whole-genome sequencing

The paper introduces MOTET, a Bayesian framework that jointly infers multimodal mutational processes in cancer genomes, improving accuracy over post hoc methods.

The paper investigates how adaptive tracking contributes to the invasion success of Drosophila suzukii by showing rapid evolution of thermal tolerance and other traits in response to environmental conditions.

The paper identifies an oxidative mutational signature in normal tissues of individuals carrying a single pathogenic MUTYH allele, suggesting a measurable mutational risk in healthy tissues.

bofasa improves orthology inference for bacterial genomes by addressing limitations of eukaryotic methods, achieving higher accuracy and better core genome recovery.

MicroDUET is a genomic foundation model that provides fast, accurate representations for pathogen surveillance by distinguishing phylogeny and function.

This study identifies 86 gene-phenotype associations for cardiovascular diseases using whole-genome sequencing data from UK Biobank participants, including 46 novel associations and insights into sex-specific and ancestry-related genetic effects.

The paper examines thermal adaptation in bacterial chaperone mRNAs, finding no strong structural differences but a significant shortening of the groL coding sequence in thermophiles.

The paper examines genomic variation across nine co-occurring plant species in an Australian mountain range, finding shared spatial patterns but differing associations with geographic and environmental factors.

This paper presents a chromosome-scale genome of Spondias tuberosa, revealing conserved genome architecture and gene family expansions in Anacardiaceae.

Genomes2Genes converts Progressive Cactus alignments into validated gene-level alignments, identifying de novo genes and enabling evolutionary analysis.

This study identifies TilR, a MarR-family regulator in Klebsiella oxytoca, as a repressor of tilimycin biosynthesis and links it to metabolic and virulence-related gene expression.

This study identifies extensive horizontal gene transfer in the fungus gnat Bradysia coprophila, showing these genes contribute to stress tolerance and ecological adaptation.

The paper identifies conserved overlapping accessory ORFs in coronavirus N genes and shows that nucleotide and codon biases drive their formation.

This study uses herbarium specimens to analyze genetic variation in Lygodium japonicum during its invasion of North America, identifying Asia as the source and finding evidence of rapid adaptation and reduced non-coding diversity.

This paper introduces MirrorDNA, a DNA language model with a strand-equivariant tokenizer that improves prediction consistency across DNA strands.

The paper updates a toolkit for genetic studies in C. briggsae by identifying indel variants and mapping mutations to genes using high-throughput sequencing.

The paper investigates how gene expression influences genome-wide mutation rates in Drosophila melanogaster and Caenorhabditis elegans, finding that highly expressed genes have lower mutation rates due to transcription-coupled repair.

GIBD detects IBD segments in pangenome graphs and annotates them with structural variants, outperforming existing methods in accuracy and speed.

This study uses genomic analysis to reclassify the Streptococcus anginosus group into four taxa, revealing diversity and lineage-associated traits linked to invasive disease.

This study identifies and characterizes VQ genes in sorghum, showing their differential expression and potential roles in salt stress tolerance.

The paper uses whole-genome analyses to challenge the two-domestication model of cattle, showing zebu originated from admixture between taurine cattle and Indian aurochs with introgression from gaur-like or banteng-like populations.

This study characterizes the MHC genomic architecture in the Midas cichlid using integrated genomic and transcriptomic analyses, revealing gene diversity, evolutionary patterns, and tissue-specific expression.

memVar links human membrane protein variants to molecular contexts and disease, revealing enrichment of pathogenic variants in transmembrane regions and interaction sites.

The paper reconstructs the asperosaponin biosynthesis pathway in Dipsacus asperoides by integrating genomics, transcriptomics, and biochemical analyses, revealing gene family diversification and glycosylation order.

Earl Grey ParTEA annotates transposable elements across multiple genomes, revealing shared and private TE families and improving annotation consistency.

The paper introduces a DNA-first framework to detect genomic architectures by analyzing raw DNA sequences, identifying potential RNA-to-DNA systems without prior protein knowledge.

GeneFamHunter recovers gene-family members from genome assemblies, outperforming existing methods in identifying divergent and tandemly arrayed genes.

The paper shows that neural RNA splicing models rely on reading frame information that the splicing machinery cannot access, leading to errors in predicting poison exons.

This study examines parallel evolution of nuclear OXPHOS genes in threespine stickleback across freshwater populations and identifies mitonuclear evolutionary coupling in specific functional modules.

This study identifies anti-phage defense systems in VREfm genomes and finds limited associations between specific systems and phage resistance, with one candidate gene reducing susceptibility.