In Press & Recent Publications

Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds
Sanne Abeln, Douwe Molenaar, K. Anton Feenstra, Huub C. J. Hoefsloot, Bas Teusink, and Jaap Heringa
Brief Bioinform first published online April 19, 2013
Gender-Dependent Associations of Metabolite Profiles and Body Fat Distribution in a Healthy Population with Central Obesity: Towards Metabolomics Diagnostics
Ewa Szymańska, Jildau Bouwman, Katrin Strassburg, Jacques Vervoort, Antti J. Kangas, Pasi Soininen, Mika Ala-Korpela, Johan Westerhuis, John P.M. van Duynhoven, David J. Mela, Ian A. Macdonald, Rob J. Vreeken, Age K. Smilde, and Doris M. Jacobs
Omics, 16:12 (2012) pages 652 - 667
Individual differences in metabolomics: individualised responses and between-metabolite relationships
Jeroen J. Jansen, Ewa Szymańska, Huub C. J. Hoefsloot, Age K. Smilde
Omics, 8:1 (2012) pages 94 - 104
A critical assessment of feature selection methods for biomarker discovery in clinical proteomics
Christin Christin, Huub C.J. Hoefsloot, Age K. Smilde, Berend Hoekman, Frank Suits, Rainer Bischoff and Peter Horvatovich
Molecular & Cellular Proteomics (2012)
DISCO-SCA and Properly Applied GSVD as Swinging Methods to Find Common and Distinctive Processes
Deun, K. Van, Mechelen, I. van, Thorrez, L., Schouteden, M., Moor, B. de, Werf, M.J. van der, Lathauwer, L. De, Smilde, A.K. and Kiers, H.A.
PLoS One, 7(5), e37840 (2012)
Editorial-data analysis in metabolomics
Jansen, J.J. and Westerhuis, J.A.
Metabolomics 8 (Suppl. 1) (2012)
Assessing the metabolic effects of prednisolone in healthy volunteers using urine metabolic profiling
Sandrine Ellero-Simatos, Ewa Szymańska, Ton Rullmann, Wim HA Dokter, Raymond Ramaker, Ruud Berger, Thijs MP van Iersel, Age K Smilde, Thomas Hankemeier and Wynand Alkema
Genome Medicine 4:94 (2012)
A lipidomic analysis approach to evaluate the response to cholesterol-lowering food intake
Ewa Szymańska, Ferdinand A. van Dorsten, Jorne Troost, Iryna Paliukhovich, Ewoud J. J. van Velzen, Margriet M. W. B. Hendriks, Elke A. Trautwein, John P. M. van Duynhoven, Rob J. Vreeken, Age K. Smilde
Metabolomics, 8:5 (2012), pages 894 - 906
A critical assessment of SELDI-TOF-MS for biomarker discovery in serum and tissue of patients with an ovarian mass
Wegdam Wouter, Moerland D Perry, Meijer Danielle, de Jong M Shreyas, Hoefsloot CJ Huub, Kenter G Gemma, Buist R Marrije, Aerts MFG Johannes
Proteome Science, 10:45 (2012)
Topology of Transcriptional Regulatory Networks: Testing and Improving
Dicle Hasdemir, Gertien J. Smits, Johan A. Westerhuis, Age K. Smilde
PLoS ONE 7(7) (2012), article number e40082
Nutrikinetics: Concept, technologies, applications, perspectives
J.P.M. van Duynhoven, E.J.J. van Velzen, J.A. Westerhuis, M. Foltz, D.M. Jacobs,A.K. Smilde
TRENDS IN FOOD SCIENCE & TECHNOLOGY, Volume 26(1) (2012) pages 4 - 13
Inferring differences in the distribution of reaction rates across conditions.
Diana M. Hendrickx, Huub C.J. Hoefsloot, Margriet M.W.B. Hendriks, Daniël J. Vis, André B. Canelas, Bas Teusink and Age K. Smilde
Mol. BioSyst., 8(9) (2012), pages 2415 - 2423
Global test for metabolic pathway differences between conditions
Diana M. Hendrickx, Huub C.J. Hoefsloot, Margriet M.W.B. Hendriks, André. Canelas and Age K. Smilde
Analytica Chimica Acta, Volume 719 (2012), pages 8 - 15
Identification of prognostic and diagnostic biomarkers of glucose intolerance in ApoE3Leiden micex
Suzan Wopereis, Marijana Radonjic, Carina Rubingh, Marjan van Erk, Age Smilde, Wim van Duyvenvoorde, Nicole Cnubben, Teake Kooistra, Ben van Ommen, and Robert Kleemann
Physiological genomisc, Volume 44(5) (2012), pages 293 - 304
Detecting Regulatory Mechanisms in Endocrine Time Series Measurements
Daniel J. Vis, Johan A. Westerhuis, Huub C. J. Hoefsloot, Ferdinand Roelfsema, Margriet M. W. B. Hendriks, and Age K. Smilde
PloS ONE Volume 7(3) (2012), article number: e32985
Generic framework for highdimensional fixed-effects ANOVA
Age K. Smilde, Marieke E.Timmerman, Margriet M.W.B. Hendriks, Jeroen J. Jansen and Huub C.J. Hoefsloot
Briefings in bioinformatics, Volume 13(5) (2012), pages 524 - 535
Tracy-Widom statistic for the largest eigenvalue of autoscaled real matrices
Edoardo Saccenti1, Age K. Smilde1, Johan A. Westerhuis1, Margriet M. W. B. Hendriks
Journal of Chemometrics, Volume 25(12) (2011), pages 644 - 65
CHRISTMAS 2011: DIAGNOSIS Beethoven's deafness and his three styles
Saccenti, E; Smilde, AK; Saris, WHM
British Medical Journal, Volume 343 (2011), d7589
Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness
Anna Zakrzewska, Gerco van Eikenhorst, Johanna E. C. Burggraaff, Daniel J. Vis, Huub Hoefsloot, Daniela Delneri, Stephen G. Oliver, Stanley Brul, and Gertien J. Smits
Molecular Biology of the Cell, Volume 22(22) (2011), pages 4435-4446
Data-processing strategies for metabolomics studies
Margriet M.W.B. Hendriks, Fred A.van Eeuwijk, Renger H. Jellema, Johan A. Westerhuis, Theo H. Reijmers, Huub C.J. Hoefsloot, Age K. Smilde
TrAC Trends in Analytical Chemistry, Volume 30(10) (2011), pages 1685-1698
On the increase of predictive performance with high-level data fusion
T.G. Doeswijk, A.K. Smilde, J.A. Hageman, J.A. Westerhuis, F.A. van Eeuwijk
Analytica Chimica Acta, Volume 705 (1-2) (2011), pages 41 - 47
Application of NMR-based metabonomics suggests a relationship between betaine absorption and elevated creatine plasma concentrations in catheterised sows
Christian Clement Yde, Johan A. Westerhuis, Hanne Christine Bertram and Knud Erik Bach Knudsen
Br J Nutr, Volume 107(11) (2012), pages 1603-1615
ANOVA-principal component analysis and ANOVA-simultaneous component analysis: a comparison
Gooitzen Zwanenburg, Huub C.J. Hoefsloot, Johan A. Westerhuis, Jeroen J. Jansen, Age K. Smilde
J Chemometrics, Volume 25 (2011), pages 561 - 567
Canonical correlation analysis of multiple sensory directed metabolomics data blocks reveals corresponding parts between data blocks
T .G. Doeswijk, J.A. Hageman, J.A. Westerhuis, Y. Tikunov, A. Bovy, F.A. van Eeuwijk
Chemometrics and Intelligent Laboratory Systems, Volume 107(2) (2011) pages 371-376
Between Metabolite Relationships: an essential aspect of metabolic change
Jeroen J. Jansen, Ewa Szymańska, Huub C. J. Hoefsloot, Doris M. Jacobs, Karin Strassburg and Age K. Smilde
Metabolomics, Volume 8 (2012), pages 422 - 432
DISCO-SCA and Properly Applied GSVD as Swinging Methods to Find Common and Distinctive Processes
Katrijn Van Deun, Iven Van Mechelen, Lieven Thorrez, Martijn Schouteden, Bart De Moor, Mariët J. van der Werf, Lieven De Lathauwer, Age K. Smilde, Henk A.L. Kiers
PLoS ONE, Volume 7(3) (2012), article number e32985
Double-check: validation of diagnostic statistics for PLS-DA models in metabolomics studies
Ewa Szymańska, Edoardo Saccenti, Age K. Smilde, Johan A. Westerhuis
Metabolomics, Volume 8(1) (2012), pages 3 - 16
To aggregate or not to aggregate high-dimensional classifiers
Xu, CJ; Hoefsloot, HCJ; Smilde, AK
BMC Bioinformatics, Volume 12, article number 153 (2011)
Simplivariate Models: Uncovering the Underlying Biology in Functional Genomics Data
Saccenti E, Westerhuis JA, Smilde AK, van der Werf MJ, Hageman JA, Hendriks MMWB
PloS ONE, Volume 6(6) (2011), article number e20747
New Figures of Merit for Comprehensive Functional Genomics Data: The Metabolomics Case
Van Batenburg MF, Coulier L, van Eeuwijk F, Smilde AK, Westerhuis JA
Analytical Chemistry, Volume 83(9) (2011), pages 3267-3274
Comparability problems in the analysis of multiway data
Van Mechelen I, Smilde AK
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, Volume 106 (2011) pages 2-11
Discovery of subtle effects in a human intervention trial through multilevel modeling
Rubingh CM, van Erk MJ, Wopereis S, van Vliet T, Verheij ER, Cnubben NHP, van Ommen B, van der Greef J, Hendriks HFJ, Smilde AK
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, Volume 106 (2011), pages 108-114
Multiway and multiset data analysis
Smilde A, Tauler R
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, Volume 106 (2011), pages 1-1
Metabolic fate of polyphenols in the human superorganism
van Duynhoven J, Vaughan EE, Jacobs DM, Kemperman RA, van Velzen EJJ, Gross G, Roger LC, Possemiers S, Smilde AK, Dore J, Westerhuis JA, Van de Wiele T
PNAS, Volume 108 (2011)i, pages 4531-4538
Real-time synchronization of batch trajectories for on-line multivariate statistical process control using Dynamic Time Warping
J.M. González-Martínez, A. Ferrer, J.A. Westerhuis
Chemometrics and Intelligent Laboratory Systems, Volume 105(2) (2011) pages 195-206
Reverse engineering of metabolic networks, a critical assessment
Diana M. Hendrickx, Margriet M. W. B. Hendriks, Paul H. C. Eilers, Age K. Smilde and Huub C. J. Hoefsloot
Mol. BioSyst, Volume 7:2 (2011) pages 511-520
Dynamic metabolomic data analysis: a tutorial review
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.
Metabolomics, Volume 6:1 (2010) pages 3-17
Multivariate paired data analysis: multilevel PLSDA versus OPLSDA
Johan A. Westerhuis, Ewoud J.J. van Velzen, Huub C.J. Hoefsloot, Age K. Smilde
Metabolomics, Vol. 6:1 (2010) pages 119-128
A generic linked-mode decomposition model for data fusion
Iven van Mechelen, Age K. Smilde
Chemometrics and Intelligent Laboratory Systems, Volume 104(1) (2010) pages 83-94
Time Alignment Algorithms Based on Selected Mass Traces for Complex LC-MS Data
Christin Christin, Age K. Smilde, Huub C. Hoefsloot, Frank Suits, Rainer Bischoff, Peter L. Horvatovich
J. Proteome Res., Vol. 9:3 (2010) pages 1483-1495
Computational modeling of the human serum proteome response to colon resection surgery
Xu, Cheng-Jian, Hoefsloot, Huub C. J., Dijkstra, Martijn, Havenga, Klaas, Roelofsen, Han, Vonk, Roel J., Smilde, Age K.
Analytica Chimica Acta, Vol. 661:1 (2010) pages 20-27
Optimal Measurement Design for Monitoring Batch Processes
Stanimirovic, Olja, Hoefsloot, Huub C. J., Smilde, Age K.
AICHE Journal, Vol. 56:3 (2010) pages 837-840
Endocrine pulse identification using penalized methods and a minimum set of assumptions
Vis, Daniel J., Westerhuis, Johan A., Hoefsloot, Huub C. J., Pijl, Hanno, Roelfsema, Ferdinand, van der Greef, Jan, Smilde, Age K.
Am J Physiol Endocrinol Metab, Vol. 298:2 (2010) pages E146-E155
The Photographer and the Greenhouse: How to Analyse Plant Metabolomics Data
Jansen JJ, Smit S, Hoefsloot HCJ, Smilde AK
Phytochemical Analysis, Vol. 21:1, (2010), pages 48-60
Crossfit analysis: a novel method to characterize the dynamics of induced plant responses
Jeroen Jansen, Nicole M van Dam, Huub CJ Hoefsloot, and Age K. Smilde
BMC Bioinformatics Vol. 10:425 (2009)
Exploring the analysis of structured metabolomics data
Maikel P.H. Verouden, Johan A. Westerhuis, Mariët J. van der Werf and Age K Smilde.
Chemometrics and Intelligent Laboratory Systems, Vol. 22 (2009), pages 88 - 96
Multi-way analysis of flux distributions across multiple conditions
Maikel P.H. Verouden, Richard A. Notebaard, Johan A. Westerhuis, Mariët J. van der Werf, Bas Teusink and Age K Smilde.
Journal of Chemometrics, Vol. 23 (2009), pages 406 - 420
Metabolic network discovery through reverse engineering of metabolome data
T. Cakir, M.M.W.B. Hendriks, J.A. Westerhuis and A.K. Smilde
Metabolomics, Januari 2009
Multilevel Data Analysis of a Crossover Designed Human Nutritional Intervention Study
Ewoud J. J. van Velzen, Johan A. Westerhuis, John P. M. van Duynhoven, Ferdi A. van Dorsten, Huub C. J. Hoefsloot, Doris M. Jacobs,§ Suzanne Smit, Richard Draijer, Christine I. Kroner, and Age K. Smilde
J. Proteome Res. Vol. 7 (2008), pages 4483 - 4491
The geomentry of ASCA
Age K. Smilde, Huub. C.J. Hoefsloot, Johan. A. Westerhuis
The Journal of Chemometrics, 22 (2008), pages 464 - 471
Discriminant Q² (DQ²) for improved discrimination in PLSDA models
Johan A. Westerhuis, Ewoud J. J. van Velzen, Huub C. J. Hoefsloot and Age K. Smilde
Metabolomics: Springer link date 30 August 2008
Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways
A.M. Willemsen, G.A. Jansen, J.C. Komen, S. van Hooff, H.R. Waterham, P.M.T. Brites, R.J.A. Wanders and A.H.C. van Kampen
ECCB: Vol. 24 (2008), pages i21-i27
A Classification Model for the Leiden Proteomics Competition
Hoefsloot, Huub C. J.; Smit, Suzanne; and Smilde, AgeK.
Statistical Applications in Genetics and Molecular Biology: Vol. 7 : Iss. 2, (2008) Article 8
Assessment of PLSDA cross validation
Johan A. Westerhuis, Huub C. J. Hoefsloot, Suzanne Smit, Daniel J. Vis, Age K. Smilde, Ewoud J. J. van Velzen, John P. M. van Duijnhoven and Ferdi A. van Dorsten
Metabolomics Volume 4, Number 1 / March, 2008
Variable Selection Methods as a Tool To Find Sensor Locations for Distributed Parameter Systems
Stanimirovic, O.; Hoefsloot, H. C. J.; De Bokx, P. K.; Smilde, A. K.
Ind. Eng. Chem. Res., 47(4) (2008), 1184-1191
Mechanistic insights on Sonogashira cross-coupling via high-throughput kinetics and descriptor modelling
Markus an der Heiden, Herbert Plennio, Enrico Burello, Huub C. J. Hoefsloot and Gadi Rothenberg
Chemistry - A European Journal, Volume 14, Issue 9, (2008), Pages 2857-2866
PARAFASCA: ASCA combined with PARAFAC for the analysis of metabolic fingerprinting data
Jeroen J. Jansen, Rasmus Bro, Huub C. J. Hoefsloot, Frans W. J. van den Berg, Johan A. Westerhuis, Age K. Smilde
Journal of Chemometrics, Volume 22 Issue 2, (2008), 114-121
Optimal sensor location and the relation between derivatives and PCA
Olja Stanimirovic, Huub C.J. Hoefsloot, Age K. Smilde, Pieter de Bokx
Accepted in Journal of Chemometrics
Statistical validation of megavariate effects in ASCA
Daniel J Vis, Johan A Westerhuis, Age K Smilde1 and Jan van der Greef
BMC BioInformatics, 8:322 (2007)
Grey component analysis for decomposing complex data using prior information
Johan A Westerhuis, Eduard PPA Derks, Huub CJ Hoefsloot and Age K Smilde
Journal of Chemometrics 21 (10-11) (OCT-NOV 2007), 474-485
Understanding Ligand Diversity
Westerhuis JA, Hageman JA, Fruhauf HW, et al.,
CHIMICA OGGI-CHEMISTRY TODAY Volume: 25 (2) (2007) Pages: 28- Supplement: Suppl. S
How to distinguish healthy from diseased? Classification strategy for mass spectrometry-based clinical proteomics
Hendriks MMWB, Smit S, Akkermans WLMW, Reijmers TH , Eilers PHC , Hoefsloot HCJ, Rubingh CM, de Koster CG , Aerts JM, Smilde AK
PROTEOMICS 7 (20) (OCT 2007), 3672-3680
Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA
Nueda MJ, Conesa A, Westerhuis JA, Hoefsloot HCJ, Smilde AK, Talon M, Ferrer A
BIOINFORMATICS 23 (14) (JUL 15 2007), 1792-1800
Applications of a new subspace clustering algorithm (COSA) in medical systems biology
Doris Damian, Matej Orešic, Elwin Verheij, Jacqueline Meulman, Jerome Friedman, Aram Adourian, Nicole Morel, Age Smilde and Jan van der Greef
Metabolomics, 3 (1) (2007), 69-77
Conditional Monte Carlo sampling to find branching architectures of polymers from radical polymerizations with transfer to polymer and recombination termination
Iedema PD, Wulkow M, Hoefsloot HCJ
POLYMER 48 (6) (MAR 8 2007), 1770-1784
Assessing the statistical validity of proteomics based biomarkers
Suzanne Smit, Mariëlle J. van Breemen, Huub C.J. Hoefsloot, Age K. Smilde, Johannes M.F.G. Aerts and Chris G. de Koster
Analytica Chimica Acta, 592 (2) (2007), 210-217
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Examples of NIR based real time release in tablet manufacturing
E.T.S. Skibsted, J.A. Westerhuis, A.K. Smilde and D.T. Witte
Journal of Pharmaceutical and Biomedical Analysis, 43 (4) (2007), 1297-1305
Maximum likelihood scaling (MALS)
Huub C. J. Hoefsloot, Maikel P. H. Verouden, Johan A. Westerhuis and Age K. Smilde
Journal of Chemometrics, 20(3-4) (2006), 120-127
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Linking PCA and time derivatives of dynamic systems
Olja Stanimirovic, Huub C. J. Hoefsloot, Pieter K. de Bokx and Age K. Smilde
Journal of Chemometrics, 20(1-2) (2006), 43-53
Modelling multi-viscosity systems with dissipative particle dynamics
Visser DC, Hoefsloot HCJ, Iedema PD
Journal of Computational Physics 214 (2) (MAY 20, 2006), 491-504
Conditional Monte Carlo sampling to find branching architectures of polymers from radical polymerizations with transfer to polymer
Iedema PD, Hoefsloot HCJ
MACROMOLECULES 39 (8) (APR 18 2006), 3081-3088
Bagged K-means clustering of metabolome data
J.A. Hageman, R.A. van den Berg, J.A. Westerhuis, H.C.J. Hoefsloot and A.K. Smilde
Critical Reviews in Analytical Chemistry, 36 (3-4) (2006), 211-220
Centering, scaling, and transformations: improving the biological information content of metabolomics data
Robert A. van den Berg , Huub C.J. Hoefsloot , Johan A. Westerhuis , Age K. Smilde and Mariët J van der Werf
B MC Genomics, 142 (2006)
Performance assesment and improvement of control charts for statistical batch process monitoring
Henk-Jan Ramaker, Eric N.M. van Sprang, Johan A. Westerhuis, Stephen P. Gurden, Frank H. van der Meulen and Age K. Smilde
Statistica Neerlandica, 60 (3) (2006), 339-360
Large-Scale Human Metabolomics Studies: A Strategy for Data (Pre-) Processing and Validation
Sabina Bijlsma, Ivana Bobeldijk, Elwin R. Verheij, Raymond Ramaker, Sunil Kochhar, Ian A. Macdonald, Ben van Ommen, and Age K. Smilde
Analytical Chemistry, 78 (2) (2006), 567-574
How to find the best homogeneous catalyst
G. Rothenberg, J. A. Hageman, F. Clerc, H.-W. Frühauf and J. A. Westerhuis
Chemical Industries (CRC Press), 115 (2006) (Catal. Org. React.), 261-270
Single Channel Event (SCE) for managing sensor failures in MSPC
Henk-Jan Ramaker, Eric N.M. van Sprang, Johan A. Westerhuis and Age K. Smilde
Computers & Chemical Engineering, 30 (6-7) (2006), 961-969
Design and Assembly of Virtual Homogeneous Catalyst Libraries — Towards in silico Catalyst Optimisation
Jos A. Hageman, Johan A. Westerhuis, Hans-Werner Frühauf, Gadi Rothenberg
Advanced Synthesis & Catalysis, 348 (2006), 361-369