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Environmental stresses are universally encountered by microbes, plants, and animals. Yet systematic studies of stress-responsive transcription factor (TF) networks in multicellular organisms have been limited. The phytohormone abscisic acid (ABA) influences the expression of thousands of genes, allowing us to characterize complex stress-responsive(More)
A cross-sectional analysis of the Cambodia Demographic Health Surveys from 2000, 2005 and 2010 was conducted to observe the national trends in infant and young child feeding practices. The results showed that rates of exclusive breastfeeding among infants aged 0-5.9 months have increased substantially since 2000, concurrent with an increase in the rates of(More)
MOTIVATION Current methods for reconstructing dynamic regulatory networks are focused on modeling a single response network using model organisms or cell lines. Unlike these models or cell lines, humans differ in their background expression profiles due to age, genetics and life factors. In addition, there are often differences in start and end times for(More)
Measurement of intracellular calcium release following agonist challenge within cells expressing the relevant membrane protein is a commonly used format to derive structure-activity relationship (SAR) data within a compound profiling assay. The Fluorometric Imaging Plate Reader (FLIPR) has become the gold standard for this purpose. FLIPR traditionally uses(More)
Genes are often combinatorially regulated by multiple transcription factors (TFs). Such combinatorial regulation plays an important role in development and facilitates the ability of cells to respond to different stresses. While a number of approaches have utilized sequence and ChIP-based datasets to study combinational regulation, these have often ignored(More)
Carbon catabolite repression (CCR) is critical for optimal bacterial growth, and in bacterial (and yeast) cells it leads to their selective consumption of a single substrate from a complex environment. However, the root cause(s) for the development of this regulatory mechanism is unknown. Previously, a flux balance model (FBAwMC) of Escherichia coli(More)
MOTIVATION With the vast increase in the number of gene expression datasets deposited in public databases, novel techniques are required to analyze and mine this wealth of data. Similar to the way BLAST enables cross-species comparison of sequence data, tools that enable cross-species expression comparison will allow us to better utilize these datasets:(More)
Drug discovery has successfully exploited the superfamily of seven transmembrane receptors (7TMR), with over 35% of clinically marketed drugs targeting them. However, it is clear that there remains an undefined potential within this protein family for successful drugs of the future. The human genome sequencing project identified approximately 720 genes that(More)
Microarray technology allows for the expression levels of thousands of genes in a cell to be measured simultaneously. The technology provides great potential in the fields of biology and medicine as the analysis of data obtained from microarray experiments gives insight into the roles of specific genes and the associated changes across experimental(More)
Motivation: Cancer is a complex and evolving disease, making it difficult to discover effective treatments. Traditional drug discovery relies on high-throughput screening on reductionist models in order to enable the testing of 105 or 106 compounds. These assays lack the complexity of the human disease. Functional assays overcome this limitation by testing(More)