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A Bioinformatics Pipeline for Cancer Epigenetics

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Epigenetics has become a cornerstone of cancer research and is an increasingly important factor in the continuous efforts to try and unravel the biology of oncogenesis. Consequently the analyses of epigenetic data have evolved towards genome wide and high-throughput approaches, generating large data sets for which computational data mining is indispensable. Bioinformatics has proven to be useful and beneficial for a plethora of tasks, going beyond elemental data management, and is now crucial for adequate candidate gene selection, data integration, comparison and correlation as well as providing insights into cancer biology. Computational approaches are used even in routine tasks like primer design, since multiple layers of information can be incorporated into a more efficient and consistent strategy. Almost every analysis feeds back information into both the biology and the tools we use during these experiments. As the cancer epigenetics field evolves rapidly, the combination with bioinformatics will create a synergy that increases our insights into cancer biology rapidly. This review summarizes some of the frequently used bioinformatics tools in large-scale or nextgeneration analyses in epigenetics that would not have been possible without the use of well-conceived computational strategies.

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Keywords: Epigenetics; cancer; computational pipeline; methylation; microarray

Document Type: Research Article

Publication date: September 1, 2010

More about this publication?
  • Current Bioinformatics aims to publish all the latest and outstanding developments in bioinformatics. Each issue contains a series of timely, in-depth reviews written by leaders in the field, covering a wide range of the integration of biology with computer and information science.

    The journal focuses on reviews on advances in computational molecular/structural biology, encompassing areas such as computing in biomedicine and genomics, computational proteomics and systems biology, and metabolic pathway engineering. Developments in these fields have direct implications on key issues related to health care, medicine, genetic disorders, development of agricultural products, renewable energy, environmental protection, etc.

    Current Bioinformatics is an essential journal for all academic and industrial researchers who want expert knowledge on all major advances in bioinformatics.
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