Publications

Peer-reviewed journals

2016
Approximate search of short patterns with high error rates using the 01∗0 lossless seeds (C. Vroland, M. Salson, S. Bini, H. Touzet), In Journal of Discrete Algorithms, 2016. [bib] [pdf]
High-throughput sequencing in acute lymphoblastic leukemia: Follow-up of minimal residual disease and emergence of new clones (Mikaël Salson, Mathieu Giraud, Aurélie Caillault, Nathalie Grardel, Nicolas Duployez, Yann Ferret, Marc Duez, Ryan Herbert, Tatiana Rocher, Shéhérazade Sebda, Sabine Quief, Céline Villenet, Martin Figeac, Claude Preudhomme), In Leukemia Research, 2016. (Accepted) [bib] [doi]
Efficient dynamic range minimum query (Alice Heliou, Martine Léonard, Laurent Mouchard, Mikaël Salson), In Theor. Comput. Sci., 2016. [bib] [pdf] [doi]
Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis (Y. Ferret, A. Caillault, S. Sebda, M. Duez, N. Gradel, N. Duployez, C. Villenet, M. Figeac, C. Preudhomme, M. Salson, M. Giraud), In British J. of Haematology, 2016. [bib] [pdf] [doi]
Vidjil: A web platform for analysis of high-throughput repertoire sequencing (Marc Duez, Mathieu Giraud, Ryan Herbert, Tatiana Rocher, Mikaël Salson, Florian Thonier), In PLOS One, volume 11, 2016. [bib] [pdf] [doi]
2015
The predictive strength of next-generation sequencing MRD detection for relapse compared with current methods in childhood ALL (Michaela Kotrova, Katerina Muzikova, Ester Mejstrikova, Michaela Novakova, Violeta Bakardjieva-Mihaylova, Karel Fiser, Jan Stuchly, Mathieu Giraud, Mikaël Salson, Christiane Pott, Monika Brüggemann, Marc Füllgrabe, Jan Stary, Jan Trka, Eva Fronkova), In Blood, American Society of Hematology, volume 126, 2015. [bib] [pdf] [doi]
2014
Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing (Mathieu Giraud, Mikaël Salson, Marc Duez, Céline Villenet, Sabine Quief, Aurélie Caillault, Nathalie Grardel, Christophe Roumier, Claude Preudhomme, Martin Figeac), In BMC Genomics, volume 15, 2014. [bib] [pdf] [doi]
2013
CRAC: an integrated approach to the analysis of RNA-seq reads (N. Philippe, M. Salson, T. Commes, É. Rivals), In Genome Biology, volume 14, 2013. [bib] [pdf] [doi]
2011
Querying large read collections in main memory: a versatile data structure (N. Philippe, M. Salson, T. Lecroq, M. Léonard, T. Commes, É. Rivals), In BMC Bioinformatics, 2011. [bib] [pdf] [doi]
On the number of elements to reorder when updating a suffix array (M. Léonard, L. Mouchard, M. Salson), In Journal of Discrete Algorithms, 2011. [bib] [pdf] [doi]
2010
Dynamic Extended Suffix Arrays (M. Salson, T. Lecroq, M. Léonard, L. Mouchard), In Journal of Discrete Algorithms, volume 8, 2010. [bib] [pdf] [doi]
2009
A Four-Stage Algorithm for Updating a Burrows-Wheeler Transform (M. Salson, T. Lecroq, M. Léonard, L. Mouchard), In Theor. Comput. Sci., volume 410, 2009. [bib] [pdf] [doi]
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Peer-reviewed conferences

2015
Lossless seeds for searching short patterns with high error rates (C. Vroland, M. Salson, H. Touzet), In Proc. of International Workshop On Combinatorial Algorithms (IWOCA), volume 8986, 2015. [bib] [pdf]
2008
Dynamic Burrows-Wheeler Transform (M. Salson, T. Lecroq, M. Léonard, L. Mouchard), In Proc. of Prague Stringology Conference (PSC), 2008. [bib] [pdf]
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Miscellaneous

2016
A Dataset of Sequences with Manually Curated V(D)J Designations (Mikaël Salson, Aurélie Caillault, Marc Duez, Yann Ferret, Alice Fievet, Michaela Kotrova, Florian Thonier, Patrick Villarese, Stephanie Wakeman, Gary Wright, Mathieu Giraud), RepSeq workshop, 2016. [bib] [pdf]
2009
Structures d'indexation compressées et dynamiques pour le texte (M. Salson), PhD thesis, Université de Rouen, 2009. [bib] [pdf]
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