Metabolic pathway predictions for metabolomics: A molecular structure matching approach

Journal of Chemical Information and Modeling

Volumn 55, Issue 3, 2015, Pages 709-718

  Hamdalla, Mai A ^a,b   Rajasekaran, Sanguthevar ^a   Grant, David F ^a   Məndoiu, Ion I ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

^b HELWAN UNIVERSITY   (Egypt)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR STRUCTURE;

BIO-CHEMICAL COMPOUNDS; BIOCHEMICAL PATHWAY; CHEMINFORMATICS; GENOMIC DATA SETS; METABOLIC PATHWAYS; SMALL MOLECULES; STRUCTURAL SIMILARITY; STRUCTURE MATCHING;

METABOLISM;

ALGORITHM; CHEMICAL STRUCTURE; COMPUTER PROGRAM; METABOLISM; METABOLOMICS; PROCEDURES; REPRODUCIBILITY;

ALGORITHMS; METABOLIC NETWORKS AND PATHWAYS; METABOLOMICS; MOLECULAR STRUCTURE; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 84925422918     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci500517v     Document Type: Article

References (20)

1. Pireddu, L.; Szafron, D.; Lu, P.; Greiner, R. Nucleic Acids Res. 2006, 34, W714-9
2. Chen, N.; del Val, I. J.; Kyriakopoulos, S.; Polizzi, K. M.; Kontoravdi, C. Curr. Opin. Biotechnol. 2012, 23, 77-82
3. Dale, J. M.; Popescu, L.; Karp, P. D. BMC Bioinform. 2010, 11, 15
4. Kanehisa, M.; Goto, S.; Hattori, M.; Aoki-Kinoshita, K. F.; Itoh, M.; Kawashima, S.; Katayama, T.; Araki, M.; Hirakawa, M. Nucleic Acids Res. 2006, 34, D354-7
5. Mithani, A.; Preston, G. M.; Hein, J. Bioinformatics (Oxford, England) 2009, 25, 1831-2
6. Karp, P. D.; Paley, S. M.; Krummenacker, M.; Latendresse, M.; Dale, J. M.; Lee, T. J.; Kaipa, P.; Gilham, F.; Spaulding, A.; Popescu, L.; Altman, T.; Paulsen, I.; Keseler, I. M.; Caspi, R. Briefings Bioinf. 2010, 11, 40-79
7. Gao, J.; Ellis, L. B. M.; Wackett, L. P. Nucleic Acids Res. 2010, 38, D488-91
8. Moriya, Y.; Shigemizu, D.; Hattori, M.; Tokimatsu, T.; Kotera, M.; Goto, S.; Kanehisa, M. Nucleic Acids Res. 2010, 38, W138-43
9. Kanehisa, M.; Goto, S.; Kawashima, S.; Nakaya, A. Nucleic Acids Res. 2002, 30, 42-46
10. Hu, L.-L.; Chen, C.; Huang, T.; Cai, Y.-D.; Chou, K.-C. PloS One 2011, 6, e29491
11. Hamdalla, M.; Mandoiu, I.; Hill, D.; Rajasekaran, S.; Grant, D. J. Chem. Inf. Model. 2013, 53, 601-612
12. Menikarachchi, L. C.; Cawley, S.; Hill, D. W.; Hall, L. M.; Hall, L.; Lai, S.; Wilder, J.; Grant, D. F. Anal. Chem. 2012, 84, 9388-9394
13. Menikarachchi, L. C.; Hamdalla, M. A.; Hill, D. W.; Grant, D. F. Comput. Struct. Biotechnol. J. 2013, 5, e201302005
14. Menikarachchi, L.; Hill, D.; Hamdalla, M.; Mandoiu, I.; Grant, D. J. Chem. Inf. Model. 2013, 53, 2483-2492
15. Macchiarulo, A.; Thornton, J. M.; Nobeli, I. J. Chem. Inf. Model. 2009, 49, 2272-2289
16. Nobeli, I.; Thornton, J. M. BioEssays 2006, 28, 534-45
17. Cai, Y.-D.; Qian, Z.; Lu, L.; Feng, K.-Y.; Meng, X.; Niu, B.; Zhao, G.-D.; Lu, W.-C. Mol. Diversity 2008, 12, 131-7
18. Breiman, L. Machine Learning, 45 th ed.; Kluwer Academic Publishers: 2001; Vol. 45, pp 5-32.
19. Gao, Y.-F.; Chen, L.; Cai, Y.-D.; Feng, K.-Y.; Huang, T.; Jiang, Y. PloS One 2012, 7, e45944
20. Rahman, S. A.; Bashton, M.; Holliday, G. L.; Schrader, R.; Thornton, J. M. J. Cheminform. 2009, 10.1186/1758-2946-1-12