James Ferguson
Genomics Software Engineer at Garvan Institute of Medical Research
Sydney, New South Wales, Australia
Summary
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RockstarJames Ferguson is a Genomics Software Engineer and senior bioinformatician in Sydney with nine years’ experience specializing in long-read sequencing for medical research. He has progressed at the Garvan Institute from research student to Genomic Systems Analyst and now Genomics Software Engineer, building production pipelines, LIMS integrations and clinical-quality QC. James combines clinical genomics work (including NIPTv2 reporting) with startup experience as CTO/co‑founder of a rapid infectious-disease testing company, demonstrating product delivery from lab to clinic. Unusually, his background spans bench skills in histopathology and microtomy through to multi-language engineering (Python, C, Perl, shell and even COBOL), and he routinely handles sensitive data under HREC approvals. His GitHub bio’s wry remark about “weird” code hints at pragmatic, idiosyncratic craftsmanship—his portfolio is at jmferguson.science.
10 years of coding experience
7 years of employment as a software developer
Github Skills (114)
converting10
eel10
genome-assembly10
genomics10
autoencoder10
convolutional-neural-network10
guppy10
cytoscapejs10
bioinformatics10
signal-processing9
convolutional-neural-networks9
electrophysiology9
libtorch9
rnaseq9
rna-seq9
Programming languages (12)
Github contributions (5)
Psy-Fer/fast5_fetcher
Aug 2018 - Feb 2019
A tool for fetching nanopore fast5 files after filtering via demultiplexing, alignment, or other, to improve downstream processing efficiency
Contributions:2 releases, 28 commits, 23 pushes in 5 months
fetchingnanoporealignmentdemultiplexingstdin
Psy-Fer/misc
May 2021 - Aug 2022
Contributions:8 commits, 7 pushes, 1 branch in 1 year 4 months
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