Simone Rubinacci

This study identifies genetic loci associated with antihypertensive medication switching, implicating neurotensin-NTSR1 signaling in ACE inhibitor-induced cough and CYP3A4*22 in dCCB intolerance.

The paper identifies 43,617 mosaic chromosomal alterations in blood from 484,081 UK Biobank participants, revealing genomic hotspots and associations with age-related clonal expansions and genetic pathways.

MetaGLIMPSE improves low coverage sequencing imputation by combining multiple reference panels, outperforming single-panel methods for modern and ancient DNA samples across various coverage and allele frequency ranges.

The paper analyzes DNA repeat instability in 700,000 participants to identify genetic modifiers of repeat expansion and contraction rates and their clinical associations.

The paper infers parent-of-origin effects in ~265,000 individuals using a novel method, identifying over 30 novel POEs and confirming known associations, supporting the parental conflict hypothesis.

This study assesses the progress and limitations of polygenic risk score prediction accuracy for common diseases, showing diminishing returns from recent GWAS and highlighting the need for broader variant coverage.

SURFBAT approximates transmission-disequilibrium tests using imputed haplotypes to detect genotype-phenotype associations while being robust to population stratification.

The paper introduces BGE, a sequencing method that combines low-pass whole genome and deep whole exome data, showing high accuracy and cost-effectiveness for genetic variant discovery.

This paper builds a haplotype reference panel from Genomics England data and imputes UK Biobank data, revealing more rare variants and suggesting limitations in detecting rare variant associations with current sample sizes.

The paper introduces RESHAPE, a method to anonymize reference panels by simulating descendant genomes, enabling genotype imputation while protecting privacy.

This study evaluates how post-mortem damage and contamination affect imputation performance in ancient DNA, finding that ATLAS improves results for highly damaged genomes and contamination above 5% reduces accuracy.

The paper introduces GLIMPSE v2.0.0, a scalable imputation method for low-coverage genomes, reducing computational costs while maintaining high accuracy for rare variants and low-coverage samples.

This paper introduces SHAPEIT5, a phasing method that accurately phases rare variants in UK Biobank WGS and WES data, improving imputation accuracy and identifying gene essentiality through compound heterozygous events.

The paper introduces μ-PBWT, a memory-efficient method for haplotype matching, reducing memory usage by up to 25 times and enabling storage of large datasets on a commodity laptop.

The paper infers parent-of-origin effects in the UK Biobank using a novel probabilistic method, identifying 101 significant associations across 59 biomarkers and 38 phenotypes.

The paper integrates multi-omic data to identify genetic and microbiome factors associated with severe COVID-19, independent of ancestry and social factors.

This study evaluates the accuracy of genotype imputation for ancient genomes and finds it comparable to modern DNA, with some population-specific biases.

The paper identifies local gene co-expression patterns across human tissues and links them to eQTLs associated with multiple traits.

This study introduces GLIMPSE, a method for efficient phasing and imputation of low-coverage sequencing data, showing improved accuracy and cost-effectiveness compared to existing methods.

IMPUTE5 improves genotype imputation by scaling sub-linearly with reference panel size and using the Positional Burrows Wheeler Transform for efficient haplotype selection.

This paper develops a high-throughput method to generate host and pathogen genomic data from single nasopharyngeal swabs of COVID-19 patients.