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.