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Research Output 1996 2019

  • 24015 Citations
  • 60 h-Index
  • 430 Article
  • 18 Conference contribution
  • 8 Chapter
  • 1 Book
2019

Chlorococcum turfosum comb. nov. (Volvocales, Chlorophyceae) and visualization of chimeric sequences

Nakada, T., Watanabe, S., Lewis, L. A. & Tomita, M., 2019 Jan 1, (Accepted/In press) In : Phycological Research.

Research output: Contribution to journalArticle

Chlorococcum
Comb and Wattles
Chlorophyceae
rRNA Genes
visualization

Comparative genomics of Bacteria commonly identified in the built environment

Merino, N., Zhang, S., Tomita, M. & Suzuki, H., 2019 Jan 28, In : BMC Genomics. 20, 1, 92.

Research output: Contribution to journalArticle

Genomics
Genome
Bacteria
Life Style
Genome Size
1 Citation (Scopus)

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., 2019 Feb 1, In : Clinica Chimica Acta. 489, p. 41-48 8 p.

Research output: Contribution to journalArticle

Metabolomics
Saliva
Mouth Diseases
Xerostomia
Capillary electrophoresis

Fast and global detection of periodic sequence repeats in large genomic resources

Mori, H., Evans-Yamamoto, D., Ishiguro, S., Tomita, M. & Yachie, N., 2019 Jan 25, In : Nucleic Acids Research. 47, 2, p. e8

Research output: Contribution to journalArticle

Software
DNA
Periodicity
Proteins
Clustered Regularly Interspaced Short Palindromic Repeats
Volvocaceae
Chlamydomonas
Chlorophyceae
Phylogeny
phylogeny

Metabolome profiling of various seaweed species discriminates between brown, red, and green algae

Hamid, S. S., Wakayama, M., Ichihara, K., Sakurai, K., Ashino, Y., Kadowaki, R., Soga, T. & Tomita, M., 2019 Jan 1, In : Planta.

Research output: Contribution to journalArticle

Phaeophyta
Rhodophyta
Seaweed
metabolome
Chlorophyta

Metabolomics Platform with Capillary Electrophoresis Coupled with High-Resolution Mass Spectrometry for Plasma Analysis

Sasaki, K., Sagawa, H., Suzuki, M., Yamamoto, H., Tomita, M., Soga, T. & Ohashi, Y., 2019 Jan 15, In : Analytical Chemistry. 91, 2, p. 1295-1301 7 p.

Research output: Contribution to journalArticle

Capillary electrophoresis
Metabolites
Mass spectrometry
Plasmas
Plasma (human)

Perioperative serum and urine metabolome analyses in patients with hepatocellular carcinoma undergoing partial hepatectomy

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., 2019 Feb 1, In : Nutrition. 58, p. 110-119 10 p.

Research output: Contribution to journalArticle

Metabolome
Hepatectomy
Hepatocellular Carcinoma
Urine
Serum

Stable and efficient delivery of DNA to Bacillus subtilis (natto) using pLS20 conjugational transfer plasmids

Itaya, M., Nagasaku, M., Shimada, T., Ohtani, N., Shiwa, Y., Yoshikawa, H., Kaneko, S., Tomita, M. & Sato, M., 2019 Feb 1, In : FEMS microbiology letters. 366, 4

Research output: Contribution to journalArticle

Bacillus subtilis
Plasmids
DNA
Genetic Engineering
Genome
2018

Accelerated Laboratory Evolution Reveals the Influence of Replication on the GC Skew in Escherichia coli

Kono, N., Tomita, M. & Arakawa, K., 2018 Nov 1, In : Genome Biology and Evolution. 10, 11, p. 3110-3117 8 p.

Research output: Contribution to journalArticle

Bacterial Genomes
mutation
Escherichia coli
machinery
Mutation

A metabologenomic approach reveals changes in the intestinal environment of mice fed on american diet

Ishii, C., Nakanishi, Y., Murakami, S., Nozu, R., Ueno, M., Hioki, K., Aw, W., Hirayama, A., Soga, T., Ito, M., Tomita, M. & Fukuda, S., 2018 Jan 1, In : International Journal of Molecular Sciences. 19, 12, 4079.

Research output: Contribution to journalArticle

diets
Butyrates
Nutrition
mice
sequencing

Base-pairing probability in the microRNA stem region affects the binding and editing specificity of human A-to-I editing enzymes ADAR1-p110 and ADAR2

Ishiguro, S., Galipon, J., Ishii, R., Suzuki, Y., Kondo, S., Okada-Hatakeyama, M., Tomita, M. & Ui-Tei, K., 2018 Jan 1, (Accepted/In press) In : RNA Biology.

Research output: Contribution to journalArticle

MicroRNAs
Base Pairing
Enzymes
Adenosine Deaminase
RNA

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., 2018 Jan 1, In : Chemical Communications. 54, 83, p. 11745-11748 4 p.

Research output: Contribution to journalArticle

Biomarkers
beta-Galactosidase
Tumors
Acetaminophen
Antigens
5 Citations (Scopus)

Development of a sheathless CE-ESI-MS interface

Hirayama, A., Abe, H., Yamaguchi, N., Tabata, S., Tomita, M. & Soga, T., 2018 Jun 1, In : Electrophoresis. 39, 11, p. 1382-1389 8 p.

Research output: Contribution to journalArticle

Metabolites
Dialysis membranes
Cracks
Metabolomics
Plastics
1 Citation (Scopus)

Drying and extraction effects on three edible brown seaweeds for metabolomics

Hamid, S. S., Wakayama, M., Soga, T. & Tomita, M., 2018 Jan 1, (Accepted/In press) In : Journal of Applied Phycology.

Research output: Contribution to journalArticle

Phaeophyceae
metabolomics
seaweed
metabolite
drying
2 Citations (Scopus)

Effect of storage conditions on salivary polyamines quantified via liquid chromatography-mass spectrometry

Tomita, A., Mori, M., Hiwatari, K., Yamaguchi, E., Itoi, T., Sunamura, M., Soga, T., Tomita, M. & Sugimoto, M., 2018 Dec 1, In : Scientific Reports. 8, 1, 12075.

Research output: Contribution to journalArticle

polyamines
storage conditions
liquid chromatography
mass spectrometry
saliva

Efficient delivery of large DNA from Escherichia coli to Synechococcus elongatus PCC7942 by broad-host-range conjugal plasmid pUB307

Itaya, M., Kusakabe, H., Sato, M., Tomita, M. & Sato, R., 2018 Jul 1, In : Journal of Biochemistry. 164, 1, p. 15-20 6 p.

Research output: Contribution to journalArticle

Synechococcus
Host Specificity
Escherichia coli
Plasmids
DNA
6 Citations (Scopus)

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. & 1 othersSunamura, M., 2018 Feb 5, In : Cancers. 10, 2, 43.

Research output: Contribution to journalArticle

Polyamines
Pancreatic Neoplasms
Saliva
Biomarkers
Spermine

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., 2018 Dec 1, In : Scientific Reports. 8, 1, 8792.

Research output: Contribution to journalArticle

Bacilli
Genes
DNA
Cloning
Molecules
1 Citation (Scopus)

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., 2018 Jan 1, Methods in Molecular Biology. Humana Press Inc., p. 167-183 17 p. (Methods in Molecular Biology; vol. 1823).

Research output: Chapter in Book/Report/Conference proceedingChapter

RNA Sequence Analysis
Inosine
RNA Editing
Adenosine
RNA
2 Citations (Scopus)

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. & 7 othersKojima, S., Tomita, M., Soga, T., Noma, T., Nonoyama, S., Nakahata, T. & Saito, M. K., 2018 Mar 4, In : Biochemical and Biophysical Research Communications. 497, 2, p. 719-725 7 p.

Research output: Contribution to journalArticle

Stem cells
Induced Pluripotent Stem Cells
Energy Metabolism
Stem Cells
Adenosine Triphosphate

Metabolic characterization of antifolate responsiveness and nonresponsiveness in malignant pleural mesothelioma cells

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., 2018 Oct 12, In : Frontiers in Pharmacology. 9, OCT, 1129.

Research output: Contribution to journalArticle

Pemetrexed
Folic Acid Antagonists
Hypoxanthine
Metabolic Networks and Pathways
Thymidine
1 Citation (Scopus)

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., 2018 Dec 1, In : Bone Reports. 9, p. 11-18 8 p.

Research output: Contribution to journalArticle

Metabolomics
Bone Density
Bone and Bones
Osteoporosis
Estrogens

MICOP: Maximal information coefficient-based oscillation prediction to detect biological rhythms in proteomics data

Iuchi, H., Sugimoto, M. & Tomita, M., 2018 Jun 28, In : BMC Bioinformatics. 19, 1, 249.

Research output: Contribution to journalArticle

Proteomics
Periodicity
Oscillation
Prediction
Coefficient
2 Citations (Scopus)

Microglena redcarensis sp. nov. (Volvocales, Chlorophyceae), a brackish water chlamydomonad with contractile vacuoles

Nakada, T., Takahashi, S. & Tomita, M., 2018 Oct 1, In : Phycological Research. 66, 4, p. 310-317 8 p.

Research output: Contribution to journalArticle

Microglena
Chlorophyceae
Vacuoles
brackish water
green alga
7 Citations (Scopus)

Reliability of plasma polar metabolite concentrations in a large-scale cohort study using capillary electrophoresis-mass spectrometry

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. M. D., Elliott, P., Tomita, M., Sato, A., Suzuki, C., Sugimoto, M., Soga, T. & Takebayashi, T., 2018 Jan 1, In : PLoS One. 13, 1, e0191230.

Research output: Contribution to journalArticle

Capillary electrophoresis
capillary electrophoresis
Capillary Electrophoresis
Metabolites
cohort studies
1 Citation (Scopus)
Amino Acyl-tRNA Synthetases
Transfer RNA
Anticodon
Archaea
Eukaryota
2 Citations (Scopus)

The complete mitochondrial genome of Eumeta variegata (Lepidoptera: Psychidae)

Arakawa, K., Kono, N., Ohtoshi, R., Nakamura, H. & Tomita, M., 2018 Jul 3, In : Mitochondrial DNA Part B: Resources. 3, 2, p. 812-813 2 p.

Research output: Contribution to journalArticle

Lepidoptera
Mitochondrial Genome
Nanopores
AT Rich Sequence
Moths
2 Citations (Scopus)
Bacilli
Bacillus subtilis
Genetic Recombination
Genes
DNA

Thymidine catabolism promotes NADPH oxidase-derived reactive oxygen species (ROS) signalling in KB and yumoto cells

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. & 2 othersFurukawa, T. & Akiyama, S. I., 2018 Dec 1, In : Scientific Reports. 8, 1, 6760.

Research output: Contribution to journalArticle

Thymidine Phosphorylase
KB Cells
NADPH Oxidase
Thymidine
Reactive Oxygen Species
2 Citations (Scopus)

Tuning Gene Activity by Inducible and Targeted Regulation of Gene Expression in Minimal Bacterial Cells

Mariscal, A. M., Kakizawa, S., Hsu, J. Y., Tanaka, K., González-González, L., Broto, A., Querol, E., Lluch-Senar, M., Piñero-Lambea, C., Sun, L., Weyman, P. D., Wise, K. S., Merryman, C., Tse, G., Moore, A. J., Hutchison, C. A., Smith, H. O., Tomita, M., Venter, J. C., Glass, J. I. & 2 othersPiñol, J. & Suzuki, Y., 2018 Jun 15, In : ACS Synthetic Biology. 7, 6, p. 1538-1552 15 p.

Research output: Contribution to journalArticle

Clustered Regularly Interspaced Short Palindromic Repeats
Mycoplasma
Gene Expression Regulation
Gene expression
Tuning
1 Citation (Scopus)

Ultralow input genome sequencing library preparation from a single tardigrade specimen

Yoshida, Y., Konno, S., Nishino, R., Murai, Y., Tomita, M. & Arakawa, K., 2018 Jul 15, In : Journal of Visualized Experiments. 2018, 137, e57615.

Research output: Contribution to journalArticle

Genomic Library
Animals
Libraries
Contamination
DNA
3 Citations (Scopus)

Urinary polyamine biomarker panels with machine-learning differentiated colorectal cancers, benign disease, and healthy controls

Nakajima, T., Katsumata, K., Kuwabara, H., Soya, R., Enomoto, M., Ishizaki, T., Tsuchida, A., Mori, M., Hiwatari, K., Soga, T., Tomita, M. & Sugimoto, M., 2018 Mar 7, In : International Journal of Molecular Sciences. 19, 3, 756.

Research output: Contribution to journalArticle

machine learning
biomarkers
Polyamines
Biomarkers
Learning systems
2017
4 Citations (Scopus)

Alteration of fatty acid chain length of Chlamydomonas reinhardtii by simultaneous expression of medium-chain-specific thioesterase and acyl carrier protein

Inaba, Y., Nakahigashi, K., Ito, T. & Tomita, M., 2017 Jan 1, In : Phycological Research. 65, 1, p. 94-99 6 p.

Research output: Contribution to journalArticle

Acyl Carrier Protein
acyl carrier protein
Chlamydomonas reinhardtii
algae
medium chain fatty acids
1 Citation (Scopus)

An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus

Ikeda, Y., Okada, Y., Sato, A., Kanai, T., Tomita, M., Atomi, H. & Kanai, A., 2017 Dec 1, In : Scientific Reports. 7, 1, 12674.

Research output: Contribution to journalArticle

Archaeal RNA
Pyrococcus
Archaeal Proteins
Thermococcus
RNA-Binding Proteins
8 Citations (Scopus)

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. & 1 othersToyama, Y., 2017 Feb 1, In : Bone. 95, p. 1-4 4 p.

Research output: Contribution to journalArticle

Metabolomics
Bone Density
Osteoporosis
Cystine
Hydroxyproline

Combination of quantitative changes in ionic components to enhance the contractile force during T-tubule development

Wakita, M., Sano, H. I., Naito, Y. & Tomita, M., 2017 Mar 1, Computing in Cardiology Conference, CinC 2016. IEEE Computer Society, Vol. 43. p. 1093-1096 4 p. 7868937

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Rats
Sarcoplasmic Reticulum
Ryanodine Receptor Calcium Release Channel
Rodentia
Guinea Pigs

Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan

Suzuki, H., Tomita, M., Tsai, P. J., Ko, W. C., Hung, Y. P., Huang, I. H. & Chen, J. W., 2017 Nov 29, In : Gut Pathogens. 9, 1, 70.

Research output: Contribution to journalArticle

Ribotyping
Clostridium difficile
Taiwan
Prophages
Genome
29 Citations (Scopus)

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

Yoshida, Y., Koutsovoulos, G., Laetsch, D. R., Stevens, L., Kumar, S., Horikawa, D. D., Ishino, K., Komine, S., Kunieda, T., Tomita, M., Blaxter, M. & Arakawa, K., 2017 Jul 27, In : PLoS Biology. 15, 7, e2002266.

Research output: Contribution to journalArticle

Tardigrada
Genomics
Genes
Arthropods
Gene transfer
1 Citation (Scopus)
oxidative phosphorylation
Phosphorylation
Adenosinetriphosphate
Oxidative Phosphorylation
Adenosine Triphosphate
7 Citations (Scopus)

Differential binding of three major human ADAR isoforms to coding and long non-coding transcripts

Galipon, J., Ishii, R., Suzuki, Y., Tomita, M. & Ui-Tei, K., 2017 Feb 1, In : Genes. 8, 2, 68.

Research output: Contribution to journalArticle

RNA Isoforms
Adenosine Deaminase
RNA
RNA Editing
Alternative Splicing
40 Citations (Scopus)

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, M. T., Wendt, K. S., Okada, Y., Nagai, T. & Maeshima, K., 2017 Jul 20, In : Molecular Cell. 67, 2, p. 282-293.e7

Research output: Contribution to journalArticle

Nucleosomes
Chromatin
Heterochromatin
Mitosis
Cell Differentiation
7 Citations (Scopus)

Effect of masticatory stimulation on the quantity and quality of saliva and the salivary metabolomic profile

Okuma, N., Saita, M., Hoshi, N., Soga, T., Tomita, M., Sugimoto, M. & Kimoto, K., 2017 Aug 1, In : PLoS One. 12, 8, e0183109.

Research output: Contribution to journalArticle

Metabolomics
metabolomics
Metabolites
saliva
Saliva
16 Citations (Scopus)

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., Tomita, M. & Iino, M., 2017 Apr 1, In : Amino Acids. 49, 4, p. 761-770 10 p.

Research output: Contribution to journalArticle

Metabolomics
Mouth Neoplasms
Biomarkers
Metabolites
Saliva
4 Citations (Scopus)

Eggshell membrane powder ameliorates intestinal inflammation by facilitating the restitution of epithelial injury and alleviating microbial dysbiosis

Jia, H., Hanate, M., Aw, W., Itoh, H., Saito, K., Kobayashi, S., Hachimura, S., Fukuda, S., Tomita, M., Hasebe, Y. & Kato, H., 2017 Mar 8, In : Scientific Reports. 7, 43993.

Research output: Contribution to journalArticle

Dysbiosis
Egg Shell
Inflammatory Bowel Diseases
Powders
Inflammation
Genome
Bacteria
Replication Origin
DNA Replication
Microbial Genome
3 Citations (Scopus)

Evolutionary analysis of HIV-1 pol proteins reveals representative residues for viral subtype differentiation

Nagata, S., Imai, J., Makino, G., Tomita, M. & Kanai, A., 2017 Nov 2, In : Frontiers in Microbiology. 8, NOV, 2151.

Research output: Contribution to journalArticle

Human Immunodeficiency Virus pol Gene Products
pol Gene Products
RNA-Directed DNA Polymerase
HIV-1
Ribonuclease H
25 Citations (Scopus)

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, M. M., Kushida, Y. & 7 othersHaba, R., Okano, K., Tomita, M., Suzuki, Y., Fukuda, S., Aoki, M. & Soga, T., 2017 Sep 12, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 37, p. E7697-E7706

Research output: Contribution to journalArticle

Adenoma
Colorectal Neoplasms
Genes
Carcinogenesis
Organelle Biogenesis
7 Citations (Scopus)

Metabolomic Profiling as a Possible Reverse Engineering Tool for Estimating Processing Conditions of Dry-Cured Hams

Sugimoto, M., Obiya, S., Kaneko, M., Enomoto, A., Honma, M., Wakayama, M., Soga, T. & Tomita, M., 2017 Jan 18, In : Journal of Agricultural and Food Chemistry. 65, 2, p. 402-410 9 p.

Research output: Contribution to journalArticle

Metabolomics
Reverse engineering
metabolomics
ham
Metabolites
7 Citations (Scopus)

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., 2017 Apr 1, In : International Journal of Molecular Sciences. 18, 4, 767.

Research output: Contribution to journalArticle

Metabolomics
Biliary Tract Neoplasms
Metabolites
Pancreatic Neoplasms
serums