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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

オープンアクセス版の論文は「つくばリポジトリ」で読むことができます。

1. 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
2. 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)
3. 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)
4. 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
5. 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
6. 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
7. 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
8. 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
9. 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
10. 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
11. 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
12. 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
13. 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
14. 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
15. 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
16. 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)
17. 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
18. Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host Takuro Nakayama; Mami Nomura; Yoshihito Takano; Goro Tanifuji (+3 著者) Masakado Kawata
Proceedings of the National Academy of Sciences 116: 15973 (2019) Semantic Scholar
19. The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites Goro Tanifuji; Shun Takabayashi; Keitaro Kume; Mizue Takagi (+3 著者) Tetsuo Hashimoto
PLoS ONE 13: (2018) Semantic Scholar
20. Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms Takuro Nakayama; Yuji Inagaki
SCIENTIFIC REPORTS 7: 13075 (2017) 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. 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
10. 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
11. 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
12. 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
13. tARP is an actin-related protein required for ciliary function that is conserved in ciliates and related eukaryotic groups. Kagawa, Miku; Takuro, Nakayama; Shiba, Kogiku; Takako, Kato-Minoura; Matsuda, Shinya; Inaba, Kazuo; INAGAKI, Yuji; Kentaro, Nakano
第77回日本細胞生物学会・第58回日本発生生物学会合同大会
14. 光合成をやめたシアノバクテリアのゲノム進化中山, 卓郎
大隅基礎科学創成財団微生物機能探究コンソーシアムG4定例会招待有り
15. 緑色渦鞭毛藻TGD株のヌクレオモルフゲノムが示す二次共生ゲノム進化の新たなスナップショット藤代彩花; 磯貝龍邑; 鈴木重勝; 高橋和也; 岩滝光儀; 稲垣, 祐司; 中山卓郎
日本植物学会第89回大会
16. Hidden microbial diversity: Novel microbial lineages discovered in dinoflagellate symbioses NAKAYAMA, Takuro
AIMEC Science Salon 招待有り
17. 珪藻に共生する窒素固定シアノバクテリアと「ニトロプラスト」中山, 卓郎
藍藻の分子生物学2024 招待有り
18. 単細胞ゲノム増幅産物から発見された極小古細菌ゲノム．原田亮; 西村祐貴; 野村真未; 矢吹彬憲; 稲垣, 祐司; 中山卓郎
日本微生物生態学会第37回大会
19. 原生生物の核ゲノム転写物におけるRNA Editingの探索．磯貝龍邑; 原田亮; 矢﨑裕規; 中山卓郎; 稲垣, 祐司; 矢吹彬憲
日本共生生物学会第8回大会
20. Metamonadaとの近縁性が示唆される好気性原生生物の系統分類学的研究．白鳥峻志; 原田亮; 磯貝龍邑; 中山卓郎; 稲垣, 祐司
日本共生生物学会第8回大会