M. Adam, B. Murali, N. Glenn, and S. Potter, Epigenetic inheritance based evolution of antibiotic resistance in bacteria, BMC Evolutionary Biology, vol.8, issue.1, p.12, 2008.
DOI : 10.1186/1471-2148-8-52

C. Adami, Digital genetics: unravelling the genetic basis of evolution, Nature Reviews Genetics, vol.96, issue.103, pp.109-118, 2006.
DOI : 10.1038/nrg1771

B. Batut, D. P. Parsons, S. Fischer, G. Beslon, and C. Knibbe, In silico experimental evolution: a tool to test evolutionary scenarios, BMC Bioinformatics, vol.14, issue.Suppl 15, pp.14-25, 2013.
DOI : 10.1016/j.jtbi.2006.09.005

URL : https://hal.archives-ouvertes.fr/hal-00873232

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

G. Beslon, D. P. Parsons, Y. Sanchez-dehesa, J. Peña, and C. Knibbe, Scaling laws in bacterial genomes: A side-effect of selection of mutational robustness?, Biosystems, vol.102, issue.1, pp.32-40, 2010.
DOI : 10.1016/j.biosystems.2010.07.009

URL : https://hal.archives-ouvertes.fr/inria-00593709

R. Bonduriansky and T. Day, Nongenetic Inheritance and Its Evolutionary Implications, Annual Review of Ecology, Evolution, and Systematics, vol.40, issue.1, pp.103-125, 2009.
DOI : 10.1146/annurev.ecolsys.39.110707.173441

S. Casjens, The diverse and dynamic structure of bacterial genomes. Annual review of genetics, pp.339-377, 1998.

E. Danchin, A. Charmantier, F. A. Champagne, A. Mesoudi, B. Pujol et al., Beyond DNA: integrating inclusive inheritance into an extended theory of evolution, Nature Reviews Genetics, vol.439, issue.7, pp.12475-486, 2011.
DOI : 10.1038/nrg3028

T. Hindré, 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, pp.352-365, 2012.
DOI : 10.1038/nrmicro2750

E. Jablonka, B. Oborny, I. Molnar, E. Kisdi, J. Hofbauer et al., The Adaptive Advantage of Phenotypic Memory in Changing Environments, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.350, issue.1332, pp.133-141, 1995.
DOI : 10.1098/rstb.1995.0147

C. Knibbe, A. Coulon, O. Mazet, J. Fayard, and G. Beslon, A Long-Term Evolutionary Pressure on the Amount of Noncoding DNA, Molecular Biology and Evolution, vol.24, issue.10, pp.242344-2353, 2007.
DOI : 10.1093/molbev/msm165

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

C. Knibbe, J. Fayard, and G. Beslon, The Topology of the Protein Network Influences the Dynamics of Gene Order: From Systems Biology to a Systemic Understanding of Evolution, Artificial Life, vol.14, issue.1, pp.149-156, 2008.
DOI : 10.1016/0165-0114(78)90029-5

URL : https://hal.archives-ouvertes.fr/hal-00391448

M. Lachmann and E. Jablonka, The Inheritance of Phenotypes: an Adaptation to Fluctuating Environments, Journal of Theoretical Biology, vol.181, issue.1, pp.1-9, 1996.
DOI : 10.1006/jtbi.1996.0109

D. Misevic, A. Frénoy, A. B. Lindner, and F. Taddei, Shape matters: Lifecycle of cooperative patches promotes cooperation in bulky populations, Evolution, vol.108, issue.3, pp.69788-802, 2015.
DOI : 10.1111/evo.12616

C. Pál, Plasticity, memory and the adaptive landscape of the genotype, Proceedings of the Royal Society B: Biological Sciences, vol.265, issue.1403, pp.1319-1323, 1998.
DOI : 10.1098/rspb.1998.0436

C. Pál and L. D. Hurst, Epigenetic inheritance and evolutionary adaptation, Organelles, Genomes and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics . CRCpress, 2004.

D. P. Parsons, C. Knibbe, and G. Beslon, Importance of the rearrangement rates on the organization of transcription, Proceedings of Artificial Life XII, pp.479-486, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00697043