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 2023-04 -- 2027-03 INAGAKI Yuji JSPS/Grant-in-Aid for Scientific Research(B) 18,330,000Yen 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 INAGAKI Yuji 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 2018-10 -- 2024-03 Yuji INAGAKI JSPS/Fund for the Promotion of Joint International Research (Fostering Joint International Research(B)) 17,810,000Yen 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) Study on the residual green alga-derived nucleomorphs in dinoflagellates 2016 -- 2018 INAGAKI Yuji Japan Society for the Promotion of Science/Grant-in-Aid for Scientific Research(B) 17,420,000Yen Investigation on the evolutionary process integrating an endosymbiotic cyanobacterium into the host cellular system 2011-04 -- 2016-03 INAGAKI Yuji JSPS/Grant-in-Aid for Scientific Research on Innovative Areas(Research in a proposed research area) 112,580,000Yen 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 ミトコンドリアを持たない真核微生物群フォルニカータの多様性の解明 2011 -- 2013 Japan Society of for the Promotion of Science/基盤研究(B) 1,500,000Yen 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
- The diversity and evolution of DNA polymerases localized in organelles: What we have unveiled and what we are uncertain about.
稲垣 祐司; 原田亮
月刊アグリバイオ/8(12)/pp.43-47, 2024-10 - 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, 2024-11 - Encyclopaedia of family A DNA polymerases localized in organelles: Evolutionary contribution of bacteria including the proto-mitochodrion.
Harada Ryo; Hirakawa Yoshihisa; Yabuki Akinori; Kim E...
MOLECULAR BIOLOGY AND EVOLUTION/41(2)/p.msae014, 2024-01 - Convergent reductive evolution of cyanobacteria in symbiosis with Dinophysiales dinoflagellates.
Nakayama Takuro; Nomura Mami; Yabuki Akinori; Shiba K...
Scientific Reports/14(1)/pp.12774-12774, 2024-06 - Is rdxPolA a piece of the ancient system for DNA maintenance in mitochondria?
原田亮; 稲垣 祐司
The Japanese Journal of Phycology (Sôrui)/72(2)/pp.104-117, 2024-07 - Dinotoms possess two evolutionary distinct autophagy-related ubiquitin-like conjugation systems.
Yazaki Euki; Uehara Tadaaki; Sakaoto Hirokazu; Inagaki...
Protist/175(6)/pp.126067-126067, 2024-10 - Convergent reductive evolution of cyanobacteria in symbiosis with Dinophysiales dinoflagellates.
Nakayama Takuro; Nomura Mami; Yabuki Akinori; Kogiku ...
bioRχiv, 2024-01 - Gleaning Euglenozoa-specific DNA polymerases in public single-cell transcriptome data
Harada Ryo; Inagaki Yuji
PROTIST/174(6)/p.125997, 2023-12 - Encyclopaedia of family A DNA polymerases localized in organelles: Evolutionary contribution of 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/12(11)/pp.e0050623-e0050623, 2023-11 - 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; Tam...
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 - more...
- The diversity and evolution of DNA polymerases localized in organelles: What we have unveiled and what we are uncertain about.
- 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.
- 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...
日本共生生物学会第8回大会/2024-10-19--2024-10-20 - Two evolutionarily distinct autophagy-related ubiquitin-like conjugation systems in dinotoms.
Euki Yazaki; Tadaaki Ueraha; Hirokazu Sakamoto; Inagak...
APCOP-V 2024/2024/11/04--2024/11/06 - 緑色渦鞭毛藻TGD株にみられるヌクレオモルフのゲノム解析 ー既知ヌクレオモルフゲノムとの共通点・相違点を探るー
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
日本共生生物学会第8回大会/2024-10-19--2024-10-20 - Recent endosymbiosis between a haptophyte and a Kareniacean dinoflagellate and “Full-furnished apartment hypothesis.”
INAGAKI Yuji
5ᵗʰ Asian Marine Biology Symposium/2024/10/28--2024/10/30 - 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/2024-10-19--2024-10-20 - 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/2024-10-28--2024-10-31 - 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/2024-10-19--2024-10-20 - CRuMsクレードの進化を解明する系統的所属不明真核生物Glissandra oviformis.
矢﨑裕規; 原田亮; 磯貝龍邑; 石田健一郎; 稲垣 祐司; 白鳥峻志.
日本共生生物学会第8回大会/2024-10-19--2024-10-20 - AUTOEB:AU検定により系統樹の二分岐を評価するソフトウェア.
番場浩平; 原田亮; 稲垣 祐司
日本共生生物学会第8回大会/2024-10-19--2024-10-20 - Myzozoa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
日本共生生物学会第8回大会/2024-10-19--2024-10-20 - 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/2024-09-06--2024-09-06 - 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/2024-10-02--2024-10-04 - Dinotoms possess two evolutionary distinct autophagy-related ubiquitin-like conjugation systems.
Euki Yazaki; Tadaaki Ueraha; Hirokazu Sakamoto; Inagak...
Annual Meeting of the Society for Molecular Biology and Evolution 2024/2024/07/07--2024/07/11 - 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/2024/03/22--2024/03/23 - Transition of the gene repertoire with adaptation to parasitic lifestyle in Diplomonads: orthology analysis with related free-living species
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...
The 93rd Annual Meeting of the Japanese Society of Parasitology/2024-03-09--2024-03-10 - Exploring symbiotic cyanobacteria using size-fractionated environmental DNA samples.
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/2023-11-18--2023-11-19 - Taxon sampling affects the internal relationship of Archaeplastida: Is either Rhodophyta or Glaucophyta the earliest branch in Archaeplastida?
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/2023-11-18--2023-11-19 - Evolution of PCNA complex in Crenarchaota.
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/2023-11-18--2023-11-19 - A novel form of Rubisco that is ancestral to forms I and I’.
番場浩平; 稲垣 祐司
日本共生生物学会第7回大会/2023-11-18--2023-11-19 - 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/2023/09/07--2023/09/09 - 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 - more...
- 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.
- Teaching
2024-10 -- 2025-02 General Biology II University of Tsukuba. 2024-10 -- 2025-02 Seminar on Genomics and Bioinformatics VF University of Tsukuba. 2024-07 -- 2024-07 Fundamental Biology, Laboratory II University of Tsukuba. 2024-10 -- 2025-02 Methodology on Genomics and Bioinformatics IIF University of Tsukuba. 2024-10 -- 2024-12 Molecular Evolution II University of Tsukuba. 2024-12 -- 2025-02 Fundamental Biology, Laboratory III University of Tsukuba. 2024-04 -- 2024-08 Seminar on Genomics and Bioinformatics IIIS University of Tsukuba. 2024-04 -- 2024-08 Methodology on Genomics and Bioinformatics IS University of Tsukuba. 2024-10 -- 2025-02 Seminar on Genomics and Bioinformatics IIIF University of Tsukuba. 2024-10 -- 2025-02 Methodology on Genomics and Bioinformatics IF 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: 2024-11-06)