1. Yang X, Jones IR, Chen PB, Yang H, Ren X, Zheng L, Li B, Li YE, Sun Q, Wen J, Beaman C, Cui X, Li Y, Wang W, Hu M, Ren B, Shen Y. Functional characterization of gene regulatory elements and neuropsychiatric disease-associated risk loci in iPSCs and iPSC-derived neurons. bioRxiv. 2023 Aug 30. doi: 10.1101/2023.08.30.555359

  2. Yang X, Wen J, Yang H, Jones IR, Zhu X, Liu W, Li B, Clelland CD, Luo W, Wong MY, Ren X, Cui X, Song M, Liu H, Chen C, Eng N, Ravichandran M, Sun Y, Lee D, Van Buren E, Jiang MZ, Chan CSY, Ye CJ, Perera RM, Gan L, Li Y#, Shen Y#. Functional characterization of Alzheimer’s disease genetic variants in microglia. Nature Genetics. 2023 Sep 21. doi: 10.1038/s41588-023-01506-8.

  3. Ren X, Yang H, Nierenberg JL, Sun Y, Chen J, Beaman C, Pham T, Nobuhara M, Takagi MA, Narayan V, Li Y, Ziv E, Shen Y. High throughput PRIME editing screens identify functional DNA variants in the human genome. bioRxiv [Preprint]. 2023 Jul 12:2023.07.12.548736. doi: 10.1101/2023.07.12.548736. PMID: 37502948; PMCID: PMC10370011.

  4. Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Mol Cell. 2023 Aug 3;83(15):2624-2640. doi: 10.1016/j.molcel.2023.06.018. Epub 2023 Jul 6. PMID: 37419111.

  5. Ren X, Takagi MA, Shen Y. Efficient bi-allelic tagging in human induced pluripotent stem cells using CRISPR. STAR Protoc. 2023 Feb 1;4(1):102084. doi: 10.1016/j.xpro.2023.102084. Epub ahead of print. PMID: 36853689; PMCID: PMC9918420.

  6. Sun W, Wang N, Liu H, Yu B, Jin L, Ren X, Shen Y, Wang L. Genetically encoded chemical crosslinking of RNA in vivo. Nat Chem. 2023 Jan;15(1):21-32. doi: 10.1038/s41557-022-01038-4. Epub 2022 Oct 6. PMID: 36202986; PMCID: PMC9840682.

  7. Wu D, Poddar A, Ninou E, Hwang E, Cole MA, Liu SJ, Horlbeck MA, Chen J, Replogle JM, Carosso GA, Eng NWL, Chang J, Shen Y, Weissman JS, Lim DA. Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells. Cell Genom. 2022 Nov 9;2(11):100177. doi: 10.1016/j.xgen.2022.100177. Epub 2022 Sep 14. PMID: 36381608; PMCID: PMC9648144.

  8. Jones IR, Ren X, Shen Y. High-throughput CRISPRi and CRISPRa technologies in 3D genome regulation for neuropsychiatric diseases. Human Molecular Genetics. 2022, Aug 16.

  9. Ravichandran M, Hu J, Cai C, Ward NP, Venida A, Foakes C, Kuljanin M, Yang A, Hennessey CJ, Yang Y, Desousa BR, Rademaker G, Staes AAL, Cakir Z, Jain IH, Aguirre AJ, Mancias JD, Shen Y, DeNicola GM, Perera RM. Coordinated transcriptional and catabolic programs support iron dependent adaptation to RAS-MAPK pathway inhibition in pancreatic cancer. Cancer Discov. 2022, Jun 30. PMID: 35771494.

  10. Yang H, Ting X, Geng YH, Xie Y, Nierenberg JL, Huo YF, Zhou YT, Huang Y, Yu YQ, Yu XY, Li ZF, Ziv E, Zhang H,Fang WG, Shen Y, Tian XX. The risk variant rs11836367 contributes to breast cancer onset and metastasis by attenuating Wnt signaling via regulating NTN4 expression. Sci Adv 2022, June 10.

  11. Ypsilanti AR, Pattabiraman K, Catta-Preta R, Golonzhka O, Lindtner S, Tang K, Jones IR, Abnousi A, Juric I, Hu M, Shen Y, Dickel DE, Visel A, Pennachio LA, Hawrylycz M, Thompson CL, Zeng H, Barozzi I, Nord AS, Rubenstein JL. Transcriptional network orchestrating regional patterning of cortical progenitors. PNAS, 2021, Dec 21.

  12. Li YE, Preissl S, Hou X, Zhang Z, Zhang K, Qiu Y, Poirion OB, Li B, Chiou J, Liu H, Pinto-Duarte A, Kubo N, Yang X, Fang R, Wang X, Han JY, Lucero J, Yan Y, Miller M, Kuan S, Gorkin D, Gaulton KJ, Shen Y, Nunn M, Mukamel EA, Behrens MM, Ecker JR, Ren B. An atlas of gene regulatory elements in adult mouse cerebrum. Nature, 2021, Oct 6.

  13. Ren X, Wang M, Li B, Jamieson K, Zheng L, Jones IR, Li B, Takagi MA, Lee J, Maliskova L, Tam TW, Yu M, Hu R, Lee L, Abnousi A, Li G, Li Y, Hu M, Ren B, Wang W, Shen Y. Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath. Sci Adv, 2021, Sep 17

  14. Ushiki A, Zhang Y, Xiong C, Zhao J, Georgakopoulos-Soares I, Kane L, Jamieson K, Bamshad MJ, Nickerson DA; University of Washington Center for Mendelian Genomics, Shen Y, Lettice LA, Silveira-Lucas EL, Petit F, Ahituv N. Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia. Nat Commun, 2021, Apr 16

  15. Wang X, Jiang W, Luo S, Yang X, Wang C, Wang B, Dang Y, Shen Y, Ma DK. The C. elegans homolog of human panic-disorder risk gene TMEM132D orchestrates neuronal morphogenesis through the WAVE-regulatory complex. Mol Brain, 2021, Mar 16.

  16. Song M, Pebworth MP, Yang X, Abnousi A, Fan C, Wen J, Rosen JD, Choudhary MNK, Cui X, Jones IR, Bergenholtz S, Eze UC, Juric I, Bingkun L, Maliskova L, Liu W, Pollen AA, Li Y, Wang T, Hu M, Kriegstein AR, Shen Y. Cell-type-specific 3D epigenomes in the developing human cortex. Nature, 2020, October 14.

  17. The ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi Ali, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chheteri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Bilber DM, Dekker J, Rinn J, Mendenhall EM, Ecker DR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry MJ, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. (2020) Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature, 2020, July 29. 

  18. Gorkin D, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, Afzal V, Akiyama JA, Plajzerv-Frick I, Novak CS, Kato M, Garvin TH, Pham QT, Harrington AN, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, He Y, Preissl S, Chee S, Han JY, Williams BA, Trout D, Amrhein H, Yang H, Cherry JM, Wang W, Gaulton K, Ecker JR, Shen Y, Dickel DE, Visel A, Pennacchio LA, Ren B. (2020) An atlas of dynamic chromatin landscapes in mouse fetal development. Nature, 2020, July 29.

  19. Yang X, Bergenholtz S, Maliskova L, Pebworth MP, Kriegstein AR, Li Y, Shen Y. (2020) SMART-Q: An Integrative Pipeline Quantifying Cell Type-Specific RNA Transcription. PLOS ONE, 2020, April 29.

  20. Huh R, Yang Y, Jiang Y, Shen Y, Li Y. (2019) SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble. Nucleic Acids Research, 2019, November 28.

  21. Song M, Yang X, Ren X, Maliskova L, Li B, Jones I, Wang C, Jacob F, Wu K, Traglia M, Tam TW, Jamieson K, Lu SY, Ming GL, Li Y, Yao J, Weiss LA, Dixon J, Judge LM, Conklin BR, Song H, Gan L, Shen Y. (2019) Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes. Nature Genetics, 2019, July 31.

  22. Alexander J, Guan J, Li B, Maliskova L, Song M, Shen Y, Huang B, Lomvardas S, Weiner OD. (2019) Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity. eLIFE, 2019, May 24.

  23. Zhan L, Krabbe G, Du F, Jones I, Reichert MC, Telpoukhovskaia M, Kodama L, Wang C, Cho S, Sayed F, Li Y, Le D, Zhou Y, Shen Y, West B, Gan L. (2019) Proximal recolonization by self-renewing microglia re-establishes microglial homeostasis in the adult mouse brain. PLos Biol, 2019 Feb 8.

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

  25. 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]

  26. 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]

  27. 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.

  28. 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).

  29. 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.

  30. 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)

  31. 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)

  32. 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.

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

  34. 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)

  35. 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.

  36. 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. 

  37. 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.

  38. 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.

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

  40. 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.

  41. 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.

  42. 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.

  43. 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.