Vishwanath R Iyer, Ph.D. - Publications

Affiliations: 
2000- Molecular Biosciences University of Texas at Austin, Austin, Texas, U.S.A. 

69 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Shivram H, Le SV, Iyer VR. PRC2 activates interferon-stimulated genes indirectly by repressing miRNAs in glioblastoma. Plos One. 14: e0222435. PMID 31513636 DOI: 10.1371/journal.pone.0222435  0.68
2019 Shivram H, Le SV, Iyer VR. MicroRNAs reinforce repression of PRC2 transcriptional targets independently and through a feed-forward regulatory network. Genome Research. PMID 30651280 DOI: 10.1101/gr.238311.118  0.68
2018 Shivram H, Iyer VR. Identification and removal of sequencing artifacts produced by mispriming during reverse transcription in multiple RNA-seq technologies. Rna (New York, N.Y.). PMID 29950518 DOI: 10.1261/rna.066217.118  0.68
2018 Hall AW, Battenhouse AM, Shivram H, Morris AR, Cowperthwaite MC, Shpak M, Iyer VR. Bivalent chromatin domains in glioblastoma reveal a subtype-specific signature of glioma stem cells. Cancer Research. PMID 29549165 DOI: 10.1158/0008-5472.CAN-17-1724  0.68
2017 Popowski M, Lee BK, Rhee C, Iyer VR, Tucker HO. Arid3a regulates mesoderm differentiation in mouse embryonic stem cells. Journal of Stem Cell Therapy and Transplantation. 1: 52-62. PMID 31080945 DOI: 10.29328/journal.jsctt.1001005  0.96
2017 Lee BS, Lee BK, Iyer VR, Sleckman BP, Shaffer AL, Ippolito GC, Tucker HO, Dekker JD. BCL11A is a critical component of a transcriptional network that activates RAG expression and VDJ recombination. Molecular and Cellular Biology. PMID 29038163 DOI: 10.1128/MCB.00362-17  0.96
2017 Lee BS, Dekker JD, Lee BK, Iyer VR, Sleckman BP, Shaffer AL, Ippolito GC, Tucker PW. Retraction for Lee et al., "The BCL11A Transcription Factor Directly Activates RAG Gene Expression and V(D)J Recombination". Molecular and Cellular Biology. 37. PMID 29030471 DOI: 10.1128/MCB.00358-17  0.96
2017 Lee Y, Park D, Iyer VR. 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 Research. 45: 8646. PMID 28854740 DOI: 10.1093/nar/gkx636  1
2017 Wang L, Zhang F, Rode S, Chin KK, Ko EE, Kim J, Iyer VR, Qiao H. Ethylene induces combinatorial effects of histone H3 acetylation in gene expression in Arabidopsis. Bmc Genomics. 18: 538. PMID 28716006 DOI: 10.1186/s12864-017-3929-6  1
2017 Lee Y, Park D, Iyer VR. 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 Research. PMID 28460001 DOI: 10.1093/nar/gkx321  1
2016 Ellefson JW, Gollihar J, Shroff R, Shivram H, Iyer VR, Ellington AD. Synthetic evolutionary origin of a proofreading reverse transcriptase. Science (New York, N.Y.). 352: 1590-3. PMID 27339990 DOI: 10.1126/science.aaf5409  1
2016 Zhang D, Park D, Zhong Y, Lu Y, Rycaj K, Gong S, Chen X, Liu X, Chao HP, Whitney P, Calhoun-Davis T, Takata Y, Shen J, Iyer VR, Tang DG. Stem cell and neurogenic gene-expression profiles link prostate basal cells to aggressive prostate cancer. Nature Communications. 7: 10798. PMID 26924072 DOI: 10.1038/ncomms10798  1
2016 Dekker JD, Park D, Shaffer AL, Kohlhammer H, Deng W, Lee BK, Ippolito GC, Georgiou G, Iyer VR, Staudt LM, Tucker HO. Subtype-specific addiction of the activated B-cell subset of diffuse large B-cell lymphoma to FOXP1. Proceedings of the National Academy of Sciences of the United States of America. PMID 26787899 DOI: 10.1073/pnas.1524677113  1
2015 Mohanty S, Hall AW, Mohanty P, Prakash S, Trivedi C, Di Biase L, Santangeli P, Bai R, Burkhardt JD, Gallinghouse GJ, Horton R, Sanchez JE, Hranitzky PM, Al-Ahmad A, Iyer VR, et al. Novel association of polymorphic genetic variants with predictors of outcome of catheter ablation in atrial fibrillation: new directions from a prospective study (DECAF). Journal of Interventional Cardiac Electrophysiology : An International Journal of Arrhythmias and Pacing. PMID 26497660 DOI: 10.1007/s10840-015-0069-2  1
2015 Polioudakis D, Abell NS, Iyer VR. MiR-191 Regulates Primary Human Fibroblast Proliferation and Directly Targets Multiple Oncogenes. Plos One. 10: e0126535. PMID 25992613 DOI: 10.1371/journal.pone.0126535  0.76
2015 Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E. Correction: Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. Plos Genetics. 11: e1005177. PMID 25919664 DOI: 10.1371/journal.pgen.1005177  1
2015 Polioudakis D, Abell NS, Iyer VR. miR-503 represses human cell proliferation and directly targets the oncogene DDHD2 by non-canonical target pairing. Bmc Genomics. 16: 40. PMID 25653011 DOI: 10.1186/s12864-015-1279-9  1
2014 Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E. Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. Plos Genetics. 10: e1004798. PMID 25411781 DOI: 10.1371/journal.pgen.1004798  1
2014 Park D, Shivram H, Iyer VR. Chd1 co-localizes with early transcription elongation factors independently of H3K36 methylation and releases stalled RNA polymerase II at introns. Epigenetics & Chromatin. 7: 32. PMID 25395991 DOI: 10.1186/1756-8935-7-32  1
2014 Ki S, Park D, Selden HJ, Seita J, Chung H, Kim J, Iyer VR, Ehrlich LI. Global transcriptional profiling reveals distinct functions of thymic stromal subsets and age-related changes during thymic involution. Cell Reports. 9: 402-15. PMID 25284794 DOI: 10.1016/j.celrep.2014.08.070  1
2014 Wortham M, Guo C, Zhang M, Song L, Lee BK, Iyer VR, Furey TS, Crawford GE, Yan H, He Y. Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma. Plos One. 9: e107156. PMID 25198066 DOI: 10.1371/journal.pone.0107156  1
2014 Shpak M, Hall AW, Goldberg MM, Derryberry DZ, Ni Y, Iyer VR, Cowperthwaite MC. An eQTL analysis of the human glioblastoma multiforme genome. Genomics. 103: 252-63. PMID 24607568 DOI: 10.1016/j.ygeno.2014.02.005  1
2014 Ippolito GC, Dekker JD, Wang YH, Lee BK, Shaffer AL, Lin J, Wall JK, Lee BS, Staudt LM, Liu YJ, Iyer VR, Tucker HO. Dendritic cell fate is determined by BCL11A. Proceedings of the National Academy of Sciences of the United States of America. 111: E998-1006. PMID 24591644 DOI: 10.1073/pnas.1319228111  1
2014 Popowski M, Templeton TD, Lee BK, Rhee C, Li H, Miner C, Dekker JD, Orlanski S, Bergman Y, Iyer VR, Webb CF, Tucker H. Bright/Arid3A acts as a barrier to somatic cell reprogramming through direct regulation of Oct4, Sox2, and Nanog. Stem Cell Reports. 2: 26-35. PMID 24511468 DOI: 10.1016/j.stemcr.2013.12.002  1
2014 Park D, Morris AR, Battenhouse A, Iyer VR. Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements. Nucleic Acids Research. 42: 3736-49. PMID 24413663 DOI: 10.1093/nar/gkt1366  1
2013 Park D, Lee Y, Bhupindersingh G, Iyer VR. Widespread misinterpretable ChIP-seq bias in yeast. Plos One. 8: e83506. PMID 24349523 DOI: 10.1371/journal.pone.0083506  1
2013 Mohr S, Ghanem E, Smith W, Sheeter D, Qin Y, King O, Polioudakis D, Iyer VR, Hunicke-Smith S, Swamy S, Kuersten S, Lambowitz AM. Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing. Rna (New York, N.Y.). 19: 958-70. PMID 23697550 DOI: 10.1261/rna.039743.113  1
2013 Lee BS, Dekker JD, Lee BK, Iyer VR, Sleckman BP, Shaffer AL, Ippolito GC, Tucker PW. The BCL11A transcription factor directly activates RAG gene expression and V(D)J recombination. Molecular and Cellular Biology. 33: 1768-81. PMID 23438597 DOI: 10.1128/MCB.00987-12  1
2013 Polioudakis D, Bhinge AA, Killion PJ, Lee BK, Abell NS, Iyer VR. A Myc-microRNA network promotes exit from quiescence by suppressing the interferon response and cell-cycle arrest genes. Nucleic Acids Research. 41: 2239-54. PMID 23303785 DOI: 10.1093/nar/gks1452  1
2012 Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, ... ... Iyer VR, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 22: 1813-31. PMID 22955991 DOI: 10.1101/gr.136184.111  1
2012 Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, ... ... Iyer VR, et al. The accessible chromatin landscape of the human genome. Nature. 489: 75-82. PMID 22955617 DOI: 10.1038/nature11232  1
2012 Lee BK, Iyer VR. Genome-wide studies of CCCTC-binding factor (CTCF) and cohesin provide insight into chromatin structure and regulation. The Journal of Biological Chemistry. 287: 30906-13. PMID 22952237 DOI: 10.1074/jbc.R111.324962  1
2012 Ni Y, Hall AW, Battenhouse A, Iyer VR. Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data. Bmc Genetics. 13: 46. PMID 22950704 DOI: 10.1186/1471-2156-13-46  1
2012 Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, London D, Song L, Lee BK, Iyer VR, Parker SC, Margulies EH, Wray GA, Furey TS, Crawford GE. Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. Plos Genetics. 8: e1002789. PMID 22761590 DOI: 10.1371/journal.pgen.1002789  1
2012 Iyer VR. Nucleosome positioning: bringing order to the eukaryotic genome. Trends in Cell Biology. 22: 250-6. PMID 22421062 DOI: 10.1016/j.tcb.2012.02.004  1
2012 Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Research. 22: 9-24. PMID 22090374 DOI: 10.1101/gr.127597.111  1
2011 Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, ... ... Iyer VR, et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Research. 21: 1757-67. PMID 21750106 DOI: 10.1101/gr.121541.111  1
2011 Lee BK, Bhinge AA, Iyer VR. Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis. Nucleic Acids Research. 39: 3558-73. PMID 21247883 DOI: 10.1093/nar/gkq1313  1
2011 Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Research. 21: 456-64. PMID 21106903 DOI: 10.1101/gr.112656.110  1
2010 Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR. Allele-specific and heritable chromatin signatures in humans. Human Molecular Genetics. 19: R204-9. PMID 20846943 DOI: 10.1093/hmg/ddq404  1
2010 McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, Erdos MR, Scott LJ, Morken MA, Kucera KS, Battenhouse A, Keefe D, Collins FS, Willard HF, Lieb JD, Furey TS, ... ... Iyer VR, et al. Heritable individual-specific and allele-specific chromatin signatures in humans. Science (New York, N.Y.). 328: 235-9. PMID 20299549 DOI: 10.1126/science.1184655  1
2008 Killion PJ, Iyer VR. ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets. Genome Biology. 9: R159. PMID 19014503 DOI: 10.1186/gb-2008-9-11-r159  1
2008 Niu W, Li Z, Zhan W, Iyer VR, Marcotte EM. Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae. Plos Genetics. 4: e1000120. PMID 18617996 DOI: 10.1371/journal.pgen.1000120  1
2008 Shivaswamy S, Bhinge A, Zhao Y, Jones S, Hirst M, Iyer VR. Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. Plos Biology. 6: e65. PMID 18351804 DOI: 10.1371/journal.pbio.0060065  1
2008 Kim J, Lee JH, Iyer VR. Global identification of Myc target genes reveals its direct role in mitochondrial biogenesis and its E-box usage in vivo. Plos One. 3: e1798. PMID 18335064 DOI: 10.1371/journal.pone.0001798  1
2008 Shivaswamy S, Iyer VR. Stress-dependent dynamics of global chromatin remodeling in yeast: dual role for SWI/SNF in the heat shock stress response. Molecular and Cellular Biology. 28: 2221-34. PMID 18212068 DOI: 10.1128/MCB.01659-07  1
2008 Yadav N, Cheng D, Richard S, Morel M, Iyer VR, Aldaz CM, Bedford MT. CARM1 promotes adipocyte differentiation by coactivating PPARgamma. Embo Reports. 9: 193-8. PMID 18188184 DOI: 10.1038/sj.embor.7401151  1
2008 Wang P, Yu W, Hu Z, Jia L, Iyer VR, Sanders BG, Kline K. Involvement of JNK/p73/NOXA in vitamin E analog-induced apoptosis of human breast cancer cells. Molecular Carcinogenesis. 47: 436-45. PMID 18058804 DOI: 10.1002/mc.20400  1
2007 Morgan XC, Ni S, Miranker DP, Iyer VR. Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining. Bmc Bioinformatics. 8: 445. PMID 18005433 DOI: 10.1186/1471-2105-8-445  1
2007 Bhinge AA, Kim J, Euskirchen GM, Snyder M, Iyer VR. Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Research. 17: 910-6. PMID 17568006 DOI: 10.1101/gr.5574907  1
2007 Carlson MW, Iyer VR, Marcotte EM. Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways. Bmc Genomics. 8: 117. PMID 17493265 DOI: 10.1186/1471-2164-8-117  1
2007 Hu Z, Killion PJ, Iyer VR. Genetic reconstruction of a functional transcriptional regulatory network. Nature Genetics. 39: 683-7. PMID 17417638 DOI: 10.1038/ng2012  1
2007 Shivaswamy S, Iyer VR. Genome-wide analysis of chromatin status using tiling microarrays. Methods (San Diego, Calif.). 41: 304-11. PMID 17309841 DOI: 10.1016/j.ymeth.2006.11.002  1
2007 Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research. 17: 877-85. PMID 17179217 DOI: 10.1101/gr.5533506  1
2006 Gu J, Iyer VR. PI3K signaling and miRNA expression during the response of quiescent human fibroblasts to distinct proliferative stimuli. Genome Biology. 7: R42. PMID 16737555 DOI: 10.1186/gb-2006-7-5-r42  1
2006 Mulligan MK, Ponomarev I, Hitzemann RJ, Belknap JK, Tabakoff B, Harris RA, Crabbe JC, Blednov YA, Grahame NJ, Phillips TJ, Finn DA, Hoffman PL, Iyer VR, Koob GF, Bergeson SE. Toward understanding the genetics of alcohol drinking through transcriptome meta-analysis. Proceedings of the National Academy of Sciences of the United States of America. 103: 6368-73. PMID 16618939 DOI: 10.1073/pnas.0510188103  1
2006 Narayanaswamy R, Niu W, Scouras AD, Hart GT, Davies J, Ellington AD, Iyer VR, Marcotte EM. Systematic profiling of cellular phenotypes with spotted cell microarrays reveals mating-pheromone response genes. Genome Biology. 7: R6. PMID 16507139 DOI: 10.1186/gb-2006-7-1-r6  1
2006 Liu J, Lewohl JM, Harris RA, Iyer VR, Dodd PR, Randall PK, Mayfield RD. Patterns of gene expression in the frontal cortex discriminate alcoholic from nonalcoholic individuals. Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology. 31: 1574-82. PMID 16292326 DOI: 10.1038/sj.npp.1300947  1
2005 Kim J, Iyer VR. 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.]. Unit 21.10. PMID 18265357 DOI: 10.1002/0471142727.mb2110s72  1
2005 Oglesby AG, Murphy ER, Iyer VR, Payne SM. Fur regulates acid resistance in Shigella flexneri via RyhB and ydeP. Molecular Microbiology. 58: 1354-67. PMID 16313621 DOI: 10.1111/j.1365-2958.2005.04920.x  1
2005 Kim J, Bhinge AA, Morgan XC, Iyer VR. Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment. Nature Methods. 2: 47-53. PMID 15782160 DOI: 10.1038/nmeth726  1
2005 Hon T, Lee HC, Hu Z, Iyer VR, Zhang L. The heme activator protein Hap1 represses transcription by a heme-independent mechanism in Saccharomyces cerevisiae. Genetics. 169: 1343-52. PMID 15654089 DOI: 10.1534/genetics.104.037143  1
2004 Killion PJ, Iyer VR. Microarray data visualization and analysis with the Longhorn Array Database (LAD). Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 7.10. PMID 18428730 DOI: 10.1002/0471250953.bi0710s08  1
2004 Iyer VR. Exploring the post-transcriptional RNA world with DNA microarrays. Trends in Biotechnology. 22: 498-500. PMID 15450741 DOI: 10.1016/j.tibtech.2004.08.006  1
2004 Kim J, Iyer VR. Global role of TATA box-binding protein recruitment to promoters in mediating gene expression profiles. Molecular and Cellular Biology. 24: 8104-12. PMID 15340072 DOI: 10.1128/MCB.24.18.8104-8112.2004  1
2004 Hahn JS, Hu Z, Thiele DJ, Iyer VR. Genome-wide analysis of the biology of stress responses through heat shock transcription factor. Molecular and Cellular Biology. 24: 5249-56. PMID 15169889 DOI: 10.1128/MCB.24.12.5249-5256.2004  1
2003 Killion PJ, Sherlock G, Iyer VR. The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD). Bmc Bioinformatics. 4: 32. PMID 12930545 DOI: 10.1186/1471-2105-4-32  1
2003 Iyer VR. Translating genome sequences into biological understanding. Genome Biology. 4: 324. PMID 12801409 DOI: 10.1186/gb-2003-4-6-324  1
2002 Pollack JR, Iyer VR. Characterizing the physical genome. Nature Genetics. 32: 515-21. PMID 12454647 DOI: 10.1038/ng1035  1
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