AIMC Topic: Chromatin Assembly and Disassembly

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DeepCAGE: Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility.

Genomics, proteomics & bioinformatics Mar 12, 2022
Although computational approaches have been complementing high-throughput biological experiments for the identification of functional regions in the human genome, it remains a great challenge to systematically decipher interactions between transcript...
Genome, Human Binding Sites Regulatory Sequences, Nucleic Acid Chromatin Chromatin Assembly and Disassembly Humans Deep Learning Protein Binding Transcription Factors
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Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities.

Genome biology May 3, 2021
A complete understanding of biological processes requires synthesizing information across heterogeneous modalities, such as age, disease status, or gene expression. Technological advances in single-cell profiling have enabled researchers to assay mul...
Computational Biology Gene Expression Regulation Organ Specificity Chromatin Gene Expression Profiling Transcriptome Single-Cell Analysis Chromatin Assembly and Disassembly Machine Learning
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TADKB: Family classification and a knowledge base of topologically associating domains.

BMC genomics Mar 14, 2019
BACKGROUND: Topologically associating domains (TADs) are considered the structural and functional units of the genome. However, there is a lack of an integrated resource for TADs in the literature where researchers can obtain family classifications a...
Chromosomes, Mammalian Algorithms Gene Expression Regulation Animals Genome Mice Chromatin Assembly and Disassembly Knowledge Bases Genomics Multigene Family RNA, Long Noncoding Humans
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Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus.

Nature communications Feb 21, 2018
Although Hi-C technology is one of the most popular tools for studying 3D genome organization, due to sequencing cost, the resolution of most Hi-C datasets are coarse and cannot be used to link distal regulatory elements to their target genes. Here w...
High-Throughput Nucleotide Sequencing Chromosomes Chromatin Assembly and Disassembly Humans Deep Learning
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Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.

Nucleic acids research Nov 29, 2016
The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF b...
Organ Specificity K562 Cells Histones Chromatin Chromatin Assembly and Disassembly Binding Sites Primary Cell Culture DNA CD4-Positive T-Lymphocytes Hepatocytes Hep G2 Cells Gene Expression Regulation Cell Line Human Embryonic Stem Cells Principal Component Analysis Humans Algorithms Protein Binding Machine Learning Transcription Factors Cell Line, Tumor
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Genes with high penetrance for syndromic and non-syndromic autism typically function within the nucleus and regulate gene expression.

Molecular autism Mar 15, 2016
BACKGROUND: Intellectual disability (ID), autism, and epilepsy share frequent yet variable comorbidities with one another. In order to better understand potential genetic divergence underlying this variable risk, we studied genes responsible for mono...
Neurogenesis Nuclear Proteins Cell Nucleus Protein Interaction Maps Autistic Disorder Penetrance Gene Expression Regulation Databases, Genetic Epilepsy Nerve Tissue Proteins Syndrome Humans Autism Spectrum Disorder Comorbidity Genetic Association Studies Epigenomics Body Patterning Chromatin Assembly and Disassembly Intellectual Disability Risk Gene Ontology
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Integrative approaches for predicting protein network perturbations through machine learning and structural characterization.

Journal of proteomics May 30, 2025
Chromatin remodeling complexes, such as the Saccharomyces cerevisiae INO80 complex, exemplify how dynamic protein interaction networks govern cellular function through a balance of conserved structural modules and context-dependent functional partner...
Protein Interaction Maps Saccharomyces cerevisiae Saccharomyces cerevisiae Proteins Chromatin Assembly and Disassembly Humans Machine Learning
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Deep learning with a small dataset predicts chromatin remodelling contribution to winter dormancy of apple axillary buds.

Tree physiology Jul 2, 2024
Epigenetic changes serve as a cellular memory for cumulative cold recognition in both herbaceous and tree species, including bud dormancy. However, most studies have discussed predicted chromatin structure with respect to histone marks. In the presen...
Cold Temperature Malus Gene Expression Regulation, Plant Chromatin Assembly and Disassembly Deep Learning Bayes Theorem Epigenesis, Genetic Seasons Flowers Plant Dormancy
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Computational methods for the prediction of chromatin interaction and organization using sequence and epigenomic profiles.

Briefings in bioinformatics Sep 2, 2021
The exploration of three-dimensional chromatin interaction and organization provides insight into mechanisms underlying gene regulation, cell differentiation and disease development. Advances in chromosome conformation capture technologies, such as h...
Sequence Analysis, DNA Unsupervised Machine Learning Supervised Machine Learning Base Sequence Humans Epigenesis, Genetic Genome, Human Chromatin Chromatin Assembly and Disassembly
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Functional interpretation of genetic variants using deep learning predicts impact on chromatin accessibility and histone modification.

Nucleic acids research Nov 18, 2019
Identifying functional variants underlying disease risk and adoption of personalized medicine are currently limited by the challenge of interpreting the functional consequences of genetic variants. Predicting the functional effects of disease-associa...
Genome-Wide Association Study Epigenesis, Genetic Sequence Analysis, DNA Histone Code Polymorphism, Genetic Chromatin Assembly and Disassembly Humans Deep Learning
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