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List of works by Yuji Inagaki

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)

scientific article published on 14 October 2005

A deviant genetic code in the green alga-derived plastid in the dinoflagellate Lepidodinium chlorophorum ⬇️

scientific article published on April 22, 2011

A deviant mitochondrial genetic code in prymnesiophytes (yellow-algae): UGA codon for tryptophan.

scientific article

A non-photosynthetic diatom reveals early steps of reductive evolution in plastids

scientific article

A novel spliceosome-mediated trans-splicing can change our view on genome complexity of the divergent eukaryote Giardia intestinalis.

scientific article

A wide diversity of previously undetected free-living relatives of diplomonads isolated from marine/saline habitats.

scientific article

Algae or protozoa: phylogenetic position of euglenophytes and dinoflagellates as inferred from mitochondrial sequences.

scientific article published in September 1997

An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyte Chrysochromulina sp. NIES-1333.

scientific article

Assessing functional divergence in EF-1alpha and its paralogs in eukaryotes and archaebacteria

scientific article

Assessing the monophyly of chlorophyll-c containing plastids by multi-gene phylogenies under the unlinked model conditions.

scientific article published on 25 May 2007

Capsaspora owczarzaki is an independent opisthokont lineage.

scientific article published in November 2004

Centrohelida is still searching for a phylogenetic home: analyses of seven Raphidiophrys contractilis genes

scientific article published on 14 September 2007

Cercozoa comprises both EF-1α-containing and EFL-containing members

scientific article published on 10 November 2010

Characterization of spliced leader trans-splicing in a photosynthetic rhizarian amoeba, Paulinella micropora, and its possible role in functional gene transfer

scientific article published on 19 July 2018

Class I release factors in ciliates with variant genetic codes

scientific article

Comparative Plastid Genomics of Cryptomonas Species Reveals Fine-Scale Genomic Responses to Loss of Photosynthesis

scientific article published on 01 February 2020

Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle

scientific article

Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificity.

scientific article published on January 2002

Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies.

scientific article published on 19 March 2004

Cryptic diversity of free-living parabasalids, Pseudotrichomonas keilini and Lacusteria cypriaca n. g., n. sp., as inferred from small subunit rDNA sequences.

scientific article

Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesis

scientific article published on 24 February 2020

Direct phylogenetic evidence for lateral transfer of elongation factor-like gene

scientific article (publication date: 13 May 2008)

Directionally evolving genetic code: the UGA codon from stop to tryptophan in mitochondria.

scientific article

Distinctive origins of group I introns found in the COXI genes of three gree algae.

scientific article published in June 1998

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.

scientific article published on 10 March 2008

Evolution of Elongation Factor‐Like (EFL) Protein in Rhizaria is Revised by Radiolarian EFL Gene Sequences ⬇️

scientific article published on July 1, 2012

Evolution of the eukaryotic translation termination system: origins of release factors

scientific article published on 01 June 2000

Expanded phylogenies of canonical and non-canonical types of methionine adenosyltransferase reveal a complex history of these gene families in eukaryotes

scientific article published on 03 July 2009

Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPase.

scientific article published on 27 March 2018

Fates of Evolutionarily Distinct, Plastid-type Glyceraldehyde 3-phosphate Dehydrogenase Genes in Kareniacean Dinoflagellates

scientific article

Fragmentation of mitochondrial large subunit rRNA in the dinoflagellate Alexandrium catenella and the evolution of rRNA structure in alveolate mitochondria.

scientific article published on 7 February 2007

Gene content evolution in Discobid mitochondria deduced from the phylogenetic position and complete mitochondrial genome of Tsukubamonas globosa.

scientific article published on February 2014

Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis.

scientific article published on 15 September 2017

Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms

scientific article published on 12 October 2017

Global Kinetoplastea phylogeny inferred from a large-scale multigene alignment including parasitic species for better understanding transitions from a free-living to a parasitic lifestyle.

scientific article published on 20 February 2017

Green-colored Plastids in the Dinoflagellate Genus Lepidodinium are of Core Chlorophyte Origin ⬇️

scientific article published on September 15, 2010

Horizontally-acquired genetic elements in the mitochondrial genome of a centrohelid Marophrys sp. SRT127

scientific article published on 19 March 2019

Identification of a bacteria-like ferrochelatase in Strongyloides venezuelensis, an animal parasitic nematode.

scientific article

In Silico Structural Modeling and Analysis of Elongation Factor-1 Alpha and Elongation Factor-like Protein

scientific article published on 23 April 2019

Inventory and Evolution of Mitochondrion-localized Family A DNA Polymerases in Euglenozoa

scientific article published on 01 April 2020

Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, telonemia and centroheliozoa, are related to photosynthetic chromalveolates

scientific article

Lateral Transfer of an EF-1α Gene

article

Metabolic Capacity of Mitochondrion-related Organelles in the Free-living Anaerobic Stramenopile Cantina marsupialis.

scientific article published on 29 August 2015

Mitochondrial Genome of Palpitomonas bilix: Derived Genome Structure and Ancestral System for Cytochrome c Maturation

scientific article

Morphological Identities of Two Different Marine Stramenopile Environmental Sequence Clades: Bicosoeca kenaiensis (Hilliard, 1971) and Cantina marsupialis (Larsen and Patterson, 1990) gen. nov., comb. nov.

scientific article

Multigene Phylogenies of Diverse Carpediemonas-like Organisms Identify the Closest Relatives of ‘Amitochondriate’ Diplomonads and Retortamonads

scientific article published on 23 February 2012

Multiple conversion between the genes encoding bacterial class-I release factors

scientific article published on 10 August 2015

On inconsistency of the neighbor-joining, least squares, and minimum evolution estimation when substitution processes are incorrectly modeled.

scientific article published on 21 May 2004

Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes.

scientific article

Origins of plastids and glyceraldehyde-3-phosphate dehydrogenase genes in the green-colored dinoflagellate Lepidodinium chlorophorum.

scientific article

Palpitomonas bilix gen. et sp. nov.: A novel deep-branching heterotroph possibly related to Archaeplastida or Hacrobia.

scientific article

Patterns in evolutionary origins of heme, chlorophyll and isopentenyl diphosphate biosynthetic pathways suggest non-photosynthetic periods prior to plastid replacements in dinoflagellates

scientific article published on 03 August 2018

Phylogenetic analysis of diatom coxI genes and implications of a fluctuating GC content on mitochondrial genetic code evolution

scientific article published on 01 January 2000

Phylogenetic estimation under codon models can be biased by codon usage heterogeneity

scientific article published on 02 May 2006

Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group

scientific article published on 19 January 2018

Phylogeny of Asian primate malaria parasites inferred from apicoplast genome-encoded genes with special emphasis on the positions of Plasmodium vivax and P. fragile.

scientific article

Plasticity of the domain structure in FlgJ, a bacterial protein involved in flagellar rod formation.

scientific article published in December 2006

Prasinoxanthin is absent in the green-colored dinoflagellate Lepidodinium chlorophorum strain NIES-1868: pigment composition and 18S rRNA phylogeny.

scientific article published on 23 March 2012

Proposal of a Twin Arginine Translocator System-Mediated Constraint against Loss of ATP Synthase Genes from Nonphotosynthetic Plastid Genomes. [Corrected].

scientific article published on 5 June 2015

Putative genome features of relic green alga-derived nuclei in dinoflagellates and future perspectives as model organisms

scientific article published on 21 June 2020

Rooting for the root of elongation factor-like protein phylogeny.

scientific article published on 5 May 2010

Secondary loss of a cis-spliced intron during the divergence of Giardia intestinalis assemblages.

scientific article

Separate origins of group I introns in two mitochondrial genes of the katablepharid Leucocryptos marina

scientific article

Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host

scientific article published on 24 June 2019

Split introns in the genome of Giardia intestinalis are excised by spliceosome-mediated trans-splicing.

scientific article published in February 2011

Testing for differences in rates-across-sites distributions in phylogenetic subtrees.

scientific article published in September 2002

The closest lineage of Archaeplastida is revealed by phylogenomics analyses that include Microheliella maris

article published on April 23, 2022

The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites.

scientific article published on 28 March 2018

Translation of synonymous codons in family boxes by Mycoplasma capricolum tRNAs with unmodified uridine or adenosine at the first anticodon position

scientific article published on 01 August 1995

Tsukubamonas globosa n. gen., n. sp., a novel excavate flagellate possibly holding a key for the early evolution in "Discoba".

scientific article published on 13 May 2011

Ungulate malaria parasites

scientific article published on 21 March 2016

Use of a deviant mitochondrial genetic code in yellow-green algae as a landmark for segregating members within the phylum ⬇️

scientific article published on August 1, 1997

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