Papers - Tomita, Masaru
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Metabolomics profiles alterations in cigarette smokers and heated tobacco product users.
Harada S, Ohmomo H, Matsumoto M, Sata M, Iida M, Hirata A, Miyagawa N, Kuwabara K, Kato S, Toki R, Edagawa S, Sugiyama D, Sato A, Hirayama A, Sugimoto M, Soga T, Tomita M, Shimizu A, Okamura T, Takebayashi T
Journal of epidemiology 2023.11
ISSN 0917-5040
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Saito M., Inose R., Sato A., Tomita M., Suzuki H., Kanai A.
Journal of Molecular Evolution (Journal of Molecular Evolution) 91 ( 5 ) 669 - 686 2023.10
ISSN 00222844
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Abhinand C.S., Galipon J., Mori M., Ramesh P., Prasad T.S.K., Raju R., Sudhakaran P.R., Tomita M.
Journal of Cell Communication and Signaling (Journal of Cell Communication and Signaling) 17 ( 3 ) 1067 - 1079 2023.09
ISSN 18739601
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Hirayama A., Ishikawa T., Takahashi H., Yamanaka S., Ikeda S., Hirata A., Harada S., Sugimoto M., Soga T., Tomita M., Takebayashi T.
Metabolites (Metabolites) 13 ( 4 ) 2023.04
ISSN 2218-1989
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iDMET: network-based approach for integrating differential analysis of cancer metabolomics
Matsuta R., Yamamoto H., Tomita M., Saito R.
BMC Bioinformatics (BMC Bioinformatics) 23 ( 1 ) 508 2022.12
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Yoshida Y., Satoh T., Ota C., Tanaka S., Horikawa D.D., Tomita M., Kato K., Arakawa K.
BMC Genomics (BMC Genomics) 23 ( 1 ) 405 2022.12
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Morita T., Majdalani N., Miura M.C., Inose R., Oshima T., Tomita M., Kanai A., Gottesman S.
mBio (mBio) 13 ( 6 ) 2022.12
ISSN 21612129
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1000 spider silkomes: Linking sequences to silk physical properties
Arakawa K., Kono N., Malay A.D., Tateishi A., Ifuku N., Masunaga H., Sato R., Tsuchiya K., Ohtoshi R., Pedrazzoli D., Shinohara A., Ito Y., Nakamura H., Tanikawa A., Suzuki Y., Ichikawa T., Fujita S., Fujiwara M., Tomita M., Blamires S.J., Chuah J.A., Craig H., Foong C.P., Greco G., Guan J., Holland C., Kaplan D.L., Sudesh K., Mandal B.B., Norma-Rashid Y., Oktaviani N.A., Preda R.C., Pugno N.M., Rajkhowa R., Wang X., Yazawa K., Zheng Z., Numata K.
Science Advances (Science Advances) 8 ( 41 ) eabo6043 2022.10
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Salivary metabolomics with machine learning for colorectal cancer detection
Kuwabara H., Katsumata K., Iwabuchi A., Udo R., Tago T., Kasahara K., Mazaki J., Enomoto M., Ishizaki T., Soya R., Kaneko M., Ota S., Enomoto A., Soga T., Tomita M., Sunamura M., Tsuchida A., Sugimoto M., Nagakawa Y.
Cancer Science (Cancer Science) 113 ( 9 ) 3234 - 3243 2022.09
ISSN 13479032
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Tsurumaki M., Saito M., Tomita M., Kanai A.
RNA (RNA) 28 ( 8 ) 1041 - 1057 2022.08
ISSN 13558382
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Iwai H., Mori M., Tomita M., Kono N., Arakawa K.
Frontiers in Ecology and Evolution (Frontiers in Ecology and Evolution) 10 2022.06
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Suzuki Y., Hayasaka R., Hasebe M., Ikeda S., Soga T., Tomita M., Hirayama A., Kuroda H.
Metabolites (Metabolites) 12 ( 6 ) 2022.06
ISSN 2218-1989
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Yoshida Y, Shaikhutdinov N, Kozlova O, Itoh M, Tagami M, Murata M, Nishiyori-Sueki H, Kojima-Ishiyama M, Noma S, Cherkasov A, Gazizova G, Nasibullina A, Deviatiiarov R, Shagimardanova E, Ryabova A, Yamaguchi K, Bino T, Shigenobu S, Tokumoto S, Miyata Y, Cornette R, Yamada TG, Funahashi A, Tomita M, Gusev O, Kikawada T
NAR genomics and bioinformatics (NAR Genomics and Bioinformatics) 4 ( 2 ) lqac029 2022.06
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Saito Y, Matsuda S, Ohnishi N, Endo K, Ashitani S, Ohishi M, Ueno A, Tomita M, Ueda K, Soga T, Muthuswamy SK
Communications biology (Communications Biology) 5 ( 1 ) 403 2022.05
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Nakayama J, Konno Y, Maruyama A, Tomita M, Makinoshima H
Journal of natural medicines (Journal of Natural Medicines) 76 ( 3 ) 686 - 692 2022.04
ISSN 1340-3443
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Kurihara Y, Iwai H, Kono N, Tomita M, Arakawa K
Biology open (Biology Open) 11 ( 3 ) 2022.02
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Kimura A, Hirayama A, Matsumoto T, Sato Y, Kobayashi T, Ikeda S, Maruyama M, Kaneko M, Shigeta M, Ito E, Soma T, Miyamoto K, Soga T, Tomita M, Oya A, Matsumoto M, Nakamura M, Kanaji A, Miyamoto T
Metabolites (Metabolites) 12 ( 1 ) 2022.01
ISSN 2218-1989
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Watanabe K, Iida M, Harada S, Kato S, Kuwabara K, Kurihara A, Takeuchi A, Sugiyama D, Okamura T, Suzuki A, Amano K, Hirayama A, Sugimoto M, Soga T, Tomita M, Kobayashi Y, Banno K, Aoki D, Takebayashi T
Maturitas (Maturitas) 155 54 - 62 2022.01
ISSN 0378-5122
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Miura MC, Nagata S, Tamaki S, Tomita M, Kanai A
Frontiers in microbiology (Frontiers in Microbiology) 13 849080 2022
ISSN 1664-302X
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Hayasaka R, Tabata S, Hasebe M, Ikeda S, Hikita T, Oneyama C, Yoshitake J, Onoshima D, Takahashi K, Shibata T, Uchida K, Baba Y, Soga T, Tomita M, Hirayama A
Frontiers in molecular biosciences (Frontiers in Molecular Biosciences) 9 1049402 2022
ISSN 2296-889X
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Okamoto L, Watanabe S, Deno S, Nie X, Maruyama J, Tomita M, Hatano A, Yugi K
Neuroscience research (Neuroscience Research) 175 82 - 97 2021.12
ISSN 0168-0102
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Decoding gut microbiota by imaging analysis of fecal samples.
Furusawa C, Tanabe K, Ishii C, Kagata N, Tomita M, Fukuda S
iScience (iScience) 24 ( 12 ) 103481 2021.12
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Ishibashi Y., Harada S., Takeuchi A., Iida M., Kurihara A., Kato S., Kuwabara K., Hirata A., Shibuki T., Okamura T., Sugiyama D., Sato A., Amano K., Hirayama A., Sugimoto M., Soga T., Tomita M., Takebayashi T.
Scientific Reports 11 ( 1 ) 7407 2021.12
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Guo J., Satoh K., Tabata S., Mori M., Tomita M., Soga T.
BMC Cancer 21 ( 1 ) 174 2021.12
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Nakasuka F., Tabata S., Sakamoto T., Hirayama A., Ebi H., Yamada T., Umetsu K., Ohishi M., Ueno A., Goto H., Sugimoto M., Nishioka Y., Yamada Y., Tomita M., Sasaki A.T., Yano S., Soga T.
Communications Biology 4 ( 1 ) 782 2021.12
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Murai Y, Yagi-Utsumi M, Fujiwara M, Tanaka S, Tomita M, Kato K, Arakawa K
BMC genomics (BMC Genomics) 22 ( 1 ) 813 2021.11
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Iwai H., Kurihara Y., Kono N., Tomita M., Arakawa K.
Insectes Sociaux (Insectes Sociaux) 68 ( 4 ) 375 - 382 2021.11
ISSN 00201812
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Saito R., Hirayama A., Akiba A., Kamei Y., Kato Y., Ikeda S., Kwan B., Pu M., Natarajan L., Shinjo H., Akiyama S., Tomita M., Soga T., Maruyama S.
Metabolites (Metabolites) 11 ( 10 ) 2021.10
ISSN 2218-1989
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Multicomponent nature underlies the extraordinary mechanical properties of spider dragline silk
Kono N., Nakamura H., Mori M., Yoshida Y., Ohtoshi R., Malay A.D., Pedrazzoli Moran D.A., Tomita M., Numata K., Arakawa K.
Proceedings of the National Academy of Sciences of the United States of America 118 ( 31 ) 2021.08
ISSN 00278424
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RNA sequencing data for gamma radiation response in the extremotolerant tardigrade <i>Ramazzottius varieornatus</i>.
Yoshida Y, Horikawa DD, Sakashita T, Yokota Y, Kobayashi Y, Tomita M, Arakawa K
Data in brief 36 107111 2021.06
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Quality assessment of untargeted analytical data in a large-scale metabolomic study
Saito R., Sugimoto M., Hirayama A., Soga T., Tomita M., Takebayashi T.
Journal of Clinical Medicine (Journal of Clinical Medicine) 10 ( 9 ) 2021.05
ISSN 2077-0383
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A metabolomic profile predictive of new osteoporosis or sarcopenia development
Miyamoto K., Hirayama A., Sato Y., Ikeda S., Maruyama M., Soga T., Tomita M., Nakamura M., Matsumoto M., Yoshimura N., Miyamoto T.
Metabolites (Metabolites) 11 ( 5 ) 2021.05
ISSN 2218-1989
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Hayasaka R., Tabata S., Hasebe M., Ikeda S., Ohnuma S., Mori M., Soga T., Tomita M., Hirayama A.
Metabolites (Metabolites) 11 ( 4 ) 2021.04
ISSN 2218-1989
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Xanthurenic acid is the main pigment of trichonephila clavata gold dragline silk
Fujiwara M., Kono N., Hirayama A., Malay A.D., Nakamura H., Ohtoshi R., Numata K., Tomita M., Arakawa K.
Biomolecules 11 ( 4 ) 2021.04
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Shibutami E., Ishii R., Harada S., Kurihara A., Kuwabara K., Kato S., Iida M., Akiyama M., Sugiyama D., Hirayama A., Sato A., Amano K., Sugimoto M., Soga T., Tomita M., Takebayashi T.
PLoS ONE 16 ( 2 February ) e0246456 2021.02
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Guo J., Wang J., Iino K., Tomita M., Soga T.
Evidence-based Complementary and Alternative Medicine 2021 6646507 2021
ISSN 1741427X
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Sato Y, Tomita M, Soga T, Ochiai A, Makinoshima H
Frontiers in pharmacology (Frontiers in Pharmacology) 12 718675 2021
ISSN 1663-9812
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Hikichi S., Sugimoto M., Tomita M.
Scientific Reports (Scientific Reports) 10 ( 1 ) 7923 2020.12
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Kono N., Nakamura H., Mori M., Tomita M., Arakawa K.
Scientific Reports (Scientific Reports) 10 ( 1 ) 15721 2020.12
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Aw W., Jia H., Lyu W., Fukuda S., Tomita M., Otani L., Kato H.
npj Science of Food (npj Science of Food) 4 ( 1 ) 5 2020.12
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Ishikawa S., Hiraka T., Kirii K., Sugimoto M., Shimamoto H., Sugano A., Kitabatake K., Toyoguchi Y., Kanoto M., Nemoto K., Soga T., Tomita M., Iino M.
Journal of Clinical Medicine (Journal of Clinical Medicine) 9 ( 12 ) 1 - 8 2020.12
ISSN 2077-0383
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Ozawa H., Hirayama A., Shoji F., Maruyama M., Suzuki K., Yamanaka-Okumura H., Tatano H., Morine Y., Soga T., Shimada M., Tomita M.
Metabolites (Metabolites) 10 ( 11 ) 1 - 11 2020.11
ISSN 2218-1989
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Effects of feed crops and boiling on chicken egg yolk and white determined by a metabolome analysis
Ogura T., Wakayama M., Ashino Y., Kadowaki R., Sato M., Soga T., Tomita M.
Food Chemistry (Food Chemistry) 327 127077 2020.10
ISSN 03088146
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Fujishima H., Okada N., Matsumoto K., Shimizu E., Fukuda S., Tomita M.
Journal of Clinical Medicine (Journal of Clinical Medicine) 9 ( 10 ) 1 - 9 2020.10
ISSN 2077-0383
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Kondo K., Mori M., Tomita M., Arakawa K.
FEBS Open Bio (FEBS Open Bio) 10 ( 9 ) 1774 - 1781 2020.09
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Ozawa H., Hirayama A., Ishikawa T., Kudo R., Maruyama M., Shoji F., Doke T., Ishimoto T., Maruyama S., Soga T., Tomita M.
Analytical Chemistry (Analytical Chemistry) 92 ( 14 ) 9799 - 9806 2020.07
ISSN 00032700
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Base editors for simultaneous introduction of C-to-T and A-to-G mutations
Sakata R.C., Ishiguro S., Mori H., Tanaka M., Tatsuno K., Ueda H., Yamamoto S., Seki M., Masuyama N., Nishida K., Nishimasu H., Arakawa K., Kondo A., Nureki O., Tomita M., Aburatani H., Yachie N.
Nature Biotechnology (Nature Biotechnology) 38 ( 7 ) 865 - 869 2020.07
ISSN 10870156
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Draft Genome Sequence of Geobacter sp. Strain SVR, Isolated from Antimony Mine Soil
Warashina T., Harada M., Nakajima N., Yamamura S., Tomita M., Suzuki H., Amachi S.
Microbiology Resource Announcements (Microbiology Resource Announcements) 9 ( 26 ) 2020.06
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Hirayama A., Tabata S., Kudo R., Hasebe M., Suzuki K., Tomita M., Soga T.
Journal of Chromatography A (Journal of Chromatography A) 1619 460914 2020.05
ISSN 00219673
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Hamid S.S., Wakayama M., Ashino Y., Kadowaki R., Soga T., Tomita M.
Algal Research 47 2020.05
ISSN 22119264
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Chromatin Remodeling and Immediate Early Gene Activation by SLFN11 in Response to Replication Stress
Murai J., Zhang H., Pongor L., Tang S.W., Jo U., Moribe F., Ma Y., Tomita M., Pommier Y.
Cell Reports (Cell Reports) 30 ( 12 ) 4137 - 4151.e6 2020.03
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Sensory properties and metabolomic profiles of dry-cured ham during the ripening process
Sugimoto M., Sugawara T., Obiya S., Enomoto A., Kaneko M., Ota S., Soga T., Tomita M.
Food Research International (Food Research International) 129 108850 2020.03
ISSN 09639969
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Mass Spectrometry-Compatible Subcellular Fractionation for Proteomics
Masuda T., Sugiyama N., Tomita M., Ohtsuki S., Ishihama Y.
Journal of Proteome Research (Journal of Proteome Research) 19 ( 1 ) 75 - 84 2020.01
ISSN 15353893
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Itaya M., Sato M., Watanabe S., Yoshikawa H., Tomita M., Sato R.
Journal of Biochemistry (Journal of Biochemistry) 25 ( 1 ) 231 - 236 2020.01
ISSN 0021924X
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Does the Gut Microbiota Modulate Host Physiology through Polymicrobial Biofilms?
Yang J, Yang Y, Ishii M, Nagata M, Aw W, Obana N, Tomita M, Nomura N, Fukuda S.
Microbes Environ 2020
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Draft Genome Sequences of Bifidobacterium animalis Consecutively Isolated from Healthy Japanese Individuals
Tsukimi T, Watabe T, Tanaka K, Sato MP, Suzuki H, Tomita M, Fukuda S.
J Genomics 8 37 - 42 2020
ISSN 1839-9940
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Comparison of the transcriptomes of two tardigrades with different hatching coordination
Yoshida Y., Sugiura K., Tomita M., Matsumoto M., Arakawa K.
BMC Developmental Biology (BMC Developmental Biology) 19 ( 1 ) 24 2019.12
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Orb-weaving spider Araneus ventricosus genome elucidates the spidroin gene catalogue
Kono N., Nakamura H., Ohtoshi R., Moran D., Shinohara A., Yoshida Y., Fujiwara M., Mori M., Tomita M., Arakawa K.
Scientific Reports (Scientific Reports) 9 ( 1 ) 8380 2019.12
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Kondo K., Mori M., Tomita M., Arakawa K.
Genes to Cells (Genes to Cells) 24 ( 12 ) 768 - 780 2019.12
ISSN 13569597
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The bagworm genome reveals a unique fibroin gene that provides high tensile strength
Kono N., Nakamura H., Ohtoshi R., Tomita M., Numata K., Arakawa K.
Communications Biology (Communications Biology) 2 ( 1 ) 148 2019.12
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Peptide Synthesis under the Alkaline Hydrothermal Conditions on Enceladus
Takahagi W., Seo K., Shibuya T., Takano Y., Fujishima K., Saitoh M., Shimamura S., Matsui Y., Tomita M., Takai K.
ACS Earth and Space Chemistry 3 ( 11 ) 2559 - 2568 2019.11
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Fukushima K., Harada S., Takeuchi A., Kurihara A., Iida M., Fukai K., Kuwabara K., Kato S., Matsumoto M., Hirata A., Akiyama M., Tomita M., Hirayama A., Sato A., Suzuki C., Sugimoto M., Soga T., Sugiyama D., Okamura T., Takebayashi T.
Journal of Clinical Lipidology (Journal of Clinical Lipidology) 13 ( 6 ) 932 - 939.e2 2019.11
ISSN 19332874
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Draft Genome Sequences of Enterococcus faecalis Strains Isolated from Healthy Japanese Individuals
Tanaka K., Watabe T., Kato K., Tsukimi T., Sato M.P., Odamaki T., Tomita M., Fukuda S.
Microbiology Resource Announcements (Microbiology Resource Announcements) 8 ( 40 ) 2019.10
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Murata T., Yanagisawa T., Kurihara T., Kaneko M., Ota S., Enomoto A., Tomita M., Sugimoto M., Sunamura M., Hayashida T., Kitagawa Y., Jinno H.
Breast Cancer Research and Treatment (Breast Cancer Research and Treatment) 177 ( 3 ) 591 - 601 2019.10
ISSN 01676806
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Saito M., Sato A., Nagata S., Tamaki S., Tomita M., Suzuki H., Kanai A.
Genome Biology and Evolution (Genome Biology and Evolution) 11 ( 10 ) 2713 - 2726 2019.09
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Chlorococcum turfosum comb. nov. (Volvocales, Chlorophyceae) and visualization of chimeric sequences
Nakada T., Watanabe S., Lewis L., Tomita M.
Phycological Research 67 ( 3 ) 239 - 243 2019.07
ISSN 13220829
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Harada M., Ito K., Nakajima N., Yamamura S., Tomita M., Suzuki H., Amachi S.
G3: Genes, Genomes, Genetics (G3: Genes, Genomes, Genetics) 9 ( 5 ) 1321 - 1329 2019.05
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Itaya M., Nagasaku M., Shimada T., Ohtani N., Shiwa Y., Yoshikawa H., Kaneko S., Tomita M., Sato M.
FEMS Microbiology Letters (FEMS Microbiology Letters) 366 ( 4 ) 2019.02
ISSN 03781097
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Effects of inter-day and intra-day variation on salivary metabolomic profiles
Kawanishi N., Hoshi N., Masahiro S., Enomoto A., Ota S., Kaneko M., Soga T., Tomita M., Kimoto K.
Clinica Chimica Acta (Clinica Chimica Acta) 489 41 - 48 2019.02
ISSN 00098981
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Kajiura D., Yamanaka-Okumura H., Hirayama A., Tatano H., Endo K., Honma M., Igarashi K., Shoji F., Ikeda S., Yamaguchi N., Katayama T., Morine Y., Imura S., Utsunomiya T., Soga T., Tomita M., Shimada M.
Nutrition (Nutrition) 58 110 - 119 2019.02
ISSN 08999007
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Comparative genomics of Bacteria commonly identified in the built environment
Merino N., Zhang S., Tomita M., Suzuki H.
BMC Genomics (BMC Genomics) 20 ( 1 ) 92 2019.01
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Fast and global detection of periodic sequence repeats in large genomic resources
Mori H., Evans-Yamamoto D., Ishiguro S., Tomita M., Yachie N.
Nucleic acids research (Nucleic Acids Research) 47 ( 2 ) e8 2019.01
ISSN 03051048
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Sasaki K., Sagawa H., Suzuki M., Yamamoto H., Tomita M., Soga T., Ohashi Y.
Analytical Chemistry (Analytical Chemistry) 91 ( 2 ) 1295 - 1301 2019.01
ISSN 00032700
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Reconsidering plasmid maintenance factors for computational plasmid design
Yano H., Shintani M., Tomita M., Suzuki H., Oshima T.
Computational and Structural Biotechnology Journal (Computational and Structural Biotechnology Journal) 17 70 - 81 2019.01
ISSN 2001-0370
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Nakada T., Tsuchida Y., Tomita M.
Molecular Phylogenetics and Evolution (Molecular Phylogenetics and Evolution) 130 1 - 8 2019.01
ISSN 10557903
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Metabolome profiling of various seaweed species discriminates between brown, red, and green algae
Hamid S., Wakayama M., Ichihara K., Sakurai K., Ashino Y., Kadowaki R., Soga T., Tomita M.
Planta (Planta) 249 ( 6 ) 1921 - 1947 2019
ISSN 00320935
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Yasuda Y., Zhang K., Sasaki O., Tomita M., Rival D., Galipon J.
Journal of the Electrochemical Society 166 ( 9 ) B3302 - B3308 2019
ISSN 00134651
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Yang J., Tsukimi T., Yoshikawa M., Suzuki K., Takeda T., Tomita M., Fukuda S.
mSystems (mSystems) 4 ( 6 ) 2019
ISSN 2379-5077
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Strand-specific Single-stranded DNA Sequencing (4S-seq) of E. coli genomes
Masuda T, Kono N, Tomita M, Arakawa K.
Bio-protocol (Bio-protocol) 9 ( 15 ) e3329 2019
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Complete Genome Sequence of Arthrobacter sp. Strain MN05-02, a UV-Resistant Bacterium from a Manganese Deposit in the Sonoran Desert
Ii KM, Kono N, Paulino-Lima IG, Tomita M, Rothschild LJ, Arakawa K.
Journal of genomics 7 18 - 25 2019
ISSN 1839-9940
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Far rapid synthesis of giant DNA in the Bacillus subtilis genome by a conjugation transfer system
Itaya M., Sato M., Hasegawa M., Kono N., Tomita M., Kaneko S.
Scientific Reports (Scientific Reports) 8 ( 1 ) 8792 2018.12
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Tomita A., Mori M., Hiwatari K., Yamaguchi E., Itoi T., Sunamura M., Soga T., Tomita M., Sugimoto M.
Scientific Reports (Scientific Reports) 8 ( 1 ) 12075 2018.12
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Drying and extraction effects on three edible brown seaweeds for metabolomics
Hamid S., Wakayama M., Soga T., Tomita M.
Journal of Applied Phycology 30 ( 6 ) 3335 - 3350 2018.12
ISSN 09218971
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Tabata S., Yamamoto M., Goto H., Hirayama A., Ohishi M., Kuramoto T., Mitsuhashi A., Ikeda R., Haraguchi M., Kawahara K., Shinsato Y., Minami K., Saijo A., Toyoda Y., Hanibuchi M., Nishioka Y., Sone S., Esumi H., Tomita M., Soga T., Furukawa T., Akiyama S.
Scientific Reports (Scientific Reports) 8 ( 1 ) 6760 2018.12
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Metabolomics-based profiles predictive of low bone mass in menopausal women
Miyamoto T., Hirayama A., Sato Y., Koboyashi T., Katsuyama E., Kanagawa H., Fujie A., Morita M., Watanabe R., Tando T., Miyamoto K., Tsuji T., Funayama A., Soga T., Tomita M., Nakamura M., Matsumoto M.
Bone Reports (Bone Reports) 9 11 - 18 2018.12
ISSN 2352-1872
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Yamamoto Y., Nakanishi Y., Murakami S., Aw W., Tsukimi T., Nozu R., Ueno M., Hioki K., Nakahigashi K., Hirayama A., Sugimoto M., Soga T., Ito M., Tomita M., Fukuda S.
Microorganisms (Microorganisms) 6 ( 4 ) 2018.12
ISSN 2076-2607
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Sato Y., Matsuda S., Maruyama A., Nakayama J., Miyashita T., Udagawa H., Umemura S., Yanagihara K., Ochiai A., Tomita M., Soga T., Tsuchihara K., Makinoshima H.
Frontiers in Pharmacology (Frontiers in Pharmacology) 9 ( OCT ) 1129 2018.10
ISSN 1663-9812
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Nakada T., Takahashi S., Tomita M.
Phycological Research 66 ( 4 ) 310 - 317 2018.10
ISSN 13220829
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Ultralow input genome sequencing library preparation from a single tardigrade specimen
Yoshida Y., Konno S., Nishino R., Murai Y., Tomita M., Arakawa K.
Journal of Visualized Experiments (Journal of Visualized Experiments) 2018 ( 137 ) 2018.07
ISSN 1940087X
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Ishiguro S., Galipon J., Ishii R., Suzuki Y., Kondo S., Okada-Hatakeyama M., Tomita M., Ui-Tei K.
RNA Biology (RNA Biology) 15 ( 7 ) 976 - 989 2018.07
ISSN 15476286
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The complete mitochondrial genome of Eumeta variegata (Lepidoptera: Psychidae)
Arakawa K., Kono N., Ohtoshi R., Nakamura H., Tomita M.
Mitochondrial DNA Part B: Resources (Mitochondrial DNA Part B: Resources) 3 ( 2 ) 812 - 813 2018.07
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Itaya M., Kusakabe H., Sato M., Tomita M., Sato R.
Journal of Biochemistry (Journal of Biochemistry) 164 ( 1 ) 15 - 20 2018.07
ISSN 0021924X
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Iuchi H., Sugimoto M., Tomita M.
BMC Bioinformatics (BMC Bioinformatics) 19 ( 1 ) 249 2018.06
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Mariscal A., Kakizawa S., Hsu J., Tanaka K., González-González L., Broto A., Querol E., Lluch-Senar M., Piñero-Lambea C., Sun L., Weyman P., Wise K., Merryman C., Tse G., Moore A., Hutchison C., Smith H., Tomita M., Venter J., Glass J., Piñol J., Suzuki Y.
ACS Synthetic Biology (ACS Synthetic Biology) 7 ( 6 ) 1538 - 1552 2018.06
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Development of a sheathless CE-ESI-MS interface
Hirayama A., Abe H., Yamaguchi N., Tabata S., Tomita M., Soga T.
Electrophoresis (Electrophoresis) 39 ( 11 ) 1382 - 1389 2018.06
ISSN 01730835
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Nakajima T., Katsumata K., Kuwabara H., Soya R., Enomoto M., Ishizaki T., Tsuchida A., Mori M., Hiwatari K., Soga T., Tomita M., Sugimoto M.
International Journal of Molecular Sciences (International Journal of Molecular Sciences) 19 ( 3 ) 2018.03
ISSN 16616596
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Human AK2 links intracellular bioenergetic redistribution to the fate of hematopoietic progenitors
Oshima K., Saiki N., Tanaka M., Imamura H., Niwa A., Tanimura A., Nagahashi A., Hirayama A., Okita K., Hotta A., Kitayama S., Osawa M., Kaneko S., Watanabe A., Asaka I., Fujibuchi W., Imai K., Yabe H., Kamachi Y., Hara J., Kojima S., Tomita M., Soga T., Noma T., Nonoyama S., Nakahata T., Saito M.
Biochemical and Biophysical Research Communications (Biochemical and Biophysical Research Communications) 497 ( 2 ) 719 - 725 2018.03
ISSN 0006291X
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Elevated polyamines in saliva of pancreatic cancer
Asai Y., Itoi T., Sugimoto M., Sofuni A., Tsuchiya T., Tanaka R., Tonozuka R., Honjo M., Mukai S., Fujita M., Yamamoto K., Matsunami Y., Kurosawa T., Nagakawa Y., Kaneko M., Ota S., Kawachi S., Shimazu M., Soga T., Tomita M., Sunamura M.
Cancers (Cancers) 10 ( 2 ) 2018.02
ISSN 2072-6694
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Tamaki S., Tomita M., Suzuki H., Kanai A.
Frontiers in Genetics (Frontiers in Genetics) 8 ( JAN ) 227 2018.01
ISSN 1664-8021
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Harada S., Hirayama A., Chan Q., Kurihara A., Fukai K., Iida M., Kato S., Sugiyama D., Kuwabara K., Takeuchi A., Akiyama M., Okamura T., Ebbels T., Elliott P., Tomita M., Sato A., Suzuki C., Sugimoto M., Soga T., Takebayashi T.
PLoS ONE (PLoS ONE) 13 ( 1 ) e0191230 2018.01
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High-quality overlapping paired-end reads for the detection of A-to-I editing on small RNA
Galipon J., Ishii R., Ishiguro S., Suzuki Y., Kondo S., Okada-Hatakeyama M., Tomita M., Ui-Tei K.
Methods in Molecular Biology 1823 167 - 183 2018
ISSN 10643745
-
Beta-galactosidase-responsive synthetic biomarker for targeted tumor detection
Nishihara T., Kuno S., Nonaka H., Tabata S., Saito N., Fukuda S., Tomita M., Sando S., Soga T.
Chemical Communications (Chemical Communications) 54 ( 83 ) 11745 - 11748 2018
ISSN 13597345
-
Kono N., Tomita M., Arakawa K.
Genome Biology and Evolution (Genome Biology and Evolution) 10 ( 11 ) 3110 - 3117 2018
-
Ishii C., Nakanishi Y., Murakami S., Nozu R., Ueno M., Hioki K., Aw W., Hirayama A., Soga T., Ito M., Tomita M., Fukuda S.
International Journal of Molecular Sciences (International Journal of Molecular Sciences) 19 ( 12 ) 2018
ISSN 16616596
-
Itaya M., Hasegawa M., Tomita M., Sato M.
Bioscience, Biotechnology and Biochemistry (Bioscience, Biotechnology and Biochemistry) 82 ( 2 ) 356 - 362 2018
ISSN 09168451
-
Morphology and Phylogeny of a Japanese Strain of Chlamydomonas augustae (Volvocales, Chlorophyceae)
Takahashi S, Tomita M, Nakada T.
J. Jpn. Bot 2018
-
Changes of liver metabolites following hepatectomy with ischemia reperfusion towards liver regeneration
Saito Y, Morine Y, Iwahashi S, Ikemoto T, Imura S, Yamanaka-Okumura H, Hirayama A, Soga T, Tomita M, Shimada M.
Ann Gastroenterol Surg 2 ( 3 ) 204 - 211 2018
-
Genomic Analysis of Rhodococcus sp. Br-6, a Bromate Reducing Bacterium Isolated From Soil in Chiba, Japan
Ito K, Harada M, Nakajima N, Yamamura S, Tomita M, Suzuki H, Amachi S.
J Genomics 6 122 - 126 2018
ISSN 1839-9940
-
Suzuki H, Tomita M, Tsai PJ, Ko WC, Hung YP, Huang IH, Chen JW.
Gut Pathogens (Gut Pathogens) 9 ( 1 ) 70 2017.10
ISSN 1757-4749
-
Kono N, Tomita M, Arakawa K.
BMC Genomics (BMC Genomics) 18 ( 1 ) 784 2017.09
-
Global metabolic reprogramming of colorectal cancer occurs at adenoma stage and is induced by MYC
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 MM, Kushida Y, Haba R, Okano K, Tomita M, Suzuki Y, Fukuda S, Aoki M, Soga T.
Proc Natl Acad Sci U S A. (Proceedings of the National Academy of Sciences of the United States of America) 114 ( 37 ) E7697-E7706 - E7706 2017.09
ISSN 00278424
-
Ikeda Y, Okada Y, Sato A, Kanai T, Tomita M, Atomi H, Kanai A.
Scientific Reports (Scientific Reports) 7 ( 1 ) 12674 2017.09
-
Okuma N, Saita M, Hoshi N, Soga T, Tomita M, Sugimoto M, Kimoto K.
PLoS ONE (PLoS ONE) 12 ( 8 ) e0183109 2017.08
-
Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus
Yoshida Y, Koutsovoulos G, Laetsch DR, Stevens L, Kumar S, Horikawa DD, Ishino K, Komine S, Kunieda T, Tomita M, Blaxter M, Arakawa K.
PLoS Biology (PLoS Biology) 15 ( 7 ) e2002266 2017.07
ISSN 15449173
-
Synthetic Biomarker Design by Using Analyte-Responsive Acetaminophen
Nishihara T, Inoue J, Tabata S, Murakami S, Ishikawa T, Saito N, Fukuda S, Tomita M, Soga T.
ChemBioChem (ChemBioChem) 18 ( 10 ) 910-913 - 913 2017.05
ISSN 14394227
-
Draft Genome Sequence of Roseovarius sp. A-2, an Iodide-Oxidizing Bacterium Isolated from Natural Gas
Yuliana T, Nakajima N, Yamamura S, Tomita M, Suzuki H, Amachi S.
J Genomics. 6 ( 5 ) 51-53 2017.04
-
Effect of timing of collection of salivary metabolomic biomarkers on oral cancer detection
Ishikawa S., Sugimoto M., Kitabatake K., Tu M., Sugano A., Yamamori I., Iba A., Yusa K., Kaneko M., Ota S., Hiwatari K., Enomoto A., Masaru T., Iino M.
Amino Acids 49 ( 4 ) 761 - 770 2017.04
ISSN 09394451
-
Robotic crowd biology with Maholo LabDroids
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.
Nat Biotechnol 35 ( 4 ) 310-312 2017.04
-
Serum Metabolomic Profiles for Human Pancreatic Cancer Discrimination
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.
International Journal of Molecular Sciences (International Journal of Molecular Sciences) 18 ( 4 ) 767 2017.04
ISSN 16616596
-
Jia H, Hanate M, Aw W, Itoh H, Saito K, Kobayashi S, Hachimura S, Fukuda S, Tomita M, Hasebe Y, Kato H.
Scientific Reports (Scientific Reports) 7 43993 2017.03
-
Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging
Nozaki T, Imai R, Tanbo M, Nagashima R, Tamura S, Tani T, Joti Y, Tomita M, Hibino K, Kanemaki MT, Wendt KS, Okada Y, Nagai T, Maeshima K.
Molecular Cell (Molecular Cell) 67 ( 2 ) 282-293 - 293.e7 2017
ISSN 10972765
-
A serum metabolomics-based profile in low bone mineral density postmenopausal women
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., Toyama Y.
Bone (Bone) 95 1 - 4 2017
Joint Work, Accepted, ISSN 87563282
-
Sugimoto M, Obiya S, Kaneko M, Enomoto A, Honma M, Wakayama M, Soga T, Tomita M.
Journal of Agricultural and Food Chemistry (Journal of Agricultural and Food Chemistry) 65 ( 2 ) 402 - 410 2017
Joint Work, Accepted, ISSN 00218561
-
Rearing and observation of immature stages of the hoverfly Microdon katsurai (Diptera, Syrphidae)
Iwai,H., Horikawa, D., Arakawa, K., Tomita, M., Komatsu, T. and Maruyama, M.
Biodiversity Data Journal (Biodiversity Data Journal) 4 ( 1 ) e10185 2017
Joint Work, Accepted, ISSN 1314-2828
-
*Inaba, Y., Nakahigashi, K., Ito, T. and Tomita, M.
Phycological Research 65 ( 1 ) 94 - 99 2017
Joint Work, Accepted, ISSN 13220829
-
Differential binding of three major human ADAR isoforms to coding and long non-coding transcripts.
Galipon, J., Ishii, R., Suzuki, Y., Tomita, M., and * Ui-Tei, K.
Genes (Genes) 8 ( 2 ) 68 2017
Joint Work, Accepted, ISSN 2073-4425
-
Sano HI, Toki T, Naito Y, Tomita M.
Journal of Theoretical Biology (Journal of Theoretical Biology) 419 269 - 277 2017
Joint Work, Accepted, ISSN 00225193
-
Nagata S, Imai J, Makino G, Tomita M, Kanai A.
Frontiers in Microbiology (Frontiers in Microbiology) 8 ( NOV ) 2151 2017
ISSN 1664-302X
-
Thymidine Catabolism as a Metabolic Strategy for Cancer Survival
Tabata S, Yamamoto M, Goto H, Hirayama A, Ohishi M, Kuramoto T, Mitsuhashi A, Ikeda R, Haraguchi M, Kawahara K, Shinsato Y, Minami K, Saijo A, Hanibuchi M, Nishioka Y, Sone S, Esumi H, Tomita M, Soga T, Furukawa T, Akiyama SI.
Cell Reports (Cell Reports) 19 ( 7 ) 1313-1321 - 1321 2017
-
Draft Genome Sequence of Roseovarius sp. A-2, an Iodide-Oxidizing Bacterium Isolated from Natural Gas Brine Water, Chiba, Japan.
Yuliana T, Nakajima N, Yamamura S, Tomita M, Suzuki H, Amachi S
Journal of genomics 5 51 - 53 2017
ISSN 1839-9940
-
18S Ribosomal RNA Gene Phylogeny of a Colonial Volvocalean Lineage (Tetrabaenaceae-Goniaceae-Volvocaceae, Volvocales, Chlorophyceae) and Its Close Relatives
Takashi Nakada, Takuro Ito, Masaru Tomita
The Journal of Japanese Botany 345 - 354 2016.12
-
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.
World Journal of Gastroenterology (World Journal of Gastroenterology) 22 ( 27 ) 6224 - 6234 2016.07
ISSN 10079327
-
Erratum to: Metabolomic profiling reveals novel biomarkers of alcohol intake and alcohol-induced liver injury in community-dwelling men.
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, Tomita M
Environmental health and preventive medicine 21 ( 4 ) 283 - 284 2016.07
ISSN 1342-078X
-
Smad2/3 proteins are required for immobilization-induced skeletal muscle atrophy
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, Toyama Y, Miyamoto T.
Journal of Biological Chemistry (Journal of Biological Chemistry) 291 ( 23 ) 12184 - 12194 2016.06
ISSN 00219258
-
Munakata H., Nakada T., Nakahigashi K., Nozaki H., Tomita M.
Journal of Eukaryotic Microbiology (Journal of Eukaryotic Microbiology) 63 ( 3 ) 340 - 348 2016.05
ISSN 10665234
-
Wakita M., Sano H.I., Naito Y., Tomita M.
Computing in Cardiology 43 1093 - 1096 2016.03
ISSN 23258861
-
Sano H.I., Naito Y., Tomita M.
Computing in Cardiology 43 249 - 252 2016.03
ISSN 23258861
-
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., Tomita M.
Environmental Health and Preventive Medicine (Environmental Health and Preventive Medicine) 21 ( 1 ) 18 - 26 2016.01
ISSN 1342078X
-
Shindo Y, Iwamoto K, Mouri K, Hibino K, Tomita M, Kosako H, Sako Y, Takahashi K.
Nature Communications (Nature Communications) 7 10485 2016.01
-
Expansion of noncanonical V-Arm-containing tRNAs in eukaryotes
Hamashima K., Tomita M., Kanai A.
Molecular Biology and Evolution (Molecular Biology and Evolution) 33 ( 2 ) 530 - 540 2016
Joint Work, ISSN 07374038
-
Yoshida Y., Tomiyama T., Maruta T., Tomita M., Ishikawa T., Arakawa K.
BMC Genomics (BMC Genomics) 17 ( 1 ) 182 2016
Joint Work
-
Nakada, T., Tomita, M., Wu, J. T. and Nozaki, H.
Journal of Phycology (Journal of Phycology) 52 ( 2 ) 208 - 304 2016
Research paper (scientific journal), Joint Work, ISSN 00223646
-
Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly
Kono N., Nakamura H., Ito Y., Tomita M., Arakawa K.
Molecular Ecology Resources (Molecular Ecology Resources) 16 ( 3 ) 662 - 672 2016
Research paper (scientific journal), Joint Work, ISSN 1755098X
-
Draft Genome Sequences of 37 Salmonella enterica Strains Isolated from Poultry Sources in Nigeria
Useh, N.,M., Ngbede, E.,O., Akange, N., Thomas, M., Foley, A., Keena, M., C., Nelson, E., Christopher-Hennings, J., Tomita, M., *Suzuki, H. and *Scaria, J.
Genome Announc 4 ( 3 ) e00315 - e00316 2016
Joint Work
-
Li Q., Guo S., Jiang X., Bryk J., Naumann R., Enard W., Tomita M., Sugimoto M., Khaitovich P., Pääbo S.
Proc Natl Acad Sci U S A (Proceedings of the National Academy of Sciences of the United States of America) 113 ( 19 ) 5358 - 5363 2016
Joint Work, ISSN 00278424
-
Sugimoto, M., Obiya, S., Kaneko, M., Enomoto, A., Honma, M., Wakayama, M., and Tomita, M.
Meat Science (Meat Science) 120 210 - 215 2016
Joint Work, ISSN 03091740
-
Genome sequencing of a single tardigrade Hypsibius dujardini individual
Arakawa, K., Yoshida, Y., Tomita, M.
Scientific Data (Scientific Data) 3 160063 2016
Joint Work
-
Identification of salivary metabolomic biomarkers for oral cancer screening
Ishikawa S., Sugimoto M., Kitabatake K., Sugano A., Nakamura M., Kaneko M., Ota S., Hiwatari K., Enomoto A., Soga T., Tomita M., Iino M.
Scientific Reports (Scientific Reports) 6 31520 2016
Joint Work
-
Profiling of plasma metabolites in postmenopausal women with metabolic syndrome
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., Takebayashi T.
Menopause (Menopause) 23 ( 7 ) 749 - 758 2016
Joint Work, ISSN 10723714
-
Metabolic profiling of total physical activity and sedentary behavior in community dwelling men
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.
PLoS ONE (PLoS ONE) 11 ( 10 ) e0164877 2016
Joint Work
-
Ito, K., Nakajima, N., Yamamura, S., Tomita, M., Suzuki, H. and Amachi, S.
Genome Announcements (Genome Announcements) 4 ( 5 ) e01155-16 2016
Joint Work, ISSN 2169-8287
-
Nakada, T. and Tomita, M.
Journal of Phycology (Journal of Phycology) 53 ( 1 ) JPY12484 - 117 2016
ISSN 00223646
-
Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth
Noro, E., Mori, M., Makino, G., Takai, Y., Ohnuma, S., Sato, A., Tomita, M., Nakahigashi, K. and Kanai, A.
RNA Biology (RNA Biology) 16 ( 2 ) 1 - 13 2016
Joint Work, Accepted, ISSN 15476286
-
Bri CA: A modular software platform for whole brain architecture
Itaya K., Takahashi K., Nakamura M., Koizumi M., Arakawa N., Tomita M., Yamakawa H.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 9947 LNCS 334 - 341 2016
ISSN 03029743
-
Ohtani N, Tomita M, Itaya M.
Applied and Environmental Microbiology (Applied and Environmental Microbiology) 28;82 ( 5 ) 1537 - 48 2015.12
ISSN 00992240
-
Tsurumaki M., Kotake M., Iwasaki M., Saito M., Tanaka K., Aw W., Fukuda S., Tomita M.
Nutrition and Diabetes (Nutrition and Diabetes) 5 ( 11 ) e185 2015.11
ISSN 2044-4052
-
Kawasaki Y, Nakada T, Tomita M.
Journal of Phycology (Journal of Phycology) 51 ( 5 ) 1000 - 16 2015.10
ISSN 00223646
-
Tracking global gene expression responses in T cell differentiation
Simeoni O., Piras V., Tomita M., Selvarajoo K.
Gene (Gene) 569 ( 2 ) 259 - 266 2015.09
ISSN 03781119
-
Operation of a 130-MHz/9-mm Compact HTS Annulus Magnet With a Micro-NMR Probe.
Hahn S, Kim Y, Song J, Voccio JP, Chu Y, Bascuñán J, Tomita M, Iwasa Y
IEEE transactions on applied superconductivity : a publication of the IEEE Superconductivity Committee 25 ( 3 ) 1 - 5 2015.06
ISSN 1051-8223
-
Bozek K., Wei Y., Yan Z., Liu X., Xiong J., Sugimoto M., Tomita M., Pääbo S., Sherwood C., Hof P., Ely J., Li Y., Steinhauser D., Willmitzer L., Giavalisco P., Khaitovich P.
Neuron (Neuron) 85 ( 4 ) 695 - 702 2015.02
ISSN 08966273
-
Modeling and simulation of developmental changes in contractile apparatus of ventricular cells
Takiguchi M., Toki T., Sano H., Naito Y., Tomita M.
Computing in Cardiology 42 1097 - 1100 2015.02
ISSN 23258861
-
Sensitivity analysis of ectopic electrical activity in the pulmonary vein myocardium
Sano H., Tanaka Y., Naito Y., Tomita M.
Computing in Cardiology 42 861 - 864 2015.02
ISSN 23258861
-
Ikeda K., Hirose Y., Hiraoka K., Noro E., Fujishima K., Tomita M., Kanai A.
RNA (RNA) 21 ( 2 ) 230 - 242 2015.02
ISSN 13558382
-
A Generic Software Platform for Brain-inspired Cognitive Computing
Takahashi, K., Itaya, K., Nakamura, M., Koizumi, M., Arakawa, N., Tomita, M. and Yamakawa, H.
Procedia Computer Science 71 31 - 37 2015
Joint Work
-
The Consumption of Bicarbonate-Rich Mineral Water Improves Glycemic Control
Murakami S, Goto Y, Ito K, Hayasaka S, Kurihara S, Soga T, Tomita M, Fukuda S.
Evid Based Complement Alternat Med. (Evidence-based Complementary and Alternative Medicine) 2015 10 2015
ISSN 1741427X
-
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.
Toxicology Reports (Toxicology Reports) 2 1281 - 1290 2015
Joint Work, ISSN 22147500
-
Analysis of genetic code ambiguity arising from nematode-specific misacylated tRNAs
Hamashima, K., Mori, M., Andachi, Y., Yuji Kohara, Y., M. and Kanai, A.
PLoS ONE (PLoS ONE) 10 ( 1 ) e0116981 2015
Joint Work
-
Alteration of metabolomic profiles by titanium dioxide nanoparticles in human gingivitis model
Garcia-Contreras, R., Sugimoto, M., Umemura, N., Kaneko, M., Hatakeyama, Y., Soga, T., Tomita, M., Scougall-Vilchis, R., J., Contreras-Bulnes, R., Nakajima, H. and *Sakagami, H.
Biomaterials (Biomaterials) 57 33 - 40 2015
Joint Work, ISSN 01429612
-
Method of preparing an equimolar DNA mixture for one-step DNA assembly of over 50 fragments
Tsuge, K., Sato, Y., Kobayashi, Y., Gondo, M., Hasebe, M., Togashi, T., Tomita, M. and Itaya, M.
Scientific Reports (Scientific Reports) 5 10655 2015
Joint Work
-
Effects of processing and storage conditions on charged metabolomic profiles in blood
Hirayama, A., Sugimoto, M., Suzuki, A., Hatakeyama, Y., Enomoto, A., Harada, S., Soga, T., Tomita, M. and Takebayashi, T.
Electrophoresis (Electrophoresis) 36 ( 18 ) 2148 - 2155 2015
Joint Work, ISSN 01730835
-
Metabolomic alterations in human cancer cells by Vitamin C-induced oxidative stress
Uetaki M., Tabata S., Nakasuka F., Soga T., Tomita M.
Scientific Reports (Scientific Reports) 5 13896 2015
Joint Work
-
Comprehensive analysis of microbes and metabolites in human tear fluids
Murakami, S., Baba, F., Fukuda, S., Soga, T., Fujishima, H. and Tomita, M.
KEIO SFC JOURNAL 382 - 400 2015
Joint Work
-
Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes
Shimo H., Arjunan S.N.V., Machiyama H., Nishino T., Suematsu M., Fujita H., Tomita M., Takahashi K.
PLoS Computational Biology (PLoS Computational Biology) 11 ( 6 ) e1004210 2015
Joint Work, ISSN 1553734X
-
Hirose Y., Ikeda K., Noro E., Hiraoka K., Tomita M., Kanai A.
BMC Genetics (BMC Genetics) 16 ( 1 ) 83 2015
Joint Work
-
Nakada T., Matsuzaki R., Krienitz L., Tomita M., Nozaki H.
Acta Phytotaxonomica et Geobotanica 66 ( 1 ) 23 - 33 2015
ISSN 13467565
-
Systems biology strategy reveals PKCd is key for sensitizing TRAIL-resistant human fibrosarcoma
Hayashi K., Tabata S., Piras V., Tomita M., Selvarajoo K.
Frontiers in Immunology (Frontiers in Immunology) 6 ( JAN ) 659 2015
ISSN 1664-3224
-
G-Links: A gene-centric link acquisition service
Arakawa K., Oshita K., Tomita M.
F1000Research (F1000Research) 3 285 2015
ISSN 20461402
-
Hirayama A., Igarashi K., Tomita M., Soga T.
Journal of Chromatography A (Journal of Chromatography A) 1369 161 - 169 2014.11
ISSN 00219673
-
Amariei C., Machné R., Stolc V., Soga T., Tomita M., Murray D.B.
Microbial Cell (Microbial Cell) 1 ( 9 ) 279 - 288 2014.09
ISSN 2311-2638
-
Temporal Enhancement of Trapped Field in a Compact NMR Magnet Comprising YBCO Annuli.
Hahn S, Kim Y, Voccio JP, Song J, Bascuñán J, Tomita M, Iwasa Y
IEEE transactions on applied superconductivity : a publication of the IEEE Superconductivity Committee 24 ( 3 ) 2014.06
ISSN 1051-8223
-
Sano, I., H., Toki, T., Naito, Y. and Tomita, M.
Computing in Cardiology 41 ( January ) 73 - 76 2014
ISSN 23258861
-
Cheng K., Lee B., Masuda T., Ito T., Ikeda K., Hirayama A., Deng L., Dong J., Shimizu K., Soga T., Tomita M., Palsson B., Robert M.
Nature Communications (Nature Communications) 31 3233 2014
Joint Work
-
Sakagami H., Sugimoto M., Tanaka S., Onuma H., Ota S., Kaneko M., Soga T., Tomita M.
Metabolomics 10 ( 2 ) 270 - 279 2014
Joint Work, ISSN 15733882
-
Quantifying periodicity in omics data
Amariei, A., Tomita, M. and Murray, B.D.
Frontiers in Cell and Developmental Biology (Frontiers in Cell and Developmental Biology) 2 ( AUG ) 40 2014
Joint Work, ISSN 2296-634X
-
Transcriptome-wide variability in single embryonic development cells
Piras V., Tomita M., Selvarajoo K.
Scientific Reports (Scientific Reports) 4 7137 2014
Joint Work
-
Genome Analysis Workshop: a Personal Genomics class at Keio SFC
Arakawa, K. and Tomita, M.
KEIO SFC JOURNAL 14 158 - 197 2014
Joint Work
-
Undesigned selection for replication termination of bacterial chromosomes
Kono, N., Arakawa, K., Mitsuru Sato; Yoshikawa, H., Masaru Tomita, M. and Itaya, M.
Journal of Molecular Biology (Journal of Molecular Biology) 426 ( 16 ) 2918 - 2927 2014
Joint Work, ISSN 00222836
-
Jia, H., Aw, W., Hanate, M., Takahashi, S., Kenji, S., Tanaka, H., Tomita, M., and Kato, H.
Journal of Functional Foods 11 ( C ) 438 - 448 2014
Joint Work, ISSN 17564646
-
Nakada T, Tsuchida Y, Arakawa K, Ito T and Tomita M.
Phycological Research 62 ( 3 ) 232 - 266 2014
Joint Work, ISSN 13220829
-
Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo
Nakahigashi, K., Takai, Y., Shiwa, Y., Wada, M., Honma, M., Yoshikawa, H., Tomita, M., Kanai, A. and Mori, H
BMC Genomics (BMC Genomics) 15 ( 1 ) 1115 2014
Joint Work
-
Sato D., Sugimoto M., Akashi H., Tomita M., Soga T.
Molecular BioSystems (Molecular BioSystems) 10 ( 4 ) 909 - 915 2014
ISSN 1742206X
-
Bozek K., Wei Y., Yan Z., Liu X., Xiong J., Sugimoto M., Tomita M., Pääbo S., Pieszek R., Sherwood C.C., Hof P.R., Ely J.J., Steinhauser D., Willmitzer L., Bangsbo J., Hansson O., Call J., Giavalisco P., Khaitovich P.
PLoS Biology (PLoS Biology) 12 ( 5 ) e1001871 2014
ISSN 15449173
-
Nakada T., Tomita M.
Acta Phytotaxonomica et Geobotanica 65 ( 2 ) 67 - 73 2014
ISSN 13467565
-
Saito T, Sugimoto M, Igarashi K, Saito K, Shao L, Katsumi T, Tomita K, Sato C, Okumoto K, Nishise Y, Watanabe H, Tomita M, Ueno Y, Soga T.
Metabolism (Metabolism: Clinical and Experimental) 62 ( 11 ) 1577 - 1586 2013.11
Joint Work, ISSN 00260495
-
The dynamics of cellular energetics during continuous yeast culture
Amariei C., Machne R., Sasidharan K., Gottstein W., Tomita M., Soga T., Lloyd D., Murray D.B.
Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS) 2013 2708 - 2711 2013.10
ISSN 1557170X
-
Time-resolved metabolomics of a novel trebouxiophycean alga using 13CO2 feeding
Ito T., Sugimoto M., Toya Y., Ano Y., Kurano N., Soga T., Tomita M.
Journal of Bioscience and Bioengineering (Journal of Bioscience and Bioengineering) 116 ( 3 ) 408 - 415 2013.09
ISSN 13891723
-
Nishino T., Yachie-Kinoshita A., Hirayama A., Soga T., Suematsu M., Tomita M.
PLoS ONE (PLoS ONE) 8 ( 8 ) e71060 2013.08
-
GEMBASSY: An EMBOSS associated software package for comprehensive genome analyses
Itaya H, Oshita K, Arakawa K, Tomita M.
Source Code for Biology and Medicine (Source Code for Biology and Medicine) 8 ( 17 ) 17 2013.08
Joint Work, ISSN 1751-0473
-
Global microRNA elevation by inducible Exportin 5 regulates cell cycle entry
Iwasaki Y.W., Kiga K., Kayo H., Fukuda-Yuzawa Y., Weise J., Inada T., Tomita M., Ishihama Y., Fukao T.
RNA (RNA) 19 ( 4 ) 490 - 497 2013.04
ISSN 13558382
-
Changes of metabolic profiles in an oral squamous cell carcinoma cell line induced by eugenol
Koh T, Murakami Y, Tanaka S, Machino M, Onuma H, Kaneko M, Sugimoto M, Soga T, Tomita M, Sakagami H.
In Vivo (In Vivo) 27 ( 2 ) 233 - 243 2013.03
Joint Work, ISSN 0258851X
-
Martínez P., Gálvez S., Ohtsuka N., Budinich M., Cortés M.P., Serpell C., Nakahigashi K., Hirayama A., Tomita M., Soga T., Martínez S., Maass A., Parada P.
Metabolomics (Metabolomics) 9 ( 1 ) 247 - 257 2013.02
ISSN 15733882
-
Ohtani, N., Tomita, M. and Itaya, M.
Extremophiles. (Extremophiles) 17 ( 1 ) 15 - 28 2013
Joint Work, Accepted, ISSN 14310651
-
Ito, T., Tanaka, M., Shinkawa, H., Nakada, T., Ano, Y., Kurano, N., Soga, T. and Tomita, M.
Metabolomics (Metabolomics) 9 ( (Suppl 1) ) 178-187 - 187 2013
Research paper (scientific journal), Joint Work, Accepted, ISSN 15733882
-
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.
Metabolomics (Metabolomics) 9 ( 2 ) 444-453 - 453 2013
Research paper (scientific journal), Joint Work, Accepted, ISSN 15733882
-
Sugimoto, M., Saruta, J., Matsuki, C., To, M., Onuma, H., Kaneko, M., Soga, T., M Tomita, M. and Tsukinoki, K.
Metabolomics 9 ( 2 ) 454-463 - 463 2013
Research paper (scientific journal), Joint Work, Accepted, ISSN 15733882
-
Computational analysis of associations between alternative splicing and histone modifications
Shindo, Y., Nozaki, T., Saito, R., Tomita, M.
FEBS LETTERS (FEBS Letters) 587 ( 5 ) 516-21 - 521 2013
Research paper (scientific journal), Joint Work, Accepted, ISSN 00145793
-
Physical Laws Shape Biology
Selvarajoo, K. and Tomita, M.
Science Feb 8 339 646 2013
Research paper (scientific journal), Single Work, Accepted
-
Matsui, M., Tomita, M. and Kanai, A.
Genome Biol Evol (Genome Biology and Evolution) 5 ( 2 ) 267-282 - 282 2013
Research paper (scientific journal), Joint Work
-
Quantitative assay for TALEN activity at endogenous genomic loci
Hisano, Y., Ota, S., Arakawa, K., Muraki, M., Kono, N., Oshita, K., Sakuma, T., Tomita, M., Yamamoto, T., Okada, Y. and *Kawahara, A.
Biology Open (Biology Open) 2 ( 4 ) 363-367 - 367 2013
Research paper (scientific journal), Joint Work, Accepted
-
Okubo, C., Sano, H., Naito, Y. and Tomita, M.
Journal of Physiological Sciences (Journal of Physiological Sciences) 63 ( 5 ) 355-67 - 367 2013
Research paper (scientific journal), Joint Work, Accepted, ISSN 18806546
-
Tsuruoka, M., Hara, J., Hirayama, A., Sugimoto, M., Soga, T., R. Shankle, R., W., and Tomita, M.
Electrophoresis (Electrophoresis) 34 ( 19 ) 2865-2872 - 2872 2013
Research paper (scientific journal), Joint Work, Accepted, ISSN 01730835
-
Commensal microbe-derived butyrate induces the Differentiation of colonic regulatory T cells
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.
Nature (Nature) 504 ( 7480 ) 446 - 450 2013
Joint Work, ISSN 00280836
-
A systems biology approach to suppress TNF-induced proinflammatory gene expressions
Hayashi K, Piras V, Tabata S, Tomita M, Selvarajoo K.
Cell Communication and Signaling (Cell Communication and Signaling) 11 ( 1 ) 84 2013
Joint Work
-
Sato, D., Akashi, H., Sugimoto, M., Tomita, M. and Soga, T.
J Chromatogr B Analyt Technol Biomed Life Sci. (Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences) 925 95 - 103 2013
Joint Work, Accepted, ISSN 15700232
-
Merging multiple omics datasets in silico: statistical analyses and data interpretation.
Arakawa, K. and Tomita, M.
Methods Mol Biol. (Methods in Molecular Biology) 985 459 - 470 2013
Joint Work, Accepted, ISSN 10643745
-
Sano H., Naito Y., Tomita M.
Computing in Cardiology 39 877 - 880 2012.12
ISSN 2325887X
-
Okubo C., Sano H., Naito Y., Tomita M.
Computing in Cardiology 39 301 - 304 2012.12
ISSN 2325887X
-
Deguchi K., Sato D., Sugimoto M., Hara H., Kawasaki Y., Demura S., Watanabe T., Denholme S., Okazaki H., Ozaki T., Yamaguchi T., Takeya H., Soga T., Tomita M., Takano Y.
Superconductor Science and Technology 25 ( 8 ) 2012.08
ISSN 09532048
-
The rice proteogenomics database OryzaPG-DB: Development, expansion, and new features
Helmy M., Sugiyama N., Tomita M., Ishihama Y.
Frontiers in Plant Science (Frontiers in Plant Science) 3 ( APR ) 65 2012.04
-
Sugimoto M., Kaneko M., Onuma H., Sakaguchi Y., Mori M., Abe S., Soga T., Tomita M.
Journal of Agricultural and Food Chemistry (Journal of Agricultural and Food Chemistry) 60 ( 10 ) 2586 - 2593 2012.03
ISSN 00218561
-
Genomic heterogeneity in a natural archaeal population suggests a model of tRNA gene disruption
Sugahara J, Fujishima K, Nunoura T, Takaki Y, Takami H, Takai K, Tomita M, Kanai A.
PLoS ONE (PLoS ONE) 7 ( 3 ) 1-8 2012.03
Research paper (scientific journal), Joint Work
-
Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis
Sugimoto, Masahiro; Kawakami, Masato; Robert, Martin; Soga, Tomoyoshi; Tomita, Masaru
Current Bioinformatics (Current Bioinformatics) 7 ( 1 ) 96-108 - 108 2012.03
Research paper (scientific journal), Joint Work, ISSN 15748936
-
Measures of Compositional Strand Bias Related to Replication Machinery and its Applications
Arakawa K., Tomita M.
Current Genomics (Current Genomics) 13 ( 1 ) 4 - 15 2012.03
ISSN 13892029
-
Murakami S., Fujishima K., Tomita M., Kanai A.
Applied and Environmental Microbiology (Applied and Environmental Microbiology) 78 ( 4 ) 1015-1022 - 1022 2012.02
Research paper (scientific journal), Joint Work, ISSN 00992240
-
MMMDB: Mouse multiple tissue metabolome database
Sugimoto M., Ikeda S., Niigata K., Tomita M., Sato H., Soga T.
Nucleic Acids Research (Nucleic Acids Research) 40 ( D1 ) D809 - 14 2012.01
ISSN 03051048
-
Time-structure of the yeast metabolism in vivo
Sasidharan K., Tomita M., Aon M., Lloyd D., Murray D.B.
Advances in Experimental Medicine and Biology 2012
ISSN 00652598
-
Peptide Identification by Searching Large-Scale Tandem Mass Spectra against Large Databases: Bioinformatics Methods in Proteogenomics
Helmy, M, Tomita M, Ishihama Y
Genes, Genome and Genomics 6 76-85 2012
Research paper (scientific journal), Joint Work, Accepted
-
Iino¸ K., Sugimoto¸ M., Soga¸ T. and Tomita, M.
Metabolomics 8 ( 1 ) 99-108 - 108 2012
Research paper (scientific journal), Joint Work, ISSN 15733882
-
Validation of Bacterial Replication Termination Models Using Simulation of Genomic Mutations
Kono, N., Arakawa, K.,and Tomita, M.
PLoS ONE (PLoS ONE) 7 ( 4 ) e34526 2012
Research paper (scientific journal), Joint Work, Accepted
-
Nematode-specific tRNAs that decode an alternative genetic code for leucine
Hamashima, K., Fujishima, K., Masuda, T., Sugahara, J., Tomita, M. and Kanai, A.
Nucleic Acids Research (Nucleic Acids Research) 40 ( 8 ) 3653-3662 - 3662 2012
Research paper (scientific journal), Joint Work, Accepted, ISSN 03051048
-
The role of Staphylococcal enterotoxin in atopic keratoconjunctivitis and corneal ulceration
Fujishima, H., Okada, N., Dogru., M., Baba, F., Tomita, M., Abe, J., Matsumoto, K. and Saito, H.
Allergy 67 ( 6 ) 799-803 - 803 2012
Research paper (scientific journal), Joint Work, Accepted, ISSN 01054538
-
Systems Biology, Metabolomics, and Cancer Metabolism
Tomita, M.,Kami, K.
Science 336 990-991 2012
Research paper (scientific journal), Joint Work, Accepted
-
Ohtani., N., Tomita, M. and Itaya, M.
Extremophiles (Extremophiles) 16 ( 2 ) 237-44 - 244 2012
Research paper (scientific journal), Joint Work, ISSN 14310651
-
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.
BMC Medical Informatics and Decision Making (BMC Medical Informatics and Decision Making) 12 ( 1 ) 54 2012
Research paper (scientific journal), Joint Work, Accepted
-
Sasidharan, K., Amariei, C., Tomita, M., and Murray, D, B.
Yeast (Yeast) 29 ( 8 ) 311-22 - 322 2012
Research paper (scientific journal), Joint Work, Accepted, ISSN 0749503X
-
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.
Breast Cancer Research and Treatment 134 ( 2 ) 661-70 - 670 2012
Research paper (scientific journal), Joint Work, Accepted, ISSN 01676806
-
Non-targeted metabolite profiling in activated macrophage secretion
Sugimoto, M., Sakagami, H., Yokote, Y., Onuma, H., Kaneko, M., Mori, M., Sakaguchi, Y., Soga, T. and Tomita, M.
Metabolomics 8 ( 4 ) 624–633 - 633 2012
Research paper (scientific journal), Joint Work, Accepted, ISSN 15733882
-
Helmy, M., Sugiyama, N., Tomita, M. and Ishihama, Y.
Genes to Cells (Genes to Cells) 17 ( 8 ) 633-44 - 644 2012
Research paper (scientific journal), Joint Work, Accepted, ISSN 13569597
-
Investigation of stochasticity in TRAIL signaling cancer model
Piras, V., Hayashi, K., Tomita, M. and Selvarajoo, K.
IEEE/ICME Com. Med. Eng. 609-614. - 614 2012
Research paper (scientific journal), Joint Work, Accepted
-
A Yeast Metabolite Extraction Protocol Optimised for Time-Series Analyses
Sasidharan, K., Soga, T., Tomita, M. and Murray, D., B.
PLoS ONE (PLoS ONE) 7 ( 8 ) e44283 2012
Research paper (scientific journal), Joint Work, Accepted
-
Toya, Y., Nakahigashi, K., Tomita, M., and Shimizu, K.
Molecular BioSystems (Molecular BioSystems) 8 ( 10 ) 2593-604. - 2604 2012
Research paper (scientific journal), Joint Work, Accepted, ISSN 1742206X
-
Temporal profiling of lapatinib-suppressed phosphorylation signals inEGFR/HER2 pathways
Imami, K., Sugiyama, N., Imamura, H., Wakabayashi, M., Tomita, M., Taniguchi, M., Ueno, T., Toi, M. and Ishihama, Y.
Mol Cell Proteomics (Molecular and Cellular Proteomics) 11 ( 12 ) [Epub ahead of print] - 1757 2012
Research paper (scientific journal), Joint Work, Accepted, ISSN 15359476
-
Hirayama, A., Tomita, M. and Soga, T.
Analyst (Analyst) 137 ( 21 ) 5026-5033 - 5033 2012
Research paper (scientific journal), Joint Work, Accepted, ISSN 00032654
-
Pilot Study of Changes in Salivary Metabolic Profiles Induced by Template Therapy
Tanaka, S., Taga, H., Maehara, K., Kaneshima, A., Machino, M., Onuma, H., Kaneko, M., Sakagami, H., Sugimoto, M., Soga, T. and Tomita, M.
InVivo. (In Vivo) 26 ( 6 ) 1015-1020 - 1020 2012
Research paper (scientific journal), Joint Work, Accepted, ISSN 0258851X
-
Is central dogma a global property of cellular information flow?
Piras, V., Tomita, M. and Selvarajoo, K
Front. Physiol. (Frontiers in Physiology) 3 439 2012
Research paper (scientific journal), Joint Work, Accepted
-
Metabolomics: A New Omics Technology for Traditional Herbal Medicine Analysis
Iino, K., Sugimoto, M., Soga, T. and Tomita, M.
Chinese Medicine: Acupuncture, Herbal Medicine and Therapies 45-55 2012
Research paper (scientific journal), Joint Work, Accepted
-
Metabolic profiling reveals new serum biomarkers for differentiating diabetic nephropathy
Hirayama, A., Nakashima, E., Sugimotoa, M., Akiyama, S., Sato, W., Maruyama, S., Matsuo, S., Tomita, M., Yuzawa, Y. and Soga, T.
Anal Bioanal Chem (Analytical and Bioanalytical Chemistry) 404 ( 10 ) 3101-9 - 3109 2012
Research paper (scientific journal), Joint Work, Accepted, ISSN 16182642
-
Itaya, M., Kawata, Y., Sato, M., Tomita, M. and Nakahigashi, K.
J. Biochem. (Journal of Biochemistry) 152 ( 6 ) 501–504 - 504 2012
Research paper (scientific journal), Joint Work, Accepted, ISSN 0021924X
-
A medium-chain fatty acid as an alternative energy source in mouse preimplantation development
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.
Sci Rep. (Scientific Reports) 2 930 2012
Research paper (scientific journal), Joint Work, Accepted
-
Light Microscopy and Phylogenetic Analyses of Chlamydomonas Species (Volvocales, Chlorophyceae). : I. Chlamydomonas pseudomacrostigma and Chlamydomonas media
Nakada, T., Nozaki, H. and Tomita, M.
Acta phytotaxonomica et geobotanica 62:69-78 62 69 - 78 2012
Joint Work
-
Ohtani, N., Hasegawa, M., Sato, M., Tomita, M., Kaneko, S. and Itaya, M.
Biotechnol J. (Biotechnology Journal) 7 ( 7 ) 867 - 76 2012
Joint Work, Accepted, ISSN 18606768
-
Kami, K., Fujita, Y., Igarashi, S., Koike, S., Sugawara, S., Ikeda, S., Sato, N., Ito, M., Tanaka, M., Tomita, M. and Soga, T.
Mitochondrion. (Mitochondrion) 12 ( 6 ) 644 - 653 2012
Accepted, ISSN 15677249
-
Seike, Masayoshi; Saitou, Takeo; Kouchi, Yasuhiro; Ohara, Takeshi; Matsuhisa, Munehide; Sakaguchi, Kazuhiko; Tomita, Koji; Kosugi, Keisuke; Kashiwagi, Atsunori; Kasuga, Masato; Tomita, Masaru; Naito, Yasuhiro; Nakajima, Hiromu
Journal of Physiological Sciences (Journal of Physiological Sciences) 61 ( 4 ) 321-330 - 330 2011.07
Research paper (scientific journal), Joint Work, ISSN 18806546
-
A novel mechanism regulates H2S and SO2 production in Saccharomyces cerevisiae
Yoshida S., Imoto J., Minato T., Oouchi R., Kamada Y., Tomita M., Soga T., Yoshimoto H.
Yeast 28 ( 2 ) 109 - 121 2011.02
ISSN 0749503X
-
Fujishima K., Sugahara J., Miller C.S., Baker B.J., Di Giulio M., Takesue K., Sato A., Tomita M., Banfield J.F., Kanai A.
Nucleic Acids Research (Nucleic Acids Research) 39 ( 22 ) 9695-9704 - 9704 2011
Research paper (scientific journal), Joint Work, ISSN 03051048
-
Redox Regulation in Respiring Saccharomyces cerevisiae
Murray, D.B., Haynes, K. and Tomita, M.
Biochim Biophys Acta. (Biochimica et Biophysica Acta - General Subjects) 1810 ( 10 ) 945-58 - 958 2011
Research paper (scientific journal), Joint Work, Accepted, ISSN 03044165
-
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
J Hepatology (Journal of Hepatology) 55 ( 4 ) 896-905 - 905 2011
Research paper (scientific journal), Joint Work, Accepted, ISSN 01688278
-
Shimo, H., Nishino, T. and Tomita, M.
Adv Hematol. (Advances in Hematology) 2011 398945 2011
Research paper (scientific journal), Joint Work, Accepted, ISSN 16879104
-
Enhancing apoptosis in TRAIL-resistant cancer cells using fundamental response rules
Piras, V., Hayashi, K., Tomita, M. and Selvarajoo, K
Scientific Reports (Scientific Reports) 1 144 2011
Research paper (scientific journal), Joint Work, Accepted
-
Sato, A., Soga, T., Igarashi, K., Takesue, K., Tomita, M. and Kanai, A.
Genes to Cells (Genes to Cells) 16 ( 12 ) 1190-1199 - 1199 2011
Research paper (scientific journal), Joint Work, Accepted, ISSN 13569597
-
Microscale phosphoproteome analysis of 10,000 cells from human cancer cell lines
Masuda, T., Sugiyama, N., Tomita, M.. and Ishihama, Y.
Anal. Chem 83 7698-703 2011
Research paper (scientific journal), Joint Work, Accepted
-
A screening system for artificial small RNAs that inhibit the growth of Escherichia coli
Komasa M., Fujishima K., Hiraoka K., Shinhara A., Lee B., Tomita M., Kanai A.
Journal of Biochemistry 150 ( 3 ) 289-294 - 294 2011
Research paper (scientific journal), Joint Work, Accepted, ISSN 0021924X
-
Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes
Kono N., Arakawa K., Tomita M.
BMC Genomics (BMC Genomics) 12 19 2011
Research paper (scientific journal), Joint Work, Accepted
-
Integrative features of the yeast phosphoproteome and protein-protein interaction map
Yachie N., Saito R., Sugiyama N., Tomita M., Ishihama Y.
PLoS Computational Biology (PLoS Computational Biology) 7 ( 1 ) e1001064 2011
Research paper (scientific journal), Joint Work, Accepted, ISSN 1553734X
-
Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA
Nozaki T., Yachie N., Ogawa R., Saito R., Tomita M.
Gene (Gene) 476 ( 1-2 ) 10-14 - 14 2011
Research paper (scientific journal), Joint Work, Accepted, ISSN 03781119
-
Metabolomic anatomy of an animal model revealing homeostatic imbalances in dyslipidaemia
Ooga, Takushi ; Sato, Hajime ; Nagashima, Atsushi ; Sasaki, Kazunori ; Tomita, Masaru ; Soga, Tomoyoshi ; Ohashi, Yoshiaki
Molecular BioSystems (Molecular BioSystems) 7 ( 4 ) 1217-1223 - 1223 2011
Research paper (scientific journal), Joint Work, ISSN 1742-206X
-
OryzaPG-DB: Rice Proteome Database based on Shotgun Proteogenomics
Helmy, M., Tomita, M. and Ishihama
BMC Plant Biol. (BMC Plant Biology) 11 63 2011
Research paper (scientific journal), Joint Work, Accepted
-
Positive Autoregulation Delays the Expression Phase of Mammalian Clock Gene Per2
Ogawa, Y., Koike, N., Kurosawa, G., Soga, T., Tomita, M. and Tei, H.
PLoS ONE (PLoS ONE) 6 ( 4 ) e18663 2011
Research paper (scientific journal), Joint Work, Accepted
-
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.
BMC Med. Genomics (BMC Medical Genomics) 4 42 2011
Research paper (scientific journal), Joint Work, Accepted
-
KBWS: an EMBOSS associated package for accessing bioinformatics web services
Oshita, K., Arakawa, K. and Tomita, M.
Source Code Biol Med. (Source Code for Biology and Medicine) 6 8 2011
Research paper (scientific journal), Joint Work, Accepted
-
Nakada, T. and Tomita,
Phycol. Res. 59 ( 3 ) 194–199 - 199 2011
Research paper (scientific journal), Joint Work, Accepted, ISSN 13220829
-
Metabolic flux analysis and visualization
Toya, Y., Kono, N., Arakawa, K. and Tomita, M.
J. Proteome Res. (Journal of Proteome Research) 10 ( 8 ) 3313–3323 - 3323 2011
Research paper (scientific journal), Joint Work, Accepted, ISSN 15353893
-
Nozaki, T., Yachie, N., Ogawa, R., Kratz, A., Saito, R. and Tomita, M.
BMC Genomics (BMC Genomics) 12 416 2011
Research paper (scientific journal), Joint Work, Accepted
-
Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli
Shinhara, A., Matsui, M., Hiraoka, K., Nomura, W., Hirano, R., Nakahigashi, K., Tomita, M., Mori, H. and Kanai, A.
BMC Genomics (BMC Genomics) 12 428 2011
Research paper (scientific journal), Joint Work, Accepted
-
The Salivary Gland and Systemic Health: Towards the Creation of Salivary Gland and Health Medicine
Tsukinoki K., Saruta J., Yamano S., Tomita M.
Journal of Oral Biosciences 53 ( 4 ) 330 - 337 2011
ISSN 13490079
-
An Extreme Thermophile, Thermus thermophilus, Is a Polyploid Bacterium
Ohtani N, Tomita M, Itaya M.
J Bacteriol (Journal of Bacteriology) 192 ( 20 ) 5499-5505 - 5505 2010.10
Research paper (scientific journal), Joint Work, ISSN 0021-9193
-
Toya Y., Ishii N., Nakahigashi K., Hirasawa T., Soga T., Tomita M., Shimizu K.
Biotechnology Progress 26 ( 4 ) 975 - 992 2010.07
ISSN 87567938
-
Horiguchi K, Toi M, Horiguchi S, Sugimoto M, Naito Y, Hayashi Y, Ueno T, Ohno S, Funata N, Kuroi K, Tomita M, Eishi Y.
J Med Dent Sci (Journal of Medical and Dental Sciences) 57 ( 2 ) 165-175 - 175 2010.06
Research paper (scientific journal), Joint Work, ISSN 1342-8810
-
Kitamura S., Fujishima K., Sato A., Tsuchiya D., Tomita M., Kanai A.
Biochemical Journal (Biochemical Journal) 426 ( 3 ) 337 - 344 2010.03
ISSN 02646021
-
Volvulina compacta ( Volvocaceae, Chlorophyceae ), new to Japan, and its phylogenetic position
Nakada, T., Tomita, M. and Nozaki, H.
J. Jpn. Bot. 85 ( 6 ) 364–369 - 369 2010
Research paper (scientific journal), Joint Work, Accepted, ISSN 00222062
-
Nakada, T., Soga, T. and Tomita, M.
Phycol. Res. 58 ( 1 ) 62-68 - 68 2010
Research paper (scientific journal), Joint Work, Accepted, ISSN 13220829
-
Arjunan, S. N. V. and Tomita, M.
Syst Synth Biol. (Systems and Synthetic Biology) 4 ( 1 ) 35-53 - 53 2010
Research paper (scientific journal), Joint Work, Accepted, ISSN 18725325
-
Takane, K., Fujishima, K., Watanabe, Y., Sato, A., Saito, N., Tomita, M and Kanai, A.
BMC Genomics (BMC Genomics) 11 ( 1 ) 101 2010
Research paper (scientific journal), Joint Work, Accepted
-
Sato, M. 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.
PLoS ONE (PLoS ONE) 5 ( 2 ) e9289 2010
Research paper (scientific journal), Joint Work, Accepted
-
Nakada, T., Soga, T., Tomita, M. and Nozaki, H.
Eur. J. Phycol. 45 ( 1 ) 97-107 - 106 2010
Research paper (scientific journal), Joint Work, Accepted, ISSN 09670262
-
Ogawa, R., Kitagawa, N., Ashida, H., Saito, R. and Tomita, M.
FEBS Letters (FEBS Letters) 584 ( 8 ) 1498-1502 - 1502 2010
Research paper (scientific journal), Joint Work, Accepted, ISSN 00145793
-
Iwasaki, M., Miwa, S., Ikegami, T., Tomita, M., Tanaka, N. and Ishihama, Y.
Anal. Chem. (Analytical Chemistry) 82 ( 7 ) 2616-2620 - 2620 2010
Research paper (scientific journal), Joint Work, Accepted, ISSN 00032700
-
Gene knockout and metabolome analysis of carnitine/organic cation transporter OCTN1
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.
Pharm Res 27 ( 5 ) 832-840 - 40 2010
Research paper (scientific journal), Joint Work, Accepted, ISSN 0724-8741
-
Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data
Imamura, H., Yachie, N., Saito, R., Ishihama, Y. and Tomita, M.
BMC Bioinformatics (BMC Bioinformatics) 11 232 2010
Research paper (scientific journal), Joint Work, Accepted
-
Kim, H., Lee, B. S., Tomita, M. and Kanai, A.
PLoS ONE (PLoS ONE) 5 ( 5 ) e10567 2010
Research paper (scientific journal), Joint Work, Accepted
-
Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns
Kratz, A., Arner, E., Saito, R., Kubosaki, A., Kawai, J., Suzuki, H., Carninci, P., Arakawa, T., Tomita, M., Hayashizaki, Y. and Daub, C.O.
BMC Genomics (BMC Genomics) 11 ( 1 ) 257 2010
Research paper (scientific journal), Joint Work, Accepted
-
Unveiling cellular biochemical reactions via metabolomics-driven approaches
Saito, N., Ohashi, Y., Soga, T. and Tomita, M.
Curr Opin Microbiol. (Current Opinion in Microbiology) 13 ( 3 ) 358-362 - 362 2010
Research paper (scientific journal), Joint Work, Accepted, ISSN 13695274
-
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
Mol. BioSyst. (Molecular BioSystems) 6 ( 7 ) 1216-1226 - 1226 2010
Research paper (scientific journal), Joint Work, Accepted, ISSN 1742206X
-
Differential metabolomics software for capillary electrophoresis-mass spectrometry data analysis
Sugimoto, Masahiro ; Hirayama, Akiyoshi ; Ishikawa, Takamasa ; Robert, Martin ; Baran, Richard ; Uehara, Keizo ; Kawai, Katsuya ; Soga, Tomoyoshi ; Tomita, Masaru
METABOLOMICS 6 ( 1 ) 27-41 - 41 2010
Research paper (scientific journal), Joint Work, ISSN 1573-3882
-
Nakada, T., Nozaki, H. and Tomita, M.
J. Eukaryot. Microbiol. (Journal of Eukaryotic Microbiology) 57 ( 4 ) 379-382 - 382 2010
Research paper (scientific journal), Joint Work, Accepted, ISSN 10665234
-
Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants
Nakagami, H., Sugiyama, N., Mochida, K., Daudi, A., Yoshida, Y., Toyoda, T., Tomita, M., Ishihama, Y. and Shirasu, K.
Plant Physiology (Plant Physiology) 153 ( 3 ) 1161-1174 - 1174 2010
Research paper (scientific journal), Joint Work, Accepted, ISSN 00320889
-
Sugimoto, M., Hirayama, A., Robert, M., Abe, S., Soga, T. and Tomita, M.
Electrophoresis (Electrophoresis) 31 ( 14 ) 2311–2318 - 2318 2010
Research paper (scientific journal), Joint Work, Accepted, ISSN 01730835
-
Ozawa, Y., Saito, R., Fujimori, S., Kashima, H., Ishizaka, Hiroshi Yanagawa, H., Miyamoto-Sato, E. and Tomita, M.
BMC Bioinformatics (BMC Bioinformatics) 11 350 2010
Research paper (scientific journal), Joint Work, Accepted
-
Kyono, Y., Sugiyama, N., Tomita, M. and Ishihama, Y.
Rapid Commun. Mass Spectrom. (Rapid Communications in Mass Spectrometry) 24 ( 15 ) 2277–2282 - 2282 2010
Research paper (scientific journal), Joint Work, Accepted, ISSN 09514198
-
Sugimoto, M., Goto, H., Otomo, K., Ito, M., Onuma, H., Suzuki, A., Sugawara, M., Abe, S., Tomita, M. and Soga, T.
J Agric Food Chem. (Journal of Agricultural and Food Chemistry) 58 ( 14 ) 8418–8425 - 8425 2010
Research paper (scientific journal), Joint Work, Accepted, ISSN 00218561
-
G-language genome analysis environment with REST and SOAP web service interfaces
Arakawa, K., Kido, N., Oshita, K. and Tomita, M.
Nucleic Acids Res. (Nucleic Acids Research) 38 ( SUPPL. 2 ) W700–W705 - 5 2010
Research paper (scientific journal), Joint Work, Accepted, ISSN 03051048
-
Tsuchiya, M., Piras, V., Giuliani, A., Tomita, M. and Selvarajoo
PLoS One (PLoS ONE) 5 ( 8 ) e12116 2010
Research paper (scientific journal), Joint Work, Accepted
-
Fujishima, K., Sugahara, J., Tomita, M. and Kanai, A.
Mol. Biol. Evol. (Molecular Biology and Evolution) 27 ( 10 ) 2233–2243 - 2243 2010
Research paper (scientific journal), Joint Work, Accepted, ISSN 07374038
-
A Metabolic Model of Human Erythrocytes: Practical Application of the E-Cell Simulation Environment
Yachie, A. K., Nishino, T., Shimo, H., Suematsu, M., and Tomita, M.
J. Biomed. Biotechnol. (Journal of Biomedicine and Biotechnology) 2010 642420 2010
Research paper (scientific journal), Joint Work, Accepted, ISSN 11107243
-
Unbiased quantitation of Escherichia coli membrane proteome using phase-transfer surfactants
Masuda,T., Saito, N., Tomita, M. and Ishihama, M.
Mol Cell Proteomics. (Molecular and Cellular Proteomics) 8 ( 12 ) 2770-2777 - 2777 2009.12
Research paper (scientific journal), Joint Work, Accepted, ISSN 15359476
-
Nock A., Ascano J.M., Jones T., Barrero M.J., Sugiyama N., Tomita M., Ishihama Y., Malik S.
Journal of Biological Chemistry (Journal of Biological Chemistry) 284 ( 30 ) 19915 - 19926 2009.07
ISSN 00219258
-
Ooga T., Ohashi Y., Kuramitsu S., Koyama Y., Tomita M., Soga T., Masui R.
Journal of Biological Chemistry (Journal of Biological Chemistry) 284 ( 23 ) 15549 - 15556 2009.06
ISSN 00219258
-
Benzodiazepine and antidepressant use in elderly patients with anxiety disorders: a survey of 796 outpatients in Japan.
Uchida H, Suzuki T, Mamo DC, Mulsant BH, Kikuchi T, Takeuchi H, Tomita M, Watanabe K, Yagi G, Kashima H
Journal of anxiety disorders 23 ( 4 ) 477 - 81 2009.05
ISSN 0887-6185
-
Kanai A., Sato A., Fukuda Y., Okada K., Matsuda T., Sakamoto T., Muto Y., Yokoyama S., Kawai G., Tomita M.
RNA 15 ( 3 ) 420 - 431 2009.03
ISSN 13558382
-
Six classes of nuclear localization signals specific to different binding grooves of importin α
Kosugi S., Hasebe M., Matsumura N., Takashima H., Miyamoto-Sato E., Tomita M., Yanagawa H.
Journal of Biological Chemistry 284 ( 1 ) 478 - 485 2009.01
ISSN 00219258
-
Shinoda, K., Tomita, M. and Ishihama,Y.
Bioinformatics (Bioinformatics) 26 ( 4 ) 576-577 - 577 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 13674803
-
Cooperativity of two active sites in bacterial homodimeric aconitases
Tsuchiya D, Shimizu N, Tomita M
Biochem Biophys Res Commun 379 ( 2 ) 485-488 - 488 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 0006291X
-
Predicting novel features of toll-like receptor 3 signaling in macrophages
Helmy, M., Gohda, J, Inoue, J., Tomita, M. Tsuchiya, M. and Selvarajoo, K.
PLoS ONE. 4 ( 11 ) e4661 2009
Research paper (scientific journal), Joint Work, Accepted
-
Fujishima, K., Sugahara, J., Kikuta, K. Hirano, R.,Sato, A., Tomita, M. and Kanai
Proc Natl Acad Sci U S A. 106 ( 8 ) 2683-7 - 2687 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 00278424
-
Genome Projector: zoomable genome map with multiple views
Arakawa, K., Tamaki, S., Kono, N., Kido, N., Ikegami, K., Ogawa, R.and Tomita, M
BMC Bioinformatics 10 31 2009
Research paper (scientific journal), Joint Work, Accepted
-
Local and Global responses in complex gene regulation networks
Tsuchiya, M., Selvarajoo, K., Piras, V., Tomita, M. and Giuliani, A.
Physica A 388 ( 8 ) 1738-1746 - 1746 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 03784371
-
Can complex cellular processes be governed by simple linear rules?
Selvarajoo, K., Tomita, M. and Tsuchiya, M.
J Bioinform Comput Biol. (Journal of Bioinformatics and Computational Biology) 7 ( 1 ) 243-268 - 268 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 02197200
-
Yachie, N., Saito, R., Sugahara, J., Tomita, M. and Ishihama, Y
Mol Cell Proteomics. (Molecular and Cellular Proteomics) 8 ( 5 ) 1061-71 - 1071 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 15359476
-
Chemical Cleavage-Assisted Tryptic Digestion for Membrane Proteome Analysis
Iwasaki, M., Masuda, T., Tomita, M. and Ishihama, Y.
J. Proteome Re (Journal of Proteome Research) 8 ( 6 ) 1061-71 - 3175 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 15353893
-
Saito, N., Robert, M., Kochi, H., Matsuo, G., Kakazu, Y., Soga, T. and Tomita, M.
J. Biol. Chem. (Journal of Biological Chemistry) 284 ( 24 ) 16442-51 - 16451 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 00219258
-
Tsuchiya, M., Piras, V., Choi, S., Akira, S., Tomita, M., Giuliani, A. and Selvarajoo, K.
PLoS One 4 ( 3 ) e4905 2009
Research paper (scientific journal), Joint Work, Accepted
-
Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non-pathogenic Pseudomonas species
Ravichandran, A., Sugiyama, N., Tomita, M., Swarup, S. and Ishihama, Y.
Proteomics. (Proteomics) 9 ( 10 ) 2764-2775 - 2775 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 16159853
-
Network features and pathway analyses of a signal transduction cascade
Yanashima, R, Kitagawa N., Matsubara, Y., Weatheritt, R., Oka, K., Kikuchi, S., Tomita, M,and Ishizaki, S.
Front Neuroinform. 3 ( MAY ) 13 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 16625196
-
Hirayama, A., Kami, K., Sugimoto, M., Sugawara, M., Toki, N., Onozuka, H., Kinoshita, T., Saito, N., Ochiai, A., Tomita, M., Esumi, H. and Soga, T.
Cancer Res (Cancer Research) 69 ( 11 ) 4918-25 - 4925 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 00085472
-
Measure of synonymous codon usage diversity among genes in bacteria
Suzuki, H., Saito, R. and Tomita, M
BMC Bioinformatics (BMC Bioinformatics) 10 167 2009
Research paper (scientific journal), Joint Work, Accepted
-
Metabolomic Profiling of Anionic Metabolites by Capillary Electrophoresis Mass Spectrometry
Soga, T., Igarashi, K., Itoh, C., Mizobuchi, K., Zimmermann, H. P. and Tomita, M.
Analytical Chemistry (Analytical Chemistry) 81 ( 15 ) 6165-6174 - 6174 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 00032700
-
Kosugi, S., Hasebe, M., Tomita, M. and Yanagawa, H.
Proc Natl Acad Sci U S A. (Proceedings of the National Academy of Sciences of the United States of America) 106 ( 31 ) 13142. - 10176 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 00278424
-
Nakahigashi, K., Toya, Y., Ishii, N., Soga, T., Hasegawa, M., Watanabe, H., Takai, Y., Honma, M., Mori, H. and Tomita, M.
Molecular Systems Biology 5 306 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 17444292
-
A web server for interactive and zoomable Chaos Game Representation images
Arakawa, K., Oshita, K. and Tomita, M.
Source Code for Biology and Medicine (Source Code for Biology and Medicine) 4 6 2009
Research paper (scientific journal), Joint Work, Accepted
-
Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System
Arjunan, S. N. V., and Tomita, M.
International Journal of Computer Science and Information Security 3 ( 1 ) 211-216 2009
Research paper (scientific journal), Joint Work, Accepted
-
Nishino, T., Yachie, A. K., Hirayama. A., Soga, T., Suematsu, T., and Tomita, M.
Journal of Biotechnology (Journal of Biotechnology) 144 ( 3 ) 212-223 - 223 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 01681656
-
Pathway Projector: Web-based Zoomable Pathway Browser using KEGG Atlas and Google Maps API
Kono, N., Arakawa, K., Ogawa, R., Kido, N., Oshita, K., Ikegami, K., Tamaki, S. and Tomita, M.
PLoS ONE (PLoS ONE) 4 ( 11 ) e7710 2009
Research paper (scientific journal), Joint Work, Accepted
-
Disrupted tRNA Gene Diversity and Possible Evolutionary Scenarios
Sugahara, J., Fujishima, K., Morita, K., Tomita, M. and Kanai , A.
Journal of Molecular Evolution (Journal of Molecular Evolution) 69 ( 5 ) 497-504 - 504 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 00222844
-
Update on the Keio collection of Escherichia coli single-gene deletion mutants
Yamamoto, N., Nakahigashi, K., Nakamichi, T., Yoshino, M., Takai, Y., Touda, Y., Furubayashi, A., Kinjyo, S., Dose, H., Hasegawa, M., Datsenko, K. A., Toru Nakayashiki, T., Tomita, M., Barry L Wanner, L. B. and Hirotada Mori, H.
Molecular Systems Biology 5 335 2009
Research paper (scientific journal), Joint Work, Accepted
-
Recharacterization of Chlamydomonas reinhardtii and its relatives with new isolates from Japan
Nakada, T., Shinkawa, H., Ito, T., and Tomita, M.
J Plant Res (Journal of Plant Research) 123 ( 1 ) 67–78 - 78 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 09189440
-
Arakawa, K., Suzuki, H. and Tomita, M.
BMC Genomics (BMC Genomics) 10 640 2009
Research paper (scientific journal), Joint Work, Accepted
-
Correlation between Sensory Evaluation Scores of Japanese Sakeand Metabolome Profiles
Sugimoto, M., Koseki ,T., Hirayama, A., Abe, S., Sano, T., Tomita, M., and Soga, T.
J. Agric. FoodChem 2010 (Journal of Agricultural and Food Chemistry) 58 ( 1 ) 374–383 - 383 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 00218561
-
Sugimoto, M., Wong, D. T., Hirayama, A., Soga, T. and Tomita
Metabolomics (Metabolomics) 6 ( 1 ) 78-95 - 95 2009
Research paper (scientific journal), Joint Work, Accepted, ISSN 15733882
-
Imami, K., Sugiyama, N., Tomita, M. and Ishihama, Y.
Mol. BioSyst. (Molecular BioSystems) 6 ( 3 ) 594-602 - 602 2009
Research paper (scientific journal), Joint Work, ISSN 1742206X
-
Sugahara J., Kikuta K., Fujishima K., Yachie N., Tomita M., Kanai A.
Molecular Biology and Evolution 25 ( 12 ) 2709 - 2716 2008.12
ISSN 07374038
-
Kami K., Tomitsuka E., Kita K., Tomita M., Soga T., Esumi H.
Japanese Journal of Clinical Chemistry 37 ( 4 ) 361 - 367 2008.12
ISSN 03705633
-
Role of Na<sup>+</sup>-Ca<sup>2+</sup> exchange in neonatal and adult ventricular cells
Sano H., Naito Y., Tomita M.
WMSCI 2008 - The 12th World Multi-Conference on Systemics, Cybernetics and Informatics, Jointly with the 14th International Conference on Information Systems Analysis and Synthesis, ISAS 2008 - Proc. 2 142 - 144 2008.12
-
Signaling flux redistribution at toll-like receptor pathway junctions
Selvarajoo K., Takada Y., Gohda J., Helmy M., Akira S., Tomita M., Tsuchiya M., Inoue J.I., Matsuo K.
PLoS ONE 3 ( 10 ) e3430 2008.10
-
Design of Peptide Inhibitors for the Importin α/β Nuclear Import Pathway by Activity-Based Profiling
Kosugi S., Hasebe M., Entani T., Takayama S., Tomita M., Yanagawa H.
Chemistry and Biology 15 ( 9 ) 940 - 949 2008.09
ISSN 10745521
-
Stabilizing synthetic data in the DNA of living organisms
Yachie N, Ohashi Y, Tomita M
Syst Synth Biol. 2 ( 1-2 ) 19-25 - 25 2008.06
Research paper (scientific journal), Joint Work, ISSN 18725325
-
GANDivAWeb: A web server for detecting early folding units ("foldons") from protein 3D structures
Laborde T., Tomita M., Krishnan A.
BMC Structural Biology 8 2008.05
-
Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis
Sugiyama,N., Nakagami,H., Mochida,K., Daudi,A., Tomita,M., Shirasu,K., and Ishihama,Y.
Mol Syst Biol. 4 193 2008.05
Research paper (scientific journal), Joint Work, ISSN 17444292
-
Yoshida S., Imoto J., Minato T., Oouchi R., Sugihara M., Imai T., Ishiguro T., Mizutani S., Tomita M., Soga T., Yoshimoto H.
Applied and Environmental Microbiology 74 ( 9 ) 2787 - 2796 2008.05
ISSN 00992240
-
Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis
Masuda T., Tomita M., Ishihama Y.
Journal of Proteome Research 7 ( 2 ) 731 - 740 2008.02
ISSN 15353893
-
Watanabe Y., Tomita M., Kanai A.
Progress of Theoretical Physics Supplement ( 173 ) 219 - 228 2008
ISSN 03759687
-
Nuclear export signal consensus sequences defined using a localization-based yeast selection system
Kosugi, S., Hasebe, M., Tomita, M. and Yanagawa, H.
Traffic 9 ( 12 ) 2053 - 2062 2008
Joint Work, ISSN 13989219
-
Computational Genome Analysis Using The G-language System
Arakawa,K., Suzuki,H. and Tomita,M.
Genges,Genomes and Genomics 2 1-13 2008
Research paper (scientific journal), Joint Work
-
Visualizing Conplex Omics Information-Scientific Visualization for Genomics and Systems Biology
Arakawa, K., Yachie, N. and Tomita M.
BIOforum Europe 6 27-29 2008
Research paper (scientific journal), Joint Work
-
Junction ribonuclease activity specified in RNases HII/2
Ohtani, N., Tomita, M. and Itaya, M.
FEBS J. 275 ( 21 ) 5444-55 - 5455 2008
Research paper (scientific journal), Joint Work, ISSN 1742464X
-
Tsuchiya D., Shimizu N., and Tomita M.
BBA - Proteins and Proteomics. 1784 ( 11 ) 1847-56. - 1856 2008
Research paper (scientific journal), Joint Work, ISSN 15709639
-
Shinoda, K., Tomita, M., Ishihama, Y.
Bioinformatics. 24 ( 14 ) 1590-5 - 1595 2008
Research paper (scientific journal), Joint Work, ISSN 13674803
-
Restriction on conjugational transfer of pLS20 in Bacillus subtilis 168
Ohtani, N., Sato, M., Tomita, M. and Itaya, M ,
Biosci. Biotechnol. Biochem. , 72 ( 9 ) 2472-5 - 2475 2008
Research paper (scientific journal), Joint Work, ISSN 09168451
-
Ohtani, N., Tomita, M. and Itaya, M.
Biochem. J. 412 ( 3 ) 517-26 - 526 2008
Research paper (scientific journal), Joint Work, ISSN 02646021
-
GeNESiS: Gene Network Evolution SImulation Software
Anton Kratz, Masaru Tomita and Arun Krishnan
BMC Bioinformatics 9 541 2008
Research paper (scientific journal), Joint Work
-
Kyono, Y.,Sugiyama, N., Imami, K., Tomita, M. and Ishihama, Y.
Journal of Proteome Research 7 ( 10 ) 4585-4593 - 4593 2008
Research paper (scientific journal), Joint Work, ISSN 15353893
-
Fujishima K., Komasa M., Kitamura S., Tomita M., Kanai A.
Progress of Theoretical Physics Supplement ( 173 ) 206 - 218 2008
ISSN 03759687
-
Ohno, H., Naito, Y., Nakajima, H. and Tomita, M.
Artificial Life 14 ( 1 ) 3-28 - 28 2008
Research paper (scientific journal), Joint Work, ISSN 10645462
-
Comparative Study of Circadian Oscillatory Network Models of Drosophila
Ogawa, Y., Arakawa, K., Kaizu, K., Miyoshi, F., Nakayama, Y. and Tomita, M.
Artificial Life 14 ( 1 ) 29-48 - 48 2008
Research paper (scientific journal), Joint Work, ISSN 10645462
-
Algebraic Method for the Analysis of Signaling Crosstalk
Matsubara, Y., Kikuchi, S., Sugimoto, M., Oka, K. and Tomita, M.
Artificial Life 14 ( 1 ) 81-94 - 94 2008
Research paper (scientific journal), Joint Work, ISSN 10645462
-
Imami, K., Sugiyama, N., Kyono, Y., Tomita, M. and Ishihama, Y.
Innovations in Analytical Sciences 24 ( 1 ) 161 - 166 2008
Research paper (scientific journal), Joint Work, ISSN 09106340
-
Depiction of metabolome changes in histidine-starved Escherichia coli by CE-TOFMS
Ohashi,Y.,Hirayama,A.,Ishikawa,T.,Nakamura,S.,Shimizu,K.,Ueno,Y.,Tomita,M.and Soga,T.
Mol.BioSyst 4 ( 2 ) 135-147 - 147 2008
Research paper (scientific journal), Joint Work, ISSN 1742206X
-
Evolution of gene regulatory networks:Robustness as an emergent property of evolution
Krishnan,A.,Tomita,M.and Giuliani,A.
Physica A:Statistical Mechanics nad its Applications 387 ( 8-9 ) 2170-2186 - 2186 2008
Research paper (scientific journal), Joint Work, ISSN 03784371
-
Reshuffling of the Bacillus subtilis 168 genome by multifold inversion
Kuroki,A.,TOda,T.,Matsui,K.,Uotsu-Tomita,R.,Tomita,M.and Itaya,M.
Journal of Biochemistry 143 ( 1 ) 97-105 - 105 2008
Research paper (scientific journal), Joint Work, ISSN 0021924X
-
Informatics for Peptide Retention Properties in Proteomic LC-MS
Shinoda, K., Sugimoto, M., Tomita, M. and Ishihama, Y.
Proteomics 8 ( 4 ) 787-98 - 798 2008
Research paper (scientific journal), Joint Work, ISSN 16159853
-
Proteins as Networks: Usefulness of Graph Theory in Protein Science
Krishnan, A., Zbilut, P.J., Tomita, M. and Giuliani, A.
Currents in Protein and Peptide Science 9 ( 1 ) 28-38 - 38 2008
Research paper (scientific journal), Joint Work, ISSN 13892037
-
Fujishima, K., Sugahara, J., Tomita, M. and Kanai, A.
PLoS ONE journal 3 ( 2 ) e1622 2008
Research paper (scientific journal), Joint Work
-
Comparative expression analysis uncovers novel features of endogenous antisense transcription
Yuki Okada, Chiaki Tashiro, Koji Numata, Kazufumi Watanabe, Hajime Nakaoka, Naoyuki Yamamoto, Kazue Okubo, Rieko Ikeda, Rintaro Saito, Akio Kanai, Kuniya Abe, Masaru Tomita, and Hidenori Kiyosawa
Hum. Mol. Genet. 17 ( 11 ) 1631-1640 - 1640 2008
Research paper (scientific journal), Joint Work, ISSN 09646906
-
Implications from a Network-Based Topological Analysis of Ubiquitin Unfolding Simulations
Arun Krishnan, Alessandro Giuliani, Joseph P. Zbilut, Masaru Tomita
PLoS ONE 3 ( 5 ) e2149 2008
Research paper (scientific journal), Joint Work
-
Time-resolved metabolomics reveals metabolic modulation in rice foliage
Shigeru Sato , Masanori Arita , Tomoyoshi Soga , Takaaki Nishioka and Masaru Tomita
BMC Systems Biology 2 51 2008
Research paper (scientific journal), Joint Work
-
E. coli metabolomics: Capturing the complexity of a "simple" model
Robert M., Soga T., Tomita M.
Topics in Current Genetics 18 189 - 234 2007.09
ISSN 16106970
-
Bioinformatic analysis of post-transcriptional regulation by uORF in human and mouse
Matsui M., Yachie N., Okada Y., Saito R., Tomita M.
FEBS Letters 581 ( 22 ) 4184 - 4188 2007.09
ISSN 00145793
-
Sequential logic model deciphers dynamic transciptional control of gene expressions
Yeo Z., Wong S., Vel Arjunan S., Piras V., Tomita M., Selvarajoo K., Giuliani A., Tsuchiya M.
PLoS ONE 2 ( 8 ) 2007.08
-
P-BOSS: A new filtering method for treasure hunting in metabolomics
Morohashi M., Shimizu K., Ohashi Y., Abe J., Mori H., Tomita M., Soga T.
Journal of Chromatography A 1159 ( 1-2 ) 142 - 148 2007.08
ISSN 00219673
-
Distinguishing enzymes using metabolome data for the hybrid dynamic/static method
Ishii N., Nakayama Y., Tomita M.
Theoretical Biology and Medical Modelling 4 2007.06
-
Gene expression waves: Cell cycle independent collective dynamics in cultured cells
Tsuchyia M., Wong S., Yeo Z., Colosimo A., Palumbo M., Farina L., Crescenzi M., Mazzola A., Negri R., Bianchi M., Selvarajoo K., Tomita M., Giuliani A.
FEBS Journal 274 ( 11 ) 2878 - 2886 2007.06
ISSN 1742464X
-
Arakawa K., Uno R., Nakayama Y., Tomita M.
Gene 392 ( 1-2 ) 239 - 246 2007.05
ISSN 03781119
-
Kinoshita A., Tsukada K., Soga T., Hishiki T., Ueno Y., Nakayama Y., Tomita M., Suematsu M.
Journal of Biological Chemistry 282 ( 14 ) 10731 - 10741 2007.04
ISSN 00219258
-
Kinoshita A., Nakayama Y., Kitayama T., Tomita M.
FEBS Journal 274 ( 6 ) 1449 - 1458 2007.03
ISSN 1742464X
-
Miyoshi, Fumihiko ; Nakayama, Yoichi ; Kaizu, Kazunari ; Iwasaki, Hideo ; Tomita, Masaru
JOURNAL OF BIOLOGICAL RHYTHMS 22 ( 1 ) 69-80 - 80 2007.02
Research paper (scientific journal), Joint Work, ISSN 0748-7304
-
Noise-reduction filtering for accurate detection of replication termini in bacterial genomes
Arakawa, Kazuharu ; Saito, Rintaro ; Tomita, Masaru
FEBS LETTERS 581 ( 2 ) 253-258 - 258 2007.01
Research paper (scientific journal), Joint Work, ISSN 0014-5793
-
eXpanda: an Integrated Platform for Network Analysis and Visualization
Negishi, Y., Nakamura, H., Yachie, N., Saito, R. and Tomita, M.
In silico Biology 7 ( 2 ) 141 - 144 2007
ISSN 13866338
-
Toya, Y., Ishii, N., Hirasawa, T., Tomita, M. and Soga, T.
Journal of Chromatography A 1159 ( 1-2 ) 134–141 - 141 2007
Research paper (scientific journal), Joint Work, ISSN 00219673
-
Soga, T., Ishikawa, T., Igarashi, S., Sugawara, K., Kakazu, Y. and Tomita, M.
Journal of Chromatography A 1159 ( 1-2 ) 125–133 - 133 2007
Research paper (scientific journal), Joint Work, ISSN 00219673
-
Conjugational transfer system to shuttle giant DNA cloned by Bacillus subtilis genome (BGM) vector
Kuroki, A., Ohtani, N., Tsuge, K., Tomita, M. and Itaya, M.
Gene 399 ( 1 ) 72-80 - 80 2007
Research paper (scientific journal), Joint Work, ISSN 03781119
-
Fujishima, K., Komasa, M., Kitamura, S., Suzuki, H., Tomita, M. and Kanai, A.
DNA Research 14 ( 3 ) 91-102 - 102 2007
Research paper (scientific journal), Joint Work, ISSN 13402838
-
Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes
Kochiwa, H., Tomita, M. and Kanai, A.
BMC Evolutionary Biology 7 128 2007
Research paper (scientific journal), Joint Work
-
Indeterminacy of Reverse Engineering of Gene Regulatory Networks: The Curse of Gene Elasticity
Krishnan, A., Giuliani, A. and Tomita, M
PLoS ONE 2 ( 6 ) e562 2007
Research paper (scientific journal), Joint Work
-
Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics
Tamaki, S., Arakawa, K., Kono, N. and Tomita, M.
Genomics Proteomics Bioinformatics 5; 53-58(2007) 5 ( 1 ) 53-58 - 58 2007
Research paper (scientific journal), Joint Work, ISSN 16720229
-
Computational analysis of microRNA-mediated antiviral defense in humans
Watanabe, Y., Kishi, A., Yachie, N., Kanai, A. and Tomita, M.
FEBS Letters 581 ( 24 ) 4603-4610 - 4610 2007
Research paper (scientific journal), Joint Work, ISSN 00145793
-
Monton, M., Tomita, M., Soga, T. and Ishihama, Y.
Analytical Chemistry 79 ( 20 ) 7838-7844 - 7844 2007
Research paper (scientific journal), Joint Work, ISSN 00032700
-
Sugiyama, N., Masuda, T., Shinoda, K., Nakamura, A., Tomita, M. and Ishihama, Y.
Mol Cell Proteomics 6 ( 6 ) 1103-1109 - 1109 2007
Research paper (scientific journal), Joint Work, ISSN 15359476
-
Statistical Analysis of Gene Expression in Innate Immune Responses: Dynamic Interactions between MicroRNA and Signaling Molecules
Piras, V., Selvarajoo, K., Fujikawa, N., Choi, S., Tomita, M., Giuliani, A. and Tsuchiya, M.
Genomics and Informatics 5 107-112 2007
Research paper (scientific journal), Joint Work
-
Multiple high throughput analyses monitor the response of E. coli to perturbations
Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Yee, Ho, Pei., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, T., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H. and Tomita, M.
Science 316 ( 5824 ) 593-597 - 597 2007
Research paper (scientific journal), Joint Work, ISSN 00368075
-
Network scaling invariants help to elucidate basic topological principles of proteins
Krishnan, A., Giuliani, A., Zbilut, J.P. and Tomita, M.
Journal of Proteome Research 6 ( 10 ) 3924-3934 - 3934 2007
Research paper (scientific journal), Joint Work, ISSN 15353893
-
Inferring rules of Escherichia coli translational efficiency using an artificial neural network
Mori, K., Saito, R., Kikuchi, S. and Tomita, M.
BioSystems 90 ( 2 ) 414-420 - 420 2007
Research paper (scientific journal), Joint Work, ISSN 03032647
-
Computational Methods for MicroRNA Target Prediction
Watanabe, Y., Tomita, M. and Kanai, A.
Methods in Enzymology 427 65-86 - 86 2007
Research paper (scientific journal), Joint Work, ISSN 00766879
-
Arakawa, K. and Tomita, M.
Evolutionary Bioinformatics 3 279-286 - 286 2007
Research paper (scientific journal), Joint Work
-
Sugahara, J., Yachie, N., Arakawa, K. and Tomita, M.
RNA 13 ( 5 ) 671-681 - 681 2007
Research paper (scientific journal), Joint Work, ISSN 13558382
-
Inhibitory effect of phosphoenolpyruvate on glycolytic enzymes in Escherichia coli
Ogawa, T., Mori, H., Tomita, M. and Yoshino, M.
Research in Microbiology 158 ( 2 ) 159-163 - 163 2007
Research paper (scientific journal), Joint Work, ISSN 09232508
-
Simulation of developmental changes in action potentials with ventricular cell models
Itoh, H., Naito, Y. and Tomita, M.
Systems and Synthetic Biology 1 ( 1 ) 11-23 - 23 2007
Research paper (scientific journal), Joint Work, ISSN 18725325
-
Visualization of three-way comparisons of omics data
Baran, R., Robert, M., Suematsu, M., Soga, T. and Tomita, M.
BMC Bioinformatics 8 72 2007
Research paper (scientific journal), Joint Work
-
Alignment-Based Approach for Durable Data Storage into Living Organisms
Yachie, N., Sekiyama, K., Sugahara, J., Ohashi, Y. and Tomita, M.
Biotechnology Progress 23 ( 2 ) 501-505 - 505 2007
Research paper (scientific journal), Joint Work, ISSN 87567938
-
Dynamic simulation of an in vitro multi-enzyme system
Ishii, N., Suga, Y., Hagiya, A., Watanabe, H., Mori, H., Yoshino, M, and Tomita, M.
FEBS Letters 581 ( 3 ) 413-420 - 420 2007
Research paper (scientific journal), Joint Work, ISSN 00145793
-
Comparative analysis of cis-encoded antisense RNAs in eukaryotes
Numata, K., Okada, Y., Saito, R., Kiyosawa, H., Kanai, A. and Tomita, M.
Gene 392 392 ( 1-2 ) 134-141 - 141 2007
Research paper (scientific journal), Joint Work, ISSN 03781119
-
Hu, B. and Tomita, M.
Systems and Synthetic Biology 1 ( 1 ) 47-58 - 58 2007
Research paper (scientific journal), Joint Work, ISSN 18725325
-
Arakawa, K. and Tomita, M.
Evolutionary Bioinformatics 3 159 - 168 2007
Research paper (scientific journal), Joint Work
-
Robust effects of Tsr-CheBp and CheA-CheYp affinity in bacterial chemotaxis
Matsuzaki, Y., Kikuchi, S. and Tomita, M.
Artificial intelligence in medicine 41 ( 2 ) 145-150 - 150 2007
Research paper (scientific journal), Joint Work, ISSN 09333657
-
Hashimoto, M., Ishihama, Y., Tomita, M. and Soga, T.
Rapid Communications in Mass Spectrometry 21 ( 22 ) 3579 - 3584 - 3584 2007
Research paper (scientific journal), Joint Work, ISSN 09514198
-
Permuted tRNA Genes Expressed via a Circular RNA Intermediate in Cyanidioschyzon merolae
Soma, A., Onodera, A., Sugahara, J., Kanai, A., Yachie, N., Tomita, M., Kawamura, F., Sekine, Y.
Science 318 ( 5849 ) 450-453 - 453 2007
Research paper (scientific journal), Joint Work, ISSN 00368075
-
Morohashi, M., Ohashi, Y., Tani, S., Ishii, K., Itaya, M., Nanamiya, H., Kawamura, F., Tomita, M. and Soga, T.
Journal of Biochemistry 142 ( 2 ) 183-191 - 191 2007
Research paper (scientific journal), Joint Work, ISSN 0021924X
-
Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria
Suzuki H, Saito R, Tomita M.
EURASIP J Bioinform Syst Biol. 2007 ( 61374 ) 2007
Research paper (scientific journal), Joint Work, ISSN 16874145
-
Chua G.H., Krishnan A., Li K.B., Tomita M.
Journal of Bioinformatics and Computational Biology 4 ( 6 ) 1245 - 1267 2006.12
ISSN 02197200
-
Shinoda K., Sugimoto M., Yachie N., Sugiyama N., Masuda T., Robert M., Soga T., Tomita M.
Journal of Proteome Research 5 ( 12 ) 3312 - 3317 2006.12
ISSN 15353893
-
HybGFS: a hybrid method for genome-fingerprint scanning
Shinoda, Kosaku ; Yachie, Nozomu ; Masuda, Takeshi ; Sugiyama, Naoyuki ; Sugimoto, Masahiro ; Soga, Tomoyoshi ; Tomita, Masaru
BMC Bioinformatics 7 8 2006.10
Research paper (scientific journal), Joint Work, ISSN 1471-2105
-
Evaluation of metabolic alteration in transgenic rice overexpressing dihydroflavonol-4-reductase
Takahashi, Hideyuki ; Hayashi, Mitsunori ; Goto, Fumiyuki ; Sato, Shigeru ; Soga, Tomoyoshi ; Nishioka, Takaaki ; Tomita, Masaru ; Kawai-Yamada, Maki ; Uchimiya, Hirofumi
Annals of Botany 98 ( 4 ) 819-825 - 825 2006.10
Research paper (scientific journal), Joint Work, ISSN 0305-7364
-
Over-representation of Chi sequences caused by di-codon increase in Escherichia coli K-12
Uno, Reina ; Nakayama, Yoichi ; Tomita, Masaru
Gene 380 ( 1 ) 30-37 - 37 2006.09
Research paper (scientific journal), Joint Work, ISSN 0378-1119
-
Metabolomics approach for enzyme discovery
Saito, Natsumi ; Robert, Martin ; Kitamura, Sayaka ; Baran, Richard ; Soga, Tomoyoshi ; Mori, Hirotada ; Nishioka, Takaaki ; Tomita, Masaru
Journal of Proteome Research 5 ( 8 ) 1979-1987 - 1987 2006.08
Research paper (scientific journal), Joint Work, ISSN 1535-3893
-
Kitayama, Tomoya ; Kinoshita, Ayako ; Sugimoto, Masahiro ; Nakayama, Yoichi ; Tomita, Masaru
Theor Biol Med Model 3 24 2006.07
Research paper (scientific journal), Joint Work, ISSN 1742-4682
-
Modeling Hsp70-mediated Protein Folding
Hu B, Mayer MP, Tomita M.
Biophysical Journal 91 ( 2 ) 496-507 - 507 2006.07
Research paper (scientific journal), Joint Work, ISSN 00063495
-
Comparative analysis of base correlations in 5′ untranslated regions of various species
Osada Y., Saito R., Tomita M.
Gene 375 ( 1-2 ) 80 - 86 2006.06
ISSN 03781119
-
Soga, Tomoyoshi; Baran, Richard; Suematsu, Makoto; Ueno, Yuki; Ikeda, Satsuki; Sakurakawa, Tadayuki; Kakazu, Yuji; Ishikawa, Takamasa; Robert, Martin; Nishioka, Takaaki; Tomita, Masaru
Journal of Biological Chemistry 281 ( 24 ) 16768-16776 - 16776 2006.06
Research paper (scientific journal), Joint Work, ISSN 0021-9258
-
Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model
Yachie, Nozomu ; Numata, Koji ; Saito, Rintaro ; Kanai, Akio ; Tomita, Masaru
Gene 372 ( 1-2 ) 171-181 - 181 2006.05
Research paper (scientific journal), Joint Work, ISSN 0378-1119
-
Large-scale identification of protein-protein interaction of Escherichia coli K-12
Arifuzzaman, M. ; Maeda, M. ; Itoh, A. ; Nishikata, K. ; Takita, C. ; Saito, R. ; Ara, T. ; Nakahigashi, K. ; Huang, H. C. ; Hirai, A. ; Tsuzuki, K. ; Nakamura, S. ; Altaf-Ul-Amin, M. ; Oshima, T. ; Baba, T. ; Yamamoto, N. ; Kawamura, T. ; Ioka-Nakamichi, T. ; Kitagawa, M. ; Tomita, M. ; Kanaya, S. ; Wada, C. ; Mori, H. ; Tomita, M
Genome Research 16 ( 5 ) 686-691 - 691 2006.05
Research paper (scientific journal), Joint Work, ISSN 1088-9051
-
Parameter estimation for stiff equations of biosystems using radial basis function networks
Matsubara, Yoshiya ; Kikuchi, Shinichi ; Sugimoto, Masahiro ; Tomita, Masaru
BMC Bioinformatics 7 11 2006.04
Research paper (scientific journal), Joint Work, ISSN 1471-2105
-
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes
Arakawa, Kazuharu ; Yamada, Yohei ; Shinoda, Kosaku ; Nakayama, Yoichi ; Tomita, Masaru
BMC Bioinformatics 7 11 2006.03
Research paper (scientific journal), Joint Work, ISSN 1471-2105
-
Characteristics and clustering of human ribosomal protein genes
Ishii, Kyota, Washio, Takanori, Uechi, Tamayo, Yoshihama, Maki, Kenmochi, Naoya, Tomita, Masaru
Bmc Genomics 7 37 2006.02
Research paper (scientific journal), Joint Work, ISSN 1471-2164
-
Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein
Kanai A., Sato A., Imoto J., Tomita M.
Biochemical Journal 393 ( 1 ) 373 - 379 2006.01
ISSN 02646021
-
Kochiwa H., Itaya M., Tomita M., Kanai A.
FEBS Journal 273 ( 2 ) 420 - 429 2006.01
ISSN 1742464X
-
Computational analysis of microRNA targets in Caenorhabditis elegans
Watanabe, Yuka, Yachie, Nozomu, Numata, Koji, Saito, Rintaro, Kanai, Akio, Tomita, Masaru
Gene 365 ( 1-2 SPEC. ISS. ) 2-10 - 10 2006.01
Research paper (scientific journal), Joint Work, ISSN 0378-1119
-
SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level
Sugahara, Junichi ; Yachie, Nozomu ; Sekine, Yasuhiko ; Soma, Akiko ; Matsui, Motomu ; Tomita, Masaru ; Kanai, Akio
In Silico Biology 6 ( 5 ) 411-418 - 418 2006
Research paper (scientific journal), Joint Work, ISSN 1386-6338
-
Fujita, Hideki ; Samejima, Hazuki ; Kitagawa, Noriyuki ; Mitsuhashi, Takayuki ; Washio, Takanori ; Yonemoto, Junzo ; Tomita, Masaru ; Takahashi, Takao ; Kosaki, Kenjiro
Congenital Anomalies 46 ( 3 ) 135-143 - 143 2006
Research paper (scientific journal), Joint Work, ISSN 0914-3505
-
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection
Baba, Tomoya ; Ara, Takeshi ; Hasegawa, Miki ; Takai, Yuki ; Okumura, Yoshiko ; Baba, Miki ; Datsenko, Kirill A. ; Tomita, Masaru ; Wanner, Barry L. ; Mori, Hirotada
Molecular Systems Biology 2 2006.0008. 2006
Research paper (scientific journal), Joint Work, ISSN 1744-4292
-
GPAC: benchmarking the sensitivity of genome informatics analysis to genome annotation completeness
Arakawa, Kazuharu ; Nakayama, Yoichi ; Tomita, Masaru
In Silico Biology 6 ( 1-2 ) 49-60 - 60 2006
Research paper (scientific journal), Joint Work, ISSN 1386-6338
-
MEGU: pathway mapping Web-service based on KEGG and SVG
Kono, Nobuaki ; Arakawa, Kazuharu ; Tomita, Masaru
In Silico Biology 6 ( 6 ) 621-625 - 625 2006
Research paper (scientific journal), Joint Work, ISSN 1386-6338
-
Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila
Inagaki S., Numata K., Kondo T., Tomita M., Yasuda K., Kanai A., Kageyama Y.
Genes to Cells 10 ( 12 ) 1163 - 1173 2005.12
ISSN 13569597
-
A problem in multivariate analysis of codon usage data and a possible solution
Suzuki H., Saito R., Tomita M.
FEBS Letters 579 ( 28 ) 6499 - 6504 2005.11
ISSN 00145793
-
Hoque M., Ushiyama H., Tomita M., Shimizu K.
Biochemical Engineering Journal 26 ( 1 ) 38 - 49 2005.11
ISSN 1369703X
-
A comprehensive software suite for the analysis of cDNAs
Arakawa K., Suzuki H., Fujishima K., Fujimoto K., Ueda S., Matsui M., Tomita M.
Genomics, Proteomics and Bioinformatics 3 ( 3 ) 179 - 188 2005.08
ISSN 16720229
-
All systems go: launching cell simulation fueled by integrated experimental biology data
Arita, M; Robert, M; Tomita, M
Current Opinion in Biotechnology 16 ( 3 ) 344-349 - 349 2005.06
Research paper (scientific journal), Joint Work, ISSN 09581669
-
Ohtani, Naoto Saito, Natsumi Tomita, Masaru Itaya, Mitsuhiro Itoh, Aya
FEBS Journal 272 ( 11 ) 2828-2837 - 2837 2005.06
Research paper (scientific journal), Joint Work, ISSN 1742464X
-
Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico
Takahashi, Kouichi Arjunan, Satya Nanda Vel Tomita, Masaru
Febs Letters 579 ( 8 ) 1783-1788 2005.03
Research paper (scientific journal), Joint Work, ISSN 00145793
-
GC-compositional strand bias around transcription start sites in plants and fungi
Fujimori S., Washio T., Tomita M.
BMC Genomics 6 2005.02
ISSN 14712164
-
Sugimoto M., Kikuchi S., Arita M., Soga T., Nishioka T., Tomita M.
Analytical Chemistry 77 ( 1 ) 78 - 84 2005.01
ISSN 00032700
-
A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks
Yugi K, Nakayama Y, Kojima S, Kitayama T, Tomita M.
BMC Bioinformatics 6 ( 299 ) 2005
Research paper (scientific journal), Joint Work, ISSN 14712105
-
Reverse engineering of biochemical equations from time-course data by means of genetic programming
Sugimoto M., Kikuchi S., Tomita M.
Biosystems 80 ( 2 ) 155 - 164 2005
Research paper (scientific journal), Joint Work, ISSN 03032647
-
In silico diagnosis of inherently inhibited gene expression focusing on initial codon combinations
Ohashi Y., Yamashiro A., Washio T., Ishii N., Ohshima H., Michishita T., Tomita M., Itaya M.
Gene 347 ( 1 ) 11 - 19 2005
Research paper (scientific journal), Joint Work, ISSN 03781119
-
Kitagawa, Noriyuki ; Washio, Takanori ; Kosugi, Shunichi ; Yamashita, Tomoya ; Higashi, Kenji ; Yanagawa, Hiroshi ; Higo, Kenichi ; Satoh, Koji ; Ohtomo, Yasuhiro ; Sunako, Tomomi ; Murakami, Kazuo ; Matsubara, Kenichi ; Kawai, Jun ; Carninci, Piero ; Hayashizaki, Yoshihide ; Kikuchi, Shoshi ; Tomita, Masaru
Bioinformatics 21 ( 9 ) 1758-1763 - 1763 2005
Research paper (scientific journal), Joint Work, ISSN 13674803
-
Hybrid dynamic/static method for large-scale simulation of metabolism
Yugi, K., Nakayama, Y., Kinoshita, A., and Tomita, M.
Theoretical Biology and Medical Modeling 2 ( 42 ) 2005
Research paper (scientific journal), Joint Work, ISSN 17424682
-
KEGG-based pathway visualization tool for complex omics data
Arakawa, K., Kono, N., Yamada, Y. and Tomita, M.
In Silico Biology 5 ( 0039 ) 419 - 423 2005
Research paper (scientific journal), Joint Work, ISSN 13866338
-
Metabolome Analysis and Metabolic Simulation
Ishii N., Soga T., Nishioka T. and Tomita M.
Metabolomics 1 ( 1 ) 29-37 - 37 2005
Research paper (scientific journal), Joint Work, ISSN 15733882
-
Nakayama Y., Kinoshita A., Tomita M.
Theoretical Biology and Medical Modeling 2 ( 18 ) 2005
Research paper (scientific journal), Joint Work, ISSN 17424682
-
Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7
Ohtani N., Yanagawa H., Tomita M., Itaya M.
Nucleic Acids Research 32 ( 19 ) 5809 - 5819 2004.12
ISSN 03051048
-
Comparative Analysis of Physical Maps of Four Bacillus subtilis (natto) Genomes
Qiu, Dongru Fujita, Kyoko Sakuma, Yuko Tanaka, Teruo Ohashi, Yoshiaki Ohshima, Hideyuki Tomita, Masaru Itaya, Mitsuhiro
Applied & Environmental Microbiology 70 ( 10 ) 6247-6256 - 6256 2004.10
Research paper (scientific journal), Joint Work, ISSN 00992240
-
Itoh H, Washio T, Tomita M.
RNA 10 ( 7 ) 1005-1018 - 1018 2004.07
Research paper (scientific journal), Joint Work, ISSN 13558382
-
Yano Y., Saito R., Yoshida N., Yoshiki A., Wynshaw-Boris A., Tomita M., Hirotsune S.
Journal of Molecular Medicine 82 ( 7 ) 414 - 422 2004.07
ISSN 09462716
-
Sustained MAPK activation is dependent on continual NGF receptor regeneration
Qiu, D., Mao, L., Kikuchi, S. and Tomita, M.
Development, Growth & Differentiation 46 ( 5 ) 393 - 403 2004.06
Research paper (conference, symposium, etc.), Joint Work, Accepted, ISSN 00121592
-
Kitamura-Abe S., Itoh H., Washio T., Tsutsumi A., Tomita M.
Journal of Bioinformatics and Computational Biology 2 ( 2 ) 309 - 331 2004.06
ISSN 02197200
-
Application of capillary electrophoresis-mass spectrometry to syntheitc in vitro glycolysis studies
Itoh A., Ohashi Y., Soga T., Mori H., Nishioka T. and Tomita M.
Electrophoresis 25 1996-2002 2004
Research paper (scientific journal), Joint Work
-
Simultaneous determination of the main metabolites in rice leaves using capillary electrophoresis mass spectrometry and capillary electrophoresis diode array detection
Sato, S., Soga, T., Nishioka, T. and Tomita, M.
Plant Journal 40 ( 1 ) 151-163 2004
Research paper (scientific journal), Joint Work, Accepted
-
A general computational model of mitochondrial metabolism in a whole organelle scale
Yugi K., Tomita M.
Bioinformatics 20 ( 20 ) 1795-1796 - 1796 2004
Research paper (scientific journal), Joint Work, Accepted, ISSN 13674803
-
Position-specific expression of Hox genes along the gastrointestinal tract
Yahagi N, Kosaki R, Ito T, Mitsuhashi T, Shimada H, Tomita M, Takahashi T, and Kosaki K
Congenital Anomalies 44 ( 1 ) 18-26 - 26 2004
Research paper (scientific journal), Joint Work, Accepted, ISSN 09143505
-
A multi-algorithm, multi-timescale method for cell simulation
Takahashi, K., Kaizu, K., Bin, H., Tomita, M
Bioinformatics 20 ( 4 ) 538-546 - 546 2004
Research paper (scientific journal), Joint Work, Accepted, ISSN 13674803
-
Otani, N., Yanagawa, H., Tomita, M. and Itaya, M
Biochemical Journal 381 ( 3 ) 795-802 - 802 2004
Research paper (scientific journal), Joint Work, Accepted, ISSN 02646021
-
Toward large-scale modeling of the microbial cell for computer simulation
Ishii, N., Robert, M. Nakayama, Y., Kanai, A. and Tomita, M
Journal of Biotechnology 113 ( 1-3 ) 281-294 - 294 2004
Research paper (scientific journal), Joint Work, Accepted, ISSN 01681656
-
The 'weighted sum of relative entropy': a new index for synonymous codon usage bias
Suzuki, H., Saito, R. and Tomita, M
GENE 335 ( 335 ) 19-23 - 23 2004
Research paper (scientific journal), Joint Work, Accepted, ISSN 03781119
-
Qualitative and quantitative analysis of amino acids by capillary electrophresis Electrospray ionization tandem mass spectrometry
Soga, T., Kakazu Yuji, Robert, M., Tomita, M. and Nishioka, T
Electrophoresis ( 25 ) 1964-1972 2004
Research paper (scientific journal), Joint Work, Accepted
-
On dynamics of overlapping genes in bacterial genomes
Fukuda Y., Nakayama Y., Tomita M.
Gene 323 ( 1-2 ) 181 - 187 2003.12
ISSN 03781119
-
Fujimori S, Washio T, Higo K, Ohtomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Tomita M
FEBS LETTERS 554 ( 1-2 ) 17 - 22 2003.11
Research paper (scientific journal), Single Work, ISSN 0014-5793
-
Kikuchi S., Fujimoto K., Kitagawa N., Fuchikawa T., Abe M., Oka K., Takei K., Tomita M.
Neural Networks 16 ( 9 ) 1389 - 1398 2003.11
ISSN 08936080
-
E-cell 2: Multi-platform E-Cell simulation system
Takahashi K, Ishikawa N, Sadamoto Y, Sasamoto H, Ohta S, Shiozawa A, Miyoshi F, Naito Y, Nakayama Y, Tomita M
BIOINFORMATICS 19 ( 13 ) 1727 - 1729 2003.09
Research paper (scientific journal), Single Work, ISSN 1367-4803
-
Comparative study of translation termination sites and release factors (RF1 and RF2) in procaryotes
Ozawa Y., Saito R., Washio T., Tomita M.
Journal of Molecular Evolution 56 ( 6 ) 665 - 672 2003.06
ISSN 00222844
-
Dynamics modeling of genetic networks using genetic algorithm and S-system
Kikuchi S., Tominaga D., Arita M., Takahashi K., Tomita M.
Bioinformatics 19 ( 5 ) 643 - 650 2003.03
ISSN 13674803
-
E-cell simulation system and its application to the modeling of circadian rhythm
Miyoshi F, Nakayama Y, Tomita M
Seikagaku 75 ( 1 ) 5-16 - 16 2003.01
Research paper (scientific journal), Single Work, ISSN 0037-1017
-
G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining
Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Kobayashi, Y., and Tomita, M.
Bioinformatics 19 ( 2 ) 305 - 306 2003
Research paper (scientific journal), Joint Work, ISSN 13674803
-
M. Hucka, A. Finney, H. M. Sauro, H. Bolouri, J. C. Doyle, H. Kitano, A. P. Arkin, B. J. Bornstein, D. Bray, A. Cornish-Bowden, A. A. Cuellar, S. Dronov, E. D. Gilles, M. Ginkel, V. Gor, I. I. Goryanin, W. J. Hedley, T. C. Hodgman, J.-H. Hofmeyr, P. J. Hunter, N. S. Juty, J. L. Kasberger, A.Kremling, U. Kummer, N. Le Novere, L. M. Loew, D. Lucio, P. Mendes, E. D.Mjolsness, Y. Nakayama, M. R. Nelson, P. F. Nielsen, T. Sakurada, J. C.Schaff, B. E. Shapiro, T. S. Shimizu, H. D. Spence, J. Stelling, K.Takahashi, M. Tomita, J. Wagner, J. Wang
Bioinformatics 19 ( 4 ) 524 - 531 2003
Research paper (scientific journal), Joint Work, Accepted, ISSN 13674803
-
Sato, A., Kanai, A., Itaya, M. and Tomita, M
Biochemical and Biophysical Research Communication 309 ( 1 ) 247 - 252 2003
Research paper (scientific journal), Joint Work, ISSN 0006291X
-
Computational analysis of stop codon readthrough in D.melanogaster
Sato, M., Umeki, H., Saito, R., Kanai, A. and Tomita, M.
Bioinformatics 19 ( 11 ) 1371 - 1380 2003
Research paper (scientific journal), Joint Work, ISSN 13674803
-
Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection.
Numata K., Kanai, A., Saito, R., Kondo, S., Adachi, J., Wilming, L.G., Hume, D.A., Hayashizaki, Y. and Tomita, M. ;RIKEN GER Group; GSL Members. Hayashizaki, Y. and Tomita, M.
Genome Research 13 ( 6 B ) 1301 - 1306 2003
Research paper (scientific journal), Joint Work, ISSN 10889051
-
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
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 CAM, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R
Nature 420 ( 6915 ) 563-573 - 573 2002.12
Research paper (scientific journal), Joint Work, ISSN 0028-0836
-
Comprehensive sequence analysis of translation termination sites in various eukaryotes
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
Gene 300 ( 1-2 ) 79-87 - 87 2002.10
Research paper (scientific journal), Joint Work, ISSN 0378-1119
-
Towards Computer Aided Design (CAD) of Useful Microorganisms
Tomita, M.
Bioinformatics 17 1091-1092 2002
Research paper (scientific journal), Single Work
-
Fujita H, Hasegawa T, Takahashi T, Matsuo N, and Kosaki K, Tomita M.
Teratology 65 ( 1 ) 10 - 18 2002
Joint Work, ISSN 00403709
-
Causal analysis of CpG suppression in the Mycoplasma genome
Goto, M., Washio, T. Tomita M.
Microbial and Comparative Genomics 5 51-58 2002
Joint Work
-
Soga, T. Ueno, Y., Naraoka, H., Ohashi, O., Nishioka, T. Tomita M.
Analytical Chemistry 74 ( 10 ) 2233-2239 - 2239 2002
Research paper (scientific journal), Joint Work, Accepted, ISSN 00032700
-
Integrative modeling of gene expression and metabolism with E-CELL simulation system
Hashimoto, K., Seno, S., Dhar, P.K. and Tomita, M
Artificial Life and Robotics 6 99-107 2002
Research paper (scientific journal), Joint Work, Accepted
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Proposition of cortical connectivity between 30 cytoarchitectural areas of human cerebral cortex
Fukuda, R., Hara, J., Shankle, W. R., Tomita M.
Neurocomputing 32-33 ( 33 ) 749-755 - 755 2002
Research paper (scientific journal), Joint Work, ISSN 09252312
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Soga, T., Ueno, Y., Naraoka, H., Matsuda, K., Tomita, M., and Nishioka, T
Analytical Chemistry 74 ( 24 ) 6224-6229 - 6229 2002
Research paper (scientific journal), Joint Work, ISSN 00032700
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On biased distribution of introns in various eukaryotes
Sakurai, A., Fujimori, S., Kochiwa, H., Kitamura-Abe, S., Washio, T., Saito, R., The RIKEN Genome Exploration Research Group Phase II Team, Carninci, P., Hayashizaki, Y., and Tomita, M.
Gene, 300 ( 1-2 ) 89-95 - 95 2002
Research paper (scientific journal), Joint Work, ISSN 03781119
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Kochiwa, H., Suzuki, R., Washio, T., Saito, R., The RIKEN Genome Exploration Research Group Phase II Team, Bono, H., Carninci, P., Okazaki, Y., Miki, R., Hayashizaki, Y., and Tomita, M.
Genome Research 12 ( 8 ) 1286-1293 - 1293 2002
Research paper (scientific journal), Joint Work, ISSN 10889051
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Computational challenges in cell simulation: A software engineering approach
Takahashi, K., Yugi, K., Hashimoto, K., Yamada, Y., Pickett, C., and Tomita, M
IEEE Intelligent Systems 17 ( 5 ) 64-71 2002
Research paper (scientific journal), Joint Work
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Complete mutation analysis panel of the 39 human HOX genes
Kosaki K, Takahashi T, Sasaki K, Tomita M, McGinnis W, and Matsuo N.
Teratology 65 ( 2 ) 50-62 - 62 2002
Research paper (scientific journal), Joint Work, ISSN 00403709
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Computer analysis of potential stem structures of rRNA operons in various procaryote genomes
Saito, R., Ozawa, Y., Kuzuno, N., Tomita M.
Gene 259 ( 1-2 ) 217-222 - 222 2001.12
Research paper (scientific journal), Joint Work, ISSN 03781119
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Bernardi G., Macaya G., Tomita M.
Gene 276 ( 1-2 ) 2001.10
ISSN 03781119
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Sakai H., Washio T., Saito R., Shinagawa A., Itoh M., Shibata K., Carninci P., Konno H., Kawai J., Hayashizaki Y., Tomita M.
Gene 276 ( 1-2 ) 101 - 105 2001.10
ISSN 03781119
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Functional annotation of a full-length mouse cDNA collection
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
Nature 409 ( 6821 ) 685-690 - 689 2001.02
Research paper (scientific journal), Joint Work, ISSN 0028-0836
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Correlation between Shine-Dalgarno sequence conservation and codon usage of bacterial genes
Sakai, H., Imamura, C., Osada, Y., Saito, R., Washio, T. and Tomita, M.
Journal of Molecular Evolution 52 ( 2 ) 164-170 - 170 2001
Research paper (scientific journal), Joint Work, ISSN 00222844
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The E-CELL Project: Towards Integrative Simulation of Cellular Processes
Hashimoto, K., Takahashi, K., Matsuzaki, Y., Matsushima, R., Saito, K., Yugi, K., Miyoshi, F., Nakano, H., Tanida, S., Saito, Y., Kawase, A., Watanabe, N., Shimizu, T. and Nakayama, Y., Tomita M.
New Generation Computing 18 ( 1 ) 1-12 2001
Joint Work
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Preferential usage of some minor codons in bacteria
Ohno, H., Sakai, H., Washio, T. and Tomita, M.
Gene 276 ( 1-2 ) 107-15 - 115 2001
Research paper (scientific journal), Joint Work, ISSN 03781119
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Whole cell simulation: A grand challenge of the 21st century
Tomita, M
Trends in Biotechnology 19 ( 6 ) 205-210 - 210 2001
Research paper (scientific journal), Single Work, ISSN 01677799
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E-cell project: towards computer modeling of the whole cell
Tomita M.
Annals of Biomedical Engineering (Annals of Biomedical Engineering) 28 ( SUPPL. 1 ) 2000.12
ISSN 00906964
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Characteristic Sequence Pattern in the 5-to 20-bp Upstream Region of Primate Alu Elements
Toda, Y., Saito, R. and Tomita, M.
Journal of Molecular Evolution 50 ( 3 ) 232-237 - 237 2000
Research paper (scientific journal), Joint Work, ISSN 00222844
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The orientation bias of Chi sequences is a general tendency of G-rich oligomers
Uno R., Nakayama Y., Arakawa K., Tomita M.
Gene 36 ( 1-2 ) 207-215 - 215 2000
Research paper (scientific journal), Joint Work, ISSN 03781119
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Computer Simulation of Human erythrocyte Using the E-CELL Simulation System
Yoichi Nakayama, Ryo Matsushima, Hisako Nakano, Akiko Kawase, Kouichi Takahashi and Masaru Tomita
BRIDGING THE GAP BETWEEN WEQUENCE & FUNCTION 1999.09
Joint Work
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ApA dinucleotide periodicity in prokaryote, eukaryote, and organelle genomes
Tomita M., Wada M., Kawashima Y.
Journal of Molecular Evolution 49 ( 2 ) 182 - 192 1999.08
ISSN 00222844
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Osada, Y., Saito, R. and Tomita, M.
Bioinformatics 15 ( 7-8 ) 578-581 - 581 1999
Research paper (scientific journal), Joint Work, ISSN 13674803
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Saito, R. and Tomita, M.
Gene 238 ( 1 ) 79-83 - 83 1999
Research paper (scientific journal), Joint Work, ISSN 03781119
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E-CELL: Software environment for whole cell simulation
Tomita, M., Hashimoto, K., Takahashi, K., Shimizu, T., Matsuzaki, Y., Miyoshi, F., Saito, K., Tanida, S., Yugi, K., Venter, J.,C., Hutchison, C.,A .,3rd.
Bioinformatics 15 ( 1 ) 72 - 84 1999
Research paper (scientific journal), Joint Work, ISSN 13674803
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Fukuda, Y., Washio, T. and Tomita, M.
Nucleic Acids Research 27 ( 8 ) 1847-1853 - 1853 1999
Research paper (scientific journal), Joint Work, ISSN 03051048
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Sequence patterns observed in 5' flanking regions of primate Alu elements
Toda, Y., Saito, R. and Tomita, M.
Annals of the New York Academy of Sciences 18 369-374 - 374 1999
Research paper (scientific journal), Joint Work, ISSN 00778923
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On negative selection against ATG triplets near start codons in eukaryotic and prokaryotic genomes
Saito R, Tomita M
Journal of Molecular Evolution 26 ( 23 ) 5456-5463 - 217 1998.12
Research paper (scientific journal), Joint Work, ISSN 0022-2844
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Washio T., Sasayama J., Tomita M.
Nucleic Acids Research 26 ( 23 ) 5456 - 5463 1998.12
ISSN 03051048
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Alu elements as an aid in deciphering genome rearrangements
Toda, Y. and Tomita, M.
Gene 205 ( 1-2 ) 173 - 176 1997
Research paper (scientific journal), Joint Work, ISSN 03781119
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CpG distribution patterns in methylated and nonmethylated species
Shimizu, T., Takahashi, K. and Tomita, M.
Gene 205 ( 1-2 ) 103-107 - 107 1997
Research paper (scientific journal), Joint Work, ISSN 03781119
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Introns and reading frames: Correlation between splicing sites and their codon positions
Tomita, M., Shimizu, N. and Brutlag, D.L.
Molecular Biology and Evolution 13 ( 9 ) 1219-1223 - 1223 1996
Research paper (scientific journal), Joint Work, ISSN 07374038
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CMU Project
72-82 1989