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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
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Posts
Accuracy Is a Bad Way to Judge a Predictor
Published:
If your accuracy score can be improved by a model that is calibrated worse, the score is broken. Proportion classified correctly is exactly such a score. It is not a minor imperfection to note in the discussion section. It is a metric that will, given the chance, hand you the wrong model and a straight face.
BBMap: Alignment and Contamination Filtering Without the Ceremony
Published:
This is part of a series on the BBTools suite. The overview introduces the tools and the BBDuk post builds the demo data used here.
Your Classifier Is Answering the Wrong Question
Published:
A classifier forces a choice. A probability model quantifies a tendency and hands the choice back to whoever is actually equipped to make it. In most of the problems I work on, the second thing is what I want, and the first thing is what I built by accident.
BBDuk: Adapter Trimming and Quality Filtering That Actually Makes Sense
Published:
This is part of a series on the BBTools suite. If you haven’t read the overview post, that’s a good place to start.
Visualize your Experimental Results with a dotplot in ggplot2
Published:
How to generate a quick dotplot of your data in R with ggplot2
Beyond Bar Charts: What I wish I knew as a benchtop biologist.
Published:
Barcharts could be worse, but we can do better.
portfolio
Everything Correlates With Survival
Published:
An interactive page: pick any gene, or the weather in Dublin, and watch it split a survival curve. Then shuffle the patients and watch it happen again.
SciComp4Bio: A Satirical Class Project
Published:
A lighthearted project for the geese-averse among us 
Genomic Data Analysis Course
Published:
Course Design in Genomic Data Analysis 
Sinhala & Cherokee Alphabet Learning Apps
Published:
Interactive web applications for learning new alphabet scripts 
Introducing Paralogs: A New Dimension in Gene Expression Analysis
Published:
An R Package for Visualizing Differential Paralog Expression in KEGG Gene Pathways
R Shiny App for Automated Grading
Published:
An automated grading system that saves over 100 hours per semester 
R Package for Weighted Spectral Difference
Published:
Analyze Far UV Circular Dichroism data reproducibly 
Yeast Knockout Doubling Times Database
Published:
A searchable database for doubling times of haploid lab yeast knock-out strains 
MULTIPOOL Mapping Software in Python 3
Published:
An updated Python 3 implementation of the MULTIPOOL mapping software for BSA analyses 
publications
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
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
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
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
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
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
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
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
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
talks
Paralogs: Visualizing Gene Expression with Precision
Published:
To use Paralogs, go to visit the GitHub repository.
Interpretable Ordinal Analysis for Complex Designs in Cell and Molecular Biology
Published:
Poster presented at the 2025 Joint Statistical Meetings on ordinal regression for MIC and other ordered phenotype assays in cell and molecular biology, with Jeffrey A. Lewis.
Precisely Wrong: Conformal Prediction for Honest Precision Oncology
Published:
Stacy, C. L. and Das, S.
Post-hoc Bayesian Uncertainty for a Deployed Tumour Classifier: Calibration and Out-of-Distribution Detection Under Platform Shift
Published:
Stacy, C. L. and Das, S.
AI in Medicine: Improving Cancer Diagnosis
Published:
Stacy, C. and Das, S.
teaching
Supplemental Instruction (SI) Leader - General Chemistry II, Honors General Chemistry II, and Fundamentals of Chemistry
Undergraduate Supplemental Instruction Course, University of Arkansas, Department of Student Success, 2015
During my sophomore through senior years of college, I served as a Supplemental Instruction (SI) Leader for General Chemistry II, Honors General Chemistry II, and Fundamentals of Chemistry. This role allowed me to support students in mastering challenging chemistry concepts through collaborative learning sessions.
Peace Corps Volunteer: General Chemistry
High School course, Kolahun High School, 2017
As a Peace Corps Volunteer in Liberia, I had the rewarding experience of teaching high school chemistry. During my service, I developed and implemented a comprehensive chemistry curriculum tailored to the needs of my students, who were eager to learn despite the challenging circumstances. My approach was hands-on and interactive, emphasizing practical experiments and real-world applications of chemical principles.
Teaching Assistant - Principles of Biology Lab
Undergraduate Laboratory Course, University of Arkansas, Department of Biological Sciences, 2022
From August 2022 to December 2023, I served as a Teaching Assistant for the Principles of Biology Lab, where I played a crucial role in guiding students through foundational biological concepts and laboratory techniques. My responsibilities spanned a range of instructional and support activities aimed at creating a dynamic and effective learning environment.
Teaching Assistant - Human Physiology Lab
Undergraduate Laboratory Course, University of Arkansas, Department of Biological Sciences, 2024
As a Teaching Assistant for the Human Physiology Lab, I played a pivotal role in enhancing students’ understanding of complex physiological concepts through hands-on learning and interactive instruction. My responsibilities encompassed a range of tasks designed to support both students and faculty, ensuring a comprehensive and effective learning experience.
Teaching Assistant - Genomic Data Analysis
Graduate Bioinformatics Course, University of Arkansas, Department of Biological Sciences, 2025
As a Teaching Assistant for the Genomic Data Analysis Course, I support an advanced graduate curriculum that I co-developed with my graduate advisor in 2023. This course integrates theoretical insights with practical applications in high-throughput sequencing and bioinformatics, empowering students to tackle complex genomic datasets with confidence.