Michael C. Zody

A comprehensive assessment of tandem repeat genotyping methods for Nanopore long-read genomes

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.

A global view of human centromere variation and evolution

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graph

Lancet2 improves somatic variant calling with faster runtime and better performance, especially for InDels, using enhanced methods and machine learning.

Complex genetic variation in nearly complete human genomes

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.

A comprehensive catalog of 3D genome organization in diverse human genomes facilitates understanding of the impact of structural variation on chromatin structure

The paper develops a Hi-C analysis pipeline to catalog TADs and loops in human genomes and quantifies the impact of SVs on chromatin structure and gene expression.

Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation

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.

Impact and characterization of serial structural variations across humans and great apes

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.

Rare genetic variation in Fibronectin 1 (FN1) protects against APOEe4 in Alzheimer's disease

The paper identifies rare FN1 variants that protect APOEε4 carriers from Alzheimer's disease by modulating extracellular matrix deposition and gliosis.

Multi-OMIC analysis of Huntington disease reveals a neuroprotective astrocyte state

This study uses multi-omic analysis to identify a neuroprotective astrocyte state in Huntington disease that correlates with delayed disease onset and neuroprotection.

Whole genome error-corrected sequencing for sensitive circulating tumor DNA cancer monitoring

This study applies low-cost whole genome sequencing to detect circulating tumor DNA at high sensitivity in plasma samples, achieving error rates as low as 10^-7 and enabling cancer monitoring without matched tumor sequencing.

High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

The paper presents a high coverage whole genome sequencing resource of 3,202 samples, including 602 trios, generated from the expanded 1000 Genomes Project.

Pangenome-based genome inference

PanGenie improves variant calling by using a pangenome reference and k-mer counts, achieving higher accuracy and speed compared to traditional methods.

De Novo Mutation in an Enhancer of EBF3 in simplex autism

Whole-genome sequencing in thousands of families reveals variants relevant to simplex autism in a brain enhancer of the well-established neurodevelopmental disorder gene EBF3.

Mako: a graph-based pattern growth approach to detect complex structural variants

Mako detects complex structural variants using a graph-based pattern growth approach, achieving 70% validation rate on real data and identifying 15 CSV types including two novel ones.

De novo assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation

The paper presents 64 haplotype-resolved human genomes using long-read sequencing and identifies structural variants, SV-eQTLs, and adaptive selection candidates.

Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium

The paper identifies eQTLs for ACE2 and TMPRSS2 in children's airway transcriptomes and links their expression to T2 inflammation and interferon responses, influencing SARS-CoV-2 infectivity.

Somatic variant analysis of linked-reads sequencing data with Lancet

The paper introduces an updated version of the Lancet somatic variant caller that supports linked-reads sequencing data analysis by integrating barcodes and haplotype read assignments.

Genome wide-association study identifies novel loci in the Primary Open-Angle African American Glaucoma Genetics (POAAGG) study

The paper identifies a novel POAG-associated SNP in African Americans using a genome-wide association study.

Recent ultra-rare inherited mutations identify novel autism candidate risk genes

The paper identifies ultra-rare inherited mutations that are younger and preferentially transmitted to autism probands, revealing novel candidate genes and functional networks.

Deep sequencing of 3 cancer cell lines on 2 sequencing platforms

The paper benchmarks a new sequencing platform and develops a somatic calling pipeline using deep sequencing of cancer cell lines on two platforms.

Novel patterns of complex structural variation revealed across thousands of cancer genome graphs

The paper identifies three novel complex structural variation patterns in cancer genomes using genome graph analysis across 2,833 tumor WGS.

Mapping and characterization of structural variation in 17,795 deeply sequenced human genomes

The paper maps and characterizes structural variants in 17,795 human genomes, revealing their frequency, impact, and relationship to gene dosage and regulatory elements.

Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects

The paper defines functional equivalence standards for genome sequencing pipelines to enable harmonized variant calling across diverse datasets with minimal batch effects.

WHOLE GENOME BISULPHITE SEQUENCING USING THE ILLUMINA HISEQ X SYSTEM

The paper optimizes library preparation and sequencing for whole genome bisulphite sequencing on the Illumina HiSeq X system, eliminating an artefact affecting several percent of reads.

taxMaps - Ultra-comprehensive and highly accurate taxonomic classification of short-read data in reasonable time

taxMaps provides fast and accurate taxonomic classification of short-read metagenomic data with significantly reduced computational cost compared to BLASTn.

Lancet: genome-wide somatic variant calling using localized colored DeBruijn graphs

Lancet improves somatic variant calling accuracy, especially for indels, using colored DeBruijn graphs and local assembly across synthetic and real whole-genome sequencing data.

Indel variant analysis of short-read sequencing data with Scalpel

This paper introduces Scalpel, an open-source tool for accurate indel detection from short-read sequencing data, and demonstrates its application in various analysis modes.