Professor SATOU Kenji
Faculty, Affiliation
Faculty of Transdisciplinary Sciences, Institute of Philosophy in Interdisciplinary Sciences
College and School Educational Field
Division of Electrical Engineering and Computer Science, Graduate School of Natural Science and Technology
Division of Electrical Engineering and Computer Science, Graduate School of Natural Science and Technology
Course in Bioengineering, School of Biological Science and Technology, College of Science and Engineering
School of Entrepreneurial and Innovation Studies, College of Transdisciplinary Sciences for Innovation
Laboratory
Laboratory of Bioinformatics TEL:076-234-4889 FAX:076-234-4900
Academic Background
【Academic background(Doctoral/Master's Degree)】
Kyushu University Master Graduate School, Division of Engineering 198903 Completed
【Academic background(Bachelor's Degree)】
Kyushu University Department of Computer Science and Communication Engineering 198703
【Degree】
Doctor of Engineering
Career
Educational Center for Information Processing, Kyushu University Research Associate(1989/04-1993/03)
Department of Computer Science and Communication Engineering, Kyushu University Research Associate(1993/04-1994/12)
Human Genome Center, Institute of Medical Science, The University of Tokyo Research Associate(1995/01-1998/03)
Graduate School of Knowledge Science, Japan Advanced Institute of Science and Technology Associate Professor(1998/04-2007/09)
Graduate School of Natural Science and Technology, Kanazawa University(2007/10-)
Year & Month of Birth
1963/12
Academic Society
Information Processing Society of Japan
The Institute of Electronics, Information and Communication Engineers
The Japanese Society for Artificial Intelligence
The Japanese Society for Artificial Intelligence
Japanese Society for Bioinformatics
Japanese Society for Bioinformatics
Japanese Society for Bioinformatics
Award
Specialities
、Intelligent informatics、、
Speciality Keywords
analysis of biological data
Research Themes
Data mining from biological and medical data
Due to the amazing advances in molecular biology, various and huge amount of biomedical data are now available. Objective of this theme is discovery of novel knowledge of life through combination of various data and application of advanced data mining algorithms. Specific research topics include; prediction of protein function and structure, species identification from RNA sequence, discovery of genes distinctive in a gene expression dataset, etc.
Text mining and intelligent search for biomedical literature
In the field of life science, so many papers are published every year and it is impossible for a researcher to browse through all of them. Therefore, it is desired to search the papers intelligently and extract precious information and knowledge. Objective of this theme is, through the calculation of semantic similarity among words, enabling intelligent search of biomedical papers and automatic information extraction, rather than simple keyword matching and template matching, respectively.
Books
Papers
- A deductive database system PACADE for the three dimensional structure of protein Kuhara,S., Satou,K., Furuichi,E., Takagi,T., Takehara,H., Sakaki,Y. Proc. of the Twenty-Fourth Annual Hawaii International Conference on System Sciences (HICSS24) 1 653-659 1991/01
- A deductive database system PACADE for analyzing 3-D and secondary structures of protein Satou,K., Furuichi,E., Takiguchi,K., Takagi,T., Kuhara,S. Computer Applications in the Biosciences 9 3 259-265 1993/03
- Similar structure search in a deductive database Satou,K., Furuichi,E., Takagi,T., Kuhara,S., Ushijima,K. Proc. of International Symposium on Next Generation Database Systems and Their Applications (NDA'93) 130-137 1993/09
- Searches for topologically and three dimensionally similar structures in proteins Satou,K., Furuichi,E., Kuhara,S., Takagi,T. Genome Informatics Series 4 25-35 1993/12
- Equipments for statistical analysis in a deductive database system -their implementation and their application to protein structural analysis- Nishikawa,A., Satou,K., Furuichi,E., Kuhara,S., Ushijima,K. Proc. of International Symposium on Advanced Database Technologies and Their Integration (ADTI'94) 237-244 1994/01
- Application of a deductive database system PACADE toward discovery of clusters of similar structures in proteins Satou,K., Furuichi,E., Takagi,T., Kuhara,S. Proc. of the Twenty-Seventh Annual Hawaii International Conference on System Sciences (HICSS27) 5 160-169 1994/01
- Data classification component in a deductive database system and its application to protein structural analysis Nishikawa,A., Satou,K., Furuichi,E., Kuhara,S., Ushijima,K. IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS E78-D 11 1377-1387 1995/11
- GenomeNet: overview and recent enhancements Satou,K., Takagi,T., Kanehisa,M. Proc. of the Eighth Asian- Australasian Association of Animal Production Societies (AAAP) Animal Science Congress 1 541-544 1996/01
- Development of a deductive database system for computing closures of similarity relationships among protein structures Satou,K., Furuichi,E., Hashimoto,S., Tsukamoto,Y., Kuhara,S., Takagi,T., Ushijima,K. Journal of Japanese Society for Artificial Intelligence 11 3 440-450 1996/05
- Finding association rules on heterogeneous genome data Satou,K., Shibayama,G., Ono,T., Yamamura,Y., Furuichi,E., Kuhara,S., Takagi,T. Biocomputing 2 397-408 1997/01
- Application of a deductive database system to search for topological and similar three-dimensional structures in protein Tsukamoto,Y., Takiguchi,K., Satou,K., Furuichi,E., Takagi,T., Kuhara,S. Computer Applications in the Biosciences 13 2 183-190 1997/04
- Extraction of substructures of proteins essential to their biological functions by a data mining technique Satou,K., Ono,T., Yamamura,Y., Furuichi,E., Kuhara,S., Takagi,T. Proc. of the Fifth International Conference on Intelligent Systems for Molecular Biology (ISMB'97) 254-257 1997/06
- A framework for quick-and-pinpoint data mining and its application to heterogeneous genome databases Satou,K., Fuseda,Y., Konagaya,A., Takagi,T. Knowledge-Based Intelligent Information Engineering Systems & Allied Technologies 5 773-777 2001/09
- Extraction of knowledge on protein-protein interaction by association rule discovery Oyama,T., Kitano,K., Satou,K., Ito,T. BIOINFORMATICS 18 5 705-714 2002/05
- Prediction of protein-protein interaction sites using support vector machines Minakuchi,Y., Satou,K., Konagaya,A. Proc. of the 2003 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'03) 22-28 2003/06
- Development of support tool for NMR spectrum analysis Tatsumoto,S., Satou,K., Konagaya,A.,Kurita,J., Shimahara,H., Tate,S. Proc. of the 2003 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'03) 159-164 2003/06
- Conformational change of calmodulin: A molecular dynamics simulation study Li,H., Yokota,K., Satou,K. Proc. of the 7th World Multiconference on Systemics, Cybernetics and Informatics (SCI2003) 8 47-52 2003/07
- Asynchronous peer-to-peer communication for failure resilient distributed genetic algorithms Clemente,J.C., Defago,X., Satou,K. Proc. of the 15th IASTED Intl. Conf. on Parallel and Distributed Computing and Systems (PDCS2003) 2 769-773 2003/11
- Prediction and analysis of beta-turns in proteins by support vector machine Pham,T.H., Satou,K., Ho,T.B. Genome Informatics Series 14 196-205 2003/12
- The superstructure toward open bioinformatics grid Konagaya,A., Konishi,F., Hatakeyama,M., Satou,K. NEW GENERATION COMPUTING 22 2 167-176 2004/02
- An integrated system for distributed bioinformatics environment on grids Satou,K., Nakashima,Y.,Tsuji,S., Defago,X., Konagaya,A. Grid Computing in Life Science 1 5-13 2004/05
- Prediction of protein secondary structure from PDB structure information based on sequence fragments Homology searching Tatsumoto,S., Satou,K., Konagaya,A. Proc. of the 2004 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'04) 250-255 2004/06
- Automated template discovery for information extraction from biomedical literature Kamegai,S., Satou,K., Konagaya,A. Proc. of the International Conference on Cybernetics and Information Technologies, Systems and Applications (CITSA 2004) 2 39-44 2004/07
- Improving the identification of non-anaphoric it using support vector machines Clemente,J.C., Satou,K., Torisawa,K. Proc. of the International Workshop on Natural Language Processing in Biomedicine and its Applications (NLPBA/BioNLP 2004) 58-61 2004/08
- Drug interaction ontology (DIO) for inferences of possible drug-drug interactions Yoshikawa,S., Satou,K., Konagaya,A. Proc. of Medinfo 2004 454-458 2004/09
- Mining yeast transcriptional regulatory modules from factor DNA-binding sites and gene expression data Pham,T.H., Satou,K., Ho,T.B. Genome Informatics Series 15 287-295 2004/12
- Detection and normalization of biases present in spotted cDNA microarray data: A composite method addressing dye, intensity-dependent, spatially-dependent, and print-order biases Uchida,S., Nishida,Y., Satou,K., Muta,S., Tashiro,K., Kuhara,S. DNA Research 12 1 1-7 2005/02
- Utilizing weakly controlled vocabulary for sentence segmentation in biomedical literature Satou,K., Yamamoto,K. In Silico Biology 5 1 67-79 2005/03
- Support vector machines for prediction and analysis of beta and gamma-turns in proteins Pham,T.H., Satou,K., Ho,T.B. Journal of Bioinformatics and Computational Biology 3 2 343-358 2005/04
- Rule evaluation heuristics for knowledge discovery Pham,T.H., Clemente,J.C., Satou,K., Ho,T.B. Proc. of the Workshop on Knowledge Discovery and Data Management in Biomedical Science (KDDMBS) in conjunction with PAKDD-05 29-44 2005/05
- Contractive conformational change of calmodulin caused by the central linker: A molecular dynamics simulation study Li,H., Yokota,K., Satou,K. Proc. of the 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'05) 225-230 2005/06
- Computational discovery of transcriptional regulatory rules Pham,T.H., Clemente,J.C., Satou,K., Ho,T.B. BIOINFORMATICS 21 Suppl.2 101-107 2005/09
- Comparison of phrase indexing for biomedical and newswire documents Clemente,J.C., Torisawa,K., Satou,K. Proc. of the First International Congress of the International Federation for Systems Research (IFSR2005) S5-4-2 (6 pages in CD proceedings) 2005/11
- Reconstruction of Phylogenetic relationships from metabolic pathways based on the enzyme hierarchy and the gene ontology Clemente,J.C., Satou,K., Valiente,G. Genome Informatics Series 16 2 45-55 2005/12
- Qualitatively predicting acetylation and methylation areas in DNA sequences Pham,T.H., Tran,D.H., Ho,T.B., Satou,K., Valiente,G. Genome Informatics Series 16 2 3-11 2005/12
- Conditional random fields for predicting and analyzing histone occupancy, acetylation and methylation areas in DNA sequences Tran,D.H., Pham,T.H., Satou,K., Ho,T.B. Proc. of EvoBio 2006 221-230 2006/04
- Comparative analysis of protein thermostability: difference in contents and substitutions of amino acid types on the surface and in the core regions of thermophilic and mesophilic proteins Yokota,K., Satou,K., Ohki,S. Science and Technology of Advanced Materials 7 255-262 2006/06
- Fuzzy clustering improves phylogenetic relationships reconstruction from metabolic pathways Casasnovas,J., Clemente,J.C., Miro-Julia,J., Rossello,F., Satou,K., Valiente,G. Proc. of the 11th International Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems (IPMU 2006) 2807-2814 2006/07
- Parallel and pipelined database transfer in a grid environment for bioinformatics Satou,K., Tsuji,S., Nakashima,Y.,Konagaya,A. Grid Computing in Life Science 2 255-262 2006/10
- Finding conserved and non-conserved reactions using a metabolic pathway alignment algorithm Clemente,J.C., Satou,K., Valiente,G. Genome Informatics Series 17 1 46-56 2006/12
- Phylogenetic reconstruction from non-genomic data Clemente,J.C., Satou,K., Valiente,G. BIOINFORMATICS 23 2 110-115 2007/01
- Prediction of Histone Modifications in DNA sequences Pham,T.H., Tran,D.H., Ho,T.B., Satou,K. Proc. of the 7th IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2007) 959-966 2007/10
- Comparison of Cluster Identification Methods for Selection of GO Terms related to Gene Clusters Yamada,Y., Miyata,Y., Higashihara,M., Satou,K. WSEAS Transactions on Biology and Biomedicine 5 3 54-63 2008/03
- Prediction of microRNA Hairpins Using One-class Support Vector Machines Tran,D.H., Pham,T.H., Satou,K., Ho,T.B. Proc. of the 2nd International Conference on Bioinformatics and Biomedical Engineering (ICBBE 2008) 33-36 2008/05
- Application of a Feature Selection Method to Nucleosome Data: Accuracy Improvement and Comparison with Other Methods Higashihara,M., Rebolledo-Mendez,J.D., Yamada,Y., Satou,K. WSEAS Transactions on Biology and Biomedicine 5 5 95-104 2008/05
- Estimation of Identification Methods of Gene Clusters Using GO Term Annotations from a Hierarchical Cluster Tree Yamada,Y., Miyata,Y., Higashihara,M., Satou,K. Proc. of the 9th WSEAS International Conference on MATHEMATICS & COMPUTERS IN BIOLOGY & CHEMISTRY (MCBC '08) 194-198 2008/06
- Ranking and Selection of Features for Improved Prediction of Nucleosome Occupancy and Modification Higashihara,M., Rebolledo-Mendez,J.D., Yamada,Y., Satou,K. Proc. of the 9th WSEAS International Conference on MATHEMATICS & COMPUTERS IN BIOLOGY & CHEMISTRY (MCBC '08) 188-193 2008/06
- Prediction of Genomic Methylation Status on CpG Islands Using DNA Sequence Features Yamada,Y., Satou,K. WSEAS Transactions on Biology and Biomedicine 5 7 153-162 2008/07
- Characterization and Clustering of GO Terms by Feature Importance Vectors Obtained from Microarray Data Rebolledo-Mendez,J.D., Higashihara,M., Yamada,Y., Satou,K. WSEAS Transactions on Biology and Biomedicine 5 7 163-172 2008/07
- Performance Evaluation of Parallel Processing Environment for Molecular Dynamics Satou,K., Konno,K., Ohta,O., Mikami,K., Teranishi,K., Yamada,Y., Ohki,S. WSEAS Transactions on Biology and Biomedicine 5 7 173-182 2008/07
- Prediction of human microRNA hairpins using only positive sample learning Tran,D.H., Pham,T.H., Satou,K., Ho,T.B. Journal of Biomedical Science and Engineering 1 2 141-146 2008/08
- Effect of Parallel Processing and Optimization Techniques in Molecular Dynamics Satou,K., Konno,K., Ohta,O., Mikami,K., Teranishi,K., Yamada,Y., Ohki,S. Proc. of the WSEAS International Conference on BIOMEDICAL ELECTRONICS and BIOMEDICAL INFORMATICS (BEBI'08) 228-233 2008/08
- Prediction of methylation status on DNA sequences and identification of its important DNA sequence features Yamada,Y., Satou,K. Proc. of the WSEAS International Conference on BIOMEDICAL ELECTRONICS and BIOMEDICAL INFORMATICS (BEBI'08) 223-227 2008/08
- Finding Hidden Relationship among Biological Concepts in Gene Ontology Rebolledo-Mendez,J.D., Higashihara,M., Yamada,Y., Satou,K. Proc. of the WSEAS International Conference on BIOMEDICAL ELECTRONICS and BIOMEDICAL INFORMATICS (BEBI'08) 237-241 2008/08
- Constructing Signal Transduction Networks Using Multiple Signaling Feature Data Nguyen,T.P., Satou,K., Ho,T.B., Takabayashi,K Proc. of Statistical and Relational Learning in Bioinformatics (StReBio) 1-8 2008/09
- A computational method for classifying and analyzing tumor samples using microRNA expression profiles Tran,D.H., Ho,T.B., Satou,K., Pham,T.H. Proc. of 3rd International Conference on Knowledge, Information and Creativity Support Systems (KICSS 2008) 120-127 2008/12
- Finding microRNA regulatory modules in human genome using rule induction Tran,D.H., Pham,T.H., Satou,K., Ho,T.B. BMC Bioinformatics 9 12 S5 2008/12
- An identification method of data-specific GO terms from a microarray data set Yamada,Y., Hirotani,K., Satou,K., Muramoto,K. IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS E92-D 5 1093-1102 2009/05
- Computational Discovery of miR-TF Regulatory Modules in Human Genome Tran, D.H., Satou, K., Ho, T.B., Pham, T.H. Bioinformation 4 8 371-377 2010/02
- MicroRNA expression profiles for classification and analysis of tumor samples Tran, D.H., Ho, T.B., Pham, T.H., Satou, K. IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS E94-D 3 416-422 2011/03
- PLU1 histone demethylase decreases the expression of KAT5 and enhances the invasive activity of the cells Yoshida, M., Ishimura, A., Terashima, M., Enkhbaatar, Z., Nozaki, N., Satou, K., Suzuki, T. BIOCHEMICAL JOURNAL 437 3 555-564 2011/08
- Inflammation-induced repression of tumor suppressor miR-7 in gastric tumor cells Kong,D., Piao,Y.S., Yamashita,S., Oshima,H., Oguma,K., Fushida,S., Fujimura,T., Minamoto,T., Seno,H., Yamada,Y., Satou,K., Ushijima,T., Ishikawa,T., Oshima,M. Oncogene 31 35 3949–3960 2011/12
- IMPACT: A Novel Clustering Algorithm based on Attraction Tran,V.A., Clemente,J.C., Nguyen,D.T., Li,J., Dang,X.T., Le,T.T.K., Nguyen,T.L.A., Saethang,T., Kubo,M., Yamada,Y., Satou,K. Journal of Computers 7 3 653-665 2012/03
- EpicCapo: epitope prediction using combined information of amino acid pairwise contact potentials and HLA-peptide contact site information Saethang,T., Hirose,O., Kimkong,I., Tran,V.A., Dang,X.T., Nguyen,T.L.A., Le,T.T.K., Kubo,M., Yamada,Y., Satou,K. BMC Bioinformatics 13 13:313 2012/11
- Validation of MIMGO: a method to identify differentially expressed GO terms in a microarray dataset Yamada, Y., Sawada, H., Hirotani, K., Oshima,M., Satou,K. BMC Research Notes 5 5:680 2012/12
- A Novel Over-Sampling Method and its Application to Cancer Classification from Gene Expression Data Dang,X.T., Hirose,O., Bui,D.H., Saethang,T., Tran,V.A., Nguyen,T.L.A., Le,T.T.K., Kubo,M., Yamada,Y., Satou,K. Chem-Bio Informatics Journal 13 19-29 2013/01
- PAAQD: Predicting immunogenicity of MHC class I binding peptides using amino acid pairwise contact potentials and quantum topological molecular similarity descriptors Saethang,T., Hirose,O., Kimkong,I., Tran,V.A., Dang,X.T., Nguyen,T.L.A., Le,T.T.K., Kubo,M., Yamada,Y., Satou,K. JOURNAL OF IMMUNOLOGICAL METHODS 387 1-2 293-302 2013/01
- A novel over-sampling method and its application to miRNA prediction Dang,X.T., Hirose,O., Saethang,T., Tran,V.A., Nguyen,T.L.A., Le,T.T.K., Kubo,M., Yamada,Y., Satou,K. Journal of Biomedical Science and Engineering 6 2A 236-248 2013/02
- Improving the Prediction of Protein-Protein Interaction Sites Using a Novel Over-Sampling Approach and Predicted Shape Strings Nguyen,T.L.A., Hirose,O., Dang,X.T., Le,T.T.K., Saethang,T., Tran,V.A., Kubo,M., Yamada,Y., Satou,K. Annual Review & Research in Biology 3 2 92-106 2013/03
- Inferring microRNA and transcription factor regulatory networks in heterogeneous data Le,T.D., Liu,L., Liu,B., Tsykin,A., Goodall,G.J., Satou,K., Li,J. BMC Bioinformatics 14 14:92 2013/03
Conference Presentations
Others
Arts and Fieldwork
Patent
Theme to the desired joint research
Grant-in-Aid for Scientific Research
○「一度しか出現しない単語の意味推定とその応用に関する研究」(2010-2012)
Competitive research funding,Contribution
Collaborative research,Consignment study
Classes (Bachelors)
○Molecular and Cellular Biology(2017)
○Molecular and Cellular Biology(2017)
○Molecular and Cellular Biology(2017)
○Presentation and Debate (Freshman Seminar II)(2017)
○Molecular and Cellular Biology(2017)
○Presentation and Debate (Freshman Seminar II)(2017)
○Internships B(2017)
○Research Project(2017)
○Design of Biological Information System(2017)
○Bioinformatics(2017)
○Theory of Dataset Analysis and Exercise(2017)
○Internships A(2017)
○Presentation and Debate (Freshman Seminar II)(2017)
○Presentation and Debate (Freshman Seminar II)(2017)
○Bioinformatics(2017)
○Freshman Seminar I(2017)
○Introduction to Region-studies(2017)
○Freshman Seminar I(2017)
○Molecular and Cellular Biology(2017)
○Molecular and Cellular Biology(2017)
○Molecular and Cellular Biology(2017)
○Molecular and Cellular Biology(2017)
○Molecular and Cellular Biology(2016)
○Molecular and Cellular Biology(2016)
○Molecular and Cellular Biology(2016)
○Molecular and Cellular Biology(2016)
○Molecular and Cellular Biology(2016)
○Molecular and Cellular Biology(2016)
○Freshman Seminar I(2016)
○Freshman Seminar I(2016)
○Bioinformatics(2016)
○Introduction to Electronics， Computer Engineering and Bioinformatics B(2016)
○Design of Biological Information System(2016)
○Research Project(2016)
○Bioinformatics(2016)
○Research Project(2016)
○Theory of Dataset Analysis and Exercise(2016)
○Research Project(2016)
○Presentation and Debate (Freshman Seminar II)(2016)
○Presentation and Debate (Freshman Seminar II)(2016)
○Introduction to Region-studies(2016)
Classes (Graduate Schools)
○Bioinformatics and Recent Advances in Biology(2017)
○Exercise for Technical Intern(2017)
○Advanced Bioinformatics(2017)
○Advanced Bioinformatics(2017)
○Advanced Bioinformatics(2017)
○Advanced Bioinformatics(2017)
○Advanced Bioinformatics(2016)
○Bioinformatics and Recent Advances in Biology(2016)