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This study shows that C9orf72 repeat expansions alter chromatin loops in neurons, linking RNA-DNA interactions to gene dysregulation in ALS.

The paper introduces co-expression-based models to improve eQTL predictions and identifies novel schizophrenia-associated genes using brain RNA-seq data.

The paper investigates TDG's role in cell differentiation by showing its involvement in ATF4-dependent gene transcription during retinoic acid-induced neural fate commitment.

Seq-Scope-X improves spatial transcriptomics resolution by expanding tissues, revealing detailed nuclear and cytoplasmic transcriptome differences in liver cells and enabling proteomic analysis in other tissues.

This study investigates whether dietary and ethanol exposures alter germline structural variation in mice, finding no significant changes in SV profiles across different conditions.

This paper introduces the EDEN family of foundation models for AI-programmable therapeutic design, demonstrating their ability to generate functional gene insertions, antibiotic peptides, and synthetic microbiomes.

The paper characterizes the gene model of Ilp4 ortholog in D. simulans as part of a study on IIS pathway evolution.

The paper argues that scaling model capacity alone is insufficient for Virtual Cells, emphasizing the need for contextual diversity and causal representation learning over data volume.

The paper introduces tyPPing, a method for detecting and typing phage-plasmids with high accuracy, outperforming existing tools in sensitivity and scalability.

The paper examines sex-specific regulation of EndMT in atherosclerosis using bulk RNA-seq and single-cell transcriptomics, identifying key regulators and stage-dependent differences.

This study integrates genomic and transcriptomic analyses across lactation stages in dairy cattle to identify temporal genetic variants and molecular mechanisms associated with feed intake.

The paper uses metagenomic sequencing to investigate undiagnosed febrile illness in Nigeria, identifying viruses and bacteria but finding no clear etiological agent for most cases.

This study benchmarks 27 computational tools for transferring cell type labels from scRNA-seq to scATAC-seq data across human and mouse tissues, finding Bridge and GLUE as top performers.

panREPET identifies shared transposable elements across genomes to trace their dynamics, revealing TE bursts linked to climate events in Brachypodium distachyon.

This study identifies genetic loci and pre-vaccination transcriptomic signatures associated with immune response persistence to an Influenza A vaccine in pigs.

ReDeNovo infers both known and novel mutational signatures from cancer genomes, outperforming existing methods and identifying new signatures in real data.

This paper introduces LIVI, a deep learning framework for mapping trans-eQTLs at single-cell resolution, and shows it detects more trans-eQTLs than existing methods and identifies cell types and genes involved in autoimmune disease risk.

The paper introduces TRTL, a modular method for targeted single-cell transcriptomics that enables scalable, atlas-aligned, and clonotype-resolved analysis of user-defined transcript panels.

This study identifies genetic loci associated with migration distance and links them to neurodevelopmental genes, cognition, and economic growth.