Publications in 2010-2014

Nakayama T†, Inagaki Y. Unique genome evolution in an intracellular N2-fixing symbiont of a rhopalodiacean diatom. Acta Societatis Botanicorum Poloniae 2014 83(4):409-413. abstract  (doi: 10.5586/asbp.2014.046)

Nakayama T†, Kamiawa R, Tanifuji G, Kashiyama Y, Ohkouchi N, Archibald JM, Inagaki Y. Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intercellular lifestyle. Proceedings of the National Academy of Sciences of the United States of America 111(31):11407-11412. pubmed (doi: 10.1073/pnas.1405222111)

Kamikawa R†, Inagaki Y, Hashimoto T. Secondary loss of a cis-spliced intron after the diversification of Giardia intestinalis assemblages. BMC Research Notes 2014 7:413. pubmed (doi: 10.1186/1756-0500-7-413)

Nishimura Y, Kamikawa R, Hashimoto T, Inagaki Y†. An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyte Chrysochromulina sp. NIES-1333. Mobile Genetic Elements 2014 4(1):e29384. pubmed (doi: 10.4161/mge.29384)

Yabuki A†*, Kamikawa R*, Ishikawa SA, Kolisko M, Kim E, Tanabe AS, Kume K, Ishida K, Inagaki Y. Palpitomonas bilix represents a basal cryptist lineage: Insight into the character evolution in Cryptista. 2014 Scientific Reports 4:4641. 【*Joint first authors】 pubmed (doi: 10.1038/srep04641)

Kamikawa R†, Kolisko M, Nishimura Y, Yabuki A, Brown MW, Ishikawa SA, Ishida K, Roger AJ, Hashimoto T, Inagaki Y. Gene content evolution in discobid mitochondria deduced from the phylogenetic position and complete mitochondrial genome of Tsukubamonas globosa. 2014 Genome Biology and Evolution 6(2):306-315. pubmed (doi: 10.1093/gbe/evu015)

石川奏太, 中尾昌広, 稲垣祐司, 橋本哲男, 佐藤三久. Non-homogeneous置換モデルに基づく進化系統樹推測のMPI/OpenMP HYBRID並列化：大規模計算システム向けプログラムの開発と性能評価. ハイパフォーマンスコンピューティングと計算科学シンポジウム（HPCS2014）論文集，情報処理学会 10-20.

Ishikawa SA†, Nakao H, Inagaki Y, Hashimoto T, Sato M. Non-homogeneous置換モデルを搭載した系統解析プログラムのMPI/OpenMPハイブリッド並列化：大規模遺伝子データセットへの適応に向けて． Accepted to be published in Proceedings of High Performance Computing Symposium 2014. web page

Kamikawa R†, Brown MW, Nishimura Y, Sako Y, Heiss AA, Yubuki N, Gawryluk R, Simpson AGB, Roger AJ, Hashimoto T, Inagaki Y. Parallel re-modeling of EF-1α function in eukaryotic evolution: Divergent, low-expressed EF-1α genes co-occur with EFL genes in diverse distantly related eukaryotes. 2013 BMC Evolutionary Biology 13:131. pubmed (doi:10.1186/1471-2148-13-131)

Nagayasu E, Ishikawa S, Taketani S, Ooka T, Chakraborty G, Yoshida A, Inagaki Y, Hayashi T, Maruyama H†. Identification of a bacteria-like ferrochelatase gene in Strongyloides venezuelensis, an animal parasitic nematode. 2013 PLoS ONE 8(3):e58458. pubmed (doi:10.1371/journal.pone.0058458)

Matsumoto T, Kawachi M, Miyashita H, Inagaki Y†. Prasinoxanthin is absent in the green-colored dinoflagellate Lepidodinium chlorophorum strain NIES-1868: Pigment composition and 18S rRNA phylogeny. 2012 Journal of Plant Research 125(6):705-711. pubmed  (doi:10.1007/s10265-012-0486-6)

Tsuji M†, Sato M, Tanabe AS, Inagaki Y, Hashimoto T. An asynchronous parallel genetic algorithm for the maximum likelihood phylogenetic tree search. 2012 Proceedings of 2012 IEEE Congress on Evolutionary Computation. Abstract  (doi: 10.1109/CEC.2012.6256560)

Ishitani Y†, Kamikawa R, Yabuki A, Tsuchiya M, Inagaki Y, Takishita K. Evolution of elongation factor-like (EFL) protein in Rhizaria is revised by radiolarian EFL gene sequences. 2012 Journal of Eukaryotic Microbiology 59(4):367-373. pubmed  (doi: 10.1111/j.1550-7408.2012.00626.x) 

Ishikawa SA, Inagaki Y†, Hashimoto T. RY-coding and non-homogeneous models ameliorate the maximum-likelihood inferences from nucleotide sequence data with parallel compositional heterogeneity. 2012 Evolutionary Bioinformatics 8:357-371. pubmed article (doi: 10.4137/EBO.S9017)

Nishimura Y*, Kamikawa R*, Hashimoto T, Inagaki Y†. Separate origins of group I introns in two mitochondrial genes of the katablepharid Leucocryptos marina. 2012 PLoS One 7(5):e37307. 【*Joint 1st authors】 pubmed (doi:10.1371/journal.pone.0037307)

Takishita K*, Kolisko M*, Komatsuzaki H, Yabuki A, Inagaki Y, Cepicka I, Smejkalova P, Silberman JD, Hashimoto T, Roger AJ, Simpson AGB†. Multigene phylogenies of diverse Carpediemonas-like organisms identify the closest relatives of 'amitochndriate' diplomonads and retortamonads. 2012 Protist 163(3):344-355. pubmed  【*Joint 1st authors】(doi:10.1016/j.protis.2011.12.007)

Kamikawa R†, Inagaki Y, Hashimoto T. A novel spliceosome-mediated trans-splicing can change our view on the genome complexity of the divergent eukaryote Giardia intestinalis. 2011 Biophysical Reviews 3(4):193-197. Abstract

Ishitani Y*†, Ishikawa SA*, Inagaki Y, Tsuchiya M, Takahashi K, Takishita K. Multigene phylogenetic analyses including diverse radiolarian species support the "Retaria" hypothesis -- the sister relationship of Radiolaria and Foraminifera. 【*Joint 1st authors】 2011 Marine Micropaleontology 81(1-2):32-42. abstract 

Yabuki A, Nakayama T, Yubuki N, Hashimoto T, Ishida K, Inagaki Y†. Tsukubamonas globosa n. g., n. sp., a novel excavate flagellate possibly holding a key for the early evolution in "Discoba." 2011 Journal of Eukaryotic Microbiology 58(4):319-331. pubmed  【鞭毛装置の図が、58巻4号の表紙になりました】

Kamikawa R†, Inagaki Y, Roger AJ, Hashimoto T. Splintrons in Giardia intestinalis: spliceosomal introns in a split form. 2011 Communicative & Integrative Biology 4(4):1-3. pubmed

Matsumoto T, Ishikawa SA, Hashimoto T, Inagaki Y†. A deviant genetic code in the green alga-derived plastid in the dinoflagellate Lepidodinium chlorophorum. 2011 Molecular Phylogenetics and Evolution 60(1):68‐72. pubmed

Matsumoto T, Shinozaki F, Chikuni T, Yabuki A, Takishita K, Kawachi M, Nakayama T, Inouye I, Hashimoto T, Inagaki Y†. Green-colored plastids in the dinoflagellate genus Lepidodinium are of core chlorophyte origin. 2011 Protist 162(2):268-276. pubmed 

Kamikawa R†, Inagaki Y, Tokoro M, Roger AJ, Hashimoto T. Split introns in the genome of Giarida intestinalis are excised by spliceosome-mediated trans-splicing. 2011 Current Biology 21(4):311-315. pubmed   《Also see a Dispatch about our work by T. Blumenthal》

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

【Selected as one of Top25 Hottest Articles published in European Journal of Protistology in 2011】

Masuda I*, Kamikawa R*†, Ueda M, Oyama K, Yoshimatsu S, Inagaki Y, Sako Y. Mitochondrial genomes from two red-tide forming raphidophycean algae, Heterosigma akashiwo and Chattonella var. marina. 【*Joint 1st authors】 2011 Harmful Algae 10(2):130-137. Abstract  

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

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, Hashimoto T†. Comprehensive SSU rRNA phylogeny of Eukaryota.  2010 Journal of Endocytobiosis and Cell Research 20:81-88. Abstract

Yubuki N†, Céza V, Cepicka I, Yabuki A, Inagaki Y, Nakayama T, Inouye I, Leander BS. Cryptic diversity of free-living parabasalids, Pseudotrichomonas keilini and Lacusteria cypriaca n. gen. et sp., as inferred from SSU rDNA sequences. 2010 Journal of Eukaryotic Microbiology 57(6):554-561. pubmed 

Minge MA, Shalchian-Tabrizi K, Torresen OK, Takishita K, Probert I, Inagaki Y, Klaveness D, Jakobsen KS†. A phylogenetic mosaic plastid proteome and unusual platid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum. 2010 BMC Evolutionary Biology 10(1):191. pubmed

Kamikawa R†, Sakaguchi M, Matsumoto T, Hashimoto T, Inagaki Y. Rooting for the root of elongation factor-like protein phylogeny. 2010 Molecular Phylogenetics and Evolution 56(3):1082-1088. pubmed.

Kolisko M, Silberman JD, Cepicka I, Yubuki N, Takishita K, Yabuki A, Leander BS, Inouye I, Inagaki Y, Roger AJ, Simpson AGB†. A wide diversity of previously undetected relatives of diplomonads isolated from marine/saline habitats. 2010 Environmental Microbiology 12(10):2700-2710. pubmed

Yabuki A, Inagaki Y, Ishida K†. Palpitomonas bilix gen. et sp. nov.: A novel deep-branching heterotroph possibly related to Archaeplastida or Hacrobia. 2010 Protist 210(4):523-538. pubmed

Mitsui H, Arisue N, Sakihama N, Inagaki Y, Horii T, Hasegawa M, Tanabe K, Hashimoto T†. Phylogeny of Asian primate malaria parasites inferred from apicoplast genome-encoded genes with special emphasis on the positions of Plasmodium vivax and P. fragile. 2010 Gene 450(1):32-38. pubmed