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David Alvarez-Ponce, Ph.D.
Assistant Professor

Thomas Parchman

Contact Information

Degrees

  • Postdoctoral, Consejo Superior de Investigaciones Cientificas, Spain, 2012-2014
  • Postdoctoral, Trinity College Dublin, 2012
  • Postdoctoral, National University of Ireland Maynooth, 2010-2012
  • Ph.D. Genetics, University of Barcelona, 2010
  • M.Sc. Genetics, University of Barcelona, 2007
  • B.Sc. Computer Science, Open University of Catalonia (92% completed)
  • B.Sc. Biology, University of Barcelona, 2005

Research interests

During evolution, DNA sequences accumulate mutations, resulting in genetic diversity. Mutations are subject to the filtering of natural selection, and standing patterns and levels of DNA variability contain invaluable information about the evolutionary history of genes, genomes and organisms. Research in the lab broadly focuses on understanding why different genes are subject to different evolutionary forces (e.g. purifying and positive selection). With this aim, we make extensive use of large-scale comparative genomics and bioinformatics analyses.

Genes and proteins rarely work in isolation; instead, they work as parts of networks of interacting molecules, such as metabolic networks, signal transduction networks, protein-protein interaction networks, etc. We are interested in how these networks have generated and grown during evolution, and in how the position of genes within such networks affect their evolution.

Other research areas in the lab include the origin of Eukaryotes (which are thought to have arisen from a fusion event involving an archaebacterium and a eubacterium), organism's genomic adaptation to different temperatures, and the development of bioinformatics software.

Publications

  • David Alvarez-Ponce (2014): Why proteins evolve at different rates: The determinants of proteins' rates of evolution. In M. Fares (editor): Natural Selection: Methods and Applications. Taylor & Francis (in press).
  • David Bogumil, David Alvarez-Ponce, Giddy Landan, James McInerney, Tal Dagan (2014): Integration of two ancestral chaperone systems into one: the evolution of eukaryotic molecular chaperones in light of eukaryogenesis. Molecular Biology and Evolution 31(2):410-418.
  • David Alvarez-Ponce, Philippe Lopez, Eric Bapteste, James McInerney (2013): Gene similarity networks provide tools for understanding eukaryote origins and evolution. Proceedings of the National Academy of Sciences USA 110(17):E1594-E1603.
  • David Alvarez-Ponce, Montserrat Aguadé, Julio Rozas (2013): Comment on "The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway". Evolutionary Bioinformatics 9:229-234.
  • David Alvarez-Ponce, Mario A. Fares (2012): Evolutionary rate and duplicability in the Arabidopsis thaliana protein-protein interaction network. Genome Biology and Evolution 4:1263-1274.
  • David Alvarez-Ponce (2012): The relationship between the hierarchical position of proteins in the human signal transduction network and their rate of evolution. BMC Evolutionary Biology 12:192.
  • Aoife Doherty*, David Alvarez-Ponce*, James McInerney (*Co-first authors) (2012): Increased genome sampling reveals a dynamic relationship between gene duplicability and the structure of the primate protein-protein interaction network. Molecular Biology and Evolution 29:3563-3573.
  • Pierre Luisi, David Alvarez-Ponce, Giovanni Marco Dall'Olio, Martin Sikora, Jaume Bertranpetit, Hafid Laayouni (2012): Network-level and population genetics analysis of the insulin/TOR signal transduction pathway across human populations. Molecular Biology and Evolution 29:1379-1392.
  • David Alvarez-Ponce*, Sara Guirao-Rico*, Dorcas Orengo*, Carmen Segarra, Julio Rozas, Montserrat Aguadé (*Co-first authors) (2012): Molecular population genetics of the insulin/TOR signal transduction pathway: A network-level analysis in Drosophila melanogaster. Molecular Biology and Evolution 29:123-132.
  • David Alvarez-Ponce, James McInerney (2011): The human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differences. Genome Biology and Evolution 3:782-790.
  • David Alvarez-Ponce, Montserrat Aguadé, Julio Rozas (2011): Comparative genomics of the vertebrate insulin/TOR signal transduction pathway genes: A network-level analysis of selective pressures along the pathway. Genome Biology and Evolution 3:87-101.
  • Kirkness et al. (2010): Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle. Proceedings of the National Academy of Sciences USA 107(27): 12168-73.
  • David Alvarez-Ponce, Montserrat Aguadé, Julio Rozas (2009): Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes. Genome Research 19(2): 234-42.

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