Randomized controlled trial of molnupiravir SARS-CoV-2 viral and antibody response in at-risk adult outpatients

Standing, J., Buggiotti, L., Guerra-Assuncao, J., Woodall, M., Ellis, S., Agyeman, A., Miller, C., Okechukwu, M., Kirkpatrick, E., Jacobs, A., Williams, C., Roy, S., Martin-Bernal, L., Williams, R., Smith, C., Sanderson, T., Ashford, F., Emmanuel, B., Afzal, Z., Shields, A., Richter, A., Dorward, J., Gbinigie, O., Van Hecke, O., Lown, M., Francis, N., Jani, B., Richards, D., Rahman, N., Yu, L., Thomas, N., Hart, N., Evans, P., Andersson, M., Hayward, G., Hood, K., Nguyen-Van-Tam, J., Little, P., Hobbs, F., Khoo, S., Butler, C., Lowe, D., Breuer, J., PANORAMIC Virology Group, Allen, J., Bayzid, N., Brown, J., Burns, D., Hadley, E., Hatcher, J., McHugh, T., Thalasselis, C., Tomlinson, M., Yongblah, F.

Nature Communications, 15:1652

Divergent performance of vaccines in the UK autumn 2023 COVID-19 booster campaign

Shawe-Taylor, M., Greenwood, D., Hobbs, A., Dowgier, G., Penn, R., Sanderson, T., Stevenson-Leggett, P., Bazire, J., Harvey, R., Libri, V., Kassiotis, G., Gamblin, S., Lewis, N., Williams, B., Swanton, C., Gandhi, S., Carr, E., Wu, M., Bauer, D., Wall, E.

The Lancet, 403:1133--1136

A web tool for exploring the usage of medicines in hospitals in England

Sanderson, T.

Wellcome Open Research, 9:147

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

Turakhia, Y., Thornlow, B., Hinrichs, A., De Maio, N., Gozashti, L., Lanfear, R., Haussler, D., Corbett-Detig, R.

bioRxiv

Application of barcode sequencing to increase the throughput and complexity of Plasmodium falciparum genetic screening

Muhwezi, A., Ghorbal, M., Sanderson, T., Ivanova, M., Ansari, R., Harper, S., Wong, W., Schulte, R., Girling, G., Schwach, F., Bushell, E., Beaver, C., Billker, O., Rayner, J.

bioRxiv:2024--09

Real-time estimation of immunological responses against emerging SARS-CoV-2 variants in the UK: a mathematical modelling study

Russell, T., Townsley, H., Hellewell, J., Gahir, J., Shawe-Taylor, M., Greenwood, D., Hodgson, D., Hobbs, A., Dowgier, G., Penn, R., Sanderson, T., Stevenson-Leggett, P., Bazire, J., Harvey, R., Fowler, A., Miah, M., Smith, C., Miranda, M., Bawumia, P., Mears, H., Adams, L., Hatipoglu, E., O'Reilly, N., Warchal, S., Ambrose, K., Strange, A., Kelly, G., Kjar, S., Papineni, P., Corrah, T., Gilson, R., Libri, V., Kassiotis, G., Gamblin, S., Lewis, N., Williams, B., Swanton, C., Gandhi, S., Beale, R., Wu, M., Bauer, D., Carr, E., Wall, E., Kucharski, A.

The Lancet Infectious Diseases

A molnupiravir-associated mutational signature in global SARS-CoV-2 genomes

Sanderson, T., Hisner, R., Donovan-Banfield, I., Hartman, H., Løchen, A., Peacock, T., Ruis, C.

Nature, 623:594--600

ProteInfer, deep neural networks for protein functional inference

Sanderson, T., Bileschi, M., Belanger, D., Colwell, L.

Elife, 12:e80942

Regulators of male and female sexual development are critical for transmission of a malaria parasite

Russell, A., Sanderson, T., Bushell, E., Talman, A., Anar, B., Girling, G., Hunziker, M., Kent, R., Metcalf, T., Montandon, R., Pandey, V., Brett Roberts, A., Sayers, C., Schwach, F., Rayner, J., Voet, T., Modrzynska, K., Waters, A., Lawniczak, M., Billker, O.

Cell Host & Microbe, 31:1229-1240.e6

Treenome Browser: co-visualization of enormous phylogenies and millions of genomes

Kramer, A., Sanderson, T., Corbett-Detig, R.

Bioinformatics, 39:btac772

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Cotton, S., McHugh, M., Dewar, R., Haas, J., Templeton, K., Robson, S., Connor, T., Loman, N., Golubchik, T., Nunez, R., others

Journal of Hospital Infection, 135:28--36

Independent SARS-CoV-2 staff testing protected academic and health-care institutions in northwest London

Bailey, C., Sanderson, T., Townsley, H., Goldman, J., Black, J., Young, G., Goldstone, R., Fowler, A., Ward, S., Jackson, D., Cubitt, L., Dearing, V., O'Neil, O., Crawford, M., Snell, D., Finadis, M., Edwards, A., Perez-Lloret, J., Gahir, J., Carr, E., Riddell, A., Aitken, J., Ambrose, K., Sawyer, C., O'Reilly, N., Caidan, S., Wu, M., Walker, P., Hindmarsh, S., Howell, M., Jordan, A., Fleming, J., Houlihan, C., Nastouli, E., Moores, R., Hsu, D., Papineni, P., Corrah, T., Gilson, R., MacRae, J., Hubank, M., Van As, N., Turajlic, S., Beale, R., Levi, M., Barrell, S., Williams, B., Gamblin, S., Nicod, J., Gandhi, S., Bauer, D., Wall, E., Swanton, C.

The Lancet

Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA. 1 and BA. 2

Pastorio, C., Zech, F., Noettger, S., Jung, C., Jacob, T., Sanderson, T., Sparrer, K., Kirchhoff, F.

Cell host & microbe, 30:1255--1268

Using deep learning to annotate the protein universe

Bileschi, M., Belanger, D., Bryant, D., Sanderson, T., Carter, B., Sculley, D., DePristo, M., Colwell, L.

Nature Biotechnology, 40:932--937

Taxonium, a web-based tool for exploring large phylogenetic trees

Sanderson, T.

eLife, 11:e82392

The origins and molecular evolution of SARS-CoV-2 lineage B. 1.1. 7 in the UK

Hill, V., Du Plessis, L., Peacock, T., Aggarwal, D., Colquhoun, R., Carabelli, A., Ellaby, N., Gallagher, E., Groves, N., Jackson, B., McCrone, J., O’Toole, Á., Price, A., Sanderson, T., Scher, E., Southgate, J., Volz, E., The COVID-19 genomics UK (COG-UK) consortium, Barclay, W., Barrett, J., Chand, M., Connor, T., Goodfellow, I., Gupta, R., Harrison, E., Loman, N., Myers, R., Robertson, D., Pybus, O., Rambaut, A.

Virus Evolution, 8:veac080

Barcoding genetically distinct Plasmodium falciparum strains for comparative assessment of fitness and antimalarial drug resistance

Carrasquilla, M., Drammeh, N., Rawat, M., Sanderson, T., Zenonos, Z., Rayner, J., Lee, M.

Mbio, 13:e00937--22

Emergence of new subgenomic mRNAs in SARS-CoV-2

Mears, H., Young, G., Sanderson, T., Harvey, R., Crawford, M., Snell, D., Fowler, A., Hussain, S., Nicod, J., Peacock, T., Emmott, E., Finsterbusch, K., Luptak, J., Wall, E., Williams, B., Gandhi, S., Swanton, C., Bauer, D.

BioRxiv:2022--04

CRISPR/Cas9 and genetic screens in malaria parasites: small genomes, big impact

Ishizaki, T., Hernandez, S., Paoletta, M., Sanderson, T., Bushell, E.

Biochemical Society Transactions, 50:1069--1079

Genomic reconstruction of the SARS-CoV-2 epidemic in England

Vöhringer, H., Sanderson, T., Sinnott, M., Maio, N., Nguyen, T., Goater, R., Schwach, F., Harrison, I., Hellewell, J., Ariani, C., Gonçalves, S., Jackson, D., Johnston, I., Jung, A., Saint, C., Sillitoe, J., Suciu, M., Goldman, N., Panovska-Griffiths, J., The Wellcome Sanger Institute Covid-19 Surveillance Team, The COVID-19 Genomics UK (COG-UK) Consortium, Birney, E., Volz, E., Funk, S., Kwiatkowski, D., Chand, M., Martincorena, I., Barrett, J., Gerstung, M.

Nature, 600:506--511

Using Plasmodium knowlesi as a model for screening Plasmodium vivax blood-stage malaria vaccine targets reveals new candidates

Ndegwa, D., Hostetler, J., Marin-Menendez, A., Sanderson, T., Mwikali, K., Verzier, L., Coyle, R., Adjalley, S., Rayner, J.

PLoS Pathogens, 17:e1008864

Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections

Hellewell, J., Russell, T., The SAFER Investigators and Field Study Team, The Crick COVID-19 Consortium, CMMID COVID-19 working group, Beale, R., Kelly, G., Houlihan, C., Nastouli, E., Kucharski, A.

BMC medicine, 19:1--10

The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

de Silva, T., Liu, G., Lindsey, B., Dong, D., Shah, D., Mentzer, A., Angyal, A., Brown, R., Parker, M., Yin, Z., Yao, X., Turtle, L., Dunachie, S., Maini, M., Ogg, G., Knight, J., Peng, Y., Rowland-Jones, S., Dong, T.

Iscience, 24

An apicoplast-resident folate transporter is essential for sporogony of malaria parasites

Korbmacher, F., Drepper, B., Sanderson, T., Martin, P., Stach, T., Maier, A., Matuschewski, K., Matz, J.

Cellular microbiology, 23:e13266

Clinical outcomes of COVID-19 in long-term care facilities for people with epilepsy

Balestrini, S., Koepp, M., Gandhi, S., Rickman, H., Shin, G., Houlihan, C., Anders-Cannon, J., Silvennoinen, K., Xiao, F., Zagaglia, S., Hudgell, K., Ziomek, M., Haimes, P., Sampson, A., Parker, A., for The Meath, Nastouli, E., Swanton, C., for the CCC, Sander, J., Sisodiya, S., for the ASAP Consortium

Epilepsy & Behavior, 115:107602

Variation at Spike position 142 in SARS-CoV-2 Delta genomes is a technical artifact caused by dropout of a sequencing amplicon

Sanderson, T., Barrett, J.

Wellcome Open Research

Chronumental: time tree estimation from very large phylogenies

Sanderson, T.

bioRxiv:2021--10

Mixology: a tool for calculating required masses and volumes for laboratory solutions

Sanderson, T.

Systematic Errors Associated with Some Implementations of ARTIC V4 and a Fast Workflow to Prescreen Samples for New Problematic Sites

Sanderson, T., De Maio, N., Hinrichs, A., Schneider, A., Walker, C., Goldman, N., Turakhia, Y., Lanfear, R., Corbett-Detig, R.

Virological.org

Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys

Aunin, E., Böhme, U., Sanderson, T., Simons, N., Goldberg, T., Ting, N., Chapman, C., Newbold, C., Berriman, M., Reid, A.

PLoS pathogens, 16:e1008717

Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers

Houlihan, C., Vora, N., Byrne, T., Lewer, D., Kelly, G., Heaney, J., Gandhi, S., Spyer, M., Beale, R., Cherepanov, P., others

The Lancet, 396:e6--e7

Scalable and Robust SARS-CoV-2 Testing in an Academic Center

Consortium, C.

Nature biotechnology, 38:927-931

Critiquing protein family classification models using sufficient input subsets

Carter, B., Bileschi, M., Smith, J., Sanderson, T., Bryant, D., Belanger, D., Colwell, L.

Journal of Computational Biology, 27:1219--1231

Defining multiplicity of vector uptake in transfected Plasmodium parasites

Carrasquilla, M., Adjalley, S., Sanderson, T., Marin-Menendez, A., Coyle, R., Montandon, R., Rayner, J., Pance, A., Lee, M.

Scientific Reports, 10:10894

Standard operating procedures for SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay

Buck, M., Poirier, E., Cardoso, A., Frederico, B., Canton, J., Barrell, S., Beale, R., Byrne, R., Caidan, S., Crawford, M., others

medRxiv:2020--06

Landscape of the Plasmodium interactome reveals both conserved and species-specific functionality

Hillier, C., Pardo, M., Yu, L., Bushell, E., Sanderson, T., Metcalf, T., Herd, C., Anar, B., Rayner, J., Billker, O., Choudhary, J.

Cell reports, 28:1635--1647

Genome-scale identification of essential metabolic processes for targeting the Plasmodium liver stage

Stanway, R., Bushell, E., Chiappino-Pepe, A., Roques, M., Sanderson, T., Franke-Fayard, B., Caldelari, R., Golomingi, M., Nyonda, M., Pandey, V., Schwach, F., Chevalley, S., Ramesar, J., Metcalf, T., Herd, C., Burda, P., Rayner, J., Soldati-Favre, D., Janse, C., Hatzimanikatis, V., Billker, O., Heussler, V.

Cell, 179:1112--1128

Plasmodium knowlesi as a model system for characterising Plasmodium vivax drug resistance candidate genes

Verzier, L., Coyle, R., Singh, S., Sanderson*, T., Rayner*, J.

PLoS neglected tropical diseases, 13:e0007470

Quantitation of vector uptake reveals non-Poissonian transfection dynamics in Plasmodium falciparum

Carrasquilla, M., Sanderson, T., Montandon, R., Rayner, J., Pance, A., Lee, M.

BioRxiv:681981

Synergistic malaria vaccine combinations identified by systematic antigen screening

Bustamante, L., Powell, G., Lin, Y., Macklin, M., Cross, N., Kemp, A., Cawkill, P., Sanderson, T., Crosnier, C., Muller-Sienerth, N., Doumbo, O., Traore, B., Crompton, P., Cicuta, P., Tran, T., Wright, G., Rayner, J.

Proceedings of the National Academy of Sciences, 114:12045--12050

Functional profiling of a Plasmodium genome reveals an abundance of essential genes

Bushell, E., Gomes, A., Sanderson, T., Anar, B., Girling, G., Herd, C., Metcalf, T., Modrzynska, K., Schwach, F., Martin, R., Mather, M., McFadden, G., Parts, L., Rutledge, G., Vaidya, A., Wengelnik, K., Rayner, J., Billker, O.

Cell, 170:260--272

PhenoPlasm: a database of disruption phenotypes for malaria parasite genes

Sanderson, T., Rayner, J.

Wellcome Open Research, 2:45

PlasmoTron: an open-source platform for automated culture of malaria parasites

Sanderson, T., Rayner, J.

BioRxiv:241596

Open hardware for random access plate storage

Sanderson, T.

Authorea Preprints

Plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism

Pinheiro, M., Ahmed, M., Millar, S., Sanderson, T., Otto, T., Lu, W., Krishna, S., Rayner, J., Cox-Singh, J.

Plos one, 10:e0121303

How synthetic biology will reconsider natural bioluminescence and its applications

Reeve, B., Sanderson, T., Ellis, T., Freemont, P.

Bioluminescence: Fundamentals and Applications in Biotechnology-Volume 2:3--30