Vishwanath R Iyer

Vishwanath R Iyer

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Vishwanath R Iyer

Publications by authors named "Vishwanath R Iyer"

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PRC2 activates interferon-stimulated genes indirectly by repressing miRNAs in glioblastoma.

PLoS One 2019 12;14(9):e0222435. Epub 2019 Sep 12.

Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Livestrong Cancer Institutes, University of Texas at Austin, Austin, Texas, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0222435PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6742368PMC
September 2019

MicroRNAs reinforce repression of PRC2 transcriptional targets independently and through a feed-forward regulatory network.

Genome Res 2019 02 16;29(2):184-192. Epub 2019 Jan 16.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA.

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http://dx.doi.org/10.1101/gr.238311.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360819PMC
February 2019

Identification and removal of sequencing artifacts produced by mispriming during reverse transcription in multiple RNA-seq technologies.

RNA 2018 09 27;24(9):1266-1274. Epub 2018 Jun 27.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA.

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http://dx.doi.org/10.1261/rna.066217.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097653PMC
September 2018

Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data.

PeerJ 2018 31;6:e5362. Epub 2018 Jul 31.

Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Livestrong Cancer Institutes, University of Texas at Austin, Austin, TX, USA.

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http://dx.doi.org/10.7717/peerj.5362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6074801PMC
July 2018

Bivalent Chromatin Domains in Glioblastoma Reveal a Subtype-Specific Signature of Glioma Stem Cells.

Cancer Res 2018 05 16;78(10):2463-2474. Epub 2018 Mar 16.

Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-1724DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5955797PMC
May 2018

Arid3a regulates mesoderm differentiation in mouse embryonic stem cells.

J Stem Cell Ther Transplant 2017 7;1(1):52-62. Epub 2017 Sep 7.

Department of Molecular Biosciences, USA.

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http://dx.doi.org/10.29328/journal.jsctt.1001005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6510499PMC
September 2017

The ATP-dependent chromatin remodeler Chd1 is recruited by transcription elongation factors and maintains H3K4me3/H3K36me3 domains at actively transcribed and spliced genes.

Nucleic Acids Res 2017 08;45(14):8646

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.

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http://academic.oup.com/nar/article/45/14/8646/3976500
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http://dx.doi.org/10.1093/nar/gkx636DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737436PMC
August 2017

The ATP-dependent chromatin remodeler Chd1 is recruited by transcription elongation factors and maintains H3K4me3/H3K36me3 domains at actively transcribed and spliced genes.

Nucleic Acids Res 2017 Jul;45(12):7180-7190

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkx321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499586PMC
July 2017

Ethylene induces combinatorial effects of histone H3 acetylation in gene expression in Arabidopsis.

BMC Genomics 2017 07 17;18(1):538. Epub 2017 Jul 17.

Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, 78712, Texas, USA.

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http://dx.doi.org/10.1186/s12864-017-3929-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5512946PMC
July 2017

The Determinants of Directionality in Transcriptional Initiation.

Trends Genet 2016 06 7;32(6):322-333. Epub 2016 Apr 7.

Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2016.03.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4874897PMC
June 2016

Synthetic evolutionary origin of a proofreading reverse transcriptase.

Science 2016 Jun;352(6293):1590-3

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas, 2500 Speedway, Austin, TX 78712, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.aaf5409
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http://dx.doi.org/10.1126/science.aaf5409DOI Listing
June 2016

MiR-191 Regulates Primary Human Fibroblast Proliferation and Directly Targets Multiple Oncogenes.

PLoS One 2015 20;10(5):e0126535. Epub 2015 May 20.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126535PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4439112PMC
April 2016

Subtype-specific addiction of the activated B-cell subset of diffuse large B-cell lymphoma to FOXP1.

Proc Natl Acad Sci U S A 2016 Feb 19;113(5):E577-86. Epub 2016 Jan 19.

Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712;

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http://dx.doi.org/10.1073/pnas.1524677113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4747717PMC
February 2016

Stem cell and neurogenic gene-expression profiles link prostate basal cells to aggressive prostate cancer.

Nat Commun 2016 Feb 29;7:10798. Epub 2016 Feb 29.

Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, 78957 Texas, USA.

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http://dx.doi.org/10.1038/ncomms10798DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4773505PMC
February 2016

Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma.

PLoS One 2014 8;9(9):e107156. Epub 2014 Sep 8.

Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0107156PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157845PMC
January 2016

miR-503 represses human cell proliferation and directly targets the oncogene DDHD2 by non-canonical target pairing.

BMC Genomics 2015 Feb 5;16:40. Epub 2015 Feb 5.

Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas, USA.

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http://dx.doi.org/10.1186/s12864-015-1279-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4326481PMC
February 2015

Chd1 co-localizes with early transcription elongation factors independently of H3K36 methylation and releases stalled RNA polymerase II at introns.

Epigenetics Chromatin 2014 27;7(1):32. Epub 2014 Oct 27.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas, 2500 Speedway, Austin, TX 78712 USA.

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http://dx.doi.org/10.1186/1756-8935-7-32DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230344PMC
November 2014

Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.

PLoS Genet 2014 Nov 20;10(11):e1004798. Epub 2014 Nov 20.

The European Molecular Biology Laboratory, The European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1004798DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4238955PMC
November 2014

Global transcriptional profiling reveals distinct functions of thymic stromal subsets and age-related changes during thymic involution.

Cell Rep 2014 Oct 2;9(1):402-415. Epub 2014 Oct 2.

Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.08.070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4194175PMC
October 2014

Widespread misinterpretable ChIP-seq bias in yeast.

PLoS One 2013 9;8(12):e83506. Epub 2013 Dec 9.

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.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0083506PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3857294PMC
September 2014

Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements.

Nucleic Acids Res 2014 Apr 10;42(6):3736-49. Epub 2014 Jan 10.

Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA.

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https://academic.oup.com/nar/article/42/6/3736/2437385
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http://dx.doi.org/10.1093/nar/gkt1366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973313PMC
April 2014

An eQTL analysis of the human glioblastoma multiforme genome.

Genomics 2014 Apr 4;103(4):252-63. Epub 2014 Mar 4.

Texas Advanced Computing Center, University of Texas, Austin, TX 78758, USA.

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http://dx.doi.org/10.1016/j.ygeno.2014.02.005DOI Listing
April 2014

Dendritic cell fate is determined by BCL11A.

Proc Natl Acad Sci U S A 2014 Mar 3;111(11):E998-1006. Epub 2014 Mar 3.

Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712.

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http://dx.doi.org/10.1073/pnas.1319228111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964079PMC
March 2014

The BCL11A transcription factor directly activates RAG gene expression and V(D)J recombination.

Mol Cell Biol 2013 May 25;33(9):1768-81. Epub 2013 Feb 25.

Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.

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http://dx.doi.org/10.1128/MCB.00987-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3624176PMC
May 2013

A Myc-microRNA network promotes exit from quiescence by suppressing the interferon response and cell-cycle arrest genes.

Nucleic Acids Res 2013 Feb 8;41(4):2239-54. Epub 2013 Jan 8.

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.

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http://dx.doi.org/10.1093/nar/gks1452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575845PMC
February 2013

Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data.

BMC Genet 2012 Sep 5;13:46. Epub 2012 Sep 5.

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.

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http://dx.doi.org/10.1186/1471-2156-13-46DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3434080PMC
September 2012

Genome-wide studies of CCCTC-binding factor (CTCF) and cohesin provide insight into chromatin structure and regulation.

J Biol Chem 2012 Sep 5;287(37):30906-13. Epub 2012 Sep 5.

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.

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http://www.jbc.org/lookup/doi/10.1074/jbc.R111.324962
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http://dx.doi.org/10.1074/jbc.R111.324962DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3438923PMC
September 2012

Nucleosome positioning: bringing order to the eukaryotic genome.

Trends Cell Biol 2012 May 14;22(5):250-6. Epub 2012 Mar 14.

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.

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http://dx.doi.org/10.1016/j.tcb.2012.02.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3348441PMC
May 2012

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells.

Genome Res 2012 Jan 16;22(1):9-24. Epub 2011 Nov 16.

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.

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http://dx.doi.org/10.1101/gr.127597.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246210PMC
January 2012

Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis.

Nucleic Acids Res 2011 May 18;39(9):3558-73. Epub 2011 Jan 18.

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.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkq1313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3089461PMC
May 2011

Allele-specific and heritable chromatin signatures in humans.

Hum Mol Genet 2010 Oct 16;19(R2):R204-9. Epub 2010 Sep 16.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1093/hmg/ddq404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953746PMC
October 2010

Heritable individual-specific and allele-specific chromatin signatures in humans.

Science 2010 Apr 18;328(5975):235-9. Epub 2010 Mar 18.

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.

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http://dx.doi.org/10.1126/science.1184655DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929018PMC
April 2010

ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets.

Genome Biol 2008 12;9(11):R159. Epub 2008 Nov 12.

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.

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http://dx.doi.org/10.1186/gb-2008-9-11-r159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614491PMC
February 2009

Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae.

PLoS Genet 2008 Jul 11;4(7):e1000120. Epub 2008 Jul 11.

Center for Systems and Synthetic Biology, University of Texas, Austin, Texas, United States of America.

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https://dx.plos.org/10.1371/journal.pgen.1000120
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http://dx.doi.org/10.1371/journal.pgen.1000120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2438615PMC
July 2008

Involvement of JNK/p73/NOXA in vitamin E analog-induced apoptosis of human breast cancer cells.

Mol Carcinog 2008 Jun;47(6):436-45

Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712, USA.

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http://doi.wiley.com/10.1002/mc.20400
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http://dx.doi.org/10.1002/mc.20400DOI Listing
June 2008

Stress-dependent dynamics of global chromatin remodeling in yeast: dual role for SWI/SNF in the heat shock stress response.

Mol Cell Biol 2008 Apr 22;28(7):2221-34. Epub 2008 Jan 22.

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.

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http://dx.doi.org/10.1128/MCB.01659-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2268435PMC
April 2008

Global identification of Myc target genes reveals its direct role in mitochondrial biogenesis and its E-box usage in vivo.

PLoS One 2008 Mar 12;3(3):e1798. Epub 2008 Mar 12.

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.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001798PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2258436PMC
March 2008

Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.

PLoS Biol 2008 Mar;6(3):e65

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.

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http://dx.doi.org/10.1371/journal.pbio.0060065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2267817PMC
March 2008

CARM1 promotes adipocyte differentiation by coactivating PPARgamma.

EMBO Rep 2008 Feb 11;9(2):193-8. Epub 2008 Jan 11.

Department of Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Science Park, Smithville, Texas 78957, USA.

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http://embor.embopress.org/cgi/doi/10.1038/sj.embor.7401151
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http://dx.doi.org/10.1038/sj.embor.7401151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246418PMC
February 2008

Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining.

BMC Bioinformatics 2007 Nov 15;8:445. Epub 2007 Nov 15.

Institute for Cellular and Molecular Biology and Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712-0159, USA.

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http://dx.doi.org/10.1186/1471-2105-8-445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2211755PMC
November 2007

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin.

Genome Res 2007 Jun 19;17(6):877-85. Epub 2006 Dec 19.

Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA.

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http://dx.doi.org/10.1101/gr.5533506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891346PMC
June 2007

Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE).

Genome Res 2007 Jun;17(6):910-6

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.

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http://dx.doi.org/10.1101/gr.5574907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891349PMC
June 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Genetic reconstruction of a functional transcriptional regulatory network.

Nat Genet 2007 May 8;39(5):683-7. Epub 2007 Apr 8.

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.

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http://dx.doi.org/10.1038/ng2012DOI Listing
May 2007

Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways.

BMC Genomics 2007 May 10;8:117. Epub 2007 May 10.

Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA.

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http://dx.doi.org/10.1186/1471-2164-8-117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1878486PMC
May 2007

Genome-wide analysis of chromatin status using tiling microarrays.

Methods 2007 Mar;41(3):304-11

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.

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http://dx.doi.org/10.1016/j.ymeth.2006.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1876658PMC
March 2007

Systematic profiling of cellular phenotypes with spotted cell microarrays reveals mating-pheromone response genes.

Genome Biol 2006 31;7(1):R6. Epub 2006 Jan 31.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, 2500 Speedway, University of Texas, Austin, TX 78712, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2006-7-1-r6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1431703PMC
August 2006

PI3K signaling and miRNA expression during the response of quiescent human fibroblasts to distinct proliferative stimuli.

Genome Biol 2006 31;7(5):R42. Epub 2006 May 31.

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.

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http://dx.doi.org/10.1186/gb-2006-7-5-r42DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779520PMC
August 2006

Patterns of gene expression in the frontal cortex discriminate alcoholic from nonalcoholic individuals.

Neuropsychopharmacology 2006 Jul 2;31(7):1574-82. Epub 2005 Nov 2.

Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX 78712, USA.

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http://dx.doi.org/10.1038/sj.npp.1300947DOI Listing
July 2006

Fur regulates acid resistance in Shigella flexneri via RyhB and ydeP.

Mol Microbiol 2005 Dec;58(5):1354-67

Section of Molecular Genetics and Microbiology, The University of Texas at Austin, Austin, TX 78712, USA.

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http://dx.doi.org/10.1111/j.1365-2958.2005.04920.xDOI Listing
December 2005

Identifying chromosomal targets of DNA-binding proteins by Sequence Tag Analysis of Genomic Enrichment (STAGE).

Curr Protoc Mol Biol 2005 Nov;Chapter 21:Unit 21.10

University of Texas at Austin, Austin, Texas, USA.

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http://dx.doi.org/10.1002/0471142727.mb2110s72DOI Listing
November 2005

The heme activator protein Hap1 represses transcription by a heme-independent mechanism in Saccharomyces cerevisiae.

Genetics 2005 Mar 16;169(3):1343-52. Epub 2005 Jan 16.

Department of Environmental Health Sciences, Columbia University, Mailman School of Public Health, New York, New York 10032, USA.

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http://dx.doi.org/10.1534/genetics.104.037143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449556PMC
March 2005

Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment.

Nat Methods 2005 Jan 21;2(1):47-53. Epub 2004 Dec 21.

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 78712-0159, USA.

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http://dx.doi.org/10.1038/nmeth726DOI Listing
January 2005

Microarray data visualization and analysis with the Longhorn Array Database (LAD).

Curr Protoc Bioinformatics 2004 Dec;Chapter 7:Unit 7.10

University of Texas at Austin, Austin, Texas, USA.

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http://dx.doi.org/10.1002/0471250953.bi0710s08DOI Listing
December 2004

Exploring the post-transcriptional RNA world with DNA microarrays.

Trends Biotechnol 2004 Oct;22(10):498-500

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.

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October 2004

Global role of TATA box-binding protein recruitment to promoters in mediating gene expression profiles.

Mol Cell Biol 2004 Sep;24(18):8104-12

Institute for Cellular and Molecular Biology and Section of Molecular Genetics and Microbiology, University of Texas at Austin, 78712-0159, USA.

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http://dx.doi.org/10.1128/MCB.24.18.8104-8112.2004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC515063PMC
September 2004

Genome-wide analysis of the biology of stress responses through heat shock transcription factor.

Mol Cell Biol 2004 Jun;24(12):5249-56

Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109-0606, USA.

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http://dx.doi.org/10.1128/MCB.24.12.5249-5256.2004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC419887PMC
June 2004

The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD).

BMC Bioinformatics 2003 Aug 20;4:32. Epub 2003 Aug 20.

Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712-0159, USA.

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http://dx.doi.org/10.1186/1471-2105-4-32DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC194174PMC
August 2003

Translating genome sequences into biological understanding.

Genome Biol 2003 23;4(6):324. Epub 2003 May 23.

Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.

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http://dx.doi.org/10.1186/gb-2003-4-6-324DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC193614PMC
July 2003

Characterizing the physical genome.

Nat Genet 2002 Dec;32 Suppl:515-21

Department of Pathology, Stanford University School of Medicine, CCSR Building, Room 3245A, 269 Campus Drive, Stanford, California 94305-5176, USA.

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http://dx.doi.org/10.1038/ng1035DOI Listing
December 2002