multiome

TopOmics: Topic Modelling for All Omics

TopOmics introduces a flexible topic modeling framework for multi-omics data, demonstrating competitive performance and interpretability across diverse datasets.

PRISMA: A tensor-based framework for deconstructing the genetic architecture of complex diseases, with application to diabetic retinopathy

PRISMA decomposes GWAS signals into tissue-specific genetic axes for diabetic retinopathy, revealing novel targets and regulatory patterns.

Interconnecting ADC Structure with Tumor Cell Biology with Multimodal Learning

The paper develops a multimodal machine learning framework to predict ADC cytotoxicity by integrating structural parameters with tumor cell biology data.

Monitoring in vivo transcription with synthetic serum markers

This paper introduces a platform called INTACT that non-invasively monitors specific mRNA levels in vivo by using synthetic serum markers and RNA-based sensors.

GAE-Δ: A Graph-Learning Framework for Gene Network Rewiring and Clinical Outcome Prediction from Multi-Omics Data

GAE-Δ uses a graph autoencoder to analyze multi-omics data and predict clinical outcomes while identifying gene network rewiring associated with cancer progression.

Redistribution of codon-optimality effects: measurement strategy alters the division of labor between translation and mRNA decay

The paper shows that measurement strategies affect how codon optimality influences translation versus mRNA decay, altering the perceived division of labor between these processes.

Modeling Genetic Diversity in Sickle Cell Disease Reveals Heterogeneous Responses to HbF-Inducing Therapies

This paper uses iPSC-derived erythroid cells to model genetic diversity in sickle cell disease and shows they reflect heterogeneous responses to HbF-inducing therapies like hydroxyurea.

Modular mRNA platform for in vivo antigen-specific immune tolerance

This paper introduces Tol-mRNA, a modular mRNA platform that induces antigen-specific immune tolerance by delivering PD-L1 and TGF-β along with antigen, showing therapeutic benefits in murine models and human immune settings.

Rapid receptor internalization potentiates CD7-targeted lipid nanoparticles for efficient mRNA delivery to T cells and in vivo CAR T-cell engineering

This paper compares T-cell receptor-targeted lipid nanoparticles for mRNA delivery, finding CD7-targeting achieves highest efficiency due to rapid internalization.

Spatiotemporal graph neural networks reveal conformational binding signature in protein dynamics

This paper introduces a deep learning method to identify conformational binding signatures in protein dynamics from molecular simulations.

Fine scale structural information substantially improves multivariate regression model for mRNA in-vial degradation prediction

This paper improves mRNA stability prediction by incorporating fine-scale structural metrics into a regression model, achieving better accuracy than existing methods.

T cell dysregulation and remodeling in pediatric obesity and weight loss

This study identifies T cell dysregulation in pediatric obesity and shows that these changes persist despite weight loss.

ProtmRNA: Cross-Modal Knowledge Transfer from Proteins to Messenger RNA

ProtmRNA transfers knowledge from protein language models to mRNA sequences, achieving competitive performance with less computational resources.

MetaNet: a scalable and integrated tool for reproducible omics network analysis

MetaNet is an R package for scalable multi-omics network analysis, offering faster computation and better memory efficiency than existing tools, with applications in microbial and exposome-transcriptome studies.

Ablation of glypican-3 enhances radiosensitivity in liver cancer by prolonging G2/M arrest and activating the ATM/CHK2 pathway

This study shows that reducing GPC3 in liver cancer cells increases their sensitivity to radiation by extending G2/M arrest and activating the ATM/CHK2 pathway, with clinical evidence linking high GPC3 to worse outcomes in radiotherapy-treated HCC patients.

Towards harmonized spectral quantification in MRSI: Comparative analysis of Backward-Linear-Predicted and original 1H-FID-MRSI dephased data

The paper compares Backward-Linear-Prediction (BLP) and original 1H-FID-MRSI data to assess quantification biases caused by acquisition delay and shows BLP improves consistency across different delays.

Toward Accurate RNA Folding Thermodynamics: Evaluation of Enhanced Sampling Methods for Force Field Benchmarking

This study evaluates enhanced sampling methods for RNA force field benchmarking using an 8-mer tetraloop, finding T-REMD most robust for accurate folding free energy estimates.

Cross-Species Insights from ART-D to Uncover Evolutionarily Conserved Oncogenic Mechanisms

The paper establishes ART-D, a cross-species platform analyzing Ras-driven tumors in Drosophila to identify conserved oncogenic mechanisms across stages of tumorigenesis.

Cell Type-informed Characterization of Spatial Niches from Spatial Multimodal and Multi-omics Data

SpaNECT is a framework for characterizing cell niches from spatial multimodal and multi-omics data, outperforming existing methods in diverse biological contexts.

Amino Acid Insertion Energetics in a POPC Bilayer from Unbiased Molecular Dynamics

The paper quantifies amino acid side-chain insertion energetics in a POPC bilayer using unbiased molecular dynamics simulations and derives potentials of mean force to characterize bilayer partitioning.

Engineering a pacemaker-driven human mini-heart guided by spatial multi-omics of sinoatrial node development

This paper develops a pacemaker-driven human mini-heart using spatial multi-omics and stem-cell engineering to study cardiac conduction and drug discovery.

Optimization of a liver Trm cell-inducing mRNA vaccine by reduction of type I interferon response

This study optimizes an mRNA vaccine to enhance liver Trm cell induction by reducing type I interferon responses through improved manufacturing.

Clone-level multi-modal prediction of tumour drug response

This paper introduces scClone2DR, a framework predicting tumour drug response at the clone level using single-cell DNA/RNA sequencing and drug-screening data, showing improved accuracy in identifying clonal sensitivities and resistance.

PEARL: Integrative multi-omics classification and omics feature discovery via deep graph learning

PEARL is a deep graph learning method for multi-omics integration that outperforms existing methods and identifies functionally important genes in Alzheimer's disease.

IRES-TrAPPr reveals novel insights into viral and cellular mRNA translation

The paper introduces IRES-TrAPPr, a method to quantify CDI and IRES activity, revealing that viral IRESes from warm-blooded hosts are more structurally stable and many DNA-based IRES candidates have negligible activity.

Reprogramming of Cellular Plasticity via ETS and MYC Core-regulatory Circuits During Response to MAPK Inhibition in BRAF-mutant Colorectal Cancer

This study shows BET + MAPK inhibitors improve efficacy against BRAFV600E CRC by inducing epigenetic reprogramming and cellular plasticity through enhancer dynamics disruption.

Cyclic azapeptide cluster of differentiation-36 receptor modulator attenuates left ventricular injury and temporarily reduces long-chain fatty acid accumulation after myocardial ischemia-reperfusion in mice

This study shows that the CD36 modulator MPE-298 reduces infarct size and LCFA accumulation in mice after myocardial ischemia-reperfusion.

Short RNA chaperones promote aggregation-resistant TDP-43 conformers to mitigate neurodegeneration

Short UG-rich RNAs bind and stabilize TDP-43 RNA-recognition motifs to allosterically destabilize its prion-like domain helical region, preventing aggregation and mitigating neurodegeneration in cells and mice.

Tumor cell specific total mRNA expression informed neural networks predicts cancer progression

TmSNet predicts tumor cell-specific total mRNA expression from multi-omic data, achieving high accuracy across cancer types and external cohorts.

Biodistribution of mRNA vaccines in rats: Enrichment in injection site and lymph tissues and rapid clearance without tissue persistence

Three mRNA-LNP products sharing one lipid matrix show rat intramuscular biodistribution (injection site, lymph nodes, spleen) and rapid clearance, with no Spike accumulation after repeat dosing.