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40


Journal articles22 documents

  • Monika Brüggemann, Michaela Kotrova, Henrik Knecht, Jack Bartram, Myriam Boudjogrha, et al.. Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study. Leukemia, Nature Publishing Group: Open Access Hybrid Model Option B, 2019, ⟨10.1038/s41375-019-0496-7⟩. ⟨hal-02169053⟩
  • Tatiana Rocher, Mathieu Giraud, Mikaël Salson. Indexing labeled sequences. PeerJ Computer Science, PeerJ, 2018, 4, pp.1-14. ⟨10.7717/peerj-cs.148⟩. ⟨hal-01743104⟩
  • Jérôme Audoux, Nicolas Philippe, Rayan Chikhi, Mikael Salson, Mélina Gallopin, et al.. DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition. Genome Biology, BioMed Central, 2017, 18 (1), pp.1-15. ⟨10.1186/s13059-017-1372-2⟩. ⟨hal-01728770⟩
  • Mikael Salson, Mathieu Giraud, Aurélie Caillault, Nathalie Grardel, Nicolas Duployez, et al.. High-throughput sequencing in acute lymphoblastic leukemia: Follow-up of minimal residual disease and emergence of new clones. Leukemia Research, Elsevier, 2017, 53, pp.1-7. ⟨10.1016/j.leukres.2016.11.009⟩. ⟨hal-01404817⟩
  • Jérôme Audoux, Mikaël Salson, Christophe Grosset, Sacha Beaumeunier, Jean-Marc Holder, et al.. SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines. BMC Bioinformatics, BioMed Central, 2017, 18 (1), pp.428. ⟨10.1186/s12859-017-1831-5⟩. ⟨inserm-02437931⟩
  • Alice Héliou, Martine Léonard, Laurent Mouchard, Mikael Salson. Efficient dynamic range minimum query. Theoretical Computer Science, Elsevier, 2016, 656, pp.108-117. ⟨10.1016/j.tcs.2016.07.002⟩. ⟨hal-01255499v2⟩
  • Marc Duez, Mathieu Giraud, Ryan Herbert, Tatiana Rocher, Mikael Salson, et al.. Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing. PLoS ONE, Public Library of Science, 2016, 11 (11), ⟨10.1371/journal.pone.0166126⟩. ⟨hal-01397079⟩
  • Christophe Vroland, Mikael Salson, Sébastien Bini, Hélène Touzet. Approximate search of short patterns with high error rates using the 01⁎0 lossless seeds. Journal of Discrete Algorithms, Elsevier, 2016, 37, pp.3-16. ⟨10.1016/j.jda.2016.03.002⟩. ⟨hal-01360485⟩
  • Yann Ferret, Aurélie Caillault, Shéhérazade Sebda, Marc Duez, Nathalie Grardel, et al.. Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis. British Journal of Haematology, Wiley, 2016, 173 (3), pp.413-420. ⟨10.1111/bjh.13981⟩. ⟨hal-01279160⟩
  • Michaela Kotrova, Katerina Muzikova, Ester Mejstrikova, Michaela Novakova, Violeta Bakardjieva-Mihaylova, et al.. The predictive strength of next-generation sequencing MRD detection for relapse compared with current methods in childhood ALL.. Blood, American Society of Hematology, 2015, 126 (8), pp.1045-7. ⟨10.1182/blood-2015-07-655159⟩. ⟨hal-01241663⟩
  • Mathieu Giraud, Mikaël Salson, Marc Duez, Céline Villenet, Sabine Quief, et al.. Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing. BMC Genomics, BioMed Central, 2014, 15 (1), pp.409. ⟨10.1186/1471-2164-15-409⟩. ⟨hal-01009173⟩
  • Nicolas Philippe, Mikaël Salson, Thérèse Commes, Eric Rivals. CRAC: an integrated approach to the analysis of RNA-seq reads. Genome Biology, BioMed Central, 2013, 14 (3), pp.R30. ⟨10.1186/gb-2013-14-3-r30⟩. ⟨inserm-00850972⟩
  • Eric Rivals, Nicolas Philippe, Mikael Salson, Martine Léonard, Thérèse Commes, et al.. A Scalable Indexing Solution to Mine Huge Genomic Sequence Collections. ERCIM News, ERCIM, 2012, 2012 (89), pp.20-21. ⟨lirmm-00712653⟩
  • Martine Léonard, Laurent Mouchard, Mikaël Salson. On the number of elements to reorder when updating a suffix array. Journal of Discrete Algorithms, Elsevier, 2012, 11, pp.87-99. ⟨10.1016/j.jda.2011.01.002⟩. ⟨inria-00636066⟩
  • Mathieu Giraud, Mikaël Salson. Les séquenceurs à haut débit. Interstices, INRIA, 2011. ⟨hal-01350176⟩
  • Nicolas Philippe, Mikael Salson, Thérèse Commes, Eric Rivals. A combinatorial and integrated method to analyse RNA-seq reads. EMBnet.journal, EMBnet, 2011, 17 (Supplement B), pp.1. ⟨lirmm-00757979⟩
  • Nicolas Philippe, Mikael Salson, Thierry Lecroq, Martine Léonard, Thérèse Commes, et al.. Read indexing. EMBnet.journal, EMBnet, 2011, 17 (Supplement B), pp.1. ⟨lirmm-00757983⟩
  • Nicolas Philippe, Mikael Salson, Thierry Lecroq, Martine Léonard, Thérèse Commes, et al.. Querying Large Read Collections in Main Memory: A Versatile data Structure. BMC Bioinformatics, BioMed Central, 2011, 12, pp.242-258. ⟨10.1186/1471-2105-12-242⟩. ⟨lirmm-00632958⟩
  • Mikael Salson, Thierry Lecroq, Martine Léonard, Laurent Mouchard. Dynamic Extended Suffix Arrays. Journal of Discrete Algorithms, Elsevier, 2010, 8 (2), pp.241-257. ⟨hal-00468910⟩
  • Mikael Salson, T. Lecroq, M. Léonard, L. Mouchard. Dynamic Extended Suffix Array. Journal of Discrete Algorithms, Elsevier, 2010, 8 (2), pp.241--257. ⟨hal-00474818⟩
  • Mikael Salson, M. Léonard, L. Mouchard. A four-stage algorithm for updating a Burrows-Wheeler Tranform. Theoretical Computer Science, Elsevier, 2009, 410 (43), pp.4350--4359. ⟨hal-00474814⟩
  • Mikael Salson, Thierry Lecroq, Martine Léonard, Laurent Mouchard. A Four-Stage Algorithm for Updating a Burrows-Wheeler Transform. Theoretical Computer Science, Elsevier, 2009, 43 (10), pp.4350-4359. ⟨hal-00469113⟩

Conference papers15 documents

  • Tatiana Rocher, Mathieu Giraud, Mikael Salson. Indexer un ensemble de séquences ADN annotées. JOBIM, Jun 2016, Lyon, France. ⟨hal-01576319⟩
  • Nathalie Grardel, Mikaël Salson, Aurélie Caillault, Marc Duez, Céline Villenet, et al.. Diagnostic et suivi des leucémies aiguës lymphoblastiques (LAL) par séquençage haut-débit (HTS). Congrès de la Société Française d'Hématologie (SFH), 2014, Paris, France. ⟨hal-01100152⟩
  • Evguenia Kopylova, Laurent Noé, Pierre Pericard, Mikaël Salson, Hélène Touzet. SortMeRNA 2: ribosomal RNA classification for taxonomic assignation. Workshop on Recent Computational Advances in Metagenomics, ECCB 2014, Sep 2014, Strasbourg, France. ⟨hal-01094011⟩
  • Christophe Vroland, Mikaël Salson, Hélène Touzet. Lossless seeds for searching short patterns with high error rates. International Workshop On Combinatorial Algorithms, Oct 2014, Duluth, United States. ⟨hal-01079840⟩
  • 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⟩
  • Nicolas Philippe, Mikael Salson, Thierry Lecroq, Martine Léonard, Thérèse Commes, et al.. A solution to index large set of short reads. seqBi11 - Workshop Algorithmique, combinatoire du texte et applications en bio-informatique, 2011, Rennes, France. ⟨hal-00560731⟩
  • Martine Leonard, Laurent Mouchard, Mikael Salson. Coût d'une mise à jour de la table des suffixes. Journées GdT COMATEGE du GDR IM, 2010, Montpellier, France. ⟨hal-00516722⟩
  • M. Léonard, L. Mouchard, M. Salson. Average Complexity for Updating a Suffix Array. London Stringology Days, 2010, United Kingdom. Accepted. ⟨hal-00474822⟩
  • Maxime Crochemore, L. Mouchard, Mikael Salson, B. Smyth. Efficient Dynamic Range Minimum Query. International Stringology Conference, 2010, Tel Aviv, Israel. ⟨hal-00474828⟩
  • A. Al-Hafeed, L. Mouchard, M. Salson, B. Smyth. Sliding a Suffix Array Along a Text. London Stringology Days, 2010, United Kingdom. Accepted. ⟨hal-00474821⟩
  • Mikael Salson, Thierry Lecroq, Martine Leonard, Laurent Mouchard. Dynamic Burrows-Wheeler Transform. Stringology Research Workshop 09, 2009, Tel Aviv, Israel. ⟨hal-00516727⟩
  • Mikael Salson, Thierry Lecroq, Martine Léonard, Laurent Mouchard. Dynamic Extended Suffix Arrays. London String Days and London Algorithmics Workshop, 2009, France. ⟨hal-00516719⟩
  • Mikael Salson, Thierry Lecroq, Martine Leonard, Laurent Mouchard. Dynamic Suffix Array with experiments and a specific emphasis on LCP arrays. Stringology Research Workshop 09, 2009, Tel Aviv, Israel. ⟨hal-00516720⟩
  • Mikael Salson, Thierry Lecroq, Martine Leonard, Laurent Mouchard. Dynamic Burrows-Wheeler Transform. Prague Stringology Conference, 2008, Prague, Czech Republic. pp.13-25. ⟨hal-00469530⟩
  • Mikael Salson, M. Léonard, L. Mouchard. Dynamic Burrows-Wheeler Transform. Prague Stringology Conference, 2008, Czech Republic. pp.13--25. ⟨hal-00474813⟩

Poster communications1 document

  • Nathalie Grardel, Mathieu Giraud, Mikaël Salson, Marc Duez. Multiclonal Diagnosis and MRD Follow-up in ALL with HTS Coupled with a Bioinformatic Analysis. American Society of Hematology Annual Meeting, 2014, San Francisco, France. 2014. ⟨hal-01100290⟩

Other publications1 document

  • Mikael Salson, Aurélie Caillault, Marc Duez, Yann Ferret, Alice Fievet, et al.. A dataset of sequences with manually curated V(D)J designations. 2016. ⟨hal-01331556⟩

Preprints, Working Papers, ...1 document

  • Camille Marchet, Christina Boucher, Simon Puglisi, Paul Medvedev, Mikaël Salson, et al.. Data structures based on k-mers for querying large collections of sequencing datasets. 2019. ⟨hal-02414162⟩