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Items: 1 to 20 of 47

1.

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 Aug 10. doi: 10.1101/gr.233346.117. [Epub ahead of print]

2.

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.

3.

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 Jul 10. pii: S2405-4712(18)30247-3. doi: 10.1016/j.cels.2018.06.007. [Epub ahead of print]

PMID:
30031775
4.

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 Apr 25. doi: 10.1093/bioinformatics/bty324. [Epub ahead of print]

PMID:
29701825
5.

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
6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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
12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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