AIMC Topic: Computational Biology

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PSSM-Sumo: deep learning based intelligent model for prediction of sumoylation sites using discriminative features.

BMC bioinformatics Aug 30, 2024
Post-translational modifications (PTMs) are fundamental to essential biological processes, exerting significant influence over gene expression, protein localization, stability, and genome replication. Sumoylation, a PTM involving the covalent additio...
Sumoylation Position-Specific Scoring Matrices Support Vector Machine Protein Processing, Post-Translational Humans Deep Learning Algorithms Computational Biology
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TriFusion enables accurate prediction of miRNA-disease association by a tri-channel fusion neural network.

Communications biology Aug 30, 2024
The identification of miRNA-disease associations is crucial for early disease prevention and treatment. However, it is still a computational challenge to accurately predict such associations due to improper information encoding. Previous methods char...
Humans MicroRNAs Ovarian Neoplasms Breast Neoplasms Prostatic Neoplasms Genetic Predisposition to Disease Male Computational Biology Deep Learning Neural Networks, Computer Female
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Deciphering the Language of Protein-DNA Interactions: A Deep Learning Approach Combining Contextual Embeddings and Multi-Scale Sequence Modeling.

Journal of molecular biology Aug 29, 2024
Deciphering the mechanisms governing protein-DNA interactions is crucial for understanding key cellular processes and disease pathways. In this work, we present a powerful deep learning approach that significantly advances the computational predictio...
Neural Networks, Computer Deep Learning Computational Biology DNA Protein Binding DNA-Binding Proteins Binding Sites
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Artificial neural network inference analysis identified novel genes and gene interactions associated with skeletal muscle aging.

Journal of cachexia, sarcopenia and muscle Aug 29, 2024
BACKGROUND: Sarcopenia is an age-related muscle disease that increases the risk of falls, disabilities, and death. It is associated with increased muscle protein degradation driven by molecular signalling pathways including Akt and FOXO1. This study ...
Computational Biology Muscle, Skeletal Gene Expression Profiling Transcriptome Gene Regulatory Networks Middle Aged Exercise Aged Young Adult Male Aging Adult Humans Neural Networks, Computer Female
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Developing a low-cost, open-source, locally manufactured workstation and computational pipeline for automated histopathology evaluation using deep learning.

EBioMedicine Aug 27, 2024
BACKGROUND: Deployment and access to state-of-the-art precision medicine technologies remains a fundamental challenge in providing equitable global cancer care in low-resource settings. The expansion of digital pathology in recent years and its poten...
Computational Biology Deep Learning Image Processing, Computer-Assisted Algorithms Neoplasms Humans
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Rapid discrimination between deleterious and benign missense mutations in the CAGI 6 experiment.

Human genomics Aug 27, 2024
We describe the machine learning tool that we applied in the CAGI 6 experiment to predict whether single residue mutations in proteins are deleterious or benign. This tool was trained using only single sequences, i.e., without multiple sequence align...
Humans Machine Learning Proteins Mutation, Missense Software Computational Biology
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Optimizing protein sequence classification: integrating deep learning models with Bayesian optimization for enhanced biological analysis.

BMC medical informatics and decision making Aug 27, 2024
Efforts to enhance the accuracy of protein sequence classification are of utmost importance in driving forward biological analyses and facilitating significant medical advancements. This study presents a cutting-edge model called ProtICNN-BiLSTM, whi...
Humans Proteins Deep Learning Bayes Theorem Computational Biology Sequence Analysis, Protein
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An end-to-end framework for the prediction of protein structure and fitness from single sequence.

Nature communications Aug 27, 2024
Significant research progress has been made in the field of protein structure and fitness prediction. Particularly, single-sequence-based structure prediction methods like ESMFold and OmegaFold achieve a balance between inference speed and prediction...
Neural Networks, Computer Protein Conformation Algorithms Proteins Sequence Analysis, Protein Models, Molecular Mutation Computational Biology Protein Stability
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Multi-modal deep learning enables efficient and accurate annotation of enzymatic active sites.

Nature communications Aug 27, 2024
Annotating active sites in enzymes is crucial for advancing multiple fields including drug discovery, disease research, enzyme engineering, and synthetic biology. Despite the development of numerous automated annotation algorithms, a significant trad...
Algorithms Catalytic Domain Molecular Sequence Annotation Enzymes Computational Biology Databases, Protein Deep Learning
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DRpred: A Novel Deep Learning-Based Predictor for Multi-Label mRNA Subcellular Localization Prediction by Incorporating Bayesian Inferred Prior Label Relationships.

Biomolecules Aug 26, 2024
The subcellular localization of messenger RNA (mRNA) not only helps us to understand the localization regulation of gene expression but also helps to understand the relationship between RNA localization pattern and human disease mechanism, which has ...
Bayes Theorem Deep Learning Computational Biology Humans RNA, Messenger Neural Networks, Computer
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