Publications

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T
Tremblay P-L, Summers ZM, Glaven RH, Nevin KP, Zengler K, Barrett CL, Qiu Y, Palsson BO, Lovley DR.  2011.  A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution.. Environ Microbiol. 13(1):13-23.
Thomas A, Rahmanian S, Bordbar A, Palsson BØ, Jamshidi N.  2014.  Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance.. Sci Rep. 4:3925.
Thiele I, Vo TD, Price ND, Palsson BØ.  2005.  Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants.. Journal of bacteriology. 187(16):5818-30.
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.
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.
Thiele I, Palsson BØ.  2010.  A protocol for generating a high-quality genome-scale metabolic reconstruction.. Nature protocols. 5(1):93-121.
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, Palsson BØ.  2010.  Reconstruction annotation jamborees: a community approach to systems biology.. Molecular systems biology. 6:361.
Thiele I, Price ND, Vo TD, Palsson BØ.  2005.  Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet.. The Journal of biological chemistry. 280(12):11683-95.
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.
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.
Tan J, Zuniga C, Zengler K.  2015.  Unraveling interactions in microbial communities - from co-cultures to microbiomes.. J Microbiol. 53(5):295-305.

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