|
| [27] | Alignment-free detection and seed-based identification of multi-loci V(D)J recombinations in Vidjil-algo (Cyprien Borée, Mathieu Giraud and Mikaël Salson), In Peer Community Journal, volume 5, 2025. |
| [26] | CREMSA: Compressed indexing of (ultra) large multiple sequence alignments (M. Salson, A. Boddaert, A.B. Gueye, L. Bulteau, Y. Hernandez--Courbevoie, C. Marchet, N. Pan, S. Will and Y. Ponty), In Bioinformatics [Accepted at ISMB], 2025. |
|
| [25] | Midostaurin shapes macroclonal and microclonal evolution of FLT3-mutated acute myeloid leukemia (Romane Joudinaud, Augustin Boudry, Laurène Fenwarth, Sandrine Geffroy, Mikaël Salson, Hervé Dombret, Celine Berthon, Arnaud Pigneux, Delphine Lebon, Pierre Peterlin, Simon Bouzy, Pascale Flandrin-Gresta, Emmanuelle Tavernier, Martin Carre, Sylvie Tondeur, Lamya Haddaoui, Raphaël Itzykson, Sarah Bertoli, Audrey Bidet, Eric Delabesse, Mathilde Hunault, Christan Récher and Claude Preudhomme, Nicolas Duployez and Pierre-Yves Dumas), In Blood Advances, 2024. |
| [24] | Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data (Chloé Bessière, Haoliang Xue, Benoit Guibert, Anthony Boureux, Florence Rufflé, Julien Viot, Rayan Chikhi, Mikaël Salson, Camille Marchet, Thérèse Commes and Daniel Gautheret), In Genome Biology, BioMed Central, volume 25, 2024. |
|
| [23] | Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r (Augustin Boudry, Sasha Darmon, Nicolas Duployez, Martin Figeac, Sandrine Geffroy, Maxime Bucci, Karine Celli-Lebras, Matthieu Duchmann, Romane Joudinaud, Laurène Fenwarth, Olivier Nibourel, Laure Goursaud, Raphael Itzykson, Hervé Dombret, Mathilde Hunault, Claude Preudhomme and Mikaël Salson), In BMC Bioinformatics, volume 23, 2022. |
| [22] | Sequence Indexing (Thierry Lecroq and Mikaël Salson), Chapter in From Sequences to Graphs: Discrete Methods and Structures for Bioinformatics, John Wiley & Sons, Inc. Hoboken, NJ, USA, 2022. |
| [21] | From Sequences to Graphs: Discrete Methods and Structures for Bioinformatics (Annie Chateau and Mikaël Salson), John Wiley & Sons, 2022. |
| [20] | One-Step Next-Generation Sequencing of Immunoglobulin and T-Cell Receptor Gene Recombinations for MRD Marker Identification in Acute Lymphoblastic Leukemia (P. Villarese, C. Abdo, M. Bertrand, F. Thonier, M. Giraud, M. Salson and E. Macintyre), Chapter in Immunogenetics (Langerak A.W., ed.), Methods in molecular biology (Clifton, NJ), volume 2453, 2022. |
| [19] | Immunoglobulin Gene Mutational Status Assessment by Next Generation Sequencing in Chronic Lymphocytic Leukemia (A. Langlois de Septenville, M. Boudjoghra, C. Bravetti, M. Armand, M. Salson, M. Giraud and F. Davi), Chapter in Immunogenetics (Langerak A.W., ed.), Methods in molecular biology (Clifton, NJ), volume 2453, 2022. |
|
| [18] | Data structures based on k-mers for querying large collections of sequencing data sets (C. Marchet, C. Boucher, S. J. Puglisi, P. Medvedev, M. Salson and R. Chikhi), In Genome Research, Cold Spring Harbor Lab, volume 31, 2021. |
|
| [17] | REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets (C. Marchet, Z. Iqbal, D. Gautheret, M. Salson and R. Chikhi), In Bioinformatics, volume 36, 2020. |
|
| [16] | 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 (Monika Brüggemann, Michaela Kotrova, Henrik Knecht, Jack Bartram, Myriam Boudjogrha, Vojtech Bystry, Grazia Fazio, Eva Froňková, Mathieu Giraud, Andrea Grioni, Jeremy Hancock, Dietrich Herrmann, Cristina Jimenez, Adam Krejci, John Moppett, Tomas Reigl, Mikaël Salson, Blanca Scheijen, Martin Schwarz, Simona Songia, Michael Svaton, Jacques J. M. Van Dongen, Patrick Villarese, Stephanie Wakeman, Gary Wright, Giovanni Cazzaniga, Frédéric Davi, Ramón García-Sanz, David Davi, Patricia Groenen, Michael Hummel, Elizabeth Macintyre, Kostas C Stamatopoulos, Christiane Pott, Jan Trka, Nikos Darzentas and Anton Langerak), In Leukemia, 2019. |
|
| [15] | Indexing labeled sequences (Tatiana Rocher, Mathieu Giraud and Mikaël Salson), In PeerJ CS, volume 4, 2018. |
|
| [14] | 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 and Claude Preudhomme), In Leukemia Research, volume 53, 2017. |
| [13] | SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines (Jérôme Audoux, Mikaël Salson, Christophe F. Grosset, Sacha Beaumeunier, Jean-Marc Holder, Thérèse Commes and Nicolas Philippe), In BMC Bioinformatics, volume 18, 2017. |
| [12] | DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition (Jérôme Audoux, Nicolas Philippe, Rayan Chikhi, Mikaël Salson, Mélina Gallopin, Marc Gabriel, Jérémy Le Coz, Émilie Drouineau, Thérèse Commes and Daniel Gautheret), In Genome Biology, volume 18, 2017. |
|
| [11] | Approximate search of short patterns with high error rates using the 01∗0 lossless seeds (C. Vroland, M. Salson, S. Bini and H. Touzet), In Journal of Discrete Algorithms, volume 37, 2016. |
| [10] | Efficient dynamic range minimum query (Alice Heliou, Martine Léonard, Laurent Mouchard and Mikaël Salson), In Theor. Comput. Sci., 2016. |
| [9] | 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 and M. Giraud), In British J. of Haematology, 2016. |
| [8] | Vidjil: A web platform for analysis of high-throughput repertoire sequencing (Marc Duez, Mathieu Giraud, Ryan Herbert, Tatiana Rocher, Mikaël Salson and Florian Thonier), In PLOS One, volume 11, 2016. |
|
| [7] | 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 and Eva Fronkova), In Blood, American Society of Hematology, volume 126, 2015. |
|
| [6] | 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 and Martin Figeac), In BMC Genomics, volume 15, 2014. |
|
| [5] | CRAC: an integrated approach to the analysis of RNA-seq reads (N. Philippe, M. Salson, T. Commes and É. Rivals), In Genome Biology, volume 14, 2013. |
|
| [4] | Querying large read collections in main memory: a versatile data structure (N. Philippe, M. Salson, T. Lecroq, M. Léonard, T. Commes and É. Rivals), In BMC Bioinformatics, 2011. |
| [3] | On the number of elements to reorder when updating a suffix array (M. Léonard, L. Mouchard and M. Salson), In Journal of Discrete Algorithms, 2011. |
|
| [2] | Dynamic Extended Suffix Arrays (M. Salson, T. Lecroq, M. Léonard and L. Mouchard), In Journal of Discrete Algorithms, volume 8, 2010. |
|
| [1] | A Four-Stage Algorithm for Updating a Burrows-Wheeler Transform (M. Salson, T. Lecroq, M. Léonard and L. Mouchard), In Theor. Comput. Sci., volume 410, 2009. |
