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DNA Storage & Bioinformatics

Several large colourful test tubes containing models of DNA double helixes.

The long-term storage of data is one of the fundamental problems of the digital information age. Together with researchers from a variety of disciplines, we are currently exploring approaches to use DNA molecules as a promising future storage medium with high capacity and long-term availability. In particular, we try to increase the storage density and the fault tolerance of writing to and reading from DNA through novel rateless erasure codes.

Our further work in bioinformatics includes deep learning algorithms to detect and segment morphologically complex eukaryotic cells in fluorescence microscopy images, efficient approaches to compare protein binding sites, GPU-based simulation of yeast cell flocculation, and Cloud-based approaches for metabolic flux analysis.

Selected Publications

  • Michael Schwarz, Marius Welzel, Tolganay Kabdullayeva, Anke Becker, Bernd Freisleben, Dominik Heider:
    MESA: Automated Assessment of Synthetic DNA Fragments and Simulation of DNA Synthesis, Storage, Sequencing and PCR Errors. Bioinformatics 36(11): 3322-3326, 2020
  • Marius Welzel, Anja Lange, Dominik Heider, Michael Schwarz, Bernd Freisleben, Manfred Jensen, Jens Boenigk, Daniela Beisser:
    Natrix: A Snakemake-based Workflow for Processing, Clustering, and Taxonomically Assigning Amplicon Sequencing Reads. BMC Bioinformatics 21(1): 526, 2020
  • Nikolaus Korfhage, Markus Mühling, Stefan Ringshandl, Anke Becker, Bernd Schmeck, Bernd Freisleben:
    Detection and Segmentation of Morphologically Complex Eukaryotic Cells in Fluorescence Microscopy Images via Feature Pyramid Fusion. PLOS Computational Biology 16(9): e1008179, 2020
  • Matthias Leinweber, Thomas Fober, Bernd Freisleben:
    GPU-Based Point Cloud Superpositioning for Structural Comparisons of Protein Binding Sites. IEEE ACM Transactions on Computatonal Biology and Bioinformatics, 15(3): 740-752, 2018
  • Matthias Leinweber, Thomas Fober, Marc Strickert, Lars Baumgärtner, Gerhard Klebe, Bernd Freisleben, Eyke Hüllermeier:
    CavSimBase: A Database for Large Scale Comparison of Protein Binding Sites. IEEE Transactions on Knowledge and Data Engineering, 28(6): 1423-1434, 2016
  • Matthias Leinweber, Patrick Bitter, Stefan Brueckner, Hans-Ulrich Moesch, Peter Lenz, Bernd Freisleben:
    GPU-Based Simulation of Yeast Cell Flocculation. 22nd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, Torino, Italy, 601-608, IEEE, 2014
  • Tolga Dalman, Tim Dörnemann, Ernst Juhnke, Michael Weitzel, Wolfgang Wiechert, Katharina Nöh, Bernd Freisleben:
    Cloud MapReduce for Monte Carlo bootstrap Applied to Metabolic Flux Analysis. Future Generation Computer Systems 29(2): 582-590, 2013

Further information