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Deyou Zheng, Ph.D. - Publications

Affiliations: 
Albert Einstein College of Medicine, New York, New York, United States 
 2003 Rutgers University, New Brunswick, New Brunswick, NJ, United States 
Area:
Biochemistry, General Biophysics
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Year Citation  Score
2021 Cohen I, Bar C, Liu H, Valdes VJ, Zhao D, Galbo PM, Silva JM, Koseki H, Zheng D, Ezhkova E. Polycomb complexes redundantly maintain epidermal stem cell identity during development. Genes & Development. PMID 33602871 DOI: 10.1101/gad.345363.120  0.301
2020 Adam RC, Yang H, Ge Y, Infarinato NR, Gur-Cohen S, Miao Y, Wang P, Zhao Y, Lu CP, Kim JE, Ko JY, Paik SS, Gronostajski RM, Kim J, Krueger JG, ... Zheng D, et al. NFI transcription factors provide chromatin access to maintain stem cell identity while preventing unintended lineage fate choices. Nature Cell Biology. PMID 32393888 DOI: 10.1038/S41556-020-0513-0  0.391
2020 Liu H, Barnes J, Pedrosa E, Herman NS, Salas F, Wang P, Zheng D, Lachman HM. Transcriptome analysis of neural progenitor cells derived from Lowe syndrome induced pluripotent stem cells: identification of candidate genes for the neurodevelopmental and eye manifestations. Journal of Neurodevelopmental Disorders. 12: 14. PMID 32393163 DOI: 10.1186/S11689-020-09317-2  0.346
2019 Martynova E, Zhao Y, Xie Q, Zheng D, Cvekl A. Transcriptomic analysis and novel insights into lens fibre cell differentiation regulated by Gata3. Open Biology. 9: 190220. PMID 31847788 DOI: 10.1098/Rsob.190220  0.397
2019 Ji Z, Kiparaki M, Folgado V, Kumar A, Blanco J, Rimesso G, Chuen J, Liu Y, Zheng D, Baker NE. Drosophila RpS12 controls translation, growth, and cell competition through Xrp1. Plos Genetics. 15: e1008513. PMID 31841522 DOI: 10.1371/Journal.Pgen.1008513  0.377
2019 Ito K, Lee J, Chrysanthou S, Zhao Y, Josephs K, Sato H, Teruya-Feldstein J, Zheng D, Dawlaty MM, Ito K. Non-catalytic Roles of Tet2 Are Essential to Regulate Hematopoietic Stem and Progenitor Cell Homeostasis. Cell Reports. 28: 2480-2490.e4. PMID 31484061 DOI: 10.1016/J.Celrep.2019.07.094  0.352
2019 Ravichandran M, Lei R, Tang Q, Zhao Y, Lee J, Ma L, Chrysanthou S, Lorton BM, Cvekl A, Shechter D, Zheng D, Dawlaty MM. Rinf Regulates Pluripotency Network Genes and Tet Enzymes in Embryonic Stem Cells. Cell Reports. 28: 1993-2003.e5. PMID 31433977 DOI: 10.1016/J.Celrep.2019.07.080  0.421
2019 Ren Z, Ahn JH, Liu H, Tsai YH, Bhanu NV, Koss B, Allison DF, Ma A, Storey AJ, Wang P, Mackintosh SG, Edmondson RD, Groen RWJ, Martens AC, Garcia BA, ... ... Zheng D, et al. PHF19 promotes multiple myeloma tumorigenicity through PRC2 activation. Blood. PMID 31383640 DOI: 10.1182/Blood.2019000578  0.388
2019 Liu Y, Lu P, Wang Y, Morrow BE, Zhou B, Zheng D. Spatiotemporal Gene Coexpression and Regulation in Mouse Cardiomyocytes of Early Cardiac Morphogenesis. Journal of the American Heart Association. 8: e012941. PMID 31322043 DOI: 10.1161/Jaha.119.012941  0.38
2019 Bar C, Cohen I, Zhao D, Pothula V, Litskevitch A, Koseki H, Zheng D, Ezhkova E. Polycomb Repressive Complex 1 Controls Maintenance of Fungiform Papillae by Repressing Sonic Hedgehog Expression. Cell Reports. 28: 257-266.e5. PMID 31269445 DOI: 10.1016/J.Celrep.2019.06.011  0.384
2019 Zhao Y, Zheng D, Cvekl A. Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways. Epigenetics & Chromatin. 12: 27. PMID 31053165 DOI: 10.1186/S13072-019-0272-Y  0.404
2019 Limi S, Zhao Y, Guo P, Lopez-Jones M, Zheng D, Singer RH, Skoultchi AI, Cvekl A. Bidirectional Analysis of Cryba4-Crybb1 Nascent Transcription and Nuclear Accumulation of Crybb3 mRNAs in Lens Fibers. Investigative Ophthalmology & Visual Science. 60: 234-244. PMID 30646012 DOI: 10.1167/Iovs.18-25921  0.387
2019 Lee E, Wongvipat J, Choi D, Wang P, Lee YS, Zheng D, Watson PA, Gopalan A, Sawyers CL. amplifies androgen receptor output in human prostate cancer and contributes to antiandrogen resistance. Elife. 8. PMID 30644358 DOI: 10.7554/Elife.41913  0.328
2019 Wang P, Mokhtari R, Pedrosa E, Zheng D, Lachman H. Transcriptome Analysis Of Wnt7A-Mediated Gene Expression In Human Neural Progenitor Cells Derived From Control And Chd8 Haploinsufficient Induced Pluripotent Stem Cells European Neuropsychopharmacology. 29. DOI: 10.1016/J.Euroneuro.2017.08.203  0.407
2018 Cohen I, Zhao D, Menon G, Nakayama M, Koseki H, Zheng D, Ezhkova E. PRC1 preserves epidermal tissue integrity independently of PRC2. Genes & Development. PMID 30567998 DOI: 10.1101/Gad.319939.118  0.372
2018 Diacou R, Zhao Y, Zheng D, Cvekl A, Liu W. Six3 and Six6 Are Jointly Required for the Maintenance of Multipotent Retinal Progenitors through Both Positive and Negative Regulation. Cell Reports. 25: 2510-2523.e4. PMID 30485816 DOI: 10.1016/J.Celrep.2018.10.106  0.363
2018 Zhao Y, Wilmarth PA, Cheng C, Limi S, Fowler VM, Zheng D, David LL, Cvekl A. Proteome-transcriptome analysis and proteome remodeling in mouse lens epithelium and fibers. Experimental Eye Research. PMID 30359574 DOI: 10.1016/J.Exer.2018.10.011  0.336
2018 Zhao Y, Zheng D, Cvekl A. A comprehensive spatial-temporal transcriptomic analysis of differentiating nascent mouse lens epithelial and fiber cells. Experimental Eye Research. PMID 29883638 DOI: 10.1016/J.Exer.2018.06.004  0.37
2018 Cohen I, Zhao D, Bar C, Valdes VJ, Dauber-Decker KL, Nguyen MB, Nakayama M, Rendl M, Bickmore WA, Koseki H, Zheng D, Ezhkova E. PRC1 Fine-tunes Gene Repression and Activation to Safeguard Skin Development and Stem Cell Specification. Cell Stem Cell. 22: 726-739.e7. PMID 29727681 DOI: 10.1016/J.Stem.2018.04.005  0.391
2018 Xu B, Cai L, Butler JM, Chen D, Lu X, Allison DF, Lu R, Rafii S, Parker JS, Zheng D, Wang GG. The Chromatin Remodeler BPTF Activates a Stemness Gene-Expression Program Essential for the Maintenance of Adult Hematopoietic Stem Cells. Stem Cell Reports. PMID 29456179 DOI: 10.1016/J.Stemcr.2018.01.020  0.386
2018 Adam RC, Yang H, Ge Y, Lien WH, Wang P, Zhao Y, Polak L, Levorse J, Baksh SC, Zheng D, Fuchs E. Temporal Layering of Signaling Effectors Drives Chromatin Remodeling during Hair Follicle Stem Cell Lineage Progression. Cell Stem Cell. PMID 29337183 DOI: 10.1016/J.Stem.2017.12.004  0.351
2018 Wang P, Zhao D, Lachman HM, Zheng D. Enriched expression of genes associated with autism spectrum disorders in human inhibitory neurons. Translational Psychiatry. 8: 13. PMID 29317598 DOI: 10.1038/S41398-017-0058-6  0.321
2018 Ran L, Chen Y, Wong WPE, Li D, Cao Z, Shukla S, Xie Y, Zheng D, Koche RP, Antonescu CR, Chen Y, Chi P. Abstract 3358: FOXF1 defines the core-regulatory circuitry in gastrointestinal stromal tumor (GIST) Cancer Research. 78: 3358-3358. DOI: 10.1158/1538-7445.Am2018-3358  0.341
2018 Cohen I, Zhao D, Zheng D, Ezhkova E. 1358 PRC1 fine-tunes gene repression and activation to safeguard skin epithelium development and stem cell specification Journal of Investigative Dermatology. 138. DOI: 10.1016/J.Jid.2018.03.1375  0.356
2017 Zhang D, Wang Y, Lu P, Wang P, Yuan X, Yan J, Cai C, Chang CP, Zheng D, Wu B, Zhou B. REST regulates the cell cycle for cardiac development and regeneration. Nature Communications. 8: 1979. PMID 29215012 DOI: 10.1038/S41467-017-02210-Y  0.337
2017 Ran L, Chen Y, Sher J, Wong WPE, Murphy D, Zhang JQ, Li D, Deniz K, Sirota I, Cao Z, Wang S, Guan Y, Shukla S, Li KY, Chramiec A, ... ... Zheng D, et al. FOXF1 defines the core-regulatory circuitry in gastrointestinal stromal tumor (GIST). Cancer Discovery. PMID 29162563 DOI: 10.1158/2159-8290.Cd-17-0468  0.352
2017 Zhao D, Lin M, Pedrosa E, Lachman HM, Zheng D. Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis. Bmc Genomics. 18: 860. PMID 29126398 DOI: 10.1186/S12864-017-4261-X  0.359
2017 Seki Y, Suzuki M, Guo X, Glenn AS, Vuguin PM, Fiallo A, Du Q, Ko YA, Yu Y, Susztak K, Zheng D, Greally JM, Katz EB, Charron MJ. In Utero Exposure to a High-Fat Diet Programs Hepatic Hypermethylation and Gene Dysregulation and Development of Metabolic Syndrome in Male Mice. Endocrinology. 158: 2860-2872. PMID 28911167 DOI: 10.1210/En.2017-00334  0.344
2017 Cvekl A, Zhao Y, McGreal R, Xie Q, Gu X, Zheng D. Evolutionary Origins of Pax6 Control of Crystallin Genes. Genome Biology and Evolution. 9: 2075-2092. PMID 28903537 DOI: 10.1093/Gbe/Evx153  0.372
2017 Cavalheiro GR, Matos-Rodrigues GE, Zhao Y, Gomes AL, Anand D, Predes D, de Lima S, Abreu JG, Zheng D, Lachke SA, Cvekl A, Martins RAP. N-myc regulates growth and fiber cell differentiation in lens development. Developmental Biology. PMID 28716713 DOI: 10.1016/J.Ydbio.2017.07.002  0.358
2017 Bose R, Karthaus WR, Armenia J, Abida W, Iaquinta PJ, Zhang Z, Wongvipat J, Wasmuth EV, Shah N, Sullivan PS, Doran MG, Wang P, Patruno A, Zhao Y, ... Zheng D, et al. ERF mutations reveal a balance of ETS factors controlling prostate oncogenesis. Nature. PMID 28614298 DOI: 10.1038/Nature22820  0.329
2017 Zhao D, Mokhtari R, Pedrosa E, Birnbaum R, Zheng D, Lachman HM. Transcriptome analysis of microglia in a mouse model of Rett syndrome: differential expression of genes associated with microglia/macrophage activation and cellular stress. Molecular Autism. 8: 17. PMID 28367307 DOI: 10.1186/S13229-017-0134-Z  0.37
2017 Racedo SE, Hasten E, Lin M, Devakanmalai GS, Guo T, Ozbudak EM, Cai CL, Zheng D, Morrow BE. Reduced dosage of β-catenin provides significant rescue of cardiac outflow tract anomalies in a Tbx1 conditional null mouse model of 22q11.2 deletion syndrome. Plos Genetics. 13: e1006687. PMID 28346476 DOI: 10.1371/Journal.Pgen.1006687  0.316
2017 Wang P, Mokhtari R, Pedrosa E, Kirschenbaum M, Bayrak C, Zheng D, Lachman HM. CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in cerebral organoids derived from iPS cells. Molecular Autism. 8: 11. PMID 28321286 DOI: 10.1186/S13229-017-0124-1  0.409
2017 Shen Y, Stanislauskas M, Li G, Zheng D, Liu L. Epigenetic and genetic dissections of UV-induced global gene dysregulation in skin cells through multi-omics analyses. Scientific Reports. 7: 42646. PMID 28211524 DOI: 10.1038/Srep42646  0.354
2017 Cvekl A, Limi S, Zhao Y, McGreal R, Zheng D. Transcriptional dynamics, denucleation, and gene regulation in embryonic lens development Acta Ophthalmologica. 95. DOI: 10.1111/J.1755-3768.2017.01165  0.377
2017 Cohen I, Valdes J, Dauber K, Bar C, Zhao D, Zheng D, Bickmore W, Koseki H, Ezhkova E. 864 Catalytic-dependent and -independent activities of Polycomb repressive complex 1 differentially regulate skin stem cell specification Journal of Investigative Dermatology. 137. DOI: 10.1016/J.Jid.2017.02.890  0.328
2016 Zhang D, Wu B, Wang P, Wang Y, Lu P, Nechiporuk T, Floss T, Greally JM, Zheng D, Zhou B. Non-CpG methylation by DNMT3B facilitates REST binding and gene silencing in developing mouse hearts. Nucleic Acids Research. PMID 27956497 DOI: 10.1093/Nar/Gkw1258  0.37
2016 Zhu Z, Li C, Zeng Y, Ding J, Qu Z, Gu J, Ge L, Tang F, Huang X, Zhou C, Wang P, Zheng D, Jin Y. PHB Associates with the HIRA Complex to Control an Epigenetic-Metabolic Circuit in Human ESCs. Cell Stem Cell. PMID 27939217 DOI: 10.1016/J.Stem.2016.11.002  0.383
2016 Lin M, Pedrosa E, Hrabovsky A, Chen J, Puliafito BR, Gilbert SR, Zheng D, Lachman HM. Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion. Bmc Systems Biology. 10: 105. PMID 27846841 DOI: 10.1186/S12918-016-0366-0  0.32
2016 Sun J, Zhao Y, McGreal R, Cohen-Tayar Y, Rockowitz S, Wilczek C, Ashery-Padan R, Shechter D, Zheng D, Cvekl A. Pax6 associates with H3K4-specific histone methyltransferases Mll1, Mll2, and Set1a and regulates H3K4 methylation at promoters and enhancers. Epigenetics & Chromatin. 9: 37. PMID 27617035 DOI: 10.1186/S13072-016-0087-Z  0.347
2016 Choo SW, Rayko M, Tan TK, Hari R, Komissarov A, Wee WY, Yurchenko A, Kliver S, Tamazian G, Antunes A, Wilson RK, Warren WC, Koepfli KP, Minx P, Krasheninnikova K, ... ... Zheng D, et al. Pangolin genomes and the evolution of mammalian scales and immunity. Genome Research. PMID 27510566 DOI: 10.1101/Gr.203521.115  0.3
2016 Perdigoto CN, Dauber KL, Bar C, Tsai PC, Valdes VJ, Cohen I, Santoriello FJ, Zhao D, Zheng D, Hsu YC, Ezhkova E. Polycomb-Mediated Repression and Sonic Hedgehog Signaling Interact to Regulate Merkel Cell Specification during Skin Development. Plos Genetics. 12: e1006151. PMID 27414999 DOI: 10.1371/Journal.Pgen.1006151  0.368
2016 Lu R, Wang P, Parton T, Zhou Y, Chrysovergis K, Rockowitz S, Chen WY, Abdel-Wahab O, Wade PA, Zheng D, Wang GG. Epigenetic Perturbations by Arg882-Mutated DNMT3A Potentiate Aberrant Stem Cell Gene-Expression Program and Acute Leukemia Development. Cancer Cell. PMID 27344947 DOI: 10.1016/J.Ccell.2016.05.008  0.374
2016 Yuan Z, Claros CS, Suzuki M, Maggi EC, Kaner JD, Kinstlinger N, Gorecka J, Quinn TJ, Geha R, Corn A, Pastoriza J, Jing Q, Adem A, Wu H, Alemu G, ... ... Zheng D, et al. Loss of MEN1 activates DNMT1 implicating DNA hypermethylation as a driver of MEN1 tumorigenesis. Oncotarget. PMID 26871472 DOI: 10.18632/Oncotarget.7279  0.319
2016 Nebel RA, Zhao D, Pedrosa E, Kirschen J, Lachman HM, Zheng D, Abrahams BS. Reduced CYFIP1 in Human Neural Progenitors Results in Dysregulation of Schizophrenia and Epilepsy Gene Networks. Plos One. 11: e0148039. PMID 26824476 DOI: 10.1371/Journal.Pone.0148039  0.353
2016 Yang H, Schramek D, Adam R, Levorse J, Keyes B, Wang P, Zheng D, Fuchs E. Abstract 881: Dissecting chromatin dynamics in malignant progression Cancer Research. 76: 881-881. DOI: 10.1158/1538-7445.Am2016-881  0.416
2016 Cvekl A, Limi S, Zhao Y, McGreal R, Xie Q, Zheng D. The α A-crystallin gene expression in differentiating lens fiber cells, FGF signaling, and transcriptional factories Acta Ophthalmologica. 94. DOI: 10.1111/J.1755-3768.2016.0393  0.34
2015 Lin M, Lachman HM, Zheng D. Transcriptomics analysis of iPSC-derived neurons and modeling of neuropsychiatric disorders. Molecular and Cellular Neurosciences. PMID 26631648 DOI: 10.1016/J.Mcn.2015.11.009  0.373
2015 Yang H, Schramek D, Adam RC, Keyes BE, Wang P, Zheng D, Fuchs E. ETS family transcriptional regulators drive chromatin dynamics and malignancy in squamous cell carcinomas. Elife. 4. PMID 26590320 DOI: 10.7554/Elife.10870  0.405
2015 White RR, Milholland B, MacRae SL, Lin M, Zheng D, Vijg J. Comprehensive transcriptional landscape of aging mouse liver. Bmc Genomics. 16: 899. PMID 26541291 DOI: 10.1186/S12864-015-2061-8  0.308
2015 Wang P, Lin M, Pedrosa E, Hrabovsky A, Zhang Z, Guo W, Lachman HM, Zheng D. CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment. Molecular Autism. 6: 55. PMID 26491539 DOI: 10.1186/S13229-015-0048-6  0.415
2015 Wiesner T, Lee W, Obenauf AC, Ran L, Murali R, Zhang QF, Wong EW, Hu W, Scott SN, Shah RH, Landa I, Button J, Lailler N, Sboner A, Gao D, ... ... Zheng D, et al. Alternative transcription initiation leads to expression of a novel ALK isoform in cancer. Nature. PMID 26444240 DOI: 10.1038/Nature15258  0.365
2015 Sun J, Rockowitz S, Xie Q, Ashery-Padan R, Zheng D, Cvekl A. Identification of in vivo DNA-binding mechanisms of Pax6 and reconstruction of Pax6-dependent gene regulatory networks during forebrain and lens development. Nucleic Acids Research. 43: 6827-46. PMID 26138486 DOI: 10.1093/Nar/Gkv589  0.394
2015 Rockowitz S, Zheng D. Significant expansion of the REST/NRSF cistrome in human versus mouse embryonic stem cells: potential implications for neural development. Nucleic Acids Research. 43: 5730-43. PMID 25990720 DOI: 10.1093/Nar/Gkv514  0.404
2015 Chen J, Lin M, Hrabovsky A, Pedrosa E, Dean J, Jain S, Zheng D, Lachman HM. ZNF804A Transcriptional Networks in Differentiating Neurons Derived from Induced Pluripotent Stem Cells of Human Origin. Plos One. 10: e0124597. PMID 25905630 DOI: 10.1371/Journal.Pone.0124597  0.43
2015 Adam RC, Yang H, Rockowitz S, Larsen SB, Nikolova M, Oristian DS, Polak L, Kadaja M, Asare A, Zheng D, Fuchs E. Pioneer factors govern super-enhancer dynamics in stem cell plasticity and lineage choice. Nature. 521: 366-70. PMID 25799994 DOI: 10.1038/Nature14289  0.351
2015 Xu B, On DM, Ma A, Parton T, Konze KD, Pattenden SG, Allison DF, Cai L, Rockowitz S, Liu S, Liu Y, Li F, Vedadi M, Frye SV, Garcia BA, ... Zheng D, et al. Selective inhibition of EZH2 and EZH1 enzymatic activity by a small molecule suppresses MLL-rearranged leukemia. Blood. 125: 346-57. PMID 25395428 DOI: 10.1182/Blood-2014-06-581082  0.353
2015 Lu R, Wang P, Parton T, Zheng D, Wang GG. Epigenetic Reprogramming of Cis-Regulatory Sites By R882-Mutated DNMT3A Potentiates Aberrant Stem Cell Gene Program and Acute Leukemia Development Blood. 126: 2430-2430. DOI: 10.1182/Blood.V126.23.2430.2430  0.371
2014 Lee W, Teckie S, Wiesner T, Ran L, Prieto Granada CN, Lin M, Zhu S, Cao Z, Liang Y, Sboner A, Tap WD, Fletcher JA, Huberman KH, Qin LX, Viale A, ... ... Zheng D, et al. PRC2 is recurrently inactivated through EED or SUZ12 loss in malignant peripheral nerve sheath tumors. Nature Genetics. 46: 1227-32. PMID 25240281 DOI: 10.1038/Ng.3095  0.313
2014 Chamberlain AA, Lin M, Lister RL, Maslov AA, Wang Y, Suzuki M, Wu B, Greally JM, Zheng D, Zhou B. DNA methylation is developmentally regulated for genes essential for cardiogenesis. Journal of the American Heart Association. 3: e000976. PMID 24947998 DOI: 10.1161/Jaha.114.000976  0.345
2014 Rockowitz S, Lien WH, Pedrosa E, Wei G, Lin M, Zhao K, Lachman HM, Fuchs E, Zheng D. Comparison of REST cistromes across human cell types reveals common and context-specific functions. Plos Computational Biology. 10: e1003671. PMID 24922058 DOI: 10.1371/Journal.Pcbi.1003671  0.405
2014 Castellanos R, Xie Q, Zheng D, Cvekl A, Morrow BE. Mammalian TBX1 preferentially binds and regulates downstream targets via a tandem T-site repeat. Plos One. 9: e95151. PMID 24797903 DOI: 10.1371/Journal.Pone.0095151  0.366
2014 Lin M, Zhao D, Hrabovsky A, Pedrosa E, Zheng D, Lachman HM. Heat shock alters the expression of schizophrenia and autism candidate genes in an induced pluripotent stem cell model of the human telencephalon. Plos One. 9: e94968. PMID 24736721 DOI: 10.1371/Journal.Pone.0094968  0.372
2014 Kong P, Racedo SE, Macchiarulo S, Hu Z, Carpenter C, Guo T, Wang T, Zheng D, Morrow BE. Tbx1 is required autonomously for cell survival and fate in the pharyngeal core mesoderm to form the muscles of mastication. Human Molecular Genetics. 23: 4215-31. PMID 24705356 DOI: 10.1093/Hmg/Ddu140  0.348
2014 Guo X, Lin M, Rockowitz S, Lachman HM, Zheng D. Characterization of human pseudogene-derived non-coding RNAs for functional potential. Plos One. 9: e93972. PMID 24699680 DOI: 10.1371/Journal.Pone.0093972  0.408
2014 Bell RD, Long X, Lin M, Bergmann JH, Nanda V, Cowan SL, Zhou Q, Han Y, Spector DL, Zheng D, Miano JM. Identification and initial functional characterization of a human vascular cell-enriched long noncoding RNA. Arteriosclerosis, Thrombosis, and Vascular Biology. 34: 1249-59. PMID 24578380 DOI: 10.1161/Atvbaha.114.303240  0.351
2014 Kadaja M, Keyes BE, Lin M, Pasolli HA, Genander M, Polak L, Stokes N, Zheng D, Fuchs E. SOX9: a stem cell transcriptional regulator of secreted niche signaling factors. Genes & Development. 28: 328-41. PMID 24532713 DOI: 10.1101/Gad.233247.113  0.377
2014 Lien WH, Polak L, Lin M, Lay K, Zheng D, Fuchs E. In vivo transcriptional governance of hair follicle stem cells by canonical Wnt regulators. Nature Cell Biology. 16: 179-90. PMID 24463605 DOI: 10.1038/Ncb2903  0.377
2013 Keyes BE, Segal JP, Heller E, Lien WH, Chang CY, Guo X, Oristian DS, Zheng D, Fuchs E. Nfatc1 orchestrates aging in hair follicle stem cells. Proceedings of the National Academy of Sciences of the United States of America. 110: E4950-9. PMID 24282298 DOI: 10.1073/Pnas.1320301110  0.315
2013 Chen J, Lin M, Foxe JJ, Pedrosa E, Hrabovsky A, Carroll R, Zheng D, Lachman HM. Transcriptome comparison of human neurons generated using induced pluripotent stem cells derived from dental pulp and skin fibroblasts. Plos One. 8: e75682. PMID 24098394 DOI: 10.1371/Journal.Pone.0075682  0.376
2013 Banaszynski LA, Wen D, Dewell S, Whitcomb SJ, Lin M, Diaz N, Elsässer SJ, Chapgier A, Goldberg AD, Canaani E, Rafii S, Zheng D, Allis CD. Hira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells. Cell. 155: 107-20. PMID 24074864 DOI: 10.1016/J.Cell.2013.08.061  0.35
2013 Folgueras AR, Guo X, Pasolli HA, Stokes N, Polak L, Zheng D, Fuchs E. Architectural niche organization by LHX2 is linked to hair follicle stem cell function. Cell Stem Cell. 13: 314-27. PMID 24012369 DOI: 10.1016/J.Stem.2013.06.018  0.35
2013 Baker LA, Ueberheide BM, Dewell S, Chait BT, Zheng D, Allis CD. The yeast Snt2 protein coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress. Molecular and Cellular Biology. 33: 3735-48. PMID 23878396 DOI: 10.1128/Mcb.00025-13  0.35
2013 Xie Q, Yang Y, Huang J, Ninkovic J, Walcher T, Wolf L, Vitenzon A, Zheng D, Götz M, Beebe DC, Zavadil J, Cvekl A. Pax6 interactions with chromatin and identification of its novel direct target genes in lens and forebrain. Plos One. 8: e54507. PMID 23342162 DOI: 10.1371/Journal.Pone.0054507  0.438
2013 Cai L, Rothbart SB, Lu R, Xu B, Chen WY, Tripathy A, Rockowitz S, Zheng D, Patel DJ, Allis CD, Strahl BD, Song J, Wang GG. An H3K36 methylation-engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targeting. Molecular Cell. 49: 571-82. PMID 23273982 DOI: 10.1016/J.Molcel.2012.11.026  0.384
2012 Lin M, Hrabovsky A, Pedrosa E, Wang T, Zheng D, Lachman HM. Allele-biased expression in differentiating human neurons: implications for neuropsychiatric disorders. Plos One. 7: e44017. PMID 22952857 DOI: 10.1371/Journal.Pone.0044017  0.379
2012 Wontakal SN, Guo X, Smith C, MacCarthy T, Bresnick EH, Bergman A, Snyder MP, Weissman SM, Zheng D, Skoultchi AI. A core erythroid transcriptional network is repressed by a master regulator of myelo-lymphoid differentiation. Proceedings of the National Academy of Sciences of the United States of America. 109: 3832-7. PMID 22357756 DOI: 10.1073/Pnas.1121019109  0.381
2011 Lin M, Pedrosa E, Shah A, Hrabovsky A, Maqbool S, Zheng D, Lachman HM. RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders. Plos One. 6: e23356. PMID 21915259 DOI: 10.1371/Journal.Pone.0023356  0.393
2011 Lien WH, Guo X, Polak L, Lawton LN, Young RA, Zheng D, Fuchs E. Genome-wide maps of histone modifications unwind in vivo chromatin states of the hair follicle lineage. Cell Stem Cell. 9: 219-32. PMID 21885018 DOI: 10.1016/J.Stem.2011.07.015  0.367
2011 Pedrosa E, Sandler V, Shah A, Carroll R, Chang C, Rockowitz S, Guo X, Zheng D, Lachman HM. Development of patient-specific neurons in schizophrenia using induced pluripotent stem cells. Journal of Neurogenetics. 25: 88-103. PMID 21797804 DOI: 10.3109/01677063.2011.597908  0.326
2011 Wontakal SN, Guo X, Will B, Shi M, Raha D, Mahajan MC, Weissman S, Snyder M, Steidl U, Zheng D, Skoultchi AI. A large gene network in immature erythroid cells is controlled by the myeloid and B cell transcriptional regulator PU.1. Plos Genetics. 7: e1001392. PMID 21695229 DOI: 10.1371/Journal.Pgen.1001392  0.409
2010 Chi P, Chen Y, Zhang L, Guo X, Wongvipat J, Shamu T, Fletcher JA, Dewell S, Maki RG, Zheng D, Antonescu CR, Allis CD, Sawyers CL. ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours. Nature. 467: 849-53. PMID 20927104 DOI: 10.1038/Nature09409  0.382
2010 Abrajano JJ, Qureshi IA, Gokhan S, Molero AE, Zheng D, Bergman A, Mehler MF. Corepressor for element-1-silencing transcription factor preferentially mediates gene networks underlying neural stem cell fate decisions. Proceedings of the National Academy of Sciences of the United States of America. 107: 16685-90. PMID 20823235 DOI: 10.1073/Pnas.0906917107  0.411
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2022 Ma L, Tang Q, Gao X, Lee J, Lei R, Suzuki M, Zheng D, Ito K, Frenette PS, Dawlaty MM. Tet-mediated DNA demethylation regulates specification of hematopoietic stem and progenitor cells during mammalian embryogenesis. Science Advances. 8: eabm3470. PMID 35235365 DOI: 10.1126/sciadv.abm3470  0.215
2023 De Bono C, Liu Y, Ferrena A, Valentine A, Zheng D, Morrow BE. Single-cell transcriptomics uncovers a non-autonomous Tbx1-dependent genetic program controlling cardiac neural crest cell development. Nature Communications. 14: 1551. PMID 36941249 DOI: 10.1038/s41467-023-37015-9  0.212
2022 Trifiletti R, Lachman HM, Manusama O, Zheng D, Spalice A, Chiurazzi P, Schornagel A, Serban AM, van Wijck R, Cunningham JL, Swagemakers S, van der Spek PJ. Identification of ultra-rare genetic variants in pediatric acute onset neuropsychiatric syndrome (PANS) by exome and whole genome sequencing. Scientific Reports. 12: 11106. PMID 35773312 DOI: 10.1038/s41598-022-15279-3  0.204
2024 Wang H, Sica RA, Kaur G, Galbo PM, Jing Z, Nishimura CD, Ren X, Tanwar A, Etemad-Gilbertson B, Will B, Zheng D, Fooksman D, Zang X. TMIGD2 is an orchestrator and therapeutic target on human acute myeloid leukemia stem cells. Nature Communications. 15: 11. PMID 38167704 DOI: 10.1038/s41467-023-43843-6  0.196
2022 Piszczatowski RT, Schwenger E, Sundaravel S, Stein CM, Liu Y, Stanley P, Verma A, Zheng D, Seidel RD, Almo SC, Townley RA, Bülow HE, Steidl U. A glycan-based approach to cell characterization and isolation: Hematopoiesis as a paradigm. The Journal of Experimental Medicine. 219. PMID 36066492 DOI: 10.1084/jem.20212552  0.194
2023 Ferrena A, Zhang X, Shrestha R, Zheng D, Liu W. Six3 and Six6 jointly regulate the identities and developmental trajectories of multipotent retinal progenitor cells in the mouse retina. Biorxiv : the Preprint Server For Biology. PMID 37205402 DOI: 10.1101/2023.05.03.539288  0.19
2023 Bera BS, Thompson TV, Sosa E, Nomaru H, Reynolds D, Dubin RA, Maqbool SB, Zheng D, Morrow BE, Greally JM, Suzuki M. An optimized approach for multiplexing single-nuclear ATAC-seq using oligonucleotide-conjugated antibodies. Epigenetics & Chromatin. 16: 14. PMID 37118773 DOI: 10.1186/s13072-023-00486-7  0.186
2021 Xu C, Tsai YH, Galbo PM, Gong W, Storey AJ, Xu Y, Byrum SD, Xu L, Whang YE, Parker JS, Mackintosh SG, Edmondson RD, Tackett AJ, Huang J, Zheng D, et al. Cistrome analysis of YY1 uncovers a regulatory axis of YY1:BRD2/4-PFKP during tumorigenesis of advanced prostate cancer. Nucleic Acids Research. PMID 33849067 DOI: 10.1093/nar/gkab252  0.186
2024 Wang J, Ferrena A, Zhang R, Singh S, Viscarret V, Al-Harden W, Aldahamsheh O, Borjihan H, Singla A, Yaguare S, Tingling J, Zi X, Lo Y, Gorlick R, Schwartz EL, ... ... Zheng D, et al. Targeted inhibition of SCF confers anti-tumor activities resulting in a survival benefit in osteosarcoma. Oncogene. PMID 38355807 DOI: 10.1038/s41388-024-02942-4  0.183
2022 Singh VK, Misra R, Almo SC, Steidl UG, Bülow HE, Zheng D. HSMotifDiscover: identification of motifs in sequences composed of non-single-letter elements. Bioinformatics (Oxford, England). PMID 35771633 DOI: 10.1093/bioinformatics/btac437  0.173
2022 Wang F, Liu Y, Qiu W, Shum E, Feng M, Zhao D, Zheng D, Borczuk A, Cheng H, Halmos B. Functional analysis of MET exon 14 skipping alteration in cancer invasion and metastatic dissemination. Cancer Research. PMID 35078819 DOI: 10.1158/0008-5472.CAN-21-1327  0.167
2020 Ilaltdinov AW, Gong Y, Leong DJ, Gruson KI, Zheng D, Fung DT, Sun L, Sun HB. Advances in the development of gene therapy, noncoding RNA, and exosome-based treatments for tendinopathy. Annals of the New York Academy of Sciences. PMID 32501571 DOI: 10.1111/nyas.14382  0.159
2022 Ren X, Peng M, Xing P, Wei Y, Galbo PM, Corrigan D, Wang H, Su Y, Dong X, Sun Q, Li Y, Zhang X, Edelmann W, Zheng D, Zang X. Blockade of the immunosuppressive KIR2DL5/PVR pathway elicits potent human NK cell-mediated antitumor immunity. The Journal of Clinical Investigation. 132. PMID 36377656 DOI: 10.1172/JCI163620  0.157
2021 Wang L, Liu Y, Stratigopoulos G, Panigrahi SK, Sui L, LeDuc CA, Glover HJ, De Rosa MC, Burnett LC, Williams DJ, Shang L, Goland R, Tsang SH, Wardlaw SL, Egli D, ... Zheng D, et al. Bardet-Biedl Syndrome proteins regulate intracellular signaling and neuronal function in patient-specific iPSC-derived neurons. The Journal of Clinical Investigation. PMID 33630762 DOI: 10.1172/JCI146287  0.156
2023 Cui J, Zhang C, Lee JE, Bartholdy BA, Yang D, Liu Y, Erler P, Galbo PM, Hodge DQ, Huangfu D, Zheng D, Ge K, Guo W. MLL3 loss drives metastasis by promoting a hybrid epithelial-mesenchymal transition state. Nature Cell Biology. PMID 36604594 DOI: 10.1038/s41556-022-01045-0  0.155
2023 Lu P, Wu B, Wang Y, Russell M, Liu Y, Bernard DJ, Zheng D, Zhou B. Prerequisite endocardial-mesenchymal transition for murine cardiac trabecular angiogenesis. Developmental Cell. PMID 37023750 DOI: 10.1016/j.devcel.2023.03.009  0.153
2022 Patel AJ, Warda S, Maag JLV, Misra R, Miranda-Roman MA, Pachai MR, Lee CJ, Li D, Wang N, Bayshtok G, Fishinevich E, Meng Y, Wong EWP, Yan J, Giff E, ... ... Zheng D, et al. PRC2 Inactivating Mutations in Cancer Enhance Cytotoxic Response to DNMT1 Targeted Therapy via Enhanced Viral Mimicry. Cancer Discovery. PMID 35789380 DOI: 10.1158/2159-8290.CD-21-1671  0.152
2023 Liu Y, John P, Nishitani K, Cui J, Nishimura CD, Christin JR, Couturier N, Ren X, Wei Y, Pulanco MC, Galbo PM, Zhang X, Fu W, Cui W, Bartholdy BA, ... Zheng D, et al. A SOX9-B7x axis safeguards dedifferentiated tumor cells from immune surveillance to drive breast cancer progression. Developmental Cell. PMID 37963469 DOI: 10.1016/j.devcel.2023.10.010  0.152
2023 Racedo SE, Liu Y, Shi L, Zheng D, Morrow BE. Dgcr8 functions in the secondary heart field for outflow tract and right ventricle development in mammals. Developmental Biology. 506: 72-84. PMID 38110169 DOI: 10.1016/j.ydbio.2023.12.005  0.146
2022 John P, Pulanco MC, Galbo PM, Wei Y, Ohaegbulam KC, Zheng D, Zang X. The immune checkpoint B7x expands tumor-infiltrating Tregs and promotes resistance to anti-CTLA-4 therapy. Nature Communications. 13: 2506. PMID 35523809 DOI: 10.1038/s41467-022-30143-8  0.146
2021 Zhang Y, Zheng D. Pseudogene Profiling for Cancer Subtype Classification. Methods in Molecular Biology (Clifton, N.J.). 2324: 307-317. PMID 34165723 DOI: 10.1007/978-1-0716-1503-4_19  0.146
2021 Wang J, Aldahamsheh O, Ferrena A, Borjihan H, Singla A, Yaguare S, Singh S, Viscarret V, Tingling J, Zi X, Lo Y, Gorlick R, Zheng D, Schwartz EL, Zhao H, et al. The interaction of SKP2 with p27 enhances the progression and stemness of osteosarcoma. Annals of the New York Academy of Sciences. PMID 33594717 DOI: 10.1111/nyas.14578  0.144
2021 Wei Y, Ren X, Galbo PM, Moerdler S, Wang H, Sica RA, Etemad-Gilbertson B, Shi L, Zhu L, Tang X, Lin Q, Peng M, Guan F, Zheng D, Chinai JM, et al. KIR3DL3-HHLA2 is a human immunosuppressive pathway and a therapeutic target. Science Immunology. 6. PMID 34244312 DOI: 10.1126/sciimmunol.abf9792  0.143
2024 Zhang D, Wang Y, Lu P, Wang P, Yuan X, Yan J, Cai C, Chang CP, Zheng D, Wu B, Zhou B. Retraction Note: REST regulates the cell cycle for cardiac development and regeneration. Nature Communications. 15: 1623. PMID 38388651 DOI: 10.1038/s41467-024-46055-8  0.135
2023 Ferrena A, Wang J, Zhang R, Karadal-Ferrena B, Al-Hardan W, Singh S, Borjihan H, Schwartz E, Zhao H, Yang R, Geller D, Hoang B, Zheng D. SKP2 knockout in Rb1/p53 deficient mouse models of osteosarcoma induces immune infiltration and drives a transcriptional program with a favorable prognosis. Biorxiv : the Preprint Server For Biology. PMID 37214958 DOI: 10.1101/2023.05.09.540053  0.134
2023 Jing Z, Galbo P, Ovando L, Demouth M, Welte S, Park R, Chandran K, Wu Y, MacCarthy T, Zheng D, Fooksman D. Fine-tuning spatial-temporal dynamics and surface receptor expression support plasma cell-intrinsic longevity. Biorxiv : the Preprint Server For Biology. PMID 36891288 DOI: 10.1101/2023.02.15.527913  0.126
2023 Galbo PM, Madsen AT, Liu Y, Peng M, Wei Y, Ciesielski MJ, Fenstermaker RA, Graff S, Montagna C, Segall JE, Sidoli S, Zang X, Zheng D. Functional Contribution and Clinical Implication of Cancer-Associated Fibroblasts in Glioblastoma. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 38060213 DOI: 10.1158/1078-0432.CCR-23-0493  0.124
2022 Ren Z, Liang H, Galbo PM, Dharmaratne M, Kulkarni AS, Fard AT, Aoun ML, Martinez-Lopez N, Suyama K, Benard O, Zheng W, Liu Y, Albanese J, Zheng D, Mar JC, et al. Redox signaling by glutathione peroxidase 2 links vascular modulation to metabolic plasticity of breast cancer. Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35193955 DOI: 10.1073/pnas.2107266119  0.121
2024 Kadamb R, Anton ML, Purwin TJ, Chua V, Seeneevassen L, Teh J, Angela Nieto M, Sato T, Terai M, Roman SR, De Koning L, Zheng D, Aplin AE, Aguirre-Ghiso J. Lineage commitment pathways epigenetically oppose oncogenic Gαq/11-YAP signaling in dormant disseminated uveal melanoma. Biorxiv : the Preprint Server For Biology. PMID 38496663 DOI: 10.1101/2024.03.05.583565  0.12
2022 Yan J, Chen Y, Patel AJ, Warda S, Lee CJ, Nixon BG, Wong EW, Miranda-Román MA, Yang N, Wang Y, Pachai MR, Sher J, Giff E, Tang F, Khurana E, ... ... Zheng D, et al. Tumor-intrinsic PRC2 inactivation drives a context-dependent immune-desert microenvironment and is sensitized by immunogenic therapeutic viruses. The Journal of Clinical Investigation. PMID 35852856 DOI: 10.1172/JCI153437  0.113
2022 Astorkia M, Lachman HM, Zheng D. Characterization of cell-cell communication in autistic brains with single-cell transcriptomes. Journal of Neurodevelopmental Disorders. 14: 29. PMID 35501678 DOI: 10.1186/s11689-022-09441-1  0.109
2022 Picarda E, Galbo PM, Zong H, Rajan MR, Wallenius V, Zheng D, Börgeson E, Singh R, Pessin J, Zang X. The immune checkpoint B7-H3 (CD276) regulates adipocyte progenitor metabolism and obesity development. Science Advances. 8: eabm7012. PMID 35476450 DOI: 10.1126/sciadv.abm7012  0.109
2023 Li R, Chen B, Kubota A, Hanna A, Humeres C, Hernandez SC, Liu Y, Ma R, Tuleta I, Huang S, Venugopal H, Zhu F, Su K, Li J, Zhang J, ... Zheng D, et al. Protective effects of macrophage-specific integrin α5 in myocardial infarction are associated with accentuated angiogenesis. Nature Communications. 14: 7555. PMID 37985764 DOI: 10.1038/s41467-023-43369-x  0.109
2019 Lister R, Chamberlain A, Einstein F, Wu B, Zheng D, Zhou B. Intrauterine Programming of Diabetes Induced Cardiac Embryopathy. Diabetes & Obesity International Journal. 4. PMID 32537569  0.102
2021 Galbo PM, Zang X, Zheng D. Implication of cancer associated fibroblast subtypes on cancer pathogenesis, prognosis, and immunotherapy resistance. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 33622705 DOI: 10.1158/1078-0432.CCR-20-4226  0.097
2020 Zhu Z, Li C, Zeng Y, Ding J, Qu Z, Gu J, Ge L, Tang F, Huang X, Zhou C, Wang P, Zheng D, Jin Y. PHB Associates with the HIRA Complex to Control an Epigenetic-Metabolic Circuit in Human ESCs. Cell Stem Cell. 26: 294. PMID 32032527 DOI: 10.1016/j.stem.2020.01.001  0.096
2021 Akhmetzyanova I, Aaron T, Galbo P, Tikhonova A, Dolgalev I, Tanaka M, Aifantis I, Zheng D, Zang X, Fooksman D. Tissue-resident macrophages promote early dissemination of multiple myeloma via IL-6 and TNFα. Blood Advances. 5: 3592-3608. PMID 34550328 DOI: 10.1182/bloodadvances.2021005327  0.094
2022 Lu P, Wang P, Wu B, Wang Y, Liu Y, Cheng W, Feng X, Yuan X, Atteya MM, Ferro H, Sugi Y, Rydquist G, Esmaily M, Butcher JT, Chang CP, ... ... Zheng D, et al. A SOX17-PDGFB signaling axis regulates aortic root development. Nature Communications. 13: 4065. PMID 35831318 DOI: 10.1038/s41467-022-31815-1  0.084
2021 Lu P, Wang Y, Liu Y, Wang Y, Wu B, Zheng D, Harvey RP, Zhou B. Perinatal angiogenesis from pre-existing coronary vessels via DLL4-NOTCH1 signalling. Nature Cell Biology. PMID 34497373 DOI: 10.1038/s41556-021-00747-1  0.079
2023 Alex L, Tuleta I, Hernandez SC, Hanna A, Venugopal H, Astorkia M, Humeres C, Kubota A, Su K, Zheng D, Frangogiannis NG. Cardiac Pericytes Acquire a Fibrogenic Phenotype and Contribute to Vascular Maturation After Myocardial Infarction. Circulation. PMID 37350296 DOI: 10.1161/CIRCULATIONAHA.123.064155  0.079
2023 Lü J, Zhao Q, Guo Y, Li D, Xie H, Liu C, Hu X, Liu S, Hou Z, Wei X, Zheng D, Pestell RG, Yu Z. Regulation of ERα-dependent breast cancer metastasis by a miR-29a signaling. Journal of Experimental & Clinical Cancer Research : Cr. 42: 93. PMID 37081505 DOI: 10.1186/s13046-023-02665-6  0.072
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