publications 2013-2010

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Publications 2013

Nelson Lee Afanador, T.N. Tran, L.M.C. Buydens
Use of the bootstrap and permuation methods for a more robust variable importance in the projection metric for partial least squares regression.
Analytica Chimica Acta, 768, 49-56 

C. Ruckebusch and L. Blanchet 
Multivariate Curve Resolution: Advanced and Tailored Applications, Challenges
Analytica Chimica Acta, 765 (2013) 28- 36, 2013 

M. Kounelakis, M. Zervakis, G. Giakos, G. Postma, L. Buydens, X. Kotsiakis 
On the Relevance of Glycolysis Process on Brain Gliomas
IEEE Journal of Biomedical and Health Informatics17 (1), 128-135

Jeroen J. Jansen, L. Blanchet, L.M.C. Buydens
Theory of Chemometrics
Metabonews, issue 18, February 2013

E. Szymanska
Why isn't Chemometrics Center Stage?
The Analytical Scientist, issue 0313, March 2013

T.M. Fortuna, J.B. Woelke, C.A. Hordijk, J.J. Jansen, N.M. van Dam, L.E.M. Vet, J.A. Harvey.
A tritrophic approach to the preference-performance hypothesis involving an exotic and a native plant.
Biological Invasions, 15(11), 2387-2401

Tone Frost Bathen, Brigitte Geurts, Beathe Sitter, Hans E Fjøsne, Steinar Lundgren, Lutgarde Buydens, Ingrid S Gribbestad, Geert Postma, Guro F Giskeødegård
Feasibility of MR metabolomics for immediate analysis of resection margins during breast cancer surgery.
PloS one, 8(4), 1-17

Tom Bloemberg
New Warping and Multivariate Analysis Methodologies for Complex Proteomic and Metabolomic Data 
PhD thesis, May 7, 2013

Tom Bloemberg, Jan Gerretzen, Anton Lunshof, Ron Wehrens, Lutgarde Buydens
Warping Methods for Spectroscopic and Chromatographic Signal Alignment: A Tutorial.
Analytica Chimica Acta, 781, (2013) 14-32 

Tom O.G. Tytgat, K.J.F. Verhoeven, J.J. Jansen, C.E. Raaijmakers, T. Bakx-Schotman, L.M. McIntyre, W.H. van der Putten, A. Biere, N.M. van Dam
Plants Know where it Hurts. Root and Shoot Jasmonic Acid Induction Elicit Differential Responses in Brassica oleracea.
PLoS One, 8(6)

Jan Andries, Yvan Vander Heyden ,Lutgarde Buydens
Predictive-Property-Ranked Variable Reduction with Final Complexity Adapted Models in Partial Least Squares Modelling for Multiple Responses
Analytical Chemistry 2013, 85, 5444-5453

Jasper Engel; Jan Gerretzen; Ewa Szymanska, Jeroen J Jansen, Gerard Downey, Lionel Blanchet, Lutgarde Buydens,
Breaking with trends in pre-processing?
TrAC 50, 96-106

Vebjorn Ljosa, Peter D. Caie, Rob ter Horst, Katherine L. Sokolnicki, Emma L. Cooke, Sandeep Daya, Mark E. Roberts, Thouis R. Jones, Paul A. Clemons, Neil. O. Carragher, Anne E. Carpenter
Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment.
Journal of Biomolecular ScreeningSeptember 17, 2013

Nikola Dordevic, F. Camin, M.R. Marianella, G.J. Postma, L.M.C. Buydens, R. Wehrens
Detecting the addition of sugar and water to wine
Australian Journal of Grape and Wine Research, 19 (3), 324-330

Lutgarde Buydens
Towards Tsunami-Resistant Chemometrics
The Analytical Scientist, nr. 813 (pdf, 710 kB), 24-30. Cover Article

Stijn F.M. van Dongen, J. Clerx, K. Norgaard, T. G. Bloemberg, J. J. L.M. Cornelissen, M. A. Trakselis, S. W. Nelsson, S.J. Benkovic, A. E. Rowan ,R. J.M. Nolte
A clamp-like biohybrid catalyst for DNA oxidation
Nature Chemistry, 5(11), 945-951

Luisa Amo, Jeroen J. Jansen, Nicole van Dam, Marcel Dicke & Marcel E. Visser
Birds exploit herbivore-induced plant volatiles to locate herbivorous prey 
Ecology Letters,16(11), 1348-1355

Brigitte Geurts
Personalized health: the doctor is watching you
Volonté Générale, nr. 3 (docx, 20 kB), 6-9. aug.2013

Smeenk, N.J., Engel, J., Mulder, P., Bauhuis, G.J., Bissels,G., Schermer, J.J., Vlieg, E. & Kelly, J.J.
Arsenic formation on GaAs during etching in HF Solutions: relevance for the epitaxial Lift-off process. 
Ecs Journal of Solid State Science & Technology, 2(3), 58-65

Vartika Mathur, Tom O. G. Tytgat, Cornelis A. Hordijk, Harry R. Harhangi, Jeroen J. Jansen, A. Sankara Reddy, Jeffrey A. Harvey, Louise E. M. Vet and Nicole M. van Dam
An ecogenomic analysis of herbivore induced plant volatiles in Brassica juncea
Molecular Ecology 22(24), 6179-6196

Beers, J.J. van, Willemze, A., Jansen, J.J., Engbers, G.H., Salden, M., Raats, J., Drijfhout, J.W., Mil, A.H. van der Helm-van, Toes, R.E. & Pruijn, G.J.
ACPA fine-specificity profiles in early rheumatoid arthritis patients do not correlate with clinical features at baseline or with disease progression. 
Arthritis Research & Therapy, 15(5), R140

Publications 2012

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Jeroen J. Jansen, Ewa Szymańska, Huub C. J. Hoefsloot and Age K. Smilde
Individual differences in metabolomics: individualised responses and between-metabolite relationships 
Metabolomics, 8 (1): p. 94-104

Jeroen J. Jansen, Johan A. Westerhuis
Editorial - Data analysis in metabolomics 
Metabolomics, 8 (1): p. 1-2

Agnieszka Smolinska, Joram Posma, Lionel Blanchet, Kirsten Ampt, Amos Attali, Tinka Tuinstra, Theo Luider, Marek Doskocz, Paul J. Michiels, Frederic C. Girard, Lutgarde M.C. Buydens, and Sybren S. Wijmenga
Simultaneous analysis of plasma and CSF by NMR and Hierarchical Model Fusion
Analytical and Bioanalytical Chemistry,  403 (4,), 947-959

Jasper Engel, Lionel Blanchet, Lutgarde Buydens, Gerard Downey
Confirmation of brand identity of a Trappist beers by mid-infrared spectroscopy coupled with multivariate data analysis
Talanta, 99 (1), 426-432

Alain J van Gool and Ronald C Hendrickson 
The proteomic toolbox for studying cerebrospinal fluid
Expert Review of Proteomics, 9( 2), 165-179

Patrick W. T. Krooshof, Geert J. Postma, Willem J. Melssen, Lutgarde M. C. Buydens
Evaluation of Spectroscopic Images 
In:Biomedical Imaging: Principles and Applications, 2012, 1-29

Agnieszka Smolinska, Lionel Blanchet, Leon Coulier, Kirsten A. M. Ampt, Theo Luider, Rogier Q. Hintzen, Sybren S. Wijmenga, Lutgarde M. C. Buydens
Interpretation and visualization of non-linear data fusion in kernel space: study on metabolomic characterization of progression of Multiple Sclerosis
PLoS one 7 (6): e38163

Marcel P. Stoop, Therese Rosenling, Amos Attali, Roland J. W. Meesters, Christoph Stingl, Lennard J. Dekker, Hans van Aken, Ernst Suidgeest, Rogier Q. Hintzen, Tinka Tuinstra, Alain van Gool, Theo M. Luider, and Rainer Bischoff
Minocycline Effects on the Cerebrospinal Fluid Proteome of Experimental Autoimmune Encephalomyelitis Rats
J. Proteome Res., 11 (8), 4315-4325

Hans J.C.T. Wessels, Tom G. Bloemberg, Maurice van Dael, Ron Wehrens, Lutgarde M.C. Buydens, Lambert P. van den Heuvel, Jolein Gloerich 
A comprehensive full factorial LC-MS/MS proteomics benchmark dataset.
Proteomics, 12 (14), 2237-2400

A. Smolinska
Chemometrics and NMR spectroscopy for metabolomics analysis of neurological disorders.
PhD Thesis. Nijmegen, August 28, 2012

C.C. Yde, J.J. Jansen, P. K.Theil, H.C. Bertram, K.E.B. Knudsen
Different metabolic and absorption patterns of betaine in response to dietary intake of whole-wheat grain, wheat aleurone or rye aleurone in catheterized pigs
European Food Research and Technology, 235 (5), 939-949, 2012

A. Smolinska, L. Blanchet, L. M. C. Buydens,S. Wijmenga
NMR and pattern recognition methods in metabolomics: From data acquisition to biomarker discovery: A review
Analytica Chimica Acta, 750, 82-97
Nikola Dordevic, Ron Wehrens, Geert J Postma, Lutgarde M C Buydens,Federica Camin
Statistical methods for improving verification of claims of origin for Italian wines based on stable isotope ratios
Analytica Chimica Acta, 757, 19-25

Guro F. Giskeødegård, Steinar Lundgren, Beathe Sitter, Hans E. Fjøsne, Geert Postma, Lutgarde M. C. Buydens, Ingrid S. Gribbestad, Tone F. Bathen
Lactate and glycine-potential MR biomarkers of prognosis in estrogen receptor-positive breast cancers
NMR in Biomedicine, 25 (11), 1271-1279

J. Andries, Yvan vander Heijden, Lutgarde Buydens
Predictive-Property-Ranked Variable Reduction in Partial Least Squares Modelling with Final Complexity Adapted Models: Comparison of Properties for Ranking
Analytica Chimica Acta, 760, 34-45, 2012 

Publications 2011

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Jorn de Haan
Improvements in the analysis of microarray data
PHD-Thesis, february 10, 2011

Alberto Mezzetti, Lionel Blanchet, Anna de Juan, Winfried Leibl and Cyril Ruckebusch
Ubiquinol formation in isolated photosynthetic reaction centres monitored by time-resolved differential FTIR in combination with 2D correlation spectroscopy and multivariate curve resolution 
Analytical and Bioanalytical Chemistry, 399 (6),1999-2014

G.J. Postma, J. Luts, A.J. Idema, M. Julià-Sapé, Á. Moreno-Torres, W. Gajewicz, J. Suykens, A. Heerschap, S. Van Huffel, L.M.C. Buydens. 
On the relevance of automatically selected single voxel MRS and multimodel MRI and MRSI features for brain tumor differentiation.
Computers in Biology and Medicine 41 (2011),  87-97 

Tom G. Bloemberg, Hans J. C. T. Wessels, Maurice van Dael, Jolein Gloerich, Lambert P. van den Heuvel, Lutgarde M.C. Buydens, Ron Wehrens. 
Pinpointing Biomarkers in Proteomic LC/MS Data by Moving-Window Discriminant Analysis. 
Analytical Chemistry 83 (13), 5197-5206, 2011 

G.J. Postma, P.W.T. Krooshof, L.M.C. Buydens
Opening the Kernel of Kernel Partial Least Squares and Support Vector Machines
Analytica Chimica Acta 705 (1-2),123-134

Lionel Blanchet, Agnieszka Smolinska, Amos Attali, Marcel Stoop, Kirsten Ampt, Hans van Aken, Ernst Suidgeest, Tinka Tuinstra, Syben S Wijmenga, Theo Luider and Lutgarde MC Buydens
Fusion of metabolomics and proteomics data for biomarkers discovery: case study on the experimental autoimmune encephalomyelitis
BMC Bioinformatics 12:254, June 2011 

Jan P.M. Andries, Yvan Vander Heyden, Lutgarde M.C. Buydens
Improved Variable Reduction in PLS modelling based on Predictive-Property-Ranked Variables and adaptation of PLS complexity
Analytica Chimica Acta 705 (1-2), 292-305 

A. van Gool
Progressing biomarkers from basic discovery to companion diagnostics. Conference Proceedings "Biomarkers in Diagnostics & Therapeutics", Singapore, January 24-25 2011
Pharmacogenomics 12(6), 779-781

Agnieszka Smolinska, Amos Attali, Lionel Blanchet, Kirsten Ampt, Hans van Aken, Ernst Suidgeest, Tinka Tuinstra, Alain van Gool, Theo Luider, Sybren Wijmenga and Lutgarde Buydens
NMR and pattern recognition can distinguish neuroinflammation and peripheral inflammation
Journal of Proteome Research 10 (10), 4428-4438

M.G. Kounelakis, M.E. Zervakis, G.C. Giakos, G.J.Postma, L.M.C. Buydens and X. Kotsiakis
Embedding filtering criteria into a wrapper marker selection method for brain tumor classification: an application on metabolic peak area ratios
Measurement Science and Technology, 22 114019

Guangmei Yan, Guojie Zhang, Xiaodong Fang, Yanfeng Zhang, Cai Li, Fei Ling, David N Cooper, Qiye Li, Yan Li, Alain J van Gool, Hongli Du, Jiesi Chen, Ronghua Chen, Pei Zhang, Zhiyong Huang, John R Thompson, Yuhuan Meng, Yinqi Ba, Jufang Wang, Min Zhuo, Tao Wang, Ying Huang, Liqiong Wei, Jianwen Li, Zhiwen Wang, Haofu Hu, Pengcheng Yang, Liang Le, Peter D Stenson, Bo Li, Xiaoming Liu, Edward V Ball, Na An, Quanfei Huang, Yong Zhang, Wei Fan, Xiuqing Zhang, Yingrui Li, Wen Wang, Michael G Katze, Bing Su, Rasmus Nielsen, Huanming Yang, Jun Wang, Xiaoning Wang & Jian Wang
Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques
Nature Biotechnology Letters 29, p.1019-1023

S.M. Cristescu, H.A. Gietema, L. Blanchet, C.L.J.J.Kruitwagen, P. Munnik, R.J. van Klaveren, J.W.J. Lammers, L.M.C. Buydens, F.J.M. Harren and P.Zanen
Screening for emphysema via exhaled volatile organic compounds
Journal of Breath Research 5, 046009

Alan J.Wright, Lutgarde M. C. Buydensand Arend Heerschap
A Phase and Frequency Alignment Protocol for Prostate Cancer MRSI Data Sets.
NMR in biomedicine,  25 (5), 755-765

Therese Rosenling, Marcel P. Stoop, Agnieszka Smolinska, Bas Muilwijk, Leon Coulier, Shanna Shi, Adrie Dane, Christin Christin, Frank Suits, Peter L. Horvatovich, Sybren Wijmenga, Lutgarde Buydens, Rob Vreeken, Thomas Hankemeier, Alain J. van Gool, Theo M. Luider, Rainer Bischoff
The impact of delayed storage on the proteome and metabolome profile of human cerebrospinal fluid (CSF)
Clinical Chemistry 2011; 57, 1703-1711

Lionel Blanchet, Lutgarde M.C. Buydens, Jan A.M. Smeitink, Peter H.G.M. Willems and Werner J.H. Koopman
Isolated mitochondrial complex I deficiency: Explorative data analysis of patient cell parameters 
Current Pharmaceutical Design 17(36):4023-33.

Gool, A. van 
Trends, challenges and opportunities of Biomarkers in Translational Medicine
Asia Pacific BioTech News, August 2011 Featured article 

Publications 2010

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R. Wehrens 
Self-organising maps for image segmentation 
In: Advances in Data Analysis, Data Handling and Business Intelligence. A. Fink, B. Lausen, W. Seidel and A. Ultsch (Eds.) 
Springer-Verlag, Berlin Heidelberg 2010

I. Stanimirova, B. Üstün, T. Èajka, K. Riddellova, J. Hajšlová, L.M.C. Buydens, B. Walczak 
Tracing the geographical origin of honeys based on volatile compounds profiles assessment using pattern recognition techniques 
Food Chemistry, 118, Issue 1: 171-176 

J.R. de Haan, E. Piek, R. Wehrens, R.C. van Schaik, S. Bauerschmidt and L.M.C. Buydens
Beyond single p-value cutoffs: Methods to improve decision making in GO enrichment analysis of microarray experiments 
Online Journal of Bioinformatics, 11 (1): 1-18, 2010 

Ester Piek, Laura S. Sleumer, Eugene P. van Someren, Leonie Heuver, Jorn R. de Haan, Ingrid de Grijs, Christian Gilissen, José M. Hendriks, Roselinde I. van Ravestein-van Os, Susanne Bauerschmidt, Koen J. Dechering, Everardus J. van Zoelen 
Osteo-Transcriptomics of Human Mesenchymal Stem Cells: Accelerated Gene Expression and Osteoblast Differentiation Induced by Vitamin D Reveals c-MYC as an Enhancer of BMP2-Induced Osteogenesis 
Bone  46: 613-627 

Alain J. van Gool, Brian Henry, Erik D. Sprengers 
From Biomarker Strategies to Biomarker Activities, and back 
Drug Discovery Today, 15 (3-4):121-126 

Pieter J. Nieuwland, Kaspar Koch, Noud van Harskamp, Ron Wehrens, Jan C. M. van Hest, Floris P. J. T. Rutjes 
Flash Chemistry Extensively Optimized: High-Temperature Swern-Moffatt Oxidation in an Automated Microreactor Platform 
Chemistry - an Asian journal, published online February 17, 2010 

Jorn R De Haan, Ester Piek, Rene C Van Schaik, Jacob De Vlieg, Susanne Bauerschmidt, Lutgarde Buydens and Ron Wehrens 
Integrating gene expression and GO classification for PCA by preclustering 
BMC Bioinformatics 2010, 11:158 

Franca Podo, Lutgarde M.C. Buydens, Hadassa Degani, Riet Hilhorst, Edda Klipp, Ingrid S. Gribbestad, Sabine van Huffel, Hanneke W.M. van Laarhoven, Jan Luts, Daniel Monleon, Geert J. Postma, Nicole Schneiderhan-Marra, Filippo Santoro, Hans Wouters, Hege G. Russnes, Therese Sørlie, Elda Tagliabue, Anne-Lise Børresen-Dale 
Triple-Negative Breast Cancer: Present Challenges and New Perspectives 
Molecular Oncology, 4 (3): 209-229 

Tom G. Bloemberg, Jan Gerretzen, Hans J.P. Wouters, Jolein Gloerich, Hans J.C.T. Wessels, Maurice van Dael, Lambert P van den Heuvel, Paul H.C. Eilers, Lutgarde M.C. Buydens, and Ron Wehrens 
Improved Parametric Time Warping for Proteomics 
Chemom. Intell.Lab. Syst, 104 (1), 65-74 

M.G. Kounelakis, M.E. Zervakis, G. Giakos, G.J. Postma, L.M.C.Buydens, A. Heerschap and X. Kotsiakis 
Targeting brain gliomas energy metabolism for classification purposes
Conference Proceedings: 2010 IEEE International Conference on Imaging Systems and Techniques (IST 2010) , Thessaloniki, Greece, July 1-2. 

Michail Kounelakis, Michail Zervakis, Geert Postma, Lutgarde Buydens, Arend Heerschap and Xenofon Kotsiakis
Validation of MRS metabolic markers in the classification of brain gliomas and their correlation to energy metabolism
Conference proceedings MEDICON 2010

Patrick Krooshof, Bülent Üstün, Geert Postma & Lutgarde Buydens 
Visualization and Recovery of the (Bio)chemical Interesting Variables in Data Analysis with Support Vector Machine Classification
Analytical Chemistry, 82 (16): 7000-7007 

Marcel P. Stoop, Leon Coullier, Therese Rosenling, Shanna Shi, Agnieszka M. Smolinska, Lutgarde Buydens, Kirsten Ampt, Christoph Stingl, Adrie Dane, Bas Muilwijk, Peter A. E. Sillevis Smitt, Rogier Q. Hintzen, Rainer Bischoff, Sybren S. Wijmenga, Thomas Hankemeier, Alain J. van Gool, and Theo M. Luider
Quantitative proteomics and metabolomics analysis of normal human cerebrospinal fluid samples
Molecular Cellular Proteomics, 9: 2063-2075 

L. Blanchet, P. Krooshof, G. Postma, B. Idema, B. Goraj, A. Heerschap & L. Buydens
Discrimination between Metastases and Glioblastomas multiforme based on morphometrical analysis of MR images
American Journal of Neuroradiology (ANJR), published online November 4, 2010 

Guro Giskeodegard, Tom Bloemberg, Geert Postma, Beathe Sitter, May-Britt Tessem, Ingrid Gribbestad, Tone Bathen, Lutgarde Buydens
Alignment of high resolution magic angle spinning MR spectroscopy data
Analytica Chimica Acta 683 (2010) 1-11 Featured article. 

P.M.A. Groenen, A. van Gool
Pharmacogenomics in the 21st century: moving from west to east
PharmaAsia, dec. 2010 Cover article 

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