Publications

2022

Tikhonenkov, D.V., Mikhailov, K.V., Gawryluk, R.M.R., Belyaev, A.O., Mathur, V., Karpov, S.A., Zagumyonnyi, D.G., Borodina, A.S., Prokina, K.I., Mylnikov, A.P., Aleoshin, V.V., and Keeling, P.J. 2022. Microbial predators form a new supergroup of eukaryotes. Nature, 612, 714-719 (PDF)

Giannotti, D., Boscaro, V., Husnik, F., Vannini, C., and Keeling, P.J. 2022. At the threshold of symbiosis: the genome of obligately endosymbiotic 'Candidatus Nebulobacter yamunensis' is almost indistinguishable from that of a cultivable strain. Microb. Genom., 8, 000909 (PDF)

Holt, C.C., Boscaro, V., Van Steenkiste, N.W.L., Herranz, M., Mathur, V., Irwin, N.A.T., Buckholtz, G., Leander, B.S., and Keeling, P.J. 2022. Microscopic marine invertebrates are reservoirs for cryptic and diverse protists and fungi. Microbiome, 10, 161 (PDF)

Zagumyonnyi, D.G., Radaykina, L.V., Keeling, P.J., and Tikhonenkov, D.V. 2022. Centrohelid heliozoans of Ukraine with a description of a new genus and species (Haptista: Centroplasthelida). Eur. J. Protistol., 86, 125916 (PDF)

Cooney, E.C., Leander, B.S., and Keeling, P.J. 2022. Phylogenomics shows unique traits in Noctilucales are derived rather than ancestral. PNAS Nexus, 1, pgac202 (PDF)

Needham, D.M., Poirier, C., Bachy, C., George, E.E., Wilken, S., Yung, C.C.M., Limardo, A.J., Morando, M., Sudek, L., Malmstrom, R.R., Keeling, P.J., Santoro, A.E., and Worden, A.Z. 2022. The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate. Nat. Microbiol., 7, 1466-1479 (PDF)

Ocaña-Pallarès, E., Williams, T.A., López-Escardó, D., Arroyo, A.S., Pathmanathan, J.S., Bapteste, E., Tikhonenkov, D.V., Keeling, P.J., Szöllösi, G.J., and Ruiz-Trillo, I. 2022. Divergent genomic trajectories predate the origin of animals and fungi. Nature, 609, 747-753 (PDF)

Syberg-Olsen, M.J., Garber, A.I., Keeling, P.J., McCutcheon, J.P., and Husnik, F. 2022. Pseudofinder: detection of pseudogenes in prokaryotic genomes. Mol. Biol. Evol., 39, msac153 (PDF)

Boscaro, V., Syberg-Olsen, M.J., Irwin, N.A.T., George, E.E., Vannini, C., Husnik, F., and Keeling, P.J. 2022. All essential endosymbionts of the ciliate Euplotes are cyclically replaced. Curr. Biol., 32, R1-R3 (PDF)

George, E.E., Tashyreva, D., Kwong, W.K., Okamoto, N., Horák, A., Husnik, F., Lukeš, J., and Keeling, P.J. 2022. Gene transfer agents in bacterial endosymbionts of microbial eukaryotes. Genome Biol. Evol., 14, evac099 (PDF)

Okamoto, N., Keeling, P.J., Leander, B.S., and Tai, V. 2022. Microbial communities in sandy beaches from the three domains of life differ by microhabitat and intertidal location. Mol. Ecol., 31, 3210-3227 (PDF)

Cho, A., Tikhonenkov, D.V., Hehenberger, E., Karnkowska, A., Mylnikov, A.P., and Keeling, P.J. 2022. Monophyly of diverse Bigyromonadea and their impact on phylogenomic relationships within stramenopiles. Mol. Phylogenet. Evol., 171, 107468 (PDF)

Boscaro, V., Holt, C.C, Van Steenkiste, N.W.L., Herranz, M., Irwin, N.A.T., Àlvarez-Campos, P., Grzelak, K., Holovachov, O., Kerbl, A., Mathur, V., Okamoto, N., Piercey, R.S., Worsaae, K., Leander, B.S., and Keeling, P.J. 2022. Microbiomes of microscopic marine invertebrates do not reveal signatures of phylosymbiosis. Nat. Microbiol., 7, 810-819 (PDF)

Giannotti, D., Boscaro, V., Husnik, F., Vannini, C., and Keeling, P.J. 2022. The "other" Rickettsiales: an overview of the family "Candidatus Midichloriaceae". Appl. Environ. Microbiol., 88, e02432-21 (PDF)

Tashyreva, D., Simpson, A.G.B., Prokopchuk, G., Škodová-Sveráková, I., Butenko, A., Hammond, M., George, E.E., Flegontova, O., Záhonová, K., Faktorová, D., Yabuki, A., Horák, A., Keeling P.J., and Lukeš, J. 2022. Diplonemids – A review on "new" flagellates on the oceanic block. Protist, 173, 125868 (PDF)

Irwin, N.A.T., Pittis, A.A., Richards, T.A., and Keeling, P.J. 2022. Systematic evaluation of horizontal gene transfer between eukaryotes and viruses. Nat. Microbiol., 7, 327–336 (PDF)

2021

Keeling, P.J., Mathur, V., and Kwong, W.K. 2021. Corallicolids: the elusive coral-infecting apicomplexans. PLoS Pathog., 17, e1009845 (PDF)

Irwin, N.A.T., Pittis, A.A., Mathur, V., Howe, L.J., Keeling, P.J., Lynn, D.H., and Bourland, W.A. 2021. The function and evolution of motile DNA replication systems in ciliates. Curr. Biol., 31, 66-76 (PDF)

Borodina, A.S., Mylnikov, A.P., Janouškovec, J., Keeling, P.J., and Tikhonenkov, D.V. 2021. The morphology, ultrastructure and molecular phylogeny of a new freshwater heterolobose amoeba Parafumarolamoeba stagnalis n. sp. (Vahlkampfiidae; Heterolobosea). Diversity, 13, 433 (PDF)

Husnik, F., Tashyreva, D., Boscaro, V., George, E.E., Lukeš, J., and Keeling, P.J. 2021. Bacterial and archaeal symbioses with protists. Curr. Biol., 31, R862-R877 (PDF)

Mathur, V., Wakeman, K.C., and Keeling, P.J. 2021. Parallel functional reduction in the mitochondria of apicomplexan parasites. Curr. Biol., 31, 2920-2928 (PDF)

Schön, M.E., Zlatogursky, V.V., Singh, R.P., Poirier, C., Wilken, S., Mathur, V., Strassert, J.F.H., Pinhassi, J., Worden, A.Z., Keeling, P.J., Ettema, T.J.G., Wideman, J.G., and Burki, F. 2021. Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae. Nat. Commun., 12, 6651 (PDF)

Kwong, W.K., Irwin, N.A.T., Mathur, V., Na, I., Okamoto, N., Vermeij, M.J.A., and Keeling, P.J. 2021. Taxonomy of the apicomplexan symbionts of coral, including Corallicolida ord. nov., reassignment of the genus Gemmocystis, and description of new species Corallicola aquarius gen. nov. sp. nov. and Anthozoaphila gnarlus gen. nov. sp. nov. J. Eukaryot. Microbiol., 68, e12852 (PDF)

Irwin, N.A.T., Twynstra, C.S., Mathur, V., and Keeling, P.J. 2021. The molecular phylogeny of Chionaster nivalis reveals a novel order of psychrophilic and globally distributed Tremellomycetes (Fungi, Basidiomycota). PLoS One, 16, e0247594 (PDF)

Singh, R.A, Boscaro, V., James, E.R., Karnkowska, A., Kolisko, M., Gavelis, G.S., Okamoto, N., del Campo, J., Fiorito, R., Hehenberger, E., Irwin, N.A.T., Mathur, V., Scheffrahn, R.H., and Keeling, P.J. 2021. Characterization of new cristamonad species from kalotermitid termites including a novel genus, Runanympha. Sci. Rep., 11, 7270 (PDF)

Little, M., George, E.E., Arts, M.G.I., Shivak, J., Benler, S., Huckeba, J., Quinlan, Z.A., Boscaro, V., Mueller, B., Cobián Güemes, A.G., Rojas, M.I., White, B., Petras, D., Silveira, C.B., Haas, A.F., Kelly, L.W., Vermeij, M.J.A., Quinn, R.A., Keeling, P.J., Dorrestein, P.C., Rohwer, F., and Roach, T.N.F. 2021. Three-dimensional molecular cartography of the Caribbean reef-building coral Orbicella faveolata. Front. Mar. Sci., 8, 627724 (PDF)

Mathur, V., Kwong, W.K., Husnik, F., Irwin, N.A.T., Kristmundsson, Á., Gestal, C., Freeman, M., and Keeling, P.J. 2021. Phylogenomics identifies a new major subgroup of apicomplexans, Marosporida class nov., with extreme apicoplast genome reduction. Genome Biol. Evol., 13, evaa244 (PDF)

Lax, G., Kolisko, M., Eglit, Y., Lee, W.J., Yubuki, N., Karnkowska, A., Leander, B.S., Burger, G., Keeling, P.J., and Simpson, A.G.B. 2021. Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs. Mol. Phylogenet. Evol., 159,107088 (PDF)

Tikhonenkov, D.V., Gawryluk, R.M.R., Mylnikov, A.P., and Keeling, P.J. 2021. First finding of free-living representatives of Prokinetoplastina and their nuclear and mitochondrial genomes. Sci. Rep., 11, 2946 (PDF)

Lemay, M.A., Chen, M.Y., Mazel, F., Hind, K.R., Starko, S., Keeling, P.J., Martone, P.T., and Wegener Parfrey, L. 2021. Morphological complexity affects the diversity of marine microbiomes. ISME J., 15, 1372-1386 (PDF)

Prokina, K.I., Keeling, P.J., and Tikhonenkov, D.V. 2021. Heterotrophic flagellates and centrohelid heliozoans from marine waters of Curacao, the Netherlands Antilles. Eur. J. Protistol., 77, 125758 (PDF)

Massana, R., Labarre, A., López-Escardó, D., Obiol, A., Bucchini, F., Hackl, T., Fischer, M.G., Vandepoele, K., Tikhonenkov, D.V., Husnik, F., and Keeling, P.J. 2021. Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate. ISME J., 15, 154-167 (PDF)

2020

Wideman, J.G., Monier, A., Rodríguez-Martínez, R., Leonard, G., Cook, E., Poirier, C., Maguire, F., Milner, D.S., Irwin, N.A.T., Moore, K., Santoro, A.E., Keeling, P.J., Worden, A.Z., and Richards, T.A. 2020. Unexpected mitochondrial genome diversity revealed by targeted single-cell genomics of heterotrophic flagellated protists. Nat. Microbiol., 5, 154-165 (PDF)

Butenko, A., Opperdoes, F.R., Flegontova, O., Horák, A., Hampl, V., Keeling, P., Gawryluk, R.M.R., Tikhonenkov, D., Flegontov, P., and Lukeš, J. 2020. Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids. BMC Biol., 18, 23 (PDF)

George, E.E., Husnik, F., Tashyreva, D., Prokopchuk, G., Horák, A., Kwong, W.K., Lukeš, J., and Keeling, P.J. 2020. Highly reduced genomes of protist endosymbionts show evolutionary convergence. Curr. Biol., 30, 925-933 (PDF)

Rodríguez-Martínez, R., Leonard, G., Milner, D.S., Sudek, S., Conway, M., Moore, K., Hudson, T., Mahé, F., Keeling, P.J., Santoro, A.E., Worden, A.Z., and Richards, T.A. 2020. Controlled sampling of ribosomally active protistan diversity in sediment-surface layers identifies putative players in the marine carbon sink. ISME J., 14, 984-998 (PDF)

Fukuda, K., Cooney, E.C., Irwin, N.A.T., Keeling, P.J., and Hirakawa, Y. 2020. High-efficiency transformation of the chlorarachniophyte Amorphochlora amoebiformis by electroporation. Algal Res., 48, 101903 (PDF)

Faktorová, D., Nisbet, R.E.R., Fernández Robledo, J.A., Casacuberta, E., Sudek, L., Allen, A.E., Ares, M., Aresté, C., Balestreri, C., Barbrook, A.C., Beardslee, P., Bender, S., Booth, D.S., Bouget, F.-Y., Bowler, C., Breglia, S.A., Brownlee, C., Burger, G., Cerutti, H., Cesaroni, R., Chiurillo, M.A., Clemente, T., Coles, D.B., Collier, J.L., Cooney, E.C., Coyne, K., Docampo, R., Dupont, C.L., Edgcomb, V., Einarsson, E., Elustondo, P.A., Federici, F., Freire-Beneitez, V., Freyria, N.J., Fukuda, K., García, P.A., Girguis, P.R., Gomaa, F., Gornik, S.G., Guo, J., Hampl, V., Hanawa, Y., Haro-Contreras, E.R., Hehenberger, E., Highfield, A., Hirakawa, Y., Hopes, A., Howe, C.J., Hu, I., Ibañez, J., Irwin, N.A.T., Ishii, Y., Janowicz, N.E., Jones, A.C., Kachale, A., Fujimura-Kamada, K., Kaur, B., Kaye, J.Z., Kazana, E., Keeling, P.J., King, N., Klobutcher, L.A., Lander, N., Lassadi, I., Li, Z., Lin, S., Lozano, J.-C., Luan, F., Maruyama, S., Matute, T., Miceli, C., Minagawa, J., Moosburner, M., Najle, S.R., Nanjappa, D., Nimmo, I.C., Noble, L., Novák Vanclová, A.M.G., Nowacki, M., Nuñez, I., Pain, A., Piersanti, A., Pucciarelli, S., Pyrih, J., Rest, J.S., Rius, M., Robertson, D., Ruaud, A., Ruiz-Trillo, I., Sigg, M.A., Silver, P.A., Slamovits, C.H., Smith, G.J., Sprecher, B.N., Stern, R., Swart, E.C., Tsaousis, A.D., Tsypin, L., Turkewitz, A., Turnšek, J., Valach, M., Vergé, V., von Dassow, P., von der Haar, T., Waller, R.F., Wang, L., Wen, X., Wheeler, G., Woods, A., Zhang, H., Mock, T., Worden, A.Z., and Lukeš, J. 2020. Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nat. Methods, 17, 481-494 (PDF)

Hehenberger, E., Eitel, M., Fortunato, S.A.V., Miller, D.J., Keeling, P.J., and Cahill, M.A. 2020. Early eukaryotic origins and metazoan elaboration of MAPR family proteins. Mol. Phylogenet. Evol., 148, 106814 (PDF)

Tikhonenkov, D.V., Hehenberger, E., Esaulov, A.S., Belyakova, O.I., Mazei, Y.A., Mylnikov, A.P., and Keeling, P.J. 2020. Insights into the origin of metazoan multicellularity from predatory unicellular relatives of animals. BMC Biol., 18, 39 (PDF)

Tikhonenkov, D.V., Strassert, J.F.H., Janouškovec, J., Mylnikov, A.P., Aleoshin, V.V., Burki, F., and Keeling P.J. 2020. Predatory colponemids are the sister group to all other alveolates. Mol. Phylogenet. Evol., 149, 106839 (PDF)

del Campo, J., Bass, D., and Keeling, P.J. 2020. The eukaryome: diversity and role of microeukaryotic organisms associated with animal hosts. Funct. Ecol., 34, 2045-2054 (PDF)

Cooney, E.C., Okamoto, N., Cho, A., Hehenberger, E., Richards, T.A., Santoro, A.E., Worden, A.Z., Leander, B.S., and Keeling, P.J. 2020. Single-cell transcriptomics of Abedinium reveals a new early-branching dinoflagellate lineage. Genome Biol. Evol., 12, 2417-2428 (PDF)

Tikhonenkov, D.V., Mikhailov, K.V., Hehenberger, E., Karpov, S.A., Prokina, K.I., Esaulov, A.S., Belyakova, O.I., Mazei, Y.A., Mylnikov, A.P., Aleoshin, V.V., and Keeling, P.J. 2020. New lineage of microbial predators adds complexity to reconstructing the evolutionary origin of animals. Curr. Biol., 30, 4500-4509 (PDF)

2019

Treitli, S.C., Kolisko, M., Husnik, F., Keeling, P.J., and Hampl, V. 2019. Revealing the metabolic capacity of Streblomastix strix and its bacterial symbionts using single-cell metagenomics. Proc. Natl. Acad. Sci. USA, 116, 19675-19684 (PDF)

del Campo, J., Heger, T.J., Rodríguez-Martínez, R., Worden, A.Z., Richards, T.A., Massana, R., and Keeling, P.J. 2019. Assessing the diversity and distribution of apicomplexans in host and free-living environments using high-throughput amplicon data and a phylogenetically informed reference framework. Front. Microbiol., 10, 2373 (PDF)

Keeling, P.J. 2019. Combining morphology, behaviour, and genomics to understand the evolution and ecology of microbial eukaryotes. Phil. Trans. R. Soc. B, 374, 20190085 (PDF)

Needham, D.M., Yoshizawa, S., Hosaka, T., Poirier, C., Choi, C.J., Hehenberger, E., Irwin, N.A.T., Wilken, S., Yung, C.-M., Bachy, C., Kurihara, R., Nakajima, Y., Kojima, K., Kimura-Someya, T., Leonard, G., Malmstrom, R.R., Mende, D.R., Olson, D.K., Sudo, Y., Sudek, S., Richards, T.A., DeLong, E.F., Keeling, P.J., Santoro, A.E., Shirouzu, M., Iwasaki, W., and Worden, A.Z. 2019. A distinct lineage of giant virus brings a rhodopsin photosystem to unicellular marine predators. Proc. Natl. Acad. Sci. USA, 116, 20574-20583 (PDF)

Husnik, F., and Keeling, P.J. 2019. The fate of obligate endosymbionts: reduction, integration, or extinction. Curr. Opin. Genet. Dev., 58-59, 1-8 (PDF)

Hehenberger, E., Gast, R.J., and Keeling, P.J. 2019. A kleptoplastidic dinoflagellate and the tipping point between transient and fully integrated plastid endosymbiosis. Proc. Natl. Acad. Sci. USA, 116, 17934–17942 (PDF)

Keeling, P.J., and Burki, F. 2019. Progress towards the Tree of Eukaryotes. Curr. Biol., 29, R808-R817 (PDF)

Mathur, V., Kolísko, M., Hehenberger, E., Irwin, N.A.T., Leander, B.S., Kristmundsson, Á., Freeman, M.A., and Keeling, P.J. 2019. Multiple independent origins of apicomplexan-like parasites. Curr. Biol., 29, 2936-2941 (PDF)

Gawryluk, R.M.R., Tikhonenkov, D.V., Hehenberger, E., Husnik, F., Mylnikov, A.P., and Keeling, P.J. 2019. Non-photosynthetic predators are sister to red algae. Nature, 572, 240-243 (PDF)

Boscaro, V., Husnik, F., Vannini, C., and Keeling, P.J. 2019. Symbionts of the ciliate Euplotes: diversity, patterns and potential as models for bacteria–eukaryote endosymbioses. Proc. R. Soc. B, 286, 20190693 (PDF)

del Campo, J., Pons, M.J., Herranz, M., Wakeman, K.C., del Valle, J., Vermeij, M.J.A., Leander, B.S., and Keeling, P.J. 2019. Validation of a universal set of primers to study animal-associated microeukaryotic communities. Environ. Microbiol., 21, 3855-3861 (PDF)

Van Steenkiste, N.W.L., Stephenson, I., Herranz, M., Husnik, F., Keeling, P.J., and Leander, B.S. 2019. A new case of kleptoplasty in animals: marine flatworms steal functional plastids from diatoms. Sci. Adv., 5, eaaw4337 (PDF)

Starko, S., Soto Gomez, M., Darby, H., Demes, K.W., Kawai, H., Yotsukura, N., Lindstrom, S.C., Keeling, P.J., Graham, S.W., and Martone, P.T. 2019. A comprehensive kelp phylogeny sheds light on the evolution of an ecosystem. Mol. Phylogenet. Evol., 136, 138-150 (PDF)

Deeg, C.M., Zimmer, M.M., George, E.E., Husnik, F., Keeling, P.J., and Suttle, C.A. 2019. Chromulinavorax destructans, a pathogen of microzooplankton that provides a window into the enigmatic candidate phylum Dependentiae. PLoS Pathog., 15, e1007801 (PDF)

John, U., Lu, Y., Wohlrab, S., Groth, M., Janouškovec, J., Kohli, G.S., Mark, F.C., Bickmeyer, U., Farhat, S., Felder, M., Frickenhaus, S., Guillou, L., Keeling, P.J., Moustafa, A., Porcel, B.M., Valentin, K., and Glöckner, G. 2019. An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome. Sci. Adv., 5, eaav1110 (PDF)

Kwong, W.K., del Campo, J., Mathur, V., Vermeij, M.J.A., and Keeling, P.J. 2019. A widespread coral-infecting apicomplexan with chlorophyll biosynthesis genes. Nature, 568, 103-107 (PDF)

Irwin, N.A.T., and Keeling, P.J. 2019. Extensive reduction of the nuclear pore complex in nucleomorphs. Genome Biol. Evol., 11, 678-687 (PDF)

Sakamoto, H., Hirakawa, Y., Ishida, K., Keeling, P.J., Kita, K., and Matsuzaki, M. 2019. Puromycin selection for stable transfectants of the oyster-infecting parasite Perkinsus marinus. Parasitol. Int., 69, 13-16 (PDF)

Gavelis, G.S., Herranz, M., Wakeman, K.C., Ripken, C., Mitarai, S., Gile, G.H., Keeling, P.J., and Leander, B.S. 2019. Dinoflagellate nucleus contains an extensive endomembrane network, the nuclear net. Sci. Rep., 9, 839 (PDF)

Irwin, N.A.T., Tikhonenkov, D.V., Hehenberger, E., Mylnikov, A.P., Burki, F., and Keeling, P.J. 2019. Phylogenomics supports the monophyly of the Cercozoa. Mol. Phylogenet. Evol., 130, 416-423 (PDF)

Votýpka, J., Kment, P., Kriegová, E., Vermeij, M.J.A., Keeling, P.J., Yurchenko, V., and Lukeś, J. 2019. High prevalence and endemism of trypanosomatids on a small Caribbean island. J. Eukaryot. Microbiol., 66, 600-607 (PDF)

Strassert, J.F.H., Hehenberger, E., del Campo, J., Okamoto, N., Kolisko, M., Richards, T.A., Worden, A.Z., Santoro, A.E., and Keeling, P.J. 2019. Phylogeny, evidence for a cryptic plastid, and distribution of Chytriodinium parasites (Dinophyceae) infecting copepods. J. Eukaryot. Microbiol., 66, 574-581 (PDF)

Okamoto, N., Gawryluk, R.M.R., del Campo, J., Strassert, J.F.H., Lukeś, J., Richards, T.A., Worden, A.Z., Santoro, A.E., and Keeling, P.J. 2019. A revised taxonomy of diplonemids including the Eupelagonemidae n. fam. and a type species, Eupelagonema oceanica n. gen. & sp. J. Eukaryot. Microbiol., 66, 519-524 (PDF)

Levy-Booth, D.J., Giesbrecht, I.J.W., Kellogg, C.T.E., Heger, T.J., D’Amore, D.V., Keeling, P.J., Hallam, S.J., and Mohn, W.W. 2019. Seasonal and ecohydrological regulation of active microbial populations involved in DOC, CO₂, and CH₄ fluxes in temperate rainforest soil. ISME J., 13, 950-963 (PDF)

Boscaro, V., Syberg-Olsen, M.J., Irwin, N.A.T., del Campo, J., and Keeling, P.J. 2019. What can environmental sequences tell us about the distribution of low-rank taxa? The case of Euplotes (Ciliophora, Spirotrichea), including a description of Euplotes enigma sp. nov. J. Eukaryot. Microbiol., 66, 281-293 (PDF)

2018

Vacek, V., Novák, L.V.F., Treitli, S.C., Táborský, P., Čepička, I., Kolísko, M., Keeling, P.J., and Hampl, V. 2018. Fe–S cluster assembly in oxymonads and related protists. Mol. Biol. Evol., 35, 2712-2718 (PDF)

Boscaro, V., Santoferrara, L.F., Zhang, Q., Gentekaki, E., Syberg-Olsen, M.J., del Campo, J., and Keeling, P.J. 2018. EukRef-Ciliophora: a manually curated, phylogeny-based database of small subunit rRNA gene sequences of ciliates. Environ. Microbiol., 20, 2218-2230 (PDF)

Mathur, V., del Campo, J., Kolisko, M., and Keeling, P.J. 2018. Global diversity and distribution of close relatives of apicomplexan parasites. Environ. Microbiol., 20, 2824-2833 (PDF)

Irwin, N.A.T., Martin, B.J.E., Young, B.P., Browne, M.J.G., Flaus, A., Loewen, C.J.R., Keeling, P.J., and Howe, L.J. 2018. Viral proteins as a potential driver of histone depletion in dinoflagellates. Nat. Commun., 9, 1535 (PDF)

Bass, D., Tikhonenkov, D.V., Foster, R., Dyal, P., Janouškovec, J., Keeling, P.J., Gardner, M., Neuhauser, S., Hartikainen, H., Mylnikov, A.P., and Berney, C. 2018. Rhizarian ‘Novel Clade 10’ revealed as abundant and diverse planktonic and terrestrial flagellates, including Aquavolon n. gen. J. Eukaryot. Microbiol., 65, 828-842 (PDF)

Záhonová, K., Petrželková, R., Valach, M., Yazaki, E., Tikhonenkov, D.V., Butenko, A., Janouškovec, J., Hrdá, Š., Klimeš, V., Burger, G., Inagaki, Y., Keeling, P.J., Hampl, V., Flegontov, P., Yurchenko, V., and Eliáš, M. 2018. Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPase. Sci. Rep., 8, 5239 (PDF)

Heger, T.J., Giesbrecht, I.J.W., Gustavsen, J., del Campo, J., Kellogg, C.T.E., Hoffman, K.M., Lertzman, K., Mohn, W.W., and Keeling, P.J. 2018. High-throughput environmental sequencing reveals high diversity of litter and moss associated protist communities along a gradient of drainage and tree productivity. Environ. Microbiol., 20, 1185-1203 (PDF)

Gile, G.H., James, E.R., Tai, V., Harper, J.T., Merrell, T.L., Boscaro, V., Husník, F., Scheffrahn, R.H., and Keeling, P.J. 2018. New species of Spirotrichonympha from Reticulitermes and the relationships among genera in Spirotrichonymphea (Parabasalia). J. Eukaryot. Microbiol., 65, 159-169 (PDF)

Lemay, M.A., Martone, P.T., Keeling, P.J., Burt, J.M., Krumhansl, K.A., Sanders, R.D., and Wegener Parfrey, L. 2018. Sympatric kelp species share a large portion of their surface bacterial communities. Environ. Microbiol., 20, 658-670 (PDF)

Orsi, W.D., Wilken, S., del Campo, J., Heger, T., James, E., Richards, T.A., Keeling, P.J., Worden, A.Z., and Santoro, A.E. 2018. Identifying protist consumers of photosynthetic picoeukaryotes in the surface ocean using stable isotope probing. Environ. Microbiol., 20, 815-827 (PDF)

Kaur, B., Valach, M., Peña-Diaz, P., Moreira, S., Keeling, P.J., Burger, G., Lukeš, J., and Faktorová, D. 2018. Transformation of Diplonema papillatum, the type species of the highly diverse and abundant marine microeukaryotes Diplonemida (Euglenozoa). Environ. Microbiol., 20, 1030-1040 (PDF)

del Campo, J., Kolisko, M., Boscaro, V., Santoferrara, L.F., Nenarokov, S., Massana, R., Guillou, L., Simpson, A., Berney, C., de Vargas, C., Brown, M.W, Keeling, P.J., and Wegener Parfrey, L. 2018. EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. PLoS Biol., 16, e2005849 (PDF)

Hehenberger, E., James, E.R., del Campo, J., Buckland-Nicks, J.A., Reimchen, T.E., and Keeling, P.J. 2018. Fish parasite dinoflagellates Haidadinium ichthyophilum and Piscinoodinium share a recent common ancestor. J. Eukaryot. Microbiol., 65, 127-131 (PDF)

Boscaro, V., Fokin, S.I., Petroni, G., Verni, F., Keeling, P.J., and Vannini, C. 2018. Symbiont replacement between bacteria of different classes reveals additional layers of complexity in the evolution of symbiosis in the ciliate Euplotes. Protist, 169, 43-52 (PDF)

Strassert, J.F.H., Karnkowska, A., Hehenberger, E., del Campo, J., Kolisko, M., Okamoto, N., Burki, F., Janouškovec, J., Poirier, C., Leonard, G., Hallam, S.J., Richards, T.A., Worden, A.Z., Santoro, A.E., and Keeling, P.J. 2018. Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates. ISME J.,12, 304-308 (PDF)

2017

Keeling, P.J., and McCutcheon, J.P. 2017. Endosymbiosis: the feeling is not mutual. J. Theor. Biol., 434, 75-79 (PDF)

del Campo, J., James, E.R., Hirakawa, Y., Fiorito, R., Kolisko, M., Irwin, N.A.T., Mathur, V., Boscaro, V., Hehenberger, E., Karnkowska, A., Scheffrahn, R.H., and Keeling, P.J. 2017. Pseudotrichonympha leei, Pseudotrichonympha lifesoni, and Pseudotrichonympha pearti, new species of parabasalian flagellates and the description of a rotating subcellular structure. Sci. Rep., 7, 16349 (PDF)

Janouškovec, J., Tikhonenkov, D.V., Burki, F., Howe, A.T., Rohwer, F.L., Mylnikov, A.P., and Keeling, P.J. 2017. A new lineage of eukaryotes illuminates early mitochondrial genome reduction. Curr. Biol., 27, 3717-3724 (PDF)

Gavelis, G.S., Keeling, P.J., and Leander, B.S. 2017. How exaptations facilitated photosensory evolution: seeing the light by accident. Bioessays, 39, 1600266 (PDF)

Keeling, P.J., and del Campo, J. 2017. Marine protists are not just big bacteria. Curr. Biol., 27, R541-R549 (PDF)

Hehenberger, E., Tikhonenkov, D.V., Kolisko, M., del Campo, J., Esaulov, A.S., Mylnikov, A.P., and Keeling, P.J. 2017. Novel predators reshape holozoan phylogeny and reveal the presence of a two-component signalling system in the ancestor of animals. Curr. Biol., 27, 2043-2050 (PDF)

Gavelis, G.S., Wakeman, K.C., Tillmann, U., Ripken, C., Mitarai, S., Herranz, M., Özbek, S., Holstein, T., Keeling, P.J., and Leander, B.S. 2017. Microbial arms race: ballistic “nematocysts” in dinoflagellates represent a new extreme in organelle complexity. Sci. Adv., 3, e1602552 (PDF)

Freeman, M.A., Fuss, J., Kristmundsson, Á., Bjorbækmo, M.F.M., Mangot, J.-F., del Campo, J., Keeling, P.J., Shalchian-Tabrizi, K., and Bass, D. 2017. X-cells are globally distributed, genetically divergent fish parasites related to perkinsids and dinoflagellates. Curr. Biol., 27, 1645-1651 (PDF)

Pyle, J.D., Keeling, P.J., and Nibert, M.L. 2017. Amalga-like virus infecting Antonospora locustae, a microsporidian pathogen of grasshoppers, plus related viruses associated with other arthropods. Virus Res., 233, 95-104 (PDF)

Boscaro, V., Kolisko, M., Felletti, M., Vannini, C., Lynn, D.H., and Keeling, P.J. 2017. Parallel genome reduction in symbionts descended from closely related free-living bacteria. Nat. Ecol. Evol., 1, 1160-1167 (PDF)

Boscaro, V., James, E.R., Fiorito, R., Hehenberger, E., Karnkowska, A., del Campo, J., Kolisko, M., Irwin, N.A.T., Mathur, V., Scheffrahn, R.H., and Keeling, P.J. 2017. Molecular characterization and phylogeny of four new species of the genus Trichonympha (Parabasalia, Trichonymphea) from lower termite hindguts. Int. J. Syst. Evol. Microbiol., 67, 3570-3575 (PDF)

del Campo, J., Pombert, J.-F., Šlapeta, J., Larkum, A., and Keeling, P.J. 2017. The 'other' coral symbiont: Ostreobium diversity and distribution. ISME J., 11, 296-299 (PDF)

Pan, J., del Campo, J., and Keeling, P.J. 2017. Reference tree and environmental sequence diversity of the Labyrinthulomycetes. J. Eukaryot. Microbiol., 64, 88-96 (PDF)

Keeling, P.J. 2017. Chlorarachniophytes. In: Handbook of the Protists: Second Edition, pp. 765-781. doi:10.1007/978-3-319-28149-0_34. [BOOK CHAPTER]

2016

Stentiford, G.D., Becnel, J., Weiss, L.M., Keeling, P.J., Didier, E.S., Williams, B.A.P., Bjornson, S., Kent, M.L., Freeman, M.A., Brown, M.J.F., Troemel, E.R., Roesel, K., Sokolova, Y., Snowden, K.F., and Solter, L. 2016. Microsporidia – Emergent pathogens in the global food chain. Trends Parasitol., 32, 336-348 (PDF)

Strassert, J.F.H., Tikhonekov, D.V., Pombert, J.-F., Kolisko, M., Tai, V., Mylnikov, A.P., and Keeling, P.J. 2016. Moramonas marocensis gen. nov., sp. nov.: a jakobid flagellate isolated from desert soil with a bacteria-like, but bloated mitochondrial genome. Open Biol., 6, 150239 (PDF)

Orsi, W.D., Smith, J.M., Liu, S., Liu, Z., Sakamoto, C.M., Wilken, S., Poirier, C., Richards, T.A., Keeling, P.J., Worden, A.Z., and Santoro, A.E. 2016. Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean. ISME J., 10, 2158-2173 (PDF)

Tai, V. Carpenter, K.J., Weber, P.K., Nalepa, C.A., Perlman, S.J., and Keeling, P.J. 2016. Genome evolution and nitrogen fixation in bacterial ectosymbionts of a protist inhabiting wood-feeding cockroaches. Appl. Environ. Microbiol., 82, 4682-4695 (PDF)

Keeling, P.J. 2016. Genomics: evolution of the genetic code. Curr. Biol., 26, R851-R853 (PDF)

Hehenberger, E., Burki, F., Kolisko, M., and Keeling, P.J. 2016. Functional relationship between a dinoflagellate host and its diatom endosymbiont. Mol. Biol. Evol., 33, 2376-2390 (PDF)

Janouskovec, J., and Keeling, P.J. 2016. Evolution: causality and the origin of parasitism. Curr. Biol., 26, R174-R177 (PDF)

Smith, D.R., and Keeling, P.J. 2016. Protists and the wild, wild west of gene expression: new frontiers, lawlessness, and misfits. Annu. Rev. Microbiol., 70, 161-178 (PDF)

Gawryluk, R.M.R., del Campo, J., Okamoto, N., Strassert, J.F.H., Lukeš, J., Richards, T.A., Worden, A.Z., Santoro, A.E., and Keeling, P.J. 2016. Morphological identification and single-cell genomics of marine diplonemids. Curr. Biol., 26, 3053-3059 (PDF)

Syberg-Olsen, M.J., Irwin, N.A.T., Vannini, C., Erra, F., Di Giuseppe, G., Boscaro, V., and Keeling, P.J. 2016. Biogeography and character evolution of the ciliate genus Euplotes (Spirotrichea, Euplotia), with description of Euplotes curdsi sp. nov. PLoS One, 11, e0165442 (PDF)

Novák, L., Zubáčová, Z., Karnkowska, A., Kolisko, M., Hroudová, M., Stairs, C.W., Simpson, A.G.B., Keeling, P.J., Roger, A.J., Čepička, I., and Hampl, V. 2016. Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes. BMC Evol. Biol., 16, 197 (PDF)

Burki, F., Kaplan, M., Tikhonenkov, D.V., Zlatogursky, V., Quang Minh, B., Radaykina, L.V., Smirnov, A., Mylnikov, A.P., and Keeling, P.J. 2016. Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista. Proc. R. Soc. B, 283, 20152802 (PDF)

Tikhonenkov, D.V., Janouškovec, J., Keeling, P.J., and Mylnikov, A.P. 2016. The morphology, ultrastructure and SSU rRNA gene sequence of a new freshwater flagellate, Neobodo borokensis n. sp. (Kinetoplastea, Excavata). J. Eukaryot. Microbiol., 63, 220-232 (PDF)

Keeling, P.J. 2017. The ten-minute Leeuwenhoek microscope. In: In the Company of Microbes: Ten Years of Small Things Considered, pp. 80-83. doi:10.1128/9781555819606.ch19. [BOOK CHAPTER]

2015

Keeling, P.J., McCutcheon, J.P., and Doolittle, W.F. 2015. Symbiosis becoming permanent: survival of the luckiest. Proc. Natl. Acad. Sci. USA, 112, 10101-10103 (PDF)

Gavelis, G.S., White, R.A., Suttle, C.A., Keeling, P.J., and Leander, B.S. 2015. Single-cell transcriptomics using spliced leader PCR: evidence for multiple losses of photosynthesis in polykrikoid dinoflagellates. BMC Genomics, 16, 528 (PDF)

Woo, Y.H., Ansari, H., Otto, T.D., Klinger, C.M., Kolisko, M., Michálek, J., Saxena, A., Shanmugam, D., Tayyrov, A., Veluchamy, A., Ali, S., Bernal, A., del Campo, J., Cihlář, J., Flegontov, P., Gornik, S.G., Hajdušková, E., Horák, A., Janouškovec, J., Katris, N.J., Mast, F.D., Miranda-Saavedra, D., Mourier, T., Naeem, R., Nair, M., Panigrahi, A.K., Rawlings, N.D., Padron-Regalado, E., Ramaprasad, A., Samad, N., Tomčala, A., Wilkes, J., Neafsey, D.E., Doerig, C., Bowler, C., Keeling, P.J., Roos, D.S., Dacks, J.B., Templeton, T.J., Waller, R.F., Lukeš, J., Oborník, M., and Pain, A. 2015. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. eLife, 4, e06974 (PDF)

Gavelis, G.S., Hayakawa, S., White, R.A., Gojobori, T., Suttle, C.A., Keeling, P.J., and Leander, B.S. 2015. Eye-like ocelloids are built from different endosymbiotically acquired components. Nature, 523, 204-207 (PDF)

Gile, G.H., James, E.R., Okamoto, N., Carpenter, K.J., Scheffrahn, R.H., and Keeling, P.J. 2015. Molecular evidence for the polyphyly of Macrotrichomonas (Parabasalia: Cristamonadea) and a proposal for Macrotrichomonoides n. gen. J. Eukaryot. Microbiol., 62, 494-504 (PDF)

Flegontov, P., Michálek, J., Janouškovec, J., Lai, D.-H., Jirků, M., Hajdušková, E., Tomčala, A., Otto, T.D., Keeling, P.J., Pain, A., Oborník, M., and Lukeš, J. 2015. Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites. Mol. Biol. Evol., 32, 1115-1131 (PDF)

Smith, D.R., and Keeling, P.J. 2015. Mitochondrial and plastid genome architecture: reoccurring themes, but significant differences at the extremes. Proc. Natl. Acad. Sci. USA, 112, 10177-10184 (PDF)

Janouškovec, J., Tikhonenhov, D.V., Burki, F., Howe, A.T., Kolisko, M., Mylnikov, A.P., and Keeling, P.J. 2015. Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives. Proc. Natl. Acad. Sci. USA, 112, 10200-10207 (PDF)

Pombert, J.-F., Haag, K.L. Beidas, S., Ebert, D., and Keeling, P.J. 2015. The Ordospora colligata genome: evolution of extreme reduction in microsporidia and host-to-parasite horizontal gene transfer. mBio, 6, e02400-14 (PDF)

Tai, V., James, E.R., Nalepa, C.A., Scheffrahn, R.H., Perlman, S.J., and Keeling, P.J. 2015. The role of host phylogeny varies in shaping microbial diversity in the hindguts of lower termites. Appl. Environ. Microbiol., 81, 1059-1070 (PDF)

Tai, V., Gile, G.H., Pan, J., James, E.R., Carpenter, K.J., Scheffrahn, R.H., and Keeling, P.J. 2015. The phylogenetic position of Kofoidia loriculata (Parabasalia) and its implications on the evolution of the Cristamonadea. J. Eukaryot. Microbiol., 62, 255-259 (PDF)

Worden, A.Z., Follows, M.J., Giovannoni, S.J., Wilken, S., Zimmerman, A.E., and Keeling, P.J. 2015. Rethinking the marine carbon cycle: factoring in mutifarious lifestyles of microbes. Science, 347, 1257594 (PDF)

Keeling, P.J., and Rayner, J.C. 2015. The origins of malaria: there are more things in heaven and earth... Parasitology, 142, S16-S25 (PDF)

2014

Mikhailov, K.V., Janouškovec, J., Tikhonenkov, D.V., Mirzaeva, G.S., Diakin, A.Y., Simdyanov, T.G., Mylnikov, A.P., Keeling, P.J., and Aleoshin, V.V. 2014. A complex distribution of elongation family GTPases EF1A and EFL in basal alveolate lineages. Genome Biol. Evol., 6, 2361-2367 (PDF)

Keeling, P.J., Fast, N.M., and Corradi, N. 2014. Microsporidian genome structure and function. In: Microsporidia: Pathogens of Opportunity, pp. 221-229. doi:10.1002/9781118395264.ch7. [BOOK CHAPTER]

Keeling, P.J. 2014. Phylogenetic place of Microsporidia in the Tree of Eukaryotes. In: Microsporidia: Pathogens of Opportunity, pp. 195-202. doi:10.1002/9781118395264.ch5. [BOOK CHAPTER]

Okamoto, N., and Keeling, P.J. 2014. A comparative overview of the flagellar apparatus of dinoflagellate, perkinsids, and colpodellids. Microorganisms, 2, 73-91 (PDF)

Hehenberger, E., Imanian, B., Burki, F., and Keeling, P.J. 2014. Evidence for the retention of two evolutionary distinct plastids in dinoflagellates with diatom endosymbionts. Genome Biol. Evol., 6, 2321-2334 (PDF)

Kolisko, M., Boscaro, V., Burki, F., Lynn, D.H., and Keeling, P.J. 2014. Single-cell transcriptomics for microbial eukaryotes. Curr. Biol., 24, R1081-R1082 (PDF)

Burki, F., Imanian, B., Hehenberger, E., Hirakawa, Y., Maruyama, S., and Keeling, P.J. 2014. Endosymbiotic gene transfer in tertiary plastid-containing dinoflagellates. Eukaryot. Cell, 13, 246-255 (PDF)

Imanian, B., and Keeling, P.J. 2014. Horizontal gene transfer and redundancy of tryptophan biosynthetic enzymes in dinotoms. Genome Biol. Evol., 6, 333-343 (PDF)

Tikhonenkov, D.V., Janouškovec, J., Mylnikov, A.P., Mikhailov, K.V., Simdyanov, T.G., Aleoshin, V.V., and Keeling, P.J. 2014. Description of Colponema vietnamica sp. n. and Acavomonas peruviana n. gen. n. sp., two new alveolate phyla (Colponemidia nom. nov. and Acavomonidia nom. nov.) and their contributions to reconstructing the ancestral state of alveolates and eukaryotes. PLoS One, 9, e95467 (PDF)

McCutcheon, J.P., and Keeling, P.J. 2014. Endosymbiosis: protein targeting further erodes the organelle/symbiont distinction. Curr. Biol., 24, R654-R655 (PDF)

Lee, R., Lai, H., Malik, S.B., Saldarriaga, J.F., Keeling, P.J., and Slamovits, C.H. 2014. Analysis of EST data of the marine protist Oxyrrhis marina, an emerging model for alveolate biology and evolution. BMC Genomics, 15, 122 (PDF)

del Campo, J., Sieracki, M.E., Molestina, R., Keeling, P.J., Massana, R., and Ruiz-Trilo, I. 2014. The others: our biased perspective of eukaryotic genomes. Trends Ecol. Evol., 29, 252-259 (PDF)

Pombert, J.-F., Blouin, N.A., Lane, C., Boucias, D., and Keeling, P.J. 2014. A lack of parasitic reduction in the obligate parasitic green alga Helicosporidium. PLoS Genet., 10, e1004355 (PDF)

Hirakawa, Y., Suzuki, S., Archibald, J.M., Keeling, P.J., and Ishida, K. 2014. Overexpression of molecular chaperone genes in nucleomorph genomes. Mol. Biol. Evol., 31, 1437-1443 (PDF)

Keeling, P.J., Burki, F., Wilcox, H.M., Allam, B., Allen, E.E., Amaral-Zettler, L.A., Armbrust, E.V., Archibald, J.M., Bharti, A.K., Bell, C.J., Beszteri, B., Bidle, K.D., Cameron, C.T., Campbell, L., Caron, D.A., Cattolico, R.A., Collier, J.L., Coyne, K., Davy, S.K., Deschamps, P., Dyhrman, S.T., Edvardsen, B., Gates, R.D., Gobler, C.J., Greenwood, S.J., Guida, S.M., Jacobi, J.L., Jakobsen, K.S., James, E.R., Jenkins, B., John, U., Johnson, M.D., Juhl, A.R., Kamp, A., Katz, L.A., Kiene, R., Kudryavtsev, A., Leander, B.S., Lin, S., Lovejoy, C., Lynn, D., Marchetti, A., McManus, G., Nedelcu, A.M., Menden-Deuer, S., Miceli, C., Mock, T., Montresor, M., Moran M.A., Murray, S., Nadathur, G., Nagai, S., Ngam, P.B., Palenik, B., Pawlowski, J., Petroni, G., Piganeau, G., Posewitz, M.C., Rengefors, K., Romano, G., Rumpho, M.E., Rynearson, T., Schilling, K.B., Schroeder, D.C., Simpson, A.G.B., Slamovits, C.H., Smith, D.R., Smith, G.J., Smith, S.R., Sosik, H.M., Stief, P., Theriot, E., Twary, S.N., Umale, P.E., Vaulot, D., Wawrik, B., Wheeler, G.L., Wilson, W.H., Xu, Y., Zingone, A., and Worden, A.Z. 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol., 12, e1001889 (PDF)

Burki, F., and Keeling, P.J. 2014. Rhizaria. Curr. Biol., 24, R103-R107 (PDF)

Okamoto, N., and Keeling, P.J. 2014. The 3D structure of the apical complex and association with the flagellar apparatus revealed by serial TEM tomography in Psammosa pacifica, a distant relative of the Apicomplexa. PLoS One, 9, e84653 (PDF)

Keeling, P.J. 2014. The impact of history on our perception of evolutionary events: endosymbiosis and the origins of eukaryotic complexity. Cold Spring Harb. Perspect. Biol., 6, a016196 (PDF)

2013

Pombert, J.-F., Janouškovec, J., Smirnov, A., Gray, M.W., James, E.R., and Keeling, P.J. 2013. The complete mitochondrial genome from an unidentified Phalansterium species. Protist Genomics, 2, 25-32 (PDF)

Janouškovec, J., Tikhonenkov, D.V., Mikhailov, K.V., Simdyanov, T.G., Aleoshin, V.V., Mylnikov, A.P., and Keeling, P.J. 2013. Colponemids represent multiple ancient alveolate lineages. Curr. Biol., 23, 2546-2552 (PDF)

Burki, F., Corradi, N., Sierra, R., Pawlowski, J., Meyer, G.R., Abbott, C.L., and Keeling, P.J. 2013. Phylogenomics of the intracellular parasite Mikrocytos mackini reveals evidence for a mitosome in Rhizaria. Curr. Biol., 23, 1541-1547 (PDF)

Corradi, N., and Keeling, P.J. 2013. Ecological genomics of the Microsporidia. In: The Ecological Genomics of Fungi, pp. 261-278. doi:10.1002/9781118735893.ch2. [BOOK CHAPTER]

Janouškovec, J., Sobotka, R., Lai, D.-H., Flegontov, P., Koník, P., Komenda, J., Ali, S., Prášil, O., Pain, A., Oborník, M., Lukeš, J., and Keeling, P.J. 2013. Split photosystem protein, linear-mapping topology, and growth of structural complexity in the plastid genome of Chromera velia. Mol. Biol. Evol., 30, 2447-2462 (PDF)

James, E.R., Tai, V., Scheffrahn, R.H., and Keeling, P.J. 2013. Trichonympha burlesquei n. sp. from Reticulitermes virginicus and evidence against a cosmopolitan distribution of Trichonympha agilis in many termite hosts. Int. J. Syst. Evol. Microbiol., 63, 3873-3876 (PDF)

Carpenter, K.J., Weber, P.K., Davisson, M.L., Pett-Ridge, J., Haverty, M.I., and Keeling, P.J. 2013. Correlated SEM, FIB-SEM, TEM, and NanoSIMS imaging of microbes from the hindgut of a lower termite: methods for in situ functional and ecological studies of uncultivable microbes. Microsc. Microanal., 19, 1490-1501 (PDF)

Gile, G.H., Carpenter, K.J., James, E.R., Scheffrahn, R.H., and Keeling, P.J. 2013. Morphology and molecular phylogeny of Staurojoenina mulleri sp. nov. (Trichonymphida, Parabasalia) from the hindgut of the kalotermitid Neotermes jouteli. J. Eukaryot. Microbiol., 60, 203-213 (PDF)

Janouškovec, J., Liu, S.-H., Martone, P.T., Carré, W., Leblanc, C., Collén, J., and Keeling, P.J. 2013. Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers. PLoS One, 8, e59001 (PDF)

Tai, V., James, E.R., Perlman, S.J., and Keeling, P.J. 2013. Single-cell DNA barcoding using sequences from the small subunit rRNA and internal transcribed spacer region identifies new species of Trichonympha and Trichomitopsis from the hindgut of the termite Zootermopsis angusticollis. PLoS One, 8, e58728 (PDF)

James, E.R., Okamoto, N., Burki, F., Scheffrahn, R.H., and Keeling, P.J. 2013. Cthulhu macrofasciculumque n. g., n. sp. and Cthylla microfasciculumque n. g., n. sp., a newly identified lineage of parabasalian termite symbionts. PLoS One, 8, e58509 (PDF)

Smith, D.R., Hamaji, T., Olson, B.J.S.C., Durand, P.M., Ferris, P., Michod, R.E., Featherston, J., Nozaki, H., and Keeling, P.J. 2013. Organelle genome complexity scales positively with organism size in volvocine green algae. Mol. Biol. Evol., 30, 793-797 (PDF)

Pan, G., Xu, J., Li, T., Xia, Q., Liu, S.-L., Zhang, G., Li, S., Li, C., Liu, H., Yang, L., Liu, T., Zhang, X., Wu, Z., Fan, W., Dang, X., Xiang, H., Tao, M., Li, Y., Hu, J., Li, Z., Lin, L., Lou, J., Geng, L., Wang, L., Long, M., Wan, Y., He, N., Zhang, Z., Lu, C., Keeling, P.J., Wang, J., Xiang, Z., and Zhou, Z. 2013. Comparative genomics of parasitic silkworm microsporidia reveal an association between genome expansion and host adaptation. BMC Genomics, 14, 186 (PDF)

Pombert, J.-F., Xu, J., Smith, D.R., Heiman, D., Young, S., Cuomo, C.A., Weiss, L.M., and Keeling, P.J. 2013. Complete genome sequences from three genetically distinct strains reveal high intraspecies genetic diversity in the microsporidian Encephalitozoon cuniculi. Eukaryot. Cell, 12, 503-511 (PDF)

James, E.R., Burki, F., Harper, J.T., Scheffrahn, R.H., and Keeling, P.J. 2013. Molecular characterization of parabasalian symbionts Coronympha clevelandii and Trichonympha subquasilla from the Hawaiian lowland tree termite Incisitermes immigrans. J. Eukaryot. Microbiol., 60, 313-316 (PDF)

Keeling, P.J. 2013. The number, speed, and impact of plastid endosymbioses in eukaryotic evolution. Annu. Rev. Plant Biol., 64, 583-607 (PDF)

Smith, D.R., and Keeling, P.J. 2013. Gene conversion shapes linear mitochondrial genome architecture. Genome Biol. Evol., 5, 905-912 (PDF)

Tai, V., and Keeling, P.J. 2013. Termite hindguts and the ecology of microbial communities in the sequencing age. J. Eukaryot. Microbiol., 60, 421-428 (PDF)

Janouškovec, J., Horák, A., Barott, K.L., Rohwer, F.L., and Keeling, P.J. 2013. Environmental distribution of coral-associated relatives of apicomplexan parasites. ISME J., 7, 444-447 (PDF)

Keeling, P.J. 2013. Elephants in the room: protists and the importance of morphology and behaviour. Environ. Microbiol. Rep., 5, 5-6 [Special issue, "Crystal Ball - 2013"] (PDF)

2012

Imanian, B., Pombert. J.-F., Dorrell, R.G., and Keeling, P.J. 2012. Tertiary endosymbiosis in two dinotoms has generated little change in the mitochondrial genomes of their dinoflagellate hosts and diatom endosymbionts. PLoS One, 7, e43763 (PDF)

Hirakawa, Y., Burki, F., and Keeling, P.J. 2012. Dual targeting of aminoacyl-tRNA synthetases to the mitochondrion and complex plastid in chlorarachniophytes. J. Cell Sci., 125, 6176-6184 (PDF)

Pawlowski, J., Audic, S., Adl, S., Bass, D., Belbahri, L., Berney, C., Bowser, S.S., Cepicka, I., Decelle, J., Dunthorn, M., Fiore-Donno, A.M., Gile, G.H., Holzmann, M., Jahn, R., Jirků, M., Keeling, P.J., Kostka, M., Kudryavtsev, A., Lara, E., Lukeš, J., Mann, D.G., Mitchell, E.A.D., Nitsche, F., Romeralo, M., Saunders, G.W., Simpson, A.G.B., Smirnov, A.V., Spouge, J.L., Stern, R.F., Stoeck, T., Zimmermann, J., Schindel, D., and de Vargas, C. 2012. CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol., 10, e1001419 (PDF)

Curtis, B.A., Tanifuji, G., Burki, F., Gruber, A., Irimia, M., Maruyama, S., Arias, M.C., Ball, S.G., Gile, G.H., Hirakawa, Y., Hopkins, J.F., Kuo, A., Rensing, S.A., Schmutz, J., Symeonidi, A., Elias, M., Eveleigh, R.J.M., Herman, E.K., Klute, M.J., Nakayama, T., Oborník, M., Reyes-Prieto, A., Armbrust, E.V., Aves, S.J., Beiko, R.G., Coutinho, P., Dacks, J.B., Durnford, D.G., Fast, N.M., Green, B.R., Grisdale, C.J., Hempel, F., Henrissat, B., Höppner, M.P., Ishida, K., Kim, E., Kořený, L., Kroth, P.G., Liu, Y., Malik, S.-B., Maier, U.G., McRose, D., Mock, T., Neilson, J.A.D., Onodera, N.T., Poole, A.M., Pritham, E.J., Richards, T.A., Rocap, G., Roy, S.W., Sarai, C., Schaack, S., Shirato, S., Slamovits, C.H., Spencer, D.F., Suzuki, S., Worden, A.Z., Zauner, S., Barry, K., Bell, C., Bharti, A.K., Crow, J.A., Grimwood, J., Kramer, R., Lindquist, E., Lucas, S., Salamov, A., McFadden, G.I., Lane, C.E., Keeling, P.J., Gray, M.W., Grigoriev, I.V., and Archibald, J.M. 2012. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature, 492, 59-65 (PDF)

Stern, R.F., Andersen, R.A., Jameson, I. Küpper, F.C., Coffroth, M.-A., Vaulot, D., Le Gall, F., Véron, B., Brand, J.J., Skelton, H., Kasai, F., Lilly, E.L., and Keeling, P.J. 2012. Evaluating the ribosomal Internal Transcribed Spacer (ITS) as a candidate dinoflagellate barcode marker. PLoS One, 7, e42780 (PDF)

Smith, D.R., Hua, J., Lee, R.W., and Keeling, P.J. 2012. Relative rates of evolution among the three genetic compartments of the red alga Porphyra differ from those of green plants and do not correlate with genome architecture. Mol. Phylogenet. Evol., 65, 339-344 (PDF)

Pombert, J.-F., Selman, M., Burki, F., Bardell, F.T., Farinelli, L., Solter, L.F., Whitman, D.W., Weiss, L.M., Corradi, N., and Keeling, P.J. 2012. Gain and loss of multiple functionally related, horizontally transferred genes in the reduced genomes of two microsporidian parasites. Proc. Natl. Acad. Sci. USA, 109, 12638-12643 (PDF)

Worden, A.Z., Janouskovec, J., McRose, D., Engman, A., Welsh, R.M., Malfatti, S., Tringe, S.G., and Keeling, P.J. 2012. Global distribution of a wild alga revealed by targeted metagenomics. Curr. Biol., 22, R675–R677 (PDF)

Pombert, J.-F., James, E.R., Janouškovec, J., and Keeling, P.J. 2012. Evidence for transitional stages in the evolution of euglenid group II introns and twintrons in the Monomorphina aenigmatica plastid genome. PLoS One, 7, e53433 (PDF)

Burki, F., Hirakawa, Y., and Keeling, P.J. 2012. Intragenomic spread of plastid-targeting presequences in the coccolithophore Emiliania huxleyi. Mol. Biol. Evol., 29, 2109-2112 (PDF)

Janouškovec, J., Horák, A., Barott, K.L., Rohwer, F.L., and Keeling, P.J. 2012. Global analysis of plastid diversity reveals apicomplexan-related lineages in coral reefs. Curr. Biol., 22, R518–R519 (PDF)

Hirakawa, Y., Burki, F., and Keeling, P.J. 2012. Genome-based reconstruction of the protein import machinery in the secondary plastid of a chlorarachniophyte alga. Eukaryot. Cell, 11, 324-333 (PDF)

Yuan, C.L., Keeling, P.J., Krause, P.J., Horak, A., Bent, S., Rollend, L., and Hua, X.G. 2012. Colpodella spp.-like parasite infection in woman, China. Emerg. Infect. Dis., 18, 125-127 (PDF)

Smith, D.R., and Keeling, P.J. 2012. Twenty-fold difference in evolutionary rates between the mitochondrial and plastid genomes of species with secondary red plastids. J. Eukaryot. Microbiol., 59, 181-184 (PDF)

Smith, D.R., Kayal, E., Yanagihara, A.A., Collins, A.G., Pirro, S., and Keeling, P.J. 2012. First complete mitochondrial genome sequence from a box jellyfish reveals a highly fragmented linear architecture and insights into telomere evolution. Genome Biol. Evol., 4, 52-58 (PDF)

Zhao, S., Burki, F., Bråte, J., Keeling, P.J., Klaveness, D., and Shalchian-Tabrizi, K. 2012. Collodictyon – an ancient lineage in the tree of eukaryotes. Mol. Biol. Evol., 29, 1557-1568 (PDF)

Burki, F., Okamoto, N., Pombert, J.-F., and Keeling, P.J. 2012. The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins. Proc. R. Soc. B, 279, 2246-2254 (PDF)

Okamoto, N., Horák, A., and Keeling, P.J. 2012. Description of two species of early branching dinoflagellates, Psammosa pacifica n. g., n. sp. and P. atlantica n. sp. PLoS One, 7, e34900 (PDF)

Ghosh, K., Nieves, E., Keeling, P., Cali, A., and Weiss, L.M. 2012. A new vesicular compartment in Encephalitozoon cuniculi. Microb. Infect., 14, 324-328 (PDF)

Burki, F., Flegontov, P., Oborník, M., Cihlár, J., Pain, A., Lukeš, J., and Keeling, P.J. 2012. Re-evaluating the green vs. red signal in eukaryotes with secondary plastid of red algal origin. Genome Biol. Evol., 4, 626-635 (PDF)

2011

Ghosh, K., Nieves, E., Keeling, P.J., Pombert, J.-F., Henrich, P.P., Cali, A., and Weiss, L.M. 2011. Branching network of proteinaceous filaments within the parasitophorous vacuole of Encephalitozoon cuniculi and Encephalitozoon hellem. Infect. Immun., 79, 1374-1385 (PDF)

Smith, D.R., Burki, F., Yamada, T., Grimwood, J., Grigoriev, I.V., Van Etten, J.L., and Keeling, P.J. 2011. The GC-rich mitochondrial and plastid genomes of the green alga Coccomyxa give insight into the evolution of organelle DNA nucleotide landscape. PLoS One, 6, e23624 (PDF)

Fernández Robledo, J.A., Caler, E., Matsuzaki, M., Keeling, P.J., Shanmugam, D., Roos, D.S., and Vasta, G.R. 2011. The search for the missing link: a relic plastid in Perkinsus? Int. J. Parasitol., 41, 1217-1229 (PDF)

Gile, G.H., James, E.R., Scheffrahn, R.H., Carpenter, K.J., Harper, J.T., and Keeling, P.J. 2011. Molecular and morphological analysis of the family Calonymphidae with a description of Calonympha chia sp. nov., Snyderella kirbyi sp. nov., Snyderella swezyae sp. nov. and Snyderella yamini sp. nov. Int. J. Syst. Evol. Microbiol., 61, 2547-2558 (PDF)

Saldarriaga, J.F., Gile, G.H., James, E.R., Horák, A., Scheffrahan, R.H., and Keeling, P.J. 2011. Morphology and molecular phylogeny of Pseudotrichonympha hertwigi and Pseudotrichonympha paulistana (Trichonymphea, Parabasalia) from neotropical rhinotermitids. J. Eukaryot. Microbiol., 58, 487-496 (PDF)

Barott, K.L., Rodriguez-Brito, B., Janouškovec, J., Marhaver, K.L., Smith, J.E., Keeling, P., and Rohwer, F.L. 2011. Microbial diversity associated with four functional groups of benthic reef algae and the reef-building coral Montastraea annularis. Environ. Microbiol., 13, 1192-1204 (PDF)

Selman, M., Pombert, J.-F., Solter, L., Farinelli, L., Weiss, L.M., Keeling, P., and Corradi, N. 2011. Acquisition of an animal gene by microsporidian intracellular parasites. Curr. Biol., 21, R576-577 (PDF)

Carpenter, K.J., Horak, A., Chow, L., and Keeling, P.J. 2011. Symbiosis, morphology, and phylogeny of Hoplonymphidae (Parabasalia) of the wood-feeding roach Cryptocercus punctulatus. J. Eukaryot. Microbiol., 58, 426-436 (PDF)

Kořený, L., Sobotka, R., Janouškovec, J., Keeling, P.J., and Oborník, M. 2011. Tetrapyrrole synthesis of photosynthetic chromerids is likely homologous to the unusual pathway of apicomplexan parasites. Plant Cell, 23, 3454-3462 (PDF)

Hirakawa, Y., Burki, F., and Keeling, P.J. 2011. Nucleus- and nucleomorph-targeted histone proteins in a chlorarachniophyte alga. Mol. Microbiol., 80, 1439-1449 (PDF)

Hirakawa, Y., Howe, A., James, E.R., and Keeling, P.J. 2011. Morphological diversity between culture strains of a chlorarachniophyte, Lotharella globosa. PLoS One, 6, e23193 (PDF)

Botté, C.Y., Yamaryo-Botté, Y., Janouškovec, J., Rupasinghe, T., Keeling, P.J., Crellin, P., Coppel, R.L., Maréchal, E., McConville, M.J., and McFadden, G.I. 2011. Identification of plant-like galactolipids in Chromera velia, a photosynthetic relative of malaria parasites. J. Biol. Chem., 286, 29893-29903 (PDF)

Doolittle, W.F., Lukeš, J., Archibald, J.M., Keeling, P.J., and Gray, M.W. 2011. Comment on "Does constructive neutral evolution play an important role in the origin of cellular complexity?". Bioessays, 33, 427-429 (PDF)

Lukeš, J., Archibald, J.M., Keeling, P.J., Doolittle, W.F., and Gray, M.W. 2011. How a neutral evolutionary ratchet can build cellular complexity. IUMBM Life, 63, 528-537 (PDF)

Keeling, P.J. 2011. Endosymbiosis: bacteria sharing the load. Curr. Biol., 21, R623-R624 (PDF)

Keeling, P.J., and Corradi, N. 2011. Shrink it or lose it: balancing loss of function with shrinking genomes in the microsporidia. Virulence, 2, 67-70 (PDF)

Slamovits, C.H., Okamoto, N., Burri, L., James, E.R., and Keeling, P.J. 2011. A bacterial proteorhodopsin proton pump in marine eukaryotes. Nat. Commun., 2, 183 (PDF)

Lowe, C.D., Keeling, P.J., Martin, L.E., Slamovits, C.H., Watts, P.C., Montagnes, D.J.S. 2011. Who is Oxyrrhis marina? Morphological and phylogenetic studies of an unusual dinoflagellate. J. Plankton Res., 33, 555-567 (PDF)

Slamovits, C.H., and Keeling, P.J. 2011. Contributions of Oxyrrhis marina to molecular biology, genomics, and organelle evolution of dinoflagellates. J. Plankton Res., 33, 591-602 (PDF)

Montagnes, D.J.S., Lowe, C.D., Roberts, E.C., Breckels, M.N., Boakes, D.E., Davidson, K., Keeling, P.J., Slamovits, C.H., Steinke, M., Yang, Z., and Watts, P.C. 2011. An introduction to the special issue: Oxyrrhis marina, a model organism? J. Plankton Res., 33, 549-554 (PDF)

Oborník, M., Vancová, M. Lai, D.-H., Janouškovec, J., Keeling, P.J., and Lukeš, J. 2011. Morphology and ultrastructure of multiple life cycle stages of the photosynthetic relative of Apicomplexa, Chromera velia. Protist, 162, 115-130 (PDF)

Williams, B.A.P., and Keeling, P.J. 2011. Microsporidia - highly reduced and derived relatives of Fungi. In: The Mycota, Volume XIV: Evolution of Fungi and Fungal-Like Organisms, pp. 25-36. [BOOK CHAPTER] (PDF)

2010

Burki, F., Kudryavtsev, A., Matz, M.V., Aglyamova, G.V., Bulman, S., Fiers, M., Keeling, P.J., and Pawlowski, J. 2010. Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists. BMC Evol. Biol., 10, 377 (PDF)

Cocquyt, E., Gile, G.H., Leliaert, F., Verbruggen, H., Keeling, P.J., and De Clerck, O. 2010. Complex phylogenetic distribution of a non-canonical genetic code in green algae. BMC Evol. Biol, 10, 327 (PDF)

Gray, M.W., Lukeš, J., Archibald, J.M., Keeling, P.J., and Doolittle, W.F. 2010. Irremediable complexity? Science, 330, 920-921 (PDF)

Hirakawa, Y., Gile, G.H., Ota, S., Keeling, P.J., and Ishida, K. 2010. Characterization of periplastidal compartment-targeting signals in chlorarachniophytes. Mol. Biol. Evol., 27, 1538-1545 (PDF)

Stern, R.F., Horak, A., Andrew, R.L., Coffroth, M.-A., Andersen, R.A., Küpper, F.C., Jameson, I., Hoppenrath, M., Véron, B., Kasai, F., Brand, J., James, E.R., and Keeling, P.J. 2010. Environmental barcoding reveals massive dinoflagellate diversity in marine environments. Plos One, 5, e13991 (PDF)

Corradi, N., Pombert, J.-F., Farinelli, L., Didier, E.S., and Keeling, P.J. 2010. The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis. Nat. Commun., 1, 77 (PDF)

Lee, S.C., Corradi, N., Doan, S., Dietrich, F.S., Keeling, P.J., and Heitman, J. 2010. Evolution of the sex-related locus and genomic features shared in Microsporidia and Fungi. Plos. One, 5, e10539 (PDF)

Imanian, B., Pombert, J.-F., and Keeling, P.J. 2010. The complete plastid genomes of the two ‘dinotoms’ Durinskia baltica and Kryptoperidinium foliaceum. Plos One, 5, e10711 (PDF)

Gile, G.H., Stern, R.F., James, E.R., and Keeling, P.J. 2010. DNA barcoding of chlorarachniophytes using nucleomorph ITS sequences. J. Phycol., 46, 743-750 (PDF)

Keeling, P.J., Corradi, N., Morrison, H.G., Haag, K.L., Ebert, D., Weiss, L.M., Akiyoshi, D.E., and Tzipori, S. 2010. The reduced genome of the parasitic microsporidian Enterocytozoon bieneusi lacks genes for core carbon metabolism. Genome Biol. Evol., 2, 304-309 (PDF)

Janouškovec, J., Horák, A., Obornik, M., Lukeš, J., and Keeling, P.J. 2010. A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids. Proc. Natl. Acad. Sci. USA, 107, 10949-10954 (PDF)

Williams, B.A., Elliot, C., Burri, L., Kido, Y., Kita, K., Moore, A.L., and Keeling, P.J. 2010. A broad distribution of the alternative oxidase in microsporidian parasites. PLoS Pathog., 6, e1000761 (PDF)

Gill, E.E., Lee, R.C.H., Corradi, N., Grisdale, C.J., Limpright, V.O., Keeling P.J., and Fast, N.M. 2010. Splicing and transcription differ between spore and intracellular life stages in the parasitic Microsporidia. Mol. Biol. Evol., 27, 1579-1584 (PDF)

Pombert J.-F., and Keeling, P.J. 2010. The mitochondrial genome of the entomoparasitic green alga Helicosporidium. PLoS One, 5, e8954 (PDF)

Keeling, P.J., Leander, B.S., and Lukeš, J. 2010. Reply to Speijer: Does complexity necessarily arise from selective advantange? Proc. Natl. Acad. Sci. USA, 107, E26 (PDF)

Keeling, P.J. 2010. The endosymbiotic origin, diversification and fate of plastids. Phil. Trans. R. Soc. B, 365, 729-748 (PDF)

Carpenter, K.J., Horak, A., and Keeling, P.J. 2010. Phylogenetic position and morphology of Spirotrichosomidae (Parabasalia): new evidence from Leptospironympha of Cryptocercus punctulatus. Protist, 161, 122-132 (PDF)

2009

Corradi, N., Haag, K.L., Pombert, J.-F., Ebert, D., and Keeling, P.J. 2009. Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions. Genome Biol., 10, R106 (PDF)

Keeling, P.J. 2009. A 1673 view of the microscopic universe. Make, 20, 125-128 (PDF)

Burki, F., Inagaki, I., Bråte, J., Archibald, J.M., Keeling, P.J., Cavalier-Smith, T., Sakaguchi, M., Hashimoto, T., Horak, A., Kumar, S., Klaveness, D., Jokobsen, K.S., Pawlowski, J., and Shalchian-Tabrizi, K. 2009. Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, Telonemia and Centroheliozoa, are related to photosynthetic chromalveolates. Genome Biol. Evol., 1, 231-238 (PDF)

Keeling, P.J. 2009. Five questions about Microsporidia. PLoS Pathog., 5, e1000489 (PDF)

Corradi, N., and Keeling, P.J. 2009. Microsporidia: a journey through radical taxonomic revisions. Fungal Biol. Rev., 23, 1-8 (PDF)

Keeling, P.J. 2009. Functional and ecological impacts of horizontal gene transfer in eukaryotes. Curr. Opin. Genet. Dev., 19, 613-619 (PDF)

Keeling, P.J. 2009. Creationists made me do it. Science, 325, 945 (PDF)

Redhead, S.A., Kirk, P.M., Keeling, P.J., and Weiss, L.M. 2009. (048-051) Proposals to exclude the phylum Microsporidia from the Code. Taxon, 58, 658-672 (PDF)

Redhead, S.A., Kirk, P.M., Keeling, P.J., and Weiss, L.M. 2009. Proposals 048-051 to amend the International Code of Botanical Nomenclature. Mycotaxon, 108, 505-507 (PDF)

Elias, M., Patron, N.J., and Keeling, P.J. 2009. The RAB family GTPase Rab1A from Plasmodium falciparum defines a unique paralog shared by chromalveolates and Rhizaria. J. Eukaryot. Microbiol., 56, 348-356 (PDF)

Okamoto, N., Chantangsi, C., Horák, A., Leander, B.S., and Keeling, P.J. 2009. Molecular phylogeny and description of the novel katablepharid Roombia truncata gen. et sp. nov., and establishment of the Hacrobia taxon nov. PLoS One, 4, e7080 (PDF)

Gile, G.H., Novis, P.M., Cragg, D.S., Zuccarello, G.C., and Keeling, P.J. 2009. The distribution of Elongation Factor-1 alpha (EF-1⍺), Elongation Factor-Like (EFL), and a non- canonical genetic code in the Ulvophyceae: discrete genetic characters support a consistent phylogenetic framework. J. Eukaryot. Microbiol., 56, 367-372 (PDF)

Lukeš, J., Leander, B.S., and Keeling, P.J. 2009. Cascades of convergent evolution: the corresponding evolutionary histories of euglenozoans and dinoflagellates. Proc. Natl. Acad. Sci. USA, 106, 9963-9970 (PDF)

Harper, J.T., Gile, G.H., James, E.R., Carpenter, K.J., and Keeling, P.J. 2009. The inadequacy of morphology for species and genus delineation in microbial eukaryotes: an example from the parabasalian termite symbiont Coronympha. PLoS One, 4, e6577 (PDF)

Slamovits, C.H., and Keeling, P.J. 2009. Evolution of ultrasmall spliceosomal introns in highly reduced nuclear genomes. Mol. Biol. Evol., 26, 1699-1705 (PDF)

Carpenter, K.J., Chow, L., and Keeling, P.J. 2009. Morphology, phylogeny, and diversity of Trichonympha (Parabasalia: Hypermastigida) of the wood-feeding cockroach Cryptocercus punctulatus. J. Eukaryot. Microbiol., 56, 305-313 (PDF)

Gile, G.H., Faktorová, D., Castlejohn, C.A., Burger, G., Lang, B.F., Farmer, M.A., Lukeš, J., and Keeling, P.J. 2009. Distribution and phylogeny of EFL and EF-1⍺ in Euglenozoa suggest ancestral co-occurrence followed by differential loss. PLoS One, 4, e5162 (PDF)

Keeling, P.J. 2009. Role of horizontal gene transfer in the evolution of photosynthetic eukaryotes and their plastids. In: Horizontal Gene Transfer: Genomes in Flux, pp. 501-515. doi:10.1007/978-1-60327-853-9_29. [BOOK CHAPTER] (PDF)

Akiyoshi, D.E., Morrison, H.G., Lei, S., Feng, X., Zhang, Q., Corradi, N., Mayanja, H., Tumwine, J.K., Keeling, P.J., Weiss, L.M., Tzipori, S. 2009. Genomic survey of the non-cultivatable opportunistic human pathogen, Enterocytozoon bieneusi. PLoS Pathog., 5, e1000261 (PDF)

Keeling, P.J. 2009. Chromalveolates and the evolution of plastids by secondary endosymbiosis. J. Eukaryot. Microbiol., 56, 1-8 (PDF)

2008

Lee, R.C.H., Williams, B.A.P., Brown, A.M.V., Adamson, M.L., Keeling, P.J., and Fast, N.M. 2008. ⍺- and β-tubulin phylogenies support a close relationship between the microsporidia Brachiola algerae and Antonospora locustae. J. Eukaryot. Microbiol., 55, 388-392 (PDF)

Williams, B.A.P., Lee, R.C.H., Becnel, J.J., Weiss, L.M., Fast, N.M., and Keeling, P.J. 2008. Genome sequence surveys of Brachiola algerae and Edhazardia aedis reveal microsporidia with low gene densities. BMC Genomics, 9, 200 (PDF)

Corradi, N., Burri, L., and Keeling, P.J. 2008. mRNA processing in Antonospora locustae spores. Mol. Genet. Genom., 280, 565-574 (PDF)

Lee, S.C., Corradi, N., Byrnes, E.J., Torres-Martinez, S., Dietrich, F.S., Keeling, P.J., and Heitman, J. 2008. Microsporidia evolved from ancestral sexual fungi. Curr. Biol., 18, 1675-1679 (PDF)

Keeling, P.J., and Archibald, J.M. 2008. Organelle evolution: what's in a name? Curr. Biol., 18, R345-R347 (PDF)

McEwan, M., Humayun, R., Slamovits, C.H., and Keeling, P.J. 2008. Nuclear genome sequence survey of the dinoflagellate Heterocapsa triquetra. J. Eukaryot. Microbiol., 55, 530-535 (PDF)

Gile, G.H., and Keeling, P.J. 2008. Nucleus-encoded periplastid-targeted EFL in chlorarachniophytes. Mol. Biol. Evol., 25, 1967-1977 (PDF)

Keeling, P.J., and Palmer, J.D. 2008. Horizontal gene transfer in eukaryotic evolution. Nat. Rev. Genet., 9, 605-618 (PDF)

Slamovits, C.H., and Keeling, P.J. 2008. Widespread recycling of processed cDNAs in dinoflagellates. Curr. Biol., 18, R550-R552 (PDF)

Slamovits, C.H., Keeling, P.J. 2008. Plastid-derived genes in the nonphotosynthetic alveolate Oxyrrhis marina. Mol. Biol. Evol., 25, 1297-1306 (PDF)

Williams, B.A.P., Cali, A., Takvorian, P.M., and Keeling, P.J. 2008. Distinct localization patterns of two putative mitochondrial proteins in the microsporidian Encephalitozoon cuniculi. J. Eukaryot. Microbiol., 55, 131-133 (PDF)

Corradi, N., Gangaeva, A., and Keeling, P.J. 2008. Comparative profiling of overlapping transcription in the compacted genomes of microsporidia Antonospora locustae and Encephalitozoon cuniculi. Genomics, 91, 388-393 (PDF)

Williams, B.A.P., Haferkamp, I., and Keeling, P.J. 2008. An ADP/ATP-specific mitochondrial carrier protein in the microsporidian Antonospora locustae. J. Mol. Biol., 375, 1249-1257. (PDF)

Carpenter, K.J., Waller, R.F., and Keelilng, P.J. 2008. Surface morphology of Saccinobaculus (Oxymonadida): implications for character evolution and function in oxymonads. Protist, 159, 209-221 (PDF)

Keeling, P.J. 2008. Bridge over troublesome plastids. Nature, 451, 896-897 (PDF)

de Koning, A.P., Noble, G.P., Heiss, A.A., Wong, J., Keeling, P.J. 2008. Envronmental PCR survey to determine the distribution of a non-canonical genetic code in uncultivable oxymonads. Environ. Microbiol., 10, 65-74 (PDF)

Keeling, P.J. 2008. Genome reduction in Microsporidia. In: Genomics and Evolution of Microbial Eukaryotes, pp. 181-191. [BOOK CHAPTER]

Kopriva, S., Patron, N.J., Keeling, P., and Leustek, T. 2008. Phylogenetic analysis of sulfate assimilation and cysteine biosynthesis in phototrophic organisms. In: Sulfur Metabolism in Phototrophic Organisms, pp. 31-58. [BOOK CHAPTER] (PDF)

2007

Corradi, N., Akiyoshi, D.E., Morrison, H.G., Feng, X., Weiss, L.M., Tzipori, S., and Keeling, P.J. 2007. Patterns of genome evolution among the microsporidian parasites Encephalitozoon cuniculi, Antonospora locustae and Enterocytozoon bieneusi. PLoS One, 2, e1277 (PDF)

Noble, G.P., Rogers, M.B., and Keeling, P.J. 2007. Complex distribution of EFL and EF-1⍺ proteins in the green algal lineage. BMC Evol. Biol., 7, 82 (PDF)

Imanian, B., and Keeling, P.J. 2007. The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum retain functionally overlapping mitochondria from two evolutionarily distinct lineages. BMC Evol. Biol., 7, 172 (PDF)

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 Biol., 5, 41 (PDF)

Keeling, P.J. 2007. Deep questions in the Tree of Life. Science, 317, 1875-1876 (PDF)

Slamovits, C.H., Saldarriaga, J.F., Larocque, A., and Keeling, P.J. 2007. The highly reduced and fragmented mitochondrial genome of the early-branching dinoflagellate Oxyrrhis marina shares characteristics with both apicomplexan and dinoflagellate mitochondrial genomes. J. Mol. Biol. 372, 356-368 (PDF)

Rogers, M.B., Patron, N.J., and Keeling, P.J. 2007. Horizontal transfer of a eukaryotic plastid-targeted protein gene to cyanobacteria. BMC Biol., 5, 26 (PDF)

Rogers, M.B., Watkins, R.F., Harper, J.T., Durnford, D.G., Gray, M.W., and Keeling, P.J. 2007. A complex and punctuate distribution of three eukaryotic genes derived by lateral gene transfer. BMC Evol. Biol., 7, 89 (PDF)

Patron, N.J., Inagaki, Y., and Keeling, P.J. 2007. Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages. Curr. Biol., 17, 887-891 (PDF)

Rogers, M.B., Gilson, P.R., Su, V., McFadden, G.I., and Keeling, P.J. 2007. The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans: evidence for independent origins of chlorarachniophyte and euglenid secondary endosymbionts. Mol. Biol. Evol., 24, 54-62 (PDF)

Keeling, P.J. 2007. Ostreococcus tauri: seeing through the genes to the genome. Trends Genet., 23, 151-154 (PDF)

Akiyoshi, D.E., Weiss, L.M., Feng, X., Williams, B.A.P., Keeling, P.J., Zhang, Q., and Tzipori, S. 2007. Analysis of the β-tubulin genes from Enterocytozoon bieneusi isolates from a human and rhesus macaque. J. Eukaryot. Microbiol., 54, 38-41 (PDF)

Burri, L., and Keeling, P.J. 2007. Protein targeting in parasites with cryptic mitochondria. Int. J. Parasitol., 37, 265-272 (PDF)

Imanian, B., Carpenter, K.J., and Keeling, P.J. 2007. Mitochondrial genome of a tertiary endosymbiont retains genes for electron transport proteins. J. Eukaryot. Microbiol., 54, 146-153 (PDF)

Koziol, A.G., Borza, T., Ishida, K., Keeling, P.J., Lee, R.W., and Durnford, D.G. 2007. Tracing the evolution of the light-harvesting antennae in chlorophyll a/b-containing organisms. Plant Physiol., 143, 1802-1816 (PDF)

Carpenter, K.J., and Keeling, P.J. 2007. Morphology and phylogenetic position of Eucomonympha imla (Parabasalia: Hypermastigida). J. Eukaryot. Microbiol., 54, 263-270 (PDF)

2006

Gile, G.H., Patron, N.J., and Keeling, P.J. 2006. EFL GTPase in cryptomonads and the distribution of EFL and EF-1⍺ in chromalveolates. Protist, 157, 435-444 (PDF)

Heiss, A.A., and Keeling, P.J. 2006. The phylogenetic position of the oxymonad Saccinobaculus based on SSU rRNA. Protist, 157, 335-344 ( PDF)

Eisen, J.A., Coyne, R.S., Wu, M., Wu, D., Thiagarajan, M., Wortman, J.R., Badger, J.H., Ren, Q., Amedeo, P., Jones, K.M., Tallon, L.J., Delcher, A.L., Salzberg, S.L., Silva, J.C., Haas, B.J., Majoros, W.H., Farzad, M., Carlton, J.M., Smith, R.K., Garg, J., Pearlman, R.E., Karrer, K.M., Sun, L., Manning, G., Elde, N.C., Turkewitz, A.P., Asai, D.J., Wilkes, D.E., Wang, Y., Cai, H., Collins, K., Stewart, B.A., Lee, S.R., Wilamowska, K., Weinberg, Z., Ruzzo, W.L., Wloga, D., Gaertig, J., Frankel, J., Tsao, C.-C., Gorovsky, M.A., Keeling, P.J., Waller, R.F., Patron, N.J., Cherry, J.M., Stover, N.A., Krieger, C.J., del Toro, C., Ryder, H.F., Williamson, S.C., Barbeau, R.A., Hamilton, E. P., and Orias, E. 2006. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol., 4, e268 (PDF)

Waller, R.F., and Keeling, P.J. 2006. Alveolate and chlorophycean mitochondrial cox2 genes split twice independently. Gene, 383, 33-37 (PDF)

Gould, S.B., Sommer, M.S., Kroth, P.G., Gile, G.H., Keeling, P.J., and Maier, U.-G. 2006. Nucleus-to-nucleus gene transfer and protein retargeting into a remnant cytoplasm of cryptophytes and diatoms. Mol. Biol. Evol., 23, 2413-2422 (PDF)

Burri, L., Williams, B.A.P., Bursac, D., Lithgow, T., and Keelilng, P.J. 2006. Microsporidian mitosomes retain elements of the general mitochondrial targeting system. Proc. Natl. Acad. Sci. USA, 103, 15916-15920 (PDF)

Waller, R.F., Slamovits, C.H., and Keeling, P.J. 2006. Lateral gene transfer of a multigene region from cyanobacteria to dinoflagellates resulting in a novel plastid-targeted fusion protein. Mol. Biol. Evol., 23, 1437-1443 (PDF)

Slamovits, C.H., Burri, L., and Keeling, P.J. 2006. Characterisation of a divergent Sec61β in Microsporidia. J. Mol. Biol., 359, 1196-1202 (PDF)

Gilson, P.R., Su, V., Slamovits, C.H., Reith, M.E., Keeling, P.J., and McFadden, G.I. 2006. Complete nucleotide sequence of the chlorarachniophyte nucleomorph: Nature's smallest nucleus. Proc. Natl. Acad. Sci. USA, 103, 9566-9571 (PDF)

Patron, N.J., Rogers, M.B., and Keeling, P.J. 2006. Comparative rates of evolution in endosymbiotic nuclear genomes. BMC Evol. Biol., 6, 46 (PDF)

Waller, R.F., Patron, N.J., and Keeling, P.J. 2006. Phylogenetic history of plastid-targeted proteins in the peridinin-containing dinoflagellate Heterocapsa triquetra. Int. J. Syst. Evol. Microbiol., 56, 1439-1447( PDF)

Keeling, P.J., and Brugerolle, G. 2006. Evidence from SSU rRNA phylogeny that Octomitus is a sister lineage to Giardia. Protist, 157, 205-212 (PDF)

Slamovits, C.H., and Keeling, P.J. 2006. A high density of ancient spliceosomal introns in oxymonad excavates. BMC Evol. Biol., 6, 34 (PDF)

de Koning, A.P., and Keeling, P.J. 2006. The complete plastid genome sequence of the parasitic green alga Helicosporidium sp. is highly reduced and structured. BMC Biol., 4, 12 (PDF)

Patron, N.J., Waller, R.F., and Keeling, P.J. 2006. A tertiary plastid uses genes from two endosymbionts. J. Mol. Biol., 357, 1373-1382 ( PDF)

Slamovits, C.H., and Keeling, P.J. 2006. Pyruvate-phosphate dikinase of oxymonads and parabasalia and the evolution of pyrophosphate-dependent glycolysis in anaerobic eukaryotes. Eukaryot. Cell, 5, 148-154 (PDF)

2005

Keeling, P.J., Burger, G., Durnford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A.J., and Gray, M.W. 2005. The tree of eukaryotes. Trends Ecol. Evol., 20, 670-676 (PDF)

Keeling, P.J., and Slamovits, C.H. 2005. Causes and effects of nuclear genome reduction. Curr. Opin. Genet. Dev., 15, 601-608 (PDF)

Patron, N.J., and Keeling, P.J. 2005. Common evolutionary origin of starch biosynthetic enzymes in green and red algae. J. Phycol.. 41, 1131-1141 (PDF)

Williams, B.A.P., Slamovits, C.H., Patron, N.J., Fast, N.M., and Keeling, P.J. 2005. A high frequency of overlapping gene expression in compacted eukaryotic genomes. Proc. Natl. Acad. Sci. USA, 102, 10936-10941 (PDF)

Takishita, K., Patron, N.J., Ishida, K., Maruyama, T., and Keeling, P.J. 2005. A transcriptional fusion of genes encoding glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and enolase in dinoflagellates. J. Eukaryot. Microbiol., 52, 343-348 (PDF)

Williams, B.A.P., and Keeling, P.J. 2005. Microsporidian mitochondrial proteins: expression in Antonospora locustae spores and identification of genes coding for two further proteins. J. Eukaryot. Microbiol., 52, 271-276 (PDF)

Patron, N.J., Waller, R.F., Archibald, J.M., and Keeling, P.J. 2005. Complex protein targeting to dinoflagellate plastids. J. Mol. Biol., 348, 1015-1024 (PDF)

de Koning, A.P., Tartar, A., Boucias, D.G., and Keeling, P.J. 2005. Expressed sequence tag (EST) survey of the highly adapted green algal parasite, Helicosporidium. Protist, 156, 181-190 (PDF)

Keeling, P.J., Fast, N.M., Law, J.S., Williams, B.A.P., and Slamovits, C.H. 2005. Comparative genomics of microsporidia. Folia Parasitol., 52, 8-14 (PDF)

Harper, J.T., Waanders, E., and Keeling, P.J. 2005. On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes. Int. J. Syst. Evol. Microbiol., 55, 487-496 (PDF)

Likić, V.A., Perry, A., Hulett, J., Derby, M., Traven, A., Waller, R.F., Keeling, P.J., Koehler, C.M., Curran, S.P., 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 (PDF)

Keeling, P.J. 2005. Progress and problems in the origin and evolution of plastids. In: Microbial Phylogeny and Evolution: Concepts and Controversies, pp. 238-260. [BOOK CHAPTER]

Fast, N.M., and Keeling, P.J. 2005. The fungal roots of Microsporidia. In: Insect-Fungal Associations. Ecology and Evolution, pp. 97-118. [BOOK CHAPTER]

2004

Keeling, P.J., Archibald, J.M., Fast, N.M., and Palmer, J.D. 2004. Comment on "The evolution of modern eukaryotic phytoplankton". Science, 306, 2191 (PDF)

McEwan, M.L., and Keeling, P.J. 2004. HSP90, tubulin and actin are retained in the tertiary endosymbiont genome of Kryptoperidinium foliaceum. J. Eukaryot. Microbiol., 51, 651-659 (PDF)

Keeling, P.J., and Slamovits, C.H. 2004. Simplicity and complexity of microsporidian genomes. Eukar. Cell, 3, 1363-1369 (PDF)

Keeling, P.J., and Inagaki, Y. 2004. A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor-1⍺. Proc. Natl. Acad. Sci. USA, 101, 15380-15385 (PDF)

Patron, N.J., Rogers, M.B., and Keeling, P.J. 2004. Gene replacement of fructose-1,6-bisphophate aldolase supports the hypothesis of a single photosynthetic ancestor of chromalveolates. Eukaryot. Cell, 3, 1169-1175 (PDF)

de Koning, A.P., and Keeling, P.J. 2004. Nucleus-encoded genes for plastid-targeted proteins in Helicosporidium: functional diversity of a cryptic plastid in a parasitic alga. Eukaryot. Cell, 3, 1198-1205 (PDF)

Rogers. M.B., Archibald, J.M., Field, M.A., Li, C., Striepen, B., and Keeling, P.J. 2004. Plastid-targeting peptides from the chlorarachniophyte Bigelowiella natans. J. Eukaryot. Microbiol., 51, 529-535 (PDF)

Harper, J.T., and Keeling, P.J. 2004. Lateral gene transfer and the complex distribution of insertions in eukaryotic enolase. Gene, 340, 227-235 (PDF)

Keeling, P.J. 2004. Diversity and evolutionary history of plastids and their hosts. Am. J. Bot., 91, 1481-1493 (PDF)

Slamovits, C.H., and Keeling, P.J. 2004. Class II photolyase in a microsporidian intracellular parasite. J. Mol. Biol., 341, 713-721 (PDF)

Rogers, M., and Keeling, P.J. 2004. Lateral transfer and recompartmentalization of Calvin cycle enzymes in plants and algae. J. Mol. Evol., 58, 367-375 (PDF)

Leander, B.S., and Keeling, P.J. 2004. Symbiotic innovation in the oxymonad Streblomastix strix. J. Eukaryot. Microbiol., 51, 291-300 (PDF)

Slamovits, C.H., Fast, N.M., Law, J.S., and Keeling, P.J. 2004. Genome compaction and stability in microsporidian intracellular parasites. Curr. Biol., 14, 891-896 (PDF)

Leander, B.S., and Keeling, P.J. 2004. Early evolutionary history of dinoflagellates and apicomplexans (Alveolata) as inferred from HSP90 and actin phylogenies. J. Phycol., 40, 341-350 (PDF)

Keeling, P.J. 2004. Polymorphic insertions and deletions in parabasalian enolase genes. J. Mol. Evol., 58, 550-556 (PDF)

Archibald, J.M., and Keeling, P.J. 2004. The evolutionary history of plastids: a molecular phylogenetic perspective. In: Organelles, Genomes and Eukaryote Phylogeny, pp. 55-74. doi:10.1201/9780203508930. [BOOK CHAPTER] (PDF)

Keeling, P.J. 2004. Reduction and compaction in the genome of the apicomplexan parasite Cryptosporidium parvum. Dev. Cell, 6, 614-616 (PDF)

Gerbod, D., Sanders, E., Moriya, S., Noël, C. Takasu, H., Fast, N.M., Delgado-Viscogliosi, P., Ohkuma, M., Kudo, T., Capron, M., Palmer, J.D., Keeling, P.J., and Viscogliosi, E. 2004. Molecular phylogenies of Parabasalia inferred from four protein genes and comparison with rRNA trees. Mol. Phylogenet. Evol., 31, 572-580 (PDF)

Archibald, J.M., and Keeling, P.J. 2004. Actin and ubiquitin protein sequences support a cercozoan/foraminieran ancestry for the plasmodiophorid plant pathogens. J. Eukaryot. Microbiol., 51, 113-118 (PDF)

Saldarriaga, J.F., Taylor, F.J.R., Cavalier-Smith, T., Menden-Deuer, S., and Keeling, P.J. 2004. Molecular data and the evolutionary history of dinoflagellates. Europ. J. Protistol., 40, 85-111 (PDF)

Slamovits, C.H., Williams, B.A.P., and Keeling, P.J. 2004. Transfer of Nosema locustae (Microsporidia) to Antonospora locustae n. comb. based on molecular and ultrastructural data. J. Eukaryot. Microbiol., 51, 207-213 (PDF)

Keeling, P.J. 2004. A brief history of plastids and their hosts. Protist, 155, 3-7 (PDF)

2003

Leander, B.S., Harper, J.T., and Keeling, P.J. 2003. Molecular phylogeny and surface morphology of marine aseptate gregarines (Apicomplexa): Selenidium spp. and Lecudina spp. J. Parasitol., 89, 1191-1205 (PDF)

Leander, B.S., Kuvardina, O.N., Aleshin, V.V., Mylnikov, A.P., and Keeling, P.J. 2003. Molecular phylogeny and surface morphology of Colpodella edax (Alveolata): insights into the phagotrophic ancestry of apicomplexans. J. Eukaryot. Microbiol., 50, 334-340 (PDF)

Fast, N.M., Law, J.S., Williams, B.A.P., and Keeling, P.J. 2003. Bacterial catalase in the microsporidian Nosema locustae: implications for microsporidian metabolism and genome evolution. Euk. Cell, 2, 1069-1075 (PDF)

Longet, D., Archibald, J.M., Keeling, P.J., and Pawlowski, J. 2003. Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies. Int. J. Syst. Evol. Microbiol., 53, 1735-1739 (PDF)

Harper, J.T., and Keeling, P.J. 2003. Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. Mol. Biol. Evol., 20, 1730-1735 (PDF)

Archibald, J.M., Rogers, M.B., Toop, M., Ishida, K., and Keeling, P.J. 2003. Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga, Bigelowiella natans. Proc. Natl. Acad. Sci. USA, 100, 7678-7683 (PDF) (Commentary)

Waller, R.F., Keeling, P.J., van Dooren, G., and McFadden, G.I. 2003. Comment on "A green algal apicoplast ancestor". Science, 301, 49 (PDF)

Williams, B.A.P., and Keeling, P.J. 2003. Cryptic organelles in parasitic protists and fungi. Adv. Parasitol., 54 , 9-68 (PDF)

Leander, B.S., and Keeling, P.J. 2003. Morphostasis in alveolate evolution. Trends Ecol. Evol., 18, 395-402 (PDF)

Ryall, K., Harper, J.T., and Keeling, P.J. 2003. Plastid-derived Type II fatty acid biosynthetic enzymes in chromists. Gene, 313, 139-148 (PDF)

Archibald, J.M., Teh, E.M., and Keeling, P.J. 2003. Novel ubiquitin fusion proteins: ribosomal protein P1 and actin. J. Mol. Biol., 328, 771-778 (PDF)

Keeling, P.J. 2003. Congruent evidence from ⍺-tubulin and β-tubulin gene phylogenies for a zygomycete origin of microsporidia. Fungal Genet. Biol., 38, 298-309 (PDF)

Keeling, P.J., and Leander, B.S. 2003. Characterisation of a non-canonical genetic code in the oxymonad Streblomastix strix. J. Mol. Biol., 326, 1337-1349 (PDF)

Archibald, J.M., and Keeling, P.J. 2003. Plant genomes: cyanobacterial genes revealed. Heredity, 90, 2-3 (PDF)

Saldarriaga, J.F., Leander, B.S., Taylor, F.J.R., and Keeling, P.J. 2003. Lessardia elongata gen. et sp. nov. (Dinoflagellata, Peridiniales, Podolampaceae) and the taxonomic position of the genus Roscoffia. J. Phycol., 39, 368-378 (PDF)

Archibald, J.M., Longet, D., Pawlowski, J., and Keeling, P.J. 2003. A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup. Mol. Biol. Evol., 20, 62-66 (PDF)

Saldarriaga, J.F., McEwan, M.L., Fast, N.M., Taylor, F.J.R., and Keeling, P.J. 2003. Multiple protein phylogenies show that Oxyrrhis marina and Perkinsus marinus are early branches of the dinoflagellate lineage. Int. J. Syst. Evol. Microbiol., 53, 355-365 (PDF)

Leander, B.S., Clopton, R.E., and Keeling, P.J. 2003. Phylogeny of gregarines (Apicomplexa) as inferred from small-subunit rDNA and ß-tubulin. Int. J. Syst. Evol. Microbiol., 53, 345-354 (PDF)

2002

Kuvardina, O.N., Leander, B.S., Aleshin, V.V., Myl'nikov, A.P., Keeling, P.J., and Simdyanov, T.G. 2002. The phylogeny of colpodellids (Alveolata) using small subunit rRNA gene sequences suggests they are the free-living sister group to apicomplexans. J. Eukaryot. Microbiol., 49, 498-504 (PDF)

Leander, B.S., Saldarriaga, J.F., and Keeling, P.J. 2002. Surface morphology of the marine parasite Haplozoon axiothellae Siebert (Dinoflagellata). Eur. J. Protistol., 38, 287-297 (cover) (PDF)

Keeling, P.J. 2002. Molecular phylogenetic position of Trichomitopsis termopsidis (Parabasalia) and evidence for the Trichomitopsiinae. Eur. J. Protistol., 38, 279-286 (PDF)

Archibald, J.M., and Keeling, P.J. 2002. Recycled plastids: a 'green movement' in eukaryotic evolution. Trends Genet., 18, 577-584 (PDF)

Brinkman, F.S.L., Blanchard, J.L., Cherkasov, A., Av-Gay, Y., Brunham, R.C., Fernandez, R.C., Finlay, B.B., Otto, S.P., Ouellette, B.F.F., Keeling, P.J., Rose, A.M., Hancock, R.E.W., and Jones, S.J.M. 2002. Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, Cyanobacteria, and the chloroplast. Genome Res. 12, 1159-1167 (PDF)

Keeling, P.J., and Fast, N.M. 2002. Microsporidia: biology and evolution of highly reduced intracellular parasites. Annu. Rev. Microbiol., 56, 93-116 (PDF)

Fast, N.M., Xue, L., Bingham, S., and Keeling, P.J. 2002. Re-examining alveolate evolution using multiple protein molecular phylogenies. J. Eukaryot. Microbiol., 49, 30-37 (PDF)

Keeling, P.J. 2002. Cellular Organelles. In: Encyclopedia of Evolution, pp. 146-149. [BOOK CHAPTER]

2001

Keeling, P.J. 2001. Parasites go the full monty. Nature, 414, 401-402 (PDF)

Fast, N.M., and Keeling, P.J. 2001. Alpha and beta subunits of pyruvate dehydrogenase E1 from the microsporidian Nosema locustae: mitochondrion-derived carbon metabolism in microsporidia. Mol. Biochem. Parasitol., 117, 201-209 (PDF)

Keeling, P.J., and Palmer, J.D. 2001. Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase. Proc. Natl. Acad. Sci. USA, 98, 10745-10750 (PDF)

Saldarriaga, J.F., Taylor, F.J.R., Keeling, P.J., and Cavalier-Smith, T. 2001. Dinoflagellate nuclear SSU rRNA phylogeny suggests multiple plastid losses and replacements. J. Mol. Evol., 53, 204-213 (PDF)

Qian, Q., and Keeling, P.J. 2001. Diplonemid glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and prokaryote-to-eukaryote lateral gene transfer. Protist, 152, 193-201 (PDF)

Fast, N.M., and Keeling, P.J. 2001. A common origin for alveolate and heterokont plastids (translated to Japanese by K. Ishida). Jpn. J. Phycol., 49, 137-140

Keeling, P.J. 2001. Foraminifera and Cercozoa are related in actin phylogeny: two orphans find a home? Mol. Biol. Evol., 18, 1551-1557 (PDF)

Fast, N.M., Kissinger, J.C., Roos, D.S., and Keeling, P.J. 2001. Nuclear-encoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids. Mol. Biol. Evol., 18, 418-426 (PDF)

Frankel, J., Williams, N.E., Nelsen, E.M., and Keeling, P.J. 2001. An evaluation of Hsp90 as a mediator of cortical patterning in Tetrahymena. J. Eukaryot. Microbiol., 48, 147-160 (PDF)

2000

de Koning, A.P., Brinkman, F.S.L., Jones, S.J.M., and Keeling, P.J. 2000. Lateral gene transfer and metabolic adaptation in the human parasite Trichomonas vaginalis. Mol. Biol. Evol., 17, 1769-1773 (Citation) (PDF)

Stibitz, T.A., Keeling, P.J., and Bhattacharya, D. 2000. Symbiotic origin of a novel actin gene in the cryptophyte Pyrenomonas helgolandii. Mol. Biol. Evol., 17, 1731-1738 (Abstract) (PDF)

Keeling, P.J., and Palmer, J.D. 2000. Parabasalian flagellates are ancient eukaryotes. Nature, 405, 635-637 (Citation) (PDF)

Keeling, P.J., Luker, M.A., and Palmer, J.D. 2000. Evidence from beta-tubulin phylogeny that Microsporidia evolved from within the Fungi. Mol. Biol. Evol., 17, 23-31 (Abstract) (PDF)

1999

Keeling, P.J., Palmer, J.D., Donald, R.G.K., Roos, D.S., Waller, R.F., and McFadden, G.I. 1999. Shikimate pathway in apicomplexan parasites. Nature, 397, 219-220 (PDF)

Keeling, P.J., Deane, J.A., Hink-Schauer, C., Douglas, S.E., Maier, U.-G., and McFadden, G.I. 1999. The secondary endosymbiont of the cryptomonad Guillardia theta contains alpha-, beta-, and gamma-tubulin genes. Mol. Biol. Evol., 16, 1308-1313 (PDF)

Keeling, P.J. 1999. Latest installment of the endocytobiology serial. Bioessays, 21, 449-450. [BOOK REVIEW] (PDF)

1998

Keeling, P.J., Poulson, N., and McFadden, G.I. 1998. Phylogenetic diversity of parabasalian symbionts from termites, including the phylogenetic position of Pseudotrypanosoma and Trichonympha. J. Eukaryot. Microbiol., 45, 643-650 (PDF)

Keeling, P.J., and McFadden, G.I. 1998. Origins of microsporidia. Trends Microbiol., 6 , 19-23 (PDF)

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 Toxoplasma gondii and Plasmodium falciparum. Proc. Natl. Acad. Sci. USA, 95, 12352-12357 (PDF)

Keeling, P.J., Fast, N.M., and McFadden, G.I. 1998. Evolutionary relationship between translation initiation factor eIF-2ɣ and selenocysteine- specific elongation factor SELB: change of function in translation factors. J. Mol. Evol., 47, 649-655 (PDF)

Keeling, P.J., Deane, J.A., and McFadden, G.I. 1998. The phylogenetic position of alpha- and beta-tubulins from the Chlorarachnion host and Cercomonas (Cercozoa). J. Eukaryot. Microbiol., 45, 561-570 (PDF)

Keeling, P.J. 1998. A kingdom's progress: Archezoa and the origin of eukaryotes. Bioessays, 20, 87-95 (PDF)

Keeling, P.J., Klenk, H.-P., Singh, R.K., Schenk, M.E., Sensen, C.W., Zillig, W., and Doolittle, W.F. 1998. Sulfolobus islandicus plasmids pRN1 and pRN2 share distant but common evolutionary ancestry. Extremophiles, 2, 391-393 (PDF)

1997

Keeling, P.J., and Doolittle, W.F. 1997. Evidence that eukaryotic triosephosphate isomerase is of alpha-proteobacterial origin. Proc. Natl. Acad. Sci. USA, 94, 1270-1275 (PDF)

Keeling, P.J., and Doolittle, W.F. 1997. Widespread and ancient distribution of a noncanonical genetic code in diplomonads. Mol. Biol. Evol., 14, 895-901 (PDF)

Keeling, P.J. 1997. Response to: 'UAR codons for glutamine'. J. Mol. Evol., 45, 207-208 (PDF)

1996

Keeling, P.J., and Doolittle, W.F. 1996. A non-canonical genetic code in an early-diverging eukaryotic lineage. EMBO J., 15, 2285-2290 (PDF)

Keeling, P.J., and Doolittle, W.F. 1996. Alpha-tubulin from early-diverging eukaryotic lineages and the evolution of the tubulin family. Mol. Biol. Evol., 13, 1295-1305 (PDF)

Keeling, P.J., Doherty-Kirby, A.L., Teh, E.M., and Doolittle, W.F. 1996. Linked genes for calmodulin and E2 ubiquitin-conjugating enzyme in Trichomonas vaginalis. J. Eukaryot. Microbiol., 43, 468-474 (PDF)

Keeling, P.J., Baldauf, S.L., Doolittle, W.F., Zillig, W., and Klenk, H.-P. 1996. An infB-homologue in Sulfolobus acidocaldarius. Syst. App. Microbiol., 19, 312-321 (PDF)

Keeling, P.J., and Logsdon, J.M. 1996. Highly-divergent Caenorhabditis and Saccharomyces tubulins evolved recently from genes encoding ɣ-tubulin. Trends Cell Biol., 6, 375 (PDF)

Keeling, P.J., Klenk, H.-P., Singh, R.K., Feeley, O., Schleper, C., Zillig, W., Doolittle, W.F., and Sensen, C.W. 1996. Complete nucleotide sequence of the Sulfolobus islandicus multicopy plasmid pRN1. Plasmid, 35, 141-144 (PDF)

Keeling, P.J., and Doolittle, W.F. 1996. Methionine aminopeptidase-1: the MAP of the mitochondrion? Trends Biochem. Sci., 21, 285-286 (PDF)

1995

Keeling, P.J., and Doolittle, W.F. 1995. Archaea: narrowing the gap between prokaryotes and eukaryotes. Proc. Natl. Acad. Sci. USA, 92, 5761-5764 (PDF)

Keeling, P.J., and Doolittle, W.F. 1995. Concerted evolution in protists: recent homogenization of a polyubiquitin gene in Trichomonas vaginalis. J. Mol. Evol., 41, 556-562 (PDF)

Keeling, P.J., and Roger, A.J. 1995. The selfish pursuit of sex. Nature, 375, 283 (PDF)

Keeling, P.J., and Doolittle, W.F. 1995. An archaebacterial eIF-1A: new grist for the mill. Mol. Microbiol., 17, 399-400 (PDF)

1994

Keeling, P.J., Charlebois, R.L., and Doolittle, W.F. 1994. Archaebacterial genomes: eubacterial form and eukaryotic content. Curr. Opin. Genet. Dev., 4, 816-822 (PDF)

Roger, A.J., Keeling, P.J., and Doolittle, W.F. 1994. Introns, the broken transposons. Soc. Gen. Physiol. Ser., 49, 27-37 (Citation)