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Curriculum Vitae – Shigehiro Kuraku 1 Shigehiro Kuraku, Ph.D. Unit Leader Laboratory for Phyloinformatics RIKEN Center for Biosystems Dynamics Research Email: [email protected] URL: www.clst.riken.jp/phylo/ GENDER Male YEAR OF BIRTH 1976 NATIONALITY Japanese Ph.D. Department of Biophysics, Graduate School of Science, Kyoto University January 2005 Discipline: Evolutionary Biology Supervisor: Prof. Yoshinori Shichida (after Prof. Takashi Miyata retired) M.Sc. Department of Biophysics, Graduate School of Science, Kyoto University March 2001 Discipline: Molecular Evolutionary Biology Supervisor: Prof. Takashi Miyata B.Sc. Faculty of Science, Kyoto University March 1999 Discipline: Molecular Evolutionary Biology Supervisor: Prof. Takashi Miyata Japanese (native) English (fluent) German (Level 3 – Diplom Deutsch in Japan. 1995) Italian (Diploma elementare di Lingua Italiana Firenze - Accadmia italiana di lingua. 1999) 2 Curriculum vitae – Shigehiro Kuraku Year Appointment 2018- Unit Leader Laboratory for Phyloinformatics RIKEN Center for Biosystems Dynamics Research in Kobe, Japan 2018- Adjunct Associate Professor Graduate School of Science, Kobe University, Japan 2014-2018 Unit Leader Phyloinformatics Unit RIKEN Center for Life Science Technologies in Kobe, Japan 2014- Adjunct Associate Professor Organization of Advanced Science and Technology, Kobe University, Japan 2013- Adjunct Associate Professor Graduate School of Science and Technology, Kwansei Gakuin University, Japan 2012-2014 Unit Leader Genome Resource and Analysis Unit, Center for Developmental Biology, RIKEN in Kobe, Japan 2007-2012 Assistant Professor (Akademischer Rat / Wissenschaftlicher Mitarbeiter) Laboratory for Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany 2005-2007 Research Scientist (postdoctoral) Laboratory for Evolutionary Morphology, Center for Developmental Biology, RIKEN in Kobe, Japan 2004-2005 Research Associate (pre-doctoral) Laboratory for Evolutionary Morphology, Center for Developmental Biology, RIKEN in Kobe, Japan 2003-2004 Junior Research Associate Laboratory for Evolutionary Morphology, Center for Developmental Biology, RIKEN in Kobe, Japan (Descending order for years of publication; *I am a corresponding author) Original papers (review papers are numbered separately and listed further below) 2018 69. Yuichiro Hara, Miki Takeuchi, Yuka Kageyama, Kaori Tatsumi, Masahiko Hibi, Hiroshi Kiyonari and Shigehiro Kuraku*. Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes BMC Biology 2018. accepted. doi: 10.1186/s12915-018-0509-4 68. Koh Onimaru, Fumio Motone, Itsuki Kiyatake, Kiyonori Nishida, and Shigehiro Kuraku*. A staging table for the embryonic development of the brownbanded bamboo shark (Chiloscyllium punctatum). Developmental Dynamics 2018. accepted. doi:10.1002/dvdy.24623 Curriculum vitae – Shigehiro Kuraku 3 2017 67. Eri Okamoto, Rie Kusakabe, Shigehiro Kuraku, Susumu Hyodo, Alexandre Robert-Moreno, Koh Onimaru, James Sharpe, and Shigeru Kuratani, Mikiko Tanaka. Migratory appendicular muscles precursor cells in the common ancestor to all vertebrates. Nature Ecology & Evolution, 2017. 1, 1784. 66. Osamu Nishimura, Yuichiro Hara, Shigehiro Kuraku*. gVolante for standardizing completeness assessment of genome and transcriptome assemblies. Bioinformatics 2017. 13, 3635-3637. doi: 10.1093/bioinformatics/btx445 65. Mitsutaka Kadota, Yuichiro Hara, Kaori Tanaka, Wataru Takagi, Chiharu Tanegashima, Osamu Nishimura, and Shigehiro Kuraku*. CTCF binding landscape in jawless fish with reference to Hox cluster evolution. Scientific Reports, 2017. 7, 4957. doi:10.1038/s41598-017-04506-x . 2016 64. Miki Takeuchi, Shingo Yamaguchi, Masayoshi Sakakibara, Takuto Hayashi, Koji Matsuda, Yuichiro Hara, Chiharu Tanegashima, Takashi Shimizu, Shigehiro Kuraku and Masahiko Hibi. Gene expression profiling of granule cells and Purkinje cells in the zebrafish cerebellum. Journal of Comparative Neurology, 2016. 525: 1558-1585. 63. Hitoshi Niwa, Akira Nakamura, Makoto Urata, Maki Shirae-Kurabayashi, Shigehiro Kuraku, Steven Russell and Satoshi Ohtsuka. The evolutionally-conserved function of group B1 Sox family members confers the unique role of Sox2 in mouse ES cells. BMC Evolutionary Biology 2016, 16:173. 62. Juliana Gutierrez-Mazariegos, Eswar Kumar Nadendla, Romain A. Studer, Susana Alvarez, Angel R. de Lera, Shigehiro Kuraku, William Bourguet, Michael Schubert & Vincent Laudet. Evolutionary diversification of retinoic acid receptor (RAR) ligand-binding pocket structure by molecular tinkering. Royal Society Open Science 2016, doi: 10.1098/rsos.150484 61. Fumiaki Sugahara, Juan Pascual-Anaya, Yasuhiro Oisi, Shigehiro Kuraku, Shin-ichi Aota, Noritaka Adachi, Wataru Takagi, Tamami Hirai, Noboru Sato, Yasunori Murakami, Shigeru Kuratani. Evidence from cyclostomes for complex regionalization of the ancestral vertebrate brain. Nature, 2016, 531: 97-100. 60. Yuuta Moriyama, Fumihiro Ito, Hiroyuki Takeda, Tohru Yano, Masataka Okabe, Shigehiro Kuraku, Fred W. Keeley and Kazuko, Koshiba-Takeuchi. Evolution of the fish heart by sub/neofunctionalization of an elastin gene. Nature Communications, 2016, 7: 10397 59. Genshiro A. Sunagawa, Kenta Sumiyama, Maki Ukai-Tadenuma, Dimitri Perrin, Hiroshi Fujishima, Hideki Ukai, Osamu Nishimura, Shoi Shi, Rei-ichiro Ohno, Ryohei Narumi, Yoshihiro Shimizu, Daisuke Tone, Koji L. Ode, Shigehiro Kuraku, Hiroki R. Ueda. Mammalian reverse genetics without crossing reveals Nr3a as a short-sleeper gene. Cell 4 Curriculum vitae – Shigehiro Kuraku Reports 2016, 14: 662-677. DOI: 10.1016/j.celrep.2015.12.052 58. Yukiko Ogino, Shigehiro Kuraku, Hiroshi Ishibashi, Hitoshi Miyakawa, Eri Sumiya, Shinichi Miyagawa, Hajime Matsubara, Gen Yamada, Michael E. Baker, Taisen Iguchi. Neofunctionalization of androgen receptor (AR) by gain-of-function mutations in teleost Fish lineage. Molecular Biology and Evolution, 2016, 33: 228-244. 2015 57. Yuichiro Hara, Kaori Tatsumi, Michio Yoshida, Eriko Kajikawa, Hiroshi Kiyonari. and Shigehiro Kuraku*. Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation. BMC Genomics 2015, 16: 977. 56. Yoko Yamaguchi, Wataru Takagi, Shigehiro Kuraku, Shunsuke Moriyama, Justin D. Bell, Andre P. Seale, Darren T. Lerner, E. Gordon Grau, Susumu Hyodo. Discovery of conventional prolactin from the holocephalan elephant fish, Callorhinchus milii. General and Comparative Endocrinology 2015, 224: 216-227. 55. Mitsumasa Koyanagi, Seiji Wada, Emi Kawano-Yamashita, Yuichiro Hara, Shigehiro Kuraku, Shigeaki Kosaka, Koichi Kawakami, Satoshi Tamotsu, Hisao Tsukamoto, Yoshinori Shichida, and Akihisa Terakita. Diversification of non-visual photopigment parapinopsin in spectral sensitivity for diverse pineal functions. BMC Biology, 2015, 13: 73. 54. Koh Onimaru, Shigehiro Kuraku, Wataru Takagi, Susumu Hyodo, James Sharpe and Mikiko Tanaka. A shift in anterior-posterior positional information underlies the fin-to-limb evolution. eLife, 2015, 4: e07048. doi: http://dx.doi.org/10.7554/eLife.07048.001. 53. Munazah Andrabi, Shigehiro Kuraku, Nozomu Takata, Yoshiki Sasai and Nick R. Love. Comparative, transcriptome analysis of self-organizing optic tissues. Scientific Data, 2015, 2: Article number: 150030. doi:10.1038/sdata.2015.30. 52. Miyuki Noro, Fumiaki Sugahara, Shigehiro Kuraku*. Reevaluating Emx gene phylogeny: homopolymeric amino acid tracts as a potential factor obscuring orthology signals in cyclostome genes. BMC Evolutionary Biology, 2015, 15:78. doi: 10.1186/s12862-015-0351-z. 51. Kaori Tatsumi, Osamu Nishimura, Kazu Itomi, Chiharu Tanegashima, Shigehiro Kuraku*. Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing. Biotechniques, 2015, 58: 253-257. doi: 10.2144/000114288. 2014 50. Benoit G Godard, Marion Coolen, Sophie Le Panse, Aurelie Gombault, Susana Ferreiro-Galve, Laurent Laguerre, Ronan Lagadec, Patrick Wincker, Julie Poulain, Corinne Da Silva, Shigehiro Kuraku, Wilfrid Carre, Agnes Boutet, and Sylvie Mazan. Mechanisms of endoderm formation in a cartilaginous fish reveal ancestral and homoplastic traits in jawed vertebrates. Biology Open, doi: 10.1242/bio.20148037. Curriculum vitae – Shigehiro Kuraku 5 49. Nathalie Feiner, Axel Meyer, Shigehiro Kuraku*. Evolution of the vertebrate Pax4/6 class of genes with focus on its novel member, the Pax10 gene. Genome Biology and Evolution, 2014. 6: 1635-1651. 2013 48. Saori Tani, Shigehiro Kuraku, Hiroshi Sakamoto, Kunio Inoue, and Rie Kusakabe. Developmental expression and evolution of muscle-specific microRNAs conserved in vertebrates. Evolution & Development, 2013 15: 293-304. 47. Nathalie Feiner, Yasunori Murakami, Lisa Breithut, Sylvie Mazan, Axel Meyer and Shigehiro Kuraku*. Saltatory evolution of the ectodermal neural cortex (ENC) gene family at the vertebrate origin. Genome Biology and Evolution, 2013. doi:10.1093/gbe/evt104. 46. Adina J. Renz, Axel Meyer and Shigehiro Kuraku*. Revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes. PLoS One, 2013. 8(6): e66400. doi:10.1371/journal.pone.0066400. 45. Zhuo Wang, et al (15th out of the 33 authros). The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nature Genetics, 2013. 45: 701–706. 44. Shigehiro Kuraku*, Christian M. Zmasek, Osamu Nishimura, and Kazutaka Katoh. aLeaves facilitates on-demand exploration of metazoan gene family trees
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