AIMC Topic: Promoter Regions, Genetic
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Rapid, portable, and sensitive detection of CaMV35S by RPA-CRISPR/Cas12a-G4 colorimetric assays with high accuracy deep learning object recognition and classification.
Talanta
Jun 20, 2024
Fast, sensitive, and portable detection of genetic modification contributes to agricultural security and food safety. Here, we developed RPA-CRISPR/Cas12a-G-quadruplex colorimetric assays that can combine with intelligent recognition by deep learning...
EPI-Trans: an effective transformer-based deep learning model for enhancer promoter interaction prediction.
BMC bioinformatics
Jun 18, 2024
BACKGROUND: Recognition of enhancer-promoter Interactions (EPIs) is crucial for human development. EPIs in the genome play a key role in regulating transcription. However, experimental approaches for classifying EPIs are too expensive in terms of eff...
DeepCBA: A deep learning framework for gene expression prediction in maize based on DNA sequences and chromatin interactions.
Plant communications
Jun 10, 2024
Chromatin interactions create spatial proximity between distal regulatory elements and target genes in the genome, which has an important impact on gene expression, transcriptional regulation, and phenotypic traits. To date, several methods have been...
promSEMBLE: Hard Pattern Mining and Ensemble Learning for Detecting DNA Promoter Sequences.
IEEE/ACM transactions on computational biology and bioinformatics
Feb 5, 2024
Accurate identification of DNA promoter sequences is of crucial importance in unraveling the underlying mechanisms that regulate gene transcription. Initiation of transcription is controlled through regulatory transcription factors binding to promote...
AI and Knowledge-Based Method for Rational Design of Sigma70 Promoters.
ACS synthetic biology
Jan 4, 2024
Expanding sigma70 promoter libraries can support the engineering of metabolic pathways and enhance recombinant protein expression. Herein, we developed an artificial intelligence (AI) and knowledge-based method for the rational design of sigma70 prom...
Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring.
Proceedings of the National Academy of Sciences of the United States of America
Jul 3, 2023
Plasma cell-free DNA (cfDNA) is a noninvasive biomarker for cell death of all organs. Deciphering the tissue origin of cfDNA can reveal abnormal cell death because of diseases, which has great clinical potential in disease detection and monitoring. D...
Designer genes courtesy of artificial intelligence.
Genes & development
May 30, 2023
The core promoter determines not only where gene transcription initiates but also the transcriptional activity in both basal and enhancer-induced conditions. Multiple short sequence elements within the core promoter have been identified in different ...
Deep Learning Prediction of Promoter Mutation Status in Thyroid Cancer Using Histologic Images.
Medicina (Kaunas, Lithuania)
Mar 9, 2023
objectives: Telomerase reverse transcriptase () promoter mutation, found in a subset of patients with thyroid cancer, is strongly associated with aggressive biologic behavior. Predicting promoter mutation is thus necessary for the prognostic strati...
Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants.
Plant communications
Feb 9, 2023
With the development of high-throughput biology techniques and artificial intelligence, it has become increasingly feasible to design and construct artificial biological parts, modules, circuits, and even whole systems. To overcome the limitations of...
A deep learning based two-layer predictor to identify enhancers and their strength.
Methods (San Diego, Calif.)
Feb 3, 2023
The enhancer is a DNA sequence that can increase the activity of promoters and thus speed up the frequency of gene transcription. The enhancer plays an essential role in activating gene expression. Currently, gene sequencing technology has been devel...
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