whole-genome sequencing

The paper investigates the mcm4Chaos3 mutation in yeast, showing it causes genome instability by impairing specific centromere-proximal origins.

This study analyzes ancient U/V sex chromosomes in Polytrichaceae mosses, showing that recombination suppression has limited SDR expansion and functional degeneration despite their 124 million-year-old origin.

NPlasmid-seq detects sub-percent contamination and sequence heterogeneity in plasmid preparations using Cas9-encoded terminal signatures, revealing structural variants missed by consensus-based methods.

This study identifies genomic regions associated with DUS traits in Pakistani wheat varieties using GWAS, aiming to improve varietal identification through molecular markers.

The paper identifies tandem repeats in methanogenic archaea and their viruses, showing they contribute to genomic diversity and adaptation potential.

CNVision is a computational framework that automates the interpretation of intragenic copy number variants by standardizing input parsing, transcript mapping, and reading-frame classification.

This study shows that proteolytic feedback regulates quorum sensing in Pseudomonas aeruginosa by controlling RhlR stability, affecting virulence and biofilm formation.

This paper adapts ACMG/AMP variant classification criteria for the non-protein-coding gene RMRP, resulting in a framework for classifying variants in cartilage-hair hypoplasia.

This paper improves variant-effect prediction in sequence-to-function models using synthetic MPRA data generated from distilled model predictions.

The paper introduces eQIF, an unsupervised machine-learning method that integrates Enformer predictions to prioritize gene-regulatory variants, showing strong performance in predicting eQTLs and GWAS variants.

This study assesses non-MHC immune gene diversity in tigers using whole-genome data, finding higher variation at immune receptor genes and signs of balancing selection on Toll-like receptors.

This paper shows PHATE can better capture continuous population structure in genomic data than PCA or UMAP by tuning scale and balancing populations.

This study identifies genetic variants in FGF5 and CELSR1 associated with long and rough coat phenotypes in guinea pigs, revealing distinct molecular mechanisms.

The paper examines ancestry patterns and temperature effects in a Culex pipiens hybrid zone, finding urbanization increases molestus ancestry while temperature influences specific loci.

The paper reports whole genome assemblies of 28 Phaeosphaeriaceae isolates from Canada, revealing genetic diversity and potential new species.

This paper develops a stable RPE1 cell line with inducible and dose-dependent transgene expression using CRISPR/Cas9 and FRT/Tet-On systems, validated through multi-omics analysis.

The paper shows guide-tree bias in whole-genome alignment can mislead phylogenomic analyses and proposes a consensus alignment strategy to reduce this bias.

The paper presents the first chromosome-scale reference genome for Mytilus planulatus, revealing structural variation and population structure in mussels.

The paper estimates whole-genome heritability of complex traits across diverse populations, finding rare and non-coding variants significantly contribute to heritability.

This paper calibrates CADD v1.7 and AlphaGenome AVI for ACMG/AMP computational evidence across variant classes, showing AVI outperforms CADD and highlights the need for class-specific thresholds.

This study identifies convergent genomic and gene-level constraints in grasses adapting to extreme environments using phylogenomic data and large language models.

This study identifies mosaic chromosomal alterations in healthy human tissues, revealing tissue-specific patterns of mitotic errors and purifying selection across aging.

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 investigates the evolutionary relationship between flagellar motility and bacterial secretion systems, finding strong coupling with T6SS but not bacteriocins.

The paper integrates long-read, short-read, and SNP data using a pangenome and imputation framework to identify structural variants associated with stature and milk traits in dairy cattle.

The paper introduces kGain, a metric quantifying k-mer frequency shifts due to mutations, and shows it predicts adaptive potential across species and experimental systems.

The paper presents 25 new microsporidian genomes, revealing extreme pangenome diversity and novel tetraploid structures in some species.

ScanFold3 improves RNA structure prediction speed and accuracy, outperforming previous versions in benchmarking and validation.

This paper identifies genomic loci and mutations associated with DDT metabolic resistance in Anopheles gambiae using bulk segregant analysis and confirms their selection in natural populations.