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Research Output

  • 37 Article
  • 2 Review article
  • 1 Comment/Letter to the editor
  • 1 Doctoral Thesis
2019

A bioinformatics workflow to decipher transcriptomic data from vitamin D studies

Muñoz García, A., Eijssen, L. M., Kutmon, M., Sarathy, C., Cengo, A., Hewison, M., Evelo, C. T., Lenz, M. & Coort, S. L., May 2019, In : Journal of Steroid Biochemistry and Molecular Biology. 189, p. 28-35 8 p.

Research output: Contribution to journalReview articleAcademicpeer-review

Open Access

CyTargetLinker app update: A flexible solution for network extension in Cytoscape

Kutmon, M., Ehrhart, F., Willighagen, E. L., Evelo, C. T. & Coort, S. L., 13 Aug 2019, In : F1000Research. 7, p. 743

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
File
36 Downloads (Pure)

Prader-Willi syndrome and Angelman syndrome: Visualisation of the molecular pathways for two chromosomal disorders

Ehrhart, F., Janssen, K. J. M., Coort, S. L., Evelo, C. T. & Curfs, L. M. G., 21 Oct 2019, In : World Journal of Biological Psychiatry. 20, 9, p. 670-682 13 p.

Research output: Contribution to journalReview articleAcademicpeer-review

Open Access

Transcriptomic analysis of vitamin D responses in uterine and peripheral NK cells

Tamblyn, J. A., Jeffery, L. E., Susarla, R., Lissauer, D. M., Coort, S. L., Garcia, A. M., Knoblich, K., Fletcher, A. L., Bulmer, J. N., Kilby, M. D. & Hewison, M., Aug 2019, In : Reproduction. 158, 2, p. 211-221 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

2018

Biological pathways leading from ANGPTL8 to Diabetes Mellitus: a co-expression network based analysis

Siddiqa, A., Cirillo, E., Tareen, S. H. K., Ali, A., Kutmon, M., Eijssen, L. M. T., Ahmad, J., Evelo, C. T. & Coort, S. L., 21 Dec 2018, In : Frontiers in physiology. 9, 15 p., 1841.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Differential protein expression of hippocampal cells associated with heavy metals (Pb, As, and MeHg) neurotoxicity: Deepening into the molecular mechanism of neurodegenerative diseases

Karri, V., Ramos, D., Bauza Martinez, J., Odena, A., Oliveira, E., Coort, S. L., Evelo, C. T., Mariman, E. C. M., Schuhmacher, M. & Kumar, V., 15 Sep 2018, In : Journal of Proteomics. 187, p. 106-125 20 p.

Research output: Contribution to journalArticleAcademicpeer-review

From SNPs to pathways: Biological interpretation of type 2 diabetes (T2DM) genome wide association study (GWAS) results

Cirillo, E., Kutmon, M., Gonzalez Hernandez, M., Hooimeijer, T., Adriaens, M. E., Eijssen, L. M. T., Parnell, L. D., Coort, S. L. & Evelo, C. T., 4 Apr 2018, In : PLOS ONE. 13, 4, p. e0193515 19 p., 0193515.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Pathway analysis of transcriptomic data shows immunometabolic effects of vitamin D

Garcia, A. M., Kutmon, M., Eijssen, L., Hewison, M., Evelo, C. T. & Coort, S. L., Feb 2018, In : Journal of Molecular Endocrinology. 60, 2, p. 95-108 14 p.

Research output: Contribution to journalArticleAcademicpeer-review

Role of 1 alpha,25-Dihydroxyvitamin D-3 in Adipogenesis of SGBS Cells: New Insights into Human Preadipocyte Proliferation

Felicidade, I., Sartori, D., Coort, S. L. M., Semprebon, S. C., Niwa, A. M., D'Epiro, G. F., Biazi, B. I., Marques, L. A., Evelo, C. T., Mantovani, M. S. & Ribeiro, L. R., 1 Jan 2018, In : Cellular Physiology and Biochemistry. 48, 1, p. 407-418 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2017

Sexual Dimorphism, Age, and Fat Mass Are Key Phenotypic Drivers of Proteomic Signatures

Curran, A. M., Fogarty Draper, C., Scott-Boyer, M-P., Valsesia, A., Roche, H. M., Ryan, M. F., Gibney, M. J., Kutmon, M., Evelo, C. T., Coort, S. L., Astrup, A., Saris, W. H., Brennan, L. & Kaput, J., 3 Nov 2017, In : Journal of Proteome Research. 16, 11, p. 4122-4133 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

Visualizing the regulatory role of Angiopoietin-like protein 8 (ANGPTL8) in glucose and lipid metabolic pathways

Siddiqa, A., Cirillo, E., Tareen, S. H. K., Ali, A., Kutmon, M., Eijssen, L., Ahmad, J., Evelo, C. T. & Coort, S. L., Oct 2017, In : Genomics. 109, 5-6, p. 408-418 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

2016

New insights in Rett syndrome using pathway analysis for transcriptomics data

Ehrhart, F., Steinbusch - Coort, S., Cirillo, E., Smeets, E., Evelo, C. T. & Curfs, L., Sep 2016, In : Wiener Medizinische Wochenschrift. 166, 11, p. 346-352 7 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Reactome from a WikiPathways Perspective

Bohler, A., Wu, G., Kutmon, M., Pradhana, L. A., Steinbusch - Coort, S., Hanspers, K., Haw, R., Pico, A. R. & Evelo, C. T., May 2016, In : PLoS Computational Biology. 12, 5, e1004941.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)

Rett syndrome - biological pathways leading from MECP2 to disorder phenotypes

Ehrhart, F., Steinbusch - Coort, S., Cirillo, E., Smeets, E., Evelo, C. T. & Curfs, L. M. G., 25 Nov 2016, In : Orphanet Journal of Rare Diseases. 11, 13 p., 158.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

WikiPathways: capturing the full diversity of pathway knowledge

Kutmon, M., Riutta, A., Nunes, N., Hanspers, K., Willighagen, E. L., Bohler, A., Melius, J., Waagmeester, A., Sinha, S. R., Miller, R., Coort, S. L., Cirillo, E., Smeets, B., Evelo, C. T. & Pico, A. R., 4 Jan 2016, In : Nucleic Acids Research. 44, D1, p. D488-D494 7 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
37 Citations (Scopus)
2015

Integrative network-based analysis of mRNA and microRNA expression in 1,25-dihydroxyvitamin D3-treated cancer cells

Kutmon, M., Coort, S. L., de Nooijer, K., Lemmens, C. & Evelo, C. T., 1 Jan 2015, In : Genes and nutrition. 10, 5, 35.

Research output: Contribution to journalArticleAcademicpeer-review

4 Citations (Scopus)
2014

A network biology workflow to study transcriptomics data of the diabetic liver

Kutmon, M., Evelo, C. T. & Coort, S. L., 1 Jan 2014, In : BMC Genomics. 15, p. 971

Research output: Contribution to journalArticleAcademicpeer-review

5 Citations (Scopus)

Identification of platelet function defects by multi-parameter assessment of thrombus formation

de Witt, S. M., Swieringa, F., Cavill, R., Lamers, M. M., van Kruchten, R., Mastenbroek, T., Baaten, C., Coort, S., Pugh, N., Schulz, A., Scharrer, I., Jurk, K., Zieger, B., Clemetson, K. J., Farndale, R. W., Heemskerk, J. W. & Cosemans, J. M., Jul 2014, In : Nature Communications. 5, 13 p., 4257.

Research output: Contribution to journalArticleAcademicpeer-review

38 Citations (Scopus)

Transcriptome analysis of peripheral blood mononuclear cells in human subjects following a 36 h fast provides evidence of effects on genes regulating inflammation, apoptosis and energy metabolism

Elliott, R. M., de Roos, B., Duthie, S. J., Bouwman, F. G., Rubio Aliaga, I., Crosley, L. K., Mayer, C., Polley, A. C., Heim, C., Coort, S., Evelo, C. T., Mulholland, F., Daniel, H., Mariman, E. C. & Johnson, I. T., Nov 2014, In : Genes and nutrition. 9, 6, 11 p., 432.

Research output: Contribution to journalArticleAcademicpeer-review

2 Citations (Scopus)
2013

CyTargetLinker: a cytoscape app to integrate regulatory interactions in network analysis

Kutmon, M., Kelder, T., Mandaviya, P., Evelo, C. T. & Coort, S. L., 5 Dec 2013, In : PLOS ONE. 8, 12, 9 p., e82160.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
25 Citations (Scopus)
2012

Marginal selenium deficiency down-regulates inflammation-related genes in splenic leukocytes of the mouse.

Kipp, A. P., Banning, A., van Schothorst, E. M., Meplan, C., Coort, S. L. M., Evelo, C. T. A., Keijer, J., Hesketh, J. & Brigelius Flohe, R., Sep 2012, In : Journal of Nutritional Biochemistry. 23, 9, p. 1170-1177 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

15 Citations (Scopus)

MicroRNA profiling identifies microRNA-155 as an adverse mediator of cardiac injury and dysfunction during acute viral myocarditis.

Corsten, M. F., Papageorgiou, A., Verhesen, W., Carai, P., Lindow, M., Obad, S., Summer, G., Coort, S. L. M., Hazebroek, M., van Leeuwen, R., Gijbels, M. J. J., Wijnands, E., Biessen, E. A., de Winther, M. P. J., Stassen, F. R. M., Carmeliet, P., Kauppinen, S., Schroen, B. & Heymans, S., 3 Aug 2012, In : Circulation Research. 111, 4, p. 415-425

Research output: Contribution to journalArticleAcademicpeer-review

72 Citations (Scopus)
2011

2D-electrophoresis and multiplex immunoassay proteomic analysis of different body fluids and cellular components reveal known and novel markers for extended fasting

Bouwman, F. G., de Roos, B., Rubio Aliaga, I., Crosley, L. K., Duthie, S. J., Mayer, C., Horgan, G., Polley, A. C., Heim, C., Coort, S. L. M., Evelo, C. T. A., Mulholland, F., Johnson, I. T., Elliott, R. M., Daniel, H. & Mariman, E. C., 1 Jan 2011, In : BMC Medical Genomics. 4, 1, p. 24

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
File
15 Citations (Scopus)
160 Downloads (Pure)

Alterations in hepatic one-carbon metabolism and related pathways following a high-fat dietary intervention

Rubio-Aliaga, I., de Roos, B., Sailer, M., McLoughlin, G. A., Boekschoten, M. V., van Erk, M., Bachmair, E. M., van Schothorst, E. M., Keijer, J., Coort, S. L. M., Evelo, C. T. A., Gibney, M. J., Daniel, H., Muller, M., Kleemann, R. & Brennan, L., 1 Jan 2011, In : Physiological genomics. 43, 8, p. 408-416

Research output: Contribution to journalArticleAcademicpeer-review

44 Citations (Scopus)

Epigenetics: prenatal exposure to genistein leaves a permanent signature on the hematopoietic lineage.

Vanhees, K., Coort, S. L. M., Ruijters, E. J. B., Godschalk, R. W. L., van Schooten, F. J. & Khosrovani, S. B., 1 Jan 2011, In : Faseb Journal. 25, 2, p. 797-807

Research output: Contribution to journalArticleAcademicpeer-review

44 Citations (Scopus)
2009

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

24 Citations (Scopus)

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

56 Citations (Scopus)

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

3 Citations (Scopus)
2008

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

5 Citations (Scopus)

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

25 Citations (Scopus)

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

199 Citations (Scopus)

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

18 Citations (Scopus)

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

30 Citations (Scopus)
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

104 Citations (Scopus)

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

45 Citations (Scopus)
2006

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

44 Citations (Scopus)
2005
Open Access
File
235 Downloads (Pure)

The subcellular compartmentation of fatty acid transporters is regulated differently by insulin and by AICAR

Chabowski, A., Coort, S. L. M., Calles-Escandon, J., Tandon, NN., Glatz, J. F., Luiken, J. J. F. P. & Bonen, A., 1 Jan 2005, In : Febs Letters. 579, p. 2428-2432

Research output: Contribution to journalArticleAcademicpeer-review

69 Citations (Scopus)
2003

Uncoupling protein 3 as a mitochondrial fatty acid anion exporter

Schrauwen, P., Hoeks, J., Schaart, G., Kornips, C. F. P., Binas, B., van der Vusse, G. J., van Bilsen, M., Luiken, J. J. F. P., Coort, S. L. M., Glatz, J. F., Saris, W. H. M. & Hesselink, M. K. C., 1 Jan 2003, In : Faseb Journal. 17, 15, p. 2272-2274 3 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
File
88 Citations (Scopus)
198 Downloads (Pure)