Publications by authors named "Quanming Shi"

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Enhancer activation from transposable elements in extrachromosomal DNA.
Katerina Kraft, Sedona E Murphy, Matthew G Jones, Quanming Shi, Aarohi Bhargava-Shah

Nat Cell Biol· November 2025

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Genetic elements promote retention of extrachromosomal DNA in cancer cells.
Venkat Sankar, King L Hung, Aditi Gnanasekar, Ivy Tsz-Lo Wong, Quanming Shi

Nature· November 2025

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Genetic elements promote retention of extrachromosomal DNA in cancer cells.
Venkat Sankar, King L Hung, Aditi Gnanasekar, Ivy Tsz-Lo Wong, Quanming Shi

bioRxiv· October 2025

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Enhancer activation from transposable elements in extrachromosomal DNA.
Katerina Kraft, Sedona E Murphy, Matthew G Jones, Quanming Shi, Aarohi Bhargava-Shah

bioRxiv· September 2025

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Massively parallel immunopeptidome by DNA sequencing provides insights into cancer antigen presentation.
Quanming Shi, Elana P Simon, Cansu Cimen Bozkus, Anna Kaminska, Leandra Velazquez

Nat Genet· August 2025

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Robust fluorescent labeling and tracking of endogenous non-repetitive genomic loci.
Alex Raterink, Rajarshi P Ghosh, Linfeng Yang, Quanming Shi, Minh Khue Nguyen

bioRxiv· August 2025

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EcDNA-borne PVT1 fusion stabilizes oncogenic mRNAs.
Hyerim Yi, Shu Zhang, Jason Swinderman, Yanbo Wang, Vishnupriya Kanakaveti, Quanming Shi

bioRxiv· April 2025

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Bidirectional epigenetic editing reveals hierarchies in gene regulation.
Naomi M Pacalin, Zachary Steinhart, Quanming Shi, Julia A Belk, Dmytro Dorovskyi

Nat Biotechnol· March 2025

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Autoantibody hotspots reveal origin and impact of immunogenic XIST ribonucleoprotein complex.
Bingyu Yan, Jinwoo Lee, Suhas Srinivasan, Quanming Shi, Diana R Dou

bioRxiv· January 2025

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Engineered cell entry links receptor biology with single-cell genomics.
Bingfei Yu, Quanming Shi, Julia A Belk, Kathryn E Yost, Kevin R Parker

Cell· December 2022

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Inducible lncRNA transgenic mice reveal continual role of in promoting breast cancer metastasis.
Qing Ma, Liuyi Yang, Karen Tolentino, Guiping Wang, Yang Zhao, Quanming Shi

Elife· December 2022

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Divergent clonal differentiation trajectories of T cell exhaustion.
Bence Daniel, Kathryn E Yost, Sunnie Hsiung, Katalin Sandor, Yu Xia, Quanming Shi, Takeshi Egawa

Nat Immunol· November 2022

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The evolutionary dynamics of extrachromosomal DNA in human cancers.
Joshua T Lange, John C Rose, Celine Y Chen, Yuriy Pichugin, Liangqi Xie, Quanming Shi

Nat Genet· October 2022

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Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence.
Julia A Belk, Winnie Yao, Nghi Ly, Katherine A Freitas, Yan-Ting Chen, Quanming Shi, Eric Shifrut

Cancer Cell· July 2022

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Spatiotemporal co-dependency between macrophages and exhausted CD8 T cells in cancer.
Kelly Kersten, Kenneth H Hu, Alexis J Combes, Bushra Samad, Tory Harwin, Quanming Shi

Cancer Cell· June 2022

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ecDNA hubs drive cooperative intermolecular oncogene expression.
King L Hung, Kathryn E Yost, Liangqi Xie, Quanming Shi, Konstantin Helmsauer

Nature· December 2021

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A human mutation in STAT3 promotes type 1 diabetes through a defect in CD8+ T cell tolerance.
Jeremy T Warshauer, Julia A Belk, Alice Y Chan, Jiaxi Wang, Alexander R Gupta, Quanming Shi

J Exp Med· August 2021

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Differential usage of transcriptional repressor Zeb2 enhancers distinguishes adult and embryonic hematopoiesis.
Xiao Huang, Stephen T Ferris, Sunkyung Kim, Mayank N K Choudhary, Julia A Belk, Quanming Shi, Takeshi Egawa

Immunity· July 2021

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B cell-specific XIST complex enforces X-inactivation and restrains atypical B cells.
Bingfei Yu, Yanyan Qi, Rui Li, Quanming Shi, Ansuman T Satpathy

Cell· April 2021

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Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions.
Ryan A Flynn, Julia A Belk, Yanyan Qi, Yuki Yasumoto, Jin Wei, Quanming Shi

Cell· April 2021

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Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing.
James K Nuñez, Jin Chen, Greg C Pommier, J Zachery Cogan, Joseph M Replogle, Quanming Shi

Cell· April 2021

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B cell-specific XIST complex enforces X-inactivation and restrains atypical B cells.
Bingfei Yu, Yanyan Qi, Rui Li, Quanming Shi, Ansuman Satpathy

bioRxiv· January 2021

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Stiff stroma increases breast cancer risk by inducing the oncogene ZNF217.
Jason J Northey, Alexander S Barrett, Irene Acerbi, Mary-Kate Hayward, Stephanie Talamantes, Quanming Shi

J Clin Invest· November 2020

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Concerted localization-resets precede YAP-dependent transcription.
J Matthew Franklin, Rajarshi P Ghosh, Quanming Shi, Michael P Reddick, Jan T Liphardt

Nat Commun· September 2020

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Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation.
Ava C Carter, Jin Xu, Meagan Y Nakamoto, Yuning Wei, Brian J Zarnegar, Quanming Shi

Elife· May 2020

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