In Press & Recent Publications
Metabolic fate of polyphenols in the human superorganism
John van Duynhoven, Elaine E. Vaughana, Doris M. Jacobsa, Robèr Kempermana,
Ewoud J. J. van Velzena, Gabriele Grossa, Laure C. Rogera, Sam Possemiers,
Age K. Smildec, Joël Doré, Johan A. Westerhuisc, and Tom Van de Wiele
PNAS, Volume 107:25 (2010)
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
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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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