Istrail2010
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