Representative publications. For complete list, please refer to [Google Scholar].

17. Radhika Mathur, Qixuan Wang, Patrick G. Schupp, Ana Nikolic, Stephanie Hilz, Chibo Hong, Nadia R. Grishanina, Darwin Kwok, Nicholas O. Stevers, Qiushi Jin, Mark W. Youngblood, Lena Ann Stasiak, Ye Hou, Juan Wang, Takafumi N. Yamaguchi, Marisa Lafontaine, Anny Shai, Ivan V. Smirnov, David A. Solomon, Susan M. Chang, Shawn L. Hervey-Jumper, Mitchel S. Berger, Janine M. Lupo, Hideho Okada, Joanna J. Phillips, Paul C. Boutros, Marco Gallo, Marco Gallo, Michael C. Oldham, Feng Yue^#, Joseph F. Costello^#. Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective. Cell (2024). Highlighted by Cell Leading Edge.

16. Tingting Liu, Juan Wang, Hongbo Yang, Qiushi Jin, Xiaotao Wang, Yihao Fu, Yu Luan, Qixuan Wang, Mark W. Youngblood, Xinyan Lu, Lucia Casadei, Raphael Pollock^#, Feng Yue^# . Enhancer Coamplification and Hijacking Promote Oncogene Expression in Liposarcoma. Cancer Research (2023).

15. Jie Xu, Fan Song, Huijue Lyu, Mikoto Kobayashi, Baozhen Zhang, Ziyu Zhao, Ye Hou, Xiaotao Wang, Yu Luan, Bei Jia, Lena Stasiak, Josiah Hiu-Yuen Wong, Qixuan Wang, Qi Jin, Qiushi Jin, Yihao Fu, Hongbo Yang, Ross C Hardison, Sinisa Dovat, Leonidas C Platanias, Yarui Diao, Yue Yang, Tomoko Yamada, Aaron D Viny, Ross L Levine, David Claxton, James R Broach, Hong Zheng^#, Feng Yue^# . Subtype-specific 3D genome alteration in acute myeloid leukaemia. Nature (2022).

14. Xiaotao Wang, Yu Luan, Feng Yue. EagleC: A deep-learning framework for detecting a full range of structural variations from bulk and single-cell contact maps. Science Advances, (2022).

13. Hongbo Yang*, Hui Zhang*, Yu Luan*, Tingting Liu, Kathryn G Roberts, Mao-xiang Qian, Bo Zhang, Wenjian Yang, Virginia Perez-Andreu, Jie Xu, Sriranga Iyyanki, Da Kuang, Shalini C. Reshmi, Julie Gastier-Foster, Colton Smith, Ching-Hon Pui, William E Evans, Stephen P Hunger, Leonidas C. Platanias, Mary V Relling, Charles G Mullighan, Mignon L Loh, Feng Yue^#, Jun J Yang^#. Non-coding germline GATA3 variants alter chromatin topology and contribute to pathogenesis of acute lymphoblastic leukemia., Nature Genetics, (2022). Highlighted by Nature Reviews Cancer.

12. Xiaotao Wang, Jie Xu, Baozhen Zhang, Ye Hou, Fan Song, Huijue Lyu, Feng Yue. Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes. Nature Methods(2021).

11. Juan Wang*, Tina Yi-Ting Huang*, Ye Hou*, Elizabeth Bartom, Xinyan Lu, Ali Shilatifard, Feng Yue^#, Amanda Saratsis^#. Epigenomic landscape and 3D genome structure in pediatric high-grade glioma. Science Advances 7:23, DOI: 0.1126/sciadv.abg4126 (2021).

10. Tejaswi Iyyanki*, Baozhen Zhang*, QixuanWang*, Ye Hou*, Qiushi Jin, Jie Xu, Hongbo Yang, Tingting Liu, Xiaotao Wang, Fan Song, Yu Luan, Hironobu Yamashita, Ruby Chien, Huijue Lyu, Lijun Zhang, Lu Wang, Joshua Warrick, Jay D. Raman, Joshua J. Meeks, David J. DeGraff^# and Feng Yue^# . Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer. Genome Biology 22:105, (2021).

9. Hongbo Yang*, Yu Luan*, Tingting Liu*, Hyung Joo Lee, Li Fang, Yanli Wang, Xiaotao Wang, Bo Zhang, Qiushi Jin, Khai Chung Ang, Xiaoyun Xing, Juan Wang, Jie Xu, Fan Song, Iyyanki Sriranga, Chachrit Khunsriraksakul, Tarik Salameh, Daofeng Li, Mayank N. K. Choudhary, Jacek Topczewski, Kai Wang, Glenn S. Gerhard, Ross C. Hardison, Ting Wang, Keith C. Cheng, Feng Yue. A map of cis-regulatory elements and 3D genome structures in zebrafish. Nature (2020).

8. Jing Zhang*, Donghoon Lee*, Vineet Dhiman*, Peng Jiang*, Jie Xu*, Patrick McGillivray*, Hongbo Yang*, ..., Feng Yue^#, X. Shirley Liu^#, Kevin White^#, Mark Gerstein^#. An integrative ENCODE resource for cancer genomics. Nature Commmunications, 11:3696, (2020).

7. Tarik J Salameh, Xiaotao Wang, Fan Song, Bo Zhang, Sage M. Wright, Chachrit Khunsriraksakul, Feng Yue. A supervised learning framework for chromatin loop detection in genome-wide contact maps.. Nature Communications 11:3428, (2020).

6. Yali Ding*, Bo Zhang*, Jonathon L. Payne, ... Kimberly J. Payne, Feng Yue^#, Sinisa Dovat^#. Ikaros tumor suppressor function includes induction of active enhancers and super-enhancers along with pioneering activity. Leukemia, (2019).

5. Jesse Dixon*^#, Jie Xu*, Vishnu Dileep*, Ye Zhan*, Fan Song*, Victoria T. Le, Galip Gurkan Yardimci, Abhijit Chakraborty, ... Ferhat Ay^#, William Stafford Noble^#, Job Dekker^#, David M. Gilbert^#, Feng Yue^#. Integrative Framework For Detecting Structural Variations In Cancer Genomes. Nature Genetics 50, 1388-1398, (2018).

4. Yanli Wang, Bo Zhang, Lijun Zhang, Lin An, Jie Xu, Daofeng Li, Mayank NK Choudhary, Yun Li, Ming Hu, Ross Hardison, Ting Wang^#, Feng Yue^#. The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. Genome Biology 19:151, 2018.

3. Yan Zhang*, Lin An*, Jie Xu, Bo Zhang, W. Jim Zheng, Ming Hu, Jijun Tang and Feng Yue. Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus. Nature Communications 9, 750, 2018.

2. Tao Yang, Feipeng Zhang, Galip Gurkan Yardimci, Ross C Hardison, William Stafford Noble, Feng Yue^#, Qunhua Li^#. HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Genome Research 2017.

1. Feng Yue*, Yong Cheng*, Alessandra Breschi*, Jeff Vierstra*, Weisheng Wu*, Tyrone Ryba*, Richard Sandstrom*, Zhihai Ma*, Carrie Davis*, Benjamin D. Pope*, Yin Shen*, ..., Yanli Wang,... , John Stamatoyannopoulos#, Michael P. Snyder#, Roderic Guigo#, Thomas R. Gingeras#, David M. Gilbert#, Ross C. Hardison#, Michael A. Beer#,*, Bing Ren# & The mouse ENCODE Consortium. An Integrated and Comparative Encyclopedia of DNA Elements in the Mouse Genome. Nature 515, 355-364, 2014.