BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files
Payne, Alexander, Holmes, Nadine, Rakyan, Vardhman, Loose, Matthew
Published in Bioinformatics (Oxford, England) (01.07.2019)
Published in Bioinformatics (Oxford, England) (01.07.2019)
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Journal Article
Telomere-to-telomere assembly of a complete human X chromosome
Miga, Karen H., Koren, Sergey, Rhie, Arang, Vollger, Mitchell R., Gershman, Ariel, Bzikadze, Andrey, Brooks, Shelise, Howe, Edmund, Porubsky, David, Logsdon, Glennis A., Schneider, Valerie A., Potapova, Tamara, Wood, Jonathan, Chow, William, Armstrong, Joel, Fredrickson, Jeanne, Pak, Evgenia, Tigyi, Kristof, Kremitzki, Milinn, Markovic, Christopher, Maduro, Valerie, Dutra, Amalia, Bouffard, Gerard G., Chang, Alexander M., Hansen, Nancy F., Wilfert, Amy B., Thibaud-Nissen, Françoise, Schmitt, Anthony D., Belton, Jon-Matthew, Selvaraj, Siddarth, Dennis, Megan Y., Soto, Daniela C., Sahasrabudhe, Ruta, Kaya, Gulhan, Quick, Josh, Loman, Nicholas J., Holmes, Nadine, Loose, Matthew, Surti, Urvashi, Risques, Rosa ana, Graves Lindsay, Tina A., Fulton, Robert, Hall, Ira, Paten, Benedict, Howe, Kerstin, Timp, Winston, Young, Alice, Mullikin, James C., Pevzner, Pavel A., Gerton, Jennifer L., Sullivan, Beth A., Eichler, Evan E., Phillippy, Adam M.
Published in Nature (London) (03.09.2020)
Published in Nature (London) (03.09.2020)
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Journal Article
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
Quick, Joshua, Grubaugh, Nathan D, Pullan, Steven T, Claro, Ingra M, Smith, Andrew D, Gangavarapu, Karthik, Oliveira, Glenn, Robles-Sikisaka, Refugio, Rogers, Thomas F, Beutler, Nathan A, Burton, Dennis R, Lewis-Ximenez, Lia Laura, de Jesus, Jaqueline Goes, Giovanetti, Marta, Hill, Sarah C, Black, Allison, Bedford, Trevor, Carroll, Miles W, Nunes, Marcio, Alcantara, Luiz Carlos, Sabino, Ester C, Baylis, Sally A, Faria, Nuno R, Loose, Matthew, Simpson, Jared T, Pybus, Oliver G, Andersen, Kristian G, Loman, Nicholas J
Published in Nature protocols (01.06.2017)
Published in Nature protocols (01.06.2017)
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Journal Article
Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples
Votintseva, Antonina A, Bradley, Phelim, Pankhurst, Louise, Del Ojo Elias, Carlos, Loose, Matthew, Nilgiriwala, Kayzad, Chatterjee, Anirvan, Smith, E Grace, Sanderson, Nicolas, Walker, Timothy M, Morgan, Marcus R, Wyllie, David H, Walker, A Sarah, Peto, Tim E A, Crook, Derrick W, Iqbal, Zamin
Published in Journal of clinical microbiology (01.05.2017)
Published in Journal of clinical microbiology (01.05.2017)
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Journal Article
The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks
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
Published in The Journal of infectious diseases (05.01.2022)
Published in The Journal of infectious diseases (05.01.2022)
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Journal Article
Impact of whole-genome duplications on structural variant evolution in Cochlearia
Hämälä, Tuomas, Moore, Christopher, Cowan, Laura, Carlile, Matthew, Gopaulchan, David, Brandrud, Marie K., Birkeland, Siri, Loose, Matthew, Kolář, Filip, Koch, Marcus A., Yant, Levi
Published in Nature communications (25.06.2024)
Published in Nature communications (25.06.2024)
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A single-cell atlas of pig gastrulation as a resource for comparative embryology
Simpson, Luke, Strange, Andrew, Klisch, Doris, Kraunsoe, Sophie, Azami, Takuya, Goszczynski, Daniel, Le Minh, Triet, Planells, Benjamin, Holmes, Nadine, Sang, Fei, Henson, Sonal, Loose, Matthew, Nichols, Jennifer, Alberio, Ramiro
Published in Nature communications (18.06.2024)
Published in Nature communications (18.06.2024)
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Journal Article
Reply to ‘Errors in long-read assemblies can critically affect protein prediction’
Koren, Sergey, Phillippy, Adam M., Simpson, Jared T., Loman, Nicholas J., Loose, Matthew
Published in Nature biotechnology (01.02.2019)
Published in Nature biotechnology (01.02.2019)
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Journal Article
Examining diabetic heel ulcers through an ecological lens: microbial community dynamics associated with healing and infection
Sloan, Tim J, Turton, James C, Tyson, Jess, Musgrove, Alison, Fleming, Vicki M, Lister, Michelle M, Loose, Matthew W, Sockett, R Elizabeth, Diggle, Mathew, Game, Frances L, Jeffcoate, William
Published in Journal of medical microbiology (01.02.2019)
Published in Journal of medical microbiology (01.02.2019)
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Journal Article
Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states
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
Published in Genome Biology (14.02.2022)
Published in Genome Biology (14.02.2022)
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Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements
Cahyani, Inswasti, Putro, Eko W, Ridwanuloh, Asep M, Wibowo, Satrio, Hariyatun, Hariyatun, Syahputra, Gita, Akbariani, Gilang, Utomo, Ahmad R, Ilyas, Mohammad, Loose, Matthew, Kusharyoto, Wien, Susanti, Susanti
Published in Viruses (08.04.2022)
Published in Viruses (08.04.2022)
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Journal Article
NANOG is required to establish the competence for germ-layer differentiation in the basal tetrapod axolotl
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
Published in PLoS biology (14.06.2023)
Published in PLoS biology (14.06.2023)
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Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom
Chappell, Joseph G, Tsoleridis, Theocharis, Clark, Gemma, Berry, Louise, Holmes, Nadine, Moore, Christopher, Carlile, Matthew, Sang, Fei, Debebe, Bisrat J, Wright, Victoria, Irving, William L, Thomson, Brian J, Boswell, Timothy C J, Willingham, Iona, Joseph, Amelia, Smith, Wendy, Khakh, Manjinder, Fleming, Vicki M, Lister, Michelle M, Howson-Wells, Hannah C, Holmes, Edward C, Loose, Matthew W, Ball, Jonathan K, McClure, C Patrick, On Behalf Of The Cog-Uk Consortium
Published in Journal of general virology (01.06.2021)
Published in Journal of general virology (01.06.2021)
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Journal Article
MinION Analysis and Reference Consortium: Phase 1 data release and analysis
Ip, Camilla L C, Loose, Matthew, Tyson, John R, de Cesare, Mariateresa, Brown, Bonnie L, Jain, Miten, Leggett, Richard M, Eccles, David A, Zalunin, Vadim, Urban, John M, Piazza, Paolo, Bowden, Rory J, Paten, Benedict, Mwaigwisya, Solomon, Batty, Elizabeth M, Simpson, Jared T, Snutch, Terrance P, Birney, Ewan, Buck, David, Goodwin, Sara, Jansen, Hans J, O'Grady, Justin, Olsen, Hugh E
Published in F1000 research (2015)
Published in F1000 research (2015)
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Transient Accumulation of 5-Carboxylcytosine Indicates Involvement of Active Demethylation in Lineage Specification of Neural Stem Cells
Wheldon, Lee M., Abakir, Abdulkadir, Ferjentsik, Zoltan, Dudnakova, Tatiana, Strohbuecker, Stephanie, Christie, Denise, Dai, Nan, Guan, Shengxi, Foster, Jeremy M., Corrêa, Ivan R., Loose, Matthew, Dixon, James E., Sottile, Virginie, Johnson, Andrew D., Ruzov, Alexey
Published in Cell reports (Cambridge) (12.06.2014)
Published in Cell reports (Cambridge) (12.06.2014)
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Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study
Stirrup, Oliver, Blackstone, James, Mapp, Fiona, MacNeil, Alyson, Panca, Monica, Holmes, Alison, Machin, Nicholas, Shin, Gee Yen, Mahungu, Tabitha, Saeed, Kordo, Saluja, Tranprit, Taha, Yusri, Mahida, Nikunj, Pope, Cassie, Chawla, Anu, Cutino-Moguel, Maria-Teresa, Tamuri, Asif, Williams, Rachel, Darby, Alistair, Robertson, David L, Flaviani, Flavia, Nastouli, Eleni, Robson, Samuel, Smith, Darren, Loose, Matthew, Laing, Kenneth, Monahan, Irene, Kele, Beatrix, Haldenby, Sam, George, Ryan, Bashton, Matthew, Witney, Adam A, Byott, Matthew, Coll, Francesc, Chapman, Michael, Peacock, Sharon J, Hughes, Joseph, Nebbia, Gaia, Partridge, David G, Parker, Matthew, Price, James Richard, Peters, Christine, Roy, Sunando, Snell, Luke B, de Silva, Thushan I, Thomson, Emma, Flowers, Paul, Copas, Andrew, Breuer, Judith
Published in eLife (13.09.2022)
Published in eLife (13.09.2022)
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MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry [version 1; peer review: 1 approved, 2 approved with reservations]
Jain, Miten, Tyson, John R, Loose, Matthew, Ip, Camilla L.C, Eccles, David A, O'Grady, Justin, Malla, Sunir, Leggett, Richard M, Wallerman, Ola, Jansen, Hans J, Zalunin, Vadim, Birney, Ewan, Brown, Bonnie L, Snutch, Terrance P, Olsen, Hugh E
Published in F1000 research (2017)
Published in F1000 research (2017)
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