Research of Bioinformatics Group
The Bioinformatics group focuses on fundamental and applied bioinformatics research in the green life sciences. We develop and apply novel computational methods for the analysis and integration of –omics data.
An overview of our research projects can be found in the Wageningen University & Research Library.
Our software and databases
- Geometricus: a structure-based, alignment-free embedding approach for proteins [paper]
- Paired omics Data Platform: resource for linked public genomics and metabolomics data
- Caretta: A multiple protein structure alignment and feature extraction suite [demo-server]
- AraQTL: Arabidopsis workbench and database for QTL analysis [paper]
- WormQTL2: Interactive platform for systems genetics in Caenorhabditis elegans [paper]
- OptiTools: A toolset for optical map detection (OptiScan), alignment (OptiMap), and assembly (OptiAsm)
- Ouroboros: prediction of protein-protein interactions to improve intermolecuar contact prediction [paper]
- PanTools: representation, storage, and exploration of pan-genomic data [paper]
- ACE: error correction in NGS reads using K-mer tries [paper]
- antiSMASH: identification of biosynthetic gene clusters [paper]
- Primer3Plus: primer design software [paper]
- QualitySNPng: SNP detection & visualization [paper]
- HSPVdb: Human Short Peptide Variation Database [paper]
- ProRepeat: Amino acid tandem repeats in proteins [paper]
- CyLineUp: Human Short Peptide Variation Database [paper]
- Haplosim: Haplotyping simulation pipeline
- plantiSMASH: identification of plant biosynthetic gene clusters [paper]
- TriPoly: Haplotype estimation tool for polyploids [paper]
- PopPoly: Family-based estimation of polyploid haplotypes
- PKSpop: Prediction of PKS protein-protein interactions
- Paired omics Data Platform: resource for linked public genomics and metabolomics data
- Sesquiterpene synthase database: resource for characterized plant sesquiterpene synthases [paper]
- Winter moth: web portal for the winter moth genome [paper]
Research themes
Bioinformatics
The Bioinformatics group, led by Marnix Medema, focuses on fundamental and applied bioinformatics research in the green life sciences.