Anastasia Lucas

A phylogeny-guided framework for decoding mechanisms of human endogenous retrovirus regulation in health and disease

ERVmancer is a phylogeny-informed method that resolves read-mapping ambiguity for HERVs, outperforming existing approaches and revealing new biology in breast cancer.

Taxonomy-free fecal microbiome profiles enable robust prediction of immunotherapy response and toxicity in melanoma

This study identifies microbiome-derived protein biomarkers for predicting immunotherapy response and toxicity in melanoma without relying on taxonomic classification.

Evidence of epistasis in regions of long-range linkage disequilibrium across five complex diseases in the UK Biobank and eMERGE datasets

The paper identifies epistatic SNP-SNP interactions in long-range LD across five diseases using UK Biobank and eMERGE data, finding associations involving conserved genes and essential genes.

Impact of natural selection on global patterns of genetic variation, and association with clinical phenotypes, at genes involved in SARS-CoV-2 infection.

The paper examines genetic variation and natural selection at SARS-CoV-2 host genes in diverse populations and links selected variants to clinical phenotypes in COVID-19.

hudson: A User-Friendly R Package to Extend Manhattan Plots

hudson extends Manhattan plots for genome-wide studies with interactive features and flexible frameworks for various analyses.

Multi-ancestry gene-trait connection landscape using electronic health record (EHR) linked biobank data

The paper uses multi-ancestry biobank data and integrative methods to identify gene-disease associations across different ancestry groups, finding shared and ancestry-specific genetic links.

eQTpLot: a user-friendly R package for the visualization and colocalization of eQTL and GWAS signals

eQTpLot visualizes and colocalizes eQTL and GWAS signals for gene-trait pairs through customizable plots.

Mendelian pathway analysis of laboratory traits reveals distinct roles for ciliary subcompartments in common disease pathogenesis

The paper identifies 73 gene-trait associations between ciliary genes and common laboratory traits in the UK BioBank, revealing distinct roles of ciliary subcompartments in common disease pathogenesis.

Exome-by-phenome-wide rare variant gene burden association with electronic health record phenotypes

This study identifies robust gene-phenotype associations by analyzing rare loss-of-function variants in exome-wide data linked to electronic health records.

Genome wide-association study identifies novel loci in the Primary Open-Angle African American Glaucoma Genetics (POAAGG) study

The paper identifies a novel POAG-associated SNP in African Americans using a genome-wide association study.

Polygenic Risk Scores for Cardio-renal-metabolic Diseases in the Penn Medicine Biobank

This study develops polygenic risk scores for cardio-renal-metabolic diseases in the Penn Medicine Biobank and finds limited predictive value in African ancestry individuals.

Collective feature selection to identify crucial epistatic variants

The paper introduces a collective feature selection approach to identify epistatic variants by combining multiple methods, showing improved performance in detecting true positive interactions in both simulated and real BMI data.

A simulation study investigating power estimates in Phenome-Wide Association Studies

This study simulates PheWAS to assess how sample size, case-control ratio, minor allele frequency, and disease penetrance affect statistical power for binary and quantitative traits.