Pathway analysis of high-throughput biological data within a Bayesian network framework

No abstract is available for this paper.

• Publication year

  2011

• Venue

  Bioinform.

• Publication date

  2011-06-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/btr269PMID 21551144
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2007influential reference
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  2006cited by this paper
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  1995cited by this paper
• Controlling the false discovery rate: a practical and powerful approach to multiple testing

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