Publications
(*These authors contributed equally. # Co-corresponding authors.)
2026
De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes.
Ketrin Gjoni, Xingjie Ren, Amanda Everitt, Yin Shen, and Katherine S. Pollard.
Genome Research - July 8, 2026
A druggable link between the angiotensin receptor 1 and α-synuclein pathology revealed in scalable human cellular models of Parkinson’s disease.
Daynac M, Mouilleau V, Liu Y, Yang X, Shen Y, Su Guo.
Molecular Neurodegeneration Advances (Volume 2, Article 32) - Jun 25, 2026
CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription.
Ren X, Zheng L, Liu Y, Maliskova L, Tam TW, Sun Y, Liu H, Cui X, Lee J, Takagi MA, Li B, Ren B, Wang W, Shen Y.
Nature Communications - Mar 25, 2026
2025
Cell-type specific inference from bulk RNA-sequencing data by integrating single-cell reference profiles via EPIC-unmix.
Tang C, Sun Q, Zeng X, Li G, Yang X, Liu F, Zhao J, Shen Y, Liu B, Wen J, Li Y.
Genome Biology - Nov 20, 2025
Single-cell polygenic risk scores dissect cellular and molecular heterogeneity of complex human diseases.
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.
Nature Biotechnology - July 25, 2025
Comparative characterization of human accelerated regions in neurons.
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. Nature - Feb 26, 2025
2024
Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.
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, 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#, Bayraktar O#, Habib N#, Nowakowski TJ#.
Nature Neuroscience - Dec 27, 2024
The PRC2.1 Subcomplex Opposes G1 Progression through Regulation of CCND1 and CCND2.
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.
eLife - Dec 5, 2024
Combinatorial transcription factor binding encodes cis-regulatory wiring of forebrain GABAergic neurogenesis.
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#.
Developmental Cell. - Oct 30, 2024
Widespread transposable element dysregulation in human aging brains with Alzheimer's disease.
Feng Y, Yang X, Hou Y, Zhou Y, Leverenz JB, Eng C, Pieper AA, Goate A, Shen Y, Cheng F.
Alzheimers Dementia - Oct 2, 2024
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
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#.
Nature Methods - Jul 21, 2024
MYC phase separation selectively modulates the transcriptome.
Yang J*, Chung C-I*, Koach J, Liu H, Navalkar A, He H, Ma Z, Zhao Q, Yang X, He L, Mittag T, Shen Y, Weiss WA, Shu X.
Nature Structural & Molecular Biology - May 29, 2024
A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex.
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.
PNAS - May 14, 2024
Multicenter integrated analysis of noncoding CRISPRi screens.
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, Yardımcı GG, Tewhey R, Kundaje A, Greenleaf WJ, Sabeti PC, Leslie C, Pritykin Y, Moore JE, Beer MA, Gersbach CA, Reddy TE, Shen Y, Engreitz JE, Bassik MC, Reilly SK#.
Nature Methods - Mar 19, 2024
Phase separation of YAP-MAML2 differentially regulates the transcriptome.
Chung C-I, Yang J, Yang X, Liu H, Ma Z, Szulzewsky F, Holland EC, Shen Y, Shu X.
PNAS - Feb 13, 2024
2023
High throughput PRIME editing screens identify functional DNA variants in the human genome.
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.
Molecular Cell - Dec 21, 2023
Functional characterization of gene regulatory elements and neuropsychiatric disease-associated risk loci in iPSCs and iPSC-derived neurons.
Yang X*, Jones IR*, Chen PB*, Yang H*, Ren X*, Zheng L, Li B, Li YE, Sun Q, Wen J, Beaman C, Cui X, Li Y, Wang W, Hu M, Ren B#, Shen Y#.
bioRxiv - Aug 30, 2023
Functional characterization of Alzheimer’s disease genetic variants in microglia.
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#.
Nature Genetics - Sep 21, 2023
Linking non-coding variants to function in microglia in alzheimer’s disease. [Research Briefing]
Nature Genetics - Sep 21, 2023
Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.
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, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S.
Molecular Cell - Aug 3, 2023
Efficient bi-allelic tagging in human induced pluripotent stem cells using CRISPR.
Ren X, Takagi MA, Shen Y.
STAR Protocols - Feb 1, 2023
Genetically encoded chemical crosslinking of RNA in vivo.
Sun W*, Wang N*, Liu H, Yu B, Jin L, Ren X, Shen Y, Wang L.
Nature Chemistry - Jan 15, 2023
2022
Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells.
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.
Cell Genomics - Nov 9, 2022
High-throughput CRISPRi and CRISPRa technologies in 3D genome regulation for neuropsychiatric diseases.
Jones IR, Ren X, Shen Y.
Human Molecular Genetics - Aug 16, 2022
Coordinated transcriptional and catabolic programs support iron dependent adaptation to RAS-MAPK pathway inhibition in pancreatic cancer.
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.
Cancer Discov. - Jun 30, 2022
The risk variant rs11836367 contributes to breast cancer onset and metastasis by attenuating Wnt signaling via regulating NTN4 expression.
Yang H, Ting X, Geng YH, Xie Y, Nierenberg JL, Huo YF, Zhou YT, Huang Y, Yu YQ, Yu XY, Li ZF, Ziv E, Zhang H,Fang WG, Shen Y, Tian XX.
Sci Adv - June 10, 2022
THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data.
Rowland B, Huh R, Hou Z, Crowley C, Wen J, Shen Y, Hu M, Giusti-Rodríguez P, Sullivan PF, Li Y.
PLoS Genet. - Mar 8, 2022
2021
Transcriptional network orchestrating regional patterning of cortical progenitors.
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.
PNAS - Dec 21, 2021
An atlas of gene regulatory elements in adult mouse cerebrum.
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.
Nature - Oct , 2021
Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath.
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.
Science Advances - Sep 17, 2021
HPRep: Quantifying Reproducibility in HiChIP and PLAC-Seq Datasets
Rosen, J. D., Yang, Y., Abnousi, A., Chen, J., Song, M., Jones, I. R., Shen, Y., Hu, M., & Li, Y. (2021). .
Current Issues in Molecular Biology - Sep 17, 2021
SMNN: batch effect correction for single-cell RNA-seq data via supervised mutual nearest neighbor detection.
Yang Y*, Li G*, Qian H, Wilhelmsen KC, Shen Y, Li Y.
Briefings in Bioinformatics - May 20, 2021
Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia.
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.
Nature Communications - Apr 16, 2021
The C. elegans homolog of human panic-disorder risk gene TMEM132D orchestrates neuronal morphogenesis through the WAVE-regulatory complex.
Wang X*, Jiang W*, Luo S, Yang X, Wang C, Wang B, Dang Y, Shen Y, Ma DK.
Molecular Brain - Mar 16, 2021
2020
Cell-type-specific 3D epigenomes in the developing human cortex.
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, Bingkun L, Maliskova L, Liu W, Pollen AA, Li Y, Wang T, Hu M*,#, Kriegstein AR#, Shen Y#.
Nature - Nov 14, 2020
Expanded encyclopaedias of DNA elements in the human and mouse genomes.
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.
Nature - Jul 29, 2020
An atlas of dynamic chromatin landscapes in mouse fetal development.
Gorkin D*, 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, Plajzerv-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.
Nature - Jul 29, 2020
SMART-Q: An Integrative Pipeline Quantifying Cell Type-Specific RNA Transcription.
Yang X, Bergenholtz S, Maliskova L, Pebworth MP, Kriegstein AR, Li Y, Shen Y.
PLoS One - Apr 29, 2020
SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble.
Huh R, Yang Y, Jiang Y, Shen Y, Li Y.
Nucleic Acids Research - Jan 10, 2020
2019
Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes.
Song M, Yang X, Ren X, Maliskova L, Li B, Jones I, Wang C, Jacob F, Wu K, Traglia M, Tam TW, Jamieson K, Lu SY, Ming GL, Li Y, Yao J, Weiss LA, Dixon J, Judge LM, Conklin BR, Song H, Gan L, Shen Y.
Nature Genetics - Jul 31, 2019
Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity.
Alexander J, Guan J, Li B, Maliskova L, Song M, Shen Y, Huang B, Lomvardas S, Weiner OD.
eLIFE - May 24, 2019
Proximal recolonization by self-renewing microglia re-establishes microglial homeostasis in the adult mouse brain.
Zhan L, Krabbe G, Du F, Jones I, Reichert MC, Telpoukhovskaia M, Kodama L, Wang C, Cho S, Sayed F, Li Y, Le D, Zhou Y, Shen Y, West B, Gan L.
PLos Biology - Feb 8, 2019
2018 and Earlier
Gene regulation in the 3D genome.
Human Molecular Genetics - Aug 1, 2018
Li Y, Hu M, Shen Y.
SOX2 regulates acinar cell development in the salivary gland.
eLIFE - Jun 17, 2017
Emmerson E, May A, Nathan S, Pacheco NC, Lizama CO, Maliskova L, Zovein AC, Shen Y, Muench MO, Knox SM.
A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells.
Nature Methods - Jun , 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 K, Ren B.
Improved regulatory element prediction based on tissue-specific local epigenomic signatures.
PNAS - Feb 28, 2017
He Y, Gorkin D, Dickel D, Nery J, Castanon R, Lee AY, Shen Y, Visel A, Pennacchio L, Ren B, Ecker J.
Chromatin architecture reorganization during stem cell differentiation.
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.
Nature - Feb 19, 2015
A New Class of Temporarily Phenotypic Enhancers Identified by CRISPR/Cas9 Mediated Genetic Screening.
Diao Y*, Li B, Young I, Lee AY, Meng Z, Maliskova L, Guan K, Shen Y*,#, Ren B#.
Genome Research - Jan 26, 2016
A comparative encyclopedia of DNA elements in the mouse genome.
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.
Nature - Nov 20, 2014
A panel of CpG methylation patterns distinguishes human embryonic stem cells and induced pluripotent stem cells.
Huang K*, Shen Y*, Xue Z, Bibikova M, April C, Liu Z, Cheng L, Nagy A, Pellegrini M, Fan JB, Fan G.
Stem Cell Reports - Dec 26, 2013
Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues.
Hon GC, Rajagopal N, Shen Y, McCleary DF, Yue F, Dang MD, Ren B.
Nature Genetics - Sep 1, 2013
An encyclopedia of mouse DNA elements (Mouse ENCODE).
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.
Genome Biology - Aug 13, 2012
A map of cis-regulatory sequences in the mouse genome.
Shen Y*, Yue F*, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B.
Nature - Aug 2, 2012
Topological domains in mammalian genomes identified by analysis of chromatin interactions.
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B.
Nature - Apr 11, 2012
Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome.
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.
Cell - Jun 8, 2012
Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal.
Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS#, Reiter JF#.
PLoS Genetics - March 15, 2012
Functional Modules Distinguish Human Induced Pluripotent Stem Cells from Embryonic Stem Cells.
Wang A, Huang K, Shen Y, Xue Z, Cai C, Horvath S, Fan G.
Stem Cells and Development - Nov 20, 2011
Genome-wide DNA methylation profiling: the mDIP- Chip technology.
Shen Y, Fouse SD, and Fan G.
Methods Molecular Biology - June 7, 2009
X-inactivation in female human embryonic stem cells is in a non-random pattern and prone to epigenetic alterations.
Shen Y, Matsuno Y, Fouse S, Rao N, Root S, Xu RH, Pellegrini M, Riggs A, and Fan G. PNAS - Mar 25, 2008
Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, Polycomb binding and histone H3 lys4/lys27 trimethylation.
Fouse S, Shen Y, Pellegrini M, Cole S, Meissner A, Van Neste L, Jaenisch R, and Fan G. Cell
Stem Cell - Feb 7, 2008
Abnormal CpG island methylation occurs during in vitro differentiation of human embryonic stem cells.
Shen Y, Chow J, Wang Z, Fan G.
Human Molecular Genetics - Sep 1, 2006
DNA methylation controls the timing of astrogliogenesis through regulation of JAK-STAT signaling.
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#.
Development - Aug 1, 2005