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This study identifies molecular subtypes of gastric adenocarcinoma that correlate with prognosis but find that neither histology nor a derived signature alone reliably stratifies survival.

This paper reports the genome assemblies and biosynthetic gene cluster analysis of four deep subsurface microbial isolates, identifying potential natural product pathways and shared/strain-specific enzymes.

This study shows chronic e-cigarette exposure accelerates atherosclerosis by reprogramming smooth muscle cells toward a chondrogenic phenotype through GRIN2A-dependent NMDAR signaling.

The paper integrates long-read and short-read data to analyze structural variation in canines, identifying new variants and selection signatures.

The paper develops ADhunter, a model to identify and quantify transcriptional activators in fungal genomes, expanding functional annotations across non-model species.

This study characterizes phage-plasmids in clinical Enterobacteriaceae isolates, finding they are common and associated with antimicrobial resistance and disease severity.

This study investigates the molecular consequences of epigenetic machinery disruption in neuronal progenitors by knocking out EM factors and analyzing gene expression and DNA methylation changes.

The paper develops a framework to analyze multivariate beta-lactam resistance in Streptococcus pneumoniae using MIC data from 3,628 isolates, revealing genetic mutations and lineage-specific resistance profiles.

This study uses low-coverage whole genome sequencing to assess genetic variation and structure in Swedish sand lizard populations, revealing strong population structure and low genetic diversity in some populations.

The paper presents a gap-free donkey genome assembly and identifies novel structural variants in functional genes.

The paper co-profiles nascent transcription and mature RNA in cycling human fibroblasts and finds their dynamics are concordant without a transcription-to-maturation lag.

The paper uses genomic data to compare reproductive isolation between Typha species in Europe and North America, finding stronger isolation in Europe due to prolonged sympatry.

The paper uses deep mutational scanning and structural analysis to study the functional effects of missense variants in the P2RY8 receptor and improves variant effect predictions.

This study presents a high-quality chromosome-level genome assembly of Sinibrama wui and identifies expanded gene families related to lipid metabolism and nervous system.

The paper establishes dynamic enhancer-based gene regulatory networks in human hematopoiesis, revealing that stemness loss and lineage acquisition are temporally and mechanistically uncoupled.

LongBench benchmarks long-read RNA-sequencing technologies using a cross-platform dataset of cancer cell lines, showing high gene-level concordance but reduced transcript-level consistency across platforms.

This study uses large-scale comparative genomics to analyze 131 Hymenoptera species, revealing genomic patterns and innovations linked to key evolutionary traits.

This study identifies changes in histone modifications H3K27ac and H3K9me3 in Aedes aegypti mosquitoes following Rift Valley fever virus exposure, linking these changes to gene expression patterns that support viral replication and host responses.

The paper identifies genome-wide promoter-enhancer interactions in rat brain using Hi-C data and CTCF binding sites, revealing regulatory elements linked to developmental processes.