Refereed Papers

*Check my Google Scholar site for the most updated list

• Harada R, Nishimura Y, Nomura M, Yabuki A, Shiba K, Inaba K, Allers T, Inagaki Y, Nakayama T
  A hidden archaeal lineage with an ultra-reduced genome retaining only its replicative core.
  Curr Biol 2026 [Link]

• Kagawa M, Hagita M, Nakayama T, Shiba K, Kato‐Minoura T, Matsuda S, Inaba K, Inagaki Y, Nakano K
  tArp Is an Actin‐Related Protein Required for Ciliary Function That Is Conserved in Ciliates and Related Eukaryotic Groups.
  J Eukaryot Microbiol 2026; 73(5):e70123 [Link]

• Maciszewski K, Takahashi K, Harada R, Martinek IN, Nakayama T, Iwataki M, Inagaki Y, Hehenberger E
  Recent plastid replacement in Karlodinium ballantinum (Kareniaceae, Dinoflagellata) challenges the paradigms of endosymbiotic gene transfer.
  Mol Biol Evol 2026; 43(7):msag166 [Link]

• Isogai R, Wei M, Harada R, Yazaki E, Nakayama T, Gawryluk RMR, Inagaki Y
  Diversity and evolution of DNA polymerase θ in eukaryotes and the origin of mitochondrion-localized DNA polymerase PolIA in euglenozoa.
  Protist 2026; 181:126160 [Link]

• Nakayama T, Harada R, Yabuki A, Nomura M, Shiba K, Inaba K, Inagaki Y
  Marked Genome Reduction Driven by a Parasitic Lifestyle: Two Complete Genomes of Endosymbiotic Bacteria Possibly Hosted by a Dinoflagellate.
  Microbes Environ 2025; 40(2):ME25005 [Link]

• Nakayama T, Nomura M, Yabuki A, Shiba K, Inaba K, Inagaki Y
  Convergent reductive evolution of cyanobacteria in symbiosis with Dinophysiales dinoflagellates.
  Sci Rep 2024; 14(1):12774 [Link]

• Sakamoto F, Kanamori S, Díaz LM, Cádiz A, Ishii Y, Yamaguchi K, Shigenobu S, Nakayama T, Makino T, Kawata M
  Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches in Anolis lizards.
  Ecol Evol 2024; 14(3):e11117 [Link]

• Mochizuki T, Sakamoto M, Tanizawa Y, Nakayama T, Tanifuji G, Kamikawa R, Nakamura Y
  A practical assembly guideline for genomes with various levels of heterozygosity.
  Brief Bioinform 2023; 24(6):bbad337 [Link]

• Nomura M, Ohta K, Nishigami Y, Nakayama T, Nakamura K-I, Tadakuma K, Galipon J
  Three-dimensional architecture and assembly mechanism of the egg-shaped shell in testate amoeba Paulinella micropora.
  Front Cell Dev Biol 2023; 11:1232685 [Link]

• Harada R, Kume K, Horie K, Nakayama T, Inagaki Y, Amagasa T
  AtLASS: A Scheme for End-to-End Prediction of Splice Sites Using Attention-based Bi-LSTM.
  IPSJ Transactions on Bioinformatics 2023; 16:20-27 [Link]

• Yoshinaga M, Nakayama T, Inagaki Y
  A novel structural maintenance of chromosomes (SMC)-related protein family specific to Archaea.
  Front Microbiol 2022; 13:913088 [Link]

• Matsuo E, Morita K, Nakayama T, Yazaki E, Sarai C, Takahashi K, Iwataki M, Inagaki Y
  Comparative Plastid Genomics of Green-Colored Dinoflagellates Unveils Parallel Genome Compaction and RNA Editing.
  Front Plant Sci 2022; 13:918543 [Link]

• Kamikawa R, Mochizuki T, Sakamoto M, Tanizawa Y, Nakayama T, Onuma R, Cenci U, Moog D, Speak S, Sarkozi K, Toseland A, van Oosterhout C, Oyama K, Kato M, Kume K, Kayama M, Azuma T, Ishii K-I, Miyashita H, Henrissat B, Lombard V, Win J, Kamoun S, Kashiyama Y, Mayama S, Miyagishima S-Y, Tanifuji G, Mock T, Nakamura Y
  Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida.
  Sci Adv 2022; 8(17):eabi5075 [Link]

• Yazaki E, Miyata R, Chikami Y, Harada R, Kawakubo T, Tanifuji G, Nakayama T, Yahata K, Hashimoto T, Inagaki Y
  Signs of the plastid: Enzymes involved in plastid-localized metabolic pathways in a eugregarine species.
  Parasitol Int 2021; 83:102364 [Link]

• Kawachi M, Nakayama T, Kayama M, Nomura M, Miyashita H, Bojo O, Rhodes L, Sym S, Pienaar RN, Probert I, Inouye I, Kamikawa R
  Rappemonads are haptophyte phytoplankton.
  Curr Biol 2021; 31(11):2395-2403.e4 [Link]

• Kanamori S, Cádiz A, Díaz LM, Ishii Y, Nakayama T, Kawata M
  Detection of genes positively selected in Cuban Anolis lizards that naturally inhabit hot and open areas and currently thrive in urban areas.
  Ecol Evol 2021; 11(4):1719-1728 [Link]

• Nakayama T, Takahashi K, Kamikawa R, Iwataki M, Inagaki Y, Tanifuji G
  Putative genome features of relic green alga-derived nuclei in dinoflagellates and future perspectives as model organisms.
  Commun Integr Biol 2020; 13(1):84-88 [Link]

• Sarai C, Tanifuji G, Nakayama T, Kamikawa R, Takahashi K, Yazaki E, Matsuo E, Miyashita H, Ishida K-I, Iwataki M, Inagaki Y
  Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesis.
  Proc Natl Acad Sci U S A 2020; 117(10):5364-5375 [Link]

• Nakayama T, Nomura M, Takano Y, Tanifuji G, Shiba K, Inaba K, Inagaki Y, Kawata M
  Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host.
  Proc Natl Acad Sci U S A 2019; 116(32):15973-15978 [Link]

• Tanifuji G, Takabayashi S, Kume K, Takagi M, Nakayama T, Kamikawa R, Inagaki Y, Hashimoto T
  The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites.
  PLoS One 2018; 13(3):e0194487 [Link]

• Nakayama T, Inagaki Y
  Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms.
  Sci Rep 2017; 7(1):13075 [Link]

• Tanifuji G, Cenci U, Moog D, Dean S, Nakayama T, David V, Fiala I, Curtis BA, Sibbald SJ, Onodera NT, Colp M, Flegontov P, Johnson-MacKinnon J, McPhee M, Inagaki Y, Hashimoto T, Kelly S, Gull K, Lukeš J, Archibald JM
  Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis.
  Sci Rep 2017; 7(1):11688 [Link]

• Hirakawa Y, Nakayama T, Keilert N, Ishida K
  Evolution of UhpC‐type hexose‐phosphate transporters in dinoflagellates.
  Phycol Res 2017; 65(2):166-170 [Link]

• Lhee D, Yang EC, Kim JI, Nakayama T, Zuccarello G, Andersen RA, Yoon HS
  Diversity of the Photosynthetic Paulinella Species, with the Description of Paulinella micropora sp. nov. and the Chromatophore Genome Sequence for strain KR01.
  Protist 2017; 168(2):155-170 [Link]

• Noguchi F, Shimamura S, Nakayama T, Yazaki E, Yabuki A, Hashimoto T, Inagaki Y, Fujikura K, Takishita K
  Metabolic Capacity of Mitochondrion-related Organelles in the Free-living Anaerobic Stramenopile Cantina marsupialis.
  Protist 2015; 166(5):534-550 [Link]

• Nakayama T, Inagaki Y
  Unique genome evolution in an intracellular N2-fixing symbiont of a rhopalodiacean diatom.
  Acta Soc Bot Pol 2014; 83(4):409-413 [Link]

• Nakayama T, Kamikawa 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 intracellular lifestyle.
  Proc Natl Acad Sci U S A 2014; 111(31):11407-11412 [Link]

• Nomura M, Nakayama T, Ishida K
  Detailed Process of Shell Construction in the Photosynthetic Testate Amoeba Paulinella chromatophora (Euglyphid, Rhizaria).
  J Eukaryot Microbiol 2014; 61(3):317-321 [Link]

• Demura M, Nakayama T, Kasai F, Kawachi M
  Genetic structure of Japanese Chattonella marina (Raphidophyceae) populations revealed using microsatellite markers.
  Phycol Res 2014; 62(2):102-108 [Link]

• Demura M, Kawachi M, Koshikawa H, Nakayama T, Mayuzumi Y, Watanabe MM
  Succession of Genetic Diversity of Botryococcus braunii (Trebouxiophyceae) in Two Japanese Reservoirs.
  Procedia Environ Sci 2012; 15:3-11 [Link]

• Nakayama T, Archibald JM
  Evolving a photosynthetic organelle.
  BMC Biol 2012; 10(1):35 [Link]

• Nakayama T, Ishida K-I, Archibald JM
  Broad Distribution of TPI-GAPDH Fusion Proteins among Eukaryotes: Evidence for Glycolytic Reactions in the Mitochondrion?
  PLoS One 2012; 7(12):e52340 [Link]

• Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, Arias MC, Ball SG, Gile GH, Hirakawa Y, Hopkins JF, Kuo A, Rensing SA, Schmutz J, Symeonidi A, Elias M, Eveleigh RJM, Herman EK, Klute MJ, Nakayama T, et al.
  Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs.
  Nature 2012; 492(7427):59-65 [Link]

• Nakayama T, Ikegami Y, Nakayama T, Ishida K-I, Inagaki Y, Inouye I
  Spheroid bodies in rhopalodiacean diatoms were derived from a single endosymbiotic cyanobacterium.
  J Plant Res 2011; 124(1):93-97 [Link]

• Kamikawa R, Yabuki A, Nakayama T, Ishida K-I, Hashimoto T, Inagaki Y
  Cercozoa comprises both EF-1α-containing and EFL-containing members.
  Eur J Protistol 2011; 47(1):24-28 [Link]

• Reyes-Prieto A, Yoon HS, Moustafa A, Yang EC, Andersen RA, Boo SM, Nakayama T, Ishida KI, Bhattacharya D
  Differential Gene Retention in Plastids of Common Recent Origin.
  Mol Biol Evol 2010; 27(7):1530-1537 [Link]

• Ishida K-I, Inagaki Y, Sakaguchi M, Oiwa A, Kai A, Masahiro S, Nakayama T, Chikuni T, Yabuki A, Haruyo Y, Yubuki N, Yoshida M, Nakayama T, Inouye I, Hashimoto T
  Comprehensive SSU rRNA phylogeny of eukaryota.
  J Endocytobiosis Cell Res 2010; 20:81-88

• Yoon HS, Nakayama T, Reyes-Prieto A, Andersen RA, Boo SM, Ishida K-I, Bhattacharya D
  A single origin of the photosynthetic organelle in different Paulinella lineages.
  BMC Evol Biol 2009; 9(1):98 [Link]

• Nakayama T, Ishida K-I
  Another acquisition of a primary photosynthetic organelle is underway in Paulinella chromatophora.
  Curr Biol 2009; 19(7):R284-R285 [Link]

Review Articles

• 中山卓郎. ボリューム電子顕微鏡によって明らかとなった光合成性有殻アメーバPaulinella microporaの被殻の三次元構造とその構築様式. 藻類 74(2), 85-90. (2026)

• 中山卓郎, 稲垣祐司. シアノバクテリアと真核藻類の細胞統合—「窒素固定オルガネラ」へ続く道？ 生物の科学 遺伝 ［特集：真核細胞の共生由来オルガネラ研究最前線—広がり続ける多様性と機能］　70(2):176-180. (2016)

• 稲垣祐司, 中山卓郎. 現在も続く細胞内共生細菌のオルガネラ化． 共生の生物学 Part VI 細胞内共生（化学同人） 17章p203-213. (2016)

• 中山卓郎. Paulinella chromatophoraに見る一次共生のスナップショット. 藻類 60, 142-144. (2012) [PDF]

• 中山卓郎. 新たなる一次葉緑体の獲得-Paulinella chromatophoraに見られる共生関係-. 藻類 57, 98-100. (2009) [PDF]

• 中山卓郎, 石田健一郎. 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(1), 27-31. (2008) [PDF]

Presentations in International Meetings

• Genome analysis of a symbiotic nitrogen-fixing cyanobacterium in a pelagic dinoflagellate, Histioneis depressa . 2019.7 VIII ECOP-ISOP Joint congress (Rome) Nakayama T, Takano Y, Nomura M, Shiba K, Inaba K, Tanifuji G, Inagaki Y, Kawata M

• Genome analysis of a symbiotic cyanobacterium in a dinophysialean dinoflagellate, Ornithocercus magnificus. 2018.5 XXII Meeting of the International Society of Evolutionary Protistology (Cyprus) Nakayama T, Takano Y, Nomura M, Shiba K, Inaba K, Tanifuji G, Inagaki Y, Kawata M

• Non-photosynthetic evolution of photosynthetic bacteria living inside a cell. 2017.8 3^rd Annual Data Science in Life Science and Engineering Collaboration and Symposium (Cleveland, USA) Nakayama T

• Phylogenetic positions of marine gregarines Selenidium terebellae and Lecudina tuzetae, and molecular evidence of their remnant nonphotosynthetic plastids (apicoplasts). 2016.9 ICES2016 (Kyoto, Japan) Wakeman K, Nakayama T (presenter), Tanifuji G, Matsuo E, Leander BS, Inagaki Y

• Cyanobacterial genes in the nuclear genome of a diatom bearing N₂-fixing cyanobacterial endosymbionts. 2016.6 Protist 2016 (Moscow, Russia) Nakayama T, Inagaki Y

• Genome evolution of non-photosynthetic cyanobacteria residing in diatom cells. 2015.9 International Symposium on Matryoshka-Type Evolution of Eukaryotic Cells (Tsukuba, Japan) Nakayama T

• "Green genes" in novel green colored dinoflagellates: signs of the nucleomorph genomes. 2014.8 Protist2014 (Banff, Canada) Nakayama T, Tanifuji G, Kamikawa R, Matsuo E, Sarai C, Takahashi K,Ishida K, Iwataki M, Inagaki Y

• Green dinoflagellates: their origins and implications from transcriptome analysis. 2014.6 CIFAR meeting (Liblice, Czech) Nakayama T, Inagaki Y

• Nitrogen-fixing organelle? Genome sequence of a cyanobacterial endosymbiont in a rhopalodiacean diatom. 2014.3 Microbe Evolution2014 Tsukuba (Tsukuba, Japan) Nakayama T

• Broad distribution of TPI-GAPDH fusion proteins among eukaryotes: evidence for glycolysis in the mitochondrion? 2012.7 Protist2012 (Oslo, Norway) Nakayama T, Ishida K, Archibald JM

• Paulinella chromatophora possesses TPI-GAPDH fusion protein gene presumably transferred from the stramenopile lineage 2010.7 ISEP XVIII (Kanazawa, Japan) Nakayama T, Ishida K, Kasai F

• Evidence for endosymbiotic gene transfer in a photosynthetic testate amoeba, Paulinella chromatophora 2009.8 Int.Phycological Congress (Tokyo, Japan) NakayamaT, Ishida K

• Several genes for chromatophore proteins are nuclear-encoded in Paulinella chromatophora 2008.7 Protist2008 (Halifax, Canada) NakayamaT, Ishida K

• Single origin of Paulinella chromatophora cyanelles 2007.9 10th Int. Colloq. Endocytobiol. Symbiosis (Gmunden, Austria) Nakayama T, Ishida K

• Single origin of Paulinella chromatophora cyanelles 2006.10 Marine Algae and Global Warming (Seoul, Korea) Nakayama T, Ishida K

• Another primary endosymbiosis? -Origin of Paulinella chromatophora cyanelles- 2005.8 Int. Phycological Congress (Durban, South Africa) Nakayama T, Ishida