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circDeep: deep learning approach for circular RNA classification from other long non-coding RNA

2019 Bioinformatics  
other long non-coding RNAs (lncRNAs).  ...  Prediction of circular RNA can be achieved in three steps: distinguishing non-coding RNAs from protein coding gene transcripts, separating short and long non-coding RNAs and predicting circular RNAs from  ...  Acknowledgements We would like to thank Eric Rouchka and Julia Chariker for insightful discussions and comments.  ... 
doi:10.1093/bioinformatics/btz537 pmid:31268128 pmcid:PMC6956777 fatcat:7exee2gglbdmzkdmb6q6j74jda

JEDI: Circular RNA Prediction based on Junction Encoders and Deep Interaction among Splice Sites [article]

Jyun-Yu Jiang, Chelsea Jui-Ting Ju, Junheng Hao, Muhao Chen, Wei Wang
2020 bioRxiv   pre-print
Circular RNA is a novel class of endogenous non-coding RNAs that have been largely discovered in eukaryotic transcriptome.  ...  The circular structure arises from a non-canonical splicing process, where the donor site backsplices to an upstream acceptor site.  ...  Conclusions In this paper, we propose a novel end-to-end deep learning approach for circular RNA prediction by learning to appropriately model splice sites with flanking regions around junctions and studying  ... 
doi:10.1101/2020.02.03.932038 fatcat:kxwsnb6u7je7pdlainemg2uibe

JEDI: circular RNA prediction based on junction encoders and deep interaction among splice sites

Jyun-Yu Jiang, Chelsea J -T Ju, Junheng Hao, Muhao Chen, Wei Wang
2021 Bioinformatics  
Motivation Circular RNA (circRNA) is a novel class of long non-coding RNAs that have been broadly discovered in the eukaryotic transcriptome.  ...  Recently, advanced computational methods leverage deep learning to capture the relevant patterns from RNA sequences and model their interactions to facilitate the prediction.  ...  Acknowledgement We thank all reviewers for their constructive comments and valuable suggestions. Funding  ... 
doi:10.1093/bioinformatics/btab288 pmid:34252942 fatcat:2z44svw2ovg6bccwblu3rsbkou

Attention-Based Deep Multiple-Instance Learning for Classifying Circular RNA and Other Long Non-Coding RNA

Yunhe Liu, Qiqing Fu, Xueqing Peng, Chaoyu Zhu, Gang Liu, Lei Liu
2021 Genes  
Circular RNA (circRNA) is a distinguishable circular formed long non-coding RNA (lncRNA), which has specific roles in transcriptional regulation, multiple biological processes.  ...  The identification of circRNA from other lncRNA is necessary for relevant research.  ...  Introduction Non-coding RNAs (ncRNAs), referring to RNAs without protein-coding potential, account for the majority of RNAs.  ... 
doi:10.3390/genes12122018 pmid:34946967 pmcid:PMC8701965 fatcat:ie2gecal2jhera37p6apgefxmu

Advances in Computational Methodologies for Classification and Sub-Cellular Locality Prediction of Non-Coding RNAs

Muhammad Nabeel Asim, Muhammad Ali Ibrahim, Muhammad Imran Malik, Andreas Dengel, Sheraz Ahmed
2021 International Journal of Molecular Sciences  
Apart from protein-coding Ribonucleic acids (RNAs), there exists a variety of non-coding RNAs (ncRNAs) which regulate complex cellular and molecular processes.  ...  RNA, micro RNA, long ncRNA, and circular RNA, and to determine sub-cellular localization of distinct ncRNAs and RNAs.  ...  Distinguishing Circular RNAs from Long Non-Coding RNAs Another novel sub type of long ncRNA is Circular RNA (circRNA), which is generated by the process of back-splicing.  ... 
doi:10.3390/ijms22168719 pmid:34445436 pmcid:PMC8395733 fatcat:l66viluvf5aqvimsyvmowvpjuy

Identifying Circular RNA and Predicting Its Regulatory Interactions by Machine Learning

Guishan Zhang, Yiyun Deng, Qingyu Liu, Bingxu Ye, Zhiming Dai, Yaowen Chen, Xianhua Dai
2020 Frontiers in Genetics  
Circular RNA (circRNA) is a closed long non-coding RNA (lncRNA) formed by covalently closed loops through back-splicing.  ...  Here, first we present circLGB, a machine learning-based framework to discriminate circRNA from other lncRNAs. circLGB integrates commonly used sequence-derived features and three new features containing  ...  Circular RNAs have some different attributes from other long non-coding RNAs (lncRNAs), such as back-splicing .  ... 
doi:10.3389/fgene.2020.00655 pmid:32849764 pmcid:PMC7396586 fatcat:sgre27znyrasddkjhkfhdpy3oe

Opportunities and Challenges of Predictive Approaches for the Non-coding RNA in Plants

Dong Xu, Wenya Yuan, Chunjie Fan, Bobin Liu, Meng-Zhu Lu, Jin Zhang
2022 Frontiers in Plant Science  
INTRODUCTION Non-coding RNA (ncRNA) is a key regulatory RNA with limited abilities of coding potential (Liu et al., 2015) .  ...  Khan et al., 2020 ncPro-ML ncRNA promoter identification Tang et al., 2020 circDeep circular RNA classification Chaabane et al., 2020 PredLnc-GFStack ncRNA identification Liu et al., 2019 LncADeep lncRNA  ...  National Science Foundation of China (32171814) SUPPLEMENTARY MATERIAL The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fpls.2022. 890663  ... 
doi:10.3389/fpls.2022.890663 pmid:35498708 pmcid:PMC9048598 fatcat:savtessk5newfgcoybufszuswq

Defining the landscape of circRNAs in non-small cell lung cancer and their potential as liquid biopsy biomarkers: a complete review including current methods

Carlos Pedraz-Valdunciel, Rafael Rosell
2021 Extracellular Vesicles and Circulating Nucleic Acids  
Circular RNAs (circRNAs) are a re-discovered type of RNAs featuring stable structure and high tissue-specific expression.  ...  Despite the significant decrease in population-level mortality of lung cancer patients as reflected in the Surveillance Epidemiology and End Results program national database, lung cancer, with non-small  ...  Acknowledgments We would like to thank Stephanie Davis for language editing assistance, and Dr. Cristina Aguado-Esteban for her deep insights. Figure 1 created with BioRender.com.  ... 
doi:10.20517/evcna.2020.07 fatcat:bfjrciy7drhydmzlkxldlp3kje

RNA Sequence Classification Using Secondary Structure Fingerprints, Sequence-Based Features, and Deep Learning

Kevin Sutanto, University, My
2021
Therefore, we hypothesized that using a representation that includes the multiple possible secondary structures of an RNA for classification purposes may improve the classification performance.  ...  Extracting sequences from RNA samples is usually not a major limitation anymore thanks to sequencing technologies such as RNA-Seq.  ...  For instance, "circDeep" uses 3 different types of "sequence descriptor" with deep learning in order to determine whether a sequence of RNA is a circular RNA or a different type of long non-coding RNA  ... 
doi:10.20381/ruor-26098 fatcat:zk74svp5jre5tcqvs34dnhfcoq

Advances in Non-Coding RNA Sequencing

Julia Micheel, Aram Safrastyan, Damian Wollny
2021
Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules.  ...  Moreover, RNA sequencing revealed crucial roles of many ncRNAs in human health and disease.  ...  Acknowledgments: We apologize to all authors whose work could not be included and thank the anonymous reviewers for their contribution to improve this manuscript.  ... 
doi:10.3390/ncrna7040070 pmid:34842804 pmcid:PMC8628893 fatcat:trztplu7t5f5vep7ft5qwxg3qe