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PFP Compressed Suffix Trees.
Boucher C, Cvacho O, Gagie T, Holub J, Manzini G, Navarro G, Rossi M. Boucher C, et al. Among authors: gagie t. Proc Worksh Algorithm Eng Exp. 2021;2021:60-72. doi: 10.1137/1.9781611976472.5. Proc Worksh Algorithm Eng Exp. 2021. PMID: 35355938 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: gagie t. Bioinformatics. 2017 Oct 15;33(20):3181-3187. doi: 10.1093/bioinformatics/btx067. Bioinformatics. 2017. PMID: 28200001 Free PMC article.
Document retrieval on repetitive string collections.
Gagie T, Hartikainen A, Karhu K, Kärkkäinen J, Navarro G, Puglisi SJ, Sirén J. Gagie T, et al. Inf Retr Boston. 2017;20(3):253-291. doi: 10.1007/s10791-017-9297-7. Epub 2017 Apr 1. Inf Retr Boston. 2017. PMID: 28596702 Free PMC article.
Relative Suffix Trees.
Farruggia A, Gagie T, Navarro G, Puglisi SJ, Sirén J. Farruggia A, et al. Among authors: gagie t. Comput J. 2018 May;61(5):773-788. doi: 10.1093/comjnl/bxx108. Epub 2017 Nov 21. Comput J. 2018. PMID: 29795706 Free PMC article.
Practical dynamic de Bruijn graphs.
Crawford VG, Kuhnle A, Boucher C, Chikhi R, Gagie T. Crawford VG, et al. Among authors: gagie t. 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. Among authors: gagie t. 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: gagie t. 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: gagie t. 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.
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