TY - JOUR AU - Monod, J. PY - 1949 DA - 1949// TI - The growth of bacterial cultures JO - Annu Rev Microbiol VL - 3 UR - https://doi.org/10.1146/annurev.mi.03.100149.002103 DO - 10.1146/annurev.mi.03.100149.002103 ID - Monod1949 ER - TY - JOUR AU - Stülke, J. AU - Hillen, W. PY - 1999 DA - 1999// TI - Carbon catabolite repression in bacteria JO - Curr Opin Microbiol VL - 2 UR - https://doi.org/10.1016/S1369-5274(99)80034-4 DO - 10.1016/S1369-5274(99)80034-4 ID - Stülke1999 ER - TY - JOUR AU - Brückner, R. AU - Titgemeyer, F. PY - 2002 DA - 2002// TI - Carbon catabolite repression in bacteria: choice of the carbon source and autoregulatory limitation of sugar utilization JO - FEMS Microbiol Lett VL - 209 UR - https://doi.org/10.1016/S0378-1097(02)00559-1 DO - 10.1016/S0378-1097(02)00559-1 ID - Brückner2002 ER - TY - JOUR AU - Boulineau, S. AU - Tostevin, F. AU - Kiviet, D. AU - ten Wolde, P. AU - Nghe, P. AU - Tans, S. PY - 2013 DA - 2013// TI - Single-cell dynamics reveals sustained growth during diauxic shifts JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0061686 DO - 10.1371/journal.pone.0061686 ID - Boulineau2013 ER - TY - JOUR AU - Boianelli, A. AU - Bidossi, A. AU - Gualdi, L. AU - Mulas, L. AU - Mocenni, C. AU - Pozzi, G. PY - 2012 DA - 2012// TI - A non-linear deterministic model for regulation of diauxic lag on cellobiose by the pneumococcal multidomain transcriptional regulator celr JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0047393 DO - 10.1371/journal.pone.0047393 ID - Boianelli2012 ER - TY - JOUR AU - Inada, T. AU - Kimata, K. AU - Aiba, H. PY - 1996 DA - 1996// TI - Mechanism responsible for glucose-lactose diauxie in Escherichia coli: challenge to the cAMP model JO - Genes Cells VL - 1 UR - https://doi.org/10.1046/j.1365-2443.1996.24025.x DO - 10.1046/j.1365-2443.1996.24025.x ID - Inada1996 ER - TY - JOUR AU - Kompala, D. AU - Ramkrishna, D. AU - Jansen, N. AU - Tsao, G. PY - 1986 DA - 1986// TI - Investigation of bacterial growth on mixed substrates: Experimental evaluation of cybernetic models JO - Biotech Bioeng VL - 28 UR - https://doi.org/10.1002/bit.260280715 DO - 10.1002/bit.260280715 ID - Kompala1986 ER - TY - JOUR AU - New, A. AU - Cerulus, B. AU - Govers, S. AU - Perez-Samper, G. AU - Zhu, B. AU - Boogmans, S. PY - 2014 DA - 2014// TI - Different levels of catabolite repression optimize growth in stable and variable environments JO - PLoS Biology VL - 12 UR - https://doi.org/10.1371/journal.pbio.1001764 DO - 10.1371/journal.pbio.1001764 ID - New2014 ER - TY - JOUR AU - Narang, A. PY - 2006 DA - 2006// TI - Comparative analysis of some models of gene regulation in mixed-substrate microbial growth JO - J Theor Biol VL - 242 UR - https://doi.org/10.1016/j.jtbi.2006.03.017 DO - 10.1016/j.jtbi.2006.03.017 ID - Narang2006 ER - TY - JOUR AU - Narang, A. AU - Pilyugin, S. PY - 2007 DA - 2007// TI - Bacterial gene regulation in diauxic and non-diauxic growth JO - J Theor Biol VL - 244 UR - https://doi.org/10.1016/j.jtbi.2006.08.007 DO - 10.1016/j.jtbi.2006.08.007 ID - Narang2007 ER - TY - JOUR AU - Kremling, A. AU - Kremling, S. AU - Bettenbrock, K. PY - 2009 DA - 2009// TI - Catabolite repression in escherichia coli- a comparison of modelling approaches JO - FEBS J VL - 276 UR - https://doi.org/10.1111/j.1742-4658.2008.06810.x DO - 10.1111/j.1742-4658.2008.06810.x ID - Kremling2009 ER - TY - JOUR AU - Deutscher, J. PY - 2008 DA - 2008// TI - The mechanisms of carbon catabolite repression in bacteria JO - Curr Opin Microbiol VL - 11 UR - https://doi.org/10.1016/j.mib.2008.02.007 DO - 10.1016/j.mib.2008.02.007 ID - Deutscher2008 ER - TY - JOUR AU - Zabet, N. AU - Chu, D. PY - 2010 DA - 2010// TI - Computational limits to binary genes JO - J R Soc Interface VL - 7 UR - https://doi.org/10.1098/rsif.2009.0474 DO - 10.1098/rsif.2009.0474 ID - Zabet2010 ER - TY - JOUR AU - Dekel, E. AU - Alon, U. PY - 2005 DA - 2005// TI - Optimality and evolutionary tuning of the expression level of a protein JO - Nature VL - 436 UR - https://doi.org/10.1038/nature03842 DO - 10.1038/nature03842 ID - Dekel2005 ER - TY - JOUR AU - Kalisky, T. AU - Dekel, E. AU - Alon, U. PY - 2007 DA - 2007// TI - Cost-benefit theory and optimal design of gene regulation functions JO - Phys Biol VL - 4 UR - https://doi.org/10.1088/1478-3975/4/4/001 DO - 10.1088/1478-3975/4/4/001 ID - Kalisky2007 ER - TY - JOUR AU - Thattai, M. AU - van Oudenaarden, A. PY - 2004 DA - 2004// TI - Stochastic gene expression in fluctuating environments JO - Genetics VL - 167 UR - https://doi.org/10.1534/genetics.167.1.523 DO - 10.1534/genetics.167.1.523 ID - Thattai2004 ER - TY - JOUR AU - Bennett, A. AU - Lenski, R. PY - 2007 DA - 2007// TI - An experimental test of evolutionary trade-offs during temperature adaptation JO - Proc Natl Acad Sci VL - 104 UR - https://doi.org/10.1073/pnas.0702117104 DO - 10.1073/pnas.0702117104 ID - Bennett2007 ER - TY - JOUR AU - Lestas, I. AU - Paulsson, J. AU - Ross, N. AU - Vinnicombe, G. PY - 2008 DA - 2008// TI - Noise in gene regulatory networks JO - Automatic Control IEEE Trans VL - 53 UR - https://doi.org/10.1109/TAC.2007.911347 DO - 10.1109/TAC.2007.911347 ID - Lestas2008 ER - TY - JOUR AU - Chu, D. AU - Zabet, N. AU - Hone, A. PY - 2011 DA - 2011// TI - Optimal parameter settings for information processing in gene regulatory networks JO - BioSystems VL - 104 UR - https://doi.org/10.1016/j.biosystems.2011.01.006 DO - 10.1016/j.biosystems.2011.01.006 ID - Chu2011 ER - TY - BOOK AU - Alberts, B. AU - Johnson, A. AU - Lewis, J. AU - Raff, M. AU - Roberts, K. AU - Walter, P. PY - 2002 DA - 2002// TI - Molecular Biology of the Cell PB - Garland Science CY - New York ID - Alberts2002 ER - TY - JOUR AU - Chu, D. AU - Zabet, N. AU - Mitavskiy, B. PY - 2009 DA - 2009// TI - Models of transcription factor binding: sensitivity of activation functions to model assumptions JO - J Theor Biol VL - 257 UR - https://doi.org/10.1016/j.jtbi.2008.11.026 DO - 10.1016/j.jtbi.2008.11.026 ID - Chu2009 ER - TY - JOUR AU - Pfeiffer, T. AU - Schuster, S. AU - Bonhoeffer, S. PY - 2001 DA - 2001// TI - Cooperation and competition in the evolution of ATP-producing pathways JO - Science VL - 292 UR - https://doi.org/10.1126/science.1058079 DO - 10.1126/science.1058079 ID - Pfeiffer2001 ER - TY - JOUR AU - Eigen, M. AU - McCaskill, J. AU - Schuster, P. PY - 1989 DA - 1989// TI - The molecular quasi-species JO - Adv Chem Phys VL - 75 ID - Eigen1989 ER - TY - JOUR AU - Jasmin, J. AU - Dillon, M. M. AU - Zeyl, C. PY - 2012 DA - 2012// TI - The yield of experimental yeast populations declines during selection JO - Proc R Soc B Biol Sci VL - 279 UR - https://doi.org/10.1098/rspb.2012.1659 DO - 10.1098/rspb.2012.1659 ID - Jasmin2012 ER - TY - JOUR AU - Molenaar, D. AU - van Berlo, R. AU - de Ridder, D. AU - Teusink, B. PY - 2009 DA - 2009// TI - Shifts in growth strategies reflect tradeoffs in cellular economics JO - Mol Syst Biol VL - 5 UR - https://doi.org/10.1038/msb.2009.82 DO - 10.1038/msb.2009.82 ID - Molenaar2009 ER - TY - JOUR AU - Gottstein, W. AU - Müller, S. AU - Herzel, H. AU - Steuer, R. PY - 2014 DA - 2014// TI - Elucidating the adaptation and temporal coordination of metabolic pathways using in-silico evolution JO - Biosystems VL - 117 UR - https://doi.org/10.1016/j.biosystems.2013.12.006 DO - 10.1016/j.biosystems.2013.12.006 ID - Gottstein2014 ER - TY - JOUR AU - Alon, U. AU - Surette, M. AU - Barkai, N. AU - Leibler, S. PY - 1999 DA - 1999// TI - Robustness in bacterial chemotaxis JO - Nature VL - 397 UR - https://doi.org/10.1038/16483 DO - 10.1038/16483 ID - Alon1999 ER - TY - JOUR AU - Rao, C. AU - Wolf, D. AU - Arkin, A. PY - 2002 DA - 2002// TI - Control, exploitation and tolerance of intracellular noise JO - Nature VL - 420 UR - https://doi.org/10.1038/nature01258 DO - 10.1038/nature01258 ID - Rao2002 ER - TY - JOUR AU - Samoilov, M. AU - Plyasunov, S. AU - Arkin, A. PY - 2005 DA - 2005// TI - Stochastic amplification and signaling in Enzymatic futile cycles through noise-induced Bistability with oscillations JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0406841102 DO - 10.1073/pnas.0406841102 ID - Samoilov2005 ER - TY - JOUR AU - Li, F. AU - Lu, Y. AU - Tang, C. PY - 2004 DA - 2004// TI - The yeast cell-cycle network is robustly designed JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0305937101 DO - 10.1073/pnas.0305937101 ID - Li2004 ER - TY - JOUR AU - Bennett, C. PY - 1986 DA - 1986// TI - On the nature and origin of complexity in discrete, homogeneous, locally-interacting systems JO - Found Phys VL - 16 UR - https://doi.org/10.1007/BF01886523 DO - 10.1007/BF01886523 ID - Bennett1986 ER - TY - JOUR AU - Szekely, P. AU - Sheftel, H. AU - Mayo, A. AU - Alon, U. PY - 2013 DA - 2013// TI - Evolutionary tradeoffs between economy and effectiveness in biological homeostasis systems JO - PLoS Comput Biol VL - 9 UR - https://doi.org/10.1371/journal.pcbi.1003163 DO - 10.1371/journal.pcbi.1003163 ID - Szekely2013 ER - TY - JOUR AU - Elena, S. AU - Lenski, R. PY - 2003 DA - 2003// TI - Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation JO - Nat Rev Genet VL - 4 UR - https://doi.org/10.1038/nrg1088 DO - 10.1038/nrg1088 ID - Elena2003 ER - TY - JOUR AU - Francois, P. AU - Hakim, V. PY - 2004 DA - 2004// TI - Design of genetic networks with specified functions by evolution in silico JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0304532101 DO - 10.1073/pnas.0304532101 ID - Francois2004 ER - TY - JOUR AU - Jenkins, D. AU - Stekel, D. PY - 2010 DA - 2010// TI - De novo evolution of complex, global and hierarchical gene regulatory mechanisms JO - J Mol Evol VL - 71 UR - https://doi.org/10.1007/s00239-010-9369-4 DO - 10.1007/s00239-010-9369-4 ID - Jenkins2010 ER - TY - JOUR AU - Stekel, D. AU - Jenkins, D. PY - 2012 DA - 2012// TI - Evolution of resource and energy management in biologically realistic gene regulatory network models JO - Adv Exp Med Biol VL - 751 UR - https://doi.org/10.1007/978-1-4614-3567-9_14 DO - 10.1007/978-1-4614-3567-9_14 ID - Stekel2012 ER - TY - STD TI - Chu D. Replaying the tape of evolution: Evolving parameters for a simple bacterial metabolism. In: Evolutionary Computation (CEC), 2013 IEEE Congress On: 2013. p. 213–20. doi:10.1109/CEC.2013.6557573. ID - ref37 ER - TY - STD TI - Chu D. Evolving parameters for a noisy bio-systems. In: 2013 IEEE Symposion Series on Computational Intelligence: 2013. ID - ref38 ER - TY - BOOK AU - Goldberg, D. PY - 1989 DA - 1989// TI - Genetic Algorithms in Search, Optimization and Machine Learning PB - Addison-Wesley CY - Reading, Massachusetts ID - Goldberg1989 ER -