Associate Professor YAMADA Yoichi
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
Course in Bioengineering, School of Biological Science and Technology, 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
The Institute of Electronics, Information and Communication Engineers
Japanese Society for Bioinformatics
日本農芸化学会
Award
Specialities
Genomics、Molecular biology、Bioinformatics、Applied microbiology
Speciality Keywords
Genome science, Microbiology, Bioinformatics
Research Themes
酵母のグルコース抑制の研究
出芽酵母のアルコール発酵と好気呼吸の切り替えメカニズムを解明することは、酒類やエタノールの生産、そして酵母を用いた有用物質の生産に重要である。酵母におけるグルコース抑制とは、グルコースが好気呼吸代謝や他の糖代謝を抑制し，グルコースを用いたアルコール発酵を優先的に行う現象である。本研究室では、出芽酵母のリボソーム結合性分子シャペロン制御因子であるZuo1がグルコース抑制に必要であることを見いだし、Zuo1のグルコース抑制における役割を研究している(Yamada, et al., FEMS yeast research, 2023）。
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.
Yeast multidrug resistance research
Books
Papers
- In Saccharomyces cerevisiae ρ0 cells, UME6 contributes to the activation of ABC transporter genes and pleiotropic drug resistance via RPD3 and PDR3 Funasaka M., Ota M., Yamada Y., Microbiology Research 15 734–745 2024
- Zuo1, a ribosome-associated J protein, is involved in glucose repression in Saccharomyces cerevisiae. Yamada Y, Shiroma A, Hirai S, Iwasaki J, FEMS Yeast Research 2023
- UME6 Is Involved in the Suppression of Basal Transcription of ABC Transporters and Drug Resistance in the ρ+ Cells of Saccharomyces cerevisiae. Yamada Y, Microorganisms 10 601 14 pages 2022
- RPD3 and UME6 are involved in the activation of PDR5 transcription and pleiotropic drug resistance in ρ0 cells of Saccharomyces cerevisiae. Yamada Y, BMC Microbiology 21 311 2021
- A method for identifying allele-specific hydroxymethylation. Yamada Y, Sasaki S, Epigenetics 15 (3) 231-250 2020
- NF-κB-induced NOX1 activation promotes gastric tumorigenesis through the expansion of SOX2-positive epithelial cells. Echizen K, Horiuchi K, Aoki Y, Yamada Y, Minamoto T, Oshima H, Oshima M Oncogene 2019
- 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
- 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
- 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 5 680 12 pages 2012
- Highly efficient PCR assay to discriminate allelic DNA methylation status using whole genome amplification. Yamada Y., Ito T. BMC Research Notes 4 179 6 pages 2011
- 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
- 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 Neurosci. Res. 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 DNA Research 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
Others
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)
○「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-)
○「出芽酵母の分子シャペロン制御因子によるグルコース抑制の制御」(2024-2026)
Competitive research funding,Contribution
Collaborative research,Consignment study
○construction of DNA mehtylation body map by HM-PCR(2004-2006)
Classes (Bachelors)
○Guide to Biology and Bioengineering B(2019)
○Topics in Biology and Bioengineering B(2019)
○Design of Biological Information System(2019)
○Guide to Biology and Bioengineering A(2018)
○Bimolecular Informatics(2018)
○Bimolecular Informatics(2018)
○Design of Biological Information System(2018)
○International Training B(2018)
○Guide to Biology and Bioengineering B(2018)
○Topics in Biology and Bioengineering A(2018)
○Topics in Biology and Bioengineering B(2018)
○Bimolecular Informatics(2017)
○Bimolecular Informatics(2017)
○Design of Biological Information System(2017)
○Student-Initiated Project(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)
○Freshman Seminar I(2016)
○Bimolecular Informatics(2016)
○Bimolecular Informatics(2016)
Classes (Graduate Schools)
○Topics in Molecular Biology(2019)
○Foundation of Genome informatics A(2019)
○Topics in Molecular Biology(2018)
○Foundation of Genome informatics A(2018)
○Topics in Molecular Biology(2017)
○Foundation of Genome informatics A(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)