AIMC Topic: Histone Code

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An explainable artificial intelligence approach for decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila.

Genome biology Nov 8, 2021
BACKGROUND: Enhancers are non-coding regions of the genome that control the activity of target genes. Recent efforts to identify active enhancers experimentally and in silico have proven effective. While these tools can predict the locations of enhan...
Animals Epigenesis, Genetic High-Throughput Nucleotide Sequencing Artificial Intelligence Machine Learning Molecular Sequence Annotation Enhancer Elements, Genetic Histone Code Drosophila Proteins Promoter Regions, Genetic Drosophila melanogaster
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A semi-supervised deep learning approach for predicting the functional effects of genomic non-coding variations.

BMC bioinformatics Jun 2, 2021
BACKGROUND: Understanding the functional effects of non-coding variants is important as they are often associated with gene-expression alteration and disease development. Over the past few years, many computational tools have been developed to predic...
Histone Code Humans Deep Learning Algorithms Genomics Supervised Machine Learning
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An Integrative Framework for Combining Sequence and Epigenomic Data to Predict Transcription Factor Binding Sites Using Deep Learning.

IEEE/ACM transactions on computational biology and bioinformatics Feb 3, 2021
Knowing the transcription factor binding sites (TFBSs) is essential for modeling the underlying binding mechanisms and follow-up cellular functions. Convolutional neural networks (CNNs) have outperformed methods in predicting TFBSs from the primary D...
Deep Learning Transcription Factors Chromatin Immunoprecipitation Sequencing Protein Binding Binding Sites Computational Biology Histone Code Epigenesis, Genetic
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Characterizing chromatin folding coordinate and landscape with deep learning.

PLoS computational biology Sep 28, 2020
Genome organization is critical for setting up the spatial environment of gene transcription, and substantial progress has been made towards its high-resolution characterization. The underlying molecular mechanism for its establishment is much less u...
Histone Code Deep Learning Models, Biological Protein Conformation Thermodynamics Genome Chromatin Computer Simulation
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Computational methods and next-generation sequencing approaches to analyze epigenetics data: Profiling of methods and applications.

Methods (San Diego, Calif.) Sep 14, 2020
Epigenetics is mainly comprised of features that regulate genomic interactions thereby playing a crucial role in a vast array of biological processes. Epigenetic mechanisms such as DNA methylation and histone modifications influence gene expression b...
Data Analysis Animals Mice Humans Machine Learning High-Throughput Nucleotide Sequencing Histone Code Epigenesis, Genetic Epigenomics DNA Methylation
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Machine learning uncovers cell identity regulator by histone code.

Nature communications Jun 1, 2020
Conversion between cell types, e.g., by induced expression of master transcription factors, holds great promise for cellular therapy. Our ability to manipulate cell identity is constrained by incomplete information on cell identity genes (CIGs) and t...
Histone Code Chromatin Immunoprecipitation Sequencing Cells Pluripotent Stem Cells Epigenesis, Genetic Phenotype Transcription Factors RNA-Seq Databases, Genetic Humans Gene Regulatory Networks Human Umbilical Vein Endothelial Cells Machine Learning Regenerative Medicine Algorithms Gene Expression Regulation
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A computational method to predict topologically associating domain boundaries combining histone Marks and sequence information.

BMC genomics Dec 27, 2019
BACKGROUND: The three-dimensional (3D) structure of chromatins plays significant roles during cell differentiation and development. Hi-C and other 3C-based technologies allow us to look deep into the chromatin architectures. Many studies have suggest...
ROC Curve Protein Binding Area Under Curve Histones Neural Networks, Computer Chromatin Algorithms Histone Code
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Deciphering epigenomic code for cell differentiation using deep learning.

BMC genomics Sep 12, 2019
BACKGROUND: Although DNA sequence plays a crucial role in establishing the unique epigenome of a cell type, little is known about the sequence determinants that lead to the unique epigenomes of different cell types produced during cell differentiatio...
Epigenomics Cell Differentiation CD4-Positive T-Lymphocytes Histone Code Humans Nucleotide Motifs Deep Learning Cell Lineage Conserved Sequence
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Visualizing complex feature interactions and feature sharing in genomic deep neural networks.

BMC bioinformatics Jul 19, 2019
BACKGROUND: Visualization tools for deep learning models typically focus on discovering key input features without considering how such low level features are combined in intermediate layers to make decisions. Moreover, many of these methods examine ...
Databases, Genetic Base Sequence Histones Neural Networks, Computer Deep Learning Algorithms Histone Code Genomics Transcription Factors
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Predicting DNA Methylation States with Hybrid Information Based Deep-Learning Model.

IEEE/ACM transactions on computational biology and bioinformatics Apr 3, 2019
DNA methylation plays an important role in the regulation of some biological processes. Up to now, with the development of machine learning models, there are several sequence-based deep learning models designed to predict DNA methylation states, whic...
DNA Methylation Cell Line, Tumor DNA Humans Histone Code Computational Biology High-Throughput Nucleotide Sequencing Deep Learning Sequence Analysis, DNA
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