selected publications

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)

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)

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)