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Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone.
Park DJ, Dudas G, Wohl S, Goba A, Whitmer SL, Andersen KG, Sealfon RS, Ladner JT, Kugelman JR, Matranga CB, Winnicki SM, Qu J, Gire SK, Gladden-Young A, Jalloh S, Nosamiefan D, Yozwiak NL, Moses LM, Jiang PP, Lin AE, Schaffner SF, Bird B, Towner J, Mamoh M, Gbakie M, Kanneh L, Kargbo D, Massally JL, Kamara FK, Konuwa E, Sellu J, Jalloh AA, Mustapha I, Foday M, Yillah M, Erickson BR, Sealy T, Blau D, Paddock C, Brault A, Amman B, Basile J, Bearden S, Belser J, Bergeron E, Campbell S, Chakrabarti A, Dodd K, Flint M, Gibbons A, Goodman C, Klena J, McMullan L, Morgan L, Russell B, Salzer J, Sanchez A, Wang D, Jungreis I, Tomkins-Tinch C, Kislyuk A, Lin MF, Chapman S, MacInnis B, Matthews A, Bochicchio J, Hensley LE, Kuhn JH, Nusbaum C, Schieffelin JS, Birren BW, Forget M, Nichol ST, Palacios GF, Ndiaye D, Happi C, Gevao SM, Vandi MA, Kargbo B, Holmes EC, Bedford T, Gnirke A, Ströher U, Rambaut A, Garry RF, Sabeti PC. Park DJ, et al. Among authors: Kislyuk A. Cell. 2015 Jun 18;161(7):1516-26. doi: 10.1016/j.cell.2015.06.007. Cell. 2015. PMID: 26091036 Free PMC article.
Neisseria Base: a comparative genomics database for Neisseria meningitidis.
Katz LS, Humphrey JC, Conley AB, Nelakuditi V, Kislyuk AO, Agrawal S, Jayaraman P, Harcourt BH, Olsen-Rasmussen MA, Frace M, Sharma NV, Mayer LW, Jordan IK. Katz LS, et al. Among authors: Kislyuk AO. Database (Oxford). 2011 Sep 18;2011:bar035. doi: 10.1093/database/bar035. Print 2011. Database (Oxford). 2011. PMID: 21930505 Free PMC article.
A computational genomics pipeline for prokaryotic sequencing projects.
Kislyuk AO, Katz LS, Agrawal S, Hagen MS, Conley AB, Jayaraman P, Nelakuditi V, Humphrey JC, Sammons SA, Govil D, Mair RD, Tatti KM, Tondella ML, Harcourt BH, Mayer LW, Jordan IK. Kislyuk AO, et al. Bioinformatics. 2010 Aug 1;26(15):1819-26. doi: 10.1093/bioinformatics/btq284. Epub 2010 Jun 2. Bioinformatics. 2010. PMID: 20519285 Free PMC article.
Multiple whole-genome alignments without a reference organism.
Dubchak I, Poliakov A, Kislyuk A, Brudno M. Dubchak I, et al. Among authors: Kislyuk A. Genome Res. 2009 Apr;19(4):682-9. doi: 10.1101/gr.081778.108. Epub 2009 Jan 28. Genome Res. 2009. PMID: 19176791 Free PMC article.
Frameshift detection in prokaryotic genomic sequences.
Kislyuk A, Lomsadze A, Lapidus AL, Borodovsky M. Kislyuk A, et al. Int J Bioinform Res Appl. 2009;5(4):458-77. doi: 10.1504/IJBRA.2009.027519. Int J Bioinform Res Appl. 2009. PMID: 19640832
Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases.
Schadt EE, Banerjee O, Fang G, Feng Z, Wong WH, Zhang X, Kislyuk A, Clark TA, Luong K, Keren-Paz A, Chess A, Kumar V, Chen-Plotkin A, Sondheimer N, Korlach J, Kasarskis A. Schadt EE, et al. Among authors: Kislyuk A. Genome Res. 2013 Jan;23(1):129-41. doi: 10.1101/gr.136739.111. Epub 2012 Oct 23. Genome Res. 2013. PMID: 23093720 Free PMC article.
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