Publications

2007
2006
2005
2004
2003
2002
2000
1999
1998
1997
1996
1995
1993

2007

"A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data", Reuben Thomas, Carlos J. Paredes, Sanjay Mehrotra, Eleftherios T. Papoutsakis and Vassily Hatzimanikatis, BMC Bioinformatics, in press (2007)

"A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1261 ORFs and thermodynamic information", Adam M. Feist, Chris S. Henry, Jennifer L. Reed, Markus Krummenacker, A. R. Joyce, Peter D. Karp, Linda J. Broadbelt, Vassily Hatzimanikatis, and Bernhard O. Palsson, Molecular Systems Biology, In press (2007)

"Thermodynamics-Based Metabolic Flux Analysis", Christopher Henry, Linda Broadbelt, and Vassily Hatzimanikatis, Biophysical Journal, 92 (7) 1792-1805 (2007)

"A model for protein translation: Polysome self-organization leads to maximum protein synthesis rates", Hermioni Zouridis and Vassily Hatzimanikatis, Biophysical Journal, 92 (7) 717-730 (2007)

2006

" Analysis of the Maximum Theoretical Yield for the Synthesis of Erythromycin Precursors in Escherichia coli", Joanna Gonzalez-Lergier, Linda J. Broadbelt and Vassily Hatzimanikatis, Biotechnology and Bioengineering, (95) 4, 638-644 (2006)

" Metabolic Engineering under Uncertainty. I: Framework Development", Liqing Wang, and Vassily Hatzimanikatis, Metabolic Engineering, 8 (2), 133-141 (2006)

" Metabolic Engineering under Uncertainty. II: Analysis of Yeast Metabolism", Liqing Wang, and Vassily Hatzimanikatis, Metabolic Engineering, 8 (2), 142-159 (2006)

"An algorithmic framework for genome-wide modeling and analysis of translation networks", Amit Mehra and Vassily Hatzimanikatis, Biophysical Journal, 90 (4), 1136-1146 (2006)

"Genome Scale Thermodynamic Analysis of E. coli metabolism", C.S. Henry, M.D. Jankowski, L.J. Broadbelt, and V. Hatzimanikatis, Biophysical Journal, 90 (4), 1453-1461 (2006)

"Bistability Explains Threshold Phenomena in Protein Aggregation Both in vitro and in vivo", T. R. Rieger, R. I. Morimoto and V. Hatzimanikatis, Biophysical Journal, 90 (3), 886-895 (2006)

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)

"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)

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)

"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)

"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)

2003

" Insights Into the Relation Between mRNA and Protein Expression Patterns: I. Theoretical Considerations ", Amit Mehra, Kelvin H. Lee, and Vassily Hatzimanikatis, Biotechnology & Bioengineering, 84(7), 822-833 (2003)

" Insights Into the Relation Between mRNA and Protein Expression Patterns: II. Experimental Observations in Escherichia coli ", Pat S. Lee, Leah B. Shaw, Leila H. Choe, Amit Mehra, Vassily Hatzimanikatis, and Kelvin H. Lee, Biotechnology & Bioengineering, 84(7), 836-841 (2003)

2002

"A memorial review of Jay Bailey's contribution in prokaryotic metabolic engineering", V. Hatzimanikatis and J.C. Liao, Biotechnology & Bioengineering, 79(5), 504-508 (2002)

"Jay Bailey as mentor - The students' perspective", K. F. Reardon, K. H. Lee, K. D. Wittrup, and V. Hatzimanikatis, Biotechnology & Bioengineering, 79(5), 484-489 (2002)

"Editorial Overview - Biochemical Engineering", K.H. Lee and V. Hatzimanikatis, Current Opinion in Biotechnology, 13: 85-86 (2002)

"The Integration of Proteomic, Genechip and DNA Sequence Data", L. Shaw, V. Hatzimanikatis, A. Mehra, and K.H. Lee, Protein Arrays, Biochips, and Proteomics: The Next, J. Albala and I. Humphrey-Smith, eds. Marcel-Dekker (2002)

2000

"Bioinformatics, Genomics, and the Chemical Engineer: A perspective", V. Hatzimanikatis, D. Collins, S. Browning, and K.H. Lee, Chemical Engineering Education, 34(4), 346-349 (2000)

"Bioinformatics and Functional Genomics: Challenges and Opportunities", V. Hatzimanikatis, AIChE Journal, 46(12), 2340-2343 (2000)

1999

"A Mathematical Description for the G1-S Transition of the Mammalian Cell Cycle", V. Hatzimanikatis, K.H. Lee, and J.E. Bailey, Biotechnology & Bioengineering, 65(6), 631-637 (1999)

"Nonlinear Metabolic Control Analysis", V. Hatzimanikatis, Metabolic Engineering, 1(1), 75-87 (1999)

"Proteomics: Theoretical and Experimental Considerations", V Hatzimanikatis, L.H. Choe, and K.H. Lee, Biotechnology Progress, 15(3), 312-318 (1999)

"Modeling molecular mechanisms within cellular environment", Hatzimanikatis and J.E. Bailey, J. Biotechnology, 71, 263-265 (1999)

"Dynamical Analysis of Gene Networks Requires Both mRNA and Protein Expression Information", V. Hatzimanikatis and K.H. Lee, Metabolic Engineering, 1(4), 275-281 (1999)

1998

"Application of Mathematical Tools for Metabolic Design of Microbial Ethanol Production", V. Hatzimanikatis, M. Emmerling, U. Sauer, and J.E. Bailey, Biotechnology & Bioengineering, 58(2-3), 154-161 (1998)

1997

"The AlkB monooxygenase of Pseudomonas oleovorans: Synthesis, stability and level in recombinant Escherichia coli and in the native host", I. E. Staijen, V. Hatzimanikatis, and B. Witholt, European Journal of Biochemistry, 244, 462-470 (1997)

"Metabolic Consequences of a Phosphotransferase (PTS) Mutation in a Phenylalanine-Producing Recombinant Escherichia coli", R. Chen, V. Hatzimanikatis, Y.M.G. Jaap, P. Postma, and J.E. Bailey, Biotechnology Progress, 13(6), 768-775 (1997)

"Studies on Glycolysis. I: Multiple Steady-states in Bacterial Glycolysis", V. Hatzimanikatis and J.E. Bailey, Chemical Engineering Science, 52(15), 2579-2588 (1997)

"Spatiotemporal Variations and Metabolic Control Analysis", V. Hatzimanikatis and J.E. Bailey, Biotechnology & Bioengineering, 54(2), 91-104 (1997)

"Metabolic Flux in Riboflavin-producing Bacillus subtilis Studied by Combined Use of Flux Balancing and Two-dimensional NMR Studies of Biosynthetically-directed Fractional 13C-labeling", U. Sauer, V. Hatzimanikatis, J.E. Bailey, M. Hochuli, T. Szyperski, and K. Wuthrich, Nature Biotechnology, 15, 448-452 (1997)

1996

"Analysis and Design of Metabolic Reaction Networks via Mixed-Integer Linear Optimization", V. Hatzimanikatis, C.A. Floudas, and J.E. Bailey, AIChE Journal, 42(5), 1277-1292 (1996)

"MCA Has More to Say", V. Hatzimanikatis and J.E. Bailey, Journal of Theoretical Biology, 182, 233-242 (1996)

"Optimization of Regulatory Architectures in Metabolic Reaction Networks", V. Hatzimanikatis, C.A. Floudas, and J.E. Bailey, Biotechnology & Bioengineering, 52, 485-500 (1996)

"Effect of Vitroescilla Hemoglobin Dosage on Microaerobic Escherichia coli Carbon and Energy Metabolism", P.S. Tsai, V. Hatzimanikatis, and J.E. Bailey, Biotechnology & Bioengineering, 49(2), 139-150 (1996)

"Inverse Metabolic Engineering: A Strategy for Directed Genetic Engineering of Useful Phenotypes", J.E. Bailey, A. Sburlati, V. Hatzimanikatis, K.H. Lee, W.A. Renner, and P.S. Tsai, Biotechnology & Bioengineering, 52, 109-121 (1996)

"Metabolic Flux Analysis of Hybridoma Cells in Different Culture Media Using Mass Balances", H.P.J. Bonarius, V. Hatzimanikatis, K.P.H. Meesters, C.D. de Gooijer, G. Schmid, and J. Tramper, Biotechnology & Bioengineering, 50(3), 299-318 (1996)

"Physiology and Metabolic Fluxes of Wild-Type and Riboflavin-Producing Bacillus Subtilis", U. Sauer, V. Hatzimanikatis, P. Hohmann, M. Manneberg, A.P.G.M. van Loon, and J.E. Bailey, Applied and Environmental Microbiology, 62, 3687-3696 (1996)

1995

"A Mathematical Model for the G1/S Transition of the Mammalian Cell Cycle", V. Hatzimanikatis, K.H. Lee, W.A. Renner, and J.E. Bailey, Biotechnology Letters, (7), 669-674 (1995)

"Recombinant Cyclin E Expression Activates Proliferation and Obviates Surface Attachment of Chinese Hamster Ovary (CHO) Cells in Protein-Free Medium", W.A. Renner, K.H. Lee, V. Hatzimanikatis, J.E. Bailey, and H.M. Eppenberger, Biotechnology & Bioengineering, 47, 476-482 (1995)

1993

"A Method for Pulsed Periodic Optimization of Chemical Reaction Systems", V. Hatzimanikatis, G. Lyberatos, S. Pavlou, and S. Svoronos, Chemical Engineering Science, 48(4), 789-797 (1993)