The field of machine learning has allowed researchers to generate and analyse vast amounts of data using a wide variety of methodologies. Artificial Neural Networks (ANN) are some of the most commonly used statistical models and have been successful in biomarker discovery studies in multiple disease types. This review seeks to explore and evaluate an integrated ANN pipeline for biomarker discovery and validation in Alzheimer's disease, the most common form of dementia worldwide with no proven cause and no available cure. The proposed pipeline consists of analysing public data with a categorical and continuous stepwise algorithm and further examination through network inference to predict gene interactions. This methodology can reliably generate novel markers and further examine known ones and can be used to guide future research in Alzheimer's disease.
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http://dx.doi.org/10.1016/j.csbj.2018.02.001 | DOI Listing |
Nat Commun
January 2025
Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford, UK.
The analysis of circulating tumour DNA (ctDNA) through minimally invasive liquid biopsies is promising for early multi-cancer detection and monitoring minimal residual disease. Most existing methods focus on targeted deep sequencing, but few integrate multiple data modalities. Here, we develop a methodology for ctDNA detection using deep (80x) whole-genome TET-Assisted Pyridine Borane Sequencing (TAPS), a less destructive approach than bisulphite sequencing, which permits the simultaneous analysis of genomic and methylomic data.
View Article and Find Full Text PDFBiochem Genet
January 2025
Cancer Immunology and Immunotherapy Center, Cancer Research Center, Saint Savas Cancer Hospital, 11522, Athens, Greece.
The tumor microenvironment has a significant input on prognosis and also for predicting clinical outcomes in various types of cancers. However, tumor tissue is not always available, thus, rendering peripheral blood a preferable alternative in the search for prognostic and predictive gene signatures. Head and neck squamous cell carcinoma (HNSCC) constitutes a quite heterogeneous disease characterized by poor prognosis.
View Article and Find Full Text PDFCurr Comput Aided Drug Des
January 2025
Department of Clinical Pharmacology Lab, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China.
Introduction: Astrocytoma is the most common glioma, accounting for about 65% of glioblastoma. Its malignant transformation is also one of the important causes of patient mortality, making it the most prevalent and difficult to treat in primary brain tumours. However, little is known about the underlying mechanisms of this transformation.
View Article and Find Full Text PDFEur Respir Rev
January 2025
Division of Pulmonary and Critical Care Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
Asthma is considered severe if it remains uncontrolled despite optimal conventional therapy, characterised by poor symptom control, frequent exacerbations and increased exposure to systemic corticosteroids. This has a significant impact on morbidity, mortality and healthcare resource utilisation. Recent advances in the understanding of asthma heterogeneity and immunopathogenesis have helped delineate precise disease pathways.
View Article and Find Full Text PDFJ Genet Genomics
January 2025
Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China. Electronic address:
Colitis-associated colorectal cancer (CAC), a serious complication of ulcerative colitis (UC), is associated with a poor prognosis. The vitamin D receptor (VDR) is recognized for its protective role in UC and CAC through the maintenance of intestinal barrier integrity and the regulation of inflammation. This study demonstrates a significant reduction in mA-related genes, particularly methyltransferase like 14 (METTL14), in UC and CAC patients and identifies an association between METTL14 and VDR.
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