Publications

Peer-reviewed journals

15 results
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

2 results
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 (), PhD thesis, Université de Rouen, . [bibtex] [pdf]