multiome

An integrated human forebrain organoid reveals microglia-mediated CD8⁺ T cell recruitment and neuroimmune dysfunction in Alzheimer's disease pathology

Antisense oligonucleotides targeting transcription termination windows disrupt mRNA 3' end processing and decrease gene expression

This study shows that antisense oligonucleotides targeting transcription termination windows can decrease gene expression by disrupting mRNA 3' end processing and causing off-target effects.

Lung surfactants as a component of lipid nanoparticles for pulmonary mRNA delivery

This study shows that adding lung surfactant Poractant alfa to lipid nanoparticles improves their performance for pulmonary mRNA delivery, increasing transfection efficiency and particle concentration.

Pumilio and Brain tumor regulate the expression of Smaug during the Drosophila maternal-to-zygotic transition

This study shows that Pumilio and Brain tumor regulate Smaug mRNA degradation during the Drosophila maternal-to-zygotic transition, preventing ectopic Smaug protein expression and ensuring proper mRNA clearance.

A spectral framework for measuring diversity in multiple sequence alignments

This paper introduces Leff, a spectral measure to quantify effective information in multiple sequence alignments, showing evolutionary constraints reduce sequence diversity in RNA and proteins.

ZNF121 recruits YTHDF2 to modulate mRNA stability

The paper identifies ZNF121 as a cofactor that enhances YTHDF2-mediated mRNA decay by facilitating its binding to target transcripts, thereby modulating mRNA stability and cell-cycle regulation.

The Virtual Biotech: A Multi-Agent AI Framework for Therapeutic Discovery and Development

The Virtual Biotech uses AI agents to integrate multi-omic and clinical data for drug discovery, identifying genomic features linked to trial success and proposing therapeutic strategies.

N6-methyladenosine promotes temozolomide resistance through non-canonical regulation of mRNA stability in glioblastoma cells

This study shows that m6A methylation stabilizes genes involved in temozolomide resistance in glioblastoma, and inhibiting METTL3 can restore drug sensitivity.

Observations of anisotropic paramagnetic and diamagnetic susceptibility in the primate brain

This study uses MRI and computational methods to show that paramagnetic substances contribute to susceptibility anisotropy in primate brain tissue, alongside diamagnetic components.

5-azacytosine induces cytotoxicity via 5-methylcytosine depletion on chromatin-associated RNA in leukemia

This paper shows that 5-azaC induces leukemia cell death by depleting m5C in chromatin-associated RNA, leading to transcriptional repression and disrupting key regulatory pathways.

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.

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.

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.

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.

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.

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.

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.

Supervised restricted data fusion with common, local & distinct components

PESCAR improves detection of subtle response-related patterns in multi-omics data by integrating response information into multiblock decomposition.

DIVAS: an R package for identifying shared and individual variations of multiomics data

DIVAS identifies shared and individual variations in multiomics data, revealing partially shared patterns missed by existing methods.

Exploring the sensitivity limits of neuronal current imaging with MRI and MEG in the human brain

This paper evaluates the sensitivity of spin-lock fMRI for detecting neuronal magnetic fields in vivo, finding it insufficient compared to MEG and BOLD-fMRI.

Optimising 7T-fMRI for imaging regions of magnetic susceptibility

This study improves 7T-fMRI quality in susceptibility-prone regions using multi-echo and multiband sequences, enhancing BOLD signal and GLM precision.

Mapping enhancer-gene regulatory interactions from single-cell data

The paper introduces scE2G models to predict enhancer-gene regulatory interactions from single-cell data and demonstrates their performance across multiple cell types and perturbations.

ELAVL1 and ELAVL4 are required for Musashi-dependent translational activation

This study identifies ELAVL1 and ELAVL4 as co-regulators of MSI1-dependent translational activation in Xenopus and mammals.

Continual integration of single-cell multimodal data with MIRACLE

MIRACLE enables efficient continual integration of single-cell multimodal data, updating cell atlases with new data without reintegration, and identifies novel cell types and transfers labels across datasets.

Can a history of crop rotations improve the prediction of soil organic carbon in the Andes? integrating machine learning multi-annual crop classification as a proxy of soil management

This study models soil organic carbon in the Andes using machine learning with crop rotation data, finding that fallow frequency is a key predictor of SOC when soil data are excluded.

Automated Ventricle Assessment via Three-dimensional Anatomical Reconstruction (AVA-TAR): a computational toolkit for autonomous lateral ventricle assessment in preclinical hydrocephalus models

This paper develops a deep learning tool for automated segmentation and morphological analysis of lateral ventricles in rodent MRIs, achieving high accuracy and correlation with manual measurements.

Automated Surface-Based Segmentation of Deep Gray Matter Regions Based on Diffusion Tensor Images Reveals Unique Age Trajectories Over the Healthy Lifespan

This paper introduces an automated DTI-only segmentation method for deep gray matter regions, revealing distinct age-related changes in volume, FA, and MD that differ from volumetric trajectories.

Pulmonary mRNA-LNP Vaccines for Rapid and Durable Protection Against Bacterial Infection

This paper develops a pulmonary mRNA-LNP vaccine that provides rapid and durable protection against bacterial lung infections by integrating innate and adaptive immune responses.

RAFTER: a releasing factor tethered RNA editing system for quantifying mRNA translation

RAFTER quantifies mRNA translation by labeling efficiently translated RNAs with an RNA editing enzyme and releasing factor, showing correlation with Ribo-seq and Polysome-seq but with a simpler workflow enabling single-cell analysis.