multiome

Distinct and overlapping correlates of fear acquisition and extinction across different neuroimaging modalities

The paper examines brain correlates of fear acquisition and extinction using multimodal neuroimaging data and identifies overlapping and distinct brain regions involved in these processes.

dioscRi enables transferable prediction of clinical outcomes in multi-parameter cytometry data

dioscRi improves transferability of deep learning models for cytometry data by integrating normalization, cell type hierarchies, and clinical outcome prediction.

Chemical Lithography: Selective Glyoxal Caging of mRNAs to Control Gene Expression

This paper develops a method to control gene expression by selectively caging mRNAs with glyoxal, enabling tunable and time-dependent regulation.

scDisent: regulatory-aware disentangled representation learning for multi-omic single-cell analysis

scDisent separates regulatory and expression variables in multi-omic single-cell data, improving integration and interpretability.

CodonMamba: a foundation model for programmable mRNA coding sequence design

CodonMamba is a foundation model for mRNA coding sequence design that achieves state-of-the-art performance and enables programmable codon optimization through inference-time steering.

Stimulation of rodent and human beta-cell proliferation using synthetic modified mRNAs encoding cell cycle regulators

This study uses synthetic modified mRNAs to stimulate beta-cell proliferation in rodents and humans, showing temporary activation of cell cycle pathways without sustained proliferation.

Extracellular matrix regulates lineage plasticity in prostate cancer through YAP/TEAD

Loss of extracellular matrix-integrin signaling switches off YAP/TEAD and lets prostate adenocarcinoma organoids turn neuroendocrine; LATS inhibition reverses it, and combined YAP, NOTCH and AR inhibition fully reprograms them.

Cellfoundry: a GPU-accelerated, multi-physics ABM framework for cellular microenvironment and organoid-scale studies

Cellfoundry is a GPU-accelerated agent-based modeling framework for simulating cellular microenvironments, enabling the study of complex interactions between cells, extracellular matrix, and biochemical signals.

3'UTR-directed control of poly(A) tail dynamics and mRNA stability in vertebrate embryos

The paper develops a method to study 3'UTR sequences' role in mRNA stability and poly(A) tail dynamics in zebrafish embryos, revealing how these sequences influence mRNA fate during development.

Testing the reliability of novel Voxel Placement approaches for Magnetic Resonance Spectroscopy

This study evaluates three voxel placement methods for MRS, finding that SSVR significantly improves reliability and reduces metabolite variability in challenging regions.

MOFTy: Multimodal Gaussian Process Factor Analysis with Numerical Information Field Theory

MOFTy disentangles spatial structures and recovers cross-modal patterns in multi-omics data by separating smooth gradients from fine-scale heterogeneity.

A serotonergic mechanism is involved in the pro-cognitive effect of AM6545 treatment in a mouse model of fragile X syndrome

This study shows that AM6545 treatment improves cognitive deficits in FX mice by modulating serotonergic receptors and gut microbiota.

Isoform-specific regulation of SMARCAD1 dosage in ectodermal homeostasis and dysplasia

The paper investigates how SMARCAD1 isoform-specific regulation affects protein dosage in ectodermal homeostasis and disease, identifying post-transcriptional and spatial mechanisms.

Mechanistic Dissection of Entropic Penalty upon Ligand Binding and Molecular Flexibility via Molecular Dynamics Simulations and Machine Learning

This study quantifies molecular entropy and its changes during ligand binding using MD simulations and machine learning, revealing key motions and their thermodynamic impacts.

2-arm-PEG-oligocations transiently shield the liver sinusoids to mitigate off-target hepatic expression of mRNA lipid nanoparticles

This paper demonstrates that 2-arm-PEG-oligocations transiently shield liver sinusoids to reduce off-target hepatic mRNA expression and improve iLNP delivery to spleen and tumors.

Unique CD8+ T Cell Populations Expand during ART and Predict Delayed HIV-1 Rebound

The paper identifies a unique CD8+ T cell population that expands during ART and predicts delayed HIV-1 rebound.

SpatialMOC: Accurate reconstruction of spatial multi-omics landscapes through cross-modality prediction

SpatialMOC reconstructs missing spatial multi-omics data by integrating spatial context and cross-modality learning, outperforming existing methods across multiple tissues and modalities.

Declines in mRNA synthesis set the rate of organismal aging

The paper shows that declining mRNA synthesis capacity during aging reduces mRNA abundance, driving organismal aging, and that manipulating this decline affects healthspan and lifespan.

From gHBfix to NBfix: Reweighting-Driven Refinement of Hydrogen-Bond Interactions in RNA Force Fields

This paper reparameterizes RNA force fields by replacing hydrogen-bond corrections with Lennard-Jones modifications, improving simulation accuracy without external potentials.

Five-layer systems analysis of Leishmania stage differentiation reveals an essential role for protein degradation in parasite development

The paper uses a five-layer systems analysis to show that protein degradation, not genomic changes, drives stage differentiation in Leishmania parasites.

Identifying multi-omics biomarkers for ovarian cancer survival estimation

This paper develops a multi-omics machine learning framework to estimate ovarian cancer survival, identifying a 20-biomarker signature that improves prognostic accuracy.

Gaussian Accelerated Molecular Dynamics in GROMACS

This paper implements Gaussian accelerated molecular dynamics in GROMACS, showing improved sampling of conformational and binding free-energy basins compared to conventional MD simulations.

Single-cell multiomic mapping of genetic predisposition to childhood B-cell acute lymphoblastic leukemia

The paper uses single-cell multiomic analysis to identify genetic variants and regulatory disruptions linked to childhood B-cell acute lymphoblastic leukemia.

Aperiodic neural activity links electromagnetic and hemodynamic representations of domain-general cognitive demand across the cortical hierarchy

The paper investigates how aperiodic neural activity relates to cognitive demand across the cortical hierarchy using combined fMRI and MEG data.

LagCI Enables Inference of Temporal Causal Relationships from Dense Multi-Omic Time Series

LagCI identifies temporal causal relationships in dense multi-omics time series by analyzing lag-correlation profiles and filtering spurious associations.

Impact of Coding Region Accessibility and Uridine Chemistry on Translation in mRNA-DNA Hybrid Origami

This study investigates how folding mRNA into a six-helix bundle affects translation, finding that only the start of the coding sequence needs to be accessible, and that modifications like 5-methoxyuridine and N1-methylpseudouridine influence translation levels.

Differential correlation across subpopulations of single cells in subtypes of acute myeloid leukemia

The paper introduces a method to detect differential correlations between protein pairs across subpopulations in AML samples, revealing nonlinear relationships in cytometry data.

A Physics-Inspired Classical Digital Twin of the Cell: A Composite Multi-Clock Port-Hamiltonian Neural Network Learned from Multi-Omic Circadian Data

The paper develops a physics-inspired digital twin of the cell using a multi-clock port-Hamiltonian neural network trained on multi-omic circadian data, showing aggregate phase lag agreement but no per-gene correlation.

PAIP1 couples mRNA export to cytoplasmic mRNP remodeling and poly(A) homeostasis

This study identifies PAIP1 as a cofactor for mRNA export and shows it couples nuclear to cytoplasmic mRNP remodeling and poly(A) homeostasis, affecting mRNA stability and development.

Laterality of subcortical structures predicts spontaneous brain dynamics

The paper examines how asymmetry in subcortical brain structures relates to cortical oscillatory power in resting-state MEG data from healthy adults.