Senior bioinformatician & data scientist. I take genomics pipelines from raw reads to production.

Lead Bioinformatician

Led bioinformatics strategy and end-to-end pipeline development for a commercial genomics company serving agricultural and industrial clients, including customers in Latin America and Asia.

• Architected the company's full Oxford Nanopore 16S microbiome stack, from live DNA sample to pathogen detection report: 8–20 weeks outsourced to 2 days in-house, as routine.
• Sole developer of a commercial SNP-array pipeline for a new tree species: scope, resource estimation, validation, delivery, IP handover.
• Designed the genomic selection SQL database (DbSchema) and authored SOPs to centralise reproducibility, QA, and onboarding.
• Translating complex genomic data into reports and content for non-technical stakeholders (farmers, producers, C-suite).
• 2 scientific papers under review, plus industry magazine articles and blog posts to grow scientific engagement.

Cloud Genomic Data Scientist

Led and delivered 4+ concurrent national and international programs spanning cloud genomics, AI-assisted bioinformatics, and federated learning — primarily short-read NGS, targeted pharmacogenomics, infectious-disease surveillance, and population genomics, with partners in Australia, Indonesia, Korea, France and the USA.

• Co-led GeneGuardian, a dynamic consent platform: owned FHIR, storage and cloud decisions, and researched and developed the blockchain and decentralised-storage layers (Terraform on AWS for deployment and testing). Live at a pilot hospital via geneguardian.online. 1st author, GigaScience (Q1) · GeneGuardian blog post · Future-proofing blog post.
• Led the multi-institution pangenome project (Mayo Clinic, Paris-Saclay) on reference bias in sequencing-based population analyses, coordinating 2 researchers and supervising 2 postgraduate students across 3 institutions and 3 time zones. 1st author, BioMolecules (Q1).
• Deployed PharmCAT, sVEP, VariantSpark and sBeacon into partner AWS accounts in Indonesia and Korea, with use cases including pharmacogenomics, COVID-19 / TB surveillance, and population genomics. PathsBeacon blog post.
• Pharmacogenomics & cancer genomics: on PrecisionGO (University of Sydney, Westmead Hospital) I took liver-transplant donor and recipient cohorts from raw FASTQ to VCFs, ran PharmCAT with PharmGKB and linked genotypes to EHR and clinical data to relate genetic background to transplant outcome and drug reactions; main contact and project manager across the institutes. Also built a breast-cancer PharmCAT pipeline deployed to collaborators’ AWS accounts, and a Nextflow WGS pipeline for a rat mammary-tumour study (co-author, J Mammary Gland Biol Neoplasia, 2026).
• Developed and led SpreadStopper, a serverless (AWS Lambda, S3, DynamoDB) COVID-19 variant-surveillance system tracking mutations of concern across countries from ~2M public genomes; deployed with engineers into the Indonesian partner’s AWS account. Funded by DFAT/AIHSP.
• Represented CSIRO in federated-learning consortia with Microsoft, MIT, NVIDIA and Sanofi. Mentored 15+ team members; won the CSIRO Health & Biosecurity Entrepreneurship Award (2024).

Quantitative Analyst

Six-month applied stint between the PhD and CSIRO: statistical modelling and anomaly detection on noisy, high-dimensional time-series data.

• Built predictive models and ran EDA on multi-asset time-series, applying the same feature-engineering and signal-validation rigour now used on genomic data.

PhD in Bioinformatics

Thesis: reducing reference bias in genomic data analysis using pangenome graphs and benchmarking. Three Q1 first-author papers, co-authored FAIR/CARE community standards for reproducible aDNA research — all on Illumina short-read NGS data.

• Benchmarked 30 mapping strategies (BWA-aln, BWA-mem, Bowtie2, NovoAlign) on Illumina ancient-DNA data and chromosome-22 simulations with realistic post-mortem damage (Mitty, gargammel), scoring reference bias, D-statistics, PCA and CPU cost, in Briefings in Bioinformatics (Q1, IF 9.5) · DOI 10.1093/bib/bbab076.
• Showed specific BWA-aln settings outperform BWA-mem for ancient DNA, in Ecology & Evolution (Q1) · DOI 10.1002/ece3.8297.
• Co-authored FAIR / CARE recommendations for reproducible paleogenomic analyses in The American Journal of Human Genetics (Q1).
• Built pangenome variation-graph workflows (vg, minigraph) on HPC, with ANGSD, PLINK, ADMIXTURE, smartpca and ADMIXTOOLS for low-coverage population genetics. Started retraining DeepVariant on damaged reads (unfinished, no result claimed). NGS & WGS case study →
• Designed and taught "Bioinformatics 101" (Python, Jupyter, command-line, computational thinking).

Earlier research & software roles

• Research Data Scientist & Computational Modeller · CNRS · 2017–2018: developed and published the MPEE ancestral sequence reconstruction model in PhyML (Bioinformatics, Oxford, Q1).
• Research Intern · ANU · 2016: implemented MCMC phylogeographic methods in the R package Phyloland, applying Bayesian inference to migration simulation.
• Web Developer Intern · 2014: built features and managed the SQL database for BasiCompta, a financial-tracking web app for sports associations (JavaScript, jQuery, PHP).
• Research Intern · University of Auckland · 2013: built a gene database for endometriosis research with the ENCODE consortium, annotating SNPs via the UCSC Genome Browser.