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Professor Matthew Loose's Outputs (28)

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., Tyson, J., Beggs, A., Dilthey, A., Fiddes, I., Malla, S., Marriott, H., Nieto, T., O'Grady, J., Olsen, H., Pedersen, B., Rhie, A., Richardson, H., Quinlan, A., Snutch, 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., Chatterjee, A., Smith, E. G., Sanderson, N., Walker, T. M., Morgan, M. R., Wyllie, D. H., Walker, A. S., Peto, T. E., Crook, D. W., & 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.-A., Bachvarova, R. F., Ferjentsik, Z., Redwood, C., Walmsley, M., Patient, R., Loose, 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.

Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe (2014)
Journal Article
Brown, W. R., Thomas, G., Lee, N. C., Blythe, M., Liti, G., Warringer, J., & Loose, M. W. (2014). Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe. Proceedings of the National Academy of Sciences, 111(5), https://doi.org/10.1073/pnas.1216934111

Kinetochores in multicellular eukaryotes are usually associated with heterochromatin. Whether this heterochromatin simply promotes the cohesion necessary for accurate chromosome segregation at cell division or whether it also has a role in kinetochor... Read More about Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe.