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Vassily Hatzimanikatis - Publications

Affiliations: 
2000-2006 Chemical Engineering Northwestern University, Evanston, IL 
 2006- Chemistry and Chemical Engineering École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland 
Area:
General Biophysics, Applied Mathematics, Molecular Biology
Website:
http://lcsb.epfl.ch/page-56751-en.html
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132 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Oftadeh O, Hatzimanikatis V. Genome-scale models of metabolism and expression predict the metabolic burden of recombinant protein expression. Metabolic Engineering. 84: 109-116. PMID 38880390 DOI: 10.1016/j.ymben.2024.06.005  0.328
2022 Choudhury S, Moret M, Salvy P, Weilandt D, Hatzimanikatis V, Miskovic L. Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks. Nature Machine Intelligence. 4: 710-719. PMID 37790987 DOI: 10.1038/s42256-022-00519-y  0.341
2022 Vayena E, Chiappino-Pepe A, MohammadiPeyhani H, Francioli Y, Hadadi N, Ataman M, Hafner J, Pavlou S, Hatzimanikatis V. A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions. Proceedings of the National Academy of Sciences of the United States of America. 119: e2211197119. PMID 36343249 DOI: 10.1073/pnas.2211197119  0.767
2022 MohammadiPeyhani H, Hafner J, Sveshnikova A, Viterbo V, Hatzimanikatis V. Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx. Nature Communications. 13: 1560. PMID 35322036 DOI: 10.1038/s41467-022-29238-z  0.322
2021 Oftadeh O, Salvy P, Masid M, Curvat M, Miskovic L, Hatzimanikatis V. A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics. Nature Communications. 12: 4790. PMID 34373465 DOI: 10.1038/s41467-021-25158-6  0.352
2021 MohammadiPeyhani H, Chiappino-Pepe A, Haddadi K, Hafner J, Hadadi N, Hatzimanikatis V. NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism. Elife. 10. PMID 34340747 DOI: 10.7554/eLife.65543  0.713
2021 Hafner J, Hatzimanikatis V. Finding metabolic pathways in large networks through atom-conserving substrate-product pairs. Bioinformatics (Oxford, England). PMID 34003971 DOI: 10.1093/bioinformatics/btab368  0.316
2021 Tsouka S, Ataman M, Hameri T, Miskovic L, Hatzimanikatis V. Constraint-based metabolic control analysis for rational strain engineering. Metabolic Engineering. 66: 191-203. PMID 33895366 DOI: 10.1016/j.ymben.2021.03.003  0.339
2021 Chiappino-Pepe A, Hatzimanikatis V. PhenoMapping: a protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models. Star Protocols. 2: 100280. PMID 33532729 DOI: 10.1016/j.xpro.2020.100280  0.756
2020 Masid M, Ataman M, Hatzimanikatis V. Author Correction: Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN. Nature Communications. 11: 3757. PMID 32703980 DOI: 10.1038/S41467-020-17694-4  0.356
2020 Masid M, Ataman M, Hatzimanikatis V. Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN. Nature Communications. 11: 2821. PMID 32499584 DOI: 10.1038/S41467-020-16549-2  0.44
2020 Hafner J, MohammadiPeyhani H, Sveshnikova A, Scheidegger A, Hatzimanikatis V. Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power. Acs Synthetic Biology. PMID 32421310 DOI: 10.1021/Acssynbio.0C00052  0.308
2020 Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, ... ... Hatzimanikatis V, et al. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. 38: 504. PMID 32265554 DOI: 10.1038/S41587-020-0477-4  0.352
2020 Tokic M, Hatzimanikatis V, Miskovic L. Large-scale kinetic metabolic models of KT2440 for consistent design of metabolic engineering strategies. Biotechnology For Biofuels. 13: 33. PMID 32140178 DOI: 10.1186/S13068-020-1665-7  0.436
2020 Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, ... ... Hatzimanikatis V, et al. MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. PMID 32123384 DOI: 10.1038/S41587-020-0446-Y  0.363
2020 Tsouka S, Hatzimanikatis V. redLips: a comprehensive mechanistic model of the lipid metabolic network of yeast. Fems Yeast Research. 20. PMID 32068831 DOI: 10.1093/Femsyr/Foaa006  0.415
2020 Krishnan A, Kloehn J, Lunghi M, Chiappino-Pepe A, Waldman BS, Nicolas D, Varesio E, Hehl A, Lourido S, Hatzimanikatis V, Soldati-Favre D. Functional and Computational Genomics Reveal Unprecedented Flexibility in Stage-Specific Toxoplasma Metabolism. Cell Host & Microbe. PMID 31991093 DOI: 10.1016/J.Chom.2020.01.002  0.779
2020 Salvy P, Hatzimanikatis V. The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models. Nature Communications. 11: 30. PMID 31937763 DOI: 10.1038/S41467-019-13818-7  0.443
2019 Hameri T, Boldi MO, Hatzimanikatis V. Statistical inference in ensemble modeling of cellular metabolism. Plos Computational Biology. 15: e1007536. PMID 31815929 DOI: 10.1371/Journal.Pcbi.1007536  0.378
2019 Stanway RR, Bushell E, Chiappino-Pepe A, Roques M, Sanderson T, Franke-Fayard B, Caldelari R, Golomingi M, Nyonda M, Pandey V, Schwach F, Chevalley S, Ramesar J, Metcalf T, Herd C, ... ... Hatzimanikatis V, et al. Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage. Cell. 179: 1112-1128.e26. PMID 31730853 DOI: 10.1016/J.Cell.2019.10.030  0.755
2019 Miskovic L, Béal J, Moret M, Hatzimanikatis V. Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties. Plos Computational Biology. 15: e1007242. PMID 31430276 DOI: 10.1371/Journal.Pcbi.1007242  0.414
2019 Weilandt DR, Hatzimanikatis V. Particle-Based Simulation Reveals Macromolecular Crowding Effects on the Michaelis-Menten Mechanism. Biophysical Journal. 117: 355-368. PMID 31311624 DOI: 10.1016/J.Bpj.2019.06.017  0.358
2019 Borer B, Ataman M, Hatzimanikatis V, Or D. Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH). Plos Computational Biology. 15: e1007127. PMID 31216273 DOI: 10.1371/Journal.Pcbi.1007127  0.373
2019 Abrami L, Denhardt-Eriksson RA, Hatzimanikatis V, van der Goot FG. Dynamic Radiolabeling of S-Palmitoylated Proteins. Methods in Molecular Biology (Clifton, N.J.). 2009: 111-127. PMID 31152399 DOI: 10.1007/978-1-4939-9532-5_9  0.335
2019 Pandey V, Hadadi N, Hatzimanikatis V. Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models. Plos Computational Biology. 15: e1007036. PMID 31083653 DOI: 10.1371/Journal.Pcbi.1007036  0.439
2019 Pandey V, Hatzimanikatis V. Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data. Plos Computational Biology. 15: e1006760. PMID 31002661 DOI: 10.1371/Journal.Pcbi.1006760  0.431
2019 Hadadi N, MohammadiPeyhani H, Miskovic L, Seijo M, Hatzimanikatis V. Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites. Proceedings of the National Academy of Sciences of the United States of America. PMID 30910961 DOI: 10.1073/Pnas.1818877116  0.335
2019 Salvy P, Fengos G, Ataman M, Pathier T, Soh KC, Hatzimanikatis V. pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis. Bioinformatics (Oxford, England). 35: 167-169. PMID 30561545 DOI: 10.1093/Bioinformatics/Bty499  0.304
2019 Miskovic L, Tokic M, Savoglidis G, Hatzimanikatis V. Control Theory Concepts for Modeling Uncertainty in Enzyme Kinetics of Biochemical Networks Industrial & Engineering Chemistry Research. 58: 13544-13554. DOI: 10.1021/Acs.Iecr.9B00818  0.352
2018 Hameri T, Fengos G, Ataman M, Miskovic L, Hatzimanikatis V. Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations. Metabolic Engineering. 52: 29-41. PMID 30455161 DOI: 10.1016/J.Ymben.2018.10.005  0.441
2018 Tokić M, Hadadi N, Ataman M, Neves D, Ebert BE, Blank LM, Miskovic L, Hatzimanikatis V. Discovery and Evaluation of Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors. Acs Synthetic Biology. PMID 30021444 DOI: 10.1021/Acssynbio.8B00049  0.384
2018 Panayiotou C, Mastrogeorgopoulos S, Ataman M, Hadadi N, Hatzimanikatis V. Molecular thermodynamics of metabolism: hydration quantities and the equation-of-state approach. Physical Chemistry Chemical Physics : Pccp. 18: 32570-32592. PMID 27874110 DOI: 10.1039/C6Cp06281D  0.322
2017 Abrami L, Dallavilla T, Sandoz PA, Demir M, Kunz B, Savoglidis G, Hatzimanikatis V, van der Goot FG. Identification and dynamics of the human ZDHHC16-ZDHHC6 palmitoylation cascade. Elife. 6. PMID 28826475 DOI: 10.7554/Elife.27826  0.324
2017 Ataman M, Hatzimanikatis V. lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites. Plos Computational Biology. 13: e1005513. PMID 28727789 DOI: 10.1371/Journal.Pcbi.1005513  0.439
2017 Ataman M, Hernandez Gardiol DF, Fengos G, Hatzimanikatis V. redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models. Plos Computational Biology. 13: e1005444. PMID 28727725 DOI: 10.1371/Journal.Pcbi.1005444  0.455
2017 Miskovic L, Alff-Tuomala S, Soh KC, Barth D, Salusjärvi L, Pitkänen JP, Ruohonen L, Penttilä M, Hatzimanikatis V. A design-build-test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models. Biotechnology For Biofuels. 10: 166. PMID 28674555 DOI: 10.1186/S13068-017-0838-5  0.377
2017 Ahsanul Islam M, Hadadi N, Ataman M, Hatzimanikatis V, Stephanopoulos G. Exploring Biochemical Pathways for Mono-Ethylene Glycol (MEG) Synthesis from Synthesis Gas. Metabolic Engineering. PMID 28433737 DOI: 10.1016/J.Ymben.2017.04.005  0.387
2017 Chiappino-Pepe A, Tymoshenko S, Ataman M, Soldati-Favre D, Hatzimanikatis V. Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks. Plos Computational Biology. 13: e1005397. PMID 28333921 DOI: 10.1371/Journal.Pcbi.1005397  0.779
2017 Berset Y, Merulla D, Joublin A, Hatzimanikatis V, van der Meer JR. Mechanistic Modeling of Genetic Circuits for ArsR Arsenic Regulation. Acs Synthetic Biology. PMID 28215088 DOI: 10.1021/Acssynbio.6B00364  0.316
2017 Mastrogeorgopoulos S, Hatzimanikatis V, Panayiotou C. Toward a Simple Predictive Molecular Thermodynamic Model for Bulk Phases and Interfaces Industrial & Engineering Chemistry Research. 56: 10900-10910. DOI: 10.1021/Acs.Iecr.7B02286  0.302
2017 Chiappino-Pepe A, Pandey V, Ataman M, Hatzimanikatis V. Integration of metabolic, regulatory and signaling networks towards analysis of perturbation and dynamic responses Current Opinion in Systems Biology. 2: 59-66. DOI: 10.1016/J.Coisb.2017.01.007  0.423
2016 Hadadi N, Hafner J, Soh KC, Hatzimanikatis V. Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites. Biotechnology Journal. PMID 27897385 DOI: 10.1002/Biot.201600464  0.351
2016 Wayne G, Graves A, Hassabis D, Saha S, Weber CA, Hyman AA, Juelicher F, Stroud DA, Ryan MT, Potvin-Trottier L, Paulsson J, Geiler-Samerotte KA, Siegal ML, Uhlen M, Edfors F, ... ... Hatzimanikatis V, et al. Principles of Systems Biology, No. 11 Cell Systems. 3: 406-410. PMID 27883884 DOI: 10.1016/J.Cels.2016.11.010  0.326
2016 Kiparissides A, Hatzimanikatis V. Thermodynamics-based Metabolite Sensitivity Analysis in metabolic networks. Metabolic Engineering. 39: 117-127. PMID 27845184 DOI: 10.1016/J.Ymben.2016.11.006  0.466
2016 Hadadi N, Hafner J, Shajkofci A, Zisaki A, Hatzimanikatis V. ATLAS of Biochemistry: A Repository of All Possible Biochemical Reactions for Synthetic Biology and Metabolic Engineering Studies. Acs Synthetic Biology. 5: 1155-1166. PMID 27404214 DOI: 10.1021/Acssynbio.6B00054  0.422
2016 Vieira JP, Racle J, Hatzimanikatis V. Analysis of Translation Elongation Dynamics in the Context of an Escherichia coli Cell. Biophysical Journal. 110: 2120-31. PMID 27166819 DOI: 10.1016/J.Bpj.2016.04.004  0.321
2016 Savoglidis G, da Silveira Dos Santos AX, Riezman I, Angelino P, Riezman H, Hatzimanikatis V. A method for analysis and design of metabolism using metabolomics data and kinetic models: Application on lipidomics using a novel kinetic model of sphingolipid metabolism. Metabolic Engineering. 37: 46-62. PMID 27113440 DOI: 10.1016/J.Ymben.2016.04.002  0.454
2016 Dallavilla T, Abrami L, Sandoz PA, Savoglidis G, Hatzimanikatis V, van der Goot FG. Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin. Plos Computational Biology. 12: e1004774. PMID 26900856 DOI: 10.1371/Journal.Pcbi.1004774  0.371
2016 Andreozzi S, Chakrabarti A, Soh KC, Burgard A, Yang TH, Van Dien S, Miskovic L, Hatzimanikatis V. Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models. Metabolic Engineering. 35: 148-59. PMID 26855240 DOI: 10.1016/J.Ymben.2016.01.009  0.433
2016 Andreozzi S, Miskovic L, Hatzimanikatis V. iSCHRUNK--In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks. Metabolic Engineering. 33: 158-68. PMID 26474788 DOI: 10.1016/J.Ymben.2015.10.002  0.45
2016 Morales M, Ataman M, Badr S, Linster S, Kourlimpinis I, Papadokonstantakis S, Hatzimanikatis V, Hungerbühler K. Sustainability assessment of succinic acid production technologies from biomass using metabolic engineering Energy & Environmental Science. 9: 2794-2805. DOI: 10.1039/C6Ee00634E  0.357
2015 Ataman M, Hatzimanikatis V. Heading in the right direction: thermodynamics-based network analysis and pathway engineering. Current Opinion in Biotechnology. 36: 176-82. PMID 26360871 DOI: 10.1016/J.Copbio.2015.08.021  0.403
2015 Miskovic L, Tokic M, Fengos G, Hatzimanikatis V. Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes. Current Opinion in Biotechnology. 36: 146-53. PMID 26342586 DOI: 10.1016/J.Copbio.2015.08.019  0.404
2015 Hatzimanikatis V, Saez-Rodriguez J. Integrative approaches for signalling and metabolic networks. Integrative Biology : Quantitative Biosciences From Nano to Macro. 7: 844-5. PMID 26198436 DOI: 10.1039/C5Ib90030A  0.333
2015 Hadadi N, Hatzimanikatis V. Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways. Current Opinion in Chemical Biology. 28: 99-104. PMID 26177079 DOI: 10.1016/J.Cbpa.2015.06.025  0.386
2015 Tymoshenko S, Oppenheim RD, Agren R, Nielsen J, Soldati-Favre D, Hatzimanikatis V. Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis. Plos Computational Biology. 11: e1004261. PMID 26001086 DOI: 10.1371/Journal.Pcbi.1004261  0.442
2015 Zisaki A, Miskovic L, Hatzimanikatis V. Antihypertensive drugs metabolism: an update to pharmacokinetic profiles and computational approaches. Current Pharmaceutical Design. 21: 806-22. PMID 25341854 DOI: 10.2174/1381612820666141024151119  0.397
2015 Hadadi N, Ataman M, Hatzimanikatis V, Panayiotou C. Molecular thermodynamics of metabolism: Quantum thermochemical calculations for key metabolites Physical Chemistry Chemical Physics. 17: 10438-10453. DOI: 10.1039/C4Cp05825A  0.354
2014 Soh KC, Hatzimanikatis V. Constraining the flux space using thermodynamics and integration of metabolomics data. Methods in Molecular Biology (Clifton, N.J.). 1191: 49-63. PMID 25178783 DOI: 10.1007/978-1-4939-1170-7_3  0.392
2014 Almquist J, Cvijovic M, Hatzimanikatis V, Nielsen J, Jirstrand M. Kinetic models in industrial biotechnology - Improving cell factory performance. Metabolic Engineering. 24: 38-60. PMID 24747045 DOI: 10.1016/J.Ymben.2014.03.007  0.357
2014 Hadadi N, Cher Soh K, Seijo M, Zisaki A, Guan X, Wenk MR, Hatzimanikatis V. A computational framework for integration of lipidomics data into metabolic pathways. Metabolic Engineering. 23: 1-8. PMID 24395008 DOI: 10.1016/J.Ymben.2013.12.007  0.404
2014 Gill RT, Hatzimanikatis V. Introduction to metabolic engineering communications Metabolic Engineering Communications. 1: 29. DOI: 10.1016/J.Meteno.2014.11.002  0.32
2013 Fierro-Monti I, Racle J, Hernandez C, Waridel P, Hatzimanikatis V, Quadroni M. A novel pulse-chase SILAC strategy measures changes in protein decay and synthesis rates induced by perturbation of proteostasis with an Hsp90 inhibitor. Plos One. 8: e80423. PMID 24312217 DOI: 10.1371/Journal.Pone.0080423  0.341
2013 Racle J, Picard F, Girbal L, Cocaign-Bousquet M, Hatzimanikatis V. A genome-scale integration and analysis of Lactococcus lactis translation data. Plos Computational Biology. 9: e1003240. PMID 24130467 DOI: 10.1371/Journal.Pcbi.1003240  0.365
2013 Mattanovich D, Hatzimanikatis V. Editorial: metabolic modeling in biotechnology and medical research. Biotechnology Journal. 8: 962-3. PMID 24031032 DOI: 10.1002/Biot.201300378  0.411
2013 Chakrabarti A, Miskovic L, Soh KC, Hatzimanikatis V. Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints. Biotechnology Journal. 8: 1043-57. PMID 23868566 DOI: 10.1002/Biot.201300091  0.478
2013 Tymoshenko S, Oppenheim RD, Soldati-Favre D, Hatzimanikatis V. Functional genomics of Plasmodium falciparum using metabolic modelling and analysis. Briefings in Functional Genomics. 12: 316-27. PMID 23793264 DOI: 10.1093/Bfgp/Elt017  0.361
2013 Mier-y-Terán-Romero L, Silber M, Hatzimanikatis V. Mechanistically consistent reduced models of synthetic gene networks. Biophysical Journal. 104: 2098-109. PMID 23663853 DOI: 10.1016/J.Bpj.2013.03.031  0.366
2012 Radivojevic A, Chachuat B, Bonvin D, Hatzimanikatis V. Exploration of trade-offs between steady-state and dynamic properties in signaling cycles Physical Biology. 9. PMID 22872041 DOI: 10.1088/1478-3975/9/4/045010  0.343
2012 Racle J, Overney J, Hatzimanikatis V. A computational framework for the design of optimal protein synthesis. Biotechnology and Bioengineering. 109: 2127-33. PMID 22334333 DOI: 10.1002/Bit.24463  0.307
2012 Soh KC, Miskovic L, Hatzimanikatis V. From network models to network responses: integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks. Fems Yeast Research. 12: 129-43. PMID 22129227 DOI: 10.1111/J.1567-1364.2011.00771.X  0.438
2012 Brunk E, Neri M, Tavernelli I, Hatzimanikatis V, Rothlisberger U. Integrating computational methods to retrofit enzymes to synthetic pathways. Biotechnology and Bioengineering. 109: 572-82. PMID 21928337 DOI: 10.1002/Bit.23334  0.363
2011 Singh A, Cher Soh K, Hatzimanikatis V, Gill RT. Manipulating redox and ATP balancing for improved production of succinate in E. coli. Metabolic Engineering. 13: 76-81. PMID 21040799 DOI: 10.1016/J.Ymben.2010.10.006  0.4
2011 Mišković L, Hatzimanikatis V. Modeling of uncertainties in biochemical reactions. Biotechnology and Bioengineering. 108: 413-23. PMID 20830674 DOI: 10.1002/Bit.22932  0.408
2010 Jol SJ, Kümmel A, Hatzimanikatis V, Beard DA, Heinemann M. Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks. Biophysical Journal. 99: 3139-44. PMID 21081060 DOI: 10.1016/J.Bpj.2010.09.043  0.372
2010 Soh KC, Hatzimanikatis V. DREAMS of metabolism. Trends in Biotechnology. 28: 501-8. PMID 20727603 DOI: 10.1016/J.Tibtech.2010.07.002  0.446
2010 Miskovic L, Hatzimanikatis V. Production of biofuels and biochemicals: in need of an ORACLE. Trends in Biotechnology. 28: 391-7. PMID 20646768 DOI: 10.1016/J.Tibtech.2010.05.003  0.351
2010 Soh KC, Hatzimanikatis V. Network thermodynamics in the post-genomic era. Current Opinion in Microbiology. 13: 350-7. PMID 20378394 DOI: 10.1016/J.Mib.2010.03.001  0.334
2010 Mier-y-Terán-Romero L, Silber M, Hatzimanikatis V. The origins of time-delay in template biopolymerization processes. Plos Computational Biology. 6: e1000726. PMID 20369012 DOI: 10.1371/Journal.Pcbi.1000726  0.327
2010 Finley SD, Broadbelt LJ, Hatzimanikatis V. In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene. Bmc Systems Biology. 4: 7. PMID 20122273 DOI: 10.1186/1752-0509-4-7  0.312
2010 Henry CS, Broadbelt LJ, Hatzimanikatis V. Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate. Biotechnology and Bioengineering. 106: 462-73. PMID 20091733 DOI: 10.1002/Bit.22673  0.374
2009 Finley SD, Broadbelt LJ, Hatzimanikatis V. Computational framework for predictive biodegradation. Biotechnology and Bioengineering. 104: 1086-97. PMID 19650084 DOI: 10.1002/Bit.22489  0.339
2009 Finley SD, Broadbelt LJ, Hatzimanikatis V. Thermodynamic analysis of biodegradation pathways. Biotechnology and Bioengineering. 103: 532-41. PMID 19288443 DOI: 10.1002/Bit.22285  0.301
2008 Zouridis H, Hatzimanikatis V. Effects of codon distributions and tRNA competition on protein translation. Biophysical Journal. 95: 1018-33. PMID 18359800 DOI: 10.1529/Biophysj.107.126128  0.315
2007 Thomas R, Paredes CJ, Mehrotra S, Hatzimanikatis V, Papoutsakis ET. A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data. Bmc Bioinformatics. 8: 228. PMID 17603872 DOI: 10.1186/1471-2105-8-228  0.317
2007 Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BØ. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular Systems Biology. 3: 121. PMID 17593909 DOI: 10.1038/Msb4100155  0.436
2007 Henry CS, Broadbelt LJ, Hatzimanikatis V. Thermodynamics-based metabolic flux analysis. Biophysical Journal. 92: 1792-805. PMID 17172310 DOI: 10.1529/Biophysj.106.093138  0.408
2007 Zouridis H, Hatzimanikatis V. A model for protein translation: polysome self-organization leads to maximum protein synthesis rates. Biophysical Journal. 92: 717-30. PMID 17098800 DOI: 10.1529/Biophysj.106.087825  0.339
2006 González-Lergier J, Broadbelt LJ, Hatzimanikatis V. Analysis of the maximum theoretical yield for the synthesis of erythromycin precursors in Escherichia coli. Biotechnology and Bioengineering. 95: 638-44. PMID 16619212 DOI: 10.1002/Bit.20925  0.374
2006 Wang L, Hatzimanikatis V. Metabolic engineering under uncertainty. I: framework development. Metabolic Engineering. 8: 133-41. PMID 16414298 DOI: 10.1016/J.Ymben.2005.11.003  0.431
2006 Wang L, Hatzimanikatis V. Metabolic engineering under uncertainty--II: analysis of yeast metabolism. Metabolic Engineering. 8: 142-59. PMID 16413809 DOI: 10.1016/J.Ymben.2005.11.002  0.46
2006 Mehra A, Hatzimanikatis V. An algorithmic framework for genome-wide modeling and analysis of translation networks. Biophysical Journal. 90: 1136-46. PMID 16299083 DOI: 10.1529/Biophysj.105.062521  0.586
2006 Rieger TR, Morimoto RI, Hatzimanikatis V. Bistability explains threshold phenomena in protein aggregation both in vitro and in vivo. Biophysical Journal. 90: 886-95. PMID 16299080 DOI: 10.1529/Biophysj.105.066662  0.748
2006 Henry CS, Jankowski MD, Broadbelt LJ, Hatzimanikatis V. Genome-scale thermodynamic analysis of Escherichia coli metabolism. Biophysical Journal. 90: 1453-61. PMID 16299075 DOI: 10.1529/Biophysj.105.071720  0.421
2006 Hatzimanikatis V, Wang L. The systems engineering of cellular processes Computer Aided Chemical Engineering. 21: 71-80. DOI: 10.1016/S1570-7946(06)80028-3  0.438
2005 González-Lergier J, Broadbelt LJ, Hatzimanikatis V. Theoretical considerations and computational analysis of the complexity in polyketide synthesis pathways. Journal of the American Chemical Society. 127: 9930-8. PMID 15998100 DOI: 10.1021/Ja051586Y  0.355
2005 Rieger TR, Morimoto RI, Hatzimanikatis V. Mathematical modeling of the eukaryotic heat-shock response: dynamics of the hsp70 promoter. Biophysical Journal. 88: 1646-58. PMID 15626701 DOI: 10.1529/Biophysj.104.055301  0.76
2005 Hatzimanikatis V, Li C, Ionita JA, Henry CS, Jankowski MD, Broadbelt LJ. Exploring the diversity of complex metabolic networks. Bioinformatics (Oxford, England). 21: 1603-9. PMID 15613400 DOI: 10.1093/Bioinformatics/Bti213  0.554
2005 Rieger TR, Hatzimanikatis V. Understanding the ultrasensitive responses of tricyclic cascade networks Aiche Annual Meeting, Conference Proceedings. 11697.  0.757
2005 Wang L, Hatzimanikatis V. Quantitative target identification for metabolic engineering of yeast saccharomyces cerevisiae: Impacts of bioreactor environment Aiche Annual Meeting, Conference Proceedings. 8461.  0.353
2005 Hatzimanikatis V, Mehra A. Genome-scale analysis of translation in s. cerevisiae: Insights into system response and regulation Aiche Annual Meeting, Conference Proceedings. 8600.  0.573
2004 Wang L, Birol I, Hatzimanikatis V. Metabolic control analysis under uncertainty: framework development and case studies. Biophysical Journal. 87: 3750-63. PMID 15465856 DOI: 10.1529/Biophysj.104.048090  0.461
2004 Thomas R, Mehrotra S, Papoutsakis ET, Hatzimanikatis V. A model-based optimization framework for the inference on gene regulatory networks from DNA array data. Bioinformatics (Oxford, England). 20: 3221-35. PMID 15247105 DOI: 10.1093/Bioinformatics/Bth389  0.318
2004 Hatzimanikatis V, Li C, Ionita JA, Broadbelt LJ. Metabolic networks: enzyme function and metabolite structure. Current Opinion in Structural Biology. 14: 300-6. PMID 15193309 DOI: 10.1016/J.Sbi.2004.04.004  0.572
2004 Li C, Henry CS, Jankowski MD, Ionita JA, Hatzimanikatis V, Broadbelt LJ. Computational discovery of biochemical routes to specialty chemicals Chemical Engineering Science. 59: 5051-5060. DOI: 10.1016/J.Ces.2004.09.021  0.5
2003 Lee PS, Shaw LB, Choe LH, Mehra A, Hatzimanikatis V, Lee KH. Insights into the relation between mrna and protein expression patterns: II. Experimental observations in Escherichia coli. Biotechnology and Bioengineering. 84: 834-41. PMID 14708124 DOI: 10.1002/Bit.10841  0.663
2003 Mehra A, Lee KH, Hatzimanikatis V. Insights into the relation between mRNA and protein expression patterns: I. Theoretical considerations. Biotechnology and Bioengineering. 84: 822-33. PMID 14708123 DOI: 10.1002/Bit.10860  0.666
2002 Bailey JE, Sburlati A, Hatzimanikatis V, Lee K, Renner WA, Tsai PS. Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes. Biotechnology and Bioengineering. 79: 568-79. PMID 12209828 DOI: 10.1002/bit.10441  0.639
2002 Hatzimanikatis V, Liao JC. A memorial review of Jay Bailey's contribution in prokaryotic metabolic engineering. Biotechnology and Bioengineering. 79: 504-8. PMID 12209822 DOI: 10.1002/Bit.10406  0.339
2002 Reardon KF, Lee KH, Wittrup KD, Hatzimanikatis V. Jay Bailey as mentor--the students' perspective. Biotechnology and Bioengineering. 79: 484-9. PMID 12209819 DOI: 10.1002/Bit.10402  0.689
1999 Hatzimanikatis V, Lee KH. Dynamical Analysis of Gene Networks Requires Both mRNA and Protein Expression Information Metabolic Engineering. 1: 275-281. PMID 10937820 DOI: 10.1006/Mben.1999.0115  0.568
1999 Hatzimanikatis V. Nonlinear Metabolic Control Analysis Metabolic Engineering. 1: 75-87. PMID 10935756 DOI: 10.1006/Mben.1998.0108  0.457
1999 Hatzimanikatis V, Lee KH, Bailey JE. A mathematical description of regulation of the G1-S transition of the mammalian cell cycle Biotechnology and Bioengineering. 65: 631-637. PMID 10550769 DOI: 10.1002/(Sici)1097-0290(19991220)65:6<631::Aid-Bit3>3.0.Co;2-7  0.626
1999 Hatzimanikatis V, Choe LH, Lee KH. Proteomics: Theoretical and experimental considerations Biotechnology Progress. 15: 312-318. PMID 10356248 DOI: 10.1021/Bp990004B  0.574
1999 Hatzimanikatis V, Bailey JE. Modelling molecular mechanisms within their cellular environment Journal of Biotechnology. 71: 263-265. DOI: 10.1016/S0168-1656(99)00032-2  0.539
1998 Hatzimanikatis V, Emmerling M, Sauer U, Bailey JE. Application of mathematical tools for metabolic design of microbial ethanol production Biotechnology and Bioengineering. 58: 154-161. PMID 10191385 DOI: 10.1002/(Sici)1097-0290(19980420)58:2/3<154::Aid-Bit7>3.0.Co;2-K  0.557
1997 Hatzimanikatis V, Bailey JE. Effects of spatiotemporal variations on metabolic control: approximate analysis using (log)linear kinetic models. Biotechnology and Bioengineering. 54: 91-104. PMID 18634077 DOI: 10.1002/(Sici)1097-0290(19970420)54:2<91::Aid-Bit1>3.0.Co;2-Q  0.56
1997 Chen R, Hatzimanikatis V, Yap WMGJ, Postma PW, Bailey JE. Metabolic consequences of phosphotransferase (PTS) mutation in a phenylalanine-producing recombinant Escherichia coli Biotechnology Progress. 13: 768-775. PMID 9413135 DOI: 10.1021/Bp970060H  0.457
1997 Sauer U, Hatzimanikatis V, Bailey JE, Hochuli M, Szyperski T, Wüthrich K. Metabolic fluxes in riboflavin-producing Bacillus subtilis Nature Biotechnology. 15: 448-452. PMID 9131624 DOI: 10.1038/Nbt0597-448  0.557
1997 Hatzimanikatis V, Bailey JE. Studies on glycolysis-I. Multiple steady states in bacterial glycolysis Chemical Engineering Science. 52: 2579-2588. DOI: 10.1016/S0009-2509(97)00074-2  0.478
1997 Hatzimanikatis V, Bailey JE. Effects of spatiotemporal variations on metabolic control: Approximate analysis using (log)linear kinetic models Biotechnology and Bioengineering. 54: 91-104. DOI: 10.1002/(SICI)1097-0290(19970420)54:2<91::AID-BIT1>3.0.CO;2-Q  0.474
1996 Hatzimanikatis V, Floudas CA, Bailey JE. Optimization of regulatory architectures in metabolic reaction networks. Biotechnology and Bioengineering. 52: 485-500. PMID 18629921 DOI: 10.1002/(Sici)1097-0290(19961120)52:4<485::Aid-Bit4>3.0.Co;2-L  0.579
1996 Bailey JE, Sburlati A, Hatzimanikatis V, Lee K, Renner WA, Tsai PS. Inverse metabolic engineering: A strategy for directed genetic engineering of useful phenotypes. Biotechnology and Bioengineering. 52: 109-21. PMID 18629857 DOI: 10.1002/(Sici)1097-0290(19961005)52:1<109::Aid-Bit11>3.0.Co;2-J  0.666
1996 Tsai PS, Hatzimanikatis V, Bailey JE. Effect of Vitreoscilla hemoglobin dosage on microaerobic Escherichia coli carbon and energy metabolism. Biotechnology and Bioengineering. 49: 139-50. PMID 18623564 DOI: 10.1002/(Sici)1097-0290(19960120)49:2<139::Aid-Bit3>3.0.Co;2-R  0.499
1996 Hatzimanikatis V, Bailey JE. MCA has more to say Journal of Theoretical Biology. 182: 233-242. PMID 8944154 DOI: 10.1006/Jtbi.1996.0160  0.581
1996 Sauer U, Hatzimanikatis V, Hohmann HP, Manneberg M, Van Loon APGM, Bailey JE. Physiology and metabolic fluxes of wild-type and riboflavin-producing Bacillus subtilis Applied and Environmental Microbiology. 62: 3687-3696. PMID 8837424 DOI: 10.1128/Aem.62.10.3687-3696.1996  0.497
1996 Hatzimanikatis V, Floudas CA, Bailey JE. Analysis and design of metabolic reaction networks via mixed-integer linear optimization Aiche Journal. 42: 1277-1292. DOI: 10.1002/Aic.690420509  0.563
1996 Bonarius HPJ, Hatzimanikatis V, Meesters KPH, De Gooijer CD, Schmid G, Tramper J. Metabolic flux analysis of hybridoma cells in different culture media using mass balances Biotechnology and Bioengineering. 50: 299-318. DOI: 10.1002/(Sici)1097-0290(19960505)50:3<299::Aid-Bit9>3.0.Co;2-B  0.358
1996 Hatzimanikatis V, Floudas CA, Bailey JE. Analysis and Design of Metabolic Reaction Networks via Mixed-Integer Linear Optimization Aiche Journal. 42: 1277-1290.  0.31
1995 Renner WA, Lee KH, Hatzimanikatis V, Bailey JE, Eppenberger HM. Recombinant cyclin E expression activates proliferation and obviates surface attachment of chinese hamster ovary (CHO) cells in protein-free medium. Biotechnology and Bioengineering. 47: 476-82. PMID 18623424 DOI: 10.1002/Bit.260470409  0.461
1995 Hatzimanikatis V, Lee KH, Renner WA, Bailey JE. A mathematical model for the G1/S transition of the mammalian cell cycle Biotechnology Letters. 17: 669-674. DOI: 10.1007/Bf00130348  0.627
1995 Renner WA, Lee KH, Hatzimanikatis V, Bailey JE, Eppenberger HM. Recombinant cyclin E expression activates proliferation and obviates surface attachment of Chinese hamster ovary (CHO) cells in protein-free medium Biotechnology and Bioengineering. 47: 476-482. DOI: 10.1002/bit.260470409  0.464
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