Arabidopsis Ensemble Reverse-Engineered Gene Regulatory Network Discloses Interconnected Transcription Factors in Oxidative Stress[W]

No abstract is available for this paper.

• Publication year

  2014

• Venue

  The Plant Cell

• Publication date

  2014-12-01

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1105/tpc.114.131417PMID 25549671PMCID PMC4311199
• 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.

• Resource: A comprehensive catalogue of human RNA-binding protein reagents

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