Computational Non-coding RNA Biology - 1st Edition - ISBN: 9780128143650

Computational Non-coding RNA Biology

1st Edition

Authors: Yun Zheng
Paperback ISBN: 9780128143650
Imprint: Academic Press
Published Date: 1st October 2018
Page Count: 350
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Non-coding RNAs are molecules that play important roles in biological systems and human disease. The development of high throughput sequencing technologies has led to the critical task of identifying different classes of non-coding RNAs and predicting the possible functions of these molecules. Finding, quantifying, and visualizing non-coding RNAs from high throughput sequencing datasets at high volume is complex. It is therefore not usually possible for biologists to complete all necessary steps for analysis independently. Computational Non-coding of RNA Biology is a resource for the computation of non-coding RNAs. The book covers computational methods for the identification and quantification of non-coding RNAs, including miRNAs, tasiRNAs, phasiRNAs, lariat originated circRNAs and back-spliced circRNAs, identification of miRNA/siRNA targets, and identification of mutations and editing sites in miRNAs. The book introduces basic ideas of computational methods, and the computational steps are given in sufficient detail for the reader to replicate the method on their own datasets.

Key Features

  • Presents a comprehensive resource for computational methods for the identification and quantification of non-coding RNAs
  • Provides a guide to assist biologists and other researchers dealing with complex datasets
  • Introduces basic computational methods, and provides guidelines for their replication by researchers
  • Offers a solution to researchers approaching large and complex sequencing datasets


Biologists, computational biologists, researchers in proteins and proteomics, botanists; researchers and graduate researchers working on non-coding RNA data

Table of Contents

SECTION I: Genetic and Epigenetic effect on cancer through noncoding RNA
1. miRNA and Cancer
2. miRNA biogenesis disruption and cancer
3. Genetic alteration of miRNA affecting cancer pathways
4. The epigenetic control of microRNA expression and cancer
5. Effects of miRNAs on epigenetic machinery
6. Histone modifiers of deregulated miRNAs in cancer
7. miRNA genes epigenetically regulated by DNA methylation in cancer
8. Circulating miRNA increasing the risk of cancer
9. lncRNA as cancer biomarker
10. Genetic variation of lncRNA in cancer
11. Implications of lncRNAs in cancer epigenetics
12. Charting DNA methylation of long non-coding RNA in cancer.
13. Competing endogenous RNA and cancer
14. miRNA-lncRNA-ceRNA network in cancer
15. Noncoding function of protein-coding genes: mRNA 3´ UTR as ceRNAs in cancer
16. Long noncoding RNAs and pseudogenes as ceRNA in cancer
17. Epigenetic programming mechanism guided by piRNAs in cancer.
18. Epigenetic loss of the PIWI/piRNA machinery in human tumorigenesis
19. tRNA and cancer
20. Dynamic reprogramming of tRNA modifications in cancer
21. Post-transcriptional modifications of tRNA linked to cancer
22. Circular RNA: a novel non-coding RNA in Cancer
23. Other ncRNA and cancer

SECTION II: Cancer Epigenetic Mechanisms modulated by non-coding RNA
24. Assessing DNA methylation and demethylation of noncoding RNA in cancer
25. Noncoding RNAs act as chromatin scaffold of histone modification complexes in cancer
26. Heterochromatin modulation by noncoding RNA in cancer
27. Noncoding RNAs (ncRNAs) mediate the recruitment of PcG control of gene expression in cancer.

SECTION III: Therapeutic implications of ncRNA in cancer
28. Non-coding RNA involved in Cancer Stem Cell Therapy
29. Therapeutic strategies based on targeting ncRNAs for selective silencing
30. Clinical relevance of non-coding RNAs in Cancer
31. Non-coding RNAs: Novel Targets in anticancer drug development

SECTION IV: Bioinformatics’ detection of ncRNA in cancer
32. Cancer ncRNA discovery via High Throughput Sequencing
33. Non-coding RNAs as a cause of cancer: evidence from GWAS and reverse genetics.
34. A comparative evaluation of emerging tools for cancer ncRNA retrieval
35. Databases: a comprehensive resource of noncoding RNAs



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© Academic Press 2019
Academic Press
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About the Author

Yun Zheng

Yun Zheng is Associate Professor in Bioinformatics at Kunming University of Science and Technology in China. He has been working in bioinformatics for more than 10 years, concentrating on non-coding RNAs, and has published over 30 papers in the area. He has developed novel tools for a wide-range of computational topics in non-coding RNAs, validated by influential work in the field of non-coding RNAs. Yun Zheng holds a PhD from the National University of Singapore.

Affiliations and Expertise

Kunming University of Science and Technology

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