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Researcher Information

last modified:2018/04/02

Associate Professor YAMADA Yoichi

Mail

Faculty, Affiliation

Faculty of Biological Science and Technology,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

Laboratory

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
【Degree】
Doctor of Philosophy

Career

Year & Month of Birth

Academic Society

Japanese Society for Bioinformatics

Award

Specialities

Genomics、Molecular biology、Bioinformatics

Speciality Keywords

Genome, Bioinformatics

Research Themes

Genomic methylation analysis

DNA methylation is a chemical reaction in which methyl group is added to 5-position of the cytocine of CpG dinucleotides in the 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 method based on genomic sequences. Then, we first identified a sequence-dependent allele-specific methylation on human chromosome 21 in peripheral blood leukocytes using the HM-PCR method. Since sequence-dependent allele-speific methylation is currently shown to be ubiquitous on human genome, it is expected to reveal a mechanism of disease susceptibility difference caused by polymorphisms.
We therefore study the sequence-dependent allele-speific methylation by whole genome bisulfite sequencing and computer analysis.

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.

Books

Papers

  •  Intestinal cancer progression by mutant p53 through the acquisition of invasiveness associated with complex glandular formation. Nakayama M, Sakai E, Echizen K, Yamada Y, Oshima H, Han T-S, Ohki R, Fujii S, Ochiai A, Robine S, Voon DC, Tanaka T, Taketo MM and Oshima M Oncogene 36 42 5885-5896. 2017
  •  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

show all

  •  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
  •  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
  •  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
  •  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
  •  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

Patent

Theme to the desired joint research

Grant-in-Aid for Scientific Research

○「配列依存的アレル特異的ヒドロキシメチル化の普遍性の検証」(2015-2017) 
○「配列依存的アレル特異的ヒドロキシメチル化の探索」(2012-2014)
○「配列依存的アレル特異的ヒドロキシメチル化の探索」(2012-2014) 
○「転写因子遺伝子群に限定した網羅的ヒトインプリント遺伝子の探索」(2007-) 
○「網羅的アレル別メチル化解析によるヒトメチル化ボディマップの作成」(2005-) 

Classes (Bachelors)

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

Classes (Graduate Schools)

○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)
○Topics in Molecular Biology(2017)
○Topics in Molecular Biology(2017)
○Topics in Molecular Biology(2016)
○Foundation of Genome informatics A(2016)

International Project

International Students

Lecture themes

Others (Social Activities)

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