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.
(2022). Treenome Browser: co-visualization of enormous phylogenies and millions of genomes. bioRxiv.
(2022). Regulators of male and female sexual development critical for transmission of a malaria parasite. Cell, Host and Microbe (in Press).
(2022). Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA. 1 and BA. 2. Cell Host & Microbe.
(2022). The origins and molecular evolution of SARS-CoV-2 lineage B. 1.1. 7 in the UK. Virus Evolution.
(2022). Using deep learning to annotate the protein universe. Nature Biotechnology.
(2022). Emergence of new subgenomic mRNAs in SARS-CoV-2. bioRxiv.
(2022). CRISPR/Cas9 and genetic screens in malaria parasites: small genomes, big impact. Biochemical Society Transactions.
(2022). Barcoding genetically distinct Plasmodium falciparum strains for comparative assessment of fitness and antimalarial drug resistance. mBio.
(2021). Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature.
(2021). ProteInfer: deep networks for protein functional inference. bioRxiv.
(2021). Using Plasmodium knowlesi as a model for screening Plasmodium vivax blood-stage malaria vaccine targets reveals new candidates. PLoS Pathogens.
(2021). Systematic Errors Associated with Some Implementations of ARTIC V4 and a Fast Workflow to Prescreen Samples for New Problematic Sites. Virological.org.
(2021). Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections. BMC medicine.
(2021). Clinical outcomes of COVID-19 in long-term care facilities for people with epilepsy. Epilepsy & Behavior.
(2021). An apicoplast-resident folate transporter is essential for sporogony of malaria parasites. Cellular Microbiology.
(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.
(2020). Using Plasmodium knowlesi as a model for screening Plasmodium vivax blood-stage malaria vaccine targets reveals new candidates. BioRxiv.
(2020). Standard operating procedures for SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay. medRxiv.
(2020). Scalable and Robust SARS-CoV-2 Testing in an Academic Center. Nature Biotechnology.
(2020). Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers. The Lancet.
(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.
(2020). Defining multiplicity of vector uptake in transfected Plasmodium parasites. Scientific reports.
(2020). Critiquing protein family classification models using sufficient input subsets. Journal of Computational Biology.
(2019). Using deep learning to annotate the protein universe. Nature Biotechnology.
(2019). Quantitation of vector uptake reveals non-Poissonian transfection dynamics in Plasmodium falciparum. bioRxiv.
(2019). Plasmodium knowlesi as a model system for characterising Plasmodium vivax drug resistance candidate genes. PLoS neglected tropical diseases.
(2019). Landscape of the Plasmodium interactome reveals both conserved and species-specific functionality. Cell reports.
(2019). Genome-scale identification of essential metabolic processes for targeting the Plasmodium liver stage. Cell.
(2017). PhenoPlasm: a database of disruption phenotypes for malaria parasite genes. In Wellcome Open Research.
(2017). Functional profiling of a Plasmodium genome reveals an abundance of essential genes. In Cell.
(2017). Synergistic malaria vaccine combinations identified by systematic antigen screening. Proceedings of the National Academy of Sciences.
(2017). PhenoPlasm: a database of disruption phenotypes for malaria parasite genes. Wellcome open research.
(2017). Open hardware for random access plate storage. Authorea Preprints.
(2017). Functional profiling of a Plasmodium genome reveals an abundance of essential genes. Cell.
(2015). Plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism. PLOS one.
(2014). How synthetic biology will reconsider natural bioluminescence and its applications. Bioluminescence: Fundamentals and Applications in Biotechnology-Volume 2.