Inagaki Yuji
- Affiliation
- Center for Computational Sciences
- Official title
- Professor
- ORCID
- 0000-0003-0101-8483
- URL
- Research fields
Evolutionary biology Biodiversity/Systematics - Research keywords
eukaryotes orgenelle evolution molecular evolution genome evolution protein facotrs involved in translation gene duplication lataral gene transfer - Research projects
真核生物ゲノムデータに混入している原核共生体ゲノムの体系的探索 2023 -- 2026 稲垣 祐司 Japan Society for the Promotion of Science/Grant-in-Aid for Scientific Research(B) 18,330,000Yen 真核生物ゲノムデータに混入している原核共生体ゲノムの体系的探索 2023-04 -- 2027-03 稲垣祐司 日本学術振興会/基盤研究(B) 3次葉緑体をもつ渦鞭毛藻類における葉緑体進化 2023-04 -- 2025-03 稲垣祐司 日本学術振興会/二国間交流事業 共同研究 ミトコンドリアDNAポリメラーゼの多様性と進化の全容解明 2019 -- 2022 稲垣 祐司 Japan Society for the Promotion of Science/Grant-in-Aid for Scientific Research(B) 17,030,000Yen 海洋原生生物に共生する細菌多様性の実態解明 2018 -- 2022 Yuji Inagaki 日本学術振興会/国際共同研究加速基金(国際共同研究強化(B)) 海洋バクテリアの長期炭素隔離機能に対する海洋酸性化の影響評価 2016 -- 2019 濱健夫 日本学術振興会/科学研究費補助金 基盤研究(B) 非光合成生物の光適応進化の全容解明 2017 -- 2020 谷藤吾朗 日本学術振興会/科学研究費補助金 基盤研究(B) 渦鞭毛藻細胞内に発見された新たな共生体痕跡核ゲノムの解読 2016 -- 2018 稲垣 祐司 Japan Society for the Promotion of Science/Grant-in-Aid for Scientific Research(B) 17,420,000Yen 新型分割イントロン切り出し因子同定に基づく真核生物mRNA成熟機構進化の解明 2011 -- 2015 Japan Society of for the Promotion of Science/基盤研究(A) 2,000,000Yen ミトコンドリア・色素体以外の共生オルガネラ成立過程の解明 2011 -- 2015 Ministry of Education, Culture, Sports, Science and Technology, Japan/新学術領域研究 50,960,000Yen more... - Career history
1996-01 -- 1996-03 日本学術振興会名古屋大学特別研究員 1996-04 -- 1998-03 ㈱JT生命誌研究館奨励研究員 1998-04 -- 2000-03 日本学術振興会派遣先:カナダ・ダルハウジー大学海外特別研究員 2000-04 -- 2004-03 ダルハウジー大学(カナダ)博士研究員 2004-04 -- 2005-07 長浜バイオ大学バイオサイエンス学部バイオサイエンス学科講師 2005-08 -- 2007-03 筑波大学大学院生命環境科学研究科助教授 2007-04 -- 2011-09 筑波大学大学院生命環境科学研究科准教授 2011-10 -- 2016-03 筑波大学生命環境系准教授 2016-04 -- (current) 筑波大学計算科学研究センター教授 - Academic background
1987-04 -- 1991-03 Nagoya University Faculty of Science 1991-04 -- 1993-03 Nagoya University Graduate School, Division of Natural Science 生物学専攻博士課程(前期) 1993-04 -- 1995-12 Nagoya University Graduate School, Division of Natural Science 生物学専攻博士課程(後期) - Degree
1995-12 博士(理学) Nagoya University - Academic societies
2004 -- (current) SOCIETY OF EVOLUTIONARY STUDIES, JAPAN 2005 -- (current) THE JAPANESE SOCIETY OF PHYCOLOGY 2004 -- (current) The Molecular Biology Society of Japan -- (current) International Society for Evolutionary Protistology 2008 -- (current) International Society of Protistologists 2004 -- (current) Society for Molecular Biology and Evolution - Honors & Awards
1993-04-01 公益信託森安大学院生奨学基金 2007-04-17 科学技術分野の文部科学大臣表彰若手科学者賞 2008-08-23 日本進化学会研究奨励賞 - Articles
- Encyclopedia of family A DNA polymerases localized in organelles: Contribution of genes from diverse bacteria including the proto-mitochodrion.
Harada Ryo; Hirakawa Yoshihisa; Yabuki Akinori; Kim E...
bioRχiv, 2023-08 - Transcriptome data sets of free-living diplomonads, Treponema sp, and Hexamita sp.
Kume Keitaro; Tsubasa Gen; Kazuki Abe; Hiroshi Komats...
Microbiology Resource Announcements, 2023-12 - AtLASS: A scheme for end-to-end prediction of splice sites using attention-based bi-LSTM.
Harada Ryo; Kume Keitaro; Horie Kazumasa; Nakayama Takur...
IPSJ Transactions on Bioinformatics/16/pp.20-27, 2023-07 - 遺伝子水平伝播が支配するオルガネラ局在ファミリーA DNAポリメラーゼの進化
原田亮; 稲垣 祐司
月刊 細胞/55(6)/pp.33-36, 2023-04 - Fascinating strategies of marine organisms to cope with coming pollutant: Titanium dioxide nanoparticles.
Ishitani Yoshiyuki; Ciacci Caterina; Ujiié Yurika; Tame ...
Environmental Pollution/330/p.121538, 2023-04 - Draft genome sequence of Aduncisulcus paluster, a free-living microaerophilic eukaryote belonging to Fornicata.
Ikuko Yuyama; Kume Keitaro; Tamura Takumi; Inagaki Yu...
MICROBIOLOGY RESOURCE ANNOUNCEMENTS/12(2)/p.e0053922, 2023-02 - Phylogenomics invokes the clade housing Cryptista, Archaeplastida, and Microheliella maris.
矢﨑裕規; 矢吹彬憲; 稲垣 祐司
Sôrui/70/pp.199-204, 2022-11 - Microheliella maris possesses the most gene-rich mitochondrial genomes in Diaphoretickes.
Yazaki Euki; Yabuki Akinori; Nishimura Yuki; Shiratori T...
Frontiers in Ecology and Evolution/10/p.1030570, 2022-11 - A novel structural maintenance of chromosomes (SMC)-related protein family specific to Archaea
Yoshinaga Mari; Nakayama Takuro; Inagaki Yuji
FRONTIERS IN MICROBIOLOGY/13/p.913088, 2022-08 - Comparative Plastid Genomics of Green-Colored Dinoflagellates Unveils Parallel Genome Compaction and RNA Editing
Eriko Matsuo; Kounosuke Morita; Takuro Nakayama; Yazaki ...
FRONTIERS IN PLANT SCIENCE/13/p.918543, 2022-07 - The closest relative of Archaeplastida is revealed by phylogenomic analyses that include Microheliella maris.
Yazaki Euki; Yabuki Akinori; Imaizumi Ayaka; Kume Keitar...
OPEN BIOLOGY/12(4)/p.210376, 2022-04 - Ubiquity and origins of structural maintenance of chromosomes (SMC) proteins in eukaryotes
Yoshinaga Mari; Inagaki Yuji
Genome Biology and Evolution/13(12)/p.evab256, 2021-12 - Phylogenomics invokes the clade housing Cryptista, Archaeplastida, and Microheliella maris.
Yazaki Euki; Yabuki Akinori; Imaizumi Ayaka; Kume Keitar...
bioRχiv, 2021-08 - Signs of the plastid: Enzymes involved in plastid-localized metabolic pathways in a eugregarine species
Yazaki Euki; Miyata Ryosuke; Chikami Yasuhiko; Harada Ry...
Parasitology International/83/p.102364, 2021-08 - Phage origin of mitochondrion-localized family A DNA polymerases in kinetoplastids and diplonemids.
Ryo Harada; Inagaki Yuji
Genome Biology and Evolution/13(2)/p.evab003, 2021-02 - Experimental analysis of diurnal variations in humic-like fluorescent dissolved organic matters in surface seawater.
Omori Yuko; Saeki AKira; Wada Shigeki; Inagaki Yuji; Hama...
Frontiers in Marine Science/7/p.589064, 2020-10 - Phage origin of mitochondrion-localized family A DNA polymerases in kinetoplastids and diplonemids.
Ryo Harada; Inagaki Yuji
bioRχiv, 2020-09 - Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP
Euki Yazaki; Kume Keitaro; Takashi Shiratori; Yana Eglit...
Proceedings of the Royal Society B/287(1934)/p.20201538, 2020-09 - Putative genome features of the relic green alga-derived nuclei in the dinoflagellates and the future perspectives as model organisms.
Nakayama Takuro; Takahashi Kazuya; Kamikawa Ryoma; Iwatak...
Communicative & Integrative Biology/13(1)/pp.84-88, 2020-06 - Mitochondrial genomes of Hemiarma marina and Leucocryptos marina revised the evolution of cytochrome c maturation in Cryptista.
Yuki Nishimura; Keitaro Kume; Keito Sonehara; Goro Tanif...
Frontiers in Ecology and Evolution/8/p.140, 2020-05 - Inventory and evolution of mitochondrion-localized family A DNA polymerases in Euglenoza.
Ryo Harada; Yoshihisa Hirakawa; Akinori Yabuki; Yuichiro ...
Pathogens/9(4), 2020-04 - Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesis
Sarai Chihiro; Tanifuji Goro; Nakayama Takuro; Kamikawa ...
Proceedings of the National Academy of Sciences of the United States of America/117(10)/pp.5364-5375, 2020-02 - Comparative plastid genomics of Cryptomonas species reveals fine-scale genomic responses to loss of photosynthesis.
Tanifuji Goro; Kamikawa Ryoma; Moore Christa E; Mills Ty...
Genome Biology and Evolution/12(2)/pp.3926-3937, 2020-02 - Large DNA virus promoted the endosymbiotic evolution to make a photosynthetic eukaryote
Matsuo Mitsuhiro; Katahata Atsushi; Tchikawa Makoto; Mina...
bioRχiv, 2019-10 - Barthelonids represent a deep-branching Matamonada clade with mitochondrion-related organelles generating no ATP.
Euki Yazaki; Kume Keitaro; Takashi Shiratori; Yana Edlit...
bioRχiv, 2019-10 - more...
- Encyclopedia of family A DNA polymerases localized in organelles: Contribution of genes from diverse bacteria including the proto-mitochodrion.
- Books
- Protein Folding and Evolution
Harada Ryuhei; Inagaki Yuji; Shigeta Yasuteru
Reference modules in Materials Science and Engineering 2016, 2016-06 - 第17章 現在も続く細胞内共生細菌のオルガネラ化.
稲垣 祐司; 中山卓郎
共生微生物/化学同人/pp.203-212, 2016-10 - 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
The Japanese Journal of Phycology, 2004-01 - 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
The Japanese Journal of Phycology, 2007-07
- Protein Folding and Evolution
- Conference, etc.
- 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/2023-06-29--2023-07-01 - 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/2023-06-29--2023-07-01 - Evolution and switching of mitochondrion-localized DNA polymerases in Euglenozoa.
Ryo Harada; Hirakawa Yoshihisa; Yabuki Akinori; Kim Enso...
3ʳᵈ Annual International Congress on Euglenoids 2023/2023/07/17--2023/07/18 - A non-kareniacean dinoflagellate with a haptophyte-derived plastid indicates multiple tertiary endosymbioses.
Takahashi Kazuya; Nakayama Takuro; Inagaki Yuji; Hehenber...
IX ECOP-ISOP joint meeting 2023/2023/07/09--2023/07/14 - 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 2023/2023/07/09--2023/07/14 - Repeated haptophyte endosymbioses in the dinoflagellate family Kareniaceae.
Inagaki Yuji; Benico Garry; Takahashi Kazuya; Ryo Harada...
IX ECOP-ISOP joint meeting 2023/2023/07/09--2023/07/14 - Has the DNA polymerase of the proto-mitochondrion been retained in Discoba, Malawimonadidae, and Ancyromonadida?: a novel mitochondrion-localized DNA polymerase with the phylogenetic affinity to the alpha-proteobacterial PolI.
Ryo Harada; Inagaki Yuji
IX ECOP-ISOP joint meeting 2023/2023/07/09--2023/07/14 - Serial secondary and serial tertiary endosymbioses in dinoflagellates.
Inagaki Yuji
ICG seminor/2023/03/21--2023/03/21 - Search for free-living-related proteins in free-living diplomonads that transitioned from a parasitic ancestor
厳翼; 久米慶太郎; 阿部一貴; 矢﨑裕規; 小松崎洋志; 谷藤吾朗; 神川龍馬; 稲垣 祐司; 橋本哲男
第92回寄生虫学会大会/2023/03/30--2023/03/31 - 真核生物の大系統:最近の研究成果から見る多様性の広がり、まとまり、今後の展望
稲垣 祐司
第92回寄生虫学会大会サテライトシンポジウム 原生生物学・共生生物学談話会/2023/03/29--2023/03/29 - Recent progress in resolving the diversity and evolution of deep eukaryotic phylogeny
Inagaki Yuji
ISEP23/2023/01/20--2023/01/20 - A factor that hinders the accurate phylogenetic inferences: The monophyly of Archaeplastida as a case study.
Inagaki Yuji
EPCC-CCS Workshop 2022/2022-12-14--2022-12-15 - Endosymbiotic origin of the DNA polymerase localized in euglenid plastids.
Harada Ryo; Eliáš Marek; Inagaki Yuji
2nd Annual International Congress of Euglenids/2022-11-07--2022-11-10 - A novel type of mitochondrion-localized DNA polymerase hints the phylognetic affinity among Malawimonadida, Ancyromonadida, and Discoba, and the possible root of the eukaryotic phylogeny
原田亮; Eliáš Marek; 中野健太郎; 白鳥峻志; 矢吹彬憲; Ensoo Kim; 石田健一郎; 稲垣 祐司
第81回日本寄生虫学会東日本支部大会・日本共生生物学会第6回大会/2022-10-01--2022-10-02 - Euglenids have a plastid-localized DNA polymerase from a green alga related to Pyramimonas
原田亮; Eliáš Marek; 稲垣 祐司
第81回日本寄生虫学会東日本支部大会・日本共生生物学会第6回大会/2022-10-01--2022-10-02 - Draft nucleomorph genomes of green-colored dinoflagellates
Inagaki Yuji; Nakayama Takuro; Kawakubo Takashi; Matsuo ...
21st Symposium of the International Society of Endocytobiology/2022-7-19--2022-7-22 - 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/2022-03-29--2022-03-30 - 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/2021-11-27--2021-11-28 - Microheriella maris units Archaeplastida and Cryptista in phylogenomics.
Euki Yazaki; Akinori Yabuki; Ayaka Imaizumi; Keitaro Kum...
Asian Congress of Protistology IV/2021-11-19--2021-11-21 - Single-cell transcriptome data from diverse euglenids revised the evolution of mitochondrion-localized DNA polymerase in Euglenozoa.
Harada Ryo; Inagaki Yuji
1st Annual International Cogress on Euglenoids 2021/2021-11-08--2021-11-11 - 古細菌SMC関連タンパク質ClsNとSphは同一の新規SMCタンパクサブファミリーから派生した
吉永真理; 稲垣 祐司
日本微生物生態学会第34回大会/2021-10-30--2021-11-02 - Draft nucleomorph genome of a green-colored dinoflagellate
Inagaki Yuji
ISEP seminor/2021-05-20--2021-05-20 - 真核生物におけるSMCタンパク質ファミリーの多様化と二次的喪失
吉永真理; 稲垣 祐司
日本共生生物学会第4回大会/2020-10-30--2020-11-01 - キネトプラスチダ類及びディプロネマ類に特異的なミトコンドリア局在DNAポリメラーゼはファージ起源である.
原田亮; 稲垣 祐司
日本共生生物学会第4回大会/2020-10-30--2020-11-01 - 新奇ミトコンドリア局在DNAポリメラーゼは新たな真核生物高次系統群を示唆するか?
原田亮; 中野賢太郎; 矢吹彬憲; 白鳥峻志; Kim Ensoo; 稲垣 祐司
第17回原生生物・寄生虫・進化セミナー/2020-05-29--2020-5-29 - more...
- 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.
- Teaching
2023-10 -- 2024-02 Seminar on Genomics and Bioinformatics EII University of Tsukuba. 2023-04 -- 2023-08 Seminar on Genomics and Bioinformatics EI University of Tsukuba. 2023-05 -- 2023-06 Introduction to Phylogenomics University of Tsukuba. 2023-04 -- 2023-08 Methodology on Genomics and Bioinformatics IS University of Tsukuba. 2023-04 -- 2023-08 Seminar on Genomics and Bioinformatics IIIS University of Tsukuba. 2023-04 -- 2023-08 Seminar on Genomics and Bioinformatics VS University of Tsukuba. 2023-04 -- 2023-08 Seminar on Genomics and Bioinformatics IS University of Tsukuba. 2023-10 -- 2024-02 Seminar on Genomics and Bioinformatics IVF University of Tsukuba. 2023-04 -- 2023-07 Molecular Evolution I University of Tsukuba. 2023-10 -- 2024-02 Thesis Research in Genomics and Bioinformatics F University of Tsukuba. more... - Other educational activities
2017-03 -- 2017-03 さくらサイエンスプラン実習 筑波大学およびマレーシア工科大学
(Last updated: 2023-09-27)