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This paper develops a low-cost amplicon sequencing assay to rapidly characterize Staphylococcus aureus intrahost diversity directly from samples, enabling transmission analysis without whole-genome sequencing.

This paper shows RNA-seq can detect most mutations found by WGS in pediatric tumors and provides additional insights into their pathogenicity.

This paper reviews methodological challenges in GWAS of biobank data with time-to-event outcomes, proposing a two-step martingale residual approach for efficient analysis.

This study benchmarks four peak calling methods for CUT&RUN data, revealing variability in performance across histone marks and highlighting method-specific strengths.

This study uses genomic and modeling approaches to show Asian pika populations responded to Pleistocene glaciation events with population bottlenecks and expansions, revealing low effective population sizes and informing conservation strategies.

This study assesses genetic diversity and population structure of Atlantic bottlenose dolphins in Mississippi Sound using whole mitogenomes from stranded animals, identifying four distinct populations.

The paper develops a MAGIC population for eggplant, identifies a gene linked to root morphology, and shows its potential for trait mapping and breeding.

The paper finds that positive genetic interactions have greater scientific impact but are underrepresented in literature, despite equal detection capability.

This study constructs a reference-free pangenome of Arabidopsis thaliana using 93 assemblies, revealing gene and pseudogene diversity across geographic regions.

This study constructs a transcriptional and epigenetic atlas of T cell development in neonatal and adult mice, identifying age-related gene regulatory programs and a conserved regulator, Zbtb20.

This paper benchmarks three statistical phasing methods using synthetic diploids, finding consistent error patterns across methods and populations.

The paper uses Nanopore duplex sequencing to analyze 5hmC and 5mC distribution in medaka brain DNA, revealing strand-specific patterns in CpG dinucleotides.

MintFlow is a generative AI algorithm that predicts how tissue perturbations reprogram cell states in disease, revealing novel cell populations and therapeutic targets in three human conditions.

This study presents a chromosome-level genome assembly of the spider mite Tetranychus cinnabarinus, identifying key detoxification genes relevant to pesticide resistance.

The paper de novo assembles the genome of Agropyron cristatum and identifies genes for wheat improvement, developing a genome-selection model for breeding derivatives.

This study uses ancient DNA to show genetic continuity and differences in kinship systems among Early Copper Age communities in the Carpathian Basin.

This paper applies HERRO error correction to Oxford Nanopore sequencing data to resolve a neonatal ICU MRSA outbreak at the SNV level, achieving results comparable to Illumina sequencing.

MITScan performs genome-wide association analysis between microbiome and host transcriptome using zero-inflated negative binomial models, achieving computational efficiency with score tests and permutation methods.

The paper analyzes allelic coverage in oysters to identify SNPs associated with polymorphic duplications, finding 15% of variants linked to copy number variations across chromosomes.

The paper introduces a comprehensive database integrating 16S, 23S, and 5S rRNA sequences, alignments, intragenomic heterogeneity, and secondary structures from around 5000 microbial genomes.