Approximation of Greedy Algorithms for Max-ATSP, Maximal Compression, Maximal Cycle Cover, and Shortest Cyclic Cover of Strings

Bastien Cazaux , Eric Rivals

PSC: Prague Stringology Conference, Czech Technical University in Prague, Sep 2014, Prague, Czech Republic. pp.148-161

Communication dans un congrès lirmm-01100683v1

Functional annotation of polymorphisms identified by NGS approaches in P.falciparum

Ankit Dwivedi , Emmanuel Cornillot , Christelle Reynes , Nimol Khim , Didier Menard et al.

SeqBio, Nov 2014, Montpellier, France

Communication dans un congrès lirmm-01397406v1
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Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data

Niko Välimäki , Eric Rivals

ISBRA'2013: International Symposium on Bioinformatics Research and Applications, May 2013, Charlotte, NC, United States. pp.237-248

Communication dans un congrès lirmm-00806103v1
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Building the Assembly De Bruijn Graph from an Implicit Suffix Tree

Eric Rivals

Mini-Workshop on the Storage, Search and Annotation of Multiple Similar Genomes, Dec 2013, Bielefeld, Germany

Communication dans un congrès lirmm-00938959v1

Analysis of genomic data from high throughput sequencing: concepts and basic methods

Eric Rivals

Palaeogenomics Summer School, Oct 2011, Cargese, France

Communication dans un congrès lirmm-00832551v1

A solution to index large set of short reads

Nicolas Philippe , Mikael Salson , Thierry Lecroq , Martine Léonard , Thérèse Commes et al.

seqBi11 - Workshop Algorithmique, combinatoire du texte et applications en bio-informatique, 2011, Rennes, France

Communication dans un congrès hal-00560731v1

CRAC: A multi-purpose program to analyse large read collections

Eric Rivals

Analyse bio-informatique des données NGS, Dec 2011, Institut Pasteur de Lille, France

Communication dans un congrès lirmm-00832549v1
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Approximate Common Intervals in Multiple Genome Comparison

Pierre Riou , Eric Rivals , Annie Chateau

BIBM'11: Bioinformatics and Biomedicine, Nov 2011, Atlanta, United States. pp.131-134, ⟨10.1109/BIBM.2011.96⟩

Communication dans un congrès lirmm-00659473v1
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Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps

Raluca Uricaru , Alban Mancheron , Eric Rivals

RECOMB-CG: Comparative Genomics, Oct 2010, Ottawa, Canada. pp.161-172, ⟨10.1007/978-3-642-16181-0_14⟩

Communication dans un congrès lirmm-00527915v1

An integrated approach to read analysis

Eric Rivals

LIX Bioinformatics Colloquium 2010, Nov 2010, Ecole Polytechnique, Palaiseau, France

Communication dans un congrès lirmm-00832548v1
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Improved sensitivity and reliability of anchor based genome alignment

Raluca Uricaru , Célia Michotey , Laurent Noé , Helene H. Chiapello , Eric Rivals

JOBIM - Journées Ouvertes en Biologie Informatique Mathématiques2009 - Nantes :, Jun 2009, Nantes, France. 259 p

Communication dans un congrès hal-02751358v1
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Investigating the transcriptomic repertoire based on High Throughput Sequencing data

Eric Rivals

Colloque 2009 du GDR de Bioinformatique Moléculaire, Nov 2009, Paris, France

Communication dans un congrès lirmm-00833124v1
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Improved Sensitivity And Reliability Of Anchor Based Genome Alignment

Raluca Uricaru , Célia Michotey , Laurent Noé , Hélène Chiapello , Eric Rivals

JOBIM 2009 - 10es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2009, Nantes, France. pp.31-36

Communication dans un congrès lirmm-00407215v1
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MPSCAN: Fast Localisation of Multiple Reads in Genomes

Eric Rivals , Leena Salmela , Petri Kalsi , Petteri Kiiskinen , Jorma Tarhio

WABI: Workshop on Algorithms in Bioinformatics, Sep 2009, Philadelphie, United States. pp.246-260, ⟨10.1007/978-3-642-04241-6_21⟩

Communication dans un congrès lirmm-00407173v1

Ehrlichia Ruminantium Genome Segmentations Reveal Novel Homologous Genes

Alban Mancheron , Raluca Uricaru , Eric Rivals

ISCB Africa ASBCB Joint Conference on Bioinformatics of Infectious Diseases, Nov 2009, Bamako, Mali

Communication dans un congrès lirmm-00491362v1

Estimation of Sequence Errors and Prediction Capacity in Transcriptomic and DNA-Protein Interaction Assays

Nicolas Philippe , Anthony Boureux , Laurent Brehelin , Jorma Tarhio , Thérèse Commes et al.

SMPGD'09: Statistical Methods for Post-genomic Data Workshop, Jan 2009, Paris, France. pp.3

Communication dans un congrès lirmm-00375005v1

Estimation of Sequence Errors and Prediction Capacity in Transcriptomic and DNA-Protein Interaction Assays

Eric Rivals

Journée Thématique : Nouveaux Séquenceurs (NGS), Apr 2009, Rennes, France

Communication dans un congrès lirmm-00375010v1
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Evolutionary Process of a Tetranucleotide Microsatellite Locus in Acipenseriforms

Eric Rivals , Zhaojun Shao , Patrick Berrebi , Bin Zhu , Na Zhao et al.

MIEP: Mathematics and Informatics in Evolution and Phylogeny, Jun 2008, St Martin de Londres, France. pp.20-21

Communication dans un congrès lirmm-00345813v1
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Evolutionary Dynamics of a Locus of Fertility Restoration in Plants

José R. Hernández Mora , Eric Rivals , Hakim Mireau , Françoise Budar

JOBIM 2008 - 9es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2008, Lille, France. pp.273-274

Communication dans un congrès lirmm-00343902v1
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Combining SAGE Tags to Predict Genomic Transcribed Regions

Eric Rivals , Anthony Boureux , Mireille Lejeune , Florence Ottones , Oscar Pecharromàn Pérez et al.

JOBIM 2008 - 9es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2008, Lille, France. pp.141-146

Communication dans un congrès lirmm-00343895v1
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Combinatorics of Periods in Strings

Eric Rivals

Workshop on Algorithms on Words, Mar 2007, Turku, Finland. pp.43-44

Communication dans un congrès lirmm-00193520v1
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Analysis of four polymorphic minisatellites suggests frequent genetic exchanges among House Mouse subspecies

Eric Rivals , François Bonhomme , Annie Orth , Gemma R Grant , Alec J Jeffreys et al.

JOBIM 2007 - 8es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2007, Marseille, France. pp.123-124

Communication dans un congrès lirmm-00195503v1
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A new type of Hidden Markov Models to predict complex domain architecture in protein sequences

Raluca Uricaru , Laurent Brehelin , Eric Rivals

JOBIM 2007 - 8es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2007, Marseille, France. pp.97-102

Communication dans un congrès lirmm-00195493v1
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Evolutionary Dynamics of the Restorer and a non-restorer Allelic Rfo Locus.

José R. Hernández Mora , Eric Rivals , Hakim Mireau , Françoise Budar

SFBV'07: VIIe Colloque National de la Société Française de Biologie Végétale, Sep 2007, Versailles, France. pp.113

Communication dans un congrès lirmm-00203886v1
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Minisatellite Markers Reveals Frequent Genetic Exchanges among House Mouse Subspecies

Eric Rivals

Rencontres ALPHY - Génomique Evolutive, Bioinformatique, Alignement et Phylogénie, Feb 2007, Montpellier, France. pp.1

Communication dans un congrès lirmm-00195524v1
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L'analyse de marqueurs minisatellites variables suggèrent de fréquents échanges génétiques entre sous-espèces de la souris commune

Eric Rivals

Bioinformatique, Modélisation des Systèmes Biologiques, Oct 2007, Paris, France

Communication dans un congrès lirmm-00193841v1
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On the Detection of Recombination in Minisatellite Data

Eric Rivals , Ezekiel Adebiyi

First Southern African Bioinformatics Workshop, Jan 2007, Johannesburg, South-Africa, pp.25-32

Communication dans un congrès lirmm-00193849v1
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Transcriptome annotation using tandem SAGE tags

Eric Rivals , Anthony Boureux , Mireille Lejeune , Florence Ottones , Oscar Pecharromàn Pérez et al.

Réunion satellite "Transcriptome et bioinformatique", Jul 2007, Marseille, France. pp.8

Communication dans un congrès lirmm-00203923v1

Distribution of very short microsatellites are not consistent with a neutral model of apparition by substitution

Sébastien Leclercq , Philippe Jarne , Eric Rivals

Conférences Jacque-Monod: "Evolutionary Genomics", May 2007, Roscoff, France

Communication dans un congrès hal-02756290v1

Tandem Repeats Analysis

Eric Rivals

Southern African Bioinformatics Workshop, Jan 2007, Johannesburg, South Africa. pp.2

Communication dans un congrès lirmm-00193478v1

Human Transcriptome Annotation using Tandem SAGE Tags

Eric Rivals , Anthony Boureux , Mireille Lejeune , Florence Ottones , Oscar Pecharromàn Pérez et al.

Integrative Post-Genomics, Nov 2006, Lyon, France. pp.39

Communication dans un congrès lirmm-00120164v1

Detecting microsatellites within genomes: no exact solution?

Sébastien Leclercq , Eric Rivals , Philippe Jarne

Integrative Post-Genomics, Nov 2006, Lyon, pp.27

Communication dans un congrès lirmm-00120181v1

A new type of Hidden Markov Models to predict complex motif organization in protein sequences

Raluca Uricaru , Laurent Brehelin , Eric Rivals

Integrative Post-Genomics, 2006, Lyon, pp.43

Communication dans un congrès lirmm-00120171v1
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Tiling an Interval of the Discrete Line

Olivier Bodini , Eric Rivals

CPM: Combinatorial Pattern Matching, Jul 2006, Barcelona, Spain. pp.117-128, ⟨10.1007/11780441_12⟩

Communication dans un congrès lirmm-00120188v1

Formation of the Arabidopsis Pentatricopeptide Repeat (PPR) Protein Family

Eric Rivals , Clémence Bruyère , Claire Toffano-Nioche , Alain Lecharny

JOBIM 2005 - 6es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2005, Lyon, France. pp.291-298

Communication dans un congrès lirmm-00106048v1
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Modular Data Compression to Optimally Locate Regular Segments in Sequences. Application to DNA Sequence Analysis

O. Delgrange , Eric Rivals

IT'05: 26th Symposium on Information Theory in the Benelux, May 2005, Bruxelles (Belgique), pp.105-112

Communication dans un congrès lirmm-00106467v1
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Hardness of Optimal Spaced Seed Design

François Nicolas , Eric Rivals

CPM: Combinatorial Pattern Matching, Jun 2005, Jeju City, South Korea. pp.144-155, ⟨10.1007/11496656_13⟩

Communication dans un congrès lirmm-00106448v1

Analyse des génomes: Quels enjeux algorithmiques ?

Eric Rivals

Rencontres des ASTI : Sciences et Technologies de l'Information, Oct 2005

Communication dans un congrès lirmm-00106555v1

Complexities of the Centre and Median String Problems

François Nicolas , Eric Rivals

CPM: Combinatorial Pattern Matching, Jun 2003, Morelia, Mexico. pp.315-327

Communication dans un congrès lirmm-00269556v1
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Comparaison de Séquences avec Amplifications et Contractions

Sèverine Bérard , Eric Rivals

ROADEF 2003 - 4e Congrès de la Société Française de Recherche Opérationnelle et d'Aide à la Décision, 2003, Avignon, France. pp.169-170

Communication dans un congrès lirmm-00269459v1
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Histoires de Duplication et Répétitions en Tandem

Eric Rivals

ALBIO, Montpellier (France), France. pp.P nd

Communication dans un congrès lirmm-00269427v1
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Comparison of Minisatellites

Sèverine Bérard , Eric Rivals

RECOMB 2002 - 6th International Conference on Computational Molecular Biology, Apr 2002, Whashington, DC, United States. pp.67-76, ⟨10.1145/565196.565205⟩

Communication dans un congrès lirmm-00090351v1

Comparaison de Minisatellites

Sèverine Bérard , Eric Rivals

JOBIM 2002 - 3es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2002, St Malo, France. pp.261-262

Communication dans un congrès lirmm-00268469v1
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Histoires de Duplication et Répétitions en Tandem

Eric Rivals

ALBIO, Montpellier, France. pp.P nd

Communication dans un congrès lirmm-00191527v1

Comparaison de Minisatellites

Sèverine Bérard , Eric Rivals

Réunion Annuelle du Groupe de Génétique et Biologie des Populations, Aug 2002, Montpellier, France. pp.128

Communication dans un congrès lirmm-00269317v1

Purification Process Of Nascent DNA

Marcel Méchali , Philippe Coulombe , C Cayrou , Eric Rivals

United States, Patent n° : US 61/238 315 - WO2011023827 (A1). 2011, pp.N/A

Brevet lirmm-00832553v1

Purification Process Of Nascent DNA

Marcel Méchali , Christelle Cayrou , Philippe Coulombe , Eric Rivals

United States, Patent n° : US 61/238 315 - WO2011023827 (A1). 2010

Brevet hal-03102676v1