Author / Use of biological information analysis system / with acknowledgements
Tomoyuki Shikata, Fumio Takahashi, Hiroyo Nishide, Shuji Shigenobu, Yasuhiro Kamei, Setsuko Sakamoto, Kouki Yuasa, Yoshitaka Nishiyama, Yasuhiro Yamasaki and Ikuo Uchiyama
RNA-Seq Analysis Reveals Genes Related to Photoreception, Nutrient Uptake, and Toxicity in a Noxious Red-Tide Raphidophyte Chattonella antiqua
Front. Microbiol. 31 (2019)
doi.org/10.3389/fmicb.2019.01764
Use of biological information analysis system / with acknowledgements
Masafumi Harada, Kohei Ito, Nobuyoshi Nakajima, Shigeki Yamamura, Masaru Tomita, Haruo Suzuki and Seigo Amachi
Genomic Analysis of Pseudomonas sp. Strain SCT, an Iodate-Reducing Bacterium Isolated from Marine Sediment, Reveals a Possible Use for Bioremediation
G3 Genes Genomes Genetics Volume 9 May 2019
1321 ORCID ID: 0000-0003-1447-6109 (H.S.)
Hiromu Kameoka, Ippo Tsutsui, Katsuharu Saito, Yusuke Kikuchi, Yoshihiro Handa, Tatsuhiro Ezawa, Hideo Hayashi, Masayoshi Kawaguchi and Kohki Akiyama
Stimulation of asymbiotic sporulation in arbuscular mycorrhizal fungi by fatty acids
Nature Microbiology Vol. 4 1654–1660 (2019)
doi.org/10.1038/s41564-019-0485-7
Hiromu Kameoka, Taro Maeda, Nao Okuma and Masayoshi Kawaguchi
Structure-Specific Regulation of Nutrient Transport and Metabolism in Arbuscular Mycorrhizal Fungi
Plant Cell Physiol. 60(10): 2272–2281 (2019)
doi:10.1093/pcp/pcz122
Ryo Nagao, Koji Kato, Takehiro Suzuki, Kentaro Ifuku, Ikuo Uchiyama, Yasuhiro Kashino, Naoshi Dohmae, Seiji Akimoto, Jian-Ren Shen, Naoyuki Miyazaki and Fusamichi Akita
Structural basis for energy harvesting and dissipation in a diatom PSII–FCPII supercomplex
Nature Plants Vol. 5 890–901 (2019)
doi.org/10.1038/s41477-019-0477-x
Masaki Ishikawa, Mio Morishita, Yohei Higuchi1, Shunsuke Ichikawa, Takaaki Ishikawa, Tomoaki Nishiyama, Yukiko Kabeya, Yuji Hiwatashi, Tetsuya Kurata, Minoru Kubo, Shuji Shigenobu, Yosuke Tamada, Yoshikatsu Sato and Mitsuyasu Hasebe
Physcomitrella STEMIN transcription factor induces stem cell formation with epigenetic reprogramming
Nature Plants Vol. 5 681-690 (2019)
doi.org/10.1038/s41477-019-0464-2
Yuu Ishii, Shinichiro Maruyama, Hiroki Takahashi, Yusuke Aihara, Takeshi Yamaguchi, Katsushi Yamaguchi, Shuji Shigenobu, Masakado Kawata, Naoto Ueno and Jun Minagawa
Global Shifts in Gene Expression Profiles Accompanied with Environmental Changes in Cnidarian-Dinoflagellate Endosymbiosis
G3 Genes Genomes Genetics Volume 9 July 2019
orcid.org/0000-0002-3028-3203
Shinichi Morita, Toshiya Ando, Akiteru Maeno, Takeshi Mizutani, Mutsuki Mase, Shuji Shigenobu and Teruyuki Niimi
Precise staging of beetle horn formation in Trypoxylus dichotomus reveals the pleiotropic roles of doublesex depending on the spatiotemporal developmental contexts
PLOS Genetics PLoS Genet 15(4): e1008063
doi.org/10.1371/journal.pgen.1008063
Yasukazu Okada, Masako Katsuki, Naoki Okamoto, Haruna Fujioka and Kensuke Okada
A specific type of insulin-like peptide regulates the conditional growth of a beetle weapon
PLOS Biology November 27, (2019)
doi.org/10.1371/journal.pbio.3000541
Tetsuya Komatsu, Kenji Ohya, Kotaro Sawai, Justice Opare Odoi, Keiko Otsu, Atsushi Ota, Toshihiro Ito, Mikihiko Kawai and Fumito Maruyama
Draft genome sequences of Mycolicibacterium peregrinum isolated from a pig with lymphadenitis and from soil on the same Japanese pig farm
BMC Research Notes volume 12, Article number: 341 (2019)
doi.org/10.1186/s13104-019-4380-3
without acknowledgements
Ayana Okada, Satoshi Kikuchi, Yoichiro Hoshino, Hisato Kunitake and Makiko Mimura
Phylogeny and trait variation of Japanese Rubus subgenus Ideaobatus
Scientia Horticulturae Vol. 264 109150 (2020)
doi.org/10.1016/j.scienta.2019.109150
Yusuke Sakai, Masayuki Hatta, Seishiro Furukawa, Masakado Kawata, Naoto Ueno and Shinichiro Maruyama
Environmental factors explain spawning day deviation from full moon in the scleractinian coral Acropora
Biology Letters 16: (2019)
doi.org/10.1098/rsbl.2019.0760
Author / Use of Biological Information Analysis System / with acknowledgements
Ikuo Uchiyama, Motohiro Mihara, Hiroyo Nishide, Hirokazu Chiba and Masaki Kato
MBGD update 2018: microbial genome database based on hierarchical orthology relations covering closely related and distantly related comparisons
Nucleic Acids Research (2019) 47 D1 D382–D389
doi: 10.1093/nar/gky1054
Use of biological information analysis system / with acknowledgements
Toshihiro Ito, Kotaro Sawai, Mikihiko Kawai, Keiko Nozaki, Keiko Otsu, Hideto Fukushi, Kenji Ohya and Fumito Maruyama
Draft Genome Sequences of Mycolicibacter senuensis Isolate GF74 and Mycobacterium colombiense Isolates GF28 and GF76 from a Swine Farm in Japan
Microbiology Resource Announcements (2018) 7 (10) e00936-18
doi: 10.1128/MRA.00936-18
Kohei Ito, Masafumi Harada, Nobuyoshi Nakajima, Shigeki Yamamura, Masaru Tomita, Haruo Suzuki and Seigo Amachi
Genomic Analysis of Rhodococcus sp. Br-6, a Bromate Reducing Bacterium Isolated From Soil in Chiba, Japan
Journal of Genomics (2018) 6: 122-126
doi: 10.7150/jgen.27741
Kazuki Sato, Yasuhiro Kadota, Pamela Gan, Takahiro Bino, Taketo Uehara, Katsushi Yamaguchi, Yasunori Ichihashi, Noriko Maki, Hideaki Iwahori, Takamasa Suzuki, Shuji Shigenobu and Ken Shirasu
High-Quality Genome Sequence of the Root-Knot Nematode Meloidogyne arenaria Genotype A2-O
Genome Announcements (2018) 6 (26) e00519-18
doi: 10.1128/genomeA.00519-18.
Yusuke Aihara, Shinichiro Maruyama, Andrew H. Baird, Akira Iguchi, Shunichi Takahashia and Jun Minagawa
Green fluorescence from cnidarian hosts attracts symbiotic algae
PNAS (2019) 116 (6) :2118-2123
doi: 10.1073/pnas.1812257116
Taro Maeda, Yuuki Kobayashi, Hiromu Kameoka, Nao Okuma, Naoya Takeda, Katsushi Yamaguchi, Takahiro Bino, Shuji Shigenobu and Masayoshi Kawaguchi
Evidence of non-tandemly repeated rDNAs and their intragenomic heterogeneity in Rhizophagus irregularis
Communications Biology (2018) 1: 87
doi: 10.1038/s42003-018-0094-7
Yuuki Kobayashi, Taro Maeda, Katsushi Yamaguchi, Hiromu Kameoka, Sachiko Tanaka, Tatsuhiro Ezawa, Shuji Shigenobu and Masayoshi Kawaguchi
The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi
BMC Genomics (2018) 19: 465
doi: 10.1186/s12864-018-4853-0
Hirokazu Yano, Masaki Shintani, Masaru Tomita, Haruo Suzuki and Taku Oshima
Reconsidering plasmid maintenance factors for computational plasmid design
Computational and Structural Biotechnology Journal (2019) 17, 70-81
doi: 10.1016/j.csbj.2018.12.001
Nancy Merino, Shu Zhang, Masaru Tomita and Haruo Suzuki
Comparative genomics of Bacteria commonly identified in the built environment
BMC Genomics (2019) 20: 92
doi: 10.1186/s12864-018-5389-z
Yasuhiro Sugime, Kohei Oguchi, Hiroki Gotoh, Yoshinobu Hayashi, Masatoshi Matsunami, Shuji Shigenobu, Shigeyuki Koshikawa and Toru Miura
Yoshikatsu Sato, Yosuke Tamada, Mitsuyasu Hasebe
Termite soldier mandibles are elongated by dachshund under hormonal and Hox gene controls
Development (2019) 146: dev171942
doi: 10.1242/dev.171942
Hiromu Kameoka, Taro Maeda, Nao Okuma and Masayoshi Kawaguchi
Structure-specific regulation of nutrient absorption, metabolism and transfer in arbuscular mycorrhizal fungi
BioRxiv (2019)
doi: 10.1101/491811
Satoshi Ishishita, Mayuko Takahashi, Katsushi Yamaguchi, Keiji Kinoshita, Mikiharu Nakano, Mitsuo Nunome, Shumpei Kitahara, Shoji Tatsumoto, Yasuhiro Go, Shuji Shigenobu and Yoichi Matsuda
Nonsense mutation in PMEL is associated with yellowish plumage colour phenotype in Japanese quail
Scientific Reports (2018) 8, 16732
doi: 10.1038/s41598-018-34827-4
Nobuhiko Muramoto, Arisa Oda, Hidenori Tanaka, Takahiro Nakamura, Kazuto Kugou, Kazuki Suda, Aki Kobayashi, Shiori Yoneda, Akinori Ikeuchi, Hiroki Sugimoto, Satoshi Kondo, Chikara Ohto, Takehiko Shibata, Norihiro Mitsukawa and Kunihiro Ohta
Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double-strand breaks
Nature Communications (2018) 9, 1995
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Wan-Yi Chiou, Tadafumi Kawamoto, Eiko Himi, Kazuhide Rikiishi, Manabu Sugimoto, Mika Hayashi-Tsugane, Kazuo Tsugane and Masahiko Maekawa
LARGE GRAIN Encodes a Putative RNA-Binding Protein that Regulates Spikelet Hull Length in Rice
Plant and Cell Physiology (2019) 60 (3) 503–515
doi: 10.1093/pcp/pcz014
Toshiya Ando, Takeshi Matsuda, Kumiko Goto, Kimiko Hara, Akinori Ito, Junya Hirata, Joichiro Yatomi, Rei Kajitani, Miki Okuno, Katsushi Yamaguchi, Masaaki Kobayashi, Tomoyuki Takano, Yohei Minakuchi, Masahide Seki, Yutaka Suzuki, Kentaro Yano, Takehiko Itoh, Shuji Shigenobu, Atsushi Toyoda and Teruyuki Niimi
Repeated inversions within a pannier intron drive diversification of intraspecific colour patterns of ladybird beetles
Nature Communications (2018) 9, 3843
doi: 10.1038/s41467-018-06116-1
without acknowledgements
Chihiro Miura, Katsushi Yamaguchi, Ryohei Miyahara, Tatsuki Yamamoto, Masako Fuji, Takahiro Yagame, Haruko Imaizumi-Anraku, Masahide Yamato, Shuji Shigenobu, and Hironori Kaminaka
The Mycoheterotrophic Symbiosis Between Orchids and Mycorrhizal Fungi Possesses Major Components Shared with Mutualistic Plant-Mycorrhizal Symbioses
Molecular Plant-Microbe Interactions (2018) 31 (10) 1033
doi: 1 0.1094/MPMI-01-18-0029-R
Yudai Masuoka, Hajime Yaguchi, Kouhei Toga, Shuji Shigenobu and Kiyoto Maekawa
TGFβ signaling related genes are involved in hormonal mediation during termite soldier differentiation
PLoS Genetics (2018) 14 (4): e1007338
doi: 10.1371/journal.pgen.1007338
Hajime Yaguchi, Shuji Shigenobu, Yoshinobu Hayashi, Satoshi Miyazak, Kouhei Toga, Yudai Masuoka and Kiyoto Maekawa
A lipocalin protein, Neural Lazarillo, is key to social interactions that promote termite soldier differentiation
Proceedings of the Royal Society B (2018) 285 20180707
doi: 10.1098/rspb.2018.0707
Naruo Nikoh, Tsutomu Tsuchida, Taro Maeda, Katsushi Yamaguchi, Shuji Shigenobu, Ryuichi Koga and Takema Fukatsu
Genomic Insight into Symbiosis-Induced Insect Color Change by a Facultative Bacterial Endosymbiont, “Candidatus Rickettsiella viridis”
mBio (2018) 9 (3) e00890-18
doi: 10.1128/mBio.00890-18
Huimin Cai1, Qiye Li, Xiaodong Fang, Ji Li, Nicholas E. Curtis, Andreas Altenburger, Tomoko Shibata, Mingji Feng, Taro Maeda, Julie A. Schwartz, Shuji Shigenobu, Nina Lundholm, Tomoaki Nishiyama, Huanming Yang, Mitsuyasu Hasebe, Shuaicheng Li, Sidney K. Pierce and Jian Wang
A draft genome assembly of the solar-powered sea slug Elysia chlorotica
Scientific Data (2019) 6: 190022
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情報管理解析室利用
Tominaga, H., Satoh, N., Ueno, N., and Takahashi, H.
Enhancer activities of amphioxus Brachyury genes in embryos of the ascidian, Ciona intestinalis.
Genesis (2018) e23240.
Author / Use of Biological Information Analysis System / with acknowledgements
Ikuo Uchiyama
Ortholog Identification and Comparative Analysis of Microbial Genomes Using MBGD and RECOG
Protein Function Prediction (2017) 1611, 147-168
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Takashi Ikeda, Ikuo Uchiyama, Mio Iwasaki, Tetsuhiko Sasaki, Masato Nakagawa, Keisuke Okita, Shinji Masui
Artificial acceleration of mammalian cell reprogramming by bacterial proteins
Genes to Cells (2017) 22, 918-928
doi: 10.1111/gtc.12519
Use of biological information analysis system / with acknowledgement / written report of use
Ayako Gotoh, Shuji Shigenobu, Katsushi Yamaguchi, Satoru Kobayashi, Fuminori Ito, Kazuki Tsuji
Transcriptome profiling of the spermatheca identifies genes potentially involved in the long-term sperm storage of ant queens
Scientific reports (2017) 7: 5972
doi: 10.1038/s41598-017-05818-8
A. Gotoh, S. Shigenobu, K. Yamaguchi, S. Kobayashi, F. Ito, K. Tsuji
Transcriptome characterization of male accessory glands in ants to identify molecules involved in their reproductive success
Insect Molecular Biology (2018) 27(2), 212–220
doi: 10.1111/imb.12364
Yoshinobu Hayashi, Kiyoto Maekawa, Christine A. Nalepa, Toru Miura, Shuji Shigenobu
Transcriptome sequencing and estimation of DNA methylation level in the subsocial wood‑feeding cockroach Cryptocercus punctulatus (Blattodea: Cryptocercidae)
Applied Entomology and Zoology (2017) 52(4), 643-651
doi: 10.1007/s13355-017-0519-7
Sergio Seoane, Kiwamu Hyodo, Shoko Ueki
Chloroplast Genome Sequences of Seven Strains of the Bloom-Forming Raphidophyte Heterosigma akashiwo
Genome announcements (2017) 41(5)
doi: 10.1128,/genomeA. 01030-17
Aiko Higashi, Satoshi Nagai, Paulo S. Salomon, Shoko Ueki
A unique, highly variable mitochondrial gene with coding capacity of Heterosigma akashiwo, class Raphidophyceae
Journal of Applied Phycology (2017) 29(6), 2961-2969
doi: 10.1007/s10811-017-1142-2
Aiko Higashi, Satoshi Nagai, Sergio Seone, Shoko Ueki
A hypervariable mitochondrial protein coding sequence associated with geographical origin in a cosmopolitan bloom-forming alga, Heterosigma akashiwo
Biology letters (2017) 13(4)
doi: 10.1098/rsbl.2016.0976
Haruo Suzuki, Masaru Tomita, Pei-Jane Tsai, Wen-Chien Ko, Yuan-Pin Hung, I-Hsiu Huang, Jenn-Wei Chen
Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan
Gut Pathog (2017) 9:70
Doi: 10.1186/s13099-017-0219-4
Rumiko Kofuji, Yasushi Yagita, Takashi Murata, Mitsuyasu Hasebe
Antheridial development in the moss Physcomitrella patens: implications for understanding stem cells in mosses
Phylosophical transaction of the royal society (2017)
doi: 10.1098/rstb.2016.0494
Tsuyoshi Shimmura, Tomoya Nakayama, Ai Shinomiya, Shoji Fukamachi, Masaki Yasugi, Eiji Watanabe, Takayuki Shimo, Takumi Senga, Toshiya Nishimura, Minoru Tanaka, Yasuhiro Kamei, Kiyoshi Naruse, Takashi Yoshimura
Dynamic plasticity in phototransduction regulates seasonal changes in color perception
Nature communications (2017) 8:412
doi: 10.1038/s41467-017-00432-8
Shizuka Koshimizu, Rumiko Kofuji, Yuko Sasaki-Sekimoto, Masahide Kikkawa, Mie Shimojima, Hiroyuki Ohta, Shuji Shigenobu, Yukiko Kabeya, Yuji Hiwatashi, Yosuke Tamada, Takashi Murata, Mitsuyasu Hasebe
Physcomitrella MADS-box genes regulate water supply and sperm movement for fertilization
Nature plants (2018) 4, 36-45
doi: 10.1038/s41477-017-0082-9
Nobuhiko Muramoto, Arisa Oda, Hidenori Tanaka, Takahiro Nakamura, Kazuto Kugou, Kazuki Suda, Aki Kobayashi, Shiori Yoneda, Akinori Ikeuchi, Hiroki Sugimoto, Satoshi Kondo, Chikara Ohto, Takehiko Shibata, Norihiro Mitsukawa, Kunihiro Ohta
Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA doublestrand breaks
Nature Communications (2018) 9:1995
doi: 10.1038/s41467-018-04256-y
Taro Maeda, Yuuki Kobayashi, Hiromu Kameoka, Nao Okuma, Naoya Takeda, Katsushi Yamaguchi, Takahiro Bino, Shuji Shigenobu, Masayoshi Kawaguchi
Evidence of non-tandemly repeated rDNAs and their intragenomic heterogeneity in Rhizophagus irregularis
bioRxiv (2017)
doi: 10.1101/205864
Yuu Ishii, Shinichiro Maruyama, Konomi Fujimura-Kamada, Natsumaro Kutsuna, Shunichi Takahashi, Masakado Kawata, Jun Minagawa
Isolation of uracil auxotroph mutants of coral symbiont alga for symbiosis studies
Scientific Reports(2018) 8:3237
doi: 10.1038/s41598-018-21499-3
without acknowledgements
Fukushima, K., Fang, X., Alvarez-Ponce, D., Cai, H., Carretero-Paulet, L., Chen, C., Chang, T.H., Farr, K.M., Fujita, T., Hiwatashi, Y., Hoshi, Y., Imai, T., Kasahara, M., Librado, P., Mao, L., Mori, H., Nishiyama, T., Nozawa, M., Palfalvi, G., Pollard, S.T. Rozas, J., Sanchez-Gracia, A., Sankoff, D., Shibata, T.F., Shigenobu, S., Sumikawa, N., Uzawa, T., Xie, M., Zheng, C., Pollock, D.D., Albert, V.A., Li, S., Hasebe, M.
Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory.
Nature ecology & evolution(2017) vol. 1, 59.
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