Search Results - "Nicholls, Samuel"

Ultra-deep, long-read nanopore sequencing of mock microbial community standards by Nicholls, Samuel M, Quick, Joshua C, Tang, Shuiquan, Loman, Nicholas J

“…Long sequencing reads are information-rich: aiding de novo assembly and reference mapping, and consequently have great potential for the study of microbial…”
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SARS-CoV-2 within-host diversity and transmission by Lythgoe, Katrina A, Hall, Matthew, Ferretti, Luca, de Cesare, Mariateresa, MacIntyre-Cockett, George, Trebes, Amy, Andersson, Monique, Otecko, Newton, Wise, Emma L, Moore, Nathan, Lynch, Jessica, Kidd, Stephen, Cortes, Nicholas, Mori, Matilde, Williams, Rebecca, Vernet, Gabrielle, Justice, Anita, Green, Angie, Nicholls, Samuel M, Ansari, M Azim, Abeler-Dörner, Lucie, Moore, Catrin E, Peto, Timothy E A, Eyre, David W, Shaw, Robert, Simmonds, Peter, Buck, David, Todd, John A, Connor, Thomas R, Ashraf, Shirin, da Silva Filipe, Ana, Shepherd, James, Thomson, Emma C, Bonsall, David, Fraser, Christophe, Golubchik, Tanya

“…Extensive global sampling and sequencing of the pandemic virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have enabled researchers to monitor…”
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Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic by Jackson, Ben, Boni, Maciej F., Bull, Matthew J., Colleran, Amy, Colquhoun, Rachel M., Darby, Alistair C., Haldenby, Sam, Hill, Verity, Lucaci, Anita, McCrone, John T., Nicholls, Samuel M., O’Toole, Áine, Pacchiarini, Nicole, Poplawski, Radoslaw, Scher, Emily, Todd, Flora, Webster, Hermione J., Whitehead, Mark, Wierzbicki, Claudia, Loman, Nicholas J., Connor, Thomas R., Robertson, David L., Pybus, Oliver G., Rambaut, Andrew

“…We present evidence for multiple independent origins of recombinant SARS-CoV-2 viruses sampled from late 2020 and early 2021 in the United Kingdom. Their…”
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Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK by du Plessis, Louis, McCrone, John T, Zarebski, Alexander E, Hill, Verity, Ruis, Christopher, Gutierrez, Bernardo, Raghwani, Jayna, Ashworth, Jordan, Colquhoun, Rachel, Connor, Thomas R, Faria, Nuno R, Jackson, Ben, Loman, Nicholas J, O'Toole, Áine, Nicholls, Samuel M, Parag, Kris V, Scher, Emily, Vasylyeva, Tetyana I, Volz, Erik M, Watts, Alexander, Bogoch, Isaac I, Khan, Kamran, Aanensen, David M, Kraemer, Moritz U G, Rambaut, Andrew, Pybus, Oliver G

“…The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined…”
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On the complexity of haplotyping a microbial community by Nicholls, Samuel M, Aubrey, Wayne, De Grave, Kurt, Schietgat, Leander, Creevey, Christopher J, Clare, Amanda

“…Abstract Motivation Population-level genetic variation enables competitiveness and niche specialization in microbial communities. Despite the difficulty in…”
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CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance by Nicholls, Samuel M, Poplawski, Radoslaw, Bull, Matthew J, Underwood, Anthony, Chapman, Michael, Abu-Dahab, Khalil, Taylor, Ben, Colquhoun, Rachel M, Rowe, Will P M, Jackson, Ben, Hill, Verity, O'Toole, Áine, Rey, Sara, Southgate, Joel, Amato, Roberto, Livett, Rich, Gonçalves, Sónia, Harrison, Ewan M, Peacock, Sharon J, Aanensen, David M, Rambaut, Andrew, Connor, Thomas R, Loman, Nicholas J

“…In response to the ongoing SARS-CoV-2 pandemic in the UK, the COVID-19 Genomics UK (COG-UK) consortium was formed to rapidly sequence SARS-CoV-2 genomes as…”
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Goldilocks: a tool for identifying genomic regions that are 'just right' by Nicholls, Samuel M, Clare, Amanda, Randall, Joshua C

“…: We present Goldilocks: a Python package providing functionality for collecting summary statistics, identifying shifts in variation, discovering outlier…”
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A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK by Colquhoun, Rachel, O’Toole, Áine, Hill, Verity, McCrone, J T, Yu, Xiaoyu, Nicholls, Samuel M, Poplawski, Radoslaw, Whalley, Thomas, Groves, Natalie, Ellaby, Nicholas, Loman, Nick, Connor, Tom, Rambaut, Andrew

“…Abstract In response to the escalating SARS-CoV-2 pandemic, in March 2020 the COVID-19 Genomics UK (COG-UK) consortium was established to enable national-scale…”
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Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package by Griffiths, Emma J, Timme, Ruth E, Mendes, Catarina Inês, Page, Andrew J, Alikhan, Nabil-Fareed, Fornika, Dan, Maguire, Finlay, Campos, Josefina, Park, Daniel, Olawoye, Idowu B, Oluniyi, Paul E, Anderson, Dominique, Christoffels, Alan, da Silva, Anders Gonçalves, Cameron, Rhiannon, Dooley, Damion, Katz, Lee S, Black, Allison, Karsch-Mizrachi, Ilene, Barrett, Tanya, Johnston, Anjanette, Connor, Thomas R, Nicholls, Samuel M, Witney, Adam A, Tyson, Gregory H, Tausch, Simon H, Raphenya, Amogelang R, Alcock, Brian, Aanensen, David M, Hodcroft, Emma, Hsiao, William W L, Vasconcelos, Ana Tereza R, MacCannell, Duncan R

“…Abstract Background The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to…”
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Genomics-informed outbreak investigations of SARS-CoV-2 using civet by O'Toole, Áine, Hill, Verity, Jackson, Ben, Dewar, Rebecca, Sahadeo, Nikita, Colquhoun, Rachel, Rooke, Stefan, McCrone, J T, Duggan, Kate, McHugh, Martin P, Nicholls, Samuel M, Poplawski, Radoslaw, Aanensen, David, Holden, Matt, Connor, Tom, Loman, Nick, Goodfellow, Ian, Carrington, Christine V F, Templeton, Kate, Rambaut, Andrew

“…The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 13 million sequences shared publicly at the time of writing…”
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Renewable and Responsive Cross-Linked Systems Based on Polyurethane Backbones from Clickable Biobased Bismaleimide Architecture by Tremblay-Parrado, Khantutta-Kim, Bordin, Clément, Nicholls, Samuel, Heinrich, Benoit, Donnio, Betrand, Avérous, Luc

“…A new biobased bismaleimide architecture from methyl oleate, consisting of an aliphatic branched structure, denoted methyl oleate bismaleimide (MO BMI), was…”
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Recurrent SARS-CoV-2 mutations in immunodeficient patients by Wilkinson, S A J, Richter, Alex, Casey, Anna, Osman, Husam, Mirza, Jeremy D, Stockton, Joanne, Quick, Josh, Ratcliffe, Liz, Sparks, Natalie, Cumley, Nicola, Poplawski, Radoslaw, Nicholls, Samuel N, Kele, Beatrix, Harris, Kathryn, Peacock, Thomas P, Loman, Nicholas J

“…Abstract Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunodeficient patients are an important source of variation for…”
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Computational recovery of enzyme haplotypes from a metagenome by Nicholls, Samuel

“…Population-level diversity of microbial communities (microbiomes) represent a biotechnological resource for biomining, biorefining and synthetic biology; but…”
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Genomics-informed outbreak investigations of SARS-CoV-2 using civet by Áine O’Toole, Verity Hill, Ben Jackson, Rebecca Dewar, Nikita Sahadeo, Rachel Colquhoun, Stefan Rooke, J. T. McCrone, Kate Duggan, Martin P. McHugh, Samuel M. Nicholls, Radoslaw Poplawski, David Aanensen, Matt Holden, Tom Connor, Nick Loman, Ian Goodfellow, Christine V. F. Carrington, Kate Templeton, Andrew Rambaut

“…The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 13 million sequences shared publicly at the time of writing…”
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Routes of War: The World of Movement in the Confederate South by Nicholls, Samuel A.

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NO. VI. LATHE-BAND HOOK by Nicholls, Samuel

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PAPERS IN MANUFACTURES by JONES, EDWIN, SCORRAR, THOMAS, Nicholls, Samuel, Swinscow, Thomas, Morris, William

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PAPERS IN AGRICULTURE by LEE, H. P., NICHOLLS, SAMUEL, JOHNES, THOMAS, CURWEN, J. C., PETRE, J. BERNEY, Lloyd, Thomas, Cooper, T. H., TOWERS, RICHARD, BALLS, THOMAS, ASTLEY, J. H., BAKER, JOHN, JEFFERY, WILLIAM, HUTTON, JOSEPH

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