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4
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PLoS One. 2012;7(2):e31345. doi: 10.1371/journal.pone.0031345. Epub 2012 Feb 15.
5
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6
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7
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Nat Biotechnol. 2008 Nov;26(11):1251-9. doi: 10.1038/nbt.1499.
8
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Bioinformatics. 2003 Oct;19 Suppl 2:ii238-44. doi: 10.1093/bioinformatics/btg1084.
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