Timothy E. Reddy - Publications, H-index & Citations

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Timothy E. Reddy

Duke University

53H-index

152Paper Count

2.5WCitation Count

Published Papers 60

Publication Date

An expanded registry of candidate cis-regulatory elements

Nature

IF48.5

2026-01-07

OAAI

Jill E. Moore; Henry E. Pratt; Kaili Fan; Nishigandha Phalke; Jonathan Fisher; Shaimae I. Elhajjajy; Gregory Andrews; Mingshi Gao; Nicole Shedd; Yu Fu; Matthew C. Lacadie; Jair Meza; Mansi Khandpekar; Mohit Ganna; Eva Choudhury; Ross Swofford; Huong Phan; Christian C. Ramirez; Maxwell Campbell; Mary Likhite; Nina P. Farrell; Annika K. Weimer; Anusri Pampari; Vivekanandan Ramalingam; Fairlie Reese; Beatrice Borsari; Xuezhu Yu; Eve Wattenberg; Marina Ruiz-Romero; Milad Razavi-Mohseni; Jinrui Xu; Timur Galeev; Andres Colubri; Michael A. Beer; Roderic Guigó; Mark B. Gerstein; Jesse M. Engreitz; Mats Ljungman; Timothy E. Reddy; Michael P. Snyder; Charles B. Epstein; Elizabeth Gaskell; Bradley E. Bernstein; Diane E. Dickel; Axel Visel; Len A. Pennacchio; Ali Mortazavi; Anshul Kundaje; Zhiping Weng

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The IGVF catalog-from genetic variation to function

NUCLEIC ACIDS RESEARCH

IF13.1

2025-12-01

PREAI

Li, Daofeng; Liu, Shane; Assis, Pedro R.; Li, Mingjie; Dong, Shengcheng; Whaling, Ian; Jolanki, Otto; Kagda, Meenakshi; Zhang, Wenjin; Macias-Velasco, Juan F.; Liu, Tianjie; Cody, Sarah; Antonacci-Fulton, Lucinda; Huang, Yuanhao; Liu, Jie; Montgomery, Michael T.; Zeiberg, Daniel; Jain, Shantanu; Pejaver, Vikas; Bergquist, Timothy; Chen, Yile; Radivojac, Predrag; Gersbach, Charles A.; Sherpa, Rintsen N.; Castro, Christopher P.; Boyle, Alan P.; Starita, Lea M.; Fowler, Douglas M.; Ahituv, Nadav; Dey, Kushal K.; Majoros, William H.; Reddy, Timothy E.; Craven, Mark; Sinha, Riya; Sverchkov, Yuriy; Cai, Xiangmeng; Nzima, Mpathi Z.; Calderwood, Michael A.; Rozowsky, Joel; Gerstein, Mark; Ma, Jian; Yue, Feng; Cherry, J. Michael; Love, Michael, I; Engreitz, Jesse M.; Hitz, Benjamin C.; Wang, Ting

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Comprehensive evaluation of diverse massively parallel reporter assays to functionally characterize human enhancers genome-wide

Genome Biology

IF9.4

2025-11-04

OAAI

Junke Zhang; Alden King-Yung Leung; Yutong Zhu; Li Yao; Avery Willis; Xiuqi Pan; Abdullah Ozer; Zhou Zhou; Keith Siklenka; Alejandro Barrera; Jin Liang; Nathaniel D. Tippens; Timothy E. Reddy; John T. Lis; Haiyuan Yu

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Mediator kinase inhibition impedes transcriptional plasticity and prevents resistance to ERK/MAPK-targeted therapy in KRAS-mutant cancers

NPJ PRECISION ONCOLOGY

IF8

2024-05-31

OAAI

Nussbaum, Daniel P.; Martz, Colin A.; Waters, Andrew M.; Barrera, Alejandro; Liu, Annie; Rutter, Justine C.; Cerda-Smith, Christian G.; Stewart, Amy E.; Wu, Chao; Cakir, Merve; Levandowski, Cecilia B.; Kantrowitz, David E.; Mccall, Shannon J.; Pierobon, Mariaelena; Petricoin III, Emanuel F.; Joshua Smith, J.; Reddy, Timothy E.; Der, Channing J.; Taatjes, Dylan J.; Wood, Kris C.

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Multicenter integrated analysis of noncoding CRISPRi screens

NATURE METHODS

IF32.1

2024-03-19

OAAI

Yao, David; Tycko, Josh; Oh, Jin Woo; Bounds, Lexi R.; Gosai, Sager J.; Lataniotis, Lazaros; Mackay-Smith, Ava; Doughty, Benjamin R.; Gabdank, Idan; Schmidt, Henri; Guerrero-Altamirano, Tania; Siklenka, Keith; Guo, Katherine; White, Alexander D.; Youngworth, Ingrid; Andreeva, Kalina; Ren, Xingjie; Barrera, Alejandro; Luo, Yunhai; Yardimci, Galip Gurkan; Tewhey, Ryan; Kundaje, Anshul; Greenleaf, William J.; Sabeti, Pardis C.; Leslie, Christina; Pritykin, Yuri; Moore, Jill E.; Beer, Michael A.; Gersbach, Charles A.; Reddy, Timothy E.; Shen, Yin; Engreitz, Jesse M.; Bassik, Michael C.; Reilly, Steven K.

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Transcriptional and epigenetic regulators of human CD8+ T cell function identified through orthogonal CRISPR screens

NATURE GENETICS

IF31.8

2023-11-09

OAAI

McCutcheon, Sean R.; Swartz, Adam M.; Brown, Michael C.; Barrera, Alejandro; Amador, Christian McRoberts; Siklenka, Keith; Humayun, Lucas; ter Weele, Maria A.; Isaacs, James M.; Reddy, Timothy E.; Allen, Andrew S.; Nair, Smita K.; Antonia, Scott J.; Gersbach, Charles A.

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Integrin α3 promotes TH17 cell polarization and extravasation during autoimmune neuroinflammation

SCIENCE IMMUNOLOGY

IF16.3

2023-10-27

OAAI

Park, Eunchong; Barclay, William E.; Barrera, Alejandro; Liao, Tzu-Chieh; Salzler, Harmony R.; Reddy, Timothy E.; Shinohara, Mari L.; Ciofani, Maria

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Cooperative regulation of coupled oncoprotein synthesis and stability in triple-negative breast cancer by EGFR and CDK12/13

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IF9.1

2023-09-11

OAAI

Ang, Hazel X.; Sutiman, Natalia; Deng, Xinyue L.; Liu, Annie; Cerda-Smith, Christian G.; Hutchinson, Haley M.; Kim, Holly; Bartelt, Luke C.; Chen, Qiang; Barrera, Alejandro; Lin, Jiaxing; Sheng, Zhecheng; McDowell, Ian C.; Reddy, Timothy E.; Nicchitta, Christopher V.; Wood, Kris C.

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The Hypersensitive Glucocorticoid Response Specifically Regulates Period 1 and Expression of Circadian Genes

MOLECULAR AND CELLULAR BIOLOGY

IF2.7

2023-03-20

144

OAAI

Reddy, Timothy E.; Gertz, Jason; Crawford, Gregory E.; Garabedian, Michael J.; Myers, Richard M.

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ZBTB7A promotes virus-host homeostasis during human coronavirus 229E infection

CELL REPORTS

IF6.9

2022-10-01

OAAI

Zhu, Xinyu; Trimarco, Joseph D.; Williams, Courtney A.; Barrera, Alejandro; Reddy, Timothy E.; Heaton, Nicholas S.

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Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data

GENOME RESEARCH

IF5.5

2022-05-24

OAAI

Luo, Kaixuan; Zhong, Jianling; Safi, Alexias; Hong, Linda K.; Tewari, Alok K.; Song, Lingyun; Reddy, Timothy E.; Ma, Li; Crawford, Gregory E.; Hartemink, Alexander J.

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Epigenetic basis of oncogenic-Kras-mediated epithelial-cellular proliferation and plasticity

DEVELOPMENTAL CELL

IF8.7

2022-02-01

OAAI

Murthy, Preetish Kadur Lakshminarasimha; Xi, Rui; Arguijo, Diana; Everitt, Jeffrey, I; Kocak, Dewran D.; Kobayashi, Yoshihiko; Bozec, Aline; Vicent, Silvestre; Ding, Shengli; Crawford, Gregory E.; Hsu, David; Tata, Purushothama Rao; Reddy, Timothy; Shen, Xiling

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Epigenome editing of the CFTR-locus for treatment of cystic fibrosis

JOURNAL OF CYSTIC FIBROSIS

IF6

2022-01-01

OAAI

Kabadi, Ami M.; Machlin, Leah; Dalal, Nikita; Lee, Rhianna E.; McDowell, Ian; Shah, Nirav N.; Drowley, Lauren; Randell, Scott H.; Reddy, Timothy E.

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Transgenic mice for in vivo epigenome editing with CRISPR-based systems

NATURE METHODS

IF32.1

2021-08-02

OAAI

Gemberling, Matthew; Siklenka, Keith; Rodriguez, Erica; Tonn-Eisinger, Katherine R.; Barrera, Alejandro; Liu, Fang; Kantor, Ariel; Li, Liqing; Cigliola, Valentina; Hazlett, Mariah F.; Williams, Courtney; Bartelt, Luke C.; Madigan, Victoria J.; Bodle, Josephine; Daniels, Heather; Rouse, Douglas C.; Hilton, Isaac B.; Asokan, Aravind; Ciofani, Maria; Poss, Kenneth D.; Reddy, Timothy E.; West, Anne E.; Gersbach, Charles A.

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Targeted long-read sequencing identifies missing disease-causing variation

AMERICAN JOURNAL OF HUMAN GENETICS

IF8.1

2021-08-01

137

OAAI

Miller, Danny E.; Sulovari, Arvis; Wang, Tianyun; Loucks, Hailey; Hoekzema, Kendra; Munson, Katherine M.; Lewis, Alexandra P.; Fuerte, Edith P. Almanza; Paschal, Catherine R.; Walsh, Tom; Thies, Jenny; Bennett, James T.; Glass, Ian; Dipple, Katrina M.; Patterson, Karynne; Bonkowski, Emily S.; Nelson, Zoe; Squire, Audrey; Sikes, Megan; Beckman, Erika; Bennett, Robin L.; Earl, Dawn; Lee, Winston; Allikmets, Rando; Perlman, Seth J.; Chow, Penny; Hing, Anne, V; Wenger, Tara L.; Adam, Margaret P.; Sun, Angela; Lam, Christina; Chang, Irene; Zou, Xue; Austin, Stephanie L.; Huggins, Erin; Safi, Alexias; Iyengar, Apoorva K.; Reddy, Timothy E.; Majoros, William H.; Allen, Andrew S.; Crawford, Gregory E.; Kishnani, Priya S.; King, Mary-Claire; Cherry, Tim; Chong, Jessica X.; Bamshad, Michael J.; Nickerson, Deborah A.; Mefford, Heather C.; Doherty, Dan; Eichler, Evan E.

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Glucocorticoid receptor triggers a reversible drug-tolerant dormancy state with acquired therapeutic vulnerabilities in lung cancer

NATURE COMMUNICATIONS

IF15.7

2021-07-16

OAAI

Prekovic, Stefan; Schuurman, Karianne; Mayayo-Peralta, Isabel; Manjon, Anna G.; Buijs, Mark; Yavuz, Selcuk; Wellenstein, Max D.; Barrera, Alejandro; Monkhorst, Kim; Huber, Anne; Morris, Ben; Lieftink, Cor; Chalkiadakis, Theofilos; Alkan, Ferhat; Silva, Joana; Gyorffy, Balazs; Hoekman, Liesbeth; van den Broek, Bram; Teunissen, Hans; Debets, Donna O.; Severson, Tesa; Jonkers, Jos; Reddy, Timothy; de Visser, Karin E.; Faller, William; Beijersbergen, Roderick; Altelaar, Maarten; de Wit, Elzo; Medema, Rene; Zwart, Wilbert

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Correcting signal biases and detecting regulatory elements in STARR-seq data

GENOME RESEARCH

IF5.5

2021-03-15

OAAI

Kim, Young-Sook; Johnson, Graham D.; Seo, Jungkyun; Barrera, Alejandro; Cowart, Thomas N.; Majoros, William H.; Ochoa, Alejandro; Allen, Andrew S.; Reddy, Timothy E.

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AP-1 subunits converge promiscuously at enhancers to potentiate transcription

GENOME RESEARCH

IF5.5

2021-03-05

OAAI

Seo, Jungkyun; Kocak, D. Dewran; Bartelt, Luke C.; Williams, Courtney A.; Barrera, Alejandro; Gersbach, Charles A.; Reddy, Timothy E.

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Causal network inference from gene transcriptional time-series response to glucocorticoids

plos biology

IF3.6

2021-01-29

OAAI

Lu, Jonathan; Dumitrascu, Bianca; McDowell, Ian C.; Jo, Brian; Barrera, Alejandro; Hong, Linda K.; Leichter, Sarah M.; Reddy, Timothy E.; Engelhardt, Barbara E.

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Transcriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth

SCIENCE ADVANCES

IF12.5

2020-12-04

OAAI

Sakabe, Noboru J.; Aneas, Ivy; Knoblauch, Nicholas; Sobreira, Debora R.; Clark, Nicole; Paz, Cristina; Horth, Cynthia; Ziffra, Ryan; Kaur, Harjot; Liu, Xiao; Anderson, Rebecca; Morrison, Jean; Cheung, Virginia C.; Grotegut, Chad; Reddy, Timothy E.; Jacobsson, Bo; Hallman, Mikko; Teramo, Kari; Murtha, Amy; Kessler, John; Grobman, William; Zhang, Ge; Muglia, Louis J.; Rana, Sarosh; Lynch, Vincent J.; Crawford, Gregory E.; Ober, Carole; He, Xin; Nobrega, Marcelo A.

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Research Directions