User:Yiannis Kaznessis: Difference between revisions
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*[[Special:Emailuser/Yiannis Kaznessis|Email me through OpenWetWare]] | *[[Special:Emailuser/Yiannis Kaznessis|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. | 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 [http://synbioss.sourceforge.net/]. We are now incorporating the connection with BioBricks. | ||
In recent work, | 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== | ==Education== | ||
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==Research interests== | ==Research interests== | ||
<!-- Feel free to add brief descriptions to your research interests as well --> | <!-- Feel free to add brief descriptions to your research interests as well --> | ||
# | # Statistical mechanics (yes, it can be fun!) | ||
# | # Synthetic biology | ||
# | # Computer simulations | ||
==Publications== | ==Computational Synthetic Biology Publications== | ||
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<biblio> | <biblio> | ||
#Paper1 pmid= | #Paper10 pmid=19830714 | ||
#Paper2 pmid= | #Paper11 pmid=19644174 | ||
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# | #Paper1 pmid=17986347 | ||
#Paper2 pmid=18190181 | |||
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#Paper8 pmid=15740306 | |||
#Paper9 pmid=16183880 | |||
</biblio> | </biblio> | ||
Latest revision as of 08:49, 18 December 2009
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
- Statistical mechanics (yes, it can be fun!)
- Synthetic biology
- Computer simulations
Computational Synthetic Biology Publications
- Kaznessis YN. Computational methods in synthetic biology. Biotechnol J. 2009 Oct;4(10):1392-405. DOI:10.1002/biot.200900163 |
- 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 |
- 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 |
- Kaznessis YN. Models for synthetic biology. BMC Syst Biol. 2007 Nov 6;1:47. DOI:10.1186/1752-0509-1-47 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |
