Details of the Researcher

PHOTO

Takeshi Obayashi
Section
Graduate School of Information Sciences
Job title
Professor
Degree

  • 博士（理学）（東京工業大学）

  • 修士（理学）（東京工業大学）

e-Rad No.
50397048
Researcher ID
E-9663-2011
Profile
生命システムの進化に興味を持ち、大規模データをマイニングするアプローチで研究をしています。

Research History 9

  • 2024/04 - Present
    Advanced Institute for Marine Ecosystem Change (WPI-AIMEC)　Coastal Ecosystem Services Research Unit　Unit Leader

  • 2022/10 - Present
    Tohoku University　Graduate School of Information Sciences　Professor

  • 2012/04 - 2022/09
    Tohoku University　Graduate School of Information Sciences　Associate professor

  • 2009/12 - 2012/03
    Graduate School of Information Sciences, Tohoku University　Assistant professor

  • 2009/10 - 2009/11
    Graduate School of Information Sciences, Tohoku University　Postdoctoral Researcher

  • 2006/04 - 2009/09
    Human Genome Center, The Institute of Medical Science, The University of Tokyo　Postdoctoral Researcher

  • 2005/04 - 2006/03
    Graduate School of Pharmaceutical Sciences, Chiba University　Postdoctoral Researcher

  • 2004/10 - 2005/03
    Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology　Postdoctoral Researcher

  • 2004/04 - 2004/09
    Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology　Postdoctoral Researcher

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Education 2

  • Tokyo Institute of Technology　Graduate School of Bioscience and Biotechnology

    1997/04 - 2004/03

  • Tokyo Institute of Technology　School of Bioscience and Biotechnology

    1994/04 - 1997/03

Committee Memberships 15

  • Japanese Society for Bioinformatics　Treasurer

    2015/04 - Present

  • Japanese Society for Bioinformatics　Board Members

    2024/04 - 2026/03

  • The Japanese Society of Plant Physiologists　Handling Editor

    2023 - 2026

  • Information processing society of Japan　Steering Committee (Secretary) of The Special Interest Groups of Bioinformatics and Genomics

    2023/04 - 2025/03

  • Japanese Society for Bioinformatics　Board of Directors

    2018/04 - 2022/03

  • Information Processing Society of Japan　Steering Committee for The Special Interest Groups of Bioinformatics and Genomics (BIO)

    2017/04 - 2021/03

  • Japanese Society of Plant Physiologists　Editorial Board

    2011/01 - 2019/12

  • Japanese Society of Plant Physiologists　Secretaries of Public Relations

    2017/04 - 2019/03

  • Botanical Society of Japan　Editorial Board

    2014 - 2019

  • Japanese Society for Bioinformatics　Board of Directors

    2013/04 - 2017/03

  • The Japanese Society of Plant Physiologists　Public Relations Committee

    2012/01 - 2016/03

  • Japanese Society for Bioinformatics　Councilors

    2013/04 - 2015/03

  • Japanese Society for Bioinformatics　Execution Committee of Bioinformatics Engineer Certification Exam

    2012 - 2014

  • Japanese Society for Bioinformatics　Councilors

    2010/04 - 2012/03

  • Japanese Society for Bioinformatics　Contributor of Bioinformatics Engineer Certification Exam

    2009 - 2011

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Professional Memberships 7

  • The Japanese Society of Plant Physiologists

  • International Society for Computational Biology

  • Japanese Society for Bioinformatics

  • The Ecological Society of Japan

    2019 - Present

  • ISCB Student Council Japan Division

  • Information Processing Society of Japan

  • The Japanese Society for Artificial Intelligence

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Research Interests 10

  • Marine Biology

  • Population genetics

  • Computational linguistics

  • Bioinformatics

  • Computational biology

  • Transcriptome

  • Evolutionary Ecology

  • Database

  • Gene coexpression

  • Gene network

Research Areas 4

  • Life sciences / Ecology and environmental science /

  • Humanities & social sciences / Linguistics /

  • Life sciences / Plants: molecular biology and physiology /

  • Life sciences / Genomics /

Awards 14

  1. (Young Investigator Award)

    2017/11　Minoru Ishida Foundation

  2. Funai Information Technology Award

    2015/04　Funai Foundation

  3. The Young Scientists’ Award, The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology

    2015/04　Minister of Education, Culture, Sports, Science and Technology

  4. Young Investigator Award

    2014/03　Japanese society of plant physiologists

  5. Oxford Journals - Japanese Society for Bioinformatics Prize, 2013

    2013/10　Japanese Society for Bioinformatics

  6. BSJ Special Award, 2009

    2009/09　The Botanical Society of Japan

  7. President's Education Award

    2021/03　Tohoku University

  8. Award for Contribution to University Education

    2021/02　Tohoku University

  9. PCP Top Cited Paper Award 2020

    2020/03　Japanese Society of Plant Physiologists

  10. 第54回バイオ情報学研究発表会 優秀プレゼンテーション賞

    2018/06

  11. DBCLSオープン・サイエンス・アワード データベース部門 審査員特別賞, 2013

    2013/10　ライフサイエンス統合データベースセンター　ATTED-II / COXPRESdb

  12. J. Plant Res. Most cited paper award 2013

    2013/09　日本植物学会　Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways. (2010) J. Plant Res. 123: 311–319

  13. 第19回加齢研集談会発表コンテスト 最優秀賞

    2011/07　東北大学加齢医学研究所研究員会

  14. Award for winning debate team on the 4th AYRCOB

    2010/12　Asian Young Researchers Conference on Computational and Omics Biology (AYRCOB)

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Papers 54

  1. COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations

    Takeshi Obayashi, Shun Kodate, Himiko Hibara, Yuki Kagaya, Kengo Kinoshita

    Nucleic Acids Research　51　(D1)　D80-D87　2022/11/09

    Publisher: Oxford University Press (OUP)

    DOI： 10.1093/nar/gkac983 　

    ISSN： 0305-1048

    eISSN： 1362-4962

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    Abstract Gene coexpression is synchronization of gene expression across many cellular and environmental conditions and is widely used to infer the biological function of genes. Gene coexpression information is complex, comprising a complete graph of all genes in the genome, and requires appropriate visualization and analysis tools. Since its initial release in 2007, the animal gene expression database COXPRESdb (https://coxpresdb.jp) has been continuously improved by adding new gene coexpression data and analysis tools. Here, we report COXPRESdb version 8, which has been enhanced with new features for an overview, summary, and individual examination of coexpression relationships: CoexMap to display coexpression on a genome scale, pathway enrichment analysis to summarize the function of coexpressed genes, and CoexPub to bridges coexpression and existing knowledge. COXPRESdb also facilitates downstream analyses such as interspecies comparisons by integrating RNAseq and microarray coexpression data in a union-type gene coexpression. COXPRESdb strongly support users with the new coexpression data and enhanced functionality.

  2. ATTED-II v11: A Plant Gene Coexpression Database Using a Sample Balancing Technique by Subagging of Principal Components.

    Takeshi Obayashi, Himiko Hibara, Yuki Kagaya, Yuichi Aoki, Kengo Kinoshita

    Plant & cell physiology　63　(6)　869-881　2022/06/15

    DOI： 10.1093/pcp/pcac041 　

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    ATTED-II (https://atted.jp) is a gene coexpression database for nine plant species based on publicly available RNAseq and microarray data. One of the challenges in constructing condition-independent coexpression data based on publicly available gene expression data is managing the inherent sampling bias. Here, we report ATTED-II version 11, wherein we adopted a coexpression calculation methodology to balance the samples using principal component analysis and ensemble calculation. This approach has two advantages. First, omitting principal components with low contribution rates reduces the main contributors of noise. Second, balancing large differences in contribution rates enables considering various sample conditions entirely. In addition, based on RNAseq- and microarray-based coexpression data, we provide species-representative, integrated coexpression information to enhance the efficiency of interspecies comparison of the coexpression data. These coexpression data are provided as a standardized z-score to facilitate integrated analysis with different data sources. We believe that with these improvements, ATTED-II is more valuable and powerful for supporting interspecies comparative studies and integrated analyses using heterogeneous data.

  3. COXPRESdb v7: a gene coexpression database for 11 animal species supported by 23 coexpression platforms for technical evaluation and evolutionary inference. Peer-reviewed

    Obayashi T, Kagaya Y, Aoki Y, Tadaka S, Kinoshita K

    Nucleic acids research　2018/11

    DOI： 10.1093/nar/gky1155 　

    ISSN： 0305-1048

  4. ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index. Peer-reviewed

    Obayashi T, Aoki Y, Tadaka S, Kagaya Y, Kinoshita K

    Plant & cell physiology　59　(1)　e3　2018/01

    DOI： 10.1093/pcp/pcx191 　

    ISSN： 0032-0781

  5. ALCOdb: Gene Coexpression Database for Microalgae Peer-reviewed

    Yuichi Aoki, Yasunobu Okamura, Hiroyuki Ohta, Kengo Kinoshita, Takeshi Obayashi

    PLANT AND CELL PHYSIOLOGY　57　(1)　e3-e3　2016/01

    DOI： 10.1093/pcp/pcv190 　

    ISSN： 0032-0781

    eISSN： 1471-9053

  6. ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression Peer-reviewed

    Yuichi Aoki, Yasunobu Okamura, Shu Tadaka, Kengo Kinoshita, Takeshi Obayashi

    PLANT AND CELL PHYSIOLOGY　57　(1)　e5-e5　2016/01

    DOI： 10.1093/pcp/pcv165 　

    ISSN： 0032-0781

    eISSN： 1471-9053

  7. COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems Peer-reviewed

    Yasunobu Okamura, Yuichi Aoki, Takeshi Obayashi, Shu Tadaka, Satoshi Ito, Takafumi Narise, Kengo Kinoshita

    NUCLEIC ACIDS RESEARCH　43　(D1)　D82-D86　2015/01

    DOI： 10.1093/nar/gku1163 　

    ISSN： 0305-1048

    eISSN： 1362-4962

  8. ATTED-II in 2014: Evaluation of Gene Coexpression in Agriculturally Important Plants Peer-reviewed

    Takeshi Obayashi, Yasunobu Okamura, Satoshi Ito, Shu Tadaka, Yuichi Aoki, Matsuyuki Shirota, Kengo Kinoshita

    PLANT AND CELL PHYSIOLOGY　55　(1)　e6-e6　2014/01

    DOI： 10.1093/pcp/pct178 　

    ISSN： 0032-0781

    eISSN： 1471-9053

  9. COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals Peer-reviewed

    Takeshi Obayashi, Yasunobu Okamura, Satoshi Ito, Shu Tadaka, Ikuko N. Motoike, Kengo Kinoshita

    NUCLEIC ACIDS RESEARCH　41　(D1)　D1014-D1020　2013/01

    DOI： 10.1093/nar/gks1014 　

    ISSN： 0305-1048

  10. ATTED-II Updates: Condition-Specific Gene Coexpression to Extend Coexpression Analyses and Applications to a Broad Range of Flowering Plants Peer-reviewed

    Takeshi Obayashi, Kozo Nishida, Kota Kasahara, Kengo Kinoshita

    PLANT AND CELL PHYSIOLOGY　52　(2)　213-219　2011/02

    DOI： 10.1093/pcp/pcq203 　

    ISSN： 0032-0781

  11. COXPRESdb: a database to compare gene coexpression in seven model animals Peer-reviewed

    Takeshi Obayashi, Kengo Kinoshita

    NUCLEIC ACIDS RESEARCH　39　(Database issue)　D1016-D1022　2011/01

    DOI： 10.1093/nar/gkq1147 　

    ISSN： 0305-1048

  12. Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways Peer-reviewed

    Takeshi Obayashi, Kengo Kinoshita

    JOURNAL OF PLANT RESEARCH　123　(3)　311-319　2010/05

    DOI： 10.1007/s10265-010-0333-6 　

    ISSN： 0918-9440

    eISSN： 1618-0860

  13. Co-expression tools for plant biology: opportunities for hypothesis generation and caveats Peer-reviewed

    Bjoern Usadel, Takeshi Obayashi, Marek Mutwil, Federico M. Giorgi, George W. Bassel, Mimi Tanimoto, Amanda Chow, Dirk Steinhauser, Staffan Persson, Nicholas J. Provart

    PLANT CELL AND ENVIRONMENT　32　(12)　1633-1651　2009/12

    DOI： 10.1111/j.1365-3040.2009.02040.x 　

    ISSN： 0140-7791

  14. Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis Peer-reviewed

    Kengo Kinoshita, Takeshi Obayashi

    BIOINFORMATICS　25　(20)　2677-2684　2009/10

    DOI： 10.1093/bioinformatics/btp442 　

    ISSN： 1367-4803

  15. Rank of Correlation Coefficient as a Comparable Measure for Biological Significance of Gene Coexpression Peer-reviewed

    Takeshi Obayashi, Kengo Kinoshita

    DNA RESEARCH　16　(5)　249-260　2009/10

    DOI： 10.1093/dnares/dsp016 　

    ISSN： 1340-2838

  16. ATTED-II provides coexpressed gene networks for Arabidopsis Peer-reviewed

    Takeshi Obayashi, Shinpei Hayashi, Motoshi Saeki, Hiroyuki Ohta, Kengo Kinoshita

    NUCLEIC ACIDS RESEARCH　37　(Database issue)　D987-D991　2009/01

    DOI： 10.1093/nar/gkn807 　

    ISSN： 0305-1048

  17. COXPRESdb: a database of coexpressed gene networks in mammals Peer-reviewed

    Takeshi Obayashi, Shinpei Hayashi, Masayuki Shibaoka, Motoshi Saeki, Hiroyuki Ohta, Kengo Kinoshita

    NUCLEIC ACIDS RESEARCH　36　(Database issue)　D77-D82　2008/01

    DOI： 10.1093/nar/gkm840 　

    ISSN： 0305-1048

  18. ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis Peer-reviewed

    Takeshi Obayashi, Kengo Kinoshita, Kenta Nakai, Masayuki Shibaoka, Shinpei Hayashi, Motoshi Saeki, Daisuke Shibata, Kazuki Saito, Hiroyuki Ohta

    NUCLEIC ACIDS RESEARCH　35　(Database issue)　D863-D869　2007/01

    DOI： 10.1093/nar/gkl783 　

    ISSN： 0305-1048

  19. Distinctive features of plant organs characterized by global analysis of gene expression in Arabidopsis. International-journal Peer-reviewed

    Takeshi Obayashi, Takashi Okegawa, Yuko Sasaki-Sekimoto, Hiroshi Shimada, Tatsuru Masuda, Erika Asamizu, Yasukazu Nakamura, Daisuke Shibata, Satoshi Tabata, Ken-ichiro Takamiya, Hiroyuki Ohta

    DNA research : an international journal for rapid publication of reports on genes and genomes　11　(1)　11-25　2004/02/29

    DOI： 10.1093/dnares/11.1.11 　

    ISSN： 1340-2838

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    The distinctive features of plant organs are primarily determined by organ-specific gene expression. We analyzed the expression specificity of 8809 genes in 7 organs of Arabidopsis using a cDNA macroarray system. Using relative expression (RE) values between organs, many known and unknown genes specifically expressed in each organ were identified. We also analyzed the organ specificity of various gene groups using the GRE (group relative expression) value, the average of the REs of all genes in a group. Consequently, we found that many gene groups even ribosomal protein genes, have strong organ-specific expression. Clustering of the expression profiles revealed that the 8809 genes were classified into 9 major categories. Although 3451 genes were clustered into the largest category, which showed constitutive gene expression, 266 and 1005 genes were found to be root- and silique-specific genes, respectively. By this clustering, particular gene groups which showed multi-organ-specific expression profiles, such as bud-flower-specific, stem-silique-specific or bud-flower-root-specific profiles, could be effectively identified. From these results, major features of plant organs could be characterized by their distinct profiles of global gene expression. These data of organ-specific gene expression are available at our web site: Arabidopsis thaliana Tissue-Specific Expression Database, ATTED (http://www.atted.bio.titech.ac.jp/).

  20. Evolutionary approaches for narrowing down the candidate genes from the unannotated gene list Peer-reviewed

    Kanako Bessho-Uehara, Takeshi Obayashi

    Plant And Cell Physiology　2025/01/11

    Publisher: Oxford University Press (OUP)

    DOI： 10.1093/pcp/pcaf003 　

    ISSN： 0032-0781

    eISSN： 1471-9053

  21. Lipid Pathway Databases with a Focus on Algae. International-journal

    Naoki Sato, Takeshi Obayashi

    Methods in molecular biology (Clifton, N.J.)　2295　455-468　2021

    DOI： 10.1007/978-1-0716-1362-7_26 　

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    Pathways of lipid biosynthesis are highly complex and have been established in model organisms such as Arabidopsis thaliana and Chlamydomonas reinhardtii, whereas in other organisms, we need bioinformatic tools to map individual enzymes onto reference pathways. In this chapter, we explain representative tools that are useful in identifying algal orthologs of lipid biosynthetic enzymes and finding new enzymes that are possibly involved in the pathway of interest. All descriptions in this chapter refer to in silico (i.e., computer-based) methods rather than laboratory experiments.

  22. Lipid remodeling regulator 1 (LRL1) is differently involved in the phosphorus-depletion response from PSR1 in Chlamydomonas reinhardtii. International-journal Peer-reviewed

    Nur A Hidayati, Yui Yamada-Oshima, Masako Iwai, Takashi Yamano, Masataka Kajikawa, Nozomu Sakurai, Kunihiro Suda, Kanami Sesoko, Koichi Hori, Takeshi Obayashi, Mie Shimojima, Hideya Fukuzawa, Hiroyuki Ohta

    The Plant journal : for cell and molecular biology　100　(3)　610-626　2019/11

    DOI： 10.1111/tpj.14473 　

    ISSN： 0960-7412

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    The elucidation of lipid metabolism in microalgae has attracted broad interest, as their storage lipid, triacylglycerol (TAG), can be readily converted into biofuel via transesterification. TAG accumulates in the form of oil droplets, especially when cells undergo nutrient deprivation, such as for nitrogen (N), phosphorus (P), or sulfur (S). TAG biosynthesis under N-deprivation has been comprehensively studied in the model microalga Chlamydomonas reinhardtii, during which TAG accumulates dramatically. However, the resulting rapid breakdown of chlorophyll restricts overall oil yield productivity and causes cessation of cell growth. In contrast, P-deprivation results in oil accumulation without disrupting chloroplast integrity. We used a reverse genetics approach based on co-expression analysis to identify a transcription factor (TF) that is upregulated under P-depleted conditions. Transcriptomic analysis revealed that the mutants showed repression of genes typically associated with lipid remodeling under P-depleted conditions, such as sulfoquinovosyl diacylglycerol 2 (SQD2), diacylglycerol acyltransferase (DGTT1), and major lipid droplet protein (MLDP). As accumulation of sulfoquinovosyl diacylglycerol and TAG were suppressed in P-depleted mutants, we designated the protein as lipid remodeling regulator 1 (LRL1). LRL1 mutants showed slower growth under P-depletion. Moreover, cell size in the mutant was significantly reduced, and TAG and starch accumulation per cell were decreased. Transcriptomic analysis also suggested the repression of several genes typically upregulated in adaptation to P-depletion that are associated with the cell cycle and P and lipid metabolism. Thus, our analysis of LRL1 provides insights into P-allocation and lipid remodeling under P-depleted conditions in C. reinhardtii. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The sequencing data were made publicly available under the BioProject Accession number PRJDB6733 and an accession number LC488724 at the DNA Data Bank of Japan (DDBJ). The data is available at https://trace.ddbj.nig.ac.jp/BPSearch/bioproject?acc=PRJDB6733; http://getentry.ddbj.nig.ac.jp/getentry/na/LC488724. The metabolome data were made publicly available and can be accessed at http://metabolonote.kazusa.or.jp/SE195:/; http://webs2.kazusa.or.jp/data/nur/.

  23. ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index. Peer-reviewed

    Obayashi T, Aoki Y, Tadaka S, Kagaya Y, Kinoshita K

    Plant & cell physiology　59　(2)　440　2018/02

    DOI： 10.1093/pcp/pcx209 　

    ISSN： 0032-0781

  24. Arabinogalactan Proteins Accumulate in the Cell Walls of Searching Hyphae of the Stem Parasitic Plants, Cuscuta campestris and Cuscuta japonica Peer-reviewed

    Akitaka Hozumi, Subhankar Bera, Daiki Fujiwara, Takeshi Obayashi, Ryusuke Yokoyama, Kazuhiko Nishitani, Koh Aoki

    PLANT AND CELL PHYSIOLOGY　58　(11)　1868-1877　2017/11

    DOI： 10.1093/pcp/pcx121 　

    ISSN： 0032-0781

    eISSN： 1471-9053

  25. Root-Knot and Cyst Nematodes Activate Procambium-Associated Genes in Arabidopsis Roots Peer-reviewed

    Yasuka L. Yamaguchi, Reira Suzuki, Javier Cabrera, Satoru Nakagami, Tomomi Sagara, Chika Ejima, Ryosuke Sano, Yuichi Aoki, Rocio Olmo, Tetsuya Kurata, Takeshi Obayashi, Taku Demura, Takashi Ishida, Carolina Escobar, Shinichiro Sawa

    FRONTIERS IN PLANT SCIENCE　8　1195　2017/07

    DOI： 10.3389/fpls.2017.01195 　

    ISSN： 1664-462X

  26. Co-expressed Pathways DataBase for Tomato: a database to predict pathways relevant to a query gene Peer-reviewed

    Takafumi Narise, Nozomu Sakurai, Takeshi Obayashi, Hiroyuki Ohta, Daisuke Shibata

    BMC GENOMICS　18　(1)　437　2017/06

    DOI： 10.1186/s12864-017-3786-3 　

    ISSN： 1471-2164

  27. Editorial: Plant and Cell Physiology's 2017 Database Issue Peer-reviewed

    Hajime Ohyanagi, Takeshi Obayashi, Kentaro Yano

    PLANT AND CELL PHYSIOLOGY　58　(1)　1-3　2017/01

    DOI： 10.1093/pcp/pcw227 　

    ISSN： 0032-0781

    eISSN： 1471-9053

  28. Plant Aurora kinases interact with and phosphorylate transcription factors Peer-reviewed

    Mai Takagi, Takuya Sakamoto, Ritsuko Suzuki, Keiichirou Nemoto, Takeshi Obayashi, Takeshi Hirakawa, Tomoko M. Matsunaga, Daisuke Kurihara, Yuko Nariai, Takeshi Urano, Tatsuya Sawasaki, Sachihiro Matsunaga

    JOURNAL OF PLANT RESEARCH　129　(6)　1165-1178　2016/11

    DOI： 10.1007/s10265-016-0860-x 　

    ISSN： 0918-9440

    eISSN： 1618-0860

  29. Editorial: Plant and Cell Physiology's 2016 Online Database Issue

    Hajime Ohyanagi, Takeshi Obayashi, Kentaro Yano

    PLANT AND CELL PHYSIOLOGY　57　(1)　1-3　2016/01

    DOI： 10.1093/pcp/pcv205 　

    ISSN： 0032-0781

    eISSN： 1471-9053

  30. Comparison of Gene Coexpression Profiles and Construction of Conserved Gene Networks to Find Functional Modules Peer-reviewed

    Yasunobu Okamura, Takeshi Obayashi, Kengo Kinoshita

    PLOS ONE　10　(7)　e0132039-e0132039　2015/07

    DOI： 10.1371/journal.pone.0132039 　

    ISSN： 1932-6203

  31. Editorial: Plant and Cell Physiology's 2015 Database Issue

    Hajime Ohyanagi, Takeshi Obayashi, Kentaro Yano

    PLANT AND CELL PHYSIOLOGY　56　(1)　4-6　2015/01

    DOI： 10.1093/pcp/pcu206 　

    ISSN： 0032-0781

    eISSN： 1471-9053

  32. Molecular and Cellular Features of Murine Craniofacial and Trunk Neural Crest Cells as Stem Cell-Like Cells Peer-reviewed

    Kunie Hagiwara, Takeshi Obayashi, Nobuyuki Sakayori, Emiko Yamanishi, Ryuhei Hayashi, Noriko Osumi, Toru Nakazawa, Kohji Nishida

    PLOS ONE　9　(1)　e84072-e84072　2014/01

    DOI： 10.1371/journal.pone.0084072 　

    ISSN： 1932-6203

  33. Plant and Cell Physiology 2014 Online Database Issue

    Takeshi Obayashi, Kentaro Yano

    PLANT AND CELL PHYSIOLOGY　55　(1)　1-2　2014/01

    DOI： 10.1093/pcp/pct193 　

    ISSN： 0032-0781

    eISSN： 1471-9053

  34. Basic Helix-Loop-Helix Transcription Factors JASMONATE-ASSOCIATED MYC2-LIKE1 (JAM1), JAM2, and JAM3 Are Negative Regulators of Jasmonate Responses in Arabidopsis Peer-reviewed

    Yuko Sasaki-Sekimoto, Yusuke Jikumaru, Takeshi Obayashi, Hikaru Saito, Shinji Masuda, Yuji Kamiya, Hiroyuki Ohta, Ken Shirasu

    PLANT PHYSIOLOGY　163　(1)　291-304　2013/09

    DOI： 10.1104/pp.113.220129 　

    ISSN： 0032-0889

  35. Dmrta1 regulates proneural gene expression downstream of Pax6 in the mammalian telencephalon Peer-reviewed

    Takako Kikkawa, Takeshi Obayashi, Masanori Takahashi, Urara Fukuzaki-Dohi, Keiko Numayama-Tsuruta, Noriko Osumi

    GENES TO CELLS　18　(8)　636-649　2013/08

    DOI： 10.1111/gtc.12061 　

    ISSN： 1356-9597

  36. The 2013 Plant and Cell Physiology Database Issue

    Takeshi Obayashi, Kentaro Yano

    PLANT AND CELL PHYSIOLOGY　54　(2)　169-170　2013/02

    DOI： 10.1093/pcp/pct011 　

    ISSN： 0032-0781

  37. Role of the G-box element in regulation of chlorophyll biosynthesis in arabidopsis roots Peer-reviewed

    Koichi Kobayashi, Takeshi Obayashi, Tatsuru Masuda

    Plant Signaling and Behavior　7　(8)　922-926　2012/08

    DOI： 10.4161/psb.20760 　

    ISSN： 1559-2316 1559-2324

  38. Regulation of Root Greening by Light and Auxin/Cytokinin Signaling in Arabidopsis Peer-reviewed

    Koichi Kobayashi, Shinsuke Baba, Takeshi Obayashi, Mayuko Sato, Kiminori Toyooka, Mika Keranen, Eva-Mari Aro, Hidehiro Fukaki, Hiroyuki Ohta, Keiko Sugimoto, Tatsuru Masuda

    PLANT CELL　24　(3)　1081-1095　2012/03

    DOI： 10.1105/tpc.111.092254 　

    ISSN： 1040-4651

  39. Corticotropin-releasing hormone receptor 1 gene variants in irritable bowel syndrome. International-journal Peer-reviewed

    Naoko Sato, Naoki Suzuki, Ayaka Sasaki, Emiko Aizawa, Takeshi Obayashi, Motoyori Kanazawa, Tomoko Mizuno, Michiko Kano, Masashi Aoki, Shin Fukudo

    PloS one　7　(9)　e42450-e42450　2012

    DOI： 10.1371/journal.pone.0042450 　

    More details Close

    BACKGROUND: Corticotropin-releasing hormone (CRH) acts mainly via the CRH receptor 1 (CRH-R1) and plays a crucial role in the stress-induced pathophysiology of irritable bowel syndrome (IBS). Several studies have demonstrated that variants of the CRH-R1 gene carry a potential risk for depression, but evidence for an association between CRH-R1 genotypes and IBS is lacking. We tested the hypothesis that genetic polymorphisms and haplotypes of CRH-R1 moderate the IBS phenotype and negative emotion in IBS patients. METHODS: A total of 103 patients with IBS and 142 healthy controls participated in the study. Three single-nucleotide polymorphisms of the CRH-R1 gene (rs7209436, rs242924, and rs110402) were genotyped. Subjects' emotional states were evaluated using the Perceived-Stress Scale, the State-Trait Anxiety Inventory, and the Self-rating Depression Scale. RESULTS: The TT genotype of rs7209436 (P = 0.01) and rs242924 (P = 0.02) was significantly more common in patients with IBS than in controls. Total sample analysis showed significant association between bowel pattern (normal, diarrhea, constipation, or mixed symptoms) and the T allele of rs7209436 (P = 0.008), T allele of rs242924 (P = 0.019), A allele of rs110402 (P = 0.047), and TAT haplocopies (P = 0.048). Negative emotion was not associated with the examined CRH-R1 SNPs. CONCLUSION: These findings suggest that genetic polymorphisms and the CRH-R1 haplotypes moderate IBS and related bowel patterns. There was no clear association between CRH-R1 genotypes and negative emotion accompanying IBS. Further studies on the CRH system are therefore warranted.

  40. Normalization using ploidy and genomic DNA copy number allows absolute quantification of transcripts, proteins and metabolites in cells Peer-reviewed

    Hiroshi Shimada, Takeshi Obayashi, Naoki Takahashi, Minami Matsui, Atsushi Sakamoto

    PLANT METHODS　6　29-29　2010/12

    DOI： 10.1186/1746-4811-6-29 　

    ISSN： 1746-4811

  41. Three novel subunits of Arabidopsis chloroplastic NAD(P)H dehydrogenase identified by bioinformatic and reverse genetic approaches Peer-reviewed

    Atsushi Takabayashi, Noriko Ishikawa, Takeshi Obayashi, Satoshi Ishida, Junichi Obokata, Tsuyoshi Endo, Fumihiko Sato

    PLANT JOURNAL　57　(2)　207-219　2009/01

    DOI： 10.1111/j.1365-313X.2008.03680.x 　

    ISSN： 0960-7412

    eISSN： 1365-313X

  42. A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human. Peer-reviewed

    Hatanaka, Y., Nagasaki, M., Yamaguchi, R., Obayashi, T., Numata, K., Fujita, A., Shimamura, T., Tamada, Y., Imoto, S., Kinoshita, K., Nakai, K., Miyano, S.

    Genome informatics. International Conference on Genome Informatics　20　212-221　2008

    DOI： 10.1142/9781848163003_0018 　

  43. WoLF PSORT: protein localization predictor Peer-reviewed

    Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C. J. Adams-Collier, Kenta Nakai

    NUCLEIC ACIDS RESEARCH　35　(Web Server issue)　W585-W587　2007/07

    DOI： 10.1093/nar/gkm259 　

    ISSN： 0305-1048

  44. Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis Peer-reviewed

    Masami Yokota Hirai, Kenjiro Sugiyama, Yuji Sawada, Takayuki Tohge, Takeshi Obayashi, Akane Suzuki, Ryoichi Araki, Nozomu Sakurai, Hideyuki Suzuki, Koh Aoki, Hideki Goda, Osamu Ishizaki Nishizawa, Daisuke Shibata, Kazuki Saito

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA　104　(15)　6478-6483　2007/04

    DOI： 10.1073/pnas.0611629104 　

    ISSN： 0027-8424

  45. Application of large-scale mRNA expression data sets for comprehensive analysis of plant hormone signaling. Invited

    Ohta H, Obayashi T

    Quantum Bio-Informatics　381-388　2007

    DOI： 10.1142/9789812793171_0029 　

  46. In silico assessment of gene function involved in cysteine biosynthesis in Arabidopsis: expression analysis of multiple isoforms of serine acetyltransferase

    M Noji, CG Kawashima, T Obayashi, K Saito

    AMINO ACIDS　30　(2)　163-171　2006/03

    DOI： 10.1007/s00726-005-0253-2 　

    ISSN： 0939-4451

  47. Protein subcellular localization prediction with WOLF PSORT Peer-reviewed

    P Horton, KJ Park, T Obayashi, K Nakai

    Proceedings of the 4th Asia-Pacific Bioinformatics Conference　3　39-48　2006

    DOI： 10.1142/9781860947292_0007 　

  48. Coordinated activation of metabolic pathways for antioxidants and defence compounds by jasmonates and their roles in stress tolerance in Arabidopsis Peer-reviewed

    Y Sasaki-Sekimoto, N Taki, T Obayashi, M Aono, F Matsumoto, N Sakurai, H Suzuki, MY Hirai, M Noji, K Saito, T Masuda, K Takamiya, D Shibata, H Ohta

    PLANT JOURNAL　44　(4)　653-668　2005/11

    DOI： 10.1111/j.1365-313X.2005.02560.x 　

    ISSN： 0960-7412

  49. 12-oxo-phytodienoic acid triggers expression of a distinct set of genes and plays a role in wound-induced gene expression in Arabidopsis Peer-reviewed

    N Taki, Y Sasaki-Sekimoto, T Obayashi, A Kikuta, K Kobayashi, T Ainai, K Yagi, N Sakurai, H Suzuki, T Masuda, K Takamiya, D Shibata, Y Kobayashi, H Ohta

    PLANT PHYSIOLOGY　139　(3)　1268-1283　2005/11

    DOI： 10.1104/pp.105.067058 　

    ISSN： 0032-0889

  50. Gene expression profiling of the tetrapyrrole metabolic pathway in Arabidopsis with a mini-array system Peer-reviewed

    F Matsumoto, T Obayashi, Y Sasaki-Sekimoto, H Ohta, K Takamiya, T Masuda

    PLANT PHYSIOLOGY　135　(4)　2379-2391　2004/08

    DOI： 10.1104/pp.104.042408 　

    ISSN： 0032-0889

  51. 44. 12-oxo-phytodienoic acid triggers expression of a distinct set of genes from jasmonates, and plays a role other than intermediate of jasmonates biosynthesis

    Taki Nozomi, Sekimoto Yuko, Obayashi Takeshi, Kikuta Akihiro, Ainai Takayuki, Kobayashi Yuichi, Sakurai Nozomu, Suzuki Hideyuki, Takamiya Kenichiro, Shibata Daisuke, Ohta Hiroyuki

    The Janapese Society for Chemical Regulation of Plants, Abstract　39　65　2004

    Publisher: The Janapese Society for Chemical Regulation of Plants

    DOI： 10.18978/jscrpanb.39.0_65 　

    ISSN： 0919-1887

    eISSN： 2189-6313

    More details Close

    Jasmonic acid (JA) and methyl jasmonate (MeJA) are cyclopentanone derivatives that originate from linolenic acid via an octadecanoid pathway. JA and MeJA (jasmonates) regulate diverse physiological processes such as wound responses, disease responses. Recent reports suggest that a cyclopentenone precursor of jasmonates, 12-oxo-phytodienoic acid (OPDA) itself induces gene expression like as JA. However, little is known about physiological significance of the OPDA-dependent gene expression. We used DNA microarray covering about 22000 genes of Arabidopsis thaliana and globally compared JA-, MeJA-, and OPDA-responsive genes and attempted to figure out OPDA-mediated physiological responses in gene expression level. Although OPDA-responsive genes were generally identical with JA- and MeJA-responsive genes, OPDA also induced expression of distinct set of genes from jasmonates. The genes which specifically responded to OPDA mainly consisted of regulation factors such as DNA binding proteins (ZAT10, DREB2A etc.) and protein kinases, and showed early and transient induction by the OPDA treatment. Many of those genes in this set were also induced by wounding. Moreover, the analysis for wounding using aos and opr3 mutants suggested that OPDA plays a role as a signaling substance, and regulates a set of genes related to wounding response via JA-independent pathway.

  52. Monitoring of 12-oxo-phytodienoic acid (OPDA)-induced expression changes in arabidopsis by cDNA macroarray

    Y Sasaki-Sekimoto, T Obayashi, M Matsuumi, Y Kobayashi, E Asamizu, D Shibata, Y Nakamura, T Masuda, H Shimada, K Takamiya, S Tabata, H Ohta

    ADVANCED RESEARCH ON PLANT LIPIDS　335-338　2003

  53. Photosynthetic regulatory gene cluster in an aerobic photosynthetic bacterium, Roseobacter denitrificans Peer-reviewed

    K Nishimura, H Shimada, T Shinmen, T Obayashi, T Masuda, H Ohta, K Takamiya

    JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY　45　(3)　129-134　1999/06

    DOI： 10.2323/jgam.45.129 　

    ISSN： 0022-1260

    eISSN： 1349-8037

  54. Properties of ORF5-disrupted and -overexpressed Rhodobacter sphaeroides mutants

    T Obayashi, H Shimada, K Nishimura, T Masuda, H Ohta, K Takamiya

    PHOTOSYNTHESIS: MECHANISMS AND EFFECTS, VOLS I-V　2893-2896　1998

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Misc. 34

  1. 共発現情報から見る遺伝子機能ネットワーク

    Obayashi T, Kinoshita K

    KASEAA　49　(1)　48-56　2011

    Publisher: Japan Society for Bioscience, Biotechnology, and Agrochemistry

    DOI： 10.1271/kagakutoseibutsu.49.48 　

    ISSN： 0453-073X

  2. 33Pを用いた遺伝子発現の網羅的解析

    Obayashi T, Sekimoto Y, Ohta H

    Isotope News　589　16-18　2003/05

    ISSN： 0285-5518

  3. 生物多様性と文化へと繋がるバイオインフォマティクス Peer-reviewed

    松前 ひろみ, 神保 宇嗣, 仲里 猛留, 畠山 剛臣, 大林 武

    JSBi Bioinformatics Review　3　(2)　88-114　2022

    DOI： 10.11234/jsbibr.2022.primer3 　

  4. 遺伝子共発現ネットワークにおけるタンパク質細胞内局在の影響

    青木裕一, 青木裕一, 大林武, 木下賢吾, 木下賢吾

    日本生化学会大会(Web)　90th　2017

  5. 藻類比較ゲノムデータベースAlgaenomeの構築

    梅津純平, 森宙史, 堀孝一, 大林武, 太田啓之, 黒川顕

    日本ゲノム微生物学会年会要旨集　10th　88　2016

  6. 遺伝子発現量データを利用した表現型の違いに影響を及ぼす遺伝子セットの検出方法の開発

    土多隆雄, 大林武, 木下賢吾

    研究報告バイオ情報学（BIO）　2013　(7)　1-2　2013/03/14

    More details Close

    マイクロアレイ解析では遺伝子単独の発現量変化に対して統計学的仮説検定を行うことで、表現型の違いに影響を及ぼす遺伝子を検出することが多い．しかし、実際には遺伝子は複数で相互に関わりあいながら機能することから、遺伝子単独ではなく複数の遺伝子による発現パターン変化にも着目する必要があるといえる．そこで、本研究では複数の遺伝子による発現パターン変化を検出する手法を新たに開発し、肺がんに関する遺伝子発現量データを用いて先行研究で提案されている手法との比較解析を行った．その結果、先行研究で提案されている手法では検出されない発現パターン変化を示す遺伝子ペアを検出することができた．

  7. Identification of functional modules in protein networks by near-clique detection

    2013　(4)　1-2　2013/03/14

  8. Gene module detection from the conservation of gene coexpression patterns among species

    2013　(5)　1-2　2013/03/14

  9. 公共の遺伝子発現データの二次利用

    Obayashi T, Kinoshita K

    Surgery Frontier　19　(2)　89-95　2012/06

  10. Comparative analysis of gene expression pattern between spieces

    Yasunobu Okamura, Takeshi Obayashi, Kengo Kinoshita

    IPSJ SIG technical reports　2012　(2)　1-2　2012/03/21

    Publisher: Information Processing Society of Japan (IPSJ)

    ISSN： 0919-6072

    More details Close

    Currently gene expression data by DNA microarray are increasing. We can construct coexpression gene families from similarity of gene expression patterns. To find core functions for living organisms and divergent function of each spices, we compared similarity of gene expression patterns. Here we found that ribosomal protein or other house keeping genes are well conserved between human and mouse and that genes involved in nervous system and signal transductions are divergent.

  11. トランスポートソーム-生体膜輸送機構の全体像に迫る 基礎,臨床,創薬応用研究の最新成果 第4章 残されたトランスポーターへのアプローチ 4 COXPRESdb: 共発現データに基づいた機能関連遺伝子の探索

    大林武, 木下賢吾

    遺伝子医学MOOK　(19)　2011

    ISSN： 1349-2527

  12. Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways.

    Obayashi, Takeshi Kinoshita, Kengo

    J Plant Res　123　(3)　311-319　2010/05

    DOI： 10.1007/s10265-010-0333-6 　

  13. Construction of CaMKII-interacting protein network obtained from affinity purified proteins in silico and its experimental verification

    Takafumi Yamada, Akihiro Iwamatsu, Takeshi Obayashi, Kengo Kinoshita, Shunji Ohsako

    NEUROSCIENCE RESEARCH　68　E345-E345　2010

    DOI： 10.1016/j.neures.2010.07.1527 　

    ISSN： 0168-0102

  14. Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

    Bjoern Usadel, Takeshi Obayashi, Marek Mutwil, Federico M. Giorgi, George W. Bassel, Mimi Tanimoto, Amanda Chow, Dirk Steinhauser, Staffan Persson, Nicholas J. Provart

    PLANT CELL AND ENVIRONMENT　32　(12)　1633-1651　2009/12

    DOI： 10.1111/j.1365-3040.2009.02040.x 　

    ISSN： 0140-7791

  15. COXPRESdb: A DATABASE OF COEXPRESSED GENE NETWORKS FOR HUMAN, MOUSE AND RAT

    Takeshi Obayashi, Kengo Kinoshita

    JOURNAL OF PHYSIOLOGICAL SCIENCES　59　444-444　2009

    ISSN： 1880-6546

  16. 共発現データベースCOXPRESの構築と利用法

    Obayashi T, Kinoshita K

    Transportsome　4　16-20　2007/05

  17. Omics-based Identification of a Transcription Factor Gene Regulating Glucosinolate Biosynthesis Genes

    Hirai Masami, Sugiyama Kenjiro, Sawada Yuji, Tohge Takayuki, Suzuki Akane, Obayashi Takeshi, Araki Ryoichi, Sakurai Nozomu, Suzuki Hideyuki, Aoki Koh, Nishizawa Osamu, Shibata Daisuke, Saito Kazuki

    Plant and Cell Physiology Supplement　2007　(0)　201-201　2007

    Publisher: The Japanese Society of Plant Physiologists

    More details Close

    We obtained time-series data of the transcriptome and metabolome of sulfur-starved Arabidopsis. By analyzing the data using batch-learning self-organizing mapping, we found that known glucosinolate (GSL) biosynthesis genes were coexpressed under sulfur deficiency. Based on the assumption that unknown genes coexpressed with known GSL biosynthesis genes are also involved in GSL biosynthesis, we found a candidate gene encoding a transcription factor regulating GSL biosynthesis genes. We also conducted coexpression analysis using publicly available 1388 microarray data of AtGenExpress, and found that this gene is coexpressed with the genes involved in Met-derived GSL (MET-GSL). To confirm the predicted function as a transcription factor regulating MET-GSL biosynthesis genes, we analyzed the transcriptome and GSL profile of a knockout mutant and overexpressing T87 cell culture lines of this gene. The results showed that this gene is actually a positive regulator specific to MET-GSL biosynthesis genes but lesser for Trp-derived GSL biosynthesis genes.

  18. KaPPA-View2: A plant metabolic pathway database and tool for gene expression correlation analysis

    Nozomu Sakurai, Kiyoshi Yamazaki, Yoshiyuki Ogata, Koh Aoki, Koei Okazaki, Takeshi Obayashi, Hideyuki Suzuki, Kazuki Saito, Daisuke Shibata

    PLANT AND CELL PHYSIOLOGY　48　(0)　S68-S68　2007

    ISSN： 0032-0781

  19. Coordinated activation of metabolic pathways for antioxidants and defence compounds by jasmonates and their roles in stress tolerance in Arabidopsis

    Y Sasaki-Sekimoto, N Taki, T Obayashi, M Aono, F Matsumoto, N Sakurai, H Suzuki, M Hirai, M Noji, K Saito, T Masuda, K Takamiya, D Shibata, H Ohta

    PLANT AND CELL PHYSIOLOGY　47　(0)　S233-S233　2006

    ISSN： 0032-0781

  20. A novel strategy for comprehensive prediction of gene function by integration of transcriptomics and metabolomics

    M Hirai, S Kanaya, Y Sawada, T Tohge, M Kusano, A Hukushima, H Akiyama, T Sakurai, Y Shimada, H Goda, T Obayashi, M Yano, K Sugiyama, N Sakurai, H Suzuki

    PLANT AND CELL PHYSIOLOGY　47　(0)　S50-S50　2006

    ISSN： 0032-0781

  21. Comprehensive functional genomics approach by integration of coexpression analysis and metabolic profiling in Arabidopsis flavonoid metabolism

    T Tohge, K Sakakibara, M Shibata, T Obayashi, K Saito

    PLANT AND CELL PHYSIOLOGY　47　(0)　S109-S109　2006

    ISSN： 0032-0781

  22. 発現情報から遺伝子機能を推定する

    Yamazaki M, Obayashi T

    Plant Organelles　4　10-16　2006

  23. 12-oxo-phytodienoic acid triggers expression of a distinct set of genes from jasmonates, and plays a role other than intermediate of jasmonates biosynthesis

    TAKI Nozomi, SASAKI SEKIMOTO Yuko, OBAYASHI Takeshi, KIKUTA Akihiro, AINAI Takayuki, KOBAYASHI Yuichi, SAKURAI Nozomu, SUZUKI Hideyuki, TAKAMIYA Ken-ichiro, SHIBATA Daisuke, OHTA Hiroyuki

    39　65-65　2005/05/28

    Publisher: The Japanese Society for Chemical Regulation of Plants

    ISSN： 1346-5406

    More details Close

    Jasmonic acid (JA) and methyl jasmonate (MeJA) are cyclopentanone derivatives that originate from linolenic acid via an octadecanoid pathway. JA and MeJA (jasmonates) regulate diverse physiological processes such as wound responses, disease responses. Recent reports suggest that a cyclopentenone precursor of jasmonates, 12-oxo-phytodienoic acid (OPDA) itself induces gene expression like as JA. However, little is known about physiological significance of the OPDA-dependent gene expression. We used DNA microarray covering about 22000 genes of Arabidopsis thaliana and globally compared JA-, MeJA-, and OPDA-responsive genes and attempted to figure out OPDA-mediated physiological responses in gene expression level. Although OPDA-responsive genes were generally identical with JA- and MeJA-responsive genes, OPDA also induced expression of distinct set of genes from jasmonates. The genes which specifically responded to OPDA mainly consisted of regulation factors such as DNA binding proteins (ZAT10, DREB2A etc.) and protein kinases, and showed early and transient induction by the OPDA treatment. Many of those genes in this set were also induced by wounding. Moreover, the analysis for wounding using aos and opr3 mutants suggested that OPDA plays a role as a signaling substance, and regulates a set of genes related to wounding response via JA-independent pathway.

  24. cis element analysis using DNA array data in Arabidopsis

    T Obayashi, K Nakai, Y Sasaki-Sekimoto, N Taki, A Kikuta, N Sakurai, H Suzuki, K Takamiya, D Shibata, H Ohta

    PLANT AND CELL PHYSIOLOGY　46　S138-S138　2005

    ISSN： 0032-0781

  25. Comprehensive analysis of jasmonate-responsive gene expression in Lotus japonicus

    S Miyachi, S Matsukura, Y Sasaki-Sekimoto, T Obayashi, T Aoki, H Kouchi, N Sakurai, H Suzuki, K Takamiya, D Shibata, H Ohta

    PLANT AND CELL PHYSIOLOGY　46　S218-S218　2005

    ISSN： 0032-0781

  26. A novel protein that interacts with SPB of Rhodobacter sphaeroides: cloning, expression and function

    K Ishida, Y Machiya, H Shimada, T Obayashi, T Masuda, H Ohta, K Takamiya

    PLANT AND CELL PHYSIOLOGY　45　S130-S130　2004

    ISSN： 0032-0781

  27. Identification of jasmonate responsive genes involved in metabolic pathways with cDNA macroarray and analysis of their metabolites.

    Y Sasaki-Sekimoto, N Taki, T Obayashi, N Sakurai, H Suzuki, M Aono, M Noji, K Saito, K Takamiya, D Shibata, H Ohta

    PLANT AND CELL PHYSIOLOGY　45　(0)　S78-S78　2004

    ISSN： 0032-0781

  28. DNAアレイ（DNAチップ）法を用いた遺伝子発現解析

    Sekimoto Y, Obayashi T, Ohta H

    Kagaku Souchi　45　(4)　32-35　2003/04

    Publisher: 工業調査会

    ISSN： 0368-4849

  29. Monitoring of 12-oxo-phytodienoic acid -responsive genes in Arabidopsis by cDNA macroarray

    N Taki, Y Sasaki-Sekimoto, T Obayashi, T Ainai, Y Kobayashi, E Asamizu, Y Nakamura, T Masuda, H Shimada, K Takamiya, D Shibata, S Tabata

    PLANT AND CELL PHYSIOLOGY　44　S112-S112　2003

    ISSN： 0032-0781

  30. cDNA macroarray analysis of light and cytokinin responses in Arabidopsis

    T Obayashi, T Okegawa, Y Sasaki-Sekimoto, H Shimada, T Masuda, D Shibata, S Tabata, K Takamiya, H Ohta

    PLANT AND CELL PHYSIOLOGY　44　S113-S113　2003

    ISSN： 0032-0781

  31. Analysis for methyl jasmonate-specific expression changes in Arabidopsis by cDNA macroarray

    Y Sasaki-Sekimoto, N Taki, T Obayashi, T Ainai, Y Kobayashi, E Asamizu, Y Nakamura, T Kuromori, T Hirayama, K Shinozaki, T Masuda, H Shimada, K Takamiya, D Shibata, S Tabata, H Ohta

    PLANT AND CELL PHYSIOLOGY　44　S112-S112　2003

    ISSN： 0032-0781

  32. Property and processing of the data of cDNA macroarray

    T Obayashi, Y Sasaki, M Horikoshi, H Shimada, T Masuda, D Shibata, S Tabata, K Takemiya, H Ohta

    PLANT AND CELL PHYSIOLOGY　43　S207-S207　2002

    ISSN： 0032-0781

  33. ANALYSIS OF THE PHOTOSYNTHETIC REGULATORY GENE CLUSTER IN RHOSEOBACTER DENITRIFICANS, AN AEROBIC PHOTOSYNTHETIC BACTERIUM

    NISHIMURA Kohji, OBAYASHI Takeshi, MANRI Naoki, MASUDA Tatsuru, SHIMADA Hiroshi, OHTA Hiroyuki, TAKAMIYA Ken-ichiro

    39　S31-S31　1998/05

    ISSN： 0032-0781

  34. GENETIC ANALYSIS OF orf5 IN PHOTOSYNTHETIC REGULATORY CLUSTER OF Rhodobacter sphaeroides

    OBAYASHI Takeshi, NISHIMURA Kohji, AWAI Koichiro, SHIMADA Hiroshi, MASUDA Tatsuru, OHTA Hiroyuki, TAKAMIYA Ken-ichiro

    39　S31-S31　1998/05

    ISSN： 0032-0781

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Books and Other Publications 6

  1. バイオインフォマティクス入門

    秋山 泰, 中井, 謙太, 冨田, 勝, 向井, 有理, 長崎, 英樹, 中村, 保一, 池田, 修己, 向井, 友花, 越中谷賢治, 飯田, 泰広, 濱田, 康太, 榊原, 康文, 舟橋 啓, 鎌田真由美, 小森 隆, 佐藤, 健吾, 浜田, 道昭, 内山, 郁夫, 阿部, 貴志, 野口, 英樹, 白井, 剛, 土方, 敦司, 諏訪, 牧子, 有田, 正規, 後藤, 修, 大林, 武, 竹本, 和弘, 櫻井 望

    慶應義塾大学出版会　2015/08/22

    ISBN: 9784766422511

  2. 実験医学2011年9月増刊号「バイオデータベースとソフトウェアアップデート」

    有田正則編

    羊土社　2011/09

    ISBN: 9784758102902

  3. ゲノムが拓く生態学―遺伝子の網羅的解析で迫る植物の生きざま

    永野 惇, 森長 真一, 種生物学会

    文一総合出版　2011/07

    ISBN: 9784829910870

    More details Close

    http://www.amazon.co.jp/dp/4829910879

  4. 実験医学MOOK「トランスポートソーム-生体膜輸送機構の全体像に迫る―基礎、臨床、創薬応用研究の最新成果」

    金井好克編

    メディカルドゥ　2011/03

    ISBN: 4944157495

    More details Close

    http://www.amazon.co.jp/dp/4944157495

  5. Protein function prediction for omics era

    Edited by, Daisuke Kihara, Purdue Univ, USA

    Springer Verlag　2010/05

    ISBN: 9400708807

  6. 「生体膜トランスポートソームの分子構築と生理機能」

    金井好克編

    2007 Spring 「共発現データベースCOXPRESの構築と利用法」（大林武，木下賢吾）　2010

Show all Show first 5

Presentations 22

  1. PlanDyO: Long-term Meta-Epigenomic Monitoring Platform to Elucidate Marine Plankton Dynamics in Onagawa Bay, Sanriku Coast.

    Obayashi T.

    the 2nd International Scientific Symposium of CSK-2　2024/11/14

  2. Long-Term Meta-Epigenomic Monitoring Platform to Elucidate Marine Plankton Dynamics in Onagawa Bay, Sanriku Coast

    Takeshi Obayashi, Toyonobu Fujii, Akane Kitamura, Gaku Kumano, Minoru Ikeda

    The 32nd International Plant and Animal Genome Conference (PAG32)　2025/01/13

  3. Establishing an Epigenomics Research Platform for Marine Plankton in Onagawa Bay:Advancing Ecological Understanding

    Obayashi T., Fujii T., Kitamura A., Kumano G., Ikeda M.

    1st Asia & Pacific Bioinformatics Joint Conference　2024/10/24

  4. ATTED-II Version 12.0: Plant Gene Coexpression Database with Enhanced SpeciesComparison for Supporting Flowering Plants

    Obayashi T.

    1st Asia & Pacific Bioinformatics Joint Conference　2024/10/24

  5. 女川湾のプランクトン動態解明に向けたゲノム解析基盤の整備

    大林武, 藤井豊展, 北村茜, 池田実

    トーゴーの日シンポジウム2024　2024/10/05

  6. 植物の遺伝子共発現データベースATTED-II version 12.0

    大林武

    トーゴーの日シンポジウム2024　2024/10/05

  7. 植物の共発現データベースATTED-IIにおける種間比較機能強化の取り組み

    大林武

    DICP研究交流会　2024/10/04

  8. Visualizing human impact on plant transmission from linguistic data

    Nishikawa Y., Obayashi T., Matsumae H.

    Cultural Evolution Society Conference 2024

  9. 生命科学分野における電界撹拌技術を用いたin situ hybridization法の迅速化の検討 Invited

    内田克哉, 大林武

    第14回迅速免疫染色研究会　2024/09/07

  10. Meta-Epigenomic Insights into Marine Plankton Dynamics in Onagawa Bay Invited

    Obayashi T.

    10th Annual Data Science in Engineering and Life Sciences Symposium　2024/08/06

  11. 変わりゆく海：海洋ビッグデータ解析の挑戦

    大林武

    Public lecture in Open Campus 2024　2024/07/31

  12. Establishing an Epigenomics Research Platform for Marine Plankton: From Individual Species Analyses to Ecological Modeling.

    Obayashi T.

    1st AIMEC colloquium　2024/07/08

  13. 非モデル植物のための遺伝子ネットワーク情報活用基盤

    大林武

    2024年度 統合化推進プログラム サイトビジット　2024/07/04

  14. Establishing an Epigenomics Research Platform for Marine Plankton Through Long-Term Monitoring in Onagawa Bay

    Obayashi T.

    AIMEC Asamushi Workshop　2024/06/17

  15. Onagawa Bay: A Model for Advanced Coastal Ecosystem Research Through Genomics and Data Integratio Invited

    Obayashi T., Ikeda M., Fujii T., Hamabata T.

    Japan Geoscience Union Meeting 2024　2024/05/27

  16. Enhancing ATTED-II Database for Diverse Plant Species Research

    Obayashi T.

    The 65th Annual Meeting of the Japanese Society of Plant Physiologists　2024/03/17

  17. Visualizing human impact on plant transmission from linguistic data

    2024/03/13

  18. Coastal Ecosystem Services Research Unit Invited

    Obayashi T.

    WPI-AIMEC Kick-off Symposium　2024/03/08

  19. 植物の伝播における人間の影響を言語データから可視化する

    西川有理, 松前ひろみ, 大林武

    東海大学 マイクロ・ナノ啓発会　2024/02/29

  20. How to measure the similarity of gene expression patterns to identify gene function International-presentation

    QBIC2011 Bio-Informatics Workshop　2011/03/11

  21. ATTED-II International-presentation

    19th International Conference on Arabidopsis Research　2011/03/11

  22. Application of large-scale mRNA expression data sets for comprehensive analysis of plant hormone signaling International-presentation

    Ohta H

    QBIC2007 Bio-Informatics Workshop　2007/03/17

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Research Projects 13

  1. 組織横断型遺伝子共発現法を用いた細胞間コミュニケーション解析 Competitive

    System: Grant-in-Aid for Scientific Research

    2015/04 - Present

  2. 遺伝子共発現に基づく生命システム進化学 Competitive

    System: Grant-in-Aid for Scientific Research

    2012/04 - Present

  3. 微細藻類の遺伝子共発現データベースALCOdbの構築・運用 Competitive

    System: JST Basic Research Programs (Core Research for Evolutional Science and Technology :CREST)

    2011/10 - Present

  4. 動物の遺伝子共発現データベースCOXPRESdbの構築・運用 Competitive

    System: Grant-in-Aid for Scientific Research

    2007/04 - Present

  5. 植物の遺伝子共発現データベースATTED-II の構築・運用 Competitive

    System: Grant-in-Aid for Scientific Research

    2005/04 - Present

  6. Key-Molecule-Network in Plant Reproduction

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research Fund for the Promotion of Joint International Research (International Leading Research )

    Category: Fund for the Promotion of Joint International Research (International Leading Research )

    Institution: The University of Tokyo

    2022/12/20 - 2029/03/31

  7. 人間活動に伴う植物の短期的適応進化の学際統合的理解

    大林 武

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 国際共同研究加速基金(国際共同研究強化(A))

    Institution: 東北大学

    2021 - 2023

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    異質倍数体はゲノム配列の種内バリエーションを単一個体に取り込み、遺伝子の新しい組み合わせを探索することで、新規の環境へ適応するという短期進化の重要な戦略である。異質倍数体を通じた短期進化の鍵は、遺伝子ネットワークの再編であり、本研究ではこれを遺伝子共発現ネットワークを用いてネットワーク再編と進化圧の関係を解き明かす。まず、遺伝子共発現ネットワークの種内バリエーションを理解するため、親ゲノムにおける遺伝子ネットワークの特徴づけを行った。シロイヌナズナの標準種を基準として、亜種における遺伝子発現を解析したところ、基本的に標準種における環境応答と類似していることがわかった。すなわち、非標準種の遺伝子発現は、標準種とは環境応答の強度が異なる一方で、環境応答の方向性は大方同じであることを示唆している。一方、非標準種との進化的距離の影響については不明であり、引き続き検討が必要である。これと並行して、異質倍数体ゲノムの再編を可視化する方法を検討した。異質倍数体ゲノムには、複数の亜種に由来する遺伝子セットが混在しており、新しい共発現関係が構築されていると推定される。そのためホメオログ関係を念頭にオーソロググループを共発現ネットワーク上で可視化すれば、共発現関係の再編成を直感的に理解できる。個別の事例について検討したところ、この可視化により遺伝子重複後の新機能獲得を明確に検出できることがわかった。網羅的な検討を行うために、任意の共発現モジュールについて、ホメオログ関係を描画するツールの開発に着手した。

  8. Improvement of gene coexpression network analysis with the construction of reference transcriptome data

    Obayashi Takeshi

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (C)

    Institution: Tohoku University

    2019/04/01 - 2022/03/31

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    Gene coexpression analysis is a method for predicting gene function by identifying groups of genes with similar expression profiles. Although a large amount of publicly available gene expression data reflects diverse environments, sample bias in the data is a severe problem in coexpression analysis. We have developed a new methodology combining principal component analysis and ensemble calculation to retrieve highly accurate coexpression information.

  9. A new molecular model for plant cell wall based on a new enzyme, cellulose endotransglucosylase

    Nishitani Kazuhiko

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (B)

    2017/04/01 - 2020/03/31

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    The molecular mechanism underlying the physical integration of cellulose microfibrils into the network architecture still remains controversial. To gain insight into this dilemma, we first investigated distribution of cellulose endotransglucosylase in land plants by phylogeny. Next, we investigated the cell wall regeneration process using mesophyll protoplasts derived from xyloglucan less mutant leaves. Based on the results obtained we propose that xyloglucan is not essential for the initial assembly of the cellulose network, and that cellulose network formation as mediated by cellulose endotransglucosylase might play a role in the land plants.

  10. Novel molecular mechanism collaborating stem neural stem cell mainteinance and differentiation

    Katsuyama Yu, IGARASHI Kazuhiko, OBAYASHI Takeshi

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research (C)

    2014/04/01 - 2017/03/31

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    We prepared polyclonal antibodies against Sbno1 protein, Western blot analysis using these antibodies detected different band pattern, suggesting that Sbno1 protein is regulated by cleavage. Sbno1 knockout mice showed premature neuronal differentiation, extinction of the neural stem cells, and apoptosis. Yeast two hybrid screening identified several molecules interacting with Sbno1. Our analyses suggested that one of these is transcription factor regulating cell differentiation, some of these are involved in regulation of cell cycle, and rest of these is deubiquitination enzyme which downregulates apoptosis. These findings suggest that Sbno1 function is regulated after protein translation, probably by protein cleavage mechanisms. Sbno1 can bind to multiple factors of different function, such as regulation of cell differentiation, cell cycle, and apoptosis. Thus, Sbno1 is a molecule which integrates these cellular processes.

  11. Structure and dynamics of the plant cell wall as information processing system

    Nishitani Kazuhiko, YOKOYAMA Ryusuke, KUROHA Takeshi

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    Institution: Tohoku University

    2012/06/28 - 2017/03/31

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    The function of the plant cell wall in information-processing largely depend on its structural features. The most widely accepted structural model for the plant cell wall was “tethered-network model” which holds that cellulose microfibrils are tethered by xyloglucan or other matrix polysaccharides to form skeletal network of cellulose. But this model has been challenged by recent reports. In the present we found that certain cell wall enzyme can mediate splitting and reconnection of cellulose molecules by transglucosylation reaction, and named this enzyme activity as Cellulose Endo Transglucosylase (CET). On the basis of this new finding we propose a new structural model for the plant cell wall, a model in which cellulose microfibrils are directly tethered via a covalent bonding between cellulose microfibrils.

  12. The plant cell wall as information processing system

    Nishitani Kazuhiko, YOKOYAMA Ryusuke, KUROHA Takeshi, OKADA Kiyotaka, SAMEJIMA Masahiro, NISHIMURA Mikio, HASEBE Mitsuyasu, FUKUDA Hiroo

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    Institution: Tohoku University

    2012/06/28 - 2017/03/31

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    Plant cell walls are capable of sensing signals from the outside and can process and respond to them. This information processing process is essential for plant life and is found ubiquitously during its life cycle, but the mechanism is unknown. The elucidation of the molecular mechanisms of this system is the goal of the overall program of this research. This project was specifically aimed at supporting researchers in this research program by stimulating exchange of ideas and methodology among themselves with different academic background, and thereby facilitating collaboration to pave the way to understanding the new function of plant cell wall as an information processing system. In this project, we intended to support young scientist such as graduate students and post-docs for their future careers in the new field of cell wall research. Another task of this project was outreach addressed to general public by developing a new model for public relations.

  13. Construction of ATTED-III, Gene Coexpression Database for Arabidopsis

    OBAYASHI Takeshi

    Offer Organization: Japan Society for the Promotion of Science

    System: Grants-in-Aid for Scientific Research

    Category: Grant-in-Aid for Young Scientists (B)

    Institution: Tohoku University

    2009 - 2010

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    ATTED-II, a coexpressed gene database for Arabidopsis, has been used to find functionally related gene groups. However, this traditional coexpression information cannot provide the detail of gene relationships. In this study, I constructed condition-specific coexpression data and two types of viewers to reveal the situation when and where the genes function together.

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Teaching Experience 6

  1. 応用データ科学　東北大学大学院情報科学研究科

  2. 生命システム情報学　東北大学工学部

  3. Basic Computer Science　東北大学工学部

  4. 生命情報システム科学　東北大学大学院情報科学研究科

  5. 計算機学　東北大学工学部

  6. システム生理学　東北大学工学部

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Social Activities 1

  1. 東北大学・飛翔型「科学者の卵養成講座」

    2014/04 - 2018/03

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    研究発展コースI

Other 4

  1. 微細藻類の遺伝子共発現データベースALCOdb

  2. COXPRESdb; gene coexpression database for animals

  3. ATTED-II; gene coexpression database for plants

  4. 植物栄養細胞をモデルとした藻類脂質生産系の戦略的構築

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    多くの藻類は、植物のような貯蔵器官を持たず、光合成を行う細胞で貯蔵脂質の合成・蓄積を行います。そのため栄養飢餓などの限られた条件で脂質の高生産が起こります。研究代表者らは最近、植物でも葉のような栄養細胞では、種子と異なり、必須元素であるリンの飢餓時に顕著な脂質蓄積が起こることを見出しました。本研究では、このような植物葉と藻類の脂質蓄積の共通性を基に、藻類脂質の高生産系を戦略的に構築することを目的とします。そのため、有用藻類のゲノムや栄養飢餓応答遺伝子の情報などを網羅した基盤情報の集積とデータベース化を行い、それらを駆使してＤＨＡなど種々の有用脂肪酸類の高生産系を創製し、バイオ燃料や有用物質を藻類で高効率に生産するための基盤技術の創出を目指します。