multiome

BrainAGE: Revisited and reframed machine learning workflow

The paper revises the BrainAGE method using Gaussian process regression, showing improved performance on UK Biobank data and disease-specific patterns in clinical samples.

Trajectory analysis of hepatic stellate cell differentiation reveals metabolic regulation of cell commitment and fibrosis

This study maps the differentiation trajectory of iPSCs to hepatic stellate cells, identifying RORA as a key regulator of metabolic reprogramming and fibrosis.

Transposable Element Derepression-mediated IFN-I Signaling Enhances Stem/Progenitor Cell Activity After Irradiation

The paper shows that transposable element derepression triggers IFN-I signaling, boosting stem/progenitor cell activity after irradiation.

Optimal Decoding of Neural Dynamics Occurs at Mesoscale Spatial and Temporal Resolutions

The paper develops a model to decode neural activity and finds optimal spatial and temporal resolutions for decoding image information from MUA data.

Multiome-seq links inflammatory bowel disease polygenic risk to TNF inhibitor response

The paper links IBD polygenic risk to TNFi response using multiome-seq and genetic data from pediatric IBD patients.

Multiscale networks in multiple sclerosis

The paper uses multilayer network analysis and multi-omics data to identify biological pathways in MS that explain disease severity and central nervous system damage.

Inhibition of CPEB3 ribozyme elevates CPEB3 protein expression and polyadenylation of its target mRNAs, and enhances object location memory

The paper shows that inhibiting the CPEB3 ribozyme increases CPEB3 protein and enhances memory by promoting mRNA polyadenylation and translation.

Translational activation by a synthetic PPR protein elucidates control of psbA translation in Arabidopsis chloroplasts

A synthetic PPR protein substitutes for HCF173, elucidating its role in activating psbA translation and demonstrating synthetic PPRs' ability to control chloroplast gene expression.

Influence of preprocessing, distortion correction and cardiac triggering on the quality of diffusion MR images of spinal cord

This study evaluates the impact of distortion correction and cardiac triggering on spinal cord diffusion MRI quality, finding that distortion correction has limited effectiveness and cardiac triggering can be omitted without significant quality loss.

Translational arrest and mRNA decay are independent activities of alphaherpesvirus virion host shutoff proteins

This study compares alphaherpesvirus vhs proteins to determine if translational arrest and mRNA decay are separate functions, finding that some induce mRNA decay while others cause translational arrest without decay.

Transdifferentiation of Human Dental Pulp Mesenchymal Stem Cells into Spiral Ganglion-like Neurons

This study differentiates human dental pulp stem cells into spiral ganglion-like neurons using in vitro protocols, showing phenotypic and nanomechanical similarities to native neurons.

Programmable RNA writing with trans-splicing

This paper introduces PRECISE, a method for programmable RNA editing that enables precise insertion, substitution, and deletion of RNA sequences in pre-mRNAs, with high efficiency and fidelity.

CAG repeat expansions create splicing acceptor sites and produce aberrant repeat-containing RNAs

This study identifies that CAG repeat expansions create new splice acceptor sites, leading to aberrant repeat-containing RNAs that are translated via canonical AUG-initiated mechanisms.

Diffusion MRI Head Motion Correction Methods are Highly Accurate but Impacted by Denoising and Sampling Scheme

This study evaluates head motion correction methods in diffusion MRI, showing both Eddy and SHORELine perform well but are affected by denoising and sampling schemes.

Rewriting endogenous human transcripts with trans-splicing

This paper introduces RESPLICE, a CRISPR-based trans-splicing system that efficiently edits endogenous human transcripts, achieving up to 90% trans-splicing efficiency in sorted cells.

Autophagy-dependent alternative splicing event produces a more stable ribosomal protein S24 isoform that aids in hypoxic cell survival

A Multiscale Spatial Modeling Framework for the Germinal Center Response

This paper develops a multiscale spatial simulation framework to model the germinal center response, recapitulating key molecular, cellular, and morphological events.

MORE interpretable multi-omic regulatory networks to characterize phenotypes

MORE constructs phenotype-specific multi-omic regulatory networks using regression-based modeling and variable selection, showing improved accuracy and efficiency over existing tools.

A dual-gene reporter-amplifier architecture for enhancing the sensitivity of molecular MRI by water exchange

This paper develops a dual-gene reporter-amplifier system to enhance MRI sensitivity by using Aqp1 to facilitate water exchange, enabling detection of low-abundance Oatp1b3-expressing cells.

M2WISH: an easy and efficient protocol for whole-mount mRNA in situ hybridization that allows 3D cell resolution of gene expression in Arabidopsis thaliana.

The paper introduces M2WISH, a protocol for whole-mount mRNA in situ hybridization in Arabidopsis that enables 3D cellular resolution of gene expression during meristem conversion.

The PCM scaffold enables RNA localization to centrosomes

The paper investigates how Plp mRNA localizes to centrosomes, showing that its coding sequence is necessary and sufficient for localization and that PCM scaffold interactions facilitate this process.

Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an Integer Programming framework

The paper develops an integer programming framework to predict RNA secondary structures with pseudoknots and local 3D motifs, showing improved accuracy when integrating motif information.

Investigating the impact of motion in the scanner on brain age predictions

This paper assesses how scanner motion affects brain age gap estimates using MRI data from two datasets, finding significant differences in predicted age with varying motion levels.

Targeted LNPs deliver mRNA encoding IL-15 superagonists to balance efficacy and toxicity in cancer therapy

This study uses targeted mRNA-LNPs to deliver IL-15 superagonists, improving anti-tumor efficacy while reducing toxicity compared to existing therapies.

Neuromark PET: A multivariate method for estimating whole brain fMRI guided intrinsic networks and connectomes from fMRI and PET data

This paper introduces a method to estimate whole brain PET and fMRI connectomes using spatially constrained independent component analysis and examines their relationship in mild cognitive impairment patients.

Aberrant activation of wound healing programs within the metastatic niche facilitates lung colonization by osteosarcoma cells

This study identifies fibrosis as a targetable vulnerability in osteosarcoma lung metastasis by showing nintedanib inhibits metastatic progression through anti-fibrotic effects.

Estrogen receptor-related receptor (Esrra) induces ribosomal protein Rplp1-mediated adaptive hepatic translation during prolonged starvation

The paper identifies Esrra as a master regulator of adaptive hepatic translation during prolonged starvation by inducing Rplp1 expression and lysosome/autophagy protein translation.

MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer

MarsGT identifies rare cell populations in multi-omics single-cell data, outperforming existing tools and revealing novel biological insights in human and mouse datasets.

The CD4 T cell epigenetic JUNB+ state is associated with proliferation and exhaustion

The paper identifies a JUNB+ epigenetic state in CD4 T cells associated with proliferation, exhaustion, and memory formation, and develops a new machine learning tool to analyze its regulation.

PCA-Plus: Enhanced principal component analysis with illustrative applications to batch effects and their quantitation

PCA-Plus enhances principal component analysis to better detect, visualize, and quantify batch effects and group differences in multi-omic data.