multiome

Decoding Single-Cell Multiomics: scMaui - A Deep Learning Framework for Uncovering Cellular Heterogeneity in Presence of Batch Effects and Missing Data

scMaui is a deep learning framework that integrates single-cell multiomics data, handles batch effects, and addresses missing data, showing improved performance in downstream analyses.

Selective attention and decision-making have separable neural bases in space and time

This study separates the neural bases of selective attention and decision-making using a two-stage task and multimodal neuroimaging data, showing attention affects stimulus representations before decision-making begins.

Single cell multiome profiling of pancreatic islets reveals physiological changes in cell type-specific regulation associated with diabetes risk

The paper uses single-cell multiome profiling to identify gene regulatory changes in pancreatic islets linked to diabetes risk factors like age, sex, and genetic variants.

Engineering ionizable lipids for rapid biodegradation balances mRNA vaccine efficacy and tolerability

This study designs and tests biodegradable ionizable lipids for mRNA vaccines, showing they balance efficacy and tolerability by reducing inflammation while maintaining strong immune responses.

mosGraphFlow: a novel integrative graph AI model mining disease targets from multi-omic data

This study introduces mosGraphFlow, a graph AI model for analyzing multi-omic data to identify AD-associated biomarkers and signaling pathways, achieving high classification accuracy.

Cancer Stemness Online: A resource for investigating cancer stemness and associations with immune response

Cancer Stemness Online provides a resource for scoring cancer stemness and analyzing its associations with immune response and cancer hallmarks.

Advancing mRNA subcellular localization prediction with graph neural network and RNA structure

The paper introduces Allocator, a deep learning framework for predicting mRNA subcellular localization by integrating sequence and structure information, showing improved performance over existing methods.

mosGraphGPT: a foundation model for multi-omic signaling graphs using generative AI

mosGraphGPT is a foundation model for multi-omic signaling graphs trained on cancer data and fine-tuned for Alzheimer's Disease, improving classification accuracy and interpretability.

Bootstrap Evaluation of Association Matrices (BEAM) for Integrating Multiple Omics Profiles with Multiple Outcomes

BEAM integrates multiple omics profiles with multiple clinical outcomes using bootstrap resampling to identify significant associations, outperforming existing methods in simulations and a pediatric leukemia application.

Genomic and transcriptomic profiles influence on brain morphology and their interactions with pain sensitivity individual differences

This study investigates how genomic and transcriptomic profiles interact with brain morphology to influence individual differences in pain sensitivity using multi-omics data from 432 participants.

Dimensions of early life adversity are differentially associated with patterns of delayed and accelerated brain maturation

The paper examines how different types of early-life adversity relate to brain age gaps in children, finding some types are linked to younger-looking brains and others to older-looking brains.

TIRR regulates mRNA export and association with P bodies in response to DNA damage

This study shows TIRR binds specific mRNAs and interacts with XPO1 and P bodies during DNA damage, aiding mRNA export and DNA repair.

MultiOmicsAgent: Guided extreme gradient-boosted decision trees-based approaches for biomarker-candidate discovery in multi-omics data

MOAgent discovers biomarker candidates in multi-omics data using gradient-boosted decision trees, addressing data challenges and providing accessible analysis tools.

Zfp106 binds to G-quadruplex RNAs and inhibits RAN translation and formation of RNA foci caused by G4C2 repeats

This study shows Zfp106 binds to G-quadruplex RNAs formed by GGGGCC repeats, inhibiting RAN translation and RNA foci formation in C9orf72-related diseases.

Variation and interaction of distinct subgenomes contribute to growth diversity in intergeneric hybrid fish

The paper investigates how subgenome interactions affect growth diversity in intergeneric hybrid fish by analyzing whole-genome sequencing and mRNA-seq data.

Dengue virus preferentially uses human and mosquito non-optimal codons

This study shows that dengue virus uses non-optimal codons in both human and mosquito cells, enhancing its fitness and suggesting synonymous codon choice is critical in host-pathogen interactions.

Feature Importance in Predicting Clinical Outcome: Statistics vs. Explainable Artificial Intelligence

The paper compares XAI and statistical methods to identify important features predicting neoadjuvant chemotherapy response in breast cancer, finding complementary insights.

The human mitochondrial mRNA structurome reveals mechanisms of gene expression

The paper maps the human mitochondrial mRNA structurome using a novel method, revealing novel mechanisms of gene expression and the role of LRPPRC in mRNA stability.

Sex Differences in the Brain's White Matter Microstructure during Development assessed using Advanced Diffusion MRI Models

The paper assesses sex differences in white matter microstructure during development using diffusion MRI models and finds the TDF model is most sensitive in detecting these differences.

Brain Age Analysis and Dementia Classification using Convolutional Neural Networks trained on Diffusion MRI: Tests in Indian and North American Cohorts

This paper evaluates CNN models for brain age prediction and dementia classification using diffusion MRI, showing improved performance after dataset harmonization across Indian and North American cohorts.

Modeling causal signal propagation in multi-omic factor space with COSMOS

The paper introduces COSMOS+ to integrate mechanistic prior knowledge with multi-omics data analysis to generate mechanistic hypotheses about disease resistance mechanisms.

TDP-43 mutations-induced defects in miRNA biogenesis and cytotoxicity by differentially obstructing Dicer activity in Drosophila and in vitro

This study shows TDP-43 mutations disrupt miRNA biogenesis by affecting Dicer activity, leading to cytotoxicity in Drosophila and in vitro models.

Pan-cancer Analysis Reveals m6A Variation and Cell-specific Regulatory Network in Different Cancer Types

The paper analyzes m6A methylomes across nine human tissues to show how m6A variation contributes to tumor heterogeneity and clinical outcomes in different cancer types.

CodonBERT: Large Language Models for mRNA Design and Optimization

CodonBERT is a large language model for mRNA design and optimization that outperforms previous methods on a flu vaccine dataset.

Piezo1 and Piezo2 channels in retinal ganglion cells and the impact of Piezo1 stimulation on light-dependent neural activity

This paper shows that Piezo1 and Piezo2 channels are expressed in retinal ganglion cells and that their activation increases light-dependent neural activity and excitability, potentially linking to glaucoma progression.

Dynamic off-resonance correction improves functional image analysis in fMRI of awake behaving non-human primates

This study improves functional MRI analysis in awake non-human primates by applying dynamic off-resonance correction, enhancing image fidelity and activation estimates.

Optimizing 5'UTRs for mRNA-delivered gene editing using deep learning

The paper uses deep learning to design optimized 5'UTRs for mRNA-delivered gene editing, showing improved editing efficiency across cell types and targets.

{Phi}-Space: Continuous phenotyping of single-cell multi-omics data

Phi-Space continuously phenotypes single-cell multi-omics data by embedding cells in a low-dimensional space defined by reference phenotypes, enabling robust annotation and analysis of transitional and novel cell states.

Telomeric lncRNA TERRA localizes to stress granules in human ALT cells

This study shows TERRA, a telomeric lncRNA, localizes to stress granules in human ALT cells under stress conditions.

Large Scale and Stable Graph Differential Analysis via Multi-Layer Node Embeddings and Ranking

This paper introduces node2vec2rank, a method for graph differential analysis that identifies biologically relevant differences between weighted networks in cancer subtypes and single-cell dynamics.