Genetics

Decoding RNA N6-Methyladenosine Methylome of Wheat Using Machine Learning and Nanopore Direct RNA Sequencing.

Nanopore direct RNA sequencing (DRS) enables transcriptome-wide detection of N6-methyladenosine (m6A), a pivotal RNA modification that regulates plant growth, development, and stress responses, at single-base resolution. However, existing Nanopore DRS-based m6A detection tools are often trained on ionic current signals from synthetic RNAs or model species, which limits their applicability to speci...

An Explainable Deep Learning Framework Integrating DNA Sequence and Transcription Initiation Signals for Gene Expression Prediction.

Gene expression is a fundamental process in cellular function and organismal phenotype formation, governed by intricate and finely tuned regulatory mechanisms. Deciphering the regulatory code of gene expression and elucidating the transcriptional effects of the genome remain critical challenges in human genetics. While numerous deep learning approaches have been developed to predict gene expressio...

A salivary protein panel for detecting malignant transformation of oral leukoplakia.

Oral leukoplakia (OLK) is the most common oral potentially malignant disorder and carries a lifetime risk of transformation to oral squamous cell carc...

BulkFormer: A large-scale foundation model for bulk transcriptomes.

Foundation models are transforming transcriptome analysis, yet most RNA sequencing (RNA-seq) foundation models are pretrained on sparse single-cell RN...

Calceolarioside B alleviates airway barrier dysfunction and inflammation via targeting P2Y6R in OVA-triggered asthma.

Asthma is a chronic inflammatory airway disease characterized by barrier dysfunction and excessive inflammatory response. In this study, we identified...

An empirical study of defect clustering in deep neural networks and its implications for testing.

DNN decision logic is vulnerable to adversarial attacks, making robustness testing essential for safety-critical intelligent systems. Existing coverag...

ClairS: a deep-learning method for long-read tumor-normal pair somatic small variant calling.

Somatic variant discovery in tumors is crucial for clinical analysis, yet most existing methods are designed for short-read sequencing, with few devel...

Cross-ancestry pleiotropic analysis of imaging-derived phenotypes enhances risk stratification of depression.

Depression arises from dynamic interactions among genetic predisposition, brain alterations, and environmental stressors. Despite genome-wide associat...

Full-Spectrum Analysis With Machine Learning for Quantitative Assessment of Lateral Flow Immunoassays: A Platform Approach.

Lateral flow immunoassays (LFIAs) provide rapid point-of-care results but lack quantitative capabilities. This study presents a platform technology in...

Integrated analysis of single-cell and bulk-RNA sequencing data reveals drug therapeutic targets and prognostic biomarkers related to ribosome biogenesis in hepatocellular carcinoma.

BACKGROUND: Ribosome biogenesis is involved in the progression of hepatocellular carcinoma (HCC), but the specific mechanisms and diagnostic values of...

Machine-learning prediction of affinity and epistasis in the bovine pancreatic trypsin inhibitor-chymotrypsin complex.

Protein-protein interactions (PPIs) are shaped by evolutionary pressures that fine-tune binding affinities and drive the epistatic relationships that ...

Pinoresinol diglucoside from Eucommia ulmoides attenuates diabetic cardiomyopathy through suppressing the store-operated calcium entry and downregulating the STIM1/Orai1/NFAT3 signaling pathway.

Pinoresinol diglucoside (PDG), an active component derived from Eucommia ulmoides, exhibits therapeutic effects against apoptosis, inflammation, and h...

A Persistent Homology Approach Enables Single-Cell Detection of Chromatin Spatial Organization Changes During Pathological Senescence Transition.

Chromatin organization changes during aging, accompanied by alterations in higher-order chromosome architecture, contributing to the acquisition of se...

An Aging Clock Based on Immune Repertoire Features: COVID-19 Accelerates Aging.

Aging induces immunosenescence, a progressive decline in immune function underpinning age-related pathogen vulnerability, yet T/B cell receptor (TCR/B...

Deep Unsupervised Domain Adaptation for Translating Cancer Dependency Maps From Cell Lines to Breast Cancer Tumor Genomics.

The Cancer dependency maps (DepMap) identify genetic dependencies in cancer cells using large-scale loss-of-function screens, providing a foundation f...

Deep learning in tumour genomics: from multi-omics integration to precision oncology.

Cancer remains a leading cause of death globally, with nearly 10 million deaths in 2020. Advances in genomic technologies have revolutionized cancer r...

Metabolic reprogramming of myeloid cells in cancer: from lactate-NAMPT axis to AI-guided therapeutics.

Myeloid cells-including macrophages, monocytes, neutrophils and dendritic cells-are metabolically plastic sentinels that shape the tumor microenvironm...

An AI-Driven Multi-Omics Framework Identifies CASP8 as a Clinically Actionable Pyroptosis Biomarker in Bladder Cancer.

Despite rapid advances in multi-omics technologies, translating candidate biomarkers into clinical practice for bladder cancer remains challenging due...

Integrative Genomic and Clinical Profiling of Colorectal Cancer Liver Metastases to Guide Personalized Surgery and Liver Transplantation.

BACKGROUND/AIM: Colorectal cancer liver metastases (CRLM) remain a leading cause of cancer-related mortality. Although hepatic resection is the only e...

Air pollution and hepatocellular carcinoma: Integrated network toxicology, machine learning, molecular docking and multiomics analysis.

Air pollution is closely related to the incidence and prognosis of hepatocellular carcinoma (HCC); however, the mechanisms remain elusive. Therefore, ...