Timothy E Reddy
Associate Professor of Biostatistics & Bioinformatics,
Current Appointments & Affiliations
- Associate Professor of Biostatistics & Bioinformatics,, Biostatistics & Bioinformatics, Basic Science Departments 2019
- 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
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tim.reddy@duke.edu
(919) 564-9536
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Website
- Background
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Education, Training, & Certifications
- Ph.D., Boston University 2007
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Previous Appointments & Affiliations
- Associate Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2017 - 2019
- Assistant Professor of Biomedical Engineering, Biomedical Engineering, Pratt School of Engineering 2016 - 2019
- 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
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In the News
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NOV 23, 2022 -
OCT 3, 2018 Duke Med Alumni News -
APR 9, 2018 -
AUG 25, 2016 -
OCT 27, 2015 -
MAY 26, 2015 -
FEB 5, 2015 Duke Today -
FEB 5, 2015 -
JAN 6, 2015
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- Expertise
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Subject Headings
- Alleles
- Binding Sites
- Cell Adhesion
- Cell Differentiation
- Cell Movement
- Chromatin
- Chromatin Immunoprecipitation
- Chromosomes, Human
- Chromosomes, Human, X
- DNA
- DNA Methylation
- DNA-Binding Proteins
- Databases, Genetic
- Deoxyribonuclease I
- E1A-Associated p300 Protein
- Encyclopedias as Topic
- Epithelial Cells
- Exons
- Female
- Gene Expression Profiling
- Gene Expression Regulation
- Genetic Predisposition to Disease
- Genetic Variation
- Genetic Vectors
- Genome
- Genome, Human
- Genome-Wide Association Study
- Genomics
- HEK293 Cells
- High-Throughput Nucleotide Sequencing
- Histones
- Humans
- Immunohistochemistry
- Interleukin 1 Receptor Antagonist Protein
- Internet
- Introns
- Mammals
- Microarray Analysis
- Molecular Sequence Annotation
- Polymorphism, Single Nucleotide
- Promoter Regions, Genetic
- Protein Engineering
- RNA Editing
- RNA Polymerase II
- RNA, Guide
- Regulatory Elements, Transcriptional
- Regulatory Sequences, Nucleic Acid
- Respiratory Mucosa
- Ribonucleases
- Sequence Analysis, RNA
- Transcription Factors
- Transcription, Genetic
- Transcriptional Activation
- X Chromosome Inactivation
- Research
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Selected Grants
- Deciphering the role of noncoding variation in the pathogenesis of multiple sclerosis awarded by National Institutes of Health 2021 - 2026
- Design, prediction, and prioritization of systematic perturbations of the human genome awarded by National Institutes of Health 2021 - 2026
- High-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular Phenotypes awarded by National Institutes of Health 2021 - 2026
- Beyond GWAS: High Throughput Functional Genomics & Epigenome Editing to Elucidate the Effects of Genetic Associations for Schizophrenia awarded by National Institutes of Health 2021 - 2026
- Genetic and Genomics Training Grant awarded by National Institutes of Health 2020 - 2025
- Elucidating the Genetic Architecture of Metabolic and Reproductive PCOS Subtypes in Diverse Populations awarded by Icahn School of Medicine at Mount Sinai 2022 - 2025
- Uncovering novel gene regulatory mechanisms underlying glucocorticoid response phenotypes through targeted mutagenesis of an essential transcription factor awarded by National Institutes of Health 2022 - 2025
- Defining the effects of noncoding genetic variation on human regulatory element activity awarded by National Institutes of Health 2021 - 2024
- The function and regulation of the novel pregnancy-specific hexokinase HKDC1 awarded by University of Illinois at Chicago 2017 - 2023
- The Duke FUNCTION Center: Pioneering the comprehensive identification of combinatorial noncoding causes of disease awarded by National Institutes of Health 2020 - 2023
- Epigenome Editing Technologies for Treating Diverse Disease awarded by National Institutes of Health 2019 - 2023
- Preparing Genetic Counselors for Genomic Medicine Research awarded by National Institutes of Health 2017 - 2023
- Quantifying the genetic diversity of human regulatory element activity awarded by National Institutes of Health 2019 - 2023
- Postdoctoral Training in Genomic Medicine Research awarded by National Institutes of Health 2017 - 2023
- IRES Track 1 IRTG Engaged in Dissecting and Reengineering the Regulatory Genome awarded by National Science Foundation 2019 - 2023
- Duke CTSA (TL1) Year 5 awarded by National Institutes of Health 2018 - 2023
- Thwarting Influenza with RNA-powered Modulators (ThIRM) awarded by Georgia Institute of Technology 2019 - 2023
- Genetics of glucocorticoid-induced intraocular pressure rise awarded by Massachusetts Eye and Ear Infirmary 2021 - 2022
- Identification and Characterization of Novel Cis-Regulatory Elements Controlling PTEN Expression awarded by National Institutes of Health 2020 - 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 - 2022
- Predicting Newborn and Childhood Adiposity: An Integrated Omics Approach awarded by Northwestern University 2018 - 2022
- Regulatory Mechanisms of CD4+ T Cell Differentiation awarded by National Institutes of Health 2017 - 2022
- Identifying Pathogenic Non-Coding Mutations in Rare Mendelian Disease awarded by National Institutes of Health 2019 - 2022
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- Epigenome Editing Technologies to Control Diverse Biological Functions awarded by Allen Institute for Brain Science 2017 - 2021
- 3/3 Chromatin regulation during brain development and in ASD awarded by National Institutes of Health 2018 - 2021
- Multiethnic Fine-Mapping of Polycystic Ovary Syndrome Susceptibility Loci awarded by Mount Sinai School of Medicine 2017 - 2021
- Interdisciplinary Training Program in Lung Disease awarded by National Institutes of Health 2009 - 2021
- Genetics Training Grant awarded by National Institutes of Health 1979 - 2020
- Functional characterization of regulatory variants associated with maternal hyperglycemia awarded by National Institutes of Health 2017 - 2020
- Cellular and Molecular Systems Biology of Preterm Birth awarded by University of Chicago 2015 - 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
- 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
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External Relationships
- Element Genomics
- Publications & Artistic Works
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Selected Publications
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Academic Articles
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Mangan, Riley J., Fernando C. Alsina, Federica Mosti, Jesús Emiliano Sotelo-Fonseca, Daniel A. Snellings, Eric H. Au, Juliana Carvalho, et al. “Adaptive sequence divergence forged new neurodevelopmental enhancers in humans.” Cell 185, no. 24 (November 23, 2022): 4587-4603.e23. https://doi.org/10.1016/j.cell.2022.10.016.Full Text Link to Item
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Zhu, Xinyu, Joseph D. Trimarco, Courtney A. Williams, Alejandro Barrera, Timothy E. Reddy, and Nicholas S. Heaton. “ZBTB7A promotes virus-host homeostasis during human coronavirus 229E infection.” Cell Rep 41, no. 4 (October 25, 2022): 111540. https://doi.org/10.1016/j.celrep.2022.111540.Full Text Link to Item
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Luo, Kaixuan, Jianling Zhong, Alexias Safi, Linda K. Hong, Alok K. Tewari, Lingyun Song, Timothy E. Reddy, Li Ma, Gregory E. Crawford, and Alexander J. Hartemink. “Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data.” Genome Res 32, no. 6 (June 2022): 1183–98. https://doi.org/10.1101/gr.272203.120.Full Text Link to Item
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Kadur Lakshminarasimha Murthy, Preetish, Rui Xi, Diana Arguijo, Jeffrey I. Everitt, Dewran D. Kocak, Yoshihiko Kobayashi, Aline Bozec, et al. “Epigenetic basis of oncogenic-Kras-mediated epithelial-cellular proliferation and plasticity.” Dev Cell 57, no. 3 (February 7, 2022): 310-328.e9. https://doi.org/10.1016/j.devcel.2022.01.006.Full Text Link to Item
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Kabadi, Ami M., Leah Machlin, Nikita Dalal, Rhianna E. Lee, Ian McDowell, Nirav N. Shah, Lauren Drowley, Scott H. Randell, and Timothy E. Reddy. “Epigenome editing of the CFTR-locus for treatment of cystic fibrosis.” J Cyst Fibros 21, no. 1 (January 2022): 164–71. https://doi.org/10.1016/j.jcf.2021.04.008.Full Text Link to Item
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Miller, Danny E., Arvis Sulovari, Tianyun Wang, Hailey Loucks, Kendra Hoekzema, Katherine M. Munson, Alexandra P. Lewis, et al. “Targeted long-read sequencing identifies missing disease-causing variation.” Am J Hum Genet 108, no. 8 (August 5, 2021): 1436–49. https://doi.org/10.1016/j.ajhg.2021.06.006.Full Text Link to Item
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Gemberling, Matthew P., Keith Siklenka, Erica Rodriguez, Katherine R. Tonn-Eisinger, Alejandro Barrera, Fang Liu, Ariel Kantor, et al. “Transgenic mice for in vivo epigenome editing with CRISPR-based systems.” Nat Methods 18, no. 8 (August 2021): 965–74. https://doi.org/10.1038/s41592-021-01207-2.Full Text Link to Item
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Prekovic, Stefan, Karianne Schuurman, Isabel Mayayo-Peralta, Anna G. Manjón, Mark Buijs, Selçuk Yavuz, Max D. Wellenstein, et al. “Glucocorticoid receptor triggers a reversible drug-tolerant dormancy state with acquired therapeutic vulnerabilities in lung cancer.” Nat Commun 12, no. 1 (July 16, 2021): 4360. https://doi.org/10.1038/s41467-021-24537-3.Full Text Link to Item
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Hu, Benxia, Hyejung Won, Won Mah, Royce B. Park, Bibi Kassim, Keeley Spiess, Alexey Kozlenkov, et al. “Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders.” Nat Commun 12, no. 1 (June 25, 2021): 3968. https://doi.org/10.1038/s41467-021-24243-0.Full Text Link to Item
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Kim, Young-Sook, Graham D. Johnson, Jungkyun Seo, Alejandro Barrera, Thomas N. Cowart, William H. Majoros, Alejandro Ochoa, Andrew S. Allen, and Timothy E. Reddy. “Correcting signal biases and detecting regulatory elements in STARR-seq data.” Genome Res 31, no. 5 (May 2021): 877–89. https://doi.org/10.1101/gr.269209.120.Full Text Link to Item
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Seo, Jungkyun, D Dewran Koçak, Luke C. Bartelt, Courtney A. Williams, Alejandro Barrera, Charles A. Gersbach, and Timothy E. Reddy. “AP-1 subunits converge promiscuously at enhancers to potentiate transcription.” Genome Res 31, no. 4 (April 2021): 538–50. https://doi.org/10.1101/gr.267898.120.Full Text Link to Item
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Lu, Jonathan, Bianca Dumitrascu, Ian C. McDowell, Brian Jo, Alejandro Barrera, Linda K. Hong, Sarah M. Leichter, Timothy E. Reddy, and Barbara E. Engelhardt. “Causal network inference from gene transcriptional time-series response to glucocorticoids.” Plos Comput Biol 17, no. 1 (January 2021): e1008223. https://doi.org/10.1371/journal.pcbi.1008223.Full Text Link to Item
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Black, Joshua B., Sean R. McCutcheon, Shataakshi Dube, Alejandro Barrera, Tyler S. Klann, Grayson A. Rice, Shaunak S. Adkar, Scott H. Soderling, Timothy E. Reddy, and Charles A. Gersbach. “Master Regulators and Cofactors of Human Neuronal Cell Fate Specification Identified by CRISPR Gene Activation Screens.” Cell Rep 33, no. 9 (December 1, 2020): 108460. https://doi.org/10.1016/j.celrep.2020.108460.Full Text Link to Item
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Sakabe, Noboru J., Ivy Aneas, Nicholas Knoblauch, Debora R. Sobreira, Nicole Clark, Cristina Paz, Cynthia Horth, et al. “Transcriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth.” Sci Adv 6, no. 49 (December 2020). https://doi.org/10.1126/sciadv.abc8696.Full Text Link to Item
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Majoros, William H., Young-Sook Kim, Alejandro Barrera, Fan Li, Xingyan Wang, Sarah J. Cunningham, Graham D. Johnson, et al. “Bayesian estimation of genetic regulatory effects in high-throughput reporter assays.” Bioinformatics 36, no. 2 (January 15, 2020): 331–38. https://doi.org/10.1093/bioinformatics/btz545.Full Text Link to Item
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Parker, Morgan E., Alejandro Barrera, Joshua D. Wheaton, Matthew K. Zuberbuehler, David S. J. Allan, James R. Carlyle, Timothy E. Reddy, and Maria Ciofani. “c-Maf regulates the plasticity of group 3 innate lymphoid cells by restraining the type 1 program.” J Exp Med 217, no. 1 (January 6, 2020). https://doi.org/10.1084/jem.20191030.Full Text Link to Item
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Cunningham, Sarah J., Liping Feng, Terrence K. Allen, and Timothy E. Reddy. “Functional Genomics of Healthy and Pathological Fetal Membranes.” Front Physiol 11 (2020): 687. https://doi.org/10.3389/fphys.2020.00687.Full Text Link to Item
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Johnson, Graham D., Alejandro Barrera, Ian C. McDowell, Anthony M. D’Ippolito, William H. Majoros, Christopher M. Vockley, Xingyan Wang, Andrew S. Allen, and Timothy E. Reddy. “Human genome-wide measurement of drug-responsive regulatory activity.” Nat Commun 9, no. 1 (December 21, 2018): 5317. https://doi.org/10.1038/s41467-018-07607-x.Full Text Link to Item
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Lea, Amanda J., Christopher M. Vockley, Rachel A. Johnston, Christina A. Del Carpio, Luis B. Barreiro, Timothy E. Reddy, and Jenny Tung. “Genome-wide quantification of the effects of DNA methylation on human gene regulation.” Elife 7 (December 21, 2018). https://doi.org/10.7554/eLife.37513.Full Text Link to Item
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Majoros, William H., Carson Holt, Michael S. Campbell, Doreen Ware, Mark Yandell, and Timothy E. Reddy. “Predicting gene structure changes resulting from genetic variants via exon definition features.” Bioinformatics 34, no. 21 (November 1, 2018): 3616–23. https://doi.org/10.1093/bioinformatics/bty324.Full Text Link to Item
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McDowell, Ian C., Alejandro Barrera, Anthony M. D’Ippolito, Christopher M. Vockley, Linda K. Hong, Sarah M. Leichter, Luke C. Bartelt, et al. “Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding.” Genome Res 28, no. 9 (September 2018): 1272–84. https://doi.org/10.1101/gr.233346.117.Full Text Link to Item
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D’Ippolito, Anthony M., Ian C. McDowell, Alejandro Barrera, Linda K. Hong, Sarah M. Leichter, Luke C. Bartelt, Christopher M. Vockley, et al. “Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids.” Cell Syst 7, no. 2 (August 22, 2018): 146-160.e7. https://doi.org/10.1016/j.cels.2018.06.007.Full Text Link to Item
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Bryois, Julien, Melanie E. Garrett, Lingyun Song, Alexias Safi, Paola Giusti-Rodriguez, Graham D. Johnson, Annie W. Shieh, et al. “Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia.” Nat Commun 9, no. 1 (August 7, 2018): 3121. https://doi.org/10.1038/s41467-018-05379-y.Full Text Link to Item
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Klann, Tyler S., Gregory E. Crawford, Timothy E. Reddy, and Charles A. Gersbach. “Screening Regulatory Element Function with CRISPR/Cas9-based Epigenome Editing.” Methods Mol Biol 1767 (2018): 447–80. https://doi.org/10.1007/978-1-4939-7774-1_25.Full Text Link to Item
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McDowell, Ian C., Dinesh Manandhar, Christopher M. Vockley, Amy K. Schmid, Timothy E. Reddy, and Barbara E. Engelhardt. “Clustering gene expression time series data using an infinite Gaussian process mixture model.” Plos Comput Biol 14, no. 1 (January 2018): e1005896. https://doi.org/10.1371/journal.pcbi.1005896.Full Text Link to Item
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Vockley, Christopher M., Ian C. McDowell, Antony M. D’Ippolito, and Timothy E. Reddy. “A long-range flexible billboard model of gene activation.” Transcription 8, no. 4 (August 8, 2017): 261–67. https://doi.org/10.1080/21541264.2017.1317694.Full Text Link to Item
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Klann, Tyler S., Joshua B. Black, Malathi Chellappan, Alexias Safi, Lingyun Song, Isaac B. Hilton, Gregory E. Crawford, Timothy E. Reddy, and Charles A. Gersbach. “CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.” Nat Biotechnol 35, no. 6 (June 2017): 561–68. https://doi.org/10.1038/nbt.3853.Full Text Link to Item
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Guo, Cong, Ian C. McDowell, Michael Nodzenski, Denise M. Scholtens, Andrew S. Allen, William L. Lowe, and Timothy E. Reddy. “Transversions have larger regulatory effects than transitions.” Bmc Genomics 18, no. 1 (May 19, 2017): 394. https://doi.org/10.1186/s12864-017-3785-4.Full Text Link to Item
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Majoros, William H., Michael S. Campbell, Carson Holt, Erin K. DeNardo, Doreen Ware, Andrew S. Allen, Mark Yandell, and Timothy E. Reddy. “High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE.” Bioinformatics 33, no. 10 (May 15, 2017): 1437–46. https://doi.org/10.1093/bioinformatics/btw799.Full Text Link to Item
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Hivert, Marie-France, Denise M. Scholtens, Catherine Allard, Michael Nodzenski, Luigi Bouchard, Diane Brisson, Lynn P. Lowe, et al. “Genetic determinants of adiponectin regulation revealed by pregnancy.” Obesity (Silver Spring) 25, no. 5 (May 2017): 935–44. https://doi.org/10.1002/oby.21805.Full Text Link to Item
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Vockley, Christopher M., Alejandro Barrera, and Timothy E. Reddy. “Decoding the role of regulatory element polymorphisms in complex disease.” Curr Opin Genet Dev 43 (April 2017): 38–45. https://doi.org/10.1016/j.gde.2016.10.007.Full Text Link to Item
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Black, Joshua B., Andrew F. Adler, Hong-Gang Wang, Anthony M. D’Ippolito, Hunter A. Hutchinson, Timothy E. Reddy, Geoffrey S. Pitt, Kam W. Leong, and Charles A. Gersbach. “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 1, 2016): 406–14. https://doi.org/10.1016/j.stem.2016.07.001.Full Text Link to Item
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Ludvik, Anton E., Carolina M. Pusec, Medha Priyadarshini, Anthony R. Angueira, Cong Guo, Amy Lo, Korri S. Hershenhouse, et al. “HKDC1 Is a Novel Hexokinase Involved in Whole-Body Glucose Use.” Endocrinology 157, no. 9 (September 2016): 3452–61. https://doi.org/10.1210/en.2016-1288.Full Text Link to Item
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Vockley, Christopher M., Anthony M. D’Ippolito, Ian C. McDowell, William H. Majoros, Alexias Safi, Lingyun Song, Gregory E. Crawford, and Timothy E. Reddy. “Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome.” Cell 166, no. 5 (August 25, 2016): 1269-1281.e19. https://doi.org/10.1016/j.cell.2016.07.049.Full Text Link to Item
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PsychENCODE Consortium, Nenad, Schahram Akbarian, Chunyu Liu, James A. Knowles, Flora M. Vaccarino, Peggy J. Farnham, Gregory E. Crawford, et al. “The PsychENCODE project.” Nat Neurosci 18, no. 12 (December 2015): 1707–12. https://doi.org/10.1038/nn.4156.Full Text Open Access Copy Link to Item
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Thakore, Pratiksha I., Anthony M. D’Ippolito, Lingyun Song, Alexias Safi, Nishkala K. Shivakumar, Ami M. Kabadi, Timothy E. Reddy, Gregory E. Crawford, and Charles A. Gersbach. “Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements.” Nat Methods 12, no. 12 (December 2015): 1143–49. https://doi.org/10.1038/nmeth.3630.Full Text Link to Item
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Lowe, William L., and Timothy E. Reddy. “Genomic approaches for understanding the genetics of complex disease.” Genome Res 25, no. 10 (October 2015): 1432–41. https://doi.org/10.1101/gr.190603.115.Full Text Link to Item
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Vockley, Christopher M., Cong Guo, William H. Majoros, Michael Nodzenski, Denise M. Scholtens, M Geoffrey Hayes, William L. Lowe, and Timothy E. Reddy. “Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort.” Genome Res 25, no. 8 (August 2015): 1206–14. https://doi.org/10.1101/gr.190090.115.Full Text Link to Item
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Polstein, Lauren R., Pablo Perez-Pinera, D Dewran Kocak, Christopher M. Vockley, Peggy Bledsoe, Lingyun Song, Alexias Safi, Gregory E. Crawford, Timothy E. Reddy, and Charles A. Gersbach. “Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators.” Genome Res 25, no. 8 (August 2015): 1158–69. https://doi.org/10.1101/gr.179044.114.Full Text Link to Item
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Guo, Cong, Anthony M. D’Ippolito, and Timothy E. Reddy. “From Prescription to Transcription: Genome Sequence as Drug Target.” Cell 162, no. 1 (July 2, 2015): 16–17. https://doi.org/10.1016/j.cell.2015.06.033.Full Text Link to Item
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Kabadi, Ami M., Pratiksha I. Thakore, Christopher M. Vockley, David G. Ousterout, Tyler M. Gibson, Farshid Guilak, Timothy E. Reddy, and Charles A. Gersbach. “Enhanced MyoD-induced transdifferentiation to a myogenic lineage by fusion to a potent transactivation domain.” Acs Synth Biol 4, no. 6 (June 19, 2015): 689–99. https://doi.org/10.1021/sb500322u.Full Text Link to Item
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Hilton, Isaac B., Anthony M. D’Ippolito, Christopher M. Vockley, Pratiksha I. Thakore, Gregory E. Crawford, Timothy E. Reddy, and Charles A. Gersbach. “Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers.” Nat Biotechnol 33, no. 5 (May 2015): 510–17. https://doi.org/10.1038/nbt.3199.Full Text Link to Item
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Ousterout, D. G., A. M. Kabadi, P. I. Thakore, P. Perez-Pinera, M. T. Brown, W. H. Majoros, T. E. Reddy, and C. A. Gersbach. “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 5, 2015): 523–32. https://doi.org/10.1038/mt.2014.234.Full Text
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Ousterout, David G., Ami M. Kabadi, Pratiksha I. Thakore, Pablo Perez-Pinera, Matthew T. Brown, William H. Majoros, Timothy E. Reddy, and Charles A. Gersbach. “Correction of dystrophin expression in cells from Duchenne muscular dystrophy patients through genomic excision of exon 51 by zinc finger nucleases.” Mol Ther 23, no. 3 (March 2015): 523–32. https://doi.org/10.1038/mt.2014.234.Full Text Link to Item
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Ousterout, David G., Ami M. Kabadi, Pratiksha I. Thakore, William H. Majoros, Timothy E. Reddy, and Charles A. Gersbach. “Multiplex CRISPR/Cas9-based genome editing for correction of dystrophin mutations that cause Duchenne muscular dystrophy.” Nat Commun 6 (February 18, 2015): 6244. https://doi.org/10.1038/ncomms7244.Full Text Link to Item
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Guo, Cong, Anton E. Ludvik, Michelle E. Arlotto, M Geoffrey Hayes, Loren L. Armstrong, Denise M. Scholtens, Christopher D. Brown, et al. “Coordinated regulatory variation associated with gestational hyperglycaemia regulates expression of the novel hexokinase HKDC1.” Nat Commun 6 (February 4, 2015): 6069. https://doi.org/10.1038/ncomms7069.Full Text Link to Item
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Angueira, Anthony R., Anton E. Ludvik, Timothy E. Reddy, Barton Wicksteed, William L. Lowe, and Brian T. Layden. “New insights into gestational glucose metabolism: lessons learned from 21st century approaches.” Diabetes 64, no. 2 (February 2015): 327–34. https://doi.org/10.2337/db14-0877.Full Text Link to Item
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Gertz, Jason, Daniel Savic, Katherine E. Varley, E Christopher Partridge, Alexias Safi, Preti Jain, Gregory M. Cooper, Timothy E. Reddy, Gregory E. Crawford, and Richard M. Myers. “Distinct properties of cell-type-specific and shared transcription factor binding sites.” Mol Cell 52, no. 1 (October 10, 2013): 25–36. https://doi.org/10.1016/j.molcel.2013.08.037.Full Text Link to Item
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Hayes, M. G., M. Urbanek, M. F. Hivert, L. L. Armstrong, J. Morrison, C. Guo, L. P. Lowe, 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 62, no. 10 (October 1, 2013): 3641. https://doi.org/10.2337/db13-er10.Full Text
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Perez-Pinera, Pablo, D Dewran Kocak, Christopher M. Vockley, Andrew F. Adler, Ami M. Kabadi, Lauren R. Polstein, Pratiksha I. Thakore, et al. “RNA-guided gene activation by CRISPR-Cas9-based transcription factors.” Nat Methods 10, no. 10 (October 2013): 973–76. https://doi.org/10.1038/nmeth.2600.Full Text Link to Item
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Hayes, M Geoffrey, Margrit Urbanek, Marie-France Hivert, Loren L. Armstrong, Jean Morrison, Cong Guo, Lynn P. Lowe, et al. “Identification of HKDC1 and BACE2 as genes influencing glycemic traits during pregnancy through genome-wide association studies.” Diabetes 62, no. 9 (September 2013): 3282–91. https://doi.org/10.2337/db12-1692.Full Text Link to Item
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Urbanek, Margrit, M Geoffrey Hayes, Loren L. Armstrong, Jean Morrison, Lynn P. Lowe, Sylvia E. Badon, Doug Scheftner, 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 22, no. 17 (September 1, 2013): 3583–96. https://doi.org/10.1093/hmg/ddt168.Full Text Link to Item
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Gao, Xia, Christopher M. Vockley, Florencia Pauli, Kimberly M. Newberry, Yan Xue, Scott H. Randell, Timothy E. Reddy, and Brigid L. M. Hogan. “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): 9356–61. https://doi.org/10.1073/pnas.1307589110.Full Text Link to Item
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Varley, Katherine E., Jason Gertz, Kevin M. Bowling, Stephanie L. Parker, Timothy E. Reddy, Florencia Pauli-Behn, Marie K. Cross, et al. “Dynamic DNA methylation across diverse human cell lines and tissues.” Genome Res 23, no. 3 (March 2013): 555–67. https://doi.org/10.1101/gr.147942.112.Full Text Link to Item
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Perez-Pinera, P., D. D. Kocak, C. M. Vockley, A. F. Adler, A. M. Kabadi, L. R. Polstein, P. I. Thakore, et al. “RNA-guided gene activation by CRISPR-Cas9-based transcription factors.” Nature Methods 10, no. 10 (2013): 973–76. https://doi.org/10.1038/nmeth.2600.Full Text
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Gertz, Jason, Timothy E. Reddy, Katherine E. Varley, Michael J. Garabedian, and Richard M. Myers. “Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner.” Genome Res 22, no. 11 (November 2012): 2153–62. https://doi.org/10.1101/gr.135681.111.Full Text Link to Item
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Gerstein, Mark B., Anshul Kundaje, Manoj Hariharan, Stephen G. Landt, Koon-Kiu Yan, Chao Cheng, Xinmeng Jasmine Mu, et al. “Architecture of the human regulatory network derived from ENCODE data.” Nature 489, no. 7414 (September 6, 2012): 91–100. https://doi.org/10.1038/nature11245.Full Text Link to Item
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ENCODE Project Consortium, Bernie. “An integrated encyclopedia of DNA elements in the human genome.” Nature 489, no. 7414 (September 6, 2012): 57–74. https://doi.org/10.1038/nature11247.Full Text Link to Item
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Reddy, Timothy E., Jason Gertz, Gregory E. Crawford, Michael J. Garabedian, and Richard M. Myers. “The hypersensitive glucocorticoid response specifically regulates period 1 and expression of circadian genes.” Mol Cell Biol 32, no. 18 (September 2012): 3756–67. https://doi.org/10.1128/MCB.00062-12.Full Text Link to Item
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Landt, Stephen G., Georgi K. Marinov, Anshul Kundaje, Pouya Kheradpour, Florencia Pauli, Serafim Batzoglou, Bradley E. Bernstein, et al. “ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.” Genome Res 22, no. 9 (September 2012): 1813–31. https://doi.org/10.1101/gr.136184.111.Full Text Link to Item
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Sumen, Cenk, Timothy E. Reddy, Mark S. Alber, and Peter P. Lee. “Corrigendum to:Agent-based modeling of the context dependency in T cell recognition.” J Theor Biol 303 (June 21, 2012): 152–53. https://doi.org/10.1016/j.jtbi.2012.03.018.Full Text Link to Item
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Reddy, Timothy E., Jason Gertz, Florencia Pauli, Katerina S. Kucera, Katherine E. Varley, Kimberly M. Newberry, Georgi K. Marinov, et al. “Effects of sequence variation on differential allelic transcription factor occupancy and gene expression.” Genome Res 22, no. 5 (May 2012): 860–69. https://doi.org/10.1101/gr.131201.111.Full Text Link to Item
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Kucera, Katerina S., Timothy E. Reddy, Florencia Pauli, Jason Gertz, Jenae E. Logan, Richard M. Myers, and Huntington F. Willard. “Allele-specific distribution of RNA polymerase II on female X chromosomes.” Hum Mol Genet 20, no. 20 (October 15, 2011): 3964–73. https://doi.org/10.1093/hmg/ddr315.Full Text Link to Item
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Gertz, Jason, Katherine E. Varley, Timothy E. Reddy, Kevin M. Bowling, Florencia Pauli, Stephanie L. Parker, Katerina S. Kucera, Huntington F. Willard, and Richard M. Myers. “Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation.” Plos Genet 7, no. 8 (August 2011): e1002228. https://doi.org/10.1371/journal.pgen.1002228.Full Text Link to Item
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ENCODE Project Consortium, G. E. “A user's guide to the encyclopedia of DNA elements (ENCODE).” Plos Biol 9, no. 4 (April 2011): e1001046. https://doi.org/10.1371/journal.pbio.1001046.Full Text Link to Item
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Reddy, Timothy E., Florencia Pauli, Rebekka O. Sprouse, Norma F. Neff, Kimberly M. Newberry, Michael J. Garabedian, and Richard M. Myers. “Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation.” Genome Res 19, no. 12 (December 2009): 2163–71. https://doi.org/10.1101/gr.097022.109.Full Text Link to Item
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Brunner, Alayne L., David S. Johnson, Si Wan Kim, Anton Valouev, Timothy E. Reddy, Norma F. Neff, Elizabeth Anton, et al. “Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver.” Genome Res 19, no. 6 (June 2009): 1044–56. https://doi.org/10.1101/gr.088773.108.Full Text Link to Item
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Reddy, Timothy E., Charles DeLisi, and Boris E. Shakhnovich. “Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites.” Plos Comput Biol 3, no. 5 (May 2007): e90. https://doi.org/10.1371/journal.pcbi.0030090.Full Text Link to Item
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Reddy, Timothy E., Boris E. Shakhnovich, Daniel S. Roberts, Shelley J. Russek, and Charles DeLisi. “Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes.” Nucleic Acids Res 35, no. 3 (2007): e20. https://doi.org/10.1093/nar/gkl1062.Full Text Link to Item
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Casal, Arancha, Cenk Sumen, Timothy E. Reddy, Mark S. Alber, and Peter P. Lee. “Agent-based modeling of the context dependency in T cell recognition.” J Theor Biol 236, no. 4 (October 21, 2005): 376–91. https://doi.org/10.1016/j.jtbi.2005.03.019.Full Text Link to Item
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Reddy, Timothy E., Charles DeLisi, and Boris E. Shakhnovich. “Assessing transcription factor motif drift from noisy decoy sequences.” Genome Inform 16, no. 1 (2005): 59–67.Link to Item
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Casal, A., C. Sumen, T. Reddy, M. Alber, and P. P. Lee. “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 (January 1, 2004): 553–60. https://doi.org/10.1007/978-3-540-30479-1_57.Full Text
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Shakhnovich, Boris E., Timothy E. Reddy, Kevin Galinsky, Joseph Mellor, and Charles Delisi. “Comparisons of predicted genetic modules: identification of co-expressed genes through module gene flow.” Genome Inform 15, no. 1 (2004): 221–28.Link to Item
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Book Sections
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Reddy, T. E. “The functional genome: epigenetics and epigenomics.” In Genomic and Precision Medicine: Oncology, Third Edition, 29–54, 2022. https://doi.org/10.1016/B978-0-12-800684-9.00017-4.Full Text
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Reddy, T. E. “The Functional Genome: Epigenetics and Epigenomics.” In Genomic and Precision Medicine: Foundations, Translation, and Implementation: Third Edition, 21–44, 2017. https://doi.org/10.1016/B978-0-12-800681-8.00002-5.Full Text
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Conference Papers
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Pickar-Oliver, Adrian, Joshua B. Black, Mae M. Lewis, Kevin J. Mutchnick, Tyler S. Klann, Kylie A. Gilcrest, Madeleine J. Sitton, et al. “Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells.” In Nat Biotechnol, 37:1493–1501, 2019. https://doi.org/10.1038/s41587-019-0235-7.Full Text Link to Item
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Thakore, Pratiksha I., Anthony D’Ippolito, Lingyun Song, Alexias Safi, Nishkala K. Shivakumar, Ami M. Kabadi, Peggy Bledsoe, Timothy E. Reddy, Gregory E. Crawford, and Charles A. Gersbach. “485. Targeted Epigenome Editing by CRISPR/Cas9-Based Repressors for Silencing of Distal Regulatory Elements.” In Molecular Therapy, 23:S192–93. Elsevier BV, 2015. https://doi.org/10.1016/s1525-0016(16)34094-1.Full Text
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Thakore, Pratiksha I., David G. Ousterout, Ami M. Kabadi, Victoria E. Deneke, Gregory E. Crawford, Timothy E. Reddy, and Charles A. Gersbach. “CRISPR/Cas9-Based Transcriptional Repressors for Control of Human Gene Expression.” In Molecular Therapy, 22:S214–15. NATURE PUBLISHING GROUP, 2014.Link to Item
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