multiome

Control of Epithelial Tissue Organization by mRNA Localization

This study shows that Net1 mRNA localization at the dermal-epidermal junction influences epithelial tissue organization by regulating RhoA activity and DEJ structure.

A versatile information retrieval framework for evaluating profile strength and similarity

The paper introduces a statistical framework using mean average precision (mAP) to evaluate phenotypic activity and consistency in high-dimensional profiling data across various modalities and perturbation types.

Translation-specific disruption of Col1a1 expression in multiple models of Spinal Muscular Atrophy can be rescued by Risdiplam.

The paper identifies COL1A1 as a translation-specific biomarker of SMA severity and shows it can be rescued by SMN-restoring therapies in multiple models.

Tumor microenvironment governs the prognostic landscape of immunotherapy for head and neck squamous cell carcinoma: A computational model-guided analysis

This study develops a computational model of the HNSCC tumor microenvironment to identify subtype-specific resistance mechanisms and predict therapeutic targets for immunotherapy.

HEAL-KGGen: A Hierarchical Multi-Agent LLM Framework with Knowledge Graph Enhancement for Genetic Biomarker-Based Medical Diagnosis

HEAL-KGGen improves LLM performance in genetic diagnostics by integrating a knowledge graph with a multi-agent framework for multi-omics data interpretation.

Hierarchical Extended Linkage Method (HELM)'s Deep Dive into Hybrid Clustering Strategies

This paper introduces HELM, a hybrid clustering method combining k-means efficiency with hierarchical flexibility, and demonstrates its application to protein-DNA and protein folding simulations.

Carotenoid-based immune response in sea cucumbers relies on newly identified coelomocytes -- the carotenocytes

This study identifies carotenoid-rich coelomocytes in sea cucumbers, challenging the assumption that hemocytes contain haemoglobin and proposing a new classification as carotenocytes.

Securing diagonal integration of multimodal single-cell data against ambiguous mapping

The paper introduces SONATA, a diagnostic method to detect artificial integrations in diagonal multimodal single-cell data integration, showing its effectiveness across simulated and real datasets.

Biomni: A General-Purpose Biomedical AI Agent

An LLM agent with a literature-mined environment of 150 tools, 105 packages and 59 databases plans in code, matching reported human accuracy on database and sequence question answering.

WAGO-1 is a sexually dimorphic Argonaute protein required for proper germ granule structure and gametogenesis

This study identifies sex-specific roles of WAGO-1, an Argonaute protein, in C. elegans germ granule structure and gametogenesis through structural and functional analysis.

Expression of a RAS degrader via synthetic nanocarrier-mediated mRNA delivery reduces pancreatic tumors

The paper demonstrates that synthetic nanocarriers deliver RAS-degrading mRNA to pancreatic tumors, reducing RAS levels and tumor growth.

The Effects of Early Life Pain and Juvenile Fear Conditioning on CRF-Receptor Expression in the Amygdala and Hypothalamus

This study investigates how early life pain and fear conditioning affect CRH receptor expression in brain regions, finding no significant changes in amygdala receptors but modest hypothalamic changes.

Human CCR4 deadenylase homolog Angel1 is a Non-Stop mRNA Decay factor

The paper identifies Angel1 as a key factor in non-stop mRNA decay by showing its role in destabilizing mRNAs lacking stop codons.

scExploreR: a flexible platform for democratized analysis of multimodal single-cell data by non-programmers

scExploreR provides a user-friendly platform for non-programmers to analyze multimodal single-cell data with customizable plots and seamless handling of different input formats.

Evidence-driven biases in alternative splicing inferred from NCBI Eukaryotic Genome Annotation Pipeline metadata

This study quantifies biases in alternative splicing estimates from the NCBI EGAP pipeline and introduces a normalization method to reduce evidence-driven biases.

Spatiotemporal Single-Cell Analysis Reveals T Cell Clonal Dynamics and Phenotypic Plasticity in Human Graft-versus-Host Disease

This study uses spatiotemporal single-cell analysis to track T cell clonal dynamics and phenotypic plasticity in GVHD, revealing links between TCR features, clonal expansion, and disease severity.

Clonal lineage tracing and parallel multiomics profiling reveal transcriptional diversification induced by ARID1A deficiency

This study uses an integrated platform to show that ARID1A deficiency increases transcriptomic and epigenetic heterogeneity in cancer cells through stochastic and constrained chromatin changes.

Cross-site harmonization of diffusion MRI data without matched training subjects

This paper introduces RISH-GLM, a method to harmonize diffusion MRI data across sites without requiring matched training subjects, showing effectiveness with unmatched groups and multiple sites.

Extracellular Ca2+-Sensing Receptor (CaSR) Regulates Hypothalamic Function to Control Energy and Skeletal Metabolism in Mice

This study shows that neuronal CaSR regulates energy and skeletal metabolism by modulating hypothalamic function in mice, affecting growth, bone mass, and metabolic parameters.

Post-transcriptional regulation of cyclin A and cyclin B mRNAs is mediated by Bruno 1 and Cup, and further fine-tuned within P-bodies

This study shows that Bruno 1 and Cup regulate cyclin A and B mRNAs, with P-bodies modulating cyclin B mRNA levels in a stage-specific manner.

Evaluating the predictive power of combined gene expression dynamics from single cells on antibiotic survival

The paper uses Bayesian inference to predict antibiotic survival in E. coli by integrating gene expression and growth rate data from single cells.

An integrative systems-biology approach defines mechanisms of Alzheimer's disease neurodegeneration

This study integrates multi-omics data from Drosophila and human Alzheimer's disease models to identify pathways involved in neurodegeneration.

Multimodal cortical connectome in the default mode network across the adult lifespan

The paper examines age-related changes in multimodal connectivity within the default mode network using MRI and MEG data from adults aged 18 to 88.

An RNA binding regulatory cascade controls the switch from proliferation to differentiation in the Drosophila male germ line stem cell lineage

The paper shows that Bam represses how RNA to control the switch from proliferation to differentiation in Drosophila male germ line stem cells.

Rudhira-mediated microtubule stability controls TGFβ signaling during mouse vascular development

This paper shows Rudhira regulates TGFβ signaling and microtubule stability during mouse vascular development through both direct and transcriptional mechanisms.

Compensatory Mechanisms in γδ T Cell-Deficient Chickens Following Salmonella infection

This study shows that γδ T cells help protect chickens early against Salmonella infection, but their role is replaced by other cells later.

Decoding Plasticity Regulators and Transition Trajectories in Glioblastoma with Single-cell Multiomics

This study uses single-cell multiomics to identify regulatory programs and plasticity regulators in glioblastoma, revealing MYT1L as a key repressor of malignant plasticity.

Single cell multiomics reveals drivers of metabolic dysfunction-associated steatohepatitis

This study uses single-cell multi-omics to identify cell type-specific regulatory networks and novel therapeutic targets in MASLD.

Restoring AIBP expression in the retina provides neuroprotection in glaucoma

This study shows that restoring AIBP expression in glaucomatous retinas protects retinal ganglion cells and reduces neuroinflammation in mouse models.

MAPT Splicing Modulators as a Therapeutic Strategy for Tauopathies

Discovery of SMCs that correct MAPT splicing, reduce 4R tau, and rescue pathology in patient-derived neuronal and in vivo models of 4R tauopathies.