• Universiteitssingel50, UNS50

    6229 ER Maastricht

    Netherlands

Research Output

2010

A combined transcriptomics and lipidomics analysis of subcutaneous, epididymal and mesenteric adipose tissue reveals marked functional differences

Caesar, R., Manieri, M., Kelder, T. A. J., Boekschoten, M., Evelo, C. T. A., Muller, M., Kooistra, T., Cinti, S., Kleemann, R. & Drevon, C. A., 12 Jul 2010, In : PLOS ONE. 5, 7, 14 p., e11525.

Research output: Contribution to journalArticleAcademicpeer-review

Biotransformation pathway maps in WikiPathways enable direct visualization of drug metabolism related expression changes.

Jennen, D. G. J., Gaj, S., Giesbertz, P. J., van Delft, J. H. M., Evelo, C. T. A. & Kleinjans, J. C. S., 1 Jan 2010, In : Drug Discovery Today. 15, 19-20, p. 851-858

Research output: Contribution to journalArticleAcademicpeer-review

Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies

van Ommen, B., Bouwman, J., Dragsted, L. O., Drevon, C. A., Elliott, R., de Groot, P., Kaput, J., Mathers, J. C., Muller, M., Pepping, F., Saito, J. T., Scalbert, A., Radonjic, M., Rocca Serra, P., Travis, A., Wopereis, S. & Evelo, C. T. A., 1 Jan 2010, In : Genes and nutrition. 5, 3, p. 189-203

Research output: Contribution to journalArticleAcademicpeer-review

Connecting the Human Variome Project to nutrigenomics

Kaput, J., Evelo, C. T. A., Perozzi, G., van Ommen, B. & Cotton, R., 1 Jan 2010, In : Genes and nutrition. 5, 4, p. 275-283

Research output: Contribution to journalArticleAcademicpeer-review

Data integration with biological pathways

van Iersel, M. P., 1 Jan 2010, Maastricht: Maastricht University. 120 p.

Research output: ThesisDoctoral ThesisInternal

Open Access
File
515 Downloads (Pure)

Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets

Kelder, T. A. J., Conklin, B. R., Evelo, C. T. A. & Pico, A. R., Aug 2010, In : Plos Biology. 8, 8, 5 p., e1000472.

Research output: Contribution to journalArticleAcademicpeer-review

From nanotechnology to nanomedicine: applications to cancer research

Seigneuric, R., Markey, L., Nuyten, D. S., Dubernet, C., Evelo, C. T. A., Finot, E. & Garrido, C., Oct 2010, In : Current Molecular Medicine. 10, 7, p. 640-652 13 p.

Research output: Contribution to journalArticleAcademicpeer-review

Nature Europe site should highlight most productive countries

Evelo, C. T. A. & Waagmeester, A. S., 10 Jun 2010, In : Nature. 465, 7299, p. 685-685 1 p.

Research output: Contribution to journalComment/Letter to the editorAcademicpeer-review

The BioPAX community standard for pathway data sharing

Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martinez Flores, I., Hu, Z., Jimenez Jacinto, V., Joshi Tope, G., Kandasamy, K., Lopez Fuentes, A. C., Mi, H., Pichler, E., Rodchenkov, I. & 70 others, Splendiani, A., Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, O., Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray Rust, P., Neumann, E., Reubenacker, O., Samwald, M., van Iersel, M. P., Wimalaratne, S., Allen, K., Braun, B., Whirl Carrillo, M., Cheung, K. H., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren, L., Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K. H., Rzhetsky, A., Schachter, V., Sobral, B. S., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado Vides, J., Goto, S., Hucka, M., Le Novere, N., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P. D., Sander, C. & Bader, G. D., 1 Jan 2010, In : Nature Biotechnology. 28, 9, p. 935-42

Research output: Contribution to journalArticleAcademicpeer-review

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

van Iersel, M. P., Pico, A. R., Kelder, T. A. J., Gao, J., Ho, I., Hanspers, K., Conklin, B. R. & Evelo, C. T. A., 4 Jan 2010, In : BMC Bioinformatics. 11, p. 5 7 p., 5.

Research output: Contribution to journalArticleAcademicpeer-review

The Micronutrient Genomics Project: a community-driven knowledge base for micronutrient research

van Ommen, B., El Sohemy, A., Hesketh, J., Kaput, J., Fenech, M., Evelo, C. T. A., McArdle, H. J., Bouwman, J., Lietz, G., Mathers, J. C., Fairweather Tait, S., van Kranen, H., Elliott, R., Wopereis, S., Ferguson, L. R., Meplan, C., Perozzi, G., Allen, L. & Rivero, D., Dec 2010, In : Genes and nutrition. 5, 4, p. 285-296 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

Time-resolved and tissue-specific systems analysis of the pathogenesis of insulin resistance

Kleemann, R., van Erk, A., Verschuren, L., van den Hoek, A. M., Koek, M., Wielinga, P. Y., Jie, A., Pellis, L., Bobeldijk Pastorova, I., Kelder, T., Toet, K., Wopereis, S., Cnubben, N., Evelo, C., van Ommen, B. & Kooistra, T., 21 Jan 2010, In : PLOS ONE. 5, 1, 17 p., 8817.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2009

An integrated bioinformatics approach to improve two-color microarray quality-control: impact on biological conclusions.

van Haaften, R. I., Luceri, C., van Erk, A. & Evelo, C. T., 1 Jan 2009, In : Genes and nutrition. 4, 2, p. 123-127

Research output: Contribution to journalArticleAcademicpeer-review

Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway

Orton, R. J., Michiel Adriaens, M. E., Gormand, A., Sturm, O. E., Kolch, W. & Gilbert, D. R., 1 Jan 2009, In : BMC Systems Biology. 3, p. 100

Research output: Contribution to journalArticleAcademicpeer-review

Etomoxir-induced partial carnitine palmitoyltransferase-I (CPT-I) inhibition in vivo does not alter cardiac long-chain fatty acid uptake and oxidation rates

Luiken, J. J. F. P., Niessen, H. E. C., Coort, S. L. M., Hoebers, N., Coumans, W. A., Schwenk, R. W., Bonen, A. & Glatz, J. F., 1 Jan 2009, In : Biochemical Journal. 419, 2, p. 447-55

Research output: Contribution to journalArticleAcademicpeer-review

Four selenoproteins, protein biosynthesis, and Wnt signalling are particularly sensitive to limited selenium intake in mouse colon

Kipp, A., Banning, A., van Schothorst, E. M., Meplan, C., Schomburg, L., Evelo, C., Coort, S., Gaj, S., Keijer, J., Hesketh, J. & Brigelius Flohe, R., 1 Jan 2009, In : Molecular Nutrition & Food Research. 53, 12, p. 1561-72

Research output: Contribution to journalArticleAcademicpeer-review

Mining biological pathways using WikiPathways web services.

Kelder, T. A., Pico, A. R., Hanspers, K., van Iersel, M. P., Evelo, C. T. A. & Conklin, B. R., 1 Jan 2009, In : PLOS ONE. 4, 7, e6447.

Research output: Contribution to journalArticleAcademicpeer-review

Pathway Enrichment Based on Text Mining and Its Validation on Carotenoid and Vitamin A Metabolism

Waagmeester, A. S., Pezik, P., Coort, S., Tourniaire, F., Evelo, C. & Rebholz Schuhmann, D., 1 Jan 2009, In : OMICS-a journal of Integrative Biology. 13, 5, p. 367-379

Research output: Contribution to journalArticleAcademicpeer-review

Reduction of colonic inflammation in HLA-B27 transgenic rats by feeding Marie Ménard apples, rich in polyphenols.

Castagnini, C., Luceri, C., Toti, S., Bigagli, E., Caderni, G., Femia, A. P., Giovannelli, L., Lodovici, M., Pitozzi, V., Salvadori, M., Messerini, L., Martin, R., Zoetendal, E. G., Gaj, S., Eijssen, L. M., Evelo, C. T., Renard, C. M., Baron, A. & Dolara, P., 1 Jan 2009, In : British Journal of Nutrition. 102, 11, p. 1620-1628

Research output: Contribution to journalArticleAcademicpeer-review

2008

Altered myocardial gene expression reveals possible maladaptive processes in heterozygous and homozygous cardiac myosin-binding protein C knockout mice.

Eijssen, L. M. T., van den Bosch, B. J. C., Vignier, N., Lindsey, P. J., van den Burg, C. M. M., Carrier, L., Doevendans, P. A. F. M., van der Vusse, G. J. & Smeets, H. J., 1 Jan 2008, In : Genomics. 91, 1, p. 52-60

Research output: Contribution to journalArticleAcademicpeer-review

A novel stepwise analysis procedure of genome-wide expression profiles identifies transcript signatures of thiamine genes as classifiers of mitochondrial mutants.

Eijssen, L. M. T., Lindsey, P. J., Peeters, R., Westra, R. L., van Eijsden, R. G. E., Bolotin-Fukuhara, M., Smeets, H. J. & Vlietinck, R. F. M., 1 Jan 2008, In : Yeast. 25, 2, p. 129-140

Research output: Contribution to journalArticleAcademicpeer-review

Bioinformatic interrogation of expression array data to identify nutritionally regulated genes potentially modulated by DNA methylation

McKay, J. A., Michiel Adriaens, M. E., Ford, D., Relton, C. L., Evelo, C. T. & Mathers, J. C., 1 Jan 2008, In : Genes and nutrition. 3, 3-4, p. 167-71

Research output: Contribution to journalArticleAcademicpeer-review

Bioinformatics for the NuGO proof of principle study: analysis of gene expression in muscle of ApoE3*Leiden mice on a high-fat diet using PathVisio

Coort, S. L., van Iersel, M. P., van Erk, M., Kooistra, T., Kleemann, R. & Evelo, C. T., 1 Jan 2008, In : Genes and nutrition. 3, 3-4, p. 185-91

Research output: Contribution to journalArticleAcademicpeer-review

Identification of protein kinase D as a novel contraction-activated kinase linked to GLUT4-mediated glucose uptake independent of AMPK

Luiken, J. J. F. P., Vertommen, D., Coort, S. L. M., Habets, D. D. J., El Hasnaoui, M. M., Pelsers, M. M. A. L., Viollet, B., Bonen, A., Hue, L., Rider, M. H. & Glatz, J. F., 1 Jan 2008, In : Cellular Signalling. 20, p. 543-555

Research output: Contribution to journalArticleAcademicpeer-review

Presenting and exploring biological pathways with PathVisio

van Iersel, M. P., Kelder, T. A. J., Pico, A. R., Hanspers, K., Coort, S. L., Conklin, B. R. & Evelo, C., 1 Jan 2008, In : BMC Bioinformatics. 9, p. 399

Research output: Contribution to journalArticleAcademicpeer-review

Termination of damaged protein repair defines the occurrence of symptoms in carriers of the m.3243A > G tRNA(Leu) mutation.

van Eijsden, R., Eijssen, L. M., Lindsey, P., van den Burg, C., de Wit, E., Rubio-Gozalbo, M. E., de Die-Smulders, C. E. M., Ayoubi, T., Sluiter, W., de Coo, I. & Smeets, H., 1 Jan 2008, In : Journal of Medical Genetics. 45, 8, p. 525-534

Research output: Contribution to journalArticleAcademicpeer-review

The emerging world of wikis

Hu, J. C., Aramayo, R., Bolser, D., Conway, T., Elsik, C. G., Gribskov, M., Kelder, T. A. J., Kihara, D., Knight, T. F. . J., Pico, A. R., Siegele, D. A., Wanner, B. L. & Welch, R. D., 1 Jan 2008, In : Science. 320, 5881, p. 1289-90

Research output: Contribution to journalComment/Letter to the editorAcademicpeer-review

The NuGO proof of principle study package: a collaborative research effort of the European Nutrigenomics Organisation

Baccini, M., Bachmaier, E. M., Biggeri, A., Boekschoten, M. V., Bouwman, F. G., Brennan, L., Caesar, R., Cinti, S., Coort, S. L. M., Crosley, K., Daniel, H., Drevon, C. A., Duthie, S. J., Eijssen, L. M. T., Elliott, R. M., van Erk, M., Evelo, C. T. A., Gibney, M., Heim, C., Horgan, G. W. & 1 others, Johnson, I. T., 1 Jan 2008, In : Genes and nutrition. 3(3-4), p. 147-151

Research output: Contribution to journalArticleAcademicpeer-review

The public road to high-quality curated biological pathways

Michiel Adriaens, M. E., Jaillard, M., Waagmeester, A. S., Coort, S. L., Pico, A. R. & Evelo, C. T., 1 Jan 2008, In : Drug Discovery Today. 13, 19-20, p. 856-862

Research output: Contribution to journalArticleAcademicpeer-review

The role of bioinformatics in pathway curation

Waagmeester, A. S., Kelder, T. A. J. & Evelo, C. T., 1 Jan 2008, In : Genes and nutrition. 3, 3-4, p. 139-142

Research output: Contribution to journalArticleAcademicpeer-review

Validating nutrient-related gene expression changes from microarrays using RT(2) PCR-arrays

Gaj, S., Eijssen, L. M., Mensink, R. P. & Evelo, C. T., 1 Jan 2008, In : Genes and nutrition. 3, 3-4, p. 153-7

Research output: Contribution to journalArticleAcademicpeer-review

WikiPathways: pathway editing for the people

Pico, A. R., Kelder, T. A. J., van Iersel, M. P., Hanspers, K., Conklin, B. R. & Evelo, C., 1 Jan 2008, In : Plos Biology. 6, 7, e184.

Research output: Contribution to journalArticleAcademicpeer-review

2007

Cardiac contractile dysfunction in insulin-resistant rats fed a high-fat diet is associated with elevated CD36-mediated fatty acid uptake and esterification

Ouwens, DM., Diamant, M., Fodor, M., Habets, D. D. J., Pelsers, M. M. A. L., El Hasnaoui, M. M., Dang, Z. C., van den Brom, C. E., Vlasblom, R., Rietdijk, A., Boer, C., Coort, S. L. M., Glatz, J. F. & Luiken, J. J. F. P., 1 Jan 2007, In : Diabetologia. 50, 9, p. 1938-48

Research output: Contribution to journalArticleAcademicpeer-review

Cardiac substrate uptake and metabolism in obesity and type-2 diabetes: Role of sarcolemmal substrate transporters

Coort, S. L. M., Bonen, A., van der Vusse, G. J., Glatz, J. F. & Luiken, J. J. F. P., 1 Jan 2007, In : Molecular and Cellular Biochemistry. 299, 1-2, p. 5-18

Research output: Contribution to journalArticleAcademicpeer-review

Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases.

Cavalieri, D., Castagnini, C., Toti, S., Maciag, K., Kelder, T. A. J., Gambineri, L., Anqioli, S. & Dolara, P., 1 Jan 2007, In : Bioinformatics. 23, 19, p. 2631-2632

Research output: Contribution to journalArticleAcademicpeer-review

Impact of supervised gene signatures of early hypoxia on patient survival.

Seigneuric, R., Starmans, M. H. W., Fung, G., Krishnapuram, B., Nuyten, D. S. A., van Erk, A. A., Magagnin, M. G., Rouschop, K. M. A., Krishnan, S., Rao, R. B., Evelo, C. T. A., Beqq, A. C., Wouters, B. G. & Lambin, P., 1 Jan 2007, In : Radiotherapy and Oncology. 83, 3, p. 374-382

Research output: Contribution to journalArticleAcademicpeer-review

Linking microarray reporters with protein functions

Gaj, S., van Erk, A. A., van Haaften, R. I. & Evelo, C. T., 1 Jan 2007, In : BMC Bioinformatics. 8, 1, p. 360

Research output: Contribution to journalArticleAcademicpeer-review

2006

Biologically relevant effects of mRNA amplification on gene expression profiles

van Haaften, R. I. M., Schroen, B. L., Janssen, B. J., van Erk, A. A., Debets, J. J., Smeets, H. J., Smits, J. F., van den Wijngaard, A., Pinto, Y. M. & Evelo, C. T., 1 Jan 2006, In : BMC Bioinformatics. 7, p. 200

Research output: Contribution to journalArticleAcademicpeer-review

Blue Obelisk - Interoperability in chemical informatics

Guha, R., Howard, MT., Hutchison, GR., Murray-Rust, P., Rzepa, H., Steinbeck, C., Wegner, J. & Willighagen, EL., May 2006, In : Journal of Chemical Information and Modeling. 46, 3, p. 991-998 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

Chip-based mtDNA mutation screening enables fast and reliable genetic diagnosis of OXPHOS patients

van Eijsden, R. G., Gerards, M., Eijssen, L. M., Hendrickx, A. T., Jongbloed, R. J. E., Wokke, J. H., Hintzen, R. Q., Rubio-Gozalbo, M. E., De Coo, I. F., Briem, E., Tiranti, V. & Smeets, H. J., 1 Jan 2006, In : Genetics in Medicine. 8, 10, p. 620-627

Research output: Contribution to journalArticleAcademicpeer-review

Prolonged AMPK activation increases the expression of fatty acid transporters in cardiac myocytes and perfused hearts

Chabowski, A. M. I., Coort, S. L. M., Calles-Escandon, J. T. NN., Glatz, J. F. & Luiken, J. J. F. P., 1 Jan 2006, In : Molecular and Cellular Biochemistry. 288, p. 201-212

Research output: Contribution to journalArticleAcademicpeer-review

2004

Childhood asthma: exhaled markers of airway inflammation, asthma control score, and lung function tests

Rosias, P. P. R., Dompeling, E. D., Dentener, M. A., Pennings, H. J., Hendriks, H., van Iersel, M. P. & Jöbsis, Q., 1 Jan 2004, In : Pediatric Pulmonology. 38, 2, p. 107-114

Research output: Contribution to journalArticleAcademicpeer-review