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Hybrid indexes for repetitive datasets.
Ferrada H, Gagie T, Hirvola T, Puglisi SJ. Ferrada H, et al. Among authors: gagie t. Philos Trans A Math Phys Eng Sci. 2014 Apr 21;372(2016):20130137. doi: 10.1098/rsta.2013.0137. Print 2014 May 28. Philos Trans A Math Phys Eng Sci. 2014. PMID: 24751871
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.
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.
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: gagie t. 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.
Finding Maximal Exact Matches Using the r-Index.
Rossi M, Oliva M, Bonizzoni P, Langmead B, Gagie T, Boucher C. Rossi M, et al. Among authors: gagie t. J Comput Biol. 2022 Feb;29(2):188-194. doi: 10.1089/cmb.2021.0445. Epub 2022 Jan 17. J Comput Biol. 2022. PMID: 35041518 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
39 results