Selected Work
Open-source tools and peer-reviewed research contributions in bioinformatics, metagenomics, and carbohydrate-active enzyme analysis.
The work spans population-scale cohort screening, RNA-seq differential expression, phylogenetic placement, scientific software development, and HPC pipeline engineering — methods that transfer across biological systems. If the problem looks familiar, a scoping call will quickly establish whether there's a fit.
Open Source Tools
SACCHARIS 2
Sequence Analysis and Clustering of CarboHydrate Active enzymes for Rapid Informed prediction of Specificity
A bioinformatics pipeline for phylogenetic functional prediction of carbohydrate-active enzymes (CAZymes). Embeds novel sequences within phylogenetic trees of biochemically characterised CAZymes to enable informed predictions of substrate specificity.
Role: Lead developer who rewrote the original Perl pipeline in Python, added proper packaging and Bioconda distribution, and designed and implemented a full GUI from scratch.
Publications
Bespoke plant glycoconjugates for gut microbiota-mediated drug targeting
A targeted drug delivery system (GlycoCaging) using plant oligosaccharides to trigger site-specific release of anti-inflammatory drugs via gut bacterial glycosidases, validated in inflammatory bowel disease models.
Alex's contribution
Owned the full metagenomics component — from raw HMP2 reads to the figures underpinning the paper's central targeting claim.
Designed and executed the metagenomics component: aligned HMP2 longitudinal fecal metagenomes (n=124 across healthy controls, ulcerative colitis, and Crohn's Disease cohorts) against xyloglucan utilization locus references using Magic-BLAST on the Digital Research Alliance of Canada HPC cluster. Longitudinal presence/absence tracking of five GH5_4 endo-xyloglucanase genes across up to 24 bi-weekly timepoints per individual, with dual-threshold validation and systematic QC annotation. Downstream analysis and visualization in Python (pandas, NumPy, seaborn, Matplotlib).
Transcriptional delineation of polysaccharide utilization loci in Segatella copri DSM18205 and co-culture with exemplar Bacteroides species on dietary plant glycans
RNA-seq characterisation of polysaccharide utilization loci (PULs) and CAZymes in a key human gut commensal, revealing differential transcriptional responses across plant polysaccharides including mixed-linkage β-glucans, xyloglucans, xylans, pectins, and inulin.
Alex's contribution
Ran the RNA-seq analysis pipeline and produced the RNA-seq data visualisations for the published manuscript.
Analyzed RNA-seq data and generated all data visualisations. Pipeline: FastQC/MultiQC for QC, Trimmomatic for trimming, Salmon for transcript quantification, and DESeq2 for differential expression analysis.
The molecular basis of cereal mixed-linkage β-glucan utilization by the human gut bacterium Segatella copri
Structural and mechanistic study of how S. copri recognises and degrades cereal β-glucans, combining biochemistry, X-ray crystallography, and molecular analysis to characterise a novel MLG-specific PUL.
Alex's contribution
Conducted population-scale metagenomics screening across four continents and GH5_4 phylogenetic analysis contextualising the paper's enzyme specificity findings.
Conducted population-scale metagenomics screening of human stool metagenomes (NCBI + HMP2 datasets representing cross-sections from North America, Europe, Asia, and Africa) for presence of Segatella MLG-PULs across 15 species. Also performed GH5_4 phylogenetic analysis using SACCHARIS.
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