Michael C. Schatz

The paper analyzes genetic variation, ancestry, and DNA methylation in Hispanic/Latino participants using long-read sequencing, identifying novel variants and phenotype associations.

The paper introduces the Microbiology Galaxy Lab, a community-driven platform for reproducible and FAIR microbial data analysis, offering tools for various omics data types and use cases.

This paper demonstrates agentic science on public infrastructure to ensure reproducibility by making all agent actions and workflows publicly accessible.

Alignment-free pan-k-mer profiles track minimap2 similarity (whole-chromosome r^2 0.959-0.968), profile 605 vertebrate genomes in about a day on 40 cores, and nominate trait-linked loci across plants and animals.

Perseus improves taxonomic classification of long-read metagenomes by refining Kraken2 results with lineage-aware confidence estimation, reducing false assignments and improving precision.

The paper identifies SNPC-1.2 as a female-specific piRNA transcription factor in C. elegans, revealing how gene duplication and functional specialization generate sex-specific piRNA expression.

The paper presents a large reference panel of 515,579 genomes to improve rare-variant imputation across underrepresented populations, enhancing accuracy for variants with frequencies as low as 0.002%.

The paper constructs a high-resolution human pangenome structural variant resource, identifies disease-associated SVs, and demonstrates its utility in filtering variants from probands and associating SVs with traits in a large cohort.

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.

AniAnns annotates tandem repeat arrays by leveraging high ANI between repeat units, improving annotation accuracy and speed across plant and animal genomes.

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.

This study identifies genes linked to cancer risk variation across species, showing indirect effects on body size dominate cancer suppression, while direct effects increase tumour prevalence.

The paper describes the Common Fund Data Ecosystem (CFDE), which integrates NIH Common Fund data resources to enable discovery, analysis, and collaboration across heterogeneous datasets.

The paper assembles unmapped reads from South Asian genomes to reveal hidden genetic variation not captured by traditional reference-based methods.

The paper shows a neofunctionalized gene in Solanaceae plants became a flowering antagonist, influencing adaptation across species and environments.

The paper demonstrates a framework using BRC-Analytics and agentic AI to standardize RNA-seq analysis of fungal pathogens, achieving reproducible results across studies with differing annotations.

This study surveys the AnVIL community to understand user needs, training preferences, and platform adoption opportunities.

This paper uses CRISPR/Cas9 to engineer compact Physalis peruviana plants to improve yield and scalability for agricultural production.

The paper analyzes long-read sequencing data from the All of Us Research Program to identify structural variants and their associations with diseases in a large cohort of Black or African American participants.

This study compares the genomics of seven Trichomonas species, revealing convergent genome size expansions in human-infecting lineages and genes involved in host-switching from birds to humans.

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

The paper integrates long-read sequencing and gene expression to prioritize functional structural variants and tandem repeats in rare disease patients, identifying potential causal variants in a neurodevelopmental disorder.

Uncalled4 improves nanopore signal alignment for DNA and RNA modification detection, identifying more modifications than existing tools in human cell lines.

The paper uses long-read sequencing data to analyze STR variability across 2,645 individuals, identifying disease-associated STR loci with elevated allelic variability and introducing the PLVI metric.

The paper identifies bi-directionally expressed enhancers in maize with domestication signatures using integrated epigenomic and transcriptomic data from multiple tissues and inbred lines.

This paper demonstrates that ONT Duplex sequencing combined with Pore-C data can assemble complete, high-quality human and plant chromosomes with base accuracy over 99.999%.

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.

BEATRICE identifies causal variants from GWAS summary data using a Bayesian framework, outperforming baselines in coverage and finding the APOEε2 allele in Alzheimer's disease.

The paper uses pan-genomics and genome editing in Solanum to show that paralog diversification hinders genotype-phenotype predictability in crop domestication.

The paper investigates convergent evolution of plant prickles, finding that mutations in a cytokinin gene repeatedly cause prickle loss across species.