Computational Pangenomics: We develop methods and tools to work with tens of thousands of genomes and analyze and integrate the corresponding data. See here for our Survey. Particular research highlights:
Genome Data Mining: We have developed various tools for mining relevant patterns in (huge) genomes and networks. Research highlights:
- SAVAGE - De Novo Viral Quasispecies Assembly.
- PROSIC - Enhancing sensitivity in somatic insertion and deletion discovery and discovering particularly hard-to-discover ones.
- WhatsHap - Phasing directly from (in particular third-generation) sequencing reads.
De Novo Viral Quasispecies Assembly using Overlap Graphs Baaijens et al., Genome Research, 2017.
A high-quality reference panel reveals the complexity and distribution of structural genome changes in a human population, Hehir-Kwa et al., Nature Communications, 2016.
Computational Pan-Genomics: Status, Promises and Challenges
Marschall et al., Briefings in Bioinformatics, 2016.
- Jasmijn received the Best Talk Award at the ISMB-HitSeq 2017, for her talk on SAVAGE, see here for our Paper and Software.
- Alex has been Program Faculty at the Computational Genomics Summer Institute, IPAM, UC Los Angeles, July 6 - 26, 2017.
- Alex presented a poster on Single Cell Variant Calling at the Workshop on Statistical Challenges in Single Cell Biology in Ascona, 2017.
- Alex was Publicity Chair of the RECOMB, Hongkong, April/May 2017.
- Alex gave a Keynote Talk at the ISBRA 2016.
- Alex was Program Committee Chair at the RECOMB-SEQ 2016.