TY - JOUR AU - Loewe, L. AU - Charlesworth, B. AU - Bartolomé, C. AU - Nöel, V. PY - 2006 DA - 2006// TI - Estimating selection on non-synonymous mutations JO - Genetics VL - 172 ID - Loewe2006 ER - TY - JOUR AU - Eyre-Walker, A. AU - Keightley, P. D. PY - 2007 DA - 2007// TI - The distribution of fitness effects of new mutations JO - Nat Rev Genet VL - 8 ID - Eyre-Walker2007 ER - TY - JOUR AU - Papin, J. A. AU - Price, N. D. AU - Wiback, S. J. AU - Fell, D. A. AU - Palsson, B. O. PY - 2003 DA - 2003// TI - Metabolic pathways in the post-genome era JO - Trends Biochem Sci VL - 28 ID - Papin2003 ER - TY - JOUR AU - Joyce, A. R. AU - Palsson, B. O. PY - 2008 DA - 2008// TI - Predicting gene essentiality using genome-scale in silico models JO - Methods Mol Biol VL - 416 ID - Joyce2008 ER - TY - JOUR AU - Bruggeman, F. J. AU - Westerhoff, H. V. PY - 2007 DA - 2007// TI - The nature of systems biology JO - Trends Microbiol VL - 15 ID - Bruggeman2007 ER - TY - JOUR AU - Heuett, W. J. AU - Beard, D. A. AU - Qian, H. PY - 2008 DA - 2008// TI - Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory JO - BMC Syst Biol VL - 2 ID - Heuett2008 ER - TY - JOUR AU - Schuetz, R. AU - Kuepfer, L. AU - Sauer, U. PY - 2007 DA - 2007// TI - Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli JO - Mol Syst Biol VL - 3 ID - Schuetz2007 ER - TY - JOUR AU - Snitkin, E. S. AU - Segrè, D. PY - 2008 DA - 2008// TI - Optimality criteria for the prediction of metabolic fluxes in yeast mutants JO - Genome Informatics VL - 20 ID - Snitkin2008 ER - TY - JOUR AU - Snitkin, E. S. AU - Dudley, A. M. AU - Janse, D. M. AU - Wong, K. AU - Church, G. M. AU - Segre, D. PY - 2008 DA - 2008// TI - Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions JO - Genome Biol VL - 9 ID - Snitkin2008 ER - TY - JOUR AU - Papp, B. AU - Teusink, B. AU - Notebaart, R. A. PY - 2009 DA - 2009// TI - A critical view of metabolic network adaptations JO - HFSP Journal VL - 1 ID - Papp2009 ER - TY - JOUR AU - Edwards, J. S. AU - Ibarra, R. U. AU - Palsson, B. O. PY - 2001 DA - 2001// TI - In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data JO - Nat Biotechnol VL - 19 ID - Edwards2001 ER - TY - JOUR AU - Shlomi, T. AU - Berkman, O. AU - Ruppin, E. PY - 2005 DA - 2005// TI - Regulatory on/off minimization of metabolic flux changes after genetic perturbations JO - Proc Natl Acad Sci USA VL - 102 ID - Shlomi2005 ER - TY - JOUR AU - Papp, B. AU - Pal, C. AU - Hurst, L. D. PY - 2004 DA - 2004// TI - Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast JO - Nature VL - 429 ID - Papp2004 ER - TY - JOUR AU - Förster, J. AU - Famili, I. AU - Palsson, B. O. AU - Nielsen, J. PY - 2003 DA - 2003// TI - Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae JO - OMICS VL - 7 ID - Förster2003 ER - TY - JOUR AU - Famili, I. AU - Förster, J. AU - Nielsen, J. AU - Palsson, B. O. PY - 2003 DA - 2003// TI - Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network JO - Proc Natl Acad Sci USA VL - 100 ID - Famili2003 ER - TY - JOUR AU - Segre, D. AU - Deluna, A. AU - Church, G. M. AU - Kishony, R. PY - 2005 DA - 2005// TI - Modular epistasis in yeast metabolism JO - Nat Genet VL - 37 ID - Segre2005 ER - TY - JOUR AU - Kacser, H. AU - Burns, J. A. PY - 1973 DA - 1973// TI - The control of flux JO - Symp Soc Exp Biol VL - 27 ID - Kacser1973 ER - TY - JOUR AU - Murphy, M. P. AU - Partridge, L. PY - 2008 DA - 2008// TI - Toward a Control Theory Analysis of Aging JO - Annu Rev Biochem VL - 77 ID - Murphy2008 ER - TY - BOOK AU - Fell, D. PY - 1996 DA - 1996// TI - Understanding the control of metabolism PB - Portland Press CY - London ID - Fell1996 ER - TY - JOUR AU - Fell, D. A. PY - 2005 DA - 2005// TI - Enzymes, metabolites and fluxes JO - J Exp Bot VL - 56 ID - Fell2005 ER - TY - JOUR AU - Carlson, R. AU - Fell, D. AU - Srienc, F. PY - 2002 DA - 2002// TI - Metabolic pathway analysis of a recombinant yeast for rational strain development JO - Biotechnol Bioeng VL - 79 ID - Carlson2002 ER - TY - JOUR AU - Fell, D. A. PY - 1992 DA - 1992// TI - Metabolic control analysis: a survey of its theoretical and experimental development JO - Biochem J VL - 286 ID - Fell1992 ER - TY - JOUR AU - Gillespie, D. T. PY - 2007 DA - 2007// TI - Stochastic simulation of chemical kinetics JO - Annu Rev Phys Chem VL - 58 ID - Gillespie2007 ER - TY - JOUR AU - Gibson, M. A. AU - Bruck, J. PY - 2000 DA - 2000// TI - Efficient exact stochastic simulation of chemical systems with many species and many channels JO - Journal of Physical Chemistry A VL - 104 ID - Gibson2000 ER - TY - CHAP AU - Calder, M. AU - Gilmore, S. AU - Hillston, J. PY - 2005 DA - 2005// TI - Automatically deriving ODEs from process algebra models of signalling pathways BT - Computational Methods in Systems Biology 2005 PB - LFCS CY - University of Edinburgh ID - Calder2005 ER - TY - JOUR AU - Loewe, L. AU - Hillston, J. PY - 2008 DA - 2008// TI - Meeting report: Computational models in systems biology JO - Genome Biol VL - 9 ID - Loewe2008 ER - TY - JOUR AU - Alberts, B. PY - 1998 DA - 1998// TI - The cell as a collection of protein machines: preparing the next generation of molecular biologists JO - Cell VL - 92 ID - Alberts1998 ER - TY - JOUR AU - Cassman, M. PY - 2005 DA - 2005// TI - Barriers to progress in systems biology JO - Nature VL - 438 ID - Cassman2005 ER - TY - JOUR AU - Westerhoff, H. V. AU - Palsson, B. O. PY - 2004 DA - 2004// TI - The evolution of molecular biology into systems biology JO - Nat Biotechnol VL - 22 ID - Westerhoff2004 ER - TY - JOUR AU - Kitano, H. PY - 2002 DA - 2002// TI - Systems biology: a brief overview JO - Science VL - 295 ID - Kitano2002 ER - TY - JOUR AU - Kitano, H. PY - 2002 DA - 2002// TI - Computational systems biology JO - Nature VL - 420 ID - Kitano2002 ER - TY - BOOK AU - Boogerd, F. C. AU - Bruggeman, F. J. AU - Hofmeyr, J. -. H. S. AU - Westerhoff, H. V. PY - 2007 DA - 2007// TI - Systems Biology – philosophical foundations PB - Elsevier CY - Amsterdam, The Netherlands ID - Boogerd2007 ER - TY - BOOK AU - Palsson, B. PY - 2006 DA - 2006// TI - Systems biology: properties of reconstructed networks PB - Cambridge University Press CY - Cambridge; New York ID - Palsson2006 ER - TY - BOOK AU - Alberghina, L. AU - Westerhoff, H. V. PY - 2008 DA - 2008// TI - Systems biology: definitions and perspectives PB - Springer CY - Berlin ID - Alberghina2008 ER - TY - CHAP AU - Schaff, J. AU - Loew, L. M. PY - 1999 DA - 1999// TI - The virtual cell BT - Pac Symp Biocomput ID - Schaff1999 ER - TY - JOUR AU - Chory, J. AU - Ecker, J. R. AU - Briggs, S. AU - Caboche, M. AU - Coruzzi, G. M. AU - Cook, D. AU - Dangl, J. AU - Grant, S. AU - Guerinot, M. L. AU - Henikoff, S. PY - 2000 DA - 2000// TI - 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 JO - Plant Physiol VL - 123 ID - Chory2000 ER - TY - JOUR AU - Jones, D. PY - 2008 DA - 2008// TI - All systems go: How might systems biology approaches be applied in drug discovery and development? JO - Nature Reviews Drug Discovery VL - 7 ID - Jones2008 ER - TY - JOUR AU - Hood, L. AU - Heath, J. R. AU - Phelps, M. E. AU - Lin, B. PY - 2004 DA - 2004// TI - Systems biology and new technologies enable predictive and preventative medicine JO - Science VL - 306 ID - Hood2004 ER - TY - JOUR AU - Werner, E. PY - 2005 DA - 2005// TI - Meeting report: the future and limits of systems biology JO - Sci STKE VL - 2005 ID - Werner2005 ER - TY - JOUR AU - Wolkenhauer, O. PY - 2001 DA - 2001// TI - Systems biology: the reincarnation of systems theory applied in biology? JO - Brief Bioinform VL - 2 ID - Wolkenhauer2001 ER - TY - JOUR AU - Wiegert, R. G. PY - 1975 DA - 1975// TI - Simulation Models of Ecosystems JO - Annu Rev Ecol Syst VL - 6 ID - Wiegert1975 ER - TY - BOOK AU - Balding, D. J. AU - Bishop, M. J. AU - Cannings, C. PY - 2007 DA - 2007// TI - Handbook of statistical genetics PB - Sons CY - Chichester, England; Hoboken, NJ ID - Balding2007 ER - TY - BOOK AU - Barton, N. H. AU - Briggs, D. E. G. AU - Eisen, J. A. AU - Goldstein, D. B. AU - Patel, N. H. PY - 2007 DA - 2007// TI - Evolution PB - Cold Spring Harbor Laboratory Press CY - Cold Spring Harbor, N.Y. ID - Barton2007 ER - TY - BOOK AU - Crow, J. F. AU - Kimura, M. PY - 1970 DA - 1970// TI - An Introduction to Population Genetics Theory PB - Burgess International Group Incorporated CY - Edina, MN, USA ID - Crow1970 ER - TY - BOOK AU - Fisher, R. A. PY - 1930 DA - 1930// TI - The genetical theory of natural selection PB - Clarendon Press CY - Oxford ID - Fisher1930 ER - TY - JOUR AU - Wright, S. PY - 1931 DA - 1931// TI - Evolution in mendelian populations JO - Genetics VL - 16 ID - Wright1931 ER - TY - BOOK AU - Kimura, M. PY - 1983 DA - 1983// TI - The neutral theory of molecular evolution PB - Cambridge University Press CY - Cambridge ID - Kimura1983 ER - TY - BOOK AU - Fox, C. W. AU - Wolf, J. B. PY - 2006 DA - 2006// TI - Evolutionary genetics: concepts and case studies PB - Oxford University Press CY - New York ID - Fox2006 ER - TY - JOUR AU - Barton, N. H. AU - Turelli, M. PY - 1991 DA - 1991// TI - Natural and sexual selection on many loci JO - Genetics VL - 127 ID - Barton1991 ER - TY - JOUR AU - Kirkpatrick, M. AU - Johnson, T. AU - Barton, N. PY - 2002 DA - 2002// TI - General models of multilocus evolution JO - Genetics VL - 161 ID - Kirkpatrick2002 ER - TY - BOOK AU - Lynch, M. AU - Walsh, B. PY - 1998 DA - 1998// TI - Genetics and analysis of quantitative traits PB - Sinauer Associates CY - Sunderland, Massachusetts ID - Lynch1998 ER - TY - BOOK AU - Falconer, D. S. AU - Mackay, T. F. C. PY - 1996 DA - 1996// TI - Introduction to quantiative genetics PB - Longman CY - Harlow, Essex, UK ID - Falconer1996 ER - TY - JOUR AU - Haldane, J. B. S. PY - 1924 DA - 1924// TI - The mathematical theory of natural and artificial selection. Part I JO - Trans Camb Philos Soc VL - 23 ID - Haldane1924 ER - TY - JOUR AU - Ohta, T. PY - 1992 DA - 1992// TI - The nearly neutral theory of molecular evolution JO - Annu Rev Ecol Syst VL - 23 ID - Ohta1992 ER - TY - JOUR AU - McVean, G. A. T. AU - Charlesworth, B. PY - 1999 DA - 1999// TI - A population genetic model for the evolution of synonymous codon usage: patterns and predictions JO - Genet Res VL - 74 ID - McVean1999 ER - TY - BOOK AU - Rose, M. R. AU - Lauder, G. V. PY - 1996 DA - 1996// TI - Adaptation PB - Academic Press CY - San Diego ID - Rose1996 ER - TY - BOOK AU - Darwin, C. PY - 1859 DA - 1859// TI - On the origin of species by means of natural selection PB - J. Murray CY - London ID - Darwin1859 ER - TY - JOUR AU - Grafen, A. PY - 2006 DA - 2006// TI - A theory of Fisher's reproductive value JO - J math Biol VL - 53 ID - Grafen2006 ER - TY - JOUR AU - Grafen, A. PY - 2007 DA - 2007// TI - The formal Darwinism project: a mid-term report JO - J Evol Biol VL - 20 ID - Grafen2007 ER - TY - JOUR AU - Andolfatto, P. PY - 2005 DA - 2005// TI - Adaptive evolution of non-coding DNA in Drosophila JO - Nature VL - 437 ID - Andolfatto2005 ER - TY - JOUR PY - 2005 DA - 2005// TI - Initial sequence of the chimpanzee genome and comparison with the human genome JO - Nature VL - 437 ID - ref61 ER - TY - JOUR AU - Lander, E. S. AU - Linton, L. M. AU - Birren, B. AU - Nusbaum, C. AU - Zody, M. C. AU - Baldwin, J. AU - Devon, K. AU - Dewar, K. AU - Doyle, M. AU - FitzHugh, W. PY - 2001 DA - 2001// TI - Initial sequencing and analysis of the human genome JO - Nature VL - 409 ID - Lander2001 ER - TY - JOUR AU - Begun, D. J. AU - Holloway, A. K. AU - Stevens, K. AU - Hillier, L. W. AU - Poh, Y. P. AU - Hahn, M. W. AU - Nista, P. M. AU - Jones, C. D. AU - Kern, A. D. AU - Dewey, C. N. PY - 2007 DA - 2007// TI - Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans JO - PLoS Biol VL - 5 ID - Begun2007 ER - TY - JOUR AU - Chamary, J. V. AU - Parmley, J. L. AU - Hurst, L. D. PY - 2006 DA - 2006// TI - Hearing silence: non-neutral evolution at synonymous sites in mammals JO - Nat Rev Genet VL - 7 ID - Chamary2006 ER - TY - JOUR AU - Eyre-Walker, A. PY - 2006 DA - 2006// TI - The genomic rate of adaptive evolution JO - Trends Ecol Evol VL - 21 ID - Eyre-Walker2006 ER - TY - JOUR AU - Nielsen, R. AU - Williamson, S. AU - Kim, Y. AU - Hubisz, M. J. AU - Clark, A. G. AU - Bustamante, C. PY - 2005 DA - 2005// TI - Genomic scans for selective sweeps using SNP data JO - Genome Res VL - 15 ID - Nielsen2005 ER - TY - JOUR AU - Nielsen, R. AU - Bustamante, C. AU - Clark, A. G. AU - Glanowski, S. AU - Sackton, T. B. AU - Hubisz, M. J. AU - Fledel-Alon, A. AU - Tanenbaum, D. M. AU - Civello, D. AU - White, T. J. PY - 2005 DA - 2005// TI - A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees JO - PLoS Biol VL - 3 ID - Nielsen2005 ER - TY - JOUR AU - Rokyta, D. R. AU - Joyce, P. AU - Caudle, S. B. AU - Wichman, H. A. PY - 2005 DA - 2005// TI - An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus JO - Nat Genet VL - 37 ID - Rokyta2005 ER - TY - JOUR AU - Betancourt, A. J. AU - Bollback, J. P. PY - 2006 DA - 2006// TI - Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution JO - Curr Opin Genet Dev VL - 16 ID - Betancourt2006 ER - TY - CHAP AU - Betancourt, A. J. PY - 2009 DA - 2009// TI - Genome-wide Patterns of Subsitution in Adaptively Evolving Populations of the RNA Bacteriophage MS2 BT - Genetics ID - Betancourt2009 ER - TY - JOUR AU - Lenski, R. E. AU - Travisano, M. PY - 1994 DA - 1994// TI - Dynamics of adaptation and diversification: A 10,000-generation experiment with bacterial populations JO - Proc Natl Acad Sci USA VL - 91 ID - Lenski1994 ER - TY - JOUR AU - Elena, S. F. AU - Lenski, R. E. PY - 2003 DA - 2003// TI - Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation JO - Nature Review Genetics VL - 4 ID - Elena2003 ER - TY - JOUR AU - Lenski, R. E. AU - Winkworth, C. L. AU - Riley, M. A. PY - 2003 DA - 2003// TI - Rates of DNA sequence evolution in experimental populations of Escherichia coli during 20,000 generations JO - J Mol Evol VL - 56 ID - Lenski2003 ER - TY - JOUR AU - Philippe, N. AU - Crozat, E. AU - Lenski, R. E. AU - Schneider, D. PY - 2007 DA - 2007// TI - Evolution of global regulatory networks during a long-term experiment with Escherichia coli JO - Bioessays VL - 29 ID - Philippe2007 ER - TY - JOUR AU - Novak, M. AU - Pfeiffer, T. AU - Lenski, R. E. AU - Sauer, U. AU - Bonhoeffer, S. PY - 2006 DA - 2006// TI - Experimental tests for an evolutionary trade-off between growth rate and yield in E. coli JO - Am Nat VL - 168 ID - Novak2006 ER - TY - JOUR AU - Silander, O. K. AU - Tenaillon, O. AU - Chao, L. PY - 2007 DA - 2007// TI - Understanding the evolutionary fate of finite populations: the dynamics of mutational effects JO - PLoS Biol VL - 5 ID - Silander2007 ER - TY - JOUR AU - Poon, A. AU - Chao, L. PY - 2005 DA - 2005// TI - The Rate of Compensatory Mutation in the DNA Bacteriophage {phi}X174 JO - Genetics VL - 170 ID - Poon2005 ER - TY - JOUR AU - Burch, C. L. AU - Chao, L. PY - 1999 DA - 1999// TI - Evolution by small steps and rugged landscapes in the RNA virus phi 6 JO - Genetics VL - 151 ID - Burch1999 ER - TY - JOUR AU - Burch, C. L. AU - Chao, L. PY - 2000 DA - 2000// TI - Evolvability of an RNA virus is determined by its mutational neighbourhood JO - Nature VL - 406 ID - Burch2000 ER - TY - JOUR AU - Chao, L. PY - 1990 DA - 1990// TI - Fitness of RNA virus decreased by Muller's ratchet JO - Nature VL - 348 ID - Chao1990 ER - TY - JOUR AU - Chao, L. AU - Tran, T. T. AU - Tran, T. T. PY - 1997 DA - 1997// TI - The advantage of sex in the RNA Virus f6 JO - Genetics VL - 147 ID - Chao1997 ER - TY - JOUR AU - Biebricher, C. K. AU - Gardiner, W. C. PY - 1997 DA - 1997// TI - Molecular evolution of RNA in vitro JO - Biophys Chem VL - 66 ID - Biebricher1997 ER - TY - JOUR AU - Lawrence, M. S. AU - Bartel, D. P. PY - 2005 DA - 2005// TI - New ligase-derived RNA polymerase ribozymes JO - RNA VL - 11 ID - Lawrence2005 ER - TY - JOUR AU - Müller, U. F. AU - Bartel, D. P. PY - 2008 DA - 2008// TI - Improved polymerase ribozyme efficiency on hydrophobic assemblies JO - RNA VL - 14 ID - Müller2008 ER - TY - JOUR AU - Kudla, G. AU - Lipinski, L. AU - Caffin, F. AU - Helwak, A. AU - Zylicz, M. PY - 2006 DA - 2006// TI - High guanine and cytosine content increases mRNA levels in mammalian cells JO - PLoS Biol VL - 4 ID - Kudla2006 ER - TY - JOUR AU - Warnecke, T. AU - Hurst, L. D. PY - 2007 DA - 2007// TI - Evidence for a trade-off between translational efficiency and splicing regulation in determining synonymous codon usage in Drosophila melanogaster JO - Mol Biol Evol VL - 24 ID - Warnecke2007 ER - TY - JOUR AU - Hurst, L. D. AU - Pal, C. AU - Lercher, M. J. PY - 2004 DA - 2004// TI - The evolutionary dynamics of eukaryotic gene order JO - Nat Rev Genet VL - 5 ID - Hurst2004 ER - TY - JOUR AU - Jasnos, L. AU - Korona, R. PY - 2007 DA - 2007// TI - Epistatic buffering of fitness loss in yeast double deletion strains JO - Nat Genet VL - 39 ID - Jasnos2007 ER - TY - JOUR AU - Moore, J. H. PY - 2003 DA - 2003// TI - The ubiquitous nature of epistasis in determining susceptibility to common human diseases JO - Hum Hered VL - 56 ID - Moore2003 ER - TY - BOOK AU - Wolf, J. B. AU - Brodie, E. D. AU - Wade, M. J. PY - 2000 DA - 2000// TI - Epistasis and the evolutionary process PB - Oxford University Press CY - New York ID - Wolf2000 ER - TY - JOUR AU - Poelwijk, F. J. AU - Kiviet, D. J. AU - Weinreich, D. M. AU - Tans, S. J. PY - 2007 DA - 2007// TI - Empirical fitness landscapes reveal accessible evolutionary paths JO - Nature VL - 445 ID - Poelwijk2007 ER - TY - JOUR AU - Weinreich, D. M. AU - Watson, R. A. AU - Chao, L. PY - 2005 DA - 2005// TI - Perspective: Sign epistasis and genetic constraint on evolutionary trajectories JO - Evolution VL - 59 ID - Weinreich2005 ER - TY - JOUR AU - Loewe, L. AU - Charlesworth, B. PY - 2006 DA - 2006// TI - Inferring the distribution of mutational effects on fitness in Drosophila JO - Biol Lett VL - 2 ID - Loewe2006 ER - TY - JOUR AU - Sanjuan, R. AU - Elena, S. F. PY - 2006 DA - 2006// TI - Epistasis correlates to genomic complexity JO - Proc Natl Acad Sci USA VL - 103 ID - Sanjuan2006 ER - TY - JOUR AU - Dean, A. M. AU - Thornton, J. W. PY - 2007 DA - 2007// TI - Mechanistic approaches to the study of evolution: the functional synthesis JO - Nat Rev Genet VL - 8 ID - Dean2007 ER - TY - JOUR AU - Watt, W. B. AU - Dean, A. M. PY - 2000 DA - 2000// TI - Molecular-functional studies of adaptive genetic variation in prokaryotes and eukaryotes JO - Annu Rev Genet VL - 34 ID - Watt2000 ER - TY - JOUR AU - Halligan, D. L. AU - Eyre-Walker, A. AU - Andolfatto, P. AU - Keightley, P. D. PY - 2004 DA - 2004// TI - Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila JO - Genome Res VL - 14 ID - Halligan2004 ER - TY - JOUR AU - Gaffney, D. J. AU - Keightley, P. D. PY - 2006 DA - 2006// TI - Genomic selective constraints in murid noncoding DNA JO - PLoS Genetics VL - 2 ID - Gaffney2006 ER - TY - BOOK AU - Lynch, M. PY - 2007 DA - 2007// TI - The origins of genome architecture PB - Sinauer Associates CY - Sunderland, Mass. ID - Lynch2007 ER - TY - JOUR AU - Lynch, M. PY - 2007 DA - 2007// TI - The evolution of genetic networks by non-adaptive processes JO - Nat Rev Genet VL - 8 ID - Lynch2007 ER - TY - JOUR AU - Lynch, M. PY - 2007 DA - 2007// TI - The frailty of adaptive hypotheses for the origins of organismal complexity JO - Proc Natl Acad Sci USA VL - 104 ID - Lynch2007 ER - TY - JOUR AU - Loewe, L. AU - Cutter, A. PY - 2008 DA - 2008// TI - On the potential for extinction by Muller's Ratchet in Caenorhabditis elegans JO - BMC Evol Biol VL - 8 ID - Loewe2008 ER - TY - JOUR AU - Gould, S. J. AU - Lewontin, R. C. PY - 1979 DA - 1979// TI - The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme JO - Proc R Soc Lond B Biol Sci VL - 205 ID - Gould1979 ER - TY - JOUR AU - Gould, S. J. PY - 1997 DA - 1997// TI - The exaptive excellence of spandrels as a term and prototype JO - Proc Natl Acad Sci USA VL - 94 ID - Gould1997 ER - TY - JOUR AU - Kreitman, M. PY - 2000 DA - 2000// TI - Methods to detect selection in populations with applications to the human JO - Annu Rev Genomics Hum Genet VL - 1 ID - Kreitman2000 ER - TY - JOUR AU - Dobzhansky, T. PY - 1973 DA - 1973// TI - Nothing in biology makes sense except in the light of evolution JO - American Biology Teacher VL - 35 ID - Dobzhansky1973 ER - TY - JOUR AU - Rajasingh, H. AU - Gjuvsland, A. B. AU - Vage, D. I. AU - Omholt, S. W. PY - 2008 DA - 2008// TI - When parameters in dynamic models become phenotypes:a case study on flesh pigmentation in the Chinook salmon (Oncorhynchus tshawytscha) JO - Genetics VL - 179 ID - Rajasingh2008 ER - TY - JOUR AU - Ibarra, R. U. AU - Edwards, J. S. AU - Palsson, B. O. PY - 2002 DA - 2002// TI - Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth JO - Nature VL - 420 ID - Ibarra2002 ER - TY - JOUR AU - Endy, D. AU - You, L. AU - Yin, J. AU - Molineux, I. J. PY - 2000 DA - 2000// TI - Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes JO - Proc Natl Acad Sci USA VL - 97 ID - Endy2000 ER - TY - CHAP AU - Locke, J. C. AU - Southern, M. M. AU - Kozma-Bognar, L. AU - Hibberd, V. AU - Brown, P. E. AU - Turner, M. S. AU - Millar, A. J. PY - 2005 DA - 2005// TI - Extension of a genetic network model by iterative experimentation and mathematical analysis BT - Mol Syst Biol ID - Locke2005 ER - TY - JOUR AU - Watt, W. B. PY - 1985 DA - 1985// TI - Bioenergetics and Evolutionary Genetics – Opportunities for New Synthesis JO - Am Nat VL - 125 ID - Watt1985 ER - TY - JOUR AU - Miller, S. P. AU - Lunzer, M. AU - Dean, A. M. PY - 2006 DA - 2006// TI - Direct demonstration of an adaptive constraint JO - Science VL - 314 ID - Miller2006 ER - TY - JOUR AU - Zhu, G. AU - Golding, G. B. AU - Dean, A. M. PY - 2005 DA - 2005// TI - The selective cause of an ancient adaptation JO - Science VL - 307 ID - Zhu2005 ER - TY - JOUR AU - Kacser, H. AU - Burns, J. A. PY - 1981 DA - 1981// TI - The molecular basis of dominance JO - Genetics VL - 97 ID - Kacser1981 ER - TY - JOUR AU - Hartl, D. L. PY - 1989 DA - 1989// TI - The physiology of weak selection JO - Genome VL - 31 ID - Hartl1989 ER - TY - JOUR AU - Watt, W. B. PY - 1986 DA - 1986// TI - Power and Efficiency as Indexes of Fitness in Metabolic Organization JO - Am Nat VL - 127 ID - Watt1986 ER - TY - JOUR AU - Wright, S. PY - 1932 DA - 1932// TI - The roles of mutation, inbreeding, crossbreeding, and selection in evolution JO - Proceedings of the Sixth International Congress of Genetics VL - 1 ID - Wright1932 ER - TY - BOOK AU - Gavrilets, S. PY - 2004 DA - 2004// TI - Fitness landscapes and the origin of species PB - Princeton University Press CY - Princeton, NJ ID - Gavrilets2004 ER - TY - CHAP AU - Provine, W. B. ED - Provine, W. B. PY - 1986 DA - 1986// TI - Wrinkles in the surface of selective value BT - Sewall Wright and Evolutionary Biology, Hull DL (Series Editor): Science and its conceptual foundations PB - The University of Chicago Press CY - Chicago ID - Provine1986 ER - TY - JOUR AU - Arnold, S. J. AU - Pfrender, M. E. AU - Jones, A. G. PY - 2001 DA - 2001// TI - The adaptive landscape as a conceptual bridge between micro- and macroevolution JO - Genetica VL - 112-113 ID - Arnold2001 ER - TY - BOOK AU - McGhee, G. R. PY - 2007 DA - 2007// TI - The geometry of evolution: adaptive landscapes and theoretical morphospaces PB - Cambridge University Press CY - Cambridge, UK ID - McGhee2007 ER - TY - JOUR AU - Bonhoeffer, S. AU - Stadler, P. F. PY - 1993 DA - 1993// TI - Error thresholds on correlated fitness landscapes JO - J Theor Biol VL - 164 ID - Bonhoeffer1993 ER - TY - JOUR AU - Biebricher, C. K. AU - Eigen, M. PY - 2005 DA - 2005// TI - The error threshold JO - Virus Res VL - 107 ID - Biebricher2005 ER - TY - JOUR AU - Rice, S. H. PY - 2002 DA - 2002// TI - A general population genetic theory for the evolution of developmental interactions JO - Proc Natl Acad Sci USA VL - 99 ID - Rice2002 ER - TY - JOUR AU - Rice, S. H. PY - 2004 DA - 2004// TI - Developmental associations between traits: covariance and beyond JO - Genetics VL - 166 ID - Rice2004 ER - TY - JOUR AU - Rice, S. H. PY - 2008 DA - 2008// TI - Theoretical approaches to the evolution of development and genetic architecture JO - Ann N Y Acad Sci VL - 1133 ID - Rice2008 ER - TY - JOUR AU - Gillespie, J. H. PY - 1984 DA - 1984// TI - Molecular evolution over the mutational landscape JO - Evolution VL - 38 ID - Gillespie1984 ER - TY - BOOK AU - Gillespie, J. H. PY - 1991 DA - 1991// TI - The Causes of Molecular Evolution PB - Oxford University Press CY - New York ID - Gillespie1991 ER - TY - JOUR AU - Lande, R. PY - 1976 DA - 1976// TI - Natural-Selection and Random Genetic Drift in Phenotypic Evolution JO - Evolution VL - 30 ID - Lande1976 ER - TY - JOUR AU - Lande, R. PY - 1975 DA - 1975// TI - The maintenance of genetic variability by mutation in a polygenic character with linked loci JO - Genet Res VL - 26 ID - Lande1975 ER - TY - JOUR AU - Lande, R. PY - 1979 DA - 1979// TI - Quantitative genetic analysis of multivariate evolution applied to brain:body size allometry JO - Evolution VL - 33 ID - Lande1979 ER - TY - JOUR AU - Lande, R. PY - 1982 DA - 1982// TI - A Quantitative Genetic Theory of Life-History Evolution JO - Ecology VL - 63 ID - Lande1982 ER - TY - JOUR AU - Lande, R. AU - Arnold, S. J. PY - 1983 DA - 1983// TI - The measurement of selection on correlated characters JO - Evolution VL - 37 ID - Lande1983 ER - TY - JOUR AU - Lande, R. PY - 2007 DA - 2007// TI - Expected relative fitness and the adaptive topography of fluctuating selection JO - Evolution VL - 61 ID - Lande2007 ER - TY - JOUR AU - Lande, R. PY - 2008 DA - 2008// TI - Adaptive topography of fluctuating selection in a Mendelian population JO - J Evol Biol VL - 21 ID - Lande2008 ER - TY - JOUR AU - Phillips, P. C. PY - 2007 DA - 2007// TI - 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 JO - Genetics Research VL - 89 ID - Phillips2007 ER - TY - JOUR AU - Barton, N. H. AU - Turelli, M. PY - 1987 DA - 1987// TI - Adaptive landscapes, genetic distance and the evolution of quantitative characters JO - Genet Res VL - 49 ID - Barton1987 ER - TY - JOUR AU - Waxman, D. AU - Welch, J. J. PY - 2005 DA - 2005// TI - Fisher's microscope and Haldane's ellipse JO - Am Nat VL - 166 ID - Waxman2005 ER - TY - JOUR AU - Welch, J. J. AU - Waxman, D. PY - 2003 DA - 2003// TI - Modularity and the cost of complexity JO - Evolution VL - 57 ID - Welch2003 ER - TY - JOUR AU - Martin, G. AU - Lenormand, T. PY - 2006 DA - 2006// TI - A general multivariate extension of Fisher's geometrical model and the distribution of mutation fitness effects across species JO - Evolution VL - 60 ID - Martin2006 ER - TY - JOUR AU - Martin, G. AU - Lenormand, T. PY - 2008 DA - 2008// TI - The distribution of beneficial and fixed mutation fitness effects close to an optimum JO - Genetics VL - 179 ID - Martin2008 ER - TY - JOUR AU - Orr, H. A. PY - 2005 DA - 2005// TI - The genetic theory of adaptation: a brief history JO - Nature Review Genetics VL - 6 ID - Orr2005 ER - TY - JOUR AU - Martin, G. AU - Elena, S. F. AU - Lenormand, T. PY - 2007 DA - 2007// TI - Distributions of epistasis in microbes fit predictions from a fitness landscape model JO - Nat Genet VL - 39 ID - Martin2007 ER - TY - JOUR AU - Barton, N. H. AU - Keightley, P. D. PY - 2002 DA - 2002// TI - Understanding quantitative genetic variation JO - Nature Review Genetics VL - 3 ID - Barton2002 ER - TY - BOOK AU - Maynard Smith, J. AU - Szathmáry, E. PY - 1995 DA - 1995// TI - The major transitions in evolution PB - W.H. Freeman Spektrum CY - Oxford; New York ID - Maynard Smith1995 ER - TY - JOUR AU - Szathmáry, E. AU - Maynard Smith, J. PY - 1995 DA - 1995// TI - The major evolutionary transitions JO - Nature VL - 374 ID - Szathmáry1995 ER - TY - CHAP AU - Gardner, A. AU - Grafen, A. PY - 2009 DA - 2009// TI - Capturing the superorganism: a formal theory of group adaptation BT - J Evol Biol ID - Gardner2009 ER - TY - BOOK AU - Okasha, S. PY - 2006 DA - 2006// TI - Evolution and the levels of selection PB - Oxford University Press CY - Oxford ID - Okasha2006 ER - TY - JOUR AU - Grafen, A. PY - 2006 DA - 2006// TI - Optimization of inclusive fitness JO - J Theor Biol VL - 238 ID - Grafen2006 ER - TY - JOUR AU - Rice, S. H. PY - 2008 DA - 2008// TI - A stochastic version of the Price equation reveals the interplay of deterministic and stochastic processes in evolution JO - BMC Evol Biol VL - 8 ID - Rice2008 ER - TY - BOOK AU - Jolliffe, I. T. PY - 2002 DA - 2002// TI - Principal component analysis PB - Springer CY - New York ID - Jolliffe2002 ER - TY - JOUR AU - Kingsolver, J. G. AU - Hoekstra, H. E. AU - Hoekstra, J. M. AU - Berrigan, D. AU - Vignieri, S. N. AU - Hill, C. E. AU - Hoang, A. AU - Gibert, P. AU - Beerli, P. PY - 2001 DA - 2001// TI - The strength of phenotypic selection in natural populations JO - Am Nat VL - 157 ID - Kingsolver2001 ER - TY - JOUR AU - Arnold, S. J. PY - 1983 DA - 1983// TI - Morphology, Performance and Fitness JO - Am Zoologist VL - 23 ID - Arnold1983 ER - TY - JOUR AU - Arnold, S. J. PY - 2003 DA - 2003// TI - Performance surfaces and adaptive landscapes JO - Integrative and Comparative Biology VL - 43 ID - Arnold2003 ER - TY - JOUR AU - Jones, A. G. AU - Arnold, S. J. AU - Borger, R. PY - 2003 DA - 2003// TI - Stability of the G-matrix in a population experiencing pleiotropic mutation, stabilizing selection, and genetic drift JO - Evolution VL - 57 ID - Jones2003 ER - TY - JOUR AU - Gu, X. PY - 2007 DA - 2007// TI - Evolutionary framework for protein sequence evolution and gene pleiotropy JO - Genetics VL - 175 ID - Gu2007 ER - TY - JOUR AU - Weinreich, D. M. AU - Delaney, N. F. AU - Depristo, M. A. AU - Hartl, D. L. PY - 2006 DA - 2006// TI - Darwinian evolution can follow only very few mutational paths to fitter proteins JO - Science VL - 312 ID - Weinreich2006 ER - TY - JOUR AU - Furnham, N. AU - de Bakker, P. I. AU - Gore, S. AU - Burke, D. F. AU - Blundell, T. L. PY - 2008 DA - 2008// TI - Comparative modelling by restraint-based conformational sampling JO - BMC Struct Biol VL - 8 ID - Furnham2008 ER - TY - JOUR AU - Dalton, J. A. AU - Jackson, R. M. PY - 2007 DA - 2007// TI - An evaluation of automated homology modelling methods at low target template sequence similarity JO - Bioinformatics VL - 23 ID - Dalton2007 ER - TY - JOUR AU - Alber, T. PY - 1989 DA - 1989// TI - Mutational effects on protein stability JO - Annu Rev Biochem VL - 58 ID - Alber1989 ER - TY - BOOK AU - Lutz, S. AU - Bornscheuer, U. T. PY - 2009 DA - 2009// TI - Protein Engineering Handbook ID - Lutz2009 ER - TY - JOUR AU - Burke, D. F. AU - Worth, C. L. AU - Priego, E. M. AU - Cheng, T. AU - Smink, L. J. AU - Todd, J. A. AU - Blundell, T. L. PY - 2007 DA - 2007// TI - Genome bioinformatic analysis of nonsynonymous SNPs JO - BMC Bioinformatics VL - 8 ID - Burke2007 ER - TY - JOUR AU - Sunyaev, S. AU - Ramensky, V. AU - Koch, I. AU - Lathe, W. AU - Kondrashov, A. S. AU - Bork, P. PY - 2001 DA - 2001// TI - Prediction of deleterious human alleles JO - Hum Mol Genet VL - 10 ID - Sunyaev2001 ER - TY - JOUR AU - Helles, G. PY - 2008 DA - 2008// TI - A comparative study of the reported performance of ab initio protein structure prediction algorithms JO - J R Soc Interface VL - 5 ID - Helles2008 ER - TY - JOUR AU - Stein, M. AU - Gabdoulline, R. R. AU - Wade, R. C. PY - 2007 DA - 2007// TI - Bridging from molecular simulation to biochemical networks JO - Curr Opin Struct Biol VL - 17 ID - Stein2007 ER - TY - JOUR AU - Richter, S. AU - Wenzel, A. AU - Stein, M. AU - Gabdoulline, R. R. AU - Wade, R. C. PY - 2008 DA - 2008// TI - webPIPSA: a web server for the comparison of protein interaction properties JO - Nucleic Acids Res VL - 36 ID - Richter2008 ER - TY - JOUR AU - Gabdoulline, R. R. AU - Stein, M. AU - Wade, R. C. PY - 2007 DA - 2007// TI - qPIPSA: relating enzymatic kinetic parameters and interaction fields JO - BMC Bioinformatics VL - 8 ID - Gabdoulline2007 ER - TY - JOUR AU - Bogatyreva, N. S. AU - Osypov, A. A. AU - Ivankov, D. N. PY - 2009 DA - 2009// TI - KineticDB: a database of protein folding kinetics JO - Nucleic Acids Res VL - 37 ID - Bogatyreva2009 ER - TY - JOUR AU - Kumar, P. AU - Han, B. C. AU - Shi, Z. AU - Jia, J. AU - Wang, Y. P. AU - Zhang, Y. T. AU - Liang, L. AU - Liu, Q. F. AU - Ji, Z. L. AU - Chen, Y. Z. PY - 2008 DA - 2008// TI - Update of KDBI: Kinetic Data of Bio-molecular Interaction database JO - Nucleic Acids Res VL - 37 ID - Kumar2008 ER - TY - JOUR AU - Markiewicz, P. AU - Kleina, L. G. AU - Cruz, C. AU - Ehret, S. AU - Miller, J. H. PY - 1994 DA - 1994// TI - 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 JO - J Mol Biol VL - 240 ID - Markiewicz1994 ER - TY - JOUR AU - Drummond, D. A. AU - Iverson, B. L. AU - Georgiou, G. AU - Arnold, F. H. PY - 2005 DA - 2005// TI - Why high-error-rate random mutagenesis libraries are enriched in functional and improved proteins JO - J Mol Biol VL - 350 ID - Drummond2005 ER - TY - JOUR AU - Tokuriki, N. AU - Stricher, F. AU - Serrano, L. AU - Tawfik, D. S. PY - 2008 DA - 2008// TI - How protein stability and new functions trade off JO - PLoS Comput Biol VL - 4 ID - Tokuriki2008 ER - TY - JOUR AU - Tokuriki, N. AU - Stricher, F. AU - Schymkowitz, J. AU - Serrano, L. AU - Tawfik, D. S. PY - 2007 DA - 2007// TI - The stability effects of protein mutations appear to be universally distributed JO - J Mol Biol VL - 369 ID - Tokuriki2007 ER - TY - JOUR AU - Peisajovich, S. G. AU - Tawfik, D. S. PY - 2007 DA - 2007// TI - Protein engineers turned evolutionists JO - Nat Methods VL - 4 ID - Peisajovich2007 ER - TY - JOUR AU - Peisajovich, S. G. AU - Rockah, L. AU - Tawfik, D. S. PY - 2006 DA - 2006// TI - Evolution of new protein topologies through multistep gene rearrangements JO - Nat Genet VL - 38 ID - Peisajovich2006 ER - TY - JOUR AU - Bershtein, S. AU - Segal, M. AU - Bekerman, R. AU - Tokuriki, N. AU - Tawfik, D. S. PY - 2006 DA - 2006// TI - Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein JO - Nature VL - 444 ID - Bershtein2006 ER - TY - JOUR AU - Aharoni, A. AU - Gaidukov, L. AU - Khersonsky, O. AU - Mc, Q. G. S. AU - Roodveldt, C. AU - Tawfik, D. S. PY - 2005 DA - 2005// TI - The 'evolvability' of promiscuous protein functions JO - Nat Genet VL - 37 ID - Aharoni2005 ER - TY - JOUR AU - Voigt, C. A. AU - Kauffman, S. AU - Wang, Z. G. PY - 2000 DA - 2000// TI - Rational evolutionary design: the theory of in vitro protein evolution JO - Adv Protein Chem VL - 55 ID - Voigt2000 ER - TY - JOUR AU - Hayashi, Y. AU - Aita, T. AU - Toyota, H. AU - Husimi, Y. AU - Urabe, I. AU - Yomo, T. PY - 2006 DA - 2006// TI - Experimental rugged fitness landscape in protein sequence space JO - PLoS ONE VL - 1 ID - Hayashi2006 ER - TY - JOUR AU - Zhao, J. AU - Ridgway, D. AU - Broderick, G. AU - Kovalenko, A. AU - Ellison, M. PY - 2008 DA - 2008// TI - Extraction of elementary rate constants from global network analysis of E. coli central metabolism JO - BMC Syst Biol VL - 2 ID - Zhao2008 ER - TY - JOUR AU - Pey, A. L. AU - Rodriguez-Larrea, D. AU - Bomke, S. AU - Dammers, S. AU - Godoy-Ruiz, R. AU - Garcia-Mira, M. M. AU - Sanchez-Ruiz, J. M. PY - 2008 DA - 2008// TI - Engineering proteins with tunable thermodynamic and kinetic stabilities JO - Proteins VL - 71 ID - Pey2008 ER - TY - JOUR AU - Landry, C. R. AU - Lemos, B. AU - Rifkin, S. A. AU - Dickinson, W. J. AU - Hartl, D. L. PY - 2007 DA - 2007// TI - Genetic properties influencing the evolvability of gene expression JO - Science VL - 317 ID - Landry2007 ER - TY - JOUR AU - Qian, W. AU - Zhang, J. PY - 2008 DA - 2008// TI - Gene dosage and gene duplicability JO - Genetics VL - 179 ID - Qian2008 ER - TY - JOUR AU - Kondrashov, F. A. AU - Koonin, E. V. PY - 2004 DA - 2004// TI - A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications JO - Trends Genet VL - 20 ID - Kondrashov2004 ER - TY - JOUR AU - Wright, S. PY - 1934 DA - 1934// TI - Physiological and evolutionary theories of dominance JO - Am Nat VL - 68 ID - Wright1934 ER - TY - JOUR AU - Hartl, D. L. AU - Dykhuizen, D. E. AU - Dean, A. M. PY - 1985 DA - 1985// TI - Limits of adaptation: The evolution of selective neutrality JO - Genetics VL - 111 ID - Hartl1985 ER - TY - JOUR AU - Dykhuizen, D. E. AU - Dean, A. M. AU - Hartl, D. L. PY - 1987 DA - 1987// TI - Metabolic flux and fitness JO - Genetics VL - 115 ID - Dykhuizen1987 ER - TY - JOUR AU - Swarup, R. AU - Kramer, E. M. AU - Perry, P. AU - Knox, K. AU - Leyser, H. M. AU - Haseloff, J. AU - Beemster, G. T. AU - Bhalerao, R. AU - Bennett, M. J. PY - 2005 DA - 2005// TI - Root gravitropism requires lateral root cap and epidermal cells for transport and response to a mobile auxin signal JO - Nat Cell Biol VL - 7 ID - Swarup2005 ER - TY - JOUR AU - Shreenivasaiah, P. K. AU - Rho, S. H. AU - Kim, T. AU - Kim do, H. PY - 2008 DA - 2008// TI - An overview of cardiac systems biology JO - J Mol Cell Cardiol VL - 44 ID - Shreenivasaiah2008 ER - TY - JOUR AU - Southern, J. AU - Pitt-Francis, J. AU - Whiteley, J. AU - Stokeley, D. AU - Kobashi, H. AU - Nobes, R. AU - Kadooka, Y. AU - Gavaghan, D. PY - 2008 DA - 2008// TI - Multi-scale computational modelling in biology and physiology JO - Prog Biophys Mol Biol VL - 96 ID - Southern2008 ER - TY - JOUR AU - McCulloch, A. D. AU - Paternostro, G. PY - 2005 DA - 2005// TI - Cardiac systems biology JO - Ann N Y Acad Sci VL - 1047 ID - McCulloch2005 ER - TY - BOOK AU - Stearns, S. C. AU - Koella, J. C. PY - 2008 DA - 2008// TI - Evolution in health and disease PB - Oxford University Press CY - Oxford; New York ID - Stearns2008 ER - TY - JOUR AU - Feist, A. M. AU - Herrgard, M. J. AU - Thiele, I. AU - Reed, J. L. AU - Palsson, B. Ø. PY - 2009 DA - 2009// TI - Reconstruction of Biochemical Networks in Microbial Organisms JO - Nature Reviews Microbiology VL - 7 ID - Feist2009 ER - TY - JOUR AU - Gutenkunst, R. N. AU - Waterfall, J. J. AU - Casey, F. P. AU - Brown, K. S. AU - Myers, C. R. AU - Sethna, J. P. PY - 2007 DA - 2007// TI - Universally sloppy parameter sensitivities in systems biology models JO - PLoS Comput Biol VL - 3 ID - Gutenkunst2007 ER - TY - JOUR AU - Ibarra, R. U. AU - Fu, P. AU - Palsson, B. O. AU - DiTonno, J. R. AU - Edwards, J. S. PY - 2003 DA - 2003// TI - Quantitative analysis of Escherichia coli metabolic phenotypes within the context of phenotypic phase planes JO - J Mol Microbiol Biotechnol VL - 6 ID - Ibarra2003 ER - TY - JOUR AU - Loewe, L. AU - Hillston, J. PY - 2008 DA - 2008// TI - The distribution of mutational effects on fitness in a simple circadian clock JO - Lecture Notes in Bioinformatics VL - 5307 ID - Loewe2008 ER - TY - JOUR AU - Kauffman, K. J. AU - Pajerowski, J. D. AU - Jamshidi, N. AU - Palsson, B. O. AU - Edwards, J. S. PY - 2002 DA - 2002// TI - Description and analysis of metabolic connectivity and dynamics in the human red blood cell JO - Biophys J VL - 83 ID - Kauffman2002 ER - TY - JOUR AU - Covert, M. W. AU - Schilling, C. H. AU - Famili, I. AU - Edwards, J. S. AU - Goryanin, I. I. AU - Selkov, E. AU - Palsson, B. O. PY - 2001 DA - 2001// TI - Metabolic modeling of microbial strains in silico JO - Trends Biochem Sci VL - 26 ID - Covert2001 ER - TY - JOUR AU - von Dassow, G. AU - Meir, E. AU - Munro, E. M. AU - Odell, G. M. PY - 2000 DA - 2000// TI - The segment polarity network is a robust developmental module JO - Nature VL - 406 ID - von Dassow2000 ER - TY - JOUR AU - Munteanu, A. AU - Sole, R. V. PY - 2008 DA - 2008// TI - Neutrality and robustness in evo-devo: emergence of lateral inhibition JO - PLoS Comput Biol VL - 4 ID - Munteanu2008 ER - TY - JOUR AU - Johnson, L. J. AU - Brookfield, J. F. PY - 2003 DA - 2003// TI - Evolution of spatial expression pattern JO - Evol Dev VL - 5 ID - Johnson2003 ER - TY - JOUR AU - Arthur, W. PY - 2002 DA - 2002// TI - The emerging conceptual framework of evolutionary developmental biology JO - Nature VL - 415 ID - Arthur2002 ER - TY - JOUR AU - Raff, R. A. PY - 2000 DA - 2000// TI - Evo-devo: the evolution of a new discipline JO - Nat Rev Genet VL - 1 ID - Raff2000 ER - TY - JOUR AU - Arthur, W. PY - 2000 DA - 2000// TI - The concept of developmental reprogramming and the quest for an inclusive theory of evolutionary mechanisms JO - Evol Dev VL - 2 ID - Arthur2000 ER - TY - JOUR AU - Lamm, E. AU - Jablonka, E. PY - 2008 DA - 2008// TI - Integrating evolution and development: from theory to practice JO - Perspect Biol Med VL - 51 ID - Lamm2008 ER - TY - JOUR AU - De Robertis, E. M. PY - 2008 DA - 2008// TI - Evo-devo: variations on ancestral themes JO - Cell VL - 132 ID - De Robertis2008 ER - TY - JOUR AU - Carroll, S. B. PY - 2008 DA - 2008// TI - Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution JO - Cell VL - 134 ID - Carroll2008 ER - TY - JOUR AU - Wagner, G. P. AU - Pavlicev, M. AU - Cheverud, J. M. PY - 2007 DA - 2007// TI - The road to modularity JO - Nat Rev Genet VL - 8 ID - Wagner2007 ER - TY - JOUR AU - Muller, G. B. PY - 2007 DA - 2007// TI - Evo-devo: extending the evolutionary synthesis JO - Nat Rev Genet VL - 8 ID - Muller2007 ER - TY - JOUR AU - Raff, R. A. PY - 2007 DA - 2007// TI - Written in stone: fossils, genes and evo-devo JO - Nat Rev Genet VL - 8 ID - Raff2007 ER - TY - JOUR AU - Canestro, C. AU - Yokoi, H. AU - Postlethwait, J. H. PY - 2007 DA - 2007// TI - Evolutionary developmental biology and genomics JO - Nat Rev Genet VL - 8 ID - Canestro2007 ER - TY - BOOK PY - 2007 DA - 2007// TI - Systems Biology: a vision for engineering and medicine. London ID - ref212 ER - TY - BOOK PY - 2007 DA - 2007// TI - Systems Biology: a Grand Challenge for Europe PB - European Science Foundation CY - Strasbourg, France ID - ref213 ER - TY - JOUR AU - Welch, J. J. AU - Waxman, D. PY - 2005 DA - 2005// TI - The nk model and population genetics JO - J Theor Biol VL - 234 ID - Welch2005 ER - TY - JOUR AU - Brommer, J. E. PY - 2000 DA - 2000// TI - The evolution of fitness in life-history theory JO - Biol Rev Camb Philos Soc VL - 75 ID - Brommer2000 ER - TY - BOOK AU - Stearns, S. C. PY - 1992 DA - 1992// TI - The evolution of life histories PB - Oxford University Press CY - Oxford ID - Stearns1992 ER - TY - JOUR AU - Stearns, S. C. PY - 2000 DA - 2000// TI - Life history evolution: successes, limitations, and prospects JO - Naturwissenschaften VL - 87 ID - Stearns2000 ER - TY - JOUR AU - Martin, G. AU - Lenormand, T. PY - 2006 DA - 2006// TI - The fitness effect of mutations across environments: a survey in light of fitness landscape models JO - Evolution VL - 60 ID - Martin2006 ER - TY - JOUR AU - Förster, J. AU - Famili, I. AU - Fu, P. AU - Palsson, B. O. AU - Nielsen, J. PY - 2003 DA - 2003// TI - Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network JO - Genome Res VL - 13 ID - Förster2003 ER - TY - JOUR AU - Kulheim, C. AU - Agren, J. AU - Jansson, S. PY - 2002 DA - 2002// TI - Rapid regulation of light harvesting and plant fitness in the field JO - Science VL - 297 ID - Kulheim2002 ER - TY - JOUR AU - Isalan, M. AU - Lemerle, C. AU - Michalodimitrakis, K. AU - Horn, C. AU - Beltrao, P. AU - Raineri, E. AU - Garriga-Canut, M. AU - Serrano, L. PY - 2008 DA - 2008// TI - Evolvability and hierarchy in rewired bacterial gene networks JO - Nature VL - 452 ID - Isalan2008 ER - TY - JOUR AU - Fischer, E. AU - Sauer, U. PY - 2005 DA - 2005// TI - Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism JO - Nat Genet VL - 37 ID - Fischer2005 ER - TY - JOUR AU - Elena, S. F. AU - Cooper, V. S. AU - Lenski, R. E. PY - 1996 DA - 1996// TI - Punctuated evolution caused by selection of rare beneficial mutations JO - Science VL - 272 ID - Elena1996 ER - TY - JOUR AU - Cooper, V. S. AU - Lenski, R. E. PY - 2000 DA - 2000// TI - The population genetics of ecological specialization in evolving Escherichia coli populations JO - Nature VL - 407 ID - Cooper2000 ER - TY - JOUR AU - Kacser, H. AU - Acerenza, L. PY - 1993 DA - 1993// TI - A universal method for achieving increases in metabolite production JO - Eur J Biochem VL - 216 ID - Kacser1993 ER - TY - JOUR AU - Ouyang, Y. AU - Andersson, C. R. AU - Kondo, T. AU - Golden, S. S. AU - Johnson, C. H. PY - 1998 DA - 1998// TI - Resonating circadian clocks enhance fitness in cyanobacteria JO - Proc Natl Acad Sci USA VL - 95 ID - Ouyang1998 ER - TY - JOUR AU - Dodd, A. N. AU - Salathia, N. AU - Hall, A. AU - Kevei, E. AU - Toth, R. AU - Nagy, F. AU - Hibberd, J. M. AU - Millar, A. J. AU - Webb, A. A. R. PY - 2005 DA - 2005// TI - Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage JO - Science VL - 309 ID - Dodd2005 ER - TY - JOUR AU - Dekel, E. AU - Alon, U. PY - 2005 DA - 2005// TI - Optimality and evolutionary tuning of the expression level of a protein JO - Nature VL - 436 ID - Dekel2005 ER - TY - JOUR AU - Bloom, J. D. AU - Drummond, D. A. AU - Arnold, F. H. AU - Wilke, C. O. PY - 2006 DA - 2006// TI - Structural determinants of the rate of protein evolution in yeast JO - Mol Biol Evol VL - 23 ID - Bloom2006 ER - TY - JOUR AU - Drummond, D. A. AU - Wilke, C. O. PY - 2008 DA - 2008// TI - Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution JO - Cell VL - 134 ID - Drummond2008 ER - TY - JOUR AU - Wilke, C. O. AU - Bloom, J. D. AU - Drummond, D. A. AU - Raval, A. PY - 2005 DA - 2005// TI - Predicting the tolerance of proteins to random amino acid substitution JO - Biophys J VL - 89 ID - Wilke2005 ER - TY - JOUR AU - Wilke, C. O. AU - Drummond, D. A. PY - 2006 DA - 2006// TI - Population genetics of translational robustness JO - Genetics VL - 173 ID - Wilke2006 ER - TY - JOUR AU - Pfeiffer, T. AU - Soyer, O. S. AU - Bonhoeffer, S. PY - 2005 DA - 2005// TI - The evolution of connectivity in metabolic networks JO - PLoS Biol VL - 3 ID - Pfeiffer2005 ER - TY - JOUR AU - Soyer, O. S. AU - Bonhoeffer, S. PY - 2006 DA - 2006// TI - Evolution of complexity in signaling pathways JO - Proc Natl Acad Sci USA VL - 103 ID - Soyer2006 ER - TY - JOUR AU - Soyer, O. S. AU - Pfeiffer, T. AU - Bonhoeffer, S. PY - 2006 DA - 2006// TI - Simulating the evolution of signal transduction pathways JO - J Theor Biol VL - 241 ID - Soyer2006 ER - TY - JOUR AU - Soyer, O. S. AU - Salathe, M. AU - Bonhoeffer, S. PY - 2006 DA - 2006// TI - Signal transduction networks: topology, response and biochemical processes JO - J Theor Biol VL - 238 ID - Soyer2006 ER - TY - JOUR AU - Charlesworth, B. AU - Borthwick, H. AU - Bartolome, C. AU - Pignatelli, P. PY - 2004 DA - 2004// TI - Estimates of the genomic mutation rate for detrimental alleles in Drosophila melanogaster JO - Genetics VL - 167 ID - Charlesworth2004 ER - TY - JOUR AU - Lynch, M. AU - Blanchard, J. AU - Houle, D. AU - Kibota, T. AU - Schultz, S. AU - Vassilieva, L. AU - Willis, J. PY - 1999 DA - 1999// TI - Perspective: Spontaneous deleterious mutation JO - Evolution VL - 53 ID - Lynch1999 ER - TY - JOUR AU - Drake, J. W. AU - Charlesworth, B. AU - Charlesworth, D. AU - Crow, J. F. PY - 1998 DA - 1998// TI - Rates of spontaneous mutation JO - Genetics VL - 148 ID - Drake1998 ER - TY - JOUR AU - Kassen, R. AU - Bataillon, T. PY - 2006 DA - 2006// TI - Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria JO - Nat Genet VL - 38 ID - Kassen2006 ER - TY - JOUR AU - Sanjuan, R. AU - Moya, A. AU - Elena, S. F. PY - 2004 DA - 2004// TI - The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus JO - Proc Natl Acad Sci USA VL - 101 ID - Sanjuan2004 ER - TY - JOUR AU - Davies, E. K. AU - Peters, A. D. AU - Keightley, P. D. PY - 1999 DA - 1999// TI - High frequency of cryptic deleterious mutations in Caenorhabditis elegans JO - Science VL - 285 ID - Davies1999 ER - TY - JOUR AU - Keightley, P. D. AU - Eyre-Walker, A. PY - 2007 DA - 2007// TI - Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies JO - Genetics VL - 177 ID - Keightley2007 ER - TY - JOUR AU - Li, H. AU - Stephan, W. PY - 2006 DA - 2006// TI - Inferring the demographic history and rate of adaptive substitution in Drosophila JO - PLoS Genet VL - 2 ID - Li2006 ER - TY - JOUR AU - Williamson, S. H. AU - Hernandez, R. AU - Fledel-Alon, A. AU - Zhu, L. AU - Nielsen, R. AU - Bustamante, C. D. PY - 2005 DA - 2005// TI - Simultaneous inference of selection and population growth from patterns of variation in the human genome JO - Proc Natl Acad Sci USA VL - 102 ID - Williamson2005 ER - TY - JOUR AU - Kitano, H. PY - 2007 DA - 2007// TI - Towards a theory of biological robustness JO - Mol Syst Biol VL - 3 ID - Kitano2007 ER - TY - JOUR AU - Flatt, T. PY - 2005 DA - 2005// TI - The evolutionary genetics of canalization JO - Q Rev Biol VL - 80 ID - Flatt2005 ER - TY - JOUR AU - de Visser, J. A. AU - Hermisson, J. AU - Wagner, G. P. AU - Ancel Meyers, L. AU - Bagheri-Chaichian, H. AU - Blanchard, J. L. AU - Chao, L. AU - Cheverud, J. M. AU - Elena, S. F. AU - Fontana, W. PY - 2003 DA - 2003// TI - Perspective: Evolution and detection of genetic robustness JO - Evolution VL - 57 ID - de Visser2003 ER - TY - JOUR AU - Gjuvsland, A. B. AU - Plahte, E. AU - Omholt, S. W. PY - 2007 DA - 2007// TI - Threshold-dominated regulation hides genetic variation in gene expression networks JO - BMC Syst Biol VL - 1 ID - Gjuvsland2007 ER - TY - JOUR AU - Bergman, A. AU - Siegal, M. L. PY - 2003 DA - 2003// TI - Evolutionary capacitance as a general feature of complex gene networks JO - Nature VL - 424 ID - Bergman2003 ER - TY - JOUR AU - Waddington, C. H. PY - 1942 DA - 1942// TI - Canalization of development and the inheritance of acquired characters JO - Nature VL - 150 ID - Waddington1942 ER - TY - JOUR AU - Gibson, G. AU - Wagner, G. PY - 2000 DA - 2000// TI - Canalization in evolutionary genetics: a stabilizing theory? JO - Bioessays VL - 22 ID - Gibson2000 ER - TY - JOUR AU - Queitsch, C. AU - Sangster, T. A. AU - Lindquist, S. PY - 2002 DA - 2002// TI - Hsp90 as a capacitor of phenotypic variation JO - Nature VL - 417 ID - Queitsch2002 ER - TY - JOUR AU - Hermisson, J. AU - Wagner, G. P. PY - 2004 DA - 2004// TI - The population genetic theory of hidden variation and genetic robustness JO - Genetics VL - 168 ID - Hermisson2004 ER - TY - JOUR AU - Wagner, A. PY - 2001 DA - 2001// TI - The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes JO - Mol Biol Evol VL - 18 ID - Wagner2001 ER - TY - BOOK AU - Wagner, A. PY - 2005 DA - 2005// TI - Robustness and evolvability in living systems PB - Princeton University Press CY - Princeton, N.J. ID - Wagner2005 ER - TY - JOUR AU - Wagner, A. PY - 2000 DA - 2000// TI - Robustness against mutations in genetic networks of yeast JO - Nat Genet VL - 24 ID - Wagner2000 ER - TY - JOUR AU - Wagner, A. PY - 2008 DA - 2008// TI - Neutralism and selectionism: a network-based reconciliation JO - Nat Rev Genet VL - 9 ID - Wagner2008 ER - TY - JOUR AU - Wagner, A. PY - 2008 DA - 2008// TI - Gene duplications, robustness and evolutionary innovations JO - Bioessays VL - 30 ID - Wagner2008 ER - TY - JOUR AU - Wagner, A. PY - 2008 DA - 2008// TI - Robustness and evolvability: a paradox resolved JO - Proc Biol Sci VL - 275 ID - Wagner2008 ER - TY - JOUR AU - de Visser, J. A. AU - Elena, S. F. PY - 2007 DA - 2007// TI - The evolution of sex: empirical insights into the roles of epistasis and drift JO - Nat Rev Genet VL - 8 ID - de Visser2007 ER - TY - JOUR AU - Szathmary, E. PY - 1993 DA - 1993// TI - Do deleterious mutations act synergistically? Metabolic control theory provides a partial answer JO - Genetics VL - 133 ID - Szathmary1993 ER - TY - JOUR AU - Elena, S. F. AU - Lenski, R. E. PY - 1997 DA - 1997// TI - Test of synergistic interactions among deleterious mutations in bacteria JO - Nature VL - 390 ID - Elena1997 ER - TY - JOUR AU - Gjuvsland, A. B. AU - Hayes, B. J. AU - Meuwissen, T. H. AU - Plahte, E. AU - Omholt, S. W. PY - 2007 DA - 2007// TI - Nonlinear regulation enhances the phenotypic expression of trans-acting genetic polymorphisms JO - BMC Syst Biol VL - 1 ID - Gjuvsland2007 ER - TY - JOUR AU - Gjuvsland, A. B. AU - Hayes, B. J. AU - Omholt, S. W. AU - Carlborg, O. PY - 2007 DA - 2007// TI - Statistical epistasis is a generic feature of gene regulatory networks JO - Genetics VL - 175 ID - Gjuvsland2007 ER - TY - JOUR AU - Harrison, R. AU - Papp, B. AU - Pal, C. AU - Oliver, S. G. AU - Delneri, D. PY - 2007 DA - 2007// TI - Plasticity of genetic interactions in metabolic networks of yeast JO - Proc Natl Acad Sci USA VL - 104 ID - Harrison2007 ER - TY - JOUR AU - Huelsenbeck, J. P. AU - Rannala, B. PY - 1997 DA - 1997// TI - Phylogenetic methods come of age: testing hypotheses in an evolutionary context JO - Science VL - 276 ID - Huelsenbeck1997 ER - TY - JOUR AU - Welch, J. J. AU - Bromham, L. PY - 2005 DA - 2005// TI - Molecular dating when rates vary JO - Trends Ecol Evol VL - 20 ID - Welch2005 ER - TY - JOUR AU - Drummond, A. J. AU - Ho, S. Y. AU - Phillips, M. J. AU - Rambaut, A. PY - 2006 DA - 2006// TI - Relaxed phylogenetics and dating with confidence JO - PLoS Biol VL - 4 ID - Drummond2006 ER - TY - JOUR AU - Drummond, A. J. AU - Rambaut, A. PY - 2007 DA - 2007// TI - BEAST: Bayesian evolutionary analysis by sampling trees JO - BMC Evol Biol VL - 7 ID - Drummond2007 ER - TY - JOUR AU - Welch, J. J. AU - Eyre-Walker, A. AU - Waxman, D. PY - 2008 DA - 2008// TI - Divergence and polymorphism under the nearly neutral theory of molecular evolution JO - J Mol Evol VL - 67 ID - Welch2008 ER - TY - JOUR AU - Li, H. AU - Stephan, W. PY - 2005 DA - 2005// TI - Maximum-likelihood methods for detecting recent positive selection and localizing the selected site in the genome JO - Genetics VL - 171 ID - Li2005 ER - TY - JOUR AU - Loewe, L. PY - 2006 DA - 2006// TI - Quantifying the genomic decay paradox due to Muller's ratchet in human mitochondrial DNA JO - Genet Res VL - 87 ID - Loewe2006 ER - TY - JOUR AU - Charlesworth, B. PY - 1979 DA - 1979// TI - Evidence against Fisher's theory of dominance JO - Nature VL - 278 ID - Charlesworth1979 ER - TY - JOUR AU - Orr, H. A. PY - 1991 DA - 1991// TI - A test of Fisher's theory of dominance JO - Proc Natl Acad Sci USA VL - 88 ID - Orr1991 ER - TY - JOUR AU - Fisher, R. A. PY - 1931 DA - 1931// TI - The evolution of dominance JO - Biol Rev (Camb) VL - 6 ID - Fisher1931 ER - TY - JOUR AU - Mayo, O. AU - Bürger, R. PY - 1997 DA - 1997// TI - The evolution of dominance: A theory whose time has passed? JO - Biol Rev Camb Philos Soc VL - 72 ID - Mayo1997 ER - TY - JOUR AU - Briggs, G. E. AU - Haldane, J. B. PY - 1925 DA - 1925// TI - A Note on the Kinetics of Enzyme Action JO - Biochem J VL - 19 ID - Briggs1925 ER - TY - JOUR AU - Medina, M. PY - 2005 DA - 2005// TI - Genomes, phylogeny, and evolutionary systems biology JO - Proc Natl Acad Sci USA VL - 102 ID - Medina2005 ER - TY - JOUR AU - Koonin, E. V. AU - Wolf, Y. I. PY - 2006 DA - 2006// TI - Evolutionary systems biology: links between gene evolution and function JO - Curr Opin Biotechnol VL - 17 ID - Koonin2006 ER - TY - BOOK AU - Monroe, D. AU - Bergman, A. AU - Siegal, M. L. AU - Michor, F. PY - 2008 DA - 2008// TI - Meeting report: Convergent revolution: evolutionary systems biology PB - New York Academy of Sciences CY - New York ID - Monroe2008 ER - TY - JOUR AU - Barabasi, A. L. AU - Oltvai, Z. N. PY - 2004 DA - 2004// TI - Network biology: understanding the cell's functional organization JO - Nat Rev Genet VL - 5 ID - Barabasi2004 ER - TY - JOUR AU - Yuan, J. S. AU - Galbraith, D. W. AU - Dai, S. Y. AU - Griffin, P. AU - Stewart, C. N. PY - 2008 DA - 2008// TI - Plant systems biology comes of age JO - Trends Plant Sci VL - 13 ID - Yuan2008 ER - TY - JOUR AU - Kitano, H. PY - 2007 DA - 2007// TI - A robustness-based approach to systems-oriented drug design JO - Nature Reviews Drug Discovery VL - 6 ID - Kitano2007 ER - TY - JOUR AU - Greaves, M. PY - 2007 DA - 2007// TI - Darwinian medicine: a case for cancer JO - Nat Rev Cancer VL - 7 ID - Greaves2007 ER - TY - JOUR AU - Kitano, H. PY - 2003 DA - 2003// TI - Cancer robustness: tumour tactics JO - Nature VL - 426 ID - Kitano2003 ER - TY - JOUR AU - Boulesteix, A. L. AU - Strimmer, K. PY - 2007 DA - 2007// TI - Partial least squares: a versatile tool for the analysis of high-dimensional genomic data JO - Brief Bioinform VL - 8 ID - Boulesteix2007 ER - TY - JOUR AU - Ahmed, F. E. AU - Vos, P. W. AU - Holbert, D. PY - 2007 DA - 2007// TI - Modeling survival in colon cancer: a methodological review JO - Mol Cancer VL - 6 ID - Ahmed2007 ER - TY - JOUR AU - Greenman, C. AU - Wooster, R. AU - Futreal, P. A. AU - Stratton, M. R. AU - Easton, D. F. PY - 2006 DA - 2006// TI - Statistical analysis of pathogenicity of somatic mutations in cancer JO - Genetics VL - 173 ID - Greenman2006 ER - TY - JOUR AU - Goriely, A. AU - McVean, G. A. AU - van Pelt, A. M. AU - O'Rourke, A. W. AU - Wall, S. A. AU - de Rooij, D. G. AU - Wilkie, A. O. PY - 2005 DA - 2005// TI - Gain-of-function amino acid substitutions drive positive selection of FGFR2 mutations in human spermatogonia JO - Proc Natl Acad Sci USA VL - 102 ID - Goriely2005 ER - TY - JOUR AU - Cirz, R. T. AU - Chin, J. K. AU - Andes, D. R. AU - de Crecy-Lagard, V. AU - Craig, W. A. AU - Romesberg, F. E. PY - 2005 DA - 2005// TI - Inhibition of mutation and combating the evolution of antibiotic resistance JO - PLoS Biol VL - 3 ID - Cirz2005 ER - TY - JOUR AU - Norrby, S. R. AU - Nord, C. E. AU - Finch, R. PY - 2005 DA - 2005// TI - Lack of development of new antimicrobial drugs: a potential serious threat to public health JO - Lancet Infect Dis VL - 5 ID - Norrby2005 ER - TY - JOUR AU - D'Costa, V. M. AU - McGrann, K. M. AU - Hughes, D. W. AU - Wright, G. D. PY - 2006 DA - 2006// TI - Sampling the antibiotic resistome JO - Science VL - 311 ID - D'Costa2006 ER - TY - JOUR AU - Rambaut, A. AU - Posada, D. AU - Crandall, K. A. AU - Holmes, E. C. PY - 2004 DA - 2004// TI - The causes and consequences of HIV evolution JO - Nat Rev Genet VL - 5 ID - Rambaut2004 ER - TY - JOUR AU - Butler, S. J. AU - Vickery, J. A. AU - Norris, K. PY - 2007 DA - 2007// TI - Farmland biodiversity and the footprint of agriculture JO - Science VL - 315 ID - Butler2007 ER - TY - JOUR AU - Belostotsky, D. A. AU - Rose, A. B. PY - 2005 DA - 2005// TI - Plant gene expression in the age of systems biology: integrating transcriptional and post-transcriptional events JO - Trends Plant Sci VL - 10 ID - Belostotsky2005 ER - TY - JOUR AU - Hammer, G. AU - Cooper, M. AU - Tardieu, F. AU - Welch, S. AU - Walsh, B. AU - van Eeuwijk, F. AU - Chapman, S. AU - Podlich, D. PY - 2006 DA - 2006// TI - Models for navigating biological complexity in breeding improved crop plants JO - Trends Plant Sci VL - 11 ID - Hammer2006 ER - TY - JOUR AU - Schauer, N. AU - Fernie, A. R. PY - 2006 DA - 2006// TI - Plant metabolomics: towards biological function and mechanism JO - Trends Plant Sci VL - 11 ID - Schauer2006 ER - TY - JOUR AU - Benner, S. A. AU - Sismour, A. M. PY - 2005 DA - 2005// TI - Synthetic biology JO - Nat Rev Genet VL - 6 ID - Benner2005 ER - TY - JOUR AU - O'Malley, M. A. AU - Powell, A. AU - Davies, J. F. AU - Calvert, J. PY - 2008 DA - 2008// TI - Knowledge-making distinctions in synthetic biology JO - Bioessays VL - 30 ID - O'Malley2008 ER - TY - JOUR AU - Sprinzak, D. AU - Elowitz, M. B. PY - 2005 DA - 2005// TI - Reconstruction of genetic circuits JO - Nature VL - 438 ID - Sprinzak2005 ER - TY - JOUR AU - Jamshidi, N. AU - Palsson, B. O. PY - 2006 DA - 2006// TI - Systems biology of SNPs JO - Mol Syst Biol VL - 2 ID - Jamshidi2006 ER - TY - JOUR AU - Adami, C. PY - 2006 DA - 2006// TI - Digital genetics: unravelling the genetic basis of evolution JO - Nat Rev Genet VL - 7 ID - Adami2006 ER - TY - JOUR AU - Wilke, C. O. AU - Wang, J. L. AU - Ofria, C. AU - Lenski, R. E. AU - Adami, C. PY - 2001 DA - 2001// TI - Evolution of digital organisms at high mutation rates leads to survival of the flattest JO - Nature VL - 412 ID - Wilke2001 ER - TY - JOUR AU - Lenski, R. E. AU - Ofria, C. AU - Pennock, R. T. AU - Adami, C. PY - 2003 DA - 2003// TI - The evolutionary origin of complex features JO - Nature VL - 423 ID - Lenski2003 ER - TY - JOUR AU - Papp, B. AU - Pal, C. AU - Hurst, L. D. PY - 2003 DA - 2003// TI - Dosage sensitivity and the evolution of gene families in yeast JO - Nature VL - 424 ID - Papp2003 ER - TY - JOUR AU - Reed, J. L. AU - Patel, T. R. AU - Chen, K. H. AU - Joyce, A. R. AU - Applebee, M. K. AU - Herring, C. D. AU - Bui, O. T. AU - Knight, E. M. AU - Fong, S. S. AU - Palsson, B. O. PY - 2006 DA - 2006// TI - Systems approach to refining genome annotation JO - Proc Natl Acad Sci USA VL - 103 ID - Reed2006 ER - TY - CHAP AU - Rigler, F. H. AU - Peters, R. H. ED - Rigler, F. H. ED - Peters, R. H. PY - 1995 DA - 1995// TI - Reductionism versus holism: An old problem rejuvenated by the computer BT - Science and limnology PB - Ecology Institute CY - Oldendorf/Luhe, Germany ID - Rigler1995 ER - TY - CHAP AU - Wolkenhauer, O. AU - Ullah, M. ED - Boogerd, F. C. ED - Bruggeman, F. J. ED - Hofmeyr, J. -. H. S. ED - Westerhoff, H. V. PY - 2007 DA - 2007// TI - All models are wrong ... some more than others BT - Systems Biology – philosophical foundations PB - Elsevier CY - Amsterdam, The Netherlands ID - Wolkenhauer2007 ER - TY - BOOK AU - Popper, K. R. PY - 1962 DA - 1962// TI - Conjectures and refutations; the growth of scientific knowledge PB - Basic Books CY - New York, ID - Popper1962 ER - TY - BOOK AU - Gelman, A. PY - 2004 DA - 2004// TI - Bayesian data analysis PB - Hall/CRC CY - Boca Raton, Fla. ID - Gelman2004 ER - TY - BOOK AU - Bishop, C. M. PY - 2006 DA - 2006// TI - Pattern recognition and machine learning PB - Springer CY - New York ID - Bishop2006 ER - TY - JOUR AU - Charlesworth, D. AU - Charlesworth, B. AU - McVean, G. A. PY - 2001 DA - 2001// TI - Genome sequences and evolutionary biology, a two-way interaction JO - Trends in Ecol Evol VL - 16 ID - Charlesworth2001 ER - TY - JOUR AU - Peters, D. P. C. AU - Herrick, J. E. AU - Urban, D. L. AU - Gardner, R. H. AU - Breshears, D. D. PY - 2004 DA - 2004// TI - Strategies for ecological extrapolation JO - Oikos VL - 106 ID - Peters2004 ER - TY - CHAP AU - O'Neill, R. V. ED - Nelson, D. J. PY - 1973 DA - 1973// TI - Error analysis of ecological models BT - Radionuclides in ecosystems: Proceedings of the Third National Symposium on Radioecology, May 10–12, 1971, Oak Ridge, Tennessee PB - National Technical Information Service CY - Springfield, Virginia, USA ID - O'Neill1973 ER - TY - JOUR AU - Grimm, V. AU - Revilla, E. AU - Berger, U. AU - Jeltsch, F. AU - Mooij, W. M. AU - Railsback, S. F. AU - Thulke, H. H. AU - Weiner, J. AU - Wiegand, T. AU - DeAngelis, D. L. PY - 2005 DA - 2005// TI - Pattern-oriented modeling of agent-based complex systems: lessons from ecology JO - Science VL - 310 ID - Grimm2005 ER - TY - JOUR AU - Loehle, C. PY - 1990 DA - 1990// TI - A Guide to Increased Creativity in Research – Inspiration or Perspiration JO - Bioscience VL - 40 ID - Loehle1990 ER - TY - BOOK AU - Taylor, H. M. AU - Karlin, S. PY - 1998 DA - 1998// TI - An introduction to stochastic modeling PB - Academic Press CY - San Diego ID - Taylor1998 ER - TY - BOOK AU - McConnell, S. PY - 2004 DA - 2004// TI - Code complete 2nd Edition PB - Microsoft Press CY - Redmond, Wash. ID - McConnell2004 ER - TY - BOOK AU - Law, A. M. AU - Kelton, W. D. PY - 2000 DA - 2000// TI - Simulation modeling and analysis PB - McGraw-Hill CY - Boston ID - Law2000 ER - TY - BOOK AU - Grimm, V. AU - Railsback, S. F. PY - 2005 DA - 2005// TI - Individual-based modeling and ecology PB - Princeton University Press CY - Princeton ID - Grimm2005 ER - TY - JOUR AU - Bart, J. PY - 1995 DA - 1995// TI - Acceptance criteria for using individual-based models to make management decisions JO - Ecol Applic VL - 5 ID - Bart1995 ER - TY - JOUR AU - Hopkins, J. C. AU - Leipold, R. J. PY - 1996 DA - 1996// TI - On the dangers of adjusting the parameters values of mechanism-based mathematical models JO - J Theor Biol VL - 183 ID - Hopkins1996 ER - TY - BOOK AU - Gershenfeld, N. PY - 1999 DA - 1999// TI - The nature of mathematical modeling PB - Cambridge University Press CY - Cambridge ID - Gershenfeld1999 ER - TY - JOUR AU - May, R. M. PY - 2004 DA - 2004// TI - Uses and abuses of mathematics in biology JO - Science VL - 303 ID - May2004 ER - TY - JOUR AU - Nicolson, C. R. AU - Starfield, A. M. AU - Kofinas, G. P. AU - Kruse, J. A. PY - 2002 DA - 2002// TI - Ten heuristics for interdisciplinary modeling projects JO - Ecosystems VL - 5 ID - Nicolson2002 ER - TY - BOOK AU - Aceto, L. AU - Anna, I. AU - Larsen, K. G. AU - Srba PY - 2007 DA - 2007// TI - Reactive systems: modelling, specification and verification PB - Cambridge University Press CY - Cambridge; New York ID - Aceto2007 ER - TY - JOUR AU - Regev, A. AU - Shapiro, E. PY - 2002 DA - 2002// TI - Cells as computation JO - Nature VL - 419 ID - Regev2002 ER - TY - JOUR AU - Beaumont, M. A. AU - Rannala, B. PY - 2004 DA - 2004// TI - The Bayesian revolution in genetics JO - Nat Rev Genet VL - 5 ID - Beaumont2004 ER -