Author
Amgen (United States)ORCID 0000-0002-2011-6946Unclaimed ORCID profile · follow to get notified of new preprints
12 papers
Recent·Most cited
Xiaowei Yan, Ivy Tsz Lo Wong, Muhammad Murtaza Hassan, Rui Li, Katerina Kraft, Aditi Gnanasekar, Paul S. Mischel, Howard Y. Chang
This study identifies mitosis as a critical window for ecDNA hub organization in cancer cells and shows WEE1 regulates hub integrity and oncogene expression.
bioRxiv · Oct 9, 2026 · PreprintCancer Biology
Yanbo Wang, Xiaowei Yan, Natasha E. Weiser, Ivy Tsz-Lo Wong, Shu Zhang, Yung‐Hsin Huang, Rui Li, Katerina Kraft, Aditi Gnanasekar, Jun Tang, Cy Chittenden, Lotte Brückner, Imran Noorani, Charles Swanton, Anton George Henssen, , Paul S. Mischel
The paper shows ecDNA localizes to the nuclear periphery in cancer, resisting silencing and enhancing transcriptional output through interactions with the nuclear lamina.
bioRxiv · Sep 17, 2026 · PreprintCancer Biology
Matthew G. Jones, Natasha E. Weiser, King L. Hung, Xiaowei Yan, Sangya Agarwal, Jens Luebeck, Aditi Gnanasekar, Brooke E. Howitt, Ellis J. Curtis, Kevin Yu, John C. Rose, Katerina Kraft, Valeh Valiollah Pour Amiri, Leena Satpathy, Vineet Bafna, , Howard Y. Chang
scAmp detects and analyzes ecDNA at single-cell resolution, showing its impact on chromatin accessibility in cancer cells.
bioRxiv · Feb 15, 2026 · PreprintCancer Biology
Biswanath Chowdhury, Kaiyuan Zhu, Chaohui Li, Jessica Alsing, Jens Luebeck, Maria E. Stefanova, Owen S. Chapman, Katerina Kraft, Shu Zhang, Jun Yi Stanley Lim, Yipeng Xie, Yoon Jung Kim, Sihan Wu, Lukas Chávez, Guy Nir, , Vineet Bafna
The paper introduces ec3D, a method to reconstruct 3D structures of ecDNA from Hi-C data, revealing spherical configurations and unique long-range interactions in cancer.
Nature Communications · Dec 20, 2025Peer-reviewedCancer Biology
Venkat Sankar, King L. Hung, Aditi Gnanasekar, Ivy Tsz-Lo Wong, Quanming Shi, Katerina Kraft, Matthew G. Jones, Britney Jiayu He, Xiaowei Yan, Julia A. Belk, Kevin J. Liu, Sangya Agarwal, Sean K. Wang, Anton George Henssen, Paul S. Mischel, Howard Y. Chang
A genome-wide plasmid screen, Retain-seq, identifies thousands of CpG-rich promoter-like human elements that tether episomes to mitotic chromosomes, shape ecDNA structure, and lose function when methylated.
Nature · Nov 19, 2025Peer-reviewedCancer Biology✦ In-depth digest
Katerina Kraft, Sedona E. Murphy, Matthew G. Jones, Quanming Shi, Aarohi Bhargava-Shah, Christy Luong, King L. Hung, Britney Jiayu He, Rui Li, Seung Kuk Park, Michael T. Montgomery, Natasha E. Weiser, Yanbo Wang, Jens Luebeck, Vineet Bafna, , Howard Y. Chang
The paper identifies enhancer-like elements on ecDNA in colorectal cancer that are derived from transposable elements and are functionally active in cancer cell fitness.
Nature Cell Biology · Oct 21, 2025Peer-reviewedGenetics
Hyerim Yi, Shu Zhang, Jason T. Swinderman, Yanbo Wang, Vishnupriya Kanakaveti, King L. Hung, Ivy Tsz-Lo Wong, Suhas Srinivasan, Ellis J. Curtis, Aarohi Bhargava-Shah, Rui Li, Matthew G. Jones, Jens Luebeck, Yanding Zhao, Julia A. Belk, , Howard Y. Chang
The paper shows that ecDNA-borne PVT1 fusions stabilize oncogenic mRNAs by interacting with SRSF1, enhancing RNA stability and supporting MYC dependency in cancer.
bioRxiv · Apr 1, 2025 · PreprintCancer Biology
Naomi M. Pacalin, Zachary Steinhart, Quanming Shi, Julia A. Belk, Dmytro Dorovskyi, Katerina Kraft, Kevin R. Parker, Brian Rudolph Shy, Alexander Marson, Howard Y. Chang
This study introduces CRISPRai, a bidirectional epigenetic editing system, to investigate gene regulation hierarchies and interactions in T cells and hematopoietic lineage transcription factors.
Nature Biotechnology · May 17, 2024Peer-reviewedGenomics
Diana R. Dou, Yanding Zhao, Julia A. Belk, Yang Zhao, Kerriann M. Casey, Derek C. Chen, Rui Li, Bingfei Yu, Suhas Srinivasan, Brian T. Abe, Katerina Kraft, Cecilia Hellström, Ronald Sjöberg, Sarah Esther Chang, Allan Feng, , Howard Y. Chang
This study shows that Xist ribonucleoprotein complexes drive sex-biased autoimmunity in males, leading to autoimmune pathology and reprogramming of immune cells to resemble female patterns.
Cell · Feb 1, 2024Peer-reviewedMolecular Biology
Sean K. Wang, Surag Nair, Rui Li, Katerina Kraft, Anusri Pampari, Aman Patel, Joyce B. Kang, Christy Luong, Anshul Bharat Kundaje, Howard Y. Chang
The paper uses a single-cell multiome atlas of the human retina and deep learning to identify causal noncoding variants in eye diseases.
Cell Genomics · Jul 27, 2022Peer-reviewedGenomics
Katerina Kraft, Kathryn E. Yost, Sedona E. Murphy, Andreas Magg, Yicheng Long, M. Ryan Corces, Jeffrey M. Granja, Lars Wittler, Stefan Mundlos, Thomas R. Cech, Alistair Nicol Boettiger, Howard Y. Chang
The paper investigates how Polycomb-mediated genome architecture facilitates long-range H3K27 methylation spreading in ESCs and iPSCs, revealing RNA-dependent DNA looping and developmental gene roles in chromatin organization.
Proceedings of the National Academy of Sciences · May 26, 2022Peer-reviewedGenetics
Jiao Sima, Abhijit Chakraborty, Vishnu Dileep, Marco Michalski, Kyle N. Klein, Nicolas P. Holcomb, Jesse L. Turner, Michelle T. Paulsen, Juan Carlos Rivera‐Mulia, Claudia Trevilla‐García, Daniel A. Bartlett, Peiyao A Zhao, Brian K. Washburn, Elphège Pierre Nora, Katerina Kraft, , David M. Gilbert
The paper identifies cis-regulatory elements (ERCEs) that control domain-wide replication timing, chromatin compartmentalization, and transcription in mouse embryonic stem cells.
Cell · Dec 27, 2018Peer-reviewedMolecular Biology