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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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53 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
2025 Zou X, Gomez ZW, Reddy TE, Allen AS, Majoros WH. Bayesian Estimation of Allele-Specific Expression in the Presence of Phasing Uncertainty. Bioinformatics (Oxford, England). PMID 40326704 DOI: 10.1093/bioinformatics/btaf283  0.333
2024 Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, Andrews G, Gao M, Shedd N, Fu Y, Lacadie MC, Meza J, Ganna M, Choudhury E, Swofford R, ... ... Reddy TE, et al. An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation. Biorxiv : the Preprint Server For Biology. PMID 39763870 DOI: 10.1101/2024.12.26.629296  0.566
2024 Zou X, Gomez ZW, Reddy TE, Allen AS, Majoros WH. Bayesian Estimation of Allele-Specific Expression in the Presence of Phasing Uncertainty. Biorxiv : the Preprint Server For Biology. PMID 39211106 DOI: 10.1101/2024.08.09.607371  0.333
2022 Luo K, Zhong J, Safi A, Hong LK, Tewari AK, Song L, Reddy TE, Ma L, Crawford GE, Hartemink AJ. Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data. Genome Research. PMID 35609992 DOI: 10.1101/gr.272203.120  0.318
2021 Lu J, Dumitrascu B, McDowell IC, Jo B, Barrera A, Hong LK, Leichter SM, Reddy TE, Engelhardt BE. Causal network inference from gene transcriptional time-series response to glucocorticoids. Plos Computational Biology. 17: e1008223. PMID 33513136 DOI: 10.1371/journal.pcbi.1008223  0.314
2020 Cunningham SJ, Feng L, Allen TK, Reddy TE. Functional Genomics of Healthy and Pathological Fetal Membranes. Frontiers in Physiology. 11: 687. PMID 32655414 DOI: 10.3389/Fphys.2020.00687  0.304
2019 Parker ME, Barrera A, Wheaton JD, Zuberbuehler MK, Allan DSJ, Carlyle JR, Reddy TE, Ciofani M. c-Maf regulates the plasticity of group 3 innate lymphoid cells by restraining the type 1 program. The Journal of Experimental Medicine. PMID 31570496 DOI: 10.1084/Jem.20191030  0.311
2019 Pickar-Oliver A, Black JB, Lewis MM, Mutchnick KJ, Klann TS, Gilcrest KA, Sitton MJ, Nelson CE, Barrera A, Bartelt LC, Reddy TE, Beisel CL, Barrangou R, Gersbach CA. Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells. Nature Biotechnology. PMID 31548729 DOI: 10.1038/S41587-019-0235-7  0.33
2019 Majoros WH, Kim YS, Barrera A, Li F, Wang X, Cunningham SJ, Johnson GD, Guo C, Lowe WL, Scholtens DM, Hayes MG, Reddy TE, Allen AS. Bayesian Estimation of Genetic Regulatory Effects in High-throughput Reporter Assays. Bioinformatics (Oxford, England). PMID 31368479 DOI: 10.1093/Bioinformatics/Btz545  0.368
2018 Johnson GD, Barrera A, McDowell IC, D'Ippolito AM, Majoros WH, Vockley CM, Wang X, Allen AS, Reddy TE. Human genome-wide measurement of drug-responsive regulatory activity. Nature Communications. 9: 5317. PMID 30575722 DOI: 10.1038/S41467-018-07607-X  0.379
2018 Lea AJ, Vockley CM, Johnston RA, Del Carpio CA, Barreiro LB, Reddy TE, Tung J. Genome-wide quantification of the effects of DNA methylation on human gene regulation. Elife. 7. PMID 30575519 DOI: 10.7554/Elife.37513  0.384
2018 McDowell IC, Barrera A, D'Ippolito AM, Vockley CM, Hong LK, Leichter SM, Bartelt LC, Majoros WH, Song L, Safi A, Koçak DD, Gersbach CA, Hartemink AJ, Crawford GE, Engelhardt BE, ... Reddy TE, et al. Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding. Genome Research. PMID 30097539 DOI: 10.1101/Gr.233346.117  0.434
2018 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. Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids. Cell Systems. PMID 30031775 DOI: 10.1016/J.Cels.2018.06.007  0.451
2018 Majoros WH, Holt C, Campbell MS, Ware D, Yandell M, Reddy TE. Predicting Gene Structure Changes Resulting from Genetic Variants via Exon Definition Features. Bioinformatics (Oxford, England). PMID 29701825 DOI: 10.1093/Bioinformatics/Bty324  0.468
2018 Klann TS, Crawford GE, Reddy TE, Gersbach CA. Screening Regulatory Element Function with CRISPR/Cas9-based Epigenome Editing. Methods in Molecular Biology (Clifton, N.J.). 1767: 447-480. PMID 29524151 DOI: 10.1007/978-1-4939-7774-1_25  0.354
2018 McDowell IC, Manandhar D, Vockley CM, Schmid AK, Reddy TE, Engelhardt BE. Clustering gene expression time series data using an infinite Gaussian process mixture model. Plos Computational Biology. 14: e1005896. PMID 29337990 DOI: 10.1371/Journal.Pcbi.1005896  0.358
2018 Lea AJ, Vockley CM, Johnston RA, Carpio CAD, Barreiro LB, Reddy TE, Tung J. Author response: Genome-wide quantification of the effects of DNA methylation on human gene regulation Elife. DOI: 10.7554/Elife.37513.046  0.378
2017 Vockley CM, McDowell IC, D'Ippolito AM, Reddy TE. A Long-range Flexible Billboard Model of Gene Activation. Transcription. 0. PMID 28598247 DOI: 10.1080/21541264.2017.1317694  0.42
2017 Guo C, McDowell IC, Nodzenski M, Scholtens DM, Allen AS, Lowe WL, Reddy TE. Transversions have larger regulatory effects than transitions. Bmc Genomics. 18: 394. PMID 28525990 DOI: 10.1186/S12864-017-3785-4  0.439
2017 Klann TS, Black JB, Chellappan M, Safi A, Song L, Hilton IB, Crawford GE, Reddy TE, Gersbach CA. CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome. Nature Biotechnology. PMID 28369033 DOI: 10.1038/Nbt.3853  0.353
2016 Majoros WH, Campbell MS, Holt C, DeNardo E, Ware D, Allen AS, Yandell M, Reddy TE. High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. Bioinformatics (Oxford, England). PMID 28011790 DOI: 10.1093/Bioinformatics/Btw799  0.407
2016 Vockley CM, Barrera A, Reddy TE. Decoding the role of regulatory element polymorphisms in complex disease. Current Opinion in Genetics & Development. 43: 38-45. PMID 27984826 DOI: 10.1016/J.Gde.2016.10.007  0.408
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  0.462
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  0.436
2016 Kabadi AM, Klann TS, Chellappan M, Kwon J, Reddy TE, Gersbach CA. 525. Directed Molecular Evolution of Transcription Factors in Mammalian Cells for Enhanced Directed Cell Differentiation Molecular Therapy. 24: S210. DOI: 10.1016/S1525-0016(16)33334-2  0.4
2015 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, ... ... Reddy TE, et al. The PsychENCODE project. Nature Neuroscience. 18: 1707-1712. PMID 26605881 DOI: 10.1038/Nn.4156  0.539
2015 Thakore PI, D'Ippolito AM, Song L, Safi A, Shivakumar NK, Kabadi AM, Reddy TE, Crawford GE, Gersbach CA. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nature Methods. PMID 26501517 DOI: 10.1038/Nmeth.3630  0.468
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  0.38
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  0.392
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  0.499
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  0.445
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  0.381
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  0.323
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  0.414
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  0.4
2015 Thakore PI, D'Ippolito A, Song L, Safi A, Shivakumar NK, Kabadi AM, Bledsoe P, Reddy TE, Crawford GE, Gersbach CA. 485. Targeted Epigenome Editing by CRISPR/Cas9-Based Repressors for Silencing of Distal Regulatory Elements Molecular Therapy. 23: S192-S193. DOI: 10.1016/S1525-0016(16)34094-1  0.468
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  0.416
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  0.387
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  0.398
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  0.348
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  0.472
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  0.344
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  0.442
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  0.502
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  0.483
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  0.33
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  0.404
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  0.508
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  0.745
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  0.749
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 DOI: 10.11234/Gi1990.16.59  0.741
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  0.721
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:Identification of Co-Expressed Genes through Module Gene Flow Genome Informatics. 15: 221-228. DOI: 10.11234/Gi1990.15.221  0.716
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