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Comparative analysis of protease-inhibitor gene family counts under different counting units and genome annotations

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

Molecule-resolved inference reveals the spatial organization of transcriptional programs

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.

Venom toxin genes are tandem-arrayed beyond gene-family-size expectations in four venomous bilaterian species

The paper examines the clustering of toxin genes in four venomous species and finds that toxin genes are tandem-arrayed beyond family-size expectations, with the excess mainly in homologous arrays.

Evolutionary conservation and divergence of regional fructose-responsive gene regulation in the intestine

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

An invariant network architecture with broadly expressed regulators distinguishes cell-type from cell-state identity in situ

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: cross-species bacterial promoter prediction using element-resolved promoter definitions

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

Shared genomic signatures of Arctic adaptation among distantly related plant lineages

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.

Variation in hypoxia tolerance is driven by evolutionary changes in gene regulation in the eastern oyster

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.

Characterisation of cis-regulatory elements and genome wide enhancer prediction in Heliconiini butterflies

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.

Antimicrobial use contributes to resistance gene enrichment across cattle groups on commercial dairy farms

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.

MutQA: A Cross-Validated Q&A Dataset for Genetic Mutations

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.

Nucleotide-resolution Mapping of RNA N6-Methyladenosine (m6A) modifications and comprehensive analysis of global polyadenylation events in mRNA 3' end processing in malaria pathogen Plasmodium falciparum

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.

3D-genome impacts of TAD-boundary-disrupting ultra-rare structural variants identified in schizophrenia

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: Phylogeny-Guided Stagewise Pretraining for Plant Genome Foundation Models across 1,000 Species

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.

Genetic integration with cell-specific nucleosome positioning resolves causal relationships underlying chromatin accessibility profiles

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.

Tandem repeat variation shapes immune cell type-specific gene expression

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

Engineered Tn5 Variants Enhance CUT&Tag Fidelity for Transcription Factors

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.

Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system

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.

Scalable variant-to-function screens using prime editing perturb-seq

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.

Promises and limitations of current ancient human epigenetic clocks

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.