Richard A. Gibbs

This study develops an oligonucleotide capture sequencing method to generate SARS-CoV-2 genomic and transcriptome sequences from clinical samples, revealing differential transcriptional activity and ORF10 expression.

Neptune delivers structured genomic data to EHR systems through customizable reports and variant reanalysis, supporting over 15,000 clinical reports.

This paper describes the implementation of HL7 FHIR standards for representing clinical genomics results in the eMERGE Networks, improving interoperability for genetic data management.

The paper presents the first genome sequence for a thysanopteran insect, providing insights into its biology and evolution as a crop pest.

This study identifies COPB2 haploinsufficiency as a cause of a coatopathy with osteoporosis and developmental delay, showing disrupted collagen trafficking and potential treatment with ascorbic acid.

The paper catalogs structural variants across 19,652 genomes and identifies their associations with proteomic measurements and disease phenotypes.

The paper investigates PRUNE1 variants causing NMIHBA, showing they disrupt exopolyphosphatase activity and lead to neurodevelopmental defects in mice.

The paper analyzes gene and protein domain content changes across 76 arthropod genomes to understand evolutionary patterns and their association with phenotypic adaptations.

This study evaluates five SV genotyping software methods using simulated and real data to assess their sensitivity, reliability, and compatibility with VCF formats.

The paper reports exome sequencing of 457 ASD families, identifying 10.4% with known ASD genes and 3.4% with possibly associated variants, and provides statistical support for 34 ASD risk genes using the TADA framework.

Hem1 loss-of-function mutations cause congenital immunodysregulation by disrupting WAVE2 and mTORC2 complexes, leading to immunodeficiency and immune hyperresponsiveness.

ARBoR tracks versioned clinical reports using a blockchain-inspired system to ensure authenticity and tamper-proof lineage in clinical genetics.

The paper presents the milkweed bug genome and comparative analyses to study molecular evolution and feeding ecology in Hemiptera.

Atlas-CNV identifies single-exon CNVs in targeted sequencing data with reduced false discovery rate using C-scores and ExonQC thresholds.

The paper reports the sequencing and manual annotation of the Gerris buenoi genome, identifying gene expansions linked to adaptations for aquatic life.

The paper describes the establishment of a harmonized clinical sequencing network for the eMERGE III Network, enabling standardized protocols and integration of genomic results into electronic health records.

Parliament2 combines multiple structural variant callers to improve accuracy and speed, offering a Docker-based solution for efficient variant calling.

The paper identifies additional DDX3X variants in individuals with intellectual disability and expands the known phenotypic spectrum of DDX3X disorders.

The paper presents the genome of the Colorado potato beetle to study its rapid evolutionary changes, herbivory adaptations, and insecticide resistance mechanisms.

The paper analyzes the house spider genome to identify an ancient whole-genome duplication shared by spiders and scorpions, distinct from horseshoe crab duplications.

This study characterizes genomic, transcriptomic, and epigenomic artifacts in FFPE tissues and provides best practices to mitigate their impact on molecular analysis.

The paper improves KIR allele discovery in Mauritian cynomolgus macaques using high-throughput sequencing and develops a new target capture reagent, finding nine novel alleles.

The paper develops a novel HWE filtering strategy to improve variant calling quality control in large-scale sequencing by optimizing p-value cutoffs based on site frequency spectra.