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
21 Mar 2023 | Algorithmic Bioinformatics presenting at DSB 2023
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 “.
20 Sep 2022 | Poster presentation at GI 2022
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.
15 Jun 2022 | Paper accepted at WABI 2022
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.
13 Jun 2022 | Algorithmic Bioinformatics presenting at DSB 2022
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”.
11 Apr 2022 | Summer semester 2022 has started
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.
08 Mar 2022 | Algorithmic Bioinformatics supports an art project of Alicja Kwade
The Berlin-based artist Alicja Kwade had her personal genome printed out for her exhibition “In Absence” – on 314,000 DIN A4 pages of paper. To do this, she collaborated with Sven Rahmann, bioinformatics professor at Saarland University. The exhibition can be visited at the Berlinische Galerie until April 4.
The human genome consists of 3.1 billion base pairs - a number that is difficult to grasp. “Even for us bioinformaticians, this is an abstractly high number, although we work with genome data almost every day. This is because we usually only have the data as files on the computer,” says Saarbrücken bioinformatics professor Sven Rahmann.
The dimensions of the human genome can be better understood through a project by the Berlin artist Alicja Kwade. She has had her personal genome printed out on 314,000 A4 pages and is exhibiting it publicly in her exhibition “In Absence” at the Berlinische Galerie. 12,000 pages have been hung on the walls of the hall, the rest are in copper archive boxes distributed around the room. If all the pages of this genome document were laid side by side, they would stretch over a length of around 66 kilometers.
More information is available in the press release by Saarland Informatics Campus, or in an article of Saarbrücker Zeitung.
(Photograph by Frank Tschentscher)
07 Mar 2022 | Borja Freire Castro - Visiting Researcher from University of A Coruña, Spain.
We welcome Borja, who is finishing his PhD thesis at University of A Coruña, Spain, as a short-term guest researcher in our group.
He has worked on the reconstruction of viral quasispecies, and is interested in learning about alignment-free algorithms and statistical methods in bioinformatics.
19 Oct 2021 | Busy Beaver Award for "Algorithms on Sequence Analysis" lecture
The summer term lecture “Algorithms for Sequence Analysis” by Sven Rahmann has received a Busy Beaver Award by the Student Council.
This award is handed out for lectures that were well received and received very positive evaluations by students.
18 Oct 2021 | Winter semester 2021/22 is starting
During the winter semester, Prof. Sven Rahmann is offering the following courses:
Lecture and tutorials in “Statistics, Probability and Applications in Bioinformatics”. More information is on the website, or directly in the SIC CMS, where you also need to register for the course with your UdS student account.
Master Seminar “Current Topics in Sequence Analysis”, for students who have previously passed the “Algorithms for Sequence Analysis course”. More information is on the website, or directly in the SIC Seminar System, where you choose your preferred seminar(s). Note that you need to go through the assignment process and cannot directly register for the seminar.