Publications by date

Here you find the publications from projects in the NMC. They are sorted by date of publication, in descending order.

High-performance Liquid Chromatography (HPLC)-Mass Spectrometry (MS) analysis of plant metabolites in Brassicaceae.
De Vos, R.C.H., Schipper, B., Hall, R.D.
03/2012
Plant associate projects

Global test for metabolic pathway differences between conditions
Diana M. Hendrickx, Huub C.J. Hoefsloot, Margriet M.W.B. Hendriks, Andre B. Canelas and Age K. Smilde
02/2012
Biostatistics

Lipidomics Reveals Multiple Pathway Effects of a Multi-Components Preparation on Lipid Biochemistry in ApoE*3Leiden.CETP Mice
Heng Wei, Chunxiu Hu, Mei Wang, Anita M. van den Hoek, Theo H Reijmers, Suzan Wopereis, Jildau Bouwman, Raymond Ramaker, Henrie A.A.J. Korthout, Marco Vennik, Thomas Hankemeier, Louis M. Havekes, Renger F. Witkamp, Elwin R. Verheij, Guowang Xu, Jan van der Greef
01/2012
Biomedical

Understanding and Classifying Metabolite Space and Metabolite-Likeness
Julio E. Peironcely, Theo Reijmers, Leon Coulier, Andreas Bender, Thomas Hankemeier
12/2011
Metabolite identification

Perspective: All systems go
Jan van der Greef
12/2011
Biomedical

Tracy-Widom statistic for the largest eigenvalue of autoscaled real matrices
E. Saccenti, J.A. Westerhuis, A.K. Smilde and M.M.W.B. Hendriks
11/2011
Biostatistics

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
11/2011
Biomedical

Tracy-Widom statistic for the largest eigenvalue of autoscaled real matrices
E. Saccenti, J. A. Westerhuis, A. K. Smilde and M. M. W. B. Hendriks
11/2011
Biomedical

Enrichment of viable bacteria in a micro-volume by free-flow electrophoresis
S. Podszun, P. Vulto, H. Heinz, S. Hakenberg, C. Hermann, T. Hankemeier, G.A. Urban
10/2011
Biomedical

Mesenchymal Stem Cells Induce Resistance to Chemotherapy through the Release of platinum-Induced Fatty Acids
Jeanine M.L. Roodhart, Laura G.M. Daenen, Edwin C.A. Stiger, Henk-Jan Prins, Johan Gerrits, Julia M. Houthuijzen, Marije G. Gerritsen, Henk S. Schipper, Marieke J.G. Backer, Miranda van Amersfoort, Joost S.P. Vermaat, Petra Moerer, Kenji Ishihara, Eric Kalkhoven, Jos H. Beijnen, Patrick W.B. Derksen, Rene H. Medema, Anton C. Martens, Arjan B. Brenkman and Emile E. Voest
09/2011
Quantitative profiling

Double-check: validation of diagnostic statistics for PLS-DA models in metabolomics studies
Ewa Szymanska, Edoardo Saccenti, Age K. Smilde, Johan A. Westerhuis
08/2011
Biostatistics

Single-Electrolyte isotachophoresis Using a Nanochannel-Induced Depletion Zone
Jos Quist*, Kjeld G.H. Janssen* (equally contributing), Paul Vulto, Thomas Hankemeier, Heiko J. van der Linden
08/2011
Biomedical

Linking biological activity with herbal constituents by systems biology-based approaches: effects of Panax ginseng in type 2 diabetic Goto-Kakizaki rats
Chunxiu Hu, Heng Wei, Hongwei Kong, Jildau Bouwman, Vanessa Gonzalez-Covarrubias, Rob van der Heijden, Theo H. Reijmers, Xu Bao, Elwin R. Verheij, Thomas Hankemeier, Guowang Xu, Jan van der Greef and Mei Wang
08/2011
Nutrition & Health

Elemental Composition determination based on MSn
Miguel-Rojas-Cherto, Piotr T. Kasper, Egon L. Willighagen, Rob Vreeken, Thomas Hankemeier and Theo Reijmers
07/2011
Metabolite identification

Quantitative profiling of oxylipins via comprehensive LC-MS/MS analysis: Application to patients undergoing cardiac surgery
Katrin Strassburg, Annemarie M.L. Huijbrechts, Kirsten Koortekaas, Jan Lindeman, Theresa L. Pedersen, John W. Newman, Adrie Dane, Ruud Berger, Thomas Hankemeier, John van Duynhoven, Eric Kalkhoven, Rob Vreeken
06/2011
Biomedical

Quantitative profiling of oxylipins via comprehensive LC-MS/MS analysis: Application to patients undergoing cardiac surgery
Katrin Strassburg, Annemarie M.L. Huijbrechts, Kirsten Koortekaas, Jan Lindeman, Theresa L. Pedersen, John W. Newman, Adrie Dane, Ruud Berger, Thomas Hankemeier, John van Duynhoven, Eric Kalkhoven, Rob Vreeken
06/2011
Biomedical

Simplivariate Models: Uncovering the Underlying Biology in Functional Genomics Data
Saccenti E, Westerhuis JA, Smilde AK, van der Werf MJ, Hageman JA, Hendriks MMWB
06/2011
Biostatistics

Between Metabolite Relationships: an essential aspect of metabolic change
Jeroen J. Jansen, Ewa Szymanska, Huub C.J. Hoefsloot, Doris M. Jacobs, Katrin Strassburg and Age K. Smilde
05/2011
Biostatistics

Untargeted metabolite discovery in kinetic data from multi-dose intervention studies
Peters, S., Janssen, H., Vivó-Truyols, G
05/2011
Nutrition & Health

Procyanidins in fruit from Sour cherry (Prunus cerasus) differ strongly in chainlength from those in Laurel cherry (Prunus lauracerasus) and Cornelian cherry (Cornus mas)

Capanoglu, E., Boyacioglu, D., De Vos, R.C.H., Hall, R.D., Beekwilder, J.
04/2011
Plant associate projects

Phaseguides: A paradigm shift in microfluidic priming and emptying
P. Vulto, S. Podszun, P. Meyer, C. Hermann, A. Manz, G. Urban
03/2011
Biomedical

Lab-on-a-chip technologies for massive parallel data generation in the life sciences: a tutorial review
S. Trietsch, H. van der Linden and Th. Hankemeier,
03/2011
Quantitative profiling

New figures of merit for comprehensive functional genomics data: the metabolomics case
Van Batenburg M.F., Coulier L., Van Eeuwijk F., Smilde A.K., and Westerhuis J.A.
03/2011
Biostatistics

On the increase of predictive performance with high-level data fusion
Doeswijk T.G., Smilde A.K., Hageman, J.A., Westerhuis J.A. and van Eeuwijk F.A.
03/2011
Plant associate projects

Crops and tasty, nutrtious food-How can metabolomics help?
Stewart D.W., Shepherd L.V.T., Hall R.D., Fraser P.D.
03/2011
Plant associate projects

Metabolomics of a model fruit: tomato.
De Vos, R.C.H., Hall, R.D., Moing, A.
03/2011
Plant associate projects

Plant Metabolomics in a nutshell
Hall, R.D.
03/2011
Plant associate projects

Biology of plant metabolomics.
Hall, R.D. (Ed.)
03/2011
Plant associate projects

Discovery of early-stage biomarkers for diabetic kidney disease using MS-based metabolomics (FinnDiane Study)
F. van der Kloet, F. Tempels, N. Ismail, R. van der Heijden, P. Kasper; M. Rojas Cherto, R. van Doorn, G. Spijksma, M. Koek, J. van der Greef, V.P. M„kinen, C. Forsblom, H.Holth”fer, P.H. Groop, T.H. Reijmers, T. Hankemeier
02/2011
Quantitative profiling

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
01/2011
Biostatistics

Genome-wide computational function prediction of Arabidopsis thaliana proteins by integration of multiple data sources.
Kourmpetis, Y. A. I., van Dijk, A. D. J., van Ham, R. C. H. J. and ter Braak, C. J. F.
01/2011
Plant associate projects

Plant Metabolomics and its Potential for Systems Biology Research: Background Concepts, Technology, and Methodology
Allwood J.W., De Vos R.C.H., Moing A., Deborde C., Erban A., Kokpa, J., Goodacre R., Hall, R.D.
01/2011
Plant associate projects

Measuring plant volatiles.
Verhoeven, H.A., Jonker, H., De Vos, R.C.H., Hall, R.D.
01/2011
Plant associate projects

Plant metabolomics, Methods and Protocols
Hardy, N.G. & Hall, R.D. (Eds)
01/2011
Plant associate projects

Extensive metabolic cross-talk in melon fruit revealed by spatial and developmental combinatorial metabolomics
Moing, Annick, Asaph Aharoni, Benoit Biais, Ilana Rogachev, Sagit Meir, Leonid Brodsky, J. William Allwood, Alexander Erban, Warwick B. Dunn, Lorraine Kay, Sjaak de Koning, Ric C.H. de Vos, Harry Jonker, Roland Mumm, Catherine Deborde, Michael Maucourt, St
01/2011
Plant associate projects

In-vivo D2O labeling in C57Bl/6 mice to quantify static and dynamic changes in cholesterol and cholesterol esters by high resolution LC mass-spectrometry
Castro-Perez JM, Previs SF, McLaren DG, Shah V, Herath K, Bhat G, Johns DG, Wang SP, Mitnaul L, Jensen K, Vreeken R, Hankemeier T, Roddy TP, Hubbard BK
01/2011
Biomedical

Sub-Typing of Rheumatic Diseases Based on a Systems Diagnosis Questionnaire
Herman A. van Wietmarschen, Theo H. Reijmers, Anita J. van der Kooij, Jan Schroen, Heng Wei, Thomas Hankemeier, Jacqueline J. Meulman, Jan van der Greef
01/2011
Biomedical

Polyphenol Identification Based on Systematic and Robust High-Resolution Accurate Mass Spectrometry Fragmentation Analytical Chemistry
J. van der Hooft, J. Vervoort, R. Bino and R. de Vos
12/2010
Metabolite identification

Gene Regulatory Networks from Multifactorial Perturbations Using Graphical Lasso: Application to the DREAM4 Challenge
Menendez, P., Kourmpetis, Y.A.I., ter Braak, C.J.F., van Eeuwijk, F.A.
12/2010
Plant associate projects

Human ultra-weak photon emission in relation to the 'Yin/ Yang' concept of Chinese Medicine
Van Wijk R, Van Wijk EPA, Van der Greef, J.
12/2010
Biomedical

Online capillary liquid-liquid electroextraction of peptides as fast pre-concentration prior to LC-MS
Lindenburg PW, Seitzinger R, Tempels FW, Tjaden UR, van der Greef J, Hankemeier T
11/2010
Biomedical

The DNA damage repair protein Ku70 interacts with FOXO4 to coordinate a conserved cellular stress response
Brenkman AB, van den Broek NJ, de Keizer PL, van Gent DC, Burgering BM
11/2010
Biomedical

Depletion zone isotachophoresis, a new micro/nanofluidic electrokinetic method
J. Quist, KGH Janssen, HJ. van der Linden, T. Hankemeier
11/2010
Biomedical

Multi-Stage Elemental Formula Tool for Metabolite Identification
M. Rojas Cherto
11/2010
Metabolite identification

The Effect of Industrial Food Processing on Potentially Health-Beneficial Tomato Antioxidants
Capanoglu, E. , Beekwilder, Jules , Boyacioglu, Dilek , De Vos, Ric C. H. and Hall, Robert D.
11/2010
Plant associate projects

Nutrikinetics

Velzen, E. van
11/2010
Nutrition & Health

Chip-based heaterless nano-API-MS
R.-J. Raterink, H. van der Linden and Th. Hankemeier
10/2010
Biomedical

Activation of forkhead box O transcription factors by oncogenic BRAF promotes p21cip1-dependent senescence.
de Keizer PL, Packer LM, Szypowska AA, Riedl-Polderman PE, van den Broek NJ, de Bruin A, Dansen TB, Marais R, Brenkman AB*, Burgering BM
08/2010
Biomedical

Chemometrics in analytical chemistry from an industrial perspective
R. Jellema, S. Krishnan
08/2010
Biomedical

Comparative Transcriptional Profiling and Preliminary Study on Heterosis Mechanism of Super-Hybrid Rice
Song GS, Zhai HL, Peng YG, Zhang L, Wei G, Chen XY, Xiao YG, Wang L, Chen YJ, Wu B, Chen B, Zhang Y, Chen H, Feng XJ, Gong WK, Liu Y, Yin ZJ, Wang F, Liu GZ, Xu HL, Wei XL, Zhao XL, Ouwerkerk PB, Hankemeier T, Reijmers T, Heijden RV, Lu CM, Wang M, Greef JV, Zhu Z.
08/2010
Biomedical

Deconvolution using signal segmentation
R. Jellema, S. Krishnan, M. Hendriks, B. Muilwijk, J. Vogels,
07/2010
Quantitative profiling

Carotenoid and Fatty Acid Metabolism in Light-Stressed Dunaliella salina
Lamers Packo P, Carlien C.W. van de Laak, Petrouchka S. Kaasenbrood, Jeroen Lorier, Marcel Janssen, Ric C.H. De Vos, Raoul J. Bino, Rene H. Wijffels
07/2010
Plant associate projects

Metabolic profiling of oxylipids at Netherlands Metabolomics Centre
Katrin Strassburg, Annemarie Huijbrechts, Arjan Brenkman, John Newman, Ruud Berger, Thomas Hankemeier, John van Duynhoven, Eric Kalkhoven, Rob Vreeken
06/2010
Quantitative profiling

Micro/nanofluidic preconcentrator for single cell metabolomics
J. Quist, KGH Janssen, HJ. van der Linden, T. Hankemeier
06/2010
Biomedical

An inter-laboratory comparison demonstrates that [H-1]-NMR metabolite fingerprinting is a robust technique for collaborative plant characterization and data collection.
Ward JL, Baker JM, Miller SJ, Deborde C, Maucourt M, Biais B, Rolin D, Moing A, Moco S, Vervoort J, Lommen A, Schafer H, Humpfer E, Beale MH.
06/2010
Metabolite identification

Metabolite identification pipeline based on MS fragmentation
M. Rojas Cherto
06/2010
Metabolite identification

Discovery of subtle effects in a human intervention trial through multilevel modeling
C.M. Rubingh, M.J. van Erk, S. Wopereis, T van Vliet, E.R. Verheij, N.H. Cnubbem, B. van Ommen, J. van der Greef and A.K. Smilde
06/2010
Biostatistics

Metabolic profiling of oxylipids at Netherlands Metabolomics Centre
Katrin Strassburg, Annemarie Huijbrechts, Arjan Brenkman, John Newman, Ruud Berger, Thomas Hankemeier, John van Duynhoven, Eric Kalkhoven, Rob Vreeken
06/2010
Nutrition & Health

Statistical analysis of the spontaneously emitted photon signals from palm and dorsal sides of both hands in human subjects
Van Wijk EP, Van Wijk R, Bajpai R, Van der Greef J.
06/2010
Biomedical

LC-MS-SPE-NMR for the Isolation and Characterization of neo-Clerodane Diterpenoids from Teucrium luteum subsp flavovirens
Castro A, Moco S, Coll J and Vervoort J.
05/2010
Metabolite identification

Production of novel antioxidative phenolic amides through heterologous expression of the plant's chlorogenic acid biosynthesis genes in yeast
Moglia A., Cominoa C., Lanteria S., de Vos R., de Waard P., van Beek T.A., Goitred L., Rettad S.F., Beekwilder J.
05/2010
Plant associate projects

Strategies to optimise the flavonoid content of tomato fruit
Bovy, A.G., Gomez-Roldan, V., Hall, R.D.
04/2010
Plant associate projects

Comprehensive LC-MS(E) Lipidomic Analysis using a Shotgun Approach and Its Application to Biomarker Detection and Identification in Osteoarthritis Patients
Castro-Perez JM, Kamphorst J, Degroot J, Lafeber F, Goshawk J, Yu K, Shockcor JP, Vreeken RJ, Hankemeier T
03/2010
Quantitative profiling

Stable Single Walled Carbon Nanotube-Streptavidin Complex for Bio-Recognition
Liu ZF., Galli F, Janssen, KGH, Jiang, LH, Van der Linden, HJ, De Geus, DC, Voskamp P, Kuil ME, Olsthoorn RCL, Oosterkamp TH, Hankemeier T, Abrahams JP
03/2010
Quantitative profiling

From QTL to candidate gene: Genetical genomics of simple and complex traits in potato using a pooling strategy
Kloosterman, B., M. Oortwijn, J. uitdeWilligen, T. America, R. de Vos, R.G.F. Visser & C.W.B. Bachem
03/2010
Plant associate projects

Using ultra-weak photon emission to determine the effect of oligomeric proanthocyanidins on oxidative stress of human skin.
Van Wijk EPA, Van Wijk R, Bosman S.
03/2010
Biomedical

Regulation of Treg functionality by acetylation-mediated Foxp3 protein stabilization
van Loosdregt J, Vercoulen Y, Guichelaar T, Gent YY, Beekman JM, van Beekum O, Brenkman AB, Hijnen DJ, Mutis T, Kalkhoven E, Prakken BJ, Coffer PJ
02/2010
Quantitative profiling

Insight in modulation of inflammation by gene, protein and metabolite profiling in mildly obese males: a human intervention study
M.J. van Erk, S.Wopereis, C.M. Rubingh, T. van Vliet, E.Verheij, N.H.P. Cnubben, T.L. Pedersen, J.W. Newman, A.K. Smilde, J. van der Greef, H.F.J. Hendriks and B. van Ommen
02/2010
Biostatistics

Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data
Kourmpetis Y.A.I, van Dijk A.D.J., Bink M.C.A.M., van Ham R.C.H.J., ter Braak C.J.F.
02/2010
Plant associate projects

Equating or Correction for Between-Block Effects with Application to Body Fluid LC-MS and NMR Metabolomics Data Sets
H. Draisma, T. Reijmers, F. van der Kloet, I. Bobeldijk-Pastorova, E. Spies-Faber, J. Vogels, J. Meulman, D. Boomsma, J. van der Greef, T. Hankemeier
01/2010
Biomedical

Acute and 2-week exposure to prednisolone impair different aspects of beta-cell function in healthy men
Van Raalte D.H., Nofrate V., Bunck M.C., Van Iersel T., Elassaiss Schaap J., Nassander U.K., Heine R.J., Mari A., Dokter W.H., Diamant M.
01/2010
Biomedical

Endocrine pulse identification using penalized methods and a minimum set of assumptions
D.J. Vis, J.A. Westerhuis, H.C.J. Hoefsloot, H. Pijl, F. Roelfsema, J. van der Greef, A.K. Smilde
01/2010
Biostatistics

The photographer and the greenhouse: how to analyze plant metabolomics data
J. J. Jansen, S. Smit, H.C.J. Hoefsloot and A.K. Smilde
01/2010
Biostatistics

Multivariate paired data analysis: Multilevel PLSDA versus OPLSDA
J.A. Westerhuis, E.J.J. van Velzen, H.C.J. Hoefsloot and A.K. Smilde
01/2010
Biostatistics

Dynamic Metabolomics Data Analysis: a Tutorial Review
A.K. Smilde, J.A. Westerhuis, H.C.J. Hoefsloot, S. Bijlsma, C.M. Rubingh, D.J. Vis, R.H. Jellema, H. Pijl, F. Roelfsema and J. van der Greef
01/2010
Biostatistics

Deconvolution using signal segmentation
Renger H. Jellema, Shaji Krishnan, Margriet M.W.B. Hendriks, Bas Muilwijk a, Jack T.W.E. Vogels
01/2010
Biostatistics

Plant molecular stress responses face climate change
Ahuja I., R.C.H. De Vos, A.M. Bones & R.D. Hall
01/2010
Plant associate projects

Biochemical and Molecular Analysis of Pink Tomatoes: Deregulated Expression of the Gene Encoding Transcription Factor S1MYB12 Leads to Pink Tomato Fruit Color
Ballester, A. R., Molthoff, J., de Vos, R C.H., Hekkert, B. T. L., Orzaez, D., Fernandez-Moreno, J. P., Tripodi, P., Grandillo, S., Martin, C., Heldens, J., Ykema, M., Granell, A., Bovy, A.
01/2010
Plant associate projects

A Role for Differential Glycoconjugation in the Emission of Phenylpropanoid Volatiles from Tomato Fruit Discovered Using a Metabolic Data Fusion Approach
Tikunov, Y. M., de Vos, R. C. H., Paramas, A. M. G., Hall, R. D., Bovy, A. G.
01/2010
Plant associate projects

Unusual optical properties of collagen and implications for the primo-vascular system.
Van Wijk EPA, Groeneveld M, Van der Greef J, Van Wijk R.
01/2010
Biomedical

Systems Biology-Based Diagnostic Principles as Pillars of the Bridge between Chinese and Western Medicine
Van der Greef J, van Wietmarschen H, Schro
01/2010
Biomedical

The Metabolic Fate of Red Wine and Grape Juice Polyphenols in Humans Assessed by Metabolomics
Dorsten, F. van Grün, C., Velzen, E., van, Jacobs, D., Draijer, R., Duynhoven, J. van
01/2010
Nutrition & Health

The metabolic fate of polyphenols in the human superorganism
Duynhoven, J. van, Vaughan, E., Jacobs, D, Kemperman, R., Velzen, E. van, Gross, G., Roger, R., Possemiers, S., Smilde, A., Doré, J., Westerhuis,J., Wiele T. van de
01/2010
Nutrition & Health

NMR-based metabonomics approaches for the assessment of the metabolic impact of dietary polyphenols on humans (2009Magnetic Resonance in Food Science
Duynhoven, J. van, Velzen, E. van, Gross, G., Dorsten, F. van, Jacobs, D., Bingham, M. Draijer, R., Mulder, T., Koning, T., Vaughan, E., Wiele, T van der, Westerhuis, J., Smilde, AS.
01/2010
Nutrition & Health

Food and Nutritional Science Applications of Magnetic Resonance

Duynhoven, J. van
01/2010
Nutrition & Health

Novel Approaches for Analysing Gut Microbes and Dietary Polyphenols, Challenges and Opportunities
Kemperman, R., Bolca, S., Roger, L., Vaughan, E
01/2010
Nutrition & Health

Trend analysis of time-series data: a novel method for untargeted metabolite discovery
Peters, S., Janssen, H., Vivó-Truyols, G.
01/2010
Nutrition & Health

Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies
Ommen,Ben van, Jildau Bouwman, Lars O. Dragsted, Christian A. Drevon, Ruan Elliott, Philip Groot, Jim Kaput, et al.
01/2010
Nutrition & Health

Peroxisome proliferator-activated receptor beta/delta (PPARbeta/delta) but not PPARalpha serves as a plasma free fatty acid sensor in liver
Sanderson LM, Degenhardt T, Koppen A, Kalkhoven E, Desvergne B, Mller M, Kersten S
12/2009
Biomedical

Reduced expression of ATP7B affected by Wilson disease-causing mutations is rescued by pharmacological folding chaperones 4-phenylbutyrate and curcumin
Peter V. E. van den Berghe, Janneke M. Stapelbroek, Elmar Krieger, Prim de Bie, Stan F. J. van de Graaf, Reinoud E. A. de Groot, Ellen van Beurden, Ellen Spijker, Roderick H. J. Houwen, Ruud Berger, and Leo W. J. Klomp
12/2009
Biomedical

Systems toxicology study of doxorubicin on rats using ultra performance liquid chromatography coupled with mass spectrometry based metabolomics
Wang J, Reijmers T, Chen L, Van Der Heijden R, Wang M, Peng, S, Hankemeier T, Xu G, Van Der Greef J.
12/2009
Metabolite identification

Characterization of Chinese Liquor Starter, "Daqu", by Flavor Type with H-1 NMR-Based Nontargeted Analysis
Wu XH , Zheng XW , Han BZ, Vervoort J, Nout MJR
12/2009
Metabolite identification

Crossfit analysis: a novel method to characterize the dynamics of induced plant responses
J.J. Jansen, N.M. van Dam, H.C.J. Hoefsloot and A.K. Smilde
12/2009
Biostatistics

Improved cholesterol phenotype analysis by a model describing how lipoprotein lifecycle processes depend on particle size
D.B. van Schalkwijk, B. van Ommen, K. van Bochove, P.C. Rensen, L.M. Havekes, N.C.A. van de Pas, A. de Graaf, H.C.J. Hoefsloot, J. van der Greef and A. Freidig
12/2009
Biostatistics

Topical formulation containing natural oligomeric proanthocyanidins (OPCS) reduces UV-induced oxidative stress in skin as assessed by ultra-weak photon emission (UPE)
Van Wijk EP, Bosman S, Achanta G, Van Wijk R.
12/2009
Biomedical

Functional implications of genetic variation in human PPARgamma
Jeninga EH, Gurnell M, Kalkhoven E
10/2009
Biomedical

Nuclear receptor-coregulator interaction profiling identifies TRIP3 as a novel peroxisome proliferator-activated receptor gamma cofactor?
Koppen A, Houtman R, Pijnenburg D, Jeninga EH, Ruijtenbeek R, Kalkhoven E.
10/2009
Quantitative profiling

RNAi-mediated transgenic Tospovirus resistance broken by intraspecies silencing suppressor protein complementation
Hassani-Mehraban A, Brenkman AB, van den Broek NJ, Goldbach R, Kormelink R
10/2009
Biomedical

Metabolomics data exploration guided by prior knowledge
R.A. van den Berg, C.M. Rubingh, J.A. Westerhuis, M.J. van der Werf and A.K. Smilde
10/2009
Biostatistics

Integrating functional genomics data using maximum likelihood based simultaneous component analysis
R.A. van den Berg, I. van Mechelen, T.F. Wilderjans, K. van Deun, H.A.L. Kiers and A.K. Smilde
10/2009
Biostatistics

Identification of a quality marker of the fermented off-note in coffee by a non-targeted chemometric approach
Lindinger, C, P. Pollien, R.C.H. de Vos, Y. Tikunov, J. A. Hageman, C. Lambot, R. Fumeaux, E. Voirol-Baliguet and I. Blank.
10/2009
Plant associate projects

Quality and safety of Chinese herbal medicines guided by a systems biology perspective
Jiangshan Wang, Rob van der Heijden, Shannon Spruit, Thomas Hankemeier, Kelvin Chan, Jan van der Greef, Guowang Xu, Mei Wang
10/2009
Biomedical

Systems biology guided by Chinese medicine reveals new markers for sub-typing rheumatoid arthritis patients.
Van Wietmarschen, H., Yuan, K., Lu, C., Gao, P., Wang, J, Xiao, C., Yan, X., Wang, M, Schro
10/2009
Biomedical

Non-Digestible Food Ingredients, Colonic Microbiota and the Impact on Gut Health and Immunity: A Role for Metabolomics
Jacobs, D., Gaudier, E., Duynhoven, J. van, Vaughan, E
10/2009
Nutrition & Health

Peroxisome proliferator-activated receptor gamma regulates expression of the anti-lipolytic G-protein-coupled receptor 81 (GPR81/Gpr81)
Jeninga EH, Bugge A, Nielsen R, Kersten S, Hamers N, Dani C, Wabitsch M, Berger R, Stunnenberg HG, Mandrup S, Kalkhoven E
09/2009
Biomedical

Analyzing longitudinal microbial metabolomics data
C.M. Rubingh, S. Bijlsma, R.H. Jellema, K.M. Overkamp, M.J. van der Werf, A.K. Smilde
09/2009
Biostatistics

Characterizing the precision of mass-spectrometry based metabolic profiling platforms
A.K. Smilde, M.J. van der Werf, C. Kistemaker and J.P. Schaller
09/2009
Biostatistics

Analytical strategies in lipidomics and applications in disease biomarker discovery
Hu C., Van der Heijden R., Wang M., Van der Greef J., Hankemeier T., Xu G.
09/2009
Biomedical

Tissue Selectivity in Multiple Endocrine Neoplasia Type 1-Associated Tumorigenesis
Ana Gracanin, Koen M. A. Dreijerink, Rob B. van der Luijt, Cornelis J. M. Lips and Jo W. M. Höppener
08/2009
Biomedical

Exploring the analysis of structured metabolomics data
M. Verouden, J.A. Westerhuis, M.J. van der Werf and A.K. Smilde
08/2009
Biostatistics

Developmental, genetic and environmental factors affect the expression of flavonoid genes, enzymes and metabolites in strawberry fruits
Carbone, F., Preuss, A., De Vos, R. C. H., D'Amico, E., Perrotta, G., Bovy, A. G., Martens, S., Rosati, C.
08/2009
Plant associate projects

The influence of adaptogens on ultraweak biophoton emission: a pilot experiment
Schutgens F.W.G., Neogi P., Van Wijk E.P.A., Van Wijk R., Wikman G., Wiegant F.A.C.
08/2009
Biomedical

Medullary thyroid carcinoma and biomarkers: past, present and future
W. van Veelen, J. W. B. de Groot, D. S. Acton, R. M. W. Hofstra, J. W. M. Hoppener, T. P. Links & C. J. M. Lips
07/2009
Biomedical

Characterization of rhamnosidases from Lactobacillus plantarum and Lactobacillus acidophilus
Jules Beekwilder, Daniela Marcozzi, Samuele Vecchi, Ric de Vos, Patrick Janssen, Christof Francke, Johan van Hylckama Vlieg and Robert D. Hall
06/2009
Plant associate projects

Systems toxiology study of doxorubicin on rats using ultra performance liquid chromatography coupled with mass spectrometry based metabolomics
Wang, J., Reijmers, T., Chen, L., Van der Hoeve, R., Wang, M., Peng, S., Hankemeier, T., Zu, G., Van der Greef, J.
05/2009
Biomedical

Automated procedure for candidate compound selection in GC-MS metabolomics based on prediction of Kovats retention index
Mihaleva VV, Verhoeven HA, de Vos RC, Hall RD, van Ham RC.
03/2009
Plant associate projects

Bioconversion of red ginseng saponines in the gastro-intestinal tract in-vitro model studied by high-performance liquid chromatography-high resolution Fourier transform ion cyclotron resonance mass spectrometry
Hongwei Kong, Mei Wang, Koen Venema, Annet Maathuis, Rob van der Heijden, Jan van der Greef , Guowang Xu and Thomas Hankemeier
03/2009
Biomedical

Alkaloid profiling of the Chinese herbal medicine Fuzi by combination of matrix-assisted laser desorption ionization mass spectrometry with liquid chromatography-mass spectrometry 4
Wang, J., van der, Heiden, R., Spijksma, G., Reijmers, T., Wang, M., Xu, G., Hankemeier, T., and van der Greef. J.
03/2009
Biomedical

Improving the analysis of designed studies by combining statistical modelling with study design information
U. Thissen, S.Wopereis, S.A.A. van den Berg, I.Bobeldijk, R. Kleemann, T. Kooistra, K.Willems van Dijk, B. van Ommen and A.K. Smilde
02/2009
Biomedical

Posttranslational modifications of PPAR-gamma: fine-tuning the metabolic master regulator
van Beekum O, Fleskens V, Kalkhoven E.
02/2009
Biomedical

Metabolic network discovery through reverse engineering of metabolome data
T. Cakir, M.M.W.B. Hendriks, J.A. Westerhuis and A.K. Smilde
02/2009
Biostatistics

Metabolic profiling of the response to an oral glucose tolerance test detects subtle metabolic changes
S. Wopereis, C.M. Rubingh, M.J. van Erk, E.R Verheij, T. van Vliet, N.H.P. Cnubben, A.K Smilde, J. van der Greef, B. van Ommen, and H.F.J. Hendriks
02/2009
Biostatistics

More than a grain of rice: the quest for quality
Fitzgerald, M.E., Mccouch, S., Hall, R.D.
02/2009
Plant associate projects

Biophoton detection and low-intensity light therapy: A potential clinical partnership
Tafur J., Van Wijk E.P.A., Van Wijk R., Mills P.
02/2009
Biomedical

Multiset Data Analysis: ANOVA Simultaneous Component Analysis and Related Methods.
H. C. J. Hoefsloot, D. J. Vis, J. A. Westerhuis, A. K. Smilde, and J. J. Jansen
02/2009
Biostatistics

Analytical strategies in lipidomics and applications in disease biomarker discovery.
Hu C, van der Heijden R, Wang M, van der Greef J, Hankemeier T, Xu G
01/2009
Biomedical

Feasibility of electrodialysis as a fast and selective sample preparation method for the profiling of low-abundant peptides in biofluids
Kamphorst JJ, Tjaden UR, van der Heijden R, DeGroot J, van der Greef J, Hankemeier T
01/2009
Biomedical

Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research
Scalbert A, Brennan L, Fiehn O, Hankemeier T, Kristal BS, van Ommen B, Pujos-Guillot E, Verheij E, Wishart D, Wopereis S
01/2009
Biomedical

P18 is a tumor suppressor gene involved in human medullary thyroid carcinoma and pheochromocytoma development
Wendy van Veelen , Rob Klompmaker , Martijn Gloerich, Carola J.R. van Gasteren, Eric Kalkhoven, Ruud Berger, Cornelis J.M. Lips, Rene H. Medema, Jo W.M. Hoppener and Dennis S. Acton
01/2009
Biomedical

Analytical error reduction using single point calibration for accurate and precise metabolomic phenotyping
F. van der Kloet, I. Bobeldijk, E. Verheij, R. Jellema,
01/2009
Biomedical

Plant Micrometabolomics: The Analysis of Endogenous Metabolites Present in a Plant Cell or Tissue
Moco S, B Schneider, J Vervoort
01/2009
Metabolite identification

Regression by L1 regularization of smart contrasts and sums (ROSCAS) beats PLS and elastic net in latent variable model
Ter Braak C. J. F.
01/2009
Plant associate projects

Fruit-Surface Flavonoid Accumulation in Tomato Is Controlled by a SlMYB12-Regulated Transcriptional Network
Avital Adato, Tali Mandel, Shira Mintz-Oron, Ilya Venger, Dorit Levy, Merav Yativ, Eva Dominguez, Zhonghua Wang, Ric C. H. De Vos, Reinhard Jetter, Lukas Schreiber, Antonio Heredia, Ilana Rogachev, Asaph Aharoni
01/2009
Plant associate projects

Metabolomic and genetic analyses of flavonol synthesis in Arabidopsis thaliana support the in vivo involvement of leucoanthocyanidin dioxygenase
Ralf Stracke, Ric C. H. De Vos, Lutz Bartelniewoehner, Hirofumi Ishihara, Martin Sagasser, Stefan Martens and Bernd Weisshaar
01/2009
Plant associate projects

System-wide molecular evidence for phenotypic buffering in Arabidopsis
Jingyuan Fu, Joost J B Keurentjes, Harro Bouwmeester, Twan America, Francel WA Verstappen, Jane L Ward, Michael H Beale, Ric C H De Vos, Martijn Dijkstra, Richard A Scheltema, Frank Johannes, Maarten Koornneef, Dick Vreugdenhil, Rainer Breitling & Ritsert C Jansen
01/2009
Plant associate projects

The effect of environmental conditions on extracellular protease activity in controlled fermentations of Aspergillus niger
M. Braaksma, A.K. Smilde, M.J. van der Werf and Peter J. Punt
01/2009
Industrial biotechnology

Separation and identification of malonyl-ginsenosides in white ginseng using HPLC-LTQ-FTMS
Hongwei Kong, Mei Wang, Rob van der Heijden, Jan van der Greef , Thomas Hankemeier and Guowang Xu
01/2009
Biomedical

Commentary: "A systems view on the future of medicine: Inspiration from Chinese medicine?"
Verpoorte, R., Crommelin, D., Danhof, M., Gilissen, L. J. W. J., Schuitmaker, H., van der Greef, J., and Witkamp, R. F.
01/2009
Biomedical

NMR-based metabonomics approaches for the assessment of the metabolic impact of dietary polyphenols on humans
Duynhoven, J.P.M. van, Velzen, E.J.J. van, Gross, G., Dorsten, F.A. van, Westerhuis, J.A. & Smilde, A.K.
01/2009
Biostatistics

Parameter selection for peak alignment in chromatographic sample profiling: objective quality indicators and use of control samples
Peters, S., Velzen, E. van, Janssen, H.G.
01/2009
Nutrition & Health

Phenotyping tea consumers by nutrikinetic analysis of polyphenolic end-metabolites
Velzen, E. van, Westerhuis, J., van Duynhoven, J., van Dorsten, F., Jacobs, D., Gruen, C., Duchateau, G., Vis, D., Smilde, A
01/2009
Nutrition & Health

Multivariate paired data analysis: Multilevel PLSDA versus OPLSDA
Westerhuis J.A., Velzen E.J.J. van, Hoefsloot H.C.J., Smilde A.K.
01/2009
Nutrition & Health

Solution Titration by Wall Deprotonation During Capillary Filling of Silicon Oxide Nanochannels
Janssen KGH, Hoang HT, ,Floris J, De Vries J, Tas NR, Eijkel JCT, Hankemeier T
11/2008
Quantitative profiling

Exploring and exploiting carotenoid accumulation in Dunaliella salina for cell-factory applications
Packo P. Lamers, Marcel Janssen, Ric C.H. De Vos, Raoul J. Bino and Rene H. Wijffels
11/2008
Plant associate projects

Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors
Butelli, E., TIitta, L., Georgio, M., Mock, H-P.,Matros, A., Peterek, S., Schijlen, E.G.W.M., Hall, R.D., Bovy, A.G., Martin, C.A.
11/2008
Plant associate projects

RPLC-FTMS Method for Lipid Profiling of Plasma: Method Validation and Application to p53 mutant Mouse Model
Hu C., VAn Dommelen J., Van der Heijden R., Spijksma G., Reijmers T.H., Wang M., Xu G., Slee E., Lu X., Van der Greef J., Hankemeier T.
10/2008
Biomedical

The peptidyl-isomerase Pin1 regulates p27Kip1 expression through inhibition of FOXO tumorsuppressors.
Brenkman AB, de Keizer PLJ, van den Broek NJF, van der Groep P, van Diest PJ, van der Horst A, Smits AMM, Burgering BMT
09/2008
Biomedical

Lipodomic approach to evaluate rosuvastatin and atorvastatin at various dosages: investigating defferential effects among statins
Bergheanu S.C., Reijmers T., Zwinderman A.H., Bobeldijk I., Ramaker R., Liem A.H., Van der Greef J., Hankemeier T., Jukema J.W.
08/2008
Biomedical

Multilevel data analysis of a cross-over designed human nutritional study
E.J.J. van Velzen, J.A. Westerhuis, J.P.M. van Duynhoven, F.A. van Dorsten, H.C.J. Hoefsloot, D.M. Jacobs, S. Smit, R. Draijer, C.I. Kroner and A.K. Smilde
08/2008
Biostatistics

Discriminant Q2 (DQ2) statistic for improved discrimination in PLSDA models
J.A. Westerhuis, E.J.J. van Velzen, H.C.J. Hoefsloot and A.K. Smilde
08/2008
Biostatistics

Predicting sub-Golgi localization of type ii membrane proteins
Van Dijk, A. D. J., Bosch, D., ter Braak, C. J. F., van der Krol, A. R. and van Ham, R. C. H. J.
08/2008
Plant associate projects

Stress-induced biosynthesis of dicaffeoylquinic acids in globe artichoke
Moglia A, Lanteri S, Comino C, Acquadro A, de Vos R, Beekwilder J.
08/2008
Plant associate projects

The geometry of ASCA
A.K. Smilde, H.C.J. Hoefsloot and J.A. Westerhuis
07/2008
Biostatistics

Flavour metabolomics - Holistic versus targeted profiling in flavour research
De Vos, R.C.H., Y. Tikunov, A.G. Bovy & R.D. Hall.
07/2008
Plant associate projects

Coffee chemometrics as a new concept: Untargeted metabolic profiling of coffee
Lindinger, C., R.C.H De Vos, C. Lambot, P. Pollien, A. Rytz, E. Voirol-Baliguet, R. Fumeaux, F. Robert, C. Yeretzian & I. Blank
07/2008
Plant associate projects

The impact of the absence of aliphatic glucosinolates on insect herbivory in Arabidopsis.
Beekwilder, J., Van Leeuwen, W., Van Dam, N.M., Bertossi, M., Grandi, V., Mizzi, L., Soloviev, M., Szabados, L., Molthoff, J.W., Schipper, B., Verbocht, H., De Vos, R.C.H., Morandini, P., Aarts, M.G.M., Bovy, A.G.
04/2008
Plant associate projects

Comprehensive analysis of the metabolome of Pseudomonas putida S12 grown on different carbon sources
Van der Werf MJ, Overkamp KM, Muilwijk B, Koek MM, van der Werff-van der Vat BJ, Jellema RH, Coulier L, Hankemeier T
04/2008
Industrial biotechnology

Similarities and differences in lipidomics profiles among healthy monoygotic twin pairs
Draisma H.H.M., Reijmers T.H., Bobeldijk-Pastorova I., Meulman J.J., Estourgie-van Burk G.F., Bartels M., Ramaker R., Van der Greef J., Boomsma D.I., Hankemeier T.
03/2008
Biomedical

Higher mass loadability in GCxGC-MS: improved analytical performance for metabolomics analysis
Koek M, Muilwijk B, Van Stee LLP, Hankemeier T
01/2008
Biomedical

Parafasca: ASCA combined with Parafac for the analysis of metabolic fingerprinting data
J.J. Jansen, R. Bro, H.C.J. Hoefsloot, F.W.J. van den Berg, J.A. Westerhuis and A.K. Smilde
01/2008
Biostatistics

Assessment of PLSDA cross validation
J.A. Westerhuis, H.C.J. Hoefsloot, S. Smit, D.J. Vis, A.K. Smilde, E.J.J. van Velzen, J.P.M. van Duijnhoven and F.A. van Dorsten
01/2008
Biostatistics

Simplivariate models: ideas and first results
J.A. Hageman, M.M.W.B. Hendriks, J.A. Westerhuis, M.J. van der Werf, R. Berger and A.K. Smilde
01/2008
Biostatistics

Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control
Van Dijk, A.D.J., ter Braak, C.J.F. Immink, G..H., Angenent, G.C., van Ham, R.C.H.J.
01/2008
Plant associate projects

Bootstrap Confidence Intervals for Principal Response Curves
Timmerman, M. E. & ter Braak, C. J. F.
01/2008
Plant associate projects

Plant metabolomics applications in the Brassicaceae: added value for science and industry
Hall, R.D., De Vos, R.C.H., Ward, J.L.
01/2008
Plant associate projects

Tomato strigolactones are derived from carotenoids and their biosynthesis is promoted by phosphate starvation
Juan Antonio L
01/2008
Plant associate projects

Accurate mass error correction in liquid chromatography time-of-flight mass spectrometry based metabolomics
Mihaleva, V.V., Vorst, O., Maliepaard, C., Verhoeven, H.A., De Vos, C.H.R., Hall, R.D., van Ham, R.C.H.J.
01/2008
Plant associate projects

Plant metabolomics and its potential for human nutrition
Hall, R.D., Brouwer, I., Fitzgerald, M.E.
01/2008
Plant associate projects

Boosting beneficial phytochemicals in vegetable crop plants
Schijlen, E.G.W.M., Beekwilder, J., Hall, R.D., van der Meer, I.M.
01/2008
Plant associate projects

Changes in Antioxidant and Metabolite Profiles during Production of Tomato Paste
Esra Capanoglu, Jules Beekwilder, Dilek Boyacioglu, Robert Hall and Ric de Vos
01/2008
Plant associate projects

Antioxidants, Phenolic Compounds, and Nutritional Quality of Different Strawberry Genotypes
Tulipani S, Mezzetti B, Capocasa F, Bompadre S, Beekwilder J, De Vos RCH, Capanoglu E, Bovy A, Battino M.
01/2008
Plant associate projects

Plant Metabolomics and its potential for human nutrition
Hall, R.D., Brouwer, I., Fitzgerald, M.E.
01/2008
Plant associate projects

1H NMR metabolite profiling of faeces as a tool to assess the impact of nutrition on the human microbiome
Jacobs, D., Deltimple, N., Velzen, E. van, Bingham, M., Vaughan, E., Bingham, M., Duynhoven, J
01/2008
Nutrition & Health

GC–MS methods for metabolic profiling of microbial fermentation products of dietary polyphenols in human and in vitro intervention studies
Grun, C., Dorsten, F. van, Jacobs, D., Le Belleguic, M., Velzen, E. van, Bingham, M., Janssen, H.G., Duynhoven, J. van
01/2008
Nutrition & Health

Multilevel data analysis of a human nutritional crossover designed study
Velzen, E. van, Westerhuis, J, Duynhoven, J. van Dorsten, F. van, Hoefsloot, H., Smit, S., Draijer, R., Kroner, C.I., Smilde, A.K.
01/2008
Nutrition & Health

Assessment of PLSDA crossvalidation
Westerhuis, J., Hoefsloot, H., Smit, S., Vis, D., Smilde, A., Velzen, E. van, Duynhoven, J. van, Dorsten, F. van
01/2008
Nutrition & Health

The metabolic fate of polyphenols in the human superorganism
J. van Duynhoven, E.E. Vaughan, D. Jacobs, R. Kemperman, E.J.J. van Velzen, G. Gross, L. Roger, S. Possemiers, A.K. Smilde, J. Dore, J.A. Westerhuis and T. van der Wiele
06/2007
Biostatistics

Chemical identification strategies by liquid chromatography (LC)-photo diode array (PDA)-solid phase extraction (SPE)-nuclear magnetic resonance (NMR) / mass spectrometry (MS).
Moco S and Vervoort J
01/2007
Metabolite identification

Production of novel antioxidative phenolic amides through heterologous expression of the plant?s chlorogenic acid biosynthesis genes in yeast
Moglia Andrea, Cinzia Cominoa, Sergio Lanteria, Ric de Vos, Pieter de Waard, Teris A. van Beek, Luca Goitred, Saverio Francesco Rettad, Jules Beekwilder
01/2007
Plant associate projects

C3?H Isolation and mapping of a C3'H gene (CYP98A49) from globe artichoke, and its expression upon UV-C stress.
Moglia A, Comino C, Portis E, Acquadro A, De Vos RC, Beekwilder J, Lanteri S.
01/2007
Plant associate projects

In vitro bioconversion of polyphenols from black tea and red wine/grape juice by human intestinal microbiota displays strong inter-individual variability
Gross, G., Jacobs, D., Peters, S., Possemiers, S., van Duynhoven, J., Vaughan, E., Van de Wiele, T
01/2007
Nutrition & Health

Rapid and validated NMR quantification approaches for complex metabolite mixtures
Braganti, B., Peters, S., Jacobs, D., Eymond, T., Klinkenberg, M., Duynhoven, J. van
01/2007
Nutrition & Health

Towards identification of polyphenol metabolites in biofluids by SPE-LC-MS-SPE-NMR
Klinkenberg, M., Roo, N., Alexandre, P., Mahlous, I., Jacobs, D., Janssen, H., Duynhoven, J. van
01/2007
Nutrition & Health

Response of green tea extract on human metabolism at rest and during moderate intensity exercise
Hodgson, A., Randell, R., Fuhrmann, J.C., Rennefahrt, U., Garczarek, U., Jeukendrup, A., Jacobs, D.
01/2007
Nutrition & Health

Health space visualization and identification of personalized molecular phenotype and treatment responses according to the underlying relevant biological processes
Jildau Bouwman, Jack T.W.E. Vogels, Suzan Wopereis, Carina M. Rubingh, Sabina Bijlsma, Ben van Ommen
01/2007
Nutrition & Health

Practical applications of metabolomics in plant biology
Hall, R.D., Hardy, N.G.
Plant associate projects