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Publications
 
In press

  01.Giuliani, Alessandro; Tsuchiya, Masa; Hashimoto, Midori; Tomita, Masaru; Yoshikawa, Keinichi (2014) Collective Genome-Wide Expression Modes: Major Roles of Low-Variance Genes. FEBS. (In Press).

 

  02.Ikeda KT, Hirose Y, Hiraoka K, Noro E, Fujishima K, Tomita M, Kanai A. (2014) Identification, expression, and molecular evolution of microRNAs in the “living fossil” Triops cancriformis (tadpole shrimp). RNA (In press).

 

  03.

Nakada T, Matsuzaki R, Krienitz L, Tomita M, Nozaki H. (2014) Taxonomic 
reassessment of strains formerly classified as Chloromonas insignis (Volvocales, Chlorophyceae), and description of Gloeomonas anomalipyrenoides sp. nov. Acta Phytotaxonomica et Geobotanica. (In Press).

 

 

 

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2015
 
2014

 

01.Sakagami, H., Sugimoto, M., Tanaka, S., Onuma, H., Ota, S., Kaneko, M., Soga, T. and Tomita, M. (2014) Metabolomic profiling of sodium fluoride-induced cytotoxicity in an oral squamous cell carcinoma cell line. Metabolomics. 10: 270–9.

02.Sugimoto M, Takada M, Toi M. (2014) Development of Web tools to predict axillary lymph node metastasis and pathological response to neoadjuvant chemotherapy in breast cancer patients. Int J Biol Markers, doi: 10.5301/jbm.5000103.

03.Bozek K, Wei Y, Yan Z, Liu X, Xiong J, Sugimoto M, Tomita M, Pääbo S, Pieszek R, Sherwood CC, Hof PR, Ely JJ, Steinhauser D, Willmitzer L, Bangsbo J, Hansson O, Call J, Giavalisco P, Khaitovich P. (2014) Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness. PLoS Biol., 12(5):e1001871.

04.Sato D, Sugimoto M, Akashi H, Tomita M, Soga T. (2014) Comparative metabolite profiling of foxglove aphids (Aulacorthum solani Kaltenbach) on leaves of resistant and susceptible soybean strains. Mol Biosyst., 10(4):909-15.

05. Kono N, Arakawa K, Sato M, Yoshikawa H, Tomita M, Itaya M. (2014) Undesigned selection for replication termination of bacterial chromosomes. J Mol Biol., 426(16):2918-27.

 06.Amariei C, Tomita M, Murray DB. (2014) Quantifying periodicity in omics data. Front Cell Dev Biol., 2:40. doi: 10.3389/fcell.2014.00040

07. Nakahigashi K, Takai Y, Shiwa Y, Wada M, Honma M, Yoshikawa H, Tomita M, Kanai A and Mori H. (2014) Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo. BMC Genomics, 15:1115 DOI: 10.1186/1471-2164-15-1115

 08.Hayashi K, Tabata S, Piras V, Tomita M and Selvarajoo K. (2014) Systems Biology Strategy Reveals PKC-delta is Key for SensitizingTRAIL-Resistant Human Fibrosarcoma. Front. Immunol. 5:659.doi:10.3389/fimmu.2014.00659

09.Piras V, Tomita M, and Selvarajoo K. (2014) Transcriptome-wide Variability in Single Embryonic Development Cells. Sci Rep, 4, 7137 doi:10.1038/srep07137

10.Cheng KK, Lee BS, Masuda T, Ito T, Ikeda K, Hirayama A, Deng L, Dong J, Shimizu K, Soga T, Tomita M, Palsson BO, Robert M. (2014) Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol. Nat Commun, 5:3233. doi:10.1038/ncomms4233

11.Hirayama A, Wakayama M, Soga T. (2014) Metabolome analysis based on capillary electrophoresis-mass spectrometry. Trend Anal Chem,  doi:10.1016/j.trac.2014.05.005

 12. Nakada, T. and Tomita, M. (2014) Light microscopy and phylogenetic analyses of Chlamydomonas species (Volvocales, Chlorophyceae). II. Molecular phylogeny, 
secondary structure of ITS-2, cell morphology, and nomenclature of Microglena 
opisthopyren, and M. media, comb. nov. Acta Phytotax. Geobot. 65, 67-73

13.Nakada T, Tsuchida Y, Arakawa K, Ito T and Tomita M. (2014) Hybridization between Japanese and North American Chlamydomonas reinhardtii (Volvocales, Chlorophyceae). Phycol. Res. 62, 232-236.
 

 
2013

 

01.Martínez, P., Gálvez, S., Ohtsuka, N., Budinich, M., Paz Cortés, M., Serpell, C., Nakahigashi, K.., Hirayama, A., Tomita, M., Soga. T., Martínez, S., Maass, A. and Parada, P. (2013) Metabolomic study of of Chilean biomining bacteria Acidithiobacillus ferrooxidans strain Wenelen and Acidithiobacillus thiooxidans strain Licananta. Metabolomics. 9: 247–57.
 

02.Matsui, M., Tomita, M. and Kanai, A. (2013) Comprehensive Computational Analysis of Bacterial CRP/FNR Superfamily and its Target Motifs Reveals Stepwise Evolution of Transcriptional Networks. Genome Biol Evol. 5: 267–82.

03.Selvarajoo K. and Tomita M. (2013) Physical laws shape biology. Science. 339: 6120-646.

04.Soga, T. (2013) Cancer metabolism: key players in metabolic reprogramming. Cancer Sci. 104: 275-81.

05.Takubo, K., Nagamatsu, G., Kobayashi, C. I, Nakamura-Ishizu, A., Kobayashi, H., Ikeda, E., Goda, N., Johnson, R. S, Rahimi, Y., Soga, T., Hirao, A., Suematsu, M., and Suda, T. (2013) Regulation of Glycolysis by Pdk Functions as a Metabolic Checkpoint for Cell Cycle Quiescence in Hematopoietic Stem Cells. Cell Stem Cell. 12: 49-61.

06.Maekawa, K.*, Hirayama, A.*, Iwata Y.*, Tajima Y., Nishimaki-Mogami T., Sugawara S., Ueno, N., Abe, H., Ishikawa M., Murayama M., Matsuzawa Y., Nakanishi H., Ikeda K., Arita M., Taguchi, R., Minamino N., Wakabayashi, S., Soga T., and Saito, Y. (2013) Global metabolomic analysis of heart tissue in a hamster model for dilated cardiomyopathy. J. Mol. Cell. Cardiol. 59: 76-85.

07.Takeuchi, K., Ohishi, M., Ota, S., Suzumura, K., Naraoka, H., Ohata, T., Seki, J., Miyamae, Y., Honma, M., and Soga, T. (2013) Metabolic Profiling to Identify Potential Serum Biomarkers for gastric ulceration induced by non-steroid anti-inflammatory drugs. J. Proteome Res.12, 1399-407.

08.Hisano, Y., Ota, S., Arakawa, K., Muraki, M., Kono, N., Oshita, K., Sakuma, T., Tomita, M., Yamamoto, T., Okada, Y., and Kawahara, A. (2013) Quantitative assay for TALEN activity at endogenous genomic loci. Biology Open. 363-7.

09.Shindo, Y., Nozaki, T., Saito, R., Tomita M. (2013) Computational analysis of associations between alternative splicing and histone modifications. FEBS LETTERS. 587: 516–21.

10.Iwasaki, W., Y., Kiga, K., Kayo, H., Fukuda-Yuzawa, Y., Weise, J., Inada, T., Tomita, M., Ishihama, Y. and Fukao, T. (2013) Global MicroRNA Elevation by Inducible Exportin 5 Regulates Cell Cycle Entry. RNA. 490-7.

11.Sugimoto, M., Saruta, J., Matsuki, C., To, M., Onuma, H., Kaneko, M., Soga, T., Tomita, M. and Tsukinoki, K. (2013) Physiological and environmental parameters associated with mass   spectrometry-based salivary metabolomic profiles. Metabolomics. 454-63.

12.Kami, K., Fujimori, T., Sato, H., Sato, M., Yamamoto, H., Ohashi, Y., Sugiyama, N., Ishihama, Y., Onozuka, H., Kinoshita, T., Saito, N., Ochiai, A., *Esumi, H., Soga, T. and Tomita, M. (2013) Metabolomic Profiling of Lung and Prostate Tumor Tissues by Capillary Electrophoresis Time-of-flight Mass Spectrometry. Metabolomics. 444-53.

13.Ito, T., Tanaka, M., Shinkawa,  H., Nakada, T., Ano, Y., Kurano, N., Soga, T. and Tomita, M. (2013) Metabolic and morphological changes of an oil accumulating trebouxiophycean alga in nitrogen-deficient conditions. Metabolomics. 9: 178-87.

14.Tsuruoka, M., Hara, J., Hirayama, A., Sugimoto, M., Soga, T., Shankle, W.R., Tomita, M. (2013) Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 34: 2865–72.

15.Okubo, C., Sano, HI., Naito, Y., Tomita, M. (2013) Contribution of quantitative changes in individual ionic current systems to the embryonic development of ventricular myocytes: a simulation study. J Physiol Sci. 63: 355-67.

16.Itaya, H., Oshita, K., Arakawa, K. and Tomita, M. (2013) GEMBASSY: an EMBOSS Associated Software Package for Comprehensive Genome Analyses. Source Code Biol Med. 8: 17.

17.Ito, T., Sugimoto, M., Toya, Y., Ano, Y., Kurano N, Soga., T, Tomita, M. (2013) Time-resolved metabolomics of a novel trebouxiophycean alga using 13CO2 feeding. J Biosci Bioeng. 116: 408-15.
 

18.Nishino. T., Yachie-Kinoshita.A., Hirayama, A., Soga, T., Suematsu, M. and Tomita, M. (2013) Dynamic simulation and metabolome analysis of long-term erythrocyte storage in adenine–guanosine solution. PLOS ONE. 144: 212-23.
 

19.Migita, T., Okabe, S., Ikeda, K., Igarashi, S., Sugawara, S., Tomida, A., Taguchi, R., Soga, T., and Seimiya, H. (2013) Inhibition of ATP citrate lyase induces an anticancer effect via reactive oxygen species: AMPK as a predictive biomarker for therapeutic impact. Am J Pathol. 182: 1800-10.

20.Adam, J., Yang, M., Bauerschmidt, C., Kitagawa, M., O’Flaherty, L., Maheswaran, P., O¨ zkan, G., Sahgal, N., Baban, D., Kato, K., Saito, K., Iino, K., Igarashi, K., Stratford, M., Pugh, C., Tenant, D., Ludwig, C., Davies, B., Ratcliffe, P. J., El-Bahrawy, M., Ashrafian, H., Soga, T., and Pollard, P. J. (2013) A Role for Cytosolic Fumarate Hydratase in Urea Cycle Metabolism and Renal Neoplasia. Cell Rep. 3: 1440-48.
                

21.Ternette N., Yang M., Laroyia M., Kitagawa M., O'Flaherty L., Wolhulter K., Igarashi K., Saito K., Kato K., Fischer R., Berquand A., Kessler B.M., Lappin T., Frizzell N., Soga T., Adam J, Pollard P.J. (2013) Inhibition of Mitochondrial Aconitase by Succination in Fumarate Hydratase Deficiency. Cell Rep. 3: 689-700.

22.Furusawa, Y., Obata, Y., Fukuda, S., Endo, T., A., Nakato, G., Takahashi, D., Nakanishi, Y., Uetake, C., Kato, K., Kato, T., Takahashi, M., Fukuda, N., N., Murakami, S., Miyauchi, E., Hino, S., Atarashi, K., Onawa, S., Fujimura, Y., Lockett, T., Clarke, J., M., Topping, D., L., Tomita, M., Hori, S., Ohara, O., Morita, T., Koseki, H., Kikuchi, J., Honda, K., Hase, K. and Ohno, H. (2013) Commensal microbe-derived butyrate
                  induces the Differentiation of colonic regulatory T cells.
Nature. 504: 446-50.
                

23.Hayashi, K., Piras, V., Tabata, S., Tomita, M., and  Selvarajoo, K. (2013) Systems Biology Approach to Suppress TNF-induced Proinflammatory Gene Expressions. Cell Communication and Signaling. 11: 84.

24.Karasawa T., Saito T., Ueno .Y., Sugimoto M., Soga T. (2013) Metabolome analysis of erythrocytes from patients with chronic hepatitis C reveals the etiology of ribavirin-induced hemolysis. International Journal of Medical Sciences,10 ,1575-1577.

25.Saito T., Sugimoto M., Igarashi K., Saito K., Shao L., Katsumi T., Tomita K., Sato C., Aso R., Okumoto K., Nishise Y., Watanabe H., Tomita M., Ueno Y., Soga T. (2013) Dynamics of serum metabolites in patients with chronic hepatitis C receiving pegylated interferon plus ribavirin: A metabolomics analysis, Metabolism, 62, 1577-1586.

26.Sato D., Akashi H., Sugimoto M., Tomita M., Soga T. (2013) Metabolomic profiling of the response of susceptible and resistant soybean strains to foxglove aphid, Aulacorthum solani Kaltenbach, Journal of Chromatography B, 925(5): 95-103.

27.Koh T., Murakami Y., Machino M., Onuma H., Kaneko M., Sugimoto M., Soga T., Tomita M. (2013) Changes of Metabolic Profiles in an Oral Squamous Cell Carcinoma Cell Line Induced by Eugenol, In Vivo, 27(2): 233-243.

28.Atarashi, K., Tanoue, T., Suda, W., Oshima, K., Nagano, Y., Nishikawa, H., Fukuda, S., Saito, T., Narushima, S., Hase, K., Kim, S.W., Fritz, J.V., Wilmes, P., Ueha, S., Matsushima, K., Ohno, H., Olle, B., Sakaguchi, S., Taniguchi, T., Morita, H., Hattori, M., Honda, K. (2013) Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota, Nature 500: 232-236.

29.Amariei C, Machné R, Sasidharan K, Gottstein W, Tomita M, Soga T, Lloyd D, Murray DB. (2013) The dynamics of cellular energetics during continuous yeast culture, Conf Proc IEEE Eng Med Biol Soc. 2708–2711. doi: 10.1109/EMBC.2013.6610099

30.Soma, A., Sugahara, J., Onodera, A., Yachie, N., Kanai, A., Watanabe, S., Yoshikawa, H., Ohnuma, M., Kuroiwa, H., Kuroiwa, T. and Sekine, Y. (2013) Identification of highly-disrupted tRNA genes in nuclear genome of the red alga, Cyanidioschyzon merolae 10D. Sci Rep. 3:2321. doi: 10.1038/srep02321

31.Okuda, J., Niizuma, S., Shioi, T., Kato, T., Inuzuka, Y., Kawashima, T., Tamaki, Y., Kawamoto, A., Tanada, Y., Iwanaga, Y., Narazaki, M., Matsuda, T., Adachi, S., Soga, T., Takemura, G., Kondoh, H., Kita, T., Kimura, T. (2013) Persistent overexpression of phosphoglycerate mutase, a glycolytic enzyme, modifies energy metabolism and reduces stress resistance of heart in mice. PLoS ONE. 8(8):e72173.
                  doi:10.1371/journal.pone.0072173

32.Karasawa, T., Saito, T., Ueno, Y., Sugimoto, M., Soga, T. (2013) Metabolome analysis of erythrocytes from patients with chronic hepatitis C reveals the etiology of ribavirin-induced hemolysis. Int J Med Sci. 10(11):1575-1577. doi:10.7150/ijms.6436

33.Saito, T., Sugimoto, M., Igarashi, K., Saito, K., Shao, L., Katsumi, T., Tomita, K., Sato, C., Ishii, R., Okumoto, K., Nishise, Y., Watanabe, H., Tomita, M., Ueno, Y., Soga, T. (2013) Dynamics of serum metabolites in patients with chronic hepatitis C receiving pegylated interferon plus ribavirin: A metabolomics analysis. Metabolism. 62(11):1577-1586. doi:10.1016/j.metabol.2013.07.002

34.Uema, N., Ooshio, T., Harada, K., Naito, M., Naka, K., Hoshii, T., Tadokoro, Y., Ohta, K., Ali, MA., Katano, M., Soga, T., Nakanuma, Y., Okuda, A., Hirao, A. (2013) Abundant nucleostemin expression supports the undifferentiated properties of germ cell tumors. Am J Pathol. 183(2):592-603. doi:10.1016/j.ajpath.2013.04.018

35.Yang, M., Soga, T., and Pollard, P. J. (2013) Oncometabolites: Linking Altered Metabolism with Cancer?  J. Clin. Invest. 123(9):3652-3658. doi:10.1172/JCI67228




 

 

 
2012

  01.Selvarajoo, K. (2012) The recognition of chaos in host-pathogen response. Front. Physio. 3:7.

02.Murakami, S., Fujishima, K., Tomita, M. and Kanai, A. (2012) Metatranscriptomic analysis of microbes in an ocean-front deep subsurface hot spring reveals novel small RNAs and type-specific tRNA degradation. Applied and Environmental Microbiology. 78(4): 1015-1022. 

03.Sugimoto, M., Sakagami, H., Yokote, Y., Onuma, H., Kaneko, M., Mori, H., Sakaguchi, Y., Soga, T., and Tomita, M. (2012) Non-targeted metabolite profiling in activated macrophage secretion. Metabolomics. 8: 624-33.

04.Sugimoto, M., Kaneko, M., Onuma, H., Sakaguchi, Y., Mori, M., Abe, S., Soga, T., and Tomita, M. (2012) Changes in the Charged Metabolite and Sugar Profiles of Pasteurized and Unpasteurized Japanese Sake with Storage. J. Agric. Food Chem. 60 (10): 2586–2593.

05.Sugahara, J., Fujishima, K., Nunoura, T., Takaki, Y., Takami, H., Takai, K., Tomita M., and Kanai, A. (2012) Genomic Heterogeneity in a Natural Archaeal Population Suggests a Model of tRNA Gene Disruption. PLoS ONE. 7(3):e32504. 

06.Arakawa, K. and Tomita, M. (2012) Measures of Compositional Strand Bias Related to Replication Machinery and its Applications. Current Genomics. 13(1):4-15.

07.Tomita, M. and Kami, K. (2012) Systems Biology, Metabolomics, and Cancer Metabolism. Science. 336:990-991.

08.Selvarajoo K., and Giuliani A. (2012) Finding Self-organization from the Dynamic Gene Expressions of Innate Immune Responses. Front. Physiol. 3:192.

09.Selvarajoo K. (2012) Understanding multimodal biological decisions from single cell and population dynamics. Wiley Interdiscip Rev Syst Biol Med.4(4) 385-99.  

10.Kono, N., Arakawa, K., and Tomita, M. (2012) Validation of bacterial replication termination models using simulation of genomic mutations. PLoS One.7(4):e34526.  

11.Hamashima, K., Fujishima, K., Masuda, T., Sugahara, J., Tomita, M., and Kanai, A.(2012) Nematode-specific tRNAs that decode an alternative genetic code for leucine. Nucleic Acids Res. 40: 3653-3662.

12.Sugimoto, M., Kawakami, M., Robert, M., Soga, T. and Tomita, M. (2012) Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis. Current Bioinformatics. 7: 96-108.

13.Helmy, M., Tomita, M. and Ishihama, Y.(2012) Peptide Identification by Searching Large-Scale Tandem Mass Spectra against Large Databases: Bioinformatics Methods in Proteogenomics. Genes Genomes Genomics. 6: 76-85.

14.Helmy, M., Sugiyama, N., Tomita, M. and  Ishihama, Y. (2012) Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics. Genesto Cells Manuscript.(2012). 17: 633-44.

15.Fujishima, H., Okada, N., Dogru, M., Baba, F., Tomita, M., Abe, J., Matsumoto, K., and Saito, H. (2012) The role of Staphylococcal enterotoxin in atopic keratoconjunctivitis and corneal ulceration. Allergy. 67: 799–803.

16.Sasidharan, K., Amariei, C., Tomita, M., and Murray, D.B. (2012) Rapid DNA, RNA and protein extraction protocols optimised for slow continuously growing yeast cultures. Yeast Journal. 29:311-322.

17.Piras, V., Tomita, M., and Selvarajoo, K. (2012) Is central dogma a global property of cellular information flow? Front. Physiol.3,439.

18. Hirayama, A., Nakashima, E., Sugimoto, M., Akiyama, S., Sato, W., Maruyama, S., Matsuo, S., Tomita, M., Yuzawa, Y. and Soga, T. (2012) Metabolic profiling reveals new serum biomarkers for differentiating diabetic nephropathy. Anal Bioanal Chem. 404:3101-9.

19. Iino, K., Sugimoto, M., Soga, T. and Tomita, M. (2012) Metabolomics: A New Omics Technology for Traditional Herbal Medicine Analysis. Chinese Medicine: Acupuncture, Herbal Medicine and Therapies. 45-55.                         

20. Tanaka, S., Taga, H., Maehara, K., Kaneshima, A., Machino, M., Onuma, H., Kaneko, M., Sakagami, H., Sugimoto, M., Soga, T. and Tomita, M. (2012) Pilot Study of Changes in Salivary Metabolic Profiles Induced by Template Therapy. In Vivo. 26:1015-20.

21.Hirayama, A., Tomita, M. and Soga, T. (2012) Sheathless capillary electrophoresis-mass spectrometry with a high- sensitivity porous sprayer for cationic metabolome analysis. Analyst. 137:5026-5033.

22.Imami, K., Sugiyama, N., Imamura, H., Wakabayashi, M., Tomita, M., Taniguchi, M., Ueno, T., Toi, M. and Ishihama, Y. (2012) Temporal profiling of lapatinib-suppressed phosphorylation signals inEGFR/HER2 pathways. Mol Cell Proteomics. 12:1741-57.

23.Sasidharan, K., Soga, T., Tomita, M. and Murray, D., B. (2012) A Yeast Metabolite Extraction Protocol Optimised for Time-Series Analyses. PLoS ONE. 7:e44283.
                                                                                                                                                  

24.Piras, V., Hayashi, K., Tomita, M. and Selvarajoo, K. (2012) Investigation of stochasticity in TRAIL signaling cancer model. IEEE/ICME Com. Med. Eng. 609-614.

25.Takada, M., Sugimoto, M., Ohno, S., Kuroi, K., N. Sato , H., Bando, H.,  Masuda, N., Iwata, H., Kondo, M., Sasano, H.,  Chow, L., W., C., Inamoto, T., Naito, Y., Tomita, M. and Toi, M. (2012) Predictions of the pathological response to neoadjuvant chemotherapy in patients with primary breast cancer using a data mining technique. Breast Cancer Res Treat. 134:661-70.

26.Sasidharan, K., Tomita, M., Aon, M., Lloyd, D. and Murray, D, B.(2012) Time-structure of the yeast metabolism in vivo. Adv Exp Med Biol. 736:359-79.
  

27. Takada, M., Sugimoto, M., Naito, Y., Moon, H., G., Han, W., Noh, D., Y., Kondo, M., Kuroi, K., Sasano, H., Inamoto, T., Tomita, M., and Toi, M. (2012) Prediction of axillary lymph node metastasis in primary breast cancer patients using a decision tree-based model. BMC Med Inform Decis Mak 12:54.

28.Ohtani., N., Tomita, M. and Itaya, M. (2012) The third plasmid pVV8 from Thermus thermophilus HB8: isolation, characterization, and sequence determination. Extremophiles. 16:237-44.

29. Helmy, M., Sugiyama, N., Tomita, M. and Ishihama, Y. (2012) The rice proteogenomics database OryzaPG-DB: development, expansion and new features. Front. Plant Sci. 3:65.
 

30. Jeelani G., Sato D., Husain A., Cadiz A.E., Sugimoto M., Soga T., Suematsu M., Nozaki T.(2012) Metabolic Profiling of the Protozoan Parasite Entamoeba invadens Revealed Activation of Unpredicted Pathway during Encystation, Plos One, 7(5), e37740.

31. Sugimoto, M., Ikeda, S., Niigata, K., Tomita, M., Sato, H. and Soga, T. (2012) MMMDB: Mouse Multiple Tissue Metabolome Database. Nucleic Acids Res. 40: D809–D814.
    

32.Itaya,M., Kawata, Y., Sato. M., Tomita. M. and Nakahigashi. K. (2012) A simple method to provide a shuttling plasmid for delivery to other host ascertained by prolonged stability of extracellular plasmid DNA released from Escherichia coli K12 endA mutant, deficient in major endonuclease. J. Biochem. 152:501–504.

33.Toya, Y., Nakahigashi, K., Tomita, M., and Shimizu, K. (2012) Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data. Molecular BioSystems. 8: 2593–604.

34.Yamada, M., Takanashi, K., Hamatani, T., Hirayama, A., Akutsu, H., Fukunaga, T., Ogawa, S., Sugawara, K., Shinoda, K., Soga, T., Umezawa, A., Kuji, N., Yoshimura, Y. and Tomita, M. (2012) A medium-chain fatty acid as an alternative energy source in mouse preimplantation development. Scientific Reports. 2.

35.Kami, K., Fujimori, T., Sato, H., Sato, M., Yamamoto, H., Ohashi, Y., Sugiyama, N., Ishihama, Y., Onozuka, H., Kinoshita, T., Saito, N., Ochiai, A., Esumi, H., Soga, T. and Tomita, M.(2012) Metabolomic Profiling of Lung and Prostate Tumor Tissues by Capillary Electrophoresis Time-of-flight Mass Spectrometry. Metabolomics. 1–10.

36. Hoshi, T., Tadokoro, Y., Naka, K., Ooshio, T., Muraguchi, T., Sugiyama, N., Soga, T., Araki, K., Yamamura, K., and Hirao, A. (2012) mTORC1 is Essential for Leukemia Propagation but Not Stem Cell Self- renewal. J. Clin. Invest. 122, 2114–29.

37. Kasukawa, T., Sugimoto, M., Hida, A., Minami, Y., Mori, M., Honma, S., Honma, K., Mishima, K., Soga, T., and Ueda, H.R. (2012) Human blood metabolite timetable indicates internal body time. Proc. Natl. Acad. Sci. USA. 109, 15036-141.

38. Imaizumi, Y., Okada, Y., Akamatsu, W., Koike, M., Kuzumaki, N., Hayakawa, H., Nihira, T.,  Kobayashi, T., Ohyama, M., ,Sato, S., Takanashi, M., Funayama, M., Hirayama, A., Soga, T., Hishiki, T., Suematsu, M., Yagi, T., Ito, D., Kosakai, A., Hayashi, K., Shouji, M., Nakanishi, A., Suzuki, N., Mizuno, Y., Mizushima, N., Amagai, M., Uchiyama, Y., Mochizuki, H., Hattori, N., and Okano H. (2012) Mitochondrial dysfunction associated with increased oxidative stress and α-synuclein accumulation in PARK2 iPSC-derived neurons and postmortem brain tissue. Mol Brain. 5: 35.

39. Takahashi, M., Miyata, S., Fujii, J., Inai, Y., Ueyama, S., Araki, M., Soga, T., Fujinawa, R., Nishitani C., Ariki S., Shimizu T., Abe T., Ihara Y., Nishikimi, M., Kozutsumi Y., Taniguchi N., and Kuroki, Y. (2012) In vivo role of aldehyde reductase. Biochim. Biophys. Acta. 1820: 1787–96.

40. Akiyama, Y., Takeuchi, Y., Kikuchi, K., Mishima, E., Yamamoto, Y., Suzuki, C., Toyohara, T., Suzuki, T., Hozawa, A., Ito, S., Soga, T., and Abe, T. (2012) A Metabolomic approach for clarifying the effect of AST-120 on 5/6 nephrectomized rats by Capillary Electrophoresis with Mass Spectrometry(CE-MS). Toxins. 4: 1309-22.

42. Omori, Y., Ohtani, T., Sakata, Y., Mano, T., Takeda, Y., Tamaki, S., Tsukamoto. Y., Kamimura, D., Aizawa, Y., Miwa, T., Komuro, I., Soga, T., and Yamamoto, K. (2012) L-Carnitine Prevents the Development of Ventricular Fibrosis and Heart Failure with Preserved Ejection Fraction in Hypertensive Heart Disease . J. Hypertens. 30: 1834-44.

43. Yang, M., Soga, T., Pollard, P.J., and Adam, J. (2012) The emerging role of fumarate as an oncometabolite. Front. Oncol. 2: 85.

44. Hirata, Y., Ikeda, K., Sudoh, M., Tokunaga, Y., Suzuki, A., Weng, L., Ohta, M., Tobita, Y., Okano, K., Ozeki, K., Kawasaki, K., Tsukuda, T., Katsume, A., Aoki, Y., Umehara, T., Sekiguchi, S., Toyoda, T., Shimotohno, K., Soga, T., Nishijima, M., Taguchi, R., and Kohara, M. (2012) Self-enhancement of hepatitis C virus replication by promotion of specific sphingolipid biosynthesis. PLoS Pathog. 8.

45. Husain, A., Sato, D., Jeelani, G., Soga, T., and Nozaki, T. (2012) Dramatic Increase in Glycerol Biosynthesis upon Oxidative Stress in the Anaerobic Protozoan Parasite Entamoeba histolytica. PLoS Negl. Trop. Dis. 6

46. Liu, C., Kurakane, S., Takita, J., Itano R., Soga, T., Oikawa A., and Igarashi, K. (2012) Antihypertensive Effects of Unripe Persimmon (Diospyros kaki L.cv. Hiratanenashi) Fruit and Its Component in Spontaneously Hypertensive Rats. Food Sci. Technol. Res. 18, 391-8.

47. Deguchi, K., Sato, D., Sugimoto, M., Hara, H., Kawasaki, Y., Demura, S., Watanabe, T., Denholme, S. J., Okazaki, H., Ozaki, T., Yamaguchi, T., Takeya, H., Soga, T., Tomita, M., and Takano, Y. (2012) Clarification as to why alcoholic beverages have the ability to induce superconductivity in Fe1+dTe1−xSx. Supercond. Sci. Technol. 25(8), 084025.

48. Jeelani G., Sato D., Husain A., Cadiz A.E., Sugimoto M., Soga T., Suematsu M., Nozaki T.(2012) Metabolic Profiling of the Protozoan Parasite Entamoeba invadens Revealed Activation of Unpredicted Pathway during Encystation, Plos One, 7(5), e37740.

 49.Nakada T, Nozaki H, Tomita M. (2012) Light microscopy and phylogenetic analyses of 
Chlamydomonas species (Volvocales, Chlorophyceae). I. Chlamydomonas pseudomacrostigma and Chlamydomonas media. Acta Phytotaxonomica et Geobotanica, 62, 69-78

 

 
2011

01. Yachie, N., Saito, R., Sugiyama, N., Tomita, M. and Ishihama, Y. (2011) Integrative features of the yeast phosphoproteome and protein-protein interaction map. PLoS Comput. Biol., 7(1), e1001064.

02.Kono, N., Arakawa, K. and Tomita, M. (2011) Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes. BMC Genomics, 12(1), 19.

03.Yoshida, S., Imoto, J., Minato, T., Oouchi, R., Kamada, Y., Tomita, M., Soga, T. and Yoshimoto, H. (2011) A novel mechanism regulates H(2) S and SO(2) production in Saccharomyces cerevisiae. Yeast, 28(2), 109-21.

04.Hayashi, K., Sasamura, H., Hishiki, T., Suematsu, M., Ikeda, S., Soga, T., and Itoh, H. (2011) Use of Serum and Urine Metabolome Analysis for the Detection of Metabolic Changes in Patients with Stage 1-2 Chronic Kidney Disease. Nephro-Urol. Mon. 3: 164-71.
 

05. Nozaki, T., Yachie, N., Ogawa, R., Saito, R. and Tomita, M. (2011) Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA.  Gene, 476(1-2), 10-4.

06.Ogawa, Y., Koike, N., Kurosawa, G., Soga, T., Tomita, M. and Tei, H. (2011) Positive Autoregulation Delays the Expression Phase of Mammalian Clock Gene Per2. PLoS ONE, 6(4), e18663.

07. Selvarajoo, K. (2011) Macroscopic law of conservation revealed in the population dynamics of Toll-like receptor signaling. Cell Communication and Signaling, 9(9).

08. Nakada, T. and Tomita, M. (2011) Chlamydomonas neoplanoconvexa nom. nov. and its unique phylogenetic position within Volvocales (Chlorophyceae). Phycological  Research, 59(3), 194–9.
 

09. Murray, B.D., Haynes, K. and Tomita, M. (2011) Redox Regulation in Respiring Saccharomyces cerevisiae.  Biochim Biophys Acta. 1810(10), 945-58.

10.Ooga, T., Sato, H., Nagashima, A., Sasaki, K., Tomita, M., Soga T. and Ohashi, Y. (2011) Metabolomic Anatomy of Animal Model Revealing Homeostatic Imbalances in Dyslipidemia. Y. Mol. BioSyst.,7, 1217-23.

11.Oshita,K., Arakawa, K., and Tomita, M. (2011) KBWS: an EMBOSS associated package for accessing bioinformatics webservices. Source Code Biol. Med., 6, 8.

12.Komasa, M., Fujishima, K., Hiraoka, K., Shinhara, A., Lee, Baek-Seok., Tomita, M. and Kanai, A. (2011) A screening system for artificial small RNAs that inhibit the growth of Escherichia coli. J. Biochem., 150(3), 289-94.

13.Helmy, M., Tomita, M., Ishihama, Y. (2011) OryzaPG-DB: rice proteome database based on shotgun proteogenomics. BMC Plant Biol., 11, 13.

14.Saito, R., Kohno, K., Okada, Y., Osada, Y., Numata, K., Kohama, C., Watanabe, K., Nakaoka, H., Yamamoto, N., Kanai, A., Yasue, H., Murata, S., Abe, K., Tomita, M., Ohkohchi, N. and Kiyosawa, H. (2011) Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes. BMC Med Genomics., 4, 42.

15.Toya, Y., Kono, N., Arakawa, K., Tomita, M. (2011) Metabolic flux analysis and visualization. J. Proteome Res., 10(8), 3313-23.

16.Takane, K., Kanai, A. (2011) Vertebrate Virus-Encoded MicroRNAs and Their Sequence Conservation. Jpn. J. Infect. Dis., 64(5), 357-66.

17.Nozaki, T., Yachie, N., Ogawa, R., Kratz, A., Saito, R., Tomita, M. (2011) Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification. BMC Genomics, 12, 416.

18.Shinhara, A., Matsui, M., Hiraoka, K., Nomura, W., Hirano, R., Nakahigashi, K., Tomita, M., Mori, H., Kanai, A. (2011) Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. BMC Genomics, 12, 428.

19.Soga, T., Sugimoto, M., Honma, M., Mori, M., Igarashi, K., Kashikura, K., Ikeda, S., Hirayama, A., Yamamoto, T., Yoshida, H., Otsuka, M., Tsuji, S., Yatomi, Y., Sakuragawa, T., Watanabe, H., Nihei, K., Saito, T., Kawata, S., Suzuki, H., Tomita, M., Suematsu, M. (2011) Serum metabolomics reveals γ-glutamyl dipeptides as biomarkers for discrimination among different forms of liver disease. J. Hepatol., 55(4), 896-905.
               

20.Piras, V., Hayashi, K., Tomita, M., Selvarajoo, K. (2011) Enhancing apoptosis in TRAIL-resistant cancer cells using fundamental response rules.  Sci. Rep., 1,144.

21.Sato, A., Soga, T., Igarashi, K., Takesue, K., Tomita, M., Kanai, A. (2011) GTP-dependent RNA 3'-terminal phosphate cyclase from the hyperthermophilic archaeon Pyrococcus furiosus. Genes Cells, 16(12), 1190-1199.

22.Adam, J., Hatipoglu, E., O’Flaherty, L., Ternette, N., Sahgal, N., Lockstone, H., Baban D., Nye, E., Stamp, G.W., Wolhuter, K., Stevens, M., Fischer, R., Carmeliet, P., Maxwell, P.H., Pugh, C.W., Frizzell, N., Soga, T., Kessler, B.M., El-Bahrawy, M., Ratcliffe, P.J., Pollard, P.J. (2011) Renal Cyst Formation in Fh1-Deficient Mice Is Independent of the Hif/Phd Pathway: Roles for Fumarate in KEAP1 Succination and Nrf2 Signaling, Cancer Cell, 20, 524-537.
                

23.Deng, L., Shoji, I., Ogawa, W., Kaneda, S., Soga, T., Jiang, D., Ide, Y., Hotta, H. (2011) Hepatitis C Virus Infection Promotes Hepatic Gluconeogenesis through an NS5A-Mediated, FoxO1-Dependent Pathway, J. Virol. 85, 8556-8568.
 

24.Kato, T., Niizuma, S., Inuzuka, Y., Kawashima, T., Okuda, J., Kawamoto A., Tamai, Y., Iwanaga, Y., Soga, T., Kita, T., Kimura, T., Shioi, T. (2011) Analysis of Liver Metabolism in a Rat Model of Heart Failure, Int. J. Cardiol.  online doi:10.1016/j.ijcard.2011.07.056.
 

25.Ochiai, D., Goda, N., Hishiki, T., Kanai, M., Senoo-Matsuda, N., Soga, T., Johnson, R.S.,  Yoshimura, Y., Suematsu, M. (2011) Disruption of HIF-1α in Hepatocytes Impairs Glucose Metabolism in Diet-induced Obesity Mice, Biochem. Biophys. Res. Commun, 415(3):445-9
 

26.Toyoda, Y., Tamai, M., Kashikura, K., Kobayashi, S., Fujiyama, Y., Soga, T., Tawaga, Y.(2011), Acetaminophen-induced Hepatotoxicity in a Liver Tissue Model Consisting of Primary Hepatocytes Assembling Around an Endothelial Cell Network, Drug Metab. Dispos. 40(1):169-77.
 

27.Suzuki, T., Toyohara, T., Akiyama, Y., Takeuchi, Y., Mishima, E., Suzuki, C., Ito, S., Soga, T., Abe, T.(2011), Transcriptional Regulation of Organic Anion Transporting Polypeptide SLCO4C1 as a New Therapeutic Modality to Prevent Chronic Kidney Disease, J. Pharm. Sci., 100, 3696-3707.
 

28.Gustavsson, C., Soga, T., Wahlström, E, Vesterlund, M, Azimi, A., Norstedt, G., Tollet-Egnell, P.(2011) Sex-dependent Hepatic Transcripts and Metabolites in the Development of Glucose Intolerance and Insulin Resistance in Zucker Diabetic Fatty Rats, J. Mol. Endcrinol. 47, 129-143.
 

29.Kimura, T., Takabatake, Y., Takahashi, A., Kaimori, J., Matsui, I., Namba, T., Kitamura, H., Niimura, F., Matsusaka, T., Soga, T., Rakugi, H., Isaka, Y.(2011) Autophagy Protects the Proximal Tubule from Degeneration and Acute Ischemic Injury, J. Am. Soc. Nephrol. 22, 902-913.
 

30.Masuda, T., Sugiyama, N., Tomita, M., Ishihama, Y. (2011) Microscale Phosphoproteome Analysis of 10 000 Cells from Human Cancer Cell Lines. Anal. Chem. 83:7698-703.

31.Fujishima, K., Sugahara, J., Miller, CS., Baker, BJ., Di Giulio, M., Takesue, K., Sato, A., Tomita, M., Banfield, JF., Kanai, A. (2011) A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity. Nucleic Acids Res. 39:9695-9704.

32.Ooga, T., Sato, H., Nagashima, A., Sasaki, K., Tomita, M., Soga, T., and Ohashi, Y. (2011) Metabolomic Anatomy of an Animal Model Revealing Homeostatic Imbalances in Dyslipidaemia. Mol. Biosyst. 7: 1217-23.
 

 

 

 

 

 

 

 
2010

01. Kitamura, S., Fujishima, K., Sato, A., Tsuchiya, D., Tomita, M. and Kanai, A. (2010) Characterization of RNase HII substrate recognition using RNase HII-Argonaute chimeric enzymes from Pyrococcus furiosus. Biochem. J.,  426(3), 337-44.

02. Arjunan, S.N.V. and Tomita, M. (2010) A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation. Syst. Synth. Biol., 4(1), 35-53.

03. Takane, K., Fujishima, K., Watanabe, Y., Sato, A., Saito, N., Tomita, M. and Kanai, A., (2010) Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals. BMC Genomics, 11(1), 101.

04. Imami, K., Sugiyama, N., Tomita, M. and Ishihama, Y. (2010) Quantitative Proteome and Phosphoproteome Analysis of Cultured Cells Based on SILAC Labeling without Requirement of Serum Dialysis, Mol Biosyst., 6(3), 594-602.

05. Shinoda, K., Tomita, M. and Ishihama, Y. (2010) emPAI Calc -- for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry. Bioinformatics, 26(4), 576-7.

06. Ogawa, R., Kitagawa, N., Ashida, H., Saito, R. and Tomita, M. (2010) Computational prediction of nucleosome positioning by calculating the relative fragment frequency index of nucleosomal sequences. FEBS Lett., 584(8), 1498-1502.

 07.Iwasaki, M., Miwa, S., Ikegami, T., Tomita, M., Tanaka, N. and Ishihama, Y. (2010) One-Dimensional Capillary Liquid Chromatographic Separation Coupled with Tandem Mass Spectrometry Unveils the Escherichia coli Proteome on a Microarray Scale. Anal. Chem., 82(7), 2616-2620.

08.Sato, D., Kobayashi, S., Yasui, H., Shibata, N., Toru, T., Yamamoto, M., Tokoro, G., Ali, V., Soga, T., Takeuchi, T., Suematsu, M., Nozaki, T. (2010) Cytotoxic Effect of Amide Derivatives of Trifluoromethionine against The Enteric Protozoan Parasite Entamoeba histolytica. Int. J. Antimicrob. Agents., 35(1), 56-61. [Erratum in: Int. J. Antimicrob. Agents., 35(4) 417.]

09.Nakada, T., Shinkawa, H., Ito, T. and Tomita, M. (2010) Recharacterization of Chlamydomonas reinhardtii and its relatives with new isolates from Japan. J. Plant Res., 123(1), 67-78.

10.Nakada, T., Soga, T. and Tomita, M. (2010) Phylogenetic position of a rare loricated green alga, Cephalomonas granulata N. L. Higinb. (Volvocales, Chiorophyceae). Phycol. Res., 58(1), 62-68.

11.Nakada, T. (2010) Nomenclatural notes on some ambiregnal generic names (comments to Özdikmen, 2009). Mun. Ent. Zool., 5(1), 204-208.

12.Kato, T., Niizuma, S., Inuzuka, Y., Kawashima, T., Okuda, J., Tamaki, Y., Iwanaga, Y., Narazaki, M., Matsuda, T., Soga, T., Kita, T., Kimura, T. and Shioi, T. (2010) Analysis of Metabolic Remodeling in Compensated Left Ventricular Hypertrophy and Heart Failure. Circ. Heart Fail., ePub. 3(3), 420-30.

13.Nakada, T., Soga, T., Tomita, M. and Nozaki, H. (2010) Chlorogonium complexum sp. nov. (Volvocales, Chlorophyceae), and morphological evolution of Chlorogonium. Eur. J. Phycol., 45(1), 97-107.

14.Nozaki, H., Nakada, T. and Watanabe, S. (2010) Evolutionary origin of Gloeomonas (Volvocales, Chlorophyceae), based on ultrastructure of chloroplasts and molecular phylogeny. J. Phycol., 46(1), 195-201.

15.Maruyama, S., Sugahara, J., Kanai, A. and Nozaki, H. (2010) Permuted tRNA genes in the nuclear and nucleomorph genomes of photosynthetic eukaryotes. Mol Biol Evol., 27(5), 1070-1076.

16.Imamura, H., Yachie, N., Saito, R., Ishihama, Y. and Tomita, M. (2010) Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. BMC Bioinformatics, 11:232.

17. Fujishima, K., Sugahara, J., Tomita, M., Kanai, A. (2010) Large-scale tRNA intron transposition in the archaeal order Thermoproteales represents a novel mechanism of intron gain. Mol Biol Evol. 27(10), 2233-2243.

18.Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language genome analysis environment with REST and SOAP web service interfaces. Nucleic Acids Research, 38, W700-W705.

 19  Kim, H., Lee, B.S., Tomita, M., Kanai, A. (2010) Transcription-Associated Mutagenesis Increases Protein Sequence Diversity More Effectively than Does Random Mutagenesis in Escherichia coli. PLoS One, 5(5), e10567

20.Saito, N., Ohashi, Y., Soga, T. and Tomita, M. (2010) Unveiling cellular biochemical reactions via metabolomics-driven approaches. Curr Opin Microbiol., 13, 358–362.
 

21.Fujiwara, K., Ishihama, Y., Nakahigashi, K., Soga, T. and Taguchi, H. (2010) A Systematic Survey of in vivo Obligate Shaperonin-dependent Substrates. EMBO J., 29, 1552 - 1564.
 

22.Kato, Y., Kubo, Y., Iwata, D., Kato, S., Sudo, T., Sugiura, T., Kagaya, T., Wakayama, T., Hirayama, A., Sugimoto, M., Sugihara, K., Kaneko, S., Soga, T., Asano, M., Tomita, M., Matsui, T., Wada, M. and Tsuji, A. (2010) Gene knockout and metabolome analysis of carnitine/organic cation transporter OCTN1. Pharm. Res., 27(5), 832-404.
 

23.Kratz, A., Arner, E., Saito, R., Kubosaki, A., Kawai, J., Suzuki, H., Carninci, P., Arakawa, T., Tomita, M., Hayashizaki, Y. and Daub, C.O. (2010) Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns. BMC Genomics, 11, 257.
  

24.Nakada, T., Nozaki, H., and Tomita, M. (2010) Another Origin of Coloniality in Volvocaleans: The Phylogenetic Position of Pyrobotrys Arnoldi (Spondylomoraceae, Volvocales). J. Eukaryot. Microbiol., 57(4):379-82.
    

25.Ozawa Y., Saito R., Fujimori S., Kashima H., Ishizaka M., Yanagawa H., Miyamoto-Sato E. and Tomita M. (2010) Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions. BMC Bioinformatics.,11,350.

 26.Kyono Y., Sugiyama N., Tomita M., Ishihama Y.(2010) Chemical dephosphorylation for identification of multiply phosphorylated peptides and phosphorylation site determination. Rapid communications in mass spectrometry.,24(15), 2277-82.
    

27.Sugimoto M., Hirayama A., Robert M., Abe S., Soga T., Tomita M.(2010) Prediction of metabolite identity from accurate mass, migration time prediction and isotopic pattern information in CE-TOFMS data. ELECTROPHORESIS,31(14), 2311-18.
    

28.Tsuchiya M., Piras V., Giuliani A., Tomita M., Selvarajoo K.(2010) Collective dynamics of specific gene ensembles crucial for neutrophil differentiation: the existence of genome vehicles revealed. PLoS One,5(8), e12116.
     

 29.Katayama T., Arakawa K., Nakao M., Ono K., Aoki-Kinoshita F K., Yamamoto Y., Yamaguchi A., Kawashima S., Chun H., Aerts J., et al.(2010) The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J. Biomed. Semantics,1(1)8.
     

30.Nakada, T. (2010) (138) A proposal on the designation of cultures of fungi and algae as types. Taxon, 59(3), 983.
      

31.Nishito, Y., Osana, Y., Hachiya, T., Popendorf, K., Toyoda, A., Fujiyama, A., Itaya, M. and Sakakibara, Y. (2010) Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data. BMC Genomics, 11, 243.
      

32.Kaneko, S. and Itaya, M. (2010) Designed horizontal transfer of stable giant DNA released from Escherichia coli. J. Biochem., 147(6), 819-822.
     

33.Itaya, M. and Kaneko, S. (2010) Integration of stable extra-cellular DNA released from Escherichia coli into the Bacillus subtilis genome vector by culture mix method. Nucleic Acids Res., 38(8), 2551–2557.
      

34.Sakuragawa, T., Hishiki, T., Ueno, Y., Ikeda, S., Soga, T., Yachie, A.K., Kajimura, M. and Suematsu, M. (2010) Hypotaurine is an Energy-Saving Hepatoprotective Compound against Ischemia-Reperfusion Injury of Rat Liver. J. Clin. Biochem. Nutr., 46(2), 126-134.
   

35.Hayama, H., Nakada, T., Hamaji, T. and Nozaki, H. (2010) Morphology, molecular phylogeny and taxonomy of Gonium maiaprilis sp. nov. (Goniaceae, Chlorophyta) from Japan. Phycologia, 49(3), 221-234.
    

36.Matsuzaki, R., Nakada, T., Hara, Y. and Nozaki, H. (2010) Light and electron microscopy and molecular phylogenetic analyses of Chloromonas pseudoplatyrhyncha (Volvocales, Chlorophyceae). Phycol. Res., 58(3) 202-209.
   

37.Toya, Y., Ishii, N., Nakahigashi, K., Hirasawa, T., Soga, T., Tomita, M. and Shimizu, K. (2010) 13C-metabolic flux analysis for batch culture of Escherichia coli and its pyk and pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites. Biotechnol. Prog., 26(4):975-992.
    

 38.Kitagawa, M., Ikeda, S., Tashiro, E., Soga, T., Imoto, M. (2010) Metabolomic Identification of the Target of the Filopodia Protrusion Iinhibitor Glucopiericidin A. Chem Biol. 17(9):989-998.
   

39. Jeelani, G., Husain, A., Sato, D., Ali, V., Suematsu, M., Soga, T., Nozaki, T.(2010) Two Atypical L-cysteine-regulated NADPH-dependent Oxidoreductases Involved in Redox Maintenance, L-cystine and Iron Reduction, and Metronidazole Activation in the Enteric Protozoon Entamoeba Histolytica, J. Biol. Chem., 285, 26889-26899.
 

 40.Miyamoto-Sato, E., Fujimori, S., Ishizaka, M., Hirai1, N., Masuoka1, K., Saito, R., Ozawa, Y., Hino, K., Washio, T., Tomita, M., Yamashita, T., Oshikubo, T., Akasaka, H., Sugiyama, J., Matsumoto, Y. and Yanagawa, H. (2010) A Comprehensive Resource of Interacting Protein Regions for Refining Human Transcription Factor Networks. Electrophoresis, 5(2):e9289.
    

41.Aono,  E., Baba, T., Ara, T., Nishi, T., Nakamichi, T., Inamoto, E., Toyonaga, H., Hasegawa, M., Takai, Y., Okumura,Y., Baba, M., Tomita, M., Kato, C., Oshima, T., Nakasone, K. and Mori, H. (2010) Complete genome sequence and comparative analysis of Shewanella violacea, a psychrophilic and piezophilic bacterium from deep sea floor sediments. Mol. Biosyst., 6(7):1216-26.
     

 42.Nakagami, H., Sugiyama, N., Mochida, K., Daudi, A., Yoshida, Y., Toyoda, T., Tomita, M., Ishihama, Y. and Shirasu, K. (2010) Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants. Plant Physiol., 153(3):1161-74.
    

 43.Sugimoto, M., Goto, H., Otomo, K., Ito, M., Onuma, H., Suzuki, A., Sugawara, M., Abe, S., Tomita, M. and Soga, T. (2010) Metabolomic Profiles and Sensory Attributes of Edamame under Various Storage Duration and Temperature Conditions. J. Agric. Food Chem., 58(14):8418-25.
    

44.Yachie, A. K., Nishino, T., Shimo, H., Suematsu, M., and Tomita, M. (2010) A Metabolic Model of Human Erythrocytes: Practical Application of the E-Cell Simulation Environment. J. Biomed. Biotechnol., 2010,642420.
   

45.Nakada, T., Tomita, M. and Nozaki, H. (2010) Volvulina compacta ( Volvocaceae, Chlorophyceae ), new to Japan, and its phylogenetic position. J. Jpn. Bot., 85, 364–369.
    

46.Horiguchi, K., Toi, M., Horiguchi, S., Sugimoto, M., Naito, Y., Hayashi, Y., Ueno, T., Ohno, S., Funata, N., Kuroi, K., Tomita, M. and Eishi, Y. (2010) Predictive value of CD24 and CD44 for neoadjuvant chemotherapy response and prognosis in primary breast cancer patients. J. Med. Dent. Sci., 57(2), 165-75.

47. Sugimoto, M., Wong, D. T., Hirayama, A., Soga, T. and Tomita, M. (2010) Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles. Metabolomics, 6, 78-95.

48. Horai, H., Arita, M., Kanaya, S., Nihei, Y., Ikeda, T., Suwa, K., Ojima, Y., Tanaka, K., Tanaka, S., Aoshima, K., Oda, Y., Kakazu, Y., Kusano, M., Tohge, T., Matsuda, F., Sawada, Y., Hirai, Y. M., Nakanishi, H., Ikeda, K., Akimoto, N., Maoka, T., Takahashi, H., Ara, T., Sakurai, N., Suzuki, H., Shibata, D., Neumann, S., Iida, T., Tanaka, K., Funatsu, K., Matsuura, F., Soga, T., Taguchi, R., Saito, K., Nishioka, T. (2010) MassBank: A Public Repository for Sharing Mass Spectral Data for Life Sciences. J. Mass Spectro. 45, 703-714.

49. Sugimoto, M., Koseki, T., Hirayama, A., Abe, S., Sano, T., Tomita, M. and Soga, T. (2010) Correlation between Sensory Evaluation Scores of Japanese Sake and Metabolome Profiles, J. Agric. Food Chem., 58, 374-383.

50. Sugimoto, M., Hirayama, A., Ihiskawa, T., Robert, M., Baran, R., Uehara, K., Kawai, K., Soga, T., Tomita, M. (2010) Differential Metabolomics Software for Capillary Electrophoresis-Mass Spectrometry Data Analysis, Metabolomics, 6, 27-41.

51. Husain, A., Sato, D., Jeelani, G., Suematsu, M., Soga, T., Nozaki, T.(2010) Metabolome Analysis Revealed Increase in S-methylcysteine and Phosphatidylisopropanolamine Synthesis upon L-cysteine Deprivation in The Anaerobic Protozoan Parasite Entamoeba Histolytica, J. Biol. Chem., 285, 39160-39170.

52. Toyohara, T., Akiyama, Y., Suzuki, T., Takeuchi, Y., Mishima, E., Tanemoto, M., Momose, A., Toki, N., Sato, H., Nakayama, M., Hozawa, A., Tsuji, I., Ito, S., Soga, T. and Abe. T (2010) Metabolomic profiling of uremic solutes in CKD patients, Hypertens. Res. 33, 944-952.

53. Kitagawa, M., Ikeda, S., Tashiro, E., Soga, T., and Imoto, M. (2010) Metabolomic Identification of the Target of the Filopodia Protrusion Inhibitor Glucopiericidin A. Chem. Biol. 17, 989-998.

54. Sugiura, T., Kato, S., Shimizu, T., Wakayama, T., Nakamichi, N., Kubo, Y., Iwata, D., Suzuki, K., Soga, T., Asano, M., Iseki, S., Tamai, I., Tsuji, A., and Kato, Y. (2010) Functional Expression of Carnitine/Organic Cation Transporter OCTN1/SLC22A4 in Mouse Small Intestine and Liver. Drug Metab Dispos. 38: 1665-72. 


 

 
2009

01.Yachie N, Saito R, Sugahara J, Tomita M, Ishihama Y (2009) In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution, Mol Cell Proteomics, 8, 1061-1071

02.Tsuchiya M, Selvarajoo K, Piras V, Tomita M, Giuliani A (2009) Local and global responses in complex gene regulation networks, Physica A: Statistical Mechanics and its Applications, 388, 1738-1746

03.Tsuchiya M, Piras V, Choi S, Akira S, Tomita M, Giuliani A, Selvarajoo K (2009) Emergent genome-wide control in wildtype and genetically mutated lipopolysaccarides-stimulated macrophages, PLoS One, 4, e4905

04.Toyohara T, Suzuki T, Morimoto R, Akiyama Y, Souma T, Shiwaku HO, Takeuchi Y, Mishima E, Abe M, Tanemoto M, Masuda S, Kawano H, Maemura K, Nakayama M, Sato H, Mikkaichi T, Yamaguchi H, Fukui S, Fukumoto Y, Shimokawa H, Inui K, Terasaki T, Goto J, Ito S, Hishinuma T, Rubera I, Tauc M, Fujii-Kuriyama Y, Yabuuchi H, Moriyama Y, Soga T, Abe T (2009) SLCO4C1 transporter eliminates uremic toxins and attenuates hypertension and renal inflammation, J Am Soc Nephrol, 20, 2546-2555

05.Tajima T, Goda N, Fujiki N, Hishiki T, Nishiyama Y, Senoo-Matsuda N, Shimazu M, Soga T, Yoshimura Y, Johnson RS, Suematsu M (2009) HIF-1alpha is necessary to support gluconeogenesis during liver regeneration, Biochem Biophys Res Commun, 387, 789-794

06.Suzuki H, Saito R, Tomita M (2009) Measure of synonymous codon usage diversity among genes in bacteria, BMC Bioinformatics, 10, 167

07.Sugahara J, Fujishima K, Morita K, Tomita M, Kanai A (2009) Disrupted tRNA gene diversity and possible evolutionary scenarios, J Mol Evol, 69, 497-504

08.Soga T, Igarashi K, Ito C, Mizobuchi K, Zimmermann HP, Tomita M (2009) Metabolomic profiling of anionic metabolites by capillary electrophoresis mass spectrometry, Anal Chem, 81, 6165-6174

09.Shintani T, Iwabuchi T, Soga T, Kato Y, Yamamoto T, Takano N, Hishiki T, Ueno Y, Ikeda S, Sakuragawa T, Ishikawa K, Goda N, Kitagawa Y, Kajimura M, Matsumoto K, Suematsu M (2009) Cystathionine beta-synthase as a carbon monoxide-sensitive regulator of bile excretion, Hepatology, 49, 141-150

10.Selvarajoo K, Tomita M, Tsuchiya M (2009) Can complex cellular processes be governed by simple linear rules?, J Bioinform Comput Biol, 7, 243-268

11.Sato D, Nozaki T (2009) Methionine gamma-lyase: the unique reaction mechanism, physiological roles, and therapeutic applications against infectious diseases and cancers, IUBMB Life, 61, 1019-1028

12.Saito N, Robert M, Kochi H, Matsuo G, Kakazu Y, Soga T, Tomita M (2009) Metabolite profiling reveals YihU as a novel hydroxybutyrate dehydrogenase for alternative succinic semialdehyde metabolism in Escherichia coli, J Biol Chem, 284, 16442-16451

13.Ravichandran A, Sugiyama N, Tomita M, Swarup S, Ishihama Y (2009) Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non-pathogenic Pseudomonas species, Proteomics, 9, 2764-2775

14.Ooga T, Ohashi Y, Kuramitsu S, Koyama Y, Tomita M, Soga T, Masui R (2009) Degradation of ppGpp by nudix pyrophosphatase modulates the transition of growth phase in the bacterium Thermus thermophilus, J Biol Chem, 284, 15549-15556

15.Numata K, Osada Y, Okada Y, Saito R, Hiraiwa N, Nakaoka H, Yamamoto N, Watanabe K, Okubo K, Kohama C, Kanai A, Abe K, Kiyosawa H (2009) Identification of novel endogenous antisense transcripts by DNA microarray analysis targeting complementary strand of annotated genes, BMC Genomics, 10, 392

16.Nock A, Ascano JM, Jones T, Barrero MJ, Sugiyama N, Tomita M, Ishihama Y, Malik S (2009) Identification of DNA-dependent protein kinase as a cofactor for the forkhead transcription factor FoxA2, J Biol Chem, 284, 19915-19926

17.Nishino T, Yachie-Kinoshita A, Hirayama A, Soga T, Suematsu M, Tomita M (2009) In silico modeling and metabolome analysis of long-stored erythrocytes to improve blood storage methods, J Biotechnol, 144, 212-223

18.Nakahigashi K, Toya Y, Ishii N, Soga T, Hasegawa M, Watanabe H, Takai Y, Honma M, Mori H, Tomita M (2009) Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism, Mol Syst Biol, 5, 306

19.Minami Y, Kasukawa T, Kakazu Y, Iigo M, Sugimoto M, Ikeda S, Yasui A, van der Horst GT, Soga T, Ueda HR (2009) Measurement of internal body time by blood metabolomics, Proc Natl Acad Sci U S A, 106, 9890-9895

20.Masuda T, Saito N, Tomita M, Ishihama Y (2009) Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants, Mol Cell Proteomics, 8, 2770-2777

21.Kuramori C, Hase Y, Hoshikawa K, Watanabe K, Nishi T, Hishiki T, Soga T, Nashimoto A, Kabe Y, Yamaguchi Y, Watanabe H, Kataoka K, Suematsu M, Handa H (2009) Mono-(2-ethylhexyl) phthalate targets glycogen debranching enzyme and affects glycogen metabolism in rat testis, Toxicol Sci, 109, 143-151

22.Kosugi S, Hasebe M, Tomita M, Yanagawa H (2009) Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs, Proc Natl Acad Sci U S A, 106, 10171-10176

23.Kosugi S, Hasebe M, Matsumura N, Takashima H, Miyamoto-Sato E, Tomita M, Yanagawa H (2009) Six classes of nuclear localization signals specific to different binding grooves of importin alpha, J Biol Chem, 284, 478-485

24.Kono N, Arakawa K, Ogawa R, Kido N, Oshita K, Ikegami K, Tamaki S, Tomita M (2009) Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API, PLoS One, 4, e7710

25.Kaneko S, Takeuchi T, Itaya M (2009) Genetic connection of two contiguous bacterial artificial chromosomes using homologous recombination in Bacillus subtilis genome vector, J Biotechnol, 139, 211-213

26.Kanai A, Sato A, Fukuda Y, Okada K, Matsuda T, Sakamoto T, Muto Y, Yokoyama S, Kawai G, Tomita M (2009) Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus, RNA, 15, 420-431

27.Iwasaki M, Masuda T, Tomita M, Ishihama Y (2009) Chemical cleavage-assisted tryptic digestion for membrane proteome analysis, J Proteome Res, 8, 3169-3175

28.Iuchi Y, Okada F, Takamiya R, Kibe N, Tsunoda S, Nakajima O, Toyoda K, Nagae R, Suematsu M, Soga T, Uchida K, Fujii J (2009) Rescue of anaemia and autoimmune responses in SOD1-deficient mice by transgenic expression of human SOD1 in erythrocytes, Biochem J, 422, 313-320

29.Hirayama A, Kami K, Sugimoto M, Sugawara M, Toki N, Onozuka H, Kinoshita T, Saito N, Ochiai A, Tomita M, Esumi H, Soga T (2009) Quantitative metabolome profiling of colon and stomach cancer microenvironment by capillary electrophoresis time-of-flight mass spectrometry, Cancer Res, 69, 4918-4925

30.Helmy M, Gohda J, Inoue J, Tomita M, Tsuchiya M, Selvarajoo K (2009) Predicting novel features of toll-like receptor 3 signaling in macrophages, PLoS One, 4, e4661

31.Fujishima K, Sugahara J, Kikuta K, Hirano R, Sato A, Tomita M, Kanai A (2009) Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea, Proc Natl Acad Sci U S A, 106, 2683-2687

32.Asai N, Nishioka T, Takabayashi J, Furuichi T (2009) Plant volatiles regulate the activities of Ca2+ -permeable channels and promote cytoplasmic calcium transients in Arabidopsis leaf cells, Plant Signal Behav, 4, 294-300

33.Arjunan SNaT, M (2009) Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System, International Journal of Computer Science and Information Security,, 211-216, />

34.Arakawa K, Tamaki S, Kono N, Kido N, Ikegami K, Ogawa R, Tomita M (2009) Genome Projector: zoomable genome map with multiple views, BMC Bioinformatics, 10, 31

35.Arakawa K, Suzuki H, Tomita M (2009) Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index, BMC Genomics, 10, 640

36.Arakawa K, Oshita K, Tomita M (2009) A web server for interactive and zoomable Chaos Game Representation images, Source Code Biol Med, 4, 6

 
2008

01.Yoshida S, Imoto J, Minato T, Oouchi R, Sugihara M, Imai T, Ishiguro T, Mizutani S, Tomita M, Soga T, Yoshimoto H (2008) Development of bottom-fermenting saccharomyces strains that produce high SO2 levels, using integrated metabolome and transcriptome analysis, Appl Environ Microbiol, 74, 2787-2796

02.Yachie N, Ohashi Y, Tomita M (2008) Stabilizing synthetic data in the DNA of living organisms, Syst Synth Biol, 2, 19-25

03.Watanabe Y, Tomita, M. and Kanai, A. (2008) Perspective in the Evolution of Human MicroRNAs : Copy Number Expansion and Acquisition of Target Gene Speciallization., Progress of Theoretical Physics, Supplement No.173, 219-228

04.Tsuchiya D, Shimizu N, Tomita M (2008) Versatile architecture of a bacterial aconitase B and its catalytic performance in the sequential reaction coupled with isocitrate dehydrogenase, Biochim Biophys Acta, 1784, 1847-1856

05.Sugiyama N, Nakagami H, Mochida K, Daudi A, Tomita M, Shirasu K, Ishihama Y (2008) Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis, Mol Syst Biol, 4, 193

06.Sugahara J, Kikuta K, Fujishima K, Yachie N, Tomita M, Kanai A (2008) Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales, Mol Biol Evol, 25, 2709-2716

07.Shinoda K, Tomita M, Ishihama Y (2008) Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments, Bioinformatics, 24, 1590-1595

08.Shinoda K, Sugimoto M, Tomita M, Ishihama Y (2008) Informatics for peptide retention properties in proteomic LC-MS, Proteomics, 8, 787-798

09.Selvarajoo K, Takada Y, Gohda J, Helmy M, Akira S, Tomita M, Tsuchiya M, Inoue J, Matsuo K (2008) Signaling flux redistribution at toll-like receptor pathway junctions, PLoS One, 3, e3430

10.Sato S, Arita M, Soga T, Nishioka T, Tomita M (2008) Time-resolved metabolomics reveals metabolic modulation in rice foliage, BMC Syst Biol, 2, 51

11.Sato D, Yamagata W, Harada S, Nozaki T (2008) Kinetic characterization of methionine gamma-lyases from the enteric protozoan parasite Entamoeba histolytica against physiological substrates and trifluoromethionine, a promising lead compound against amoebiasis, FEBS J, 275, 548-560

12.Sato D, Karaki T, Shimizu A, Kamei K, Harada S, Nozaki T (2008) Crystallization and preliminary X-ray analysis of L-methionine gamma-lyase 1 from Entamoeba histolytica, Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 697-699

13.Sagane K, Ishihama Y, Sugimoto H (2008) LGI1 and LGI4 bind to ADAM22, ADAM23 and ADAM11, Int J Biol Sci, 4, 387-396

14.Okada Y, Tashiro C, Numata K, Watanabe K, Nakaoka H, Yamamoto N, Okubo K, Ikeda R, Saito R, Kanai A, Abe K, Tomita M, Kiyosawa H (2008) Comparative expression analysis uncovers novel features of endogenous antisense transcription, Hum Mol Genet, 17, 1631-1640

15.Ohtani N, Tomita M, Itaya M (2008) Junction ribonuclease: a ribonuclease HII orthologue from Thermus thermophilus HB8 prefers the RNA-DNA junction to the RNA/DNA heteroduplex, Biochem J, 412, 517-526

16.Ohtani N, Tomita M, Itaya M (2008) Junction ribonuclease activity specified in RNases HII/2, FEBS J, 275, 5444-5455

17.Ohtani N, Sato M, Tomita M, Itaya M (2008) Restriction on conjugational transfer of pLS20 in Bacillus subtilis 168, Biosci Biotechnol Biochem, 72, 2472-2475

18.Ohno H, Naito Y, Nakajima H, Tomita M (2008) Construction of a biological tissue model based on a single-cell model: a computer simulation of metabolic heterogeneity in the liver lobule, Artif Life, 14, 3-28

19.Ohashi Y, Hirayama A, Ishikawa T, Nakamura S, Shimizu K, Ueno Y, Tomita M, Soga T (2008) Depiction of metabolome changes in histidine-starved Escherichia coli by CE-TOFMS, Mol Biosyst, 4, 135-147

20.Ogawa Y, Arakawa K, Kaizu K, Miyoshi F, Nakayama Y, Tomita M (2008) Comparative study of circadian oscillatory network models of Drosophila, Artif Life, 14, 29-48

21.Miyamoto K, Hara T, Kobayashi H, Morisaka H, Tokuda D, Horie K, Koduki K, Makino S, Nunez O, Yang C, Kawabe T, Ikegami T, Takubo H, Ishihama Y, Tanaka N (2008) High-efficiency liquid chromatographic separation utilizing long monolithic silica capillary columns, Anal Chem, 80, 8741-8750

22.Matsubara Y, Kikuchi S, Sugimoto M, Oka K, Tomita M (2008) Algebraic method for the analysis of signaling crosstalk, Artif Life, 14, 81-94

23.Masuda T, Tomita M, Ishihama Y (2008) Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis, J Proteome Res, 7, 731-740

24.Laborde T, Tomita M, Krishnan A (2008) GANDivAWeb: a web server for detecting early folding units ("foldons") from protein 3D structures, BMC Struct Biol, 8, 15

25.Kyono Y, Sugiyama N, Imami K, Tomita M, Ishihama Y (2008) Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography, J Proteome Res, 7, 4585-4593

26.Kuroki A, Toda T, Matsui K, Uotsu-Tomita R, Tomita M, Itaya M (2008) Reshuffling of the Bacillus subtilis 168 genome by multifold inversion, J Biochem, 143, 97-105

27.Krishnan A, Zbilut JP, Tomita M, Giuliani A (2008) Proteins as networks: usefulness of graph theory in protein science, Curr Protein Pept Sci, 9, 28-38

28.Krishnan A, Tomita M, Giuliani A (2008) Evolution of gene regulatory networks: Robustness as an emergent property of evolution, Physica A: Statistical Mechanics and its Applications, 387, 2170-2186

29.Krishnan A, Giuliani A, Zbilut JP, Tomita M (2008) Implications from a network-based topological analysis of ubiquitin unfolding simulations, PLoS One, 3, e2149

30.Kratz A, Tomita M, Krishnan A (2008) GeNESiS: gene network evolution simulation software, BMC Bioinformatics, 9, 541

31.Kosugi S, Hasebe M, Tomita M, Yanagawa H (2008) Nuclear export signal consensus sequences defined using a localization-based yeast selection system, Traffic, 9, 2053-2062

32.Kosugi S, Hasebe M, Entani T, Takayama S, Tomita M, Yanagawa H (2008) Design of peptide inhibitors for the importin alpha/beta nuclear import pathway by activity-based profiling, Chem Biol, 15, 940-949

33.Itaya M, Fujita K, Kuroki A, Tsuge K (2008) Bottom-up genome assembly using the Bacillus subtilis genome vector, Nat Methods, 5, 41-43

34.Ishii K, Nakamura S, Morohashi M, Sugimoto M, Ohashi Y, Kikuchi S, Tomita M (2008) Comparison of metabolite production capability indices generated by network analysis methods, Biosystems, 91, 166-170

35.Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008) Protein abundance profiling of the Escherichia coli cytosol, BMC Genomics, 9, 102

36.Ishihama Y (2008) NanoLC-MS systems in proteomics., Chromatography, 29, 25-31

37.Ishihama Y (2008) Molecular dynamics in cellular signal transduction systems, The Japan Society of Mechanical Engineers, 111, 578-581

38.Imami K, Sugiyama N, Kyono Y, Tomita M, Ishihama Y (2008) Automated phosphoproteome analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined titania/C18 biphasic column, Anal Sci, 24, 161-166

39.Imami K, Ishihama Y, Terabe S (2008) On-line selective enrichment and ion-pair reaction for structural determination of sulfated glycopeptides by capillary electrophoresis-mass spectrometry, J Chromatogr A, 1194, 237-242

40.Horai HaN, T (2008) Automatic Generation of Structure of Phospholipids, Journal of Computer Aided Chemistry, 55-61, />

41.Fujishima K, Sugahara J, Tomita M, Kanai A (2008) Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5' and 3' tRNA halves, PLoS One, 3, e1622

42.Fujishima K, Komasa, M., Kitamura, S., Tomita, M. and Kanai, A. (2008) Comparison and Characterization of Proteomes in the Three Domains of Life Using 2D Correlation Analysis, Progress of Theoretical Physics, Supplement No.173, 206-218

43.Asti KG. B-FJ, Cini M., De Ninno A., Del Giudice E., Drago A, Elia V., Farina L., Gagliasso E., Germano R., Giuliani A., Krishnan A., Levy Leblond JM., Licata I., Modonesi C., Rossi PA., Selvarajoo K., Silvestrini V., Tamino G., Tomita M., Tsuchiya M., Verma C., Vitiello G., Webber CL. and Zbilut JP. (2008) Web era Theatrum Mundi: Another Big Chill in Science?, Alliage, 61, 41-46

44.Arakawa. K, Suzuki. H, Tomita. M (2008) Computational Genome Analysis Using The G-language System., Genes, Genomes and Genomics, 2, 1-13

45.Arakawa K, Yachie, N. and Tomita, M (2008) Visualizing Conplex Omics Information - Scientific Visualization for Genomics and Systems Biology., BIOforum Europe, 6, 27-29

46.Aon MA, Roussel MR, Cortassa S, O'Rourke B, Murray DB, Beckmann M, Lloyd D (2008) The scale-free dynamics of eukaryotic cells, PLoS One, 3, e3624

 
2007

01.Zbilut JP, Chua GH, Krishnan A, Bossa C, Rother K, Webber CL, Jr., Giuliani A (2007) A topologically related singularity suggests a maximum preferred size for protein domains, Proteins, 66, 621-629

02.Yeo ZX, Wong ST, Arjunan SN, Piras V, Tomita M, Selvarajoo K, Giuliani A, Tsuchiya M (2007) Sequential logic model deciphers dynamic transcriptional control of gene expressions, PLoS One, 2, e776

03.Yachie N, Sekiyama K, Sugahara J, Ohashi Y, Tomita M (2007) Alignment-based approach for durable data storage into living organisms, Biotechnol Prog, 23, 501-505

04.Watanabe Y, Tomita M, Kanai A (2007) Computational methods for microRNA target prediction, Methods Enzymol, 427, 65-86

05.Watanabe Y, Kishi A, Yachie N, Kanai A, Tomita M (2007) Computational analysis of microRNA-mediated antiviral defense in humans, FEBS Lett, 581, 4603-4610

06.Tsuchiya M, Wong ST, Yeo ZX, Colosimo A, Palumbo MC, Farina L, Crescenzi M, Mazzola A, Negri R, Bianchi MM, Selvarajoo K, Tomita M, Giuliani A (2007) Gene expression waves. Cell cycle independent collective dynamics in cultured cells, FEBS J, 274, 2878-2886

07.Toya Y, Ishii N, Hirasawa T, Naba M, Hirai K, Sugawara K, Igarashi S, Shimizu K, Tomita M, Soga T (2007) Direct measurement of isotopomer of intracellular metabolites using capillary electrophoresis time-of-flight mass spectrometry for efficient metabolic flux analysis, J Chromatogr A, 1159, 134-141

08.Tamaki S, Arakawa K, Kono N, Tomita M (2007) Restauro-G: a rapid genome re-annotation system for comparative genomics, Genomics Proteomics Bioinformatics, 5, 53-58

09.Suzuki H, Saito R, Tomita M (2007) Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria, EURASIP Journal on Bioinformatics and Systems Biology, 2007, 61374

10.Sugiyama N, Masuda T, Shinoda K, Nakamura A, Tomita M, Ishihama Y (2007) Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications, Mol Cell Proteomics, 6, 1103-1109

11.Sugahara J, Yachie N, Arakawa K, Tomita M (2007) In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs, RNA, 13, 671-681

12.Soma A, Onodera A, Sugahara J, Kanai A, Yachie N, Tomita M, Kawamura F, Sekine Y (2007) Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae, Science, 318, 450-453

13.Soga T, Ishikawa T, Igarashi S, Sugawara K, Kakazu Y, Tomita M (2007) Analysis of nucleotides by pressure-assisted capillary electrophoresis-mass spectrometry using silanol mask technique, J Chromatogr A, 1159, 125-133

14.Sato T, Ishihama Y, Oda Y (2007) Quantitative proteomics of mouse brain and specific protein-interaction studies using stable isotope labeling, Methods Mol Biol, 359, 53-70

15.Robert M, Soga T, Tomita M (2007) E. coli metabolomics: capturing the complexity of a “simple” model., Metabolomics. Topics in Current Genetics., 18, 189-234

16.Rappsilber J, Mann M, Ishihama Y (2007) Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips, Nat Protoc, 2, 1896-1906

17.Piras V, Selvarajpp, K., Fujikawa, N., Choi, S., Tomita, M., Giuliani, A. and Tsuchiya M. (2007) Statistical Analysis of Gene Expression in Innate Immune Responses Dynamic Interactions between MicroRNA and Signaling Molecules., Genomics and Informatics, 5, 107-112

18.Ogawa T, Mori H, Tomita M, Yoshino M (2007) Inhibitory effect of phosphoenolpyruvate on glycolytic enzymes in Escherichia coli, Res Microbiol, 158, 159-163

19.Numata K, Okada Y, Saito R, Kiyosawa H, Kanai A, Tomita M (2007) Comparative analysis of cis-encoded antisense RNAs in eukaryotes, Gene, 392, 134-141

20.Murray DB, Lloyd D (2007) A tuneable attractor underlies yeast respiratory dynamics, Biosystems, 90, 287-294

21.Murray DB, Beckmann M, Kitano H (2007) Regulation of yeast oscillatory dynamics, Proc Natl Acad Sci U S A, 104, 2241-2246

22.Morohashi M, Shimizu K, Ohashi Y, Abe J, Mori H, Tomita M, Soga T (2007) P-BOSS: a new filtering method for treasure hunting in metabolomics, J Chromatogr A, 1159, 142-148

23.Morohashi M, Ohashi Y, Tani S, Ishii K, Itaya M, Nanamiya H, Kawamura F, Tomita M, Soga T (2007) Model-based definition of population heterogeneity and its effects on metabolism in sporulating Bacillus subtilis, J Biochem, 142, 183-191

24.Mori K, Saito R, Kikuchi S, Tomita M (2007) Inferring rules of Escherichia coli translational efficiency using an artificial neural network, Biosystems, 90, 414-420

25.Monton MR, Tomita M, Soga T, Ishihama Y (2007) Polymer entrapment in polymerized silicate for preparing highly stable capillary coatings for CE and CE-MS, Anal Chem, 79, 7838-7844

26.Monton MR, Soga T (2007) Metabolome analysis by capillary electrophoresis-mass spectrometry, J Chromatogr A, 1168, 237-246; discussion 236

27.Miyoshi F, Nakayama Y, Kaizu K, Iwasaki H, Tomita M (2007) A mathematical model for the Kai-protein-based chemical oscillator and clock gene expression rhythms in cyanobacteria, J Biol Rhythms, 22, 69-80

28.Matsuzaki Y, Kikuchi S, Tomita M (2007) Robust effects of Tsr-CheBp and CheA-CheYp affinity in bacterial chemotaxis, Artif Intell Med, 41, 145-150

29.Matsui M, Yachie N, Okada Y, Saito R, Tomita M (2007) Bioinformatic analysis of post-transcriptional regulation by uORF in human and mouse, FEBS Lett, 581, 4184-4188

30.Lloyd D, Murray DB (2007) Redox rhythmicity: clocks at the core of temporal coherence, Bioessays, 29, 465-473

31.Lee HJ, Chua GH, Krishnan A, Lane DP, Verma CS (2007) Substrate specificity of cyclins determined by electrostatics, Cell Cycle, 6, 2219-2226

32.Kuroki A, Ohtani N, Tsuge K, Tomita M, Itaya M (2007) Conjugational transfer system to shuttle giant DNA cloned by Bacillus subtilis genome (BGM) vector, Gene, 399, 72-80

33.Krishnan J, Selvarajoo, K., Tsuchiya, M., Lee, G. and Choi, S. (2007) Toll-like receptor signal transduction, Exp Mol Med, 39, 421-438

34.Krishnan A, Giuliani A, Zbilut JP, Tomita M (2007) Network scaling invariants help to elucidate basic topological principles of proteins, J Proteome Res, 6, 3924-3934

35.Krishnan A, Giuliani A, Tomita M (2007) Indeterminacy of reverse engineering of Gene Regulatory Networks: the curse of gene elasticity, PLoS One, 2, e562

36.Kotake Y, Sagane K, Owa T, Mimori-Kiyosue Y, Shimizu H, Uesugi M, Ishihama Y, Iwata M, Mizui Y (2007) Splicing factor SF3b as a target of the antitumor natural product pladienolide, Nat Chem Biol, 3, 570-575

37.Kochiwa H, Tomita M, Kanai A (2007) Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes, BMC Evol Biol, 7, 128

38.Kinoshita A, Tsukada K, Soga T, Hishiki T, Ueno Y, Nakayama Y, Tomita M, Suematsu M (2007) Roles of hemoglobin Allostery in hypoxia-induced metabolic alterations in erythrocytes: simulation and its verification by metabolome analysis, J Biol Chem, 282, 10731-10741

39.Kinoshita A, Nakayama Y, Kitayama T, Tomita M (2007) Simulation study of methemoglobin reduction in erythrocytes. Differential contributions of two pathways to tolerance to oxidative stress, FEBS J, 274, 1449-1458

40.Itoh H, Naito Y, Tomita M (2007) Simulation of developmental changes in action potentials with ventricular cell models, Syst Synth Biol, 1, 11-23

41.Ishii N, Suga Y, Hagiya A, Watanabe H, Mori H, Yoshino M, Tomita M (2007) Dynamic simulation of an in vitro multi-enzyme system, FEBS Lett, 581, 413-420

42.Ishii N, Nakayama Y, Tomita M (2007) Distinguishing enzymes using metabolome data for the hybrid dynamic/static method, Theor Biol Med Model, 4, 19

43.Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, Ho PY, Kakazu Y, Sugawara K, Igarashi S, Harada S, Masuda T, Sugiyama N, Togashi T, Hasegawa M, Takai Y, Yugi K, Arakawa K, Iwata N, Toya Y, Nakayama Y, Nishioka T, Shimizu K, Mori H, Tomita M (2007) Multiple high-throughput analyses monitor the response of E. coli to perturbations, Science, 316, 593-597

44.Ishihama Y, Wei FY, Aoshima K, Sato T, Kuromitsu J, Oda Y (2007) Enhancement of the efficiency of phosphoproteomic identification by removing phosphates after phosphopeptide enrichment, J Proteome Res, 6, 1139-1144

45.Ishihama Y (2007) Optimization of Nano-Liquid Chromatography Coupled with Mass Spectrometry for Proteomics, J Mass Spectrom Soc Jpn, 55, 157-164

46.Imami K, Monton MR, Ishihama Y, Terabe S (2007) Simple on-line sample preconcentration technique for peptides based on dynamic pH junction in capillary electrophoresis-mass spectrometry, J Chromatogr A, 1148, 250-255

47.Hu B, Tomita M (2007) The Hsp70 chaperone system maintains high concentrations of active proteins and suppresses ATP consumption during heat shock, Syst Synth Biol, 1, 47-58

48.Hashimoto M, Ishihama Y, Tomita M, Soga T (2007) Microelectrospray interface with coaxial sheath flow for high-resolution capillary electrophoresis/mass spectrometry separation, Rapid Commun Mass Spectrom, 21, 3579-3584

49.Fujishima K, Komasa M, Kitamura S, Suzuki H, Tomita M, Kanai A (2007) Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in the hyperthermophilic archaeon Pyrococcus furiosus, DNA Res, 14, 91-102

50.Baran R, Robert M, Suematsu M, Soga T, Tomita M (2007) Visualization of three-way comparisons of omics data, BMC Bioinformatics, 8, 72

51.Arakawa K, Uno R, Nakayama Y, Tomita M (2007) Validating the significance of genomic properties of Chi sites from the distribution of all octamers in Escherichia coli, Gene, 392, 239-246

52.Arakawa K, Tomita M (2007) Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes, Evol Bioinform Online, 3, 279-286

53.Arakawa K, Tomita M (2007) The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection, Evol Bioinform Online, 3, 159-168

54.Arakawa K, Saito R, Tomita M (2007) Noise-reduction filtering for accurate detection of replication termini in bacterial genomes, FEBS Lett, 581, 253-258

 
2006

01.Zbilut JP, Chua GH, Krishnan A, Bossa C, Colafranceschi M, Giuliani A (2006) Entropic criteria for protein folding derived from recurrences: six residues patch as the basic protein word, FEBS Lett, 580, 4861-4864

02.Yachie N, Numata K, Saito R, Kanai A, Tomita M (2006) Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model, Gene, 372, 171-181

03.Yachie N, Arakawa K, Tomita M (2006) On the interplay of gene positioning and the role of rho-independent terminators in Escherichia coli, FEBS Lett, 580, 6909-6914

04.Watanabe Y, Yachie N, Numata K, Saito R, Kanai A, Tomita M (2006) Computational analysis of microRNA targets in Caenorhabditis elegans, Gene, 365, 2-10

05.Wakabayashi Y, Kobayashi M, Akashi-Takamura S, Tanimura N, Konno K, Takahashi K, Ishii T, Mizutani T, Iba H, Kouro T, Takaki S, Takatsu K, Oda Y, Ishihama Y, Saitoh S, Miyake K (2006) A protein associated with toll-like receptor 4 (PRAT4A) regulates cell surface expression of TLR4, J Immunol, 177, 1772-1779

06.Uno R, Nakayama Y, Tomita M (2006) Over-representation of Chi sequences caused by di-codon increase in Escherichia coli K-12, Gene, 380, 30-37

07.Takahashi H, Hayashi M, Goto F, Sato S, Soga T, Nishioka T, Tomita M, Kawai-Yamada M, Uchimiya H (2006) Evaluation of metabolic alteration in transgenic rice overexpressing dihydroflavonol-4-reductase, Ann Bot, 98, 819-825

08.Sugahara J, Yachie N, Sekine Y, Soma A, Matsui M, Tomita M, Kanai A (2006) SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level, In Silico Biol, 6, 411-418

09.Soga T, Baran R, Suematsu M, Ueno Y, Ikeda S, Sakurakawa T, Kakazu Y, Ishikawa T, Robert M, Nishioka T, Tomita M (2006) Differential metabolomics reveals ophthalmic acid as an oxidative stress biomarker indicating hepatic glutathione consumption, J Biol Chem, 281, 16768-16776

10.Shinoda K, Yachie N, Masuda T, Sugiyama N, Sugimoto M, Soga T, Tomita M (2006) HybGFS: a hybrid method for genome-fingerprint scanning, BMC Bioinformatics, 7, 479

11.Shinoda K, Sugimoto M, Yachie N, Sugiyama N, Masuda T, Robert M, Soga T, Tomita M (2006) Prediction of liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome using artificial neural networks, J Proteome Res, 5, 3312-3317

12.Sakaya N, Kaneko S, Matsunaga S, Itaya M (2006) Experimental basis for a stable plasmid, pLS30, to shuttle between Bacillus subtilis species by conjugational transfer, J Biochem, 139, 557-561

13.Saito N, Robert M, Kitamura S, Baran R, Soga T, Mori H, Nishioka T, Tomita M (2006) Metabolomics approach for enzyme discovery, J Proteome Res, 5, 1979-1987

14.Saito H, Oda Y, Sato T, Kuromitsu J, Ishihama Y (2006) Multiplexed Two-Dimensional Liquid Chromatography for MALDI and Nanoelectrospray Ionization Mass Spectrometry in Proteomics, Journal of Proteome Research, 5, 1803-1807

15.Osada Y, Saito R, Tomita M (2006) Comparative analysis of base correlations in 5' untranslated regions of various species, Gene, 375, 80-86

16.Okada K, Takahashi M, Sakamoto T, Kawai G, Nakamura K, Kanai A (2006) Solution structure of a GAAG tetraloop in helix 6 of SRP RNA from Pyrococcus furiosus, Nucleosides Nucleotides Nucleic Acids, 25, 383-395

17.Okada K, Matsuda T, Sakamoto T, Muto Y, Yokoyama S, Kanai A, Kawai G (2006) 1H, 13C and 15N resonance assignments of the 2'-5' RNA ligase-like protein from Pyrococcus furiosus, J Biomol NMR, 36 Suppl 1, 16

18.Murata K, Mano N, Asakawa N, Ishihama Y (2006) Simplified gradient generator for micro- and nano-liquid chromatography, J Chromatogr A, 1123, 47-52

19.Monton MR, Terabe S (2006) Sample enrichment techniques in capillary electrophoresis: focus on peptides and proteins, J Chromatogr B Analyt Technol Biomed Life Sci, 841, 88-95

20.Matsubara Y, Kikuchi S, Sugimoto M, Tomita M (2006) Parameter estimation for stiff equations of biosystems using radial basis function networks, BMC Bioinformatics, 7, 230

21.Kono N, Arakawa K, Tomita M (2006) MEGU: pathway mapping web-service based on KEGG and SVG, In Silico Biol, 6, 621-625

22.Kochiwa H, Itaya M, Tomita M, Kanai A (2006) Stage-specific expression of Caenorhabditis elegans ribonuclease H1 enzymes with different substrate specificities and bivalent cation requirements, FEBS J, 273, 420-429

23.Kitayama T, Kinoshita A, Sugimoto M, Nakayama Y, Tomita M (2006) A simplified method for power-law modelling of metabolic pathways from time-course data and steady-state flux profiles, Theor Biol Med Model, 3, 24

24.Kanai A, Sato A, Imoto J, Tomita M (2006) Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein, Biochem J, 393, 373-379

25.Kanai A (2006) Importance of systematic identification of RNA-binding proteins in a hyperthermophilic archaeon., Viva Origino, 34, 144-147

26.Itaya M, Sakaya N, Matsunaga S, Fujita K, Kaneko S (2006) Conjugational transfer kinetics of pLS20 between Bacillus subtilis in liquid medium, Biosci Biotechnol Biochem, 70, 740-742

27.Ishii K, Washio T, Uechi T, Yoshihama M, Kenmochi N, Tomita M (2006) Characteristics and clustering of human ribosomal protein genes, BMC Genomics, 7, 37

28.Ishihama Y, Rappsilber J, Mann M (2006) Modular stop and go extraction tips with stacked disks for parallel and multidimensional Peptide fractionation in proteomics, J Proteome Res, 5, 988-994

29.Hu B, Mayer MP, Tomita M (2006) Modeling Hsp70-mediated protein folding, Biophys J, 91, 496-507

30.Fujita H, Samejima H, Kitagawa N, Mitsuhashi T, Washio T, Yonemoto J, Tomita M, Takahashi T, Kosaki K (2006) Genome-wide screening of dioxin-responsive genes in fetal brain: bioinformatic and experimental approaches, Congenit Anom (Kyoto), 46, 135-143

31.Chua GH, Krishnan A, Li KB, Tomita M (2006) Multiresolution analysis uncovers hidden conservation of properties in structurally and functionally similar proteins, J Bioinform Comput Biol, 4, 1245-1267

32.Baran R, Kochi H, Saito N, Suematsu M, Soga T, Nishioka T, Robert M, Tomita M (2006) MathDAMP: a package for differential analysis of metabolite profiles, BMC Bioinformatics, 7, 530

33.Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Mol Syst Biol, 2, 2006 0008

34.Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12, Genome Res, 16, 686-691

35.Arakawa KaT, M (2006) Large-scale Modeling for Systems Biology, BIOforum Europe, 10, 54-55

36.Arakawa K TM (2006) G-langage System as a platform for large-scale analysis of high-throughput omics data, Journal of Pesticide Science, 31, 282-288

37.Arakawa K, Yamada Y, Shinoda K, Nakayama Y, Tomita M (2006) GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes, BMC Bioinformatics, 7, 168

38.Arakawa K, Nakayama Y, Tomita M (2006) GPAC: benchmarking the sensitivity of genome informatics analysis to genome annotation completeness, In Silico Biol, 6, 49-60

 
2005

01.Yugi K, Nakayama Y, Kojima S, Kitayama T, Tomita M (2005) A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks, BMC Bioinformatics, 6, 299

02.Yugi K, Nakayama Y, Kinoshita A, Tomita M (2005) Hybrid dynamic/static method for large-scale simulation of metabolism, Theor Biol Med Model, 2, 42

03.Takahashi K, Arjunan SN, Tomita M (2005) Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico, FEBS Lett, 579, 1783-1788

04.Suzuki H, Saito R, Tomita M (2005) A problem in multivariate analysis of codon usage data and a possible solution, FEBS Lett, 579, 6499-6504

05.Sugimoto M, Kikuchi S Fau - Arita M, Arita M Fau - Soga T, Soga T Fau - Nishioka T, Nishioka T Fau - Tomita M, Tomita M (2005) Large-scale prediction of cationic metabolite identity and migration time in capillary electrophoresis mass spectrometry using artificial neural networks, />

06.Sugimoto M, Kikuchi S, Tomita M (2005) Reverse engineering of biochemical equations from time-course data by means of genetic programming, Biosystems, 80, 155-164

07.Ohtani N, Saito N, Tomita M, Itaya M, Itoh A (2005) The SCO2299 gene from Streptomyces coelicolor A3(2) encodes a bifunctional enzyme consisting of an RNase H domain and an acid phosphatase domain, FEBS J, 272, 2828-2837

08.Ohashi Y, Yamashiro A, Washio T, Ishii N, Ohshima H, Michishita T, Tomita M, Itaya M (2005) In silico diagnosis of inherently inhibited gene expression focusing on initial codon combinations, Gene, 347, 11-19

09.Nakayama Y, Kinoshita A, Tomita M (2005) Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition, Theor Biol Med Model, 2, 18

10.Kitagawa N, Washio T, Kosugi S, Yamashita T, Higashi K, Yanagawa H, Higo K, Satoh K, Ohtomo Y, Sunako T, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Tomita M (2005) Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa), Bioinformatics, 21, 1758-1763

11.Jaros M, Soga T, van de Goor T, Gas B (2005) Conductivity detection in capillary zone electrophoresis: inspection by PeakMaster, Electrophoresis, 26, 1948-1953

12.Ishihama Y (2005) Proteomic LC-MS systems using nanoscale liquid chromatography with tandem mass spectrometry, J Chromatogr A, 1067, 73-83

13.Inagaki S, Numata K, Kondo T, Tomita M, Yasuda K, Kanai A, Kageyama Y (2005) Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila, Genes Cells, 10, 1163-1173

14.Hoque MA, Ushiyama H, Tomita M, Shimizu K (2005) Dynamic responses of the intracellular metabolite concentrations of the wild type and pykA mutant Escherichia coli against pulse addition of glucose or NH3 under those limiting continuous cultures, Biochemical Engineering Journal, 26, 38-49

15.Fujimori S, Washio T, Tomita M (2005) GC-compositional strand bias around transcription start sites in plants and fungi, BMC Genomics, 6, 26

16.Arita M, Robert M, Tomita M (2005) All systems go: launching cell simulation fueled by integrated experimental biology data, Curr Opin Biotechnol, 16, 344-349

17.Arakawa K, Suzuki H, Fujishima K, Fujimoto K, Ueda S, Matsui M, Tomita M (2005) A comprehensive software suite for the analysis of cDNAs, Genomics Proteomics Bioinformatics, 3, 179-188

18.Arakawa K, Kono N, Yamada Y, Mori H, Tomita M (2005) KEGG-based pathway visualization tool for complex omics data, In Silico Biol, 5, 419-423

 
2004

01.Zhao J, Baba T, Mori H, Shimizu K (2004) Global metabolic response of Escherichia coli to gnd or zwf gene-knockout, based on 13C-labeling experiments and the measurement of enzyme activities, Appl Microbiol Biotechnol, 64, 91-98

02.Zhao J, Baba T, Mori H, Shimizu K (2004) Effect of zwf gene knockout on the metabolism of Escherichia coli grown on glucose or acetate, Metab Eng, 6, 164-174

03.Yugi K, Tomita M (2004) A general computational model of mitochondrial metabolism in a whole organelle scale, Bioinformatics, 20, 1795-1796

04.Yano Y, Saito R, Yoshida N, Yoshiki A, Wynshaw-Boris A, Tomita M, Hirotsune S (2004) A new role for expressed pseudogenes as ncRNA: regulation of mRNA stability of its homologous coding gene, J Mol Med (Berl), 82, 414-422

05.Yahagi N, Kosaki R, Ito T, Mitsuhashi T, Shimada H, Tomita M, Takahashi T, Kosaki K (2004) Position-specific expression of Hox genes along the gastrointestinal tract, Congenit Anom (Kyoto), 44, 18-26

06.Takahashi K, Kaizu K, Hu B, Tomita M (2004) A multi-algorithm, multi-timescale method for cell simulation, Bioinformatics, 20, 538-546

07.Suzuki H, Saito R, Tomita M (2004) The 'weighted sum of relative entropy': a new index for synonymous codon usage bias, Gene, 335, 19-23

08.Soga T, Kakazu Y, Robert M, Tomita M, Nishioka T (2004) Qualitative and quantitative analysis of amino acids by capillary electrophoresis-electrospray ionization-tandem mass spectrometry, Electrophoresis, 25, 1964-1972

09.Sato S, Soga T, Nishioka T, Tomita M (2004) Simultaneous determination of the main metabolites in rice leaves using capillary electrophoresis mass spectrometry and capillary electrophoresis diode array detection, Plant J, 40, 151-163

10.Qiu D, Mao L, Kikuchi S, Tomita M (2004) Sustained MAPK activation is dependent on continual NGF receptor regeneration, Dev Growth Differ, 46, 393-403

11.Qiu D, Fujita K, Sakuma Y, Tanaka T, Ohashi Y, Ohshima H, Tomita M, Itaya M (2004) Comparative analysis of physical maps of four Bacillus subtilis (natto) genomes, Appl Environ Microbiol, 70, 6247-6256

12.Ohtani N, Yanagawa H, Tomita M, Itaya M (2004) Identification of the first archaeal Type 1 RNase H gene from Halobacterium sp. NRC-1: archaeal RNase HI can cleave an RNA-DNA junction, Biochem J, 381, 795-802

13.Ohtani N, Yanagawa H, Tomita M, Itaya M (2004) Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7, Nucleic Acids Res, 32, 5809-5819

14.Melnick J, Lis E, Park JH, Kinsland C, Mori H, Baba T, Perkins J, Schyns G, Vassieva O, Osterman A, Begley TP (2004) Identification of the two missing bacterial genes involved in thiamine salvage: thiamine pyrophosphokinase and thiamine kinase, J Bacteriol, 186, 3660-3662

15.Kitamura-Abe S, Itoh H, Washio T, Tsutsumi A, Tomita M (2004) Characterization of the splice sites in GT-AG and GC-AG introns in higher eukaryotes using full-length cDNAs, J Bioinform Comput Biol, 2, 309-331

16.Itoh H, Washio T, Tomita M (2004) Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes, RNA, 10, 1005-1018

17.Itoh A, Ohashi Y, Soga T, Mori H, Nishioka T, Tomita M (2004) Application of capillary electrophoresis-mass spectrometry to synthetic in vitro glycolysis studies, Electrophoresis, 25, 1996-2002

18.Ishii N, Robert M, Nakayama Y, Kanai A, Tomita M (2004) Toward large-scale modeling of the microbial cell for computer simulation, J Biotechnol, 113, 281-294

19.Hua Q, Yang C, Oshima T, Mori H, Shimizu K (2004) Analysis of gene expression in Escherichia coli in response to changes of growth-limiting nutrient in chemostat cultures, Appl Environ Microbiol, 70, 2354-2366

20.Hoque MA, Siddiquee KAZ, Shimizu K (2004) Metabolic control analysis of gene-knockout Escherichia coli based on the inverse flux analysis with experimental verification, Biochemical Engineering Journal, 19, 53-59

21.Arita M, Ohashi Y (2004) Secret signatures inside genomic DNA, Biotechnol Prog, 20, 1605-1607

 
2003

01.Zhao J, Shimizu K (2003) Metabolic flux analysis of Escherichia coli K12 grown on 13C-labeled acetate and glucose using GC-MS and powerful flux calculation method, J Biotechnol, 101, 101-117

02.Yang C, Hua Q, Baba T, Mori H, Shimizu K (2003) Analysis of Escherichia coli anaplerotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates and phosphoenolpyruvate carboxykinase knockout, Biotechnol Bioeng, 84, 129-144

03.Takahashi K, Ishikawa N, Sadamoto Y, Sasamoto H, Ohta S, Shiozawa A, Miyoshi F, Naito Y, Nakayama Y, Tomita M (2003) E-Cell 2: multi-platform E-Cell simulation system, Bioinformatics, 19, 1727-1729

04.Soga T, Ohashi Y, Ueno Y, Naraoka H, Tomita M, Nishioka T (2003) Quantitative metabolome analysis using capillary electrophoresis mass spectrometry, J Proteome Res, 2, 488-494

05.Sato M, Umeki H, Saito R, Kanai A, Tomita M (2003) Computational analysis of stop codon readthrough in D.melanogaster, Bioinformatics, 19, 1371-1380

06.Sato A, Kanai A, Itaya M, Tomita M (2003) Cooperative regulation for Okazaki fragment processing by RNase HII and FEN-1 purified from a hyperthermophilic archaeon, Pyrococcus furiosus, Biochem Biophys Res Commun, 309, 247-252

07.Ozawa Y, Saito R, Washio T, Tomita M (2003) Comparative study of translation termination sites and release factors (RF1 and RF2) in procaryotes, J Mol Evol, 56, 665-672

08.Ohashi Y, Ohshima H, Tsuge K, Itaya M (2003) Far different levels of gene expression provided by an oriented cloning system in Bacillus subtilis and Escherichia coli, FEMS Microbiol Lett, 221, 125-130

09.Ohashi Y, Inaoka T, Kasai K, Ito Y, Okamoto S, Satsu H, Tozawa Y, Kawamura F, Ochi K (2003) Expression profiling of translation-associated genes in sporulating Bacillus subtilis and consequence of sporulation by gene inactivation, Biosci Biotechnol Biochem, 67, 2245-2253

10.Numata K, Kanai A, Saito R, Kondo S, Adachi J, Wilming LG, Hume DA, Hayashizaki Y, Tomita M, Group RG, Members GSL (2003) Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection, Genome Res, 13, 1301-1306

11.Miyoshi F, Nakayama Y, Tomita M (2003) [E-Cell simulation system and its application to the modeling of circadian rhythm], Seikagaku, 75, 5-16

12.Kikuchi S, Tominaga D, Arita M, Takahashi K, Tomita M (2003) Dynamic modeling of genetic networks using genetic algorithm and S-system, Bioinformatics, 19, 643-650

13.Kikuchi S, Fujimoto K, Kitagawa N, Fuchikawa T, Abe M, Oka K, Takei K, Tomita M (2003) Kinetic simulation of signal transduction system in hippocampal long-term potentiation with dynamic modeling of protein phosphatase 2A, Neural Netw, 16, 1389-1398

14.Kanai A, Oida H, Matsuura N, Doi H (2003) Expression cloning and characterization of a novel gene that encodes the RNA-binding protein FAU-1 from Pyrococcus furiosus, Biochem J, 372, 253-261

15.Jiao Z, Baba T, Mori H, Shimizu K (2003) Analysis of metabolic and physiological responses to gnd knockout in Escherichia coli by using C-13 tracer experiment and enzyme activity measurement, FEMS Microbiol Lett, 220, 295-301

16.Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin, II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J, Forum S (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics, 19, 524-531

17.Hua Q, Yang C, Baba T, Mori H, Shimizu K (2003) Responses of the central metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts, J Bacteriol, 185, 7053-7067

18.Fukuda Y, Nakayama Y, Tomita M (2003) On dynamics of overlapping genes in bacterial genomes, Gene, 323, 181-187

19.Fujimori S, Washio T, Higo K, Ohtomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Tomita M (2003) A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription, FEBS Lett, 554, 17-22

20.Arakawa K, Mori K, Ikeda K, Matsuzaki T, Kobayashi Y, Tomita M (2003) G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining, Bioinformatics, 19, 305-306

 
2002

01.Takahashi. K, Yugi. K, Hashimoto. K, Yamada. Y, Pickett. CJF, Tomita M (2002) Computational Challenges in Cell Simulation: A Software Engineering Approach, IEEE Intelligent Systems , 17, 64-71

02.Soga T, Ueno Y, Naraoka H, Ohashi Y, Tomita M, Nishioka T (2002) Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry, Anal Chem, 74, 2233-2239

03.Soga T, Ueno Y, Naraoka H, Matsuda K, Tomita M, Nishioka T (2002) Pressure-assisted capillary electrophoresis electrospray ionization mass spectrometry for analysis of multivalent anions, Anal Chem, 74, 6224-6229

04.Sakurai A, Fujimori S, Kochiwa H, Kitamura-Abe S, Washio T, Saito R, Carninci P, Hayashizaki Y, Tomita M (2002) On biased distribution of introns in various eukaryotes, Gene, 300, 89-95

05.Ozawa Y, Hanaoka S, Saito R, Washio T, Nakano S, Shinagawa A, Itoh M, Shibata K, Carninci P, Konno H, Kawai J, Hayashizaki Y, Tomita M (2002) Comprehensive sequence analysis of translation termination sites in various eukaryotes, Gene, 300, 79-87

06.Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schonbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y, Consortium F, I RGERGP, Team II (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs, Nature, 420, 563-573

07.Kosaki K, Kosaki R, Suzuki T, Yoshihashi H, Takahashi T, Sasaki K, Tomita M, McGinnis W, Matsuo N (2002) Complete mutation analysis panel of the 39 human HOX genes, Teratology, 65, 50-62

08.Kochiwa H, Suzuki R, Washio T, Saito R, Bono H, Carninci P, Okazaki Y, Miki R, Hayashizaki Y, Tomita M, Team RGERGPI (2002) Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data, Genome Res, 12, 1286-1293

09.Hashimoto K, Seno S, Dhar P, Tomita M (2002) Integrative modeling of gene expression and metabolism with E-CELL System, Artificial Life and Robotics, 6, 99-107

10.Fujita H, Kosaki R, Yoshihashi H, Ogata T, Tomita M, Hasegawa T, Takahashi T, Matsuo N, Kosaki K (2002) Characterization of the aryl hydrocarbon receptor repressor gene and association of its Pro185Ala polymorphism with micropenis, Teratology, 65, 10-18

 
2001

01.Tomita M (2001) Whole-cell simulation: a grand challenge of the 21st century, Trends Biotechnol, 19, 205-210

02.Tomita M (2001) Towards computer aided design (CAD) of useful microorganisms, Bioinformatics, 17, 1091-1092

03.Sakai H, Washio T, Saito R, Shinagawa A, Itoh M, Shibata K, Carninci P, Konno H, Kawai J, Hayashizaki Y, Tomita M (2001) Correlation between sequence conservation of the 5' untranslated region and codon usage bias in Mus musculus genes, Gene, 276, 101-105

04.Sakai H, Imamura C, Osada Y, Saito R, Washio T, Tomita M (2001) Correlation between Shine--Dalgarno sequence conservation and codon usage of bacterial genes, J Mol Evol, 52, 164-170

05.Ohno H, Sakai H, Washio T, Tomita M (2001) Preferential usage of some minor codons in bacteria, Gene, 276, 107-115

06.Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, Kiyosawa H, Kondo S, Yamanaka I, Saito T, Okazaki Y, Gojobori T, Bono H, Kasukawa T, Saito R, Kadota K, Matsuda H, Ashburner M, Batalov S, Casavant T, Fleischmann W, Gaasterland T, Gissi C, King B, Kochiwa H, Kuehl P, Lewis S, Matsuo Y, Nikaido I, Pesole G, Quackenbush J, Schriml LM, Staubli F, Suzuki R, Tomita M, Wagner L, Washio T, Sakai K, Okido T, Furuno M, Aono H, Baldarelli R, Barsh G, Blake J, Boffelli D, Bojunga N, Carninci P, de Bonaldo MF, Brownstein MJ, Bult C, Fletcher C, Fujita M, Gariboldi M, Gustincich S, Hill D, Hofmann M, Hume DA, Kamiya M, Lee NH, Lyons P, Marchionni L, Mashima J, Mazzarelli J, Mombaerts P, Nordone P, Ring B, Ringwald M, Rodriguez I, Sakamoto N, Sasaki H, Sato K, Schonbach C, Seya T, Shibata Y, Storch KF, Suzuki H, Toyo-oka K, Wang KH, Weitz C, Whittaker C, Wilming L, Wynshaw-Boris A, Yoshida K, Hasegawa Y, Kawaji H, Kohtsuki S, Hayashizaki Y, Team RGERGPI, the FC (2001) Functional annotation of a full-length mouse cDNA collection, Nature, 409, 685-690

 
2000

01.Uno R, Nakayama Y, Arakawa K, Tomita M (2000) The orientation bias of Chi sequences is a general tendency of G-rich oligomers, Gene, 259, 207-215

02.Tomita M, Hashimoto K, Takahashi K, Matsuzaki Y, Matsushima R, Saito K, Yugi K, Miyoshi F, Nakano H, Tanida S, Saito Y, Kawase A, Watanabe N, Simizu T, Nakayama Y (2000) The E-CELL project: Towards integrative simulation of cellular processes, New Generation Computing, 18, 1-12

03.Toda Y, Saito R, Tomita M (2000) Characteristic sequence pattern in the 5- to 20-bp upstream region of primate Alu elements, J Mol Evol, 50, 232-237

04.Saito R, Ozawa Y, Kuzuno N, Tomita M (2000) Computer analysis of potential stem structures of rRNA operons in various procaryote genomes, Gene, 259, 217-222

05.Goto M, Washio T, Tomita M (2000) Causal analysis of CpG suppression in the Mycoplasma genome, Microb Comp Genomics, 5, 51-58

06.Fukuda R, Hara J, Shankle WR, Tomita M (2000) Proposition of cortical connectivity between 30 cytoarchitectural areas of human cerebral cortex, Neurocomputing, 32–33, 749-755

 
1999

01.Tomita M, Wada M, Kawashima Y (1999) ApA dinucleotide periodicity in prokaryote, eukaryote, and organelle genomes, J Mol Evol, 49, 182-192

02.Tomita M, Hashimoto K, Takahashi K, Shimizu TS, Matsuzaki Y, Miyoshi F, Saito K, Tanida S, Yugi K, Venter JC, Hutchison CA, 3rd (1999) E-CELL: software environment for whole-cell simulation, Bioinformatics, 15, 72-84

03.Toda Y, Saito R, Tomita M (1999) Sequence patterns observed in 5' flanking regions of primate Alu elements, Ann N Y Acad Sci, 870, 369-374

04.Saito R, Tomita M (1999) On negative selection against ATG triplets near start codons in eukaryotic and prokaryotic genomes, J Mol Evol, 48, 213-217

05.Saito R, Tomita M (1999) Computer analyses of complete genomes suggest that some archaebacteria employ both eukaryotic and eubacterial mechanisms in translation initiation, Gene, 238, 79-83

06.Osada Y, Saito R, Tomita M (1999) Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes, Bioinformatics, 15, 578-581

07.Fukuda Y, Washio T, Tomita M (1999) Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae, Nucleic Acids Res, 27, 1847-1853

 
1998

01.Washio T, Sasayama J, Tomita M (1998) Analysis of complete genomes suggests that many prokaryotes do not rely on hairpin formation in transcription termination, Nucleic Acids Res, 26, 5456-5463

02.Toda Y, Saito R, Tomita M (1998) Comprehensive Sequence Analyses of 5' Flanking Regions of Primate Alu Elements, Genome Inform Ser Workshop Genome Inform, 9, 41-48

 
1997

01.Tomita M, Hashimoto K, Takahashi K, Shimizu T, Matsuzaki Y, Miyoshi F, Saito K, Tanida S, Yugi K, Venter JC, Hutchison CA (1997) E-CELL: Software Environment for Whole Cell Simulation, Genome Inform Ser Workshop Genome Inform, 8, 147-155

02.Toda Y, Tomita M (1997) Alu elements as an aid in deciphering genome rearrangements, Gene, 205, 173-176

03.Shimizu TS, Takahashi K, Tomita M (1997) CpG distribution patterns in methylated and non-methylated species, Gene, 205, 103-107