AIMC Topic: RNA, Messenger
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Adenosine Triphosphate Protects from Elevated Extracellular Calcium-Induced Damage in Human Proximal Kidney Cells: Using Deep Learning to Predict Cytotoxicity.
Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology
Sep 21, 2022
BACKGROUND/AIMS: In kidney, extracellular [Ca] can modulate intracellular [Ca] to control key cellular processes. Hence, extracellular [Ca] is normally maintained within narrow range. We tested effect of extracellular ATP on viability of human proxim...
A novel ergodic cellular automaton gene network model towards efficient hardware-based genome simulator.
Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
Jul 1, 2022
In this paper, a novel ergodic cellular automaton model of Hes1 mRNA and Hes1 protein network is presented. Detailed analyses reveal that the presented network model can reproduce a typical nonlinear bifurcation phenomenon observed in a conventional ...
Deep learning tools are top performers in long non-coding RNA prediction.
Briefings in functional genomics
May 21, 2022
The increasing amount of transcriptomic data has brought to light vast numbers of potential novel RNA transcripts. Accurately distinguishing novel long non-coding RNAs (lncRNAs) from protein-coding messenger RNAs (mRNAs) has challenged bioinformatic ...
lncRNAfunc: a knowledgebase of lncRNA function in human cancer.
Nucleic acids research
Jan 7, 2022
The long non-coding RNAs associating with other molecules can coordinate several physiological processes and their dysfunction can impact diverse human diseases. To date, systematic and intensive annotations on diverse interaction regulations of lncR...
DeepAc4C: a convolutional neural network model with hybrid features composed of physicochemical patterns and distributed representation information for identification of N4-acetylcytidine in mRNA.
Bioinformatics (Oxford, England)
Dec 22, 2021
MOTIVATION: N4-acetylcytidine (ac4C) is the only acetylation modification that has been characterized in eukaryotic RNA, and is correlated with various human diseases. Laboratory identification of ac4C is complicated by factors, such as sample hydrol...
[Naringenin promotes osteogenic differentiation of BMSCs via SDF-1α/CXCR4 signaling axis].
Shanghai kou qiang yi xue = Shanghai journal of stomatology
Dec 1, 2021
PURPOSE: To explore the influence of naringenin on osteogenic differentiation of bone mesenchymal stem cells(BMSCs), and the role of SDF-1α/CXCR4 signaling axis in the osteogenic differentiation by naringenin.
Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning.
Nucleic acids research
Sep 20, 2021
N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotic mRNAs and influences many aspects of RNA processing. miCLIP (m6A individual-nucleotide resolution UV crosslinking and immunoprecipitation) is an antibody-based appr...
Feature extraction approaches for biological sequences: a comparative study of mathematical features.
Briefings in bioinformatics
Sep 2, 2021
As consequence of the various genomic sequencing projects, an increasing volume of biological sequence data is being produced. Although machine learning algorithms have been successfully applied to a large number of genomic sequence-related problems,...
Classification and gene selection of triple-negative breast cancer subtype embedding gene connectivity matrix in deep neural network.
Briefings in bioinformatics
Sep 2, 2021
Triple-negative breast cancer (TNBC) has been a challenging breast cancer subtype for oncological therapy. Normally, it can be classified into different molecular subtypes. Accurate and stable classification of the six subtypes is essential for perso...
SubLocEP: a novel ensemble predictor of subcellular localization of eukaryotic mRNA based on machine learning.
Briefings in bioinformatics
Sep 2, 2021
MOTIVATION: mRNA location corresponds to the location of protein translation and contributes to precise spatial and temporal management of the protein function. However, current assignment of subcellular localization of eukaryotic mRNA reveals import...
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