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Bacterial genomic epidemiology with mixed samples.
Mäklin T, Kallonen T, Alanko J, Samuelsen Ø, Hegstad K, Mäkinen V, Corander J, Heinz E, Honkela A. Mäklin T, et al. Among authors: alanko j. Microb Genom. 2021 Nov;7(11):000691. doi: 10.1099/mgen.0.000691. Microb Genom. 2021. PMID: 34779765 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.
Buffering updates enables efficient dynamic de Bruijn graphs.
Alanko J, Alipanahi B, Settle J, Boucher C, Gagie T. Alanko J, et al. 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.
Finding all maximal perfect haplotype blocks in linear time.
Alanko J, Bannai H, Cazaux B, Peterlongo P, Stoye J. Alanko J, et al. Algorithms Mol Biol. 2020 Feb 10;15:2. doi: 10.1186/s13015-020-0163-6. eCollection 2020. Algorithms Mol Biol. 2020. PMID: 32055252 Free PMC article.
Matchtigs: minimum plain text representation of k-mer sets.
Schmidt S, Khan S, Alanko JN, Pibiri GE, Tomescu AI. Schmidt S, et al. Among authors: alanko jn. Genome Biol. 2023 Jun 9;24(1):136. doi: 10.1186/s13059-023-02968-z. Genome Biol. 2023. PMID: 37296461 Free PMC article.
69 results