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Contact



Language Skills

R
Rust
Bash
Python
Julia
Javascript
SQL
Lisp
Haskell

Main

Jonathan Carroll, PhD

I provide software design and implementation for statistics, analysis, visualisation, exploration, curation, and storage - all things data.

I enjoy solving complex puzzles, both mathematical, algorithmic, and biological.

I am comfortable with a UNIX/Linux environment. I have successfully navigated remote positions since 2017.

Education

20092006

PhD
Theoretical Physics

University of Adelaide Adelaide, South Australia
20052002

Bachelor of Science, Honours
Physics & Theoretical Physics

University of Adelaide Adelaide, South Australia

Research Experience

20132009

Postdoc

Special Research Centre for the Subatomic Structure of Matter University of Adelaide
  • Dense matter nuclear astrophysics, hybrid stars
  • Muonic hydrogen spectroscopy, “the proton radius puzzle”

Industry Experience

I have experience working in academia, government, and in both large and small biotech.

Current2022

Senior Research Software Engineer

Human Immunology Biosciences (HI-Bio) South San Francisco (remote)
  • Development of internal tooling supporting translational science, antibody discovery, and infrastructure.
  • R (shiny), Python, Docker, AWS, Benchling, clinical trials
Current2016

Editor

RWeekly rweekly.org
  • Compliation, curation, and editing of the rweekly.org newsletter
Current2015

Principal Consultant

Irregularly Scheduled Programming Adelaide, South Australia
  • Independent contractor / consultant (ABN: 43486039320)
20222021

Technical Lead / co-Product Owner

Cancer Immunology Department @ Genentech / Roche South San Francisco, CA, USA (remote)
  • Coordinated development of a large shiny app project for interactive exploration of genomics visualisation, aimed at life-scientists without coding experience. Remotely directed a team of 10 developers located worldwide.
  • R (shiny), CSS, JavaScript, HTML, SQL/SQLite, Docker, Git, database management, statistics, computational biology/genomics, management, agile scrum, leadership
20222017

Data Curator / Integrator & Software Developer

Cancer Immunology Department @ Genentech / Roche South San Francisco, CA, USA (remote)
  • Developed software tooling supporting extraction and integration of multiple high-dimensional data modalities for FAIRification of internal data (MultiAssayExperiment / DataMart).
  • R (Bioconductor, shiny), CSS, JavaScript, HTML, Docker, Git
20172013

Senior Research Officer / Fisheries Modeller

South Australian Research and Development Institute (SARDI) Government of South Australia
  • Developed and maintained fisheries stock assessment models, spatio-temporal catch rate analyses, and geographic information system tools
  • Database management, statistics, biology, and the interface between fishers and government policy
  • R, C++ (ADMB), SQL, Microsoft Access

Selected Writings

I regularly write on my blog https://jcarroll.com.au about puzzles, syntax, and my own learnings as I explore multiple languages - R, Julia, Rust, Python, JavaScript, Lisp, Haskell, and many more.

Selected Software Packages

I contribute R packages to open-source software and engage with users, integrating feature requests and bug fixes.

{ggeasy} (author, maintainer) CRAN

  • Provides a series of aliases to commonly used but difficult to remember ‘ggplot2’ sequences

{bomrang} (contributor) CRAN

  • Australian Government Bureau of Meteorology (‘BOM’) Data Client

{datapasta} (contributor) CRAN

  • RStudio addins and R functions that make copy-pasting vectors and tables to text painless

{mathpix} (author, maintainer) CRAN

  • Support for the ‘Mathpix’ API (Image to ‘LaTeX’)

{benchlingapi} (author, maintainer) GitHub

  • Wraps the Benchling API for access in R

Selected Publications

I have experience as a first author and as a collaboator on articles in a diverse range of fields.

2022

Natural killer cell educating KIR/HLA combinations impact survival in anti-PD-L1 treated cancer patients

medRxiv
2021

Genetic variation associated with thyroid autoimmunity shapes the systemic immune response to PD-1 checkpoint blockade

Nature Communications, volume 12, number 3355
2020

Polygenic risk for skin autoimmunity impacts immune checkpoint blockade in bladder cancer

Proceedings of the National Academy of Sciences, volume 117, number 22, 12288–12294
2018

Beyond Spreadsheets with R

https://www.manning.com/books/beyond‑spreadsheets‑with‑r
  • Manning Publications
  • 352 pages
2016

Influence of Wind and Swelloncatch Rates in a Dive Fishery: A Case Study from the South Australian Abalone Fishery

Journal of Shellfish Research, volume 35, number 3, 685-694
2016

Setting quotas using provisional data: a case study from the South Australian abalone fisheries

New Zealand Journal of Marine and Freshwater Research, volume 50, number 3, 371-388
2016

Spawning biomass of jack mackerel (Trachurus declivis) off eastern Australia: Critical knowledge for managing a controversial fishery

Fisheries Research, volume 179, 10-22
2014

Quark-meson coupling model, nuclear matter constraints, and neutron star properties

Physical Review C - Nuclear Physics, volume 89, number 6
2012

Nuclear quasielastic electron scattering limits nucleon off-mass shell properties

Physical Review C - Nuclear Physics, volume 86, number 6
2011

Nonperturbative relativistic calculation of the muonic hydrogen spectrum

Physical Review A - Atomic, Molecular, and Optical Physics, volume 84, number 1
2009

Phase transition from quark-meson coupling hyperonic matter to deconfined quark matter

Physical Review C - Nuclear Physics, volume 79, number 4
2005

Neutral pion decay into νν̄ in dense Skyrmion matter

Physical Review D - Particles, Fields, Gravitation and Cosmology, volume 71, number 11

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Last updated on 2023-07-03.