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Items: 1 to 50 of 92

1.

Creating a Reliable Mass Spectral-Retention Time Library for All Ion Fragmentation-Based Metabolomics.

Tada I, Tsugawa H, Meister I, Zhang P, Shu R, Katsumi R, Wheelock CE, Arita M, Chaleckis R.

Metabolites. 2019 Oct 26;9(11). pii: E251. doi: 10.3390/metabo9110251.

2.

Characterization of Lipid Profiles after Dietary Intake of Polyunsaturated Fatty Acids Using Integrated Untargeted and Targeted Lipidomics.

Naoe S, Tsugawa H, Takahashi M, Ikeda K, Arita M.

Metabolites. 2019 Oct 21;9(10). pii: E241. doi: 10.3390/metabo9100241.

3.

Mass Spectrometry Data Repository Enhances Novel Metabolite Discoveries with Advances in Computational Metabolomics.

Tsugawa H, Satoh A, Uchino H, Cajka T, Arita M, Arita M.

Metabolites. 2019 Jun 24;9(6). pii: E119. doi: 10.3390/metabo9060119.

4.

Cancer Stem-Cell Marker CD44v9-Positive Cells Arise From Helicobacter pylori-Infected CAPZA1-Overexpressing Cells.

Tsugawa H, Kato C, Mori H, Matsuzaki J, Kameyama K, Saya H, Hatakeyama M, Suematsu M, Suzuki H.

Cell Mol Gastroenterol Hepatol. 2019;8(3):319-334. doi: 10.1016/j.jcmgh.2019.05.008. Epub 2019 May 27.

5.

Neutrophil-activating Protein Polymorphism of Helicobacter pylori Determines the Host Risk of Dyspepsia.

Matsuzaki J, Tsugawa H, Kashiwazaki Y, Mori H, Yamamoto Y, Kameyama H, Masaoka T, Kanai T, Suzuki H.

Cell Mol Gastroenterol Hepatol. 2019;8(2):295-297.e6. doi: 10.1016/j.jcmgh.2019.05.004. Epub 2019 May 18. No abstract available.

6.

Publisher Correction: A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms.

Tsugawa H, Nakabayashi R, Mori T, Yamada Y, Takahashi M, Rai A, Sugiyama R, Yamamoto H, Nakaya T, Yamazaki M, Kooke R, Bac-Molenaar JA, Oztolan-Erol N, Keurentjes JJB, Arita M, Saito K.

Nat Methods. 2019 May;16(5):446. doi: 10.1038/s41592-019-0423-x.

PMID:
30992571
7.

A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms.

Tsugawa H, Nakabayashi R, Mori T, Yamada Y, Takahashi M, Rai A, Sugiyama R, Yamamoto H, Nakaya T, Yamazaki M, Kooke R, Bac-Molenaar JA, Oztolan-Erol N, Keurentjes JJB, Arita M, Saito K.

Nat Methods. 2019 Apr;16(4):295-298. doi: 10.1038/s41592-019-0358-2. Epub 2019 Mar 28. Erratum in: Nat Methods. 2019 Apr 16;:.

PMID:
30923379
8.

Inhibiting xCT Improves 5-Fluorouracil Resistance of Gastric Cancer Induced by CD44 Variant 9 Expression.

Miyoshi S, Tsugawa H, Matsuzaki J, Hirata K, Mori H, Saya H, Kanai T, Suzuki H.

Anticancer Res. 2018 Nov;38(11):6163-6170. doi: 10.21873/anticanres.12969.

PMID:
30396933
9.

CAPZA1 determines the risk of gastric carcinogenesis by inhibiting Helicobacter pylori CagA-degraded autophagy.

Tsugawa H, Mori H, Matsuzaki J, Sato A, Saito Y, Imoto M, Suematsu M, Suzuki H.

Autophagy. 2019 Feb;15(2):242-258. doi: 10.1080/15548627.2018.1515530. Epub 2018 Sep 10.

10.

Advances in computational metabolomics and databases deepen the understanding of metabolisms.

Tsugawa H.

Curr Opin Biotechnol. 2018 Dec;54:10-17. doi: 10.1016/j.copbio.2018.01.008. Epub 2018 Feb 6. Review.

PMID:
29413746
11.

Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics.

Lai Z, Tsugawa H, Wohlgemuth G, Mehta S, Mueller M, Zheng Y, Ogiwara A, Meissen J, Showalter M, Takeuchi K, Kind T, Beal P, Arita M, Fiehn O.

Nat Methods. 2018 Jan;15(1):53-56. doi: 10.1038/nmeth.4512. Epub 2017 Nov 27.

12.

Enteric Glial Dysfunction Evoked by Apolipoprotein E Deficiency Contributes to Delayed Gastric Emptying.

Fukuhara S, Masaoka T, Nishimura S, Nakamura M, Matsuzaki J, Tsugawa H, Miyoshi S, Mori H, Kawase S, Shibata S, Okano H, Kanai T, Suzuki H.

Dig Dis Sci. 2017 Dec;62(12):3359-3369. doi: 10.1007/s10620-017-4820-7. Epub 2017 Nov 2.

PMID:
29098550
13.

Critical Assessment of Small Molecule Identification 2016: automated methods.

Schymanski EL, Ruttkies C, Krauss M, Brouard C, Kind T, Dührkop K, Allen F, Vaniya A, Verdegem D, Böcker S, Rousu J, Shen H, Tsugawa H, Sajed T, Fiehn O, Ghesquière B, Neumann S.

J Cheminform. 2017 Mar 27;9(1):22. doi: 10.1186/s13321-017-0207-1.

14.

Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy.

Blaženović I, Kind T, Torbašinović H, Obrenović S, Mehta SS, Tsugawa H, Wermuth T, Schauer N, Jahn M, Biedendieck R, Jahn D, Fiehn O.

J Cheminform. 2017 May 25;9(1):32. doi: 10.1186/s13321-017-0219-x.

15.

Using MS-FINDER for identifying 19 natural products in the CASMI 2016 contest.

Vaniya A, Samra SN, Palazoglu M, Tsugawa H, Fiehn O.

Phytochem Lett. 2017 Sep;21:306-312. doi: 10.1016/j.phytol.2016.12.008. Epub 2016 Dec 9.

16.

Integrated Strategy for Unknown EI-MS Identification Using Quality Control Calibration Curve, Multivariate Analysis, EI-MS Spectral Database, and Retention Index Prediction.

Matsuo T, Tsugawa H, Miyagawa H, Fukusaki E.

Anal Chem. 2017 Jun 20;89(12):6766-6773. doi: 10.1021/acs.analchem.7b01010. Epub 2017 May 26.

PMID:
28520403
17.

The importance of bioinformatics for connecting data-driven lipidomics and biological insights.

Tsugawa H, Ikeda K, Arita M.

Biochim Biophys Acta Mol Cell Biol Lipids. 2017 Aug;1862(8):762-765. doi: 10.1016/j.bbalip.2017.05.006. Epub 2017 May 14. Review. No abstract available.

PMID:
28514647
18.

Identification of small molecules using accurate mass MS/MS search.

Kind T, Tsugawa H, Cajka T, Ma Y, Lai Z, Mehta SS, Wohlgemuth G, Barupal DK, Showalter MR, Arita M, Fiehn O.

Mass Spectrom Rev. 2018 Jul;37(4):513-532. doi: 10.1002/mas.21535. Epub 2017 Apr 24. Review.

PMID:
28436590
19.

Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library.

Tsugawa H, Ikeda K, Tanaka W, Senoo Y, Arita M, Arita M.

J Cheminform. 2017 Mar 15;9:19. doi: 10.1186/s13321-017-0205-3. eCollection 2017.

20.

Sigma-2 receptor and progesterone receptor membrane component 1 (PGRMC1) are two different proteins: Proofs by fluorescent labeling and binding of sigma-2 receptor ligands to PGRMC1.

Pati ML, Groza D, Riganti C, Kopecka J, Niso M, Berardi F, Hager S, Heffeter P, Hirai M, Tsugawa H, Kabe Y, Suematsu M, Abate C.

Pharmacol Res. 2017 Mar;117:67-74. doi: 10.1016/j.phrs.2016.12.023. Epub 2016 Dec 19.

PMID:
28007569
21.

Cystathionine β-synthase and PGRMC1 as CO sensors.

Kabe Y, Yamamoto T, Kajimura M, Sugiura Y, Koike I, Ohmura M, Nakamura T, Tokumoto Y, Tsugawa H, Handa H, Kobayashi T, Suematsu M.

Free Radic Biol Med. 2016 Oct;99:333-344. doi: 10.1016/j.freeradbiomed.2016.08.025. Epub 2016 Aug 24. Review.

PMID:
27565814
22.

Flavor characteristics of the juices from fresh market tomatoes differentiated from those from processing tomatoes by combined analysis of volatile profiles with sensory evaluation.

Iijima Y, Iwasaki Y, Otagiri Y, Tsugawa H, Sato T, Otomo H, Sekine Y, Obata A.

Biosci Biotechnol Biochem. 2016 Dec;80(12):2401-2411. Epub 2016 Aug 30.

PMID:
27573376
23.

Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies.

Treutler H, Tsugawa H, Porzel A, Gorzolka K, Tissier A, Neumann S, Balcke GU.

Anal Chem. 2016 Aug 16;88(16):8082-90. doi: 10.1021/acs.analchem.6b01569. Epub 2016 Aug 2.

PMID:
27452369
24.

Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software.

Tsugawa H, Kind T, Nakabayashi R, Yukihira D, Tanaka W, Cajka T, Saito K, Fiehn O, Arita M.

Anal Chem. 2016 Aug 16;88(16):7946-58. doi: 10.1021/acs.analchem.6b00770. Epub 2016 Aug 4.

PMID:
27419259
25.

Rifabutin-based 10-day and 14-day triple therapy as a third-line and fourth-line regimen for Helicobacter pylori eradication: A pilot study.

Mori H, Suzuki H, Matsuzaki J, Tsugawa H, Fukuhara S, Miyoshi S, Hirata K, Seino T, Matsushita M, Nishizawa T, Masaoka T, Kanai T.

United European Gastroenterol J. 2016 Jun;4(3):380-7. doi: 10.1177/2050640615618043. Epub 2015 Nov 13.

26.

Boosting Sensitivity in Liquid Chromatography-Fourier Transform Ion Cyclotron Resonance-Tandem Mass Spectrometry for Product Ion Analysis of Monoterpene Indole Alkaloids.

Nakabayashi R, Tsugawa H, Kitajima M, Takayama H, Saito K.

Front Plant Sci. 2015 Dec 17;6:1127. doi: 10.3389/fpls.2015.01127. eCollection 2015.

27.

Efficacy of 10-day Sitafloxacin-Containing Third-Line Rescue Therapies for Helicobacter pylori Strains Containing the gyrA Mutation.

Mori H, Suzuki H, Matsuzaki J, Tsugawa H, Fukuhara S, Miyoshi S, Hirata K, Seino T, Matsushita M, Masaoka T, Kanai T.

Helicobacter. 2016 Aug;21(4):286-94. doi: 10.1111/hel.12286. Epub 2015 Nov 27.

PMID:
26612407
28.

BH3-only protein Bim is associated with the degree of Helicobacter pylori-induced gastritis and is localized to the mitochondria of inflammatory cells in the gastric mucosa.

Akazawa Y, Matsuda K, Isomoto H, Matsushima K, Kido Y, Urabe S, Yamaghchi N, Ohnita K, Takeshima F, Kondo H, Tsugawa H, Suzuki H, Moss J, Nakao K, Nakashima M.

Int J Med Microbiol. 2015 Sep;305(6):553-62. doi: 10.1016/j.ijmm.2015.07.002. Epub 2015 Jul 9.

29.

Nordihydroguaiaretic Acid Disrupts the Antioxidant Ability of Helicobacter pylori through the Repression of SodB Activity In Vitro.

Tsugawa H, Mori H, Matsuzaki J, Masaoka T, Hirayama T, Nagasawa H, Sakakibara Y, Suematsu M, Suzuki H.

Biomed Res Int. 2015;2015:734548. doi: 10.1155/2015/734548. Epub 2015 Apr 6.

30.

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis.

Tsugawa H, Cajka T, Kind T, Ma Y, Higgins B, Ikeda K, Kanazawa M, VanderGheynst J, Fiehn O, Arita M.

Nat Methods. 2015 Jun;12(6):523-6. doi: 10.1038/nmeth.3393. Epub 2015 May 4.

31.

MRM-DIFF: data processing strategy for differential analysis in large scale MRM-based lipidomics studies.

Tsugawa H, Ohta E, Izumi Y, Ogiwara A, Yukihira D, Bamba T, Fukusaki E, Arita M.

Front Genet. 2015 Jan 30;5:471. doi: 10.3389/fgene.2014.00471. eCollection 2014.

32.

Mucosal expression of aquaporin-4 in the stomach of histamine type 2 receptor knockout mice and Helicobacter pylori-infected mice.

Fukuhara S, Matsuzaki J, Tsugawa H, Masaoka T, Miyoshi S, Mori H, Fukushima Y, Yasui M, Kanai T, Suzuki H.

J Gastroenterol Hepatol. 2014 Dec;29 Suppl 4:53-9. doi: 10.1111/jgh.12771.

PMID:
25521734
33.

Bulk RNA degradation by nitrogen starvation-induced autophagy in yeast.

Huang H, Kawamata T, Horie T, Tsugawa H, Nakayama Y, Ohsumi Y, Fukusaki E.

EMBO J. 2015 Jan 13;34(2):154-68. doi: 10.15252/embj.201489083. Epub 2014 Dec 2.

34.

[Study of infection strategies of Helicobacter pylori and host cell response against CagA oncoprotein].

Tsugawa H.

Nihon Saikingaku Zasshi. 2014;69(4):565-75. Review. Japanese.

35.

Novel strategy for non-targeted isotope-assisted metabolomics by means of metabolic turnover and multivariate analysis.

Nakayama Y, Tamada Y, Tsugawa H, Bamba T, Fukusaki E.

Metabolites. 2014 Aug 25;4(3):722-39. doi: 10.3390/metabo4030722.

36.

MRMPROBS suite for metabolomics using large-scale MRM assays.

Tsugawa H, Kanazawa M, Ogiwara A, Arita M.

Bioinformatics. 2014 Aug 15;30(16):2379-80. doi: 10.1093/bioinformatics/btu203. Epub 2014 Apr 20.

PMID:
24753485
37.

Different-batch metabolome analysis of Saccharomyces cerevisiae based on gas chromatography/mass spectrometry.

Kawase N, Tsugawa H, Bamba T, Fukusaki E.

J Biosci Bioeng. 2014 Feb;117(2):248-255. doi: 10.1016/j.jbiosc.2013.07.008. Epub 2013 Aug 19.

PMID:
23968869
38.

Method for assessing the statistical significance of mass spectral similarities using basic local alignment search tool statistics.

Matsuda F, Tsugawa H, Fukusaki E.

Anal Chem. 2013 Sep 3;85(17):8291-7. doi: 10.1021/ac401564v. Epub 2013 Aug 14.

PMID:
23944154
39.

Bile acids increase levels of microRNAs 221 and 222, leading to degradation of CDX2 during esophageal carcinogenesis.

Matsuzaki J, Suzuki H, Tsugawa H, Watanabe M, Hossain S, Arai E, Saito Y, Sekine S, Akaike T, Kanai Y, Mukaisho K, Auwerx J, Hibi T.

Gastroenterology. 2013 Dec;145(6):1300-11. doi: 10.1053/j.gastro.2013.08.008. Epub 2013 Aug 8.

PMID:
23933602
40.

Highly sensitive and selective analysis of widely targeted metabolomics using gas chromatography/triple-quadrupole mass spectrometry.

Tsugawa H, Tsujimoto Y, Sugitate K, Sakui N, Nishiumi S, Bamba T, Fukusaki E.

J Biosci Bioeng. 2014 Jan;117(1):122-8. doi: 10.1016/j.jbiosc.2013.06.009. Epub 2013 Jul 16.

PMID:
23867096
41.

CD44 variant 9 expression in primary early gastric cancer as a predictive marker for recurrence.

Hirata K, Suzuki H, Imaeda H, Matsuzaki J, Tsugawa H, Nagano O, Asakura K, Saya H, Hibi T.

Br J Cancer. 2013 Jul 23;109(2):379-86. doi: 10.1038/bjc.2013.314. Epub 2013 Jun 18.

42.

MRMPROBS: a data assessment and metabolite identification tool for large-scale multiple reaction monitoring based widely targeted metabolomics.

Tsugawa H, Arita M, Kanazawa M, Ogiwara A, Bamba T, Fukusaki E.

Anal Chem. 2013 May 21;85(10):5191-9. doi: 10.1021/ac400515s. Epub 2013 May 1.

PMID:
23581547
43.

Impaired heme oxygenase-1 induction in the gastric antrum induces disruption of the interstitial cells of Cajal network in a rat model of streptozotocin-induced diabetes.

Mogami S, Suzuki H, Tsugawa H, Fukuhara S, Hibi T.

Neurogastroenterol Motil. 2013 Jul;25(7):609-e465. doi: 10.1111/nmo.12122. Epub 2013 Mar 27.

PMID:
23534481
44.

Current metabolomics: technological advances.

Putri SP, Yamamoto S, Tsugawa H, Fukusaki E.

J Biosci Bioeng. 2013 Jul;116(1):9-16. doi: 10.1016/j.jbiosc.2013.01.004. Epub 2013 Mar 7. Review.

PMID:
23466298
45.

Molecular approaches and modern clinical strategies for the management of Helicobacter pylori infection in Japan.

Suzuki H, Nishizawa T, Tsugawa H, Hibi T.

Keio J Med. 2012;61(4):109-19. Review.

46.

Reactive oxygen species-induced autophagic degradation of Helicobacter pylori CagA is specifically suppressed in cancer stem-like cells.

Tsugawa H, Suzuki H, Saya H, Hatakeyama M, Hirayama T, Hirata K, Nagano O, Matsuzaki J, Hibi T.

Cell Host Microbe. 2012 Dec 13;12(6):764-77. doi: 10.1016/j.chom.2012.10.014.

47.

Overexpression of miR-142-5p and miR-155 in gastric mucosa-associated lymphoid tissue (MALT) lymphoma resistant to Helicobacter pylori eradication.

Saito Y, Suzuki H, Tsugawa H, Imaeda H, Matsuzaki J, Hirata K, Hosoe N, Nakamura M, Mukai M, Saito H, Hibi T.

PLoS One. 2012;7(11):e47396. doi: 10.1371/journal.pone.0047396. Epub 2012 Nov 28. Erratum in: PLoS One. 2013;8(7). doi:10.1371/annotation/53d1898f-d0ae-4e5c-a585-c084a5c881bf.

48.

The tumor suppressor microRNA-29c is downregulated and restored by celecoxib in human gastric cancer cells.

Saito Y, Suzuki H, Imaeda H, Matsuzaki J, Hirata K, Tsugawa H, Hibino S, Kanai Y, Saito H, Hibi T.

Int J Cancer. 2013 Apr 15;132(8):1751-60. doi: 10.1002/ijc.27862. Epub 2012 Oct 17.

49.

Development of a novel microRNA promoter microarray for ChIP-on-chip assay to identify epigenetically regulated microRNAs.

Saito Y, Suzuki H, Taya T, Nishizawa M, Tsugawa H, Matsuzaki J, Hirata K, Saito H, Hibi T.

Biochem Biophys Res Commun. 2012 Sep 14;426(1):33-7. doi: 10.1016/j.bbrc.2012.08.012. Epub 2012 Aug 11.

PMID:
22906743
50.

Identification of biomarkers of stent restenosis with serum metabolomic profiling using gas chromatography/mass spectrometry.

Hasokawa M, Shinohara M, Tsugawa H, Bamba T, Fukusaki E, Nishiumi S, Nishimura K, Yoshida M, Ishida T, Hirata K.

Circ J. 2012;76(8):1864-73. Epub 2012 May 16.

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