Cell-type-specific 3D epigenomes in the developing human cortex
Song, Michael, Pebworth, Mark-Phillip, Yang, Xiaoyu, Abnousi, Armen, Fan, Changxu, Wen, Jia, Rosen, Jonathan D., Choudhary, Mayank N. K., Cui, Xiekui, Jones, Ian R., Bergenholtz, Seth, Eze, Ugomma C., Juric, Ivan, Li, Bingkun, Maliskova, Lenka, Lee, Jerry, Liu, Weifang, Pollen, Alex A., Li, Yun, Wang, Ting, Hu, Ming, Kriegstein, Arnold R., Shen, Yin
Published in Nature (London) (26.11.2020)
Published in Nature (London) (26.11.2020)
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SMART-Q: An Integrative Pipeline Quantifying Cell Type-Specific RNA Transcription
Yang, Xiaoyu, Bergenholtz, Seth, Maliskova, Lenka, Pebworth, Mark-Phillip, Kriegstein, Arnold R, Li, Yun, Shen, Yin
Published in PloS one (29.04.2020)
Published in PloS one (29.04.2020)
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MOCHA’s advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts
Rachid Zaim, Samir, Pebworth, Mark-Phillip, McGrath, Imran, Okada, Lauren, Weiss, Morgan, Reading, Julian, Czartoski, Julie L., Torgerson, Troy R., McElrath, M. Juliana, Bumol, Thomas F., Skene, Peter J., Li, Xiao-jun
Published in Nature communications (09.08.2024)
Published in Nature communications (09.08.2024)
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Trimodal single-cell profiling reveals a novel pediatric CD8αα+ T cell subset and broad age-related molecular reprogramming across the T cell compartment
Thomson, Zachary, He, Ziyuan, Swanson, Elliott, Henderson, Katherine, Phalen, Cole, Zaim, Samir Rachid, Pebworth, Mark-Phillip, Okada, Lauren Y., Heubeck, Alexander T., Roll, Charles R., Hernandez, Veronica, Weiss, Morgan, Genge, Palak C., Reading, Julian, Giles, Josephine R., Manne, Sasikanth, Dougherty, Jeanette, Jasen, C. J., Greenplate, Allison R., Becker, Lynne A., Graybuck, Lucas T., Vasaikar, Suhas V., Szeto, Gregory L., Savage, Adam K., Speake, Cate, Buckner, Jane H., Li, Xiao-jun, Bumol, Thomas F., Wherry, E.John, Torgerson, Troy R., Vella, Laura A., Henrickson, Sarah E., Skene, Peter J., Gustafson, Claire E.
Published in Nature immunology (01.11.2023)
Published in Nature immunology (01.11.2023)
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Tri-modal single cell (TEA-seq) profiling reveals a novel, epigenetically distinct T cell subset in children and global molecular reprogramming across age
Gustafson, Claire E, Thomson, Zachary, He, Ziyuan, Swanson, Elliot, Henderson, Katherine, Pebworth, Mark-Phillip, Okada, Lauren, Heubeck, Alexander, Roll, Charles, Hernandez, Veronica, Weiss, Morgan, Genge, Palak, Reading, Julian, Giles, Josephine, Manne, Sasikanth, Dougherty, Jeanette, Jasen, CJ, Greenplate, Allison, Becker, Lynne, Graybuck, Lucas, Vasaikar, Suhas, Szeto, Gregory Lee, Savage, Adam, Speake, Cate, Buckner, Jane H, Li, Xiaojun, Bumol, Thomas, Wherry, E. John, Torgerson, Troy, Vella, Laura, Henrickson, Sarah E., Skene, Peter
Published in The Journal of immunology (1950) (01.05.2023)
Published in The Journal of immunology (1950) (01.05.2023)
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Author Correction: Trimodal single-cell profiling reveals a novel pediatric CD8αα+ T cell subset and broad age-related molecular reprogramming across the T cell compartment
Thomson, Zachary, He, Ziyuan, Swanson, Elliott, Henderson, Katherine, Phalen, Cole, Zaim, Samir Rachid, Pebworth, Mark-Phillip, Okada, Lauren Y., Heubeck, Alexander T., Roll, Charles R., Hernandez, Veronica, Weiss, Morgan, Genge, Palak C., Reading, Julian, Giles, Josephine R., Manne, Sasikanth, Dougherty, Jeanette, Jasen, C. J., Greenplate, Allison R., Becker, Lynne A., Graybuck, Lucas T., Vasaikar, Suhas V., Szeto, Gregory L., Savage, Adam K., Speake, Cate, Buckner, Jane H., Li, Xiao-jun, Bumol, Thomas F., Wherry, E.John, Torgerson, Troy R., Vella, Laura A., Henrickson, Sarah E., Skene, Peter J., Gustafson, Claire E.
Published in Nature immunology (01.03.2024)
Published in Nature immunology (01.03.2024)
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Longitudinal immune dynamics of mild COVID-19 define signatures of recovery and persistence
Talla, Aarthi, Vasaikar, Suhas V, Lemos, Maria P, Moodie, Zoe, Lee Pebworth, Mark-Phillip, Henderson, Kathy E, Cohen, Kristen W, Czartoski, Julie L, Lai, Lilin, Suthar, Mehul S, Heubeck, Alexander T, Genge, Palak C, Roll, Charles R, Weiss, Morgan, Reading, Julian, Kondza, Nina, MacMillan, Hugh, Fong, Olivia C, Thomson, Zachary James, Graybuck, Lucas T, Okada, Lauren Y, Newell, Evan W, Coffey, Ernest M, Meijer, Paul, Becker, Lynne A, De Rosa, Stephen C, Skene, Peter J, Torgerson, Troy R, Li, Xiao-Jun, Szeto, Gregory Lee, McElrath, M Juliana, Bumol, Thomas F
Published in bioRxiv (19.08.2021)
Published in bioRxiv (19.08.2021)
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Systemic inflammation and lymphocyte activation precede rheumatoid arthritis
He, Ziyuan, Glass, Marla C, Venkatesan, Pravina, Feser, Marie L, Lazaro, Leander, Okada, Lauren Y, Tran, Nhung T T, He, Yudong D, Rachid Zaim, Samir, Bennett, Christy E, Ravisankar, Padmapriyadarshini, Dornisch, Elisabeth M, Arishi, Najeeb A, Asamoah, Ashley G, Barzideh, Saman, Becker, Lynne A, Bemis, Elizabeth A, Buckner, Jane H, Collora, Christopher E, Criley, Megan A L, Demoruelle, M Kristen, Fleischer, Chelsie L, Garber, Jessica, Genge, Palak C, Gong, Qiuyu, Graybuck, Lucas T, Gustafson, Claire E, Hattel, Brian C, Hernandez, Veronica, Heubeck, Alexander T, Kawelo, Erin K, Krishnan, Upaasana, Kuan, Emma L, Kuhn, Kristine A, LaFrance, Christian M, Lee, Kevin J, Li, Ruoxin, Lord, Cara, Mettey, Regina R, Moss, LauraKay, Musgrove, Blessing, Nguyen, Kathryn, Ochoa, Andrea, Parthasarathy, Vaishnavi, Pebworth, Mark-Phillip, Pedrick, Chong, Peng, Tao, Phalen, Cole G, Reading, Julian, Roll, Charles R, Seifert, Jennifer A, Siedschlag, Marguerite D, Speake, Cate, Striebich, Christopher C, Stuckey, Tyanna J, Swanson, Elliott G, Takada, Hideto, Thai, Tylor, Thomson, Zachary J, Trieu, Nguyen, Tsaltskan, Vlad, Wang, Wei, Weiss, Morgan D A, Westermann, Amy, Zhang, Fan, Boyle, David L, Goldrath, Ananda W, Bumol, Thomas F, Li, Xiao-Jun, Holers, V Michael, Skene, Peter J, Savage, Adam K, Firestein, Gary S, Deane, Kevin D, Torgerson, Troy R, Gillespie, Mark A
Published in bioRxiv (12.11.2024)
Published in bioRxiv (12.11.2024)
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Journal Article
MOLECULAR SIGNATURES OF LONG-TERM COVID-19 AND TREATMENT THEREOF
TORGERSON, Troy, MCELRATH, Juliana M, TALLA, Aarthi, LI, Xiaojun, BUMOL, Thomas F, SKENE, Peter, SZETO, Gregory Lee, VASAIKAR, Suhas, PEBWORTH, Mark-Phillip
Year of Publication 04.07.2024
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Year of Publication 04.07.2024
Patent
MOLECULAR SIGNATURES OF LONG-TERM COVID-19 AND TREATMENT THEREOF
TORGERSON, Troy, TALLA, Aarthi, MCELRATH, M. Juliana, LI, Xiaojun, BUMOL, Thomas F, SKENE, Peter, SZETO, Gregory Lee, VASAIKAR, Suhas, PEBWORTH, Mark-Phillip
Year of Publication 06.03.2024
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Year of Publication 06.03.2024
Patent
MOLECULAR SIGNATURES OF LONG-TERM COVID-19 AND TREATMENT THEREOF
TORGERSON, Troy, TALLA, Aarthi, MCELRATH, M. Juliana, LI, Xiaojun, BUMOL, Thomas F, SKENE, Peter, SZETO, Gregory Lee, VASAIKAR, Suhas, PEBWORTH, Mark-Phillip
Year of Publication 03.11.2022
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Year of Publication 03.11.2022
Patent
Distinct Heterogeneity in the Naive T cell Compartments of Children and Adults
Gustafson, Claire E, Thomson, Zachary, He, Ziyuan, Swanson, Elliott, Henderson, Katherine, Pebworth, Mark-Phillip L, Okada, Lauren Y, Heubeck, Alexander T, Roll, Charles R, Hernandez, Veronica, Morgan Da Weiss, Genge, Palak C, Reading, Julian, Giles, Josephine R, Manne, Sasikanth, Dougherty, Jeanette, Jasen, Cj, Greenplate, Allison R, Becker, Lynne A, Graybuck, Lucas T, Vasaikar, Suhas V, Szeto, Gregory L, Savage, Adam K, Speake, Cate, Buckner, Jane H, Xiao-Jun, Li, Torgerson, Troy R, Wherry, E John, Bumol, Thomas F, Vella, Laura A, Henrickson, Sarah H, Skene, Peter J
Published in bioRxiv (07.10.2022)
Published in bioRxiv (07.10.2022)
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Paper
3D Epigenomic Characterization Reveals Insights Into Gene Regulation and Lineage Specification During Corticogenesis
Song, Michael, Mark-Phillip Pebworth, Yang, Xiaoyu, Abnousi, Armen, Fan, Changxu, Jia Wen, Rosen, Jonathan, Choudhary, Mayank, Cui, Xiekui, Jones, Ian, Bergenholtz, Seth, Eze, Ugomma, Juric, Ivan, Li, Bingkun, Maliskova, Lenka, Liu, Weifang, Pollen, Alex, Li, Yun, Wang, Ting, Hu, Ming, Kriegstein, Arnold, Shen, Yin
Published in bioRxiv (25.02.2020)
Published in bioRxiv (25.02.2020)
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