Please find attached the publications below belonging to the session "Data extraction"

Reviews

Brown, M., Dunn, W.B., Ellis, D.I., Goodacre, R., Handl, J., Knowles, J.D., O'Hagan, S., Spasic, I. and Kell, D.B. (2005) A metabolome pipeline: from concept to data to knowledge. Metabolomics 1, 39-51.

Shurubor, Y.I., Paolucci, U., Krasnikov, B.F., Matson, W.R. and Kristal, B.S. (2005) Analytical precision, biological variation, and mathematical normalization in high data density metabolomics. Metabolomics 1, 75-85.

Alignment

Vorst, O., Vos, C.H.R.d., Lommen, A., Staps, R.V., Visser, R.G.F., Bino, R.J. and Hall, R.D. (2005) A non-directed approach to the differential analysis of multiple LC-MS-derived metabolic profiles. Metabolomics 1, 169-180.

Smith, C.A., Want, E.J., O'Maille, G., Abagyan, R. and Siuzdak, G. (2006) XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification. Anal. Chem. 78, 779-787.

Katajamaa, M. and Oresic, M. (2005) Processing methods for differential analysis of LC/MS profile data. Bmc Bioinformatics 6, Art. No. 179.

Kind, T., Tolstikov, V., Fiehn, O. and Weiss, R.H. (2007) A comprehensive urinary metabolomic approach for identifying kidney cancer. Analytical Biochemistry 363, 185-195.

Normalization

Wagner, S., Scholz, K., Sieber, M., Kellert, M. and Voelkel, W. (2007) Tools in metabonomics: An integrated validation approach for LC-MS metabolic profiling of mercapturic acids in human urine. Analytical Chemistry 79, 2918-2926.

Saude, E., Adamko, D., Rowe, B., Marrie, T. and Sykes, B. (2007) Variation of metabolites in normal human urine. Metabolomics.

Kemperman, R.F.J., Horvatovich, P.L., Hoekman, B., Reijmers, T.H., Muskiet, F.A.J. and Bischoff, R. (2007) Comparative Urine Analysis by Liquid Chromatography-Mass Spectrometry and Multivariate Statistics: Method Development, Evaluation, and Application to Proteinuria. J. Proteome Res. 6, 194-206.

Craig, A., Cloareo, O., Holmes, E., Nicholson, J.K. and Lindon, J.C. (2006) Scaling and normalization effects in NMR spectroscopic metabonomic data sets. Analytical Chemistry 78, 2262-2267.

Dieterle, F., Ross, A., Schlotterbeck, G. and Senn, H. (2006) Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in H-1 NMR metabonomics. Analytical Chemistry 78, 4281-4290.

Bijlsma, S., Bobeldijk, I., Verheij, E.R., Ramaker, R., Kochhar, S., Macdonald, I.A., van Ommen, B. and Smilde, A.K. (2006) Large-Scale Human Metabolomics Studies: A Strategy for Data (Pre-) Processing and Validation. Anal Chem 78, 567-574.

Baran, R., Kochi, H., Saito, N., Suematsu, M., Soga, T., Nishioka, T., Robert, M. and Tomita, M. (2006) MathDAMP: a package for differential analysis of metabolite profiles. BMC Bioinformatics 7, 530.

van den Berg, R.A., Hoefsloot, H.C.J., Westerhuis, J.A., Smilde, A.K. and van der Werf, M.J. (2006) Centering, scaling, and transformations: improving the biological information content of metabolomics data. Bmc Genomics 7, Art. No. 142.

GC-GC-Tof

Shellie, R.A., Welthagen, W., Zrostlikova, J., Spranger, J., Ristow, M., Fiehn, O. and Zimmermann, R. (2005) Statistical methods for comparing comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry results: Metabolomic analysis of mouse tissue extracts. Journal of Chromatography A 1086, 83-90.

Standardization

Goodacre, R., Broadhurst, D., Smilde, A., Kristal, B., Baker, J., Beger, R., Bessant, C., Connor, S., Capuani, G., Craig, A., Ebbels, T., Kell, D., Manetti, C., Newton, J., Paternostro, G., Somorjai, R., SjÃstrÃm, M., Trygg, J. and Wulfert, F. (2007) Proposed minimum reporting standards for data analysis in metabolomics. Metabolomics 3, 231-241.  

Attachments
	Brown.pdf Brown M. et al.	447 KB
	Shurubor.pdf Shurubor Y.I. et al.	255 KB
	Vorst.pdf Vorst O. et al.	605 KB
	Smith XCMS.pdf Smith C.A. et al.	526 KB
	Katajamaa 2005.pdf Katajamaa M. et al.	1516 KB
	Kind. 2007 (kidney cancer).pdf Kind T. et al.	494 KB
	Wagner.pdf Wagner S. et al.	518 KB
	Saude.pdf Saude E. et al.	631 KB
	Kemperman.pdf Kemperman R.F.J. et al.	532 KB
	Craig.pdf Craig A. et al.	294 KB
	Dieterle.pdf Dieterle F. et al.	707 KB
	Bijlsma 2006.pdf Bijlsma S. et al.	1327 KB
	Baran.pdf Baran R. et al.	770 KB
	Van den Berg.pdf van den Berg R.A. et al.	601 KB
	Shellie.pdf Shellie R.A. et al.	414 KB
	Goodacre.pdf Goodacre R. et al.	328 KB