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A molnupiravir-associated mutational signature in global SARS-CoV-2 genomes
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SVG export from DeckGL
Taxonium, my tool for exploring large phylogenetic trees, uses a few tricks to be fast even when exploring trees of 15 million sequences.
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Independent SARS-CoV-2 staff testing protected academic and health-care institutions in northwest London
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LabGPT
Yesterday, GPT-4 was released.
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ProteInfer: deep networks for protein functional inference
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Regulators of male and female sexual development critical for transmission of a malaria parasite
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Taxonium, a web-based tool for exploring large phylogenetic trees
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Treenome Browser: co-visualization of enormous phylogenies and millions of genomes
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Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA. 1 and BA. 2
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Identifying malaria phenotype papers with GPT-3
Visit papers.phenoplasm.org Some years ago I launched PhenoPlasm which aims to catalogue all reported phenotypes in Plasmodium in a systematic machine- (and human-) readable format.
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The origins and molecular evolution of SARS-CoV-2 lineage B. 1.1. 7 in the UK
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Using deep learning to annotate the protein universe
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Emergence of new subgenomic mRNAs in SARS-CoV-2
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CRISPR/Cas9 and genetic screens in malaria parasites: small genomes, big impact
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Barcoding genetically distinct Plasmodium falciparum strains for comparative assessment of fitness and antimalarial drug resistance
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Genomic reconstruction of the SARS-CoV-2 epidemic in England
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Two tips for experimental design of barseq experiments
In my time I’ve done various bits of analysis for barcode-sequencing (barseq) experiments (in Plasmodium), and sometimes have chats with people who are starting for the first time.
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FlowAlign
Python package / CLI tool for easy alignment of viral sequences to reference (using minimap2 under the hood)
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LFD, PCR, PPV, TLA
People are very interested in the positive predictive value of lateral flow tests.
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Mixology: a tool for calculating required masses and volumes for laboratory solutions
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Five lines of R
Somebody on Twitter asked me whether B.1.1.7 data from Florida was still compatible with a logistic increase.
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Turning a graph back into data
Summary: The ONS Coronavirus Infection Survey is an immensely valuable scientific project measuring prevalence of coronavirus in the community.
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Looking again at Maccabi data for efficacy after initial Pfizer dose
Update(2021-02-03): Maccabi have also now released a different report looking at a cohort, which gives a less rosy picture of initial efficacy.
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Analysing Maccabi data on initial efficacy of first vaccine dose
This exciting chart has emerged from the Maccabi study, providing evidence for efficacy of the Pfizer vaccine after the first dose.
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New-variant compatibility in the ONS infection survey
Code behind this analysis: https://github.com/theosanderson/theo.io/tree/master/content/post/2021-01-22-ons-data The ONS infection survey has come out and there has been a lot of discussion on the apparent decrease in proportion of “new variant compatible”
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Investigating the latest round of REACT
The latest round of the REACT study has come out, and been quite controversial.
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The virus vs. the vaccine
One framing for thinking about COVID is as a race between vaccination and infection, since we expect the former to have at least some mitigating effect on the latter.
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Variation at Spike position 142 in SARS-CoV-2 Delta genomes is a technical artifact caused by dropout of a sequencing amplicon
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Using Plasmodium knowlesi as a model for screening Plasmodium vivax blood-stage malaria vaccine targets reveals new candidates
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Systematic Errors Associated with Some Implementations of ARTIC V4 and a Fast Workflow to Prescreen Samples for New Problematic Sites
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Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections
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Covince
I built the first version of the Covince lineage explorer and then led a small team of two that continued its development.
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Clinical outcomes of COVID-19 in long-term care facilities for people with epilepsy
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Chronumental: time tree estimation from very large phylogenies
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An apicoplast-resident folate transporter is essential for sporogony of malaria parasites
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Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys
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COVID-19 and the categorical imperative
I recently asked on Twitter: And got reassuring results: Then I asked another question.
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Community testing for COVID-19: reaching 25 million tests per week
Until recently, the strategy for COVID testing in many countries has been focused on people who have a significantly likelihood of having COVID-19.
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Controlled infection with COVID-19 as a safer means of establishing herd immunity
Update: it seems (although clarity is lacking) that the UK has moved away from the herd-immunity strategy.
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Using Plasmodium knowlesi as a model for screening Plasmodium vivax blood-stage malaria vaccine targets reveals new candidates
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Standard operating procedures for SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay
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Scalable and Robust SARS-CoV-2 Testing in an Academic Center
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Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers
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Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys
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Defining multiplicity of vector uptake in transfected Plasmodium parasites
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Critiquing protein family classification models using sufficient input subsets
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Slides
Create slides in Markdown with Wowchemy Wowchemy | Documentation Features Efficiently write slides in Markdown 3-in-1: Create, Present, and Publish your slides Supports speaker notes Mobile friendly slides Controls Next: Right Arrow or Space Previous: Left
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PubTweet
There are a lot of tweets to PubMed pages – not least from @MalariaPapers.
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eMotion 5075 teardown
In my PhD lab we had an epMotion 5075 pipetting robot.
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Using deep learning to annotate the protein universe