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List of Publications 2019
2018 2017

 
Tanoue T, Morita S, Plichta DR, Skelly AN, Suda W, Sugiura Y, Narushima S, Vlamakis H, Motoo I, Sugita K, Shiota A, Takeshita K, Yasuma-Mitobe K, Riethmacher D, Kaisho T, Norman JM, Mucida D, Suematsu M, Yaguchi T, Bucci V, Inoue T, Kawakami Y, Olle B, Roberts B, Hattori M, Xavier RJ, Atarashi K, Honda K. A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. (2019) Nature, 565, 600-605. doi: 10.1038/s41586-019-0878-z


Soyano, T., Shimoda, Y., Kawaguchi, M., Hayashi, M. A shared gene drives lateral root development and root nodule symbiosis pathways in Lotus. (2019) Science. 366: 1021-1023. doi: 10.1126/science.aax2153


Yoshida, S., Kim, S., Wafula, E. K., Tanskanen, J., Kim, Y. M., Honaas, L., Yang, Z., Spallek, T., Conn, C. E., Ichihashi, Y., Cheong, K., Cui, S., Der, J. P., Gundlach, H., Jiao, Y., Hori, C., Ishida, J. K., Kasahara, H., Kiba, T., Kim, M. S., Koo, N., Laohavisit, A., Lee, Y. H., Lumba, S., McCourt, P., Mortimer, J. C., Mutuku, J. M., Nomura, T., Sekimoto, Y. S., Seto, Y., Wang, Y., Wakatake, T., Sakakibara, H., Demura, T., Yamaguchi, S., Yoneyama, K., Manabe, R., Nelson, D. C., Schulman, A. H., Timko, M. P., dePamphilis, C. W., Choi, D., and Shirasu, K. Genome sequence of Striga asiatica provides insight into the evolution of plant parasitism. (2019) Curr. Biol. 29: 3041-3052.E4. doi: 10.1016/j.cub.2019.07.086


Tsugawa, H*., Nakabayashi, R*., Mori, T., Yamada, Y., Takahashi, M., Rai, A., Sugiyama, R., Yamamoto, H., Nakaya, T., Yamazaki, M., Kooke, R., Bac-Molenaar, A. J., Oztolan-Erol, N., Keurentjes, J.B. J., Arita, M., and Saito, K. * equally contributed. A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms. (2019) Nat. Methods, 16, 295-298. doi: s41592-019-0358-2


Ali, A., Abouleila, Y., Germond, A. An Integrated Raman Spectroscopy and Mass Spectrometry Platform to Study Single-Cell Drug Uptake, Metabolism, and Effect. (2019) JoVE (in press)


Ali, A., Abouleila, Y., Shimizu, Y., Hiyama, E., Watanabe, M. T., Yanagida, T., Germond, A. Single-cell screening of tamoxifen abundance and effect using mass spectrometry and Raman-spectroscopy. (2019) Analytical Chemistry. doi: 10.1021/acs.analchem.8b04393


Shimizu, Y., Abouleila, Y., Ali, A., Onidani, K., Watanabe, M. T., Germond, A., Honda, K. Metabolome Analysis by Single-Cell Mass Spectrometry. (2019) Proteome letters, 4: 1 pp 1-7. doi: 10.14889/jpros.4.1_1


Nakabayashi, R., Hashimoto, K., Toyooka, K., Saito, K. Keeping the shape of plant tissue for visualizing metabolite features in segmentation and correlation analysis of imaging mass spectrometry in Asparagus officinalis. (2019) Metabolomics, 15, 24. doi: 10.1007/s11306-019-1486-5


Yonekura-Sakakibara, K., Higashi, Y., Nakabayashi, R. The origin and evolution of plant flavonoid metabolism. (2019) Front. Plant Sci., 10, 943. doi: 10.3389/fpls.2019.00943


Kato, S., Hirai, M., Ohkuma, M., Suzuki, K. Microbial metabolisms in an abyssal ferromanganese crust from the Takuyo-Daigo Seamount as revealed by metagenomics. (2019) PLoS One 14(11): e0224888. doi: 10.1371/journal.pone.0224888


Kuncharoen, N., Kudo, T., Yuki, M., Ohkuma, M., Booncharoen, A., Tanasupawat, S. Micromonospora musae sp. nov., an endophytic actinomycete isolated from roots of Musa species. (2019) Systematic and Applied Microbiology, 42(6):126020. doi: 10.1016/j.syapm.2019.126020


Kato, S., Itoh, T., Yuki, M., Nagamori, M., Ohnishi, M., Uematsu, K., Suzuki, K., Takashina, T., Ohkuma, M. Isolation and characterization of a thermophilic sulfur- and iron-reducing thaumarchaeote from a terrestrial acidic hot spring. (2019) The ISME Journal, 13(10): 2465-2474. doi: 10.1038/s41396-019-0447-3


Kuncharoen, N., Kudo, T., Yuki, M., Okuma, M., Pittayakhajonwut, P., Tanasupawat, S. Micromonospora radicis sp. nov., isolated from roots of Azadirachta indica var. siamensis Valenton, and reclassification of Jishengella zingiberis as Micromonospora zingiberis comb. nov. (2019) International Journal of Systematic and Evolutionary Microbiology, 69(9): 2884-2891. doi: 10.1099/ijsem.0.003574


Kunthiphun, S., Wattanagonniyom, T., Endoh, R., Takashima, M., Ohkuma, M., Tanasupawat, S., Savarajara, A. Heterocephalacria mucosa sp. nov., a new basidiomycetous yeast species isolated from a mangrove forest in Thailand. (2019) International Journal of Systematic and Evolutionary Microbiology, 69(9): 2823-2827. doi: 10.1099/ijsem.0.003562


Kato, S., Nakano, S., Kouduka, M., Hirai, M., Suzuki, K., Itoh, T., Ohkuma, M., Suzuki, Y. Metabolic potential of as-yet-uncultured archaeal lineages of Candidatus Hydrothermarchaeota thriving in deep-sea metal sulfide deposits. (2019) Microbes and Environments, 34(3):293-303. doi: 10.1264/jsme2.ME19021


Hirao, S. A., Imai, R., Endoh, R., Ohkuma, M., Degawa, Y. Draft genome sequence of novel Metschnikowia sp. strain JCM 33374, a nectar yeast isolated from a bumblebee. (2019) Microbiology Resource Announcements, 8(37): e00704-19. doi: 10.1128/MRA.00704-19


Sriswasdi, S., Takashima, M., Manabe, RI., Ohkuma, M., Iwasaki, W. Genome and transcriptome evolve separately in recently hybridized Trichosporon fungi. (2019) Communications Biology, 2: 263. doi: 10.1038/s42003-019-0515-2
Maejima, Y., Iino, T., Muraguchi, Y., Ohkuma, M., Kimbara, K., Shintani, M. Algoriphagus sanaruensis sp. nov., a member of the family Cyclobacteriaceae, isolated from a brackish lake in Hamamatsu, Japan. (2019) International Journal of Systematic and Evolutionary Microbiology, 69(7): 2108-2113. doi: 10.1099/ijsem.0.003447


Takashima, M., Manabe, RI., Nishimura, Y., Endoh, R., Ohkuma, M., Sriswasdi, S., Sugita, T., Iwasaki, W. Recognition and delineation of yeast genera based on genomic data: Lessons from Trichosporonales. (2019) Fungal Genetics and Biology, 130: 31-42. doi: 10.1016/j.fgb.2019.04.013


Ikeyama, N., Ohkuma, M., Sakamoto, M. Draft genome sequence of Mesosutterella multiformis JCM 32464T, a member of the family Sutterellaceae, isolated from human feces. (2019) Microbiology Resource Announcements, 8(24): e00478-19. doi: 10.1128/MRA.00478-19


Takashima, M., Manabe, RI., Ohkuma, M. Draft genome sequences of Basidiomycetous epiphytic phylloplane yeast type strains Dioszegia crocea JCM 2961 and Dioszegia aurantiaca JCM 2956. (2019) Microbiology Resource Announcements, 8(26): e01727-18. doi: 10.1128/MRA.01727-18


Kunthiphun, S., Endoh, R., Takashima, M., Ohkuma, M., Tanasupawat, S., Savarajara, A. Prototheca paracutis sp. nov., a novel oleaginous achlorophyllous microalga isolated from a mangrove forest. (2019) Mycoscience 60(3): 165-169. doi: 10.1016/j.myc.2019.02.003


Sakamoto, M., Ikeyama, N., Murakami, T., Mori, H., Yuki, M., Ohkuma, M. Comparative genomics of Parolsenella catena and Libanicoccus massiliensis: Reclassification of Libanicoccus massiliensis as Parolsenella massiliensis comb. nov. (2019) International Journal of Systematic and Evolutionary Microbiology, 69(4): 1123-1129. doi: 10.1099/ijsem.0.003283


Dekio, I., McDowell, A., Sakamoto, M., Tomida, S., Ohkuma, M. Proposal of new combination, Cutibacterium acnes subsp. elongatum comb. nov., and emended descriptions of the genus Cutibacterium, Cutibacterium acnes subsp. acnes and Cutibacterium acnes subsp. defendens. (2019) International Journal of Systematic and Evolutionary Microbiology, 69(4): 1087-1092. doi: 10.1099/ijsem.0.003274


Tohno, M., Tanizawa, Y., Kojima, Y., Sakamoto, M., Nakamura, Y., Ohkuma, M., Kobayashi, H. Lactobacillus salitolerans sp. nov., a novel lactic acid bacterium isolated from spent mushroom substrates. (2019) International Journal of Systematic and Evolutionary Microbiology, 69(4): 964-969. doi: 10.1099/ijsem.0.003224


Nishimura, Y., Shiratori, T., Ishida, KI., Hashimoto, T., Ohkuma, M., Inagaki, Y. Horizontally-acquired genetic elements in the mitochondrial genome of a centrohelid Marophrys sp. SRT127. (2019) Scientific Reports, 9(1): 4850. doi: 10.1038/s41598-019-41238-6 Ridwan, R., Rusmana, I., Widyastuti, Y., Wiryawan, G. K., Prasetya, B., Sakamoto, M., Ohkuma, M. Bacteria and methanogen community in the rumen fed different levels of grass-legume silages. (2019) Biodiversitas 20: 1055-1062. doi: 10.13057/biodiv/d200417 Kobayashi, H., Tanizawa, Y., Sakamoto, M., Nakamura, Y., Ohkuma, M., Tohno, M. Reclassification of Paenibacillus thermophilus Zhou et al. 2013 as a later heterotypic synonym of Paenibacillus macerans (Schardinger 1905) Ash et al. 1994. (2019) International Journal of Systematic and Evolutionary Microbiology, 69(2): 417-421. doi: 10.1099/ijsem.0.003160
Shintani, M., Ohkuma, M., Kimbara, K. High-resolution comparison of bacterial conjugation frequencies. (2019) Journal of Visualized Experiments, 143: e57812. doi: 10.3791/57812


Kuncharoen, N., Kudo, T., Ohkuma, M., Tanasupawat, S. Micromonospora azadirachtae sp. nov., isolated from roots of Azadirachta indica A. Juss. var. siamensis Valeton. (2019) Antonie van Leeuwenhoek 112(2): 253-262. doi: 10.1007/s10482-018-1152-3


Ogata, Y., Suda, W., Hattori, M., Ohkuma, M., Sakamoto, M. Complete genome sequence of Phascolarctobacterium faecium JCM 30894, isolated from human feces. (2019) Microbiology Resource Announcements, 8(3): e01487-18. doi: 10.1128/MRA.01487-18


Murakami, T., Onouchi, S., Igai, K., Ohkuma, M., Hongoh, Y. Ectosymbiotic bacterial microbiota densely colonize the surface of thelastomatid nematodes in the gut of the wood-feeding cockroach Panesthia angustipennis. (2019) FEMS Microbiology Ecology, 95(2): fiy238. doi: 10.1093/femsec/fiy238


Utami, D. Y., Kuwahara, H., Igai, K., Murakami, T., Sugaya, K., Morikawa, T., Nagura, Y., Yuki, M., Deevong, P., Inoue, T., Kihara, K., Lo, N., Yamada, A., Ohkuma, M., Hongoh, Y. Genome analyses of uncultured TG2/ZB3 bacteria in 'Margulisbacteria' specifically attached to ectosymbiotic spirochetes of protists in the termite gut. (2019) The ISME Journal, 13(2): 455–467. doi: 10.1038/s41396-018-0297-4


Sakamoto, M., Ikeyama, N., Kunihiro, T., Iino, T., Yuki, M., Ohkuma, M. Mesosutterella multiformis gen. nov., sp. nov., a member of the family Sutterellaceae and Sutterella megasphaeroides sp. nov., isolated from human faeces. (2018) International Journal of Systematic and Evolutionary Microbiology, 68(12): 3942-3950. doi: 10.1099/ijsem.0.003096
Noda, S., Sakamoto, M., Aihara, C., Yuki, M., Katsuhara, M., Ohkuma, M. Lactococcus termiticola sp. nov., isolated from the gut of the wood-feeding higher termite Nasutitermes takasagoensis. (2018) International Journal of Systematic and Evolutionary Microbiology, 68(12): 3832-3836. doi: 10.1099/ijsem.0.003068


Sakamoto, M., Ikeyama, N., Yuki, M., Ohkuma, M. Draft genome sequence of Faecalimonas umbilicata JCM 30896T, an acetate-producing bacterium isolated from human feces. (2018) Microbiology Resource Announcements, 7 (9): e01091-18. doi: 10.1128/MRA.01091-18


Sugiyama, Y., Nagashima, Y., Wakazaki, M., Sato M., Toyooka, K., Fukuda, H., Oda, Y. A Rho-actin signaling pathway shapes cell wall boundaries in Arabidopsis xylem vessels. (2019) Nature Communication 10, 468. doi: s41467-019-08396-7


Usui, K., Kadono, N., Furuichi, Y., Shiraga, K., Saitou, T., Kawasaki, H., Toyooka, K., Tamura, H., Kubo, A., Amagai, M., Matsui, T. 3D in vivo imaging of the keratin filament network in the mouse stratum granulosum reveals profilaggrin-dependent regulation of keratin bundling. (2019) J Dermatol Sci. 94(3):346-349. doi: 10.1016/j.jdermsci.2019.04.006 Ito-Inaba, Y., Sato, M., Sato, MP., Kurayama, Y., Yamamoto, H., Ohata, M., Ogura, Y., Hayashi, T., Toyooka, K., Inaba, T. Alternative Oxidase Capacity of Mitochondria in Microsporophylls May Function in Cycad Thermogenesis. (2019) Plant Physiol. 180(2):743-756. doi: 10.1104/pp.19.00150


Toyooka K, Shinozaki-Narikawa N. Efficient fluorescence recovery using antifade reagents in correlative light and electron microscopy. (2019) Microscopy, 68(5) 417-421. doi: 10.1093/jmicro/dfz029


Hiwatashi T, Goh H, Yasui Y, Koh LQ, Takami H, Kajikawa M, Kirita H, Kanazawa T, Minamino N, Togawa T, Sato M, Wakazaki M, Yamaguchi K, Shigenobu S, Fukaki H, Mimura T, Toyooka K, Sawa S, Yamato KT, Ueda T, Urano D, Kohchi T, Ishizaki K. The RopGEF KARAPP*O Is Essential for the Initiation of Vegetative Reproduction in Marchantia polymorpha. (2019) Current biology : CB 29(20) 3525-3531.e7. doi: 10.1101/385682


Kato S, Ozasa K, Maeda M, Tanno Y, Tamaki S, Higuchi-Takeuchi M, Numata K, Kodama Y, Sato M, Toyooka K, Shinomura T. Carotenoid in the eyespot apparatus is required for triggering phototaxis in Euglena gracilis. (2019) Plant journal : for cell and molecular biology (in press)


Naramoto S, Jones VAS, Trozzi N, Sato M, Toyooka K, Shimamura M,Ishida S, Nishitani K, Ishizaki K, Nishihama R, Kohchi T, Dolan L and Kyozuka J.A conserved regulatory mechanism mediates the convergent evolution of plant shoot lateral organs. PLOS Biology (in press)


Kim SG, Becattini S, Moody TU, Shliaha PV, Littmann ER, Seok R, Gjonbalaj M, Eaton V, Fontana E, Amoretti L, Wright R, Caballero S, Wang ZX, Jung HJ, Morjaria SM, Leiner IM, Qin W, Ramos RJJF, Cross JR, Narushima S, Honda K, Peled JU, Hendrickson RC, Taur Y, van den Brink MRM, Pamer EG. Microbiota-derived lantibiotic restores resistance against vancomycin-resistant Enterococcus (2019) Nature, 572, :665-669. doi: 10.1038/s41586-019-1501-z


Skelly AN, Sato Y, Kearney S, Honda K. Mining the microbiota for microbial and metabolite-based immunotherapies. (2019) Nat Rev Immunol, 19, 305-323. doi: 10.1038/s41577-019-0144-5


Ladinsky MS, Araujo LP, Zhang X, Veltri J, Galan-Diez M, Soualhi S, Lee C, Irie K, Pinker EY, Narushima S, Bandyopadhyay S, Nagayama M, Elhenawy W, Coombes BK, Ferraris RP, Honda K, Iliev ID, Gao N, Bjorkman PJ, Ivanov II. Endocytosis of commensal antigens by intestinal epithelial cells regulates mucosal T cell homeostasis. (2019) Science, 363, pii: eaat4042. doi: 10.1126/science.aat4042


Kanoh N., Kawamata A., Suzuki K., Takahashi Y., Miyazawa T., Nakamura T., Moriya T., Hirano H., Osada H., Iwabuchi Y., and Takahashi S. An integrated cytochrome P450 substrate screening system enables the analysis of transition in the global substrate selectivity of engineered P450 BM3 mutants. Sci. Rep. (in press)


Panthee S., Takahashi S.*, Hayashi T., Shimizu T, and Osada H.* β-carboline biomediators induce reveromycin production in Streptomyces sp. SN-593. Sci. Rep. 9 (1): 5802, 2019. doi: 10.1038/s41598-019-42268-w. *Corresponding


Kim J.W., Son S., Kim G.S., Otaka J., Miura Y., Muranaka A., Uchiyama M., Lee J.-S., Jang M., Ko S.-K., Takahashi S., Osada H., Jang J.-H., Ahn J.S. Aromatic butenolides produced by a soil ascomycete Auxarthron sp. KCB15F070 derived from a volcanic island. Tetrahedron Lett. 60 (45): 7, 151227, 2019. doi: 10.1016/j.tetlet.2019.151227


Hashimoto T., Hashimoto J., Kozone I., Amagai K., Kawahara T., Takahashi S., Ikeda H., Shin-ya K. Biosynthesis of quinolidomicin, the largest known macrolide of terrestrial origin: Identification and heterologous expression of a biosynthetic gene cluster over 200 kb. Org. Lett. 20 (24): 7996-7999, 2018. doi: 10.1021/acs.orglett.8b03570


Yazaki, J., Kawashima, Y., Ogawa, T., Kobayashi, A., Okoshi, M., Watanabe, T., Yoshida, S., Kii, I., Egami, S., Amagai, M., Hosoya, T., Shiroguchi, K., Ohara, O. HaloTag-based conjugation of proteins to barcoding-oligonucleotides. (2019) Nucleic Acids Research, gkz1086. doi: 10.1093/nar/gkz1086


Motoyama, T., Nogawa, T., Hayashi, T., Hirota, H., Osada, H. Induction of nectriapyrone biosynthesis in the rice blast fungus Pyricularia oryzae by disturbance of the two-component signal transduction system. (2019) Chembiochem, 20, 693-700. doi: 10.1002/cbic.201800620


Nogawa, T., Kawatani, M., Okano, A., Futamura, Y., Aono, H., Shimizu, T., Kato, N., Kikuchi, H., Osada, H. Structure and biological activity of Metarhizin C, a stereoisomer of BR-050 from Tolypocladium album RK17-F0007. (2019) Journal of Antibiotics, 72, 996-1000. doi: 10.1038/s41429-019-0229-1


Simpkins, W. S., Deshpande, R., Nelson, J., Li, C. S., Piotrowski, S. J., Ward, N. H., Yashiroda, Y., Osada, H., Yoshida, M., Boone, C., Myers, L. C., Using BEAN-counter to quantify genetic interactions from multiplexed barcode sequencing experiments. (2019) Nature Protocols, 14, 415-440. doi: 10.1038/s41596-018-0099-1


Panthee, S., Takahashi, S., Hayashi, T., Shimizu, T., Osada, H. β-carboline biomediators induce reveromycin production in Streptomyces sp. SN-593. (2019) Scientific Reports, 9, 5802. doi: 10.1038/s41598-019-42268-w


Lopez, V. J.A., Nogawa, T., Futamura, Y., Shimizu, T., Osada, H. Nocardamin glucuronide, a new member of the ferrioxamine siderophores isolated from the ascamycin-producing strain Streptomyces sp. 80H647. (2019) Journal of Antibiotics, 72, 991-995. doi: 10.1038/s41429-019-0217-5


Yamamoto, K., Futamura, Y., Uson-Lopez, A. R., Aono, H., Shimizu, T., Osada, H. YO-001A, a new antifungal agent produced by Streptomyces sp. YO15-A001. (2019) Journal of Antibiotics, 72, 986-990. doi: 10.1038/s41429-019-0239-z 


Suzuki K, Vogelzang A, & Fagarasan S (2019) MZB1 folding and unfolding the role of IgA. Proc Natl Acad Sci U S A 116(27):13163-13165. doi: 10.1073/pnas.1908012116


Vogelzang A, Guerrini MM, Minato N, & Fagarasan S (2018) Microbiota - an amplifier of autoimmunity. Curr Opin Immunol 55:15-21. doi: 10.1016/j.coi.2018.09.003


Guerrini MM, Vogelzang A, & Fagarasan S (2018) A Hen in the Wolf Den: A Pathobiont Tale. Immunity 48(4):628-631. doi: 10.1016/j.immuni.2018.04.003


Wu, J., Ichihashi, Y., Suzuki, T., Shibata, A., Shirasu, K., Yamaguchi, N., Ito, T. (2019) Abscisic acid-dependent histone demethylation during postgermination growth arrest in Arabidopsis. (2019) Plant Cell Environ. 42(7): 2198-2214. doi: 10.1111/pce.13547


Lee, H. Z., Tatsumi, Y., Ichihashi, Y., Suzuki, T., Shibata, A., Shirasu, K., Yamaguchi, N., Ito, T. CRABS CLAW and SUPERMAN Coordinate Hormone-, Stress-, and Metabolic-Related Gene Expression During Arabidopsis Stamen Development. (2019) Front. Ecol. Evol. doi: 10.3389/fevo.2019.00437


Sato, T., Hachiya, S., Inamura, N., Ezawa, T., Cheng, W., Tawaraya, K. Secretion of acid phosphatase from extraradical hyphae of the arbuscular mycorrhizal fungus Rhizophagus clarus is regulated in response to phosphate availability. (2019) Mycorrhiza. doi: 10.1007/s00572-019-00923-0


Bramson, A., Baland, A., Iriki, A. Measuring Dynamical Uncertainty with Revealed Dynamics Markov Models. (2019) Front Appl Math Stats, 5, article 7, doi: 10.3389/fams.2019.00007


Lin, M.K., Takahashi, Y.S., Huo, B.X., Hanada, M., Nagashima, J., Hata, J., Tolpygo, A.S., Ram, K., Lee, B., Miller, M., Rosa, M.G.P., Sasaki, E., Iriki, A., Okano, H., Mitra, P.P. A High-throughput Neurohistological Pipeline for Brain-Wide Mesoscale Connectivity Mapping of the Common Marmoset. (2019) eLife, 8, e40042. doi: 10.7554/eLife.40042


Gumert, M.D., Tan, A., Luncz, L., Chua, C.T., Kulik, L., Switzer, A., Haslam, M., Iriki, A., Malaivijitnond S. Prevalence of tool behaviour is associated with pelage phenotype in intraspecific hybrid long-tailed macaques (Macaca fascicularis aurea x M. f. fascicularis). (2019) Behav, 156, 1083-1125. doi: 10.1163/1568539X-00003557


Kosugi, A., Castagnola, E., Carli, S., Ricci, D., Fadiga, L., Taoka, M., Iriki, A., Ushiba, J. Fast electrophysiological mapping of rat cortical motor representation on a time scale of minutes during skin stimulation. (2019) Neurosci., 414,245-254. doi: 10.1016/j.neuroscience.2019.07.011


Tramacere, A., Wada, K., Okanoya, K., Iriki, A., Ferrari, P.F. Auditory-motor matching in vocal recognition and imitative learning. (2019) Neurosci, 409, 222-234. doi: 10.1016/j.neuroscience.2019.01.056


Bretas, R.V., Taoka, M., Suzuki, H., Iriki, A. Secondary somatosensory cortex of primates: Beyond body maps, towards conscious “self-in-the-world” map. (2020) Exp Brain Res, in press.


Bretas, R.V., Yamazaki, Y., Iriki, A. Phase Transitions of Brain Evolution that Produced Human Language..., and Beyond. (2020) Neurosci Res, in press.


Yi X, Son S, Ando R, Miyawaki A, Weiss S (2019). Moments reconstruction and local dynamic range compression of high order super-resolution optical fluctuation imaging. Biomed. Opt. Express. 10, 2430-2445. doi: 10.1364/BOE.10.002430


Margarete Diaz-Cuadros, Daniel E. Wagner, Christoph Budjan, Alexis Hubaud, Oscar A. Tarazona, Sophia Donelly, Arthur Michaut, Ziad Al Tanoury, Kumiko Yoshioka-Kobayashi, Yusuke Niino, Ryoichiro Kageyama, Atsushi Miyawaki, Jonathan Touboul, and Olivier Pourquié. In vitro characterization of the human segmentation clock. Nature in press.


Kumiko Yoshioka-Kobayashi, Marina Matsumiya, Yusuke Niino, Akihiro Isomura, Hiroshi Kori, Atsushi Miyawaki, and Ryoichiro Kageyama. Dynamic control of coupling delay for synchronized oscillations in the segmentation clock. Nature in press.


Nakamoto N, Sasaki N, Aoki R, Miyamoto K, Suda W, Teratani T, Suzuki T, Koda Y, Chu PS, Taniki N, Yamaguchi A, Kanamori M, Kamada N, Hattori M, Ashida H, Sakamoto M, Atarashi K, Narushima S, Yoshimura A, Honda K, Sato T, Kanai T. Gut pathobionts underlie intestinal barrier dysfunction and liver T helper 17 cell immune response in primary sclerosing cholangitis. Nat Microbiol. 4(3): 492–503 (2019). doi: 10.1038/s41564-018-0333-1


Ohtsu A, Takeuchi Y, Katagiri S, Suda W, Maekawa S, Shiba T, Komazaki R, Udagawa S, Sasaki N, Hattori M, Izumi Y. Influence of Porphyromonas gingivalis in gut microbiota of streptozotocin-induced diabetic mice. Oral Dis. 25(3): 868–880 (2019). doi: 10.1111/odi.13044


Ikeda E, Shiba T, Ikeda Y, Suda W, Nakasato A, Takeuchi Y, Azuma M, Hattori M, Izumi Y. Deep sequencing reveals specific bacterial signatures in the subgingival microbiota of healthy subjects. Cli Oral Investig. 23(3): 1489–1493 (2019). doi: 10.1007/s00784-019-02805-3


Song J, Kang I, Joung Y, Yoshizawa S, Kaneko R, Oshima K, Hattori M, Hamasaki K, Kogure K, Kim S, Lee K, Cho JC. Genome analysis of Rubritalea profundi SAORIC-165T, the first deep-sea verrucomicrobial isolate, from the northwestern Pacific Ocean. J Microbiol. 57(5): 413–422 (2019). doi: 10.1007/s12275-019-8712-8


Nagata N, Tohya M, Fukuda S, Suda W, Nishijima S, Takeuchi F, Ohsugi M, Tsujimoto T, Nakamura T, Shimomura A, Yanagisawa N, Hisada Y, Watanabe K, Imbe K, Akiyama J, Mizokami M, Miyoshi-Akiyama T, Uemura N, Hattori M. Effects of bowel preparation on the human gut microbiome and metabolome. Sci Rep. 9(1): 4042 (2019). doi: 10.1038/s41598-019-40182-9


Nikoh N, Koga R, Oshima K, Hattori M, Fukatsu T. Genome Sequence of "Candidatus Serratia symbiotica" Strain IS, a Facultative Bacterial Symbiont of the Pea Aphid Acyrthosiphon pisum. Microbiol Resour Announc. 8(19) (2019). doi: 10.1128/MRA.00272-19


Okazaki S, Sano N, Yamada T, Ishii K, Kojima K, Djedidi S, Artigas Ramírez MD, Yuan K, Kanekatsu M, Ohkama-Ohtsu N, Hirose Y, Oshima K, Hattori M, Yokoyama T. Complete Genome Sequence of Plant Growth-Promoting Bacillus pumilus TUAT1. Microbiol Resour Announc. 8(21) (2019). doi: 10.1128/MRA.00076-19


Suzuki Y, Nishijima S, Furuta Y, Yoshimura J, Suda W, Oshima K, Hattori M, Morishita S. Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut. Microbiome 7(1): 119 (2019). doi: 10.1186/s40168-019-0737-z


Yamazaki Y, Sakai Y, Mino S, Suda W, Hattori M, Meirelles PM, Thompson F, Sawabe T. Repeated selective enrichment process of sediment microbiota occurred in sea cucumber guts. Environ Microbiol Rep. 11(6):797-807 (2019). doi: 10.1111/1758-2229.12791


Ikeda E, Shiba T, Ikeda Y, Suda W, Nakasato A, Takeuchi Y, Azuma M, Hattori M, Izumi Y. Japanese subgingival microbiota in health vs disease and their roles in predicted functions associated with periodontitis. Odontology 2019 Sep 9. doi: 10.1007/s10266-019-00452-4


Yamada T, Hino S, Iijima H, Genda T, Aoki R, Nagata R, Han KH, Hirota M, Kinashi Y, Oguchi H, Suda W, Furusawa Y, Fujimura Y, Kunisawa J, Hattori M, Fukushima M, Morita T, Hase K. Mucin O-glycans facilitate symbiosynthesis to maintain gut immune homeostasis. EBioMedicine 48:513-525 (2019). doi: 10.1016/j.ebiom.2019.09.008


Chiou TY, Suda W, Oshima K, Hattori M, Matsuzaki C, Yamamoto K, Takahashi T. Draft Genome Sequence of Sporolactobacillus inulinus NBRC 111894, Isolated from Kôso, a Japanese Sugar-Vegetable Fermented Beverage. Microbiol Resour Announc. 8(41). pii: e00751-19 (2019). doi: 10.1128/MRA.00751-19


Nagata N, Tohya M, Takeuchi F, Suda W, Nishijima S, Ohsugi M, Ueki K, Tsujimoto T, Nakamura T, Kawai T, Miyoshi-Akiyama T, Uemura N, Hattori M. Effects of storage temperature, storage time, and Cary-Blair transport medium on the stability of the gut microbiota. Drug Discov Ther. 13(5):256-260 (2019). doi: 10.5582/ddt.2019.01071


Sakamoto M, Ikeyama N, Ogata Y, Suda W, Iino T, Hattori M, Ohkuma M. Alistipes communis sp. nov., Alistipes dispar sp. nov. and Alistipes onderdonkii subsp. vulgaris subsp. nov., isolated from human faeces, and creation of Alistipes onderdonkii subsp. onderdonkii subsp. nov. Int J Syst Evol Microbiol. 2019 Oct 21. doi: 10.1099/ijsem.0.003778


Nadatani Y, Watanabe T, Suda W, Nakata A, Matsumoto Y, Kosaka S, Higashimori A, Otani K, Hosomi S, Tanaka F, Nagami Y, Kamata N, Taira K, Yamagami H, Tanigawa T, Hattori M, Fujiwara Y. Gastric acid inhibitor aggravates indomethacin-induced small intestinal injury via reducing Lactobacillus johnsonii. Sci Rep. 9(1):17490 (2019). doi: 10.1038/s41598-019-53559-7


Kawashima Y, Watanabe E, Umeyama T, Nakajima D, Hattori M, Honda K, Ohara O. Optimization of Data-Independent Acquisition Mass Spectrometry for Deep and Highly Sensitive Proteomic Analysis. Int J Mol Sci. 20(23). pii: E5932 (2019). doi: 10.3390/ijms20235932


Hirata M, Asano N, Katayama K, Yoshida A, Tsuda Y, Sekimizu M, Mitani S, Kobayashi E, Komiyama M, Fujimoto H, Goto T, Iwamoto Y, Naka N, Iwata S, Nishida Y, Hiruma T, Hiraga H, Kawano H, Motoi T, Oda Y, Matsubara D, Fujita M, Shibata T, Nakagawa H, Nakamaya R, Kondo T, Imoto S, Miyano S, Kawai A, Yamaguchi R, Ichikawa H, and Matsuda K. Integrated exome and RNA sequencing of differentiated liposarcoma. Nat Commun in press


Mizuno K, Akamatsu S, Sumiyoshi T, Wong J, Fujita M, Maejima K, Nakano K, Ono A, Aikata H, Ueno M, Hayami S, Yamaue H, Chayama K, Inoue T, Ogawa O, Nakagawa H, and Fujimoto A. eVIDENCE: a practical variant filtering for low-frequency variants detection in cell-free DNA. Sci Rep (2019). doi: 10.1038/s41598-019-51459-4 (in press)


Takata R, Takahashi A, Fujita M, Momozawa Y, Saunders EJ, Yamada H, Maejima K, Nakano K, Yamaji T, Sawada N, Iwasaki M, Tsugane S, Sasaki M, Shimizu A, Tanno K, Minegishi N, Suzuki K, Matsuda K, Kubo K, Inazawa J, Egawa S, Haiman CA, Ogawa O, Obara W, Kamatani Y, Akamatsu S, and Nakagawa H. 12 new susceptibility loci for prostate cancer identified by genome-wide association study in Japanese population. Nat Commun 10(1):4422 (2019). doi: 10.1038/s41467-019-12267-6


Yang F, Kim DK, Nakagawa H, Hayashi S, Imoto S, Stein L, and Roth F, Quantifying immune-based counterselection of somatic mutations. PLoS Genet 15 (7): e1008227 (2019) doi: 10.1371/journal.pgen.1008227


Wong JH, Shigemizu D, Yoshii Y, Akiyama S, Tanaka A, Nakagawa H, Narumiya S, and Fujimoto A. Identification of intermediate-sized deletions and inference of their impact on gene expression in a human population. Genome Med 11(1): 44 (2019). doi: 10.1186/s13073-019-0656-4


Momozawa Y, Iwasaki Y, Hirata M, Liu X, Kamatani Y, Takahashi A, Sugano K, Yoshida T, Murakami Y, Matsuda K, Nakagawa H, Spurdle AB, and Kubo M. Germline pathogenic variants of BRCA1/2, HOXB13, and ATM in 7,636 Japanese prostate cancer patients and 12,366 controls. J Natl Cancer Inst (2019) doi: 10.1093/jnci/djz124


Tsuda Y, Hirata M, Katayama K, Motoi T, Matsubara D, Oda Y, Fujita M, Kobayashi H, Kawano H, Nishida Y, Sakai T, Okuma T, Goto T, Ogura K, Kawai A, Ae K, Anazawa U, Suehara Y, Iwata S, Miyano S, Imoto S, Shibata T, Nakagawa H, Yamaguchi R, Tanaka S, and Matsuda K. Massively parallel sequencing of tenosynovial giant cell tumors reveals novel CSF1 fusion transcripts and novel somatic CBL mutations. Int J Cancer (2019). doi: 10.1002/ijc.32421


Mateos RN, Nakagawa H, Hirono S, Takano S, Fukasawa M, Yanagi-sawa A, Yasukawa S, Maejima K, Oku-Sasaki A, Nakano K, Dutta M, Tanaka H, Miyano S, Enomoto N, Yamaue H, Nakai K, and Fujita M. Genomic analysis of pancreatic juice DNA assesses malignant risk of intraductal papillary mucinous neoplasm of pancreas. Cancer Med 8:4565-4573 (2019). doi: 10.1002/cam4.2340


Xue R, Chen L, Zhang C, Fujita M, Li R, Yan SM, Ong CK, Liao X, Gao Q, Sasagawa S, Li Y, Wang J, Guo H, Huang QT, Zhong Q, Tan J, Qi L, Gong W, Hong Z, Li M, Zhao J, Peng T, Lu Y, Lim KHT, Boot A, Ono A, Chayama K, Zhang Z, Rozen SG, Teh BT, Wang XW, Nakagawa H,* Zeng MS,* Bai F* and Zhang N*. Genomic and transriptomic profiling of combined hepatocellular and intrahepatic cholangio-carcinoma reveals distinct molecular subtypes. Cancer Cell 35: 932-947 (2019). doi: 10.1016/j.ccell.2019.04.007 *equally corresponding


Yamamoto Y, Uemura M, Fujita M, Maejima K, Koh Y, Matsushita M, Nakano K, Hayashi Y, Wang C, Ishizuya Y, Kinouchi T, Hayashi T, Matsuzaki K, Jingushi K, Kato T, Kawashima A, Ujike T, Nagahara A, Fujita K, Imamura R, Nakagawa H, and Nonomura N. Clinical significance of the mutational landscape and fragmentation of circulating-tumor DNA in renal cell carcinoma. Cancer Sci 110:617-628 (2019). doi: 10.1111/cas.13906


Hayashi S, Morimoto T, Yamaguchi R, Mizuno S, Uemura M, Miyano S, Nakagawa H, and Imoto S. ALPHLARD-NT: Bayesian method for HLA genotyping and mutation calling through simultaneous analysis of normal and tumor whole-genome sequence data. J Comput Biol 26(9):923-937 (2019). doi: 10.1089/cmb.2018.0224


Furumai R, Tamada K, Liu X, Takumi T. UBE3A regulates the transcription of IRF, an antiviral immunity. (2019) Hum Mol Genet, 28, 1947-1958. doi: 10.1093/hmg/ddz019


Choi Y, Kim H, Choi M, Yang EJ, Takumi T, Kim HS. Fetal neural stem cells from a mouse model of 15q11-13 duplication syndrome exhibit altered differentiation into neurons and astrocytes. (2019) J Pharmacol Sci, 139, 249-253. doi: 10.1016/j.jphs.2018.12.007


Mori K, Tamada K, Kurooka H, Matsui M, Takumi T, Yokota Y. Gene expression profile data of the developing small intestine of Id2-deficient mice. (2019) Data Brief, 24:103717. doi: 10.1016/j.dib.2019.103717


Takumi T, Tamada K, Hatanaka F, Nakai N, Bolton PF. Behavioral neuroscience of autism. (2019) Neurosci Biobehav Rev, pii: S0149-7634(18)30372-5. doi: 10.1016/j.neubiorev.2019.04.012


Imada Y, Kurisu K, Takumi T, Aoyama H, Sadatomo T, Migita K, Yuki K. Morphological Pattern and Classification of the Superficial Middle Cerebral Vein by Cadaver Dissections: An Embryological Viewpoint. (2019) Neurol Med Chir, 59, 264-270. doi: 10.2176/nmc.oa.2018-0284


Nakanishi M, Anderson MP, Takumi T. Recent genetic and functional insights in autism spectrum disorder. (2019) Curr Opin Neurol, 32, 627-634. doi: 10.1097/WCO.0000000000000718


Wang J, Lou SS, Wang T, Wu RJ, Li G, Zhao M, Lu B, Li YY, Zhang J, Cheng X, Shen Y, Wang X, Zhu ZC, Li MJ, Takumi T, Yang H, Yu X, Liao L, Xiong ZQ. UBE3A-mediated PTPA ubiquitination and degradation regulate PP2A activity and dendritic spine morphology. (2019) Proc Natl Acad Sci U S A, 116, 12500-12505. doi: 10.1073/pnas.1820131116


Nishino T, Tamada K, Maeda A, Abe T, Kiyonari H, Funahashi Y, Kaibuchi K, Takumi T, Konishi H. Behavioral analysis in mice deficient for GAREM2 (Grb2-associated regulator of Erk/MAPK subtype2) that is a subtype of highly expressing in the brain. (2019) Mol Brain, 12, 94. doi: 10.1186/s13041-019-0512-x


Tsurugizawa T, Tamada K, Ono N, Karakawa S, Kodama Y, Debacker C, Hata J, Okano H, Kitamura A, Zalesky A, Takumi T. Awake functional MRI detects neural circuit dysfunction in a mouse model of autism. (2019) Science Adv, in press


Ooka, H., McGlynn, S., Nakamura, R. Electrochemistry at deep-sea hydrothermal vents: utilization of the thermodynamic driving force towards the autotrophic origin of life. (2019) ChemElectroChem, 6, 1316-1323. doi: 10.1002/celc.201801432


Shimoda, Y., Imaizumi-Anraku, H., Hayashi, M. Kinase activity-dependent stability of calcium/calmodulin-dependent protein kinase of Lotus japonicus. (2019) Planta. 250: 1773-1779. doi: 10.1007/s00425-019-03264-6


Liu, M., Soyano, T., Yano, K., Hayashi, M., Kawaguchi, M. ERN1 and CYCLOPS coordinately activate NIN signaling to promote infection thread formation in Lotus japonicus. (2019) J. Plant Res. 132: 641-653. doi:10.1007/s10265-019-01122-w


Sogawa, A., Yamazaki, A., Yamasaki, H., Komi, M., Manabe, T., Tajima, S., Hayashi, M., Nomura, M. SNARE Proteins LjVAMP72a and LjVAMP72b Are Required for Root Symbiosis and Root Hair Formation in Lotus japonicus. (2019) Front. Plant Sci. 9: 1992. doi:10.3389/fpls.2018.01992


Chow, S., Inaba, N., Nagai, S., Kurogi, H., Nakamura, Y., Yanagimoto, T., Tanaka, H., Hasegawa, D., Asakura, T., Kikuchi, J., Tomoda, T. and Kodama, T. “Molecular diet analysis of Anguilliformes leptocephalus larvae collected in the western North Pacific” PLoS One. doi: 10.1371/journal.pone.0225610 (in press)


Mega, R., Abe, F., Kim, J.-S., Tsuboi, Y., Tanaka, K., Kobayashi, H., Sakata, Y., Hanada, K., Tsujimoto, H., Kikuchi, J., Cutler, S. R. and Okamoto, M. “Tuning water use efficiency and drought tolerance in wheat using abscisic acid receptors” Nature Plants 5, 153-159 (2019). doi: s41477-019-0361-8


Yamada, S., Ito, K., Kurotani, A., Yamada, Y., Chikayama, E. and Kikuchi, J. “InterSpin: Integrated supportive webtools for low and high-field NMR analysis toward molecular complexity” ACS Omega. 4, 3361-3369 (2019). doi: 10.1021/acsomega.8b02714


Kato, T., Yamazaki, K., Nakajima, M., Date, Y., Kikuchi, J., Hase, K., Ohno, H and Yamazaki, K. "Oral administration of Porphyromonas gingivalis alters the gut microbiome and serum metabolome" mSphere 3, e00460-18 (2019). doi: 10.1128/mSphere.00460-18


Kikuchi, J. “Practical aspects of the analysis of low- and high-field NMR data from environmental complexity” Methods in Molecular Biology (Raftery, Gowda Ed.) 2037, 315-331 (2019). doi: 10.1007/978-1-4939-9690-2_17


Mekuchi, M., Asakura, T. and Kikuchi, J. “New aquaculture technology based on host-symbiotic co-metabolism” Marine Metagenomics (Gojobori, Wada, Kobayashi, Mineta Ed.) 189-218 (2019). doi: 10.1007/978-981-13-8134-8_13


和田時夫、渡部終五、伊藤文成、菊地淳、良永知義、伊藤暁、黒萩真悟 “持続可能な水産養殖業を目指して -研究開発・事業・政策の現状と展開方向-” 生物の科学 遺伝 73, 314-323 (2019).


Kadota, M., Nishimura, O., Miura, H., Tanaka, K., Hiratani, I., Kuraku, S. Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding? (2019) GigaScience, accepted in principle. doi: 10.1101/659623v1


Kishida, T., Go, Y., Tatsumoto, S., Tatsumi, K., Kuraku, S., Toda, M. Loss of olfaction in sea snakes provides new perspectives on the aquatic adaptation of amniotes. (2019) Proceedings of the Royal Society B, 286(1910), 20191828. doi: 10.1098/rspb.2019.1828


Opazo, JC., Kuraku, S., Zavala, K., Toloza-Villalobos, J., Hoffmann, FG. Evolution of nodal and nodal‐related genes and the putative composition of the heterodimers that trigger the nodal pathway in vertebrates. (2019) Evolution & Development, 21(4), 205-217. doi: 10.1111/ede.12292


Imaseki, I., Wakabayashi, M., Hara, Y., Watanabe, T., Takabe, S., Kakumura, K., Honda, Y., Ueda, K., Murakumo, K., Matsumoto, R., Matsumoto, Y., Nakamura., Takagi, W., Kuraku, S., Hyodo, S. Comprehensive analysis of genes contributing to euryhalinity in the bull shark, Carcharhinus leucas; Na+-Cl- co-transporter is one of the key renal factors up-regulated in acclimation to low-salinity environment in bull sharks, but not in houndsharks, Triakis scyllium. (2019) Journal of Experimental Biology, jeb.201780. doi: 10.1242/jeb.201780


Feiner, N., Motone, F., Meyer, A., Kuraku, S. Asymmetric paralog evolution between the “cryptic” gene Bmp16 and its well-studied sister genes Bmp2 and Bmp4. (2019) Scientific Reports, 9, 3136. doi: 10.1038/s41598-019-40055-1


Hor YY, Lew LC, Jaafar MH, Lau AS, Ong JS, Kato T, Nakanishi Y, Azzam G, Azlan A, Ohno H, Liong MT. Lactobacillus sp. improved microbiota and metabolite profiles of aging rats. Pharmacol Res 146: 104312, 2019. doi: 10.1016/j.phrs.2019.104312


Lew LC, Hor YY, Jaafar MH, Lau AS, Khoo BY, Sasidharan S, Choi SB, Ong KL, Kato T, Nakanishi Y, Ohno H, Liong MT. Effects of Potential Probiotic Strains on the Fecal Microbiota and Metabolites of D-Galactose-Induced Aging Rats Fed with High-Fat Diet. Probiotics Antimicrob Proteins 2019. doi: 10.1007/s12602-019-09545-6


Matsuda C, Kato T, Inoue-Suzuki S, Kikuchi J, Ohta T, Kagawa M, Hattori M, Kobayashi H, Shiba D, Shirakawa M, Mizuno H, Furukawa S, Mukai C, Ohno H. Dietary intervention of mice using an improved Multiple Artificial-gravity Research System (MARS) under artificial 1 g. NPJ Microgravity 5, 16, 2019. doi: s41526-019-0077-0


Ong JS, Taylor TD, Wong CB, Khoo BY, Sasidharan S, Choi SB, Ohno H, Liong MT. Extracellular transglycosylase and glyceraldehyde-3-phosphate dehydrogenase attributed to the anti-staphylococcal activity of Lactobacillus plantarum USM8613. J Biotechnol 300: 20-31, 2019. doi: 10.1016/j.jbiotec.2019.05.006


Dissanayake E, Tani Y, Nagai K, Sahara M, Mitsuishi C, Togawa Y, Suzuki Y, Nakano T, Yamaide F, Ohno H, Shimojo N. Skin Care and Synbiotics for Prevention of Atopic Dermatitis or Food Allergy in Newborn Infants: A 2 × 2 Factorial, Randomized, Non-Treatment Controlled Trial. Int Arch Allergy Immunol. 180(3):202-211, 2019. doi: 10.1159/000501636


Fikri B, Tani Y, Nagai K, Sahara M, Mitsuishi C, Togawa Y, Nakano T, Yamaide F, Ohno H, Shimojo N. Soluble CD14 in Breast Milk and Its Relation to Atopic Manifestations in Early Infancy. Nutrients. 11(9): pii: E2118, 2019 doi: 10.3390/nu11092118


Hara S, Sasaki T, Satoh-Takayama N, Kanaya T, Kato T, Takikawa Y, Takahashi M, Tachibana N, Kim KS, Surh CD, Ohno H. Dietary Antigens Induce Germinal Center Responses in Peyer's Patches and Antigen-Specific IgA Production. Front Immunol. 10:2432, 2019 doi: 10.3389/fimmu.2019.02432


Sato Y, Sakurai K, Tanabe H, Kato T, Nakanishi Y, Ohno H, Mori C. Maternal gut microbiota is associated with newborn anthropometrics in a sex-specific manner. J Dev Orig Health Dis. 10(6):659-666, 2019. doi: 10.1017/S2040174419000138


Stanifer ML, Mukenhirn M, Muenchau S, Pervolaraki K, Kanaya T, Albrecht D, Odendall C, Hielscher T, Haucke V, Kagan JC, Bartfeld S, Ohno H, Boulant S. Asymmetric distribution of TLR3 leads to a polarized immune response in human intestinal epithelial cells. Nat Microbiol. 2019. doi: 10.1038/s41564-019-0594-3


Tanabe H, Sakurai K, Kato T, Kawasaki Y, Nakano T, Yamaide F, Taguchi-Atarashi N, Watanabe M, Ochiai S, Ohno H, Fukuoka H, Shimojo N, Mori C. Association of the maternal microbiome in Japanese pregnant women with the cumulative prevalence of dermatitis in early infancy: A pilot study from the Chiba study of Mother and Child Health birth cohort. World Allergy Organ J. 12(10):100065, 2019. doi: 10.1016/j.waojou.2019.100065


Sakurai K, Kato T, Tanabe H, Taguchi-Atarashi N, Sato Y, Eguchi A, Watanabe M, Ohno H, Mori C. Association between gut microbiota composition and glycoalbumin level during pregnancy in Japanese women: Pilot study from Chiba Study of Mother and Child Health. J Diabetes Investig. 2019. doi: 10.1111/jdi.13177


Kadota, Y., Liebrand, T. W., Goto, Y., Sklenar, J., Derbyshire, P., Menke, F. L., Torres, M., Molina, A., Zipfel, C., Coaker, G. and Shirasu, K. Quantitative phosphoproteomic analysis reveals common regulatory mechanisms between effector‐ and PAMP‐triggered immunity in plants. (2019) New Phytol. 221:2160-2175. doi: 10.1111/nph.15523


Mutuku, J. M., and Shirasu, K. Striga (2019) Curr. Biol. 20: R1064-R1065. doi: 10.1016/j.cub.2019.06.075


Tsushima, A., Gan, P., Kumakura, N., Narusaka, M., Takano, Y., Narusaka, Y., Shirasu, K. Genomic plasticity mediated by transposable elements in the plant pathogenic fungus Colletotrichum higginsianum (2019) Genome Biology and Evolution, evz087 doi: 10.1093/gbe/evz087


Gan, P., Tsushima, A., Hiroyama, R., Narusaka, M., Takano, Y., Narusaka, Y., Kawaradani, M., Damm, U., and Shirasu, K. Colletotrichum shisoi sp. nov., an anthracnose pathogen of Perilla frutescens in Japan: molecular phylogenetic, morphological and genomic evidence. (2019) Sci. Rep. 9:13349. doi: 10.1038/s41598-019-50076-5


Mutuku, J. M., Cui, S., Hori, C., Takeda, Y., Tobimatsu, Y., Nakabayashi, R., Mori, T., Saito, K., Demura, T., Umezawa, T., Yoshida, Y., Shirasu, K. The structural integrity of lignin is crucial for resistance against Striga hermonthica parasitism in rice. (2019) Plant Physiol. doi: 10.1104/pp.18.01133


Gan, P., Tsushima, A., Narusaka, M., Narusaka, Y., Takano, Y., Kubo, Y., Shirasu, K. Genome sequence resources for four phytopathogenic fungi from the Colletotrichum orbiculare species complex (2019) MPMI doi: 10.1094/MPMI-12-18-0352-A


Goto, Y., Maki, N., Ichihashi, Y., Kitazawa, D., Igarashi, D., Kadota, Y., Shirasu, K. Exogenous treatment with glutamate induces immune responses in Arabidopsis. (2019) MPMI. doi: 10.1094/MPMI-09-19-0262-R


Bart, R. and Shirasu, K. Biotic Interactions - hosts, microbes and a changing environment. (2019) Curr Opinion Plant Biol. 50:iv-vi. doi: 10.1016/j.pbi.2019.08.001


Sato, K., Kadota, Y., Shirasu, K. Plant immune responses to parasitic nematodes. (2019) Front Plant Sci 10:1165. doi: 10.3389/fpls.2019.01165


Tsushima, A., Gan, P., Shirasu, K. Method for Assessing virulence of Colletotrichum higginsianum on Arabidopsis thaliana leaves using automated lesion area detection and measurement. (2019) Bio-protocol. 9: e3434.10.21769/BioProtoc.3434


Vong, K., Eda, S., Kadota, Y., Nasibullin, I., Wakatake, T., Ykoshima, S., Shirasu, K., Tanaka, K. An artificial metalloenzyme biosensor can detect ethylene gas in fruits and Arabidopsis leaves. (2019) Nature Comm. in press.


Goyet, V., Wada, S., Cui, S., Wakatake, T., Shirasu, K., Montiel, G., Simier, P., Yoshida, S. Haustorium Inducing Factors for Parasitic Orobanchaceae. (2019) Front Plant Sci. 10:1056. doi:10.3389/fpls.2019.01056


Asai, S., Ayukawa, Y., Gan, P., Masuda, S., Komatsu, K., Shirasu, K., Arie, T. A high-quality draft genome sequence of Fusarium oxysporum f. sp. cubense strain 160527, a causal agent of Panama disease. (2019) Microbiol Resource Announcement. 8: e00654-19. doi: 10.1128/MRA.00654-19


Takagi, M., Hamano, K., Takagi, H., Morimoto, T., Akimitsu, K., Terauchi, R., Shirasu, K., Ichimura, K. Disruption of the MAMP-induced MEKK1-MKK1/MKK2-MPK4 pathway activates the TNL immune receptor SMN1/RPS6. (2019) Plant Cell and Physiology. doi:10.1093/pcp/pcy243 

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