Jordan Douglas

This paper introduces phylogenetic pairwise contrasts (PPC) to analyze the relationship between molecular evolutionary rates and biological traits, showing it outperforms PGLS in calibration and accuracy.

This paper introduces a hierarchical clock-mixture model for Bayesian phylogenetic dating to better handle uncertainty in clock choice and improve timescale estimation.

The paper uses population genomics to identify three yellow-eyed penguin subspecies and links candidate genes to respiratory distress syndrome.

This paper introduces a new package for reconstructing substitution histories on phylogenies, showing improved accuracy and precision using relaxed clocks and codon-partition models.

The paper uses phylogenomic and fossilized birth-death dating to show Cicadidae diversified extensively after the K-Pg extinction event.

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

This study investigates the function, structure, and evolution of CtdA, showing its role in preventing canavanine toxicity in Salmonella and E. coli.

The paper develops substitution models that account for changes in the coding alphabet size over time, finding support for a reduced ancient alphabet in old proteins and rejecting it in young ones.

This paper introduces a probabilistic framework to detect evolutionary bursts during branching events, showing evidence in proteins, morphologies, and languages.

The paper identifies a functional urzyme, GlyCA, from an arctic fox genome that exhibits enhanced catalytic activity compared to known urzymes, supporting the idea that urzymes represent ancestral catalytic activities in genetic coding.

AARS Online provides a curated database of aminoacyl-tRNA synthetases with sequence, structure, and evolutionary information, accessible via an interactive platform.

This paper uses tertiary-interaction characters to improve structural phylogenetics beyond the twilight zone, achieving accurate results with fast computation.

The paper analyzes SARS-CoV-2 genomic data from Colombia to study variant transmission dynamics and the impact of control measures during the first two years of the pandemic.

StarBeast3 improves Bayesian inference of the multispecies coalescent model with faster computation and parallelization, outperforming previous versions and *BEAST on real and synthetic datasets.

This paper improves the efficiency of Bayesian phylogenetic inference by developing adaptive MCMC operators for relaxed clock models, achieving up to 65x speedup in parameter estimation.

The paper reviews the evolutionary history of cotranscriptional editing in paramyxoviruses, showing multiple switches between P and V default modes and losses of the editing system.

The paper compares 12 stochastic transcription elongation models using Bayesian inference and force-velocity data from E. coli, S. cerevisiae, and T7 polymerases, showing differences in translocation rates and model applicability.

The paper compares 128 kinetic models of transcriptional pausing using approximate Bayesian computation to predict pause site locations in E. coli, finding structural parameters and translocation dynamics are key, while hypertranslocation and backtracking are not required.