Selected Publications


  1. Hayakawa, E., Guzman, C., Horiguchi, O., Kawano, C., Shiraishi, A., Mohri, K., Lin, M. H., Nakamura, R., Nakamura, R., Kawai, E., Komoto, S., Jokura, K., Shiba, K., Shigenobu, S., Satake, H., Inaba, K., & Watanabe, H. Mass spectrometry of short peptides reveals common features of metazoan peptidergic neurons. Nature Ecology & Evolution, doi: 10.1038/s41559-022-01835-7 (2022)

  2. Masuda-Ozawa, T., Fujita, S., Nakamura, R.Watanabe, H., Kuranaga, E., & Nakajima, Y. siRNA-mediated gene knockdown via electroporation in hydrozoan jellyfish embryos. Scientific Reports, doi: 10.1038/s41598-022-20476-1 (2022)


  1. Shikaya, Y., Takase, Y., Tadokoro, R., Nakamura, R., Inaba, M., & Takahashi, Y. Distribution Map of Peristaltic Waves in the Chicken Embryonic Gut Reveals Importance of Enteric Nervous System and Inter-Region Cross Talks Along the Gut Axis. Frontiers in Cell and Developmental Biology, doi: 10.3389/fcell.2022.827079 (2022)


  1. Yi, R., Fahrenbach, A., Hongo Y. Radiolytically Driven Chemical Evolution. Journal of Geography, 129(6), 837­851, doi:10.5026/jgeography.129.837 (2020)

  2. Atrigenio, M. P., Conaco, C., Guzman, C., Yap, H. T., Aliño, P. M. Distribution and abundance of Heliopora coerulea (Cnidaria: Coenothecalia) and notes on its aggressive behavior against scleractinian corals: Temperature mediated? Regional Studies in Marine Science, 40. doi:10.1016/j.rsma.2020.101502 (2020)

  3. Mohri, K., Tanaka, R., Nagano, S. Live cell imaging of cell movement and transdifferentiation during regeneration of an amputated multicellular body of the social amoeba Dictyostelium discoideum. Developmental Biology457(1), 140–149, doi: 10.1016/j.ydbio.2019.09.014 (2020)


  1. Shoemark D.K., Ziegler B., Watanabe H., Strompen J., Tucker R.P., Özbek S., Adams J.C. (2019) Emergence of a Thrombospondin Superfamily at the Origin of Metazoans. Molecular Biology and Evolution 36(6), 1220-1238, doi:10.1093/molbev/msz060 (2019)

  2. Guzman, C., Atrigenio, M., Shinzato, C., Aliño, P., Conaco, C. (2019) Warm Seawater temperature promotes substrate colonization by the blue coral, Heliopora coerulea. Peer J, doi: 10.7717/peerj.7785 (2019)


  1. Lin, M.-F., Takahashi, S., Forêt, S., Davy, S., Miller, D.J. (2018) Transcriptomic analyses highlight the likely metabolic consequences of infection of a cnidarian host (Ricordea yuma) with homologous or heterologous Symbiodinium phylotypes. Review. Biology Open 2019 Mar 27;8(3). pii: bio038281. doi: 10.1242/bio.038281.

  2. 渡邉寛(2018) 分担執筆:第2章「脳の起源︱中枢神経系の誕生」遺伝子から解き明かす脳の不思議な世界 (Mystery world of the brains revealed by genes. – 500 million years of the evolutionary history) ISBN: 4909383050


  1. Watanabe, H. "Back through time: how cnidarians and basal metazoans shed light on ancient nervous systems." Brain Evolution by Design, Springer (Eds.: Shigeo S, Murakami Y, Nomura T) 45-75, Chapter 3 Jan. (2017). Review


  1. Hayakawa, E., Fujimura, Y. & Miura, D.  MSIdV: a versatile tool to visualize biological indices from mass spectrometry imaging data. Bioinformatics 32, 3852-3854, doi:10.1093/bioinformatics/btw548 (2016).

Before OIST

  1. Watanabe, T*., Nakamura, R*., Takase, Y., Susaki, E. A., Ueda, H. R., Tadokoro, R. and Takahashi, Y. (*Equal contribution) Comparison of the 3-D patterns of the parasympathetic nervous system in the lung at late developmental stages between mouse and chicken. Developmental Biology., Elsevier, 444(1), pp S325-S336 (2018)
  2. Nakamura, R., Koshiba-Takeuchi, K., Tsuchiya, M., Kojima, M., Miyazawa, A., Ito, K., Ogawa, H. and Takeuchi, J. K. Expression analysis of Baf60c during heart regeneration in axolotls and neonatal mice. Development, Growth & Differentiation., Wiley-Blackwell, 58(4), pp 367-382 (2016)
  3. Koshiba-Takeuchi, K., Morita, Y., Nakamura, R., Takeuchi, J.K. Combinatorial Functions of Transcription Factors and Epigenetic Factors in Heart Development and Disease (In English). In: Nakanishi T., Markwald R., Baldwin H., Keller B., Srivastava D., Yamagishi H. (eds) Etiology and Morphogenesis of Congenital Heart Disease. Springer, Tokyo. (2016)
  4. Buts, K., Michielssens, S., Hertog, M. L., Hayakawa, E., Cordewener, J., America, A. H., Nicolai, B. M. & Carpentier, S. C.  Improving the identification rate of data independent label-free quantitative proteomics experiments on non-model crops: a case study on apple fruit. J. Proteomics 105, 31-45, doi:10.1016/j.jprot.2014.02.015 (2014).
  5. Watanabe, H.**, Kuhn, A., Fushiki, M., Agata, K., Özbek, S., Fujisawa, T., Holstein, T. W.** “Sequential actions of β-Catenin and Bmp pattern the oral nerve net in Nematostella vectensis.” Nat. Commun. 5, 5536, (2014) **Co-corresponding authors.
  6. Watanabe, H.**, Schmidt, H. A., Kuhn, A., Höger, S. K., Kocagöz, Y., Laumann-Lipp, N., Özbek, S., Holstein, T. W.** “Nodal signalling determines biradial asymmetry in Hydra.” Nature 112-115, 515, 2014. **Co-corresponding authors.
  7. Hayakawa, E., Landuyt, B., Baggerman, G., Cuyvers, R., Lavigne, R., Luyten, W. & Schoofs, L.  Peptidomic analysis of human reflex tear fluid. Peptides 42, 63-69, doi:10.1016/j.peptides.2012.11.018 (2013).
  8. Hayakawa, E., Menschaert, G., De Bock, P. J., Luyten, W., Gevaert, K., Baggerman, G. & Schoofs, L.  Improving the identification rate of endogenous peptides using electron transfer dissociation and collision-induced dissociation. J. Proteome Res. 12, 5410-5421, doi:10.1021/pr400446z (2013).
  9. Crappe, J., Van Criekinge, W., Trooskens, G., Hayakawa, E., Luyten, W., Baggerman, G. & Menschaert, G.  Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs. BMC Genomics 14, 648, doi:10.1186/1471-2164-14-648 (2013).
  10. Hori, Y., Morishita, T., Nakamura, R., Koshiba-Takeuchi, K., and Takeuchi, J. K. Epigenetic factors and 
heart development/failure (In Japanese). Dictionary of Epigenetic Keywords.  , p192-200 (2013)
  11. Menschaert, G., Hayakawa, E., Schoofs, L., Van Criekinge, W. & Baggerman, G.  Spectral clustering in peptidomics studies allows homology searching and modification profiling: HomClus, a versatile tool. J. Proteome Res. 11, 2774-2785, doi:10.1021/pr201114m (2012).
  12. Nakamura, R., Tsukahara, Y., and Takeuchi, J. K. Epigenetics in
heart development and disease (In Japanese). Experimental Medicine. Vol.30 No.18 p2923-2931(2012)
  13. Holstein, T. W., Watanabe, H., Özbek, S. "Signaling pathways and axis formation in the lower metazoa." Curr. Top. Dev. Biol. 137-177, 97, 2011. Review
  14. Watanabe, H.*, Hongu, T.*, Yamazaki, M., Kanaho, Y. "Phospholipase D2 activation by p38 MAP kinase is involved in neurite outgrowth." Biochem. Biophys. Res. Commun. 288-293, 413, 2011.  *equal authorship.
  15. Van Dijck, A., Hayakawa, E., Landuyt, B., Baggerman, G., Van Dam, D., Luyten, W., Schoofs, L. & De Deyn, P. P.  Comparison of extraction methods for peptidomics analysis of mouse brain tissue. J. Neurosci. Methods 197, 231-237, doi:10.1016/j.jneumeth.2011.02.023 (2011).
  16. Suzuki, A., Arikawa, C., Kuwahara, Y., Itoh, K., Watanabe, M., Watanabe, H., Suzuki, T.,  Funakoshi, Y., Hasegawa, H., Kanaho, Y. "The scaffold protein JIP3 functions as a downstream effector of the small GTPase ARF6 to regulate neurite morphogenesis of cortical neurons." FEBS Lett. 2801-2806, 584, 2010.
  17. Chapman, J. A., Kirkness, E. F., Simakov, O., Hampson, S. E., Mitros, T., Weinmaier, T., Rattei, T., Balasubramanian, P. G., Borman, J., Busam, J. D., Disbennett, K., Pfannkoch, C., Sumin, N., Sutton, G. G., Viswanathan, L. D., Walenz, B., Goodstein, D. M., Hellsten, U., Kawashima, T., Prochnik, S. E., Putnam, N. H., Shu, S., Blumberg, B., Dana, C. E., Gee, L., Kibler, D. F., Law, L., Lindgens, D., Martinez, D. E., Peng, J., Wigge, P. A., Bertulat, B., Guder, C., Nakamura, Y., Özbek, S., Watanabe, H., Khalturin, K., Hemmrich, G., Franke, A., Augustin, R., Fraune, S., Hayakawa, E., Hayakawa, S., Hirose, M., Hwang, J. S., Ikeo, K., Nishimiya-Fujisawa, C., Ogura, A., Takahashi, T., Steinmetz, P. R., Zhang, X., Aufschnaiter, R., Eder, M. K., Gorny, A. K., Salvenmoser, W., Heimberg, A. M., Wheeler, B. M., Peterson, K.J., Böttger, A., Tischler, P., Wolf, A., Gojobori, T., Remington, K. A., Strausberg, R. L., Venter, J. C., Technau, U., Hobmayer, B., Bosch, T. C., Holstein, T. W., Fujisawa, T., Bode, H. R., David, C. N., Rokhsar, D. S., Steele, R. E. “The dynamic genome of Hydra.” Nature 592-596, 464, 2010.
  18. Watanabe, H., Hoang, V. T., Mättner, R., Holstein, T. W. “Immortality and the base of multicellular life: Lessons from cnidarian stem cells.” Semin. Cell Dev. Biol. 1114-1125, 20, 2009. Review
  19. Menschaert, G., Vandekerckhove, T. T., Landuyt, B., Hayakawa, E., Schoofs, L., Luyten, W. & Van Criekinge, W.  Spectral clustering in peptidomics studies helps to unravel modification profile of biologically active peptides and enhances peptide identification rate. Proteomics 9, 4381-4388, doi:10.1002/pmic.200900248 (2009).
  20. Watanabe H, Fujisawa T, Holstein TW “Cnidarians and the evolutionary origin of the nervous system.” Dev. Growth Differ. 167-183, 51, 2009.
  21. Philipp I, Aufschnaiter R, Özbek S, Pontasch S, Jenewein M, Watanabe H, Rentzsch F, Holstein TW, Hobmayer B “Wnt/beta-catenin and noncanonical Wnt signaling interact in tissue evagination in the simple eumetazoan Hydra.” Proc. Natl. Acad. Sci. U. S. A. 4290-4295, 106, 2009.
  22. Lengfeld T*, Watanabe H*, Simakov O, Lindgens D, Gee L, Law L, Schmidt HA, Özbek S, Bode H, Holstein TW “Multiple Wnts are involved in Hydra organizer formation and regeneration.“ Dev. Biol. 186-199, 330, 2009. *equal authorship.
  23. Nishio M, Watanabe K, Sasaki J, Taya C, Takasuga S, Iizuka R, Balla T, Yamazaki M, Watanabe H, Itoh R, Kuroda S, Horie Y, Forster I, Mak TW, Yonekawa H, Penninger JM, Kanaho Y, Suzuki A, Sasaki T "Control of cell polarity and motility by the PtdIns(3,4,5)P(3) phosphatase SHIP1." Nat. Cell Biol. 36-44, 9, 2007.
  24. Hayakawa, E., Takahashi, T., Nishimiya-Fujisawa, C. & Fujisawa, T.  A novel neuropeptide (FRamide) family identified by a peptidomic approach in Hydra magnipapillata. FEBS J. 274, 5438-5448, doi:10.1111/j.1742-4658.2007.06071.x (2007).
  25. Guder C, Philipp I, Lengfeld T, Watanabe H, Hobmayer B, Holstein TW "The Wnt code: cnidarians signal the way." Oncogene 7450-7460, 25, 2006  Review
  26. Miyazaki H, Yamazaki M, Watanabe H, Maehama T, Yokozeki T, Kanaho Y "The small GTPase ADP-ribosylation factor 6 negatively regulates dendritic spine formation." FEBS Lett. 6834-6838, 579, 2005.
  27. Sasaki J, Sasaki T, Yamazaki M, Matsuoka K, Taya C, Shitara H, Takasuga S, Nishio M, Mizuno K, Wada T, Miyazaki H, Watanabe H, Iizuka R, Kubo S, Murata S, Chiba T, Maehama T, Hamada K, Kishimoto H, Frohman MA, Tanaka K, Penninger JM, Yonekawa H, Suzuki A, Kanaho Y "Regulation of anaphylactic responses by phosphatidylinositol phosphate kinase type I {alpha}." J. Exp. Med. 859-870, 201, 2005.
  28. Kanaho Y and Watanabe H. "Measurement of Phospholipase D Activity." Methods for Intracellular Signal Transduction Studies (Ed.: Y. Fukui) Center for Academic Publications Japan, 115-122, Review, Japanese
  29. Watanabe H, Yokozeki T, Yamazaki M, Miyazaki H, Sasaki T, Maehama T, Itoh K, Frohman MA, Kanaho Y “Essential role for phospholipase D2 activation downstream of ERK MAP kinase in NGF-stimulated neurite outgrowth from PC12 cells.” J. Biol. Chem. 37870-37877, 279, 2004.
  30. Watanabe H, Yamazaki M, Miyazaki H, Arikawa C, Itoh K, Sasaki T, Maehama T, Frohman MA, Kanaho Y “Phospholipase D2 functions as a downstream signaling molecule of MAP kinase pathway in L1-stimulated neurite outgrowth of cerebellar granule neurons.” J. Neurochem. 142-151, 89, 2004.
  31. Nogami M, Yamazaki M, Watanabe H, Okabayashi Y, Kido Y, Kasuga M, Sasaki T, Maehama T, Kanaho Y "Requirement of autophosphorylated tyrosine 992 of EGF receptor and its docking protein phospholipase C gamma 1 for membrane ruffle formation." FEBS Lett. 71-76, 536, 2003.
  32. Yamazaki M, Miyazaki H, Watanabe H, Sasaki T, Maehama T, Frohman MA, Kanaho Y "Phosphatidylinositol 4-phosphate 5-kinase is essential for ROCK-mediated neurite remodeling." J. Biol. Chem. 17226-17230, 277, 2002.
  33. Watanabe H, Kanaho Y “Inhibition of Phosphatidylinositol 4,5-Bisphosphate-Stimulated Phospholipase D2 Activity by Ser/Thr Phosphorylation.” Biochim. Biophys. Acta –Mol. Cell Res. 121-124, 1495, 2000. 
  34. Honda A, Nogami M, Yokozeki T, Yamazaki M, Nakamura H, Watanabe H, Kawamoto K, Nakayama K, Morris AJ, Frohman MA, Kanaho Y "Phosphatidylinositol 4-phosphate 5-kinase a is a Downstream Effector of the Small G Protein ARF6 in Membrane Ruffle Formation." Cell  521-532, 99, 1999.
  35. Yamazaki M, Zhang Y, Watanabe H, Yokozeki T, Ohno S, Kaibuchi K, Shibata H, Mukai H, Ono Y, Frohman MA, Kanaho Y "Interaction of the Small G Protein RhoA with the C Terminus of Human Phospholipase D1" J. Biol. Chem. 6035-6038, 274, 1999.