Publications by authors named "Eric Rivals"

32Publications

PEWO: a collection of workflows to benchmark phylogenetic placement.

Bioinformatics 2020 Jul 22. Epub 2020 Jul 22.

LIRMM, University of Montpellier, CNRS, Montpellier, France.

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http://dx.doi.org/10.1093/bioinformatics/btaa657DOI Listing
July 2020

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

Nat Commun 2019 07 11;10(1):3072. Epub 2019 Jul 11.

Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, 27709, USA.

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http://dx.doi.org/10.1038/s41467-019-10905-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6624317PMC
July 2019

AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees.

Bioinformatics 2019 09;35(17):3163-3165

Department of Computer Science, LIRMM, UMR 5506, CNRS and Université Montpellier, Montpellier, France.

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http://dx.doi.org/10.1093/bioinformatics/btz011DOI Listing
September 2019

De novo assembly of viral quasispecies using overlap graphs.

Genome Res 2017 05 10;27(5):835-848. Epub 2017 Apr 10.

Centrum Wiskunde and Informatica, 1098 XG Amsterdam, Netherlands.

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http://dx.doi.org/10.1101/gr.215038.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411778PMC
May 2017

Ribo-seq enlightens codon usage bias.

DNA Res 2017 Jun;24(3):303-210

Department of Computer Science, Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM), CNRS et Université de Montpellier, 34095 Montpellier Cedex 5, France.

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http://dx.doi.org/10.1093/dnares/dsw062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499818PMC
June 2017

Read mapping on de Bruijn graphs.

BMC Bioinformatics 2016 Jun 16;17(1):237. Epub 2016 Jun 16.

IRISA Inria Rennes Bretagne Atlantique, GenScale team, Campus de Beaulieu, Rennes, 35042, France.

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http://dx.doi.org/10.1186/s12859-016-1103-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4910249PMC
June 2016

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

Bioinformatics 2017 03;33(6):799-806

Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland.

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http://dx.doi.org/10.1093/bioinformatics/btw321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5351550PMC
March 2017

YOC, A new strategy for pairwise alignment of collinear genomes.

BMC Bioinformatics 2015 Apr 2;16:111. Epub 2015 Apr 2.

LIRMM, UMR 5506, Computational Biology Institute, CNRS, University of Montpellier 2, Montpellier, France.

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http://dx.doi.org/10.1186/s12859-015-0530-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4411659PMC
April 2015

The ancient Yakuts: a population genetic enigma.

Philos Trans R Soc Lond B Biol Sci 2015 Jan;370(1660):20130385

Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France Institut Médico-Légal, Université Paris Descartes, Paris, France.

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http://dx.doi.org/10.1098/rstb.2013.0385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275892PMC
January 2015

LoRDEC: accurate and efficient long read error correction.

Bioinformatics 2014 Dec 26;30(24):3506-14. Epub 2014 Aug 26.

Department of Computer Science and Helsinki Institute for Information Technology HIIT, FI-00014 University of Helsinki, Finland and LIRMM and Institut de Biologie Computationelle, CNRS and Université Montpellier, 34095 Montpellier Cedex 5, France.

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http://dx.doi.org/10.1093/bioinformatics/btu538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253826PMC
December 2014

Diversity of Prdm9 zinc finger array in wild mice unravels new facets of the evolutionary turnover of this coding minisatellite.

PLoS One 2014 13;9(1):e85021. Epub 2014 Jan 13.

Institut des Sciences de l'Evolution Montpellier, Université Montpellier 2, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Montpellier, France.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0085021PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890296PMC
September 2014

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

Nucleic Acids Res 2014 Mar 18;42(5):2820-32. Epub 2013 Dec 18.

Transcriptomics, bioinformatics and myeloid leukaemia, INSERM, U1040, Institute for Research in Biotherapy, Montpellier F-34197, France, Université Montpellier 2, Montpellier, France, Institut de Biologie Computationnelle, Maison de la modélisation, Université Montpellier 2, France, LIRMM, MAB, CNRS UMR 5506, Université Montpellier 2, Montpellier, France and Genomic instability of pluripotent stem cells, INSERM, U1040, Institute for Research in Biotherapy, Montpellier F-34197, France.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkt1300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950697PMC
March 2014

Novel definition and algorithm for chaining fragments with proportional overlaps.

J Comput Biol 2011 Sep;18(9):1141-54

Department of Computer Science, LIRMM, CNRS, Université de Montpellier 2, Montpellier, France.

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http://dx.doi.org/10.1089/cmb.2011.0126DOI Listing
September 2011

Evolutionary process of a tetranucleotide microsatellite locus in Acipenseriformes.

J Genet 2011 Aug;90(2):217-27

Institute of Hydroecology, Ministry of Water Resources, Chinese Academy of Sciences, Wuhan 430079, People's Republic of China.

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http://dx.doi.org/10.1007/s12041-011-0055-0DOI Listing
August 2011

Querying large read collections in main memory: a versatile data structure.

BMC Bioinformatics 2011 Jun 17;12:242. Epub 2011 Jun 17.

LIRMM, UMR 5506, CNRS and Université de Montpellier 2, CC 477, 161 rue Ada, 34095 Montpellier, France.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-12-242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3163563PMC
June 2011

An alternative approach to multiple genome comparison.

Nucleic Acids Res 2011 Aug 6;39(15):e101. Epub 2011 Jun 6.

LIRMM - CNRS, Université Montpellier 2 - CC 477, 161, rue Ada, 34095 Montpellier Cedex 5, France.

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http://dx.doi.org/10.1093/nar/gkr177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159434PMC
August 2011

DNA slippage occurs at microsatellite loci without minimal threshold length in humans: a comparative genomic approach.

Genome Biol Evol 2010 Jul 12;2:325-35. Epub 2010 Jul 12.

Centre d'Ecologie Fonctionnelle et d'Evolution, UMR 5175 CNRS, 1919 route de Mende, 34095 Montpellier cedex 5, France.

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http://dx.doi.org/10.1093/gbe/evq023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2997547PMC
July 2010

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 Biol 2010 Feb 24;10:35. Epub 2010 Feb 24.

Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Route de St-Cyr, Versailles Cedex France.

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http://dx.doi.org/10.1186/1471-2229-10-35DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848758PMC
February 2010

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

Nucleic Acids Res 2009 Aug 16;37(15):e104. Epub 2009 Jun 16.

Laboratoire d'Informatique, de Robotique et de Microélectronique, Université de Montpellier II, UMR 5506 CNRS, 34392 Montpellier, France.

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http://dx.doi.org/10.1093/nar/gkp492DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2731892PMC
August 2009

Transcriptome annotation using tandem SAGE tags.

Nucleic Acids Res 2007 20;35(17):e108. Epub 2007 Aug 20.

Laboratoire d'Informatique, de Robotique et de Microélectronique, UMR 5506 CNRS-Université de Montpellier II, 161 rue Ada, 34392 Montpellier 05, France.

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http://dx.doi.org/10.1093/nar/gkm495DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2034470PMC
November 2007

Detecting microsatellites within genomes: significant variation among algorithms.

BMC Bioinformatics 2007 Apr 18;8:125. Epub 2007 Apr 18.

LIRMM, UMR 5506 CNRS--Université de Montpellier II, Montpellier, France.

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http://dx.doi.org/10.1186/1471-2105-8-125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1876248PMC
April 2007

Formation of the Arabidopsis pentatricopeptide repeat family.

Plant Physiol 2006 Jul;141(3):825-39

Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5506, Université de Montpellier II, 34392 Montpellier cedex 5, France.

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http://dx.doi.org/10.1104/pp.106.077826DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1489915PMC
July 2006

A fast and specific alignment method for minisatellite maps.

Evol Bioinform Online 2007 Feb 22;2:303-20. Epub 2007 Feb 22.

INRA, Département MIA, Toulouse, France.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674676PMC
February 2007

STAR: an algorithm to Search for Tandem Approximate Repeats.

Bioinformatics 2004 Nov 4;20(16):2812-20. Epub 2004 Jun 4.

Université de Mons Hainaut, Service d'Informatique Générale, Avenue du champ de Mars, 6, Mons, 7000, Belgique and LIRMM, CNRS UMR 5506, 161, rue Ada, Montpellier Cedex 5, 34392, France.

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http://dx.doi.org/10.1093/bioinformatics/bth335DOI Listing
November 2004

Comparison of minisatellites.

J Comput Biol 2003 ;10(3-4):357-72

L.I.R.M.M., UMR CNRS 5506, 161 rue Ada, F34392 Montpellier Cedex 5, France.

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http://dx.doi.org/10.1089/10665270360688066DOI Listing
March 2004