In Press & Recent Publications
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, published online 4 January 2012
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, published online 23 December, 2011
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
British Journal of Nutrition, online September, 2011
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 (online) (2011)
Double-check: validation of diagnostic statistics for PLS-DA
models in metabolomics studies
Ewa Szymańska, Edoardo Saccenti, Age K. Smilde, Johan A. Westerhuis
Metabolomics (online) (2011)
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) 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
Download files used
in this article. (zip - 2.8 KB)
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