研究成果

2021年度（令和3年度）

Siriwach R., Matsuzaki J., Saito T., Nishimura H., Isozaki M., Isoyama Y., Sato M., Arita M., Akaho S., Higashide T., Yano K., and Hirai M. Y. Assessment of Greenhouse Tomato Anthesis Rate Through Metabolomics Using LASSO Regularized Linear Regression Model Front. Mol. Biosci., 01 DOI:10.3389/fmolb.2022.839051, (2022)

Imoto H., Yamashiro S, and Okada M. A text-based computational framework for patient -specific modeling for classification of cancers iScience DOI:10.1016/j.isci.2022.103944, (2022)

Haga M., and Okada M. Systems approaches to investigate the role of NF-κB signaling in aging Biochem J 479 (2), (2022)

Yesudhas D., Dharshini A. P., Taguchi ,Y-h. and Gromiha M. M. Tumor Heterogeneity and Molecular Characteristics of Glioblastoma Revealed by Single-Cell RNA-Seq Data Analysis Genes 13 (3), (2022)

Taguchi Y-h. and Turki T. Novel feature selection method via kernel tensor decomposition for improved multi-omics data analysis BMC Medical Genomics 15 (37), (2022)

Uematsu S., Ohno S., Tanaka K., Y., Hatano A., Kokaji T., Ito Y., Kubota H., Hironaka K., Suzuki Y., Matsumoto M., Nakayama K., I., Hirayama A., Soga T., and Kuroda S. Multi-omics-based label-free metabolic flux inference reveals obesity-associated dysregulatory mechanisms in liver glucose metabolism iScience, DOI: 10.1016/j.isci.2022.103787 (2022)
東京大学プレスリリース

Sugawara T., Miya F., Ishikawa T., Lysenko A., Nishino J., Kamatani T., Takemoto A., Boroevich K. A., Kakimi K., Kinugasa Y., Tanabe M. and Tsunoda T. Immune subtypes and neoantigen-related immune evasion in advanced colorectal cancer iScience 25(2), 103740. (2022)

Miyauchi K., Ki S., Ukai M., Suzuki Y., Inoue K., Suda W., Matsui T., Ito Y., Honda K., Koseki H., Ohara O., Tanaka RJ., Okada-Hatakeyama M., and Kubo M. Essential Role of STAT3 Signaling in Hair Follicle Homeostasis. Front. Immunol. 11, (2021)

Ando M., Magi S., Seki M., Suzuki Y., Kasukawa T., Lefaudeux D., Hoffmann A., and Okada M. IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells. NPJ Syst. Biol. Appl. 7(1), 42. (2021)

Magi S., Ki S., Ukai M., Domínguez-Hüttinger E., Naito AT., Suzuki Y., and Okada M. A combination approach of pseudotime analysis and mathematical modeling for understanding drug-resistant mechanisms. Sci. Rep. 11(1), 18511. (2021)

Yoshizawa R., Umeki N., Yamamoto A., Okada M., Murata M., and Sako Y. p52Shc regulates the sustainability of ERK activation in a RAF-independent manner. Mol. Biol. Cell. 32(19), 1838-1848. (2021)

Matsumura Y., Ito R., Yajima A., Yamaguchi R., Tanaka T., Kawamura T., Magoori K., Abe Y., Uchida A., Yoneshiro T., Hirakawa H., Zhang J., Arai M., Yang C., Yang G., Takahashi H., Fujihashi H., Nakaki R., Yamamoto S., Ota S., Tsutsumi S., Inoue S., Kimura H., Wada Y., Kodama T., Inagaki T., Osborne T. F., Aburatani H., Node K., and Sakai J. Spatiotemporal dynamics of SETD5-containing NCoR–HDAC3 complex determines enhancer activation for adipogenesis Nat. Commun. 12(1), 7045. (2021)
東北大学プレスリリース
 東京大学プレスリリース

Taguchi Y-h. and Turki T. Effects of Collagen–Glycosaminoglycan Mesh on Gene Expression as Determined by Using Principal Component Analysis-Based Unsupervised Feature Extraction. Polymers 13(23), 4117. (2021)

Ishibashi R. and Taguchi Y-h. Identification of Enhancers and Promoters in the Genome by Multidimensional Scaling. Genes 12(11), 1671. (2021)

Taguchi Y-h. and Turki T. Tensor-Decomposition-Based Unsupervised Feature Extraction in Single-Cell Multiomics Data Analysis. Genes 12(9), 1442. (2021)

Fujisawa K., Shimo M., Taguchi Y.-H., Ikematsu S., and Miyata R. PCA-based unsupervised feature extraction for gene expression analysis of COVID-19 patients. Scientific Reports 11, 17351. (2021)
琉球大学プレスリリース

Sugiyama T., Murao N., Kadowaki H., Takao K., Miyakawa T., Matsushita Y., Katagiri T., Futatsugi A., Shinmyo Y., Kawasaki H., Sakai J., Shiomi K., Nakazato M., Takeda K., Mikoshiba K., Ploegh H. L., Ichijo H., and Nishitoh H. ERAD components Derlin-1 and Derlin-2 are essential for postnatal brain development and motor function. iScience 24(7), 102758. (2021)

Sharma A., Lysenko A., Boroevich K., A., Vans E., and Tsunoda T. DeepFeature: feature selection in nonimage data using convolutional neural network. Brief. Bioinform., bbab297 (2021)

Yamagishi M., Kubokawa M., Kuze Y., Suzuki A., Yokomizo A., Kobayashi S., Nakashima M., Makiyama J., Iwanaga M., Fukuda T., Watanabe T., Suzuki Y., and Uchimaru K. Chronological genome and single-cell transcriptome integration characterizes the evolutionary process of adult T cell leukemia-lymphoma. Nat. Commun. 12, 4821 (2021)

Sakamoto Y., Zaha S., Suzuki Y., Seki M., and Suzuki A. Application of long-read sequencing to the detection of structural variants in human cancer genomes. Comput. Struct. Biotechnol. J., DOI: 10.1016/j.csbj.2021.07.030 (2021)

Nagasawa S., Kashima Y., Suzuki A., and Suzuki Y. Single-cell and spatial analyses of cancer cells: toward elucidating the molecular mechanisms of clonal evolution and drug resistance acquisition. Inflamm. Regener. 41, 22. (2021)

Kholodenko B. N., and Okada M. Reengineering protein-phosphorylation switches. Science, 373, 6550. (2021)

Mita M., Sugawara I., Harada K., Ito M., Takizawa M., Ishida K., Ueda H., Kitaguchi T., and Tsuboi T. Development of red genetically encoded biosensor for visualization of intracellular glucose dynamics. Cell Chem. Biol., DOI: 10.1016/j.chembiol.2021.06.002. (2021)
東京大学プレスリリース

Watabe E., Togo‐Ohno M., Ishigami Y., Wani S., Hirota K., Kimura‐Asami M., Hasan S., Takei S., Fukamizu A., Suzuki Y., Suzuki T., and Kuroyanagi H. m⁶A-mediated alternative splicing coupled with nonsense-mediated mRNA decay regulates SAM synthetase homeostasis. The EMBO Journal, e106434. (2021)
東京医科歯科大学プレスリリース

Itoh T. D., Horinouchi T., Uchida H., Takahashi K., and Ozaki H. Optimal Scheduling for Laboratory Automation of Life Science Experiments with Time Constraints. SLAS Technol., 247263032110217 (2021)

Nakasone S., Suzuki A., Okazaki H., Onodera K., Zenkoh J., Ishii G., Suzuki Y., Tsuboi M., and Tsuchihara K. Predictive markers based on transcriptome modules for vinorelbine-based adjuvant chemotherapy for lung adenocarcinoma patients. Lung Cancer, 158, 115–125. (2021)

Marutani E., Morita M., Hirai S., Kai S., Grange R. M. H., Miyazaki Y., Nagashima F., Traeger L., Magliocca A., Ida T., Matsunaga T., Flicker D. R., Corman B., Mori N., Yamazaki Y., Batten A., Li R., Tanaka T., Ikeda T., … Motohashi H. and Ichinose F. Sulfide catabolism ameliorates hypoxic brain injury. Nature Communications, 12(1), 3108. (2021)

Onoki T., Izumi Y., Takahashi M., Murakami S., Matsumaru D., Ohta N., Wati S. M., Hatanaka N., Katsuoka F., Okutsu M., Yabe Y., Hagiwara Y., Kanzaki M., Bamba T., Itoi E., and Motohashi H. Skeletal muscle-specific Keap1 disruption modulates fatty acid utilization and enhances exercise capacity in female mice. Redox Biology, 43, 101966. (2021)

Watanabe M., Chiba Y., and Hirai M. Y. Metabolism and Regulatory Functions of O-Acetylserine, S-Adenosylmethionine, Homocysteine, and Serine in Plant Development and Environmental Responses. Frontiers in Plant Science, 12, 593. (2021)

Okamura E., Ohtaka K., Nishihama R., Uchida K., Kuwahara A., Mochida K., and Hirai M. Y. Diversified amino acid-mediated allosteric regulation of phosphoglycerate dehydrogenase for serine biosynthesis in land plants. Biochemical Journal, BCJ20210191. (2021)

Sugiyama R., Li R., Kuwahara A., Nakabayashi R., Sotta N., Mori T., Ito T., Ohkama-Ohtsu N., Fujiwara T., Saito K., Nakano R. T., Bednarek P., and Hirai M. Y. Retrograde sulfur flow from glucosinolates to cysteine in Arabidopsis thaliana. Proceedings of the National Academy of Sciences, 118(22), e2017890118. (2021)

Sakamoto Y., Zaha S., Nagasawa S., Miyake S., Kojima Y., Suzuki A., Suzuki Y., and Seki, M. Long-read whole-genome methylation patterning using enzymatic base conversion and nanopore sequencing. Nucleic Acids Research, gkab397, (2021)

Ebata K., Yamashiro S., Iida K., and Okada, M. Building patient‐specific models for receptor tyrosine kinase signaling networks. The FEBS Journal, DOI: 10.1111/febs.15831 (2021)

Kanazawa T., Michida H., Uchino Y., Ishihara A., Zhang S., Tabata S., Suzuki Y., Imamoto A., and Okada, M. Cell shape-based chemical screening reveals an epigenetic network mediated by focal adhesions. The FEBS Journal, DOI: 10.1111/febs.15840 (2021)

Taguchi Y-h. and Turki T. Unsupervised tensor decomposition-based method to extract candidate transcription factors as histone modification bookmarks in post-mitotic transcriptional reactivation. PLoS ONE, 16 (5): e0251032. (2021)

Yoneshiro T., Kataoka N., Walejko J. M., Ikeda K., Brown Z., Yoneshiro M., Crown S. B., Osawa T., Sakai J., McGarrah R. W., White P. J., Nakamura K., and Kajimura S. Metabolic flexibility via mitochondrial BCAA carrier SLC25A44 is required for optimal fever. ELife, 10. DOI: 10.7554/eLife.66865 (2021)

Zhang J., Matsumura Y., Kano Y., Yoshida A., Kawamura T., Hirakawa H., Inagaki T., Tanaka T., Kimura H., Yanagi S., Fukami K., Doi T., Osborne T. F., Kodama T., Aburatani H., and Sakai J. Ubiquitination dependent and independent repression of target genes by SETDB1 reveals a context dependent role for its methyltransferase activity during adipogenesis. Genes to Cells, gtc.12868. (2021)

Roy S.S., and Taguchi Y-h. Identification of genes associated with altered gene expression and m6A profiles during hypoxia using tensor decomposition based unsupervised feature extraction. Sci. Rep. 11, 8909 (2021).

Nagasawa S., Kuze Y., Maeda I., Kojima Y., Motoyoshi Ai, Onishi T., Iwatani T., Yokoe T., Koike J., Chosokabe M., Kubota M., Seino H., Suzuki A., Seki M., Tsuchihara K., Inoue E., Tsugawa K., Ohta T., and Suzuki Y. Genomic proﬁling reveals heterogeneous populations of ductal carcinoma in situ of the breast. Communications Biology, DOI: 10.1038/s42003-021-01959-9 (2021).

2020年度（令和2年度）

Egami R., Kokaji T., Hatano A., Yugi K., Eto M., Morita K., Ohno S., Fujii M., Hironaka K., Uematsu S., Terakawa A., Bai Y., Pan Y., Tsuchiya T., Ozaki H., Inoue H., Uda S., Kubota H., Suzuki Y., Matsumoto M., Nakayama K. I., Hirayama A., Soga T., and Kuroda S. Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle. iScience, DOI: 10.1016/j.isci.2021.102217 (2021).
東京大学プレスリリース

Taguchi Y-h. and Turki T. Application of Tensor Decomposition to Gene Expression of Infection of Mouse Hepatitis Virus can Identify Critical Human Genes and Efffective Drugs for SARS-CoV-2 Infection IEEE J-STSP, DOI: 10.1109/JSTSP.2021.3061251 (2021).

Ranjith A., Jemimah S., Taguchi Y-h., and Gromiha M. Exploring common therapeutic targets for neurodegenerative disorders using transcriptome study. Front. Genet., DOI: 10.3389/fgene.2021.639160 (2021).

Abe K., Hirayama M., Ohno K., and Shimamura T. Hierarchical non-negative matrix factorization using clinical information for microbial communities. BMC Genomics, 22(1), 104, (2021).

Minoura K., Abe K., Maeda Y., Nishikawa H., Shimamura T. CYBERTRACK2.0: zero-inflated model-based cell clustering and population tracking method for longitudinal mass cytometry data. Bioinformatics, btaa873, (2020).

Abe K., Minoura K., Maeda Y., Nishikawa H., and Shimamura T. Model-based clustering for flow and mass cytometry data with clinical information. BMC Bioinform.,, 21(Suppl 13), 393, (2020).

Taguchi Y-h. and Turki T. Mathematical formulation and application of kernel tensor decomposition based unsupervised feature extraction. Knowl.-Based Syst., 106834, (2021).

Turki T. and Taguchi Y-h. Discriminating the Single-cell Gene Regulatory Networks of Human Pancreatic Islets: A Novel Deep Learning Application. Comput. Biol. Med., 104257, (2021).

Taguchi Y-h. and Turki T. Novel method for the prediction of drug-drug Interaction based on Gene Expression profiles. Eur. J. Pharm. Sci., 105742, (2021).

Oka M., Xu L., Suzuki T., Yoshikawa T., Sakamoto H., Uemura H., Yoshizawa A. C., Suzuki Y., Nakatsura T., Ishihama Y., Suzuki A., and Seki M. Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer. Genome. Biol., 22, 9, (2021).

Taguchi Y-h., Dharshini S.A.P., Gromiha M.M. Identification of Transcription Factors, Biological Pathways, and Diseases as Mediated by N6-methyladenosine Using Tensor Decomposition-Based Unsupervised Feature Extraction. Appl. Sci., 11(1), 213, (2021).

Umezu, T., Tsuneyama, K., Kanekura, Hayakawa　M., Tanahashi T., Kawano T., Taguchi Y-h. , Toyoda H., Tamori A., Kuroda M., and Murakami Y. Comprehensive analysis of liver and blood miRNA in precancerous conditions. Sci. Rep., 10, 21766, (2020).

Taguchi Y-h. and Turki T. Tensor-Decomposition-Based Unsupervised Feature Extraction Applied to Prostate Cancer Multiomics Data. Genes, 11, 1493, (2020).

Esaki T., Horinouchi T., Natsume-Kitatani Y., Nojima Y., Sakane I., and Matsui H. Estimation of relationships between chemical substructures and antibiotic resistance-related gene expression in bacteria: Adapting a canonical correlation analysis for small sample data of gathered features using consensus clustering. Chem-Bio Info. J., 20, 58-61 (2020).

Maeda T., Iwasawa J., Kotani H., Sakata N., Kawada M., Horinouchi T., Sakai A., Tanabe K., and Furusawa C. High-throughput laboratory evolution reveals evolutionary constraints in Escherichia coli. Nat. Commun., 11, 5970 (2020).

Ochiai K., Motozawa N., Terada M., Horinouchi T., Masuda T., Kudo T., Kamei M., Tsujikawa A., Matsukuma K., Natsume T., Kanda G. N., Takahashi M., and Takahashi K. A Variable Scheduling Maintenance Culture Platform for Mammalian Cells. SLAS Technol., 2472630320972109 (2020).

Kokaji T., Hatano A., Ito Y., Yugi K., Eto M., Morita K., Ohno S., Fujii M., Hironaka K., Egami R., Terakawa A., Tsuchiya T., Ozaki H., Inoue H., Uda S., Kubota H., Suzuki Y., Ikeda K., Arita M., Matsumoto M., Nakayama K.I., Hirayama A., Soga T.,and Kuroda S. Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity Sci. Signal., 13(660) (2020).

Hashimoto S., Zhao H., Hayakawa M., Nakajima K., Taguchi Y-h., and Murakami Y. Developing a diagnostic method for latent tuberculosis infection using circulating miRNA Transl. Med. Commun., 5, 25 (2020).

Okazaki K., Anzawa H., Liu Z., Ota N., Kitamura H., Onodera Y., Alam M. M., Matsumaru D., Suzuki T., Katsuoka F., Tadaka S, Motoike I., Watanabe M., Hayasaka K., Sakurada A., Okada Y., Yamamoto M., Suzuki T., Kinoshita K., Sekine H., and Motohashi H. Enhancer remodelig promotes tumor-initiating activity in NRF2-activated non-small cell lung cancers. Nat. Commun., 11, 5911 (2020).

Oishi T., Matsumaru D., Ota N., Kitamura H., Zhang T., Honkura Y., Katori Y., and Motohashi H. Activation of the NRF2 pathway in Keap1-knockdown mice attenuates progression of age-related hearing loss. npj Aging Mech. Dis., in press.

Wati S. M., Matsumaru D.,and Motohashi H. NRF2 pathway activation by KEAP1 inhibition attenuates the manifestation of aging phenotypes in salivary glands. Redox Biol., 36, 101603, (2020).

Schneider J. W., Oommen S., Qureshi M. Y., Goetsch S. C., Pease D. R., Sundsbak R. S., Guo W., Sun M., Sun H., Kuroyanagi H.,... and Wanek Program Preclinical Pipeline Dysregulated ribonucleoprotein granules promote cardiomyopathy in RBM20 gene-edited pigs Nat. Med., DOI: 10.1038/s41591-020-1087-x (2020).

Harada K., Chihara T., Hayasaka Y., Mita M., Takizawa M., Ishida K., Arai M., Tsuno S., Matsumoto M., Ishihara T., Ueda H., Kitaguchi T., and Tsuboi T. Green fluorescent protein-based lactate and pyruvate indicators suitable for biochemical assays and live cell imaging Sci. Rep., 10(1), 19562, (2020).

Imoto H., Zhang S., and Okada M. A Computational Framework for Prediction and Analysis of Cancer Signaling Dynamics from RNA Sequencing Data—Application to the ErbB Receptor Signaling Pathway Cancers, 12(10), 2878. (2020).

Cherng B. W., Islam T., Torigoe M., Tsuboi T., and Okamoto H. The Dorsal Lateral Habenula-Interpeduncular Nucleus Pathway Is Essential for Left-Right-Dependent Decision Making in Zebrafish. Cell Rep., 32(11), 108143. (2020).

Hoshino D., Kawata K., Kunida K., Hatano A., Yugi K., Wada T., Fujii M., Sano T., Ito Y., Furuichi Y., Manabe Y., Suzuki Y., Fujii N.L., Soga T., and Kuroda S. Trans-omic analysis reveals ROS-dependent pentose phosphate pathway activation after high-frequency electrical stimulation in C2C12 myotubes. iScience, DOI: 10.1016/j.isci.2020.101558 (2020).

Kawata K., Wakida H., Yamada T., Taniue K., Han H., Seki M., Suzuki Y., and Akimitsu N. Metabolic labeling of RNA using multiple ribonucleoside analogs enables the simultaneous evaluation of RNA synthesis and degradation rates. Genome Research, DOI: 10.1101/gr.264408.120 (2020)

Uchiyama J., Ishihama Y., and Imami K. Quantitative nascent proteome profiling by dual pulse labeling with O-propargyl-puromycin and stable isotope labeled amino acids. J. Biochem., DOI: 10.1093/jb/mvaa104 (2020).

Roy S.S., Rodrigues N. and Taguchi Y-h. Incremental Dilations Using CNN for Brain Tumor Classification. Appl. Sci. 10, 4915. (2020).

Taguchi Y-h., and Turki T. A new advanced in silico drug discovery method for novel coronavirus (SARS-CoV-2) with tensor decomposition-based unsupervised feature extraction. PLoS ONE 15(9): e0238907. (2020).

Ng K. L., and Taguchi Y-h. Identification of miRNA signatures for kidney renal clear cell carcinoma using the tensor-decomposition method Sci. Rep., DOI: 10.1038/s41598-020-71997-6 (2020).

Sakamoto Y., Xu L., Seki M., Yokoyama T. T., Kasahara M., Kashima Y., Ohashi A., Shimada Y., Motoi N., Tsuchihara K., Kobayashi S. S., Kohno T., Shiraishi Y., Suzuki A., and Suzuki Y. Long-read sequencing for non-small-cell lung cancer genomes. Genome Research, DOI: 10.1101/gr.261941.120 (2020).

Ohno S., Quek L.-E., Krycer J. R., Yugi K., Hirayama A., Ikeda S., Shoji F., Suzuki K., Soga T., James D. E., and Kuroda S. Kinetic trans-omic analysis reveals key regulatory mechanisms for insulin-regulated glucose metabolism in adipocytes. iScience, 23(9), 101479. (2020).

Wada T., Hironaka K., Wataya M., Fujii M., Eto M., Uda S., Hoshino D., Kunida K., Inoue H., Kubota H., Takizawa T., Karasawa Y., Nakatomi H., Saito N., Hamaguchi H., Furuichi Y., Manabe Y., Fujii N. L., and Kuroda S. Single-Cell Information Analysis Reveals That Skeletal Muscles Incorporate Cell-to-Cell Variability as Information Not Noise. Cell Rep., 32(9), 108051. (2020).

Matsuda N., Hironaka K., Fujii M., Wada T., Kunida K., Inoue H., Eto M., Hoshino D., Furuichi Y., Manabe Y., Fujii N. L., Noji H., Imamura H., and Kuroda S. Monitoring and mathematical modeling of mitochondrial ATP in myotubes at single-cell level reveals two distinct population with different kinetics. Quant. Biol., DOI: 10.1007/s40484-020-0211-8 (2020).

Handa T., Harada A., Maehara K., Sato S., Nakao M., Goto N., Kurumizaka H., Ohkawa Y., and Kimura H. Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input. Nat. Protoc., DOI: 10.1038/s41596-020-0375-8 (2020).

Horisawa. K, Udono. M, Ueno. K, Ohkawa. Y, Nagasaki. M, Sekiya. S, and Suzuki. A. The Dynamics of Transcriptional Activation by Hepatic Reprogramming Factors. Mol. Cell., DOI: 10.1016/j.molcel.2020.07.0122 (2020).

Ochiai. H, Hayashi. T, Umeda. M, Yoshimura. M, Harada. A, Shimizu. Y, Nakano. K, Saitoh. N, Liu. Z, Yamamoto. T, Okamura. T, Ohkawa. Y, Kimura. H, and Nikaido. I. Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells. Sci. Adv., DOI: 10.1126/sciadv.aaz6699. (2020).

Kurihara. M, Kato. K, Sanbo. C, Shigenobu. S, Ohkawa. Y, Fuchigami. T, and Miyanari. Y. Genomic Profiling by ALaP-Seq Reveals Transcriptional Regulation by PML Bodies through DNMT3A Exclusion. Mol. Cell., DOI: 10.1016/j.molcel.2020.04.004. (2020).

Yuda. J, Odawara. J, Minami. M, Muta. T, Kohno. K, Tanimoto. K, Eto. T, Shima. T, Kikushige. Y, Kato. K, Takenaka. K, Iwasaki. H, Minami. Y, Ohkawa. Y, Akashi. K, and Miyamoto. T. Tyrosine kinase inhibitors induce alternative spliced BCR-ABLIns35bp variant via inhibition of RNA polymerase II on genomic BCR-ABL. Cancer Sci., DOI: 10.1111/cas.14424. (2020).

Nakajo H., Chou M.-Y., Kinoshita M., Appelbaum L., Shimazaki H., Tsuboi T., and Okamoto H. Hunger Potentiates the Habenular Winner Pathway for Social Conflict by Orexin-Promoted Biased Alternative Splicing of the AMPA Receptor Gene. Cell Rep. , 31(12), 107790. (2020).

Taguchi Y-h., and Turki T. Universal nature of drug treatment responses of drug-tissue-wide model-animal experiments. Front. Genet., DOI: 10.3389/fgene.2020.00695 (2020).

Michida H., Imoto H., Shinohara H., Yumoto N., Seki M., Umeda M., ... and Okada-Hatakeyama, M. The Number of Transcription Factors at an Enhancer Determines Switch-like Gene Expression. Cell Rep., 31(9), 107724. (2020).

Matsuoka Y., Izumi Y., Takahashi M., Bamba T. and Yamada K. I. Method for Structural Determination of Lipid-derived Radicals Analytical Chemistry, DOI: 10.1021/acs.analchem.0c00053 (2020).

Horinouchi T. and Furusawa C. Understanding metabolic adaptation by using bacterial laboratory evolution and trans-omics analysis Biophysical Reviews, DOI: 10.1007/s12551-020-00695-4 (2020).

Siriwach R., Matsuda F., Yano K., and Hirai M. Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of Arabidopsis thaliana Metabolites , 10(4), 159, (2020).

2019年度（平成31年度・令和元年度）

Uda S. Application of information theory in systems biology Biophysical Reviews, DOI: 10.1007/s12551-020-00665-w (2020).

Okazaki K., Papagiannakopoulos T. and Motohashi H. Metabolic features of cancer cells in NRF2 addiction status Biophysical Reviews, DOI: 10.1007/s12551-020-00659-8 (2020).

Horinouchi T., Maeda T., Kotani H., and Furusawa C. Suppression of antibiotic resistance evolution by single-gene deletion Sci. Rep. , 10 4178 (2020).

Quek L., Krycer J., Ohno S., Yugi K., Fazakerley D., Scalzo R., Elkington S., Dai Z., Hirayama A., Ikeda S., Shoji F., Suzuki K., Locasale J., Soga T., James D., and Kuroda S. Dynamic 13 C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response to Insulin iScience , DOI: 10.1016/j.isci.2020.100855 (2020).

Hirayama A., Tabata S., Kudo R., Hasebe M., Suzuki K., Tomita M. and Soga T. The use of a double coaxial electrospray ionization sprayer improves the peak resolutions of anionic metabolites in capillary ion chromatography-mass spectrometry Journal of Chromatography A , DOI: 10.1016/j.chroma.2020.460914 (2020).

Chiang S., Huang J., Tsai H., and Okada M. Inferring the transcriptional regulatory mechanism of signal-dependent gene expression via an integrative computational approach FEBS Letters , DOI: 10.1002/1873-3468.13757, (2020).

Imamoto A., Ki S., Li L., Iwamoto K., Maruthamuthu V., Devany J., Lu O., Kanazawa T., Zhang S., Yamada T., Hirayama A., Fukuda S., and Okada M. Essential role of the Crk family-dosage in DiGeorge-like anomaly and metabolic homeostasis. Life Science Alliance , DOI: 10.26508/lsa.201900635 (2020).
大阪大学プレスリリース
 日本経済新聞電子版

Nishino J., Watanabe S., Miya F., Kamatani T., Sugawara T., Boroevich K., and Tsunoda T. Quantification of multicellular colonization in tumor metastasis using exome sequencing data International Journal of Cancer , 10.1002/ijc.32910 (2020).

Chandra A., Sharma A., Dehzangi A., Shigemizu D., and Tsunoda T. Bigram-PGK: phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix BMC Molecular and Cell Biology , 20 57 (2019).

Shigemizu D., Akiyama S., Asanomi Y., Boroevich K.A., Sharma A., Tsunoda T. Sakurai T., Ozaki K., Ochiya T., and Niida S. A comparison of machine learning classifiers for dementia with Lewy bodies using miRNA expression data. BMC Med Genomics , 12 ,150 (2019).

Araki H., Miura F., Watanabe A., Morinaga C., Kitaoka F., Kitano Y., Sakai N., Shibata Y., Terada M., Goto S., Yamanaka S., Takahashi M., and Ito T. Base-Resolution Methylome of Retinal Pigment Epithelial Cells Used in the First Trial of Human Induced Pluripotent Stem Cell-Based Autologous Transplantation Stem Cell Rep. , DOI: 10.1016/j.stemcr.2019.08.014 (2019).

Osawa T., Shimamura T., Saito K., Hasegawa Y., Ishii N., Nishida M., Ando R., Kondo A., Anwar M., Tsuchida R., Hino S., Sakamoto A., Igarashi K., Saitoh K., Kato K., Endo K., Yamano S.,Kanki Y., Matsumura Y., Minami T., Tanaka T., Anai M, Wada Y., Wanibuchi H., Hayashi M., Hamada A., Yoshida M., Yachida S., Nakao M., Saki J., Aburatani H., Shibuya M., Hanada K., Miyano S., Soga T. and Kodama T. Phosphoethanolamine Accumulation Protects Cancer Cells under Glutamine Starvation through Downregulation of PCYT2 Cell Rep. , Volume 29, ISSUE 1 P89-103.e7(2019).

Kimura S., Tokuhisa M., and Okada M. Inference of genetic networks using random forests: Assigning different weights for gene expression data J Bioinform Comput Biol. , 10:1950015. (2019).

Mino T., Iwai N., Endo M., Inoue K., Akaki K., Hia F., Uehata T., Emura T., Hidaka K., Suzuki Y., Standley D.M., Okada-Hatakeyama M., Ohno S., Sugiyama H., Yamashita A., and Takeuchi O. Translation-dependent unwinding of stem-loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs Nucleic Acids Res. , gkz628 (2019).

Imoto H. and Okada M. Signal-dependent regulation of early-response genes and cell cycle: a quantitative view Current Opinion in Systems Biology , 15 100-108 (2019).

Morita M., Siddiqui N., Katsumura S., Rouya C., Larsson O., Nagashima T., Hekmatnejad B., Takahashi A., Kiyonari H., Zang M., St-Arnaud R., Giguère V., Topisirovic I., Okada-Hatakeyama M., Yamamoto T., and Sonenberg N. A hepatic post-transcriptional network comprised of CCR4-NOT deadenylase and FGF21 maintains systemic metabolic homeostasis PNAS , 116(16) 7973-7981 (2019).

Suzuki T., Kikuguchi C., Nishijima S., Nagashima T., Takahashi S., Okada M., and Yamamoto T. Postnatal liver functional maturation requires Cnot complex-mediated decay of mRNAs encoding cell cycle and immature liver genes Development , 146 dev.168146 (2019).

Fujii M., Murakami Y., Karasawa Y., Sumitomo Y., Fujita S., Koyama M., Uda S., Kubota H., Inoue H., Konishi K., Oba S., Ishii S., and Kuroda, S. Logical design of oral glucose ingestion pattern minimizing blood glucose in humans npj System Biology and Applications , 5, 31 (2019).

Sharma, A., Vans, E., Shigemizu, D., Boroevich, K. A. and Tsunoda, T. DeepInsight: A methodology to transform a non-image data to an image for convolution neural network architecture. Sci. Rep., 9(1), 11399, (2019).
東京大学プレスリリース
 理化学研究所プレスリリース
 科学技術振興機構プレスリリース
東京医科歯科大学プレスリリース

Yachida, S., Mizutani, S., Shiroma, H., Shiba, S., Nakajima, T., Sakamoto, T., Watanabe, H., Masuda, K., Nishimoto, Y., Kubo, M., Hosoda, F., Rokutan, H., Matsumoto, M., Takamaru, H., Yamada, M., Matsuda, T., Iwasaki, M., Yamaji, T., Yachida, T., Soga, T., Kurokawa, K., Toyoda, A., Ogura, Y., Hayashi, T., Hatakeyama, M., Nakagama, H., Saito, Y., Fukuda, S., Shibata, T., and Yamada, T. Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer Nature Medicine , 25, 968-976 (2019).

Kikuchi, K., Saigusa, D., Kanemitsu, Y., Matsumoto, Y., Thanai, P., Suzuki, N., Mise, K., Yamaguchi, H., Nakamura, T., Asaji, K., Mukawa, C., Tsukamoto, H., Sato, T., Oikawa, Y., Iwasaki, T., Oe, Y., Tsukimi, T., Fukuda, N., HO, H., Nanto-Hara, F., Ogura, J., Saito, R., Nagao, S., Ohsaki, Y., Shimada, S., Suzuki, T., Toyohara, T., Mishima, E., Shima, H., Akiyama, Y., Akiyama, Y., Ichijo, M., Matsuhashi, T., Matsuo, A., Ogata. Y., Yang, C., Suzuki, C., Breeggemann, M., Heymann, J., Shimizu, M. Ogawa S., Takahashi, N., Suzuki, T., Owada, Y., Kure, S., Mano, N., Soga, T., Wada, T., Kopp, J., Fukuda, S. , Hozawa, A., Yamamoto, M., Ito, S., Wada. J. Tomioka, Y., and Abe, T. Gut microbiome-derived phenyl sulfate contributes to albuminuria in diabetic kidney disease Nat. Commun. , 10, 1835 (2019).

Yugi, K., Ohno, S., Krycer, J., James, D., and Kuroda, S. Rate-oriented trans-omics: integration of multiple omic data on the basis of reaction kinetics Current Opinion in Systems Biology , 15, 109-120 (2019).

Arai Hojo, M., Masuda K., Hojo, H., Nagahata, Y., Yasuda, K., Ohara, D., Takeuchi, Y., Hirota, K., Suzuki, Y., Kawamoto, H., and Kawaoka, S. Identification of a genomic enhancer that enforces proper apoptosis induction in thymic negative selection Nat. Commun. , 10, 2603 (2019).

Miura, F., Shibata, Y., Miura, M., Sangatsuda, Y., Hisano, O., Araki, H., and Ito, T. Highly efficient single-stranded DNA ligation technique improves low-input whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. Nucleic Acids Research , gkz435 (2019).

Chandra, AA., Sharma, A., Dehzangi, A., and Tsunoda, T. EvolStruct-Phogly: incorporating structural properties and evolutionary information from profile bigrams for the phosphoglycerylation prediction. BMC Genomics , 19(Suppl 9), 984 (2019).

2018年度（平成30年度）

Horinouchi T., Maeda T., and Furusawa C. Understanding and engineering alcohol-tolerant bacteria using OMICS technology World Journal of Microbiology and Biotechnology , 34 157 (2018).

Ishii, C., Nakanishi, Y., Murakami, S., Nozu, R., Ueno, M., Hioki, K., Aw, W., Hirayama, A., Soga, T., Ito, M., Tomita, M., and Fukuda, S. A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet International Journal of Molecular Sciences , 19(12), 4079 (2018).

Yamamoto, Y., Nakanishi, Y., Murakami, S., Aw, W., Tsukimi, T., Nozu, R., Ueno, M., Nakahigashi, K., Hirayama, A., Sugimoto, M., Soga, T., Ito, M., Tomita, M., and Fukuda, S. A Metabolomic-Based Evaluation of the Role of Commensal Microbiota throughout the Gastrointestinal Tract in Mice Microorganisms , 6(4), 101 (2018).

Nishiguchi, H., Hiasa, N., Uebayashi, K., Liao, J., Shimizu, H. and Matsuda, F. Transomics data-driven, ensemble kinetic modeling for system-level understanding and engineering of the cyanobacteria central metabolism. Metab. Eng., 52(July 2018), 273–283, (2019).

Okahashi, N., Maeda, K., Kawana, S., Iida, J., Shimizu, H. and Matsuda, F. Sugar phosphate analysis with baseline separation and soft ionization by gas chromatography-negative chemical ionization-mass spectrometry improves flux estimation of bidirectional reactions in cancer cells. Metab. Eng., 51, 43–49, (2019).
島津製作所プレスリリース
 大阪大学プレスリリース
 日本経済新聞プレスリリース

Hayakawa, K., Matsuda, F. and Shimizu, H. 13C-metabolic flux analysis of ethanol-assimilating Saccharomyces cerevisiae for S-adenosyl-l-methionine production. Microb. Cell Fact., 17(1), 82, (2018).

Uebayashi, K., Shimizu, H. and Matsuda, F. Comparative analysis of fermentation and enzyme expression profiles among industrial Saccharomyces cerevisiae strains. Appl. Microbiol. Biotechnol., 102(16), 7071–7081, (2018).

Araki, C., Okahashi, N., Maeda, K., Shimizu, H. and Matsuda, F. Mass Spectrometry-Based Method to Study Inhibitor-Induced Metabolic Redirection in the Central Metabolism of Cancer Cells. Mass Spectrom., 7(1), A0067–A0067, (2018).

Nagai, H., Masuda, A., Toya, Y., Matsuda, F. and Shimizu, H. Metabolic engineering of mevalonate-producing Escherichia coli strains based on thermodynamic analysis. Metab. Eng., 47, 1–9, (2018).

Chandra, A., Sharma, A., Dehzangi, A., Ranganathan, S., Jokhan, A., Chou, K.-C. and Tsunoda, T. PhoglyStruct: Prediction of phosphoglycerylated lysine residues using structural properties of amino acids. Sci. Rep., 8(1), 17923, (2018).

Harada, A., Maehara, K., Handa, T., Arimura, Y., Nogami, J., Hayashi-Takanaka, Y., Shirahige, K., Kurumizaka, H., Kimura, H. and Ohkawa, Y. A chromatin integration labelling method enables epigenomic profiling with lower input. Nat. Cell Biol. ,1, (2018).

Kawata, K., Yugi, K., Hatano, A., Kokaji, T., Tomizawa, Y., Fujii, M., Uda, S., Kubota, H., Matsumoto, M., Nakayama, K. I. and Kuroda, S. Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data. Genes to Cells ,gtc.12655, (2018).

Cortes, E., Lachowski, D., Robinson, B., Sarper, M., Teppo, J. S., Thorpe, S. D., Lieberthal, T. J., Iwamoto, K., Lee, D. A., Okada-Hatakeyama, M., Varjosalo, M. T. and Del Río Hernández, A. E. Tamoxifen mechanically reprograms the tumor microenvironment via HIF-1A and reduces cancer cell survival. EMBO Rep. ,e46557, (2018).

Lysenko, A., Sharma, A., Boroevich, K. A. and Tsunoda, T. An integrative machine learning approach for prediction of toxicity-related drug safety. Life Sci. Alliance ,1(6), e201800098, (2018).

Liu, R., Wang, J., Ukai, M., Sewon, K., Chen, P., Suzuki, Y., Wang, H., Aihara, K., Okada-Hatakeyama, M. and Chen, L. Hunt for the tipping point during endocrine resistance process in breast cancer by dynamic network biomarkers. J. Mol. Cell Biol. ,(2018).

Fujiwara, S., Hoshizaki, M., Ichida, Y., Lex, D., Kuroda, E., Ishii, K. J., Magi, S., Okada, S.,… Imai, Y. Pulmonary phagocyte-derived NPY controls the pathology of severe influenza virus infection. Nat. Microbiol. ,1, (2018).

Kawata, K., Hatano, A., Yugi, K., Kubota, H., Sano, T., Fujii, M.,Tomizawa, Y., Kokaji, T., Tanaka, K.Y., Uda, S., Suzuki, Y., Matsumoto, M., Nakayama, K.I., Saitoh, K., Kato, K., Ueno, A., Ohishi, M., Hirayama, A., Soga, T., Kuroda, S. Trans-omic Analysis Reveals Selective Responses to Induced and Basal Insulin across Signaling, Transcriptional, and Metabolic Networks. iScience ,7, 212–229, (2018).
東京大学プレスリリース

Takahashi, M., Izumi, Y., Iwahashi, F., Nakayama, Y., Iwakoshi, M., Nakao, M., Yamato, S., Fukusaki, E. and Bamba, T. Highly Accurate Detection and Identification Methodology of Xenobiotic Metabolites Using Stable Isotope Labeling, Data Mining Techniques, and Time-Dependent Profiling Based on LC/HRMS/MS. Anal. Chem., 90(15), 9068–9076, (2018).

Kubota, H., Uda, S., Matsuzaki, F., Yamauchi, Y., and Kuroda, S. In Vivo Decoding Mechanisms of the Temporal Patterns of Blood Insulin by the Insulin-AKT Pathway in the Liver. Cell Syst. 7, 118-128.E3 (2018).

Yamaguchi-Kabata, Y., Morihara, T., Ohara, T., Ninomiya, T., Takahashi, A., Akatsu, H., Hashizume, Y., Hayashi, N., Shigemizu, D., Boroevich, K.A., Ikeda, M., Kubo, M., Takeda, M., and Tsunoda, T. Integrated analysis of human genetic association study and mouse transcriptome suggests LBH and SHF genes as novel susceptible genes for amyloid-β accumulation in Alzheimer’s disease. Hum. Genet. 137, 521-533 (2018).

Wang, Y., Cao, L., Lee, C.-Y., Matsuo, T., Wu, K., Asher, G., Tang, L., Saitoh, T., Russell, J., Klewe-Nebenius, D., Wang, L., Soya, S., Hasegawa, E., Chérasse, Y., Zhou, J., Li, Y., Wang, T., Zhan, X., Miyoshi, C., Irukayama, Y., Cao, J., Meeks, J.P., Gautron, L., Wang, Z., Sakurai, K., Funato, H., Sakurai, T., Yanagisawa, M., Nagase, H., Kobayakawa, R., Kobayakawa, K., Beutler, B. and Liu, Q. Large-scale forward genetics screening identifies Trpa1 as a chemosensor for predator odor-evoked innate fear behaviors. Nat. Commun. 9, 2041 (2018).

Miura, F., Fujino, T., Kogashi, K., Shibata, Y., Miura, M., Isobe, H., and Ito, T. Triazole linking for preparation of a next-generation sequencing library from single-stranded DNA. Nucleic Acids Res. gky452, (2018).

Enya, S., Kawakami, K., Suzuki, Y., and Kawaoka, S. A novel zebrafish intestinal tumor model reveals a role for cyp7a1 -dependent tumor–liver crosstalk in causing adverse effects on the host. Dis. Model. Mech. 11, dmm032383 (2018).

Takeda, H., Izumi, Y., Takahashi, M., Paxton, T., Tamura, S., Koike, T., Yu, Y., Kato, N., Nagase, K., Shiomi, M. and Bamba, T. Widely-targeted quantitative lipidomics method by supercritical fluid chromatography triple quadrupole mass spectrometry. J. Lipid Res., 59(7), 1283–1293, (2018).

Harada, A., Maehara, K., Ono, Y., Taguchi, H., Yoshioka, K., Kitajima, Y., Xie, Y., Sato, Y., Iwasaki, T., Nogami, J., Okada, S., Komatsu, T., Semba, Y., Takemoto, T., Kimura, H., Kurumizaka, H., and Ohkawa, Y. Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration. Nat. Commun. 9, (2018).

Saqi, M., Lysenko, A., Guo, Y.-K., Tsunoda, T., and Auffray, C. Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. Brief. Bioinform. 1-15 (2018).

2017年度（平成29年度）

Morita, M., Sato, T., Nomura, M., Sakamoto, Y., Inoue, Y., Tanaka, R., Ito, S., Kurosawa, K., Yamaguchi, K., Sugiura, Y., Takizaki, H., Yamashita, Y., Katakura, R., Sato, I., Kawai, M., Okada, Y., Watanabe, H., Kondoh, G., Matsumoto, S., Kishimoto, A., Obata, M., Matsumoto, M., Fukuhara, T., Motohashi, H., Suematsu, M., Komatsu, M., Nakayama, K.I., Watanabe, T., Soga, T., & Tanuma, N. PKM1 Confers Metabolic Advantages and Promotes Cell-Autonomous Tumor Cell Growth. Cancer Cell. 33, 355-367.e7 (2018).

Ohashi, K., Fujii, M., Uda, S., Kubota, H., Komada, H., Sakaguchi, K., Ogawa, W. and Kuroda, S. Increase in hepatic and decrease in peripheral insulin clearance characterize abnormal temporal patterns of serum insulin in diabetic subjects. npj Syst. Biol. Appl. 4, 14 (2018). 4:14.

Fukushima, H., Shimizu, K., Watahiki, A., Hoshikawa, S., Kosho, T., Oba, D., Sakano, S., Arakaki, M., Yamada, A., Nagashima, K., Okabe, K., Fukumoto, S., Jimi, E., Bigas, A., Nakayama, K.I., Nakayama, K., Aoki, Y., Wei, W., & Inuzuka, H. NOTCH2 Hajdu-Cheney Mutations Escape SCFFBW7-Dependent Proteolysis to Promote Osteoporosis. Mol. Cell. 68, 645-658 (2017).

Yonehara, R., Nada, S., Nakai, T., Nakai, M., Kitamura, A., Ogawa, A., Nakatsumi, H., Nakayama, K.I., Li, S., Standley, D.M., Yamashita, E., Nakagawa, A., & Okada, M. Structural basis for the assembly of the Ragulator-Rag GTPase complex. Nat. Commun. 8, (2017).

Nakayama, S., Yumimoto, K., Kawamura, A., & Nakayama, K.I. Degradation of the endoplasmic reticulum–anchored transcription factor MyRF by the ubiquitin ligase SCF^Fbxw7 in a manner dependent on the kinase GSK-3. J. Biol. Chem. jbc.ra117.000741 (2018).

Yugi, K., & Kuroda, S. Metabolism as a signal generator across trans-omic networks at distinct time scales. Curr. Opin. Syst. Biol. 8, 59-66 (2017).

Nakatsumi, H., Matsumoto, M., & Nakayama, K.I. Noncanonical Pathway for Regulation of CCL2 Expression by an mTORC1-FOXK1 Axis Promotes Recruitment of Tumor-Associated Macrophages. Cell Rep. 21, 2471-2486 (2017).

Krycer J.R., Yugi, K., Hirayama, A., Fazakerley, D.J., Quek, L.-E., Scalzo, R., Ohno, S., Hodson, M.P., Ikeda, S., Shoji, F., Suzuki, K., Domanova, W., Parker, B.L., Nelson, M.E., Humphrey, S.J., Turner, N., Hoehn, K.L., Cooney, G.J., Soga, T., Kuroda, S., & James, D. Dynamic metabolomics reveals that insulin primes the adipocyte for glucose metabolism. Cell Rep. 21, 3536-3547 (2017).

Umeyama, T. & Ito, T. DMS-seq for in vivo genome-wide mapping of protein-DNA interactions and nucleosome centers. Cell Rep. 21, 289-300 (2017).