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2021 10
2022 5
2023 11
2024 6

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PFP-FM: An Accelerated FM-index.
Hong A, Oliva M, Köppl D, Bannai H, Boucher C, Gagie T. Hong A, et al. Res Sq [Preprint]. 2023 Oct 30:rs.3.rs-3487536. doi: 10.21203/rs.3.rs-3487536/v1. Res Sq. 2023. PMID: 37961504 Free PMC article. Updated. Preprint.
Pfp-fm: an accelerated FM-index.
Hong A, Oliva M, Köppl D, Bannai H, Boucher C, Gagie T. Hong A, et al. Algorithms Mol Biol. 2024 Apr 10;19(1):15. doi: 10.1186/s13015-024-00260-8. Algorithms Mol Biol. 2024. PMID: 38600518 Free PMC article.
PFP Compressed Suffix Trees.
Boucher C, Cvacho O, Gagie T, Holub J, Manzini G, Navarro G, Rossi M. Boucher C, et al. 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.
Finding Maximal Exact Matches Using the r-Index.
Rossi M, Oliva M, Bonizzoni P, Langmead B, Gagie T, Boucher C. Rossi M, et al. 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.
Syotti: scalable bait design for DNA enrichment.
Alanko JN, Slizovskiy IB, Lokshtanov D, Gagie T, Noyes NR, Boucher C. Alanko JN, et al. Bioinformatics. 2022 Jun 24;38(Suppl 1):i177-i184. doi: 10.1093/bioinformatics/btac226. Bioinformatics. 2022. PMID: 35758776 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. 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.
Pangenomic genotyping with the marker array.
Mun T, Vaddadi NSK, Langmead B. Mun T, et al. Algorithms Mol Biol. 2023 May 5;18(1):2. doi: 10.1186/s13015-023-00225-3. Algorithms Mol Biol. 2023. PMID: 37147657 Free PMC article.
Pangenomic Genotyping with the Marker Array.
Mun T, Vaddadi NSK, Langmead B. Mun T, et al. Algorithms Bioinform. 2022 Sep;242:19. Algorithms Bioinform. 2022. PMID: 36409181 Free PMC article.
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.
32 results