Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases. - Morris A. Swertz; Engbert 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 (Bioinform., 2004)

Combining microarrays and genetic analysis. - Rudi Alberts; Jingyuan Fu; Morris A. Swertz; L. Alrik Lubbers; Casper J. Albers; Ritsert C. Jansen (Briefings Bioinform., 2005)

SIMAGE: simulation of DNA-microarray gene expression data. - Casper J. Albers; Ritsert C. Jansen; Jan Kok; Oscar P. Kuipers; Sacha A. F. T. van Hijum (BMC Bioinform., 2006)

A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat. - Rudi Alberts; Peter Terpstra; Menno Hardonk; Leonid V. Bystrykh; Gerald de Haan; Rainer Breitling; Jan Peter Nap; Ritsert C. Jansen (BMC Bioinform., 2007)

Towards dynamic database infrastructures for mouse genetics. - Morris A. Swertz; Damian Smedley; Katy Wolstencroft; Rudi Alberts; Michael Zouberakis; Vassilis Aidinis; Klaus Schughart; Paul N. Schofield; Ritsert C. Jansen (BIBE, 2008)

affyGG: computational protocols for genetical genomics with Affymetrix arrays. - Rudi Alberts; Gonzalo Vera; Ritsert C. Jansen (Bioinform., 2008)

R/parallel - speeding up bioinformatics analysis with R. - Gonzalo Vera; Ritsert C. Jansen; Remo Suppi (BMC Bioinform., 2008)

designGG: an R-package and web tool for the optimal design of genetical genomics experiments. - Yang Li 036; Morris A. Swertz; Gonzalo Vera; Jingyuan Fu; Rainer Breitling; Ritsert C. Jansen (BMC Bioinform., 2009)

R/qtl: high-throughput multiple QTL mapping. - Danny Arends; Pjotr Prins; Ritsert C. Jansen; Karl W. Broman (Bioinform., 2010)

Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq. - 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 (Bioinform., 2010)

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button. - Morris A. Swertz; Martijn Dijkstra; Tomasz Adamusiak; K. Joeri van der Velde; Alexandros Kanterakis; Erik T. Roos; Joris Lops; Gudmundur A. Thorisson; Danny Arends; George Byelas; Juha Muilu; Anthony J. Brookes; et al. (BMC Bioinform., 2010)

DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules. - Bruno M. Tesson; Rainer Breitling; Ritsert C. Jansen (BMC Bioinform., 2010)

MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects. - Harm-Jan Westra; Ritsert C. Jansen; Rudolf S. N. Fehrmann; Gerard J. te Meerman; David van Heel; Cisca Wijmenga; Lude Franke (Bioinform., 2011)

Bioinformatics tools and database resources for systems genetics analysis in mice - a short review and an evaluation of future needs. - Caroline Durrant; Morris A. Swertz; Rudi Alberts; Danny Arends; Steffen Möller; Richard Mott; Pjotr Prins; K. Joeri van der Velde; Ritsert C. Jansen; Klaus Schughart (Briefings Bioinform., 2012)

xQTL workbench: a scalable web environment for multi-level QTL analysis. - Danny Arends; K. Joeri van der Velde; Pjotr Prins; Karl W. Broman; Steffen Möller; Ritsert C. Jansen; Morris A. Swertz (Bioinform., 2012)

WormQTL - public archive and analysis web portal for natural variation data in Caenorhabditis spp. - L. Basten Snoek; K. Joeri van der Velde; Danny Arends; Yang Li 036; Antje Beyer; Mark Elvin; Jasmin Fisher; Alex Hajnal; Michael O. Hengartner; Gino B. Poulin; Miriam Rodriguez; Tobias Schmid; et al. (Nucleic Acids Res., 2013)

WormQTLHD - a web database for linking human disease to natural variation data in C. elegans. - K. Joeri van der Velde; Mark de Haan; Konrad Zych; Danny Arends; L. Basten Snoek; Jan E. Kammenga; Ritsert C. Jansen; Morris A. Swertz; Yang Li 036 (Nucleic Acids Res., 2014)

Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains. - Konrad Zych; Yang Li 036; K. Joeri van der Velde; Ronny Joosen; Wilco Ligterink; Ritsert C. Jansen; Danny Arends (BMC Bioinform., 2015)

Correlation Trait Loci (CTL) mapping: phenotype network inference subject to genotype. - Danny Arends; Yang Li 036; Gudrun A. Brockmann; Ritsert C. Jansen; Robert W. Williams; Pjotr Prins (J. Open Source Softw., 2016)

FitTetra 2.0 - improved genotype calling for tetraploids with multiple population and parental data support. - Konrad Zych; Gerrit Gort; Chris A. Maliepaard; Ritsert C. Jansen; Roeland E. Voorrips (BMC Bioinform., 2019)