Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration
Toth, Andrea, Kannan, Paranthaman, Snowball, John, Kofron, Matthew, Wayman, Joseph A., Bridges, James P., Miraldi, Emily R., Swarr, Daniel, Zacharias, William J.
Published in Nature communications (19.12.2023)
Published in Nature communications (19.12.2023)
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maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks
Cazares, Tareian A, Rizvi, Faiz W, Iyer, Balaji, Chen, Xiaoting, Kotliar, Michael, Bejjani, Anthony T, Wayman, Joseph A, Donmez, Omer, Wronowski, Benjamin, Parameswaran, Sreeja, Kottyan, Leah C, Barski, Artem, Weirauch, Matthew T, Prasath, V B Surya, Miraldi, Emily R
Published in PLoS computational biology (01.01.2023)
Published in PLoS computational biology (01.01.2023)
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Toward a genome scale sequence specific dynamic model of cell-free protein synthesis in Escherichia coli
Horvath, Nicholas, Vilkhovoy, Michael, Wayman, Joseph A., Calhoun, Kara, Swartz, James, Varner, Jeffrey D.
Published in Metabolic engineering communications (01.06.2020)
Published in Metabolic engineering communications (01.06.2020)
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Journal Article
Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates
Toth, Andrea, Steinmeyer, Shelby, Kannan, Paranthaman, Gray, Jerilyn, Jackson, Courtney M, Mukherjee, Shibabrata, Demmert, Martin, Sheak, Joshua R, Benson, Daniel, Kitzmiller, Joseph, Wayman, Joseph A, Presicce, Pietro, Cates, Christopher, Rubin, Rhea, Chetal, Kashish, Du, Yina, Miao, Yifei, Gu, Mingxia, Guo, Minzhe, Kalinichenko, Vladimir V, Kallapur, Suhas G, Miraldi, Emily R, Xu, Yan, Swarr, Daniel, Lewkowich, Ian, Salomonis, Nathan, Miller, Lisa, Sucre, Jennifer S, Whitsett, Jeffrey A, Chougnet, Claire A, Jobe, Alan H, Deshmukh, Hitesh, Zacharias, William J
Published in Science translational medicine (30.03.2022)
Published in Science translational medicine (30.03.2022)
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Sequence Specific Modeling of E. coli Cell-Free Protein Synthesis
Vilkhovoy, Michael, Horvath, Nicholas, Shih, Che-Hsiao, Wayman, Joseph A, Calhoun, Kara, Swartz, James, Varner, Jeffrey D
Published in ACS synthetic biology (17.08.2018)
Published in ACS synthetic biology (17.08.2018)
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Biological systems modeling of metabolic and signaling networks
Wayman, Joseph A, Varner, Jeffrey D
Published in Current opinion in chemical engineering (01.11.2013)
Published in Current opinion in chemical engineering (01.11.2013)
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Nutrient starvation activates ECM remodeling gene enhancers associated with inflammatory bowel disease risk in fibroblasts
Secchia, Stefano, Beilinson, Vera, Chen, Xiaoting, Yang, Zi F, Wayman, Joseph A, Dhaliwal, Jasbir, Jurickova, Ingrid, Angerman, Elizabeth, Denson, Lee A, Miraldi, Emily R, Weirauch, Matthew T, Ikegami, Kohta
Published in bioRxiv (12.09.2024)
Published in bioRxiv (12.09.2024)
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Journal Article
TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation
Ho, Jessica Sook Yuin, Mok, Bobo Wing-Yee, Campisi, Laura, Jordan, Tristan, Yildiz, Soner, Parameswaran, Sreeja, Wayman, Joseph A., Gaudreault, Natasha N., Meekins, David A., Indran, Sabarish V., Morozov, Igor, Trujillo, Jessie D., Fstkchyan, Yesai S., Rathnasinghe, Raveen, Zhu, Zeyu, Zheng, Simin, Zhao, Nan, White, Kris, Ray-Jones, Helen, Malysheva, Valeriya, Thiecke, Michiel J., Lau, Siu-Ying, Liu, Honglian, Zhang, Anna Junxia, Lee, Andrew Chak-Yiu, Liu, Wen-Chun, Jangra, Sonia, Escalera, Alba, Aydillo, Teresa, Melo, Betsaida Salom, Guccione, Ernesto, Sebra, Robert, Shum, Elaine, Bakker, Jan, Kaufman, David A., Moreira, Andre L., Carossino, Mariano, Balasuriya, Udeni B.R., Byun, Minji, Albrecht, Randy A., Schotsaert, Michael, Garcia-Sastre, Adolfo, Chanda, Sumit K., Miraldi, Emily R., Jeyasekharan, Anand D., TenOever, Benjamin R., Spivakov, Mikhail, Weirauch, Matthew T., Heinz, Sven, Chen, Honglin, Benner, Christopher, Richt, Juergen A., Marazzi, Ivan
Published in Cell (13.05.2021)
Published in Cell (13.05.2021)
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37 SINGLE-CELL-RESOLVED CHROMATIN ACCESSIBLITY MAPS OF INFLAMMATORY BOWEL DISEASE INTESTINE NOMINATE CELL TYPES AND CONTEXTS MEDIATING GENETIC DISEASE RISK
Wayman, Joseph A., Yang, Zi, Angerman, Elizabeth, Bonkowski, Erin, Jurickova, Ingrid, Chen, Xiaoting, Parks, Lois, Bejjani, Anthony, Miethke, Alexander, VanDussen, Kelli L., Dhaliwal, Jasbir, Weirauch, Matthew, Kottyan, Leah C., Denson, Lee A., Miraldi, Emily R.
Published in Gastroenterology (New York, N.Y. 1943) (18.05.2024)
Published in Gastroenterology (New York, N.Y. 1943) (18.05.2024)
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Elevated CD153 Expression on Aged T Follicular Helper Cells is Vital for B cell Responses
Thomas, Alyssa L, Wayman, Joseph A, Almanan, Maha, Bejjani, Anthony T, Miraldi, Emily R, Chougnet, Claire A, Hildeman, David A
Published in bioRxiv : the preprint server for biology (07.04.2023)
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Published in bioRxiv : the preprint server for biology (07.04.2023)
Journal Article
Accessible chromatin maps of inflammatory bowel disease intestine nominate cell-type mediators of genetic disease risk
Wayman, Joseph A, Yang, Zi, Angerman, Elizabeth, Bonkowski, Erin, Jurickova, Ingrid, Chen, Xiaoting, Bejjani, Anthony T, Parks, Lois, Parameswaran, Sreeja, Miethke, Alexander G, VanDussen, Kelli L, Dhaliwal, Jasbir, Weirauch, Matthew T, Kottyan, Leah C, Denson, Lee A, Miraldi, Emily R
Published in bioRxiv : the preprint server for biology (13.02.2024)
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Published in bioRxiv : the preprint server for biology (13.02.2024)
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Cholestasis alters polarization and suppressor function of hepatic regulatory T cells
Kudira, Ramesh, Yang, Zi F, Osuji, Immaculeta, Karns, Rebekah, Bariya, Priya, Pfuhler, Liva, Mullen, Mary, Taylor, Amy, Ji, Hong, Lages, Celine S, Yang Vom Hofe, Annika, Shi, Tiffany, Pasula, Srikar, Wayman, Joseph A, Bernieh, Anas, Zhang, Wujuan, Chougnet, Claire A, Hildeman, David, Tiao, Gregory M, Huppert, Stacey S, Subramanian, Sajay, Salomonis, Nathan, Miraldi, Emily, Miethke, Alexander Gerhard
Published in bioRxiv (21.05.2024)
Published in bioRxiv (21.05.2024)
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An atlas of gene regulatory networks for memory CD4 + T cells in youth and old age
Wayman, Joseph A, Thomas, Alyssa, Bejjani, Anthony, Katko, Alexander, Almanan, Maha, Godarova, Alzbeta, Korinfskaya, Svetlana, Cazares, Tareian A, Yukawa, Masashi, Kottyan, Leah C, Barski, Artem, Chougnet, Claire A, Hildeman, David A, Miraldi, Emily R
Published in bioRxiv : the preprint server for biology (03.04.2023)
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Published in bioRxiv : the preprint server for biology (03.04.2023)
Journal Article
Topoisomerase 1 inhibition therapy protects against SARS-CoV-2-induced inflammation and death in animal models
Yuin Ho, Jessica Sook, Wing-Yee Mok, Bobo, Campisi, Laura, Jordan, Tristan, Yildiz, Soner, Parameswaran, Sreeja, Wayman, Joseph A, Gaudreault, Natasha N, Meekins, David A, Indran, Sabarish V, Morozov, Igor, Trujillo, Jessie D, Fstkchyan, Yesai S, Rathnasinghe, Raveen, Zhu, Zeyu, Zheng, Simin, Zhao, Nan, White, Kris, Ray-Jones, Helen, Malysheva, Valeriya, Thiecke, Michiel J, Lau, Siu-Ying, Liu, Honglian, Junxia Zhang, Anna, Chak-Yiu Lee, Andrew, Liu, Wen-Chun, Aydillo, Teresa, Salom Melo, Betsaida, Guccione, Ernesto, Sebra, Robert, Shum, Elaine, Bakker, Jan, Kaufman, David A, Moreira, Andre L, Carossino, Mariano, Balasuriya, Udeni B R, Byun, Minji, Miraldi, Emily R, Albrecht, Randy A, Schotsaert, Michael, Garcia-Sastre, Adolfo, Chanda, Sumit K, Jeyasekharan, Anand D, TenOever, Benjamin R, Spivakov, Mikhail, Weirauch, Matthew T, Heinz, Sven, Chen, Honglin, Benner, Christopher, Richt, Juergen A, Marazzi, Ivan
Published in bioRxiv (01.12.2020)
Published in bioRxiv (01.12.2020)
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maxATAC: genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks
Cazares, Tareian A, Rizvi, Faiz W, Iyer, Balaji, Chen, Xiaoting, Kotliar, Michael, Wayman, Joseph A, Bejjani, Anthony, Donmez, Omer, Wronowski, Benjamin, Parameswaran, Sreeja, Kottyan, Leah C, Barski, Artem, Weirauch, Matthew T, Vb Surya Prasath, Miraldi, Emily R
Published in bioRxiv (29.01.2022)
Published in bioRxiv (29.01.2022)
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