Genetics

Dynamic evolution of chaperone-mediated autophagy is associated with tumor microenvironment remodeling and prognostic stratification in lung adenocarcinoma: insights from single-cell transcriptomics, ensemble machine learning, and experimental validation.

BACKGROUND: Lung adenocarcinoma (LUAD) shows prognostic heterogeneity, and tumor-node-metastasis (TNM) staging is limited for individualized management. Chaperone-mediated autophagy (CMA) maintains proteostasis, but its role during adenocarcinoma in situ (AIS)-minimally invasive adenocarcinoma (MIA)-invasive adenocarcinoma (IAC) progression remains unclear. METHODS: Single-cell RNA sequencing (scR...

Integrative structural biology of protein-RNA interactions in four dimensions.

Protein-RNA complexes underlie essential cellular processes and understanding their functional mechanisms requires structural analysis. Yet, their inherent flexibility, multi-valency, and dynamics make them challenging targets for structural biology. Integrative approaches, combining nuclear magnetic resonance (NMR), small-angle scattering, cryo-electron microscopy (cryo-EM), cryo-electron tomogra...

Integrating Multimodal Data and Genomics for a Comprehensive Assessment of Cardiovascular Aging and Its Impact.

BACKGROUND: Age-related structural and functional remodeling of the heart and vessels increases cardiovascular disease (CVD) risk, yet comprehensive a...

Integrating structurally defined DNA-carbon nanotube sensors with machine learning for cancer detection.

Liquid biopsy is a promising, noninvasive approach for cancer detection, but current methods often trade off accuracy, operability, and cost. To addre...

Silkworm synthetic biology: Toolkit development, chassis engineering, and biomanufacturing applications.

The silkworm, Bombyx mori, is not only an economically important insect but also an increasingly promising chassis for insect synthetic biology. This ...

abCRISPR: deep learning-based design of abasic gRNA sequences for specific CRISPR-Cas genome editing.

SUMMARY: CRISPR-Cas9 has become a widely used tool for genome editing. However, its off-target cleavage caused by partial sequence matches with guide ...

Comparative Phylogenomics and Transcriptional Regulatory Networks of AQPs, HSPs, and LEA Proteins in Salt-Stressed Portulaca oleracea.

Soil salinization severely threatens global food security, necessitating systematic investigations of halophytes like Portulaca oleracea to decode the...

Genomic, epigenomic and transcriptomic regulation of cellular senescence.

Cellular senescence is a complex, highly regulated cell state induced by cellular damage and stress. Senescence is central to many areas of biology, w...

Reconsidering Molecular Docking Practices in Aptamer Research.

Molecular docking is increasingly used to infer aptamer-target interactions, yet most studies rely on computationally predicted aptamer structures rat...

Artificial intelligence in pediatric medical genetics and genomics.

PURPOSE OF REVIEW: Artificial intelligence (AI) is being rapidly but unevenly integrated into many aspects of medicine as well as society more broadly...

scReGAT: Leveraging Knowledge of Regulatory Interactions to Predict Long-range Gene Regulation at Single-cell Resolution.

Understanding gene regulation at single-cell resolution is crucial for unraveling development, disease, and cellular identity. We introduce single-cel...

Beyond Invariable Sites: Using Evolutionary Stasis to Map Multi-Layered Constraints on the Evolution of Viral and Mammalian Genomes.

The quantification of genomic conservation has progressed from foundational statistical modeling of evolutionary rates to state-of-the-art deep learni...

A novel support vector regression approach for detecting gene-environment interactions and predicting trait values.

Genome-wide association studies and genomic prediction are fundamental for investigating complex traits, but they have different objectives and are ra...

A machine learning-derived and functionally validated circadian rhythm signature predicts clinical outcomes and in silico drug sensitivity in colorectal cancer.

BACKGROUND: Colorectal cancer (CRC) displays considerable heterogeneity in clinical outcomes, highlighting the need for reliable prognostic biomarkers...

Drug repurposing opportunities across 92 CNS-related conditions using deep learning and whole-genome sequencing.

CNS-related conditions span tumors, vascular, neurodevelopmental, and psychiatric disorders, yet therapeutic development for CNS disorders continues t...

Screening of potential targets of (2S)-2'-methoxykurarinone against sepsis and in vivo verification in zebrafish model.

OBJECTIVE: To screen the potential core targets of (2S)-2'-Methoxykurarinone, a dimethyldihydroflavonoid derived from Sophora flavescens, against seps...

Mechanistic advances in nanomedicine, nucleic acid therapies, and AI-driven research on cervical cancer.

Cervical cancer pharmacotherapy is significantly limited by physiological and cellular barriers that restrict drug access to therapeutic targets, resu...

Health databases and early identification of autism spectrum disorder: a scoping review.

OBJECTIVES: To map the available evidence on the use of health databases for the early identification of autism spectrum disorder (ASD) across diverse...

Combined Analysis of scRNA-seq and Bulk RNA-seq Sequencing Revealing the Heterogeneity of Recurrent Respiratory Papillomatosis and Key Molecular Mechanisms of Its Occurrence and Development.

OBJECTIVE: Recurrent respiratory papillomatosis (RRP) is a benign tumor that is highly prone to recurrence and has the potential to become malignant, ...

Single-cell and spatial transcriptomic landscapes reveal PIGT as a pivotal regulator of immunometabolic remodeling in colorectal cancer liver metastasis.

Colorectal cancer liver metastasis (CRLM) represents the leading cause of mortality in colorectal cancer (CRC). However, the molecular mechanisms enab...