- FJ Whelan, RJ Hall, JO McInerney. Evidence for selection in a prokaryote pangenome. (2021). Molecular Biology & Evolution, msab139.
- FJ Whelan*, M Rusilowicz*, JO McInerney. Coinfinder: detecting significant associations and dissociations in pangenomes. (2020). Microbial Genomics 6 (3).
- FJ Whelan, B Waddell, SA Syed, S Shekarriz, HR Rabin, MD Parkins, MG Surette. Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota. (2020). Nature Microbiology 5 (2), 379-390.
- FJ Whelan, AA Heirali, L Rossi, HR Rabin, MD Parkins, MG Surette. Longitudinal sampling of the lung microbiota in individuals with cystic fibrosis. PloS one 12 (3), e0172811
- FJ Whelan, MG Surette. Clinical Insights into Pulmonary Exacerbations in Cystic Fibrosis from the Microbiome. What Are We Missing? Annals of the American Thoracic Society 12 (Supplement 2), S207-S211.
- FJ Whelan, CP Verschoor, JC Stearns, L Rossi, K Luinstra, M Loeb, M Smieja, J Johnstone, MG Surette, DME Bowdish. The Loss of Topography in the Microbial Communities of the Upper Respiratory Tract in the Elderly. Annals of the American Thoracic Society 11 (4), 513-521.
- FJ Whelan, CJ Meehan, GB Golding, BJ McConkey, DME Bowdish. The evolution of the class A scavenger receptors. BMC evolutionary biology 12 (1), 1-11.
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