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
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
Previous Appointments & Affiliations
- 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
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
- 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
- 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 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
- Quantifying the genetic diversity of human regulatory element activity awarded by National Institutes of Health 2019 - 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
- The function and regulation of the novel pregnancy-specific hexokinase HKDC1 awarded by University of Illinois at Chicago 2017 - 2022
- Predicting Newborn and Childhood Adiposity: An Integrated Omics Approach awarded by Northwestern University 2018 - 2022
- Preparing Genetic Counselors for Genomic Medicine Research awarded by National Institutes of Health 2017 - 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
- Postdoctoral Training in Genomic Medicine Research awarded by National Institutes of Health 2017 - 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
External Relationships
- Element Genomics
Publications & Artistic Works
Selected Publications
- Academic Articles
  - 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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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  - ENCODE Project Consortium, David B. “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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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- Book Sections
  - 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.
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- Conference Papers
  - 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.
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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.
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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.
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Teaching & Mentoring
Recent Courses
- CBB 510S: Computational Biology Seminar 2022
- CBB 511: Journal Club 2022
- CBB 591: Independent Study 2022
- CBB 700: Internship 2022
- CBB 510S: Computational Biology Seminar 2021
- CBB 511: Journal Club 2021
- CBB 591: Independent Study 2021
- CBB 510S: Computational Biology Seminar 2020
- CBB 511: Journal Club 2020
- CBB 591: Independent Study 2020

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