Genetics

Neural Latent Filtering for Gene Discovery in Breast Cancer Subtypes.

Gene selection from expression data represents a challenging task, primarily due to the high data dimensionality and the vast number of genes that would be identified, many of which may be unrelated to cancer-relevant biological processes. To tackle this issue, filtering methods constitute an effective solution to identify the most informative genes, which can serve as potential biomarkers to tail...

Optimized primer and model improve precision of X chromosome telomere length determination in the Han population.

The attrition of telomere length is associated with cellular aging and plays a role in multiple age-related disorders. This study analyzed the relationship between telomere length on the X chromosome and age in the Han population (n = 492) using whole-genome sequencing and long-read sequencing data from 32 individuals. We developed three pairs of primers and completed measurements in a cohort of 1...

Deep-learning/transfer-learning based Overall Survival prediction conditional on Progression-Free Interval with TCGA RNA-seq expression and KEGG-pathways.

We developed a novel deep-learning network that integrated Progression-Free Interval (PFI) as a condition based on transfer learning and fine tuning, ...

LEAP: Long sequence enhancer activity analysis and prediction framework.

BACKGROUND AND OBJECTIVE: Enhancer activity is central to the regulation of gene expression. Despite extensive computational research on enhancers, th...

Improvements to Casanovo, a Deep Learning De Novo Peptide Sequencer.

Casanovo is a state-of-the-art deep learning model for de novo peptide sequencing from mass spectrometry and proteomics data. Here, we report on a ser...

Artificial Intelligence for the Treatment and Management of Colorectal Liver Metastases.

Colorectal cancer (CRC) is the third most commonly diagnosed malignancy worldwide. Prognosis is significantly worsened in patients with colorectal liv...

A machine learning-based model for the prediction of thyroid eye disease with oxidative stress-related biomarkers.

Thyroid eye disease (TED), the most common adult orbital disease, can significantly impair patients' quality of life. Currently, effective diagnostic ...

Machine learning-assisted prognosis of multiple myeloma side population cells via SRGs and OCLR stemness index.

BACKGROUND AND OBJECTIVE: Relapse in Multiple Myeloma, driven by therapy-resistant cancer stem cells, necessitates the development of more specific an...

MetaChrome: an open-source, user-friendly tool for automated metaphase chromosome analysis.

DNA Fluorescence In Situ Hybridization (DNA FISH) is an essential technique to study chromosome biology and genetics, enabling precise visualization o...

NAD+ restores proteostasis through splicing-dependent autophagy.

Autophagy preserves neuronal integrity by clearing damaged proteins and organelles, but its efficiency declines with aging and neurodegeneration. Depl...

A chalcone-rich extract from licorice root inhibits liver steatosis and fibrosis via regulating PPARα and TGFβ signaling.

BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a major liver disorder, which seriously affects human health globally....

Polyploid giant cancer cells: A novel target in future cancer therapy.

Under intense therapeutic stress-including chemotherapy, radiotherapy, and targeted therapies-tumor cells can undergo ploidy reprogramming to generate...

Morphological regulation of filamentous fungi improves industrial production.

Filamentous fungi have emerged as ideal chassis cells for high-value products such as industrial enzymes, therapeutic proteins, and antibiotics, due t...

Integrating Genomic Data and Imaging in Lung Cancer Prediction Using a Hybrid Deep Learning Approach.

OBJECTIVES: Lung cancer remains one of the leading causes of cancer-related mortality worldwide, underscoring the urgent need for improved diagnostic ...

cncFinder: A graph-attention-network-based interpretable learning model to identify bifunctional long non-coding RNAs.

Certain RNAs exhibit both protein-coding and regulatory non-coding functions, termed bifunctional RNAs or coding and non-coding RNAs. Long non-coding ...

Causal Inference and Prognostic Modeling in Colorectal Cancer through Integration of Computational Pathology and Mendelian Randomization.

BACKGROUND: While traditional pathology supports the diagnosis and staging of colorectal cancer (CRC), computational pathology provides novel prognost...

Integrating molecular diagnostics and artificial intelligence in chronic microbial disease.

Chronic microbial diseases, often driven by biofilm formation, pose a persistent global health burden due to their complex diagnosis, resistance mecha...

Graph neural network-based mutation-aware regression test ordering using code dependency graphs and execution traces.

The mutation-aware test prioritisation system in this paper uses Graph Neural Networks (GNNs) to combine static program structure, dynamic execution t...

PlantscRNAdb 4.0: Improved marker identification and annotation under a cell-type uniformity for plants.

Single-cell RNA sequencing (scRNA-seq) has revolutionized plant biology by enabling high-resolution analysis of cellular heterogeneity, gene expressio...

Urinary Tumor DNA to Identify Candidates for Repeat Transurethral Resection in Non-Muscle-Invasive Bladder Cancer.

Repeat transurethral resection of bladder tumor (re-TURBT) is commonly recommended for patients with non-muscle-invasive bladder cancer (NMIBC) with h...