AIMC Topic: Chromatin
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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...
Chromatin Assembly and Disassembly
Human Embryonic Stem Cells
Binding Sites
Primary Cell Culture
Chromatin
Humans
Machine Learning
Algorithms
DNA
CD4-Positive T-Lymphocytes
Hepatocytes
K562 Cells
Histones
Hep G2 Cells
Gene Expression Regulation
Cell Line, Tumor
Cell Line
Organ Specificity
Protein Binding
Principal Component Analysis
Transcription Factors
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 ...
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...
deepTAD: an approach for identifying topologically associated domains based on convolutional neural network and transformer model.
Briefings in bioinformatics
Mar 4, 2025
MOTIVATION: Topologically associated domains (TADs) play a key role in the 3D organization and function of genomes, and accurate detection of TADs is essential for revealing the relationship between genomic structure and function. Most current method...
Predicting gene expression from histone marks using chromatin deep learning models depends on histone mark function, regulatory distance and cellular states.
Nucleic acids research
Feb 8, 2025
To understand the complex relationship between histone mark activity and gene expression, recent advances have used in silico predictions based on large-scale machine learning models. However, these approaches have omitted key contributing factors li...
Machine and Deep Learning Methods for Predicting 3D Genome Organization.
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2025
Three-dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, topologically associating domains (TADs), and A/B compartments, play critical roles in a wide range of cellular processes by regulating gene expressi...
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