E. Coli

Analysis of the E. coli Network by Other Research Groups

(If your publication is missing from this list, please send it to us and we will add it. The studies have been categorized into five categories based on analysis we performed in this review article.)

Metabolic Engineering Applications

• Burgard, A.P., Pharkya, P. & Maranas, C.D. "Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization" Biotechnol Bioeng 84, 647-657 (2003).

• Pharkya, P., Burgard, A.P. & Maranas, C.D. "Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock" Biotechnol Bioeng 84, 887-899 (2003).

• Pharkya, P., Burgard, A.P. & Maranas, C.D. "OptStrain: a computational framework for redesign of microbial production systems" Genome Res 14, 2367-2376 (2004).

• Alper, H., Jin, Y.S., Moxley, J.F. & Stephanopoulos, G. "Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli" Metab Eng 7, 155-164 (2005).

• Alper, H., Miyaoku, K. & Stephanopoulos, G. "Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets" Nat Biotechnol 23, 612-616 (2005).

• Lee, S.J., Lee, D.-Y., Kim, T.Y., Kim, B.H., Lee, J. & Lee, S.Y. "Metabolic Engineering of Escherichia coli for Enhanced Production of Succinic Acid, Based on Genome Comparison and In Silico Gene Knockout Simulation" Appl Environ Microbiol 71, 7880-7887 (2005).

• Lee, K.H., Park, J.H., Kim, T.Y., Kim, H.U. & Lee, S.Y. "Systems metabolic engineering of Escherichia coli for L-threonine production" Mol Syst Biol 3, 149 (2007).

• Park, J.H., Lee, K.H., Kim, T.Y. & Lee, S.Y. "Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation" Proc Natl Acad Sci USA 104, 7797–7802 (2007).

• Pharkya, P. & Maranas, C.D. "An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems" Metab Eng 8, 1-13 (2006).

• Wang, Q., Chen, X., Yang, Y. & Zhao, X. "Genome-scale in silico aided metabolic analysis and flux comparisons of Escherichia coli to improve succinate production" Appl Microbiol Biotechnol V73, 887-894 (2006).

Studies for Biological Discovery

• Chen, L. & Vitkup, D. "Predicting genes for orphan metabolic activities using phylogenetic profiles" Genome Biol 7, R17 (2006).

• Kharchenko, P., Chen, L., Freund, Y., Vitkup, D. & Church, G.M. "Identifying metabolic enzymes with multiple types of association evidence" BMC Bioinformatics 7 (2006).

• Satish Kumar, V., Dasika, M.S. & Maranas, C.D. "Optimization based automated curation of metabolic reconstructions" BMC Bioinformatics 8, 212 (2007).

• Fuhrer, T., Chen, L., Sauer, U. & Vitkup, D. "Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli" J Bacteriol 189, 8073–8079 (2007).

Studies of Phenotypic Behavior

• Burgard, A.P., Vaidyaraman, S. & Maranas, C.D. "Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments" Biotechnol Prog 17, 791-797 (2001).

• Beard, D.A., Liang, S.D. & Qian, H. "Energy balance for analysis of complex metabolic networks" Biophys J 83, 79-86 (2002).

• Segre, D., Vitkup, D. & Church, G.M. "Analysis of optimality in natural and perturbed metabolic networks" Proc Natl Acad Sci USA 99, 15112-15117 (2002).

• Imielinski, M., Belta, C., Halasz, A. & Rubin, H. "Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities" Bioinformatics 21, 2008-2016 (2005).

• Shlomi, T., Berkman, O. & Ruppin, E. "Regulatory on/off minimization of metabolic flux changes after genetic perturbations" Proc Natl Acad Sci USA 102, 7695-7700 (2005).

• Ghim, C.M., Goh, K.I. & Kahng, B. "Lethality and synthetic lethality in the genome-wide metabolic network of Escherichia coli" J theor Biol 237, 401-411 (2005).

• Henry, C.S., Jankowski, M.D., Broadbelt, L.J. & Hatzimanikatis, V. "Genome-scale thermodynamic analysis of Escherichia coli metabolism" Biophys J 90, 1453-1461 (2006).

• Samal, A., Singh, S., Giri, V., Krishna, S., Raghuram, N. & Jain, S. "Low degree metabolites explain essential reactions and enhance modularity in biological networks" BMC Bioinformatics 7, 118 (2006).

• Kümmel, A., Panke, S. & Heinemann, M. "Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data" Mol Syst Biol 2, 2006.0034 (2006).

• Wunderlich, Z. & Mirny, L.A. "Using the topology of metabolic networks to predict viability of mutant strains" Biophys J 91, 2304-2311 (2006).

• Kümmel, A., Panke, S. & Heinemann, M. "Systematic assignment of thermodynamic constraints in metabolic network models" BMC Bioinformatics 7 (2006).

• Gerdes, S., Edwards, R., Kubal, M., Fonstein, M., Stevens, R. & Osterman, A. "Essential genes on metabolic maps" Curr Opin Biotechnol 17, 448-456 (2006).

• Lyubetskaya, A.V., Rubanov, L.I. & Gelfand, M.S. "Use of the flux model of amino acid metabolism of Escherichia coli" Biochemistry (Mosc) 71, 1256-1260 (2006).

• Henry, C.S., Broadbelt, L.J. & Hatzimanikatis, V. "Thermodynamics-Based Metabolic Flux Analysis" Biophys J 92, 1792-1805 (2007).

• Ederer, M. & Gilles, E.D. "Thermodynamically feasible kinetic models of reaction networks" Biophys J 92, 1846-1857 (2007).

• Choi, H.S., Kim, T.Y., Lee, D.Y. & Lee, S.Y. "Incorporating metabolic flux ratios into constraint-based flux analysis by using artificial metabolites and converging ratio determinants" J Biotechnol 129, 696–705 (2007).

• Hoppe, A., Hoffmann, S. & Holzhutter, H.G. "Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks" BMC Syst Biol 1, 23 (2007).

• Guimera, R., Sales-Pardo, M. & Amaral, L.A. "A network-based method for target selection in metabolic networks" Bioinformatics 23, 1616–1622 (2007).

• Beg, Q.K. et al. "Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity" Proc Natl Acad Sci USA 104, 12663–12668 (2007).

• Kim, P.J. et al. "Metabolite essentiality elucidates robustness of Escherichia coli metabolism" Proc Natl Acad Sci USA 104, 13638–13642 (2007).

• Warren, P.B. & Jones, J.L. "Duality, thermodynamics, and the linear programming problem in constraint-based models of metabolism" Phys Rev Lett 99, 108101 (2007).

• Schuetz, R., Kuepfer, L. & Sauer U. "Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli" Mol Syst Biol 3, 119 (2007).

• Vazquez, A. et al. "Impact of the solvent capacity constraint on E. coli metabolism" BMC Syst Biol 2, 7 (2008).

• Motter, A.E., Gulbahce, N., Almaas, E. & Barabasi, A.L. "Predicting synthetic rescues in metabolic networks" Mol Syst Biol 4, 168 (2008).

• Ow, D.S., Lee, D.Y., Yap, M.G. & Oh, S.K. "Identification of cellular objective for elucidating the physiological state of plasmid-bearing Escherichia coli using genome-scale in silico analysis" Biotechnol Prog 25, 61-67 (2008)

Biological Network Analysis

• Gagneur, J., Jackson, D.B. & Casari, G. "Hierarchical analysis of dependency in metabolic networks" Bioinformatics 19, 1027-1034 (2003).

• Burgard, A.P., Nikolaev, E.V., Schilling, C.H. & Maranas, C.D. "Flux Coupling Analysis of Genome-Scale Metabolic Network Reconstructions" Genome. Res 14, 301-312 (2004).

• Almaas, E., Kovacs, B., Vicsek, T., Oltvai, Z.N. & Barabasi, A.L. "Global organization of metabolic fluxes in the bacterium Escherichia coli" Nature 427, 839-843 (2004). See Cover Art below

• Nikolaev, E.V., Burgard, A.P. & Maranas, C.D. "Elucidation and structural analysis of conserved pools for genome-scale metabolic reconstructions" Biophys J 88, 37-49 (2005).

• Almaas, E., Oltvai, Z.N. & Barabasi, A.L. "The Activity Reaction Core and Plasticity of Metabolic Networks" PLoS Comput Biol 1, e68 (2005).

• Imielinski, M., Belta, C., Rubin, H. & Halasz, A. "Systematic Analysis of Conservation Relations in Escherichia coli Genome-Scale Metabolic Network Reveals Novel Growth Media" Biophys J 90, 2659-2672 (2006).

• Samal, A. & Jain, S. "The regulatory network of E. coli metabolism as a boolean dynamical system exhibits both homeostasis and flexibility of response" Under Review (2007).

• Shlomi, T., Eisenberg, Y., Sharan, R. & Ruppin, E. "A genome-scale computational study of the interplay between transcriptional regulation and metabolism" Mol Syst Biol 3, 101 (2007).

• Beasley, J.E. & Planes, F.J. "Recovering metabolic pathways via optimization" Bioinformatics 23, 92-98 (2007).

• Almaas, E. "Optimal flux patterns in cellular metabolic networks" Chaos (Woodbury, N.Y.) 17, 026107 (2007).

• Sales-Pardo, M., Guimera, R., Moreira, A.A. & Amaral, L.A. "Extracting the hierarchical organization of complex systems" Proc Natl Acad Sci USA 104, 15224–15229 (2007).

• Notebaart, R.A., Teusink, B., Siezen, R.J. & Papp, B. "Co-regulation of metabolic genes is better explained by flux coupling than by network distance" PLoS Comput Biol 4, e26 (2008).

• Mahadevan, R. & Lovley, D.R. "The degree of redundancy in metabolic genes is linked to mode of metabolism" Biophys J 94, 1216–1220 (2008).

Studies of Bacterial Evolution

• Pal, C., Papp, B. & Lercher, M.J. "Horizontal gene transfer depends on gene content of the host" Bioinformatics 21 Suppl 2, ii222-ii223 (2005).

• Pal, C., Papp, B. & Lercher, M.J. "Adaptive evolution of bacterial metabolic networks by horizontal gene transfer" Nat Genet 37, 1372-1375 (2005).

• Pal, C., Papp, B., Lercher, M.J., Csermely, P., Oliver, S.G. & Hurst, L.D. "Chance and necessity in the evolution of minimal metabolic networks" Nature 440, 667-670 (2006).

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