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Timothy E. Reddy, Ph.D. - Publications

Affiliations: 
2008 Boston University, Boston, MA, United States 
Area:
Genetics, Bioinformatics Biology, Biostatistics Biology
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34 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Vockley CM, D'Ippolito AM, McDowell IC, Majoros WH, Safi A, Song L, Crawford GE, Reddy TE. Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome. Cell. 166: 1269-1281.e19. PMID 27565349 DOI: 10.1016/j.cell.2016.07.049  0.48
2016 Black JB, Adler AF, Wang HG, D'Ippolito AM, Hutchinson HA, Reddy TE, Pitt GS, Leong KW, Gersbach CA. Targeted Epigenetic Remodeling of Endogenous Loci by CRISPR/Cas9-Based Transcriptional Activators Directly Converts Fibroblasts to Neuronal Cells. Cell Stem Cell. PMID 27524438 DOI: 10.1016/j.stem.2016.07.001  0.48
2016 Ludvik AE, Pusec CM, Priyadarshini M, Angueira AR, Guo C, Lo A, Hershenhouse KS, Yang GY, Ding X, Reddy TE, Lowe WL, Layden BT. HKDC1 is a novel hexokinase involved in whole body glucose utilization. Endocrinology. en20161288. PMID 27459389 DOI: 10.1210/en.2016-1288  0.48
2015 Lowe WL, Reddy TE. Genomic approaches for understanding the genetics of complex disease. Genome Research. 25: 1432-41. PMID 26430153 DOI: 10.1101/gr.190603.115  0.48
2015 Vockley CM, Guo C, Majoros WH, Nodzenski M, Scholtens DM, Hayes MG, Lowe WL, Reddy TE. Massively parallel quantification of the regulatory effects of non-coding genetic variation in a human cohort. Genome Research. PMID 26084464 DOI: 10.1101/gr.190090.115  0.48
2015 Polstein LR, Perez-Pinera P, Kocak DD, Vockley CM, Bledsoe P, Song L, Safi A, Crawford GE, Reddy TE, Gersbach CA. Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators. Genome Research. PMID 26025803 DOI: 10.1101/gr.179044.114  0.48
2015 Hilton IB, D'Ippolito AM, Vockley CM, Thakore PI, Crawford GE, Reddy TE, Gersbach CA. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nature Biotechnology. 33: 510-7. PMID 25849900 DOI: 10.1038/nbt.3199  0.48
2015 Ousterout DG, Kabadi AM, Thakore PI, Majoros WH, Reddy TE, Gersbach CA. Multiplex CRISPR/Cas9-based genome editing for correction of dystrophin mutations that cause Duchenne muscular dystrophy. Nature Communications. 6: 6244. PMID 25692716 DOI: 10.1038/ncomms7244  0.48
2015 Guo C, Ludvik AE, Arlotto ME, Hayes MG, Armstrong LL, Scholtens DM, Brown CD, Newgard CB, Becker TC, Layden BT, Lowe WL, Reddy TE. Coordinated regulatory variation associated with gestational hyperglycaemia regulates expression of the novel hexokinase HKDC1. Nature Communications. 6: 6069. PMID 25648650 DOI: 10.1038/ncomms7069  0.48
2015 Angueira AR, Ludvik AE, Reddy TE, Wicksteed B, Lowe WL, Layden BT. New insights into gestational glucose metabolism: lessons learned from 21st century approaches. Diabetes. 64: 327-34. PMID 25614666 DOI: 10.2337/db14-0877  0.48
2015 Kabadi AM, Thakore PI, Vockley CM, Ousterout DG, Gibson TM, Guilak F, Reddy TE, Gersbach CA. Enhanced MyoD-Induced Transdifferentiation to a Myogenic Lineage by Fusion to a Potent Transactivation Domain. Acs Synthetic Biology. 4: 689-99. PMID 25494287 DOI: 10.1021/sb500322u  0.48
2015 Ousterout DG, Kabadi AM, Thakore PI, Perez-Pinera P, Brown MT, Majoros WH, Reddy TE, Gersbach CA. Correction of dystrophin expression in cells from duchenne muscular dystrophy patients through genomic excision of exon 51 by zinc finger nucleases. Molecular Therapy : the Journal of the American Society of Gene Therapy. 23: 523-32. PMID 25492562 DOI: 10.1038/mt.2014.234  0.48
2015 Guo C, D'Ippolito AM, Reddy TE. From Prescription to Transcription: Genome Sequence as Drug Target Cell. 162: 16-17. DOI: 10.1016/j.cell.2015.06.033  0.48
2013 Gertz J, Savic D, Varley KE, Partridge EC, Safi A, Jain P, Cooper GM, Reddy TE, Crawford GE, Myers RM. Distinct properties of cell-type-specific and shared transcription factor binding sites. Molecular Cell. 52: 25-36. PMID 24076218 DOI: 10.1016/j.molcel.2013.08.037  0.48
2013 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, ... ... Reddy TE, et al. Identification of HKDC1 and BACE2 as genes influencing glycemic traits during pregnancy through genome-wide association studies. Diabetes. 62: 3282-91. PMID 23903356 DOI: 10.2337/db12-1692  0.48
2013 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. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nature Methods. 10: 973-6. PMID 23892895 DOI: 10.1038/nmeth.2600  0.48
2013 Gao X, Vockley CM, Pauli F, Newberry KM, Xue Y, Randell SH, Reddy TE, Hogan BL. Evidence for multiple roles for grainyhead-like 2 in the establishment and maintenance of human mucociliary airway epithelium.[corrected]. Proceedings of the National Academy of Sciences of the United States of America. 110: 9356-61. PMID 23690579 DOI: 10.1073/pnas.1307589110  0.48
2013 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, ... ... Reddy TE, et al. The chromosome 3q25 genomic region is associated with measures of adiposity in newborns in a multi-ethnic genome-wide association study. Human Molecular Genetics. 22: 3583-96. PMID 23575227 DOI: 10.1093/hmg/ddt168  0.48
2013 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. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Research. 23: 555-67. PMID 23325432 DOI: 10.1101/gr.147942.112  0.48
2012 Gertz J, Reddy TE, Varley KE, Garabedian MJ, Myers RM. Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner. Genome Research. 22: 2153-62. PMID 23019147 DOI: 10.1101/gr.135681.111  0.48
2012 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, ... ... Reddy TE, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 22: 1813-31. PMID 22955991 DOI: 10.1101/gr.136184.111  0.48
2012 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, ... ... Reddy TE, et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 489: 91-100. PMID 22955619 DOI: 10.1038/nature11245  0.48
2012 Reddy TE, Gertz J, Crawford GE, Garabedian MJ, Myers RM. The hypersensitive glucocorticoid response specifically regulates period 1 and expression of circadian genes. Molecular and Cellular Biology. 32: 3756-67. PMID 22801371 DOI: 10.1128/MCB.00062-12  0.48
2012 Sumen C, Reddy TE, Alber MS, Lee PP. Corrigendum to:Agent-based modeling of the context dependency in T cell recognition. Journal of Theoretical Biology. 303: 152-3. PMID 22783551 DOI: 10.1016/j.jtbi.2012.03.018  0.48
2012 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. Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Research. 22: 860-9. PMID 22300769 DOI: 10.1101/gr.131201.111  0.48
2011 Gertz J, Varley KE, Reddy TE, Bowling KM, Pauli F, Parker SL, Kucera KS, Willard HF, Myers RM. Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. Plos Genetics. 7: e1002228. PMID 21852959 DOI: 10.1371/journal.pgen.1002228  0.48
2011 Kucera KS, Reddy TE, Pauli F, Gertz J, Logan JE, Myers RM, Willard HF. Allele-specific distribution of RNA polymerase II on female X chromosomes. Human Molecular Genetics. 20: 3964-73. PMID 21791549 DOI: 10.1093/hmg/ddr315  0.48
2009 Reddy TE, Pauli F, Sprouse RO, Neff NF, Newberry KM, Garabedian MJ, Myers RM. Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation. Genome Research. 19: 2163-71. PMID 19801529 DOI: 10.1101/gr.097022.109  0.48
2009 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. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Research. 19: 1044-56. PMID 19273619 DOI: 10.1101/gr.088773.108  0.48
2007 Reddy TE, DeLisi C, Shakhnovich BE. Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites. Plos Computational Biology. 3: e90. PMID 17500587 DOI: 10.1371/journal.pcbi.0030090  0.48
2007 Reddy TE, Shakhnovich BE, Roberts DS, Russek SJ, DeLisi C. Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes. Nucleic Acids Research. 35: e20. PMID 17204484 DOI: 10.1093/nar/gkl1062  0.48
2005 Reddy TE, DeLisi C, Shakhnovich BE. Assessing transcription factor motif drift from noisy decoy sequences. Genome Informatics. International Conference On Genome Informatics. 16: 59-67. PMID 16362907  0.48
2005 Casal A, Sumen C, Reddy TE, Alber MS, Lee PP. Agent-based modeling of the context dependency in T cell recognition. Journal of Theoretical Biology. 236: 376-91. PMID 15899504 DOI: 10.1016/j.jtbi.2005.03.019  0.48
2004 Shakhnovich BE, Reddy TE, Galinsky K, Mellor J, Delisi C. Comparisons of predicted genetic modules: identification of co-expressed genes through module gene flow. Genome Informatics. International Conference On Genome Informatics. 15: 221-8. PMID 15712124  0.48
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