1. Li Y, Hu M, Shen Y. (2018) Gene regulation in the 3D genome. Human Molecular Genetics, 2018 May 14.

  2. Emmerson E, May A, Nathan S, Pacheco NC, Lizama CO, Maliskova L, Zovein AC, Shen Y, Muench MO, Knox SM. (2017) SOX2 regulates acinar cell development in the salivary gland. eLIFE, 2017, Jun 17. [Epub ahead of print]

  3. Diao Y, Fang R, Li B, Meng Z, Yu J, Qiu Y, Lin KC, Huang H, Liu T, Marina RJ, Jung I, Shen Y, Guan K, Ren B. (2017) A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. Nature Method, 2017 Apr 17. [Epub ahead of print]

  4. He Y, Gorkin D, Dickel D, Nery J, Castanon R, Lee AY, Shen Y, Visel A, Pennacchio L, Ren B, Ecker J. (2017) Improved regulatory element prediction based on tissue-specific local epigenomic signatures. PNAS, 2017 Jan 9;114(9):1633-1640.

  5. Diao Y*, Li B, Young I, Lee AY, Meng Z, Maliskova L, Guan K, Shen Y*,#, Ren B#. (2016) A New Class of Temporarily Phenotypic Enhancers Identified by CRISPR/Cas9 Mediated Genetic Screening. Genome Research, 2016 Jan 26. [Epub ahead of print] (*equal contribution, # co-correspondence author).

  6. Dixon JR*, Jung I*, Selvaraj S*, Shen Y, Antosiewicz-Bourget JE, Lee AY, Ye Z, Kim A, Rajagopal N, Xie W, Diao Y, Liang J, Zhao H, Lobanenkov VV, Ecker JR, Thomson JA, Ren B. (2015) Chromatin architecture reorganization during stem cell differentiation. Nature 2015; 518 (7539): 33.

  7. Yue F*, Cheng Y*, Breschi A*, Vierstra J*, Wu W*, Ryba T*, Sandstrom R*, Ma Z*, Davis C*, Pope BD*, Shen Y*, et al (2014) A comparative encyclopedia of DNA elements in the mouse genome. Nature, 2014 Nov 20;515(7527):355-64. (*co-first author)

  8. Huang K*, Shen Y*, Xue Z, Bibikova M, April C, Liu Z, Cheng L, Nagy A, Pellegrini M, Fan JB, Fan G. (2014) A panel of CpG methylation patterns distinguishes human embryonic stem cells and induced pluripotent stem cells. Stem Cell Reports. (*co-first author)

  9. Hon GC, Rajagopal N, Shen Y, McCleary DF, Yue F, Dang MD, Ren B. (2013) Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nature Genetics 2013 Oct;45(10):1198-206.

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

  11. Shen Y*, Yue F*, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B. (2012) A map of cis-regulatory sequences in the mouse genome. Nature, 488, 116-120. (* co-first author)

  12. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485, 376-380.

  13. Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A, Li X, Dai Q, Shen Y, Park B, Min JH, Jin P, Ren B, He C (2012) Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome. Cell 149(6):1368-80. 

  14. Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS, Reiter JF. (2012) Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal. PLoS Genet. Mar;8(3):e1002576. Epub 2012 Mar 15.

  15. Wang A, Huang K, Shen Y, Xue Z, Cai C, Horvath S, Fan G (2011). Functional Modules Distinguish Human Induced Pluripotent Stem Cells from Embryonic Stem Cells. Stem Cells Dev. 2011 Jun 20.

  16. Shen Y, Fouse SD, and Fan G (2009) Genome-wide DNA methylation profiling: the mDIP- Chip technology. Methods Mol Biol. 2009;568:203-16.

  17. Shen Y, Matsuno Y, Fouse S, Rao N, Root S, Xu RH, Pellegrini M, Riggs A, and Fan G. (2008). X-inactivation in female human embryonic stem cells is in a non-random pattern and prone to epigenetic alterations. Proc Natl Acad Sci U S A 2008 Mar 25; 105(12):4709-14. Epub 2008 Mar 13.

  18. Fouse S, Shen Y, Pellegrini M, Cole S, Meissner A, Van Neste L, Jaenisch R, and Fan G. (2008). Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, Polycomb binding and histone H3 lys4/lys27 trimethylation. Cell Stem Cell 2008 Feb; 2(2): 160-169.

  19. Shen Y, Chow J, Wang Z, Fan G. (2006). Abnormal CpG island methylation occurs during in vitro differentiation of human embryonic stem cells. Human Molecular Genetics 2006 Sep 1;15(17):2623-35.

  20. Fan G, Martinowich K, Chin M, He F, Fouse S., Hutnick L, Hattori D, Ge W, Shen Y, Wu H, ten Hoeve T, Shuai K, and Sun Y. (2005) DNA methylation controls the timing of astrogliogenesis through regulation of JAK-STAT signaling. Development 2005 Aug; 132(15):3345-56.