AIMC Topic: Computational Biology

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Identification of diagnostic genes and drug prediction in metabolic syndrome-associated rheumatoid arthritis by integrated bioinformatics analysis, machine learning, and molecular docking.

Frontiers in immunology Jul 29, 2024
BACKGROUND: Interactions between the immune and metabolic systems may play a crucial role in the pathogenesis of metabolic syndrome-associated rheumatoid arthritis (MetS-RA). The purpose of this study was to discover candidate biomarkers for the diag...
Transcriptome Biomarkers Arthritis, Rheumatoid Protein Interaction Maps Molecular Docking Simulation Computational Biology Gene Regulatory Networks Humans Gene Expression Profiling Metabolic Syndrome Machine Learning
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RACGAP1 is a pivotal gene in lung adenocarcinoma-associated membranous nephropathy: Based on comprehensive bioinformatics analysis and machine learning.

International immunopharmacology Jul 27, 2024
BACKGROUND: This study performs a detailed bioinformatics and machine learning analysis to investigate the genetic foundations of membranous nephropathy (MN) in lung adenocarcinoma (LUAD).
Prognosis Female Male Middle Aged Gene Expression Profiling Lung Neoplasms GTPase-Activating Proteins Humans Machine Learning Glomerulonephritis, Membranous Collagen Type III Computational Biology Adenocarcinoma of Lung Gene Expression Regulation, Neoplastic Databases, Genetic
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DeepPGD: A Deep Learning Model for DNA Methylation Prediction Using Temporal Convolution, BiLSTM, and Attention Mechanism.

International journal of molecular sciences Jul 26, 2024
As part of the field of DNA methylation identification, this study tackles the challenge of enhancing recognition performance by introducing a specialized deep learning framework called DeepPGD. DNA methylation, a crucial biological modification, pla...
Neural Networks, Computer Computational Biology DNA Algorithms DNA Methylation Humans Deep Learning
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Hybrid framework for membrane protein type prediction based on the PSSM.

Scientific reports Jul 26, 2024
Membrane proteins are considered the major source of drug targets and are indispensable for drug design and disease prevention. However, traditional biomechanical experiments are costly and time-consuming; thus, many computational methods for predict...
Humans Neural Networks, Computer Machine Learning Databases, Protein Computational Biology Algorithms Position-Specific Scoring Matrices Membrane Proteins Deep Learning
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DeepDRA: Drug repurposing using multi-omics data integration with autoencoders.

PloS one Jul 26, 2024
Cancer treatment has become one of the biggest challenges in the world today. Different treatments are used against cancer; drug-based treatments have shown better results. On the other hand, designing new drugs for cancer is costly and time-consumin...
Antineoplastic Agents Deep Learning Computational Biology Humans Machine Learning Neoplasms Multiomics Drug Repositioning
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BiRNN-DDI: A Drug-Drug Interaction Event Type Prediction Model Based on Bidirectional Recurrent Neural Network and Graph2Seq Representation.

Journal of computational biology : a journal of computational molecular cell biology Jul 25, 2024
Research on drug-drug interaction (DDI) prediction, particularly in identifying DDI event types, is crucial for understanding adverse drug reactions and drug combinations. This work introduces a Bidirectional Recurrent Neural Network model for DDI ev...
Drug Interactions Recurrent Neural Networks Neural Networks, Computer Algorithms Computational Biology Humans
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Potential Shared Mitochondrial-Related Gene Signatures and Molecular Mechanisms Between Polycystic Ovary Syndrome (PCOS) and Major Depressive Disorder (MDD): Evidence from Transcriptome Data and Machine Learning.

Molecular biotechnology Jul 24, 2024
Polycystic ovary syndrome (PCOS) is strongly associated with major depressive disorder (MDD), but the shared pathophysiological mechanisms between them are ambiguous, and the aim of this study was to explore the shared genetic features and associated...
Gene Expression Profiling Transcriptome Protein Interaction Maps Machine Learning Female Depressive Disorder, Major Databases, Genetic Mitochondria Polycystic Ovary Syndrome Gene Regulatory Networks Computational Biology Humans Support Vector Machine
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AAontology: An Ontology of Amino Acid Scales for Interpretable Machine Learning.

Journal of molecular biology Jul 24, 2024
Amino acid scales are crucial for protein prediction tasks, many of them being curated in the AAindex database. Despite various clustering attempts to organize them and to better understand their relationships, these approaches lack the fine-grained ...
Computational Biology Cluster Analysis Proteins Databases, Protein Amino Acids Machine Learning
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Robust evaluation of deep learning-based representation methods for survival and gene essentiality prediction on bulk RNA-seq data.

Scientific reports Jul 24, 2024
Deep learning (DL) has shown potential to provide powerful representations of bulk RNA-seq data in cancer research. However, there is no consensus regarding the impact of design choices of DL approaches on the performance of the learned representatio...
Humans Computational Biology Genes, Essential Neoplasms Deep Learning RNA-Seq
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A personalized mRNA signature for predicting hypertrophic cardiomyopathy applying machine learning methods.

Scientific reports Jul 24, 2024
Hypertrophic cardiomyopathy (HCM) may lead to cardiac dysfunction and sudden death. This study was designed to develop a HCM signature applying bioinformatics and machine learning methods. Data of HCM and normal tissues were obtained from public data...
Humans Computational Biology RNA, Messenger Gene Expression Profiling Disease Models, Animal Transcriptome Machine Learning Zebrafish Gene Regulatory Networks Animals Cardiomyopathy, Hypertrophic
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