Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays. - Henrik Bjørn Nielsen; Rasmus Wernersson; Steen Knudsen (Nucleic Acids Res., 2003)

RevTrans: multiple alignment of coding DNA from aligned amino acid sequences. - Rasmus Wernersson; Anders Gorm Pedersen (Nucleic Acids Res., 2003)

FeatureExtract - extraction of sequence annotation made easy. - Rasmus Wernersson (Nucleic Acids Res., 2005)

OligoWiz 2.0 - integrating sequence feature annotation into the design of microarray probes. - Rasmus Wernersson; Henrik Bjørn Nielsen (Nucleic Acids Res., 2005)

Virtual Ribosome - a comprehensive DNA translation tool with support for integration of sequence feature annotation. - Rasmus Wernersson (Nucleic Acids Res., 2006)

FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB. - Rasmus Wernersson; Kristoffer Rapacki; Hans Henrik Stærfeldt; Peter Wad Sackett; Anne Mølgaard (Nucleic Acids Res., 2006)

SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. - Frank Panitz; Henrik Stengaard; Henrik Hornshøj; Jan Gorodkin; Jakob Hedegaard; Susanna Cirera; Bo Thomsen; Lone B. Madsen; Anette Høj; Rikke K. Vingborg; Bujie Zahn; Xuegang Wang; et al. (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Cyclebase.org - a comprehensive multi-organism online database of cell-cycle experiments. - Nicholas Paul Gauthier; Malene Erup Larsen; Rasmus Wernersson; Ulrik de Lichtenberg; Lars Juhl Jensen; Søren Brunak; Thomas Skøt Jensen (Nucleic Acids Res., 2008)

InterMap3D: predicting and visualizing co-evolving protein residues. - Rodrigo Gouveia-Oliveira; Francisco S. Roque; Rasmus Wernersson; Thomas Sicheritz-Pontén; Peter Wad Sackett; Anne Mølgaard; Anders Gorm Pedersen (Bioinform., 2009)

Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. - Nicholas Paul Gauthier; Lars Juhl Jensen; Rasmus Wernersson; Søren Brunak; Thomas Skøt Jensen (Nucleic Acids Res., 2010)

The strength of intron donor splice sites in human genes displays a bell-shaped pattern. - Kai Wang; Rasmus Wernersson; Søren Brunak (Bioinform., 2011)

PHUSER (Primer Help for USER): a novel tool for USER fusion primer design. - Lars Rønn Olsen; Niels Bjørn Hansen; Mads Tvillinggaard Bonde; Hans Jasper Genee; Dorte Koefoed Holm; Simon Carlsen; Bjarne Gram Hansen; Kiran Raosaheb Patil; Uffe Hasbro Mortensen; Rasmus Wernersson (Nucleic Acids Res., 2011)

Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes. - Alberto Santos; Rasmus Wernersson; Lars Juhl Jensen (Nucleic Acids Res., 2015)