I study how we live with the microbes and viruses in our bodies, and how those relationships shape immunity, vaccine responses and disease.
Dr Feargal J. Ryan is a leading computational biologist, working across microbiology, bioinformatics and systems biology. His discoveries, published in journals including Nature and Science, have started clinical trials and are cited in health guidance from the UK, US, Germany, the European Union and the World Health Organization. He is on the Stanford/Elsevier list of the world's top 2% of scientists.
Why do some people respond strongly to vaccines and others don't? In infants, gut Bifidobacteria turn out to be essential for optimal responses to the PCV13 pneumococcal vaccine, and antibiotics given in the first days of life blunt those responses for up to seven months. In adults, a multi-omics atlas of the immune system compared innate and adaptive responses to mRNA and adenovirus-vectored COVID-19 vaccines.
Some of the earliest molecular evidence for long COVID: immune gene-expression signatures that persist months after SARS-CoV-2 infection, and trace-level cytokines that impair heart muscle cell function.
Multi-omic profiling of more than 850 patients across Ireland and North America, with over 340 biopsies. It showed that the microbiome modulates inflammation through epigenetic mechanisms and that medication drives much of the variation.
Mapping the viruses of the gut, especially the bacteriophages that prey on our bacteria. The virome is highly personal and stable over time. It changes in disease and is easily distorted by analysis choices.
Taxon set enrichment analysis. Turn a ranked list of differentially abundant taxa into interpretable signatures from BugSigDB, MiMeDB and other curated databases in seconds.
BiocManager::install("TaxSEA")One workflow from raw shotgun reads to results: QC, host removal, taxonomic profiling, assembly and functional annotation, locally or on SLURM clusters.
The common traps in human metagenome studies, from sparse and low-prevalence taxa to reproducibility, and how to avoid them. Illustrated with public stool metagenomes, with all analysis code available.
Collaborations, PhD and postdoc opportunities, speaking invitations and software questions.