Mark Chaisson

Isocall is a scalable method for joint transcript identification from long-read RNA-seq data, showing high precision and handling large datasets efficiently.

Owl quantifies microsatellite instability from long-read data, identifying MSI-high genomes and motif-specific patterns in cancer samples.

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.

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

This paper develops a pangenome-based method to improve trait association and genomic prediction by capturing complex genetic variation missed by traditional approaches.

This study uses long-read sequencing to map transposable element variation in human brain tissue, revealing regulatory and epigenetic effects across cell types and ancestries.

The paper introduces CLASH, a method to quantify how genetic variation, methylation, and CTCF occupancy affect chromatin loop strength across individuals.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

The paper identifies FGF14 GAA repeat expansions in Parkinson's disease using long-read sequencing and finds they occur in both patients and controls.

The paper introduces ctyper, a method for genotyping CNV and CMR genes using pangenomes, showing improved accuracy in copy number and expression divergence of duplicated genes.

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.

TRUHiC enhances low-resolution Hi-C data using deep generative modeling to improve 3D chromatin structure characterization across cell lines and species.

The paper uses long-read sequencing to identify structural variants and their impacts on gene expression and methylation in diverse human brain samples.

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.

The paper introduces a new TR catalog, TRExplorer v1.0, containing 4.86 million loci, designed for both short-read and long-read analyses and includes variation clusters identified using long-read HiFi data.

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 constructs TRCompDB, a database of 4.4 million tandem repeat loci across 832 human genomes, revealing mutation rates and dynamics influenced by recombination and duplication context.

VISTA improves structural variant detection by integrating multiple callers with a novel filtering algorithm, achieving high accuracy across various SV types and genomic contexts.

The paper presents a scalable pipeline for reference genome assembly and evaluation, demonstrating its effectiveness across 51 vertebrate species using Galaxy.

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

HQAlign improves structural variant detection from nanopore reads by incorporating sequencing physics and SV-specific alignment adjustments, capturing more SVs than minimap2 with comparable performance.

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

The paper identifies VNTR motifs linked to gene expression using a repeat-pangenome graph, showing motif variation explains more associations than VNTR length.

The paper presents a comprehensive catalog of structural variants across 138,134 individuals, identifying novel variants and their associations with cardio-metabolic and hematologic traits.

This paper develops a scalable protocol for Oxford Nanopore long-read sequencing, achieving high SNP and structural variant detection with haplotype-resolved methylation calls, suitable for large-scale genomics projects.

This paper presents a haplotype-resolved genome assembly of the Nile rat, revealing unique genomic features relevant to type 2 diabetes and metabolic dysfunctions.

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 vamos, a method to annotate VNTRs by selecting representative motifs, and applies it to 32 haplotype-resolved human genomes, finding an average of 3.1-4.0 alleles per locus.

TT-Mars evaluates structural variant calls by comparing them to haplotype-resolved assemblies, showing high accuracy and additional variant detection compared to existing methods.