User:Yiannis Kaznessis

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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 1.0.2 is available on Sourceforge.net [1]. We are now incorporating the connection with BioBricks.

In recent work (Ramalingam, KI, Tomshine, JR, Maynard, JA, Kaznessis YN. " Forward engineering of synthetic bio-logical AND gates" Biochemical Engineering Journal, 2009, 47(1-3):38-47), we used multiscale models of gene regulatory networks to design, build and test bio-logical AND gates.

We are also participating in the iGEM competition. We were awarded a Gold Medal in 2009 for SynBioSS work.

Education

• 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. Computational methods in synthetic biology. Biotechnol J. 2009 Oct;4(10):1392-405. DOI:10.1002/biot.200900163 |
2. Sotiropoulos V, Contou-Carrere MN, Daoutidis P, and Kaznessis YN. Model reduction of multiscale chemical langevin equations: a numerical case study. IEEE/ACM Trans Comput Biol Bioinform. 2009 Jul-Sep;6(3):470-82. DOI:10.1109/TCBB.2009.23 |
3. Hill AD, Tomshine JR, Weeding EM, Sotiropoulos V, and Kaznessis YN. SynBioSS: the synthetic biology modeling suite. Bioinformatics. 2008 Nov 1;24(21):2551-3. DOI:10.1093/bioinformatics/btn468 |
4. Kaznessis YN. Models for synthetic biology. BMC Syst Biol. 2007 Nov 6;1:47. DOI:10.1186/1752-0509-1-47 |
5. 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 |
6. 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 |
7. 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 |
8. 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 |
9. 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 |
10. 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 |
11. 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 |
12. 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 |

Useful links

• Introductory tutorial
• OpenWetWare help pages