Matthew W. Mitchell

New iPSC resource with long-read whole genome sequencing characterizations for enhanced in vitro modeling

The paper introduces a new iPSC resource with long-read whole-genome sequencing data for in vitro modeling and genomic analysis.

A complete diploid human genome benchmark for personalized genomics

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.

A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos

This study presents a pan-pangenome of humans, chimpanzees, and bonobos, revealing structural variation, selection patterns, and adaptations related to immunity and malaria resistance.

Recurrent structural variation and recent turnover at the 17q21.31 locus in humans and great apes

The paper characterizes structural variation at the 17q21.31 locus in humans and great apes, identifying new haplotypes and evolutionary dynamics.

Haplotype-resolved centromeric chromatin organization from a complete diploid human genome

The paper uses a complete diploid human genome to study centromeric chromatin organization, revealing that DNA methylation regulates centromere structure and plasticity.

Community member, community liaison and researcher perspectives on the creation of HapMap and 1000 Genomes Project iPSCs

The paper surveys community and researcher perspectives on creating iPSCs from HapMap and 1000 Genomes Project biospecimens, finding broad support but also concerns.

Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance

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

Whole-Genome Sequencing Reveals Individual and Cohort Level Insights into Chromosome 9p Syndromes

This study uses whole-genome sequencing to analyze 9p deletion and duplication syndromes, identifying key genes and structural variants, and introduces a machine learning model for syndrome prediction.

A new NHGRI Sample Repository for Human Genetic Research collection of induced pluripotent stem cell lines.

The paper describes a new NHGRI Sample Repository containing seven iPSC lines generated from PBMCs, with genomic data for studying genetic variation and its functional implications.

Environmentally-mediated selection parallels population divergence across a chimpanzee subspecies contact zone

This study identifies genes under selection in chimpanzee subspecies at a contact zone, linking environmental variation to genetic divergence and adaptation.

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.

Automated assembly of high-quality diploid human reference genomes

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.

A fast machine-learning-guided primer design pipeline for selective whole genome amplification

The paper introduces swga2.0, a machine-learning-guided pipeline for designing selective whole genome amplification primers, significantly reducing runtime and improving amplification performance for microbial DNA.