Multi-Timescale Complex Adaptation
Final rept. 5 Sep 2001-31 Dec 2005
THOMAS JEFFERSON UNIV PHILADELPHIA PA
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The overall goal of the project was to develop structured approaches to modeling complex gene regulation dynamics underlying cellular adaptation in mammalian systems. This involves integration of two erstwhile disjoint aspects mathematical modeling and bioinformatics of high-throughput biological data. As part of a structured approach to tackle this problem, we have developed methods and software tools for identification of 1 robust patterns of gene expression using a meta-clustering approach, 2 network structures from these patterns, and 3 a continuous-time regulatory network model based on temporally discrete gene expression data and predicted network structures. A web-based, graphical user interface was developed for the network structure prediction software, PAINT, and has been released as a DARPA BioSPICE module. We have successfully employed our structured approach in the study of various gene regulatory networks from in silico model systems, yeast cell cycle, neuronal differentiation and adaptation, circadian rhythms, and cellular response to pathogens.
- Genetic Engineering and Molecular Biology
- Operations Research
- Computer Programming and Software