Faculty of Environment and Information Studies

Research Output

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Review article
2020

A "philosophical molecule," hydrogen may overcome senescence and intractable diseases

Hirano, S. I., Ichikawa, Y., Kurokawa, R., Takefuji, Y. & Satoh, F., 2020 Jan 1, In : Medical gas research. 10, 1, p. 47-49 3 p.

Research output: Contribution to journalReview article

2019

Nanopore sequencing: Review of potential applications in functional genomics

Kono, N. & Arakawa, K., 2019 Jan 1, In : Development Growth and Differentiation.

Research output: Contribution to journalReview article

13 Citations (Scopus)

On the correlation between total condensate and moist heating in tropical cyclones and applications for diagnosing intensity

Nolan, D. S., Miyamoto, Y., Wu, S. N. & Soden, B. J., 2019 Jan 1, In : Monthly Weather Review. 147, 10, p. 3759-3784 26 p.

Research output: Contribution to journalReview article

Preventing explosions of hydrogen gas inhalers

Kurokawa, R., Hirano, S. I., Ichikawa, Y., Matsuo, G. & Takefuji, Y., 2019 Sep, In : Medical gas research. 9, 3, p. 160-162 3 p.

Research output: Contribution to journalReview article

Reconsidering plasmid maintenance factors for computational plasmid design

Yano, H., Shintani, M., Tomita, M., Suzuki, H. & Oshima, T., 2019 Jan 1, In : Computational and Structural Biotechnology Journal. 17, p. 70-81 12 p.

Research output: Contribution to journalReview article

4 Citations (Scopus)
2016

A systematic review of the economic evaluation of telemedicine in Japan

Akiyama, M. & Yoo, B. K., 2016 Jul, In : Journal of Preventive Medicine and Public Health. 49, 4, p. 183-196 14 p.

Research output: Contribution to journalReview article

13 Citations (Scopus)
2015

Disrupted tRNA genes and tRNA fragments: A perspective on tRNA gene evolution

Kanai, A., 2015 Jan 26, In : Life. 5, 1, p. 321-331 11 p.

Research output: Contribution to journalReview article

19 Citations (Scopus)
2014

BioHackathon series in 2011 and 2012: Penetration of ontology and linked data in life science domains

Katayama, T., Wilkinson, M. D., Aoki-Kinoshita, K. F., Kawashima, S., Yamamoto, Y., Yamaguchi, A., Okamoto, S., Kawano, S., Kim, J. D., Wang, Y., Wu, H., Kano, Y., Ono, H., Bono, H., Kocbek, S., Aerts, J., Akune, Y., Antezana, E., Arakawa, K., Aranda, B. & 65 others, Baran, J., Bolleman, J., Bonnal, R. J. P., Buttigieg, P. L., Campbell, M. P., Chen, Y. A., Chiba, H., Cock, P. J. A., Cohen, K. B., Constantin, A., Duck, G., Dumontier, M., Fujisawa, T., Fujiwara, T., Goto, N., Hoehndorf, R., Igarashi, Y., Itaya, H., Ito, M., Iwasaki, W., Kalaš, M., Katoda, T., Kim, T., Kokubu, A., Komiyama, Y., Kotera, M., Laibe, C., Lapp, H., Lütteke, T., Marshall, M. S., Mori, T., Mori, H., Morita, M., Murakami, K., Nakao, M., Narimatsu, H., Nishide, H., Nishimura, Y., Nystrom-Persson, J., Ogishima, S., Okamura, Y., Okuda, S., Oshita, K., Packer, N. H., Prins, P., Ranzinger, R., Rocca-Serra, P., Sansone, S., Sawaki, H., Shin, S. H., Splendiani, A., Strozzi, F., Tadaka, S., Toukach, P., Uchiyama, I., Umezaki, M., Vos, R., Whetzel, P. L., Yamada, I., Yamasaki, C., Yamashita, R., York, W. S., Zmasek, C. M., Kawamoto, S. & Takagi, T., 2014, In : Journal of Biomedical Semantics. 5, 1, 5.

Research output: Contribution to journalReview article

23 Citations (Scopus)

Concise review: Genetic dissection of hypoxia signaling pathways in normal and leukemic stem cells

Gezer, D., Vukovic, M., Soga, T., Pollard, P. J. & Kranc, K. R., 2014 Jun, In : Stem Cells. 32, 6, p. 1390-1397 8 p.

Research output: Contribution to journalReview article

20 Citations (Scopus)

Mechanotransduction in epidermal Merkel cells

Nakatani, M., Maksimovic, S., Baba, Y. & Lumpkin, E. A., 2014, In : Pflugers Archiv European Journal of Physiology. 467, 1, p. 101-108 8 p.

Research output: Contribution to journalReview article

20 Citations (Scopus)

Metabolome analysis based on capillary electrophoresis-mass spectrometry

Hirayama, A., Wakayama, M. & Soga, T., 2014 Oct 1, In : TrAC - Trends in Analytical Chemistry. 61, p. 215-222 8 p.

Research output: Contribution to journalReview article

60 Citations (Scopus)

Pattern classification in Kampo medicine

Yakubo, S., Ito, M., Ueda, Y., Okamoto, H., Kimura, Y., Amano, Y., Togo, T., Adachi, H., Mitsuma, T. & Watanabe, K., 2014, In : Evidence-based Complementary and Alternative Medicine. 2014, 535146.

Research output: Contribution to journalReview article

29 Citations (Scopus)

Radiation-driven migration: The case of Minamisoma City, Fukushima, Japan, after the Fukushima nuclear accident

Zhang, H., Yan, W., Oba, A. & Zhang, W., 2014 Sep 9, In : International journal of environmental research and public health. 11, 9, p. 9286-9305 20 p.

Research output: Contribution to journalReview article

24 Citations (Scopus)

Rare insights into cancer biology

Adam, J., Yang, M., Soga, T. & Pollard, P. J., 2014 May 15, In : Oncogene. 33, 20, p. 2547-2556 10 p.

Research output: Contribution to journalReview article

54 Citations (Scopus)

tRNA gene diversity in the three domains of life

Fujishima, K. & Kanai, A., 2014 Jan 1, In : Frontiers in Genetics. 5, MAY, 142.

Research output: Contribution to journalReview article

35 Citations (Scopus)

Unexpected tRNAs that do not consistently obey the universal genetic code

Hamashima, K. & Kanai, A., 2014 Jan 1, In : Seikagaku. 86, 4, p. 483-488 6 p.

Research output: Contribution to journalReview article

2013

A blueprint for building a quantum computer

Van Meter, R. & Horsman, C., 2013 Oct 22, In : Communications of the ACM. 56, 10, p. 84-93 10 p.

Research output: Contribution to journalReview article

42 Citations (Scopus)

Alternative genetic code for amino acids and transfer RNA revisited

Hamashima, K. & Kanai, A., 2013 Jun 1, In : Biomolecular Concepts. 4, 3, p. 309-318 10 p.

Research output: Contribution to journalReview article

7 Citations (Scopus)

Cancer metabolism: Key players in metabolic reprogramming

Soga, T., 2013 Mar 1, In : Cancer science. 104, 3, p. 275-281 7 p.

Research output: Contribution to journalReview article

141 Citations (Scopus)

Oncometabolites: Linking altered metabolism with cancer

Yang, M., Soga, T. & Pollard, P. J., 2013 Sep 3, In : Journal of Clinical Investigation. 123, 9, p. 3652-3658 7 p.

Research output: Contribution to journalReview article

175 Citations (Scopus)
2012

Knowledge, beliefs, and concerns about opioids, palliative care, and homecare of advanced cancer patients: A nationwide survey in Japan

Akiyama, M., Takebayashi, T., Morita, T., Miyashita, M., Hirai, K., Matoba, M., Akizuki, N., Shirahige, Y., Yamagishi, A. & Eguchi, K., 2012 May 1, In : Supportive Care in Cancer. 20, 5, p. 923-931 9 p.

Research output: Contribution to journalReview article

14 Citations (Scopus)

Measures of Compositional Strand Bias Related to Replication Machinery and its Applications

Arakawa, K. & Tomita, M., 2012 Mar 1, In : Current Genomics. 13, 1, p. 4-15 12 p.

Research output: Contribution to journalReview article

9 Citations (Scopus)

The rice proteogenomics database OryzaPG-DB: Development, expansion, and new features

Helmy, M., Sugiyama, N., Tomita, M. & Ishihama, Y., 2012 Apr 2, In : Frontiers in Plant Science. 3, APR, 65.

Research output: Contribution to journalReview article

10 Citations (Scopus)

Usage and attitudes of physicians in Japan concerning traditional Japanese medicine (Kampo Medicine): A descriptive evaluation of a representative questionnaire-based survey

Moschik, E. C., Mercado, C., Yoshino, T., Matsuura, K. & Watanabe, K., 2012 Mar 19, In : Evidence-based Complementary and Alternative Medicine. 2012, 139818.

Research output: Contribution to journalReview article

24 Citations (Scopus)
2011

[Virus, phage, transposon and their regulatory small non-coding RNAs].

Kanai, A., 2011 Jun, In : Uirusu. 61, 1, p. 25-34 10 p.

Research output: Contribution to journalReview article

Open Access
1 Citation (Scopus)

Redox regulation in respiring Saccharomyces cerevisiae

Murray, D. B., Haynes, K. & Tomita, M., 2011 Oct 1, In : Biochimica et Biophysica Acta - General Subjects. 1810, 10, p. 945-958 14 p.

Research output: Contribution to journalReview article

40 Citations (Scopus)

Systems biology reveals microRNA-mediated gene regulation

Watanabe, Y. & Kanai, A., 2011 Dec 1, In : Frontiers in Genetics. 2, JUNE, Article 29.

Research output: Contribution to journalReview article

21 Citations (Scopus)

Traditional Japanese Kampo medicine: Clinical research between modernity and traditional medicine - The state of research and methodological suggestions for the future

Witt, C. M., Watanabe, K., Matsuura, K., Gao, P., Hottenbacher, L., Tokunaga, H., Nishimura, K., Imazu, Y. & Reissenweber, H., 2011 Apr 6, In : Evidence-based Complementary and Alternative Medicine. 2011, 513842.

Research output: Contribution to journalReview article

69 Citations (Scopus)

Transcriptional regulation of organic anion transporting polypeptide SLCO4C1 as a new therapeutic modality to prevent chronic kidney disease

Suzuki, T., Toyohara, T., Akiyama, Y., Takeuchi, Y., Mishima, E., Suzuki, C., Ito, S., Soga, T. & Abe, T., 2011 Sep, In : Journal of Pharmaceutical Sciences. 100, 9, p. 3696-3707 12 p.

Research output: Contribution to journalReview article

21 Citations (Scopus)

Vertebrate virus-encoded microRNAs and their sequence conservation

Takane, K. & Kanai, A., 2011 Sep 27, In : Japanese Journal of Infectious Diseases. 64, 5, p. 357-366 10 p.

Research output: Contribution to journalReview article

10 Citations (Scopus)
2010

A metabolic model of human erythrocytes: Practical application of the E-Cell Simulation Environment

Yachie-Kinoshita, A., Nishino, T., Shimo, H., Suematsu, M. & Tomita, M., 2010 Aug 13, In : Journal of Biomedicine and Biotechnology. 2010, 642420.

Research output: Contribution to journalReview article

17 Citations (Scopus)

The DBCLS BioHackathon: Standardization and interoperability for bioinformatics web services and workflows

Katayama, T., Arakawa, K., Nakao, M., Ono, K., Aoki-Kinoshita, K. F., Yamamoto, Y., Yamaguchi, A., Kawashima, S., Chun, H. W., Aerts, J., Aranda, B., Barboza, L. H., Bonnal, R. J. P., Bruskiewich, R., Bryne, J. C., Fernández, J. M., Funahashi, A., Gordon, P. M. K., Goto, N., Groscurth, A. & 37 others, Gutteridge, A., Holland, R., Kano, Y., Kawas, E. A., Kerhornou, A., Kibukawa, E., Kinjo, A. R., Kuhn, M., Lapp, H., Lehvaslaiho, H., Nakamura, H., Nakamura, Y., Nishizawa, T., Nobata, C., Noguchi, T., Oinn, T. M., Okamoto, S., Owen, S., Pafilis, E., Pocock, M., Prins, P., Ranzinger, R., Reisinger, F., Salwinski, L., Schreiber, M., Senger, M., Shigemoto, Y., Standley, D. M., Sugawara, H., Tashiro, T., Trelles, O., Vos, R. A., Wilkinson, M. D., York, W., Zmasek, C. M., Asai, K. & Takagi, T., 2010 Aug 21, In : Journal of Biomedical Semantics. 1, 8.

Research output: Contribution to journalReview article

21 Citations (Scopus)

The treatment of menopausal symptoms by traditional East Asian medicines: Review and perspectives

Scheid, V., Ward, T., Cha, W. S., Watanabe, K. & Liao, X., 2010 Jun 1, In : Maturitas. 66, 2, p. 111-130 20 p.

Research output: Contribution to journalReview article

38 Citations (Scopus)

Unveiling cellular biochemical reactions via metabolomics-driven approaches

Saito, N., Ohashi, Y., Soga, T. & Tomita, M., 2010 Jun 1, In : Current Opinion in Microbiology. 13, 3, p. 358-362 5 p.

Research output: Contribution to journalReview article

23 Citations (Scopus)
2009

Can complex cellular processes be governed by simple linear rules?

Selvarajoo, K., Tomita, M. & Tsuchiya, M., 2009 May 11, In : Journal of Bioinformatics and Computational Biology. 7, 1, p. 243-268 26 p.

Research output: Contribution to journalReview article

14 Citations (Scopus)

Disrupted tRNA gene diversity and possible evolutionary scenarios

Sugahara, J., Fujishima, K., Morita, K., Tomita, M. & Kanai, A., 2009 Nov 1, In : Journal of Molecular Evolution. 69, 5, p. 497-504 8 p.

Research output: Contribution to journalReview article

25 Citations (Scopus)

Kampo medicine as an integrative medicine in Japan

Nishimura, K., Plotnikoff, G. A. & Watanabe, K., 2009 May 1, In : Japan Medical Association Journal. 52, 3, p. 147-149 3 p.

Research output: Contribution to journalReview article

25 Citations (Scopus)
2008

Informatics for peptide retention properties in proteomic LC-MS

Shinoda, K., Sugimoto, M., Tomita, M. & Ishihama, Y., 2008 Feb 1, In : Proteomics. 8, 4, p. 787-798 12 p.

Research output: Contribution to journalReview article

31 Citations (Scopus)

Palliative care in Japan: Current status and a nationwide challenge to improve palliative care by the cancer control act and the Outreach Palliative Care Trial of Integrated Regional Model (OPTIM) study

Yamagishi, A., Morita, T., Miyashita, M., Akizuki, N., Kizawa, Y., Shirahige, Y., Akiyama, M., Kei Hirai, H., Kudo, T., Yamaguchi, T., Fukushima, A. & Eguchi, K., 2008 Oct 1, In : American Journal of Hospice and Palliative Medicine. 25, 5, p. 412-418 7 p.

Research output: Contribution to journalReview article

40 Citations (Scopus)

Proteins as networks: Usefulness of graph theory in protein science

Krishnan, A., Zbilut, J. P., Tomita, M. & Giuliani, A., 2008 Dec 1, In : Current Protein and Peptide Science. 9, 1, p. 28-38 11 p.

Research output: Contribution to journalReview article

78 Citations (Scopus)

Stabilizing synthetic data in the DNA of living organisms

Yachie, N., Ohashi, Y. & Tomita, M., 2008 Jun 1, In : Systems and Synthetic Biology. 2, 1-2, p. 19-25 7 p.

Research output: Contribution to journalReview article

18 Citations (Scopus)
2007

Metabolome analysis by capillary electrophoresis-mass spectrometry

Monton, M. R. N. & Soga, T., 2007 Oct 19, In : Journal of Chromatography A. 1168, 1-2, p. 237-246 10 p.

Research output: Contribution to journalReview article

229 Citations (Scopus)
2006

Architectural implications of quantum computing technologies

Van Meter, R. & Oskin, M., 2006, In : ACM Journal on Emerging Technologies in Computing Systems. 2, 1, p. 31-63 33 p.

Research output: Contribution to journalReview article

52 Citations (Scopus)

A whole genome cloning in the BGM vector

Itaya, M., Tsuge, K., Koizumi, M. & Fujita, K., 2006 Jan, In : Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme. 51, 1, p. 61-67 7 p.

Research output: Contribution to journalReview article

English and multiculturalism - From the language user's perspective

Tanaka, S., 2006 Dec 1, In : RELC Journal. 37, 1, p. 47-66 20 p.

Research output: Contribution to journalReview article

6 Citations (Scopus)

G-language System as a platform for large-scale analysis of high-throughput omics data

Arakawa, K. & Tomita, M., 2006 Aug 31, In : Journal of Pesticide Science. 31, 3, p. 282-288 7 p.

Research output: Contribution to journalReview article

26 Citations (Scopus)
2005

All systems go: Launching cell simulation fueled by integrated experimental biology data

Arita, M., Robert, M. & Tomita, M., 2005 Jun, In : Current Opinion in Biotechnology. 16, 3 SPEC. ISS., p. 344-349 6 p.

Research output: Contribution to journalReview article

21 Citations (Scopus)

Metabolome analysis and metabolic simulation

Ishii, N., Soga, T., Nishioka, T. & Tomita, M., 2005 Mar 1, In : Metabolomics. 1, 1, p. 29-37 9 p.

Research output: Contribution to journalReview article

13 Citations (Scopus)
2004

A new role for expressed pseudogenes as ncRNA: Regulation of mRNA stability of is homologous coding gene

Yano, Y., Saito, R., Yoshida, N., Yoshiki, A., Wynshaw-Boris, A., Tomita, M. & Hirotsune, S., 2004 Jul, In : Journal of Molecular Medicine. 82, 7, p. 414-422 9 p.

Research output: Contribution to journalReview article

58 Citations (Scopus)
2 Citations (Scopus)