Joseph W. Thornton

The paper investigates the evolutionary origin of NELL-Robo interactions and shows that dual-ligand responsiveness is conserved in chordates but not protostomes.

This study shows that allostery in vertebrate hemoglobin evolved from a non-allosteric dimer through three key substitutions, leveraging inherent conformational flexibility of the globin fold.

The paper reconstructs ancestral transcription factors to study how ancient genotype-phenotype maps influenced the evolution of protein function.

This study evaluates how realistic evolutionary heterogeneity affects ancestral sequence reconstruction and finds that ASR is robust to such heterogeneity, with phylogenetic signal being the primary determinant.

This study investigates how vertebrate hemoglobin evolved from a homodimeric ancestor to a heterotetramer through simple genetic changes that exploited symmetry in its structure.

The paper investigates the evolutionary dynamics of self-assembly in prokaryotic citrate synthases, finding frequent transitions between different assembly types without strong functional consequences.

The paper responds to criticisms of their reference-free analysis method by addressing claims about high-order epistasis and methodological equivalences.

Reference-free analysis with a sigmoid link shows additive plus pairwise effects explain a median 96% of phenotypic variance across 20 combinatorial protein mutagenesis datasets.

The paper develops a framework to account for multi-nucleotide substitutions and synonymous rate variation in natural selection analyses, showing they significantly impact detection of positive selection.

This study presents crystal structures of Kirrel receptors, showing their homodimerization mechanism and its role in axon coalescence into glomeruli in the mouse olfactory system.