Recent News

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.

02 Sep 2024 | Swiftly Identifying Strongly Unique k-Mers at WABI 2022

Jens presented his paper “Swiftly Identifying Strongly Unique k-Mers” at the Wonderful Algorithms in Bioinformatics conference.

04 Apr 2024 | ISMB 24 - Tutorial Just-in-time compiled Python for bioinformatics research

We are happy to announce that Sven, Jens and Johanna are organizing a whole day tutorial at the ISMB 2024 in Montréal. We will give an introduction on Just-in-time compiled Python for bioinformatics research.

04 Apr 2024 | GCB 24 - Workshop Just-in-time compiled Python for bioinformatics research

We are happy to announce that Sven, Jens and Johanna are organizing a half day workshop at the GCB 2024 in Bielefeld. We will give an introduction on Just-in-time compiled Python for bioinformatics research.

25 Mar 2024 | Günther Hotz Medal

At the graduation ceremony of the SIC, Johanna was awarded the Günther Hotz Medal for an outstanding Master’s degree in Bioinformatics.

18 Mar 2024 | Data Structures in Bioinformatics

Sven, Jens and Johanna visited the workshop Data Structures in Bioinformatics in Montpellier. Johanna gave a talk about EpiSegMix, a new tool for chromatin segmentation based on epigentic marks using HMMs.

20 Dec 2023 | Christmas Party

Andrea Volkamer, Sven Rahmann, and Alexey Gurevich hosted an inauguration / Christmas party at the Center of Bioinformatics.

15 Sep 2023 | German Conference on Bioinformatics

The group visited the German Conference on Bioinformatics (GCB) in Hamburg. Sven co-organized the workshop Education in Bioinformatics. Johanna, Vu Lam and Andre presented posters about their current work. Jens gave a talk about the new Xengsort version.

23 Jun 2023 | CPM summer school

Vu Lam Dang and Jens Zentgraf participated in the CPM summer school at the École normale supérieure in Paris. Vu Lam presented a poster about his work on factorization of binary matrices and the possibility of using them to calculate polygenic risk score. Jens presented a poster about the possibility to combine super-k-mers and multi-way bucketed parallel Cuckoo hashing.

14 Jun 2023 | Algorithmic Bioinformatics at the HLA-Workshop

From 14.06. to 16.06 Andre Holzer, Sven Rahmann, Johanna Schmitz, Johannes Schreieck and Jens Zentgraf participated in the HLA-Workshop by the Stefan Morsch Foundation. Andre gave a talk about the Opportunities and Challenges of Long-Read Sequencing.

15 May 2023 | Visit of the working group of Jan Fostier

Sven Rahmann and Jens Zentgraf visited the group of Jan Fostier in Ghent. We had an interesting exchange about search schemes, k-mers and different applications.

21 Apr 2023 | Algorithmic Bioinformatics visiting the Stefan Morsch foundation

We visited the Stefan Morsch Foundation and had the opportunity to visit the laboratories and look at the procedure. We discussed the possibilities, difficulties and advantages of long read sequencing in HLA typing.

01 Apr 2023 | Johanna Schmitz joined the Algorithmic Bioinformatics group

On 01.04 we could welcome Johanna Schmitz as a new member of the group. She has already written her master thesis entitled “Multivariate Hidden Markov Models with Flexible Distributions for Chromatin–State Discovery” in the group and is working on:

• Development of an efficient and accurate chromatin segmentation method based on epigenetic marks
• Investigating the diversity or species richness of a large population