TY - JOUR AU - Orth, J. D. AU - Thiele, I. AU - Palsson, B. Ø. 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 - 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 - Schuetz, R. AU - Zamboni, N. AU - Zampieri, M. AU - Heinemann, M. AU - Sauer, U. PY - 2012 DA - 2012// TI - Multidimensional optimality of microbial metabolism JO - Science VL - 336 UR - https://doi.org/10.1126/science.1216882 DO - 10.1126/science.1216882 ID - Schuetz2012 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 - 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 U S A VL - 99 UR - https://doi.org/10.1073/pnas.232349399 DO - 10.1073/pnas.232349399 ID - Segrè2002 ER - TY - JOUR AU - Harcombe, W. R. AU - Delaney, N. F. AU - Leiby, N. AU - Klitgord, N. AU - Marx, C. J. PY - 2013 DA - 2013// TI - The ability of flux balance analysis to predict evolution of central metabolism scales with the initial distance to the optimum JO - PLoS Comput Biol VL - 9 UR - https://doi.org/10.1371/journal.pcbi.1003091 DO - 10.1371/journal.pcbi.1003091 ID - Harcombe2013 ER - TY - JOUR AU - Pramanik, J. AU - Keasling, J. D. PY - 1998 DA - 1998// TI - Effect of Escherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model JO - Biotechnol Bioeng VL - 60 UR - https://doi.org/3.0.CO;2-Q DO - 3.0.CO;2-Q ID - Pramanik1998 ER - TY - JOUR AU - Gianchandani, E. P. AU - Oberhardt, M. A. AU - Burgard, A. P. AU - Maranas, C. D. AU - Papin, J. A. PY - 2008 DA - 2008// TI - Predicting biological system objectives de novo from internal state measurements JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-43 DO - 10.1186/1471-2105-9-43 ID - Gianchandani2008 ER - TY - JOUR AU - Burgard, A. P. AU - Maranas, C. D. PY - 2003 DA - 2003// TI - Optimization-based framework for inferring and testing hypothesized metabolic objective functions JO - Biotechnol Bioeng VL - 82 UR - https://doi.org/10.1002/bit.10617 DO - 10.1002/bit.10617 ID - Burgard2003 ER - TY - JOUR AU - Knorr, A. L. AU - Jain, R. AU - Srivastava, R. PY - 2007 DA - 2007// TI - Bayesian-based selection of metabolic objective functions JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btl619 DO - 10.1093/bioinformatics/btl619 ID - Knorr2007 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. 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 - Collins, S. B. AU - Reznik, E. AU - Segrè, D. PY - 2012 DA - 2012// TI - Temporal expression-based analysis of metabolism JO - PLoS Comput Biol VL - 8 UR - https://doi.org/10.1371/journal.pcbi.1002781 DO - 10.1371/journal.pcbi.1002781 ID - Collins2012 ER - TY - JOUR AU - Blazier, A. S. AU - Papin, J. A. PY - 2012 DA - 2012// TI - Integration of expression data in genome-scale metabolic network reconstructions JO - Front Physiol VL - 3 UR - https://doi.org/10.3389/fphys.2012.00299 DO - 10.3389/fphys.2012.00299 ID - Blazier2012 ER - TY - JOUR AU - Machado, D. AU - Herrgård, M. PY - 2014 DA - 2014// TI - Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism JO - PLoS Comput Biol VL - 10 UR - https://doi.org/10.1371/journal.pcbi.1003580 DO - 10.1371/journal.pcbi.1003580 ID - Machado2014 ER - TY - JOUR AU - Taniguchi, Y. AU - Choi, P. J. AU - Li, G. -. W. AU - Chen, H. AU - Babu, M. AU - Hearn, J. PY - 2010 DA - 2010// TI - Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells JO - Science VL - 329 UR - https://doi.org/10.1126/science.1188308 DO - 10.1126/science.1188308 ID - Taniguchi2010 ER - TY - JOUR AU - Sharma, K. AU - Schmitt, S. AU - Bergner, C. G. AU - Tyanova, S. AU - Kannaiyan, N. AU - Manrique-Hoyos, N. PY - 2015 DA - 2015// TI - Cell type– and brain region–resolved mouse brain proteome JO - Nat Neurosci VL - 18 UR - https://doi.org/10.1038/nn.4160 DO - 10.1038/nn.4160 ID - Sharma2015 ER - TY - JOUR AU - Vemuri, G. N. AU - Altman, E. AU - Sangurdekar, D. P. AU - Khodursky, A. B. AU - Eiteman, M. A. PY - 2006 DA - 2006// TI - Overflow metabolism in Escherichia coli during steady-state growth: transcriptional regulation and effect of the redox ratio JO - Appl Environ Microbiol VL - 72 UR - https://doi.org/10.1128/AEM.72.5.3653-3661.2006 DO - 10.1128/AEM.72.5.3653-3661.2006 ID - Vemuri2006 ER - TY - JOUR AU - Beg, Q. K. AU - Zampieri, M. AU - Klitgord, N. AU - Collins, S. B. AU - Altafini, C. AU - Serres, M. H. PY - 2012 DA - 2012// TI - Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gks467 DO - 10.1093/nar/gks467 ID - Beg2012 ER - TY - JOUR AU - Maddamsetti, R. AU - Lenski, R. E. AU - Barrick, J. E. PY - 2015 DA - 2015// TI - Adaptation, clonal interference, and frequency-dependent interactions in a long-term evolution experiment with Escherichia coli JO - Genetics VL - 200 UR - https://doi.org/10.1534/genetics.115.176677 DO - 10.1534/genetics.115.176677 ID - Maddamsetti2015 ER - TY - JOUR AU - Wiser, M. J. AU - Ribeck, N. AU - Lenski, R. E. PY - 2013 DA - 2013// TI - Long-term dynamics of adaptation in asexual populations JO - Science VL - 342 UR - https://doi.org/10.1126/science.1243357 DO - 10.1126/science.1243357 ID - Wiser2013 ER - TY - JOUR AU - Woods, R. J. AU - Barrick, J. E. AU - Cooper, T. F. AU - Shrestha, U. AU - Kauth, M. R. AU - Lenski, R. E. PY - 2011 DA - 2011// TI - Second-order selection for evolvability in a large Escherichia coli population JO - Science VL - 331 UR - https://doi.org/10.1126/science.1198914 DO - 10.1126/science.1198914 ID - Woods2011 ER - TY - JOUR AU - Plucain, J. AU - Hindré, T. AU - Gac, M. AU - Tenaillon, O. AU - Cruveiller, S. AU - Médigue, C. PY - 2014 DA - 2014// TI - Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli JO - Science VL - 343 UR - https://doi.org/10.1126/science.1248688 DO - 10.1126/science.1248688 ID - Plucain2014 ER - TY - JOUR AU - Burgard, A. P. AU - Nikolaev, E. V. AU - Schilling, C. H. AU - Maranas, C. D. PY - 2004 DA - 2004// TI - Flux coupling analysis of genome-scale metabolic network reconstructions JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.1926504 DO - 10.1101/gr.1926504 ID - Burgard2004 ER - TY - JOUR AU - Nagrath, D. AU - Avila-Elchiver, M. AU - Berthiaume, F. AU - Tilles, A. W. AU - Messac, A. AU - Yarmush, M. L. PY - 2010 DA - 2010// TI - Soft constraints-based multiobjective framework for flux balance analysis JO - Metab Eng VL - 12 UR - https://doi.org/10.1016/j.ymben.2010.05.003 DO - 10.1016/j.ymben.2010.05.003 ID - Nagrath2010 ER - TY - JOUR AU - Shoval, O. AU - Sheftel, H. AU - Shinar, G. AU - Hart, Y. AU - Ramote, O. AU - Mayo, A. PY - 2012 DA - 2012// TI - Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space JO - Science VL - 336 UR - https://doi.org/10.1126/science.1217405 DO - 10.1126/science.1217405 ID - Shoval2012 ER - TY - JOUR AU - Fischer, E. AU - Sauer, U. PY - 2003 DA - 2003// TI - Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS JO - Eur J Biochem VL - 270 UR - https://doi.org/10.1046/j.1432-1033.2003.03448.x DO - 10.1046/j.1432-1033.2003.03448.x ID - Fischer2003 ER - TY - STD TI - Tervo CJ, Reed JL. MapMaker and PathTracer for tracking carbon in genome-scale metabolic models. Biotechnol J. 2016;11(5):648-61. ID - ref27 ER - TY - JOUR AU - Beg, Q. K. AU - Vazquez, A. AU - Ernst, J. AU - Menezes, M. A. AU - Bar-Joseph, Z. AU - Barabási, A. -. L. PY - 2007 DA - 2007// TI - Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity JO - Proc Natl Acad Sci U S A VL - 104 UR - https://doi.org/10.1073/pnas.0609845104 DO - 10.1073/pnas.0609845104 ID - Beg2007 ER - TY - STD TI - Zhao Q, Stettner AI, Reznik E, Segrè D, Paschalidis IC. Learning cellular objectives from fluxes by inverse optimization, Proceedings of the 54th IEEE Conference on Decision and Control, 2015:1271-1276. ID - ref29 ER - TY - JOUR AU - Bertsimas, D. AU - Gupta, V. AU - Paschalidis, I. C. PY - 2015 DA - 2015// TI - Data-driven estimation in equilibrium using inverse optimization JO - Math Program VL - 153 UR - https://doi.org/10.1007/s10107-014-0819-4 DO - 10.1007/s10107-014-0819-4 ID - Bertsimas2015 ER -