Finding maximum colorful subtrees in practice

Journal of Computational Biology

Volumn 20, Issue 4, 2013, Pages 311-321

  Rauf, Imran ^a   Rasche, Florian ^b   Nicolas, François ^b   Böcker, Sebastian ^b  

^a NATIONAL UNIVERSITY OF COMPUTER AND EMERGING SCIENCES   (Pakistan)

^b FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

Author keywords

Computational mass spectrometry; Maximum colorful subtree problem; Maximum subtree problem; Metabolomics; NP hard problems; Small molecules

Indexed keywords

RESERPINE;

ALGORITHM; ARTICLE; DATA BASE; MASS SPECTROMETRY; METABOLISM; METABOLOME; METABOLOMICS; METHODOLOGY; SYSTEM ANALYSIS; TIME;

ALGORITHMS; DATABASES AS TOPIC; MASS SPECTROMETRY; METABOLOME; METABOLOMICS; PROGRAMMING, LINEAR; RESERPINE; TIME FACTORS;

EID: 84876246881     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2012.0083     Document Type: Article

References (21)

1. Björklund, A., Husfeldt, T., Kaski, P., and Koivisto, M. 2007. Fourier meets Möbius: fast subset convolution. Proc. of ACM Symposium on Theory of Computing (STOC 2007), ACM Press, New York, 67-74.
2. Böcker, S., and Rasche, F. 2008. Towards de novo identification of metabolites by analyzing tandem mass spectra. Bioinformatics 24, I49-I55.
3. Dondi, R., Fertin, G., and Vialette, S. 2009. Maximum motif problem in vertex-colored graphs. Proc. of Symposium on Combinatorial Pattern Matching (CPM 2009), Lect. Notes Comput. Sci. Vol. 5577 Springer, Berlin, 221-235.
4. Dreyfus, S.E., and Wagner, R.A. 1972. The Steiner problem in graphs, Networks 1, 195-207.
5. Fellows, M.R., Gramm, J., and Niedermeier, R. 2006. On the parameterized intractability of motif search problems. Combinatorica 26, 141-167.
6. Fernie, A.R., Trethewey, R.N., Krotzky, A.J., and Willmitzer, L. 2004. Metabolite profiling: from diagnostics to systems biology. Nat. Rev. Mol. Cell Biol. 5, 763-769.
7. Guillemot, S., and Sikora, F. 2010. Finding and counting vertex-colored subtrees. Proc. of Mathematical Foundations of Computer Science (MFCS 2010), Lect. Notes Comput. Sci. Vol. 6281, Springer, Berlin 405-416.
8. Hill, D.W., Kertesz, T.M., Fontaine, D., et al. 2008. Mass spectral metabonomics beyond elemental formula: Chemical database querying by matching experimental with computational fragmentation spectra. Anal. Chem. 80, 5574-5582.
9. Hufsky, F., Dührkop, K., Rasche, F., et al. 2012a. Fast alignment of fragmentation trees. Bioinformatics 28, i265-i273. Proc. of Intelligent Systems for Molecular Biology (ISMB 2012).
10. Hufsky, F., Rempt, M., Rasche, F., et al. 2012. De novo analysis of electron impact mass spectra of metabolites using fragmentation trees. Anal. Chim Acta. 739, 67-76.
11. Ito, T. (2011). Finding maximum weight arborescence in an edge-weighted DAG. Available at: http://cstheory.stackexchange.com/q/4088/189 Accessed Oct 12, 2011.
12. Koutis, I., and Williams, R. 2009. Limits and applications of group algebras for parameterized problems, Proc. of International Colloquium on Automata, Languages and Programming (ICALP 2009), Lect. Notes Comput. Sci., Vol. 5555. Springer, Berlin, 653-664.
13. Li, J.W.-H., and Vederas, J.C. 2009. Drug discovery and natural products: end of an era or an endless frontier? Science 325, 161-165.
14. Ljubić, I., Weiskircher, R., Pferschy, U., et al. 2005. Solving the prize-collecting steiner tree problem to optimality. Proc. of Algorithm Engineering and Experiments (ALENEX 2005), SIAM, Philadelphia, 68-76.
15. Oberacher, H., Pavlic, M., Libiseller, K., et al. 2009. On the inter-instrument and inter-laboratory transferability of a tandem mass spectral reference library: 1. results of an Austrian multicenter study. J. Mass Spectrom. 44, 485-493.
16. Rasche, F., Scheubert, K., Hufsky, F., et al. 2012. Identifying the unknowns by aligning fragmentation trees. Anal. Chem. 84, 3417-26.
17. Rasche, F., Svatoš, A., Maddula, R.K., et al. 2011. Computing fragmentation trees from tandem mass spectrometry data. Anal. Chem. 83, 1243-1251.
18. Scheubert, K., Hufsky, F., Rasche, F., and Böcker, S. 2011. Computing fragmentation trees from metabolite multiple mass spectrometry data. J. Comput. Biol. 18, 1383-1397.
19. Sikora, F. 2010. An (almost complete) state of the art around the graph motif problem. Technical report. Université Paris-Est, France. Available at: www-igm.univ-mlv.fr/fsikora/pub/GraphMotif-Resume.pdf
20. Sikora, F. 2011. Aspects algorithmiques de la comparaison d'éléments biologiques. [PhD thesis]. Université Paris-Est, France.
21. Xu, K., and Li, W. 2006. Many hard examples in exact phase transitions. Theor. Comput. Sci. 355, 291-302.