Outputs (15)

‘Vivaldi’: an amplicon-based whole-genome sequencing method for the four seasonal human coronaviruses, 229E, NL63, OC43 and HKU1, alongside SARS-CoV-2 (2025)
Journal Article
McClure, P. C., Tsoleridis, T., Hill, J. D., Holmes, N., Chappell, J. G., Byaruhanga, T., Duncan, J., Tofan, M., Berry, L., Clark, G., L. Irving, W., Tarr, A. W., Ball, J. K., Astbury, S., & Loose, M. (2025). ‘Vivaldi’: an amplicon-based whole-genome sequencing method for the four seasonal human coronaviruses, 229E, NL63, OC43 and HKU1, alongside SARS-CoV-2. Microbial Genomics, 11, Article 001451. https://doi.org/10.1099/mgen.0.001451

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 and HKU1, alongside SARS-CoV-2.

ROBIN: A unified nanopore-based assay integrating intraoperative methylome classification and next-day comprehensive profiling for ultra-rapid tumor diagnosis (2025)
Journal Article
Deacon, S., Cahyani, I., Holmes, N., Fox, G., Munro, R., Wibowo, S., Murray, T., Mason, H., Housley, M., Martin, D., Sharif, A., Patel, A., Goldspring, R., Brandner, S., Sahm, F., Smith, S., Paine, S., & Loose, M. (2025). ROBIN: A unified nanopore-based assay integrating intraoperative methylome classification and next-day comprehensive profiling for ultra-rapid tumor diagnosis. Neuro-Oncology, https://doi.org/10.1093/neuonc/noaf103

Background
Advances in our technological capacity to interrogate CNS tumor biology have led to the ever increasing use of genomic sequencing in diagnostic decision making. Presently, CNS tumors are classified based on their epigenetic signatures, le... Read More about ROBIN: A unified nanopore-based assay integrating intraoperative methylome classification and next-day comprehensive profiling for ultra-rapid tumor diagnosis.

An optimised toolkit for high molecular weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride (2025)
Journal Article
Cahyani, I., Tyson, J., Holmes, N., Quick, J., Moore, C., Loman, N., & Loose, M. (2025). An optimised toolkit for high molecular weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride. Genome Research, 35(5), 1154-1166. https://doi.org/10.1101/gr.279943.124

Since the advent of long-read sequencing, achieving longer read lengths has been a key goal for many users. Ultra-long-read sets (N50 ≥ 100 kb) produced from Oxford Nanopore sequencers have improved genome assemblies in recent years. However, despite... Read More about An optimised toolkit for high molecular weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride.

Programming of pluripotency and the germ line co-evolved from a Nanog ancestor (2025)
Journal Article
Crowley, D., Simpson, L., Chatfield, J., Forey, T., Allegrucci, C., Sang, F., Holmes, N., Genikhovich, G., Technau, U., Cunningham, D., Silva, E., Mullin, N., Dixon, J. E., Loose, M., Alberio, R., & Johnson, A. D. (2025). Programming of pluripotency and the germ line co-evolved from a Nanog ancestor. Cell Reports, 44(3), Article 115396. https://doi.org/10.1016/j.celrep.2025.115396

Francois Jacob proposed that evolutionary novelty arises through incremental tinkering with pre-existing genetic mechanisms. Vertebrate evolution was predicated on pluripotency, the ability of embryonic cells to form somatic germ layers and primordia... Read More about Programming of pluripotency and the germ line co-evolved from a Nanog ancestor.

Paternal undernutrition and overnutrition 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 undernutrition and overnutrition modify semen composition and preimplantation embryo developmental kinetics in mice. BMC Biology, 22(1), 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 undernutrition and overnutrition 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.