User:Yiannis Kaznessis

From OpenWetWare
Revision as of 08:24, 8 November 2008 by Yiannis Kaznessis (talk | contribs) (Contact Info)
Jump to: navigation, search

I am a new member of OpenWetWare!

Contact Info

  • Yiannis Kaznessis
  • Department of Chemical Engineering and Materials Science
  • University of Minnesota
  • 421 Washington Ave SE
  • Minneapolis, MN 55455, USA
  • Email me through OpenWetWare

In my group we are interested in computational synthetic biology. We are developing the Synthetic Biology Software Suite, a publicly available software suite that assists in rationally designing synthetic gene regulatory networks. We combine components from BioBricks to generate networks of biomolecular reactions. We combine stochastic-discrete, stochastic-continuous and continuous-deterministic models to simulate these reaction networks. Version 1.0.1 is available on [1]. We are now incorporating the connection with BioBricks.

In recent work, we developed multiscale models of gene regulatory networks with synthetic biology applications.Simulations have been used that model all biomolecular interactions in transcription, translation, regulation, and induction of gene regulatory networks, guiding the design of synthetic systems.

We are also participating in the iGEM competition. We are developing computer-aided designs of a comparator, an important component of control systems and implementing them in the lab[2].


  • 1999, PhD, University of Notre Dame
  • 1994, BS, Aristotle University in Thessaloniki

Research interests

  1. Statistical mechanics (yes, it can be fun!)
  2. Synthetic biology
  3. Computer simulations

Computational Synthetic Biology Publications

  1. Kaznessis YN. Models for synthetic biology. BMC Syst Biol. 2007 Nov 6;1:47. DOI:10.1186/1752-0509-1-47 | PubMed ID:17986347 | HubMed [Paper1]
  2. Sotiropoulos V and Kaznessis YN. An adaptive time step scheme for a system of stochastic differential equations with multiple multiplicative noise: chemical Langevin equation, a proof of concept. J Chem Phys. 2008 Jan 7;128(1):014103. DOI:10.1063/1.2812240 | PubMed ID:18190181 | HubMed [Paper2]
  3. Sotiropoulos V and Kaznessis YN. Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes. BMC Syst Biol. 2007 Jan 9;1:7. DOI:10.1186/1752-0509-1-7 | PubMed ID:17408514 | HubMed [Paper3]
  4. Salis H and Kaznessis YN. Computer-aided design of modular protein devices: Boolean AND gene activation. Phys Biol. 2006 Dec 22;3(4):295-310. DOI:10.1088/1478-3975/3/4/007 | PubMed ID:17200605 | HubMed [Paper4]
  5. Tomshine J and Kaznessis YN. Optimization of a stochastically simulated gene network model via simulated annealing. Biophys J. 2006 Nov 1;91(9):3196-205. DOI:10.1529/biophysj.106.083485 | PubMed ID:16920827 | HubMed [Paper5]
  6. Salis H, Sotiropoulos V, and Kaznessis YN. Multiscale Hy3S: hybrid stochastic simulation for supercomputers. BMC Bioinformatics. 2006 Feb 24;7:93. DOI:10.1186/1471-2105-7-93 | PubMed ID:16504125 | HubMed [Paper6]
  7. Salis H and Kaznessis YN. An equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks. J Chem Phys. 2005 Dec 1;123(21):214106. DOI:10.1063/1.2131050 | PubMed ID:16356038 | HubMed [Paper7]
  8. Salis H and Kaznessis Y. Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions. J Chem Phys. 2005 Feb 1;122(5):54103. DOI:10.1063/1.1835951 | PubMed ID:15740306 | HubMed [Paper8]
  9. Tuttle LM, Salis H, Tomshine J, and Kaznessis YN. Model-driven designs of an oscillating gene network. Biophys J. 2005 Dec;89(6):3873-83. DOI:10.1529/biophysj.105.064204 | PubMed ID:16183880 | HubMed [Paper9]
All Medline abstracts: PubMed | HubMed

Useful links