whole-genome sequencing

THRESHER calculates data-driven SNP thresholds for bacterial genomes to improve strain classification compared to fixed cutoffs.

The paper presents draft genome assemblies for two ant species, analyzing genome size variation and gene family expansions related to brood management strategies.

GLARE is a TE classifier that outperforms existing methods across multiple taxonomic groups and sequence quality conditions using a genomic language model fine-tuned on harmonized reference data.

The paper presents the genomes of Ayahuasca source plants, revealing retrotransposon-derived centromeres and distinct biosynthetic pathways for DMT and beta-carbolines.

The paper characterizes HPV integration structures in oropharyngeal cancer and links Type2 integration to oncogenic features and aggressive tumor behavior.

The paper investigates rDNA instability in aging yeast, identifying new forms of instability beyond ERCs that contribute to lifespan variability.

The paper compares recombination rates in intracellular and encapsidated reovirus RNA, finding higher recombination in intracellular RNA and suggesting recombination occurs more frequently during plus-strand synthesis.

This study establishes genetic tractability in Jeongeupia sacculi HS-3 by disrupting rpoS, showing it regulates biofilm formation under low-nutrient conditions but not general stress survival.

The paper exposes eastern oyster larvae to combined stressors and finds compositional genomic synergy despite additive survival and allele-frequency change.

This study shows bovine H5N1 influenza viruses have adapted to efficiently use NeuGc receptors in cattle, enhancing replication without significantly altering zoonotic risk.

The paper compares the rate of decline in gene-level evolutionary conservation and human constraint scores with disease onset age across Mendelian diseases.

The paper presents a chromosome-level genome assembly for the chilli thrips Scirtothrips dorsalis, providing genomic resources for studying its biology and pest status.

This study analyzes complete PEDV genomes to reveal temporal genetic differentiation and recombination in US PEDV populations, expanding the known geographic distribution of S1 clades.

The paper shows that routine strain handling of Komagataeibacter rhaeticus exposes recurrent genome reduction at a dynamic accessory locus, leading to phenotypic variation.

This study compares genomic adaptations of cheese-associated Nectriaceae fungi, revealing contrasting evolutionary paths involving gene family expansions, reductions, and horizontal gene transfer.

The paper develops a model to predict NMD outcomes for protein-truncating variants using RNA-seq data, achieving ~78% ROC-AUC and identifying non-canonical determinants.

The paper examines how demographic history affects genetic diversity and performance traits in insular and mainland lizard populations, finding elevated genetic load correlates with reduced bite force.

This paper evaluates genomic foundation models using splice-variant perturbations, finding they match task-specific networks and generalize across mutation types.

The paper introduces a structured-evidence framework for predicting bacteriophage-host interactions using a large language model, achieving high accuracy and enabling interpretable inference.

This study examines genomic divergence and diversity in three Hydrophis sea snake species, finding shared demographic patterns and linked selection, with chemosensory genes showing elevated diversity.

The paper introduces Cerberus, an improved regulatory sequence model using bidirectional state space blocks, achieving higher accuracy and efficiency than existing models like Borzoi.

The paper uses long-read sequencing to study how nucleosome positioning affects isoform expression by analyzing chromatin and RNA in yeast.

The paper presents nine T2T genomes of Lake Malawi cichlids, revealing a novel centromeric satellite structure with inverted elements and potential implications for speciation.

This paper presents a statistical framework for correcting SARS-CoV-2 genomic sequences using phylogenetic priors, improving call rate and accuracy in challenging regions.

PRISM estimates sample-specific correlation networks for cross-sectional and longitudinal omics data, improving accuracy and uncertainty quantification over existing methods.

The paper investigates recombination near the mating-type locus in Cladorrhinum fungi, finding no evidence of large recombination suppression despite pseudo-homothallic life cycles.

The paper investigates the relationship between mutation rates and selective constraint in the human genome, finding higher mutation rates in protein-coding genes compared to non-coding regions.

Anvaya analyzes chromosome fusion and mixing events to infer phylogenetic trees and detect whole-genome duplications using synteny data.

This study investigates how coevolution between phages and bacteria affects interaction networks by analyzing genetic changes in both hosts and phages.

The paper examines the evolutionary fate of the nebulin superfamily after teleost-specific genome duplication in zebrafish and medaka, showing lineage-specific retention and expression divergence of duplicated LASP genes.