AIMC Topic: Computational Biology
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Four Genes with Seven Targeted Drugs might be Treatment for Diabetic Nephropathy and Acute Coronary Syndrome.
The Tohoku journal of experimental medicine
Jun 27, 2024
Diabetes nephropathy (DN) is a main risk factor for acute coronary syndrome (ACS), but the molecular mechanism is unknown. This research used bioinformatics approaches to uncover potential molecular mechanisms and drugs for DN and ACS. GSE142153 and ...
Inference of Essential Genes of the Parasite via Machine Learning.
International journal of molecular sciences
Jun 27, 2024
Over the years, comprehensive explorations of the model organisms (elegant worm) and (vinegar fly) have contributed substantially to our understanding of complex biological processes and pathways in multicellular organisms generally. Extensive func...
ST-CellSeg: Cell segmentation for imaging-based spatial transcriptomics using multi-scale manifold learning.
PLoS computational biology
Jun 27, 2024
Spatial transcriptomics has gained popularity over the past decade due to its ability to evaluate transcriptome data while preserving spatial information. Cell segmentation is a crucial step in spatial transcriptomic analysis, as it enables the avoid...
Cracking AlphaFold2: Leveraging the power of artificial intelligence in undergraduate biochemistry curriculums.
PLoS computational biology
Jun 27, 2024
AlphaFold2 is an Artificial Intelligence-based program developed to predict the 3D structure of proteins given only their amino acid sequence at atomic resolution. Due to the accuracy and efficiency at which AlphaFold2 can generate 3D structure predi...
Identification and validation of cuproptosis-related genes in acetaminophen-induced liver injury using bioinformatics analysis and machine learning.
Frontiers in immunology
Jun 27, 2024
BACKGROUND: Acetaminophen (APAP) is commonly used as an antipyretic analgesic. However, acetaminophen overdose may contribute to liver injury and even liver failure. Acetaminophen-induced liver injury (AILI) is closely related to mitochondrial oxidat...
Identification of endoplasmic reticulum stress genes in human stroke based on bioinformatics and machine learning.
Neurobiology of disease
Jun 26, 2024
After ischemic stroke (IS), secondary injury is intimately linked to endoplasmic reticulum (ER) stress and body-brain crosstalk. Nonetheless, the underlying mechanism systemic immune disorder mediated ER stress in human IS remains unknown. In this st...
PT-KGNN: A framework for pre-training biomedical knowledge graphs with graph neural networks.
Computers in biology and medicine
Jun 26, 2024
Biomedical knowledge graphs (KGs) serve as comprehensive data repositories that contain rich information about nodes and edges, providing modeling capabilities for complex relationships among biological entities. Many approaches either learn node fea...
NPI-DCGNN: An Accurate Tool for Identifying ncRNA-Protein Interactions Using a Dual-Channel Graph Neural Network.
Journal of computational biology : a journal of computational molecular cell biology
Jun 26, 2024
Noncoding RNA (NcRNA)-protein interactions (NPIs) play fundamentally important roles in carrying out cellular activities. Although various predictors based on molecular features and graphs have been published to boost the identification of NPIs, most...
mACPpred 2.0: Stacked Deep Learning for Anticancer Peptide Prediction with Integrated Spatial and Probabilistic Feature Representations.
Journal of molecular biology
Jun 25, 2024
Anticancer peptides (ACPs), naturally occurring molecules with remarkable potential to target and kill cancer cells. However, identifying ACPs based solely from their primary amino acid sequences remains a major hurdle in immunoinformatics. In the pa...
scHolography: a computational method for single-cell spatial neighborhood reconstruction and analysis.
Genome biology
Jun 24, 2024
Spatial transcriptomics has transformed our ability to study tissue complexity. However, it remains challenging to accurately dissect tissue organization at single-cell resolution. Here we introduce scHolography, a machine learning-based method desig...
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