生物情報解析システム利用/謝辞あり/利用報告書記載
Reimi Tada, Takuya Higashidate, Takanori Amano, Shoma Ishikawa,Chifuyu Yokoyama, Suzu Kobari, Saki Nara, Koshiro Ishida, Akane Kawaguchi, Haruki Ochi, Hajime Ogino, Nayuta Yakushiji-Kaminatsui, Joe Sakamoto, Yasuhiro Kamei, Koji Tamura, Hitoshi Yokoyama
The shh limb enhancer is activated in patterned limb regeneration but not in hypomorphic limb regeneration in Xenopus laevis
ELSEVIER, May 2023
doi.org/10.1016/j.ydbio.2023.05.009
Maho Tokuda, Masahiro Yuki, Moriya Ohkuma, Kazuhide Kimbara,Haruo Suzuki and Masaki Shintani
Transconjugant range of PromA plasmids in microbial communities is predicted by sequence similarity with the bacterial host chromosome
MICROBIOLOGY SOCIETY,Volume9,Issue6, June 2023
https://doi.org/10.1099/mgen.0.001043
Kenji Toyota, Takeo Yamamoto, Tomoko Mori, Miyuki Mekuchi, Shinichi Miyagawa, Masaru Ihara, Shuji Shigenobu & Tsuyoshi Ohira
Eyestalk transcriptome and methyl farnesoate titers provide insight into the physiological changes in the male snow crab, Chionoecetes opilio, after its terminal molt
Scientific Reports,13,Article number:7204, May 2023
https://doi.org/10.1038/s41598-023-34159-y
Kenji Toyota , Miyuki Mekuchi, Hiroshi Akashi, Shinichi Miyagawa, Tsuyoshi Ohira
Sexual dimorphic eyestalk transcriptome of kuruma prawn Marsupenaeus japonicus Author links open overlay panel
ELSEVIER,gene. Volume885,November 2023
https://doi.org/10.1016/j.gene.2023.147700
Kenji Toyota,, Hiroshi Akashi, Momoka Ishikawa, Katsushi Yamaguchi,Shuji Shigenobu, Tomomi Sato, Anke Lange, Charles R. Tyler, Taisen Iguchi,Shinichi Miyagawa
Comparative analysis of gonadal transcriptomes between turtle and alligator identifies common molecular cues activated during the temperature-sensitive period for sex determination
ELSEVIER,Gene888(2023)
https://doi.org/10.1016/j.gene.2023.147763
Hiromu Kameoka, Shota Shimazaki, Kiyoshi Mashiguchi, ..., Takahito Nomura, Shinjiro Yamaguchi, Junko Kyozuka
DIENELACTONE HYDROLASE LIKE PROTEIN1 negatively regulates the KAI2-ligand pathway in Marchantia polymorpha
Current Biology33,August 2023
https://doi.org/10.1016/j.cub.2023.06.083
Shinichi Morita, Tomoko F. Shibata, Tomoaki Nishiyama, Yuuki Kobayashi, Katsushi Yamaguchi, Kouhei Toga, Takahiro Ohde, Hiroki Gotoh, Takaaki Kojima, Jesse N. Weber, Marco Salvemini, Takahiro Bino, Mutsuki Mase, Moe Nakata, Tomoko Mori, Shogo Mori, Richard Cornette, Kazuki Sakura, Laura C. Lavine, Douglas J. Emlen, Teruyuki Niimi & Shuji Shigenobu
The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation
Scientific Reports,13,Article number:8735,May 2023
https://www.nature.com/articles/s41598-023-35246-w
Shizuka Koshimizu, Sachiko Masuda, Arisa Shibata, Takayoshi Ishii, Ken Shirasu, Atsushi Hoshino and Masanori Arita
Genome and transcriptome analyses reveal genes involved in the formation of fine ridges on petal epidermal cells in Hibiscus trionum
DNA Research,Volume 30, September 2023
https://doi.org/10.1093/dnares/dsad019
Kohei Kakino,Hiroaki Mon,Takeru Ebihara,Masato Hino,Akitsu Masuda,Jae Man Lee andTakahiro Kusakabe
Comprehensive Transcriptome Analysis in the Testis of the Silkworm, Bombyx mori
Insects 2023, 14(8), 684;
https://doi.org/10.3390/insects14080684
Yoko Otsubo, Akira Yamashita, Yuhei Goto, Keiichiro Sakai,Tetsushi Iida, Shinji Yoshimura, Katsuki Johzuka
Cellular responses to compound stress induced by atmospheric-pressure plasma in fission yeast
Journal of Cell Science,volume 136,Issue2,December 2023
https://doi.org/10.1242/jcs.261292
生物情報解析システム利用/謝辞あり/利用報告書記載漏れ
Hiroyuki Sekimoto, Ayumi Komiya, Natsumi Tsuyuki, Junko Kawai, Naho Kanda, Ryo Ootsuki, Yutaka Suzuki, Atsushi Toyoda, Asao Fujiyama, Masahiro Kasahara, Jun Abe, Yuki Tsuchikane, Tomoaki Nishiyama
A divergent RWP-RK transcription factor determines mating type in heterothallic Closterium
New Phylogist Foundation,Volume237,Issue5,March 2023
https://doi.org/10.1111/nph.18662Ci
Satoshi Ansai, Atsushi Toyoda, Kohta Yoshida, Jun Kitano
Repositioning of centromere-associated repeats during karyotype evolution in Oryzias fishes
First published: 28 November 2023
https://doi.org/10.1111/mec.17222
Kazunori Yamahira, Hirozumi Kobayashi, Ryo Kakioka, Javier Montenegro, Kawilarang W. A. Masengi, Noboru Okuda, Atsushi J. Nagano, Rieko Tanaka, Kiyoshi Naruse, Shoji Tatsumoto
Ghost introgression in ricefishes of the genus Adrianichthys in an ancient Wallacean lake
Journal of Evolutionary Biology, Volume 36, Issue 10, 1 October 2023
https://doi.org/10.1111/jeb.14223
Yuu Ishii,Hironori Ishii,Takeshi Kuroha,Ryusuke Yokoyama,Ryusaku Deguchi,Kazuhiko Nishitani,Jun Minagawa,Masakado Kawata,Shunichi Takahashi,Shinichiro Maruyama
Environmental pH signals the release of monosaccharides from cell wall in coral symbiotic alga
eLife,Microbiology and Infectious Disease,Aug 18, 2023
https://doi.org/10.7554/eLife.80628
Chihiro Miura, Yuki Furui, Tatsuki Yamamoto, Yuri Kanno, Masaya Honjo, Katsushi Yamaguchi, Kenji Suetsugu, Takahiro Yagame, Mitsunori Seo, Shuji Shigenob, Masahide Yamato, Hironori Kaminaka
Autoactivation of mycorrhizal symbiosis signaling through gibberellin deactivation in orchid seed germination
Plant Physiology, Volume 194, Issue 1, January 2024
https://doi.org/10.1093/plphys/kiad517
Hiroyuki Kakui, Tokuko Ujino-Ihara, Yoichi Hasegawa, Eriko Tsurisaki, Norihiro Futamura, Junji Iwai, Yuumi Higuchi, Takeshi Fujino, Yutaka Suzuki, Masahiro Kasahara
A single-nucleotide substitution of CjTKPR1 determines pollen production in the gymnosperm plant Cryptomeria japonica
PNAS Nexus, Volume 2, Issue 8, August 2023
https://doi.org/10.1093/pnasnexus/pgad236
Franziska Saul, Mathias Scharmann, Takanori Wakatake, Sitaram Rajaraman, André Marques, Matthias Freund, Gerhard Bringmann, Louisa Channon, Dirk Becker, Emily Carroll, Yee Wen Low, Charlotte Lindqvist, Kadeem J. Gilbert, Tanya Renner, Sachiko Masuda, Michaela Richter, Gerd Vogg, Ken Shirasu, Todd P. Michael, Rainer Hedrich, Victor A. Albert & Kenji Fukushima
Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis
nature plants 9, November 2023
https://www.nature.com/articles/s41477-023-01562-2
Kazutoshi Masuda,Hiroaki Setoguchi,Koki Nagasawa,Suzuki Setsuko,Shosei Kubota,Shin S. Satoh,Shota Sakaguchi
Phylogenetic Origin of Dioecious Callicarpa (Lamiaceae) Species Endemic to the Ogasawara Islands Revealed by Chloroplast and Nuclear Whole Genome Analyses
SSRN, Posted:Mar 2024
http://dx.doi.org/10.2139/ssrn.4753241
Satoko Ishii, Taishi Kakizuka, Sung-Joon Park, Ayako Tagawa, Chiaki Sanbo,Hideyuki Tanabe, Yasuyuki Ohkawa, Mahito Nakanishi, Kenta Nakai & Yusuke Miyanari
Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility
Nature Genetics 56,February 2024
https://www.nature.com/articles/s41588-024-01658-1
Naoki Minamino, Haruki Fujii, Haruhiko Murata, Sho Hachinoda, Yohei Kondo, Kazuhiro Hotta, Takashi Ueda
Analysis of Plant-Specific ANTH Domain–Containing Protein in Marchantia polymorpha
Plant and Cell Physiology, Volume 64, Issue 11, November 2023
https://doi.org/10.1093/pcp/pcad118
Tetsuya Komatsu, Kenji Ohya, Atsushi Ota, Yukiko Nishiuchi, Hirokazu Yano, Kayoko Matsuo, Justice Opare Odo, Shota Suganuma, Kotaro Sawai, Akemi Hasebe, Tetsuo Asai, Tokuma Yanai, Hideto Fukushi, Takayuki Wada, Shiomi Yoshida, Toshihiro Ito, Kentaro Arikawa, Mikihiko Kawai, Manabu Ato, Anthony D. Baughn, Tomotada Iwamoto, Fumito Maruyama
Unique genomic sequences in a novel Mycobacterium avium subsp. hominissuis lineage enable fine scale transmission route tracing during pig movement
One Health,May (2023) 10055
https://doi.org/10.1016/j.onehlt.2023.100559
Ai Shinomiya, Daisuke Adachi, Tsuyoshi Shimmura, Miki Tanikawa, Naoshi Hiramatsu, Shigeho Ijiri, Kiyoshi Naruse, Mitsuru Sakaizumi & Takashi Yoshimura
Variation in responses to photoperiods and temperatures in Japanese medaka from different latitudes
SPRINGERLINK,Volume9, July 2023
https://link.springer.com/article/10.1186/s40851-023-00215-8
生物情報解析システム利用/謝辞なし/利用報告書記載
Ryohei H. Suzuki,Takumi Hanada, Yoshinobu Hayashi,Shuji Shigenobu,Kiyoto Maekawa,Masaru K. Hojo
Gene expression profiles of chemosensory genes of termite soldier and worker antennae
Insect Molecular Biology, March 2023
https://doi.org/10.1111/imb.12841
Keita Furuminato, Saki Minatoya, Eriko Senoo, TatsukiGoto, Sho Yamazaki, Moeka Sakaguchi, KenjiToyota, Taisen Iguchi & Shinichi Miyagawa
The role of mesenchymal estrogen receptor 1 in mouse uterus in response to estrogen
Scientic reports,2023
https://doi.org/10.1038/s41598-023-39474-y
Masaki Shintani, Haruo Suzuki, Hideaki Nojiri, Masato Suzuki
Reconsideration of the previously classified incompatibility groups of plasmids, IncP-1 and IncP-11
ENVIRONMENTAL MICROBIOLOGY, Volume25,Issue6, June 2023
https://doi.org/10.1111/1462-2920.16345
Yuh Shiwa, Tomoya Baba, Maria A. Sierra, JangKeun Kim, Christopher E. Mason & Haruo Suzuki
Evaluation of rRNA depletion methods for capturing the RNA virome from environmental surfaces
BMC Research Notes 142, July 2023
https://doi.org/ 10.1186/s13104-023-06417-9.
Jun Wu, Yige Hu, Michael H Perlin, David Danko, Jun Lu, Manuela Oliveira, Johannes Werner, Maria M Zambrano, Maria A Sierra, Olayinka O Osuolale, Paweł Łabaj, Nicolás Rascovan, Nur Hazlin Hazrin-Chong, Soojin Jang, Haruo Suzuki, Marina Nieto-Caballero, Bharath Prithiviraj, Patrick K H Lee, Agnieszka Chmielarczyk, Anna Różańska, Yongxiang Zhao, Lan Wang, Christopher E Mason, Tieliu Shi
Landscape of global urban environmental resistome and its association with local socioeconomic and medical status
SPRINGERLINK,March 2024
生物情報解析システム利用/謝辞あり/利用報告書記載
Dewa A.P. Rasmika Dewi, Yuh Shiwa, Krista Ryon, Christopher E. Mason, Tstsuya Matsumoto, Haruo Suzuki
Urban Microbiomes in Narita, Chiba, Japan: Shotgun Metagenome Sequences of a Train Station
Microbiology Resource Announcements Volume 12, January 2023
doi.org/10.1128/mra.01092-2
Yuki Kobayashi, Tomoko F. Shibata, Hideki Hirakawa, Tomoaki Nishiyama, Akiyoshi Yamada, Mitsuyasu Hasebe, Shuji Shigenobu and Masayoshi Kawaguchi
The genome of Lyophyllum shimeji provides insight into the initial evolution of ectomycorrhizal fungal genomes
DNA Research,2023,30,1-8 January 2023
doi.org/10.1093/dnares/dsac053
Masaki Ishikawa, Ayaka Fujiwara, Ken Kosetsu, Yuta Horiuchi, Naoya Kamamoto, Naoyuki Umakawa, Yosuke Tamada, Liechi Zhang, Katsuyoshi Matsushita, Gergo Palfalvi, Tomoaki Nishiyama, Sota Kitasaki, Yuri Masuda, Yoshiki Shiroza, Munenori Kitagawa, Toru Nakamura, Hongchang Cui, Yuji Hiwatashi, Yukiko Kabeya, Shuji Shigenobu, Tsuyoshi Aoyama, Kagayaki Kato, Takashi Murata, Koichi Fujimoto, Philip N.Benfey, Mitsuyasu Hasebe and Rumiko Kofuji
GRAS transcription factors regulate cell division planes in moss overriding the default rule
PNAS 2023 Vol.120 No.4, January 2023
doi.org/10.1073/pnas.2210632120
Masanao Sato, Masahide Seki, Yutaka Suzuki, Shoko Ueki
The dataset of de novo assembly and inferred functional annotation of the transcriptome of Heterosigma akashiwo, a bloom-forming, cosmopolitan raphidophyte
ELSEVIER Data in Brief 48 (2023), March 2023
doi.org/10.1016/j.dib.2023.109071
Kazuki Sakura, Shinichi Morita and Teruyuki Niimi
RNA Interference Method for Gene Function Analysis in the Japanese Rhinoceros Beetle Trypoxylus dichotomus
Bio-protocol, Apr 2022
DOI: 10.1038/s41598-020-75709-y
Munetaka Kawamoto, Takashi Kiuchi and Susumu Katsuma
SilkBase: an integrated transcriptomic and genomic database for Bombyx mori and related species
Database,Volume.00,Article ID baac040, June 2022
doi.org/10.1093/database/baac040
Yoshinobu Hayashi, Kohei Oguchi, Mayuko Nakamura, Shigeyuki Koshikawa and Toru Miura
Construction of a massive genetic resource by transcriptome sequencing and genetic characterization of Megasyllis nipponica (Annelida: Syllidae)
Genes Genet. Syst.(2022) 97
doi.org/10.1266/ggs.21-00137
Shunta Yorimoto, Mitsuru Hattori, Maki Kondo, Shuji Shigenobu
Complex host/symbiont integration of a multi-partner symbiotic system in the eusocial aphid Ceratovacuna japonica
iScience 25, 105478, December 2022
doi.org/10.1016/j.isci.2022.105478
Meng Yu, Naoki Arai, Tadahiro Ochiai and Takashi Ohyama
Expression and function of an S1-type nuclease in the digestive fluid of a sundew, Drosera adelae
Annals of Botany131, Issue 2, February 2023
doi.org/10.1093/aob/mcac150
Hiroyuki Sekimoto, Ayumi Komiya, Natsumi Tsuyuki, Junko Kawai, Naho Kanda, Ryo Ootsuki,Yutaka Suzuki, Atsushi Toyoda, Asao Fujiyama, Masahiro Kasahara, Jun Abe, Yuki Tsuchikane and Tomoaki Nishiyama
A divergent RWP-RK transcription factor determines mating type in heterothallic Closterium
New Phytologist Volume 237, Issue 5, March 2023
doi.org/10.1111/nph.18662
Yuki Yoshida, Nurislam Shaikhutdinov, Olga Kozlova, Masayoshi Itoh, Michihira Tagami, Mitsuyoshi Murata, Hiromi Nishiyori-Sueki, Miki Kojima-Ishiyama, Shohei Noma, Alexander Cherkasov, Guzel Gazizova, Aigul Nasibullina, Ruslan Deviatiiarov, Elena Shagimardanova, Alina Ryabova, Katsushi Yamaguchi, Takahiro Bino, Shuji Shigenobu, Shoko Tokumoto, Yugo Miyata, Richard Cornette, Takahiro G. Yamada, Akira Funahashi, Masaru Tomita, Oleg Gusev and Takahiro Kikawada
High quality genome assembly of the anhydrobiotic midge provides insights on a single chromosome-based emergence of extreme desiccation tolerance
NAR Genomics and Bioinformatics, Volume 4, No.2 (2022)
doi.org/10.1093/nargab/lqac029
Yasuhiko Chikami, Miki Okuno, Atsushi Toyoda, Takehiko Itoh and Teruyuki Niimi
Evolutionary history of sexual differentiation mechanism in insects
Mol. Biol. Evol.39 (7):msac145 July 2022
https://doi.org/10.1093/molbev/msac145
Munetaka Kawamoto and Susumu Katsuma
Silk Baseのアップデート-タンパク質立体構造情報の配備-
SANSHI-KONCHU BIOTEC Volume 91 (3), 2022
Yuki Kobayashi and Shuji Shigenobu
Hygrocybe griseonigricans(ハラタケ目ヌメリガサ科)の日本新産報告
日菌報63:17-21, May 2022
doi:10.18962/jjom.jjom.R3-10
生物情報解析システム利用/謝辞あり/利用報告書記載漏れ
Hajime Yaguchi, Shogo Suzuki, Naoto Kanasaki, Yudai Masuoka, Ryutaro Suzuki, Ryouhei H. Suzuki, Yoshinobu Hayashi, Shuji Shigenobu, Kiyoto Maekawa
Evolution and functionalization of vitellogenin genes in the termite Reticulitermes speratus
J Exp Zool B Mol Dev Evol.2023:3402022
doi.org/10.1002/jez.b.23141
Shizuka Koshimizu, Naoki Minamino, Tomoaki Nishiyama, Emiko Yoro, Mayuko Sato, Mayumi Wakazaki, Kiminori Toyooka, Kazuo Ebine, Keiko Sakakibara, Takashi Ueda and Kentaro Yano
Phylogenetic distribution and expression pattern analyses identified a divergent basal body assembly protein involved in land plant spermatogenesis
New Phytologist (2022) 236
doi.org/10.1111/nph.18385
Meng Liu, Hiromu Kameoka, Akiko Oda, Taro Maeda, Takashi Goto, Koji Yano, Takashi Soyano and Masayoshi Kawaguchi
The effects of ERN1 on gene expression during early rhizobial infection in Lotus japonicus
Frontiers in Plant Science Volume 13, January 2023
doi.org/10.3389/fpls.2022.995589
Hiroaki Mon, Masanao Sato, Jae Man Lee, Takahiro Kusakabe
Construction of gene co-expression networks in cultured silkworm cells and identification of previously uncharacterized lepidopteran-specific genes required for chromosome dynamics
ELSEVIER Science Direct Volume 151,December 2022
doi.org/10.1016/j.ibmb.2022.103875
Taro Maeda, Shigeo S. Sugano, Makoto Shirakawa, Mayu Sagara, Toshiro Ito, Satoshi Kondo and Atsushi J.Nagano
Single-Cell RNA Sequencing of Arabidopsis Leaf Tissues Identifies Multiple Specialized Cell Types: Idioblast Myrosin Cells and Potential Glucosinolate-Producing Cells
Plant & Cell Physiology, Volume 64, February 2023
doi.org/10.1093/pcp/pcac167
生物情報解析システム利用/謝辞なし/利用報告書記載
Ryo Nagao, Koji Kato, Minoru Kumazawa, Kentaro Ifuku, Makio Yokono, Takehiro Suzuki, Naoshi Dohmae, Fusamichi Akita, Seiji Akimoto, Naoyuki Miyazaki and Jian-Ren Shen
Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex
NATURE COMMUNICATIONS | (2022) 13:1764
doi.org/10.1038/s41467-022-29294-5
Ayako Gotoh, MikaTakeshima and Ken‐ichi Mizutani
Near‐anoxia induces immobilization and sustains viability of sperm stored in ant queens
Scientific Reports 13:3029 March (2023)
doi.org/10.1038/s41598-023-29705-7
Masatoshi Matsunami, Dai Watanabe, Kokuto Fujiwara, Yoshinobu Hayashi, Shuji Shigenobu, Toru Miura and Kiyoto Maekawa
Transcriptomics on Social Interactions in Termites: Effects of Soldier Presence
Frontiers in Ecology and Evolution Volume 10, June 2022
doi: 10.3389/fevo.2022.924151
Ryota Saiki, Yoshinobu Hayashi, Kouhei Toga, Hajime Yaguchi, Yudai Masuoka, Ryutaro Suzuki, Kokuto Fujiwara, Shuji Shigenobu and Kiyoto Maekawa
Comparison of gene expression profles among caste diferentiations in the termite Reticulitermes speratus
Scientifc Reports | (2022) 12:11947
doi.org/10.1038/s41598-022-15984-z
Akimasa Fukui and Masatoshi Matsunami
Gene Structure Analysis of Chemokines and Their Receptors in Allotetraploid Frog, Xenopus laevis
Front. Genet. Volume 12, January 2022
doi: 10.3389/fgene.2021.787979
著者
Minoru Kumazawa, Hiroyo Nishide, Ryo Nagao, Natsuko Inoue-Kashino, Jian-Ren Shen, Takeshi Nakano, Ikuo Uchiyama Yasuhiro Kashino, Kentaro Ifuku
Molecular phylogeny of fucoxanthin-chlorophyll a/c proteins from Chaetoceros gracilis and Lhcq/Lhcf diversity
Physiologia Plantarum,November 2021
doi.org/10.1111/ppl.13598
生物情報解析システム利用/謝辞あり
Shuji Shigenobua, Yoshinobu Hayashi, Dai Watanabe, Gaku Tokuda, Masaru Y. Hojo, Kouhei Toga,Ryota Saiki, Hajime Yaguchi, Yudai Masuoka, Ryutaro Suzuki, Shogo Suzuki, Moe Kimura, Masatoshi Matsunami, Yasuhiro Sugime, Kohei Oguchi, Teruyuki Niimi, Hiroki Gotoh, Masaru K. Hojo, Satoshi Miyazaki, Atsushi Toyoda, Toru Miura and Kiyoto Maekawa
Genomic and transcriptomic analyses of the subterranean termite Reticulitermes speratus: Gene duplication facilitates social evolution
PNAS, January 2022 Vol. 119
doi/full/10.1073/pnas.2110361119
Kazuki Sato, Taketo Uehara, Julia Holbein, Yuko Sasaki-Sekimoto, Pamela Gan,Takahiro Bino, Katsushi Yamaguchi, Yasunori Ichihashi, Noriko Maki,Shuji Shigenobu, Hiroyuki Ohta, Rochus B. Franke, Shahid Siddique,Florian M. W. Grundler, Takamasa Suzuki, Yasuhiro Kadota and Ken Shirasu
Transcriptomic Analysis of Resistant and Susceptible Responses in a New Model Root-Knot Nematode Infection System Using Solanum torvum and Meloidogyne arenaria
Frontiers in Plant Science, May 2021
doi.org/10.3389/fpls.2021.680151
Takaaki Yoshimoto, Shuntaro Okazaki, Motofumi Sumiya, Haruka K. Takahashi, Eri Nakagawa, Takahiko Koike, Ryo Kitada, Shiki Okamoto, Masanori Nakata, Toshihiko Yada, Hirotaka Kosaka, Norihiro Sadato, Junichi Chikazoe
Coexistence of sensory qualities and value representations in human orbitofrontal cortex
ELSEVIER Neuroscience Research, Feb.2022
doi.org/10.1016/j.neures.2022.02.004
David Danko, Daniela Bezdan, Evan E. Afshin, Sofia Ahsanuddin, Chandrima Bhattacharya, Daniel J. Butler, Kern Rei Chng, Daisy Donnellan, Jochen Hecht, Katelyn Jackson, Katerina Kuchin, Mikhail Karasikov, Abigail Lyons, Lauren Mak, Dmitry Meleshko, Harun Mustafa, Beth Mutai, Russell Y. Neches, Amanda Ng, Olga Nikolayeva, Tatyana Nikolayeva, Eileen Png, Krista A. Ryon, Jorge L. Sanchez, Heba Shaaban, Maria A. Sierra, Dominique Thomas, Ben Young, Omar O. Abudayyeh, Josue Alicea, Malay Bhattacharyya, Ran Blekhman, Eduardo Castro-Nallar, Ana M. Can˜ as, Aspassia D. Chatziefthimiou, Robert W. Crawford, Francesca De Filippis, Youping Deng, Christelle Desnues, Emmanuel Dias-Neto, Marius Dybwad, Eran Elhaik, Danilo Ercolini, Alina Frolova, Dennis Gankin, Jonathan S. Gootenberg, Alexandra B. Graf, David C. Green, Iman Hajirasouliha, Jaden J.A. Hastings, Mark Hernandez, Gregorio Iraola, Soojin Jang, Andre Kahles, Frank J. Kelly, Kaymisha Knights, Nikos C. Kyrpides, Pawe1 P. qabaj, Patrick K.H. Lee, Marcus H.Y. Leung, Per O. Ljungdahl, Gabriella Mason-Buck, Ken McGrath, Cem Meydan, Emmanuel F. Mongodin, Milton Ozorio Moraes, Niranjan Nagarajan, Marina Nieto-Caballero, Houtan Noushmehr, Manuela Oliveira, Stephan Ossowski, Olayinka O. Osuolale, Orhan O¨ zcan, David Paez-Espino, Nicola´ s Rascovan, Hugues Richard, Gunnar Ra¨ tsch,Lynn M. Schriml,Torsten Semmler, Osman U. Sezerman, Leming Shi, Tieliu Shi, Rania Siam, Le Huu Song, Haruo Suzuki, Denise Syndercombe Court, Scott W. Tighe, Xinzhao Tong, Klas I. Udekwu, Juan A. Ugalde, Brandon Valentine, Dimitar I. Vassilev, Elena M. Vayndorf, Thirumalaisamy P. Velavan, Jun Wu, Marı´a M. Zambrano, Jifeng Zhu, Sibo Zhu,Christopher E. Mason and The International MetaSUB Consortium
A global metagenomic map of urban microbiomes and antimicrobial resistance
Cell Press, June, 2021
doi.org/10.1016/j.cell.2021.05.002
Yuanhai You, Kaisa Thorell, Lihua He, Koji Yahara, Yoshio Yamaoka, Jeong-Heon Cha, Kazunari Murakami, Yukako Katsura, TEAMHp, Ichizo Kobayashi, Daniel Falush and Jianzhong Zhang
Genomic differentiation within East Asian Helicobacter pylori
Microbial Genomics, February, 2022
doi.org/10.1099/mgen.0.000676
Hiroyuki Koga, Mikiko Kojima, Yumiko Takebayashi, Hitoshi Sakakibara and Hirokazu Tsukaya
Identification of the unique molecular framework of heterophylly in the amphibious plant Callitriche palustris L.
THE PLANT CELL, January, 2021
doi:10.1093/plcell/koab192
Taro Maeda, Shunichi Takahashi, Takao Yoshida, Shigeru Shimamura, Yoshihiro Takaki, Yukiko Nagai, Atsushi Toyoda, Yutaka Suzuki, Asuka Arimoto, Hisaki Ishii, Nori Satoh, Tomoaki Nishiyama, Mitsuyasu Hasebe, Tadashi Maruyama, Jun Minagawa, Junichi Obokata, Shuji Shigenobu
Chloroplast acquisition without the gene transfer in kleptoplastic sea slugs, Plakobranchus ocellatus
eLife, April 2021
doi.org/10.7554/eLife.60176
Natsu Katayama, Satoshi Koi, Akira Sassa, Tetsuya Kurata, Ryoko Imaichi, Masahiro Kato & Tomoaki Nishiyama
Elevated mutation rates underlie the evolution of the aquatic plant family Podostemaceae
COMMUNICATIONS BIOLOGY, January (2022)
doi.org/10.1038/s42003-022-03003-w
Kazuki Sato, Taketo Uehara, Julia Holbein, Yuko Sasaki-Sekimoto, Pamela Gan, Takahiro Bino, Katsushi Yamaguchi, Yasunori Ichihashi, Noriko Maki, Shuji Shigenobu, Hiroyuki Ohta, Rochus B. Franke, Shahid Siddique, Florian M. W. Grundler, Takamasa Suzuki, Yasuhiro Kadota and Ken Shirasu
Transcriptomic Analysis of Resistant and Susceptible Responses in a New Model Root-Knot Nematode Infection System Using Solanum torvum and Meloidogyne arenaria
Bio Rxiv, April 2021
doi.org/10.1101/2021.04.02.438176
Takashi Goto, Takashi Soyano, Meng Liu, Tomoko Mori and Masayoshi Kawaguchi
Auxin methylation by IAMT1, duplicated in the legume lineage, promotes root nodule development in Lotus japonicus
PNAS, March,2022 Vol. 119
doi.org/10.1073/pnas.2116549119
Trung Quang Pham, Shota Nishiyama, Norihiro Sadato and Junichi Chikazoe
Distillation of Regional Activity Reveals Hidden Content of Neural Information in Visual Processing
Frontiers in Human Neuroscience, November 2021
doi.org/10.3389/fnhum.2021.777464
Tetsuya Komatsu, Kenji Ohya, Atsushi Ota, Yukiko Nishiuchi, Hirokazu Yano, Kayoko Matsuo, Justice Opare Odoi, Shota Suganuma, Kotaro Sawai, Akemi Hasebe, Tetsuo Asai, Tokuma Yanai, Hideto Fukushi, Takayuki Wada, Shiomi Yoshida, Toshihiro Ito, Kentaro Arikawa, Mikihiko Kawai, Manabu Ato, Anthony D Baughn, Tomotada Iwamoto and Fumito Maruyama
Genomic features of Mycobacterium avium subsp. hominissuis isolated from pigs in Japan
Gigabyte, November,2021,
doi.org/10.46471/gigabyte.33
Haruna Fujioka, Masatoshi S. Abe, Yasukazu Okada
Individual Ants Do Not Show Activity–rest Rhythms in Nest Conditions
Journal of Biological Rhythms, April (2021)
doi.org/10.1177%2F07487304211002934
Katsuya Kiyose, Masako Katsuki, Yu Suzaki, Kensuke Okada, Yasukazu Okada
Octopaminergic system orchestrates combat and mating behaviors: a potential regulator of alternative male mating tactics in an armed beetle
Journal of Insect Physiology, May-June (2021)
doi.org/10.1016/j.jinsphys.2021.104211
Katsuya Kiyose, Yasukazu Okada, Masako Katsuki, Yu Suzaki, Kensuke Okada
Sexually selected traits and life history traits of larger and smaller males of the horned flour beetle Gnatocerus cornutus
Ecological Entomology, April 2021
DOI: 10.1111/(ISSN)1365-2311
生物情報解析システム利用/謝辞あり/利用報告書記載なし
Trieu-Duc Vu , Yuki Iwasaki, Kenshiro Oshima, Ming-Tzu Chiu, Masato Nikaido, Norihiro Okada
Data of RNA-seq transcriptomes in the brain associated with aggression in males of the fish Betta splendens
ELSEVIER (2021)
doi.org/10.1016/j.dib.2021.107448
Hiroyuki Kakui, Tokuko UjinoIhara, Yoichi Hasegawa, Eriko Tsurisaki, Norihiro Futamura, Junji Iwai, Yuumi Higuchi, Takeshi Fujino, Yutaka Suzuki, Masahiro Kasahara, Katsushi Yamaguchi, Shuji Shigenobu, Masahiro Otani, Masaru Nakano, Saneyoshi Ueno, Yoshinari Moriguchi
Single-nucleotide substitution determines pollen production in Japanese cedar
bioRxiv, March, 2022
doi.org/10.1101/2022.03.17.484665
生物情報解析システム利用/謝辞あり/利用報告書記載なし
Asano Ishikawa, Yoel E. Stuart, Daniel I. Bolnick and Jun Kitano
Copy number variation of a fatty acid desaturase gene Fads2 associated with ecological divergence in freshwater stickleback populations
Biology Letters, August, 2021
doi.org/10.1098/rsbl.2021.0204
Masaki Shintani, Haruo Suzuki, Hideaki Nojiri and Masato Suzuki
Precise classification of antimicrobial resistance-associated IncP-2 megaplasmids for molecular epidemiological studies on Pseudomonas species
Journal of Antimicrobial Chemotherapy, March, 2022
doi.org/10.1093/jac/dkac006
Cheng‑Hung Tsai, Tzu‑Chieh Lin, Yi‑Hsien Chang, Huai‑Kuang Tsai and Jia‑Hsin Huang
Identification and comparative analysis of long non‑coding RNAs in the brain of fire ant queens in two different reproductive states
BMC Genomics, (2021)
doi.org/10.1186/s12864-022-08539-z
Takaya Tominaga, Chihiro Miura, Yuuka Sumigawa, Yukine Hirose, Katsushi Yamaguchi, Shuji Shigenobu, Akira Mine and Hironori Kaminaka
Conservation and Diversity in Gibberellin-Mediated Transcriptional Responses Among Host Plants Forming Distinct Arbuscular Mycorrhizal Morphotypes
Frontiers in Plant Science, December 2021
doi.org/10.3389/fpls.2021.795695
Takashi Takeuchi, Haruka Matsubara, Fumina Minamitani, Yukio Satoh, Sayo Tozawa, Tomoki Moriyama, Kohei Maruyama, Ken-ichi T. Suzuki, Shuji Shigenobu, Takeshi Inoue, Koji Tamura, Kiyokazu Agata and Toshinori Hayashi
Newt Hoxa13 has an essential and predominant role in digit formation during development and regeneration
The Company of Biologists, January,2022
doi:10.1242/dev.200282
著者/生物情報解析システム利用/謝辞あり
Midori Iida, Miyuki Suzuki, Yuto Sakane, Hiroyo Nishide, Ikuo Uchiyama, Takashi Yamamoto,
Ken-ichi T. Suzuki, Satoshi Fujii
A simple and practical workflow for genotyping of CRISPR–Cas9-based knockout phenotypes using multiplexed amplicon sequencing
Genes to Cells( 2020)
doi: 10.1111/gtc.12775
Ryo Nagao, Koji Kato, Kentaro Ifuku, Takehiro Suzuki, Minoru Kumazawa, Ikuo Uchiyama, Yasuhiro Kashino, Naoshi Dohmae, Seiji Akimoto, Jian-Ren Shen, Naoyuki Miyazaki & Fusamichi Akita
Structural basis for assembly and function of a diatom photosystem I-light-harvesting supercomplex
NATURE COMMUNICATIONS (2020) 11:2481
doi.org/10.1038/s41467-020-16324-3
Takashi Okubo, Atsushi Toyoda, Kohei Fukuhara, Ikuo Uchiyama, Yuhki Harigaya, Megumi Kuroiwa, Takuma Suzuki, Yuka Murakami, Yuichi Suwa, Hideto Takami
The physiological potential of anammox bacteria as revealed by their core genome structure.
DNA Res. 28, dsaa028(2021)
doi:10.1093/dnares/dsaa028
生物情報解析システム利用/謝辞あり/利用報告書記載
Tamiris I. Yassumoto, Mana Nakatsukasa, Atsushi J. Nagano, Masaki Yasugi, Takashi Yoshimura,
Ai Shinomiya
Genetic analysis of body weight in wild populations of medaka fish from different latitudes
PLOS ONE (2020)
doi.org/10.1371/journal.pone.0234803
Satoshi Ansai, Koji Mochida, Shingo Fujimoto, Daniel F. Mokodongan, Bayu Kreshna Adhitya Sumarto, Kawilarang W. A. Masengi, Renny K. Hadiaty, Atsushi J. Nagano, Atsushi Toyoda, Kiyoshi Naruse, Kazunori Yamahira & Jun Kitano
Genome editing reveals fitness effects of a gene for sexual dichromatism in Sulawesian fishes
NATURE COMMUNICATIONS (2021) 12:1350
doi.org/10.1038/s41467-021-21697-0
Yuki Doll, Hiroyuki Koga and Hirokazu Tsukaya
The diversity of stomatal development regulation in Callitriche is related to the intrageneric diversity in lifestyles
PNAS (2021) Vol. 118 No. 14 e2026351118
doi.org/10.1073/pnas.2026351118
Trung Quang Pham, Takaaki Yoshimoto, Haruki Niwa, Haruka K Takahashi, Ryutaro Uchiyama, Teppei Matsui, Adam K Anderson, Norihiro Sadato, Junichi Chikazoe
Vision-to-value transformations in artificial network and human brains
Bio Rxiv (2021)
doi.org/10.1101/2021.03.18.435929
Maho Tokuda, Haruo Suzuki, Kosuke Yanagiya, Masahiro Yuki, Kengo Inoue, Moriya Ohkuma, Kazuhide Kimbara and Masaki Shintani
Determination of Plasmid pSN1216-29 Host Range and the Similarity in Oligonucleotide Composition Between Plasmid and Host Chromosomes
Frontiers in Microbiology (2020)
doi.org/10.3389/fmicb.2020.01187
Tomoro Warashina, Masafumi Harad, Nobuyoshi Nakajima, Shigeki Yamamura, Masaru Tomita,
Haruo Suzuki, Seigo Amachi
Draft Genome Sequence of Geobacter sp. Strain SVR, Isolated from Antimony Mine Soil
Microbiology Resource Announcements (2020)
doi.org/10.1128/MRA.00461-20
Nan Gu, Yosuke Tamada, Akihiro Ima, Gergo Palfalvi, Yukiko Kabeya, Shuji Shigenobu, Masaki Ishikawa, Karel J. Angelis, Chunli Chen and Mitsuyasu Hasebe
DNA damage triggers reprogramming of differentiated cells into stem cells in Physcomitrella
Nature Plants Vol. 1098 6 (2020) 1098–1105
doi.org/10.1038/s41477-020-0745-9
Misuzu Kurihara, Kagayaki Kato, Chiaki Sanbo, Shuji Shigenobu, Yasuyuki Ohkawa, Takeshi Fuchigami,
Yusuke Miyanari
Genomic Profiling by ALaP-Seq Reveals Transcriptional Regulation by PML Bodies through DNMT3A Exclusion
Molecular Cell / 78, 1–13:(2020)
doi.org/10.1016/j.molcel.2020.04.004
Mikihiko Kawai, Atsushi Ota, Taichiro Takemura, Toshihiro Nakai and Fumito Maruyama
Continuation and replacement of Vibrio cholerae non-O1 clonal genomic groups isolated from Plecoglossus altivelis fish in freshwaters
Environmental Microbiology (2020) 22(10) 4473–4484
doi:10.1111/1462-2920.15199
Nancy Merino, Mikihiko Kawai, Eric S. Boyd, Daniel R. Colman, Shawn E. McGlynn, Kenneth H. Nealson, Ken Kurokawa and Yuichi Hongoh
Single-Cell Genomics of Novel Actinobacteria With the Wood–Ljungdahl Pathway Discovered in a Serpentinizing System
Frontiers in Microbiology (2020)
doi.org/10.3389/fmicb.2020.01031
Nao Okuma, Takashi Soyano, Takuya Suzaki & Masayoshi Kawaguchi
MIR2111-5 locus and shoot-accumulated mature miR2111 systemically enhance nodulation depending on HAR1 in Lotus japonicus
NATURE COMMUNICATIONS (2020) 11:5192
doi.org/10.1038/s41467-020-19037-9
生物情報解析システム利用/謝辞あり/利用報告書記載なし
Masatoshi Okura, Jean‑Philippe Auger, Tomoyuki Shibahara, Guillaume Goyette‑Desjardins, Marie‑Rose Van Calsteren, Fumito Maruyama, Mikihiko Kawai, Makoto Osaki, Mariela Segura, Marcelo Gottschalk &
Daisuke Takamatsu
Capsular polysaccharide switching in Streptococcus suis modulates host cell interactions and virulence
nature portfolio (2021) 11:6513
doi.org/10.1038/s41598-021-85882-3
Mami Sakai, Satoshi Kakutani, Shin-ichiro Asano, Masanao Satoh, Hisanori Bando
Proliferetion of Bombyx mori nucleopolyhedrovirus strain H4 in BmN cells is enhanced by exchange of the F gene sequence with type strain T3
ELSEVIER Volume291 (2021)
doi.org/10.1016/j.virusres.2020.198195
Trieu-Duc Vu, Yuki Iwasaki, Kenshiro Oshima, Ming-Tzu Chi, Masato Nikaido, Norihiro Okada
A unique neurogenomic state emerges after aggressive confrontations in males of the fish Betta aplendens
ELSEVIER Volume784 (2021)
doi.org/10.1016/j.gene.2021.145601
Hiroyuki Koga, Mikiko Kojima, Yumiko Takebayashi, Hitoshi Sakakibara and Hirokazu Tsukaya
The molecular framework of heterophylly in Callitriche palustris L. differs from that in other amphibious plants
bioRxiv (2020)
doi.org/10.1101/2020.12.19.423571
生物情報解析システム利用/謝辞なし/利用報告書記載あり
Trieu-Duc Vu, Yuki Iwasaki, Shuji Shigenobu, Akiko Maruko, Kenshiro Oshima, Erica Iioka,
Chao-Li Huang, Takashi Abe, Satoshi Tamaki, Yi Wen Lin, Chih-Kuan Chen, Mei-Yeh Lu, Masaru Hojo, Hao-Ven Wang, Shun-Fen Tzeng, Hao-Jen Huang, Akio Kanai, Takashi Gojobori, Tzen-Yuh, Chiang, H.Sunny Sun, Wen-Hsiung Li, Norihiro Okada
Behavioral and brain- transcriptomic synchronization between the two opponents of a fighting pair of the fish Betta splendens
PLOS Genetics (2020)
doi.org/10.1371/journal.pgen.1008831
Yasuhiko Chikami, Haruka Kawaguchi, Takamasa Suzuki, Hirofumi Yoshioka, Yutaka Sato, Toshinobu Yaginuma, Teruyuki Niimi
Oral RNAi of diap1 results in rapid reduction of damage to potatoes in Henosepilachna vigintioctopunctata
Journal of Pest Science (2021) 94:505–515
doi.org/10.1007/s10340-020-01276-w
Ryo Nagao, Makio Yokono, Yoshifumi Ueno, Takehiro Suzuki, Minoru Kumazawa, Ka-Ho Kato, Naoki Tsuboshita, Naoshi Dohmae, Kentaro Ifuku, Jian-Ren Shen, Seiji Akimoto
Enhancement of excitation-energy quenching in fucoxanthin chlorophyll a/ c-binding proteins isolated from a diatom Phaeodactylum tricornutum upon excess-light illumination
BBA – Bioenergetics (2020)
doi.org/10.1016/j.bbabio.2020.148350
Shoko Onodera, Akiko Saito, Hironori Hojo, Takashi Nakamura, Denise Zujur, Katsuhito Watanabe, Nana Morita, Daigo Hasegawa, Hideki Masaki, Hiromitsu Nakauchi, Takeshi Nomura, Takahiko Shibahara, Akira Yamaguchi, Ung-il Chung, Toshifumi Azuma and Shinsuke Ohba
Hedgehog Activation Regulates Human Osteoblastogenesis
Stem Cell Reports Vol. 15(2020) 125–139
doi.org/10.1016/j.stemcr.2020.05.008
Akio Ooki, Shoko Onodera, Akiko Saito, Akiko Oguchi, Yasuhiro Murakawa, Teruo Sakamoto, Kenji Sueishi, Yasushi Nishii, Toshifumi Azuma
CAGE-seq analysis of osteoblast derived from cleidocranial dysplasia human induced pluripotent stem cells
ELSEVIER Bone Volume141 (2020)
doi.org/10.1016/j.bone.2020.115582
Gergo Palfalvi, Thomas Hackl, Niklas Terhoeven, Tomoko F. Shibata, Tomoaki Nishiyama, Markus Ankenbrand, Dirk Becker, Frank Fo¨ rster, Matthias Freund, Anda Iosip, Ines Kreuzer, Franziska Saul, Chiharu Kamida, Kenji Fukushima, Shuji Shigenobu, Yosuke Tamada, Lubomir Adamec, Yoshikazu Hoshi, Kunihiko Ueda, Traud Winkelmann, Jo¨ rg Fuchs, Ingo Schubert, Rainer Schwacke, Khaled Al-Rasheid, Jo¨ rg Schultz, Mitsuyasu Hasebe and Rainer Hedrich
Genomes of the Venus Flytrap and Close Relatives Unveil the Roots of Plant Carnivory
Current Biology Cell Press 30 (2020) 2312–2320
doi.org/10.1016/j.cub.2020.04.051
Takaya Tominaga, Katsushi Yamaguchi, Shuji Shigenobu, Masahide Yamato & Hironori Kaminaka
The effects of gibberellin on the expression of symbiosis-related genes in Paris-type arbuscular mycorrhizal symbiosis in Eustoma grandiflorum
Plant Signaling &Behavior (2020) VOL. 15 NO. 9
doi.org/10.1080/15592324.2020.1784544
Haruna Fujioka, Yasukazu Okada and Masato S. Abe
Bipartite network analysis of ant-task associations reveals task groups and absence of colonial daily activity
Royal Society Open Science (2020) 8
doi.org/10.10198/rsos.201637
Tatsuya Saga, Masaki Okuno, Kevin J. Loope, Koji Tsuchida, Kako Ohbayashi, Masakazu Shimada and Yasukazu Okada
Polyandry and paternity affect disease resistance in eusocial wasps
Behavioral Ecology (2020) 31(5) 1172–1179.
doi:10.1093/beheco/araa062
Kensuke Okada, Masako Katsuki, Katsuya Kiyose, Yasukazu Okada
Older males are more competitive in male fights and more aggressive toward females in the broad-horned flour beetle Gnatocerus cornutus
Behavioral Ecology and Sociobiology (2020) 74: 36
doi.org/10.1007/s00265-020-2815-4
著者/生物情報解析システム利用/謝辞あり
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
生物情報解析システム利用/謝辞あり
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
生物情報解析システム利用/謝辞なし/利用報告書記載あり
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
著者/生物情報解析システム利用/謝辞あり
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
生物情報解析システム利用/謝辞あり
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
doi: 10.1038/s41467-018-04256-y
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
謝辞なし
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
doi: 10.1038/sdata.2019.22
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.
著者/生物情報解析システム利用/謝辞あり
Ikuo Uchiyama
Ortholog Identification and Comparative Analysis of Microbial Genomes Using MBGD and RECOG
Protein Function Prediction (2017) 1611, 147-168
doi: 10.1007/978-1-4939-7015-5_12
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
生物情報解析システム利用/謝辞あり/利用報告書記載
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
生物情報解析システム利用/謝辞なし
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.
doi: 10.1038/s41559-016-0059