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Results: 1 to 20 of 28

1.

Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern.

Potok ME, Nix DA, Parnell TJ, Cairns BR.

Cell. 2013 May 9;153(4):759-72. doi: 10.1016/j.cell.2013.04.030.

PMID:
23663776
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

DNA methylation profiling in zebrafish.

Wu SF, Zhang H, Hammoud SS, Potok M, Nix DA, Jones DA, Cairns BR.

Methods Cell Biol. 2011;104:327-39. doi: 10.1016/B978-0-12-374814-0.00018-5.

PMID:
21924171
[PubMed - indexed for MEDLINE]
3.

Genome-wide analysis identifies changes in histone retention and epigenetic modifications at developmental and imprinted gene loci in the sperm of infertile men.

Hammoud SS, Nix DA, Hammoud AO, Gibson M, Cairns BR, Carrell DT.

Hum Reprod. 2011 Sep;26(9):2558-69. doi: 10.1093/humrep/der192. Epub 2011 Jun 17.

PMID:
21685136
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes.

Rowley JW, Oler AJ, Tolley ND, Hunter BN, Low EN, Nix DA, Yost CC, Zimmerman GA, Weyrich AS.

Blood. 2011 Oct 6;118(14):e101-11. doi: 10.1182/blood-2011-03-339705. Epub 2011 May 19. Erratum in: Blood. 2014 Jun 12;123(24):3843.

PMID:
21596849
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

ENCODE tiling array analysis identifies differentially expressed annotated and novel 5' capped RNAs in hepatitis C infected liver.

Folkers ME, Delker DA, Maxwell CI, Nelson CA, Schwartz JJ, Nix DA, Hagedorn CH.

PLoS One. 2011 Feb 16;6(2):e14697. doi: 10.1371/journal.pone.0014697.

PMID:
21359205
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Next generation tools for genomic data generation, distribution, and visualization.

Nix DA, Di Sera TL, Dalley BK, Milash BA, Cundick RM, Quinn KS, Courdy SJ.

BMC Bioinformatics. 2010 Sep 9;11:455. doi: 10.1186/1471-2105-11-455.

PMID:
20828407
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Dicer's helicase domain is required for accumulation of some, but not all, C. elegans endogenous siRNAs.

Welker NC, Pavelec DM, Nix DA, Duchaine TF, Kennedy S, Bass BL.

RNA. 2010 May;16(5):893-903. doi: 10.1261/rna.2122010. Epub 2010 Mar 30.

PMID:
20354150
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Distinctive chromatin in human sperm packages genes for embryo development.

Hammoud SS, Nix DA, Zhang H, Purwar J, Carrell DT, Cairns BR.

Nature. 2009 Jul 23;460(7254):473-8. doi: 10.1038/nature08162. Epub 2009 Jun 14.

PMID:
19525931
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks.

Nix DA, Courdy SJ, Boucher KM.

BMC Bioinformatics. 2008 Dec 5;9:523. doi: 10.1186/1471-2105-9-523.

PMID:
19061503
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping.

Dutrow N, Nix DA, Holt D, Milash B, Dalley B, Westbroek E, Parnell TJ, Cairns BR.

Nat Genet. 2008 Aug;40(8):977-86. doi: 10.1038/ng.196. Epub 2008 Jul 20.

PMID:
18641648
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.

Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS.

Genome Res. 2008 Mar;18(3):393-403. doi: 10.1101/gr.7080508. Epub 2008 Feb 7.

PMID:
18258921
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

PMID:
17571346
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

RNA maps reveal new RNA classes and a possible function for pervasive transcription.

Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR.

Science. 2007 Jun 8;316(5830):1484-8. Epub 2007 May 17.

PMID:
17510325
[PubMed - indexed for MEDLINE]
Free Article
14.

Large-scale turnover of functional transcription factor binding sites in Drosophila.

Moses AM, Pollard DA, Nix DA, Iyer VN, Li XY, Biggin MD, Eisen MB.

PLoS Comput Biol. 2006 Oct;2(10):e130. Epub 2006 Aug 21.

PMID:
17040121
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array.

Biemar F, Nix DA, Piel J, Peterson B, Ronshaugen M, Sementchenko V, Bell I, Manak JR, Levine MS.

Proc Natl Acad Sci U S A. 2006 Aug 22;103(34):12763-8. Epub 2006 Aug 14.

PMID:
16908844
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Genome-wide analysis of Polycomb targets in Drosophila melanogaster.

Schwartz YB, Kahn TG, Nix DA, Li XY, Bourgon R, Biggin M, Pirrotta V.

Nat Genet. 2006 Jun;38(6):700-5. Epub 2006 May 28.

PMID:
16732288
[PubMed - indexed for MEDLINE]
17.

Flexible promoter architecture requirements for coactivator recruitment.

Chiang DY, Nix DA, Shultzaberger RK, Gasch AP, Eisen MB.

BMC Mol Biol. 2006 Apr 28;7:16.

PMID:
16646957
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Factors that predict prematurity and preeclampsia in pregnancies that are complicated by systemic lupus erythematosus.

Chakravarty EF, Colón I, Langen ES, Nix DA, El-Sayed YY, Genovese MC, Druzin ML.

Am J Obstet Gynecol. 2005 Jun;192(6):1897-904.

PMID:
15970846
[PubMed - indexed for MEDLINE]
19.

GATA: a graphic alignment tool for comparative sequence analysis.

Nix DA, Eisen MB.

BMC Bioinformatics. 2005 Jan 17;6:9.

PMID:
15655071
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

The actin-regulating kinase Prk1p negatively regulates Scd5p, a suppressor of clathrin deficiency, in actin organization and endocytosis.

Henry KR, D'Hondt K, Chang JS, Nix DA, Cope MJ, Chan CS, Drubin DG, Lemmon SK.

Curr Biol. 2003 Sep 2;13(17):1564-9.

PMID:
12956961
[PubMed - indexed for MEDLINE]
Free Article

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