Design and implementation of three incoherent feed-forward motif based biological concentration sensors

No abstract is available for this paper.

• Publication year

  2007

• Venue

  Journal of Systems and Synthetic Biology

• Publication date

  2007-11-01

• Fields of study

  Biology, Chemistry, Computer Science, Engineering, Medicine

• Identifiers
  DOI 10.1007/s11693-007-9008-6PMID 19003446PMCID PMC2398716
• 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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  2002influential reference
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  2000cited by this paper
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