Atsushi Toyoda

Scopus Author ID Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 108

Top Venues

Nature communications

Scientific reports

Communications biology

Molecular biology and evolution

This page only lists publications with an associated author ORCID identifier.

Publications

Kiyoshi Yamazaki, Yoshihiro Ohmori, Hirokazu Takahashi, Atsushi Toyoda, Yutaka Sato, Mikio Nakazono, Toru Fujiwara
Transcriptome Analysis of Rice Root Tips Reveals Auxin, Gibberellin and Ethylene Signaling Underlying Nutritropism. Plant & cell physiology 65 (4) (2024)
Kiyoshi Yamazaki, Yoshihiro Ohmori, Hirokazu Takahashi, Atsushi Toyoda, Yutaka Sato, Mikio Nakazono, Toru Fujiwara
Transcriptome analysis of rice root tips reveals auxin, gibberellin, and ethylene signalling underlying nutritropism. Plant & cell physiology (2024)
Yasuhiko Kato, Joel H Nitta, Christelle Alexa Garcia Perez, Nikko Adhitama, Pijar Religia, Atsushi Toyoda, Wataru Iwasaki, Hajime Watanabe
Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna. Scientific reports 14 (1) (2024)
Junji Konuma, Tomochika Fujisawa, Tomoaki Nishiyama, Masahiro Kasahara, Tomoko F Shibata, Masafumi Nozawa, Shuji Shigenobu, Atsushi Toyoda, Mitsuyasu Hasebe, Teiji Sota
odd-paired is involved in morphological divergence of snail-feeding beetles. Molecular biology and evolution (2024)
Junji Konuma, Tomochika Fujisawa, Tomoaki Nishiyama, Masahiro Kasahara, Tomoko F Shibata, Masafumi Nozawa, Shuji Shigenobu, Atsushi Toyoda, Mitsuyasu Hasebe, Teiji Sota
Odd-Paired is Involved in Morphological Divergence of Snail-Feeding Beetles. Molecular biology and evolution 41 (6) (2024)
Yoshihito Niimura, Bhim B Biswa, Takushi Kishida, Atsushi Toyoda, Kazumichi Fujiwara, Masato Ito, Kazushige Touhara, Miho Inoue-Murayama, Scott H Jenkins, Christopher Adenyo, Boniface B Kayang, Tsuyoshi Koide
Synchronized Expansion and Contraction of Olfactory, Vomeronasal, and Taste Receptor Gene Families in Hystricomorph Rodents. Molecular biology and evolution 41 (4) (2024)
Yasuhiko Kato, Joel H Nitta, Christelle Alexa Garcia Perez, Nikko Adhitama, Pijar Religia, Atsushi Toyoda, Wataru Iwasaki, Hajime Watanabe
Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna. Scientific reports 14 (1) (2024)
Kiyoshi Yamazaki, Yoshihiro Ohmori, Hirokazu Takahashi, Atsushi Toyoda, Yutaka Sato, Mikio Nakazono, Toru Fujiwara
Transcriptome Analysis of Rice Root Tips Reveals Auxin, Gibberellin and Ethylene Signaling Underlying Nutritropism. Plant & cell physiology 65 (4) (2024)
Yoshihito Niimura, Bhim B Biswa, Takushi Kishida, Atsushi Toyoda, Kazumichi Fujiwara, Masato Ito, Kazushige Touhara, Miho Inoue-Murayama, Scott H Jenkins, Christopher Adenyo, Boniface B Kayang, Tsuyoshi Koide
Synchronized Expansion and Contraction of Olfactory, Vomeronasal, and Taste Receptor Gene Families in Hystricomorph Rodents. Molecular biology and evolution 41 (4) (2024)
Yoshihito Niimura, Bhim B Biswa, Takushi Kishida, Atsushi Toyoda, Kazumichi Fujiwara, Masato Ito, Kazushige Touhara, Miho Inoue-Murayama, Scott H Jenkins, Christopher Adenyo, Boniface B Kayang, Tsuyoshi Koide
Synchronized Expansion and Contraction of Olfactory, Vomeronasal, and Taste Receptor Gene Families in Hystricomorph Rodents. Molecular biology and evolution 41 (4) (2024)
Kaoru Yamano, Akane Haseda, Keisuke Iwabuchi, Takayuki Osabe, Yuki Sudo, Babil Pachakkil, Keisuke Tanaka, Yutaka Suzuki, Atsushi Toyoda, Hideki Hirakawa, Yasuyuki Onodera
QTL analysis of femaleness in monoecious spinach and fine mapping of a major QTL using an updated version of chromosome-scale pseudomolecules. PloS one 19 (2) (2024)
Haruka Aoyama, Toshihiro Arae, Yui Yamashita, Atsushi Toyoda, Satoshi Naito, Naoyuki Sotta, Yukako Chiba
Impact of translational regulation on diel expression revealed by time-series ribosome profiling in Arabidopsis. The Plant journal : for cell and molecular biology (2024)
Kentaro Fukuta, Dai-Ichiro Kato, Juri Maeda, Atsuhiro Tsuruta, Hirobumi Suzuki, Yukio Nagano, Hisao Tsukamoto, Kazuki Niwa, Makoto Terauchi, Atsushi Toyoda, Asao Fujiyama, Hideki Noguchi
Genome assembly of Genji firefly (Nipponoluciola cruciata) reveals novel luciferase-like luminescent proteins without peroxisome targeting signal. DNA research : an international journal for rapid publication of reports on genes and genomes 31 (2) (2024)
Kaoru Yamano, Akane Haseda, Keisuke Iwabuchi, Takayuki Osabe, Yuki Sudo, Babil Pachakkil, Keisuke Tanaka, Yutaka Suzuki, Atsushi Toyoda, Hideki Hirakawa, Yasuyuki Onodera
QTL analysis of femaleness in monoecious spinach and fine mapping of a major QTL using an updated version of chromosome-scale pseudomolecules. PloS one 19 (2) (2024)
Junji Konuma, Tomochika Fujisawa, Tomoaki Nishiyama, Masahiro Kasahara, Tomoko F Shibata, Masafumi Nozawa, Shuji Shigenobu, Atsushi Toyoda, Mitsuyasu Hasebe, Teiji Sota
Odd-Paired is Involved in Morphological Divergence of Snail-Feeding Beetles. Molecular biology and evolution 41 (6) (2024)
Haruka Aoyama, Toshihiro Arae, Yui Yamashita, Atsushi Toyoda, Satoshi Naito, Naoyuki Sotta, Yukako Chiba
Impact of translational regulation on diel expression revealed by time-series ribosome profiling in Arabidopsis. The Plant journal : for cell and molecular biology 118 (6) (2024)
Haruka Aoyama, Toshihiro Arae, Yui Yamashita, Atsushi Toyoda, Satoshi Naito, Naoyuki Sotta, Yukako Chiba
Impact of translational regulation on diel expression revealed by time-series ribosome profiling in Arabidopsis. The Plant journal : for cell and molecular biology 118 (6) (2024)
Kaoru Yamano, Akane Haseda, Keisuke Iwabuchi, Takayuki Osabe, Yuki Sudo, Babil Pachakkil, Keisuke Tanaka, Yutaka Suzuki, Atsushi Toyoda, Hideki Hirakawa, Yasuyuki Onodera
QTL analysis of femaleness in monoecious spinach and fine mapping of a major QTL using an updated version of chromosome-scale pseudomolecules. PloS one 19 (2) (2024)
Yasuhiko Kato, Joel H Nitta, Christelle Alexa Garcia Perez, Nikko Adhitama, Pijar Religia, Atsushi Toyoda, Wataru Iwasaki, Hajime Watanabe
Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna. Scientific reports 14 (1) (2024)
Junji Konuma, Tomochika Fujisawa, Tomoaki Nishiyama, Masahiro Kasahara, Tomoko F Shibata, Masafumi Nozawa, Shuji Shigenobu, Atsushi Toyoda, Mitsuyasu Hasebe, Teiji Sota
Odd-Paired is Involved in Morphological Divergence of Snail-Feeding Beetles. Molecular biology and evolution 41 (6) (2024)
Kentaro Fukuta, Dai-Ichiro Kato, Juri Maeda, Atsuhiro Tsuruta, Hirobumi Suzuki, Yukio Nagano, Hisao Tsukamoto, Kazuki Niwa, Makoto Terauchi, Atsushi Toyoda, Asao Fujiyama, Hideki Noguchi
Genome assembly of Genji firefly (Nipponoluciola cruciata) reveals novel luciferase-like luminescent proteins without peroxisome targeting signal. DNA research : an international journal for rapid publication of reports on genes and genomes 31 (2) (2024)
Yasuhiko Kato, Joel H Nitta, Christelle Alexa Garcia Perez, Nikko Adhitama, Pijar Religia, Atsushi Toyoda, Wataru Iwasaki, Hajime Watanabe
Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna. Scientific reports 14 (1) (2024)
Junji Konuma, Tomochika Fujisawa, Tomoaki Nishiyama, Masahiro Kasahara, Tomoko F Shibata, Masafumi Nozawa, Shuji Shigenobu, Atsushi Toyoda, Mitsuyasu Hasebe, Teiji Sota
Odd-Paired is Involved in Morphological Divergence of Snail-Feeding Beetles. Molecular biology and evolution 41 (6) (2024)
Yoshihito Niimura, Bhim B Biswa, Takushi Kishida, Atsushi Toyoda, Kazumichi Fujiwara, Masato Ito, Kazushige Touhara, Miho Inoue-Murayama, Scott H Jenkins, Christopher Adenyo, Boniface B Kayang, Tsuyoshi Koide
Synchronized Expansion and Contraction of Olfactory, Vomeronasal, and Taste Receptor Gene Families in Hystricomorph Rodents. Molecular biology and evolution 41 (4) (2024)
Kiyoshi Yamazaki, Yoshihiro Ohmori, Hirokazu Takahashi, Atsushi Toyoda, Yutaka Sato, Mikio Nakazono, Toru Fujiwara
Transcriptome Analysis of Rice Root Tips Reveals Auxin, Gibberellin and Ethylene Signaling Underlying Nutritropism. Plant & cell physiology 65 (4) (2024)
Kiyoshi Yamazaki, Yoshihiro Ohmori, Hirokazu Takahashi, Atsushi Toyoda, Yutaka Sato, Mikio Nakazono, Toru Fujiwara
Transcriptome Analysis of Rice Root Tips Reveals Auxin, Gibberellin and Ethylene Signaling Underlying Nutritropism. Plant & cell physiology 65 (4) (2024)
Masaru Ito, Asako Furukohri, Kenichiro Matsuzaki, Yurika Fujita, Atsushi Toyoda, Akira Shinohara
FIGNL1 AAA+ ATPase remodels RAD51 and DMC1 filaments in pre-meiotic DNA replication and meiotic recombination. Nature communications 14 (1) (2023)
Miki Okuno, Yuta Mochimaru, Kentaro Matsuoka, Takahiro Yamabe, Luisa Matiz-Ceron, Takamichi Jogahara, Atsushi Toyoda, Asato Kuroiwa, Takehiko Itoh
Chromosomal-level assembly of Tokudaia osimensis, Tokudaia tokunoshimensis, and Tokudaia muenninki genomes. Scientific data 10 (1) (2023)
Osamu Miura, Atsushi Toyoda, Tetsuya Sakurai
Chromosome-Scale Genome Assembly of the Freshwater Snail Semisulcospira habei from the Lake Biwa Drainage System. Genome biology and evolution 15 (11) (2023)
Muran Xiao, Shinji Kondo, Masaki Nomura, Shinichiro Kato, Koutarou Nishimura, Weijia Zang, Yifan Zhang, Tomohiro Akashi, Aaron D Viny, Tsukasa Shigehiro, Tomokatsu Ikawa, Hiromi Yamazaki, Miki Fukumoto, Atsushi Tanaka, Yasutaka Hayashi, Yui Koike, Yumi Aoyama, Hiromi Ito, Hiroyoshi Nishikawa, Toshio Kitamura, Akinori Kanai, Akihiko Yokoyama, Tohru Fujiwara, Susumu Goyama, Hideki Noguchi, Stanley C Lee, Atsushi Toyoda, Kunihiko Hinohara, Omar Abdel-Wahab, Daichi Inoue
BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state. Nature communications 14 (1) (2023)
Miki Okuno, Yuta Mochimaru, Kentaro Matsuoka, Takahiro Yamabe, Luisa Matiz-Ceron, Takamichi Jogahara, Atsushi Toyoda, Asato Kuroiwa, Takehiko Itoh
Chromosomal-level assembly of Tokudaia osimensis, Tokudaia tokunoshimensis, and Tokudaia muenninki genomes. Scientific data 10 (1) (2023)
Hiroki Ayabe, Atsushi Toyoda, Akitoshi Iwamoto, Nobuhiro Tsutsumi, Shin-Ichi Arimura
Mitochondrial gene defects in Arabidopsis can broadly affect mitochondrial gene expression through copy number. Plant physiology (2023)
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. The New phytologist 237 (5) (2023)
Takahiko Kubo, Yoshiyuki Yamagata, Hiroaki Matsusaka, Atsushi Toyoda, Yutaka Sato, Toshihiro Kumamaru
MiRiQ database: a platform for in silico rice mutant screening. Plant & cell physiology (2023)
Muran Xiao, Shinji Kondo, Masaki Nomura, Shinichiro Kato, Koutarou Nishimura, Weijia Zang, Yifan Zhang, Tomohiro Akashi, Aaron D Viny, Tsukasa Shigehiro, Tomokatsu Ikawa, Hiromi Yamazaki, Miki Fukumoto, Atsushi Tanaka, Yasutaka Hayashi, Yui Koike, Yumi Aoyama, Hiromi Ito, Hiroyoshi Nishikawa, Toshio Kitamura, Akinori Kanai, Akihiko Yokoyama, Tohru Fujiwara, Susumu Goyama, Hideki Noguchi, Stanley C Lee, Atsushi Toyoda, Kunihiko Hinohara, Omar Abdel-Wahab, Daichi Inoue
BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state. Nature communications 14 (1) (2023)
Muran Xiao, Shinji Kondo, Masaki Nomura, Shinichiro Kato, Koutarou Nishimura, Weijia Zang, Yifan Zhang, Tomohiro Akashi, Aaron D Viny, Tsukasa Shigehiro, Tomokatsu Ikawa, Hiromi Yamazaki, Miki Fukumoto, Atsushi Tanaka, Yasutaka Hayashi, Yui Koike, Yumi Aoyama, Hiromi Ito, Hiroyoshi Nishikawa, Toshio Kitamura, Akinori Kanai, Akihiko Yokoyama, Tohru Fujiwara, Susumu Goyama, Hideki Noguchi, Stanley C Lee, Atsushi Toyoda, Kunihiko Hinohara, Omar Abdel-Wahab, Daichi Inoue
BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state. Nature communications 14 (1) (2023)
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. The New phytologist 237 (5) (2023)
Miki Okuno, Yuta Mochimaru, Kentaro Matsuoka, Takahiro Yamabe, Luisa Matiz-Ceron, Takamichi Jogahara, Atsushi Toyoda, Asato Kuroiwa, Takehiko Itoh
Chromosomal-level assembly of Tokudaia osimensis, Tokudaia tokunoshimensis, and Tokudaia muenninki genomes. Scientific data 10 (1) (2023)
Miki Okuno, Yuta Mochimaru, Kentaro Matsuoka, Takahiro Yamabe, Luisa Matiz-Ceron, Takamichi Jogahara, Atsushi Toyoda, Asato Kuroiwa, Takehiko Itoh
Chromosomal-level assembly of Tokudaia osimensis, Tokudaia tokunoshimensis, and Tokudaia muenninki genomes. Scientific data 10 (1) (2023)
Kim Nhung Ta, Mari W Yoshida, Takumi Tezuka, Sae Shimizu-Sato, Misuzu Nosaka-Takahashi, Atsushi Toyoda, Takamasa Suzuki, Gohta Goshima, Yutaka Sato
Control of Plant Cell Growth and Proliferation by MO25A, a Conserved Major Component of the Mammalian Sterile 20-Like Kinase Pathway. Plant & cell physiology 64 (3) (2023)
Takahiro Yamabe, Rei Kajitani, Atsushi Toyoda, Takehiko Itoh
Chromosomal-level genome assembly of the coffee bee hawk moth reveals the evolution of chromosomes and the molecular basis of distinct phenotypes. Genome biology and evolution (2023)
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. The New phytologist 237 (5) (2023)
Taku Sasaki, Kae Kato, Awie J Hosaka, Yu Fu, Atsushi Toyoda, Asao Fujiyama, Yoshiaki Tarutani, Tetsuji Kakutani
Arms race between anti-silencing and RdDM in noncoding regions of transposable elements. EMBO reports (2023)
Kohei Nagao, Yoshiki Tanaka, Rei Kajitani, Atsushi Toyoda, Takehiko Itoh, Souichirou Kubota, Yuji Goto
Bioinformatic and fine-scale chromosomal mapping reveal the nature and evolution of eliminated chromosomes in the Japanese hagfish, Eptatretus burgeri, through analysis of repetitive DNA families. PloS one 18 (8) (2023)
Mizue Anda, Shun Yamanouchi, Salvatore Cosentino, Mitsuo Sakamoto, Moriya Ohkuma, Masako Takashima, Atsushi Toyoda, Wataru Iwasaki
Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years. Nature communications 14 (1) (2023)
Muran Xiao, Shinji Kondo, Masaki Nomura, Shinichiro Kato, Koutarou Nishimura, Weijia Zang, Yifan Zhang, Tomohiro Akashi, Aaron D Viny, Tsukasa Shigehiro, Tomokatsu Ikawa, Hiromi Yamazaki, Miki Fukumoto, Atsushi Tanaka, Yasutaka Hayashi, Yui Koike, Yumi Aoyama, Hiromi Ito, Hiroyoshi Nishikawa, Toshio Kitamura, Akinori Kanai, Akihiko Yokoyama, Tohru Fujiwara, Susumu Goyama, Hideki Noguchi, Stanley C Lee, Atsushi Toyoda, Kunihiko Hinohara, Omar Abdel-Wahab, Daichi Inoue
BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state. Nature communications 14 (1) (2023)
Yawako W Kawaguchi, Yuki Tsuchikane, Keisuke Tanaka, Teruaki Taji, Yutaka Suzuki, Atsushi Toyoda, Motomi Ito, Yasuyuki Watano, Tomoaki Nishiyama, Hiroyuki Sekimoto, Takashi Tsuchimatsu
Extensive Copy Number Variation Explains Genome Size Variation in the Unicellular Zygnematophycean Alga, Closterium peracerosum-strigosum-littorale Complex. Genome biology and evolution (2023)
Hiroshi Mori, Tamotsu Kato, Hiroaki Ozawa, Mitsuo Sakamoto, Takumi Murakami, Todd D Taylor, Atsushi Toyoda, Moriya Ohkuma, Ken Kurokawa, Hiroshi Ohno
Assessment of metagenomic workflows using a newly constructed human gut microbiome mock community. DNA research : an international journal for rapid publication of reports on genes and genomes 30 (3) (2023)
Miki Okuno, Yuta Mochimaru, Kentaro Matsuoka, Takahiro Yamabe, Luisa Matiz-Ceron, Takamichi Jogahara, Atsushi Toyoda, Asato Kuroiwa, Takehiko Itoh
Chromosomal-level assembly of Tokudaia osimensis, Tokudaia tokunoshimensis, and Tokudaia muenninki genomes. Scientific data 10 (1) (2023)
Muran Xiao, Shinji Kondo, Masaki Nomura, Shinichiro Kato, Koutarou Nishimura, Weijia Zang, Yifan Zhang, Tomohiro Akashi, Aaron D Viny, Tsukasa Shigehiro, Tomokatsu Ikawa, Hiromi Yamazaki, Miki Fukumoto, Atsushi Tanaka, Yasutaka Hayashi, Yui Koike, Yumi Aoyama, Hiromi Ito, Hiroyoshi Nishikawa, Toshio Kitamura, Akinori Kanai, Akihiko Yokoyama, Tohru Fujiwara, Susumu Goyama, Hideki Noguchi, Stanley C Lee, Atsushi Toyoda, Kunihiko Hinohara, Omar Abdel-Wahab, Daichi Inoue
BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state. Nature communications 14 (1) (2023)
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. The New phytologist (2022)
Jessica Kim, Masafumi Muraoka, Hajime Okada, Atsushi Toyoda, Rieko Ajima, Yumiko Saga
The RNA helicase DDX6 controls early mouse embryogenesis by repressing aberrant inhibition of BMP signaling through miRNA-mediated gene silencing. PLoS genetics 18 (10) (2022)
Tetsuo Kon, Kentaro Fukuta, Zelin Chen, Koto Kon-Nanjo, Kota Suzuki, Masakazu Ishikawa, Hikari Tanaka, Jason W Sinclair, Hideki Noguchi, Atsushi Toyoda, Yoshihiro Omori
Single-cell transcriptomics of the goldfish retina reveals genetic divergence in the asymmetrically evolved subgenomes after allotetraploidization. Communications biology 5 (1) (2022)
Tetsuo Kon, Kentaro Fukuta, Zelin Chen, Koto Kon-Nanjo, Kota Suzuki, Masakazu Ishikawa, Hikari Tanaka, Jason W Sinclair, Hideki Noguchi, Atsushi Toyoda, Yoshihiro Omori
Single-cell transcriptomics of the goldfish retina reveals genetic divergence in the asymmetrically evolved subgenomes after allotetraploidization. Communications biology 5 (1) (2022)
Tetsuo Kon, Kentaro Fukuta, Zelin Chen, Koto Kon-Nanjo, Kota Suzuki, Masakazu Ishikawa, Hikari Tanaka, Jason W Sinclair, Hideki Noguchi, Atsushi Toyoda, Yoshihiro Omori
Single-cell transcriptomics of the goldfish retina reveals genetic divergence in the asymmetrically evolved subgenomes after allotetraploidization. Communications biology 5 (1) (2022)
Hidefumi Suzuki, Ryota Abe, Miho Shimada, Tomonori Hirose, Hiroko Hirose, Keisuke Noguchi, Yoko Ike, Nanami Yasui, Kazuki Furugori, Yuki Yamaguchi, Atsushi Toyoda, Yutaka Suzuki, Tatsuro Yamamoto, Noriko Saitoh, Shigeo Sato, Chieri Tomomori-Sato, Ronald C Conaway, Joan W Conaway, Hidehisa Takahashi
The 3' Pol II pausing at replication-dependent histone genes is regulated by Mediator through Cajal bodies' association with histone locus bodies. Nature communications 13 (1) (2022)
Shuji Shigenobu, 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, Kiyoto Maekawa
Genomic and transcriptomic analyses of the subterranean termite Reticulitermes speratus : Gene duplication facilitates social evolution. Proceedings of the National Academy of Sciences of the United States of America 119 (3) (2022)
Masaru Konishi Nobu, Ryosuke Nakai, Satoshi Tamazawa, Hiroshi Mori, Atsushi Toyoda, Akira Ijiri, Shino Suzuki, Ken Kurokawa, Yoichi Kamagata, Hideyuki Tamaki
Unique H 2 -utilizing lithotrophy in serpentinite-hosted systems. The ISME journal (2022)
Arikuni Uchimura, Hirotaka Matsumoto, Yasunari Satoh, Yohei Minakuchi, Sayaka Wakayama, Teruhiko Wakayama, Mayumi Higuchi, Masakazu Hashimoto, Ryutaro Fukumura, Atsushi Toyoda, Yoichi Gondo, Takeshi Yagi
Early embryonic mutations reveal dynamics of somatic and germ cell lineages in mice. Genome research 32 (5) (2022)
Miho Terao, Yuya Ogawa, Shuji Takada, Rei Kajitani, Miki Okuno, Yuta Mochimaru, Kentaro Matsuoka, Takehiko Itoh, Atsushi Toyoda, Tomohiro Kono, Takamichi Jogahara, Shusei Mizushima, Asato Kuroiwa
Turnover of mammal sex chromosomes in the Sry -deficient Amami spiny rat is due to male-specific upregulation of Sox9 . Proceedings of the National Academy of Sciences of the United States of America 119 (49) (2022)
Tsubasa Kawai, Kyosuke Shibata, Ryosuke Akahoshi, Shunsaku Nishiuchi, Hirokazu Takahashi, Mikio Nakazono, Takaaki Kojima, Misuzu Nosaka-Takahashi, Yutaka Sato, Atsushi Toyoda, Nonawin Lucob-Agustin, Mana Kano-Nakata, Roel R Suralta, Jonathan M Niones, Ying-Long Chen, Kadambot H M Siddique, Akira Yamauchi, Yoshiaki Inukai
WUSCHEL-related homeobox family genes in rice control lateral root primordium size. Proceedings of the National Academy of Sciences of the United States of America 119 (1) (2022)
Tetsuo Kon, Kentaro Fukuta, Zelin Chen, Koto Kon-Nanjo, Kota Suzuki, Masakazu Ishikawa, Hikari Tanaka, Jason W Sinclair, Hideki Noguchi, Atsushi Toyoda, Yoshihiro Omori
Single-cell transcriptomics of the goldfish retina reveals genetic divergence in the asymmetrically evolved subgenomes after allotetraploidization. Communications biology 5 (1) (2022)
Ahammad Kabir, Risa Ieda, Sho Hosoya, Daigaku Fujikawa, Kazufumi Atsumi, Shota Tajima, Aoi Nozawa, Takashi Koyama, Shotaro Hirase, Osamu Nakamura, Mitsutaka Kadota, Osamu Nishimura, Shigehiro Kuraku, Yasukazu Nakamura, Hisato Kobayashi, Atsushi Toyoda, Satoshi Tasumi, Kiyoshi Kikuchi
Repeated translocation of a supergene underlying rapid sex chromosome turnover in Takifugu pufferfish. Proceedings of the National Academy of Sciences of the United States of America 119 (23) (2022)
Taisei Kikuchi, Mehmet Dayi, Vicky L Hunt, Kenji Ishiwata, Atsushi Toyoda, Asuka Kounosu, Simo Sun, Yasunobu Maeda, Yoko Kondo, Belkisyole Alarcon de Noya, Oscar Noya, Somei Kojima, Toshiaki Kuramochi, Haruhiko Maruyama
Genome of the fatal tapeworm Sparganum proliferum uncovers mechanisms for cryptic life cycle and aberrant larval proliferation. Communications biology 4 (1) (2021)
Masafumi Nozawa, Yohei Minakuchi, Kazuhiro Satomura, Shu Kondo, Atsushi Toyoda, Koichiro Tamura
Shared evolutionary trajectories of three independent neo-sex chromosomes in Drosophila. Genome research 31 (11) (2021)
Narges Aghaallaei, Advaita M Dick, Erika Tsingos, Daigo Inoue, Eva Hasel, Thomas Thumberger, Atsushi Toyoda, Maria Leptin, Joachim Wittbrodt, Baubak Bajoghli
αβ/γδ T cell lineage outcome is regulated by intrathymic cell localization and environmental signals. Science advances 7 (29) (2021)
Amit Rai, Hideki Hirakawa, Ryo Nakabayashi, Shinji Kikuchi, Koki Hayashi, Megha Rai, Hiroshi Tsugawa, Taiki Nakaya, Tetsuya Mori, Hideki Nagasaki, Runa Fukushi, Yoko Kusuya, Hiroki Takahashi, Hiroshi Uchiyama, Atsushi Toyoda, Shoko Hikosaka, Eiji Goto, Takashi Hashimoto, Mami Yamazaki
Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis. Nature communications 12 (1) (2021)
Yuki Matsumoto, Hiromichi Nagayama, Hirofumi Nakaoka, Atsushi Toyoda, Tatsuhiko Goto, Tsuyoshi Koide
Combined change of behavioral traits for domestication and gene-networks in mice selectively bred for active tameness. Genes, brain, and behavior 20 (3) (2021)
Guillem Ylla, Taro Nakamura, Takehiko Itoh, Rei Kajitani, Atsushi Toyoda, Sayuri Tomonari, Tetsuya Bando, Yoshiyasu Ishimaru, Takahito Watanabe, Masao Fuketa, Yuji Matsuoka, Austen A Barnett, Sumihare Noji, Taro Mito, Cassandra G Extavour
Insights into the genomic evolution of insects from cricket genomes. Communications biology 4 (1) (2021)
Mitsuo Sakamoto, Nao Ikeyama, Atsushi Toyoda, Takumi Murakami, Hiroshi Mori, Sho Morohoshi, Tadao Kunihiro, Takao Iino, Moriya Ohkuma
Coprobacter secundus subsp. similis subsp. nov. and Solibaculum mannosilyticum gen. nov., sp. nov., isolated from human feces. Microbiology and immunology 65 (6) (2021)
Kenta Shirasawa, Shunichi Kosugi, Kazuhiro Sasaki, Andrea Ghelfi, Koei Okazaki, Atsushi Toyoda, Hideki Hirakawa, Sachiko N Isobe
Genome features of common vetch (Vicia sativa) in natural habitats. Plant direct 5 (10) (2021)
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 12 (1) (2021)
Michiharu Nakano, Hideki Hirakawa, Eigo Fukai, Atsushi Toyoda, Rei Kajitani, Yohei Minakuchi, Takehiko Itoh, Yohei Higuchi, Toshiaki Kozuka, Hidemasa Bono, Kenta Shirasawa, Ippei Shiraiwa, Katsuhiko Sumitomo, Tamotsu Hisamatsu, Michio Shibata, Sachiko N Isobe, Kenji Taniguchi, Makoto Kusaba
A chromosome-level genome sequence of Chrysanthemum seticuspe, a model species for hexaploid cultivated chrysanthemum. Communications biology 4 (1) (2021)
Kayoko Yamamoto, Takashi Hamaji, Hiroko Kawai-Toyooka, Ryo Matsuzaki, Fumio Takahashi, Yoshiki Nishimura, Masanobu Kawachi, Hideki Noguchi, Yohei Minakuchi, James G Umen, Atsushi Toyoda, Hisayoshi Nozaki
Three genomes in the algal genus Volvox reveal the fate of a haploid sex-determining region after a transition to homothallism. Proceedings of the National Academy of Sciences of the United States of America 118 (21) (2021)
Yukako Katsura, Toshimichi Ikemura, Rei Kajitani, Atsushi Toyoda, Takehiko Itoh, Mitsuaki Ogata, Ikuo Miura, Kennosuke Wada, Yoshiko Wada, Yoko Satta
Comparative genomics of Glandirana rugosa using unsupervised AI reveals a high CG frequency. Life science alliance 4 (5) (2021)
Keiichiro Koiwai, Takashi Koyama, Soichiro Tsuda, Atsushi Toyoda, Kiyoshi Kikuchi, Hiroaki Suzuki, Ryuji Kawano
Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process. eLife 10 (2021)
Taro Maeda, Shunichi Takahashi, Takao Yoshida, Shigeru Shimamura, Yoshihiro Takaki, Yukiko Nagai, Atsushi Toyoda, Yutaka Suzuki, Asuka Arimoto, Hisaki Ishii, Noriyuki 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 10 (2021)
Mariko Takeuchi, Hirokazu Kuwahara, Takumi Murakami, Kazuki Takahashi, Rei Kajitani, Atsushi Toyoda, Takehiko Itoh, Moriya Ohkuma, Yuichi Hongoh
Parallel reductive genome evolution in Desulfovibrio ectosymbionts independently acquired by Trichonympha protists in the termite gut. The ISME journal 14 (9) (2020)
Hideo Matsumura, Min-Chien Hsiao, Ya-Ping Lin, Atsushi Toyoda, Naoki Taniai, Kazuhiko Tarora, Naoya Urasaki, Shashi S Anand, Narinder P S Dhillon, Roland Schafleitner, Cheng-Ruei Lee
Reply to Renner: Meticulous investigation, not sequencing effort, leads to robust conclusion. Proceedings of the National Academy of Sciences of the United States of America 117 (40) (2020)
Hideo Matsumura, Min-Chien Hsiao, Ya-Ping Lin, Atsushi Toyoda, Naoki Taniai, Kazuhiko Tarora, Naoya Urasaki, Shashi S Anand, Narinder P S Dhillon, Roland Schafleitner, Cheng-Ruei Lee
Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of nonclassic domestication. Proceedings of the National Academy of Sciences of the United States of America 117 (25) (2020)
Omaya Dudin, Andrej Ondracka, Xavier Grau-Bové, Arthur Ab Haraldsen, Atsushi Toyoda, Hiroshi Suga, Jon Bråte, Iñaki Ruiz-Trillo
Correction: A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization. eLife 9 (2020)
Taiko Kim To, Yuichiro Nishizawa, Soichi Inagaki, Yoshiaki Tarutani, Sayaka Tominaga, Atsushi Toyoda, Asao Fujiyama, Frederic Berger, Tetsuji Kakutani
RNA interference-independent reprogramming of DNA methylation in Arabidopsis. Nature plants 6 (12) (2020)
Yasunari Satoh, Jun-Ichi Asakawa, Mayumi Nishimura, Tony Kuo, Norio Shinkai, Harry M Cullings, Yohei Minakuchi, Jun Sese, Atsushi Toyoda, Yoshiya Shimada, Nori Nakamura, Arikuni Uchimura
Characteristics of induced mutations in offspring derived from irradiated mouse spermatogonia and mature oocytes. Scientific reports 10 (1) (2020)
Takashi Gakuhari, Shigeki Nakagome, Simon Rasmussen, Morten E Allentoft, Takehiro Sato, Thorfinn Korneliussen, Blánaid Ní Chuinneagáin, Hiromi Matsumae, Kae Koganebuchi, Ryan Schmidt, Souichiro Mizushima, Osamu Kondo, Nobuo Shigehara, Minoru Yoneda, Ryosuke Kimura, Hajime Ishida, Tadayuki Masuyama, Yasuhiro Yamada, Atsushi Tajima, Hiroki Shibata, Atsushi Toyoda, Toshiyuki Tsurumoto, Tetsuaki Wakebe, Hiromi Shitara, Tsunehiko Hanihara, Eske Willerslev, Martin Sikora, Hiroki Oota
Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations. Communications biology 3 (1) (2020)
Songkui Cui, Tomoya Kubota, Tomoaki Nishiyama, Juliane Karine Ishida, Shuji Shigenobu, Tomoko F Shibata, Atsushi Toyoda, Mitsuyasu Hasebe, Ken Shirasu, Satoko Yoshida
Ethylene signaling mediates host invasion by parasitic plants. Science advances 6 (44) (2020)
Taro Tsujimura, Osamu Takase, Masahiro Yoshikawa, Etsuko Sano, Matsuhiko Hayashi, Kazuto Hoshi, Tsuyoshi Takato, Atsushi Toyoda, Hideyuki Okano, Keiichi Hishikawa
Controlling gene activation by enhancers through a drug-inducible topological insulator. eLife 9 (2020)
Tomohiko Kazama, Miki Okuno, Yuta Watari, Shungo Yanase, Chie Koizuka, Yu Tsuruta, Hajime Sugaya, Atsushi Toyoda, Takehiko Itoh, Nobuhiro Tsutsumi, Kinya Toriyama, Nobuya Koizuka, Shin-Ichi Arimura
Curing cytoplasmic male sterility via TALEN-mediated mitochondrial genome editing. Nature plants 5 (7) (2019)
Satoshi Hiraoka, Yusuke Okazaki, Mizue Anda, Atsushi Toyoda, Shin-Ichi Nakano, Wataru Iwasaki
Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community. Nature communications 10 (1) (2019)
Rei Kajitani, Dai Yoshimura, Miki Okuno, Yohei Minakuchi, Hiroshi Kagoshima, Asao Fujiyama, Kaoru Kubokawa, Yuji Kohara, Atsushi Toyoda, Takehiko Itoh
Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions. Nature communications 10 (1) (2019)
Asano Ishikawa, Naoki Kabeya, Koki Ikeya, Ryo Kakioka, Jennifer N Cech, Naoki Osada, Miguel C Leal, Jun Inoue, Manabu Kume, Atsushi Toyoda, Ayumi Tezuka, Atsushi J Nagano, Yo Y Yamasaki, Yuto Suzuki, Tomoyuki Kokita, Hiroshi Takahashi, Kay Lucek, David Alexander Marques, Yusuke Takehana, Kiyoshi Naruse, Seiichi Mori, Oscar Monroig, S Nemiah Ladd, Carsten J Schubert, Blake Matthews, Catherine L Peichel, Ole Seehausen, Goro Yoshizaki, Jun Kitano
A key metabolic gene for recurrent freshwater colonization and radiation in fishes. Science (New York, N.Y.) 364 (6443) (2019)
Yuta Kobayashi, Yosui Nojima, Takuma Sakamoto, Kikuo Iwabuchi, Takeru Nakazato, Hidemasa Bono, Atsushi Toyoda, Asao Fujiyama, Michael R Kanost, Hiroko Tabunoki
Comparative analysis of seven types of superoxide dismutases for their ability to respond to oxidative stress in Bombyx mori. Scientific reports 9 (1) (2019)
Omaya Dudin, Andrej Ondracka, Xavier Grau-Bové, Arthur Ab Haraldsen, Atsushi Toyoda, Hiroshi Suga, Jon Bråte, Iñaki Ruiz-Trillo
A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization. eLife 8 (2019)
Zelin Chen, Yoshihiro Omori, Sergey Koren, Takuya Shirokiya, Takuo Kuroda, Atsushi Miyamoto, Hironori Wada, Asao Fujiyama, Atsushi Toyoda, Suiyuan Zhang, Tyra G Wolfsberg, Koichi Kawakami, Adam M Phillippy, null null, May Christine V Malicdan, Jason W Sinclair
De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication. Science advances 5 (6) (2019)
Hirotsugu Shiroma, Sayaka Mizutani, Hirotsugu Shiroma, Satoshi Shiba, Takeshi Nakajima, Taku Sakamoto, Hikaru Watanabe, Keigo Masuda, Yuichiro Nishimoto, Masaru Kubo, Fumie Hosoda, Hirofumi Rokutan, Minori Matsumoto, Hiroyuki Takamaru, Masayoshi Yamada, Takahisa Matsuda, Motoki Iwasaki, Taiki Yamaji, Tatsuo Yachida, Tomoyoshi Soga, Ken Kurokawa, Atsushi Toyoda, Yoshitoshi Ogura, Tetsuya Hayashi, Masanori Hatakeyama, Hitoshi Nakagama, Yutaka Saito, Shinji Fukuda, Tatsuhiro Shibata, Takuji Yamada
Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer. Nature medicine 25 (6) (2019)
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, Teruyuki Niimi
Repeated inversions within a pannier intron drive diversification of intraspecific colour patterns of ladybird beetles. Nature communications 9 (1) (2018)
Kazue Nakanaga, Yoshitoshi Ogura, Atsushi Toyoda, Mitsunori Yoshida, Hanako Fukano, Nagatoshi Fujiwara, Yuji Miyamoto, Noboru Nakata, Yuko Kazumi, Shinji Maeda, Tadasuke Ooka, Masamichi Goto, Kazunari Tanigawa, Satoshi Mitarai, Koichi Suzuki, Norihisa Ishii, Manabu Ato, Tetsuya Hayashi, Yoshihiko Hoshino
Naturally occurring a loss of a giant plasmid from Mycobacterium ulcerans subsp. shinshuense makes it non-pathogenic. Scientific reports 8 (1) (2018)
Hugh McColl, Fernando Racimo, Lasse Vinner, Fabrice Demeter, Takashi Gakuhari, J Víctor Moreno-Mayar, George van Driem, Uffe Gram Wilken, Andaine Seguin-Orlando, Constanza de la Fuente Castro, Sally Wasef, Rasmi Shoocongdej, Viengkeo Souksavatdy, Thongsa Sayavongkhamdy, Mohd Mokhtar Saidin, Morten E Allentoft, Takehiro Sato, Anna-Sapfo Malaspinas, Farhang A Aghakhanian, Thorfinn Sand Korneliussen, Ana Prohaska, Ashot Margaryan, Peter de Barros Damgaard, Supannee Kaewsutthi, Patcharee Lertrit, Thi Mai Huong Nguyen, Hsiao-Chun Hung, Thi Minh Tran, Huu Nghia Truong, Giang Hai Nguyen, Shaiful Shahidan, Ketut Wiradnyana, Hiromi Matsumae, Nobuo Shigehara, Minoru Yoneda, Hajime Ishida, Tadayuki Masuyama, Yasuhiro Yamada, Atsushi Tajima, Hiroki Shibata, Atsushi Toyoda, Tsunehiko Hanihara, Shigeki Nakagome, Thibaut Deviese, Anne-Marie Bacon, Philippe Duringer, Jean-Luc Ponche, Laura Shackelford, Elise Patole-Edoumba, Anh Tuan Nguyen, Bérénice Bellina-Pryce, Jean-Christophe Galipaud, Rebecca Kinaston, Hallie Buckley, Christophe Pottier, Simon Rasmussen, Thomas Higham, Robert A Foley, Marta Mirazón Lahr, Ludovic Orlando, Martin Sikora, Maude E Phipps, Hiroki Oota, Charles Higham, David M Lambert, Eske Willerslev
The prehistoric peopling of Southeast Asia. Science (New York, N.Y.) 361 (6397) (2018)
Takashi Hamaji, Hiroko Kawai-Toyooka, Haruka Uchimura, Masahiro Suzuki, Hideki Noguchi, Yohei Minakuchi, Atsushi Toyoda, Asao Fujiyama, Shin-Ya Miyagishima, James G Umen, Hisayoshi Nozaki
Anisogamy evolved with a reduced sex-determining region in volvocine green algae. Communications biology 1 (2018)
Tomoyo Ujisawa, Akane Ohta, Tatsuya Ii, Yohei Minakuchi, Atsushi Toyoda, Miki Ii, Atsushi Kuhara
Endoribonuclease ENDU-2 regulates multiple traits including cold tolerance via cell autonomous and nonautonomous controls in Caenorhabditis elegans. Proceedings of the National Academy of Sciences of the United States of America 115 (35) (2018)
Stefan Reuscher, Tomoyuki Furuta, Kanako Bessho-Uehara, Michele Cosi, Kshirod K Jena, Atsushi Toyoda, Asao Fujiyama, Nori Kurata, Motoyuki Ashikari
Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species. Communications biology 1 (2018)

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Atsushi Toyoda