Charles J. Markello

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

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.

A Draft Human Pangenome Reference

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

Recombination between heterologous human acrocentric chromosomes

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

A Complete Pedigree-Based Graph Workflow for Rare Candidate Variant Analysis

The paper introduces a pedigree-aware workflow using pangenome graphs to improve variant calling in rare disease analysis, detecting more deleterious variants in probands than unaffected siblings.

Benchmarking challenging small variants with linked and long reads

This paper expands genome benchmarking to include difficult-to-map regions using linked and long reads, identifying more false negatives in variant calling.

Federated analysis of BRCA1 and BRCA2 variation in a Japanese cohort

The paper demonstrates federated analysis of BRCA1 and BRCA2 variants in a Japanese cohort to interpret variants of uncertain significance without transferring sensitive data.

Genotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkit

The paper introduces Giraffe, a pangenome mapper that improves genotyping of SNVs, indels, and SVs in 5,202 human genomes using the vg toolkit.

A Diploid Assembly-based Benchmark for Variants in the Major Histocompatibility Complex

The paper develops a diploid assembly-based benchmark for variants in the MHC region using HG002 data, identifying 21496 small variants with high concordance to clinical HLA types.

Sequence variation aware genome references and read mapping with the variation graph toolkit

The paper introduces vg, a toolkit for creating and using variation graphs as genome references, improving read mapping and variant calling accuracy over linear references.