Julian Lucas

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

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 constructs an atlas of telomere variation across humans using long-read sequencing and reveals heritable telomere variant repeats and telomerase-independent extension mechanisms.

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

DeepPolisher improves genome assembly accuracy by reducing errors using a transformer model and phasing method, achieving over 70% indel error reduction.

This paper demonstrates that ONT Duplex sequencing combined with Pore-C data can assemble complete, high-quality human and plant chromosomes with base accuracy over 99.999%.

The paper introduces methods for haplotype-resolved de novo assembly using Shasta and GFAse, showing improved assembly quality with newer Oxford Nanopore reads.

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.

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

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

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.

The paper assesses SNVs within human segmental duplications, finding increased mutation rates and interlocus gene conversion, along with distinct mutational spectra.

The paper presents a comprehensive analysis of fully assembled human centromeres, revealing their architecture, variation, and evolutionary dynamics at high resolution.

The paper describes AnVIL, a cloud-based platform that enables genomic data analysis without data transfer, improving security, scalability, and collaboration.