Research Activities

Research Activities

Home › Research Activities › Principal Investigators › Wataru Fujibuchi (Professor)

Principal Investigators

Dept. of Life Science Frontiers 
Wataru Fujibuchi (Professor)

Publications

Kim JH, Kurtz A, Yuan BZ, Zeng F, Lomax G, Loring JF, Crook J, Ju JH, Clarke L, Inamdar MS, Pera M, Firpo MT, Sheldon M, Rahman N, O'Shea O, Pranke P, Zhou Q, Isasi R, Rungsiwiwut R, Kawamata S, Oh S, Ludwig T, Masui T, Novak TJ, Takahashi T, Fujibuchi W, Koo SK, Stacey GN.

Report of the International Stem Cell Banking Initiative Workshop Activity: Current Hurdles and Progress in Seed-Stock Banking of Human Pluripotent Stem Cells. Stem Cells Translational Medicine 6(11):1956-1962 (2017).

Katayama H, Tamai K, Shibuya R, Nakamura M, Mochizuki M, Yamaguchi K, Kawamura S, Tochigi T, Sato I, Okanishi T, Sakurai K, Fujibuchi W, Arai Y, Satoh K.

Long non-coding RNA HOTAIR promotes cell migration by upregulating insulin growth factor-binding protein 2 in renal cell carcinoma. Scientific Reports 7(1):12016 (2017).

Iki T, Tanaka M, Kitajiri SI, Kita T, Kawasaki Y, Mizukoshi A, Fujibuchi W, Nakagawa T, Nakahata T, Ito J, Omori K, Saito MK.

Microarray analyses of otospheres derived from the cochlea in the inner ear identify putative transcription factors that regulate the characteristics of otospheres. PLOS ONE 12(6):e0179901 (2017).

Aiba T, Saito T, Hayashi A, Sato S, Yunokawa H, Maruyama T, Fujibuchi W, Kurita H, Tohyama C, Ohsako S.

Methylated Site Display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles. BMC Molecular Biology 18(7) (2017).

Yamane J, Mori T, Taniyama N, Kobayashi K, Fujibuchi W.

Development of Enhanced Reduced Representation Bisulfite Sequencing Method for Single-cell Methylome Analysis. Genomics and Computational Biology 3(2):e49 (2017).

Sakurai K, Fujibuchi W.

Developing Global Cellular Information Retrieval System with Minimum Reporting Guidelines on Cellular Data for Regenerative Medicine. Genomics and Computational Biology 3(2):e50 (2017).

Mori T, Yamane J, Kobayashi K, Taniyama N, Tano T, Fujibuchi W.

Development of 3D Tissue Reconstruction Method from Single-cell RNA-seq Data. Genomics and Computational Biology 3(1):e53 (2017).

Sakurai K, Kurtz A, Stacey G, Sheldon M, Fujibuchi W.

First Proposal of Minimum Information About a Cellular Assay for Regenerative Medicine. Stem Cells Translational Medicine. 5(10): 1345-1361 (2016).

Yamane J, Aburatani S, Imanishi S, Akanuma H, Nagano R, Kato T, Sone H, Ohsako S, Fujibuchi W.

Prediction of Developmental Chemical Toxicity based on Gene Networks of Human Embryonic Stem Cells. Nucleic Acids Research. 44(12): 5515-5528 (2016).

Matsuda Y, Miura K, Yamane J, Shima H, Fujibuchi W, Ishida K, Fujishima F, Ohnuma S, Sasaki H, Nagao M, Tanaka N, Satoh K, Naitoh T, Unno M.

SERPINI1 regulates epithelial-mesenchymal transition in an orthotopic implantation model of colorectal cancer. Cancer Science. 107(5): 619-628 (2016).

Akiyama H, Ueda Y, Nobumasa H, Ooshima H, Ishizawa Y, Kitahiro K, Miyagawa I, Watanabe K, Nakamura T, Tanaka R, Yamamoto N, Nakae H, Kawase M, Gemma N, Sekiguchi Y, Fujibuchi W, Matoba R.

A set of external reference controls/probes that enable quality assurance between different microarray platforms. Analytical Biochemistry. 472: 75-83 (2015).

Tanaka T, Maeda Y, Veluchamy A, Tanaka M, Abida H, Maréchal E, Bowler C, Muto M, Sunaga Y, Tanaka M, Yoshino T, Taniguchi T, Fukuda Y, Nemoto M, Matsumoto M, Wong P.S, Aburatani S, Fujibuchi W.

Oil Accumulation by the Oleaginous Diatom Fistulifera solaris as Revealed by the Genome and Transcriptome. The Plant Cell. 27(1): 162-176 (2015).

Wong P.S, Tanaka M, Sunaga Y, Tanaka M, Taniguchi T, Yoshino T, Tanaka T, Fujibuchi W, Aburatani S.

Tracking difference in gene expression in a time-course experiment using gene set enrichment analysis. PLoS One. 9(9): e107629 (2014).

Nakano S, Ikebe E, Tsukamoto Y, Wang Y, Matsumoto T, Mitsui T, Yahiro T, Inoue K, Kawazato H, Yasuda A, Ito K, Yokoyama S, Takahashi N, Hori M, Shimada T, Moriyama M, Kubota T, Ono K, Fujibuchi W, Jeang K.T, Iha H, Nishizono A.

Commensal microbiota contributes to chronic endocarditis in TAX1BP1 deficient mice. PLoS One. 8(9): e73205 (2013).

Pessiot J.F, Kim H, Fujibuchi W.

Pairwise ranking component analysis. Knowledge and Information Systems. 36(2): 459-487 (2013).

Aburatani S, Fujibuchi W, Yamane J, Imanishi S, Nagano R, Sone H, Ohsako S.

Inference of Gene Regulatory Networks to Detect Toxicity-Specific Effects in Human Embryonic Stem Cells. International Journal on Advances in Life Sciences. 5(1&2): 103-114 (2013).

Pessiot J.F, Wong P.S, Maruyama T, Morioka R, Aburatani S, Tanaka M, Fujibuchi W.

The impact of collapsing data on microarray analysis and DILI prediction. Systems Biomedicine. 1(2): 137-143 (2013).

Kinouchi M, Miura K, Mizoi T, Ishida K, Fujibuchi W, Sasaki H, Ohnuma S, Saito K, Katayose Y, Naitoh T, Motoi F, Shiiba K, Egawa S, Shibata C, Unno M.

Infiltration of CD40-positive tumor-associated macrophages indicates a favorable prognosis in colorectal cancer patients. Hepato-Gastroenterology. 60(121): 83-88 (2013).

Aburatani S, Fujibuchi W.

Inference of Specific Gene Regulation by Environmental Chemicals in Human Embryonic Stem Cells. Journal of Molecular Biology Research. 2(1): 54-64 (2012).

Miura K, Fujibuchi W, Unno M.

Review: Splice isoforms as therapeutic targets for colorectal cancer. Carcinogenesis. 33(12): 2311-2319 (2012).

Aburatani S, Fujibuchi W.

Application of Structural Equation Modeling for Inferring Toxicity-Dependent Regulation in Human Embryonic Stem Cells. Proceeding of GLOBAL HEALTH 2012, The First International Conference on Global Health Challenges, 27-32, Venice, Italy. (2012).

Miura K, Fujibuchi W, Unno M.

Review: Splice variants in apoptotic pathway. Experimental Oncology. 34(3): 212-217 (2012).

He X, Imanishi S, Sone H, Nagano R, Qin X.Y, Yoshinaga J, Akanuma H, Yamane J, Fujibuchi W, Ohsako S.

Effects of methylmercury exposure on neuronal differentiation of mouse and human embryonic stem cells. Toxicology Letters. 212(1): 1-10 (2012).

Pessiot J.F, Wong P.S, Maruyama T, Morioka R, Aburatani S, Tanaka M, Fujibuchi W.

The impact of collapsing data on microarray analysis and DILI prediction. Proceedings of Critical Assessment of Massive Data Analysis 2012 (CAMDA2012). (2012).

Miura K, Ishida K, Fujibuchi W, Ito A, Niikura H, Ogawa H, Sasaki I.

Review: Differentiating rectal carcinoma by an immunohistological analysis of carcinomas of pelvic organs based on the NCBI Literature Survey and the Human Protein Atlas database. Surgery Today. 42(6): 515-525 (2012).

Hamada S, Satoh K, Fujibuchi W, Hirota M, Kanno A, Unno J, Masamune A, Kikuta K, Kume K, Shimosegawa T.

MiR-126 acts as a tumor suppressor in pancreatic cancer cells via the regulation of ADAM9. Molecular Cancer Research. 10(1): 3-10(2012).

Fujibuchi W, Aburatani S, Yamane J, Imanishi S, Akanuma H, Sone H, Ohsako S.

Prediction of Chemical Toxicity by Network-based SVM on ES-cell Validation System The Proceedings of the 2011 Joint Conference of CBI-Society and JSBi, Kobe (2011).

Hatano A, Chiba H, Moesa H.A, Taniguchi T, Nagaie S, Yamanegi K, Takai-Igarashi T, Tanaka H, Fujibuchi W.

CELLPEDIA: a repository for human cell information for cell studies and differentiation analyses Database (Oxford). bar046 (2011).

Sugihara M, Fujibuchi W, Suwa M.

Structural elements of the signal propagation pathway in squid rhodopsin and bovine rhodopsin. The Journal of Physical Chemistry B. 115(19): 6172-6179 (2011).

Kinouchi M, Miura K, Mizoi T, Ishida K, Fujibuchi W, Ando T, Yazaki N, Saito K, Shiiba K, Sasaki I.

Infiltration of CD14-positive macrophages at the invasive front indicates a favorable prognosis in colorectal cancer patients with lymph node metastasis. Hepato-Gastroenterology. 58(106): 352-358 (2011).

Miura K, Fujibuchi W, Ishida K, Naitoh T, Ogawa H, Ando T, Yazaki N, Watanabe K, Haneda S, Shibata C, Sasaki I.

Invited Review: Inhibitor of apoptosis protein family as diagnostic markers and therapeutic targets of colorectal cancer. Surgery Today. 41(2): 175-182 (2011).

Miura K, Fujibuchi W, Sasaki I.

Review: Alternative pre-mRNA splicing in digestive tract malignancy. Cancer Science. 102(2): 309-316 (2011).

Wijaya E, Pessiot J.F, Frith M.C, Fujibuchi W, Asai K, Horton P.

In search of true reads: A classification approach to next generation sequencing data selection. International Conference on Bioinformatics and Biomedicine Workshops (BIBMW). 37: 561-566 (2010).

Miura K, Kinouchi M, Ishida K, Fujibuchi W, Naitoh T, Ogawa H, Ando T, Yazaki N, Watanabe K, Haneda S, Shibata C, Sasaki I.

5-FU metabolism in cancer and orally-administrable 5-FU drugs. Cancers (Basel). 2(3): 1717-1730 (2010).

Pessiot J.F, Chiba H, Hyakkoku H, Taniguchi T, Fujibuchi W.

PeakRegressor identifies composite sequence motifs responsible for STAT1 binding sites and their potential rSNPs PLoS One. 5(8): e11881 (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. Analytical Chemistry. 82(13): 5768-5776 (2010).

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. The Journal of Toxicological Sciences. 35(1): 115-123 (2010).

Pessiot J.F, Chiba H, Hyakkoku H, Taniguchi T, 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 (CAMDA 2009). 4-11, Chicago (2009).

Fujibuchi W, Chiba H, Akiyama H, 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 (IFPT'6). 253-257, Beijing (2009).

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, Sasaki I.

Down-regulation of cIAP2 enhances 5-FU sensitivity through the apoptotic pathway in human colon cancer cells Cancer Science. 100(5): 903-913 (2009).

Hamada S, Satoh K, Hirota M, Fujibuchi W, Kanno A, Umino J, Ito H, Satoh A, Kikuta K, Kume K, Masamune A, Shimosegawa T.

Expression of the calcium-binding protein S100P is regulated by bone morphogenetic protein in pancreatic duct epithelial cell lines Cancer Science. 100(1): 103-110 (2009).

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. 145(1): 57-68 (2009).

Satoh K, Hamada S, Kimura K, Kanno A, Hirota M, Umino J, Fujibuchi W, Masamune A, Tanaka N, Miura K, Egawa S, Motoi F, Unno M, Vonderhaar B.K, Shimosegawa T.

Up-Regulation of MSX2 Enhances the Malignant Phenotype and Is Associated with Twist 1 Expression in Human Pancreatic Cancer Cells The American Journal of Pathology. 172(4): 926-939 (2008).

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, Sasaki I.

Orthotopic implantation mouse model and cDNA microarray analysis indicates several genes potentially involved in lymph node metastasis of colorectal cancer Cancer Science. 99(4): 711-719 (2008).

Horton P, Fujibuchi W.

An upper bound on the hardness of exact matrix based motif discovery. Journal of Discrete Algorithms. 5(4): 706-713 (2007).

Fujibuchi W, Kiseleva L, Taniguchi T, Harada H, Horton P.

CellMontage: Similar Expression Profile Search Server Bioinformatics 23(22): 3103-3104 (2007).

Fujibuchi W, Kato T.

Classification of Heterogeneous Microarray Data by Maximum Entropy Kernel BMC Bioinformatics. 8(267) (2007).

Okada Y, Fujibuchi W. Horton P.

A biclustering method for gene expression module discovery using a closed itemset enumeration algorithm IPSJ Transactions on Bioinformatics 48(SIG 5(TBIO2)). 39-48 (2007).

Okada Y, Fujibuchi W, Horton P.

Exhaustive search of maximal biclusters in gene expression data IAENG. 2-1: 307-312 (2007).

Okada Y, Okubo K, Horton P, 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, 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).

Kato T, Murata Y, Miura K, Asai K, Horton P.B, Tsuda K, Fujibuchi W.

Network-based de-noising improves prediction from microarray data BMC Bioinformatics. 7(Suppl. 1): S4 (2006).

Polouliakh N, Natsume T, Harada H, Fujibuchi W, Horton P.

Comparative genomic analysis of transcription regulation elements involved in human MAP-kinase G-protein coupling pathway Journal of Bioinformatics and Computational Biology. 4(2): 469-482 (2006).

Kato T, Fujibuchi W, Asai K.

Learning Kernels from Distance Constraints IPSJ. 47(SIG10): 1-11 (2006).

Horton P.B, Kiseleva L, Fujibuchi W.

RaPiDS: An Algorithm for Rapid Expression Profile Database Search Genome Informatics. 17(2): 67-76 (2006).

Kato T, Fujibuchi W, Asai K.

Kernel analysis for noisy microarray data CBRC Technical Report. AIST02-J00001-8 (2006).

Kato T, Murata Y, Miura K, Asai K, Horton P.B, Tsuda K, Fujibuchi W.

Drug-response prediction from microarray data using network-based de-noising IPSJ SIG technical reports 2006. 47-52 BIO-5-(8) (2006).

Kato T, Fujibuchi W, Asai K.

Kernel construction from distance constraints CBRC Technical Report. AIST02-J00001-7 (2005).

Barrett T, Suzek T.O, Troup D.B, Wilhite S.E, Ngau W.C, Ledoux P, Rudnev D, Lash A.E, Fujibuchi W, Edgar R.

NCBI GEO: mining millions of expression profiles - database and tools Nucleic Acids Research. 33 (Database issue): D562-566 (2005).

Ono Y, Fujibuchi W, Suwa M.

Automatic gene collection system for genome-scale overview of G-protein coupled receptors in Eukaryotes Gene. 364: 63-73 (2005).

Horton P, Fujibuchi W.

An Upper Bound on the Hardness of Exact Matrix Based Motif Discovery Combinatorial Pattern Matching. 16th Annual Symposium 3537: 219-228 (2005).

Fujibuchi W, Anderson J.S, Landsman D.

PROSPECT improves cis-acting regulatory element prediction by integrating expression profile data with consensus pattern searches Nucleic Acids Research. 29(19): 3988-3996 (2001).

Fujibuchi W, Ogata H, Matsuda H, Kanehisa M.

Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping Nucleic Acids Research. 28(20): 4029-4036 (2000).

Ogata H, Fujibuchi W, Goto S, Kanehisa M.

A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters Nucleic Acids Research. 28(20): 4021-4028 (2000).

Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M.

KEGG: Kyoto Encyclopedia of Genes and Genomes Nucleic Acids Research. 27(1): 29-34 (1999).

Ogata H, Goto S, Fujibuchi W, Kanehisa M.

Computation with the KEGG pathway database BioSystems. 47(1-2): 119-128 (1998).

Bono H, Goto S, Fujibuchi W, Ogata H, Kanehisa M.

Systematic prediction of orthologous units of genes in the complete genomes. Genome Informatics. Workshop on Genome Informatics. 9: 32-40 (1998).

Fujibuchi W, Sato K, Ogata H, Goto S, Kanehisa M.

KEGG and DBGET/LinkDB: Integration of biological relationships in divergent molecular biology data AAAI Technical Report WS-98-04. 35-40 (1998).

Fujibuchi W, Goto S, Migimatsu H, Uchiyama I, Ogiwara A, Akiyama Y, Kanehisa M.

DBGET/LinkDB: an integrated database retrieval system Pacific Symposium on Biocomputing 1998. 683-694 (1998).

Fujibuchi W, Kanehisa M.

Prediction of gene expression specificity by promoter sequence patterns DNA Research. 4(2): 81-90 (1997).

Ogata H, Fujibuchi W, Kanehisa M.

The size differences among mammalian introns are due to the accumulation of small deletions FEBS Letters. 390(1): 99-103 (1996).

Ogata H, Bono H, Fujibuchi W, Goto S, Kanehisa M.

Analysis of binary relations and hierarchies of enzymes in the metabolic pathways Proc. 7th Workshop on Genome Informatics. 128-136 (1996).

Goto S, Bono H, Ogata H, Fujibuchi W, Nishioka T, Sato K, Kanehisa M.

Organizing and computing metabolic pathway data in terms of binary relations Pacific Symposium on Biocomputing '97. 175-186 (1997).

Fujibuchi W, Kanehisa M.

A method to extract functional motifs for transcriptional regulation in eukaryotic sequences Bulletin of the Institute for Chemical Research. Kyoto University. 71(3): 317-326 (1993).
Books

Kato T, and Fujibuchi W.

"Kernel classification methods for cancer microarray data" Medical Biostatistics for Complex Diseases. 279-303,
WILEY-VCH, Weinheim, Germany (2010).

Fujibuchi W, Kim H, Okada Y, Taniguchi T, Sone H.

"High-performance gene expression module analysis tool and its application to chemical toxicity data" Methods in Molecular Biology. 577: 55-65, Humana Press Inc., U.S.A. (2009).
go top