CV Publications Projects Software Contact Impressum

SecureEpiLinker (SEL)

S. Stammler, T. Kussel, P. Schoppmann, F. Stampe, G. Tremper, S. Katzenbeisser, K. Hamacher, M. Lablans. Mainzelliste SecureEpiLinker (MainSEL): Privacy-Preserving Record Linkage using Secure Multi-Party Computation, Bioinformatics, accepted, 2020.
Code on GitHub


P. Kunzmann, K. Hamacher. Biotite: A unifying open source computational biology framework in Python, BMC Bioinformatics, 19:346, 2018.
Abstract & PDF-Version

Code on GitHub


R package to analyze MD trajectories in a graph-semantic fashion

J. Comp. Chem., 39:1666-1674, 2018.
Abstract & PDF-Version
Cover Page


R package to compute transfer entropy (under statistical permutation test)

15th conference on Computational Methods for Systems Biology
Lecture Notes in Bioinformatics (LNBI 10545), 285-290, 2017.
Abstract & PDF-Version


Efficient, reliable covalent docking in Molecular Operating Environment (MOE)

SVL-Source-Code at MOE repository
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J. Chem. Inf. Model. 55(2):398-406, 2015.

Resampling in Lisp

a domain-specific language (DSL) for statistical tests of arbitrary S-expressions (and more)
Source code (tar.gz)


Molecular (Co)evolution and Biophysical/Molecular Dynamics in R;
uses Information Theory, Elastic Network Models, Multi-Core Computations etc.

Code at CRAN
Our BioPhysConnectoR-Website
BMC Bioinformatics 2010, 11:199


Compute transfer entropy (including statistical permutation test) for time series Frontiers in Physics 3(2015)10


Visual Analytics for Phylogenies


IEEE Conference on Visual Analytics Science and Technology (VAST2011), 31-40, 2011

CoMIC - Coevolution via MI on CUDA

We've implemented a massively-parallel version of our normalization procedure for mutual information values in molecular (co)evolution. To this end we compute replica-wise Z-scores and percentiles of a parameter-free model of neutral evolution.


Visual Analytics for (Co)evolutionary Matrices


BMC Bioinformatics, 11:330, 2010