AIMC Topic: Computational Biology

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Compressed Representation of Extreme Learning Machine with Self-Diffusion Graph Denoising Applied for Dissecting Molecular Heterogeneity.

Journal of computational biology : a journal of computational molecular cell biology Mar 19, 2025
Molecular heterogeneity exists in many biological systems, such as major malignancies or diverse cell populations. Clustering of gene expression profiles has been widely used to dissect molecular heterogeneity. One drawback common to most clustering ...
Humans Machine Learning Algorithms Neoplasms Gene Expression Profiling Computational Biology Cluster Analysis Extreme Learning Machines
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Multitask learning model for predicting non-coding RNA-disease associations: Incorporating local and global context.

Methods (San Diego, Calif.) Mar 18, 2025
Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are crucial non-coding RNAs involved in various diseases. Understanding these interactions is vital for advancing diagnostic, preventive, and therapeutic strategies. Existing computational methods...
Machine Learning Liver Neoplasms Computational Biology Genetic Predisposition to Disease MicroRNAs Humans RNA, Long Noncoding
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ListPred: A predictive ML tool for virulence potential and disinfectant tolerance in Listeria monocytogenes.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases Mar 18, 2025
Despite current surveillance and sanitation strategies, foodborne pathogens continue to threaten the food industry and public health. Whole genome sequencing (WGS) has reached an unprecedented resolution to analyse and compare pathogenic bacterial is...
Disinfectants Genome, Bacterial Listeriosis Listeria monocytogenes Whole Genome Sequencing Virulence Machine Learning Drug Resistance, Bacterial Humans Computational Biology
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CacPred: a cascaded convolutional neural network for TF-DNA binding prediction.

BMC genomics Mar 18, 2025
BACKGROUND: Transcription factors (TFs) regulate the genes' expression by binding to DNA sequences. Aligned TFBSs of the same TF are seen as cis-regulatory motifs, and substantial computational efforts have been invested to find motifs. In recent yea...
Protein Binding Computational Biology Transcription Factors DNA Binding Sites Software Neural Networks, Computer Chromatin Immunoprecipitation Sequencing Algorithms Convolutional Neural Networks
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Identification and validation of endoplasmic reticulum stress-related diagnostic biomarkers for type 1 diabetic cardiomyopathy based on bioinformatics and machine learning.

Frontiers in endocrinology Mar 18, 2025
BACKGROUND: Diabetic cardiomyopathy (DC) is a serious complication in patients with type 1 diabetes mellitus and has become a growing public health problem worldwide. There is evidence that endoplasmic reticulum stress (ERS) is involved in the pathog...
Mice Humans Endoplasmic Reticulum Stress Computational Biology Biomarkers Machine Learning Diabetic Cardiomyopathies Diabetes Mellitus, Type 1 Animals Gene Expression Profiling
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PlantPathoPPI: An Ensemble-based Machine Learning Architecture for Prediction of Protein-Protein Interactions between Plants and Pathogens.

Journal of molecular biology Mar 17, 2025
This study aimed to develop a machine learning-based tool for predicting protein-protein interactions (PPIs) between plant-pathogen systems, addressing the challenges of experimental PPI identification. Identifying PPIs in plant-pathogen interactions...
Algorithms Protein Interaction Maps Computational Biology Neural Networks, Computer Machine Learning Software Support Vector Machine Plant Proteins Plants Host-Pathogen Interactions Plant Diseases Protein Interaction Mapping
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Artificial Intelligence: A New Tool for Structure-Based G Protein-Coupled Receptor Drug Discovery.

Biomolecules Mar 17, 2025
Understanding protein structures can facilitate the development of therapeutic drugs. Traditionally, protein structures have been determined through experimental approaches such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy...
Drug Discovery Computational Biology Humans Ligands Receptors, G-Protein-Coupled Artificial Intelligence Protein Conformation Algorithms Molecular Docking Simulation
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A novel seven-tier framework for the classification of MEFV missense variants using adaptive and rigid classifiers.

Scientific reports Mar 17, 2025
There is a great discrepancy between the clinical categorization of MEFV gene variants and in silico tool predictions. In this study, we developed a seven-tier classification system for MEFV missense variants of unknown significance and recommended a...
Machine Learning Algorithms Computer Simulation Humans Computational Biology Familial Mediterranean Fever Databases, Genetic Pyrin Mutation, Missense
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Generative AI extracts ecological meaning from the complex three dimensional shapes of bird bills.

PLoS computational biology Mar 17, 2025
Data on the three dimensional shape of organismal morphology is becoming increasingly available, and forms part of a new revolution in high-throughput phenomics that promises to help understand ecological and evolutionary processes that influence phe...
Computational Biology Beak Birds Deep Learning Imaging, Three-Dimensional Artificial Intelligence Animals
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Predictive reward-prediction errors of climbing fiber inputs integrate modular reinforcement learning with supervised learning.

PLoS computational biology Mar 17, 2025
Although the cerebellum is typically associated with supervised learning algorithms, it also exhibits extensive involvement in reward processing. In this study, we investigated the cerebellum's role in executing reinforcement learning algorithms, wit...
Supervised Machine Learning Cerebellum Reward Computational Biology Models, Neurological Mice, Inbred C57BL Reinforcement, Psychology Purkinje Cells Algorithms Animals Male Mice
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