I'm a PhD candidate in Crop Science, soon to be a recent graduate, with a passion for applying computational and data-driven approaches to understand complex biological systems in agriculture. My research focuses on the intersection of plant science, microbiology, and genomics, with a particular interest in leveraging bioinformatics and statistical analysis to address real-world challenges in crop health and resilience.
I'm currently wrapping up my PhD research at Niab East Malling and the University of Reading, where my work has involved studying the apple root microbiome, conducting waterlogging experiments, and analyzing bacterial genomics data to study bacterial biocontrols.
My doctoral research has spanned several key areas:
- Apple root microbiome: Investigating the effects of site, planting date, and scion genotype on the apple root microbiome and its association with European apple canker expression. This involves amplicon metabarcoding, sequence data analysis, community profiling, and understanding host-microbe interactions.
- Waterlogging: Developing and applying statistical models and data visualization techniques to analyze data from experiments studying crop responses to waterlogging.
- Bacterial Genomics: Analyzing bacterial genomes to identify potential mechanisms for biocontrol activity in candidate bacteria. This includes genome assembly, annotation, and comparative genomics.
You can find code and resources related to these projects in the following repositories:
- Apple root microbiome: Code for ITS and 16S rRNA gene sequencing analysis of apple root microbiome. (The interplay between scion genotype, root microbiome, and Neonectria ditissima apple canker - Published in FEMS Microbiology Ecology)
- Waterlogging: R scripts and data pipelines for analyzing physiological and canker expression data from waterlogged plants.
- Waterlogging microbiome: Code for ITS and 16S rRNA gene sequencing analysis of apple root and soil microbiome of waterlogged plants.
- Bacterial biocontrols: Scripts for assembling, annotating, and analysing bacterial genomes from Sphingomonas canker biocontrol candidates.
Beyond my core PhD work, I enjoy exploring various areas of computing and bioinformatics:
-
NixOS: My declarative system configuration managed with NixOS, reflecting my interest in reproducible development environments.
-
Home manager: My declarative dotfiles managed with home-manager.
-
Rosalind: Solutions to bioinformatics practice problems from Rosalind used for sharpening coding skills with a focus on bioinformatics, particularly in Julia.
-
Exercism: Solutions to general programming practice problems from Exercism used for sharpening coding skills, particularly in Julia, R, python, and bash.
Here are some of the tools and technologies I commonly use:
- Languages: R, Julia, Python, Bash
- Bioinformatics: Bakta, PLaBAse, antiSMASH, BiG-SCAPE, DADA2, USEARCH
- Data Analysis & Statistics: data.table, DESeq2, DHARMa, ggplot2, statistical modeling, data visualization
- Systems & Tools: Git, GitHub, Docker, Nix, NixOS, Linux command line
- Domains: Bioinformatics, Genomics, Microbiology, Data Science, Statistics, Crop Science
Here are some of the publications resulting from my research:
- The interplay between scion genotype, root microbiome, and Neonectria ditissima apple canker - FEMS Microbiology Ecology, 2025. https://doi.org/10.1093/femsec/fiaf014
- ORCID: https://orcid.org/0000-0002-9073-4897
- ResearchGate: https://www.researchgate.net/profile/Hamish-Mclean
- LinkedIn: https://www.linkedin.com/in/hscmclean/
Feel free to explore my repositories and reach out.