Submitted

1. 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." BioRxiv, 2017.

2. 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. "An Integrative Framework For Detecting Structural Variations In Cancer Genomes." BioRxiv, 2017.

3. Yan Zhang*, Lin An*, Ming Hu, Jijun Tang, Feng Yue. "HiCPlus: Resolution Enhancement of Hi-C interaction heatmap." Biorxiv, 2017.

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." Biorxiv, 2017.

Most Representative

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

2. 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. (2015) "Epigenetic Priming of Enhancers Predicts Developmental Competence to hESC-Derived Endodermal Lineage Intermediates", Cell Stem Cell , 2015 Apr 2;16(4):386-99. (*Co-first author).

3. 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)

4. 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

All Publications [Google Scholar]

19. 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, (co-corresponding author, accepted).

18. Yu Zhang, Lin An, Feng Yue, Ross Hardison (2016) "Jointly characterizing epigenetic dynamics across multiple human cell types", Nucleic Acids Research , 2016; doi: 10.1093/nar/gkw278

17. Xu Z, Zhang G, Duan Q, Chai S, Zhang B, Wu C, Jin F, Yue F , Li Y, HuM (2016) "HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants", BMC Res Notes, 2016 Mar 11;9:159. doi: 10.1186/s13104-016-1947-0.

16. 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. (2015) "Epigenetic Priming of Enhancers Predicts Developmental Competence to hESC-Derived Endodermal Lineage Intermediates", Cell Stem Cell , 2015 Apr 2;16(4):386-99. (*Co-first author).

14. Danny Leung, Inkyung Jung, Nisha Rajagopal, Anthony Schmitt, Siddarth Selvaraj, Ah Young Lee, Chia-An Yen, Shin Lin, Yiing Lin, Yunjiang Qiu, Wei Xie, Feng Yue, Manoj Hariharan, Pradipta Ray, Samantha Kuan, Lee Edsall, Hongbo Yang, Neil C. Chi, Michael Q. Zhang, Joseph R. Ecker, and Bing Ren. (2015) "Integrative analysis of haplotype-resolved epigenomes across human tissues.", Nature, 2015 Feb 19;518(7539):350-4.

13. 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).

12. 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.

11. 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].

10. 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

10. 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)

9. 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

8. 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

7. 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.

6. 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.

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

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

3. 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.

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

1. 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.