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Jansen, Prof. Ritsert

Ritsert Jansen
Ritsert Jansen

Ritsert Jansen is professor of bio-informatics and head of the Groningen Bioinformatics Centre. Jansen studied mathematics at the University of Groningen and then went to work for a research institute in Wageningen. The advent of new biomolecular tools led him to develop new statistical tools for mapping QTLs (‘quantitative trait loci’, stretches of DNA containing or linked to the genes that underlie a quantitative trait) in plants, and this research formed the basis of his PhD thesis. In 2002, he returned to the University of Groningen where he holds a joint appointment at the Faculty of Science and Engineering and the Faculty of Medical Sciences as a professor of bioinformatics. At present, his research group is interested in designing, modelling and analysing quantitative biomolecular experiments on populations, using ‘genetic genomics’ strategies that combine the merits of genetics with the power of genomics.

Jansen is also a ‘Dean of Talent Development’ at the University of Groningen. As an acclaimed researcher he likes to give young colleagues a helping hand. In 2011 his book Developing a Talent for Science was published by Cambridge University Press, in which he discusses the stressful life of modern scientists in an increasingly competitive academic environment. ‘You are an entrepreneur in the land of research’, says Jansen. ‘In the past you would be welcomed to your new research place with a big bag of money, but nowadays scientists have to gather their own funds by winning grants.’ In 2013 Funding your career in Science was released by Cambridge University Press.

As Dean, Jansen is involved in matters such as training courses for academics in the field of applying for grants and holding presentations, as well as in the Grants Week, a large event for researchers seeking to acquire grants.

Article UG
Article UG

Contact and further information

Publications

2019

Zych, K., Gort, G., Maliepaard, C. A., Jansen, R. C., & Voorrips, R. E. (2019). FitTetra 2.0-improved genotype calling for tetraploids with multiple population and parental data support. Bmc Bioinformatics, 20, [148]. https://doi.org/10.1186/s12859-019-2703-y
Prins, P., Smant, G., Arends, D., Mulligan, M. K., Williams, R. W., & Jansen, R. C. (2019). Systems Genetics for Evolutionary Studies. In M. Anisimova (Ed.), Evolutionary Genomics (pp. 635-652). (Methods in Molecular Biology; Vol. 1910). Springer. https://doi.org/10.1007/978-1-4939-9074-0_21

2017

Zych, K., Snoek, L. B., Elvin, M., Rodriguez, M., van der Velde, K. J., Arends, D., Westra, H-J., Swertz, M. A., Poulin, G., Kammenga, J. E., Breitling, R., Jansen, R. C., & Li, Y. (2017). reGenotyper: Detecting mislabeled samples in genetic data. PLoS ONE, 12(2), [e0171324]. https://doi.org/10.1371/journal.pone.0171324

2015

Westra, H-J., Arends, D., Esko, T., Peters, M. J., Schurmann, C., Schramm, K., Kettunen, J., Yaghootkar, H., Fairfax, B. P., Andiappan, A. K., Li, Y., Fu, J., Karjalainen, J., Platteel, M., Visschedijk, M., Weersma, R. K., Kasela, S., Milani, L., Tserel, L., ... Franke, L. (2015). Cell Specific eQTL Analysis without Sorting Cells. PLoS genetics, 11(5), [1005223]. https://doi.org/10.1371/journal.pgen.1005223
Fehrmann, R. S. N., Karjalainen, J. M., Krajewska, M., Westra, H-J., Maloney, D., Simeonov, A., Pers, T. H., Hirschhorn, J. N., Jansen, R. C., Schultes, E. A., van Haagenl, H. H. H. B. M., de Vries, E. G. E., te Meerman, G., Wijmenga, C., van Vugt, M. A. T. M., & Franke, L. (2015). Gene expression analysis identifies global gene dosage sensitivity in cancer. Nature Genetics, 47(2), 115-125. https://doi.org/10.1038/ng.3173
Zych, K., Li, Y., van der Velde, J. K., Joosen, R. V. L., Ligterink, W., Jansen, R. C., & Arends, D. (2015). Pheno2Geno: High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains. Bmc Bioinformatics, 16(1), [51]. https://doi.org/10.1186/s12859-015-0475-6
van der Graaf, A., Wardenaar, R., Neumann, D. A., Taudt, A., Shaw, R. G., Jansen, R. C., Schmitz, R. J., Colome-Tatche, M., & Johannes, F. (2015). Rate, spectrum, and evolutionary dynamics of spontaneous epimutations. Proceedings of the National Academy of Sciences of the United States of America, 112(21), 6676-6681. https://doi.org/10.1073/pnas.1424254112
Prins, P., de Ligt, J., Tarasov, A., Jansen, R. C., Cuppen, E., & Bourne, P. E. (2015). Toward effective software solutions for big biology. Nature Biotechnology, 33(7), 686-687. https://doi.org/10.1038/nbt.3240

2014

Cortijo, S., Wardenaar, R., Colome-Tatche, M., Gilly, A., Etcheverry, M., Labadie, K., Caillieux, E., Hospital, F., Aury, J-M., Wincker, P., Roudier, F., Jansen, R. C., Colot, V., & Johannes, F. (2014). Mapping the Epigenetic Basis of Complex Traits. Science, 343(6175), 1145-1148. https://doi.org/10.1126/science.1248127
Rintisch, C., Heinig, M., Bauerfeind, A., Schafer, S., Mieth, C., Patone, G., Hummel, O., Chen, W., Cook, S., Cuppen, E., Colomé Tatché, M., Johannes, F., Jansen, R. C., Neil, H., Werner, M., Pravenec, M., Vingron, M., & Hubner, N. (2014). Natural variation of histone modification and its impact on gene expression in the rat genome. Genome Research, 24(6), 942-953. https://doi.org/10.1101/gr.169029.113
Pino Del Carpio, D., Basnet, R. K., Arends, D., Lin, K., De Vos, R. C. H., Muth, D., Kodde, J., Boutilier, K., Bucher, J., Wang, X., Jansen, R., & Bonnema, G. (2014). Regulatory network of secondary metabolism in Brassica rapa: insight into the glucosinolate pathway. PLoS ONE, 9(9), [e107123]. https://doi.org/10.1371/journal.pone.0107123
Snoek, L. B., Joeri van der Velde, K., Li, Y., Jansen, R. C., Swertz, M. A., & Kammenga, J. E. (2014). Worm variation made accessible: Take your shopping cart to store, link, and investigate! Worm, 3(2), [e28357]. https://doi.org/10.4161/worm.28357
Velde, K. J. V. D., Haan, M. D., Zych, K., Arends, D., Snoek, L. B., Kammenga, J. E., Jansen, R. C., Swertz, M. A., & Li, Y. (2014). WormQTL(HD)-a web database for linking human disease to natural variation data in C. elegans. Nucleic Acids Research, 42(D1), D794-D801. https://doi.org/10.1093/nar/gkt1044

2013

Joosen, R. V. L., Arends, D., Li, Y., Willems, L. A. J., Keurentjes, J. J. B., Ligterink, W., Jansen, R. C., & Hilhorst, H. W. M. (2013). Identifying Genotype-by-Environment Interactions in the Metabolism of Germinating Arabidopsis Seeds Using Generalized Genetical Genomics. Plant Physiology, 162(2), 553-566. https://doi.org/10.1104/pp.113.216176
Westra, H-J., Peters, M. J., Esko, T., Yaghootkar, H., Schurmann, C., Kettunen, J., Christiansen, M. W., Fairfax, B. P., Schramm, K., Powell, J. E., Zhernakova, A., Zhernakova, D. V., Veldink, J. H., Van den Berg, L. H., Karjalainen, J., Withoff, S., Uitterlinden, A. G., Hofman, A., Rivadeneira, F., ... Hoen, P. A. C. . (2013). Systematic identification of trans eQTLs as putative drivers of known disease associations. Nature Genetics, 45(10), 1238-1243. https://doi.org/10.1038/ng.2756
Snoek, L. B., Van der Velde, K. J., Arends, D., Li, Y., Beyer, A., Elvin, M., Fisher, J., Hajnal, A., Hengartner, M. O., Poulin, G. B., Rodriguez, M., Schmid, T., Schrimpf, S., Xue, F., Jansen, R. C., Kammenga, J. E., & Swertz, M. A. (2013). WormQTL-public archive and analysis web portal for natural variation data in Caenorhabditis spp. Nucleic Acids Research, 41(D1), D738-D743. https://doi.org/10.1093/nar/gks1124

2012

Durrant, C., Swertz, M. A., Alberts, R., Arends, D., Moeller, S., Mott, R., Prins, P., van der Velde, K. J., Jansen, R. C., & Schughart, K. (2012). Bioinformatics tools and database resources for systems genetics analysis in mice-a short review and an evaluation of future needs. Briefings in Bioinformatics, 13(2), 135-142. https://doi.org/10.1093/bib/bbr026
Colomé Tatché, M., Cortijo, S., Wardenaar, R., Monteiro Morgado, L., Lahouze, B., Sarazin, A., Etcheverry, M., Martin, A., Feng, S., Duvernois-Berthet, E., Labadie, K., Wincker, P., Jacobsen, S. E., Jansen, R. C., Colot, V., & Johannes, F. (2012). Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation. Proceedings of the National Academy of Sciences of the United States of America, 109(40), 16240-16245. https://doi.org/10.1073/pnas.1212955109
Prins, P., Smant, G., & Jansen, R. C. (2012). Genetical Genomics for Evolutionary Studies. Methods in Molecular Biology, 856, 469-485. https://doi.org/10.1007/978-1-61779-585-5_19
Demirkan, A., van Duijn, C. M., Ugocsai, P., Isaacs, A., Pramstaller, P. P., Liebisch, G., Wilson, J. F., Johansson, A., Rudan, I., Aulchenko, Y. S., Kirichenko, A. V., Janssens, A. C. J. W., Jansen, R. C., Gnewuch, C., Domingues, F. S., Pattaro, C., Wild, S. H., Jonasson, I., Polasek, O., ... EUROSPAN Consortium (2012). Genome-Wide Association Study Identifies Novel Loci Associated with Circulating Phospho- and Sphingolipid Concentrations. PLoS genetics, 8(2), [e1002490]. https://doi.org/10.1371/journal.pgen.1002490
Lendvai, Á., Johannes, F., Grimm, C., Eijsink, J. J. H., Wardenaar, R., Volders, H. H., Klip, H. G., Hollema, H., Jansen, R. C., Schuuring, E., Wisman, G. B. A., & van der Zee, A. G. J. (2012). Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia. Epigenetics, 7(11), 1268-1278. https://doi.org/10.4161/epi.22301
Diekstra, F. P., Saris, C. G. J., van Rheenen, W., Franke, L., Jansen, R. C., van Es, M. A., van Vught, P. W. J., Blauw, H. M., Groen, E. J. N., Horvath, S., Estrada, K., Rivadeneira, F., Hofman, A., Uitterlinden, A. G., Robberecht, W., Andersen, P. M., Melki, J., Meininger, V., Hardiman, O., ... Brown Jr., R. H. (2012). Mapping of Gene Expression Reveals CYP27A1 as a Susceptibility Gene for Sporadic ALS. PLoS ONE, 7(4), [e35333]. https://doi.org/10.1371/journal.pone.0035333
Zych, K., Arends, D., & Jansen, R. (2012). Pheno2geno; generating genetic markers and maps from molecular phenotypes. http://pheno2geno.nl
Neto, E. C., Keller, M. P., Broman, A. F., Attie, A. D., Jansen, R. C., Broman, K. W., & Yandell, B. S. (2012). Quantile-Based Permutation Thresholds for Quantitative Trait Loci Hotspots. Genetics, 191(4), 1355-1365. https://doi.org/10.1534/genetics.112.139451
Fu, J., Wolfs, M. G. M., Deelen, P., Westra, H. J., Fehrmann, R. S. N., te Meerman, G., Buurman, W. A., Rensen, S. S. M., Groen, H., Weersma, R. K., van den Berg, L. H., Veldink, J., Ophoff, R. A., Snieder, H., van Heel, D., Jansen, R. C., Hofker, M. H., Wijmenga, C., & Franke, L. (2012). Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression. PLoS genetics, 8(1), [e1002431]. https://doi.org/10.1371/journal.pgen.1002431
Joosen, R. V. L., Arends, D., Willems, L. A. J., Ligterink, W., Jansen, R. C., & Hilhorst, H. W. M. (2012). Visualizing the Genetic Landscape of Arabidopsis Seed Performance. Plant Physiology, 158(2), 570-589. https://doi.org/10.1104/pp.111.186676
Arends, D., van der Velde, K. J., Prins, P., Broman, K. W., Moller, S., Jansen, R. C., & Swertz, M. A. (2012). xQTL workbench: a scalable web environment for multi-level QTL analysis. Bioinformatics, 28(7), 1042-1044. https://doi.org/10.1093/bioinformatics/bts049

2011

Trelles, O., Prins, P., Snir, M., & Jansen, R. C. (2011). Big data, but are we ready? Nature Reviews Genetics, 12(3), 224-224. https://doi.org/10.1038/nrg2857-c1
Roux, F., Colomé-Tatché, M., Edelist, C., Wardenaar, R., Guerche, P., Hospital, F., Colot, V., Jansen, R. C., & Johannes, F. (2011). Genome-Wide Epigenetic Perturbation Jump-Starts Patterns of Heritable Variation Found in Nature. Genetics, 188(4), 1015-1017. https://doi.org/10.1534/genetics.111.128744
Westra, H-J., Jansen, R. C., Fehrmann, R. S. N., te Meerman, G. J., van Heel, D., Wijmenga, C., Franke, L., & te Meerman, G. (2011). MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects. Bioinformatics, 27(15), 2104-2111. https://doi.org/10.1093/bioinformatics/btr323
Scheltema, R. A., Jankevics, A., Jansen, R. C., Swertz, M. A., & Breitling, R. (2011). PeakML/mzMatch: A File Format, Java Library, R Library, and Tool-Chain for Mass Spectrometry Data Analysis. Analytical Chemistry, 83(7), 2786-2793. https://doi.org/10.1021/ac2000994
Seinen, E., Burgerhof, J. G., Jansen, R. C., & Sibon, O. C. (2011). RNAi-induced off-target effects in Drosophila melanogaster: frequencies and solutions. Briefings in Functional Genomics, 10(4), 206-214. https://doi.org/10.1093/bfgp/elr017
Fehrmann, R. S. N., Jansen, R. C., Veldink, J. H., Westra, H. J., Arends, D., Bonder, M. J., Fu, J., Deelen, P., Groen, H., Smolonska, J., Weersma, R. K., Hofstra, R. M. W., Buurman, W. A., Rensen, S., Wolfs, M. G. M., Platteel, M., Zhernakova, A., Elbers, C. C., Festen, E. A., ... Franke, L. (2011). Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA. PLoS genetics, 7(8), [1002197]. https://doi.org/10.1371/journal.pgen.1002197

2010

Johannes, F., Wardenaar, R., Colomé Tatché, M., Mousson, F., de Graaf, P., Mokry, M., Guryev, V., Timmers, H. T. M., Cuppen, E., & Jansen, R. C. (2010). Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq. Bioinformatics, 26(8), 1000-1006. https://doi.org/10.1093/bioinformatics/btq087
Li, Y., Tesson, B. M., Churchill, G. A., & Jansen, R. C. (2010). Critical reasoning on causal inference in genome-wide linkage and association studies. Trends in Genetics, 26(12), 493-498. https://doi.org/10.1016/j.tig.2010.09.002
Tesson, B. M., Breitling, R., & Jansen, R. C. (2010). DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules. Bmc Bioinformatics, 11(1), 497-1-497-9. [497]. https://doi.org/10.1186/1471-2105-11-497
Li, Y., Breitling, R., Snoek, L. B., van der Velde, K. J., Swertz, M. A., Riksen, J., Jansen, R. C., & Kammenga, J. E. (2010). Global Genetic Robustness of the Alternative Splicing Machinery in Caenorhabditis elegans. Genetics, 186(1), 405-U620. https://doi.org/10.1534/genetics.110.119677
Seinen, E., Burgerhof, J. G. M., Jansen, R. C., & Sibon, O. C. M. (2010). RNAi Experiments in D. melanogaster: Solutions to the Overlooked Problem of Off-Targets Shared by Independent dsRNAs. PLoS ONE, 5(10), [13119]. https://doi.org/10.1371/journal.pone.0013119
Arends, D., Prins, P., Jansen, R. C., & Broman, K. W. (2010). R/qtl: high-throughput multiple QTL mapping. Bioinformatics, 26(23), 2990-2992. https://doi.org/10.1093/bioinformatics/btq565
Nieselt, K., Battke, F., Herbig, A., Bruheim, P., Wentzel, A., Jakobsen, O. M., Sletta, H., Alam, M. T., Merlo, M. E., Moore, J., Omara, W. A. M., Morrissey, E. R., Juarez-Hermosillo, M. A., Rodriguez-Garcia, A., Nentwich, M., Thomas, L., Iqbal, M., Legaie, R., Gaze, W. H., ... Morrisey, E. R. (2010). The dynamic architecture of the metabolic switch in Streptomyces coelicolor. BMC Genomics, 11, [10]. https://doi.org/10.1186/1471-2164-11-10
Swertz, M. A., Dijkstra, M., Adamusiak, T., van der Velde, J. K., Kanterakis, A., Roos, E. T., Lops, J., Thorisson, G. A., Arends, D., Byelas, G., Muilu, J., Brookes, A. J., de Brock, E. O., Jansen, R. C., & Parkinson, H. (2010). The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button. Bmc Bioinformatics, 11 suppl 12 (S12), S12-1-S12-9. [12]. https://doi.org/10.1186/1471-2105-11-S12-S12
Swertz, M. A., van der Velde, K. J., Tesson, B. M., Scheltema, R. A., Arends, D., Vera, G., Alberts, R., Dijkstra, M., Schofield, P., Schughart, K., Hancock, J. M., Smedley, D., Wolstencroft, K., Goble, C., de Brock, E. O., Jones, A. R., Parkinson, H. E., & Jansen, R. C. (2010). XGAP: A uniform and extensible data model and software platform for genotype and phenotype experiments. Genome Biology, 11(3), [27]. https://doi.org/10.1186/gb-2010-11-3-r27

2009

Heap, G. A., Trynka, G., Jansen, R. C., Bruinenberg, M., Swertz, M. A., Dinesen, L. C., Hunt, K. A., Wijmenga, C., vanHeel, D. A., Franke, L., & Heel, D. A. V. (2009). Complex nature of SNP genotype effects on gene expression in primary human leucocytes. BMC Medical Genomics, 2(1), [1]. https://doi.org/10.1186/1755-8794-2-1
Jansen, R. C., Tesson, B. M., Fu, J., Yang, Y., McIntyre, L. M., & McInttyre, L. M. (2009). Defining gene and QTL networks. Current Opinion in Plant Biology, 12(2), 241-246. https://doi.org/10.1016/j.pbi.2009.01.003
Li, Y., Swertz, M. A., Vera, G., Fu, J., Breitling, R., & Jansen, R. C. (2009). designGG: an R-package and web tool for the optimal design of genetical genomics experiments. Bmc Bioinformatics, 10(188), [188]. https://doi.org/10.1186/1471-2105-10-188
Franke, L., & Jansen, R. C. (2009). eQTL Analysis in Humans. In K. DiPetrillo (Ed.), Cardiovascular Genomics: Methods and Protocols (Vol. 573, pp. 311-328). (Methods in Molecular Biology; No. 573). Springer. https://doi.org/10.1007/978-1-60761-247-6_17
Franke, L. H., & Jansen, R. C. (2009). eQTL Analysis in Humans in Methods in Molecular Biology. In Dipetrello (Ed.), Cardiovascular Genomics
Tesson, B. M., & Jansen, R. C. (2009). eQTL Analysis in Mice and Rats. In K. DiPetrillo (Ed.), Cardiovascular Genomics: Methods and Protocols (573 ed., pp. 285-309). (Methods in Molecular Biology; No. 573). Springer. https://doi.org/10.1007/978-1-60761-247-6_16
Tesson, B. M., & Jansen, R. C. (2009). eQTL Analysis in mice and rats Methods in Molecular Biology. In Dipetrello K. (Ed.), Cardiovascular Genetics
Gerrits, A., Li, Y., Tesson, B. M., Bystrykh, L. V., Weersing, E., Ausema, A., Dontje, B., Wang, X., Breitling, R., Jansen, R. C., de Haan, G., & Dethmers-Ausema, B. (2009). Expression Quantitative Trait Loci Are Highly Sensitive to Cellular Differentiation State. PLoS genetics, 5(10), [1000692]. https://doi.org/10.1371/journal.pgen.1000692
Dijkstra, M., & Jansen, R. C. (2009). Optimal analysis of complex protein mass spectra. Proteomics, 9(15), 3869-3876. https://doi.org/10.1002/pmic.200701064
Scheltema, R. A., Decuypere, S., Dujardin, J. C., Watson, D. G., Jansen, R. C., & Breitling, R. (2009). Simple data-reduction method for high-resolution LC-MS data in metabolomics. Bioanalysis, 1(9), 1551-1557. https://doi.org/10.4155/BIO.09.146
Fu, J., Keurentjes, J. J. B., Bouwmeester, H., America, T., Verstappen, F. W. A., Ward, J. L., Beale, M. H., de Vos, R. C. H., Dijkstra, M., Scheltema, R. A., Johannes, F., Koornneef, M., Vreugdenhil, D., Breitling, R., & Jansen, R. C. (2009). System-wide molecular evidence for phenotypic buffering in Arabidopsis. Nature Genetics, 41(2), 166-167. https://doi.org/10.1038/ng.308

2008

Alberts, R., Vera, G., & Jansen, R. C. (2008). affyGG: computational protocols for genetical genomics with Affymetrix arrays. Bioinformatics, 24(3), 433-434. https://doi.org/10.1093/bioinformatics/btm614
Johannes, F., Colot, V., & Jansen, R. C. (2008). Epigenome dynamics: a quantitative genetics perspective. Nature Reviews Genetics, 9, 883 - 890. http://www.rug.nl/biologie/onderzoek/onderzoekGroepen/bioinformatics/pdfPapers/nrg2467johannes.pdf
Li, Y., Breitling, R., & Jansen, R. C. (2008). Generalizing genetical genomics: getting added value from environmental perturbation. Trends in Genetics, 24(10), 518-524. https://doi.org/10.1016/j.tig.2008.08.001
Breitling, R., Li, Y., Tesson, B. M., Fu, J., Wu, C., Wiltshire, T., Gerrits, A., Bystrykh, L. V., de Haan, G., Su, A. I., & Jansen, R. C. (2008). Genetical Genomics: Spotlight on QTL Hotspots. PLoS genetics, 4(10), [e1000232]. https://doi.org/10.1371/journal.pgen.1000232
Scheltema, R. A., Kamleh, A., Wildridge, D., Ebikeme, C., Watson, D. G., Barrett, M. R., Jansen, R. C., Breitling, R., & Barrett, M. P. (2008). Increasing the mass accuracy of high-resolution LC-MS data using background ions - a case study on the LTQ-Orbitrap. Proteomics, 8(22), 4647-4656. https://doi.org/10.1002/pmic.200800314
Johannes, F., Colot, V., & Jansen, R. C. (2008). OPINION Epigenome dynamics: a quantitative genetics perspective. Nature Reviews Genetics, 9(11), 883-890. https://doi.org/10.1038/nrg2467
Lam, A. C., Fu, J., Jansen, R. C., Haley, C. S., & de Koning, D-J. (2008). Optimal Design of Genetic Studies of Gene Expression With Two-Color Microarrays in Outbred Crosses. Genetics, 180(3), 1691-1698. https://doi.org/10.1534/genetics.108.090308
Vera, G., Jansen, R. C., & Suppi, R. L. (2008). R/parallel - speeding up bioinformatics analysis with R. Bmc Bioinformatics, 22(9), 390. [390]. https://doi.org/10.1186/1471-2105-9-390
Swertz, M. A., Smedley, D., Wolstencroft, K., Alberts, R., Zouberakis, M., Aidinis, V., Schughart, K., Schofield, P. N., & Jansen, R. C. (2008). Towards dynamic database infrastructures for mouse genetics. In 8th IEEE International Conference on BioInformatics and BioEngineering, 2008. BIBE 2008 University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute (GBB).

2007

Alberts, R., Terpstra, P., Hardonk, M., Bystrykh, L. V., de Haan, G., Breitling, R., Nap, J-P., & Jansen, R. C. (2007). A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat. Bmc Bioinformatics, 8(1), [132]. https://doi.org/10.1186/1471-2105-8-132
Nolte, I. M., Vries, A. R. D., Spijker, G. T., Jansen, R. C., Brinza, D., Zelikovsky, A., & Meerman, G. J. T. (2007). Association testing by haplotype-sharing methods applicable to whole-genome analysis. BMC Proceedings, 1 Suppl 1, S129. https://doi.org/10.1186/1753-6561-1-s1-s129
Swertz, M. A., & Jansen, R. C. (2007). Beyond standardization: dynamic software infrastructures for systems biology. Nature Reviews Genetics, 8(3), 235-243. https://doi.org/10.1038/nrg2048
Fu, J., Swertz, M. A., Keurentjes, J. J. B., & Jansen, R. C. (2007). MetaNetwork: A computational protocol for the genetic study of metabolic networks. Nature protocols, 2(3), 685-694. https://doi.org/10.1038/nprot.2007.96
Nyangoma, S. O., Van Kampen, A. A., Reijmers, T. H., Govorukhina, N. I., van der Zee, A. G., Billingham, I. 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 nois in LC-MS data sets. Statistical applications in genetics and molecular biology, 6(article 23). http://www.ncbi.nlm.nih.gov/pubmed/17910529?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
Nyangoma, S. O., van Kampen, A. A. H. C., Reijmers, T. H., Govorukhina, N. I., van der Zee, A. G. J., 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. Statistical applications in genetics and molecular biology, 6(1), [23].
Keurentjes, J. J. B., Fu, J., Terpstra, I. R., Garcia, J. M., Ackerveken, G. V. D., Snoek, L. B., Peeters, A. J. M., Vreugdenhil, D., Koornneef, M., & Jansen, R. C. (2007). Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. Proceedings of the National Academy of Sciences of the United States of America, 104(5), 1708-1713. https://doi.org/10.1073/pnas.0610429104
Keurentjes, J. J. B., Fu, J. J., Terpstra, I. R., Garcia, J. M., van den Ackerveken, G., Snoek, L. B., Peeters, A. J. M., Vreugdenhil, D., Koornreef, M., & Jansen, R. C. (2007). Regulatory Network Construction in Arabidopsis using genome-wide gene expression QTLs. PNAS, 104, 1708 - 1713. http://www.pnas.org/cgi/reprint/104/5/1708
Dijkstra, M., Vonk, R., & Jansen, R. C. (2007). SELDI-TOF mass spectra: A view on sources of variation. Journal of Chromatography B, 847(1), 12-23. https://doi.org/10.1016/j.jchromb.2006.11.004
Alberts, R., Terpstra, P., Li, Y., Breitling, R., Nap, J., & Jansen, R. C. (2007). Sequence Polymorphisms Cause Many False cis eQTLs. PLoS ONE, 2(7), 132 - 136. [622]. https://doi.org/10.1371/journal.pone.0000622

2006

Govorukhina, N. I., Reijmers, T. H., Nyangoma, S. O., van der Zee, A. GJ., Jansen, R. C., & Bischoff, R. (2006). Analysis of human serum by liquid chromatography-mass spectrometry: Improved sample preparation and data analysis: Improved sample preparation and data analysis. Journal of Chromatography A, 1120(1-2), 142 - 150. https://doi.org/10.1016/j.chroma.2006.02.088
Nyangoma, S. O., Fung, W-K., & Jansen, R. C. (2006). Identifying influential multinomial observations by perturbation. Computational Statistics %26 Data Analysis, 50(10), 2799 - 2821. https://doi.org/10.1016/j.csda.2005.04.023
Li, Y., Gutteling, E. W., Tijsterman, M., Fu, J., Riksen, J. A. G., Hazendonk, E., Prins, P., Plasterk, R. H. A., Jansen, R. C., Breitling, R., Kammenga, J. E., & Álvarez, O. A. (2006). Mapping determinants of gene expression plasticity by genetical genomics in C-elegans. PLoS genetics, 2(12), 2155 - 2161. [222]. https://doi.org/10.1371/journal.pgen.0020222
Fu, J., & Jansen, R. C. (2006). Optimal Design and Analysis of Genetic Studies on Gene Expression. Genetics, 172(3), 1993-1999. https://doi.org/10.1534/genetics.105.047001
Dijkstra, M., Roelofsen, H., Vonk, R. J., & Jansen, R. C. (2006). Peak quantification in surface-enhanced laser desorption/ionization by using mixture models. Proteomics, 6(19), 5106 - 5116. https://doi.org/10.1002/pmic.200600181
Albers, C. J., Jansen, R. C., Kok, J., Kuipers, O. P., & Hijum, S. A. F. T. V. (2006). SIMAGE: simulation of DNA-microarray gene expression data. Bmc Bioinformatics, 7(205), [205]. https://doi.org/10.1186/1471-2105-7-205
Keurentjes, J. J. B., Fu, J., Vos, C. H. R. D., Lommen, A., Hall, R. D., Bino, R. J., Plas, L. H. W. V. D., Jansen, R. C., Vreugdenhil, D., Koornneef, M., Hall, RD., Bino, RJ., & van der Plas, LHW. (2006). The genetics of plant metabolism. Nature Genetics, 38(7), 842 - 849. https://doi.org/10.1038/ng1815

2005

Alberts, R., Terpstra, P., Bystrykh, L. V., Haan, G. D., & Jansen, R. C. (2005). A statistical multiprobe model for analyzing cis and trans genes in genetical genomics experiments with short-oligonucleotide arrays. Genetics, 171(3), 1437 - 1439. https://doi.org/10.1534/genetics.105.045930
Horvatovich, P., Govorukhina, N. I., Reijmers, T. H., Nyangoma, S., Jansen, R. C., & Bischoff, R. (2005). Biomarker discovery for the early diagnosis of cervical cancer. Febs Journal, 272, 494 - 495.
Alberts, R., Fu, J., Swertz, M. A., Lubbers, L. A., Albers, C. J., & Jansen, R. C. (2005). Combining microarrays and genetic analysis. Briefings in Bioinformatics, 6(2), 135-145. https://doi.org/10.1093/bib/6.2.135
Spijker, G. T., Nolte, I. M., Jansen, R. C., & te Meerman, G. J. (2005). Genetic association studies in complex disease: Disentangling additional predisposing loci from associated neutral loci using a constrained - permutation approach. Annals of Human Genetics, 69(1), 90 - 101. https://doi.org/10.1046/j.1529-8817.2004.00129.x
de Haan, G., Bystrykh, L. V., Weersing, E., Sutton, S., Manly, K., Chesler, E., Jansen, R. C., Vellenga, E., Williams, R. W., & Cooke, M. P. (2005). Genetical genomics to identify gene networks in hematopoietic stem cells. Experimental Hematology, 33(7), 60 - 60.
Fu, J. J., & Jansen, R. C. (2005). Optimal Design and Analysis of Genetic Studies on Gene Expression. Genetics, 172, 1993 - 1999.
Bystrykh, L., Weersing, E., Dontje, B., Sutton, S., Pletcher, M. T., Wiltshire, T., Su, A. I., Vellenga, E., Wang, J., Manly, K. F., Lu, L., Chesler, E. J., Alberts, R., Jansen, R. C., Williams, R. W., Cooke, M., Pletcher, MT., de Haan, G., Su, AI., ... Williams, O. (2005). Uncovering regulatory pathways that effect hematopoietic stem cell function using 'genetical genomics'. Nature Genetics, 37(3), 225 - 232. https://doi.org/10.1038/ng1497

2004

Swertz, M. A., Brock, E. O. B. D., Hijum, S. A. F. T. V., Jong, A. D., Buist, G., Baerends, R. J. S., Kok, J., Kuipers, O. P., & Jansen, R. C. (2004). Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases. Bioinformatics, 20(13), 2075 - 2083. https://doi.org/10.1093/bioinformatics/bth206
Jansen, R. C., & Nap, J-P. (2004). Regulating gene expression: surprises still in store. Trends in Genetics, 20(5), 223 - 225. https://doi.org/10.1016/j.tig.2004.03.002
Churchill, G. A., Jansen, R. C., Airey, D. C., Allayee, H., Angel, J. M., Attie, A. D., Beatty, J., Beavis, W. D., Belknap, J. K., Bennett, B., Berrettini, W., Bleich, A., Bogue, M., Broman, K. W., Buck, K. J., Buckler, E., Burmeister, M., Chesler, E. J., Cheverud, J. M., ... Complex Trait Consortium (2004). The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nature Genetics, 36(11), 1133-1137. https://doi.org/10.1038/ng1104-1133

2003

Jansen, R. C. (2003). Levensecht puzzelen. s.n.
Jansen, R. C., Jannink, J-L., & Beavis, W. D. (2003). Mapping quantitative trait loci in plant breeding populations: Use of parental haplotype sharing. Crop Science, 43(3), 829-834. https://doi.org/10.2135/cropsci2003.0829
Jansen, R. C. (2003). Studying complex biological systems using multifactorial perturbation. Nature Reviews Genetics, 4(2), 145-151. https://doi.org/10.1038/nrg996
Abiola, O., Angel, JM., Avner, P., Bachmanov, AA., Belknap, JK., Bennett, B., Blankenhorn, EP., Blizard, DA., Bolivar, N. V., Brockmann, GA., Buck, KJ., Bureau, JF., Casley, WL., Chesler, EJ., Cheverud, JM., Churchill, GA., Cook, M., Crabbe, JC., Crusio, WE., ... Complex Trait Consortium (2003). The nature and identification of quantitative trait loci: a community's view. Nature Reviews Genetics, 4(11), 911-916. https://doi.org/10.1038/nrg1206

2002

Boer, M. P., Braak, C. J. F. T., & Jansen, R. C. (2002). A penalized likelihood method for mapping epistatic quantitative trait loci with one-dimensional genome searches. Genetics, 162(2), 951-960. http://keur.eldoc.ub.rug.nl/wetenschappers/9//FILES/wetenschappers/9/62/62.pdf
Mlynárová, L., Loonen, A., Mietkiewska, E., Jansen, R. C., & Nap, J-P. (2002). Assembly of Two Transgenes in an Artificial Chromatin Domain Gives Highly Coordinated Expression in Tobacco. Genetics, 160, 727-740.
Balding, DJ., Carothers, AD., Marchini, JL., Cardon, LR., Vetta, A., Griffiths, B., Weir, BS., Hill, WG., Goldstein, D., Strimmer, K., Myers, S., Beaumont, MA., Glasbey, CA., Mayer, CD., Richardson, S., Marshall, C., Durrett, R., Nielsen, R., Visscher, PM., ... Gabrielson, E. (2002). Discussion on the meeting on 'Statistical modelling and analysis of genetic data'. Journal of the Royal Statistical Society. Series B: Statistical Methodology, 64, 737-775. https://doi.org/10.1111/1467-9868.00359
Jansen, R. C., Nap, J-P., & Mlynárová, L. (2002). Errors in genomics and proteomics. Nature Biotechnology, 20(19). https://doi.org/10.1038/nbt0102-19b
van Ooien, J. W., Boer, M. P., Jansen, R. C., & Maliepaard, C. (2002). MapQTL 4.0: Software For The Calculation Of QTL Positions On Genetic Maps. Plant Research International.
Bink, M. C. A. M., Uimari, P., Sillanpää, M. J., Janss, L. L. G., & Jansen, R. C. (2002). Multiple QTL mapping in related plant populations via a pedigree-analysis approach. Theoretical and Applied Genetics, 104(5), 751-762. https://doi.org/10.1007/s00122-001-0796-x

2001

Jansen, R. C., Geerlings, H., Oeveren, A. J. V., & Schaik, R. C. V. (2001). A Comment on Codominant Scoring of AFLP Markers. Genetics.
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