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Yin Shen - Publications

Affiliations: 
University of California, San Francisco, San Francisco, CA 
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55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2025 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, ... ... Shen Y, et al. Comparative characterization of human accelerated regions in neurons. Nature. PMID 40011774 DOI: 10.1038/s41586-025-08622-x  0.397
2024 Bonev B, Gonçalo CB, 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, ... ... Shen Y, et al. Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery. Nature Neuroscience. 27: 2292-2309. PMID 39627587 DOI: 10.1038/s41593-024-01806-0  0.318
2024 Gjoni K, Ren X, Everitt A, Shen Y, Pollard KS. De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes. Biorxiv : the Preprint Server For Biology. PMID 39574698 DOI: 10.1101/2024.11.06.621353  0.384
2024 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, et al. Combinatorial transcription factor binding encodes cis-regulatory wiring of mouse forebrain GABAergic neurogenesis. Developmental Cell. PMID 39481376 DOI: 10.1016/j.devcel.2024.10.004  0.363
2024 Ren X, Zheng L, Maliskova L, Tam TW, Sun Y, Liu H, Lee J, Takagi MA, Li B, Ren B, Wang W, Shen Y. CRISPR tiling deletion screens reveal functional enhancers of neuropsychiatric risk genes and allelic compensation effects (ACE) on transcription. Biorxiv : the Preprint Server For Biology. PMID 39416108 DOI: 10.1101/2024.10.08.616922  0.525
2024 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, ... ... Shen Y, et al. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature Methods. PMID 38849569 DOI: 10.1038/s41592-024-02298-3  0.334
2024 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, ... ... Shen Y, et al. Multicenter integrated analysis of noncoding CRISPRi screens. Nature Methods. PMID 38504114 DOI: 10.1038/s41592-024-02216-7  0.317
2023 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. Molecular Cell. 83: 4633-4645.e9. PMID 38134886 DOI: 10.1016/j.molcel.2023.11.021  0.336
2023 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 : the Preprint Server For Biology. PMID 37502948 DOI: 10.1101/2023.07.12.548736  0.316
2023 Catta-Preta R, Lindtner S, Ypsilanti A, Price J, Abnousi A, Su-Feher L, Wang Y, Juric I, Jones IR, Akiyama JA, Hu M, Shen Y, Visel A, Pennacchio LA, Dickel D, et al. Combinatorial transcription factor binding encodes cis-regulatory wiring of forebrain GABAergic neurogenesis. Biorxiv : the Preprint Server For Biology. PMID 37425940 DOI: 10.1101/2023.06.28.546894  0.358
2023 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, ... ... Shen Y, et al. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Molecular Cell. PMID 37419111 DOI: 10.1016/j.molcel.2023.06.018  0.548
2023 Ren X, Takagi MA, Shen Y. Efficient bi-allelic tagging in human induced pluripotent stem cells using CRISPR. Star Protocols. 4: 102084. PMID 36853689 DOI: 10.1016/j.xpro.2023.102084  0.34
2022 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 Genomics. 2. PMID 36381608 DOI: 10.1016/j.xgen.2022.100177  0.358
2022 Jones IR, Ren X, Shen Y. High throughput CRISPRi and CRISPRa technologies in 3D genome regulation for neuropsychiatric diseases. Human Molecular Genetics. PMID 35972825 DOI: 10.1093/hmg/ddac193  0.321
2022 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, et al. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. PMID 35474001 DOI: 10.1038/s41586-021-04226-3  0.552
2021 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, ... ... Shen Y, et al. An atlas of gene regulatory elements in adult mouse cerebrum. Nature. 598: 129-136. PMID 34616068 DOI: 10.1038/s41586-021-03604-1  0.603
2021 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, ... ... Shen Y, et al. Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath. Science Advances. 7: eabi4360. PMID 34524848 DOI: 10.1126/sciadv.abi4360  0.453
2021 Ushiki A, Zhang Y, Xiong C, Zhao J, Georgakopoulos-Soares I, Kane L, Jamieson K, Bamshad MJ, Nickerson DA, 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. Nature Communications. 12: 2282. PMID 33863876 DOI: 10.1038/s41467-021-22470-z  0.365
2021 Shen Y, Chen LL, Gao J. CharPlant: A De Novo Open Chromatin Region Prediction Tool for Plant Genomes. Genomics, Proteomics & Bioinformatics. PMID 33662624 DOI: 10.1016/j.gpb.2020.06.021  0.403
2021 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, ... Shen Y, et al. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. PMID 33398137 DOI: 10.1038/s41586-020-03089-4  0.418
2020 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, ... ... Shen Y, et al. Cell-type-specific 3D epigenomes in the developing human cortex. Nature. PMID 33057195 DOI: 10.1038/s41586-020-2825-4  0.397
2020 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, ... Shen Y, et al. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. PMID 33037424 DOI: 10.1038/s41586-020-2841-4  0.396
2020 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, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 583: 699-710. PMID 32728249 DOI: 10.1038/S41586-020-2493-4  0.652
2020 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, ... ... Shen Y, et al. An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. 583: 744-751. PMID 32728240 DOI: 10.1038/S41586-020-2093-3  0.631
2020 Yang Y, Li G, Qian H, Wilhelmsen KC, Shen Y, Li Y. SMNN: batch effect correction for single-cell RNA-seq data via supervised mutual nearest neighbor detection. Briefings in Bioinformatics. PMID 32591778 DOI: 10.1093/Bib/Bbaa097  0.346
2020 Yang X, Bergenholtz S, Maliskova L, Pebworth MP, Kriegstein AR, Li Y, Shen Y. SMART-Q:  An Integrative Pipeline Quantifying Cell Type-Specific RNA Transcription. Plos One. 15: e0228760. PMID 32348304 DOI: 10.1371/Journal.Pone.0228760  0.378
2020 Sturtevant D, Lu S, Zhou ZW, Shen Y, Wang S, Song JM, Zhong J, Burks DJ, Yang ZQ, Yang QY, Cannon AE, Herrfurth C, Feussner I, Borisjuk L, Munz E, et al. The genome of jojoba (): A taxonomically isolated species that directs wax ester accumulation in its seeds. Science Advances. 6: eaay3240. PMID 32195345 DOI: 10.1126/Sciadv.Aay3240  0.315
2019 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, ... Shen Y, et al. Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes. Nature Genetics. 51: 1252-1262. PMID 31367015 DOI: 10.1038/S41588-019-0472-1  0.708
2019 Alexander JM, Guan J, Li B, Maliskova L, Song M, Shen Y, Huang B, Lomvardas S, Weiner OD. Live-cell imaging reveals enhancer-dependent transcription in the absence of enhancer proximity. Elife. 8. PMID 31124784 DOI: 10.7554/Elife.41769  0.436
2019 Alexander JM, Guan J, Li B, Maliskova L, Song M, Shen Y, Huang B, Lomvardas S, Weiner OD. Author response: Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity Elife. DOI: 10.7554/Elife.41769.054  0.328
2018 Li Y, Hu M, Shen Y. Gene Regulation in the 3D Genome. Human Molecular Genetics. PMID 29767704 DOI: 10.1093/Hmg/Ddy164  0.513
2017 Emmerson E, May A, Nathan S, Cruz Pacheco N, Lizama CO, Maliskova L, Zovein AC, Shen Y, Muench MO, Knox SM. SOX2 regulates acinar cell development in the salivary gland. Elife. 6. PMID 28623666 DOI: 10.7554/Elife.26620  0.39
2017 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. A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. Nature Methods. PMID 28417999 DOI: 10.1038/Nmeth.4264  0.764
2017 He Y, Gorkin DU, Dickel DE, Nery JR, Castanon RG, Lee AY, Shen Y, Visel A, Pennacchio LA, Ren B, Ecker JR. Improved regulatory element prediction based on tissue-specific local epigenomic signatures. Proceedings of the National Academy of Sciences of the United States of America. PMID 28193886 DOI: 10.1073/Pnas.1618353114  0.623
2017 Emmerson E, May AJ, Nathan S, Cruz-Pacheco N, Lizama CO, Maliskova L, Zovein AC, Shen Y, Muench MO, Knox SM. Author response: SOX2 regulates acinar cell development in the salivary gland Elife. DOI: 10.7554/Elife.26620.041  0.327
2016 Diao Y, Li B, Meng Z, Jung I, Lee A, Dixon J, Maliskova L, Guan KL, Shen Y, Ren B. A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9 mediated genetic screening. Genome Research. PMID 26813977 DOI: 10.1101/Gr.197152.115  0.792
2015 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, et al. Chromatin architecture reorganization during stem cell differentiation. Nature. 518: 331-6. PMID 25693564 DOI: 10.1038/Nature14222  0.777
2015 Yue F, Shen Y, Ye Z, Ren B. Abstract 2211: A comparative analysis of the cis-regulatory landscape between human and mouse Cancer Research. 75: 2211-2211. DOI: 10.1158/1538-7445.Am2015-2211  0.683
2014 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, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515: 355-64. PMID 25409824 DOI: 10.1038/Nature13992  0.748
2014 Huang K, Shen Y, Xue Z, Bibikova M, April C, Liu Z, Cheng L, Nagy A, Pellegrini M, Fan JB, Fan G. A panel of CpG methylation sites distinguishes human embryonic stem cells and induced pluripotent stem cells. Stem Cell Reports. 2: 36-43. PMID 24511466 DOI: 10.1016/J.Stemcr.2013.11.003  0.414
2013 Hon GC, Rajagopal N, Shen Y, McCleary DF, Yue F, Dang MD, Ren B. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nature Genetics. 45: 1198-206. PMID 23995138 DOI: 10.1038/Ng.2746  0.75
2013 Hon GC, Shen Y, McCleary DF, Edsall L, Kuan S, Ren B. Abstract 1111: Whole genome bisulfite sequencing reveals tissue-specific DNA methylation in a normal mouse. Cancer Research. 73: 1111-1111. DOI: 10.1158/1538-7445.Am2013-1111  0.749
2012 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, ... ... Shen Y, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology. 13: 418. PMID 22889292 DOI: 10.1186/Gb-2012-13-8-418  0.696
2012 Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B. A map of the cis-regulatory sequences in the mouse genome. Nature. 488: 116-20. PMID 22763441 DOI: 10.1038/Nature11243  0.784
2012 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. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell. 149: 1368-80. PMID 22608086 DOI: 10.1016/J.Cell.2012.04.027  0.738
2012 Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 485: 376-80. PMID 22495300 DOI: 10.1038/Nature11082  0.756
2012 Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS, Reiter JF. Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal. Plos Genetics. 8: e1002576. PMID 22438827 DOI: 10.1371/Journal.Pgen.1002576  0.58
2011 Wang A, Huang K, Shen Y, Xue Z, Cai C, Horvath S, Fan G. Functional modules distinguish human induced pluripotent stem cells from embryonic stem cells. Stem Cells and Development. 20: 1937-50. PMID 21542696 DOI: 10.1089/Scd.2010.0574  0.443
2009 Shen Y, Fouse SD, Fan G. Genome-wide DNA methylation profiling: the mDIP-chip technology. Methods in Molecular Biology (Clifton, N.J.). 568: 203-16. PMID 19582429 DOI: 10.1007/978-1-59745-280-9_13  0.475
2008 Fouse SD, Shen Y, Pellegrini M, Cole S, Meissner A, Van Neste L, Jaenisch R, Fan G. 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. 2: 160-9. PMID 18371437 DOI: 10.1016/J.Stem.2007.12.011  0.506
2008 Shen Y, Matsuno Y, Fouse SD, Rao N, Root S, Xu R, Pellegrini M, Riggs AD, Fan G. X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations. Proceedings of the National Academy of Sciences of the United States of America. 105: 4709-14. PMID 18339804 DOI: 10.1073/Pnas.0712018105  0.374
2006 Shen Y, Chow J, Wang Z, Fan G. Abnormal CpG island methylation occurs during in vitro differentiation of human embryonic stem cells. Human Molecular Genetics. 15: 2623-35. PMID 16870691 DOI: 10.1093/Hmg/Ddl188  0.444
2005 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. DNA methylation controls the timing of astrogliogenesis through regulation of JAK-STAT signaling. Development (Cambridge, England). 132: 3345-56. PMID 16014513 DOI: 10.1242/Dev.01912  0.436
1997 Huq AH, Sutcliffe JS, Nakao M, Shen Y, Gibbs RA, Beaudet AL. Sequencing and functional analysis of the SNRPN promoter: in vitro methylation abolishes promoter activity. Genome Research. 7: 642-8. PMID 9199937 DOI: 10.1101/Gr.7.6.642  0.372
1995 Timms KM, Lu F, Shen Y, Pierson CA, Muzny DM, Gu Y, Nelson DL, Gibbs RA. 130 kb of DNA sequence reveals two new genes and a regional duplication distal to the human iduronate-2-sulfate sulfatase locus. Genome Research. 5: 71-8. PMID 8717057 DOI: 10.1101/Gr.5.1.71  0.319
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