Systems Biology (Methods in Molecular Biology)

Acknowledgments

We thank all the members of Dr. Lorenza Putignani’s laboratories,

Unit of Human Microbiome, Genetic and Rare Diseases Area,

Bambino Gesu`Children’s Hospital, IRCCSRome, Italy and Unit

of Parasitology, Bambino Gesu`Children’s Hospital, IRCCSRome,

Italy, for providing the samples and the clinical data for the meta-

bolomics study here described.We are grateful to Dr. Alessandro

Giuliani, Department of Environment and Primary Prevention,

Istituto Superiore di Sanita`, Rome, Italy for his useful comments

and suggestions on the data analysis.

References

1. Chen R, Snyder M (2012) Systems biology:
   personalized medicine for the future? Curr
   Opin Pharmacol 12:623–628


2. Saqi M, Pellet J, Roznovat I et al (2016) Sys-
   tems medicine: the future of medical genomics,
   healthcare, and wellness. Methods Mol Biol
   1386:43–60


3. Wishart DS (2016) Emerging applications of
   metabolomics in drug discovery and precision
   medicine. Nat Rev Drug Discov 15:473–484


4. Nicholson JK, Lindon JC (2008) Metabo-
   nomics. Nature 445:1054–1056


5. Nicholson JK, Holmes E, Kinross JM et al
   (2012) Metabolic phenotyping in clinical and
   surgical environments. Nature 491:384–392


6. Everett JR (2015) Pharmacometabonomics in
   humans: A new tool for personalized medicine.
   Pharmacogenomics 16:737–754


7. Priori R, Casadei L, Valerio M et al (2015)^1 H-
   NMR-based metabolomic study for identifying
   serum profiles associated with the response to
   etanercept in patients with rheumatoid arthri-
   tis. PLoS One 10(11):e0138537


8. Ludwig C, G€unther UL (2011) MetaboLab –
   advanced NMR data processing and analysis for
   metabolomics. BMC Bioinformatics 12:366


9. Thrippleton MJ, Edden RA, Keeler J (2005)
   Suppression of strong coupling artefacts in
   J-spectra. J Magn Reson 174:97–109


10. Dieterle F, Ross A, Schlotterbeck G et al
    (2006) Probabilistic quotient normalization as
    robust method to account for dilution of com-
    plex biological mixtures. Application in H-1

NMR metabonomics. Anal Chem

78:4281–4290

11. Dieterle F, Riefke B, Schlotterbeck G et al
    (2011) NMR and MS methods for metabolo-
    mics. Methods Mol Biol 691:385–415


12. Purohit PV, Rocke DM, Viant MR et al (2004)
    Discrimination models using variance-
    stabilizing transformation of metabolomic
    NMR data. OMICS J Integr Biol 8:118–130


13. Parsons HM, Ludwig C, Gunther UL et al
    (2007) Improved classification accuracy in
    1-and 2-dimensional NMR metabolomics
    data using the variance stabilising generalised
    logarithm transformation. BMC Bioinformat-
    ics 8:234–250


14. Dieterle F, Ross A, Schlotterbeck G et al
    (2006) Metabolite projection analysis for fast
    identification of metabolites in metabonomics.
    Application in an amiodarone study. Anal
    Chem 78:3551–3561


15. Davis RA, Charlton AJ, Godward J et al (2007)
    Adaptive binning: an improved binning
    method for metabolomics data using the unde-
    cimated wavelet transform. Chemometr Intell
    Lab 85:144–154


16. De Meyer T, Sinnaeve D, Van Gasse B et al
    (2008) NMR-based characterization of meta-
    bolic alterations in hypertension using an adap-
    tive, intelligent binning algorithm. Anal Chem
    80:3783–3790


17. Anderson PE, Mahle DA, Doom TE et al
    (2011) Dynamic adaptive binning: an
    improved quantification technique for NMR
    spectroscopic data. Metabolomics 7:179–190

336 Luca Casadei et al.