Carson Stacy

Carson Stacy

Postdoctoral Research Fellow at RCSI, Dublin. Statistical modeling, machine learning, and reproducible data analysis for genomics.

Publications

Genome-wide assessment of DNA methylation fidelity identifies representative ovarian cancer cell line models

Published in Journal of Cellular and Molecular Medicine, 2026

Infinium 450K/EPIC profiles of 60 ovarian cancer cell lines and 108 tumours, compared by correlation and effect size across genomic and epigenomic domains, identify cell lines that faithfully represent each histotype.

Recommended citation: Jordan, A., Caffrey, A., **Stacy, C.**, Huang, R. Y., Tan, T. Z., McCabe, A., Dean, K., Das, S., & Perry, A. S. (2026). *Genome-wide assessment of DNA methylation fidelity identifies representative ovarian cancer cell line models.* **Journal of Cellular and Molecular Medicine**, 30(16), e71334. https://doi.org/10.1111/jcmm.71334

Surprising regulatory plasticity for the conserved HOG pathway in diverse Saccharomyces cerevisiae strains

Published in bioRxiv (preprint), 2025

Comparing hog1Δ mutants in a laboratory strain and diverse wild Saccharomyces cerevisiae strains reveals an expanded role for Hog1 in cross-stress protection and gene expression beyond its canonical osmotic-stress function.

Recommended citation: **Stacy, C. L.**, Scholes, A. N., Stuecker, T. N., Hood, S. E., Crook, C. C., Espana-Pena, M., Paré, A. C., & Lewis, J. A. (2025). *Surprising regulatory plasticity for the conserved HOG pathway in diverse Saccharomyces cerevisiae strains.* **bioRxiv**. doi:10.64898/2025.12.28.696518 https://doi.org/10.64898/2025.12.28.696518

Bicycle-related trauma trends in a region of expanding cycling infrastructure

Published in The American Surgeon, 2025

A retrospective trauma-registry cohort (2014–2022) at a level II trauma centre, relating bicycle-related hospitalisation trends to regional trail usage and state crash data.

Recommended citation: VanDyke, L., Mantooth, R., **Stacy, C.**, Robinson, S., Fischer, P., Mosley, C., Beauford, H., & Jensen, H. (2026). *Bicycle-related trauma trends in a region of expanding cycling infrastructure.* **The American Surgeon**, 92(6), 1630–1636. https://doi.org/10.1177/00031348251405546

MIC*: A framework for interpretable analysis of ordinal viability data

Published in bioRxiv (preprint), 2025

Proportional-odds models with biologically scaled thresholds give an interpretable, uncertainty-quantified alternative to conventional MIC readouts, with companion software (ordinalMIC, MICalculator, BLISS).

Recommended citation: **Stacy, C. L.**, Lenaduwe, S., Stuecker, T. N., & Lewis, J. A. (2025). *MIC\*: A framework for interpretable analysis of ordinal viability data.* **bioRxiv**. doi:10.1101/2025.10.13.682067 https://doi.org/10.1101/2025.10.13.682067

Diet driven differences in host tolerance are linked to shifts in global gene expression in a common avian host-pathogen system

Published in Molecular Ecology, 2025

In this paper, we examine the transcriptomic effects of diet on the immune response of canaries

Recommended citation: **Sauer, E. L.***, **Stacy, C. L.***, Perrine, W., Love, A. C., Lewis, J. A., & DuRant, S. E. (2025). *Diet driven differences in host tolerance are linked to shifts in global gene expression in a common avian host-pathogen system.* **Molecular Ecology**, 34(12), e17793. *Co-first authors.* https://doi.org/10.1111/mec.17793

Stability comparisons between natural versus engineered archaeal heat-shock proteins.

Published in Microorganisms, 2024

In this paper, I developed an analytical workflow and subsequently quantified weighted spectral differences between natural and engineered heat shock proteins.

Recommended citation: Furr, M., Badiee, S. A., Basha, S., Agrawal, S., Alraawi, Z., Heng, S., **Stacy, C. L.**, Ahmed, Y., Moradi, M., Kumar, T. K. S., & Ceballos, R. M. (2024). *Structural Stability Comparisons Between Natural and Engineered Group II Chaperonins: Are Crenarchaeal “Heat Shock” Proteins Also “pH Shock” Resistant?* **Microorganisms**, 12(11), 2348. https://doi.org/10.3390/microorganisms12112348

Natural variation in yeast reveals multiple paths for acquiring higher stress resistance

Published in BMC Biology, 2024

In this paper, I introduce ordinal logistic regression of yeast survival data for analyzing changes in acquired stress resistatnce

Recommended citation: Scholes, Amanda N., Tara N. Stuecker, Stephanie E. Hood, Cader J. Locke, Carson L. Stacy, Qingyang Zhang, and Jeffrey A. Lewis. "Natural variation in yeast reveals multiple paths for acquiring higher stress resistance." BMC biology 22, no. 1 (2024): 149. https://doi.org/10.1186/s12915-024-01945-7

Quantifying relative virulence: when $\mu$ max fails and AUC alone just is not enough

Published in Journal of General Virology, 2021

This paper is about a temporally weighted metric of differences in growth inhibition resulting from viral infection in microbial populations.

Recommended citation: Ceballos, Ruben Michael, and Carson Len Stacy. "Quantifying relative virulence: when μ max fails and AUC alone just is not enough." Journal of General Virology 102, no. 1 (2021): 001515. https://doi.org/10.1099/jgv.0.001515

Host-dependent differences in replication strategy of the Sulfolobus spindle-shaped virus strain SSV9 (aka, SSVK1): infection profiles in hosts of the family Sulfolobaceae.

Published in Frontiers in Microbiology, 2020

In this paper, I quantified differential viral pathogen loads as determined by ESI/MS spectra assays and modelled inferred infection dynamics.

Recommended citation: Ceballos, Ruben Michael, Coyne Gareth Drummond, Carson Len Stacy, Elizabeth Padilla-Crespo, and Kenneth Mark Stedman. "Host-dependent differences in replication strategy of the Sulfolobus spindle-shaped virus strain SSV9 (aka, SSVK1): infection profiles in hosts of the family Sulfolobaceae." Frontiers in Microbiology 11 (2020): 1218. https://doi.org/10.3389/fmicb.2020.01218