Jean-Stéphane Varré

professeur des universités
CNU : SECTION 27 - INFORMATIQUE
jean-stephane_varre.png

Jean-Stéphane Varré

professeur des universités

Publications

Article dans des revues

  • Delphine Beury, Léa Fléchon, Florence Maurier, Ségolène Caboche, Jean-Stéphane Varré, et al.. Use of whole-genome sequencing in the molecular investigation of care-associated HCoV-OC43 infections in a hematopoietic stem cell transplant unit. Journal of Clinical Virology, Elsevier, 2020, 122, pp.104206. ⟨10.1016/j.jcv.2019.104206⟩. ⟨hal-02403094⟩
  • Florence Maurier, Delphine Beury, Léa Fléchon, Jean-Stéphane Varré, Hélène Touzet, et al.. A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43. Virology, Elsevier, 2019, 531, pp.141-148. ⟨10.1016/j.virol.2019.03.006⟩. ⟨hal-02167880⟩
  • Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré. Graph analysis of fragmented long-read bacterial genome assemblies. Bioinformatics, Oxford University Press (OUP), 2019, ⟨10.1093/bioinformatics/btz219⟩. ⟨hal-02167175⟩
  • Jean-Stéphane Varré, Nunzio D'agostino, Pascal Touzet, Sophie Gallina, Rachele Tamburino, et al.. Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome. International Journal of Molecular Sciences, MDPI, 2019, 20, ⟨10.3390/ijms20194788⟩. ⟨hal-02298474⟩
  • Samuel Blanquart, Jean-Stéphane Varré, Paul Guertin, Amandine Perrin, Anne Bergeron, et al.. Assisted transcriptome reconstruction and splicing orthology. BMC Genomics, BioMed Central, 2016, Proceedings of the 14th Annual Research in Computational Molecular Biology (RECOMB) Comparative Genomics Satellite Workshop: genomics, 17 (Suppl 10), pp.786. ⟨10.1186/s12864-016-3103-6⟩. ⟨hal-01396410⟩
  • Amandine Perrin, Jean-Stéphane Varré, Samuel Blanquart, Aïda Ouangraoua. ProCARs: Progressive Reconstruction of Ancestral Gene Orders. BMC Genomics, BioMed Central, 2015, 16 (Suppl 5), pp.S6. ⟨10.1186/1471-2164-16-S5-S6⟩. ⟨hal-01217311⟩
  • A. Darracq, J.S. Varré, L. Maréchal-Drouard, A. Courseaux, V. Castric, et al.. Structural and content diversity of the mitochondrial genome in beet. A comparative genomic analysis. .. Genome Biology, BioMed Central, 2011, 3, pp.723-736. ⟨hal-00621021⟩
  • Antoine Thomas, Jean-Stéphane Varré, Aïda Ouangraoua. Genome dedoubling by DCJ and reversal. BMC Bioinformatics, BioMed Central, 2011, 12 (Suppl 9), pp.S20. ⟨10.1186/1471-2105-12-S9-S20⟩. ⟨hal-00784416⟩
  • Mathieu Giraud, Jean-Stéphane Varré. Parallel Position Weight Matrices Algorithms. Parallel Computing, Elsevier, 2011, 37, pp.466-478. ⟨10.1016/j.parco.2010.10.001⟩. ⟨hal-00623404⟩
  • Antoine Thomas, Jean-Stéphane Varré, Ouangraoua Aïda. Genome Dedoubling by DCJ and Reversal. BMC Bioinformatics, BioMed Central, 2011, 12 (Suppl 9), pp.S20. ⟨inria-00635003⟩
  • Aude Darracq, Jean-Stéphane Varré, L. Maréchal-Drouard, A. Courseaux, V. Castric, et al.. Structural and content diversity of mitochondrial genome in beet: a comparative genomic analysis. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2011, 3, pp.723-736. ⟨10.1093/gbe/evr042⟩. ⟨hal-00616508⟩
  • Tonon Laurie, Hélène Touzet, Jean-Stéphane Varré. TFM-Explorer: mining cis-regulatory regions in genomes. Nucleic Acids Research, Oxford University Press, 2010, 38 (S2), pp.W286-W292. ⟨10.1093/nar/gkq473⟩. ⟨hal-00823465⟩
  • Aude Darracq, Jean-Stéphane Varré, P. Touzet. A scenario of mitochondrial genome evolution in maize based on rearrangement events. BMC Genomics, BioMed Central, 2010, 11, pp.233. ⟨10.1186/1471-2164-11-233⟩. ⟨hal-00468454⟩
  • Helene Touzet, Jean-Stéphane Varré. Efficient and accurate P-value computation for Position Weight Matrices. Algorithms for Molecular Biology, BioMed Central, 2007, 2 (15), pp.1-12. ⟨inria-00270263⟩
  • Alexandra Coppin, Jean-Stéphane Varré, Luc Lienard, David Dauvillee, Yann Guerardel, et al.. Evolution of plant-like crystalline storage polysaccharide in the protozoan parasite Toxoplasma gondii argues for a red alga ancestry.. Journal of Molecular Evolution, Springer Verlag, 2005, 60, pp.257-267. ⟨hal-00085577⟩
  • Alexandra Coppin, Jean-Stéphane Varré, Luc Lienard, David Dauvillée, Yann Guerardel, et al.. Evolution of plant-like crystalline storage polysaccharide in the protozoan parasite Toxoplasma gondii argues for a red alga ancestry. Journal of Molecular Evolution, Springer Verlag, 2005, 60 (2), pp.257-267. ⟨10.1007/s00239-004-0185-6⟩. ⟨hal-02680299⟩

Communication dans un congrès

  • Tuan Tu Tran, Mathieu Giraud, Jean-Stéphane Varré. Perfect Hashing Structures for Parallel Similarity Searches. International Workshop on High Performance Computational Biology (HiCOMB 2015) / International Parallel and Distributed Processing Symposium (IPDPS 2015), 2015, Hyderabad, India. pp.332-341, ⟨10.1109/IPDPSW.2015.105⟩. ⟨hal-01153893⟩
  • Mathieu Giraud, Mikaël Salson, Marc Duez, Jean-Stéphane Varré, Céline Villenet, et al.. Suivi de la leucémie résiduelle par séquençage haut-débit. JOBIM, Jul 2013, Toulouse, France. ⟨hal-00857581⟩
  • Antoine Thomas, Aïda Ouangraoua, Jean-Stéphane Varré. Tandem Halving Problems by DCJ. Workshop on Algorithms in Bioinformatics, Sep 2012, Ljubljana, Slovenia. pp.417-429, ⟨10.1007/978-3-642-33122-0_33⟩. ⟨hal-00749019⟩
  • Antoine Thomas, Aïda Ouangraoua, Jean-Stéphane Varré. Genome Halving by Block Interchange. BIOINFORMATICS, Feb 2012, Lisboa, Portugal. pp.58-65. ⟨hal-00749026⟩
  • Jean-Frédéric Berthelot, Charles Deltel, Mathieu Giraud, Stéphane Janot, Laetitia Jourdan, et al.. biomanycores.org: a repository of interoperable open-source code for many-core bioinformatics. JOBIM 2011, Jul 2011, Paris, France. ⟨hal-00637847⟩
  • Mathieu Giraud, Stéphane Janot, Jean-Frédéric Berthelot, Charles Deltel, Laetitia Jourdan, et al.. Biomanycores, open-source parallel code for many-core bioinformatics. Bioinformatics Open Source Conference (BOSC 2011), 2011, Vienne, Austria. ⟨inria-00623390⟩
  • Tuan Tu Tran, Mathieu Giraud, Jean-Stéphane Varré. Bit-Parallel Multiple Pattern Matching. Parallel Processing and Applied Mathematics / Parallel Biocomputing Conference (PPAM / PBC 11), 2011, Torun, Poland. ⟨inria-00637227⟩
  • Mathieu Giraud, Jean-Stéphane Varré. Parallel Position Weight Matrices Algorithms. International Symposium on Parallel and Distributed Computing (ISPDC 2009), Jul 2009, Lisboa, Portugal. pp.65-69, ⟨10.1109/ISPDC.2009.31⟩. ⟨inria-00438215⟩
  • Jean-Stéphane Varré, Stéphane Janot, Mathieu Giraud. Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics. Bioinformatics Open Source Conference (BOSC), Jun 2009, Stockholm, Sweden. ⟨inria-00438224⟩
  • Aude Liefooghe, Helene Touzet, Jean-Stéphane Varré. Self-Overlapping Occurrences and Knuth-Morris-Pratt Algorithm for Weighted Matching. 3rd International Conference on Language and Automata Theory and Applications, Apr 2009, Tarragona, Spain. pp.481-492. ⟨inria-00365411⟩
  • Aude Liefooghe, Helene Touzet, Jean-Stéphane Varré. Large Scale Matching for Position Weight Matrices. Combinatorial Pattern Matching, Jul 2006, Barcelona, Spain. pp.401-412, ⟨10.1007/11780441_36⟩. ⟨inria-00270270⟩

Poster

  • Nicolas Guillaudeux, Catherine Belleannée, Samuel Blanquart, Jean-Stéphane Varré. Predicting isoform transcripts: What does the comparison of known transcripts in human, mouse and dog tell us?. JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. 8, pp.1, 2019, ⟨10.7490/f1000research.1117311.1⟩. ⟨hal-02267357⟩
  • Pierre Marijon, Jean-Stéphane Varré, Rayan Chikhi. Debugging long-read genome and metagenome assemblies using string graph analysis. JOBIM 2017- Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France. ⟨hal-01574824⟩

Chapitre d'ouvrage

  • Jean-Stéphane Varré, Bertil Schmidt, Stéphane Janot, Mathieu Giraud. Manycore high-performance computing in bioinformatics. Laura Elnitski, Helen Piontkivska, Lonnie R Welch. Advances in Genomic Sequence Analysis and Pattern Discovery, World Scientific, chapter 8, 2011. ⟨hal-00563408⟩

HDR

  • Jean-Stéphane Varré. Algorithmes pour la comparaison de génomes et la recherche de signaux cis-régulateurs. Bio-informatique [q-bio.QM]. Université des Sciences et Technologie de Lille - Lille I, 2008. ⟨tel-00832685⟩