Hailey Loucks

The paper introduces Centrolign, a tool for aligning centromeric regions, revealing mutation dynamics and enabling variant calling in human centromeres.

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

The paper presents the first telomere-to-telomere genome for the common marmoset, revealing genomic features and a pangenome resource for biomedical research.

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.

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

The paper uses a complete diploid human genome to study centromeric chromatin organization, revealing that DNA methylation regulates centromere structure and plasticity.

HMM-Flagger evaluates genome assemblies by detecting structural errors using read coverage modeling, showing improved accuracy in human assemblies.

The paper uses fully phased telomere-to-telomere assemblies and long-read epigenomes to study centromere genetic and epigenetic dynamics across inheritance and cell-fate transitions, finding positional stability of CDRs and dynamic epigenetic changes.

The paper presents T2T reference genomes from a multi-generational pedigree to study genetic and epigenetic inheritance across the complete genome.

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

This paper introduces targeted long-read sequencing to identify complex structural variants and disease-causing mutations missed by conventional methods, improving diagnostic accuracy in genetic disorders.