Angie S. Hinrichs

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 estimates neutral mutation rates and fitness effects of mutations in influenza proteins using phylogenetic analysis of over 100,000 sequences, revealing context-dependent patterns across viruses.

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

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.

The paper estimates mutation rates across SARS-CoV-2 genome sites and identifies factors influencing these rates, finding significant variability and patterns related to gene boundaries, sequence context, and RNA structure.

This study compares pangoLEARN and pUShER for SARS-CoV-2 lineage assignment, finding pUShER more stable and accurate across pangolin versions.

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.

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.

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

The paper introduces UShER, a method for ultrafast phylogenetic placement of SARS-CoV-2 sequences, enabling real-time genomic contact tracing and maintaining an updated reference phylogeny.

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.

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.

The paper identifies lab-specific recurrent mutations in SARS-CoV-2 sequences that affect phylogenetic inference and proposes tools to improve sequence quality and phylogeny comparison.

The paper describes a SARS-CoV-2 genome browser that integrates molecular data from multiple sources for visualization and analysis.

The paper updates the UCSC Genome Browser with new features and data sets, including improved human genome assembly hg38/GRCh38 and new tools for data integration.