The Osier Lab at RIT

Our lab group focusses on the analysis of "large" biological data sets. We emphasize databases and Web interfaces to ease collaboration within user research labs. For analysis we often utilize biological ontologies and Genetic Algorithms. Our tools of choice are usually Perl and MySQL. Our current projects involve metabolomics analysis, data mining of NHANES III, categorizing mitochondrial genome variation, and the evolution of viral genomes.

Taylor SL, Ganti S, Bukanov NO, Chapman A, Fiehn O, Osier M, Kim K, and Weiss RH. (2010) A metabolomics approach using juvenile cystic mice to identify urinary biomarkers and altered pathways in polycystic kidney disease. American Journal of Physiology - Renal Physiology, 298:F909-F922. Uduman M, Reynolds C, Osier MV. (2006) A Genetic Algorithm and a Searching Heuristic for Application in Bioinformatics. In "Intelligent Engineering Systems Through Artificial Neural Networks-Volume 16." ASME Press. Osier, M.V., Zhao, H., and Cheung, K.-H. (2004) Handling multiple testing while interpreting microarrays with the Gene Ontology. BMC Bioinformatics, 5:124. Osier, M.V., Pakstis, A.J., Goldman, D., Edenberg, H.J., Kidd, J.R., and Kidd, K.K. (2002) A Proline-Threonine substitution in codon 351 of ADH1C is common in Native Americans. Alcoholism Clinical and Experimental Research, 26:1759-1763. Osier, M.V., Pakstis, A.J., Soodyall, H., Comas, D., Goldman, D., Odunsi, K., Okonofua, F., Parnas, J., Schulz, L., Bertranpetit, J., Bonne-Tamir, B., Lu, R.-B., Kidd, J.R., and Kidd, K.K. (2002) A Global Perspective on Genetic Variation at the ADH Genes Reveals Unusual Patterns of Linkage Disequilibrium and Diversity. American Journal of Human Genetics, 71:84-99. Cheung, K.H.*, Miller, P.L, Kidd, J.R., Kidd, K.K., Osier, M.V.*, Pakstis, A.J. (2000) ALFRED: a Web-accessible allele frequency database. Pacific Symposium on Biocomputing 639-650. * Joint first-author Full CV

	Kyle Dewey: The mtHaplogroups database.
	Christopher Fucile: Data mining of the NHANES III data set
	Benjamin Hopkins: A Visualization and Exploration Tool Designed to Assist in the Analysis of Experimental Metabolic Data
	Melissa Ruda: Rethinking the mitochondrial haplogroups.

• Sean Connolly - Presbycusis database development
• Anthony Corbett - Web Service classification
• Adam Cornwell - Meta-ontology for biology as a tool for managing public domain multimedia.
• Sherry Dadgar - Data mining of influenza genomic sequence.
• Kyle Dewey - Presbycusis glossary
• Lee Edsall - NatureSpy development
• T.J. Esposito - Permutation of Cluster Rank Analysis
• Chris Fucile - Development of a Web-accessible database for presbycusis research.
• Adam Handen - Permutation correction for t-tests of presbycusis data.
• Alex Haugh - Development of a Web Service to provide the maximum biclique solution for data in ALFRED
• Jonathan Keeling - NatureSpy data collection through cellular networks
• Brandon Marzullo - Mining the NHanes III Data set for a relationship between Vitamin D levels and heart disease.
• Amanda McFedries - Comparative identification of transcription factor binding sites
• Psalm Mizuki - Primer design using mtHaplogroups data.
• Phil Plummer - NatureSpy development
• Rhea Sanchez - Automated extraction of RT-PCR data and analysis of mitochondrial genetic variation for presbycusis.
• Bindhu Satheeshkumar - Development of a searchable influenza sequence database.
• Brian Selinsky - Neural network for analysis of high dimensionality data
• Ben Snider - Analysis of presbycusis genetics data
• Brent Strong - Comparative genomics
• Vishal Thovarai - Data mining of influenza genomic sequence.
• Mohamed Uduman - Solving the maximum biclique in human population genetics data from ALFRED
• Mellisa Wilbert - Data mining of influenza genomic sequence.
• Christina Witkowski - Cluster Rank Analysis development
• Greg Wyllie - Automated validation of Presbycusis Database contents.
• Michael Zeller - Meta-ontology for biology as a tool for managing public domain multimedia.

Last updated 7/8/11