Preprint(Under review)

1. 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." [Manuscript] .

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

1. 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 18, 661–668 (2021).

2. 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).

3. 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).

4. 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, DOI:10.1038/s41586-020-2962-9. (2020).

5. 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." [Manuscript]. Nature Commmunications, 11:3696, (2020).

6. 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." [Manuscript], [Download predicted loops]. Nature Communications 11:3428, (2020).

7. 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).

8. Galip Yardimci, Hakan Ozadam, Michael E.G. Sauria, Oana Ursu, Koon-Kiu Yan, Tao Yang, Abhijit Chakraborty, Arya Kaul, Bryan R Lajoie, Fan Song, Ye Zhan, Ferhat Ay, Mark Gerstein, Anshul Kundaje, Qunhua Li, James Taylor, Feng Yue, Job Dekker, William S Noble. "Measuring the reproducibility and quality of Hi-C data." Genome Biology 20:57, (2019).

9. 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).

10. 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.

11. 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 2018, Link .750, (2018).

12. Job Dekker, Andrew S. Belmont, Mitchell Guttman, et. al., and the 4D Nucleome Network. "The 4D nucleome project." Nature 549, 219–226, 2017.

13. 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.

14. Bing Ren and Feng Yue. (2015) "Transcriptional Enhancers: Bridging the Genome and Phenome." Cold Spring Harb Symp Quant Biol. 2015 Nov 18.

15. Allen Wang*, Feng Yue*, Yan Li*, Ruiyu Xie, Thomas Harper, Nisha A. Patel, Kayla Muth, Jeffrey Palmer, Jeffrey C. Raum, Doris A. Stoffers, Bing Ren, Maike Sander. "Epigenetic Priming of Enhancers Predicts Developmental Competence to hESC-Derived Endodermal Lineage Intermediates", Cell Stem Cell , Apr 2;16(4):386-99 2015.

16. 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.

17. Yin Shen*, Feng Yue*, David F McCleary, Zhen Ye, Lee Edsall, Samantha Kuan, Ulrich Wagner, Jesse Dixon, Leonard Lee, Victor V Lobanenkov, Bing Ren, "A map of the cis-regulatory sequences in the mouse genome", Nature, 2012 488 (7409), 116-120. (*Co-first author)

18. Jesse R. Dixon, Siddarth Selvaraj, Feng Yue, Audrey Kim, Yan Li, Yin Shen, Ming Hu, Jun S. Liu, Bing Ren, "Topological domains in mammalian genomes identified by analysis of chromatin interactions", Nature, 2012, 485, 376-380

19. Mouse ENCODE Consortium, "An encyclopedia of mouse DNA elements (Mouse ENCODE)", Genome Biology, 2012 Aug 13; 13(8)418.

21. Feng Yue, Jian Shi, and Jijun Tang, "Simultaneous phylogeny reconstruction and multiple sequence alignment", BMC Bioinformatics, 2009, 10(Suppl. 1):S11.

22. Feng Yue and Jijun Tang, "A space-efficient algorithm for three sequence alignment and ancestor inference", Intl Journal of Data Mining and Bioinformatics, 2009, 3(2), 192-204.

23. Feng Yue, Meng Zhang, and Jijun Tang, "Phylogenetic reconstruction from transposit ion", BMC Genomics, 2008, 9 (Suppl. 2):S15.

24. Feng Yue, Liying Cui, Claude W. dePamphilis, Bernard ME Moretand Jijun Tang, "Gene rearrangement Analysis from Chloroplast Genomes with Inverted Repeat", BMC Genomics, 2008, 9(Suppl 1):S25.