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WMC Bioinformatics Faculty
 
WMC Bioinformatics Faculty
 

Prof. Kazuo Ishii

Professor of Genome Science
Tokyo University of Agriculture and Technology
3-5-8 Saiwai-cho, Fuchu, Tokyo
Japan
183-8509

 
 

Brief Biography:

Kazuo Ishii, Ph.D. is the Professor of Genome Science, School of Agriculture and Graduate School of Agriculture, Tokyo University of Agriculture and Technology. He dedicates to the Human Resource Development Program in Agricultural Genome Sciences in Tokyo University of Agriculture and Technology, funding supported from the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT).

Educational history:

1. 1982-1986: BS, Pharmacy, Shizuoka College of Pharmacy, Shizuoka, Japan
2. 1986-1988: MS, Pharmacy, Shizuoka College of Pharmacy, Shizuoka, Japan
3. 1991-1995: Ph.D., Medical Science, University of Tokushima, Tokushima, Japan

Professional history:

1. 1988-1991: Research Scientist, Nissui Pharmaceutical Co. Ltd., Ibaraki, Japan
2. 1995-1997: Research Scientist, Gene Analysis Center, TAKARA Shuzo Co. Ltd., Shiga, Japan
3. 1997-1998: Research Associate, Human Genome Center Institute of Medical Science, University of Tokyo, Tokyo, Japan
4. 1998-2000: Research Scientist, RIKEN-GSC, Yokohama, Japan
5. 2000-2002: Research Scientist, Centre National de Genotypage, Evry, France
6. 2003-2005: Research Scientist, Osaka Medical Center for Cancer and Cardiovascular Disease, Osaka, Japan
7. 2005-2009: Research Scientist, Tokyo University of Science, Chiba, Japan
8. 2010-2010: Bioinformatics Specialist, Northwestern University, Chicago, IL, USA
9. 2011-present: Professor of Genome Science, Tokyo University of Agriculture and Technology, Tokyo, Japan

 

Academic positions:

Professor of Genome Science

 

Research interests:

Bioinformatics, Statistics, Genome Science, Big Data & Cloud

 

Any other information:

Dr. Ishii specializes in bioinformatics, statistical genetics and biostatistics with computational statistics and statistical computing, especially using R/Bioconductor, Matlab, Perl/Python/Ruby scripting and MySQL database management system on the UNIX (Linux and *BSD) platform. His main research target is data analysis and data mining for next generation sequencing, microarray and protein mass analysis with MALDI-TOF-MS and LC/MS/MS for medical and agricultural applications. His main applications of NGS include de novo sequencing, resequencing, RNA-Seq, ChIP-Seq and metagenomics. Dr. Ishii also dedicates to several free software and open source software projects such as Debian GNU/Linux and Ruby.

Specialties:
Bioscience; Molecular biology, biochemistry, bioinformatics, biostatistics and pharmaceutics.
Computer Science; Programming (Java, Perl, Python, Ruby, Lisp, Haskell, C/C++), statistics (R/BioConductor, S-PLUS, Matrlab, Octave), database (MySQL, PostgreSQL) and Linux OS (Debian, Fedora, Ubuntu and *BSD).
Big Data and cloud computing; Hadoop MapReduce, Apache Mahout, NoSQL(HDFS, Hive, Pig), CloudStack and OpenStack

 

Publications:

1. G. Nagao, K. Ishii, K. Hirota, K. Makano, and H. Terada Role of lipid rafts in innate immunity and phagocytosis of polystyrene latex microspheres. Colloids Surf B Biointerfaces. 84(2):317-24. (2011) PMID: 21316932
2. G. Nagao, K. Ishii, K. Hirota, K. Makano, and H. Terada Role of lipid rafts in phagocytic uptake of polystyrene latex microspheres by macrophages. Anticancer Res , 30(8):3167-76. (2010) PMID:20871036
3. Ishii K, Kurita-Taniguchi M, Aoki M, Kimura T, Kashiwazaki Y, Matsumoto M, Seya T. Gene-inducing program of human dendritic cells in response to BCG cell-wall skeleton (CWS), which reflects adjuvancy required for tumor immunotherapy Immunology Letters, 98(2):280-90 (2005) PMID:15860229
4. Begum NA, Ishii K, Kurita-Taniguchi M, Tanabe M, Kobayashi M, Moriwaki Y, Matsumoto M, Fukumori Y, Azuma I, Toyoshima K, Seya T. Mycobacterium bovis BCG Cell Wall-Specific Differentially Expressed Genes Identified by Differential Display and cDNA Subtraction in Human Macrophages Infection and Immunity, 72(2), 937-948 (2004) PMID:14742539
5. Ichikawa Y, Goto J, Hattori M, Toyoda A, Ishii K, Jeong SY, Hashida H, Masuda N, Ogata K, Kasai F, Hirai M, Maciel P, Rouleau GA, Sakaki Y, Kanazawa I The genomic structure and expression of MJD, the Machado-Joseph desesase gene. Journal of Human Genetics, 46, 413-422 (2001) PMID:11450850
6. Hayashi T, Makino K, Ohnishi M, Kurokawa K, Ishii K, Yokoyama K, Han CG, Ohtsubo E, Nakayama K, Murata T, Tanaka M, Tobe T, Iida T, Takami H, Honda T, Sasakawa C, Ogasawara N, Yasunaga T, Kuhara S, Shiba T, Hattori M, Shinagawa H. Complete genome sequence of enterohemorrhagic Escherichia coliO157:H7 and genomic comparison with a laboratory strain K-12. DNA Research, 8, 11-22 (2001) PMID:11258796
7. Katsushi Yokoyama, Kozo Makino, Yoshino Kubota, Motoji Watanabe, Sigenobu Kimura, Chikako H. Yutsudo, Ken Kurokawa, Kazuo Ishii, Masahira Hattori, Ichiro Tatsuno, Hiroyuki Abe, Myonsun Yoh, Tetsuya Iida, Makoto Ohnishi, Tetsuya Hayashi, Teruo Yasunaga, Takeshi Honda, Chihiro Sasakawa and Hideo Shinagawa Complete nucleotide sequence of the prophage VT1-Sakai carrying the Shiga toxin 1 genes of the enterohemorrhagic Escherichia coli O157:H7 strain derived from the Sakai
outbreak. Gene, 258, 127-39 (2000)
8. Mutsunori Shirai, Hideki Hirakawa, Mitsuaki Kimoto, Mitsuaki Tabuchi, Fumio Kishi, Kazunobu Ouchi, Tadayoshi Shiba, Kazuo Ishii, Masahira Hattori, Satoru Kuhara and Teruko Nakazawa Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA. Nucleic Acids Research, 28, 2311-2314 (2000)
9. Mutsunori Shirai, Hideki Hirakawa, Kazunobu Ouchi, Mitsuaki Tabuchi, Fumio Kishi, Mitsuaki Kimoto, Hiroaki Takeuchi, Junko Nishida, Kaori Shibata, Ryutaro Fujinaga, Hiroshi Yoneda, Hiroshi Matsushima, Chiho Tanaka, Susumu Furukawa, Koshiro Miura, Atsushi Nakazawa, Kazuo Ishii, Tadayoshi Shiba, Masahira Hattori, Satoru Kuhara, and Teruko Nakazawa Comparison of outer membrane protein genes omp and pmp in the whole genome sequences of Chlamydia pneumoniae isolates from Japan and the United States. The Journal of Infectious Disease, 181, S524-S527 (2000)
10. M. Hattori, A. Fujiyama, T. D. Taylor, H. Watanabe, T. Yada, H.-S. Park, A. Toyoda, K. Ishii, Y. Totoki, D.-K. Choi, E. Soeda, M. Ohki, T. Takagi, Y. Sakaki, S. Taudien, K. Blechschmidt, A. Polley, U. Menzel, J. Delabara, K. Kumpf, R. Lehmann, D. Patterson, K. Reichwald, A. Rump, M. Schillhabel, A. Schudy, W. Zimmermann, A. Rosenthal, J. Kudoh, K. Shibuya, K. Kawasaki, S. Asakawa, A. Shintani, T. Sasaki, K. Nagamine, S. Mistuyama, S. E. Antonarakis, S. Minoshima, N. Shimizu, G. Nordsiek, K. Hornischer, P. Brandt, M. Scharfe, O. Schon, A. Desario, J. Reichelt, G. Kauer, H. Blocker, J. Ramser, A. Beck, S. Klages, S. Hennig, L. Riesselmann, E. Dagand, T. Haaf, S. Wehrmeyer, K. Borzym, K. Gardiner, D. Nizetic, F. Francis, H. Lehrach, R. Reinhardt and M.-L. Yaspo The DNA sequence of human chromosome 21. Nature, 405, 311 - 319 (2000)
11. Makoto Ohnishi, Chiho Tanaka, Satoru Kuhara, Kazuo Ishii, Masahira Hattori, Ken Kurokawa, Teruo Yasunaga, Kozo Makino, Hideo Shinagawa, Takahiro Murata, Keisuke Nakayama, Yoshiro Terawaki, and Testuya Hayashi Chromosome of the Enterohemorrhagic Escherichia coli O157:H7; Comparative Analysis with K-12 MG1655 Revealed the Acquisition of a Large Amount of Foreign DNAs. DNA Research, 6, 361-368 (1999)
12. Kozo Makino, Katsushi Yokoyama, Yoshino Kubota, Chikako H. Yutsudo, Sigenobu Kimura, Ken Kurosawa, Kazuo Ishii, Masahira Hattori, Ichiro Tatsuno, Hiroyuki Abe, Tetsuya Iida, Koichiro Yamamoto, Makoto Onishi, Tetsuya Hayashi, Teruo Yasunaga, Takeshi Handa, Chihiro Sasakawa, and Hideo Shinagawa. Complete Nucleotide Sequence of the Prophage VT2-Sakai Carring the Verotoxin 2 Genes of the Enterohemorrhagic Escherichia coli O157:H7 Derived from the Sakai Outbreak Genes
Genet. Syst., 74, 227-239 (1999)
13. Guipponi M, Scott HS, Hattori M, Ishii K, Sakaki Y, Antonarakis SE. Genomic structure, sequence, and refined mapping of the human intersectin gene (ITSN), which encompasses 250 kb on chromosome 21q22.1-->q22.2. Cytogenet Cell Genet. 83(3-4):218-20(1998). PMID:10072581
14. Fumihiko Matsuda, Kazuo Ishii, Patrice Bourvagnet, Kei-ichi Kuma, Hidenori Hayashida, Takashi Miyata, and Tasuku Honjyo The Complete Nucleotide Sequence of the Human Immunoglobulin Heavy Chain Variable Region Locus. Jounal of Exp. Med., 188, 2151-2162 (1998)
15. Takanobu Imanaka, Hideki Hayashi, Kazuhiro Kishi, Lihong Wang, Kazuo Ishii,
Osamu Hazeki, Toshiaki Katada, and Yousuke Ebina Reconstitution of Insulin Signaling Pathways in Rat 3Y1 Cells Lacking Insulin Receptor and Insulin Receptor Substrate-1. The Journal of Biological Chemistry, 273, 25347-25355 (1998)
16. Kozo Makino, Kazuo Ishii, Teruo Yasunaga, Masahira Hattori, Katsushi Yokayama, Chikako H. Yutsudo, Yoshino Kubota, Yoshiharu Yamaichi, Tetsuya Iida, Koichiro Yamamoto, Takeshi Honda, Chang-Gyun Han, Eiichi Otstubo, Masaaki Kasamastu, Tetsuya Hayashi, Satoru Kuhara, and Hideo Shinagawa Complete Nucleotide Sequences of 93-kb and 3.3-kb Plasmids of an Enterohemorrhagic
Escherichia coli O157:H7 Derived from Sakai Outbreak. DNA Research, 5, 1-9 (1998)
17. Lihong Wang, Hideki Hayashi, Yasumasa Mitani, Kazuo Ishii, Tetsuo Ohnishi, Yasuharu Niwa, Hiroshi Kida, and Yosuke Ebina Cloning of a cDNA Encoding a 190-kDa Insulin Receptor Substrate-1-like Protein of Simian COS Cells. Biochemical and Biophysical Research Communications, 216, 321-328 (1995)
18. Kazuo Ishii, Hideki Hayashi, Mikio Todaka, Seika Kamohara, Fumihiko Kanai, Hideaki Jinnouchi, Lihong Wang, and Yousuke Ebina Possible Domains Responsible for Intracellular Targeting and Insulin-Dependent Translocation of Glucose Transporter Type 4. Biochemical Journal, 309, 813-823 (1995)
19. Seika Kamohara, Hideki Hayashi, Mikio Todaka, Fumihiko Kanai, Kazuo Ishii, Takanobu Imanaka, Jaime A. Escobedo, Lewis T. Williams, and Yosuke Ebina Platelet-Derived Growth Factor Triggers Translocation of the Insulin-Regulatable Glucose Transporter (Type 4) Predominantly through Phosphatidylinositol 3-Kinase Binding Sites on the Receptor. Proceeding National Academy of Science USA 92, 1077-1081 (1995)
20. Kazuo Ishii, Seika Kamohara, Hideki Kayashi, Mikio Todaka, Fumihiko Kanai, Takanobu Imanaka, and Yousuke Ebina Epidermal Growth Factor Triggers the Translocation of Insulin-responsive Glucose Transporter (GLUT4). Biochemical and Biophysical Research Communications, 205, 857-863 (1994)
21. Mikio Todaka, Toshihiko Nishiyama, Takashi Murakami, Seiichiro Saito, Kimio Ito, Fumihiko Kanai, Masaharu Kan, Kazuo Ishii, Hideki Hayashi, Motoaki Shichiri, and Yousuke Ebina The Role of Insulin in Activation of Two Enhancers in the Mouse GLUT1 Gene. The Journal of Biological Chemistry, 269, 29265-29270 (1994)
22. Fumihiko Kanai, Kimio Ito, Mikio Todaka, Hideki Hayashi, Seika Kamohara, Kazuo Ishii, Taro Okada, Osamu Hazeki, Michi Ui, and Yousuke Ebina Insulin-Stimulated GLUT4 Translocation is Relevant to the Phosphorylation of IRS-1 and the Activity of PI3-Kinase. Biochemical and Biophysical Research Communications, 195, 762-768 (1993)
23. Hideki Hayashi, Yasuhiko Nishioka, Seika Kamohara, Fumihiko Kanai, Kazuo Ishii, Yasuhira Fukui, Fitoshi Shibasaki, Tadaomi Takenawa, Hiroshi Kido, Nobuhiko Kastunuma, and Yousike Ebina
The a-Type 85-kDa Subunit of Phosphatidylinositol 3-Kinase is Phosphoryrated at Tyrosines 368, 580, and 607 by the Insulin Receptor. The Journal of Biological Chemistry, 268, 7107-7117 (1993)
24. Takashi Murakami, Toshihiko Nishiyama, Tetsuya Shirotani, Yasuo Shinohara, Masaharu Kan, Kazuo Ishii, Fumihiko Kanai, Shoichi Nakazuru, and Yousuke Ebina Identification of Two Enhancer Elements in the Gene Encoding the Type 1 Glucose Transporter from the Nouse Which Are Responsive to Serum, Growth Factor, and Oncogenes. The Journal of Biological Chemistry, 267, 9300-9306(1992)
25. Takao Taki, Shigeru Nishiwaki, Kazuo Ishii, and Shizuo Handa A Simple and Specific Assey of Glycosyltransferase and Glycosidase Activities by an Enzyme-Linked Immunosorbent Assey Method, and Its Application to Assey of Galactosyltransferase Activity in Sera from Patients with Cancer. Journal of Biochemistry, 107, 493-498(1990)
26. Takao Taki, Kaname Yamamoto, Miki Takamatsu, Kazuo Ishii, Akio Myoga, Kiyoshi Sekiguchi, Isao Ikeda, Kunio Kurata, Jun Nakayama, Shizuo Handa, and Makoto Matsumoto Accumulation of Gangliosides With N-Acetylneuraminisyl(a2-6)lactosamine Structure in Primary Human Hepatoma.
Cancer Research, 50, 1284-1290 (1990)

 

What I think of the idea behind WebmedCentral:

I think it is very good idea. I would like to perform any contribution for WebmedCentral, such as an editor, a reviewer, an adviser, a colsultant and a conference master in bioinformatics and computational biology.