Tom Kelly
Scientist at The New Zealand Institute for Bioeconomy Science Limited
Dunedin, Otago, New Zealand
Summary
👤
Senior🎓
Top SchoolTom Kelly is an interdisciplinary scientist combining 11 years of expertise in bioinformatics, quantitative genetics, and computational biology, currently working in New Zealand's national bioeconomy institute. He builds and maintains production-grade genomics pipelines and compute infrastructure, with hands-on experience taking algorithms (notably adding the Leiden clustering method) into widely used single-cell tools like Seurat. His background spans academia and industry—from a PhD in biomathematics at Otago and postdoctoral work at RIKEN to leading bioinformatics R&D and clinical-testing workflows in large healthcare organisations. He mentors teams, teaches digital research skills through The Carpentries, and champions open science, diversity in STEM, and pragmatic technology adoption. Fluent across R, Linux/HPC and cloud (AWS) stacks, he pairs mathematical rigor with practical engineering to accelerate translational genomics. A Kiwi who built a career in Japan, he brings cross-cultural collaboration and multilingual communication to international research programs.
11 years of coding experience
7 years of employment as a software developer
PhD, Biomathematics, Bioinformatics, and Computational Biology, Enrolled April 2014; Submitted June 2017; Graduated December 2017, PhD, Biomathematics, Bioinformatics, and Computational Biology, Enrolled April 2014; Submitted June 2017; Graduated December 2017 at University of OtagoNCEA Levels 1-3, Excellence, NCEA Levels 1-3, Excellence at Rotorua Boys' High
English, 日本語 (japanese), italiano (italian), français (french), nederlands (dutch), te reo māori, deutsch (german)
Stackoverflow
1,538reputation
420kreached
29answers
2questions
r
top-5%
parallel-processing
top-5%
Github Skills (18)
algorithm10
algorithms10
single-cell-genomics10
python10
r10
parallel-processing9
data-analysis9
rna-seq9
data-visualization6
cran6
heatmap6
assert6
language-design6
package6
rstudio6
Programming languages (18)
Github contributions (5)
satijalab/seurat
Jan 2019 - Jan 2020
R toolkit for single cell genomics
Role in this project:
Back-end Developer & Data Scientist
Back-end Developer & Data ScientistContributions:24 commits, 5 PRs, 86 comments in 1 year
Contributions summary:Tom primarily contributed to the implementation and refinement of the Leiden algorithm for clustering single-cell genomics data. They added the Leiden algorithm to the Seurat's FindClusters function and made modifications to integrate it with the existing codebase. Their work involved refactoring the code, optimizing performance, and addressing dependencies related to the Leiden algorithm and its integration. The user also incorporated functionalities related to partition types and argument passing within the python implementation.
single-cell-genomicscranhuman-cell-atlasgenomicsbioinformatics
TomKellyGenetics/vioplot
Feb 2018 - Dec 2022
Development version of vioplot R package (CRAN maintainer)
Contributions:10 releases, 192 commits, 1 PR in 4 years 10 months
r-packagecrancustomisationviolin-plotboxplot
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