Melvin's digital garden


CREATED: 200808140303 Title: The Regulatory Genome and the Computing: Theory and Practice

Joint work with Erik Davidson

** CYRENE Project The Gene Naming Problem

  • translation table approach
  • “the fight for data”

The Sequence Bottleneck Problem

  • how to represent the binding sites
  • consensus sequence not good enough

The Logic Inference Problem

  • how to determine the logic of cis regulation from experiments

** Sea Urchin: genome, transcriptome, logicome

The sea urchin provided fundamental insights into basic biology

The logicome

  • combinatorial logic functions
  • and, short range repression, switch toggle, etc

The regulatory genome and the computer (ref Von Neumann’s book)

Example of Rube Goldberg’s pencil sharpener

The cis-trans embrace, cis = DNA, trans = transcription factor

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