Crow JF., Kimura M (1970, 2009) An introduction to population genetics theory. Blackburn Press, Caldwell
Google Scholar
Charlesworth B (1994) Evolution in age-structured populations. Cambridge studies in mathematical biology, vol 13, 2nd edn. Cambridge University Press, Cambridge
Google Scholar
Brommer JE (2000) The evolution of fitness in life-history theory. Biol Rev Camb Philos Soc 75(3):377–404
PubMed
CrossRef
CAS
Google Scholar
Kingsolver JG, Hoekstra HE, Hoekstra JM, Berrigan D, Vignieri SN, Hill CE, Hoang A, Gibert P, Beerli P (2001) The strength of phenotypic selection in natural populations. Am Nat 157(3):245–261
PubMed
CrossRef
CAS
Google Scholar
Endler JA (1986) Natural selection in the wild. Monographs in population biology, vol 21. Princeton University Press, NJ
Google Scholar
Mitton JB (1997) Selection in natural populations. Oxford University Press, Oxford
Google Scholar
Sunyaev S, Ramensky V, Koch I, Lathe W 3rd, Kondrashov AS, Bork P (2001) Prediction of deleterious human alleles. Hum Mol Genet 10(6):591–597
PubMed
CrossRef
CAS
Google Scholar
Eyre-Walker A, Keightley PD (2007) The distribution of fitness effects of new mutations. Nat Rev Genet 8(8):610–618
PubMed
CrossRef
CAS
Google Scholar
Loewe L, Charlesworth B (2006) Inferring the distribution of mutational effects on fitness in Drosophila. Biol Lett 2(3):426–430
PubMed
CrossRef
Google Scholar
Loewe L, Charlesworth B, Bartolomé C, Nöel V (2006) Estimating selection on non-synonymous mutations. Genetics 172:1079–1092
PubMed
CrossRef
CAS
Google Scholar
Eyre-Walker A, Woolfit M, Phelps T (2006) The distribution of fitness effects of new deleterious amino acid mutations in humans. Genetics 173(2):891–900
PubMed
CrossRef
CAS
Google Scholar
Keightley PD, Halligan DL (2011) Inference of site frequency spectra from high-throughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humans. Genetics 188(4):931–940 doi:10.1534/genetics.111.128355
PubMed
CrossRef
Google Scholar
Schneider A, Charlesworth B, Eyre-Walker A, Keightley PD (2011) A method for inferring the rate of occurrence and fitness effects of advantageous mutations. Genetics 189:1427–1437
PubMed
CrossRef
CAS
Google Scholar
Keightley PD, Eyre-Walker A (2007) Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies. Genetics 177(4):2251–2261
PubMed
CrossRef
CAS
Google Scholar
Keightley PD, Eyre-Walker A (2010) What can we learn about the distribution of fitness effects of new mutations from DNA sequence data? Philos Trans Roy Soc Lond B Biol Sci 365(1544):1187–1193 doi:10.1098/rstb.2009.0266
CrossRef
Google Scholar
Orr HA (2005) The genetic theory of adaptation: a brief history. Nat Rev Genet 6(2):119–127
PubMed
CrossRef
CAS
Google Scholar
Orr HA (2010) The population genetics of beneficial mutations. Philos Trans Roy Soc Lond B Biol Sci 365:1195–1201
CrossRef
Google Scholar
Kitano H (2002) Computational systems biology. Nature 420(6912):206–210
PubMed
CrossRef
CAS
Google Scholar
Kitano H (2002) Systems biology: a brief overview. Science 295(5560):1662–1664
PubMed
CrossRef
CAS
Google Scholar
Loewe L (2007) Poster: An evolutionary framework for systems biology. In: 41th Population Genetics Group Meeting, Warwick, UK. http://www.populationgeneticsgroup.org/wpcontent/uploads/2010/01/PGGWarwickProgramme.pdf and http://evolution.ws/people/loewe/posters
Loewe L (2009) A framework for evolutionary systems biology. BMC Syst Biol 3:27
PubMed
CrossRef
Google Scholar
Loewe L, Hillston J (2008) The distribution of mutational effects on fitness in a simple circadian clock. Lect Notes Bioinform 5307:156–175
Google Scholar
Gavrilets S (2004) Fitness landscapes and the origin of species, Monographs in population biology, Princeton University Press, NJ 41:476
Google Scholar
Joyce AR, Palsson BO (2008) Predicting gene essentiality using genome-scale in silico models. Meth Mol Biol 416:433–457
CrossRef
CAS
Google Scholar
Samal A, Matias Rodrigues JF, Jost J, Martin OC, Wagner A (2010) Genotype networks in metabolic reaction spaces. BMC Syst Biol 4:30
PubMed
CrossRef
Google Scholar
Cowperthwaite MC, Economo EP, Harcombe WR, Miller EL, Meyers LA (2008) The ascent of the abundant: how mutational networks constrain evolution. PLoS Comput Biol 4(7):e1000110
PubMed
CrossRef
Google Scholar
Dodd AN, Salathia N, Hall A, Kevei E, Toth R, Nagy F, Hibberd JM, Millar AJ, Webb AAR (2005) Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage. Science 309(5734):630–633
PubMed
CrossRef
CAS
Google Scholar
Loewe L, Hillston J (2012) Evolutionary systems biology estimates of distributions of mutational effects in a circadian clock (in preparation)
Google Scholar
MacLean RC, Perron GG, Gardner A (2010) Diminishing returns from beneficial mutations and pervasive epistasis shape the fitness landscape for rifampicin resistance in Pseudomonas aeruginosa. Genetics 186(4):1345–1354. doi:10.1534/genetics.110.123083
PubMed
CrossRef
CAS
Google Scholar
You L., Yin J (2002) Dependence of epistasis on environment and mutation severity as revealed by in silico mutagenesis of phage t7. Genetics 160(4):1273–1281
PubMed
Google Scholar
You L, Suthers PF, Yin J (2002) Effects of Escherichia coli physiology on growth of phage T7 in vivo and in silico. J Bacteriol 184(7):1888–1894
PubMed
CrossRef
CAS
Google Scholar
Endy D, You L, Yin J, Molineux IJ (2000) Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes. Proc Natl Acad Sci USA 97(10):5375–5380
PubMed
CrossRef
CAS
Google Scholar
Segre D, Deluna A, Church GM, Kishony R (2005) Modular epistasis in yeast metabolism. Nat Genet 37(1):77–83
PubMed
CAS
Google Scholar
Medina M (2005) Genomes, phylogeny, and evolutionary systems biology. Proc Natl Acad Sci USA 102(1):6630–6635
PubMed
CrossRef
CAS
Google Scholar
Koonin EV, Wolf YI (2006) Evolutionary systems biology: links between gene evolution and function. Curr Opin Biotechnol 17(5):481–487
PubMed
CrossRef
CAS
Google Scholar