Eric Rivals's Main Publications
External lists: in life sciences PubMed , computer science Facetted DBLP , general Google Scholar , Microsoft academic or Web of Knowledge ; most are uncomplete. A list in PDF format.
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In press / Up coming
2011
Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features.
Cayrou C, Coulombe P, Vigneron A, Stanojcik S, Ganier O, Peiffer I, Rivals E, Puy A, Laurent-Chabalier S, Desprat R, Mechali M. Genome Research Vol. 21, No. 9, p. 1438-1449, Jul 12, 2011
Novel definition and algorithm for chaining fragments with proportional overlaps
R. Uricaru, A. Mancheron, E. Rivals
in press in Journal of Computational Biology Vol. 18, No. 9, p. 1141-1154, 2011.
Evolutionary process of a tetranucleotide microsatellite locus in Acipenseriforms
Z. Shao, E. Rivals, N. Zhao, S. Lek, J. Chang, P. Berrebi,
J. of Genetics Vol. 90, Number 2, p. 217-227, August 2011.
An alternative approach to multiple genome comparison
A. Mancheron, R. Uricaru, E. Rivals Nucleic Acids Research
(NAR) Vol. 39, No. 15, p. e101, doi:10.1093/nar/gkr177; 2011
Querying large read collections in main memory: a versatile data structure
N. Philippe, M. Salson, T. Lecroq, M. Leonard, T. Commes and E. Rivals
BMC Bioinformatics , Vol. 12, p. 42, doi:10.1186/1471-2105-12-242, 2011.
Exact Search Algorithms for Biological Sequences
E. Rivals, L. Salmela, J. Tarhio, pages 91-111, chap. 5, in Algorithms in
Computational Molecular Biology: Techniques , Approaches and
Applications, ISBN : 978-0470505199, Wiley Series in Bioinformatics,
Wiley, 2011.
2010
Novel definition and algorithm for chaining fragments with proportional overlaps
R. Uricaru, A. Mancheron, E. Rivals
RECOMB Comparative Genomics , Lecture Notes in Computer Science
(LNCS), Springer-Verlag, Vol. 6398, p. 161-172 , 2010. (free pdf )
Reliable Bacterial Genome Comparison Tools
E. Rivals, A. Mancheron, R. Uricaru
ERCIM News , Vol. 82, p. 17-18, 2010.
DNA Slippage Occurs at Microsatellite Loci without Minimal Threshold Length in Humans: A Comparative Genomic Approach
S. Leclercq , E. Rivals, P. Jarne
Genome Biology and Evolution , Vol. 2, p. 325-35, 2010.
Sequence analysis of two alleles reveals that intra-and intergenic recombination played a role in the evolution of the radish fertility restorer (Rfo) JR Hernandez Mora, E. Rivals, H. Mireau, F. Budar BMC Plant Biology Vol. 10:35, doi:10.1186/1471-2229-10-35; 2010
2009
Using reads to annotate the genome: influence of length,
background distribution, and sequence errors on prediction capacity N. Philippe*,
A. Boureux*, L. Bréhèlin, J. Tarhio, T. Commes, E. Rivals Nucleic Acids Research
(NAR) Vol. 37, No. 15 e104, doi:10.1093/nar/gkp492; 2009. *: joint first co-authors
MPSCAN: fast localisation
of multiple reads in genomes E. Rivals, L. Salmela,
P. Kiiskinen, P. Kalsi,
J. Tarhio Proc. 9th Workshop on
Algorithms in Bioinformatics Lecture Notes in BioInformatics
(LNBI), Springer-Verlag, Vol. 5724, p. 246-260 , 2009.
2008
2007
Transcriptome
Annotation using Tandem SAGE Tags E. Rivals*,
A. Boureux*, M. Lejeune, F. Ottones, O. Pecharroman Pérez,
J. Tarhio, F. Pierrat, F. Ruffle, T. Commes, J. Marti Nucleic Acids Research
(NAR) , Vol. 35(17):e108, http://dx.doi.org/10.1093/nar/gkm495 . *: joint first co-authors
Available at http://nar.oxfordjournals.org/cgi/content/full/35/17/e108
Detection of Recombination in Variable Number Tandem Repeat
Sequences E. Adebiyi, E. Rivals South African Computer Journal
(SACJ) Vol. 39, p. 1-7, 2007.
Species-wide distribution
of highly polymorphic minisatellite markers suggests past and
present genetic exchanges among House Mouse subspecies
F. Bonhomme*, E. Rivals*, A. Orth, G.R. Grant, A.J. Jeffreys,
P.J. Bois Genome
Biology , Vol. 8, p. R80, 2007. *: joint first co-authors
Available at http://genomebiology.com/2007/8/5/R80
Detecting microsatellites within genomes: significant variation among algorithms
S. Leclercq , E. Rivals, P. Jarne
BMC Bioinformatics , Vol. 8, p. 125, 2007. Available at
http://www.biomedcentral.com/1471-2105/8/125/abstract
Longest Common Subsequence Problem for Unoriented and Cyclic Strings
F. Nicolas, E. Rivals
Theoretical Computer Science (TCS) , Vol. 370, p. 1-18, 2007.
doi:10.1016/j.tcs.2006.10.002
On the Detection of Recombination in Minisatellite Data
E. Adebiyi, E. Rivals
Proc. of the first Southern African Bioinformatics Workshop , p. 25-32, 2007
2006
A fast and specific alignment method for minisatellite maps
S. Bérard, F. Nicolas, J. Buard, O. Gascuel, E. Rivals
Evolutionary Bioinformatics 2:327-344, 2006.
Also available at http://la-press.com/journals.php?pa=abstract&content_id=127
Formation of the Arabidopsis pentatricopeptide family
E. Rivals, C. Bruyère, C. Toffano-Nioche, A. Lecharny
Plant Physiology 141:825-839, 2006 .
http://www.plantphysiol.org/cgi/content/abstract/141/3/825
Tiling an Interval of the Discrete Line
O. Bodini, E. Rivals
Proc. of the 17th Annual Symposium on Combinatorial Pattern Matching (CPM) , LNCS 4009, p. 117-128, 2006
2005
Algorithmes d'analyse de séquences en bioinformatique. Périodicité et répétitions in French
Eric Rivals
Habilitation à diriger des recherches, Univ. of Montpellier II, 2005
Hardness Results for the Center and
Median String Problems under the Weighted and Unweighted Edit
Distances
François Nicolas, Eric Rivals
J. of Discrete
Algorithms , 3(2-4), p. 390-415, June 2005
Extended version of the paper in CPM 03
Modular Data Compression to Optimally Locate Regular Segments in Sequences. Application to DNA Sequence Analysis
O.Delgrange, E. Rivals
26th Symposium on Information Theory in the Benelux (IT05) , May 2005.
pp. 105-112, J. Cardinal, N. Cerf, O. Delgrange, O. Markowich Eds, ISBN 90-71048-21-7.
Hardness of Optimal Spaced Seed Design
F. Nicolas, E. Rivals
Proc. of the 16th Annual Symposium on Combinatorial Pattern Matching (CPM) , LNCS 3537, p. 144-155, 2005
2004
2003
Combinatorics of
Periods in Strings
E. Rivals, S. Rahmann
Journal of Combinatorial Theory - Series A , 104(1), p. 95-113, October 2003
The Number of Missing Words in Random Texts
S. Rahmann, E. Rivals
Combinatorics, Probability and Computing , 12, p. 73-87, 2003
Comparison of Minisatellites
S. Bérard, E. Rivals
J. of Computational Biology , 10(3-4), p. 357-372, 2003
Mary-Ann Liebert Inc. publishers
Long version of the RECOMB 2002 abstract
Complexities of the Centre and Median String Problems
François Nicolas, Eric Rivals
Proceedings of the
Fourteenth Annual Symposium on Combinatorial Pattern Matching (CPM 2003)
Lecture Notes in Computer Science, Vol. 2676, p. 315 - 327, Springer Verlag, Heidelberg, 2003.
2002
2001
Combinatorics of
Periods in Strings
E. Rivals, S. Rahmann
Proc. of the 28th International
Colloquium on Automata, Languages, andProgramming ,
P. Orejas, P. G. Spirakis, J. van Leuween editors.
Lecture Notes in Computer Science vol. 2076, pp. 615-626. Springer Verlag, Heidelberg, 2001.
Research report 01-017 of the LIRMM , Januar 2001.
Improved version of the Research Report 99-297
Apports futurs de la bioinformatique
É. Rivals
in Des modèles biologiques à l'amélioration des plantes ,
S. Hamon (editor),
IRD Editions, Collection "Colloques et Séminaires", 892 pages.
Full version of the abstract published at Colloque
AUF-AUPELF "Des modèles biologiques à l'amélioration des
plantes" ,
Montpellier, 3-5 July 2000.
2000
GeneNest: automated generation and visualization of gene indices
S. Haas, T. Beissbarth, É. Rivals, A. Krause, M. Vingron
Trends in Genetics , p. 521-2, vol. 16(11), Nov. 2000
Exact and Efficient Computation of the Expected Number of Missing and Common Words in Random Texts
S. Rahmann, É. Rivals
Proceedings of the 11th Annual
Symposium on Combinatorial Pattern Matching ,
Lecture Notes in Computer Science, Number 1848, pp. 375-387,
Springer-Verlag, Heidelberg, 2000.
also a Research Report 99-229 of the
LIRMM , November 1999.
1999
Location of Repetitive Regions in Sequences By Optimizing a
Compression Method
O. Delgrange, M. Dauchet, É. Rivals
4th Pacific Symposium on Biocomputing (PSB99) ,
Hawai, 4-9. Jan, 1999
The Transformation Distance: a Dissimilarity Measure Based
on Movements of Segments
J.-S. Varré, J.-P. Delahaye, É. Rivals
Bioinformatics ,
p. 194-202, vol. 15(3), March 1999.
Full version of the extended abstract
published in the
German Conference on Bioinformatics (GCB98) ,
Cologne, Germany, 7-10 Oct. 1998,
also as a poster in the 8th
Workshop on Genome and Informatics (GIW97) ,
Tokyo, 12-13 dec 1997
q-gram Based Database Searching Using a Suffix Array (QUASAR)
Stefan Burkhardt, Andreas Crauser, Paolo Ferragina,
Hans-Peter Lenhof, Éric Rivals, Martin Vingron
Third Annual International Conference on Computational
Molecular Biology (RECOMB99) ,
Lyon 11-14 April 1999,
also as a Tech. Report
MPI-I-98-1-024 , Max
Planck Institute für Informatik, Saarbrücken .
Automatic Clustering of Protein and EST Sequence Databases
A. Krause, É. Rivals, M. Rehmsmeier, S. Haas, T.Beissbarth, M. Vingron
poster and abstract at the
DHGP Genome Meeting 1999 ,
Munich, Nov. 28th - Dec. 1st 1999
1998
Average Optimal Representation using Kolmogorov Complexity
É. Rivals et J-P. Delahaye,
Theoretical Computer Science (TCS) ,
p. 261-287, vol. 200(1-2), June 1998.
Strategies for Identifying Leucine Zippers
E. Bornberg-Bauer, É. Rivals, M. Vingron
Nucleic Acids Research (NAR) ,
p. 2740-2746, vol. 26(11), June 1998.
also as a poster and abstract in the
Second Annual International Conference on
Computational Molecular Biology (RECOMB98) ,
New York, NY, 22-25 March 1998.
1997
Detection of
significant patterns by compression algorithms: the case of
Approximate Tandem Repeats
É. Rivals, O. Delgrange, J-P. Delahaye, M. Dauchet, M-O. Delorme, A. Hénaut, E. Ollivier
Computer Applications in BIOSciences (CABIOS) ,
p. 131-136, vol. 13(2), April 1997
Fast Discerning Repeats in DNA
Sequences with a Compression Algorithm
É. Rivals, M. Dauchet, J-P. Delahaye, O. Delgrange
Extended abstract in the 8th
Workshop on Genome and Informatics (GIW97) ,
Tokyo, 12-13 Dec 1997
1996
Compression and
genetic sequences analysis
É. Rivals, M. Dauchet, J-P. Delahaye, O. Delgrange
Biochimie ,
p. 315-322, vol. 78, 1996
A Guaranteed Compression Scheme for Repetitive DNA Sequences
É. Rivals, J-P. Delahaye, M. Dauchet, O. Delgrange,
abstract in the 6th Data Compression Conference IEEE
Computer Science Press, Snowbird (Utah), April 1-3, 1996
Algorithmes de
compression et applications à l'analyse de séquences génétiques
É. Rivals
PhD thesis in computer science (in French),1996
LIFL
Lille I University ,
1995
A First Step Towards Chromosome Analysis by Compression Algorithms
É. Rivals, O. Delgrange, J-P. Delahaye, M. Dauchet
IEEE Symposium on Intelligence in Neural and Biological Systems (INBS)
N.G. Bourbakis ed., Herndon, May 29-31, 1995
Compression optimale en moyenne et complexité de Kolmogorov
É. Rivals et J-P. Delahaye
LIFL
Lille I University ,
technical report IT-266 (in French)
A Guaranteed Compression Scheme for Repetitive DNA Sequences
É. Rivals, J-P. Delahaye, M. Dauchet, O. Delgrange
LIFL
Lille I University ,
technical report IT-285
1994
Compression pour l'analyse de séquences
É. Rivals
CNRS G.D.R. "Informatique et génomes" workshop
Rencontre pour la Recherche de Motifs dans les Séquences ,
M. Crochemore ed., Marseille, February 24-25, 1994 (in French)
ADN, recherches de régularités
É. Rivals
abstract in the Forum InterDisciplinaire Génome et Informatique ,
M-O. Delorme ed., Aussois, June 15-17, 1994 (in French)
Eric
Rivals Updated in September 2011