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The paper compares protease-inhibitor gene family counts across species, showing how annotation methods and counting units affect results.

The paper introduces FICTURE2, a statistical model that infers transcriptional programs from individual RNA molecules in spatial transcriptomics data, revealing spatial organization and cellular identity without segmentation.

The paper compares toxin gene clustering in venomous species to random genes and non-toxin families, finding higher odds of toxin clustering in four bilaterians.

This study examines how fructose-responsive gene regulation varies across intestinal regions in mice and fruit flies, finding conserved pathways and divergent metabolic responses.

The paper constructs state-level regulatory networks in mouse liver hepatocytes, revealing an invariant sub-network of broadly expressed TFs that defines cell-type identity, distinct from state-specific variations.

GBactPro improves cross-species bacterial promoter prediction using element-resolved promoter definitions, achieving high AUROC across multiple species and outperforming existing predictors.

The paper identifies shared genomic signatures of Arctic adaptation across distantly related plant species by comparing genome assemblies and analyzing selection pressures and repetitive elements.

The paper investigates the genomic basis of hypoxia tolerance divergence between two eastern oyster populations, finding that gene regulation, not protein-coding evolution, drives population-specific differences.

This study characterizes cis-regulatory elements and predicts enhancers in Heliconiini butterflies using ATAC-seq and histone modification data, revealing temporal divergence and developing a CNN for enhancer prediction.

The paper links antimicrobial use (AMU) on dairy farms to variations in resistance gene profiles across cattle groups, showing that higher AMU correlates with increased resistance to certain drug classes.

The paper introduces MutQA, a cross-validated Q&A dataset linking genetic mutations to their functional consequences, and demonstrates its utility in improving LLM performance.

The paper maps m6A modifications and polyadenylation events in Plasmodium falciparum mRNAs, identifying stage-specific m6A sites and their potential role in 3' end processing.

The paper identifies and functionally characterizes TAD-boundary-disrupting ultra-rare structural variants in schizophrenia using CRISPR/Cas9 in iPSCs, showing cell-type-specific effects on 3D-genome organization and gene expression.

Creator 1.0 is a plant genome foundation model pretrained on 1,000 species using phylogeny-guided stagewise pretraining, achieving strong performance on plant-related tasks.

The paper maps cell type-specific genetic effects on nucleosome-free regions and nucleosome occupancy using snATAC-seq data from human muscle biopsies, showing causal relationships between these elements and GWAS traits.

The paper identifies immune cell type-specific gene expression regulated by tandem repeats using multi-omics data from large cohorts.

This paper improves CUT&Tag for transcription factors by engineering Tn5 variants, enhancing recovery of TF binding sites in mouse cells and revealing distinct chromatin interaction modes.

The paper identifies two rodent-specific transposable element subfamilies that function as cell-type-specific enhancers in the mouse immune system, contributing to cell identity and gene regulation.

This paper introduces PEP-seq, a method linking genetic variants to transcriptomic states, and shows it can detect functional effects of eQTLs and nonsense-mediated decay.

This study evaluates epigenetic clocks for age estimation in ancient human DNA, finding they are unreliable for continuous age-at-death but accurate for sex determination.