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Yugi Inagaki - Publications

Affiliations: 
Dalhousie University, Halifax, Nova Scotia, Canada 
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56 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Harada R, Hirakawa Y, Yabuki A, Kashiyama Y, Maruyama M, Onuma R, Soukal P, Miyagishima S, Hampl V, Tanifuji G, Inagaki Y. Inventory and Evolution of Mitochondrion-localized Family A DNA Polymerases in Euglenozoa. Pathogens (Basel, Switzerland). 9. PMID 32244644 DOI: 10.3390/Pathogens9040257  0.558
2020 Nishimura Y, Kume K, Sonehara K, Tanifuji G, Shiratori T, Ishida K, Hashimoto T, Inagaki Y, Ohkuma M. Mitochondrial Genomes of Hemiarma marina and Leucocryptos marina Revised the Evolution of Cytochrome c Maturation in Cryptista Frontiers in Ecology and Evolution. 8. DOI: 10.3389/Fevo.2020.00140  0.331
2019 Nakayama T, Nomura M, Takano Y, Tanifuji G, Shiba K, Inaba K, Inagaki Y, Kawata M. Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host. Proceedings of the National Academy of Sciences of the United States of America. 116: 15973-15978. PMID 31235587 DOI: 10.1073/pnas.1902538116  0.365
2018 Matsuo M, Katahata A, Satoh S, Matsuzaki M, Nomura M, Ishida KI, Inagaki Y, Obokata J. Characterization of spliced leader trans-splicing in a photosynthetic rhizarian amoeba, Paulinella micropora, and its possible role in functional gene transfer. Plos One. 13: e0200961. PMID 30024971 DOI: 10.1371/Journal.Pone.0200961  0.313
2018 Záhonová K, Petrželková R, Valach M, Yazaki E, Tikhonenkov DV, Butenko A, Janouškovec J, Hrdá Š, Klimeš V, Burger G, Inagaki Y, Keeling PJ, Hampl V, Flegontov P, Yurchenko V, et al. Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPase. Scientific Reports. 8: 5239. PMID 29588502 DOI: 10.1038/S41598-018-23575-0  0.594
2018 Kamikawa R, Yazaki E, Tahara M, Sakura T, Matsuo E, Nagamune K, Hashimoto T, Inagaki Y. Fates of Evolutionarily Distinct, Plastid-type Glyceraldehyde 3-phosphate Dehydrogenase Genes in Kareniacean Dinoflagellates. The Journal of Eukaryotic Microbiology. PMID 29478272 DOI: 10.1111/jeu.12512  0.329
2018 Brown MW, Heiss AA, Kamikawa R, Inagaki Y, Yabuki A, Tice AK, Shiratori T, Ishida KI, Hashimoto T, Simpson AGB, Roger AJ. Phylogenomics places orphan protistan lineages in a novel eukaryotic super-group. Genome Biology and Evolution. PMID 29360967 DOI: 10.1093/Gbe/Evy014  0.686
2017 Tanifuji G, Cenci U, Moog D, Dean S, Nakayama T, David V, Fiala I, Curtis BA, Sibbald SJ, Onodera NT, Colp M, Flegontov P, Johnson-MacKinnon J, McPhee M, Inagaki Y, et al. Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis. Scientific Reports. 7: 11688. PMID 28916813 DOI: 10.1038/S41598-017-11866-X  0.739
2017 Leger MM, Kolisko M, Kamikawa R, Stairs CW, Kume K, Čepička I, Silberman JD, Andersson JO, Xu F, Yabuki A, Eme L, Zhang Q, Takishita K, Inagaki Y, Simpson AGB, et al. Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes. Nature Ecology & Evolution. 1: 0092. PMID 28474007 DOI: 10.1038/S41559-017-0092  0.663
2015 Kamikawa R, Tanifuji G, Ishikawa SA, Ishii KI, Matsuno Y, Onodera NT, Ishida KI, Hashimoto T, Miyashita H, Mayama S, Inagaki Y. Proposal of a Twin Aarginine Translocator System-Mediated Constraint against Loss of ATP Synthase Genes from Nonphotosynthetic Plastid Genomes. Molecular Biology and Evolution. PMID 26576845 DOI: 10.1093/Molbev/Msv247  0.345
2015 Noguchi F, Shimamura S, Nakayama T, Yazaki E, Yabuki A, Hashimoto T, Inagaki Y, Fujikura K, Takishita K. Metabolic Capacity of Mitochondrion-related Organelles in the Free-living Anaerobic Stramenopile Cantina marsupialis. Protist. 166: 534-550. PMID 26436880 DOI: 10.1016/j.protis.2015.08.002  0.323
2015 Takeuchi F, Sekizuka T, Ogasawara Y, Yokoyama H, Kamikawa R, Inagaki Y, Nozaki T, Sugita-Konishi Y, Ohnishi T, Kuroda M. The Mitochondrial Genomes of a Myxozoan Genus Kudoa Are Extremely Divergent in Metazoa. Plos One. 10: e0132030. PMID 26148004 DOI: 10.1371/journal.pone.0132030  0.369
2015 Kamikawa R, Tanifuji G, Ishikawa SA, Ishii KI, Matsuno Y, Onodera NT, Ishida KI, Hashimoto T, Miyashita H, Mayama S, Inagaki Y. Proposal of a Twin Aarginine Translocator System-Mediated Constraint against Loss of ATP Synthase Genes from Nonphotosynthetic Plastid Genomes. Molecular Biology and Evolution. PMID 26048548 DOI: 10.1093/molbev/msv134  0.345
2015 Kamikawa R, Tanifuji G, Kawachi M, Miyashita H, Hashimoto T, Inagaki Y. Plastid genome-based phylogeny pinpointed the origin of the green-colored plastid in the dinoflagellate Lepidodinium chlorophorum. Genome Biology and Evolution. 7: 1133-40. PMID 25840416 DOI: 10.1093/gbe/evv060  0.31
2014 Kamikawa R, Kolisko M, Nishimura Y, Yabuki A, Brown MW, Ishikawa SA, Ishida K, Roger AJ, Hashimoto T, Inagaki Y. Gene content evolution in Discobid mitochondria deduced from the phylogenetic position and complete mitochondrial genome of Tsukubamonas globosa. Genome Biology and Evolution. 6: 306-15. PMID 24448982 DOI: 10.1093/Gbe/Evu015  0.754
2013 Kamikawa R, Brown MW, Nishimura Y, Sako Y, Heiss AA, Yubuki N, Gawryluk R, Simpson AG, Roger AJ, Hashimoto T, Inagaki Y. Parallel re-modeling of EF-1α function: divergent EF-1α genes co-occur with EFL genes in diverse distantly related eukaryotes. Bmc Evolutionary Biology. 13: 131. PMID 23800323 DOI: 10.1186/1471-2148-13-131  0.72
2012 Ishitani Y, Kamikawa R, Yabuki A, Tsuchiya M, Inagaki Y, Takishita K. Evolution of elongation factor-like (EFL) protein in Rhizaria is revised by radiolarian EFL gene sequences. The Journal of Eukaryotic Microbiology. 59: 367-73. PMID 22672006 DOI: 10.1111/j.1550-7408.2012.00626.x  0.344
2012 Nishimura Y, Kamikawa R, Hashimoto T, Inagaki Y. Separate origins of group I introns in two mitochondrial genes of the katablepharid Leucocryptos marina. Plos One. 7: e37307. PMID 22606358 DOI: 10.1371/journal.pone.0037307  0.356
2012 Takishita K, Kolisko M, Komatsuzaki H, Yabuki A, Inagaki Y, Cepicka I, Smejkalová P, Silberman JD, Hashimoto T, Roger AJ, Simpson AG. Multigene phylogenies of diverse Carpediemonas-like organisms identify the closest relatives of 'amitochondriate' diplomonads and retortamonads. Protist. 163: 344-55. PMID 22364773 DOI: 10.1016/J.Protis.2011.12.007  0.777
2011 Kamikawa R, Inagaki Y, Roger AJ, Hashimoto T. Splintrons in Giardia intestinalis: Spliceosomal introns in a split form. Communicative & Integrative Biology. 4: 454-6. PMID 21966569 DOI: 10.4161/cib.4.4.15466  0.541
2011 Kamikawa R, Inagaki Y, Tokoro M, Roger AJ, Hashimoto T. Split introns in the genome of Giardia intestinalis are excised by spliceosome-mediated trans-splicing. Current Biology : Cb. 21: 311-5. PMID 21315596 DOI: 10.1016/j.cub.2011.01.025  0.52
2011 Kamikawa R, Yabuki A, Nakayama T, Ishida K, Hashimoto T, Inagaki Y. Cercozoa comprises both EF-1α-containing and EFL-containing members. European Journal of Protistology. 47: 24-8. PMID 21071191 DOI: 10.1016/J.Ejop.2010.08.002  0.312
2010 Matsumoto T, Shinozaki F, Chikuni T, Yabuki A, Takishita K, Kawachi M, Nakayama T, Inouye I, Hashimoto T, Inagaki Y. Green-colored plastids in the dinoflagellate genus Lepidodinium are of core chlorophyte origin. Protist. 162: 268-76. PMID 20829107 DOI: 10.1016/j.protis.2010.07.001  0.327
2010 Kolisko M, Silberman JD, Cepicka I, Yubuki N, Takishita K, Yabuki A, Leander BS, Inouye I, Inagaki Y, Roger AJ, Simpson AG. A wide diversity of previously undetected free-living relatives of diplomonads isolated from marine/saline habitats. Environmental Microbiology. 12: 2700-10. PMID 20482740 DOI: 10.1111/J.1462-2920.2010.02239.X  0.761
2009 Burki F, Inagaki Y, Bråte J, Archibald JM, Keeling PJ, Cavalier-Smith T, Sakaguchi M, Hashimoto T, Horak A, Kumar S, Klaveness D, Jakobsen KS, Pawlowski J, Shalchian-Tabrizi K. Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, telonemia and centroheliozoa, are related to photosynthetic chromalveolates. Genome Biology and Evolution. 1: 231-8. PMID 20333193 DOI: 10.1093/Gbe/Evp022  0.42
2009 Kamikawa R, Sanchez-Perez GF, Sako Y, Roger AJ, Inagaki Y. Expanded phylogenies of canonical and non-canonical types of methionine adenosyltransferase reveal a complex history of these gene families in eukaryotes. Molecular Phylogenetics and Evolution. 53: 565-70. PMID 19577655 DOI: 10.1016/J.Ympev.2009.06.016  0.763
2009 Takishita K, Yamaguchi H, Maruyama T, Inagaki Y. A hypothesis for the evolution of nuclear-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase genes in "chromalveolate" members. Plos One. 4: e4737. PMID 19270733 DOI: 10.1371/journal.pone.0004737  0.377
2008 Sakaguchi M, Takishita K, Matsumoto T, Hashimoto T, Inagaki Y. Tracing back EFL gene evolution in the cryptomonads-haptophytes assemblage: separate origins of EFL genes in haptophytes, photosynthetic cryptomonads, and goniomonads. Gene. 441: 126-31. PMID 18585873 DOI: 10.1016/j.gene.2008.05.010  0.332
2008 Kamikawa R, Inagaki Y, Sako Y. Direct phylogenetic evidence for lateral transfer of elongation factor-like gene. Proceedings of the National Academy of Sciences of the United States of America. 105: 6965-9. PMID 18458344 DOI: 10.1073/pnas.0711084105  0.314
2008 Takishita K, Inagaki Y. Eukaryotic origin of glyceraldehyde-3-phosphate dehydrogenase genes in Clostridium thermocellum and Clostridium cellulolyticum genomes and putative fates of the exogenous gene in the subsequent genome evolution. Gene. 441: 22-7. PMID 18420358 DOI: 10.1016/j.gene.2008.03.001  0.32
2008 Takishita K, Kawachi M, Noël MH, Matsumoto T, Kakizoe N, Watanabe MM, Inouye I, Ishida K, Hashimoto T, Inagaki Y. Origins of plastids and glyceraldehyde-3-phosphate dehydrogenase genes in the green-colored dinoflagellate Lepidodinium chlorophorum. Gene. 410: 26-36. PMID 18191504 DOI: 10.1016/J.Gene.2007.11.008  0.309
2007 Sakaguchi M, Inagaki Y, Hashimoto T. Centrohelida is still searching for a phylogenetic home: analyses of seven Raphidiophrys contractilis genes. Gene. 405: 47-54. PMID 17931802 DOI: 10.1016/j.gene.2007.09.003  0.331
2007 Patron NJ, Inagaki Y, Keeling PJ. Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages. Current Biology : Cb. 17: 887-91. PMID 17462896 DOI: 10.1016/J.Cub.2007.03.069  0.359
2007 Kamikawa R, Inagaki Y, Sako Y. Fragmentation of mitochondrial large subunit rRNA in the dinoflagellate Alexandrium catenella and the evolution of rRNA structure in alveolate mitochondria. Protist. 158: 239-45. PMID 17291829 DOI: 10.1016/j.protis.2006.12.002  0.302
2006 Inagaki Y, Roger AJ. Phylogenetic estimation under codon models can be biased by codon usage heterogeneity. Molecular Phylogenetics and Evolution. 40: 428-34. PMID 16647273 DOI: 10.1016/j.ympev.2006.03.020  0.509
2006 Inagaki Y, Susko E, Roger AJ. Recombination between elongation factor 1alpha genes from distantly related archaeal lineages. Proceedings of the National Academy of Sciences of the United States of America. 103: 4528-33. PMID 16537397 DOI: 10.1073/Pnas.0600744103  0.555
2006 Simpson AG, Inagaki Y, Roger AJ. Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes. Molecular Biology and Evolution. 23: 615-25. PMID 16308337 DOI: 10.1093/Molbev/Msj068  0.716
2005 Takishita K, Inagaki Y, Tsuchiya M, Sakaguchi M, Maruyama T. A close relationship between Cercozoa and Foraminifera supported by phylogenetic analyses based on combined amino acid sequences of three cytoskeletal proteins (actin, alpha-tubulin, and beta-tubulin). Gene. 362: 153-60. PMID 16226855 DOI: 10.1016/j.gene.2005.08.013  0.331
2005 SIMPSON AG, INAGAKI Y, ROGER AJ. The evolutionary relationships amongst excavates: a concatened protein analysis The Journal of Eukaryotic Microbiology. 52: 7S-27S. DOI: 10.1111/J.1550-7408.2005.05202003_1_68.X  0.714
2004 Ruiz-Trillo I, Inagaki Y, Davis LA, Sperstad S, Landfald B, Roger AJ. Capsaspora owczarzaki is an independent opisthokont lineage. Current Biology : Cb. 14: R946-7. PMID 15556849 DOI: 10.1016/J.Cub.2004.10.037  0.696
2004 Keeling PJ, Inagaki Y. A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor 1α Proceedings of the National Academy of Sciences of the United States of America. 101: 15380-15385. PMID 15492217 DOI: 10.1073/Pnas.0404505101  0.344
2004 Inagaki Y, Simpson AGB, Dacks JB, Roger AJ. Phylogenetic artifacts can be caused by leucine, serine, and arginine codon usage heterogeneity: Dinoflagellate plastid origins as a case study Systematic Biology. 53: 582-593. PMID 15371248 DOI: 10.1080/10635150490468756  0.533
2004 Susko E, Inagaki Y, Roger AJ. On inconsistency of the neighbor-joining, least squares, and minimum evolution estimation when substitution processes are incorrectly modeled. Molecular Biology and Evolution. 21: 1629-42. PMID 15155796 DOI: 10.1093/Molbev/Msh159  0.449
2004 Inagaki Y, Susko E, Fast NM, Roger AJ. Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies. Molecular Biology and Evolution. 21: 1340-9. PMID 15034136 DOI: 10.1093/Molbev/Msh130  0.503
2003 Inagaki Y, Blouin C, Susko E, Roger AJ. Assessing functional divergence in EF-1alpha and its paralogs in eukaryotes and archaebacteria. Nucleic Acids Research. 31: 4227-37. PMID 12853641 DOI: 10.1093/Nar/Gkg440  0.444
2002 Susko E, Inagaki Y, Field C, Holder ME, Roger AJ. Testing for differences in rates-across-sites distributions in phylogenetic subtrees. Molecular Biology and Evolution. 19: 1514-23. PMID 12200479 DOI: 10.1093/Oxfordjournals.Molbev.A004214  0.444
2002 Inagaki Y, Doolittle WF, Baldauf SL, Roger AJ. Lateral transfer of an EF-1alpha gene: origin and evolution of the large subunit of ATP sulfurylase in eubacteria. Current Biology : Cb. 12: 772-6. PMID 12007424 DOI: 10.1016/S0960-9822(02)00816-3  0.649
2002 Inagaki Y, Blouin C, Doolittle WF, Roger AJ. Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificity. Nucleic Acids Research. 30: 532-44. PMID 11788716 DOI: 10.1093/Nar/30.2.532  0.612
2001 Inagaki Y, Doolittle WF. Class I release factors in ciliates with variant genetic codes. Nucleic Acids Research. 29: 921-7. PMID 11160924 DOI: 10.1093/Nar/29.4.921  0.485
2000 Inagaki Y, Dacks JB, Doolittle WF, Watanabe KI, Ohama T. Evolutionary relationship between dinoflagellates bearing obligate diatom endosymbionts: insight into tertiary endosymbiosis. International Journal of Systematic and Evolutionary Microbiology. 50: 2075-81. PMID 11155982 DOI: 10.1099/00207713-50-6-2075  0.57
2000 Inagaki Y, Doolittle WF. Evolution of the eukaryotic translation termination system: Origins of release factors Molecular Biology and Evolution. 17: 882-889. PMID 10833194 DOI: 10.1093/Oxfordjournals.Molbev.A026368  0.526
2000 Ehara M, Inagaki Y, Watanabe KI, Ohama T. Phylogenetic analysis of diatom coxI genes and implications of a fluctuating GC content on mitochondrial genetic code evolution. Current Genetics. 37: 29-33. PMID 10672441 DOI: 10.1007/s002940050004  0.33
1998 Watanabe KI, Ehara M, Inagaki Y, Ohama T. Distinctive origins of group I introns found in the COXI genes of three gree algae. Gene. 213: 1-7. PMID 9714606 DOI: 10.1016/S0378-1119(98)00235-2  0.321
1997 Hayashi-Ishimaru Y, Ehara M, Inagaki Y, Ohama T. A deviant mitochondrial genetic code in prymnesiophytes (yellow-algae): UGA codon for tryptophan. Current Genetics. 32: 296-9. PMID 9342410 DOI: 10.1007/s002940050280  0.336
1997 Inagaki Y, Hayashi-Ishimaru Y, Ehara M, Igarashi I, Ohama T. Algae or protozoa: phylogenetic position of euglenophytes and dinoflagellates as inferred from mitochondrial sequences. Journal of Molecular Evolution. 45: 295-300. PMID 9302324 DOI: 10.1007/PL00006233  0.402
1997 Ehara M, Hayashi-Ishimaru Y, Inagaki Y, Ohama T. Use of a deviant mitochondrial genetic code in yellow-green algae as a landmark for segregating members within the phylum. Journal of Molecular Evolution. 45: 119-24. PMID 9236270 DOI: 10.1007/PL00006210  0.303
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