Computational methods in synthetic biology

Yiannis N. Kaznessis

Research output: Contribution to journalReview articlepeer-review

15 Scopus citations


We discuss how a theoretical synthetic biology research programme may liberate empiricism in biological sciences beyond the unaided human brain. Because synthetic biological systems are relatively small and largely independent of evolutionary contexts, they can be represented with mathematical models strongly founded on first principles of molecular biology and laws of statistical thermodynamics. A universal mathematical formalism for describing synthetic constructs may then be plausibly used to explain in unambiguous, quantitative terms how biological phenotypic complexity emerges as a result of well-defined biomolecular interactions. SynBioSS, a publicly available software package, is described that implements this mathematical formalism.

Original languageEnglish (US)
Pages (from-to)1392-1405
Number of pages14
JournalBiotechnology Journal
Issue number10
StatePublished - Oct 2009
Externally publishedYes


  • Biochemical networks
  • Hybrid stochastic simulation
  • Markov processes
  • Stochastic chemical kinetics
  • SynbioSS


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