Nicholas Joseph Matzke

Statistical Model Comparison Supports a Pitcher Origin of Utricularia Suction Traps

The paper tests the pitcher hypothesis for the evolution of Utricularia bladder traps using statistical model comparison of phylogenetic data.

Molecular and structural innovations of the stator motor complex at the dawn of flagellar motility

This study classifies and characterizes MotAB stator complexes across bacterial phyla, identifying structural innovations linked to flagellar motility.

Adding 3Di characters to amino acid datasets can improve resolution, but the effect is weaker in shorter and alpha-helical proteins

This study shows that combining 3Di characters with sequence data improves phylogenetic resolution in protein superfamilies, but 3Di's effectiveness is reduced in alpha-helical proteins.

Mapping the loss of flagellar motility across the tree of life

The paper maps the evolution of flagellar motility across bacterial species by analyzing genome data and developing a classifier to predict motility based on protein homology.

On use of tertiary structure characters in hidden Markov models for protein fold prediction

The paper uses structure-based hidden Markov models to predict protein folds and infer function, particularly for proteins with weak sequence homology.

A new method for determining ribosomal DNA copy number shows differences between Saccharomyces cerevisiae populations

The paper introduces a method to estimate rDNA copy number using modal coverage and applies it to yeast isolates, finding population-level variation in copy numbers.