Students and collaborators

Here is the list of graduate or doctoral students I am or was the mentor of, and the list of the researchers I collaborate with.

Students

Raluca Uricaru

2006-now, Master student in Computer Science. Subject: Hidden Markov Models for repeat detection. [24] PhD studen, subject: algorithms for genome sequences comparison.

Sébastien Leclercq

2004-now, PhD student in Evolutionary Biology under supervision of P. Jarne (CEFE). Subject: microsatellite evolution. [23].

François Nicolas

2001-2005, PhD student in Computer Science, University of Montpellier, France. PhD defended on the 13th of December 2005. Title: "Alignment, consensus sequence, similarity search: complexity and approximability." [12,13,2,14].

Sèverine Bérard

2000-2003, PhD student in Computer Science, University of Montpellier, France. PhD defended on the 5th of December 2003. Subject: pairwise alignment of tandem repeat sequences and analysis of minisatellite data. [7,8,2].

Sven Rahmann

1999-2000, Diploma student in Mathematics, German Cancer Research Center, Heidelberg, Germany. Diploma in 2000. Subject: statistics of words in random texts and the analysis of approximate pattern matching algorithms. [15,16].

Jean-Stéphane Varré

1996-2000, graduatate and doctoral student, PhD in Computer Science in 2000, University of Lille, France, Subject: the Transformation Distance: a new approach in genetic sequence comparison. [25]

PhD directors at the University of Lille, France.

Prof. Max Dauchet

Subject: compression for analysis of genetic sequences. [18,20,9].

Prof. Jean-Paul Delahaye

Subjects: compression for analysis of genetic sequences, Kolmogorov complexity and optimal representation, sequence comparison. [18,20,19,25].

Collaborators

Text algorithms

• Multi pattern matching for biological motifs [21]
  Team of Jorma Tarhio, Laboratory of Software Technology, Helsinki University of Technology, Espoo, Finland.

On algorithms for approximate tandem repeats

• Detection of approximate tandem repeats by compression algorithms, [18,20,9,10]
  Olivier Delgrange, Service Informatique, University of Mons-Hainaut, Belgium.

• Alignment of tandem repeats, [7,8,2]
  Sèverine Bérard INRA, MIA, Toulouse, France.
  F. Nicolas, O. Gascuel, LIRMM, Montpellier, France.

• Detection of recombination in tandem repeats alleles, [1]
  Ezekiel Adebiyi Department of Computer and Information Sciences, Covenant University, PMB 1023, Ota, Nigeria

On biological analysis of tandem repeats

• Analysis of approximate tandem repeats in Yeast [20]
  Alain Hénaut, Emmanuelle Ollivier, Marie-Odile Delorme, Université Versailles St-Quentin.

• Analysis of microsatellite in complete genomes [23]
  Philippe Jarne, Sébastien Leclercq, François Munoz, CEFE, CNRS, Montpellier, France.

• Analysis of human minisatellites [2]
  Jérôme Buard, IGH, CNRS, Montpellier, France.

• Evolution of the PCMP protein family in Arabidopsis thaliana [17]
  Alain Lecharny, Clémence Bruyère, C. Toffano-Nioche, from the Institut de Biotechnologie des Plantes, Orsay and URGV, Evry, France.

• Analysis of mouse minisatellites [4]
  F. Bonhomme, A. Orth, Univ. Montpellier II, CNRS, Montpellier, France
  G. Grant, A.J. Jeffreys, Dpt of Genetics, Univ. of Leicester, GB
  Ph. Bois, St Jude Children's Research Hospital, Dpt of Biochemisry, Memphis, TN, USA.

On biological sequence analysis

• Detection of protein motifs (Leucine Zipper) [5]
  Martin Vingron, MPI Molekular Biologie, Berlin, Germany¹
  Dr. Erich Bornberg-Bauer, unknown address¹.

• Similarity search algorithms for large sequence database [6]
  Martin Vingron, MPI Molekular Biologie, Berlin, Germany¹
  Stefan Burkhardt, Andreas Crauser, Hens-Peter Lenhof, MPI für Informatik, Saarbrücken, Germany.
  Paolo Ferragina, University of Pisa, Italy.

• EST clustering and construction of gene indices [11].
  Tim Beissbarth, Stefan Haas, Antje Krause, Martin Vingron, MPI Molekular Biologie, Berlin, Germany¹.

Genomics

• Exploiting SAGE data to annotate the transcriptome on the genome [21]
  Team of T. Commes and J. Marti, IGH, CNRS, Montpellier, France.
  Skuld Tech company, Montpellier, France.
  Team of Jorma Tarhio, Laboratory of Software Technology, Helsinki University of Technology, Espoo, Finland.

Combinatorics and statistics of texts.

• Periodicity of strings [22]
  Sven Rahmann, MPI Molekular Biologie, and Freie Universität, Berlin, Germany.

• Tillings of $\mathbb{N}$ and periodicity [3]
  Olivier Bodini, LIRMM, Montpellier.

Bibliography

1

Ezekiel Adebiyi and Eric Rivals.
On the Detection of Recombination in Minisatellite Data.
In Scott Hazelhurst and Michèle Ramsay, editors, Proc. of the first Southern African Bioinformatics Workshop, pages 25-32, University of the Witwatersrand, Johannesburg, South Africa, January 2007.

2

Sèverine Bérard, François Nicolas, Jérôme Buard, Olivier Gascuel, and Eric Rivals.
A fast and specific alignment method for minisatellite maps.
Evolutionary Bioinformatics, 2:327-344, 2006.

3

Olivier Bodini and Eric Rivals.
Tiling an Interval of the Discrete Line.
In M. Lewenstein and G. Valiente, editors, Proc. of the 17th Annual Symposium on Combinatorial Pattern Matching (CPM), volume 4009 of Lecture Notes in Computer Science, pages 117-128. Springer Verlag, 2006.

4

François Bonhomme, Eric Rivals, Annie Orth, Gemma R. Grant, Alec J. Jeffreys, and Philippe R.J. Bois.
Species-wide distribution of highly polymorphic minisatellite markers suggests past and present genetic exchanges among House Mouse subspecies.
Genome Biology, 8:R80, 2007.

5

Erich Bornberg-Bauer, Eric Rivals, and Martin Vingron.
Computational Approaches to Identify Leucine Zippers.
Nucleic Acids Research, 26(11):2740-2746, 1998.

6

S. Burkhardt, A. Crauser, P. Ferragina, H.-P. Lenhof, E. Rivals, and M. Vingron.
$q$-gram Based Database Searching Using a Suffix Array (QUASAR).
In Third Annual International Conference on Computational Molecular Biology, pages 77-83, Lyon, France, 11-14 April 1999. ACM Press.

7

Sèverine Bérard and Eric Rivals.
Comparison of Minisatellites.
In G. Myers, S. Hannenhalli, S. Istrail, P. Pevzner, and M. Waterman, editors, Proc. of the Sixth Annual International Conference on Computational Molecular Biology, pages 67-76, Washington DC, USA, 2002. ACM Press.

8

Sèverine Bérard and Eric Rivals.
Comparison of minisatellites.
J. of Computational Biology, 10(3-4):357-372, 2003.

9

O. Delgrange, M. Dauchet, and E. Rivals.
Location of Repetitive Regions in Sequences By Optimizing A Compression Method.
In Russ Altman, editor, Proc. of the 4th Pacific Symposium on Biocomputing, volume 4, Hawai, Jan 4-9 1999.

10

Olivier Delgrange and Eric Rivals.
STAR: an algorithm to Search for Tandem Approximate Repeats.
Bioinformatics, 20(16):2812-2820, Nov 2004.

11

S.A. Haas, T. Beissbarth, E. Rivals, A. Krause, and M. Vingron.
GeneNest: automated generation and visualization of gene indices.
Trends in Genetics, 16(11):521-523, 2000.

12

François Nicolas and Eric Rivals.
Hardness of Optimal Spaced Seed Design.
In A. Apostolico, M. Crochemore, and K. Park, editors, Proc. of the 16th Annual Symposium on Combinatorial Pattern Matching (CPM), volume 3537 of Lecture Notes in Computer Science, pages 144-155. Springer Verlag, 2005.

13

François Nicolas and Eric Rivals.
Hardness Results for the Center and Median String Problems under the Weighted and Unweighted Edit Distances.
J. of Discrete Algorithms, 3(2-4):390-415, June 2005.

14

François Nicolas and Eric Rivals.
Longest Common Subsequence Problem for Unoriented and Cyclic Strings.
Theorical Computer Science, 370:1-18, 2007.

15

Sven Rahmann and Eric Rivals.
Exact and Efficient Computation of the Expected Number of Missing and Common Words in Random Texts.
In R. Giancarlo and D. Sankoff, editors, Proc. of the 11th Symposium on Combinatorial Pattern Matching, volume 1848 of Lecture Notes in Computer Science, pages 375-387. Springer-Verlag, Berlin, 2000.

16

Sven Rahmann and Eric Rivals.
The number of missing words in random texts.
Combinatorics, Probability and Computing, 12:73-87, 2003.

17

E. Rivals, C. Bruyère, C. Toffano-Nioche, and A. Lecharny.
Formation of the Arabidopsis Pentatricopeptide Repeat Family.
Plant Physiology, 141:825-839, 2006.

18

E. Rivals, M. Dauchet, J-P. Delahaye, and O. Delgrange.
Compression and genetic sequences analysis.
Biochimie, 78(4):315-322, 1996.

19

E. Rivals and J-P. Delahaye.
Optimal Representation in Average using Kolmogorov Complexity.
Theorical Computer Science, 200(1-2):261-287, June 1998.

20

E. Rivals, O. Delgrange, J-P. Delahaye M. Dauchet, M-O. Delorme, A. Hénaut, and E. Ollivier.
Detection of significant patterns by compression algorithms: the case of Approximate Tandem Repeats in DNA sequences.
CABIOS, 13(2):131-136, 1997.

21

Eric Rivals, Anthony Boureux, Mireille Lejeune, Florence Ottones, Oscar Pecharromàn Pérez, Jorma Tarhio, Fabien Pierrat, Florence Ruffle, Thérèse Commes, and Jacques Marti.
Transcriptome Annotation using Tandem SAGE Tags.
Nucleic Acids Research, 2007.
In press.

22

Eric Rivals and Sven Rahmann.
Combinatorics of Periods in Strings.
J. of Combinatorial Theory series A, 104(1):95-113, October 2003.

23

Sébastien Leclercq and Eric Rivals and Philippe Jarne.
Detecting microsatellites within genomes: significant variation among algorithms.
BMC Bioinformatics, 8:125, 2007.
http://www.biomedcentral.com/1471-2105/8/125/abstract.

24

Raluca Uricaru, Laurent Bréhélin, and Eric Rivals.
A new type of Hidden Markov Models to predict complex motif organization in protein sequences.
In O. Gandrillon, editor, Integrative Post-Genomics, page 42, Lyon, France, November 2006.
poster.

25

Jean-Stéphane Varré, Jean-Paul Delahaye, and Eric Rivals.
The Transformation Distance: A Dissimilarity Measure Based on Movements of Segments.
Bioinformatics, 15(3):194-202, March 1999.

Footnotes

... Germany¹

At that time at German Cancer Research Center (DKFZ), Heidelberg, Germany.