Jonathan Carroll, PhD
Quantitative Scientist & Research Software Engineer
Profile
Senior quantitative scientist and research software engineer with 10+ years across multi-modal biomedical research, clinical trial analysis, and fisheries science. Experienced in statistical modelling, data analysis, and production analytics pipelines; author of Beyond Spreadsheets with R. Specialist in R with production experience across the full analytical pipeline; from data ingestion and curation through modelling, visualisation, and reporting to non-technical audiences.
Extensive experience with clinical trial data standards (ADaM, SDTM), multi-modal biomedical data integration, and survival and longitudinal analyses. Background in translational immunology, genomics, and large-scale cohort data (UK Biobank). Comfortable operating independently or leading distributed teams in remote environments since 2017.
Beyond Spreadsheets with R: A beginner's guide to R and RStudio Manning Publications, 2018, 352 pp.
Technical Skills
Industry Experience
- Built analytical infrastructure and exploratory dashboards supporting translational science and antibody discovery; connected data across internal systems via REST APIs.
- Migrated a production LIMS from Benchling to Sapio, preserving data integrity and provenance across complex experimental workflows.
- Processed and retrieved petabytes of UK Biobank genotype data for allele-frequency analyses; productionised and extended C++ likelihood code (TrypLik), orchestrating parallel execution via Bash.
- Managed deployment of GoAnywhere secure file transfer for regulated data exchange.
- Integrated AI/LLM tooling into R shiny dashboards for exploratory clinical data analysis; prompt engineering for biomedical summarisation tasks.
- Data processing and analysis in Redshift; exploration of ADaM and SDTM clinical trial datasets.
- Led development of a large-scale interactive genomics visualisation platform (R shiny) for life scientists without coding experience; coordinated a distributed team of 10 developers across multiple time zones.
- Platform incorporated DGE, GSEA, Kaplan–Meier survival analyses, volcano plots, t-tests, and laboratory result trend visualisations for clinical trial cohorts.
- Managed agile delivery, devOps, CI/CD pipelines, database design (SQLite/SQL), and Docker-based deployment.
- Curated and integrated multi-modal high-dimensional data (genomics, proteomics, clinical trial outcomes) from ADaM/SDTM-structured datasets into a FAIRified internal DataMart (MultiAssayExperiment).
- Performed Kaplan–Meier and Cox proportional hazards survival analyses for clinical trial cohorts; longitudinal modelling of concomitant medications and laboratory results across trial timepoints.
- Conducted in silico analyses linking multi-omics data to patient outcomes; contributed analyses to peer-reviewed publications (Nature Communications, PNAS, medRxiv).
- Developed R/Bioconductor tooling and shiny applications; authored reusable packages supporting downstream analytical teams.
- Independent statistical and data science consulting; selected clients include Gate Biosciences and Lander Analytics.
- Engagements covering R-based analytical pipelines, data infrastructure, visualisation, and reporting.
- Developed and maintained stock assessment models for South Australian fisheries using GLMs, GAMs, mixed effects models, and custom likelihood-based approaches in C++ (ADMB).
- Conducted spatiotemporal catch rate analyses and geographic information system analyses to characterise population dynamics under environmental covariates (wind, swell).
- Produced annual statistical reports and peer-reviewed publications; provided statistically rigorous briefings with uncertainty quantification to government policymakers to inform quota-setting decisions.
Research Experience
- Dense matter nuclear astrophysics: equation-of-state modelling for hybrid neutron stars via numerical simulation in Fortran with MPI parallelisation.
- Muonic hydrogen spectroscopy and the proton radius puzzle; nonperturbative relativistic quantum mechanical calculations.
Education
- Thesis: Applications of the Octet Baryon Quark-Meson Coupling Model to Hybrid Stars — arXiv:1001.4318
Selected Publications
Book
Carroll J. (2018). Beyond Spreadsheets with R. Manning Publications, 352 pp.
Peer-reviewed articles (selected)
Negative impact of the GABA pathway on αPD-1/PD-L1 immunotherapy. Submitted 2025.
Natural killer cell educating KIR/HLA combinations impact survival in anti-PD-L1 treated cancer patients. medRxiv, 2022.
Genetic variation associated with thyroid autoimmunity shapes the systemic immune response to PD-1 checkpoint blockade. Nature Communications 12, 3355 (2021).
Polygenic risk for skin autoimmunity impacts immune checkpoint blockade in bladder cancer. PNAS 117(22), 12288–12294 (2020).
Influence of wind and swell on catch rates in a dive fishery. Journal of Shellfish Research 35(3), 685–694 (2016).
Nonperturbative relativistic calculation of the muonic hydrogen spectrum. Physical Review A 84(1) (2011).
Selected Open-Source Software
Published R packages (author & maintainer unless noted): {ggeasy} · {charcuterie} · {ntfy} · {mathpix} · {DFplyr} (Bioconductor) · {benchlingapi} · {weatherOz} (contributor) · {datapasta} (contributor)
Community & Communication
- Blog: Regular technical writing at jcarroll.com.au covering R, data analysis, and multi-language programming explorations (R, Rust, Haskell, Julia, APL, and others).
- rweekly.org: Editor — compilation, curation, and editing of the weekly R community newsletter (2016 – present).
- Conference presentations: DataEngBytes and other data science venues.
- Governing Council: Highbury Preschool / Highbury Primary / Modbury High (Chair, Vice Chair; 2016 – present).
- Chess Club Teacher (volunteer): Highbury Primary School (2022 – present).
Last updated: July 2026