Understanding Science Through the Lens of Computation. Richard M. Karp Nov. 3, 2007. The Power of the Computational Perspective . Exposes the computational nature of natural processes and provides a language for their description.
Richard M. Karp
Nov. 3, 2007
Left Middle Right
Top 0/0 1,2 2,1
Middle 2,1 0.0 1,2
Bottom 1,2 2,1 0,0
The eukaryotic cell
“We can approach understanding how the whole genome works by breaking it down into groups of genes that interact strongly with each other. Once researchers identify and understand these network modules, the next step will be to figure out the interactions within networks of networks, and so on until we eventually understand how the whole genome works, many years from now. ”
“ Regulatory interactions mandated by circuitry encoded in the genome determine whether each gene is expressed in each cell, throughout developmental space and time, and, if so, at what amplitude.” Eric Davidson
M: AAAAGAGTCAOccurrences of A Motif
Signaling and regulatory pathways and protein complexes consist of genes, proteins and small molecules ``wired’’ together in a complex network of intermolecular interactions.
Two proteins interact if they bind to each other or one of them binds to the control regions of the other’s gene.
Many complexes and pathways are conserved – they have evolved over evolutionary time and occur, in modified forms, in many organisms.
Our goal: using databases of protein-protein interactions in several species, in conjunction with data about protein sequence, structure, function and expression, identify conserved protein complexes and signaling pathways.
Discovery of conserved pathways and complexes allows transfer of functional annotation and prediction of interactions from one species tto another.
Kelley et al. PNAS 2003
Sharan et al. RECOMB 2004
173 complexes associated with:
DNA, RNA and phosphorus metabolism
regulation of transcription
protein folding, synthesis and degradation
cell proliferation, development and growth