Fotograaf: Age Smilde

dhr. prof. dr. A.K. (Age) Smilde


  • Faculteit der Natuurwetenschappen, Wiskunde en Informatica
    SILS
  • Bezoekadres
    Science Park A
    Science Park 904  Amsterdam
    Kamernummer: C2.269
  • Postadres:
    Postbus  94215
    1090 GE  Amsterdam
  • A.K.Smilde@uva.nl
    T: 0205255062
    T: 0205256970

2016

  • van der Kloet, F. M., Sebastián-León, P., Conesa, A., Smilde, A. K., & Westerhuis, J. A. (2016). Separating common from distinctive variation. BMC Bioinformatics, 17(Suppl 5), [195]. DOI: 10.1186/s12859-016-1037-2 [details / files]
  • Fazelzadeh, P., Hangelbroek, R. W. J., Tieland, M., de Groot, C. P. G. M., Verdijk, L. B., van Loon, L. J. C., ... Boekschoten, M. V. (2016). The Muscle Metabolome Differs between Healthy and Frail Older Adults. Journal of Proteome Research, 15(2), 499-509. DOI: 10.1021/acs.jproteome.5b00840 [details]
  • Gardlo, A., Smilde, A. K., Hron, K., Hrda, M., Karlikova, R., & Friedecky, D. (2016). Normalization techniques for PARAFAC modeling of urine metabolomics. Metabolomics[details]
  • Mitra, V., Govorukhina, N., Zwanenburg, G., Westra, I., Smilde, A., Reijmers, T., ... Horvatovich, P. (2016). Identification of Analytical Factors Affecting Complex Proteomics Profiles Acquired in a Factorial Design Study with Analysis of Variance: Simultaneous Component Analysis. Analytical Chemistry, 88(8), 4229-38. DOI: 10.1021/acs.analchem.5b03483 [details]
  • Stroeve, J. H. M., Saccenti, E., Bouwman, J., Dane, A., Strassburg, K., Vervoort, J., ... Saris, W. H. M. (2016). Weight loss predictability by plasma metabolic signatures in adults with obesity and morbid obesity of the DiOGenes study. Obesity, 24(2), 379-388. DOI: 10.1002/oby.21361 [details]

2015

  • Hasdemir, D., Hoefsloot, H. C. J., & Smilde, A. K. (2015). Validation and selection of ODE based systems biology models: how to arrive at more reliable decisions. BMC Systems Biology, 9, 32. DOI: 10.1186/s12918-015-0180-0 [details / files]
  • Kutzera, J., Smilde, A. K., Wilderjans, T. F., & Hoefsloot, H. C. J. (2015). Towards a Hierarchical Strategy to Explore Multi-Scale IP/MS Data for Protein Complexes. PLoS One, 10(10), [0139704]. DOI: 10.1371/journal.pone.0139704 [details / files]
  • Reshetova, P., Smilde, A. K., Westerhuis, J. A., & van Kampen, A. H. C. (2015). Using Petri nets for experimental design in a multi-organ elimination pathway. Computers in Biology and Medicine, 63, 19-27. DOI: 10.1016/j.compbiomed.2015.05.001 [details]
  • Vis, D. J., Westerhuis, J. A., Jacobs, D. M., van Duynhoven, J. P. M., Wopereis, S., van Ommen, B., ... Smilde, A. K. (2015). Analyzing metabolomics-based challenge test. Metabolomics, 11(1), 50-63. DOI: 10.1007/s11306-014-0673-7 [details]
  • Westerhuis, J. A., van Velzen, E. J. J., Jansen, J. J., Hoefsloot, H. C. J., & Smilde, A. K. (2015). Analysis of high-dimensional data from designed metabolomics studies. In M. Grootveld (Ed.), Metabolic profiling: disease and xenobiotics (pp. 117-136). (Issues in Toxicology; No. 21). Cambridge: Royal Society of Chemistry. DOI: 10.1039/9781849735162 [details]
  • Horvatovich, P., Christin, C., Hoefsloot, H. C. J., Hoekman, B., Suits, F., Smilde, A. K., & Bischoff, R. (2015). Comparing the t-test, the Mann-Whitney-Wilcoxon test, nearest shrunken centroid, linear support vector machine - recursive features elimination, principal component discriminant analysis, and partial least squares discriminant analysis in biomarker discovery. In V. R. Preedy (Ed.), Biomarkers in Disease: Methods, Discoveries and Applications. (Biomarkers in Disease: Methods, Discoveries and Applications). Springer. [details]
  • Saccenti, E., van Duynhoven, J., Jacobs, D. M., Smilde, A. K., & Hoefsloot, H. C. J. (2015). Strategies for individual phenotyping of linoleic and arachidonic acid metabolism using an oral glucose tolerance test. PLoS One, 10(3), e0119856. DOI: 10.1371/journal.pone.0119856 [details] [PDF]
  • Timmerman, M. E., Hoefsloot, H. C. J., Smilde, A. K., & Ceulemans, E. (2015). Scaling in ANOVA-simultaneous component analysis. Metabolomics, 11(5), 1265-1276. DOI: 10.1007/s11306-015-0785-8 [details / files]
  • Willemsen, A. M., Hendrickx, D. M., Hoefsloot, H. C. J., Hendriks, M. M. W. B., Wahl, S. A., Teusink, B., ... van Kampen, A. H. C. (2015). MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis. Molecular BioSystems, 11(1), 137-145. DOI: 10.1039/c4mb00510d [details / files]
  • van Deun, K., Thorrez, L., van Berg, R. A., Smilde, A. K., & Van Mechelen, I. (2015). Not Just a Sum? Identifying Different Types of Interplay between Constituents in Combined Interventions. PLoS One, 10(5), [e0125334]. DOI: 10.1371/journal.pone.0125334 [details] [PDF]

2014

  • Hasdemir, D., Hoefsloot, H. C. J., Westerhuis, J. A., & Smilde, A. K. (2014). How informative is your kinetic model?: using resampling methods for model invalidation. BMC Systems Biology, 8, 61. DOI: 10.1186/1752-0509-8-61 [details] [PDF]
  • Kaduk, M., Hoefsloot, H. C. J., Vis, D. J., Reijmers, T., van der Greef, J., Smilde, A. K., & Hendriks, M. M. W. B. (2014). Correlated measurement error hampers association network inference. Journal of Chromatography B, 966, 93-99. DOI: 10.1016/j.jchromb2014.04.048 [details]
  • Mihaleva, V. V., van Schalkwijk, D. B., de Graaf, A. A., van Duynhoven, J., van Dorsten, F. A., Vervoort, J., ... Jacobs, D. M. (2014). A systematic approach to obtain validated Partial Least Square models for predicting lipoprotein subclasses from serum NMR spectra. Analytical Chemistry, 86(1), 543-550. DOI: 10.1021/ac402571z [details]
  • Reshetova, P., Smilde, A. K., van Kampen, A. H. C., & Westerhuis, J. A. (2014). Use of prior knowledge for the analysis of high-throughput transcriptomics and metabolomics data. BMC Systems Biology, 8(suppl 2), S2. DOI: 10.1186/1752-0509-8-S2-S2 [details / files]
  • Saccenti, E., Tenori, L., Verbruggen, P., Timmerman, M. E., Bouwman, J., van der Greef, J., ... Smilde, A. K. (2014). Of monkeys and men: a metabolomic analysis of static and dynamic urinary metabolic phenotypes in two species. PLoS One, 9(9), e106077. DOI: 10.1371/journal.pone.0106077 [details] [PDF]
  • Saccenti, E., Hoefsloot, H. C. J., Smilde, A. K., Westerhuis, J. A., & Hendriks, M. M. W. B. (2014). Reflections on univariate and multivariate analysis of metabolomics data. Metabolomics, 10(3), 361-374. DOI: 10.1007/s11306-013-0598-6 [details]
  • Smit, S., Szymańska, E., Kunz, I., Gomez Roldan, V., van Tilborg, M. W. E. M., Weber, P., ... Bendik, I. (2014). Nutrikinetic modeling reveals order of genistein phase II metabolites appearance in human plasma. Molecular nutrition & food research, 58(11), 2111-2121. DOI: 10.1002/mnfr.201400325 [details / files]
  • Vis, D. J., Hendriks, M. M. W. B., Sailer, M., Smilde, A. K., Daniel, H., & Westerhuis, J. A. (2014). A technical note on challenge tests in human volunteers for multidimensional phenotyping. Chemometrics and Intelligent Laboratory Systems, 136, 81-84. DOI: 10.1016/j.chemolab.2014.05.006 [details]
  • Vis, D. J., Westerhuis, J. A., Hoefsloot, H. C. J., Roelfsema, F., van der Greef, J., Hendriks, M. M. W. B., & Smilde, A. K. (2014). Network identification of hormonal regulation. PLoS One, 9(5), e96284. DOI: 10.1371/journal.pone.0096284 [details / files]
  • Zha, Y., Westerhuis, J. A., Muilwijk, B., Overkamp, K. M., Nijmeijer, B. M., Coulier, L., ... Punt, P. J. (2014). Identifying inhibitory compounds in lignocellulosic biomass hydrolysates using an exometabolomics approach. BMC Biotechnology, 14, 22. DOI: 10.1186/1472-6750-14-22 [details / files]
  • van Velzen, E. J. J., Westerhuis, J. A., Grün, C. H., Jacobs, D. M., Eilers, P. H. C., Mulder, T. P., ... Smilde, A. K. (2014). Population-based nutrikinetic modeling of polyphenol exposure. Metabolomics, 10(6), 1059-1073. DOI: 10.1007/s11306-014-0645-y [details]
  • Bro, R., & Smilde, A. K. (2014). Principal component analysis. Analytical Methods, 6(9), 2812-2831. DOI: 10.1039/c3ay41907j [details] [PDF]
  • Kvalheim, O. M., Arneberg, R., Bleie, O., Rajalahti, T., Smilde, A. K., & Westerhuis, J. A. (2014). Variable importance in latent variable regression models. Journal of Chemometrics, 28(8), 615-622. DOI: 10.1002/cem.2626 [details]
  • Mitra, V., Smilde, A., Hoefsloot, H., Suits, F., Bischoff, R., & Horvatovich, P. (2014). Inversion of peak elution order prevents uniform time alignment of complex liquid-chromatography coupled to mass spectrometry datasets. Journal of Chromatography A, 1373, 61-72. DOI: 10.1016/j.chroma.2014.10.101 [details]

2013

  • Kutzera, J., Hoefsloot, H. C. J., Malovannaya, A., Smit, A. B., Van Mechelen, I., & Smilde, A. K. (2013). Inferring protein-protein interaction complexes from immunoprecipitation data. BMC Research Notes, 6, [468]. DOI: 10.1186/1756-0500-6-468 [details / files]
  • Rubingh, C. M., Martens, H., van der Voet, H., & Smilde, A. K. (2013). The costs of complex model optimization. Chemometrics and Intelligent Laboratory Systems, 125, 139-146. DOI: 10.1016/j.chemolab.2013.04.004 [details]
  • Smilde, A. K., Hendriks, M. M. W. B., Westerhuis, J., & Hoefsloot, H. C. J. (2013). Data Processing in Metabolomics. In M. Lämmerhofer, & W. Weckwerth (Eds.), Metabolomics in Practice: Successful Strategies to Generate and Analyze Metabolic Data. (pp. 261- 284). Weinheim: Wiley‐VCH Verlag GmbH & Co. KGaA. DOI: 10.1002/9783527655861.ch11 [details]
  • Christin, C., Hoefsloot, H. C. J., Smilde, A. K., Hoekman, B., Suits, F., Bischoff, R., & Horvatovich, P. (2013). A critical assessment of feature selection methods for biomarker discovery in clinical proteomics. Molecular & Cellular Proteomics, 12(1), 263-276. DOI: 10.1074/mcp.M112.022566 [details]
  • van Deun, K., Smilde, A. K., Thorrez, L., Kiers, H. A. L., & van Mechelen, I. (2013). Identifying common and distinctive processes underlying multiset data. Chemometrics and Intelligent Laboratory Systems, 129, 40-51. DOI: 10.1016/j.chemolab.2013.07.005 [details]

2012

  • Hasdemir, D., Smits, G. J., Westerhuis, J. A., & Smilde, A. K. (2012). Topology of transcriptional regulatory networks: testing and improving. PLoS One, 7(7), [e40082]. [details] [PDF]
  • Hendrickx, D. M., Hoefsloot, H. C. J., Hendriks, M. M. W. B., Canelas, A. B., & Smilde, A. K. (2012). Global test for metabolic pathway differences between conditions. Analytica Chimica Acta, 719, 8-15. DOI: 10.1016/j.aca.2011.12.051 [details]
  • Hendrickx, D. M., Hoefsloot, H. C. J., Hendriks, M. M. W. B., Vis, D. J., Canelas, A. B., Teusink, B., & Smilde, A. K. (2012). Inferring differences in the distribution of reaction rates across conditions. Molecular BioSystems, 8(9), 2415-2423. DOI: 10.1039/c2mb25015b [details]
  • Jansen, J. J., Szymanska, E., Hoefsloot, H. C. J., Jacobs, D. M., Strassburg, K., & Smilde, A. K. (2012). Between Metabolite Relationships: an essential aspect of metabolic change. Metabolomics, 8, 422-432. DOI: 10.1007/s11306-011-0316-1 [details]
  • Jansen, J. J., Szymanska, E., Hoefsloot, H. C. J., & Smilde, A. K. (2012). Individual differences in metabolomics: individualised responses and between-metabolite relationships. Metabolomics, 8(Suppl 1), 94-104. DOI: 10.1007/s11306-012-0414-8 [details]
  • Smilde, A. K., Timmerman, M. E., Hendriks, M. M. W. B., Jansen, J. J., & Hoefsloot, H. C. J. (2012). Generic framework for high-dimensional fixed-effects ANOVA. Briefings in Bioinformatics, 13(5), 524-535. DOI: 10.1093/bib/bbr071 [details]
  • Szymanska, E., Saccenti, E., Smilde, A. K., & Westerhuis, J. A. (2012). Double-check: validation of diagnostic statistics for PLS-DA models in metabolomics studies. Metabolomics, 8(suppl. 1), 3-16. DOI: 10.1007/s11306-011-0330-3 [details]
  • Szymańska, E., van Dorsten, F. A., Troost, J., Paliukhovich, I., van Velzen, E. J. J., Hendriks, M. M. W. B., ... Smilde, A. K. (2012). A lipidomic analysis approach to evaluate the response to cholesterol-lowering food intake. Metabolomics, 8(5), 894-906. DOI: 10.1007/s11306-011-0384-2 [details]
  • Szymańska, E., Bouwman, J., Strassburg, K., Vervoort, J., Kangas, A. J., Soininen, P., ... Jacobs, D. M. (2012). Gender-dependent associations of metabolite profiles and body fat distribution in a healthy population with central obesity: towards metabolomics diagnostics. Omics, 16(12), 652-667. DOI: 10.1089/omi.2012.0062 [details / files]
  • Vis, D. J., Westerhuis, J. A., Hoefsloot, H. C., Roelfsema, F., Hendriks, M. M. W. B., & Smilde, A. K. (2012). Detecting regulatory mechanisms in endocrine time series measurements. PLoS One, 7(3), [e32985]. DOI: 10.1371/journal.pone.0032985 [details] [PDF]
  • Ellero-Simatos, S., Szymańska, E., Rullmann, T., Dokter, W. H. A., Ramaker, R., Berger, R., ... Alkema, W. (2012). Assessing the metabolic effects of prednisolone in healthy volunteers using urine metabolic profiling. Genome Medicine, 4(11), 94. DOI: 10.1186/gm395 [details / files]
  • Wopereis, S., Radonjic, M., Rubingh, C., van Erk, M., Smilde, A., van Duyvenvoorde, W., ... Kleemann, R. (2012). Identification of prognostic and diagnostic biomarkers of glucose intolerance in ApoE3Leiden mice. Physiological Genomics, 44(5), 293-304. DOI: 10.1152/physiolgenomics.00072.2011 [details]
  • van Deun, K., van Mechelen, I., Thorrez, L., Schouteden, M., de Moor, B., van der Werf, M. J., ... Kiers, H. A. L. (2012). DISCO-SCA and properly applied GSVD as swinging methods to find common and distinctive processes. PLoS One, 7(5), e37840. DOI: 10.1371/journal.pone.0037840 [details] [PDF]
  • van Duynhoven, J. P. M., van Velzen, E. J. J., Westerhuis, J. A., Foltz, M., Jacobs, D. M., & Smilde, A. K. (2012). Nutrikinetics: concept, technologies, applications, perspectives. Trends in Food Science & Technology, 26(1), 4-13. DOI: 10.1016/j.tifs.2012.01.004 [details]

2011

  • Hendrickx, D. M., Hendriks, M. M. W. B., Eilers, P. H. C., Smilde, A. K., & Hoefsloot, H. C. J. (2011). Reverse engineering of metabolic networks, a critical assessment. Molecular BioSystems, 7(2), 511-520. DOI: 10.1039/c0mb00083c [details]
  • Rubingh, C. M., van Erk, M. J., Wopereis, S., van Vliet, T., Verheij, E. R., Cnubben, N. H. P., ... Smilde, A. K. (2011). Discovery of subtle effects in a human intervention trial through multilevel modeling. Chemometrics and Intelligent Laboratory Systems, 106(1), 108-114. DOI: 10.1016/j.chemolab.2010.06.003 [details]
  • Saccenti, E., Smilde, A. K., & Saris, W. H. M. (2011). Beethoven's deafness and his three styles. BMJ : British medical journal, 343, d7589. [d7589]. DOI: 10.1136/bmj.d7589 [details]
  • Saccenti, E., Smilde, A. K., Westerhuis, J. A., & Hendriks, M. M. W. B. (2011). Tracy-Widom statistic for the largest eigenvalue of autoscaled real matrices. Journal of Chemometrics, 25(12), 644-652. DOI: 10.1002/cem.1411 [details]
  • Saccenti, E., Westerhuis, J. A., Smilde, A. K., van der Werf, M. J., Hageman, J. A., & Hendriks, M. M. W. B. (2011). Simplivariate models: uncovering the underlying biology in functional genomics data. PLoS One, 6(6). DOI: 10.1371/journal.pone.0020747 [details] [PDF]
  • Smilde, A., & Tauler, R. (2011). Multiway and multiset data analysis. Chemometrics and Intelligent Laboratory Systems, 106, 1-1. DOI: 10.1016/j.chemolab.2010.09.009 [details]
  • Xu, C. J., Hoefsloot, H. C. J., & Smilde, A. K. (2011). To aggregate or not to aggregate high-dimensional classifiers. BMC Bioinformatics, 12. DOI: 10.1186/1471-2105-12-153 [details] [PDF]
  • Zwanenburg, G., Hoefsloot, H. C. J., Westerhuis, J. A., Jansen, J. J., & Smilde, A. K. (2011). ANOVA-principal component analysis and ANOVA-simultaneous component analysis: a comparison. Journal of Chemometrics, 25(10), 561-567. DOI: 10.1002/cem.1400 [details]
  • van Batenburg, M. F., Coulier, L., van Eeuwijk, F., Smilde, A. K., & Westerhuis, J. A. (2011). New figures of merit for comprehensive functional genomics data: the metabolomics case. Analytical Chemistry, 83(9), 3267-3274. DOI: 10.1021/ac102374c [details]
  • Doeswijk, T. G., Smilde, A. K., Hageman, J. A., Westerhuis, J. A., & van Eeuwijk, F. A. (2011). On the increase of predictive performance with high-level data fusion. Analytica Chimica Acta, 705(1-2), 41-47. DOI: 10.1016/j.aca.2011.03.025 [details]
  • Hendriks, M. M. W. B., van Eeuwijk, F. A., Jellema, R. H., Westerhuis, J. A., Reijmers, T. H., Hoefsloot, H. C. J., & Smilde, A. K. (2011). Data-processing strategies for metabolomics studies. Trends in Analytical Chemistry, 30(10), 1685-1698. DOI: 10.1016/j.trac.2011.04.019 [details]
  • van Duynhoven, J., Vaughan, E. E., Jacobs, D. M., Kemperman, R. A., van Velzen, E. J. J., Gross, G., ... van der Wiele, T. (2011). Metabolic fate of polyphenols in the human superorganism. Proceedings of the National Academy of Sciences of the United States of America, 108 Suppl, 4531-4538. DOI: 10.1073/pnas.1000098107 [details]
  • van Mechelen, I., & Smilde, A. K. (2011). Comparability problems in the analysis of multiway data. Chemometrics and Intelligent Laboratory Systems, 106(1), 2-11. DOI: 10.1016/j.chemolab.2010.08.006 [details]

2010

  • Jansen, J. J., Smit, S., Hoefsloot, H. C. J., & Smilde, A. K. (2010). The photographer and the greenhouse: how to analyse plant metabolomics data. Phytochemical Analysis, 21(1), 48-60. DOI: 10.1002/pca.1181 [details]
  • Smilde, A. K., Westerhuis, J. A., Hoefsloot, H. C. J., Bijlsma, S., Rubingh, C. M., Vis, D. J., ... van der Greef, J. (2010). Dynamic metabolomic data analysis: a tutorial review. Metabolomics, 6(1), 3-17. DOI: 10.1007/s11306-009-0191-1 [details] [PDF]
  • Stanimirovic, O., Hoefsloot, H. C. J., & Smilde, A. K. (2010). Optimal measurement design for monitoring batch processes. AIChE Journal, 56(3), 837-840. DOI: 10.1002/aic.11968 [details]
  • Vis, D. J., Westerhuis, J. A., Hoefsloot, H. C. J., Pijl, H., Roelfsema, F., van der Greef, J., & Smilde, A. K. (2010). Endocrine pulse identification using penalized methods and a minimum set of assumptions. American Journal of Physiology. Endocrinology and Metabolism, 298(2), E146-E155. DOI: 10.1152/ajpendo.00048.2009 [details]
  • Westerhuis, J. A., van Velzen, E. J. J., Hoefsloot, H. C. J., & Smilde, A. K. (2010). Multivariate paired data analysis: multilevel PLSDA versus OPLSDA. Metabolomics, 6(1), 119-128. DOI: 10.1007/s11306-009-0185-z [details] [PDF]
  • Xu, C. J., Hoefsloot, H. C. J., Dijkstra, M., Havenga, K., Roelofsen, H., Vonk, R. J., & Smilde, A. K. (2010). Computational modeling of the human serum proteome response to colon resection surgery. Analytica Chimica Acta, 661(1), 20-27. DOI: 10.1016/j.aca.2009.12.003 [details]
  • Christin, C., Hoefsloot, H. C. J., Smilde, A. K., Suits, F., Bischoff, R., & Horvatovich, P. L. (2010). Time alignment algorithms based on selected mass traces for complex LC-MS data. Journal of Proteome Research, 9(3), 1483-1495. DOI: 10.1021/pr9010124 [details]
  • van Erk, M. J., Wopereis, S., Rubingh, C., van Vliet, T., Verheij, E., Cnubben, N. H. P., ... van Ommen, B. (2010). Insight in modulation of inflammation in response to diclofenac intervention: a human intervention study. BMC Medical Genomics, 3, 5. DOI: 10.1186/1755-8794-3-5 [details] [PDF]
  • van Mechelen, I., & Smilde, A. K. (2010). A generic linked-mode decomposition model for data fusion. Chemometrics and Intelligent Laboratory Systems, 104(1), 83-94. DOI: 10.1016/j.chemolab.2010.04.012 [details]

2009

  • Hoefsloot, H. C. J., Vis, D. J., Westerhuis, J. A., Smilde, A. K., & Jansen, J. J. (2009). Multiset data analysis: ANOVA simultaneous component analysis and related methods. In S. D. Brown, R. Tauler, & B. Walczak (Eds.), Comprehensive chemometrics: chemical and biochemical data analysis. - Vol. 2. (pp. 453-472). Amsterdam: Elsevier. DOI: 10.1016/B978-044452701-1.00054-5 [details]
  • Jansen, J. J., van Dam, N. M., Hoefsloot, H. C. J., & Smilde, A. K. (2009). Crossfit analysis: a novel method to characterize the dynamics of induced plant responses. BMC Bioinformatics, 10, 425. DOI: 10.1186/1471-2105-10-425 [details] [PDF]
  • Smilde, A. K., Kiers, H. A. L., Bijlsma, S., Rubingh, C. M., & van Erk, M. J. (2009). Matrix correlations for high-dimensional data: the modified RV-coefficient. Bioinformatics, 25(3), 401-405. DOI: 10.1093/bioinformatics/btn634 [details]
  • Smilde, A. K., van der Werf, M. J., Schaller, J. P., & Kistemaker, C. (2009). Characterizing the precision of mass-spectrometry-based metabolic profiling platforms. Analyst, 134(11), 2281-2285. DOI: 10.1039/b902242b [details]
  • Verouden, M. P. H., Nootebaart, R. A., Westerhuis, J. A., van der Werf, M. J., Teusink, B., & Smilde, A. K. (2009). Multi-way analysis of flux distributions across multiple conditions. Journal of Chemometrics, 23(7-8), 406-420. DOI: 10.1002/cem.1238 [details]
  • Verouden, M. P. H., Westerhuis, J. A., van der Werf, M. J., & Smilde, A. K. (2009). Exploring the analysis of structured metabolomics data. Chemometrics and Intelligent Laboratory Systems, 98(1), 88-96. DOI: 10.1016/j.chemolab.2009.05.004 [details]
  • Westerhuis, J., van Velzen, E., Hoefsloot, H., & Smilde, A. (2009). Data analysis strategies in nutritional metabolomics. GIT Laboratory Journal Europe, 13(1-2), 17-19. [details] [PDF]
  • van Velzen, E. J. J., Westerhuis, J. A., van Duynhoven, J. P. M., van Dorsten, F. A., Grün, C. H., Jacobs, D. M., ... Smilde, A. K. (2009). Phenotyping tea consumers by nutrikinetic analysis of polyphenolic end-metabolites. Journal of Proteome Research, 8(7), 3317-3330. DOI: 10.1021/pr801071p [details]
  • van den Berg, R. A., van Mechelen, I., Wilderjans, T. F., van Deun, K., Kiers, H. A. L., & Smilde, A. K. (2009). Integrating functional genomics data using maximum likelihood based simultaneous component analysis. BMC Bioinformatics, 10, 340. DOI: 10.1186/1471-2105-10-340 [details] [PDF]
  • van den Berg, R. A., Rubingh, C. M., Westerhuis, J. A., van der Werf, M. J., & Smilde, A. K. (2009). Metabolomics data exploration guided by prior knowledge. Analytica Chimica Acta, 651(2), 173-181. DOI: 10.1016/j.aca.2009.08.029 [details]
  • Çakir, T., Hendriks, M. M. W. B., Westerhuis, J. A., & Smilde, A. K. (2009). Metabolic network discovery through reverse engineering of metabolome data. Metabolomics, 5(3), 318-329. DOI: 10.1007/s11306-009-0156-4 [details] [PDF]
  • Boot, R. G., van Breemen, M. J., Wegdam, W., Sprenger, R. R., de Jong, S., Speijer, D., ... Aerts, J. M. F. G. (2009). Gaucher disease: a model disorder for biomarker discovery. Expert Review of Proteomics, 6(4), 411-419. DOI: 10.1586/epr.09.54 [details]
  • Braaksma, M., Smilde, A. K., van der Werf, M. J., & Punt, P. J. (2009). The effect of environmental conditions on extracellular protease activity in controlled fermentations of Aspergillus niger. Microbiology - SGM, 155(10), 3430-3439. DOI: 10.1099/mic.0.031062-0 [details]
  • Thissen, U., Wopereis, S., van Berg, S. A. A., Bobeldijk, I., Kleemann, R., Kooistra, T., ... Smilde, A. K. (2009). Improving the analysis of designed studies by combining statistical modelling with study design information. BMC Bioinformatics, 10, 52. DOI: 10.1186/1471-2105-10-52 [details] [PDF]
  • Timmerman, M. E., Kiers, H. A. L., Smilde, A. K., Ceulemans, E., & Stouten, J. (2009). Bootstrap confidence intervals in multi-level simultaneous component analysis. British Journal of Mathematical & Statistical Psychology, 62(2), 299-318. DOI: 10.1348/000711007X265894 [details]
  • Wopereis, S., Rubingh, C. M., van Erk, M. J., Verheij, E. R., van Vliet, T., Cnubben, N. H. P., ... Hendriks, H. F. J. (2009). Metabolic profiling of the response to an oral glucose tolerance test detects subtle metabolic changes. PLoS One, 4(2), e4525. DOI: 10.1371/journal.pone.0004525 [details] [PDF]
  • van Deun, K., Smilde, A. K., van der Werf, M. J., Kiers, H. A. L., & van Mechelen, I. (2009). A structured overview of simultaneous component based data integration. BMC Bioinformatics, 10, 246. DOI: 10.1186/1471-2105-10-246 [details] [PDF]
  • van Duynhoven, J., van Velzen, E., Gross, G., van Dorsten, F., Jacobs, D., Bingham, M., ... Smilde, A. (2009). NMR-based metabonomics approaches for the assessment of the metabolic impact of dietary polyphenols on humans. Special Publication - Royal Society of Chemistry, 20-28. DOI: 10.1039/9781847559494-00020 [details]

2008

  • Cruz, S. C., Rothenberg, G., Westerhuis, J. A., & Smilde, A. K. (2008). Estimating kinetic parameters of complex catalytic reactions using a curve resolution based method. Chemometrics and Intelligent Laboratory Systems, 91(2), 101-109. DOI: 10.1016/j.chemolab.2007.10.003 [details]
  • Hageman, J. A., Hendriks, M. M. W. B., Westerhuis, J. A., van der Werf, M. J., Berger, R., & Smilde, A. K. (2008). Simplivariate models: Ideas and first examples. PLoS One, 3(9), e3259. DOI: 10.1371/journal.pone.0003259 [details] [PDF]
  • Hageman, J. A., van den Berg, R. A., Westerhuis, J. A., van der Werf, M. J., & Smilde, A. K. (2008). Genetic algorithm based two-mode clustering of metabolomics data. Metabolomics, 4(2), 141-149. DOI: 10.1007/s11306-008-0105-7 [details] [PDF]
  • Jansen, J. J., Bro, R., Hoefsloot, H. C. J., van den Berg, F. W. J., Westerhuis, J. A., & Smilde, A. K. (2008). PARAFASCA: ASCA combined with PARAFAC for the analysis of metabolic fingerprinting data. Journal of Chemometrics, 22(2), 114-121. DOI: 10.1002/cem.1105 [details]
  • Smilde, A. K., Hoefsloot, H. C. J., & Westerhuis, J. A. (2008). The geometry of ASCA. Journal of Chemometrics, 22(8), 464-471. DOI: 10.1002/cem.1175 [details]
  • Smit, S., Hoefsloot, H. C. J., & Smilde, A. K. (2008). Statistical data processing in clinical proteomics. Journal of Chromatography B, 866(1-2), 77-88. DOI: 10.1016/j.jchromb.2007.10.042 [details]
  • Stanimirovic, O., Hoefsloot, H. C. J., de Bokx, P. K., & Smilde, A. K. (2008). Variable selection methods as a tool to find sensor locations for distributed parameter systems. Industrial & Engineering Chemistry Research, 47(4), 1184-1191. DOI: 10.1021/ie070946i [details]
  • Westerhuis, J. A., Hoefsloot, H. C. J., Smit, S., Vis, D. J., Smilde, A. K., van Velzen, E. J. J., ... van Dorsten, F. A. (2008). Assessment of PLSDA cross validation. Metabolomics, 4(1), 81-89. DOI: 10.1007/s11306-007-0099-6 [details] [PDF]
  • Westerhuis, J. A., van Velzen, E. J. J., Hoefsloot, H. C. J., & Smilde, A. K. (2008). Discriminant Q2 (DQ2) for improved discrimination in PLSDA models. Metabolomics, 4(4), 293-296. DOI: 10.1007/s11306-008-0126-2 [details] [PDF]
  • van Velzen, E. J. J., Westerhuis, J. A., van Duynhoven, J. P. M., van Dorsten, F. A., Hoefsloot, H. C. J., Jacobs, D. M., ... Smilde, A. K. (2008). Multilevel data analysis of a crossover designed human nutritional intervention study. Journal of Proteome Research, 7(10), 4483-4491. DOI: 10.1021/pr800145j [details]
  • Aerts, J. M., van Breemen, M. J., Bussink, A. P., Ghauharali, K., Sprenger, R., Boot, R. G., ... de Koster, C. G. (2008). Biomarkers for lysosomal storage disorders: Identification and application as exemplified by chitotriosidase in Gaucher disease. Acta Paediatrica, 97(s457), 7-14. DOI: 10.1111/j.1651-2227.2007.00641.x [details]
  • Bro, R., Kjeldahl, K., Smilde, A. K., & Kiers, H. A. L. (2008). Cross-validation of component models: A critical look at current methods. Analytical and Bioanalytical Chemistry, 390(5), 1241-1251. DOI: 10.1007/s00216-007-1790-1 [details]
  • Christin, C., Smilde, A. K., Hoefsloot, H. C. J., Suits, F., Bischoff, R., & Horvatovich, P. L. (2008). Optimized time alignment algorithm for LC-MS data: Correlation optimized warping using component detection algorithm-selected mass chromatograms. Analytical Chemistry, 80(18), 7012-7021. DOI: 10.1021/ac800920h [details]

2008

  • Hoefsloot, H. C. J., Smit, S., & Smilde, A. K. (2008). A classification model for the Leiden proteomics competition. Statistical Applications in Genetics and Molecular Biology, 7(2), 8. [details] [PDF]

2011

  • Saccenti, E. (Author), & Smilde, A. K. (Author). (2011). Beethoven's deafness and his three styles. British Medical Journal. [details]

2017

  • Reshetova, P. V. (2017). Use of prior knowledge in biological systems modelling [details / files]
This list of publications is extracted from the UvA-Current Research Information System. Questions? Ask the library or the Pure staff of your faculty / institute. Log in to Pure to edit your publications.
  • University of Copenhagen
    Deeltijd hoogleraar Computational Systems Biology

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