A map of cis-regulatory elements and 3D genome structures in zebrafish

No abstract is available for this paper.

• Publication year

  2020

• Venue

  Nature

• Publication date

  2020-11-25

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1038/s41586-020-2962-9PMID 33239788PMCID PMC8183574
• 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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  2017cited by this paper
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  2017cited by this paper
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