| 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 |
0.392 |
|
| 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 |
0.388 |
|
| 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 |
0.342 |
|
| 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 |
0.317 |
|
| 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 |
0.301 |
|
| 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 |
0.417 |
|
| 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 |
0.374 |
|
| 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 |
0.406 |
|
| 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 |
0.416 |
|
| 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 |
0.366 |
|
| 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 |
0.405 |
|
| 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 |
0.431 |
|
| 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 |
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| 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 |
0.372 |
|
| 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 |
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| 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 |
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| 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 |
0.406 |
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| 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 |
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| 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 |
0.373 |
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| 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 |
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| 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 |
0.409 |
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| 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 |
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| 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 |
0.378 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.368 |
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| 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 |
0.327 |
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| 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 |
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| 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 |
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| 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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| 2010 |
Pedrosa E, Shah A, Tenore C, Capogna M, Villa C, Guo X, Zheng D, Lachman HM. β-catenin promoter ChIP-chip reveals potential schizophrenia and bipolar disorder gene network. Journal of Neurogenetics. 24: 182-93. PMID 20615089 DOI: 10.3109/01677063.2010.495182 |
0.336 |
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| 2010 |
Goldberg AD, Banaszynski LA, Noh KM, Lewis PW, Elsaesser SJ, Stadler S, Dewell S, Law M, Guo X, Li X, Wen D, Chapgier A, DeKelver RC, Miller JC, Lee YL, ... ... Zheng D, et al. Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell. 140: 678-91. PMID 20211137 DOI: 10.1016/J.Cell.2010.01.003 |
0.344 |
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| 2009 |
McLellan AS, Dubin RA, Jing Q, Maqbool SB, Olea R, Westby G, Broin PÓ, Fazzari MJ, Zheng D, Suzuki M, Greally JM. The Einstein Center for Epigenomics: studying the role of epigenomic dysregulation in human disease. Epigenomics. 1: 33-8. PMID 22122636 DOI: 10.2217/Epi.09.9 |
0.307 |
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| 2009 |
Abrajano JJ, Qureshi IA, Gokhan S, Zheng D, Bergman A, Mehler MF. REST and CoREST modulate neuronal subtype specification, maturation and maintenance. Plos One. 4: e7936. PMID 19997604 DOI: 10.1371/Journal.Pone.0007936 |
0.374 |
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| 2009 |
Abrajano JJ, Qureshi IA, Gokhan S, Zheng D, Bergman A, Mehler MF. Differential deployment of REST and CoREST promotes glial subtype specification and oligodendrocyte lineage maturation. Plos One. 4: e7665. PMID 19888342 DOI: 10.1371/Journal.Pone.0007665 |
0.394 |
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| 2009 |
Liu YJ, Zheng D, Balasubramanian S, Carriero N, Khurana E, Robilotto R, Gerstein MB. Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity. Bmc Genomics. 10: 480. PMID 19835609 DOI: 10.1186/1471-2164-10-480 |
0.34 |
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| 2009 |
Guo X, Zhang Z, Gerstein MB, Zheng D. Small RNAs originated from pseudogenes: cis- or trans-acting? Plos Computational Biology. 5: e1000449. PMID 19649160 DOI: 10.1371/Journal.Pcbi.1000449 |
0.324 |
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| 2009 |
Zheng D, Zhao K, Mehler MF. Profiling RE1/REST-mediated histone modifications in the human genome. Genome Biology. 10: R9. PMID 19173732 DOI: 10.1186/Gb-2009-10-1-R9 |
0.358 |
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| 2009 |
Balasubramanian S, Zheng D, Liu YJ, Fang G, Frankish A, Carriero N, Robilotto R, Cayting P, Gerstein M. Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes. Genome Biology. 10: R2. PMID 19123937 DOI: 10.1186/Gb-2009-10-1-R2 |
0.313 |
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| 2009 |
Cvekl A, Zheng D. Gene sharing and evolution Human Genomics. 4: 66. DOI: 10.1186/1479-7364-4-1-66 |
0.318 |
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| 2008 |
Zheng D. Gene duplication in the epigenomic era. Epigenetics. 3: 250-3. PMID 19013828 DOI: 10.4161/Epi.3.5.6991 |
0.38 |
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| 2008 |
Zheng D. Asymmetric histone modifications between the original and derived loci of human segmental duplications. Genome Biology. 9: R105. PMID 18598352 DOI: 10.1186/Gb-2008-9-7-R105 |
0.312 |
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| 2007 |
Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Zheng D, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874 |
0.376 |
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| 2007 |
Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigó R, Harrow J, et al. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Research. 17: 839-51. PMID 17568002 DOI: 10.1101/Gr.5586307 |
0.376 |
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| 2007 |
Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R, Gingeras TR, Weissman S, Miller P, Snyder M, Gerstein MB. The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Research. 17: 732-45. PMID 17567993 DOI: 10.1101/Gr.5696007 |
0.374 |
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| 2007 |
Trinklein ND, Karaöz U, Wu J, Halees A, Force Aldred S, Collins PJ, Zheng D, Zhang ZD, Gerstein MB, Snyder M, Myers RM, Weng Z. Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Research. 17: 720-31. PMID 17567992 DOI: 10.1101/Gr.5716607 |
0.381 |
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| 2007 |
Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M. What is a gene, post-ENCODE? History and updated definition. Genome Research. 17: 669-81. PMID 17567988 DOI: 10.1101/Gr.6339607 |
0.392 |
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| 2007 |
Zheng D, Gerstein MB. The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they? Trends in Genetics : Tig. 23: 219-24. PMID 17382428 DOI: 10.1016/J.Tig.2007.03.003 |
0.317 |
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| 2007 |
Emanuelsson O, Nagalakshmi U, Zheng D, Rozowsky JS, Urban AE, Du J, Lian Z, Stolc V, Weissman S, Snyder M, Gerstein MB. Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. Genome Research. 17: 886-97. PMID 17119069 DOI: 10.1101/Gr.5014606 |
0.336 |
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| 2006 |
Rozowsky J, Wu J, Lian Z, Nagalakshmi U, Korbel JO, Kapranov P, Zheng D, Dyke S, Newburger P, Miller P, Gingeras TR, Weissman S, Gerstein M, Snyder M. Novel transcribed regions in the human genome. Cold Spring Harbor Symposia On Quantitative Biology. 71: 111-6. PMID 17381286 DOI: 10.1101/Sqb.2006.71.054 |
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| 2006 |
Zheng D, Gerstein MB. A computational approach for identifying pseudogenes in the ENCODE regions. Genome Biology. 7: S13.1-10. PMID 16925835 DOI: 10.1186/Gb-2006-7-S1-S13 |
0.347 |
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| 2006 |
Gerstein M, Zheng D. The real life of pseudogenes. Scientific American. 295: 48-55. PMID 16866288 DOI: 10.1038/Scientificamerican0806-48 |
0.316 |
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| 2006 |
Zhang Z, Carriero N, Zheng D, Karro J, Harrison PM, Gerstein M. PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics (Oxford, England). 22: 1437-9. PMID 16574694 DOI: 10.1093/Bioinformatics/Btl116 |
0.331 |
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| 2005 |
Zheng D, Zhang Z, Harrison PM, Karro J, Carriero N, Gerstein M. Integrated pseudogene annotation for human chromosome 22: evidence for transcription. Journal of Molecular Biology. 349: 27-45. PMID 15876366 DOI: 10.1016/J.Jmb.2005.02.072 |
0.409 |
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| 2005 |
Harrison PM, Zheng D, Zhang Z, Carriero N, Gerstein M. Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Research. 33: 2374-83. PMID 15860774 DOI: 10.1093/Nar/Gki531 |
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| 2005 |
Zheng D, Swapna GVT, Hunter M, Montelione G. Resonance Assignments for the Z Domain of Staphylococcal Protein A using a 2H, 13C, 15N enriched, selective methyl protonated sample Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr5656 |
0.437 |
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| 2004 |
Zheng D, Aramini JM, Montelione GT. Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data. Protein Science : a Publication of the Protein Society. 13: 549-54. PMID 14718654 DOI: 10.1110/Ps.03351704 |
0.452 |
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| 2003 |
Li W, Zhang Y, Kihara D, Huang YJ, Zheng D, Montelione GT, Kolinski A, Skolnick J. TOUCHSTONEX: Protein structure prediction with sparse NMR data Proteins: Structure, Function and Genetics. 53: 290-306. PMID 14517980 DOI: 10.1002/Prot.10499 |
0.648 |
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| 2003 |
Zheng D, Cort JR, Chiang Y, Acton T, Kennedy MA, Montelione GT. 1H, 13C and 15N resonance assignments for methionine sulfoxide reductase B from Bacillus subtilis. Journal of Biomolecular Nmr. 27: 183-4. PMID 12913416 DOI: 10.1023/A:1024991310929 |
0.423 |
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| 2003 |
Goh CS, Lan N, Echols N, Douglas SM, Milburn D, Bertone P, Xiao R, Ma LC, Zheng D, Wunderlich Z, Acton T, Montelione GT, Gerstein M. SPINE 2: a system for collaborative structural proteomics within a federated database framework. Nucleic Acids Research. 31: 2833-8. PMID 12771210 DOI: 10.1093/Nar/Gkg397 |
0.449 |
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| 2003 |
Zheng D, Huang YJ, Moseley HN, Xiao R, Aramini J, Swapna GV, Montelione GT. Automated protein fold determination using a minimal NMR constraint strategy. Protein Science : a Publication of the Protein Society. 12: 1232-46. PMID 12761394 DOI: 10.1110/Ps.0300203 |
0.654 |
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| 2002 |
Cort JR, Chiang Y, Zheng D, Montelione GT, Kennedy MA. NMR structure of conserved eukaryotic protein ZK652.3 from C. elegans: a ubiquitin-like fold. Proteins. 48: 733-6. PMID 12211038 DOI: 10.1002/Prot.10197 |
0.514 |
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| 2001 |
Bertone P, Kluger Y, Lan N, Zheng D, Christendat D, Yee A, Edwards AM, Arrowsmith CH, Montelione GT, Gerstein M. SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. Nucleic Acids Research. 29: 2884-98. PMID 11433035 DOI: 10.1093/Nar/29.13.2884 |
0.478 |
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| 2000 |
Montelione GT, Zheng D, Huang YJ, Gunsalus KC, Szyperski T. Protein NMR spectroscopy in structural genomics. Nature Structural Biology. 7: 982-5. PMID 11104006 DOI: 10.1038/80768 |
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