The following publications from within the Department of Surgery and Cancer, form the basis of the experiments performed as part of the training courses we offer. We would recommend them as good introductory publications within the field of metabolic profiling. Publications from external organisations are also listed and form the pre-course reading materials.

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Publications from external organisations

We would also recommend the following publications as further reading in the field of metabolic profiling.

General Metabolic Profiling

Fiehn, O. (2002). "Metabolomics--the link between genotypes and phenotypes." Plant Molecular Biology 48(1-2): 155-171.

NMR data pre-processing
 
Hoch, J. C. and A. S. Stern (1996). NMR Data Processing. New York, Wiley-Liss.
 
Aberg, K. M., E. Alm and R. J. Torgrip (2009). "The correspondence problem for metabonomics datasets." Anal Bioanal Chem 394(1): 151-162.
 
LC-MS data pre-processing
 
Pluskal, T., S. Castillo, A. Villar-Briones and M. Oresic (2010). "MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data." BMC Bioinformatics 11: 395.
 
Multivariate Analysis - Unsupervised
 
Bro, R. and A. K. Smilde (2014). "Principal component analysis." Analytical Methods 6(9): 2812-2831.
 
Multivariate Analysis - Supervised
 
Wold, S., M. Sjostrom and L. Eriksson (2001). "PLS-regression: a basic tool of chemometrics."
Chemometrics and Intelligent Laboratory Systems 58(2): 109-130.
 
Trygg, J. and S. Wold (2002). "Orthogonal projections to latent structures (O-PLS)." Journal of
Chemometrics 16(3): 119-128.
 
Trygg, J. and S. Wold (2003). "O2-PLS, a two-block (X-Y) latent variable regression (LVR) method with an integral OSC filter." Journal of Chemometrics 17(1): 53-64.
 
Löfstedt, T. and J. Trygg (2011). "OnPLS—a novel multiblock method for the modelling of predictive and orthogonal variation." Journal of Chemometrics 25(8): 441-455.
 
Pathway Analysis
 
Khatri, P., M. Sirota and A. J. Butte (2012). "Ten years of pathway analysis: current approaches and outstanding challenges." PLoS Comput Biol 8(2): e1002375.
 
Xia, J. and D. S. Wishart (2010). "MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data." Nucleic Acids Res 38(Web Server issue): W71-77.
 
Metabolite Identification
 
Kuhl, C., R. Tautenhahn, C. Bottcher, T. R. Larson and S. Neumann (2012). "CAMERA: An integrated strategy for compound spectra extraction and annotation of LC/MS data sets." Analytical Chemistry 84(1): 283-289.
 
Kind, T., K.-H. Liu, D. Y. Lee, B. DeFelice, J. K. Meissen and O. Fiehn (2013). "LipidBlast in silico
tandem mass spectrometry database for lipid identification." Nat Meth 10(8): 755-758.