Carl J. Stone

Professional Summary

Molecular microbiologist finishing a Ph.D. in bacterial evolution and genomics. Research spans genome-scale epigenetics (6mA methylome characterization), Bayesian hierarchical modeling for longitudinal fitness analysis, and production R package development. Seeking postdoc or scientist positions in computational microbiology.

Education

Vanderbilt University — Nashville, TN Ph.D. in Biological Sciences (May 2026) August 2020 – May 2026 Advisor: Dr. Megan Behringer

University of Minnesota – Twin Cities — Minneapolis, MN Bachelor of Science, magna cum laude, in Microbiology August 2014 – May 2018

Key Skills

Molecular biology: DNA/RNA extraction, PCR/qPCR, molecular cloning, plasmid construction, phage transduction, transposon mutagenesis

Sequencing: NGS and TGS execution, analysis, and QC; Nanopore MinION library prep; basecalling including methylation calling

Microbiology: Bacterial culture, aseptic technique, strain construction, selective/differential media assays

Functional genomics: RB-TnSeq fitness screens, transposon library construction, experimental design, statistical analysis

Bioinformatics: Expert in R (genomic/epigenomic datasets, Bayesian modeling, package development); strong Bash; proficient Python; reproducible workflows; expert data visualization

Research Experience

Ph.D. Researcher — Vanderbilt University, Nashville, TN Dr. Megan Behringer, Department of Biological Sciences August 2020 – May 2026

• Produced the most detailed per-site characterization of the E. coli Dam methylome, identifying 177 reproducibly hypomethylated GATC sites at regulatory DNA-protein interaction sites
• Developed a Bayesian hierarchical model (Stan/brms) for longitudinal RB-TnSeq fitness analysis; constructed an empirical fitness seascape that predicts evolutionary outcomes in long-term evolution experiments
• Developed and published commaKit, an R package for differential bacterial methylation analysis; Bioconductor submission pending
• Two first-author publications (mBio 2023; bioRxiv 2026, in review at MBE)
• Designed genome-scale fitness assay using RB-TnSeq with Bayesian modeling

Research Assistant — Georgetown University, Washington, DC Dr. Shaun Brinsmade, Department of Biology September 2018 – June 2020

• Studied nutritional regulation of virulence in Staphylococcus aureus
• Used molecular cloning, phage transduction, qPCR, fluorescent reporter strains
• Trained and mentored 4 students; maintained lab protocols

Undergraduate Researcher — University of Minnesota, St. Paul, MN Dr. Michael Sadowsky May 2017 – May 2018

• Compared accuracy of microbial community ecology pipelines (mothur, QIIME, DADA2) using soil microbiome datasets
• Completed undergraduate honors thesis with Latin honors

Student Lab Technician — University of Minnesota Veterinary Diagnostic Lab, St. Paul, MN April 2016 – August 2017

• Performed microbiological testing on bovine mastitis samples (culture, plate counts, antibiotic sensitivity, MALDI-TOF)

Publications

• Stone CJ, Behringer MG. 2026. Bayesian analysis of longitudinal RB-TnSeq resolves the fitness seascape in fluctuating environments. bioRxiv. https://doi.org/10.64898/2026.02.11.703069 (in review at Molecular Biology and Evolution)

• Stone CJ, Boyer GF, Behringer MG. 2023. Differential adenine methylation analysis reveals increased variability in 6mA in the absence of methyl-directed mismatch repair. mBio 14, e01289-23.

• Pendleton A, Yeo W-S, Alqahtani S, DiMaggio DA Jr., Stone CJ, et al. 2022. Regulation of the Sae two-component system by branched-chain fatty acids in Staphylococcus aureus. mBio 13, e01472-22.

• Behringer MG, Ho W-C, Meraz JC, Miller SF, Boyer GF, Stone CJ, et al. 2022. Complex ecotype dynamics evolve in response to fluctuating resources. mBio 13, e03467-21.

• Mlynek KD, Bulock LL, Stone CJ, et al. 2020. Genetic and biochemical analysis of CodY-mediated cell aggregation in Staphylococcus aureus reveals an interaction between extracellular DNA and polysaccharide in the extracellular matrix. Journal of Bacteriology 202, e00593-19.

Conference Presentations

• Stone CJ, Behringer MG. A Bayesian framework for longitudinal analysis of transposon insertion-based fitness screens. Oral presentation, 3rd Joint Congress on Evolutionary Biology, Montreal, Canada. July 2024. Watch on YouTube

• Stone CJ, Behringer MG. Differential adenine methylation analysis reveals 6mA variability after experimental evolution. Poster, The Allied Genetics Conference, National Harbor, MD. March 2024.

• Stone CJ, Behringer MG. Increased variability in adenine methylation in the absence of methyl-directed mismatch repair in Escherichia coli. Evolution 2022, Cleveland, OH. July 2022.

• Stone CJ, Behringer MG. Epigenetic changes during long-term experimental evolution in E. coli. SouthEastern Population Ecology and Evolutionary Genetics Conference, Athens, GA. October 2021.

Honors and Awards

• Best Oral Presentation, Department of Biological Sciences Annual Retreat — Vanderbilt University (May 2024)
• Best Graduate Student Presentation — SouthEastern Population Ecology and Evolutionary Genetics Conference (October 2021)

Teaching and Mentoring

Teaching Assistant, Principles of Genetics — Vanderbilt University Fall 2021, Fall 2022

• Led weekly recitation sessions with 10–20 undergraduates; graded assessments

Graduate Mentor — Behringer Lab, Vanderbilt University Fall 2021 – Fall 2022

• Mentored junior graduate students and guided lab onboarding as the lab’s most senior graduate student