Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy

Random Forests

Breiman, L. (2001) · Machine Learning · doi:10.1023/a:1010933404324 · Cited by 133,538

The Elements of Statistical Learning

Hastie, T., Friedman, J., & Tibshirani, R. (2001) · Springer Series in Statistics · doi:10.1007/978-0-387-21606-5 · Cited by 24,162

The sequence of the human genome

Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909

Proposed minimum reporting standards for chemical analysis: Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI)

Sumner, L. W., Amberg, A., Barrett, D., Beale, M. H., Beger, R., Daykin, C. A., Fan, T. W.-M., Fiehn, O., Goodacre, R., Griffin, J. L., et al. (2007) · Metabolomics · doi:10.1007/s11306-007-0082-2 · Cited by 5,368

Hierarchical Organization of Modularity in Metabolic Networks

Ravasz, E., Somera, A. L., Mongru, D. A., Oltvai, Z. N., & Barabási, A.-L. (2002) · Science · doi:10.1126/science.1073374 · Cited by 4,224

A branched-chain amino acid-related metabolic signature that differentiates obese and lean humans and contributes to insulin resistance

Newgard, C. B., An, J., Bain, J. R., Muehlbauer, M. J., Stevens, R. D., Lien, L. F., Haqq, A. M., Shah, S. H., Arlotto, M., Slentz, C. A., et al. (2009) · Cell Metabolism · doi:10.1016/j.cmet.2009.02.002 · Cited by 3,165

Centering, scaling, and transformations: improving the biological information content of metabolomics data

van den Berg, R. A., Hoefsloot, H. C., Westerhuis, J. A., Smilde, A. K., & van der Werf, M. J. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-142 · Cited by 2,450

Severe hypercholesterolemia and atherosclerosis in apolipoprotein E-deficient mice created by homologous recombination in ES cells

Plump, A. S., Smith, J. D., Hayek, T., Aalto-Setälä, K., Walsh, A., Verstuyft, J. G., Rubin, E. M., & Breslow, J. L. (1992) · Cell · doi:10.1016/0092-8674(92)90362-g · Cited by 2,263

Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry

Kind, T., & Fiehn, O. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-105 · Cited by 1,201

Molecular and metabolic mechanisms of insulin resistance and β-cell failure in type 2 diabetes

Muoio, D. M., & Newgard, C. B. (2008) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2327 · Cited by 1,177

Diabetes, a New Mutation in the Mouse

Hummel, K. P., Dickie, M. M., & Coleman, D. L. (1966) · Science · doi:10.1126/science.153.3740.1127 · Cited by 990

Gut microorganisms, mammalian metabolism and personalized health care

Nicholson, J. K., Holmes, E., & Wilson, I. D. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1152 · Cited by 945

Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum

Gieger, C., Geistlinger, L., Altmaier, E., Hrabé de Angelis, M., Kronenberg, F., Meitinger, T., Mewes, H.-W., Wichmann, H.-E., Weinberger, K. M., Adamski, J., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000282 · Cited by 737

Modeling the Heart--from Genes to Cells to the Whole Organ

Noble, D. (2002) · Science · doi:10.1126/science.1069881 · Cited by 622

Data processing for mass spectrometry-based metabolomics

Katajamaa, M., & Orešič, M. (2007) · Journal of Chromatography A · doi:10.1016/j.chroma.2007.04.021 · Cited by 616

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Herrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1492 · Cited by 588

Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases

Kell, D. B. (2009) · BMC Medical Genomics · doi:10.1186/1755-8794-2-2 · Cited by 554

Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis‐driven science in the post‐genomic era

Kell, D. B., & Oliver, S. G. (2004) · BioEssays · doi:10.1002/bies.10385 · Cited by 535

Metabolomics and systems biology: making sense of the soup

KELL, D. (2004) · Current Opinion in Microbiology · doi:10.1016/j.mib.2004.04.012 · Cited by 529

The Metabolomics Standards Initiative (MSI)

Fiehn, O., Robertson, D., Griffin, J., van der Werf, M., Nikolau, B., Morrison, N., Sumner, L. W., Goodacre, R., Hardy, N. W., Taylor, C., et al. (2007) · Metabolomics · doi:10.1007/s11306-007-0070-6 · Cited by 518

Analysis of the Adult Human Plasma Metabolome

Lawton, K. A., Berger, A., Mitchell, M., Milgram, K. E., Evans, A. M., Guo, L., Hanson, R. W., Kalhan, S. C., Ryals, J. A., & Milburn, M. V. (2008) · Pharmacogenomics · doi:10.2217/14622416.9.4.383 · Cited by 490

Biomarkers in nutritional epidemiology: applications, needs and new horizons

Jenab, M., Slimani, N., Bictash, M., Ferrari, P., & Bingham, S. A. (2009) · Human Genetics · doi:10.1007/s00439-009-0662-5 · Cited by 448

The Edinburgh human metabolic network reconstruction and its functional analysis

Ma, H., Sorokin, A., Mazein, A., Selkov, A., Selkov, E., Demin, O., & Goryanin, I. (2007) · Molecular Systems Biology · doi:10.1038/msb4100177 · Cited by 435

Probiotic modulation of symbiotic gut microbial–host metabolic interactions in a humanized microbiome mouse model

Martin, F. J., Wang, Y., Sprenger, N., Yap, I. K. S., Lundstedt, T., Lek, P., Rezzi, S., Ramadan, Z., van Bladeren, P., Fay, L. B., et al. (2008) · Molecular Systems Biology · doi:10.1038/msb4100190 · Cited by 421

Metabolite profiling of fecal water extracts from human colorectal cancer

Monleón, D., Morales, J. M., Barrasa, A., López, J. A., Vázquez, C., & Celda, B. (2009) · NMR in Biomedicine · doi:10.1002/nbm.1345 · Cited by 186

Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour ’rules’

Draper, J., Enot, D. P., Parker, D., Beckmann, M., Snowdon, S., Lin, W., & Zubair, H. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-227 · Cited by 169

A combined1H-NMR spectroscopy- and mass spectrometry-based metabolomic study of the PPAR-α null mutant mouse defines profound systemic changes in metabolism linked to the metabolic syndrome

Atherton, H. J., Bailey, N. J., Zhang, W., Taylor, J., Major, H., Shockcor, J., Clarke, K., & Griffin, J. L. (2006) · Physiological Genomics · doi:10.1152/physiolgenomics.00060.2006 · Cited by 159

High-resolution magic angle spinning (HR MAS) MR spectroscopy in metabolic characterization of human cancer

Sitter, B., Bathen, T. F., Tessem, M.-B., & Gribbestad, I. S. (2009) · Progress in Nuclear Magnetic Resonance Spectroscopy · doi:10.1016/j.pnmrs.2008.10.001 · Cited by 91

Effects of Probiotic Lactobacillus Paracasei Treatment on the Host Gut Tissue Metabolic Profiles Probed via Magic-Angle-Spinning NMR Spectroscopy

Martin, F.-P. J., Wang, Y., Sprenger, N., Holmes, E., Lindon, J. C., Kochhar, S., & Nicholson, J. K. (2007) · Journal of Proteome Research · doi:10.1021/pr060596a · Cited by 87

ENU mutagenesis identifies mice with cardiac fibrosis and hepatic steatosis caused by a mutation in the mitochondrial trifunctional protein β-subunit

Kao, H.-J., Cheng, C.-F., Chen, Y.-H., Hung, S.-I., Huang, C.-C., Millington, D., Kikuchi, T., Wu, J.-Y., & Chen, Y.-T. (2006) · Human Molecular Genetics · doi:10.1093/hmg/ddl433 · Cited by 47

Metabonomics studies of intact hepatic and renal cortical tissues from diabetic db/db mice using high-resolution magic-angle spinning 1H NMR spectroscopy

Xu, J., Zhang, J., Cai, S., Dong, J., Yang, J. Y., & Chen, Z. (2009) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-009-2623-1 · Cited by 43

Detection of Metabolic Alterations in Non-tumor Gastrointestinal Tissue of the ApcMin/+ Mouse by 1H MAS NMR Spectroscopy

Backshall, A., Alferez, D., Teichert, F., Wilson, I. D., Wilkinson, R. W., Goodlad, R. A., & Keun, H. C. (2009) · Journal of Proteome Research · doi:10.1021/pr800793w · Cited by 42

Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry.

The Human Serum Metabolome (HUSERMET) Consortium, Dunn, W. B., Broadhurst, D., Begley, P., Zelena, E., Francis-McIntyre, S., Anderson, N., Brown, M., Knowles, J. D., Halsall, A., et al. (2011) · Nature Protocols · doi:10.1038/nprot.2011.335 · Cited by 3,294

Multi-omics approaches to disease

Hasin, Y., Seldin, M., & Lusis, A. (2017) · Genome Biology · doi:10.1186/s13059-017-1215-1 · Cited by 2,953

Metabolomics enables precision medicine: “A White Paper, Community Perspective”

for “Precision Medicine and Pharmacometabolomics Task Group”-Metabolomics Society Initiative, Beger, R. D., Dunn, W., Schmidt, M. A., Gross, S. S., Kirwan, J. A., Cascante, M., Brennan, L., Wishart, D. S., Oresic, M., et al. (2016) · Metabolomics · doi:10.1007/s11306-016-1094-6 · Cited by 592

Genome-wide association study identifies multiple loci influencing human serum metabolite levels

Kettunen, J., Tukiainen, T., Sarin, A.-P., Ortega-Alonso, A., Tikkanen, E., Lyytikäinen, L.-P., Kangas, A. J., Soininen, P., Würtz, P., Silander, K., et al. (2012) · Nature Genetics · doi:10.1038/ng.1073 · Cited by 553

The food metabolome: a window over dietary exposure

Scalbert, A., Brennan, L., Manach, C., Andres-Lacueva, C., Dragsted, L. O., Draper, J., Rappaport, S. M., van der Hooft, J. J., & Wishart, D. S. (2014) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.113.076133 · Cited by 519