multiome

Divergent role of CD8 T cells with distinct metabolic phenotypes during curative radio-immunotherapy in hot versus cold tumors

This study examines how CD8 T cells with different metabolic profiles contribute to tumor cure in hot versus cold murine tumors using radio-immunotherapy.

All You Need Is Water: Converging Ligand Binding Simulations with Hydration Collective Variables

This paper introduces a data-driven method to construct solvation-based collective variables for molecular dynamics simulations, achieving accurate binding free energy landscapes with improved efficiency.

Bayesian Cooperative Learning for Multimodal Integration

This paper introduces BayesCOOP, a Bayesian method for multimodal integration that avoids MCMC and variational approaches, showing improved performance in estimation and uncertainty assessment.

Extrinsic Apoptosis and Necroptosis in Telencephalic Development: A Single-Cell Mass Cytometry Study

This study uses single-cell mass cytometry to show that deleting RIPK3 and Caspase-8 increases cell count in the mouse telencephalon, indicating non-exclusive roles for extrinsic apoptosis and necroptosis in developmental cell elimination.

Multi-omics integration and batch correction using a modality-agnostic deep learning framework

This paper introduces MIMA, a deep learning framework for multi-omics integration and batch correction, which effectively removes batch effects and preserves biological information across modalities.

Limited generalizability of dynamic fMRI correlates of adolescent rumination

The paper examines dynamic fMRI correlates of adolescent rumination and finds that adult models do not generalize, suggesting developmental differences in neural correlates of rumination.

A simple, open-source restraint system for magnetic resonance imaging in awake rats

This paper introduces an open-source restraint system for awake rat fMRI that eliminates anesthesia, reducing stress and motion artifacts while enabling high-quality imaging and behavioral integration.

Cortical Iron in Schizophrenia: A Quantitative Susceptibility Mapping and Diffusion Tensor Imaging MRI Study

This study uses MRI to investigate cortical iron levels in schizophrenia patients and finds elevated iron in specific brain regions.

Molecular and cellular dynamics of measurable residual disease progression in myelodysplastic syndromes

This study identifies molecular features of MRD progression in MDS using single-cell multi-omic profiling, revealing dynamic evolutionary processes and immunoevasive mechanisms.

Gene regulatory innovations from transposable elements in mammalian cerebellum development

The paper identifies TE fragments with regulatory potential in cerebellar development across species and introduces a framework to analyze their contribution to gene regulation.

Computationally designed mRNA-launched protein nanoparticle vaccines

This paper develops an mRNA-launched nanoparticle vaccine that combines protein nanoparticle and mRNA vaccine advantages, showing enhanced antibody and T cell responses in mice.

CSDE1 regulates miR-20a-5p/ TMBIM6 axis in melanoma

The paper identifies a regulatory axis involving CSDE1, miR-20a-5p, and TMBIM6 in melanoma, showing CSDE1 enhances TMBIM6 expression through post-transcriptional mechanisms.

Decoding Chromatin Dynamics in Cardiac Organoids Reveals Genetic Drivers of Human Heart Development and Disease

The paper uses a single-cell multi-omic atlas and deep learning to identify cis-regulatory elements and genetic drivers of heart development and disease.

Senescent Activated Naive B Cells Promote Anti-Citrullinated Antigen T Cell Responses and the Transition to Clinical Rheumatoid Arthritis

This study identifies senescent activated naive B cells in ACPA+ individuals that promote anti-citrullinated antigen T cell responses and drive progression to clinical RA.

AP-1 Primes Transcriptional Noise-Led Cancer Treatment Adaptation Through KDM5 Chromatin Rewiring

The paper identifies transcriptional noise as a driver of cancer treatment adaptation through AP-1 and KDM5-mediated chromatin rewiring in neuroblastoma and hepatoblastoma.

Deep Learning of Brain-Behavior Dimensions Identifies Transdiagnostic Biotypes in Youth with ADHD and Anxiety Disorders

The paper uses deep learning to identify brain-behavior dimensions and biotypes in youth with ADHD and anxiety disorders, revealing distinct symptom profiles and brain development patterns.

Hypoxia Imaging as a Radiomics Signature in Tumors Using Novel 19F-Eu-Based Contrast Agents for Magnetic Resonance Imaging

This paper demonstrates the use of 19F-Eu-based contrast agents for real-time hypoxia imaging in tumors, showing reliable delivery and integration with spatial biology for biomarker identification.

Limbic System White Matter in Children and Adolescents with ADHD: A Longitudinal Diffusion MRI Analysis

This study uses diffusion MRI to examine limbic system white matter development in children and adolescents with ADHD, finding reduced microstructural organization and connectivity linked to symptom severity.

mRNA poly(A)-tail length is a battleground for coronavirus-host competition

This study shows coronavirus infection limits PABPC1 activity, destabilizing short-tailed host mRNAs and enabling viral mRNAs to maintain specific poly(A)-tail lengths through synthesis and capping mechanisms.

SRSF12 is a primate-specific splicing factor that induces a tissue-specific gene expression program

This study identifies SRSF12 as a primate-specific splicing factor that induces tissue-specific gene expression programs in human cells.

Loss of tight junction protein claudin 18 uncovers alveolar epithelial stem cell plasticity and emergence of non-fibrogenic transitional progenitors

The paper identifies regeneration-associated transitional progenitors (RATPs) in Cldn18 knockout mice, showing they are less fibrogenic and contribute to lung repair rather than fibrosis.

CDH3-AS1 antisense RNA enhances P-cadherin translation and acts as a tumor suppressor in melanoma

Domain shifts in infant brain diffusion MRI: Quantification and mitigation for fODF estimation

This study evaluates deep learning models for fODF estimation in infant brain MRI, finding that U-Net performs best with fewer gradient directions, while MLP and Transformer improve with more directions.

mcRigor: a statistical method to enhance the rigor of metacell partitioning in single-cell data analysis

mcRigor improves metacell partitioning reliability by detecting heterogeneous metacells and optimizing hyperparameters for single-cell RNA-seq and multiome data.

A Tonic Signaling Code Predicts CAR-T Cell Efficacy in Diffuse Midline Glioma

This study identifies tonic signaling as a key factor in CAR-T cell efficacy for diffuse midline glioma, showing that restrained tonic signaling improves therapeutic outcomes.

Programmable Aptamer-Embedded Circular RNAs for Targeted Antigen-Presenting Cells Immunotherapy

This paper develops Apt-circRNAs for targeted antigen-presenting cell immunotherapy, showing efficacy in tumors and clinical trials.

Cinematic Simulation of Substrate-to-Product Chemical Reactions with Chemical Accuracy Using QuantaMind MD

This study uses a deep learning-based MLFF to simulate the PETase-catalyzed reaction with DFT-level accuracy, capturing key events and free energy barriers consistent with experiments and previous QM/MM studies.

RNA-binding proteins provide specificity to the PAN2-PAN3 mRNA deadenylation complex

This study shows that the PAN2-PAN3 deadenylation complex can be recruited to specific mRNAs via RNA adaptors, adding to the specificity of mRNA degradation.

scPhoenix: A Contrastive Learning-based Framework with Aux-Core Feature Disentanglement Enhances Sparse Cellular Multi-omics Translation

scPhoenix enhances sparse cellular multi-omics translation using contrastive learning and aux-core feature disentanglement, preserving heterogeneity and improving performance in high sparsity and spatial heterogeneity scenarios.

The DND1-NANOS3 complex shapes the primordial germ cell transcriptome via a heptanucleotide sequence in mRNA 3'UTRs

The paper identifies an RNA sequence motif recognized by the DND1-NANOS3 complex in germ cells and shows its role in regulating mRNA expression.