multiome

This study identifies age-acquired enhancers in mouse hearts and shows that exercise can reverse their activation.

This paper develops an injectable, bioresorbable device for localized mRNA delivery to the heart after myocardial infarction, showing improved cardiac function and reduced remodeling in mice.

MUTUAL enables cross-modality analysis between transcriptome and chromatin by learning a shared RNA-ATAC space from multiome data without refitting.

This study creates a time-resolved multi-omics map of gene regulation in Toxoplasma gondii by integrating perturbation data with single-cell measurements, revealing regulatory networks and novel interactions.

This study identifies three splicing regulation patterns mediated by UAP56 and URH49 and their association with mRNA export pathways.

This study uses single-nucleus RNA-sequencing and multiome data to identify neuronal mitochondrial gene suppression as a driver of Alzheimer's dementia, revealing genetic and epigenetic mechanisms underlying cognitive resilience.

SPARK reconstructs enhancer-based gene regulatory networks using single-cell multiomics data and prior knowledge, revealing regulatory links associated with immune disease GWAS variants.

The paper identifies DGKK as the primary target of SNORD116, showing increased DGKK RNA and protein levels upon SNORD116 depletion in human and mouse models.

MINT Block integrates multi-omics data across studies to identify generalisable signatures while accounting for study-specific variation, improving prediction accuracy.

XplainTDA identifies molecular determinants of topological structures in single-cell multi-omics data through perturbation-based analysis.

This study shows ABCA7 deficiency in microglia disrupts lysosomal and lipid homeostasis, impairs phagocytosis, and negatively affects neuronal health in Alzheimer's disease.

The paper shows that the m6A writer spares canonical 3' splice sites from methylation, allowing efficient splicing despite cotranscriptional methylation.

This study identifies molecular and architectural changes in normal-adjacent field tissue in HNSCC that disrupt epithelial differentiation and may promote cancer development.

The paper uses CRISPR activation to engineer regulatory states in RPE-1 cells, revealing hidden genetic effects in AMD by analyzing chromatin accessibility and transcriptional interactions.

The paper uses MD simulations and machine learning to compare residue-pair fluctuations in STING under different conditions, identifying distinct dynamic patterns.

Regulon-based clustering of islet scRNA-seq finds an IRF1-high, cytokine-driven beta cell state with reduced identity and autoantigen genes, enriched in type 1 diabetes donors.

The paper identifies a branched RNA stem-loop (hp3) as a major regulator of RNase E synthesis in Escherichia coli, showing it binds RNase E with high affinity and functions additively with hp2.

The paper identifies PUM1 and PUM2 as cofactors for viral noncoding RNAs HSUR1 and HSUR2 in mRNA repression, showing PUM binding is required for productive HSUR-mRNA engagement.

The paper describes a synthetic circRNA-derived IRES-like element, SynFarsa, that enhances translation of an endogenous protein, HSP90, in trans by targeting its 3'UTR.

This study shows that Pumilio and Brain tumor regulate Smaug mRNA degradation during the Drosophila maternal-to-zygotic transition, preventing ectopic Smaug protein expression and ensuring proper mRNA clearance.

Haruka identifies condition-specific and shared spatial domains across tissues and conditions using contrastive learning, demonstrating improved detection of spatially heterogeneous perturbation responses.

The paper identifies a Wolbachia protein that enhances Drosophila resistance to virus infection via the IMD pathway.

DeepSCENIC uses transfer learning from sequence-to-function models to infer causal gene regulatory networks from single-cell multiome data.

The paper identifies ZNF121 as a cofactor that enhances YTHDF2-mediated mRNA decay by facilitating its binding to target transcripts, thereby modulating mRNA stability and cell-cycle regulation.

This paper introduces mRNA-OG, a programmable mRNA nanostructure that affects protein expression, delivery, and immune response through its architecture.

This study shows ERBB2 controls the timing of progesterone responsiveness in the uterus, ensuring proper receptivity for implantation.

This paper introduces an RNA-fragment end joining (REJ) platform for gene complementation that enables precise and efficient splicing of RNA units into functional mRNAs.

40S subunit binding to a previously unrecognised RRM in LARP1 activates its TOP-binding HEAT repeats, licensing repression of ribosomal protein mRNA translation in human cells.

The paper identifies an exitron in UBQLN2 that generates an alternatively spliced isoform with distinct properties linked to ALS.

This study shows that a root pathogen activates antimicrobial production in beneficial bacteria, enhancing plant defense against itself.