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Researcher Information

last modified:2017/07/16

Associate Professor YAMADA Yoichi


Faculty, Affiliation

Faculty of Electrical and Computer Engineering, Institute of Science and Engineering

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
School of Electrical and Computer Engineering, College of Science and Engineering


genome informatics TEL:076-234-4898 FAX:076-234-4900

Academic Background

【Academic background(Doctoral/Master's Degree)】
The University of Tokyo Doctor Completed
【Academic background(Bachelor's Degree)】
University of Tsukuba
Doctor of Philosophy


Year & Month of Birth

Academic Society

Japanese Society for Bioinformatics



、Molecular biology、

Speciality Keywords

Research Themes

Development of a body map of human genome methylation

DNA methylation is a chemical reaction in which methyl group is added to 5-position of cytocine of CpG dinucleotides in mammalian genome. If a gene promoter region is methylated, the gene will be inactivated due to its chromatin condensation, or because transcription factors are physically unable to directly bind to the promoter region. In this context, we have developed HpaII-McrBC PCR (HM-PCR) method, which is a methylation analysis approach based on genome sequence information. Then, we have identified promoters on human chromosome 21 and 11 in silico, and by using HM-PCR method, have also investigated methylation status of these promoters in the genome from human peripheral blood leukocytes. Furthermore, since it was proved that HM-PCR method is also capable of detecting allele-specific methylation (ASM), comprehensive isolation of imprint genes, which exist near ASM region and are known for its relationships with various diseases, is also expected.

computational identification of useful knowledge from gene expression data

Microarray is a genetic engineering technology that is capable of quantifying the gene expression of 20,000-30,000 simultaneously. However, manual works have limitations when discovering valuable findings from such massive amount of data. In this context, we have been working on developing algorithms for discovering valuable findings from microarray data by utilizing a computer-based statistic analysis or a clustering method.



  •  Myeloid Differentiation Factor 88 Signaling in Bone Marrow-Derived Cells Promotes Gastric Tumorigenesis by Generation of Inflammatory Microenvironment. Maeda Y, Echizen K, Oshima H, Yu L, Sakulsak N, Hirose O, Yamada Y, Taniguchi T, Jenkins BJ, Saya H, Oshima M. Cancer Prev Res 9 3 253-263 2016
  •  Factors to preserve CpG-rich sequences in methylated CpG islands Miyahara H., Hirose O., Satou K., Yamada Y. BMC Genomics 16 144 2015
  •  D-IMPACT: A Data Preprocessing Algorithm to Improve the Performance of Clustering Tran V.A., Hirose O., Saethang T., Nguyen L.A.T., Dang X.T., Le T.K.T., Ngo D.L., Gavrilov S., Kubo M., Yamada Y., Satou K. Journal of Software Engineering and Applications 7 8 639-654 2014
  •  Le T.K.T., Hirose O., Tran V.A., Saethang T., Nguyen L.A.T., Dang X.T., Ngo D.L., Kubo M., Yamada Y., Satou K. Le T.K.T., Hirose O., Tran V.A., Saethang T., Nguyen L.A.T., Dang X.T., Ngo D.L., Kubo M., Yamada Y., Satou K. Journal of Biomedical Science and Engineering 7 1 28-37 2014
  •  Regional DNA methylation differences between humans and chimpanzees are associated with genetic changes, transcriptional divergence and disease genes Fukuda K., Ichiyanagi K., Yamada Y., Go Y., Udono T., Wada S., Maeda T., Soejima H., Saitou N., Ito T., Sasaki H. Journal of Human Genetics 58(7) 446-454 2013

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  •  TNF-α/TNFR1 signaling promotes gastric tumorigenesis through induction of Noxo1 and Gna14 in tumor cells Oshima H., Ishikawa T., Yoshida G.J., Naoi K., Maeda Y., Naka K., Ju X., Yamada Y., Minamoto T., Mukaida N., Saya H., Oshima M. Oncogene 33(29) 3820-3829 2013
  •  An identification method of data-specific GO terms from a microarray data set Yoichi Yamada, Ken-ichi Hirotani, Kenji Satou, Ken-ichiro Muramoto IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS E92-D 5 1093-1102 2009/05
  •  Prediction of Genomic Methylation Status on CpG Islands Using DNA Sequence Features Yoichi Yamada, Kenji Satou 5 153-162 2008
  •  Changes of phospho-growth associated protein 43 (phospho-GAP43) in zebrafish retina after optic nerve injury: a long term observation Manabu Kaneda, Mikiko Nagashima, Tomoya Nunome, Takanori Muramatsu, Yoichi Yamada, Mamoru Kubo, Ken-ichiro Muramoto, Toru Matsukawa, Yoshiki Koriyama, Kayo Sugitani, Ivan H. Vachkov, Kazuhiro Mawatari, Satoru Kato 61 281-288 2008
  •  Diverse DNA Methylation Status at Alternative Promoters of Human Genes in Various Normal Tissues Jieun Cheong, Yoichi Yamada, Riu Yamashita, Takuma Irie, Akinori Kanai, Hiroyuki Wakaguri, Kenta Nakai, Takashi Ito, Izumu Saito, Sumio Sugano, Yutaka Suzuki 13 155-167 2006
  •  A comprehensive allelic methylation analysis of CpG islands on human chromosome 11q Yoichi Yamada, Tomoyo Shirakawa, Todd Taylor, Kohji Okamura, Hidenobu Soejima, Michiko Uchiyama, Tsuyoshi Iwasaka, Tsunehiro Mukai, Ken-ichiro Muramoto, Yoshiyuki Sakaki, Takashi Ito DNA SEQUENCE 17 300-306 2006
  •  A yeast one-hybrid system to detect methylation-dependent DNA-protein interactions. Shu-Ying Feng, Kazuhisa Ota, Yoichi Yamada, Nobuaki Sawabu, Takashi Ito BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 23 922-925 2004
  •  A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q. Yoichi Yamada, Hidemi Watanabe, Fumihito Miura, Hidenobu Soejima, Michiko Uchiyama, Tsuyoshi Iwasaka, Tsunehiro Mukai, Yoshiyuki Sakaki, Takashi Ito GENOME RESEARCH 14 247-266 2004/02

Conference Presentations

Arts and Fieldwork


Theme to the desired joint research

Grant-in-Aid for Scientific Research


Classes (Bachelors)

○Design of Biological Information System(2017)
○Bimolecular Informatics(2017)
○Bimolecular Informatics(2017)
○Student-Initiated Project(2016)
○Freshman Seminar I(2016)
○Bimolecular Informatics(2016)
○Bimolecular Informatics(2016)
○Design of Biological Information System(2016)
○Presentation and Debate (Freshman Seminar II)(2016)
○Presentation and Debate (Freshman Seminar II)(2016)
○Freshman Seminar I(2016)

Classes (Graduate Schools)

○Topics in Molecular Biology(2017)
○Topics in Molecular Biology(2017)
○Foundation of Genome informatics A(2017)
○Topics in Molecular Biology(2017)
○Fostering the independence of researchers(2017)
○Fostering the independence of researchers(2017)
○Topics in Molecular Biology(2017)
○Foundation of Genome informatics A(2016)
○Topics in Molecular Biology(2016)

International Project

International Students

Lecture themes

Others (Social Activities)

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