Jakob McBroome

EMS Mutation and SNP Detection in Intracellular Wolbachia Genomes

This paper demonstrates the successful detection of EMS-induced mutations in Wolbachia genomes using circle sequencing, revealing a significant enrichment of C/G>T/A transitions.

Pandemic-scale phylogenetics

The paper develops a phylogenetic package to handle pandemic-scale SARS-CoV-2 genomic data, enabling real-time analysis and visualization of large mutation-annotated phylogenetic trees.

Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Approaches

This study compares online and de novo phylogenetic methods for SARS-CoV-2, finding that maximum parsimony online approaches are more accurate and efficient than maximum likelihood or de novo methods.

A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees

The paper introduces a daily-updated database of SARS-CoV-2 mutation-annotated trees and associated tools for querying and manipulating the data.

A phylogeny-based metric for estimating changes in transmissibility from recurrent mutations in SARS-CoV-2

The paper estimates changes in SARS-CoV-2 transmissibility using a phylogeny-based metric, finding that Delta is the most transmissible clade and transmissibility within clades slightly decreases over time.

A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control

The paper reports a SARS-CoV-2 lineage with mutations from known variants of concern that is rejected by sequence repositories due to a deletion, suggesting underestimation of its frequency.

Chromosome-scale genome assembly of a single outbred Drosophila melanogaster

The paper demonstrates a chromosome-scale genome assembly of a single outbred Drosophila melanogaster using a hybrid method with low input DNA.