R. Assis

A tale of too many trees: a conundrum for phylogenetic regression

This paper investigates the consequences of gene tree-species tree mismatch in phylogenetic regression and finds high false positive rates when trees are mismatched.

Robust Phylogenetic Regression

This paper introduces robust phylogenetic regression to improve trait association tests by reducing sensitivity to model violations while maintaining statistical power.

Predicting expression divergence and its evolutionary parameters between single-copy genes in two species

PiXi predicts gene expression divergence and its evolutionary parameters between single-copy genes in two species, showing 20% divergence in Drosophila and involvement in mitochondrial electron transport.

Learning retention mechanisms and evolutionary parameters of duplicate genes from their expression data

The paper develops CLOUD, a neural network that classifies duplicate gene retention mechanisms and predicts evolutionary parameters, outperforming the existing CDROM method.

Population-specific sequence and expression differentiation in Europeans

The paper examines population-specific sequence and expression differentiation in four human populations to identify genes involved in adaptation.

Rapid functional divergence of grass duplicate genes

The paper analyzes gene expression in grasses to show that small-scale duplications lead to rapid functional divergence, particularly in younger gene copies and anther-specific expression.