Related publications

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.

Citation

BibTex format

@article{Holmes:2008:10.1038/nature06882,
author = {Holmes, E and Loo, RL and Stamler, J and Bictash, M and Yap, IKS and Chan, Q and Ebbels, T and De, Iorio M and Brown, IJ and Veselkov, KA and Daviglus, ML and Kesteloot, H and Ueshima, H and Zhao, L and Nicholson, JK and Elliott, P},
doi = {10.1038/nature06882},
journal = {NATURE},
pages = {396--U50},
title = {Human metabolic phenotype diversity and its association with diet and blood pressure},
url = {http://dx.doi.org/10.1038/nature06882},
volume = {453},
year = {2008}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AU  - Holmes,E
AU  - Loo,RL
AU  - Stamler,J
AU  - Bictash,M
AU  - Yap,IKS
AU  - Chan,Q
AU  - Ebbels,T
AU  - De,Iorio M
AU  - Brown,IJ
AU  - Veselkov,KA
AU  - Daviglus,ML
AU  - Kesteloot,H
AU  - Ueshima,H
AU  - Zhao,L
AU  - Nicholson,JK
AU  - Elliott,P
DO  - 10.1038/nature06882
EP  - 50
PY  - 2008///
SN  - 0028-0836
SP  - 396
TI  - Human metabolic phenotype diversity and its association with diet and blood pressure
T2  - NATURE
UR  - http://dx.doi.org/10.1038/nature06882
UR  - https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000255868400053&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=a2bf6146997ec60c407a63945d4e92bb
VL  - 453
ER  -
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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.