AIMC Topic: MicroRNAs

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miRBaseConverter: an R/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase.

BMC bioinformatics
BACKGROUND: miRBase is the primary repository for published miRNA sequence and annotation data, and serves as the "go-to" place for miRNA research. However, the definition and annotation of miRNAs have been changed significantly across different vers...

Identification of pre-microRNAs by characterizing their sequence order evolution information and secondary structure graphs.

BMC bioinformatics
BACKGROUND: Distinction between pre-microRNAs (precursor microRNAs) and length-similar pseudo pre-microRNAs can reveal more about the regulatory mechanism of RNA biological processes. Machine learning techniques have been widely applied to deal with ...

Model based on GA and DNN for prediction of mRNA-Smad7 expression regulated by miRNAs in breast cancer.

Theoretical biology & medical modelling
BACKGROUND: The Smad7 protein is negative regulator of the TGF-β signaling pathway, which is upregulated in patients with breast cancer. miRNAs regulate proteins expressions by arresting or degrading the mRNAs. The purpose of this work is to identify...

Prediction of plant-derived xenomiRs from plant miRNA sequences using random forest and one-dimensional convolutional neural network models.

BMC genomics
BACKGROUND: An increasing number of studies reported that exogenous miRNAs (xenomiRs) can be detected in animal bodies, however, some others reported negative results. Some attributed this divergence to the selective absorption of plant-derived xenom...

Dual Convolutional Neural Network Based Method for Predicting Disease-Related miRNAs.

International journal of molecular sciences
Identification of disease-related microRNAs (disease miRNAs) is helpful for understanding and exploring the etiology and pathogenesis of diseases. Most of recent methods predict disease miRNAs by integrating the similarities and associations of miRNA...

Gene Ontology-based function prediction of long non-coding RNAs using bi-random walk.

BMC medical genomics
BACKGROUND: With the development of sequencing technology, more and more long non-coding RNAs (lncRNAs) have been identified. Some lncRNAs have been confirmed that they play an important role in the process of development through the dosage compensat...

Application of Artificial Neural Network in miRNA Biomarker Selection and Precise Diagnosis of Colorectal Cancer.

Iranian biomedical journal
BACKGROUND: The early diagnosis of colorectal cancer (CRC) is associated with improved survival rates, and development of novel non-invasive, sensitive, and specific diagnostic tests is highly demanded. The objective of this paper was to identify com...

A Supervised Ensemble Approach for Sensitive microRNA Target Prediction.

IEEE/ACM transactions on computational biology and bioinformatics
MicroRNAs, a class of small non-coding RNAs, regulate important biological functions via post-transcriptional regulation of messenger RNAs (mRNAs). Despite rapid development in miRNA research, precise experimental methods to determine miRNA target in...

miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts.

PLoS computational biology
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by binding to partially complementary regions within the 3'UTR of their target genes. Computational methods play an important role in target prediction and assume that the miR...

Expanding the horizons of microRNA bioinformatics.

RNA (New York, N.Y.)
MicroRNA regulation of key biological and developmental pathways is a rapidly expanding area of research, accompanied by vast amounts of experimental data. This data, however, is not widely available in bioinformatic resources, making it difficult fo...