Outputs (27)

Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock (2022)
Journal Article
Maciel-Guerra, A., Baker, M., Hu, Y., Wang, W., Zhang, X., Rong, J., Zhang, Y., Zhang, J., Kaler, J., Renney, D., Loose, M., Emes, R. D., Liu, L., Chen, J., Peng, Z., Li, F., & Dottorini, T. (2023). Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock. ISME Journal, 17(1), 21-35. https://doi.org/10.1038/s41396-022-01315-7

A debate is currently ongoing as to whether intensive livestock farms may constitute reservoirs of clinically relevant antimicrobial resistance (AMR), thus posing a threat to surrounding communities. Here, combining shotgun metagenome sequencing, mac... Read More about Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock.

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.

Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements (2022)
Journal Article
Cahyani, I., Putro, E. W., Ridwanuloh, A. M., Wibowo, S., Hariyatun, H., Syahputra, G., Akbariani, G., Utomo, A. R., Ilyas, M., Loose, M., Kusharyoto, W., & Susanti, S. (2022). Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements. Viruses, 14(4), Article 778. https://doi.org/10.3390/v14040778

Whole-genome sequencing (WGS) has played a significant role in understanding the epidemiology and biology of SARS-CoV-2 virus. Here, we investigate the use of SARS-CoV-2 WGS in Southeast and East Asian countries as a genomic surveillance during the C... Read More about Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements.

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.

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.

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.

Pluripotency and X chromosome dynamics revealed in pig pre-gastrulating embryos by single cell analysis (2019)
Journal Article
Ramos-Ibeas, P., Sang, F., Zhu, Q., Wang, W. W., Withey, S., Klisch, D., Wood, L., Loose, M., Surani, M. A., & Alberio, R. (2019). Pluripotency and X chromosome dynamics revealed in pig pre-gastrulating embryos by single cell analysis. Nature Communications, 10, Article 500. https://doi.org/10.1038/s41467-019-08387-8

High-resolution molecular programmes delineating the cellular foundations of mammalian embryogenesis have emerged recently. Similar analysis of human embryos is limited to pre-implantation stages, since early post-implantation embryos are largely ina... Read More about Pluripotency and X chromosome dynamics revealed in pig pre-gastrulating embryos by single cell analysis.

Examining diabetic heel ulcers through an ecological lens: microbial community dynamics associated with healing and infection (2019)
Journal Article
Sloan, T. J., Turton, J. C., Tyson, J., Musgrove, A., Fleming, V. M., Lister, M. M., Loose, M. W., Sockett, R. E., Diggle, M., Game, F. L., & Jeffcoate, W. (2019). Examining diabetic heel ulcers through an ecological lens: microbial community dynamics associated with healing and infection. Journal of Medical Microbiology, 68(2), 230-240. https://doi.org/10.1099/jmm.0.000907

Purpose: While some micro-organisms, such as Staphylococcus aureus, are clearly implicated in causing tissue damage in diabetic foot ulcers (DFUs), our knowledge of the contribution of the entire microbiome to clinical outcomes is limited. We profile... Read More about Examining diabetic heel ulcers through an ecological lens: microbial community dynamics associated with healing and infection.

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.