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Genetic risk and inflammatory signaling converge on cell type-specific regulatory programs in type 1 diabetes

This study identifies T1D-associated SNPs that alter chromatin accessibility at TF binding sites in pancreatic islets, linking genetic risk to cell type-specific regulatory programs.

EWS::WT1 Isoform-Dependent Regulation of Neogenes in Desmoplastic Small Round Cell Tumors

This study identifies DSRCT-specific neogenes regulated by the EWS::WT1 fusion protein and shows their potential as biomarkers and therapeutic targets in desmoplastic small round cell tumors.

When to Trust Epigenetic Clocks: Avoiding False Positives in Aging Interventions.

This study evaluates epigenetic clocks for aging interventions, finding newer clocks trained on mortality or aging rates are more reliable than those based on chronological age.

The role of methylation and structural variants in shaping the recombination landscape of barley

This study identifies genomic features that explain recombination variation in barley, showing methylation and structural variants jointly determine recombination hotspots and coldspots.

Fetal signatures in the 3D genome of iPSC-derived neurons and their implications for disease modeling

This study compares chromatin architecture in iPSC-derived neurons to fetal and mature neurons, finding iPSC-derived neurons resemble fetal neurons and have distinct chromatin features.

A systematic delineation of 3' UTR regulatory elements and their contextual associations

The paper identifies 3'UTR regulatory elements using synthetic inserts and a deep learning model, revealing their effects on gene expression and nuclear-cytoplasmic partitioning, and highlights disease-relevant variants.

Historical plant embryos as alternative sources of ancient DNA for whole genome sequencing

The paper isolates DNA from seed embryos of historical plant specimens to improve ancient DNA quality for whole genome sequencing, finding embryos provide better DNA preservation than leaves in some species.

The Genome In A Bottle HG002 assembly-based variant benchmark set enables comprehensive benchmarking of small and structural variants.

The paper introduces a comprehensive variant benchmark set derived from a high-quality diploid assembly, improving small and structural variant detection across complex genomic regions.

Chromosome-level genome assembly of the Olympia oyster (Ostrea lurida), the only oyster species native to the West Coast of North America

The paper presents a chromosome-level genome assembly of the Olympia oyster, enabling insights into its biology and aiding conservation and restoration efforts.

When clades collide: Genomic admixture in blacklegged ticks (Ixodes scapularis) from the Great Plains

This study analyzes genomic admixture in Ixodes scapularis ticks from the Great Plains, finding admixed populations in Nebraska with no B. burgdorferi infection, suggesting genomic factors influence Lyme disease transmission.

Reconstruction of the Prox gene family evolution in vertebrates reveals multiple lineage-specific gene losses

This study reconstructs the evolutionary history of the Prox gene family in vertebrates, revealing lineage-specific gene losses and identifying a fourth ancestral Prox gene.

Predicted Effector Gene Aggregation, Standards and Unified Schema (PEGASUS): A Community Framework for Effector Gene Reporting

PEGASUS defines a community reporting standard for GWAS predicted effector genes: a metadata record, a full locus-by-gene evidence matrix, and a derived author-prioritised gene list.

Integrated transcriptomic analysis identifies Paternally Expressed Gene 10 as a novel candidate biomarker associated with aggressive features in liposarcoma

The paper identifies PEG10 as a biomarker associated with aggressive liposarcoma features through transcriptomic analysis and validation in multiple datasets.

Comparative analysis of Illumina and Ultima-Genomics sequencing for plasma cell-free small RNA profiling in pancreatic cancer

This study compares Illumina and Ultima-Genomics platforms for plasma cell-free small RNA profiling in pancreatic cancer, finding both produce biologically relevant results with platform-specific differences.

Factors underlying creativity show distinct genetic architecture and genetic correlations with psychiatric disorders

This study identifies two distinct genetic factors underlying creativity, showing different genetic correlations with education and psychiatric disorders.

Phylodynamic analysis reveals asymmetric and accelerating global spread of dengue virus

This study uses phylogeographic and phylodynamic methods to analyze DENV genome data, revealing asymmetric global spread patterns and the role of travel over climate in DENV transmission.

GeoEPred: A Multimodal Structure-Aware Geometric Deep Learning Framework for Gram-Negative Bacterial Secreted Effector Prediction with Sequence Semantics

GeoEPred improves effector protein prediction by integrating sequence and structural information to better model functional motifs and spatial conformations.

Cellular-Resolution Spatial Transcriptomics Reveals Laminar VSMC Phenotypic Remodeling and a Hypoxic Medial Core in Human Thoracic Aortic Dissection

The paper uses spatial transcriptomics to identify hypoxia-adapted VSMC remodeling in human aortic dissection, linking it to interlamellar separation.

Whole-genome characterization of Plasmodium falciparum population structure and drug resistance across Uganda and neighboring countries

The paper characterizes the population structure and drug resistance of Plasmodium falciparum in Uganda and neighboring countries using whole-genome data, identifying key resistance-associated haplotypes.

Genome-wide DNA methylation profiling of the zebrafish forebrain

The paper generates a genome-wide DNA methylation map of the adult zebrafish forebrain using long-read sequencing, revealing patterns of 5mC, 5hmC, and 6mA modifications.