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1.

Prevalence of persistent SARS-CoV-2 in a large community surveillance study.

Ghafari, Mahan; Hall, Matthew; Golubchik, Tanya; Ayoubkhani, Daniel; House, Thomas; MacIntyre-Cockett, George; Fryer, Helen R; Thomson, Laura; Nurtay, Anel; Kemp, Steven A; Ferretti, Luca; Buck, David; Green, Angie; Trebes, Amy; Piazza, Paolo; Lonie, Lorne J; Studley, Ruth; Rourke, Emma; Smith, Darren L; Bashton, Matthew; Nelson, Andrew; Crown, Matthew; McCann, Clare; Young, Gregory R; Santos, Rui Andre Nunes Dos; Richards, Zack; Tariq, Mohammad Adnan; Cahuantzi, Roberto; Barrett, Jeff; Fraser, Christophe; Bonsall, David; Walker, Ann Sarah; Lythgoe, Katrina.

Nature ; 626(8001): 1094-1101, 2024 Feb.

Article in English | MEDLINE | ID: mdl-38383783

2.

Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias.

Fryer, Helen R; Golubchik, Tanya; Hall, Matthew; Fraser, Christophe; Hinch, Robert; Ferretti, Luca; Thomson, Laura; Nurtay, Anel; Pellis, Lorenzo; House, Thomas; MacIntyre-Cockett, George; Trebes, Amy; Buck, David; Piazza, Paolo; Green, Angie; Lonie, Lorne J; Smith, Darren; Bashton, Matthew; Crown, Matthew; Nelson, Andrew; McCann, Clare M; Adnan Tariq, Mohammed; Elstob, Claire J; Nunes Dos Santos, Rui; Richards, Zack; Xhang, Xin; Hawley, Joseph; Lee, Mark R; Carrillo-Barragan, Priscilla; Chapman, Isobel; Harthern-Flint, Sarah; Bonsall, David; Lythgoe, Katrina A.

PLoS Pathog ; 19(8): e1011461, 2023 08.

Article in English | MEDLINE | ID: mdl-37578971

3.

Correction: Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias.

Fryer, Helen R; Golubchik, Tanya; Hall, Matthew; Fraser, Christophe; Hinch, Robert; Ferretti, Luca; Thomson, Laura; Nurtay, Anel; Pellis, Lorenzo; House, Thomas; MacIntyre-Cockett, George; Trebes, Amy; Buck, David; Piazza, Paolo; Green, Angie; Lonie, Lorne J; Smith, Darren; Bashton, Matthew; Crown, Matthew; Nelson, Andrew; McCann, Clare M; Tariq, Mohammed Adnan; Elstob, Claire J; Dos Santos, Rui Nunes; Richards, Zack; Xhang, Xin; Hawley, Joseph; Lee, Mark R; Carrillo-Barragan, Priscilla; Chapman, Isobel; Harthern-Flint, Sarah; Bonsall, David; Lythgoe, Katrina A.

PLoS Pathog ; 19(10): e1011706, 2023 Oct.

Article in English | MEDLINE | ID: mdl-37801435

4.

The genomic landscape of acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21.

Gao, Qingsong; Ryan, Sarra L; Iacobucci, Ilaria; Ghate, Pankaj S; Cranston, Ruth E; Schwab, Claire; Elsayed, Abdelrahman H; Shi, Lei; Pounds, Stanley; Lei, Shaohua; Baviskar, Pradyuamna; Pei, Deqing; Cheng, Cheng; Bashton, Matthew; Sinclair, Paul; Bentley, David R; Ross, Mark T; Kingsbury, Zoya; James, Terena; Roberts, Kathryn G; Devidas, Meenakshi; Fan, Yiping; Chen, Wenan; Chang, Ti-Cheng; Wu, Gang; Carroll, Andrew; Heerema, Nyla; Valentine, Virginia; Valentine, Marcus; Yang, Wenjian; Yang, Jun J; Moorman, Anthony V; Harrison, Christine J; Mullighan, Charles G.

Blood ; 142(8): 711-723, 2023 08 24.

Article in English | MEDLINE | ID: mdl-37216686

5.

Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey.

Lythgoe, Katrina A; Golubchik, Tanya; Hall, Matthew; House, Thomas; Cahuantzi, Roberto; MacIntyre-Cockett, George; Fryer, Helen; Thomson, Laura; Nurtay, Anel; Ghafani, Mahan; Buck, David; Green, Angie; Trebes, Amy; Piazza, Paolo; Lonie, Lorne J; Studley, Ruth; Rourke, Emma; Smith, Darren; Bashton, Matthew; Nelson, Andrew; Crown, Matthew; McCann, Clare; Young, Gregory R; Andre Nunes Dos Santos, Rui; Richards, Zack; Tariq, Adnan; Fraser, Christophe; Diamond, Ian; Barrett, Jeff; Walker, Ann Sarah; Bonsall, David.

Proc Biol Sci ; 290(2009): 20231284, 2023 10 25.

Article in English | MEDLINE | ID: mdl-37848057

6.

SPEAR: Systematic ProtEin AnnotatoR.

Crown, Matthew; Teruel, Natália; Najmanovich, Rafael; Bashton, Matthew.

Bioinformatics ; 38(15): 3827-3829, 2022 08 02.

Article in English | MEDLINE | ID: mdl-35695776

7.

Molecular characterization and clinical outcome of B-cell precursor acute lymphoblastic leukemia with IG-MYC rearrangement.

Bomken, Simon; Enshaei, Amir; Schwalbe, Edward C; Mikulasova, Aneta; Dai, Yunfeng; Zaka, Masood; Fung, Kent T M; Bashton, Matthew; Lim, Huezin; Jones, Lisa; Karataraki, Nefeli; Winterman, Emily; Ashby, Cody; Attarbaschi, Andishe; Bertrand, Yves; Bradtke, Jutta; Buldini, Barbara; Burke, G A Amos; Cazzaniga, Giovanni; Gohring, Gudrun; De Groot-Kruseman, Hesta A; Haferlach, Claudia; Nigro, Luca Lo; Parihar, Mayur; Plesa, Adriana; Seaford, Emma; Sonneveld, Edwin; Strehl, Sabine; Van der Velden, Vincent H J; Rand, Vikki; Hunger, Stephen P; Harrison, Christine J; Bacon, Chris M; Van Delft, Frederik W; Loh, Mignon L; Moppett, John; Vormoor, Josef; Walker, Brian A; Moorman, Anthony V; Russell, Lisa J.

Haematologica ; 108(3): 717-731, 2023 03 01.

Article in English | MEDLINE | ID: mdl-35484682

8.

Loss of ALK hotspot mutations in relapsed neuroblastoma.

Allinson, Lisa M; Potts, Aaron; Goodman, Angharad; Bown, Nick; Bashton, Matthew; Thompson, Dean; Basta, Nermine O; Gabriel, Alem S; McCorkindale, Michael; Ng, Antony; McNally, Richard J Q; Tweddle, Deborah A.

Genes Chromosomes Cancer ; 61(12): 747-753, 2022 12.

Article in English | MEDLINE | ID: mdl-36029175

9.

Persistent SARS-CoV-2 infection in patients with secondary antibody deficiency: successful clearance following combination casirivimab and imdevimab (REGN-COV2) monoclonal antibody therapy.

Taha, Yusri; Wardle, Hayley; Evans, Adam B; Hunter, Ewan R; Marr, Helen; Osborne, Wendy; Bashton, Matthew; Smith, Darren; Burton-Fanning, Shirelle; Schmid, Matthias L; Duncan, Christopher J A.

Ann Clin Microbiol Antimicrob ; 20(1): 85, 2021 Dec 30.

Article in English | MEDLINE | ID: mdl-34969393

10.

Dynamic clonal progression in xenografts of acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21.

Sinclair, Paul B; Blair, Helen H; Ryan, Sarra L; Buechler, Lars; Cheng, Joanna; Clayton, Jake; Hanna, Rebecca; Hollern, Shaun; Hawking, Zoe; Bashton, Matthew; Schwab, Claire J; Jones, Lisa; Russell, Lisa J; Marr, Helen; Carey, Peter; Halsey, Christina; Heidenreich, Olaf; Moorman, Anthony V; Harrison, Christine J.

Haematologica ; 103(4): 634-644, 2018 04.

Article in English | MEDLINE | ID: mdl-29449437

11.

Critical roles of arginine in growth and biofilm development by Streptococcus gordonii.

Jakubovics, Nicholas S; Robinson, Jill C; Samarian, Derek S; Kolderman, Ethan; Yassin, Sufian A; Bettampadi, Deepti; Bashton, Matthew; Rickard, Alexander H.

Mol Microbiol ; 97(2): 281-300, 2015 Jul.

Article in English | MEDLINE | ID: mdl-25855127

12.

OMEinfo: global geographic metadata for -omics experiments.

Crown, Matthew; Bashton, Matthew.

Bioinform Adv ; 4(1): vbae025, 2024.

Article in English | MEDLINE | ID: mdl-38456126

13.

Environmental microbiome in the home and daycare settings during the COVID-19 pandemic, and potential risk of non-communicable disease in children.

McKay, Jill A; Crown, Matthew; Bashton, Matthew; Pearce, David; Entwistle, Jane A; Sangal, Vartul.

Environ Microbiol Rep ; 16(1): e13233, 2024 Feb.

Article in English | MEDLINE | ID: mdl-38217304

14.

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.

Hunt, Martin; Hinrichs, Angie S; Anderson, Daniel; Karim, Lily; Dearlove, Bethany L; Knaggs, Jeff; Constantinides, Bede; Fowler, Philip W; Rodger, Gillian; Street, Teresa; Lumley, Sheila; Webster, Hermione; Sanderson, Theo; Ruis, Christopher; de Maio, Nicola; Amenga-Etego, Lucas N; Amuzu, Dominic S Y; Avaro, Martin; Awandare, Gordon A; Ayivor-Djanie, Reuben; Bashton, Matthew; Batty, Elizabeth M; Bediako, Yaw; De Belder, Denise; Benedetti, Estefania; Bergthaler, Andreas; Boers, Stefan A; Campos, Josefina; Carr, Rosina Afua Ampomah; Cuba, Facundo; Dattero, Maria Elena; Dejnirattisai, Wanwisa; Dilthey, Alexander; Duedu, Kwabena Obeng; Endler, Lukas; Engelmann, Ilka; Francisco, Ngiambudulu M; Fuchs, Jonas; Gnimpieba, Etienne Z; Groc, Soraya; Gyamfi, Jones; Heemskerk, Dennis; Houwaart, Torsten; Hsiao, Nei-Yuan; Huska, Matthew; Hölzer, Martin; Iranzadeh, Arash; Jarva, Hanna; Jeewandara, Chandima; Jolly, Bani.

bioRxiv ; 2024 Apr 30.

Article in English | MEDLINE | ID: mdl-38746185

15.

Integrative genomic analysis of childhood acute lymphoblastic leukaemia lacking a genetic biomarker in the UKALL2003 clinical trial.

Schwab, Claire; Cranston, Ruth E; Ryan, Sarra L; Butler, Ellie; Winterman, Emily; Hawking, Zoe; Bashton, Matthew; Enshaei, Amir; Russell, Lisa J; Kingsbury, Zoya; Peden, John F; Barretta, Emilio; Murray, James; Gibson, Jude; Hinchliffe, Andrew C; Bain, Robert; Vora, Ajay; Bentley, David R; Ross, Mark T; Moorman, Anthony V; Harrison, Christine J.

Leukemia ; 37(3): 529-538, 2023 03.

Article in English | MEDLINE | ID: mdl-36550215

16.

Single-cell multi-omics identifies chronic inflammation as a driver of TP53-mutant leukemic evolution.

Rodriguez-Meira, Alba; Norfo, Ruggiero; Wen, Sean; Chédeville, Agathe L; Rahman, Haseeb; O'Sullivan, Jennifer; Wang, Guanlin; Louka, Eleni; Kretzschmar, Warren W; Paterson, Aimee; Brierley, Charlotte; Martin, Jean-Edouard; Demeule, Caroline; Bashton, Matthew; Sousos, Nikolaos; Moralli, Daniela; Subha Meem, Lamia; Carrelha, Joana; Wu, Bishan; Hamblin, Angela; Guermouche, Helene; Pasquier, Florence; Marzac, Christophe; Girodon, François; Vainchenker, William; Drummond, Mark; Harrison, Claire; Chapman, J Ross; Plo, Isabelle; Jacobsen, Sten Eirik W; Psaila, Bethan; Thongjuea, Supat; Antony-Debré, Iléana; Mead, Adam J.

Nat Genet ; 55(9): 1531-1541, 2023 09.

Article in English | MEDLINE | ID: mdl-37666991

17.

The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities.

Aggarwal, Dinesh; Myers, Richard; Hamilton, William L; Bharucha, Tehmina; Tumelty, Niamh M; Brown, Colin S; Meader, Emma J; Connor, Tom; Smith, Darren L; Bradley, Declan T; Robson, Samuel; Bashton, Matthew; Shallcross, Laura; Zambon, Maria; Goodfellow, Ian; Chand, Meera; O'Grady, Justin; Török, M Estée; Peacock, Sharon J; Page, Andrew J.

Lancet Microbe ; 3(2): e151-e158, 2022 02.

Article in English | MEDLINE | ID: mdl-34608459

18.

Emergence and maintenance of actionable genetic drivers at medulloblastoma relapse.

Richardson, Stacey; Hill, Rebecca M; Kui, Christopher; Lindsey, Janet C; Grabovksa, Yura; Keeling, Claire; Pease, Louise; Bashton, Matthew; Crosier, Stephen; Vinci, Maria; André, Nicolas; Figarella-Branger, Dominique; Hansford, Jordan R; Lastowska, Maria; Zakrzewski, Krzysztof; Jorgensen, Mette; Pickles, Jessica C; Taylor, Michael D; Pfister, Stefan M; Wharton, Stephen B; Pizer, Barry; Michalski, Antony; Joshi, Abhijit; Jacques, Thomas S; Hicks, Debbie; Schwalbe, Edward C; Williamson, Daniel; Ramaswamy, Vijay; Bailey, Simon; Clifford, Steven C.

Neuro Oncol ; 24(1): 153-165, 2022 01 05.

Article in English | MEDLINE | ID: mdl-34272868

19.

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.

Elife ; 112022 Sep 13.

Article in English | MEDLINE | ID: mdl-36098502

20.

Domain-ligand mapping for enzymes.

Bashton, Matthew; Thornton, Janet M.

J Mol Recognit ; 23(2): 194-208, 2010.

Article in English | MEDLINE | ID: mdl-19810051

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