AIMC Topic: Mutagenesis

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Selene: a PyTorch-based deep learning library for sequence data.

Nature methods Mar 28, 2019
To enable the application of deep learning in biology, we present Selene (https://selene.flatironinstitute.org/), a PyTorch-based deep learning library for fast and easy development, training, and application of deep learning model architectures for ...
Software Algorithms Deep Learning Humans Neural Networks, Computer Models, Statistical Area Under Curve Mutation Genomics Computational Biology Sequence Analysis, DNA Normal Distribution Alzheimer Disease Gene Library Programming Languages Mutagenesis
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Identifying mouse developmental essential genes using machine learning.

Disease models & mechanisms Dec 13, 2018
The genes that are required for organismal survival are annotated as 'essential genes'. Identifying all the essential genes of an animal species can reveal critical functions that are needed during the development of the organism. To inform studies o...
Genes, Developmental Mutagenesis Molecular Sequence Annotation Gene Ontology Conserved Sequence Point Mutation Chromosomes, Mammalian Mice Databases, Genetic Genes, Essential Reproducibility of Results Animals Protein Interaction Maps Humans Algorithms Phenotype Machine Learning Software
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Genotoxicity evaluation of titanium dioxide nanoparticles using the mouse lymphoma assay and the Ames test.

Mutation research. Genetic toxicology and environmental mutagenesis Dec 1, 2018
Titanium dioxide nanoparticles (TiO-NPs) are widely used in the cosmetics, health, and food industries, but their safety and genotoxicity remain a matter of debate. We investigated whether TiO-NPs could induce gene mutations in mouse lymphoma L5178Y ...
Titanium Mutagenesis Mutagenicity Tests Salmonella typhimurium Mutation Rate Metal Nanoparticles DNA Damage Animals Cell Line, Tumor Mice
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Machine-Learning-Guided Mutagenesis for Directed Evolution of Fluorescent Proteins.

ACS synthetic biology Aug 20, 2018
Molecular evolution based on mutagenesis is widely used in protein engineering. However, optimal proteins are often difficult to obtain due to a large sequence space. Here, we propose a novel approach that combines molecular evolution with machine le...
Directed Molecular Evolution Escherichia coli Luminescent Proteins Mutagenesis Machine Learning Green Fluorescent Proteins
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Enhancing the Biological Relevance of Machine Learning Classifiers for Reverse Vaccinology.

International journal of molecular sciences Feb 1, 2017
Reverse vaccinology (RV) is a bioinformatics approach that can predict antigens with protective potential from the protein coding genomes of bacterial pathogens for subunit vaccine design. RV has become firmly established following the development of...
Area Under Curve Bacterial Proteins Epitopes Mutagenesis Antigens, Bacterial Epitope Mapping Bacterial Vaccines ROC Curve Vaccines, Subunit Computational Biology Humans Support Vector Machine Machine Learning
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Extending (Q)SARs to incorporate proprietary knowledge for regulatory purposes: A case study using aromatic amine mutagenicity.

Regulatory toxicology and pharmacology : RTP Feb 13, 2016
Statistical-based and expert rule-based models built using public domain mutagenicity knowledge and data are routinely used for computational (Q)SAR assessments of pharmaceutical impurities in line with the approach recommended in the ICH M7 guidelin...
Amines Models, Molecular Molecular Structure Knowledge Bases Computer Simulation Humans Quantitative Structure-Activity Relationship Data Mining Animals Databases, Factual Mutagenesis Risk Assessment Pattern Recognition, Automated Mutagenicity Tests Mutagens
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Identification of Clonal Hematopoiesis Driver Mutations through In Silico Saturation Mutagenesis.

Cancer discovery Sep 4, 2024
Clonal hematopoiesis (CH) is a phenomenon of clonal expansion of hematopoietic stem cells driven by somatic mutations affecting certain genes. Recently, CH has been linked to the development of hematologic malignancies, cardiovascular diseases, and o...
Hematologic Neoplasms Mutation Mutagenesis Clonal Hematopoiesis Humans Machine Learning Computer Simulation
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SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models.

Bioinformatics (Oxford, England) Jun 3, 2024
SUMMARY: The increasing development of sequence-based machine learning models has raised the demand for manipulating sequences for this application. However, existing approaches to edit and evaluate genome sequences using models have limitations, suc...
Computer Simulation Computational Biology Mutagenesis Humans Machine Learning Software
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Optimizing machine-learning models for mutagenicity prediction through better feature selection.

Mutagenesis Oct 26, 2022
Assessing a compound's mutagenicity using machine learning is an important activity in the drug discovery and development process. Traditional methods of mutagenicity detection, such as Ames test, are expensive and time and labor intensive. In this c...
Neural Networks, Computer Machine Learning Mutagens Mutagenesis
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fastISM: performant in silico saturation mutagenesis for convolutional neural networks.

Bioinformatics (Oxford, England) Apr 28, 2022
MOTIVATION: Deep-learning models, such as convolutional neural networks, are able to accurately map biological sequences to associated functional readouts and properties by learning predictive de novo representations. In silico saturation mutagenesis...
Mutation Neural Networks, Computer Mutagenesis
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