Gastvorlesung Ivo Große

Ivo Große von der Universität Halle wird uns am 13. Januar besuchen und eine Gastvorlesung zum Thema Motif Finding und EM-Algorithmus halten – klassische Themen der Bioinformatik, die in Jena leider nicht mehr gelehrt werden.

Die Vorlesung findet am Mittwoch den 13. Januar von 9:30 bis 12:00 Uhr im Seminarraum 119, August-Bebel-Str. 4 statt.

Die Veranstaltung ist für alle Studierenden der Bioinformatik, insbesondere für alle Master-Studenten interessant. Alle Interessierten sind herzlich eingeladen.

We have published a paper in PNAS

Our paper “Searching molecular structure databases with tandem mass spectra using CSI:FingerID” has just appeared in the online issue of Proceedings of the National Academy of Sciences USA. Also see the press release by the Friedrich-Schiller-University Jena (here for German). The metabolite search engine CSI:FingerID is available from This is joint work with Juho Rousu and his group at Aalto University (Finland).

SIRIUS 3.0 release

We present SIRIUS 3.0, a java-based software for discovering a landscape of de-novo identification of metabolites using single and tandem mass spectrometry.
SIRIUS uses isotope pattern analysis for detecting the molecular formula and further analyses the fragmentation pattern of a compound using fragmentation trees.

The version 3.0 is a complete rewrite of our previous software. It uses faster algorithms for the fragmentation tree computation and a revised scoring based on Bayesian statistics.

A command line tool is available here. We will add a graphical user interface soon.

COCONUT released!

We present the first release of our renewed tool for estimating the composition distribution from mass spectra of synthetic copolymers. COCONUT provides an easy-to-use graphical user interface and can be downloaded here.

Gecko3 released!

We released the new version of Gecko — our software for finding gene clusters. Gecko3 offers an easy-to-use graphical user interface, but can also be used as a command line tool in an analysis pipeline. Downloads are available here.

GCB 2012 website has been moved

The website of the German Conference on Bioinformatics 2012 has been moved from to The content will be made available permanently under the new URL.