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 crassaNature, 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 cerevisiaeGenome 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:

Additional materials are forthcoming.