AIMC Topic: Chromatin
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De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture.
Proceedings of the National Academy of Sciences of the United States of America
Oct 31, 2017
Inside the cell nucleus, genomes fold into organized structures that are characteristic of cell type. Here, we show that this chromatin architecture can be predicted de novo using epigenetic data derived from chromatin immunoprecipitation-sequencing ...
EP-DNN: A Deep Neural Network-Based Global Enhancer Prediction Algorithm.
Scientific reports
Dec 8, 2016
We present EP-DNN, a protocol for predicting enhancers based on chromatin features, in different cell types. Specifically, we use a deep neural network (DNN)-based architecture to extract enhancer signatures in a representative human embryonic stem c...
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...
Algorithms
Histones
Cell Line, Tumor
Binding Sites
Humans
Protein Binding
Primary Cell Culture
Machine Learning
Cell Line
Transcription Factors
Human Embryonic Stem Cells
Gene Expression Regulation
Chromatin
Principal Component Analysis
Hep G2 Cells
DNA
Organ Specificity
CD4-Positive T-Lymphocytes
K562 Cells
Chromatin Assembly and Disassembly
Hepatocytes
A knowledgebase of the human Alu repetitive elements.
Journal of biomedical informatics
Jan 28, 2016
Alu elements are the most abundant retrotransposons in the human genome with more than one million copies. Alu repeats have been reported to participate in multiple processes related with genome regulation and compartmentalization. Moreover, they hav...
Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features.
BMC bioinformatics
Jan 11, 2016
BACKGROUND: Understanding the mechanisms by which transcription factors (TF) are recruited to their physiological target sites is crucial for understanding gene regulation. DNA sequence intrinsic features such as predicted binding affinity are often ...
CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers.
Nucleic acids research
Jul 7, 2025
We present CGeNArateWeb, a new web tool for the three-dimensional simulation of naked DNA and protein-bound chromatin fibers. The server allows the user to obtain a dynamic representation of long segments of linear, circular, or protein-DNA segments ...
Temporally discordant chromatin accessibility and DNA demethylation define short- and long-term enhancer regulation during cell fate specification.
Cell reports
May 27, 2025
Chromatin and DNA modifications mediate the transcriptional activity of lineage-specifying enhancers, but recent work challenges the dogma that joint chromatin accessibility and DNA demethylation are prerequisites for transcription. To understand thi...
CREATE: cell-type-specific cis-regulatory element identification via discrete embedding.
Nature communications
May 17, 2025
Cis-regulatory elements (CREs), including enhancers, silencers, promoters and insulators, play pivotal roles in orchestrating gene regulatory mechanisms that drive complex biological traits. However, current approaches for CRE identification are pred...
Quantitative spatial analysis of chromatin biomolecular condensates using cryoelectron tomography.
Proceedings of the National Academy of Sciences of the United States of America
May 13, 2025
Phase separation is an important mechanism to generate certain biomolecular condensates and organize the cell interior. Condensate formation and function remain incompletely understood due to difficulties in visualizing the condensate interior at hig...
Unraveling the three-dimensional genome structure using machine learning.
BMB reports
May 1, 2025
The study of chromatin interactions has advanced considerably with technologies such as high-throughput chromosome conformation capture (Hi-C) sequencing, providing a genome-wide view of physical interactions within the nucleus. These techniques have...
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