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Yin Shen, Ph.D.
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Topological domains in mammalian genomes identified by analysis of chromatin interactions
JR Dixon, S Selvaraj, F Yue, A Kim, Y Li, Y Shen, M Hu, JS Liu, B Ren
Nature 485 (7398), 376-380, 2012
72312012
A comparative encyclopedia of DNA elements in the mouse genome
F Yue, Y Cheng, A Breschi, J Vierstra, W Wu, T Ryba, R Sandstrom, Z Ma, ...
Nature 515 (7527), 355-364, 2014
19932014
Chromatin architecture reorganization during stem cell differentiation
JR Dixon, I Jung, S Selvaraj, Y Shen, JE Antosiewicz-Bourget, AY Lee, ...
Nature 518 (7539), 331-336, 2015
17712015
A map of the cis-regulatory sequences in the mouse genome
Y Shen, F Yue, DF McCleary, Z Ye, L Edsall, S Kuan, U Wagner, J Dixon, ...
Nature 488 (7409), 116-120, 2012
15802012
Expanded encyclopaedias of DNA elements in the human and mouse genomes
JE Moore, MJ Purcaro, HE Pratt, CB Epstein, N Shoresh, J Adrian, T Kawli, ...
Nature 583 (7818), 699-710, 2020
14462020
Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome
M Yu, GC Hon, KE Szulwach, CX Song, L Zhang, A Kim, X Li, Q Dai, ...
Cell 149 (6), 1368-1380, 2012
11362012
Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation
SD Fouse, Y Shen, M Pellegrini, S Cole, A Meissner, L Van Neste, ...
Cell stem cell 2 (2), 160-169, 2008
5322008
Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues
GC Hon, N Rajagopal, Y Shen, DF McCleary, F Yue, MD Dang, B Ren
Nature genetics 45 (10), 1198-1206, 2013
5032013
DNA methylation controls the timing of astrogliogenesis through regulation of JAK-STAT signaling
G Fan, K Martinowich, MH Chin, F He, SD Fouse, L Hutnick, D Hattori, ...
Oxford University Press for The Company of Biologists Limited 132 (15), 3345 …, 2005
4962005
An encyclopedia of mouse DNA elements (Mouse ENCODE)
JA Stamatoyannopoulos, M Snyder, R Hardison, B Ren, T Gingeras, ...
Genome Biology 13 (8), 418, 2012
3762012
An atlas of dynamic chromatin landscapes in mouse fetal development
DU Gorkin, I Barozzi, Y Zhao, Y Zhang, H Huang, AY Lee, B Li, J Chiou, ...
Nature 583 (7818), 744-751, 2020
3052020
Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity
JM Alexander, J Guan, B Li, L Maliskova, M Song, Y Shen, B Huang, ...
elife 8, e41769, 2019
2982019
A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells
Y Diao, R Fang, B Li, Z Meng, J Yu, Y Qiu, KC Lin, H Huang, T Liu, ...
Nature methods 14 (6), 629-635, 2017
2852017
X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations
Y Shen, Y Matsuno, SD Fouse, N Rao, S Root, R Xu, M Pellegrini, ...
Proceedings of the National Academy of Sciences 105 (12), 4709-4714, 2008
2482008
Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes
M Song, X Yang, X Ren, L Maliskova, B Li, IR Jones, C Wang, F Jacob, ...
Nature genetics 51 (8), 1252-1262, 2019
1742019
A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening
Y Diao, B Li, Z Meng, I Jung, AY Lee, J Dixon, L Maliskova, K Guan, ...
Genome research 26 (3), 397-405, 2016
1562016
Proximal recolonization by self-renewing microglia re-establishes microglial homeostasis in the adult mouse brain
L Zhan, G Krabbe, F Du, I Jones, MC Reichert, M Telpoukhovskaia, ...
PLoS biology 17 (2), e3000134, 2019
1512019
An encyclopedia of mouse DNA elements (Mouse ENCODE)
EC Mouse, JA Stamatoyannopoulos, M Snyder, R Hardison, B Ren, ...
Genome Biol 13 (8), 418, 2012
1512012
An atlas of gene regulatory elements in adult mouse cerebrum
YE Li, S Preissl, X Hou, Z Zhang, K Zhang, Y Qiu, OB Poirion, B Li, ...
Nature 598 (7879), 129-136, 2021
1442021
Cell-type-specific 3D epigenomes in the developing human cortex
M Song, MP Pebworth, X Yang, A Abnousi, C Fan, J Wen, JD Rosen, ...
Nature 587 (7835), 644-649, 2020
1322020
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