Software
- Peacock (2017): Phylogenies Visualization library
- PEDCA (2017): Ploidy Estimation by Dynamic Coverage Analysis
- GenomeTools (2017): Collection of algorithms to manipulate genomics related file format
- Homokaryon-Expression (2017): The discovery and analysis of homokaryon specific expression (bioRxiv 2017)
- BrainScope (2017): Interactive visual exploration of the brain (NAR 2017)
- REVEAL (2016): REcursiVe Exact-matching ALigner; can be used to (multi) align whole genomes (bioRxiv 2016)
- MEREDITH (2016): Multi-omic data integration approach. The corresponding R package implementing MEREDITH is available here. (Scientific Reports 2016)
- SANEFALCON (2016): Calculating the fetal fraction for noninvasive prenatal testing based on genome-wide nucleosome profiles (Prenatal Diagnosis 2016)
- Proteny (2015): A tool to analyze synteny at the protein level (Bioinformatics 2015)
- Pilon (2014): Automated genome assembly improvement and variant detection tool (PLoS ONE 2014)
- TSSA (2014): Scale-aware Topology Measures (STMs) can be used to characterize the topology of a graph on multiple scale levels (ISMB 2014)
- SPiCE (2014): Web-based software tool for exploring sequence-based features of proteins in predefined classes (BMC Bioinformatics 2014)
- WISECONDOR (2014): Detecting fetal trisomies and smaller CNV's in maternal plasma samples using whole-genome data (NAR 2014)
- MaryGold (2013): An algorithm for finding and visualising variation within and between metagenome sequence datasets (Bioinformatics 2013)
- HATSEQ (2013): Method to analyze your ChIP-array or ChIP-Seq data (AABC 2013)
- IBIDAS (2013): Environment for data handling and exploration (DILS 2013)
- GRASS (2012): Generic algorithm for scaffolding next-generation sequencing assemblies (Bioinformatics 2012)
- HIPSEC (2012): Predicting high-level production of secreted proteins in Aspergillus niger (PLoS ONE 2012)
- Magnolya (2012): De novo detection of copy number variation by co-assembly (Bioinformatics 2012)
- GenomeView (2011): Next-generation genome browser (NAR 2011)
- Cytoscape RPC (2011): Plugin to create, modify and query Cytoscape networks from scripting languages (Bioinformatics 2011)
- MAIA (2010): Integrating genome assemblies (Bioinformatics 2010)
- Java-ML (2009): Java Machine Learning Library (JMLR 2009)
- MaRIboES (2009): Metabolite and reaction inference based on enzyme specificities (Bioinformatics 2009)
- CSSC_GeneVisualizer 2009