Graph-theoretic topological control of biological genetic networks
Anil Aswani, Nicholas Boyd, Claire Tomlin

Citation
Anil Aswani, Nicholas Boyd, Claire Tomlin. "Graph-theoretic topological control of biological genetic networks". ACC 2009, 1700–1705, 10, June, 2009.

Abstract
The control of biological genetic networks is an important problem. If the system is abstracted into a graph, then the affect of drugs, pharmaceuticals, and gene therapy can be abstracted as changing the topology of the graph. We consider the control objective of removing the stable oscillations of the genetic network. This control is done using several theorems relating the topology of the network to the dynamics of the system. These theorems suggest that the controller should remove all the negative feedback in the networks.We prove that the problem of minimizing the edges and vertices to remove, in order to remove negative feedback, is NP-hard. In light of this result, a heuristic algorithm to solve this graph problem is presented. The algorithm is applied to several genetic networks, and it is shown that the heuristic gives reasonable results. Additionally, we consider the p53 network and show that the algorithm gives biologically relevant results.

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Citation formats

• HTML

  Anil Aswani, Nicholas Boyd, Claire Tomlin. <a
  href="http://chess.eecs.berkeley.edu/pubs/605.html"
  >Graph-theoretic topological control of biological
  genetic networks</a>, ACC 2009, 1700–1705, 10,
  June, 2009.

• Plain text

  Anil Aswani, Nicholas Boyd, Claire Tomlin.
  "Graph-theoretic topological control of biological
  genetic networks". ACC 2009, 1700–1705, 10,
  June, 2009.

• BibTeX

  @inproceedings{AswaniBoydTomlin09_GraphtheoreticTopologicalControlOfBiologicalGenetic,
      author = {Anil Aswani and Nicholas Boyd and Claire Tomlin},
      title = {Graph-theoretic topological control of biological
                genetic networks},
      booktitle = {ACC 2009},
      pages = {1700–1705},
      day = {10},
      month = {June},
      year = {2009},
      abstract = {The control of biological genetic networks is an
                important problem. If the system is abstracted
                into a graph, then the affect of drugs,
                pharmaceuticals, and gene therapy can be
                abstracted as changing the topology of the graph.
                We consider the control objective of removing the
                stable oscillations of the genetic network. This
                control is done using several theorems relating
                the topology of the network to the dynamics of the
                system. These theorems suggest that the controller
                should remove all the negative feedback in the
                networks.We prove that the problem of minimizing
                the edges and vertices to remove, in order to
                remove negative feedback, is NP-hard. In light of
                this result, a heuristic algorithm to solve this
                graph problem is presented. The algorithm is
                applied to several genetic networks, and it is
                shown that the heuristic gives reasonable results.
                Additionally, we consider the p53 network and show
                that the algorithm gives biologically relevant
                results.},
      URL = {http://chess.eecs.berkeley.edu/pubs/605.html}
  }
  

Posted by Anil Aswani on 17 Jun 2009.
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