Theo Sanderson

The paper introduces viral_usher, a tool for scalable viral phylogenetics, and demonstrates that replication machinery explains most variance in viral mutation spectra.

The paper reprocesses SARS-CoV-2 genomic data to correct systematic errors in phylogenies using a novel assembly tool, resulting in a cleaner global tree of 4.47 million samples.

This study uses mutational spectra to infer influenza virus transmission routes and adaptive mutations enabling sustained respiratory transmission.

The paper uses barcoded P. falciparum gene knockouts with BarSeq to phenotype parasite life cycle traits at scale.

A uniformly processed set of 2,440,377 bacterial and archaeal genomes with search tools and annotations, plus an AI-mined peptide set yielding ATB20, active in a mouse skin infection model.

ProteInfer uses deep convolutional neural networks to predict protein functions from amino acid sequences, offering efficient and accurate predictions with a lightweight software interface.

The paper identifies ten genes critical for male and female sexual development in Plasmodium berghei and reveals a regulatory cascade governing gametogenesis.

Treenome Browser allows interactive visualization of millions of genomes with large phylogenetic trees.

Taxonium enables exploration of large phylogenetic trees, including SARS-CoV-2 sequences, using WebGL for scalability and metadata linking.

This paper uses deep learning to improve protein function annotation by training on Pfam data, achieving better accuracy and efficiency than BLASTp.

Chronumental estimates time trees from large phylogenies using stochastic gradient descent, scaling to millions of nodes and providing accurate chronological predictions without metadata.

Mixology calculates required masses and volumes for laboratory solutions, converting between volumetric, mass, and concentration units using molecular masses from ChEBI.

The paper presents genomic and transcriptomic evidence showing Hepatocystis parasites are closely related to Plasmodium but lack blood replication and have lost genes involved in red blood cell invasion.

The paper critiques protein family classification models by identifying sufficient input subsets to understand their decision-making criteria.

PlasmoTron automates malaria parasite culture using an open-source liquid-handling robot and database, maintaining cultures at desired parasitaemias.

Phenoplasm curates and integrates phenotypic data from gene disruptions in Plasmodium parasites, enabling cross-species comparisons of genetic effects.