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The paper presents a new phased assembly of the Antarctic spiny plunderfish and identifies genomic features linked to cold adaptation in notothenioids.

This study analyzes genomic diversity of Plasmodium vivax in Vietnam, finding decreasing infection complexity, increasing clonal inbreeding, and stable drug resistance allele frequencies over a 10-year period.

The paper constructs a DNA methylation atlas for 106 Chinese individuals using nanopore long-read sequencing, identifying CpG sites and environmental influences on methylation.

The paper identifies CAD risk variants that alter VSMC gene programs via ox-LDL-induced enhancer remodelling using multi-omics approaches.

The paper analyzes transcriptomic changes in human fibroblasts under different senescence-inducing conditions, finding shared pathway-level responses and inducer-specific gene-level variations.

This study investigates the origin and evolution of grapevines through phylogenomic analysis of 29 genome assemblies, revealing evolutionary relationships and genomic features contributing to their adaptation.

This study identifies cryptic species within the honeypot ant M. mendax complex using phylogenomic and population genomic analyses of UCE data.

This study uses molecular pixelation to profile CAR protein organization dynamics in CAR-T therapy, revealing co-localization network remodeling linked to clinical outcomes.

Concordia detects spatial domains in population-level spatial proteomics data using a GNN-based framework, revealing a cancer-associated fibroblast subset linked to clinical outcomes in lung cancer.

The paper identifies transcription factor collaborations that shape CD8+ T cell states and demonstrates how engineering these interactions can influence cell fate for therapeutic applications.

This study compares short and long read sequencing technologies for human genome profiling, finding they are equivalent for SNVs but long reads excel in structural variants and haplotype phasing.

The paper engineers an essential neo-chromosome III in yeast to enable genome minimisation by relocating essential genes, demonstrating stability and cross-species complementation.

This study uses genomic data from Roman Dacia to show sex-biased ancestry patterns, indicating male-mediated gene flow and complex demographic interactions in Roman frontier communities.

The paper develops a genomic toolkit for Seychelles warblers, enabling genetic pedigree assignment and correcting sample identity errors using high-quality genomic data.

The paper systematically perturbs enhancer sequences to study their functional properties and robustness, revealing insights into regulatory sequence space and enhancer activity.

REPLAY automates DNA replication timing analysis from Repli-seq data, providing a reproducible and user-friendly tool without requiring programming expertise.

The paper introduces DBCO-modified PCR primers for enzyme-free click chemistry ligation in nanopore amplicon sequencing, achieving higher pore occupation and reads than commercial solutions.

MetaMuse curates and harmonizes biomedical metadata using a multi-agent AI system, achieving high accuracy and scalability in standardizing unstructured data from repositories like GEO.

The paper evaluates improved text embeddings for gene representations, showing consistent performance gains across multiple tasks.

The paper evaluates 24 metagenomic sequencing workflows for SARS-CoV-2 detection in saliva, finding that RNA-Seq library preparation has a greater impact on viral read recovery than extraction methods.