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BACKGROUND In recent years, the maturation of microarray technology has allowed the genome-wide analysis of gene expression patterns to identify tissue-specific and ubiquitously expressed ('housekeeping') genes. We have performed a functional and topological analysis of housekeeping and tissue-specific networks to identify universally necessary biological(More)
BACKGROUND The identification of key target nodes within complex molecular networks remains a common objective in scientific research. The results of pathway analyses are usually sets of fairly complex networks or functional processes that are deemed relevant to the condition represented by the molecular profile. To be useful in a research or clinical(More)
The challenge of predicting the metabolism or toxicity of a drug in humans has been approached using in vivo animal models, in vitro systems, high throughput genomics and proteomics methods, and, more recently, computational approaches. Understanding the complexity of biological systems requires a broader perspective rather than focusing on just one method(More)
OBJECTIVE This study aimed to discover "signature pathways" that characterize biologic processes, based on genes differentially expressed in the uterine cervix before and after spontaneous labor. STUDY DESIGN The cervical transcriptome was characterized previously from biopsy specimens taken before and after term labor. Pathway analysis was used to study(More)
We identified a set of genes with an unexpected bimodal distribution among breast cancer patients in multiple studies. The property of bimodality seems to be common, as these genes were found on multiple microarray platforms and in studies with different end-points and patient cohorts. Bimodal genes tend to cluster into small groups of four to six genes(More)
BACKGROUND The problem of prostate cancer progression to androgen independence has been extensively studied. Several studies systematically analyzed gene expression profiles in the context of biological networks and pathways, uncovering novel aspects of prostate cancer. Despite significant research efforts, the mechanisms underlying tumor progression are(More)
Over the past several years there has been a paradigm shift in life science research as a result of the unprecedented advances in several laboratory techniques , such as automated DNA sequencing, global gene expression measurements, and proteomics and metabonomics techniques. The high throughput data collectively referred to as 'OMICs' data are ubiquitous(More)
Over the last two decades there have been tremendous advances with quantitative experimental techniques in physiology and signal transduction. On the cellular level these techniques include the scanning confocal microscopy, single channel recordings from intracellular channels, fluorescent dyes that allow visualization of the spatial and temporal dynamics(More)
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