Timothy E Reddy

Education

• Ph.D. Boston University, 2007

Positions

• Associate Professor of Biostatistics & Bioinformatics,
• Associate Professor of Biomedical Engineering
• Associate Professor in Molecular Genetics and Microbiology

Courses Taught

• UPGEN 778C: University Program in Genetics and Genomics Biological Solutions Module Ill

Publications

• Beaman MM, Yin W, Smith AJ, Sears PR, Leigh MW, Ferkol TW, et al. Promoter Deletion Leading to Allele Specific Expression in a Genetically Unsolved Case of Primary Ciliary Dyskinesia. Am J Med Genet A. 2025 Feb;197(2):e63880.
• Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, et al. An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation. bioRxiv. 2024 Dec 26;
• Zou X, Gomez ZW, Reddy TE, Allen AS, Majoros WH. Bayesian Estimation of Allele-Specific Expression in the Presence of Phasing Uncertainty. bioRxiv. 2024 Aug 13;
• Melore SM, Hamilton MC, Reddy TE. HyperCas12a enables highly-multiplexed epigenome editing screens. bioRxiv. 2024 Jul 9;
• Nussbaum DP, Martz CA, Waters AM, Barrera A, Liu A, Rutter JC, et al. Mediator kinase inhibition impedes transcriptional plasticity and prevents resistance to ERK/MAPK-targeted therapy in KRAS-mutant cancers. NPJ Precis Oncol. 2024 May 31;8(1):124.
• Yao D, Tycko J, Oh JW, Bounds LR, Gosai SJ, Lataniotis L, et al. Multicenter integrated analysis of noncoding CRISPRi screens. Nat Methods. 2024 Apr;21(4):723u201334.
• McCutcheon SR, Swartz AM, Brown MC, Barrera A, McRoberts Amador C, Siklenka K, et al. Transcriptional and epigenetic regulators of human CD8+ T cell function identified through orthogonal CRISPR screens. Nat Genet. 2023 Dec;55(12):2211u201323.
• Park E, Barclay WE, Barrera A, Liao T-C, Salzler HR, Reddy TE, et al. Integrin u03b13 promotes TH17 cell polarization and extravasation during autoimmune neuroinflammation. Sci Immunol. 2023 Oct 20;8(88):eadg7597.
• Ang HX, Sutiman N, Deng XL, Liu A, Cerda-Smith CG, Hutchinson HM, et al. Cooperative regulation of coupled oncoprotein synthesis and stability in triple-negative breast cancer by EGFR and CDK12/13. Proc Natl Acad Sci U S A. 2023 Sep 19;120(38):e2221448120.
• Mangan RJ, Alsina FC, Mosti F, Sotelo-Fonseca JE, Snellings DA, Au EH, et al. Adaptive sequence divergence forged new neurodevelopmental enhancers in humans. Cell. 2022 Nov 23;185(24):4587-4603.e23.
• Zhu X, Trimarco JD, Williams CA, Barrera A, Reddy TE, Heaton NS. ZBTB7A promotes virus-host homeostasis during human coronavirus 229E infection. Cell Rep. 2022 Oct 25;41(4):111540.
• Luo K, Zhong J, Safi A, Hong LK, Tewari AK, Song L, et al. Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data. Genome Res. 2022 Jun;32(6):1183u201398.
• Kadur Lakshminarasimha Murthy P, Xi R, Arguijo D, Everitt JI, Kocak DD, Kobayashi Y, et al. Epigenetic basis of oncogenic-Kras-mediated epithelial-cellular proliferation and plasticity. Dev Cell. 2022 Feb 7;57(3):310-328.e9.
• Kabadi AM, Machlin L, Dalal N, Lee RE, McDowell I, Shah NN, et al. Epigenome editing of the CFTR-locus for treatment of cystic fibrosis. Journal of cystic fibrosisu202f: official journal of the European Cystic Fibrosis Society. 2022 Jan;21(1):164u201371.
• Reddy TE. The functional genome: epigenetics and epigenomics. In: Genomic and Precision Medicine: Oncology, Third Edition. 2022. p. 29u201354.
• Miller DE, Sulovari A, Wang T, Loucks H, Hoekzema K, Munson KM, et al. Targeted long-read sequencing identifies missing disease-causing variation. Am J Hum Genet. 2021 Aug 5;108(8):1436u201349.
• Gemberling MP, Siklenka K, Rodriguez E, Tonn-Eisinger KR, Barrera A, Liu F, et al. Transgenic mice for in vivo epigenome editing with CRISPR-based systems. Nat Methods. 2021 Aug;18(8):965u201374.
• Prekovic S, Schuurman K, Mayayo-Peralta I, Manju00f3n AG, Buijs M, Yavuz S, et al. Glucocorticoid receptor triggers a reversible drug-tolerant dormancy state with acquired therapeutic vulnerabilities in lung cancer. Nature communications. 2021 Jul;12(1):4360.
• Hu B, Won H, Mah W, Park RB, Kassim B, Spiess K, et al. Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders. Nat Commun. 2021 Jun 25;12(1):3968.
• Kim Y-S, Johnson GD, Seo J, Barrera A, Cowart TN, Majoros WH, et al. Correcting signal biases and detecting regulatory elements in STARR-seq data. Genome Res. 2021 May;31(5):877u201389.
• Seo J, Kou00e7ak DD, Bartelt LC, Williams CA, Barrera A, Gersbach CA, et al. AP-1 subunits converge promiscuously at enhancers to potentiate transcription. Genome Res. 2021 Apr;31(4):538u201350.
• Lu J, Dumitrascu B, McDowell IC, Jo B, Barrera A, Hong LK, et al. Causal network inference from gene transcriptional time-series response to glucocorticoids. PLoS Comput Biol. 2021 Jan;17(1):e1008223.
• Black JB, McCutcheon SR, Dube S, Barrera A, Klann TS, Rice GA, et al. Master Regulators and Cofactors of Human Neuronal Cell Fate Specification Identified by CRISPR Gene Activation Screens. Cell Rep. 2020 Dec 1;33(9):108460.
• Sakabe NJ, Aneas I, Knoblauch N, Sobreira DR, Clark N, Paz C, et al. Transcriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth. Sci Adv. 2020 Dec;6(49).
• Majoros WH, Kim Y-S, Barrera A, Li F, Wang X, Cunningham SJ, et al. Bayesian estimation of genetic regulatory effects in high-throughput reporter assays. Bioinformatics. 2020 Jan 15;36(2):331u20138.
• Parker ME, Barrera A, Wheaton JD, Zuberbuehler MK, Allan DSJ, Carlyle JR, et al. c-Maf regulates the plasticity of group 3 innate lymphoid cells by restraining the type 1 program. J Exp Med. 2020 Jan 6;217(1).
• Cunningham SJ, Feng L, Allen TK, Reddy TE. Functional Genomics of Healthy and Pathological Fetal Membranes. Front Physiol. 2020;11:687.
• Pickar-Oliver A, Black JB, Lewis MM, Mutchnick KJ, Klann TS, Gilcrest KA, et al. Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells. In: Nat Biotechnol. 2019. p. 1493u2013501.
• Lea AJ, Vockley CM, Johnston RA, Del Carpio CA, Barreiro LB, Reddy TE, et al. Genome-wide quantification of the effects of DNA methylation on human gene regulation. Elife. 2018 Dec 21;7.
• Johnson GD, Barrera A, McDowell IC, Du2019Ippolito AM, Majoros WH, Vockley CM, et al. Human genome-wide measurement of drug-responsive regulatory activity. Nat Commun. 2018 Dec 21;9(1):5317.
• 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. 2018 Nov 1;34(21):3616u201323.
• McDowell IC, Barrera A, Du2019Ippolito AM, Vockley CM, Hong LK, Leichter SM, et al. Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding. Genome Res. 2018 Sep;28(9):1272u201384.
• Du2019Ippolito AM, McDowell IC, Barrera A, Hong LK, Leichter SM, Bartelt LC, et al. Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids. Cell Syst. 2018 Aug 22;7(2):146-160.e7.
• Bryois J, Garrett ME, Song L, Safi A, Giusti-Rodriguez P, Johnson GD, et al. Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia. Nat Commun. 2018 Aug 7;9(1):3121.
• Klann TS, Crawford GE, Reddy TE, Gersbach CA. Screening Regulatory Element Function with CRISPR/Cas9-based Epigenome Editing. Methods Mol Biol. 2018;1767:447u201380.
• 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 Comput Biol. 2018 Jan;14(1):e1005896.
• Vockley CM, McDowell IC, Du2019Ippolito AM, Reddy TE. A long-range flexible billboard model of gene activation. Transcription. 2017 Aug 8;8(4):261u20137.
• Klann TS, Black JB, Chellappan M, Safi A, Song L, Hilton IB, et al. CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome. Nat Biotechnol. 2017 Jun;35(6):561u20138.
• Guo C, McDowell IC, Nodzenski M, Scholtens DM, Allen AS, Lowe WL, et al. Transversions have larger regulatory effects than transitions. BMC Genomics. 2017 May 19;18(1):394.
• Majoros WH, Campbell MS, Holt C, DeNardo EK, Ware D, Allen AS, et al. High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. Bioinformatics. 2017 May 15;33(10):1437u201346.
• Hivert M-F, Scholtens DM, Allard C, Nodzenski M, Bouchard L, Brisson D, et al. Genetic determinants of adiponectin regulation revealed by pregnancy. Obesity (Silver Spring). 2017 May;25(5):935u201344.
• Vockley CM, Barrera A, Reddy TE. Decoding the role of regulatory element polymorphisms in complex disease. Curr Opin Genet Dev. 2017 Apr;43:38u201345.
• Reddy TE. The Functional Genome: Epigenetics and Epigenomics. In: Genomic and Precision Medicine: Foundations, Translation, and Implementation: Third Edition. 2017. p. 21u201344.
• Black JB, Adler AF, Wang H-G, Du2019Ippolito AM, Hutchinson HA, Reddy TE, et al. Targeted Epigenetic Remodeling of Endogenous Loci by CRISPR/Cas9-Based Transcriptional Activators Directly Converts Fibroblasts to Neuronal Cells. Cell Stem Cell. 2016 Sep 1;19(3):406u201314.
• Ludvik AE, Pusec CM, Priyadarshini M, Angueira AR, Guo C, Lo A, et al. HKDC1 Is a Novel Hexokinase Involved in Whole-Body Glucose Use. Endocrinology. 2016 Sep;157(9):3452u201361.
• Vockley CM, Du2019Ippolito AM, McDowell IC, Majoros WH, Safi A, Song L, et al. Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome. Cell. 2016 Aug 25;166(5):1269-1281.e19.
• PsychENCODE Consortium, Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, et al. The PsychENCODE project. Nat Neurosci. 2015 Dec;18(12):1707u201312.
• Thakore PI, Du2019Ippolito AM, Song L, Safi A, Shivakumar NK, Kabadi AM, et al. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat Methods. 2015 Dec;12(12):1143u20139.
• Lowe WL, Reddy TE. Genomic approaches for understanding the genetics of complex disease. Genome Res. 2015 Oct;25(10):1432u201341.
• Polstein LR, Perez-Pinera P, Kocak DD, Vockley CM, Bledsoe P, Song L, et al. Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators. Genome Res. 2015 Aug;25(8):1158u201369.
• Vockley CM, Guo C, Majoros WH, Nodzenski M, Scholtens DM, Hayes MG, et al. Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort. Genome Res. 2015 Aug;25(8):1206u201314.
• Guo C, Du2019Ippolito AM, Reddy TE. From Prescription to Transcription: Genome Sequence as Drug Target. Cell. 2015 Jul 2;162(1):16u20137.
• Kabadi AM, Thakore PI, Vockley CM, Ousterout DG, Gibson TM, Guilak F, et al. Enhanced MyoD-induced transdifferentiation to a myogenic lineage by fusion to a potent transactivation domain. ACS Synth Biol. 2015 Jun 19;4(6):689u201399.
• Thakore PI, Du2019Ippolito A, Song L, Safi A, Shivakumar NK, Kabadi AM, et al. 485. Targeted Epigenome Editing by CRISPR/Cas9-Based Repressors for Silencing of Distal Regulatory Elements. In: Molecular Therapy. Elsevier BV; 2015. p. S192u20133.
• Hilton IB, Du2019Ippolito AM, Vockley CM, Thakore PI, Crawford GE, Reddy TE, et al. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol. 2015 May;33(5):510u20137.
• Ousterout DG, Kabadi AM, Thakore PI, Perez-Pinera P, Brown MT, Majoros WH, et al. Correction of dystrophin expression in cells from Duchenne muscular dystrophy patients through genomic excision of exon 51 by zinc finger nucleases. Molecular Therapy. 2015 Mar 5;23(3):523u201332.
• Ousterout DG, Kabadi AM, Thakore PI, Perez-Pinera P, Brown MT, Majoros WH, et al. Correction of dystrophin expression in cells from Duchenne muscular dystrophy patients through genomic excision of exon 51 by zinc finger nucleases. Mol Ther. 2015 Mar;23(3):523u201332.
• 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. Nat Commun. 2015 Feb 18;6:6244.
• Guo C, Ludvik AE, Arlotto ME, Hayes MG, Armstrong LL, Scholtens DM, et al. Coordinated regulatory variation associated with gestational hyperglycaemia regulates expression of the novel hexokinase HKDC1. Nat Commun. 2015 Feb 4;6:6069.
• 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. 2015 Feb;64(2):327u201334.
• Thakore PI, Ousterout DG, Kabadi AM, Deneke VE, Crawford GE, Reddy TE, et al. CRISPR/Cas9-Based Transcriptional Repressors for Control of Human Gene Expression. In: MOLECULAR THERAPY. NATURE PUBLISHING GROUP; 2014. p. S214u20135.
• Gertz J, Savic D, Varley KE, Partridge EC, Safi A, Jain P, et al. Distinct properties of cell-type-specific and shared transcription factor binding sites. Mol Cell. 2013 Oct 10;52(1):25u201336.
• Perez-Pinera P, Kocak DD, Vockley CM, Adler AF, Kabadi AM, Polstein LR, et al. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods. 2013 Oct;10(10):973u20136.
• Hayes MG, Urbanek M, Hivert MF, Armstrong LL, Morrison J, Guo C, et al. Erratum: Identification of HKDC1 and BACE2 as genes influencing glycemic traits during pregnancy through genome-wide association studies (Diabetes (2013) 62 (3282-3291)). Diabetes. 2013 Oct 1;62(10):3641.
• Hayes MG, Urbanek M, Hivert M-F, Armstrong LL, Morrison J, Guo C, et al. Identification of HKDC1 and BACE2 as genes influencing glycemic traits during pregnancy through genome-wide association studies. Diabetes. 2013 Sep;62(9):3282u201391.
• Urbanek M, Hayes MG, Armstrong LL, Morrison J, Lowe LP, Badon SE, et al. The chromosome 3q25 genomic region is associated with measures of adiposity in newborns in a multi-ethnic genome-wide association study. Hum Mol Genet. 2013 Sep 1;22(17):3583u201396.
• Gao X, Vockley CM, Pauli F, Newberry KM, Xue Y, Randell SH, et al. Evidence for multiple roles for grainyhead-like 2 in the establishment and maintenance of human mucociliary airway epithelium.[corrected]. Proc Natl Acad Sci U S A. 2013 Jun 4;110(23):9356u201361.
• Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F, et al. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res. 2013 Mar;23(3):555u201367.
• Perez-Pinera P, Kocak DD, Vockley CM, Adler AF, Kabadi AM, Polstein LR, et al. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nature Methods. 2013;10(10):973u20136.
• 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 Res. 2012 Nov;22(11):2153u201362.
• Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan K-K, Cheng C, et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 6;489(7414):91u2013100.
• ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57u201374.
• Reddy TE, Gertz J, Crawford GE, Garabedian MJ, Myers RM. The hypersensitive glucocorticoid response specifically regulates period 1 and expression of circadian genes. Mol Cell Biol. 2012 Sep;32(18):3756u201367.
• Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep;22(9):1813u201331.
• Sumen C, Reddy TE, Alber MS, Lee PP. Corrigendum to:Agent-based modeling of the context dependency in T cell recognition. J Theor Biol. 2012 Jun 21;303:152u20133.
• Reddy TE, Gertz J, Pauli F, Kucera KS, Varley KE, Newberry KM, et al. Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res. 2012 May;22(5):860u20139.
• Kucera KS, Reddy TE, Pauli F, Gertz J, Logan JE, Myers RM, et al. Allele-specific distribution of RNA polymerase II on female X chromosomes. Hum Mol Genet. 2011 Oct 15;20(20):3964u201373.
• Gertz J, Varley KE, Reddy TE, Bowling KM, Pauli F, Parker SL, et al. Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet. 2011 Aug;7(8):e1002228.
• ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr;9(4):e1001046.
• Reddy TE, Pauli F, Sprouse RO, Neff NF, Newberry KM, Garabedian MJ, et al. Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation. Genome Res. 2009 Dec;19(12):2163u201371.
• Brunner AL, Johnson DS, Kim SW, Valouev A, Reddy TE, Neff NF, et al. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 2009 Jun;19(6):1044u201356.
• Reddy TE, DeLisi C, Shakhnovich BE. Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites. PLoS Comput Biol. 2007 May;3(5):e90.
• 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 Res. 2007;35(3):e20.
• Casal A, Sumen C, Reddy TE, Alber MS, Lee PP. Agent-based modeling of the context dependency in T cell recognition. J Theor Biol. 2005 Oct 21;236(4):376u201391.
• Reddy TE, DeLisi C, Shakhnovich BE. Assessing transcription factor motif drift from noisy decoy sequences. Genome Inform. 2005;16(1):59u201367.
• Casal A, Sumen C, Reddy T, Alber M, Lee PP. A cellular automata model of early t cell recognition. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2004 Jan 1;3305:553u201360.
• 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 Inform. 2004;15(1):221u20138.

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