Vishwanath Iyer

Summary

Affiliation: University of Texas
Country: USA

Publications

  1. pmc The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD)
    Patrick J Killion
    Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712 0159, USA
    BMC Bioinformatics 4:32. 2003
  2. ncbi request reprint Genetic reconstruction of a functional transcriptional regulatory network
    Zhanzhi Hu
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas at Austin, 1 University Station A4800, Austin, Texas 78712, USA
    Nat Genet 39:683-7. 2007
  3. pmc 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
  4. pmc ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets
    Patrick J Killion
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station A4800, Austin, Texas 78712, USA
    Genome Biol 9:R159. 2008
  5. pmc Global identification of Myc target genes reveals its direct role in mitochondrial biogenesis and its E-box usage in vivo
    Jonghwan Kim
    Section of Molecular Genetics and Microbiology, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
    PLoS ONE 3:e1798. 2008
  6. pmc 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
  7. pmc PI3K signaling and miRNA expression during the response of quiescent human fibroblasts to distinct proliferative stimuli
    Jian Gu
    Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, University of Texas at Austin, 1 University Station A4800, Austin, TX 78712 0159, USA
    Genome Biol 7:R42. 2006
  8. pmc Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining
    Xochitl C Morgan
    Institute for Cellular and Molecular Biology and Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712 0159, USA
    BMC Bioinformatics 8:445. 2007
  9. ncbi request reprint Exploring the post-transcriptional RNA world with DNA microarrays
    Vishwanath R Iyer
    Center for Systems and Synthetic Biology, and Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station A4800, Austin, TX 78712 0159, USA
    Trends Biotechnol 22:498-500. 2004
  10. pmc Translating genome sequences into biological understanding
    Vishwanath R Iyer
    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Genome Biol 4:324. 2003

Research Grants

Detail Information

Publications30

  1. pmc The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD)
    Patrick J Killion
    Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712 0159, USA
    BMC Bioinformatics 4:32. 2003
    ..The power of microarray analysis can be realized only if data is systematically archived and linked to biological annotations as well as analysis algorithms...
  2. ncbi request reprint Genetic reconstruction of a functional transcriptional regulatory network
    Zhanzhi Hu
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas at Austin, 1 University Station A4800, Austin, Texas 78712, USA
    Nat Genet 39:683-7. 2007
    ..The enrichment of promoter motifs and Gene Ontology annotations provide insight into the biological functions of the transcription factors...
  3. pmc 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...
  4. pmc ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets
    Patrick J Killion
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station A4800, Austin, Texas 78712, USA
    Genome Biol 9:R159. 2008
    ..ArrayPlex is available at http://sourceforge.net/projects/arrayplex/...
  5. pmc Global identification of Myc target genes reveals its direct role in mitochondrial biogenesis and its E-box usage in vivo
    Jonghwan Kim
    Section of Molecular Genetics and Microbiology, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
    PLoS ONE 3:e1798. 2008
    ..This study thus sheds light on the transcriptional regulatory networks mediated by Myc in vivo...
  6. pmc 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...
  7. pmc PI3K signaling and miRNA expression during the response of quiescent human fibroblasts to distinct proliferative stimuli
    Jian Gu
    Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, University of Texas at Austin, 1 University Station A4800, Austin, TX 78712 0159, USA
    Genome Biol 7:R42. 2006
    ..We have profiled the global transcriptional program of human fibroblasts from two different tissue sources to distinct growth stimuli, and identified a striking conservation in their gene-expression signatures...
  8. pmc Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining
    Xochitl C Morgan
    Institute for Cellular and Molecular Biology and Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712 0159, USA
    BMC Bioinformatics 8:445. 2007
    ....
  9. ncbi request reprint Exploring the post-transcriptional RNA world with DNA microarrays
    Vishwanath R Iyer
    Center for Systems and Synthetic Biology, and Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station A4800, Austin, TX 78712 0159, USA
    Trends Biotechnol 22:498-500. 2004
    ..The challenges ahead relate to extending such approaches to larger genomes and to integrating this type of information with that generated by standard expression profiling...
  10. pmc Translating genome sequences into biological understanding
    Vishwanath R Iyer
    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Genome Biol 4:324. 2003
  11. ncbi request reprint Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment
    Jonghwan Kim
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology and Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712 0159, USA
    Nat Methods 2:47-53. 2005
    ..STAGE provides a means of identifying the chromosomal targets of DNA-associated proteins in any sequenced genome...
  12. pmc 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...
  13. pmc 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...
  14. ncbi request reprint Patterns of gene expression in the frontal cortex discriminate alcoholic from nonalcoholic individuals
    Jianwen Liu
    Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX 78712, USA
    Neuropsychopharmacology 31:1574-82. 2006
    ..These results revealed a consistent re-programming of gene expression in alcohol abusers that reliably discriminates alcoholic from non-alcoholic individuals...
  15. doi request reprint Microarray data visualization and analysis with the Longhorn Array Database (LAD)
    Patrick J Killion
    University of Texas at Austin, Austin, Texas, USA
    Curr Protoc Bioinformatics . 2004
    ..This unit provides the complete set of information needed to successfully deploy, configure, and use LAD for the purposes of two-color DNA microarray analysis and visualization...
  16. pmc Stress-dependent dynamics of global chromatin remodeling in yeast: dual role for SWI/SNF in the heat shock stress response
    Sushma Shivaswamy
    Institute for Cellular and Molecular Biology and Section of Molecular Genetics and Microbiology, University of Texas at Austin, 1 University Station A4800, Austin, TX 78712 0159, USA
    Mol Cell Biol 28:2221-34. 2008
    ..Our results suggest a broad and direct dual role for SWI/SNF in chromatin remodeling, during heat shock activation as well as repression, at promoters and coding regions...
  17. pmc Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE)
    Akshay A Bhinge
    Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712, USA
    Genome Res 17:910-6. 2007
    ..STAGE is thus a viable method for identifying the chromosomal targets of transcription factors and generating meaningful biological hypotheses that further our understanding of transcriptional regulatory networks...
  18. pmc Toward understanding the genetics of alcohol drinking through transcriptome meta-analysis
    Megan K Mulligan
    Waggoner Center for Alcohol and Addiction Research and Sections of Neurobiology, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 103:6368-73. 2006
    ..The present study demonstrates the use of (i) a microarray meta-analysis to analyze a behavioral phenotype (in this case, alcohol preference) and (ii) a congenic strain for identification of cis regulation...
  19. pmc Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways
    Mark W Carlson
    Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
    BMC Genomics 8:117. 2007
    ..We used gene expression profiling to quantitatively assess the gene expression of nine cell line models of cervical cancer...
  20. pmc Global role of TATA box-binding protein recruitment to promoters in mediating gene expression profiles
    Jonghwan Kim
    Institute for Cellular and Molecular Biology and Section of Molecular Genetics and Microbiology, University of Texas at Austin, 78712 0159, USA
    Mol Cell Biol 24:8104-12. 2004
    ..The primary data reported here are available at http://www.iyerlab.org/tbp...
  21. ncbi request reprint Fur regulates acid resistance in Shigella flexneri via RyhB and ydeP
    Amanda G Oglesby
    Section of Molecular Genetics and Microbiology, The University of Texas at Austin, Austin, TX 78712, USA
    Mol Microbiol 58:1354-67. 2005
    ..These results demonstrate that the acid sensitivity defect of the S. flexneri fur mutant is due to repression of ydeP by RyhB, most likely via repression of evgA...
  22. pmc Systematic profiling of cellular phenotypes with spotted cell microarrays reveals mating-pheromone response genes
    Rammohan Narayanaswamy
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, 2500 Speedway, University of Texas, Austin, TX 78712, USA
    Genome Biol 7:R6. 2006
    ..Besides morphology assays, cell microarrays should be valuable for high-throughput in situ hybridization and immunoassays, enabling new classes of genetic assays based on cell imaging...
  23. ncbi request reprint Involvement of JNK/p73/NOXA in vitamin E analog-induced apoptosis of human breast cancer cells
    Pei Wang
    Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712, USA
    Mol Carcinog 47:436-45. 2008
    ..Taken together, these findings suggest a role for JNK activation in mediating full length p73 expression and add to our understanding of the mechanisms of anticancer actions of alpha-TEA, a potential chemotherapeutic agent...
  24. doi request reprint Identifying chromosomal targets of DNA-binding proteins by Sequence Tag Analysis of Genomic Enrichment (STAGE)
    Jonghwan Kim
    University of Texas at Austin, Austin, Texas, USA
    Curr Protoc Mol Biol . 2005
    ..STAGE can be applied to any sequenced genome to identify targets of DNA-binding proteins without requiring extensive microarray resources...
  25. pmc Genome-wide analysis of the biology of stress responses through heat shock transcription factor
    Ji Sook Hahn
    Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109 0606, USA
    Mol Cell Biol 24:5249-56. 2004
    ..This genome-wide identification of HSF target genes provides novel insights into the role of HSF in growth, development, disease, and aging and in the complex metabolic reprogramming that occurs in all cells in response to stress...
  26. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  27. ncbi request reprint Characterizing the physical genome
    Jonathan R Pollack
    Department of Pathology, Stanford University School of Medicine, CCSR Building, Room 3245A, 269 Campus Drive, Stanford, California 94305 5176, USA
    Nat Genet 32:515-21. 2002
    ..Methods based on microarrays are beginning to provide a detailed picture of this physical genome, and they complement the genome-wide studies of mRNA expression profiling that have previously been so successful...
  28. pmc The heme activator protein Hap1 represses transcription by a heme-independent mechanism in Saccharomyces cerevisiae
    Thomas Hon
    Department of Environmental Health Sciences, Columbia University, Mailman School of Public Health, New York, New York 10032, USA
    Genetics 169:1343-52. 2005
    ..Further, we found that repression by Hap1 requires the function of Hsp70 (Ssa), but not Hsp90. These results show that Hap1 binds to its own promoter and represses transcription in a heme-independent but Hsp70-dependent manner...
  29. pmc FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
    Paul G Giresi
    Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 3280, USA
    Genome Res 17:877-85. 2007
    ..FAIRE has utility as a positive selection for genomic regions associated with regulatory activity, including regions traditionally detected by nuclease hypersensitivity assays...
  30. pmc CARM1 promotes adipocyte differentiation by coactivating PPARgamma
    Neelu Yadav
    Department of Carcinogenesis, The University of Texas M D Anderson Cancer Center, Science Park, Smithville, Texas 78957, USA
    EMBO Rep 9:193-8. 2008
    ..Together, these results show that CARM1 promotes adipocyte differentiation by coactivating PPARgamma-mediated transcription and thus might be important in energy balance...

Research Grants1

  1. STAGE and FAIRE for Regulatory Element Identification
    Vishwanath Iyer; Fiscal Year: 2006
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