Algorithms for Computational Genomics

Overview

The Algorithms for Computational Genomics group is headed by Tobias Marschall and is affiliated with the Center for Bioinformatics at Saarland University and the Max Planck Institute for Informatics.

The group develops algorithms and statistical methods for computational genomics. In particular, we work on methods to analyze high-throughput sequencing data to study genetic diversity, epigenetics, and cancer. On the one hand, we develop the required theoretical foundations in algorithmic statistics, combinatorial optimization, and sequence algorithms and, on the other hand, we apply the resulting methods in collaboration with biomedical researchers to gain biological insights. Topics addressed in the group range from algorithms for low level data processing to questions of population genetics.

News

  • 1 June 2016: The paper on Jana's Bachelor thesis on Genotyping of Inversions and Tandem Duplications has been accepted for presentation at HitSeq 2016. Congratuations! A preprint is at biorxiv.
  • 30 May 2016: Our joint paper with Kathrin Trappe and Bernard Renard (RKI, Berlin) on Detecting Horizontal Gene Transfer by Mapping Sequencing Reads Across Species Boundaries has been accepted at ECCB 2016.
  • 19 February 2016: Our paper Read-Based Phasing of Related Individuals has been conditionally accepted at ISMB 2016.
  • 17 February 2016: Workshop proposal accepted: Tobias will co-organize a workshop on Computational Pan-Genomics at ECCB together with Zamin Iqbal (Oxford) and Benedict Paten (UCSC).
  • 27 January 2016: David Porubsky from ERIBA, Groningen won an EMBO Short Term Followship to join us from March to Mai. Congrats David!
  • 12 January 2016: Tobias joins the program committee of RECOMB-SEQ 2016 and GCB 2016.
  • 7 September 2015: Tobias is on the program committee of RECOMB 2016.
  • 31 July 2015: Tobias' talk was accepted at GCB 2015, he will present an overview of our work.
  • 15 April 2015: Ali Ghaffaari joins the group as a PhD student. Welcome Ali!
  • 3 April 2015: GoNL paper on de novo structural variation has been accepted in Genome Research.
  • 19 January 2015: Tobias is on the program committee of RECOMB-SEQ 2015.
  • 19 December 2014: We are organizing a special session on Modeling and Optimization in Computational Biology at MCO 2015 to be held in Metz, France, on May 11-13.
  • 29 July 2014: Our proposal for a Workshop on Future Perspectives in Computational Pan-Genomics was approved. The workshop will be held at the Lorentz Center in June 2015. It is jointly organized by Victor Guryev, Tobias Marschall, Alexander Schönhuth, Fabio Vandin, and Kai Ye.
  • 29 June 2014: The Genome of the Netherlands Consortium has published its first main findings in Nature Genetics (doi: 10.1038/ng.3021). Tobias Marschall is part of the consortium and contributed to discovery and genotyping of structural variations.
  • 1 April 2014: The Algorithms for Computational Genomics group is established.

Research

Information on current research projects can be found on the Research page.

Publications

A list of publications can be found on the Publications page.

Jobs

We are looking for talented students on all levels (bachelor, master, PhD). If you are interested in working in the group, please contact Tobias Marschall.

Contact

  • Email: t.marschall at mpi-inf dot mpg dot de
  • Office: Building E2.1, Room 201
  • Address:
    Center for Bioinformatics
    Campus E2.1
    66041 Saarbrücken
    Germany