AIMC Topic: Promoter Regions, Genetic

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Explainable artificial intelligence as a reliable annotator of archaeal promoter regions.

Scientific reports Jan 31, 2023
Archaea are a vast and unexplored cellular domain that thrive in a high diversity of environments, having central roles in processes mediating global carbon and nutrient fluxes. For these organisms to balance their metabolism, the appropriate regulat...
Artificial Intelligence Machine Learning Transcription Factors Promoter Regions, Genetic Archaea
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Ensemble learning based assessment of the role of transcription factors in gene expression.

Computers in biology and medicine Dec 21, 2022
Cancer cells are formed when the associated, active genes fail to function the way they are meant to function. Multiple genes collectively control cell growth by activating a proper set of genes. Regulation of gene expression is controlled through th...
Machine Learning Cell Line, Tumor Transcription Factors Gene Expression Gene Expression Regulation Promoter Regions, Genetic
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DeepTSS: multi-branch convolutional neural network for transcription start site identification from CAGE data.

BMC bioinformatics Dec 12, 2022
BACKGROUND: The widespread usage of Cap Analysis of Gene Expression (CAGE) has led to numerous breakthroughs in understanding the transcription mechanisms. Recent evidence in the literature, however, suggests that CAGE suffers from transcriptional an...
Neural Networks, Computer Software Promoter Regions, Genetic Chromatin Transcription Initiation Site
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CFA: An explainable deep learning model for annotating the transcriptional roles of cis-regulatory modules based on epigenetic codes.

Computers in biology and medicine Nov 29, 2022
Metazoa gene expression is controlled by modular DNA segments called cis-regulatory modules (CRMs). CRMs can convey promoter/enhancer/insulator roles, generating additional regulation layers in transcription. Experiments for understanding CRM roles a...
Deep Learning Epigenesis, Genetic Promoter Regions, Genetic
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DPProm: A Two-Layer Predictor for Identifying Promoters and Their Types on Phage Genome Using Deep Learning.

IEEE journal of biomedical and health informatics Oct 4, 2022
With the number of phage genomes increasing, it is urgent to develop new bioinformatics methods for phage genome annotation. Promoter, a DNA region, is important for gene transcriptional regulation. In the era of post-genomics, the availability of da...
Humans Deep Learning Genomics DNA Promoter Regions, Genetic Bacteriophages
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iCREPCP: A deep learning-based web server for identifying base-resolution cis-regulatory elements within plant core promoters.

Plant communications Sep 28, 2022
Deep Learning Plants Promoter Regions, Genetic Regulatory Sequences, Nucleic Acid
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DeeProPre: A promoter predictor based on deep learning.

Computational biology and chemistry Sep 13, 2022
The promoter is a DNA sequence recognized, bound and transcribed by RNA polymerase. It is usually located at the upstream or 5'end of the transcription start site (TSS). Studies have shown that the structure of the promoter affects its affinity for R...
Neural Networks, Computer Software Algorithms Deep Learning Promoter Regions, Genetic
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iPromoter-CLA: Identifying promoters and their strength by deep capsule networks with bidirectional long short-term memory.

Computer methods and programs in biomedicine Aug 28, 2022
BACKGROUND AND OBJECTIVE: The promoter is a fragment of DNA and a specific sequence with transcriptional regulation function in DNA. Promoters are located upstream at the transcription start site, which is used to initiate downstream gene expression....
Neural Networks, Computer Promoter Regions, Genetic
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BERT-Promoter: An improved sequence-based predictor of DNA promoter using BERT pre-trained model and SHAP feature selection.

Computational biology and chemistry Jul 14, 2022
A promoter is a sequence of DNA that initializes the process of transcription and regulates whenever and wherever genes are expressed in the organism. Because of its importance in molecular biology, identifying DNA promoters are challenging to provid...
Machine Learning Natural Language Processing DNA Promoter Regions, Genetic
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Development and Application of Two Inducible Expression Systems for Streptococcus suis.

Microbiology spectrum Jun 27, 2022
Streptococcus suis is an important zoonotic bacterial pathogen posing a threat to the pig industry as well as public health, for which the mechanisms of growth and cell division remain largely unknown. Developing convenient genetic tools that can ach...
Animals Swine Bacterial Proteins Base Sequence Promoter Regions, Genetic Isopropyl Thiogalactoside Cell Division Streptococcus suis
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