AIMC Topic: Promoter Regions, Genetic
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CapsProm: a capsule network for promoter prediction.
Computers in biology and medicine
Jun 1, 2022
Locating the promoter region in DNA sequences is of paramount importance in bioinformatics. This problem has been widely studied in the literature, but it has not yet been fully resolved. Some researchers have shown remarkable results using convoluti...
A successful hybrid deep learning model aiming at promoter identification.
BMC bioinformatics
May 31, 2022
BACKGROUND: The zone adjacent to a transcription start site (TSS), namely, the promoter, is primarily involved in the process of DNA transcription initiation and regulation. As a result, proper promoter identification is critical for further understa...
EPI-Mind: Identifying Enhancer-Promoter Interactions Based on Transformer Mechanism.
Interdisciplinary sciences, computational life sciences
May 28, 2022
MOTIVATION: Enhancer-Promoter Interactions (EPIs) is an essential step in the gene regulation process. However, the detection of EPIs by traditional wet experimental techniques is time-consuming and expensive. Thus, computational methods would be ver...
iProm-Zea: A two-layer model to identify plant promoters and their types using convolutional neural network.
Genomics
May 6, 2022
A promoter is a short DNA sequence near the start codon, responsible for initiating the transcription of a specific gene in the genome. The accurate recognition of promoters is important for achieving a better understanding of transcriptional regulat...
PredPromoter-MF(2L): A Novel Approach of Promoter Prediction Based on Multi-source Feature Fusion and Deep Forest.
Interdisciplinary sciences, computational life sciences
Apr 30, 2022
Promoters short DNA sequences play vital roles in initiating gene transcription. However, it remains a challenge to identify promoters using conventional experiment techniques in a high-throughput manner. To this end, several computational predictors...
Promoter prediction in nannochloropsis based on densely connected convolutional neural networks.
Methods (San Diego, Calif.)
Mar 31, 2022
Promoter is a key DNA element located near the transcription start site, which regulates gene transcription by binding RNA polymerase. Thus, the identification of promoters is an important research field in synthetic biology. Nannochloropsis is an im...
An Extensive Examination of Discovering 5-Methylcytosine Sites in Genome-Wide DNA Promoters Using Machine Learning Based Approaches.
IEEE/ACM transactions on computational biology and bioinformatics
Feb 3, 2022
It is well-known that the major reason for the rapid proliferation of cancer cells are the hypomethylation of the whole cancer genome and the hypermethylation of the promoter of particular tumor suppressor genes. Locating 5-methylcytosine (5mC) sites...
Precise Prediction of Promoter Strength Based on a De Novo Synthetic Promoter Library Coupled with Machine Learning.
ACS synthetic biology
Dec 19, 2021
Promoters are one of the most critical regulatory elements controlling metabolic pathways. However, the fast and accurate prediction of promoter strength remains challenging, leading to time- and labor-consuming promoter construction and characteriza...
BiLSTM-5mC: A Bidirectional Long Short-Term Memory-Based Approach for Predicting 5-Methylcytosine Sites in Genome-Wide DNA Promoters.
Molecules (Basel, Switzerland)
Dec 7, 2021
An important reason of cancer proliferation is the change in DNA methylation patterns, characterized by the localized hypermethylation of the promoters of tumor-suppressor genes together with an overall decrease in the level of 5-methylcytosine (5mC)...
An explainable artificial intelligence approach for decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila.
Genome biology
Nov 8, 2021
BACKGROUND: Enhancers are non-coding regions of the genome that control the activity of target genes. Recent efforts to identify active enhancers experimentally and in silico have proven effective. While these tools can predict the locations of enhan...
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