Outputs (27)

Enhancing nanopore adaptive sampling for PromethION using readfish at scale (2025)
Journal Article
Munro, R., Payne, A., Holmes, N., Moore, C., Cahyani, I., & Loose, M. (in press). Enhancing nanopore adaptive sampling for PromethION using readfish at scale. Genome Research, https://doi.org/10.1101/gr.279329.124

A unique feature of Oxford Nanopore Technologies sequencers, adaptive sampling, allows precise DNA molecule selection from sequencing libraries. Here we present enhancements to our tool, readfish, enabling all features for the industrial scale Promet... Read More about Enhancing nanopore adaptive sampling for PromethION using readfish at scale.

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.

Impact of whole-genome duplications on structural variant evolution in Cochlearia (2024)
Journal Article
Hämälä, T., Moore, C., Cowan, L., Carlile, M., Gopaulchan, D., K. Brandrud, M. K., Birkeland, S., Loose, M., Kolář, F., Koch, M., & Yant, L. (2024). Impact of whole-genome duplications on structural variant evolution in Cochlearia. Nature Communications, 15, Article 5377. https://doi.org/10.1038/s41467-024-49679-y

Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding of their fitness consequences. Here, we study whether WGDs result in... Read More about Impact of whole-genome duplications on structural variant evolution in Cochlearia.

A single-cell atlas of pig gastrulation as a resource for comparative embryology (2024)
Journal Article
Simpson, L., Strange, A., Klisch, D., Kraunsoe, S., Azami, T., Goszczynski, D., Le Minh, T., Planells, B., Holmes, N., Sang, F., Henson, S., Loose, M., Nichols, J., & Alberio, R. (2024). A single-cell atlas of pig gastrulation as a resource for comparative embryology. Nature Communications, 15(1), Article 5210. https://doi.org/10.1038/s41467-024-49407-6

Cell-fate decisions during mammalian gastrulation are poorly understood outside of rodent embryos. The embryonic disc of pig embryos mirrors humans, making them a useful proxy for studying gastrulation. Here we present a single-cell transcriptomic at... Read More about A single-cell atlas of pig gastrulation as a resource for comparative embryology.

Sarbecoviruses of British Horseshoe Bats; Sequence Variation and Epidemiology (2023)
Journal Article
Apaa, T., Withers, A. J., Staley, C. E., Blanchard, A. M., Bennett, M., Bremner-Harrison, S., Chadwick, E. A., Hailer, F., Harrison, S. W. R., Loose, M., Mathews, F., & Tarlinton, R. E. (2023). Sarbecoviruses of British Horseshoe Bats; Sequence Variation and Epidemiology. Journal of General Virology, 104(6), Article 001859. https://doi.org/10.1101/2023.02.14.528476

Horseshoe bats are the natural hosts of the Sarbecovirus subgenus that includes SARS-CoV and SARS-CoV- 2. Despite the devastating impact of the COVID-19 pandemic, there is still little known about the underlying epidemiology and virology of sarbecovi... Read More about Sarbecoviruses of British Horseshoe Bats; Sequence Variation and Epidemiology.

NANOG is required to establish the competence for germ-layer differentiation in the basal tetrapod axolotl (2023)
Journal Article
Simpson, L. A., Crowley, D., Forey, T., Acosta, H., Ferjentsik, Z., Chatfield, J., Payne, A., Simpson, B. S., Redwood, C., Dixon, J. E., Holmes, N., Sang, F., Alberio, R., Loose, M., & Johnson, A. D. (2023). NANOG is required to establish the competence for germ-layer differentiation in the basal tetrapod axolotl. PLoS Biology, 21(6), Article e3002121. https://doi.org/10.1371/journal.pbio.3002121

Pluripotency defines the unlimited potential of individual cells of vertebrate embryos, from which all adult somatic cells and germ cells are derived. Understanding how the programming of pluripotency evolved has been obscured in part by a lack of da... Read More about NANOG is required to establish the competence for germ-layer differentiation in the basal tetrapod axolotl.

Genomics and biochemical analyses reveal a metabolon key to β-L-ODAP biosynthesis in Lathyrus sativus (2023)
Journal Article
Edwards, A., Njaci, I., Sarkar, A., Jiang, Z., Kaithakottil, G. G., Moore, C., Cheema, J., Stevenson, C. E. M., Rejzek, M., Novák, P., Vigouroux, M., Vickers, M., Wouters, R. H. M., Paajanen, P., Steuernagel, B., Moore, J. D., Higgins, J., Swarbreck, D., Martens, S., Kim, C. Y., …Emmrich, P. M. F. (2023). Genomics and biochemical analyses reveal a metabolon key to β-L-ODAP biosynthesis in Lathyrus sativus. Nature Communications, 14, Article 876. https://doi.org/10.1038/s41467-023-36503-2

Grass pea (Lathyrus sativus L.) is a rich source of protein cultivated as an insurance crop in Ethiopia, Eritrea, India, Bangladesh, and Nepal. Its resilience to both drought and flooding makes it a promising crop for ensuring food security in a chan... Read More about Genomics and biochemical analyses reveal a metabolon key to β-L-ODAP biosynthesis in Lathyrus sativus.

Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design (2023)
Journal Article
Weilguny, L., De Maio, N., Munro, R., Manser, C., Birney, E., Loose, M., & Goldman, N. (2023). Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design. Nature Biotechnology, 41, 1018–1025. https://doi.org/10.1038/s41587-022-01580-z

Nanopore sequencers can select which DNA molecules to sequence, rejecting a molecule after analysis of a small initial part. Currently, selection is based on predetermined regions of interest that remain constant throughout an experiment. Sequencing... Read More about Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design.

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.

Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study (2022)
Journal Article
Colton, H., Parker, M. D., Stirrup, O., Blackstone, J., Loose, M., McClure, C. P., Roy, S., Williams, C., McLeod, J., Smith, D., Taha, Y., Zhang, P., Hsu, S. N., Kele, B., Harris, K., Mapp, F., Williams, R., COG-UK HOCI Investigators, COVID-19 Genomics UK (COG-UK) Consortium, Flowers, P., Breuer, J., …de Silva, T. I. (2023). Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study. Journal of Hospital Infection, 131, 34-42. https://doi.org/10.1016/j.jhin.2022.09.022

Background
Barriers to rapid return of sequencing results can affect the utility of sequence data for infection prevention and control decisions.

Aim
To undertake a mixed-methods analysis to identify challenges that sites faced in achieving a ra... Read More about Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study.