Dr. ir. H.C.J. (Huub) Hoefsloot
Faculteit der Natuurwetenschappen, Wiskunde en Informatica
Swammerdam Institute for Life Sciences
Bezoekadres
- Science Park 904
- Kamernummer: C2.206
Postadres
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Postbus 1212
1000 BE Amsterdam
Contactgegevens
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Publicaties
2023
García-Valiente, R., Merino Tejero, E., Stratigopoulou, M., Balashova, D., Jongejan, A., Lashgari, D., Pélissier, A., Caniels, T. G., Claireaux, M. A. F., Musters, A., van Gils, M. J., Rodríguez Martínez, M., de Vries, N., Meyer-Hermann, M., Guikema, J. E. J., Hoefsloot, H., & van Kampen, A. H. C. (2023). Understanding repertoire sequencing data through a multiscale computational model of the germinal center. Npj Systems Biology and Applications, 9, Article 8. https://doi.org/10.1038/s41540-023-00271-y [details]
2022
- Khakimov, B., Hoefsloot, H. C. J., Mobaraki, N., Aru, V., Kristensen, M., Lind, M. V., Holm, L., Castro-Mejía, J. L., Nielsen, D. S., Jacobs, D. M., Smilde, A. K., & Engelsen, S. B. (2022). Human Blood Lipoprotein Predictions from 1H NMR Spectra: Protocol, Model Performances, and Cage of Covariance. Analytical Chemistry, 94(2), 628–636. Advance online publication. https://doi.org/10.1101/2021.02.24.432509, https://doi.org/10.1021/acs.analchem.1c01654 [details]
- Lashgari, D., Merino Tejero, E., Meyer-Hermann, M., Claireaux, M. A. F., van Gils, M. J., Hoefsloot, H. C. J., & Van Kampen, A. H. C. (2022). From affinity selection to kinetic selection in Germinal Centre modelling. PLoS Computational Biology, 18(6), Article e1010168. https://doi.org/10.1371/journal.pcbi.1010168 [details]
- Li, L., Hoefsloot, H., de Graaf, A. A., Acar, E., & Smilde, A. K. (2022). Exploring dynamic metabolomics data with multiway data analysis: a simulation study. BMC Bioinformatics, 23(1), Article 31. https://doi.org/10.1186/s12859-021-04550-5 [details]
2021
- Merino Tejero, E., Lashgari, D., García-Valiente, R., Gao, X., Crauste, F., Robert, P. A., Meyer-Hermann, M., Rodríguez Martínez, M., van Ham, S. M., Guikema, J. E. J., Hoefsloot, H., & van Kampen, A. H. C. (2021). Multiscale Modeling of Germinal Center Recapitulates the Temporal Transition From Memory B Cells to Plasma Cells Differentiation as Regulated by Antigen Affinity-Based Tfh Cell Help. Frontiers in Immunology, 11, Article 620716. https://doi.org/10.3389/fimmu.2020.620716 [details]
- Merino Tejero, E., Lashgari, D., García-Valiente, R., He, J., Robert, P. A., Meyer-Hermann, M., Guikema, J. E. J., Hoefsloot, H., & van Kampen, A. H. C. (2021). Coupled Antigen and BLIMP1 Asymmetric Division With a Large Segregation Between Daughter Cells Recapitulates the Temporal Transition From Memory B Cells to Plasma Cells and a DZ-to-LZ Ratio in the Germinal Center. Frontiers in Immunology, 12, Article 716240. https://doi.org/10.3389/fimmu.2021.716240 [details]
2020
- Monsonis-Centelles, S., Hoefsloot, H. C. J., Engelsen, S. B., Smilde, A. K., & Lind, M. V. (2020). Repeatability and reproducibility of lipoprotein particle profile measurements in plasma samples by ultracentrifugation. Clinical chemistry and laboratory medicine, 58(1), 103-115. Advance online publication. https://doi.org/10.1515/cclm-2019-0729 [details]
- Swarge, B., Abhyankar, W., Jonker, M., Hoefsloot, H., Kramer, G., Setlow, P., Brul, S., & de Koning, L. J. (2020). Integrative Analysis of Proteome and Transcriptome Dynamics during Bacillus subtilis Spore Revival. mSphere, 5(4), Article e00463-20. https://doi.org/10.1128/mSphere.00463-20 [details]
2018
- Fazelzadeh, P., Hoefsloot, H. C. J., Hankemeier, T., Most, J., Kersten, S., Blaak, E. E., Boekschoten, M., & van Duynhoven, J. (2018). Global testing of shifts in metabolic phenotype. Metabolomics, 14(10), Article 139. https://doi.org/10.1007/s11306-018-1435-8 [details]
- Feenstra, K. A., Abeln, S., Westerhuis, J. A., Brancos dos Santos, F., Molenaar, D., Teusink, B., Hoefsloot, H. C. J., & Heringa, J. (2018). Training for translation between disciplines: a philosophy for life and data sciences curricula. Bioinformatics, 34(13), i4–i12. https://doi.org/10.1093/bioinformatics/bty233 [details]
- Folch-Fortuny, A., Teusink, B., Hoefsloot, H. C. J., Smilde, A. K., & Ferrer, A. (2018). Dynamic elementary mode modelling of non-steady state flux data. BMC Systems Biology, 12, Article 71. https://doi.org/10.1186/s12918-018-0589-3 [details]
- Naue, J., Hoefsloot, H. C. J., Kloosterman, A. D., & Verschure, P. J. (2018). Forensic DNA methylation profiling from minimal traces: How low can we go? Forensic Science International. Genetics, 33, 17-23. https://doi.org/10.1016/j.fsigen.2017.11.004 [details]
- Naue, J., Sänger, T., Hoefsloot, H. C. J., Lutz-Bonengel, S., Kloosterman, A. D., & Verschure, P. J. (2018). Proof of concept study of age-dependent DNA methylation markers across different tissues by massive parallel sequencing. Forensic Science International. Genetics, 36, 152-159. https://doi.org/10.1016/j.fsigen.2018.07.007 [details]
- Stelder, S. K., Benito de Moya, C., Hoefsloot, H. C. J., de Koning, L. J., Brul, S., & de Koster, C. G. (2018). Correction to "Stoichiometry, Absolute Abundance, and Localization of Proteins in the Bacillus cereus Spore Coat Insoluble Fraction Determined Using a QconCAT Approach". Journal of Proteome Research, 17(7), 2562. https://doi.org/10.1021/acs.jproteome.8b00313
- Stelder, S. K., Benito de Moya, C., Hoefsloot, H. C. J., de Koning, L. J., Brul, S., & de Koster, C. G. (2018). Stoichiometry, Absolute Abundance, and Localization of Proteins in the Bacillus cereus Spore Coat Insoluble Fraction Determined Using a QconCAT Approach. Journal of Proteome Research, 17(2), 903-917. https://doi.org/10.1021/acs.jproteome.7b00732 [details]
2017
- Aru, V., Lam, C., Khakimov, B., Hoefsloot, H. C. J., Zwanenburg, G., Lind, M. V., Schäfer, H., van Duynhoven, J., Jacobs, D. M., Smilde, A. K., & Engelsen, S. B. (2017). Quantification of lipoprotein profiles by nuclear magnetic resonance spectroscopy and multivariate data analysis. Trends in Analytical Chemistry, 94, 210-219. https://doi.org/10.1016/j.trac.2017.07.009 [details]
- Hoefsloot, H. C. J., van der Kloet, F. M., & Westerhuis, J. A. (2017). Why orthogonal rotations might be not so orthogonal as you think. Journal of Chemometrics, 31(10), Article e2920. https://doi.org/10.1002/cem.2920 [details]
- Julkowska, M. M., Koevoets, I. T., Mol, S., Hoefsloot, H., Feron, R., Tester, M. A., Keurentjes, J. J. B., Korte, A., Haring, M. A., de Boer, G. J., & Testerink, C. (2017). Genetic Components of Root Architecture Remodeling in Response to Salt Stress. The Plant Cell, 29(12), 3198-3213. https://doi.org/10.1105/tpc.16.00680 [details]
- Monsonis Centelles, S., Hoefsloot, H. C. J., Khakimov, B., Ebrahimi, P., Lind, M. V., Kristensen, M., de Roo, N., Jacobs, D. M., van Duynhoven, J., Cannet, C., Fang, F., Humpfer, E., Schäfer, H., Spraul, M., Engelsen, S. B., & Smilde, A. K. (2017). Toward Reliable Lipoprotein Particle Predictions from NMR Spectra of Human Blood: An Interlaboratory Ring Test. Analytical Chemistry, 89(15), 8004-8012. Advance online publication. https://doi.org/10.1021/acs.analchem.7b01329 [details]
- Naue, J., Hoefsloot, H. C. J., Mook, O. R. F., Rijlaarsdam-Hoekstra, L., van der Zwalm, M. C. H., Henneman, P., Kloosterman, A. D., & Verschure, P. J. (2017). Chronological age prediction based on DNA methylation: Massive parallel sequencing and random forest regression. Forensic Science International. Genetics, 31, 19-28. https://doi.org/10.1016/j.fsigen.2017.07.015 [details]
- Oka, R., Zicola, J., Weber, B., Anderson, S. N., Hodgman, C., Gent, J. I., Wesselink, J-J., Springer, N. M., Hoefsloot, H. C. J., Turck, F., & Stam, M. (2017). Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biology, 18, Article 137. https://doi.org/10.1186/s13059-017-1273-4 [details]
2016
- Angermayr, S. A., van Alphen, P., Hasdemir, D., Kramer, G., Iqbal, M., van Grondelle, W., Hoefsloot, H. C., Choi, Y. H., & Hellingwerf, K. J. (2016). Culturing Synechocystis sp. Strain PCC 6803 with N2 and CO2 in a Diel Regime Reveals Multiphase Glycogen Dynamics with Low Maintenance Costs. Applied and Environmental Microbiology, 82(14), 4180-4189. Advance online publication. https://doi.org/10.1128/AEM.00256-16 [details]
- Mitra, V., Govorukhina, N., Zwanenburg, G., Hoefsloot, H., Westra, I., Smilde, A., Reijmers, T., van der Zee, A. G. J., Suits, F., Bischoff, R., & 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), 4229-4238. Advance online publication. https://doi.org/10.1021/acs.analchem.5b03483 [details]
2015
- Borirak, O., Rolfe, M. D., de Koning, L. J., Hoefsloot, H. C. J., Bekker, M., Dekker, H. L., Roseboom, W., Green, J., de Koster, C. G., & Hellingwerf, K. J. (2015). Time-series analysis of the transcriptome and proteome of Escherichia coli upon glucose repression. Biochimica et Biophysica Acta. Proteins and Proteomics, 1854(10, Part A), 1269-1279. https://doi.org/10.1016/j.bbapap.2015.05.017 [details]
- Borirak, O., de Koning, L. J., van der Woude, A. D., Hoefsloot, H. C. J., Dekker, H. L., Roseboom, W., de Koster, C. G., & Hellingwerf, K. J. (2015). Quantitative proteomics analysis of an ethanol- and a lactate-producing mutant strain of Synechocystis sp. PCC6803. Biotechnology for Biofuels, 8, Article 111. https://doi.org/10.1186/s13068-015-0294-z [details]
- 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. https://doi.org/10.1186/s12918-015-0180-0 [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.
- 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), Article 0139704. https://doi.org/10.1371/journal.pone.0139704 [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. https://doi.org/10.1371/journal.pone.0119856 [details]
- Smilde, A. K., Timmerman, M. E., Saccenti, E., Jansen, J. J., & Hoefsloot, H. C. J. (2015). Covariances Simultaneous Component Analysis: a new method within a framework for modeling covariances. Journal of Chemometrics, 29(5), 277-288. https://doi.org/10.1002/cem.2707 [details]
- Timmerman, M. E., Hoefsloot, H. C. J., Smilde, A. K., & Ceulemans, E. (2015). Scaling in ANOVA-simultaneous component analysis. Metabolomics, 11(5), 1265-1276. https://doi.org/10.1007/s11306-015-0785-8 [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). Royal Society of Chemistry. https://doi.org/10.1039/9781849735162 [details]
- Willemsen, A. M., Hendrickx, D. M., Hoefsloot, H. C. J., Hendriks, M. M. W. B., Wahl, S. A., Teusink, B., Smilde, A. K., & van Kampen, A. H. C. (2015). MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis. Molecular BioSystems, 11(1), 137-145. Advance online publication. https://doi.org/10.1039/c4mb00510d [details]
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. https://doi.org/10.1186/1752-0509-8-61 [details]
- Julkowska, M. M., Hoefsloot, H. C. J., Mol, S., Feron, R., de Boer, G. J., Haring, M. A., & Testerink, C. (2014). Capturing Arabidopsis Root Architecture Dynamics with root-fit Reveals Diversity in Responses to Salinity. Plant Physiology, 166(3), 1387-1402. Advance online publication. https://doi.org/10.1104/pp.114.248963 [details]
- 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. https://doi.org/10.1016/j.jchromb2014.04.048 [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. https://doi.org/10.1016/j.chroma.2014.10.101 [details]
- 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. https://doi.org/10.1007/s11306-013-0598-6 [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. https://doi.org/10.1371/journal.pone.0096284 [details]
2013
- Abeln, S., Molenaar, D., Feenstra, K. A., Hoefsloot, H. C. J., Teusink, B., & Heringa, J. (2013). Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds. Briefings in Bioinformatics, 14(5), 589-598. https://doi.org/10.1093/bib/bbt023 [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. https://doi.org/10.1074/mcp.M112.022566 [details]
- Hoefsloot, H. C. J. (2013). Statistical Analysis and validation. In P. Horvatovich, & R. Bischoff (Eds.), Comprehensive Biomarker Discovery and Validation for Clinical Application (pp. 226-242). (RSC Drug Discovery; No. 33). RSC Publishing. https://doi.org/10.1039/9781849734363-00226 [details]
- 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, Article 468. https://doi.org/10.1186/1756-0500-6-468 [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). Wiley-VCH. https://doi.org/10.1002/9783527655861.ch11 [details]
2012
- 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. https://doi.org/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. Advance online publication. https://doi.org/10.1039/c2mb25015b [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. Advance online publication. https://doi.org/10.1007/s11306-012-0414-8 [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. https://doi.org/10.1007/s11306-011-0316-1 [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. Advance online publication. https://doi.org/10.1093/bib/bbr071 [details]
- 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), Article e32985. https://doi.org/10.1371/journal.pone.0032985 [details]
- Wegdam, W., Moerland, P. D., Meijer, D., de Jong, S. M., Hoefsloot, H. C. J., Kenter, G. G., Buist, M. R., & Aerts, J. M. F. G. (2012). A critical assessment of SELDI-TOF-MS for biomarker discovery in serum and tissue of patients with an ovarian mass. Proteome Science, 10(1), Article 45. https://doi.org/10.1186/1477-5956-10-45 [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. https://doi.org/10.1039/c0mb00083c [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. https://doi.org/10.1016/j.trac.2011.04.019 [details]
- Xu, C. J., Hoefsloot, H. C. J., & Smilde, A. K. (2011). To aggregate or not to aggregate high-dimensional classifiers. BMC Bioinformatics, 12. https://doi.org/10.1186/1471-2105-12-153 [details]
- Zakrzewska, A., van Eikenhorst, G., Burggraaff, J. E. C., Vis, D. J., Hoefsloot, H., Delneri, D., Oliver, S. G., Brul, S., & Smits, G. J. (2011). Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness. Molecular Biology of the Cell, 22(22), 4435-4446. https://doi.org/10.1091/mbc.E10-08-0721 [details]
- 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. https://doi.org/10.1002/cem.1400 [details]
2010
- 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. https://doi.org/10.1021/pr9010124 [details]
- 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. https://doi.org/10.1002/pca.1181 [details]
- Smilde, A. K., Westerhuis, J. A., Hoefsloot, H. C. J., Bijlsma, S., Rubingh, C. M., Vis, D. J., Jellema, R. H., Pijl, H., Roelfsema, F., & van der Greef, J. (2010). Dynamic metabolomic data analysis: a tutorial review. Metabolomics, 6(1), 3-17. https://doi.org/10.1007/s11306-009-0191-1 [details]
- Stanimirovic, O., Hoefsloot, H. C. J., & Smilde, A. K. (2010). Optimal measurement design for monitoring batch processes. AIChE Journal, 56(3), 837-840. https://doi.org/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. https://doi.org/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. https://doi.org/10.1007/s11306-009-0185-z [details]
- 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. https://doi.org/10.1016/j.aca.2009.12.003 [details]
2009
- Boot, R. G., van Breemen, M. J., Wegdam, W., Sprenger, R. R., de Jong, S., Speijer, D., Hollak, C. E. M., van Dussen, L., Hoefsloot, H. C. J., Smilde, A. K., de Koster, C. G., Vissers, J. P. C., & Aerts, J. M. F. G. (2009). Gaucher disease: a model disorder for biomarker discovery. Expert Review of Proteomics, 6(4), 411-419. https://doi.org/10.1586/epr.09.54 [details]
- 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). Elsevier. https://doi.org/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. https://doi.org/10.1186/1471-2105-10-425 [details]
- Wegdam, W., Moerland, P. D., Buist, M. R., Ver Loren van Themaat, E., Bleijlevens, B., Hoefsloot, H. C. J., de Koster, C. G., & Aerts, J. F. M. G. (2009). Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets. Proteome Science, 7, 19. https://doi.org/10.1186/1477-5956-7-19 [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. http://www.laboratory-journal.com/science/lebensmittel/data-analysis-strategies-nutritional-metabolomics [details]
- van Schalkwijk, D. B., de Graaf, A. A., van Ommen, B., van Bochove, K., Rensen, P. C. N., Havekes, L. M., van de Pas, N. C. A., Hoefsloot, H. C. J., van der Greef, J., & Freidig, A. P. (2009). Improved cholesterol phenotype analysis by a model relating lipoprotein life cycle processes to particle size. Journal of Lipid Research, 50(12), 2398-2411. https://doi.org/10.1194/jlr.M800354-JLR200 [details]
2008
- Aerts, J. M., van Breemen, M. J., Bussink, A. P., Ghauharali, K., Sprenger, R., Boot, R. G., Groener, J. E., Hollak, C. E., Maas, M., Smit, S., Hoefsloot, H. C., Smilde, A. K., Vissers, J. P. C., de Jong, S., Speijer, D., & 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. https://doi.org/10.1111/j.1651-2227.2007.00641.x [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. https://doi.org/10.1021/ac800920h [details]
- 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. https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/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 Duijnhoven, J. P. M., & van Dorsten, F. A. (2008). Assessment of PLSDA cross validation. Metabolomics, 4(1), 81-89. https://doi.org/10.1007/s11306-007-0099-6 [details]
- 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. https://doi.org/10.1007/s11306-008-0126-2 [details]
- an der Heiden, M. R., Plenio, H., Immel, S., Burello, E., Rothenberg, G., & Hoefsloot, H. C. J. (2008). Insights into Sonogashira cross-coupling by high-throughput kinetics and descriptor modeling. Chemistry - A European Journal, 14(9), 2857-2866. https://doi.org/10.1002/chem.200701418 [details]
- van Velzen, E. J. J., Westerhuis, J. A., van Duynhoven, J. P. M., van Dorsten, F. A., Hoefsloot, H. C. J., Jacobs, D. M., Smit, S., Draijer, R., Kroner, C. I., & Smilde, A. K. (2008). Multilevel data analysis of a crossover designed human nutritional intervention study. Journal of Proteome Research, 7(10), 4483-4491. https://doi.org/10.1021/pr800145j [details]
2019
- Aru, V., Lam, C., Khakimov, B., Hoefsloot, H. C. J., Zwanenburg, G., Lind, M. V., Schäfer, H., van Duynhoven, J., Jacobs, D. M., Smilde, A. K., & Engelsen, S. B. (2019). Corrigendum to “Quantification of lipoprotein profiles by nuclear magnetic resonance spectroscopy and multivariate data analysis” [Trends Anal Chem 94 (2017) 210–219](S0165993617301024)(10.1016/j.trac.2017.07.009)). TrAC - Trends in Analytical Chemistry, 119, Article 115631. https://doi.org/10.1016/j.trac.2019.115631
2015
- Smelt, J. P., Hoefsloot, H. C., de Koster, C. G., Schuurmans, J. M., ter Kuile, B. H., & Brul, S. (2015). Simulation of the rate of transfer of antibiotic resistance between Escherichia coli strains cultured under well controlled environmental conditions. Food Microbiology, 45(Part B), 189-194. Advance online publication. https://doi.org/10.1016/j.fm.2014.03.019 [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. http://www.bepress.com/sagmb/vol7/iss2/art8 [details]
2013
- Borirak, O., Bekker, M., Rolfe, M. D., Dekker, H. L., de Jong, L., de Koster, C. G., Hoefsloot, H. C. J., de Koning, L. J., & Hellingwerf, K. J. (2013). Dynamic changes of the Escherichia coli transcriptome and proteome exerted by glucose repression. The FASEB Journal, 27(1 Supplement), Article lb136. http://www.fasebj.org/content/27/1_Supplement/lb136.abstract [details]
2017
- Oka, R., Wesselink, J.-J., Zicola, J., Weber, B., Anderson, S. N., Hodgman, C., Gent, J. I., Springer, N. M., Hoefsloot, H. C. J., Turck, F. & Stam, M. (2017). Additional file 4: of Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Figshare. https://doi.org/10.6084/m9.figshare.c.3833383_d4.v1
- Oka, R., Wesselink, J.-J., Zicola, J., Weber, B., Anderson, S. N., Hodgman, C., Gent, J. I., Springer, N. M., Hoefsloot, H. C. J., Turck, F. & Stam, M. (2017). Additional file 5: of Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Figshare. https://doi.org/10.6084/m9.figshare.c.3833383_d5.v1
- Oka, R., Wesselink, J.-J., Zicola, J., Weber, B., Anderson, S. N., Hodgman, C., Gent, J. I., Springer, N. M., Hoefsloot, H. C. J., Turck, F. & Stam, M. (2017). Additional file 6: of Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Figshare. https://doi.org/10.6084/m9.figshare.c.3833383_d6.v1
- Oka, R., Wesselink, J.-J., Zicola, J., Weber, B., Anderson, S. N., Hodgman, C., Gent, J. I., Springer, N. M., Hoefsloot, H. C. J., Turck, F. & Stam, M. (2017). Additional file 3: of Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Figshare. https://doi.org/10.6084/m9.figshare.c.3833383_d3.v1
- Oka, R., Wesselink, J.-J., Zicola, J., Weber, B., Anderson, S. N., Hodgman, C., Gent, J. I., Springer, N. M., Hoefsloot, H. C. J., Turck, F. & Stam, M. (2017). Additional file 2: of Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Figshare. https://doi.org/10.6084/m9.figshare.c.3833383_d2.v1
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García-Valiente, R., Merino Tejero, E., Stratigopoulou, M., Balashova, D., Jongejan, A., Lashgari, D., Pélissier, A., Caniels, T. G., Claireaux, M. A. F., Musters, A., van Gils, M. J., Rodríguez Martínez, M., de Vries, N., Meyer-Hermann, M., Guikema, J. E. J., Hoefsloot, H., & van Kampen, A. H. C. (2023). Understanding repertoire sequencing data through a multiscale computational model of the germinal center. Npj Systems Biology and Applications, 9, Article 8.