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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.
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.
The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera.
Ahola V, Lehtonen R, Somervuo P, Salmela L, Koskinen P, Rastas P, Välimäki N, Paulin L, Kvist J, Wahlberg N, Tanskanen J, Hornett EA, Ferguson LC, Luo S, Cao Z, de Jong MA, Duplouy A, Smolander OP, Vogel H, McCoy RC, Qian K, Chong WS, Zhang Q, Ahmad F, Haukka JK, Joshi A, Salojärvi J, Wheat CW, Grosse-Wilde E, Hughes D, Katainen R, Pitkänen E, Ylinen J, Waterhouse RM, Turunen M, Vähärautio A, Ojanen SP, Schulman AH, Taipale M, Lawson D, Ukkonen E, Mäkinen V, Goldsmith MR, Holm L, Auvinen P, Frilander MJ, Hanski I. Ahola V, et al. Among authors: makinen v. Nat Commun. 2014 Sep 5;5:4737. doi: 10.1038/ncomms5737. Nat Commun. 2014. PMID: 25189940 Free PMC article.
Recombination-aware alignment of diploid individuals.
Mäkinen V, Valenzuela D. Mäkinen V, et al. BMC Genomics. 2014;15 Suppl 6(Suppl 6):S15. doi: 10.1186/1471-2164-15-S6-S15. Epub 2014 Oct 17. BMC Genomics. 2014. PMID: 25572943 Free PMC article.
Computational pan-genomics: status, promises and challenges.
Computational Pan-Genomics Consortium. Computational Pan-Genomics Consortium. Brief Bioinform. 2018 Jan 1;19(1):118-135. doi: 10.1093/bib/bbw089. Brief Bioinform. 2018. PMID: 27769991 Free PMC article. Review.
154 results