Kyushu University Academic Staff Educational and Research Activities Database
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Osamu Maruyama Last modified date:2016.09.16

Graduate School
Undergraduate School

Academic Degree
Dr. Sci.
Field of Specialization
Systems biology, Machine learning, Computer science
Outline Activities
Research activities:
It is important to elucidate various the structures, mechanisms and
regulations of organisms, which are designed according to the
blueprints called 'genomes', in order to understand them as complex
systems. I’m tackling this problem by designing and analyzing
algorithms to discover biological knowledge and rules from existing
data. I’m also carrying out computational experiments on various
biological data with the implemented algorithms.

Educational activities:
An educational purpose is to train computer scientists who can
understand biology.

Social activities:
A manager of Japanese Society for Bioinformatics
Research Interests
  • Systems Biology, Computational Biology
    keyword : protein-protein interaction, gene regulatory network, algorithm, pattern recognition, machine learning
Academic Activities
1. Osamu Maruyama, Yuki Kuwahara, RocSampler: Regularizing Overlapping Protein Complexes in Protein-Protein Interaction Networks, BMC Bioinformatics, To appear, 2016.10.
2. Osamu Maruyama, Limsoon Wong, Regularizing predicted complexes by mutually exclusive protein-protein interactions, Proceedings of the 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining 2015, 2015.08.
3. So Kobiki, Osamu Maruyama, ReSAPP: Predicting overlapping protein complexes by merging multiple-sampled partitions of proteins, Journal of bioinformatics and computational biology, 12, 6, 1442004, 2014.12.
4. Chern Han Yong, Osamu Maruyama, Limsoon Wong, Discovery of small protein complexes from PPI networks with size-specific supervised weighting, BMC systems biology 8, S3-S3, 2014., 2014.12.
5. Osamu Maruyama, Shota Shikita, A scale-free structure prior for Bayesian inference of Gaussian graphical models, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2014. , 2014.11.
6. Chasanah Kusumastuti Widita, Osamu Maruyama, PPSampler2: Predicting Protein Complexes More Accurately and Efficiently by Sampling, BMC Systems Biology, 7, Suppl 6, 2013.12.
7. Daisuke Tatsuke, Osamu Maruyama, Sampling Strategy for Protein Complex Prediction Using Cluster Size Frequency, Gene, Special issue of the 23rd International Conference on Genome Informatics (GIW), 2012.12.
8. Osamu Maruyama, Heterodimeric Protein Complex Identification, ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011, 2011.08.
9. Osamu Maruyama and Ayaka Chihara, NWE: Node-Weighted Expansion for Protein Complex Prediction Using Random Walk Distances, Proc. IEEE International Conference on Bioinformatics & Biomedicine (IEEE BIBM 2010), 590-594, 2010.12.
10. Yukio Yasukochi, Osamu Maruyama, Milind C. Mahajan, Carolyn Pad- den, Ghia M. Euskirchen, Vincent Schulz, Hideki Hirakawa, Satoru Kuhara, Xing-Hua Pan, Peter E. Newburger, Michael Snyder, and Sherman M. Weiss- man, X chromosome-wide analyses of genomic DNA methylation states and
gene expression in male and female neutrophils
, Proceedings of the National Academy of Sciences of the United States of America (PNAS), 107, 3704-3709, 2010.02.
11. Osamu Maruyama, Hideki Hirakawa, Takao Iwayanagi, Yoshiko Ishida, Shizu Takeda, Jun Otomo, Satoru Kuhara, Evaluating Protein Sequence Signatures Inferred
from Protein-Protein Interaction Data by Gene Ontology Annotations, 2008 IEEE International Conference on Bioinformatics and Biomedicine, 417-420, 2008.11.
12. Osamu Maruyama, Akiko Matsuda, and Satoru Kuhara, Reconstructing phylogenetic trees of prokaryote genomes by randomly sampling oligopeptides, International Journal of Bioinformatics Research and Applicaions (IJBRA) 1(4), 429-446, 2005. (preliminary version has appeared in the Proceedings of the 5th International Conference on Computational Science (ICCS 2005), Lecture Notes in Computer Science 3514-6, Springer-Verlag, II-911-918, 2005). , 2005.11.
13. Daichi Shigemizu and Osamu Maruyama., Searching for Regulatory Elements of Alternative Splicing Events Using Phylogenetic Footprinting,, Proceedings of the 4th Workshop on Algorithms in Bioinformatics, Lecture Notes in Bioinformatics 3240, Springer-Verlag, 3240, 147-158, 2004.09.
14. Osamu Maruyama, Extensive Search for Discriminative Features of Alternative Splicing, Pacific Symposium on Biocomputing 2004, 54-65, 2004.01.
15. Osamu Maruyama, Finding optimal degenerate patterns in DNA sequences, Bioinformatics, 19, 19(supplement 2), 206-214, 2003.09.
Works, Software and Database
1. .
1. Osamu Maruyama, Limsoon Wong, Regularizing predicted complexes by mutually exclusive protein-protein interactions, International Symposium on Network Enabled Health Informatics, Biomedicine and Bioinformatics, HI-BI-BI 2015, 2015.08.26.
2. , [URL].
3. , [URL].
Membership in Academic Society
  • Institute of Electronics, Information and Communication Engineers(IEICE)