Jean-Stéphane Varré
Contact
jean-stephane.varre[chez]univ-lille[point].fr
+33 3 28 77 85 57
Campus Cité Scientifique, M3 extension, 207
Publications
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"title_s":["yacrd and fpa: upstream tools for long-read genome assembly"],
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"citationRef_s":"<i>Journal of Clinical Virology</i>, 2020, 122, pp.104206. <a target=\"_blank\" href=\"https://dx.doi.org/10.1016/j.jcv.2019.104206\">⟨10.1016/j.jcv.2019.104206⟩</a>",
"citationFull_s":"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. <i>Journal of Clinical Virology</i>, 2020, 122, pp.104206. <a target=\"_blank\" href=\"https://dx.doi.org/10.1016/j.jcv.2019.104206\">⟨10.1016/j.jcv.2019.104206⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-02403094v1\">⟨hal-02403094⟩</a>",
"title_s":["Use of whole-genome sequencing in the molecular investigation of care-associated HCoV-OC43 infections in a hematopoietic stem cell transplant unit"],
"authFullName_s":["Delphine Beury","Léa Fléchon","Florence Maurier","Ségolène Caboche","Jean-Stéphane Varré","Helene Touzet","Jean Dubuisson","David Hot","Benoît Guéry","Anne Goffard"],
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"citationFull_s":"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?. <i>JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques</i>, Jul 2019, Nantes, France. 8, pp.1, 2019, <a target=\"_blank\" href=\"https://dx.doi.org/10.7490/f1000research.1117311.1\">⟨10.7490/f1000research.1117311.1⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-02267357v1\">⟨hal-02267357⟩</a>",
"title_s":["Predicting isoform transcripts: What does the comparison of known transcripts in human, mouse and dog tell us?"],
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"citationRef_s":"<i>Virology</i>, 2019, 531, pp.141-148. <a target=\"_blank\" href=\"https://dx.doi.org/10.1016/j.virol.2019.03.006\">⟨10.1016/j.virol.2019.03.006⟩</a>",
"citationFull_s":"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. <i>Virology</i>, 2019, 531, pp.141-148. <a target=\"_blank\" href=\"https://dx.doi.org/10.1016/j.virol.2019.03.006\">⟨10.1016/j.virol.2019.03.006⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-02167880v1\">⟨hal-02167880⟩</a>",
"title_s":["A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43"],
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"citationFull_s":"Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré. Graph analysis of fragmented long-read bacterial genome assemblies. <i>Bioinformatics</i>, 2019, <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioinformatics/btz219\">⟨10.1093/bioinformatics/btz219⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-02167175v1\">⟨hal-02167175⟩</a>",
"title_s":["Graph analysis of fragmented long-read bacterial genome assemblies"],
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"citationFull_s":"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. <i>International Journal of Molecular Sciences</i>, 2019, 20, <a target=\"_blank\" href=\"https://dx.doi.org/10.3390/ijms20194788\">⟨10.3390/ijms20194788⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-02298474v1\">⟨hal-02298474⟩</a>",
"title_s":["Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome"],
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"citationFull_s":"Pierre Marijon, Jean-Stéphane Varré, Rayan Chikhi. Debugging long-read genome and metagenome assemblies using string graph analysis. <i>JOBIM 2017- Journées Ouvertes en Biologie, Informatique et Mathématiques</i>, Jul 2017, Lille, France. <a target=\"_blank\" href=\"https://project.inria.fr/jobim2017/\"></a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-01574824v1\">⟨hal-01574824⟩</a>",
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"citationFull_s":"Samuel Blanquart, Jean-Stéphane Varré, Paul Guertin, Amandine Perrin, Anne Bergeron, et al.. Assisted transcriptome reconstruction and splicing orthology. <i>BMC Genomics</i>, 2016, Proceedings of the 14th Annual Research in Computational Molecular Biology (RECOMB) Comparative Genomics Satellite Workshop: genomics, 17 (Suppl 10), pp.786. <a target=\"_blank\" href=\"https://dx.doi.org/10.1186/s12864-016-3103-6\">⟨10.1186/s12864-016-3103-6⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-01396410v1\">⟨hal-01396410⟩</a>",
"title_s":["Assisted transcriptome reconstruction and splicing orthology"],
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"citationFull_s":"Tuan Tu Tran, Mathieu Giraud, Jean-Stéphane Varré. Perfect Hashing Structures for Parallel Similarity Searches. <i>International Workshop on High Performance Computational Biology (HiCOMB 2015) / International Parallel and Distributed Processing Symposium (IPDPS 2015)</i>, 2015, Hyderabad, India. pp.332-341, <a target=\"_blank\" href=\"https://dx.doi.org/10.1109/IPDPSW.2015.105\">⟨10.1109/IPDPSW.2015.105⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-01153893v1\">⟨hal-01153893⟩</a>",
"title_s":["Perfect Hashing Structures for Parallel Similarity Searches"],
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"citationFull_s":"Amandine Perrin, Jean-Stéphane Varré, Samuel Blanquart, Aïda Ouangraoua. ProCARs: Progressive Reconstruction of Ancestral Gene Orders. <i>BMC Genomics</i>, 2015, 16 (Suppl 5), pp.S6. <a target=\"_blank\" href=\"https://dx.doi.org/10.1186/1471-2164-16-S5-S6\">⟨10.1186/1471-2164-16-S5-S6⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-01217311v1\">⟨hal-01217311⟩</a>",
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"citationFull_s":"Mathieu Giraud, Mikaël Salson, Marc Duez, Jean-Stéphane Varré, Céline Villenet, et al.. Suivi de la leucémie résiduelle par séquençage haut-débit. <i>JOBIM</i>, Jul 2013, Toulouse, France. <a target=\"_blank\" href=\"https://inria.hal.science/hal-00857581v1\">⟨hal-00857581⟩</a>",
"title_s":["Suivi de la leucémie résiduelle par séquençage haut-débit"],
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"title_s":["Tandem Halving Problems by DCJ"],
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"citationRef_s":"<i>BIOINFORMATICS</i>, Feb 2012, Lisboa, Portugal. pp.58-65",
"citationFull_s":"Antoine Thomas, Aïda Ouangraoua, Jean-Stéphane Varré. Genome Halving by Block Interchange. <i>BIOINFORMATICS</i>, Feb 2012, Lisboa, Portugal. pp.58-65. <a target=\"_blank\" href=\"https://hal.science/hal-00749026v1\">⟨hal-00749026⟩</a>",
"title_s":["Genome Halving by Block Interchange"],
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"citationFull_s":"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. <i>JOBIM 2011</i>, Jul 2011, Paris, France. <a target=\"_blank\" href=\"https://hal.science/hal-00637847v1\">⟨hal-00637847⟩</a>",
"title_s":["biomanycores.org: a repository of interoperable open-source code for many-core bioinformatics"],
"authFullName_s":["Jean-Frédéric Berthelot","Charles Deltel","Mathieu Giraud","Stéphane Janot","Laetitia Jourdan","Dominique Lavenier","Helene Touzet","Jean-Stéphane Varré"],
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"citationFull_s":"Mathieu Giraud, Stéphane Janot, Jean-Frédéric Berthelot, Charles Deltel, Laetitia Jourdan, et al.. Biomanycores, open-source parallel code for many-core bioinformatics. <i>Bioinformatics Open Source Conference (BOSC 2011)</i>, 2011, Vienne, Austria. <a target=\"_blank\" href=\"https://inria.hal.science/inria-00623390v1\">⟨inria-00623390⟩</a>",
"title_s":["Biomanycores, open-source parallel code for many-core bioinformatics"],
"authFullName_s":["Mathieu Giraud","Stéphane Janot","Jean-Frédéric Berthelot","Charles Deltel","Laetitia Jourdan","Dominique Lavenier","Helene Touzet","Jean-Stéphane Varré"],
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"title_s":["Genome Dedoubling by DCJ and Reversal"],
"authFullName_s":["Antoine Thomas","Jean-Stéphane Varré","Ouangraoua Aïda"],
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"citationFull_s":"Aude Darracq, Jean-Stéphane Varré, Laurence Maréchal-Drouard, Adeline Courseaux, Vincent Castric, et al.. Structural and content diversity of mitochondrial genome in beet: a comparative genomic analysis. <i>Genome Biology and Evolution</i>, 2011, 3, pp.723-736. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/gbe/evr042\">⟨10.1093/gbe/evr042⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-00616508v1\">⟨hal-00616508⟩</a>",
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"citationFull_s":"Antoine Thomas, Jean-Stéphane Varré, Aïda Ouangraoua. Genome dedoubling by DCJ and reversal. <i>BMC Bioinformatics</i>, 2011, 12 (Suppl 9), pp.S20. <a target=\"_blank\" href=\"https://dx.doi.org/10.1186/1471-2105-12-S9-S20\">⟨10.1186/1471-2105-12-S9-S20⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-00784416v1\">⟨hal-00784416⟩</a>",
"title_s":["Genome dedoubling by DCJ and reversal"],
"authFullName_s":["Antoine Thomas","Jean-Stéphane Varré","Aïda Ouangraoua"],
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"citationRef_s":"<i>Parallel Processing and Applied Mathematics / Parallel Biocomputing Conference (PPAM / PBC 11)</i>, 2011, Torun, Poland",
"citationFull_s":"Tuan Tu Tran, Mathieu Giraud, Jean-Stéphane Varré. Bit-Parallel Multiple Pattern Matching. <i>Parallel Processing and Applied Mathematics / Parallel Biocomputing Conference (PPAM / PBC 11)</i>, 2011, Torun, Poland. <a target=\"_blank\" href=\"https://inria.hal.science/inria-00637227v1\">⟨inria-00637227⟩</a>",
"title_s":["Bit-Parallel Multiple Pattern Matching"],
"authFullName_s":["Tuan Tu Tran","Mathieu Giraud","Jean-Stéphane Varré"],
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"citationRef_s":"Laura Elnitski, Helen Piontkivska, Lonnie R Welch. <i>Advances in Genomic Sequence Analysis and Pattern Discovery</i>, World Scientific, chapter 8, 2011",
"citationFull_s":"Jean-Stéphane Varré, Bertil Schmidt, Stéphane Janot, Mathieu Giraud. Manycore high-performance computing in bioinformatics. Laura Elnitski, Helen Piontkivska, Lonnie R Welch. <i>Advances in Genomic Sequence Analysis and Pattern Discovery</i>, World Scientific, chapter 8, 2011. <a target=\"_blank\" href=\"https://hal.science/hal-00563408v1\">⟨hal-00563408⟩</a>",
"title_s":["Manycore high-performance computing in bioinformatics"],
"authFullName_s":["Jean-Stéphane Varré","Bertil Schmidt","Stéphane Janot","Mathieu Giraud"],
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"citationRef_s":"<i>Parallel Computing</i>, 2011, 37, pp.466-478. <a target=\"_blank\" href=\"https://dx.doi.org/10.1016/j.parco.2010.10.001\">⟨10.1016/j.parco.2010.10.001⟩</a>",
"citationFull_s":"Mathieu Giraud, Jean-Stéphane Varré. Parallel Position Weight Matrices Algorithms. <i>Parallel Computing</i>, 2011, 37, pp.466-478. <a target=\"_blank\" href=\"https://dx.doi.org/10.1016/j.parco.2010.10.001\">⟨10.1016/j.parco.2010.10.001⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-00623404v1\">⟨hal-00623404⟩</a>",
"title_s":["Parallel Position Weight Matrices Algorithms"],
"authFullName_s":["Mathieu Giraud","Jean-Stéphane Varré"],
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"citationRef_s":"<i>Nucleic Acids Research</i>, 2010, 38 (S2), pp.W286-W292. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/nar/gkq473\">⟨10.1093/nar/gkq473⟩</a>",
"citationFull_s":"Tonon Laurie, Hélène Touzet, Jean-Stéphane Varré. TFM-Explorer: mining cis-regulatory regions in genomes. <i>Nucleic Acids Research</i>, 2010, 38 (S2), pp.W286-W292. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/nar/gkq473\">⟨10.1093/nar/gkq473⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-00823465v1\">⟨hal-00823465⟩</a>",
"title_s":["TFM-Explorer: mining cis-regulatory regions in genomes"],
"authFullName_s":["Tonon Laurie","Hélène Touzet","Jean-Stéphane Varré"],
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"citationRef_s":"<i>BMC Genomics</i>, 2010, 11, pp.233. <a target=\"_blank\" href=\"https://dx.doi.org/10.1186/1471-2164-11-233\">⟨10.1186/1471-2164-11-233⟩</a>",
"citationFull_s":"Aude Darracq, Jean-Stéphane Varré, Pascal Touzet. A scenario of mitochondrial genome evolution in maize based on rearrangement events. <i>BMC Genomics</i>, 2010, 11, pp.233. <a target=\"_blank\" href=\"https://dx.doi.org/10.1186/1471-2164-11-233\">⟨10.1186/1471-2164-11-233⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-00468454v1\">⟨hal-00468454⟩</a>",
"title_s":["A scenario of mitochondrial genome evolution in maize based on rearrangement events"],
"authFullName_s":["Aude Darracq","Jean-Stéphane Varré","Pascal Touzet"],
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