Bioinformatics Facility

Initially part of the Cologne Center for Genomics (CCG), the CECAD Bioinformatics Facility has been relocated to the CECAD building at the end of 2013. The facility has recruited new coworkers who take responsibility for bioinformatics data analysis and software development. In addition, bioinformatics PhD students from several CECAD labs were embedded into the facility to take advantage of its infrastructure and expertise. The IT hardware used by the Bioinformatics Facility is operated by the Regional Computing Center of the University of Cologne (RRZK).

Services: The newly founded Bioinformatics Facility provides support in all areas of biological data analysis. In particular, it helps with handling the enormous amounts of data from high-throughput technologies in the genomics (Next-Generation Sequencing) as well as the proteomics and metabolomics (Mass Spectrometry) fields. For this purpose, the platform develops very efficient analysis pipelines using state-of-the-art analysis algorithms, but also aims at offering more individualized support.

Scientific achievements: Apart from the basic data processing, the group is particularly interested in innovative data-driven methods for the identification of regulatory molecular circuits. This work relies on public resources as well as large in-house RNA-Seq/ChIP-Seq databases growing with every single sample that is being processed by the analysis pipelines. This data pool is used to establish networks of molecular regulation on the transcriptional as well as the post-transcriptional level which are then made accessible as a high-level support to several collaborative projects with research labs from CECAD.

Future plans: The platform pursues the particular goal to participate in projects involving data integration between different levels of biological information, for instance integrated genomics/proteomics analyses, which open a more system-wide view on biological questions. The Bioinformatics Facility is supported by independent funding from the German Research Foundation (DFG, grant FR3313/2-1 to PF) and the Federal Ministry of Economy and Technology (BMWi, grant KF2429610MS2 to PF).

Dr. Peter Frommolt
Head of Bioinformatics Facility
Tel.  +49 221 478 84017

CECAD Cologne / Bioinformatics
CECAD Forschungszentrum
Joseph-Stelzmann-Str. 26
50931 Köln
Profile Page

Peter Frommolt
Figure 1
Figure 2

Figure 1: The QuickNGS framework developed by the facility combines a broad collection of widely adopted Next-Generation Sequencing (NGS) data analysis softwares into a professional high-end analysis system enabling rapid in-depth analysis of tens or hundreds of samples from NGS experiments with extremely low hands-on time. The sample information simply needs to be fed into a MySQL database by the lab operators and all the rest is running fully automated, ending up in a convenient web interface for easy user access.

Figure 2: The lab operates an in-house software package which trains models of molecular regulatory networks by taking advantage of the large and ever increasing RNA-Seq/ChIP-Seq databases behind the QuickNGS framework. Integration of these networks with additional a-priori knowledge from public databases has established a very powerful tool for downstream analysis of RNA-Seq data from the labs within CECAD.
The figure shows a sub-network of a trained miRNA regulatory network in Caenorhabditis elegans enriched for genes involved in lifespan regulation and aging.

  • Schermer B, Bartels V, Frommolt P, Habermann B, Braun F, Schultze JL, Roodbergen M, Hoeijmakers JH, Schumacher B, Nürnberg P, Dollé ME, Benzing T, Müller RU, Kurschat CE. (2013) Transcriptional profiling reveals progeroid Ercc1 (-/Δ) mice as a model system for glomerular aging. BMC Genomics; 14:559.
  • Gharbi H, Fabretti F, Bharill P, Rinschen MM, Brinkkötter S, Frommolt P, Burst V, Schermer B, Benzing T, Müller RU. (2013) Loss of the Birt-Hogg-Dub. gene product folliculin induces longevity in a hypoxiainducible factor-dependent manner. Aging Cell; 12(4): 593-603.
  • Rynes J, Donohoe CD, Frommolt P, Brodesser S, Jindra M, Uhlirova M. (2012) Activating transcription factor 3 regulates immune and metabolic homeostasis. Mol Cell Biol; 32(19): 3949-62.
  • Frommolt P, Abdallah AT, Altmüller J, Motameny S, Thiele H, Becker C, Stemshorn K, Fischer M, Freilinger T, Nürnberg P. (2012) Assessing the enrichment performance in targeted resequencing experiments. Hum Mutat; 33(4):635-41.
  • Meimaridou E, Kowalczyk J, Guasti L, Hughes CR, Wagner F, Frommolt P, Nürnberg P, Mann NP, Banerjee R,Saka HN, Chapple JP, King PJ, Clark AJ, Metherell LA. (2012) Mutations in NNT encoding nicotinamide nucleotide transhydrogenase cause familial glucocorticoid deficiency. Nat Genet; 44(7): 740-2.