fujibuchi

Wataru Fujibuchi, Ph.D.

Current Job:
Professor
Center for iPS Research and Application (CiRA)
Kyoto University
(Concurrently) Computational Biology Research Center, AIST
(Concurrently) Faculty of Science and Engineering, Waseda Univ.
53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, JAPAN
Voice: +81-75-366-7012, Email: w.fujibuchi(a)cira.kyoto-u.ac.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
2012.4- Invited Senior Researcher, CBRC
2012.4- Professor, Center for iPS Research and Application, Kyoto University
2007.4-2012.3 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
【Reviewed Publications】 *…Corresponding

  1. CELLPEDIA: a repository for human cell information for cell studies and differentiation analyses, Hatano, A., Chiba, H., Moesa, H.A., Taniguchi, T., Nagaie, S., Yamanegi, K., Takai, T., Tanaka, H., *Fujibuchi, W., Database 2011, bar046 (2011).
  2. Prediction of Chemical Toxicity by Network-based SVM on ES-cell Validation System, *Fujibuchi, W., Aburatani, S., Yamane, J., Imanishi, S., Akanuma, H., Sone, H., Ohsako, S.,The Proceedings of the 2011 Joint Conference of CBI-Society and JSBi, Kobe (2011).
  3. Differential diagnosis of rectal carcinoma using immunohistochemistry of carcinomas from other pelvic organs with NCBI literature survey and the Human Protein Atlas database. Miura, K., Ishida, K., Fujibuchi, W., Ito, A., Niikura, H., Ogawa, H., Sasaki, I., Surg Today (In press).
  4. Infiltration of CD14-positive macrophages at the invasive front indicates a favorable prognosis in colorectal cancer patients with lymph node metastasis. Kinouchi M, Miura K, Mizoi T, Ishida K, Fujibuchi W, Ando T, Yazaki N, Saito K, Shiiba K, Sasaki I. Hepatogastroenterology. 58(106):352-8 (2011).
  5. Structural elements of the signal propagation pathway in squid rhodopsin and bovine rhodopsin. Sugihara M, Fujibuchi W, Suwa M. J Phys Chem B. 115(19):6172-9 (2011).
  6. Invited Review: Inhibitor of apoptosis protein family as diagnostic markers and therapeutic targets of colorectal cancer. Miura K, Fujibuchi W, Ishida K, Naitoh T, Ogawa H, Ando T, Yazaki N, Watanabe K, Haneda S, Shibata C, Sasaki I. Surg Today. 41(2):175-82 (2011).
  7. Review: Alternative pre-mRNA splicing in digestive tract malignancy. Miura K, Fujibuchi W, Sasaki I. Cancer Sci. 102(2):309-16 (2011).
  8. In search of true reads: A classification approach to next generation sequencing data, E. Wijaya, J.F. Pessiot, M.C. Frith, W. Fujibuchi, K. Asai & P. Horton, Intl. Conference on Bioinformatics and Biomedicine Workshops, 37:561-6 (2011).
  9. PeakRegressor identifies composite sequence motifs responsible for STAT1 binding sites and their potential rSNPs, Pessiot, J.F., Chiba, H., Hyakkoku, H., Taniguchi, T., and *Fujibuchi, W., PLoS ONE, 5(8):e11881 (2010).
  10. Sensitive and convenient yeast reporter assay for high-throughput analysis by using a secretory luciferase from Cypridina noctiluca. Tochigi Y, Sato N, Sahara T, Wu C, Saito S, Irie T, Fujibuchi W, Goda T, Yamaji R, Ogawa M, Ohmiya Y, Ohgiya S., Analytical Chemistry, 82(13):5768-76 (2010).
  11. Profiles of Chemical Effects on Cells (pCEC): a toxicogenomics database with a toxicoinformatics system for risk evaluation and toxicity prediction of environmental chemicals.Sone H, Okura M, Zaha H, Fujibuchi W, Taniguchi T, Akanuma H, Nagano R, Ohsako S, Yonemoto J. J Toxicol Sci. 35(1):115-23 (2010).
  12. Invited Review: Miura, K., Kinouchi, M., Ishida, K., Fujibuchi, W., Naitoh, T., Ogawa, H., Ando, T., Yazaki, N., Watanabe, K., Haneda, S., Shibata, C., Sasaki, I. Cancers, Special Issue: Cell Death and Cancer (Edited by Prof. Samali A) 5-FU Metabolism in Cancer and Orally-Administrable 5-FU Drugs. 2, 1717-1730 (2010).
  13. PeakRegressor identifies composite sequence motifs responsible for STAT1 binding sites and their potential rSNPs, Pessiot, J.F., Chiba, H., Hyakkoku, H., Taniguchi, T., and Fujibuchi, W., Proceedings of Critical Assessment of Massive Data Analysis 2009, pp.4-11, Chicago (2009).
  14. Designing Pyro-Primer Sequences Using a Simulated Annealing Algorithm, to Critically Target mRNAs in Quantitative Cell Analysis, *Fujibuchi, W., Chiba, H., Akiyama, H., and Shiku, H., Proceedings of the 6'th International Forum on Post-genome Technologies, pp.253-7, Beijing (2009).
  15. Expression of the calcium-binding protein S100P is regulated by bone morphogenetic protein in pancreatic duct epithelial cell lines, 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., Cancer Sci. 100(1):103-10 (2009).
  16. Down-regulation of cIAP2 enhances 5-FU sensitivity through the apoptotic pathway in human colon cancer cells, 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. Cancer Sci. 100(5):903-13 (2009).
  17. Cancer-associated splicing variants of the CDCA1 and MSMB genes expressed in cancer cell lines and surgically resected gastric cancer tissues, 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., Surgery 145(1):57-68 (2009).
  18. Up-regulation of MSX2 enhances the malignant phenotype and associates with Twist 1 expression in human pancreatic cancer cells, Sato, K., Hamada, S., Kimura, K., Kanno, A., Hirota, M., Fujibuchi, W., Tanaka, N., Miura, K., Masamune, A., Vonderhaar, B.K. and Shimosegawa, T., American Journal of Pathology, 172(4):926-939, 2008.
  19. An orthotopic implantation mice model and cDNA microarray analysis demonstrates several genes potentially involved in the lymph node metastasis of colorectal cancer, 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., Cancer Science, 99(4):711-9 (2008).
  20. Classification of Heterogeneous Microarray Data by Maximum Entropy Kernel, *Fujibuchi, W. and Kato, T., BMC Bioinformatics 8(267) (2007).
  21. CellMontage: Similar Expression Profile Search Server, Fujibuchi, W., Kiseleva, L., Taniguchi, T., Harada, H. and Horton, P., Bioinformatics 23(22):3103-3104 (2007).
  22. A biclustering method for gene expression module discovery using closed itemset enumeration algorithm, Okada, Y., Fujibuchi, W. and Horton, P., IPSJ Transactions on Bioinformatics 48(SIG 5(TBIO2)):39-48, 2007.
  23. Exhaustive search of maximal biclusters in gene expression data, Okada, Y., Fujibuchi, W. and Horton, P., IAENG,2-1:307-312 (2007).
  24. Exhaustive Search Method of Gene Expression Modules and Its Application to Human Tissue Data, Okada, Y., Okubo, K., Horton, P. and *Fujibuchi, W., IAENG International Journal of Computer Science 34(1), 119-126 (2007).
  25. Mining a Large-scale Microarray Database for Similar Gene Expression Modules to Find Distant Relationships between Down Syndrome and Huntington's Disease, Okada, Y. and *Fujibuchi, W., Proceedings of Critical Assessment of Microarray Data Analysis 07, Valencia, Spain (2007).
  26. Network-based de-noising improves prediction from microarray data, Kato, T., Murata, Y., Miura, K., Asai, K., Horton, P., Tsuda, K. and *Fujibuchi, W., BMC Bioinformatics 7(Suppl. 1):S4 (2006).
  27. Comparative genomic analysis of transcription regulation elements involved in the human MAP-kinase G-protein coupling pathway, Polouliakh N, Natsume, T., Harada, H., Fujibuchi, W. and Horton, P., Journal of Bioinformatics and Computational Biology 4:469-482 (2006).
  28. Learning Kernels from Distance Constraints, Kato, T., Fujibuchi, W. and Asai, K., IPSJ 47(SIG10):1-11 (2006).
  29. RaPiDS: An Algorithm for Rapid Expression Profile Database Search, Horton, P., Kiseleva, L. and Fujibuchi, W., Genome Informatics 17(2):67-76 (2006).
  30. Kernels for Noisy Microarray Data, Tsuyoshi Kato, Wataru Fujibuchi, Kiyoshi Asai, CBRC Technical Report AIST-02-J00001-8 (2006).
  31. Drug-response prediction from microarray using network-based de-noising, Tsuyoshi Kato, Yukio Murata, Koh Miura, Kiyoshi Asai, Paul B. Horton, Koji Tsuda, Wataru Fujibuchi, IPSJ SIG technical reports 2006:47-52 BIO-5-(8) (2006).
  32. Kernel construction from distance constraints, Tsuyoshi Kato, Wataru Fujibuchi, Kiyoshi Asai, CBRC Technical Report AIST02-J00001-7 (2005).
  33. NCBI GEO: Mining millions of expression profiles - database and tools, Tanya Barrett, Tugba Suzek, Dennis Troup, Stephen Wilhite, Wing-Chi Ngau, Pierre Ledoux, Dmitry Rudnev, Alex Lash, Fujibuchi, W., Ron Edgar, Nucleic Acids Res. 33:D562-566 (2005).
  34. Automatic gene collection system for genome-scale overview of G-protein coupled receptors in eukaryotes, Ono, Y., Fujibuchi, W. and Suwa, M., GENE 364:53-62 (2005).
  35. An Upper Bound on the Hardness of Exact Matrix Based Motif Discovery, Horton, P. and Fujibuchi, W., Combinatorial Pattern Matching,16th Annual Symposium pp.219-228 (2005).
  36. PROSPECT improves cis-acting regulatory element prediction by integrating expression profile data with consensus pattern searches, Fujibuchi, W., John S. Anderson and David Landsman, Nucleic Acids Res. 29(19):3988-96 (2001).
  37. Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping, Fujibuchi, W., Ogata, H., Matsuda,H. and Kanehisa, M., Nucleic Acids Res. 28(20):4029-36 (2000).
  38. A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters, Ogata, H., Fujibuchi, W., Goto, S. and Kanehisa, M., Nucleic Acids Res. 28(20):4021-28 (2000).
  39. KEGG: Kyoto Encyclopedia of Genes and Genomes, Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H. and Kanehisa, M., Nucleic Acids Res. 27(1):29-34 (1999).
  40. Computation with the KEGG pathway database, Ogata, H., Goto, S., Fujibuchi, W. and Kanehisa, M., BioSystems 47(1-2):119-128 (1998).
  41. Systematic prediction of orthologous units of genes in the complete genomes, Bono, H., Goto, S., Fujibuchi, W., Ogata, H. and Kanehisa, M., Genome Informatics 9:32-40 (1998).
  42. KEGG and DBGET/LinkDB: Integration of biological relationships in divergenet molecular biology data, Fujibuchi, W., Sato, K., Ogata, H., Goto, S. and Kanehisa, M., Knowledge Sharing Across Biological and Medical Knowledge Based Systems, Technical Report WS-98-04:35-40 (1998).
  43. Prediction of gene expression specificity by promoter sequence patterns, Fujibuchi, W. and Kanehisa, M., DNA Res., 4(2):81-90 (1997).
  44. DBGET/LinkDB: an Integrated Database Retrieval System, Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, J., Akiyama, Y. and Kanehisa, M., Pacific Symposium on Biocomputing '98, pp.683-694 (1997).
  45. The size differences among mammalian introns are due to the accumulation of small deletions, Ogata, H., Fujibuchi, W. and Kanehisa, M., FEBS Lett. 390(1):99-103 (1996).
  46. Analysis of binary relations and hierarchies of enzymes in the metabolic pathways, Ogata, H., Bono, H., Fujibuchi, W., Goto, S. and Kanehisa, M., Genome Informatics 7, pp.128-136 (1996).
  47. Organizing and computing metabolic pathway data in terms of binary relations, Goto, S., Bono, H., Ogata, H., Fujibuchi, W., Nishioka, T., Sato, K. and Kanehisa, M., Pacific Symposium on Biocomputing '97, pp.175-186 (1996).
  48. A method to extract functional motifs for transcriptional regulation in eukaryotic sequences, Fujibuchi, W. and Kanehisa, M., Bull. Inst. Chem. Res., Kyoto Univ. 71:317-26 (1993).
【Books】
  1. 千葉啓和、藤渕航「細胞情報解析に役立つツール―幹細胞研究の進展とその創薬応用に向けて」実験医学28(19)pp.3171-4、羊土社2010.
  2. Kato, T., and Fujibuchi, W., “Kernel classification methods for cancer microarray data”, Medical Biostatistics for Complex Diseases, WILEY-VCH, Weinheim, Germany 2010.
  3. 藤渕航「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」、シングルセル解析の最前線、シーエムシー出版 2010.
  4. 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.
  5. 「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）.
  6. 「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, 実験医学、羊土社, 25-26, 2007.
  7. 「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.
  8. 「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.
  9. 「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.
  10. 「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.
  11. 「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.
  12. 「遺伝子クラスター解析」藤渕 航, 金久 實, 数理科学別冊, 2001.
  13. 「遺伝子クラスター解析」藤渕 航, 金久 實, 数理科学、432, 12-18, 1999.
  14. 「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.
  15. 「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.
  16. 「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.
  17. 「インターネットを利用した遺伝情報検索システム最前線」中井謙太, 藤渕 航, 薬学図書館, 41(4), 359-364, 1996.
【Patents】
  1. 核酸標準物質検出用プローブの設計方法、核酸標準物質検出用プローブ及び当該核酸標準物質検出用プローブを有する該酸検出系, 藤渕 航(40)、関口 勇地(20)、秋山英雄(30)（JMAC）、的場亮(10)（JMAC）特願2010-113343、産業技術総合研究所、バイオチップコンソーシアム2010.05.17
  2. 「プライマーセット探索装置、方法およびプログラム」, 藤渕　航(50)、千葉　啓和(50), 特願2009-212703, 2009.9.15.
  3. 遺伝子発現モジュール探索装置、遺伝子発現モジュール探索方法及び遺伝子発現モジュール探索プログラム、岡田吉史(50)、藤渕航(50), 特願2007-320636、産業技術総合研究所2007.12.12
  4. 細胞輪郭抽出装置、細胞輪郭抽出方法およびプログラム，藤渕 航(100)，特願2006-331416、産業技術総合研究所、2006.12.08
  5. 遺伝子発現プロファイル比較装置，Horton Paul(75)、藤渕 航(25)，特願2005-236198、産業技術総合研究所、2005.08.17
  6. 生物学的情報処理装置、生物学的情報処理方法および生物学的情報処理プログラム，加藤 毅(70)、藤渕 航(30)，特願2005-235562、産業技術総合研究所、2005.08.15
  7. 遺伝子発現プロファイル検索装置、遺伝子発現プロファイル検索方法およびプログラム，藤渕 航(75)、Horton Paul(25)，特願2004-280257、産業技術総合研究所、2004.09.27
【International Patens】
  1. 核酸標準物質検出用プローブの設計方法、核酸標準物質検出用プローブ及び当該核酸標準物質検出用プローブを有する該酸検出系, 藤渕 航(40)、関口 勇地(20)、秋山英雄(30)（JMAC）、的場亮(10)（JMAC）PCT/JP2011/061310、産業技術総合研究所、バイオチップコンソーシアム2011.05.17
  2. 遺伝子発現プロファイル検索装置、遺伝子発現プロファイル検索方法およびプログラム，藤渕 航(75)、Horton Paul(25)，11/235150（米国）、産業技術総合研究所2005.09.27

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