multiome

Growing a Root from Its Genome : Emergent Tissue Layers and Zones in a GPU-Native Simulation of the Arabidopsis Root Tip

This paper simulates Arabidopsis root tip development from a genome, showing emergent cell identities and zones without pre-defined structures, but with limitations in niche maintenance and regeneration.

A Minimal Synthetic Cleavage Module Enables Selective Degradation of Pathogenic r(CUG) Repeats in Cells

This study develops a synthetic cleavage module that selectively degrades pathogenic r(CUG) repeats in cells, reducing DM1-associated pathology without DNA damage.

Aging activates latent enhancers that can be reversed withexercise

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

RBM25 selectively stabilizes XBP1s mRNA independently of splicing factor activity

This study identifies RBM25 as a post-transcriptional regulator that selectively stabilizes XBP1s mRNA during ER stress, enhancing UPR signaling and cellular survival.

Engineering morphology of tetrasulfide-incorporated mesoporous silica nanoparticles for enhanced mRNA delivery

This study develops tetrasulfide-incorporated mesoporous silica nanoparticles to enhance mRNA delivery by optimizing morphology and chemistry, showing improved cellular uptake and mRNA stability.

Integrated transcriptomic and epigenomic profiling of human cartilage reveals coordinated changes in fibronectin expression, splicing, and receptor signaling during osteoarthritis progression

This study profiles human cartilage across OA grades, revealing changes in fibronectin expression, splicing, and receptor signaling during disease progression.

Bioresorbable, Injectable In Situ-Formed Electroactive mRNA-Delivering Device for Precision Gene Therapy after Myocardial Infarction

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.

A single-cell multimodal foundation model enables cross modality analysis between transcriptome and chromatin

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

Impact of RNA modification and IL-12 boosts on mRNA-LNP vaccine-elicited CD8+ T cell responses

This study compares CD8+ T cell and antibody responses in non-human primates using different ratios of modified and unmodified mRNA-LNP vaccines with IL-12 boosting.

PHENOMS: Open-Source Software for Rust-Accelerated Hydrogen-Bond Analysis in Molecular Dynamics Simulations

PHENOMS analyzes hydrogen-bond networks in molecular dynamics simulations using Rust-accelerated code, achieving significant speedup over Python-based tools and demonstrating its utility with HDX-MS data.

A MultiOmics time-resolved systems map of gene regulation in Toxoplasma gondii

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.

Two closely related RNA helicases, UAP56 and URH49, couple mRNA splicing and export pathways with their distinct complexes

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

Single-Nucleus Profiling Reveals Neuronal Metabolic Collapse During the Transition to Alzheimer's Disease Dementia

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.

Multiplex-GCN Predicts Clinically Actionable Tumor Microenvironment Subtypes in Pancreatic Cancer

The paper develops a multi-layered GCN to identify TME-guided PDAC subtypes, revealing seven subtypes with distinct molecular and prognostic features.

Structural basis for repeat-associated non-AUG translation initiation on C9orf72 mRNA

The paper determines the structure of C9orf72 RAN translation initiation complexes and identifies a key RNA-RNA interaction that drives DPR production, suggesting a therapeutic target.

Identification of gene kinetics patterns improves RNA velocity and cell fate prediction using JuloVelo

JuloVelo improves RNA velocity and cell fate prediction by incorporating gene kinetics patterns, outperforming existing methods across multiple differentiation programs.

SPARK: Bayesian structure learning of enhancer-based gene regulatory networks from single-cell multiomics data and prior knowledge

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

Sensitized infants who tolerate peanut have more dendritic cells and HLA-DR+ memory CD4 T cells

The paper identifies increased dendritic cells and HLA-DR+ memory CD4 T cells in sensitized infants who tolerate peanut, highlighting the importance of controlling staining batches in mass cytometry studies.

Language models annotate mass cytometry clusters within the range where human experts disagree

This paper uses large language models to annotate mass cytometry clusters, achieving high concordance with expert annotations and outperforming baselines.

RNA promotes MAPK signaling through direct interaction with BRAF

This study shows RNA directly interacts with BRAF to regulate MAPK signaling by facilitating RAF complex formation and MEK1/2 phosphorylation.

The DGKK mRNA is a primary target of the Prader-Willi syndrome-associated snoRNA SNORD116

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: multivariate integration across independent studies to identify multi-omics signatures

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

XplainTDA: Explaining the topological structure of single-cell multi-omics data through perturbation

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

Optimal transport reveals unresolved cells in single cell multi-omics

This paper introduces optimal transport to explicitly reveal cell correspondences in single-cell multi-omics, improving integration and label transfer by identifying and removing ambiguous cells.

The Alzheimer's disease risk gene ABCA7 regulates microglial lysosomal and lipid homeostasis and promotes phagocytosis to maintain neuronal health

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

The m6A motif is an anti-3' splice site

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

Dysregulation of epithelial differentiation architecture underlies field cancerization in head and neck cancer

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

Cirrhosis-associated immune dysfunction reflects impaired intestinal CD8ab⁺ intraepithelial lymphocyte compartmentalization

The paper investigates immune dysfunction in cirrhosis by analyzing CD8ab⁺ intraepithelial lymphocytes and identifies CCL25-CCR9 axis disruption as a key factor.

Engineered regulatory states resolve context-dependent genetics in macular degeneration

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.

Latent-Space Residue-Pair Networks from Molecular Dynamics Distinguish Ligand-Activated and SAVI-Associated STING

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