A single-cell atlas of bobtail squid visual and nervous system highlights molecular principles of convergent evolution

No abstract is available for this paper.

• Publication year

  2022

• Venue

  bioRxiv

• Publication date

  2022-05-28

• Fields of study

  Biology

• Identifiers
  DOI 10.1101/2022.05.26.490366
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

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• The octopus genome and the evolution of cephalopod neural and morphological novelties

  2015influential reference
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• Molecular Evidence for Convergence and Parallelism in Evolution of Complex Brains of Cephalopod Molluscs: Insights from Visual Systems.

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• The Sequence Alignment/Map format and SAMtools

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• Guidelines for Proper Conduct of Animal Experiments by the Science Council of Japan

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