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John Kenny

Research Officer

Research Interests

John is a Senior Research Officer, his research focusses on solving questions of function in microbial communities. This builds on his decade long experience in running a next generation sequencing laboratory where he developed methods such as long and short read sequencing platforms, FACS and microfluidics platforms for single cell studies, and synthetic biology approaches.  These were applied to a diverse range of research topics, including human, crop, outbreak and microbiome studies.

John’s interests lie in using new methods 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.


PhD. University College Cork, Ireland. 2006

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


  1. Alessandra Frau et al., DNA extraction and amplicon production strategies deeply influence the outcome of gut mycobiome studies. Scientific Reports. 2019.
  2. Goodhead I et al., Large scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont. Microbial Genomics. In Press.
  3. Siddharth Jayaraman, et al., Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. PLOS Neglected Tropical Diseases. 2019
  4. Laura-Jayne Gardiner et al., Hidden variation in polyploid wheat drives local adaptation. Genome Res. 2018
  5. Lisa Olohan et al., A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample.  BMC Genomics. 2018
  6. Rosalinda D’Amore et al., SMRT Gate: A method for validation of synthetic constructs on Pacific Biosciences sequencing platforms. BioTechniques. 2017
  7. Rosalinda D'Amore et al., A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. BMC Genomics. 2016
  8. Miles Carroll et al., Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa. Nature. 2015