Shiratori Takashi, Suzuki Shigekatsu, Kakizawa Yukako, Ishida Ken-ichiro (2019) Phagocytosis-like cell engulfment by a planctomycete bacterium. Nature Communications 10:5529 (DOI:10.1038/s41467-019-13499-2).

Thakur Rabindra, Shiratori Takashi, Ishida Ken-ichiro (2019) Taxon-rich Multigene Phylogenetic Analyses Resolve the Phylogenetic Relationship Among Deep-branching Stramenopiles. Protist 170(5):UNSP 125682 (DOI:10.1016/j.protis.2019.125682).

Sakarnoto Hirokazu, Hirakawa Yoshihisa, Ishida Ken-ichiro, Keeling Patrick J., Kita Kiyoshi, Matsuzaki Motomichi (2019) Puromycin selection for stable transfectants of the oyster-infecting parasite Perkinsus marinus. Parasitology International 69:13-16 (DOI:10.1016/j.parint.2018.10.011).

Nishimura Yuki, Shiratori Takashi, Ishida Ken-ichiro, Hashimoto Tetsuo, Ohkuma Moriya, Inagaki Yuji (2019) Horizontally-acquired genetic elements in the mitochondrial genome of a centrohelid Marophrys sp.SRT127. Scientific Reports 9:4850 (DOI:10.1038/s41598-019-41238-6).

Nomura Mami, Atsuji Kohei, Hirose Keiko, Shiba Kogiku, Yanase Ryuji, Nakayama Takeshi, Ishida Ken-ichiro, Inaba Kazuo (2019) Microtubule stabilizer reveals requirement of Ca2+-dependent conformational changes of microtubules for rapid coiling of haptonema in haptophyte algae. Biology Open 8(2):UNSP bio036590 (DOI:10.1242/bio.036590).

Araie Hiroya, Nakamura Hideto, Toney Jaime L., Haig Heather A., Plancq Julien, Shiratori Takashi, Leavitt Peter R., Seki Osamu, Ishida Ken-ichiro, Sawada Ken, Suzuki Iwane, Shiraiwa Yoshihiro (2018-07) Novel alkenone-producing strains of genus Isochrysis (Haptophyta) isolated from Canadian saline lakes show temperature sensitivity of alkenones and alkenoates. Organic Geochemistry 121:89-103.

Matsuo Mitsuhiro, Katahata Atsushi, Satoh Soichirou, Matsuzaki Motomichi, Nomura Mami, Ishida Ken-ichiro, Inagaki Yuji, Obokata Junichi (2018) Characterization of spliced leader trans-splicing in a photosynthetic rhizarian amoeba, Paulinella micropora, and its possible role in functional gene transfer. PLOS ONE 13(7):e0200961.

Brown Matthew R, Heiss Aaron A, Kamikawa Ryoma, Inagaki Yuji, Yabuki Akinori, Alexander Tice T, Shiratori Takashi, Ishida Ken-ichiro, Hashimoto, Tetsuo, Simpson Alastair GB, J Roger Andrew (2018) Phylogenomics places orpha protistan lineages in a novel candidate supergroup. Genome Biology and Evolution/10(2)/pp.427-433.

Tashyreva Daria, Prokopchuk Galina, Yabuki Akinori, Kaur Binnypreet, Faktorová Drahomíra, Votýpka Jan, Kusaka Chiho, Fujikura Katsunori, Shiratori Takashi, Ishida Ken-Ichiro, Horák Aleš, Lukeš Julius (2018) Phylogeny and morphology of new diplonemids from Japan. Protist, 169:158-179.

Yabuki Akinori, Ishida Ken-ichiro (2018) An Orphan Protist Quadricilia rotundata Finally Finds Its Phylogenetic Home in Cercozoa. The Journal of eukaryotic microbiology.

Shiratori T.,, Takur R., Ishida K. (2017) Pseudophyllomitus vesiculosus (Larsen and Patterson 1990) Lee, 2002, a poorly studied phagotrophic biflagellate is the first characterized member of stramenopile environmental clade MAST-6. Protist 168(4):439-451.

Shiratori T., Fujita S., Shimizu T., Nakayama T., Ishida K. (2017) Viridiuvalis adhaerensgen. et sp. nov., a novel colony-forming chlorarachniophyte. Journal of Plant Research 130:999-1012.

Kamikawa R., Moog D., Zauner S., Tanifuji G., Ishida K., Miyashita H., Mayama S., Hashimoto T., Maier U. -G., Archibald J. M., Inagaki Y. (2017) A nonphotosynthetic diatom reveals early steps of reductive evolution in plastids. Molecular Biology and Evolution 34(9): 2355–2366.

Hirakawa Y., Nakayama T., Keilert N., Ishida K. (2017) Evolution of UhpC-type hexose-phosphate transporters in dinoflagellates. Phycological Research 65(2):166-170.

Shiratori T., Ishida K.(2016) A New Heterotrophic Cryptomonad: Hemiarma marina n. g., n. sp.. Journal of Eukaryotic Microbiology 63(6):804-812.

Shiratori T., Ishida K. (2016) Trachyrhizium urniformis n. g., n. sp., a Novel Marine Filose Thecate Amoeba Related to a Cercozoan Environmental Clade (Novel Clade 4). Journal of Eukaryotic Microbiology 63(6):722-731.

Suzuki S., Ishida K.,Hirakawa Y.,(2016) Diurnal Transcriptional Regulation of Endosymbiotically Derived Genes in the chlorarachniophyte Bigelowiella natans. Genome Biology and Evolution 8(9):2672-2682.

Nakamura Hideto, Sawada Ken, Araie Hiroya, Shiratori Takashi, Ishida Ken-ichiro, Suzuki Iwane, and Shiraiwa Yoshihiro (2016) Composition of long chain alkenones and alkenoates as a function of growth temperature in marine haptophyte Tisochrysis lutea. Organic Geochemistry 99:78-89 (DOI: 10.1016/j.orggeochem.2016.06.006.

Nomura M., Ishida K. (2016) Fine-structural observations on siliceous scale production and shell assembly in the testate amoeba Paulinella chromatophora. Protist 167 (4):303-318.

Suzuki S., Hirakawa Y., Kofuji R., Sugita M., Ishida K. (2016) Plastid genome sequences of Gymnochlora stellata, Lotharella vacuolata, and Partenskyella glossopodia reveal remarkable structural conservation among chlorarachniophyte species. Journal of Plant Research 129(4):581-590.

Shiratori T., Ishida K. (2016) Entamoeba marina n. sp.; a New Species of Entamoeba Isolated from Tidal Flat Sediment of Iriomote Island, Okinawa, Japan. Journal of Eukaryotic Microbiology 63(3):280-286.

Kamikawa R., Shiratori T., Ishida K., Miyashita H., Roger A. (2016) Group II intron-mediated trans-splicing in the gene-rich mitochondrial genome of an enigmatic eukaryote, Diphylleia rotans. Genome Biology and Evolution 8(2):458-466.

Hirakawa Y., Ishida K. (2015) Prospective function of FtsZ proteins in the secondary plastid of chlorarachniophyte algae. BMC Plant Biology 15: 276.

Kamikawa R., Tanifuji G., Ishikawa S.A., Ishii KI., Matsuno, Y., Onodera N.T., Ishida K., Hashimoto T., Miyashita H., Mayama S., Inagaki Y. (2015) Proposal of a Twin Aarginine Translocator System-Mediated Constraint against Loss of ATP Synthase Genes from Nonphotosynthetic Plastid Genomes. Molecular Biology and Evolution 32(10):2598-2604.

Heiss, Aaron A., Lee, Won J., Ishida, Ken-ichiro, Simpson, Alastair G. B. (2015) Cultivation and Characterisation of New Species of Apusomonads (the Sister Group to Opisthokonts), Including Close Relatives of Thecamonas (Chelonemonas n. gen.). Journal of Eukaryotic Microbiology 62(5):637-649.

Shiratori T., Nakayama T., Ishida K (2015) A new deep-branching stramenopile, Platysulcus tardus gen. nov. sp. nov. Protist 166:337-348.

Suzuki S., Shirato S., Hirakawa Y., Ishida K (2015) Nucleomorph genome sequences of two chlorarachniophytes, Amorphochlora amoebiformis and Lotharella vacuolata. Genome Biology and Evolution 7(6):15336-1545.

Tanabe Y., Okazaki Y., Yoshida M., Matsuura H., Kai A., Shiratori T., Ishida K, Nakano S., Watanabe M. M. (2015) A novel alphaproteobacterial ectosymbiont promotes the growth of the hydrocarbon-rich green alga Botryococcus braunii. Scientific Reports (in press).

Yamaguchi H., Suzuki S., Tanabe Y., Osana Y., Shimura Y., Ishida K., Kawachi M. (2015) Complete Genome Sequence of Microcystis aeruginosa NIES-2549, a Bloom-Forming Cyanobacterium from Lake Kasumigaura, Japan. Genome Announcements 3(3):e00551-15.

Heiss A. A., Lee W. J., Ishida K., Simpson A. G. B.  (2015) Cultivation and Characterisation of New Species of Apusomonads (the Sister Group to Opisthokonts), Including Close Relatives of Thecamonas (Chelonemonas n. gen.). Protist (in press).

Nakayama T., Nakamura A., Yokoyama A., Shiratori T., Inouye I., Ishida K. (2015) Taxonomic study of a new eustigmatophycean alga, Vacuoliviride crystalliferum gen. et sp. nov. Journal of Plant Research 128(2):249-257.

Kamikawa R., Yubuki N., Yoshida M., Taira M. Nakamura N., Ishida K., Leander B. S.,Miyashita H., Hashimoto T., Mayama S., Inagaki Y. (2015) Multiple losses of photosynthesis in Nitzschia (Bacillariophyceae). Phycological Research 63(1):19-28.

Shiratori T.,Yokoyama A., Ishida K. (2014) Phylogeny, ultrastructure, and flagellar apparatus of a new marimonad flagellate Abollifer globosa sp. nov. (Imbricatea, Cercozoa). Protist165(6):808-824.

Hirakawa Y., Ishida K. (2014) Polyploidy of endosymbiotically derived genomes in complex algae. Genome Biology and Evolution 6(4):974-980.

Yabuki A., Kamikawa R., Ishikawa S., Kolisko M., Kim E., Tanabe A., Kume K., Ishida K., Inagaki Y. (2014) Palpitomonas bilix represents a basal cryptist lineage: insight into the character evolution in Cryptista. Scientific Reports 4: 4641 (DOI: 10.1038/srep04641).

Kamikawa R., Kolisko M., Nishimura Y., Yabuki A. Brown M. W., Ishikawa S. A., Ishida K., Roger A. J., Hashimoto T., Inagaki Y. (2014) Gene Content Evolution in Discobid Mitochondria Deduced from the Phylogenetic Position and Complete Mitochondrial Genome of Tsukubamonas globosa. Genome Biology and Evolution 6(2):306-315.

Hirakawa Y., Suzuki S., Archibald J. M., Keeling P. J., Ishida K. (2014) Overexpression of molecular chaperone genes in nucleomorph genomes. Molecular Biology and Evolution 31(6):1437-1443.

Nomura M., Nakayama T., Ishida K. (2014) Detailed Process of Shell Construction in the Photosynthetic Testate Amoeba Paulinella chromatophora (Euglyphid, Rhizaria). Journal of Eukaryotic Microbiology 61:317-321.

Owari A., Hayashi A., Ishida K. (2014) Subcellular localization of minicircle DNA in the dinoflagellate Amphidinium massartii. Phycological Research 62:1-8.

Fukuda S., Iwamoto K., Atsumi M., Yokoyama A., Nakayama T., Ishida K., Inouye I., Shiraiwa Y. (2014) Screening of microalgae and aquatic plants that can eliminate radioactive cesium, iodine and strontium by bioaccumulation from radio-contaminated aquatic environment. Journal of Plant Research 127:79-89.

Yabuki A., Ishida K. and Cavalier-Smith T. (2013) Rigifila ramosa n. gen., n. sp., a filose apusozoan with a distinctive pellicle, is related to Micronuclearia. Protist 164(1):75-88.

Nakayama T., Ishida K., Kasai F., Archibald J. M. (2012) Broad distribution of TPI-GAPDH fusion proteins among eukaryotes: evidence for glycolytic reactions in the mitochondrion?Pros One 7(12):e52340.

Curtis B. 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., 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., Archibald J. M. (2012) Algal nuclear genomes reveal evolutionary mosaicism and fate of nucleomorphs. Nature 492:59-65.

Kashiyama Y., Yokoyama A., Kinoshita Y., Shoji S., Miyashita H., Shiratori T., Suga H., Ishikawa K., Ishikawa A., Inouye I., Ishida K., Fujimura D., Aoki K., Kobayashi M., Nomoto S., Mizoguchi T. and Tamiaki H. (2012) Ubiquity and quantitative significance of detoxification catabolism of chlorophyll associated with protistan herbivory Proc. Natl. acad. Sci. USA 109(43):17328-17335.

Shiratori T., Yabuki A., Ishida K. (2012) Esquamula lacrimiformis n. g., n. sp., a new member of thaumatomonads that lacks siliceous scales. J. Eukaryot. Microbiol. 59(6):527-536.

Yabuki A., Chao E. E., Ishida K. and Cavalier-Smith T. (2012) Microheliella maris (Microhelida ord. n.), an ultrastructurally highly distinctive new axopodial protist species and genus, and the unity of phylum Heliozoa. Protist 163(3):356-388.

Arima H., Horiguchi N., Takaichi S., Kofuji R., Ishida K., Wada K. and Sakamoto T. (2012) Molecular genetic and chemotaxonomic characterization of the terrestrial cyanobacterium Nostoc commune and its neighboring species. FEMS Microbiol. Ecol. 79(1):34-45.

Yabuki A., Nakayama T., Yubuki N., Hashimoto T., Ishida K. and Inagaki Y. (2011) Tsukubamonas globosa gen. et sp. nov.; a novel excavate flagellate possibly hold a key for the early evolution in “Discoba”. J. Euk. Microbiol. 58 (2):94-102.

Ota S., Kudo A. and Ishida K.(2011) Gymnochlora dimorpha sp. nov., a new chlorarachniophyte that has a unique behaviour of daughter cells. Phycologia 50(3):317-326.

Ishida K., Endo H., Koike S. (2011) Partenskyella glossopodia (Chlorarachniophyceae) possesses a nucleomorph genome of approximetely 1 Mbp. Phycol. Res. 59(2):120-122.

Yabuki A. and Ishida K. (2011) Mataza hastifera n. gen., n. sp.: a possible new lineage in the Thecofilosea (Cercozoa). J. Euk. Microbiol.58(2):94-102.

Ishida K., Yabuki A., Ota S. (2011) Amorphochlora amoebiformis gen. et comb. nov. (Chlorarachniophyceae). Phycol. Res. 59(1):52-53.

Kamikawa R., Yabuki A., Nakayama T., Ishida K., Hashimoto T., and Inagaki Y. (2011) Cercozoa comprises both EF-1α-containing and EFL-containing members. European Journal of Protistology. 47:24-28.

Nakayama T., Ikegami Y., Nakayama T., Ishida K., Inagaki Y. and Inouye I. (2011) Spheroid bodies in rhopalodiacean diatoms were derived from a single endosymbiotic cyanobacterium. Journal of Plant Research 124(1):93-97.

Ishida K., Inagaki Y., Sakaguchi M., Oiwa A., Kai A., Suzuki M., Nakayama T., Chikuni T., Yabuki A., Yamaguchi H., Yubuki N., Yoshida M., Nakayama T., Inouye I. and Hashimoto T. (2010) Comprehensive SSU rRNA Phylogeny of Eukaryota. Journal of Endocytobiosis and Cell Research 20:

Hirakawa Y. and Ishida K.(2010) Internal plastid-targeting signal found in a RubisCO small subunit protein of a chlorarachniophyte alga. The Plant Journal. 64:402-410.

Yabuki A., Inagaki Y. and Ishida K. (2010) Palpitomonas bilix gen. et sp. nov.: a novel deep-branching heterotroph possibly related to Archaeplastida or Hacrobia. Protist 161(4):523-538.

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(7):1538-1545.

Reyes-Prieto A., Yoon H.S., Moustafa A., Yang E.C., Andersen R.A., Boo S.M., Nakayama T., Ishida K. and Bhattacharya D. (2010) Differential gene retention in plastids of common recent origin. Mol. Biol. Evol. 27(7):1530-1537.

Hirakawa Y., Nagamune K. and Ishida K. (2009) Protein targeting into secondary plastids of chlorarachniophytes. Proceedings of National Academy of Science USA 106(31):12820-12825.

Yoon H.-S., Nakayama T., Reyes-Prieto A., Andersen R.A., Boo S.-M., Ishida K. and Bhattacharya D. (2009) A single origin of the photosynthetic organelle in different Paulinella chromatophora lineages. BMC Evol. Biol. 9:98 (http://www.biomedcentral.com/1471-2148/9/98)

Ota S., Silver T.D., Archibald J. M. and Ishida K. (2009) Lotharella oceanica sp. nov. – a new planktonic chlorarachniophyte studied by light and electron microscopy. Phycologia 48(5):315-323.

Nakayama T. and Ishida K. (2009) Another acquisition of primary photosynthetic organelle is underway in Paulinella chromatophora. Curr. Biol. 19(7):R284-R285.

Bass D., Chao E., Nikolaevb S., Yabuki A., Ishida K., Berney C., Pakzad U., Wyleziche C., and Cavalier-Smith T. (2009) Phylogeny of novel naked filose and reticulose cercozoa: Granofilosea cl. n. and Proteomyxidea revised. Protist 160(1):75-109.

Ota S., D Vaulot, Le Gall F., Yabuki A. and Ishida K. (2009) Partenskyella glossopodia gen. et sp. nov., the first report of a chlorarachniophyte that lacks a pyrenoid. Protist 160(1):137-150.

Hirakawa Y., Kofuji R. and Ishida K. (2008) Transient transformation of a chlorarachniophyte alga, Lotharella amoebiformis (Chlorarachniophyceae), with uidA and egfp reporter genes. J. Phycol. 44:814-820

Takishita K., Kawachi M., Noël M.-H., Matsumoto T., Kakizoe N., Watanabe M. M., Inouye I., Ishida K., Hashimoto T. and Inagaki Y. (2008) Origins of plastids and glyceraldehyde-3-phosphate dehydrogenase genes in the green-colored dinoflagellate Lepidodinium chlorophorum. Gene 410:26-36.

Ota S., Ueda K. and Ishida K. (2007) Norrisiella sphaerica gen. et sp. nov., a new coccoid chlorarachniophyte from Baja California, Mexico. J. Plant Res. 120(6):661-670.

Silver T.D., Koike S., Yabuki A., Kofuji R., Archibald J.M. and Ishida K. (2007) Phylogeny and nucleomorph karyotype diversity of chlorarachniophyte algae. J. Euk. Microbiol. 54(5):403-410.

Nelson M.J., Dang Y., Filek E., Zhang Z, Yu V.W.C., Ishida K. and Green B.R. (2007) Identification and transcription of transfer RNA genes in dinoflagellate plastid minicircles. Gene 392:291-298.

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.

Ota S., Ueda K. and Ishida K. (2007) Taxonomic study of Bigelowiella longifila sp. nov. (Chlorarachniophyta) and a time lapse video observation on the unique migration of amoeboid cells. J. Phycol. 43:333-343.

Tanifuji G., Erata M., Ishida K., Onodera N. and Hara Y.  (2006) Diversity of secondary endosymbiont-derived actin-coding genes in cryptomonads and their evolutionary implications. J. Plant Res. 119:205-215.

Ota S., Ueda K. and Ishida K. (2005) Lotharella vacuolata sp. nov., a new species of chlorarachniophyte algae, and time-lapse video observations on its unique post-cell division behavior. Phycological Research 53:275-286.

Bentley F., Harnett J., Ishida K. and Green B.R. (2005) Investigation of PSI-associated light-harvesting proteins in a chromophyte alga. In: Photosynthesis: Fundamental Aspects to Global Perspectives (Eds: van der Est A. and Bruce D.) pp. 161-163.

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. Journal of Eukaryotic Microbiology 52(4):343-348.

Nishi A., Ishida K. and Endoh H. (2005) Reevaluation of the evolutionary position of opalinids based on beta-tubulin and 18S rDNA phylogenies. Journal of Molecular Evolution 60:695-705.

Takishita K., Ishida K., Ishikura M. and Maruyama T. (2005) Phylogeny of the psbC gene, coding a photosystem II component CP43, suggests separate origins for the peridinin- and the fucoxanthin derivertive-containing plastids of dinoflagellates. Phycologia 44(1):26-34.

Takishita K., Ishida K. and Maruyama T. (2004) Phylogeny of nuclear-encoded plastid-targeted GAPDH gene supports origins for the peridinin- and the fucoxanthin derivative-containing plastids of dinoflagellates. Protist 155(4):447-458.

Bok J.-W., Ishida K. and Griffiths A. J. F. (2003) Ultrastructural changes in Neurospora cells undergoing scenescence induced by kalilo plasmids. Mycologia 95:500-505.

Takishita K., Ishida K. and Maruyama T. (2003) An enigmatic GAPDH gene in the symbiotic dinoflagellate genus Symbiodinium and its related species (the order Suessiales): possible gene transfer between two eukaryotic algae, dinoflagellate and euglenophyte. Protist 154:443-454.

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 prastid-containing alga, Bigelowiella natans. Proceedings of National Academy of Science USA 100(13):7678-7683.

Chaal B. K., Ishida K. and Green B. R. (2003) A thylakoidal processing peptidase from the heterokont alga Heterosigma akashiwo. Plant Molecular Bology 52(2):463-472.

Ishida K. and Green B. R. (2002) Second- and third-hand chloroplasts in dinoflagellates: phylogeny of oxygen-evolving enhancer 1 (PsbO) protein reveals replacement of a nuclear-encoded plastid gene by that of a haptophyte tertiary endosymbiont. Proceedings of National Academy of Science USA 99(14):9294-9299.

Ishida K., Cavalier-Smith T. and Green B. R. (2000) Endomembrane structure and the chloroplast protein targeting pathway in Heterosigma akashiwo (Raphidophyceae, Chromista). Journal of Phycology 36:1135-1144.

Ishida K., Ishida N. and Hara Y. (2000) Lotharella amoeboformis sp. nov.: a new species of chlorarachniophytes from Japan. Phycological Research 48(4):221-230.

Ishida K., Green B. R. and Cavalier-Smith T. (1999) Diversification of a chimaeric algal group, the chlorarachniophytes: phylogeny of nuclear and nucleomorph small subunit rRNA genes. Molecular Biology and Evolution 16(3):321-331.

Ishida K., Cao Y., Hasegawa M., Okada N. and Hara Y. (1997) The origin of chlorarachniophyte plastids, as inferred from phylogenetic comparisons of amino acid sequences of EF-Tu. Journal of Molecular Evolution 45:682-687.

Ishida K., Nakayama T. and Hara Y. (1996) Taxonomic studies on the Chlorarachniophyta II. Genetic delimitation of the chlorarachniophytes and description of Gymnochlora stellata gen. et sp. nov. and Lotharella gen. nov. Phycological Research 44(1):37-45.

Ishida K. and Hara Y. (1994) Taxonomic studies on the Chlorarachniophyta I. Chlorarachnion globosum sp. nov. Phycologia 33(5):351-358.

津田吉晃、廣田充、山中勤、安立美奈子、立花 敏、出川洋介、山川陽祐、田中健太、上野健一、松岡憲知、沼田治、石田健一郎、津村義彦（2018）「登山白書2017」ヤマケイ登山総合研究所（編）、山と渓谷社・東京　p. 126-129.

石田健一郎（2016）「共生微生物-生物と密接に関わるミクロな生命体」大野博司（編）、化学同人・京都　p. 202-212.

石田健一郎（2015）「進化の謎をゲノムで解く」長谷部光泰（監修）（細胞工学別冊）、秀潤社・東京　p. 166-175.

石田健一郎（2012）「藻類ハンドブック」渡邉　信（監修）、NTS・東京　p. 93-96.

石田健一郎（2012）「進化学事典」日本進化学会（編）、共立出版・東京　p. 70-73.

石田健一郎（2010）「あたらしいエネルギー　藻類バイオマス」渡邉　信（編）、みみずく舍、東京　p. 67-76、139-140．

石田健一郎（2009）海洋生命系のダイナミクスシリーズ第1巻「海洋の生命史 生命は海洋でどう進化したか」西田睦（編）、東海大学出版会、東京　p. 170-181．

Ota S. and Ishida K. (2008) Chlorarachniophytes. In: ENCYCLOPEDIA OF LIFE SCIENCES. John Wiley & Sons, Ltd: Chichester http://www.els.net/ [DOI: 10.1002/9780470015902.a0003060.pub2]

Ishida K., Yabuki A. and Ota S. (2007) The chlorarachniophytes: evolution and classification. In Brodie J. and Lewis J. (eds) Unravelling the Algae: The Past, Present, and Future of Algal Systematics. CRC Press, Boca Raton, FL., pp. 171-182.

石田健一郎、小池さやか、平川泰久（2007）葉緑体の誕生と水平伝播．細胞工学別冊　植物細胞工学シリーズ23「植物の進化」（清水健太郎、長谷部光泰　監修）秀潤社　P. 183-191．

石田健一郎（1999）コラム13　共生核の運命．バイオディバーシティ・シリーズ３、「藻類の多様性と系統」（岩槻邦男・馬渡俊輔　監修、千原光雄　編集）裳華房、東京　p. 25８-25９．

原慶明・石田健一郎（1999）10章　クロララクニオン植物門．バイオディバーシティ・シリーズ３、「藻類の多様性と系統」（岩槻邦男・馬渡俊輔　監修、千原光雄　編集）裳華房、東京　p. 256-257．

石田健一郎（1997）11章　クロララクニオン植物門．「藻類多様性の生物学」（千原光雄　編・著）内田老鶴圃、東京　p. 241-249．

石田健一郎（1996）クロララクニオン藻綱．週刊朝日百科「植物の世界−139号、藻類、緑藻類」朝日新聞社、東京　P. 12:221．

石田健一郎（1993）９章クロララクニオン藻綱．「藻類の生活史集成」第３巻　単細胞性・鞭毛藻類　（堀輝三　編）内田老鶴圃、東京　p. 203-213．

中山卓郎・石田健一郎（2008）もう一つの一次共生？ -Paulinella　chromatophoraとそのシアネレ-。原生動物学雑誌41:27-31

瀧下清貴・石田健一郎、丸山正（2006）真核生物におけるGAPDH遺伝子の複雑な進化．生体の科学57：410-412.

Ishida K. (2005) Protein targeting into plastids: a key to understand the symbiogenetic acquisitions of plastids. Journal of Plant Research 118:237-245.

石田健一郎・中山剛（2003）葉緑体の水平伝搬がもたらした藻類多様性：切っても切れない原生動物との関係．生物科学 55(2):95-103．

原慶明・堀口健雄・半澤直人・石田健一郎・横山亜紀子・保科亮・工藤創・越智昭彦・近野麻里（2002）パラオ海水湖における海産大型藻類の固有進化．月刊海洋　号外29：19-26．

Ishida K. and McFadden G. I. (2001) Chlorarachniophytes. Tree of Life Web Project (ed. Maddison D. R.): =>Web site.

原慶明・恵良田真由美・石田健一郎（1992）ヌクレオモルフ−新しい細胞像−．植物細胞工学　14(6):373-382．

クラーク「分子生物学」丸善（2007）（分担）

レーヴン・ジョンソン「生物学（下）」培風館（2007）（分担）

石田健一郎（訳）アルベオラータと不等毛藻の葉緑体は共通の起源から進化した。（Fast N. M. and Keeling P. J. A common origin for alveolate and heterokont plastids.) 藻類: Jap. J. Phycol. 49(2):137-140．

瀧下清貴・石田健一郎（2007）光合成をする繊毛虫ーその巧妙な生存戦略。遺伝 61(3):4-5.

石田健一郎（2001）藻類はなぜカラフルになりえたか？　藻類: Jap. J. Phycol. 49(3):212-214．

石田健一郎（2001）一生使える使い捨て葉緑体−ウミウシのクレプトクロロプラスト−．　藻類: Jap. J. Phycol. 49(1):14-15．

石田健一郎（2000）葉緑体の誕生は１回だった？　藻類: Jap. J. Phycol. 48(3):241-242．

石田健一郎（2000）ルビスコ遺伝子群の複雑な進化．　藻類: Jap. J. Phycol. 48(2):181-182．

石田健一郎（2000）二次共生由来の葉緑体へのタンパク質輸送機構−ユーグレナの場合−．　藻類: Jap. J. Phycol. 48(1):37-38．

石田健一郎（1999）葉緑体包膜の起源．　藻類: Jap. J. Phycol. 47(3):237-238．