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Bioinformatics Approaches to the Study of MicroRNAs

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Non-coding RNAs and Cancer

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Abstract

The introduction of Next-Generation Sequencing (NGS) technologies has opened new avenues, including determination of the relationship of genomic and epigenomic variation and phenotypes to disease. These technologies are particularly well suited for discovery of both small RNAs, around 30–75 base pairs long, and long RNAs, longer than 75 base pairs, because the NGS sequencers can produce millions of short reads in a relatively rapid period of time. However, the large amounts (terabases) of data generated require proper computational resources and analytical methods to translate the rich source of genomic data into meaningful information for biomedical applications. In this chapter, we describe various bioinformatics methods for performing integrative analysis for the identification of miRNAs and their target mRNAs from the NGS sequencers. We describe the most commonly used databases and prediction programs that are available on the World Wide Web and demonstrate the use of some of these programs by an example. We provide a list of these programs along with their Web URLs and suggest guidelines for successful application.

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Authors and Affiliations

  1. Center for Systems and Computational Biology, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA

    Ravi Gupta & Ramana V. Davuluri

  2. Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA

    Ravi Gupta & Ramana V. Davuluri

  3. SciGenom Labs. Pvt. Ltd., Cochin, Kerala, India

    Ravi Gupta

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  1. Ravi Gupta
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  2. Ramana V. Davuluri
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Correspondence to Ramana V. Davuluri .

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  1. Pediatrics and Molecular Microbiology &, University of Southern California Children's Hospital Los Angeles, Los Angeles, California, USA

    Muller Fabbri

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Gupta, R., Davuluri, R.V. (2014). Bioinformatics Approaches to the Study of MicroRNAs. In: Fabbri, M. (eds) Non-coding RNAs and Cancer. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-8444-8_9

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