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C
Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen F-C, Fleming RMT, Hsiung CA et al..  2011.  A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.. BMC Syst Biol. 5:8.
Thiele I, Swainston N, Fleming RMT, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD et al..  2013.  A community-driven global reconstruction of human metabolism.. Nat Biotechnol.
F
Thiele I, Fleming RMT, Bordbar A, Schellenberger J, Palsson BØ.  2010.  Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery.. Biophysical journal. 98(10):2072-81.
G
Thiele I, Jamshidi N, Fleming RMT, Palsson BØ.  2009.  Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization.. PLoS computational biology. 5(3):e1000312.
M
Paglia G, Hrafnsdóttir S, Magnúsdóttir M, Fleming RMT, Thorlacius S, Palsson BØ, Thiele I.  2012.  Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS).. Anal Bioanal Chem. 402(3):1183-98.
Thiele I, Fleming RMT, Que R, Bordbar A, Diep D, Palsson BO.  2012.  Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage.. PLoS One. 7(9):e45635.
Q
Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S et al..  2011.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.. Nat Protoc. 6(9):1290-307.