AIMC Topic: Lysine

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Comprehensive analysis of scRNA-seq and bulk RNA-seq data via machine learning and bioinformatics reveals the role of lysine metabolism-related genes in gastric carcinogenesis.

BMC cancer Apr 9, 2025
BACKGROUND: Gastric cancer (GC) is a highly aggressive and heterogeneous cancer with extremely complex biological characteristics. Lysine and its metabolism are closely related to human cancer, but little is known about how lysine metabolism-related ...
Single-Cell Gene Expression Analysis Computational Biology Sequence Analysis, RNA RNA-Seq Gene Regulatory Networks Carcinogenesis Vimentin Lysine Gene Expression Regulation, Neoplastic Nomograms Cell Proliferation Prognosis Stomach Neoplasms Biomarkers, Tumor Cell Line, Tumor Single-Cell Analysis Humans Machine Learning
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Lipid discovery enabled by sequence statistics and machine learning.

eLife Dec 10, 2024
Bacterial membranes are complex and dynamic, arising from an array of evolutionary pressures. One enzyme that alters membrane compositions through covalent lipid modification is MprF. We recently identified that MprF synthesizes lysyl-phosphatidylgl...
Glycolipids Lysine Enterococcus Bacterial Proteins Streptococcus agalactiae Phosphatidylglycerols Substrate Specificity Machine Learning
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Machine Learning Guided Rational Design of a Non-Heme Iron-Based Lysine Dioxygenase Improves its Total Turnover Number.

Chembiochem : a European journal of chemical biology Dec 5, 2024
Highly selective C-H functionalization remains an ongoing challenge in organic synthetic methodologies. Biocatalysts are robust tools for achieving these difficult chemical transformations. Biocatalyst engineering has often required directed evolutio...
Iron Mutation Molecular Dynamics Simulation Machine Learning Dioxygenases Lysine Protein Engineering
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DeepKlapred: A deep learning framework for identifying protein lysine lactylation sites via multi-view feature fusion.

International journal of biological macromolecules Nov 19, 2024
Lysine lactylation (Kla) is a post-translational modification (PTM) that holds significant importance in the regulation of various biological processes. While traditional experimental methods are highly accurate for identifying Kla sites, they are bo...
Amino Acid Sequence Lysine Protein Processing, Post-Translational Proteins Algorithms Deep Learning Computational Biology
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iBhb-Lys: Identify lysine β-hydroxybutyrylation sites using autoencoder feature representation and fuzzy SVM algorithm.

Analytical biochemistry Nov 7, 2024
Lysine β-hydroxybutyrylation (Kbhb) is newly discovered β-hydroxybutyrylate-derived histone modification which has been associated with the pathogenesis of many human diseases. To further elucidate the biological significance and molecular mechanism ...
Algorithms Support Vector Machine Fuzzy Logic Lysine Humans
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KbhbXG: A Machine learning architecture based on XGBoost for prediction of lysine β-Hydroxybutyrylation (Kbhb) modification sites.

Methods (San Diego, Calif.) Apr 27, 2024
Lysine β-hydroxybutyrylation is an important post-translational modification (PTM) involved in various physiological and biological processes. In this research, we introduce a novel predictor KbhbXG, which utilizes XGBoost to identify β-hydroxybutyry...
Humans Machine Learning Software Proteomics Algorithms Protein Processing, Post-Translational Computational Biology Lysine
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Predicting lysine methylation sites using a convolutional neural network.

Methods (San Diego, Calif.) Apr 9, 2024
Protein lysine methylation is a particular type of post translational modification that plays an important role in both histone and non-histone function regulation in proteins. Deregulation caused by lysine methyltransferases has been identified as t...
Methylation Lysine Histone-Lysine N-Methyltransferase Machine Learning Computational Biology Protein Processing, Post-Translational Humans Neural Networks, Computer
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An Automated Deep Learning-Based Framework for Uptake Segmentation and Classification on PSMA PET/CT Imaging of Patients with Prostate Cancer.

Journal of imaging informatics in medicine Apr 8, 2024
Uptake segmentation and classification on PSMA PET/CT are important for automating whole-body tumor burden determinations. We developed and evaluated an automated deep learning (DL)-based framework that segments and classifies uptake on PSMA PET/CT. ...
Humans Aged Lysine Antigens, Surface Glutamate Carboxypeptidase II Male Deep Learning Positron Emission Tomography Computed Tomography Prostatic Neoplasms Urea
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DeepNphos: A deep-learning architecture for prediction of N-phosphorylation sites.

Computers in biology and medicine Jan 28, 2024
MOTIVATION: Phosphorylation, a prevalent post-translational modification, plays a crucial role in regulating cellular activities. This process encompasses O-phosphorylation (e.g., phosphoserine) and N-phosphorylation (e.g., phospho-lysine (pK), phosp...
Deep Learning Protein Processing, Post-Translational Arginine Phosphorylation Histidine Lysine
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Prediction of lysine HMGylation sites using multiple feature extraction and fuzzy support vector machine.

Analytical biochemistry Dec 30, 2022
Protein 3-hydroxyl-3-methylglutarylation (HMGylation) is newly discovered lysine acylation modification in mitochondrion. The accurate identification of HMGylation sites is the premise and key to further explore the molecular mechanisms of HMGylation...
Amino Acids Support Vector Machine Algorithms Lysine Protein Processing, Post-Translational Computational Biology Proteins
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