Publications

Peer-reviewed publications

[1] M. Matsuura, H. Nishihara, K. Onimaru, N. Kokubo, S. Kuraku, R. Kusakabe, N. Okada, S. Kuratani, and M. Tanaka, "Identification of four Engrailed genes in the Japanese Lamprey, Lethenteron japonicum" Dev. Dyn., vol. 237, no. 6, pp. 1581–1589, 2008.

[2] K. Sakamoto, K. Onimaru, K. Munakata, N. Suda, M. Tamura, H. Ochi, and M. Tanaka, "Heterochronic shift in Hox-mediated activation of Sonic hedgehod leads to morphological changes during fin development" PLoS One, vol. 4, no. 4, 2009.

[3] N. Kokubo, M. Matsuura, K. Onimaru, E. Tiecke, S. Kuraku, S. Kuratani, and M. Tanaka, "Mechanisms of heart development in the Japanese lamprey, Lethenteron japonicum" Evol. Dev., vol. 12, no. 1, pp. 34–44, 2010.

[4] K. Onimaru, E. Shoguchi, S. Kuratani, and M. Tanaka, "Development and evolution of the lateral plate mesoderm: Comparative analysis of amphioxus and lamprey with implications for the acquisition of paired fins" Dev. Biol., vol. 359, no. 1, pp. 124–136, 2011.

[5] (Review) M. Tanaka and K. Onimaru, "Acquisition of the paired fins: a view from the sequential evolution of the lateral plate mesoderm" Evol. Dev., vol. 14, no. 5, pp. 412–420, 2012.

[6] K. Onimaru, S. Kuraku, W. Takagi, S. Hyodo, J. Sharpe, and M. Tanaka, "A shift in anterior–posterior positional information underlies the fin-to-limb evolution" Elife, vol. 4, p. e07048, 2015. link

[7] K. Onimaru, L. Marcon, M. Musy, M. Tanaka, and J. Sharpe, "The fin-to-limb transition as the re-organization of a Turing pattern" Nat. Commun., vol. 7, p. 11582, 2016. link

[8] E. Okamoto, R. Kusakabe, S. Kuraku, S. Hyodo, A. Robert-Moreno, K. Onimaru, J. Sharpe, S. Kuratani, and M. Tanaka, “Migratory appendicular muscles precursor cells in the common ancestor to all vertebrates” Nat. Ecol. Evol., vol. 1, p. 1731–1736, 2017.

[9] K. Onimaru, F. Motone, I. Kiyatake, K. Nishida, S. Kuraku, "A staging table for the embryonic development of the brownbanded bamboo shark (Chiloscyllium punctatum)" Dev. Dyn., 247, 712-723, 2018. DOI: 10.1002/dvdy.24623 link

[10] (Review) K. Onimaru and S. Kuraku, "Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications" Brief. Funct. Genomics, 17 (5), 352-361, 2018.

[11] K. Onimaru K. Tatsumi, K. Shibagaki and S. Kuraku, "A de novo transcriptome assembly of the zebra bullhead shark, Heterodontus zebra" Sci. Data, 5, 180197, 2018. DOI: https://doi.org/10.1038/sdata.2018.197

[12] Y. Hara, K. Yamaguchi, K. Onimaru, …(20 authors)…., S. Kuraku, "Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates" Nat. Ecol. Evol., 2 (11), 1761, 2018. DOI: https://doi.org/10.1038/s41559-018-0673-5

[13] K. Onimaru, O. Nishimura, and S. Kuraku, "Predicting gene regulatory regions with a convolutional neural network for processing double-strand genome sequence information" PloS one 15 (7), e0235748, 2020. link

[14] K. Onimaru, K. Tatsumi, C. Tanegashima, M. Kadota, O. Nishimura, S. Kuraku "Developmental hourglass and heterochronic shifts in fin and limb development" Elife 10, e62865, 2021. link

Preprints

[1] K. Onimaru, O. Nishimura, and S. Kuraku, "A regulatory-sequence classifier with a neural network for genomic information processing" bioRxiv, DOI: https://doi.org/10.1101/355974, 2018. (published at PLOS ONE)

[1] (Review) K. Onimaru, L. Marcon, "Systems biology approach to the origin of the tetrapod limb" arXiv, arXiv:1907.02730, 2019 . link

[2] K. Onimaru, K. Tatsumi, C. Tanegashima, M. Kadota, O. Nishimura, S. Kuraku "Developmental hourglass and heterochronic shifts in fin and limb development" bioRxiv, DOI: https://doi.org/10.1101/2020.01.10.901173 , 2020. link (published at eLIFE)

etc

[1] Itsuki Kiyatake, Koh Onimaru, Shigehiro Kuraku, and Kiyonori Nishida, "A study of the embryonic development of the brown-banded bamboo shark (イヌザメの発生研究)" Journal of Osaka Aquarium Kaiyukan, KAIYU (海遊館機関誌かいゆう), vol. 22, p1-11, 2019. link