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Items: 1 to 20 of 39

1.

Features that define the best ChIP-seq peak calling algorithms.

Thomas R, Thomas S, Holloway AK, Pollard KS.

Brief Bioinform. 2017 May 1;18(3):441-450. doi: 10.1093/bib/bbw035.

2.

Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis.

Luna-Zurita L, Stirnimann CU, Glatt S, Kaynak BL, Thomas S, Baudin F, Samee MA, He D, Small EM, Mileikovsky M, Nagy A, Holloway AK, Pollard KS, Müller CW, Bruneau BG.

Cell. 2016 Feb 25;164(5):999-1014. doi: 10.1016/j.cell.2016.01.004. Epub 2016 Feb 11.

3.

Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor.

Holloway AK, Bruneau BG, Sukonnik T, Rubenstein JL, Pollard KS.

Mol Biol Evol. 2016 Apr;33(4):1008-18. doi: 10.1093/molbev/msv344. Epub 2015 Dec 29.

4.
5.

From scientific discovery to cures: bright stars within a galaxy.

Williams RS, Lotia S, Holloway AK, Pico AR.

Cell. 2015 Sep 24;163(1):21-3. doi: 10.1016/j.cell.2015.09.007.

6.

RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis.

Williams AG, Thomas S, Wyman SK, Holloway AK.

Curr Protoc Hum Genet. 2014 Oct 1;83:11.13.1-20. doi: 10.1002/0471142905.hg1113s83.

7.

Long-read sequencing of chicken transcripts and identification of new transcript isoforms.

Thomas S, Underwood JG, Tseng E, Holloway AK; Bench To Basinet CvDC Informatics Subcommittee.

PLoS One. 2014 Apr 15;9(4):e94650. doi: 10.1371/journal.pone.0094650. eCollection 2014.

8.

A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design.

Smith RP, Riesenfeld SJ, Holloway AK, Li Q, Murphy KK, Feliciano NM, Orecchia L, Oksenberg N, Pollard KS, Ahituv N.

Genome Biol. 2013 Jul 18;14(7):R72. doi: 10.1186/gb-2013-14-7-r72.

9.

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage.

Shaffer HB, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, Bruneau BG, Buck LT, Capel B, Castoe TA, Czerwinski M, Delehaunty KD, Edwards SV, Fronick CC, Fujita MK, Fulton L, Graves TA, Green RE, Haerty W, Hariharan R, Hernandez O, Hillier LW, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning AP, Li Y, Literman R, McGaugh SE, Mork L, O'Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, St John J, Schwartz T, Sethuraman A, Spinks PQ, Storey KB, Thane N, Vinar T, Zimmerman LM, Warren WC, Mardis ER, Wilson RK.

Genome Biol. 2013 Mar 28;14(3):R28. doi: 10.1186/gb-2013-14-3-r28.

10.

Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage.

Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, Bruneau BG.

Cell. 2012 Sep 28;151(1):206-20. doi: 10.1016/j.cell.2012.07.035. Epub 2012 Sep 12.

11.

Genomic variation in natural populations of Drosophila melanogaster.

Langley CH, Stevens K, Cardeno C, Lee YC, Schrider DR, Pool JE, Langley SA, Suarez C, Corbett-Detig RB, Kolaczkowski B, Fang S, Nista PM, Holloway AK, Kern AD, Dewey CN, Song YS, Hahn MW, Begun DJ.

Genetics. 2012 Oct;192(2):533-98. doi: 10.1534/genetics.112.142018. Epub 2012 Jun 5.

12.

The microRNA expression changes associated with malignancy and SDHB mutation in pheochromocytoma.

Patterson E, Webb R, Weisbrod A, Bian B, He M, Zhang L, Holloway AK, Krishna R, Nilubol N, Pacak K, Kebebew E.

Endocr Relat Cancer. 2012 Apr 10;19(2):157-66. doi: 10.1530/ERC-11-0308. Print 2012 Apr.

13.

MiR-886-3p regulates cell proliferation and migration, and is dysregulated in familial non-medullary thyroid cancer.

Xiong Y, Zhang L, Holloway AK, Wu X, Su L, Kebebew E.

PLoS One. 2011;6(10):e24717. doi: 10.1371/journal.pone.0024717. Epub 2011 Oct 5.

14.

A high-resolution map of human evolutionary constraint using 29 mammals.

Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC; Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK; Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M.

Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530.

15.

Chromosomal haplotypes by genetic phasing of human families.

Roach JC, Glusman G, Hubley R, Montsaroff SZ, Holloway AK, Mauldin DE, Srivastava D, Garg V, Pollard KS, Galas DJ, Hood L, Smit AF.

Am J Hum Genet. 2011 Sep 9;89(3):382-97. doi: 10.1016/j.ajhg.2011.07.023.

16.

Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules.

He BZ, Holloway AK, Maerkl SJ, Kreitman M.

PLoS Genet. 2011 Apr;7(4):e1002053. doi: 10.1371/journal.pgen.1002053. Epub 2011 Apr 28.

17.

MicroRNA profiling of adrenocortical tumors reveals miR-483 as a marker of malignancy.

Patterson EE, Holloway AK, Weng J, Fojo T, Kebebew E.

Cancer. 2011 Apr 15;117(8):1630-9. doi: 10.1002/cncr.25724. Epub 2010 Nov 8.

18.

Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution.

Lambert N, Lambot MA, Bilheu A, Albert V, Englert Y, Libert F, Noel JC, Sotiriou C, Holloway AK, Pollard KS, Detours V, Vanderhaeghen P.

PLoS One. 2011 Mar 18;6(3):e17753. doi: 10.1371/journal.pone.0017753.

19.

Chromatin remodelling complex dosage modulates transcription factor function in heart development.

Takeuchi JK, Lou X, Alexander JM, Sugizaki H, Delgado-Olguín P, Holloway AK, Mori AD, Wylie JN, Munson C, Zhu Y, Zhou YQ, Yeh RF, Henkelman RM, Harvey RP, Metzger D, Chambon P, Stainier DY, Pollard KS, Scott IC, Bruneau BG.

Nat Commun. 2011 Feb 8;2:187. doi: 10.1038/ncomms1187.

20.

Identification of differentially expressed microRNA in parathyroid tumors.

Rahbari R, Holloway AK, He M, Khanafshar E, Clark OH, Kebebew E.

Ann Surg Oncol. 2011 Apr;18(4):1158-65. doi: 10.1245/s10434-010-1359-7. Epub 2010 Nov 18.

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