Ryan M. Layer

The landscape of polygenic score prediction accuracy and transportability across the phenome in ancestrally diverse populations

This study evaluates polygenic score prediction accuracy and cross-ancestry portability across 3,994 PGSs in diverse populations, identifying factors affecting their performance and equity.

Population-scale interpretation of RNA isoform diversity enabled by Isopedia

Isopedia reduces apparent isoform novelty by up to 26-fold in HG002 benchmarks and provides a reference-agnostic framework for population-scale isoform annotation.

TEPEAK : A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations

TEPEAK identifies and characterizes polymorphic transposable elements in non-model species populations using genome and SRA data, revealing genetic disruptions and TE presence in related species.

STABIX: Summary statistic-based GWAS indexing and compression

STABIX improves GWAS data compression and query efficiency by enabling summary-statistic-based queries and achieving smaller file sizes and faster decompression speeds compared to tabix.

Rapid, Reliable, and Interpretable CNV Curation Visualizations for Diagnostic Settings with SeeNV

SeeNV is a tool for rapid, reliable, and interpretable CNV curation in diagnostic settings, achieving high precision and recall with minimal user time.

Hypothesis Generation For Rare and Undiagnosed Diseases Through Clustering and Classifying Time-Versioned Biological Ontologies

This paper identifies potential gene-to-phenotype connections for undiagnosed diseases by clustering time-versioned biological ontologies and analyzing network data.

GenoSiS: A Biobank-Scale Genotype Similarity Search Architecture for Creating Dynamic Patient-Match Cohorts

GenoSiS dynamically finds patient-matched cohorts across populations using genotype similarity search to improve clinical analyses.

PARMIK: PArtial Read Matching with Inexpensive K-mers

PARMIK improves metagenomic sequence search by using inexpensive k-mers to achieve higher recall and faster alignment than BLAST.

STIX: Long-reads based Accurate Structural Variation Annotation at Population Scale

STIX annotates structural variants using long-read data, achieving high accuracy and identifying common SVs in population-scale datasets.

Implications of noncoding regulatory functions in the development of insulinomas

This study identifies noncoding regulatory regions and their mutations in insulinomas, linking them to altered β-cell function and tumor development.

The effects of biological knowledge graph topology on embedding-based link prediction

The paper evaluates how knowledge graph topology affects link prediction performance in rare disease variant prioritization, finding that a filtered knowledge graph improves model performance.

A complete reference genome improves analysis of human genetic variation

The T2T-CHM13 reference genome improves read mapping and variant calling across diverse samples, reducing false positives and enabling novel variant discovery.

RAREsim: A simulation method for very rare genetic variants

RAREsim simulates rare genetic variants using real data parameters and annotations to improve method evaluation for complex trait studies.

Samplot: A Platform for Structural Variant Visual Validation and Automated Filtering

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

Mining Thousands of Genomes to Classify Somatic and Pathogenic Structural Variants

The paper presents a method to index and search raw alignments from thousands of samples to improve the classification of somatic and pathogenic structural variants.

The structural variation landscape in 492 Atlantic salmon genomes

This study identifies 15,483 high-confidence structural variants in 492 Atlantic salmon genomes, revealing their role in population structure, functional impact, and domestication traits.

Learning What a Good Structural Variant Looks Like.

This paper develops Samplot-ML, a CNN that reduces false positives in structural variant detection by 47% while retaining 97% of true positives using visualization-based training.

Regulatory Sharing Between Estrogen Receptor α Bound Enhancers

The paper investigates how estrogen receptor α bound enhancers cooperate to regulate gene expression, finding that full ERE motifs and pre-existing chromatin states are critical for enhancer activity.

svtools: population-scale analysis of structural variation

svtools enables population-scale structural variation analysis by providing a fast, scalable toolkit and cloud pipeline for high-quality SV mapping across thousands of human genomes.

Limited contribution of rare, noncoding variation to autism spectrum disorder from sequencing of 2,076 genomes in quartet families

This study examines the role of noncoding variation in autism spectrum disorder using whole genome sequencing of 2,076 genomes, finding no significant association after correction for multiple testing.

Mapping and characterization of structural variation in 17,795 deeply sequenced human genomes

The paper maps and characterizes structural variants in 17,795 human genomes, revealing their frequency, impact, and relationship to gene dosage and regulatory elements.

A map of constrained coding regions in the human genome.

The paper creates a detailed map of constrained coding regions in the human genome using variation data from 123,136 individuals, identifying regions under strong purifying selection and enriched for pathogenic variants.

SV-plaudit: A cloud-based framework for manually curating thousands of structural variants

SV-plaudit enables rapid manual curation of thousands of structural variants through a cloud-based framework with image visualization and collaborative reporting.

GIGGLE: a search engine for large-scale integrated genome analysis

GIGGLE is a search engine that identifies significant shared genomic loci between query features and large genomic datasets, improving data integration and hypothesis generation.