Aaron R. Quinlan

The paper identifies genetic variants associated with placental abnormalities in stillbirths by analyzing exome sequencing data from placental and fetal samples.

The paper shows that DNA lesions in C. elegans can be inherited and generate multi-allelic mutations across generations.

The paper investigates mutation and recombination patterns in human acrocentric chromosome short arms using multiple sequencing technologies and a four-generation pedigree.

This study identifies genomic factors influencing tandem repeat mutagenesis using long-read sequencing in a large family, finding that de novo mutations are more common at longer, uninterrupted, and heterozygous loci.

The paper uses AVITI sequencing to analyze homopolymer mutation rates in a CEPH/Utah pedigree, confirming lower mutation rates and no significant paternal age effect compared to other STRs.

The paper analyzes mutations in colon crypts to determine if colibactin is linked to early-onset CRC, finding that its association reflects anatomy rather than oncogenesis.

This study examines how interruptions at short tandem repeats (STRs) affect mutability and functional importance, finding that coding STRs with purifying selection have higher synonymous interruptions, while noncoding regulatory STRs have fewer interruptions.

The paper evaluates genetic-constraint metrics across the human noncoding genome and identifies regions where they underperform due to model bias and low signal-to-noise ratios.

The paper directly identifies de novo mobile element insertions in human sperm using long-read sequencing and finds age-related increases in retrotransposition rates.

This paper optimizes variant prioritization parameters for Exomiser and Genomiser to improve diagnostic yield in rare disease cases using WES and WGS data.

The paper creates a long-read benchmark for genetic variants using a large pedigree, improving variant calling performance and introducing new truth sets for tandem repeats and structural variants.

The paper uses a four-generation family to systematically assess de novo mutations and recombination, finding high mutation rates and paternal bias, along with a detailed recombination map.

STRchive provides a dynamic resource for interpreting TR variants at disease loci, showing most TR diseases affect children and pathogenic genotypes exist in gnomAD without known disease prevalence.

This paper evaluates avidity sequencing for single-cell RNA-seq, showing it accurately sequences through homopolymers and improves alignment workflows.

TRGT-denovo accurately detects de novo tandem repeat mutations in family trios, reducing false positives and improving precision compared to genotype-based methods.

vcfexpress is a high-performance tool for filtering and formatting VCF files using Lua expressions, offering speed and flexibility comparable to existing tools.

The paper reanalyzes RNA-seq data to show pre-mRNA levels vary across cell types, affecting gene length bias and normalization methods, and highlights the impact of bioinformatic processing over assay choice.

The paper investigates how parental age and STR composition affect de novo mutation rates, finding that maternal age influences STR mutations even when oocytes are not replicating.

The paper identifies epistasis between mutator alleles in mice, showing that combined mutator alleles at two loci increase C>A mutations compared to single mutator alleles.

The paper introduces TRGT, a tool for tandem repeat genotyping, and a database of 937,122 TRs across 100 genomes, achieving high concordance and detecting repeat expansions, methylation, and mosaicism.

STRling detects short tandem repeat expansions at known and novel loci using k-mer counting, achieving high sensitivity and base pair accuracy.

SVAFotate annotates structural variants with allele frequency data from multiple datasets to help classify them as common or rare, aiding in rare disease analysis.

This paper introduces ConSpliceML, a machine learning model that improves the identification of deleterious splicing variants by integrating genetic constraint and alternative splicing predictions.

This paper estimates offspring genetic risk scores from parental DNA and finds that they can be accurately estimated with percent errors below 10% for most traits.

The paper establishes variant filtering guidelines for rare disease studies and estimates candidate variant yields for different inheritance modes using slivar software.

The paper introduces the D4 format and d4tools to efficiently store and analyze read depth data, achieving smaller file sizes and faster analysis speeds compared to existing formats.

Unfazed detects the parental gamete of origin for de novo mutations using read-based phasing and scales to large datasets.

Samplot creates visualizations for structural variant validation and includes a machine learning tool to reduce false positives across multiple sequencing technologies.