AIMC Topic: Promoter Regions, Genetic

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Assessing the effects of data selection and representation on the development of reliable E. coli sigma 70 promoter region predictors.

PloS one
As the number of sequenced bacterial genomes increases, the need for rapid and reliable tools for the annotation of functional elements (e.g., transcriptional regulatory elements) becomes more desirable. Promoters are the key regulatory elements, whi...

[Synthetic promoters: theory, design, and prospects].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology
Synthetic promoters are novel promoters artificially designed and do not exist in nature. They can initiate the expression of target genes with specific regulatory modes, offering advantages such as high expression efficiency, precise regulation, and...

Paternally Expressed Gene 10 Promoter Methylation Level as a Predictor of HBeAg Seroconversion in Chronic Hepatitis B Patients.

Journal of medical virology
The management of chronic hepatitis B (CHB) encounters challenges like suboptimal antiviral response and the lack of predictive biomarkers. In this study, the role of paternally expressed gene 10 (PEG10) in hepatitis B e antigen (HBeAg) seroconversio...

CREATE: cell-type-specific cis-regulatory element identification via discrete embedding.

Nature communications
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...

AI-Driven Drug Target Screening Platform Identified Oncogene CACNA2D1 Activated by Enhancer Infestation in Epstein-Barr Virus-Associated Nasopharyngeal Carcinoma.

International journal of molecular sciences
The management of nasopharyngeal cancer (NPC) is rapidly evolving, with immune checkpoint inhibitors emerging as a prominent treatment approach. However, drug development targeting specific molecular and cellular abnormalities in NPC has slowed. Rece...

EPIPDLF: a pretrained deep learning framework for predicting enhancer-promoter interactions.

Bioinformatics (Oxford, England)
MOTIVATION: Enhancers and promoters, as regulatory DNA elements, play pivotal roles in gene expression, homeostasis, and disease development across various biological processes. With advancing research, it has been uncovered that distal enhancers may...

Negative dataset selection impacts machine learning-based predictors for multiple bacterial species promoters.

Bioinformatics (Oxford, England)
MOTIVATION: Advances in bacterial promoter predictors based on machine learning have greatly improved identification metrics. However, existing models overlooked the impact of negative datasets, previously identified in GC-content discrepancies betwe...

[Machine learning-aided design of synthetic biological parts and circuits].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology
Synthetic biology is an emerging interdisciplinary field at the convergence of biology, engineering, and computer science. It employs a bottom-up approach to progressively design biological parts, devices, and circuits, aiming to create artificial bi...

[Intelligent design of nucleic acid elements in biomanufacturing].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology
Nucleic acid elements are essential functional sequences that play critical roles in regulating gene expression, optimizing pathways, and enabling gene editing to enhance the production of target products in biomanufacturing. Therefore, the design an...

Predicting gene expression from histone marks using chromatin deep learning models depends on histone mark function, regulatory distance and cellular states.

Nucleic acids research
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...