Publications

Publications as a member of the COG-UK Consortium (main roles: sample prioritisation and quality-control) are excluded below, but can be found here.
Theo Sanderson, Maxwell Bileschi, David Belanger, Lucy Colwell (2023). ProteInfer: deep networks for protein functional inference. eLife.
Theo Sanderson, Ryan Hisner, I'ah Donovan-Banfield, Thomas Peacock, Christopher Ruis (2023). Identification of a molnupiravir-associated mutational signature in SARS-CoV-2 sequencing databases. medRxiv.
Andrew JC Russell, Theo Sanderson, Ellen Bushell, Arthur M Talman, Burcu Anar, Gareth Girling, Mirjam Hunziker, Robyn S Kent, Tom Metcalf, Ruddy Montandon, others (2023). Regulators of male and female sexual development critical for transmission of a malaria parasite. Cell Host & Microbe.
Theo Sanderson (2022). Taxonium, a web-based tool for exploring large phylogenetic trees. eLife.
Alexander M Kramer, Theo Sanderson, Russell Corbett-Detig (2022). Treenome Browser: co-visualization of enormous phylogenies and millions of genomes. Bioinformatics.
Chiara Pastorio, Fabian Zech, Sabrina Noettger, Christoph Jung, Timo Jacob, Theo Sanderson, Konstantin MJ Sparrer, Frank Kirchhoff (2022). Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA. 1 and BA. 2. Cell Host & Microbe.
Verity Hill, Louis Du Plessis, Thomas P Peacock, Dinesh Aggarwal, Rachel Colquhoun, Alesandro M Carabelli, Nicholas Ellaby, Eileen Gallagher, Natalie Groves, Ben Jackson, J T McCrone, Áine O’Toole, Anna Price, Theo Sanderson, Emily Scher, Joel Southgate, Erik Volz, The COVID-19 Genomics UK (COG-UK) Consortium, Wendy S Barclay, Jeffrey C Barrett, Meera Chand, Thomas Connor, Ian Goodfellow, Ravindra K Gupta, Ewan M Harrison, Nicholas Loman, Richard Myers, David L Robertson, Oliver G Pybus, Andrew Rambaut (2022). The origins and molecular evolution of SARS-CoV-2 lineage B. 1.1. 7 in the UK. Virus Evolution.
Maxwell L Bileschi, David Belanger, Drew H Bryant, Theo Sanderson, Brandon Carter, D Sculley, Alex Bateman, Mark A DePristo, Lucy J Colwell (2022). Using deep learning to annotate the protein universe. Nature Biotechnology.
Harriet V Mears, George R Young, Theo Sanderson, Ruth Harvey, Margaret Crawford, Daniel M Snell, Ashley S Fowler, Saira Hussain, Jerome Nicod, Thomas P Peacock, others (2022). Emergence of new subgenomic mRNAs in SARS-CoV-2. bioRxiv.
Takahiro Ishizaki, Sophia Hernandez, Martina S Paoletta, Theo Sanderson, Ellen SC Bushell (2022). CRISPR/Cas9 and genetic screens in malaria parasites: small genomes, big impact. Biochemical Society Transactions.
Manuela Carrasquilla, Ndey Fatou Drammeh, Mukul Rawat, Theo Sanderson, Zenon Zenonos, Julian C Rayner, Marcus Lee (2022). Barcoding genetically distinct Plasmodium falciparum strains for comparative assessment of fitness and antimalarial drug resistance. mBio.
Harald S Vohringer, Theo Sanderson, Matthew Sinnott, Nicola De Maio, Thuy Nguyen, Richard Goater, Frank Schwach, Ian Harrison, Joel Hellewell, Cristina Ariani, others (2021). Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature.
Theo Sanderson (2021). Mixology: a tool for calculating required masses and volumes for laboratory solutions. Wellcome Open Research.
Theo Sanderson, Jeffrey C Barrett (2021). Variation at Spike position 142 in SARS-CoV-2 Delta genomes is a technical artifact caused by dropout of a sequencing amplicon. medRxiv.
Duncan N Ndegwa, Prasun Kundu, Jessica B Hostetler, Alejandro Marin-Menendez, Theo Sanderson, Kioko Mwikali, Lisa H Verzier, Rachael Coyle, Sophie Adjalley, Julian C Rayner (2021). Using Plasmodium knowlesi as a model for screening Plasmodium vivax blood-stage malaria vaccine targets reveals new candidates. PLoS Pathogens.
Theo Sanderson, Nicola De Maio, Angie S. Hinrichs, Adriano de Bernardi Schneider, Conor Walker, Nick Goldman, Yatish Turakhia, Robert Lanfear, Russell Corbett-Detig (2021). Systematic Errors Associated with Some Implementations of ARTIC V4 and a Fast Workflow to Prescreen Samples for New Problematic Sites. Virological.org.
Joel Hellewell, Timothy W Russell, Rupert Beale, Gavin Kelly, Catherine Houlihan, Eleni Nastouli, [..] (as member of Crick Covid Consortium) (2021). Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections. BMC medicine.
Simona Balestrini, Matthias J Koepp, Sonia Gandhi, Hannah M Rickman, Gee Yen Shin, Catherine F Houlihan, Jonny Anders-Cannon, Katri Silvennoinen, Fenglai Xiao, Sara Zagaglia, [..] (as member of Crick Covid Consortium) (2021). Clinical outcomes of COVID-19 in long-term care facilities for people with epilepsy. Epilepsy & Behavior.
Theo Sanderson (2021). Chronumental: time tree estimation from very large phylogenies. bioRxiv.
Francois Korbmacher, Benjamin Drepper, Theo Sanderson, Peer Martin, Thomas Stach, Alexander G Maier, Kai Matuschewski, Joachim M Matz (2021). An apicoplast-resident folate transporter is essential for sporogony of malaria parasites. Cellular Microbiology.
Eerik Aunin, Ulrike Böhme, Theo Sanderson, Noah D. Simons, Tony L. Goldberg, Nelson Ting, Colin A. Chapman, Chris I. Newbold, Matthew Berriman, Adam J. Reid (2020). Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys. PLoS Pathogens.
Duncan N Ndegwa, Jessica B Hostetler, Alejandro Marin-Menendez, Theo Sanderson, Kioko Mwikali, Lisa H Verzier, Rachael Coyle, Sophie Adjalley, Julian C Rayner (2020). Using Plasmodium knowlesi as a model for screening Plasmodium vivax blood-stage malaria vaccine targets reveals new candidates. BioRxiv.
Michael D Buck, Enzo Z Poirier, Ana Cardoso, Bruno Frederico, Johnathan Canton, Sam Barrell, Rupert Beale, Richard Byrne, Simon Caidan, Margaret Crawford, others (2020). Standard operating procedures for SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay. medRxiv.
Crick Covid Consortium (2020). Scalable and Robust SARS-CoV-2 Testing in an Academic Center. Nature Biotechnology.
Catherine F Houlihan, Nina Vora, Thomas Byrne, Dan Lewer, Gavin Kelly, Judith Heaney, Sonia Gandhi, Moira J Spyer, Rupert Beale, Peter Cherepanov, others (2020). Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers. The Lancet.
Eerik Aunin, Ulrike Böhme, Theo Sanderson, Noah D Simons, Tony L Goldberg, Nelson Ting, Colin A Chapman, Chris I Newbold, Matthew Berriman, Adam J Reid (2020). Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys. PLoS pathogens.
Manuela Carrasquilla, Sophie Adjalley, Theo Sanderson, Alejandro Marin-Menendez, Rachael Coyle, Ruddy Montandon, Julian C Rayner, Alena Pance, Marcus CS Lee (2020). Defining multiplicity of vector uptake in transfected Plasmodium parasites. Scientific reports.
Brandon Carter, Maxwell Bileschi, Jamie Smith, Theo Sanderson, Drew Bryant, David Belanger, Lucy J Colwell (2020). Critiquing protein family classification models using sufficient input subsets. Journal of Computational Biology.
Maxwell L Bileschi, David Belanger, Drew H Bryant, Theo Sanderson, Brandon Carter, D Sculley, Mark A DePristo, Lucy J Colwell (2019). Using deep learning to annotate the protein universe. Nature Biotechnology.
Manuela Carrasquilla, Theo Sanderson, Ruddy Montandon, Julian Rayner, Alena Pance, Marcus Lee (2019). Quantitation of vector uptake reveals non-Poissonian transfection dynamics in Plasmodium falciparum. bioRxiv.
Lisa H Verzier, Rachael Coyle, Shivani Singh, Theo Sanderson, Julian C Rayner (2019). Plasmodium knowlesi as a model system for characterising Plasmodium vivax drug resistance candidate genes. PLoS neglected tropical diseases.
Charles Hillier, Mercedes Pardo, Lu Yu, Ellen Bushell, Theo Sanderson, Tom Metcalf, Colin Herd, Burcu Anar, Julian C Rayner, Oliver Billker, others (2019). Landscape of the Plasmodium interactome reveals both conserved and species-specific functionality. Cell reports.
Rebecca R Stanway*, Ellen Bushell, Anush Chiappino-Pepe*, Magali Roques*, Theo Sanderson, Blandine Franke-Fayard, Reto Caldelari, Murielle Golomingi, Mary Nyonda, Vikash Pandey, others (2019). Genome-scale identification of essential metabolic processes for targeting the Plasmodium liver stage. Cell.
Theo Sanderson, Julian C Rayner (2018). PlasmoTron: an open-source platform for automated culture of malaria parasites. BioRxiv.
Theo Sanderson, Julian C. Rayner (2017). PhenoPlasm: a database of disruption phenotypes for malaria parasite genes. In Wellcome Open Research.
Ellen Bushell, Ana Rita Gomes, Theo Sanderson, Burcu Anar, Gareth Girling, Colin Herd, Tom Metcalf, Katarzyna Modrzynska, Frank Schwach, Rowena E. Martin, Michael W. Mather, Geoffrey I. McFadden, Leopold Parts, Gavin G. Rutledge, Akhil B. Vaidya, Kai Wengelnik, Julian C. Rayner, Oliver Billker (2017). Functional profiling of a Plasmodium genome reveals an abundance of essential genes. In Cell.
Leyla Y Bustamante, Gareth T Powell, Yen-Chun Lin, Michael D Macklin, Nadia Cross, Alison Kemp, Paula Cawkill, Theo Sanderson, Cecile Crosnier, Nicole Muller-Sienerth, others (2017). Synergistic malaria vaccine combinations identified by systematic antigen screening. Proceedings of the National Academy of Sciences.
Theo Sanderson, Julian C Rayner (2017). PlasmoTron: an open-source platform for automated culture of malaria parasites. BioRxiv.
Theo Sanderson, Julian C Rayner (2017). PhenoPlasm: a database of disruption phenotypes for malaria parasite genes. Wellcome open research.
Theo Sanderson (2017). Open hardware for random access plate storage. Authorea Preprints.
Ellen Bushell, Ana Rita Gomes, Theo Sanderson, Burcu Anar, Gareth Girling, Colin Herd, Tom Metcalf, Katarzyna Modrzynska, Frank Schwach, Rowena E Martin, others (2017). Functional profiling of a Plasmodium genome reveals an abundance of essential genes. Cell.
Miguel M Pinheiro, Md Atique Ahmed, Scott B Millar, Theo Sanderson, Thomas D Otto, Woon Chan Lu, Sanjeev Krishna, Julian C Rayner, Janet Cox-Singh (2015). Plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism. PLOS one.
Theo Sanderson (2015). Investigating the Plasmodium invadome with high-throughput reverse genetics.
Benjamin Reeve, Theo Sanderson, Tom Ellis, Paul Freemont (2014). How synthetic biology will reconsider natural bioluminescence and its applications. Bioluminescence: Fundamentals and Applications in Biotechnology-Volume 2.