Gustavo Caetano-Anolles

Professor

Dr. Caetano-Anollés explores molecular diversity and how molecular structure determines biological function in plants, animals, fungi and microbes of significance to agriculture. He studies the origin, structure, and evolution of genomes, proteomes, RNomes, and functionomes for applications including bioengineering, biomedicine, and systems biology.

Research Interests

  • Interaction of plants and microbes
  • The spontaneous mutation process
  • Evolution of biological networks
  • Function and structure in proteins and ncRNA
  • Evolution of macromolecular structure

Selected Articles in Journals

  • Mughal F, G Caetano-Anolles (2019) MANET 3.0: Hierarchy and modularity in evolving metabolic networks. PLoS ONE 14(10): e0224201 (abstract) Press release: Tracking metabolic history
  • Caetano-Anolles G, F Aziz, F Mughal, F Graeter, I Koc, K Caetano-Anolles, D Caetano-Anolles (2019) Emergence of hierarchical modularity in evolving networks uncovered by phylogenomic analysis. Evolutionary Bioinformatics 15: 1176934319872980 (abstract)
  • Jeong H, B Arif, G Caetano-Anolles, KM Kim, A Nasir (2019) Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation. Scientific Reports 9(1): 12173 (abstract) Press release: Horizontal gene transfer in the microbiome
  • Caetano-Anolles G, A Nasir, KM Kim, D Caetano-Anolles (2018) Rooting phylogenies and the Tree of Life while minimizing ad hoc and auxiliary assumptions. Evolutionary Bioinformatics 14: 1176934318805101 (abstract)
  • Koc I, I Yuksel, G Caetano-Anolles G (2018) Metabolite-centric reporter pathway and tripartite network analysis of Arabidopsis under cold stress. Frontiers in Bioengineering and Biotechnology 6: 121 (abstract) Press release: Whole system view of plant cold stress
  • Koc I, G Caetano-Anolles (2017) A natural history of molecular functions inferred from an extensive phylogenomic analysis of Gene Ontology data. PLoS ONE 12(5): e0176129 (abstract) Press release: History of molecular functions
  • Malik SS, S Azem-e-Zhara, KM Kim, G Caetano-Anolles, A Nasir (2017) Do viruses exchange genes across superkingdoms of life? Frontiers in Microbiology 8: 2110 (abstract) Press release: Viruses share genes across life
  • Aziz MF, K Caetano-Anolles, G Caetano-Anolles (2016) The early history and emergence of molecular functions and modular scale-free network behavior. Scientific Reports 6: 25058 (abstract)
  • Caetano-Anolles D, G Caetano-Anolles (2016) Piecemeal buildup of the genetic code, ribosomes, and genomes from primordial tRNA building blocks. Life 6: 43 (abstract)
  • Nasir A, G Caetano-Anolles (2015) A phylogenomic data-driven exploration of viral origins and evolution. Science Advances 1: e1500527 (abstract) Press release: Viruses are alive
  • Caetano-Anolles G, D Caetano-Anolles (2015) Computing the origin and evolution of the ribosome from its structure – Uncovering processes of macromolecular accretion benefitting synthetic biology. Computational and Structural Biotechnology Journal 13: 427-447 (abstract)
  • Caetano-Anolles G, M Wang, D Caetano-Anolles (2013) Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility. PLoS ONE 8(8): e72225 (abstract) Press release: Insights onto the origin of the genetic code
  • Debes C, M Wang, G Caetano-Anolles, F Graeter (2013) Folding rate evolution of protein domain structure. PLoS Computational Biology 9: e1002861 (abstract) Press release: Protein folds unravel origins of life
  • Nasir A, KM Kim, G Caetano-Anolles (2012) Giant viruses coexisted with cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya. BMC Evolutionary Biology 15: 156 (abstract) Press release: Shaking up the tree of life
  • Mittenthal JE, D Caetano-Anolles, G Caetano-Anolles (2012) Biphasic patterns of diversification and the emergence of modules. Frontiers in Genetics 3: 147 (abstract)
  • Harish A, G Caetano-Anolles (2012) Ribosomal history reveals the origin of modern protein synthesis. PLoS ONE 7: e32776 (abstract) Press release: Challenging of the RNA world hypothesis
  • Kim KM, T Qin, Y-Y Jiang, L-L Chen, M Xiong, D Caetano-Anolles, H-Y Zhang, G Caetano-Anolles (2012) Protein domain structure uncovers the origin of aerobic metabolism and the rise of planetary oxygenation. Structure 20: 67-76 (abstract) Press release: Researchers identify molecular culprit in rise of planetary oxygen
  • Wang M, CG Kurland, G Caetano-Anolles (2011) Reductive evolution of proteomes and protein structures. Proceedings of the National Academy of Sciences USA 108: 11954-11958 (abstract) (pdf)
  • Wang M, YY Jiang, KM Kim, G Qu, HF Ji, JE Mittenthal, HY Zhang, G Caetano-Anolles (2011) A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation. Molecular Biology and Evolution 28: 567-582 (abstract)
  • Sun F-J, G Caetano-Anolles (2010) The ancient history of the structure of ribonuclease P and the early origins of Archaea. BMC Bioinformatics 11:153 (abstract)
  • Dupont CL, A Butcher, RE Valas, PE Bourne, G Caetano-Anolles (2010) History of biological metal utilization inferred through phylogenomic analysis of protein structure. Proceedings of the National Academy of Sciences USA 107 (23): 10567-10572 (abstract)
  • Caetano-Anolles D, KM Kim, Caetano-Anolles (2010) Proteome evolution and the metabolic origins of translation and cellular life. Journal of Molecular Evolution 72: 14-32 (abstract)
  • Caetano-Anolles G, M Wang, D Caetano-Anolles, JE Mittenthal (2009) The origin, evolution and structure of the protein world. Biochemical Journal 417: 621-637 (abstract)(pdf).
  • Wang M, G Caetano-Anolles (2009) The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world. Structure 17: 66-78 (abstract) Press release: Study of protein structures reveals key events in evolutionary history
  • Sun F-J, G Caetano-Anolles (2008) Evolutionary patterns in the sequence and structure of transfer RNA: a window into early translation and the genetic code. PLoS ONE 3: e2799 (abstract)(pdf) Press release: Study reveals surprising details of the evolution of protein translation
  • Sun F-J, G Caetano-Anolles (2008) Evolutionary patterns in the sequence and structure of transfer RNA: early origins of Archaea and viruses. PLoS Computational Biology 4: e1000018. (abstract) (pdf) Press release: Researchers see history of life in the structure of transfer RNA
  • Wang M, LS Yafremava, D Caetano-Anolles, JE Mittenthal, G Caetano-Anolles (2007) Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world. Genome Research 17: 1572-1585 (abstract)
  • Caetano-Anolles G, HS Kim, JE Mittenthal (2007) The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture. Proceedings of the National Academy of Sciences USA 104: 9358-9363 (abstract)