I have a broad background in biology and computer science. One of the most straightforward intersections between those two areas is bioinformatics, the specialized set of programming techniques used to transform nucleotide reads to a useable piece of data. I most often work with Oxford Nanopore whole genome sequencing and adaptive sequencing datasets, though I occasionally am lucky enough to work with exciting metagenomic environmental data. My two areas of expertise are in post-sequencing processing of long read sequencing data and dimensionality reduction for any large dataset.
I have experience writing programs and scripts in several computer programming languages including the bash shell, rust, R, python, and Java. This flexibility has made it easier to adapt existing software to meet the needs of particular projects, and to develop new programs to fit more specialized biological ideas. One example is the generalized hidden markov model I helped develop to model the unique uridylation/adenylation of mRNA transcript tails by trypanosomes; another more recent project is my software suite, Methylation Operation Wizard (MeOW). These projects required mathematical expertise to generalize probabilistic models, skill in programming, and an understanding of relevant molecular biology concepts and lab methods that needed to be integrated.
My statistical specialization is multivariate analysis of large compositional datasets. I also have an enduring interest in expanding what can be inferred through network analysis by using classic computer science concepts like maximum flow. Additionally, I've previously used my skills with ArcGIS, python, and java to automate workflows and generally perform advanced spatial analysis with wildlife and environmental data.
Current Projects
Improving Fungal Identification with ITS1
A current project to improve the taxonomic identification of ITS1 DNA sequences by improving alignment and establishing hierarchical thresholds.
Assessment of Microbes for Improving Wild Rice Restoration
As part of as large project identifying microbes and fungi involved in the health and life cycle of wild rice (Zizania palustris), I am focusing on wetland biogeochemical cycles using high throughput sequencing.
Psychrophilic and Extremely Acidophilic Sulfate-Reducing Bacteria and Acidic Mine Drainage
Collaboration with University of Alaska to identify microbes isolated in Acid Mine Drainage treatment
Source Sink Modeling of Raw Sewage Microbial Communities
Raw sewage samples are often used as stand-ins for human stool signal in environmental source tracking studies. I'm using SourceTracker to determine the relative contribution of human and other animal feces to the signal.
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Publications
3-hour genome sequencing and targeted analysis to rapidly assess genetic risk
Miranda Galey, Jonas Gustafson, Stephanie Bohaczuk, Ben Mallory, Paxton Reed, Tara Wenger, Erika Beckman, Irene J. Chang, Cate R. Paschal, Jillian G. Buchan, Christina M. Lockwood, Mihai Puia-Dumitrescu, Daniel R. Garalde, Joseph Guillory, Androo J. Markham, Michael J. Bamshad, Evan E. Eichler, Andrew B. Stergachis, Danny E. Miller
Genetics in Medicine Open, 2024, p. 101833
Danny Miller, Camille Dash, David Miller, Miranda Galey, Jasmine Lin, Jill A. Madden, Alan Beggs, Pankaj Agrawal, Casie Genetti, Monica Wojcik
Genetics in Medicine Open, vol. 1, Elsevier {BV}, 2023, p. 100737
Cate Paschal, Anita Beck, Madelyn Gillentine, Jaya Narayanan, Paxton Reed, Miranda Galey, Danny Miller
Genetics in Medicine Open, vol. 1, Elsevier {BV}, 2023, p. 100459
Haosheng Li, Erica Berent, Savannah Hadjipanteli, Miranda Galey, Nigel Muhammad-Lahbabi, Danny E. Miller, K. Nicole Crown
R. Scott Hawley, {PLOS} Genetics, vol. 19, Public Library of Science ({PLoS}), 2023 Apr, pp. e1010702
GENOME REPORT: Chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus)
Elizabeth Dong Nguyen, Vahid Nikoonejad Fard, Bernard Y. Kim, Sarah Collins, Miranda Galey, Branden R. Nelson, Paul Wakenight, Simone M. Gable, Aaron McKenna, Theo K. Bammler, Jim MacDonald, Daryl M. Okamura, Jay Shendure, David R. Beier, Jan Marino Ramirez, Mark W. Majesky, Kathleen J. Millen, Marc Tollis, Danny E. Miller
Cold Spring Harbor Laboratory, 2023 Apr
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