The best models of metabolism

Voit, Eberhard O.

doi:10.1002/wsbm.1391

Title: The best models of metabolism

Journal Article · Fri May 19 00:00:00 EDT 2017 · Wiley Interdisciplinary Reviews: Systems Biology and Medicine

DOI:https://doi.org/10.1002/wsbm.1391· OSTI ID:1399160

Voit, Eberhard O. ^[1]

Department of Biomedical Engineering Georgia Institute of Technology Atlanta GA USA

Biochemical systems are among of the oldest application areas of mathematical modeling. Spanning a time period of over one hundred years, the repertoire of options for structuring a model and for formulating reactions has been constantly growing, and yet, it is still unclear whether or to what degree some models are better than others and how the modeler is to choose among them. In fact, the variety of options has become overwhelming and difficult to maneuver for novices and experts alike. This review outlines the metabolic model design process and discusses the numerous choices for modeling frameworks and mathematical representations. It tries to be inclusive, even though it cannot be complete, and introduces the various modeling options in a manner that is as unbiased as that is feasible. However, the review does end with personal recommendations for the choices of default models. WIREs Syst Biol Med 2017, 9:e1391. doi: 10.1002/wsbm.1391 This article is categorized under: Analytical and Computational Methods > Dynamical Methods Models of Systems Properties and Processes > Mechanistic Models Biological Mechanisms > Metabolism

View Accepted Manuscript (Publisher)

Cite

Export

Save

Sponsoring Organization:: USDOE

Grant/Contract Number:: DE‐AC05‐00OR22725

OSTI ID:: 1399160

Journal Information:: Wiley Interdisciplinary Reviews: Systems Biology and Medicine, Journal Name: Wiley Interdisciplinary Reviews: Systems Biology and Medicine Vol. 9 Journal Issue: 6; ISSN 1939-5094

Publisher:: Wiley Blackwell (John Wiley & Sons)Copyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 27 works

Citation information provided by
Web of Science

References (251)

Mathematical Contributions to the Theory of Evolution. XIX. Second Supplement to a Memoir on Skew Variation Pearson, K. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 216, Issue 538-548 https://doi.org/10.1098/rsta.1916.0009	journal	January 1916
Challenges in lin-log modelling of glycolysis in Lactococcus lactis del Rosario, R. C. H.; Mendoza, E.; Voit, E. O. IET Systems Biology, Vol. 2, Issue 3 https://doi.org/10.1049/iet-syb:20070030	journal	January 2008
Parameter estimation and optimal experimental design Banga, Julio R.; Balsa-Canto, Eva Essays in Biochemistry, Vol. 45 https://doi.org/10.1042/bse0450195	journal	September 2008
Estimating age-related trends in cross-sectional studies using S-distributions Sorribas, A.; March, J.; Voit, E. O. Statistics in Medicine, Vol. 19, Issue 5 https://doi.org/10.1002/(SICI)1097-0258(20000315)19:5<697::AID-SIM378>3.0.CO;2-Y	journal	March 2000
Lotka-Volterra representation of general nonlinear systems Hernández-Bermejo, Benito; Fairén, Víctor Mathematical Biosciences, Vol. 140, Issue 1 https://doi.org/10.1016/S0025-5564(96)00131-9	journal	February 1997
On Identifiability of Nonlinear ODE Models and Applications in Viral Dynamics Miao, Hongyu; Xia, Xiaohua; Perelson, Alan S. SIAM Review, Vol. 53, Issue 1 https://doi.org/10.1137/090757009	journal	January 2011
Mathematical modelling and assessment of the pH homeostasis mechanisms in Aspergillus niger while in citric acid producing conditions García, Jacqueline; Torres, Néstor Journal of Theoretical Biology, Vol. 282, Issue 1 https://doi.org/10.1016/j.jtbi.2011.04.028	journal	August 2011
Tendency Modeling: A New Approach to Obtain Simplified Kinetic Models of Metabolism Applied to Saccharomyces cerevisiae Visser, Diana; van der Heijden, René; Mauch, Klaus Metabolic Engineering, Vol. 2, Issue 3 https://doi.org/10.1006/mben.2000.0150	journal	July 2000
Metabolic ensemble modeling for strain engineers Tan, Yikun; Liao, James C. Biotechnology Journal, Vol. 7, Issue 3 https://doi.org/10.1002/biot.201100186	journal	October 2011
Modeling forest growth I. Canonical approach Voit, Eberhard O.; Sands, Peter J. Ecological Modelling, Vol. 86, Issue 1 https://doi.org/10.1016/0304-3800(94)00192-8	journal	April 1996
New insights into the complex regulation of the glycolytic pathway in Lactococcus lactis. II. Inference of the precisely timed control system regulating glycolysis Dolatshahi, Sepideh; Fonseca, Luis L.; Voit, Eberhard O. Molecular BioSystems, Vol. 12, Issue 1 https://doi.org/10.1039/C5MB00726G	journal	January 2016
A steady-state kinetic method for the verification of the rapid-equilibrium assumption in allosteric enzymes Symcox, Marina M.; Reinhart, Gregory D. Analytical Biochemistry, Vol. 206, Issue 2 https://doi.org/10.1016/0003-2697(92)90384-J	journal	November 1992
Parameter estimation for differential equations: a generalized smoothing approach: Parameter Estimation for Differential Equations Ramsay, J. O.; Hooker, G.; Campbell, D. Journal of the Royal Statistical Society: Series B (Statistical Methodology), Vol. 69, Issue 5 https://doi.org/10.1111/j.1467-9868.2007.00610.x	journal	October 2007
Enzyme Kinetics: From Diastase to Multi-enzyme Systems Schulz, Arthur R. https://doi.org/10.1017/CBO9780511608438	book	January 1994
Magnesium-ATP and fructose 6-phosphate interactions with phosphofructokinase from Escherichia coli Johnson, Jason L.; Reinhart, Gregory D. Biochemistry, Vol. 31, Issue 46 https://doi.org/10.1021/bi00161a032	journal	November 1992
Advances in flux balance analysis Kauffman, Kenneth J.; Prakash, Purusharth; Edwards, Jeremy S. Current Opinion in Biotechnology, Vol. 14, Issue 5 https://doi.org/10.1016/j.copbio.2003.08.001	journal	October 2003
Hypercooperativity Induced by Interface Mutations in the Phosphofructokinase fromEscherichia coli Auzat, Isabelle; Le Bras, Gisèle; Garel, Jean-Renaud Journal of Molecular Biology, Vol. 246, Issue 2 https://doi.org/10.1006/jmbi.1994.0080	journal	February 1995
Development of fractal kinetic theory for enzyme-catalysed reactions and implications for the design of biochemical pathways Savageau, Michael A. Biosystems, Vol. 47, Issue 1-2 https://doi.org/10.1016/S0303-2647(98)00020-3	journal	June 1998
GS-distributions: A new family of distributions for continuous unimodal variables Muiño, J. M.; Voit, E. O.; Sorribas, A. Computational Statistics & Data Analysis, Vol. 50, Issue 10 https://doi.org/10.1016/j.csda.2005.04.016	journal	June 2006
Exact stochastic simulation of coupled chemical reactions Gillespie, Daniel T. The Journal of Physical Chemistry, Vol. 81, Issue 25 https://doi.org/10.1021/j100540a008	journal	December 1977
Efficient algorithms for ordinary differential equation model identification of biological systems Wedelin, D.; Gennemark, P. IET Systems Biology, Vol. 1, Issue 2 https://doi.org/10.1049/iet-syb:20050098	journal	March 2007
Fermentation pathway kinetics and metabolic flux control in suspended and immobilized Saccharomyces cerevisiae Galazzo, Jorge L.; Bailey, James E. Enzyme and Microbial Technology, Vol. 12, Issue 3 https://doi.org/10.1016/0141-0229(90)90033-M	journal	March 1990
BioModel Engineering with Petri Nets Blätke, Mary Ann; Heiner, Monika; Marwan, Wolfgang Algebraic and Discrete Mathematical Methods for Modern Biology https://doi.org/10.1016/B978-0-12-801213-0.00007-1	book	January 2015
Dynamic modeling of the central carbon metabolism ofEscherichia coli Chassagnole, Christophe; Noisommit-Rizzi, Naruemol; Schmid, Joachim W. Biotechnology and Bioengineering, Vol. 79, Issue 1 https://doi.org/10.1002/bit.10288	journal	May 2002
Spatiotemporal modeling of microbial metabolism Chen, Jin; Gomez, Jose A.; Höffner, Kai BMC Systems Biology, Vol. 10, Issue 1 https://doi.org/10.1186/s12918-016-0259-2	journal	March 2016
Comparison of different algorithms for simultaneous estimation of multiple parameters in kinetic metabolic models Baker, Syed Murtuza; Schallau, Kai; Junker, Björn H. Journal of Integrative Bioinformatics, Vol. 7, Issue 3 https://doi.org/10.1515/jib-2010-133	journal	December 2010
A high-order conservative Patankar-type discretisation for stiff systems of production–destruction equations Burchard, Hans; Deleersnijder, Eric; Meister, Andreas Applied Numerical Mathematics, Vol. 47, Issue 1 https://doi.org/10.1016/S0168-9274(03)00101-6	journal	October 2003
Utility of in vitro drug metabolism data in predicting in vivo metabolic clearance Brian Houston, J. Biochemical Pharmacology, Vol. 47, Issue 9 https://doi.org/10.1016/0006-2952(94)90520-7	journal	April 1994
Estimation of metabolic pathway systems from different data sources Chou, I. -C.; Voit, E. O.; Fonseca, L. L. IET Systems Biology, Vol. 3, Issue 6 https://doi.org/10.1049/iet-syb.2008.0180	journal	November 2009
Network regulation of the immune response: alternative control points for suppressor modulation of effector lymphocytes. Irvine, D. H.; Savageau, M. A. The Journal of Immunology, Vol. 134, Issue 4 https://doi.org/10.4049/jimmunol.134.4.2100	journal	April 1985
Quantitative approaches to the analysis of the control and regulation of microbial metabolism Westerhoff, Hans V.; van Heeswijk, Wally; Kahn, Daniel Antonie van Leeuwenhoek, Vol. 60, Issue 3-4 https://doi.org/10.1007/BF00430365	journal	September 1991
The Spatial Organization of Metabolism Within the Plant Cell Sweetlove, Lee J.; Fernie, Alisdair R. Annual Review of Plant Biology, Vol. 64, Issue 1 https://doi.org/10.1146/annurev-arplant-050312-120233	journal	April 2013
Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems Lomnitz, Jason G.; Savageau, Michael A. Frontiers in Genetics, Vol. 7 https://doi.org/10.3389/fgene.2016.00118	journal	July 2016
Symmetry structure in discrete models of biochemical systems: natural subsystems and the weak control hierarchy in a new model of computation driven by interactions Nehaniv, Chrystopher L.; Rhodes, John; Egri-Nagy, Attila Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 373, Issue 2046 https://doi.org/10.1098/rsta.2014.0223	journal	July 2015
Cause and cure of sloppiness in ordinary differential equation models Tönsing, Christian; Timmer, Jens; Kreutz, Clemens Physical Review E, Vol. 90, Issue 2 https://doi.org/10.1103/PhysRevE.90.023303	journal	August 2014
Decoupling dynamical systems for pathway identification from metabolic profiles Voit, E. O.; Almeida, J. Bioinformatics, Vol. 20, Issue 11 https://doi.org/10.1093/bioinformatics/bth140	journal	February 2004
A rigorous derivation of the chemical master equation Gillespie, Daniel T. Physica A: Statistical Mechanics and its Applications, Vol. 188, Issue 1-3 https://doi.org/10.1016/0378-4371(92)90283-V	journal	September 1992
Order Reduction of the Chemical Master Equation via Balanced Realisation López-Caamal, Fernando; Marquez-Lago, Tatiana T. PLoS ONE, Vol. 9, Issue 8 https://doi.org/10.1371/journal.pone.0103521	journal	August 2014
Mathematical and computational techniques to deduce complex biochemical reaction mechanisms Crampin, E. Progress in Biophysics and Molecular Biology, Vol. 86, Issue 1 https://doi.org/10.1016/j.pbiomolbio.2004.04.002	journal	September 2004
Phenotypes and tolerances in the design space of biochemical systems Savageau, M. A.; Coelho, P. M. B. M.; Fasani, R. A. Proceedings of the National Academy of Sciences, Vol. 106, Issue 16 https://doi.org/10.1073/pnas.0809869106	journal	March 2009
Stochastic Approaches for Systems Biology Ullah, Mukhtar; Wolkenhauer, Olaf https://doi.org/10.1007/978-1-4614-0478-1	book	January 2011
Constructing stochastic models from deterministic process equations by propensity adjustment Wu, Jialiang; Vidakovic, Brani; Voit, Eberhard O. BMC Systems Biology, Vol. 5, Issue 1 https://doi.org/10.1186/1752-0509-5-187	journal	January 2011
An interval approach for dealing with flux distributions and elementary modes activity patterns Llaneras, F.; Picó, J. Journal of Theoretical Biology, Vol. 246, Issue 2 https://doi.org/10.1016/j.jtbi.2006.12.029	journal	May 2007
Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy Penas, David R.; González, Patricia; Egea, Jose A. BMC Bioinformatics, Vol. 18, Issue 1 https://doi.org/10.1186/s12859-016-1452-4	journal	January 2017
Parameter estimation of kinetic models from metabolic profiles: two-phase dynamic decoupling method Jia, Gengjie; Stephanopoulos, Gregory N.; Gunawan, Rudiyanto Bioinformatics, Vol. 27, Issue 14 https://doi.org/10.1093/bioinformatics/btr293	journal	May 2011
Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations Ishii, N.; Nakahigashi, K.; Baba, T. Science, Vol. 316, Issue 5824 https://doi.org/10.1126/science.1132067	journal	April 2007
Modeling and Simulation of Molecular Biology Systems Using Petri Nets: Modeling Goals of Various Approaches Hardy, Simon; Robillard, Pierre N. Journal of Bioinformatics and Computational Biology, Vol. 02, Issue 04 https://doi.org/10.1142/S0219720004000764	journal	December 2004
Isotopically non-stationary metabolic flux analysis: complex yet highly informative Wiechert, Wolfgang; Nöh, Katharina Current Opinion in Biotechnology, Vol. 24, Issue 6 https://doi.org/10.1016/j.copbio.2013.03.024	journal	December 2013
Computation and analysis of time-dependent sensitivities in Generalized Mass Action systems Schwacke, John H.; Voit, Eberhard O. Journal of Theoretical Biology, Vol. 236, Issue 1 https://doi.org/10.1016/j.jtbi.2005.02.013	journal	September 2005
Parameter optimization in S-system models Vilela, Marco; Chou, I-Chun; Vinga, Susana BMC Systems Biology, Vol. 2, Issue 1 https://doi.org/10.1186/1752-0509-2-35	journal	April 2008
Determining identifiable parameter combinations using subset profiling Eisenberg, Marisa C.; Hayashi, Michael A. L. Mathematical Biosciences, Vol. 256 https://doi.org/10.1016/j.mbs.2014.08.008	journal	October 2014
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1 Sigurdsson, Martin I.; Jamshidi, Neema; Steingrimsson, Eirikur BMC Systems Biology, Vol. 4, Issue 1 https://doi.org/10.1186/1752-0509-4-140	journal	January 2010
Recasting nonlinear models as S-systems Voit, Eberhard O. Mathematical and Computer Modelling, Vol. 11 https://doi.org/10.1016/0895-7177(88)90469-4	journal	January 1988
Network regulation of the immune response: modulation of suppressor lymphocytes by alternative signals including contrasuppression. Irvine, D. H.; Savageau, M. A. The Journal of Immunology, Vol. 134, Issue 4 https://doi.org/10.4049/jimmunol.134.4.2117	journal	April 1985
Flux analysis and metabolomics for systematic metabolic engineering of microorganisms Toya, Yoshihiro; Shimizu, Hiroshi Biotechnology Advances, Vol. 31, Issue 6 https://doi.org/10.1016/j.biotechadv.2013.05.002	journal	November 2013
Mathematical analysis of models for reaction kinetics in intracellular environments Bajzer, Željko; Huzak, Miljenko; Neff, Kevin L. Mathematical Biosciences, Vol. 215, Issue 1 https://doi.org/10.1016/j.mbs.2008.05.003	journal	September 2008
Flux duality in nonlinear GMA systems: Implications for metabolic engineering Marin-Sanguino, Alberto; Mendoza, Eduardo R.; Voit, Eberhard O. Journal of Biotechnology, Vol. 149, Issue 3 https://doi.org/10.1016/j.jbiotec.2009.12.009	journal	September 2010
New insights into the complex regulation of the glycolytic pathway in Lactococcus lactis. I. Construction and diagnosis of a comprehensive dynamic model Dolatshahi, Sepideh; Fonseca, Luis L.; Voit, Eberhard O. Molecular BioSystems, Vol. 12, Issue 1 https://doi.org/10.1039/C5MB00331H	journal	January 2016
Estimation of dynamic flux profiles from metabolic time series data Chou, I-Chun; Voit, Eberhard O. BMC Systems Biology, Vol. 6, Issue 1 https://doi.org/10.1186/1752-0509-6-84	journal	January 2012
Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation Mendes, P.; Kell, D. Bioinformatics, Vol. 14, Issue 10 https://doi.org/10.1093/bioinformatics/14.10.869	journal	November 1998
A constrained wavelet smoother for pathway identification tasks in systems biology Dolatshahi, Sepideh; Vidakovic, Brani; Voit, Eberhard O. Computers & Chemical Engineering, Vol. 71 https://doi.org/10.1016/j.compchemeng.2014.07.019	journal	December 2014
Biochemical systems analysis Savageau, Michael A. Journal of Theoretical Biology, Vol. 25, Issue 3 https://doi.org/10.1016/S0022-5193(69)80027-5	journal	December 1969
New types of experimental data shape the use of enzyme kinetics for dynamic network modeling Tummler, Katja; Lubitz, Timo; Schelker, Max FEBS Journal, Vol. 281, Issue 2 https://doi.org/10.1111/febs.12525	journal	November 2013
Joining forces of Bayesian and frequentist methodology: a study for inference in the presence of non-identifiability Raue, Andreas; Kreutz, Clemens; Theis, Fabian Joachim Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 371, Issue 1984 https://doi.org/10.1098/rsta.2011.0544	journal	February 2013
Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws Schnell, S.; Turner, T. E. Progress in Biophysics and Molecular Biology, Vol. 85, Issue 2-3 https://doi.org/10.1016/j.pbiomolbio.2004.01.012	journal	June 2004
Stepwise inference of likely dynamic flux distributions from metabolic time series data Faraji, Mojdeh; Voit, Eberhard O. Bioinformatics, Vol. 33, Issue 14 https://doi.org/10.1093/bioinformatics/btx126	journal	March 2017
Biochemical systems analysis of genome-wide expression data Voit, E. O.; Radivoyevitch, T. Bioinformatics, Vol. 16, Issue 11 https://doi.org/10.1093/bioinformatics/16.11.1023	journal	November 2000
Growth equations: A general equation and a survey of special cases Savageau, Michael A. Mathematical Biosciences, Vol. 48, Issue 3-4 https://doi.org/10.1016/0025-5564(80)90061-9	journal	April 1980
A graph-theoretical analysis of metabolic regulation Kohn, Michael C.; Letzkus, William J. Journal of Theoretical Biology, Vol. 100, Issue 2 https://doi.org/10.1016/0022-5193(83)90353-3	journal	January 1983
Automated smoother for the numerical decoupling of dynamics models Vilela, Marco; Borges, Carlos CH; Vinga, Susana BMC Bioinformatics, Vol. 8, Issue 1 https://doi.org/10.1186/1471-2105-8-305	journal	August 2007
Smooth functional tempering for nonlinear differential equation models Campbell, David; Steele, Russell J. Statistics and Computing, Vol. 22, Issue 2 https://doi.org/10.1007/s11222-011-9234-3	journal	March 2011
Framework for network modularization and Bayesian network analysis to investigate the perturbed metabolic network Kim, Hyun; Kim, Tae; Lee, Sang BMC Systems Biology, Vol. 5, Issue Suppl 2 https://doi.org/10.1186/1752-0509-5-S2-S14	journal	January 2011
Kinetic modeling using S-systems and lin-log approaches Wang, Feng-Sheng; Ko, Chih-Lung; Voit, Eberhard O. Biochemical Engineering Journal, Vol. 33, Issue 3 https://doi.org/10.1016/j.bej.2006.11.002	journal	March 2007
Algebraic Systems Biology: Theses and Hypotheses Mishra, Bud Algebraic Biology https://doi.org/10.1007/978-3-540-73433-8_1	book	January 2007
Approximative kinetic formats used in metabolic network modeling Heijnen, Joseph J. Biotechnology and Bioengineering, Vol. 91, Issue 5 https://doi.org/10.1002/bit.20558	journal	January 2005
The Determination of Enzyme Dissociation Constants Lineweaver, Hans; Burk, Dean Journal of the American Chemical Society, Vol. 56, Issue 3 https://doi.org/10.1021/ja01318a036	journal	March 1934
Identification of metabolic system parameters using global optimization methods Polisetty, Pradeep K.; Voit, Eberhard O.; Gatzke, Edward P. Theoretical Biology and Medical Modelling, Vol. 3, Issue 1 https://doi.org/10.1186/1742-4682-3-4	journal	January 2006
A detailed metabolic flux analysis of an underdetermined network of CHO cells Zamorano, F.; Wouwer, A. Vande; Bastin, G. Journal of Biotechnology, Vol. 150, Issue 4 https://doi.org/10.1016/j.jbiotec.2010.09.944	journal	December 2010
Systems Analysis of the Role of Bone Morphogenic Protein 4 in Endothelial Inflammation Yin, Weiwei; Jo, Hanjoong; Voit, Eberhard O. Annals of Biomedical Engineering, Vol. 38, Issue 2 https://doi.org/10.1007/s10439-009-9822-y	journal	October 2009
Universally Sloppy Parameter Sensitivities in Systems Biology Models Gutenkunst, Ryan N.; Waterfall, Joshua J.; Casey, Fergal P. PLoS Computational Biology, Vol. 3, Issue 10 https://doi.org/10.1371/journal.pcbi.0030189	journal	January 2007
The intricate side of systems biology Voit, E.; Neves, A. R.; Santos, H. Proceedings of the National Academy of Sciences, Vol. 103, Issue 25 https://doi.org/10.1073/pnas.0603337103	journal	June 2006
Ueber die chemische Affinität. § 1. Einleitung Guldberg, C. M.; Waage, P. Journal für Praktische Chemie, Vol. 19, Issue 1 https://doi.org/10.1002/prac.18790190111	journal	March 1879
Systems biology: parameter estimation for biochemical models: Parameter estimation in systems biology Ashyraliyev, Maksat; Fomekong-Nanfack, Yves; Kaandorp, Jaap A. FEBS Journal, Vol. 276, Issue 4 https://doi.org/10.1111/j.1742-4658.2008.06844.x	journal	January 2009
Michaelis-Menten mechanism reconsidered: implications of fractal kinetics Savageau, Michael A. Journal of Theoretical Biology, Vol. 176, Issue 1 https://doi.org/10.1006/jtbi.1995.0181	journal	September 1995
An Automated Procedure for the Extraction of Metabolic Network Information from time Series data Marino, Simeone; Voit, Eberhard O. Journal of Bioinformatics and Computational Biology, Vol. 04, Issue 03 https://doi.org/10.1142/S0219720006002259	journal	June 2006
Construction and Customization of Stable Oscillation Models in Biology Yin, Weiwei; Voit, Eberhard O. Journal of Biological Systems, Vol. 16, Issue 04 https://doi.org/10.1142/S0218339008002502	journal	December 2008
Comparing systemic properties of ensembles of biological networks by graphical and statistical methods Alves, R.; Savageau, M. A. Bioinformatics, Vol. 16, Issue 6 https://doi.org/10.1093/bioinformatics/16.6.527	journal	June 2000
The Importance of Compartmentalization in Metabolic flux Models: Yeast as an Ecosystem of Organelles Klitgord, Niels; SegrÈ, Daniel Proceedings of the 9th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2009), Genome Informatics 2009 https://doi.org/10.1142/9781848165786_0005	conference	January 2012
Structural identifiability of polynomial and rational systems Němcová, Jana Mathematical Biosciences, Vol. 223, Issue 2 https://doi.org/10.1016/j.mbs.2009.11.002	journal	February 2010
Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics Visser, Diana; Heijnen, Joseph J. Metabolic Engineering, Vol. 5, Issue 3 https://doi.org/10.1016/S1096-7176(03)00025-9	journal	July 2003
Computational Prediction of Protein–Protein Interaction Networks: Algorithms and Resources Zahiri, Javad; Bozorgmehr, Joseph; Masoudi-Nejad, Ali Current Genomics, Vol. 14, Issue 6 https://doi.org/10.2174/1389202911314060004	journal	September 2013
A pharmacodynamic model for the action of the antibiotic imipenem onPseudomonas aeruginosa populationsin vitro Berg, Paul H.; Voit, Eberhard O.; White, Roger L. Bulletin of Mathematical Biology, Vol. 58, Issue 5 https://doi.org/10.1007/BF02459490	journal	September 1996
Mathematical Modeling and Validation of the Ergosterol Pathway in Saccharomyces cerevisiae Alvarez-Vasquez, Fernando; Riezman, Howard; Hannun, Yusuf A. PLoS ONE, Vol. 6, Issue 12 https://doi.org/10.1371/journal.pone.0028344	journal	December 2011
System estimation from metabolic time-series data Goel, Gautam; Chou, I-Chun; Voit, Eberhard O. Bioinformatics, Vol. 24, Issue 21 https://doi.org/10.1093/bioinformatics/btn470	journal	September 2008
Optimization in integrated biochemical systems Voit, Eberhard O. Biotechnology and Bioengineering, Vol. 40, Issue 5 https://doi.org/10.1002/bit.260400504	journal	August 1992
150 Years of the Mass Action Law Voit, Eberhard O.; Martens, Harald A.; Omholt, Stig W. PLoS Computational Biology, Vol. 11, Issue 1 https://doi.org/10.1371/journal.pcbi.1004012	journal	January 2015
Dynamic sensitivities in chaotic dynamical systems Shiraishi, Fumihide; Hatoh, Yuji Applied Mathematics and Computation, Vol. 186, Issue 2 https://doi.org/10.1016/j.amc.2006.07.141	journal	March 2007
Metabolic network modelling: Including stochastic effects Ao, P. Computers & Chemical Engineering, Vol. 29, Issue 11-12 https://doi.org/10.1016/j.compchemeng.2005.05.007	journal	October 2005
Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets Goss, P. J. E.; Peccoud, J. Proceedings of the National Academy of Sciences, Vol. 95, Issue 12 https://doi.org/10.1073/pnas.95.12.6750	journal	June 1998
Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum Faraji, Mojdeh; Fonseca, Luis L.; Escamilla-Treviño, Luis Biotechnology for Biofuels, Vol. 8, Issue 1 https://doi.org/10.1186/s13068-015-0334-8	journal	September 2015
Biomedical Engineering Strategies in System Design Space Savageau, Michael A. Annals of Biomedical Engineering, Vol. 39, Issue 4 https://doi.org/10.1007/s10439-010-0220-2	journal	January 2011
Growth of complex systems can be related to the properties of their underlying determinants Savageau, M. A. Proceedings of the National Academy of Sciences, Vol. 76, Issue 11 https://doi.org/10.1073/pnas.76.11.5413	journal	November 1979
Fluxes through plant metabolic networks: measurements, predictions, insights and challenges Kruger, Nicholas J.; Ratcliffe, R. George Biochemical Journal, Vol. 465, Issue 1 https://doi.org/10.1042/BJ20140984	journal	December 2014
The Mathematics of Metabolic Control Analysis Revisited Visser, Diana; Heijnen, Joseph J. Metabolic Engineering, Vol. 4, Issue 2 https://doi.org/10.1006/mben.2001.0216	journal	April 2002
ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context Margolin, Adam A.; Nemenman, Ilya; Basso, Katia BMC Bioinformatics, Vol. 7, Issue S1 https://doi.org/10.1186/1471-2105-7-S1-S7	journal	March 2006
Network Inference, Analysis, and Modeling in Systems Biology Albert, Réka The Plant Cell, Vol. 19, Issue 11 https://doi.org/10.1105/tpc.107.054700	journal	November 2007
Universal canonical forms for time-continuous dynamical systems Brenig, L.; Goriely, A. Physical Review A, Vol. 40, Issue 7 https://doi.org/10.1103/PhysRevA.40.4119	journal	October 1989
Pre-steady State Quantification of the Allosteric Influence of Escherichia coli Phosphofructokinase Pham, Audrey S.; Reinhart, Gregory D. Journal of Biological Chemistry, Vol. 276, Issue 37 https://doi.org/10.1074/jbc.M102785200	journal	July 2001
The dawn of a new era of metabolic systems analysis Voit, Eberhard O. Drug Discovery Today: BIOSILICO, Vol. 2, Issue 5 https://doi.org/10.1016/S1741-8364(04)02419-9	journal	September 2004
The Regulation of Cellular Systems Heinrich, Reinhart; Schuster, Stefan https://doi.org/10.1007/978-1-4613-1161-4	book	January 1996
Modeling formalisms in Systems Biology Machado, Daniel; Costa, Rafael S.; Rocha, Miguel AMB Express, Vol. 1, Issue 1 https://doi.org/10.1186/2191-0855-1-45	journal	January 2011
Identification of regulatory structure and kinetic parameters of biochemical networks via mixed-integer dynamic optimization Guillén-Gosálbez, Gonzalo; Miró, Antoni; Alves, Rui BMC Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1186/1752-0509-7-113	journal	January 2013
Parameter uncertainty in biochemical models described by ordinary differential equations Vanlier, J.; Tiemann, C. A.; Hilbers, P. A. J. Mathematical Biosciences, Vol. 246, Issue 2 https://doi.org/10.1016/j.mbs.2013.03.006	journal	December 2013
Genome-scale models of bacterial metabolism: reconstruction and applications Durot, Maxime; Bourguignon, Pierre-Yves; Schachter, Vincent FEMS Microbiology Reviews, Vol. 33, Issue 1 https://doi.org/10.1111/j.1574-6976.2008.00146.x	journal	January 2009
Approximation of delays in biochemical systems Mocek, W. T.; Rudnicki, R.; Voit, E. O. Mathematical Biosciences, Vol. 198, Issue 2 https://doi.org/10.1016/j.mbs.2005.08.001	journal	December 2005
Estimating parameters for generalized mass action models using constraint propagation Tucker, Warwick; Kutalik, Zoltán; Moulton, Vincent Mathematical Biosciences, Vol. 208, Issue 2 https://doi.org/10.1016/j.mbs.2006.11.009	journal	August 2007
On the nature of allosteric transitions: A plausible model Monod, Jacque; Wyman, Jeffries; Changeux, Jean-Pierre Journal of Molecular Biology, Vol. 12, Issue 1 https://doi.org/10.1016/S0022-2836(65)80285-6	journal	May 1965
Canonical Modeling: Review of Concepts with Emphasis on Environmental Health Voit, Eberhard O. Environmental Health Perspectives, Vol. 108, Issue s5 https://doi.org/10.1289/ehp.00108s5895	journal	October 2000
Equation discovery for systems biology: finding the structure and dynamics of biological networks from time course data Džeroski, Sašo; Todorovski, Ljupčo Current Opinion in Biotechnology, Vol. 19, Issue 4 https://doi.org/10.1016/j.copbio.2008.07.002	journal	August 2008
In vivo nuclear magnetic resonance studies of glycolytic kinetics inLactococcus lactis Neves, Ana Rute; Ramos, Ana; Nunes, Marta C. Biotechnology and Bioengineering, Vol. 64, Issue 2 https://doi.org/10.1002/(SICI)1097-0290(19990720)64:2<200::AID-BIT9>3.0.CO;2-K	journal	July 1999
What is flux balance analysis? Orth, Jeffrey D.; Thiele, Ines; Palsson, Bernhard Ø Nature Biotechnology, Vol. 28, Issue 3 https://doi.org/10.1038/nbt.1614	journal	March 2010
Cooperativity and saturation in biochemical networks: A saturable formalism using Taylor series approximations Sorribas, Albert; Hernández-Bermejo, Benito; Vilaprinyo, Ester Biotechnology and Bioengineering, Vol. 97, Issue 5 https://doi.org/10.1002/bit.21316	journal	January 2007
Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism Trinh, Cong T.; Wlaschin, Aaron; Srienc, Friedrich Applied Microbiology and Biotechnology, Vol. 81, Issue 5 https://doi.org/10.1007/s00253-008-1770-1	journal	November 2008
Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: Model validation and dynamic behavior Sorribas, Albert; Curto, Raul; Cascante, Marta Mathematical Biosciences, Vol. 130, Issue 1 https://doi.org/10.1016/0025-5564(94)00094-G	journal	November 1995
Slow-scale tau-leaping method Cao, Yang; Petzold, Linda Computer Methods in Applied Mechanics and Engineering, Vol. 197, Issue 43-44 https://doi.org/10.1016/j.cma.2008.02.024	journal	August 2008
Metabolic network discovery through reverse engineering of metabolome data Çakır, Tunahan; Hendriks, Margriet M. W. B.; Westerhuis, Johan A. Metabolomics, Vol. 5, Issue 3 https://doi.org/10.1007/s11306-009-0156-4	journal	February 2009
Path finding approaches and metabolic pathways Planes, F. J.; Beasley, J. E. Discrete Applied Mathematics, Vol. 157, Issue 10 https://doi.org/10.1016/j.dam.2008.06.035	journal	May 2009
Calculating as Many Fluxes as Possible in Underdetermined Metabolic Networks Klamt, Steffen; Schuster, Stefan Molecular Biology Reports, Vol. 29, Issue 1/2, p. 243-248 https://doi.org/10.1023/A:1020394300385	journal	January 2002
Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation Becker, Scott A.; Palsson, Bernhard Ø. BMC Microbiology, Vol. 5, Issue 1 https://doi.org/10.1186/1471-2180-5-8	journal	March 2005
The inverse problem in mathematical biology Clermont, Gilles; Zenker, Sven Mathematical Biosciences, Vol. 260 https://doi.org/10.1016/j.mbs.2014.09.001	journal	February 2015
Contributions to the Mathematical Theory of Evolution. II. Skew Variation in Homogeneous Material Pearson, K. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 186, Issue 0 https://doi.org/10.1098/rsta.1895.0010	journal	January 1895
Qualitatively distinct phenotypes in the design space of biochemical systems Savageau, Michael A.; Fasani, Rick A. FEBS Letters, Vol. 583, Issue 24 https://doi.org/10.1016/j.febslet.2009.10.073	journal	October 2009
Metabolism of citric acid production byAspergillus niger: Model definition, steady-state analysis and constrained optimization of citric acid production rate Alvarez-Vasquez, Fernando; González-Alcón, Carlos; Torres, Néstor V. Biotechnology and Bioengineering, Vol. 70, Issue 1 https://doi.org/10.1002/1097-0290(20001005)70:1<82::AID-BIT10>3.0.CO;2-V	journal	January 2000
Strategies for representing metabolic pathways within biochemical systems theory: Reversible pathways Sorribas, Albert; Savageau, Michael A. Mathematical Biosciences, Vol. 94, Issue 2 https://doi.org/10.1016/0025-5564(89)90066-7	journal	June 1989
Approximate accelerated stochastic simulation of chemically reacting systems Gillespie, Daniel T. The Journal of Chemical Physics, Vol. 115, Issue 4 https://doi.org/10.1063/1.1378322	journal	July 2001
The Attractions of Proteins for Small Molecules and ions Scatchard, George Annals of the New York Academy of Sciences, Vol. 51, Issue 4 https://doi.org/10.1111/j.1749-6632.1949.tb27297.x	journal	May 1949
Mathematical formalisms based on approximated kinetic representations for modeling genetic and metabolic pathways Alves, Rui; Vilaprinyo, Ester; Hernández-Bermejo, Benito Biotechnology and Genetic Engineering Reviews, Vol. 25, Issue 1 https://doi.org/10.5661/bger-25-1	journal	January 2008
Biochemical systems theory and metabolic control theory: 1. fundamental similarities and differences Savageau, Michael A.; Voit, Eberhard O.; Irvine, Douglas H. Mathematical Biosciences, Vol. 86, Issue 2 https://doi.org/10.1016/0025-5564(87)90007-1	journal	October 1987
A genetic network for the clock of Neurospora crassa Yu, Y.; Dong, W.; Altimus, C. Proceedings of the National Academy of Sciences, Vol. 104, Issue 8 https://doi.org/10.1073/pnas.0611005104	journal	February 2007
XS-systems: eXtended S-Systems and Algebraic Differential Automata for Modeling Cellular Behavior Antoniotti, Marco; Policriti, Alberto; Ugel, Nadia High Performance Computing — HiPC 2002 https://doi.org/10.1007/3-540-36265-7_41	book	January 2002
Taming the complexity of biochemical models through bisimulation and collapsing: theory and practice Antoniotti, M.; Piazza, C.; Policriti, A. Theoretical Computer Science, Vol. 325, Issue 1 https://doi.org/10.1016/j.tcs.2004.03.064	journal	September 2004
Determining Enzyme Kinetics for Systems Biology with Nuclear Magnetic Resonance Spectroscopy Eicher, Johann; Snoep, Jacky; Rohwer, Johann Metabolites, Vol. 2, Issue 4 https://doi.org/10.3390/metabo2040818	journal	November 2012
On the relationship between sloppiness and identifiability Chis, Oana-Teodora; Villaverde, Alejandro F.; Banga, Julio R. Mathematical Biosciences, Vol. 282 https://doi.org/10.1016/j.mbs.2016.10.009	journal	December 2016
Large-Scale Kinetic Parameter Identification of Metabolic Network Model of <i>E. coli</i> Using PSO Adam Kunna, Mohammed; Abdul Kadir, Tuty Asmawaty; Jaber, Aqeel S. Advances in Bioscience and Biotechnology, Vol. 06, Issue 02 https://doi.org/10.4236/abb.2015.62012	journal	January 2015
Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments Monk, J. M.; Charusanti, P.; Aziz, R. K. Proceedings of the National Academy of Sciences, Vol. 110, Issue 50 https://doi.org/10.1073/pnas.1307797110	journal	November 2013
Global structure of sloppiness in a nonlinear model: Sloppiness structure identification in a nonlinear model Tafintseva, Valeria; Tøndel, Kristin; Ponosov, Arcady Journal of Chemometrics, Vol. 28, Issue 8 https://doi.org/10.1002/cem.2651	journal	June 2014
Detection of stoichiometric inconsistencies in biomolecular models Gevorgyan, A.; Poolman, M. G.; Fell, D. A. Bioinformatics, Vol. 24, Issue 19 https://doi.org/10.1093/bioinformatics/btn425	journal	August 2008
Ab initio reconstruction of metabolic pathways Boyer, F.; Viari, A. Bioinformatics, Vol. 19, Issue Suppl 2 https://doi.org/10.1093/bioinformatics/btg1055	journal	September 2003
Kinetics of the allosteric interactions of phosphofructokinase from Escherichia coli Blangy, D.; Buc, H.; Monod, J. Journal of Molecular Biology, Vol. 31, Issue 1 https://doi.org/10.1016/0022-2836(68)90051-X	journal	January 1968
A New Family of Probability Distributions with Applications to Monte Carlo Studies Johnson, Mark E.; Tietjen, Gary L.; Beckman, Richard J. Journal of the American Statistical Association, Vol. 75, Issue 370 https://doi.org/10.1080/01621459.1980.10477464	journal	June 1980
Benchmarks for identification of ordinary differential equations from time series data Gennemark, Peter; Wedelin, Dag Bioinformatics, Vol. 25, Issue 6 https://doi.org/10.1093/bioinformatics/btp050	journal	January 2009
Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: Steady-state analysis Cascante, Marta; Curto, Raul; Sorribas, Albert Mathematical Biosciences, Vol. 130, Issue 1 https://doi.org/10.1016/0025-5564(94)00093-F	journal	November 1995
Integration of kinetic information on yeast sphingolipid metabolism in dynamical pathway models Alvarez-Vasquez, Fernando; Sims, Kellie J.; Hannun, Yusuf A. Journal of Theoretical Biology, Vol. 226, Issue 3 https://doi.org/10.1016/j.jtbi.2003.08.010	journal	February 2004
Predicting Network Activity from High Throughput Metabolomics Li, Shuzhao; Park, Youngja; Duraisingham, Sai PLoS Computational Biology, Vol. 9, Issue 7 https://doi.org/10.1371/journal.pcbi.1003123	journal	July 2013
A Linear Steady-State Treatment of Enzymatic Chains. Critique of the Crossover Theorem and a General Procedure to Identify Interaction Sites with an Effector Heinrich, Reinhart; Rapoport, Tom A. European Journal of Biochemistry, Vol. 42, Issue 1 https://doi.org/10.1111/j.1432-1033.1974.tb03319.x	journal	February 1974
Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome Steinway, Steven N.; Biggs, Matthew B.; Loughran, Thomas P. PLOS Computational Biology, Vol. 11, Issue 6 https://doi.org/10.1371/journal.pcbi.1004338	journal	June 2015
Biochemical systems analysis Savageau, Michael A. Journal of Theoretical Biology, Vol. 25, Issue 3 https://doi.org/10.1016/S0022-5193(69)80026-3	journal	December 1969
Computing with Membranes Păun, Gheorghe Journal of Computer and System Sciences, Vol. 61, Issue 1 https://doi.org/10.1006/jcss.1999.1693	journal	August 2000
Mathematical models of purine metabolism in man Curto, Raul; O. Voit, Eberhard; Sorribas, Albert Mathematical Biosciences, Vol. 151, Issue 1 https://doi.org/10.1016/S0025-5564(98)10001-9	journal	July 1998
Biochemical systems analysis Savageau, Michael A. Journal of Theoretical Biology, Vol. 26, Issue 2 https://doi.org/10.1016/S0022-5193(70)80013-3	journal	February 1970
Automated construction and analysis of the design space for biochemical systems Fasani, R. A.; Savageau, M. A. Bioinformatics, Vol. 26, Issue 20 https://doi.org/10.1093/bioinformatics/btq479	journal	September 2010
Universal formats for nonlinear ordinary differential systems Kerner, Edward H. Journal of Mathematical Physics, Vol. 22, Issue 7 https://doi.org/10.1063/1.525074	journal	July 1981
Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways Alves, R.; Savageau, M. A. Bioinformatics, Vol. 16, Issue 6 https://doi.org/10.1093/bioinformatics/16.6.534	journal	June 2000
Inferring Cellular Networks Using Probabilistic Graphical Models Friedman, N. Science, Vol. 303, Issue 5659 https://doi.org/10.1126/science.1094068	journal	February 2004
Biochemical systems theory and metabolic control theory: 2. the role of summation and connectivity relationships Savageau, Michael A.; Voit, Eberhard O.; Irvine, Douglas H. Mathematical Biosciences, Vol. 86, Issue 2 https://doi.org/10.1016/0025-5564(87)90008-3	journal	October 1987
Dynamic Modeling of Cell-Free Biochemical Networks Using Effective Kinetic Models Wayman, Joseph; Sagar, Adithya; Varner, Jeffrey Processes, Vol. 3, Issue 1 https://doi.org/10.3390/pr3010138	journal	March 2015
The Behavior of Intact Biochemical Control Systems Savageau, Michael A. Current Topics in Cellular Regulation https://doi.org/10.1016/B978-0-12-152806-5.50010-2	book	January 1972
Stochastic Simulation of Chemical Kinetics Gillespie, Daniel T. Annual Review of Physical Chemistry, Vol. 58, Issue 1 https://doi.org/10.1146/annurev.physchem.58.032806.104637	journal	May 2007
Identification of Biochemical Network Modules Based on Shortest Retroactive Distances Sridharan, Gautham Vivek; Hassoun, Soha; Lee, Kyongbum PLoS Computational Biology, Vol. 7, Issue 11 https://doi.org/10.1371/journal.pcbi.1002262	journal	November 2011
An efficient method for calculation of dynamic logarithmic gains in biochemical systems theory Shiraishi, Fumihide; Hatoh, Yuji; Irie, Toshinori Journal of Theoretical Biology, Vol. 234, Issue 1 https://doi.org/10.1016/j.jtbi.2004.11.015	journal	May 2005
Modelling metabolic networks using power-laws and S-systems Voit, Eberhard O. Essays in Biochemistry, Vol. 45 https://doi.org/10.1042/bse0450029	journal	September 2008
A Mathematical Model for the Influence of Fructose 6-Phosphate, ATP, Potassium, Ammonium and Magnesium on the Phosphofructokinase from Rat Erythrocytes Otto, Matthias; Heinrich, Reinhart; Kuhn, Brigitte European Journal of Biochemistry, Vol. 49, Issue 1 https://doi.org/10.1111/j.1432-1033.1974.tb03822.x	journal	November 1974
Exploring the Space of Viable Configurations in a Model of Metabolism–Boundary Co-construction Agmon, Eran; Gates, Alexander J.; Churavy, Valentin Artificial Life, Vol. 22, Issue 2 https://doi.org/10.1162/ARTL_a_00196	journal	May 2016
Cellular concentrations of enzymes and their substrates Albe, Kathy R.; Butler, Margaret H.; Wright, Barbara E. Journal of Theoretical Biology, Vol. 143, Issue 2 https://doi.org/10.1016/S0022-5193(05)80266-8	journal	March 1990
Petri nets: Properties, analysis and applications Murata, T. Proceedings of the IEEE, Vol. 77, Issue 4 https://doi.org/10.1109/5.24143	journal	April 1989
BiomeNet: A Bayesian Model for Inference of Metabolic Divergence among Microbial Communities Shafiei, Mahdi; Dunn, Katherine A.; Chipman, Hugh PLoS Computational Biology, Vol. 10, Issue 11 https://doi.org/10.1371/journal.pcbi.1003918	journal	November 2014
Genome-scale modelling of microbial metabolism with temporal and spatial resolution Henson, Michael A. Biochemical Society Transactions, Vol. 43, Issue 6 https://doi.org/10.1042/BST20150146	journal	November 2015
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions Gillespie, Daniel T. Journal of Computational Physics, Vol. 22, Issue 4 https://doi.org/10.1016/0021-9991(76)90041-3	journal	December 1976
Flux balance analysis of biological systems: applications and challenges Raman, K.; Chandra, N. Briefings in Bioinformatics, Vol. 10, Issue 4 https://doi.org/10.1093/bib/bbp011	journal	March 2009
Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: Model definition and nomenclature Curto, Raul; Sorribas, Albert; Cascante, Marta Mathematical Biosciences, Vol. 130, Issue 1 https://doi.org/10.1016/0025-5564(94)00092-E	journal	November 1995
New results for the analysis of linear systems with time-invariant delays Zhang, Jianrong; Knospe, Carl R.; Tsiotras, Panagiotis International Journal of Robust and Nonlinear Control, Vol. 13, Issue 12 https://doi.org/10.1002/rnc.834	journal	January 2003
Accuracy of alternative representations for integrated biochemical systems Voit, Eberhard O.; Savageau, Michael A. Biochemistry, Vol. 26, Issue 21 https://doi.org/10.1021/bi00395a042	journal	October 1987
Validation of Fractal-Like Kinetic Models by Time-Resolved Binding Kinetics of Dansylamide and Carbonic Anhydrase in Crowded Media Neff, Kevin L.; Offord, Chetan P.; Caride, Ariel J. Biophysical Journal, Vol. 100, Issue 10 https://doi.org/10.1016/j.bpj.2011.04.016	journal	May 2011
Polynomial algebra of discrete models in systems biology Veliz-Cuba, Alan; Jarrah, Abdul Salam; Laubenbacher, Reinhard Bioinformatics, Vol. 26, Issue 13 https://doi.org/10.1093/bioinformatics/btq240	journal	May 2010
A Model Checking Approach to the Parameter Estimation of Biochemical Pathways Donaldson, Robin; Gilbert, David Computational Methods in Systems Biology https://doi.org/10.1007/978-3-540-88562-7_20	book	January 2008
A quantitative model of the generation of N∊-(carboxymethyl)lysine in the Maillard reaction between collagen and glucose Ferreira, António E. N.; Ponces Freire, Ana M. J.; Voit, Eberhard O. Biochemical Journal, Vol. 376, Issue 1 https://doi.org/10.1042/bj20030496	journal	November 2003
Spatial Modeling of Cell Signaling Networks Cowan, Ann E.; Moraru, Ion I.; Schaff, James C. Methods in Cell Biology https://doi.org/10.1016/B978-0-12-388403-9.00008-4	book	January 2012
Enzyme kinetics in vitro and in vivo: Michaelis-Menten revisited Savageau, Michael A. Principles of Medical Biology https://doi.org/10.1016/S1569-2582(06)80007-3	book	January 1995
Dialogue on Reverse-Engineering Assessment and Methods: The DREAM of High-Throughput Pathway Inference Stolovitzky, G.; Monroe, D.; Califano, A. Annals of the New York Academy of Sciences, Vol. 1115, Issue 1 https://doi.org/10.1196/annals.1407.021	journal	October 2007
Design principles for elementary gene circuits: Elements, methods, and examples Savageau, Michael A. Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol. 11, Issue 1 https://doi.org/10.1063/1.1349892	journal	January 2001
The S-Distribution: Approximation of Discrete Distributions Voit, Eberhard O.; Yu, Shuiyang Biometrical Journal, Vol. 36, Issue 2 https://doi.org/10.1002/bimj.4710360215	journal	January 1994
A Perfect Smoother Eilers, Paul H. C. Analytical Chemistry, Vol. 75, Issue 14 https://doi.org/10.1021/ac034173t	journal	July 2003
Flux analysis of underdetermined metabolic networks: the quest for the missing constraints Bonarius, Hendrik P. J.; Schmid, Georg; Tramper, Johannes Trends in Biotechnology, Vol. 15, Issue 8 https://doi.org/10.1016/S0167-7799(97)01067-6	journal	August 1997
Flux-based estimation of parameters in S-systems Sands, P. J.; Voit, E. O. Ecological Modelling, Vol. 93, Issue 1-3 https://doi.org/10.1016/0304-3800(95)00215-4	journal	December 1996
ODEion — A SOFTWARE MODULE FOR STRUCTURAL IDENTIFICATION OF ORDINARY DIFFERENTIAL EQUATIONS Gennemark, Peter; Wedelin, Dag Journal of Bioinformatics and Computational Biology, Vol. 12, Issue 01 https://doi.org/10.1142/S0219720013500157	journal	January 2014
Reverse engineering of regulatory networks in human B cells Basso, Katia; Margolin, Adam A.; Stolovitzky, Gustavo Nature Genetics, Vol. 37, Issue 4 https://doi.org/10.1038/ng1532	journal	March 2005
Recent developments in parameter estimation and structure identification of biochemical and genomic systems Chou, I-Chun; Voit, Eberhard O. Mathematical Biosciences, Vol. 219, Issue 2 https://doi.org/10.1016/j.mbs.2009.03.002	journal	June 2009
A comparison of variant theories of intact biochemical systems. I. enzyme-enzyme interactions and biochemical systems theory Sorribas, Albert; Savageau, Michael A. Mathematical Biosciences, Vol. 94, Issue 2 https://doi.org/10.1016/0025-5564(89)90064-3	journal	June 1989
A method for the determination of flux in elementary modes, and its application toLactobacillus rhamnosus Poolman, M. G.; Venkatesh, K. V.; Pidcock, M. K. Biotechnology and Bioengineering, Vol. 88, Issue 5 https://doi.org/10.1002/bit.20273	journal	January 2004
Nonlinear Differential Equations of Chemically Reacting Systems Gavalas, George R. Springer Tracts in Natural Philosophy https://doi.org/10.1007/978-3-642-87643-1	book	January 1968
The Predator-Prey Model: Do We Live in a Volterra World? Peschel, Manfred; Mende, Werner https://doi.org/10.1515/9783112621349	book	December 1986
Biochemical systems theory: Operational differences among variant representations and their significance Savageau, Michael A. Journal of Theoretical Biology, Vol. 151, Issue 4 https://doi.org/10.1016/S0022-5193(05)80367-4	journal	August 1991
TheS-Distribution A Tool for Approximation and Classification of Univariate, Unimodal Probability Distributions Voit, Eberhard O. Biometrical Journal, Vol. 34, Issue 7 https://doi.org/10.1002/bimj.4710340713	journal	January 1992
Biochemical Systems Theory: A Review Voit, Eberhard O. ISRN Biomathematics, Vol. 2013 https://doi.org/10.1155/2013/897658	journal	January 2013
KINETIC MODEL OF PHOSPHOFRUCTOKINASE-1 FROM ESCHERICHIA COLI Peskov, Kirill; Goryanin, Igor; Demin, Oleg Journal of Bioinformatics and Computational Biology, Vol. 06, Issue 04 https://doi.org/10.1142/S0219720008003643	journal	August 2008
Hybrid Modeling in Biochemical Systems Theory by Means of Functional Petri nets Wu, Jialiang; Voit, Eberhard Journal of Bioinformatics and Computational Biology, Vol. 07, Issue 01 https://doi.org/10.1142/S0219720009004047	journal	February 2009
Integrating Bioinformatics and Computational Biology: Perspectives and Possibilities for In Silico Network Reconstruction in Molecular Systems Biology Alves, Rui; Vilaprinyo, Ester; Sorribas, Albert Current Bioinformatics, Vol. 3, Issue 2 https://doi.org/10.2174/157489308784340694	journal	May 2008
Parameter identifiability of power-law biochemical system models Srinath, Sridharan; Gunawan, Rudiyanto Journal of Biotechnology, Vol. 149, Issue 3 https://doi.org/10.1016/j.jbiotec.2010.02.019	journal	September 2010
Parameter estimation of dynamic biological network models using integrated fluxes Liu, Yang; Gunawan, Rudiyanto BMC Systems Biology, Vol. 8, Issue 1 https://doi.org/10.1186/s12918-014-0127-x	journal	November 2014
Reverse engineering and identification in systems biology: strategies, perspectives and challenges Villaverde, Alejandro F.; Banga, Julio R. Journal of The Royal Society Interface, Vol. 11, Issue 91 https://doi.org/10.1098/rsif.2013.0505	journal	February 2014
Flux Estimation Using Isotopic Tracers: Common Ground for Metabolic Physiology and Metabolic Engineering Kelleher, Joanne K. Metabolic Engineering, Vol. 3, Issue 2 https://doi.org/10.1006/mben.2001.0185	journal	April 2001
13C Metabolic Flux Analysis Wiechert, Wolfgang Metabolic Engineering, Vol. 3, Issue 3 https://doi.org/10.1006/mben.2001.0187	journal	July 2001
Inference of biochemical network models in S-system using multiobjective optimization approach Liu, Pang-Kai; Wang, Feng-Sheng Bioinformatics, Vol. 24, Issue 8 https://doi.org/10.1093/bioinformatics/btn075	journal	March 2008
A Universal Framework for 13C Metabolic Flux Analysis Wiechert, Wolfgang; Möllney, Michael; Petersen, Sören Metabolic Engineering, Vol. 3, Issue 3 https://doi.org/10.1006/mben.2001.0188	journal	July 2001
Parameter estimation of ODE’s via nonparametric estimators Brunel, Nicolas J-B. Electronic Journal of Statistics, Vol. 2, Issue 0 https://doi.org/10.1214/07-EJS132	journal	January 2008
Modeling in Systems Biology: The Petri Net Approach Koch, Ina; Reisig, Wolfgang; Schreiber, Falk Computational Biology https://doi.org/10.1007/978-1-84996-474-6	book	January 2011
Recasting nonlinear differential equations as S-systems: a canonical nonlinear form Savageau, Michael A.; Voit, Eberhard O. Mathematical Biosciences, Vol. 87, Issue 1 https://doi.org/10.1016/0025-5564(87)90035-6	journal	November 1987
A cybernetic view of microbial growth: Modeling of cells as optimal strategists Dhurjati, P.; Ramkrishna, D.; Flickinger, M. C. Biotechnology and Bioengineering, Vol. 27, Issue 1 https://doi.org/10.1002/bit.260270102	journal	January 1985
Characterizability of metabolic pathway systems from time series data Voit, Eberhard O. Mathematical Biosciences, Vol. 246, Issue 2 https://doi.org/10.1016/j.mbs.2013.01.008	journal	December 2013
Gene and Metabolite Regulatory Network Analysis of Early Developing Fruit Tissues Highlights New Candidate Genes for the Control of Tomato Fruit Composition and Development Mounet, Fabien; Moing, Annick; Garcia, Virginie Plant Physiology, Vol. 149, Issue 3 https://doi.org/10.1104/pp.108.133967	journal	January 2009
Mining the Unknown: A Systems Approach to Metabolite Identification Combining Genetic and Metabolic Information Krumsiek, Jan; Suhre, Karsten; Evans, Anne M. PLoS Genetics, Vol. 8, Issue 10 https://doi.org/10.1371/journal.pgen.1003005	journal	October 2012
Biokinetic Modeling and in Vitro – in Vivo Extrapolations Blaauboer, Bas J. Journal of Toxicology and Environmental Health, Part B, Vol. 13, Issue 2-4 https://doi.org/10.1080/10937404.2010.483940	journal	June 2010
Estimating parameters for generalized mass action models with connectivity information Ko, Chih-Lung; Voit, Eberhard O.; Wang, Feng-Sheng BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-140	journal	January 2009
Hybrid Modeling in Computational Neuropsychiatry Marin-Sanguino, A.; Mendoza, E. Pharmacopsychiatry, Vol. 41, Issue S 01 https://doi.org/10.1055/s-2008-1081464	journal	September 2008
Machine Learning Biochemical Networks from Temporal Logic Properties Calzone, Laurence; Chabrier-Rivier, Nathalie; Fages, François Transactions on Computational Systems Biology VI https://doi.org/10.1007/11880646_4	book	January 2006
Models-of-data and models-of-processes in the post-genomic era Voit, Eberhard O. Mathematical Biosciences, Vol. 180, Issue 1-2 https://doi.org/10.1016/S0025-5564(02)00115-3	journal	November 2002
The tricarboxylic acid cycle in Dictyostelium discoideum. I. Formulation of alternative kinetic representations Shiraishi, F.; Savageau, M. A. Journal of Biological Chemistry, Vol. 267, Issue 32 https://doi.org/10.1016/S0021-9258(18)50034-X	journal	November 1992
Supervised enzyme network inference from the integration of genomic data and chemical information Yamanishi, Y.; Vert, J. -P.; Kanehisa, M. Bioinformatics, Vol. 21, Issue Suppl 1 https://doi.org/10.1093/bioinformatics/bti1012	journal	June 2005
A Comparison of Deterministic and Stochastic Modeling Approaches for Biochemical Reaction Systems: On Fixed Points, Means, and Modes Hahl, Sayuri K.; Kremling, Andreas Frontiers in Genetics, Vol. 7 https://doi.org/10.3389/fgene.2016.00157	journal	August 2016
Kinetic modeling of β-chloroprene metabolism: Probabilistic in vitro–in vivo extrapolation of metabolism in the lung, liver and kidneys of mice, rats and humans Yang, Yuching; Himmelstein, Matthew W.; Clewell, Harvey J. Toxicology in Vitro, Vol. 26, Issue 6 https://doi.org/10.1016/j.tiv.2012.04.004	journal	September 2012
Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies Dräger, Andreas; Kronfeld, Marcel; Ziller, Michael J. BMC Systems Biology, Vol. 3, Issue 1 https://doi.org/10.1186/1752-0509-3-5	journal	January 2009
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks Shannon, P. Genome Research, Vol. 13, Issue 11 https://doi.org/10.1101/gr.1239303	journal	November 2003
A comparison of variant theories of intact biochemical systems. II. flux-oriented and metabolic control theories Sorribas, Albert; Savageau, Michael A. Mathematical Biosciences, Vol. 94, Issue 2 https://doi.org/10.1016/0025-5564(89)90065-5	journal	June 1989
A new framework for the estimation of control parameters in metabolic pathways using lin-log kinetics: Control parameter estimation using lin-log kinetics Wu, Liang; Wang, Weiming; Van Winden, Wouter A. European Journal of Biochemistry, Vol. 271, Issue 16 https://doi.org/10.1111/j.0014-2956.2004.04269.x	journal	July 2004
What if the Fit is Unfit? Criteria for Biological Systems Estimation beyond Residual Errors Voit, Eberhard O. Applied Statistics for Network Biology: Methods in Systems Biology, Volume 1 https://doi.org/10.1002/9783527638079.ch9	book	April 2011
Translating biochemical network models between different kinetic formats Hadlich, Frieder; Noack, Stephan; Wiechert, Wolfgang Metabolic Engineering, Vol. 11, Issue 2 https://doi.org/10.1016/j.ymben.2008.10.002	journal	March 2009
Metabolic Control Analysis: A Tool for Designing Strategies to Manipulate Metabolic Pathways Moreno-Sánchez, Rafael; Saavedra, Emma; Rodríguez-Enríquez, Sara Journal of Biomedicine and Biotechnology, Vol. 2008 https://doi.org/10.1155/2008/597913	journal	January 2008
Reverse Engineering Cellular Networks with Information Theoretic Methods Villaverde, Alejandro; Ross, John; Banga, Julio Cells, Vol. 2, Issue 2 https://doi.org/10.3390/cells2020306	journal	May 2013
Genome-Scale Metabolic Network Inference Ebenhöh, Oliver; Kempa, Stefan Encyclopedia of Systems Biology https://doi.org/10.1007/978-1-4419-9863-7_1146	book	January 2013
Identification of neutral biochemical network models from time series data Vilela, Marco; Vinga, Susana; Maia, Marco A. Grivet Mattoso BMC Systems Biology, Vol. 3, Issue 1 https://doi.org/10.1186/1752-0509-3-47	journal	May 2009
$\sqrt n$-consistent parameter estimation for systems of ordinary differential equations: bypassing numerical integration via smoothing Gugushvili, Shota; Klaassen, Chris A. J. Bernoulli, Vol. 18, Issue 3 https://doi.org/10.3150/11-BEJ362	journal	August 2012
Integrative Comparative Analyses of Transcript and Metabolite Profiles from Pepper and Tomato Ripening and Development Stages Uncovers Species-Specific Patterns of Network Regulatory Behavior Osorio, Sonia; Alba, Rob; Nikoloski, Zoran Plant Physiology, Vol. 159, Issue 4 https://doi.org/10.1104/pp.112.199711	journal	June 2012
Metabolic reconstruction using shortest paths Arita, Masanori Simulation Practice and Theory, Vol. 8, Issue 1-2 https://doi.org/10.1016/S0928-4869(00)00006-9	journal	April 2000
Reaction Centric Layout for Metabolic Networks El Kaissi, Muhieddine; Jia, Ming; Reiners, Dirk Advances in Visual Computing https://doi.org/10.1007/978-3-642-10520-3_8	book	January 2009
Reverse engineering of metabolic networks, a critical assessment Hendrickx, Diana M.; Hendriks, Margriet M. W. B.; Eilers, Paul H. C. Mol. BioSyst., Vol. 7, Issue 2 https://doi.org/10.1039/C0MB00083C	journal	January 2011
Time Hierarchies and Model Reduction in Canonical Non-linear Models Löwe, Hannes; Kremling, Andreas; Marin-Sanguino, Alberto Frontiers in Genetics, Vol. 7 https://doi.org/10.3389/fgene.2016.00166	journal	September 2016
An indirect optimization method for biochemical systems: Description of method and application to the maximization of the rate of ethanol, glycerol, and carbohydrate production inSaccharomyces cerevisiae Torres, Néstor V.; Voit, Eberhard O.; Glez-Alcón, Carlos Biotechnology and Bioengineering, Vol. 55, Issue 5 https://doi.org/10.1002/(SICI)1097-0290(19970905)55:5<758::AID-BIT6>3.0.CO;2-A	journal	September 1997
Simpathica: A Computational Systems Biology Tool Within the Valis Bioinformatics Environment Mishra, Bud; Antoniotti, Marco; Paxia, Salvatore Computational Systems Biology https://doi.org/10.1016/B978-012088786-6/50024-1	book	January 2006
A Suprasystem of Probability Distributions Savageau, M. A. Biometrical Journal, Vol. 24, Issue 4 https://doi.org/10.1002/bimj.4710240402	journal	January 1982
Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations1: equations and parameter refinement Mulquiney, Peter J.; Kuchel, Philip W. Biochemical Journal, Vol. 342, Issue 3 https://doi.org/10.1042/bj3420581	journal	September 1999
An ensemble method for identifying regulatory circuits with special reference to the qa gene cluster of Neurospora crassa Battogtokh, D.; Asch, D. K.; Case, M. E. Proceedings of the National Academy of Sciences, Vol. 99, Issue 26 https://doi.org/10.1073/pnas.262658899	journal	December 2002

Similar Records

Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms

Journal Article · Thu Sep 01 00:00:00 EDT 2016 · Wiley Interdisciplinary Reviews: Computational Molecular Science · OSTI ID:1399160

Sousa, Sérgio Filipe; Ribeiro, António J. M.; Neves, Rui P. P.; +4 more

The Doomsday Equation and 50 years beyond: new perspectives on the human‐water system

Journal Article · Wed Mar 11 00:00:00 EDT 2015 · WIRES. Water · OSTI ID:1399160

Parolari, Anthony J.; Katul, Gabriel G.; Porporato, Amilcare

Mandating better buildings: a global review of building codes and prospects for improvement in the United States

Journal Article · Wed Mar 11 00:00:00 EDT 2015 · Wiley Interdisciplinary Reviews. Energy and Environment · OSTI ID:1399160

Sun, Xiaojing; Brown, Marilyn A.; Cox, Matt; +1 more

Title: The best models of metabolism

Citation Formats

References (251)

Similar Records

Related Subjects