2022/03/01 更新

ヤダ テツシ
矢田 哲士
YADA Tetsushi
Scopus 論文情報  
総論文数: 0  総Citation: 0  h-index: 7

Citation Countは当該年に発表した論文の被引用数

所属
大学院情報工学研究院 生命化学情報工学研究系
職名
教授
研究室住所
福岡県飯塚市川津680-4
外部リンク

研究キーワード

  • ゲノム生物学

  • バイオインフォマティクス

出身学校

  • 1988年03月   九州大学   理学部   生物学科   卒業   日本国

取得学位

  • 東京大学  -  博士(理学)   1998年06月

学内職務経歴

  • 2019年04月 - 現在   九州工業大学   大学院情報工学研究院   生命化学情報工学研究系     教授

  • 2017年04月 - 2018年03月   九州工業大学   情報工学部     情報工学部生命情報工学科長

  • 2017年04月 - 2018年03月   九州工業大学   大学院情報工学府     情報工学府学際情報工学専攻長・情報システム専攻長

  • 2017年04月 - 2018年03月   九州工業大学   大学院情報工学府     情報工学府情報工学専攻長

  • 2017年04月 - 2018年03月   九州工業大学   大学院情報工学研究院     情報工学研究院生命情報工学研究系長

  • 2013年05月 - 2019年03月   九州工業大学   大学院情報工学研究院   生命情報工学研究系     教授

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学外略歴

  • 2007年04月 - 2013年04月   京都大学   大学院情報学研究科   准教授   日本国

  • 2003年10月 - 2007年03月   京都大学   大学院情報学研究科   助教授   日本国

  • 2001年04月 - 2003年09月   東京大学   医科学研究所   助教授   日本国

  • 1999年04月 - 2001年03月   理化学研究所   ゲノム科学総合研究センター   研究員   日本国

  • 1988年04月 - 1999年03月   株式会社三菱総合研究所   研究員   日本国

論文

  • Genome sequence alignment 招待有り 査読有り

    Tetsushi Yada

    Encyclopedia of Bioinformatics and Computational Biology   2018年09月

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    担当区分:責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)

  • Asymmetry in indegree and outdegree distributions of gene regulatory networks arising from dynamical robustness 査読有り

    Ichinose N., Yada T., Wada H.

    Physical Review E   97 ( 6 )   2018年06月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)

    © 2018 American Physical Society. Although outdegree distributions of gene regulatory networks have scale-free characteristics similar to other biological networks, indegree distributions have single-scale characteristics with significantly lower variance than that of outdegree distributions. In this study, we mathematically explain that such asymmetric characteristics arise from dynamical robustness, which is the property of maintaining an equilibrium state of gene expressions against inevitable perturbations to the networks, such as gene dysfunction and mutation of promoters. We reveal that the expression of a single gene is robust to a perturbation for a large number of inputs and a small number of outputs. Applying these results to the networks, we also show that an equilibrium state of the networks is robust if the variance of the indegree distribution is low (i.e., single-scale characteristics) and that of the outdegree distribution is high (i.e., scale-free characteristics). These asymmetric characteristics are conserved across a wide range of species, from bacteria to humans.

    DOI: 10.1103/PhysRevE.97.062315

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  • Micropeptides encoded in transcripts previously identified as long noncoding RNAs: A new chapter in transcriptomics and proteomics 査読有り

    Yeasmin F., Yada T., Akimitsu N.

    Frontiers in Genetics   9 ( APR )   2018年04月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)

    © 2018 Yeasmin, Yada and Akimitsu. Integrative analysis using omics-based technologies results in the identification of a large number of putative short open reading frames (sORFs) with protein-coding capacity within transcripts previously identified as long noncoding RNAs (lncRNAs) or transcripts of unknown function (TUFs). sORFs were previously overlooked because of their diminutive size and the difficulty of identification by bioinformatics analyses. There is now growing evidence of the existence of potentially functional micropeptides produced from sORFs within cells of diverse species. Recent characterization of a few of these revealed their significant divergent roles in many fundamental biological processes, where some also show important relationships with pathogenesis. Recent works therefore provide new insights for exploring the wealth of information that may lie within sORF-encoded short proteins. Here, we summarize the current progress and view of micropeptides encoded in sORFs of protein-coding genes.

    DOI: 10.3389/fgene.2018.00144

    Scopus

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  • A new computational method to predict transcriptional activity of a DNA sequence from diverse datasets of massively parallel reporter assays 査読有り

    Liu Y., Irie T., Yada T., Suzuki Y.

    Nucleic Acids Research   45 ( 13 )   2017年07月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)

    © 2017 The Author(s). In recent years, the dramatic increase in the number of applications for massively parallel reporter assay (MPRA) technology has produced a large body of data for various purposes. However, a computational model that can be applied to decipher regulatory codes for diverse MPRAs does not exist yet. Here, we propose a new computational method to predict the transcriptional activity of MPRAs, as well as luciferase reporter assays, based on the TRANScription FACtor database. We employed regression trees and multivariate adaptive regression splines to obtain these predictions and considered a feature redundancy-dependent formula for conventional regression trees to enable adaptation to diverse data. The developed method was applicable to various MPRAs despite the use of different types of transfected cells, sequence lengths, construct numbers and sequence types. We demonstrate that this method can predict the transcriptional activity of promoters in HEK293 cells through predictive functions that were estimated by independent assays in eight tumor cell lines. The prediction was generally good (Pearson’s r = 0.68) which suggested that common active transcription factor binding sites across different cell types make greater contributions to transcriptional activity and that known promoter activity could confer transcriptional activity of unknown promoters in some instances, regardless of cell type.

    DOI: 10.1093/nar/gkx396

    Scopus

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  • Estimating optimal sparseness of developmental gene networks using a semiquantitative model' 査読有り

    Ichinose N., Yada T., Wada H.

    PLoS ONE   12 ( 4 )   2017年04月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)

    © 2017 Ichinose et al. To estimate gene regulatory networks, it is important that we know the number of connections, or sparseness of the networks. It can be expected that the robustness to perturbations is one of the factors determining the sparseness. We reconstruct a semi-quantitative model of gene networks from gene expression data in embryonic development and detect the optimal sparseness against perturbations. The dense networks are robust to connectionremoval perturbation, whereas the sparse networks are robust to misexpression perturbation. We show that there is an optimal sparseness that serves as a trade-off between these perturbations, in agreement with the optimal result of validation for testing data. These results suggest that the robustness to the two types of perturbations determines the sparseness of gene networks.

    DOI: 10.1371/journal.pone.0176492

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  • Long Noncoding RNA NEAT0-Dependent SFPQ relocation from promoter region to paraspeckle mediates IL8 expression upon immune stimuli

    Imamura K., Imamachi N., Akizuki G., Kumakura M., Kawaguchi A., Nagata K., Kato A., Kawaguchi Y., Sato H., Yoneda M., Kai C., Yada T., Suzuki Y., Yamada T., Ozawa T., Kaneki K., Inoue T., Kobayashi M., Kodama T., Wada Y., Sekimizu K., Akimitsu N.

    Molecular Cell ( Molecular Cell )   54 ( 6 )   2014年06月

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    記述言語:日本語   掲載種別:記事・総説・解説・論説等(大学・研究所紀要)

    DOI: 10.0006/j.molcel.2004.06.003

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  • miRNA-target prediction based on transcriptional regulation. 査読有り

    Fujiwara T., Yada T.

    BMC genomics   14 Suppl 2   2013年06月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)

    microRNAs (miRNAs) are tiny endogenous RNAs that have been discovered in animals and plants, and direct the post-transcriptional regulation of target mRNAs for degradation or translational repression via binding to the 3'UTRs and the coding exons. To gain insight into the biological role of miRNAs, it is essential to identify the full repertoire of mRNA targets (target genes). A number of computer programs have been developed for miRNA-target prediction. These programs essentially focus on potential binding sites in 3'UTRs, which are recognized by miRNAs according to specific base-pairing rules. Here, we introduce a novel method for miRNA-target prediction that is entirely independent of existing approaches. The method is based on the hypothesis that transcription of a miRNA and its target genes tend to be co-regulated by common transcription factors. This hypothesis predicts the frequent occurrence of common cis-elements between promoters of a miRNA and its target genes. That is, our proposed method first identifies putative cis-elements in a promoter of a given miRNA, and then identifies genes that contain common putative cis-elements in their promoters. In this paper, we show that a significant number of common cis-elements occur in ~28% of experimentally supported human miRNA-target data. Moreover, we show that the prediction of human miRNA-targets based on our method is statistically significant. Further, we discuss the random incidence of common cis-elements, their consensus sequences, and the advantages and disadvantages of our method. This is the first report indicating prevalence of transcriptional regulation of a miRNA and its target genes by common transcription factors and the predictive ability of miRNA-targets based on this property.

    Scopus

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  • Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability 査読有り

    Tani H., Tani H., Imamachi N., Salam K., Mizutani R., Ijiri K., Irie T., Yada T., Suzuki Y., Akimitsu N.

    RNA Biology   9 ( 11 )   1370 - 1379   2012年01月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)

    UPF1 eliminates aberrant mRNAs harboring premature termination codons, and regulates the steady-state levels of normal physiological mRNAs. Although genome-wide studies of UPF1 targets performed, previous studies did not distinguish indirect UPF1 targets because they could not determine UPF1-dependent altered RNA stabilities. Here, we measured the decay rates of the whole transcriptome in UPF1-depleted HeLa cells using BRIC-seq, an inhibitor-free method for directly measuring RNA stability. We determined the half-lives and expression levels of 9,229 transcripts. An amount of 785 transcripts were stabilized in UPF1-depleted cells. Among these, the expression levels of 76 transcripts were increased, but those of the other 709 transcripts were not altered. RNA immunoprecipitation showed UPF1 bound to the stabilized transcripts, suggesting that UPF1 directly degrades the 709 transcripts. Many UPF1 targets in this study were newly identified. This study clearly demonstrates that direct determination of RNA stability is a powerful approach for identifying targets of RNA degradation factors. © 2012 Landes Bioscience.

    DOI: 10.4161/rna.22360

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  • Large-scale motif discovery using DNA Gray code and equiprobable oligomers 査読有り

    Ichinose N., Yada T., Gotoh O.

    Bioinformatics   28 ( 1 )   25 - 31   2012年01月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)

    Motivation: How to find motifs from genome-scale functional sequences, such as all the promoters in a genome, is a challenging problem. Word-based methods count the occurrences of oligomers to detect excessively represented ones. This approach is known to be fast and accurate compared with other methods. However, two problems have hampered the application of such methods to largescale data. One is the computational cost necessary for clustering similar oligomers, and the other is the bias in the frequency of fixedlength oligomers, which complicates the detection of significant words. Results: We introduce a method that uses a DNA Gray code and equiprobable oligomers, which solve the clustering problem and the oligomer bias, respectively. Our method can analyze 18 000 sequences of ~1 kbp long in 30 s. We also show that the accuracy of our method is superior to that of a leading method, especially for large-scale data and small fractions of motif-containing sequences. © The Author(s) 2011. Published by Oxford University Press. All rights reserved.

    DOI: 10.1093/bioinformatics/btr606

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  • Linear regression models predicting strength of transcriptional activity of promoters. 査読有り

    Yada T., Yoshida K., Morita M., Taniguchi T., Irie T., Suzuki Y.

    Genome informatics. International Conference on Genome Informatics   25 ( 1 )   53 - 60   2011年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)

    We developed linear regression models which predict strength of transcriptional activity of promoters from their sequences. Intrinsic transcriptional strength data of 451 human promoter sequences in three cell lines (HEK293, MCF7 and 3T3), which were measured by systematic luciferase reporter gene assays, were used to build the models. The models sum up contributions of CG dinucleotide content and transcription factor binding sites (TFBSs) to transcriptional strength. We evaluated prediction accuracies of the models by cross validation tests and found that they have adequate ability for predicting transcriptional strength of promoters in spite of their simple formalization. We also evaluated statistical significance of the contributions and proposed a picture of regulatory code hidden in promoter sequences. That is, CG dinucleotide content and TFBSs mainly determine strength of transcriptional activity under ubiquitous and specific environments, respectively.

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  • Predicting promoter activities of primary human DNA sequences 査読有り

    Irie T., Park S., Yamashita R., Seki M., Yada T., Sugano S., Nakai K., Suzuki Y.

    Nucleic Acids Research   39 ( 11 )   2011年06月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)

    We developed a computer program that can predict the intrinsic promoter activities of primary human DNA sequences. We observed promoter activity using a quantitative luciferase assay and generated a prediction model using multiple linear regression. Our program achieved a prediction accuracy correlation coefficient of 0.87 between the predicted and observed promoter activities. We evaluated the prediction accuracy of the program using massive sequencing analysis of transcriptional start sites in vivo. We found that it is still difficult to predict transcript levels in a strictly quantitative manner in vivo; however, it was possible to select active promoters in a given cell from the other silent promoters. Using this program, we analyzed the transcriptional landscape of the entire human genome. We demonstrate that many human genomic regions have potential promoter activity, and the expression of some previously uncharacterized putatively non-protein-coding transcripts can be explained by our prediction model. Furthermore, we found that nucleosomes occasionally formed open chromatin structures with RNA polymerase II recruitment where the program predicted significant promoter activities, although no transcripts were observed. © 2011 The Author(s).

    DOI: 10.1093/nar/gkr173

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科研費獲得実績

  • 次世代シークエンサー解析と情報科学解析で迫る転写調節コードの普遍性と多様性

    研究課題番号:15H01358  2015年04月 - 2017年03月   新学術領域研究

  • プロモーター配列の情報科学的解体と再構成による遺伝子回路の設計

    研究課題番号:26119717  2014年04月 - 2016年03月   新学術領域研究

  • 遺伝子のde novo誕生の機序に迫るバイオインフォマティクス研究

    研究課題番号:25640112  2013年04月 - 2016年03月   挑戦的萌芽研究

担当授業科目(学内)

  • 2020年度   バイオインフォマティクス特論

  • 2020年度   科学技術英語Ⅱ

  • 2020年度   遺伝情報科学

  • 2020年度   生命化学情報工学入門

  • 2020年度   コンピュテーショナル・ゲノミクス

  • 2020年度   解析Ⅰ・同演習

  • 2019年度   バイオインフォマティクス特論

  • 2019年度   バイオインフォマティクス

  • 2019年度   科学技術英語Ⅱ

  • 2019年度   生命化学情報工学入門

  • 2019年度   解析Ⅰ・同演習

  • 2018年度   科学技術英語Ⅱ

  • 2018年度   バイオインフォマティクス

  • 2018年度   バイオインフォマティクス特論

  • 2018年度   学際情報講究Ⅲ

  • 2018年度   学際情報特別実験及び演習Ⅲ

  • 2018年度   解析Ⅰ・同演習

  • 2018年度   情報工学概論

  • 2018年度   データベースB

  • 2017年度   学際情報特別実験及び演習Ⅲ

  • 2017年度   学際情報講究Ⅲ

  • 2017年度   バイオインフォマティクス特論

  • 2017年度   バイオインフォマティクス

  • 2017年度   科学技術英語Ⅱ

  • 2017年度   データベースB

  • 2017年度   解析Ⅰ・演習

  • 2017年度   教育実習

  • 2016年度   バイオインフォマティクス特論

  • 2016年度   バイオインフォマティクス

  • 2016年度   科学技術英語Ⅱ

  • 2016年度   データベースB

  • 2016年度   解析Ⅰ・演習

  • 2016年度   教育実習

  • 2015年度   解析Ⅰ・演習

  • 2015年度   データヘ゛ースB

  • 2015年度   科学技術英語Ⅱ

  • 2015年度   バイオインフォマティクス

  • 2015年度   バイオインフォマティクス特論

  • 2014年度   解析Ⅰ・演習

  • 2014年度   データヘ゛ースB

  • 2014年度   科学技術英語Ⅱ

  • 2014年度   バイオインフォマティクス

  • 2014年度   バイオインフォマティクス特論

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