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1.  Assessment of Pharmacologic Area Under the Curve When Baselines are Variable 
Pharmaceutical research  2011;28(5):1081-1089.
The area under the curve (AUC) is commonly used to assess the extent of exposure of a drug. The same concept can be applied to generally assess pharmacodynamic responses and the deviation of a signal from its baseline value. When the initial condition for the response of interest is not zero, there is uncertainty in the true value of the baseline measurement. This necessitates the consideration of the AUC relative to baseline to account for this inherent uncertainty and variability in baseline measurements.
An algorithm to calculate the AUC with respect to a variable baseline is developed by comparing the AUC of the response curve with the AUC of the baseline while taking into account uncertainty in both measurements. Furthermore, positive and negative components of AUC (above and below baseline) are calculated separately to allow for the identification of biphasic responses.
This algorithm is applied to gene expression data to illustrate its ability to capture transcriptional responses to a drug that deviate from baseline and to synthetic data to quantitatively test its performance.
The variable nature of the baseline is an important aspect to consider when calculating the AUC.
PMCID: PMC3152796  PMID: 21234658
AUC; baseline; bioinformatics; microarrays; pharmacogenomics
2.  A New Symbolic Representation for the Identification of Informative Genes in Replicated Microarray Experiments 
Microarray experiments generate massive amounts of data, necessitating innovative algorithms to distinguish biologically relevant information from noise. Because the variability of gene expression data is an important factor in determining which genes are differentially expressed, analysis techniques that take into account repeated measurements are critically important. Additionally, the selection of informative genes is typically done by searching for the individual genes that vary the most across conditions. Yet because genes tend to act in groups rather than individually, it may be possible to glean more information from the data by searching specifically for concerted behavior in a set of genes. Applying a symbolic transformation to the gene expression data allows the detection overrepresented patterns in the data, in contrast to looking only for genes that exhibit maximal differential expression. These challenges are approached by introducing an algorithm based on a new symbolic representation that searches for concerted gene expression patterns; furthermore, the symbolic representation takes into account the variance in multiple replicates and can be applied to long time series data. The proposed algorithm's ability to discover biologically relevant signals in gene expression data is exhibited by applying it to three datasets that measure gene expression in the rat liver.
PMCID: PMC3133780  PMID: 20455749

Results 1-2 (2)