Publications

Peer-reviewed journals, book chapters and books

23 results
2022
[23] Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r (, , , , , , , , , , , , , , , and ), In BMC Bioinformatics, volume 23, . [bibtex] [pdf] [doi]
[22]Sequence Indexing ( and ), Chapter in From Sequences to Graphs: Discrete Methods and Structures for Bioinformatics, John Wiley & Sons, Inc. Hoboken, NJ, USA, . [bibtex] [doi]
[21]From Sequences to Graphs: Discrete Methods and Structures for Bioinformatics ( and ), John Wiley & Sons, . [bibtex] [doi]
[20] One-Step Next-Generation Sequencing of Immunoglobulin and T-Cell Receptor Gene Recombinations for MRD Marker Identification in Acute Lymphoblastic Leukemia (, , , , , and ), Chapter in Immunogenetics (Langerak A.W., ed.), Methods in molecular biology (Clifton, NJ), volume 2453, . [bibtex] [pdf] [doi]
[19] Immunoglobulin Gene Mutational Status Assessment by Next Generation Sequencing in Chronic Lymphocytic Leukemia (, , , , , and ), Chapter in Immunogenetics (Langerak A.W., ed.), Methods in molecular biology (Clifton, NJ), volume 2453, . [bibtex] [pdf] [doi]
2021
[18] Data structures based on k-mers for querying large collections of sequencing data sets (, , , , and ), In Genome Research, Cold Spring Harbor Lab, volume 31, . [bibtex] [pdf]
2020
[17] REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets (, , , and ), In Bioinformatics, volume 36, . [bibtex] [pdf] [doi]
2019
[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 (, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , and ), In Leukemia, . [bibtex] [pdf] [doi]
2018
[15] Indexing labeled sequences (, and ), In PeerJ CS, volume 4, . [bibtex] [pdf] [doi]
2017
[14] High-throughput sequencing in acute lymphoblastic leukemia: Follow-up of minimal residual disease and emergence of new clones (, , , , , , , , , , , , and ), In Leukemia Research, volume 53, . [bibtex] [pdf] [doi]
[13] SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines (, , , , , and ), In BMC Bioinformatics, volume 18, . [bibtex] [pdf] [doi]
[12] DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition (, , , , , , , , and ), In Genome Biology, volume 18, . [bibtex] [pdf] [doi]
2016
[11] Approximate search of short patterns with high error rates using the 01∗0 lossless seeds (, , and ), In Journal of Discrete Algorithms, volume 37, . [bibtex] [pdf] [doi]
[10] Efficient dynamic range minimum query (, , and ), In Theor. Comput. Sci., . [bibtex] [pdf] [doi]
[9] Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis (, , , , , , , , , and ), In British J. of Haematology, . [bibtex] [pdf] [doi]
[8] Vidjil: A web platform for analysis of high-throughput repertoire sequencing (, , , , and ), In PLOS One, volume 11, . [bibtex] [pdf] [doi]
2015
[7] The predictive strength of next-generation sequencing MRD detection for relapse compared with current methods in childhood ALL (, , , , , , , , , , , , , and ), In Blood, American Society of Hematology, volume 126, . [bibtex] [pdf] [doi]
2014
[6] Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing (, , , , , , , , and ), In BMC Genomics, volume 15, . [bibtex] [pdf] [doi]
2013
[5] CRAC: an integrated approach to the analysis of RNA-seq reads (, , and ), In Genome Biology, volume 14, . [bibtex] [pdf] [doi]
2011
[4] Querying large read collections in main memory: a versatile data structure (, , , , and ), In BMC Bioinformatics, . [bibtex] [pdf] [doi]
[3] On the number of elements to reorder when updating a suffix array (, and ), In Journal of Discrete Algorithms, . [bibtex] [pdf] [doi]
2010
[2] Dynamic Extended Suffix Arrays (, , and ), In Journal of Discrete Algorithms, volume 8, . [bibtex] [pdf] [doi]
2009
[1] A Four-Stage Algorithm for Updating a Burrows-Wheeler Transform (, , and ), In Theor. Comput. Sci., volume 410, . [bibtex] [pdf] [doi]

Peer-reviewed conferences

2 results
2015
[2] Lossless seeds for searching short patterns with high error rates (, and ), In Proc. of International Workshop On Combinatorial Algorithms (IWOCA), volume 8986, . [bibtex] [pdf]
2008
[1] Dynamic Burrows-Wheeler Transform (, , and ), In Proc. of Prague Stringology Conference (PSC), . [bibtex] [pdf]

Miscellaneous

4 results
2023
[4] Méthodes sans alignement et indexation pour l'analyse de données nucléiques massives (), Habilitation à diriger des recherches, . [bibtex] [pdf]
2021
[3] SARS-CoV-2 Through the Lens of Computational Biology: How bioinformatics is playing a key role in the study of the virus and its origins (, , , , , , , and ), . [bibtex] [pdf]
2016
[2] A Dataset of Sequences with Manually Curated V(D)J Designations (, , , , , , , , , and ), RepSeq workshop, . [bibtex] [pdf]
2009
[1] Structures d'indexation compressées et dynamiques pour le texte (), PhD² thesis, Université de Rouen, . [bibtex] [pdf]