selected publications

 

Previous publications

Morgan X, Shulin N, Miranker DP and Iyer V.R. (2007)  Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining

BMC Bioinformatics 8:445 (Download PDF)


The ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Nature 447:799-816 (Download PDF)


Bhinge, A.A., Kim, J., Euskirchen, G., Snyder, M. and Iyer, V.R. (2007) Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE)

Genome Research 17: 910-916 (Download PDF)


Giresi P.G., Kim J., McDaniell R.M., Iyer V.R. and Lieb J.D. (2007) FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin Genome Research 17: 877-885 (Download PDF)


Hu Z., Killion, P.J., and Iyer V.R. (2007) Genetic reconstruction of a functional transcriptional regulatory network

Nature Genetics 39: 683-687 (Download PDF)


Shivaswamy S. and Iyer V.R. (2007) Genome-wide analysis of chromatin status using tiling microarrays

Methods 41: 304-11 (Download PDF)


Gu J. & Iyer V.R. (2006) PI3K signaling and miRNA expression during the response of quiescent human fibroblasts to distinct proliferative stimuli

Genome Biol. 7: R42 (Download PDF)


Narayanaswamy, R., Niu, W., Scouras, A., Hart, G. T., Davies, J.,

Ellington, A. D., Iyer, V. R. & Marcotte, E. M. (2006) Systematic profiling of cellular phenotypes with spotted cell microarrays reveals mating-pheromone response genes

Genome Biol.7: R6 (Download PDF)


Kim J., Bhinge A.A., Morgan X.C. & Iyer V.R. (2005) Mapping DNA-Protein Interactions in Large Genomes by Sequence Tag Analysis of Genomic Enrichment

Nature Methods 2: 47-53. (Download PDF)


Iyer, V. R. (2004) Exploring the posttranscriptional RNA world with DNA microarrays

Trends Biotechnol. 22: 498-500 (Download PDF)


Kim J. & Iyer V.R. (2004) Global role of TATA-box binding protein recruitment to promoters in mediating gene expression profiles

Mol. Cell. Biol. 24: 8104-8112 (Download PDF)


Hahn, J.S., Hu Z., Thiele D. J.* and Iyer V.R.* (2004) Genome-Wide Analysis of the Biology of Stress Responses through Heat Shock Transcription Factor

Mol. Cell. Biol. 24: 5249-5256 (Download PDF)


Killion P. J., Sherlock G. & Iyer V. R. (2003) The Longhorn Array Database (LAD): An Open-Source, MIAME compliant implementation of the Stanford Microarray Database (SMD)

BMC Bioinformatics 4:32 (Download PDF)


Pollack J. R. & Iyer V.R. (2002) Characterizing the physical genome

Nature Genetics 32 suppl: 515-521 (Download PDF)

Park D., Lee Y., Bhupindersingh G. & Iyer V.R. Widespread Misinterpretable ChIP-seq Bias in Yeast (2013) PLoS ONE 8(12): e83506



Polioudakis D., Bhinge A.A., Killion P.J., Lee B.K., Abell N.S. & Iyer V.R. A Myc-microRNA network promotes exit from quiescence by suppressing the interferon response and cell-cycle arrest genes. (2013) Nucleic Acids Res 41: 2239-54


Lee B.S., Dekker J.D., Lee B.K., Iyer V.R., Sleckman B.P., Shaffer A.L., 3rd, Ippolito G.C. & Tucker P.W. The BCL11A Transcription Factor Directly Activates RAG Gene Expression and V(D)J Recombination. (2013) Mol Cell Biol 33: 1768-81


Shibata Y., Sheffield N.C., Fedrigo O., Babbitt C.C., Wortham M., Tewari A.K., London D., Song L., Lee B.K., Iyer V.R., Parker S.C., Margulies E.H., Wray G.A., Furey T.S. & Crawford G.E. Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection. (2012) PLoS Genet 8: e1002789


Ni Y., Hall A.W., Battenhouse A. & Iyer V.R. Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data. (2012) BMC Genetics 13:46


The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. (2012) Nature 489: 57–74


Lee B.K., Bhinge A.A., Battenhouse A., McDaniell R.M., Liu Z., Song L., Ni Y., Birney E., Lieb J.D., Furey T.S., Crawford G.E., & Iyer V.R. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. (2012) Genome Res. 22: 9-24


The ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). (2011) PLoS Biol 9: e1001046


Lee B.K., Bhinge A.A. & Iyer V.R. Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis. (2011) Nucleic Acids Res. 39: 3558-3573


Boyle A.P., Song L., Lee B.K., London D., Keefe D., Birney E., Iyer V.R., Crawford G.E. & Furey T.S. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. (2011) Genome Res. 21: 456-464


Birney E., Lieb J.D., Furey T.S., Crawford G.E. & Iyer V.R. Allele-specific and heritable chromatin signatures in humans. (2010) Hum. Mol. Genet. 19: R204-9 (Download PDF)


McDaniell R., Lee B.K., Song L., Liu Z., Boyle A.P., Erdos M.R., Scott L.J., Morken M.A., Kucera K.S., Battenhouse A., Keefe D., Collins F.S., Willard H.F., Lieb J.D., Furey T.S., Crawford G.E.*,
Iyer V.R.*, Birney E.* (2010) Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans. Science 328: 235-239 (Download PDF)


Killion P.J. and Iyer V.R. (2008) ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets

Genome Biol. Nov 12;9(11):R159. (Download PDF)


Niu W., Li Z., Zhan W., Iyer V.R. and Marcotte E.M. (2008) Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae

PLoS Genet. vol. 4 (7) pp. e100012. (Download PDF)


Kim J., Lee J. and Iyer V.R. (2008) Global identification of Myc target genes reveals its direct role in mitochondrial biogenesis and its E-box usage in vivo

PLoS ONE vol. 3 (3) pp. e1798.(Download PDF)


Shivaswamy S, Bhinge A., Zhao Y., Jones S., Hirst M. and Iyer V.R. (2008) Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation

PLoS Biol. vol. 6 (3) pp. e65 (Download PDF)


Shivaswamy S and Iyer V.R. (2008) Stress-dependent dynamics of global chromatin remodeling in yeast: A dual role for SWI/SNF in the heat shock stress response

Mol Cell. Biol. 28: 2221-2234 (Download PDF)


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