Tina A. Graves-Lindsay

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 investigates methylation patterns of polymorphic transposable elements using long-read sequencing and the Human Pangenome Reference, revealing distinct methylation profiles and context-dependent interactions.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

This study shows that using graph-based pangenomes and inferred donor-specific assemblies improves somatic variant detection compared to GRCh38.

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.

This study uses whole-genome sequencing to analyze 9p deletion and duplication syndromes, identifying key genes and structural variants, and introduces a machine learning model for syndrome prediction.

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.

The paper develops a pangenomic method to create a benchmark resource for somatic variant detection using HapMap mixtures, identifying millions of variants across different genomic regions.

The paper evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

This paper completes the linear assembly of human chromosome 8, resolves long-standing gaps, and analyzes the evolutionary history of its centromeric regions across great apes.

The paper presents a chromosome-level genome of surface fish Astyanax mexicanus and uses it to identify genetic factors contributing to trait evolution in cavefish populations.

The paper presents a gapless, telomere-to-telomere assembly of the human X chromosome using ultra-long-read nanopore sequencing and complementary technologies.