Publications by SQC Users
SQC Publication Archives
(last update 2024.4)
*SQC members are underlined.
SQC members in Author
Kei Kudo, Takehiro Nishimura, Miho Izumikawa, Ikuko Kozone, Junko Hashimoto, Manabu Fujie, Hikaru Suenaga, Haruo Ikeda, Nori Satoh & Kazuo Shin-ya
Capability of a large bacterial artificial chromosome clone harboring multiple biosynthetic gene clusters for the production of diverse compounds
The Journal of Antibiotics (2024).
Published: 04 March 2024
https://doi.org/10.1038/s41429-024-00711-9
Taiga Uchida, Yuki Yoshioka, Yu Yoshida, Manabu Fujie, Ayuta Yamaki, Akira Sasaki, Koji Inoue, Chuya Shinzato
Genomic and transcriptomic analyses illuminate the molecular basis of the unique lifestyle of a tubeworm, Lamellibrachia satsuma
DNA Research, Volume 30, Issue 4, August 2023, dsad014,
Published: 26 June 2023
https://doi.org/10.1093/dnares/dsad014
Tri Kustono Adi, Manabu Fujie, Nori Satoh, Tatsuya Ueki
The acidic amino acid-rich C-terminal domain of VanabinX enhances reductase activity, attaining 1.3- to 1.7-fold vanadium reduction
Biochemistry and Biophysics Reports, 32, 101349 (2022)
Available online: 16 September 2022
https://doi.org/10.1016/j.bbrep.2022.101349
Takeshi Takeuchi, Yoshihiko Suzuki, Shugo Watabe, Kiyohito Nagai, Tetsuji Masaoka, Manabu Fujie, Mayumi Kawamitsu, Noriyuki Satoh, Eugene W. Myers
A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster
DNA Research, Volume 29, Issue 6, December 2022, dsac035,
Published:10 November 2022
https://doi.org/10.1093/dnares/dsac035
Kojin Tsuchiya, Yuna Zayasu, Yuichi Nakajima, Nana Arakaki, Go Suzuki, Noriyuki Satoh, Chuya Shinzato
Genomic analysis of a reef-building coral, Acropora digitifera, reveals complex population structure and a migration network in the Nansei Islands, Japan
Molecular Biology, Volume31, Issue20 October 2022, Pages 5270-5284
Published: 09 September 2022
https://doi.org/10.1111/mec.16665
Atina Rizkiya Choirunnisa, Kuga Arima, Yo Abe, Noritaka Kagaya, Kei Kudo, Hikaru Suenaga, Junko Hashimoto, Manabu Fujie, Noriyuki Satoh, Kazuo Shin-ya, Kenichi Matsuda and Toshiyuki Wakimoto
New azodyrecins identified by a genome mining-directed reactivity-based screening
Beilstein J. Org. Chem. 2022, 18, 1017–1025.
Published:10 Aug 2022
https://doi.org/10.3762/bjoc.18.102
Kojin Tsuchiya, Yuna Zayasu, Yuichi Nakajima, Nana Arakaki, Go Suzuki, Nori Satoh, Chuya Shinzato
Kojin Tsuchiya, Yuna Zayasu, Yuichi Nakajima ,Nana Arakaki ,Go Suzuki, Nori Satoh, Chuya Shinzato
Molecular Ecology
Accepted: 08 Aug 2022
https://doi.org/10.22541/au.163935025.51395391/v1
Konstantin Khalturin, Natalia Shunatova, Sergei Shchenkov, Yasunori Sasakura, Mayumi Kawamitsu, Noriyuki Satoh
Polyzoa is back: The effect of complete gene sets on the placement of Ectoprocta and Entoprocta
Science Advances
Published:July 01, 2022
https://doi.org/10.1126/sciadv.abo4400
Yasuda N, Inoue J, Hall MR, Nair MR, Adjeroud M, Fortes MD, Nishida M, Tuivavalagi N, Ravago-Gotanco R, Forsman ZH, Soliman T, Koyanagi R, Hisata K, Motti CA and Satoh N
Two Hidden mtDNA-Clades of Crown-of-Thorns Starfish in the Pacific Ocean
Front. Mar. Sci. 9:831240
Published:27 April 2022
https://doi.org/10.3389/fmars.2022.831240
Kyosuke Yamamoto, Yasuko Yoneda, Ayaka Makino, Yasuhiro Tanaka, Xian-Ying Meng, Junko Hashimoto, Kazuo Shin-ya, Nori Satoh, Manabu Fujie, Tadashi Toyama, Kazuhiro Mori, Michihiko Ike, Masaaki Morikawa, Yoichi Kamagata, and Hideyuki Tamaki
Complete Genome Sequence of Luteitalea sp. Strain TBR-22
Microbiology Resource Announcements
Published:17 February 2022
https://doi.org/10.1128/mra.00455-21
Kyosuke Yamamoto, Yasuko Yoneda, Ayaka Makino, Yasuhiro Tanaka, Xian-Ying Meng, Junko Hashimoto, Kazuo Shin-ya, Nori Satoh, Manabu Fujie, Tadashi Toyama, Kazuhiro Mori, Michihiko Ike, Masaaki Morikawa, Yoichi Kamagata, and Hideyuki Tamaki
Draft genome sequence of Bryobacteraceae strain F-183
Microbiology Resource Announcements
Published: 13 January 2022
https://doi.org/10.1128/mra.00453-21
Kojin Tsuchiya, Yuna Zayasu, Yuichi Nakajima, Nana Arakaki, Go Suzuki, Nori Satoh, Chuya Shinzato
Genomic analysis of a reef-building coral, Acropora digitifera, reveals complex population structure and a migration network in the Nansei Islands, Japan
Authorea
Published: December 12, 2021
https://doi.org/10.22541/au.163935025.51395391/v1
Ken Maeda, Chuya Shinzato, Ryo Koyanagi, Taiga Kunishima, Hirozumi Kobayashi, Noriyuki Satoh, Herminie P. Palla
Two new species of Rhinogobius (Gobiiformes: Oxudercidae) from Palawan, Philippines, with their phylogenetic placement
Zootaxa 5068(1): 81-98
Published: 15 November 2021
https://doi.org/10.11646/zootaxa.5068.1.3
Ken Maeda, Hirozumi Kobayashi, Herminie P. Palla, Chuya Shinzato, Ryo Koyanagi, Javier Montenegro, Atsushi J. Nagano, Toshifumi Saeki, Taiga Kunishima, Takahiko Mukai, Katsunori Tachihara, Vincent Laudet, Noriyuki Satoh, and Kazunori Yamahira
Do colour-morphs of an amphidromous goby represent different species? Taxonomy of Lentipes (Gobiiformes) from Japan and Palawan, Philippines, with phylogenomic approaches
Systematics and Biodiversity
Published: 4th Oct 2021
https://doi.org/10.1080/14772000.2021.1971792
Yuna Zayasu, Takeshi Takeuchi, Tomofumi Nagata, Megumi Kanai, Manabu Fujie, Mayumi Kawamitsu, Wakana Chinen, Chuya Shinzato, Noriyuki Satoh
Genome-wide SNP genotyping reveals hidden population structure of an acroporid species at a subtropical coral island: Implications for coral restoration
Aquatic Conservation
Published: June 21, 2021
https://doi.org/10.1002/aqc.3626
Anzhelika Koldaeva, Cary Zhang, Yu-Pei Huang, Janine K Reinert, Seiya Mizuno, Fumihiro Sugiyama, Satoru Takahashi, Taha Soliman, Hiroaki Matsunami and Izumi Fukunaga
Generation and characterisation of a cell-type specific, inducible Cre-driver line to study olfactory processing
Generation and characterisation of a cell-type specific, inducible Cre-driver line to study olfactory processing
Published: June 7, 2021
https://doi.org/10.1523/JNEUROSCI.3076-20.2021
Takeshi Takeuchi, Manabu Fujie, Ryo Koyanagi, Laurent Plasseraud, Isabelle Ziegler-Devin, Nicolas Brosse, Cédric Broussard, Noriyuki Satoh and Frédéric Marin
The ‘Shellome’ of the Crocus Clam Tridacna crocea Emphasizes Essential Components of Mollusk Shell Biomineralization
Front. Genet. 12:674539. doi: 10.3389/fgene.2021.674539
Published: 08 June 2021
https://doi.org//10.3389/fgene.2021.674539
Yasuko Yoneda, Kyosuke Yamamoto, Ayaka Makino, Yasuhiro Tanaka, Xian-Ying Meng, Junko Hashimoto, Kazuo Shin-ya, Noriyuki Satoh, Manabu Fujie, Tadashi Toyama, Kazuhiro Mori, Michihiko Ike, Masaaki Morikawa, Yoichi Kamagata, Hideyuki Tamaki
Novel Plant-Associated Acidobacteria Promotes Growth of Common Floating Aquatic Plants, Duckweeds
Microorganisms 2021, 9(6), 1133;
Published:24 May 2021
https://doi.org/10.3390/microorganisms9061133
Shinya Okubo, Eri Ena, Akifumi Okuda, Ikuko Kozone, Junko Hashimoto, Yoshie Nishitsuji, Manabu Fujie, Noriyuki Satoh, Haruo Ikeda & Kazuo Shin-ya
Identification of functional cytochrome P450 and ferredoxin from Streptomyces sp. EAS-AB2608 by transcriptional analysis and their heterologous expression
Applied Microbiology and Biotechnology
Published:04 May 2021
https://doi.org/10.1007/s00253-021-11304-z
Yutaka Satou, Atsuko Sato, Hitoyoshi Yasuo, Yukie Mihirogi, John Bishop, Manabu Fujie, Mayumi Kawamitsu, Kanako Hisata, and Noriyuki Satoh
Chromosomal inversion polymorphisms in two sympatric ascidian lineages
Genome Biology and Evolution, evab068
Published:02 April 2021
https://doi.org/10.1093/gbe/evab068
Noriyuki Satoh, Koji Kinjo, Kohei Shintaku, Daisuke Kezuka, Hiroo Ishimori, Atsushi Yokokura, Kazutaka Hagiwara, Kanako Hisata, Mayumi Kawamitsu, Koji Koizumi, Chuya Shinzato, Yuna Zayasu
Color morphs of the coral, Acropora tenuis, show different responses to environmental stress and different expression profiles of fluorescent-protein genes
G3 Genes|Genomes|Genetics, jkab018
Published:23 January 2021
https://doi.org/10.1093/g3journal/jkab018
Ran Zhao, Takeshi Takeuchi, Ryo Koyanagi, Alejandro Villar-Briones, Lixy Yamada, Hitoshi Sawada, Akito Ishikawa, Shunsuke Iwanaga, Kiyohito Nagai, Yuqi Che, Noriyuki Satoh & Kazuyoshi Endo
Phylogenetic comparisons reveal mosaic histories of larval and adult shell matrix protein deployment in pteriomorph bivalves
Scientific Reports
Published: 17 December 2020
https://doi.org/10.1038/s41598-020-79330-x
Anna Prokhorova, Mami Kainuma, Rie Hiyane, Susan Boerner, Igor Goryanin
Concurrent treatment of raw and aerated swine wastewater using an electrotrophic denitrification system
Bioresource Technology
Published: 2 December 2020
https://doi.org/10.1016/j.biortech.2020.124508
Toshihiko Nogawa, Atsutaka Terai, Keita Amagai, Junko Hashimoto, Yushi Futamura, Akiko Okano, Manabu Fujie, Noriyuki Satoh, Haruo Ikeda, Kazuo Shin-ya, Hiroyuki Osada, Shunji Takahashi
Heterologous expression of the biosynthetic gene cluster for verticilactam and identification of new analogues
Journal of Natural Products
Published: 20 November 2020
https://doi.org/10.1021/acs.jnatprod.0c00755
Yuki Yoshioka, Hiroshi Yamashita, Go Suzuki, Yuna Zayasu, Ipputa Tada, Miyuki Kanda, Noriyuki Satoh, Eiichi Shoguchi, Chuya Shinzato
Whole-genome transcriptome analyses of native symbionts reveal host coral genomic novelties for establishing coral-algae symbioses
Genome Biology and Evolution, evaa240
Published: 13 November 2020
https://doi.org/10.1093/gbe/evaa240
Chuya Shinzato, Konstantin Khalturin, Jun Inoue, Yuna Zayasu, Miyuki Kanda, Mayumi Kawamitsu, Yuki Yoshioka, Hiroshi Yamashita, Go Suzuki, Noriyuki Satoh
Eighteen coral genomes reveal the evolutionary origin of Acropora strategies to accommodate environmental changes
Molecular Biology and Evolution
Published: 02 September 2020
https://doi.org/10.1093/molbev/msaa216
Koki Nishitsuji, Asuka Arimoto, Yoshitaka Yonashiro, Kanako Hisata, Manabu Fujie, Mayumi Kawamitsu, Eiichi Shoguchi, Noriyuki Satoh
Comparative genomics of four strains of the edible brown alga, Cladosiphon okamuranus
BMC Genomics
Published: 26 June 2020
https://doi.org/10.1186/s12864-020-06792-8
Akito Ishikawa, Keisuke Shimizu, Yukinobu Isowa, Takeshi Takeuchi, Ran Zhao, Keiji Kito, Manabu Fujie, Noriyuki Satoh, and Kazuyoshi Endo
Functional shell matrix proteins tentatively identified by asymmetric snail shell morphology
Scientific Reports
Published: 17 June 2020
https://doi.org/10.1038/s41598-020-66021-w
Fabienne Ziadi-Künzli, Taha Soliman, Hideyuki Imai, Momoko Sakurai, Ken Maeda, Katsunori Tachihara
Re-evaluation of deep-sea dogfishes (genus Squalus) in Japan using phylogenetic inference
Deep-Sea Research Part I: Oceanographic Research Papers.
Published: June 2020
https://doi.org/10.1016/j.dsr.2020.103261
Kazuo Shin-ya, Takuya Hashimoto, Ikuko Kozone, Junko Hashimoto, Hikaru Suenaga, Manabu Fujie, Noriyuki Sato, and Haruo Ikeda
Identification, cloning and heterologous expression of biosynthetic gene cluster for desertomycin
The Journal of Antibiotics
Published: 26 May 2020
https://doi.org/10.1038/s41429-020-0319-0
Takashi Miyake, Natsuki Aihara, Ken Maeda, Chuya Shinzato, Ryo Koyanagi, Hirozumi Kobayashi, Kazunori Yamahira
Bloodmeal host identification with inferences to feeding habits of a fish-fed mosquito, Aedes baisasi
Scientific Reports 9: 4002 (2019)
Published: 8 March 2019
https://doi.org/10.1038/s41598-019-40509-6
Kazuo Shin-ya, Takuya Hashitomo, Ikuko Kozone, Junko Hashimoto, Reiko Ueoka, Noritaka Kagaya, Manabu Fujie, Noriyuki Sato, Haruo Ikeda
Novel macrolactam compound produced by heterologous expression of a large cryptic biosynthetic gene cluster of Streptomyces rochei IFO12908
Journal of Antibiotics
Published: 18 Dec 2019
https://doi.org/10.1038/s41429-019-0265-x
Takeshi Takeuchi, Tetsuji Masaoka, Hideo Aoki, Ryo Koyanagi, Manabu Fujie, Noriyuki Satoh
Divergent northern and southern populations and demographic history of the pearl oyster in the western Pacific revealed with genomic SNPs
Evolutionary Applications
Published: 13 December 2019
https://doi.org/10.1111/eva.12905
Nozomi Hanahara, Takuo Higashiji, Chuya Shinzato, Ryo Koyanagi, Ken Maeda
First record of Larsonella pumilus (Teleostei: Gobiidae) from Japan, with phylogenetic placement of the genus Larsonella
Zootaxa
Published: 11 Nov 2019
https://doi.org/10.11646/zootaxa.4695.4.4
Yutaka Satou, Ryohei Nakmura, Yu Deli, Reiko Yoshida, Mayuko Hamada, Manabu Fujie, Kanako Hisata, Hiroyuki Takeda, and Noriyuki Satoh
A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona
Genome Biol. Evol. In Press.
Published: 22 October 2019
https://doi.org/10.1093/gbe/evz228
Ogawa T, Oda-Ueda N, Hisata K, Nakamura H, Chijiwa T, Hattori S, Isomoto A, Yugeta H, Yamasaki S, Fukumaki Y, Ohno M, Satoh N, Shibata H
Alternative mRNA Splicing in Three Venom Families Underlying a Possible Production of Divergent Venom Proteins of the Habu Snake, Protobothrops flavoviridis.
Toxins (Basel). 2019 Oct 9;11(10). pii: E581
Published online: 9 Oct 2019
https://doi.org/10.3390/toxins11100581
Lu TM, Kanda M, Furuya H, Satoh N.
Dicyemid Mesozoans: a unique parasitic lifestyle and a reduced genome.
Genome biology and evolution. 2019 Aug;11(8):2232-43.
Published: 26 July 2019
https://doi.org/10.1093/gbe/evz157
Hosam E.Elsaieda, Taha Soliman, Hany T .Abu-Taleb, Hiroki Goto, and Holger Jenke-Kodam.
Phylogenetic characterization of eukaryotic and prokaryotic gut flora of Nile tilapia, Oreochromis niloticus, along niches of Lake Nasser, Egypt, based on rRNA gene high-throughput sequences
Ecological Genetics and Genomics. Volume 11
Published: May 2019
https://doi.org/10.1016/j.egg.2019.100037
Konstantin Khalturin, Chuya Shinzato, Maria Khalturina, Mayuko Hamada, Manabu Fujie, Ryo Koyanagi, Miyuki Kanda, Hiroki Goto, Friederike Anton-Erxleben, Masaya Toyokawa, Sho Toshino, and Noriyuki Satoh
Medusozoan genomes inform the evolution of the jellyfish body plan
Nature Ecology & Evolution volume 3, pages 811–822 (2019)
Published: 15 April 2019
https://doi.org/10.1038/s41559-019-0853-y
Arimoto A, Nishitsuji K, Higa Y, Arakaki N, Hisata K, Shinzato C, Satoh N, Shoguchi E.
A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants.
DNA Research. 2019 Apr 1;26(2):183-92
Published: 28 March 2019
https://doi.org/10.1093/dnares/dsz002
Nishitsuji, K., Arimoto, A., Higa, Y., Mekaru, M., Kawamitsu, M., Satoh, N., and Shoguchi, E.
Draft genome of the brown alga, Nemacystus decipiens, Onna-1 strain: Fusion of genes involved in the sulfated fucan biosynthesis pathway
Scientific Reports, 9: 4607, 2019
Published: 14 March 2019
https://doi.org/10.1038/s41598-019-40955-2
Iwasaka H, Koyanagi R, Satoh R, Nagano A, Watanabe K, Hisata K, Satoh N, Aki T.
A Possible Trifunctional β-Carotene Synthase Gene Identified in the Draft Genome of Aurantiochytrium sp. Strain KH105.
Genes 2018, 9(4), 200
Published: 9 April 2018
https://doi.org/10.3390/genes9040200
Shinzato C, Zayasu Y, Kanda M, Kawamitsu M, Satoh N, Yamashita H and Suzuki G
Using seawater to document coral-zoothanthella diversity: A new approach to coral reef monitoring using environmental DNA.
Front. Mar. Sci.
Published: 20 February 2018
https://doi.org/10.3389/fmars.2018.00028
Nakano H, Miyazawa H, Maeno A, Shiroishi T, Kakui K, Koyanagi R, Kanda M, Satoh N, Omori A, Kohtsuka H.
A new species of Xenoturbella from the western Pacific Ocean and the evolution of Xenoturbella.
BMC Evol Biol. 2017 Dec 18;17(1):245.
Published: 18 December 2017
https://doi.org/10.1186/s12862-017-1080-2
Luo YJ, Kanda M, Koyanagi R, Hisata K, Akiyama T, Sakamoto H, Sakamoto T, Satoh N.
Nemertean and phoronid genomes reveal lophotrochozoan evolution and the origin of bilaterian heads.
Nat Ecol Evol. 2017
Published: 04 December 2017
https://doi.org/10.1038/s41559-017-0389-y
Maeda K, Saeki T, Shinzato C, Koyanagi R, and Satoh N.
Review of Schismatogobius (Gobiidae) from Japan, with the description of a new species.
Ichtyol. Res. (2017)
Published: 25 July 2017
https://doi.org/10.1007/s10228-017-0593-4
Hasan Z, Koizumi S, Sasaki D, Yamada H, Arakaki N, Fujihara Y, Okitsu S, Shirahata H, and Ishikawa H.
JunB is essential for IL-23-dependent pathogenicity of Th17 cells.
Nature Communications, 8: 15628 (2017)
Published: 30 May 2017
https://doi.org/10.1038/ncomms15628
Lu TM, Kanda M, Satoh N, and Furuya H.
The phylogenetic position of dicyemid mesozoans offers insights into spiralian evolution.
Zoological Letters 3: 6 (2017)
Published: 29 May 2017
https://doi.org/10.1186/s40851-017-0068-5
Hall MR, Kocot KM, Baughman KW, Fernandez-Valverde SL, Gauthier MEA, Hatleberg WL, Krishnan A, McDougall C, Motti CA, Shoguchi E, Wang T, Xiang X, Zhao M, Bose U, Shinzato C, Hisata K, Fujie M, Kanda M, Cummins SF, Satoh N, Degnan SM, and Degnan BM.
The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest.
Nature (2017)
Published: 13 April 2017
https://doi.org/10.1038/nature22033
Campbell MA, Nielsen JG, Sado T, Shinzato C, Kanda M, Satoh TP, and Miya M.
Evolutionary affinities of the unfathomable Parabrotulidae: Molecular data indicate placement of Parabrotula within the family Bythitidae, Ophidiiformes.
Molecular Phylogenetics and Evolution, 109, 337-342 (2017)
Published online: 6 February 2017
https://doi.org/10.1016/j.ympev.2017.02.004
SQC in Acknowledgement
Roger Huerlimann, Natacha Roux, Ken Maeda, Polina Pilieva, Saori Miura, Hsiao Chian, Michael Izumiyama, Vincent Laudet, Timothy Ravasi
The transcriptional landscape underlying larval development and metamorphosis in the Malabar grouper (Epinephelus malabaricus)
eLife
Reviewed preprint version: March 22, 2024
https://doi.org/10.7554/eLife.94573.1
Shinju Sugiyama, Keiko Kono
Exocytic plasma membrane flows remodel endoplasmic reticulum–plasma membrane tethering for septin collar assembly
Science Advances, Vol 10, Issue 11
Published: 13 Mar 2024
https://doi.org/10.1126/sciadv.adj1512
Shoguchi, E., Kawachi, M., Shinzato, C. & Beedessee, G. (2024)
Functional analyses of bacterial genomes found in Symbiodiniaceae genome assemblies
Environmental Microbiology Reports, 16(2), e13238.
First published: 05 March 2024
https://doi.org/10.1111/1758-2229.13238
Hinako Tamotsu, Koji Koizumi, Alejandro Villar Briones & Reina Komiya
Spatial distribution of three ARGONAUTEs regulates the anther phasiRNA pathway
Nature Communications volume 14, Article number: 3333 (2023)
Published: 07 June 2023
https://doi.org/10.1038/s41467-023-38881-z
Rachapun Rotrattanadumrong, Yohei Yokobayashi
Experimental exploration of a ribozyme neutral network using evolutionary algorithm and deep learning
Nature Communications volume 13, Article number: 4847 (2022)
Published: 17 August 2022
https://doi.org/10.1038/s41467-022-32538-z
Swathy Babu, Yuki Takeuchi, Ichiro Masai
Banp regulates DNA damage response and chromosome segregation during the cell cycle in zebrafish retina
eLife
Published: Aug 9, 2022
https://doi.org/10.7554/eLife.74611
Agneesh Barua, Ivan Kolidarov, Alexander S. Mikheyev
Co-option of the same ancestral gene family gave rise to mammalian and reptilian toxins
BMC Biology
Published: 23 December 2021
https://doi.org/10.1186/s12915-021-01191-1
Vienna Kowallik, Alexander S. Mikheyev
Honey Bee Larval and Adult Microbiome Life Stages Are Effectively Decoupled with Vertical Transmission Overcoming Early Life Perturbations
mBio Volume 12 • Number 6
Published: 21 December 2021
https://doi.org/10.1128/mBio.02966-21
Guohong Albert Wu, Chikatoshi Sugimoto, Hideyasu Kinjo, Chika Azama, Fumimasa Mitsube, Manuel Talon, Frederick G. Gmitter Jr. & Daniel S. Rokhsar
Diversification of mandarin citrus by hybrid speciation and apomixis
Nature Communications volume 12, Article number: 4377 (2021)
Published: 26 July 2021
https://doi.org/10.1038/s41467-021-24653-0
Agneesh Barua, Alexander S. Mikheyev
An ancient, conserved gene regulatory network led to the rise of oral venom systems
PNAS April 6, 2021 118 (14) e2021311118;
Published: April 6, 2021
https://doi.org/10.1073/pnas.2021311118
Matin Miryeganeh, Ferdinand Marlétaz, Daria Gavriouchkina, Hidetoshi Saze
An ancient, conserved gene regulatory network led to the rise of oral venom systems
New Phytologist
Published: 16 September 2021
https://doi.org/10.1111/nph.17738
Keisuke Fukunaga, Yohei Yokobayashi
Directed evolution of orthogonal RNA–RBP pairs through library-vs-library in vitro selection
Nucleic Acids Research, gkab527,
Published: 5 July 2021
https://doi.org/10.1093/nar/gkab527
Noriyuki Satoh, Hitoshi Tominaga, Masato Kiyomoto, Kanako Hisata, Jun Inoue and Koki Nishitsuji
A Preliminary Single-Cell RNA-Seq Analysis of Embryonic Cells That Express Brachyury in the Amphioxus, Branchiostoma japonicum
Front. Cell Dev. Biol.
Published: 15 July 2021
https://doi.org/10.3389/fcell.2021.696875
Guohong Albert Wu, Chikatoshi Sugimoto, Hideyasu Kinjo, Chika Azama, Fumimasa Mitsube, Manuel Talon, Frederick G. Gmitter Jr. & Daniel S. Rokhsar
Diversification of mandarin citrus by hybrid speciation and apomixis
Nature Communications volume 12, Article number: 4377 (2021)
Published: 26 July 2021
https://doi.org/10.1038/s41467-021-24653-0
Gustavo Sanchez, Fernando Á. Fernández-Álvarez, Morag Taite, Chikatoshi Sugimoto, Jeffrey Jolly, Oleg Simakov, Ferdinand Marlétaz, Louise Allcock & Daniel S. Rokhsar
Phylogenomics illuminates the evolution of bobtail and bottletail squid (order Sepiolida)
Communications Biology
Article number: 819 (2021)
Published: 29 June 2021
https://doi.org/10.1038/s42003-021-02348-y
Kaz Kawamura · Koki Nishitsuji · Eiichi Shoguchi · Shigeki Fujiwara · Noriyuki Satoh
Establishing Sustainable Cell Lines of a Coral, Acropora tenuis
Marine Biotechnology(2021)
Published: 26 April 2021
https://doi.org/10.1007/s10126-021-10031-w
Agneesh Barua, Alexander S. Mikheyev
De novo genome assembly and in natura epigenomics reveal salinity-induced DNA methylation in the mangrove tree Bruguiera gymnorhiza
PNAS April 6, 2021 118 (14) e2021311118;
Published in issue: April 6, 2021.
https://doi.org/10.1073/pnas.2021311118
Chuang, Po-Shun, Kota Ishikawa, and Satoshi Mitarai
Morphological and genetic recovery of coral polyps after bail-out
Frontiers in Marine Science 8 (2021): 280.
Published: 25 March 2021
https://doi.org/10.3389/fmars.2021.609287
Agneesh Baruaa, Alexander S. Mikheyev
An ancient, conserved gene regulatory network led to the rise of oral venom systems
Proceedings of the national Academy of Sciences of the United States of America
Published: March 29, 2021
https://doi.org/10.1073/pnas.2021311118
Jun Inoue,Kanako Hisata,Nina Yasuda,Noriyuki Satoh
An Investigation into the Genetic History of Japanese Populations of Three Starfish,Acanthaster planci,Linckia laevigata,and Asterias amurensis,Based on Complete Mitochondrial DNA Sequences
G3 Genes|Genomes|Genetics
Published: July 1, 2020
https://doi.org/10.1534/g3.120.401155
Takahashi A, Suzuki T, Soeda S, Takaoka S, Kobori S, Yamaguchi T, Mohamed HM, Yanagiya A, Abe T, Shigeta M, Furuta Y.
The CCR4–NOT complex maintains liver homeostasis through mRNA deadenylation.
Life science alliance;3(5)
Published: 1 April 2020
https://doi.org/10.26508/lsa.201900494
Ilsley GR, Suyama R, Noda T, Satoh N, Luscombe NM.
Finding cell-specific expression patterns in the early Ciona embryo with single-cell RNA-seq.
Scientific reports;10(1):1-0
Published: 18 Mar 2020
https://doi.org/10.1038/s41598-020-61591-1
Espinas NA, Furci L, Shimajiri Y, Harukawa Y, Miura S, Takuno S, Saze H.
Transcriptional regulation of genes bearing intronic heterochromatin in the rice genome.
PLoS genetics;16(3):e1008637.
Published: 18 March 2020
https://doi.org/10.1371/journal.pgen.1008637
Shoguchi E, Yoshioka Y, Shinzato C, Arimoto A, Bhattacharya D, Satoh N.
Correlation between organelle genetic variation and RNA editing in dinoflagellates associated with the coral Acropora digitifera.
Genome biology and evolution;12(3):203-9.
Published: 27 February 2020
https://doi.org/10.1093/gbe/evaa042
Mostafa D, Takahashi A, Yanagiya A, Yamaguchi T, Abe T, Kureha T, Kuba K, Kanegae Y, Furuta Y, Yamamoto T, Suzuki T.
Essential functions of the CNOT7/8 catalytic subunits of the CCR4-NOT complex in mRNA regulation and cell viability.
RNA biology.
Published: 10 Jan 2020
https://doi.org/10.1080/15476286.2019.1709747
Sanchez G, Jolly J, Reid A, Sugimoto C, Azama C, Marlétaz F, Simakov O, Rokhsar DS.
New bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu islands revealed by molecular and morphological analysis.
Communications biology; 2(1):1-5
Published: 11 December 2019
https://doi.org/10.1038/s42003-019-0661-6
Darwell CT, Fischer G, Sarnat EM, Friedman NR, Liu C, Baiao G, Mikheyev AS, Economo EP.
Genomic and phenomic analysis of island ant community assembly.
Molecular Ecology.
Published: 10 Dec 2019
https://doi.org/10.1111/mec.15326
Lu TM, Furuya H, Satoh N.
Gene expression profiles of dicyemid life-cycle stages may explain how dispersing larvae locate new hosts.
Zoological Letters; 1;5(1):32
Published: Dec 2019
https://doi.org/10.1186/s40851-019-0146-y
Arimoto A, Nishitsuji K, Narisoko H, Shoguchi E, Satoh N.
Differential gene expression in fronds and stolons of the siphonous macroalga, Caulerpa lentillifera.
Development, growth & differentiation
Published: 11 November 2019
https://doi.org/10.1111/dgd.12634
Takahashi A, Takaoka S, Kobori S, Yamaguchi T, Ferwati S, Kuba K, Yamamoto T, Suzuki T.
The CCR4–NOT deadenylase complex maintains adipocyte identity.
International journal of molecular sciences. 20(21):5274
Published: 24 Oct 2019
https://doi.org/10.3390/ijms20215274
Techer MA, Rane RV, Grau ML, Roberts JM, Sullivan ST, Liachko I, Childers AK, Evans JD, Mikheyev AS.
Divergent selection following speciation in two ectoparasitic honey bee mites.
bioRxiv
Published: 1 Oct 2019
https://doi.org/10.1038/s42003-019-0606-0
Techer MA, Rane RV, Grau ML, Roberts JMK, Sullivan ST, Liachko I, Childers AK, Evans JD, Mikheyev AS
Divergent evolutionary trajectories following speciation in two ectoparasitic honey bee mites.
Communications Biology; 2:357
Published: 1 Oct 2019
https://doi.org/10.1038/s42003-019-0606-0
Nomura Y, Yokobayashi Y.
Systematic minimization of RNA ligase ribozyme through large-scale design-synthesis-sequence cycles.
Nucleic acids research; 47(17):8950-60
Published: 26 Sep 2019
https://doi.org/10.1093/nar/gkz729
Kawamura K, Maruyama IN.
Forward genetic screen for Caenorhabditis elegans mutants with a shortened locomotor healthspan.
G3: Genes, Genomes, Genetics;9(8):2415-23
Published: 8 Aug 2019
https://doi.org/10.1534/g3.119.400241
Techer MA, Rane RV, Grau ML, Roberts JM, Sullivan ST, Liachko I, Childers AK, Evans JD, Mikheyev AS.
Genomic analyses of sibling honey bee ectoparasitic mite species show divergent strategies of adaptation.
bioRxiv
Published: 2 July 2019
https://doi.org/10.1101/512988
Marion Mennesson, Ken Maeda, Philippe Keith
Evolutionary aspects of cephalic sensory papillae of the Indo-Pacific species of Eleotris (Teleostei: Eleotridae).
Zoologica Scripta 48: 627–639 (2019)
Published: 2 July 2019
https://doi.org/10.1111/zsc.12366
Dehm D, Krumbholz J, Baunach M, Wiebach V, Hinrichs K, Guljamow A, Tabuchi T, Jenke-Kodama H, Sussmuth RD, Dittmann E.
Unlocking the spatial control of secondary metabolism uncovers hidden natural product diversity in Nostoc punctiforme.
ACS chemical biology ;14(6):1271-9
Published: 24 May 2019
https://doi.org/10.1021/acschembio.9b00240
Beedessee G.
Genomic insights on secondary metabolism in symbiotic dinoflagellates.
Thesis or Dissertation
Published: 2019 Apr
https://doi.org/10.15102/1394.00000779
Brisbin MM, Conover AE, Mitarai S.
Hydrothermal activity and water mass composition shape microbial eukaryote diversity and biogeography in the Okinawa Trough.
bioRxiv
Published: 1 Jan 2019
https://doi.org/10.1101/714816
Kawamura, Kazuto.
Forward genetic screen for Caenorhabditis elegans mutants with a progressive decline in adult locomotor function.
Thesis or Dissertation
Published: Jan 2019
https://doi.org/10.15102/1394.00000766
Poetsch AR, Boulton SJ, Luscombe NM
Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis.
BioRxiv
Published: 07 December 2018
https://doi.org/10.1101/168153
Brisbin MM, Mesrop LY, Grossmann MM, Mitarai S.
Intra-host symbiont diversity and extended symbiont maintenance in photosymbiotic Acantharea (clade F).
bioRxiv
Published: 27 August 2018
https://doi.org/10.1101/299495
Inoue T, Barker CS, Matsunami H, Aizawa SI, Samatey FA.
The FlaG regulator is involved in length control of the polar flagella of Campylobacter jejuni.
Microbiology
Published: 01 May 2018
https://doi.org/10.1099/mic.0.000648
Sajiki K, Tahara Y, Villar-Briones A, Pluskal T, Teruya T, Mori A, Hatanaka M, Ebe M, Nakamura T, Aoki K, Nakaseko Y, Yanagida M.
Genetic defects in SAPK signalling, chromatin regulation, vesicle transport and CoA-related lipid metabolism are rescued by rapamycin in fission yeast.
Open Biol. 2018 Mar;8(3). pii: 170261.
Published:28 March 2018
https://doi.org/10.1098/rsob.170261
Kobori S, Yokobayashi Y.
Analyzing and Tuning Ribozyme Activity by Deep Sequencing to Modulate Gene Expression Level in Mammalian Cells.
ACS Synthetic Biolology.
Published: 17 Jan 2018
https://doi.org/10.1021/acssynbio.7b00367
Soliman T, Yang SY, Yamazaki T, Jenke-Kodama H.
Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise.
PeerJ. 2017 Dec 19;5:e4178.
Published: 19 Dec 2017
https://doi.org/10.7717/peerj.4178
Soliman T, Reimer JD, Yang SY, Villar-Briones A, Roy MC, Jenke-Kodama H.
Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro) in Okinawa Island, Japan.
Front Microbiol.
Published: 11 Dec 2017
https://doi.org/10.3389/fmicb.2017.02451
Nomura Y, Chien HC, Yokobayashi Y.
Direct screening for ribozyme activity in mammalian cells.
Chem Commun (Camb).
Published: 7 Nov 2017
https://doi.org/10.1039/c7cc07815c
Dhamodharan V, Kobori S, Yokobayashi Y.
Large Scale Mutational and Kinetic Analysis of a Self-Hydrolyzing Deoxyribozyme.
ACS Chem Biol.
Published: 23 Oct 2017
https://doi.org/10.1021/acschembio.7b00621
Mikheyev AS, Zwick A, Magrath MJL, Grau ML, Qiu L, Su YN, Yeates D.
Museum Genomics Confirms that the Lord Howe Island Stick Insect Survived Extinction.
Curr Biol. 2017 Oct 4. pii: S0960-9822(17)31098-9.
Published: 23 October 2017
https://doi.org/10.1016/j.cub.2017.08.058
Khilyas IV, Sorokin AA, Kiseleva L, Simpson DJW, Fedorovich V, Sharipova MR, Kainuma M, Cohen MF, Goryanin I.
Comparative Metagenomic Analysis of Electrogenic Microbial Communities in Differentially Inoculated Swine Wastewater-Fed Microbial Fuel Cells.
Scientifica (Cairo).
Published: 12 Oct 2017
https://doi.org/10.1155/2017/7616359
Aird SD, Arora J, Barua A, Qiu L, Terada K, Mikheyev AS.
Population Genomic Analysis of a Pitviper Reveals Microevolutionary Forces Underlying Venom Chemistry.
Genome Biol Evol. 2017 Oct 1;9(10):2640-2649.
Published: 27 September 2017
https://doi.org/10.1093/gbe/evx199
Kobori S, Takahashi K, and Yokobayashi Y.
Deep Sequencing Analysis of Aptazyme Variants Based on a Pistol Ribozyme.
ACS Synthetic Biology (2017)
Published: 11 April 2017
https://doi.org/10.1021/acssynbio.7b00057
SQC in Materials and Methods
Ben E Clifton, Muhammad A Fariz, Gen-Ichiro Uechi, Paola Laurino
Evolutionary repair reveals an unexpected role of the tRNA modification m1G37 in aminoacylation
Nucleic Acids Research
Published: 11 November 2021
https://doi.org/10.1093/nar/gkab1067
Douglas B. Booher, Joshua C. Gibson, Cong Liu,John T. Longino, Brian L. Fisher, Milan Janda,Nitish Narula,Evropi Toulkeridou, Alexander S. Mikheyev, Andrew V. Suarez, Evan P. Economo
Functional innovation promotes diversification of form in the evolution of an ultrafast trap-jaw mechanism in ants. .
PLoS biology 19.3 (2021): e3001031.
Published: 2 March 2021
https://doi.org/10.1371/journal.pbio.3001031
Mars Brisbin M, Mitarai S.
Differential Gene Expression Supports a Resource‐Intensive, Defensive Role for Colony Production in the Bloom‐Forming Haptophyte, Phaeocystis globosa.
Journal of Eukaryotic Microbiology;66(5):788-801.
Published: 12 March 2019
https://doi.org/10.1111/jeu.12727
Marlétaz F, Peijnenburg KT, Goto T, Satoh N, Rokhsar DS.
A new spiralian phylogeny places the enigmatic arrow worms among gnathiferans.
Current Biology ;29(2):312-8.
Published: 21 Jan 2019
https://doi.org/10.1016/j.cub.2018.11.042