Computational methods in synthetic biology: towards computer-aided part design

Curr Opin Chem Biol. 2012 Aug;16(3-4):318-22. doi: 10.1016/j.cbpa.2012.05.003. Epub 2012 Jun 20.


A number of computational tools have been developed for composing synthetic gene circuits, managing workflows, and simulating their behavior. Less attention has been directed towards the underlying parts that go into these designs. New computational approaches nonetheless are being developed for engineering these parts and relating their underlying DNA or amino-acid sequences to functional parameters. These approaches range from detailed mechanistic models to simple ones based on statistical correlations. The challenges will be to integrate the disparate tools into a common framework for the computer-aided design of synthetic gene circuits.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Base Sequence
  • Computational Biology / methods*
  • Gene Regulatory Networks / genetics
  • Genetic Engineering / methods*
  • Promoter Regions, Genetic / genetics
  • Protein Biosynthesis / genetics
  • Transcription Factors / metabolism


  • Transcription Factors