Osier lab at RIT

The Osier Lab at RIT

Michael V. Osier, Ph.D.
Associate Professor of Biological Sciences
Office: 08-1338
Email: mvoscl@rit.edu
Current schedule and courses

Research interests

Our lab group studies genomics and transcriptomics of agricultural and invasive plant species. We combine use of existing bioinformatics and computational biology tools with development of our own tools.

Select publications

Kesel E, Hudson AO, Osier MV. (2022) Whole-Genome Sequence, Assembly and Annotation of an Invasive Plant, Lonicera maackii (Amur Honeysuckle). Plants, 11:3253. https://doi.org/10.3390/plants11233253
Musich R, Cadle-Davidson L, Osier MV. (2021) Comparison of Short-Read Sequence Aligners Indicates Strengths and Weaknesses for Biologists to Consider. Frontiers in Plant Science, https://doi.org/10.3389/fpls.2021.657240.
Barba P, Lillis J, Stephen Luce R, Travadon R, Osier M, Baumgartner K, Wilcox WF, Reisch BI, and Cadle-Davidson L. (2018) Two dominant loci determine resistance to Phomopsis cane lesions in F1 families of hybrid grapevines. Theoretical and Applied Genetics, https://doi.org/10.1007/s00122-018-3070-1.
Thomas JA, Quintana ADB, Bosch MA, De Pena AC, Aguilera E, Coulibaly A, Wu W, Osier MV, Hudson AO, Weintraub ST, and Black LW. (2016) Identification of Essential Genes in the Salmonella Phage SPN3US Reveals Novel Insights into Giant Phage Head Structure and Assembly. Journal of Virology, 90:10284-10298.
Osier MV. (2016) VitisPathways: gene pathway analysis for V. vinifera. Vitis, 55:129-133.
Osier MV. (2014) A Board Game for Undergraduate Genetics Vocabulary and Concept Review: The Pathway Shuffle. Journal of Microbiology and Biology Education, 15:328-329.
Ganti S, Taylor SL, Aboud OA, Yang J, Evans C, Osier MV, Alexander DC, Kim K, and Weiss RH. (2012) Kidney Tumor Biomarkers Revealed by Simultaneous Multiple Matrix Metabolomics Analysis. Cancer Research, 72:3471-9.
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., 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

Current student researchers

Sarah Teeter
Samantha Tran

Past student researchers

Sean Connolly - Presbycusis database development
Anthony Corbett - Web Service classification
* Anthony Corbett - Assessment of Alignment Algorithms, Variant Discovery and Genotype Calling Strategies in Exome Sequencing Data
* Adam Cornwell - Meta-ontology for biology as a tool for managing public domain multimedia.
Sherry Dadgar - Data mining of influenza genomic sequence.
* Kyle Dewey - The mtHaplogroups database
Kyle Dewey - Presbycusis glossary
Lee Edsall - NatureSpy development
* T.J. Esposito - Permutation of Cluster Rank Analysis
Connor Fortin - Web crawling for mtDNA variation
* Connor Fortin - Developing a new data storage and retrieval system for grape breeders
Chris Fucile - Development of a Web-accessible database for presbycusis research.
* Christopher Fucile - Data mining NHANES: Utilizing a Genetic Algorithm to Detect Correlation Between Birth Sex Ratio and Epidemiological Factors
* Adam Handen - Determining new alignment scoring matrix for disordered proteins.
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
Benjamin Hopkins - A Visualization and Exploration Tool Designed to Assist in the Analysis of Experimental Metabolic Data
Jonathan Keeling - NatureSpy data collection through cellular networks
* Erin Kesel - Assembly and annotation of the genome of an invasive bush honeysuckle, Amur honeysuckle (Lonicera maackii)
* David Kim - Determining a substitution matrix for the alignment of disordered proteins.
Dakota Kosiorek
* Jacquelyn Lillis - Characterization of the Ren4 resistance locus through the analysis of Genotyping-by-Sequencing and RNA-Sequencing data
Spencer Lopp - Assembly of a plant genome.
* Brandon Marzullo - The NHANES III database: Design and a retrospective study to identify associations between vitamin D and hypertension
Amanda McFedries - Comparative identification of transcription factor binding sites
* Psalm Mizuki - Primer design using mtHaplogroups data.
Nadia Moore - Assembly of a plant genome.
* Ryan Musich - A Recent (2020) Comparative Analysis of Genome Aligners Shows HISAT2 and BWA are Among the Best Tools
* Isabelle O'Bryon - Analysis of Grape Berry Epiphytic Microbiomes via QIIME
Lars Olsen - HTS Analysis of PM
* Lars Olsen - Functional Comparison of Current Software Tools for Genomic Assembly from High Throughput Sequencing Data
* Cal Palumbo - Investigation of Cold Stress Induced Disease Resistance (SIDR) in Grapevines and Arabidopsis
Phil Plummer - NatureSpy development
Makayla Reed - Assembly of a plant genome.
* Melissa Ruda - A Study of phylogenetic trees versus networks to objectively identify haplogroups in mitochondrial DNA
* Patrick Rynkiewicz - SecretePEPPr: Computational Prediction and Characterization of Effector-like Proteins Secreted from Vitis vinifera
* 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
Michael Shearer - Powdery Mildew Variation
Ben Snider - Analysis of presbycusis genetics data
* Chris Snyder - Comparative Transcriptomics of Grapevine Powdery Mildew
Brent Strong - Comparative genomics
* Daniel Surdyk - A Composite Interface for Bioinformatics Applications (CIBA)
Vishal Thovarai - Data mining of influenza genomic sequence.
Serena Tuytschaevers
* Mohamed Uduman - Solving the maximum biclique in human population genetics data from ALFRED
* Gaochan Wang - Genetic duplication in L. maackii genome.
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.

* Master of Science theses

Last updated 11/30/22