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Novel bioinformatics tools for miRNA-Seq analysis, RNA structure visualization, and genome-wide repeat detection

Shi, Jieming
http://orcid.org/0000-0003-1086-9538
http://rave.ohiolink.edu/etdc/view?acc_num=miami15003113547315

Abstract Details

2017, Doctor of Philosophy, Miami University, Cell, Molecular and Structural Biology (CMSB).
This dissertation addresses four main questions in molecular biology with our newly developed bioinformatics software. Chapter I and VI give the overview of introduction and conclusions to the dissertation respectively. Chapter II titled "mirPRo - a novel standalone program for differential expression and variation analysis of miRNAs", addresses the problem of accurate miRNA quantification and comprehensive miRNA variation detection from high-throughput sequencing data. Here, we developed a new tool called "mirPRo" to quantify known miRNAs and predict novel miRNAs. Compared with the most widely used tool - miRDeep2, mirPRo is more accurate in known miRNA quantification, and offers new functions such as read cataloging based on genome annotation, miRNA isoform identification, and "arm switching" detection. The paper is published in Nature Scientific Reports: Sci. Rep. 5, 14617 (2015). Chapter III titled "JNSViewer - a JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures", addresses the problem of interactive RNA/DNA secondary structure visualization in web computational platforms. Here, we developed JNSViewer, a highly interactive web service bundled with several popular tools for DNA/RNA secondary structure prediction, providing precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. We also predicted some RNA structures for Arabidopsis by incorporating in vivo high-throughput profiling data as a useful resource for plant RNA study. The relevant manuscript is under review in PLoS One. Chapter IV titled "GRF: a generic and accurate tool for genome-wide de novo repeat detection", addresses the problem of accurate and exhaustive repeat search in genomes. Here, we developed GRF, a tool for genome-wide repeat detection based on fast, exhaustive numerical calculation algorithms integrated with optimized dynamic programming. GRF can accurately identify terminal inverted/direct repeats and interspersed repeats, and detect DNA or RNA transposon elements characterized by these repeats in genomes. GRF proves to be more accurate than other repeat detection tools such as detectIR, detectMITE, IRF, and LTR_FINDER. Chapter V titled "Genome-wide study of inverted repeats, MITEs, and their relationship with DNA methylation and gene expression in human";, investigates the interconnection of inverted repeats and MITEs, DNA methylation, and associated gene expression in human. Using our novel repeat detection tool - GRF, we provided more comprehensive and accurate annotations of inverted repeats and MITEs in human, Arabidopsis and mouse. We also investigated the sequence features of inverted repeats and MITEs, their DNA methylation levels, and expression levels of associated genes in different human tissues.
Liang Chun (Advisor)
Bioinformatics

Recommended Citations

Citations

  • Shi, J. (2017). Novel bioinformatics tools for miRNA-Seq analysis, RNA structure visualization, and genome-wide repeat detection [Doctoral dissertation, Miami University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=miami15003113547315

    APA Style (7th edition)

  • Shi, Jieming. Novel bioinformatics tools for miRNA-Seq analysis, RNA structure visualization, and genome-wide repeat detection. 2017. Miami University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=miami15003113547315.

    MLA Style (8th edition)

  • Shi, Jieming. "Novel bioinformatics tools for miRNA-Seq analysis, RNA structure visualization, and genome-wide repeat detection." Doctoral dissertation, Miami University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=miami15003113547315

    Chicago Manual of Style (17th edition)

miami15003113547315
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© 2017, some rights reserved.Creative Commons License Novel bioinformatics tools for miRNA-Seq analysis, RNA structure visualization, and genome-wide repeat detection by Jieming Shi is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. Based on a work at etd.ohiolink.edu.
This open access ETD is published by Miami University and OhioLINK.