Edward Louis Braun   Assistant Professor Department of Zoology University of Florida ebraun68 -AT- ufl -dot- edu Telephone: (352) 846-1124 Office: 514 Carr Hall Ph.D. (Biology), University of New Mexico, 1997 Research Interests: Evolutionary Genomics and Bioinformatics

General Research Interests:

• Patterns of genome change, especially changes involving the loss of genes or protein domains.
• The evolution of transcriptional regulation, with a special focus on the transcription factors.
• The theory and practice of phylogenetic estimation, including marker development for phylogenetics.
• Computational approaches for large-scale comparisons of genomic data.

Current Projects:

• Resolving of deep nodes in avian phylogeny as a part of the Early Bird collaboration.
• Patterns of genome evolution in reptiles.
• Comparative genomics, especially studies focused on the loss of genes.
• Examining ancient evolutionary divergences using genome-scale approaches.
• Genomics in the lower fungi, especially chytrids.
  

Background:

• Ph.D. reseach in the control of growth and proliferation for the yeast Saccharomyces cerevisiae. This work was done with Dr. Margaret Werner-Washburne in the Department of Biology at the University of New Mexico.
• Post-doctoral research in fungal genomics, working with the Neurospora genome projectat the University of New Mexico. This work was done when I worked at the National Center for Genome Resources and the University of New Mexico with Dr. Donald Natvig.
• Post-doctoral research in plant transcription factors. This work was done in the Department of Plant Biology (now the Department of Plant Cellular and Molecular Biology/Molecular and Cellular Biochemistry) at the Ohio State University, working with Dr. Erich Grotewold. I was supported by a fellowship from the USDA while working at the Ohio State University.

Courses:

• Fall 2001: Genetics (PCB3063)
• Spring 2002: Seminar in Phylogenetic Comparative Methods (Graduate course), with Dr. Rebecca T. Kimball
• Fall 2002: Introductory Biology (BSC2011), with Dr. Rebecca T. Kimball
• Spring 2003: Genetics (PCB3063)
• Fall 2003: Models and Simulations in Molecular Evolution (Graduate course)
• Spring 2004: Genetics (PCB3063)
• Spring 2004: Journal Club in Phylogenomics (ZOO 6927)
• Fall 2004: Introductory Biology (BSC2011), with Dr. Rebecca T. Kimball
• Spring 2005: Genetics (PCB3063)
• Fall 2005: Topics in Phylogenetics - Hadamard conjugation, Vertebrate gene duplication, and other topics (Graduate course)
• Spring and Fall 2006: Genetics (PCB3063)

Graduate Students:

• Jena Chojnowski (Fall 2003 – present) – Jena’s primary interests are development and evolution. Jena has been part of the Early Bird project and has worked on examining the isochore structure of reptiles. For her thesis project, Jena is using genomic approaches to examine development in the Red-eared Slider (Trachemys scripta).
• Sarah Haas (Fall 2004 – Summer 2007) – Sarah joined the lab after recieving her degree from Southwest Texas State University and she worked on projects with implications for conservation biology.
  
• Deena Westbrook (Fall 2004 – Fall 2007) – Deena graduated with a MST (Masters of science teaching) degree. While attending UF she acted as my Genetics TA for two semesters and taught at the middle school level.
• Jordan Smith (Fall 2007 – present) – Jordan has been working on deep avian phylogenetics, both contributing to the Early Bird project and moving in some novel directions.

Publications:

1. Braun, EL & N Phillips. 2008. Phylogenomics and secondary plastids: A look back and a look ahead. Journal of Phycology, 44:2-6.
        [abstract] and additional information.
2. Chojnowski, JL & EL Braun. 2008. Turtle isochore structure is intermediate between amphibians and other amniotes. Integrative and Comparative Biology, in press; Advance Access published on June 24, 2008. doi:10.1093/icb/icn062.
        [abstract] and additional information.
3. Chojnowski, JL, RT Kimball & EL Braun. 2008. Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes. Gene, 410:89-96.
        [abstract] and additional information.
4. Georgelis N, EL Braun & LC Hannah. 2008. Duplication and functional divergence of ADP-glucose pyrophosphorylase genes in plants. BMC Evolutionary Biology, 8:232.
        [abstract] and additional information or [full text pdf].
5. Hackett, SJ, RT Kimball, S Reddy, RCK Bowie, EL Braun, MJ Braun, JL Chojnowski, WA Cox, K-L Han, J Harshman, CJ Huddleston, BD Marks, KJ Miglia, WS Moore, FH Sheldon, DW Steadman, CC Witt & T Yuri. 2008. A phylogenomic study of birds reveals their evolutionary history. Science, 320:1763-1768.
        [abstract] and additional information.
6. Harshman, J, EL Braun, MJ Braun, CJ Huddleston, S Reddy, RCK Bowie, JL Chojnowski, K-L Han, SJ Hackett, RT Kimball, BD Marks, KJ Miglia, WS Moore, FH Sheldon, DW Steadman, SJ Steppan, CC Witt & T Yuri. 2008. Phylogenomic evidence for multiple losses of flight in ratite birds. Proceedings of the National Academy of Sciences USA, 105:13462-13467.
        [abstract] and additional information.
7. Kimball, RT & EL Braun. 2008. A multigene phylogeny of Galliformes supports a single origin of erectile ability in non-feathered facial traits. Journal of Avian Biology, 39:438-445.
        [abstract] and additional information.
8. Phillips, N, S Calhoun, A Moustafa, D Bhattacharya & EL Braun. 2008. Genomic insights into evolutionary relationships among heterokont lineages emphasizing the Phaephyceae. Journal of Phycology, 44:15-18.
        [abstract] and additional information.
9. Yuri, T, RT Kimball, EL Braun & MJ Braun. 2008. Duplication and accelerated evolution of growth hormone gene in passerine birds. Molecular Biology and Evolution, 25:352-361.
        [abstract] and additional information.
10. Chojnowski, JL, J Franklin, Y Katsu, T Iguchi, LJ Guillette Jr, RT Kimball & EL Braun. 2007. Patterns of vertebrate isochore evolution revealed by comparison of expressed mammalian, avian, and crocodilian genes. Journal of Molecular Evolution, 65: 259-266.
         [abstract] and additional information.
11. Cox, WA, EL Braun & RT Kimball. 2007. Phylogenetic position of the New World Quail (Odontophoridae): Eight nuclear loci and three mitochondrial regions contradict morphology and the Sibley-Ahlquist Tapestry. The Auk, 124: 71-84.
         [abstract] and additional information.
12. Georgelis, N, EL Braun, JR Shaw & LC Hannah. 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.
         [abstract] and additional information.
13. Gibb, GC, O Kardailsky, RT Kimball, EL Braun & D Penny. 2007. Mitochondrial genomes and avian phylogeny: Complex characters and resolvability without explosive radiations. Molecular Biology and Evolution, 24: 269-280.
         [abstract] and additional information.
14. Sassi, SO, EL Braun & SA Benner SA. 2007. The evolution of seminal ribonuclease: Pseudogene reactivation or multiple gene inactivation events? Molecular Biology and Evolution, 24: 1012-1024.
         [abstract] and additional information.
15. Crowe, TM, P Bloomer, E Randi, V Lucchini, RT Kimball, EL Braun & JG Groth. 2006. Supra-generic cladistics of landfowl (Order Galliformes). Acta Zoologica Sinica, 52(Supplement): 358-361.
         [abstract] and additional information or [full text pdf].
16. Kimball, RT, EL Braun, JD Ligon, E Randi & V Lucchini. 2006. Using molecular phylogenetics to interpret evolutionary changes in morphology and behavior in the Phasianidae. Acta Zoologica Sinica, 52(Supplement): 362-365.
         [abstract] and additional information or [full text pdf].
17. Braun, EL, DO Natvig, M Werner-Washburne & MA Nelson. 2004. Genomics in Neurospora crassa: From One-Gene-One-Enzyme to 10,000 Genes. Applied Mycology and Biotechnology, Volume 4. Fungal Genomics (DK Arora & GG Khachatourians, editors), pp. 295-313.
         [abstract] and additional information or [full text pdf].
18. Katsu, Y, DS Bermudez, EL Braun, C Helbing, S Miyagawa, MP Gunderson, S Kohno, TA Bryan, LJ Guillette Jr, & T Iguchi. 2004. Molecular cloning of the estrogen and progesterone receptors of the American alligator. General and Comparative Endocrinology, 136: 122-133.
         [abstract] and additional information.
19. Braun, EL. 2003. Innovation from reduction: Gene loss, domain loss and sequence divergence in genome evolution. Applied Bioinformatics, 2:13-34.
         [abstract] and additional information or [full text pdf].
20. Dias, AP, EL Braun, MD McMullen & E Grotewold. 2003. Recently duplicated maize R2R3 Myb genes provide evidence for distinct mechanisms of evolutionary divergence after duplication. Plant Physiology, 131: 610-620.
         [abstract] and additional information.
21. Galagan, JE, et al. (76 co-authors). 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature, 422: 859-868.
         [abstract] and additional information.
22. Braun, EL & RT Kimball. 2002. Examining basal avian divergences with mitochondrial sequences: Model complexity, taxon sampling and sequence length. Systematic Biology, 51:614-625.
         [description] of the paper and additional information.
23. Armstrong, MH, EL Braun & RT Kimball. 2001. Phylogenetic utility of avian ovomucoid intron G: A comparison of nuclear and mitochondrial phylogenies in the Galliformes. The Auk, 118:799-804.
         [abstract] and additional information or [full text pdf].
24. Bean, LE, WH Dvorachek Jr, EL Braun, A Errett, GS Saenz, M Giles, M Werner-Washburne, MA Nelson & DO Natvig. 2001. Analysis of the pdx-1 (snz-1/sno-1) region of the Neurospora crassa genome: Correlation of pyridoxine-requiring phenotypes with mutations in two structural genes. Genetics, 157:1067-1075.
         [abstract] and additional information.
25. Braun, EL, AP Dias, TJ Matulnik & E Grotewold. 2001. Transcription factors and metabolic engineering: Novel applications for ancient tools. Recent Advances in Phytochemistry, 35:79-109.
         [description] of the paper and additional information or [full text pdf].
26. Braun, EL & E Grotewold. 2001. Fungal Zuotin proteins evolved from MIDA1-like factors by lineage-specific loss of MYB domains. Molecular Biology and Evolution, 18:1401-1412.
         [abstract] and additional information.
27. Braun, EL & RT Kimball. 2001. Polytomies, the power of phylogenetic inferences, and the stochastic nature of molecular evolution: A comment on Walsh et al. (1999). Evolution, 55:1261-1263.
         [description] of the paper and additional information.
28. Dong X, EL Braun & E Grotewold. 2001. Functional conservation of plant secondary metabolic enzymes revealed by complementation of Arabidopsis flavonoid mutants with maize genes. Plant Physiology, 127:46-57.
         [abstract] and additional information.
29. Kimball RT, EL Braun, JD Ligon, V Lucchini & E Randi. 2001. A molecular phylogeny of the peacock-pheasants (Galliformes: Polyplectron spp.) indicates loss and reduction of ornamental traits and display behaviours. Biological Journal of the Linnean Society, 73:187-198.
         [abstract] and additional information.
30. Randi, E, V Lucchini, A Hennache, RT Kimball, EL Braun & JD Ligon. 2001. Evolution of the mitochondrial DNA control region and cytochrome b genes, and the inference of phylogenetic relationships in the avian genus Lophura (Galliformes). Molecular Phylogenetics and Evolution, 19:187-201.
         [abstract] and additional information.
31. Braun, EL, AL Halpern, MA Nelson & DO Natvig. 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 Research, 10:416-430.
         [abstract] and additional information or [full text pdf].
32. Randi, E, V Lucchini, T Armijo-Prewitt, RT Kimball, EL Braun & JD Ligon. 2000. Mitochondrial DNA phylogeny and speciation of the Tragopans. The Auk, 117:1003-1015.
         [abstract] and additional information or [full text pdf].
33. Bieszke, JA, EL Braun, LE Bean, S Kang, DO Natvig & KA Borkovich. 1999. The nop-1 gene of Neurospora crassa encodes a seven transmembrane helix, retinal-binding protein homologous to archaeal rhodopsins. Proceedings of the National Academy of Sciences USA, 96:8034-8039.
         [abstract] from NCBI and [full text] from PNAS.
34. Braun, EL & E Grotewold. 1999. Newly discovered plant c-myb-like genes rewrite the evolution of the plant myb gene family. Plant Physiology, 121:21-24.
         [full text] from Plant Physiology.
35. Kimball, RT, EL Braun, PW Zwartjes, TM Crowe & JD Ligon. 1999. A molecular phylogeny of the pheasants and partridges suggests that these lineages are not monophyletic. Molecular Phylogenetics and Evolution, 11:38-54.
         [abstract] from NCBI and [full text pdf] from the Science Direct web site.
36. Rabinowicz, PD, EL Braun, AD Wolfe, B Bowen & E Grotewold. 1999. Maize R2R3 Myb genes: Sequence analysis reveals amplification in the higher plants. Genetics, 153:427-444.
         [abstract] from NCBI and [full text] from Genetics.
37. Braun, EL, S Kang, MA Nelson & DO Natvig. 1998. Identification of the first fungal annexin: Analysis of annexin gene duplications and implications for eukaryotic evolution. Journal of Molecular Evolution, 47: 531-543.
         [abstract] and [full text pdf] from the Journal of Molecular Evolution.
38. Kimball, RT, EL Braun & JD Ligon. 1997. Resolution of the phylogenetic position of the Congo Peafowl, Afropavo congensis: A biogeographic and evolutionary enigma. Proceedings of the Royal Society of London, series B, 264: 1517-1523.
         [abstract] from NCBI or [full text pdf].
39. Nelson, MA, S Kang, EL Braun, ME Crawford, PL Dolan, PM Leonard, J Mitchell, AM Armijo, L Bean, E Blueyes, T Cushing, A Errett, M Fleharty, M Gorman, K Judson, R Miller, J Ortega, I Pavlova, J Perea, S Todisco, R Trujillo, J Valentine, A Wells, M Werner-Washburne, S Yazzie & DO Natvig. 1997. Expressed sequences from conidial, mycelial and sexual stages of Neurospora crassa. Fungal Genetics and Biology, 21:348-363.
         [abstract] from NCBI or [full text pdf].
40. Braun, EL, EK Fuge, PA Padilla & M Werner-Washburne. 1996. A stationary-phase gene in Saccharomyces cerevisiae is a member of a novel, highly conserved gene family. Journal of Bacteriology, 178:6865-6872.
         [abstract] from NCBI or [full text pdf].
41. Werner-Washburne, M, EL Braun, ME Crawford & VM Peck. 1996. Stationary phase in Saccharomyces cerevisiae. Molecular Microbiology, 19:1159-1166.
42. Fuge, EK, EL Braun & M Werner-Washburne. 1994. Protein synthesis in long-term stationary phase cultures of Saccharomyces cerevisiae. Journal of Bacteriology, 176:5802-5813.
         [abstract] from NCBI or [full text pdf] (also see [PubMed central] for high resolution scans of the 2D PAGE images).
43. Werner-Washburne, M, E Braun, GC Johnston & RA Singer. 1993. Stationary phase in the yeast Saccharomyces cerevisiae. Microbiological Reviews, 57:383-401.
         [abstract] from PubMed centrol or [full text pdf].
44. Werner-Washburne, M, D Brown & E Braun. 1991. Bcy1, the regulatory subunit of cAMP-dependent protein kinase in yeast, is differentially modified in response to the physiological status of the cell. Journal of Biological Chemistry, 266:19704-19709.
         [abstract] from NCBI or [full text pdf].

Links to Seminars at the University of Florida:

• Department of Zoology Seminar Series.
• Seminars and Events Sponsored by the University of Florida Genetics Institute.
• Schedule of Botany Colloquia.
• College of Medicine Research Seminar Series.
• Plant Molecular and Cellular Biology (PMCB) Program Workshops and Seminars.