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Results: 1 to 20 of 140

1.

Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility.

Dogan N, Wu W, Morrissey CS, Chen KB, Stonestrom A, Long M, Keller CA, Cheng Y, Jain D, Visel A, Pennacchio LA, Weiss MJ, Blobel GA, Hardison RC.

Epigenetics Chromatin. 2015 Apr 23;8:16. doi: 10.1186/s13072-015-0009-5. eCollection 2015.

2.

Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution.

Denas O, Sandstrom R, Cheng Y, Beal K, Herrero J, Hardison RC, Taylor J.

BMC Genomics. 2015 Feb 14;16:87. doi: 10.1186/s12864-015-1245-6.

3.

The effects of chromatin organization on variation in mutation rates in the genome.

Makova KD, Hardison RC.

Nat Rev Genet. 2015 Apr;16(4):213-23. doi: 10.1038/nrg3890. Epub 2015 Mar 3. Review.

4.

Dynamics of GATA1 binding and expression response in a GATA1-induced erythroid differentiation system.

Jain D, Mishra T, Giardine BM, Keller CA, Morrissey CS, Magargee S, Dorman CM, Long M, Weiss MJ, Hardison RC.

Genom Data. 2015 Jun 1;4:1-7.

PMID:
25729644
5.

Functions of BET proteins in erythroid gene expression.

Stonestrom AJ, Hsu SC, Jahn KS, Huang P, Keller CA, Giardine BM, Kadauke S, Campbell AE, Evans P, Hardison RC, Blobel GA.

Blood. 2015 Apr 30;125(18):2825-34. doi: 10.1182/blood-2014-10-607309. Epub 2015 Feb 18.

PMID:
25696920
6.

Pluripotent stem cells reveal erythroid-specific activities of the GATA1 N-terminus.

Byrska-Bishop M, VanDorn D, Campbell AE, Betensky M, Arca PR, Yao Y, Gadue P, Costa FF, Nemiroff RL, Blobel GA, French DL, Hardison RC, Weiss MJ, Chou ST.

J Clin Invest. 2015 Mar 2;125(3):993-1005. doi: 10.1172/JCI75714. Epub 2015 Jan 26.

7.

Topologically associating domains are stable units of replication-timing regulation.

Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, G├╝lsoy G, Dennis JH, Snyder MP, Stamatoyannopoulos JA, Taylor J, Hardison RC, Kahveci T, Ren B, Gilbert DM.

Nature. 2014 Nov 20;515(7527):402-5. doi: 10.1038/nature13986.

8.

Principles of regulatory information conservation between mouse and human.

Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B; Mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP.

Nature. 2014 Nov 20;515(7527):371-5. doi: 10.1038/nature13985.

9.

A comparative encyclopedia of DNA elements in the mouse genome.

Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium.

Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.

10.

Genome accessibility is widely preserved and locally modulated during mitosis.

Hsiung CC, Morrissey CS, Udugama M, Frank CL, Keller CA, Baek S, Giardine B, Crawford GE, Sung MH, Hardison RC, Blobel GA.

Genome Res. 2015 Feb;25(2):213-25. doi: 10.1101/gr.180646.114. Epub 2014 Nov 4.

11.

Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis.

Pimkin M, Kossenkov AV, Mishra T, Morrissey CS, Wu W, Keller CA, Blobel GA, Lee D, Beer MA, Hardison RC, Weiss MJ.

Genome Res. 2014 Dec;24(12):1932-44. doi: 10.1101/gr.164178.113. Epub 2014 Oct 15.

12.

Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis.

Wu W, Morrissey CS, Keller CA, Mishra T, Pimkin M, Blobel GA, Weiss MJ, Hardison RC.

Genome Res. 2014 Dec;24(12):1945-62. doi: 10.1101/gr.164830.113. Epub 2014 Oct 15.

13.

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.

Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos J, Weng Z, White KP, Hardison RC.

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3366. No abstract available.

14.

A comprehensive and high-resolution genome-wide response of p53 to stress.

Chang GS, Chen XA, Park B, Rhee HS, Li P, Han KH, Mishra T, Chan-Salis KY, Li Y, Hardison RC, Wang Y, Pugh BF.

Cell Rep. 2014 Jul 24;8(2):514-27. doi: 10.1016/j.celrep.2014.06.030. Epub 2014 Jul 17.

15.

Discovering enhancers directly by activity.

Hardison RC.

Nat Methods. 2014 May;11(5):491-2. doi: 10.1038/nmeth.2933. No abstract available.

16.

Defining functional DNA elements in the human genome.

Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6131-8. doi: 10.1073/pnas.1318948111. Epub 2014 Apr 21. Review.

17.

MRHMMs: multivariate regression hidden Markov models and the variantS.

Lee Y, Ghosh D, Hardison RC, Zhang Y.

Bioinformatics. 2014 Jun 15;30(12):1755-6. doi: 10.1093/bioinformatics/btu070. Epub 2014 Feb 19.

18.

Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development.

Paralkar VR, Mishra T, Luan J, Yao Y, Kossenkov AV, Anderson SM, Dunagin M, Pimkin M, Gore M, Sun D, Konuthula N, Raj A, An X, Mohandas N, Bodine DM, Hardison RC, Weiss MJ.

Blood. 2014 Mar 20;123(12):1927-37. doi: 10.1182/blood-2013-12-544494. Epub 2014 Feb 4.

19.

Function of GATA factors in the adult mouse liver.

Zheng R, Rebolledo-Jaramillo B, Zong Y, Wang L, Russo P, Hancock W, Stanger BZ, Hardison RC, Blobel GA.

PLoS One. 2013 Dec 18;8(12):e83723. doi: 10.1371/journal.pone.0083723. eCollection 2013.

20.

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.

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