Ritsert C Jansen

Summary

Affiliation: University of Groningen
Country: The Netherlands

Publications

  1. pmc Expression quantitative trait loci are highly sensitive to cellular differentiation state
    Alice Gerrits
    Department of Cell Biology, Section Stem Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
    PLoS Genet 5:e1000692. 2009
  2. pmc Sequence polymorphisms cause many false cis eQTLs
    Rudi Alberts
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, Netherlands
    PLoS ONE 2:e622. 2007
  3. pmc XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments
    Morris A Swertz
    Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
    Genome Biol 11:R27. 2010
  4. pmc Association testing by haplotype-sharing methods applicable to whole-genome analysis
    Ilja M Nolte
    Department of Epidemiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
    BMC Proc 1:S129. 2007
  5. pmc The dynamic architecture of the metabolic switch in Streptomyces coelicolor
    Kay Nieselt
    Center for Bioinformatics Tubingen, Department of Information and Cognitive Sciences, University of Tubingen, D 72076 Tubingen, Germany
    BMC Genomics 11:10. 2010
  6. pmc The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button
    Morris A Swertz
    Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen and Department of Genetics, University Medical Center Groningen, P O Box 30001, 9700 RB Groningen, The Netherlands
    BMC Bioinformatics 11:S12. 2010
  7. pmc DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules
    Bruno M Tesson
    Groningen Bioinformatics Center, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
    BMC Bioinformatics 11:497. 2010
  8. pmc R/parallel--speeding up bioinformatics analysis with R
    Gonzalo Vera
    Computer Architecture and Operating Systems Department, Universitat Autonoma de Barcelona, Bellaterra, Spain
    BMC Bioinformatics 9:390. 2008
  9. pmc WormQTLHD--a web database for linking human disease to natural variation data in C. elegans
    K Joeri van der Velde
    Genomics Coordination Center, University of Groningen, University Medical Center Groningen, P O Box 30001, 9700 RB Groningen, The Netherlands, Groningen Bioinformatics Center, University of Groningen, P O Box 11103, 9700 CC Groningen, The Netherlands, Department of Genetics, University of Groningen, University Medical Center Groningen, P O Box 30001, 9700 RB Groningen, The Netherlands, Department of Bioinformatics, Hanze University of Applied Sciences, Groningen, Zernikeplein 11, 9747 AS, The Netherlands and Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
    Nucleic Acids Res 42:D794-801. 2014
  10. pmc xQTL workbench: a scalable web environment for multi-level QTL analysis
    Danny Arends
    Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands
    Bioinformatics 28:1042-4. 2012

Collaborators

Detail Information

Publications36

  1. pmc Expression quantitative trait loci are highly sensitive to cellular differentiation state
    Alice Gerrits
    Department of Cell Biology, Section Stem Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
    PLoS Genet 5:e1000692. 2009
    ..Therefore, future genetical genomics studies should aim at studying multiple well-defined and highly purified cell types in order to construct as comprehensive a picture of the changing functional regulatory relationships as possible...
  2. pmc Sequence polymorphisms cause many false cis eQTLs
    Rudi Alberts
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, Netherlands
    PLoS ONE 2:e622. 2007
    ..Applying this approach to recent mouse and human eQTL data, we demonstrate that indeed many local eQTLs are falsely reported as "cis-acting" or "cis" and can be successfully detected and eliminated with this approach...
  3. pmc XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments
    Morris A Swertz
    Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
    Genome Biol 11:R27. 2010
    ..Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans...
  4. pmc Association testing by haplotype-sharing methods applicable to whole-genome analysis
    Ilja M Nolte
    Department of Epidemiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
    BMC Proc 1:S129. 2007
    ..In conclusion, haplotype sharing methods, particularly the CROSS test, show great promise for identifying disease gene loci...
  5. pmc The dynamic architecture of the metabolic switch in Streptomyces coelicolor
    Kay Nieselt
    Center for Bioinformatics Tubingen, Department of Information and Cognitive Sciences, University of Tubingen, D 72076 Tubingen, Germany
    BMC Genomics 11:10. 2010
    ..We have studied gene expression patterns during this switch, using a specifically designed Affymetrix genechip and a high-resolution time-series of fermenter-grown samples...
  6. pmc The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button
    Morris A Swertz
    Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen and Department of Genetics, University Medical Center Groningen, P O Box 30001, 9700 RB Groningen, The Netherlands
    BMC Bioinformatics 11:S12. 2010
    ..We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed...
  7. pmc DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules
    Bruno M Tesson
    Groningen Bioinformatics Center, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
    BMC Bioinformatics 11:497. 2010
    ..Here, sensitive and untargeted means that the method should be able to construct de novo modules by grouping genes based on shared, but subtle, differential correlation patterns...
  8. pmc R/parallel--speeding up bioinformatics analysis with R
    Gonzalo Vera
    Computer Architecture and Operating Systems Department, Universitat Autonoma de Barcelona, Bellaterra, Spain
    BMC Bioinformatics 9:390. 2008
    ..Although these tools can finally speed up the calculations, the time, skills and additional resources required to use them are an obstacle for most bioinformaticians...
  9. pmc WormQTLHD--a web database for linking human disease to natural variation data in C. elegans
    K Joeri van der Velde
    Genomics Coordination Center, University of Groningen, University Medical Center Groningen, P O Box 30001, 9700 RB Groningen, The Netherlands, Groningen Bioinformatics Center, University of Groningen, P O Box 11103, 9700 CC Groningen, The Netherlands, Department of Genetics, University of Groningen, University Medical Center Groningen, P O Box 30001, 9700 RB Groningen, The Netherlands, Department of Bioinformatics, Hanze University of Applied Sciences, Groningen, Zernikeplein 11, 9747 AS, The Netherlands and Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
    Nucleic Acids Res 42:D794-801. 2014
    ..All software is available as open source, built on MOLGENIS and xQTL workbench. ..
  10. pmc xQTL workbench: a scalable web environment for multi-level QTL analysis
    Danny Arends
    Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands
    Bioinformatics 28:1042-4. 2012
    ..All data involved can be uploaded and queried online: markers, genotypes, microarrays, NGS, LC-MS, GC-MS, NMR, etc. When new data types come available, xQTL workbench is quickly customized using the Molgenis software generator...
  11. doi request reprint System-wide molecular evidence for phenotypic buffering in Arabidopsis
    Jingyuan Fu
    Groningen Bioinformatics Centre, University of Groningen, 9751NN Haren, The Netherlands
    Nat Genet 41:166-7. 2009
    ..We found six QTL hot spots with major, system-wide effects, suggesting there are six breakpoints in a system otherwise buffered against many of the 500,000 SNPs...
  12. pmc designGG: an R-package and web tool for the optimal design of genetical genomics experiments
    Yang Li
    Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
    BMC Bioinformatics 10:188. 2009
    ..The optimal design of such genetical genomics experiments in a cost-efficient and effective way is not trivial...
  13. pmc A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat
    Rudi Alberts
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
    BMC Bioinformatics 8:132. 2007
    ..To determine the accuracy of Affymetrix arrays, we developed an extensive verification protocol, for mouse arrays incorporating the NCBI RefSeq, NCBI UniGene Unique, NIA Mouse Gene Index, and UCSC mouse genome databases...
  14. pmc Global genetic robustness of the alternative splicing machinery in Caenorhabditis elegans
    Yang Li
    Groningen Bioinformatics Centre, University of Groningen, 9751 NN, Haren, The Netherlands
    Genetics 186:405-10. 2010
    ..Our findings suggest that the regulatory mechanism of alternative splicing in C. elegans is robust toward genetic variation at the genome-wide scale, which is in striking contrast to earlier observations in humans...
  15. doi request reprint Generalizing genetical genomics: getting added value from environmental perturbation
    Yang Li
    Groningen Bioinformatics Centre, University of Groningen, 9751 NN Haren, The Netherlands
    Trends Genet 24:518-24. 2008
    ..Here we outline a strategy for selecting and allocating individuals to particular treatments, and we discuss the promises and pitfalls of the generalized genetical genomics approach...
  16. ncbi request reprint affyGG: computational protocols for genetical genomics with Affymetrix arrays
    Rudi Alberts
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
    Bioinformatics 24:433-4. 2008
    ..Affymetrix arrays use multiple probes per gene to measure mRNA abundances. Standard software takes averages over probes. Important information may be lost if polymorphisms in the mRNA affect the hybridization of individual probes...
  17. pmc Optimal design and analysis of genetic studies on gene expression
    Jingyuan Fu
    Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751NN Haren, The Netherlands
    Genetics 172:1993-9. 2006
    ..Our results will aid the design and analysis of future studies on gene expression and will help to shed more light on gene regulatory networks...
  18. doi request reprint Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq
    Frank Johannes
    Groningen Bioinformatics Centre, University of Groningen, Kerklaan 30, Biologisch Centrum, 9751 NN Haren, The Netherlands
    Bioinformatics 26:1000-6. 2010
    ..This shortcoming presents a bottleneck in biological interpretations of multiple sample data...
  19. doi request reprint eQTL analysis in mice and rats
    Bruno M Tesson
    Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
    Methods Mol Biol 573:285-309. 2009
    ..In this chapter, we provide a step-by-step guide to performing genome-wide linkage analysis in an eQTL mapping experiment by using the R statistical software framework...
  20. ncbi request reprint MetaNetwork: a computational protocol for the genetic study of metabolic networks
    Jingyuan Fu
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, NL 9751 NN Haren, The Netherlands
    Nat Protoc 2:685-94. 2007
    ..This way MetaNetwork will contribute to a better integration of such data into systems biology...
  21. doi request reprint eQTL analysis in humans
    Lude Franke
    Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
    Methods Mol Biol 573:311-28. 2009
    ..2007, Nature 448, 470-473): associated genetic variants have been identified that affect levels of gene expression in cis or in trans, providing insight into the biological pathways affected by these diseases...
  22. pmc A statistical multiprobe model for analyzing cis and trans genes in genetical genomics experiments with short-oligonucleotide arrays
    Rudi Alberts
    Groningen Bioinformatics Centre GBiC, Groningen Biomolecular Sciences and Biotechnology Institute GBB, University of Groningen, 9751 NN, Haren, The Netherlands
    Genetics 171:1437-9. 2005
    ..It can also help in detecting alternative splicing, start, or termination...
  23. doi request reprint PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis
    Richard A Scheltema
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
    Anal Chem 83:2786-93. 2011
    ..The PeakML/mzMatch software is freely available at http://mzmatch.sourceforge.net, with documentation, tutorials, and a community forum...
  24. pmc SIMAGE: simulation of DNA-microarray gene expression data
    Casper J Albers
    Groningen Bioinformatics Centre, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands
    BMC Bioinformatics 7:205. 2006
    ....
  25. doi request reprint Increasing the mass accuracy of high-resolution LC-MS data using background ions: a case study on the LTQ-Orbitrap
    Richard A Scheltema
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
    Proteomics 8:4647-56. 2008
    ..The accuracy of this approach will facilitate many downstream systems biology applications, including mass-based molecule identification, ab initio metabolic network reconstruction, and untargeted metabolomics in general...
  26. pmc R/qtl: high-throughput multiple QTL mapping
    Danny Arends
    Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands
    Bioinformatics 26:2990-2. 2010
    ..MQM for R/qtl is the first free and open source implementation of MQM that is multi-platform, scalable and suitable for automated procedures and large genetical genomics datasets...
  27. pmc Critical reasoning on causal inference in genome-wide linkage and association studies
    Yang Li
    Groningen Bioinformatics Centre, University of Groningen, The Netherlands
    Trends Genet 26:493-8. 2010
    ..We conclude that causal inference methods can still be of use in the iterative process of mathematical modeling and biological validation...
  28. ncbi request reprint Combining microarrays and genetic analysis
    Rudi Alberts
    Groningen Bioinformatics Centre, University of Groningen, Kerklaan 30, 9751 NN, Haren, The Netherlands
    Brief Bioinform 6:135-45. 2005
    ..It is shown how to fully exploit the power of genetics through optimal experimental design and analysis for two major microarray technologies, cDNA two-colour arrays and Affymetrix short oligonucleotide arrays...
  29. pmc Mapping determinants of gene expression plasticity by genetical genomics in C. elegans
    Yang Li
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
    PLoS Genet 2:e222. 2006
    ..Our results suggest widespread genetic variation of differential expression responses to environmental impacts and demonstrate the potential of genetical genomics for mapping the molecular determinants of phenotypic plasticity...
  30. ncbi request reprint Beyond standardization: dynamic software infrastructures for systems biology
    Morris A Swertz
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, NL 9751 NN Haren, The Netherlands
    Nat Rev Genet 8:235-43. 2007
    ..We argue that a minimal computer language, and a software tool called a generator, can be used to quickly produce customized software infrastructures that 'systems biologists really want to have'...
  31. pmc Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation
    Maria Colomé-Tatché
    Groningen Bioinformatics Centre, University of Groningen, 9747 AG Groningen, The Netherlands
    Proc Natl Acad Sci U S A 109:16240-5. 2012
    ..This level of robustness is remarkable, considering that this population represents an extreme with key recombination barriers having been forced to a minimum...
  32. doi request reprint Defining gene and QTL networks
    Ritsert C Jansen
    Groningen Bioinformatics Centre, University of Groningen, The Netherlands
    Curr Opin Plant Biol 12:241-6. 2009
    ..These methods are becoming increasingly popular in plant genetic studies as well as in studies on many other organisms...
  33. doi request reprint Epigenome dynamics: a quantitative genetics perspective
    Frank Johannes
    Frank Johannes and Ritsert C Jansen are at the Groningen Bioinformatics Centre, University of Groningen, NL 9751 NN, Haren, The Netherlands
    Nat Rev Genet 9:883-90. 2008
    ..Here we argue that it is timely to consider novel experimental strategies and analysis models to capture the potentially dynamic interplay between chromatin and DNA sequence factors in complex traits...
  34. doi request reprint Optimal analysis of complex protein mass spectra
    Martijn Dijkstra
    Groningen Bioinformatics Centre, University of Groningen, Haren, The Netherlands
    Proteomics 9:3869-76. 2009
    ....
  35. pmc Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor
    Mohammad T Alam
    Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
    BMC Genomics 11:202. 2010
    ..Here we have explored the underlying reorganization of the metabolome by combining computational predictions based on constraint-based modeling and detailed transcriptomics time course observations...
  36. ncbi request reprint SELDI-TOF mass spectra: a view on sources of variation
    Martijn Dijkstra
    Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, P O Box 800, NL 9700 AV Groningen, The Netherlands
    J Chromatogr B Analyt Technol Biomed Life Sci 847:12-23. 2007
    ....