Vishwanath R Iyer

Summary

Publications

  1. pmc Widespread misinterpretable ChIP-seq bias in yeast
    Daechan Park
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas, Austin, Texas, United States of America
    PLoS ONE 8:e83506. 2013
  2. pmc 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
  3. 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
  4. pmc Dendritic cell fate is determined by BCL11A
    Gregory C Ippolito
    Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
    Proc Natl Acad Sci U S A 111:E998-E1006. 2014
  5. pmc 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
  6. pmc 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
  7. 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
  8. 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
  9. 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
  10. 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

Collaborators

Detail Information

Publications36

  1. pmc Widespread misinterpretable ChIP-seq bias in yeast
    Daechan Park
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas, Austin, Texas, United States of America
    PLoS ONE 8:e83506. 2013
    ..Caution is therefore warranted regarding the interpretation of data that seemingly show the association of various transcription and chromatin factors with highly transcribed genes in yeast. ..
  2. pmc 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...
  3. 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...
  4. pmc Dendritic cell fate is determined by BCL11A
    Gregory C Ippolito
    Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
    Proc Natl Acad Sci U S A 111:E998-E1006. 2014
    ..Our results identify BCL11A as an essential, lineage-specific factor that regulates pDC development, supporting a model wherein differentiation into pDCs represents a primed "default" pathway for common dendritic cell progenitors. ..
  5. pmc 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...
  6. pmc 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...
  7. 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...
  8. 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...
  9. 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
    ....
  10. 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...
  11. 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...
  12. pmc 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...
  13. pmc Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements
    Daechan Park
    Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    Nucleic Acids Res 42:3736-49. 2014
    ....
  14. pmc 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...
  15. pmc Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing
    Sabine Mohr
    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
    RNA 19:958-70. 2013
    ..Our findings demonstrate novel biochemical activities and inherent advantages of group II intron RTs for research, biotechnological, and diagnostic methods, with potentially wide applications...
  16. 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...
  17. pmc Genome-wide analysis of chromatin status using tiling microarrays
    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
    Methods 41:304-11. 2007
    ..Here, we describe current methods based on recent advances in microarray technology to conduct such studies...
  18. 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...
  19. 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...
  20. 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...
  21. 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...
  22. 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...
  23. 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...
  24. 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...
  25. 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/...
  26. 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...
  27. 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...
  28. 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...
  29. 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...
  30. ncbi request reprint An eQTL analysis of the human glioblastoma multiforme genome
    Max Shpak
    NeuroTexas Institute, St David s HealthCare, Austin, TX 78705, USA Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712, USA Fresh Pond Research Institute, Cambridge MA 02140, USA Electronic address
    Genomics 103:252-63. 2014
    ..These results suggest several loci that may serve as hubs in gene regulatory pathways associated with GBM. ..
  31. 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...
  32. 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...
  33. pmc 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...
  34. 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...
  35. 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...
  36. 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