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Vishwanath Iyer

Research Profile

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Oligonucleotide Array Sequence Analysis

Chemicals & Drugs

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Physiology

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Saccharomyces cerevisiae

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Genes & Molecular Sequences

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Baeck-seung Lee; Arthur L Shaffer; Barry P Sleckman; Joseph D Dekker; Gregory C Ippolito; Vishwanath R Iyer; Bum-kyu Lee; Philip W Tucker
The BCL11A transcription factor directly activates RAG gene expression and V(D)J recombination.
Damon Polioudakis; Nathan S Abell; Akshay A Bhinge; Patrick J Killion; Bum-Kyu Lee; Vishwanath R Iyer
A Myc-microRNA network promotes exit from quiescence by suppressing the interferon response and cell-cycle arrest genes.
Bum-Kyu Lee; Vishwanath R Iyer
Genome-wide studies of CCCTC-binding factor (CTCF) and cohesin provide insight into chromatin structure and regulation.

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All Publications

2013: Baeck-seung Lee; Arthur L Shaffer; Barry P Sleckman; Joseph D Dekker; Gregory C Ippolito; Vishwanath R Iyer; Bum-kyu Lee; Philip W Tucker
The BCL11A transcription factor directly activates RAG gene expression and V(D)J recombination.
Molecular and cellular biology 2013;33(9):1768-81.
2013: Damon Polioudakis; Nathan S Abell; Akshay A Bhinge; Patrick J Killion; Bum-Kyu Lee; Vishwanath R Iyer
A Myc-microRNA network promotes exit from quiescence by suppressing the interferon response and cell-cycle arrest genes.
Nucleic acids research 2013;41(4):2239-54.
2012: Bum-Kyu Lee; Vishwanath R Iyer
Genome-wide studies of CCCTC-binding factor (CTCF) and cohesin provide insight into chromatin structure and regulation.
The Journal of biological chemistry 2012;287(37):30906-13.
2012: Yoichiro Shibata; Lingyun Song; Alok K Tewari; Matthew Wortham; Gregory A Wray; Courtney C Babbitt; Olivier Fedrigo; Terrence S Furey; Vishwanath R Iyer; Bum-Kyu Lee; Darin London; Elliott H Margulies; Stephen C J Parker; Nathan C Sheffield; Gregory E Crawford
Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.
PLoS genetics 2012;8(6):e1002789.
2012: Vishwanath R Iyer
Nucleosome positioning: bringing order to the eukaryotic genome.
Trends in cell biology 2012;22(5):250-6.
2012: Yunyun Ni; Amelia Weber Hall; Anna Battenhouse; Vishwanath R Iyer
Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data.
BMC genetics 2012;13():46.
2011: Lingyun Song; Teresa Vales; Tianyuan Wang; Deborah Winter; Zhancheng Zhang; Zhuzhu Zhang; Ewan Birney; Alan P Boyle; Neil D Clarke; Gregory E Crawford; Paul G Giresi; Stefan Gräf; Linda L Grasfeder; Mikael Huss; Vishwanath R Iyer; Damian Keefe; Bum-Kyu Lee; Jason Dillon Lieb; Zheng Liu; Darin London; Ryan M McDaniell; Nathan C Sheffield; Yoichiro Shibata; Kimberly A Showers; Jeremy M Simon; Terrence S Furey
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.
Genome research 2011;21(10):1757-67.
2011: Bum-Kyu Lee; Akshay A Bhinge; Vishwanath R Iyer
Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis.
Nucleic acids research 2011;39(9):3558-73.
2011: Alan P Boyle; Lingyun Song; Bum-Kyu Lee; Darin London; Damian Keefe; Ewan Birney; Vishwanath R Iyer; Gregory E Crawford; Terrence S Furey
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.
Genome research 2011;21(3):456-64.
2010: Ryan McDaniell; Bum-Kyu Lee; Lingyun Song; Zheng Liu; Alan P Boyle; Michael R Erdos; Laura J Scott; Mario A Morken; Katerina S Kucera; Anna Battenhouse; Damian Keefe; Francis S Collins; Huntington F Willard; Jason Dillon Lieb; Terrence S Furey; Gregory E Crawford; Vishwanath R Iyer; Ewan Birney
Heritable individual-specific and allele-specific chromatin signatures in humans.
Science (New York, N.Y.) 2010;328(5975):235-9.
2008: Wei Niu; Zhihua Li; Wenjing Zhan; Vishwanath R Iyer; Edward M Marcotte
Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae.
PLoS genetics 2008;4(7):e1000120.
2008: Pei Wang; Weiping Yu; Zhanzhi Hu; Li Jia; Vishwanath R Iyer; Bob G Sanders; Kimberly Kline
Involvement of JNK/p73/NOXA in vitamin E analog-induced apoptosis of human breast cancer cells.
Molecular carcinogenesis 2008;47(6):436-45.
2008: Sushma Shivaswamy; Vishwanath R Iyer
Stress-dependent dynamics of global chromatin remodeling in yeast: dual role for SWI/SNF in the heat shock stress response.
Molecular and cellular biology 2008;28(7):2221-34.
2008: Sushma Shivaswamy; Akshay Bhinge; Yongjun Zhao; Steven Jones; Martin Hirst; Vishwanath R Iyer
Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.
PLoS biology 2008;6(3):e65.
2008: Neelu Yadav; Donghang Cheng; Stephane Richard; Melanie Morel; Vishwanath R Iyer; C Marcelo Aldaz; Mark T Bedford
CARM1 promotes adipocyte differentiation by coactivating PPARgamma.
EMBO reports 2008;9(2):193-8.
2008: Patrick J Killion; Vishwanath R Iyer
ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets.
Genome biology 2008;9(11):R159.
2008: Jonghwan Kim; Ji-hoon Lee; Vishwanath R Iyer
Global identification of Myc target genes reveals its direct role in mitochondrial biogenesis and its E-box usage in vivo.
PloS one 2008;3(3):e1798.
2007: Akshay A Bhinge; Jonghwan Kim; Ghia Euskirchen; Michael Snyder; Vishwanath R Iyer
Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE).
Genome research 2007;17(6):910-6.
2007: Paul G Giresi; Jonghwan Kim; Ryan M McDaniell; Vishwanath R Iyer; Jason Dillon Lieb
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin.
Genome research 2007;17(6):877-85.
2007: Zhanzhi Hu; Patrick J Killion; Vishwanath R Iyer
Genetic reconstruction of a functional transcriptional regulatory network.
Nature genetics 2007;39(5):683-7.
2007: Sushma Shivaswamy; Vishwanath R Iyer
Genome-wide analysis of chromatin status using tiling microarrays.
Methods (San Diego, Calif.) 2007;41(3):304-11.
2007: Xochitl C Morgan; Shulin Ni; Daniel P Miranker; Vishwanath R Iyer
Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining.
BMC bioinformatics 2007;8():445.
2007: Mark W Carlson; Vishwanath R Iyer; Edward M Marcotte
Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways.
BMC genomics 2007;8():117.
2006: Jianwen Liu; Joanne M Lewohl; R Adron Harris; Vishwanath R Iyer; Peter R Dodd; Patrick K Randall; R Dayne Mayfield
Patterns of gene expression in the frontal cortex discriminate alcoholic from nonalcoholic individuals.
Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology 2006;31(7):1574-82.
2006: Megan K Mulligan; Igor Ponomarev; Robert Hitzemann; John K Belknap; Boris Tabakoff; R Adron Harris; John C Crabbe; Yuri A Blednov; Nicholas J Grahame; Tamara J Phillips; Deborah A Finn; Paula L Hoffman; Vishwanath R Iyer; George F Koob; Susan E Bergeson
Toward understanding the genetics of alcohol drinking through transcriptome meta-analysis.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(16):6368-73.
2006: Jian Gu; Vishwanath R Iyer
PI3K signaling and miRNA expression during the response of quiescent human fibroblasts to distinct proliferative stimuli.
Genome biology 2006;7(5):R42.
2006: Rammohan Narayanaswamy; Wei Niu; Alexander D Scouras; G Traver Hart; Jonathan Davies; Andrew D Ellington; Vishwanath R Iyer; Edward M Marcotte
Systematic profiling of cellular phenotypes with spotted cell microarrays reveals mating-pheromone response genes.
Genome biology 2006;7(1):R6.
2005: Amanda Oglesby-Sherrouse; Erin R Murphy; Vishwanath R Iyer; Shelley M Payne
Fur regulates acid resistance in Shigella flexneri via RyhB and ydeP.
Molecular microbiology 2005;58(5):1354-67.
2005: Jonghwan Kim; Vishwanath R Iyer
Identifying chromosomal targets of DNA-binding proteins by Sequence Tag Analysis of Genomic Enrichment (STAGE).
Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.] 2005;Chapter 21():Unit 21.10.
2005: Thomas Hon; Hee Chul Lee; Zhanzhi Hu; Vishwanath R Iyer; Li Zhang
The heme activator protein Hap1 represses transcription by a heme-independent mechanism in Saccharomyces cerevisiae.
Genetics 2005;169(3):1343-52.
2005: Jonghwan Kim; Akshay A Bhinge; Xochitl C Morgan; Vishwanath R Iyer
Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment.
Nature methods 2005;2(1):47-53.
2004: Patrick J Killion; Vishwanath R Iyer
Microarray data visualization and analysis with the Longhorn Array Database (LAD).
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2004;Chapter 7():Unit 7.10.
2004: Igor Ponomarev; Gwen L Schafer; Yuri A Blednov; Robert Williams; Vishwanath R Iyer; R Adron Harris
Convergent analysis of cDNA and short oligomer microarrays, mouse null mutants and bioinformatics resources to study complex traits.
Genes, brain, and behavior 2004;3(6):360-8.
2004: Vishwanath R Iyer
Exploring the post-transcriptional RNA world with DNA microarrays.
Trends in biotechnology 2004;22(10):498-500.
2004: Jonghwan Kim; Vishwanath R Iyer
Global role of TATA box-binding protein recruitment to promoters in mediating gene expression profiles.
Molecular and cellular biology 2004;24(18):8104-12.
2004: Ji-Sook Hahn; Zhanzhi Hu; Dennis J Thiele; Vishwanath R Iyer
Genome-wide analysis of the biology of stress responses through heat shock transcription factor.
Molecular and cellular biology 2004;24(12):5249-56.
2003: Patrick J Killion; Gavin Sherlock; Vishwanath R Iyer
The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD).
BMC bioinformatics 2003;4():32.
2003: Vishwanath R Iyer
Translating genome sequences into biological understanding.
Genome biology 2003;4(6):324.
2002: Jonathan R Pollack; Vishwanath R Iyer
Characterizing the physical genome.
Nature genetics 2002;32 Suppl():515-21.
2001: Rika Miki; Koji Kadota; Hidemasa Bono; Yosuke Mizuno; Yasuhiro Tomaru; piero carninci; Masayoshi Itoh; Kazuhiro Shibata; Jun Kawai; H Konno; S Watanabe; K Sato; Y Tokusumi; N Kikuchi; Y Ishii; Yohei Hamaguchi; Itaru Nishizuka; Hitoshi Goto; Hiroyuki Nitanda; S Satomi; A Yoshiki; M Kusakabe; Joe L DeRisi; Michael B Eisen; Vishwanath R Iyer; P O Brown; Masami Muramatsu; Hiroshi Shimada; Yasushi Okazaki; Yoshihide Hayashizaki
Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(5):2199-204.
2001: Vishwanath R Iyer; C E Horak; C S Scafe; David Botstein; M Snyder; Patrick O Brown
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF.
Nature 2001;409(6819):533-8.
1999: Joe L DeRisi; Vishwanath R Iyer
Genomics and array technology.
Current opinion in oncology 1999;11(1):76-9.
1999: Vishwanath R Iyer; Michael B Eisen; Douglas T Ross; G Schuler; T Moore; JC Lee; Jeffrey M. Trent; Louis M Staudt; J Hudson; Mark S Boguski; DA Lashkari; D Shalon; David Botstein; Patrick O Brown
The transcriptional program in the response of human fibroblasts to serum.
Science (New York, N.Y.) 1999;283(5398):83-7.
1998: Paul Spellman; Gavin Sherlock; M Q Zhang; Vishwanath R Iyer; K Anders; Michael B Eisen; Patrick O Brown; David Botstein; Bruce Futcher
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.
Molecular biology of the cell 1998;9(12):3273-97.
1998: Matthew J Marton; Joe L DeRisi; Holly Bennett; Vishwanath R Iyer; Michael R Meyer; C J Roberts; Roland B Stoughton; Julja Burchard; D Slade; H Dai; D E Bassett; Leland H Hartwell; P O Brown; S H Friend
Drug target validation and identification of secondary drug target effects using DNA microarrays.
Nature medicine 1998;4(11):1293-301.
1997: Joe DeRisi; Vishwanath R Iyer; Patrick O Brown
Exploring the metabolic and genetic control of gene expression on a genomic scale.
Science (New York, N.Y.) 1997;278(5338):680-6.