multiome

Integrating Single-Molecule Sequencing and Deep Learning to Predict Haplotype-Specific 3D Chromatin Organization in a Mendelian Condition

This paper introduces FiberFold, a deep learning model that predicts haplotype-specific 3D chromatin organization using Fiber-seq data, revealing changes in TADs in a Mendelian disease.

Heparanase, a host gene that potently restricts retrovirus transcription

This study identifies HPSE as a host factor that restricts retrovirus infection by inhibiting proviral transcription through sequestration of the SP1 transcription factor.

AggreBots: configuring CiliaBots through guided, modular tissue aggregation

The paper introduces AggreBots, a platform for creating designer motility patterns in multicellular tissues by spatially controlling the aggregation of epithelial spheroids, achieving greater motility than traditional CiliaBots.

Immunogenicity of Rabies Virus G-Protein mRNA Formulated with Muscle Targeting Lipid Nanoparticles in Mice

This study evaluates an mRNA vaccine encoding the Rabies Virus G-protein formulated with muscle-targeting lipid nanoparticles, showing high immunogenicity and protection in mice.

AI-Driven Breeding Enhances Stress Tolerance in High-Elevation Extremophytes: A Proof-of-Concept Study with Cross-Component Validation

This study demonstrates an AI platform that predicts and enhances stress tolerance in high-elevation extremophytes using multi-omics data and machine learning techniques.

A KIF1C-CNBP motor-adaptor complex for trafficking mRNAs to cell protrusions

The paper identifies CNBP as a factor required for mRNA localization to cell protrusions by forming a motor-adaptor complex with KIF1C.

Destabilisation of bam transcripts terminates the mitotic phase of Drosophila female germline differentiation

The paper shows that Bam transcript instability, regulated by Rbp9 and Rbfox1, terminates the mitotic phase of Drosophila female germline differentiation.

Shared brain basis of aggression in clinical, forensic, and healthy samples: A meta-analysis

This study identifies a common neural network associated with aggression across clinical, forensic, and healthy populations through a meta-analysis of neuroimaging studies.

Yeast poly(A)-binding protein (Pab1) controls translation initiation in vivo primarily by blocking mRNA decapping and decay

This study shows that Pab1 in yeast primarily controls translation by blocking mRNA decapping and decay, with reduced mRNA abundance driving translational changes.

Iterative Multiscale Molecular Dynamics: Accelerating Conformational Sampling of Biomolecular Systems by Iterating All-Atom and Coarse-Grained Molecular Dynamics Simulations

This paper introduces iMMD, an iterative multiscale MD workflow combining all-atom and coarse-grained simulations to accelerate conformational sampling of biomolecules.

An RNA Splicing System that Excises Transposons from Animal mRNAs

This paper describes a novel RNA splicing system, SOS splicing, that removes transposons from mRNAs in C. elegans and human cells, protecting genes from TE-mediated disruption.

Single-cell multiome analysis supports α-to-β transdifferentiation in human pancreas

The paper identifies transitional cell states between alpha and beta cells in human islets using single-cell multiome data, suggesting potential for alpha-to-beta transdifferentiation.

MicroRNAs and mRNA Regulatory Network of Parenchymal Hematoma after Endovascular Mechanical Reperfusion for Acute Ischemic Stroke in Rat

The paper identifies microRNA and mRNA regulatory networks associated with parenchymal hematoma after mechanical reperfusion in a rat stroke model.

Sex-specific role of epigenetic modification of a leptin upstream enhancer in the adipose tissue

The paper investigates how maternal thyroid hormone exposure affects DNA methylation at a leptin upstream enhancer in adipose tissue, with sex-specific impacts on body fat percentage.

Annotation Comparison Explorer (ACE): connecting brain cell types across studies of health and Alzheimer's Disease

ACE compares cell type annotations across studies, enabling users to align and analyze cell type classifications and metadata in health and Alzheimer's Disease research.

Simultaneous single-cell CRISPR, RNA, and ATAC-seq enables multiomic CRISPR screens to identify gene regulatory relationships

The paper introduces CAT-ATAC, a method combining CRISPR, RNA, and ATAC-seq in single cells to identify gene regulatory relationships and validate them with loss-of-function experiments.

Diverse mechanisms of DDX3Y suppression by DDX3X

This study shows DDX3X suppresses DDX3Y through both transcript and protein stabilization mechanisms in male cancer cells, revealing cell-type-specific cross-regulation between X- and Y-linked paralogs.

M3NetFlow: A novel multi-scale multi-hop graph AI model for integrative multi-omic data analysis

M3NetFlow is a multi-scale multi-hop graph model for multi-omic data analysis that ranks targets and infers signaling pathways, achieving high accuracy in drug response and Alzheimer's disease studies.

ISME - Incoherent Sampling of Multi-Echo data to minimize cardiac-induced noise in brain maps of R2* and magnetic susceptibility

The paper introduces ISME, a sampling strategy that reduces cardiac-induced noise in brain maps of R2* and magnetic susceptibility, improving reproducibility.

An attention-based deep neural network model to detect cis-regulatory elements at the single-cell level from multi-omics data

This paper introduces an attention-based deep neural network to detect cis-regulatory elements at the single-cell level using multi-omics data, showing improved accuracy and cell state clustering.

TSC1 mRNA processing alterations in tuberous sclerosis complex (TSC) patients with negative or inconclusive genetic testing results

This study identifies mRNA processing errors in TSC patients with negative or inconclusive genetic tests using cDNA analysis, reclassifying a variant of uncertain significance as pathogenic.

Telomemore enables single-cell analysis of cell cycle and chromatin condensation

Telomemore quantifies subtelomeric reads from single-cell data to assess chromatin condensation and complements cell cycle analysis in single-cell RNA-seq.

Tumour-derived glucocorticoids amplify ROR1 and are exploited with glucocorticoid-resistant ROR1 CAR-T cells

The paper shows that tumor-derived glucocorticoids increase ROR1 expression while suppressing T cell activity, and GC-resistant CAR-T cells can overcome this by preserving ROR1 expression in tumor cells.

PBAE-PEG based lipid nanoparticles for lung cell-specific gene delivery

This paper develops PBAE-PEG and PBAE lipid nanoparticles for targeted mRNA delivery to lung cells, showing differential efficacy in transfecting pulmonary endothelial and epithelial cells via different routes.

A trans-amplifying mRNA vaccine with consensus spike elicits broadly cross-neutralizing antibody response against multiple SARS-CoV-2 variants

This study evaluates a trans-amplifying mRNA vaccine with a consensus spike protein, showing it elicits broad cross-neutralizing antibodies against multiple SARS-CoV-2 variants with reduced antigen dose.

Mapping cells through time and space with moscot

moscot unifies optimal transport for temporal, spatial and spatiotemporal single-cell mapping, using multimodal cost spaces and low-rank solvers to scale to 1.7 million mouse embryo cells.

The Proton Resonance Enhancement for CEST imaging and Shift Exchange (PRECISE) family of RF pulse shapes for Chemical Exchange Saturation Transfer MRI

The paper develops a new RF pulse shape for CEST MRI using gradient ascent optimization, showing improved contrast in phantoms and live mice compared to Gaussian and Fermi pulses.

plasma: Partial LeAst Squares for Multiomics Analysis

plasma is a supervised multiomics method that integrates features into biologically relevant components to predict patient outcomes, outperforming unsupervised and single-omics models.

VDR-calcium axis regulates the diet-driven metabolic shift during weaning

This study shows that the VDR-calcium axis is critical for metabolic adaptation during weaning, with dietary fat preventing energy deprivation in VDR-deficient mice.

Bi-allelic variants in the aminopeptidase XPNPEP3 cause mitochondrial disease with pediatric cardiomyopathy

This study identifies bi-allelic XPNPEP3 variants causing mitochondrial disease with pediatric cardiomyopathy, revealing impaired mitochondrial protein processing as the underlying mechanism.