Joshua G. Schraiber

Characterizing and mitigating confounding by unreplicated evolutionary events in phylogenetic regression

This paper introduces a method to reduce false positives in phylogenetic regression by incorporating eigenvectors of the phylogenetic variance-covariance matrix and presents a new R package for visualization.

Accounting for recurrent mutation in the frequency spectrum of rare alleles

The paper introduces the single mutation frequency spectrum (SMFS) to account for recurrent mutations in the site frequency spectrum of rare alleles, showing its application to human exome data.

Observational epidemiological studies can mitigate genetic confounding with the genetic relatedness matrix

This paper introduces a method using genetic relatedness matrices to control genetic confounding in observational studies, showing improved performance over existing approaches in smaller datasets.

Interspecific divergence of gene expression biophysics driven by both evolutionary systems drift and strong selective constraints on bursting rate

This study estimates biophysical parameters of gene expression in multiple vertebrate species and finds coordinated evolution under evolutionary systems drift and additional constraints on transcriptional bursting.

Estimation of demography and mutation rates from one million haploid genomes

This paper introduces DR EVIL, a method to estimate mutation rates and demographic history from large haploid genome datasets, revealing mutation-rate heterogeneity and the impact of multiple mutation events on rare variants.

Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias

This study improves allele frequency and ancestry proportion estimation by adjusting genotype likelihoods to reduce mapping bias in ancient DNA sequencing.

Convergent expansions of keystone gene families drive metabolic innovation in a major eukaryotic clade

The paper investigates the relationship between gene family expansions and metabolic traits in yeasts, finding that keystone gene families drive multiple metabolic innovations.

Phylogenetic analysis reveals how selection and mutation shape the coevolution of mRNA and protein abundances

This study uses a phylogenetic model to analyze multi-species data and finds that protein abundances are under strong stabilizing selection, while mRNA abundances adapt more quickly due to mutational opportunity.

A path integral approach for allele frequency dynamics under polygenic selection

This paper extends a path integral method to polygenic selection scenarios, deriving analytic expressions for allele frequency transitions under stabilizing and adaptive selection to improve evolve-and-resequence experiments.

Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations

This paper unifies statistical genetics and phylogenetics by developing a general model for genetic covariance, showing how GWAS and phylogenetic regression are special cases and demonstrating improved association testing through shared methodology.

Heritability within groups is uninformative about differences among groups: cases from behavioral, evolutionary, and statistical genetics

The paper shows that within-group heritability cannot determine the genetic vs. environmental basis of between-group phenotypic differences, using mathematical analysis and simulations.

Tree-based QTL mapping with expected local geneticrelatedness matrices

This paper introduces a QTL mapping method using expected local genetic relatedness matrices derived from ancestral recombination graphs, improving detection of QTLs in populations with limited imputation resources.

The landscape of tolerated genetic variation in humans and primates

The paper uses primate genetic data to predict human variant pathogenicity with a deep learning classifier trained on 4.3 million common missense variants.

A global catalog of whole-genome diversity from 233 primate species

This study presents whole-genome data from 233 primate species, revealing patterns of genetic diversity, mutation rates, and recurrent missense mutations across primate clades.

Rare penetrant mutations confer severe risk of common diseases

The paper identifies rare variant polygenic risk scores as more effective than common variant polygenic risk scores in identifying individuals with outlier phenotypes in common human diseases and complex traits.

Ancestry Inference Using Reference Labeled Clusters of Haplotypes

ARCHes infers ancestry composition using haplotype-based models, outperforming RFMix in global and local ancestry assignment across diverse populations.

AN ADMIXTURE SIGNAL IN ARMENIANS AROUND THE END OF THE BRONZE AGE REVEALS WIDESPREAD POPULATION MOVEMENT ACROSS THE MIDDLE EAST

This study analyzes genomic data to show Armenians remained unadmixed until the Bronze Age, then experienced a Sardinian-like genetic input, suggesting large-scale population movements in the Middle East.