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PHONI: Streamed Matching Statistics with Multi-Genome References.
Boucher C, Gagie T, Tomohiro I, Köppl D, Langmead B, Manzini G, Navarro G, Pacheco A, Rossi M. Boucher C, et al. Proc Data Compress Conf. 2021 Mar;2021:193-202. doi: 10.1109/dcc50243.2021.00027. Epub 2021 May 10. Proc Data Compress Conf. 2021. PMID: 34778549 Free PMC article.
Succinct colored de Bruijn graphs.
Muggli MD, Bowe A, Noyes NR, Morley PS, Belk KE, Raymond R, Gagie T, Puglisi SJ, Boucher C. Muggli MD, et al. Among authors: boucher c. Bioinformatics. 2017 Oct 15;33(20):3181-3187. doi: 10.1093/bioinformatics/btx067. Bioinformatics. 2017. PMID: 28200001 Free PMC article.
Practical dynamic de Bruijn graphs.
Crawford VG, Kuhnle A, Boucher C, Chikhi R, Gagie T. Crawford VG, et al. Among authors: boucher c. Bioinformatics. 2018 Dec 15;34(24):4189-4195. doi: 10.1093/bioinformatics/bty500. Bioinformatics. 2018. PMID: 29939217
Prefix-free parsing for building big BWTs.
Boucher C, Gagie T, Kuhnle A, Langmead B, Manzini G, Mun T. Boucher C, et al. Algorithms Mol Biol. 2019 May 24;14:13. doi: 10.1186/s13015-019-0148-5. eCollection 2019. Algorithms Mol Biol. 2019. PMID: 31149025 Free PMC article.
Matching Reads to Many Genomes with the r-Index.
Mun T, Kuhnle A, Boucher C, Gagie T, Langmead B, Manzini G. Mun T, et al. Among authors: boucher c. J Comput Biol. 2020 Apr;27(4):514-518. doi: 10.1089/cmb.2019.0316. Epub 2020 Mar 16. J Comput Biol. 2020. PMID: 32181686 Free PMC article.
Pan-genomic matching statistics for targeted nanopore sequencing.
Ahmed O, Rossi M, Kovaka S, Schatz MC, Gagie T, Boucher C, Langmead B. Ahmed O, et al. Among authors: boucher c. iScience. 2021 Jun 8;24(6):102696. doi: 10.1016/j.isci.2021.102696. eCollection 2021 Jun 25. iScience. 2021. PMID: 34195571 Free PMC article.
Buffering updates enables efficient dynamic de Bruijn graphs.
Alanko J, Alipanahi B, Settle J, Boucher C, Gagie T. Alanko J, et al. Among authors: boucher c. Comput Struct Biotechnol J. 2021 Jul 6;19:4067-4078. doi: 10.1016/j.csbj.2021.06.047. eCollection 2021. Comput Struct Biotechnol J. 2021. PMID: 34377371 Free PMC article.
MONI: A Pangenomic Index for Finding Maximal Exact Matches.
Rossi M, Oliva M, Langmead B, Gagie T, Boucher C. Rossi M, et al. Among authors: boucher c. J Comput Biol. 2022 Feb;29(2):169-187. doi: 10.1089/cmb.2021.0290. Epub 2022 Jan 17. J Comput Biol. 2022. PMID: 35041495 Free PMC article.
839 results