The potential for non-adaptive origins of evolutionary innovations in central carbon metabolism
暂无分享,去创建一个
[1] S. Carroll,et al. Gene co-option in physiological and morphological evolution. , 2002, Annual review of cell and developmental biology.
[2] Bret J. Pearson,et al. Recruitment of a hedgehog regulatory circuit in butterfly eyespot evolution. , 1999, Science.
[3] Andreas Wagner,et al. A comparison of genotype-phenotype maps for RNA and proteins. , 2012, Biophysical journal.
[4] Sayed-Rzgar Hosseini,et al. Exhaustive genotype-phenotype mapping in metabolic genotype space , 2013 .
[5] J. Piatigorsky,et al. Lens Crystallins of Invertebrates , 1996 .
[6] B. Griffin,et al. Network Context and Selection in the Evolution to Enzyme Specificity , 2014 .
[7] Ronan M. T. Fleming,et al. Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide. , 2010, EcoSal Plus.
[8] B. Palsson,et al. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) , 2003, Genome Biology.
[9] Andreas Wagner,et al. Genotype networks in metabolic reaction spaces , 2010, BMC Systems Biology.
[10] Andreas Wagner,et al. Genotype networks, innovation, and robustness in sulfur metabolism , 2010, BMC Systems Biology.
[11] Yu. V. Boltyanskaya,et al. Osmoadaptation of haloalkaliphilic bacteria: Role of osmoregulators and their possible practical application , 2007, Microbiology.
[12] Andreas Wagner,et al. Exhaustive Analysis of a Genotype Space Comprising 1015 Central Carbon Metabolisms Reveals an Organization Conducive to Metabolic Innovation , 2015, PLoS Comput. Biol..
[13] J. Edwards,et al. Systems Properties of the Haemophilus influenzaeRd Metabolic Genotype* , 1999, The Journal of Biological Chemistry.
[14] D. Lipman,et al. Modelling neutral and selective evolution of protein folding , 1991, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[15] Jeffrey D Orth,et al. What is flux balance analysis? , 2010, Nature Biotechnology.
[16] Bernhard Ø. Palsson,et al. Description and Interpretation of Adaptive Evolution of Escherichia coli K-12 MG1655 by Using a Genome-Scale In Silico Metabolic Model , 2003, Journal of bacteriology.
[17] C. Pál,et al. Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast , 2004, Nature.
[18] Telmo Pievani,et al. Exaptation in human evolution: how to test adaptive vs exaptive evolutionary hypotheses. , 2011, Journal of anthropological sciences = Rivista di antropologia : JASS.
[19] Juhan Kim,et al. Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5′-phosphate synthesis , 2010, Molecular systems biology.
[20] D. Phillips,et al. Pentachlorophenol measurements in body fluids of people in log homes and workplaces , 1989, Archives of environmental contamination and toxicology.
[21] Andreas Wagner,et al. Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks , 2009, PLoS Comput. Biol..
[22] L. Rehmann,et al. Enhancement of PCB degradation by Burkholderia xenovorans LB400 in biphasic systems by manipulating culture conditions , 2008, Biotechnology and bioengineering.
[23] Walter J. Bock,et al. PREADAPTATION AND MULTIPLE EVOLUTIONARY PATHWAYS , 1959 .
[24] B. Palsson,et al. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[25] G. Church,et al. Analysis of optimality in natural and perturbed metabolic networks , 2002 .
[26] Richard A. Notebaart,et al. Network-level architecture and the evolutionary potential of underground metabolism , 2014, Proceedings of the National Academy of Sciences.
[27] R. Milo,et al. Glycolytic strategy as a tradeoff between energy yield and protein cost , 2013, Proceedings of the National Academy of Sciences.
[28] Oliver Ebenhöh,et al. Functional Classification of Genome-Scale Metabolic Networks , 2009, EURASIP J. Bioinform. Syst. Biol..
[29] G. Church,et al. Bacteria Subsisting on Antibiotics , 2007, Science.
[30] Adam M. Feist,et al. Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli , 2013, Molecular systems biology.
[31] B. Palsson,et al. Genome-scale models of microbial cells: evaluating the consequences of constraints , 2004, Nature Reviews Microbiology.
[32] Ronan M. T. Fleming,et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.
[33] Robert R. Sokal,et al. A statistical method for evaluating systematic relationships , 1958 .
[34] A. Wagner. Metabolic networks and their evolution. , 2012, Advances in experimental medicine and biology.
[35] P. Schuster,et al. From sequences to shapes and back: a case study in RNA secondary structures , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[36] Denis Duboule,et al. Hox genes in digit development and evolution , 1999, Cell and Tissue Research.
[37] B. Palsson,et al. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. , 2003, Genome research.
[38] P. Bork,et al. Variation and evolution of the citric-acid cycle: a genomic perspective. , 1999, Trends in microbiology.
[39] Jason A. Papin,et al. Applications of genome-scale metabolic reconstructions , 2009, Molecular systems biology.
[40] Dan S. Tawfik,et al. Enzyme promiscuity: a mechanistic and evolutionary perspective. , 2010, Annual review of biochemistry.
[41] Andreas Wagner,et al. Arrival of the Fittest: Solving Evolution's Greatest Puzzle , 2014 .
[42] J. R. van der Meer,et al. Evolution of a Pathway for Chlorobenzene Metabolism Leads to Natural Attenuation in Contaminated Groundwater , 1998, Applied and Environmental Microbiology.
[43] Adam M. Feist,et al. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information , 2007, Molecular systems biology.
[44] J. Piatigorsky,et al. Lens crystallins of invertebrates--diversity and recruitment from detoxification enzymes and novel proteins. , 1996, European journal of biochemistry.
[45] B. Palsson,et al. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data , 2001, Nature Biotechnology.
[46] S. Copley,et al. Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach. , 2000, Trends in biochemical sciences.
[47] B. Palsson,et al. Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods , 2012, Nature Reviews Microbiology.
[48] Eric L. Miller,et al. The Ascent of the Abundant: How Mutational Networks Constrain Evolution , 2008, PLoS Comput. Biol..
[49] Reinhart Heinrich,et al. Theoretical approaches to the evolutionary optimization of glycolysis--chemical analysis. , 1997, European journal of biochemistry.
[50] Jianzhi Zhang,et al. Abundant Indispensable Redundancies in Cellular Metabolic Networks , 2009, Genome biology and evolution.
[51] Stephen S Fong,et al. Metabolic gene–deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes , 2004, Nature Genetics.
[52] Andreas Wagner,et al. Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms , 2014, BMC Systems Biology.
[53] R. Hunter,et al. Histochemical demonstration of enzymes separated by zone electrophoresis in starch gels. , 1957, Science.
[54] B. Palsson,et al. Metabolic modelling of microbes: the flux-balance approach. , 2002, Environmental microbiology.
[55] Maria Papagianni,et al. Recent advances in engineering the central carbon metabolism of industrially important bacteria , 2012, Microbial Cell Factories.
[56] Andreas Wagner,et al. A latent capacity for evolutionary innovation through exaptation in metabolic systems , 2013, Nature.
[57] R. Milo,et al. Central carbon metabolism as a minimal biochemical walk between precursors for biomass and energy. , 2010, Molecular cell.
[58] A. Wagner,et al. The organization of metabolic genotype space facilitates adaptive evolution in nitrogen metabolism , 2014 .
[59] Adam M. Feist,et al. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli , 2008, Nature Biotechnology.
[60] B. Palsson,et al. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth , 2002, Nature.
[61] S. Gould,et al. Exaptation—a Missing Term in the Science of Form , 1982, Paleobiology.
[62] A. Wagner,et al. Superessential reactions in metabolic networks , 2012, Proceedings of the National Academy of Sciences.
[63] Ronan M. T. Fleming,et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.