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

123 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
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  0.44
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  0.76
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  0.76
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  0.44
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.44
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.76
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  0.44
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  0.76
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  0.76
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  0.96
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  0.44
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  0.96
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  0.96
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  0.76
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  0.96
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  0.96
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  0.76
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  0.76
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  0.76
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  0.96
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  0.76
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  0.96
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  0.96
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  0.76
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.76
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  0.96
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  0.96
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  0.96
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  0.96
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  0.76
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  0.96
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  0.96
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  0.96
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  0.96
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  0.72
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  0.96
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  0.76
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.76
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  0.76
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  0.76
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  0.76
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.76
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  0.56
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.76
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.8
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.8
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  0.96
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  0.8
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  0.96
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  0.96
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  0.96
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  0.96
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  0.8
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  0.96
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  0.96
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  0.96
2008 Schones DE, Zhao K. Genome-wide approaches to studying chromatin modifications. Nature Reviews. Genetics. 9: 179-91. PMID 18250624 DOI: 10.1038/nrg2270  0.8
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  0.96
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  0.96
2006 Cuddapah S, Zhao K. Genome-wide mapping of histone modifications by GMAT. Biotechnology & Genetic Engineering Reviews. 23: 93-103. PMID 22530504  0.96
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  0.96
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  0.96
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  0.44
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  0.96
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