Yasin Uzun

Assistant Professor of Pediatrics

Yasin Uzun

Research Summary

Developing and applying systems biology approaches to better understand gene regulation at the molecular level in development and disease by using single-cell genomic sequencing data.

Huck Graduate Students

Huck Affiliations

Links

Most Recent Publications

Noncoding RNA, ncRNA-a3, Epigenetically Regulates TAL1 Transcriptional Program During Erythropoiesis

Meghana Matur, Yasin Uzun, Xiangguo Shi, Karina Hamamoto, Yi Qiu, Suming Huang, 2025, Molecular and Cellular Biology on p. 169-184

Longitudinal single-cell multiomic atlas of high-risk neuroblastoma reveals chemotherapy-induced tumor microenvironment rewiring

Wenbao Yu, Rumeysa Biyik-Sit, Yasin Uzun, Chia Hui Chen, Anusha Thadi, Jonathan H. Sussman, Minxing Pang, Chi Yun Wu, Liron D. Grossmann, Peng Gao, David W. Wu, Aliza Yousey, Mei Zhang, Christina S. Turn, Zhan Zhang, Shovik Bandyopadhyay, Jeffrey Huang, Tasleema Patel, Changya Chen, Daniel Martinez, Lea F. Surrey, Michael D. Hogarty, Kathrin Bernt, Nancy R. Zhang, John M. Maris, Kai Tan, 2025, Nature Genetics

Identification and Characterization of Chemotherapy-Resistant High-Risk Neuroblastoma Persister Cells

Liron D. Grossmann, Chia Hui Chen, Yasin Uzun, Anusha Thadi, Adam J. Wolpaw, Kevin Louault, Yael Goldstein, Lea F. Surrey, Daniel Martinez, Matteo Calafatti, Mark Gerelus, Peng Gao, Lobin Lee, Khushbu Patel, Rebecca S. Kaufman, Guy Shani, Alvin Farrel, Sharon Moshitch-Moshkovitz, Paris Grimaldi, Matthew Shapiro, Nathan M. Kendsersky, Jarrett M. Lindsay, Colleen E. Casey, Kateryna Krytska, Laura Scolaro, Matthew Tsang, David Groff, Smita Matkar, Josh R. Kalna, Emily Mycek, Jayne McDevitt, Erin Runbeck, Tasleema Patel, Kathrin M. Bernt, Shahab Asgharzadeh, Yves A. Declerck, Yael P. Mossé, Kai Tan, John M. Maris, 2024, Cancer Discovery on p. 2387-2406

ER stress elicits non-canonical CASP8 (caspase 8) activation on autophagosomal membranes to induce apoptosis

Tatsuya Hattori, Kevin A. Fundora, Kouta Hamamoto, David M. Opozda, Xinwen Liang, Xiaoming Liu, Jiawen Zhang, Yasin Uzun, Yoshinori Takahashi, Hong Gang Wang, 2024, Autophagy on p. 349-364

Analysis of Gene Regulatory Networks from Gene Expression Using Graph Neural Networks

Hakan Otal, Abdulhamit Subasi, Furkan Kurt, M Canbaz, Yasin Uzun, 2024, arXiv preprint arXiv:2409.13664

Approaches for Benchmarking Single-Cell Gene Regulatory Network Methods

Karamveer, Yasin Uzun, 2024, Bioinformatics and Biology Insights

Advances in computational and experimental approaches for deciphering transcriptional regulatory networks: Understanding the roles of cis-regulatory elements is essential, and recent research utilizing MPRAs, STARR-seq, CRISPR-Cas9, and machine learning has yielded valuable insights

Camille Moeckel, Ioannis Mouratidis, Nikol Chantzi, Yasin Uzun, Ilias Georgakopoulos-Soares, 2024, BioEssays

584 Crohn's disease epithelial cells exhibit sustained inflammatory progenitor cell states

Tatiana Karakasheva, Clara Martinez, Yusen Zhou, Joshua Rhoades, Olivia Hix, Gloria Soto, Shaneice Nettleford, Daana Roach, Alyssa Laguerta, Anusha Thadi, Daniel Aleynick, Oliver Pickering, Yelizaveta Borodyanskaya, Marykate Fulton, Yasin Uzun, Ning Li, Meenakshi Bewtra, Judith Kelsen, Kai Tan, Andy Minn, Christopher Legner, Kathryn Hamilton, 2024, Gastroenterology on p. S--141

Integrating Single-Cell Methylome and Transcriptome Data with MAPLE

Yasin Uzun, Hao Wu, Kai Tan, 2023, on p. 43--54

Ncrna-a3 Epigenetically Regulates TAL1 and Its Target Genes to Drive Erythroid Differentiation

Meghana Matur, Yasin Uzun, Y Qiu, S Huang, 2023, Blood on p. 1077

Most-Cited Papers

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

Orit Rozenblatt-Rosen, Aviv Regev, Philipp Oberdoerffer, Tal Nawy, Anna Hupalowska, Jennifer E. Rood, Orr Ashenberg, Ethan Cerami, Robert J. Coffey, Emek Demir, Li Ding, Edward D. Esplin, James M. Ford, Jeremy Goecks, Sharmistha Ghosh, Joe W. Gray, Justin Guinney, Sean E. Hanlon, Shannon K. Hughes, E. Shelley Hwang, Christine A. Iacobuzio-Donahue, Judit Jané-Valbuena, Bruce E. Johnson, Ken S. Lau, Tracy Lively, Sarah A. Mazzilli, Dana Pe'er, Sandro Santagata, Alex K. Shalek, Denis Schapiro, Michael P. Snyder, Peter K. Sorger, Avrum E. Spira, Sudhir Srivastava, Kai Tan, Robert B. West, Elizabeth H. Williams, Denise Aberle, Samuel I. Achilefu, Foluso O. Ademuyiwa, Andrew C. Adey, Rebecca L. Aft, Rachana Agarwal, Ruben A. Aguilar, Fatemeh Alikarami, Viola Allaj, Christopher Amos, Robert A. Anders, Michael R. Angelo, Yasin Uzun, 2020, Cell on p. 236-249

Integrative bulk and single-cell profiling of premanufacture t-cell populations reveals factors mediating long-term persistence of car t-cell therapy

Gregory M. Chen, Changya Chen, Rajat K. Das, Peng Gao, Chia Hui Chen, Shovik Bandyopadhyay, Yang Yang Ding, Yasin Uzun, Wenbao Yu, Qin Zhu, Regina M. Myers, Stephan A. Grupp, David M. Barrett, Kai Tan, 2021, Cancer Discovery on p. 2186-2199

Developmental trajectory of prehematopoietic stem cell formation from endothelium

Qin Zhu, Peng Gao, Joanna Tober, Laura Bennett, Changya Chen, Yasin Uzun, Yan Li, Elizabeth D. Howell, Melanie Mumau, Wenbao Yu, Bing He, Nancy A. Speck, Kai Tan, 2020, Blood on p. 845-856

Single-cell multiomics reveals increased plasticity, resistant populations, and stem-cell–like blasts in KMT2A-rearranged leukemia

Changya Chen, Wenbao Yu, Fatemeh Alikarami, Qi Qiu, Chia hui Chen, Jennifer Flournoy, Peng Gao, Yasin Uzun, Li Fang, James W. Davenport, Yuxuan Hu, Qin Zhu, Kai Wang, Clara Libbrecht, Alex Felmeister, Isaiah Rozich, Yang yang Ding, Stephen P. Hunger, Carolyn A. Felix, Hao Wu, Patrick A. Brown, Erin M. Guest, David M. Barrett, Kathrin M. Bernt, Kai Tan, 2022, Blood on p. 2198-2211

Identifying noncoding risk variants using disease-relevant gene regulatory networks

Long Gao, Yasin Uzun, Peng Gao, Bing He, Xiaoke Ma, Jiahui Wang, Shizhong Han, Kai Tan, 2018, Nature Communications

Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells

Peng Gao, Changya Chen, Elizabeth D. Howell, Yan Li, Joanna Tober, Yasin Uzun, Bing He, Long Gao, Qin Zhu, Arndt F. Siekmann, Nancy A. Speck, Kai Tan, 2020, Genes and Development

MITI minimum information guidelines for highly multiplexed tissue images

Denis Schapiro, Clarence Yapp, Artem Sokolov, Sheila M. Reynolds, Yu An Chen, Damir Sudar, Yubin Xie, Jeremy Muhlich, Raquel Arias-Camison, Sarah Arena, Adam J. Taylor, Milen Nikolov, Madison Tyler, Jia Ren Lin, Erik A. Burlingame, Daniel L. Abravanel, Samuel Achilefu, Foluso O. Ademuyiwa, Andrew C. Adey, Rebecca Aft, Khung Jun Ahn, Fatemeh Alikarami, Shahar Alon, Orr Ashenberg, Ethan Baker, Gregory J. Baker, Shovik Bandyopadhyay, Peter Bayguinov, Jennifer Beane, Winston Becker, Kathrin Bernt, Courtney B. Betts, Julie Bletz, Tim Blosser, Adrienne Boire, Genevieve M. Boland, Edward S. Boyden, Elmar Bucher, Raphael Bueno, Qiuyin Cai, Francesco Cambuli, Joshua Campbell, Song Cao, Wagma Caravan, Ronan Chaligné, Joseph M. Chan, Sara Chasnoff, Deyali Chatterjee, Alyce A. Chen, Yasin Uzun, 2022, Nature Methods on p. 262-267

ScATAC-pro: A comprehensive workbench for single-cell chromatin accessibility sequencing data

Wenbao Yu, Yasin Uzun, Qin Zhu, Changya Chen, Kai Tan, 2020, Genome Biology

Epigenetic state determines inflammatory sensing in neuroblastoma

Adam J. Wolpaw, Liron D. Grossmann, Jessica L. Dessau, May M. Dong, Bailey J. Aaron, Patricia A. Brafford, Darya Volgina, Guillem Pascual-Pasto, Alba Rodriguez-Garcia, Yasin Uzun, Marie Arsenian-Henriksson, Daniel J. Powell, Kristopher R. Bosse, Andrew Kossenkov, Kai Tan, Michael D. Hogarty, John M. Maris, Chi V. Dang, 2022, Proceedings of the National Academy of Sciences of the United States of America

Risk variants disrupting enhancers of T<sub>H</sub>1 and T<sub>REG</sub> cells in type 1 diabetes

Peng Gao, Yasin Uzun, Bing He, Sarah E. Salamati, Julie K.M. Coffey, Eva Tsalikian, Kai Tan, 2019, Proceedings of the National Academy of Sciences of the United States of America on p. 7581-7590