Timothy E Reddy | Scholars@Duke

Timothy E Reddy
Associate Professor of Biostatistics & Bioinformatics

Current Appointments & Affiliations

Associate Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2017
Assistant Professor of Biomedical Engineering, Biomedical Engineering, Pratt School of Engineering 2016
Associate Professor in Molecular Genetics and Microbiology, Molecular Genetics and Microbiology, Basic Science Departments 2017

Contact Information

101 Science Drive, 2347 Ciemas, Duke Box 3382, Durham, NC 27708
Duke Box 3382, Durham, NC 27710
tim.reddy@duke.edu (919) 564-9536
Website

Background
Education, Training, & Certifications
- Ph.D., Boston University 2007
Duke Appointment History
- Assistant Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2011 - 2017
- Assistant Professor in Molecular Genetics and Microbiology, Molecular Genetics and Microbiology, Basic Science Departments 2012 - 2017
Recognition
In the News
- OCT 3, 2018 Duke Med Alumni News
  
  From Innovation to Impact
- APR 9, 2018
  
  Faculty Startup Sold to Belgian Pharma for $30 Million
- AUG 25, 2016
  
  Hormone Activation Of Genes Takes Teamwork
- OCT 27, 2015
  
  Pratt Research Brings Precise Control to Gene Expression
- MAY 26, 2015
  
  Studying the Harm and Healing Power of Steroids
- FEB 5, 2015
  
  Newly Discovered Protein Has Link to Gestational Diabetes
- JAN 6, 2015
  
  Genomics Team Wins $5.9 Million Grant
Expertise
Subject Headings
Research
Selected Grants
- Duke CTSA (KL2) awarded by National Institutes of Health 2018 - 2023
- Duke CTSA (TL1) awarded by National Institutes of Health 2018 - 2023
- Summer Scholars Program in Genome Sciences and Medicine awarded by National Institutes of Health 2017 - 2022
- Postdoctoral Training in Genomic Medicine Research awarded by National Institutes of Health 2017 - 2022
- Training Program in Developmental and Stem Cell Biology awarded by National Institutes of Health 2001 - 2022
- To support research on the development of CRISPR-based epigenome editing tools to refine genome wide association studies awarded by Open Philanthropy Project 2018 - 2021
- Regulatory Mechanisms of CD4+ T Cell Differentiation awarded by National Institutes of Health 2017 - 2021
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- Cellular and Molecular Systems Biology of Preterm Birth awarded by University of Chicago 2015 - 2020
- Epigenome Editing Technologies to Control Diverse Biological Functions awarded by Allen Institute for Brain Science 2017 - 2020
- Functional characterization of regulatory variants associated with maternal hyperglycemia awarded by National Institutes of Health 2017 - 2020
- Genetics Training Grant awarded by National Institutes of Health 1979 - 2020
- Interdisciplinary Training Program in Lung Disease awarded by National Institutes of Health 2009 - 2020
- 3/3 Chromatin regulation during brain development and in ASD awarded by National Institutes of Health 2018 - 2019
- Multiethnic Fine-Mapping of Polycystic Ovary Syndrome Susceptibility Loci awarded by Mount Sinai School of Medicine 2017 - 2019
- Decoding schizophrenia-From GWAS to functional regulatory variants awarded by National Institutes of Health 2014 - 2019
- Decoding and Reprogramming the Corticosteroid Transcriptional Regulatory Network awarded by National Institutes of Health 2015 - 2018
- Trans-regulatory mechanisms of glucocorticoid-mediated transcriptional repression awarded by National Institutes of Health 2016 - 2018
- Progenitor Cells in Lung Development and Repair awarded by National Institutes of Health 1992 - 2018
- The function and regulation of the novel pregnancy-specific hexokinase HKDC1 awarded by University of Illinois at Chicago 2017 - 2018
- Genetics and Genomics of Maternal Glycemia During Pregnancy awarded by Northwestern University 2013 - 2018
- Engineering Targeted Epigenetic Modifiers for Precise Control of Gene Regulation awarded by National Institutes of Health 2013 - 2018
- Genetics and Evolution of Fetal Human Fat Accretion During Development awarded by Northwestern University 2013 - 2018
- University of Utah awarded by University of Utah 2017 - 2018
- Toward a Comprehensive Functional Annotation of the Human Genome awarded by HudsonAlpha Institute for Biotechnology 2012 - 2017
- Multiethnic Fine-Mapping of Polycystic Ovary Syndrome Susceptibility Loci awarded by Northwestern University 2016 - 2017
- HARDAC+:Reproducible HPC for next-generation genomics awarded by North Carolina Biotechnology Center 2016 - 2017
- Genome Editing of Stem Cells for Analysis of Osteoarthritis Causal Variants awarded by National Institutes of Health 2014 - 2017
- EAGER: Graph-based Genome Annotation and Analyses for Plant Genomes awarded by University of Utah 2016 - 2017
- Testing novel models of glucocorticoid-induced transcription regulation awarded by National Institutes of Health 2015 - 2016
- The function and regulation of the novel pregnancy-specific hexokinase HKDC1 awarded by Northwestern University 2015 - 2016
- Identifying Regulatory Variants Associated with Maternal Hyperglycemia awarded by National Institutes of Health 2015 - 2016
Publications & Artistic Works
Selected Publications
- Book Sections
  - Reddy, TE. "The Functional Genome: Epigenetics and Epigenomics." In Genomic and Precision Medicine: Foundations, Translation, and Implementation: Third Edition, 21-44. December 15, 2016. Full Text
- Conference Papers
  - Thakore, PI, D'Ippolito, A, Song, L, Safi, A, Shivakumar, NK, Kabadi, AM, Bledsoe, P, Reddy, TE, Crawford, GE, and Gersbach, CA. "485. Targeted Epigenome Editing by CRISPR/Cas9-Based Repressors for Silencing of Distal Regulatory Elements." May 2015. Full Text
  - Thakore, PI, Ousterout, DG, Kabadi, AM, Deneke, VE, Crawford, GE, Reddy, TE, and Gersbach, CA. "CRISPR/Cas9-Based Transcriptional Repressors for Control of Human Gene Expression." May 2014. Link to Item
- Journal Articles
  - Majoros, WH, Holt, C, Campbell, MS, Ware, D, Yandell, M, and Reddy, TE. "Predicting gene structure changes resulting from genetic variants via exon definition features." Bioinformatics (Oxford, England) 34, no. 21 (November 2018): 3616-3623. Full Text
  - 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, and Reddy, TE. "Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding." Genome Res 28, no. 9 (September 2018): 1272-1284. Full Text Link to Item
  - 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, and Reddy, TE. "Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids." Cell Systems 7, no. 2 (August 2018): 146-160.e7. Full Text
  - McDowell, IC, Manandhar, D, Vockley, CM, Schmid, AK, Reddy, TE, and Engelhardt, BE. "Clustering gene expression time series data using an infinite Gaussian process mixture model." Plos Computational Biology 14, no. 1 (January 16, 2018): e1005896-null. Full Text
  - Klann, TS, Crawford, GE, Reddy, TE, and Gersbach, CA. "Screening Regulatory Element Function with CRISPR/Cas9-based Epigenome Editing." Methods in molecular biology (Clifton, N.J.) 1767 (January 2018): 447-480. Full Text
  - Vockley, CM, McDowell, IC, D'Ippolito, AM, and Reddy, TE. "A long-range flexible billboard model of gene activation." Transcription 8, no. 4 (August 2017): 261-267. Full Text
  - Klann, TS, Black, JB, Chellappan, M, Safi, A, Song, L, Hilton, IB, Crawford, GE, Reddy, TE, and Gersbach, CA. "CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome." Nature Biotechnology 35, no. 6 (June 2017): 561-568. Full Text
  - Guo, C, McDowell, IC, Nodzenski, M, Scholtens, DM, Allen, AS, Lowe, WL, and Reddy, TE. "Transversions have larger regulatory effects than transitions." BMC genomics 18, no. 1 (May 19, 2017): 394-. Full Text
  - Hivert, M-F, Scholtens, DM, Allard, C, Nodzenski, M, Bouchard, L, Brisson, D, Lowe, LP, McDowell, I, Reddy, T, Dastani, Z, Richards, JB, Hayes, MG, and Lowe, WL. "Genetic determinants of adiponectin regulation revealed by pregnancy." Obesity (Silver Spring, Md.) 25, no. 5 (May 2017): 935-944. Full Text
  - Majoros, WH, Campbell, MS, Holt, C, DeNardo, EK, Ware, D, Allen, AS, Yandell, M, and Reddy, TE. "High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE." Bioinformatics (Oxford, England) 33, no. 10 (May 2017): 1437-1446. Full Text
  - Vockley, CM, Barrera, A, and Reddy, TE. "Decoding the role of regulatory element polymorphisms in complex disease." Current Opinion in Genetics & Development 43 (April 2017): 38-45. (Review) Full Text
  - Black, JB, Adler, AF, Wang, H-G, D'Ippolito, AM, Hutchinson, HA, Reddy, TE, Pitt, GS, Leong, KW, and Gersbach, CA. "Targeted Epigenetic Remodeling of Endogenous Loci by CRISPR/Cas9-Based Transcriptional Activators Directly Converts Fibroblasts to Neuronal Cells." Cell Stem Cell 19, no. 3 (September 2016): 406-414. Full Text
  - Ludvik, AE, Pusec, CM, Priyadarshini, M, Angueira, AR, Guo, C, Lo, A, Hershenhouse, KS, Yang, G-Y, Ding, X, Reddy, TE, Lowe, WL, and Layden, BT. "HKDC1 Is a Novel Hexokinase Involved in Whole-Body Glucose Use." Endocrinology 157, no. 9 (September 2016): 3452-3461. Full Text
  - Vockley, CM, D'Ippolito, AM, McDowell, IC, Majoros, WH, Safi, A, Song, L, Crawford, GE, and Reddy, TE. "Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome." Cell 166, no. 5 (August 2016): 1269-1281.e19. Full Text
  - 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, FCP, 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, CCY, Wray, GA, Wu, EY, Xu, X, Yao, L, Senthil, G, Lehner, T, Sklar, P, and Sestan, N. "The PsychENCODE project." Nature Neuroscience 18, no. 12 (December 2015): 1707-1712. (Review) Full Text Open Access Copy
  - Thakore, PI, D'Ippolito, AM, Song, L, Safi, A, Shivakumar, NK, Kabadi, AM, Reddy, TE, Crawford, GE, and Gersbach, CA. "Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements." Nature Methods 12, no. 12 (December 2015): 1143-1149. Full Text
  - Lowe, WL, and Reddy, TE. "Genomic approaches for understanding the genetics of complex disease." Genome Research 25, no. 10 (October 2015): 1432-1441. Full Text
  - Polstein, LR, Perez-Pinera, P, Kocak, DD, Vockley, CM, Bledsoe, P, Song, L, Safi, A, Crawford, GE, Reddy, TE, and Gersbach, CA. "Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators." Genome Research 25, no. 8 (August 2015): 1158-1169. Full Text
  - Polstein, LR, Perez-Pinera, P, Kocak, DD, Vockley, CM, Bledsoe, P, Song, L, Safi, A, Crawford, GE, Reddy, TE, and Gersbach, CA. "Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators." GENOME RESEARCH 25, no. 8 (August 2015): 1158-1169. Full Text Link to Item
  - Vockley, CM, Guo, C, Majoros, WH, Nodzenski, M, Scholtens, DM, Hayes, MG, Lowe, WL, and Reddy, TE. "Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort." Genome Research 25, no. 8 (August 2015): 1206-1214. Full Text
  - Guo, C, D'Ippolito, AM, and Reddy, TE. "From Prescription to Transcription: Genome Sequence as Drug Target." Cell 162, no. 1 (July 2015): 16-17. Full Text
  - Kabadi, AM, Thakore, PI, Vockley, CM, Ousterout, DG, Gibson, TM, Guilak, F, Reddy, TE, and Gersbach, CA. "Enhanced MyoD-induced transdifferentiation to a myogenic lineage by fusion to a potent transactivation domain." Acs Synthetic Biology 4, no. 6 (June 2015): 689-699. Full Text
  - Hilton, IB, D'Ippolito, AM, Vockley, CM, Thakore, PI, Crawford, GE, Reddy, TE, and Gersbach, CA. "Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers." Nature Biotechnology 33, no. 5 (May 2015): 510-517. Full Text
  - Ousterout, DG, Kabadi, AM, Thakore, PI, Perez-Pinera, P, Brown, MT, Majoros, WH, Reddy, TE, and 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, no. 3 (March 2015): 523-532. Full Text
  - Ousterout, DG, Kabadi, AM, Thakore, PI, Perez-Pinera, P, Brown, MT, Majoros, WH, Reddy, TE, and 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 23, no. 3 (March 2015): 523-532. Full Text Link to Item
  - Ousterout, DG, Kabadi, AM, Thakore, PI, Majoros, WH, Reddy, TE, and Gersbach, CA. "Multiplex CRISPR/Cas9-based genome editing for correction of dystrophin mutations that cause Duchenne muscular dystrophy." Nature Communications 6 (February 18, 2015): 6244-null. Full Text
  - Guo, C, Ludvik, AE, Arlotto, ME, Hayes, MG, Armstrong, LL, Scholtens, DM, Brown, CD, Newgard, CB, Becker, TC, Layden, BT, Lowe, WL, and Reddy, TE. "Coordinated regulatory variation associated with gestational hyperglycaemia regulates expression of the novel hexokinase HKDC1." Nature communications 6 (February 4, 2015): 6069-. Full Text
  - Angueira, AR, Ludvik, AE, Reddy, TE, Wicksteed, B, Lowe, WL, and Layden, BT. "New insights into gestational glucose metabolism: lessons learned from 21st century approaches." Diabetes 64, no. 2 (February 2015): 327-334. Full Text
  - Ousterout, DG, Kabadi, AM, Thakore, PI, Perez-Pinera, P, Brown, MT, Majoros, WH, Reddy, TE, and 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 23, no. 3 (January 1, 2015): 523-532. Full Text
  - Gertz, J, Savic, D, Varley, KE, Partridge, EC, Safi, A, Jain, P, Cooper, GM, Reddy, TE, Crawford, GE, and Myers, RM. "Distinct properties of cell-type-specific and shared transcription factor binding sites." Molecular Cell 52, no. 1 (October 2013): 25-36. Full Text
  - Hayes, M, Urbanek, M, Hivert, M-F, Armstrong, L, Morrison, J, Guo, C, Lowe, L, Scheftner, D, Pluzhnikov, A, Levine, D, McHugh, C, Ackerman, C, Bouchard, L, Brisson, D, Layden, B, Mirel, D, Doheny, K, Leya, M, Lown-Hecht, R, Dyer, A, Metzger, B, Reddy, T, Cox, N, and Lowe, W. "Identification of HKDC1 and BACE2 as genes influencing glycemic traits during pregnancy through genome-wide association studies. Diabetes 2013;62:3282-3291." Diabetes 62, no. 10 (October 1, 2013): 3641-3641. Full Text
  - 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, and Gersbach, CA. "RNA-guided gene activation by CRISPR-Cas9-based transcription factors." Nat Methods 10, no. 10 (October 2013): 973-976. Full Text Link to Item
  - Hayes, MG, Urbanek, M, Hivert, M-F, 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, and HAPO Study Cooperative Research Group, . "Identification of HKDC1 and BACE2 as genes influencing glycemic traits during pregnancy through genome-wide association studies." Diabetes 62, no. 9 (September 2013): 3282-3291. Full Text
  - 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, and HAPO Study Cooperative Research Group, . "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, no. 17 (September 2013): 3583-3596. Full Text
  - Gao, X, Vockley, CM, Pauli, F, Newberry, KM, Xue, Y, Randell, SH, Reddy, TE, and Hogan, BLM. "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 110, no. 23 (June 4, 2013): 9356-9361. Full Text Link to Item
  - 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, and Myers, RM. "Dynamic DNA methylation across diverse human cell lines and tissues." Genome Research 23, no. 3 (March 2013): 555-567. Full Text
  - Gertz, J, Savic, D, Varley, KE, Partridge, EC, Safi, A, Jain, P, Cooper, GM, Reddy, TE, Crawford, GE, and Myers, RM. "Distinct properties of cell-type-specific and shared transcription factor binding sites." Molecular Cell 52, no. 1 (2013): 25-36. Full Text
  - 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, and Gersbach, CA. "RNA-guided gene activation by CRISPR-Cas9-based transcription factors." Nature Methods 10, no. 10 (2013): 973-976. Full Text
  - ENCODE Project Consortium, . "An integrated encyclopedia of DNA elements in the human genome." Nature 489, no. 7414 (September 2012): 57-74. Full Text
  - Gerstein, MB, Kundaje, A, Hariharan, M, Landt, SG, Yan, K-K, 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, and Snyder, M. "Architecture of the human regulatory network derived from ENCODE data." Nature 489, no. 7414 (September 2012): 91-100. Full Text
  - 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, and Snyder, M. "ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia." Genome Research 22, no. 9 (September 2012): 1813-1831. Full Text
  - Reddy, TE, Gertz, J, Crawford, GE, Garabedian, MJ, and Myers, RM. "The hypersensitive glucocorticoid response specifically regulates period 1 and expression of circadian genes." Molecular and Cellular Biology 32, no. 18 (September 2012): 3756-3767. Full Text
  - 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, and Myers, RM. "Effects of sequence variation on differential allelic transcription factor occupancy and gene expression." Genome Research 22, no. 5 (May 2012): 860-869. Full Text
  - Gertz, J, Reddy, TE, Varley, KE, Garabedian, MJ, and 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, no. 11 (2012): 2153-2162. Full Text
  - Sumen, C, Reddy, TE, Alber, MS, and Lee, PP. "Corrigendum to: "Agent-based modeling of the context dependency in T cell recognition" [J. Theor. Biol. 236 (2005) 376-391]." Journal of Theoretical Biology 303 (2012): 152-153. Full Text
  - Kucera, KS, Reddy, TE, Pauli, F, Gertz, J, Logan, JE, Myers, RM, and Willard, HF. "Allele-specific distribution of RNA polymerase II on female X chromosomes." Hum Mol Genet 20, no. 20 (October 15, 2011): 3964-3973. Full Text Link to Item
  - Gertz, J, Varley, KE, Reddy, TE, Bowling, KM, Pauli, F, Parker, SL, Kucera, KS, Willard, HF, and Myers, RM. "Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation." Plos Genetics 7, no. 8 (August 11, 2011): e1002228-null. Full Text
  - "A User's Guide to the Encyclopedia of DNA Elements (ENCODE)." Edited by Becker, PB. Plos Biology 9, no. 4 (April 19, 2011): e1001046-e1001046. Full Text
  - Reddy, TE, Pauli, F, Sprouse, RO, Neff, NF, Newberry, KM, Garabedian, MJ, and Myers, RM. "Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation." Genome Research 19, no. 12 (December 2009): 2163-2171. Full Text
  - 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, and Myers, RM. "Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver." Genome Research 19, no. 6 (June 2009): 1044-1056. Full Text
  - Reddy, TE, DeLisi, C, and Shakhnovich, BE. "Binding site graphs: A new graph theoretical framework for prediction of transcription factor binding sites." PLoS Computational Biology 3, no. 5 (2007): 0844-0854. Full Text
  - Reddy, TE, Shakhnovich, BE, Roberts, DS, Russek, SJ, and DeLisi, C. "Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABA_A receptor subunit genes." Nucleic Acids Research 35, no. 3 (2007). Full Text
  - Casal, A, Sumen, C, Reddy, TE, Alber, MS, and Lee, PP. "Agent-based modeling of the context dependency in T cell recognition." Journal of Theoretical Biology 236, no. 4 (2005): 376-391. Full Text
  - Reddy, TE, DeLisi, C, and Shakhnovich, BE. "Assessing transcription factor motif drift from noisy decoy sequences." Genome informatics series : proceedings of the .. Workshop on Genome Informatics. Workshop on Genome Informatics. 16, no. 1 (2005): 59-67.
  - Casal, A, Sumen, C, Reddy, T, Alber, M, and 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) 3305 (2004): 553-560.
  - Shakhnovich, BE, Reddy, TE, Galinsky, K, Mellor, J, and Delisi, C. "Comparisons of predicted genetic modules: identification of co-expressed genes through module gene flow." Genome informatics series : proceedings of the . Workshop on Genome Informatics. Workshop on Genome Informatics 15, no. 1 (2004): 221-228.
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