Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function.

Tian W, Zhang LV, Taşan M, Gibbons FD, King OD, Park J, Wunderlich Z, Cherry JM, Roth FP.

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PMID: 18613951 [PubMed - indexed for MEDLINE]

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PMID: 15929793 [PubMed - indexed for MEDLINE]

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Barutcuoglu Z, Schapire RE, Troyanskaya OG.

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Science. 2002 Oct 25;298(5594):799-804.

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