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September 2015: Participants of the UCSC Genome Browser Workshop held by Robert Kuhn, Associate Director of the Genome Browser Project (4th from the left, sitting), organized by Mario Looso

Bioinformatics and ECCPS bioinformatics service group

The group of Dr. Mario Looso focuses on applied bioinformatics. The group provides support in several types of bioinformatic tasks but works on own projects as well. To achieve a highly efficient infrastructure for bioinformatic workflows, it works closely with the IT service group. The goal is to ensure that scientists across the institute are able to exploit existing and emerging computational technologies. By consulting of scientists we help to identify bioinformatic approaches to scientist’s research problems and help to frame the questions to “omics” terms. Typical supported bioinformatic tasks are:

Analysis of next-generation data

RNAseq, miRNAseq and ChIPseq approaches are often used to investigate differences in transcription between two or more conditions or within time series experiments. Besides quality analysis and general data statistics, we offer experiment orientated quantitative analysis of such next-generation sequencing datasets. Nevertheless, when working with niche model organisms or focusing on new proteins or protein variants, data from next-generation sequencing cannot be analysed in a standardized way, but needs de novo assembly of transcriptomes or genomes to unravel unknown structures of interest, like new transcripts or splice-variants. We provide the necessary computational infrastructure and software environment to apply to such approaches.

Integration of -omics approaches

Modern molecular biology is often driven by large screenings on genome, transcriptome and proteome level. Such screenings and their basal analysis become more and more standardized. In contrast the comparison and correlation of such datasets on different molecular levels is not trivial. We offer the integration and visualization of such datasets based on ID mappings and expression correlations. A fundamental understanding of the biological background and experiment, which can only be supplied by the scientists who has done the work, is essential for an appropriate analysis.

Management of large data sets

Recent high throughput technologies provide large amounts of data that highly raised demands on computational infrastructures and data management. We allocate adapted systems and management solutions. Development of user and data specific databases is a typical task in this field.

Generation of automated workflows

Laboratories often have repetitive tasks that can be automated by writing scripts. We help to identify these repetitive tasks and write the necessary scripts to streamline the processes (blasting, masking, database searches, pattern finding).

Contact

Group Leader:

Dr. Mario Looso

Max Planck Institute for Heart and Lung Research

Ludwigstrasse 43 / FGI 109

D-61231 Bad Nauheim

Tel.: +49 (0)6032 705-1763

Fax: +49 (0)6032 705-419

© 2017 Max-Planck-Institut für Herz- und Lungenforschung, Bad Nauheim