Identifying combinatorial regulation of transcription factors and binding motifs.

Kato M, Hata N, Banerjee N, Futcher B, Zhang MQ.

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PMID: 15287978 [PubMed - indexed for MEDLINE]

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PMID: 14627835 [PubMed - indexed for MEDLINE]

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Wu WS, Li WH, Chen BS.

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PMID: 17010188 [PubMed - indexed for MEDLINE]

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PMID: 15113405 [PubMed - indexed for MEDLINE]

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