Maxwell D. Sanderford

Evolutionary sparse learning with paired species contrast reveals the shared genetic basis of convergent traits

This study uses evolutionary sparse learning to identify shared genetic bases for convergent traits in different species, finding common genes involved in C4 photosynthesis and echolocation.

MEGA12: Molecular Evolutionary Genetic Analysis version 12 for adaptive and green computing

MEGA12 adds filtered substitution-model selection, matching full-search choices in all 240 simulated nucleotide alignments, and adaptive bootstrapping with an 81% average speed-up, accelerating maximum-likelihood phylogenetics.

TopHap: Rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity

TopHap infers phylogenetic structures from common haplotypes in large genome collections, improving accuracy and speed for SARS-CoV-2 variant phylogeny.

TreeMap: A Structured Approach to Fine Mapping of eQTL Variants

TreeMap identifies causal eQTL variants by accounting for multisite effects and linkage, showing improved accuracy and enabling genome-wide analysis of long-range eQTL.