AIMC Topic: Genes, Essential

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Essential genes identification model based on sequence feature map and graph convolutional neural network.

BMC genomics Jan 10, 2024
BACKGROUND: Essential genes encode functions that play a vital role in the life activities of organisms, encompassing growth, development, immune system functioning, and cell structure maintenance. Conventional experimental techniques for identifying...
Genomics Genes, Essential Entropy Neural Networks, Computer Algorithms
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Untangling the Context-Specificity of Essential Genes by Means of Machine Learning: A Constructive Experience.

Biomolecules Dec 22, 2023
Gene essentiality is a genetic concept crucial for a comprehensive understanding of life and evolution. In the last decade, many essential genes (EGs) have been determined using different experimental and computational approaches, and this informatio...
Machine Learning Genes, Essential
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XA4C: eXplainable representation learning via Autoencoders revealing Critical genes.

PLoS computational biology Oct 2, 2023
Machine Learning models have been frequently used in transcriptome analyses. Particularly, Representation Learning (RL), e.g., autoencoders, are effective in learning critical representations in noisy data. However, learned representations, e.g., the...
Gene Expression Profiling Genes, Essential Databases, Factual Neoplasms Humans Artificial Intelligence
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An unsupervised deep learning framework for predicting human essential genes from population and functional genomic data.

BMC bioinformatics Sep 18, 2023
BACKGROUND: The ability to accurately predict essential genes intolerant to loss-of-function (LOF) mutations can dramatically improve the identification of disease-associated genes. Recently, there have been numerous computational methods developed t...
Humans Cell Line Genes, Essential Metagenomics Mice Genomics Animals Deep Learning
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EPGAT: Gene Essentiality Prediction With Graph Attention Networks.

IEEE/ACM transactions on computational biology and bioinformatics Jun 3, 2022
Identifying essential genes and proteins is a critical step towards a better understanding of human biology and pathology. Computational approaches helped to mitigate experimental constraints by exploring machine learning (ML) methods and the correla...
Neural Networks, Computer Machine Learning Humans Proteins Genes, Essential Algorithms Protein Interaction Maps
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Prediction of Essential Genes in Comparison States Using Machine Learning.

IEEE/ACM transactions on computational biology and bioinformatics Oct 7, 2021
Identifying essential genes in comparison states (EGS) is vital to understanding cell differentiation, performing drug discovery, and identifying disease causes. Here, we present a machine learning method termed Prediction of Essential Genes in Compa...
Genetic Markers Transcriptome Gene Regulatory Networks Computational Biology Genes, Essential Machine Learning
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Cross-Predicting Essential Genes between Two Model Eukaryotic Species Using Machine Learning.

International journal of molecular sciences May 11, 2021
Experimental studies of and have contributed substantially to our understanding of molecular and cellular processes in metazoans at large. Since the publication of their genomes, functional genomic investigations have identified genes that are esse...
Caenorhabditis elegans Proteins Gene Ontology Caenorhabditis elegans Genomics Machine Learning Evolution, Molecular Animals Genes, Essential Drosophila Proteins Drosophila melanogaster
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Essential gene prediction using limited gene essentiality information-An integrative semi-supervised machine learning strategy.

PloS one Nov 30, 2020
Essential gene prediction helps to find minimal genes indispensable for the survival of any organism. Machine learning (ML) algorithms have been useful for the prediction of gene essentiality. However, currently available ML pipelines perform poorly ...
Genetic Diseases, Inborn Algorithms Humans Metabolic Networks and Pathways Cluster Analysis Machine Learning Support Vector Machine Area Under Curve Genes, Essential
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A Computational Framework Based on Ensemble Deep Neural Networks for Essential Genes Identification.

International journal of molecular sciences Nov 28, 2020
Essential genes contain key information of genomes that could be the key to a comprehensive understanding of life and evolution. Because of their importance, studies of essential genes have been considered a crucial problem in computational biology. ...
Algorithms Reproducibility of Results Sequence Analysis, DNA Genes, Essential Deep Learning Neural Networks, Computer Area Under Curve Species Specificity
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DeeplyEssential: a deep neural network for predicting essential genes in microbes.

BMC bioinformatics Sep 30, 2020
BACKGROUND: Essential genes are those genes that are critical for the survival of an organism. The prediction of essential genes in bacteria can provide targets for the design of novel antibiotic compounds or antimicrobial strategies.
Codon Neural Networks, Computer Gram-Negative Bacteria Gram-Positive Bacteria Cluster Analysis ROC Curve Genes, Essential Bacteria Area Under Curve
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