Quantitative and Computational Biology

Our group works on two broad topics. First, we develop computational and statistical methods for predicting the structure and function of proteins from their amino acid sequences. Our HH-suite software for remote homology detection and the HHpred web server have become standard tools in their fields. We also develop a software suite MMseqs for very fast yet sensitive sequence searching for metagenomics and other very high-throughput applications, which addresses the challenge brought about by the next gene sequencing revolution in quantitative biology.

Second, we want to better understand transcriptional regulation, which represents the most important level of cellular regulation. We want to know how transcriptional programs are encoded in each gene's regulatory region, and we want to understand how genomic enhancers selectively activate their target genes, which are often not the nearest in sequence. For this purpose, we develop software and statistical models to analyze regulatory nucleotide sequences. In collaboration with the Department of Molecular Biology at the Max Planck Institute for Biophysical Chemistry, we probe transcription and RNA maturation using functional genomics techniques to obtain insights into the molecular processes needed for its regulation.