Computational Biology (CBI)

The Computational Biology Junior Group (CBI) started its work at HITS in 2013 and grew over the course of the year to its current size of four. Philipp Kämpfer and Philipp Bongartz, two PhD scholarship holders, joined in June and August respectively, and Martin Pippel joined in July as a postdoc. Furthermore, the group receives mentorship from Gene Myers, one of the pioneers in the field of genome assembly. Gene is a director at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden and holds the Klaus Tschira Chair of Systems Biology.

The CBI group works at the interface(s) between computer science, mathematics, and the biological sciences. Our research focuses on the computational and algorithmic foundations of genome biology. Of the multitude of issues encountered in that field, we are especially interested in whole-genome assembly, the reconstruction of a genome’s sequence from the data produced by a DNA sequencer. The basic principle applied for assembly is to randomly (over-)sample overlapping fragments from the genome, sequence them, and computationally reconstruct the full sequence from those fragments.

The complexity of this task is largely dependent on two characteristics of the fragments, average length and accuracy. The current generation of sequencers produces very long fragments, but with high error rates, so new approaches to the problem of efficient assembly under such conditions are needed. The development of such algorithms and their efficient implementation and application in genome sequencing projects are the main goals of the group.