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稲垣祐司

Inagaki, Yuji

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

http://sites.google.com/site/yujiswebsite/Home

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. 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. Colponemidia questions the ancestry of an ATG10-lacking ATG8-ATG12 conjugation system in Alveolata. Yazaki, Euki; Isogai, Ryu; INAGAKI, Yuji
Journal of Protistology 57: e008 (2026)
3. Morphology, ultrastructure, and classification of barthelonids (Metamonada incertae sedis): with description of Microbarthelona gen. nov., and Parabarthelona gen. nov. Takashi, Shiratori; Yana, Egli; Euki, Yazaki; INAGAKI, Yuji (+1 著者) Simpson Alastair
Journal of Eukaryotic Micobiology 73: e70080 (2026)
4. Protists with Uncertain Phylogenetic Affiliations for Resolving the Deep Tree of Eukaryotes Yazaki, Euki; Shiratori, Takashi; INAGAKI, Yuji
Microorganisms 13: 1926 (2025) Semantic Scholar
5. Protists with uncertain phylogenetic affiliations for resolving the deep tree of eukaryotes. Yazaki, Euki; Shiratori, Takashi; INAGAKI, Yuji
Microorganisms 13: 1926 (2025)
6. A deeply branching lineage in Heterolobosea (Discoba) with multiflagellated and multigrooved life stages. Prokina; Kristina I.; Yubuki, Naoji; Galindo, Luis Javier (+4 著者) Moreira, David
Journal of Eukaryotic Micobiology 72: e70037 (2025)
7. Glissandra oviformis n. sp.: a novel predatory flagellate illuminates the character evolution within the eukaryotic clade CRuMs. Yazaki, Euki; Harada, Ryo; Isogai, Ryu; Bamba, Kohei (+2 著者) Shiratori, Takashi
Open Biology 15: 250057 (2025)
8. Marked genome reduction driven by a 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
9. 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
10. 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)
11. An expanded phylogenomic analysis of Heterolobosea reveals the deep relationships, non-canonical genetic codes, and cryptic flagellate stages in the group. Pánek, Tomáš; Tice, Alexander K.; Corre, Pia; Hrubá, Pavla (+13 著者) Čepička, Ivan
Molecular Phylogenetics and Evolution 204: 108289 (2025)
12. Complete mitochondrial genomes of ancyromonads provide clues for the gene content and genome structures of ancestral mitochondria. Harada, Ryo; Shiratori, Takashi; Yabuki, Akinori; INAGAKI, Yuji (+1 著者) Kamikawa, Ryoma
bioRχiv 72: e70012 (2025)
13. 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
14. AUTOEB: A software for systematically evaluating bipartitions in a phylogenetic tree employing an approximately unbiased test. Kohei, Bamba; Ryo, Harada; INAGAKI, Yuji
IPSJ Transactions on Bioinformatics 17: 72 (2024) Semantic Scholar
15. Dinotoms possess two evolutionary distinct autophagy-related ubiquitin-like conjugation systems. Yazaki, Euki; Uehara, Tadaaki; Sakaoto, Hirokazu; Inagaki, Yuji
Protist 175: 126067 (2024) Semantic Scholar
16. オルガネラ局在DNAポリメラーゼの多様性と進化：現状とこれからの課題．稲垣, 祐司; 原田亮
月刊アグリバイオ 8: 43 (2024)
17. 新奇DNAポリメラーゼrdxPolAは、古のミトコンドリアDNA維持装置の遺産か？原田亮; 稲垣, 祐司
The Japanese Journal of Phycology (Sôrui) 72: 104 (2024)
18. Convergent reductive evolution of cyanobacteria in symbiosis with Dinophysiales dinoflagellates Takuro Nakayama; Mami Nomura; Akinori Yabuki; Kogiku Shiba (+1 著者) Yuji Inagaki
Scientific Reports 14: 12774 (2024) Semantic Scholar
19. Gleaning Euglenozoa-specific DNA polymerases in public single-cell transcriptome data Harada, Ryo; Inagaki, Yuji
PROTIST 174: 125997 (2023) Semantic Scholar
20. Transcriptome data sets of free-living diplomonads, Treponema sp, and Hexamita sp. Kume, Keitaro; Tsubasa, Gen; Kazuki, Abe; Hiroshi, Komatsuzaki (+4 著者) Hashimoto, Tetsuo
MICROBIOLOGY RESOURCE ANNOUNCEMENTS 12: e0050623 (2023) Semantic Scholar

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1. 共生微生物稲垣,祐司; 中山卓郎 (担当:分担執筆, 範囲:第17章現在も続く細胞内共生細菌のオルガネラ化．)
化学同人 2016年10月 (ISBN: 9784759817287)
2. Reference modules in Materials Science and Engineering 2016 Harada, Ryuhei; Inagaki, Yuji; Shigeta, Yasuteru (担当:分担執筆, 範囲:Protein Folding and Evolution)
2016年6月
3. ロングブランチの誘惑--分子系統解析のダークサイド稲垣祐司 (担当:監修)
藻類 2007年7月
4. アピコンプレクサ類の退化葉緑体は緑藻起源か？稲垣祐司 (担当:監修)
藻類 2004年1月

161. 寄生虫化に伴うディプロモナス類の遺伝子レパートリーの変化．久米, 慶太郎; 若島, 朋幸; 厳, 翼; 岩本, 亮介; 井上, 貴史; 谷藤, 吾朗; 神川, 龍馬; 稲垣, 祐司; 橋本, 哲男
日本共生生物学会第8回大会
162. アピコンプレクサおよびその近縁系統におけるオルガネラ局在DNAポリメラーゼの多様性と進化．稲垣, 祐司; 原田亮
奄美医科学研究シンポジウム
163. Recent endosymbiosis between a haptophyte and a Kareniacean dinoflagellate and “Full-furnished apartment hypothesis.” INAGAKI, Yuji
5ᵗʰ Asian Marine Biology Symposium
164. AUTOEB: A software for systematically evaluating bipartitions in a phylogenetic tree employing an approximately unbiased test. Kohei, Bamba; Ryo, Harada; INAGAKI, Yuji
第79回バイオ情報学研究会
165. Dinotoms possess two evolutionary distinct autophagy-related ubiquitin-like conjugation systems. Euki, Yazaki; Tadaaki, Ueraha; Hirokazu, Sakamoto; Inagaki, Yuji
Annual Meeting of the Society for Molecular Biology and Evolution 2024
166. 緑色渦鞭毛藻TGD株のヌクレオモルフゲノムの解析．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88回大会
167. 光合成関連遺伝子に着目した緑色渦鞭毛藻TGD株のヌクレオモルフゲノムの解析．藤代彩花; 磯貝龍邑; 高橋和也; 岩滝光儀; 稲垣, 祐司; 中山卓郎
日本藻類学会第48回大会
168. ディプロモナス類の寄生虫化に伴う遺伝子レパートリーの変化：近縁自由生活種とのオルソログ比較解析久米, 慶太郎; 若島, 朋幸; 厳, 翼; 岩本, 亮介; 井上, 貴史; 谷藤, 吾朗; 神川, 龍馬; 稲垣, 祐司; 橋本, 哲男
第93回日本寄生虫学会大会
169. 寄生性ユーグレナ類Euglenaformis parasiticaにおける非光合成性葉緑体の存在とその機能加藤孝一朗; 南波紀昭; 稲垣, 祐司; 中山剛; 中山卓郎
日本植物学会第87回大会
170. I″型ルビスコの発見：I/I′型ルビスコに対する祖先的タンパク質群．番場浩平; 稲垣, 祐司
日本共生生物学会第7回大会
171. クレン古細菌におけるPCNA複合体の進化．上西慧莉紗; 原田亮; 吉永真理; 稲垣, 祐司
日本共生生物学会第7回大会
172. 一次植物内部系統関係におけるタクソンサンプリングの影響：紅藻類と灰色藻類のどちらが初期分岐系統なのか？磯貝龍邑; 原田亮; 中山卓郎; 稲垣, 祐司
日本共生生物学会第7回大会
173. 細胞サイズ別環境 DNA を用いた共生性シアノバクテリアの探索．宮本知世; 矢吹彬憲; 野村真未; 柴小菊; 稲葉一男; 稲垣, 祐司; 中山卓郎
日本共生生物学会第7回大会
174. Repeated haptophyte endosymbioses in the dinoflagellate family Kareniaceae. Inagaki, Yuji; Benico, Garry; Takahashi, Kazuya; Ryo, Harada; Martinek, Inga; Maciszewski, Kacper; Nakayama, Takuro; Iwataki, Mitsunori; Kolisko, Martin; Hehenberger, Elisabeth
IX ECOP-ISOP joint meeting 2023 ECOP
175. Impact of taxon sampling on the relationship among Rhodophyta, Glaucophyta, and Chloroplastida inferred from nuclear gene-based phylogenomic analyses. Isogai, Ryu; Ryo, Harada; Nakayama, Takuro; Inagaki, Yuji
IX ECOP-ISOP joint meeting 2023 ECOP
176. A non-kareniacean dinoflagellate with a haptophyte-derived plastid indicates multiple tertiary endosymbioses. Takahashi, Kazuya; Nakayama, Takuro; Inagaki, Yuji; Hehenberger, Elisabeth; Iwataki, Mitsunori
IX ECOP-ISOP joint meeting 2023 ECOP
177. Evolution and switching of mitochondrion-localized DNA polymerases in Euglenozoa. Ryo, Harada; Hirakawa, Yoshihisa; Yabuki, Akinori; Kim, Ensoo; Yazaki, Euki; Ryoma, Kamikawa; Nakano, Kentaro; Eliáš, Marek; Inagaki, Yuji
3ʳᵈ Annual International Congress on Euglenoids 2023 Euglena International Network
178. AtLASS: A Scheme for end-to-end prediction of splice sites using attention-based bi-LSTM. 原田亮; 久米慶太郎; 堀江和正; 中山卓郎; 稲垣, 祐司; 天笠俊之
第74回バイオ情報学(SIGBIO)研究会
179. 最尤系統樹中の2分岐の信頼性に対する新たな評価手法．番場浩平; 稲垣, 祐司; 原田亮; 中山卓郎; 磯貝龍邑
第74回バイオ情報学(SIGBIO)研究会
180. Evolution and switching of mitochondrion-localized DNA polymerases in Euglenozoa. Ryo, Harada; Hirakawa, Yoshihisa; Yabuki, Akinori; Kim, Ensoo; Yazaki, Euki; Ryoma, Kamikawa; Nakano, Kentaro; Elia?, Marek; Inagaki, Yuji
3?? Annual International Congress on Euglenoids 2023 Euglena International Network