REFERENCES

MANET DATABASE
1. Kim, H.S., Mittenthal, J.E., Caetano-Anollés, G. (2006) MANET: tracing evolution of protein architecture in metabolic networks. BMC Bioinformatics 7:351. [Abstract][Full Text].
2. Kim, H. S., Mittenthal, J. E., Caetano-Anollés, G. (2013) Widespread recruitment of ancient domain structures in modern enzymes during metabolic evolution. Journal of integrative bioinformatics 10(1): 1-18. [Abstract].
3. Mughal, F., Caetano-Anollés, G. (2019) MANET 3.0: Hierarchy and modularity in evolving metabolic networks. PLoS ONE14(10): e0224201. [Abstract][Press release: Tracking metabolic history].
EVOLUTION OF METABOLIC NETWORKS
1. Caetano-Anollés, G., Kim, H.S., Mittenthal, J.E. (2007) The origins of modern metabolic networks inferred from phylogenomic analysis of protein structure. Proceeding of the National Academy of Sciences USA 104: 9358-9363. [Abstract][Full Text].
2. Aziz, M.F., Chan, P., Osorio, J.S., Minhas, B.F., Parekatt, V., Caetano-Anollés, G. (2012) Stress induces biphasic-rewiring and modularization patterns in the metabolomic networks of Escherichia coli. The 2012 IEEE International Conference on BioInformation and BioMedicine (BIBM 2012). [Full Text] [Online supplementary material (pdf)] [Network Images (html)] [Network Animated (html)].
3. Caetano-Anollés, K., Caetano-Anollés, G. (2013) ) Structural phylogenomics reveals gradual evolutionary replacement of abiotic chemistries by protein enzymes in purine metabolism. PLoS ONE 8: e59300. [Abstract]
PROTEOME EVOLUTION
1. Caetano-Anollés, G., Caetano-Anollés, D. (2003) An evolutionarily structured universe of protein architecture. Genome Research 13: 1563-1571. [Abstract] [Full Text]
2. Caetano-Anollés, G. (2004) Protein evolution: charting the universe of macromolecular structure. Chemistry Today 21: 20-22. [Full Text]
3. Caetano-Anollés, G., Caetano-Anollés, D. (2005) Universal sharing patterns in proteomes and evolution of protein fold architecture and life. Journal of Molecular Evolution 60:484-498. [Abstract] [Full Text]
4. Wang M and Caetano-Anollés (2006) Global phylogeny determined by the combination of protein domains in proteomes. Molecular Biology and Evolution 23: 2444-2453. [Abstract][Full Text].
5. Wang, M., Boca, S.M., Kalelkas, R., Mittenthal, J.E., and Caetano-Anollés, G. (2006) A phylogenomics reconstruction of the protein world based on a genomic census of protein fold architecture. Complexity 12:27-40. [Abstract][Full Text]
OTHER
1. Sun F-J., Caetano-Anollés G. (2009) The evolutionary history of the structure of 5S ribosomal RNA. Journal of Molecular Evolution 69: 430-443. [Abstract] [Full Text] [Online supplementary material (pdf)]
   
   
   
   
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