Research

At the University of Oregon, data science researchers focus on tackling complex challenges and exploring novel methodologies to extract insights from massive datasets.

Areas of Research Interest:

Social Justice and Data Science

Biostatistics

Statistical Forensic Genetics

Data Optimization

Geometric Deep Learning

AI-Assisted Decision Making

Population Genetics

Microbiome Research

Evolutionary Biology

Generative Deep Learning

Digital Health/Pathology

Computational Biology

a seadragon positioned in a lab tube for scanning by a large machine

Read the latest research from our faculty

From conference presentations to academic journals, browse some of UO's published data science research.

test begin

2023
How Useful Are Tax Disclosures in Predicting Effective Tax Rates? A Machine Learning Approach Guenther, D.A., Peterson, K., Searcy, J., Williams, BM. The Accounting Review, 1-26. 2023	Improving biology faculty diversity through a co-hiring policy and faculty agents of change Harris, M., Rosser, S., Goldman, M., Márquez-Magaña, L., Rohlfs, R.V. PLoS ONE: 18(5): e0285602, 2023
Deep learning for denoising High-Rate Global Navigation Satellite System data Thomas, A., Melgar, D., Dybing, S.N., Searcy, J. Seismica 2. 2023	Frontline Data Science: Lessons Learned From a Pandemic Beck, E.A., Tavalire, H., Searcy J. PubPub 5. 2023
Reaching Latinx Communities With Algorithmic Optimization for SARS-CoV-2 Testing Locations Searcy, J., Cioffi, C.C., Tavalire, H.F., Budd, E.L., Cresko W.A., DeGarmo, D. and others Prevention Science, 1-12. 2023	Low-Altitude UAV Imaging Accurately Quantifies Eelgrass Wasting Disease From Alaska to California Yang, B., T. L. Hawthorne, L. Aoki, and others Geophysical Research Letters 50: e2022GL101985. 2023
UAV High-Resolution Imaging and Disease Surveys Combine to Quantify Climate-Related Decline in Seagrass Meadows Aoki, L. R., B. Yang, O. J. Graham, C. Gomes, B. Rappazzo, T. L. Hawthorne, E. J. Duffy, and D. Harvell. 2023. Oceanography 36: 38–39. 2023	Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy in Antarctic Notothenioids Minhas, B.F. , Beck, E.A., Cheng, C.-H., Catchen, J. Scientific Reports. 2023
Genome-wide analysis facilitates estimation of the amount of male contribution in meiotic gynogenetic threespine stickleback (Gasterosteus aculeatus) Currey, M., Walker, C, Bassham, S., Healey, H.M., Beck, E.A., Cresko, W.A. Journal of Fish Biology. 2023	Host genomic variation shapes gut microbiome diversity in threespine stickleback fish. bioRxiv preprint available Small C.M., Beck E.A., Currey M.C., Tavalire H.F., Bassham S., Cresko W.A. 2023
Ovarian transcriptional response to Wolbachia infection in D. melanogaster in the context of between-genotype variation in gene expression Frantz S.I, Small C.M., Cresko W.A., Singh N.D. G3. 2023

2022
Associations between forensic loci and neighboring gene expression levels may compromise medical privacy Bañuelos, M., Zavaleta, Y.J.A., Roldan, A., Reyes,R.-J., Guardado, M., Chavez Rojas, B., Nyein, T., Rodriguez Vega, A., Santos, M., Huerta Sanchez, E., Rohlfs R.V. Proceedings of the National Academy of Sciences of the United States of America 119: e2121024119, 2022	Video abstract: Do forensic profiles reveal medical information? Roldan, A., Reyes, R.-J., Zavaleta, Y.J.A., Bañuelos, M., Rohlfs R.V. 2022
Predictable Changes in Eelgrass Microbiomes with Increasing Wasting Disease Prevalence across 23° Latitude in the Northeastern Pacific Beatty, D. S., L. R. Aoki, B. Rappazzo, and others mSystems 7: e00224-22. 2022	Preparing Aquatic Research for an Extreme Future: Call for Improved Definitions and Responsive, Multidisciplinary Approaches Aoki, L. R., M. M. Brisbin, A. G. Hounshell, and others BioScience 72: 508–520. 2022
Disease surveillance by artificial intelligence links eelgrass wasting disease to ocean warming across latitudes Aoki, L. R., Rappazzo, B., Beatty, D. S., and others Limnology and Oceanography 67: 1577–1589. 2022	Extreme intraspecific divergence in mitochondrial haplotypes makes threespine stickleback fish an emerging evolutionary mutant model for mito-nuclear interactions Beck, E. A., Bassham, S., Cresko, W. A. Frontiers in Genetics 13:925786. 2022
Leafy and Weedy Seadragon Genomes connect Genic and Repetitive DNA Features to the extravagant Biology of Syngnathid Fishes Small, C. M., Healey, H. M., Currey, M. C., Beck, E. A., Catchen, J., Lin, A. S. P., Cresko, W. A., Bassham, S. Proceedings of the National Academy of Sciences of the United States of America 119:e2119602119 (cover article). 2022	The evolution of the testis transcriptome in pregnant male pipefishes and seahorses Johnson, B. D., Anderson, A. P., Small, C. M., Rose, E., Flanagan, S. P., Hendrickson-Rose, C., Jones, A. G. Evolution 76:2162-2180. 2022
Evolution and developmental expression of the sodium iodide symporter (NIS, slc5a5) gene family: Implications for perchlorate toxicology Petersen, A. M., Small, C. M., Yan, Y., Wilson, C., Bremiller, R. A., Buck, L. C., von Hippel, F. A., Cresko, W. A., Postlethwait, J. H. Evolutionary Applications 15:1079-1098. 2022	Rapid Ground Motion Forecasting for Large Earthquakes with HR-GNSS and Deep Learning Lin, J.T., Melgar, D., Thomas, A.M., Sahakian, V.J., Searcy, J. AGU Fall Meeting Abstracts 2022, NH33A-08. 2022
Learning source, path and site effects: CNN-based on-site intensity prediction for earthquake early warning Zhang, H., Melgar, D., Sahakian, V., Searcy, J., Lin, J.T. Geophysical Journal International 231 (3), 2186-2204. 2022	Workflow Analysis To Understand Ease of Preparation and Importation of 3D Exemplar Head Scan Data to 3D Modeling Software Programs for N95 Mask Sizing and Fit Sokolowski, S.L., Zou, Y., Searcy, J. International Textile and Apparel Association Annual Conference Proceedings. 2022
Effectiveness of a COVID-19 Testing Outreach Intervention for Latinx Communities: A Cluster Randomized Trial DeGarmo, D.S., De Anda, S., Cioffi, C.C., Tavalire, H.F., Searcy, J.A., Budd, E.L. JAMA Network Open 5 (6), e2216796-e2216796. 2022

2021
Elucidating the adaptive potential of coral holobionts under thermal stress Avila-Magaña V., Kamel, B., DeSalvo, M., Kitano, H., Rohlfs, R.,Iglesias-Prieto, R., Medina, M. Nature Communications: 12: Article number 5731, 2021	Comparative regulomics reveals pervasive selection on gene dosage following whole genome duplication Gillard, G., Grønvold, L., Røsæg, L., Mekrog Holen, M., Monsen, Ø., Koop, B., Rondeau, E., Kumar Gundappa, M., Mendoza, J., Macqueen, D., Rohlfs, R., Sandve, S., Hvidsten, T. Genome Biology: 22: 103, 2021
The Future Is Big—and Small: Remote Sensing Enables Cross-Scale Comparisons of Microbiome Dynamics and Ecological Consequences Beatty, D. S., Aoki, L. R., Graham, O. J., and Yang, B. mSystems 6: e01106-21. 2021	Advancing Human Disease Research with Fish Evolutionary Mutant Models Beck, E. A., Healey, H. M., Small, C. M., Currey, M. C., Desvignes, T., Cresko, W. A., Postlethwait, J. H. TRENDS in Genetics 38(1):22-44. 2021. PMID:34334238
Rapid Determination of Magnitude, Location, and Source Extent with HR-GNSS and Deep Learning Lin, J. T., Melgar, D., Thomas, A., Sahakian, V., Searcy, J. AGU Fall Meeting Abstracts 2021, S14A-05. 2021	Early warning for great earthquakes from characterization of crustal deformation patterns with deep learning Lin, J. T., Melgar, D., Thomas, A. M., Searcy, J. Journal of Geophysical Research: Solid Earth 126(10): e2021JB022703. 2021
Identification of Low‐Frequency Earthquakes on the San Andreas Fault With Deep Learning Thomas, A. M., Inbal, A., Searcy, J., Shelly, D. R., Bürgmann, R. Geophysical Research Letters 48(13): e2021GL093157. 2021	Towards Automatic Sizing for PPE with a Point Cloud Based Variational Autoencoder Searcy, J. A., Sokolowski, S. L. arXiv preprint arXiv:2105.10067. 2021

2020
QTL Mapping of Intestinal Neutrophil Variation in Threespine Stickleback Reveals Possible Gene Targets Connecting Intestinal Inflammation and Systemic Health Beck, E. A., Currey, M., Small, C. M., Cresko, W. A. G3 (Bethesda). 2020	Comparative regulomics reveals pervasive selection on gene dosage following whole genome duplication Gillard, G., Grønvold, L., Røsæg, L., Mekrog Holen, L., Monsen, Ø., Koop, B., Rondeau, E., Kumar Gundappa, M., Mendoza, J., Macqueen, D., Rohlfs, R., Sandve, S., Hvidsten, T. Genome Biology: 22: 103, 2021
Ten simple rules for an inclusive summer coding program for non-CS undergraduates Pennings, P., Banuelos, M., Catalan, F., Caudill, V., Chakalov, B., Hernandez, S., Jones, J., Okorie, C., Modrek, S., Rohlfs, R., Adelstein, N. PLoS Computational Biology: 16(9): e1007833, 2020	Reckoning with our eugenic roots and cultivating anti-racism in science Rohlfs, R. Summer Institute in Statistical Genetics Op-Ed talk: 2020
Understanding our eugenic past to take steps towards scientific accountability Rohlfs, R. Genes to Genomes Blog: 8 June 2020	Eugenics on Campus Tam, R., Kaur, J., Tam, C., Reynolds, M., and Rohlfs, R. Longmore Institute Disability Remix Blog: 3 Jan 2020

2019
Highly reproducible 16S sequencing facilitates measurement of host genetic influences on the stickleback microbiome Small, C. M., Currey, M., Beck, E. A., Bassham, S., Cresko, W. A. mSystems 4: e00331-19. PMID: 31409661. 2019	Developmental tuning of mineralization drives morphological diversity of gill cover bones in sculpins and their relatives Cytrynbaum, E. G., Small, C. M., Kwon, R. Y., Boaz, H., Kent, D., Yan, Y., Knope, M. L., Bremiller, R. A., Desvignes, T., Kimmel, C. B. Evolution Letters 3:374-391. 2019

Search this site

School of Computer and Data Sciences Menu

School of Computer and Data Sciences

Read the latest research from our faculty