TY - JOUR AU - Lewis, N. E. AU - Nagarajan, H. AU - Palsson, B. O. PY - 2012 DA - 2012// TI - Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods JO - Nat Rev Microbiol VL - 10 ID - Lewis2012 ER - TY - JOUR AU - Thorleifsson, S. G. AU - Thiele, I. PY - 2011 DA - 2011// TI - rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks JO - Bioinf (Oxford, England) VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr308 DO - 10.1093/bioinformatics/btr308 ID - Thorleifsson2011 ER - TY - JOUR AU - Thiele, I. AU - Palsson, B. O. PY - 2010 DA - 2010// TI - A protocol for generating a high-quality genome-scale metabolic reconstruction JO - Nat Protoc VL - 5 UR - https://doi.org/10.1038/nprot.2009.203 DO - 10.1038/nprot.2009.203 ID - Thiele2010 ER - TY - JOUR AU - Beard, D. a. AU - Liang, S. d. AU - Qian, H. PY - 2002 DA - 2002// TI - Energy balance for analysis of complex metabolic networks JO - Biophys j VL - 83 UR - https://doi.org/10.1016/S0006-3495(02)75150-3 DO - 10.1016/S0006-3495(02)75150-3 ID - Beard2002 ER - TY - JOUR AU - Varma, A. AU - Palsson, B. O. PY - 1993 DA - 1993// TI - Metabolic capabilities of escherichia coli: I. synthesis of biosynthetic precursors and cofactors JO - J Theor Biol VL - 165 UR - https://doi.org/10.1006/jtbi.1993.1202 DO - 10.1006/jtbi.1993.1202 ID - Varma1993 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 / FEBS 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 - Henry, C. S. AU - Broadbelt, L. J. AU - Hatzimanikatis, V. PY - 2007 DA - 2007// TI - Thermodynamics-based metabolic flux analysis JO - Biophys J VL - 92 UR - https://doi.org/10.1529/biophysj.106.093138 DO - 10.1529/biophysj.106.093138 ID - Henry2007 ER - TY - JOUR AU - Fleming, R. M. T. AU - Thiele, I. AU - Provan, G. AU - Nasheuer, H. P. PY - 2010 DA - 2010// TI - Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism JO - J Theor Biol VL - 264 UR - https://doi.org/10.1016/j.jtbi.2010.02.044 DO - 10.1016/j.jtbi.2010.02.044 ID - Fleming2010 ER - TY - JOUR AU - Fleming, R. M. T. AU - Thiele, I. PY - 2011 DA - 2011// TI - von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models JO - Bioinf (Oxford, England) VL - 27 UR - https://doi.org/10.1093/bioinformatics/btq607 DO - 10.1093/bioinformatics/btq607 ID - Fleming2011 ER - TY - JOUR AU - Cogne, G. AU - Rügen, M. AU - Bockmayr, A. AU - Titica, M. AU - Dussap, C. G. AU - Cornet, J. F. AU - Legrand, J. PY - 2011 DA - 2011// TI - A model-based method for investigating bioenergetic processes in autotrophically growing eukaryotic microalgae: application to the green algae Chlamydomonas reinhardtii JO - Biotechnol Prog VL - 27 UR - https://doi.org/10.1002/btpr.596 DO - 10.1002/btpr.596 ID - Cogne2011 ER - TY - JOUR AU - Noor, E. AU - Bar-Even, A. AU - Flamholz, A. AU - Lubling, Y. AU - Davidi, D. AU - Milo, R. PY - 2012 DA - 2012// TI - An integrated open framework for thermodynamics of reactions that combines accuracy and coverage JO - Bioinf (Oxford, England) VL - 27 UR - https://doi.org/10.1093/bioinformatics/bts317 DO - 10.1093/bioinformatics/bts317 ID - Noor2012 ER - TY - JOUR AU - De Martino, D. AU - Figliuzzi, M. AU - De Martino, A. AU - Marinari, E. PY - 2012 DA - 2012// TI - A scalable algorithm to explore the Gibbs energy landscape of genome-scale metabolic networks JO - PLoS Computat Biol VL - 8 UR - https://doi.org/10.1371/journal.pcbi.1002562 DO - 10.1371/journal.pcbi.1002562 ID - De Martino2012 ER - TY - JOUR AU - Lewis, N. E. AU - Hixson, K. K. AU - Conrad, T. M. AU - Lerman, J. a. AU - Charusanti, P. AU - Polpitiya, A. D. AU - Adkins, J. N. AU - Schramm, G. AU - Purvine, S. O. AU - Lopez-Ferrer, D. AU - Weitz, K. K. AU - Eils, R. AU - König, R. AU - Smith, R. D. AU - Palsson, B. O. PY - 2010 DA - 2010// TI - Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models JO - Mol Syst Biol VL - 6 ID - Lewis2010 ER - TY - JOUR AU - Klitgord, N. AU - Segre, D. PY - 2010 DA - 2010// TI - The importance of compartmentalization in metabolic flux models: yeast as an ecosystem of organelles JO - Genome Inform Ser VL - 2009 ID - Klitgord2010 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 - Thiele, I. AU - Fleming, R. M. T. AU - Bordbar, A. AU - Schellenberger, J. AU - Palsson, B. O. PY - 2010 DA - 2010// TI - Functional characterization of alternate optimal solutions of Escherichia coli’s transcriptional and translational machinery JO - Biophys J VL - 98 UR - https://doi.org/10.1016/j.bpj.2010.01.060 DO - 10.1016/j.bpj.2010.01.060 ID - Thiele2010 ER - TY - JOUR AU - Schellenberger, J. AU - Lewis, N. E. AU - Palsson, B. O. PY - 2011 DA - 2011// TI - Elimination of thermodynamically infeasible loops in steady-state metabolic models JO - Biophys J VL - 100 UR - https://doi.org/10.1016/j.bpj.2010.12.3707 DO - 10.1016/j.bpj.2010.12.3707 ID - Schellenberger2011 ER - TY - JOUR AU - Lewis, N. E. AU - Cho, B. K. AU - Knight, E. M. AU - Palsson, B. O. PY - 2009 DA - 2009// TI - Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content JO - J bacteriol VL - 191 UR - https://doi.org/10.1128/JB.00034-09 DO - 10.1128/JB.00034-09 ID - Lewis2009 ER -