Ph.D., Massachusetts Institute of Technology, 2001
Metabolic engineering with emphasis in metabolic flux analysis and metabolic profiling, functional genomics, mathematical modeling of biological networks, quantitative systems biology.
Current Research Projects
Quantitative Systems Biology of the Plant Arabidopsis thaliana
In April 2007, Dr. Klapa graduated two Ph.D. students who had been working since 2002-2003 in analyzing the transcriptional and metabolic, respectively, profile of Arabidopsis thaliana liquid culture system under various environmental stresses using cDNA microarrays and Gas Chromatography-Mass Spectrometry. This study lead to two US Patent applications, while the metabolomic methodology that was developed received the "Outstanding Invention of 2005" in the Information Sciences award from the Office of Technology Commercialization of University of Maryland.
Metabolic Engineering and Systems Biology Laboratory at the Institute of Chemical Engineering and High-Temperature Chemical Processes of the Foundation for Research and Technology-Hellas (FORTH/ICE-HT)
The research of Dr. Klapa's lab at FORTH/ICE-HT focuses on (a) the experimental and computational analysis of metabolic networks with emphasis in methodology development for metabolic flux quantification and Gas Chromatography-Mass Spectrometry (GC-MS) metabolomics (it is actually the first and currently only laboratory in Greece and South-Eastern Europe that develops and uses this analytical platform), (b) quantitative systems biology with
emphasis in the integrated analyses of high-throughput "omic" data from various levels of cellular function, and (c) mathematical modeling of biological systems.
Outside Research Projects:
Dr. Klapa is the PI of a contract with Bayer HealthCare, Berkeley, CA, USA on metabolomics in cell culture engineering and has coordinated a U.S.-NSF project on integrated transcriptomics and metabolomics. She is or has been a partner/member in 1 GSRT ESPA-Collaboration project, 1 EC-FP6-ICT Integrated Project, 1 EC-FP7-HEALTH Large-Scale Project, 1 EC-FP6-Life Long Learning Project and the EC-FP6 European Network of Excellence in Nanobiotechnology, Nano2Life. She is also an external collaborator of the University of Patras Interdepartmental Network on Research and Applications in Medical Molecular Genetics.
Honors and Awards
Postdoctoral Fellow, Functional Genomics, The Institute for Genomics Research (TIGR), 2002
Postdoctoral Research Associate, Chemical Engineering, Massachusetts Institute of Technology (MIT), 2001
- Associate Member of the American Institute of Chemical Engineers (AIChE)
- Member of the American Chemical Society (ACS)
- Member of the American Association for the Advancement of Science (AAAS)
- Member of the American Society of Plant Biologists (ASPB)
- Associate Member of the Sigma Xi Research Society
- Member of the American Mathematical Society (AMS)
- Member of the Hellenic Society of Chemical Engineers (ΠΣΧΜ)
- Member of the Technical Chamber of Greece (Τ.Ε.Ε.)
- Member of the Hellenic Society of Biochemistry and Molecular Biology (HSBB)
- Member of the Hellenic Society of Neurosciences (HSN)
Β. Dutta, R. Snyder and M.I. Klapa. 2007. Significance analysis of time-series transcriptomic data: A methodology that enables the identification and further exploration of the differentially expressed
genes at each time-point. Biotecnology and Bioengineering (Ιn Print) (published online on March 29 2007 - DOI: 10.1002/bit.21432)
Ι.C. Tsandili, M.N. Karim, M. I. Klapa. 2007. Quantifying the Metabolic Capabilities of the Engineered Zymomonas mobilis using Linear Programming Analysis. Microbial Cell Factories 6:8.
Η. Κanani and M.I. Klapa. 2007. Data Correction Strategy for Metabolomics Analysis Using Gas Chromatography-Mass Spectrometry, Metabolic Engineering 9: 39-51 (published online August 18, 2006 doi:10.1016/j.ymben.2006.08.001)
K. Lai and M.I Klapa. 2004. Alternative pathways of galactose assimilation: Could Inverse Metabolic Engineering provide an alternative for galactosemic patients? Metab Eng. 6:239-44.
Klapa M.I. and Quackenbush J. 2003. The quest for the mechanisms of life (submitted to Biotechnology and Bioengineering for the special issue on Systems Biology and Bioinformatics)
Klapa, M.I., Aon, J.C. and Stephanopoulos, Gregory 2003. Systematic quantification of complex metabolic flux networks using stable isotopes and mass spectrometry (in press in European Journal of Biochemistry).
Klapa, M.I., Aon, J.C. and Stephanopoulos, Gregory. 2003. Using ion trap Mass Spectrometry in combination with gas chromatography for high resolution metabolic flux determination Biotechniques 34:832-40.
Saeed A.I., Sharov V., White J., Li J., Liang W., Bhagabati N., Braisted J., Klapa M., Currier T., Thiagarajan M., Sturn A., Snuffin M., Rezantsev A., Popov D., Ryltsov A., Kostukovich E., Borisovsky I., Liu Z., Vinsavich A., Trush V, and Quackenbush J. 2003. TM4: A Free, Open Source System for Microarray Data Management and Analysis. BioTechniques 34:374-378.
Varela C., Agosin E., Baez M., Klapa M. and Stephanopoulos G. 2003. Metabolic flux redistribution in Corynebacterium glutamicum in response to osmotic stress. Appl Microbiol Biotechnol 60:547-555.
Klapa M.I., Park S.M., Sinskey A.J., Stephanopoulos G.N. 1999. Metabolite and isotopomer balancing in the analysis of metabolic cylces: I. Theory. Biotechnol Bioeng. 62: 375-391.
Park S.M., Klapa M.I., Sinskey A.J., Stephanopoulos G.N. 1999. Metabolite and isotopomer balancing in the analysis of metabolic cylces: II. Applications. Biotechnol Bioeng. 62: 392-401.
M.I. Klapa. 2007. Metabolic Flux Analysis in Metabolic Pathway Engineering Handbook, Christina Smolke (ed.), CRC Press, scheduled to be published on 15/2/2008 (submitted/invited contribution).
H. Kanani, B. Dutta, J. Quackenbush and M.I. Klapa. 2007. Time-series integrated high- throughput transcriptomic and metabolomic profiling analyses; Short-term effect of elevated CO2 levels on Arabidopsis thaliana primary metabolism: A case-study (Chapter 7), in Concepts in Plant Metabolomics, Nikolau B. and Wurtele E. (eds), Springer-Verlag (invited contribution).
Klapa M.I., and Stephanopoulos, Gregory. 2000. Metabolic Engineering: A Framework for the Integration of Genomic and Physiological Data. In: Barbotin/Portais (eds) NMR in Microbiology: Theory and Applications. Horizon Scientific Press, UK, pp. 453-477.
Klapa M.I. and Stephanopoulo,s Gregory. 2000. Metabolic Flux Analysis. In: Schugerl/Bellgardt (eds) Bioreaction Engineering: Modeling and Control, Springer, Berlin Heidelberg New York.
Ι.C. Tsandili, M.N. Karim, M. I. Klapa. 2007. Quantifying the Metabolic Capabilities of Zymomonas mobilis using Linear Programming Analysis. Proceedings of the Conference "Foundations of Systems Biology in Engineering (FOSBE) 2007.
C. H. Syriopoulos, A. Panayotarou, C. Katsikani, P. Patiou, B. Pesheva, K. Lai and M. I. Klapa. 2007. In vivo analysis of galactosemia using yeast as the model system. Proceedings of the 6th Hellenic Conference in Chemical Engineering, Volume B, pp.1109-1112.
M.A. Kostourou, G.N. Koumoundouros, C.N. Flytzanis and M.I. Klapa. 2007. Metabolomic analysis of adult male and female zebrafish for the identification of sex-determining metabolic
biomarkers using gas chromatography-mass spectrometry. Proceedings of the 6th Hellenic Conference in Chemical Engineering, Volume B, pp.1121-1124 (in Greek).
Ι.C.Tsandili, M.N. Karim, M.I. Klapa. 2007. Evaluating the Metabolic Boundaries of the Genetically Engineered Zymomonas mobilis using Linear Programming. Proceedings of the 6th Hellenic Conference in Chemical Engineering, Volume B, pp.1153-1156.
M.I. Klapa and Gregory Stephanopoulos, Design of Isotopic-Tracer Experiments for Flux Quantification, Metabolic Engineering Conference, Elmau, Germany, 25-30 October, 1998.
Eduardo Agosin, Maria I. Klapa and Gregory Stephanopoulos, Metabolic Flux Redistribution in Response to Osmotic Stress in Corynebacterium glutamicum, Metabolic Engineering Conference, Elmau, Germany, 25-30 October, 1998.
M.I. Klapa, S.K. Rijhwani and Gregory Stephanopoulos, Design of Isotopic-Tracer Experiments for Flux Quantification, 1998 AIChE Annual Meeting, Session: Advances in Metabolic Engineering, Miami, Florida, 15-20 November 1998.
Eduardo Agosin, Maria I. Klapa, Cristian Varela and Gregory Stephanopoulos, Metabolic Flux Redistribution in Response to Osmotic Stress in Corynebacterium glutamicum, IXth International conference on bacteriology and Applied Microbiology, IUMS, Sydney, Australia 16-20 August 1999.
M.I. Klapa and Gregory Stephanopoulos, Observability and Redundancy Classification in Complex Metabolic Networks, 2000 ASBMB/ASPET joint Satellite and Annual Meeting, Session: Modeling of Cellular Networks, Boston, MA, 3-8 June 2000.
M.I. Klapa, J.C.Aon and Gregory Stephanopoulos, Quantification of Corynebacterium glutamicum metabolic flux network using stable isotopes and Mass Spectrometry, 2000 AIChE Annual Meeting, Session: Advances in Bioinformatics, Los Angeles, CA, 12-17 November 2000.
M.I. Klapa, J.C. Aon and Gregory Stephanopoulos, Measurement of Mass Isotopomer Fractions by Gas Chromatography- Mass Spectrometry for High Resolution Metabolic Flux Quantification, 2001 AIChE Annual Meeting, Session: Advances in Metabolic Engineering: From Genomics to Pathways, Reno, NV, 4-9 November 2001.
M.I. Klapa, J.C. Aon and Gregory Stephanopoulos, Quantifying the effect of different carbon sources on the Corynebacterium glutamicum physiology using flux analysis and mass spectrometry, 2002 ΑCS Annual Meeting, Session: Bioinformatics, Genomics and Proteomics, August 18-25, 2002, Boston, MA.
Chair of the workshop on experimental techniques and the challenge of multiplexing in Metabolic Engineering Conference IV, October 2002, Tuscany, Italy.
Chair of the session Metabolic Engineering and Bioinformatics II: Scope and Future of Metabolic Engineering (panel discussion), Bioinformatics Topical Conference, AIChE Annual Meeting, 3-8 November 2002, Indianapolis, Indiana, USA.
Chair of the session Metabolic Engineering and Bioinformatics I: Perspectives and Applications, Bioinformatics Topical Conference, AIChE Annual Meeting, 3-8 November 2002, Indianapolis, Indiana, USA.