A framework for evolutionary systems biology

BMC Systems Biology

Volumn 3, Issue , 2009, Pages

  Loewe, Laurence ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; ALGORITHM; ARTICLE; BIOLOGICAL MODEL; EVOLUTION; GENETICS; GENOMICS; METHODOLOGY; MUTATION; POPULATION GENETICS; SYSTEMS BIOLOGY;

ADAPTATION, BIOLOGICAL; ALGORITHMS; EVOLUTION; GENETICS, POPULATION; GENOMICS; MODELS, GENETIC; MUTATION; SYSTEMS BIOLOGY;

EID: 64049093033     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-3-27     Document Type: Article

References (329)

1. Loewe L Charlesworth B Bartolomé C Nöel V Estimating selection on non-synonymous mutations Genetics 2006, 172:1079-1092 1456207 16299397
2. Eyre-Walker A Keightley PD The distribution of fitness effects of new mutations Nat Rev Genet 2007, 8:610-618 17637733
3. Papin JA Price ND Wiback SJ Fell DA Palsson BO Metabolic pathways in the post-genome era Trends Biochem Sci 2003, 28:250-258 12765837
4. Joyce AR Palsson BO Predicting gene essentiality using genome-scale in silico models Methods Mol Biol 2008, 416:433-457 18392986
5. Bruggeman FJ Westerhoff HV The nature of systems biology Trends Microbiol 2007, 15:45-50 17113776
6. Heuett WJ Beard DA Qian H Linear analysis near a steady-state of biochemical networks: Control analysis, correlation metrics and circuit theory BMC Syst Biol 2008, 2:44 2435235 18482450
7. Schuetz R Kuepfer L Sauer U Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli Mol Syst Biol 2007, 3:119 1949037 17625511
8. Snitkin ES Segrè D Optimality criteria for the prediction of metabolic fluxes in yeast mutants Genome Informatics 2008, 20:123-134
9. Snitkin ES Dudley AM Janse DM Wong K Church GM Segre D Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions Genome Biol 2008, 9:R140 2592718 18808699
10. Papp B Teusink B Notebaart RA A critical view of metabolic network adaptations HFSP Journal 2009, 1:83
11. Edwards JS Ibarra RU Palsson BO In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data Nat Biotechnol 2001, 19:125-130 11175725
12. Shlomi T Berkman O Ruppin E Regulatory on/off minimization of metabolic flux changes after genetic perturbations Proc Natl Acad Sci USA 2005, 102:7695-7700 1140402 15897462
13. Papp B Pal C Hurst LD Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast Nature 2004, 429:661-664 15190353
14. Förster J Famili I Palsson BO Nielsen J Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae OMICS 2003, 7:193-202 14506848
15. Famili I Förster J Nielsen J Palsson BO Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network Proc Natl Acad Sci USA 2003, 100:13134-13139 263729 14578455
16. Segre D Deluna A Church GM Kishony R Modular epistasis in yeast metabolism Nat Genet 2005, 37:77-83 15592468
17. Kacser H Burns JA The control of flux Symp Soc Exp Biol 1973, 27:65-104 4148886
18. Murphy MP Partridge L Toward a Control Theory Analysis of Aging Annu Rev Biochem 2008, 77:777-798 18318658
19. Fell D Understanding the control of metabolism London: Portland Press; 1996.
20. Fell DA Enzymes, metabolites and fluxes J Exp Bot 2005, 56:267-272 15545297
21. Carlson R Fell D Srienc F Metabolic pathway analysis of a recombinant yeast for rational strain development Biotechnol Bioeng 2002, 79:121-134 12115428
22. Fell DA Metabolic control analysis: A survey of its theoretical and experimental development Biochem J 1992, 286(Pt 2):313-330 1132899 1530563
23. Gillespie DT Stochastic simulation of chemical kinetics Annu Rev Phys Chem 2007, 58:35-55 17037977
24. Gibson MA Bruck J Efficient exact stochastic simulation of chemical systems with many species and many channels Journal of Physical Chemistry A 2000, 104:1876-1889
25. Calder M Gilmore S Hillston J Automatically deriving ODEs from process algebra models of signalling pathways Computational Methods in Systems Biology 2005 LFCS, University of Edinburgh 2005, 204-215
26. Loewe L Hillston J Meeting report: Computational models in systems biology Genome Biol 2008, 9:328 2646271 19090975
27. Alberts B The cell as a collection of protein machines: Preparing the next generation of molecular biologists Cell 1998, 92:291-294 9476889
28. Cassman M Barriers to progress in systems biology Nature 2005, 438:1079 16371982
29. Westerhoff HV Palsson BO The evolution of molecular biology into systems biology Nat Biotechnol 2004, 22:1249-1252 15470464
30. Kitano H Systems biology: A brief overview Science 2002, 295:1662-1664 11872829
31. Kitano H Computational systems biology Nature 2002, 420:206-210 12432404
32. Boogerd FC Bruggeman FJ Hofmeyr J-HS Westerhoff HV Systems Biology - philosophical foundations Amsterdam, The Netherlands: Elsevier 2007.
33. Palsson B Systems biology: Properties of reconstructed networks Cambridge; New York: Cambridge University Press; 2006.
34. Alberghina L Westerhoff HV Systems biology: Definitions and perspectives Berlin: Springer; 2008.
35. Schaff J Loew LM The virtual cell Pac Symp Biocomput 1999, 228-239 10380200
36. Chory J Ecker JR Briggs S Caboche M Coruzzi GM Cook D Dangl J Grant S Guerinot ML Henikoff S et al National Science Foundation-Sponsored Workshop Report: "The 2010 Project" functional genomics and the virtual plant. A blueprint for understanding how plants are built and how to improve them Plant Physiol 2000, 123:423-426 1539254 10859172
37. Jones D All systems go: How might systems biology approaches be applied in drug discovery and development? Nature Reviews Drug Discovery 2008, 7:278-279
38. Hood L Heath JR Phelps ME Lin B Systems biology and new technologies enable predictive and preventative medicine Science 2004, 306:640-643 15499008
39. Werner E Meeting report: The future and limits of systems biology Sci STKE 2005, 2005:pE16 15811911
40. Wolkenhauer O Systems biology: The reincarnation of systems theory applied in biology? Brief Bioinform 2001, 2:258-270 11589586
41. Wiegert RG Simulation Models of Ecosystems Annu Rev Ecol Syst 1975, 6:311-338
42. Balding DJ Bishop MJ Cannings C Handbook of statistical genetics Chichester, England; Hoboken, NJ: John Wiley & Sons 3 2007.
43. Barton NH Briggs DEG Eisen JA Goldstein DB Patel NH Evolution Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press; 2007.
44. Crow JF Kimura M An Introduction to Population Genetics Theory Edina, MN, USA: Burgess International Group Incorporated 1970.
45. Fisher RA The genetical theory of natural selection Oxford: Clarendon Press 1 1930.
46. Wright S Evolution in mendelian populations Genetics 1931, 16:97-159 1201091 17246615
47. Kimura M The neutral theory of molecular evolution Cambridge: Cambridge University Press 1983.
48. Fox CW Wolf JB Evolutionary genetics: Concepts and case studies New York: Oxford University Press; 2006.
49. Barton NH Turelli M Natural and sexual selection on many loci Genetics 1991, 127:229-255 1204308 2016044
50. Kirkpatrick M Johnson T Barton N General models of multilocus evolution Genetics 2002, 161:1727-1750 1462196 12196414
51. Lynch M Walsh B Genetics and analysis of quantitative traits Sunderland, Massachusetts: Sinauer Associates 1998.
52. Falconer DS Mackay TFC Introduction to quantiative genetics Harlow, Essex, UK: Longman 4 1996.
53. Haldane JBS The mathematical theory of natural and artificial selection. Part I Trans Camb Philos Soc 1924, 23:19-41
54. Ohta T The nearly neutral theory of molecular evolution Annu Rev Ecol Syst 1992, 23:263-286
55. McVean GAT Charlesworth B A population genetic model for the evolution of synonymous codon usage: Patterns and predictions Genet Res 1999, 74:145-158
56. Rose MR Lauder GV Eds Adaptation San Diego: Academic Press 1996.
57. Darwin C On the origin of species by means of natural selection London,: J. Murray 1859.
58. Grafen A A theory of Fisher's reproductive value J math Biol 2006, 53:15-60 16791649
59. Grafen A The formal Darwinism project: A mid-term report J Evol Biol 2007, 20:1243-1254 17584220
60. Andolfatto P Adaptive evolution of non-coding DNA in Drosophila Nature 2005, 437:1149-1152 16237443
61. The Chimpanzee Sequencing and Analysis Consortium Initial sequence of the chimpanzee genome and comparison with the human genome Nature 2005, 437:69-87 16136131
62. Lander ES Linton LM Birren B Nusbaum C Zody MC Baldwin J Devon K Dewar K Doyle M FitzHugh W et al Initial sequencing and analysis of the human genome Nature 2001, 409:860-921 11237011
63. Begun DJ Holloway AK Stevens K Hillier LW Poh YP Hahn MW Nista PM Jones CD Kern AD Dewey CN et al Population genomics: Whole-genome analysis of polymorphism and divergence in Drosophila simulans PLoS Biol 2007, 5:e310 2062478 17988176
64. Chamary JV Parmley JL Hurst LD Hearing silence: Non-neutral evolution at synonymous sites in mammals Nat Rev Genet 2006, 7:98-108 16418745
65. Eyre-Walker A The genomic rate of adaptive evolution Trends Ecol Evol 2006, 21:569-575 16820244
66. Nielsen R Williamson S Kim Y Hubisz MJ Clark AG Bustamante C Genomic scans for selective sweeps using SNP data Genome Res 2005, 15:1566-1575 1310644 16251466
67. Nielsen R Bustamante C Clark AG Glanowski S Sackton TB Hubisz MJ Fledel-Alon A Tanenbaum DM Civello D White TJ et al A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees PLoS Biol 2005, 3:e170 1088278 15869325
68. Rokyta DR Joyce P Caudle SB Wichman HA An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus Nat Genet 2005, 37:441-444 15778707
69. Betancourt AJ Bollback JP Fitness effects of beneficial mutations: The mutational landscape model in experimental evolution Curr Opin Genet Dev 2006, 16:618-623 17055718
70. Betancourt AJ Genome-wide Patterns of Subsitution in Adaptively Evolving Populations of the RNA Bacteriophage MS2 Genetics 2009. DOI: 10.1534/ genetics.1107.085837 19189959
71. Lenski RE Travisano M Dynamics of adaptation and diversification: A 10,000-generation experiment with bacterial populations Proc Natl Acad Sci USA 1994, 91:6808-6814 44287 8041701
72. Elena SF Lenski RE Evolution experiments with microorganisms: The dynamics and genetic bases of adaptation Nature Review Genetics 2003, 4:457-469
73. Lenski RE Winkworth CL Riley MA Rates of DNA sequence evolution in experimental populations of Escherichia coli during 20,000 generations J Mol Evol 2003, 56:498-508 12664169
74. Philippe N Crozat E Lenski RE Schneider D Evolution of global regulatory networks during a long-term experiment with Escherichia coli Bioessays 2007, 29:846-860 17691099
75. Novak M Pfeiffer T Lenski RE Sauer U Bonhoeffer S Experimental tests for an evolutionary trade-off between growth rate and yield in E. coli Am Nat 2006, 168:242-251 16874633
76. Silander OK Tenaillon O Chao L Understanding the evolutionary fate of finite populations: The dynamics of mutational effects PLoS Biol 2007, 5:e94 1845161 17407380
77. Poon A Chao L The Rate of Compensatory Mutation in the DNA Bacteriophage {phi}X174 Genetics 2005, 170:989-999 1451187 15911582
78. Burch CL Chao L Evolution by small steps and rugged landscapes in the RNA virus phi 6 Genetics 1999, 151:921-927 1460516 10049911
79. Burch CL Chao L Evolvability of an RNA virus is determined by its mutational neighbourhood Nature 2000, 406:625-628 10949302
80. Chao L Fitness of RNA virus decreased by Muller's ratchet Nature 1990, 348:454-455 2247152
81. Chao L Tran TT Tran TT The advantage of sex in the RNA Virus f6 Genetics 1997, 147:953-959 1208270 9383044
82. Biebricher CK Gardiner WC Molecular evolution of RNA in vitro Biophys Chem 1997, 66:179-192 9362559
83. Lawrence MS Bartel DP New ligase-derived RNA polymerase ribozymes RNA 2005, 11:1173-1180 1370801 15987804
84. Müller UF Bartel DP Improved polymerase ribozyme efficiency on hydrophobic assemblies RNA 2008, 14:552-562 2248263 18230767
85. Kudla G Lipinski L Caffin F Helwak A Zylicz M High guanine and cytosine content increases mRNA levels in mammalian cells PLoS Biol 2006, 4:e180 1463026 16700628
86. Warnecke T Hurst LD Evidence for a trade-off between translational efficiency and splicing regulation in determining synonymous codon usage in Drosophila melanogaster Mol Biol Evol 2007, 24:2755-2762 17905999
87. Hurst LD Pal C Lercher MJ The evolutionary dynamics of eukaryotic gene order Nat Rev Genet 2004, 5:299-310 15131653
88. Jasnos L Korona R Epistatic buffering of fitness loss in yeast double deletion strains Nat Genet 2007, 39:550-554 17322879
89. Moore JH The ubiquitous nature of epistasis in determining susceptibility to common human diseases Hum Hered 2003, 56:73-82 14614241
90. Wolf JB Brodie ED III Wade MJ Eds Epistasis and the evolutionary process New York: Oxford University Press; 2000.
91. Poelwijk FJ Kiviet DJ Weinreich DM Tans SJ Empirical fitness landscapes reveal accessible evolutionary paths Nature 2007, 445:383-386 17251971
92. Weinreich DM Watson RA Chao L Perspective: Sign epistasis and genetic constraint on evolutionary trajectories Evolution 2005, 59:1165-1174 16050094
93. Loewe L Charlesworth B Inferring the distribution of mutational effects on fitness in Drosophila Biol Lett 2006, 2:426-430 1686194 17148422
94. Sanjuan R Elena SF Epistasis correlates to genomic complexity Proc Natl Acad Sci USA 2006, 103:14402-14405 1599975 16983079
95. Dean AM Thornton JW Mechanistic approaches to the study of evolution: the functional synthesis Nat Rev Genet 2007, 8:675-688 2488205 17703238
96. Watt WB Dean AM Molecular-functional studies of adaptive genetic variation in prokaryotes and eukaryotes Annu Rev Genet 2000, 34:593-622 11092840
97. Halligan DL Eyre-Walker A Andolfatto P Keightley PD Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila Genome Res 2004, 14:273-279 327102 14762063
98. Gaffney DJ Keightley PD Genomic selective constraints in murid noncoding DNA PLoS Genetics 2006, 2:e204 1657059 17166057
99. Lynch M The origins of genome architecture Sunderland, Mass.: Sinauer Associates; 2007.
100. Lynch M The evolution of genetic networks by non-adaptive processes Nat Rev Genet 2007, 8:803-813 17878896
101. Lynch M The frailty of adaptive hypotheses for the origins of organismal complexity Proc Natl Acad Sci USA 2007, 104(Suppl 1):8597-8604 1876435 17494740
102. Loewe L Cutter A On the potential for extinction by Muller's Ratchet in Caenorhabditis elegans BMC Evol Biol 2008, 8:125 2408595 18447910
103. Gould SJ Lewontin RC The spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist programme Proc R Soc Lond B Biol Sci 1979, 205:581-598 42062
104. Gould SJ The exaptive excellence of spandrels as a term and prototype Proc Natl Acad Sci USA 1997, 94:10750-10755 23474 11038582
105. Kreitman M Methods to detect selection in populations with applications to the human Annu Rev Genomics Hum Genet 2000, 1:539-559 11701640
106. Dobzhansky T Nothing in biology makes sense except in the light of evolution American Biology Teacher 1973, 35:125-129 http://people.delphiforums.com/lordorman/light.htm
107. Rajasingh H Gjuvsland AB Vage DI Omholt SW When parameters in dynamic models become phenotypes: A case study on flesh pigmentation in the Chinook salmon (Oncorhynchus tshawytscha) Genetics 2008, 179:1113-1118 2429864 18505867
108. Ibarra RU Edwards JS Palsson BO Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth Nature 2002, 420:186-189 12432395
109. Endy D You L Yin J Molineux IJ Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes Proc Natl Acad Sci USA 2000, 97:5375-5380 25836 10792041
110. Locke JC Southern MM Kozma-Bognar L Hibberd V Brown PE Turner MS Millar AJ Extension of a genetic network model by iterative experimentation and mathematical analysis Mol Syst Biol 2005, 1 2005 0013 1681447 16729048
111. Watt WB Bioenergetics and Evolutionary Genetics - Opportunities for New Synthesis Am Nat 1985, 125:118-143
112. Miller SP Lunzer M Dean AM Direct demonstration of an adaptive constraint Science 2006, 314:458-461 17053145
113. Zhu G Golding GB Dean AM The selective cause of an ancient adaptation Science 2005, 307:1279-1282 15653464
114. Kacser H Burns JA The molecular basis of dominance Genetics 1981, 97:639-666 1214416 7297851
115. Hartl DL The physiology of weak selection Genome 1989, 31:183-189 2687089
116. Watt WB Power and Efficiency as Indexes of Fitness in Metabolic Organization Am Nat 1986, 127:629-653
117. Wright S The roles of mutation, inbreeding, crossbreeding, and selection in evolution Proceedings of the Sixth International Congress of Genetics 1932, 1:356-366
118. Gavrilets S Fitness landscapes and the origin of species Princeton, NJ: Princeton University Press 2004 2004.
119. Provine WB Wrinkles in the surface of selective value Sewall Wright and Evolutionary Biology, Hull DL (Series Editor): Science and its conceptual foundations Chicago: The University of Chicago Press Provine WB 1986, 307-317
120. Arnold SJ Pfrender ME Jones AG The adaptive landscape as a conceptual bridge between micro- and macroevolution Genetica 2001, 112-113:9-32 11838790
121. McGhee GR The geometry of evolution: Adaptive landscapes and theoretical morphospaces Cambridge, UK: Cambridge University Press; 2007.
122. Bonhoeffer S Stadler PF Error thresholds on correlated fitness landscapes J Theor Biol 1993, 164:359-372
123. Biebricher CK Eigen M The error threshold Virus Res 2005, 107:117-127 15649558
124. Rice SH A general population genetic theory for the evolution of developmental interactions Proc Natl Acad Sci USA 2002, 99:15518-15523 137749 12438697
125. Rice SH Developmental associations between traits: Covariance and beyond Genetics 2004, 166:513-526 1470672 15020440
126. Rice SH Theoretical approaches to the evolution of development and genetic architecture Ann N Y Acad Sci 2008, 1133:67-86 18559816
127. Gillespie JH Molecular evolution over the mutational landscape Evolution 1984, 38:1116-1129
128. Gillespie JH The Causes of Molecular Evolution New York: Oxford University Press; 1991.
129. Lande R Natural-Selection and Random Genetic Drift in Phenotypic Evolution Evolution 1976, 30:314-334
130. Lande R The maintenance of genetic variability by mutation in a polygenic character with linked loci Genet Res 1975, 26(3):221-235 1225762
131. Lande R Quantitative genetic analysis of multivariate evolution applied to brain:bOdy size allometry Evolution 1979, 33:402-416
132. Lande R A Quantitative Genetic Theory of Life-History Evolution Ecology 1982, 63:607-615
133. Lande R Arnold SJ The measurement of selection on correlated characters Evolution 1983, 37:1210-1226
134. Lande R Expected relative fitness and the adaptive topography of fluctuating selection Evolution 2007, 61:1835-1846 17683427
135. Lande R Adaptive topography of fluctuating selection in a Mendelian population J Evol Biol 2008, 21:1096-1105 18422529
136. Phillips PC What maintains genetic variation in natural populations? A commentary on 'The maintenance of genetic variability by mutation in a polygenic character with linked loci' by Russell Lande Genetics Research 2007, 89:371-372 18976524
137. Barton NH Turelli M Adaptive landscapes, genetic distance and the evolution of quantitative characters Genet Res 1987, 49:157-174 3596236
138. Waxman D Welch JJ Fisher's microscope and Haldane's ellipse Am Nat 2005, 166:447-457 16224701
139. Welch JJ Waxman D Modularity and the cost of complexity Evolution 2003, 57:1723-1734 14503615
140. Martin G Lenormand T A general multivariate extension of Fisher's geometrical model and the distribution of mutation fitness effects across species Evolution 2006, 60:893-907 16817531
141. Martin G Lenormand T The distribution of beneficial and fixed mutation fitness effects close to an optimum Genetics 2008, 179:907-916 2429884 18505866
142. Orr HA The genetic theory of adaptation: A brief history Nature Review Genetics 2005, 6:119-127
143. Martin G Elena SF Lenormand T Distributions of epistasis in microbes fit predictions from a fitness landscape model Nat Genet 2007, 39:555-560 17369829
144. Barton NH Keightley PD Understanding quantitative genetic variation Nature Review Genetics 2002, 3:11-21
145. Maynard Smith J Szathmáry E The major transitions in evolution Oxford; New York: W.H. Freeman Spektrum; 1995.
146. Szathmáry E Maynard Smith J The major evolutionary transitions Nature 1995, 374:227-232 7885442
147. Gardner A Grafen A Capturing the superorganism: A formal theory of group adaptation J Evol Biol 2009. 19210588
148. Okasha S Evolution and the levels of selection Oxford: Oxford University Press; 2006.
149. Grafen A Optimization of inclusive fitness J Theor Biol 2006, 238:541-563 16046225
150. Rice SH A stochastic version of the Price equation reveals the interplay of deterministic and stochastic processes in evolution BMC Evol Biol 2008, 8:262 2577117 18817569
151. Jolliffe IT Principal component analysis New York: Springer 2 2002.
152. Kingsolver JG Hoekstra HE Hoekstra JM Berrigan D Vignieri SN Hill CE Hoang A Gibert P Beerli P The strength of phenotypic selection in natural populations Am Nat 2001, 157:245-261 18707288
153. Arnold SJ Morphology, Performance and Fitness Am Zoologist 1983, 23:347-361
154. Arnold SJ Performance surfaces and adaptive landscapes Integrative and Comparative Biology 2003, 43:367-375
155. Jones AG Arnold SJ Borger R Stability of the G-matrix in a population experiencing pleiotropic mutation, stabilizing selection, and genetic drift Evolution 2003, 57:1747-1760 14503617
156. Gu X Evolutionary framework for protein sequence evolution and gene pleiotropy Genetics 2007, 175:1813-1822 1855142 17277368
157. Weinreich DM Delaney NF Depristo MA Hartl DL Darwinian evolution can follow only very few mutational paths to fitter proteins Science 2006, 312:111-114 16601193
158. Furnham N de Bakker PI Gore S Burke DF Blundell TL Comparative modelling by restraint-based conformational sampling BMC Struct Biol 2008, 8:7 2275734 18237407
159. Dalton JA Jackson RM An evaluation of automated homology modelling methods at low target template sequence similarity Bioinformatics 2007, 23:1901-1908 17510171
160. Alber T Mutational effects on protein stability Annu Rev Biochem 1989, 58:765-798 2673021
161. Lutz S Bornscheuer UT Eds Protein Engineering Handbook Wiley-VCH 2009.
162. Burke DF Worth CL Priego EM Cheng T Smink LJ Todd JA Blundell TL Genome bioinformatic analysis of nonsynonymous SNPs BMC Bioinformatics 2007, 8:301 1978506 17708757
163. Sunyaev S Ramensky V Koch I Lathe W 3rd Kondrashov AS Bork P Prediction of deleterious human alleles Hum Mol Genet 2001, 10:591-597 11230178
164. Helles G A comparative study of the reported performance of ab initio protein structure prediction algorithms J R Soc Interface 2008, 5:387-396 2405928 18077243
165. Stein M Gabdoulline RR Wade RC Bridging from molecular simulation to biochemical networks Curr Opin Struct Biol 2007, 17:166-172 17395455
166. Richter S Wenzel A Stein M Gabdoulline RR Wade RC webPIPSA: A web server for the comparison of protein interaction properties Nucleic Acids Res 2008, 36:W276-280 2447742 18420653
167. Gabdoulline RR Stein M Wade RC qPIPSA: Relating enzymatic kinetic parameters and interaction fields BMC Bioinformatics 2007, 8:373 2174957 17919319
168. Bogatyreva NS Osypov AA Ivankov DN KineticDB: A database of protein folding kinetics Nucleic Acids Res 2009, 37:D342-D346 18842631
169. Kumar P Han BC Shi Z Jia J Wang YP Zhang YT Liang L Liu QF Ji ZL Chen YZ Update of KDBI: Kinetic Data of Bio-molecular Interaction database Nucleic Acids Res 2008 37 Database issue D636-D641 18971255
170. Markiewicz P Kleina LG Cruz C Ehret S Miller JH Genetic studies of the lac repressor. XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as "spacers" which do not require a specific sequence J Mol Biol 1994, 240:421-433 8046748
171. Drummond DA Iverson BL Georgiou G Arnold FH Why high-error-rate random mutagenesis libraries are enriched in functional and improved proteins J Mol Biol 2005, 350:806-816 15939434
172. Tokuriki N Stricher F Serrano L Tawfik DS How protein stability and new functions trade off PLoS Comput Biol 2008, 4:e1000002 2265470 18463696
173. Tokuriki N Stricher F Schymkowitz J Serrano L Tawfik DS The stability effects of protein mutations appear to be universally distributed J Mol Biol 2007, 369:1318-1332 17482644
174. Peisajovich SG Tawfik DS Protein engineers turned evolutionists Nat Methods 2007, 4:991-994 18049465
175. Peisajovich SG Rockah L Tawfik DS Evolution of new protein topologies through multistep gene rearrangements Nat Genet 2006, 38:168-174 16415885
176. Bershtein S Segal M Bekerman R Tokuriki N Tawfik DS Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein Nature 2006, 444:929-932 17122770
177. Aharoni A Gaidukov L Khersonsky O Mc QGS Roodveldt C Tawfik DS The 'evolvability' of promiscuous protein functions Nat Genet 2005, 37:73-76 15568024
178. Voigt CA Kauffman S Wang ZG Rational evolutionary design: The theory of in vitro protein evolution Adv Protein Chem 2000, 55:79-160 11050933
179. Hayashi Y Aita T Toyota H Husimi Y Urabe I Yomo T Experimental rugged fitness landscape in protein sequence space PLoS ONE 2006, 1:e96 1762315 17183728
180. Zhao J Ridgway D Broderick G Kovalenko A Ellison M Extraction of elementary rate constants from global network analysis of E. coli central metabolism BMC Syst Biol 2008, 2:41 2396597 18462493
181. Pey AL Rodriguez-Larrea D Bomke S Dammers S Godoy-Ruiz R Garcia-Mira MM Sanchez-Ruiz JM Engineering proteins with tunable thermodynamic and kinetic stabilities Proteins 2008, 71:165-174 17932922
182. Landry CR Lemos B Rifkin SA Dickinson WJ Hartl DL Genetic properties influencing the evolvability of gene expression Science 2007, 317:118-121 17525304
183. Qian W Zhang J Gene dosage and gene duplicability Genetics 2008, 179:2319-2324 2516101 18689880
184. Kondrashov FA Koonin EV A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications Trends Genet 2004, 20:287-290 15219392
185. Wright S Physiological and evolutionary theories of dominance Am Nat 1934, 68:24-53
186. Hartl DL Dykhuizen DE Dean AM Limits of adaptation: The evolution of selective neutrality Genetics 1985, 111:655-674 1202663 3932127
187. Dykhuizen DE Dean AM Hartl DL Metabolic flux and fitness Genetics 1987, 115:25-32 1203059 3104135
188. Swarup R Kramer EM Perry P Knox K Leyser HM Haseloff J Beemster GT Bhalerao R Bennett MJ Root gravitropism requires lateral root cap and epidermal cells for transport and response to a mobile auxin signal Nat Cell Biol 2005, 7:1057-1065 16244669
189. Shreenivasaiah PK Rho SH Kim T Kim do H An overview of cardiac systems biology J Mol Cell Cardiol 2008, 44:460-469 18261742
190. Southern J Pitt-Francis J Whiteley J Stokeley D Kobashi H Nobes R Kadooka Y Gavaghan D Multi-scale computational modelling in biology and physiology Prog Biophys Mol Biol 2008, 96:60-89 17888502
191. McCulloch AD Paternostro G Cardiac systems biology Ann N Y Acad Sci 2005, 1047:283-295 16093504
192. Stearns SC Koella JC Evolution in health and disease Oxford; New York: Oxford University Press 2 2008.
193. Feist AM Herrgard MJ Thiele I Reed JL Palsson BØ Reconstruction of Biochemical Networks in Microbial Organisms Nature Reviews Microbiology 2009, 7:129-143 19116616
194. Gutenkunst RN Waterfall JJ Casey FP Brown KS Myers CR Sethna JP Universally sloppy parameter sensitivities in systems biology models PLoS Comput Biol 2007, 3:1871-1878 2000971 17922568
195. Ibarra RU Fu P Palsson BO DiTonno JR Edwards JS Quantitative analysis of Escherichia coli metabolic phenotypes within the context of phenotypic phase planes J Mol Microbiol Biotechnol 2003, 6:101-108 15044828
196. Loewe L Hillston J The distribution of mutational effects on fitness in a simple circadian clock Lecture Notes in Bioinformatics 2008, 5307:156-175
197. Kauffman KJ Pajerowski JD Jamshidi N Palsson BO Edwards JS Description and analysis of metabolic connectivity and dynamics in the human red blood cell Biophys J 2002, 83:646-662 1302176 12124254
198. Covert MW Schilling CH Famili I Edwards JS Goryanin II Selkov E Palsson BO Metabolic modeling of microbial strains in silico Trends Biochem Sci 2001, 26:179-186 11246024
199. von Dassow G Meir E Munro EM Odell GM The segment polarity network is a robust developmental module Nature 2000, 406:188-192 10910359
200. Munteanu A Sole RV Neutrality and robustness in evo-devo: Emergence of lateral inhibition PLoS Comput Biol 2008, 4:e1000226 2577890 19023404
201. Johnson LJ Brookfield JF Evolution of spatial expression pattern Evol Dev 2003, 5:593-599 14984041
202. Arthur W The emerging conceptual framework of evolutionary developmental biology Nature 2002, 415:757-764 11845200
203. Raff RA Evo-devo: The evolution of a new discipline Nat Rev Genet 2000, 1:74-79 11262880
204. Arthur W The concept of developmental reprogramming and the quest for an inclusive theory of evolutionary mechanisms Evol Dev 2000, 2:49-57 11256417
205. Lamm E Jablonka E Integrating evolution and development: From theory to practice Perspect Biol Med 2008, 51:636-647 19013853
206. De Robertis EM Evo-devo: Variations on ancestral themes Cell 2008, 132:185-195 2280037 18243095
207. Carroll SB Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution Cell 2008, 134:25-36 18614008
208. Wagner GP Pavlicev M Cheverud JM The road to modularity Nat Rev Genet 2007, 8:921-931 18007649
209. Muller GB Evo-devo: Extending the evolutionary synthesis Nat Rev Genet 2007, 8:943-949 17984972
210. Raff RA Written in stone: Fossils, genes and evo-devo Nat Rev Genet 2007, 8:911-920 18007648
211. Canestro C Yokoi H Postlethwait JH Evolutionary developmental biology and genomics Nat Rev Genet 2007, 8:932-942 18007650
212. Academy of Medical Sciences, Royal Academy of Engineering Systems Biology: A vision for engineering and medicine. London 2007 http://www.acmedsci.ac.uk ISBN No. 1-904401-13-5
213. European Science Foundation Systems Biology: A Grand Challenge for Europe Strasbourg, France: European Science Foundation 2007 http://www.esf.org ISBN: 2-912049-65-2
214. Welch JJ Waxman D The nk model and population genetics J Theor Biol 2005, 234:329-340 15784268
215. Brommer JE The evolution of fitness in life-history theory Biol Rev Camb Philos Soc 2000, 75:377-404 11034016
216. Stearns SC The evolution of life histories Oxford: Oxford University Press; 1992.
217. Stearns SC Life history evolution: Successes, limitations, and prospects Naturwissenschaften 2000, 87:476-486 11151666
218. Martin G Lenormand T The fitness effect of mutations across environments: A survey in light of fitness landscape models Evolution 2006, 60:2413-2427 17263105
219. Förster J Famili I Fu P Palsson BO Nielsen J Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network Genome Res 2003, 13:244-253 420374 12566402
220. Kulheim C Agren J Jansson S Rapid regulation of light harvesting and plant fitness in the field Science 2002, 297:91-93 12098696
221. Isalan M Lemerle C Michalodimitrakis K Horn C Beltrao P Raineri E Garriga-Canut M Serrano L Evolvability and hierarchy in rewired bacterial gene networks Nature 2008, 452:840-845 18421347
222. Fischer E Sauer U Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism Nat Genet 2005, 37:636-640 15880104
223. Elena SF Cooper VS Lenski RE Punctuated evolution caused by selection of rare beneficial mutations Science 1996, 272:1802-1804 8650581
224. Cooper VS Lenski RE The population genetics of ecological specialization in evolving Escherichia coli populations Nature 2000, 407:736-739 11048718
225. Kacser H Acerenza L A universal method for achieving increases in metabolite production Eur J Biochem 1993, 216:361-367 8375376
226. Ouyang Y Andersson CR Kondo T Golden SS Johnson CH Resonating circadian clocks enhance fitness in cyanobacteria Proc Natl Acad Sci USA 1998,
227. Dodd AN Salathia N Hall A Kevei E Toth R Nagy F Hibberd JM Millar AJ Webb AAR Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage Science 2005, 309:630-633 16040710
228. Dekel E Alon U Optimality and evolutionary tuning of the expression level of a protein Nature 2005, 436:588-592 16049495
229. Bloom JD Drummond DA Arnold FH Wilke CO Structural determinants of the rate of protein evolution in yeast Mol Biol Evol 2006, 23:1751-1761 16782762
230. Drummond DA Wilke CO Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution Cell 2008, 134:341-352 18662548
231. Wilke CO Bloom JD Drummond DA Raval A Predicting the tolerance of proteins to random amino acid substitution Biophys J 2005, 89:3714-3720 1366941 16150971
232. Wilke CO Drummond DA Population genetics of translational robustness Genetics 2006, 173:473-481 1461446 16489231
233. Pfeiffer T Soyer OS Bonhoeffer S The evolution of connectivity in metabolic networks PLoS Biol 2005, 3:e228 1157096 16000019
234. Soyer OS Bonhoeffer S Evolution of complexity in signaling pathways Proc Natl Acad Sci USA 2006, 103:16337-16342 1621048 17060629
235. Soyer OS Pfeiffer T Bonhoeffer S Simulating the evolution of signal transduction pathways J Theor Biol 2006, 241:223-232 16403533
236. Soyer OS Salathe M Bonhoeffer S Signal transduction networks: Topology, response and biochemical processes J Theor Biol 2006, 238:416-425 16045939
237. Charlesworth B Borthwick H Bartolome C Pignatelli P Estimates of the genomic mutation rate for detrimental alleles in Drosophila melanogaster Genetics 2004, 167:815-826 1470907 15238530
238. Lynch M Blanchard J Houle D Kibota T Schultz S Vassilieva L Willis J Perspective: Spontaneous deleterious mutation Evolution 1999, 53:645-663
239. Drake JW Charlesworth B Charlesworth D Crow JF Rates of spontaneous mutation Genetics 1998, 148:1667-1686 1460098 9560386
240. Kassen R Bataillon T Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria Nat Genet 2006, 38:484-488 16550173
241. Sanjuan R Moya A Elena SF The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus Proc Natl Acad Sci USA 2004, 101:8396-8401 420405 15159545
242. Davies EK Peters AD Keightley PD High frequency of cryptic deleterious mutations in Caenorhabditis elegans Science 1999, 285:1748-1751 10481013
243. Keightley PD Eyre-Walker A Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies Genetics 2007, 177:2251-2261 2219502 18073430
244. Li H Stephan W Inferring the demographic history and rate of adaptive substitution in Drosophila PLoS Genet 2006, 2:e166 1599771 17040129
245. Williamson SH Hernandez R Fledel-Alon A Zhu L Nielsen R Bustamante CD Simultaneous inference of selection and population growth from patterns of variation in the human genome Proc Natl Acad Sci USA 2005, 102:7882-7887 1142382 15905331
246. Kitano H Towards a theory of biological robustness Mol Syst Biol 2007, 3:137 2013924 17882156
247. Flatt T The evolutionary genetics of canalization Q Rev Biol 2005, 80:287-316 16250465
248. de Visser JA Hermisson J Wagner GP Ancel Meyers L Bagheri-Chaichian H Blanchard JL Chao L Cheverud JM Elena SF Fontana W et al Perspective: Evolution and detection of genetic robustness Evolution 2003, 57:1959-1972 14575319
249. Gjuvsland AB Plahte E Omholt SW Threshold-dominated regulation hides genetic variation in gene expression networks BMC Syst Biol 2007, 1:57 2238762 18062810
250. Bergman A Siegal ML Evolutionary capacitance as a general feature of complex gene networks Nature 2003, 424:549-552 12891357
251. Waddington CH Canalization of development and the inheritance of acquired characters Nature 1942, 150:563-565
252. Gibson G Wagner G Canalization in evolutionary genetics: A stabilizing theory? Bioessays 2000, 22:372-380 10723034
253. Queitsch C Sangster TA Lindquist S Hsp90 as a capacitor of phenotypic variation Nature 2002, 417:618-624 12050657
254. Hermisson J Wagner GP The population genetic theory of hidden variation and genetic robustness Genetics 2004, 168:2271-2284 1448756 15611191
255. Wagner A The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes Mol Biol Evol 2001, 18:1283-1292 11420367
256. Wagner A Robustness and evolvability in living systems Princeton, N.J.: Princeton University Press; 2005.
257. Wagner A Robustness against mutations in genetic networks of yeast Nat Genet 2000, 24:355-361 10742097
258. Wagner A Neutralism and selectionism: A network-based reconciliation Nat Rev Genet 2008, 9:965-974 18957969
259. Wagner A Gene duplications, robustness and evolutionary innovations Bioessays 2008, 30:367-373 18348184
260. Wagner A Robustness and evolvability: A paradox resolved Proc Biol Sci 2008, 275:91-100 2562401 17971325
261. de Visser JA Elena SF The evolution of sex: Empirical insights into the roles of epistasis and drift Nat Rev Genet 2007, 8:139-149 17230200
262. Szathmary E Do deleterious mutations act synergistically? Metabolic control theory provides a partial answer Genetics 1993, 133:127-132 1205292 8417983
263. Elena SF Lenski RE Test of synergistic interactions among deleterious mutations in bacteria Nature 1997, 390:395-398 9389477
264. Gjuvsland AB Hayes BJ Meuwissen TH Plahte E Omholt SW Nonlinear regulation enhances the phenotypic expression of trans-acting genetic polymorphisms BMC Syst Biol 2007, 1:32 1994684 17651484
265. Gjuvsland AB Hayes BJ Omholt SW Carlborg O Statistical epistasis is a generic feature of gene regulatory networks Genetics 2007, 175:411-420 1774990 17028346
266. Harrison R Papp B Pal C Oliver SG Delneri D Plasticity of genetic interactions in metabolic networks of yeast Proc Natl Acad Sci USA 2007, 104:2307-2312 1892960 17284612
267. Huelsenbeck JP Rannala B Phylogenetic methods come of age: Testing hypotheses in an evolutionary context Science 1997, 276:227-232 9092465
268. Welch JJ Bromham L Molecular dating when rates vary Trends Ecol Evol 2005, 20:320-327 16701388
269. Drummond AJ Ho SY Phillips MJ Rambaut A Relaxed phylogenetics and dating with confidence PLoS Biol 2006, 4:e88 1395354 16683862
270. Drummond AJ Rambaut A BEAST: Bayesian evolutionary analysis by sampling trees BMC Evol Biol 2007, 7:214 2247476 17996036
271. Welch JJ Eyre-Walker A Waxman D Divergence and polymorphism under the nearly neutral theory of molecular evolution J Mol Evol 2008, 67:418-426 18818860
272. Li H Stephan W Maximum-likelihood methods for detecting recent positive selection and localizing the selected site in the genome Genetics 2005, 171:377-384 1456529 15972464
273. Loewe L Quantifying the genomic decay paradox due to Muller's ratchet in human mitochondrial DNA Genet Res 2006, 87:133-159 16709275
274. Charlesworth B Evidence against Fisher's theory of dominance Nature 1979, 278:848-849
275. Orr HA A test of Fisher's theory of dominance Proc Natl Acad Sci USA 1991, 88:11413-11415 53145 1763055
276. Fisher RA The evolution of dominance Biol Rev (Camb) 1931, 6:345-368
277. Mayo O Bürger R The evolution of dominance: A theory whose time has passed? Biol Rev Camb Philos Soc 1997, 72:97-110
278. Briggs GE Haldane JB A Note on the Kinetics of Enzyme Action Biochem J 1925, 19:338-339 1259181 16743508
279. Medina M Genomes, phylogeny, and evolutionary systems biology Proc Natl Acad Sci USA 2005, 102(Suppl 1):6630-6635 1131869 15851668
280. Koonin EV Wolf YI Evolutionary systems biology: Links between gene evolution and function Curr Opin Biotechnol 2006, 17:481-487 16962765
281. Monroe D Bergman A Siegal ML Michor F Meeting report: Convergent revolution: Evolutionary systems biology New York: New York Academy of Sciences 2008. http://www.nyas.org/evosysbio Meeting held at 1st July 2008.
282. Barabasi AL Oltvai ZN Network biology: Understanding the cell's functional organization Nat Rev Genet 2004, 5:101-113 14735121
283. Yuan JS Galbraith DW Dai SY Griffin P Stewart CN Jr Plant systems biology comes of age Trends Plant Sci 2008, 13:165-171 18329321
284. Kitano H A robustness-based approach to systems-oriented drug design Nature Reviews Drug Discovery 2007, 6:202-210 17318209
285. Greaves M Darwinian medicine: A case for cancer Nat Rev Cancer 2007, 7:213-221 17301845
286. Kitano H Cancer robustness: Tumour tactics Nature 2003, 426:125 14614483
287. Boulesteix AL Strimmer K Partial least squares: A versatile tool for the analysis of high-dimensional genomic data Brief Bioinform 2007, 8:32-44 16772269
288. Ahmed FE Vos PW Holbert D Modeling survival in colon cancer: A methodological review Mol Cancer 2007, 6:15 1810545 17295918
289. Greenman C Wooster R Futreal PA Stratton MR Easton DF Statistical analysis of pathogenicity of somatic mutations in cancer Genetics 2006, 173:2187-2198 1569711 16783027
290. Goriely A McVean GA van Pelt AM O'Rourke AW Wall SA de Rooij DG Wilkie AO Gain-of-function amino acid substitutions drive positive selection of FGFR2 mutations in human spermatogonia Proc Natl Acad Sci USA 2005, 102:6051-6056 1087921 15840724
291. Cirz RT Chin JK Andes DR de Crecy-Lagard V Craig WA Romesberg FE Inhibition of mutation and combating the evolution of antibiotic resistance PLoS Biol 2005, 3:e176 1088971 15869329
292. Norrby SR Nord CE Finch R Lack of development of new antimicrobial drugs: A potential serious threat to public health Lancet Infect Dis 2005, 5:115-119 15680781
293. D'Costa VM McGrann KM Hughes DW Wright GD Sampling the antibiotic resistome Science 2006, 311:374-377 16424339
294. Rambaut A Posada D Crandall KA Holmes EC The causes and consequences of HIV evolution Nat Rev Genet 2004, 5:52-61 14708016
295. Butler SJ Vickery JA Norris K Farmland biodiversity and the footprint of agriculture Science 2007, 315:381-384 17234947
296. Belostotsky DA Rose AB Plant gene expression in the age of systems biology: Integrating transcriptional and post-transcriptional events Trends Plant Sci 2005, 10:347-353 15951220
297. Hammer G Cooper M Tardieu F Welch S Walsh B van Eeuwijk F Chapman S Podlich D Models for navigating biological complexity in breeding improved crop plants Trends Plant Sci 2006, 11:587-593 17092764
298. Schauer N Fernie AR Plant metabolomics: Towards biological function and mechanism Trends Plant Sci 2006, 11:508-516 16949327
299. Benner SA Sismour AM Synthetic biology Nat Rev Genet 2005, 6:533-543 15995697
300. O'Malley MA Powell A Davies JF Calvert J Knowledge-making distinctions in synthetic biology Bioessays 2008, 30:57-65 18081015
301. Sprinzak D Elowitz MB Reconstruction of genetic circuits Nature 2005, 438:443-448 16306982
302. Jamshidi N Palsson BO Systems biology of SNPs Mol Syst Biol 2006, 2:38 1681509 16820779
303. Adami C Digital genetics: Unravelling the genetic basis of evolution Nat Rev Genet 2006, 7:109-118 16418746
304. Wilke CO Wang JL Ofria C Lenski RE Adami C Evolution of digital organisms at high mutation rates leads to survival of the flattest Nature 2001, 412:331-333 11460163
305. Lenski RE Ofria C Pennock RT Adami C The evolutionary origin of complex features Nature 2003, 423:139-144 12736677
306. Papp B Pal C Hurst LD Dosage sensitivity and the evolution of gene families in yeast Nature 2003, 424:194-197 12853957
307. Reed JL Patel TR Chen KH Joyce AR Applebee MK Herring CD Bui OT Knight EM Fong SS Palsson BO Systems approach to refining genome annotation Proc Natl Acad Sci USA 2006, 103:17480-17484 1859954 17088549
308. Rigler FH Peters RH Reductionism versus holism: An old problem rejuvenated by the computer Science and limnology Oldendorf/Luhe, Germany: Ecology Institute Rigler FH, Peters RH 1995 95-115
309. Wolkenhauer O Ullah M All models are wrong⋯ some more than others Systems Biology - philosophical foundations Amsterdam, The Netherlands: Elsevier Boogerd FC, Bruggeman FJ, Hofmeyr J-HS, Westerhoff HV 2007 163-180
310. Popper KR Conjectures and refutations; the growth of scientific knowledge New York,: Basic Books; 1962.
311. Gelman A Bayesian data analysis Boca Raton, Fla.: Chapman & Hall/CRC 2 2004.
312. Bishop CM Pattern recognition and machine learning New York: Springer; 2006.
313. Charlesworth D Charlesworth B McVean GA Genome sequences and evolutionary biology, a two-way interaction Trends in Ecol Evol 2001, 16(5):235-242 11301152
314. Peters DPC Herrick JE Urban DL Gardner RH Breshears DD Strategies for ecological extrapolation Oikos 2004, 106:627-636
315. O'Neill RV Error analysis of ecological models Radionuclides in ecosystems: Proceedings of the Third National Symposium on Radioecology, May 10-12, 1971, Oak Ridge, Tennessee Springfield, Virginia, USA: National Technical Information Service Nelson DJ 1973 898-908
316. Grimm V Revilla E Berger U Jeltsch F Mooij WM Railsback SF Thulke HH Weiner J Wiegand T DeAngelis DL Pattern-oriented modeling of agent-based complex systems: Lessons from ecology Science 2005, 310:987-991 16284171
317. Loehle C A Guide to Increased Creativity in Research - Inspiration or Perspiration Bioscience 1990, 40:123-129
318. Taylor HM Karlin S An introduction to stochastic modeling San Diego: Academic Press 3 1998.
319. McConnell S Code complete 2nd Edition Redmond, Wash.: Microsoft Press 2 2004.
320. Law AM Kelton WD Simulation modeling and analysis Boston: McGraw-Hill 3 2000.
321. Grimm V Railsback SF Individual-based modeling and ecology Princeton: Princeton University Press; 2005.
322. Bart J Acceptance criteria for using individual-based models to make management decisions Ecol Applic 1995, 5:411-420
323. Hopkins JC Leipold RJ On the dangers of adjusting the parameters values of mechanism-based mathematical models J Theor Biol 1996, 183:417-427 9015457
324. Gershenfeld N The nature of mathematical modeling Cambridge: Cambridge University Press; 1999.
325. May RM Uses and abuses of mathematics in biology Science 2004, 303:790-793 14764866
326. Nicolson CR Starfield AM Kofinas GP Kruse JA Ten heuristics for interdisciplinary modeling projects Ecosystems 2002, 5:376-384
327. Aceto L Anna I Larsen KG Srba Jr Reactive systems: Modelling, specification and verification Cambridge; New York: Cambridge University Press; 2007.
328. Regev A Shapiro E Cells as computation Nature 2002, 419:343 12353013
329. Beaumont MA Rannala B The Bayesian revolution in genetics Nat Rev Genet 2004, 5:251-261 15131649