Yin Shen, PhD

Title(s)Professor, Neurology
SchoolSchool of Medicine
Address1651 4th Street, #581E
San Francisco CA 94158
PronounsShe/Her/Hers
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
    Study of Selective Cell and System Vulnerability in Alzheimer's Disease
    NIH/NIA R01AG079291May 1, 2023 - Apr 30, 2028
    Role: co-Principal Investigator
    Elucidate the roles of Alzheimer's disease risk genes and variants in gene expression and AD-related phenotypes
    NIH/NIA RF1AG079557Sep 15, 2022 - Aug 31, 2025
    Role: Principal Investigator
    Single Cell Characterization of FTLD-GRN
    NIH/NINDS RF1NS128908Sep 15, 2022 - Aug 31, 2025
    Role: co-Principal Investigator
    Dissecting functional roles of MeCP2 condensates in neurons with chemogenetic tools
    NIH/NIDA R21DA056293Aug 1, 2022 - Jul 31, 2024
    Role: Principal Investigator
    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 Bibliographic 
    Collapse selected 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. Comparative characterization of human accelerated regions in neurons. Nature. 2025 Apr; 640(8060):991-999. Cui X, Yang H, Cai C, Beaman C, Yang X, Liu H, Ren X, Amador Z, Jones IR, Keough KC, Zhang M, Fair T, Abnousi A, Mishra S, Ye Z, Hu M, Pollen AA, Pollard KS, Shen Y. PMID: 40011774.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    2. The PRC2.1 subcomplex opposes G1 progression through regulation of CCND1 and CCND2. Elife. 2025 Feb 04; 13. Longhurst AD, Wang K, Suresh HG, Ketavarapu M, Ward HN, Jones IR, Narayan V, Hundley FV, Hassan AZ, Boone C, Myers CL, Shen Y, Ramani V, Andrews BJ, Toczyski DP. PMID: 39903505; PMCID: PMC11793871.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    3. Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery. Nat Neurosci. 2024 Dec; 27(12):2292-2309. Bonev B, Castelo-Branco G, Chen F, Codeluppi S, Corces MR, Fan J, Heiman M, Harris K, Inoue F, Kellis M, Levine A, Lotfollahi M, Luo C, Maynard KR, Nitzan M, Ramani V, Satijia R, Schirmer L, Shen Y, Sun N, Green GS, Theis F, Wang X, Welch JD, Gokce O, Konopka G, Liddelow S, Macosko E, Ali Bayraktar O, Habib N, Nowakowski TJ. PMID: 39627587; PMCID: PMC11999325.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    4. Author Correction: MYC phase separation selectively modulates the transcriptome. Nat Struct Mol Biol. 2024 Nov; 31(11):1808. Yang J, Chung CI, Koach J, Liu H, Navalkar A, He H, Ma Z, Zhao Q, Yang X, He L, Mittag T, Shen Y, Weiss WA, Shu X. PMID: 38867115.
      View in: PubMed   Mentions:    Fields:    
    5. Combinatorial transcription factor binding encodes cis-regulatory wiring of mouse forebrain GABAergic neurogenesis. Dev Cell. 2025 Jan 20; 60(2):288-304.e6. Catta-Preta R, Lindtner S, Ypsilanti A, Seban N, Price JD, Abnousi A, Su-Feher L, Wang Y, Cichewicz K, Boerma SA, Juric I, Jones IR, Akiyama JA, Hu M, Shen Y, Visel A, Pennacchio LA, Dickel DE, Rubenstein JLR, Nord AS. PMID: 39481376; PMCID: PMC11753952.
      View in: PubMed   Mentions:    Fields:    
    6. The PRC2.1 Subcomplex Opposes G1 Progression through Regulation of CCND1 and CCND2. bioRxiv. 2024 Oct 16. Longhurst AD, Wang K, Suresh HG, Ketavarapu M, Ward HN, Jones IR, Narayan V, Hundley FV, Hassan AZ, Boone C, Myers CL, Shen Y, Ramani V, Andrews BJ, Toczyski DP. PMID: 38562687; PMCID: PMC10983909.
      View in: PubMed   Mentions:
    7. CRISPR tiling deletion screens reveal functional enhancers of neuropsychiatric risk genes and allelic compensation effects (ACE) on transcription. bioRxiv. 2024 Oct 10. Ren X, Zheng L, Maliskova L, Tam TW, Sun Y, Liu H, Lee J, Takagi MA, Li B, Ren B, Wang W, Shen Y. PMID: 39416108; PMCID: PMC11483005.
      View in: PubMed   Mentions:
    8. Widespread transposable element dysregulation in human aging brains with Alzheimer's disease. Alzheimers Dement. 2024 Nov; 20(11):7495-7517. Feng Y, Yang X, Hou Y, Zhou Y, Leverenz JB, Eng C, Pieper AA, Goate A, Shen Y, Cheng F. PMID: 39356058; PMCID: PMC11567813.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    9. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nat Methods. 2024 Jul; 21(7):1349-1363. Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez Martinez JM, Hunt T, Lagarde J, Liang CE, Li H, Meade MJ, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Çelik MH, Chen Y, Du MRM, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Li JL, Lienhard M, Mikheenko A, Mulligan D, Nip KM, Pertea M, Ritchie ME, Sim AD, Tang AD, Wan YK, Wang C, Wong BY, Yang C, Barnes I, Berry AE, Capella-Gutierrez S, Cousineau A, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Götz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Ren X, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Smith ML, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Maehr R, Shen Y, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Au KF, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN. PMID: 38849569; PMCID: PMC11543605.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansAnimalsCells
    10. MYC phase separation selectively modulates the transcriptome. Nat Struct Mol Biol. 2024 Oct; 31(10):1567-1579. Yang J, Chung CI, Koach J, Liu H, Navalkar A, He H, Ma Z, Zhao Q, Yang X, He L, Mittag T, Shen Y, Weiss WA, Shu X. PMID: 38811792; PMCID: PMC11479839.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    11. Deconvolution of polygenic risk score in single cells unravels cellular and molecular heterogeneity of complex human diseases. bioRxiv. 2024 May 14. Zhang S, Shu H, Zhou J, Rubin-Sigler J, Yang X, Liu Y, Cooper-Knock J, Monte E, Zhu C, Tu S, Li H, Tong M, Ecker JR, Ichida JK, Shen Y, Zeng J, Tsao PS, Snyder MP. PMID: 38798507; PMCID: PMC11118500.
      View in: PubMed   Mentions:
    12. A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex. Proc Natl Acad Sci U S A. 2024 May 14; 121(20):e2321711121. Liang XG, Hoang K, Meyerink BL, Kc P, Paraiso K, Wang L, Jones IR, Zhang Y, Katzman S, Finn TS, Tsyporin J, Qu F, Chen Z, Visel A, Kriegstein A, Shen Y, Pilaz LJ, Chen B. PMID: 38713624; PMCID: PMC11098099.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    13. Multicenter integrated analysis of noncoding CRISPRi screens. Nat Methods. 2024 Apr; 21(4):723-734. Yao D, Tycko J, Oh JW, Bounds LR, Gosai SJ, Lataniotis L, Mackay-Smith A, Doughty BR, Gabdank I, Schmidt H, Guerrero-Altamirano T, Siklenka K, Guo K, White AD, Youngworth I, Andreeva K, Ren X, Barrera A, Luo Y, Yardimci GG, Tewhey R, Kundaje A, Greenleaf WJ, Sabeti PC, Leslie C, Pritykin Y, Moore JE, Beer MA, Gersbach CA, Reddy TE, Shen Y, Engreitz JM, Bassik MC, Reilly SK. PMID: 38504114; PMCID: PMC11009116.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    14. Phase separation of YAP-MAML2 differentially regulates the transcriptome. Proc Natl Acad Sci U S A. 2024 Feb 13; 121(7):e2310430121. Chung CI, Yang J, Yang X, Liu H, Ma Z, Szulzewsky F, Holland EC, Shen Y, Shu X. PMID: 38315854; PMCID: PMC10873646.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    15. High-throughput PRIME-editing screens identify functional DNA variants in the human genome. Mol Cell. 2023 Dec 21; 83(24):4633-4645.e9. 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. PMID: 38134886; PMCID: PMC10766087.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    16. Functional characterization of Alzheimer's disease genetic variants in microglia. Nat Genet. 2023 Oct; 55(10):1735-1744. 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. PMID: 37735198; PMCID: PMC10939305.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    17. Efficient bi-allelic tagging in human induced pluripotent stem cells using CRISPR. STAR Protoc. 2023 03 17; 4(1):102084. Ren X, Takagi MA, Shen Y. PMID: 36853689; PMCID: PMC9918420.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    18. High-throughput CRISPRi and CRISPRa technologies in 3D genome regulation for neuropsychiatric diseases. Hum Mol Genet. 2022 10 20; 31(R1):R47-R53. Jones IR, Ren X, Shen Y. PMID: 35972825; PMCID: PMC9585669.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    19. Genetically encoded chemical crosslinking of RNA in vivo. Nat Chem. 2023 01; 15(1):21-32. Sun W, Wang N, Liu H, Yu B, Jin L, Ren X, Shen Y, Wang L. PMID: 36202986; PMCID: PMC9840682.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    20. Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells. Cell Genom. 2022 Nov 09; 2(11). 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. PMID: 36381608; PMCID: PMC9648144.
      View in: PubMed   Mentions: 11     Fields:    
    21. Coordinated Transcriptional and Catabolic Programs Support Iron-Dependent Adaptation to RAS-MAPK Pathway Inhibition in Pancreatic Cancer. Cancer Discov. 2022 09 02; 12(9):2198-2219. 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. PMID: 35771494; PMCID: PMC9444964.
      View in: PubMed   Mentions: 27     Fields:    Translation:Humans
    22. THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data. PLoS Genet. 2022 03; 18(3):e1010102. Rowland B, Huh R, Hou Z, Crowley C, Wen J, Shen Y, Hu M, Giusti-Rodríguez P, Sullivan PF, Li Y. PMID: 35259165; PMCID: PMC8932604.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    23. 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: 22     Fields:    Translation:Animals
    24. 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: 79     Fields:    Translation:HumansAnimalsCells
    25. 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: 12     Fields:    
    26. SMNN: batch effect correction for single-cell RNA-seq data via supervised mutual nearest neighbor detection. Brief Bioinform. 2021 05 20; 22(3). Yang Y, Li G, Qian H, Wilhelmsen KC, Shen Y, Li Y. PMID: 32591778; PMCID: PMC8324985.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    27. 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: 22     Fields:    Translation:HumansAnimalsCells
    28. 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: 6     Fields:    Translation:HumansAnimalsCells
    29. 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: 73     Fields:    Translation:HumansCells
    30. 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: 172     Fields:    Translation:HumansAnimalsCells
    31. 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: 948     Fields:    Translation:HumansAnimalsCells
    32. 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: 2     Fields:    Translation:HumansCells
    33. 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: 36     Fields:    Translation:HumansCells
    34. 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: 93     Fields:    Translation:HumansCells
    35. 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: 171     Fields:    Translation:AnimalsCells
    36. 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: 80     Fields:    Translation:AnimalsCells
    37. 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: 30     Fields:    Translation:HumansAnimalsCells
    38. 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: 52     Fields:    Translation:HumansAnimalsCells
    39. 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: 147     Fields:    Translation:HumansCells
    40. 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: 41     Fields:    Translation:HumansCells
    41. 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: 70     Fields:    Translation:HumansCells
    42. 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: 827     Fields:    Translation:HumansCells
    43. 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: 929     Fields:    Translation:HumansAnimalsCells
    44. 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.
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    45. 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.
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    46. 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.
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    47. 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.
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    48. 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.
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    49. 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.
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    50. 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.
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    51. 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.
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    52. Genome-wide DNA methylation profiling: the mDIP-chip technology. Methods Mol Biol. 2009; 568:203-16. Shen Y, Fouse SD, Fan G. PMID: 19582429.
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    53. 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.
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    54. 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.
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    55. 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.
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    56. 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.
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