Lily Karim

Real-time accessible phylogenetics for every highly sampled virus

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

Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes

Panmap efficiently aligns, genotypes, and places reads on large pangenomes using phylogenetic compression, enabling rapid analysis of up to 8 million genomes.

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

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.