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Whole genome sequencing of Salmonella Typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014.
Published in:
BMC Microbiology, 2016, v. 16, p. 1, doi. 10.1186/s12866-016-0831-3
By:
- Phillips, Anastasia;
- Sotomayor, Cristina;
- Qinning Wang;
- Holmes, Nadine;
- Furlong, Catriona;
- Ward, Kate;
- Howard, Peter;
- Octavia, Sophie;
- Ruiting Lan;
- Sintchenko, Vitali
Publication type:
Article
Use of Bulk Segregant Analysis for Determining the Genetic Basis of Azole Resistance in the Opportunistic Pathogen Aspergillus fumigatus.
Published in:
Frontiers in Cellular & Infection Microbiology, 2022, v. 12, p. 1, doi. 10.3389/fcimb.2022.841138
By:
- Ashton, George D.;
- Fei Sang;
- Blythe, Martin;
- Zadik, Daniel;
- Holmes, Nadine;
- Malla, Sunir;
- Camps, Simone M. T.;
- Wright, Victoria;
- Melchers, Willem J. G.;
- Verweij, Paul E.;
- Dyer, Paul S.
Publication type:
Article
Readfish enables targeted nanopore sequencing of gigabase-sized genomes.
Published in:
Nature Biotechnology, 2021, v. 39, n. 4, p. 442, doi. 10.1038/s41587-020-00746-x
By:
- Payne, Alexander;
- Holmes, Nadine;
- Clarke, Thomas;
- Munro, Rory;
- Debebe, Bisrat J.;
- Loose, Matthew
Publication type:
Article
minoTour, real-time monitoring and analysis for nanopore sequencers.
Published in:
Bioinformatics, 2022, v. 38, n. 4, p. 1133, doi. 10.1093/bioinformatics/btab780
By:
- Munro, Rory;
- Santos, Roberto;
- Payne, Alexander;
- Forey, Teri;
- Osei, Solomon;
- Holmes, Nadine;
- Loose, Matthew
Publication type:
Article
Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states.
Published in:
Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02617-x
By:
- Rodriguez-Algarra, Francisco;
- Seaborne, Robert A. E.;
- Danson, Amy F.;
- Yildizoglu, Selin;
- Yoshikawa, Harunori;
- Law, Pui Pik;
- Ahmad, Zakaryya;
- Maudsley, Victoria A.;
- Brew, Ama;
- Holmes, Nadine;
- Ochôa, Mateus;
- Hodgkinson, Alan;
- Marzi, Sarah J.;
- Pradeepa, Madapura M.;
- Loose, Matthew;
- Holland, Michelle L.;
- Rakyan, Vardhman K.
Publication type:
Article
Stat3 oxidation-dependent regulation of gene expression impacts on developmental processes and involves cooperation with Hif-1α.
Published in:
PLoS ONE, 2020, v. 15, n. 12, p. 1, doi. 10.1371/journal.pone.0244255
By:
- Grillo, Michela;
- Palmer, Carolyn;
- Holmes, Nadine;
- Sang, Fei;
- Larner, Andrew C.;
- Bhosale, Rahul;
- Shaw, Peter E.
Publication type:
Article
Genome Reference Assembly for Bottlenecked Southern Australian Koalas.
Published in:
Genome Biology & Evolution, 2023, v. 15, n. 1, p. 1, doi. 10.1093/gbe/evac176
By:
- Blanchard, Adam Mark;
- Emes, Richard David;
- Greenwood, Alex David;
- Holmes, Nadine;
- Loose, Matthew William;
- McEwen, Gail Katherine;
- Meers, Joanne;
- Speight, Natasha;
- Tarlinton, Rachael Eugenie
Publication type:
Article
NANOG is required to establish the competence for germ-layer differentiation in the basal tetrapod axolotl.
Published in:
PLoS Biology, 2023, v. 21, n. 6, p. 1, doi. 10.1371/journal.pbio.3002121
By:
- Simpson, Luke A.;
- Crowley, Darren;
- Forey, Teri;
- Acosta, Helena;
- Ferjentsik, Zoltan;
- Chatfield, Jodie;
- Payne, Alexander;
- Simpson, Benjamin S.;
- Redwood, Catherine;
- Dixon, James E.;
- Holmes, Nadine;
- Sang, Fei;
- Alberio, Ramiro;
- Loose, Matthew;
- Johnson, Andrew D.
Publication type:
Article
Identifying Likely Transmission Pathways within a 10-Year Community Outbreak of Tuberculosis by High-Depth Whole Genome Sequencing.
Published in:
PLoS ONE, 2016, v. 11, n. 3, p. 1, doi. 10.1371/journal.pone.0150550
By:
- Outhred, Alexander C.;
- Holmes, Nadine;
- Sadsad, Rosemarie;
- Martinez, Elena;
- Jelfs, Peter;
- Hill-Cawthorne, Grant A.;
- Gilbert, Gwendolyn L.;
- Marais, Ben J.;
- Sintchenko, Vitali
Publication type:
Article
Rapid-CNS<sup>2</sup>: rapid comprehensive adaptive nanopore-sequencing of CNS tumors, a proof-of-concept study.
Published in:
Acta Neuropathologica, 2022, v. 143, n. 5, p. 609, doi. 10.1007/s00401-022-02415-6
By:
- Patel, Areeba;
- Dogan, Helin;
- Payne, Alexander;
- Krause, Elena;
- Sievers, Philipp;
- Schoebe, Natalie;
- Schrimpf, Daniel;
- Blume, Christina;
- Stichel, Damian;
- Holmes, Nadine;
- Euskirchen, Philipp;
- Hench, Jürgen;
- Frank, Stephan;
- Rosenstiel-Goidts, Violaine;
- Ratliff, Miriam;
- Etminan, Nima;
- Unterberg, Andreas;
- Dieterich, Christoph;
- Herold-Mende, Christel;
- Pfister, Stefan M.
Publication type:
Article
Paternal undernutrition and overnutrition modify semen composition and preimplantation embryo developmental kinetics in mice.
Published in:
BMC Biology, 2024, v. 22, n. 1, p. 1, doi. 10.1186/s12915-024-01992-0
By:
- Morgan, Hannah L.;
- Eid, Nader;
- Holmes, Nadine;
- Henson, Sonal;
- Wright, Victoria;
- Coveney, Clare;
- Winder, Catherine;
- O'Neil, Donna M.;
- Dunn, Warwick B.;
- Boocock, David J.;
- Watkins, Adam J.
Publication type:
Article
A framework for real-time monitoring, analysis and adaptive sampling of viral amplicon nanopore sequencing.
Published in:
Frontiers in Genetics, 2023, v. 14, p. 1, doi. 10.3389/fgene.2023.1138582
By:
- Munro, Rory;
- Holmes, Nadine;
- Moore, Christopher;
- Carlile, Matthew;
- Payne, Alexander;
- Tyson, John R.;
- Williams, Thomas;
- Alder, Christopher;
- Snell, Luke B.;
- Nebbia, Gaia;
- Santos, Roberto;
- Loose, Matt
Publication type:
Article
The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks.
Published in:
Journal of Infectious Diseases, 2022, v. 225, n. 1, p. 10, doi. 10.1093/infdis/jiab483
By:
- Francis, Rodric V;
- Billam, Harriet;
- Clarke, Mitch;
- Yates, Carl;
- Tsoleridis, Theocharis;
- Berry, Louise;
- Mahida, Nikunj;
- Irving, William L;
- Moore, Christopher;
- Holmes, Nadine;
- Ball, Jonathan K;
- Loose, Matthew;
- McClure, C Patrick;
- consortium, COVID-19 Genomics UK (COG-UK);
- COVID-19 Genomics UK (COG-UK) consortium
Publication type:
Article
Genome sequencing reveals novel deletions associated with secondary resistance to pyrazinamide in MDR Mycobacterium tuberculosis.
Published in:
Journal of Antimicrobial Chemotherapy (JAC), 2015, v. 70, n. 9, p. 2511, doi. 10.1093/jac/dkv128
By:
- Martinez, Elena;
- Holmes, Nadine;
- Jelfs, Peter;
- Sintchenko, Vitali
Publication type:
Article
BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files.
Published in:
Bioinformatics, 2019, v. 35, n. 13, p. 2193, doi. 10.1093/bioinformatics/bty841
By:
- Payne, Alexander;
- Holmes, Nadine;
- Rakyan, Vardhman;
- Loose, Matthew
Publication type:
Article
Paternal low protein diet perturbs inter-generational metabolic homeostasis in a tissue-specific manner in mice.
Published in:
Communications Biology, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s42003-022-03914-8
By:
- Morgan, Hannah L.;
- Furse, Samuel;
- Dias, Irundika H. K.;
- Shabir, Kiran;
- Castellanos, Marcos;
- Khan, Iqbal;
- May, Sean T.;
- Holmes, Nadine;
- Carlile, Matthew;
- Sang, Fei;
- Wright, Victoria;
- Koulman, Albert;
- Watkins, Adam J.
Publication type:
Article
Paternal low protein diet perturbs inter-generational metabolic homeostasis in a tissue-specific manner in mice.
Published in:
Communications Biology, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s42003-022-03914-8
By:
- Morgan, Hannah L.;
- Furse, Samuel;
- Dias, Irundika H. K.;
- Shabir, Kiran;
- Castellanos, Marcos;
- Khan, Iqbal;
- May, Sean T.;
- Holmes, Nadine;
- Carlile, Matthew;
- Sang, Fei;
- Wright, Victoria;
- Koulman, Albert;
- Watkins, Adam J.
Publication type:
Article
Sub-Optimal Paternal Diet at the Time of Mating Disrupts Maternal Adaptations to Pregnancy in the Late Gestation Mouse.
Published in:
Nutrients, 2024, v. 16, n. 12, p. 1879, doi. 10.3390/nu16121879
By:
- Khoshkerdar, Afsaneh;
- Eid, Nader;
- Batra, Vipul;
- Baker, Nichola;
- Holmes, Nadine;
- Henson, Sonal;
- Sang, Fei;
- Wright, Victoria;
- McLaren, Jane;
- Shakesheff, Kevin;
- Woad, Kathryn J.;
- Morgan, Hannah L.;
- Watkins, Adam J.
Publication type:
Article

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