multiome

ESGI: Efficient splitting of generic indices in single-cellsequencing data

ESGI provides a flexible framework for demultiplexing and processing single-cell sequencing data with arbitrary barcode architectures, supporting complex and emerging experimental designs.

Spligation enables programmable chimeric RNA generation in living cells

This paper introduces spligation, a method using CRISPR-Csm complexes to generate chimeric RNA in living cells by enabling site-specific RNA cleavage and trans-ligation.

From Prefix to Path: Learning Temporally Consistent Biomolecular Dynamics from Limited Initial Data

This paper introduces a Transformer-based framework to predict full molecular dynamics trajectories from limited initial data, showing it captures long-range temporal structures and improves sampling compared to traditional methods.

Cost adjusted hierarchical defense strategies enables stratified oxidative stress tolerance

This study shows how E. coli uses different oxidative stress tolerance strategies based on stress magnitude, revealing modular defense programs.

Prefrontal Cortical Deficits are a Putative Susceptibility Factor for PTSD

The paper investigates prefrontal cortical deficits as a potential susceptibility factor for PTSD using an animal model and human data, finding mPFC dysfunction before trauma in susceptible individuals.

Atlas-scale spatially aware clustering with support for 3D and multimodal data using SpatialLeiden

The paper extends SpatialLeiden to handle atlas-scale, 3D, and multimodal spatial omics data, improving modularity and scalability across multiple samples.

Quiescence improves Candida albicans survival of fungicidal drug exposure

This study shows that quiescence in Candida albicans enhances survival during antifungal drug exposure by altering cellular properties and gene expression.

Poly(acrylamido) PEG-alternatives Enhance mRNA-LNP Efficacy in Immune Cells and Evade anti-PEG Antibodies During Repeated Dosing

This study develops PAM-lipids as PEG alternatives for mRNA-LNPs, showing improved transfection in immune cells and evasion of anti-PEG antibodies during repeated dosing.

PantheonOS: An Evolvable Multi-Agent Framework for Automatic Genomics Discovery

PantheonOS introduces a multi-agent framework for automated genomics analysis, achieving super-human performance in batch correction and gene panel selection across diverse biological tasks.

Lipid Nanoparticles with Aptamers Enable Targeted mRNA Delivery to CD4⁺ T Cells

This paper develops aptamer-functionalized lipid nanoparticles for targeted mRNA delivery to CD4+ T cells, showing enhanced in vitro transfection and in vivo tissue enrichment with safety profiles.

Dogme: A nextflow pipeline for reprocessing nanopore RNA and DNA modifications

Dogme is a Nextflow pipeline that automates reprocessing of ONT data for modification detection and transcript quantification, showing reproducible results across biological replicates.

Evaluating the quality of brainstem ROI registration using structural and diffusion MRI

The paper evaluates diffusion MRI's role in improving brainstem ROI registration accuracy compared to T1w-only methods, showing better performance with diffusion-based pipelines.

Modelling motion-induced signal corruption in steady-state diffusion MRI

This paper models and corrects motion-induced signal corruption in DW-SSFP diffusion MRI using an extended phase graph framework and provides open-source software for future studies.

NeuroMDAVIS: Visualization of single-cell multi-omics data under deep learning framework

NeuroMDAVIS is a multi-omics visualization model that integrates multiple data modalities to generate low-dimensional embeddings preserving local and global structures, outperforming existing methods.

Synthesis and Assembly of a New-generation Bifunctional Lipid Nanoparticle for Selective Delivery of mRNA to Antigen Presenting Cells

This paper develops a new mRNA-BLNP3 nanoparticle that selectively delivers mRNA to antigen-presenting cells, showing improved immune responses and reduced liver accumulation compared to previous versions.

SimHS-AFMfit-MD: An Integrative Approach to Deciphering Alpha-Actinin Atomic Conformational Dynamics

This paper introduces SimHS-AFMfit-MD, a framework combining HS-AFM, MD simulations, and AFMfit to reconstruct atomic-scale conformational dynamics of alpha-actinin.

Temporal and cell-type specific SPAK-NKCC1 disruption following severe TBI in the developing gyrencephalic brain.

This study examines age-dependent changes in NKCC1 and SPAK expression following TBI in piglets, identifying potential therapeutic targets for pediatric TBI.

Single-Cell and Spatial Methods for Multimodal Functional Glycan Profiling in Tissues

The paper introduces two methods to profile functional glycan-lectin interactions in tissues using single-cell and spatial multiomic approaches, revealing stimulus-specific glycan remodeling and spatial glycan programs in immune cells and follicular lymphoma.

Expanded gene targeting in RNA hacking with G-tract-supply Staple oligomer

This paper introduces Gs-Staple oligomers to expand RNAh's target range by alleviating sequence constraints, enabling broader mRNA targeting and precise gene suppression in mammalian cells and in vivo.

SuperCell2.0 enables semi-supervised construction of multimodal metacell atlases

SuperCell2.0 constructs multimodal metacell atlases from blood and tumor samples, identifying interferon-primed monocytes and macrophages with improved inter-modality consistency.

Activating FGFR1 restores Integrin-β1--mediated fibronectin sensing in satellite cells of aged mice

This study shows that activating FGFR1 restores Integrin-β1-mediated fibronectin sensing in aged satellite cells, improving their regenerative capacity.

Comparing Multislice Projections of MD Simulations with CryoEM Exposes Structural Prediction Errors

This paper compares multislice projections of MD simulations with cryoEM to identify structural prediction errors in coarse-grained and all-atom MD simulations of membranes.

Integration of Multiomic and Multi-phenotypic Data Identifies Biological Pathways Associated with Physical Fitness

This paper introduces PhenoMol, a framework that integrates multiomic and multi-phenotypic data to identify biological pathways linked to physical fitness, outperforming traditional regression models.

Crosslinking of Lipid Nanoparticles Enhances the Delivery Efficiency and Efficacy of mRNA Vaccines

This paper introduces a crosslinking method to improve mRNA LNP stability and delivery efficiency, showing enhanced structural integrity and transfection performance in vitro and in vivo.

Visualizing single base RNA mutations in living cells through DNA nanostructure mediated amplification

The paper introduces a DNA nanostructure-based platform for single-base RNA mutation detection in living cells, demonstrating its ability to distinguish insulin mRNAs and detect KRASG12D mutations with high specificity.

Elevated ferritin as a companion biomarker of myeloid-driven inflammation in RNP/Sm co-positive, treatment-resistant SLE endotype

This paper identifies an RNP/Sm co-positive SLE endotype with myeloid-driven inflammation, hyperferritinaemia, and treatment resistance, suggesting targeted therapies are needed.

tensorOmics: Data integration for longitudinal omics data using tensor factorisation

tensorOmics integrates longitudinal multi-omics data using tensor factorisation to capture coordinated molecular responses across time and omic layers.

Nup42 safeguards heat-induced mRNAs from nuclear condensation tosupport chaperone synthesis

The paper identifies Nup42 as a key factor preventing heat-induced chaperone mRNAs from condensing in the nucleus, ensuring their translation and chaperone production during heat shock.

Eicosapentaenoic Acid Enhances Angiogenesis and Reperfusion After Ischemia: Comparative Effects of Omega-3 Fatty Acids in a Murine Hind Limb Model

This study compares the effects of EPA and DHA on angiogenesis and reperfusion in a murine hind limb ischemia model, finding EPA enhances reperfusion and angiogenesis while DHA does not.

Stemness factor Mex3a times translation and protein trafficking to ensure robust differentiation of olfactory sensory neurons

This study shows that Mex3a regulates neuronal differentiation by controlling translation and trafficking of cell surface proteins, cilia structure, and planar cell polarity in olfactory sensory neurons.