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Items: 18

1.

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals.

Battle A, Mostafavi S, Zhu X, Potash JB, Weissman MM, McCormick C, Haudenschild CD, Beckman KB, Shi J, Mei R, Urban AE, Montgomery SB, Levinson DF, Koller D.

Genome Res. 2014 Jan;24(1):14-24. doi: 10.1101/gr.155192.113. Epub 2013 Oct 3.

2.

BAP1 loss defines a new class of renal cell carcinoma.

Peña-Llopis S, Vega-Rubín-de-Celis S, Liao A, Leng N, Pavía-Jiménez A, Wang S, Yamasaki T, Zhrebker L, Sivanand S, Spence P, Kinch L, Hambuch T, Jain S, Lotan Y, Margulis V, Sagalowsky AI, Summerour PB, Kabbani W, Wong SW, Grishin N, Laurent M, Xie XJ, Haudenschild CD, Ross MT, Bentley DR, Kapur P, Brugarolas J.

Nat Genet. 2012 Jun 10;44(7):751-9. doi: 10.1038/ng.2323. Erratum in: Nat Genet. 2012 Sep;44(9):1072.

3.

An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation.

Harhay GP, Smith TP, Alexander LJ, Haudenschild CD, Keele JW, Matukumalli LK, Schroeder SG, Van Tassell CP, Gresham CR, Bridges SM, Burgess SC, Sonstegard TS.

Genome Biol. 2010;11(10):R102. doi: 10.1186/gb-2010-11-10-r102. Epub 2010 Oct 20.

4.

A comprehensive catalogue of somatic mutations from a human cancer genome.

Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordóñez GR, Bignell GR, Ye K, Alipaz J, Bauer MJ, Beare D, Butler A, Carter RJ, Chen L, Cox AJ, Edkins S, Kokko-Gonzales PI, Gormley NA, Grocock RJ, Haudenschild CD, Hims MM, James T, Jia M, Kingsbury Z, Leroy C, Marshall J, Menzies A, Mudie LJ, Ning Z, Royce T, Schulz-Trieglaff OB, Spiridou A, Stebbings LA, Szajkowski L, Teague J, Williamson D, Chin L, Ross MT, Campbell PJ, Bentley DR, Futreal PA, Stratton MR.

Nature. 2010 Jan 14;463(7278):191-6. doi: 10.1038/nature08658. Epub 2009 Dec 16.

5.

Accurate whole human genome sequencing using reversible terminator chemistry.

Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ.

Nature. 2008 Nov 6;456(7218):53-9. doi: 10.1038/nature07517.

6.

SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries.

Van Tassell CP, Smith TP, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, Moore SS, Warren WC, Sonstegard TS.

Nat Methods. 2008 Mar;5(3):247-52. doi: 10.1038/nmeth.1185. Epub 2008 Feb 24.

PMID:
18297082
7.

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.

Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE.

Nature. 2008 Mar 13;452(7184):215-9. doi: 10.1038/nature06745. Epub 2008 Feb 17.

8.

Transcription factor expression in lipopolysaccharide-activated peripheral-blood-derived mononuclear cells.

Roach JC, Smith KD, Strobe KL, Nissen SM, Haudenschild CD, Zhou D, Vasicek TJ, Held GA, Stolovitzky GA, Hood LE, Aderem A.

Proc Natl Acad Sci U S A. 2007 Oct 9;104(41):16245-50. Epub 2007 Oct 3.

9.

Transcriptomic analysis of growth heterosis in larval Pacific oysters (Crassostrea gigas).

Hedgecock D, Lin JZ, DeCola S, Haudenschild CD, Meyer E, Manahan DT, Bowen B.

Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2313-8. Epub 2007 Feb 2.

10.

Use of massively parallel signature sequencing to study genes expressed during the plant defense response.

Meyers BC, Haudenschild CD, Vemaraju K.

Methods Mol Biol. 2007;354:105-19.

PMID:
17172749
11.

Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods.

Gowda M, Venu RC, Raghupathy MB, Nobuta K, Li H, Wing R, Stahlberg E, Couglan S, Haudenschild CD, Dean R, Nahm BH, Meyers BC, Wang GL.

BMC Genomics. 2006 Dec 8;7:310.

12.

Massively parallel signature sequencing.

Zhou D, Rao MS, Walker R, Khrebtukova I, Haudenschild CD, Miura T, Decola S, Vermaas E, Moon K, Vasicek TJ.

Methods Mol Biol. 2006;331:285-311.

PMID:
16881523
13.

Elucidation of the small RNA component of the transcriptome.

Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ.

Science. 2005 Sep 2;309(5740):1567-9.

14.

An atlas of human gene expression from massively parallel signature sequencing (MPSS).

Jongeneel CV, Delorenzi M, Iseli C, Zhou D, Haudenschild CD, Khrebtukova I, Kuznetsov D, Stevenson BJ, Strausberg RL, Simpson AJ, Vasicek TJ.

Genome Res. 2005 Jul;15(7):1007-14.

15.

Statistical analysis of MPSS measurements: application to the study of LPS-activated macrophage gene expression.

Stolovitzky GA, Kundaje A, Held GA, Duggar KH, Haudenschild CD, Zhou D, Vasicek TJ, Smith KD, Aderem A, Roach JC.

Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1402-7. Epub 2005 Jan 24.

16.

The use of MPSS for whole-genome transcriptional analysis in Arabidopsis.

Meyers BC, Tej SS, Vu TH, Haudenschild CD, Agrawal V, Edberg SB, Ghazal H, Decola S.

Genome Res. 2004 Aug;14(8):1641-53.

17.

Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing.

Meyers BC, Vu TH, Tej SS, Ghazal H, Matvienko M, Agrawal V, Ning J, Haudenschild CD.

Nat Biotechnol. 2004 Aug;22(8):1006-11. Epub 2004 Jul 11.

PMID:
15247925
18.

Molecular engineering of monoterpene production.

Haudenschild CD, Croteau RB.

Genet Eng (N Y). 1998;20:267-80. Review. No abstract available.

PMID:
9666564

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