Justin M. Zook

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

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 uses long-read sequencing to characterize lentiviral provirus insertions in clonal CAR-T cell lines, revealing structural variations missed by short-read and ddPCR methods.

Aardvark benchmarks genomic variant calling accuracy by comparing haplotype sequences with a basepair score, supporting multiple variant types and outperforming hap.py.

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

The paper creates a long-read benchmark for genetic variants using a large pedigree, improving variant calling performance and introducing new truth sets for tandem repeats and structural variants.

The paper describes a comprehensive genomic dataset from a tumor-normal pair with broad consent, generated using multiple sequencing technologies for benchmarking somatic variant detection.

The paper creates a variant benchmark for X and Y chromosomes using a complete assembly of HG002, highlighting challenges in variant detection in complex regions.

The paper develops a benchmark for detecting low-frequency mosaic variants in the HG002 reference material using high-coverage sequencing data and validates its utility across multiple technologies.

The paper uses long-read sequencing on 100 samples from the 1000 Genomes Project to identify structural variants and improve understanding of human genetic variation.

The paper introduces genomic stratifications for human reference genomes GRCh37, GRCh38, and T2T-CHM13v2.0 to benchmark variant caller performance in difficult regions.

StratoMod predicts variant calling errors using interpretable machine learning to help design better variant calling pipelines.

GrapHiC improves Hi-C read imputation by integrating Hi-C and ChIP-seq data in a graph framework, enhancing performance on sparse and cross-cell-type inputs.

This work extends vcfdist to jointly benchmark SNPs, INDELs, and SVs, showing error reductions and improved accuracy over previous methods.

This paper introduces LongTR, a tool for accurately genotyping tandem repeats from long reads, and provides its code repository.

The paper benchmarks small and large variants in tandem repeats across 86 samples, creating a benchmark dataset and comparison method for TR variant calling.

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 a pangenome research toolkit to analyze complex genomic variations across multiple scales, improving the interpretation of repetitive and clinically relevant genes.

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 introduces FixItFelix and a modified GRCh38 reference to improve variant calling and expression analysis in genes with reference errors, showing benefits across multiple sequencing types and populations.

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

The paper evaluates variant calling in difficult genomic regions using short- and long-read sequencing, showing improved performance with new methods and multi-technology approaches.

The paper improves a telomere-to-telomere human genome assembly by developing a repeat-aware polishing strategy, fixing 51% of errors and increasing assembly quality.

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

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

The T2T-CHM13 reference genome improves read mapping and variant calling across diverse samples, reducing false positives and enabling novel variant discovery.

This paper creates a comprehensive benchmark for challenging medically-relevant autosomal genes, improving variant recall from 8% to 100% by addressing reference-specific false duplications.

The paper evaluates the detection of technically challenging variants in NGS workflows using synthetic specimens and clinical data from 450,000 patients, finding significant variability in detection rates.

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.