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
Duke Appointment History
- 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
- 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
- IRES Track 1 IRTG Engaged in Dissecting and Reengineering the Regulatory Genome awarded by National Science Foundation 2019 - 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
- 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
- Cellular and Molecular Systems Biology of Preterm Birth awarded by University of Chicago 2015 - 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
- The function and regulation of the novel pregnancy-specific hexokinase HKDC1 awarded by University of Illinois at Chicago 2017 - 2019
- Integrated Omics awarded by Northwestern University 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
- 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
- Academic Articles
  - 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..” Nature Communications 9, no. 1 (December 21, 2018). https://doi.org/10.1038/s41467-018-07607-x.
    Full Text
  - 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
  - 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
  - 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
  - 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..” Nature Communications 9, no. 1 (August 7, 2018). https://doi.org/10.1038/s41467-018-05379-y.
    Full Text
  - 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 Systems 7, no. 2 (August 2018): 146-160.e7. https://doi.org/10.1016/j.cels.2018.06.007.
    Full Text
  - 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 Computational Biology 14, no. 1 (January 16, 2018). https://doi.org/10.1371/journal.pcbi.1005896.
    Full Text
  - Klann, Tyler S., Gregory E. Crawford, Timothy E. Reddy, and Charles A. Gersbach. “Screening Regulatory Element Function with CRISPR/Cas9-based Epigenome Editing..” Methods in Molecular Biology (Clifton, N.J.) 1767 (January 2018): 447–80. https://doi.org/10.1007/978-1-4939-7774-1_25.
    Full Text
  - 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 2017): 261–67. https://doi.org/10.1080/21541264.2017.1317694.
    Full Text
  - 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
  - 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). https://doi.org/10.1186/s12864-017-3785-4.
    Full Text Link to Item
  - 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, Md.) 25, no. 5 (May 2017): 935–44. https://doi.org/10.1002/oby.21805.
    Full Text
  - 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 (Oxford, England) 33, no. 10 (May 2017): 1437–46. https://doi.org/10.1093/bioinformatics/btw799.
    Full Text
  - Vockley, Christopher M., Alejandro Barrera, and Timothy E. Reddy. “Decoding the role of regulatory element polymorphisms in complex disease..” Current Opinion in Genetics & Development 43 (April 2017): 38–45. https://doi.org/10.1016/j.gde.2016.10.007.
    Full Text
  - 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 2016): 406–14. https://doi.org/10.1016/j.stem.2016.07.001.
    Full Text
  - 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
  - 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
  - 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
  - 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
  - Lowe, William L., and Timothy E. Reddy. “Genomic approaches for understanding the genetics of complex disease..” Genome Research 25, no. 10 (October 2015): 1432–41. https://doi.org/10.1101/gr.190603.115.
    Full Text
  - 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 Research 25, no. 8 (August 2015): 1158–69. https://doi.org/10.1101/gr.179044.114.
    Full Text
  - 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 Research 25, no. 8 (August 2015): 1158–69. https://doi.org/10.1101/gr.179044.114.
    Full Text Link to Item
  - 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 Research 25, no. 8 (August 2015): 1206–14. https://doi.org/10.1101/gr.190090.115.
    Full Text
  - Guo, Cong, Anthony M. D’Ippolito, and Timothy E. Reddy. “From Prescription to Transcription: Genome Sequence as Drug Target..” Cell 162, no. 1 (July 2015): 16–17. https://doi.org/10.1016/j.cell.2015.06.033.
    Full Text
  - 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
  - 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
  - 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
  - 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..” Molecular Therapy : The Journal of the American Society of Gene Therapy 23, no. 3 (March 2015): 523–32. https://doi.org/10.1038/mt.2014.234.
    Full Text
  - 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.” Molecular Therapy 23, no. 3 (March 1, 2015): 523–32. https://doi.org/10.1038/mt.2074.234.
    Full Text Link to Item
  - 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..” Nature Communications 6 (February 18, 2015). https://doi.org/10.1038/ncomms7244.
    Full Text
  - 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). https://doi.org/10.1038/ncomms7069.
    Full Text Link to Item
  - 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
  - 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
  - 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). https://doi.org/10.2337/db13-er10.
    Full Text
  - 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
  - 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
  - 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..” Human Molecular Genetics 22, no. 17 (September 2013): 3583–96. https://doi.org/10.1093/hmg/ddt168.
    Full Text
  - 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]..” Proceedings of the National Academy of Sciences of the United States of America 110, no. 23 (June 2013): 9356–61. https://doi.org/10.1073/pnas.1307589110.
    Full Text
  - 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 Research 23, no. 3 (March 2013): 555–67. https://doi.org/10.1101/gr.147942.112.
    Full Text
  - Gertz, J., D. Savic, K. E. Varley, E. C. Partridge, A. Safi, P. Jain, G. M. Cooper, T. E. Reddy, G. E. Crawford, and R. M. Myers. “Distinct properties of cell-type-specific and shared transcription factor binding sites.” Molecular Cell 52, no. 1 (2013): 25–36. https://doi.org/10.1016/j.molcel.2013.08.037.
    Full Text
  - 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
  - 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 Research 22, no. 11 (November 2012): 2153–62. https://doi.org/10.1101/gr.135681.111.
    Full Text
  - ENCODE Project Consortium, Racquel. “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
  - 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 2012): 91–100. https://doi.org/10.1038/nature11245.
    Full Text
  - 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
  - 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..” Molecular and Cellular Biology 32, no. 18 (September 2012): 3756–67. https://doi.org/10.1128/MCB.00062-12.
    Full Text
  - 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..” Journal of Theoretical Biology 303 (June 2012): 152–53. https://doi.org/10.1016/j.jtbi.2012.03.018.
    Full Text
  - 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
  - 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..” Human Molecular Genetics 20, no. 20 (October 2011): 3964–73. https://doi.org/10.1093/hmg/ddr315.
    Full Text
  - 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). https://doi.org/10.1371/journal.pgen.1002228.
    Full Text Link to Item
  - ENCODE Project Consortium, S. L. “A user's guide to the encyclopedia of DNA elements (ENCODE)..” Plos Biol 9, no. 4 (April 2011). https://doi.org/10.1371/journal.pbio.1001046.
    Full Text Link to Item
  - 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
  - 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 Research 19, no. 6 (June 2009): 1044–56. https://doi.org/10.1101/gr.088773.108.
    Full Text
  - 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 Computational Biology 3, no. 5 (May 2007). https://doi.org/10.1371/journal.pcbi.0030090.
    Full Text
  - 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 Research 35, no. 3 (January 3, 2007). https://doi.org/10.1093/nar/gkl1062.
    Full Text
  - 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..” Journal of Theoretical Biology 236, no. 4 (October 2005): 376–91. https://doi.org/10.1016/j.jtbi.2005.03.019.
    Full Text
  - Reddy, Timothy E., Charles DeLisi, and Boris E. Shakhnovich. “Assessing transcription factor motif drift from noisy decoy sequences..” Genome Informatics. International Conference on Genome Informatics 16, no. 1 (January 2005): 59–67.
  - 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 (December 1, 2004): 553–60.
  - 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 Informatics. International Conference on Genome Informatics 15, no. 1 (January 2004): 221–28.
- Book Sections
  - Reddy, T. E. “The Functional Genome: Epigenetics and Epigenomics.” In Genomic and Precision Medicine: Foundations, Translation, and Implementation: Third Edition, 21–44, 2016. https://doi.org/10.1016/B978-0-12-800681-8.00002-5.
    Full Text
- Conference Papers
  - 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
  - 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
Teaching & Mentoring
Recent Courses

Some information on this profile has been compiled automatically from Duke databases and external sources. (Our About page explains how this works.) If you see a problem with the information, please write to Scholars@Duke and let us know. We will reply promptly.

Education, Training, & Certifications

Duke Appointment History

In the News

Subject Headings

Selected Grants

Selected Publications

Academic Articles

Book Sections

Conference Papers

Recent Courses