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Widespread epistasis shapes RNA polymerase II active site function and evolution.

Publication: Journal Article

Duan, Bingbing, Chenxi Qiu, Sing-Hoi Sze, and Craig Kaplan. 2025. “Widespread Epistasis Shapes RNA Polymerase II Active Site Function and Evolution.”. Nature Communications 16 (1): 7993.

Team And Collaborators: Mark Zeidel, MD, Principal Investigator Bryce MacIver, PhD, Project Coordinator Aaron Grant, PhD, Director, Preclinical MRI Core at BIDMC Dave Alsop, PhD, Director, Division of Magnetic Resonance Research at BIDMC Cody Callahan, BS, Department of Radiology at BIDMC John Mac...

Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser.

Publication: Journal Article

Lin, Guowu, Christopher O Barnes, Simon Weiss, Bercem Dutagaci, Chenxi Qiu, Michael Feig, Jihnu Song, et al. 2024. “Structural Basis of Transcription: RNA Polymerase II Substrate Binding and Metal Coordination Using a Free-Electron Laser.”. Proceedings of the National Academy of Sciences of the United States of America 121 (36): e2318527121.

Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning.

Publication: Journal Article

Dutagaci, Bercem, Bingbing Duan, Chenxi Qiu, Craig D Kaplan, and Michael Feig. 2023. “Characterization of RNA Polymerase II Trigger Loop Mutations Using Molecular Dynamics Simulations and Machine Learning.”. PLoS Computational Biology 19 (3): e1010999.

Inhibition of death-associated protein kinase 1 attenuates cis P-tau and neurodegeneration in traumatic brain injury.

Publication: Journal Article

Kim, Nami, Bin Wang, Kazuhiro Koikawa, Yutaka Nezu, Chenxi Qiu, Tae Ho Lee, and Xiao Zhen Zhou. 2021. “Inhibition of Death-Associated Protein Kinase 1 Attenuates Cis P-Tau and Neurodegeneration in Traumatic Brain Injury.”. Progress in Neurobiology 203: 102072.

Molecular mechanisms of voiding dysfunction in a novel mouse model of acute urinary retention.

Publication: Journal Article

Xie, Xiang, Huan Chen, Lanlan Zhang, Daniel Chan, Warren G Hill, Mark L Zeidel, and Weiqun Yu. 2021. “Molecular Mechanisms of Voiding Dysfunction in a Novel Mouse Model of Acute Urinary Retention.”. FASEB Journal 35 (4): e21447.

Functional Neuroimaging of Voiding in Mice

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These studies were funded by an NIH P20 grant [DK108276], to form a Resource Development Project within the BIDMC Department of Medicine’s Center for Interdisciplinary Research in Benign Urology. This Project brings together Department of Radiology Magnetic Resonance Imaging (MRI) physicists and...

Reciprocal antagonism of PIN1-APC/CCDH1 governs mitotic protein stability and cell cycle entry.

Publication: Journal Article

Ke, Shizhong, Fabin Dang, Lin Wang, Jia-Yun Chen, Mandar T Naik, Wenxue Li, Abhishek Thavamani, et al. 2024. “Reciprocal Antagonism of PIN1-APC/CCDH1 Governs Mitotic Protein Stability and Cell Cycle Entry.”. Nature Communications 15 (1): 3220.