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Machine Learning and Genome Annotation: a Match Meant to Be?

Overview
Journal Genome Biol
Specialties Biology
Genetics
Date 2013 Jun 5
PMID 23731483
Citations 36
Authors
Affiliations
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Abstract

By its very nature, genomics produces large, high-dimensional datasets that are well suited to analysis by machine learning approaches. Here, we explain some key aspects of machine learning that make it useful for genome annotation, with illustrative examples from ENCODE.

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References
1.
Garber M, Grabherr M, Guttman M, Trapnell C . Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods. 2011; 8(6):469-77. DOI: 10.1038/nmeth.1613. View

2.
Levine M, Davidson E . Gene regulatory networks for development. Proc Natl Acad Sci U S A. 2005; 102(14):4936-42. PMC: 555974. DOI: 10.1073/pnas.0408031102. View

3.
Lawrence C, Altschul S, Boguski M, Liu J, Neuwald A, Wootton J . Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science. 1993; 262(5131):208-14. DOI: 10.1126/science.8211139. View

4.
Simonatto M, Barozzi I, Natoli G . Non-coding transcription at cis-regulatory elements: computational and experimental approaches. Methods. 2013; 63(1):66-75. DOI: 10.1016/j.ymeth.2013.03.021. View

5.
King D, Taylor J, Elnitski L, Chiaromonte F, Miller W, Hardison R . Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Res. 2005; 15(8):1051-60. PMC: 1182217. DOI: 10.1101/gr.3642605. View