Yin Shen, PhD

Title(s)Associate Professor, Neurology
SchoolSchool of Medicine
Address513 Parnassus Ave, HSE
San Francisco CA 94143
Phone415-502-3403
ORCID ORCID Icon0000-0001-9901-5613 Additional info
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    Other Positions
    Title(s)UCSF Weill Institute for Neurosciences


    Collapse Biography 
    Collapse Education and Training
    UCLAPh.D.Human Genetics
    Ludwig Institute for Cancer Research/UCSDPostdocGenomics and gene regulation
    UCSF2021Diversity, Equity, and Inclusion Champion Training
    Collapse Awards and Honors
    2016  - 2018AFAR new investigator award in Alzheimer's disease
    2016  - 2019UCSF Weill Institute for Neurosciences Innovation Award
    2021Weill Neurohub Investigator

    Collapse Overview 

    Collapse Research 
    Collapse Research Activities and Funding
    Charting the 3D epigenome in human brain development and diseases
    NIH U01DA052713Sep 30, 2020 - Aug 31, 2025
    Role: Principal Investigator
    Development of massively parallel reporter assays that use cognate promoters
    NIH/NHGRI 1R21HG010065May 1, 2018 - Apr 30, 2020
    Role: Principle Investigator
    Transcriptional regulation of BEST1 in retina pigment epithelium.
    NIH R01EY027789Sep 30, 2017 - Jun 30, 2022
    Role: Principal Investigator
    Functional characterization of Alzheimer's disease associated genetic variants
    NIH R01AG057497Sep 30, 2017 - May 31, 2022
    Role: Principal Investigator
    High throughput CRISPR-mediated functional validation of regulatory elements
    NIH UM1HG009402Feb 1, 2017 - Jan 31, 2022
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications
    Collapse Student Projects

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Transcriptional network orchestrating regional patterning of cortical progenitors. Proc Natl Acad Sci U S A. 2021 12 21; 118(51). 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. PMID: 34921112; PMCID: PMC8713794.
      View in: PubMed   Mentions:
    2. An atlas of gene regulatory elements in adult mouse cerebrum. Nature. 2021 10; 598(7879):129-136. 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. PMID: 34616068; PMCID: PMC8494637.
      View in: PubMed   Mentions:    Fields:    
    3. Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath. Sci Adv. 2021 Sep 17; 7(38):eabi4360. 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. PMID: 34524848; PMCID: PMC8443183.
      View in: PubMed   Mentions:    Fields:    
    4. Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia. Nat Commun. 2021 04 16; 12(1):2282. 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. PMID: 33863876; PMCID: PMC8052326.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    5. The C. elegans homolog of human panic-disorder risk gene TMEM132D orchestrates neuronal morphogenesis through the WAVE-regulatory complex. Mol Brain. 2021 03 16; 14(1):54. Wang X, Jiang W, Luo S, Yang X, Wang C, Wang B, Dang Y, Shen Y, Ma DK. PMID: 33726789; PMCID: PMC7962252.
      View in: PubMed   Mentions:    Fields:    
    6. Cell-type-specific 3D epigenomes in the developing human cortex. Nature. 2020 11; 587(7835):644-649. 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, Li B, Maliskova L, Lee J, Liu W, Pollen AA, Li Y, Wang T, Hu M, Kriegstein AR, Shen Y. PMID: 33057195; PMCID: PMC7704572.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    7. An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. 2020 07; 583(7818):744-751. Gorkin DU, 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, Plajzer-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. PMID: 32728240; PMCID: PMC7398618.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansAnimalsCells
    8. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 07; 583(7818):699-710. 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 A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. PMID: 32728249; PMCID: PMC7410828.
      View in: PubMed   Mentions: 129     Fields:    Translation:HumansAnimalsCells
    9. SMART-Q:  An Integrative Pipeline Quantifying Cell Type-Specific RNA Transcription. PLoS One. 2020; 15(4):e0228760. Yang X, Bergenholtz S, Maliskova L, Pebworth MP, Kriegstein AR, Li Y, Shen Y. PMID: 32348304; PMCID: PMC7190163.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    10. SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble. Nucleic Acids Res. 2020 01 10; 48(1):86-95. Huh R, Yang Y, Jiang Y, Shen Y, Li Y. PMID: 31777938; PMCID: PMC6943136.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    11. Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes. Nat Genet. 2019 08; 51(8):1252-1262. Song M, Yang X, Ren X, Maliskova L, Li B, Jones IR, Wang C, Jacob F, Wu K, Traglia M, Tam TW, Jamieson K, Lu SY, Ming GL, Li Y, Yao J, Weiss LA, Dixon JR, Judge LM, Conklin BR, Song H, Gan L, Shen Y. PMID: 31367015; PMCID: PMC6677164.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    12. Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity. Elife. 2019 05 24; 8. Alexander JM, Guan J, Li B, Maliskova L, Song M, Shen Y, Huang B, Lomvardas S, Weiner OD. PMID: 31124784; PMCID: PMC6534382.
      View in: PubMed   Mentions: 47     Fields:    Translation:AnimalsCells
    13. Proximal recolonization by self-renewing microglia re-establishes microglial homeostasis in the adult mouse brain. PLoS Biol. 2019 02; 17(2):e3000134. Zhan L, Krabbe G, Du F, Jones I, Reichert MC, Telpoukhovskaia M, Kodama L, Wang C, Cho SH, Sayed F, Li Y, Le D, Zhou Y, Shen Y, West B, Gan L. PMID: 30735499; PMCID: PMC6383943.
      View in: PubMed   Mentions: 33     Fields:    Translation:AnimalsCells
    14. Gene regulation in the 3D genome. Hum Mol Genet. 2018 08 01; 27(R2):R228-R233. Li Y, Hu M, Shen Y. PMID: 29767704; PMCID: PMC6061806.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    15. SOX2 regulates acinar cell development in the salivary gland. Elife. 2017 06 17; 6. Emmerson E, May AJ, Nathan S, Cruz-Pacheco N, Lizama CO, Maliskova L, Zovein AC, Shen Y, Muench MO, Knox SM. PMID: 28623666; PMCID: PMC5498133.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansAnimalsCells
    16. A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. Nat Methods. 2017 Jun; 14(6):629-635. 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 KL, Ren B. PMID: 28417999; PMCID: PMC5490986.
      View in: PubMed   Mentions: 84     Fields:    Translation:HumansCells
    17. Improved regulatory element prediction based on tissue-specific local epigenomic signatures. Proc Natl Acad Sci U S A. 2017 02 28; 114(9):E1633-E1640. He Y, Gorkin DU, Dickel DE, Nery JR, Castanon RG, Lee AY, Shen Y, Visel A, Pennacchio LA, Ren B, Ecker JR. PMID: 28193886; PMCID: PMC5338528.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
    18. A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening. Genome Res. 2016 Mar; 26(3):397-405. Diao Y, Li B, Meng Z, Jung I, Lee AY, Dixon J, Maliskova L, Guan KL, Shen Y, Ren B. PMID: 26813977; PMCID: PMC4772021.
      View in: PubMed   Mentions: 47     Fields:    Translation:HumansCells
    19. Chromatin architecture reorganization during stem cell differentiation. Nature. 2015 Feb 19; 518(7539):331-6. 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. PMID: 25693564; PMCID: PMC4515363.
      View in: PubMed   Mentions: 504     Fields:    Translation:HumansCells
    20. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 2014 Nov 20; 515(7527):355-64. Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B, Mouse ENCODE Consortium. PMID: 25409824; PMCID: PMC4266106.
      View in: PubMed   Mentions: 606     Fields:    Translation:HumansAnimalsCells
    21. A panel of CpG methylation sites distinguishes human embryonic stem cells and induced pluripotent stem cells. Stem Cell Reports. 2014 Jan 14; 2(1):36-43. Huang K, Shen Y, Xue Z, Bibikova M, April C, Liu Z, Cheng L, Nagy A, Pellegrini M, Fan JB, Fan G. PMID: 24511466; PMCID: PMC3916755.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    22. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat Genet. 2013 Oct; 45(10):1198-206. Hon GC, Rajagopal N, Shen Y, McCleary DF, Yue F, Dang MD, Ren B. PMID: 23995138; PMCID: PMC4095776.
      View in: PubMed   Mentions: 219     Fields:    Translation:AnimalsCells
    23. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012 Aug 13; 13(8):418. Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB. PMID: 22889292; PMCID: PMC3491367.
      View in: PubMed   Mentions: 246     Fields:    Translation:HumansAnimals
    24. A map of the cis-regulatory sequences in the mouse genome. Nature. 2012 Aug 02; 488(7409):116-20. Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B. PMID: 22763441; PMCID: PMC4041622.
      View in: PubMed   Mentions: 666     Fields:    Translation:AnimalsCells
    25. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell. 2012 Jun 08; 149(6):1368-80. 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. PMID: 22608086; PMCID: PMC3589129.
      View in: PubMed   Mentions: 440     Fields:    Translation:HumansAnimalsCells
    26. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012 Apr 11; 485(7398):376-80. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. PMID: 22495300; PMCID: PMC3356448.
      View in: PubMed   Mentions: 2208     Fields:    Translation:HumansAnimalsCells
    27. Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal. PLoS Genet. 2012; 8(3):e1002576. Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS, Reiter JF. PMID: 22438827; PMCID: PMC3305387.
      View in: PubMed   Mentions: 40     Fields:    Translation:AnimalsCells
    28. Functional modules distinguish human induced pluripotent stem cells from embryonic stem cells. Stem Cells Dev. 2011 Nov; 20(11):1937-50. Wang A, Huang K, Shen Y, Xue Z, Cai C, Horvath S, Fan G. PMID: 21542696; PMCID: PMC3202894.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimalsCells
    29. Genome-wide DNA methylation profiling: the mDIP-chip technology. Methods Mol Biol. 2009; 568:203-16. Shen Y, Fouse SD, Fan G. PMID: 19582429.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    30. X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations. Proc Natl Acad Sci U S A. 2008 Mar 25; 105(12):4709-14. Shen Y, Matsuno Y, Fouse SD, Rao N, Root S, Xu R, Pellegrini M, Riggs AD, Fan G. PMID: 18339804; PMCID: PMC2290804.
      View in: PubMed   Mentions: 92     Fields:    Translation:HumansCells
    31. Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell. 2008 Feb 07; 2(2):160-9. Fouse SD, Shen Y, Pellegrini M, Cole S, Meissner A, Van Neste L, Jaenisch R, Fan G. PMID: 18371437; PMCID: PMC3070208.
      View in: PubMed   Mentions: 193     Fields:    Translation:AnimalsCells
    32. Abnormal CpG island methylation occurs during in vitro differentiation of human embryonic stem cells. Hum Mol Genet. 2006 Sep 01; 15(17):2623-35. Shen Y, Chow J, Wang Z, Fan G. PMID: 16870691.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansCells
    33. DNA methylation controls the timing of astrogliogenesis through regulation of JAK-STAT signaling. Development. 2005 Aug; 132(15):3345-56. Fan G, Martinowich K, Chin MH, He F, Fouse SD, Hutnick L, Hattori D, Ge W, Shen Y, Wu H, ten Hoeve J, Shuai K, Sun YE. PMID: 16014513.
      View in: PubMed   Mentions: 167     Fields:    Translation:AnimalsCells
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