Publications

2025

Takata, K., Nonaka, M., Xia, F., Kikuchi, T., Gibu, K. & Yasuda, N. (2025) The complete mitochondrial genome of Pleurocorallium inutile (Octocora llia: Scleralcyonacea: Coralliidae). Molecular Biology Reports 52.

Lastik, D., Kounosu, A., Dayi, M., Yoshida, A., Fujihira, A., Reynolds, K., Hunt, V. L. & Kikuchi, T. (2025) Small non-coding RNAs have predicted roles in reproductive biology and transposable element regulation in the parasitic worm Strongyloides v enezuelensis. Scientific Reports 15.

Hikima, A., Sun, S., Okino, T., Kinoshita, K., Yoshida, A., Maeda, Y., Ishiwata, K., Kanuka, H. & Kikuchi, T. (2025) A chromosome-level genome resource for the lethal tapeworm Sparganum proliferum, with candidate genomic safe harbours for functional genetics.

Fujihira, A., Kinoshita, K., Hikima, A., Kounosu, A., Maeda, Y., Sakamoto, K., Kondo, Y. & Kikuchi, T. (2025) Proteomic Dataset of Sparganum proliferum and Spirometra mansoni to Understand Asexual Proliferation in Hosts. Scientific Data.

Yoshida, K., Witte, H., Hatashima, R., Sun, S., Kikuchi, T., Röseler, W. & Sommer, R. J. (2024) Rapid chromosome evolution and acquisition of thermosensitive stochastic sex determination in nematode androdioecious hermaphrodites. Nature Communications 15.

2024

Tokiwa, T., Fushimi, M., Chou, S., Yoshida, A., Kinoshita, K., Hikima, A., Kikuchi, T. & Ozaki, K. (2024) Aberrant sparganosis in cat caused by Spirometra mansoni (Cestoda: Dip hyllobothriidae): a case report. BMC Veterinary Research 20.

Tamagawa, K., Dayi, M., Sun, S., Hata, R., Kikuchi, T., Haruta, N., Sugimoto, A. & Makino, T. (2024) Evolutionary changes of noncoding elements associated with transition of sexual mode in Caenorhabditis nematodes. Science Advances 10.

Sukmawinata, E., Uemura, R., Nishiki, I., Yoshida, T., Sueyoshi, M. & Kikuchi, T. (2024) IncX3 plasmid carrying blaSHV-12 and qnrS1 in a Japanese racehorse-origin Escherichia coli isolate. Veterinarski Glasnik 78, 81-87.

Kounosu, A., Sun, S., Maeda, Y., Dayi, M., Yoshida, A., Maruyama, H., Hunt, V., Sugimoto, A. & Kikuchi, T. (2024) Syntenic relationship of chromosomes in Strongyloides species and Rhabditophanes diutinus based on the chromosome-level genome assemblies. Philosophical Transactions of the Royal Society B Biological Sciences 379.

Isomura, N., Inoha, K., Shimura, A., Yasuda, N., Kikuchi, T., Iwao, K., Kitanobo, S., Ohki, S., Morita, M. & Fukami, H. (2024) Effect of the frequency of multi-specific synchronous spawning on genetic introgression among three Acropora species. Coral Reefs 43, 1497-1509.

Arif, R., Sukmawinata, E., Nurhidayah, N., Satrija, F., Nuradji, H., Wienanto, R. & Kikuchi, T. (2024) Gastrointestinal Nematode Infections of Deer and Sheep in An Agritourism Farm in Bogor, Indonesia. Philippine Journal of Veterinary Medicine 61.

Al-Jawabreh, R., Anderson, R., Atkinson, L. E., Bickford-Smith, J., Bradbury, R. S., Breloer, M., Bryant, A. S., Buonfrate, D., Cadd, L. C., Crooks, B., Deiana, M., Grant, W., Hallem, E., Hedtke, S. M., Hunt, V., Khieu, V., Kikuchi, T., Kounosu, A., Lastik, D., Van Lieshout, L., Liu, Y., McSorley, H. J., McVeigh, P., Mousley, A., Murcott, B., Nevin, W. D., Nosková, E., Pomari, E., Reynolds, K., Ross, K., Streit, A., Suleiman, M., Tiberti, N. & Viney, M. (2024) Strongyloides questions – a research agenda for the future. Philosophical Transactions of the Royal Society B Biological Sciences 379.

2023

Yoshida, K., Rödelsperger, C., Röseler, W., Riebesell, M., Sun, S., Kikuchi, T. & Sommer, R. J. (2023) Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation. Nature Ecology and Evolution 7, 424-439.

Sildever, S., Nishi, N., Tazawa, S., Kasai, H., Hirai, J., Shiomoto, A., Kikuchi, T., Katakura, S. & Nagai, S. (2023) Eight years of weekly eDNA monitoring in the North-Western Pacific. Environmental DNA 5, 1202-1215.

Sakaguchi, M., Urbanczyk, Y., Kikuchi, T. & Urbanczyk, H. (2023) Grimontia kaedaensis sp. nov., isolated from the estuary of Kaeda river in Miyazaki, Japan. International Journal of Systematic and Evolutionary Microbiology 73.

Owashi, Y., Minami, T., Kikuchi, T., Yoshida, A., Nakano, R., Kageyama, D. & Adachi-Hagimori, T. (2023) Microbiome of Zoophytophagous Biological Control Agent Nesidiocoristenuis. Microbial Ecology 86, 2923-2933.

Lee, Y. C., Ke, H. M., Liu, Y. C., Lee, H. H., Wang, M. C., Tseng, Y. C., Kikuchi, T. & Tsai, I. J. (2023) Single-worm long-read sequencing reveals genome diversity in free-livi ng nematodes. Nucleic Acids Research 51, 8035-8047.

Lai, C. K., Lee, Y. C., Ke, H. M., Lu, M. R., Liu, W. A., Lee, H. H., Liu, Y. C., Yoshiga, T., Kikuchi, T., Chen, P. J. & Tsai, I. J. (2023) The Aphelenchoides genomes reveal substantial horizontal gene transfer s in the last common ancestor of free-living and major plant-parasitic nematodes. Molecular Ecology Resources 23, 905-919.

Kawahara, K., Inada, T., Tanaka, R., Dayi, M., Makino, T., Maruyama, S., Kikuchi, T., Sugimoto, A. & Kawata, M. (2023) Differentially Expressed Genes Associated with Body Size Changes and T ransposable Element Insertions between Caenorhabditis elegans and Its Sister Species, Caenorhabditis inopinata. Genome Biology and Evolution 15.

Kaneko, C., Shinohara, A., Kikuchi, T., Tokuda, A., Irie, T., Yamada, K., Misawa, N. & Yoshida, A. (2023) Distinctly different gut microbiota in Japanese badgers and Japanese r accoon dogs despite sharing similar food habits and environments. Mammalian Biology 103, 363-373.

Iguchi, A., Takemura, T., Ogura, Y., Nguyen, T. T. H., Kikuchi, T., Okuno, M., Tokizawa, A., Iwashita, H., Pham, H. Q. A., Doan, T. H., Tran, N. L., Tran, T. L., Nguyen, T. H., Tran, T. H., Pham, T. N. L., Dao, T. D., Vu, T. M. H., Nguyen, T. N., Vu, H., Nguyen, V. T., Vu, T. T. H., Le, T. H., Lai, T. A., Ngo, T. C., Hasebe, F., Nguyen, D. T. & Yamashiro, T. (2023) Genomic characterization of endemic diarrheagenic Escherichia coli and Escherichia albertii from infants with diarrhea in Vietnam. Plos Neglected Tropical Diseases 17.

2022

Yokogami, K., Kikuchi, T., Watanabe, T., Nakatake, Y., Yamashita, S., Mizuguchi, A. & Takeshima, H. (2022) Methionine regulates self-renewal, pluripotency, and cell death of GIC through cholesterol?rRNA axis. BMC Cancer 22.

Sun, S., Kanzaki, N., Dayi, M., Maeda, Y., Yoshida, A., Tanaka, R. & Kikuchi, T. (2022) The compact genome of Caenorhabditis niphades n. sp., isolated from a wood-boring weevil, Niphades variegatus. BMC Genomics 23.

Suleiman, M., Kohnosu, A., Murcott, B., Dayi, M., Pawluk, R., Yoshida, A., Viney, M., Kikuchi, T. & Hunt, V. L. (2022) piRNA-like small RNAs target transposable elements in a Clade IV paras itic nematode. Biorxiv.

Shinya, R., Sun, S., Dayi, M., Tsai, I. J., Miyama, A., Chen, A. F., Hasegawa, K., Antoshechkin, I., Kikuchi, T. & Sternberg, P. W. (2022) Possible stochastic sex determination in Bursaphelenchus nematodes. Nature Communications 13.

Murase, K., Arakawa, E., Izumiya, H., Iguchi, A., Takemura, T., Kikuchi, T., Nakagawa, I., Thomson, N. R., Ohnishi, M. & Morita, M. (2022) Genomic dissection of the Vibrio cholerae O-serogroup global reference strains: reassessing our view of diversity and plasticity between two chromosomes. Microbial Genomics 8.

Broitman-Maduro, G., Sun, S., Kikuchi, T. & Maduro, M. F. (2022) The GATA factor ELT-3 specifies endoderm in Caenorhabditis angaria in an ancestral gene network. Development Cambridge 149.

2021

Taninaka, H., Maggioni, D., Seveso, D., Huang, D., Townsend, A., Richards, Z. T., Tang, S. L., Wada, N., Kikuchi, T., Yuasa, H., Kanai, M., De Palmas, S., Phongsuwan, N. & Yasuda, N. (2021) Phylogeography of Blue Corals (Genus Heliopora) Across the Indo-West P acific. Frontiers in Marine Science 8.

Takata, K., Iwase, F., Iguchi, A., Yuasa, H., Taninaka, H., Iwasaki, N., Uda, K., Suzuki, T., Nonaka, M., Kikuchi, T. & Yasuda, N. (2021) Genome-Wide SNP Data Revealed Notable Spatial Genetic Structure in the Deep-Sea Precious Coral Corallium japonicum. Frontiers in Marine Science 8.

Nguyen, T. T. H., Kikuchi, T., Tokunaga, T., Iyoda, S. & Iguchi, A. (2021) Diversity of the Tellurite Resistance Gene Operon in Escherichia coli. Frontiers in Microbiology 12.

Murase, K., Aikawa, C., Nozawa, T., Nakatake, A., Sakamoto, K., Kikuchi, T. & Nakagawa, I. (2021) Biological Effect of Streptococcus pyogenes-Released Extracellular Ves icles on Human Monocytic Cells, Induction of Cytotoxicity, and Inflamm atory Response. Frontiers in Cellular and Infection Microbiology 11.

Mokodongan, D. F., Taninaka, H., Sara, L., Kikuchi, T., Yuasa, H., Suyama, Y. & Yasuda, N. (2021) Spatial Autocorrelation Analysis Using MIG-seq Data Indirectly Estimat ed the Gamete and Larval Dispersal Range of the Blue Coral, Heliopora coerulea, Within Reefs. Frontiers in Marine Science 8.

Kikuchi, T., Dayi, M., Hunt, V. L., Ishiwata, K., Toyoda, A., Kounosu, A., Sun, S., Maeda, Y., Kondo, Y., Noya, B. A., Noya, O., Kojima, S., Kuramochi, T. & Maruyama, H. (2021) Genome of the fatal tapeworm Sparganum proliferum uncovers mechanisms for cryptic life cycle and aberrant larval proliferation. Communications Biology 4.

Horoiwa, M., Nakamura, T., Yuasa, H., Kajitani, R., Ameda, Y., Sasaki, T., Taninaka, H., Kikuchi, T., Yamakita, T., Toyoda, A., Itoh, T. & Yasuda, N. (2021) Integrated population genomic analysis and numerical simulation to est imate larval dispersal of Acanthaster cf. Solaris between Ogasawara an d other Japanese regions. Biorxiv.

Dayi, M., Kanzaki, N., Sun, S., Ide, T., Tanaka, R., Masuya, H., Okabe, K., Kajimura, H. & Kikuchi, T. (2021) Additional description and genome analyses of Caenorhabditis auricular iae representing the basal lineage of genus Caenorhabditis. Scientific Reports 11.

2020

Sun, S., Shinya, R., Dayi, M., Yoshida, A., Sternberg, P. W. & Kikuchi, T. (2020) Telomere-to-Telomere Genome Assembly of Bursaphelenchus okinawaensis S train SH1. Microbiology Resource Announcements 9.

Murase, K., Nozawa, T., Aikawa, C., Nagao, M., Ikebe, T., Yoshida, A., Kikuchi, T. & Nakagawa, I. (2020) Complete genome sequences of Streptococcus pyogenes serotype M3, M28, and M89 strains isolated from human patients in Japan, 1994 to 2009. Microbiology Resource Announcements 9.

Mondal, S. I., Akter, A., Koga, R., Hosokawa, T., Dayi, M., Murase, K., Tanaka, R., Shigenobu, S., Fukatsu, T. & Kikuchi, T. (2020) Reduced Genome of the Gut Symbiotic Bacterium ?Candidatus Benitsuchiph ilus tojoi? Provides Insight Into Its Possible Roles in Ecology and Ad aptation of the Host Insect. Frontiers in Microbiology 11.

Minowa-Nozawa, A., Nozawa, T., Takamatsu, D., Yoshida, A., Murase, K., Kikuchi, T., Ishida-Kuroki, K., Nitta, Y., Sekizaki, T. & Nakagawa, I. (2020) Complete genome sequences of two streptococcus suis strains isolated f rom asymptomatic pigs. Microbiology Resource Announcements 9.

Kikuchi, T. & Maruyama, H. (2020) Human proliferative sparganosis update. Parasitology International 75.
Iguchi, A., Nishii, H., Seto, K., Mitobe, J., Lee, K., Konishi, N., Obata, H., Kikuchi, T. & Iyoda, S. (2020) Additional og-typing PCR techniques targeting escherichia coli-novel a nd shigella-unique O-antigen biosynthesis gene clusters. Journal of Clinical Microbiology 58.

Dayi, M., Sun, S., Maeda, Y., Tanaka, R., Yoshida, A., Tsai, I. J. & Kikuchi, T. (2020) Nearly complete genome assembly of the pinewood nematode bursaphelench us xylophilus strain Ka4C1. Microbiology Resource Announcements 9.

2019

Tanaka, S. E., Dayi, M., Maeda, Y., Tsai, I. J., Tanaka, R., Bligh, M., Takeuchi-Kaneko, Y., Fukuda, K., Kanzaki, N. & Kikuchi, T. (2019) Stage-specific transcriptome of Bursaphelenchus xylophilus reveals tem poral regulation of effector genes and roles of the dauer-like stages in the lifecycle. Scientific Reports 9.

Takata, K., Taninaka, H., Nonaka, M., Iwase, F., Kikuchi, T., Suyama, Y., Nagai, S. & Yasuda, N. (2019) Multiplexed ISSR genotyping by sequencing distinguishes two precious c oral species (Anthozoa: Octocorallia: Coralliidae) that share a mitoch ondrial haplotype. Peerj 2019.

Nagaoka, K., Konno, S., Murase, K., Kikuchi, T., Morinaga, Y., Yanagihara, K. & Nakagawa, I. (2019) Complete genome sequences of streptococcus pneumoniae Strains HU-OH (S erotype 3, Sequence Type 183 [ST183]), NU83127 (Serotype 4, ST246), an d ATCC 49619 (Serotype 19F, ST1203). Microbiology Resource Announcements 8.

Maeda, Y., Palomares-Rius, J. E., Hino, A., Afrin, T., Mondal, S. I., Nakatake, A., Maruyama, H. & Kikuchi, T. (2019) Secretome analysis of Strongyloides venezuelensis parasitic stages reveals that soluble and insoluble proteins are involved in its parasitism. Parasites and Vectors 12.

Kudo, R., Masuya, H., Endoh, R., Kikuchi, T. & Ikeda, H. (2019) Gut bacterial and fungal communities in ground-dwelling beetles are as sociated with host food habit and habitat. Isme Journal 13, 676-685.

Kounosu, A., Murase, K., Yoshida, A., Maruyama, H. & Kikuchi, T. (2019) Improved 18S and 28S rDNA primer sets for NGS-based parasite detection. Scientific Reports 9.

Hombu, A., Yoshida, A., Kikuchi, T., Nagayasu, E., Kuroki, M. & Maruyama, H. (2019) Treatment of larva migrans syndrome with long-term administration of a lbendazole. Journal of Microbiology Immunology and Infection 52, 100-105.

Hikichi, M., Nagao, M., Murase, K., Aikawa, C., Nozawa, T., Yoshida, A., Kikuchi, T. & Nakagawa, I. (2019) Complete genome sequences of eight methicillin-resistant staphylococcus aureus strains isolated from patients in Japan. Microbiology Resource Announcements 8.

Coghlan, A., Tyagi, R., Cotton, J. A., Holroyd, N., Rosa, B. A., Tsai, I. J., Laetsch, D. R., Beech, R. N., Day, T. A., Hallsworth-Pepin, K., Ke, H. M., Kuo, T. H., Lee, T. J., Martin, J., Maizels, R. M., Mutowo, P., Ozersky, P., Parkinson, J., Reid, A. J., Rawlings, N. D., Ribeiro, D. M., Swapna, L. S., Stanley, E., Taylor, D. W., Wheeler, N. J., Zamanian, M., Zhang, X., Allan, F., Allen, J. E., Asano, K., Babayan, S. A., Bah, G., Beasley, H., Bennett, H. M., Bisset, S. A., Castillo, E., Cook, J., Cooper, P. J., Cruz-Bustos, T., Cuéllar, C., Devaney, E., Doyle, S. R., Eberhard, M. L., Emery, A., Eom, K. S., Gilleard, J. S., Gordon, D., Harcus, Y., Harsha, B., Hawdon, J. M., Hill, D. E., Hodgkinson, J., Horak, P., Howe, K. L., Huckvale, T., Kalbe, M., Kaur, G., Kikuchi, T., Koutsovoulos, G., Kumar, S., Leach, A. R., Lomax, J., Makepeace, B., Matthews, J. B., Muro, A., O?Boyle, N. M., Olson, P. D., Osuna, A., Partono, F., Pfarr, K., Rinaldi, G., Foronda, P., Rollinson, D., Samblas, M. G., Sato, H., Schnyder, M., Scholz, T., Shafie, M., Tanya, V. N., Toledo, R., Tracey, A., Urban, J. F., Wang, L. C., Zarlenga, D., Blaxter, M. L., Mitreva, M. & Berriman, M. (2019) Comparative genomics of the major parasitic worms. Nature Genetics 51, 163-174.

Afrin, T., Murase, K., Kounosu, A., Hunt, V. L., Bligh, M., Maeda, Y., Hino, A., Maruyama, H., Tsai, I. J. & Kikuchi, T. (2019) Sequential Changes in the Host Gut Microbiota during Infection with th e Intestinal Parasitic Nematode Strongyloides venezuelensis. Frontiers in Cellular and Infection Microbiology 9.

2018

Vicente, C. S. L., Mondal, S. I., Akter, A., Ozawa, S., Kikuchi, T. & Hasegawa, K. (2018) Genome analysis of new Blattabacterium spp., obligatory endosymbionts of Periplaneta fuliginosa and P. japonica. Plos One 13.

Richards, Z. T., Yasuda, N., Kikuchi, T., Foster, T., Mitsuyuki, C., Stat, M., Suyama, Y. & Wilson, N. G. (2018) Integrated evidence reveals a new species in the ancient blue coral ge nus Heliopora (Octocorallia). Scientific Reports 8.

Nagaoka, K., Konno, S., Murase, K., Kikuchi, T. & Nakagawa, I. (2018) Complete genome sequence of streptococcus agalactiae serotype iii, mul tilocus sequence type 335 strain hu-gs5823, isolated from a human pati ent in Japan with severe invasive infection. Microbiology Resource Announcements 7.

Kitazume, H., Dayi, M., Tanaka, R. & Kikuchi, T. (2018) Assessment of the behaviour and survival of nematodes under low oxygen concentrations. Plos One 13.

Kanzaki, N., Tsai, I. J., Tanaka, R., Hunt, V. L., Liu, D., Tsuyama, K., Maeda, Y., Namai, S., Kumagai, R., Tracey, A., Holroyd, N., Doyle, S. R., Woodruff, G. C., Murase, K., Kitazume, H., Chai, C., Akagi, A., Panda, O., Ke, H. M., Schroeder, F. C., Wang, J., Berriman, M., Sternberg, P. W., Sugimoto, A. & Kikuchi, T. (2018) Biology and genome of a newly discovered sibling species of Caenorhabd itis elegans. Nature Communications 9.

Hunt, V. L., Hino, A., Yoshida, A. & Kikuchi, T. (2018) Comparative transcriptomics gives insights into the evolution of paras itism in Strongyloides nematodes at the genus, subclade and species le vel. Scientific Reports 8.

Banjo, M., Iguchi, A., Seto, K., Kikuchi, T., Harada, T., Scheutz, F. & Iyoda, S. (2018) Escherichia coli H-Genotyping PCR: A complete and practical platform f or molecular h typing. Journal of Clinical Microbiology 56.

Afrin, T., Kounosu, A., Billah, M. M., Murase, K. & Kikuchi, T. (2018) Evaluation of magnetic cellulose bead-based DNA extraction from faecal materials for high-throughput bacterial community analyses. Applied Entomology and Zoology 53, 281-286.

2017

Viney, M. & Kikuchi, T. (2017) Strongyloides ratti and S. venezuelensis – Rodent models of Strongyloi des infection. Parasitology 144, 285-294.

Tsubokawa, D., Hatta, T., Kikuchi, T., Maeda, H., Mikami, F., Alim, M. A., Maruyama, H. & Tsuji, N. (2017) Venestatin, a Ca++-binding protein from the parasitic nematode Strongy loides venezuelensis, is involved in the larval migration process. International Journal for Parasitology 47, 501-509.

Nagayasu, E., Aung, M. P. P. T. H. H., Hortiwakul, T., Hino, A., Tanaka, T., Higashiarakawa, M., Olia, A., Taniguchi, T., Win, S. M. T., Ohashi, I., Odongo-Aginya, E. I., Aye, K. M., Mon, M., Win, K. K., Ota, K., Torisu, Y., Panthuwong, S., Kimura, E., Palacpac, N. M. Q., Kikuchi, T., Hirata, T., Torisu, S., Hisaeda, H., Horii, T., Fujita, J., Htike, W. W. & Maruyama, H. (2017) A possible origin population of pathogenic intestinal nematodes, Stron gyloides stercoralis, unveiled by molecular phylogeny. Scientific Reports 7.

Klopfenstein, N. B., Stewart, J. E., Ota, Y., Hanna, J. W., Richardson, B. A., Ross-Davis, A. L., Elías-Román, R. D., Korhonen, K., Ke?a, N., Iturritxa, E., Alvarado-Rosales, D., Solheim, H., Brazee, N. J., akomy, P., Cleary, M. R., Hasegawa, E., Kikuchi, T., Garza-Ocañas, F., Tsopelas, P., Rigling, D., Prospero, S., Tsykun, T., Bérubé, J. A., Stefani, F. O. P., Jafarpour, S., Antonín, V., Tom?ovsk, M., McDonald, G. I., Woodward, S. & Kim, M. S. (2017) Insights into the phylogeny of northern hemisphere Armillaria: Neighbo r-net and bayesian analyses of translation elongation factor 1-? gene sequences. Mycologia 109, 75-91.

Kikuchi, T., Eves-Van Den Akker, S. & Jones, J. T. (2017) Genome Evolution of Plant-Parasitic Nematodes. Annual Review of Phytopathology 55, 333-354.

Iguchi, A., Mentzer, A., Kikuchi, T. & Thomson, N. R. (2017) An untypeable enterotoxigenic Escherichia coli represents one of the d ominant types causing human disease. Microbial Genomics 3.

Chung, C. L., Lee, T. J., Akiba, M., Lee, H. H., Kuo, T. H., Liu, D., Ke, H. M., Yokoi, T., Roa, M. B., Lu, M. Y. J., Chang, Y. Y., Ann, P. J., Tsai, J. N., Chen, C. Y., Tzean, S. S., Ota, Y., Hattori, T., Sahashi, N., Liou, R. F., Kikuchi, T. & Tsai, I. J. (2017) Comparative and population genomic landscape of Phellinus noxius: A hy pervariable fungus causing root rot in trees. Molecular Ecology 26, 6301-6316.

2016

Yoshida, A., Matsuo, K., Moribe, J., Tanaka, R., Kikuchi, T., Nagayasu, E., Misawa, N. & Maruyama, H. (2016) Venison, another source of Paragonimus westermani infection. Parasitology International 65, 607-612.

Yoshida, A., Kikuchi, T., Nakagaki, S. & Maruyama, H. (2016) Optimal ELISA antigen for the diagnosis of Ascaris suum infection in h umans. Parasitology Research 115, 4701-4705.

Vicente, C. S. L., Nascimento, F. X., Barbosa, P., Ke, H. M., Tsai, I. J., Hirao, T., Cock, P. J. A., Kikuchi, T., Hasegawa, K. & Mota, M. (2016) Evidence for an Opportunistic and Endophytic Lifestyle of the Bursaphe lenchus xylophilus-Associated Bacteria Serratia marcescens PWN146 Isol ated from Wilting Pinus pinaster. Microbial Ecology 72, 669-681.

Tsai, I. J., Tanaka, R., Kanzaki, N., Akiba, M., Yokoi, T., Espada, M., Jones, J. T. & Kikuchi, T. (2016) Transcriptional and morphological changes in the transition from mycet ophagous to phytophagous phase in the plant-parasitic nematode Bursaph elenchus xylophilus. Molecular Plant Pathology 17, 77-83.

Mondal, S. I., Mahmud, Z., Elahi, M., Akter, A., Jewel, N. A., Muzahidul Islam, M., Ferdous, S. & Kikuchi, T. (2016) Study of intra-inter species protein-protein interactions for potential drug targets identification and subsequent drug design for Escherichia coli O104:H4 C277-11. In Silico Pharmacol 5, 1.

Kikuchi, T., Hino, A., Tanaka, T., Aung, M. P. P. T. H. H., Afrin, T., Nagayasu, E., Tanaka, R., Higashiarakawa, M., Win, K. K., Hirata, T., Htike, W. W., Fujita, J. & Maruyama, H. (2016) Genome-Wide Analyses of Individual Strongyloides stercoralis (Nematoda : Rhabditoidea) Provide Insights into Population Structure and Reprodu ctive Life Cycles. Plos Neglected Tropical Diseases 10.

Kikuchi, T., Afrin, T. & Yoshida, M. (2016) Complete mitochondrial genomes of four entomopathogenic nematode speci es of the genus Steinernema. Parasites and Vectors 9.

Hunt, V. L., Tsai, I. J., Coghlan, A., Reid, A. J., Holroyd, N., Foth, B. J., Tracey, A., Cotton, J. A., Stanley, E. J., Beasley, H., Bennett, H. M., Brooks, K., Harsha, B., Kajitani, R., Kulkarni, A., Harbecke, D., Nagayasu, E., Nichol, S., Ogura, Y., Quail, M. A., Randle, N., Xia, D., Brattig, N. W., Soblik, H., Ribeiro, D. M., Sanchez-Flores, A., Hayashi, T., Itoh, T., Denver, D. R., Grant, W., Stoltzfus, J. D., Lok, J. B., Murayama, H., Wastling, J., Streit, A., Kikuchi, T., Viney, M. & Berriman, M. (2016) The genomic basis of parasitism in the Strongyloides clade of nematode s. Nature Genetics 48, 299-307.

Hino, A., Maruyama, H. & Kikuchi, T. (2016) A novel method to assess the biodiversity of parasites using 18S rDNA Illumina sequencing; parasitome analysis method. Parasitology International 65, 572-575.

Cotton, J. A., Steinbiss, S., Yokoi, T., Tsai, I. J. & Kikuchi, T. (2016) An expressed, endogenous Nodavirus-like element captured by a retrotra nsposon in the genome of the plant parasitic nematode Bursaphelenchus xylophilus. Scientific Reports 6.

Cotton, J. A., Bennuru, S., Grote, A., Harsha, B., Tracey, A., Beech, R., Doyle, S. R., Dunn, M., Hotopp, J. C. D., Holroyd, N., Kikuchi, T., Lambert, O., Mhashilkar, A., Mutowo, P., Nursimulu, N., Ribeiro, J. M. C., Rogers, M. B., Stanley, E., Swapna, L. S., Tsai, I. J., Unnasch, T. R., Voronin, D., Parkinson, J., Nutman, T. B., Ghedin, E., Berriman, M. & Lustigman, S. (2016) The genome of Onchocerca volvulus, agent of river blindness. Nature Microbiology 2.

2015

Palomares-Rius, J. E., Tsai, I. J., Karim, N., Akiba, M., Kato, T., Maruyama, H., Takeuchi, Y. & Kikuchi, T. (2015) Genome-wide variation in the pinewood nematode Bursaphelenchus xylophi lus and its relationship with pathogenic traits. BMC Genomics 16.

Ogura, N., Takeuchi, T., Kikuchi, T., Tanaka, R., Yamaguchi, M. & Dayi, M. (2015) Development and validation of SSR markers for the plant-parasitic nema tode Subanguina moxae using genome assembly of Illumina pair-end reads. Nematology 17, 515-522.

Masuya, H., Kikuchi, T. & Sahashi, N. (2015) New insights to develop studies on witch’s broom caused by Taphrina wi esneri. Nihon Ringakkai Shi Journal of the Japanese Forestry Society 97, 153-157.
Iguchi, A., Iyoda, S., Kikuchi, T., Ogura, Y., Katsura, K., Ohnishi, M., Hayashi, T. & Thomson, N. R. (2015) A complete view of the genetic diversity of the Escherichia coli O-ant igen biosynthesis gene cluster. DNA Research 22, 101-107.

Bird, D. M., Jones, J. T., Opperman, C. H., Kikuchi, T. & Danchin, E. G. J. (2015) Signatures of adaptation to plant parasitism in nematode genomes. Parasitology 142, S71-S84.

Akiba, M., Ota, Y., Tsai, I. J., Hattori, T., Sahashi, N. & Kikuchi, T. (2015) Genetic differentiation and spatial structure of Phellinus noxius, the causal agent of brown root rot of woody plants in Japan. Plos One 10.

Tsai, I. J., Tanaka, E., Masuya, H., Tanaka, R., Hirooka, Y., Endoh, R., Sahashi, N. & Kikuchi, T. (2014) Comparative genomics of taphrina fungi causing varying degrees of tumo rous deformity in plants. Genome Biology and Evolution 6, 861-872.

2014

Tsai, I. J., Hunt, M., Holroyd, N., Huckvale, T., Berriman, M. & Kikuchi, T. (2014) Summarizing specific profiles in illumina sequencing from whole-genome amplified DNA. DNA Research 21, 243-254.

Tanaka, R., Hino, A., Tsai, I. J., Palomares-Rius, J. E., Yoshida, A., Ogura, Y., Hayashi, T., Maruyama, H. & Kikuchi, T. (2014) Assessment of helminth biodiversity in wild rats using 18S rDNA based metagenomics. Plos One 9.

Palomares-Rius, J. E., Kikuchi, T., Cantalapiedra-Navarrete, C. & Castillo, P. (2014) Integrative diagnosis of the needle nematode Longidorus jonesi affecti ng forest in southern Japan. Forest Pathology 44, 246-249.

Palomares-Rius, J. E., Hirooka, Y., Tsai, I. J., Masuya, H., Hino, A., Kanzaki, N., Jones, J. T. & Kikuchi, T. (2014) Distribution and evolution of glycoside hydrolase family 45 cellulases in nematodes and fungi. BMC Evolutionary Biology 14.

Kikuchi, T., Helder, J., Cock, P. J. A. & Jones, J. T. (2014) Characterisation of the transcriptome of Aphelenchoides besseyi and id entification of a GHF 45 cellulase. Nematology 16, 99-107.

Hino, A., Tanaka, T., Takaishi, M., Fujii, Y., Palomares-Rius, J. E., Hasegawa, K., Maruyama, H. & Kikuchi, T. (2014) Karyotype and reproduction mode of the rodent parasite Strongyloides v enezuelensis. Parasitology 141, 1736-1745.

Cotton, J. A., Lilley, C. J., Jones, L. M., Kikuchi, T., Reid, A. J., Thorpe, P., Tsai, I. J., Beasley, H., Blok, V., Cock, P. J. A., Akker, S. E. V., Holroyd, N., Hunt, M., Mantelin, S., Naghra, H., Pain, A., Palomares-Rius, J. E., Zarowiecki, M., Berriman, M., Jones, J. T. & Urwin, P. E. (2014) The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biology 15.

~2013

Shinya, R., Morisaka, H., Kikuchi, T., Takeuchi, Y., Ueda, M. & Futai, K. (2013) Secretome Analysis of the Pine Wood Nematode Bursaphelenchus xylophilu s Reveals the Tangled Roots of Parasitism and Its Potential for Molecu lar Mimicry. Plos One 8.

Palomares-Rius, J. E. & Kikuchi, T. (2013) -Omics fields of study related to plant-parasitic nematodes. Journal of Integrated OMICS 3, 1-10.

Laing, R., Kikuchi, T., Martinelli, A., Tsai, I. J., Beech, R. N., Redman, E., Holroyd, N., Bartley, D. J., Beasley, H., Britton, C., Curran, D., Devaney, E., Gilabert, A., Hunt, M., Jackson, F., Johnston, S. L., Kryukov, I., Li, K., Morrison, A. A., Reid, A. J., Sargison, N., Saunders, G. I., Wasmuth, J. D., Wolstenholme, A., Berriman, M., Gilleard, J. S. & Cotton, J. A. (2013) The genome and transcriptome of Haemonchus contortus, a key model para site for drug and vaccine discovery. Genome Biology 14.

Jones, J. T., Haegeman, A., Danchin, E. G. J., Gaur, H. S., Helder, J., Jones, M. G. K., Kikuchi, T., Manzanilla-López, R., Palomares-Rius, J. E., Wesemael, W. M. L. & Perry, R. N. (2013) Top 10 plant-parasitic nematodes in molecular plant pathology. Molecular Plant Pathology 14, 946-961.

Hunt, M., Kikuchi, T., Sanders, M., Newbold, C., Berriman, M. & Otto, T. D. (2013) REAPR: A universal tool for genome assembly evaluation. Genome Biology 14.

Tanaka, R., Kikuchi, T., Aikawa, T. & Kanzaki, N. (2012) Simple and quick methods for nematode DNA preparation. Applied Entomology and Zoology 47, 291-294.

Kikuchi, T., Cotton, J. A., Dalzell, J. J., Hasegawa, K., Kanzaki, N., McVeigh, P., Takanashi, T., Tsai, I. J., Assefa, S. A., Cock, P. J. A., Da Otto, T., Hunt, M., Reid, A. J., Sanchez-Flores, A., Tsuchihara, K., Yokoi, T.,

Larsson, M. C., Miwa, J., Maule, A. G., Sahashi, N., Jones, J. T. & Berriman, M. (2011) Genomic insights into the origin of parasitism in the emerging plant p athogen bursaphelenchus xylophilus. Plos Pathogens 7.

Karim, N., Shibuya, H. & Kikuchi, T. (2011) Analysis of expressed sequence tags from the wood-decaying fungus Fomitopsis palustris and identification of potential genes involved in the decay process. J Microbiol Biotechnol 21, 347-358.

Kanetani, S., Kikuchi, T., Akiba, M., Nakamura, K., Ikegame, H. & Tetsuka, K. (2011) Detection of Bursaphelenchus xylophilus from old discs of dead Pinus a rmandii var. amamiana trees using a new detection kit. Forest Pathology 41, 387-391.

Hasegawa, E., Ota, Y., Hattori, T., Sahashi, N. & Kikuchi, T. (2011) Ecology of Armillaria species on conifers in Japan. Forest Pathology 41, 429-437.

Hasegawa, E., Ota, Y., Hattori, T. & Kikuchi, T. (2010) Sequence-based identification of Japanese Armillaria species using the elongation factor-1 alpha gene. Mycologia 102, 898-910.

Onozato, H., Kawabe, Y., Ota, Y., Kikuchi, T. & Kanezawa, Y. (2009) Detection of Armillaria spp. by the bait method using oak logs in a ch erry stand damaged by Armillaria tabescens. Nihon Ringakkai Shi Journal of the Japanese Forestry Society 91, 201-207.

Kikuchi, T., Li, H., Karim, N., Kennedy, M. W., Moens, M. & Jones, J. T. (2009) Identification of putative expansin-like genes from the pine wood nema tode, Bursaphelenchus xylophilus, and evolution of the expansin gene f amily within the Nematoda. Nematology 11, 355-364.

Kikuchi, T., Karim, N., Masuya, H., Ota, Y. & Kubono, T. (2009) An inexpensive high-throughput method to extract high yields of good q uality DNA from fungi. Molecular Ecology Resources 9, 41-45.

Kikuchi, T., Aikawa, T., Oeda, Y., Karim, N. & Kanzaki, N. (2009) A rapid and precise diagnostic method for detecting the pinewood nemat ode Bursaphelenchus xylophilus by loop-mediated isothermal amplificati on. Phytopathology 99, 1365-1369.

Karim, N., Jones, J. T., Okada, H. & Kikuchi, T. (2009) Analysis of expressed sequence tags and identification of genes encodi ng cell-wall-degrading enzymes from the fungivorous nematode Aphelench us avenae. BMC Genomics 10.

Aikawa, T., Anbutsu, H., Nikoh, N., Kikuchi, T., Shibata, F. & Fukatsu, T. (2009) Longicorn beetle that vectors pinewood nematode carries many Wolbachia genes on an autosome. Proceedings of the Royal Society B Biological Sciences 276, 3791-3798.

Shibuya, H. & Kikuchi, T. (2008) Purification and characterization of recombinant endoglucanases from t he pine wood nematode Bursaphelenchus xylophilus. Bioscience Biotechnology and Biochemistry 72, 1325-1332.

Kikuchi, T. (2008) Parasitism Genes of the Pine Wood Nematode. Pine Wilt Disease, 67-80.
Jones, J. T., Moens, M., Mota, M., Li, H. & Kikuchi, T. (2008) Bursaphelenchus xylophilus: Opportunities in comparative genomics and molecular host-parasite interactions. Molecular Plant Pathology 9, 357-368.

Kikuchi, T., Aikawa, T., Kosaka, H., Pritchard, L., Ogura, N. & Jones, J. T. (2007) Expressed sequence tag (EST) analysis of the pine wood nematode Bursap helenchus xylophilus and B. mucronatus. Molecular and Biochemical Parasitology 155, 9-17.

Aikawa, T. & Kikuchi, T. (2007) Estimation of virulence of Bursaphelenchus xylophilus (Nematoda: Aphel enchoididae) based on its reproductive ability. Nematology 9, 371-377.

Kikuchi, T., Shibuya, H., Aikawa, T. & Jones, J. T. (2006) Cloning and characterization of pectate lyases expressed in the esopha geal gland of the pine wood nematode Bursaphelenchus xylophilus. Molecular Plant Microbe Interactions 19, 280-287.

Aikawa, T., Kikuchi, T. & Kosaka, H. (2006) Population structure of Bursaphelenchus xylophilus within single Pinus thunbergii trees inoculated with two nematode isolates. Forest Pathology 36, 1-13.

Kikuchi, T., Shibuya, H. & Jones, J. T. (2005) Molecular and biochemical characterization of an endo-?-1,3-glucanase from the pinewood nematode Bursaphelenchus xylophilus acquired by hori zontal gene transfer from bacteria. Biochemical Journal 389, 117-125.

Kikuchi, T. (2005) Genomics of plant pathogenic microbes. Nihon Ringakkai Shi Journal of the Japanese Forestry Society 87, 251-260.

Jones, J. T., Furlanetto, C. & Kikuchi, T. (2005) Horizontal gene transfer from bacteria and fungi as a driving force in the evolution of plant parasitism in nematodes. Nematology 7, 641-646.

Kojima, K., Takano, Y., Yoshimi, A., Tanaka, C., Kikuchi, T. & Okuno, T. (2004) Fungicide activity through activation of a fungal signalling pathway. Molecular Microbiology 53, 1785-1796.

Kikuchi, T., Jones, J. T., Aikawa, T., Kosaka, H. & Ogura, N. (2004) A family of glycosyl hydrolase family 45 cellulases from the pine wood nematode Bursaphelenchus xylophilus. FEBS Letters 572, 201-205.

Aikawa, T., Kikuchi, T. & Kosaka, H. (2003) Demonstration of interbreeding between virulent and avirulent populati ons of Bursaphelenchus xylophilus (Nematoda: Aphelenchoididae) by PCR- RFLP method. Applied Entomology and Zoology 38, 565-569.

Kojima, K., Kikuchi, T., Takano, Y., Oshiro, E. & Okuno, T. (2002) The mitogen-activated protein kinase gene MAF1 is essential for the ea rly differentiation phase of appressorium formation in Colletotrichum lagenarium. Molecular Plant Microbe Interactions 15, 1268-1276.

Takano, Y., Kikuchi, T., Kubo, Y., Hamer, J. E., Mise, K. & Furusawa, I. (2000) The Colletotrichum lagenarium MAP kinase gene CMK1 regulates diverse a spects of fungal pathogenesis. Molecular Plant Microbe Interactions 13, 374-383.