Bologna University/Literature

From 2007.igem.org

(Difference between revisions)

Revision as of 10:34, 26 October 2007

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.

@@ Line 1: / Line 1: @@
 '''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.
+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.
+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
+variants of green fuorescent protein for studies of transient gene expression in bacteria. ''Appl
-uorescent protein for studies of transient gene expression in bacteria. Appl
+Environ Microbiol'', 64(6):2240-2246, Jun 1998.
-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
+Ernst-Dieter Gilles. A quantitative approach to catabolite repression in Escherichia coli. ''J
-Biol Chem, 281(5):2578{2584, Feb 2006.
+Biol Chem'', 281(5):2578-2584, Feb 2006.
-*[5] F Conti. Claude Bernard: primer of the second biomedical revolution. Nat Rev Mol Cell
+*[5] F Conti. Claude Bernard: primer of the second biomedical revolution. ''Nat Rev Mol Cell
-Biol, 2(9):703{708, Sep 2001. Biography.
+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
+ux balance models of metabolism. ''J Theor Biol'', 213(1):73-88, Nov 2001.
-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.
+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.
+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
+*[9] J S Edwards and B O Palsson. Metabolic flux balance analysis and the in silico analysis of
-ux balance analysis and the in silico analysis of
+Escherichia coli K-12 gene deletions. ''BMC Bioinformatics'', 1:1, 2000.
-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.
+''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.
+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
+expression coordinated by an operator.]. ''C R Hebd Seances Acad Sci'', 250:1727-1729, Feb
 .
 *[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.
+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.
+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.
+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.
+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{
+and model discrimination: problem formulation and solutions. ''Genome Res'', 14(9):1773-
 , 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.
+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
+*[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.
+the Escherichia coli chromosome and in multicopy plasmids: lac operator function. ''Biotechnol.
-Bioeng., 26:1372{1382, 1984a.
+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.
+the Escherichia coli chromosome and in multicopy plasmids: lac operator function. ''Biotechnol.
-Bioeng., 26:1383{1389, 1984b.
+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.
+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.
+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
-ux
+flux balance analysis of diauxic growth in Escherichia coli. ''Biophys J'', 83(3):1331-1340, Sep 2002.
-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
+Oudenaarden. Predicting stochastic gene expression dynamics in single cells. ''Proc Natl Acad
-Sci U S A, 103(19):7304{7309, May 2006.
+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.
+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.
+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,
+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,
+Van Oudenaarden. Multistability in the lactose utilization network of Escherichia coli. ''Nature'',
-(6976):737{740, Feb 2004.
+(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,
+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
+*[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.
+J'', 92(11):3830-3842, Jun 2007.
-*[31] Moises Santillan and Michael C Mackey. In
+*[31] Moises Santillan and Michael C Mackey. Influence of catabolite repression and inducer exclusion
-uence of catabolite repression and inducer exclusion
+on the bistable behavior of the lac operon. ''Biophys J'', 86(3):1282-1292, Mar 2004.
-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
+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
+genomic data using flux balances. ''Biotechnol Prog'', 15(3):288-295, May 1999.
-ux balances. Biotechnol Prog, 15(3):288{295, May 1999.
+*[34] S Strelitz. On the Routh-Hurwitz problem. ''Am. Math. Mon'', 84:542-544, 1977.
-*[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.
+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,
+transport systems in Escherichia coli K-12 and its experimental veri�cation. ''J Biotechnol'',
-(2):133{158, Dec 2001.
+(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,
+exclusion, catabolite repression, and diauxic growth on glucose and lactose. ''Biotechnol Prog'',
-(2):132{143, Mar 1997.
+(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
+bistability in a reduced model of the lac operon. ''Chaos'', 14(2):279-292, Jun 2004. Comparative
 Study.

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Bologna University/Literature

From 2007.igem.org

Revision as of 10:34, 26 October 2007