Eric Rivals's Main Publications

In press / Up coming

• Prédiction d'ARN chimériques à partir de séquençage d'ARN
  Philippe N.; Salson M.; Ruffle F; Bou Samara E; Boureux A; Commes T.; Rivals E.
  7èmes Journées du Cancéropôle GSO du 18 au 19 octobre 2011
  


• Approximate Common Intervals in Multiple Genome Comparison
  A. Chateau, P. Riou, E. Rivals
  in press in IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2011), 2011.

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

• Hardness of Optimal Spaced Seed Design
  F. Nicolas, E. Rivals
  Journal of Computer and System Sciences, Vol. 74, p. 831-849, 2008
  doi:10.1016/j.jcss.2007.10.001.

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

• STAR: an algorithm to Search for Tandem Approximate Repeats
  O.Delgrange, E. Rivals
  Bioinformatics, Vol. 20, No. 16, 2812-2820, 2004
  Available http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/16/2812


• A Survey on Algorithmic Aspects of Tandem Repeats Evolution
  E. Rivals
  International Journal of Foundations of Computer Science, Vol. 15, No. 2, 225-257, 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

• Histoire de duplication et répétitions en tandem
  Eric Rivals
  Actes des Journées Montoises d'Informatique Théorique Montpellier, 9-11 September, 2002. Keynote speaker


• Comparison of Minisatellites
  S. Bérard, E. Rivals
  Proc. of the 6th Annual International Conference on Research in Computational Molecular Biology,
  ACM Press, 2002.
  Research report 01-184 of the LIRMM, October 2001.
  

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)