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Volumn , Issue , 2012, Pages 23-38

Finding characteristic substructures for metabolite classes

Author keywords

FT BLAST; Mass spectrometry; Metabolites; Substructure prediction

Indexed keywords

COMMON SUBGRAPH; DATA SETS; FT-BLAST; ICELANDICS; STRUCTURAL ELEMENTS; STRUCTURAL SIMILARITY; STRUCTURE ELUCIDATION; TREE ALIGNMENT;

EID: 84871212197     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.4230/OASIcs.GCB.2012.23     Document Type: Conference Paper
Times cited : (6)

References (43)
  • 1
    • 79751533664 scopus 로고    scopus 로고
    • Computing bond orders in molecule graphs
    • Sebastian Böcker, Quang Bao Anh Bui, and Anke Truss. Computing bond orders in molecule graphs. Theoretical Computer Science, 412(12-14):1184-1195, 2011.
    • (2011) Theoretical Computer Science , vol.412 , Issue.12-14 , pp. 1184-1195
    • Böcker, S.1    Bao Anh Bui, Q.2    Truss, A.3
  • 2
    • 58349086772 scopus 로고    scopus 로고
    • SIRIUS: Decomposing isotope patterns for metabolite identification
    • Sebastian Böcker, Matthias Letzel, Zsuzsanna Lipták, and Anton Pervukhin. SIRIUS: Decomposing isotope patterns for metabolite identification. Bioinformatics, 25(2):218-224, 2009.
    • (2009) Bioinformatics , vol.25 , Issue.2 , pp. 218-224
    • Böcker, S.1    Letzel, M.2    Lipták, Z.3    Pervukhin, A.4
  • 3
    • 49549101405 scopus 로고    scopus 로고
    • Towards de novo identification of metabolites by analyzing tandem mass spectra
    • Proc. of European Conference on Computational Biology (ECCB 2008)
    • Sebastian Böcker and Florian Rasche. Towards de novo identification of metabolites by analyzing tandem mass spectra. Bioinformatics, 24:I49-I55, 2008. Proc. of European Conference on Computational Biology (ECCB 2008).
    • (2008) Bioinformatics , vol.24
    • Böcker, S.1    Rasche, F.2
  • 5
    • 84901022772 scopus 로고    scopus 로고
    • Chemoinformatics-an introduction for computer scientists
    • Nathan Brown. Chemoinformatics-an introduction for computer scientists. ACM Comput Surv, 41(2):8, 2009.
    • (2009) ACM Comput Surv , vol.41 , Issue.2 , pp. 8
    • Brown, N.1
  • 7
    • 3042521543 scopus 로고    scopus 로고
    • Spectral similarity versus structural similarity: Mass spectrometry
    • W. Demuth, M. Karlovits, and K. Varmuza. Spectral similarity versus structural similarity: mass spectrometry. Anal Chim Acta, 516(1-2):75-85, 2004.
    • (2004) Anal Chim Acta , vol.516 , Issue.1-2 , pp. 75-85
    • Demuth, W.1    Karlovits, M.2    Varmuza, K.3
  • 8
    • 33750055006 scopus 로고    scopus 로고
    • Enumerating molecules
    • Kenny B. Lipkowitz, Raima Larter, and Thomas R. Cundari, editors, , chapter 3 . John Wiley & Sons, Inc
    • Jean-Loup Faulon, Donald P. Visco, and Diana Roe. Enumerating molecules. In Kenny B. Lipkowitz, Raima Larter, and Thomas R. Cundari, editors, Reviews in Computational Chemistry, volume 21, chapter 3, pages 209-286. John Wiley & Sons, Inc., 2005.
    • (2005) Reviews in Computational Chemistry , vol.21 , pp. 209-286
    • Faulon, J.1    Visco, D.P.2    Roe, D.3
  • 10
    • 41049100247 scopus 로고    scopus 로고
    • Extending the breadth of metabolite profiling by gas chromatography coupled to mass spectrometry
    • Oliver Fiehn. Extending the breadth of metabolite profiling by gas chromatography coupled to mass spectrometry. Trends Analyt Chem, 27(3):261-269, 2008.
    • (2008) Trends Analyt Chem , vol.27 , Issue.3 , pp. 261-269
    • Fiehn, O.1
  • 12
    • 85008016154 scopus 로고    scopus 로고
    • Discovering frequent graph patterns using disjoint paths
    • Ehud Gudes, Solomon Eyal Shimony, and Natalia Vanetik. Discovering frequent graph patterns using disjoint paths. IEEE Trans Knowl Data En, 18(11):1441-1456, 2006.
    • (2006) IEEE Trans Knowl Data en , vol.18 , Issue.11 , pp. 1441-1456
    • Gudes, E.1    Eyal Shimony, S.2    Vanetik, N.3
  • 13
    • 56149101337 scopus 로고    scopus 로고
    • FiD: A software for ab initio structural identification of product ions from tandem mass spectrometric data
    • Markus Heinonen, Ari Rantanen, Taneli Mielikäinen, Juha Kokkonen, Jari Kiuru, Raimo A Ketola, and Juho Rousu. FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data. Rapid Commun Mass Spectrom, 22(19):3043-3052, 2008.
    • (2008) Rapid Commun Mass Spectrom , vol.22 , Issue.19 , pp. 3043-3052
    • Heinonen, M.1    Rantanen, A.2    Mielikäinen, T.3    Kokkonen, J.4    Kiuru, J.5    Ketola, R.A.6    Rousu, J.7
  • 14
    • 49049121462 scopus 로고    scopus 로고
    • Mass spectral metabonomics beyond elemental formula: Chemical database querying by matching experimental with computational fragmentation spectra
    • Dennis W. Hill, Tzipporah M. Kertesz, Dan Fontaine, Robert Friedman, and David F. Grant. Mass spectral metabonomics beyond elemental formula: Chemical database querying by matching experimental with computational fragmentation spectra. Anal Chem, 80(14):5574-5582, 2008.
    • (2008) Anal Chem , vol.80 , Issue.14 , pp. 5574-5582
    • Hill, D.W.1    Kertesz, T.M.2    Fontaine, D.3    Friedman, R.4    Grant, D.F.5
  • 16
    • 84864025665 scopus 로고    scopus 로고
    • De novo analysis of electron impact mass spectra using fragmentation trees
    • Franziska Hufsky, Martin Rempt, Florian Rasche, Georg Pohnert, and Sebastian Böcker. De novo analysis of electron impact mass spectra using fragmentation trees. Anal Chim Acta, 739:67-76, 2012.
    • (2012) Anal Chim Acta , vol.739 , pp. 67-76
    • Hufsky, F.1    Rempt, M.2    Rasche, F.3    Pohnert, G.4    Böcker, S.5
  • 17
    • 79954566035 scopus 로고    scopus 로고
    • Decision tree supported substructure prediction of metabolites from GC-MS profiles
    • Jan Hummel, Nadine Strehmel, Joachim Selbig, Dirk Walther, and Joachim Kopka. Decision tree supported substructure prediction of metabolites from GC-MS profiles. Metabolomics, 6(2):322-333, 2010.
    • (2010) Metabolomics , vol.6 , Issue.2 , pp. 322-333
    • Hummel, J.1    Strehmel, N.2    Selbig, J.3    Walther, D.4    Kopka, J.5
  • 18
    • 84974733299 scopus 로고    scopus 로고
    • An apriori-based algorithm for mining frequent substructures from graph data
    • Jan Komorowski Djamel A. Zighed and Jan Zytkow, editors, of Lect Notes Comput Sci,. Springer, Berlin
    • Akihiro Inokuchi, Takashi Washio, and Hiroshi Motoda. An apriori-based algorithm for mining frequent substructures from graph data. In Jan Komorowski Djamel A. Zighed and Jan Zytkow, editors, Proceedings of the 4th European Conference on Principles of Data Mining and Knowledge Discovery (PKDD 2000), volume 1910 of Lect Notes Comput Sci, pages 13-23. Springer, Berlin, 2000.
    • (2000) Proceedings of the 4th European Conference on Principles of Data Mining and Knowledge Discovery (PKDD 2000) , vol.1910 , pp. 13-23
    • Inokuchi, A.1    Washio, T.2    Motoda, H.3
  • 19
    • 70149092076 scopus 로고    scopus 로고
    • Analytical and statistical approaches to metabolomics research
    • Haleem J Issaq, Que N Van, Timothy J Waybright, Gary M Muschik, and Timothy D Veenstra. Analytical and statistical approaches to metabolomics research. J Sep Sci, 32(13):2183-2199, 2009.
    • (2009) J Sep Sci , vol.32 , Issue.13 , pp. 2183-2199
    • Issaq, H.J.1    Van Que, N.2    Waybright, T.J.3    Muschik, G.M.4    Veenstra, T.D.5
  • 20
    • 78650737804 scopus 로고    scopus 로고
    • Advances in structure elucidation of small molecules using mass spectrometry
    • Tobias Kind and Oliver Fiehn. Advances in structure elucidation of small molecules using mass spectrometry. Bioanal Rev, 2(1-4):23-60, 2010.
    • (2010) Bioanal Rev , vol.2 , Issue.1-4 , pp. 23-60
    • Kind, T.1    Fiehn, O.2
  • 21
    • 79957957678 scopus 로고    scopus 로고
    • Evaluation of dried blood spots as sample matrix for gas chromatography/mass spectrometry based metabolomic profiling
    • Sing Teang Kong, Hai-Shu Lin, Jianhong Ching, and Paul C Ho. Evaluation of dried blood spots as sample matrix for gas chromatography/mass spectrometry based metabolomic profiling. Anal Chem, 83(11):4314-4318, 2011.
    • (2011) Anal Chem , vol.83 , Issue.11 , pp. 4314-4318
    • Teang Kong, S.1    Lin, H.2    Ching, J.3    Ho, P.C.4
  • 22
    • 0002024882 scopus 로고    scopus 로고
    • JChemPaint-using the collaborative forces of the internet to develop a free editor for 2D chemical structures
    • Stefan Krause, Egon Willighagen, and Christoph Steinbeck. JChemPaint-using the collaborative forces of the internet to develop a free editor for 2D chemical structures. Molecules, 5(1):93-98, 2000.
    • (2000) Molecules , vol.5 , Issue.1 , pp. 93-98
    • Krause, S.1    Willighagen, E.2    Steinbeck, C.3
  • 23
    • 4544385908 scopus 로고    scopus 로고
    • An efficient algorithm for discovering frequent subgraphs
    • Michihiro Kuramochi and George Karypis. An efficient algorithm for discovering frequent subgraphs. IEEE Trans Knowl Data En, 16(9):1038-1051, 2004.
    • (2004) IEEE Trans Knowl Data en , vol.16 , Issue.9 , pp. 1038-1051
    • Kuramochi, M.1    Karypis, G.2
  • 24
    • 14944375202 scopus 로고    scopus 로고
    • The Gaston tool for frequent subgraph mining
    • Siegfried Nijssen and Joost N. Kok. The Gaston tool for frequent subgraph mining. Electron Notes Theor Comput Sci, 127(1):77-87, 2005.
    • (2005) Electron Notes Theor Comput Sci , vol.127 , Issue.1 , pp. 77-87
    • Nijssen, S.1    Kok, J.N.2
  • 25
    • 84858790233 scopus 로고    scopus 로고
    • Innovation: Metabolomics: The apogee of the omics trilogy
    • Gary J. Patti, Oscar Yanes, and Gary Siuzdak. Innovation: Metabolomics: The apogee of the omics trilogy. Nat Rev Mol Cell Biol, 13(4):263-269, 2012.
    • (2012) Nat Rev Mol Cell Biol , vol.13 , Issue.4 , pp. 263-269
    • Patti, G.J.1    Yanes, O.2    Siuzdak, G.3
  • 26
    • 60549107218 scopus 로고    scopus 로고
    • In silico methods for predicting metabolism and mass fragmentation applied to quetiapine in liquid chromatography/time-of-flight mass spectrometry urine drug screening
    • Anna Pelander, Elli Tyrkkö, and Ilkka Ojanperä. In silico methods for predicting metabolism and mass fragmentation applied to quetiapine in liquid chromatography/time-of-flight mass spectrometry urine drug screening. Rapid Commun Mass Spectrom, 23(4):506-514, 2009.
    • (2009) Rapid Commun Mass Spectrom , vol.23 , Issue.4 , pp. 506-514
    • Pelander, A.1    Tyrkkö, E.2    Ojanperä, I.3
  • 28
    • 84859400853 scopus 로고    scopus 로고
    • Identifying the unknowns by aligning fragmentation trees
    • Florian Rasche, Kerstin Scheubert, Franziska Hufsky, Thomas Zichner, Marco Kai, Aleŝ Svatoŝ, and Sebastian Böcker. Identifying the unknowns by aligning fragmentation trees. Anal Chem, 84(7):3417-3426, 2012.
    • (2012) Anal Chem , vol.84 , Issue.7 , pp. 3417-3426
    • Rasche, F.1    Scheubert, K.2    Hufsky, F.3    Zichner, T.4    Kai, M.5    Svatoŝ, A.6    Böcker, S.7
  • 29
    • 0036663707 scopus 로고    scopus 로고
    • Maximum common subgraph isomorphism algorithms for the matching of chemical structures
    • JohnWRaymond and Peter Willett. Maximum common subgraph isomorphism algorithms for the matching of chemical structures. J Comput Aided Mol Des, 16(7):521-533, 2002.
    • (2002) J Comput Aided Mol des , vol.16 , Issue.7 , pp. 521-533
    • Raymond, J.W.1    Willett, P.2
  • 30
    • 37049239596 scopus 로고
    • A computer program for classifying plants
    • D. J. Rogers and T. T. Tanimoto. A computer program for classifying plants. Science, 132(3434):1115-1118, 1960.
    • (1960) Science , vol.132 , Issue.3434 , pp. 1115-1118
    • Rogers, D.J.1    Tanimoto, T.T.2
  • 32
    • 79953228863 scopus 로고    scopus 로고
    • Computing fragmentation trees from metabolite multiple mass spectrometry data
    • of Lect Notes Comput Sci,. Springer, Berlin
    • Kerstin Scheubert, Franziska Hufsky, Florian Rasche, and Sebastian Böcker. Computing fragmentation trees from metabolite multiple mass spectrometry data. In Proc. of Research in Computational Molecular Biology (RECOMB 2011), volume 6577 of Lect Notes Comput Sci, pages 377-391. Springer, Berlin, 2011.
    • (2011) Proc. of Research in Computational Molecular Biology (RECOMB 2011) , vol.6577 , pp. 377-391
    • Scheubert, K.1    Hufsky, F.2    Rasche, F.3    Böcker, S.4
  • 33
    • 84859376463 scopus 로고    scopus 로고
    • Consensus structure elucidation combining GC/EI-MS, structure generation and calculated properties
    • Emma Louise Schymanski, Christine M J Gallampois, Martin Krauss, Markus Meringer, Steffen Neumann, Tobias Schulze, Sebastian Wolf, and Werner Brack. Consensus structure elucidation combining GC/EI-MS, structure generation and calculated properties. Anal Chem, 84(7):3287-3295, 2012.
    • (2012) Anal Chem , vol.84 , Issue.7 , pp. 3287-3295
    • Louise Schymanski, E.1    Gallampois, C.M.J.2    Krauss, M.3    Meringer, M.4    Neumann, S.5    Schulze, T.6    Wolf, S.7    Brack, W.8
  • 34
    • 0000429874 scopus 로고
    • Chemical substructure identification by mass spectral library searching
    • Stephen Stein. Chemical substructure identification by mass spectral library searching. J Am Soc Mass Spectrom, 6:644-655, 1995.
    • (1995) J Am Soc Mass Spectrom , vol.6 , pp. 644-655
    • Stein, S.1
  • 35
    • 33745135773 scopus 로고    scopus 로고
    • Recent developments of the Chemistry Development Kit (CDK)-an open-source java library for chemo-and bioinformatics
    • Christoph Steinbeck, Christian Hoppe, Stefan Kuhn, Matteo Floris, Rajarshi Guha, and Egon L Willighagen. Recent developments of the Chemistry Development Kit (CDK)-an open-source java library for chemo-and bioinformatics. Curr Pharm Des, 12(17):2111-2120, 2006.
    • (2006) Curr Pharm des , vol.12 , Issue.17 , pp. 2111-2120
    • Steinbeck, C.1    Hoppe, C.2    Kuhn, S.3    Floris, M.4    Guha, R.5    Willighagen, E.L.6
  • 36
    • 84996033884 scopus 로고
    • Recognition of largest common structural fragment among a variety of chemical structures
    • Yoshimasa Takahashi, Yuzuru Satoh, Hajime Suzuki, and Shin-ichi Sasaki. Recognition of largest common structural fragment among a variety of chemical structures. Anal Sci, 3:23-28, 1987.
    • (1987) Anal Sci , vol.3 , pp. 23-28
    • Takahashi, Y.1    Satoh, Y.2    Suzuki, H.3    Sasaki, S.4
  • 37
    • 79955501451 scopus 로고    scopus 로고
    • GC/MS based metabolomics: Development of a data mining system for metabolite identification by using soft independent modeling of class analogy (SIMCA)
    • Hiroshi Tsugawa, Yuki Tsujimoto, Masanori Arita, Takeshi Bamba, and Eiichiro Fukusaki. GC/MS based metabolomics: development of a data mining system for metabolite identification by using soft independent modeling of class analogy (SIMCA). BMC Bioinformatics, 12:131, 2011.
    • (2011) BMC Bioinformatics , vol.12 , pp. 131
    • Tsugawa, H.1    Tsujimoto, Y.2    Arita, M.3    Bamba, T.4    Fukusaki, E.5
  • 38
    • 58149411184 scopus 로고
    • Features of similarity
    • Amos Tversky. Features of similarity. Psychol Rev, 84(4):327-352, 1977.
    • (1977) Psychol Rev , vol.84 , Issue.4 , pp. 327-352
    • Tversky, A.1
  • 39
    • 0001144659 scopus 로고    scopus 로고
    • Mass spectral classifiers for supporting systematic structure elucidation
    • K. Varmuza and W. Werther. Mass spectral classifiers for supporting systematic structure elucidation. J Chem Inf Comp Sci, 36(2):323-333, 1996.
    • (1996) J Chem Inf Comp Sci , vol.36 , Issue.2 , pp. 323-333
    • Varmuza, K.1    Werther, W.2
  • 40
    • 67849104638 scopus 로고    scopus 로고
    • PubChem: A public information system for analyzing bioactivities of small molecules
    • Yanli Wang, Jewen Xiao, Tugba O Suzek, Jian Zhang, Jiyao Wang, and Stephen H Bryant. PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res, 37(Web Server issue):W623-W633, 2009.
    • (2009) Nucleic Acids Res , vol.37
    • Wang, Y.1    Xiao, J.2    Suzek, T.O.3    Zhang, J.4    Wang, J.5    Bryant, S.H.6
  • 41
    • 36348980985 scopus 로고    scopus 로고
    • Current progress in computational metabolomics
    • David S Wishart. Current progress in computational metabolomics. Brief Bioinform, 8(5):279-293, 2007.
    • (2007) Brief Bioinform , vol.8 , Issue.5 , pp. 279-293
    • Wishart, D.S.1
  • 42
    • 77952302069 scopus 로고    scopus 로고
    • In silico fragmentation for computer assisted identification of metabolite mass spectra
    • Sebastian Wolf, Stephan Schmidt, Matthias Müller-Hannemann, and Steffen Neumann. In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinformatics, 11:148, 2010.
    • (2010) BMC Bioinformatics , vol.11 , pp. 148
    • Wolf, S.1    Schmidt, S.2    Müller-Hannemann, M.3    Neumann, S.4


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