Koh Onimaru, Ph.D.

Affiliation: Special Postdoctoral Researcher at RIKEN Center for Biosystems Dynamics Research (Shigehiro Kuraku Lab)

Contact: koh.onimaru(at)gmail.com / koh.onimaru(at)riken.jp (Please replace (at) to @)

Education:

2013 Ph.D. Tokyo Institute of Technology, Japan

Positions:

2013 Postdoctoral researcher, Mikiko Tanaka Lab, Tokyo Institute of Technology, Japan

2013-2016 Postdoctoral researcher, James Sharpe Lab, Centre for Genomic Regulation, Spain

2016-2018 Postdoctoral researcher, Shigehiro Kuraku Lab, RIKEN Center for Life Science Technologies (CLST)

Scientific interest: Evolutionary biology. I am currently interested in the fin-to-limb transition. Morphogenesis is a really complicated system as it involves thousands of gene regulations and cell interactions. I am wondering how random mutations at DNA level affect such a complex system and happened to change its morphology to others. To solve this question, I am trying to combine (a) developmental biology, in which morphogenesis actually occur, (b) numerical modeling to deal with the non-linear and multibody dynamics of morphogenesis, (c) comparative genomics to identify mutations that affect the morphogenetic system. The fin-to-limb transformation is a good example to tackle. My ultimate goal is to find out the general principles of biology.

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., DOI: 10.1002/dvdy.24623, 2018. link

[10] (Review) K. Onimaru and S. Kuraku, "Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications" Brief. Funct. Genomics, ely008, DOI: https://doi.org/10.1093/bfgp/ely008, 2018.

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.


Presentations at professional conferences

Oral presentations at international conferences

1. Koh Onimaru, Shigeru Kuratani and Mikiko Tanaka " Evolution of the lateral plate mesoderm: Insights from amphioxus and lampreys development." The fourth meeting of the European Society for Evolutionary Developmental Biology, Lisbon, 10-13 July, 2012

2. Koh Onimaru, Luciano Marcon, Marco Musy, Mikiko Tanaka, James Sharpe "The fin to limb transition as the re-organisation of a Turing pattern" 13th International Limb Development & Regeneration Conference 28 June - 1 July, Florida, 2015

3. Koh Onimaru, Luciano Marcon, Marco Musy, Mikiko Tanaka, James Sharpe "A Turing pattern transition and the morphological diversity of vertebrate fins and limbs " the EMBO Conference Genetic Control of Development and Evolution, Paris, 29 September - 2 October, 2015

4. Koh Onimaru (invited speaker), Luciano Marcon, Marco Musy, Mikiko Tanaka, James Sharpe "Turing pattern in fins and limbs" The sixth meeting of the European Society for Evolutionary Developmental Biology, Uppsala, 26-29 July, 2016

Poster presentations at international conferences

1. Koh Onimaru, Eiichi Shoguchi, Shigeru Kuratani and Mikiko Tanaka "Development and Evolution of the Lateral Plate Mesoderm: Comparative Analysis of Amphioxus and Lamprey, with Implications for the Acquisition of Paired Fins" the 2011 conference of the Society for Molecular Biology and Evolution, 63, Kyoto, July, 2011

2. Koh Onimaru and Mikiko Tanaka "Insights into the Origin of the Thumb" CDB Symposium 2013, P83, Kobe, March, 2013

3. Koh Onimaru, Luciano Marcon, Marco Musy, Mikiko Tanaka, James Sharpe "Transformation of skeletal patterns from fins into limbs via a mode change of Turing mechanism" The fifth meeting of the European Society for Evolutionary Developmental Biology, P-177, Vienna, July, 2014

Selected oral presentation at domestic conferences

1. Koh Onimaru, Shigehiro Kuraku, Wataru Takagi, Susumu Hyodo, Mikiko Tanaka " Anterior-posterior patterning of pectoral fin development in cartilaginous fishes: Insight into the fin-to-limb evolution" the 47th Annual Meeting for the Japanese Society of Developmental Biologists, Aichi (Japan), 27-30 May, 2014

2. Koh Onimaru (Invited speaker), Shigehiro Kuraku, Wataru Takagi, Susumu Hyodo, James Sharpe, Mikiko Tanaka "Anterior-posterior patterning of cartilaginous fish fin development: Insights into the origin of radius and thumbs." 16th Annual Meeting of Society of Evolutionary Studies, Japan, Osaka, 21- 24 August, 2014

3. Koh Onimaru "Transformation of skeletal patterns from fins into limbs through a mode change of Turing mechanism" the 5th meeting of Spanish Society for Developmental Biology, Madrid, October, 2014

Grants and Fellowships

1. JSPS KAKENHI Grant Number 17K15132 Apr. 2017– Mar. 2019

2. Special Postdoctoral Researchers Program at RIKEN, from Apr. 2018

Software

1. DeepGMAP (https://github.com/koonimaru/DeepGMAP)