Vishwanath R Iyer

Summary

Publications

  1. ncbi Nucleosome positioning: bringing order to the eukaryotic genome
    Vishwanath R Iyer
    Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Section of Molecular Genetics and Microbiology, University of Texas at Austin, 1 University Station A4800, Austin, TX 78712 0159, USA
    Trends Cell Biol 22:250-6. 2012
  2. ncbi A Myc-microRNA network promotes exit from quiescence by suppressing the interferon response and cell-cycle arrest genes
    Damon Polioudakis
    Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Section of Molecular Genetics and Microbiology, University of Texas at Austin, 1 University Station A4800, Austin, Texas 78712 0159, USA
    Nucleic Acids Res 41:2239-54. 2013
  3. ncbi Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells
    Bum Kyu Lee
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712, USA
    Genome Res 22:9-24. 2012
  4. ncbi Genome-wide studies of CCCTC-binding factor (CTCF) and cohesin provide insight into chromatin structure and regulation
    Bum Kyu Lee
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas, Austin, Texas 78712, USA
    J Biol Chem 287:30906-13. 2012
  5. ncbi Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data
    Yunyun Ni
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX 78712, USA
    BMC Genet 13:46. 2012
  6. ncbi Heritable individual-specific and allele-specific chromatin signatures in humans
    Ryan McDaniell
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712, USA
    Science 328:235-9. 2010
  7. ncbi Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis
    Bum Kyu Lee
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX 78712, USA
    Nucleic Acids Res 39:3558-73. 2011
  8. ncbi Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation
    Sushma Shivaswamy
    Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas, United States of America
    PLoS Biol 6:e65. 2008
  9. ncbi Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae
    Wei Niu
    Center for Systems and Synthetic Biology, University of Texas, Austin, Texas, United States of America
    PLoS Genet 4:e1000120. 2008
  10. ncbi The BCL11A transcription factor directly activates RAG gene expression and V(D)J recombination
    Baeck Seung Lee
    Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
    Mol Cell Biol 33:1768-81. 2013

Collaborators

  • Terrence S Furey
  • Zheng Liu
  • Huntington F Willard
  • Bum Kyu Lee
  • Yunyun Ni
  • Akshay A Bhinge
  • Anna Battenhouse
  • Baeck Seung Lee
  • Damon Polioudakis
  • Gregory E Crawford
  • Lingyun Song
  • Ewan Birney
  • Jason D Lieb
  • Ryan McDaniell
  • Wei Niu
  • Sushma Shivaswamy
  • Patrick J Killion
  • Nathan S Abell
  • Philip W Tucker
  • Joseph D Dekker
  • Barry P Sleckman
  • Gregory C Ippolito
  • Arthur L Shaffer
  • Ryan M McDaniell
  • Amelia Weber Hall
  • Laura J Scott
  • Damian Keefe
  • Katerina S Kucera
  • Francis S Collins
  • Mario A Morken
  • Alan P Boyle
  • Michael R Erdos
  • Yongjun Zhao
  • Steven Jones
  • Wenjing Zhan
  • Akshay Bhinge
  • Zhihua Li
  • Martin Hirst
  • Edward M Marcotte

Detail Information

Publications10

  1. ncbi Nucleosome positioning: bringing order to the eukaryotic genome
    Vishwanath R Iyer
    Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Section of Molecular Genetics and Microbiology, University of Texas at Austin, 1 University Station A4800, Austin, TX 78712 0159, USA
    Trends Cell Biol 22:250-6. 2012
    ..This paper reviews recent genomic studies that have shed light on the determinants of nucleosome positioning and their impact on the genome...
  2. ncbi A Myc-microRNA network promotes exit from quiescence by suppressing the interferon response and cell-cycle arrest genes
    Damon Polioudakis
    Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Section of Molecular Genetics and Microbiology, University of Texas at Austin, 1 University Station A4800, Austin, Texas 78712 0159, USA
    Nucleic Acids Res 41:2239-54. 2013
    ..Our results implicate miR-22 in downregulating the anti-proliferative p53 and interferon pathways and reveal a new transcription factor-miRNA network that regulates the transition of primary human cells from quiescence to proliferation...
  3. ncbi Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells
    Bum Kyu Lee
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712, USA
    Genome Res 22:9-24. 2012
    ..These data illuminate how combinatorial binding of transcription factors in diverse cell types is associated with gene expression and cell-type specific biology...
  4. ncbi Genome-wide studies of CCCTC-binding factor (CTCF) and cohesin provide insight into chromatin structure and regulation
    Bum Kyu Lee
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas, Austin, Texas 78712, USA
    J Biol Chem 287:30906-13. 2012
    ..This partnership between CTCF and cohesin is emerging as a novel and perhaps pivotal aspect of gene regulatory mechanisms, in addition to playing a role in the organization of higher order chromatin architecture...
  5. ncbi Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data
    Yunyun Ni
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX 78712, USA
    BMC Genet 13:46. 2012
    ..This requirement limits the study of allele-specific effects of SNPs in primary patient samples from diseases of interest, where complete genotypes are not readily available...
  6. ncbi Heritable individual-specific and allele-specific chromatin signatures in humans
    Ryan McDaniell
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712, USA
    Science 328:235-9. 2010
    ..Our study shows that heritable chromatin status and transcription factor binding differ as a result of genetic variation and may underlie phenotypic variation in humans...
  7. ncbi Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis
    Bum Kyu Lee
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX 78712, USA
    Nucleic Acids Res 39:3558-73. 2011
    ..Taken together, our genome-wide analysis provided evidence of versatile roles of E2F4 and insights into its functions...
  8. ncbi Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation
    Sushma Shivaswamy
    Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas, United States of America
    PLoS Biol 6:e65. 2008
    ..Our study provides a detailed, high-resolution, dynamic map of single-nucleosome remodeling across the yeast genome and its relation to global transcriptional changes...
  9. ncbi Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae
    Wei Niu
    Center for Systems and Synthetic Biology, University of Texas, Austin, Texas, United States of America
    PLoS Genet 4:e1000120. 2008
    ..This work thus implicates new genes in cell cycle progression, complements previous screens, and lays the foundation for future experiments to define more precisely roles for these genes in cell cycle progression...
  10. ncbi The BCL11A transcription factor directly activates RAG gene expression and V(D)J recombination
    Baeck Seung Lee
    Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
    Mol Cell Biol 33:1768-81. 2013
    ..We conclude that BCL11A is a critical component of a transcriptional network that regulates B cell fate by controlling V(D)J recombination...