AIMC Topic: Chromatin

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A Comparative Study of Supervised Machine Learning Algorithms for the Prediction of Long-Range Chromatin Interactions.

Genes Aug 24, 2020
The role of three-dimensional genome organization as a critical regulator of gene expression has become increasingly clear over the last decade. Most of our understanding of this association comes from the study of long range chromatin interaction ma...
Humans Genome, Human K562 Cells Gene Expression Regulation, Leukemic Chromatin Algorithms Computer Simulation Support Vector Machine Supervised Machine Learning
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Cell type prioritization in single-cell data.

Nature biotechnology Jul 20, 2020
We present Augur, a method to prioritize the cell types most responsive to biological perturbations in single-cell data. Augur employs a machine-learning framework to quantify the separability of perturbed and unperturbed cells within a high-dimensio...
Machine Learning Animals Databases, Genetic Walking Nerve Net Mice Gene Expression Profiling Chromatin Computational Biology Transcriptome Sequence Analysis, RNA Single-Cell Analysis Rats
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A supervised learning framework for chromatin loop detection in genome-wide contact maps.

Nature communications Jul 9, 2020
Accurately predicting chromatin loops from genome-wide interaction matrices such as Hi-C data is critical to deepening our understanding of proper gene regulation. Current approaches are mainly focused on searching for statistically enriched dots on ...
K562 Cells Genome Chromatin Supervised Machine Learning Species Specificity Organ Specificity Humans Databases, Genetic Sequence Analysis, DNA
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Discriminant analysis and interpretation of nuclear chromatin distribution and coarseness using gray-level co-occurrence matrix features for lobular endocervical glandular hyperplasia.

Diagnostic cytopathology May 6, 2020
BACKGROUND: Lobular endocervical glandular hyperplasia (LEGH) is a disease considered to be the origin of tumorigenesis of minimal deviation adenocarcinoma, which has characteristic expression in the gastric pyloric mucosa. It is difficult to diagnos...
Uterine Cervical Neoplasms Middle Aged Papanicolaou Test Adenocarcinoma Female Aged Adult Hyperplasia Chromatin Support Vector Machine Discriminant Analysis Image Interpretation, Computer-Assisted Humans
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DDBJ Data Analysis Challenge: a machine learning competition to predict Arabidopsis chromatin feature annotations from DNA sequences.

Genes & genetic systems Mar 26, 2020
Recently, the prospect of applying machine learning tools for automating the process of annotation analysis of large-scale sequences from next-generation sequencers has raised the interest of researchers. However, finding research collaborators with ...
Computational Biology Japan High-Throughput Nucleotide Sequencing Molecular Sequence Annotation Crowdsourcing Databases, Nucleic Acid Genome, Plant Machine Learning Data Analysis Arabidopsis Chromatin
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DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure.

Genome biology Mar 26, 2020
Non-coding variants have been shown to be related to disease by alteration of 3D genome structures. We propose a deep learning method, DeepMILO, to predict the effects of variants on CTCF/cohesin-mediated insulator loops. Application of DeepMILO on v...
Whole Genome Sequencing Cell Cycle Proteins Chromatin CCCTC-Binding Factor Chromosomal Proteins, Non-Histone Insulator Elements Cohesins Neoplasms Deep Learning Cell Line, Tumor Humans Mutation
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Graph embedding and unsupervised learning predict genomic sub-compartments from HiC chromatin interaction data.

Nature communications Mar 3, 2020
Chromatin interaction studies can reveal how the genome is organized into spatially confined sub-compartments in the nucleus. However, accurately identifying sub-compartments from chromatin interaction data remains a challenge in computational biolog...
Gene Expression Markov Chains Epigenome K562 Cells Computer Graphics Chromatin Reproducibility of Results Genomics Cluster Analysis Unsupervised Machine Learning Neural Networks, Computer Data Analysis Algorithms Humans
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Deep learning models predict regulatory variants in pancreatic islets and refine type 2 diabetes association signals.

eLife Jan 27, 2020
Genome-wide association analyses have uncovered multiple genomic regions associated with T2D, but identification of the causal variants at these remains a challenge. There is growing interest in the potential of deep learning models - which predict e...
Chromatin Islets of Langerhans Epigenomics Signal Transduction Models, Theoretical Genome-Wide Association Study Diabetes Mellitus, Type 2 Genetic Predisposition to Disease Polymorphism, Single Nucleotide Humans Deep Learning
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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...
Protein Binding Area Under Curve Histones Chromatin Neural Networks, Computer Algorithms ROC Curve Histone Code
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Ranking of non-coding pathogenic variants and putative essential regions of the human genome.

Nature communications Nov 20, 2019
A gene is considered essential if loss of function results in loss of viability, fitness or in disease. This concept is well established for coding genes; however, non-coding regions are thought less likely to be determinants of critical functions. H...
Genome, Human Gene Expression Nucleic Acid Conformation Mutation INDEL Mutation Supervised Machine Learning Enhancer Elements, Genetic Humans Introns Genetic Variation Genes, Reporter Computer Simulation Chromatin DNA
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