Horizontal gene transfer as a source of conflict and cooperation in prokaryotes Rebecca J Hall, Fiona J Whelan, James O McInerney, Maria Rosa Domingo Sananes. (2020) Frontiers Microbiology. A Perspectives article on HGT and its impact on pangenomes.
Coinfinder: Detecting Significant Associations and Dissociations in Pangenomes Fiona J. Whelan*, Martin Rusilowicz*, and James O. McInerney. (2020) Microbial Genomics. A software paper introducing Coinfinder for the detection of coincident (co-occurring and avoiding) gene sets in pangenome datasets.
The Evolution of the class A Scavenger Receptors. Whelan FJ, Meehan CJ, Golding GB, McConkey BJ, & Bowdish DME (2012) BMC Evolutionary Biology. The class A scavenger receptors are a subclass of a diverse family of proteins defined based on their ability to bind modified lipoproteins. The 5 members of this family are strikingly variable in their protein structure and function, which begged the question as to their evolutionary relationships.
Horizontal gene transfer as a source of conflict and cooperation in prokaryotes Rebecca J Hall, Fiona J Whelan, James O McInerney, Maria Rosa Domingo Sananes. (2020) Frontiers Microbiology. A Perspectives article on HGT and its impact on pangenomes.
Key publications:
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FJ Whelan, RJ Hall, JO McInerney. Evidence for selection in a prokaryote pangenome. (2020). bioRxiv.
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FJ Whelan*, M Rusilowicz*, JO McInerney. Coinfinder: detecting significant associations and dissociations in pangenomes. (2020). Microbial Genomics 6 (3).
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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.
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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
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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.
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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.
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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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