Publications

Google Scholar Page

Full list of peer reviewed publications:

Undergraduate co-authors are indicated with an asterisk.

1. Shaffer, HB, P Minx, DE Warren, AM Shedlock, RC Thomson, N Valenzuela, J Abramyan, CT Amemiya, D Badenhorst, KK Biggar, GM Borchert, CW Botka, RM Bowden, EL Braun, AM Bronikowski, BG Bruneau, LT Buck, B Capel, TA Castoe, M Czerwinski, KD Delehaunty, SV Edwards, CC Fronick, MK Fujita, L Fulton, TA Graves, RE Green, W Haerty, R Hariharan, O Hernandez, LW Hillier, AK Holloway, D Janes, FJ Janzen, C Kandoth, L Kong, APJ de Koning, Y Li, R Literman, SE McGaugh, L Mork, M O’Laughlin, RT Paitz, DD Pollock, CP Ponting, S Radhakrishnan, BJ Raney, JM Richman, J St John, T Schwartz, A Sethuraman, PQ Spinks, KB Storey, N Thane, T Vinar, LM Zimmerman, WC Warren, ER Mardis & RK Wilson. 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology, in press.

2. Smith, JV, EL Braun & RT Kimball. 2013. Ratite non-monophyly: Independent evidence from 40 novel loci. Systematic Biology, 62:35-49.

3. Yuri, T, RT Kimball, J Harshman, RCK Bowie, MJ Braun, JL Chojnowski, SJ Hackett, K-L Han, SJ Hackett, CJ Huddleston, WS Moore, S Reddy, FH Sheldon, DW Steadman, CC Witt & EL Braun. 2013. Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. Biology, 2:419-444.

4. Castoe, TA, EL Braun, AM Bronikowski, CL Cox, AR Davis Rabosky, APJ de Koning, J Dobry, MK Fujita, MW Giorgianni, A Hargreaves, CV Henkel, SP Mackessy, D O’Meally, DR Rokyta, SM Secor, JW Streicher, KP Wray, KD Yokoyama & DD Pollock. 2012. Report from the first Snake Genomics and Integrative Biology meeting. Standards in Genomic Sciences, 7:1.

5. Chojnowski, JL & EL Braun. 2012. An unbiased approach to identify genes involved in development in a turtle with temperature-dependent sex determination. BMC Genomics,

6. Ponciano, JM, JG Burleigh, EL Braun & ML Taper. 2012. Assessing parameter identifiability in phylogenetic models using Data Cloning. Systematic Biology61:955-972.

7. St John, JA, EL Braun, SR Isberg, LB Miles, AY Chong, J Gongora, P Dalzell, C Moran, B Bed’hom, A Abzhanov, SC Burgess, AM Cooksey, TA Castoe, NG Crawford, LD Densmore, JC Drew, SV Edwards, BC Faircloth, MK Fujita, MJ Greenwold, FG Hoffmann, JM Howard, T Iguchi, DE Janes, SY Khan, S Kohno, APJ de Koning, SL Lance, FM McCarthy, JE McCormack, ME Merchant, DG Peterson, DD Pollock, N Pourmand, BJ Raney, KA Roessler, JR Sanford, RH Sawyer, CJ Schmidt, EW Triplett, TD Tuberville, M Venegas-Anaya, JT Howard, ED Jarvis, LJ Guillette Jr, TC Glenn, RE Green & DA Ray. 2012. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology, 13:415.

8. Wang, N, EL Braun & RT Kimball. 2012. Testing hypotheses about the sister group of the Passeriformes using an independent 30 locus dataset. Molecular Biology and Evolution, 29:737-750.

9. Braun, EL, RT Kimball, K-L Han, NR Iuhasz*, AJ Bonilla*, JL Chojnowski, JV Smith*, RCK Bowie, MJ Braun, JL Chojnowski, SJ Hackett, J Harshman, CJ Huddleston, BD Marks, KJ Miglia, WS Moore, S Reddy, FH Sheldon, CC Witt & T Yuri. 2011. Homoplastic microinversions and the Avian Tree of Life. BMC Evolutionary Biology, 11:141.

10. Feller, A, K Machemer, EL Braun & E Grotewold. 2011. Evolutionary and comparative genomics of MYB and bHLH plant transcription factors. The Plant Journal, 66:94-116. [abstract]

11. Han, K-L, EL Braun, RT Kimball, S Reddy, RCK Bowie, MJ Braun, JL Chojnowski, SJ Hackett, J Harshman, CJ Huddleston, BD Marks, KJ Miglia, WS Moore, FH Sheldon, DW Steadman, CC Witt & T Yuri. 2011. Are transposable element insertions homoplasy free? An examination using the Avian Tree of Life. Systematic Biology, 60:375-386.

12. Kimball, RT, CM St Mary & EL Braun. 2011. A macroevolutionary perspective on multiple sexual traits in the Phasianidae (Galliformes). International Journal of Evolutionary Biology, Article ID 423938, 16 pages. [full text html] [full text pdf]

13. Lim, CH, T Hamazaki, EL Braun, J Wade & N Terada. 2011. Evolutionary genomics indicates a specific function of Slc25a31 in mammalian and anole lizard germ cells. PLoS ONE, 6:e23122.

14. Bonilla, AJ*, EL Braun & RT Kimball. 2010. Comparative molecular evolution and phylogenetic utility of 3′-UTRs and introns in Galliformes. Molecular Phylogenetics and Evolution, 50:654-660. [abstract]

15. Zhu, J, EL Braun, S Kohno, M Antenos, EY Xu, RW Cook, SJ Lin, BC Moore, LJ Guillette Jr, TS Jardetzky & TK Woodruff. 2010. Phylogenomic analyses reveal the evolutionary origin of the inhibin α-subunit, a unique TGFβ superfamily antagonist. PLoS ONE, 5:e9457. [abstract] [full text].

16. Katsu, Y, EL Braun, LJ Guillette Jr & T Iguchi. 2009. From reptilian phylogenomics to reptilian genomes: Analyses of c-Jun and DJ-1 proto-oncogenes. Cytogenetic and Genome Research, 127:79-93. [abstract]

17. Kimball, RT, EL Braun, FK Barker, RCK Bowie, MJ Braun, JL Chojnowski, SJ Hackett, K-L Han, J Harshman, V Heimer-Torres*, W Holznagel, CJ Huddleston, BD Marks, KJ Miglia, WS Moore, S Reddy, FH Sheldon, JV Smith*, CC Witt & T Yuri. 2009. A well-tested set of primers to amplify regions spread across the avian genome. Molecular Phylogenetics and Evolution, 50:654-660. [full text]

18. Braun, EL & N Phillips. 2008. Phylogenomics and secondary plastids: A look back and a look ahead. Journal of Phycology, 44:2-6. [abstract]

19. Chojnowski, JL & EL Braun. 2008. Turtle isochore structure is intermediate between amphibians and other amniotes. Integrative and Comparative Biology, 48:454-462. [abstract]

20. 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]

21. Georgelis N, EL Braun & LC Hannah. 2008. Duplication and functional divergence of ADP-glucose pyrophosphorylase genes in plants. BMC Evolutionary Biology, 8:232. [abstract] [full text pdf].

22. 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]

23. 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]

24. 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]

25. 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]

26. 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]

27. 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]

28. 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]

29. 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]

30. 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]

31. 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]

32. 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] [full text pdf].

33. 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] [full text pdf].

34. 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] [full text pdf].

35. 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]

36. Braun, EL. 2003. Innovation from reduction: Gene loss, domain loss and sequence divergence in genome evolution. Applied Bioinformatics, 2:13-34. [abstract] [full text pdf].

37. 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]

38. Galagan, JE, et al.  (76 co-authors). 2003. The genome sequence of the filamentous fungus Neurospora crassaNature, 422: 859-868. [abstract]

39. 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]

40. 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] [full text pdf].

41. 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]

42. 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] [full text pdf].

43. 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]

44. 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]

45. 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]

46. 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]

47. 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]

48. 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 cerevisiaeGenome Research, 10:416-430. [abstract] [full text pdf].

49. 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] [full text pdf].

50. 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] [full text]

51. 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]

52. 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] [full text pdf]

53. 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] [full text]

54. 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] [full text pdf]

55. 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] [full text pdf].

56. 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 crassaFungal Genetics and Biology, 21:348-363. [abstract] [full text pdf].

57. 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] [full text pdf].

58. Werner-Washburne, M, EL Braun, ME Crawford & VM Peck. 1996. Stationary phase in Saccharomyces cerevisiaeMolecular Microbiology, 19:1159-1166.

59. Fuge, EK, EL Braun & M Werner-Washburne. 1994. Protein synthesis in long-term stationary phase cultures of Saccharomyces cerevisiaeJournal of Bacteriology, 176:5802-5813. [abstract] [full text pdf] (also see [PubMed central] for high resolution scans of the 2D PAGE images).

60. Werner-Washburne, M, E Braun, GC Johnston & RA Singer. 1993. Stationary phase in the yeast Saccharomyces cerevisiaeMicrobiological Reviews, 57:383-401. [abstract] [full text pdf].

61. 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] [full text pdf].