S. F. Elena and R. E. Lenski, Microbial genetics: Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation, Nature Reviews Genetics, vol.4, issue.6, pp.457-469, 2003.
DOI : 10.1038/nrg1088

T. J. Kawecki, R. E. Lenski, D. Ebert, B. Hollis, I. Olivieri et al., Experimental evolution. Trends in ecology and evolution, pp.547-560, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00162893

N. Philippe, E. Crozat, R. E. Lenski, and D. Schneider, Evolution of global regulatory networks during a long-term experiment withEscherichia coli, BioEssays, vol.59, issue.9, pp.846-860, 2007.
DOI : 10.1002/bies.20629

D. R. Hekstra and S. Leibler, Contingency and Statistical Laws in Replicate Microbial Closed Ecosystems, Cell, vol.149, issue.5, pp.1164-1173, 2012.
DOI : 10.1016/j.cell.2012.03.040

C. Raeside, J. Gaff, D. E. Deatherage, O. Tenaillon, A. M. Briska et al., Large Chromosomal Rearrangements during a Long-Term Evolution Experiment with Escherichia coli, mBio, vol.5, issue.5, pp.1377-1391, 2014.
DOI : 10.1128/mBio.01377-14

P. B. Rainey and M. Travisano, Adaptive radiation in a heterogeneous environment, Nature, vol.394, issue.6688, pp.69-72, 1998.
DOI : 10.1038/27900

Q. Zhang, G. Lambert, D. Liao, H. Kim, K. Robin et al., Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments, Science, vol.333, issue.6050, pp.333-1764, 2011.
DOI : 10.1126/science.1208747

T. Hindr, C. Knibbe, G. Beslon, and D. Schneider, New insights into bacterial adaptation through in vivo and in silico experimental evolution, Nature Reviews Microbiology, vol.1158, issue.5, pp.352-365, 2012.
DOI : 10.1038/nrmicro2750

O. Tenaillon, F. Taddei, M. Radman, and I. Matic, Second-order selection in bacterial evolution: selection acting on mutation and recombination rates in the course of adaptation, Research in Microbiology, vol.152, issue.1, pp.11-16, 2001.
DOI : 10.1016/S0923-2508(00)01163-3

M. Kirschner and J. Gerhart, Evolvability, Proceedings of the National Academy of Sciences, vol.95, issue.15, pp.8420-8427, 1998.
DOI : 10.1073/pnas.95.15.8420

J. Reisinger and R. Miikkulainen, Selecting for evolvable representations, Proceedings of the 8th annual conference on Genetic and evolutionary computation , GECCO '06, pp.1297-1304, 2006.
DOI : 10.1145/1143997.1144199

S. L. Peck, Simulation as experiment: a philosophical reassessment for biological modeling, Trends in Ecology & Evolution, vol.19, issue.10, pp.530-534, 2004.
DOI : 10.1016/j.tree.2004.07.019

C. O. Wilke, J. L. Wang, C. Ofria, R. E. Lenski, and C. Adami, Evolution of digital organisms at high mutation rates leads to survival of the flattest, Nature, issue.6844, pp.412-331, 2001.

C. Knibbe, A. Coulon, O. Mazet, J. M. Fayard, and G. Beslon, A Long-Term Evolutionary Pressure on the Amount of Noncoding DNA, Molecular Biology and Evolution, vol.24, issue.10, pp.2344-2353, 2007.
DOI : 10.1093/molbev/msm165

URL : https://hal.archives-ouvertes.fr/hal-00391447

G. Beslon, D. P. Parsons, J. M. Pena, C. Rigotti, and Y. Sanchez-dehesa, From digital genetics to knowledge discovery: Perspectives in genetic network understanding, Intelligent Data Analysis, vol.14, issue.2, pp.173-191, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00697024

A. Crombach and P. Hogeweg, Evolution of Evolvability in Gene Regulatory Networks, PLoS Computational Biology, vol.10, issue.7, p.1000112, 2008.
DOI : 10.1371/journal.pcbi.1000112.s005

T. D. Cuypers and P. Hogeweg, Virtual Genomes in Flux: An Interplay of Neutrality and Adaptability Explains Genome Expansion and Streamlining, Genome Biology and Evolution, vol.4, issue.3, pp.212-229, 2012.
DOI : 10.1093/gbe/evr141

M. R. Servedio, Y. Brandvain, S. Dhole, C. L. Fitzpatrick, E. E. Goldberg et al., Not Just a Theory???The Utility of Mathematical Models in Evolutionary Biology, PLoS Biology, vol.272, issue.12, pp.12-1002017, 2014.
DOI : 10.1371/journal.pbio.1002017.g001

P. Dittrich, J. Ziegler, and W. Banzhaf, Artificial Chemistries???A Review, Artificial Life, vol.17, issue.3, pp.225-275, 2001.
DOI : 10.1162/106454601753138998

M. B. Elowitz, A. J. Levine, E. D. Siggia, and P. S. Swain, Stochastic Gene Expression in a Single Cell, Science, vol.297, issue.5584, pp.297-1183, 2002.
DOI : 10.1126/science.1070919

J. R. Newman, S. Ghaemmaghami, J. Ihmels, D. K. Breslow, M. Noble et al., Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise, Nature, vol.99, issue.7095, pp.441-840, 2006.
DOI : 10.1038/nature04785

E. Roberts, A. Magis, J. O. Ortiz, W. Baumeister, and Z. Luthey-schulten, Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study, PLoS Computational Biology, vol.51, issue.3, p.1002010, 2011.
DOI : 10.1371/journal.pcbi.1002010.s003

V. Mozhayskiy and I. Tagkopoulos, Microbial evolution in vivo and in silico: methods and applications, Integr. Biol., vol.102, issue.103, pp.262-277, 2013.
DOI : 10.1039/C2IB20095C

C. Adami, Digital genetics: unravelling the genetic basis of evolution, Nature Reviews Genetics, vol.96, issue.103, p.109, 2006.
DOI : 10.1038/nrg1771

D. E. Rozen, N. Philippe, J. Arjan-de-visser, R. E. Lenski, and D. Schneider, Death and cannibalism in a seasonal environment facilitate bacterial coexistence, Ecology Letters, vol.155, issue.1, pp.34-44, 2009.
DOI : 10.1111/j.1461-0248.2008.01257.x

URL : https://hal.archives-ouvertes.fr/hal-00342476