Nathan L Clark

The paper uses evolutionary rate covariation across malaria parasite species to infer protein interactions and identify new functional candidates.

The paper updates the RERconverge package with faster algorithms and new analysis features for studying convergent evolution at the genomic level.

BUSTED-PH identifies genes associated with convergent phenotypes by detecting episodic diversifying selection across mammalian species.

The paper introduces motifDiff, a tool for variant effect prediction using biophysical TF binding models, showing it effectively scores variants and provides insights into human accelerated regions.

ERC2.0 improves functional interaction prediction across large phylogenies by enhancing algorithm speed, normalization, and statistical power.

The paper evaluates the reliability of phylogenetic inference using primate enamel proteins by simulating sequence fragmentation and comparing results to a reference species tree.

This study investigates how retinal specializations in mammals evolve in response to ecological factors and morphological constraints, finding support for associations between horizontal streaks and habitat type, and between orbit convergence and retinal acuity regions.

BUSTED-E detects positive selection while identifying residual alignment errors in genome-scale datasets, improving accuracy and biological interpretation.

The paper expands RERconverge to analyze multi-categorical traits by introducing methods for ancestral state reconstruction, statistical tests, and phylogenetic permutations, showing improved performance in identifying diet-related genes and pathways.

The paper identifies potential genetic modifiers of Congenital Disorders of Glycosylation (CDG) using evolutionary rate covariation analysis across glycosylation pathways and other biological processes.

The paper identifies proteins and regulatory elements associated with vocal learning by analyzing bat neural activity and epigenomic data.

The paper shows gadusol, a maternal compound in zebrafish, protects embryos from UV damage by reducing DNA damage markers, and its biosynthesis pathway is conserved in teleosts but lost in species without UV exposure.

This study shows that multiple 9-1-1 complexes are essential for meiotic DSB repair, homolog synapsis, and ATR signaling in mammals.

This study identifies MCM8IP as a DNA repair factor that promotes homologous recombination and DNA synthesis in response to DNA damage by interacting with MCM8-9 and RPA1.

The paper uses evolutionary rate covariation analysis to identify genes coevolving with Drosophila E-cadherin, revealing novel regulators of cell adhesion and actin dynamics.

The paper identifies genes involved in herbivory between butterflies and their host-plants using genome-wide association studies and comparative analyses.