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.
MCIC-Columbus
The Molecular and Cellular Imaging Center-Columbus (MCIC-Columbus) is a section of the Molecular and Cellular Imaging Center at the Ohio Agriculture Research Development Center (OARDC). The MCIC-Columbus houses analytical and molecular biology equipment for the Departments of Plant Pathology and Horticulture and Crop Science.
Responsibilities
• Bioinformatics, metabolomics, proteomics and genomics research.
• Coordinates all MCIC-Columbus core laboratory activities, including the use and maintenance of equipment; trains and assists users.
• Conducts bioinformatics research to support genomics, proteomics, and metabolomics research.
• Conducts collaborative research with the faculty from the two departments.
• Provides bioinformatics, metabolomics, genomics, proteomics, and statistical support to faculty, staff, and students from the Department of Plant Pathology and Horticulture and Crop Science.
Publications
• Hill et al, (The HPN-DREAM Consortium [Opiyo, SO]) (2016). Inferring causal molecular networks: empirical assessment through a community-based effort. Nature Methods. doi:10.1038/nmeth.3773
• Federica Eduati et al. (The NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration [Opiyo, S.O]). Prediction of human population responses to toxic compounds by a collaborative competition. Nature Biotechnology 33, 933–940 (2015)
• Asselin JA, Lin J, Perez-Quintero AL, Gentzel I, Majerczak D, Opiyo SO, Zhao W, Paek SM, Kim MG, Coplin DL, Blakeslee JJ, Mackey D. 2015. Perturbation of Maize Phenylpropanoid Metabolism by an AvrE Family Type III Effector from Pantoea stewartii. Plant Physiol. 167(3):1117-35. doi: 10.1104/pp.114.253120
• Chakraborty S, Whitehill JG, Hill AL, Opiyo SO, Cipollini D, Herms DA, Bonello P. 2014. Effects of Water Availability on Emerald Ash Borer Larval Performance and Phloem Phenolics of Manchurian and Black. Plant, Cell and Environment 37:1009–1021
• McPherson, B. A., Mori, S. R., Opiyo, S. O., Conrad, A. O., Wood, D. L., Bonello, P. 2014. Association between resistance to an introduced invasive pathogen and phenolic compounds that may serve as biomarkers in native oaks. Forest Ecology and Management 312:154-160
• Opiyo, S.O and Mackey, D 2013. Identification of proteins similar to AvrE type III effector proteins from Arabidopsidis thaliana genome with partial least squares. African Journal of Biotechnology 12 (39): 5804-5808
• Hill, A.L, Whitehill, JGA, Opiyo, SO, Phelan, PL, and Bonello, P. 2012. Nutritional attributes of Ash (Fraxinus Spp.) outer bark and phloem and their relationships to resistance against the Emarald Ash borer. Tree Physiology 32 (12): 1522-1532
• Shingqin, L., Opiyo, S. O., Manthey, K., Glanzer, J., Ashley, A., Courtney. T., Kyle, S., Shrivastav, M., Nickoloff, J., and Oakley, G. 2012. Distinct Roles for DNA-PK, ATM, and ATR in RPA Phosphorylation and Checkpoint Activation in Response to Replication Stress. Nucleic Acid Research. 40 (21): 10780-10794
• 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.
