Publications

  1. 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 
  2. Saini, E., Zeeshan, M., Brady, D., Pandey, R., Kaiser, G., Kořený, L., Sheokand, P., Thakur, V., Tatiya, S., N.J., Limenitakis, R., Kaur, I., Green, J.L., Bottrill, A.R., Guttery, D.S., Waller, R.F., Heussler V., Holder, A.A., Mohmmed, A.A., Malhotra, P. and Tewari, R. (2017) Photosensitized INA-Labelled protein 1 (PhIL1) is a novel component of the inner membrane complex and is required for Plasmodium parasite development. Sci. Rep. 7:15577
  3. Janouškovec, J., Gavelis, G.S., Burki, F., Dinh, D., Bachvaroff, T.R., Gornik, G.S., Bright, K.J., Imanian, B., Strom, S.L., Delwiche, C.F., Waller, R.F, Fensome, R.A., Leander, B.S., Rohwer, F.L., and Saldarriaga J.F. (2017) Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics. PNAS 114(2):e171-180
  4. Wall, R.J, Roques, M., Katris, N.J., Koreny, L., Stanway, R.R., Brady, D., Waller, R.F. and Tewari, R. (2016) SAS6-like protein in Plasmodium indicates that conoid-associated apical complex proteins persist in invasive stages within the mosquito vector. Sci. Rep. 6:28604
  5. Waller, R.F., Gornik, S.G., Koreny, L. and Pain, A (2016) Metabolic pathway redundancy within the apicomplexan-dinoflagellate radiation argues against an ancient chromalveolate plastid. Comm. Integrat. Biol. 9: e1116653
  6. 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
  7. Woo, Y.H., Ansari, H., et al. (2015) Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. eLife 4: e06974
  8. Gornik, S.G., Febrimarsa, Cassin, A., MacRae, J.I., Ramaprasad, A., Rchiad, Z., McConville, M.J., Bacic, A., McFadden, G.I., Pain, A. and Waller, R.F. (2015) Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate. PNAS 112: 5767-72
  9. 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
  10. 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
  11. Hewitt, V, Lithgow, T and Waller, R.F. (2014) Modifications and innovations in the evolution of mitochondrial protein import pathways. In Endosymbiosis (ed Wolfgang Loffelhardt) Springer, New York, USA pp 19-25
  12. 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
  13. 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
  14. 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
  15. Jackson, C.J. and Waller, R.F. (2013) A widespread and unusual RNA trans-splicing type in dinoflagellate mitochondria. PLoS ONE 8(2): e56777
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. Waller, R.F. (2012) Second genesis of a plastid organelle. Proc. Natl Acad. Sci. USA 109(14): 5142-3
  22. 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
  23. 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 
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. Waller, R.F. (2010) Origin of Life. In Biology: An Australian Focus. (eds Knox, Ladiges, Saint, Evans) McGraw-Hill, North Ryde, Aulstralia. pp 3-5
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. Gould, S.B., Waller, R.F. and McFadden, G.I. (2008) Plastid Evolution. Ann. Rev. Plant Biol. 59:491-517
  36. 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
  37. 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
  38. Patron, N.J. and Waller, R.F. (2007) Transit peptide diversity and divergence: a global analysis of plastid targeting signals. BioEssays 29:1048-58
  39. 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
  40. 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
  41. Waller, R.F. and Keeling, P.J. (2006) Alveolate and chlorophycean mitochondrial cox2 genes split twice independently. Gene 383: 33-37
  42. 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
  43. Eisen, J.A., et al. (2006) Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biology 4:e286
  44. Waller, R.F., Slamovitz, C.H. and Keeling, P.J. (2006) Lateral gene transfer of a multi-gene region from cyanobacteria to dinoflagellates resulting in a novel plastid-targeted fusion protein. Mol. Biol. Evol. 23:1437-43
  45. 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
  46. 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
  47. 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
  48. 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
  49. Waller, R.F. and McFadden, G.I. (2005) The apicoplast: a review of the derived plastid of apicomplexan parasites. Curr. Issues Mol. Biol. 7: 57-79Current_issues_in_molecular_biology_2005_Cover
  50. 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
  51. 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
  52. Waller, R.F. and McFadden G.I. (2004) The Apicoplast. In Genomes and the Molecular Cell Biology of Malaria Parasites. (Waters A and Janse C eds) Horizon Scientific Press.
  53. 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
  54. Waller, R.F., McConville, M.J., and McFadden, G.I. (2004) More plastids in human parasites? Trends Parasitol. 20:54-7
  55. 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
  56. 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
  57. 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
  58. Waller, R.F., Keeling, P.J., van Dooren, G., and McFadden, G.I. (2003) Comment on a green algal apicoplast ancestor. Science 301: 49a-50a
  59. 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
  60. 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
  61. Waller, R.F. and McConville, M.J. (2002) Developmental changes in lysosome morphology and function in Leishmania parasites. Int. J. Parasitol. 32: 1435-45
  62. Waller, R.F., Reed, M.B., Cowman, A.F. and McFadden, G.I. (2000) Protein trafficking to the plastid of Plasmodium falciparum is via the secretory pathway. EMBO J. 19: 1794-1802
  63. Van Dooren, G.G., Waller, R.F., Joiner, K.A., Roos, D.S. and McFadden, G.I (2000) Protein transport in Plasmodium falciparum: Traffic jams. Parasitol. Today 16:421-7
  64. 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
  65. 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
  66. Waller, R.F. and McFadden, G.I. (2000) In situ hybridization for electron microscopy. Methods. Mol. Biol. 123: 259-277
  67. Keeling, P.J., Palmer, J.D.. Donald, R. G. K , Roos, D.S., Waller, R.F. & McFadden, G.I.  (1999) Shikimate in apicomplexan parasites. Nature 397: 219-220
  68. McFadden G.I. and Waller R.F. (1999) Evolutionary pathway of the apicomplexan plastids and its implications-Response to Bodyl. Trends Microbiol.  7:267-8
  69. Waller, R.F., Keeling, P.J., Donald, R.G.K., Striepen, B., Handman, E., Lang-Unnasch, N., Cowman, A.F., Besra, G.S., Roos D.S. and McFadden G.I. (1998) Nuclear-encoded proteins target to the plastid in Toxoplamsa gondii and Plasmodium falciparum.  Proc. Natl Acad. Sci. USA 95: 12352-57
  70. Crabb, B.S., Cooke, B.M., Reeder, J.C., Waller, R.F., Caruana, S.R., Davern, K.M., Wickham, M.E., Brown, G.V., Coppel, R.L. and Cowman, A.F. (1997)  Targeted gene disruption shows that knobs enable malaria-infected red cells to cytoadhere under physiological shear stress.  Cell 89: 287-296
  71. McFadden, G.I., Waller, R.F., Reith, M., Munhollan D.J. and Lang-Unnasch, N. (1997)  The plastid of apicomplexan parasites.  In:  The evolution of the algae and their plastids,  Bhattacharya, D. (ed), Springer Verlag, Pl. Syst. Evol. [Suppl.] 11: 261-287.
  72. McFadden, G.I. and Waller, R.F. (1997) Plastids in parasites of humans.  BioEssays 19 (11): 1033-40
  73. McFadden, G.I. and Waller, R.F. (1997) Bloodthirsty plants. New Scientist 5 April: 56
  74. McFadden, G.I. and Waller, R.F. (1997) Malaria unmasked: a new handle on an old enemy. Today's Life Science. 9: 24-28
  75. Waller, R.F. and McFadden, G.I. (1995)  Morphological and cytochemical analysis of the nucleus/pyrenoid association in a unicellular red alga.  Protoplasma  186: 131-141
  76. McFadden, G.I., Gilson, P.R. and Waller, R.F. (1995)  Molecular phylogeny of chlorarachniophytes based on plastid rRNA and rbcL sequences.  Archiv. Protistenk. 145: 231-239.
  77. Gilson, P.R., Waller, R.F. and McFadden, G.I. (1995)  Preliminary characterisation of chlorarachniophyte mitochondrial DNA.  J. Euk. Microbiol. 42: 696-701

 

 

 

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