AIMC Topic: Histones
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Label-free detection of histone based on cationic conjugated polymer-mediated fluorescence resonance energy transfer.
Talanta
Dec 5, 2017
A simple and homogeneous histone assay is developed based on histone-induced DNA compressing coupled with cationic conjugated polymer (CCP)-mediated fluorescence resonance energy transfer (FRET). In this strategy, the CCP serves as the FRET donor and...
Identify and analysis crotonylation sites in histone by using support vector machines.
Artificial intelligence in medicine
Mar 7, 2017
OBJECTIVE: Lysine crotonylation (Kcr) is a newly discovered histone posttranslational modification, which is specifically enriched at active gene promoters and potential enhancers in mammalian cell genomes. Although lysine crotonylation sites can be ...
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...
Protein Binding
Transcription Factors
Hep G2 Cells
Cell Line
Humans
Machine Learning
Algorithms
Cell Line, Tumor
Histones
Binding Sites
Primary Cell Culture
Chromatin
Chromatin Assembly and Disassembly
Human Embryonic Stem Cells
Hepatocytes
Principal Component Analysis
Gene Expression Regulation
DNA
Organ Specificity
CD4-Positive T-Lymphocytes
K562 Cells
Opening up the blackbox: an interpretable deep neural network-based classifier for cell-type specific enhancer predictions.
BMC systems biology
Aug 1, 2016
BACKGROUND: Gene expression is mediated by specialized cis-regulatory modules (CRMs), the most prominent of which are called enhancers. Early experiments indicated that enhancers located far from the gene promoters are often responsible for mediating...
eRFSVM: a hybrid classifier to predict enhancers-integrating random forests with support vector machines.
Hereditas
Jun 30, 2016
BACKGROUND: Enhancers are tissue specific distal regulation elements, playing vital roles in gene regulation and expression. The prediction and identification of enhancers are important but challenging issues for bioinformatics studies. Existing comp...
Mixed Integer Linear Programming based machine learning approach identifies regulators of telomerase in yeast.
Nucleic acids research
Feb 22, 2016
Understanding telomere length maintenance mechanisms is central in cancer biology as their dysregulation is one of the hallmarks for immortalization of cancer cells. Important for this well-balanced control is the transcriptional regulation of the te...
Genotoxic mode of action predictions from a multiplexed flow cytometric assay and a machine learning approach.
Environmental and molecular mutagenesis
Jan 13, 2016
Several endpoints associated with cellular responses to DNA damage as well as overt cytotoxicity were multiplexed into a miniaturized, "add and read" type flow cytometric assay. Reagents included a detergent to liberate nuclei, RNase and propidium io...
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 ...
Identification of active transcriptional regulatory elements from GRO-seq data.
Nature methods
Mar 23, 2015
Modifications to the global run-on and sequencing (GRO-seq) protocol that enrich for 5'-capped RNAs can be used to reveal active transcriptional regulatory elements (TREs) with high accuracy. Here, we introduce discriminative regulatory-element detec...
A deep learning model for prediction of lysine crotonylation sites by fusing multi-features based on multi-head self-attention mechanism.
Scientific reports
May 29, 2025
Lysine crotonylation (Kcr) is an important post-translational modification, which is present in both histone and non-histone proteins, and plays a key role in a variety of biological processes such as metabolism and cell differentiation. Therefore, r...
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