DiplEng, University of Patras (Greece) MS. PhD, California Institute of Technology Functional genomics; mathematical and computational  biotechnology; bioinformatics

Dr. Hatzimanikatis has moved: he is now a member of the faculty at EPFL (Ecole Polytechnique Fédérale de Lausanne) in Lausanne, Switzerland.

Research Group Web Site at Northwestern University
Faculty Site at EPFL

Functional genomics

Advances in analytical methods and development of sophisticated techniques and instrumentation have provided the tools for collecting a broad spectrum of biological information, from DNA sequence to simultaneous quantitative monitoring of cellular processes. The availability of this information has significantly contributed to the development of functional genomics, an interdisciplinary field for the study and the identification of the function of the genes and their products in the context of cellular systems as living entities. Our work in the area of functional genomics involves the development of mathematical and computational frameworks for the analysis of the large-scale data on various cellular processes and from different organisms. These frameworks are tailored to the type and the origin of this information.

Mathematical and Computational Biotechnology

We employ systems engineering methods for the study of cellular processes. We develop first-principles mathematical models of transcription, translation, signal transduction and biotransformation networks and we perform theoretical and computational studies for the identification of the systemic properties of these processes. Our goal is to understand the design principles of these systems and to develop approaches for cellular engineering.

Bioinformatics

Computer science, statistics, and biology gave birth to bioinformatics as a new discipline for management and analysis of biological information. Early efforts in bioinformatics involved the design and integration of DNA sequence databases and the prediction of the function of a gene based on comparison of its sequence with sequences of genes with known function. We are developing algorithms and methods for the identification of DNA sequence domains that are involved in the regulation of transcription and translation. Our objective is the prediction of certain kinetic properties of the cellular processes from DNA sequence information.

Recent Publications

"Mathematical Modeling of the Eukaryotic Heat Shock Response: Dynamics of the hsp70 Promoter", T. R. Rieger, R. I. Morimoto and V. Hatzimanikatis, Biophysical Journal, 88 (3), 1646-1658 Supplementary Material (2005).

"Exploring the diversity of complex metabolic networks", V. Hatzimanikatis, C. Li, J. A. Ionita, C.S. Henry, M. D. Jankowski, and L. J. Broadbelt, Bioinformatics, 21 (8) 1603-1609 Supplementary Material (2005).

"Theoretical Considerations and Computational Analysis of the Complexity in Polyketide Synthesis Pathways", Joanna Gonzalez, Linda Broadbelt, and Vassily Hatzimanikatis, Journal of the American Chemical Society, 127 (27) 9930-9938 (2005).

"Computational Discovery of Biochemical Routes to Specialty Chemicals", C. Li, J. A. Ionita, C.S. Henry, M. D. Jankowski, V. Hatzimanikatis and L. J. Broadbelt, Chemical Engineering Science, 59 (22-23), 5051-5060 (2004).

"Metabolic control analysis under uncertainty: framework development and case studies", Liqing Wang, Inanc Birol, and Vassily Hatzimanikatis, Biophysical Journal, 87(6), 3703-3715 Supplementary Material (2004).

"A model-based optimization framework for the inference on gene regulatory networks from DNA array data", Reuben Thomas, Sanjay Mehrotra, Eleftherios T. Papoutsakis, Vassily Hatzimanikatis, Bioinformatics, 20(17),3221 - 3235 (2004).

"Metabolic networks: enzyme function and metabolite structure", Vassily Hatzimanikatis, Chunhui Li, Justin A Ionita and Linda J Broadbelt, Current Opinion in Structural Biology, 14, 300-306 (2004).

Prof. Vassily Hatzimanikatis
Department of Chemical and Biological Engineering
Northwestern University
2145 Sheridan Road
Evanston, IL 60208-3120

tel: 847/491-5357
fax: 847/491-3728
E-mail Professor Hatzimanikatis