Benjamin D. Kaehler

The paper introduces methods to detect neutral mutation disequilibrium (NMD) and applies them to Drosophila, mouse, and human genomes, finding NMD is common and may mislead evolutionary inferences.

This paper introduces the Inherited Rate Matrix (IRM) algorithm for non-stationary phylogenetic model selection, showing improved accuracy and speed over existing methods.

The paper introduces RESCRIPt, a software tool for reproducibly generating and managing nucleotide sequence taxonomy databases, showing that larger databases are not always better and highlighting the benefits of curation.

This paper shows that incorporating species abundance data improves taxonomy classification accuracy for amplicon sequences.

The paper benchmarks supervised learning methods for microbiome classification and regression, introducing a QIIME 2 plugin to apply these methods to microbiome data.