multiome

Supervised restricted data fusion with common, local & distinct components

PESCAR improves detection of subtle response-related patterns in multi-omics data by integrating response information into multiblock decomposition.

DIVAS: an R package for identifying shared and individual variations of multiomics data

DIVAS identifies shared and individual variations in multiomics data, revealing partially shared patterns missed by existing methods.

Exploring the sensitivity limits of neuronal current imaging with MRI and MEG in the human brain

This paper evaluates the sensitivity of spin-lock fMRI for detecting neuronal magnetic fields in vivo, finding it insufficient compared to MEG and BOLD-fMRI.

Optimising 7T-fMRI for imaging regions of magnetic susceptibility

This study improves 7T-fMRI quality in susceptibility-prone regions using multi-echo and multiband sequences, enhancing BOLD signal and GLM precision.

Mapping enhancer-gene regulatory interactions from single-cell data

The paper introduces scE2G models to predict enhancer-gene regulatory interactions from single-cell data and demonstrates their performance across multiple cell types and perturbations.

ELAVL1 and ELAVL4 are required for Musashi-dependent translational activation

This study identifies ELAVL1 and ELAVL4 as co-regulators of MSI1-dependent translational activation in Xenopus and mammals.

Continual integration of single-cell multimodal data with MIRACLE

MIRACLE enables efficient continual integration of single-cell multimodal data, updating cell atlases with new data without reintegration, and identifies novel cell types and transfers labels across datasets.

Transcript-Specific Site-Directed RNA Editing Reveals Principles for Splice-aware guide RNA Design

The paper develops an in vitro method to study how guide RNAs affect RNA editing and splicing, finding that editing can both disrupt and improve splicing outcomes depending on the target site.

Coordinated immune, chloroplast and chemical defences underpin multilayered resistance to barley yellow dwarf virus and its aphid vector associated with the Hordeum bulbosum-derived Ryd4 introgression in barley

The paper identifies resistance mechanisms in barley against barley yellow dwarf virus and its aphid vector through a Ryd4 introgression, revealing coordinated immune, chloroplast, and chemical defenses.

Cap-specific second nucleotide ribose methylase CMTR2 is required for transcriptome transition during mammalian germline development

This study shows that CMTR2 is essential for transcriptome transitions during mammalian germline development but does not trigger innate immune responses.

Individualized surface parcellation enhances characterization of resting-state brain dynamics and their alterations in schizophrenia

This study compares parcellation strategies in schizophrenia rs-fMRI, finding that individualized parcellation better captures dynamic brain dynamics and symptom associations.

Optimizing Network-Level TMS-fMRI: Benchmarking the TMS-Compatible Sushi MR Setup

The paper benchmarks a TMS-compatible Sushi MR setup for whole-brain fMRI, showing it matches a 64-channel reference in resting-state networks and improves task-fMRI with multi-echo combination.

mRNA-based prime-and-pull vaccination combines benefits of subcutaneous and mucosal BCG vaccination

This paper describes an mRNA-based prime-and-pull vaccination strategy that combines subcutaneous BCG vaccination with mucosal mRNA delivery to achieve protective immunity against tuberculosis with improved safety.

Elevated CO2 enhances tomato tolerance to Botrytis cinerea through transcriptional and metabolic defence reprogramming

This study shows elevated CO2 improves tomato tolerance to Botrytis cinerea by reprogramming transcriptional and metabolic defenses across multiple cultivars.

BioPhasor: Decoding Cellular State Tensors from Multi-Omics Phasor Dynamics for Quantum Ready Systems Biology

The paper introduces BioPhasor, a framework that models cellular states using phasor dynamics and multi-omics data, showing improved performance in cell-cycle and circadian analysis.

SpatialJEPA: JEPA-inspired graph-context distillation for spatially aware multiomics integration

SpatialJEPA transfers spatial context from spatial multiomics data to dissociated non-spatial data through graph-context distillation, improving alignment and recovery of spatially organized programs in mouse brain multiomics.

IL-32 is a stress-responsive node locked in a noncanonical NF-κB inflammatory loop during MASLD to HCC transition

This paper identifies a noncanonical NF-κB-driven IL-32 loop that promotes inflammation during MASLD to HCC transition, revealing IL-32's dual role in metabolism and inflammation.

Post-loading ribonucleic acid into lipid nanoparticle carriers

This paper introduces a post-loading method for mRNA into lipid nanoparticles to reduce cold storage requirements, achieving comparable delivery efficiency to conventional methods.

Halophytic endophytes provide transferable immune functions for crop resilience

This study shows halophytic endophytes like Kushneria enhance crop immunity against pathogens through host immune responses and a novel RNA-NLR axis, without direct antagonism.

Can a history of crop rotations improve the prediction of soil organic carbon in the Andes? integrating machine learning multi-annual crop classification as a proxy of soil management

This study models soil organic carbon in the Andes using machine learning with crop rotation data, finding that fallow frequency is a key predictor of SOC when soil data are excluded.

Study design and rationale of Boxed-Breathing-Heart: a translational ex vivo study evaluating virus-mediated gene delivery for gene therapy in normothermic machine-perfused human hearts

The paper describes an ex vivo study using normothermic machine-perfused human hearts to evaluate AAV-mediated gene delivery for cardiac gene therapy.

Calcium-binding protein expression alone is insufficient to identify and classify GABAergic neurons in macaque cortex

The paper evaluates the use of calcium-binding proteins for classifying GABAergic neurons in macaque cortex and finds that this scheme is invalid due to high non-GABAergic expression and inability to distinguish subpopulations.

Comparing Harmonization Approaches for Protocol-Related Variability in Multisite Diffusion MRI Data

The paper compares three harmonization methods for multisite diffusion MRI data to reduce protocol-related variability while preserving associations with cognitive impairment and PET biomarkers.

Automated Ventricle Assessment via Three-dimensional Anatomical Reconstruction (AVA-TAR): a computational toolkit for autonomous lateral ventricle assessment in preclinical hydrocephalus models

This paper develops a deep learning tool for automated segmentation and morphological analysis of lateral ventricles in rodent MRIs, achieving high accuracy and correlation with manual measurements.

AI-Informed neoantigen prioritization enables a multi-epitope mRNA/LNP vaccine with antigen-specific immunogenicity and antitumor activity

This paper develops a multi-epitope mRNA/LNP vaccine using AI-prioritized neoantigens, showing enhanced immunogenicity and antitumor activity in preclinical models.

Deoxyribonucleotide incorporation reshapes mRNA design beyond canonical ribonucleotide boundaries

This paper shows that substituting ribonucleotides with deoxyribonucleotides in mRNA improves translation efficiency and therapeutic potential in vivo.

Pre-existing chromatin accessibility primes δ-cells for injury-induced endocrine plasticity

This study shows that pre-existing chromatin accessibility in δ-cells enables their conversion into hybrid cells after β-cell loss in zebrafish, facilitating endocrine plasticity.

Automated Surface-Based Segmentation of Deep Gray Matter Regions Based on Diffusion Tensor Images Reveals Unique Age Trajectories Over the Healthy Lifespan

This paper introduces an automated DTI-only segmentation method for deep gray matter regions, revealing distinct age-related changes in volume, FA, and MD that differ from volumetric trajectories.

MOLA: a novel topological data analysis framework for analyzing multiomic loops in precision medicine

MOLA identifies multiomic loops in datasets, showing better capture of epigenetic alterations in Influenza A virus data and associations with progression in breast cancer.

Regulation of protein abundance in neurons by selective translation of 3'UTR isoforms

The paper shows that long 3'UTR isoforms in neurons are less efficiently translated than short ones, mediated by ELAV and Pumilio, and that disrupting this mechanism reduces viability and stress resilience.