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Functional annotation and biological interpretation of proteomics data.

Biochimica et biophysica acta
Proteomics experiments often generate a vast amount of data. However, the simple identification and quantification of proteins from a cell proteome or subproteome is not sufficient for the full understanding of complex mechanisms occurring in the bio...

Inter-species pathway perturbation prediction via data-driven detection of functional homology.

Bioinformatics (Oxford, England)
MOTIVATION: Experiments in animal models are often conducted to infer how humans will respond to stimuli by assuming that the same biological pathways will be affected in both organisms. The limitations of this assumption were tested in the IMPROVER ...

Inside a Metastatic Fracture: Molecular Bases and New Potential Therapeutic Targets.

Cancer medicine
INTRODUCTION: Bone metastases and pathological fractures significantly impact the prognosis and quality of life in cancer patients. However, clinical and radiological features alone have been shown to fail to predict skeletal related events of a bone...

Oxidative Phosphorylation Pathway in Ankylosing Spondylitis: Multi-Omics Analysis and Machine Learning.

International journal of rheumatic diseases
INTRODUCTION: Ankylosing spondylitis (AS) is a chronic inflammatory disease affecting the axial skeleton, characterized by immune microenvironment dysregulation and elevated cytokines like TNF-α and IL-17. Mitochondrial oxidative phosphorylation (OXP...

Diagnostic Power of MicroRNAs in Melanoma: Integrating Machine Learning for Enhanced Accuracy and Pathway Analysis.

Journal of cellular and molecular medicine
This study identifies microRNAs (miRNAs) with significant discriminatory power in distinguishing melanoma from nevus, notably hsa-miR-26a and hsa-miR-211, which have exhibited diagnostic potential with accuracy of 81% and 78% respectively. To enhance...

Unveiling the Immune Landscape of Delirium through Single-Cell RNA Sequencing and Machine Learning: Towards Precision Diagnosis and Therapy.

Psychogeriatrics : the official journal of the Japanese Psychogeriatric Society
BACKGROUND: Postoperative delirium (POD) poses significant clinical challenges regarding its diagnosis and treatment. Identifying biomarkers that can predict and diagnose POD is crucial for improving patient outcomes.

Leveraging Artificial Intelligence in GPCR Activation Studies: Computational Prediction Methods as Key Drivers of Knowledge.

Methods in molecular biology (Clifton, N.J.)
G protein-coupled receptors (GPCRs) are key molecules involved in cellular signaling and are attractive targets for pharmacological intervention. This chapter is designed to explore the range of algorithms used to predict GPCRs' activation states, wh...

Identification of KCNQ1 as a diagnostic biomarker related to endoplasmic reticulum stress for intervertebral disc degeneration based on machine learning and experimental evidence.

Medicine
Intervertebral disc degeneration (IDD) is a primary cause of low back pain and disability. Cellular senescence and apoptosis due to endoplasmic reticulum stress (ERS) are key in IDD pathology. Identifying biomarkers linked to ERS in IDD is crucial fo...

A transformer-based deep learning survival prediction model and an explainable XGBoost anti-PD-1/PD-L1 outcome prediction model based on the cGAS-STING-centered pathways in hepatocellular carcinoma.

Briefings in bioinformatics
Recent studies suggest cGAS-STING pathway may play a crucial role in the genesis and development of hepatocellular carcinoma (HCC), closely associated with classical pathways and tumor immunity. We aimed to develop models predicting survival and anti...

Machine Learning upon RDF Knowledge Graphs for Drug Safety: A Case Study on Reactome Data.

Studies in health technology and informatics
Artificial Intelligence (AI), particularly Machine Learning (ML), has gained attention for its potential in various domains. However, approaches integrating symbolic AI with ML on Knowledge Graphs have not gained significant focus yet. We argue that ...