Keji Zhao - Publications

Affiliations: 
Physics The George Washington University, Washington, DC, United States 
 NHLBI, Bethesda, MD, United States 
Area:
General Biophysics, Bioinformatics Biology
Website:
https://www.nhlbi.nih.gov/science/epigenome-biology/people/zhao-keji

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

Year Citation  Score
2021 Her YR, Wang L, Chepelev I, Manterola M, Berkovits B, Cui K, Zhao K, Wolgemuth DJ. Genome-wide chromatin occupancy of BRDT and gene expression analysis suggest transcriptional partners and specific epigenetic landscapes that regulate gene expression during spermatogenesis. Molecular Reproduction and Development. PMID 33469999 DOI: 10.1002/mrd.23449  0.88
2020 Zhen T, Cao Y, Ren G, Zhao L, Hyde RK, Lopez G, Feng D, Alemu L, Zhao K, Liu PP. RUNX1 and CBFβ-SMMHC transactivate target genes together in abnormal myeloid progenitors for leukemia development. Blood. PMID 32929473 DOI: 10.1182/blood.2020007747  0.52
2020 Carter B, Ku WL, Kang JY, Hu G, Perrie J, Tang Q, Zhao K. Author Correction: Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq). Nature Communications. 11: 4424. PMID 32873803 DOI: 10.1038/s41467-020-18309-8  0.56
2020 Qiu X, Ma F, Zhao M, Cao Y, Shipp L, Liu A, Dutta A, Singh A, Braikia FZ, De S, Wood WH, Becker KG, Zhou W, Ji H, Zhao K, et al. Altered 3D chromatin structure permits inversional recombination at the locus. Science Advances. 6: eaaz8850. PMID 32851160 DOI: 10.1126/sciadv.aaz8850  0.4
2020 Sawaengdee W, Cui K, Zhao K, Hongeng S, Fucharoen S, Wongtrakoongate P. Genome-Wide Transcriptional Regulation of the Long Non-coding RNA Steroid Receptor RNA Activator in Human Erythroblasts. Frontiers in Genetics. 11: 850. PMID 32849830 DOI: 10.3389/fgene.2020.00850  0.88
2020 Ma B, Trieu TJ, Cheng J, Zhou S, Tang Q, Xie J, Liu JL, Zhao K, Habib SJ, Chen X. Differential Histone Distribution Patterns in Induced Asymmetrically Dividing Mouse Embryonic Stem Cells. Cell Reports. 32: 108003. PMID 32783931 DOI: 10.1016/j.celrep.2020.108003  0.68
2020 Han Z, Cui K, Placek K, Hong N, Lin C, Chen W, Zhao K, Jin W. Diploid genome architecture revealed by multi-omic data of hybrid mice. Genome Research. PMID 32759226 DOI: 10.1101/gr.257568.119  0.88
2020 Joo Y, Xue Y, Wang Y, McDevitt RA, Sah N, Bossi S, Su S, Lee SK, Peng W, Xie A, Zhang Y, Ding Y, Ku WL, Ghosh S, Fishbein K, ... ... Zhao K, et al. Topoisomerase 3β knockout mice show transcriptional and behavioural impairments associated with neurogenesis and synaptic plasticity. Nature Communications. 11: 3143. PMID 32561719 DOI: 10.1038/s41467-020-16884-4  0.56
2020 Yang L, So JY, Skrypek N, Yang HH, Merchant AS, Nelson GW, Chen WD, Ishii H, Chen JM, Hu G, Achyut BR, Yoon EC, Han L, Huang C, Cam MC, ... Zhao K, et al. Induction of DNMT3B by PGE2 and IL6 at distant metastatic sites promotes epigenetic modification and breast cancer colonization. Cancer Research. PMID 32265226 DOI: 10.1158/0008-5472.CAN-19-3339  0.48
2020 Li L, Mitra A, Cui K, Zhao B, Choi S, Lee J, Stamos DB, El-Khoury D, Warzecha C, Pfeifer K, Hardwick J, Zhao K, Venters B, Dave UP, Love PE. Ldb1 is required for Lmo2 oncogene-induced thymocyte self-renewal and T-cell Acute Lymphoblastic Leukemia. Blood. PMID 32181817 DOI: 10.1182/blood.2019000794  0.88
2020 Shi Z, Lim C, Tran V, Cui K, Zhao K, Chen X. Single-cyst transcriptome analysis of male germline stem cell lineage. Development (Cambridge, England). PMID 32122991 DOI: 10.1242/dev.184259  0.88
2020 Li Y, Liao Z, Luo H, Benyoucef A, Kang Y, Lai Q, Dovat S, Miller B, Chepelev I, Li Y, Zhao K, Brand M, Huang S. Alteration of CTCF-associated chromatin neighborhood inhibits TAL1-driven oncogenic transcription program and leukemogenesis. Nucleic Acids Research. PMID 32086528 DOI: 10.1093/nar/gkaa098  0.8
2020 Wang P, Song X, Cao D, Cui K, Wang J, Utpatel K, Shang R, Wang H, Che L, Evert M, Zhao K, Calvisi DF, Chen X. Oncogene-dependent function of BRG1 in hepatocarcinogenesis. Cell Death & Disease. 11: 91. PMID 32019910 DOI: 10.1038/s41419-020-2289-3  0.88
2020 Wang L, Tang J, Yang X, Zanvit P, Cui K, Ku WL, Jin W, Zhang D, Goldberg N, Cain A, Ni B, Zhao K, Wu Y, Chen W. TGF-β induces ST2 and programs ILC2 development. Nature Communications. 11: 35. PMID 31911623 DOI: 10.1038/s41467-019-13734-w  0.88
2019 Zhong C, Zheng M, Cui K, Martins AJ, Hu G, Li D, Tessarollo L, Kozlov S, Keller JR, Tsang JS, Zhao K, Zhu J. Differential Expression of the Transcription Factor GATA3 Specifies Lineage and Functions of Innate Lymphoid Cells. Immunity. PMID 31882362 DOI: 10.1016/j.immuni.2019.12.001  0.88
2019 Gao W, Lai B, Ni B, Zhao K. Genome-wide profiling of nucleosome position and chromatin accessibility in single cells using scMNase-seq. Nature Protocols. PMID 31836865 DOI: 10.1038/s41596-019-0243-6  0.48
2019 Gryder BE, Pomella S, Sayers C, Wu XS, Song Y, Chiarella AM, Bagchi S, Chou HC, Sinniah RS, Walton A, Wen X, Rota R, Hathaway NA, Zhao K, Chen J, et al. Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma. Nature Genetics. 51: 1714-1722. PMID 31784732 DOI: 10.1038/s41588-019-0534-4  0.56
2019 Ren G, Zhao K. CTCF and cellular heterogeneity. Cell & Bioscience. 9: 83. PMID 31632638 DOI: 10.1186/s13578-019-0347-2  0.52
2019 Carter B, Ku WL, Kang JY, Hu G, Perrie J, Tang Q, Zhao K. Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq). Nature Communications. 10: 3747. PMID 31431618 DOI: 10.1038/s41467-019-11559-1  0.56
2019 Harly C, Kenney D, Ren G, Lai B, Raabe T, Yang Q, Cam MC, Xue HH, Zhao K, Bhandoola A. The transcription factor TCF-1 enforces commitment to the innate lymphoid cell lineage. Nature Immunology. PMID 31358996 DOI: 10.1038/s41590-019-0445-7  0.56
2019 Ku WL, Nakamura K, Gao W, Cui K, Hu G, Tang Q, Ni B, Zhao K. Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification. Nature Methods. 16: 323-325. PMID 30923384 DOI: 10.1038/s41592-019-0361-7  0.88
2019 Teague HL, Varghese NJ, Tsoi LC, Dey AK, Garshick MS, Silverman JI, Baumer Y, Harrington CL, Stempinski E, Elnabawi YA, Dagur PK, Cui K, Tunc I, Seifuddin F, Joshi AA, ... ... Zhao K, et al. Neutrophil Subsets, Platelets, and Vascular Disease in Psoriasis. Jacc. Basic to Translational Science. 4: 1-14. PMID 30847414 DOI: 10.1016/j.jacbts.2018.10.008  0.88
2018 Rodriguez J, Ren G, Day CR, Zhao K, Chow CC, Larson DR. Intrinsic Dynamics of a Human Gene Reveal the Basis of Expression Heterogeneity. Cell. PMID 30554876 DOI: 10.1016/j.cell.2018.11.026  0.52
2018 Lee SK, Xue Y, Shen W, Zhang Y, Joo Y, Ahmad M, Chinen M, Ding Y, Ku WL, De S, Lehrmann E, Becker KG, Lei EP, Zhao K, Zou S, et al. Topoisomerase 3β interacts with RNAi machinery to promote heterochromatin formation and transcriptional silencing in Drosophila. Nature Communications. 9: 4946. PMID 30470739 DOI: 10.1038/s41467-018-07101-4  0.56
2018 Lai B, Gao W, Cui K, Xie W, Tang Q, Jin W, Hu G, Ni B, Zhao K. Publisher Correction: Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing. Nature. PMID 30401810 DOI: 10.1038/s41586-018-0690-1  0.88
2018 Lai B, Gao W, Cui K, Xie W, Tang Q, Jin W, Hu G, Ni B, Zhao K. Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing. Nature. PMID 30258225 DOI: 10.1038/s41586-018-0567-3  0.88
2018 Kraushaar DC, Chen Z, Tang Q, Cui K, Zhang J, Zhao K. The gene repressor complex NuRD interacts with the histone variant H3.3 at promoters of active genes. Genome Research. PMID 30254051 DOI: 10.1101/gr.236224.118  0.88
2018 Fang D, Cui K, Mao K, Hu G, Li R, Zheng M, Riteau N, Reiner SL, Sher A, Zhao K, Zhu J. Transient T-bet expression functionally specifies a distinct T follicular helper subset. The Journal of Experimental Medicine. PMID 30232200 DOI: 10.1084/jem.20180927  0.88
2018 Lai B, Tang Q, Jin W, Hu G, Wangsa D, Cui K, Stanton BZ, Ren G, Ding Y, Zhao M, Liu S, Song J, Ried T, Zhao K. Trac-looping measures genome structure and chromatin accessibility. Nature Methods. PMID 30150754 DOI: 10.1038/s41592-018-0107-y  0.88
2018 Yu F, Sharma S, Jankovic D, Gurram RK, Su P, Hu G, Li R, Rieder S, Zhao K, Sun B, Zhu J. The transcription factor Bhlhe40 is a switch of inflammatory versus antiinflammatory Th1 cell fate determination. The Journal of Experimental Medicine. PMID 29773643 DOI: 10.1084/jem.20170155  0.52
2018 He Y, Zuo Q, Edwards J, Zhao K, Lei J, Cai W, Nie Q, Li B, Song J. DNA Methylation and Regulatory Elements during Chicken Germline Stem Cell Differentiation. Stem Cell Reports. PMID 29681542 DOI: 10.1016/j.stemcr.2018.03.018  0.48
2018 Fang D, Cui K, Hu G, Gurram RK, Zhong C, Oler AJ, Yagi R, Zhao M, Sharma S, Liu P, Sun B, Zhao K, Zhu J. Bcl11b, a novel GATA3-interacting protein, suppresses Th1 while limiting Th2 cell differentiation. The Journal of Experimental Medicine. PMID 29514917 DOI: 10.1084/jem.20171127  0.88
2018 Hu G, Cui K, Fang D, Hirose S, Wang X, Wangsa D, Jin W, Ried T, Liu P, Zhu J, Rothenberg EV, Zhao K. Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells. Immunity. 48: 227-242.e8. PMID 29466755 DOI: 10.1016/j.immuni.2018.01.013  0.88
2018 Hodges HC, Stanton BZ, Cermakova K, Chang CY, Miller EL, Kirkland JG, Ku WL, Veverka V, Zhao K, Crabtree GR. Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers. Nature Structural & Molecular Biology. 25: 61-72. PMID 29323272 DOI: 10.1038/s41594-017-0007-3  0.84
2018 Baranello L, Kouzine F, Wojtowicz D, Cui K, Zhao K, Przytycka TM, Capranico G, Levens D. Mapping DNA Breaks by Next-Generation Sequencing. Methods in Molecular Biology (Clifton, N.J.). 1672: 155-166. PMID 29043624 DOI: 10.1007/978-1-4939-7306-4_13  0.88
2017 Cooper J, Ding Y, Song J, Zhao K. Genome-wide mapping of DNase I hypersensitive sites in rare cell populations using single-cell DNase sequencing. Nature Protocols. 12: 2342-2354. PMID 29022941 DOI: 10.1038/nprot.2017.099  0.48
2017 Resto M, Kim BH, Fernandez AG, Abraham BJ, Zhao K, Lewis BA. O-GlcNAcase is an RNA polymerase II elongation factor coupled to pausing factors SPT5 and TIF1β. The Journal of Biological Chemistry. 292: 16524-16525. PMID 28986433 DOI: 10.1074/jbc.A116.751420  0.4
2017 Kidder BL, He R, Wangsa D, Padilla-Nash HM, Bernardo MM, Sheng S, Ried T, Zhao K. SMYD5 controls heterochromatin and chromosome integrity during embryonic stem cell differentiation. Cancer Research. PMID 28951459 DOI: 10.1158/0008-5472.CAN-17-0828  0.4
2017 Nakayama RT, Pulice JL, Valencia AM, McBride MJ, McKenzie ZM, Gillespie MA, Ku WL, Teng M, Cui K, Williams RT, Cassel SH, Qing H, Widmer CJ, Demetri GD, Irizarry RA, ... Zhao K, et al. SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters. Nature Genetics. PMID 28945250 DOI: 10.1038/ng.3958  0.88
2017 Ren G, Jin W, Cui K, Rodrigez J, Hu G, Zhang Z, Larson DR, Zhao K. CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression. Molecular Cell. 67: 1049-1058.e6. PMID 28938092 DOI: 10.1016/j.molcel.2017.08.026  0.88
2017 Zhang Y, Ku WL, Liu S, Cui K, Jin W, Tang Q, Lu W, Ni B, Zhao K. Genome-wide identification of histone H2A and histone variant H2A.Z-interacting proteins by bPPI-seq. Cell Research. PMID 28862252 DOI: 10.1038/cr.2017.112  0.88
2017 Placek K, Hu G, Cui K, Zhang D, Ding Y, Lee JE, Jang Y, Wang C, Konkel JE, Song J, Liu C, Ge K, Chen W, Zhao K. MLL4 prepares the enhancer landscape for Foxp3 induction via chromatin looping. Nature Immunology. PMID 28759003 DOI: 10.1038/ni.3812  0.88
2017 Northrup D, Yagi R, Cui K, Proctor WR, Wang C, Placek K, Pohl LR, Wang R, Ge K, Zhu J, Zhao K. Histone demethylases UTX and JMJD3 are required for NKT cell development in mice. Cell & Bioscience. 7: 25. PMID 28529687 DOI: 10.1186/s13578-017-0152-8  0.88
2017 Eun SH, Feng L, Cedeno-Rosario L, Gan Q, Wei G, Cui K, Zhao K, Chen X. Polycomb group gene E(z) is required for spermatogonial dedifferentiation in Drosophila adult testis. Journal of Molecular Biology. PMID 28434938 DOI: 10.1016/j.jmb.2017.04.012  0.88
2017 Stanton BZ, Hodges C, Crabtree GR, Zhao K. A General Non-Radioactive ATPase Assay for Chromatin Remodeling Complexes. Current Protocols in Chemical Biology. 9: 1-10. PMID 28253434 DOI: 10.1002/cpch.16  0.84
2017 Kidder BL, Hu G, Cui K, Zhao K. SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation. Epigenetics & Chromatin. 10: 8. PMID 28250819 DOI: 10.1186/s13072-017-0115-7  0.88
2017 Miller EL, Hargreaves DC, Kadoch C, Chang CY, Calarco JP, Hodges C, Buenrostro JD, Cui K, Greenleaf WJ, Zhao K, Crabtree GR. TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin. Nature Structural & Molecular Biology. PMID 28250416 DOI: 10.1038/nsmb.3384  0.88
2017 Barski A, Cuddapah S, Kartashov AV, Liu C, Imamichi H, Yang W, Peng W, Lane HC, Zhao K. Rapid Recall Ability of Memory T cells is Encoded in their Epigenome. Scientific Reports. 7: 39785. PMID 28054639 DOI: 10.1038/srep39785  1
2016 Stanton BZ, Hodges C, Calarco JP, Braun SM, Ku WL, Kadoch C, Zhao K, Crabtree GR. Smarca4 ATPase mutations disrupt direct eviction of PRC1 from chromatin. Nature Genetics. PMID 27941795 DOI: 10.1038/ng.3735  0.84
2016 Hu G, Zhao K. Looping around Bcl6 in Germinal Center to Sharpen B Cell Immunity. Immunity. 45: 459-61. PMID 27653595 DOI: 10.1016/j.immuni.2016.08.020  1
2016 Resto M, Kim BH, Fernandez AG, Abraham BJ, Zhao K, Lewis BA. O-GlcNAcase is an RNA pol II elongation factor coupled to pausing factors SPT5 and TIF1β. The Journal of Biological Chemistry. PMID 27601472 DOI: 10.1074/jbc.M116.751420  0.4
2016 Ni T, Yang W, Han M, Zhang Y, Shen T, Nie H, Zhou Z, Dai Y, Yang Y, Liu P, Cui K, Zeng Z, Tian Y, Zhou B, Wei G, ... Zhao K, et al. Global intron retention mediated gene regulation during CD4+ T cell activation. Nucleic Acids Research. PMID 27369383 DOI: 10.1093/nar/gkw591  1
2016 Wang RH, Zhao T, Cui K, Hu G, Chen Q, Chen W, Wang XW, Soto-Gutierrez A, Zhao K, Deng CX. Negative reciprocal regulation between Sirt1 and Per2 modulates the circadian clock and aging. Scientific Reports. 6: 28633. PMID 27346580 DOI: 10.1038/srep28633  0.88
2016 Lu F, Liu Y, Inoue A, Suzuki T, Zhao K, Zhang Y. Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development. Cell. 165: 1375-1388. PMID 27259149 DOI: 10.1016/j.cell.2016.05.050  0.56
2016 Li Y, Schulz VP, Deng C, Li G, Shen Y, Tusi BK, Ma G, Stees J, Qiu Y, Steiner LA, Zhou L, Zhao K, Bungert J, Gallagher PG, Huang S. Setd1a and NURF mediate chromatin dynamics and gene regulation during erythroid lineage commitment and differentiation. Nucleic Acids Research. PMID 27141965 DOI: 10.1093/nar/gkw327  1
2016 Baranello L, Wojtowicz D, Cui K, Devaiah BN, Chung HJ, Chan-Salis KY, Guha R, Wilson K, Zhang X, Zhang H, Piotrowski J, Thomas CJ, Singer DS, Pugh BF, Pommier Y, ... ... Zhao K, et al. RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription. Cell. 165: 357-371. PMID 27058666 DOI: 10.1016/j.cell.2016.02.036  1
2016 Zhong C, Cui K, Wilhelm C, Hu G, Mao K, Belkaid Y, Zhao K, Zhu J. Erratum: Group 3 innate lymphoid cells continuously require the transcription factor GATA-3 after commitment. Nature Immunology. 17: 469. PMID 27002848 DOI: 10.1038/ni0416-469c  0.88
2016 Kraushaar DC, Jin W, Maunakea A, Abraham B, Ha M, Zhao K. Erratum to: Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3. Genome Biology. 17: 21. PMID 26846280 DOI: 10.1186/s13059-016-0886-3  0.52
2016 He Y, Ding Y, Zhan F, Zhang H, Han B, Hu G, Zhao K, Yang N, Yu Y, Mao L, Song J. Corrigendum: The conservation and signatures of lincRNAs in Marek's disease of chicken. Scientific Reports. 6: 19422. PMID 26814149 DOI: 10.1038/srep19422  0.48
2016 Zhong C, Cui K, Wilhelm C, Hu G, Mao K, Belkaid Y, Zhao K, Zhu J. Erratum: Group 3 innate lymphoid cells continuously require the transcription factor GATA-3 after commitment. Nature Immunology. 17: 214. PMID 26784267 DOI: 10.1038/ni0216-214c  0.88
2016 Crompton JG, Narayanan M, Cuddapah S, Roychoudhuri R, Ji Y, Yang W, Patel SJ, Sukumar M, Palmer DC, Peng W, Wang E, Marincola FM, Klebanoff CA, Zhao K, Tsang JS, et al. Lineage relationship of CD8+ T cell subsets is revealed by progressive changes in the epigenetic landscape Cellular and Molecular Immunology. 13: 502-513. DOI: 10.1038/cmi.2015.32  1
2015 Jin W, Tang Q, Wan M, Cui K, Zhang Y, Ren G, Ni B, Sklar J, Przytycka TM, Childs R, Levens D, Zhao K. Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples. Nature. PMID 26605532 DOI: 10.1038/nature15740  0.96
2015 Zhong C, Cui K, Wilhelm C, Hu G, Mao K, Belkaid Y, Zhao K, Zhu J. Group 3 innate lymphoid cells continuously require the transcription factor GATA-3 after commitment. Nature Immunology. PMID 26595886 DOI: 10.1038/ni.3318  0.44
2015 He Y, Ding Y, Zhan F, Zhang H, Han B, Hu G, Zhao K, Yang N, Yu Y, Mao L, Song J. The conservation and signatures of lincRNAs in Marek's disease of chicken. Scientific Reports. 5: 15184. PMID 26471251 DOI: 10.1038/srep15184  1
2015 Nakatsukasa H, Zhang D, Maruyama T, Chen H, Cui K, Ishikawa M, Deng L, Zanvit P, Tu E, Jin W, Abbatiello B, Goldberg N, Chen Q, Sun L, Zhao K, et al. The DNA-binding inhibitor Id3 regulates IL-9 production in CD4(+) T cells. Nature Immunology. PMID 26322481 DOI: 10.1038/ni.3252  0.44
2015 Carrillo JA, He Y, Luo J, Menendez KR, Tablante NL, Zhao K, Paulson JN, Li B, Song J. Methylome Analysis in Chickens Immunized with Infectious Laryngotracheitis Vaccine. Plos One. 10: e0100476. PMID 26107953 DOI: 10.1371/journal.pone.0100476  1
2015 Zhao C, Carrillo JA, Tian F, Zan L, Updike SM, Zhao K, Zhan F, Song J. Genome-Wide H3K4me3 Analysis in Angus Cattle with Divergent Tenderness. Plos One. 10: e0115358. PMID 26086782 DOI: 10.1371/journal.pone.0115358  1
2015 Ren G, Cui K, Zhang Z, Zhao K. Division of labor between IRF1 and IRF2 in regulating different stages of transcriptional activation in cellular antiviral activities. Cell & Bioscience. 5: 17. PMID 25960866 DOI: 10.1186/s13578-015-0007-0  0.88
2015 Crompton JG, Narayanan M, Cuddapah S, Roychoudhuri R, Ji Y, Yang W, Patel SJ, Sukumar M, Palmer DC, Peng W, Wang E, Marincola FM, Klebanoff CA, Zhao K, Tsang JS, et al. Lineage relationship of CD8(+) T cell subsets is revealed by progressive changes in the epigenetic landscape. Cellular & Molecular Immunology. PMID 25914936 DOI: 10.1038/cmi.2015.032  1
2015 Mitra A, Luo J, He Y, Gu Y, Zhang H, Zhao K, Cui K, Song J. Histone modifications induced by MDV infection at early cytolytic and latency phases. Bmc Genomics. 16: 311. PMID 25896894 DOI: 10.1186/s12864-015-1492-6  1
2015 Krupovic M, Zhi N, Li J, Hu G, Koonin EV, Wong S, Shevchenko S, Zhao K, Young NS. Multiple layers of chimerism in a single-stranded DNA virus discovered by deep sequencing. Genome Biology and Evolution. 7: 993-1001. PMID 25840414 DOI: 10.1093/gbe/evv034  1
2014 Ha M, Kraushaar DC, Zhao K. Genome-wide analysis of H3.3 dissociation reveals high nucleosome turnover at distal regulatory regions of embryonic stem cells. Epigenetics & Chromatin. 7: 38. PMID 25598842 DOI: 10.1186/1756-8935-7-38  0.52
2014 Li Q, Zou J, Wang M, Ding X, Chepelev I, Zhou X, Zhao W, Wei G, Cui J, Zhao K, Wang HY, Wang RF. Critical role of histone demethylase Jmjd3 in the regulation of CD4+ T-cell differentiation. Nature Communications. 5: 5780. PMID 25531312 DOI: 10.1038/ncomms6780  1
2014 Dowen JM, Fan ZP, Hnisz D, Ren G, Abraham BJ, Zhang LN, Weintraub AS, Schuijers J, Lee TI, Zhao K, Young RA. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell. 159: 374-87. PMID 25303531 DOI: 10.1016/j.cell.2014.09.030  1
2014 Jin Q, Zhuang L, Lai B, Wang C, Li W, Dolan B, Lu Y, Wang Z, Zhao K, Peng W, Dent SY, Ge K. Gcn5 and PCAF negatively regulate interferon-β production through HAT-independent inhibition of TBK1. Embo Reports. 15: 1192-201. PMID 25269644 DOI: 10.15252/embr.201438990  0.56
2014 Li Q, Wang HY, Chepelev I, Zhu Q, Wei G, Zhao K, Wang RF. Stage-dependent and locus-specific role of histone demethylase Jumonji D3 (JMJD3) in the embryonic stages of lung development. Plos Genetics. 10: e1004524. PMID 25079229 DOI: 10.1371/journal.pgen.1004524  1
2014 Baranello L, Kouzine F, Wojtowicz D, Cui K, Przytycka TM, Zhao K, Levens D. DNA break mapping reveals topoisomerase II activity genome-wide. International Journal of Molecular Sciences. 15: 13111-22. PMID 25056547 DOI: 10.3390/ijms150713111  0.88
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  1
2014 Lhoumaud P, Hennion M, Gamot A, Cuddapah S, Queille S, Liang J, Micas G, Morillon P, Urbach S, Bouchez O, Severac D, Emberly E, Zhao K, Cuvier O. Insulators recruit histone methyltransferase dMes4 to regulate chromatin of flanking genes. The Embo Journal. 33: 1599-613. PMID 24916307 DOI: 10.15252/embj.201385965  1
2014 Escobar TM, Kanellopoulou C, Kugler DG, Kilaru G, Nguyen CK, Nagarajan V, Bhairavabhotla RK, Northrup D, Zahr R, Burr P, Liu X, Zhao K, Sher A, Jankovic D, Zhu J, et al. miR-155 activates cytokine gene expression in Th17 cells by regulating the DNA-binding protein Jarid2 to relieve polycomb-mediated repression. Immunity. 40: 865-79. PMID 24856900 DOI: 10.1016/j.immuni.2014.03.014  0.44
2014 Zhi N, Hu G, Wong S, Zhao K, Mao Q, Young NS. Reply to Naccache et al: Viral sequences of NIH-CQV virus, a contamination of DNA extraction method. Proceedings of the National Academy of Sciences of the United States of America. 111: E977. PMID 24829942 DOI: 10.1073/pnas.1318965111  1
2014 Hu G, Zhao K. Correlating histone modifi cation patterns with gene expression data during hematopoiesis Methods in Molecular Biology. 1150: 175-187. PMID 24743998 DOI: 10.1007/978-1-4939-0512-6_11  1
2014 Kidder BL, Zhao K. Efficient library preparation for next-generation sequencing analysis of genome-wide epigenetic and transcriptional landscapes in embryonic stem cells. Methods in Molecular Biology (Clifton, N.J.). 1150: 3-20. PMID 24743988 DOI: 10.1007/978-1-4939-0512-6_1  0.56
2014 Eun SH, Shi Z, Cui K, Zhao K, Chen X. A non-cell autonomous role of E(z) to prevent germ cells from turning on a somatic cell marker. Science (New York, N.Y.). 343: 1513-6. PMID 24675960 DOI: 10.1126/science.1246514  0.44
2014 Yagi R, Zhong C, Northrup DL, Yu F, Bouladoux N, Spencer S, Hu G, Barron L, Sharma S, Nakayama T, Belkaid Y, Zhao K, Zhu J. The transcription factor GATA3 is critical for the development of all IL-7Rα-expressing innate lymphoid cells. Immunity. 40: 378-88. PMID 24631153 DOI: 10.1016/j.immuni.2014.01.012  1
2014 Wang Y, Godec J, Ben-Aissa K, Cui K, Zhao K, Pucsek AB, Lee YK, Weaver CT, Yagi R, Lazarevic V. The transcription factors T-bet and Runx are required for the ontogeny of pathogenic interferon-γ-producing T helper 17 cells. Immunity. 40: 355-66. PMID 24530058 DOI: 10.1016/j.immuni.2014.01.002  1
2014 Kidder BL, Hu G, Zhao K. KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation. Genome Biology. 15: R32. PMID 24495580 DOI: 10.1186/gb-2014-15-2-r32  0.48
2014 Liang J, Lacroix L, Gamot A, Cuddapah S, Queille S, Lhoumaud P, Lepetit P, Martin PG, Vogelmann J, Court F, Hennion M, Micas G, Urbach S, Bouchez O, Nöllmann M, ... Zhao K, et al. Chromatin immunoprecipitation indirect peaks highlight long-range interactions of insulator proteins and Pol II pausing. Molecular Cell. 53: 672-81. PMID 24486021 DOI: 10.1016/j.molcel.2013.12.029  1
2014 Pattaradilokrat S, Li J, Wu J, Qi Y, Eastman RT, Zilversmit M, Nair SC, Huaman MC, Quinones M, Jiang H, Li N, Zhu J, Zhao K, Kaneko O, Long CA, et al. Plasmodium genetic loci linked to host cytokine and chemokine responses. Genes and Immunity. 15: 145-52. PMID 24452266 DOI: 10.1038/gene.2013.74  0.44
2014 Ramadoss P, Abraham BJ, Tsai L, Zhou Y, Costa-e-Sousa RH, Ye F, Bilban M, Zhao K, Hollenberg AN. Novel mechanism of positive versus negative regulation by thyroid hormone receptor β1 (TRβ1) identified by genome-wide profiling of binding sites in mouse liver. The Journal of Biological Chemistry. 289: 1313-28. PMID 24288132 DOI: 10.1074/jbc.M113.521450  1
2014 Tian Y, Ni D, Yang W, Zhang Y, Zhao K, Song J, Mao Q, Tian Z, van Velkinburgh JC, Yang D, Wu Y, Ni B. Telbivudine treatment corrects HBV-induced epigenetic alterations in liver cells of patients with chronic hepatitis B. Carcinogenesis. 35: 53-61. PMID 24067902 DOI: 10.1093/carcin/bgt317  0.68
2014 Patel B, Kang Y, Cui K, Litt M, Riberio MS, Deng C, Salz T, Casada S, Fu X, Qiu Y, Zhao K, Huang S. Aberrant TAL1 activation is mediated by an interchromosomal interaction in human T-cell acute lymphoblastic leukemia. Leukemia. 28: 349-61. PMID 23698277 DOI: 10.1038/leu.2013.158  0.88
2013 Kraushaar DC, Zhao K. The epigenomics of embryonic stem cell differentiation. International Journal of Biological Sciences. 9: 1134-44. PMID 24339734 DOI: 10.7150/ijbs.7998  0.52
2013 Kraushaar DC, Jin W, Maunakea A, Abraham B, Ha M, Zhao K. Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3. Genome Biology. 14: R121. PMID 24176123 DOI: 10.1186/gb-2013-14-10-r121  0.52
2013 Kidder BL, Hu G, Yu ZX, Liu C, Zhao K. Extended self-renewal and accelerated reprogramming in the absence of Kdm5b. Molecular and Cellular Biology. 33: 4793-810. PMID 24100015 DOI: 10.1128/MCB.00692-13  1
2013 Hu G, Tang Q, Sharma S, Yu F, Escobar TM, Muljo SA, Zhu J, Zhao K. Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation. Nature Immunology. 14: 1190-8. PMID 24056746 DOI: 10.1038/ni.2712  0.52
2013 Zhang P, Nakatsukasa H, Tu E, Kasagi S, Cui K, Ishikawa M, Konkel JE, Maruyama T, Wei G, Abbatiello B, Wang ZQ, Zhao K, Chen W. PARP-1 regulates expression of TGF-β receptors in T cells. Blood. 122: 2224-32. PMID 23940283 DOI: 10.1182/blood-2013-05-503250  0.88
2013 Maunakea AK, Chepelev I, Cui K, Zhao K. Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition Cell Research. 23: 1256-1269. PMID 23938295 DOI: 10.1038/cr.2013.110  1
2013 Jiang L, Mu J, Zhang Q, Ni T, Srinivasan P, Rayavara K, Yang W, Turner L, Lavstsen T, Theander TG, Peng W, Wei G, Jing Q, Wakabayashi Y, Bansal A, ... ... Zhao K, et al. PfSETvs methylation of histone H3K36 represses virulence genes in Plasmodium falciparum. Nature. 499: 223-7. PMID 23823717 DOI: 10.1038/nature12361  1
2013 Byeon B, Wang W, Barski A, Ranallo RT, Bao K, Schones DE, Zhao K, Wu C, Wu WH. The ATP-dependent chromatin remodeling enzyme Fun30 represses transcription by sliding promoter-proximal nucleosomes. The Journal of Biological Chemistry. 288: 23182-93. PMID 23779104 DOI: 10.1074/jbc.M113.471979  1
2013 Fu H, Maunakea AK, Martin MM, Huang L, Zhang Y, Ryan M, Kim R, Lin CM, Zhao K, Aladjem MI. Methylation of histone H3 on lysine 79 associates with a group of replication origins and helps limit DNA replication once per cell cycle. Plos Genetics. 9: e1003542. PMID 23754963 DOI: 10.1371/journal.pgen.1003542  1
2013 Deng C, Li Y, Liang S, Cui K, Salz T, Yang H, Tang Z, Gallagher PG, Qiu Y, Roeder R, Zhao K, Bungert J, Huang S. USF1 and hSET1A mediated epigenetic modifications regulate lineage differentiation and HoxB4 transcription. Plos Genetics. 9: e1003524. PMID 23754954 DOI: 10.1371/journal.pgen.1003524  1
2013 Xu B, Zhi N, Hu G, Wan Z, Zheng X, Liu X, Wong S, Kajigaya S, Zhao K, Mao Q, Young NS. Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing. Proceedings of the National Academy of Sciences of the United States of America. 110: 10264-9. PMID 23716702 DOI: 10.1073/pnas.1303744110  1
2013 Dykhuizen EC, Hargreaves DC, Miller EL, Cui K, Korshunov A, Kool M, Pfister S, Cho YJ, Zhao K, Crabtree GR. BAF complexes facilitate decatenation of DNA by topoisomerase IIα. Nature. 497: 624-7. PMID 23698369 DOI: 10.1038/nature12146  0.44
2013 Li L, Freudenberg J, Cui K, Dale R, Song SH, Dean A, Zhao K, Jothi R, Love PE. Ldb1-nucleated transcription complexes function as primary mediators of global erythroid gene activation. Blood. 121: 4575-85. PMID 23610375 DOI: 10.1182/blood-2013-01-479451  0.88
2013 Tian F, Zhan F, VanderKraats ND, Hiken JF, Edwards JR, Zhang H, Zhao K, Song J. DNMT gene expression and methylome in Marek's disease resistant and susceptible chickens prior to and following infection by MDV. Epigenetics. 8: 431-44. PMID 23538681 DOI: 10.4161/epi.24361  0.44
2013 Abraham BJ, Cui K, Tang Q, Zhao K. Dynamic regulation of epigenomic landscapes during hematopoiesis. Bmc Genomics. 14: 193. PMID 23510235 DOI: 10.1186/1471-2164-14-193  0.88
2013 Hu G, Cui K, Northrup D, Liu C, Wang C, Tang Q, Ge K, Levens D, Crane-Robinson C, Zhao K. H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation. Cell Stem Cell. 12: 180-92. PMID 23260488 DOI: 10.1016/j.stem.2012.11.003  0.88
2012 Ouyang W, Liao W, Luo CT, Yin N, Huse M, Kim MV, Peng M, Chan P, Ma Q, Mo Y, Meijer D, Zhao K, Rudensky AY, Atwal G, Zhang MQ, et al. Novel Foxo1-dependent transcriptional programs control T(reg) cell function. Nature. 491: 554-9. PMID 23135404 DOI: 10.1038/nature11581  1
2012 Jia J, Zheng X, Hu G, Cui K, Zhang J, Zhang A, Jiang H, Lu B, Yates J, Liu C, Zhao K, Zheng Y. Regulation of pluripotency and self- renewal of ESCs through epigenetic-threshold modulation and mRNA pruning. Cell. 151: 576-89. PMID 23101626 DOI: 10.1016/j.cell.2012.09.023  1
2012 Mitra A, Luo J, Zhang H, Cui K, Zhao K, Song J. Marek's disease virus infection induces widespread differential chromatin marks in inbred chicken lines. Bmc Genomics. 13: 557. PMID 23072359 DOI: 10.1186/1471-2164-13-557  1
2012 Zhu J, Jankovic D, Oler AJ, Wei G, Sharma S, Hu G, Guo L, Yagi R, Yamane H, Punkosdy G, Feigenbaum L, Zhao K, Paul WE. The transcription factor T-bet is induced by multiple pathways and prevents an endogenous Th2 cell program during Th1 cell responses. Immunity. 37: 660-73. PMID 23041064 DOI: 10.1016/j.immuni.2012.09.007  1
2012 Nie Z, Hu G, Wei G, Cui K, Yamane A, Resch W, Wang R, Green DR, Tessarollo L, Casellas R, Zhao K, Levens D. c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells. Cell. 151: 68-79. PMID 23021216 DOI: 10.1016/j.cell.2012.08.033  1
2012 Rogers H, Wang L, Yu X, Alnaeeli M, Cui K, Zhao K, Bieker JJ, Prchal J, Huang S, Weksler B, Noguchi CT. T-cell acute leukemia 1 (TAL1) regulation of erythropoietin receptor and association with excessive erythrocytosis. The Journal of Biological Chemistry. 287: 36720-31. PMID 22982397 DOI: 10.1074/jbc.M112.378398  1
2012 Wei G, Hu G, Cui K, Zhao K. Genome-wide mapping of nucleosome occupancy, histone modifications, and gene expression using next-generation sequencing technology. Methods in Enzymology. 513: 297-313. PMID 22929775 DOI: 10.1016/B978-0-12-391938-0.00013-6  0.88
2012 LeRoy G, Chepelev I, DiMaggio PA, Blanco MA, Zee BM, Zhao K, Garcia BA. Proteo-Genomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins Genome Biology. R68. PMID 22897906 DOI: 10.1186/gb-2012-13-8-r68  0.8
2012 Luo J, Mitra A, Tian F, Chang S, Zhang H, Cui K, Yu Y, Zhao K, Song J. Histone methylation analysis and pathway predictions in chickens after MDV infection. Plos One. 7: e41849. PMID 22848633 DOI: 10.1371/journal.pone.0041849  1
2012 Cuddapah S, Roh TY, Cui K, Jose CC, Fuller MT, Zhao K, Chen X. A novel human polycomb binding site acts as a functional polycomb response element in Drosophila. Plos One. 7: e36365. PMID 22570707 DOI: 10.1371/journal.pone.0036365  1
2012 Hao H, Kim DS, Klocke B, Johnson KR, Cui K, Gotoh N, Zang C, Gregorski J, Gieser L, Peng W, Fann Y, Seifert M, Zhao K, Swaroop A. Transcriptional regulation of rod photoreceptor homeostasis revealed by in vivo NRL targetome analysis. Plos Genetics. 8: e1002649. PMID 22511886 DOI: 10.1371/journal.pgen.1002649  1
2012 Cowley AW, Nadeau JH, Baccarelli A, Berecek K, Fornage M, Gibbons GH, Harrison DG, Liang M, Nathanielsz PW, O'Connor DT, Ordovas J, Peng W, Soares MB, Szyf M, Tolunay HE, ... ... Zhao K, et al. Report of the National Heart, Lung, and Blood Institute Working Group on epigenetics and hypertension. Hypertension. 59: 899-905. PMID 22431584 DOI: 10.1161/HYPERTENSIONAHA.111.190116  1
2012 Chepelev I, Wei G, Wangsa D, Tang Q, Zhao K. Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization Cell Research. 22: 490-503. PMID 22270183 DOI: 10.1038/cr.2012.15  1
2012 Cui K, Zhao K. Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq Methods in Molecular Biology. 833: 413-419. PMID 22183607 DOI: 10.1007/978-1-61779-477-3_24  1
2011 López-Barragán MJ, Lemieux J, Quiñones M, Williamson KC, Molina-Cruz A, Cui K, Barillas-Mury C, Zhao K, Su XZ. Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum. Bmc Genomics. 12: 587. PMID 22129310 DOI: 10.1186/1471-2164-12-587  0.88
2011 Dmitrieva NI, Cui K, Kitchaev DA, Zhao K, Burg MB. DNA double-strand breaks induced by high NaCl occur predominantly in gene deserts Proceedings of the National Academy of Sciences of the United States of America. 108: 20796-20801. PMID 22106305 DOI: 10.1073/pnas.1114677108  1
2011 Wohlfert EA, Grainger JR, Bouladoux N, Konkel JE, Oldenhove G, Ribeiro CH, Hall JA, Yagi R, Naik S, Bhairavabhotla R, Paul WE, Bosselut R, Wei G, Zhao K, Oukka M, et al. GATA3 controls Foxp3⁺ regulatory T cell fate during inflammation in mice. The Journal of Clinical Investigation. 121: 4503-15. PMID 21965331 DOI: 10.1172/JCI57456  1
2011 Kidder BL, Hu G, Zhao K. ChIP-Seq: technical considerations for obtaining high-quality data. Nature Immunology. 12: 918-22. PMID 21934668 DOI: 10.1038/ni.2117  1
2011 Wei G, Abraham BJ, Yagi R, Jothi R, Cui K, Sharma S, Narlikar L, Northrup DL, Tang Q, Paul WE, Zhu J, Zhao K. Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types. Immunity. 35: 299-311. PMID 21867929 DOI: 10.1016/j.immuni.2011.08.007  1
2011 Hu G, Schones DE, Cui K, Ybarra R, Northrup D, Tang Q, Gattinoni L, Restifo NP, Huang S, Zhao K. Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1. Genome Research. 21: 1650-8. PMID 21795385 DOI: 10.1101/gr.121145.111  1
2011 Peng W, Zhao K. An integrated strategy for identification of both sharp and broad peaks from next-generation sequencing data. Genome Biology. 12: 120. PMID 21787381 DOI: 10.1186/gb-2011-12-7-120  1
2011 Kang B, Pu M, Hu G, Wen W, Dong Z, Zhao K, Stillman B, Zhang Z. Phosphorylation of H4 Ser 47 promotes HIRA-mediated nucleosome assembly. Genes & Development. 25: 1359-64. PMID 21724829 DOI: 10.1101/gad.2055511  0.48
2011 Lin N, Li X, Cui K, Chepelev I, Tie F, Liu B, Li G, Harte P, Zhao K, Huang S, Zhou L. A barrier-only boundary element delimits the formation of facultative heterochromatin in Drosophila melanogaster and vertebrates. Molecular and Cellular Biology. 31: 2729-41. PMID 21518956 DOI: 10.1128/MCB.05165-11  1
2011 Wu H, D'Alessio AC, Ito S, Wang Z, Cui K, Zhao K, Sun YE, Zhang Y. Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes & Development. 25: 679-84. PMID 21460036 DOI: 10.1101/gad.2036011  1
2011 Wu H, D'Alessio AC, Ito S, Xia K, Wang Z, Cui K, Zhao K, Sun YE, Zhang Y. Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature. 473: 389-93. PMID 21451524 DOI: 10.1038/nature09934  1
2011 Tao Y, Xi S, Shan J, Maunakea A, Che A, Briones V, Lee EY, Geiman T, Huang J, Stephens R, Leighty RM, Zhao K, Muegge K. Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences. Proceedings of the National Academy of Sciences of the United States of America. 108: 5626-31. PMID 21427231 DOI: 10.1073/pnas.1017000108  0.4
2011 Xu Z, Wei G, Chepelev I, Zhao K, Felsenfeld G. Mapping of INS promoter interactions reveals its role in long-range regulation of SYT8 transcription. Nature Structural & Molecular Biology. 18: 372-8. PMID 21336277 DOI: 10.1038/nsmb.1993  1
2011 Li L, Jothi R, Cui K, Lee JY, Cohen T, Gorivodsky M, Tzchori I, Zhao Y, Hayes SM, Bresnick EH, Zhao K, Westphal H, Love PE. Nuclear adaptor Ldb1 regulates a transcriptional program essential for the maintenance of hematopoietic stem cells. Nature Immunology. 12: 129-36. PMID 21186366 DOI: 10.1038/ni.1978  1
2011 Cuddapah S, Schones DE, Cui K, Roh TY, Barski A, Wei G, Rochman M, Bustin M, Zhao K. Genomic profiling of HMGN1 reveals an association with chromatin at regulatory regions. Molecular and Cellular Biology. 31: 700-9. PMID 21173166 DOI: 10.1128/MCB.00740-10  1
2011 Yu S, Cui K, Jothi R, Zhao DM, Jing X, Zhao K, Xue HH. GABP controls a critical transcription regulatory module that is essential for maintenance and differentiation of hematopoietic stem/progenitor cells. Blood. 117: 2166-78. PMID 21139080 DOI: 10.1182/blood-2010-09-306563  1
2011 Wu K, Jiao X, Li Z, Katiyar S, Casimiro MC, Yang W, Zhang Q, Willmarth NE, Chepelev I, Crosariol M, Wei Z, Hu J, Zhao K, Pestell RG. Cell fate determination factor Dachshund reprograms breast cancer stem cell function Journal of Biological Chemistry. 286: 2132-2142. PMID 20937839 DOI: 10.1074/jbc.M110.148395  1
2010 Daniel JA, Santos MA, Wang Z, Zang C, Schwab KR, Jankovic M, Filsuf D, Chen HT, Gazumyan A, Yamane A, Cho YW, Sun HW, Ge K, Peng W, Nussenzweig MC, ... ... Zhao K, et al. PTIP promotes chromatin changes critical for immunoglobulin class switch recombination Science. 329: 917-923. PMID 20671152 DOI: 10.1126/science.1187942  1
2010 Qi HH, Sarkissian M, Hu GQ, Wang Z, Bhattacharjee A, Gordon DB, Gonzales M, Lan F, Ongusaha PP, Huarte M, Yaghi NK, Lim H, Garcia BA, Brizuela L, Zhao K, et al. Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. Nature. 466: 503-7. PMID 20622853 DOI: 10.1038/nature09261  1
2010 Gan Q, Chepelev I, Wei G, Tarayrah L, Cui K, Zhao K, Chen X. Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq Cell Research. 20: 763-783. PMID 20440302 DOI: 10.1038/cr.2010.64  1
2010 Barski A, Chepelev I, Liko D, Cuddapah S, Fleming AB, Birch J, Cui K, White RJ, Zhao K. Pol II and its associated epigenetic marks are present at Pol III-transcribed noncoding RNA genes. Nature Structural & Molecular Biology. 17: 629-34. PMID 20418881 DOI: 10.1038/nsmb.1806  1
2010 Yagi R, Junttila IS, Wei G, Urban JF, Zhao K, Paul WE, Zhu J. The transcription factor GATA3 actively represses RUNX3 protein-regulated production of interferon-gamma. Immunity. 32: 507-17. PMID 20399120 DOI: 10.1016/j.immuni.2010.04.004  1
2010 Gan Q, Schones DE, Ho Eun S, Wei G, Cui K, Zhao K, Chen X. Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis. Genome Biology. 11: R42. PMID 20398323 DOI: 10.1186/gb-2010-11-4-r42  1
2010 Zhou J, Wang C, Wang Z, Dampier W, Wu K, Casimiro MC, Chepelev I, Popov VM, Quong A, Tozeren A, Zhao K, Lisanti MP, Pestell RG. Attenuation of Forkhead signaling by the retinal determination factor DACH1 Proceedings of the National Academy of Sciences of the United States of America. 107: 6864-6869. PMID 20351289 DOI: 10.1073/pnas.1002746107  1
2010 Cuddapah S, Barski A, Zhao K. Epigenomics of T cell activation, differentiation, and memory. Current Opinion in Immunology. 22: 341-7. PMID 20226645 DOI: 10.1016/j.coi.2010.02.007  1
2010 He HH, Meyer CA, Shin H, Bailey ST, Wei G, Wang Q, Zhang Y, Xu K, Ni M, Lupien M, Mieczkowski P, Lieb JD, Zhao K, Brown M, Liu XS. Nucleosome dynamics define transcriptional enhancers. Nature Genetics. 42: 343-7. PMID 20208536 DOI: 10.1038/ng.545  0.8
2009 Cuddapah S, Barski A, Cui K, Schones DE, Wang Z, Wei G, Zhao K. Native chromatin preparation and Illumina/Solexa library construction. Cold Spring Harbor Protocols. 2009: pdb.prot5237. PMID 20147195 DOI: 10.1101/pdb.prot5237  1
2009 Barski A, Jothi R, Cuddapah S, Cui K, Roh TY, Schones DE, Zhao K. Chromatin poises miRNA- and protein-coding genes for expression. Genome Research. 19: 1742-51. PMID 19713549 DOI: 10.1101/gr.090951.109  1
2009 Wang Z, Zang C, Cui K, Schones DE, Barski A, Peng W, Zhao K. Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell. 138: 1019-31. PMID 19698979 DOI: 10.1016/j.cell.2009.06.049  1
2009 Lin B, Wang J, Hong X, Yan X, Hwang D, Cho JH, Yi D, Utleg AG, Fang X, Schones DE, Zhao K, Omenn GS, Hood L. Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor. Plos One. 4: e6589. PMID 19668381 DOI: 10.1371/journal.pone.0006589  1
2009 Jin C, Zang C, Wei G, Cui K, Peng W, Zhao K, Felsenfeld G. H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nature Genetics. 41: 941-5. PMID 19633671 DOI: 10.1038/ng.409  1
2009 Chepelev I, Wei G, Tang Q, Zhao K. Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq. Nucleic Acids Research. 37: e106. PMID 19528076 DOI: 10.1093/nar/gkp507  1
2009 Araki Y, Wang Z, Zang C, Wood WH, Schones D, Cui K, Roh TY, Lhotsky B, Wersto RP, Peng W, Becker KG, Zhao K, Weng NP. Genome-wide analysis of histone methylation reveals chromatin state-based regulation of gene transcription and function of memory CD8+ T cells. Immunity. 30: 912-25. PMID 19523850 DOI: 10.1016/j.immuni.2009.05.006  1
2009 Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics (Oxford, England). 25: 1952-8. PMID 19505939 DOI: 10.1093/bioinformatics/btp340  1
2009 Kallin EM, Cao R, Jothi R, Xia K, Cui K, Zhao K, Zhang Y. Genome-wide uH2A localization analysis highlights Bmi1-dependent deposition of the mark at repressed genes. Plos Genetics. 5: e1000506. PMID 19503595 DOI: 10.1371/journal.pgen.1000506  1
2009 Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ. Determination of enriched histone modifications in non-genic portions of the human genome. Bmc Genomics. 10: 143. PMID 19335899 DOI: 10.1186/1471-2164-10-143  1
2009 Wang Z, Schones DE, Zhao K. Characterization of human epigenomes. Current Opinion in Genetics & Development. 19: 127-34. PMID 19299119 DOI: 10.1016/j.gde.2009.02.001  1
2009 Ho L, Jothi R, Ronan JL, Cui K, Zhao K, Crabtree GR. An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Proceedings of the National Academy of Sciences of the United States of America. 106: 5187-91. PMID 19279218 DOI: 10.1073/pnas.0812888106  1
2009 Zhu J, Davidson TS, Wei G, Jankovic D, Cui K, Schones DE, Guo L, Zhao K, Shevach EM, Paul WE. Down-regulation of Gfi-1 expression by TGF-beta is important for differentiation of Th17 and CD103+ inducible regulatory T cells. The Journal of Experimental Medicine. 206: 329-41. PMID 19188499 DOI: 10.1084/jem.20081666  1
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  1
2009 Barski A, Zhao K. Genomic location analysis by ChIP-Seq. Journal of Cellular Biochemistry. 107: 11-8. PMID 19173299 DOI: 10.1002/jcb.22077  1
2009 Wei G, Wei L, Zhu J, Zang C, Hu-Li J, Yao Z, Cui K, Kanno Y, Roh TY, Watford WT, Schones DE, Peng W, Sun HW, Paul WE, O'Shea JJ, ... Zhao K, et al. Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. Immunity. 30: 155-67. PMID 19144320 DOI: 10.1016/j.immuni.2008.12.009  1
2009 Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W, Zhao K. Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell. 4: 80-93. PMID 19128795 DOI: 10.1016/j.stem.2008.11.011  1
2009 Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Research. 19: 24-32. PMID 19056695 DOI: 10.1101/gr.082800.108  1
2008 Liao W, Schones DE, Oh J, Cui Y, Cui K, Roh TY, Zhao K, Leonard WJ. Priming for T helper type 2 differentiation by interleukin 2-mediated induction of interleukin 4 receptor alpha-chain expression. Nature Immunology. 9: 1288-96. PMID 18820682 DOI: 10.1038/ni.1656  1
2008 Jothi R, Cuddapah S, Barski A, Cui K, Zhao K. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Research. 36: 5221-31. PMID 18684996 DOI: 10.1093/nar/gkn488  1
2008 Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nature Genetics. 40: 897-903. PMID 18552846 DOI: 10.1038/ng.154  1
2008 Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. Dynamic regulation of nucleosome positioning in the human genome. Cell. 132: 887-98. PMID 18329373 DOI: 10.1016/j.cell.2008.02.022  1
2008 Roh TY, Zhao K. High-resolution, genome-wide mapping of chromatin modifications by GMAT. Methods in Molecular Biology (Clifton, N.J.). 387: 95-108. PMID 18287625 DOI: 10.1007/978-1-59745-454-4_7  0.92
2008 Schones DE, Zhao K. Genome-wide approaches to studying chromatin modifications. Nature Reviews. Genetics. 9: 179-91. PMID 18250624 DOI: 10.1038/nrg2270  1
2008 Cuddapah S, Cui K, Zhao K. Transcriptional enhancer factor 1 (TEF-1/TEAD1) mediates activation of IFITM3 gene by BRGl Febs Letters. 582: 391-397. PMID 18177740 DOI: 10.1016/j.febslet.2007.12.033  1
2007 Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-Resolution Profiling of Histone Methylations in the Human Genome Cell. 129: 823-837. PMID 17512414 DOI: 10.1016/j.cell.2007.05.009  1
2007 Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. Response: Mapping Nucleosome Positions Using ChIP-Seq Data Cell. 131: 832-833. DOI: 10.1016/j.cell.2007.11.018  1
2006 Cuddapah S, Zhao K. Genome-wide mapping of histone modifications by GMAT. Biotechnology & Genetic Engineering Reviews. 23: 93-103. PMID 22530504  1
2006 Roh TY, Cuddapah S, Cui K, Zhao K. The genomic landscape of histone modifications in human T cells. Proceedings of the National Academy of Sciences of the United States of America. 103: 15782-7. PMID 17043231 DOI: 10.1073/pnas.0607617103  1
2006 Liu J, Kouzine F, Nie Z, Chung HJ, Elisha-Feil Z, Weber A, Zhao K, Levens D. The FUSE/FBP/FIR/TFIIH system is a molecular machine programming a pulse of c-myc expression. The Embo Journal. 25: 2119-30. PMID 16628215 DOI: 10.1038/sj.emboj.7601101  1
2006 Liu H, Mulholland N, Fu H, Zhao K. Cooperative activity of BRG1 and Z-DNA formation in chromatin remodeling. Molecular and Cellular Biology. 26: 2550-9. PMID 16537901 DOI: 10.1128/MCB.26.7.2550-2559.2006  0.32
2005 Yan Z, Cui K, Murray DM, Ling C, Xue Y, Gerstein A, Parsons R, Zhao K, Wang W. PBAF chromatin-remodeling complex requires a novel specificity subunit, BAF200, to regulate expression of selective interferon-responsive genes. Genes & Development. 19: 1662-7. PMID 15985610 DOI: 10.1101/gad.1323805  0.88
2005 Roh TY, Cuddapah S, Zhao K. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes & Development. 19: 542-52. PMID 15706033 DOI: 10.1101/gad.1272505  1
2004 Roh TY, Ngau WC, Cui K, Landsman D, Zhao K. High-resolution genome-wide mapping of histone modifications. Nature Biotechnology. 22: 1013-6. PMID 15235610 DOI: 10.1038/nbt990  0.92
2004 Liu H, Zhao K. Assay of Z-DNA Induction by Chromatin Remodeling Factors Methods in Enzymology. 377: 412-420. PMID 14979042 DOI: 10.1016/S0076-6879(03)77027-X  1
2004 Kang H, Cui K, Zhao K. BRG1 Controls the Activity of the Retinoblastoma Protein via Regulation of p21CIP1/WAF1/SDI Molecular and Cellular Biology. 24: 1188-1199. PMID 14729964 DOI: 10.1128/MCB.24.3.1188-1199.2004  1
2002 Chi TH, Wan M, Zhao K, Taniuchi I, Chen L, Littman DR, Crabtree GR. Reciprocal regulation of CD4/CD8 expression by SWI/SNF-like BAF complexes. Nature. 418: 195-9. PMID 12110891 DOI: 10.1038/nature00876  0.84
2002 Rando OJ, Zhao K, Janmey P, Crabtree GR. Phosphatidylinositol-dependent actin filament binding by the SWI/SNF-like BAF chromatin remodeling complex. Proceedings of the National Academy of Sciences of the United States of America. 99: 2824-9. PMID 11880634 DOI: 10.1073/pnas.032662899  1
2000 Rando OJ, Zhao K, Crabtree GR. Searching for a function for nuclear actin. Trends in Cell Biology. 10: 92-7. PMID 10675902 DOI: 10.1016/S0962-8924(99)01713-4  1
1998 Zhao K, Wang W, Rando OJ, Xue Y, Swiderek K, Kuo A, Crabtree GR. Rapid and phosphoinositol-dependent binding of the SWI/SNF-like BAF complex to chromatin after T lymphocyte receptor signaling. Cell. 95: 625-36. PMID 9845365  1
1997 Hart CM, Zhao K, Laemmli UK. The scs' boundary element: Characterization of boundary element- associated factors Molecular and Cellular Biology. 17: 999-1009. PMID 9001253 DOI: 10.1128/MCB.17.2.999  1
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