University of New
Orleans B.S. in Chemistry, 1972.
Duke University
Ph.D. in Biochemistry, 1978.
Yale University
Postdoctoral Fellow, 1978-1979.
My research has recently moved into the areas of bioinformatics and computational biology. In collaboration with scientists in the Department of Computer Science and Engineering, I am exploring ways to examine the large volumes of genomic data that are being generated as a by-product of the Human Genome Project.
One application analyzes the results of alignment of microbial genes via positional weight matrices. An example is shown below:
All the open reading frames from E. Coli have been aligned using their start
codon. The frequency of appearance of bases at each position upstream and
downstream from this fixed point is then represented via the lines on the
graph. The ribosome binding site (the Shine-Dalgarno region) clearly shows
up as a region with a preponderance of G's just upstream of the start codon.
We are using this method to cluster data from archeae. These microorganisms seem to have unusual gene regulatory regions. This approach allows for discovery of these regions. We have applied both K-means binary clustering and self-organizing maps to analysis of our weight matrices.
Wan, Xiufeng, Susan M. Bridges, John A. Boyle, and Alan P. Boyle. Interactive Clustering for Exploration of Genomic Data. In: Smart Engineering System Design: Neural Networks, Fuzzy Logic, Evolutionary Programming, Data Mining and Complex Systems, edited by C.H. Dagli, A.L. Buczak, J. Ghosh, M.J. Embrechts, O. Ersoy and S.W. Kercel. (2002) ASME Press.
Babadzanjanz, L., J. Boyle, D. Sarkissian, and J. Zhu. Parameter identification for oscillating chemical reactions modeled by systems of ODE,(2003) Journal of ComputationalMethods in Science and Engineering 3: 31 - 40.
Boyle, J.A. 2002. Using the Human Genome: A Case Study in Education. (2002) Biochemistry and Molecular Biology Education. 30: 368 - 371.
Voet, J.G., E. Bell, R. Boyer, J.A. Boyle, M. O'Leary, and J. K. Zimmerman. Recommended Curriculum for a Program in Biochemistry and Molecular Biology. (2003) Biochemistry and Molecular Biology Education. 31: 161 - 162.
Boyle, Alan P. and John A. Boyle. Visualization of Aligned Genomic Open Reading Frame Data. (2003) Biochemistry and Molecular Biology Education. 31: 64 - 68.
Boyle, Alan P. And John A. Boyle. Global Analysis of Microbial Translation Initiation Regions. (2003) Journal of the Mississippi Academy of Sciences. 48: 138 - 150.
Boyle, John A. Implementing the Recommended Curriculum in a Biochemistry and Molecular Biology Degree Program in a Biochemistry and Molecular Biology Department: The Mississippi State Experience. (2003) Biochemistry and Molecular Biology Education. 31:283-285.
Wan, Xiufeng, Susan Bridges and John A. Boyle. Revealing gene transcription and translation initiation patterns in archaea using an interactive clustering model. (2004) Extremophiles. 8: 291-299.
Boyle, John A. Bioinformatics in Undergraduate Education: Practical Examples. (2004) Biochemistry and Molecular Biology Education. 32: 236 - 238.
Phone: (662) 325-2640
Fax: (662) 325-8664
Internet: jab@Ra.MsState.edu
