Applied Bioinformatics Group

Welcome to the home of the Bioinformatics Group of the Medical University Innsbruck

The Applied Bioinformatic Group is associated with the Division of Molecular Pathophysiology, Biocenter of the Medical University Innsbruck and is closely collaborating with the SFB 021 (Cell Proliferation and Cell Death in Tumors). Our main research interests are transcriptomics with focus on the analysis of microarray data, especially Affymetrix arrays (conventional 3' arrays, Exon arrays and tiling arrays) and development of algorithms and tools to improve/facilitate array analysis and organize microarray data.
The bioinformatic analyses of data from the Expression Profiling Unit (Gene Discovery Core Facility of the Medical University Innsbruck) are also performed by our group.



Resources and tools
Resources and tools provides links to various software tools and web resources/applications developed by the group and hosted on our servers. Additionally we mirror the Ensembl database and the Ensembl and VEGA biomart databases.

CARMAweb
Web application for the analysis of microarray data. CARMAweb uses R and Bioconductor as calculation backend.

madbWeb
Web interface to the microarray database at the TCRI. The database hosts gene expression datasets generated at the TCRI (Kofler group) and provides various tools to access and analyze this data.

maDB and pgUtils Bioconductor packages
Bioconductor packages providing functions to store/retrieve microarray data to a database backend and to create such a database.

Affymetrix Exon custom CDF files
Custom CDF files and Bioconductor packages created for the Affymetrix Human Exon 1.0 st and Mouse Exon 1.0 st microarray by aligning the oligo-probe sequences to the genome and annotating them to transcripts defined in the Ensembl and the ASTD (Alternative Spliced Transcript Database) databases.

pri-miRNA prediction and Affymetrix probeset identification
Definition of potential primary transcription units of microRNAs (miRNAs) based on their genomic localization and identification of Affymetrix probesets detecting these primary transcription units.

Quick links
News
19.01.2010: updated slides for lectures Genomics: Gene Expression Profiling and Genomics: Bioinformatics online.
15.01.2010: Daniel Bindreither joins the group.
13.05.2009: Julien Lelong joins the group.
13.05.2009: pri-miRNA probesets predictions update: Ensembl 54_36p, miRBase 13.0.
25.03.2009: pri-miRNA probesets predictions update: Ensembl 53_36o, miRBase 13.0.
18.02.2009: pri-miRNA probesets predictions update: Ensembl 52_36n.
Contact
Bioinformatics Group,
Division Molecular Pathophysiology,
Biocenter, Medical University Innsbruck
Fritz-Pregel-Str 3/IV, 6020 Innsbruck, Austria

email: johannes.rainer@i-med.ac.at

phone: 0043 512 570485 13
© 2010 Bioinformatics Group, Division Molecular Pathophysiology, Biocenter, Medical University Innsbruck