Keji Zhao

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc An integrated strategy for identification of both sharp and broad peaks from next-generation sequencing data
    Weiqun Peng
    Department of Physics, The George Washington University, 725 21st Street NW, Washington, DC 20052, USA
    Genome Biol 12:120. 2011
  2. pmc Dynamic regulation of epigenomic landscapes during hematopoiesis
    Brian J Abraham
    Systems Biology Center, NHLBI, NIH, Rockville Pike, Bethesda, MD, USA
    BMC Genomics 14:193. 2013
  3. pmc An anti-cancer Smurf
    Keji Zhao
    Systems Biology Center, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, Bethesda, Maryland 20892, USA
    Cell Biosci 2:10. 2012
  4. pmc SWI/SNF-mediated chromatin remodeling induces Z-DNA formation on a nucleosome
    Niveen Mulholland
    Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Maryland, USA
    Cell Biosci 2:3. 2012
  5. pmc Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis
    Qiang Gan
    Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
    Genome Biol 11:R42. 2010
  6. pmc Profiling RE1/REST-mediated histone modifications in the human genome
    Deyou Zheng
    Institute for Brain Disorders and Neural Regeneration, Department of Neurology, Rose F Kennedy Center for the Study of Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Genome Biol 10:R9. 2009
  7. doi request reprint Genome-wide mapping of nucleosome occupancy, histone modifications, and gene expression using next-generation sequencing technology
    Gang Wei
    Systems Biology Center, NHLBI, NIH, Bethesda, Maryland, USA
    Methods Enzymol 513:297-313. 2012
  8. pmc H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation
    Gangqing Hu
    Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Cell Stem Cell 12:180-92. 2013
  9. pmc T-cell acute leukemia 1 (TAL1) regulation of erythropoietin receptor and association with excessive erythrocytosis
    Heather Rogers
    Molecular Medicine Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892 1822, USA
    J Biol Chem 287:36720-31. 2012
  10. pmc Ldb1-nucleated transcription complexes function as primary mediators of global erythroid gene activation
    Liqi Li
    Section on Cellular and Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
    Blood 121:4575-85. 2013

Collaborators

Detail Information

Publications23

  1. pmc An integrated strategy for identification of both sharp and broad peaks from next-generation sequencing data
    Weiqun Peng
    Department of Physics, The George Washington University, 725 21st Street NW, Washington, DC 20052, USA
    Genome Biol 12:120. 2011
    ..A novel integrative approach has been developed by Lieb and colleagues for analyzing genome-wide datasets of different chromatin-binding factors and epigenetic states that exhibit both sharp and diffuse signals on the genome...
  2. pmc Dynamic regulation of epigenomic landscapes during hematopoiesis
    Brian J Abraham
    Systems Biology Center, NHLBI, NIH, Rockville Pike, Bethesda, MD, USA
    BMC Genomics 14:193. 2013
    ..Transcriptional regulation has been mostly studied using in vitro systems while epigenetic changes occurring during in vivo development remain poorly understood...
  3. pmc An anti-cancer Smurf
    Keji Zhao
    Systems Biology Center, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, Bethesda, Maryland 20892, USA
    Cell Biosci 2:10. 2012
    ..ABSTRACT: A novel, cancer-fighting function was recently discovered for Smad ubiquitination regulatory factor 2 (Smurf2)...
  4. pmc SWI/SNF-mediated chromatin remodeling induces Z-DNA formation on a nucleosome
    Niveen Mulholland
    Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Maryland, USA
    Cell Biosci 2:3. 2012
    ..abstract:..
  5. pmc Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis
    Qiang Gan
    Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
    Genome Biol 11:R42. 2010
    ..Previous studies have been performed using cultured mammalian embryonic stem cells. To a lesser extent, chromatin structure has been delineated in other model organisms, such as Drosophila, to open new avenues for genetic analyses...
  6. pmc Profiling RE1/REST-mediated histone modifications in the human genome
    Deyou Zheng
    Institute for Brain Disorders and Neural Regeneration, Department of Neurology, Rose F Kennedy Center for the Study of Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Genome Biol 10:R9. 2009
    ....
  7. doi request reprint Genome-wide mapping of nucleosome occupancy, histone modifications, and gene expression using next-generation sequencing technology
    Gang Wei
    Systems Biology Center, NHLBI, NIH, Bethesda, Maryland, USA
    Methods Enzymol 513:297-313. 2012
    ..We also describe RNA-Seq protocols used to map global gene expression profiles...
  8. pmc H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation
    Gangqing Hu
    Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Cell Stem Cell 12:180-92. 2013
    ..We propose that H2A.Z mediates such contrasting activities by acting as a general facilitator that generates access for a variety of complexes, both activating and repressive...
  9. pmc T-cell acute leukemia 1 (TAL1) regulation of erythropoietin receptor and association with excessive erythrocytosis
    Heather Rogers
    Molecular Medicine Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892 1822, USA
    J Biol Chem 287:36720-31. 2012
    ..These data suggest that TAL1 binds to the EPO-R promoter to activate EPO-R expression and provides a potential link to elevated EPO-R expression leading to hypersensitivity to erythropoietin and the resultant excessive erythrocytosis...
  10. pmc Ldb1-nucleated transcription complexes function as primary mediators of global erythroid gene activation
    Liqi Li
    Section on Cellular and Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
    Blood 121:4575-85. 2013
    ..Together, these results provide a foundation for defining the mechanism and scope of Ldb1 complex activity during erythropoiesis...
  11. pmc Marek's disease virus infection induces widespread differential chromatin marks in inbred chicken lines
    Apratim Mitra
    Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA
    BMC Genomics 13:557. 2012
    ..Also, epigenetic factors are believed to be one of the major determinants of disease response...
  12. pmc The transcription factor T-bet is induced by multiple pathways and prevents an endogenous Th2 cell program during Th1 cell responses
    Jinfang Zhu
    Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Immunity 37:660-73. 2012
    ..Our study revealed redundancy and synergy among several Th1 cell-inducing pathways in regulating the expression of T-bet and IFN-γ, and a critical role of T-bet in suppressing an endogenous Th2 cell-associated program...
  13. pmc Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq
    Kairong Cui
    Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
    Methods Mol Biol 833:413-9. 2012
    ..This chapter outlines the reagents and experimental procedures of MNase-Seq for mapping nucleosome positions in the human genome...
  14. pmc Methylation of histone H3 on lysine 79 associates with a group of replication origins and helps limit DNA replication once per cell cycle
    Haiqing Fu
    Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
    PLoS Genet 9:e1003542. 2013
    ..These data are consistent with the hypothesis that dimethylated H3K79 associates with some replication origins and marks replicated chromatin during S-phase to prevent re-replication and preserve genomic stability...
  15. pmc c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells
    Zuqin Nie
    Laboratory of Pathology, NCI, Bethesda, MD 20892, USA
    Cell 151:68-79. 2012
    ..This rule of Myc action explains the vast majority of Myc biology observed in literature...
  16. pmc Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization
    Iouri Chepelev
    Systems Biology Center, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
    Cell Res 22:490-503. 2012
    ..The Gene Expression Omnibus accession number for the raw and analyzed chromatin interaction data is GSE32677...
  17. pmc Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1
    Gangqing Hu
    Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 21:1650-8. 2011
    ..Intriguingly, we find that the nucleosome shifting specifically facilitates binding of TAL1 but not GATA1 and is linked to subsequent transcriptional regulation of target genes...
  18. pmc Transcriptional regulation of rod photoreceptor homeostasis revealed by in vivo NRL targetome analysis
    Hong Hao
    Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Genet 8:e1002649. 2012
    ..Our studies identify candidate genes for retinal dystrophies, define cis-regulatory module(s) for photoreceptor-expressed genes and provide a framework for decoding transcriptional regulatory networks that dictate rod homeostasis...
  19. pmc Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types
    Gang Wei
    Laboratory of Molecular Immunology, NHLBI, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
    Immunity 35:299-311. 2011
    ....
  20. pmc GATA3 controls Foxp3⁺ regulatory T cell fate during inflammation in mice
    Elizabeth A Wohlfert
    Mucosal Immunology Unit, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
    J Clin Invest 121:4503-15. 2011
    ..Overall, our work reveals what we believe to be a new facet in the complex role of GATA3 in T cells and highlights what may be a fundamental role in controlling Treg physiology during inflammation...
  21. pmc DNA double-strand breaks induced by high NaCl occur predominantly in gene deserts
    Natalia I Dmitrieva
    Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 108:20796-801. 2011
    ..We propose that the universal presence of NaCl around animal cells has directly influenced the evolution of the structure of their genomes...
  22. pmc Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing
    Baoyan Xu
    Hematology Branch, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 110:10264-9. 2013
    ..Although more work is needed to determine the etiologic role of NIH-CQV in human disease, our data indicate that a parvovirus-like virus is highly prevalent in a cohort of patients with non-A-E hepatitis...
  23. pmc Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum
    María J López-Barragán
    Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
    BMC Genomics 12:587. 2011
    ..Antisense transcripts have widely been reported in P. falciparum; however, the extent and pattern of antisense transcripts in different developmental stages remain largely unknown...