- Manycore high-performance computing in bioinformatics.
J.-S. Varré, B. Schmidt, S. Janot and M. Giraud.
Advances in Genomic Sequence Analysis and Pattern Discovery,
ed. by L. Elnitski, H. Piontkivska, and L. Welch, Science, Engineering, and Biology Informatics - Vol. 7, 2011.
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Retention-Error Patterns in Complex Serial-Recall Tasks
Revisited by Bioinformatics.
F. Mathy
and J.-S. Varré.
Submitted, 2012.
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Structural and content diversity of mitochondrial genome in beet: a comparative genomic analysis.
A. Darracq, J.-S. Varré, L. Maréchal-Drouard, A. Courseaux, V. Castric, P. Saumitou-Laprade, S. Oztas, P. Lenoble, B. Vacherie, V. Barbe, P. Touzet.
Genome Biology and Evolution, 3, pp 723-736, 2011.
[PDF]
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Structural and content diversity of mitochondrial genome in beet: a comparative genomic analysis.
A. Darracq, J.-S. Varré, L. Maréchal-Drouard, A. Courseaux, V. Castric, P. Saumitou-Laprade, S. Oztas, P. Lenoble, B. Vacherie, V. Barbe, P. Touzet.
Genome Biology and Evolution, 3, pp 723-736, 2011.
[PDF]
- Parallel Position Weight Matrices Algorithms.
M. Giraud and J.-S. Varré.
Parallel Computing, 37(8), 2011.
[PDF]
- A scenario of mitochondrial genome evolution in maize based on rearrangement events.
A. Darracq, J.-S. Varré and P. Touzet,
BMC Genomics, 11(233), 2010.
[PDF]
- TFM-Explorer: mining cis-regulatory regions in genomes.
L. Tonon, H. Touzet and J.-S. Varré,
NAR Web Server Issue, 38(S2), 2010.
[PDF]
- Efficient and accurate p-value computation for position weight matrices.
H. Touzet and J.-S. Varré.
Algorithms for Molecular Biology, 2(15), 2007.
[PDF]
- Evolution of plant-like crystalline storage polysaccharide in the protozoan parasite toxoplasma gondii argues for a red alga ancestry.
A. Coppin, J.-S. Varré, L. Lienard, D. Dauvillée, Y. Guérardel, M.-O. Soyer-Gobillard, A. Buléon, S. Ball, and S. Tomavo.
Journal of Molecular Evolution, 60(2):257-267, 2005.
[PDF]
- Transformation Distances: a family of dissimilarity measures based on
movements of segments.
J.-S. Varré, J.-P. Delahaye and E. Rivals.
Bioinformatics, vol. 15, no. 3, pp 194-202, 1999.
[PDF]
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Tandem Halving Problems by DCJ.
A. Thomas, A. Ouangraoua, J.-S. Varré.
2012 (proceedings of WABI 2012, to appear).
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Genome Halving by Block Interchange.
A. Thomas, A. Ouangraoua, J.-S. Varré.
2012 (proceedings of BIOINFORMATICS 2012).
[PDF][slides]
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Bit-Parallel Multiple Pattern Matching.
T. T. Tran, M. Giraud, J.-S. Varré
2011 (proceedings of PPAM / PBC 2011).
[PDF][slides]
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Genome Dedoubling by DCJ and Reversal.
A. Thomas, J.-S. Varré, A. Ouangraoua.
BMC Bioinformatics, 12(Suppl 9):S20, 2011 (proceedings of RECOMB-CG'11).
[PDF][slides]
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Parallel Position Weight Matrices Algorithms.
M. Giraud
and J.-S. Varré.
2009 (proceedings of ISPDC'09).
[PDF][slides]
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Self-overlapping occurrences and Knuth-Morris-Pratt algorithm for weighted matching.
A. Liefooghe, H. Touzet and J.-S. Varré.
LNCS 5457, pp 481-492, 2009 (proceedings of LATA'09).
[PDF][slides]
- Large scale matching for Position Weight Matrices.
A. Liefooghe, H. Touzet and J.-S. Varré.
LNCS 4009, pp 401-412, 2006 (proceedings of CPM'06).
[PDF][slides]
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Sorting by Reversals with Common Intervals.
M. Figeac and J.-S. Varré.
LNCS, 3240, pp 26-37, 2004 (proceedings of WABI'04).
[PDF]
- Recherche approximative de motifs dans des mots de taille fixe.
T. T. Tran,
M. Giraud, J.-S. Varré.
Journées
Algorithmique, combinatoire du texte et applications en
bio-informatique, 2011.
- Biomanycores, open-source parallel code for many-cores bioinformatics.
J.-F. Berthelot, C. Deltel, M. Giraud, S. Janot, L. Jourdan, D. Lavenier, H. Touzet and J.-S. Varré.
BOSC'11.
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biomanycores.org: open-source parallel bioinformatics.
J.-F. Berthelot, C. Deltel, M. Giraud, S. Janot, L. Jourdan, D. Lavenier, H. Touzet and J.-S. Varré.
Journées Ouvertes en Biologie Informatique Mathématiques (JOBIM 2011).
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Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics.
J.-S. Varré, S. Janot and M. Giraud.
BOSC'09.
[slides]
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Biomanycores, une bibliothèque open-source pour la bioinformatique massivement multi-coeurs.
J.-S. Varré, S. Janot, and M. Giraud.
Atelier "Côté Calcul", Journées Ouvertes en Biologie Informatique Mathématiques (JOBIM 2009).
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A Study of Genomic Rearrangements in Maize Mitochondrial Genomes.
A. Darracq, J.-S. Varré, P. Touzet.
Journées Ouvertes en Biologie Informatique Mathématiques (JOBIM 2009)
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Evolution of the mitochondrial genome in beet. A comparative
genomic study at the intra-specific level.
A. Darracq, J.-S. Varré,
A. Courseaux, L Maréchal-Drouard, P. Touzet.
XXth International Congress of Genetics, Berlin July 12-17, 2008.
- Calcul de P-valeur efficace et exact pour un motif PWM.
H. Touzet et J.-S. Varré.
Journées algorithmique, combinatoire du texte et applications en bio-informatique, 2007.
[slides]
- Studying tumor genome architectures using genome rearrangement theory on End-Sequence
Profiling data.
J.-S. Varré.
ACI VicAnne/ARC MOCA worshop, 2006.
[slides]
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Algorithmes pour la comparaison de génomes et la recherche de signaux cis-régulateurs.
Habilitation à Diriger des Recherches, 2008.
[PDF]
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Concepts et algorithmes pour la comparaison de séquences génétiques : une approche informationnelle.
PhD thesis, 2000.
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Distances basées sur des notions de compression de données et application à la phylogénie.
MSc thesis, 1996.