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2017

01. Inaba, Y., Nakahigashi, K., Ito, T., & Tomita, M.(2017) Alteration of fatty acid chain length of Chlamydomonas reinhardtii by simultaneous expression of medium-chain-specific thioesterase and acyl carrier protein. Phycological Research. 2017,65(1), 94-99.

02. Sugimoto, M., Obiya, S., Kaneko, M., Enomoto, A., Honma, M., Wakayama, M., Soga, T. and Tomita, M.(2017)Metabolomic Profiling as a Possible Reverse Engineering Tool for Estimating Processing Conditions of Dry-Cured Hams. J Agric Food Chem. 2017 Jan 18;65(2):402-410. doi: 10.1021/acs.jafc.6b03844.

03. Nakada, T. and Tomita, M. (2017) Morphology and phylogeny of a new wall-less freshwater volvocalean flagellate, Hapalochloris nozakii gen. et sp. nov. (Volvocales, Chlorophyceae). J Phycol. 2017 Feb;53(1):108-117. doi: 10.1111/jpy.12484.

04. Nishihara, T., Inoue, J., Tabata, S., Murakami, S., Ishikawa, T., Saito, N., Fukuda, S., Tomita, M. and Soga, T.(2017) Synthetic Biomarker Design by Using Analyte-Responsive Acetaminophen. Chembiochem. 2017 Feb 25. doi: 10.1002/cbic.201700023. [Epub ahead of print]

05. Yuliana, T., Nakajima, N., Yamamura, S., Tomita, M., Suzuki, H., Amachi, S.(2017) Draft Genome Sequence of Roseovarius sp. A-2, an Iodide-Oxidizing Bacterium Isolated from Natural Gas Brine Water, Chiba, Japan . J Genomics. 2017 Apr 6;5:51-53. doi: 10.7150/jgen.19846. eCollection 2017.

06. Galipon, J., Ishii, R., Suzuki, Y., Tomita, M., and Ui-Tei, K.(2017) Differential binding of three major human ADAR isoforms to coding and long non-coding transcripts. Genes (Basel). 2017 Feb 11;8(2). pii: E68. doi: 10.3390/genes8020068.

07. Noro, E., Mori, M., Makino, G., Takai, Y., Ohnuma, S., Sato, A., Tomita, M., Nakahigashi, K. and Kanai, A.(2017) Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth. RNA Biol. 2017 Feb;14(2):206-218. doi: 10.1080/15476286.2016.1270001.

08. Miyamoto, T., Hirayama, A., Sato, Y., Koboyashi, T., Katsuyama, E., Kanagawa, H., Miyamoto, H., Mori, T., Yoshida, S., Fujie, A., Morita, M., Watanabe, R., Tando, T., Miyamoto, K., Tsuji, T., Funayama, A., Nakamura, M., Matsumoto, M., Soga, T., Tomita, M. and Toyama, Y.(2017) A serum metabolomics-based profile in low bone mineral density postmenopausal women. Bone. 2017 Feb 11;8(2). pii: E68. doi: 10.3390/genes8020068.

09. Jia, H., Hanate, M., Aw, W., Itoh, H., Saito, K., Kobayashi, S., Hachimura, S., Fukuda, S., Tomita, M., Hasebe, Y. and Kato, H. (2017) Eggshell membrane powder ameliorates intestinal inflammation by facilitating the restitution of epithelial injury and alleviating microbial dysbiosis. Sci Rep. 2017 Mar 8;7:43993. doi: 10.1038/srep43993.

10. Itoi, T., Sugimoto, M., Umeda, J., Sofuni, A., Tsuchiya, T., Tsuji, S., Tanaka, R., Tonozuka, R., Honjo, M., Moriyasu, F., Kasuya, K., Nagakawa, Y., Abe, Y., Takano, K., Kawachi, S., Shimazu, M., Soga, T., Tomita, M., Sunamura, M.(2017) Serum Metabolomic Profiles for Human Pancreatic Cancer Discrimination. Int. J. Mol. Sci. 2017 Apr 4;18(4). pii: E767. doi: 10.3390/ijms18040767.

11. Mishima, E., Fukuda, S., Mukawa, C., Yuri, A., Kanemitsu, Y., Matsumoto, Y., Akiyama, Y., Fukuda, NN., Tsukamoto, H., Asaji, K., Shima, H., Kikuchi, K., Suzuki, T., Tomioka, Y., Soga, T., Ito, S., Abe, T.(2017) Evaluation of the impact of gut microbiota on uremic solute accumulation by a CE-TOFMS-based metabolomics approach. Kidney Int. 2017 Apr 8. pii: S0085-2538(17)30116-3.

12.Aw, W. and Fukuda, S.(2017) Understanding the role of the gut ecosystem in diabetes mellitus. J Diabetes Investig. 2017 Apr 8. doi: 10.1111/jdi.12673. [Epub ahead of print]

13. Yachie, N., Robotic Biology Consortium and Natsume, T. < Collabolators> Takahashi, K., Katayama, T., Sakurada, T., Kanda, G. N., Takagi, E., Hirose, T., Katsura, T., Moriya, T., Kitano, H., Tsujii, J., Shiraki, T., Kariyazaki, H., Kamei, M., Abe, N., Fukuda, T., Sawada, Y., Hashiguchi, Y., Matsukuma, K., Murai, S., Sasaki, N., Ipposhi, T., Urabe, H., Kudo, T., Umeno, M., Ono, S., Miyauchi, K., Nakamura, M., Kizaki, T., Suyama, T., Hatta, T., Natsume, T., Ohta, T., Ozawa, Y., Ihara, S., Tamaki, S., Antezana, E., Garcia-Castro, A., Perret, J., L., Ishiguro, S., Mori, H., Evans-Yamamoto, D., Masuyama N, Tomita M, Katayama T, Matsumoto M, Nakayama H, Shirasawa A, Shimbo, K., Yamada, N., Nakayama, K., I., Shimizu, T., Saya, H., Yamashita, S., Matsushima, T., Asahara, H., Eguchi, H., Mikamori, M. and Mori, M. (2017) Robotic crowd biology with Maholo LabDroids. Nat Biotechnol. 2017 Apr 11;35(4):310-312. doi: 10.1038/nbt.3758.

14. Sano, I., H., Toki, T., Naito, Y. and Tomita, M.(2017) Developmental changes in the balance of glycolytic ATP production and oxidative phosphorylation in ventricular cells: A simulation study. J Theor Biol. 2017 Apr 21;419:269-277. doi: 10.1016/j.jtbi.2017.02.019.

15. Kim, YG., Sakamoto, K., Seo1, SU., Pickard, JM., Gillilland, M.G. 3rd, Pudlo, NA., Hoostal, M., Li, X., Feehley, T., Stefka, AT., Schmidt, TM., Martens, EC., Fukuda, S., Inohara, N., Nagler, CR., Núñez, G.(2017) Neonatal acquisition of Clostridia species protects against colonization by bacterial pathogens. Science. 2017 Apr 21;356(6335):315-319. doi: 10.1126/science.aag2029.

16. Kitazawa, S., Ebara1, S., Ando, A., Baba, Y., Satomi, Y., Soga, T., Hara, T.(2017) Succinate dehydrogenase B-deficient cancer cells are highly sensitive to bromodomain and extra-terminal inhibitors. Oncotarget. 2017 Apr 25;8(17):28922-28938. doi: 10.18632/oncotarget.15959.

17. Sakata, F., Ito, Y., Mizuno, M., Sawai, A., Suzuki, Y., Tomita, T., Tawada, M., Tanaka, A., Hirayama, A., Sagara, A., Wada, T., Maruyama, S., Soga, T., Matsuo, S., Imai, E., Takei, Y.(2017) Sodium chloride promotes tissue inflammation via osmotic stimuli in subtotal-nephrectomized mice. Lab Invest. 2017 Apr;97(4):432-446. doi: 10.1038/labinvest.2017.4.

18. Yoshitoshi-Uebayashi, E.Y., Toyoda, T., Yasuda, K., Kotaka, M., Nomoto, K., Okita, K., Yasuchika, K., Okamoto, S., Takubo, N., Nishikubo, T., Soga, T., Uemoto, S., Osafune, K.(2017) Modelling urea-cycle disorder citrullinemia type 1 with disease-specific iPSCs. Biochem Biophys Res Commun. 2017 May 6;486(3):613-619. doi: 10.1016/j.bbrc.2017.03.037.

19. Tanaka, Y., Ogawa, T., Maruta, T., Yoshida, Y., Arakawa, K., Ishikawa, T.(2017) Glucan synthase-like 2 is indispensable for paramylon synthesis in Euglena gracilis. FEBS Lett. 2017 May;591(10):1360-1370. doi: 10.1002/1873-3468.12659. Epub 2017 May 7.

20. Tabata, S., Yamamoto, M., Goto, H., Hirayama, A., Ohishi, M., Kuramoto, T., Mitsuhashi, A., Ikeda, R., Haraguchi, M., Kawahara, K., Shinsato, Y., Minami, K., Atsuro Saijo, A., Hanibuchi, M., Nishioka, Y., Sone, S., Esumi, H., Tomita, M., Soga, T., Furukawa, T. and Akiyama, S.(2017) Thymidine Catabolism as a Metabolic Strategy for Cancer Survival. Cell Rep. 2017 May 16;19(7):1313-1321. doi: 10.1016/j.celrep.2017.04.061.

21. Kon, S., Ishibashi, K., Katoh, H., Kitamoto, S., Shirai, T., Tanaka, S., Kajita, M., Ishikawa, S., Yamauchi, H., Yako, Y., Kamasaki, T., Matsumoto, T., Watanabe, H., Egami, R., Sasaki, A., Nishikawa, A., Kameda, I., Maruyama, T., Narumi, R., Morita, T., Sasaki, Y., Enoki, R., Honma, S., Imamura, H., Oshima, M., Soga, T., Miyazaki, J., Duchen, MR.., Nam, J., Onodera, Y., Yoshioka, S., Kikuta, J., Ishii, M., Imajo, M., Nishida, E., Fujioka, Y., Ohba, Y., Sato, T., Fujita, Y.(2017) Cell competition with normal epithelial cells promotes apical extrusion of transformed cells through metabolic changes. Nat. Cell Biol. 2017 May;19(5):530-541. doi: 10.1038/ncb3509.

22. Kitazawa, S., Nishizawa, S., Nakagawa, H., Funata, M., Nishimura, K., Soga, T., Hara, T.(2017) Cancer with low cathepsin D levels is susceptible to vacuolar (H+ )-ATPase inhibition. Cancer Sci. 2017 Jun;108(6):1185-1193. doi: 10.1111/cas.13240. Epub 2017 May 20.

23. Nozaki, T., Imai, R., Tanbo, M., Nagashima, R., Tamura, S., Tani, T., Joti, Y., Tomita, M., Hibino, K., Kanemaki, M.,T., Wendt, K.,S., Okada, Y., Nagai, T. and Maeshima, K.(2017) Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging. Mol Cell. 2017 Jul 20;67(2):282-293.e7. doi: 10.1016/j.molcel.2017.06.018. Epub 2017 Jul 14.

24. Yoshida, Y., Koutsovoulos, G., Laetsch, R., D., Stevens, L., Kumar, S., Horikawa, D., D., Ishino, K., Komine, S., Kunieda, T., Tomita, M., Blaxter, M. and Arakawa, K.(2017) Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius. PLoS Biol. 2017 Jul 27;15(7):e2002266. doi: 10.1371/journal.pbio.2002266. eCollection 2017 Jul.

25. Okuma, N., Saita M., Hoshi, N., Soga, T., Tomita, M., Sugimoto, M., Kimoto K.(2017) Effect of masticatory stimulation on the quantity and quality of saliva and the salivary metabolomic profile. PLoS One. 2017 Aug 15;12(8):e0183109. doi: 10.1371/journal.pone.0183109. eCollection 2017

26. Satoh, K., Yachida, S., Sugimoto, M., Oshima, M., Nakagawa, T., Akamoto, S., Tabata, S., Saitoh, K., Kato, K., Sato, S., Igarashi, K., Aizawa, Y., Kajino-Sakamoto, R., Kojima, Y., Fujishita, T., Enomoto, A., Hirayama, A., Ishikawa, T., Taketo, M., M., Kushida, Y., Haba, R., Okano, K., Tomita, M., Suzuki, Y., Fukuda, S., Aoki, M., Soga, T.(2017) Global metabolic reprogramming of colorectal cancer occurs at adenoma stage and is induced by MYC. Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):E7697-E7706 doi: 10.1073/pnas.1710366114.

27. Kono, N., Tomita, M. and Arakawa, K.(2017) eRP arrangement: a strategy for assembled genomiccontig rearrangement based on replication profiling in bacteria. BMC Genomics. 2017 Oct 13;18(1):784. doi: 10.1186/s12864-017-4162-z.


28. Nagata, S., Imai, J., Makino, G., Tomita, M. and Kanai, A.(2017) Evolutionary analysis of HIV-1 Pol proteins reveals representative residues for viral subtype differentiation. Front Microbiol. 2017 Nov 2;8:2151. doi: 10.3389/fmicb.2017.02151. eCollection 2017.


29. Ikeda. Y., Okada, Y., Sato, A. Kanai, T., Tomita, M., Atomi, H. and Kanai, A.(2017) An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus. Sci Rep. 2017 Oct 4;7(1):12674. doi: 10.1038/s41598-017-13062-3.

2016

01. Shindo, Y., Iwamoto, K., Mouri, K., Hibino, K., Tomita, M., Kosako, H., Sako, Y. and Takahashi, K. (2016) Conversion of graded phosphorylation into switch-like nuclear translocation via autoregulatory mechanisms in ERK signaling. Nat Commun. 2016 Jan 20;7:10485. doi: 10.1038/ncomms10485.

02. Harada, S., Takebayashi, T., Kurihara, A., Akiyama, M., Suzuki, A., Hatakeyama, Y., Sugiyama, D., Kuwabara, K., Takeuchi, A., Okamura, T., Nishiwaki, Y., Tanaka, T., Hirayama, A., Sugimoto, M., Soga, T. and Tomita, M.(2016) Metabolomic profiling reveals novel biomarkers of alcohol intake and alcohol-induced liver injury in community-dwelling men.Environ Health Prev Med. 2016 Jan;21(1):18-26. doi: 10.1007/s12199-015-0494-y.

03. Akiyama M, Hirai K, Takebayashi T, Morita T, Miyashita M, Takeuchi A, Yamagishi A, Kinoshita H, Shirahige Y, and Eguchi K.(2016) The effects of community-wide dissemination of information on perceptions of palliative care, knowledge about opioids, and sense of security among cancer patients, their families, and the general public.Support Care Cancer. 2016 Jan;24(1):347-56. doi: 10.1007/s00520-015-2788-4.

04. Hamashima, K., Tomita, M. and Kanai, A. (2016) Expansion of Noncanonical V-Arm-Containing tRNAs in Eukaryotes. Mol Biol Evol. 2016 Feb;33(2):530-40. doi: 10.1093/molbev/msv253.

05. Yoshida, Y., Tomiyama, T., Maruta, T., Tomita, M., Ishikawa, T. and Arakawa, K. (2016) De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions. BMC Genomics.2016 Mar 3;17:182. doi: 10.1186/s12864-016-2540-6.

06. Galipon Josephine, 石黒宗, 冨田勝, 程久美子(2016) Detecting A-to-I RNA editing in RNA-Seq data. NGS Professional シリーズRNA-Seqマスターブック(羊土社) Review (2016)

07. Nakada, T., Tomita, M., Wu, J. T. and Nozaki, H. (2016) Taxonomic revision of Chlamydomonas subg. Amphichloris (Volvocales, Chlorophyceae), with resurrection of the genus Dangeardinia and descriptions of Ixipapillifera gen. nov. and Rhysamphichloris gen. nov. J. Phycol.2016 Apr;52(2):283-304. doi: 10.1111/jpy.12397.

08. Useh, N., Ngbede, E., Akange, N., Thomas, M., Foley, A., Keena, M., Nelson, E., Christopher-Hennings, J., Tomita, M., Suzuki, H. and Scaria, J. (2016) Draft Genome Sequences of 37 Salmonella enterica Strains Isolated from Poultry Sources in Nigeria. Genome Announc.2016 May 5;4(3). pii: e00315-16. doi: 10.1128/genomeA.00315-16.

09. Li, Q., Guo, S., Jiang, X., Bryk, J., Naumann, R., Enard, W., Tomita, M., Sugimoto, M., Khaitovich, P. and Pääbo, S. (2016) Mice carrying a human GLUD2 gene recapitulate aspects of human transcriptome and metabolome development. PNAS.2016 May 10;113(19):5358-63. doi: 10.1073/pnas.1519261113.

10. Kono, N., Nakamura, H., Ito, Y., Tomita, M. and Arakawa, K. (2016) Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly. Mol Ecol Resour.2016 May;16(3):662-72. doi: 10.1038/srep31520.

11. Kimura, T., Yasuda, K., Yamamoto, R., Soga, T., Rakugi, H., Hayashi, T., Isaka, Y.(2016) Identification of biomarkers for development of end-stage kidney disease in chronic kidney disease by metabolomic profiling. Sci Rep.2016 May 18;6:26138. doi: 10.1038/srep26138.

12. Munakata, H., Nakada, T., Nakahigashi, K., Nozaki, H. and Tomita, M.(2016) Phylogenetic Position and Molecular Chronology of a Colonial Green Flagellate, Stephanosphaera pluvialis (Volvocales, Chlorophyceae), among Unicellular Algae. Eukaryot Microbiol. 2016 May;63(3):340-8. doi: 10.1111/jeu.12283.

13. Arakawa, K.(2016) No evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. PNAS.2016 May 31;113(22):E3057. doi: 10.1073/pnas.1602711113.

14. Nakada, T. & Ota, S.(2016) What is the correct name for the type species of Haematococcus Flot. (Volvocales, Chlorophyceae)? Taxon.65(2):343-348,May 2016

15. Tando, T., Hirayama, A., Furukawa, M., Sato, Y., Kobayashi, T., Funayama, A., Kanaji, A., Hao, W., Watanabe, R., Morita, M., Oike, T., Miyamoto, K., Soga, T., Nomura, M., Yoshimura, A., Tomita, M., Matsumoto, M., Nakamura, M., Yoshiaki Toyama. Y. and Miyamoto, T. (2016) Smad2/3 Proteins Are Required for Immobilization-induced Skeletal Muscle Atrophy. J Biol Chem. 2016 Jun 3;291(23):12184-94.doi: 10.1074/jbc.M115.680579.

16. Saito, T., Ichimura, Y., Taguchi, K., Suzuki, T., Mizushima, T., Takagi, K., Hirose, Y., Nagahashi, M., Iso, T., Fukutomi, T., Ohishi, M., Endo, K., Uemura, T., Nishito, Y., Okuda, S., Obata, M., Kouno, T., Imamura, R., Tada, Y., Obata, R., Yasuda, D., Takahashi, K., Fujimura, T., Pi, J., Lee, MS., Ueno, T., Ohe, T., Mashino, T., Wakai, T., Kojima, H., Okabe, T., Nagano, T., Motohashi, H., Waguri, S., Soga, T., *Yamamoto, M., *Tanaka, K., *Komatsu, M.(2016) p62/Sqstm1 promotes malignancy of HCV-positive hepatocellular carcinoma through Nrf2-dependent metabolic reprogramming. Nat Commun. 2016 Jun 27;7:12030. doi: 10.1038/ncomms12030.

17. Saito, T., Sugimoto, M., Okumoto, K., Haga, H., Katsumi, T., Mizuno, K., Nishina, T., Sato, S., Igarashi, K., Maki, H., Tomita, M., Ueno, Y., Soga, T.(2016) Serum metabolome profiles characterized by patients with hepatocellular carcinoma associated with hepatitis B and C. World J. Gastroenterol. 2016 Jul 21;22(27):6224-34. doi: 10.3748/wjg.v22.i27.6224.

18. Yamanaka, R., Tabata, S., Shindo, Y., Hotta, K., Suzuki, K., Soga, T., Oka, K.(2016) Mitochondrial Mg2+ homeostasis decides cellular energy metabolism and vulnerability to stress. Sci Rep. 2016 Jul 26;6:30027. doi: 10.1038/srep30027.

19. Iida, M., Harada, S., Kurihara, A., Fukai, K., Kuwabara, K., Sugiyama, D., Takeuchi, A., Okamura, T., Akiyama, M., Nishiwaki, Y., Suzuki, A., Hirayama, A., Sugimoto, M., Soga, T., Tomita, M., Banno, K., Aoki, D. and Takebayashi, T. (2016) Profiling of plasma metabolites in postmenopausal women with metabolic syndrome. Menopause.2016 Jul;23(7):749-58. doi: 10.1097/GME.0000000000000630.

20. Akiyama M, Abraham C.(2016) A Systematic Review of the Economic Evaluation of Telemedicine in Japan. J Prev Med Public Health.2016 Jul;49(4):183-96. doi: 10.3961/jpmph.16.043.

21. Karigane, D., Kobayashi, H., Morikawa, T., Ootomo, Y., Sakai, M., Nagamatsu, G., Kubota, Y., Goda, N., Matsumoto, M., Nishimura, E. K., Soga, T., Otsu, K., Suematsu, M., Okamoto, S., Suda, T., Takubo, K.(2016) p38α activates purine metabolism to initiate hematopoietic stem/progenitor cell cycling in response to stress. Cell Stem Cell. 2016 Aug 19;6:31520. doi: 10.1038/srep31520.

22. Ishikawa, S., Sugimoto, M., Kitabatake, K., Sugano, A., Nakamura, M., Kaneko, M., Ota, S., Hiwatari, K., Enomoto, A., Soga, T., Tomita, M. and Iino, M.(2016) Identification of salivary metabolomic biomarkers for oral cancer screening. Sci Rep. 2016 Aug 19;6:31520. doi: 10.1038/srep31520.

23. Arakawa, K., Yoshida, Y., Tomita, M.(2016) Genome sequencing of a single tardigrade Hypsibius dujardini individual. Sci Data. 2016 Aug 16;3:160063. doi: 10.1038/sdata.2016.63.

24. Hashimoto T, Horikawa DD, Saito Y, Kuwahara H, Kozuka-Hata H, Shin-I T, Minakuchi Y, Ohishi K, Motoyama A, Aizu T, Enomoto A, Kondo K, Tanaka S, Hara Y, Yoshikawa S, Sagara H, Miura T, Yokobori S, Miyazawa K, Suzuki Y, Kubo T, Oyama M, Kohara Y, Fujiyama A, Arakawa K, Katayama T, Toyoda A, and Kunieda T.(2016) Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein. Nat Commun. 2016 Sep 20;7:12808. doi: 10.1038/ncomms12808.

25. Bardella C, Al-Dalahmah O, Krell D, Brazauskas P, Al-Qahtani K, Tomkova M, Adam J, Serres S, Lockstone H, Freeman-Mills L, Pfeffer I, Sibson N, Goldin R, Schuster-Böeckler B, Pollard, PJ, Soga T, McCullagh JS, Schofield CJ, Mulholland P, Ansorge O, Kriaucionis S, Ratcliffe PJ, Szele, FG, Tomlinson I.(2016) Expression of Idh1R132H in the murine subventricular zone stem cell niche recapitulates features of early gliomagenesis. Cancer Cell. 2016 Oct 10;30(4):578-594. doi: 10.1016/j.ccell.2016.08.017.

26. Ito,K., Nakajima, N., Yamamura, S., Tomita, M., Suzuki, H. and Amachi, S. (2016) Draft Genome Sequence of Arenibacter sp. Strain C-21, an Iodine-Accumulating Bacterium Isolated from Surface Marine Sediment. Genome Announc. 2016 Oct 13;4(5). pii: e01155-16. doi:10.1128/genomeA.01155-16.

27. Fukai, K., Harada, S., Iida, M., Kurihara, A.,Takeuchi, A., Kuwabara, K., Sugiyama, D., Okamura, T., Akiyama, M.,Nishiwaki, Y., Oguma, Y., Suzuki, A., Suzuki, C., Hirayama, A., Sugimoto,M., Soga, T., Tomita, M. and Takebayashi, T. (2016) Metabolic Profiling of Total Physical Activity and Sedentary Behavior in Community-Dwelling Men. PLoS ONE. 2016 Oct 14;11(10):e0164877. doi: 10.1371/journal.pone.0164877. eCollection 2016.

28. Ogawa, T., Tsubakiyama, R., Kanai, M., Koyama , T., Fujii, T., Iefuji, H., Soga, T., Kume, K., Miyakawa, T., Hirata, D., Mizunuma, M.(2016) Stimulating S-adenosyl-L-methionine synthesis extends lifespan via activation of AMPK. Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):11913-11918.

29. Sugimoto, M., Obiya, S., Kaneko, M., Enomoto, A., Honma, M., Wakayama, M., and Tomita, M. (2016) Simultaneous analysis of consumer variables, acceptability and sensory characteristics of dry-cured ham. Meat Sci. 2016 Nov;121:210-5. doi: 10.1016/j.meatsci.2016.06.015.

30. Iwai,H., Horikawa, D., Arakawa, K., Tomita, M., Komatsu, T. and Maruyama, M.(2016) Rearing and observation of immature stages of the hoverfly Microdon katsurai (Diptera, Syrphidae). Biodivers Data J. 2016 Dec 9;(4):e10185. doi: 10.3897/BDJ.4.e10185. eCollection 2016.

2015

01. Tsuge K, Sato Y, Kobayashi Y, Gondo M, Hasebe M, Togashi T, Tomita M, Itaya M. (2015) Method of preparing an equimolar DNA mixture for one-step DNA assembly of over 50 fragments. Sci Rep, 5, 10655.

02. Simeoni O, Piras V, Tomita M, Selvarajoo K. (2015) Tracking global gene expression responses in T cell differentiation. Gene, 569, 259-266.

03. Selvarajoo K .(2015) Measuring merit: take the risk. Science, 347, 139-140.
Pubmed

04. Piras V, Selvarajoo K. (2015) The reduction of gene expression variability from single cells to populations follows simple statistical laws. Genomics, 105, 137-144.
Pubmed

05. Ogawara Y, Katsumoto T, Aikawa Y, Shima Y, Kagiyama Y, Soga T, Matsunaga H, Seki T, Araki K, Kitabayashi I .(2015) IDH2 and NPM1 Mutations Cooperate to Activate Hoxa9/Meis1 and Hypoxia Pathways in Acute Myeloid Leukemia.Cancer Res, 75, 2005-2016.
Pubmed

06. Mishima E, Fukuda S, Shima H, Hirayama A, Akiyama Y, Takeuchi Y, Fukuda NN, Suzuki T, Suzuki C, Yuri A, Kikuchi K, Tomioka Y, Ito S, Soga T, Abe T. (2015) Alteration of the Intestinal Environment by Lubiprostone Is Associated with Amelioration of Adenine-Induced CKD. J Am Soc Nephrol, 26, 1787-1794.
Pubmed

07. Matsumura T, Sugawara Y, Yutani M, Amatsu S, Yagita H, Kohda T, Fukuoka S, Nakamura Y, Fukuda S, Hase K, Ohno H, Fujinaga Y. (2015) Botulinum toxin A complex exploits intestinal M cells to enter the host and exert neurotoxicity. Nat Commun, 6, 6255.
Pubmed

08. Kume S, Yamato M, Tamura Y, Jin G, Nakano M, Miyashige Y, Eguchi A, Ogata Y, Goda N, Iwai K, Yamano E, Watanabe Y, Soga T, Kataoka Y.(2015) Potential biomarkers of fatigue identified by plasma metabolome analysis in rats. PLoS One, 10, e0120106.
Pubmed

09. Kobayashi S, Sato M, Kasakoshi T, Tsutsui T, Sugimoto M, Osaki M, Okada F, Igarashi K, Hiratake J, Homma T, Conrad M, Fujii J, Soga T, Bannai S, Sato H.(2015) Cystathionine is a novel substrate of cystine/glutamate transporter: implications for immune function. J Biol Chem, 290, 8778-8788.
Pubmed

10. Kishikawa T, Otsuka M, Tan PS, Ohno M, Sun X, Yoshikawa T, Shibata C, Takata A, Kojima K, Takehana K, Ohishi M, Ota S, Noyama T, Kondo Y, Sato M, Soga T, Hoshida Y, Koike K.(2015) Decreased miR122 in hepatocellular carcinoma leads to chemoresistance with increased arginine. Oncotarget, 6, 8339-8352.
Pubmed

11. Ikeda KT, Hirose Y, Hiraoka K, Noro E, Fujishima K, Tomita M, Kanai A.(2015) Identification, expression, and molecular evolution of microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp). RNA, 21, 230-242.
Pubmed

12. Hirayama A, Sugimoto M, Suzuki A, Hatakeyama Y, Enomoto A, Harada S, Soga T, Tomita M, Takebayashi T.(2015) Effects of processing and storage conditions on charged metabolomic profiles in blood. Electrophoresis, Pubmed

13.Hamashima K, Mori M, Andachi Y, Tomita M, Kohara Y, Kanai A.(2015) Analysis of genetic code ambiguity arising from nematode-specific misacylated tRNAs. PLoS One, 10, e0116981.
Pubmed

14.Garcia-Contreras R, Sugimoto M, Umemura N, Kaneko M, Hatakeyama Y, Soga T, Tomita M, Scougall-Vilchis RJ, Contreras-Bulnes R, Nakajima H, Sakagami H.(2015) Alteration of metabolomic profiles by titanium dioxide nanoparticles in human gingivitis model.Biomaterials, 57, 33-40.
Pubmed

15. Bozek K, Wei Y, Yan Z, Liu X, Xiong J, Sugimoto M, Tomita M, Paabo S, Sherwood CC, Hof PR, Ely JJ, Li Y, Steinhauser D, Willmitzer L, Giavalisco P, Khaitovich P.(2015) Organization and evolution of brain lipidome revealed by large-scale analysis of human, chimpanzee, macaque, and mouse tissues.Neuron, 85, 695-702.
Pubmed

16. Aw W, Fukuda S.(2015) Toward the comprehensive understanding of the gut ecosystem via metabolomics-based integrated omics approach. Semin Immunopathol, 37, 5-16.
Pubmed

17. Takahashi, K., Itaya, K., Nakamura, M., Koizumi, M., Arakawa, N., Tomita, M. and Yamakawa, H. (2015) A Generic Software Platform for Brain-Inspired Cognitive Computing. Procedia Computer Science, 71: 31-37.

18. Murakami, S., Goto, Y., Ito, K., Hayasaka, S., Kurihara, S., Soga, T., Tomita, M. and Fukuda, S. (2015) The consumption of bicarbonate-rich mineral water improves glycemic control. Evidence-Based Complementary and Alternative Medicine 2015:10.

19. Tsurumaki, M., Kotake, M., Iwasaki, M., Saito, M., Tanaka, K., Aw, W., and Fukuda, S. and Tomita, M. (2015) The application of omics technologies in the functional evaluation of inulin and inulin-containing prebiotics dietary supplementation. Nutr Diabetes. 5:e185.

20. Sakagami, H., Shimada, C., Kanda, Y., Amano, O., Sugimoto, M., Ota, S., Soga, T., Tomita, M., Sato, A., Tanuma, S., Takao, K., and Sugita, Y.(2015) Effects of 3-styrylchromones on metabolic profiles and cell death in oral squamous cell carcinoma cells. Toxicology Reports, 2:1281-1290.

21. Kawasaki, Y., Nakada, T. and Tomita, M.(2015) Taxonomic revision of oil-producing green algae, Chlorococcum oleofaciens (Volvocales, Chlorophyceae), and its relatives. J. Phycol. 51: 1000-1016.

22. Uetaki, M., Tabata, S., Nakasuka, F., Soga, T. and Tomita, M. (2015) Metabolomic alterations in human cancer cells by vitamin C-induced oxidative stress. Scientific Reports 5:13896.

23. Murakami, S., Baba, F., Fukuda, S., Soga, T., Fujishima, H. and Tomita, M. (2015) Comprehensive analysis of microbes and metabolites in human tear fluids. KEIO SFC JOURNAL, 15(1):382-400.

24. Hirose, Y., Ikeda, T., K., Noro, E., Hiraoka, K., Tomita, M. and Kanai, A. (2015) Precise mapping and dynamics of tRNA-derived fragments (tRFs) in the development of Triops cancriformis (tadpole shrimp). BMC Genetics, 16:83.

25. Shimo, H., Arjunan, S., N., V., Machiyama, H., Nishino, T., Suematsu, M., Fujita, H., Tomita, M., and Takahashi, K. (2015) Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes.PLoS Comput Biol 11(6):e1004210.

26. Nakada, T., Matsuzaki, R., Krienitz, L., Tomita, M. and Nozaki, H. (2015) Taxonomic reassessment of strains formerly classified as Chloromonas insignis (Volvocales, Chlorophyceae), and description of Gloeomonas anomalipyrenoides sp. nov. Acta phytotaxonomica et geobotanica,66(1):23-33.

27. Ohtani, N., Tomita, M. and Itaya, M. (2015) Curing the Megaplasmid pTT27 from Thermus thermophilus HB27 and Maintaining Exogenous Plasmids in the Plasmid-Free Strain. Appl Environ Microbiol. 2015 Dec 28;82(5):1537-48. doi: 10.1128/AEM.03603-15.

2014

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

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

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

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

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

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

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

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

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

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

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

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

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

14. Sano, I., H., Toki, T., Naito, Y. and Tomita, M. (2014) Contribution of developmental changes in energy metabolism to excitation-contraction coupling of a ventricular cell: a simulation study. 41: 73-76.

15. Jia, H., Aw, W., Hanate, M., Takahashi, S., Kenji, S., Tanaka, H., Tomita, M. and Kato, H. (2014) Multi-faceted integrated omics analysis revealed Parsley (Petroselinum crispum) as a novel dietary intervention in dextran sodium sulphate induced colitic mice. J. Funct. Food 11:438-448.

16. Arakawa, K. and Tomita, M. (2014) Genome Analysis Workshop: a Personal Genomics class at Keio SFC.14:158-197.

17. Hirayama, A., Igarashi, K., Tomita, M. and Soga, T. (2014) Development of quantitative method for determination of <GAMMA>-glutamyl peptides by capillary electrophoresis tandem massspectrometry: an efficient approach avoiding matrix effect . PLoS Comput Biol 11(6):e1004210.

18. Oshita K, Tomita M and Arakawa K. (2014) G-Links: a gene-centric link acquisition service [version 2; referees: 2 approved].F1000Research 2015 3:285.

2013

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

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.
PubmedPublisher

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

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

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
Publisher

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.
Publisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
Pubmed
Publisher

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.
Pubmed
Publisher

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.
Pubmed
Publisher

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.
Publisher

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.
Pubmed
Publisher

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.
Pubmed
Publisher

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
Pubmed
Publisher

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

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

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

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

2012

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

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.
PubmedPublisher

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.
Publisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
Publisher

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

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

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

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
Publisher

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.
Pubmed Publisher

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.
Pubmed Publisher

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.
Pubmed Publisher

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.
PubmedPublisher

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.
Pubmed Publisher

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.
PubmedPublisher

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.
Pubmed Publisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
Pubmed Publisher

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.
Publisher

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.
PubmedPublisher

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.
PubmedPublisher

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. PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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

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.
PubmedPublisher

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.
PubmedPublisher

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

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.
Publisher

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.
PubmedPublisher

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

2011

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

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

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.
PubmedPublisher

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.
Publisher

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.
PubmedPublisher

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.
PubmedPublisher

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

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.
Publisher

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

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.
PubmedPublisher

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

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.
PubmedPublisher

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

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.
PubmedPublisher

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

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

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

2010

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

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.]
PubmedPublisher

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.
PubmedPublisher

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.
Publisher

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

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.
PubmedPublisher

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.
Publisher

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.
Publisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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

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.
PubmedPublisher

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

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.
PubmedPublisher

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.
PubmedPublisher

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.
Publisher

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.
Publisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
Publisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
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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.
PubmedPublisher

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.
Publisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

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.
PubmedPublisher

2009

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2008

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2007

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

http://www.iab.keio.ac.jp/jp/images//publisher.png

2006

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2005

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2004

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2003

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2002

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

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

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

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

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

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

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

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

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

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

2001

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

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

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

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

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

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

2000

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

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

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

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

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

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

1999

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

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

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

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

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

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

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

1998

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

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

1997

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

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

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

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