AIMC Topic: Genome

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Chromatin interaction neural network (ChINN): a machine learning-based method for predicting chromatin interactions from DNA sequences.

Genome biology Aug 16, 2021
Chromatin interactions play important roles in regulating gene expression. However, the availability of genome-wide chromatin interaction data is limited. We develop a computational method, chromatin interaction neural network (ChINN), to predict chr...
Base Sequence Genome Leukemia Humans Neural Networks, Computer Chromatin Machine Learning Computational Biology
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A deep learning approach to automate whole-genome prediction of diverse epigenomic modifications in plants.

The New phytologist Aug 12, 2021
Epigenetic modifications function in gene transcription, RNA metabolism, and other biological processes. However, multiple factors currently limit the scientific utility of epigenomic datasets generated for plants. Here, using deep-learning approache...
DNA Methylation Oryza Genome Deep Learning Epigenesis, Genetic Epigenomics
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DeepG4: A deep learning approach to predict cell-type specific active G-quadruplex regions.

PLoS computational biology Aug 12, 2021
DNA is a complex molecule carrying the instructions an organism needs to develop, live and reproduce. In 1953, Watson and Crick discovered that DNA is composed of two chains forming a double-helix. Later on, other structures of DNA were discovered an...
G-Quadruplexes Genome Chromatin Immunoprecipitation Humans Algorithms Neural Networks, Computer Neoplasms Deep Learning
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Machine learning-based identification and characterization of 15 novel pathogenic SUOX missense mutations.

Molecular genetics and metabolism Aug 8, 2021
Isolated sulfite oxidase deficiency (ISOD) is a rare hereditary metabolic disease caused by absence of functional sulfite oxidase (SO) due to mutations of the SUOX gene. SO oxidizes toxic sulfite and sulfite accumulation is associated with neurologic...
Humans Machine Learning Genetic Variation Gene Frequency Mutation, Missense Brain Infant, Newborn Databases, Genetic Genome Oxidoreductases Acting on Sulfur Group Donors
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Application of a Poisson deep neural network model for the prediction of count data in genome-based prediction.

The plant genome Jul 29, 2021
Genomic selection (GS) is revolutionizing conventional ways of developing new plants and animals. However, because it is a predictive methodology, GS strongly depends on statistical and machine learning to perform these predictions. For continuous ou...
Neural Networks, Computer Machine Learning Genomics Bayes Theorem Genome
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Deep-learning power and perspectives for genomic selection.

The plant genome Jul 26, 2021
Deep learning (DL) is revolutionizing the development of artificial intelligence systems. For example, before 2015, humans were better than artificial machines at classifying images and solving many problems of computer vision (related to object loca...
Genome Machine Learning Deep Learning Genomics Artificial Intelligence
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Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen.

Nature communications Jun 10, 2021
Species harbor extensive structural variation underpinning recent adaptive evolution. However, the causality between genomic features and the induction of new rearrangements is poorly established. Here, we analyze a global set of telomere-to-telomere...
Genomics Polymorphism, Single Nucleotide Models, Genetic Evolution, Molecular Genetic Variation Polymorphism, Genetic Computer Simulation Chromosomes Eukaryota Machine Learning Phylogeny Arabidopsis Crossing Over, Genetic Genome Genome-Wide Association Study Ascomycota Retroelements Genes, Duplicate INDEL Mutation Pedigree Sequence Inversion Meiosis
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Machine learning for profile prediction in genomics.

Current opinion in chemical biology Jun 6, 2021
A recent deluge of publicly available multi-omics data has fueled the development of machine learning methods aimed at investigating important questions in genomics. Although the motivations for these methods vary, a task that is commonly adopted is ...
Genomics Genome Chromatin Machine Learning Protein Binding
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i4mC-EL: Identifying DNA N4-Methylcytosine Sites in the Mouse Genome Using Ensemble Learning.

BioMed research international May 29, 2021
As one of important epigenetic modifications, DNA N4-methylcytosine (4mC) plays a crucial role in controlling gene replication, expression, cell cycle, DNA replication, and differentiation. The accurate identification of 4mC sites is necessary to und...
Base Sequence Mice Genome Computational Biology Genetic Techniques Cytosine Epigenesis, Genetic Bayes Theorem Reproducibility of Results DNA Methylation Internet Machine Learning Animals Area Under Curve Data Mining Algorithms ROC Curve DNA
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HARVESTMAN: a framework for hierarchical feature learning and selection from whole genome sequencing data.

BMC bioinformatics Apr 1, 2021
BACKGROUND: Supervised learning from high-throughput sequencing data presents many challenges. For one, the curse of dimensionality often leads to overfitting as well as issues with scalability. This can bring about inaccurate models or those that re...
Deep Learning Humans Genome Genomics Breast Neoplasms Whole Genome Sequencing
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