CASMI 2017 results are out

CASMI (Critical Assessment of Small Molecule Identification) 2017 results are finally out! Kai participated with SIRIUS/CSI:FingerID, and won categories 1 (Best Structure Identification on Natural Products), 2 (Best Automatic Structural Identification – In Silico Fragmentation Only), and 4 (Best Automatic Candidate Ranking). He did not participate in category 3.

For category 4 (in silico methods for searching in molecular structure databases), CSI:FingerID correctly identified 66 of 198 compounds (33.3%). This is more than 6-fold of what the best non-CSI:FingerID contestant reached. (Submissions containing “IOKR” in their name, correspond to different variants of the Input Output Kernel Regression version of CSI:FingerID.)

Unfortunately, CASMI 2017 data did not include isotope patterns. It appears that in many cases, SIRIUS was not able to find the correct molecular formula among the top candidate. This resulted in several cases where the correct structure was excluded due to the “wrong” molecular formula. We will investigate how many compounds would have been correctly identified if isotope pattern data would have been available.

Gastvorlesung Sebastian in Halle

Sebastian wird am Montag den 25.01.2016 zwei Vorlesungen zum Thema “Genome Rearrangements und Gene Clusters” an der Universität Halle halten.

Die Vorlesungen finden von 10:15 bis 12:00 Uhr in Seminarraum 1.30 sowie von 14:00 Uhr bis 15:15 Uhr in Seminarraum 0.04 des Institut für Informatik (Von-Seckendorff-Platz 1, Halle) statt.

Interessierte 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).

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.