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Items: 7

1.

Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing.

Li K, Shrivastava S, Brownley A, Katzel D, Bera J, Nguyen AT, Thovarai V, Halpin R, Stockwell TB.

Virol J. 2012 Nov 6;9:261. doi: 10.1186/1743-422X-9-261.

2.

Computational techniques for human genome resequencing using mated gapped reads.

Carnevali P, Baccash J, Halpern AL, Nazarenko I, Nilsen GB, Pant KP, Ebert JC, Brownley A, Morenzoni M, Karpinchyk V, Martin B, Ballinger DG, Drmanac R.

J Comput Biol. 2012 Mar;19(3):279-92. doi: 10.1089/cmb.2011.0201. Epub 2011 Dec 16.

PMID:
22175250
3.

Primer design for RT-PCR.

Li K, Brownley A.

Methods Mol Biol. 2010;630:271-99. doi: 10.1007/978-1-60761-629-0_18.

PMID:
20301004
4.

Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays.

Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G, Dahl F, Fernandez A, Staker B, Pant KP, Baccash J, Borcherding AP, Brownley A, Cedeno R, Chen L, Chernikoff D, Cheung A, Chirita R, Curson B, Ebert JC, Hacker CR, Hartlage R, Hauser B, Huang S, Jiang Y, Karpinchyk V, Koenig M, Kong C, Landers T, Le C, Liu J, McBride CE, Morenzoni M, Morey RE, Mutch K, Perazich H, Perry K, Peters BA, Peterson J, Pethiyagoda CL, Pothuraju K, Richter C, Rosenbaum AM, Roy S, Shafto J, Sharanhovich U, Shannon KW, Sheppy CG, Sun M, Thakuria JV, Tran A, Vu D, Zaranek AW, Wu X, Drmanac S, Oliphant AR, Banyai WC, Martin B, Ballinger DG, Church GM, Reid CA.

Science. 2010 Jan 1;327(5961):78-81. doi: 10.1126/science.1181498. Epub 2009 Nov 5.

5.

Aggressive assembly of pyrosequencing reads with mates.

Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G.

Bioinformatics. 2008 Dec 15;24(24):2818-24. doi: 10.1093/bioinformatics/btn548. Epub 2008 Oct 24.

6.

Novel computational methods for increasing PCR primer design effectiveness in directed sequencing.

Li K, Brownley A, Stockwell TB, Beeson K, McIntosh TC, Busam D, Ferriera S, Murphy S, Levy S.

BMC Bioinformatics. 2008 Apr 11;9:191. doi: 10.1186/1471-2105-9-191.

7.

Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.

Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA 3rd, Smith HO.

Science. 2008 Feb 29;319(5867):1215-20. doi: 10.1126/science.1151721. Epub 2008 Jan 24.

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