Publications

Links:

     Braun Google Scholar Page

     Braun ORCID Page

 

Complete list (student and postdoc coauthors indicated using superscripts (U = undergraduate, G = graduate, P = postdoc)

 

  1. Tiley, GPG, A PandeyG, RT Kimball, EL Braun & JG Burleigh. 2020. Whole genome phylogeny of Gallus: introgression and data-type effects. Avian Research, 11: 7. https://doi.org/10.1186/s40657-020-00194-w
  2. Pandey, AG & EL Braun. 2020. Phylogenetic analyses of sites in different protein structural environments result in distinct placements of the metazoan root. Biology, 9: 64. https://doi.org/10.3390/biology9040064
  3. Braun, EL, J Cracraft & P Houde. 2019. Resolving the avian tree of life from top to bottom: The promise and potential boundaries of the phylogenomic era. in Avian Genomics in Ecology and Evolution – From the lab into the wild (RHS Kraus, editor) Springer, Cham, Switzerland. pp. 151-210. https://doi.org/10.1007/978-3-030-16477-5_6.
  4. Houde, P, EL Braun, N Narula, U Minjares & S Mirarab. 2019. Phylogenetic signal of indels and the neoavian radiation. Diversity, 11: 108. https://doi.org/10.3390/d11070108
  5. Kimball, RT, CH Oliveros, N Wang, ND White, FK Barker, DJ Field, DT Ksepka, RT Chesser, RG Moyle, MJ Braun, RT Brumfield, BC Faircloth, BT Smith & EL Braun. 2019. A phylogenomic supertree of birds. Diversity, 11: 109. https://doi.org/10.3390/d11070109
  6. Oliveros, CH, DJ Field, DT Ksepka, FK Barker, A Aleixo, MJ Andersen, P. Alström, BW Benz, EL Braun, MJ Braun, GA Bravo, RT Brumfield, RT Chesser,
S Claramunt, J Cracraft, AM Cuervo, EP Derryberry, TC Glenn, MG Harvey, PA Hosner, L Joseph, RT Kimball, AL Mack, CM Miskelly, AT Peterson, MB Robbins, FH Sheldon, LF Silveira, BT Smith, ND White, RG Moyle & BC Faircloth. 2019. Earth history and the passerine superradiation. Proceedings of the National Academy of Sciences, 116: 7916-7925. https://doi.org/10.1073/pnas.1813206116
  7. Tamashiro, RAU, ND White, MJ Braun, BC Faircloth, EL Braun & RT Kimball. 2019. What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data? Molecular Phylogenetics and Evolution, 130: 132-142. https://doi.org/10.1016/j.ympev.2018.10.008
  8. Braun, EL. 2018. An evolutionary model motivated by physicochemical properties of amino acids reveals variation among proteins. Bioinformatics, 34: i350-i356. https://doi.org/10.1093/bioinformatics/bty261
  9. Chen, DP, EL Braun, M Forthman, RT Kimball & Z Zhang. 2018. A simple strategy for recovering ultraconserved elements, exons, and introns from low coverage shotgun sequencing of museum specimens: placement of the partridge genus Tropicoperdix within the Galliformes. Molecular Phylogenetics and Evolution, 129: 304-314. https://doi.org/10.1016/j.ympev.2018.09.005
  10. Eimanifar, AP, RT Kimball, EL Braun & JD Ellis. 2018. Mitochondrial genome diversity and population structure of two western honey bee subspecies in the Republic of South Africa. Scientific Reports, 8: 1333. https://doi.org/10.1038/s41598-018-19759-3
  11. Liang, B, N Wang, N Li, RT Kimball & EL Braun. 2018. Comparative genomics reveals a burst of homoplasy-free numt insertions, Molecular Biology and Evolution, 35: 2060-2064. https://doi.org/10.1093/molbev/msy112
  12. Tiley, GPG, RT Kimball, EL Braun & JG Burleigh. 2018. Comparison of the Chinese bamboo partridge and red junglefowl genome sequences highlights the importance of demography in genome evolution. BMC Genomics, 19: 336. https://doi.org/10.1186/s12864-018-4711-0
  13. Ascunce, MSP, JC Huguet-TapiaP, A Ortiz-Urquiza, NO Keyhani, EL Braun & EM Goss. 2017. Phylogenomic analysis supports multiple instances of polyphyly in the oomycete peronosporalean lineage. Molecular Phylogenetics and Evolution, 114: 199-211. https://doi.org/10.1016/j.ympev.2017.06.013
  14. Hosner, PAP, JA Tobias, EL Braun & RT Kimball. 2017. How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl. Proceedings of the Royal Society B: Biological Sciences, 284: 20170210. https://doi.org/10.1098/rspb.2017.0210
  15. Feng, GG, JG Burleigh, EL Braun, W Mei & WB Barbazuk. 2017. Evolution of the 3R-MYB gene family in plants. Genome Biology and Evolution, 9: 1013-1029. https://doi.org/10.1093/gbe/evx056
  16. Reddy, S, RT Kimball, A PandeyG, PA HosnerP, MJ Braun, SJ Hackett, K-L Han, J Harshman, CJ Huddleston, S Kingston, BD Marks, KJ Miglia, WS Moore, FH Sheldon, CC Witt, T Yuri & EL Braun. 2017. Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling. Systematic Biology, 66: 857-879. (Altmetric 43; top 5%) https://doi.org/10.1093/sysbio/syx041
  17. Wang, N, RT Kimball, EL Braun, B Liang & Z Zhang. 2017. Ancestral range reconstruction of Galliformes: the effects of topology and taxon sampling. Journal of Biogeography, 44: 122-135. https://doi.org/10.1111/jbi.12782
  18. Wang, N, PA HosnerP, B Liang, EL Braun & RT Kimball. 2017. Historical relationships of three enigmatic phasianid genera (Aves: Galliformes) inferred using phylogenomic and mitogenomic data. Molecular Phylogenetics and Evolution, 109: 217-225. https://doi.org/10.1016/j.ympev.2017.01.006
  19. Corrochano, LM, A Kuo, M Marcet-Houben, S Polaino, A Salamov, JM Villalobos, MI Álvarez, J Avalos, EP Benito, I Benoit, G Burger, LP Camino, D Cánovas, E Cerdá-Olmedo, J-F Cheng, A Domínguez, M Eliáš, AP Eslava, F Glaser, J Grimwood, G Gutiérrez, J Heitman, B Henrissat, EA Iturriaga, BF Lang, JL Lavín, SC Lee, We Li, E Lindquist, S López-García, EM Luque, AT Marcos, J Martin, K McCluskey, HR Medina, A Miralles-Durán, A Miyazaki, E Muñoz-Torres, JA Oguiza, R Ohm, M Olmedo, M Orejas, L Ortiz-Castellanos, AG Pisabarro, J Rodríguez-Romero,J Ruiz-Herrera, R Ruiz-Vázquez, C Sanz, W Schackwitz, J Schmutz, M Shahriari, E Shelest, F Silva-Franco, D Soanes, K Syed, VG Tagua, NJ Talbot, M Thon, RP de Vries, A Wiebenga, JS Yadav, EL Braun, S Baker, V Garre, B Horwitz, S Torres-Martínez, A Idnurm, A Herrera-Estrella, T Gabaldón & IV Grigoriev. Expansion of signal transduction pathways in fungi by whole-genome duplication. Current Biology, 26: 1577-1584. https://doi.org/10.1016/j.cub.2016.04.038
  20. Hosner, PAP, EL Braun & RT Kimball. 2016. Rapid and recent diversification of curassows, guans, and chachalacas (Galliformes: Cracidae) out of Mesoamerica: Phylogeny inferred from mitochondrial, intron, and ultraconserved element sequences. Molecular Phylogenetics and Evolution, 102: 320-330. https://doi.org/10.1016/j.ympev.2016.06.006
  21. Hosner, PAP, BC Faircloth, TC Glenn, EL Braun & RT Kimball. 2016. Avoiding missing data biases in phylogenomic inference: an empirical study in the landfowl (Aves: Galliformes). Molecular Biology and Evolution, 33: 1110-1125. https://doi.org/10.1093/molbev/msv347
  22. Meiklejohn, KAP, BC Faircloth, TC Glenn, RT Kimball & EL Braun. 2016. Analysis of a rapid evolutionary radiation using ultraconserved elements (UCEs): Evidence for a bias in some multi-species coalescent methods. Systematic Biology, 65: 612-627.
  23. Persons, NWU, PA HosnerP, KA MeiklejohnP, EL Braun & RT Kimball. 2016. Sorting out relationships among the grouse and ptarmigan using intron, mitochondrial, and ultra-conserved element sequences. Molecular Phylogenetics and Evolution, 98: 123-132. https://doi.org/10.1016/j.ympev.2016.02.003
  24. Burleigh, JG, RT Kimball & EL Braun. 2015. Building the avian tree of life using a large-scale, sparse supermatrix. Molecular Phylogenetics and Evolution, 84: 53-63. https://doi.org/10.1016/j.ympev.2014.12.003
  25. Cracraft, J, P Houde, SYW Ho, DP Mindell, J Fjeldså, B Lindow, SV Edwards, C Rahbek, S Mirarab, T Warnow, MTP Gilbert, G Zhang, EL Braun & ED Jarvis. 2015. Response to comment on “Whole-genome analyses resolve early branches in the Tree of Life of modern birds” Science, 349: 1460. https://doi.org/10.1126/science.aab1578
  26. Hosner, PAP, EL Braun & RT Kimball. 2015. Tertiary land bridges and global cooling shaped the colonization history and diversification of New World quail (Aves: Galliformes: Odontophoridae). Journal of Biogeography, 42: 1883-1895. https://doi.org/10.1111/jbi.12555
  27. Jarvis, ED, S Mirarab, AJ Aberer, Bo Li, P Houde, C Li, SYW Ho, BC Faircloth, B Nabholz, JT Howard, A Suh, CC Weber, RR da Fonseca, A Alfaro-Núñez, N Narula, L Liu, D Burt, H Ellegren, SV Edwards, A Stamatakis, DP Mindell, J Cracraft, EL Braun, T Warnow, Wang J, MTP Gilbert, G Zhang & The Avian Phylogenomics Consortium. 2015. Phylogenomic analyses data of the Avian Phylogenomics Project. GigaScience, 4: 4. https://doi.org/10.1186/s13742-014-0038-1
  28. Pope, WH, CA Bowman, DA Russell, D Jacobs-Sera, DJ Asai, SG Cresawn, WR Jacobs, RW Hendrix, JG Lawrence, GF Hatfull, Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science, Phage Hunters Integrating Research and Education & Mycobacterial Genetics Course. 2015. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. Elife, 4: e06416. https://doi.org/10.7554/eLife.06416 (Braun contributed to this paper as an instructor in the UF SEA “phage hunters” course)
  29. Suh, A, G Churakov, MP Ramakodi, RN Platt II, J Jurka, KK Kojima, J Caballero, A Smit, FG Hoffmann, J Brosius, EL Braun, RE Green, H Ellegren, DA Ray & J Schmitz. 2015. Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes. Genome Biology and Evolution, 7: 205-217. https://doi.org/10.1093/gbe/evu256
  30. Green, RE, EL Braun, J Armstrong, D Earl, N Nguyen, MW Vandewege, JA St John, S Capella-Gutiérrez, TA Castoe, C Kern, MK Fujita, JC Opazo, J Jurka, KK Kojima, J Caballero, RM Hubley, AAF Smit, RN Platt II, CA Lavoie, M Ramakodi, JW Finger, A Suh, SR Isberg, L Miles, AY Chong, W Jaratlerdsiri, J Gongora, C Moran, A Iriarte, BC Faircloth, J McCormack, SC Burgess, SV Edwards, E Lyons, C Williams, M Breen, CR Gresham, DG Peterson, J Schmitz, DD Pollock, D Haussler, EW Triplett, G Zhang, N Irie, ED Jarvis, CA Brochu, C Schmidt, F McCarthy, FG Hoffmann, TC Glenn, T Gabaldón, B Paten & DA Ray. 2014. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science, 346: 1254449. http://doi.org/10.1126/science.1254449
  31. Jarvis, ED, S Mirarab, AJ Aberer, B Li, P Houde, C Li, SYW Ho, BC Faircloth, B Nabholz, JT Howard, A Suh, CC Weber, RR da Fonseca, J Li, F Zhang, H Li, L Zhou, N Narula, L Liu, G Ganapathy, B Boussau, Md S Bayzid, V Zavidovych, S Subramanian, T Gabaldón, S Capella-Gutiérrez, J Huerta-Cepas, B Rekepalli, K Munch, M Schierup, B Lindow, WC Warren, D Ray, RE Green, M Bruford, X Zhan, A Dixon, S Li, N Li, Y Huang, EP Derryberry, MF Bertelsen, F Sheldon, RT Brumfield, C Mello, PV Lovell, M Wirthlin, JA Samaniego, AMV Velazquez, A Alfaro-Núñez, PF Campos, T Sicheritz-Ponten, A Pas, T Bailey, P Scofield, M Bunce, D Lambert, Q Zhou, P Perelman, AC Driskell, G Ruby, B Shapiro, Z Xiong, Y Zeng, S Liu, Z Li, B Liu, K Wu, J Xiao, X Yinqi, Q Zheng, Y Zhang, H Yang, J Wang, L Smeds, FE Rheindt, M Braun, J Fjeldså, L Orlando, K Barker, KA Jønsson, W Johnson, K-P Koepfli, S O’Brien, D Haussler, OA Ryder, C Rahbek, E Willerslev, GR Graves, TC Glenn, J McCormack, D Burt, H Ellegren, P Alström, SV Edwards, A Stamatakis, DP Mindell, J Cracraft, EL Braun, T Warnow, Wang J, MTP Gilbert & G Zhang. 2014. Whole genome analyses resolve the early branches in the Tree of Life of modern birds. Science, 346: 1320-1331. https://doi.org/10.1126/science.1253451 (the link to the National Public Radio interview of ED Jarvis and myself by Geoff Brumfiel is permanently available at http://www.npr.org/blogs/health/2014/12/11/370087804/birds-of-a-feather-arent-necessarily-related)
  32. Kimball, RT & EL Braun. 2014. Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix. PeerJ, 2: e361. https://doi.org/10.7717/peerj.361
  33. Meiklejohn, KAP, MJ Danielson, BC Faircloth, TC Glenn, EL Braun & RT Kimball. 2014. Incongruence among different mitochondrial regions: A case study using complete mitogenomes. Molecular Phylogenetics and Evolution, 78:314-323. https://doi.org/10.1016/j.ympev.2014.06.003
  34. Suh, A, CC Weber, C Kehlmaier, EL Braun, RE Green, U Fritz, DA Ray & H Ellegren. 2014. Early Mesozoic coexistence of amniotes and Hepadnaviridae. PLoS Genetics, 10: e1004559. https://doi.org/10.1371/journal.pgen.1004559
  35. Sun, K, KA MeiklejohnP, BC Faircloth, TC Glenn, EL Braun & RT Kimball. 2014. The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach. Proceedings of the Royal Society B: Biological Sciences, 281:20140823. https://doi.org/10.1098/rspb.2014.0823
  36. Zhang G, C Li, Q Li, B Li, DM Larkin, C Lee, JF Storz, A Antunes, RW Meredith, A Ödeen, J Cui, Q Zhou, L Xu, H Pan, Z Wang, L Jin, P Zhang, H Hu, W Yang, J Hu, J Xiao, Z Yang, Y Liu, Q Xie, J Lian, P Wen, F Zhang, H Li, Y Zeng, Z Xiong, S Liu, L Zhou, Z Huang, N An, J Wang, Q Zheng, Y Xiong, G Wang, B Wang, J Wang, Y Fang, R da Fonseca, A Alfaro-Núñez, M Schubert, L Orlando, T Mourier, J Howard, G Ganapathy, J Smith, M Farré, J Narayan, G Slavov, MN Romanov, R Borges, JP Machado, I Khan, MS Springer, J Gatesy, FG Hoffmann, JC Opazo, O Håstad, MJ Greenwold, RH Sawyer, H Kim, K-W Kim, N Li, Y Huang, MW Bruford, X Zhan, A Dixon, M Bertelsen, E Derryberry, W Warren, S Li, DA Ray, RE Green, SJ O’Brien, D Griffin, WE Johnson, D Haussler, OA Ryder, E Willerslev, G Graves, P Alström, J Fjeldså, D Mindell, SV Edwards, EL Braun, C Rahbek, DW Burt, P Houde, Y Zhang, H Yang, J Wang, Avian Genome Consortium, ED Jarvis, MTP Gilbert & Wang J. 2014. Comparative genomics across modern bird species reveal insights into pan-avian genome evolution and trait biodiversity. Science, 346: 1311-1320. https://doi.org/10.1126/science.1251385
  37. Kimball, RT, N WangG, V Heimer-McGinnU, C FergusonU, EL Braun. 2013. Identifying localized biases in large datasets: A case study using the Avian Tree of Life. Molecular Phylogenetics and Evolution, 69: 1021-1032. https://doi.org/10.1016/j.ympev.2013.05.029
  38. Patel, SG, RT Kimball & EL Braun. 2013. Error in phylogenetic estimation for bushes in the Tree of Life. Journal of Phylogenetics & Evolutionary Biology, 1: 110. https://doi.org/10.4172/2329-9002.1000110
  39. 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: the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology, 14: R28. https://doi.org/10.1186/gb-2013-14-3-r28
  40. Smith, JVU,G, EL Braun & RT Kimball. 2013. Ratite non-monophyly: Independent evidence from 40 novel loci. Systematic Biology, 62: 35- https://doi.org/10.1093/sysbio/sys067
  41. Wang, NG, RT Kimball, EL Braun, B Liang & Z Zhang. 2013. Assessing phylogenetic relationships among Galliformes: A multigene phylogeny with expanded taxon sampling in Phasianidae. PLoS ONE, 8:e64312. https://doi.org/10.1371/journal.pone.0064312
  42. Yuri, TP, RT Kimball, J Harshman, RCK Bowie, MJ Braun, JL ChojnowskiG, SJ Hackett, K-L HanG, 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. https://doi.org/10.3390/biology2010419
  43. Chojnowski, JLG & EL Braun. 2012. An unbiased approach to identify genes involved in development in a turtle with temperature-dependent sex determination. BMC Genomics, 13: 308.
  44. Ponciano, JM, JG Burleigh, EL Braun & ML Taper. 2012. Assessing parameter identifiability in phylogenetic models using Data Cloning. Systematic Biology, 61: 955-972. https://doi.org/10.1093/sysbio/sys055
  45. 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. https://doi.org/10.1186/gb-2012-13-1-415
  46. Wang, NG, 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. https://doi.org/10.1093/molbev/msr230
  47. Braun, EL, RT Kimball, K-L HanG, N Iuhasz-VelezU,G, AJ BonillaU, JL ChojnowskiG, JV SmithU,G, RCK Bowie, MJ Braun, SJ Hackett, J Harshman, CJ Huddleston, BD Marks, KJ Miglia, WS Moore, S Reddy, FH Sheldon, CC Witt & T YuriP. Homoplastic microinversions and the avian tree of life. BMC Evolutionary Biology, 11: 141. https://doi.org/10.1186/1471-2148-11-141
  48. Feller, A, K Machemer, EL Braun & E Grotewold. 2011. Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. The Plant Journal, 66: 94-116. https://doi.org/10.1111/j.1365-313X.2010.04459.x
  49. Han,K-LG, 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 YuriP. 2011. Are transposable element insertions homoplasy free? An examination using the avian tree of life. Systematic Biology, 60: 375-386. https://doi.org/10.1093/sysbio/syq100
  50. 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. https://doi.org/10.4061/2011/423938
  51. Lim, CH, T Hamazaki, EL Braun, J Wade & N Terada. Evolutionary genomics indicates a specific function of Slc25a31 in mammalian and anole lizard germ cells. PLoS ONE, 6: e23122. https://doi.org/10.1371/journal.pone.0023122
  52. Bonilla, AJU, EL Braun & RT Kimball. 2010. Comparative molecular evolution and phylogenetic utility of 3’-UTRs and introns in Galliformes. Molecular Phylogenetics and Evolution, 56: 536-542. https://doi.org/10.1016/j.ympev.2010.04.006
  53. Zhu, JG, 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. https://doi.org/10.1371/journal.pone.0009457
  54. Katsu, YP, 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. https://doi.org/10.1159/000297715
  55. Kimball, RT, EL Braun, FK Barker, RCK Bowie, MJ Braun, JL ChojnowskiG, SJ Hackett, K-L HanG, J Harshman, V Heimer-TorresU, W Holznagel, CJ Huddleston, BD Marks, KJ Miglia, WS Moore, S Reddy, FH Sheldon, JV SmithU,G, CC Witt & T YuriP. 2009. A well-tested set of primers to amplify regions spread across the avian genome. Molecular Phylogenetics and Evolution, 50: 654-660. https://doi.org/10.1016/j.ympev.2008.11.018
  56. Braun, EL & N Phillips. 2008. Phylogenomics and secondary plastids: A look back and a look ahead. Journal of Phycology, 44: 2-6. https://doi.org/10.1111/j.1529-8817.2007.00432.x
  57. Chojnowski, JLG & EL Braun. 2008. Turtle isochore structure is intermediate between amphibians and other amniotes. Integrative and Comparative Biology, 48:454-462. https://doi.org/10.1093/icb/icn062
  58. Chojnowski, JLG, RT Kimball & EL Braun. 2008. Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes. Gene, 410: 89-96. https://doi.org/10.1016/j.gene.2007.11.016
  59. Georgelis, NG, EL Braun & LC Hannah. 2008. Duplication and functional divergence of ADP-glucose pyrophosphorylase genes in plants. BMC Evolutionary Biology, 8: 232. https://doi.org/10.1186/1471-2148-8-232
  60. Hackett, SJ, RT Kimball, S Reddy, RCK Bowie, EL Braun, MJ Braun, JL ChojnowskiG, WA CoxU, K-L HanG, J Harshman, CJ Huddleston, BD Marks, KJ Miglia, WS Moore, FH Sheldon, DW Steadman, CC Witt & T YuriP. A phylogenomic study of birds reveals their evolutionary history. Science 320: 1763-1768. https://doi.org/10.1126/science.1157704
  61. Harshman, JP, EL Braun, MJ Braun, CJ Huddleston, RCK Bowie, JL ChojnowskiG, SJ Hackett, K-L HanG, RT Kimball, BD Marks, KJ Miglia, WS Moore, S Reddy, FH Sheldon, DW Steadman, SJ Steppan, CC Witt & T YuriP. 2008. Phylogenomic evidence for multiple losses of flight in ratite birds. Proceedings of the National Academy of Sciences USA, 105: 13462-13467. https://doi.org/10.1073/pnas.0803242105 (EL Braun corresponding author)
  62. 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. https://doi.org/10.1111/j.0908-8857.2008.04270.x
  63. Phillips, N, S Calhoun, A Moustafa, D Bhattacharya & EL Braun. Genomic insights into evolutionary relationships among heterokont lineages emphasizing the Phaeophyceae. Journal of Phycology, 44: 15-18. https://doi.org/10.1111/j.1529-8817.2007.00435.x
  64. Yuri, TP, RT Kimball, EL Braun & MJ Braun. Duplication and accelerated evolution of growth hormone gene in passerine birds. Molecular Biology and Evolution, 25: 352-361. https://doi.org/10.1093/molbev/msm260 (the title was originally published as “Duplication of accelerated evolution and growth hormone gene in passerine birds,” this was corrected (https://doi.org/10.1093/molbev/msn048)
  65. Chojnowski, JLG, J FranklinU, Y Katsu, T Iguchi, LJ Guillette Jr, RT Kimball & EL Braun. Patterns of vertebrate isochore evolution revealed by comparison of expressed mammalian, avian and crocodilian genes. Journal of Molecular Evolution, 65: 259-266. https://doi.org/10.1007/s00239-007-9003-2
  66. Cox, WAU, RT Kimball & EL Braun. 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: 74-84. https://doi.org/10.1093/auk/124.1.71
  67. Georgelis, NG, 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. https://doi.org/10.1105/tpc.106.049676
  68. 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. https://doi.org/10.1093/molbev/msl158
  69. Sassi, SOG, EL Braun & SA Benner. The evolution of seminal ribonuclease: Pseudogene reactivation or multiple gene inactivation events? Molecular Biology and Evolution, 24: 1012-1024. https://doi.org/10.1093/molbev/msm020
  70. Crowe, TM, P Bloomer, E Randi, V Lucchini, RT Kimball, E Braun & JG Groth. 2006. Supra-generic cladistics of landfowl (Order Galliformes). Acta Zoologica Sinica, 52(Supplement): 358-361.
  71. 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.
  72. 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), pages 295-313. https://people.clas.ufl.edu/ebraun/files/ApplMycol-2004-Braun-295-313.pdf
  73. 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. https://doi.org/10.1016/j.ygcen.2003.11.008
  74. Braun, EL. 2003. Innovation from reduction: The roles of gene loss, domain loss, and sequence divergence in the evolution of eukaryotic genomes. Applied Bioinformatics, 2: 13-34. https://people.clas.ufl.edu/ebraun/files/ApplBioinf-2003-Braun-13-34.pdf
  75. Dias, APG, 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. https://doi.org/10.1104/pp.012047 (AP Dias and EL Braun contributed equally)
  76. Galagan, JE, SE Calvo, KA Borkovich, EU Selker, ND Read, D Jaffe, W FitzHugh, L-J Ma, S Smirnov, S Purcell, B Rehman, T Elkins, R Engels, S Wang, CB Nielsen, J Butler, M Endrizzi, D Qui, P Ianakiev, D Bell-Pedersen, MA Nelson, M Werner-Washburne, CP Selitrennikoff, JA Kinsey, EL Braun, A Zelter, U Schulte, GO Kothe, G Jedd, W Mewes, C Staben, E Marcotte, D Greenberg, A Roy, K Foley, J Naylor, N Stange-Thomann, R Barrett, S Gnerre, M Kamal, M Kamvysselis, E Mauceli, C Bielke, S Rudd, D Frishman, S Krystofova, C Rasmussen, RL Metzenberg, DD Perkins, S Kroken, C Cogoni, G Macino, D Catcheside, W Li, RJ Pratt, SA Osmani, CP DeSouza, L Glass, MJ Orbach, JA Berglund, R Voelker, O Yarden, M Plamann, S Seiler, J Dunlap, A Radford, R Aramayo, DO Natvig, LA Alex, G Mannhaupt, DJ Ebbole, M Freitag, I Paulsen, MS Sachs, ES Lander, C Nusbaum & B Birren. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature, 422: 859-868. https://doi.org/10.1038/nature01554
  77. Braun, EL & RT Kimball. 2002. Examining basal avian divergences using mitochondrial sequences: Model complexity, taxon sampling and sequence length. Systematic Biology, 51: 614-625. https://doi.org/10.1080/10635150290102294
  78. Armstrong, MHU, 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. https://doi.org/10.1093/auk/118.3.799
  79. Bean, LEU, WH Dvorachek JrG, EL Braun, A ErrettU, GS Saenz, M GilesU, 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. https://www.genetics.org/content/157/3/1067
  80. Braun, EL, AP DiasG, TJ MatulnikG & E Grotewold. 2001. Transcription factors and metabolic engineering: Novel applications for ancient tools. Recent Advances in Phytochemistry, 35: 79-109. https://people.clas.ufl.edu/ebraun/files/RecentAdvPhytochem-2001-Braun-79-109.pdf
  81. 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. https://doi.org/10.1093/oxfordjournals.molbev.a003924
  82. 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. https://doi.org/10.1111/j.0014-3820.2001.tb00647.x
  83. Dong, XG, 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. https://doi.org/10.1104/pp.127.1.46
  84. Kimball, RT, EL Braun, JD Ligon, V Lucchini & E Randi. 2001. A molecular phylogeny of the peacock-pheasants (Galliformes: Polyplectron) indicates loss and reduction of ornamental traits and display behaviours. Biological Journal of the Linnean Society, 73: 187-198. https://doi.org/10.1111/j.1095-8312.2001.tb01356.x
  85. 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. https://doi.org/10.1006/mpev.2001.0922
  86. Braun, EL, AL Halpern, MA Nelson & DO Natvig. 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. https://doi.org/10.1101/gr.10.4.416
  87. Randi, E, V Lucchini, T Armijo-PrewittU, RT Kimball, EL Braun & JD Ligon. 2000. Mitochondrial DNA phylogeny and speciation of the Tragopans. The Auk, 117: 1003-1015. https://doi.org/10.1093/auk/117.4.1003
  88. Bieszke, JA, EL Braun, LE BeanU, 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. https://doi.org/10.1073/pnas.96.14.8034
  89. 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. https://doi.org/10.1104/pp.121.1.21
  90. 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. https://doi.org/10.1006/mpev.1998.0562
  91. 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. https://www.genetics.org/content/153/1/427
  92. 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. https://doi.org/10.1007/PL00006409
  93. 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. https://doi.org/10.1098/rspb.1997.0210
  94. Nelson, MA, S Kang, EL Braun, ME Crawford, PL Dolan, PM Leonard, J MitchellU, AM ArmijoU, L BeanU, E BlueyesU, T CushingU, A ErrettU, M FlehartyU, M GormanU, K JudsonU, R Miller, J OrtegaU, I PavlovaU, J PereaU, S TodiscoU, R TrujilloU, J ValentineU, A WellsU, M Werner-Washburne, S YazzieU & DO Natvig. 1997. Expressed sequences from conidial, mycelial and sexual stages of Neurospora crassa. Fungal Genetics and Biology, 21: 348-363. https://doi.org/10.1006/fgbi.1997.0986
  95. 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. https://doi.org/10.1128/jb.178.23.6865-6872.1996
  96. Werner-Washburne, M, EL Braun, ME Crawford & VM Peck. 1996. Stationary phase in Saccharomyces cerevisiae. Molecular Microbiology, 19: 1159-1166.
  97. 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. https://doi.org/10.1111/j.1365-2958.1996.tb02461.x (EK Fuge and EL Braun contributed equally)
  98. Werner-Washburne, M, E Braun, GC Johnston & RA Singer. 1993. Stationary phase in the yeast Saccharomyces cerevisiae. Microbiological Reviews, 57: 383-401. https://mmbr.asm.org/content/57/2/383
  99. 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. https://www.jbc.org/content/266/29/19704