Research

My research foci include efforts to reconstruct the Tree of Life and understand patterns of genome evolution. A small number of representative publications are listed below and a more complete list is provided on the Publications page. Other recent scholarly work associated with the Braun lab include:

  • The “EARLY BIRD” project:
    • Details of the publications produced by the “Early Bird” project along with links to the data matrices and trees generated by the project.
    • A short description of the “Early Bird” project for the public appears in an American Paleontologist feature on the tree of life.
  • The “GATOR GENOME” project:
    • The UF portion of the Crocodialian Genome Project
    • This project integrates research and genomics education.
  • Also see below for links to my other scholarly work, including data matrices, computer programs, other publications, and web sites related to my work.

Representative Publications

I have highlighted a few publications from various periods in my career that I have selected to illustrate my interests. These publications are divided into three groups and links to the full citation are provided:

  • Phylogenetics and the Tree of Life
  1. Smith et al. 2013. Ratite non-monophyly: Independent evidence from 40 novel loci. Systematic Biology, 62:35-49. [full citation]
  2. Yuri et al. 2013. Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. Biology, 2:419-444. [full citation]
  3. Braun et al. 2011. Homoplastic microinversions and the Avian Tree of Life. BMC Evol Biol, 11:141. [full citation]
  4. Chojnowski et al. 2008. Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes. Gene, 410:89-96. [full citation]
  5. Harshman et al. 2008. Phylogenomic evidence for multiple losses of flight in ratite birds. PNAS, 105:13462-13467. [full citation]
  6. Braun & Kimball. 2002. Examining basal avian divergences with mitochondrial sequences: Model complexity, taxon sampling and sequence length. Syst Biol, 51:614-625. [full citation]
  • Molecular evolution and gene families
  1. Feller et al. 2011. Evolutionary and comparative genomics of MYB and bHLH plant transcription factors. Plant J, 66:94-116. [full citation]
  2. Chojnowski et al. 2007. Patterns of vertebrate isochore evolution revealed by comparison of expressed mammalian, avian, and crocodilian genes. J Mol Evol, 65: 259-266. [full citation]
  3. Georgelis et al. 2007. The two AGPase subunits evolve at different rates in angiosperms, yet they are equally sensitive to activity-altering amino acid changes when expressed in bacteria. Plant Cell, 19: 1458-1472. [full citation]
  4. Braun & Grotewold. 2001. Fungal Zuotin proteins evolved from MIDA1-like factors by lineage-specific loss of MYB domains. Mol Biol Evol, 18:1401-1412.  [full citation]
  • Genomics and Phylogenomics
  1. Shaffer et al. 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology, in press. [full citation]
  2. St John et al. 2012. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology, 13:415. [full citation]
  3. Braun and Phillips. 2008. Phylogenomics and secondary plastids: A look back and a look ahead. J Phycol, 44:2-6. [full citation]
  4. Braun. 2003. Innovation from reduction: Gene loss, domain loss and sequence divergence in genome evolution. Applied Bioinf, 2:13-34.  [full citation] [full text]
  5. Galagan et al. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature, 422: 859-868. [full citation]
  6. Braun et al. 2000. Large scale comparison of fungal sequence information reveals innovation in the filamentous fungus Neurospora crassa and gene loss in the budding yeast Saccharomyces cerevisiae. Genome Res, 10:416-430. [full citation]

See publications for a complete list of peer-reviewed philosophy.

Links and Other Scholarly Works

Other work produced by myself and other members of the Braun lab includes:

  • The web page for the “Early Bird” project to assemble the avian tree of life(supported by the NSF Assembling the Tree of Life program).
  • “Borrowed Chloroplasts: Secondary Endosymbiosis and the Chromalveolates”, a symposium at the 2007 Botany and Plant Biology Joint Congress was organized by Naomi Phillips, Edward Braun & Debashish Bhattacharya.
  • A short paper in the Maize Genetics Cooperation Newsletter (“Diversification of the R2R3 Myb gene family and the segmental allotetraploid origin of the maize genome”) that I co-wrote with Erich Grotewold.
Additional materials are forthcoming.