All Outputs (6)

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.

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., …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., …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.

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., …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.