News Archive

This is the group’s collection of recent and not-so-recent news.

08 Oct 2019 (2 days ago) | Paper accepted at ALENEX 2020

Our paper “Cost-optimal assignment of elements in genome-scale multi-way bucketed Cuckoo hash tables” by Jens, Henning and Sven was accepted at ALENEX 2020, taking place January 5-6, 2020 at Salt Lake City, Utah, USA. Jens will present it; you can meet us there.

07 Oct 2019 (3 days ago) | Winter semester 2019/20 has started

In the winter semester 2019/20, the Genome Informatics group offers the Master specialization course “Algorithmic Bioinformatics” at TU Dortmund.

02 Oct 2019 (8 days ago) | Bianca presents her paper on protein complex similarity at SISAP

Bianca Stöcker presents her work Protein Complex Similarity Based on Weisfeiler-Lehman Labeling at the “Similarity Search and Applications” (SISAP) conference at Newark, New Jersey, USA.

Protein complexes consist of several protein chains. The similarity between two complexes can be measured by comparing the sets or multisets of their protein chains, but it is conceivable that two complexes consist of the same (multi)set of chains, but has a different topology, i.e. different physical interactions between the chains. This should be reflected in the similarity measure. Our work defines such a similarity measure that incorporates topological information but is almost as efficiently computable than set-based measures.

This publication resulted from a collaboration within the DFG-funded Collaborative Research Center SFB 876 between members of projects A6 (Resource-efficient graph mining) and C1 (Feature selection in high dimensional data for risk prognosis in oncology). This work is also part of our long-running project on protein hypernetworks and constraints between protein interactions.

01 Oct 2019 (9 days ago) | Prof. Frank Kaiser is the new director of the Institute of Human Genetics

As of today, Prof. Dr. Frank Kaiser is the new director of the Insititute of Human Genetics at the University of Duisburg-Essen. Welcome, Frank! We look forward to many exciting new collaborations. The former director, Prof. Dr. Bernhard Horsthemke, will continue to work as a senior professor at the institute, and we are happy to continue our joint projects.

30 Sep 2019 (10 days ago) | ZiF workshop on computational pan-genomics at Bielefeld University

At a computational pan-genomics workshop at the Center for Interdisciplinary Research (ZiF) at Bielefeld University, Sven presented joint work with Jens Quedenfeld on the analysis of min-hashing for variant tolerant read mapping. Genome Informatics alumnus Tobias Marschall gave a talk about “Rapid bit parallel sequence to graph alignment”. The workshop was organized by Jens Stoye and Alexander Schönhuth.

24 Sep 2019 (16 days ago) | Friedmund Neumann Prize 2019 of the Schering Stiftung goes to Johannes Köster

The Schering Sitftung has awarded the Friedmund Neumann Prize 2019 to Johannes Köster. Congratulations, Johannes!

Image credits: Friedmund Neumann Prize 2019 of the Schering Stiftung. Award ceremony, 24.09.2019 in Berlin. Photo: Julia Zimmermann, © Schering Stiftung. Persons (left-to-right): Prof. Dr. Sven Rahmann (nominator), Dr. Johannes Köster (awardee), Prof. Dr. Dr. h. c. Stefan H. E. Kaufmann (chairman of the Foundation Concil).

There are more pictures from the award ceremony available at the Schering Stiftung website.

17 Sep 2019 (23 days ago) | Genome Informatics at GCB 2019

Several researchers from the Genome Informatics group attended the German Conference on Bioinformatics (GCB) 2019 in Heidelberg and presented their work:

  • Jan Forster: Phase-aware Neoantigen Prediction from Whole Exome and RNA Sequencing Data
  • Till Hartmann: Efficient algorithms for decoding whole-transcriptome MERFISH experiments
  • Sven Rahmann: Comprehensive analysis of allele-specific methylation in amplicons with amplikyzer2
  • Bianca Stöcker: Protein Complex Similarity Based on Weisfeiler-Lehman Labeling
  • Jens Zentgraf: Cost-optimal assignment of elements in genome-scale multi-way bucketed Cuckoo hash tables

16 Sep 2019 (24 days ago) | Tutorial on k-mer hashing at GCB 2019

Jens Zentgraf and Sven Rahmann gave a tutorial on foundations of alignment-free sequence analysis: k-mer hashing at the German Conference on Bioinformatics (GCB) 2019 in Heidelberg.

Over 20 participants attended the tutorial. It was a lot of fun; we may do it again soon.

01 Sep 2017 (769 days ago) | Best Paper Award at WABI 2017

The article “Analysis of min-hashing for variant tolerant DNA read mapping” by Jens Quedenfeld (now at TU Munich) and Sven Rahmann has received the Best Paper Award at the Workshop of Algorithms in Bioinformatics (WABI) 2017, held in Cambridge, MA, USA, August 20-23, 2017.

The authors consider an important question, as DNA read mapping has become a ubiquitous task in bioinformatics. New technologies provide ever longer DNA reads (several thousand basepairs), although at comparatively high error rates (up to 15%), and the reference genome is increasingly not considered as a simple string over ACGT anymore, but as a complex object containing known genetic variants in the population. Conventional indexes based on exact seed matches, in particular the suffix array based FM index, struggle with these changing conditions, so other methods are being considered, and one such alternative is locality sensitive hashing. Here we examine the question whether including single nucleotide polymorphisms (SNPs) in a min-hashing index is beneficial. The answer depends on the population frequency of the SNP, and we analyze several models (from simple to complex) that provide precise answers to this question under various assumptions. Our results also provide sensitivity and specificity values for min-hashing based read mappers and may be used to understand dependencies between the parameters of such methods. This article may provide a theoretical foundation for a new generation of read mappers.

The article can be freely accessed in the WABI conference proceedings (Proceedings of the 17th International Workshop on Algorithms in Bioinformatics (WABI 2017), Russell Schwartz and Knut Reinert (Eds.), LIPICS Vol. 88).

This work is part of subproject C1 of the collaborative research center SFB 876.