2010
Fleming, R.M.T, Thiele, I., Provan, G., Nasheuer, H.P., "Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism", J. Theor. Biol., 264 (3): 683-692 (2010).
Thiele, I., Fleming, R.M.T., Bordbar, A., Schellenberger, J., Palsson, B. O.,"Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery", Biophys. J., 98(10): 2072-2081 (2010).
Thiele, I., Palsson, B.O., "Reconstruction annotation jamborees: A community-approach to Systems Biology", Mol. Sys. Biol., 6:361 (2010) (Editorial)
Orth, J., Thiele, I., Palsson, B. O.,"What is flux balance analysis?", Nat. Biotech., 28(3):245-8 (2010).
Orth, J.D., Fleming, R.M.T., Palsson, B.O. Chapter 10.2.1, Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide, EcoSal, doi: 10.1128/ecosal.10.2.1 (2010).
Thiele, I. and Palsson, B. O.,"A protocol for generating a high-quality genome-scale metabolic reconstruction.", Nat. Proctols, 5(1): 93 - 121(2010).
Burgin AB, Magnusson OT, Singh J, Witte P, Staker BL, Bjornsson JM, Thorsteinsdottir M, Hrafnsdottir S, Hagen T, Kiselyov AS, Stewart LJ, Gurney ME. Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety. Nat Biotechnol., 28(1):63-70 (2010).
2009
Fleming, R.M.T., Thiele, I., Nasheuer, H.P., Quantitative assignment of reaction directionality in constraint-based models of metabolism: Application to Escherichia coli, Biophys. Chem., 145(2-3):47-56 (2009).
Cho, B.K., Zengler, K., Qiu, Y., Knight, E.M., Park, Y.S., Barrett, C.L., Gao,Y., and Palsson, B.O., Elucidation of the Transcription Unit Architecture of the Escherichia coli K-12 MG1655 Genome, Nature Biotechnology. Published online: 1 November 2009 | doi:10.1038/nbt.1582 Supplemental Data
Zhang, Y., Thiele, I., Weekes, D., li, Z., Jaroszewski, L., Ginalski, K., Deacon, A.M., Wooley, J., Lesley, S.A., Wilson, I.A., Palsson, B.O., Osterman, A., and Godzik, A., Three-dimensional Structural View of the Central Metabolic Network of Thermotoga maritima., Science, 325(5947): 1544-1549 (2009). More info: here.
Manichaikul A., Ghamsari L., Hom E.F., Lin C., Murray R.R., Chang R.L., Balaji S., Hao T., Shen Y., Chavali A.K., Thiele I., Yang X., Fan C., Mello E., Hill D.E., Vidal M., Salehi-Ashtiani K., Papin J.A., Metabolic network analysis integrated with transcript verification for sequenced genomes. Nature Methods. (2009).
Lewis, N.E., Cho, B.K., Knight, E.M., and Palsson, B.O., Gene Expression Profiling and the Use of Genome-scale ''In Silico'' Models of ''Escherichia coli'' for Analysis: Providing Context for Content, J Bacteriol, 191:3437-44 (2009).
Sigurdsson, M.I., Jamshidi, N., Jonsson J.J., and Palsson, B.O., ''Genome-scale network analysis of imprinted human metabolic genes''. Epigenetics. (2009)
Feist, A.M., Herrgard, M.J., Thiele, I., Reed, J.L., Palsson, B.Ø., "Reconstruction of Biochemical Networks in Microbial Organisms" Nature Reviews Microbiology, 7(2)(2009).
2008
Feist, A.M. and Palsson, B.Ø., The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli., Nature Biotechnology, 26(6): 659 - 667 (2008).