fujibuchi

Wataru Fujibuchi, Ph.D.

Current Job:
Team Leader
Computational Biology Research Center
National Institute of Advanced Industrial Science and Technology
AIST Tokyo Waterfront Bio-IT Research Building 10F, 2-42 Aomi, Koto-ku, Tokyo 135-0064, JAPAN
Voice: +81-3-3599-8619, Email: w.fujibuchi(a)aist.go.jp

Research Interests:
Regulatory Genomics, Systems Biology, Sequence analysis of promoter functions, Microarray data analysis, Prediction of genetic networks, Integrative analysis of cell functions

Education and Job Career
2007.4- Team Leader, CBRC
2003.10-2007.3 Research Scientist, CBRC
2003.6-2003.9 AIST Research Staff, CBRC
2002.7-2003.5 Staff Scientist, NCBI
1999.4-2002.7 Visiting Fellow, National Center for Biotechnology Information(NCBI), NIH
1995.7-1999.3 Research Associate, Institute for Chemical Research, Kyoto Univ.
1998.5 Ph.D. Biophysics, Kyoto Univ.
1993.3 M.S. Biophysics, Kyoto Univ.
1991.3 B.S. Zoology, Hiroshima Univ.

Publications

  • Fujibuchi, W. and Kanehisa, M., A method to extract functional motifs for transcriptional regulation in eukaryotic sequences, Bull. Inst. Chem. Res., Kyoto Univ., 71, 317-326, 1993.
  • Ogata, H., Fujibuchi, W. and Kanehisa, M., The size differences among mammalian introns are due to the accumulation of small deletions, FEBS Lett. 390, 99-103, 1996.
  • Ogata, H., Bono, H., Fujibuchi, W., Goto, S. and Kanehisa, M., Analysis of binary relations and hierarchies of enzymes in the metabolic pathways, Genome Informatics 7, 128-136, 1996.
  • Goto, S., Bono, H., Ogata, H., Fujibuchi, W., Nishioka, T., Sato, K. and Kanehisa, M., Organizing and computing metabolic pathway data in terms of binary relations, Pacific Symposium on Biocomputing '97, 175-186, 1996.
  • Fujibuchi, W. and Kanehisa, M., Prediction of gene expression specificity by promoter sequence patterns, DNA Res., 4, 81-90, 1997.
  • Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, J., Akiyama, Y. and Kanehisa, M., DBGET/LinkDB: an Integrated Database Retrieval System, Pacific Symposium on Biocomputing '98, 683-694, 1997.
  • Fujibuchi, W., Sato, K., Ogata, H., Goto, S. and Kanehisa, M., KEGG and DBGET/LinkDB: Integration of biological relationships in divergenet molecular biology data, Knowledge Sharing Across Biological and Medical Knowledge Based Systems, Technical Report WS-98-04, 35-40, AAAI Press, 1998.
  • Bono, H., Goto, S., Fujibuchi, W., Ogata, H. and Kanehisa, M., Systematic prediction of orthologous units of genes in the complete genomes, Genome Informatics, 9, 32-40, 1998.
  • Ogata, H., Goto, S., Fujibuchi, W. and Kanehisa, M., Computation with the KEGG pathway database, BioSystems 47, 119-128, 1998.
  • Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H. and Kanehisa, M., KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Res. 27, 29-34, 1999.
  • Fujibuchi, W., Ogata, H., Matsuda,H. and Kanehisa, M., Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping, Nucleic Acids Res., 15, 2000.
  • Ogata, H., Fujibuchi, W., Goto, S. and Kanehisa, M., A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters, Nucleic Acids Res. 28, 4021-4028, 2000.
  • Fujibuchi, W., John S. Anderson and David Landsman, PROSPECT improves cis-acting regulatory element prediction by integrating expression profile data with consensus pattern searches, Nucleic Acids Res., 29, 2001.
  • Ono, Y., Fujibuchi, W. and Suwa, M., Automatic gene collection system for genome-scale overview of G-protein coupled receptors in eukaryotes，GENE, 364, 53-62, 2005.
  • Tanya Barrett, Tugba Suzek, Dennis Troup, Stephen Wilhite, Wing-Chi Ngau, Pierre Ledoux, Dmitry Rudnev, Alex Lash, Fujibuchi, W., Ron Edgar, NCBI GEO: Mining millions of expression profiles - database and tools, NUCLEIC ACIDS RESEARCH， 33， D562-D566, 2005.
  • Horton, P. and Fujibuchi, W., An Upper Bound on the Hardness of Exact Matrix Based Motif Discovery， Combinatorial Pattern Matching，16th Annual Symposium, 219-228, 2005.
  • Kato, T., Murata, Y., Miura, K., Asai, K., Horton, P., Tsuda, K. and Fujibuchi, W., Network-based de-noising improves prediction from microarray data, BMC BIOINFORMATICS, 7-S1, S4, 2006.
  • Polouliakh N, Natsume, T., Harada, H., Fujibuchi, W. and Horton, P., Comparative genomic analysis of transcription regulation elements involved in the human MAP-kinase G-protein coupling pathway, Journal of Bioinformatics and Computational Biology, 4, 469-482, 2006.
  • Kato, T., Fujibuchi, W. and Asai, K., Learning Kernels from Distance Constraints，IPSJ, 47-SIG10, 1-11、2006.
  • Horton, P., Kiseleva, L. and Fujibuchi, W.，RaPiDS: An Algorithm for Rapid Expression Profile Database Search, Genome Informatics, 17-2, 67-76, 2006.
  • Fujibuchi, W. and Kato, T., Classification of Heterogeneous Microarray Data by Maximum Entropy Kernel, BMC BIOINFORMATICS, 8(267), 2007.
  • Fujibuchi, W., Kiseleva, L., Taniguchi, T., Harada, H. and Horton, P., CellMontage: Similar Expression Profile Search Server, Bioinformatics, 23(22), 3103-3104, 2007.
  • Okada, Y., Fujibuchi, W. and Horton, P., A biclustering method for gene expression module discovery using closed itemset enumeration algorithm, IPSJ Transactions on Bioinformatics, 48(SIG 5(TBIO2)), 39-48, 2007.
  • Okada, Y., Fujibuchi, W. and Horton, P., Exhaustive search of maximal biclusters in gene expression data， IAENG，2-1， 307-312、2007.
  • Okada, Y., Okubo, K., Horton, P. and Fujibuchi, W., Exhaustive Search Method of Gene Expression Modules and Its Application to Human Tissue Data, IAENG International Journal of Computer Science, 34(1), 119-126, 2007.
  • Okada, Y. and Fujibuchi, W., Mining a Large-scale Microarray Database for Similar Gene Expression Modules to Find Distant Relationships between Down Syndrome and Huntington's Disease, Proceedings of Critical Assessment of Microarray Data Analysis 07, Valencia, Spain, 2007.
  • Sasaki, H., Miura, K., Horii, A., Kaneko, N., Fujibuchi, W., Kiseleva, L., Gu, Z., Murata, Y., Karasawa, H., Mizoi, T., Kobayashi, T., Kinouchi, M., Ohnuma, S., Yazaki, N., Unno, M., and Sasaki, I., An orthotopic implantation mice model and cDNA microarray analysis demonstrates several genes potentially involved in the lymph node metastasis of colorectal cancer, Cancer Science 99(4):711-9, 2007.
  • Sato, K., Hamada, S., Kimura, K., Kanno, A., Hirota, M., Fujibuchi, W., Tanaka, N., Miura, K., Masamune, A., Vonderhaar, B.K. and Shimosegawa, T., Up-regulation of MSX2 enhances the malignant phenotype and associates with Twist 1 expression in human pancreatic cancer cells, American Journal of Pathology, 172(4), 926-39, 2008.
  • Hamada, S., Satoh, K., Hirota, M., Fujibuchi, W., Kanno, A., Umino, J., Ito, H., Satoh, A., Kikuta, K., Kume, K., Masamune, A., and Shimosegawa, T., "Expression of the calcium-binding protein S100P is regulated by bone morphogenetic protein in pancreatic duct epithelial cell lines, Cancer Sci. 2009, 100(1):103-10.
  • Ohnuma S, Miura K, Horii A, Fujibuchi W, Kaneko N, Gotoh O, Nagasaki H, Mizoi T, Tsukamoto N, Kobayashi T, Kinouchi M, Okabe M, Sasaki H, Shiiba K, Miyagawa K, Sasaki I., Cancer-associated splicing variants of the CDCA1 and MSMB genes expressed in cancer cell lines and surgically resected gastric cancer tissues., Surgery. 2009 Jan;145(1):57-68.
  • Karasawa, H., Miura, K., Fujibuchi, W., Ishida, K., Kaneko, N., Kinouchi, M., Okabe, M., Ando, T., Murata, Y., Sasaki, H., Takami, K., Yamamura, A., Shibata, C., and Sasaki, I. Down-regulation of cIAP2 enhances 5-FU sensitivity through the apoptotic pathway in human colon cancer cells. Cancer Sci. 2009, 100(5), 903-13.
  • Fujiubchi, W., Kim, H., Okada, Y., Taniguchi, T., and Sone, H., High-performance gene expression module analysis tool and its application to chemical toxicity data, Methods in Molecular Biology, vol. 577, pp.55-65, Humana Press Inc., U.S.A. 2009.
  • Fujibuchi, W., Chiba, H., Akiyama, H., and Shiku, H., Designing Pyro-Primer Sequences Using a Simulated Annealing Algorithm, to Critically Target mRNAs in Quantitative Cell Analysis, Proceedings of the 6'th International Forum on Post-genome Technologies, pp.253-7, Beijing 2009.
  • Pessiot, J.F., Chiba, H., Hyakkoku, H., Taniguchi, T., and Fujibuchi, W., PeakRegressor identifies composite sequence motifs responsible for STAT1 binding sites and their potential rSNPs, Proceedings of Critical Assessment of Massive Data Analysis 2009, pp.4-11, Chicago 2009.
  • Sone H, Okura M, Zaha H, Fujibuchi W, Taniguchi T, Akanuma H, Nagano R, Ohsako S, Yonemoto J., Profiles of Chemical Effects on Cells (pCEC): a toxicogenomics database with a toxicoinformatics system for risk evaluation and toxicity prediction of environmental chemicals., J Toxicol Sci. 2010;35(1):115-23.
  • Kato, T., and Fujibuchi, W., Kernel classification methods for cancer microarray data!I, Medical Biostatistics for Complex Diseases, WILEY-VCH, Weinheim, Germany (2010).
  • Tochigi Y, Sato N, Sahara T, Wu C, Saito S, Irie T, Fujibuchi W, Goda T, Yamaji R, Ogawa M, Ohmiya Y, Ohgiya S., Sensitive and Convenient Yeast Reporter Assay for High-Throughput Analysis by Using a Secretory Luciferase from Cypridina noctiluca., Anal Chem. 82, 5768-76, 2010.
  • Pessiot, J.F., Chiba, H., Hyakkoku, H., Taniguchi, T., and Fujibuchi, W., PeakRegressor identifies composite sequence motifs responsible for STAT1 binding sites and their potential rSNPs, PLoS ONE(accepted) 2010.

    日本語刊行物、テクニカルレポート
  • 「ゲノム情報解析」藤渕 航, 金久 實, AIセンターだより, 24, 14-19, 1992.
  • 「ゲノムネットのデータベース利用法」第一章, 第三章, 藤渕 航, 共立出版、1996.
  • 「遺伝子・ゲノム百科辞典」藤渕 航, 金久 實, 遺伝子医学、1(2), 119-124, 1997.
  • 「ゲノムネットのデータベース利用法（第２版）」第二章, 藤渕 航, 共立出版、1998.
  • 「遺伝子クラスター解析」藤渕 航, 金久 實, 数理科学、432, 12-18, 1999.
  • 「遺伝子クラスター解析」藤渕 航, 金久 實, 数理科学別冊, 2001.
  • 「ゲノム研究実験ハンドブック，第２章生物学データベース ７．遺伝子発現プロファイルデータベースGEOデータベース」, Polouliakh Natalia, 藤渕 航，羊土社, 2004.
  • 「タンパク質分析（研究）超基本Q＆A，Q94 タンパク質の相互作用をインターネットで調べたい」，藤渕 航，羊土社, 2005.
  • 「産総研TODAY，CellMontage 遺伝子発現プロファイル検索解析システム」，藤渕 航，独立行政法人産業技術総合研究所, 2005.
  • 「細胞の知識ベース開発と遺伝子発現プロファイルによる細胞種と特徴予測」, 藤渕 航, Larisa Kiseleva, 谷口丈晃, Paul Horton, IPSJ SIG Technical Report, 2005-BIO-2, 33-37, 2005.
  • 「極大２部クリーク列挙法による遺伝子発現モジュールの抽出」, 岡田 吉史, 藤渕 航, Horton Paul, IPSJ SIG Technical Report，2006-BIO-6， 17-23, 2006.
  • 「GSEAによるマイクロアレイデータからの遺伝子機能セットの探索法」, 藤渕 航, 岡田 吉史, 羊土社, 25-26, 2007.
  • 「バイオデータベースとウェブツールの手取り足取り利用法」「GEO」，岡田 吉史, 藤渕 航，羊土社, 150-156, 2007.
  • 「マイクロアレイ データ統合解析プロトコール」,藤渕 航／堀本 勝久（編）, 羊土社（2008）.
  • 「シングルセル解析の最前線」「シミュレーテッドアニーリングによる多重プライマー配列デザイン法‐細胞内mRNA絶対定量に向けて−」, 藤渕 航, シーエムシー出版, 265-73, 2010.




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