A prior-based integrative framework for functional transcriptional regulatory network inference
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Title
A prior-based integrative framework for functional transcriptional regulatory network inference
Authors
Keywords
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Journal
NUCLEIC ACIDS RESEARCH
Volume -, Issue -, Pages gkw963
Publisher
Oxford University Press (OUP)
Online
2016-10-12
DOI
10.1093/nar/gkw963
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- (2013) S. Roy et al. GENOME RESEARCH
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- (2011) C. G. de Boer et al. NUCLEIC ACIDS RESEARCH
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