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Professor Matthew Loose's Outputs (34)

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.

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.

Multicellular mathematical modelling of mesendoderm formation in amphibians (2016)
Journal Article
Brown, L., Middleton, A., King, J., & Loose, M. (2016). Multicellular mathematical modelling of mesendoderm formation in amphibians. Bulletin of Mathematical Biology, 78(3), 436-467. https://doi.org/10.1007/s11538-016-0150-8

The earliest cell fate decisions in a developing embryo are those associated with establishing the germ layers. The specification of the mesoderm and endoderm is of particular interest as the mesoderm is induced from the endoderm, potentially from an... Read More about Multicellular mathematical modelling of mesendoderm formation in amphibians.

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.

Transient Accumulation of 5-Carboxylcytosine Indicates Involvement of Active Demethylation in Lineage Specification of Neural Stem Cells (2014)
Journal Article
Wheldon, L. M., Abakir, A., Ferjentsik, Z., Dudnakova, T., Strohbuecker, S., Christie, D., Dai, N., Guan, S., Foster, J. M., Corrêa, I. R., Loose, M., Dixon, J. E., Sottile, V., Johnson, A. D., & Ruzov, A. (2014). Transient Accumulation of 5-Carboxylcytosine Indicates Involvement of Active Demethylation in Lineage Specification of Neural Stem Cells. Cell Reports, 7(5), 1353-1361. https://doi.org/10.1016/j.celrep.2014.05.003

5-Methylcytosine (5mC) is an epigenetic modification involved in regulation of gene activity during differentiation. Tet dioxygenases oxidize 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Both 5fC and 5... Read More about Transient Accumulation of 5-Carboxylcytosine Indicates Involvement of Active Demethylation in Lineage Specification of Neural Stem Cells.

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.

5-hydroxymethyl-cytosine enrichment of non-committed cells is not a universal feature of vertebrate development (2012)
Journal Article
Almeida, R. D., Loose, M., Sottile, V., Matsa, E., Denning, C., Young, L., Johnson, A. D., Gering, M., & Ruzov, A. (2012). 5-hydroxymethyl-cytosine enrichment of non-committed cells is not a universal feature of vertebrate development. Epigenetics, 7(4), https://doi.org/10.4161/epi.19375

5-hydroxymethyl-cytosine (5-hmc) is a cytosine modification that is relatively abundant in mammalian pre-implantation
embryos and embryonic stem cells (Esc) derived from mammalian blastocysts. Recent observations imply that both
5-hmc and Tet1/2/... Read More about 5-hydroxymethyl-cytosine enrichment of non-committed cells is not a universal feature of vertebrate development.

Semi-quantitative immunohistochemical detection of 5-hydroxymethyl-cytosine reveals conservation of its tissue distribution between amphibians and mammals (2012)
Journal Article
Almeida, R. D., Sottile, V., Loose, M., De Sousa, P. A., Johnson, A. D., & Ruzov, A. (2012). Semi-quantitative immunohistochemical detection of 5-hydroxymethyl-cytosine reveals conservation of its tissue distribution between amphibians and mammals. Epigenetics, 7(2), https://doi.org/10.4161/epi.7.2.18949

5-Hydroxymethyl-cytosine (5-hmC) is a form of modified cytosine, which has recently attracted a considerable attention due to its potential role in transcriptional regulation. According to several reports 5-hydroxymethyl-cytosine distribution is tiss... Read More about Semi-quantitative immunohistochemical detection of 5-hydroxymethyl-cytosine reveals conservation of its tissue distribution between amphibians and mammals.