Genetics

Potential role of TNFRSF12A in linking glioblastoma and alzheimer's disease via shared tumour suppressor pathways.

Tumor suppressor genes (TSGs) are critical regulators of cellular homeostasis and are extensively studied in cancer biology. However, their roles in neurodegenerative diseases, particularly Alzheimer's disease (AD), remain poorly understood. Recent evidence of an inverse association between cancer and AD suggests the existence of shared molecular mechanisms. We conducted an integrative analysis to...

Identification of CXCR4 as a potential preventive gene in clear cell renal cell carcinoma from machine learning and immune analysis.

Clear cell renal cell carcinoma (ccRCC) represents a prevalent malignant kidney tumor characterized by high metastatic potential and recurrence rates. Investigations into the molecular mechanisms and therapeutic targets of ccRCC have provided novel directions for early diagnosis and targeted therapy. The CXCR4 gene plays a pivotal role in tumor progression and metastasis. In this study, this study...

AI-enabled drug prediction and gene network analysis reveal therapeutic use of vorinostat for Rett Syndrome in preclinical models.

BACKGROUND: Many neurodevelopmental genetic disorders, such as Rett syndrome, are caused by a single gene mutation but trigger changes in expression o...

In-silico 3D molecular editing through physics-informed and preference-aligned generative foundation models.

Generating molecular structures towards desired properties is a critical task in computer-aided drug and material design. As special 3D entities, mole...

Machine learning-assisted decoding of temporal transcriptional dynamics via fluorescent timer.

Investigating the temporal dynamics of gene expression is crucial for understanding gene regulation across various biological processes. Using the Flu...

Activated cancer-associated fibroblasts correlate with poor survival and decreased lymphocyte infiltration in infiltrative type distal cholangiocarcinoma.

Cancer-associated fibroblasts promote tumor progression through growth facilitation, invasion, and immune evasion. This study investigated the impact ...

Machine learning unveils hypoxia-immune gene hub for clinical stratification of thyroid-associated ophthalmopathy.

Thyroid-associated ophthalmopathy (TAO) is an autoimmune disorder affecting the orbit, potentially resulting in blindness. This study focused on the r...

Predict the degree of secondary structures of the encoding sequences in DNA storage by deep learning model.

DNA storage has been widely considered as a promising alternative for exponentially growing data. However, the inherent complex secondary structures s...

Regulatory T cells and matrix-producing cancer associated fibroblasts contribute on the immune resistance and progression of prognosis related tumor subtypes in ccRCC.

Clear cell renal cell carcinoma (ccRCC) is a prevalent malignant tumor in the field of urology. The effect of cell heterogeneity on the prognosis and ...

A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data.

A core computational challenge in the analysis of mass spectrometry data is the de novo sequencing problem, in which the generating amino acid sequenc...

Leveraging autoencoder models and data augmentation to uncover transcriptomic diversity of gingival keratinocytes in single cell analysis.

Periodontitis, a chronic inflammatory condition of the periodontium, is associated with over 60 systemic diseases. Despite advancements, precision med...

Validation of an AI-enabled exome/transcriptome liquid biopsy platform for early detection, MRD, disease monitoring, and therapy selection for solid tumors.

Effective clinical management of patients with cancer requires highly accurate diagnosis, precise therapy selection, and highly sensitive monitoring o...

Ensemble machine learning-based pre-trained annotation approach for scRNA-seq data using gradient boosting with genetic optimizer.

Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of gene expression by allowing researchers to analyze the transcriptomes of indivi...

Can mutation abundance assess the biological behavior of BRAF-positive papillary thyroid carcinoma?

BACKGROUND: BRAF mutation is the most common genetic change in papillary thyroid carcinoma (PTC). Nevertheless, the association between BRAF mutation ...

stGRL: spatial domain identification, denoising, and imputation algorithm for spatial transcriptome data based on multi-task graph contrastive representation learning.

BACKGROUND: Spatial transcriptomics now enables sequencing while preserving the spatial location of cells. This significantly enhances researchers' un...

Chimeric mis-annotations of genes remain pervasive in eukaryotic non-model organisms.

BACKGROUND: Accurate annotation of protein-coding genes is critical for genome analysis in non-model organisms. However, limited RNA-Seq data and inco...

Identification of potential biomarkers and mechanisms for keloid disorder based on comprehensive bioinformatics analysis and machine learning algorithms.

BACKGROUND: Keloid disorder (KD) encompasses a spectrum of fibroproliferative dermal conditions, the pathogenesis remains complex and incompletely und...

Transforming heart transplantation care with multi-omics insights.

Heart transplantation (HTx) remains the definitive treatment for patients with end-stage heart disease. Despite the number of HTx performed annually i...

MRI's evolving role in rectal cancer in the era of personalized medicine.

Recent decades have seen great advances in the diagnosis and management of rectal cancer, and magnetic resonance imaging (MRI) has become pivotal for ...

Identification of key genes and development of an identifying machine learning model for sepsis.

OBJECTIVE AND DESIGN: This study aims to identify key genes of sepsis and construct a model for sepsis identification through integrated multi-organ s...