Friedrich-Schiller-Universität Jena, Fakultät für Mathematik und Informatik
Das German Network for Bioinformatics Infrastructure (de.NBI) läd ein zur de.NBI Summer School 2016 unter dem Motto “From Big Data to Big Insights: Computational methods for the analysis and interpretation of mass-spectrometric high-throughput data”
Interessenten können sich noch bis zum 1. Juni bewerben.
Mehr Infos gibt es hier.
Bertram and Franziska are visiting the 31st TBI Winterseminar in Bled from Sunday, 14 Feb 2016 to Friday, 19 Feb 2016. Bertram is giving a talk on Transcriptomics in Cyanobacteria.
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.
Ab sofort wird Franziska auf ihrem Blog wöchentlich über Forschungsfelder, aktuelle Publikationen und Karrieremöglichkeiten aus der Bioinformatik berichten.
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.
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.
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).
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 has been presented with the Teaching Award of the Faculty at the Day of the Faculty.
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.
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).
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.
Franziska wird für ihre Promotion mit dem Preis der Dekanin ausgezeichnet.
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: “Was ist Bioinformatik und kann man mit Dreck Krebs heilen?” The talk is Mon April 13, 2015 at 20:oo, Cafe Wagner.
Kai will give a talk at the 19th Annual International Conference on Research in Computational Molecular Biology in Warsaw, Poland.
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.
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.