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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: makinen v. Microb Genom. 2021 Nov;7(11):000691. doi: 10.1099/mgen.0.000691. Microb Genom. 2021. PMID: 34779765 Free PMC article.
Fast scaffolding with small independent mixed integer programs.
Salmela L, Mäkinen V, Välimäki N, Ylinen J, Ukkonen E. Salmela L, et al. Among authors: makinen v. Bioinformatics. 2011 Dec 1;27(23):3259-65. doi: 10.1093/bioinformatics/btr562. Epub 2011 Oct 13. Bioinformatics. 2011. PMID: 21998153 Free PMC article.
Towards pan-genome read alignment to improve variation calling.
Valenzuela D, Norri T, Välimäki N, Pitkänen E, Mäkinen V. Valenzuela D, et al. Among authors: makinen v. BMC Genomics. 2018 May 9;19(Suppl 2):87. doi: 10.1186/s12864-018-4465-8. BMC Genomics. 2018. PMID: 29764365 Free PMC article.
Repeat- and error-aware comparison of deletions.
Wittler R, Marschall T, Schönhuth A, Mäkinen V. Wittler R, et al. Among authors: makinen v. Bioinformatics. 2015 Sep 15;31(18):2947-54. doi: 10.1093/bioinformatics/btv304. Epub 2015 May 15. Bioinformatics. 2015. PMID: 25979471
Gap Filling as Exact Path Length Problem.
Salmela L, Sahlin K, Mäkinen V, Tomescu AI. Salmela L, et al. Among authors: makinen v. J Comput Biol. 2016 May;23(5):347-61. doi: 10.1089/cmb.2015.0197. Epub 2016 Mar 9. J Comput Biol. 2016. PMID: 26959081
Variant genotyping with gap filling.
Walve R, Salmela L, Mäkinen V. Walve R, et al. Among authors: makinen v. PLoS One. 2017 Sep 8;12(9):e0184608. doi: 10.1371/journal.pone.0184608. eCollection 2017. PLoS One. 2017. PMID: 28886164 Free PMC article.
154 results