whole-genome sequencing

This study shows that reducing insulin signaling in adulthood extends lifespan and reduces germline mutations in C. elegans, but only when the HRDE-1 pathway is functional.

The study identifies a selective sweep linked to xenobiotic detoxification in the pine processionary moth along altitudinal gradients, suggesting local selective pressures from xenobiotic exposure.

The paper investigates aneuploidy and chromosome rearrangements in Arabidopsis thaliana neo-polyploids, finding that breakpoints cluster at fragile sites linked to ancient genome rearrangements.

The paper identifies gene losses in Antarctic notothenioid fishes and links them to physiological adaptations to cold environments.

RosaSeed improves short read alignment speed while maintaining accuracy comparable to BWA-MEM2 by using a configurable seeding strategy.

The paper presents the first chromosome-level genome of the blueberry stem gall wasp, revealing repeat-driven genome expansion and insights into symbiont interactions and host adaptation.

This paper presents the first high-quality reference genome for Scalesia gordilloi, a critically endangered plant, using Oxford Nanopore sequencing to enable conservation and comparative genomics studies.

HaloClassifier distinguishes plasmid and chromosome contigs in haloarchaeal genomes with high accuracy, enabling plasmidome reconstruction in fragmented assemblies.

The paper presents gap-free telomere-to-telomere haplotype assemblies for a hybrid grouper, enabling genetic analysis and breeding applications.

This study compares genome features of Pseudomonas aeruginosa isolates from cystic fibrosis patients and environmental sources, finding smaller genomes and shorter prophage sequences in clinical isolates.

This paper improves ATAC-seq peak calling by integrating whole-genome sequencing data to control for DNA dosage biases, enhancing peak accuracy and relevance to gene regulation.

This study performs a pan-cancer multi-omic analysis of radiotherapy response, identifying genomic and transcriptomic features associated with radioresistance and poor survival.

The paper deconvolves HIV-1 mutational signatures across anatomical compartments and identifies APOBEC3-associated mutagenesis as a major contributor, showing donor-specific patterns.

The paper introduces FASTER, a method to detect accelerated evolution of function in genomic regions, finding more rapid evolution in conserved human sites linked to brain development and cognition.

The paper presents the first T2T genome assembly of Eucalyptus recurva, revealing genomic features and conservation insights.

PhAGE enables one-step integration of ~20 kb DNA fragments into E. coli genome, resolving the trade-off between simplicity and insert size in genome engineering.

This study develops a framework for designing phage cocktails against E. coli UTIs using genomic and phenotypic data, showing that complementary cocktails outperform redundant ones in time-kill assays.

The paper constructs a graph-based pangenome of Venturia inaequalis, identifies structural variants linked to population differentiation, and reveals gene repertoire conservation and virulence-associated diversity.

This study analyzes genetic diversity and evolution of European swine influenza A viruses from 2013 to 2022, identifying 150 genotypes and highlighting pig trade as a driver of viral spread.

This study evaluates a genome language model's ability to predict the effects of sequence changes in phages using experimental data, finding mixed success in distinguishing functional from nonfunctional mutations.

The paper compares somatic mutation rates and transcriptomic changes in neurons across six mammalian species, finding higher mutation accumulation and distinct age-related dysregulation in human neurons.

The paper evaluates methods for detecting and characterizing inversions in Timema stick insects, showing differences in their ability to identify and describe inversion structures.

Vir2vec is a genome-wide viral embedding model that outperforms existing models in viral genome understanding tasks and provides explainability for host adaptation mutations.

The paper identifies an insertion-deletion variant in a super-enhancer regulating LINC00636 and CD47 in breast cancer, showing its impact on chromatin accessibility and tumor-promoting features.

This study evaluates the pathogenicity of deep intronic variants in recessive retinal diseases using a high-throughput splicing assay, finding that 19.4% of variants activate cryptic exons.

This study evaluates an AI agent's ability to control biological workflows versus make biological judgments, finding it excels at orchestration but performs poorly at adjudication.

The paper investigates how molecular evolutionary rates in duckweeds correlate with acclimation strategies to high light, finding differences in mutation rates and metabolic adaptations between lineages.

The paper identifies an almost-complete Rickettsia africae chromosome in the genome of its arthropod vector, A. variegatum, demonstrating lateral gene transfer from the pathogen to the host.

The paper evaluates multi-omics prognostic models across TCGA-BRCA and METABRIC, finding limited incremental performance and highlighting issues with model transportability and feature stability.

EPIC challenges teams to predict transcription initiation from DNA sequence in non-model metazoans, aiming to assess generalizability beyond human and model species.