AIMC Topic: Mutation

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Characterizing Protein-Ligand Binding Using Atomistic Simulation and Machine Learning: Application to Drug Resistance in HIV-1 Protease.

Journal of chemical theory and computation Jan 16, 2020
Over the past several decades, atomistic simulations of biomolecules, whether carried out using molecular dynamics or Monte Carlo techniques, have provided detailed insights into their function. Comparing the results of such simulations for a few clo...
Humans Machine Learning Protein Binding Mutation HIV Protease HIV Protease Inhibitors Hydrogen Bonding Static Electricity Monte Carlo Method Molecular Dynamics Simulation HIV-1 Ligands Drug Resistance, Viral
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pVACtools: A Computational Toolkit to Identify and Visualize Cancer Neoantigens.

Cancer immunology research Jan 6, 2020
Identification of neoantigens is a critical step in predicting response to checkpoint blockade therapy and design of personalized cancer vaccines. This is a cross-disciplinary challenge, involving genomics, proteomics, immunology, and computational a...
Cancer Vaccines Algorithms Antigens, Neoplasm Neoplasms Humans Computational Biology Mutation Neural Networks, Computer Immunotherapy Data Mining Artificial Intelligence Software
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A Multiple-Instance Learning-Based Convolutional Neural Network Model to Detect the Mutation in the Histopathology Images of Glioma Tissues.

Journal of computational biology : a journal of computational molecular cell biology Jan 3, 2020
Image Processing, Computer-Assisted Glioma Mutation Isocitrate Dehydrogenase Female Male Deep Learning Humans Neural Networks, Computer
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Prediction of IDH and TERT promoter mutations in low-grade glioma from magnetic resonance images using a convolutional neural network.

Scientific reports Dec 30, 2019
Identification of genotypes is crucial for treatment of glioma. Here, we developed a method to predict tumor genotypes using a pretrained convolutional neural network (CNN) from magnetic resonance (MR) images and compared the accuracy to that of a di...
Neural Networks, Computer Female Reproducibility of Results Humans Promoter Regions, Genetic Isocitrate Dehydrogenase Telomerase Magnetic Resonance Imaging Neoplasm Staging Neoplasm Grading Biomarkers, Tumor Mutation Male Image Processing, Computer-Assisted Glioma
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Integrated structural modeling and super-resolution imaging resolve GPCR oligomers.

Progress in molecular biology and translational science Dec 6, 2019
Formation of G protein-coupled receptors (GPCRs) dimers and higher order oligomers represents a key mechanism in pleiotropic signaling, yet how individual protomers function within oligomers remains poorly understood. For the Class A/rhodopsin subfam...
Humans Neural Networks, Computer Machine Learning Software Algorithms Animals Crystallography, X-Ray Protein Interaction Mapping Protein Structure, Secondary Protein Multimerization Allosteric Site Mutation Molecular Dynamics Simulation Ligands Fluorescence Resonance Energy Transfer Protein Binding Computational Biology Support Vector Machine Receptors, G-Protein-Coupled
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Predictive models for patients with lung carcinomas to identify EGFR mutation status via an artificial neural network based on multiple clinical information.

Journal of cancer research and clinical oncology Dec 5, 2019
PURPOSE: Epidermal growth factor receptor (EGFR) mutation testing has several limitations. Therefore, we built predictive models to determine the EGFR mutation status of patients and guide therapeutic decision-making.
Neural Networks, Computer Humans Female Aged Male Middle Aged Lung Neoplasms Mutation ErbB Receptors Decision Making, Computer-Assisted
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Evaluation of colorectal cancer subtypes and cell lines using deep learning.

Life science alliance Dec 2, 2019
Colorectal cancer (CRC) is a common cancer with a high mortality rate and a rising incidence rate in the developed world. Molecular profiling techniques have been used to better understand the variability between tumors and disease models such as cel...
Humans Machine Learning Colorectal Neoplasms Sequence Analysis, DNA DNA Copy Number Variations Neoplasm Proteins Mutation Models, Biological Biomarkers, Tumor Gene Expression Profiling Deep Learning Cell Line, Tumor
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Ranking of non-coding pathogenic variants and putative essential regions of the human genome.

Nature communications Nov 20, 2019
A gene is considered essential if loss of function results in loss of viability, fitness or in disease. This concept is well established for coding genes; however, non-coding regions are thought less likely to be determinants of critical functions. H...
Nucleic Acid Conformation Mutation Genes, Reporter Introns Supervised Machine Learning Chromatin INDEL Mutation Genetic Variation Enhancer Elements, Genetic Genome, Human Humans Computer Simulation DNA Gene Expression
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Machine learning-based quantitative texture analysis of conventional MRI combined with ADC maps for assessment of IDH1 mutation in high-grade gliomas.

Japanese journal of radiology Nov 18, 2019
PURPOSE: To assess the performance of texture analysis of conventional magnetic resonance imaging (MRI) and apparent diffusion coefficient (ADC) maps in predicting IDH1 status in high-grade gliomas (HGG).
Adult Brain Neoplasms Male Middle Aged Brain Retrospective Studies Female Reproducibility of Results Image Interpretation, Computer-Assisted Isocitrate Dehydrogenase Humans Machine Learning Glioma Magnetic Resonance Imaging Predictive Value of Tests Mutation
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CPEM: Accurate cancer type classification based on somatic alterations using an ensemble of a random forest and a deep neural network.

Scientific reports Nov 15, 2019
With recent advances in DNA sequencing technologies, fast acquisition of large-scale genomic data has become commonplace. For cancer studies, in particular, there is an increasing need for the classification of cancer type based on somatic alteration...
Genetic Variation Linear Models Genomics Mutation Genetic Testing Workflow Algorithms Databases, Factual Reproducibility of Results Neoplasms Humans Neural Networks, Computer Machine Learning
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