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Hiroki Shibata Last modified date:2017.08.01

Associate Professor / Division of Medical Molecular Cell Biology, Graduate School of Systems Life Sciences
Research Center for Transomics Medicine
Medical Institute of Bioregulation


Graduate School
Other Organization
Administration Post
Other


Homepage
http://gen.kyushu-u.ac.jp/~byouin/
Introduction of research projects, publications and members of the laboratory. .
Phone
092-642-6167
Fax
092-632-2375
Academic Degree
Ph D.
Field of Specialization
Genetics、Population Genetics
Outline Activities
Two major research projects (both heavily using NGS) are ongoing:
1. Exome sequencing is a powerful technique to identify causative variants of genetic diseases (Figure). However, the filtration of numerous candidate variants can be very difficult especially diseases so rare that a single pedigree ascertained. We introduced SNP linkage information for the filtration (Linkage-assisted exome sequencing). We are currently applying the technique on the analyses of multiple hereditary neurological diseases, such as idiopathic hyper CK-emia, spastic paraplegia and familial myochronic epilepsy.
2. Venoms are promising seeds for pharmaceutical discovery. Japanese pit viper, Habu snake (Protobothrops flavoviridis) is well known for the dangerous bites. However most of the venomic proteins are uncharacterized. Also accelerated evolution has been reported in many of the venomic proteins. Towards the complete characterization of the venomic proteins and the understanding of the mechanism of their accelerated evolution, we are currently working on omics studies of Habu snake, including whole genome sequencing, RNA-sequencing and population genetics studies.
Research
Research Interests
  • Genome divergence and diversity among island populations of Japanese Habu snakes, Protobothrops.
    keyword : Protobothrops flavoviridis, Protobothrops tokarensis, Protopbothrops elegans, mitochondria genome, microsatellite marker, genetic divergence, genetic diversity,
    2012.04.
  • Construction of the full length gene catalogue of Japanese Habu viper, Protobothrops flavoviridis.
    keyword : Protobothrops flavoviridis, next generation sequencer, RNA-sequencing, cDNA, venom gland, snake venoms
    2011.09.
  • Whole genome sequencing of Japanese Habu viper, Protobothrops flavoviridis.
    keyword : Protobothrops flavoviridis, next generation sequencer, denovo assembly, scaffolding, gene prediction, snake venoms
    2012.04.
  • Exome sequencing approach to identify the responsible variant for a hereditary motor and sensory neuropathy
    keyword : Hereditary motor and sensory neuropathy, linkage analysis, next generation sequencer, exome sequencing
    2010.04.
  • Evolutionary study of schizophrenia-associated genes.
    keyword : schizophrenia, glutamate receptor, molecular evolution, genetic diversity, natural selection
    2004.04~2013.03.
Academic Activities
Papers
1. Shiroh Miura, Takuya Morikawa, Ryuta Fujioka, Kazuhito Noda, Kengo Kosaka, Takayuki Taniwaki, Hiroki Shibata, A novel missense variation (Q220R) of GNB4 encoding a guanine nucleotide-binding protein, beta-4 in a Japanese autosomal dominant motor and sensory neuropathy family., European Journal of Medical Genetics, In press., 2016.06.
2. Shiroh Miura, Takuya Morikawa, Ryuta Fujioka, Kengo Kosaka, Kohei Yamada, Kazuhito Noda, Gohsuke Hattori, Manabu Motomura, Takayuki Taniwaki, Hiroki Shibata, A novel frameshift mutation of DDHD1 in a Japanese patient with autosomal recessive spastic paraplegia., European Journal of Medical Genetics, 59, 8, 2016.05.
3. Hiroki Shibata, Takahito Chijiwa, Shosaku Hattori, Koki Terada, Motonori Ohno, Yasuyuki Fukumaki, The taxonomic position and the unexpected divergence of the Habu viper, Protobothrops among Japanese subtropical islands., Molecular Phylogenetics and Evolution, 101, 2016.04.
4. Ken Sano, Shiroh Miura, Toshiya Fujiwara, Ryuta Fujioka, Akiko Yorita, Kazuhito Noda, Hiroshi Kida, Koichi Azuma, Shinjiro Kaieda, Ken Yamamoto, Takayuki Taniwaki, Yasuyuki Fukumaki, Hiroki Shibata, A novel missense mutation of RYR1 in familial idiopathic hyper CK-emia, Journal of Neurological Sciences, 356, 1-2, 2015.09.
5. Naoki Kubo, Hidehiro Toh, Kenjiro Shirane, Takayuki Shirakawa, Hisato Kobayashi, Sato Tetsuya, Hidetoshi Sone, Yasuyuki Sato, Shin-ichi Tomizawa, Yoshinori Tsurusaki, Hiroki Shibata, Hirotomo Saitsu, Yutaka Suzuki, Naomichi Matsumoto, Tomohiro Kono, Kazuyuki Ohbo, Hiroyuki Sasaki, DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis., BMC Genomics, 16, 1, 2015.08.
6. Hiroki Shibata, Ken Yamamoto, Zhu Sun, Akira Oka, Hidetoshi Inoko, Tadao Arinami, Toshiya Inada, Hiroshi Ujike, Masanari Itokawa, Mamoru Tochigi, Yuichiro Watanabe, Toshiyuki Someya, Hiroshi Kunugi, Tatsuyo Suzuki, Nakao Iwata, Norio Ozaki, Yasuyuki Fukumaki, Genome-wide association study of schizophrenia using microsatellite markers in the Japanese population., Psychiatr Genetics, 23, 3, 2013.06.
7. Hiroki Goto, Kazunori Watanabe, Naozumi Araragi, Rui Kageyama, Kunika Tanaka, Yoko Kuroki, Atsushi Toyoda, Masahira Hattori, Yoshiyuki Sakaki, Asao Fujiyama, Yasuyuki Fukumaki, Hiroki Shibata., The identification and functional implications of human-specific "fixed" amino acid substitutions in the glutamate receptor family., BMC Evolutionary Biology., 9: 224, 2009.09, [URL].
8. Hiroki Shibata, Ayako Tani, Tomoyuki Chikuhara, Rumiko Kikuta, Mayumi Sakai, Hideaki Ninomiya, Nobutada Tashiro, Nakao Iwata, Norio Ozaki and Yasuyuki Fukumaki. , Association study of polymorphisms in the group III metabotropic glutamate receptor genes, GRM4 and GRM7, with schizophrenia. , Psychiatric Res. , 167:88-96., 2009.04.
9. Shibata H, Aramaki T, Sakai M, Ninomiya H, Tashiro N, Iwata N, Ozaki N and Fukumaki Y., Association study of polymorphisms in the GluR7, KA1 and KA2 kainate receptor genes (GRIK3, GRIK4, GRIK5) with schizophrenia., Psychiatry Res., 141: 39-51, 2006.01.
10. Makino C, Shibata H, Ninomiya H, Tashiro N, Fukumaki Y., Identification of single-nucleotide polymorphisms in the human N-methyl-D-aspartate receptor subunit NR2D gene, GRIN2D, and association study with schizophrenia., Psychiatr Genet., 15, 3, 15 (3): 215-221., 2005.09.
11. Deng XD, Shibata H, Ninomiya H, Tashiro N, Iwata N, Ozaki N and Fukumaki Y., Association study of polymorphisms in the excitatory amino acid transporter 2 gene (SLC1A2) with schizophrenia., BMC Psychiatry, 4, 4(1): 21, 2004.08.
12. Takaki H, Kikuta R, Shibata H, Ninomiya H, Tashiro N and Fukumaki Y., Positive associations of polymorphisms in the metabotropic glutamate receptor type 8 gene (GRM8) with schizophrenia., Am J Med Genet., 128B, 1, 128B: 6-14., 2004.07.
13. The Japanese Schizophrenia Sib-pair Linkage Group., Initial genome-wide scan for linkage with schizophrenia in the Japanese Schizophrenia Sib-pair Linkage Group (JSSLG) families., Am J Med Genet., 120B, 1, 120B(1): 22-8., 2003.07.
14. Fujii Y, Shibata H, Kikuta R, Makino C, Tani A, Hirata N, Shibata A, Ninomiya H, Tashiro N, Fukumaki Y., Positive associations of polymorphisms in the metabotropic glutamate receptor type 3 gene (GRM3) with schizophrenia., Psychiatric Genetics., 13, 2, 13(2):71-6., 2003.06.
15. Makino C, Fujii Y, Kikuta R, Hirata N, Tani A, Shibata A, Ninomiya H, Tashiro N, Shibata H, Fukumaki Y., Positive association of the AMPA receptor subunit GluR4 gene (GRIA4) haplotype with schizophrenia: linkage disequilibrium mapping using SNPs evenly distributed across the gene region., Am J Med Genet., 116B, 1, 116B (1): 17-22., 2003.01.
16. Shibata H, Shibata A, Ninomiya H, Tashiro N, Fukumaki Y., Association study of polymorphisms in the GluR6 kainate receptor gene (GRIK2) with schizophrenia., Psychiatry Res., 113, 1-2, 113(1-2): 59-67., 2002.12.
17. Tani A, Kikuta R, Itoh K, Joo A, Shibata H, Ninomiya H, Tashiro N and Fukumaki Y., Polymorphism analysis of upstream regions of the human N-methyl-D-aspartate receptor subunit NR1 gene (GRIN1): implications for schizophrenia., Schizophr Research, 58, 1, 58 (1):83-86., 2002.11.
18. Shibata H, Joo A, Fujii Y, Tani A, Makino C, Hirata N, Kikuta R, Ninomiya H, Tashiro N, Fukumaki Y., Association study of polymorphisms in the coding region of the GluR5 kainate receptor gene (GRIK1) with schizophrenia., Psychiatric Genetics, 11, 3, 11 (3): 139-144., 2001.09.
19. Kiehl TR, Shibata H, Huynh DP, Vo T, Pulst SM., Identification and expression of a mouse ortholog of A2BP1., Mammalian Genome., 12 (8): 595-601., 2001.08.
20. Shibata H, Huynh DP, Pulst SM., A novel protein with RNA binding motif binds to C-terminal ataxin-2., Human Molecular Genetics, 9 (9): 1303-1313., 2000.05.
21. Shibata H, Tahira T, Hayashi K., RNA-primed PCR., Genome Research, 5, 4, 5 (4): 400-403., 1995.11.
22. Shibata H, Yamazaki T., Molecular evolution of the duplicated Amy locus in the Drosophila melanogaster species subgroup: concerted evolution only in coding region and an excess of nonsynonymous substitutions in speciation., Genetics, 141, 1, 141 (1): 223-236., 1995.09.
Presentations
1. Shiroh Miura, Takuya Morikawa, Ryuta Fujioka, Kazuhito Noda, Kengo Kosaka, Takayuki Taniwaki, Hiroki Shibata, A novel missense variation (Q220R) of GNB4 encoding a guanine nucleotide-binding protein, beta-4 in a Japanese neuropathy family., The European Human Genetics Conference 2017, 2017.05.28.
2. Hiroki Shibata, Accelerated evolution of venom protein genes in the habu genome., Global Symposium GEM , 2017.03.27.
3. Tomohisa Ogawa, Takahito Chijiwa, Naoko Oda-Ueda, Hitomi Nakamura, Shousaku Hattori, Kazumi Matsubara, Yoichi Matsuda, Kazuki Mori, Kosuke Tashiro, Shinichi Yamasaki, Manabu Fujie, Hiroki Goto, Ryo Koyanagi, Yasuyuki Fukumaki, Motonori Ohn, Eiichi Shoguchi, Kanako Hisata, Noriyuki Satoh, Hiroki Shibata, Habu snake genome reveals the evolutionary strategy for generating the venom-related genes., Global Symposium GEM , 2017.03.27.
4. Takuya Morikawa, Shiroh Miura, Kengo Kosaka, Ryuta Fujioka, Ken Sano, Akiko Yorita, Kosuke Aoki, Yusuke Uchiyama, Takayuki Taniwaki, Hiroki Shibata, Heterozygous missense mutation in SEC24A encoding a coat protein complex II vesicle associated with autosomal dominant spinocerebellar ataxia., 66th Annual Meeting of The American Society of Human Genetics, 2016.10.19.
5. Ryuta Fujioka, Shiroh Miura, Kohei Yamada, Takuya Morikawa, Hiromichi Motooka, Yasuhiro Aso, Noriyuki Kimura, Ken Sano, Ken Yamamoto, Takayuki Taniwaki, Hiroki Shibata, A missense mutation in the PPIG gene encoding the peptidyl-prolyl isomerase G in patients with autosomal dominant benign adult familial myoclonic epilepsy., 66th Annual Meeting of The American Society of Human Genetics, 2016.10.19.
6. Whole genome sequencing of a Japanese endemic pit viper, habu, Protobothrops flavoviridis reveals venom-related genes enriched in microchromosomal regions..
7. 柴田 弘紀, 山本真由美, 千々岩崇仁, 服部正策, 上田直子, 大野素徳, 服巻 保幸, Genetic divergence of mitochondria genome sequence among island populations of Japanese Habu snakes, Protobothrops., 第35回日本分子生物学会年会, 2012.12.13.
8. 藤原敏弥, 柴田 弘紀, 三浦史郎, 山本真由美, 貴田浩志, 野田和人, 加來庸一郎, 岩城 明子, 綾部光芳, 谷脇考恭, 服巻 保幸, Linkage-Exome approach to identify the responsible variant for a novel type of hereditary neuropathy, 第35回日本分子生物学会年会, 2012.12.13.
9. Molecular Evolutionary Study Of The Ionotropic Glutamate-Receptor Gene Family As Schizophrenia Susceptibility Genes: Human-Specific Balancing Selection In GRIN2B Upstream Region.
Membership in Academic Society
  • The Herpetological Society of Japan
  • Society of Evolutionary Studies, Japan
  • The Genetics Society of Japan
  • The Molecular Biology Society of Japan
  • The American Society of Human Genetics
  • The Japan Society of Human Genetics