Evolution of paralogous families

4/18/07, noon, 425 HMMB. See LabMeeting

This is a follow-up to the GeneSpeciesTreeReconciliationLabMeeting.

• Roderic Page
  • Cotton JA, Page RD.  Rates and patterns of gene duplication and loss in the human genome.  Proc Biol Sci. 2005 Feb 7;272(1560):277-83.
  • Cotton JA, Page RD.  The shape of human gene family phylogenies.  BMC Evol Biol. 2006 Aug 29;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 GP, Wolf YI, Rzhetsky AY, Berezovskaya FS, Koonin EV.  Birth and death of protein domains: a simple model of evolution explains power law behavior.  BMC Evol Biol. 2002 Oct 14;2:18.
  • Unrealistic time to formation of largest families via simple BDIMs; advocacy of nonlinear BDIMs:
    • Karev GP, Wolf YI, Koonin EV.  Simple stochastic birth and death models of genome evolution: was there enough time for us to evolve?  Bioinformatics. 2003 Oct 12;19(15):1889-900.
  • Continuous approximations to BDIMs:
    • Karev GP, Berezovskaya FS, Koonin EV.  Modeling genome evolution with a diffusion approximation of a birth-and-death process.  Bioinformatics. 2005 Nov 1;21 Suppl 3:iii12-9.
  • Exhaustive BDIM studies, simulations, theory, limit results, etc.
    • Karev GP, Wolf YI, Berezovskaya FS, Koonin EV.  Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models.  BMC Evol Biol. 2004 Sep 9;4:32.

-- IanHolmes - 21 Mar 2007