Innsbruck Medical University
Applied Bioinformatics Group
home
group members
publications
teaching
open positions
resources and tools

Applied 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 high throughput sequencing derived data and 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 generated for users of the Expression Profiling Unit 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.

Affymetrix custom CDF files
Custom CDF files and Bioconductor packages created for new generation Affymetrix sense target (ST) microarrays (Human Exon 1.0 ST v2, Human Gene 1.0 ST v1 and Mouse Gene 1.0 ST v1).

Development of R/Bioconductor software packages
Various R-software packages for data analysis and visualisation. Our maDB and pgUtils packages providing functions to store/retrieve microarray data to a database backend and to create such a database are also part of Bioconductor.

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.

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.

floWeb
Web application for management and analysis of flow cytometry data.

svn repository
Subversion repository.

Quick links
  • Biocenter of the Innsbruck Medical University
  • Medical University Innsbruck
  • Tyrolean Cancer Research Institute
  • Exon array analysis
  • pri-miRNA definitions
  • CARMAweb
  • Bioconductor
    • News
    08.03.2012: Updated Affymetrix CDF files for Ensembl 66.
    02.02.2012: Updated miRNA host gene predictions for Ensembl 66.
    16.02.2012: Custom Affymetrix CDF for Mouse Exon arrays available.
    09.01.2012: Updated miRNA host gene predictions.
    14.12.2011: Custom Affymetrix CDF for Ensembl 65 available.
    18.10.2011: Custom Affymetrix CDF for Ensembl 64 available.
    13.10.2011: Custom CDF files online.
    Contact
    Applied Bioinformatics Group,
    Division Molecular Pathophysiology,
    Biocenter, Medical University Innsbruck
    Innrain 80/82 II, 6020 Innsbruck, Austria

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

    phone: +43 (0)512 9003 70961
    © 2011 Applied Bioinformatics Group, Division Molecular Pathophysiology, Biocenter, Medical University Innsbruck