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Mutation

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Diffusion-weighted MRI precisely predicts telomerase reverse transcriptase promoter mutation status in World Health Organization grade IV gliomas using a residual convolutional neural network.

The British journal of radiology
OBJECTIVES: Telomerase reverse transcriptase promoter (pTERT) mutation status plays a key role in making decisions and predicting prognoses for patients with World Health Organization (WHO) grade IV glioma. This study was conducted to assess the valu...

Gene-Specific Machine Learning Models to Classify Driver Mutations in Clonal Hematopoiesis.

Cancer discovery
There is no general consensus on the set of mutations capable of driving the age-related clonal expansions in hematopoietic stem cells known as clonal hematopoiesis, and current variant classifications typically rely on rules derived from expert know...

Identification of Clonal Hematopoiesis Driver Mutations through In Silico Saturation Mutagenesis.

Cancer discovery
Clonal hematopoiesis (CH) is a phenomenon of clonal expansion of hematopoietic stem cells driven by somatic mutations affecting certain genes. Recently, CH has been linked to the development of hematologic malignancies, cardiovascular diseases, and o...

Machine learning enables pan-cancer identification of mutational hotspots at persistent CTCF binding sites.

Nucleic acids research
CCCTC-binding factor (CTCF) is an insulator protein that binds to a highly conserved DNA motif and facilitates regulation of three-dimensional (3D) nuclear architecture and transcription. CTCF binding sites (CTCF-BSs) reside in non-coding DNA and are...

Predicting tumor mutation burden and VHL mutation from renal cancer pathology slides with self-supervised deep learning.

Cancer medicine
BACKGROUND: Tumor mutation burden (TMB) and VHL mutation play a crucial role in the management of patients with clear cell renal cell carcinoma (ccRCC), such as guiding adjuvant chemotherapy and improving clinical outcomes. However, the time-consumin...

Protein multi-level structure feature-integrated deep learning method for mutational effect prediction.

Biotechnology journal
Through iterative rounds of mutation and selection, proteins can be engineered to enhance their desired biological functions. Nevertheless, identifying optimal mutation sites for directed evolution remains challenging due to the vastness of the prote...

DDMut-PPI: predicting effects of mutations on protein-protein interactions using graph-based deep learning.

Nucleic acids research
Protein-protein interactions (PPIs) play a vital role in cellular functions and are essential for therapeutic development and understanding diseases. However, current predictive tools often struggle to balance efficiency and precision in predicting t...

Generative AI in glioma: Ensuring diversity in training image phenotypes to improve diagnostic performance for IDH mutation prediction.

Neuro-oncology
BACKGROUND: This study evaluated whether generative artificial intelligence (AI)-based augmentation (GAA) can provide diverse and realistic imaging phenotypes and improve deep learning-based classification of isocitrate dehydrogenase (IDH) type in gl...

Unravelling the metabolic landscape of cutaneous melanoma: Insights from single-cell sequencing analysis and machine learning for prognostic assessment of lactate metabolism.

Experimental dermatology
This manuscript presents a comprehensive investigation into the role of lactate metabolism-related genes as potential prognostic markers in skin cutaneous melanoma (SKCM). Bulk-transcriptome data from The Cancer Genome Atlas (TCGA) and GSE19234, GSE2...

AttABseq: an attention-based deep learning prediction method for antigen-antibody binding affinity changes based on protein sequences.

Briefings in bioinformatics
The optimization of therapeutic antibodies through traditional techniques, such as candidate screening via hybridoma or phage display, is resource-intensive and time-consuming. In recent years, computational and artificial intelligence-based methods ...