Genetics

Deconvolving cell-type-specific gene expression profiles from bulk RNA-seq samples.

Bulk RNA sequencing (bulk RNA-seq) and single-cell RNA sequencing (scRNA-seq) are two important high-throughput sequencing platforms that have wide applications in biomedical research. Bulk RNA-seq reflects the average gene expression of all cells in the sample at a low experimental cost, whereas scRNA-seq enables transcriptomics profiling at a single-cell level, although with higher experimental ...

Distinctive DNA sequence features define epigenetic longevity of inflammatory memory.

Tissues harbor memories of inflammation, which heighten sensitivity to diverse future assaults. Whether and how these adaptations are sustained through time and cell division remain poorly understood. We show that in mice, epidermal stem cells store lifelong, functional epigenetic records of psoriasis-like skin flares. Applying deep learning to investigate these chromatin dynamics, we unearth CpG ...

A Deep Learning-Driven Framework Integrating Organoid-Based Functional Validation Identifies Universal Neoantigens from Recurrent Glioma Mutations.

Glioblastoma (GBM) is the most common malignant intracranial tumor in adults, with a median survival of only 16-20 months. Neoantigen therapy has show...

Incorporating valuable prior knowledge to improve deep learning prediction of genetic perturbation responses.

Genetic perturbation response prediction plays a critical role in virtual cell research, yet the performance of current deep learning models still lea...

Computational Discovery of MERS-CoV Main Protease Inhibitors Through Screening and Molecular Dynamics Simulations.

Targeting the main protease (Mpro) of coronaviruses has emerged as a promising therapeutic strategy for combating viral infections. Despite the global...

Associations of epigenetic age acceleration with motor impairment: Evidence from the Parkinson's Progression Markers Initiative cohort.

Motor decline is a hallmark of Parkinson's disease (PD) and biological aging, yet the specific relationship between systemic biological aging and neur...

Immune gene MMP9 as a potential key mediator in TCDD exposure-associated atherosclerosis: An integrated study based on network toxicology and experimental validation.

BACKGROUND: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a highly toxic, recalcitrant persistent organic pollutant with ubiquitous environmental dist...

Subtypes estimation in single-cell multi-omics data via S-multi-SNE.

Single-cell RNA sequencing (scRNA-seq) has rapidly become an essential method in modern biology, as it allows global characterisation of transcriptomi...

Ultrasound Localization Microscopy Learned from power doppler by uncertainty frequency density estimation and semantic consistency awareness.

Ultrasound Localization Microscopy (ULM) achieves micron-level vascular visualization beyond the resolution of conventional ultrasound imaging by trac...

Machine learning-directed massively parallel programmable nucleic acid amplification.

Dynamic regulation of amplification efficiency is pivotal yet challenging in molecular diagnostics and DNA data storage. Here, we develop a thermodyna...

Human microphysiological systems of aging recreate the in vivo process expediting evaluation of anti-geronic strategies.

The search for biological mechanisms of human aging is stalled by a lack of suitable models, and it remains unknown whether and to what degree rejuven...

Evaluation of protein-RNA Docking Web Servers for Template-Free Docking and Comparison with the AlphaFold Server.

Protein-RNA docking is a valuable tool for predicting the structures of protein-RNA complexes, which allow us to understand the structural basis for g...

GRNFormer: Accurate Gene Regulatory Network Inference Using Graph Transformer.

MOTIVATION: Deciphering gene regulatory networks (GRNs) from single-cell transcriptomics data remains a fundamental challenge in computational biology...

CpGene: A Web Application for Epigenetic Signature Identification from DNA Methylation Arrays.

MOTIVATION: DNA methylation (DNAme) is the best studied epigenetic mechanism that plays pivotal role in tissue differentiation and epigenetic disrupti...

Multi-omics integration reveals ANXA6-high γδ T cell-endothelial communication as a potential link between periodontitis and MASLD.

Periodontitis (PD) and metabolic dysfunction-associated steatotic liver disease (MASLD) were highly prevalent inflammatory disorders that frequently c...

Transcriptomic advances in studies of muscle stem cell aging: From bulk to single-cell and beyond.

Advances in transcriptomic technologies have progressively transformed the questions we can ask and answer about muscle stem cells (MuSCs) during agin...

TransG4: an interpretable deep-learning approach for sequence-based G-quadruplex prediction.

G-quadruplexes (G4) are non-canonical nucleic acid secondary structures formed in guanine-rich regions and have been shown to regulate diverse cellula...

DeepMIF: A Multiview Interactive Fusion-Based Deep Learning Method for RNA-Small Molecule Binding Affinity Prediction.

Accurately predicting the binding affinity between ribonucleic acid (RNA) and small molecules (RSMA) is crucial for RNA-targeted drug discovery, yet e...

Metagenomic profiling and predictive modeling of the gut microbiome reveal signatures of gestational disease.

The gut microbiome plays a vital role in maternal health and pregnancy outcomes, yet its impact on conditions like gestational hypertension (GH) and g...

Machine learning-augmented lateral flow assays for point-of-care infectious disease diagnostics.

Lateral flow assays (LFAs) are among the most widely used point-of-care (PoC) diagnostic platforms for infectious diseases due to their rapid operatio...