25 Sep 2026 | GCB 26
Last week, our group as part of the Center for Bioinformatics Saar organized the German Conference on Bioinformatics in Saarbrücken with around 300 participants.
We had 4 interesting keynotes by Johannes Söding, Camille Marchet, Nima Aghaeepour and Pavel Pevzner.
The lineup was extended by 26 talks from multiple research areas, such as genotypes and phenotypes, single-cell & spatial transcriptomics, drugs and protein structures, AI/ML in biomedicine and others.
In addition, 145 posters were presented during two dedicated poster sessions.
On Thursday, Johanna Becher and Jens Zentgraf organized the first PhD-Meeting at a GCB where many students attended and used the time to network with colleagues.
From our group, Jens Zentgraf gave a talk about our new method for singe-cell gene expression quantification Arcane and we had two posters: Inês Alves Ferreira presented her work on gene expression in bacteria using an alignment-free pangenome approach, and Moein Karami presented his work on exact gapped-k-mer-based filtration for genome-scale sequences.
04 Sep 2026 | WABI/ECCB 26
Start of September, Johanna Elena Schmitz and Moein Karami attended the Wonderful Algorithms in Bioinformatics conference in L’Aquila and Inês Alves Ferreira, Jens Zentgraf and Sven Rahmann joined the ECCB in Geneva.
Johanna presented her work on species richness and entropy estimation from small samples and Moein presented his work on designing exact k-mer filters based on hits and coverage.
At the ECCB, Jens gave a highlight talk about Cleanifier, our new tool to remove host contamination in metagenomic samples, Inês presented a poster on PanXpress, a new method for gene expression quantification with a pan-transcriptomic gapped k-mer index and Sven presented a poster on a new modular genomic compressor Hecate.
22 Jul 2025 | Symposium on Experimental Algorithms
Jens and Johanna attended the Symposium on Experimental Algorithms (SEA) in Venice to present their paper “Blocked Bloom filters with choices”.
They also attended the Workshop “25 Years of Compressed Self-Indexes”.
10 Mar 2025 | Snakemake Hackathon
Jens and Johanna attended the Snakemake Hackathon at the Cern in Geneva.
The Hackathon ended with the release of Snakemake 9.0.
06 Mar 2025 | Data Structures in Bioinformatics
Jens and Johanna visited the workshop Data Structures in Bioinformatics in Pisa and presented their work on probabilistic filters.
Jens gave a talk about Blocked Bloom filters with Choices. This approach improved the FPR of Blocked Bloom filters by a more balanced load per block.
Johanna gave a talk about Better Cuckoo filters, introducing a windowed memory layout to increase the fill rate of Cuckoo filters.
02 Oct 2024 | GCB 2024
We had wonderful days at GCB 2024 in Bielefeld.
The group was very active:
- We organized a workshop on Just-in-time compiled Python for bioinformatics research.
- Sven co-organized the workshop on Bioinformatics Education, attempting to harmonize BSc curricula in Germany.
- Johanna presented a poster on the unseen species estimation problem.
- Jens gave a highly praised talk on efficiently computing strong vs. weak k-mers in large k-mer sets. We can mark weak k-mers in the human reference genome in 40 seconds.
- We also announced that we will host GCB in Saarbrücken in 2026.
