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John Kenny

Research Officer

Research Interests

John Kenny is a Senior Research Officer. Dr. Kenny’s research focusses on the application of technologies to solving questions of function in microbial communities. This builds on his decade long experience in running a next generation sequencing core laboratory. John’s interests lie in using new methods (e.g, sequencing and synbio) to track the microbial composition of environmental niches, to discover how these bacteria and phage interact, and to harness these microbial capabilities for biotransformation and health benefits.

Current Projects

  • Irish Coronavirus Sequencing Consortium
  • Biotransformation in Milk
  • PhageSUAS
  • Trojan Culture
  • APC Culture Collection


PhD. University College Cork, Ireland. 2006

B.Sc. (Microbiology), University College Cork, Ireland. 2000


Professional Membership

Microbiology Society

  1. Frau et al., Inter-kingdom relationships in Crohn's disease explored using a multi-omics approach. Gut Microbes. 2021. https://doi.org/10.1080/19490976.2021.1930871
  2. Carrieri et al., Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences. Scientific Reports. 2021. https://doi.org/10.1038/s41598-021-83922-6
  3. Mallon et al., Whole-genome sequencing of SARS-CoV-2 in the Republic of Ireland during waves 1 and 2 of the pandemic. MedRxiv. 2021. https://doi.org/10.1101/2021.02.09.21251402
  4. Thornton et al., Targeted Next-Generation Sequencing of 117 Routine Clinical Samples Provides Further Insights into the Molecular Landscape of Uveal Melanoma. Cancers. https://doi.org/10.3390/cancers12041039
  5. Haldenby et al., Increasing prevalence of a fluoroquinolone resistance mutation amongst Campylobacter jejuni isolates from four human infectious intestinal disease studies in the United Kingdom. PLoSONE. 2020 https://doi.org/10.1371/journal.pone.0227535
  6. Alessandra Frau et al., DNA extraction and amplicon production strategies deeply influence the outcome of gut mycobiome studies. Scientific Reports. 2019.
  7. Goodhead I et al., Large scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont. Microbial Genomics. In Press.
  8. Siddharth Jayaraman, et al., Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. PLOS Neglected Tropical Diseases. 2019
  9. Laura-Jayne Gardiner et al., Hidden variation in polyploid wheat drives local adaptation. Genome Res. 2018
  10. Lisa Olohan et al., A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample.  BMC Genomics. 2018
  11. Rosalinda D’Amore et al., SMRT Gate: A method for validation of synthetic constructs on Pacific Biosciences sequencing platforms. BioTechniques. 2017
  12. Rosalinda D'Amore et al., A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. BMC Genomics. 2016
  13. Miles Carroll et al., Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa. Nature. 2015

Emmanuel Osei, Meghana Srinivas.