Eric Rivals

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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 Analytical Chemistry, 2024, 96 (5), pp.1825-1833. ⟨10.1021/acs.analchem.3c02635⟩ Article dans une revue hal-04430022v1
	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
	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 PLoS Computational Biology, 2023, 19 (10), pp.e1011522. ⟨10.1371/journal.pcbi.1011522⟩ Article dans une revue hal-03832368v1
	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 Malaria Journal, 2023, 22 (1), pp.27-46. ⟨10.1186/s12936-022-04430-0⟩ Article dans une revue lirmm-03962752v1
	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
	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
	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
	Alteration of ribosome function upon 5-fluorouracil treatment favors cancer cell drug-tolerance Gabriel Therizols , Zeina Bash-Imam , Baptiste Panthu , Christelle Machon , Anne Vincent Nature Communications, 2022, 13 (1), pp.173-187. ⟨10.1038/s41467-021-27847-8⟩ Article dans une revue hal-03523177v1
	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 Analytical Chemistry, 2022, 94 (35), pp.11967-11972. ⟨10.1021/acs.analchem.2c01526⟩ Article dans une revue lirmm-03761119v1
	FTO-mediated cytoplasmic m6Am demethylation adjusts stem-like properties in colorectal cancer cell Sébastien Relier , Julie Ripoll , Hélène Guillorit , Amandine Amalric , Cyrinne Achour Nature Communications, 2021, 12 (1), pp.1716. ⟨10.1038/s41467-021-21758-4⟩ Article dans une revue hal-03178788v2
	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
	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
	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
	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
	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
	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 Nature Communications, 2019, 10 (1), pp.3072. ⟨10.1038/s41467-019-10905-7⟩ Article dans une revue lirmm-02383488v1
	Computational pan-genomics: status, promises and challenges Tobias Marschall , Manja Marz , Thomas Abeel , Louis Dijkstra , Bas E. Dutilh Briefings in Bioinformatics, 2018, 19 (1), pp.118-135. ⟨10.1093/bib/bbw089⟩ Article dans une revue hal-01390478v1
	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
	Population genomics of picophytoplankton unveils novel chromosome hypervariability Romain Blanc-Mathieu , Marc Krasovec , Maxime Hebrard , Sheree Yau , Elodie Desgranges Science Advances , 2017, 3 (7), pp.e1700239. ⟨10.1126/sciadv.1700239⟩ Article dans une revue lirmm-01842137v1
	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
	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
	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 BMC Genomics, 2017, 18 (1), pp.730-739. ⟨10.1186/s12864-017-4120-9⟩ Article dans une revue lirmm-01612258v1
	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
	Functional analysis of Plasmodium falciparum subpopulations associated with artemisinin resistance in Cambodia Ankit Dwivedi , Christelle Reynes , Axel Kuehn , Daniel Barry Roche , Nimol Khim Malaria Journal, 2017, 16 (1), pp.493. ⟨10.1186/s12936-017-2140-1⟩ Article dans une revue inserm-01672315v1
	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
	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
	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 GigaScience, 2016, 5 (1), ⟨10.1186/s13742-015-0105-2⟩ Article dans une revue hal-01280238v1
	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
	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
	The ancient Yakuts: a population genetic enigma Christine Keyser , Clemence Hollard , Angela Gonzalez , Jean-Luc Fausser , Eric Rivals 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
	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 BMC Genomics, 2014, 15, pp.1-11. ⟨10.1186/1471-2164-15-1103⟩ Article dans une revue hal-01130514v1
	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 Nucleic Acids Research, 2014, 42 (5), pp.2820-2832. ⟨10.1093/nar/gkt1300⟩ Article dans une revue lirmm-01233107v1
	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
	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
	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 PLoS ONE, 2014, 9 (1), pp.e85021. ⟨10.1371/journal.pone.0085021⟩ Article dans une revue hal-00937288v1
	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
	A Scalable Indexing Solution to Mine Huge Genomic Sequence Collections Eric Rivals , Nicolas Philippe , Mikael Salson , Martine Léonard , Thérèse Commes ERCIM News, 2012, 2012 (89), pp.20-21 Article dans une revue lirmm-00712653v1
	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
	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 Genome Research, 2011, 21 (9), pp.1438-1449. ⟨10.1101/gr.121830.111⟩ Article dans une revue lirmm-00631491v1
	Digital gene expression data, cross-species conservation and noncoding RNA Nicolas Philippe , Florence Ruffle , Elias Bou Samra , Anthony Boureux , Thérèse Commes EMBnet.journal, 2011, 17 (Supplement B), pp.1. ⟨10.14806/ej.17.B.288⟩ Article dans une revue lirmm-00757989v1
	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
	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
	Querying Large Read Collections in Main Memory: A Versatile data Structure Nicolas Philippe , Mikael Salson , Thierry Lecroq , Martine Léonard , Thérèse Commes BMC Bioinformatics, 2011, 12, pp.242-258. ⟨10.1186/1471-2105-12-242⟩ Article dans une revue lirmm-00632958v1
	Read indexing Nicolas Philippe , Mikael Salson , Thérèse Commes , Thierry Lecroq , Martine Léonard EMBnet.journal, 2011, 17 (Supplement B), pp.1. ⟨10.14806/ej.17.B.289⟩ Article dans une revue lirmm-00757983v1
	Evolutionary Process of a Tetranucleotide Microsatellite Locus in Acipenseriformes Zhaojun Shao , Eric Rivals , Na Zhao , Sovan Lek , Jianbo Chang Journal of Genetics, 2011, 90 (2), pp.217-227. ⟨10.1007/s12041-011-0055-0⟩ Article dans une revue lirmm-00618055v1
	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
	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
	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 Cellular Oncology, 2009, 31 (2), pp.145-146 Article dans une revue lirmm-00416012v1
	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 Nucleic Acids Research, 2009, 37 (15 e104), pp.11. ⟨10.1093/nar/gkp492⟩ Article dans une revue lirmm-00415899v1
	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
	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
	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
	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 Genome Biology, 2007, 8, pp.R80. ⟨10.1186/gb-2007-8-5-r80⟩ Article dans une revue lirmm-00193283v1
	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
	Transcriptome Annotation using Tandem SAGE Tags Eric Rivals , Anthony Boureux , Mireille Lejeune , Florence Ottones , Oscar Pecharromàn Pérez Nucleic Acids Research, 2007, 35 (17), pp.e108. ⟨10.1093/nar/gkm495⟩ Article dans une revue lirmm-00193291v1
	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
	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
	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
	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
	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
	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
	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 lirmm-00269554v1
	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 lirmm-00269581v1

	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
	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
	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
	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
	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
	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
	Fast and accurate genome-scale identification of DNA-binding sites David Martin , Vincent Maillol , Eric Rivals BIBM: Bioinformatics and Biomedicine, Dec 2018, Madrid, Spain. pp.201-205, ⟨10.1109/BIBM.2018.8621093⟩ Communication dans un congrès lirmm-01967466v1
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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 SeqBio, Nov 2014, Montpellier, France Communication dans un congrès lirmm-01397406v1
	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
	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
	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
	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
	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
	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
	A solution to index large set of short reads Nicolas Philippe , Mikael Salson , Thierry Lecroq , Martine Léonard , Thérèse Commes seqBi11 - Workshop Algorithmique, combinatoire du texte et applications en bio-informatique, 2011, Rennes, France Communication dans un congrès hal-00560731v1
	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
	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
	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
	Estimation of Sequence Errors and Prediction Capacity in Transcriptomic and DNA-Protein Interaction Assays Nicolas Philippe , Anthony Boureux , Laurent Brehelin , Jorma Tarhio , Thérèse Commes 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
	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
	Improved Sensitivity And Reliability Of Anchor Based Genome Alignment Raluca Uricaru , Célia Michotey , Laurent Noé , Hélène Chiapello , Eric Rivals JOBIM'09 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2009, Nantes, France. pp.31-36 Communication dans un congrès lirmm-00407215v1
	Evolutionary Process of a Tetranucleotide Microsatellite Locus in Acipenseriforms Eric Rivals , Zhaojun Shao , Patrick Berrebi , Bin Zhu , Na Zhao MIEP: Mathematics and Informatics in Evolution and Phylogeny, Jun 2008, St Martin de Londres, France. pp.20-21 Communication dans un congrès lirmm-00345813v1
	Evolutionary Dynamics of a Locus of Fertility Restoration in Plants José R. Hernández Mora , Eric Rivals , Hakim Mireau , Françoise Budar JOBIM'08 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2008, Lille, France, France. pp.273-274 Communication dans un congrès lirmm-00343902v1
	Comparaison de Minisatellites Sèverine Bérard , Eric Rivals JOBIM'02 : Journées Ouvertes Biologie, Informatique, Mathématiques, St Malo, France, pp.261-262 Communication dans un congrès lirmm-00268469v1
	Combining SAGE Tags to Predict Genomic Transcribed Regions Eric Rivals , Anthony Boureux , Mireille Lejeune , Florence Ottones , Oscar Pecharromàn Pérez JOBIM'08 : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2008, Lille, France, France. pp.141-146 Communication dans un congrès lirmm-00343895v1
	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 JOBIM'07 : Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2007, Marseille, pp.123-124 Communication dans un congrès lirmm-00195503v1
	A new type of Hidden Markov Models to predict complex domain architecture in protein sequences Raluca Uricaru , Laurent Brehelin , Eric Rivals JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jul 2007, Marseille, France. pp.97-102 Communication dans un congrès lirmm-00195493v1
	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
	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
	Tandem Repeats Analysis Eric Rivals Southern African Bioinformatics Workshop, Jan 2007, Johannesburg, South Africa. pp.2 Communication dans un congrès lirmm-00193478v1
	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
	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
	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
	Transcriptome annotation using tandem SAGE tags Eric Rivals , Anthony Boureux , Mireille Lejeune , Florence Ottones , Oscar Pecharromàn Pérez Réunion satellite "Transcriptome et bioinformatique", Jul 2007, Marseille, France. pp.8 Communication dans un congrès lirmm-00203923v1
	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
	Species Wide Distribution of Highly Polymorphic Minisatellite Markers Suggests Past and Present Genetic Exchanges Among House Mouse Subspecies Eric Rivals Fourth Indo-French Bioinformatics Meeting, Nov 2007, Port-Camargue, France Communication dans un congrès lirmm-00194062v1
	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
	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
	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
	Human Transcriptome Annotation using Tandem SAGE Tags Eric Rivals , Anthony Boureux , Mireille Lejeune , Florence Ottones , Oscar Pecharromàn Pérez Integrative Post-Genomics, Nov 2006, Lyon, France. pp.39 Communication dans un congrès lirmm-00120164v1
	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
	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
	Formation of the Arabidopsis Pentatricopeptide Repeat (PPR) Protein Family C. Bruyere , Eric Rivals , A. Lecharny JOBIM: Journées Ouvertes Biologie, Informatique, Mathématiques, Jul 2005, Lyon, France. pp.291-298 Communication dans un congrès lirmm-00106048v1
	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
	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
	Histoires de Duplication et Répétitions en Tandem Eric Rivals ALBIO, Montpellier, France. pp.P nd Communication dans un congrès lirmm-00191527v1
	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
	Histoires de Duplication et Répétitions en Tandem Eric Rivals ALBIO, Montpellier (France), France. pp.P nd Communication dans un congrès lirmm-00269427v1
	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

	A linear time algorithm for Shortest Cyclic Cover of Strings Bastien Cazaux , Eric Rivals [Research Report] IBC; LIRMM. 2015 Rapport lirmm-01240278v1
	From Indexing Data Structures to de Bruijn Graphs Bastien Cazaux , Thierry Lecroq , Eric Rivals [Research Report] RR-14004, LIRMM. 2014 Rapport lirmm-00950983v2
	3-Shortest Superstring is 2-approximable by a greedy algorithm Bastien Cazaux , Eric Rivals [Research Report] RR-14009, LIRMM. 2014 Rapport lirmm-01070596v1
	Approximation of greedy algorithms for Max-ATSP, Maximal Compression, and Shortest Cyclic Cover of Strings Bastien Cazaux , Eric Rivals RR-14001, 2013, pp.12 Rapport lirmm-00932660v1
	Tiling an Interval of the Discrete Line Olivier Bodini , Eric Rivals 05019, 2005, pp.10 Rapport lirmm-00106677v1
	Longest Common Subsequence Problem for Unoriented and Cyclic Strings François Nicolas , Eric Rivals [Research Report] 04003, LIRMM. 2004, pp.12 Rapport lirmm-00109196v1
	Algorithmic Aspects of Tandem Repeats Evolution Eric Rivals 03017, 2003, pp.P nd Rapport lirmm-00269557v1
	Actes de la Réunion des Actions Spécifiques "Algorithmes et Séquences" et Indexation de Texte et Découverte de Motifs" Eric Rivals , Gregory Kucherov , T. Lecroq 03032, 2003, pp.15 Rapport lirmm-00191958v1

Eric Rivals

Présentation

Publications

Mass Spectrometry-Based Pipeline for Identifying RNA Modifications Involved in a Functional Process: Application to Cancer Cell Adaptation

Computing Phylo-k-mers

Physical modeling of ribosomes along messenger RNA: estimating kinetic rates from ribosome profiling experiments with a ballistic model

FT-GPI, a highly sensitive and accurate predictor of GPI-anchored proteins, reveals the composition and evolution of the GPI proteome in Plasmodium species

EPIK: Precise and scalable evolutionary placement with informative $k$-mers

dipwmsearch: a python package for searching di-PWM motifs

The multifaceted functions of the Fat mass and Obesity-associated protein (FTO) in normal and cancer cells

Alteration of ribosome function upon 5-fluorouracil treatment favors cancer cell drug-tolerance

Multivariate Analysis of RNA Chemistry Marks Uncovers Epitranscriptomics-Based Biomarker Signature for Adult Diffuse Glioma Diagnostics

FTO-mediated cytoplasmic m6Am demethylation adjusts stem-like properties in colorectal cancer cell

Hierarchical Overlap Graph

Rapid screening and detection of inter-type viral recombinants using phylo- $k$ -mers

PEWO: a collection of workflows to benchmark phylogenetic placement

AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees

Linking indexing data structures to de Bruijn graphs: Construction and update

NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region

Computational pan-genomics: status, promises and challenges

Relationship between superstring and compression measures: New insights on the greedy conjecture

Population genomics of picophytoplankton unveils novel chromosome hypervariability

Ribo-seq enlightens codon usage bias

Accurate self-correction of errors in long reads using de Bruijn graphs

The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies

De novo assembly of viral quasispecies using overlap graphs

Functional analysis of Plasmodium falciparum subpopulations associated with artemisinin resistance in Cambodia

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

A linear time algorithm for Shortest Cyclic Cover of Strings

Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

Read mapping on de Bruijn graphs

YOC, A new strategy for pairwise alignment of collinear genomes

The ancient Yakuts: a population genetic enigma

An improved genome of the model marine alga [i]Ostreococcus tauri[/i] unfolds by assessing Illumina [i]de novo[/i] assemblies

Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome

LoRDEC: accurate and efficient long read error correction

Reverse engineering of compact suffix trees and links: A novel algorithm

Diversity of Prdm9 Zinc Finger Array in Wild Mice Unravels New Facets of the Evolutionary Turnover of this Coding Minisatellite

CRAC: an integrated approach to the analysis of RNA-seq reads

A Scalable Indexing Solution to Mine Huge Genomic Sequence Collections

Novel definition and algorithm for chaining fragments with proportional overlaps

Genome-Scale Analysis of Metazoan Replication Origins Reveals their Organization in Specific but Flexible Sites Defined by Conserved Features

Digital gene expression data, cross-species conservation and noncoding RNA

A combinatorial and integrated method to analyse RNA-seq reads

An Alternative Approach to Multiple Genome Comparison

Querying Large Read Collections in Main Memory: A Versatile data Structure

Read indexing

Evolutionary Process of a Tetranucleotide Microsatellite Locus in Acipenseriformes

DNA Slippage Occurs at Microsatellite Loci without Minimal Threshold Length in Humans: A Comparative Genomic Approach

Sequence Analysis of Two Alleles Reveals That Intra-and Intergenic Recombination Played a Role in the Evolution of the Radish Fertility Eestorer (Rfo)

Reliable Bacterial Genome Comparison Tools

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

Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity

Hardness of Optimal Spaced Seed Design

Detection of Recombination in Variable Number Tandem Repeat Sequences

Longest Common Subsequence Problem for Unoriented and Cyclic Strings

Species-wide distribution of highly polymorphic minisatellite markers suggests past and present genetic exchanges among House Mouse subspecies

Detecting Microsatellites within Genomes: Significant Variation Among Algorithms

Transcriptome Annotation using Tandem SAGE Tags

A Fast and Specific Alignment Method for Minisatellite Maps

Formation of the Arabidopsis Pentatricopeptide Repeat Family

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

STAR: An Algorithm to Search for Tandem Approximate Repeats

A Survey on Algorithmic Aspects of Tandem Repeats Evolution

Comparison of Minisatellites

Combinatorics of Periods in Strings

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

Convergence of the number of period sets in strings

Analysis of epitranscriptome for grading of glioma

A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs

Efficient Construction of Hierarchical Overlap Graphs

Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length Encoding

High performance text indexing and applications in life sciences

Perspectives and challenges of Computational Pan-Genomics

Computational Pan-Genomics

Fast and accurate genome-scale identification of DNA-binding sites

Practical lower and upper bounds for the Shortest Linear Superstring

Données génomiques massives : applications, enjeux computationnels et perspectives

Superstrings with multiplicities

Rearrangement Scenarios Guided by Chromatin Structure