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中山卓郎

Nakayama, Takuro

計算科学研究センター , 助教
Center for Computational Sciences , Assistant Professor

1. Diversity and evolution of DNA polymerase θ in eukaryotes and the origin of mitochondrion-localized DNA polymerase PolIA in Euglenozoa. Ryu, Isogai; Mingzhe, Wei; Ryo, Harada; Euki, Yazaki (+2 著者) INAGAKI, Yuji
Protist 181: 126160 (2026)
2. Diversity and evolution of DNA polymerase θ in eukaryotes and the origin of mitochondrion-localized DNA polymerase PolIA in Euglenozoa. Ryu, Isogai; Mingzhe, Wei; Ryo, Harada; Euki, Yazaki (+2 著者) INAGAKI, Yuji
SSRN (2026)
3. Drastic genome reduction driven by parasitic lifestyle: Two complete genomes of endosymbiotic bacteria possibly hosted by a dinoflagellate. Nakayama, Takuro; Harada, Ryo; Yabuki, Akinori; Nomura, Mami (+2 著者) Inagaki, Yuji
Microbes and Environments 40: ME250005 (2025) Semantic Scholar
4. A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome. Ryo, Harada; Yuki, Nishimura; Mami, Nomura; Akinori, Yabuki (+3 著者) Takuro, Nakayama
bioRχiv (2025)
5. Phylogenetic dissection provides insights into the incongruity in the tree of Archaeplastida between the analyses of nucleus- and plastid-encoded proteins. Ryu, Isogai; Ryo, Harada; Takuro, Nakayama; INAGAKI, Yuji
bioRχiv (2025) Semantic Scholar
6. Drastic genome reduction driven by parasitic lifestyle: Two complete genomes of endosymbiotic bacteria possibly hosted by a dinoflagellate. Nakayama, Takuro; Harada, Ryo; Yabuki, Akinori; Nomura, Mami (+2 著者) Inagaki, Yuji
bioRχiv (2025) Semantic Scholar
7. Convergent reductive evolution of cyanobacteria in symbiosis with Dinophysiales dinoflagellates. Nakayama, Takuro; Nomura, Mami; Yabuki, Akinori; Shiba, Kogiku (+1 著者) Inagaki, Yuji
Scientific Reports 14: 12774 (2024) Semantic Scholar
8. Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches in Anolis lizards Sakamoto, Fuku; Kanamori, Shunsuke; Díaz, Luis M.; Cádiz, Antonio (+5 著者) Kawata, Masakado
ECOLOGY AND EVOLUTION 14: (2024) Semantic Scholar
9. A practical assembly guideline for genomes with various levels of heterozygosity Takako Mochizuki; Mika Sakamoto; Yasuhiro Tanizawa; Takuro Nakayama (+2 著者) Yasukazu Nakamura
Briefings in Bioinformatics 24: (2023) Semantic Scholar
10. Three-dimensional architecture and assembly mechanism of the egg-shaped shell in testate amoeba Paulinella micropora Mami Nomura; Keisuke Ohta; Yukinori Nishigami; Takuro Nakayama (+2 著者) Josephine Galipon
Frontiers in Cell and Developmental Biology 11: (2023) Semantic Scholar
11. AtLASS: A scheme for end-to-end prediction of splice sites using attention-based bi-LSTM. Harada, Ryo; Kume, Keitaro; Horie, Kazumasa; Nakayama, Takuro (+1 著者) Amagasa, Toshiyuki
IPSJ Transactions on Bioinformatics 16: 20 (2023) Semantic Scholar
12. A novel structural maintenance of chromosomes (SMC)-related protein family specific to Archaea Yoshinaga, Mari; Nakayama, Takuro; Inagaki, Yuji
FRONTIERS IN MICROBIOLOGY 13: 913088 (2022) Semantic Scholar
13. Comparative Plastid Genomics of Green-Colored Dinoflagellates Unveils Parallel Genome Compaction and RNA Editing Eriko Matsuo; Kounosuke Morita; Takuro Nakayama; Euki Yazaki (+3 著者) Yuji Inagaki
Frontiers in Plant Science 13: (2022) Semantic Scholar
14. Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida Ryoma Kamikawa; Takako Mochizuki; Mika Sakamoto; Yasuhiro Tanizawa (+24 著者) Yasukazu Nakamura
Science Advances 8: (2022) Semantic Scholar
15. Rappemonads are haptophyte phytoplankton. Masanobu Kawachi; Takuro Nakayama; Motoki Kayama; Mami Nomura (+7 著者) Ryoma Kamikawa
Current biology : CB 31: 2395 (2021) Semantic Scholar
16. Signs of the plastid: Enzymes involved in plastid-localized metabolic pathways in a eugregarine species. Euki Yazaki; Ryosuke Miyata; Yasuhiko Chikami; Ryo Harada (+5 著者) Yuji Inagaki
Parasitology international 83: 102364 (2021) Semantic Scholar
17. Detection of genes positively selected in Cuban Anolis lizards that naturally inhabit hot and open areas and currently thrive in urban areas Shunsuke Kanamori; Antonio Cádiz; Luis M. Díaz; Yuu Ishii (+1 著者) Masakado Kawata
Ecology and Evolution 11: 1719 (2021) Semantic Scholar
18. Putative genome features of relic green alga-derived nuclei in dinoflagellates and future perspectives as model organisms Takuro Nakayama; Kazuya Takahashi; Ryoma Kamikawa; Mitsunori Iwataki (+1 著者) Goro Tanifuji
Communicative & Integrative Biology 13: 84 (2020) Semantic Scholar
19. Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesis Chihiro Sarai; Goro Tanifuji; Takuro Nakayama; Ryoma Kamikawa (+6 著者) Yuji Inagaki
Proceedings of the National Academy of Sciences of the United States of America 117: (2020)
20. Large DNA virus promoted the endosymbiotic evolution to make a photosynthetic eukaryote Matsuo, Mitsuhiro; Katahata, Atsushi; Tchikawa, Makoto; Minakuchi, Yohei (+11 著者) Obokata, Junichi
bioRχiv (2019) Semantic Scholar

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1. 原生生物学事典中山, 卓郎
朝倉書店 2023年5月 (ISBN: 4254171811)

1. 栽培される共生体：海洋渦鞭毛藻とシアノバクテリアの共生関係中山, 卓郎
日本植物学会第86回大会 2022年9月17日
2. Paulinella microporaにおけるマイクロボディの局在とその機能推定野村, 真未; 中山, 卓郎; 中村, 桂一郎; 太田, 啓介
日本植物学会第86回大会 2022年9月17日
3. Draft nucleomorph genomes of green-colored dinoflagellates Inagaki, Yuji; Nakayama, Takuro; Kawakubo, Takashi; Matsuo, Eriko; Takahashi, Kazuya; Iwataki, Mitsunori
21st Symposium of the International Society of Endocytobiology 2022年7月19日招待有り
4. 緑色渦鞭毛藻Lepidodinium chlorophorumにおけるヌクレオモルフゲノムの存在検証中山卓郎; 稲垣, 祐司
日本藻類学会第46回大会 2022年3月29日
5. 緑色渦鞭毛藻Lepidodinium chlorophorumにおけるヌクレオモルフゲノムの存在検証中山卓郎; 稲垣, 祐司
日本藻類学会第46回大会 2022年3月29日
6. 様々なヘテロ接合度の生物を用いたハプロイドセット構築のためのゲノムアセンブリ手法の評価望月, 孝子; 坂本, 美佳; 谷澤, 靖洋; 中山, 卓郎; 谷藤, 吾朗; 神川, 龍馬; 中村, 保一
日本分子生物学会年会 2021年12月1日
7. 緑色渦鞭毛藻3種のペディノ藻由来色素体ゲノム間での共通性と特異性松尾恵梨子; 森田幸之介; 中山卓郎; 皿井千裕; 高橋和也; 岩滝光儀; 稲垣, 祐司
日本共生生物学会第5回大会 2021年11月27日
8. 原生生物に共生するシアノバクテリアの進化と多様性に関する研究中山, 卓郎
日本植物学会第85回大会 2021年9月18日
9. Draft nucleomorph genome of the dinoflagellate strain TGD. Ayaka, Fujishiro; Ryu, Isogai; Shigekatsu, Suzuki; Kazuya, Takahashi; Mitsunori, Iwataki; INAGAKI, Yuji; Takuro, Nakayama
Protist Open 2026
10. Non-parametric bootstrap with the PMSF model can overestimate support values. Ryu, Isogai; Ryo, Harada; Takuro, Nakayama; INAGAKI, Yuji
Protist Open 2026
11. テトラヒメナの繊毛運動を制御する新奇アクチン関連タンパク質 tArp 加川海来; 萩田美乃里; 中山卓郎; 柴小菊; 箕浦高子; 松田真弥; 稲葉一男; 稲垣祐司; 中野賢太郎
生体運動研究合同班会議 2026
12. Recent plastid replacement in Karlodinium ballantinum challenges the paradigms of endosymbiotic gene transfer. Maciszewski, Kacper; Takahashi, Kazuya; Harada, Ryo; Martinek, Inga; Nakayama, Takuro; Iwataki, Mitsunori; INAGAKI, Yuji; Hehenberger., Elisabeth
Protist Open 2026
13. Microscopy and phylogenomics of novel deep-branching CRuMs. Packer, Julia; Harada, Ryo; Isogai, Ryu; Nakayama, Takuro; Eglit, Yana; Shiratori, Takashi; INAGAKI, Yuji; Simpson; Alastair GB
Protist Open 2026
14. 真核生物におけるDNAポリメラーゼθの多様性とユーグレノゾア特異的ミトコンドリアDNAポリメラーゼPolIAの起源．魏明哲; 磯貝龍邑; 原田亮; 矢﨑裕規; 中山卓郎; Ryan, Gawryluk; 稲垣, 祐司
第28回日本サンゴ礁学会・第9回日本共生生物学会合同大会
15. 系統解析において座位ごとのアミノ酸組成をモデル化する手法(PMSF)に起因するバイアスの検証．磯貝龍邑; 原田亮; 中山卓郎; 稲垣, 祐司
第28回日本サンゴ礁学会・第9回日本共生生物学会合同大会
16. メタモナダに近縁性が示唆された真核微生物2株のミトコンドリアゲノム解析．松浦眞子; 磯貝龍邑; 原田亮; 白鳥峻志; 中山卓郎; 稲垣, 祐司
第28回日本サンゴ礁学会・第9回日本共生生物学会合同大会
17. On the tree of Archaeplastida: The impact of rapidly evolving and heterotachious positions on nuclear and plastid phylogenomic inferences. Isogai, Ryu; Harada, Ryo; Nakayama, Takuro; INAGAKI, Yuji
ICOP/ISEP2025
18. Nucleomorph genome of the dinoflagellate TGD reveals an early stage of genome reduction following secondary endosymbiosis. Fujishiro, Ayaka; Isogai, Ryu; Suzuki, Shigekatsu; Takahashi, Kazuya; Iwataki, Mitsunori; INAGAKI, Yuji; Nakayama, Takuro
ICOP/ISEP2025
19. Recent plastid replacement in Karlodinium ballantinum (Kareniaceae, Dinoflagellata) challenges the paradigms of endosymbiotic gene transfer. Maciszewski, Kacper; Takahashi, Kazuya; Harada, Ryo; Martinek, Inga; Nakayama, Takuro; Iwataki, Mitsunori; INAGAKI, Yuji; Hehenberger, Elisabeth
ICOP/ISOP2025
20. Thermoproteota門古細菌におけるPCNA進化．上西慧莉紗; 原田亮; 中山卓郎; 稲垣, 祐司
第37回Archaea研究会