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Items: 49

1.

Human genome-wide measurement of drug-responsive regulatory activity.

Johnson GD, Barrera A, McDowell IC, D'Ippolito AM, Majoros WH, Vockley CM, Wang X, Allen AS, Reddy TE.

Nat Commun. 2018 Dec 21;9(1):5317. doi: 10.1038/s41467-018-07607-x.

2.

Genome-wide quantification of the effects of DNA methylation on human gene regulation.

Lea AJ, Vockley CM, Johnston RA, Del Carpio CA, Barreiro LB, Reddy TE, Tung J.

Elife. 2018 Dec 21;7. pii: e37513. doi: 10.7554/eLife.37513.

3.

Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding.

McDowell IC, Barrera A, D'Ippolito AM, Vockley CM, Hong LK, Leichter SM, Bartelt LC, Majoros WH, Song L, Safi A, Ko├žak DD, Gersbach CA, Hartemink AJ, Crawford GE, Engelhardt BE, Reddy TE.

Genome Res. 2018 Sep;28(9):1272-1284. doi: 10.1101/gr.233346.117. Epub 2018 Aug 10.

4.

Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia.

Bryois J, Garrett ME, Song L, Safi A, Giusti-Rodriguez P, Johnson GD, Shieh AW, Buil A, Fullard JF, Roussos P, Sklar P, Akbarian S, Haroutunian V, Stockmeier CA, Wray GA, White KP, Liu C, Reddy TE, Ashley-Koch A, Sullivan PF, Crawford GE.

Nat Commun. 2018 Aug 7;9(1):3121. doi: 10.1038/s41467-018-05379-y.

5.

Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids.

D'Ippolito AM, McDowell IC, Barrera A, Hong LK, Leichter SM, Bartelt LC, Vockley CM, Majoros WH, Safi A, Song L, Gersbach CA, Crawford GE, Reddy TE.

Cell Syst. 2018 Aug 22;7(2):146-160.e7. doi: 10.1016/j.cels.2018.06.007. Epub 2018 Jul 18.

PMID:
30031775
6.

Predicting gene structure changes resulting from genetic variants via exon definition features.

Majoros WH, Holt C, Campbell MS, Ware D, Yandell M, Reddy TE.

Bioinformatics. 2018 Nov 1;34(21):3616-3623. doi: 10.1093/bioinformatics/bty324.

PMID:
29701825
7.

Screening Regulatory Element Function with CRISPR/Cas9-based Epigenome Editing.

Klann TS, Crawford GE, Reddy TE, Gersbach CA.

Methods Mol Biol. 2018;1767:447-480. doi: 10.1007/978-1-4939-7774-1_25.

PMID:
29524151
8.

Clustering gene expression time series data using an infinite Gaussian process mixture model.

McDowell IC, Manandhar D, Vockley CM, Schmid AK, Reddy TE, Engelhardt BE.

PLoS Comput Biol. 2018 Jan 16;14(1):e1005896. doi: 10.1371/journal.pcbi.1005896. eCollection 2018 Jan.

9.

A long-range flexible billboard model of gene activation.

Vockley CM, McDowell IC, D'Ippolito AM, Reddy TE.

Transcription. 2017 Aug 8;8(4):261-267. doi: 10.1080/21541264.2017.1317694. Epub 2017 Jun 9.

10.

Transversions have larger regulatory effects than transitions.

Guo C, McDowell IC, Nodzenski M, Scholtens DM, Allen AS, Lowe WL, Reddy TE.

BMC Genomics. 2017 May 19;18(1):394. doi: 10.1186/s12864-017-3785-4.

11.

CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.

Klann TS, Black JB, Chellappan M, Safi A, Song L, Hilton IB, Crawford GE, Reddy TE, Gersbach CA.

Nat Biotechnol. 2017 Jun;35(6):561-568. doi: 10.1038/nbt.3853. Epub 2017 Apr 3.

12.

High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE.

Majoros WH, Campbell MS, Holt C, DeNardo EK, Ware D, Allen AS, Yandell M, Reddy TE.

Bioinformatics. 2017 May 15;33(10):1437-1446. doi: 10.1093/bioinformatics/btw799.

13.

Decoding the role of regulatory element polymorphisms in complex disease.

Vockley CM, Barrera A, Reddy TE.

Curr Opin Genet Dev. 2017 Apr;43:38-45. doi: 10.1016/j.gde.2016.10.007. Epub 2016 Dec 13. Review.

PMID:
27984826
14.

Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome.

Vockley CM, D'Ippolito AM, McDowell IC, Majoros WH, Safi A, Song L, Crawford GE, Reddy TE.

Cell. 2016 Aug 25;166(5):1269-1281.e19. doi: 10.1016/j.cell.2016.07.049.

15.

Targeted Epigenetic Remodeling of Endogenous Loci by CRISPR/Cas9-Based Transcriptional Activators Directly Converts Fibroblasts to Neuronal Cells.

Black JB, Adler AF, Wang HG, D'Ippolito AM, Hutchinson HA, Reddy TE, Pitt GS, Leong KW, Gersbach CA.

Cell Stem Cell. 2016 Sep 1;19(3):406-14. doi: 10.1016/j.stem.2016.07.001. Epub 2016 Aug 11.

16.

HKDC1 Is a Novel Hexokinase Involved in Whole-Body Glucose Use.

Ludvik AE, Pusec CM, Priyadarshini M, Angueira AR, Guo C, Lo A, Hershenhouse KS, Yang GY, Ding X, Reddy TE, Lowe WL Jr, Layden BT.

Endocrinology. 2016 Sep;157(9):3452-61. doi: 10.1210/en.2016-1288. Epub 2016 Jul 26.

17.

The PsychENCODE project.

PsychENCODE Consortium, Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N.

Nat Neurosci. 2015 Dec;18(12):1707-12. doi: 10.1038/nn.4156. Review. No abstract available.

18.

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements.

Thakore PI, D'Ippolito AM, Song L, Safi A, Shivakumar NK, Kabadi AM, Reddy TE, Crawford GE, Gersbach CA.

Nat Methods. 2015 Dec;12(12):1143-9. doi: 10.1038/nmeth.3630. Epub 2015 Oct 26.

19.

Genomic approaches for understanding the genetics of complex disease.

Lowe WL Jr, Reddy TE.

Genome Res. 2015 Oct;25(10):1432-41. doi: 10.1101/gr.190603.115.

20.

From Prescription to Transcription: Genome Sequence as Drug Target.

Guo C, D'Ippolito AM, Reddy TE.

Cell. 2015 Jul 2;162(1):16-7. doi: 10.1016/j.cell.2015.06.033.

21.

Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort.

Vockley CM, Guo C, Majoros WH, Nodzenski M, Scholtens DM, Hayes MG, Lowe WL Jr, Reddy TE.

Genome Res. 2015 Aug;25(8):1206-14. doi: 10.1101/gr.190090.115. Epub 2015 Jun 17.

22.

Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators.

Polstein LR, Perez-Pinera P, Kocak DD, Vockley CM, Bledsoe P, Song L, Safi A, Crawford GE, Reddy TE, Gersbach CA.

Genome Res. 2015 Aug;25(8):1158-69. doi: 10.1101/gr.179044.114. Epub 2015 May 29.

23.

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers.

Hilton IB, D'Ippolito AM, Vockley CM, Thakore PI, Crawford GE, Reddy TE, Gersbach CA.

Nat Biotechnol. 2015 May;33(5):510-7. doi: 10.1038/nbt.3199. Epub 2015 Apr 6.

24.

Multiplex CRISPR/Cas9-based genome editing for correction of dystrophin mutations that cause Duchenne muscular dystrophy.

Ousterout DG, Kabadi AM, Thakore PI, Majoros WH, Reddy TE, Gersbach CA.

Nat Commun. 2015 Feb 18;6:6244. doi: 10.1038/ncomms7244.

25.

Coordinated regulatory variation associated with gestational hyperglycaemia regulates expression of the novel hexokinase HKDC1.

Guo C, Ludvik AE, Arlotto ME, Hayes MG, Armstrong LL, Scholtens DM, Brown CD, Newgard CB, Becker TC, Layden BT, Lowe WL, Reddy TE.

Nat Commun. 2015 Feb 4;6:6069. doi: 10.1038/ncomms7069.

26.

New insights into gestational glucose metabolism: lessons learned from 21st century approaches.

Angueira AR, Ludvik AE, Reddy TE, Wicksteed B, Lowe WL Jr, Layden BT.

Diabetes. 2015 Feb;64(2):327-34. doi: 10.2337/db14-0877.

27.

Enhanced MyoD-induced transdifferentiation to a myogenic lineage by fusion to a potent transactivation domain.

Kabadi AM, Thakore PI, Vockley CM, Ousterout DG, Gibson TM, Guilak F, Reddy TE, Gersbach CA.

ACS Synth Biol. 2015 Jun 19;4(6):689-99. doi: 10.1021/sb500322u. Epub 2014 Dec 31.

28.

Correction of dystrophin expression in cells from Duchenne muscular dystrophy patients through genomic excision of exon 51 by zinc finger nucleases.

Ousterout DG, Kabadi AM, Thakore PI, Perez-Pinera P, Brown MT, Majoros WH, Reddy TE, Gersbach CA.

Mol Ther. 2015 Mar;23(3):523-32. doi: 10.1038/mt.2014.234. Epub 2014 Dec 10.

29.

Distinct properties of cell-type-specific and shared transcription factor binding sites.

Gertz J, Savic D, Varley KE, Partridge EC, Safi A, Jain P, Cooper GM, Reddy TE, Crawford GE, Myers RM.

Mol Cell. 2013 Oct 10;52(1):25-36. doi: 10.1016/j.molcel.2013.08.037. Epub 2013 Sep 26.

30.

Identification of HKDC1 and BACE2 as genes influencing glycemic traits during pregnancy through genome-wide association studies.

Hayes MG, Urbanek M, Hivert MF, Armstrong LL, Morrison J, Guo C, Lowe LP, Scheftner DA, Pluzhnikov A, Levine DM, McHugh CP, Ackerman CM, Bouchard L, Brisson D, Layden BT, Mirel D, Doheny KF, Leya MV, Lown-Hecht RN, Dyer AR, Metzger BE, Reddy TE, Cox NJ, Lowe WL Jr; HAPO Study Cooperative Research Group.

Diabetes. 2013 Sep;62(9):3282-91. doi: 10.2337/db12-1692. Epub 2013 Jul 31. Erratum in: Diabetes. 2013 Oct;62(10):3641.

31.

RNA-guided gene activation by CRISPR-Cas9-based transcription factors.

Perez-Pinera P, Kocak DD, Vockley CM, Adler AF, Kabadi AM, Polstein LR, Thakore PI, Glass KA, Ousterout DG, Leong KW, Guilak F, Crawford GE, Reddy TE, Gersbach CA.

Nat Methods. 2013 Oct;10(10):973-6. doi: 10.1038/nmeth.2600. Epub 2013 Jul 25.

32.

Evidence for multiple roles for grainyhead-like 2 in the establishment and maintenance of human mucociliary airway epithelium.[corrected].

Gao X, Vockley CM, Pauli F, Newberry KM, Xue Y, Randell SH, Reddy TE, Hogan BL.

Proc Natl Acad Sci U S A. 2013 Jun 4;110(23):9356-61. doi: 10.1073/pnas.1307589110. Epub 2013 May 20. Erratum in: Proc Natl Acad Sci U S A. 2014 Dec 9;111(49):17684.

33.

The chromosome 3q25 genomic region is associated with measures of adiposity in newborns in a multi-ethnic genome-wide association study.

Urbanek M, Hayes MG, Armstrong LL, Morrison J, Lowe LP, Badon SE, Scheftner D, Pluzhnikov A, Levine D, Laurie CC, McHugh C, Ackerman CM, Mirel DB, Doheny KF, Guo C, Scholtens DM, Dyer AR, Metzger BE, Reddy TE, Cox NJ, Lowe WL Jr; HAPO Study Cooperative Research Group.

Hum Mol Genet. 2013 Sep 1;22(17):3583-96. doi: 10.1093/hmg/ddt168. Epub 2013 Apr 10.

34.

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.

35.

Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner.

Gertz J, Reddy TE, Varley KE, Garabedian MJ, Myers RM.

Genome Res. 2012 Nov;22(11):2153-62. doi: 10.1101/gr.135681.111. Epub 2012 Sep 26.

36.

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.

37.

Architecture of the human regulatory network derived from ENCODE data.

Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M.

Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245.

38.

The hypersensitive glucocorticoid response specifically regulates period 1 and expression of circadian genes.

Reddy TE, Gertz J, Crawford GE, Garabedian MJ, Myers RM.

Mol Cell Biol. 2012 Sep;32(18):3756-67. doi: 10.1128/MCB.00062-12. Epub 2012 Jul 16.

39.

Corrigendum to:Agent-based modeling of the context dependency in T cell recognition.

Sumen C, Reddy TE, Alber MS, Lee PP.

J Theor Biol. 2012 Jun 21;303:152-3. No abstract available.

PMID:
22783551
40.

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression.

Reddy TE, Gertz J, Pauli F, Kucera KS, Varley KE, Newberry KM, Marinov GK, Mortazavi A, Williams BA, Song L, Crawford GE, Wold B, Willard HF, Myers RM.

Genome Res. 2012 May;22(5):860-9. doi: 10.1101/gr.131201.111. Epub 2012 Feb 2.

41.

Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation.

Gertz J, Varley KE, Reddy TE, Bowling KM, Pauli F, Parker SL, Kucera KS, Willard HF, Myers RM.

PLoS Genet. 2011 Aug;7(8):e1002228. doi: 10.1371/journal.pgen.1002228. Epub 2011 Aug 11.

42.

Allele-specific distribution of RNA polymerase II on female X chromosomes.

Kucera KS, Reddy TE, Pauli F, Gertz J, Logan JE, Myers RM, Willard HF.

Hum Mol Genet. 2011 Oct 15;20(20):3964-73. doi: 10.1093/hmg/ddr315. Epub 2011 Jul 26.

43.

Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation.

Reddy TE, Pauli F, Sprouse RO, Neff NF, Newberry KM, Garabedian MJ, Myers RM.

Genome Res. 2009 Dec;19(12):2163-71. doi: 10.1101/gr.097022.109. Epub 2009 Oct 2.

44.

Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver.

Brunner AL, Johnson DS, Kim SW, Valouev A, Reddy TE, Neff NF, Anton E, Medina C, Nguyen L, Chiao E, Oyolu CB, Schroth GP, Absher DM, Baker JC, Myers RM.

Genome Res. 2009 Jun;19(6):1044-56. doi: 10.1101/gr.088773.108. Epub 2009 Mar 9.

45.

Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites.

Reddy TE, DeLisi C, Shakhnovich BE.

PLoS Comput Biol. 2007 May;3(5):e90. Epub 2007 Apr 10.

46.

Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes.

Reddy TE, Shakhnovich BE, Roberts DS, Russek SJ, DeLisi C.

Nucleic Acids Res. 2007;35(3):e20. Epub 2007 Jan 3.

47.

Assessing transcription factor motif drift from noisy decoy sequences.

Reddy TE, DeLisi C, Shakhnovich BE.

Genome Inform. 2005;16(1):59-67.

PMID:
16362907
48.

Agent-based modeling of the context dependency in T cell recognition.

Casal A, Sumen C, Reddy TE, Alber MS, Lee PP.

J Theor Biol. 2005 Oct 21;236(4):376-91. Erratum in: J Theor Biol. 2012 Jun 21;303:152-3.

PMID:
15899504
49.

Comparisons of predicted genetic modules: identification of co-expressed genes through module gene flow.

Shakhnovich BE, Reddy TE, Galinsky K, Mellor J, Delisi C.

Genome Inform. 2004;15(1):221-8.

PMID:
15712124

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