Richard A. Gibbs

Genetic and Epigenetic Landscape of Self-Identified Hispanics/Latino in All Of Us

The paper analyzes genetic variation, ancestry, and DNA methylation in Hispanic/Latino participants using long-read sequencing, identifying novel variants and phenotype associations.

Microbial Dynamics Across Commercial Spaceflights of Varying Duration

This study examines microbiome and immune changes in astronauts after short and long-duration spaceflights, finding stable gut and oral microbiomes but transient skin microbiome shifts and immune activation.

Unveiling the Hidden Rules: Enhancing NMD Prediction for Protein-Truncating Variants

The paper develops a model to predict NMD outcomes for protein-truncating variants using RNA-seq data, achieving ~78% ROC-AUC and identifying non-canonical determinants.

Integrated Clinical-Genomic Reanalysis Identifies Diagnostic Gaps and Candidate Genes in a Pediatric Rare Disease Cohort

Himito: a Graph-based Toolkit for Mitochondrial Genome Analysis using Long Reads

Himito is a graph-based toolkit for analyzing mitochondrial genomes using long reads, achieving superior performance in assembly and variant calling and revealing age-related patterns in the All of Us dataset.

Expanding the Clinical and Molecular Spectrum of TUBB2B Through Distinct Variants Identified Across Multiple Families

The paper reports new TUBB2B variants in multiple families, expanding the clinical and molecular spectrum of tubulinopathies and highlighting phenotypic heterogeneity and dual molecular diagnoses.

Somatic variant detection in normal tissues from single-cell sequencing data

This study evaluates somatic variant calling in normal tissues using single-cell RNA and ATAC sequencing, showing Monopogen outperforms other tools in accuracy and sensitivity.

Multi-Omics Characterization of Human Molecular Responses to Spaceflight Across Two Independent Missions

This study analyzes multi-omics data from two spaceflight missions to identify molecular changes in immune, skeletal, and vascular systems, providing insights for mitigating health risks during space travel.

Building an Interoperable Rare Disease Multi-omic Resource: The GREGoR Data Model and Dataset

The paper introduces a data model and dataset for rare disease research, enabling interoperable multi-omic data integration across clinical sites.

Performance Characteristics of Reasoning Large Language Models for Evidence Extraction from Clinical Genomics Literature

This paper evaluates large language models for automated PS4 evidence extraction from clinical genomics literature, finding high accuracy but model-dependent performance.

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.

Expanding the Genome in a Bottle Truth Set: Detection and Validation of Novel Low-frequency Variants Using High-accuracy NanoSeq

The paper introduces NanoSeq-MBN, a method improving variant detection in whole-genome sequencing, expanding the GIAB truth set with novel low-frequency variants and enabling somatic variant benchmarking.

Phase Separation Contributes to Pathogenicity for Nonsense Mediated Decay-Escaping Variant Alleles

This study identifies NMD-escape variants as a distinct class of disease-causing mutations, showing that altered C-terminal regions drive pathogenicity through phase separation.

Enriching for Answers in Rare Diseases

TBAS enables cost-effective long-read sequencing of rare-disease trios with high variant detection accuracy and a 77% potential solve rate.

Constellation illuminates rare disease genetics

This paper evaluates Illumina Constellation sequencing for rare disease research, showing it can detect structural variants and haplotype phasing with low DNA input and existing infrastructure.

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.

Pre-Sequencing Assessment of RNA-Seq Library Quality Using Real-Time qPCR

This paper introduces a qPCR-based assay to assess rRNA depletion efficiency in RNA-Seq libraries pre-sequencing, showing strong correlation with post-sequencing rRNA rates.

Population-scale Long-read Sequencing in the All of Us Research Program

The paper analyzes long-read sequencing data from the All of Us Research Program to identify structural variants and their associations with diseases in a large cohort of Black or African American participants.

Biallelic variants in the non-coding RNA gene RNU4-2 cause a recessive neurodevelopmental syndrome with distinct white matter changes

The paper identifies biallelic variants in RNU4-2 causing a recessive neurodevelopmental syndrome with distinct white matter changes, expanding the known genotypic and phenotypic spectrum of RNU4-2-related disorders.

Evolutionary dynamics of Respiratory Syncytial Virus in pre-pandemic, pandemic, and post-pandemic periods in Houston, Texas, USA

This study analyzes RSV evolutionary dynamics across pre-pandemic, pandemic, and post-pandemic periods in Houston, finding reduced diversity during the pandemic and increased non-synonymous mutations in RSV/B.

Genomic rare variant mechanisms for congenital cardiac laterality defect: A digenic model approach

The paper identifies trans-heterozygous digenic variants in laterality defect genes using exome/genome sequencing data from CHD cohorts, finding significant enrichment in laterality cases compared to controls.

Whole genome sequence association analysis of brain structural volume measures in the NHLBI TOPMed Program highlights novel loci in diverse participants

This study uses whole-genome sequence data from diverse participants to identify novel genetic loci associated with brain structural volumes, highlighting the importance of diverse cohorts in uncovering genetic architecture.

The SHR/Akr Y chromosome reveals repeated turnover of the rat pseudoautosomal region

The paper sequences the rat Y chromosome and reveals a short pseudoautosomal region with high recombination rate and unique evolutionary features.

Celeste: A cloud-based genomics infrastructure with variant-calling pipeline suited for population-scale sequencing projects

Celeste provides a scalable cloud infrastructure for population-scale sequencing projects, including a variant-calling pipeline optimized for clinical variant detection.

K-mer analysis of long-read alignment pileups for structural variant genotyping

This paper introduces a method called kanpig for accurately genotyping structural variants using long-read alignment pileups, achieving higher concordance than existing tools.

Defining and Reducing Variant Classification Disparities

The paper analyzes variant classification disparities between European-like and non-European-like genetic ancestries and shows that MAVE data can reduce these disparities in VUS reclassification.

VizCNV: An integrated platform for concurrent phased BAF and CNV analysis with trio genome sequencing data

VizCNV is a tool for analyzing CNVs and phased BAF from trio genome sequencing data, identifying de novo and inherited CNVs in immunodeficiency cases.

Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk

The paper introduces a CN caller for KIV-2 repeats using short reads, showing high accuracy and demonstrating its correlation with Lp(a) levels and population-specific CN distributions.

Complete Genomic Characterization of Global Pathogens, Respiratory Syncytial Virus (RSV), and Human Norovirus (HuNoV) Using Probe-based Capture Enrichment.

This paper presents a probe-based capture enrichment method to obtain full-length genomes of RSV and HuNoV from clinical samples, achieving high completeness and improving variant tracking.

A common flanking variant is associated with enhanced meiotic stability of the FGF14-SCA27B locus

The paper identifies a common flanking variant linked to increased meiotic stability at the FGF14-SCA27B repeat locus.