Chagneau C, Payros D, Goman A, Goursat C, David L, Okuno M, Bordignon P, Séguy C, Massip C, Branchu P, Ogura Y, Nougayrède J, Marenda M, Oswald E. HlyF, an underestimated virulence factor of uropathogenic Escherichia coli Clin Microbiol Infect. S1198-743X(23)00352-X, 2023.
PubMed
Taniguchi T, Okuno M, Shinoda T, Kobayashi F, Takahashi K, Yuasa H, Nakamura Y, Tanaka H, Kajitani R, Itoh T.
GINGER: An integrated method for high-accuracy prediction of gene structure in higher eukaryotes at the gene and exon level DNA Res. dsad017, 2023.
PubMed
Okuno M, Tsuru N, Yoshino S, Gotoh Y, Yamamoto T, Hayashi T, Ogura Y.
Isolation and Genomic Characterization of a Heat-Labile Enterotoxin 1-Producing Escherichia fergusonii Strain from a Human Microbiol Spectr., e0049123, 2023.
PubMed
Nakazato I, Okuno M, Itoh T, Tsutsumi N, Arimura S.
Characterization and development of a plastid genome base editor, ptpTALECD The Plant Journal, 2023.
PubMed
Tamai S, Ogura Y, Okuno M, Nukazawa K, Suzuki Y.
Highly Sensitive Detection and Quantification of Dissolved Free Extracellular DNA Using Colloid Adsorption and Foam Concentration Environ. Sci.: Water Res. Technol., 9, 1792-1803, 2023.
Okuno M, Arimizu Y, Miyahara S, Wakabayashi Y, Gotoh Y, Yoshino S, Harada T, Seto K, Yamamoto T, Nakamura K, Hayashi T, Ogura Y.. Escherichia cryptic clade I is an emerging source of human intestinal pathogens. BMC Biol., 21:81, 2023.
PubMed
Iguchi A, Takemura T, Ogura Y, Nguyen TTH, Kikuchi T, Okuno M, Tokizawa A, Iwashita H, Quynh H, Pham A, Doan HT, Tran NL, Tran TL, Nguyen TH, Tran TH, Pham TNL, Dao TD, Vu TMH, Nguyen TN, Vu H, Nguyen VT, Vu TTH Le TH, Lai TA, Ngo TC, Hasebe F, Nguyen DT, Yamashiro T.
Genomic characterization of endemicdiarrheagenic Escherichia coli and Escherichia albertii from infants with diarrhea in Vietnam. PLoS Negl Trop Dis., 17(4), 2023.
PubMed
Kawamura Y, Fujimoto Y, Kutsuna R, Tomida J, Yamamoto K, Miyoshi-Akiyama T, Okuno M, Ogura Y, Matsuoka M, Kawaguchi T, Tustsuki H, and Sawa T.
Helicobacter kumamotonensis sp. nov., isolated from human clinical specimens. Int J Syst Evol Microbiol., 73.3, 2023.
PubMed
Terao M, Ogawa Y, Takada S, Kajitani R, Okuno M, Mochimaru Y, Matsuoka K, Itoh T, Toyoda A, Kono T, Jogahara T, Mizushima S, Kuroiwa A.
Turnover of mammal sex chromosomes in the Sry-deficient Amami spiny rat is due to male-specific upregulation of Sox9 Proc Natl Acad Sci U S A. 119(49), 2022.
PubMed
Yoshida M, Hirota K, Imoto J, Okuno M, Tanaka H, Kajitani R, Toyoda A, Itoh T, Ikeo K, Sasaki T, Setiamarga D.
Gene Recruitments and Dismissals in the Argonaut Genome Provide Insights into Pelagic Lifestyle Adaptation and Shell-like Eggcase Reacquisition Genome Biology and Evolution 14(11), 2022.
PubMed
Chikami Y, Okuno M, Toyoda A, Itoh T, Niimi T.
Evolutionary history of sexual differentiation mechanism in insects Molecular Biology and Evolution 39(7), 2022.
PubMed
Nakazato I, Okuno M, Zhou C, Itoh T, Tsutsumi N, Takanashi H, Arimura S.
Targeted base editing in the mitochondrial genome of Arabidopsis thaliana Proc Natl Acad Sci U S A. 119(20), 2022.
PubMed
Miyakoshi M, Okayama H, Lejars M, Kanda T, Tanaka Y, Itaya K, Okuno M, Itoh T, Iwai N, Wachi M.
Mining RNA-seq data reveals the massive regulon of GcvB small RNA and its physiological significance in maintaining amino acid homeostasis in Escherichia coli Molecular Microbiology 117(1), 2022.
PubMed
Okuno M, Mizushima S, Kuroiwa A, Itoh T.
Analysis of sex chromosome evolution in the clade Palaeognathae from phased genome assembly
Genome Biology and Evolution 13(11), evab242, 2021.
PubMed
Kajitani R, Noguchi H, Gotoh Y, Ogura Y, Yoshimura D, Okuno M, Toyoda A, Kuwahara T, Hayashi T, Itoh T.
MetaPlatanus: a metagenome assembler that combines long-range sequence links and species-specific features Nucleic Acids Research 49(22), 2021.
PubMed
Yuasa H, Kajitani R, Nakamura Y, Takahashi K, Okuno M, Kobayashi F, Shinoda S, Toyoda A, Suzuki Y, Thongtham N, Forsman Z, Bronstein O, Seveso D, Montalbetti E, Taquet C, Eyal G, Yasuda N, Itoh T.
Elucidation of the speciation history of three sister species of crown-of-thorns starfish (Acanthaster spp.) based on genomic analysis DNA Res. 28(4), 2021.
PubMed
Nakazato I, Okuno M, Yamamoto H, Tamura Y, Itoh T, Shikanai T, Takanashi H, Tsutsumi N, Arimura S.
Targeted base editing in the plastid genome of Arabidopsis thaliana Nature Plants 7(1), 2021.
PubMed
Arimura S, Ayabe H, Sugaya H, Okuno M, Tamura Y, Tsuruta Y, Watari Y, Yanase S, Yamauchi T, Itoh T, Toyoda A, Takanashi H, Tsutsumi N.
Targeted gene disruption of ATP synthases 6‐1 and 6‐2 in the mitochondrial genome of Arabidopsis thaliana by mitoTALENs The Plant Journal 104(6), 1459-1471. 2020.
PubMed
Okuno M, Miyamoto S, Itoh T, Seki M, Suzuki Y, Mizushima S, Kuroiwa A.
Expression profiling of sexually dimorphic genes in the Japanese quail, Coturnix japonica. Sci Rep. 10(1), 1-11. 2020.
PubMed
Kazama T, Okuno M, Watari Y, Yanase S, Koizuka C, Tsuruta Y, Sugaya H, Toyoda A, Itoh T, Tsutsumi N, Toriyama K, Koizuka N, Arimura S.
Curing cytoplasmic male sterility via TALEN-mediated mitochondrial genome editing. Nature Plants 8;7(5):722-730, 2020.
PubMed
Kajitani R, Yoshimura D, Okuno M, Minakuchi Y, Kagoshima H, Fujiyama A, Kubokawa K, Kohara Y, Toyoda A, Itoh T.
Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions. Nature Comm. 12;4(10):1702, 2019.
PubMed
Yoshimura D, Kajitani R, Gotoh Y, Katahira K, Okuno M, Ogura Y, Hayashi T, Itoh T.
Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP. Microb Genom. 5(5):e000261, 2019.
PubMed
Ando T, Matsuda T, Goto K, Hara K, Ito A, Hirata J, Yatomi J, Kajitani R, Okuno M, Yamaguchi K, Kobayashi M, Takano T, Minakuchi Y, Seki M, Suzuki Y, Yano K, Itoh T, Shigenobu S, Toyoda A, Niimi T.
Repeated inversions within a pannier intron drive diversification of intraspecific colour patterns of ladybird beetles. Nature Comm. 21;9(9):3843, 2018.
PubMed
Okuno M, Kajitani R, Ryusui R, Morimoto H, Kodama Y, Itoh T.
Next-generation sequencing analysis of lager brewing yeast strains reveals the evolutionary history of interspecies hybridization. DNA Res. 4;1(1):23, 2016.
PubMed
Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Okuno M, Yabana M, Ogura Y, Nagayasu E, Maruyama H, Hayashi T, Kohara Y, Fujiyama A, Itoh T.
Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res. 24(8):1384-1395, 2014.
PubMed
Nikaido M, Noguchi H, Nishihara H, Toyoda A, Suzuki Y, Kajitani R, Suzuki H, Okuno M, Aibara M, Ngatunga B, Mzighani S, Kalombo H, Masengi K, Tuda J, Nogami S, Maeda R, Iwata M, Abe Y, Fujimura K, Okabe M, Amano T, Maeno A, Shiroishi T, Itoh T, Sugano S, Kohara Y, Fujiyama A, Okada N.
Coelacanth genomes reveal signatures for evolutionary transition from water to land. Genome Res. 22(7):1740-1748, 2013.
PubMed