Lihua J Zhu

Summary

Affiliation: University of Massachusetts Medical School
Country: USA

Publications

  1. pmc Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo
    Poshen B Chen
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
    BMC Genomics 15:1104. 2014
  2. pmc Annotating the human genome with Disease Ontology
    John D Osborne
    Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
    BMC Genomics 10:S6. 2009
  3. pmc ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
    Lihua J Zhu
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    BMC Bioinformatics 11:237. 2010
  4. pmc TRIM37 is a new histone H2A ubiquitin ligase and breast cancer oncoprotein
    Sanchita Bhatnagar
    1 Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA 2 Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Nature 516:116-20. 2014
  5. pmc Specific requirement of Gli transcription factors in Hedgehog-mediated intestinal development
    He Huang
    Department of Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    J Biol Chem 288:17589-96. 2013
  6. pmc A synthetic interaction screen identifies factors selectively required for proliferation and TERT transcription in p53-deficient human cancer cells
    Li Xie
    Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    PLoS Genet 8:e1003151. 2012
  7. pmc A large-scale RNAi-based mouse tumorigenesis screen identifies new lung cancer tumor suppressors that repress FGFR signaling
    Ling Lin
    Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
    Cancer Discov 4:1168-81. 2014
  8. pmc Research resource: Monitoring endoplasmic reticulum membrane integrity in β-cells at the single-cell level
    Kohsuke Kanekura
    Department of Medicine K K, T H, F U, Division of Endocrinology, Metabolism, and Lipid Research, and Department of Pathology and Immunology F U, Washington University School of Medicine, St Louis, Missouri 63110 and Programs in Gene Function and Expression, Molecular Medicine, and Bioinformatics and Integrative Biology J O, L J Z, University of Massachusetts Medical School, Worcester, Massachusetts 01655
    Mol Endocrinol 29:473-80. 2015
  9. pmc A therapeutically targetable mechanism of BCR-ABL-independent imatinib resistance in chronic myeloid leukemia
    Leyuan Ma
    Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Sci Transl Med 6:252ra121. 2014
  10. pmc Global Promotion of Alternative Internal Exon Usage by mRNA 3' End Formation Factors
    Ashish Misra
    Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Mol Cell 58:819-31. 2015

Collaborators

Detail Information

Publications18

  1. pmc Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo
    Poshen B Chen
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
    BMC Genomics 15:1104. 2014
    ..However, these methods are less successful in measuring the accessibility of DNA sequences within nucelosome arrays...
  2. pmc Annotating the human genome with Disease Ontology
    John D Osborne
    Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
    BMC Genomics 10:S6. 2009
    ..The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally annotated for diseases...
  3. pmc ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
    Lihua J Zhu
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    BMC Bioinformatics 11:237. 2010
    ..However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome...
  4. pmc TRIM37 is a new histone H2A ubiquitin ligase and breast cancer oncoprotein
    Sanchita Bhatnagar
    1 Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA 2 Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Nature 516:116-20. 2014
    ..Collectively, our results reveal TRIM37 as an oncogenic H2A ubiquitin ligase that is overexpressed in a subset of breast cancers and promotes transformation by facilitating silencing of tumour suppressors and other genes...
  5. pmc Specific requirement of Gli transcription factors in Hedgehog-mediated intestinal development
    He Huang
    Department of Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    J Biol Chem 288:17589-96. 2013
    ..Taken together, our study reveals, for the first time, the distinct roles of Gli proteins in intestine development and suggests SLRPs as novel regulators of smooth muscle cell differentiation...
  6. pmc A synthetic interaction screen identifies factors selectively required for proliferation and TERT transcription in p53-deficient human cancer cells
    Li Xie
    Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    PLoS Genet 8:e1003151. 2012
    ..Our collective results identify a regulatory pathway involving ETV1, ATR, and TERT that is preferentially important for proliferation of diverse p53- cancer cells...
  7. pmc A large-scale RNAi-based mouse tumorigenesis screen identifies new lung cancer tumor suppressors that repress FGFR signaling
    Ling Lin
    Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
    Cancer Discov 4:1168-81. 2014
    ..Our results indicate that increased FGFR signaling promotes tumorigenesis in many hLSCCs that lack FGFR1 amplification or activating mutations...
  8. pmc Research resource: Monitoring endoplasmic reticulum membrane integrity in β-cells at the single-cell level
    Kohsuke Kanekura
    Department of Medicine K K, T H, F U, Division of Endocrinology, Metabolism, and Lipid Research, and Department of Pathology and Immunology F U, Washington University School of Medicine, St Louis, Missouri 63110 and Programs in Gene Function and Expression, Molecular Medicine, and Bioinformatics and Integrative Biology J O, L J Z, University of Massachusetts Medical School, Worcester, Massachusetts 01655
    Mol Endocrinol 29:473-80. 2015
    ..Our method could be used to develop a novel therapeutic modality targeting the ER membrane for ER-associated disorders, including β-cell death in diabetes, neurodegeneration, and Wolfram syndrome. ..
  9. pmc A therapeutically targetable mechanism of BCR-ABL-independent imatinib resistance in chronic myeloid leukemia
    Leyuan Ma
    Howard Hughes Medical Institute, Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Sci Transl Med 6:252ra121. 2014
    ..Collectively, our results identify a therapeutically targetable mechanism of BCR-ABL-independent IM resistance in CML and CML stem cells. ..
  10. pmc Global Promotion of Alternative Internal Exon Usage by mRNA 3' End Formation Factors
    Ashish Misra
    Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Mol Cell 58:819-31. 2015
    ..Collectively, our results reveal an unanticipated role for mRNA 3' end formation factors in global promotion of alternative splicing. ..
  11. pmc Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants
    Metewo Selase Enuameh
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genome Res 23:928-40. 2013
    ..These hybrids of natural and artificial fingers can be used to create functional zinc finger nucleases for editing vertebrate genomes...
  12. pmc Exploring the DNA-recognition potential of homeodomains
    Stephanie W Chu
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genome Res 22:1889-98. 2012
    ..The diversity of recovered HD recognition sequences raises important questions about the fitness barrier that restricts the evolution of alternate recognition modalities in natural systems...
  13. pmc Thioredoxin-interacting protein mediates ER stress-induced β cell death through initiation of the inflammasome
    Christine M Oslowski
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Cell Metab 16:265-73. 2012
    ..Collectively, our results suggest that TXNIP is a potential therapeutic target for diabetes and ER stress-related human diseases such as Wolfram syndrome...
  14. pmc miR-221 is required for endothelial tip cell behaviors during vascular development
    Stefania Nicoli
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Dev Cell 22:418-29. 2012
    ..These results identify miR-221 as an important regulatory node through which tip cell migration and proliferation are controlled during angiogenesis...
  15. pmc The activity of Gli transcription factors is essential for Kras-induced pancreatic tumorigenesis
    Mihir Rajurkar
    Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Proc Natl Acad Sci U S A 109:E1038-47. 2012
    ....
  16. pmc Analysis of Gal4-directed transcription activation using Tra1 mutants selectively defective for interaction with Gal4
    Ling Lin
    Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Proc Natl Acad Sci U S A 109:1997-2002. 2012
    ..Finally, we show that although Tra1 is targeted by other activators, these interactions are unaffected by GID mutations, revealing an unanticipated specificity of the Gal4-Tra1 interaction...
  17. pmc Transcription factor ATF5 is required for terminal differentiation and survival of olfactory sensory neurons
    Shu Zong Wang
    Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Proc Natl Acad Sci U S A 109:18589-94. 2012
    ..Thus, ATF5 is required for terminal differentiation and survival of OSNs...
  18. pmc BCR-ABL suppresses autophagy through ATF5-mediated regulation of mTOR transcription
    Zhi Sheng
    Howard Hughes Medical Institute, Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Blood 118:2840-8. 2011
    ..We demonstrate that imatinib-induced autophagy is because of inhibition of the BCR-ABL/PI3K/AKT/FOXO4/ATF5/mTOR pathway that we have identified in this study...