T. Rhyker Ranallo-Benavidez

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.

This study shows that telomere dysfunction in human astrocytes leads to acrocentric chromosome instability and nucleolar reorganization through a combination of cytogenetic, imaging, and chromatin-contact analyses.

KaryoScope annotates genome assemblies at base-pair resolution across multiple feature classes quickly and without alignment, revealing structural variation in centromeres and subtelomeres.

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

This study uses long-read sequencing to show that telomere length differences between chromosome arms influence structural genome changes in IDH-mutant astrocytomas.

The paper introduces HKS, a method for exact hierarchical k-mer annotation with variable-length queries, achieving high concordance in human genome assemblies.

DeepSomatic is a deep learning method for detecting somatic variants from short-read and long-read sequencing data, outperforming existing callers, especially for indels.

The paper introduces Telomere-C, a method to map telomeric 3D interactions, revealing ultra-long-range contacts and repetitive element hubs linked to telomere maintenance.

This study compares the genomics of seven Trichomonas species, revealing convergent genome size expansions in human-infecting lineages and genes involved in host-switching from birds to humans.

The paper presents diploid genome assemblies for two human fibroblast cell lines, enabling clone-specific variant calling, improved read mapping, and accurate phasing.

SVCollector selects an optimal subset of individuals for long-read sequencing to maximize genetic diversity representation across subpopulations.

The paper systematically analyzes genomic features of 26 parthenogenetic animals and finds that no feature is consistently replicated across transitions to asexuality, suggesting lineage-specific patterns.

GenomeScope 2.0 and Smudgeplots provide reference-free tools to profile polyploid genomes by analyzing k-mer frequencies to estimate genome size, ploidy, and structure.