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Results: 1 to 20 of 64

1.

Pitfalls of Mapping High-Throughput Sequencing Data to Repetitive Sequences: Piwi's Genomic Targets Still Not Identified.

Marinov GK, Wang J, Handler D, Wold BJ, Weng Z, Hannon GJ, Aravin AA, Zamore PD, Brennecke J, Toth KF.

Dev Cell. 2015 Mar 23;32(6):765-71. doi: 10.1016/j.devcel.2015.01.013.

PMID:
25805138
2.

Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming.

Kim DH, Marinov GK, Pepke S, Singer ZS, He P, Williams B, Schroth GP, Elowitz MB, Wold BJ.

Cell Stem Cell. 2015 Jan 8;16(1):88-101. doi: 10.1016/j.stem.2014.11.005.

PMID:
25575081
3.

A ratiometric-based measure of gene co-expression.

Abelin AC, Marinov GK, Williams BA, McCue K, Wold BJ.

BMC Bioinformatics. 2014 Nov 20;15:331. doi: 10.1186/1471-2105-15-331.

4.

Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: identifying ChIP-quality p300 monoclonal antibodies.

Gasper WC, Marinov GK, Pauli-Behn F, Scott MT, Newberry K, DeSalvo G, Ou S, Myers RM, Vielmetter J, Wold BJ.

Sci Rep. 2014 Jun 12;4:5152. doi: 10.1038/srep05152.

5.

Evidence for site-specific occupancy of the mitochondrial genome by nuclear transcription factors.

Marinov GK, Wang YE, Chan D, Wold BJ.

PLoS One. 2014 Jan 20;9(1):e84713. doi: 10.1371/journal.pone.0084713. eCollection 2014.

6.

Large-scale quality analysis of published ChIP-seq data.

Marinov GK, Kundaje A, Park PJ, Wold BJ.

G3 (Bethesda). 2014 Feb 19;4(2):209-23. doi: 10.1534/g3.113.008680.

7.

From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing.

Marinov GK, Williams BA, McCue K, Schroth GP, Gertz J, Myers RM, Wold BJ.

Genome Res. 2014 Mar;24(3):496-510. doi: 10.1101/gr.161034.113. Epub 2013 Dec 3.

8.

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps.

Mortazavi A, Pepke S, Jansen C, Marinov GK, Ernst J, Kellis M, Hardison RC, Myers RM, Wold BJ.

Genome Res. 2013 Dec;23(12):2136-48. doi: 10.1101/gr.158261.113. Epub 2013 Oct 29.

9.

Genome-wide analysis reveals coating of the mitochondrial genome by TFAM.

Wang YE, Marinov GK, Wold BJ, Chan DC.

PLoS One. 2013 Aug 26;8(8):e74513. doi: 10.1371/journal.pone.0074513. eCollection 2013.

10.

Transcriptional regulation by nicotine in dopaminergic neurons.

Henley BM, Williams BA, Srinivasan R, Cohen BN, Xiao C, Mackey ED, Wold BJ, Lester HA.

Biochem Pharmacol. 2013 Oct 15;86(8):1074-83. doi: 10.1016/j.bcp.2013.07.031. Epub 2013 Aug 9.

11.

Dynamic DNA methylation across diverse human cell lines and tissues.

Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F, Cross MK, Williams BA, Stamatoyannopoulos JA, Crawford GE, Absher DM, Wold BJ, Myers RM.

Genome Res. 2013 Mar;23(3):555-67. doi: 10.1101/gr.147942.112. Epub 2013 Jan 16.

12.

Using patient-provided information to refine sexually transmitted infection screening criteria among women presenting in the emergency department.

Jenkins WD, Kovach R, Wold BJ, Zahnd WE.

Sex Transm Dis. 2012 Dec;39(12):965-7. doi: 10.1097/OLQ.0b013e31826e882f.

PMID:
23191951
13.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M.

Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.

14.

RNA editing in the human ENCODE RNA-seq data.

Park E, Williams B, Wold BJ, Mortazavi A.

Genome Res. 2012 Sep;22(9):1626-33. doi: 10.1101/gr.134957.111.

15.

An encyclopedia of mouse DNA elements (Mouse ENCODE).

Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB.

Genome Biol. 2012 Aug 13;13(8):418. doi: 10.1186/gb-2012-13-8-418.

16.

Transcription factor redundancy and tissue-specific regulation: evidence from functional and physical network connectivity.

Kuntz SG, Williams BA, Sternberg PW, Wold BJ.

Genome Res. 2012 Oct;22(10):1907-19. doi: 10.1101/gr.133306.111. Epub 2012 Jun 22.

17.

Systematic evaluation of factors influencing ChIP-seq fidelity.

Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery M, Liu T, Zhang Y, Kim TK, He HH, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ, White KP, Lieb JD, Liu XS.

Nat Methods. 2012 Jun;9(6):609-14. doi: 10.1038/nmeth.1985. Epub 2012 Apr 22.

18.

Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity.

Zhang JA, Mortazavi A, Williams BA, Wold BJ, Rothenberg EV.

Cell. 2012 Apr 13;149(2):467-82. doi: 10.1016/j.cell.2012.01.056.

19.

Microglia in the cerebral cortex in autism.

Tetreault NA, Hakeem AY, Jiang S, Williams BA, Allman E, Wold BJ, Allman JM.

J Autism Dev Disord. 2012 Dec;42(12):2569-84. doi: 10.1007/s10803-012-1513-0.

PMID:
22466688
20.

Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer.

Tai PW, Fisher-Aylor KI, Himeda CL, Smith CL, Mackenzie AP, Helterline DL, Angello JC, Welikson RE, Wold BJ, Hauschka SD.

Skelet Muscle. 2011 Jul 7;1:25. doi: 10.1186/2044-5040-1-25.

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