The following references provide some pointers to important work in evolutionary systems biology. For a more comprehensive overview of existing work and a framework that details, how various approaches can be combined, see Loewe (2009) and for a substantial update Loewe (2016).



Borenstein E, Kupiec M, Feldman MW & Ruppin E (2008) Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc. Natl. Acad. Sci. USA 105:14482-14487. PubMed

Dean, A. M. & Thornton, J. W. (2007) Mechanistic approaches to the study of evolution: the functional synthesis. Nat. Rev. Genet. 8, 675-88. PubMed

Dekel E, Alon U (2005) "Optimality and evolutionary tuning of the expression level of a protein." Nature 436:588-92. PubMed

Fong SS, Nanchen A, Palsson BO, Sauer U (2006) "Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes." J Biol Chem 281:8024-33. PubMed

Gillespie, D. T. (2007) Stochastic simulation of chemical kinetics. Annu Rev Phys Chem 58, 35-55. PubMed

Harrison R, Papp B, Pál C, Oliver SG, Delneri D (2007) "Plasticity of genetic interactions in metabolic networks of yeast." Proc Natl Acad Sci U S A 104:2307-12. PubMed

Ibarra, R. U., Edwards, J. S., & Palsson, B. O. (2002) Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420, 186-9. PubMed

Lande, R. (2008) Adaptive topography of fluctuating selection in a Mendelian population. J. Evol. Biol. 21, 1096-1105. PubMed

Loewe L (2009) A framework for evolutionary systems biology. BMC Systems Biology 3:27. Journal link

Loewe, L (2015): EvoSysBio in 10 Slides. Figshare 1427128

Loewe (2016) Systems in Evolutionary Systems Biology, pp 297–318, vol 4 in: Kliman (ed) Encyclopedia of Evolutionary Biology, Academic Press, Oxford, UK.

Lynch M (2007) "The evolution of genetic networks by non-adaptive processes." Nat Rev Genet 8:803-813. PubMed

MacLean C & Gudelj I (2006) Resource competition and social conflict in experimental populations of yeast. Nature 441:498-501. PubMed

MacLean C & Buckling A (2009) The Distribution of Fitness Effects of Beneficial Mutations in Pseudomonas aeruginosa. PLoS Genet 5: e1000406. Journal link

Michel JB, Yeh PJ, Chait R, Moellering RC Jr, Kishony R (2008) "Drug interactions modulate the potential for evolution of resistance." Proc Natl Acad Sci U S A 105:14918-23. PubMed

Pál C, Papp B, Lercher MJ, Csermely P, Oliver SG, Hurst LD (2006) "Chance and necessity in the evolution of minimal metabolic networks." Nature 440:667-70. PubMed

Papp, B., Pal, C., & Hurst, L. D. (2004) Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 429, 661-4. PubMed

Schuetz R, Kuepfer L, Sauer U (2007) "Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli." Mol Syst Biol 3:119. PubMed

Segrè D, Deluna A, Church GM, Kishony R (2005) "Modular epistasis in yeast metabolism." Nat Genet 37:77-83. PubMed

Soyer O.S. (editor, 2012). Evolutionary Systems Biology. Book series: Advances in Experimental Medicine and Biology. Springer. Contents

Wagner A (2008) "Neutralism and selectionism: a network-based reconciliation.", Nat Rev Genet 9:965-74. PubMed

Weinreich DM, Delaney NF, Depristo MA, Hartl DL (2006) "Darwinian evolution can follow only very few mutational paths to fitter proteins." Science 312:111-4. PubMed

You L, Yin J (2002) "Dependence of Epistasis on Environment and Mutation Severity as Revealed by in Silico Mutagenesis of Phage T7" Genetics 160:1273-1281. PubMed

Zaslaver A, Mayo AE, Rosenberg R, Bashkin P, Sberro H, Tsalyuk M, Surette MG, Alon U (2004) "Just-in-time transcription program in metabolic pathways." Nat Genet 36:486-91. PubMed