multiome

AI-powered integration of multi-source data for TAA discovery to accelerate ADC and TCE drug development (I): TAA Target Identification and Prioritization

This paper introduces an AI framework for TAA target identification and prioritization by integrating multi-omics data and literature, aiming to improve ADC and TCE drug development.

Vessels hiding in plain sight: quantifying brain vascular morphology in anatomical MR images using deep learning

The paper trains a deep learning model to quantify brain vascular morphology from standard MR images, showing it captures aging and health-related features not found in traditional metrics.

Lifespan reference curves for harmonizing multi-site regional brain white matter metrics from diffusion MRI

The paper creates lifespan reference curves for white matter microstructure using diffusion MRI data from multiple datasets and validates them with ApoE4 risk factor analysis.

I-SVVS: Integrative stochastic variational variable selection to explore joint patterns of multi-omics microbiome data

I-SVVS improves clustering accuracy and reduces computation time for multi-omics microbiome data across soybean, mice, and human datasets.

Controlling reactogenicity while preserving immunogenicity from a self-amplifying RNA vaccine by modulating nucleocytoplasmic transport

This study shows that RNAx, a leader-protein-encoding mRNA, reduces reactogenicity while maintaining immunogenicity in saRNA-LNP vaccines.

Synthesis of ionizable lipopolymers using split-Ugi reaction for pulmonary delivery of various size RNAs and gene editing

The paper develops a method to deliver various RNA therapeutics, including mRNA and CRISPR-Cas9, to the lung using lipopolymer-lipid hybrid nanoparticles, showing improved efficacy and reduced toxicity.

Synthetic Cytosolic Splicing Enables Programmable mRNA-Encoded Receptors

This paper introduces synthetic mRNA splicing receptors that detect extracellular signals and produce anti-inflammatory responses in cells.

Extrachromosomal DNA Gives Cancer a New Evolutionary Pathway

The paper shows that ecDNA allows tumors to adapt rapidly by maintaining a spectrum of gene expression levels across cells, rather than relying on clonal expansion.

Abnormal Lipid Metabolism and Altered Neuronal Support by Astrocytes Lacking Akap11, a Risk Gene for Schizophrenia and Bipolar Disorder

This study identifies AKAP11's role in regulating lipid metabolism and neuronal support in astrocytes, linking its dysfunction to schizophrenia and bipolar disorder risk.

Enhanced Detection of Glioblastoma Vasculature with Superparamagnetic Iron Oxide Nanoparticles and MRI

This study uses superparamagnetic iron oxide nanoparticles with MRI to improve detection of glioblastoma vasculature and angiogenesis beyond conventional MRI contrast.

Deep dynamical models of single-cell multiomic velocities predict loss-of-function and rescue perturbations in B cells

Cell type-specific contributions to impaired blood-brain barrier and cerebral metabolism in presymptomatic 5XFAD mice

The paper identifies cell type-specific transcriptomic changes in 5XFAD mice that link BBB dysfunction and metabolic dysregulation to early AD pathogenesis.

Developmental dynamics and axonal transport of cerebral cortex projection neuron mRNAs in vivo

The paper investigates mRNA dynamics and axonal transport in cerebral cortex projection neurons in vivo, identifying cis-regulatory elements and transport mechanisms for specific mRNA classes.

Multi-scale gene regulatory networks for resolving transcription factor and autoimmune variant impacts on human B cell fate dynamics

ShinyCell2: An extended library for simple and sharable visualisation of spatial, peak-based and multi-omic single-cell data

ShinyCell2 provides an interactive R package for visualizing spatial, peak-based, and multi-omic single-cell data with advanced features and ease of use.

ZBP1 Senses Splicing Aberration through Z-RNA to promote Cell Death

This study shows that spliceosome inhibition generates Z-RNA, sensed by ZBP1 to trigger necroptosis in response to splicing aberrations.

INSIGHT: In Silico Drug Screening Platform using Interpretable Deep Learning Network

The paper introduces INSIGHT, a deep learning framework that predicts drug response using multiomics data and drug molecular structure, outperforming existing methods and enabling biological interpretation.

CAFE: An Integrated Web App for High-Dimensional Analysis and Visualization in Spectral Flow Cytometry

CAFE is a web app for analyzing and visualizing high-dimensional spectral flow cytometry data, enabling interactive exploration without coding expertise.

Integrated Lineage Tracing in Hepatoblastoma Finds a Plasticity-Proliferation Axis Drives Adaptation

This study uses single-cell multiomics to trace clonal and phenotypic dynamics in hepatoblastoma after cisplatin treatment, identifying a plasticity-proliferation axis driven by BIRC5.

Single cell resolution of an epigenetic signature of persister tumor cell

The paper identifies an epigenetic signature associated with persister tumor cells in ovarian cancer that correlates with chemotherapy resistance and defines the persister state.

Cross-sectional brain age assessments are limited in predicting future brain change

This study shows brain age metrics from MRI do not reliably predict future brain changes but highlight modality-specific differences as potential cross-sectional markers.

Longitudinal deformation based morphometry pipeline to study neuroanatomical differences in structural MRI based on SyN unbiased templates

This paper introduces a two-level deformation-based morphometry pipeline for longitudinal brain change analysis using MRI, showing improved sensitivity and accuracy in detecting volume changes compared to traditional methods.

A Generalized Higher-order Correlation Analysis Framework for Multi-Omics Network Inference

This paper introduces SGTCCA-Net, a framework for multi-omics network inference that addresses limitations of existing methods by incorporating higher-order correlations and improving computational efficiency.

Low-pH conditions drive transient changes in shell calcification and the microbiome in a pH-resistant strain of the the Pacific oyster Magallana gigas

The study shows low-pH conditions increase shell mass in a pH-resistant oyster strain, alter microbiome composition, and change gene expression related to calcification and immunity.

RNA Modifications and Prp24 Coordinate Lsm2-8 Binding Dynamics during S. cerevisiae U6 snRNP Assembly

This study uses CoSMoS to analyze how RNA modifications and Prp24 influence Lsm2-8 binding dynamics during U6 snRNP assembly in yeast.

Multi-omics analysis of virus-permissive versus hostile cellular states reveals protein networks controlling virus infection

The paper identifies protein networks associated with virus-permissive and hostile cellular states through multi-omics analysis, revealing discrepancies between mRNA and protein levels and the role of phosphorylation in infection control.

The ribosome directs nascent chains through two folding-dependent pathways

The paper uses structural biology techniques to study how nascent polypeptide chains fold through two distinct pathways during ribosome-mediated translation.

CHOIR improves significance-based detection of cell types and states from single-cell data

CHOIR improves cell type and state detection in single-cell data by using statistical inference to assess clustering results, outperforming existing methods across multiple data types.

Accelerated multi-shell diffusion MRI with Gaussian process estimated reconstruction of multi-band imaging

This paper introduces a method to accelerate multi-shell diffusion MRI by using Gaussian process reconstruction, improving image quality and enabling faster scans.

Spatial Metagene Discovery and Associated Molecular Pattern Characterization in Spatial Transcriptomics and Multi-Omics using SEPAR

SEPAR identifies spatial metagenes and their patterns in spatial transcriptomics and multi-omics data, improving gene expression analysis and spatial domain detection.