designGG: an R-package and web tool for the optimal design of genetical genomics experiments (2009)
Li, Yang, Swertz, Morris A, Vera, Gonzalo, Fu, Jingyuan, Breitling, Rainer, Jansen, Ritsert C
Abstract Background High-dimensional biomolecular profiling of genetically different individuals in one or more environmental conditions is an increasingly popular strategy for exploring the...
Complex nature of SNP genotype effects on gene expression in primary human leucocytes (2009)
Heap, Graham A, Trynka, Gosia, Jansen, Ritsert C, Bruinenberg, Marcel, Swertz, Morris A, Dinesen, Lotte C, ...
Abstract Background Genome wide association studies have been hugely successful in identifying disease risk variants, yet most variants do not lead to coding changes and how variants influence...
Defining gene and QTL networks (2009)
Jansen, Ritsert C., Tesson, Bruno M., Fu, Jingyuan, Yang, Yajie, McIntyre, Lauren M.
Current technologies for high-throughput molecular profiling of large numbers of genetically different individuals offer great potential for elucidating the genotype-to-phenotype relationship....
Complex nature of SNP genotype effects on gene expression in primary human leucocytes (2009)
Heap, Graham A., Trynka, Gosia, Jansen, Ritsert C., Bruinenberg, Marcel, Swertz, Morris A., Dinesen, Lotte C., ...
Background: Genome wide association studies have been hugely successful in identifying disease risk variants, yet most variants do not lead to coding changes and how variants influence biological...
System-wide molecular evidence for phenotypic buffering in Arabidopsis (2009)
Fu, Jingyuan, Keurentjes, Joost J.B., Bouwmeester, Harro, America, Twan, Verstappen, Francel W.A., Ward, Jane L., ...
We profiled 162 lines of Arabidopsis for variation in transcript, protein and metabolite abundance using mRNA microarrays, two-dimensional polyacrylamide gel electrophoresis, gas chromatography...
designGG: an R-package and web tool for the optimal design of genetical genomics experiments (2009)
Li, Yang, Swertz, Morris A., Vera, Gonzalo, Fu, Jingyuan, Breitling, Rainer, Jansen, Ritsert C.
Background: High-dimensional biomolecular profiling of genetically different individuals in one or more environmental conditions is an increasingly popular strategy for exploring the functioning of...
Optimal analysis of complex protein mass spectra (2009)
Dijkstra, Martijn, Jansen, Ritsert C.
Due to physical and chemical phenomena, a simple sample can give rise to a complex mass spectrum with many more peaks than the number of molecular species present in the sample. We link peaks within...
Scheltema, R.A., Kamleh, M.A., Wildridge, D., Ebikeme, Charles, Watson, D.G., Barrett, Michael P., ...
With the advent of a new generation of high-resolution mass spectrometers, the fields of proteomics and metabolomics have gained powerful new tools. In this paper, we demonstrate a novel...
R/parallel – speeding up bioinformatics analysis with R (2008)
Vera, Gonzalo, Jansen, Ritsert C, Suppi, Remo L
Abstract Background R is the preferred tool for statistical analysis of many bioinformaticians due in part to the increasing number of freely available analytical methods. Such methods can be quickly...
Combining microarrays and (2008)
Groningen Bioinformatics, Jingyuan Fu, Morris A. Swertz, Groningen Bioinformatics, L. Alrik Lubbers, Ritsert C. Jansen, ...
Groningen, focusing on genetical genomics in the mouse.
affyGG: computational protocols for genetical genomics with Affymetrix arrays (2008)
Alberts, Rudi, Vera, Gonzalo, Jansen, Ritsert C.
Motivation: 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...
Generalizing genetical genomics: getting added value from environmental perturbation (2008)
Li, Yang, Breitling, Rainer, Jansen, Ritsert C.
Genetical genomics is a useful approach for studying the effect of genetic perturbations on biological systems at the molecular level. However, molecular networks depend on the environmental...
Genetical Genomics: Spotlight on QTL Hotspots (2008)
Breitling, Rainer, Li, Yang, Tesson, Bruno M., Fu, Jingyuan, Wu, Chunlei, Wiltshire, Tim, ...
Epigenome dynamics: a quantitative genetics perspective (2008)
Johannes, Frank, Colot, Vincent, Jansen, Ritsert C.
Classically, quantitative geneticists have envisioned DNA sequence variants as the only source of heritable phenotypes. This view should be revised in light of accumulating evidence for widespread...
R/parallel – speeding up bioinformatics analysis with R (2008)
Vera, Gonzalo, Jansen, Ritsert C., Suppi, Remo L.
Background: R is the preferred tool for statistical analysis of many bioinformaticians due in part to the increasing number of freely available analytical methods. Such methods can be quickly reused...
Scheltema, Richard A., Kamleh, Anas, Wildridge, David, Ebikeme, Charles, Watson, David G., Barrett, Michael P., ...
With the advent of a new generation of high-resolution mass spectrometers, the fields of proteomics and metabolomics have gained powerful new tools. In this paper, we demonstrate a novel...
Lam, Alex C., Fu, Jingyuan, Jansen, Ritsert C., Haley, Chris S., Koning, Dirk-Jan De
Combining global gene-expression profiling and genetic analysis of natural allelic variation (genetical genomics) has great potential in dissecting the genetic pathways underlying complex phenotypes....
affyGG: computational protocols for genetical genomics with Affymetrix arrays (2008)
Alberts, Rudi, Vera, Gonzalo, Jansen, Ritsert C.
Motivation: 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...
Association testing by haplotype-sharing methods applicable to whole-genome analysis (2007)
Nolte, Ilja M, De Vries, André R, Spijker, Geert T, Jansen, Ritsert C, Brinza, Dumitru, Zelikovsky, Alexander, ...
Abstract We propose two new haplotype-sharing methods for identifying disease loci: the haplotype sharing statistic (HSS), which compares length of shared haplotypes between cases and controls, and...
Nyangoma, Stephen O, Reijmers, Theo H, Govorukhina, Natalia I, Billingham, Lucinda J, ...
Liquid Chromatography - Mass Spectrometry (LC-MS) is a powerful method for sensitive detection and quantification of proteins and peptides in complex biological fluids like serum. LC-MS produces...
Nyangoma, Stephen O, Reijmers, Theo H, Govorukhina, Natalia I, Billingham, Lucinda J, ...
Liquid Chromatography - Mass Spectrometry (LC-MS) is a powerful method for sensitive detection and quantification of proteins and peptides in complex biological fluids like serum. LC-MS produces...
Nyangoma, Stephen O, Reijmers, Theo H, Govorukhina, Natalia I, Billingham, Lucinda J, ...
Liquid Chromatography - Mass Spectrometry (LC-MS) is a powerful method for sensitive detection and quantification of proteins and peptides in complex biological fluids like serum. LC-MS produces...
Nyangoma, Stephen O, Reijmers, Theo H, Govorukhina, Natalia I, Billingham, Lucinda J, ...
Liquid Chromatography - Mass Spectrometry (LC-MS) is a powerful method for sensitive detection and quantification of proteins and peptides in complex biological fluids like serum. LC-MS produces...
MetaNetwork: a computational protocol for the genetic study of metabolic networks (2007)
Fu, Jingyuan, Swertz, Morris A., Keurentjes, Joost J.B., Jansen, Ritsert C.
We here describe the MetaNetwork protocol to reconstruct metabolic networks using metabolite abundance data from segregating populations. MetaNetwork maps metabolite quantitative trait loci (mQTLs)...
SELDI-TOF mass spectra: A view on sources of variation (2007)
Dijkstra, Martijn, Vonk, Roel J., Jansen, Ritsert C.
Adequate interpretation of mass spectrometry data can yield valuable biomarkers. However, spectrum interpretation is a complicated task. This paper reviews the various factors that determine a...
Beyond standardization: dynamic software infrastructures for systems biology (2007)
Swertz, Morris A., Jansen, Ritsert C.
Progress in systems biology is seriously hindered by slow production of suitable software infrastructures. Biologists need infrastructure that easily connects to work that is done in other...
Keurentjes, Joost J.B., Fu, Jingyuan, Terpstra, Inez R., Garcia, Juan M., Ackerveken, Guido Van Den, Basten Snoek, L., ...
Accessions of a plant species can show considerable genetic differences that are analyzed effectively by using recombinant inbred line (RIL) populations. Here we describe the results of genomewide...
Sequence Polymorphisms Cause Many False cis eQTLs (2007)
Alberts, Rudi, Terpstra, Peter, Li, Yang, Breitling, Rainer, Nap, Jan-Peter, Jansen, Ritsert C.
Many investigations have reported the successful mapping of quantitative trait loci (QTLs) for gene expression phenotypes (eQTLs). Local eQTLs, where expression phenotypes map to the genes...
Association testing by haplotype-sharing methods applicable to whole-genome analysis (2007)
Nolte, Ilja M., Vries, André R. De, Spijker, Geert T., Jansen, Ritsert C., Brinza, Dumitru, Zelikovsky, Alexander, ...
We propose two new haplotype-sharing methods for identifying disease loci: the haplotype sharing statistic (HSS), which compares length of shared haplotypes between cases and controls, and the CROSS...
Govorukhina, Natalia I., Reijmers, Theo H., Nyangoma, Stephen O., Billingham, Lucinda J., ...
Liquid Chromatography - Mass Spectrometry (LC-MS) is a powerful method for sensitive detection and quantification of proteins and peptides in complex biological fluids like serum. LC-MS produces...
Mapping Determinants of Gene Expression Plasticity by Genetical Genomics in C. elegans (2006)
Yang Li, Olga Alda Álvarez, Evert W. Gutteling, Marcel Tijsterman, Jingyuan Fu, ...
Recent genetical genomics studies have provided intimate views on gene regulatory networks. Gene expression variations between genetically different individuals have been mapped to the causal...
Mapping Determinants of Gene Expression Plasticity by Genetical Genomics in C. elegans (2006)
Yang Li, Olga Alda Alvarez, Evert W Gutteling, Marcel Tijsterman, Jingyuan Fu, ...
Recent genetical genomics studies have provided intimate views on gene regulatory networks. Gene expression variations between genetically different individuals were mapped to the causal regulatory...
The genetics of plant metabolism (2006)
Keurentjes, Joost J.B., Fu, Jingyuan, Lommen, Arjen, Hall, Robert D., Bino, Raoul J., ...
Variation for metabolite composition and content is often observed in plants. However, it is poorly understood to what extent this variation has a genetic basis. Here, we describe the genetic...
SIMAGE: simulation of DNA-microarray gene expression data. Software (2006)
Albers, Casper J., Jansen, Ritsert C., Kok, Jan, Kuipers, Oscar P.
Background: Simulation of DNA-microarray data serves at least three purposes: (i) optimizing the design of an intended DNA microarray experiment, (ii) comparing existing pre-processing and processing...
Peak quantification in surface-enhanced laser desorption/ionization by using mixture models (2006)
Dijkstra, Martijn, Roelofsen, Han, Vonk, Roel J., Jansen, Ritsert C.
Surface-enhanced laser desorption/ionization (SELDI) time of flight (TOF) is a mass spectrometry technology for measuring the composition of a sampled protein mixture. A mass spectrum contains peaks...
Mapping Determinants of Gene Expression Plasticity by Genetical Genomics in C. elegans (2006)
Li, Yang, Álvarez, Olga Alda, Gutteling, Evert W., Tijsterman, Marcel, Fu, Jingyuan, Riksen, Joost A.G., ...
Recent genetical genomics studies have provided intimate views on gene regulatory networks. Gene expression variations between genetically different individuals have been mapped to the causal...
Optimal Design and Analysis of Genetic Studies on Gene Expression (2006)
Fu, Jingyuan, Jansen, Ritsert C.
Whole-genome profiling of gene expression in a segregating population has the potential to identify the regulatory consequences of natural allelic variation. Costs of such studies are high and...
Bmc Bioinformatics, Casper J Albers, Ritsert C Jansen, Jan Kok, Oscar P Kuipers, Biomed Central
Software SIMAGE: simulation of DNA-microarray gene expression data
Alberts, Rudi, Terpstra, Peter, Bystrykh, Leonid V., Haan, Gerald De, Jansen, Ritsert C.
Short-oligonucleotide arrays typically contain multiple probes per gene. In genetical genomics applications a statistical model for the individual probe signals can help in separating...
Combining microarrays and genetic analysis (2005)
Alberts, Rudi, Fu, Jingyuan, Swertz, Morris A., Lubbers, L. Alrik, Albers, Casper J., Jansen, Ritsert C.
Gene expression can be studied at a genome-wide scale with the aid of modern microarray technologies. Expression profiling of tens to hundreds of individuals in a genetic population can reveal the...
Bystrykh, Leonid, Weersing, Ellen, Dontje, Bert, Sutton, Sue, Pletcher, Mathew T., Wiltshire, Tim, ...
We combined large-scale mRNA expression analysis and gene mapping to identify genes and loci that control hematopoietic stem cell (HSC) function. We measured mRNA expression levels in purified HSCs...
Combining microarrays and genetic analysis (2005)
Alberts, Rudi, Fu, Jingyuan, Swertz, Morris A., Lubbers, L. Alrik, Albers, Casper J., Jansen, Ritsert C.
Gene expression can be studied at a genome-wide scale with the aid of modern microarray technologies. Expression profiling of tens to hundreds of individuals in a genetic population can reveal the...
Regulating gene expression: suprises still in store (2004)
Jansen, Ritsert C., Nap, Jan-Peter
Understanding how genes constitute and contribute to the regulatory networks that result in phenotypic diversity is the major challenge of the post-genome era. Recently, it has been shown that major...
The Collaborative Cross, a community resource for the genetic analysis of complex traits (2004)
Churchill, Gary A., Jansen, Ritsert C., Et Al.
The goal of the Complex Trait Consortium is to promote the development of resources that can be used to understand, treat and ultimately prevent pervasive human diseases. Existing and proposed mouse...
Swertz, Morris A., Brock, E.O. (Bert) De, Jong, Anne De, Buist, Girbe, Baerends, Richard J.S., ...
Motivation: Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of...
Rational: UML Semantics Appendix M4 -Relationship to OMG Technologies (2004)
Morris A. Swertz, Anne De Jong, Girbe Buist, Jan Kok, Oscar P. Kuipers, ...
*To whom correspondence should be addressed.
Swertz, Morris A., De Brock, E. O., De Jong, Anne, Buist, Girbe, Baerends, Richard J. S., ...
Motivation: Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of...
Swertz, Morris A., (Bert) De Brock, E. O., De Jong, Anne, Buist, Girbe, Baerends, Richard J. S., ...
Motivation: Genomic research laboratories need an adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? Lack of...
Swertz, Morris A., (Bert) De Brock, E. O., De Jong, Anne, Buist, Girbe, Baerends, Richard J. S., ...
Motivation: Genomic research laboratories need an adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? Lack of...
Studying complex biological systems using multifactorial perturbation (2003)
High-throughput genomics, transcriptomics, proteomics and metabolomics have the potential to identify the functional consequences of induced and natural genetic variation. Surprisingly, the...
The nature and identification of quantitative trait loci: a community's view (2003)
Abiola, Oduola, Jansen, Ritsert C., Et Al.
This white paper by eighty members of the Complex Trait Consortium presents a community’s view on the approaches and statistical analyses that are needed for the identification of genetic loci that...
Jansen, Ritsert C., Jannink, Jean-Luc, Beavis, William D.
Applied breeding programs evaluate large numbers of progeny derived from multiple related crosses for a wide range of agronomic traits and for tens to hundreds of molecular markers. This study was...
Mlynárová, Ludmila, Loonen, Annelies, Mietkiewska, Elzbieta, Jansen, Ritsert C., Nap, Jan-Peter
The chromatin loop model predicts that genes within the same chromatin domain exhibit coordinated regulation. We here present the first direct experimental support for this model in plants. Two...
Boer, Martin P., Jansen, Ritsert C.
Epistasis is a common and important phenomenon, as indicated by results from a number of recent experiments. Unfortunately, the discovery of epistatic quantitative trait loci (QTL) is difficult since...
A Comment on Codominant Scoring of AFLP Markers (2001)
Jansen, Ritsert C., Geerlings, Henk, Oeveren, A. Jan Van, Schaik, René C. Van
Genetical genomics: the added value from segregation (2001)
Jansen, Ritsert C., Nap, Jan-Peter
The recent successes of genome-wide expression profiling in biology tend to overlook the power of genetics. We here propose a merger of genomics and genetics into ‘genetical genomics’. This...
Using complex plant pedigrees to map valuable genes (2001)
Jannink, Jean-Luc, Jansen, Ritsert C.
Statistical methods pioneered by human and animal geneticists use marker and pedigree information to detect quantitative trait loci within complex pedigrees. These methods, adapted to plants, promise...
Aharoni, Asaph, Keizer, Leopold C.P., Bouwmeester, Harro J., Sun, Zhongkui, Alvarez-Huerta, Mayte, Verhoeven, Harrie A., ...
Fruit flavor is a result of a complex mixture of numerous compounds. The formation of these compounds is closely correlated with the metabolic changes occurring during fruit maturation. Here, we...
Johnson, David L., Jansen, Ritsert C.
A mixture model approach is employed for the mapping of quantitative trait loci (QTL) for the situation where individuals, in an outbred population, are selectively genotyped. Maximum likelihood...
Genetics of refractoriness to Plasmodium falciparum in the mosquito Anopheles stephensi (1998)
Feldmann, A.M., Gemert, Geert-Jan Van, Jansen, Ritsert C.
We previously selected a line of the malaria vector mosquito Anopheles stephensi refractory (resistant) to the human malaria parasite Plasmodium falciparum, using in vitro infections with P....
Fijneman, Remond J.A., Jansen, Ritsert C., Demant, Peter
Although several genes that cause monogenic familial cancer syndromes have been identified, susceptibility to sporadic cancer remains unresolved. Animal experiments have demonstrated multigenic...
Jansen, Ritsert C., Johnson, David L.
A mixture model approach is presented for the mapping of one or more quantitative trait loci (QTLs) in complex populations. In order to exploit the full power of complete linkage maps the...
QTL Analysis of seed dormancy in Arabidopsis using recombinant inbred lines and MQM mapping (1997)
Schaar, Wybe Van Der, Alonso-Blanco, Carlos, Léon-Kloosterziel, Karen M., Jansen, Ritsert C., Ooijen, Johan W. Van, Koornneef, Maarten
The genetic differences for seed germination between two commonly used Arabidopsis thaliana ecotypes Ler and Col, both showing a low level of seed dormancy, were investigated. The analysis was...
Dissection of a Synthesized Quantitative Trait to Characterize Transgene Interactions (1997)
Nap, Jan-Peter, Conner, Anthony J., Mlynárová, Ludmila, Stiekema, Willem J., Jansen, Ritsert C.
Six transgenic tobacco lines, each homozygous for the β-glucuronidase (GUS) gene at a different locus, and wild type were selfed and intercrossed to evaluate GUS activity in all possible hemizygous,...
Bonnier, Frans J.M., Jansen, Ritsert C., Tuyl, Jaap M. Van
Effects of freezing duration, previous storage duration of bulbs at -2 °C, and partial dehydration of scales on freezing tolerance of lily (Lilium hybrids) scales were studied for a series of...
Fijneman, Remond J.A., Vries, Sandra S. De, Jansen, Ritsert C., Demant, Peter
Many complex traits, including susceptibility to lung cancer, are controlled by multiple genes - quantitative trait loci (QTLs). We facilitated the mapping of QTLs by making use of recombinant...
A General Monte Carlo Method for Mapping Multiple Quantitative Trait Loci (1996)
In this paper we address the mapping of multiple quantitative trait loci (QTLs) in line crosses for which the genetic data are highly incomplete. Such complicated situations occur, for instance, when...
Long term lily scale bulblet storage: effects of temperature and storage in polyethylene bags (1996)
Bonnier, Frans J.M., Jansen, Ritsert C., Tuyl, Jaap M. Van
Collections of lily genotypes are usually maintained by yearly planting, harvesting and storage of the bulbs. To facilitate this maintenance, a storage method has been developed for a collection of...
Mlynárová, Ľudmila, Jansen, Ritsert C., Conner, Anthony J., Stiekema, Willem J., Nap, Jan-Peter
To study the role of matrix-associated regions (MARs) in establishing independent chromatin domains in plants, two transgenes were cloned between chicken lysozyme A elements. These transgenes were...
In crop plants quantitative variation is a feature of many important traits, such as yield, quality or disease resistance. Means of analyzing quantitative variation and especially of uncovering its...
Mlynárová, Ľudmila, Loonen, Annelies, Heldens, Jos, Jansen, Ritsert C., Keizer, Paul, Stiekema, Willem J., ...
Matrix-associated regions may be useful for studying the role of chromatin architecture in transgene activity of transformed plants. The chicken lysozyme A element was shown to have specific affinity...
High Resolution of Quantitative Traits Into Multiple Loci via Interval Mapping (1994)
Jansen, Ritsert C., Stam, Piet
A very general method is described for multiple linear regression of a quantitative phenotype on genotype [putative quantitative trait loci (QTLs) and markers] in segregating generations obtained...
Controlling the Type I and Type II Errors in Mapping Quantitative Trait Loci (1994)
Although the interval mapping method is widely used for mapping quantitative trait loci (QTLs), it is not very well suited for mapping multiple QTLs. Here, we present the results of a computer...
Interval Mapping of Multiple Quantitative Trait Loci (1993)
The interval mapping method is widely used for the mapping of quantitative trait loci (QTLs) in segregating generations derived from crosses between inbred lines. The efficiency of detecting and the...
Association testing by haplotype-sharing methods applicable to whole-genome analysis
Nolte, Ilja M, De Vries, André R, Spijker, Geert T, Jansen, Ritsert C, Brinza, Dumitru, Zelikovsky, Alexander, ...
We propose two new haplotype-sharing methods for identifying disease loci: the haplotype sharing statistic (HSS), which compares length of shared haplotypes between cases and controls, and the CROSS...
Genetical Genomics: Spotlight on QTL Hotspots
Breitling, Rainer, Li, Yang, Tesson, Bruno M., Fu, Jingyuan, Wu, Chunlei, Wiltshire, Tim, ...
Complex nature of SNP genotype effects on gene expression in primary human leucocytes
Heap, Graham A, Trynka, Gosia, Jansen, Ritsert C, Bruinenberg, Marcel, Swertz, Morris A, Dinesen, Lotte C, ...
Optimal Design of Genetic Studies of Gene Expression With Two-Color Microarrays in Outbred Crosses
Lam, Alex C., Fu, Jingyuan, Jansen, Ritsert C., Haley, Chris S., De Koning, Dirk-Jan
Combining global gene-expression profiling and genetic analysis of natural allelic variation (genetical genomics) has great potential in dissecting the genetic pathways underlying complex phenotypes....
designGG: an R-package and web tool for the optimal design of genetical genomics experiments
Li, Yang, Swertz, Morris A, Vera, Gonzalo, Fu, Jingyuan, Breitling, Rainer, Jansen, Ritsert C
Expression Quantitative Trait Loci Are Highly Sensitive to Cellular Differentiation State
Gerrits, Alice, Li, Yang, Tesson, Bruno M., Bystrykh, Leonid V., Weersing, Ellen, Ausema, Albertina, ...
Genetical genomics is a strategy for mapping gene expression variation to expression quantitative trait loci (eQTLs). We performed a genetical genomics experiment in four functionally distinct but...