Continued development of an application for generation of phenotypic prototypes using simulated annealing (SAModk-prototypes). The application uses k-mode and k-means style clustering of categorical histopathology observations and numeric gene expression and clinical chemistry data respectively via simulated annealing optimization to cluster biological samples into groups which share phenotypic responses to stimuli. The clustering of the samples using SAModk-prototypes and all the data together performs better than clustering of the data using any one of the data domains separately or pairwise combinations of the data. -------------------------------------------------------------------------------------------------- Continued development of a software for biclustering of gene expression data using phenotypic measurements to constraint the clustering of the genes or by unsupervised clustering. The biclusters are phenotypically anchored to the gene expression. Constraining the clusters by Gene Onology biological processes was investigated. -------------------------------------------------------------------------------------------------- Performed additional scanning of the human and mouse genomes to search for patterns of DNA sequence and motifs related to DNA methylation. -------------------------------------------------------------------------------------------------- Continued development of computational means to analyze the S. pombe (yeast) genome across multiple time series experiments and to find transcription factor-gene regulatory units.
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