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  2. Waller, R.F. and Kořený, L. (2017) Plastid Complexity in Dinoflagellates: A Picture of Gains, Losses, Replacements and Revisions. In Secondary Endosymbioses (ed Yoshihisa Hirakawa), Vol 84, Advances in Botanical Research, UK: Academic Press, 2017, pp. 105-144 
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  7. Jacot, D., Waller, R.F., Soldati-Favre, D., MacPherson, D.A., MacRae, J.I. (2016) Apicomplexan energy metabolism: carbon source promiscuity and the quiescence hyperbole. Trends Parasitol. 32 (1), 56-70 TIP
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  10. Wetherbee, R., Gornik, S.G., Grant, B. and Waller, R.F. (2015) Andersenia, a genus of filamentous, sand-dwelling Pelagophyceae from southeastern Australia. Phycologia 54: 35-48
  11. Katris, N.J., van Dooren, G.G., McMillan, P.J., Hanssen, E., Tilley, L. and Waller, R.F. (2014) The apical complex provides a regulated gateway for secretion of invasion factors in Toxoplasma. PLOS Pathog. 10: e1004074
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  13. Bachvaroff, T.R., Gornik, S.G., Concepcion, G.T., Waller, R.F., Mednez, G.S., Lippmeier, J.C. and Delwiche, C.F. (2014) Dinoflagellate phylogeny revisited: using ribosomal proteins to resolve deep branching dinoflagellate clades. Mol. Phylogen. Evol. 70: 314-22
  14. Teng, C.Y., Dang, Y., Danne, J.C., Waller, R.F. and Green, B.R. (2013) Mitochondrial genes of dinoflagellates are transcribed by a nuclear-encoded single-subunit RNA polymerase. PLOS ONE  8(6): e65387
  15. El-Haddad, H., Pryzborski , J.M., Kraft, L.J.K., McFadden, G.I., Waller, R.F., Gould, S.B. (2013) Characterization of TtALV2, an essential charged repeat motif protein of the Tetrahymena thermophila membrane skeleton. Euk. Cell 12(6): 932-40EukCell_2013_Cover
  16. Jackson, C.J. and Waller, R.F. (2013) A widespread and unusual RNA trans-splicing type in dinoflagellate mitochondria. PLoS ONE 8(2): e56777
  17. Danne, J.C., Gornik, S.G., MacRae, J.I., McConville, M.J. and Waller, R.F. (2013) Alveolate mitochondrial metabolic evolution: dinoflagellates force reassessment of the role of parasitism as a driver of change in apicomplexans. Mol. Biol. Evol. 30(1): 123-39
  18. Gornik, S.G., Cranenburgh, A. and Waller, R.F. (2013) New host range for Hematodinium in Southern Australia and novel tools for sensitive detection of parasitic dinoflagellates. PLOS ONE 8(12): e82774
  19. Jackson, C.J., Gornik, S.G. and Waller, R.F. (2013) A tertiary plastid gains RNA editing in its new host. Mol. Biol. Evol. 30(4):788-92
  20. Grant, B., Waller, R.F., Clementson, L.A. and Wetherbee, R. (2013) Psammomonas australis gen. et sp. nov. (Raphidophyceae), a new dimorphic, sand-dwelling raphidophyte. Phycologia  52(1):57-64
  21. Gornik, S.G., Ford, K.L., Mulhern, T.D., Bacic, A., McFadden, G.I. and Waller, R.F. (2012) Loss of nucleosomal DNA condensation coincides with appearance of a novel nuclear protein in dinoflagellates. Curr. Biol. 22(24): 2303-12     [Commentary] Current_Biology_2012_CoverImage
  22. Waller, R.F. (2012) Second genesis of a plastid organelle. Proc. Natl Acad. Sci. USA 109(14): 5142-3
  23. Jackson, C.J., Gornik, S.G. and Waller, R.F. (2012) The mitochondrial genome and transcriptome of the basal dinoflagellate Hematodinium sp.: character evolution within the highly derived mitochondrial genomes of dinoflagellates. Genome Biol. Evol. 4(1):59-72
  24. Danne, J.C., Gornik, S.G. and Waller, R.F. (2012) An assessment of vertical inheritance versus endosymbiont transfer of nucleus- encoded genes for mitochondrial proteins following tertiary endosymbiosis in Karlodinium micrum. Protist 16(1):76-90 
  25. Burger, G., Jackson, C.J. and Waller, R.F. (2012) Unusual mitochondrial genomes and genes. In Organelle Genetics (ed Charles Bullerwell) Springer, New York, USA. pp 41-77
  26. Danne, J.C. and Waller, R.F. (2011) Analysis of dinoflagellate mitochondrial protein sorting signals indicates a highly stable protein targeting system across eukaryotic diversity. J. Mol. Biol. 408: 643-53
  27. Gould. S.B., Kraft, L.G.K, van Dooren, G.G., Goodman, C.D., Ford, K.L., Cassin, A.M., Bacic, A. McFadden, G.I. and Waller, R.F. (2011) Ciliate pellicular proteome identifies novel protein families with characteristic repeat motIfs that are common to Alveolates. Mol. Biol. Evol. 28: 1319-31
  28. Grant, B., Waller, R.F. and Wetherbee, R. (2011) Platychrysis moestrupii sp.nov. (Prymnesiophyceae): a new dimorphic, sand-dwelling haptophyte species from southeastern Australia. Phycologia 50(6): 608-15
  29. Kraft, L.G.K, Kraft, G.T. and Waller, R.F. (2010) Investigations into southern Australian Ulva (Ulvophyceae, Chlorophyta) taxonomy and molecular phylogeny indicate both cosmopolitanism and endemic cryptic species. J. Phycol. 46(6): 1257-77
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  31. Waller, R.F. and Jackson, C.J. (2009) Dinoflagellate mitochondrial genomes: stretching the rules of molecular biology. BioEssays 31(2):237-45     [Highlight]BioEssays_2009_Cover
  32. Waller, R.F., Jabbour, C., Chan, N.C., Celik, N., Likić, V.A., Mulhern, T.D. and Lithgow, T. (2009) Evidence of a reduced and modified mitochondrial protein import apparatus in microsporidian mitosomes. Euk. Cell 8: 19-26
  33. Osborne, S.E., Walthers, D., Tomljenovic, A.M., Mulder, D.T., Silphaduang, U., Duong, N., Lowden, M.J., Wickham, M.E., Waller, R.F., Kenney, L.J. and Coombes, B.K (2009) Pathogenic adaptation of intracellular bacteria by rewiring a cis-regulatory input function. Proc. Natl Acad. Sci. USA 106(10):3982-7
  34. Pusnik, M., Charriere, F., Maser, P., Waller, R.F., Dagley, M., Lithgow, T. and Schneider, A. (2009) The single mitochondrial porin of Trypanosoma brucei is the main metabolite transporter in the outer mitochondrial membrane. Mol. Biol. Evol. 26: 671-80
  35. Gould, S.B., Tham, W-H., Cowman, A.F., McFadden, G.I. and Waller, R.F. (2008) Alveolins, a New Family of Cortical Proteins that Define the Protist Infrakingdom Alveolata.  Mol. Biol. Evol. 25:1219-30
  36. Gould, S.B., Waller, R.F. and McFadden, G.I. (2008) Plastid Evolution. Ann. Rev. Plant Biol. 59:491-517
  37. Perry, A.J., Rimmer, K.A., Mertens, J.D., Waller, R.F., Mulhern, T.D., Lithgow, T. and Gooley, P.R. (2008) Structure, topology and function of the translocase of the outer membrane of mitochondria. Plant Physiol. Biochem. 46:265-74
  38. Carpenter, K.J., Waller, R.F. and Keeling, P.J. (2008) Surface morphology of Saccinobaculus (Oxymonadida): implications for character evolution and function in oxymonads. Protist 159: 209-21
  39. Patron, N.J. and Waller, R.F. (2007) Transit peptide diversity and divergence: a global analysis of plastid targeting signals. BioEssays 29:1048-58
  40. Jackson, C.J., Norman, J.E., Schnare, M.N., Gray, M.W., Keeling, P.J. and Waller, R.F. (2007) Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria. BMC Biology 5:4
  41. Patron, N.J., Waller, R.F., Conzijnsen, A.J., Straney, D.C., Gardiner, D.M., Nierman, W.C. and Howlett, B.J. (2007) Origin and distribution of epipolythiodioxopiperazine (ETP) gene clusters in filamentous ascomycetes. BMC Evol. Biol. 7:174
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  43. Morita, Y.S., Sena, C.B.C., Waller, R.F., Kurokawa, K., Sernee, M.F., Nakatani, F., Haites, R.E., Billman-Jacobe, H., McConville, M.J., and Maeda, Y. (2006) PimE is a polyprenol-phosphate-mannose-dependent mannosyltransferase that transfers the fifth mannose of phosphatidyl-inositol mannoside in mycobacteria. J. Biol. Chem. 281:25143-55
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  46. Waller, R.F., Patron, N.J. and Keeling, P.J. (2006) Phylogenetic history of plastid-targeted proteins in peridinin-containing dinoflagellate Heterocapsa triquestra. Int. J. Sys. Evol. Microbiol. 56: 1439-1447
  47. Patron, N.J., Waller, R.F. and Keeling, P.J. (2006) A tertiary plastid uses genes from two endosymbionts. J. Mol. Biol. 357:1373-82
  48. Chan, N.C., Likić, V.A., Waller, R.F., Mulhern, T.D. and Lithgow, T. (2006) The C-terminal TPR domain of Tom70 defines a family of mitochondrial protein import receptors found only in animals and fungi. J. Mol. Biol. 358:1010-22
  49. Patron, N.J., Waller, R.F., Archibald, J.M. and Keeling, P.J. (2005) Complex protein targeting to dinoflagellate plastids. J. Mol. Biol. 348:1015-24
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  51. Morita, Y.S., Velasquez, R., Taig, E., Waller, R.F., Patterson, J.H., Tull, D.T., Williams, S.J., Billman-Jacobe, H., McConville, M.J. (2005) Compartmentalization of lipid biosynthesis in mycobacteria.  J. Biol. Chem. 280: 21645-52
  52. Likić, V.A., Peryy, A., Hulett, J., Traven, A., Curran, S., Waller, R.F., Keeling, P.J., Gooley, P.R. and Lithgow, T. (2005) Patterns that define the four domains conserved in known and novel isoforms of the protein import receptor Tom20. J. Mol. Biol. 347: 81-93
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  54. Dodge M.A., Waller, R.F., Chow, L.M.C., Zaman, M.M., Cotton, L.M. McConville, M.J., and Wirth, D.F. (2004) Localization and activity of multi-drug resistance protein 1 in the secretory pathway of Leishmania parasites. Mol. Micro. 51: 1563-75
  55. Waller, R.F., McConville, M.J., and McFadden, G.I. (2004) More plastids in human parasites? Trends Parasitol. 20:54-7
  56. Ralph, S.R., van Dooren, G.G., Waller, R.F., Crawford, M.J., Fraunholz, M., Foth, B.J., Roos, D.S., and McFadden, G.I. (2004) Tropical infectious diseases: metabolic maps and functions of the Plasmodium falciparum apicoplast. Nature Rev. Micro. 2: 203-16
  57. Gentle, I., Gabriel, K., Beech, P., Waller, R.F., and Lithgow, T. (2004) The Omp85 family of proteins is essential for outer membrane biogenesis in mitochondria and bacteria. J. Cell Biol. 164:19-24
  58. Bandyopadhyay, S., Chatterjee, M., Pal, S., Waller, R.F., Sundar, S., McConville, M.J., Mandal, C. (2004) Purification, characterization of O-acetylated sialoglycoconjugates-specific IgM, and development of an enzyme-linked immunosorbent assay for diagnosis and follow-up of Indian visceral leishmaniasis patients. Diagnostic Micro. Infect. Dis. 50: 15-24
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  60. Waller, R.F., Ralph, S.A., Reed, M.B., Su, V., Douglas, J.D., Minnikin, D.E., Cowman, A.F., Besra, G.S., and McFadden, G.I. (2003) A type II pathway for fatty acid biosynthesis presents drug targets in Plasmodium falciparum. Antimicrob. Agents Chemoth. 47: 297-301
  61. Patterson, J.H., Waller, R.F., Jeevarajah, D., Billman-Jacobe, H. and McConville, M.J (2003) Mannose metabolism is required for mycobacterial growth. Biochem. J. 15: 77-86
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  65. Baldi, D.L., Andrews, K.T., Waller, R.F., Roos, D.S., Howard, R.F., Crabb, B.S. and Cowman, A.F. (2000) RAP1 controls rhoptry targeting of RAP in the malaria parasite Plasmodium falciparum. EMBO J. 19: 2435-2443
  66. Waterkeyn, J.G., Wickham, M.E., Davern, K.M., Cooke, B.M., Coppel, R.L., Reeder, J.C., Culvenor, J.G., Waller, R.F. and Cowman, A.F (2000) Targeted mutagenesis of Plasmodium falciparum erythrocyte membrane protein 3 (PfEMP3) disrupts cytoadherence of malaria-infected red blood cells. EMBO J. 19: 2813-2823
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