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SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. Bankevich A, et al. Among authors: alekseyev ma. J Comput Biol. 2012 May;19(5):455-77. doi: 10.1089/cmb.2012.0021. Epub 2012 Apr 16. J Comput Biol. 2012. PMID: 22506599 Free PMC article.
On pairwise distances and median score of three genomes under DCJ.
Aganezov S Jr, Alekseyev MA. Aganezov S Jr, et al. Among authors: alekseyev ma. BMC Bioinformatics. 2012;13 Suppl 19(Suppl 19):S1. doi: 10.1186/1471-2105-13-S19-S1. Epub 2012 Dec 19. BMC Bioinformatics. 2012. PMID: 23282410 Free PMC article.
Assembling single-cell genomes and mini-metagenomes from chimeric MDA products.
Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, McLean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner PA. Nurk S, et al. Among authors: alekseyev ma. J Comput Biol. 2013 Oct;20(10):714-37. doi: 10.1089/cmb.2013.0084. J Comput Biol. 2013. PMID: 24093227 Free PMC article.
Scaffold assembly based on genome rearrangement analysis.
Aganezov S, Sitdykova N; AGC Consortium, Alekseyev MA. Aganezov S, et al. Among authors: alekseyev ma. Comput Biol Chem. 2015 Aug;57:46-53. doi: 10.1016/j.compbiolchem.2015.02.005. Epub 2015 Mar 3. Comput Biol Chem. 2015. PMID: 25819137
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