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Major Publications
In press

  01.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 Phytotaxonomica et Geobotanica. (In Press).


  02.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).


  03.Nakada T, Tsuchida Y, Arakawa K, Ito T and Tomita M. (2014) Hybridization between Japanese and North American Chlamydomonas reinhardtii (Volvocales, Chlorophyceae). Phycological Research. (In press). 


  04.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).



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).






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. Scientific Reports, 4, 7137 doi:10.1038/srep07137



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., Ayako Yachie-K., 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


  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 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



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.








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. 



01. Kosugi, S., Hasebe, M., Matsumura, N., Takashima, H., Miyamoto-Sato, E., Tomita, M. and Yanagawa, H. (2009) Six classes of nuclear localization signals specific to different binding grooves of importin alpha. J. Biol. Chem., 284(1), 478-485.

02. Tsuchiya, M.Selvarajoo, K., Piras, V., Tomita, M. and Giuliani, A. (2009) Local and Global responses in complex gene regulation networks. Physica A., 388(8), 1738-1746.

03. Shintani, T., Iwabuchi, T., Soga, T., Kato,Y., Yamamoto, T., Takano, N., Hishiki, T., Ueno, Y., Ikeda, S., Sakurakawa, T., Ishikawa, K., Goda, N., Yitagawa, Y., Kajiyama, M., Matsumoto, K. and Suematsu, M. (2009) Cystathionine β-synthase as a Carbon Monoxide-sensitive Regulator of Bile Excretion. Hepatology, 49, 141-150.

04. Kanai, A., Sato, A., Fukuda, Y., Okada, K., Matsuda, T., Sakamoto, T., Muto, Y., Yokoyama, S., Kawai, G. and Tomita, M. (2009) Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus. RNA,15(3), 420-431.

05. Yachie, N., Saito, R., Sugahara, J., Tomita, M. and Ishihama, Y. (2009) In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution. Mol. Cell. Proteomics, 8(5), 1061-1071.

06. Selvarajoo, K., Tomita, M. and Tsuchiya, M. (2009) Can complex cellular processes be governed by simple linear rules? J. Bioinform. Comput. Biol., 7(1), 243-268.

07. Fujishima, K., Sugahara, J., Kikuta, K., Hirano, R., Sato, A., Tomita, M. and 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. Proceedings of the National Academy of Sciences U. S. A., 106(8), 2683-7.

08. Tsuchiya, M., Piras, V., Choi, S., Akira, S., Tomita, M., Giuliani, A. and Selvarajoo, K. (2009) Emergent genome-wide control in wildtype and genetically mutated lipopolysaccarides-stimulated macrophages. PLoS One, 4(3), e4905.

09. Nock, A., Ascano, J. M., Jones, T., Barrero, M. J., Sugiyama, N., Tomita, M., Ishihama, Y. and Malik, S. (2009) Identification of DNA-dependent protein kinase DNA-PK as a cofactor for he forkhead transcription factor FOXA2. J. Biol. Chem., 284, 19915-26.

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

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

12. Iwasaki, M., Masuda, T., Tomita, M., and Ishihama, Y. (2009) Chemical Cleavage-Assisted Tryptic Digestion for Membrane Proteome Analysis. J. Proteome Res., 8, 3169-3175.

13. 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(23), 15549-15556.

14. Shintani, T., Iwabuchi, T., Soga, T., Kato,Y., Yamamoto, T., Takano, N., Hishiki, T., Ueno, Y., Ikeda, S., Sakurakawa, T., Ishikawa, K., Goda, N., Kitagawa, Y., Kajiyama, M., Matsumoto, K., Suematsu, M. (2009) Cystathionine β-synthase as a Carbon Monoxide-sensitive Regulator of Bile Excretion. Hepatology, 49, 141-150.

15. Ravichandran, A., Sugiyama, N., Tomita, M., Swarup, S. and Ishihama, Y. (2009) Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non-pathogenic Pseudomonas species. Proteomics, 9(10), 2764-2775.

16. Hirayama, A., Kami, K., Sugimoto, M., Sugawara, M., Toki, N., Onozuka, H., Kinoshita, T., Saito, N., Ochiai, A., Tomita, M., Esumi, H. and Soga, T. (2009) Quantitative Metabolome Profiling of Colon and Stomach Cancer Microenvironment by Capillary Electrophoresis Time-of-Flight Mass Spectrometry. Cancer Res., 69(11), 4918-4925.

17. Soga, T., Igarashi, K., Ito, C., Mizobuchi, K., Zimmermann, H. and Tomita, M. (2009) Metabolomic Profiling of Anionic Metabolites by Capillary Electrophoresis Mass Spectrometry. Anal. Chem. 81: 6165-6174.

18. Kosugi, S., Hasebe, M., Tomita, M. and 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(25), 10171-10176.

19. Minami, Y., Kasukawa, T., Kakazu, Y., Iigo, M.,Sugimoto, M., Ikeda, S., Yasui, A., van der Horst, G., Soga, T. and Ueda, H. (2009) Measurement of Internal Body Time by Blood Metabolomics. Proc. Natl. Acad. Sci. U.S.A., 106(24), 9890-9895.

20. 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. and Handa, H. (2009) Mono-(2-ethylhexyl) phthalate Targets Glycogen Debranching Enzyme and Affects Glycogen Metabolism in Rat Testis. Toxicol sci., 109, 143-151.

21. Nishino, T., Yachie-Kinoshita, A., Hirayama, A., Soga, T., Suematsu, M. and Tomita, M. (2009) In silico modeling and metabolome analysis of long-stored erythrocytes to improve blood storage methods. J. Biotechnol.,144(3), 212-223.

22. Arjunan, S.N. and Tomita, M. (2009) Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System. Int. J. Comp. Sci. and Inform. Security, 3(1).

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

24. Masuda, T., Saito, N., Tomita, M. and Ishihama, Y. (2009) Unbiased quantitation of Escherichia coli membrane proteome using phase-transfer surfactants. Mol. Cell Proteomics., 8(12), 2770-2777.

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

26. Sugahara, J., Fujishima, K., Morita, K., Tomita, M. and Kanai, A. (2009) Disrupted tRNA Gene Diversity and Possible Evolutionary Scenarios. J. Mol. Evol., (epub ahead of print)

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

28. Tajima, T., Goda, N., Fujiki, N., Hishiki, T., Nishiyama, Y., Senoo-Matsuda, N., Shimazu, M., Soga, T., Yoshimura, Y., Johnson, R.S. and Suematsu, M. (2009) HIF-1α is necessary to support gluconeogenesis during liver regeneration. Biochem. Bioph. Res. Co., 387, 789-794.

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

30. Kono, N., Arakawa, K., Ogawa, R., Kido, N., Oshita, K., Ikegami, K., Tamaki, S. and Tomita, M. (2009) Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API. PLoS One, 4(11), e7710.

31. Arakawa, K., Suzuki, H., and 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.

32. Toyohara, T., Suzuki, T., Morimoto, R., Akiyama, Y., Souma, T., Shiwaku, H.O., 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., Tetasaki, T., Goto, J., Ito, S., Hishinuma, T., Rubera, I., Tauc, M., Fujii-Kuriyama, Y., Yabuuchi, H., Moriyama, Y., Soga, T. and Abe, T. (2009) SLCO4C1 transporter  eliminates uremic toxins preventing hypertension and renal inflammation J. Am. Soc. Nephrol., 20(12), 2546-2555.    

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

34. Arakawa, K., Suzuki, H. and Tomita, M. (2009) Computational Genome Analysis Using The G-language System. Genes, Genomes and Genomics, 2(1), 1-13.

35. Kaneko, S., Takeuchi, T. and Itaya, M. (2009) Genetic connection of two contiguous bacterial artificial chromosomes using homologous recombination in Bacillus subtilis genome vector. J. Biotechnol., 139(3), 211-213

36. Nakagawa, Y., Yugi, K., Tsuge, K., Itaya, M., Yanagawa, H. and Sakakibara, Y. (2009) Operon structure optimization by random self-assembly. Nat. Comp. 9(1), 173-181.

37. Asai, N., Nishioka, T., Takabayashi, J. and 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(4), 294-300.

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

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


01. Ogawa, Y., Arakawa, K., Kaizu, K., Miyoshi, F., Nakayama, Y. and Tomita, M. Comparative study of circadian oscillatory network models of Drosophila. , Artif. Life , 14(1) , 29-48.

02. Matsubara, Y., Kikuchi, S., Sugimoto, M., Oka, K. and Tomita, M. Algebraic method for the analysis of signaling crosstalk. , Artif. Life. , 14(1) , 81-94.

03. Ohno, H., Naito, Y., Nakajima, H. and Tomita, M Comstruction of at Biological Tissue Model based on a Single-Cell Model: A Computer Simulation of Metabolic Heterogeneity in the Liver Lobule. , Artif. Life. , 14(1) , 3-28.

04. Itaya, M., Fujita, K., Kuroki, A. and Tsuge, K. Bottom-up genome assembly using the Bacillus subtilis genome vector. , Nature methods. , 5(1) , 41-43.

05. Imami, K., Sugiyama, N., Kyono, Y., Tomita, M. and Ishihama, Y. Automated Phosphoproteome Analysis for Cultured Cancer Cells by Two-Dimensional NanoLC-MS using a Calcined Titania/C18 Biphasic Column. , Anal. Sci. , 24(1) , 161.

06. Ohashi, Y., Hirayama, A., Ishikawa, T., Nakamura, S., Shimizu, K., Ueno, Y., Tomita, M. and Soga, T. Depiction of metabolome changes in histidine-starved Escherichia coli by CE-TOFMS. , Mol. BioSyst. , 4 , 135-47

07. Kuroki, A., Toda, T., Matsui, K., Uotsu-Tomita, R., Tomita, M. and Itaya, M. Reshuffling of the Bacillus subtilis 168 genome by multifold inversion. , J. Biochem. , 143(1) , 97-105

08. Krishnan, A., Zbilut, P.J., Tomita, M and Giuliani, A. Proteins as Networks: Usefulness of Graph Theory in Protein Science. , Curr. Protein Pept. Sci. , 9(1) , 28-38.

09. Masuda, T., Tomita, T. and Ishihama, Y. Phase Transfer Surfactant-Aided Trypsin Digestion for Membrane Proteome Analysis. , J. Proteome Res. , 7(2) , 731-40.

10. Shinoda, K., Sugimoto, M., Tomita, M. and Ishihama, Y. Informatics for Peptide Retention Properties in Proteomic LC-MS. , Proteomics. , 8(4) , 787-98.

11. Ishihama, Y., Schmidt, T., Rappsilber, J., Mann, M., Hartl, F.U., Kerner, M.J. and Frishman, D. Protein abundance profiling of the Escherichia coli cytosol. , BMC Genomics. , 9(1) , 102

12. Fujishima, K., Sugahara, J., Tomita, M. and Kanai A. Sequence Evidence in the Archaeal Genomes that tRNAs emerged Through the Combination of Ancestral Genes as 5' and 3' tRNA Halves , PLoS ONE. , 3(2) , e1622.

13. Laborde, T., Tomita, M. and Krishnan A. GANDivAWeb: A Web Server for detecting early folding units ('foldons') from protein 3D structures. , BMC Struct. Biol. , 8(15)

14. Ishii, K., Nakamura, S., Morohashi, M., Sugimoto, M., Ohashi, Y., Kikuchi, S. and Tomita, M. (2008) Comparison of meetabolite roduction capability indices generated by networrk analysis methods. , Biosystems. , 91(1) , 166-170.

15. Krishnan, A., Giuliani, A. and Tomita, M. Evolution of Gene Regulatory Networks: Robustness as an emergent property of evolution. , Physica A. , 387(8-9) , 2170-86.

16. Okada, Y., Tashiro, C., Numata, K., Watanabe, K., Nakaoka, H., Yamamoto, N., Okubo, K., Ikeda, R., Saito, R., Kanai, A., Abe, K., Tomita, M. and Kiyosawa, H. Comparative expression analysis uncovers novel features of endogenous antisense transcription. , Hum. Mol. Genet. , 17(11) , 1631-40.

17. Krishnan, A., Giuliani, A., Zbilut, J. P. and Tomita, M. Implications from a Network-Based Topological Analysis of Ubiquitin Unfolding Simulations. , PLoS ONE. , 3(5) , e2149.

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

19. Sato, S., Arita, M., Soga, T. , Nishioka, T. and Tomita, M. Time-resolved metabolomics reveals metabolic modulation in rice foliage. , BMC Systems Biology. , 2 , 51.

20. Yoshida, S., Imoto, J., Minato, T., Oouchi, R., Sugihara, M., Imai, T., Ishigro, T., Mizutani, S., Tomita, M., Soga, T. and Yoshimoto, H. Developing Bottom-fermenting Yeast Strains That Prooduce High SO2 Levels by Integrated Metabolome and Transcriptome Analysis. , Appl. Environ. Microbiol. , 74 , 2787-96.

21. Imami, K., Ishihama, Y. and Tarabe, S. On-line selective enrichment and ion-pair reaction for structural determination of sulfated glycopeptides by capillary electrophoresis-mass spectrometry. , J. Chromatogr. A. , 1194(2) , 237-42.

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

23. Kyono, Y., Sugiyama, N., Imami, K., Tomita, M. and Ishihama, Y. Successive and Selective Release of Phosphrylated Peptides Captured by Hydroxy Acid-Modified Metal Oxide Chromatograpy. , J. Proteome Res. , 7(10) , 4585-93.

24. Kosugi, S., Hasebe, M., Entani, T., Takayama, S., Tomita, M. and Yanagawa, H. Design of Peptide Inhibitors for the Importin alpha/beta Nuclear Import Pathway by Activity-Based Profiling. , Chemistry & Biology , 15 , 940-49.

25. Fujishima, K., Komasa, M., Kitamura, S., Tomita, M. and Kanai, A. Comparison and Characterization of Proteomes in the Three Domains of Life Using 2D Correlation Analysis. , Progress of Theoretical Physics. , Supplement No.173 , 206-18

26. Watanabe, Y., Tomita, M. and Kanai, A. Perspective in the Evolution of Human MicroRNAs : Copy Number Expansion and Acquisition of Target Gene Speciallization. , Progress of Theoretical Physics. , Supplement No.173 , 219-28

27. Kosugi, S., Hasebe, M., Tomita, M. and Yanagawa, H. Nuclear Export Signal Consensus Sequences Defined Using a Localization-Based Yeast Selection System. , Traffic.

28. Sugahara, J., Kikuta, K., Fujishima, K., Yachie, N., Tomita, M. and Kanai, A. Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order Thermoproteales. , Molecular Biology and Evolution. , 25(12) , 2709-16

29. Selvarajoo, K., Takabe, Y., Gohda, J., Helmy, M., Akira, S., Tomita, M., Tsuchiya, M., Inoue, J. and Matsuo, K. Signaling Flux Redistribution at Toll-like Recepter Pathway Junctions. , PLoS ONE , 3(10) , e3430.

30. Ohtani, N., Tomita, M. and Itaya, M. Junction ribonuclease: a ribonuclease HII orthologue from Thermus thermophilus HB8 prefers the RNA-DNA junction to the RNA/DNA heteroduplex. , Biochem. J. , 412(3) , 517-26.

31. Ohtani, N., Sato, M., Tomita, M. and Itaya, M. Restriction on conjugational transfer of pLS20 in Bacillus subtilis 168. , Biosci. Biotechnol. Biochem. , 72(9) , 2472-5.

32. Ohtani, N., Tomita, M. and Itaya, M. Junction ribonuclease activity specified in RNases HII/2. , FEBS J. , 275(21) , 5444-55.

33. Horai, H. and Nishioka, T. Automatic Generation of Structure of Phospholipids. , Journal of Computer Aided Chemistry. , 9 , 55-61.

34. Sagane, K., Ishihama, Y. and Sugimoto, H. LGI1 and LGI4 bind to ADAM22, ADAM23 and ADAM11. , Int. J. Biol. Sci. , 4(6) , 387-96.

35. Miyamoto, K., Hara, T., Kobayashi, H., Morisaka, H., Tokuda, D., Horie, K., Koduki, K., Makino, S., Núñez, O., Yang, C., Kawabe, T., Ikegami, T., Takubo, H., Ishihama, Y. and Tanaka, N. High-efficiency liquid chromatographic separation utilizing long monolithic silica capillary columns. , Anal. Chem. , 80(22) , 8741-50.

36. Shinoda, K., Tomita, M., Ishihama, Y. Aligning LC Peaks by Converting Gradient Retention Times to Retention Index of Peptides in Proteomic Experiments. , Bioinformatics. , 24(14) , 1590-5.

37. Ishihama, Y. Molecular dynamics in cellular signal transduction systems. , J. Jpn. Soc. Mechanical Engineers. , 111(7) , 578-81.

38. Ishihama, Y. NanoLC-MS systems in proteomics. , Chromatography. , 29 , 25-31.

39. Tsuchiya D., Shimizu N., and Tomita M. Versatile architecture of a bacterial aconitase B and its catalytic performance in the sequential reaction coupled with isocitrate dehydrogenase. , BBA - Proteins and Proteomics. , 1784 , 1847-56.

40. Kratz, A., Tomita, M. and Krishnan, A. GeNESiS: gene network evolution simulation software. , BMC Bioinformatics. , 9 , 541.

41. Yachie, N., Ohashi, Y. and Tomita, M. Stabilizing synthetic data in the DNA of living organisms. , Syst. Synth. Biol. 2(1-2), 19-25.

42. Sato, D., Yamagata W., Harada, S. and 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 Journal. 275(3) 548–560.

43. Sato, D., Karaki, T., Shimizu, A., Kamei, K., Harada S. and Nozaki, T. (2008) Crystallization and preliminary X-ray analysis of L-methionine gamma-lyase 1 from Entamoeba histolytica., Acta Crystallographica Section F. 64(Pt 8) 697-699.

44. Aon, MA., Roussel, MR., Cortassa, S., O'Rourke, B., Murray, D.B., Beckmann, M. and  Lloyd, D. (2008) The scale-free dynamics of eukaryotic cells., PLoS ONE. 3(11):e3624.

45. Yoshida, S., Imoto, J., Minato, T., Oouchi, R., Sugihara, M., Imai, T., Ishiguro, T., Mizutani, S., Tomita, M., Soga, T., and Yoshimoto, H. (2008) Development of Bottom-fermenting Saccharomyces Strains That Produce High SO2 Levels, Using Integrated Metabolome and Transcriptome Analysis. Appl. Environ. Microbiol. 74: 2787-96.



01. Zbilut, J. P., Chua, G. H., Krishnan, A., Bossa, C., Rother, K., Webber, C. L., Jr. and Giuliani, A. (2007) A topologically related singularity suggests a maximum preferred size for protein domains. Proteins, 66(3), 621-9.

02. Yachie, N., Sekiyama, K., Sugahara, J., Ohashi, Y. and Tomita, M. (2007) Alignment-based approach for durable data storage into living organisms. Biotechnol. Prog., 23(2), 501-5.

03. Sugahara, J., Yachie, N., Arakawa, K. and Tomita, M. (2007) In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs. RNA, 13(5), 671-81.

04. Numata, K., Okada, Y., Saito, R., Kiyosawa, H., Kanai, A. and Tomita, M. (2007) Comparative analysis of cis-encoded antisense RNAs in eukaryotes. Gene, 392(1-2), 134-41.

05. Miyoshi, F., Nakayama, Y., Kaizu, K., Iwasaki, H. and Tomita, M. (2007) A mathematical model for the Kai-protein-based chemical oscillator and clock gene expression rhythms in cyanobacteria. J. Biol. Rhythms., 22(1), 69-80.

06. Kinoshita, A., Tsukada, K., Soga, T., Hishiki, T., Ueno, Y., Nakayama, Y., Tomita, M. and 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(14), 10731-41.

07. Kinoshita, A., Nakayama, Y., Kitayama, T. and Tomita, M. (2007) Simulation study of methemoglobin reduction in erythrocytes. Differential contributions of two pathways to tolerance to oxidative stress.FEBS J., 274(6), 1449-58.

08. Ishii, N., Suga, Y., Hagiya, A., Watanabe, H., Mori, H., Yoshino, M. and Tomita, M. (2007) Dynamic simulation of an in vitro multi-enzyme system. FEBS Lett., 581(3), 413-20.

09. Arakawa, K., Saito, R. and Tomita, M. (2007) Noise-reduction filtering for accurate detection of replication termini in bacterial genomes. FEBS Lett., 581(2), 253-8.

10. Arakawa, K., Uno, R., Nakayama, Y. and Tomita, M. (2007) Validating the significance of genomic properties of Chi sites from the distribution of all octamers in Escherichia coli. Gene, 392(1-2), 239-46.

11. Baran, R., Robert, M., Suematsu, M., Soga, T. and Tomita, M. (2007) Visualization of three-way comparisons of omics data. BMC Bioinformatics, 8(1), 72.

12. 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. and Tomita, M. (2007) Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science, 316(5824), 593-7.

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

14. Tsuchiya, M., Wong, ST., Yeo, ZX., Colosimo, A., Palumbo, MC., Farina, L., Crescenzi, M., Mazzola, A., Negri, R., Bianchi, MM., Selvarajoo, K., Tomita, M. and Giuliani, A. (2007) Gene expression waves. Cell cycle independent collective dynamics in cultured cells. FEBS J., 274(11), 2878-86.

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

16. Sugiyama, N., Masuda, T., Shinoda, K., Nakamura, A., Tomita, M. and 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(6), 1103-9.

17. Ishii, N., Nakayama, Y. and Tomita, M. (2007) Distinguishing enzymes using metabolome data for the hybrid dynamic/static method. Theor. Biol. Med. Model., 4(1), 19.

18. Tamaki, A., Arakawa, K., Kono, N. and Tomita, M. (2007) Restauro-G: A rapid genome re-annotation system for comparative genomics. Genomics Proteomics Bioinformatics, 5(1), 53-8.

19. Krishnan, A., Giuliani, A., Tomita, M. (2007) Indeterminacy of Reverse Engineering of Gene Regulatory Networks: The Curse of Gene Elasticity. PLoS ONE, 2(6), e562.

20. Kuroki, A., Ohtani, N., Tsuge, K., Tomita, M. and Mitsuhiro Itaya, M. (2007) Conjugational transfer system to shuttle giant DNA cloned by Bacillus subtilis genome (BGM) vector. Gene, 399(1), 72-80.

21. Fujishima, K., Komasa, M., Kitamura, S. Suzuki, H., Tomita, M. and 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 Research, 14(3),91-102.

22. Kochiwa, H., Tomita, M. and Kanai, A. (2007) Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes. BMC Evol. Biol., 7(1), 128.

23. Morohashi, M., Shimizu, K., Ohashi, Y., Abe, J., Mori, H., Tomita, M., and Soga, T. (2007) P-BOSS: A new filtering method for treasure hunting in metabolomics. J. Chromatogr. A., 1159(1-2), 142-8.

24. Toya Y., Ishii, N., Hirasawa, T., Naba, M., Hirai, K., Sugawara, K., Igarashi, S., Shimizu, K., Tomita, M., and 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(1-2) , 134-41

25. Soga, T., Ishikawa, T., Igarashi, S., Sugawara, K., Kakazu, Y. and Tomita, M. (2007) Analysis of nucleotides by pressure-assisted capillary electrophoresis-mass spectrometry using silanol mask technique. , J. Chromatogr. A. , 1159(1-2) , 125-33

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

27. Yeo, Z.X., Wong, S.T., Arjunan,S., Piras, V., Tomita, M., Selvarajoo, K., Giuliani, A. and Tsuchiya, M. (2007) Sequential Logic Model Deciphers Dynamic Transcriptional Control of Gene Expressions. , PLoS ONE , 2(8) , e776.

28. Matsui, M. Yachie, N., Okada, Y., Saito, R. and Tomita, M. (2007) Bioinformatic analysis of human and mouse post-transcriptional regulation by uORFs. , FEBS Letters. , 581(22) , 4184-8.

29. Krishnan, J., Selvarajoo, K., Tsuchiya, M., Lee, G. and Choi, S. (2007) Toll-like receptor signal transduction. , Exp. Mol. Med. , 39(4) , 421-38.

30. Watanabe, Y., Tomita, M. and Kanai, A. (2007) Computational Methods for MicroRNA Target Prediction. , Methods in Enzymology. , 427 , 65-68.

31. Watanabe, Y., Kishi, A., Yachie, N., Kanai, A. and Tomita, M. (2007) Computational analysis of microRNA-mediated antiviral defense in humans. , FEBS Letters. , 581(24) , 4603-10

32. Monton, R. M. N., Tomita, M., Soga, T., and Ishihama, Y. (2007) Polymer Entrapment in Polymerized Silicate for Preparing Highly Stable Capillary Coatings in CE and CE-MS. , Anal. Chem. , 79 , 7838-44

33. Krishnan, A., Giuliani, A., Zbilut, J. P. and Tomita, M. (2007) Network Scaling Invariants Help to Elucidate Basic Topological Principles of Proteins. , J. Proteome. Res. , 6 , 3924-34

34. Mori, K., Saito, R., Kikuchi, S. and Tomita M. (2007) Inferring Rules of Escherichia coli Translational Efficiency using an Artificial Neural Network. , Biosystems. , 90(2) , 414-20

35. 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(3) , 107-12

36. Hashimoto, M., Ishihama, Y., Tomita, M. and Soga, T. (2007) Microelectrospray Interface with Coaxial Sheath Flow for High Resolution CE-MS Separation. , Rapid Communications in Mass Spectorometry. , 21(22) , 3579-84

37. Arakawa, K. and Tomita, M. (2007) The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection. , Evolutionary Bioinformatics. , 3 , 145-154

38. Arakawa, K. and Tomita, M. (2007) Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes. , Evolutionary Bioinformatics. , 3 , 279-86

39. Matsuzaki, Y., Kikuchi, S. and Tomita, M. (2007) Robust Effects of Tsr-CheBp and CheA-CheYp Affinity in Bacterial Chemotaxis. , Artificial intelligence in medicine. , 41(2) , 145-150

40. Soma, A., Onodera, A., Sugahara, J., Kanai, A., Yachie, N., Tomita, M., Kawamura, F. and Sekine, Y. (2007) Permuted tRNA Genes Expressed via a Circular RNA Intermediate in Cyanidioschyzon merolae. , Science , 318(5849) , 450-453

41. Morohashi, M., Ohashi, Y., Tani, S., Ishii, K., Itaya, M., Nanamiya, H., Kawamura, F., Tomita, M. and Soga, T. (2007) Model based definition of population heterogeneity and its effects on metabolism in sporulating > Bacillus subtilis , J. Biochem. , 142(2) , 183-91

42. Jun, H., Chua, H.G., Krishnan, A., P.Lane, D. and Verma, C. (2007) Substrate specificity of cyclins determined by electrostatics. , Cell Cycle , 6 , 2219-26

43. Suzuki, H., Saito, R. and Tomita, M. (2007) Variation in the Correlation of G+C Composition with Synonymous Codon Usage Bias among Bacteria. , EURASIP J. Bioinform. Syst. Biol. , 2007 , 61374

44. Ogawa, T., Mori, H., Tomita, M and Yoshino, M. (2007) Inhibitory effect of phosphoenolpyruvate on glycolytic enzyme in Escherichia Coli. , Res. Microbiol. , 158 (2) , 159-63

45. Monton, M. R. N. and Soga, T (2007) Metabolome analysis by Capillary Electrophoresis-Mass Spectrometry. , J. Chromatogr. A , 1168 , 237-246

46. Imami, K., Monton, M. R, Ishihama, Y. and Tarabe, S. Simple on-line preconcentration technique for peptides based on dynamic pH junction in capillary electrophoresis – mass spectrometry. , J. Chromatogr. A , 1148 , 250-5

47. Robert, M., Soga, T., and Tomita, M. E. coli metabolomics: capturing the complexity of a “simple” model. In: Metabolomics, A Powerful Tool in Systems Biology. , Topics in Current Genetics. , 18 , J. Nielsen, M. C. Jewett (Eds.)

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

49. Kotake, Y., Sagane, K., Owa, T., Mimori-Kiyosue, Y., Shimizu, H., Uesugi, M., Ishihama, Y., Iwata, M. and Mizui, Y. Splicing factor SF3b as a target of the antitumor natural product pladienolide. , Nat. Chem. Biol. , 3 , 570-5

50. Ishihama, Y., Wei, F. Y., Aoshima, K., Sato, T., Kuromitsu, J. and Oda, Y. Enhancement of the efficiency of phosphoproteomic identification by removing phosphates after phosphopeptide enrichment. , J. Proteome Res. , 6 , 1139-44.

51. Ishihama, Y. Optimization of Nano-Liquid Chromatography Coupled with Mass Spectrometry for Proteomics. , J. Mass Spectrom. Soc. Jpn. , 55(3) , 157-164.

52. Asti KG., Bastos-Filho JB., 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. Web era Theatrum Mundi: Another Big Chill in Science? , Alliage. , 61 , 41-46

53. Murray, D.B. and Lloyd ,D. (2007) A tuneable attractor underlies yeast respiratory dynamics. , BioSystems, 90(1):287-94.

54. Murray, D.B., Beckmann ,M . and Kitano, H. (2007) Regulation of yeast oscillatory dynamics. , Proc Natl Acad Sci U S A, 104(7):2241-6.

55. Lloyd, D. and Murray, D.B. (2007) Redox rhythmicity: clocks at the core of temporal coherence. , BioEssays, 29(5):465-473.

56. Morohashi, M., Ohashi, Y., Tani S., Ishii, K., Itaya, M., Nanamiya, H., Kawamura, F.,  Tomita, M., and Soga, T. (2007) Model-based definition of population heterogeneity and its effects on metabolism in sporulating Bacillus subtilis. J. Biochem. 142: 183-91. 


01.Zbilut, J. P., Chua, G. H., Krishnan, A., Bossa, C., Colafranceschi, M. and Giuliani, A. (2006) Entropic criteria for protein folding derived from recurrences: six residues patch as the basic protein word, FEBS Lett, 580, 4861-4

02.Yachie, N., Numata, K., Saito, R., Kanai, A. and Tomita, M. (2006) Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model, Gene, 372, 171-81

03.Yachie, N., Arakawa, K. and Tomita, M. (2006) On the interplay of gene positioning and the role of rho-independent terminators in Escherichia coli, FEBS Lett, 580, 6909-14

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

05.Uno, R., Nakayama, Y. and Tomita, M. (2006) Over-representation of Chi sequences caused by di-codon increase in Escherichia coli K-12, Gene, 380, 30-7

06.Sugahara, J., Yachie, N., Sekine, Y., Soma, A., Matsui, M., Tomita, M. and Kanai, A. (2006) SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level, In Silico Biol, 6, 411-8

07.Soga, T., Baran, R., Suematsu, M., Ueno, Y., Ikeda, S., Sakurakawa, T., Kakazu, Y., Ishikawa, T., Robert, M., Nishioka, T. and Tomita, M. (2006) Differential metabolomics reveals ophthalmic acid as an oxidative stress biomarker indicating hepatic glutathione consumption, J Biol Chem, 281, 16768-76

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

09.Shinoda, K., Sugimoto, M., Yachie, N., Sugiyama, N., Masuda, T., Robert, M., Soga, T. and 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, 3312-7

10.Saito, N., Robert, M., Kitamura, S., Baran, R., Soga, T., Mori, H., Nishioka, T. and Tomita, M. (2006) Metabolomics approach for enzyme discovery, J Proteome Res, 5, 1979-87

11.Osada, Y., Saito, R. and Tomita, M. (2006) Comparative analysis of base correlations in 5' untranslated regions of various species, Gene, 375, 80-6

12.Okada, K., Takahashi, M., Sakamoto, T., Kawai, G., Nakamura, K. and Kanai, A. (2006) Solution structure of a GAAG tetraloop in helix 6 of SRP RNA from Pyrococcus furiosus, Nucleotides Nucleic Acids, 25, 383-95

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

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

15.Kochiwa, H., Itaya, M., Tomita, M. and Kanai, A. (2006) Stage-specific expression of Caenorhabditis elegans ribonuclease H1 enzymes with different substrate specificities and bivalent cation requirements, Febs J, 273, 420-9

16.Kitayama, T., Kinoshita, A., Sugimoto, M., Nakayama, Y. and 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

17.Kanai, A., Sato, A., Imoto, J. and Tomita, M. (2006) Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein, Biochem J, 393, 373-9

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

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

20.Fujita, H., Samejima, H., Kitagawa, N., Mitsuhashi, T., Washio, T., Yonemoto, J., Tomita, M., Takahashi, T. and Kosaki, K. (2006) Genome-wide screening of dioxin-responsive genes in fetal brain: bioinformatic and experimental approaches, Congenit Anom (Kyoto), 46, 135-43

21.Chua, G. H., Krishnan, A., Li, K. B. and Tomita, M. (2006) Multiresolution analysis uncovers hidden conservation of properties in structurally and functionally similar proteins, J Bioinform Comput Biol, 4, 1245-67

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

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

24.Arifuzzaman, M., Maeda, M., Itoh, A., Nishikata, K., Takita, C., Saito, R., Ara, T., Nakahigashi, K., Huang, H. C., 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. and Mori, H. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12, Genome Res, 16, 686-91

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

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

27.Numata, K., Okada, Y., Saito, R., Kiyosawa, H., Kanai, A. and Tomita, M. (2006) Comparative analysis of cis-encoded antisense RNAs in eukaryotes, Gene,

28.Mori, K., Saito, R., Kikuchi, S. and Tomita, M. (2006) Inferring rules of Escherichia coli translational efficiency using an artificial neural network, Biosystems,

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

30.Arakawa K, Tomita M. (2006) G-langage System as a platform for large-scale analysis of high-throughput omics data, Journal of Pesticide Science, 31, 282-8

31.Itaya, M., Sakaya, N., Matsunaga, S., Fujita, K. and Kaneko, S. (2006) Conjugational transfer kinetics for pLS20 between Bacillus subtilis in liquid medium, Biosci. Biotechnol. Biochem., 70, 740-42

32.Sakaya, N., Kaneko, S., Matsunaga, S. and Itaya, M. (2006) Experimental basis for a stable plasmid, pLS30, to shuttle between Bacillus subtilis species by conjugational transfer., J. Biochem.(Tokyo)., 139, 557-61

33.Monton, M. R. and Tarabe, S. (2006) Sample enrichment techniques in capillary electrophoresis: focus on peptides and proteins., J. Chromatogr. B, 841, 88-95

34.Takahashi, H., Hayashi, M., 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, 819-25

35.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-i. and Miyake, K. (2006) A Protein Associated with Toll-Like Receptor 4 (PRAT4A) Regulates Cell Surface Expression of TLR4., J. Immunol., 177, 1772-9

36.Saito, H., Oda, Y., Sato, T., Kuromitsu, J. and Ishihama, Y. (2006) Multiplexed two-dimensional liquid chromatography for MALDI and nanoelectrospray ionization mass spectrometry in proteomics., J. Proteome Res., 5, 1803-7

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

38.Ishihama, Y., Rappsilber, J. and Mann, M. (2006) Modular stop and go extraction tips with stacked disks for parallel and multidimensional Peptide fractionation in proteomics., J. Proteome Res., 5, 988-94

39.Kanai, A., Sato, A., Imoto, J. and Tomita, M. (2006) Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein., Biochemical Journal, 393, 373-9

40.Kanai, A. (2006) Importance of systematic identification of RNA-binding proteins in a hyperthermophilic archaeon., Viva Origino, 34, 144-7

41.Arakawa, K. and Tomita, M. (2006) Large-scale Modeling for Systems Biology, BIOforum Europe, 10, 54-5


01.Yugi, K., Nakayama, Y., Kojima, S., Kitayama, T. and 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. and Tomita, M. (2005) Hybrid dynamic/static method for large-scale simulation of metabolism, Theor Biol Med Model, 2, 42

03.Takahashi, K., Arjunan, S. N. and Tomita, M. (2005) Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico, FEBS Lett, 579, 1783-8

04.Suzuki, H., Saito, R. and Tomita, M. (2005) A problem in multivariate analysis of codon usage data and a possible solution, FEBS Lett, 579, 6499-504

05.Sugimoto, M., Kikuchi, S. and Tomita, M. (2005) Reverse engineering of biochemical equations from time-course data by means of genetic programming, Biosystems, 80, 155-64

06.Sugimoto, M., Kikuchi, S., Arita, M., Soga, T., Nishioka, T. and Tomita, M. (2005) Large-scale prediction of cationic metabolite identity and migration time in capillary electrophoresis mass spectrometry using artificial neural networks, Anal Chem, 77, 78-84

07.Ohtani, N., Saito, N., Tomita, M., Itaya, M. and 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, 2828-37

08.Ohashi, Y., Yamashiro, A., Washio, T., Ishii, N., Ohshima, H., Michishita, T., Tomita, M. and Itaya, M. (2005) In silico diagnosis of inherently inhibited gene expression focusing on initial codon combinations, Gene, 347, 11-9

09.Nakayama, Y., Kinoshita, A. and 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. and Tomita, M. (2005) Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa), Bioinformatics, 21, 1758-63

11.Inagaki, S., Numata, K., Kondo, T., Tomita, M., Yasuda, K., Kanai, A. and Kageyama, Y. (2005) Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila, Genes Cells, 10, 1163-73

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

13.Arita, M., Robert, M. and Tomita, M. (2005) All systems go: launching cell simulation fueled by integrated experimental biology data, Curr Opin Biotechnol, 16, 344-9

14.Arakawa, K., Suzuki, H., Fujishima, K., Fujimoto, K., Ueda, S., Matsui, M. and Tomita, M. (2005) A comprehensive software suite for the analysis of cDNAs, Genomics Proteomics Bioinformatics, 3, 179-88

15.Arakawa, K., Kono, N., Yamada, Y., Mori, H. and Tomita, M. (2005) KEGG-based pathway visualization tool for complex omics data, In Silico Biol, 5, 419-23

16.Ishii, N., Soga, T., Nishioka, T. and Tomita, M. (2005) Metabolome Analysis and Metabolic Simulation, Metabolomics, 1, 29-37

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

18.Jaros, M., Soga, Y., Van de Goor, T., Gas, B. (2005) Conductivity detection in capillary zone electrophoresis: inspection by PeakMaster, Electrophoresis, 26, 1948-53


01.Zhao, J., Baba, T., Mori, H. and 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, 91-8

02.Zhao, J., Baba, T., Mori, H. and Shimizu, K. (2004) Effect of zwf gene knockout on the metabolism of Escherichia coli grown on glucose or acetate, Metab Eng, 6, 164-74

03.Yugi, K. and Tomita, M. (2004) A general computational model of mitochondrial metabolism in a whole organelle scale, Bioinformatics, 20, 1795-6

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

05.Takahashi, K., Kaizu, K., Hu, B. and Tomita, M. (2004) A multi-algorithm, multi-timescale method for cell simulation, Bioinformatics, 20, 538-46

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

07.Soga, T., Kakazu, Y., Robert, M., Tomita, M. and Nishioka, T. (2004) Qualitative and quantitative analysis of amino acids by capillary electrophoresis-electrospray ionization-tandem mass spectrometry, Electrophoresis, 25, 1964-72

08.Sato, S., Soga, T., Nishioka, T. and 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, 151-63

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

10.Qiu, D., Fujita, K., Sakuma, Y., Tanaka, T., Ohashi, Y., Ohshima, H., Tomita, M. and Itaya, M. (2004) Comparative analysis of physical maps of four Bacillus subtilis (natto) genomes, Appl Environ Microbiol, 70, 6247-56

11.Ohtani, N., Yanagawa, H., Tomita, M. and 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

12.Ohtani, N., Yanagawa, H., Tomita, M. and Itaya, M. (2004) Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7, Nucleic Acids Res, 32, 5809-19

13.Melnick, J., Lis, E., Park, J. H., Kinsland, C., Mori, H., Baba, T., Perkins, J., Schyns, G., Vassieva, O., Osterman, A. and Begley, T. P. (2004) Identification of the two missing bacterial genes involved in thiamine salvage: thiamine pyrophosphokinase and thiamine kinase, J Bacteriol, 186, 3660-2

14.Kitamura-Abe, S., Itoh, H., Washio, T., Tsutsumi, A. and 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, 309-31

15.Itoh, H., Washio, T. and Tomita, M. (2004) Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes, Rna, 10, 1005-18

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

17.Ishii, N., Robert, M., Nakayama, Y., Kanai, A. and Tomita, M. (2004) Toward large-scale modeling of the microbial cell for computer simulation, J Biotechnol, 113, 281-94

18.Hua, Q., Yang, C., Oshima, T., Mori, H. and 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, 2354-66

19.Arita, M. and Ohashi, Y. (2004) Secret signatures inside genomic DNA, Biotechnol Prog, 20, 1605-7

20.Yano, Y., Saito, R., Yoshida, N., Yoshiki, A., Wynshaw-Boris, A., Tomita, M. and Hirotsune, S. (2004) A new role for expressed pseudogenes as ncRNA: regulation of mRNA stability of its homologous coding gene, Journal of Molecular Medicine, 20, 1605-1607

21.Hoque, M.A., Siddiquee, K.Al.Z. and Shimizu, K. (2004) Metabolic control analysis of gene-knockout Escherichia coli based on the inverse flux analysis with experimental verification, Biochemical Engineering Journal, 20, 1605-1607


01.Zhao, J. and 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, 101-17

02.Yang, C., Hua, Q., Baba, T., Mori, H. and 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, 129-44

03.Takahashi, K., Ishikawa, N., Sadamoto, Y., Sasamoto, H., Ohta, S., Shiozawa, A., Miyoshi, F., Naito, Y., Nakayama, Y. and Tomita, M. (2003) E-Cell 2: multi-platform E-Cell simulation system, Bioinformatics, 19, 1727-9

04.Soga, T., Ohashi, Y., Ueno, Y., Naraoka, H., Tomita, M. and Nishioka, T. (2003) Quantitative metabolome analysis using capillary electrophoresis mass spectrometry, J Proteome Res, 2, 488-94

05.Sato, M., Umeki, H., Saito, R., Kanai, A. and Tomita, M. (2003) Computational analysis of stop codon readthrough in D.melanogaster, Bioinformatics, 19, 1371-80

06.Sato, A., Kanai, A., Itaya, M. and 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, 247-52

07.Ozawa, Y., Saito, R., Washio, T. and Tomita, M. (2003) Comparative study of translation termination sites and release factors (RF1 and RF2) in procaryotes, J Mol Evol, 56, 665-72

08.Ohashi, Y., Ohshima, H., Tsuge, K. and 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, 125-30

09.Ohashi, Y., Inaoka, T., Kasai, K., Ito, Y., Okamoto, S., Satsu, H., Tozawa, Y., Kawamura, F. and Ochi, K. (2003) Expression profiling of translation-associated genes in sporulating Bacillus subtilis and consequence of sporulation by gene inactivation, Biosci Biotechnol Biochem, 67, 2245-53

10.Numata, K., Kanai, A., Saito, R., Kondo, S., Adachi, J., Wilming, L. G., Hume, D. A., Hayashizaki, Y. and Tomita, M. (2003) Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection, Genome Res, 13, 1301-6

11.Miyoshi, F., Nakayama, Y. and 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. and Tomita, M. (2003) Dynamic modeling of genetic networks using genetic algorithm and S-system, Bioinformatics, 19, 643-50

13.Kikuchi, S., Fujimoto, K., Kitagawa, N., Fuchikawa, T., Abe, M., Oka, K., Takei, K. and Tomita, M. (2003) Kinetic simulation of signal transduction system in hippocampal long-term potentiation with dynamic modeling of protein phosphatase 2A, Neural Netw, 16, 1389-98

14.Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A., Cuellar, A. A., Dronov, S., Gilles, E. D., Ginkel, M., Gor, V., Goryanin, II, Hedley, W. J., Hodgman, T. C., Hofmeyr, J. H., Hunter, P. J., Juty, N. S., Kasberger, J. L., Kremling, A., Kummer, U., Le Novere, N., Loew, L. M., Lucio, D., Mendes, P., Minch, E., Mjolsness, E. D., Nakayama, Y., Nelson, M. R., Nielsen, P. F., Sakurada, T., Schaff, J. C., Shapiro, B. E., Shimizu, T. S., Spence, H. D., Stelling, J., Takahashi, K., Tomita, M., Wagner, J. and Wang, J. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics, 19, 524-31

15.Hua, Q., Yang, C., Baba, T., Mori, H. and Shimizu, K. (2003) Responses of the central metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts, J Bacteriol, 185, 7053-67

16.Fukuda, Y., Nakayama, Y. and Tomita, M. (2003) On dynamics of overlapping genes in bacterial genomes, Gene, 323, 181-7

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

18.Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Kobayashi, Y. and Tomita, M. (2003) G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining, Bioinformatics, 19, 305-6

19.Kanai, A., Oida, H., Matsuura, N. and Doi, H. (2003) Expression cloning and characterization of a novel gene that encodes the RNA-binding protein FAU-1 from Pyrococus furiosus, Biochem J, 372, 253-61

20.Jiao, Z., Baba, T., Mori, H. and 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(2), 295-301


01.Soga, T., Ueno, Y., Naraoka, H., Ohashi, Y., Tomita, M. and Nishioka, T. (2002) Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry, Anal Chem, 74, 2233-9

02.Soga, T., Ueno, Y., Naraoka, H., Matsuda, K., Tomita, M. and Nishioka, T. (2002) Pressure-assisted capillary electrophoresis electrospray ionization mass spectrometry for analysis of multivalent anions, Anal Chem, 74, 6224-9

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

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

05.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, D. P., Bult, C., Hume, D. A., Quackenbush, J., Schriml, L. M., Kanapin, A., Matsuda, H., Batalov, S., Beisel, K. W., Blake, J. A., Bradt, D., Brusic, V., Chothia, C., Corbani, L. E., Cousins, S., Dalla, E., Dragani, T. A., Fletcher, C. F., Forrest, A., Frazer, K. S., Gaasterland, T., Gariboldi, M., Gissi, C., Godzik, A., Gough, J., Grimmond, S., Gustincich, S., Hirokawa, N., Jackson, I. J., Jarvis, E. D., Kanai, A., Kawaji, H., Kawasawa, Y., Kedzierski, R. M., King, B. L., Konagaya, A., Kurochkin, I. V., Lee, Y., Lenhard, B., Lyons, P. A., Maglott, D. R., Maltais, L., Marchionni, L., McKenzie, L., Miki, H., Nagashima, T., Numata, K., Okido, T., Pavan, W. J., Pertea, G., Pesole, G., Petrovsky, N., Pillai, R., Pontius, J. U., Qi, D., Ramachandran, S., Ravasi, T., Reed, J. C., Reed, D. J., Reid, J., Ring, B. Z., Ringwald, M., Sandelin, A., Schneider, C., Semple, C. A., Setou, M., Shimada, K., Sultana, R., Takenaka, Y., Taylor, M. S., Teasdale, R. D., Tomita, M., Verardo, R., Wagner, L., Wahlestedt, C., Wang, Y., Watanabe, Y., Wells, C., Wilming, L. G., 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, E. S., Rogers, J., Birney, E. and Hayashizaki, Y. (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs, Nature, 420, 563-73

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

07.Kochiwa, H., Suzuki, R., Washio, T., Saito, R., Bono, H., Carninci, P., Okazaki, Y., Miki, R., Hayashizaki, Y. and Tomita, M. (2002) Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data, Genome Res, 12, 1286-93

08.Fujita, H., Kosaki, R., Yoshihashi, H., Ogata, T., Tomita, M., Hasegawa, T., Takahashi, T., Matsuo, N. and Kosaki, K. (2002) Characterization of the aryl hydrocarbon receptor repressor gene and association of its Pro185Ala polymorphism with micropenis, Teratology, 65, 10-8

09.Ozawa, Y., Hanaoka, S., Saito, R., Washio, T., Nakano, S., Shinagawa, A., Itoh, M., Shibata, K., Carninci, P., Konno, H., Kawai, J., Hayashizaki, Y. and Tomita, M. (2002) Comprehensive sequence analysis of translation termination sites in various eukaryotes, Gene, 300(1-2), 79-87

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

11.Tomita, M. (2002) Towards computer aided design (CAD) of useful microorganisms, Bioinformatics, 17(12), 1091-2.


01.Tomita, M. (2001) Towards computer aided design (CAD) of useful microorganisms, Bioinformatics, 17, 1091-2

02.Tomita, M. (2001) Whole-cell simulation: a grand challenge of the 21st century, Trends Biotechnol, 19, 205-10

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

04.Sakai, H., Imamura, C., Osada, Y., Saito, R., Washio, T. and Tomita, M. (2001) Correlation between Shine--Dalgarno sequence conservation and codon usage of bacterial genes, J Mol Evol, 52, 164-70

05.Ohno, H., Sakai, H., Washio, T. and Tomita, M. (2001) Preferential usage of some minor codons in bacteria, Gene, 276, 107-15

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, L. M., 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, M. F., Brownstein, M. J., Bult, C., Fletcher, C., Fujita, M., Gariboldi, M., Gustincich, S., Hill, D., Hofmann, M., Hume, D. A., Kamiya, M., Lee, N. H., 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, K. F., Suzuki, H., Toyo-oka, K., Wang, K. H., Weitz, C., Whittaker, C., Wilming, L., Wynshaw-Boris, A., Yoshida, K., Hasegawa, Y., Kawaji, H., Kohtsuki, S. and Hayashizaki, Y. (2001) Functional annotation of a full-length mouse cDNA collection, Nature, 409, 685-90

07.Hashimoto K., Seno S., Dhar PK. and Tomita M. (2001) Integrative modeling of gene expression and metabolism with E-CELL System, Artificial Life and Robotics, 6, 99-107



01.Uno, R., Nakayama, Y., Arakawa, K. and Tomita, M. (2000) The orientation bias of Chi sequences is a general tendency of G-rich oligomers, Gene, 259, 207-15

02.Toda, Y., Saito, R. and Tomita, M. (2000) Characteristic sequence pattern in the 5- to 20-bp upstream region of primate Alu elements, J Mol Evol, 50, 232-7

03.Saito, R., Ozawa, Y., Kuzuno, N. and Tomita, M. (2000) Computer analysis of potential stem structures of rRNA operons in various procaryote genomes, Gene, 259, 217-22

04.Goto, M., Washio, T. and Tomita, M. (2000) Causal analysis of CpG suppression in the Mycoplasma genome, Microb Comp Genomics, 5, 51-8

05.Fukuda, R., Hara, J., Shankle, WR. and Tomita, M. (2000) Proposition of cortical connectivity between 30 cytoarchitectural areas of human cerebral cortex, Neurocomputing, 32(33), 749-55

06.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., Shimizu T. and Nakayama Y. (2000) The E-CELL Project: Towards Integrative Simulation of Cellular Processes, New Generation Computing, 18(1), 1-12


01.Tomita, M., Wada, M. and Kawashima, Y. (1999) ApA dinucleotide periodicity in prokaryote, eukaryote, and organelle genomes, J Mol Evol, 49, 182-92

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

03.Toda, Y., Saito, R. and Tomita, M. (1999) Sequence patterns observed in 5' flanking regions of primate Alu elements, Ann N Y Acad Sci, 870, 369-74

04.Saito, R. and 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

05.Saito, R. and Tomita, M. (1999) On negative selection against ATG triplets near start codons in eukaryotic and prokaryotic genomes, J Mol Evol, 48, 213-7

06.Osada, Y., Saito, R. and Tomita, M. (1999) Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes, Bioinformatics, 15, 578-81

07.Fukuda, Y., Washio, T. and Tomita, M. (1999) Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae, Nucleic Acids Res, 27, 1847-53


01.Washio, T., Sasayama, J. and Tomita, M. (1998) Analysis of complete genomes suggests that many prokaryotes do not rely on hairpin formation in transcription termination, Nucleic Acids Res, 26, 5456-63

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


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

02.Toda, Y. and Tomita, M. (1997) Alu elements as an aid in deciphering genome rearrangements, Gene, 205, 173-6

03.Shimizu, T. S., Takahashi, K. and Tomita, M. (1997) CpG distribution patterns in methylated and non-methylated species, Gene, 205, 103-7