Sarah E Hunt

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

The paper develops an automated pipeline to map genetic developmental disorder literature to Gene2Phenotype using NLP models, achieving high accuracy and scalability for biocuration.

The paper uses long-read sequencing to characterize structural variants in 1,019 samples from the 1000 Genomes Project, identifying 167,291 sequence-resolved SVs and highlighting their genomic and functional implications.

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

The paper maps MAVE data to human reference sequences to improve variant functional assay utility for genomics applications.

The paper resolves the amylase locus at nucleotide resolution in modern and ancient humans, showing AMY1 copy number variation predated agriculture and was driven by recombination.

The paper introduces NAHRwhals, a method to detect serial structural variations in long-read genomes, identifies 37 sSV loci in humans, and shows their relevance to disease.

The paper describes a structured curation process for the Gene2Phenotype project to systematically evaluate and organize genomic disease-gene relationships.

The paper describes open data sharing, analysis tools, and lessons learned from the European COVID-19 Data Platform's SARS-CoV-2 data collection and analysis efforts.

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

EyeG2P improves diagnostic genomic testing efficiency for inherited ophthalmic disorders by increasing precision while maintaining high sensitivity.

SUsPECT improves variant annotation by using custom long-read transcriptomes to better predict variant effects in clinical settings.

The paper introduces the GA4GH Variation Representation Specification (VRS), a framework for precise and federated representation of molecular variation, with a reference implementation and community resources available online.

The paper describes the Ensembl COVID-19 resource, which integrates SARS-CoV-2 genomic data and variant annotations to support research on virus variants and their impact on therapeutics and vaccines.

VEP-G2P filters genomic variants for diagnostic purposes, showing higher sensitivity but lower precision for de novo and inherited variants, with significant background noise in controls.

The paper describes the Ensembl Variant Effect Predictor, a tool for analyzing and annotating genomic variants, and highlights its features and availability.