Publications

  1. Bjerrum, J. T.§; Rantalainen, M.§; Wang, Y.; Olsen, J.; Nielsen, O.H.; Integration of transcriptomics and metabonomics: improving diagnostics, biomarker identification and phenotyping in ulcerative colitis. Metabolomics 2013, 1-11
  2. Drong, A. W.; Nicholson, G.; Hedman, A. K.; Meduri, E.; Grundberg, E.; Small, K. S.; Shin, S. Y.; Bell, J. T.; Karpe, F.; Soranzo, N.; Spector, T. D.; McCarthy, M. I.; Deloukas, P.; Rantalainen, M.§; Lindgren, C. M.§, The presence of methylation quantitative trait Loci indicates a direct genetic influence on the level of DNA methylation in adipose tissue. PLoS One 2013, 8 (2), e55923.
  3. Parts, L., Hedman, Å.K., Keildson, S., Knights, A.J., Abreu-Goodger, C., van de Bunt, M., Guerra-Assunção, J.A., Bartonicek, N., van Dongen, S., Mägi, R., Nisbet, J., Barrett, A., Rantalainen, M., Nica, A.C., Quail, M.A., Small, K.S., Glass, D., Enright, A.J., Winn, J., Deloukas, P., Dermitzakis, E.T., McCarthy, M.I., Spector, T.D., Durbin, R., Lindgren, C.M.. Extent, causes, and consequences of small RNA expression variation in human adipose tissue. PLoS genetics 2012, 8(5), e1002704.
  4. Zhao, X. J.; Hao, F.; Huang, C.; Rantalainen, M.; Lei, H.; Tang, H.; Wang, Y., Systems responses of rats to mequindox revealed by metabolic and transcriptomic profiling. Journal of proteome research 2012, 11 (9), 4712-21.
  5. Rantalainen, M., Holmes, C. C., Accounting for control mislabeling in case-control biomarker studies. J Proteome Res 2011, 10, (12), 5562-7.
  6. Rantalainen, M., Herrera, B. M., Nicholson, G., Bowden, R., Wills, Q. F., Min, J. L., Neville, M. J., Barrett, A., Allen, M., Rayner, N. W., Fleckner, J., McCarthy, M. I., Zondervan, K. T., Karpe, F., Holmes, C. C., Lindgren, C. M., MicroRNA Expression in Abdominal and Gluteal Adipose Tissue Is Associated with mRNA Expression Levels and Partly Genetically Driven. PLoS One 2011, 6, (11), e27338.
  7. Nicholson, G., Rantalainen, M., Maher, A. D., Li, J. V., Malmodin, D., Ahmadi, K. R., Faber, J. H., Hallgrimsdottir, I. B., Barrett, A., Toft, H., Krestyaninova, M., Viksna, J., Neogi, S. G., Dumas, M. E., Sarkans, U., The Molpage, C., Silverman, B. W., Donnelly, P., Nicholson, J. K., Allen, M., Zondervan, K. T., Lindon, J. C., Spector, T. D., McCarthy, M. I., Holmes, E., Baunsgaard, D., Holmes, C. C., Human metabolic profiles are stably controlled by genetic and environmental variation. Mol Syst Biol 2011, 7, 525.
  8. Nicholson, G., Rantalainen, M., Li, J. V., Maher, A. D., Malmodin, D., Ahmadi, K. R., Faber, J. H., Barrett, A., Min, J. L., Rayner, N. W., Toft, H., Krestyaninova, M., Viksna, J., Neogi, S. G., Dumas, M. E., Sarkans, U., Donnelly, P., Illig, T., Adamski, J., Suhre, K., Allen, M., Zondervan, K. T., Spector, T. D., Nicholson, J. K., Lindon, J. C., Baunsgaard, D., Holmes, E., McCarthy, M. I., Holmes, C. C., A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. PLoS Genet 2011, 7, (9), e1002270.
  9. Kato, B. S., Nicholson, G., Neiman, M., Rantalainen, M., Holmes, C. C., Barrett, A., Uhlen, M., Nilsson, P., Spector, T. D., Schwenk, J. M., Variance decomposition of protein profiles from antibody arrays using a longitudinal twin model. Proteome Sci 2011, 9, 73.
  10. Fonville, J. M., Bylesjo, M., Coen, M., Nicholson, J. K., Holmes, E., Lindon, J. C., Rantalainen, M., Non-linear modeling of 1H NMR metabonomic data using kernel-based orthogonal projections to latent structures optimized by simulated annealing. Anal Chim Acta 2011, 705, (1-2), 72-80.
  11. Wei, H., Dong, L., Wang, T. T., Zhang, M. H., Hua, W. Y., Zhang, C. H., Pang, X. Y., Chen, M. J., Su, M. M., Qiu, Y. P., Zhou, M. M., Yang, S. L., Chen, Z., Rantalainen, M., Nicholson, J. K., Jia, W., Wu, D. Z., Zhao, L. P., Structural shifts of gut microbiota as surrogate endpoints for monitoring host health changes induced by carcinogen exposure. Fems Microbiology Ecology 2010, 73, (3), 577-586.
  12. Waldram, A., Holmes, E., Wang, Y., Rantalainen, M., Wilson, I. D., Tuohy, K. M., McCartney, A. L., Gibson, G. R., Nicholson, J. K., Top-down systems biology modeling of host metabotype-microbiome associations in obese rodents. J Proteome Res 2009, 8, (5), 2361-75.
  13. Alves, A. C., Rantalainen, M., Holmes, E., Nicholson, J. K., Ebbels, T. M., Analytic properties of statistical total correlation spectroscopy based information recovery in 1H NMR metabolic data sets. Anal Chem 2009, 81, (6), 2075-84.
  14. Rantalainen, M., Cloarec, O., Ebbels, T. M., Lundstedt, T., Nicholson, J. K., Holmes, E., Trygg, J., Piecewise multivariate modelling of sequential metabolic profiling data. BMC Bioinformatics 2008, 9, 105.
  15. Li, M.§, Wang, B.§, Zhang, M.§, Rantalainen, M.§, Wang, S.§, Zhou, H., Zhang, Y., Shen, J., Pang, X., Wei, H., Chen, Y., Lu, H., Zuo, J., Su, M., Qiu, Y., Jia, W., Xiao, C., Smith, L. M., Yang, S., Holmes, E., Tang, H., Zhao, G., Nicholson, J. K., Li, L., Zhao, L., Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci U S A 2008, 105, (6), 2117-22.
  16. Bylesjo, M.§, Rantalainen, M.§, Nicholson, J. K., Holmes, E., Trygg, J., K-OPLS package: kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space. BMC Bioinformatics 2008, 9, 106.
  17. Wang, Y., Holmes, E., Comelli, E. M., Fotopoulos, G., Dorta, G., Tang, H., Rantalainen, M. J., Lindon, J. C., Corthesy-Theulaz, I. E., Fay, L. B., Kochhar, S., Nicholson, J. K., Topographical variation in metabolic signatures of human gastrointestinal biopsies revealed by high-resolution magic-angle spinning 1H NMR spectroscopy. J Proteome Res 2007, 6, (10), 3944-51.
  18. Smith, L. M., Maher, A. D., Cloarec, O., Rantalainen, M., Tang, H., Elliott, P., Stamler, J., Lindon, J. C., Holmes, E., Nicholson, J. K., Statistical correlation and projection methods for improved information recovery from diffusion-edited NMR spectra of biological samples. Anal Chem 2007, 79, (15), 5682-9.
  19. Rantalainen, M.§, Bylesjo, M§., Cloarec, O., Nicholson, J. K., Holmes, E., Trygg, J., Kernel-based orthogonal projections to latent structures (K-OPLS). Journal of Chemometrics 2007, 21, (7-9), 376-385.
  20. Williams, R. E., Lenz, E. M., Rantalainen, M., Wilson, I. D., The comparative metabonomics of age-related changes in the urinary composition of male Wistar-derived and Zucker (fa/fa) obese rats. Mol Biosyst 2006, 2, (3-4), 193-202.
  21. Rantalainen, M., Cloarec, O., Beckonert, O., Wilson, I. D., Jackson, D., Tonge, R., Rowlinson, R., Rayner, S., Nickson, J., Wilkinson, R. W., Mills, J. D., Trygg, J., Nicholson, J. K., Holmes, E., Statistically integrated metabonomic-proteomic studies on a human prostate cancer xenograft model in mice. J Proteome Res 2006, 5, (10), 2642-55.
  22. Bylesjo, M.§, Rantalainen, M.§, Cloarec, O., Nicholson, J. K., Holmes, E., Trygg, J., OPLS discriminant analysis: combining the strengths of PLS-DA and SIMCA classification. Journal of Chemometrics 2006, 20, (8-10), 341-351.
  23. Williams, R. E., Lenz, E. M., Lowden, J. S., Rantalainen, M., Wilson, I. D., The metabonomics of aging and development in the rat: an investigation into the effect of age on the profile of endogenous metabolites in the urine of male rats using 1H NMR and HPLC-TOF MS. Mol Biosyst 2005, 1, (2), 166-75.§ = equal contribution