19.7: Further Reading, Tools and Techniques

Computational Biology - Genomes, Networks, and Evolution · LibreTexts

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    From LibreTexts, under CC BY-NC-SA 4.0, as the source states it; its equations are written in TeX, which the PDF shows typeset. This page at LibreTexts.

    There are several interesting papers that are looking at chromatin states and epigenetics in general. Several urls are listed below to begin your exploration:

    1. www.nature.com/nmeth/journal/...meth.1673.html
    2. www.nature.com/nature/journal...ture09906.html
    3. www.nature.com/nbt/journal/v2.../nbt.1662.html
    4. http://www.nytimes.com/2012/09/09/op...tter.html?_r=1 5. www.nature.com/doifinder/10.1038/nature14248

    These are a few selected publications that deal with epigenetics and disease.

    1. www.nature.com/nature/journal...ture02625.html 2. http://www.sciencedirect.com/science...11124712003725
    3. www.nature.com/nbt/journal/v2...f/nbt.1685.pdf

    Tools and Techniques

    ChromHMM is the HMM described in the text. It is available free for download with instructions and examples at: http://compbio.mit.edu/ChromHMM/.

    Segway is another method for analyzing multiple tracks of functional genomics data. It uses a dynamic Bayesian network (HMMs are a particular type of dynamic Bayesian network) which enables it to analyze the entire genome at 1-bp resolution. The downside is that it is much slower than ChromHMM. It is available free for download here: http://noble.gs.washington.edu/proj/segway/.

    This page titled 19.7: Further Reading, Tools and Techniques was last modified on Wed, 17 Mar 2021 20:41:26 GMT and is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by Manolis Kellis et al. (MIT OpenCourseWare) via source content that was edited to the style and standards of the LibreTexts platform.