From 2007.igem.org

Bibliography

• [1] Kremling A, Bettenbrock K, and Gilles ED. Analysis of global control of Escherichia coli

carbohydrate uptake. BMC Syst Biol, 1(1):42, Sep 2007. JOURNAL ARTICLE.

• [2] G K Ackers, A D Johnson, and M A Shea. Quantitative model for gene regulation by lambda

phage repressor. Proc Natl Acad Sci U S A, 79(4):1129{1133, Feb 1982.

• [3] J B Andersen, C Sternberg, L K Poulsen, S P Bjorn, M Givskov, and S Molin. New unstable

variants of green fuorescent protein for studies of transient gene expression in bacteria. Appl Environ Microbiol, 64(6):2240-2246, Jun 1998.

• [4] Katja Bettenbrock, Sophia Fischer, Andreas Kremling, Knut Jahreis, Thomas Sauter, and

Ernst-Dieter Gilles. A quantitative approach to catabolite repression in Escherichia coli. J Biol Chem, 281(5):2578-2584, Feb 2006.

• [5] F Conti. Claude Bernard: primer of the second biomedical revolution. Nat Rev Mol Cell

Biol, 2(9):703-708, Sep 2001. Biography.

• [6] M W Covert, C H Schilling, and B Palsson. Regulation of gene expression in

ux balance models of metabolism. J Theor Biol, 213(1):73-88, Nov 2001.

• [7] Markus W Covert and Bernhard O Palsson. Transcriptional regulation in constraints-based

metabolic models of Escherichia coli. J Biol Chem, 277(31):28058-28064, Aug 2002.

• [8] Markus W Covert and Bernhard O Palsson. Constraints-based models: regulation of gene

expression reduces the steady-state solution space. J Theor Biol, 221(3):309-325, Apr 2003.

• [9] J S Edwards and B O Palsson. Metabolic flux balance analysis and the in silico analysis of

Escherichia coli K-12 gene deletions. BMC Bioinformatics, 1:1, 2000.

• [10] J S Edwards and B O Palsson. Robustness analysis of the Escherichia coli metabolic network.

Biotechnol Prog, 16(6):927-939, Nov 2000.

• [11] F JACOB and J MONOD. [Genes of structure and genes of regulation in the biosynthesis of

proteins.]. C R Hebd Seances Acad Sci, 249:1282-1284, Oct 1959.

• [12] F JACOB, D PERRIN, C SANCHEZ, and J MONOD. [Operon: a group of genes with the

expression coordinated by an operator.]. C R Hebd Seances Acad Sci, 250:1727-1729, Feb 1960.

• [13] A Kremling, K Bettenbrock, B Laube, K Jahreis, J W Lengeler, and E D Gilles. The

organization of metabolic reaction networks. III. Application for diauxic growth on glucose and lactose. Metab Eng, 3(4):362-379, Oct 2001.

• [14] A Kremling, S Fischer, T Sauter, K Bettenbrock, and E D Gilles. Time hierarchies in the

Escherichia coli carbohydrate uptake and metabolism. Biosystems, 73(1):57-71, Jan 2004.

• [15] A Kremling and E D Gilles. The organization of metabolic reaction networks. II. Signal

processing in hierarchical structured functional units. Metab Eng, 3(2):138-150, Apr 2001.

• [16] A Kremling, K Jahreis, J W Lengeler, and E D Gilles. The organization of metabolic reaction

networks: a signal-oriented approach to cellular models. Metab Eng, 2(3):190-200, Jul 2000. Comparative Study.

• [17] Andreas Kremling, Sophia Fischer, Kapil Gadkar, Francis J Doyle, Thomas Sauter, Eric

Bullinger, Frank Allgower, and Ernst D Gilles. A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions. Genome Res, 14(9):1773- 1785, Sep 2004.

• [18] Jong Min Lee, Erwin P Gianchandani, and Jason A Papin. Flux balance analysis in the era

of metabolomics. Brief Bioinform, 7(2):140-150, Jun 2006.

• [19] S B Lee and J E Bailey. Genetically structured models for lac promotor-operator function in

the Escherichia coli chromosome and in multicopy plasmids: lac operator function. Biotechnol. Bioeng., 26:1372-1382, 1984a.

• [20] S B Lee and J E Bailey. Genetically structured models for lac promotor{operator function in

the Escherichia coli chromosome and in multicopy plasmids: lac operator function. Biotechnol. Bioeng., 26:1383-1389, 1984b.

• [21] Santillan M and Mackey MC. Dynamic behavior in mathematical models of the tryptophan

operon. Chaos, 11(1):261-268, Mar 2001. JOURNAL ARTICLE.

• [22] Michael C Mackey, Moises Santillan, and Necmettin Yildirim. Modeling operon dynamics:

the tryptophan and lactose operons as paradigms. C R Biol, 327(3):211-224, Mar 2004.

• [23] Radhakrishnan Mahadevan, Jeremy S Edwards, and Francis J 3rd Doyle. Dynamic

flux balance analysis of diauxic growth in Escherichia coli. Biophys J, 83(3):1331-1340, Sep 2002.

• [24] Jerome T Mettetal, Dale Muzzey, Juan M Pedraza, Ertugrul M Ozbudak, and Alexander van

Oudenaarden. Predicting stochastic gene expression dynamics in single cells. Proc Natl Acad Sci U S A, 103(19):7304-7309, May 2006.

• [25] Atul Narang. Comparative analysis of some models of gene regulation in mixed-substrate

microbial growth. J Theor Biol, 242(2):489-501, Sep 2006. Comparative Study.

• [26] Atul Narang and Sergei S Pilyugin. Bacterial gene regulation in diauxic and non-diauxic

growth. J Theor Biol, 244(2):326-348, Jan 2007.

• [27] Ertugrul M Ozbudak, Mukund Thattai, Iren Kurtser, Alan D Grossman, and Alexander van

Oudenaarden. Regulation of noise in the expression of a single gene. Nat Genet, 31(1):69-73, May 2002.

• [28] Ertugrul M Ozbudak, Mukund Thattai, Han N Lim, Boris I Shraiman, and Alexander

Van Oudenaarden. Multistability in the lactose utilization network of Escherichia coli. Nature, 427(6976):737-740, Feb 2004.

• [29] M Santillan and M C Mackey. Dynamic regulation of the tryptophan operon: a modeling

study and comparison with experimental data. Proc Natl Acad Sci U S A, 98(4):1364-1369, Feb 2001.

• [30] M Santillan, M C Mackey, and E S Zeron. Origin of bistability in the lac Operon. Biophys

J, 92(11):3830-3842, Jun 2007.

• [31] Moises Santillan and Michael C Mackey. Influence of catabolite repression and inducer exclusion

on the bistable behavior of the lac operon. Biophys J, 86(3):1282-1292, Mar 2004. Comparative Study.

• [32] Moises Santillan and Michael C Mackey. Why the lysogenic state of phage lambda is so stable:

a mathematical modeling approach. Biophys J, 86(1 Pt 1):75-84, Jan 2004. Comparative Study.

• [33] C H Schilling, J S Edwards, and B O Palsson. Toward metabolic phenomics: analysis of

genomic data using flux balances. Biotechnol Prog, 15(3):288-295, May 1999.

• [34] S Strelitz. On the Routh-Hurwitz problem. Am. Math. Mon, 84:542-544, 1977.
• [35] Jose M G Vilar, Calin C Guet, and Stanislas Leibler. Modeling network dynamics: the lac

operon, a case study. J Cell Biol, 161(3):471-476, May 2003.

• [36] J Wang, E D Gilles, J W Lengeler, and K Jahreis. Modeling of inducer exclusion and

catabolite repression based on a PTS-dependent sucrose and non-PTS-dependent glycerol transport systems in Escherichia coli K-12 and its experimental veri�cation. J Biotechnol, 92(2):133-158, Dec 2001.

• [37] P Wong, S Gladney, and J D Keasling. Mathematical model of the lac operon: inducer

exclusion, catabolite repression, and diauxic growth on glucose and lactose. Biotechnol Prog, 13(2):132-143, Mar 1997.

• [38] Necmettin Yildirim, Moises Santillan, Daisuke Horike, and Michael C Mackey. Dynamics and

bistability in a reduced model of the lac operon. Chaos, 14(2):279-292, Jun 2004. Comparative Study.