Yin Shen, PhD
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Title(s) | Associate Professor, Neurology |
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School | School of Medicine |
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Address | 513 Parnassus Ave, HSE San Francisco CA 94143
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Phone | 415-502-3403 |
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ORCID
.gif) | 0000-0001-9901-5613  |
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vCard | Download vCard |
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Title(s) | UCSF Weill Institute for Neurosciences |
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Biography | 2016
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| 2018 | AFAR new investigator award in Alzheimer's disease | | 2016
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| 2019 | UCSF Weill Institute for Neurosciences Innovation Award |
Overview Research ORNG Applications Bibliographic
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.
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Click a Field or Translation tag to filter the publications.
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Cell-type-specific 3D epigenomes in the developing human cortex. Nature. 2020 Nov; 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.
View in: PubMed Mentions: Fields:
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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.
View in: PubMed Mentions: 1 Fields:
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Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 07; 583(7818):699-710.
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.
View in: PubMed Mentions: 9 Fields:
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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.
View in: PubMed Mentions: 1 Fields: Translation: HumansCells
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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.
View in: PubMed Mentions: 3 Fields: Translation: HumansCells
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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.
View in: PubMed Mentions: 11 Fields: Translation: HumansCells
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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.
View in: PubMed Mentions: 18 Fields: Translation: AnimalsCells
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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.
View in: PubMed Mentions: 16 Fields: Translation: AnimalsCells
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Gene regulation in the 3D genome. Hum Mol Genet. 2018 08 01; 27(R2):R228-R233.
Li Y, Hu M, Shen Y. PMID: 29767704.
View in: PubMed Mentions: 4 Fields: Translation: HumansAnimalsCells
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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.
View in: PubMed Mentions: 14 Fields: Translation: HumansAnimalsCells
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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.
View in: PubMed Mentions: 48 Fields: Translation: HumansCells
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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.
View in: PubMed Mentions: 23 Fields: Translation: HumansCells
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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.
View in: PubMed Mentions: 35 Fields: Translation: HumansCells
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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.
View in: PubMed Mentions: 356 Fields: Translation: HumansCells
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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. PMID: 25409824.
View in: PubMed Mentions: 455 Fields: Translation: HumansAnimalsCells
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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.
View in: PubMed Mentions: 19 Fields: Translation: HumansCells
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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.
View in: PubMed Mentions: 173 Fields: Translation: AnimalsCells
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An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012 Aug 13; 13(8):418.
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.
View in: PubMed Mentions: 231 Fields: Translation: HumansAnimals
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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.
View in: PubMed Mentions: 583 Fields: Translation: AnimalsCells
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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.
View in: PubMed Mentions: 400 Fields: Translation: HumansAnimalsCells
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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.
View in: PubMed Mentions: 1695 Fields: Translation: HumansAnimalsCells
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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.
View in: PubMed Mentions: 36 Fields: Translation: AnimalsCells
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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.
View in: PubMed Mentions: 20 Fields: Translation: HumansAnimalsCells
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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
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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.
View in: PubMed Mentions: 87 Fields: Translation: HumansCells
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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.
View in: PubMed Mentions: 183 Fields: Translation: AnimalsCells
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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: 34 Fields: Translation: HumansCells
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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: 145 Fields: Translation: AnimalsCells
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Year | Publications |
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2005 | 1 | 2006 | 1 | 2008 | 2 | 2009 | 1 | 2011 | 1 | 2012 | 5 | 2013 | 2 | 2014 | 1 | 2015 | 1 | 2016 | 1 | 2017 | 3 | 2018 | 1 | 2019 | 3 | 2020 | 5 |
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Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications.
Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written.
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This graph shows the number and percent of publications by field.
Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications.
Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written.
To see the data as text, click here.
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