Scientific publications

2000

  1. van Kampen, A. H., van Schaik, B. D., Pauws, E., Michiels, E. M., Ruijter, J. M., Caron, H. N., Versteeg, R., Heisterkamp, S. H., Leunissen, J. A., Baas, F., & van der Mee, M. (2000). USAGE: a web-based approach towards the analysis of SAGE data. Serial Analysis of Gene Expression. Bioinformatics, 16(10), 899-905.

 

2001

  1. Caron, H., van Schaik, B., van der Mee, M., Baas, F., Riggins, G., van Sluis, P., Hermus, M. C., van Asperen, R., Boon, K., Voute, P. A., Heisterkamp, S., van Kampen, A., & Versteeg, R. (2001). The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science, 291(5507), 1289-1292.
  2. Moreno, J. C., Pauws, E., van Kampen, A. H., Jedlickova, M., de Vijlder, J. J., & Ris-Stalpers, C. (2001). Cloning of tissue-specific genes using serial analysis of gene expression and a novel computational substraction approach. Genomics, 75(1-3), 70-76.
  3. Pauws, E., van Kampen, A. H., van de Graaf, S. A., de Vijlder, J. J., & Ris-Stalpers, C. (2001). Heterogeneity in polyadenylation cleavage sites in mammalian mRNA sequences: implications for SAGE analysis. Nucleic Acids Res, 29(8), 1690-1694.
  4. Spieker, N., van Sluis, P., Beitsma, M., Boon, K., van Schaik, B. D., van Kampen, A. H., Caron, H., & Versteeg, R. (2001). The MEIS1 oncogene is highly expressed in neuroblastoma and amplified in cell line IMR32. Genomics, 71(2), 214-221.

 

2002

  1. Luyf, A. C., de Gast, J., & van Kampen, A. H. (2002). Visualizing metabolic activity on a genome-wide scale. Bioinformatics, 18(6), 813-818.
  2. Ruijter, J. M., Van Kampen, A. H., & Baas, F. (2002). Statistical evaluation of SAGE libraries: consequences for experimental design. Physiol Genomics, 11(2), 37-44.

 

2003

  1. de Jonge, R. R., Vreijling, J. P., Meintjes, A., Kwa, M. S., van Kampen, A. H., van Schaik, I. N., & Baas, F. (2003). Transcriptional profile of the human peripheral nervous system by serial analysis of gene expression. Genomics, 82(2), 97-108.
  2. van Kampen, A., Ruijter, J. M., van Schaik, B., Caron, H., & Versteeg, R. (2003). Gene expression informatics and analysis. . In B. M.R. & G. I.C. (Eds.), Bioinformatics for geneticists (pp. 319-344). Chichester: John Wiley & Sons

 

2004

  1. Versteeg, R., van Schaik, B. D., van Batenburg, M. F., Roos, M., Monajemi, R., Caron, H., Bussemaker, H. J., & van Kampen, A. H. (2003). The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. Genome Res, 13(9), 1998-2004.
  2. van Passel, M. W., Bart, A., Waaijer, R. J., Luyf, A. C., van Kampen, A. H., & van der Ende, A. (2004). An in vitro strategy for the selective isolation of anomalous DNA from prokaryotic genomes. Nucleic Acids Res, 32(14), e114.

 

2005

  1. Braat, H., Stokkers, P., Hommes, T., Cohn, D., Vogels, E., Pronk, I., Spek, A., van Kampen, A., van Deventer, S., Peppelenbosch, M., & Hommes, D. (2005). Consequence of functional Nod2 and Tlr4 mutations on gene transcription in Crohn’s disease patients. J Mol Med (Berl), 83(8), 601-609.
  2. Schaaf, G. J., Ruijter, J. M., van Ruissen, F., Zwijnenburg, D. A., Waaijer, R., Valentijn, L. J., Benit-Deekman, J., van Kampen, A. H., Baas, F., & Kool, M. (2005). Full transcriptome analysis of rhabdomyosarcoma, normal, and fetal skeletal muscle: statistical comparison of multiple SAGE libraries. FASEB J, 19(3), 404-406.
  3. van Kampen, A., & Horrevoets, A. (2005). The role of bioinformatics in genomic medicine. In G. Pasterkamp & D. P. V. de Kleijn (Eds.), Cardiovascular research: new technologies, methods & applications (pp. 103-120). New York: Springer
  4. van Passel, M. W., Bart, A., Thygesen, H. H., Luyf, A. C., van Kampen, A. H., & van der Ende, A. (2005). An acquisition account of genomic islands based on genome signature comparisons. BMC Genomics, 6, 163.
  5. van Passel, M. W., Luyf, A. C., van Kampen, A. H., Bart, A., & van der Ende, A. (2005). Deltarho-web, an online tool to assess composition similarity of individual nucleic acid sequences. Bioinformatics, 21(13), 3053-3055.

 

2006

  1. Halasz, G., van Batenburg, M. F., Perusse, J., Hua, S., Lu, X. J., White, K. P., & Bussemaker, H. J. (2006). Detecting transcriptionally active regions using genomic tiling arrays. Genome Biol, 7(7), R59.
  2. Jansen, G. A., & Wanders, R. J. (2006). Alpha-oxidation. Biochim Biophys Acta, 1763(12), 1403-1412.
  3. van de Mortel, J. E., Almar Villanueva, L., Schat, H., Kwekkeboom, J., Coughlan, S., Moerland, P. D., Ver Loren van Themaat, E., Koornneef, M., & Aarts, M. G. (2006). Large expression differences in genes for iron and zinc homeostasis, stress response, and lignin biosynthesis distinguish roots of Arabidopsis thaliana and the related metal hyperaccumulator Thlaspi caerulescens. Plant Physiol, 142(3), 1127-1147.
  4. van Passel, M. W., Bart, A., Luyf, A. C., van Kampen, A. H., & van der Ende, A. (2006). Identification of acquired DNA in Neisseria lactamica. FEMS Microbiol Lett, 262(1), 77-84.
  5. van Passel, M. W., Bart, A., Luyf, A. C., van Kampen, A. H., & van der Ende, A. (2006). Compositional discordance between prokaryotic plasmids and host chromosomes. BMC Genomics, 7, 26.
  6. van Passel, M. W., Kuramae, E. E., Luyf, A. C., Bart, A., & Boekhout, T. (2006). The reach of the genome signature in prokaryotes. BMC Evol Biol, 6, 84.
  7. Vos, J. B., Datson, N. A., van Kampen, A. H., Luyf, A. C., Verhoosel, R. M., Zeeuwen, P. L., Olthuis, D., Rabe, K. F., Schalkwijk, J., & Hiemstra, P. S. (2006). A molecular signature of epithelial host defense: comparative gene expression analysis of cultured bronchial epithelial cells and keratinocytes. BMC Genomics, 7, 9.
  8. Zelinkova, Z., Derijks, L. J., Stokkers, P. C., Vogels, E. W., van Kampen, A. H., Curvers, W. L., Cohn, D., van Deventer, S. J., & Hommes, D. W. (2006). Inosine triphosphate pyrophosphatase and thiopurine s-methyltransferase genotypes relationship to azathioprine-induced myelosuppression. Clin Gastroenterol Hepatol, 4(1), 44-49.

 

2007

  1. Ferreira, J., & Nyangoma, S. (2007). A multivariate version of the Benjamini-Hochberg method. COBRA Preprint Series.
  2. Nyangoma, S. O., van Kampen, A. A., Reijmers, T. H., Govorukhina, N. I., van der Zee, A. G., Billingham, L. J., Bischoff, R., & Jansen, R. C. (2007). Multiple testing issues in discriminating compound-related peaks and chromatograms from high frequency noise, spikes and solvent-based noise in LC-MS data sets. Stat Appl Genet Mol Biol, 6, Article23.
  3. Schaaf, G. J., van Ruissen, F., van Kampen, A., Kool, M., & Ruijter, J. M. (2007). Statistical Comparison of Two or More SAGE Libraries: One Tag at the Time. In K. L. Nielsen (Ed.), Serial Analysis of Gene Expression. Methods and Protocols. Totowa: Humana Press
  4. Sokolovic, M., Wehkamp, D., Sokolovic, A., Vermeulen, J., Gilhuijs-Pederson, L. A., van Haaften, R. I., Nikolsky, Y., Evelo, C. T., van Kampen, A. H., Hakvoort, T. B., & Lamers, W. H. (2007). Fasting induces a biphasic adaptive metabolic response in murine small intestine. BMC Genomics, 8, 361.
  5. Soufan, A. T., van den Berg, G., Moerland, P. D., Massink, M. M., van den Hoff, M. J., Moorman, A. F., & Ruijter, J. M. (2007). Three-dimensional measurement and visualization of morphogenesis applied to cardiac embryology. J Microsc, 225(Pt 3), 269-274.
  6. Volger, O. L., Fledderus, J. O., Kisters, N., Fontijn, R. D., Moerland, P. D., Kuiper, J., van Berkel, T. J., Bijnens, A. P., Daemen, M. J., Pannekoek, H., & Horrevoets, A. J. (2007). Distinctive expression of chemokines and transforming growth factor-beta signaling in human arterial endothelium during atherosclerosis. Am J Pathol, 171(1), 326-337.

 

2008

  1. Biewenga, P., Buist, M. R., Moerland, P. D., Ver Loren van Themaat, E., van Kampen, A. H., ten Kate, F. J., & Baas, F. (2008). Gene expression in early stage cervical cancer. Gynecol Oncol, 108(3), 520-526.
  2. Buimer, M., Keijser, R., Jebbink, J. M., Wehkamp, D., van Kampen, A. H., Boer, K., van der Post, J. A., & Ris-Stalpers, C. (2008). Seven placental transcripts characterize HELLP-syndrome. Placenta, 29(5), 444-453.
  3. de Win, M. M., Jager, G., Booij, J., Reneman, L., Schilt, T., Lavini, C., Olabarriaga, S. D., den Heeten, G. J., & van den Brink, W. (2008). Sustained effects of ecstasy on the human brain: a prospective neuroimaging study in novel users. Brain, 131(Pt 11), 2936-2945.
  4. de Win, M. M., Jager, G., Booij, J., Reneman, L., Schilt, T., Lavini, C., Olabarriaga, S. D., Ramsey, N. F., Heeten, G. J., & van den Brink, W. (2008). Neurotoxic effects of ecstasy on the thalamus. Br J Psychiatry, 193(4), 289-296.
  5. Ferreira, J., & Nyangoma, S. (2008). A multivariate version of the Benjamini-Hochberg. Journal of Multivariate Analysis, 99(9), 2108-2124.
  6. Glatard, T., Boulebiar, K., & Olabarriaga, S. (2008). Workflow integration in VL-e medical. Paper presented at the IEEE International Symposium on Computer-Based Medical Systems, Jyväskylä, Finland.
  7. Glatard, T., & Olabarriaga, S. (2008). From gridified scripts to workflows; the FSL Feat case. Paper presented at the MICCAI Workshop on Medical imaging on grids: achievements and perspectives, New-York.
  8. Glatard, T., & Olabarriaga, S. (2008). “User friendly management of workflow results: from provenance information to grid logical file names”. Paper presented at the IEEE International Conference on e-Science, Indianapolis.
  9. Inda, M. A., van Batenburg, M. F., Roos, M., Belloum, A. S., Vasunin, D., Wibisono, A., van Kampen, A. H., & Breit, T. M. (2008). SigWin-detector: a Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences. BMC Res Notes, 1, 63.
  10. Lagarde, S. M., Ver Loren van Themaat, P. E., Moerland, P. D., Gilhuijs-Pederson, L. A., Ten Kate, F. J., Reitsma, P. H., van Kampen, A. H., Zwinderman, A. H., Baas, F., & van Lanschot, J. J. (2008). Analysis of gene expression identifies differentially expressed genes and pathways associated with lymphatic dissemination in patients with adenocarcinoma of the esophagus. Ann Surg Oncol, 15(12), 3459-3470.
  11. Martens, K., Ver Loren van Themaat, E., van Batenburg, M. F., Heinaniemi, M., Huyghe, S., Van Hummelen, P., Carlberg, C., Van Veldhoven, P. P., Van Kampen, A., & Baes, M. (2008). Coordinate induction of PPAR alpha and SREBP2 in multifunctional protein 2 deficient mice. Biochim Biophys Acta, 1781(11-12), 694-702.
  12. Olabarriaga, S. D., Glatard, T., Boulebiar, K., & de Boer, P. T. (2008). From “low hanging” to “user ready”: initial steps into a HealthGrid. Stud Health Technol Inform, 138, 70-79.
  13. Schaaf, G. J., van Ruissen, F., van Kampen, A., Kool, M., & Ruijter, J. M. (2008). Statistical comparison of two or more SAGE libraries: one tag at a time. Methods Mol Biol, 387, 151-168.
  14. Schirmer, S. H., Fledderus, J. O., Bot, P. T., Moerland, P. D., Hoefer, I. E., Baan, J., Jr., Henriques, J. P., van der Schaaf, R. J., Vis, M. M., Horrevoets, A. J., Piek, J. J., & van Royen, N. (2008). Interferon-beta signaling is enhanced in patients with insufficient coronary collateral artery development and inhibits arteriogenesis in mice. Circ Res, 102(10), 1286-1294.
  15. Sokolovic, M., Sokolovic, A., Wehkamp, D., Ver Loren van Themaat, E., de Waart, D. R., Gilhuijs-Pederson, L. A., Nikolsky, Y., van Kampen, A. H., Hakvoort, T. B., & Lamers, W. H. (2008). The transcriptomic signature of fasting murine liver. BMC Genomics, 9, 528.
  16. Soleman, R. S., Glatard, T., Veltman, D. J., Nederveen, A., & Olabarriaga, S. (2008). Large scale fMRI parameter study on a production grid. Paper presented at the MICCAI Workshop on Medical imaging on grids: achievements and perspectives, New-York.
  17. van de Mortel, J. E., Schat, H., Moerland, P. D., Ver Loren van Themaat, E., van der Ent, S., Blankestijn, H., Ghandilyan, A., Tsiatsiani, S., & Aarts, M. G. (2008). Expression differences for genes involved in lignin, glutathione and sulphate metabolism in response to cadmium in Arabidopsis thaliana and the related Zn/Cd-hyperaccumulator Thlaspi caerulescens. Plant Cell Environ, 31(3), 301-324.
  18. van der Laan, S., Sarabdjitsingh, R. A., Van Batenburg, M. F., Lachize, S. B., Li, H., Dijkmans, T. F., Vreugdenhil, E., de Kloet, E. R., & Meijer, O. C. (2008). Chromatin immunoprecipitation scanning identifies glucocorticoid receptor binding regions in the proximal promoter of a ubiquitously expressed glucocorticoid target gene in brain. J Neurochem, 106(6), 2515-2523.
  19. van Noordende, G., Olabarriaga, S., Koot, M., & de Laat, C. (2008). A Trusted Data Storage Infrastructure for Grid-Based Medical Applications. International Journal of Grid and High Performance Computing.
  20. Willemsen, A. M., Jansen, G. A., Komen, J. C., van Hooff, S., Waterham, H. R., Brites, P. M., Wanders, R. J., & van Kampen, A. H. (2008). Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways. Bioinformatics, 24(16), i21-27.
  21. Zelinkova, Z., van Beelen, A. J., de Kort, F., Moerland, P. D., Ver Loren van Themaat, E., te Velde, A. A., van Deventer, S. J., de Jong, E. C., & Hommes, D. W. (2008). Muramyl dipeptide-induced differential gene expression in NOD2 mutant and wild-type Crohn’s disease patient-derived dendritic cells. Inflamm Bowel Dis, 14(2), 186-194.

 

2009

  1. Bijl, N., Sokolovic, M., Vrins, C., Langeveld, M., Moerland, P. D., Ottenhoff, R., van Roomen, C. P., Claessen, N., Boot, R. G., Aten, J., Groen, A. K., Aerts, J. M., & van Eijk, M. (2009). Modulation of glycosphingolipid metabolism significantly improves hepatic insulin sensitivity and reverses hepatic steatosis in mice. Hepatology, 50(5), 1431-1441.
  2. Miinalainen, I. J., Schmitz, W., Huotari, A., Autio, K. J., Soininen, R., Ver Loren van Themaat, E., Baes, M., Herzig, K. H., Conzelmann, E., & Hiltunen, J. K. (2009). Mitochondrial 2,4-dienoyl-CoA reductase deficiency in mice results in severe hypoglycemia with stress intolerance and unimpaired ketogenesis. PLoS Genet, 5(7), e1000543.
  3. Olabarriaga, S., Glatard, T., Hoheisel, A., Nederveen, A., & Krefting, D. (2009). Crossing HealthGrid Borders: Early Results in Medical Imaging. Paper presented at the Healthgrid. Studies in Health Technology and Informatics.
  4. Roos, M., Marshall, M. S., Gibson, A. P., Schuemie, M., Meij, E., Katrenko, S., van Hage, W. R., Krommydas, K., & Adriaans, P. W. (2009). Structuring and extracting knowledge for the support of hypothesis generation in molecular biology. BMC Bioinformatics, 10 Suppl 10, S9.
  5. Schirmer, S. H., Fledderus, J. O., van der Laan, A. M., van der Pouw-Kraan, T. C., Moerland, P. D., Volger, O. L., Baggen, J. M., Bohm, M., Piek, J. J., Horrevoets, A. J., & van Royen, N. (2009). Suppression of inflammatory signaling in monocytes from patients with coronary artery disease. J Mol Cell Cardiol, 46(2), 177-185.
  6. Schirmer, S. H., van Royen, N., Moerland, P. D., Fledderus, J. O., Henriques, J. P., van der Schaaf, R. J., Vis, M. M., Baan, J., Jr., Koch, K. T., Horrevoets, A. J., Hoefer, I. E., & Piek, J. J. (2009). Local cytokine concentrations and oxygen pressure are related to maturation of the collateral circulation in humans. J Am Coll Cardiol, 53(23), 2141-2147.
  7. Sluimer, J. D., van der Flier, W. M., Karas, G. B., van Schijndel, R., Barnes, J., Boyes, R. G., Cover, K. S., Olabarriaga, S. D., Fox, N. C., Scheltens, P., Vrenken, H., & Barkhof, F. (2009). Accelerating regional atrophy rates in the progression from normal aging to Alzheimer’s disease. Eur Radiol, 19(12), 2826-2833.
  8. Sontrop, H., van den Ham, R., Moerland, P. D., Reinders, M., & Verhaegh, W. (2009). A sensitivity analysis of microarray feature selection and classification under measurement noise. Genomic Signal Processing and Statistics. Paper presented at the GENSIPS 2009. IEEE International Workshop.
  9. Sontrop, H. M., Moerland, P. D., van den Ham, R., Reinders, M. J., & Verhaegh, W. F. (2009). A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability. BMC Bioinformatics, 10, 389.
  10. van Hooff, S. R., Koster, J., Hulsen, T., van Schaik, B. D., Roos, M., van Batenburg, M. F., Versteeg, R., & van Kampen, A. H. (2009). The construction of genome-based transcriptional units. OMICS, 13(2), 105-114.
  11. van Munster, B. C., van Breemen, M. J., Moerland, P. D., Speijer, D., De Rooij, S. E., Pfrommer, C. J., Levi, M., Hollmann, M. W., Aerts, J. M., Zwinderman, A. H., & Korevaar, J. C. (2009). Proteomic profiling of plasma and serum in elderly patients with delirium. J Neuropsychiatry Clin Neurosci, 21(3), 284-291.
  12. van Noordende, G., Olabarriaga, S., Koot, M., & de Laat, C. (2009). A Trusted Data Storage Infrastructure for Grid-Based Medical Applications. International Journal of Grid and High Performance Computing, 1(2), 1-14.
  13. Wegdam, W., Moerland, P. D., Buist, M. R., van Themaat, E. V. L., Bleijlevens, B., Hoefsloot, H. C., de Koster, C. G., & Aerts, J. M. (2009). Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets. Proteome Sci, 7, 19.
  14. Caan, M., Vos, F. M., van Vliet, L. J., van Kampen, A., & Olabarriaga, S. (2010, 17-20 May). Gridifying a Diffusion Tensor Imaging Analysis Pipeline. Paper presented at the International Conference on Cluster, Cloud and Grid Computing, Melbourne.

 

2010

  1. Caan, M. W., Khedoe, H. G., Poot, D. H., den Dekker, A. J., Olabarriaga, S. D., Grimbergen, K. A., van Vliet, L. J., & Vos, F. M. (2010). Estimation of diffusion properties in crossing fiber bundles. IEEE Trans Med Imaging, 29(8), 1504-1515.
  2. Glatard, T., Soleman, R. S., Veltman, D. J., Nederveen, A., & Olabarriaga, S. (2010). Large scale functional MRI study on a production grid. Future Generation Computer Systems, 26(4), 685-692.
  3. Groth, P., Gibson, A., & Velterop, J. (2010). The anatomy of a nano-publication. Information Services and Use, 30(1-2), 51.
  4. Gwadry-Sridhar, F., Olabarriaga, S., van Kampen, A., Bauer, M., & Solomonides, T. (2010). Hitting the ground running: Healthgrid deployment and adoption. Paper presented at the HealthGrid 2010, Paris.
  5. Hertoghs, K. M., Moerland, P. D., van Stijn, A., Remmerswaal, E. B., Yong, S. L., van de Berg, P. J., van Ham, S. M., Baas, F., ten Berge, I. J., & van Lier, R. A. (2010). Molecular profiling of cytomegalovirus-induced human CD8+ T cell differentiation. J Clin Invest, 120(11), 4077-4090.
  6. Klarenbeek, P. L., Tak, P. P., van Schaik, B. D., Zwinderman, A. H., Jakobs, M. E., Zhang, Z., van Kampen, A. H., van Lier, R. A., Baas, F., & de Vries, N. (2010). Human T-cell memory consists mainly of unexpanded clones. Immunol Lett, 133(1), 42-48.
  7. Luyf, A. C., van Schaik, B. D., de Vries, M., Baas, F., van Kampen, A. H., & Olabarriaga, S. D. (2010). Initial steps towards a production platform for DNA sequence analysis on the grid. BMC Bioinformatics, 11, 598.
  8. Mohammed, Y., Sax, U., Dickmann, F., Lippert, J., Solodenko, J., Von Voigt, G., Smith, M., & Rienhoffo, O. (2010). Transferring the Grid Technology to the Biomedical Community. Paper presented at the Healthrid 2010, Paris.
  9. Olabarriaga, S., & Montagnat, J. (2010). Special section: Medical imaging on grids. Future Generation Computer Systems, 26(4), 678-680.
  10. Olabarriaga, S. D., Glatard, T., & de Boer, P. T. (2010). A virtual laboratory for medical image analysis. IEEE Trans Inf Technol Biomed, 14(4), 979-985.
  11. Sontrop, H., Verhaegh, W., van den Ham, R., Reinders, M., & Moerland, P. D. (2010). Subtype specific breast cancer event prediction. Paper presented at the International Workshop on Genomic Signal Processing and Statistics 2010.
  12. Tijsen, A. J., Creemers, E. E., Moerland, P. D., de Windt, L. J., van der Wal, A. C., Kok, W. E., & Pinto, Y. M. (2010). MiR423-5p as a circulating biomarker for heart failure. Circ Res, 106(6), 1035-1039.
  13. van Batenburg, M. F., Li, H., Polman, J. A., Lachize, S., Datson, N. A., Bussemaker, H. J., & Meijer, O. C. (2010). Paired hormone response elements predict caveolin-1 as a glucocorticoid target gene. PLoS One, 5(1), e8839.
  14. van der Pouw Kraan, T. C., Schirmer, S. H., Fledderus, J. O., Moerland, P. D., Baggen, J. M., Leyen, T. A., van der Laan, A. M., Piek, J. J., van Royen, N., & Horrevoets, A. J. (2010). Expression of a retinoic acid signature in circulating CD34 cells from coronary artery disease patients. BMC Genomics, 11, 388.

 

2011

  1. Benabdelkader, A., Santcroos, M., Madougou, S., van Kampen, A., & Olabarriaga, S. (2011). A Provenance approach to trace scientific experiments on a grid infrastructure. Paper presented at the International Conference on “Computing Advances in Life Sciences”.
  2. Bol, S. M., Booiman, T., Bunnik, E. M., Moerland, P. D., van Dort, K., Strauss, J. F., 3rd, Sieberer, M., Schuitemaker, H., Kootstra, N. A., & van ‘t Wout, A. B. (2011). Polymorphism in HIV-1 dependency factor PDE8A affects mRNA level and HIV-1 replication in primary macrophages. Virology, 420(1), 32-42.
  3. Bol, S. M., Moerland, P. D., Limou, S., van Remmerden, Y., Coulonges, C., van Manen, D., Herbeck, J. T., Fellay, J., Sieberer, M., Sietzema, J. G., van ‘t Slot, R., Martinson, J., Zagury, J. F., Schuitemaker, H., & van ‘t Wout, A. B. (2011). Genome-wide association study identifies single nucleotide polymorphism in DYRK1A associated with replication of HIV-1 in monocyte-derived macrophages. PLoS One, 6(2), e17190.
  4. de Vries, M., Deijs, M., Canuti, M., van Schaik, B. D., Faria, N. R., van de Garde, M. D., Jachimowski, L. C., Jebbink, M. F., Jakobs, M., Luyf, A. C., Coenjaerts, F. E., Claas, E. C., Molenkamp, R., Koekkoek, S. M., Lammens, C., Leus, F., Goossens, H., Ieven, M., Baas, F., & van der Hoek, L. (2011). A sensitive assay for virus discovery in respiratory clinical samples. PLoS One, 6(1), e16118.
  5. Hakvoort, T. B., Moerland, P. D., Frijters, R., Sokolovic, A., Labruyere, W. T., Vermeulen, J. L., Ver Loren van Themaat, E., Breit, T. M., Wittink, F. R., van Kampen, A. H., Verhoeven, A. J., Lamers, W. H., & Sokolovic, M. (2011). Interorgan coordination of the murine adaptive response to fasting. J Biol Chem, 286(18), 16332-16343.
  6. Huis in ‘t Veld, R. A., Willemsen, A. M., van Kampen, A. H., Bradley, E. J., Baas, F., Pannekoek, Y., & van der Ende, A. (2011). Deep sequencing whole transcriptome exploration of the sigmaE regulon in Neisseria meningitidis. PLoS One, 6(12), e29002.
  7. Korkhov, V., Krefting, D., Kukla, T., Terstyanszky, G., Caan, M., & Olabarriaga, S. (2011). Exploring workflow interoperability tools for neuroimaging data analysis. Paper presented at the Workshop on Workflows in Support of Large-Scale Science (WORKS’11), Seattle, USA.
  8. Krefting, D., Glatard, T., Korkhov, V., Montagnat, J., & Olabarriaga, S. (2011). Enabling Grid Interoperability at Workflow Level. Paper presented at the Grid Workflow Workshop 2011, Cologne, Germany.
  9. Mohammed, Y., Shahand, S., Korkhov, V., Luyf, A., van Schaik, B., Caan, M., van Kampen, A., Palmblad, M., & Olabarriaga, S. (2011). Data Decomposition in Biomedical e-Science Applications. Paper presented at the International Conference on “Computing Advances in Life Sciences”.
  10. Noordhuis, M. G., Fehrmann, R. S., Wisman, G. B., Nijhuis, E. R., van Zanden, J. J., Moerland, P. D., Ver Loren van Themaat, E., Volders, H. H., Kok, M., ten Hoor, K. A., Hollema, H., de Vries, E. G., de Bock, G. H., van der Zee, A. G., & Schuuring, E. (2011). Involvement of the TGF-beta and beta-catenin pathways in pelvic lymph node metastasis in early-stage cervical cancer. Clin Cancer Res, 17(6), 1317-1330.
  11. Peeters, A., Fraisl, P., van den Berg, S., Ver Loren van Themaat, E., Van Kampen, A., Rider, M. H., Takemori, H., van Dijk, K. W., Van Veldhoven, P. P., Carmeliet, P., & Baes, M. (2011). Carbohydrate metabolism is perturbed in peroxisome-deficient hepatocytes due to mitochondrial dysfunction, AMP-activated protein kinase (AMPK) activation, and peroxisome proliferator-activated receptor gamma coactivator 1alpha (PGC-1alpha) suppression. J Biol Chem, 286(49), 42162-42179.
  12. Piet, J. R., Huis in ‘t Veld, R. A., van Schaik, B. D., van Kampen, A. H., Baas, F., van de Beek, D., Pannekoek, Y., & van der Ende, A. (2011). Genome sequence of Neisseria meningitidis serogroup B strain H44/76. J Bacteriol, 193(9), 2371-2372.
  13. Ritz, K., van Schaik, B. D., Jakobs, M. E., Aronica, E., Tijssen, M. A., van Kampen, A. H., & Baas, F. (2011). Looking ultra deep: short identical sequences and transcriptional slippage. Genomics, 98(2), 90-95.
  14. Ritz, K., van Schaik, B. D., Jakobs, M. E., van Kampen, A. H., Aronica, E., Tijssen, M. A., & Baas, F. (2011). SGCE isoform characterization and expression in human brain: implications for myoclonus-dystonia pathogenesis? Eur J Hum Genet, 19(4), 438-444.
  15. Shahand, S., Santcroos, M., Mohammed, Y., Korkhov, V., Luyf, A., van Kampen, A., & Olabarriaga, S. (2011, June 2011). Front-ends to Biomedical Data Analysis on Grids. Paper presented at the HealthGrid, Bristol, UK.
  16. Sondermeijer, B. M., Bakker, A., Halliani, A., de Ronde, M. W., Marquart, A. A., Tijsen, A. J., Mulders, T. A., Kok, M. G., Battjes, S., Maiwald, S., Sivapalaratnam, S., Trip, M. D., Moerland, P. D., Meijers, J. C., Creemers, E. E., & Pinto-Sietsma, S. J. (2011). Platelets in patients with premature coronary artery disease exhibit upregulation of miRNA340* and miRNA624*. PLoS One, 6(10), e25946.
  17. Sontrop, H. M., Verhaegh, W. F., Reinders, M. J., & Moerland, P. D. (2011). An evaluation protocol for subtype-specific breast cancer event prediction. PLoS One, 6(7), e21681.
  18. Stobbe, M. D., Houten, S. M., Jansen, G. A., van Kampen, A. H., & Moerland, P. D. (2011). Critical assessment of human metabolic pathway databases: a stepping stone for future integration. BMC Syst Biol, 5, 165.
  19. van Manen, D., Delaneau, O., Kootstra, N. A., Boeser-Nunnink, B. D., Limou, S., Bol, S. M., Burger, J. A., Zwinderman, A. H., Moerland, P. D., van ‘t Slot, R., Zagury, J. F., van ‘t Wout, A. B., & Schuitemaker, H. (2011). Genome-wide association scan in HIV-1-infected individuals identifying variants influencing disease course. PLoS One, 6(7), e22208.
  20. van ‘t Noordende, G., Olabarriaga, S., Koot, M., & de Laat, C. (2011). Trusted Data Management for Grid-Based Medical Applications. In Cloud, Grid and High Performance Computing: Emerging Applications (pp. 208-220): IGI Global
  21. van ‘t Noordende, G., Olabarriaga, S., Koot, M. R., & de Laat, C. (2011). Trusted Data Management for Grid-Based Medical Applications in Cloud. Paper presented at the Grid and High Performance Computing: Emerging Applications.

 

2012

  1. Caan, M. W., Shahand, S., Vos, F. M., van Kampen, A., & Olabarriaga, S. (2012). Evolution of Grid-based Services for Diffusion Tensor Image Analysis. Future Generation Computer Systems, 28(8), 1194-1204.
  2. de Vries, M., Oude Munnink, B. B., Deijs, M., Canuti, M., Koekkoek, S. M., Molenkamp, R., Bakker, M., Jurriaans, S., van Schaik, B. D., Luyf, A. C., Olabarriaga, S. D., van Kampen, A. H., & van der Hoek, L. (2012). Performance of VIDISCA-454 in feces-suspensions and serum. Viruses, 4(8), 1328-1334.
  3. Gesing, S., Glatard, T., Kruger, J., Olabarriaga, S., Solomonides, T., Silverstein, J., Montagnat, J., Gaignard, A., & Krefting, D. (2012). Meet Science Gateways for Life Sciences. In HealthGrid Applications and Technologies (Vol. 1). Amsterdam, the Netherlands: IOS Press
  4. Helbig, C., Gentek, R., Backer, R. A., de Souza, Y., Derks, I. A., Eldering, E., Wagner, K., Jankovic, D., Gridley, T., Moerland, P. D., Flavell, R. A., & Amsen, D. (2012). Notch controls the magnitude of T helper cell responses by promoting cellular longevity. Proc Natl Acad Sci U S A, 109(23), 9041-9046.
  5. Jupp, S., Gibson, A., Malone, J., & Stevens, R. (2012, July 21-25). Taking a view on bio-ontologies. Paper presented at the International Conference on Biomedical Ontology, University of Graz.
  6. Klarenbeek, P. L., de Hair, M. J., Doorenspleet, M. E., van Schaik, B. D., Esveldt, R. E., van de Sande, M. G., Cantaert, T., Gerlag, D. M., Baeten, D., van Kampen, A. H., Baas, F., Tak, P. P., & de Vries, N. (2012). Inflamed target tissue provides a specific niche for highly expanded T-cell clones in early human autoimmune disease. Ann Rheum Dis, 71(6), 1088-1093.
  7. Klarenbeek, P. L., Remmerswaal, E. B., ten Berge, I. J., Doorenspleet, M. E., van Schaik, B. D., Esveldt, R. E., Koch, S. D., ten Brinke, A., van Kampen, A. H., Bemelman, F. J., Tak, P. P., Baas, F., de Vries, N., & van Lier, R. A. (2012). Deep sequencing of antiviral T-cell responses to HCMV and EBV in humans reveals a stable repertoire that is maintained for many years. PLoS Pathog, 8(9), e1002889.
  8. Kramer, G., Moerland, P. D., Jeeninga, R. E., Vlietstra, W. J., Ringrose, J. H., Byrman, C., Berkhout, B., & Speijer, D. (2012). Proteomic analysis of HIV-T cell interaction: an update. Front Microbiol, 3, 240.
  9. Lodder, E. M., Scicluna, B. P., Milano, A., Sun, A. Y., Tang, H., Remme, C. A., Moerland, P. D., Tanck, M. W., Pitt, G. S., Marchuk, D. A., & Bezzina, C. R. (2012). Dissection of a quantitative trait locus for PR interval duration identifies Tnni3k as a novel modulator of cardiac conduction. PLoS Genet, 8(12), e1003113.
  10. Luckow, A., Santcroos, M., Weidner, O., Merzky, A., Maddineni, S., & Jha, S. (2012). Towards a common model for pilot-jobs. Paper presented at the International symposium on High-Performance Parallel and Distributed Computing, Delft, the Netherlands.
  11. Luckow, A., Santcroos, M., Weidner, O., Merzky, A., Mantha, P., & Jha, S. (2012). A Model of Pilot-Abstractions. Paper presented at the International Conference on e-Science.
  12. Madougou, S., Santcroos, M., Benabdelkader, A., van Schaik, B., Shahand, S., Korkhov, V., van Kampen, A., & Olabarriaga, S. (2012). Provenance for distributed biomedical workflow execution. Paper presented at the HealthGrid.
  13. Marquering, H., Engelbers, J., Groot, P., Majoie, C., Beenen, L., van Kampen, A., & Olabarriaga, S. (2012, 1 October 2012). Optimization and Parallelization of the Matched Masked Bone Elimination Method for CTA. Paper presented at the MICCAI workshop on Data- and Compute-Intensive Clinical and Translational Imaging Applications, Nice, France.
  14. Mouw, E., van ‘t Noordende, G., Guido, J., van Kampen, A., Santcroos, M., & Olabarriaga, S. (2012). Legal constraints on genetic data processing in European grids. Paper presented at the HealthGrid, Amsterdam.
  15. Santcroos, M., Olabarriaga, S., Jha, S., & Katz, D. (2012, 9 October 2012). Pilot Abstractions for Compute, Data, and Network. Paper presented at the Workshop on Collaborative research using eScience infrastructure and high speed networks, eScience 2012, Chicago.
  16. Schopman, N. C., van Montfort, T., Willemsen, M., Knoepfel, S. A., Pollakis, G., van Kampen, A., Sanders, R. W., Haasnoot, J., & Berkhout, B. (2012). Selective packaging of cellular miRNAs in HIV-1 particles. Virus Res, 169(2), 438-447.
  17. Schopman, N. C., Willemsen, M., Liu, Y. P., Bradley, T., van Kampen, A., Baas, F., Berkhout, B., & Haasnoot, J. (2012). Deep sequencing of virus-infected cells reveals HIV-encoded small RNAs. Nucleic Acids Res, 40(1), 414-427.
  18. Shahand, S., Caan, M., van Kampen, A., & Olabarriaga, S. (2012). Integrated Support for Neuroscience Research: from Study Design to Publication. Paper presented at the HealthGrid.
  19. Shahand, S., Santcroos, M., van Kampen, A., & Olabarriaga, S. (2012). A Grid-enabled Gateway for Biomedical Data Analysis. Journal of Grid Computing, 10, 795-742.
  20. Stobbe, M. (2012). 18 October 2012. The road to knowledge: from biology to databases and back again. (PhD thesis). University of Amsterdam, Amsterdam. NBIC BioRange. Van Kampen,  A.H.C. (promotor), Moerland, P. D. (co-promotor)
  21. Stobbe, M. D., Houten, S. M., van Kampen, A. H., Wanders, R. J., & Moerland, P. D. (2012). Improving the description of metabolic networks: the TCA cycle as example. FASEB J, 26(9), 3625-3636.
  22. Van Houdt, J. K., Nowakowska, B. A., Sousa, S. B., van Schaik, B. D., Seuntjens, E., Avonce, N., Sifrim, A., Abdul-Rahman, O. A., van den Boogaard, M. J., Bottani, A., Castori, M., Cormier-Daire, V., Deardorff, M. A., Filges, I., Fryer, A., Fryns, J. P., Gana, S., Garavelli, L., Gillessen-Kaesbach, G., Hall, B. D., Horn, D., Huylebroeck, D., Klapecki, J., Krajewska-Walasek, M., Kuechler, A., Lines, M. A., Maas, S., Macdermot, K. D., McKee, S., Magee, A., de Man, S. A., Moreau, Y., Morice-Picard, F., Obersztyn, E., Pilch, J., Rosser, E., Shannon, N., Stolte-Dijkstra, I., Van Dijck, P., Vilain, C., Vogels, A., Wakeling, E., Wieczorek, D., Wilson, L., Zuffardi, O., van Kampen, A. H., Devriendt, K., Hennekam, R., & Vermeesch, J. R. (2012). Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome. Nat Genet, 44(4), 445-449, S441.
  23. van Schaik, B., Santcroos, M., Korkhov, V., Jongejan, A., Willemsen, M., van Kampen, A., & Olabarriaga, S. (2012). Challenges in DNA sequence analysis on a production grid. Paper presented at the EGICF12-EMITC2.
  24. van Wingen, G. A., Geuze, E., Caan, M. W., Kozicz, T., Olabarriaga, S. D., Denys, D., Vermetten, E., & Fernandez, G. (2012). Persistent and reversible consequences of combat stress on the mesofrontal circuit and cognition. Proc Natl Acad Sci U S A, 109(38), 15508-15513.
  25. Wegdam, W., Moerland, P. D., Meijer, D., de Jong, S. M., Hoefsloot, H. C., Kenter, G. G., Buist, M. R., & Aerts, J. M. (2012). A critical assessment of SELDI-TOF-MS for biomarker discovery in serum and tissue of patients with an ovarian mass. Proteome Sci, 10(1), 45.
  26. Wortmann, S. B., Vaz, F. M., Gardeitchik, T., Vissers, L. E., Renkema, G. H., Schuurs-Hoeijmakers, J. H., Kulik, W., Lammens, M., Christin, C., Kluijtmans, L. A., Rodenburg, R. J., Nijtmans, L. G., Grunewald, A., Klein, C., Gerhold, J. M., Kozicz, T., van Hasselt, P. M., Harakalova, M., Kloosterman, W., Baric, I., Pronicka, E., Ucar, S. K., Naess, K., Singhal, K. K., Krumina, Z., Gilissen, C., van Bokhoven, H., Veltman, J. A., Smeitink, J. A., Lefeber, D. J., Spelbrink, J. N., Wevers, R. A., Morava, E., & de Brouwer, A. P. (2012). Mutations in the phospholipid remodeling gene SERAC1 impair mitochondrial function and intracellular cholesterol trafficking and cause dystonia and deafness. Nat Genet, 44(7), 797-802.

 

2013

  1. Barros, R., van Geldermalsen, S., Boers, A., Belloum, A. S., Marquering, H., & Olabarriaga, S. (2013, 27 August ). Heterogeneous Platforms Programming for Faster Medical Imaging Processing. Paper presented at the International Workshop on High Performance Bioinformatics and Biomedicine, Aachen, Germany.
  2. Bergonzi, S., Albani, M. C., Ver Loren van Themaat, E., Nordstrom, K. J., Wang, R., Schneeberger, K., Moerland, P. D., & Coupland, G. (2013). Mechanisms of age-dependent response to winter temperature in perennial flowering of Arabis alpina. Science, 340(6136), 1094-1097.
  3. de Kwaasteniet, B., Ruhe, E., Caan, M., Rive, M., Olabarriaga, S., Groefsema, M., Heesink, L., van Wingen, G., & Denys, D. (2013). Relation between structural and functional connectivity in major depressive disorder. Biol Psychiatry, 74(1), 40-47.
  4. Farkas, Z., Kacsuk, P., Santcroos, M., Olabarriaga, S., Balasko, A., & Karoczkai, K. (2013). Data Bridge: solving diverse data access in scientific applications. Paper presented at the International Workshop on Science Gateways, Zurich, Switzerland.
  5. Kiezun, A., Pulit, S. L., Francioli, L. C., van Dijk, F., Swertz, M., Boomsma, D. I., van Duijn, C. M., Slagboom, P. E., van Ommen, G. J., Wijmenga, C., Genome of the Netherlands, C., de Bakker, P. I., & Sunyaev, S. R. (2013). Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency. PLoS Genet, 9(2), e1003301.
  6. Kleinrouweler, C. E., van Uitert, M., Moerland, P. D., Ris-Stalpers, C., van der Post, J. A., & Afink, G. B. (2013). Differentially expressed genes in the pre-eclamptic placenta: a systematic review and meta-analysis. PLoS One, 8(7), e68991.
  7. Korkhov, V., & Olabarriaga, S. (2013). Exploring Workflow Interoperability for Neuroimage Analysis on the SHIWA Platform. Journal of Grid Computing, 11(3), 505-522.
  8. Madougou, S., Shahand, S., Santcroos, M., van Schaik, B., Benabdelkader, A., van Kampen, A., & Olabarriaga, S. (2013). Characterizing Workflow-based Activity on a Production e-Infrastructure Using Provenance Data. Future Generation Computer Systems, 29(8), 1931-1942.
  9. McClellan, E. A., Moerland, P. D., van der Spek, P. J., & Stubbs, A. P. (2013). NetWeAvers: an R package for integrative biological network analysis with mass spectrometry data. Bioinformatics, 29(22), 2946-2947.
  10. Mouw, E., van ‘t Noordende, G., Louter, B., & Olabarriaga, S. (2013). A Model-based Information Security Risk Assessment method for Science Gateways. Paper presented at the International Workshop on Science Gateways, Zurich, Switzerland.
  11. Olabarriaga, S., Jaghoori, M., Korkhov, V., van Schaik, B., & van Kampen, A. (2013). Understanding workflows for distributed computing: nitty-gritty details. Paper presented at the Workshop on Workflows in Support of Large-Scale Science, New York, USA.
  12. Peters, B. D., Machielsen, M. W., Hoen, W. P., Caan, M. W., Malhotra, A. K., Szeszko, P. R., Duran, M., Olabarriaga, S. D., & de Haan, L. (2013). Polyunsaturated fatty acid concentration predicts myelin integrity in early-phase psychosis. Schizophr Bull, 39(4), 830-838.
  13. Rienstra, A., Groot, P. F., Spaan, P. E., Majoie, C. B., Nederveen, A. J., Walstra, G. J., de Jonghe, J. F., van Gool, W. A., Olabarriaga, S. D., Korkhov, V. V., & Schmand, B. (2013). Symptom validity testing in memory clinics: Hippocampal-memory associations and relevance for diagnosing mild cognitive impairment. J Clin Exp Neuropsychol, 35(1), 59-70.
  14. Santcroos, M., van Schaik, B., Shahand, S., Olabarriaga, S., Luckow, A., & Jha, S. (2013, 13-16 May ). Exploring dynamic enactment of scientific workflows using pilot-abstractions. Paper presented at the International Symposium on Cluster, Cloud and Grid Computing, Delft, the Netherlands.
  15. Shahand, S., Benabdelkader, A., Huguet, J., Jaghouri, M., Santcroos, M., al Mourabit, M., Groot, P., Caan, M., van Kampen, A., & Olabarriaga, S. (2013, 3-5 June). A data-centric science gateway for computational neuroscience. Paper presented at the International Workshop on Science Gateways, Zurich, Switzerland.
  16. Stobbe, M., Mishra, T., & Macintyre, G. (2013). Breaking the ice and forging links: the importance of socializing in research. PLoS Comput Biol, 9(11), e1003355.
  17. Stobbe, M. D., Swertz, M. A., Thiele, I., Rengaw, T., van Kampen, A. H., & Moerland, P. D. (2013). Consensus and conflict cards for metabolic pathway databases. BMC Syst Biol, 7, 50.
  18. Thiele, I., Swainston, N., Fleming, R. M., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., Thorleifsson, S. G., Agren, R., Bolling, C., Bordel, S., Chavali, A. K., Dobson, P., Dunn, W. B., Endler, L., Hala, D., Hucka, M., Hull, D., Jameson, D., Jamshidi, N., Jonsson, J. J., Juty, N., Keating, S., Nookaew, I., Le Novere, N., Malys, N., Mazein, A., Papin, J. A., Price, N. D., Selkov, E., Sr., Sigurdsson, M. I., Simeonidis, E., Sonnenschein, N., Smallbone, K., Sorokin, A., van Beek, J. H., Weichart, D., Goryanin, I., Nielsen, J., Westerhoff, H. V., Kell, D. B., Mendes, P., & Palsson, B. O. (2013). A community-driven global reconstruction of human metabolism. Nat Biotechnol, 31(5), 419-425.
  19. Wensveen, F. M., Klarenbeek, P. L., van Gisbergen, K. P., Pascutti, M. F., Derks, I. A., van Schaik, B. D., Ten Brinke, A., de Vries, N., Cekinovic, D., Jonjic, S., van Lier, R. A., & Eldering, E. (2013). Pro-apoptotic protein Noxa regulates memory T cell population size and protects against lethal immunopathology. J Immunol, 190(3), 1180-1191.

 

2014

  1. Backer, R. A., Helbig, C., Gentek, R., Kent, A., Laidlaw, B. J., Dominguez, C. X., de Souza, Y. S., van Trierum, S. E., van Beek, R., Rimmelzwaan, G. F., ten Brinke, A., Willemsen, A. M., van Kampen, A. H., Kaech, S. M., Blander, J. M., van Gisbergen, K., & Amsen, D. (2014). A central role for Notch in effector CD8(+) T cell differentiation. Nat Immunol, 15(12), 1143-1151.
  2. Cobos Jimenez, V., Bradley, E. J., Willemsen, A. M., van Kampen, A. H., Baas, F., & Kootstra, N. A. (2014). Next-generation sequencing of microRNAs uncovers expression signatures in polarized macrophages. Physiol Genomics, 46(3), 91-103.
  3. Cordeddu, V., Redeker, B., Stellacci, E., Jongejan, A., Fragale, A., Bradley, T. E., Anselmi, M., Ciolfi, A., Cecchetti, S., Muto, V., Bernardini, L., Azage, M., Carvalho, D. R., Espay, A. J., Male, A., Molin, A. M., Posmyk, R., Battisti, C., Casertano, A., Melis, D., van Kampen, A., Baas, F., Mannens, M. M., Bocchinfuso, G., Stella, L., Tartaglia, M., & Hennekam, R. C. (2014). Mutations in ZBTB20 cause Primrose syndrome. Nat Genet, 46(8), 815-817.
  4. Deelen, P., Menelaou, A., van Leeuwen, E. M., Kanterakis, A., van Dijk, F., Medina-Gomez, C., Francioli, L. C., Hottenga, J. J., Karssen, L. C., Estrada, K., Kreiner-Moller, E., Rivadeneira, F., van Setten, J., Gutierrez-Achury, J., Westra, H. J., Franke, L., van Enckevort, D., Dijkstra, M., Byelas, H., van Duijn, C. M., Genome of Netherlands, C., de Bakker, P. I., Wijmenga, C., & Swertz, M. A. (2014). Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands’. Eur J Hum Genet, 22(11), 1321-1326.
  5. Doorenspleet, M. E., Klarenbeek, P. L., de Hair, M. J., van Schaik, B. D., Esveldt, R. E., van Kampen, A. H., Gerlag, D. M., Musters, A., Baas, F., Tak, P. P., & de Vries, N. (2014). Rheumatoid arthritis synovial tissue harbours dominant B-cell and plasma-cell clones associated with autoreactivity. Ann Rheum Dis, 73(4), 756-762.
  6. Genome of the Netherlands, C., & van schaik, B. D. C. (2014). Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat Genet, 46(8), 818-825.
  7. Houten, S. M., Denis, S., Te Brinke, H., Jongejan, A., van Kampen, A. H., Bradley, E. J., Baas, F., Hennekam, R. C., Millington, D. S., Young, S. P., Frazier, D. M., Gucsavas-Calikoglu, M., & Wanders, R. J. (2014). Mitochondrial NADP(H) deficiency due to a mutation in NADK2 causes dienoyl-CoA reductase deficiency with hyperlysinemia. Hum Mol Genet, 23(18), 5009-5016.
  8. Kerami, Z., Duijvis, N. W., Vogels, E. W., van Dooren, F. H., Moerland, P. D., & Te Velde, A. A. (2014). Effect of interleukin-17 on gene expression profile of fibroblasts from Crohn’s disease patients. J Crohns Colitis, 8(10), 1208-1216.
  9. Koopmann, T. T., Adriaens, M. E., Moerland, P. D., Marsman, R. F., Westerveld, M. L., Lal, S., Zhang, T., Simmons, C. Q., Baczko, I., dos Remedios, C., Bishopric, N. H., Varro, A., George, A. L., Jr., Lodder, E. M., & Bezzina, C. R. (2014). Genome-wide identification of expression quantitative trait loci (eQTLs) in human heart. PLoS One, 9(5), e97380.
  10. Lodder, E. M., Scicluna, B. P., Beekman, L., Arends, D., Moerland, P. D., Tanck, M. W., Adriaens, M. E., & Bezzina, C. R. (2014). Integrative genomic approach identifies multiple genes involved in cardiac collagen deposition. Circ Cardiovasc Genet, 7(6), 790-798.
  11. Piet, J. R., Geldhoff, M., van Schaik, B. D., Brouwer, M. C., Valls Seron, M., Jakobs, M. E., Schipper, K., Pannekoek, Y., Zwinderman, A. H., van der Poll, T., van Kampen, A. H., Baas, F., van der Ende, A., & van de Beek, D. (2014). Streptococcus pneumoniae arginine synthesis genes promote growth and virulence in pneumococcal meningitis. J Infect Dis, 209(11), 1781-1791.
  12. Ramdayal, K., Stobbe, M. D., Mishra, T., & Michaut, M. (2014). Building the future of bioinformatics through student-facilitated conferencing. PLoS Comput Biol, 10(1), e1003458.
  13. Reshetova, P., Smilde, A. K., van Kampen, A. H., & Westerhuis, J. A. (2014). Use of prior knowledge for the analysis of high-throughput transcriptomics and metabolomics data. BMC Syst Biol, 8 Suppl 2, S2.
  14. Shahand, S., Jaghoori, M., Benabdelkader, A., Font-Calvo, J., Huguet, J., Caan, M., van Kampen, A., & Olabarriaga, S. (2014). Computational Neuroscience Gateway: A science gateway Based on the WS-PGRADE/gUSE. In Science Gateways for Distributed Computing Infrastructures. Development Framework and Exploitation by Scientific User Communities. (pp. 139-150). Cham: Springer
  15. Stobbe, M. D., Jansen, G. A., Moerland, P. D., & van Kampen, A. H. (2014). Knowledge representation in metabolic pathway databases. Brief Bioinform, 15(3), 455-470.
  16. Tax, D., Sontrop, H., Reinders, M., & Moerland, P. D. (2014). The effect of aggregating subtype performances depends strongly on the performance measure used. Paper presented at the International Conference on Pattern Recognition.
  17. van Oorschot, B., Hovingh, S. E., Moerland, P. D., Medema, J. P., Stalpers, L. J., Vrieling, H., & Franken, N. A. (2014). Reduced activity of double-strand break repair genes in prostate cancer patients with late normal tissue radiation toxicity. Int J Radiat Oncol Biol Phys, 88(3), 664-670.
  18. van Schaik, B., Klarenbeek, P., Doorenspleet, M., van Kampen, A., Moody, D. B., de Vries, N., & Van Rhijn, I. (2014). Discovery of invariant T cells by next-generation sequencing of the human TCR alpha-chain repertoire. J Immunol, 193(10), 5338-5344.
  19. Wegdam, W., Argmann, C. A., Kramer, G., Vissers, J. P., Buist, M. R., Kenter, G. G., Aerts, J. M., Meijer, D., & Moerland, P. D. (2014). Label-free LC-MSe in tissue and serum reveals protein networks underlying differences between benign and malignant serous ovarian tumors. PLoS One, 9(9), e108046.

 

2015

  1. Boekel, J., Chilton, J. M., Cooke, I. R., Horvatovich, P. L., Jagtap, P. D., Kall, L., Lehtio, J., Lukasse, P., Moerland, P. D., & Griffin, T. J. (2015). Multi-omic data analysis using Galaxy. Nat Biotechnol, 33(2), 137-139.
  2. Canuti, M., van Beveren, N. J., Jazaeri Farsani, S. M., de Vries, M., Deijs, M., Jebbink, M. F., Zaaijer, H. L., van Schaik, B. D., van Kampen, A. H., van der Kuyl, A. C., de Haan, L., Storosum, J. G., & van der Hoek, L. (2015). Viral metagenomics in drug-naive, first-onset schizophrenia patients with prominent negative symptoms. Psychiatry Res, 229(3), 678-684.
  3. Francioli, L. C., Polak, P. P., Koren, A., Menelaou, A., Chun, S., Renkens, I., Genome of the Netherlands, C., van Duijn, C. M., Swertz, M., Wijmenga, C., van Ommen, G., Slagboom, P. E., Boomsma, D. I., Ye, K., Guryev, V., Arndt, P. F., Kloosterman, W. P., de Bakker, P. I. W., & Sunyaev, S. R. (2015). Genome-wide patterns and properties of de novo mutations in humans. Nat Genet, 47(7), 822-826.
  4. Groen, J. L., Andrade, A., Ritz, K., Jalalzadeh, H., Haagmans, M., Bradley, T. E., Jongejan, A., Verbeek, D. S., Nurnberg, P., Denome, S., Hennekam, R. C., Lipscombe, D., Baas, F., & Tijssen, M. A. (2015). CACNA1B mutation is linked to unique myoclonus-dystonia syndrome. Hum Mol Genet, 24(4), 987-993.
  5. Groen, J. L., Ritz, K., Jalalzadeh, H., van der Salm, S. M., Jongejan, A., Mook, O. R., Haagmans, M. A., Zwinderman, A. H., Motazacker, M. M., Hennekam, R. C., Baas, F., & Tijssen, M. A. (2015). RELN rare variants in myoclonus-dystonia. Mov Disord, 30(3), 415-419.
  6. Harwig, A., Herrera-Carrillo, E., Jongejan, A., van Kampen, A. H., & Berkhout, B. (2015). Deep Sequence Analysis of AgoshRNA Processing Reveals 3′ A Addition and Trimming. Mol Ther Nucleic Acids, 4, e247.
  7. Jebbink, J. M., Boot, R. G., Keijser, R., Moerland, P. D., Aten, J., Veenboer, G. J., van Wely, M., Buimer, M., Ver Loren van Themaat, E., Aerts, J. M., van der Post, J. A., Afink, G. B., & Ris-Stalpers, C. (2015). Increased glucocerebrosidase expression and activity in preeclamptic placenta. Placenta, 36(2), 160-169.
  8. Klarenbeek, P. L., Doorenspleet, M. E., Esveldt, R. E., van Schaik, B. D., Lardy, N., van Kampen, A. H., Tak, P. P., Plenge, R. M., Baas, F., de Bakker, P. I., & de Vries, N. (2015). Somatic Variation of T-Cell Receptor Genes Strongly Associate with HLA Class Restriction. PLoS One, 10(10), e0140815.
  9. Kloosterman, W. P., Francioli, L. C., Hormozdiari, F., Marschall, T., Hehir-Kwa, J. Y., Abdellaoui, A., Lameijer, E. W., Moed, M. H., Koval, V., Renkens, I., van Roosmalen, M. J., Arp, P., Karssen, L. C., Coe, B. P., Handsaker, R. E., Suchiman, E. D., Cuppen, E., Thung, D. T., McVey, M., Wendl, M. C., Genome of Netherlands, C., Uitterlinden, A., van Duijn, C. M., Swertz, M. A., Wijmenga, C., van Ommen, G. B., Slagboom, P. E., Boomsma, D. I., Schonhuth, A., Eichler, E. E., de Bakker, P. I., Ye, K., & Guryev, V. (2015). Characteristics of de novo structural changes in the human genome. Genome Res, 25(6), 792-801.
  10. Kok, M. G., Halliani, A., Moerland, P. D., Meijers, J. C., Creemers, E. E., & Pinto-Sietsma, S. J. (2015). Normalization panels for the reliable quantification of circulating microRNAs by RT-qPCR. FASEB J, 29(9), 3853-3862.
  11. Kurakula, K., Sommer, D., Sokolovic, M., Moerland, P. D., Scheij, S., van Loenen, P. B., Koenis, D. S., Zelcer, N., van Tiel, C. M., & de Vries, C. J. (2015). LIM-only protein FHL2 is a positive regulator of liver X receptors in smooth muscle cells involved in lipid homeostasis. Mol Cell Biol, 35(1), 52-62.
  12. Liu, Y. P., Karg, M., Harwig, A., Herrera-Carrillo, E., Jongejan, A., van Kampen, A., & Berkhout, B. (2015). Mechanistic insights on the Dicer-independent AGO2-mediated processing of AgoshRNAs. RNA Biol, 12(1), 92-100.
  13. Nandal, U. K., Vlietstra, W. J., Byrman, C., Jeeninga, R. E., Ringrose, J. H., van Kampen, A. H., Speijer, D., & Moerland, P. D. (2015). Candidate prioritization for low-abundant differentially expressed proteins in 2D-DIGE datasets. BMC Bioinformatics, 16, 25.
  14. Palao, T., Sward, K., Jongejan, A., Moerland, P. D., de Vos, J., van Weert, A., Arribas, S. M., Groma, G., vanBavel, E., & Bakker, E. N. (2015). Gene Expression and MicroRNA Expression Analysis in Small Arteries of Spontaneously Hypertensive Rats. Evidence for ER Stress. PLoS One, 10(9), e0137027.
  15. Remmerswaal, E. B., Klarenbeek, P. L., Alves, N. L., Doorenspleet, M. E., van Schaik, B. D., Esveldt, R. E., Idu, M. M., van Leeuwen, E. M., van der Bom-Baylon, N., van Kampen, A. H., Koch, S. D., Pircher, H., Bemelman, F. J., Ten Brinke, A., Baas, F., Ten Berge, I. J., van Lier, R. A., & de Vries, N. (2015). Clonal evolution of CD8+ T cell responses against latent viruses: relationship among phenotype, localization, and function. J Virol, 89(1), 568-580.
  16. Reshetova, P., Smilde, A. K., Westerhuis, J. A., & van Kampen, A. H. (2015). Using Petri nets for experimental design in a multi-organ elimination pathway. Comput Biol Med, 63, 19-27.
  17. Shahand, S. (2015). 1 October 2011 – 1 October 2015. Science gateways for biomedical big data analysis. (PhD thesis). University of Amsterdam, Amsterdam. COMMIT. Van Kampen,  A. (promotor), Olabarriaga, S. (co-promotor)
  18. Shahand, S., Benabdelkader, A., Jaghoori, M., al Mourabit, M., Huguet, J., Caan, M., van Kampen, A., & Olabarriaga, S. (2015). A data-centric neuroscience gateway: design, implementation, and experiences. Paper presented at the CONCURR COMP-Pract E.
  19. Shahand, S., van Kampen, A., & Olabarriaga, S. (2015). Science Gateway Canvas: A business reference model for Science Gateways. Paper presented at the Workshop on The Science of Cyberinfrastructure: Research, Experience, Applications and Models, New York, USA.
  20. Sontrop, H. (2015). 15 January 2015. A critical perspective on microarray breast cancer gene expression profiling. (PhD thesis). TU Delft, Delft. NBIC BioRange. Reinders, M. (promotor), Moerland, P. D. (co-promotor)
  21. Te Raa, G. D., Derks, I. A., Navrkalova, V., Skowronska, A., Moerland, P. D., van Laar, J., Oldreive, C., Monsuur, H., Trbusek, M., Malcikova, J., Loden, M., Geisler, C. H., Hullein, J., Jethwa, A., Zenz, T., Pospisilova, S., Stankovic, T., van Oers, M. H., Kater, A. P., & Eldering, E. (2015). The impact of SF3B1 mutations in CLL on the DNA-damage response. Leukemia, 29(5), 1133-1142.
  22. te Raa, G. D., Moerland, P. D., Leeksma, A. C., Derks, I. A., Yigittop, H., Laddach, N., Loden-van Straaten, M., Navrkalova, V., Trbusek, M., Luijks, D. M., Zenz, T., Skowronska, A., Hoogendoorn, M., Stankovic, T., van Oers, M. H., Eldering, E., & Kater, A. P. (2015). Assessment of p53 and ATM functionality in chronic lymphocytic leukemia by multiplex ligation-dependent probe amplification. Cell Death Dis, 6, e1852.
  23. van der Meer, A. J., Scicluna, B. P., Moerland, P. D., Lin, J., Jacobson, E. W., Vlasuk, G. P., & van der Poll, T. (2015). The Selective Sirtuin 1 Activator SRT2104 Reduces Endotoxin-Induced Cytokine Release and Coagulation Activation in Humans. Crit Care Med, 43(6), e199-202.
  24. van Leeuwen, E. M., Kanterakis, A., Deelen, P., Kattenberg, M. V., Genome of the Netherlands, C., Slagboom, P. E., de Bakker, P. I., Wijmenga, C., Swertz, M. A., Boomsma, D. I., van Duijn, C. M., Karssen, L. C., & Hottenga, J. J. (2015). Population-specific genotype imputations using minimac or IMPUTE2. Nat Protoc, 10(9), 1285-1296.
  25. van Leeuwen, E. M., Karssen, L. C., Deelen, J., Isaacs, A., Medina-Gomez, C., Mbarek, H., Kanterakis, A., Trompet, S., Postmus, I., Verweij, N., van Enckevort, D. J., Huffman, J. E., White, C. C., Feitosa, M. F., Bartz, T. M., Manichaikul, A., Joshi, P. K., Peloso, G. M., Deelen, P., van Dijk, F., Willemsen, G., de Geus, E. J., Milaneschi, Y., Penninx, B. W., Francioli, L. C., Menelaou, A., Pulit, S. L., Rivadeneira, F., Hofman, A., Oostra, B. A., Franco, O. H., Mateo Leach, I., Beekman, M., de Craen, A. J., Uh, H. W., Trochet, H., Hocking, L. J., Porteous, D. J., Sattar, N., Packard, C. J., Buckley, B. M., Brody, J. A., Bis, J. C., Rotter, J. I., Mychaleckyj, J. C., Campbell, H., Duan, Q., Lange, L. A., Wilson, J. F., Hayward, C., Polasek, O., Vitart, V., Rudan, I., Wright, A. F., Rich, S. S., Psaty, B. M., Borecki, I. B., Kearney, P. M., Stott, D. J., Adrienne Cupples, L., Genome of The Netherlands, C., Jukema, J. W., van der Harst, P., Sijbrands, E. J., Hottenga, J. J., Uitterlinden, A. G., Swertz, M. A., van Ommen, G. J., de Bakker, P. I., Eline Slagboom, P., Boomsma, D. I., Wijmenga, C., & van Duijn, C. M. (2015). Genome of The Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels. Nat Commun, 6, 6065.
  26. van Uitert, M., Moerland, P. D., Enquobahrie, D. A., Laivuori, H., van der Post, J. A., Ris-Stalpers, C., & Afink, G. B. (2015). Meta-Analysis of Placental Transcriptome Data Identifies a Novel Molecular Pathway Related to Preeclampsia. PLoS One, 10(7), e0132468.
  27. Vaz, F. M., Pras-Raves, M., Bootsma, A. H., & van Kampen, A. H. (2015). Principles and practice of lipidomics. J Inherit Metab Dis, 38(1), 41-52.
  28. Vieira Braga, F. A., Hertoghs, K. M., Kragten, N. A., Doody, G. M., Barnes, N. A., Remmerswaal, E. B., Hsiao, C. C., Moerland, P. D., Wouters, D., Derks, I. A., van Stijn, A., Demkes, M., Hamann, J., Eldering, E., Nolte, M. A., Tooze, R. M., ten Berge, I. J., van Gisbergen, K. P., & van Lier, R. A. (2015). Blimp-1 homolog Hobit identifies effector-type lymphocytes in humans. Eur J Immunol, 45(10), 2945-2958.
  29. Weijer, R., Broekgaarden, M., van Golen, R. F., Bulle, E., Nieuwenhuis, E., Jongejan, A., Moerland, P. D., van Kampen, A. H., van Gulik, T. M., & Heger, M. (2015). Low-power photodynamic therapy induces survival signaling in perihilar cholangiocarcinoma cells. BMC Cancer, 15, 1014.
  30. Willemsen, A. M., Hendrickx, D. M., Hoefsloot, H. C., Hendriks, M. M., Wahl, S. A., Teusink, B., Smilde, A. K., & van Kampen, A. H. (2015). MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis. Mol Biosyst, 11(1), 137-145.
  31. Wortmann, S. B., Zietkiewicz, S., Kousi, M., Szklarczyk, R., Haack, T. B., Gersting, S. W., Muntau, A. C., Rakovic, A., Renkema, G. H., Rodenburg, R. J., Strom, T. M., Meitinger, T., Rubio-Gozalbo, M. E., Chrusciel, E., Distelmaier, F., Golzio, C., Jansen, J. H., van Karnebeek, C., Lillquist, Y., Lucke, T., Ounap, K., Zordania, R., Yaplito-Lee, J., van Bokhoven, H., Spelbrink, J. N., Vaz, F. M., Pras-Raves, M., Ploski, R., Pronicka, E., Klein, C., Willemsen, M. A., de Brouwer, A. P., Prokisch, H., Katsanis, N., & Wevers, R. A. (2015). CLPB mutations cause 3-methylglutaconic aciduria, progressive brain atrophy, intellectual disability, congenital neutropenia, cataracts, movement disorder. Am J Hum Genet, 96(2), 245-257.

 

2016

  1. Ferwerda, B., Valls Seron, M., Jongejan, A., Zwinderman, A. H., Geldhoff, M., van der Ende, A., Baas, F., Brouwer, M. C., & van de Beek, D. (2016). Variation of 46 Innate Immune Genes Evaluated for their Contribution in Pneumococcal Meningitis Susceptibility and Outcome. EBioMedicine, 10, 77-84.
  2. Hamers, A. A., Argmann, C., Moerland, P. D., Koenis, D. S., Marinkovic, G., Sokolovic, M., de Vos, A. F., de Vries, C. J., & van Tiel, C. M. (2016). Nur77-deficiency in bone marrow-derived macrophages modulates inflammatory responses, extracellular matrix homeostasis, phagocytosis and tolerance. BMC Genomics, 17, 162.
  3. Harwig, A., Jongejan, A., van Kampen, A. H., Berkhout, B., & Das, A. T. (2016). Tat-dependent production of an HIV-1 TAR-encoded miRNA-like small RNA. Nucleic Acids Res, 44(9), 4340-4353.
  4. Heinen, C. A., Jongejan, A., Watson, P. J., Redeker, B., Boelen, A., Boudzovitch-Surovtseva, O., Forzano, F., Hordijk, R., Kelley, R., Olney, A. H., Pierpont, M. E., Schaefer, G. B., Stewart, F., van Trotsenburg, A. S., Fliers, E., Schwabe, J. W., & Hennekam, R. C. (2016). A specific mutation in TBL1XR1 causes Pierpont syndrome. J Med Genet, 53(5), 330-337.
  5. Herzog, K., Pras-Raves, M. L., Vervaart, M. A., Luyf, A. C., van Kampen, A. H., Wanders, R. J., Waterham, H. R., & Vaz, F. M. (2016). Lipidomic analysis of fibroblasts from Zellweger spectrum disorder patients identifies disease-specific phospholipid ratios. J Lipid Res, 57(8), 1447-1454.
  6. Hombrink, P., Helbig, C., Backer, R. A., Piet, B., Oja, A. E., Stark, R., Brasser, G., Jongejan, A., Jonkers, R. E., Nota, B., Basak, O., Clevers, H. C., Moerland, P. D., Amsen, D., & van Lier, R. A. (2016). Programs for the persistence, vigilance and control of human CD8(+) lung-resident memory T cells. Nat Immunol, 17(12), 1467-1478.
  7. Kok, M. G., Mandolini, C., Moerland, P. D., de Ronde, M. W., Sondermeijer, B. M., Halliani, A., Nieuwland, R., Cipollone, F., Creemers, E. E., Meijers, J. C., & Pinto-Sietsma, S. J. (2016). Low miR-19b-1-5p expression in isolated platelets after aspirin use is related to aspirin insensitivity. Int J Cardiol, 203, 262-263.
  8. Lu, Y. W., Galbraith, L., Herndon, J. D., Lu, Y. L., Pras-Raves, M., Vervaart, M., Van Kampen, A., Luyf, A., Koehler, C. M., McCaffery, J. M., Gottlieb, E., Vaz, F. M., & Claypool, S. M. (2016). Defining functional classes of Barth syndrome mutation in humans. Hum Mol Genet, 25(9), 1754-1770.
  9. Nandal, U. K., van Kampen, A. H., & Moerland, P. D. (2016). compendiumdb: an R package for retrieval and storage of functional genomics data. Bioinformatics, 32(18), 2856-2857.
  10. Potze, L., Di Franco, S., Grandela, C., Pras-Raves, M. L., Picavet, D. I., van Veen, H. A., van Lenthe, H., Mullauer, F. B., van der Wel, N. N., Luyf, A., van Kampen, A. H., Kemp, S., Everts, V., Kessler, J. H., Vaz, F. M., & Medema, J. P. (2016). Betulinic acid induces a novel cell death pathway that depends on cardiolipin modification. Oncogene, 35(4), 427-437.
  11. Raemy, E., Montessuit, S., Pierredon, S., van Kampen, A. H., Vaz, F. M., & Martinou, J. C. (2016). Cardiolipin or MTCH2 can serve as tBID receptors during apoptosis. Cell Death Differ, 23(7), 1165-1174.
  12. Slot, L. M., Hoogeboom, R., Smit, L. A., Wormhoudt, T. A., Biemond, B. J., Oud, M. E., Schilder-Tol, E. J., Mulder, A. B., Jongejan, A., van Kampen, A. H., Kluin, P. M., Guikema, J. E., Bende, R. J., & van Noesel, C. J. (2016). B-Lymphoblastic Lymphomas Evolving from Follicular Lymphomas Co-Express Surrogate Light Chains and Mutated Gamma Heavy Chains. Am J Pathol, 186(12), 3273-3284.
  13. Sontrop, H. M. J., Reinders, M. J. T., & Moerland, P. D. (2016). Breast cancer subtype predictors revisited: from consensus to concordance? BMC Med Genomics, 9(1), 26.
  14. Te Velde, A. A., Bezema, T., van Kampen, A. H., Kraneveld, A. D., t Hart, B. A., van Middendorp, H., Hack, E. C., van Montfrans, J. M., Belzer, C., Jans-Beken, L., Pieters, R. H., Knipping, K., Huber, M., Boots, A. M., Garssen, J., Radstake, T. R., Evers, A. W., Prakken, B. J., & Joosten, I. (2016). Embracing Complexity beyond Systems Medicine: A New Approach to Chronic Immune Disorders. Front Immunol, 7, 587.
  15. van Altena, A. J., Moerland, P. D., Zwinderman, A. H., & Olabarriaga, S. (2016). Understanding big data themes from scientific biomedical literature through topic modeling. Journal of Big Data, 3, 23.
  16. van Kampen, A., & Moerland, P. D. (2016). Taking Bioinformatics to Systems Medicine. In U. Schmitz & O. Wolkenhauer (Eds.), Methods Mol Biol. (Vol. 1386, pp. 17-41)
  17. Zhao, J., Hakvoort, T. B., Willemsen, A. M., Jongejan, A., Sokolovic, M., Bradley, E. J., de Boer, V. C., Baas, F., van Kampen, A. H., & Lamers, W. H. (2016). Effect of Hyperglycemia on Gene Expression during Early Organogenesis in Mice. PLoS One, 11(7), e0158035.

 

2017

  1. Bennis, A., Jacobs, J. G., Catsburg, L. A. E., Ten Brink, J. B., Koster, C., Schlingemann, R. O., van Meurs, J., Gorgels, T., Moerland, P. D., Heine, V. M., & Bergen, A. A. (2017). Stem Cell Derived Retinal Pigment Epithelium: The Role of Pigmentation as Maturation Marker and Gene Expression Profile Comparison with Human Endogenous Retinal Pigment Epithelium. Stem Cell Rev Rep, 13(5), 659-669.
  2. Bennis, A., Ten Brink, J. B., Moerland, P. D., Heine, V. M., & Bergen, A. A. (2017). Comparative gene expression study and pathway analysis of the human iris- and the retinal pigment epithelium. PLoS One, 12(8), e0182983.
  3. de Ronde, M. W. J., Kok, M. G. M., Moerland, P. D., Van den Bossche, J., Neele, A. E., Halliani, A., van der Made, I., de Winther, M. P. J., Meijers, J. C. M., Creemers, E. E., & Pinto-Sietsma, S. J. (2017). High miR-124-3p expression identifies smoking individuals susceptible to atherosclerosis. Atherosclerosis, 263, 377-384.
  4. Doorenspleet, M. E., Westera, L., Peters, C. P., Hakvoort, T. B. M., Esveldt, R. E., Vogels, E., van Kampen, A. H. C., Baas, F., Buskens, C., Bemelman, W. A., D’Haens, G., Ponsioen, C. Y., Te Velde, A. A., de Vries, N., & van den Brink, G. R. (2017). Profoundly Expanded T-cell Clones in the Inflamed and Uninflamed Intestine of Patients With Crohn’s Disease. J Crohns Colitis, 11(7), 831-839.
  5. Duijvis, N. W., Moerland, P. D., Kunne, C., Slaman, M. M. W., van Dooren, F. H., Vogels, E. W., de Jonge, W. J., Meijer, S. L., Fluiter, K., & Te Velde, A. A. (2017). Inhibition of miR-142-5P ameliorates disease in mouse models of experimental colitis. PLoS One, 12(10), e0185097.
  6. Gao, A. W., Chatzispyrou, I. A., Kamble, R., Liu, Y. J., Herzog, K., Smith, R. L., van Lenthe, H., Vervaart, M. A. T., van Cruchten, A., Luyf, A. C., van Kampen, A., Pras-Raves, M. L., Vaz, F. M., & Houtkooper, R. H. (2017). A sensitive mass spectrometry platform identifies metabolic changes of life history traits in C. elegans. Sci Rep, 7(1), 2408.
  7. Hakimzadeh, N., Elias, J., Wijntjens, G. W. M., Theunissen, R., van Weert, A., Smulders, M. W., van den Akker, N., Moerland, P. D., Verberne, H. J., Hoebers, L. P., Henriques, J. P. S., van der Laan, A. M., Ilhan, M., Post, M., Bekkers, S., & Piek, J. J. (2017). Monocytic microRNA profile associated with coronary collateral artery function in chronic total occlusion patients. Sci Rep, 7(1), 1532.
  8. Jan, S. Z., Vormer, T. L., Jongejan, A., Roling, M. D., Silber, S. J., de Rooij, D. G., Hamer, G., Repping, S., & van Pelt, A. M. M. (2017). Unraveling transcriptome dynamics in human spermatogenesis. Development, 144(20), 3659-3673.
  9. Klaassen, I., de Vries, E. W., Vogels, I. M. C., van Kampen, A. H. C., Bosscha, M. I., Steel, D. H. W., Van Noorden, C. J. F., Lesnik-Oberstein, S. Y., & Schlingemann, R. O. (2017). Identification of proteins associated with clinical and pathological features of proliferative diabetic retinopathy in vitreous and fibrovascular membranes. PLoS One, 12(11), e0187304.
  10. Reshetova, P. (2017). 2 March 2017. Use of Prior Knowledge in Biological Systems Modelling. (PhD thesis). University of Amsterdam, Amsterdam. NBIC Biorange. Van Kampen,  A.H.C (promotor), Smilde, A. (promotor), Westerhuis, J. (co-promotor)
  11. Reshetova, P., van Schaik, B. D., Klarenbeek, P. L., Doorenspleet, M. E., Esveldt, R. E., Tak, P. P., Guikema, J. E., de Vries, N., & van Kampen, A. H. (2017). Computational Model Reveals Limited Correlation between Germinal Center B-Cell Subclone Abundancy and Affinity: Implications for Repertoire Sequencing. Front Immunol, 8, 221.
  12. Smith, R. L., Tan, J. M. E., Jonker, M. J., Jongejan, A., Buissink, T., Veldhuijzen, S., van Kampen, A. H. C., Brul, S., & van der Spek, H. (2017). Beyond the polymerase-gamma theory: Production of ROS as a mode of NRTI-induced mitochondrial toxicity. PLoS One, 12(11), e0187424.
  13. Tak, P. P., Doorenspleet, M. E., de Hair, M. J. H., Klarenbeek, P. L., van Beers-Tas, M. H., van Kampen, A. H. C., van Schaardenburg, D., Gerlag, D. M., Baas, F., & de Vries, N. (2017). Dominant B cell receptor clones in peripheral blood predict onset of arthritis in individuals at risk for rheumatoid arthritis. Ann Rheum Dis, 76(11), 1924-1930.
  14. van Attekum, M. H. A., Terpstra, S., Slinger, E., von Lindern, M., Moerland, P. D., Jongejan, A., Kater, A. P., & Eldering, E. (2017). Macrophages confer survival signals via CCR1-dependent translational MCL-1 induction in chronic lymphocytic leukemia. Oncogene, 36(26), 3651-3660.
  15. van Groningen, T., Koster, J., Valentijn, L. J., Zwijnenburg, D. A., Akogul, N., Hasselt, N. E., Broekmans, M., Haneveld, F., Nowakowska, N. E., Bras, J., van Noesel, C. J. M., Jongejan, A., van Kampen, A. H., Koster, L., Baas, F., van Dijk-Kerkhoven, L., Huizer-Smit, M., Lecca, M. C., Chan, A., Lakeman, A., Molenaar, P., Volckmann, R., Westerhout, E. M., Hamdi, M., van Sluis, P. G., Ebus, M. E., Molenaar, J. J., Tytgat, G. A., Westerman, B. A., van Nes, J., & Versteeg, R. (2017). Neuroblastoma is composed of two super-enhancer-associated differentiation states. Nat Genet, 49(8), 1261-1266.
  16. van Hagen, M., Piebes, D. G. E., de Leeuw, W. C., Vuist, I. M., van Roon-Mom, W. M. C., Moerland, P. D., & Verschure, P. J. (2017). The dynamics of early-state transcriptional changes and aggregate formation in a Huntington’s disease cell model. BMC Genomics, 18(1), 373.
  17. van Oorschot, B., Uitterhoeve, L., Oomen, I., Ten Cate, R., Medema, J. P., Vrieling, H., Stalpers, L. J., Moerland, P. D., & Franken, N. A. (2017). Prostate Cancer Patients with Late Radiation Toxicity Exhibit Reduced Expression of Genes Involved in DNA Double-Strand Break Repair and Homologous Recombination. Cancer Res, 77(6), 1485-1491.
  18. Weijer, R., Clavier, S., Zaal, E. A., Pijls, M. M., van Kooten, R. T., Vermaas, K., Leen, R., Jongejan, A., Moerland, P. D., van Kampen, A. H., van Kuilenburg, A. B., Berkers, C. R., Lemeer, S., & Heger, M. (2017). Multi-OMIC profiling of survival and metabolic signaling networks in cells subjected to photodynamic therapy. Cell Mol Life Sci, 74(6), 1133-1151.
  19. Zhao, J., Hakvoort, T. B. M., Jongejan, A., Ruijter, J. M., van Kampen, A. H. C., & Lamers, W. H. (2017). Unexpected regulation of miRNA abundance during adaptation of early-somite mouse embryos to diabetic pregnancy. Biochem Biophys Res Commun, 482(4), 1013-1018.
  20. Zhao, J., Hakvoort, T. B. M., Ruijter, J. M., Jongejan, A., Koster, J., Swagemakers, S. M. A., Sokolovic, A., & Lamers, W. H. (2017). Maternal diabetes causes developmental delay and death in early-somite mouse embryos. Sci Rep, 7(1), 11714.
  21. Zheng, Y., Jongejan, A., Mulder, C. L., Mastenbroek, S., Repping, S., Wang, Y., Li, J., & Hamer, G. (2017). Trivial role for NSMCE2 during in vitro proliferation and differentiation of male germline stem cells. Reproduction, 154(3), 181-195.

 

2018

  1. Adam, A. A. A., van Wenum, M., van der Mark, V. A., Jongejan, A., Moerland, P. D., Houtkooper, R. H., Wanders, R. J. A., Oude Elferink, R. P., Chamuleau, R., & Hoekstra, R. (2018). AMC-Bio-Artificial Liver culturing enhances mitochondrial biogenesis in human liver cell lines: The role of oxygen, medium perfusion and 3D configuration. Mitochondrion, 39, 30-42.
  2. de Ronde, M. W. J., Ruijter, J. M., Moerland, P. D., Creemers, E. E., & Pinto-Sietsma, S. J. (2018). Study Design and qPCR Data Analysis Guidelines for Reliable Circulating miRNA Biomarker Experiments: A Review. Clin Chem, 64(9), 1308-1318.
  3. de Weerdt, I., Hofland, T., Lameris, R., Endstra, S., Jongejan, A., Moerland, P. D., de Bruin, R. C. G., Remmerswaal, E. B. M., Ten Berge, I. J. M., Liu, N., van der Stelt, M., Faber, L. M., Levin, M. D., Eldering, E., Tonino, S. H., de Gruijl, T. D., van der Vliet, H. J., & Kater, A. P. (2018). Improving CLL Vgamma9Vdelta2-T-cell fitness for cellular therapy by ex vivo activation and ibrutinib. Blood, 132(21), 2260-2272.
  4. Fernando, F., Boussata, S., Jongejan, A., van der Post, J. A., Afink, G., & Ris-Stalpers, C. (2018). In silico analysis of the Mus musculus uterine gene expression landscape during pregnancy identifies putative upstream regulators for labour. PLoS One, 13(9), e0204236.
  5. Herzog, K., Pras-Raves, M. L., Ferdinandusse, S., Vervaart, M. A. T., Luyf, A. C. M., van Kampen, A. H. C., Wanders, R. J. A., Waterham, H. R., & Vaz, F. M. (2018). Plasma lipidomics as a diagnostic tool for peroxisomal disorders. J Inherit Metab Dis, 41(3), 489-498.
  6. Herzog, K., Pras-Raves, M. L., Ferdinandusse, S., Vervaart, M. A. T., Luyf, A. C. M., van Kampen, A. H. C., Wanders, R. J. A., Waterham, H. R., & Vaz, F. M. (2018). Functional characterisation of peroxisomal beta-oxidation disorders in fibroblasts using lipidomics. J Inherit Metab Dis, 41(3), 479-487.
  7. Jan, S. Z., Jongejan, A., Korver, C. M., van Daalen, S. K. M., van Pelt, A. M. M., Repping, S., & Hamer, G. (2018). Distinct prophase arrest mechanisms in human male meiosis. Development, 145(16).
  8. Kloek, A. T., Khan, H. N., Valls Seron, M., Jongejan, A., Zwinderman, A. H., Baas, F., van der Ende, A., van de Beek, D., Ferwerda, B., & Brouwer, M. C. (2018). Variation in coagulation and fibrinolysis genes evaluated for their contribution to cerebrovascular complications in adults with bacterial meningitis in the Netherlands. J Infect, 77(1), 54-59.
  9. Kok, M. G. M., de Ronde, M. W. J., Moerland, P. D., Ruijter, J. M., Creemers, E. E., & Pinto-Sietsma, S. J. (2018). Small sample sizes in high-throughput miRNA screens: A common pitfall for the identification of miRNA biomarkers. Biomol Detect Quantif, 15, 1-5.
  10. Michailidou, I., Jongejan, A., Vreijling, J. P., Georgakopoulou, T., de Wissel, M. B., Wolterman, R. A., Ruizendaal, P., Klar-Mohamad, N., Grootemaat, A. E., Picavet, D. I., Kumar, V., van Kooten, C., Woodruff, T. M., Morgan, B. P., van der Wel, N. N., Ramaglia, V., Fluiter, K., & Baas, F. (2018). Systemic inhibition of the membrane attack complex impedes neuroinflammation in chronic relapsing experimental autoimmune encephalomyelitis. Acta Neuropathol Commun, 6(1), 36.
  11. Musters, A., Klarenbeek, P. L., Doorenspleet, M. E., Balzaretti, G., Esveldt, R. E. E., van Schaik, B. D. C., Jongejan, A., Tas, S. W., van Kampen, A. H. C., Baas, F., & de Vries, N. (2018). In Rheumatoid Arthritis, Synovitis at Different Inflammatory Sites Is Dominated by Shared but Patient-Specific T Cell Clones. J Immunol, 201(2), 417-422.
  12. Oja, A. E., Piet, B., Helbig, C., Stark, R., van der Zwan, D., Blaauwgeers, H., Remmerswaal, E. B. M., Amsen, D., Jonkers, R. E., Moerland, P. D., Nolte, M. A., van Lier, R. A. W., & Hombrink, P. (2018). Trigger-happy resident memory CD4(+) T cells inhabit the human lungs. Mucosal Immunol, 11(3), 654-667.
  13. Seijkens, T. T. P., van Tiel, C. M., Kusters, P. J. H., Atzler, D., Soehnlein, O., Zarzycka, B., Aarts, S., Lameijer, M., Gijbels, M. J., Beckers, L., den Toom, M., Slutter, B., Kuiper, J., Duchene, J., Aslani, M., Megens, R. T. A., van ‘t Veer, C., Kooij, G., Schrijver, R., Hoeksema, M. A., Boon, L., Fay, F., Tang, J., Baxter, S., Jongejan, A., Moerland, P. D., Vriend, G., Bleijlevens, B., Fisher, E. A., Duivenvoorden, R., Gerdes, N., de Winther, M. P. J., Nicolaes, G. A., Mulder, W. J. M., Weber, C., & Lutgens, E. (2018). Targeting CD40-Induced TRAF6 Signaling in Macrophages Reduces Atherosclerosis. J Am Coll Cardiol, 71(5), 527-542.
  14. Smits, M. A. J., Wong, K. M., Mantikou, E., Korver, C. M., Jongejan, A., Breit, T. M., Goddijn, M., Mastenbroek, S., & Repping, S. (2018). Age-related gene expression profiles of immature human oocytes. Mol Hum Reprod, 24(10), 469-477.
  15. Van Altena, A. J., Moerland, P. D., Zwinderman, A. H., & Olabarriaga, S. (2018). Analysis of the term ‘Big Data’: usage in biomedical publications. Paper presented at the IEEE International Conference on Big Data (BigData2017).
  16. van Egmond, N., Hannink, G., Janssen, D., Vrancken, A. C., Verdonschot, N., & van Kampen, A. (2018). Erratum to: Relaxation of the MCL after an Open-Wedge High Tibial Osteotomy results in decreasing contact pressures of the knee over time. Knee Surg Sports Traumatol Arthrosc, 26(1), 354.
  17. van Wenum, M., Adam, A. A. A., van der Mark, V. A., Chang, J. C., Wildenberg, M. E., Hendriks, E. J., Jongejan, A., Moerland, P. D., van Gulik, T. M., Oude Elferink, R. P., Chamuleau, R., & Hoekstra, R. (2018). Oxygen drives hepatocyte differentiation and phenotype stability in liver cell lines. J Cell Commun Signal, 12(3), 575-588.
  18. van Wenum, M., Treskes, P., Adam, A. A. A., van der Mark, V. A., Jongejan, A., Moerland, P. D., van Gulik, T. M., Oude Elferink, R. P. J., Chamuleau, R., & Hoekstra, R. (2018). HepaRG-Progenitor Cell Derived Hepatocytes Cultured in Bioartificial Livers Are Protected from Healthy- and Acute Liver Failure-Plasma Induced Toxicity. Cell Physiol Biochem, 48(5), 2189-2204.
  19. Zheng, Y., Lei, Q., Jongejan, A., Mulder, C. L., van Daalen, S. K. M., Mastenbroek, S., Hwang, G., Jordan, P. W., Repping, S., & Hamer, G. (2018). The influence of retinoic acid-induced differentiation on the radiation response of male germline stem cells. DNA Repair (Amst), 70, 55-66.
  20. Zwaveling-Soonawala, N., Alders, M., Jongejan, A., Kovacic, L., Duijkers, F. A., Maas, S. M., Fliers, E., van Trotsenburg, A. S. P., & Hennekam, R. C. (2018). Clues for Polygenic Inheritance of Pituitary Stalk Interruption Syndrome From Exome Sequencing in 20 Patients. J Clin Endocrinol Metab, 103(2), 415-428.

 

2019

  1. Bleeker, J. C., Kok, I. L., Ferdinandusse, S., van der Pol, W. L., Cuppen, I., Bosch, A. M., Langeveld, M., Derks, T. G. J., Williams, M., de Vries, M., Mulder, M. F., Gozalbo, E. R., de Sain-van der Velden, M. G. M., Rennings, A. J., Schielen, P., Dekkers, E., Houtkooper, R. H., Waterham, H. R., Pras-Raves, M. L., Wanders, R. J. A., van Hasselt, P. M., Schoenmakers, M., Wijburg, F. A., & Visser, G. (2019). Impact of newborn screening for very-long-chain acyl-CoA dehydrogenase deficiency on genetic, enzymatic, and clinical outcomes. J Inherit Metab Dis, 42(3), 414-423.
  2. Bradfield, J. P., Vogelezang, S., Felix, J. F., Chesi, A., Helgeland, O., Horikoshi, M., Karhunen, V., Lowry, E., Cousminer, D. L., Ahluwalia, T. S., Thiering, E., Boh, E. T., Zafarmand, M. H., Vilor-Tejedor, N., Wang, C. A., Joro, R., Chen, Z., Gauderman, W. J., Pitkanen, N., Parra, E. J., Fernandez-Rhodes, L., Alyass, A., Monnereau, C., Curtin, J. A., Have, C. T., McCormack, S. E., Hollensted, M., Frithioff-Bojsoe, C., Valladares-Salgado, A., Peralta-Romero, J., Teo, Y. Y., Standl, M., Leinonen, J. T., Holm, J. C., Peters, T., Vioque, J., Vrijheid, M., Simpson, A., Custovic, A., Vaudel, M., Canouil, M., Lindi, V., Atalay, M., Kahonen, M., Raitakari, O. T., van Schaik, B. D. C., Berkowitz, R. I., Cole, S. A., Voruganti, V. S., Wang, Y., Highland, H. M., Comuzzie, A. G., Butte, N. F., Justice, A. E., Gahagan, S., Blanco, E., Lehtimaki, T., Lakka, T. A., Hebebrand, J., Bonnefond, A., Grarup, N., Froguel, P., Lyytikainen, L. P., Cruz, M., Kobes, S., Hanson, R. L., Zemel, B. S., Hinney, A., Teo, K. K., Meyre, D., North, K. E., Gilliland, F. D., Bisgaard, H., Bustamante, M., Bonnelykke, K., Pennell, C. E., Rivadeneira, F., Uitterlinden, A. G., Baier, L. J., Vrijkotte, T. G. M., Heinrich, J., Sorensen, T. I. A., Saw, S. M., Pedersen, O., Hansen, T., Eriksson, J., Widen, E., McCarthy, M. I., Njolstad, P. R., Power, C., Hypponen, E., Sebert, S., Brown, C. D., Jarvelin, M. R., Timpson, N. J., Johansson, S., Hakonarson, H., Jaddoe, V. W. V., Early Growth Genetics, C., & Grant, S. F. A. (2019). A trans-ancestral meta-analysis of genome-wide association studies reveals loci associated with childhood obesity. Hum Mol Genet, 28(19), 3327-3338.
  3. De Vries, L. C. S., Duarte, J. M., De Krijger, M., Welting, O., Van Hamersveld, P. H. P., Van Leeuwen-Hilbers, F. W. M., Moerland, P. D., Jongejan, A., D’Haens, G. R., De Jonge, W. J., & Wildenberg, M. E. (2019). A JAK1 Selective Kinase Inhibitor and Tofacitinib Affect Macrophage Activation and Function. Inflamm Bowel Dis, 25(4), 647-660.
  4. Duijkers, F. A., McDonald, A., Janssens, G. E., Lezzerini, M., Jongejan, A., van Koningsbruggen, S., Leeuwenburgh-Pronk, W. G., Wlodarski, M. W., Moutton, S., Tran-Mau-Them, F., Thauvin-Robinet, C., Faivre, L., Monaghan, K. G., Smol, T., Boute-Benejean, O., Ladda, R. L., Sell, S. L., Bruel, A. L., Houtkooper, R. H., & MacInnes, A. W. (2019). HNRNPR Variants that Impair Homeobox Gene Expression Drive Developmental Disorders in Humans. Am J Hum Genet, 104(6), 1040-1059.
  5. Haijes, H. A., Willemsen, M., Van der Ham, M., Gerrits, J., Pras-Raves, M. L., Prinsen, H., Van Hasselt, P. M., De Sain-van der Velden, M. G. M., Verhoeven-Duif, N. M., & Jans, J. J. M. (2019). Direct Infusion Based Metabolomics Identifies Metabolic Disease in Patients’ Dried Blood Spots and Plasma. Metabolites, 9(1).
  6. Hermkens, D. M. A., Stam, O. C. G., de Wit, N. M., Fontijn, R. D., Jongejan, A., Moerland, P. D., Mackaaij, C., Waas, I. S. E., Daemen, M., & de Vries, H. E. (2019). Profiling the unique protective properties of intracranial arterial endothelial cells. Acta Neuropathol Commun, 7(1), 151.
  7. Liu, Y. J., Janssens, G. E., McIntyre, R. L., Molenaars, M., Kamble, R., Gao, A. W., Jongejan, A., Weeghel, M. V., MacInnes, A. W., & Houtkooper, R. H. (2019). Glycine promotes longevity in Caenorhabditis elegans in a methionine cycle-dependent fashion. PLoS Genet, 15(3), e1007633.
  8. Pollastro, S., Klarenbeek, P. L., Doorenspleet, M. E., van Schaik, B. D. C., Esveldt, R. E. E., Thurlings, R. M., Boumans, M. J. H., Gerlag, D. M., Tak, P. P., Vos, K., Baas, F., van Kampen, A. H. C., & de Vries, N. (2019). Non-response to rituximab therapy in rheumatoid arthritis is associated with incomplete disruption of the B cell receptor repertoire. Ann Rheum Dis, 78(10), 1339-1345.
  9. Reiniers, M. J., de Haan, L., Weijer, R., Wiggers, J. K., Jongejan, A., Moerland, P. D., Alles, L. K., van Kampen, A. H. C., van Gulik, T. M., Heger, M., & van Golen, R. F. (2019). Effect of preoperative biliary drainage on cholestasis-associated inflammatory and fibrotic gene signatures in perihilar cholangiocarcinoma. Br J Surg, 106(1), 55-58.
  10. Slot, L. M., Wormhoudt, T. A. M., Kwakkenbos, M. J., Wagner, K., Ballering, A., Jongejan, A., van Kampen, A. C. M., Guikema, J. E. J., Bende, R. J., & van Noesel, C. J. M. (2019). De novo gene mutations in normal human memory B cells. Leukemia, 33(5), 1219-1230.
  11. Stenvers, D. J., Jongejan, A., Atiqi, S., Vreijling, J. P., Limonard, E. J., Endert, E., Baas, F., Moerland, P. D., Fliers, E., Kalsbeek, A., & Bisschop, P. H. (2019). Diurnal rhythms in the white adipose tissue transcriptome are disturbed in obese individuals with type 2 diabetes compared with lean control individuals. Diabetologia, 62(4), 704-716.
  12. van Altena, A. J., Moerland, P. D., Zwinderman, A. H., & Delgado Olabarriaga, S. (2019). Usage of the Term Big Data in Biomedical Publications: A Text Mining Approach. Big Data and Cognitive Computing, 3(1), 13.
  13. Vaz, F. M., McDermott, J. H., Alders, M., Wortmann, S. B., Kolker, S., Pras-Raves, M. L., Vervaart, M. A. T., van Lenthe, H., Luyf, A. C. M., Elfrink, H. L., Metcalfe, K., Cuvertino, S., Clayton, P. E., Yarwood, R., Lowe, M. P., Lovell, S., Rogers, R. C., Deciphering Developmental Disorders, S., van Kampen, A. H. C., Ruiter, J. P. N., Wanders, R. J. A., Ferdinandusse, S., van Weeghel, M., Engelen, M., & Banka, S. (2019). Mutations in PCYT2 disrupt etherlipid biosynthesis and cause a complex hereditary spastic paraplegia. Brain, 142(11), 3382-3397.
  14. Vergroesen, R. D., Slot, L. M., van Schaik, B. D. C., Koning, M. T., Rispens, T., van Kampen, A. H. C., Toes, R. E. M., & Scherer, H. U. (2019). N-Glycosylation Site Analysis of Citrullinated Antigen-Specific B-Cell Receptors Indicates Alternative Selection Pathways During Autoreactive B-Cell Development. Front Immunol, 10, 2092.
  15. Warrington, N. M., Beaumont, R. N., Horikoshi, M., Day, F. R., Helgeland, O., Laurin, C., Bacelis, J., Peng, S., Hao, K., Feenstra, B., Wood, A. R., Mahajan, A., Tyrrell, J., Robertson, N. R., Rayner, N. W., Qiao, Z., Moen, G. H., Vaudel, M., Marsit, C. J., Chen, J., Nodzenski, M., Schnurr, T. M., Zafarmand, M. H., Bradfield, J. P., Grarup, N., Kooijman, M. N., Li-Gao, R., Geller, F., Ahluwalia, T. S., Paternoster, L., Rueedi, R., Huikari, V., Hottenga, J. J., Lyytikainen, L. P., Cavadino, A., Metrustry, S., Cousminer, D. L., Wu, Y., Thiering, E., Wang, C. A., Have, C. T., Vilor-Tejedor, N., Joshi, P. K., Painter, J. N., Ntalla, I., Myhre, R., Pitkanen, N., van Leeuwen, E. M., Joro, R., Lagou, V., Richmond, R. C., Espinosa, A., Barton, S. J., Inskip, H. M., Holloway, J. W., Santa-Marina, L., Estivill, X., Ang, W., Marsh, J. A., Reichetzeder, C., Marullo, L., Hocher, B., Lunetta, K. L., Murabito, J. M., Relton, C. L., Kogevinas, M., Chatzi, L., Allard, C., Bouchard, L., Hivert, M. F., Zhang, G., Muglia, L. J., Heikkinen, J., Consortium, E. G. G., Morgen, C. S., van Kampen, A. H. C., van Schaik, B. D. C., Mentch, F. D., Langenberg, C., Luan, J., Scott, R. A., Zhao, J. H., Hemani, G., Ring, S. M., Bennett, A. J., Gaulton, K. J., Fernandez-Tajes, J., van Zuydam, N. R., Medina-Gomez, C., de Haan, H. G., Rosendaal, F. R., Kutalik, Z., Marques-Vidal, P., Das, S., Willemsen, G., Mbarek, H., Muller-Nurasyid, M., Standl, M., Appel, E. V. R., Fonvig, C. E., Trier, C., van Beijsterveldt, C. E. M., Murcia, M., Bustamante, M., Bonas-Guarch, S., Hougaard, D. M., Mercader, J. M., Linneberg, A., Schraut, K. E., Lind, P. A., Medland, S. E., Shields, B. M., Knight, B. A., Chai, J. F., Panoutsopoulou, K., Bartels, M., Sanchez, F., Stokholm, J., Torrents, D., Vinding, R. K., Willems, S. M., Atalay, M., Chawes, B. L., Kovacs, P., Prokopenko, I., Tuke, M. A., Yaghootkar, H., Ruth, K. S., Jones, S. E., Loh, P. R., Murray, A., Weedon, M. N., Tonjes, A., Stumvoll, M., Michaelsen, K. F., Eloranta, A. M., Lakka, T. A., van Duijn, C. M., Kiess, W., Korner, A., Niinikoski, H., Pahkala, K., Raitakari, O. T., Jacobsson, B., Zeggini, E., Dedoussis, G. V., Teo, Y. Y., Saw, S. M., Montgomery, G. W., Campbell, H., Wilson, J. F., Vrijkotte, T. G. M., Vrijheid, M., de Geus, E., Hayes, M. G., Kadarmideen, H. N., Holm, J. C., Beilin, L. J., Pennell, C. E., Heinrich, J., Adair, L. S., Borja, J. B., Mohlke, K. L., Eriksson, J. G., Widen, E. E., Hattersley, A. T., Spector, T. D., Kahonen, M., Viikari, J. S., Lehtimaki, T., Boomsma, D. I., Sebert, S., Vollenweider, P., Sorensen, T. I. A., Bisgaard, H., Bonnelykke, K., Murray, J. C., Melbye, M., Nohr, E. A., Mook-Kanamori, D. O., Rivadeneira, F., Hofman, A., Felix, J. F., Jaddoe, V. W. V., Hansen, T., Pisinger, C., Vaag, A. A., Pedersen, O., Uitterlinden, A. G., Jarvelin, M. R., Power, C., Hypponen, E., Scholtens, D. M., Lowe, W. L., Jr., Davey Smith, G., Timpson, N. J., Morris, A. P., Wareham, N. J., Hakonarson, H., Grant, S. F. A., Frayling, T. M., Lawlor, D. A., Njolstad, P. R., Johansson, S., Ong, K. K., McCarthy, M. I., Perry, J. R. B., Evans, D. M., & Freathy, R. M. (2019). Maternal and fetal genetic effects on birth weight and their relevance to cardio-metabolic risk factors. Nat Genet, 51(5), 804-814.

 

2020

  1. Adam, A. A. A., Jongejan, A., Moerland, P. D., van der Mark, V. A., Oude Elferink, R. P., Chamuleau, R., & Hoekstra, R. (2020). Genome-wide expression profiling reveals increased stability and mitochondrial energy metabolism of the human liver cell line HepaRG-CAR. Cytotechnology, 72(3), 377-395.
  2. Bagchi, U., Gegnaw, S. T., Milicevic, N., Sandu, C., Ten Brink, J. B., Jongejan, A., Hicks, D., Moerland, P. D., Felder-Schmittbuhl, M. P., & Bergen, A. A. (2020). Core-clock genes Period 1 and 2 regulate visual cascade and cell cycle components during mouse eye development. Biochim Biophys Acta Gene Regul Mech, 1863(10), 194623.
  3. Borgoni, S., Sofyali, E., Soleimani, M., Wilhelm, H., Muller-Decker, K., Will, R., Noronha, A., Beumers, L., Verschure, P. J., Yarden, Y., Magnani, L., van Kampen, A. H. C., Moerland, P. D., & Wiemann, S. (2020). Time-Resolved Profiling Reveals ATF3 as a Novel Mediator of Endocrine Resistance in Breast Cancer. Cancers (Basel), 12(10).
  4. Darwisch, W., von Spangenberg, M., Lehmann, J., Singin, O., Deubert, G., Kuhl, S., Roos, J., Horstmann, H., Korber, C., Hoppe, S., Zheng, H., Kuner, T., Pras-Raves, M. L., van Kampen, A. H. C., Waterham, H. R., Schwarz, K. V., Okun, J. G., Schultz, C., Vaz, F. M., & Islinger, M. (2020). Cerebellar and hepatic alterations in ACBD5-deficient mice are associated with unexpected, distinct alterations in cellular lipid homeostasis. Commun Biol, 3(1), 713.
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2021

to be updated