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Ritsert Jansen

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Genes & Molecular Sequences

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Oligonucleotide Array Sequence Analysis

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TOP 3
L Basten Snoek; K Joeri Van der Velde; Feng Xue; Danny Arends; Antje Beyer; Mark Elvin; Jasmin Fisher; Alex Hajnal; Michael O Hengartner; Ritsert C Jansen; Jan E Kammenga; Yang Li; Gino B Poulin; Miriam Rodriguez; Tobias Schmid; Sabine Schrimpf; Morris A Swertz
WormQTL--public archive and analysis web portal for natural variation data in Caenorhabditis spp.
Ágnes Lendvai; Haukeline H Volders; René Wardenaar; G Bea A Wisman; Jasper J H Eijsink; Christina Grimm; Harry Hollema; Ritsert C Jansen; Frank Johannes; Harry G Klip; Ed Schuuring; Ate G J van der Zee
Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia.
Maria Colomé-Tatché; Vincent Colot; Sandra Cortijo; Evelyne Duvernois-Berthet; Mathilde Etcheverry; Suhua Feng; Steven E Jacobsen; Ritsert C Jansen; Karine Labadie; Benoit Lahouze; Antoine Martin; Lionel Morgado; Alexis Sarazin; René Wardenaar; Patrick Wincker; Frank Johannes
Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation.

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All Publications

2013: L Basten Snoek; K Joeri Van der Velde; Feng Xue; Danny Arends; Antje Beyer; Mark Elvin; Jasmin Fisher; Alex Hajnal; Michael O Hengartner; Ritsert C Jansen; Jan E Kammenga; Yang Li; Gino B Poulin; Miriam Rodriguez; Tobias Schmid; Sabine Schrimpf; Morris A Swertz
WormQTL--public archive and analysis web portal for natural variation data in Caenorhabditis spp.
Nucleic acids research 2013;41(Database issue):D738-43.
2012: Ágnes Lendvai; Haukeline H Volders; René Wardenaar; G Bea A Wisman; Jasper J H Eijsink; Christina Grimm; Harry Hollema; Ritsert C Jansen; Frank Johannes; Harry G Klip; Ed Schuuring; Ate G J van der Zee
Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia.
Epigenetics : official journal of the DNA Methylation Society 2012;7(11):1268-78.
2012: Maria Colomé-Tatché; Vincent Colot; Sandra Cortijo; Evelyne Duvernois-Berthet; Mathilde Etcheverry; Suhua Feng; Steven E Jacobsen; Ritsert C Jansen; Karine Labadie; Benoit Lahouze; Antoine Martin; Lionel Morgado; Alexis Sarazin; René Wardenaar; Patrick Wincker; Frank Johannes
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 2012;109(40):16240-5.
2012: Elias Chaibub Neto; Alan D Attie; Andrew F Broman; Karl W Broman; Ritsert C Jansen; Mark P Keller; Brian S Yandell
Quantile-based permutation thresholds for quantitative trait loci hotspots.
Genetics 2012;191(4):1355-65.
2012: Danny Arends; Karl W Broman; Ritsert C Jansen; Steffen Möller; Pjotr Prins; K Joeri van der Velde; Morris A Swertz
xQTL workbench: a scalable web environment for multi-level QTL analysis.
Bioinformatics (Oxford, England) 2012;28(7):1042-4.
2012: Caroline Durrant; Ritsert C Jansen; Steffen Möller; Richard Mott; Pjotr Prins; Rudi Alberts; Danny Arends; Morris A Swertz; K Joeri van der Velde; Klaus Schughart
Bioinformatics tools and database resources for systems genetics analysis in mice--a short review and an evaluation of future needs.
Briefings in bioinformatics 2012;13(2):135-42.
2012: Ronny Viktor Louis Joosen; Wilco Ligterink; Leo Albert Jan Willems; Danny Arends; Ritsert C Jansen; Henk W M Hilhorst
Visualizing the genetic landscape of Arabidopsis seed performance.
Plant physiology 2012;158(2):570-89.
2012: Frank P Diekstra; Karol Estrada; Lude Franke; Ewout J N Groen; Orla Hardiman; Albert Hofman; Steve Horvath; Ritsert C Jansen; John E Landers; P Nigel Leigh; Vincent Meininger; Judith Melki; Roel A Ophoff; Fernando Rivadeneira; Wim Robberecht; Christiaan G J Saris; Aleksey Shatunov; Christopher E Shaw; Andre G Uitterlinden; Leonard H Van den Berg; Michael A van Es; Wouter van Rheenen; Paul van Vught; Ammar Al-Chalabi; Peter M Andersen; Hylke M Blauw; Robert H Brown; Jan Veldink
Mapping of gene expression reveals CYP27A1 as a susceptibility gene for sporadic ALS.
PloS one 2012;7(4):e35333.
2012: Pjotr Prins; Geert Smant; Ritsert C Jansen
Genetical genomics for evolutionary studies.
Methods in molecular biology (Clifton, N.J.) 2012;856():469-85.
2012: Jingyuan Fu; Harry J M Groen; Marten H Hofker; Ritsert C Jansen; Roel A Ophoff; Sander S M Rensen; Harold Snieder; Gerard te Meerman; Leonard H van den Berg; David A van Heel; Jan Veldink; Rinse Weersma; Harm-Jan Westra; Cisca Wijmenga; Marcel G M Wolfs; Wim A Buurman; Patrick Deelen; Rudolf S N Fehrmann; Lude Franke
Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression.
PLoS genetics 2012;8(1):e1002431.
2011: Rudolf S N Fehrmann; Eleanora M Festen; Danny Arends; Marc Jan Bonder; Wim A Buurman; Patrick Deelen; Clara C Elbers; Jingyuan Fu; Harry J M Groen; Marten H Hofker; Robert M W Hofstra; Ritsert C Jansen; Roel A Ophoff; Mathieu Platteel; Sander Rensen; Christiaan G J Saris; Asia Smolonska; Gerard J Te Meerman; Gosia Trynka; Leonard H van den Berg; David A van Heel; Jan H Veldink; Rinse Weersma; Harm-Jan Westra; Cisca Wijmenga; Marcel G M Wolfs; Alexandra Zhernakova; Lude Franke
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 2011;7(8):e1002197.
2011: Harm-Jan Westra; Cisca Wijmenga; Rudolf S N Fehrmann; Ritsert C Jansen; Gerard J te Meerman; David van Heel; Lude Franke
MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects.
Bioinformatics (Oxford, England) 2011;27(15):2104-11.
2011: Fabrice Roux; René Wardenaar; Maria Colomé-Tatché; Vincent Colot; Cécile Edelist; Philippe Guerche; Frédéric Hospital; Ritsert C Jansen; Frank Johannes
Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature.
Genetics 2011;188(4):1015-7.
2011: Erwin Seinen; Johannes G M Burgerhof; Ritsert C Jansen; Ody C M Sibon
RNAi-induced off-target effects in Drosophila melanogaster: frequencies and solutions.
Briefings in functional genomics 2011;10(4):206-14.
2011: Richard A Scheltema; Andris Jankevics; Ritsert C Jansen; Morris A Swertz; Rainer Breitling
PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis.
Analytical chemistry 2011;83(7):2786-93.
2011: Oswaldo Trelles; Pjotr Prins; Marc Snir; Ritsert C Jansen
Big data, but are we ready?
Nature reviews. Genetics 2011;12(3):224.
2010: Danny Arends; Pjotr Prins; Ritsert C Jansen; Karl W Broman
R/qtl: high-throughput multiple QTL mapping.
Bioinformatics (Oxford, England) 2010;26(23):2990-2.
2010: Yang Li; Bruno M Tesson; Gary A Churchill; Ritsert C Jansen
Critical reasoning on causal inference in genome-wide linkage and association studies.
Trends in genetics : TIG 2010;26(12):493-8.
2010: Yang Li; Rainer Breitling; L Basten Snoek; K Joeri van der Velde; Morris A Swertz; Joost Riksen; Ritsert C Jansen; Jan E Kammenga
Global genetic robustness of the alternative splicing machinery in Caenorhabditis elegans.
Genetics 2010;186(1):405-10.
2010: Frank Johannes; René Wardenaar; Maria Colomé-Tatché; Florence Mousson; Petra de Graaf; Michal Mokry; Victor Guryev; H Th Marc Timmers; Edwin Cuppen; Ritsert C Jansen
Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq.
Bioinformatics (Oxford, England) 2010;26(8):1000-6.
2010: Morris A Swertz; Martijn Dijkstra; Tomasz Adamusiak; Joeri K van der Velde; Alexandros Kanterakis; Erik T Roos; Joris Lops; Gudmundur A Thorisson; Danny Arends; George Byelas; Juha Muilu; Anthony J Brookes; Engbert O de Brock; Ritsert C Jansen; Helen Parkinson
The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.
BMC bioinformatics 2010;11 Suppl 12():S12.
2010: Erwin Seinen; Johannes G M Burgerhof; Ritsert C Jansen; Ody C M Sibon
RNAi experiments in D. melanogaster: solutions to the overlooked problem of off-targets shared by independent dsRNAs.
PloS one 2010;5(10):.
2010: Bruno M Tesson; Rainer Breitling; Ritsert C Jansen
DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules.
BMC bioinformatics 2010;11():497.
2010: Morris A Swertz; K Joeri van der Velde; Bruno M Tesson; Richard A Scheltema; Danny Arends; Gonzalo Vera; Rudi Alberts; Martijn Dijkstra; Paul Schofield; Klaus Schughart; John M Hancock; Damian Smedley; Katy Wolstencroft; Carole Goble; Engbert O de Brock; Andrew R Jones; Helen E Parkinson; Ritsert C Jansen
XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments.
Genome biology 2010;11(3):R27.
2009: Alice Gerrits; Yang Li; Bruno M Tesson; Leonid V Bystrykh; Ellen Weersing; Albertina Ausema; Bert Dontje; Xusheng Wang; Rainer Breitling; Ritsert C Jansen; Gerald de Haan
Expression quantitative trait loci are highly sensitive to cellular differentiation state.
PLoS genetics 2009;5(10):e1000692.
2009: Martijn Dijkstra; Ritsert C Jansen
Optimal analysis of complex protein mass spectra.
Proteomics 2009;9(15):3869-76.
2009: Ritsert C Jansen; Bruno M Tesson; Jingyuan Fu; Yajie Yang; Lauren M McIntyre
Defining gene and QTL networks.
Current opinion in plant biology 2009;12(2):241-6.
2009: Jingyuan Fu; Joost J B Keurentjes; Harro Bouwmeester; Twan America; Francel W A Verstappen; Jane L Ward; Michael H Beale; Ric C H De Vos; Martijn Dijkstra; Richard A Scheltema; Frank Johannes; Maarten Koornneef; Dick Vreugdenhil; Rainer Breitling; Ritsert C Jansen
System-wide molecular evidence for phenotypic buffering in Arabidopsis.
Nature genetics 2009;41(2):166-7.
2009: Lude Franke; Ritsert C Jansen
eQTL analysis in humans.
Methods in molecular biology (Clifton, N.J.) 2009;573():311-28.
2009: Bruno M Tesson; Ritsert C Jansen
eQTL analysis in mice and rats.
Methods in molecular biology (Clifton, N.J.) 2009;573():285-309.
2009: Yang Li; Morris A Swertz; Gonzalo Vera; Jingyuan Fu; Rainer Breitling; Ritsert C Jansen
designGG: an R-package and web tool for the optimal design of genetical genomics experiments.
BMC bioinformatics 2009;10():188.
2009: Graham A Heap; Gosia Trynka; Ritsert C Jansen; Marcel Bruinenberg; Morris A Swertz; Lotte C Dinesen; Karen A Hunt; Cisca Wijmenga; David A Vanheel; Lude Franke
Complex nature of SNP genotype effects on gene expression in primary human leucocytes.
BMC medical genomics 2009;2():1.
2008: Richard A Scheltema; Anas Kamleh; David Wildridge; Charles Ebikeme; David G Watson; Michael P Barrett; Ritsert C Jansen; Rainer Breitling
Increasing the mass accuracy of high-resolution LC-MS data using background ions: a case study on the LTQ-Orbitrap.
Proteomics 2008;8(22):4647-56.
2008: Frank Johannes; Vincent Colot; Ritsert C Jansen
Epigenome dynamics: a quantitative genetics perspective.
Nature reviews. Genetics 2008;9(11):883-90.
2008: Alex C Lam; Jingyuan Fu; Ritsert C Jansen; Chris S Haley; Dirk-Jan de Koning
Optimal design of genetic studies of gene expression with two-color microarrays in outbred crosses.
Genetics 2008;180(3):1691-8.
2008: Rainer Breitling; Yang Li; Bruno M Tesson; Jingyuan Fu; Chunlei Wu; Timothy Wiltshire; Alice Gerrits; Leonid V Bystrykh; Gerald de Haan; Andrew Su; Ritsert C Jansen
Genetical genomics: spotlight on QTL hotspots.
PLoS genetics 2008;4(10):e1000232.
2008: Yang Li; Rainer Breitling; Ritsert C Jansen
Generalizing genetical genomics: getting added value from environmental perturbation.
Trends in genetics : TIG 2008;24(10):518-24.
2008: Rudi Alberts; Gonzalo Vera; Ritsert C Jansen
affyGG: computational protocols for genetical genomics with Affymetrix arrays.
Bioinformatics (Oxford, England) 2008;24(3):433-4.
2008: Gonzalo Vera; Ritsert C Jansen; Remo L Suppi
R/parallel--speeding up bioinformatics analysis with R.
BMC bioinformatics 2008;9():390.
2007: Morris A Swertz; Ritsert C Jansen
Beyond standardization: dynamic software infrastructures for systems biology.
Nature reviews. Genetics 2007;8(3):235-43.
2007: Martijn Dijkstra; roel vonk; Ritsert C Jansen
SELDI-TOF mass spectra: a view on sources of variation.
Journal of chromatography. B, Analytical technologies in the biomedical and life sciences 2007;847(1):12-23.
2007: Joost J B Keurentjes; Jingyuan Fu; Inez R Terpstra; Juan M Garcia; Guido Van den Ackerveken; L Basten Snoek; Anton J M Peeters; Dick Vreugdenhil; Maarten Koornneef; Ritsert C Jansen
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 2007;104(5):1708-13.
2007: Ilja M Nolte; André R de Vries; Geert T Spijker; Ritsert C Jansen; Dumitru Brinza; Alexander Zelikovsky; Gerard te Meerman
Association testing by haplotype-sharing methods applicable to whole-genome analysis.
BMC proceedings 2007;1 Suppl 1():S129.
2007: Stephen O Nyangoma; Antoine A H C van Kampen; Theo H Reijmers; Natalia I Govorukhina; Ate G J van der Zee; Lucinda Billingham; Rainer Bischoff; Ritsert C Jansen
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 2007;6():Article23.
2007: Rudi Alberts; Peter Terpstra; Yang Li; Rainer Breitling; Jan-Peter Nap; Ritsert C Jansen
Sequence polymorphisms cause many false cis eQTLs.
PloS one 2007;2(7):e622.
2007: Rudi Alberts; Peter Terpstra; Menno Hardonk; Leonid V Bystrykh; Gerald de Haan; Rainer Breitling; Jan-Peter Nap; Ritsert C Jansen
A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat.
BMC bioinformatics 2007;8():132.
2007: Jingyuan Fu; Morris A Swertz; Joost J B Keurentjes; Ritsert C Jansen
MetaNetwork: a computational protocol for the genetic study of metabolic networks.
Nature protocols 2007;2(3):685-94.
2006: Yang Li; Olga Alda Alvarez; Evert W Gutteling; Marcel Tijsterman; Jingyuan Fu; J A G Riksen; Esther Hazendonk; Pjotr Prins; Ronald H Plasterk; Ritsert C Jansen; Rainer Breitling; Jan E Kammenga
Mapping determinants of gene expression plasticity by genetical genomics in C. elegans.
PLoS genetics 2006;2(12):e222.
2006: Martijn Dijkstra; Han Roelofsen; roel vonk; Ritsert C Jansen
Peak quantification in surface-enhanced laser desorption/ionization by using mixture models.
Proteomics 2006;6(19):5106-16.
2006: Natalia I Govorukhina; Theo H Reijmers; S O Nyangoma; Ate G J van der Zee; Ritsert C Jansen; Rainer Bischoff
Analysis of human serum by liquid chromatography-mass spectrometry: improved sample preparation and data analysis.
Journal of chromatography. A 2006;1120(1-2):142-50.
2006: Joost J B Keurentjes; Jingyuan Fu; C H Ric de Vos; Arjen Lommen; Robert D Hall; Raoul J Bino; Linus H W van der Plas; Ritsert C Jansen; Dick Vreugdenhil; Maarten Koornneef
The genetics of plant metabolism.
Nature genetics 2006;38(7):842-9.
2006: Jingyuan Fu; Ritsert C Jansen
Optimal design and analysis of genetic studies on gene expression.
Genetics 2006;172(3):1993-9.
2006: Casper J Albers; Ritsert C Jansen; Jan Kok; Oscar P Kuipers; Sacha A F T van Hijum
SIMAGE: simulation of DNA-microarray gene expression data.
BMC bioinformatics 2006;7():205.
2005: Rudi Alberts; Peter Terpstra; Leonid V Bystrykh; Gerald de Haan; Ritsert C Jansen
A statistical multiprobe model for analyzing cis and trans genes in genetical genomics experiments with short-oligonucleotide arrays.
Genetics 2005;171(3):1437-9.
2005: Rudi Alberts; Jingyuan Fu; Morris A Swertz; L Alrik Lubbers; Casper J Albers; Ritsert C Jansen
Combining microarrays and genetic analysis.
Briefings in bioinformatics 2005;6(2):135-45.
2005: Leonid V Bystrykh; Ellen Weersing; Bert Dontje; Sue Sutton; Mathew Pletcher; Timothy Wiltshire; Andrew Su; Edo Vellenga; Jintao Wang; Kenneth F Manly; Lu Lu; Elissa J Chesler; Rudi Alberts; Ritsert C Jansen; Robert Williams; Michael P Cooke; Gerald de Haan
Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'.
Nature genetics 2005;37(3):225-32.
2005: Geert T Spijker; Ilja M Nolte; Ritsert C Jansen; Gerard te Meerman
Genetic association studies in complex disease: disentangling additional predisposing loci from associated neutral loci using a constrained - permutation approach.
Annals of human genetics 2005;69(Pt 1):90-101.
2004: Morris A Swertz; E O De Brock; Sacha A F T van Hijum; Anne de Jong; Girbe Buist; Richard J S Baerends; Jan Kok; Oscar P Kuipers; Ritsert C Jansen
Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases.
Bioinformatics (Oxford, England) 2004;20(13):2075-83.
2004: Ritsert C Jansen; Jan-Peter Nap
Regulating gene expression: surprises still in store.
Trends in genetics : TIG 2004;20(5):223-5.
2003: Ritsert C Jansen
Studying complex biological systems using multifactorial perturbation.
Nature reviews. Genetics 2003;4(2):145-51.
2002: Martin P Boer; Cajo J F Ter Braak; Ritsert C Jansen
A penalized likelihood method for mapping epistatic quantitative trait Loci with one-dimensional genome searches.
Genetics 2002;162(2):951-60.
2002: Ludmila Mlynárová; Annelies Loonen; Elzbieta Mietkiewska; Ritsert C Jansen; Jan-Peter Nap
Assembly of two transgenes in an artificial chromatin domain gives highly coordinated expression in tobacco.
Genetics 2002;160(2):727-40.
2002: Ritsert C Jansen; Jan-Peter Nap; Ludmila Mlynárová
Errors in genomics and proteomics.
Nature biotechnology 2002;20(1):19.
2001: Ritsert C Jansen; Jan-Peter Nap
Genetical genomics: the added value from segregation.
Trends in genetics : TIG 2001;17(7):388-91.
1997: Jan-Peter Nap; Anthony J Conner; Ludmila Mlynárová; Willem J Stiekema; Ritsert C Jansen
Dissection of a synthesized quantitative trait to characterize transgene interactions.
Genetics 1997;147(1):315-20.
1997: W van Der Schaar; Carlos Alonso-Blanco; Karen M Léon-Kloosterziel; Ritsert C Jansen; J W van Ooijen; Maarten Koornneef
QTL analysis of seed dormancy in Arabidopsis using recombinant inbred lines and MQM mapping.
Heredity 1997;79 ( Pt 2)():190-200.