News | Lehrstuhl Bioinformatik Jena

Gastvorlesung Ivo Große

12/01/201607/01/2016 by Markus Fleischauer

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.

Sirius 3.1 is out and now ships with a graphical user interface!

16/01/201703/11/2015 by Kai Dührkop

It was announced for October, but as so often, it took longer than expected to do the last steps. But here it is: The newest release of SIRIUS ships with a graphical user interface that helps with importing the data and visualizing the results. You can download SIRIUS 3.1 here.

We have published a paper in PNAS

21/02/202222/09/2015 by Sebastian Böcker

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 http://www.csi-fingerid.org/. This is joint work with Juho Rousu and his group at Aalto University (Finland).

PNAS paper scheduled for Sep 21

07/09/201504/09/2015 by Sebastian Böcker

We are thrilled that our paper in “Proceedings of the National Academy of Sciences USA” is scheduled for Sep 21, 2015 online issue. More details then.

Sebastian won the Teaching Award of the Faculty.

23/07/201525/06/2015 by franzi

Sebastian has been presented with the Teaching Award of the Faculty at the Day of the Faculty.

Meet Sebastian at Metabolomics 2015

18/08/202124/06/2015 by Sebastian Böcker

Sebastian will attend the Conference of the Metabolomics Society 2015 in San Franciso, and give a talk on “Searching molecular structure databases with tandem mass spectra using CSI:FingerID”. On Tuesday after 6 pm, Steffen Neumann and Sebastian will head the BoF meeting on Computational Mass Spectrometry.

Kinderuni am Freitag 19. Juni

30/04/202016/06/2015 by Sebastian Böcker

Am Freitag 19. Juni 2015 wird Sebastian im Rahmen der KinderUni Jena einen Vortrag zum Thema “Auch Computer müssen aufräumen” halten. Start ist um 16:00 Uhr, Veranstaltungsort ist der Hörsaal 7 in der Carl Zeiss Straße 3 (neben der Mensa).

SIRIUS 3.0 release

16/01/201719/05/2015 by Kai Dührkop

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.

FIFI ist jetzt online

13/05/2015 by Sebastian Böcker

Der Förderverein des Instituts für Informatik (kurz FIFI) ist jetzt online und nimmt schon Mitgliederanträge entgegen!

Promotionspreis der Dekanin

19/06/201520/04/2015 by franzi

Franziska wird für ihre Promotion mit dem Preis der Dekanin ausgezeichnet.

We will present a paper at COCOON 2015

30/04/202017/04/2015 by franzi

Our paper “Speedy Colorful Subtrees” will be presented at the International Computing and Combinatorics Conference (COCOON 2015) in Beijing, China.

Sebastian will give a talk at the Science Pub in Jena

30/04/202013/04/2015 by Sebastian Böcker

Sebastian will give a talk at the Science Pub in Jena: “Was ist Bioinformatik und kann man mit Dreck Krebs heilen?” The talk is Mon April 13, 2015 at 20:oo, Cafe Wagner.

Meet Kai at RECOMB in Warsaw

10/04/2015 by franzi

Kai will give a talk at the 19th Annual International Conference on Research in Computational Molecular Biology in Warsaw, Poland.

COCONUT released!

10/04/201517/02/2015 by franzi

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!

10/04/201523/01/2015 by franzi

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.

Meet Sebastian at the CeBiTec symposium in Bielefeld

18/01/2015 by Sebastian Böcker

Sebastian will given a talk on Computational Mass Spectrometry in Metabolomics at the CeBiTec symposium on “Bioinformatics for Biotechnology and Biomedicine” in Bielefeld.

We will present a paper at RECOMB 2015

20/01/201518/01/2015 by Sebastian Böcker

Our paper “Fragmentation Trees reloaded” will be presented at the Research in Computational Biology (RECOMB 2015) conference in Warsaw, Poland.

GCB 2012 website has been moved

08/01/2015 by Sebastian Böcker

The website of the German Conference on Bioinformatics 2012 has been moved from http://www.gcb2012-jena.de/ to https://bio.informatik.uni-jena.de/gcb2012/. The content will be made available permanently under the new URL.

Meet Sebastian at APRS in Salzburg

14/07/201411/07/2014 by Sebastian Böcker

Sebastian will give a plenary talk at the Austrian Proteomic Research Symposium (September 22-24, 2014) in Salzburg. Title of the talk is “Elementary, my dear Watson: Fingerprint search in molecular structure databases”.

Meet Kai at the ASMS conference in Baltimore

11/07/201411/06/2014 by Sebastian Böcker

Kai will give a talk at the Conference of the American Society for Mass Spectrometry in Baltimore, USA.