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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Journal articleVeselkov KA, Lindon JC, Ebbels TMD, et al., 2009,
Recursive Segment-Wise Peak Alignment of Biological <SUP>1</SUP>H NMR Spectra for Improved Metabolic Biomarker Recovery
, ANALYTICAL CHEMISTRY, Vol: 81, Pages: 56-66, ISSN: 0003-2700- Author Web Link
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- Citations: 271
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Journal articleHolmes E, Wilson ID, Nicholson JK, 2008,
Metabolic phenotyping in health and disease
, CELL, Vol: 134, Pages: 714-717, ISSN: 0092-8674- Author Web Link
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- Citations: 571
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Journal articleHolmes E, Loo RL, Stamler J, et al., 2008,
Human metabolic phenotype diversity and its association with diet and blood pressure
, NATURE, Vol: 453, Pages: 396-U50, ISSN: 0028-0836- Author Web Link
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- Citations: 812
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Journal articleTrygg J, Holmes E, Lundstedt T, 2007,
Chemometrics in metabonomics
, JOURNAL OF PROTEOME RESEARCH, Vol: 6, Pages: 469-479, ISSN: 1535-3893- Author Web Link
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- Citations: 1028
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Journal articleCraig A, Cloareo O, Holmes E, et al., 2006,
Scaling and normalization effects in NMR spectroscopic metabonomic data sets
, ANALYTICAL CHEMISTRY, Vol: 78, Pages: 2262-2267, ISSN: 0003-2700- Author Web Link
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- Citations: 396
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Journal articleSmith CA, Want EJ, O'Maille G, et al., 2006,
XCMS: Processing mass spectrometry data for metabolite profiling using Nonlinear peak alignment, matching, and identification
, ANALYTICAL CHEMISTRY, Vol: 78, Pages: 779-787, ISSN: 0003-2700- Author Web Link
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- Citations: 3344
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Journal articleCloarec O, Dumas ME, Craig A, et al., 2005,
Statistical total correlation spectroscopy:: An exploratory approach for latent biomarker identification from metabolic <SUP>1</SUP>H NMR data sets
, ANALYTICAL CHEMISTRY, Vol: 77, Pages: 1282-1289, ISSN: 0003-2700- Author Web Link
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- Citations: 734
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Journal articleNicholson JK, Lindon JC, Holmes E, 1999,
'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data
, XENOBIOTICA, Vol: 29, Pages: 1181-1189, ISSN: 0049-8254- Author Web Link
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- Citations: 3000
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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.