TY - JOUR AU - Kitano, H. PY - 2002 DA - 2002// TI - Systems biology: a brief overview JO - Science VL - 295 UR - https://doi.org/10.1126/science.1069492 DO - 10.1126/science.1069492 ID - Kitano2002 ER - TY - JOUR AU - Dettmer, K. AU - Aronov, P. A. AU - Hammock, B. D. PY - 2007 DA - 2007// TI - Mass spectrometry-based metabolomics JO - Mass Spectrom Rev VL - 26 UR - https://doi.org/10.1002/mas.20108 DO - 10.1002/mas.20108 ID - Dettmer2007 ER - TY - JOUR AU - Moco, S. AU - Bino, R. J. AU - Vorst, O. AU - Verhoeven, H. A. AU - de Groot, J. AU - van Beek, T. A. AU - Vervoort, J. AU - de Vos, C. H. R. PY - 2006 DA - 2006// TI - A Liquid Chromatography-Mass Spectrometry-Based Metabolome Database for Tomato JO - Plant Physiol VL - 141 UR - https://doi.org/10.1104/pp.106.078428 DO - 10.1104/pp.106.078428 ID - Moco2006 ER - TY - JOUR AU - Lisec, J. AU - Schauer, N. AU - Kopka, J. AU - Willmitzer, L. AU - Fernie, A. R. PY - 2006 DA - 2006// TI - Gas chromatography mass spectrometry-based metabolite profiling in plants JO - Nat Protoc VL - 1 UR - https://doi.org/10.1038/nprot.2006.59 DO - 10.1038/nprot.2006.59 ID - Lisec2006 ER - TY - JOUR AU - Fiehn, O. PY - 2001 DA - 2001// TI - Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks JO - Comp Funct Genomics VL - 2 UR - https://doi.org/10.1002/cfg.82 DO - 10.1002/cfg.82 ID - Fiehn2001 ER - TY - JOUR AU - Mahadevan, R. AU - Edwards, J. S. AU - Doyle, J. F. PY - 2002 DA - 2002// TI - Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli JO - Biophys J VL - 83 UR - https://doi.org/10.1016/S0006-3495(02)73903-9 DO - 10.1016/S0006-3495(02)73903-9 ID - Mahadevan2002 ER - TY - JOUR AU - Luo, R. Y. AU - Liao, S. AU - Tao, G. Y. AU - Li, Y. Y. AU - Zeng, S. AU - Li, X. Y. AU - Luo, Q. PY - 2006 DA - 2006// TI - Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions JO - Mol Syst Biol VL - 2 UR - https://doi.org/10.1038/msb4100071 DO - 10.1038/msb4100071 ID - Luo2006 ER - TY - JOUR AU - Luo, R. Y. AU - Wei, H. AU - Ye, L. AU - Wang, K. AU - Chen, F. AU - Luo, L. AU - Liu, L. AU - Li, Y. AU - Crabbe, M. J. C. AU - Jin, L. AU - Li, Y. AU - Zhong, Y. PY - 2009 DA - 2009// TI - Photosynthetic metabolism of C3 plants shows highly cooperative regulation under changing environments: A systems biological analysis JO - Proc Natl Acad Sci USA VL - 106 UR - https://doi.org/10.1073/pnas.0810731105 DO - 10.1073/pnas.0810731105 ID - Luo2009 ER - TY - JOUR AU - Nägele, T. AU - Henkel, S. AU - Hörmiller, I. AU - Sauter, T. AU - Sawodny, O. AU - Ederer, M. AU - Heyer, A. G. PY - 2010 DA - 2010// TI - Mathematical Modeling of the Central Carbohydrate Metabolism in Arabidopsis Reveals a Substantial Regulatory Influence of Vacuolar Invertase on Whole Plant Carbon Metabolism JO - Plant Physiol VL - 153 UR - https://doi.org/10.1104/pp.110.154443 DO - 10.1104/pp.110.154443 ID - Nägele2010 ER - TY - JOUR AU - Rios-Estepa, R. AU - Lange, B. M. PY - 2007 DA - 2007// TI - Experimental and mathematical approaches to modeling plant metabolic networks JO - Phytochemistry VL - 68 UR - https://doi.org/10.1016/j.phytochem.2007.04.021 DO - 10.1016/j.phytochem.2007.04.021 ID - Rios-Estepa2007 ER - TY - JOUR AU - Libourel, I. G. L. AU - Shachar-Hill, Y. PY - 2008 DA - 2008// TI - Metabolic Flux Analysis in Plants: From Intelligent Design to Rational Engineering JO - Annu Rev Plant Biol VL - 59 UR - https://doi.org/10.1146/annurev.arplant.58.032806.103822 DO - 10.1146/annurev.arplant.58.032806.103822 ID - Libourel2008 ER - TY - JOUR AU - Fischer, E. AU - Zamboni, N. AU - Sauer, U. PY - 2004 DA - 2004// TI - High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13 C constraints JO - Anal Biochem VL - 325 UR - https://doi.org/10.1016/j.ab.2003.10.036 DO - 10.1016/j.ab.2003.10.036 ID - Fischer2004 ER - TY - JOUR AU - Varma, A. AU - Palsson, B. O. PY - 1994 DA - 1994// TI - Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use JO - Nat Biotechnol VL - 12 UR - https://doi.org/10.1038/nbt1094-994 DO - 10.1038/nbt1094-994 ID - Varma1994 ER - TY - JOUR AU - Gianchandani, E. P. AU - Chavali, A. K. AU - Papin, J. A. PY - 2010 DA - 2010// TI - The application of flux balance analysis in systems biology JO - Wiley Interdiscip Rev Syst Biol Med VL - 2 UR - https://doi.org/10.1002/wsbm.60 DO - 10.1002/wsbm.60 ID - Gianchandani2010 ER - TY - JOUR AU - Orth, J. D. AU - Thiele, I. AU - Palsson, B. O. PY - 2010 DA - 2010// TI - What is flux balance analysis? JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt.1614 DO - 10.1038/nbt.1614 ID - Orth2010 ER - TY - JOUR AU - Raman, K. AU - Chandra, N. PY - 2009 DA - 2009// TI - Flux balance analysis of biological systems: applications and challenges JO - Brief Bioinform VL - 10 UR - https://doi.org/10.1093/bib/bbp011 DO - 10.1093/bib/bbp011 ID - Raman2009 ER - TY - JOUR AU - Steuer, R. AU - Gross, T. AU - Selbig, J. AU - Blasius, B. PY - 2006 DA - 2006// TI - Structural kinetic modeling of metabolic networks JO - Proc Natl Acad Sci USA VL - 103 UR - https://doi.org/10.1073/pnas.0600013103 DO - 10.1073/pnas.0600013103 ID - Steuer2006 ER - TY - JOUR AU - Feist, A. M. AU - Palsson, B. O. PY - 2010 DA - 2010// TI - The biomass objective function JO - Curr Opin Microbiol VL - 13 UR - https://doi.org/10.1016/j.mib.2010.03.003 DO - 10.1016/j.mib.2010.03.003 ID - Feist2010 ER - TY - JOUR AU - Holzhütter, H. G. PY - 2004 DA - 2004// TI - The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks JO - Eur J Biochem VL - 271 UR - https://doi.org/10.1111/j.1432-1033.2004.04213.x DO - 10.1111/j.1432-1033.2004.04213.x ID - Holzhütter2004 ER - TY - JOUR AU - Schuetz, R. AU - Kuepfer, L. AU - Sauer, U. PY - 2007 DA - 2007// TI - Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli JO - Mol Syst Biol VL - 3 UR - https://doi.org/10.1038/msb4100162 DO - 10.1038/msb4100162 ID - Schuetz2007 ER - TY - JOUR AU - Segrè, D. AU - Vitkup, D. AU - Church, G. M. PY - 2002 DA - 2002// TI - Analysis of optimality in natural and perturbed metabolic networks JO - Proc Natl Acad Sci USA VL - 99 UR - https://doi.org/10.1073/pnas.232349399 DO - 10.1073/pnas.232349399 ID - Segrè2002 ER - TY - JOUR AU - Shlomi, T. AU - Berkman, O. AU - Ruppin, E. PY - 2005 DA - 2005// TI - Regulatory on/off minimization of metabolic flux changes after genetic perturbations JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0406346102 DO - 10.1073/pnas.0406346102 ID - Shlomi2005 ER - TY - JOUR AU - Emmerling, M. AU - Dauner, M. AU - Ponti, A. AU - Fiaux, J. AU - Hochuli, M. AU - Szyperski, T. AU - Wuthrich, K. AU - Bailey, J. E. AU - Sauer, U. PY - 2002 DA - 2002// TI - Metabolic Flux Responses to Pyruvate Kinase Knockout in Escherichia coli JO - J Bacteriol VL - 184 UR - https://doi.org/10.1128/JB.184.1.152-164.2002 DO - 10.1128/JB.184.1.152-164.2002 ID - Emmerling2002 ER - TY - JOUR AU - Kitano, H. PY - 2004 DA - 2004// TI - Biological robustness JO - Nat Rev Genet VL - 5 UR - https://doi.org/10.1038/nrg1471 DO - 10.1038/nrg1471 ID - Kitano2004 ER - TY - JOUR AU - Kitano, H. PY - 2007 DA - 2007// TI - Towards a theory of biological robustness JO - Mol Syst Biol VL - 3 UR - https://doi.org/10.1038/msb4100179 DO - 10.1038/msb4100179 ID - Kitano2007 ER - TY - JOUR AU - Waage, P. AU - Gulberg, C. M. PY - 1986 DA - 1986// TI - Studies concerning affinity JO - J Chem Educ VL - 63 UR - https://doi.org/10.1021/ed063p1044 DO - 10.1021/ed063p1044 ID - Waage1986 ER - TY - BOOK AU - Heinrich, R. AU - Schuster, S. PY - 1996 DA - 1996// TI - The Regulation Of Cellular Systems PB - Springer CY - USA UR - https://doi.org/10.1007/978-1-4613-1161-4 DO - 10.1007/978-1-4613-1161-4 ID - Heinrich1996 ER - TY - JOUR AU - Grimbs, S. AU - Selbig, J. AU - Bulik, S. AU - Holzhütter, H. G. AU - Steuer, R. PY - 2007 DA - 2007// TI - The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks JO - Mol Syst Biol VL - 3 UR - https://doi.org/10.1038/msb4100186 DO - 10.1038/msb4100186 ID - Grimbs2007 ER - TY - JOUR AU - Cuthrell, J. E. AU - Biegler, L. T. PY - 1987 DA - 1987// TI - On the optimization of differential-algebraic process systems JO - AICHE J VL - 33 UR - https://doi.org/10.1002/aic.690330804 DO - 10.1002/aic.690330804 ID - Cuthrell1987 ER - TY - JOUR AU - Wilhelm, T. PY - 2009 DA - 2009// TI - The smallest chemical reaction system with bistability JO - BMC Syst Biol VL - 3 UR - https://doi.org/10.1186/1752-0509-3-90 DO - 10.1186/1752-0509-3-90 ID - Wilhelm2009 ER - TY - JOUR AU - Eissing, T. AU - Conzelmann, H. AU - Gilles, E. D. AU - Allgöwer, F. AU - Bullinger, E. AU - Scheurich, P. PY - 2004 DA - 2004// TI - Bistability analyses of a caspase activation model for receptor-induced apoptosis JO - J Biol Chem VL - 279 UR - https://doi.org/10.1074/jbc.M404893200 DO - 10.1074/jbc.M404893200 ID - Eissing2004 ER - TY - JOUR AU - Veening, J. W. AU - Smits, W. K. AU - Kuipers, O. P. PY - 2008 DA - 2008// TI - Bistability, epigenetics, and bet-hedging in bacteria JO - Annu Rev Microbiol VL - 62 UR - https://doi.org/10.1146/annurev.micro.62.081307.163002 DO - 10.1146/annurev.micro.62.081307.163002 ID - Veening2008 ER - TY - CHAP AU - Bussieck, M. R. AU - Pruessner, A. PY - 2003 DA - 2003// TI - Mixed-Integer Nonlinear Programming BT - SIAM/Opt: Views & News ID - Bussieck2003 ER - TY - BOOK AU - Berg, J. AU - Tymoczko, J. AU - Stryer, L. PY - 2002 DA - 2002// TI - Biochemistry PB - WH Freeman and Company CY - New York ID - Berg2002 ER - TY - BOOK AU - Nelson, D. L. AU - Cox, M. M. PY - 2004 DA - 2004// TI - Lehninger Principles of Biochemistry PB - WH Freeman CY - USA ID - Nelson2004 ER - TY - JOUR AU - Arnold, A. AU - Nikoloski, Z. PY - 2011 DA - 2011// TI - A quantitative comparison of Calvin-Benson cycle models JO - Trends in plant science VL - 16 UR - https://doi.org/10.1016/j.tplants.2011.09.004 DO - 10.1016/j.tplants.2011.09.004 ID - Arnold2011 ER - TY - JOUR AU - Zhu, X. G. AU - Alba, R. AU - de Sturler, E. PY - 2009 DA - 2009// TI - A simple model of the Calvin cycle has only one physiologically feasible steady state under the same external conditions JO - Nonlinear Anal Real World Appl VL - 10 UR - https://doi.org/10.1016/j.nonrwa.2008.01.021 DO - 10.1016/j.nonrwa.2008.01.021 ID - Zhu2009 ER - TY - JOUR AU - Grimbs, S. AU - Arnold, A. AU - Koseska, A. AU - Kurths, J. AU - Selbig, J. AU - Nikoloski, Z. PY - 2011 DA - 2011// TI - Spatiotemporal dynamics of the Calvin cycle: Multistationarity and symmetry breaking instabilities JO - Biosystems VL - 103 UR - https://doi.org/10.1016/j.biosystems.2010.10.015 DO - 10.1016/j.biosystems.2010.10.015 ID - Grimbs2011 ER - TY - JOUR AU - Arrivault, S. AU - Guenther, M. AU - Ivakov, A. AU - Feil, R. AU - Vosloh, D. AU - Dongen, J. T. V. AU - Sulpice, R. AU - Stitt, M. PY - 2009 DA - 2009// TI - Use of reverse-phase liquid chromatography, linked to tandem mass spectrometry, to profile the Calvin cycle and other metabolic intermediates in Arabidopsis rosettes at different carbon dioxide concentrations JO - Plant J VL - 59 UR - https://doi.org/10.1111/j.1365-313X.2009.03902.x DO - 10.1111/j.1365-313X.2009.03902.x ID - Arrivault2009 ER - TY - JOUR AU - Collatz, G. J. PY - 1978 DA - 1978// TI - The interaction between photosynthesis and ribulose-P2 concentration-effects of light, CO2 and O2 JO - Year B Carnegie Inst Wash VL - 77 ID - Collatz1978 ER - TY - JOUR AU - Giersch, C. AU - Heber, U. AU - Kaiser, G. AU - Walker, D. A. AU - Robinson, S. P. PY - 1980 DA - 1980// TI - Intracellular metabolite gradients and flow of carbon during photosynthesis of leaf protoplasts JO - Arch Biochem Biophys VL - 205 UR - https://doi.org/10.1016/0003-9861(80)90105-8 DO - 10.1016/0003-9861(80)90105-8 ID - Giersch1980 ER - TY - JOUR AU - Benson, A. PY - 2002 DA - 2002// TI - Following the path of carbon in photosynthesis: a personal story JO - Photosynth Res VL - 73 UR - https://doi.org/10.1023/A:1020427619771 DO - 10.1023/A:1020427619771 ID - Benson2002 ER - TY - JOUR AU - Nöh AU - Wahl, A. AU - Wiechert, W. PY - 2006 DA - 2006// TI - Computational tools for isotopically instationary 13 C labeling experiments under metabolic steady state conditions JO - Metabolic Engineering VL - 8 UR - https://doi.org/10.1016/j.ymben.2006.05.006 DO - 10.1016/j.ymben.2006.05.006 ID - Nöh2006 ER - TY - JOUR AU - Yuan, J. AU - Bennett, B. D. AU - Rabinowitz, J. D. PY - 2008 DA - 2008// TI - Kinetic flux profiling for quantitation of cellular metabolic fluxes JO - Nat Protoc VL - 3 UR - https://doi.org/10.1038/nprot.2008.131 DO - 10.1038/nprot.2008.131 ID - Yuan2008 ER - TY - JOUR AU - Antoniewicz, M. R. AU - Kelleher, J. K. AU - Stephanopoulos, G. PY - 2007 DA - 2007// TI - Elementary metabolite units (EMU): A novel framework for modeling isotopic distributions JO - Metab Eng VL - 9 UR - https://doi.org/10.1016/j.ymben.2006.09.001 DO - 10.1016/j.ymben.2006.09.001 ID - Antoniewicz2007 ER - TY - CHAP AU - Kim, T. Y. AU - Sohn, S. B. AU - Kim, Y. B. AU - Kim, W. J. AU - Lee, S. Y. PY - 2011 DA - 2011// TI - Recent advances in reconstruction and applications of genome-scale metabolic models BT - Curr Opin Biotechnol ID - Kim2011 ER - TY - JOUR AU - Orth, J. D. AU - Conrad, T. M. AU - Na, J. AU - Lerman, J. A. AU - Nam, H. AU - Feist, A. M. AU - Palsson, B. O. PY - 2011 DA - 2011// TI - A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011 JO - Mol Syst Biol VL - 7 UR - https://doi.org/10.1038/msb.2011.65 DO - 10.1038/msb.2011.65 ID - Orth2011 ER - TY - JOUR AU - Murty, K. G. AU - Kabadi, S. N. PY - 1987 DA - 1987// TI - Some NP-complete problems in quadratic and nonlinear programming JO - Math Program VL - 39 UR - https://doi.org/10.1007/BF02592948 DO - 10.1007/BF02592948 ID - Murty1987 ER - TY - CHAP AU - Abdi, H. PY - 2007 DA - 2007// TI - Kendall rank correlation BT - Encyclopedia of Measurement and Statistics PB - Sage CY - Salkind NJ. Thousand Oaks (CA) ID - Abdi2007 ER - TY - JOUR AU - Holmström, K. PY - 1999 DA - 1999// TI - The TOMLAB Optimization Environment in MATLAB JO - Advanced Modeling and Optimization VL - 1 ID - Holmström1999 ER - TY - JOUR AU - Hoops, S. AU - Sahle, S. AU - Gauges, R. AU - Lee, C. AU - Pahle, J. AU - Simus, N. AU - Singhal, M. AU - Xu, L. AU - Mendes, P. AU - Kummer, U. PY - 2006 DA - 2006// TI - COPASI-a COmplex PAthway SImulator JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl485 DO - 10.1093/bioinformatics/btl485 ID - Hoops2006 ER - TY - JOUR AU - Schmidt, H. AU - Jirstrand, M. PY - 2006 DA - 2006// TI - Systems Biology Toolbox for MATLAB: A computational platform for research in Systems Biology JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/bti799 DO - 10.1093/bioinformatics/bti799 ID - Schmidt2006 ER -