The Algorithmic Bioinformatics group at Saarland University is headed by Prof. Sven Rahmann. It belongs to both the Mathematics and Informatics Faculty (“MI”) and the Center for Bioinformatics (ZBI) and is part of Saarland Informatics Campus (SIC). Our research focuses on method development (algorithms and data structures) for concrete problems that arise in biological data analysis. We mainly teach in the Bioinformatics degree programs.
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.
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.
At the graduation ceremony of the SIC, Johanna was awarded the Günther Hotz Medal for an outstanding Master’s degree 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.
Andrea Volkamer, Sven Rahmann, and Alexey Gurevich hosted an inauguration / Christmas party at the Center of 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.
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.
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.
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.
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.
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:
Vu Lam Dang, Sven Rahmann and Jens Zentgraf attended the Data Structures in Bioinformatics (DSB 2023) in Delft and presented parts of their work.
Sven Rahmann gave a talk about “Optimal Worst-Case Design of Gapped k-mer Masks”. Vu Lam presented joint work with Sven Rahmannm titled “Deriving polygenic risk score using non-negative matrix factorization “.
Our poster “An efficient alignment-free method for finding genetic differences between pig races from individual whole genome sequencing data” by Jens and Sven was accepted at Genome Informatics 2022, taking place September 21-23, 2022 in Hinxton, UK. Jens will present it; you can meet him there.
The 22nd Workshop on Algorithms in Bioinformatics (WABI), an annual conference with peer-reviewed proceedings published in the LIPIcs series by Dagstuhl Publishing, took place in Potsdam, Germany, this year. It was co-located with the European Symposium on Algorithms (ESA). Sven co-chaired the WABI meeting together with Christina Boucher. Jens presented his paper “Fast gapped k-mer counting with subdivided multi-way bucketed Cuckoo hash tables”.
Our paper “Fast gapped k-mer counting with subdivided multi-way bucketed Cuckoo hash tables” by Jens and Sven was accepted at WABI 2022, taking place September 5-9, 2022 in Potsdam, Germany. Jens will present it; you can meet us there.
Sven, Vu Lam and Jens attended the Data Structures in Bioinformatics (DSB 2022) in Düsseldorf and presented parts of their work.
Jens Zentgraf gave a talk about joint work with Sven Rahmann, titled “Fast gapped k-mer counting with subdivided multi-way bucketed Cuckoo hash tables”.
The summer semester 2022 will offer a mixture between in-presence and online courses.
Our group offers the popular “Algorithms for Sequences Analysis” course (lectures online, may later move to an on-campus mode; tutorials both online and on-campus). More information can be found on the course website. Registration for UdS students is required to access the course materials.
Our group also offers a (Master) seminar “Algorithms for Metagenomics”. Information and registration take place via the CS Seminar website. Registration ends Tuesday, 12.04.
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