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| http://dx.doi.org/10.4103/ijo.IJO_3496_20 | DOI Listing |
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Establishing a GRU-GCN coordination-based prediction model for miRNA-disease associations.
BMC Genom Data
January 2025
Department of Management Information Systems, National Chung Hsing University, Taichung, 402, Taiwan.
Background: miRNAs (microRNAs) are endogenous RNAs with lengths of 18 to 24 nucleotides and play critical roles in gene regulation and disease progression. Although traditional wet-lab experiments provide direct evidence for miRNA-disease associations, they are often time-consuming and complicated to analyze by current bioinformatics tools. In recent years, machine learning (ML) and deep learning (DL) techniques are powerful tools to analyze large-scale biological data.
View Article and Find Full Text PDFPreTKcat: A pre-trained representation learning and machine learning framework for predicting enzyme turnover number.
Comput Biol Chem
January 2025
College of Artificial Intelligence, Tianjin University of Science and Technology, No. 9, 13th Street, Tianjin Economic-Technological Development Area, Tianjin, 300457, China. Electronic address:
The enzyme turnover number (k) is crucial for understanding enzyme kinetics and optimizing biotechnological processes. However, experimentally measured k values are limited due to the high cost and labor intensity of wet-lab measurements, necessitating robust computational methods. To address this issue, we propose PreTKcat, a framework that integrates pre-trained representation learning and machine learning to predict k values.
View Article and Find Full Text PDFIntegrated course on ocular anatomy for ophthalmology clerkship.
BMC Med Educ
January 2025
State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University; Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Background: Obtaining a full understanding of the anatomical structure of the eyeball and the contents within the eye plays a crucial role in learning eye diseases. However, it can be challenging for beginners to quickly learn, memorize, and apply this anatomical knowledge. To improve the teaching of ocular anatomy and help students overcome learning difficulties in ophthalmology clerkship, Zhongshan Ophthalmic Center developed an integrated ocular anatomy course comprising three main components: 'online preview,' 'lecture,' and 'wetlab dissection'.
View Article and Find Full Text PDFEnhancing the reverse transcriptase function in Taq polymerase via AI-driven multiparametric rational design.
Front Bioeng Biotechnol
December 2024
AO Vector-Best, Novosibirsk, Russia.
Introduction: Modification of natural enzymes to introduce new properties and enhance existing ones is a central challenge in bioengineering. This study is focused on the development of Taq polymerase mutants that show enhanced reverse transcriptase (RTase) activity while retaining other desirable properties such as fidelity, 5'- 3' exonuclease activity, effective deoxyuracyl incorporation, and tolerance to locked nucleic acid (LNA)-containing substrates. Our objective was to use AI-driven rational design combined with multiparametric wet-lab analysis to identify and validate Taq polymerase mutants with an optimal combination of these properties.
View Article and Find Full Text PDFDesigning novel functional proteins crucially depends on accurately modeling their fitness landscape. Given the limited availability of functional annotations from wet-lab experiments, previous methods have primarily relied on self-supervised models trained on vast, unlabeled protein sequence or structure datasets. While initial protein representation learning studies solely focused on either sequence or structural features, recent hybrid architectures have sought to merge these modalities to harness their respective strengths.
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