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Influence of metabolic network structure and function on enzyme evolution
Dennis Vitkup, Peter Kharchenko, Andreas Wagner
Genome Biol. 2006; 7(5): R39. Published online 2006 May 9. doi: 10.1186/gb-2006-7-5-r39
PMCID:
PMC1779518
Abstract Full Text PDF–328K Supplementary Material
 Is Cited by the Following 24 Articles in this Archive:
Modes of Gene Duplication Contribute Differently to Genetic Novelty and Redundancy, but Show Parallels across Divergent Angiosperms
Yupeng Wang, Xiyin Wang, Haibao Tang, Xu Tan, Stephen P. Ficklin, F. Alex Feltus, Andrew H. Paterson
PLoS One. 2011; 6(12): e28150. Published online 2011 December 2. doi: 10.1371/journal.pone.0028150
PMCID:
PMC3229532
Abstract Full Text PDF–1.1M Supplementary Material
Selection for Higher Gene Copy Number after Different Types of Plant Gene Duplications
Corey M. Hudson, Emily E. Puckett, Michaël Bekaert, J. Chris Pires, Gavin C. Conant
Genome Biol Evol. 2011; 3: 1369–1380. Published online 2011 November 4. doi: 10.1093/gbe/evr115
PMCID:
PMC3240960
Abstract Full Text PDF–502K
Expression Level Drives the Pattern of Selective Constraints along the Insulin/Tor Signal Transduction Pathway in Caenorhabditis
Richard Jovelin, Patrick C. Phillips
Genome Biol Evol. 2011; 3: 715–722. Published online 2011 August 17. doi: 10.1093/gbe/evr071
PMCID:
PMC3157841
Abstract Full Text PDF–271K
Difference in the distribution pattern of substrate enzymes in the metabolic network of Escherichia coli, according to chaperonin requirement
Kazuhiro Takemoto, Tatsuya Niwa, Hideki Taguchi
BMC Syst Biol. 2011; 5: 98. Published online 2011 June 24. doi: 10.1186/1752-0509-5-98
PMCID:
PMC3146850
Abstract Full Text PDF–651K Supplementary Material
The Effects of Network Neighbours on Protein Evolution
Guang-Zhong Wang, Martin J. Lercher
PLoS One. 2011; 6(4): e18288. Published online 2011 April 12. doi: 10.1371/journal.pone.0018288
PMCID:
PMC3075247
Abstract Full Text PDF–343K
Expression level, cellular compartment and metabolic network position all influence the average selective constraint on mammalian enzymes
Corey M Hudson, Gavin C Conant
BMC Evol Biol. 2011; 11: 89. Published online 2011 April 6. doi: 10.1186/1471-2148-11-89
PMCID:
PMC3082228
Abstract Full Text PDF–1.3M Supplementary Material
The rate of the molecular clock and the cost of gratuitous protein synthesis
Germán Plata, Max E Gottesman, Dennis Vitkup
Genome Biol. 2010; 11(9): R98. Published online 2010 September 29. doi: 10.1186/gb-2010-11-9-r98
PMCID:
PMC2965390
Abstract Full Text PDF–714K
Need-Based Up-Regulation of Protein Levels in Response to Deletion of Their Duplicate Genes
Alexander DeLuna, Michael Springer, Marc W. Kirschner, Roy Kishony
PLoS Biol. 2010 March; 8(3): e1000347. Published online 2010 March 30. doi: 10.1371/journal.pbio.1000347
PMCID:
PMC2846854
Abstract Full Text PDF–963K Supplementary Material
Relative Contributions of Intrinsic Structural–Functional Constraints and Translation Rate to the Evolution of Protein-Coding Genes
Yuri I. Wolf, Irina V. Gopich, David J. Lipman, Eugene V. Koonin
Genome Biol Evol. 2010; 2: 190–199. Published online 2010 March 17. doi: 10.1093/gbe/evq010
PMCID:
PMC2940324
Abstract Full Text PDF–830K
Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species
Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Uri Gophna, Roded Sharan, Eytan Ruppin
PLoS Comput Biol. 2010 February; 6(2): e1000690. Published online 2010 February 26. doi: 10.1371/journal.pcbi.1000690
PMCID:
PMC2829043
Abstract Full Text PDF–629K Supplementary Material
Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks
João F. Matias Rodrigues, Andreas Wagner
PLoS Comput Biol. 2009 December; 5(12): e1000613. Published online 2009 December 18. doi: 10.1371/journal.pcbi.1000613
PMCID:
PMC2785887
Abstract Full Text PDF–785K Supplementary Material
Evolutionary rate patterns of the Gibberellin pathway genes
Yan-hua Yang, Fu-min Zhang, Song Ge
BMC Evol Biol. 2009; 9: 206. Published online 2009 August 18. doi: 10.1186/1471-2148-9-206
PMCID:
PMC2794029
Abstract Full Text PDF–350K Supplementary Material
Evolutionary rates and centrality in the yeast gene regulatory network
Richard Jovelin, Patrick C Phillips
Genome Biol. 2009; 10(4): R35. Published online 2009 April 9. doi: 10.1186/gb-2009-10-4-r35
PMCID:
PMC2688926
Abstract Full Text PDF–279K
Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes
David Alvarez-Ponce, Montserrat Aguadé, Julio Rozas
Genome Res. 2009 February; 19(2): 234–242. doi: 10.1101/gr.084038.108
PMCID:
PMC2652205
Abstract Full Text PDF–760K
Network-based approaches for linking metabolism with environment
Sarath Chandra Janga, M Madan Babu
Genome Biol. 2008; 9(11): 239. Published online 2008 November 24. doi: 10.1186/gb-2008-9-11-239
PMCID:
PMC2614483
Abstract Full Text PDF–135K
Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution
Maxim Y Wolf, Yuri I Wolf, Eugene V Koonin
Biol Direct. 2008; 3: 40. Published online 2008 October 7. doi: 10.1186/1745-6150-3-40
PMCID:
PMC2572155
Abstract Full Text PDF–623K Supplementary Material
Evolutionary Constraint and Adaptation in the Metabolic Network of Drosophila
Anthony J. Greenberg, Sarah R. Stockwell, Andrew G. Clark
Mol Biol Evol. 2008 December; 25(12): 2537–2546. Published online 2008 September 17. doi: 10.1093/molbev/msn205
PMCID:
PMC2721553
Abstract Full Text PDF–504K Supplementary Material
The evolution of photosynthesis…again?
Lynn J Rothschild
Philos Trans R Soc Lond B Biol Sci. 2008 August 27; 363(1504): 2787–2801. Published online 2008 May 16. doi: 10.1098/rstb.2008.0056
PMCID:
PMC2606773
Abstract Full Text PDF–347K
From Genotype to Phenotype: Systems Biology Meets Natural Variation
Philip N. Benfey, Thomas Mitchell-Olds
Science. Author manuscript; available in PMC 2009 August 17.
Published in final edited form as: Science. 2008 April 25; 320(5875): 495–497. doi: 10.1126/science.1153716
PMCID:
PMC2727942
Abstract Full Text PDF–1.6M
Investigations into the relationship between feedback loops and functional importance of a signal transduction network based on Boolean network modeling
Yung-Keun Kwon, Sun Shim Choi, Kwang-Hyun Cho
BMC Bioinformatics. 2007; 8: 384. Published online 2007 October 15. doi: 10.1186/1471-2105-8-384
PMCID:
PMC2100072
Abstract Full Text PDF–361K Supplementary Material
Modular co-evolution of metabolic networks
Jing Zhao, Guo-Hui Ding, Lin Tao, Hong Yu, Zhong-Hao Yu, Jian-Hua Luo, Zhi-Wei Cao, Yi-Xue Li
BMC Bioinformatics. 2007; 8: 311. Published online 2007 August 27. doi: 10.1186/1471-2105-8-311
PMCID:
PMC2001200
Abstract Full Text PDF–639K Supplementary Material
Impacts of yeast metabolic network structure on enzyme evolution
Chenqi Lu, Ze Zhang, Lindsey Leach, MJ Kearsey, ZW Luo
Genome Biol. 2007; 8(8): 407. Published online 2007 August 9. doi: 10.1186/gb-2007-8-8-407
PMCID:
PMC2374984
Abstract Full Text PDF–151K Supplementary Material
Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia
Timothy Hughes, Diana Ekman, Himanshu Ardawatia, Arne Elofsson, David A Liberles
Genome Biol. 2007; 8(5): 213. Published online 2007 May 22. doi: 10.1186/gb-2007-8-5-213
PMCID:
PMC1929130
Abstract Full Text PDF–102K
Flux control and excess capacity in the enzymes of glycolysis and their relationship to flight metabolism in Drosophila melanogaster
Walter F. Eanes, Thomas J. S. Merritt, Jonathan M. Flowers, Seiji Kumagai, Efe Sezgin, Chen-Tseh Zhu
Proc Natl Acad Sci U S A. 2006 December 19; 103(51): 19413–19418. Published online 2006 December 11. doi: 10.1073/pnas.0607095104
PMCID:
PMC1748240
Abstract Full Text PDF–394K
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