This is the group’s collection of recent and not-so-recent news.
29 May 2020 (130 days ago) | New preprint and software "ting" for TCR repertoire clustering
Our preprint “Rapid T cell receptor interaction grouping with ting” is online.
Clustering of antigen-specific T cell receptor repertoire (TCRR) sequences remains challenging. While established tools like gliph aim to solve this problem they suffer from serveral shortcommings, including bad performance on huge repertoires, non-determinism, potential loss of significant antigen-specific or inclusion of too many unspecific sequences.
“ting” solves these issues by applying an efficient algorithm for identifying antigen-specific k-mers based on Fisher’s Exact Test. This allows fast processing of large scale repertoires and an improved differentiation between naive and specific TCR3b sequences.
The full paper has been submitted for review.
16 May 2020 (143 days ago) | New preprint and software "xengsort" for xenograft sorting
Finally, our preprint “Fast lightweight accurate xenograft sorting” is online.
Xenograft sorting classifies the (paired-end or single-end) reads of a xenograft sample according to species of origin.
A typical application concnerns sequenced samples from patient-derived xenografts (PDX; tumors extracted from human patients and implanted into mice), where the reads have to be classified into human reads and mouse reads (and, possibly, reads that could originate from both species, reads from neither species, and ambiguous reads).
We have developed an alignment-free approach based on 3-way bucketed Cuckoo hashing.
Our tool “xengsort” is faster by a factor of 4 than existing alignment-free tools on typical PDX datasets.
A poster about this work will be presented at ISMB HiTSeq.
The full paper has been submitted for review.
21 Apr 2020 (168 days ago) | Fused lasso paper accepted at SEA 2020
Elias’ and Sven’s paper “Engineering Fused Lasso Solvers on Trees” was accepted at the 18th Symposium on Experimental Algorithms (SEA 2020), which will be held as an online conference from June 16 till June 18.
Our paper presents two practically efficient algorithms for solving fused lasso problems on tree graphs with general weights for nodes and edges, even zero weights, which other algorithms cannot easily handle.
We hope to see you at SEA’20 for our presentation.
Also, the TreeLas software is avaliable on our Software page.
20 Apr 2020 (169 days ago) | Online-Lehre und Prüfungen ab 20.04.2020
Aufgrund der Beschlüsse der Landesregierung NRW und der einzelnen Universitäten in NRW findet ab 20.04. online-Lehre statt.
Das betrifft insbesondere “Algorithmen auf Sequenzen” von Prof. Rahmann und die Vorbesprechung zum Seminar “Aktuelle Themen der Bioinformatik”.
Ferner werden ausstehende Prüfungen (z.B. zu “Algorithmische Bioinformatik”) online durchgeführt.
06 Mar 2020 (214 days ago) | Genome Informatics presenting at SIGOPT 2020
Two researchers from the Genome Informatics group attended the SIGOPT 2020 meeting in Dortmund and presented their work on continous and combinatorial optimization problems in bioinformatics.
Elias presented his fast solver for the fused lasso problem on tree graphs (joint work with Sven).
Jens gave a talk about joint work with Henning and Sven, titled “Cost-optimal assignment of elements in genome-scale multi-way bucketed Cuckoo hash tables”.
The bioinformatics session on Friday further included talks by David Blumenthal (Munich) on median graphs and by Sven Schrinner (Düsseldorf) on polyploid phasing.
04 Feb 2020 (245 days ago) | Genome Informatics presenting at DSB 2020
Researchers from the Genome Informatics group attended the Data Structures in Bioinformatics (DSB 2020) in Rennes and presented their work.
Jens Zentgraf gave a talk about joint work with Henning Timm and Sven Rahmann, titled “Cost-optimal assignment of elements in genome-scale multi-way bucketed Cuckoo hash tables”.
Sven Rahmann presented joint work with Jens Zentgraf on “Faster xenograft sorting with 3-way bucketed Cuckoo hash tables”.
Even though it was raining in Rennes and Air France wasn’t able to fly from Düsseldorf to Rennes in under 9 hours, the meeting was a lot of fun and showcased many interesting new results.
01 Dec 2019 (310 days ago) | Dr. Fabian Kilpert from Lübeck joins the group
Dr. Fabian Kilpert is joining the Genome Informatics group in December 2019.
Together with the new director of the Institute of Human Genetics, he is coming to Essen from Lübeck in Schleswig-Holstein, where he previously worked at the Institute of Neurogenetics.
19 Nov 2019 (322 days ago) | Annual meeting of INCEPTION program at Institut Pasteur, Paris
The third annual meeting of the INCEPTION program took place at Institut Pasteur in Paris on November 18 and 19. A distinguishing feature of this program is the tight collaboration between the life sciences and social sciences.
As a member of the scientific advisory board, Sven gave a talk about “reproducible genome-wide k-mer association studies”.
08 Oct 2019 (364 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 (365 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.
01 Oct 2019 (371 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.
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 (372 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 (378 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.
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 (385 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 (386 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 (1131 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.