All Outputs (11)

Paternal under and over nutrition modify semen composition and preimplantation embryo developmental kinetics in mice (2024)
Journal Article
Morgan, H. L., Eid, N., Holmes, N., Henson, S., Wright, V., Coveney, C., Winder, C., O’Neil, D. M., Dunn, W. B., Boocock, D. J., & Watkins, A. J. (2024). Paternal under and over nutrition modify semen composition and preimplantation embryo developmental kinetics in mice. BMC Biology, 22, Article 207. https://doi.org/10.1186/s12915-024-01992-0

Background: The importance of parental diet in relation to eventual offspring health is increasing in prominence due to the increased frequency of parents of reproductive age consuming poor diets. Whilst maternal health and offspring outcome have bee... Read More about Paternal under and over nutrition modify semen composition and preimplantation embryo developmental kinetics in mice.

Vivaldi: An amplicon-based whole genome sequencing method for the four seasonal human coronaviruses 229E, NL63, OC43 & HKU1, alongside SARS-CoV-2 (2024)
Preprint / Working Paper
McClure, C. P., Tsoleridis, T., Holmes, N., Chappell, J. G., Byaruhanga, T., Duncan, J., Tofan, M., Khater, A., Berry, L., Clark, G., Irving, W. L., Tarr, A. W., Ball, J. K., Astbury, S., & Loose, M. Vivaldi: An amplicon-based whole genome sequencing method for the four seasonal human coronaviruses 229E, NL63, OC43 & HKU1, alongside SARS-CoV-2

Prior to the emergence of SARS-CoV-2 in 2019, Alphacoronaviruses 229E and NL63 and Betacoronaviruses OC43 and HKU1 were already established endemic ‘common cold’ viral infections. Despite their collective contribution towards global respiratory morbi... Read More about Vivaldi: An amplicon-based whole genome sequencing method for the four seasonal human coronaviruses 229E, NL63, OC43 & HKU1, alongside SARS-CoV-2.

Sub-optimal paternal diet at the time of mating disrupts maternal adaptations to pregnancy in the late gestation mouse (2024)
Journal Article
Khoshkerdar, A., Eid, N., Batra, V., Baker, N., Holmes, N., Henson, S., Sang, F., Wright, V., McLaren, J., Shakesheff, K., Woad, K. J., Morgan, H. L., & Watkins, A. J. (2024). Sub-optimal paternal diet at the time of mating disrupts maternal adaptations to pregnancy in the late gestation mouse. Nutrients, 16(12), Article 1879. https://doi.org/10.3390/nu16121879

Pregnancy represents a stage during which maternal physiology and homeostatic regulation undergo dramatic change and adaptation. The fundamental purpose of these adaptations is to ensure the survival of her offspring through adequate nutrient provisi... Read More about Sub-optimal paternal diet at the time of mating disrupts maternal adaptations to pregnancy in the late gestation mouse.

Genome Reference Assembly for Bottlenecked Southern Australian Koalas (2022)
Journal Article
Blanchard, A. M., Emes, R. D., Greenwood, A. D., Holmes, N., Loose, M. W., McEwen, G. K., Meers, J., Speight, N., & Tarlinton, R. E. (2023). Genome Reference Assembly for Bottlenecked Southern Australian Koalas. Genome Biology and Evolution, 15(1), Article evac176. https://doi.org/10.1093/gbe/evac176

Koala populations show marked differences in inbreeding levels and in the presence or absence of the endogenous Koala retrovirus (KoRV). These genetic differences among populations may lead to severe disease impacts threatening koala population viabi... Read More about Genome Reference Assembly for Bottlenecked Southern Australian Koalas.

Paternal low protein diet perturbs inter-generational metabolic homeostasis in a tissue-specific manner in mice (2022)
Journal Article
Morgan, H. L., Furse, S., Dias, I. H. K., Shabir, K., Castellanos, M., Khan, I., May, S. T., Holmes, N., Carlile, M., Sang, F., Wright, V., Koulman, A., & Watkins, A. J. (2022). Paternal low protein diet perturbs inter-generational metabolic homeostasis in a tissue-specific manner in mice. Communications Biology, 5(1), Article 929. https://doi.org/10.1038/s42003-022-03914-8

The underlying mechanisms driving paternally-programmed metabolic disease in offspring remain poorly defined. We fed male C57BL/6 mice either a control normal protein diet (NPD; 18% protein) or an isocaloric low protein diet (LPD; 9% protein) for a m... Read More about Paternal low protein diet perturbs inter-generational metabolic homeostasis in a tissue-specific manner in mice.

Differential and defective transcription of koala retrovirus indicates the complexity of host and virus evolution (2022)
Journal Article
Tarlinton, R. E., Legione, A. R., Sarker, N., Fabijan, J., Meers, J., McMichael, L., Simmons, G., Owen, H., Seddon, J. .., Dick, G., Ryder, J. S., Hemmatzedah, F., Trott, D. J., Speight, N., Holmes, N., Loose, M., & Emes, R. D. (2022). Differential and defective transcription of koala retrovirus indicates the complexity of host and virus evolution. Journal of General Virology, 103(6), Article 001749. https://doi.org/10.1099/jgv.0.001749

Koala retrovirus (KoRV) is unique amongst endogenous (inherited) retroviruses in that its incorporation to the host genome is still active, providing an opportunity to study what drives this fundamental process in vertebrate genome evolution. Animals... Read More about Differential and defective transcription of koala retrovirus indicates the complexity of host and virus evolution.

minoTour, real-time monitoring and analysis for nanopore sequencers (2021)
Journal Article
Munro, R., Santos, R., Payne, A., Forey, T., Osei, S., Holmes, N., & Loose, M. (2022). minoTour, real-time monitoring and analysis for nanopore sequencers. Bioinformatics, 38(4), 1133-1135. https://doi.org/10.1093/bioinformatics/btab780

Summary: MinoTour offers a LIMS system for Oxford Nanopore Technology sequencers, with real-time metrics and analysis available permanently for review. Integration of unique real-time automated analysis can reduce the time required to answer biologic... Read More about minoTour, real-time monitoring and analysis for nanopore sequencers.

The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks (2021)
Journal Article
Francis, R. V., Billam, H., Clarke, M., Yates, C., Tsoleridis, T., Berry, L., Mahida, N., Irving, W. L., Moore, C., Holmes, N., Ball, J. K., Loose, M., & McClure, C. P. (2022). The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks. Journal of Infectious Diseases, 225(1), 10-18. https://doi.org/10.1093/infdis/jiab483

Nosocomial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have severely affected bed capacity and patient flow. We utilized whole-genome sequencing (WGS) to identify outbreaks and focus infection control resources and interve... Read More about The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks.

Readfish enables targeted nanopore sequencing of gigabase-sized genomes (2020)
Journal Article
Payne, A., Holmes, N., Clarke, T., Munro, R., Debebe, B., & Loose, M. (2021). Readfish enables targeted nanopore sequencing of gigabase-sized genomes. Nature Biotechnology, 39, 442-450. https://doi.org/10.1038/s41587-020-00746-x

© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. Nanopore sequencers can be used to selectively sequence certain DNA molecules in a pool by reversing the voltage across individual nanopores to reject specific sequences,... Read More about Readfish enables targeted nanopore sequencing of gigabase-sized genomes.

Nanopore native RNA sequencing of a human poly(A) transcriptome (2019)
Journal Article
Workman, R. E., Tang, A. D., Tang, P. S., Jain, M., Tyson, J. R., Razaghi, R., Zuzarte, P. C., Gilpatrick, T., Payne, A., Quick, J., Sadowski, N., Holmes, N., de Jesus, J. G., Jones, K. L., Soulette, C. M., Snutch, T. P., Loman, N., Paten, B., Loose, M., Simpson, J. T., …Timp, W. (2019). Nanopore native RNA sequencing of a human poly(A) transcriptome. Nature Methods, https://doi.org/10.1038/s41592-019-0617-2

High-throughput complementary DNA sequencing technologies have advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short and mod... Read More about Nanopore native RNA sequencing of a human poly(A) transcriptome.

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files (2018)
Journal Article
Payne, A., Holmes, N., Rakyan, V., & Loose, M. (2018). BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files. Bioinformatics, 35(13), 2193-2198. https://doi.org/10.1093/bioinformatics/bty841

Motivation: The Oxford Nanopore Technologies (ONT) MinION is used for sequencing a wide variety of sample types with diverse methods of sample extraction. Nanopore sequencers output FAST5 files containing signal data subsequently base called to FASTQ... Read More about BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files.