My research is focused on pathogen effector bioinformatics. Pathogen effector bioinformatics include identification of pathogen effector proteins from pathogen genomes (bacteria, fungi, oomycetes, and nematodes), and their effector targets from host genomes (Arabidopsis, soybean, rice, maize, etc.) using alignment-free multivariate statistics, alignment-based methods, and machine learning approaches. Publications
Opiyo, S. O, Gangadharan, A., and Mackey, D. (submitted). Mining RNA-Seq time-course data from wild-type and rps4 mutant Arabidopsis exposed to nonhost Pseudomonas bacteria. Biotechnology and Bioinformatics Symposium 2012.
Hill, A. L., Whitehill, J. G. A., Opiyo, S. O., Phelan, P. L, and Bonello, P (submitted) Nutritional attributes of Ash (Fraxinus Spp.) outer bark and phloem and their relationships to resistance against the Emarald Ash borer. Tree Physiology
Shingqin, L., Opiyo, S. O., Manthey, K., Glanzer, J., Ashley, A., Courtney. T., Kyle, S., Shrivastav, M., Nickoloff, J., and Oakley, G. (In press). Distinct Roles for DNA-PK, ATM, and ATR in RPA Phosphorylation and Checkpoint Activation in Response to Replication Stress. Nucleic Acid Research.
Opiyo, S. O. (2012) Why we need Health Information Technology for Maintaining and Accessing Health Care Information. Journal of Health and Medical Informatics.3:e103
Orshinsky, A. M., Hu, J., Opiyo, S. O., Reddyvari-Channarayappa, V., Mitchell, T. M., and Boehm, M.J. (2012) RNA-Seq Analysis of the Sclerotinia homoeocarpa Creeping Bentgrass Pathosystem. Plos ONE 7(8): e41150
Whitehill, J. G. A, Opiyo, S. O., Koch, J. L, Herms, D. A, Cipollini, D. F, and Bonello, P. (2012) Interspecific Comparison of Constitutive Ash Phloem Phenolic Chemistry Reveals Compounds Unique to Manchurian Ash, a Species Resistant to Emerald Ash Borer. Journal of Chemical Ecology 38: 499-511.
Nagle, A. M., McPherson, B. A., Wood, D. L., Garbelotto, M., Conrad, A., Opiyo, S. O., and Bonello, P. (2011) Relationship Between Field Resistance to Phytophthora ramorum and Constitutive Phenolic Chemistry of Coast Live Oak. Proceedings of the 4th International Workshop on Genetics of Host-Parasite Interactions in Forestry.
Opiyo, S. O., Pardy, R. L., Moriyama, H., and Moriyama, E. N. (2010) Evolution of the Kdo2-lipid A biosynthesis in bacteria. BMC Evolutionary Biology 10:362.
Opiyo, S. O. and Moriyama, E. N. (2010) Mining Cytochrome b561 proteins from Plant Genomes. International Journal of Bioinformatics Research and Applications. 6: 209-221
Moriyama, E. N., and Opiyo, S. O. (2010) Bioinformatics of Seven-Transmembrane Receptors in Plant Genomes. Pp. 251-277 in Yalovsky, S., Baluska, F., and Jones, A. eds. Integrated G Proteins Signaling in Plants, Springer-Verlag, Berlin Heidelberg.
Oakley, G. G., Tillison, K., Opiyo, S., Glanzer, J., Horn, J. M., and Patrick, M. S. (2009) Physical Interaction between Replication Protein A (RPA) and MRN: Involvement of RPA2 Phosphorylation and the N-terminus of RPA1. Biochemistry. 48: 7473-7481
Opiyo, S. O. and Moriyama, E. N. (2009) Mining the Arabidopsis and rice genomes for cyclophlin protein families. International Journal of Bioinformatics Research and Applications. 5: 295-309.
Opiyo, S. O. and Moriyama, E. N. (2008) Mining Cytochrome b561 proteins from Plant Genomes. Proceedings for The 5th Annual Biotechnology and Bioinformatics Symposium: BIOT-08. pp 139-145.
Karoline, C. M., Opiyo, S., Glanzer, J.G., Dimitrova, D., Elliott, J., and Oakley, G. (2007) Nbs1 mediates ATR-dependent RPA hyperphosphorylation following replication fork stall and collapse. J. Cell Sci. 120: 4221-4229
Opiyo, S. O. and Moriyama, E. N. (2007) Protein family classification with partial least squares. J. Proteome Res. 6: 846-853.
Moriyama, E. N., Strope, P. K., Opiyo, S. O., Chen, Z. and Jones, A. M. (2006) Mining the Arabidopsis thaliana genome for highly-divergent seven transmembrane receptors. Genome Biology 7: R96.
