- "EDGE(3): a web-based solution for management and analysis of Agilent two color microarray experiments"
Vollrath AL, Smith AA, Craven M, et al., BMC Bioinformatics 10 280 Sep 2009. Here, we present EDGE(3), an open-source, web-based application that allows for the storage, analysis, and controlled sharing of transcription-based microarray data generated on the Agilent DNA platform. Pubmed/NLM.
- "The aryl hydrocarbon receptor: a perspective on potential roles in the immune system"
Stevens EA, Mezrich JD, Bradfield CA, Immunology 127 (3): 299-311 Jul 2009. In this review, we will attempt to illustrate what is currently known about AHR biology in the hope that data from fields as diverse as evolutionary biology and pharmacology will help elucidate the mechanism by which AHR modifies immune responses. Keywords: Animals; Evolution, Molecular; Inflammation/immunology; Mice; Mice, Mutant Strains; Receptors, Aryl Hydrocarbon/genetics; Receptors, Aryl Hydrocarbon/immunology; Signal Transduction/immunology; T-Lymphocytes, Regulatory/immunology. Pubmed/NLM.
- "Clustered alignments of gene-expression time series data"
Smith AA, Vollrath A, Bradfield CA, et al., Bioinformatics 25 (12): 119-127 Jun 2009. We present a novel algorithm that calculates clustered alignments; the method finds clusters of genes such that the genes within a cluster share a common alignment, but each cluster is aligned independently of the others. Pubmed/NLM.
- "Genetic components of the circadian clock regulate thrombogenesis in vivo"
Westgate EJ, Cheng Y, Reilly DF et al., Circulation 117 (16): 2087-2095 Apr 2008. Key components of the molecular clock regulate the response to a thrombogenic stimulus in vivo. Such a phenomenon may interact with environmental variables, and together with the influence of these genes on blood pressure may contribute to the diurnal variation in cardiovascular events observed in humans.