Alexi M. Runnels

Benchmarking of duplex sequencing approaches to reveal somatic mutation landscapes

This study benchmarks six duplex sequencing technologies to evaluate their performance in detecting somatic mutations across different genomic contexts and tissue types.

A comprehensive view of somatic mosaicism by single-cell DNA analysis

The paper uses single-cell DNA sequencing to analyze somatic mosaicism in postmortem lung and colon tissues, revealing mutation heterogeneity, chromosomal abnormalities, and cellular ancestry.

Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read data

The paper benchmarks somatic variant and indel detection at low allele fractions using short- and long-read data, finding sensitivity and precision around 80% at 300x coverage.

Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules

This paper introduces ppmSeq, a sequencing technology that improves accuracy and efficiency in detecting SNVs by sequencing both DNA strands, showing superior performance in clinical applications like ctDNA detection.

An analysis of RNA quality metrics in human brain tissue

The paper evaluates how pre-sequencing RNA quality metrics (PMI and RIN) correlate with post-sequencing RNA quality metrics and gene expression in human brain tissue.

Large- Scale Deep Proteomic Analysis in Alzheimer's Disease Brain Regions Across Race and Ethnicity

The paper performs large-scale proteomic analysis of Alzheimer's disease brain regions across different racial and ethnic groups, identifying AD-related protein changes and APOE4 concordance with genotype.

Bridging the Gap: Multi-Omics Profiling of Brain Tissue in Alzheimer's Disease and Older Controls in Multi-Ethnic Populations

This paper presents a multi-omics dataset from multi-ethnic Alzheimer's disease brain donors, including transcriptome, genome, and proteome data, to improve precision medicine for underrepresented populations.

High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

The paper presents a high coverage whole genome sequencing resource of 3,202 samples, including 602 trios, generated from the expanded 1000 Genomes Project.

Transcriptome Analysis of Adult C. elegans Cells Reveals Tissue-specific Gene and Isoform Expression

This study analyzes the transcriptomes of four major tissues in adult C. elegans to identify tissue-specific genes, isoforms, and regulatory patterns, providing a resource for understanding adult multicellular biology.

Mating-induced Male Death and Pheromone Toxin-regulated Androstasis

This study investigates how mating affects male lifespan in Caenorhabditis species, identifying two mechanisms: germline-dependent lifespan reduction and pheromone-mediated toxicity.