Publications

Selected Publications

2018

  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.

2017

  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

2016

  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. 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).
  2. 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.
  3. 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.
  4. 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).
  5. 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).
  6. 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).
  7. 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).
  8. 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
  9. 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.
  10. 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).
  11. 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.
  12. 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.
  13. 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
  14. 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).
  15. Watanabe H, Fujisawa T, Holstein TW “Cnidarians and the evolutionary origin of the nervous system.” Dev. Growth Differ. 167-183, 51, 2009.
  16. 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.
  17. 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.
  18. 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.
  19. 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).
  20. 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
  21. 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.
  22. 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.
  23. 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
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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. 
  29. 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.
  30. 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.