CEMS Faculty
Diploma, Chemical Engineering, Aristotle University of Thessaloniki, 1994
Ph.D., Chemical Engineering, University of Notre Dame, 1999
Research Areas
Biotechnology and Bioengineering
Theory and Computation
The completion of the Human Genome Project is a magnificent milestone for
humankind. It is, however, merely the harbinger of a revolution in
biomedicine that will drastically benefit the health of humans. The
deciphering of principles that guide nature to express itself from protein
sequence to structure and function, and then on to protein-protein
interactions, and to the circuitry of cells, will not only provide us with
deep understanding of the secrets of life, but will also allow us to control
such biological phenomena as cell differentiation and cell death.
Our research efforts integrate biophysical
computations and synthetic biology methods for characterizing and engineering
biomolecular systems. From molecules, such as antimicrobial peptides, to gene regulatory networks, such as novel bio-logical AND gates, we are developing model-driven designs that are experimentally realizable with exciting biotechnological and biomedical applications.
Selected Publications
| Computer-aided design of modular protein devices: Boolean AND gene activation. (with H. Salis) Physical Biology, 3(4):295-310. (2006)
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| Driving engineering of novel antimicrobial peptides from simulations of peptide-micelle interactions. (with H. Khandelia and A. Langham) Biochim Biophys Acta. 1758(9):1224-34. (2006) |
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| Retrocyclins kill bacilli and germinating spores of Bacillus anthracis and inactivate anthrax lethal toxin. (with Wang, Mulakala, et al.) J Biol Chem. 281(43):32755-64. (2006) |
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| Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes (with V. Sotiropoulos) BMC Systems Biology, 1:7, (2007) |
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| Accurate Hybrid Stochastic Simulation of a System of Coupled Chemical or Biochemical Reactions (with H. Salis) Journal of Chemical Physics, 122, 054103 (2005) |
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| Molecular Dynamics Simulations of the N-terminus of HIV GP-41 Fusion Peptide in SDS Micelles (with A. Langham) Journal of Peptide Science, 14( 2): 316-328 (2005) |
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| Inferring Gene Regulatory Relationships by Combining Target-Target Pattern Recognition and Regulator-Specific Motif Examination (with H. Wei) Biotechnology and Bioengineering, Vol. 89(1), p. 52-77, (2005) |
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| Prediction of distant residue contacts with the use of evolutionary information (with S. Vicatos and V.B. Reddy) Proteins, Bioinformatics, Structure and Genetics, 58 (4): 935-49 (2005) |
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Current Research Staff
John Barrett, Konstantinos Biliouris, Dan Bolintineanu, Anushree Chatterjee, Andrew Hirsch, Jayne Linstad, Joel Paustian, Abdallah Sayyed Ahmad, Patrick Smadbeck, Poonam Srivastava, Bennett Swiniarski, Katherine Volzing, Ling Wu
