Biography

Kenji Satou received the B.E., M.E., and D.E. degrees in computer science and
communication engineering from Kyushu University, in 1987, 1989,
and 1996, respectively. He was a research associate of Kyushu
University, Fukuoka, Japan (1989-1994) and the University of Tokyo,
Tokyo, Japan (1995-1998). From 1998 to 2007, he was an associate
professor of Japan Advanced Institute of Science and Technology
(JAIST), Ishikawa, Japan. He is currently an associate professor of
Kanazawa University, Ishikawa, Japan. His research interests
include wide variety of topics in bioinformatics

Lecture

Introduction to Genome Sciences (for B3)
Genome Informatics (for B4)
Genome Science (for M1)

Scientific Activities

(book) Co-editor of Grid Computing in Life Science, Springer Lecture Notes in Computer Science, Vol. 3370
(2003-2008) Trustee of Initiative for Parallel Bioinformatics (IPAB)
(2006-now) Editor-in-Chief of Special Interest Group on Molecular Biology Information (SIG-MBI) in the Japanese Society for Artificial Intelligence
(2002-2004) Councilor of Japanese Society for Bioinformatics
(2005) Organizer of a workshop on Knowledge Discovery and Data Management in Biomedical Science (KDDMBS) in conjunction with The Ninth Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD-05)
(2008) Organizer of a workshop on Knowledge, Language, and Learning in Bioinformatics (KLLBI) in conjunction with The Tenth Pacific Rim International Conference on Artificial Intelligence (PRICAI-08)

Publication

JOURNAL

Satou,K., Furuichi,E., Takiguchi,K., Takagi,T., Kuhara,S.
A deductive database system PACADE for analyzing 3-D and secondary structures of protein
Computer Applications in the Biosciences, Vol.9, No.3, pp.259-265
1993.3

Satou,K., Furuichi,E., Kuhara,S., Takagi,T.
Searches for topologically and three dimensionally similar structures in proteins
Genome Informatics Series, Vol.4, pp.25-35
1993.12

Nishikawa,A., Satou,K., Furuichi,E., Kuhara,S., Ushijima,K.
Data classification component in a deductive database system and its application to protein structural analysis
IEICE (The Institute of Electronics, Information and Communication Engineers) Transactions on Information and Systems, Vol.E78-D, No.11, pp.1377-1387
1995.11

Satou,K., Furuichi,E., Hashimoto,S., Tsukamoto,Y., Kuhara,S., Takagi,T., Ushijima,K.
Development of a deductive database system for computing closures of similarity relationships among protein structures
Journal of Japanese Society for Artificial Intelligence, Vol.11, No.3, pp.440-450
1996.5

Satou,K., Shibayama,G., Ono,T., Yamamura,Y., Furuichi,E., Kuhara,S., Takagi,T.
Finding association rules on heterogeneous genome data
Biocomputing, Vol.2, pp.397-408
1997.1

Tsukamoto,Y., Takiguchi,K., Satou,K., Furuichi,E., Takagi,T., Kuhara,S.
Application of a deductive database system to search for topological and similar three-dimensional structures in protein
Computer Applications in the Biosciences, Vol.13, No.2, pp.183-190
1997.4

Satou,K., Fuseda,Y., Konagaya,A., Takagi,T.
A framework for quick-and-pinpoint data mining and its application to heterogeneous genome databases
Knowledge-Based Intelligent Information Engineering Systems & Allied Technologies, Vol.5, pp.773-777
2001.9

Oyama,T., Kitano,K., Satou,K., Ito,T.
Extraction of knowledge on protein-protein interaction by association rule discovery
Bioinformatics, Vol.18, No.5, pp.705-714
2002.5

Pham,T.H., Satou,K., Ho,T.B.
Prediction and analysis of β-turns in proteins by support vector machine
Genome Informatics Series, Vol.14, pp.196-205
2003.12

Konagaya,A., Konishi,F., Hatakeyama,M., Satou,K.
The superstructure toward open bioinformatics grid
New Generation Computing, Vol.22, No.2, pp.167-176
2004.2

Satou,K., Nakashima,Y.,Tsuji,S., Defago,X., Konagaya,A.
An integrated system for distributed bioinformatics environment on grids
Grid Computing in Life Science, Vol.1, pp.5-13
2004.5

Pham,T.H., Satou,K., Ho,T.B.
Mining yeast transcriptional regulatory modules from factor DNA-binding sites and gene expression data
Genome Informatics Series, Vol.15, pp.287-295
2004.12

Uchida,S., Nishida,Y., Satou,K., Muta,S., Tashiro,K., Kuhara,S.
Detection and normalization of biases present in spotted cDNA microarray data: A composite method addressing dye, intensity-dependent, spatially-dependent, and print-order biases
DNA Research, Vol.12, No.1, pp.1-7
2005.2

Satou,K., Yamamoto,K.
Utilizing weakly controlled vocabulary for sentence segmentation in biomedical literature
In Silico Biology, Vol.5, No. 1, pp.67-79
2005.3

Pham,T.H., Satou,K., Ho,T.B.
Support vector machines for prediction and analysis of beta and gamma-turns in proteins
Journal of Bioinformatics and Computational Biology, Vol.3, No.2, pp.343-358
2005.4

Pham,T.H., Clemente,J.C., Satou,K., Ho,T.B.
Computational discovery of transcriptional regulatory rules
Bioinformatics, Vol.21, Suppl.2, pp.101-107
2005.9

Clemente,J.C., Satou,K., Valiente,G.
Reconstruction of Phylogenetic relationships from metabolic pathways based on the enzyme hierarchy and the gene ontology
Genome Informatics Series, Vol.16, No.2, pp.45-55
2005.12

Pham,T.H., Tran,D.H., Ho,T.B., Satou,K., Valiente,G.
Qualitatively predicting acetylation and methylation areas in DNA sequences
Genome Informatics Series, Vol.16, No.2, pp.3-11
2005.12

Yokota,K., Satou,K., Ohki,S.
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
Science and Technology of Advanced Materials, Vol.7, pp.255-262
2006.6

Satou,K., Tsuji,S., Nakashima,Y.,Konagaya,A.
Parallel and pipelined database transfer in a grid environment for bioinformatics
Grid Computing in Life Science, Vol.2, pp.255-262
2006.10

Clemente,J.C., Satou,K., Valiente,G.
Finding conserved and non-conserved reactions using a metabolic pathway alignment algorithm
Genome Informatics Series, Vol.17, No.1, pp.46-56
2006.12

Clemente,J.C., Satou,K., Valiente,G.
Phylogenetic reconstruction from non-genomic data
Bioinformatics, Vol.23, No.2, pp.110-115
2007.1

Yamada,Y., Miyata,Y., Higashihara,M., Satou,K.
Comparison of Cluster Identification Methods for Selection of GO Terms related to Gene Clusters
WSEAS Transactions on Biology and Biomedicine, Vol.5, Issue 3, pp.54-63
2008.3

Higashihara,M., Rebolledo-Mendez,J.D., Yamada,Y., Satou,K.
Application of a Feature Selection Method to Nucleosome Data: Accuracy Improvement and Comparison with Other Methods
WSEAS Transactions on Biology and Biomedicine, Vol.5, Issue 5, pp.95-104
2008.5

Yamada,Y., Satou,K.
Prediction of Genomic Methylation Status on CpG Islands Using DNA Sequence Features
WSEAS Transactions on Biology and Biomedicine, Vol.5, Issue 7, pp.153-162
2008.7

Rebolledo-Mendez,J.D., Higashihara,M., Yamada,Y., Satou,K.
Characterization and Clustering of GO Terms by Feature Importance Vectors Obtained from Microarray Data
WSEAS Transactions on Biology and Biomedicine, Vol.5, Issue 7, pp.163-172
2008.7

Satou,K., Konno,K., Ohta,O., Mikami,K., Teranishi,K., Yamada,Y., Ohki,S.
Performance Evaluation of Parallel Processing Environment for Molecular Dynamics
WSEAS Transactions on Biology and Biomedicine, Vol.5, Issue 7, pp.173-182
2008.7

Tran,D.H., Pham,T.H., Satou,K., Ho,T.B.
Prediction of human microRNA hairpins using only positive sample learning
Journal of Biomedical Science and Engineering (JBiSE), Vol.1, Issue 2, pp.141-146
2008.8

Tran,D.H., Pham,T.H., Satou,K., Ho,T.B.
Finding microRNA regulatory modules in human genome using rule induction
BMC Bioinformatics, Vol.9(Suppl.12):S5(10 pages)
2008.12

CONFERENCE

Kuhara,S., Satou,K., Furuichi,E., Takagi,T., Takehara,H., Sakaki,Y.
A deductive database system PACADE for the three dimensional structure of protein (HICSS24, Hawaii, USA)
Proc. of the Twenty-Fourth Annual Hawaii International Conference on System Sciences (HICSS24), Vol.I, pp.653-659
1991.1

Satou,K., Furuichi,E., Takagi,T., Kuhara,S., Ushijima,K.
Similar structure search in a deductive database (NDA'93, Fukuoka, Japan)
Proc. of International Symposium on Next Generation Database Systems and Their Applications (NDA'93), pp.130-137
1993.9

Satou,K., Furuichi,E., Takagi,T., Kuhara,S.
Application of a deductive database system PACADE toward discovery of clusters of similar structures in proteins (HICSS27, Hawaii, USA)
Proc. of the Twenty-Seventh Annual Hawaii International Conference on System Sciences (HICSS27), Vol.V, pp.160-169
1994.1

Nishikawa,A., Satou,K., Furuichi,E., Kuhara,S., Ushijima,K.
Equipments for statistical analysis in a deductive database system -their implementation and their application to protein structural analysis- (ADTI'94, Nara, Japan)
Proc. of International Symposium on Advanced Database Technologies and Their Integration (ADTI'94), pp.237-244
1994.1

Satou,K., Takagi,T., Kanehisa,M.
GenomeNet: overview and recent enhancements (8th AAAP animal science Congress, Chiba, Japan)
Proc. of the Eighth Asian- Australasian Association of Animal Production Societies (AAAP) Animal Science Congress, Vol.I, pp.541-544
1996.1

Satou,K., Ono,T., Yamamura,Y., Furuichi,E., Kuhara,S., Takagi,T.
Extraction of substructures of proteins essential to their biological functions by a data mining technique (ISMB'97, Halkidiki, Greece)
Proc. of the Fifth International Conference on Intelligent Systems for Molecular Biology (ISMB'97), pp.254-257
1997.6

Tatsumoto,S., Satou,K., Konagaya,A.,Kurita,J., Shimahara,H., Tate,S.
Development of support tool for NMR spectrum analysis (METMBS'03, Las Vegas, USA)
Proc. of the 2003 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'03), pp.159-164
2003.6

Minakuchi,Y., Satou,K., Konagaya,A.
Prediction of protein-protein interaction sites using support vector machines (METMBS'03, Las Vegas, USA)
Proc. of the 2003 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'03), pp.22-28
2003.6

Li,H., Yokota,K., Satou,K.
Conformational change of calmodulin: A molecular dynamics simulation study (SCI2003, Florida, USA)
Proc. of the 7th World Multiconference on Systemics, Cybernetics and Informatics (SCI2003), Vol. VIII, pp.47-52
2003.7

Clemente,J.C., Defago,X., Satou,K.
Asynchronous peer-to-peer communication for failure resilient distributed genetic algorithms (PDCS2003, California, USA)
Proc. of the 15th IASTED Intl. Conf. on Parallel and Distributed Computing and Systems (PDCS2003), Vol.II, pp.769-773
2003.11

Tatsumoto,S., Satou,K., Konagaya,A.
Prediction of protein secondary structure from PDB structure information based on sequence fragments Homology searching (METMBS'04, Las Vegas, USA)
Proc. of the 2004 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'04), pp.250-255
2004.6

Kamegai,S., Satou,K., Konagaya,A.
Automated template discovery for information extraction from biomedical literature (CITSA 2004, Florida, USA)
Proc. of the International Conference on Cybernetics and Information Technologies, Systems and Applications (CITSA 2004), Vol II, pp.39-44
2004.7

Clemente,J.C., Satou,K., Torisawa,K.
Improving the identification of non-anaphoric it using support vector machines (NLPBA/BioNLP 2004, Geneva, Switzerland)
Proc. of the International Workshop on Natural Language Processing in Biomedicine and its Applications (NLPBA/BioNLP 2004), pp.58-61
2004.8

Yoshikawa,S., Satou,K., Konagaya,A.
Drug interaction ontology (DIO) for inferences of possible drug-drug interactions (Medinfo 2004, San Francisco, USA)
Proc. of Medinfo 2004, pp.454-458
2004.9

Pham,T.H., Clemente,J.C., Satou,K., Ho,T.B.
Rule evaluation heuristics for knowledge discovery (KDDMBS, Hanoi, Vietnam)
Proc. of the Workshop on Knowledge Discovery and Data Management in Biomedical Science (KDDMBS) in conjunction with PAKDD-05, pp.29-44
2005.5

Li,H., Yokota,K., Satou,K.
Contractive conformational change of calmodulin caused by the central linker: A molecular dynamics simulation study (METMBS'05, Las Vegas, USA)
Proc. of the 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'05), pp.225-230
2005.6

Clemente,J.C., Torisawa,K., Satou,K.
Comparison of phrase indexing for biomedical and newswire documents (IFSR2005, Kobe, Japan)
Proc. of the First International Congress of the International Federation for Systems Research (IFSR2005), S5-4-2 (6 pages in CD proceedings)
2005.11

Tran,D.H., Pham,T.H., Satou,K., Ho,T.B.
Conditional random fields for predicting and analyzing histone occupancy, acetylation and methylation areas in DNA sequences (EvoBio 2006, Budapest, Hungary)
Proc. of EvoBio 2006, pp.221-230
2006.4

Casasnovas,J., Clemente,J.C., Miro-Julia,J., Rossello,F., Satou,K., Valiente,G.
Fuzzy clustering improves phylogenetic relationships reconstruction from metabolic pathways (IPMU 2006, Paris, France)
Proc. of the 11th International Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems (IPMU 2006), pp.2807-2814
2006.7

Pham,T.H., Tran,D.H., Ho,T.B., Satou,K.
Prediction of Histone Modifications in DNA sequences
Proc. of the 7th IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2007), pp.959-966
2007.10

Tran,D.H., Pham,T.H., Satou,K., Ho,T.B.
Prediction of microRNA Hairpins Using One-class Support Vector Machines
Proc. of the 2nd International Conference on Bioinformatics and Biomedical Engineering (ICBBE 2008), pp.33-36
2008.5

Higashihara,M., Rebolledo-Mendez,J.D., Yamada,Y., Satou,K.
Ranking and Selection of Features for Improved Prediction of Nucleosome Occupancy and Modification
Proc. of the 9th WSEAS International Conference on MATHEMATICS & COMPUTERS IN BIOLOGY & CHEMISTRY (MCBC '08), pp.188-193
2008.6

Yamada,Y., Miyata,Y., Higashihara,M., Satou,K.
Estimation of Identification Methods of Gene Clusters Using GO Term Annotations from a Hierarchical Cluster Tree
Proc. of the 9th WSEAS International Conference on MATHEMATICS & COMPUTERS IN BIOLOGY & CHEMISTRY (MCBC '08), pp.194-198
2008.6

Yamada,Y., Satou,K.
Prediction of methylation status on DNA sequences and identification of its important DNA sequence features
Proc. of the WSEAS International Conference on BIOMEDICAL ELECTRONICS and BIOMEDICAL INFORMATICS (BEBI'08), pp.223-227
2008.8

Satou,K., Konno,K., Ohta,O., Mikami,K., Teranishi,K., Yamada,Y., Ohki,S.
Effect of Parallel Processing and Optimization Techniques in Molecular Dynamics
Proc. of the WSEAS International Conference on BIOMEDICAL ELECTRONICS and BIOMEDICAL INFORMATICS (BEBI'08), pp.228-233
2008.8

Rebolledo-Mendez,J.D., Higashihara,M., Yamada,Y., Satou,K.
Finding Hidden Relationship among Biological Concepts in Gene Ontology
Proc. of the WSEAS International Conference on BIOMEDICAL ELECTRONICS and BIOMEDICAL INFORMATICS (BEBI'08), pp.237-241
2008.8

Nguyen,T.P., Satou,K., Ho,T.B., Takabayashi,K.
Constructing Signal Transduction Networks Using Multiple Signaling Feature Data
Proc. of Statistical and Relational Learning in Bioinformatics (StReBio), pp.1-8
2008.9

Tran,D.H., Ho,T.B., Satou,K., Pham,T.H.
A computational method for classifying and analyzing tumor samples using microRNA expression profiles
3rd International Conference on Knowledge, Information and Creativity Support Systems (KICSS 2008), pp.120-127
2008.12