My laboratory is interested in the following areas:
♦ Computational Reconstruction of Biological Networks: Our goal is to understand the catalytic and regulatory mechanisms of components within biological pathways, then reconstruct and study dynamic processes of biological networks in the cell. Our primary targets are signal transduction, gene regulation and metabolic pathways. The complexity of these systems provides many interesting challenges for those who are interested in mathematical modeling and simulation. The ultimate goal is to rebuild a living cell inside a computer, which can facilitate the functional analysis of data from advancing high throughput technologies, such as genomics, transcriptomics, proteomics, and metabolomics. Unlike commonly seen oversimplified linear chemical conversion models, our focus is on the non-linear, enzyme-centric mathematical model. This modeling technique has been proven to simulate regulatory patterns in the pathway level accurately, and mimic genetic and biochemical perturbations observed experimentally. For application, we are currently interested in network reconstruction in microbes and signaling pathways/networks in human cancers.
♦ In silico Biology: Using computational models built in the laboratory, we are interested in analyzing the regulatory patterns and control theory of robust design in natural selection. Obtaining this knowledge would facilitate the development of algorithms for the automated generation of hypotheses that can help biologists to design and simulate their experiments in silico.
♦ Biological Data Mining: We are also interested in developing biologically relevant algorithms for mining information and gaining new insights from large-scale biological data sets, primarily DNA microarray gene expression and proteomic data, and applying such computational tools to help biologists solve real biological problems.
RESEARCH INTERESTS
Systems Biology
Non-linear Dynamics of Biological Networks
Bioinformatics
DNA Microarray Analysis
RECENT PUBLICATIONS
Yang, C-R., Shapiro, B. E., Mjolsness, E. D., and Hatfield, G. W., "An enzyme mechanism language for the mathematical modeling of metabolic pathways." Bioinformatics, 21:774-780, 2005
Yang, C-R., Shapiro, B. E., Hung, S-P., Mjolsness, E. D., and Hatfield, G. W., "A mathematical model for the branched chain amino acid biosynthetic pathways of Escherichia coli K12." J. Biol. Chem., 280(12):11224-11232, 2005
Yang, C-R, Najdi, T. S., Shapiro, B. E., Hatfield, G. W. and Eric D. Mjolsness., "The Generalized Monod, Wyman, Changeux Model for Mathematical Modeling of Metabolic Enzymes with Allosteric Regulation." Journal of Bioinformatics and Computational Biology, in press June 2006
SIGNIFICANT PUBLICATIONS
Yang C-R, Leskov K, Hosley-Eberlein K, Criswell T, Pink JJ, Kinsella TJ, Boothman DA., "Nuclear apoJ/XIP8, an X-ray-inducible Ku70-binding Protein That Controls Radiosensitivity." Proc. Natl. Acad. Sci., 97(11):5907-5912, 2000
Yang, C-R., Yeh, S., Leskov K., Odegaard E., Hsu, H.L., Chang, C., Kinsella, T.J., Chen, D.J., and Boothman, D.A., "Isolation of Ku70-Binding Proteins (KUBs)." Nucleic Acids Research, 27(10):2165-2174, 1999
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