AIMC Topic: Eukaryotic Cells

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scEnhancer: a single-cell enhancer resource with annotation across hundreds of tissue/cell types in three species.

Nucleic acids research Jan 7, 2022
Previous studies on enhancers and their target genes were largely based on bulk samples that represent 'average' regulatory activities from a large population of millions of cells, masking the heterogeneity and important effects from the sub-populati...
Gene Regulatory Networks Mice Animals Single-Cell Analysis Internet Genetic Heterogeneity Databases, Genetic Unsupervised Machine Learning Humans Software Molecular Sequence Annotation Consensus Sequence Cell Lineage Eukaryotic Cells Enhancer Elements, Genetic Chromatin Gene Expression Regulation Promoter Regions, Genetic Organ Specificity Drosophila melanogaster
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Tiara: deep learning-based classification system for eukaryotic sequences.

Bioinformatics (Oxford, England) Jan 3, 2022
MOTIVATION: With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step toward a better understanding ...
Software Deep Learning Metagenome Metagenomics Eukaryotic Cells Eukaryota
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Epitome: predicting epigenetic events in novel cell types with multi-cell deep ensemble learning.

Nucleic acids research Nov 8, 2021
The accumulation of large epigenomics data consortiums provides us with the opportunity to extrapolate existing knowledge to new cell types and conditions. We propose Epitome, a deep neural network that learns similarities of chromatin accessibility ...
Chromatin Immunoprecipitation Eukaryotic Cells Atlases as Topic Chromatin Cell Lineage Humans Cell Communication Epigenesis, Genetic Neural Networks, Computer Genome, Human Machine Learning Software Transcription Factors Histones Protein Binding Binding Sites
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SubLocEP: a novel ensemble predictor of subcellular localization of eukaryotic mRNA based on machine learning.

Briefings in bioinformatics Sep 2, 2021
MOTIVATION: mRNA location corresponds to the location of protein translation and contributes to precise spatial and temporal management of the protein function. However, current assignment of subcellular localization of eukaryotic mRNA reveals import...
Humans Eukaryotic Cells Support Vector Machine Databases, Genetic Proteins RNA, Messenger RNA, Long Noncoding Eukaryota Models, Genetic
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DeepLoc: prediction of protein subcellular localization using deep learning.

Bioinformatics (Oxford, England) Nov 1, 2017
MOTIVATION: The prediction of eukaryotic protein subcellular localization is a well-studied topic in bioinformatics due to its relevance in proteomics research. Many machine learning methods have been successfully applied in this task, but in most of...
Eukaryotic Cells Eukaryota Sequence Analysis, Protein Computational Biology Models, Biological Machine Learning Protein Transport Neural Networks, Computer Software Molecular Sequence Annotation
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