Publication

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. (2014) "An Integrated and Comparative Encyclopedia of DNA Elements in the Mouse Genome", Nature 515, 355-364 (*equal contribution).

2. Benjamin D. Pope*, Tyrone Ryba*, Vishnu Dileep, Feng Yue , Weisheng Wu, Olgert Denas, Daniel L. Vera, Yanli Wang, R. Scott Hansen, Theresa K. Canfield, Robert E. Thurman, Yong Cheng, G├╝nhan G10, Jonathan H. Dennis1, Michael P. Snyder, John A. Stamatoyannopoulos, James Taylor6, Ross C. Hardison, Tamer Kahveci, Bing Ren, David M. Gilbert. (2014) "Topologically-associating domains are stable units of replication-timing regulation" Nature 515, 402-405.

3. Virginia Perez-Andreu, Kathryn G. Roberts, Heng Xu, Colton Smith, Hui Zhang, Wenjian Yang, (+20 authors), Feng Yue, Yanli Wang, Ching-Hon Pui, Sima Jeha, Mary V. Relling, William E. Evans, Daniela S. Gerhard, Mignon L. Loh, Cheryl L. Willman, Stephen P. Hunger, Charles G. Mullighan, and Jun J. Yang. (2014) "A genome-wide association study of susceptibility to acute lymphoblastic leukemia in adolescents and young adults", Blood 2014-09-595744. [Epub ahead of print].

4. Virginia Perez-Andreu, Kathryn G Roberts, Richard C Harvey, Wenjian Yang, Cheng Cheng, Deqing Pei, Heng Xu, Julie Gastier-Foster, E Shuyu, Joshua Yew-Suang Lim, I-Ming Chen, Yiping Fan, Meenakshi Devidas, Michael J Borowitz, Colton Smith, Geoffrey Neale, Esteban G Burchard, Dara G Torgerson, Federico Antillon Klussmann, Cesar Rolando Najera Villagran, Naomi J Winick, Bruce M Camitta, Elizabeth Raetz, Brent Wood, Feng Yue, William L Carroll, Eric Larsen, W Paul Bowman, Mignon L Loh, Michael Dean, Deepa Bhojwani, Ching-Hon Pui, William E Evans, Mary V Relling, Stephen P Hunger, Cheryl L Willman, Charles G Mullighan, Jun J Yang. (2013) "Inherited GATA3 variants are associated with Ph-like childhood acute lymphoblastic leukemia and risk of relapse", Nature Genetics 45 (12), 1494-1498.

Before joining Penn State

5. 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)

6. 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

7. Wei Xie, Cathy L. Barr, Audrey Kim, Feng Yue, Ah Young Lee, James Eubanks, Emma L. Dempster, Bing Ren, "Base-resolution analyses of sequence and parent-of- origin dependent DNA methylation in the mouse genome", Cell, 2012, 148, 816-831

8. Gary C Hon, Nisha Rajagopal, Yin Shen, David F McCleary, Feng Yue, My D Dang, Bing Ren, "Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues", Nature Genetics, 2013 45 (10), 1198-1206.

9. Mark Rebeiz, Brian Castro, Feng Liu, Feng Yue, James W. Posakony, "Ancestral and conserved cis-regulatory architectures in developmental control genes", Developmental Biology, 2012, 362(2), 282-294.

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

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

12. 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.

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

14. 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.