Eric Rivals - Publications

Univ. Montpellier 2, France 
Transcriptomic, Genomic, Next Generation Sequencer, RNA-Sequencing, Bioinformatic, Cancer,

10/55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Keyser C, Hollard C, Gonzalez A, Fausser JL, Rivals E, Alexeev AN, Riberon A, Crubézy E, Ludes B. The ancient Yakuts: a population genetic enigma. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370: 20130385. PMID 25487336 DOI: 10.1098/rstb.2013.0385  0.56
2014 Blanc-Mathieu R, Verhelst B, Derelle E, Rombauts S, Bouget FY, Carré I, Château A, Eyre-Walker A, Grimsley N, Moreau H, Piégu B, Rivals E, Schackwitz W, Van de Peer Y, Piganeau G. An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies. Bmc Genomics. 15: 1103. PMID 25494611 DOI: 10.1186/1471-2164-15-1103  0.56
2014 Philippe N, Bou Samra E, Boureux A, Mancheron A, Rufflé F, Bai Q, De Vos J, Rivals E, Commes T. Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome. Nucleic Acids Research. 42: 2820-32. PMID 24357408 DOI: 10.1093/nar/gkt1300  0.44
2013 Philippe N, Salson M, Commes T, Rivals E. CRAC: an integrated approach to the analysis of RNA-seq reads. Genome Biology. 14: R30. PMID 23537109 DOI: 10.1186/gb-2013-14-3-r30  0.44
2011 Philippe N, Salson M, Lecroq T, Léonard M, Commes T, Rivals E. Querying large read collections in main memory: a versatile data structure. Bmc Bioinformatics. 12: 242. PMID 21682852 DOI: 10.1186/1471-2105-12-242  0.44
2010 Leclercq S, Rivals E, Jarne P. DNA slippage occurs at microsatellite loci without minimal threshold length in humans: a comparative genomic approach. Genome Biology and Evolution. 2: 325-35. PMID 20624737 DOI: 10.1093/Gbe/Evq023  0.56
2009 Philippe N, Boureux A, Bréhélin L, Tarhio J, Commes T, Rivals E. Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity. Nucleic Acids Research. 37: e104. PMID 19531739 DOI: 10.1093/nar/gkp492  0.44
2007 Rivals E, Boureux A, Lejeune M, Ottones F, Pérez OP, Tarhio J, Pierrat F, Ruffle F, Commes T, Marti J. Transcriptome annotation using tandem SAGE tags. Nucleic Acids Research. 35: e108. PMID 17709346 DOI: 10.1093/nar/gkm495  0.44
2007 Leclercq S, Rivals E, Jarne P. Detecting microsatellites within genomes: significant variation among algorithms. Bmc Bioinformatics. 8: 125. PMID 17442102 DOI: 10.1186/1471-2105-8-125  0.56
2000 Haas SA, Beissbarth T, Rivals E, Krause A, Vingron M. GeneNest: Automated generation and visualization of gene indices Trends in Genetics. 16: 521-523. PMID 12199289 DOI: 10.1016/S0168-9525(00)02116-8  0.56
Low-probability matches
2011 Uricaru R, Mancheron A, Rivals E. Novel definition and algorithm for chaining fragments with proportional overlaps. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1141-54. PMID 21899421 DOI: 10.1089/cmb.2011.0126  0.28
2011 Mancheron A, Uricaru R, Rivals E. An alternative approach to multiple genome comparison. Nucleic Acids Research. 39: e101. PMID 21646341 DOI: 10.1093/nar/gkr177  0.28
2012 Philippe N, Salson M, Commes T, Rivals E. A combinatorial and integrated method to analyse RNA-seq reads Embnet.Journal. 17: 11. DOI: 10.14806/EJ.17.B.290  0.08
2011 Shao ZJ, Rivals E, Zhao N, Lek S, Chang J, Berrebi P. Evolutionary process of a tetranucleotide microsatellite locus in Acipenseriformes. Journal of Genetics. 90: 217-27. PMID 21869470  0.04
2021 Relier S, Ripoll J, Guillorit H, Amalric A, Achour C, Boissière F, Vialaret J, Attina A, Debart F, Choquet A, Macari F, Marchand V, Motorin Y, Samalin E, Vasseur JJ, ... ... Rivals E, et al. FTO-mediated cytoplasmic mA demethylation adjusts stem-like properties in colorectal cancer cell. Nature Communications. 12: 1716. PMID 33741917 DOI: 10.1038/s41467-021-21758-4  0.01
2020 Scholz GE, Linard B, Romashchenko N, Rivals E, Pardi F. Rapid screening and detection of inter-type viral recombinants using Phylo-K-Mers. Bioinformatics (Oxford, England). PMID 33331849 DOI: 10.1093/bioinformatics/btaa1020  0.01
2020 Linard B, Romashchenko N, Pardi F, Rivals E. PEWO: a collection of workflows to benchmark phylogenetic placement. Bioinformatics (Oxford, England). PMID 32697844 DOI: 10.1093/Bioinformatics/Btaa657  0.01
2020 Cazaux B, Rivals E. Hierarchical Overlap Graph Information Processing Letters. 155: 105862. DOI: 10.1016/j.ipl.2019.105862  0.01
2019 Oldfield AJ, Henriques T, Kumar D, Burkholder AB, Cinghu S, Paulet D, Bennett BD, Yang P, Scruggs BS, Lavender CA, Rivals E, Adelman K, Jothi R. NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region. Nature Communications. 10: 3072. PMID 31296853 DOI: 10.1038/S41467-019-10905-7  0.01
2019 Cazaux B, Castel G, Rivals E. AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees. Bioinformatics (Oxford, England). PMID 30649190 DOI: 10.1093/bioinformatics/btz011  0.01
2019 Cazaux B, Lecroq T, Rivals E. Linking indexing data structures to de Bruijn graphs: Construction and update Journal of Computer and System Sciences. 104: 165-183. DOI: 10.1016/J.JCSS.2016.06.008  0.01
2018 Cazaux B, Rivals E. Relationship between superstring and compression measures: New insights on the greedy conjecture Discrete Applied Mathematics. 245: 59-64. DOI: 10.1016/j.dam.2017.04.017  0.01
2017 Dwivedi A, Reynes C, Kuehn A, Roche DB, Khim N, Hebrard M, Milanesi S, Rivals E, Frutos R, Menard D, Mamoun CB, Colinge J, Cornillot E. Functional analysis of Plasmodium falciparum subpopulations associated with artemisinin resistance in Cambodia. Malaria Journal. 16: 493. PMID 29258508 DOI: 10.1186/s12936-017-2140-1  0.01
2017 Argout X, Martin G, Droc G, Fouet O, Labadie K, Rivals E, Aury JM, Lanaud C. The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies. Bmc Genomics. 18: 730. PMID 28915793 DOI: 10.1186/S12864-017-4120-9  0.01
2017 Blanc-Mathieu R, Krasovec M, Hebrard M, Yau S, Desgranges E, Martin J, Schackwitz W, Kuo A, Salin G, Donnadieu C, Desdevises Y, Sanchez-Ferandin S, Moreau H, Rivals E, Grigoriev IV, et al. Population genomics of picophytoplankton unveils novel chromosome hypervariability. Science Advances. 3: e1700239. PMID 28695208 DOI: 10.1126/sciadv.1700239  0.01
2017 Baaijens JA, El Aabidine AZ, Rivals E, Schönhuth A. De novo assembly of viral quasispecies using overlap graphs. Genome Research. PMID 28396522 DOI: 10.1101/gr.215038.116  0.01
2017 Paulet D, David A, Rivals E. Ribo-seq enlightens codon usage bias. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. PMID 28168289 DOI: 10.1093/dnares/dsw062  0.01
2016 Limasset A, Cazaux B, Rivals E, Peterlongo P. Read mapping on de Bruijn graphs. Bmc Bioinformatics. 17: 237. PMID 27306641 DOI: 10.1186/s12859-016-1103-9  0.01
2016 Salmela L, Walve R, Rivals E, Ukkonen E. Accurate self-correction of errors in long reads using de Bruijn graphs. Bioinformatics (Oxford, England). PMID 27273673 DOI: 10.1093/bioinformatics/btw321  0.01
2016 Le Bras Y, Collin O, Monjeaud C, Lacroix V, Rivals É, Lemaitre C, Miele V, Sacomoto G, Marchet C, Cazaux B, Zine El Aabidine A, Salmela L, Alves-Carvalho S, Andrieux A, Uricaru R, et al. Colib'read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads. Gigascience. 5: 9. PMID 26870323 DOI: 10.1186/s13742-015-0105-2  0.01
2016 Cazaux B, Rivals E. A linear time algorithm for Shortest Cyclic Cover of Strings Journal of Discrete Algorithms. 37: 56-67. DOI: 10.1016/j.jda.2016.05.001  0.01
2016 Cazaux B, Rivals E. The power of greedy algorithms for approximating Max-ATSP, Cyclic Cover, and superstrings Discrete Applied Mathematics. 212: 48-60. DOI: 10.1016/j.dam.2015.06.003  0.01
2015 Uricaru R, Michotey C, Chiapello H, Rivals E. YOC, A new strategy for pairwise alignment of collinear genomes. Bmc Bioinformatics. 16: 111. PMID 25885358 DOI: 10.1186/s12859-015-0530-3  0.01
2014 Salmela L, Rivals E. LoRDEC: accurate and efficient long read error correction. Bioinformatics (Oxford, England). 30: 3506-14. PMID 25165095 DOI: 10.1093/bioinformatics/btu538  0.01
2014 Buard J, Rivals E, Dunoyer de Segonzac D, Garres C, Caminade P, de Massy B, Boursot P. Diversity of Prdm9 zinc finger array in wild mice unravels new facets of the evolutionary turnover of this coding minisatellite. Plos One. 9: e85021. PMID 24454780 DOI: 10.1371/journal.pone.0085021  0.01
2014 Cazaux B, Rivals E. Reverse engineering of compact suffix trees and links: A novel algorithm Journal of Discrete Algorithms. 28: 9-22. DOI: 10.1016/j.jda.2014.07.002  0.01
2012 Philippe N, Ruffle F, Bou-Samra E, Boureux A, Commes T, Rivals E. Digital gene expression data, cross-species conservation and noncoding RNA Embnet.Journal. 17: 32. DOI: 10.14806/EJ.17.B.288  0.01
2011 Cayrou C, Coulombe P, Vigneron A, Stanojcic S, Ganier O, Peiffer I, Rivals E, Puy A, Laurent-Chabalier S, Desprat R, Méchali M. Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features. Genome Research. 21: 1438-49. PMID 21750104 DOI: 10.1101/gr.121830.111  0.01
2010 Hernandez Mora JR, Rivals E, Mireau H, Budar F. Sequence analysis of two alleles reveals that intra-and intergenic recombination played a role in the evolution of the radish fertility restorer (Rfo). Bmc Plant Biology. 10: 35. PMID 20178653 DOI: 10.1186/1471-2229-10-35  0.01
2008 Nicolas F, Rivals E. Hardness of optimal spaced seed design Journal of Computer and System Sciences. 74: 831-849. DOI: 10.1016/j.jcss.2007.10.001  0.01
2007 Bonhomme F, Rivals E, Orth A, Grant GR, Jeffreys AJ, Bois PR. Species-wide distribution of highly polymorphic minisatellite markers suggests past and present genetic exchanges among house mouse subspecies. Genome Biology. 8: R80. PMID 17501990 DOI: 10.1186/gb-2007-8-5-r80  0.01
2007 Nicolas F, Rivals E. Longest common subsequence problem for unoriented and cyclic strings Theoretical Computer Science. 370: 1-18. DOI: 10.1016/j.tcs.2006.10.002  0.01
2006 Bérard S, Nicolas F, Buard J, Gascuel O, Rivals E. A fast and specific alignment method for minisatellite maps. Evolutionary Bioinformatics Online. 2: 303-20. PMID 19455224  0.01
2006 Rivals E, Bruyère C, Toffano-Nioche C, Lecharny A. Formation of the Arabidopsis pentatricopeptide repeat family. Plant Physiology. 141: 825-39. PMID 16825340 DOI: 10.1104/pp.106.077826  0.01
2005 Nicolas F, Rivals E. Hardness results for the center and median string problems under the weighted and unweighted edit distances Journal of Discrete Algorithms. 3: 390-415. DOI: 10.1016/j.jda.2004.08.015  0.01
2004 Delgrange O, Rivals E. STAR: an algorithm to Search for Tandem Approximate Repeats. Bioinformatics (Oxford, England). 20: 2812-20. PMID 15180940 DOI: 10.1093/bioinformatics/bth335  0.01
2004 RIVALS E. A SURVEY ON ALGORITHMIC ASPECTS OF TANDEM REPEATS EVOLUTION International Journal of Foundations of Computer Science. 15: 225-257. DOI: 10.1142/S012905410400239X  0.01
2003 Bérard S, Rivals E. Comparison of minisatellites. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 357-72. PMID 12935333 DOI: 10.1089/10665270360688066  0.01
2003 RAHMANN S, RIVALS E. On the Distribution of the Number of Missing Words in Random Texts Combinatorics, Probability and Computing. 12. DOI: 10.1017/S0963548302005473  0.01
2003 Rivals E, Rahmann S. Combinatorics of periods in strings Journal of Combinatorial Theory, Series A. 104: 95-113. DOI: 10.1016/S0097-3165(03)00123-7  0.01
1999 Delgrange O, Dauchet M, Rivals E. Location of repetitive regions in sequences by optimizing a compression method. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 254-65. PMID 10380202 DOI: 10.1142/9789814447300_0026  0.01
1999 Varré JS, Delahaye JP, Rivals E. Transformation distances: a family of dissimilarity measures based on movements of segments. Bioinformatics (Oxford, England). 15: 194-202. PMID 10222406 DOI: 10.1093/bioinformatics/15.3.194  0.01
1998 Rivals E, Delahaye J. Optimal representation in average using Kolmogorov complexity Theoretical Computer Science. 200: 261-287. DOI: 10.1016/S0304-3975(97)00275-2  0.01
1997 Rivals E, Delgrange O, Delahaye JP, Dauchet M, Delorme MO, Hénaut A, Ollivier E. Detection of significant patterns by compression algorithms: the case of approximate tandem repeats in DNA sequences. Computer Applications in the Biosciences : Cabios. 13: 131-6. PMID 9146959 DOI: 10.1093/bioinformatics/13.2.131  0.01
1997 Rivals E, Dauchet M, Delahaye JP, Delgrange O. Compression and genetic sequence analysis. Biochimie. 78: 315-22. PMID 8905150 DOI: 10.1016/0300-9084(96)84763-8  0.01
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