whole-genome sequencing

This study examines selfing rates and self-incompatibility system stability in Suillus luteus across native and introduced ranges, finding no loss of the SI system or unisexual reproduction in introduced populations.

This study shows that regional history, not phylogeny or range size, primarily shapes demographic changes in Indo-West Pacific sea snakes over the last 200 thousand years.

The paper examines how the timing of anti-CRISPR gene expression in phages affects CRISPR-Cas interactions, finding that spacers map to earlier positions in genomes containing anti-CRISPR systems.

This study uses SCID-rab PDX models to analyze genomic and transcriptomic features of multiple myeloma, revealing selection of pre-existing high-risk clones.

This study investigates the evolutionary transition of fungi from land to sea using Kluyveromyces yeasts, finding genome size reduction, phenotypic changes, and positive selection in marine species.

The paper identifies over 200 new mobile transposable element families in Arabidopsis thaliana using pangenomic analysis, showing they contribute to large-effect alleles despite being rare in most strains.

The paper identifies and corrects missed introns in tRNA genes of Asgard archaea, revealing repeated intron gains and their splicing motif preferences.

DIPLER identifies structurally complex loci using k-mer analysis and de novo assembly from low-coverage sequencing data.

This study identifies RER deficiency as a new DNA repair defect in cancer, detectable through mutational signatures and linked to therapeutic vulnerabilities.

The paper analyzes genetic structure and diversity of Coccidioides immitis in environmental and human isolates to understand disease transmission and environmental distribution.

The paper shows early NOTCH1 mutations are selected in normal tissue but suppress later cancer driver mutations through epistasis, highlighting stage-specific mutation effects in esophageal cancer.

The paper analyzes 385 Pg genomes to show Kazakhstan hosts a diverse sexual clade with many HD haplotypes, and Pgs contributes virulent alleles to wheat rust pathogens.

This paper demonstrates that lateral flow devices can be used for rabies virus genomic surveillance, enabling rapid and decentralized genome collection without additional sample collection.

This study identifies molecular and architectural changes in normal-adjacent field tissue in HNSCC that disrupt epithelial differentiation and may promote cancer development.

This study uses nanopore sequencing to analyze chromosomal structural variation and vanA plasmid dynamics in a hospital outbreak of VREfm, revealing genetic diversity beyond allele-based typing.

PlantGeneAnn is a plant-optimized gene annotation tool that outperforms existing methods on a 20-species benchmark and enables efficient fine-tuning for non-model species.

This study evaluates the accuracy of eucalypt taxonomy by comparing gene tree topologies to a concatenated species tree, revealing inconsistencies in taxonomic groupings.

This study introduces scIRES-seq to analyze CTCs from cervical cancer, revealing multimodal molecular heterogeneity through integrated genetic, epigenomic, and transcriptomic profiling.

This paper introduces Borzoi-SE, a deep learning framework that identifies super-enhancers and detects pathogenic variants directly from DNA sequence across multiple human cell lineages.

This study uses whole-genome resequencing to analyze genetic diversity and structure in Swiss grayling populations, revealing population declines, admixture, and limited genetic contribution from hatchery releases.

DNA-LLM2Vec adapts decoder DNA models to bidirectional context for genomic tasks, improving performance on extended-context tasks but varying by task and backbone.

The paper re-speciates Corynebacterium using genome data from 87 isolates and identifies four novel species candidates, resolving taxonomic conflicts and clarifying functional roles.

The paper benchmarks structural variant analysis tools on short-read WGS data, finding that ensemble pipelines significantly reduce accuracy compared to individual tools.

LOCALE improves DNA sequence search by learning variation-robust embeddings, outperforming existing methods on benchmark datasets and real biological variance tasks.

The paper introduces genomeRxiv, a web server that enables precise strain-level identification of prokaryotes using ANI-based LINs, overcoming limitations of traditional taxonomic classification.

This study constructs a pangenome for deer mice to reveal extensive structural variation and its evolutionary implications.