- 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...
- 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...
- The dynamic architecture of the metabolic switch in Streptomyces coelicolor
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...
- 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...
- designGG: an R-package and web tool for the optimal design of genetical genomics experiments
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...
- 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...
- A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat
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...
- R/parallel--speeding up bioinformatics analysis with R
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...
- 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