Abstract: The present invention relates to methods and compositions for the detection of biomarkers associated with colorectal diseases and disorders. In preferred embodiments, said colorectal disease is colorectal cancer. In some embodiments, the invention relates to the detection of said biomarkers using non-invasive methods. In further embodiments, the invention relates to the isolation and evaluation of biomarkers residing in feces from a subject at risk for or exhibiting symptoms associated with a colorectal disease or disorder. In still further embodiments, said biomarkers include exfoliated colonocytes. In additional embodiments, mRNA transcripts isolated from said colonocytes and associated with said colorectal diseases and disorders are quantified.

Abstract: The present invention describes methods for carrying out experiments on living cells, including making measurements of the operation transcriptional regulatory processes and indicators of the kinds of processes operating in the cell in response to external stimuli. Image analysis allows for gathering data concerning the flow of information through a cell's genomic regulatory network as it is executing a programmatic change in its activities as a function of said stimuli. The method also allows collection of data of the results of the information-processing in the cell by observing the decisions the cell makes when modulating cellular process activities.

Abstract: The present invention describes methods for carrying out experiments on living cells, including making measurements of the operation transcriptional regulatory processes and indicators of the kinds of processes operating in the cell in response to external stimuli. Image analysis allows for gathering data concerning the flow of information through a cell's genomic regulatory network as it is executing a programmatic change in its activities as a function of said stimuli. The method also allows collection of data of the results of the information-processing in the cell by observing the decisions the cell makes when modulating cellular process activities.

Abstract: Simulating a microarray includes defining a number of parameters. A microarray is generated according to the parameters using an imaging procedure. The microarray is compared to a known value, and the imaging procedure is evaluated in response to the comparison. A simulated microarray image can be generated based on parameters. The simulated microarray can be associated with known values. An imaging procedure is applied to the simulated microarray image to generate observed values. The known values (e.g., intensities) can be compared to the observed values to evaluate the imaging procedure.

Abstract: Embodiments of the invention encompass methods for modeling of complex systems, which include, but are not limited to gene regulatory networks, biological systems, and the like. Other embodiments of the invention include the development of computational tools for the identification and discovery of potential targets for therapeutic intervention in diseases such as cancer. The embodiments discussed utilize methods that model the potential effect of individual genes on the global dynamical network behavior, both from the view of random gene mutation as well as intervention in order to elicit desired network behavior.

Abstract: Relatedness between genes is quantified by constructing nonlinear models predicting gene expression. Effectiveness of the model is evaluated to provide a measurement of the relatedness of genes associated with the model. Various types of models, including full-logic or neural networks can be constructed. A graphical user interface presents results of the analysis to allow evaluation by a user. Each gene's contribution to the measurement of relatedness can be shown on a graph, and graphical representations of models used to predict gene expression can be displayed.

Abstract: Embodiments of the invention encompass methods for modeling of complex systems, which include, but are not limited to gene regulatory networks, biological systems, and the like. Other embodiments of the invention include the development of computational tools for the identification and discovery of potential targets for therapeutic intervention in diseases such as cancer. The embodiments discussed utilize methods that model the potential effect of individual genes on the global dynamical network behavior, both from the view of random gene mutation as well as intervention in order to elicit desired network behavior.

Abstract: Gene expression can be quantitatively analyzed by hybridizing fluor-tagged mRNA to targets on a cDNA micro-array. Comparison of gene expression levels arising from co-hybridized samples is achieved by taking ratios of average expression levels for individual genes. In an image-processing phase, a method of image segmentation identifies cDNA target sites in a cDNA micro-array image. The resulting cDNA target sites are analyzed based on a hypothesis test and confidence interval to quantify the significance of observed differences in expression ratios. In particular, the probability density of the ratio and the maximum-likelihood estimator for the distribution are derived, and an iterative procedure for signal calibration is developed.