M. DeGiorgio

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.

A spatially aware likelihood test to detect sweeps from haplotype distributions

This paper introduces a spatially aware likelihood test to detect positive selection by analyzing haplotype frequency distributions and demonstrates its effectiveness on human and rat datasets.

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.

VolcanoFinder: genomic scans for adaptive introgression

VolcanoFinder detects adaptive introgression using polymorphism data from a single population, identifying volcano-shaped patterns of increased variability around beneficial alleles.

Flexible mixture model approaches that accommodate footprint size variability for robust detection of balancing selection

This paper introduces B statistics, a set of mixture model-based tests for detecting balancing selection, showing robust performance across window sizes and datasets.

Maximum likelihood estimation of species trees from gene trees in the presence of ancestral population structure

This paper introduces TASTI, a maximum likelihood method for inferring species trees from gene trees under ancestral population structure, showing improved accuracy with more gene trees.

A likelihood approach for uncovering selective sweep signatures from haplotype data

This paper introduces a likelihood ratio test statistic to detect selective sweep signatures in haplotype data across human and Drosophila populations, identifying known candidate genes.

Identifying and classifying shared selective sweeps from multilocus data

The paper identifies and classifies shared selective sweeps across populations using a new statistic, SS-H12, and finds both known and novel sweep candidates in human genomes.

Detection of shared balancing selection in the absence of trans-species polymorphism

The paper develops methods to detect trans-species balancing selection without relying on trans-species polymorphism, finding new genomic regions linked to immunity and barrier integrity in humans and chimpanzees.

Localizing and classifying adaptive targets with trend filtered regression

This paper introduces Trendsetter, a method for detecting and classifying genomic regions under natural selection, showing it is robust to missing data and background selection.

Detection and classification of hard and soft sweeps from unphased genotypes by multilocus genotype identity

The paper develops methods to detect and classify hard and soft selective sweeps using unphased genotypes, finding they are effective for recent sweeps and population expansions.

Copy number variation of ampliconic genes across major human Y haplogroups

The paper examines copy number variation of ampliconic genes across human Y haplogroups, finding high diversity and limited haplogroup-specific patterns.