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Items: 40

1.

Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages.

Kostka D, Holloway AK, Pollard KS.

Mol Biol Evol. 2018 Aug 1;35(8):2034-2045. doi: 10.1093/molbev/msy109.

2.

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.

3.

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.

4.

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.

5.
6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster.

Kolaczkowski B, Kern AD, Holloway AK, Begun DJ.

Genetics. 2011 Jan;187(1):245-60. doi: 10.1534/genetics.110.123059. Epub 2010 Nov 8.

23.

Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences.

Lawniczak MK, Emrich SJ, Holloway AK, Regier AP, Olson M, White B, Redmond S, Fulton L, Appelbaum E, Godfrey J, Farmer C, Chinwalla A, Yang SP, Minx P, Nelson J, Kyung K, Walenz BP, Garcia-Hernandez E, Aguiar M, Viswanathan LD, Rogers YH, Strausberg RL, Saski CA, Lawson D, Collins FH, Kafatos FC, Christophides GK, Clifton SW, Kirkness EF, Besansky NJ.

Science. 2010 Oct 22;330(6003):512-4. doi: 10.1126/science.1195755.

24.

"Reverse ecology" and the power of population genomics.

Li YF, Costello JC, Holloway AK, Hahn MW.

Evolution. 2008 Dec;62(12):2984-94. doi: 10.1111/j.1558-5646.2008.00486.x. Epub 2008 Aug 26.

25.

Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans.

Lawniczak MK, Holloway AK, Begun DJ, Jones CD.

Genome Biol. 2008;9(8):R125. doi: 10.1186/gb-2008-9-8-r125. Epub 2008 Aug 12.

26.

Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster.

Holloway AK, Begun DJ, Siepel A, Pollard KS.

Genome Res. 2008 Oct;18(10):1592-601. doi: 10.1101/gr.077131.108. Epub 2008 Jun 26.

27.
28.

Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.

Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN, Pachter L, Myers E, Langley CH.

PLoS Biol. 2007 Nov 6;5(11):e310.

29.
30.

Adaptive gene expression divergence inferred from population genomics.

Holloway AK, Lawniczak MK, Mezey JG, Begun DJ, Jones CD.

PLoS Genet. 2007 Oct;3(10):2007-13.

31.

Experimental evolution of gene duplicates in a bacterial plasmid model.

Holloway AK, Palzkill T, Bull JJ.

J Mol Evol. 2007 Feb;64(2):215-22. Epub 2007 Jan 8.

PMID:
17211548
32.

Polyploids with different origins and ancestors form a single sexual polyploid species.

Holloway AK, Cannatella DC, Gerhardt HC, Hillis DM.

Am Nat. 2006 Apr;167(4):E88-101. Epub 2006 Mar 8.

PMID:
16670990
33.

Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags.

Begun DJ, Lindfors HA, Thompson ME, Holloway AK.

Genetics. 2006 Mar;172(3):1675-81. Epub 2005 Dec 15.

34.

Molecular evolution and population genetics of duplicated accessory gland protein genes in Drosophila.

Holloway AK, Begun DJ.

Mol Biol Evol. 2004 Sep;21(9):1625-8. Epub 2004 Jun 23.

PMID:
15215320
35.

Difficulties in detecting hybridization.

Holder MT, Anderson JA, Holloway AK.

Syst Biol. 2001 Nov-Dec;50(6):978-82. No abstract available.

PMID:
12116644
36.

Garden sharing and garden stealing in fungus-growing ants.

Adams RM, Mueller UG, Holloway AK, Green AM, Narozniak J.

Naturwissenschaften. 2000 Nov;87(11):491-3.

PMID:
11151668
37.

Linkage analysis of sex determination in Bracon sp. near hebetor (Hymenoptera: Braconidae).

Holloway AK, Strand MR, Black WC 4th, Antolin MF.

Genetics. 2000 Jan;154(1):205-12.

38.

Role of local contractile activity and muscle fiber type on LPL regulation during exercise.

Hamilton MT, Etienne J, McClure WC, Pavey BS, Holloway AK.

Am J Physiol. 1998 Dec;275(6 Pt 1):E1016-22.

PMID:
9843744
39.

The time has come to activate AHCA's commitment to quality.

Holloway AK.

Provider. 1986 Nov;12(11):50-1. No abstract available.

PMID:
10311760
40.

Top administrators know the value of being a good coach.

Holloway AK.

Provider. 1986 May;12(5):47-8. No abstract available.

PMID:
10276496

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