Photo of Dr John Kenny

Dr John Kenny

Sequence Production Manager, CGR Functional and Comparative Genomics

Publications

2019

Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems (Journal article)

George, P. B. L., Lallias, D., Creer, S., Seaton, F. M., Kenny, J. G., Eccles, R. M., . . . Jones, D. L. (2019). Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems. NATURE COMMUNICATIONS, 10. doi:10.1038/s41467-019-09031-1

DOI: 10.1038/s41467-019-09031-1

2018

A Framework for Multi-Omic Prediction of Treatment Response to Biologic Therapy for Psoriasis (Journal article)

Foulkes, A. C., Watson, D. S., Carr, D. F., Kenny, J. G., Slidel, T., Parslew, R., . . . Consortium, P. S. O. R. T. (2019). A Framework for Multi-Omic Prediction of Treatment Response to Biologic Therapy for Psoriasis. JOURNAL OF INVESTIGATIVE DERMATOLOGY, 139(1), 100-107. doi:10.1016/j.jid.2018.04.041

DOI: 10.1016/j.jid.2018.04.041

2017

Microbiome and infectivity studies reveal complex polyspecies tree disease in Acute Oak Decline (Journal article)

Denman, S., Doonan, J., Ransom-Jones, E., Broberg, M., Plummer, S., Kirk, S., . . . McDonald, J. E. (2018). Microbiome and infectivity studies reveal complex polyspecies tree disease in Acute Oak Decline. ISME JOURNAL, 12(2), 386-399. doi:10.1038/ismej.2017.170

DOI: 10.1038/ismej.2017.170

SMRT Gate: A method for validation of synthetic constructs on Pacific Biosciences sequencing platforms (Journal article)

D'Amore, R., Johnson, J., Haldenby, S., Hall, N., Hughes, M., Joynson, R., . . . Hall, A. (2017). SMRT Gate: A method for validation of synthetic constructs on Pacific Biosciences sequencing platforms. BIOTECHNIQUES, 63(1), 13-20. doi:10.2144/000114565

DOI: 10.2144/000114565

Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus (Journal article)

Liu, X., Speranza, E., Munoz-Fontela, C., Haldenby, S., Rickett, N. Y., Garcia-Dorival, I., . . . Hiscox, J. A. (2017). Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus. GENOME BIOLOGY, 18. doi:10.1186/s13059-016-1137-3

DOI: 10.1186/s13059-016-1137-3

2016

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling (Journal article)

D'Amore, R., Ijaz, U. Z., Schirmer, M., Kenny, J. G., Gregory, R., Darby, A. C., . . . Hall, N. (2016). A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. BMC GENOMICS, 17. doi:10.1186/s12864-015-2194-9

DOI: 10.1186/s12864-015-2194-9

2015

Genome-Wide DNA Methylation Patterns in Wild Samples of Two Morphotypes of Threespine Stickleback (Gasterosteus aculeatus) (Journal article)

Smith, G., Smith, C., Kenny, J. G., Chaudhuri, R. R., & Ritchie, M. G. (2015). Genome-Wide DNA Methylation Patterns in Wild Samples of Two Morphotypes of Threespine Stickleback (Gasterosteus aculeatus). MOLECULAR BIOLOGY AND EVOLUTION, 32(4), 888-895. doi:10.1093/molbev/msu344

DOI: 10.1093/molbev/msu344

Investigating the Influence of Ribavirin on Human Respiratory Syncytial Virus RNA Synthesis by Using a High-Resolution Transcriptome Sequencing Approach (Journal article)

Aljabr, W., Touzelet, O., Pollakis, G., Wu, W., Munday, D. C., Hughes, M., . . . Hiscox, J. A. (2016). Investigating the Influence of Ribavirin on Human Respiratory Syncytial Virus RNA Synthesis by Using a High-Resolution Transcriptome Sequencing Approach. JOURNAL OF VIROLOGY, 90(10), 4876-4888. doi:10.1128/JVI.02349-15

DOI: 10.1128/JVI.02349-15

Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa (Journal article)

Carroll, M. W., Matthews, D. A., Hiscox, J. A., Elmore, M. J., Pollakis, G., Rambaut, A., . . . Guenther, S. (2015). Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa. NATURE, 524(7563), 97-U201. doi:10.1038/nature14594

DOI: 10.1038/nature14594

Transcriptome sequencing of human breast cancer reveals aberrant intronic transcription in amplicons and dysregulation of alternative splicing with major therapeutic implications (Journal article)

Forootan, S. S., Butler, J. M., Gardener, D., Baird, A. E., Dodson, A., Darby, A., . . . Gosden, C. M. (2016). Transcriptome sequencing of human breast cancer reveals aberrant intronic transcription in amplicons and dysregulation of alternative splicing with major therapeutic implications. INTERNATIONAL JOURNAL OF ONCOLOGY, 48(1), 130-144. doi:10.3892/ijo.2015.3222

DOI: 10.3892/ijo.2015.3222

Transcriptomic Analysis of Shiga-Toxigenic Bacteriophage Carriage Reveals a Profound Regulatory Effect on Acid Resistance in Escherichia coli (Journal article)

Veses-Garcia, M., Liu, X., Rigden, D. J., Kenny, J. G., McCarthy, A. J., & Allison, H. E. (2015). Transcriptomic Analysis of Shiga-Toxigenic Bacteriophage Carriage Reveals a Profound Regulatory Effect on Acid Resistance in Escherichia coli. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 81(23), 8118-8125. doi:10.1128/AEM.02034-15

DOI: 10.1128/AEM.02034-15

2014

Phylogenomics of the killer whale indicates ecotype divergence in sympatry (Journal article)

Moura, A. E., Kenny, J. G., Chaudhuri, R. R., Hughes, M. A., Reisinger, R. R., de Bruyn, P. J. N., . . . Hoelzel, A. R. (2015). Phylogenomics of the killer whale indicates ecotype divergence in sympatry. HEREDITY, 114(1), 48-55. doi:10.1038/hdy.2014.67

DOI: 10.1038/hdy.2014.67

Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift (Journal article)

Moura, A. E., Kenny, J. G., Chaudhuri, R., Hughes, M. A., Welch, A. J., Reisinger, R. R., . . . Hoelzel, A. R. (2014). Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift. MOLECULAR ECOLOGY, 23(21), 5179-5192. doi:10.1111/mec.12929

DOI: 10.1111/mec.12929

Single-Step Selection of Bivalent Aptamers Validated by Comparison with SELEX Using High-Throughput Sequencing (Journal article)

Wilson, R., Bourne, C., Chaudhuri, R. R., Gregory, R., Kenny, J., & Cossins, A. (2014). Single-Step Selection of Bivalent Aptamers Validated by Comparison with SELEX Using High-Throughput Sequencing. PLOS ONE, 9(6). doi:10.1371/journal.pone.0100572

DOI: 10.1371/journal.pone.0100572

2013

Can long-range PCR be used to amplify genetically divergent mitochondrial genomes for comparative phylogenetics? A case study within spiders (Arthropoda: Araneae). (Journal article)

Briscoe, A. G., Goodacre, S., Masta, S. E., Taylor, M. I., Arnedo, M. A., Penney, D., . . . Creer, S. (2013). Can long-range PCR be used to amplify genetically divergent mitochondrial genomes for comparative phylogenetics? A case study within spiders (Arthropoda: Araneae).. PLOS One, 8(5), e62404. doi:10.1371/journal.pone.00624

DOI: 10.1371/journal.pone.00624

Mannitol utilisation is required for protection of Staphylococcus aureus from human skin antimicrobial fatty acids. (Journal article)

Kenny, J. G., Moran, J., Kolar, S. L., Ulanov, A., Li, Z., Shaw, L. N., . . . Horsburgh, M. J. (2013). Mannitol utilisation is required for protection of Staphylococcus aureus from human skin antimicrobial fatty acids.. PLOS One, 8(7), e67698. doi:10.1371/journal.pone.00676

DOI: 10.1371/journal.pone.00676

2010

Comparative Genomics and Transduction Potential of Enterococcus faecalis Temperate Bacteriophages (Journal article)

Yasmin, A., Kenny, J. G., Shankar, J., Darby, A. C., Hall, N., Edwards, C., & Horsburgh, M. J. (2010). Comparative Genomics and Transduction Potential of Enterococcus faecalis Temperate Bacteriophages. JOURNAL OF BACTERIOLOGY, 192(4), 1122-1130. doi:10.1128/JB.01293-09

DOI: 10.1128/JB.01293-09

2009

The Staphylococcus aureus Response to Unsaturated Long Chain Free Fatty Acids: Survival Mechanisms and Virulence Implications (Journal article)

Kenny, J. G., Ward, D., Josefsson, E., Jonsson, I. -M., Hinds, J., Rees, H. H., . . . Horsburgh, M. J. (2009). The Staphylococcus aureus Response to Unsaturated Long Chain Free Fatty Acids: Survival Mechanisms and Virulence Implications. PLOS ONE, 4(2). doi:10.1371/journal.pone.0004344

DOI: 10.1371/journal.pone.0004344

2007

Bacteriophage-Host Interaction in Lactic Acid Bacteria (Chapter)

Skovgaard Vegge, C., Kenny, J. G., Brøndsted, L., McGrath, S., & Van Sinderen, D. (2007). Bacteriophage-Host Interaction in Lactic Acid Bacteria. In S. McGrath, & D. van Sinderen (Eds.), Bacteriophage: Genetics and Molecular Biology (pp. 195-210). Wymondham, Norfolk, UK: Caister Academic Press.

2006

Bacteriophages in Biotechnology (Chapter)

Kenny, J., O'Driscoll, J., O'Mahony, J., van Sinderen, D., & McGrath, S. (2006). Bacteriophages in Biotechnology. In E. C. Hearns (Ed.), Trends in Biotechnology Research (pp. 129-154). New York: Nova Science Publishers Inc..

Characterization of the lytic–lysogenic switch of the lactococcal bacteriophage Tuc2009 (Journal article)

Kenny, J. G., Leach, S., de la Hoz, A. B., Venema, G., Kok, J., Fitzgerald, G. F., . . . van Sinderen, D. (2006). Characterization of the lytic–lysogenic switch of the lactococcal bacteriophage Tuc2009. Virology, 347(2), 434-446. doi:10.1016/j.virol.2005.11.041

DOI: 10.1016/j.virol.2005.11.041

2005

The ClgR Protein Regulates Transcription of the clpP Operon in Bifidobacterium breve UCC 2003 (Journal article)

Ventura, M., Zhang, Z., Cronin, M., Canchaya, C., Kenny, J. G., Fitzgerald, G. F., & van Sinderen, D. (2005). The ClgR Protein Regulates Transcription of the clpP Operon in Bifidobacterium breve UCC 2003. Journal of Bacteriology, 187(24), 8411-8426. doi:10.1128/JB.187.24.8411-8426.2005

DOI: 10.1128/JB.187.24.8411-8426.2005

The clpB gene of Bifidobacterium breve UCC 2003: transcriptional analysis and first insights into stress induction (Journal article)

Ventura, M. (2005). The clpB gene of Bifidobacterium breve UCC 2003: transcriptional analysis and first insights into stress induction. Microbiology, 151(9), 2861-2872. doi:10.1099/mic.0.28176-0

DOI: 10.1099/mic.0.28176-0

2004

Bacteriophage Tuc2009 Encodes a Tail-Associated Cell Wall-Degrading Activity (Journal article)

Kenny, J. G., McGrath, S., Fitzgerald, G. F., & van Sinderen, D. (2004). Bacteriophage Tuc2009 Encodes a Tail-Associated Cell Wall-Degrading Activity. Journal of Bacteriology, 186(11), 3480-3491. doi:10.1128/JB.186.11.3480-3491.2004

DOI: 10.1128/JB.186.11.3480-3491.2004