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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., …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.

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., …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.

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., …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., …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.

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., …Dottorini, T. (2023). Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock. ISME Journal, 17, 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., …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., …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.

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., …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., …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., …Alberio, R. (2019). Pluripotency and X chromosome dynamics revealed in pig pre-gastrulating embryos by single cell analysis. Nature Communications, 10, 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., …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.

Nanopore sequencing and assembly of a human genome with ultra-long reads (2018)
Journal Article
Jain, M., Koren, S., Miga, K., Quick, J., Rand, A., Sasani, T., …Loose, M. (2018). Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature Biotechnology, 36(4), 338-345. https://doi.org/10.1038/nbt.4060

© 2018 Nature Publishing Group. All rights reserved. We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, r... Read More about Nanopore sequencing and assembly of a human genome with ultra-long reads.

Virtual genome walking across the 32 Gb Ambystoma mexicanum genome; assembling gene models and intronic sequence (2018)
Journal Article
Evans, T., D. Johnson, A., & Loose, M. (in press). Virtual genome walking across the 32 Gb Ambystoma mexicanum genome; assembling gene models and intronic sequence. Scientific Reports, 8(1), Article 618. https://doi.org/10.1038/s41598-017-19128-6

Large repeat rich genomes present challenges for assembly using short read technologies. The 32 Gb axolotl genome is estimated to contain ~19 Gb of repetitive DNA making an assembly from short reads alone effectively impossible. Indeed, this model sp... Read More about Virtual genome walking across the 32 Gb Ambystoma mexicanum genome; assembling gene models and intronic sequence.

Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples (2017)
Journal Article
Votintseva, A. A., Bradley, P., Pankhurst, L., Elias, C. D. O., Loose, M., Nilgiriwala, K., …Iqbal, Z. (2017). Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples. Journal of Clinical Microbiology, 55(5), https://doi.org/10.1128/JCM.02483-16

Routine full characterization of Mycobacterium tuberculosis (TB) is culture-based, taking many weeks. Whole-genome sequencing (WGS) can generate antibiotic susceptibility profiles to inform treatment, augmented with strain information for global surv... Read More about Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples.

Real-time selective sequencing using nanopore technology (2016)
Journal Article
Loose, M., Malla, S., & Stout, M. (in press). Real-time selective sequencing using nanopore technology. Nature Methods, 13(9), https://doi.org/10.1038/nmeth.3930

The Oxford Nanopore Technologies MinION sequencer enables the selection of specific DNA molecules for sequencing by reversing the driving voltage across individual nanopores. To directly select molecules for sequencing, we used dynamic time warping t... Read More about Real-time selective sequencing using nanopore technology.

Stochastic specification of primordial germ cells from mesoderm precursors in axolotl embryos (2014)
Journal Article
Chatfield, J., O'Reilly, M., Bachvarova, R. F., Ferjentsik, Z., Redwood, C., Walmsley, M., …JOhnson, A. D. (2014). Stochastic specification of primordial germ cells from mesoderm precursors in axolotl embryos. Development, 141(12), 2429-2440. https://doi.org/10.1242/dev.105346

A common feature of development in most vertebrate models is the early segregation of the germ line from the soma. For example, in Xenopus and zebrafish embryos primordial germ cells (PGCs) are specified by germ plasm that is inherited from the egg;... Read More about Stochastic specification of primordial germ cells from mesoderm precursors in axolotl embryos.