Gene Family Evolution Lab Meeting

Evolution of paralogous families

4/18/07, noon, 425 HMMB. See Lab Meeting

This is a follow-up to the Gene Species Tree Reconciliation Lab Meeting.

• Roderic Page
  • Cotton & Page: Rates and patterns of gene duplication and loss in the human genome. Proc. Biol. Sci. 2005;272:277-83.
  • Cotton & Page: The shape of human gene family phylogenies. BMC Evol. Biol. 2006;6:66. (article in PDF on BMC)
• GP Karev, EV Koonin - Birth/Death models and Power Laws to model gene family evolution
  • Simple, linear Birth-Death-Innovation Models (BDIM):
    • Karev et al.: Birth and death of protein domains: a simple model of evolution explains power law behavior. BMC Evol. Biol. 2002;2:18.
  • Unrealistic time to formation of largest families via simple BDIMs; advocacy of nonlinear BDIMs:
    • Karev et al.: Simple stochastic birth and death models of genome evolution: was there enough time for us to evolve?. Bioinformatics 2003;19:1889-900.
  • Continuous approximations to BDIMs:
    • Karev et al.: Modeling genome evolution with a diffusion approximation of a birth-and-death process. Bioinformatics 2005;21 Suppl 3:iii12-9.
  • Exhaustive BDIM studies, simulations, theory, limit results, etc.
    • Karev et al.: Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models. BMC Evol. Biol. 2004;4:32.

-- Ian Holmes - 21 Mar 2007