Publications

†, corresponding author(s); *, equally contributed authors

• Pánek T†, Tice AK, Žihala D, Corre P, Hrubá P, Kamikawa R, Mirzoyan S, Jones R, Yazaki E, Shiratori T, Kume K, Hashimoto T, Ishida K, Zadrobílková E, Hradilová M, Silberman JD, Stairs CW, Roger AJ, Inagaki Y, Eliáš M, Brown MW, Čepička I. 2025 An expanded phylogenomic analysis of Heterolobosea reveals the deep relationships, non-canonical genetic codes, and cryptic flagellate stages in the group. Molecular Phylogenetics and Evolution 204:108289. PubMed (doi: 10.1016/j.ympev.2025.108289)

• Nakayama T†, Harada R, Yabuki A, Nomura M, Shiba K, Inaba K, Inagaki Y.  2025 Drastic genome reduction driven by parasitic lifestyle: Two complete genomes of endosymbiotic bacteria possibly hosted by a dinoflagellate. bioRχiv  (doi: 10.1101/2025.01.03.631278) 

• Bamba K, Harada R, Inagaki Y†. 2024 AUTOEB: A software for systematically evaluating bipartitions in a phylogenetic tree employing an approximately unbiased test. IPSJ Transactions on Bioinformatics 17:72-82. (doi: 10.2197/ipsjtio.17.72)

• 稲垣祐司†，原田亮．2024 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／The diversity and evolution of DNA polymerases localized in organelles: What we know and what we are uncertain about.　月刊『アグリバイオ』8(12):43-47.

• Yazaki E†, Uehara T, Sakamoto H, Inagaki Y. 2024 Dinotoms possess two evolutionary distinct autophagy-related ubiquitin-like conjugation systems.  Protist 175(6):126067. pubmed. (doi: https://doi.org/10.1016/j.protis.2024.126067)

• 原田亮†，稲垣祐司．2024 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？／Is rdxPolA a piece of the ancient system for DNA maintenance in mitochondria? 藻類 The Japanese Journal of Phycology (Sôrui) 72(2):107-114. PDF

• Nakayama T†, Yabuki A, Nomura M, Shiba K, Inaba K, Inagaki Y.  2024 Convergent reductive evolution of cyanobacteria in symbiosis with Dinophysiales dinoflagellates. Scientific Reports 14(1):12774. pubmed  (doi: 10.1038/s41598-024-63502-0)

• Harada R, Hirakawa Y, Yabuki A, Kim E, Yazaki E, Kamikawa R, Nakano K, Eliáš M†, Inagaki Y†. 2024 Encyclopaedia of DNA polymerases localized in organelles: Evolutionary contribution of bacteria including the proto-mitochodrion.  Molecular Biology and Evolution 41(2):msae014. pubmed.  (doi: 10.1093/molbev/msae014)　プレスリリース

• Nakayama T†, Yabuki A, Nomura M, Shiba K, Inaba K, Inagaki Y.  2024 Convergent reductive evolution of cyanobacteria in symbiosis with Dinophysiales dinoflagellates. bioRχiv  (doi: 10.1101/2024.01.11.574452) The version after peer-review was published in Sci Rep in 2024. See https://doi.org/10.1038/s41598-024-63502-0