AIMC Topic: RNA, Messenger

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Identification of biomarkers associated with inflammatory response in Parkinson's disease by bioinformatics and machine learning.

PloS one Jan 1, 2025
Parkinson's disease (PD) is a common and debilitating neurodegenerative disorder. The inflammatory response is essential in the pathogenesis and progression of PD. The goal of this study is to combine bioinformatics and machine learning to screen for...
Transcriptome Protein Interaction Maps Gene Regulatory Networks Biomarkers Gene Expression Profiling Parkinson Disease MicroRNAs Transcription Factor RelA Computational Biology RNA, Messenger Inflammation Humans Machine Learning
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AI techniques have facilitated the understanding of epitranscriptome distribution.

Cell genomics Dec 11, 2024
N-methyladenosine (m6A), the most prevalent internal mRNA modification in higher eukaryotes, plays diverse roles in cellular regulation. By incorporating both sequence- and genome-derived features, Fan et al. designed a novel Transformer-BiGRU framew...
Transcriptome Humans Adenosine Artificial Intelligence RNA, Messenger Epigenesis, Genetic
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miCGR: interpretable deep neural network for predicting both site-level and gene-level functional targets of microRNA.

Briefings in bioinformatics Nov 22, 2024
MicroRNAs (miRNAs) are critical regulators in various biological processes to cleave or repress translation of messenger RNAs (mRNAs). Accurately predicting miRNA targets is essential for developing miRNA-based therapies for diseases such as cancer a...
MicroRNAs Computational Biology RNA, Messenger Humans Neural Networks, Computer Algorithms Deep Learning
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A deep learning method to integrate extracelluar miRNA with mRNA for cancer studies.

Bioinformatics (Oxford, England) Nov 1, 2024
MOTIVATION: Extracellular miRNAs (exmiRs) and intracellular mRNAs both can serve as promising biomarkers and therapeutic targets for various diseases. However, exmiR expression data is often noisy, and obtaining intracellular mRNA expression data usu...
Humans Neoplasms MicroRNAs Deep Learning Computational Biology RNA, Messenger
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DPNN-ac4C: a dual-path neural network with self-attention mechanism for identification of N4-acetylcytidine (ac4C) in mRNA.

Bioinformatics (Oxford, England) Nov 1, 2024
MOTIVATION: The modification of N4-acetylcytidine (ac4C) in RNA is a conserved epigenetic mark that plays a crucial role in post-transcriptional regulation, mRNA stability, and translation efficiency. Traditional methods for detecting ac4C modificati...
Neural Networks, Computer Algorithms Computational Biology Cytidine RNA, Messenger
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siRNADiscovery: a graph neural network for siRNA efficacy prediction via deep RNA sequence analysis.

Briefings in bioinformatics Sep 23, 2024
The clinical adoption of small interfering RNAs (siRNAs) has prompted the development of various computational strategies for siRNA design, from traditional data analysis to advanced machine learning techniques. However, previous studies have inadequ...
Computational Biology RNA, Messenger Sequence Analysis, RNA RNA, Small Interfering Gene Silencing RNA Interference Humans Neural Networks, Computer Algorithms
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m6ATM: a deep learning framework for demystifying the m6A epitranscriptome with Nanopore long-read RNA-seq data.

Briefings in bioinformatics Sep 23, 2024
N6-methyladenosine (m6A) is one of the most abundant and well-known modifications in messenger RNAs since its discovery in the 1970s. Recent studies have demonstrated that m6A is involved in various biological processes, such as alternative splicing ...
Nanopore Sequencing Computational Biology RNA, Messenger Sequence Analysis, RNA Epigenesis, Genetic Transcriptome Adenosine Deep Learning Nanopores Humans RNA-Seq Software
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MSlocPRED: deep transfer learning-based identification of multi-label mRNA subcellular localization.

Briefings in bioinformatics Sep 23, 2024
Subcellular localization of messenger ribonucleic acid (mRNA) is a universal mechanism for precise and efficient control of the translation process. Although many computational methods have been constructed by researchers for predicting mRNA subcellu...
Computational Biology RNA, Messenger Software Algorithms Deep Learning Humans
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Advancing mRNA subcellular localization prediction with graph neural network and RNA structure.

Bioinformatics (Oxford, England) Aug 2, 2024
MOTIVATION: The asymmetrical distribution of expressed mRNAs tightly controls the precise synthesis of proteins within human cells. This non-uniform distribution, a cornerstone of developmental biology, plays a pivotal role in numerous cellular proce...
RNA, Messenger Software Humans Nucleic Acid Conformation Deep Learning Neural Networks, Computer Computational Biology
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Combined bioinformatics and machine learning methodologies reveal prognosis-related ceRNA network and propose ABCA8, CAT, and CXCL12 as independent protective factors against osteosarcoma.

Advances in clinical and experimental medicine : official organ Wroclaw Medical University Aug 1, 2024
BACKGROUND: Aberrant circular RNA (circRNA) acts as an oncogene or suppressor during neoplasm initiation and development. However, the functions of most circRNAs in osteosarcoma (OS) remain unclear.
Protective Factors Computational Biology RNA, Competitive Endogenous RNA, Messenger Humans Biomarkers, Tumor Osteosarcoma Chemokine CXCL12 Gene Expression Regulation, Neoplastic Machine Learning Gene Regulatory Networks ATP-Binding Cassette Transporters Bone Neoplasms Prognosis RNA, Circular MicroRNAs
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