Glennis A. Logsdon

The paper presents a population-scale Y chromosome reference panel with 142 assemblies, revealing structural and epigenetic variation across 180,000 years of evolution.

ZATELLITE enables real-time visualization and manipulation of human centromeres in live cells using synthetic zinc fingers without causing DNA damage.

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 sequences chromosome 21 centromeres in Down syndrome families, finding extreme size asymmetry in some cases and suggesting it may be a genetic risk factor.

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.

The paper identifies a segmental duplication-mediated deletion causing neocentromere formation in orangutans by analyzing structural and epigenetic variation.

This paper describes the creation of a 2 Mb human artificial chromosome (HAC) using a protein-only centromere seeding approach that bypasses genetic engineering of target cells.

The paper investigates how neocentromeres reshape chromatin and identifies conserved features of native centromeres using haplotype-resolved assemblies and multi-omics data.

The paper analyzes young KRAB-zinc finger gene clusters in mice, showing ERVs drive genetic heterogeneity through recombination and duplication mechanisms.

This paper uses rare k-mers to identify centromere haplogroups in human populations and cancer translocations, revealing structural diversity and translocation mechanisms.

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.

VAMPIRE is a k-mer-based tool for TR discovery and analysis, revealing new insights into human and nonhuman primate centromeres and subtelomeres.

The paper uses a four-generation family to systematically assess de novo mutations and recombination, finding high mutation rates and paternal bias, along with a detailed recombination map.

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.

The paper uses Fiber-seq to show that regional centromeres have dichromatin organization, with accessible and compacted chromatin, which is conserved across species despite DNA sequence differences.

This study presents genome assemblies and analyses of macaques to explore genetic variation, population history, and evolutionary differences between species and humans.

CDR-Finder identifies hypomethylated regions in centromeres using long-read sequencing data and generates BED files and plots for analysis.

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 identifies a common flanking variant linked to increased meiotic stability at the FGF14-SCA27B repeat locus.

A second complete human centromere set (CHM1) plus 31 nonhuman primate centromeres reveals extensive α-satellite higher-order repeat variation, kinetochore repositioning, and saltatory emergence of new repeats.

This paper describes a method to efficiently form single-copy human artificial chromosomes by using a large construct and yeast spheroplast fusion to avoid multimerization.

The paper identifies structurally divergent regions in primate genomes and quantifies the impact of structural variants across multiple species.

The paper describes a novel centromere structure in the mouse species Mus pahari, characterized by a divergent repeat and unique CENP-B recruitment, enabling high-fidelity segregation during cell division.

The paper presents long-read assemblies of 43 diverse human Y chromosomes, revealing extensive structural complexity and variation across 180,000 years of evolution.

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

RAmbler improves de novo genome assembly of complex repetitive regions using high-quality long reads, outperforming existing tools on synthetic and real data.

Verkko automates telomere-to-telomere diploid genome assembly using long-read sequencing and graph-based methods, achieving high accuracy in chromosome assembly.

The paper identifies and categorizes large-scale genomic differences between the T2T-CHM13 and GRCh38 human genome assemblies, highlighting their implications for disease and evolution.

GAVISUNK validates genome assemblies by comparing distances between k-mers in HiFi assemblies and Oxford Nanopore reads to detect misassemblies.

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.