Postdoctoral Fellows

Education and Training

  • Current, Postdoctoral Fellow, LICR, UCSD School of Medicine
  • Ph.D., Human Genetics, UCLA (2008)
  • M.S., Biological Sciences, Texas Tech University (2003)
  • B.S., Biological Sciences and Technologies, Nanjing University (2000)


  • The Mouse ENCODE Consortium, An Integrated and Comparative Encyclopedia of DNA Elements in the Mouse Genome. (Under review).
  • 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 http://dx.doi.org/10.1016/j.stemcr.2013.11.003. (* co-first author)
  • 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, doi:10.1038/ng.2746.
  • Yin Shen*,Feng Yue*, David F. McCleary, Zhen Ye, Lee Edsall, Ulrich Wagner, Jesse Dixon, Leonard Lee, Victor Lobanenkov, Bing Ren, A map of cis-regulatory sequences in the mouse genome. Nature, (* co-first author) 2012 Jul 1. doi: 10.1038/nature11243. [Epub ahead of print]
  • 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, 485, 376-380.
  • 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. (2012) Cell 149(6):1368-80.
  • 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. 2012 Mar;8(3):e1002576. Epub 2012 Mar 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.
  • Shen Y., Fouse S. D. and Fan G. (2009) Genome-wide DNA methylation profiling: the mDIP-Chip technology. Methods Mol Biol. 2009;568:203-16.
  • Shen Y., Matsuno Y., Fouse S., Rao N., Root S., Xu R.H., 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.
  • 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.
  • 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.
  • 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.


1. Undergraduate Scholarship, Nanjing University. 1996-2000.
2. China Merchants Bank Scholarship. 1997.
3. Deep Gene Student Travel Awards (NSF Grant DEB-0090227). 2003.
4. California Institute for Regenerative Medicine Pre-Doctoral Fellowship. 07/2006-07/2008.
5. California Institute for Regenerative Medicine Travel Award for 5th Annual Meeting of International Society for Stem Cell Research. 2007
6. Keystone Symposia scholarship. 2008.
7. International Rett Syndrome Foundation Post-doctoral Fellowship Award. 10/2009-12/2011