Molecular pathway modelling needs ideas to make sense out of massive data

Dr. Peter Frommolt

The Bioinformatics Core Facility of CECAD Cologne is headed by Dr. Peter Frommolt. He studied mathematics and physics at the universities of Hamburg and Cologne with focus on probability theory and the theory of semiparametric statistics. From 2006 to 2008, he worked at the Institute of Medical Statistics, Informatics and Epidemiology in Cologne where he was involved in the planning and analysis of clinical trials as well as in molecular data analysis. In 2009, he received his PhD on applications of bootstrap methods for multiple hypothesis testing. Since then, he has been a postdoc at the Cologne Center for Genomics where he strengthened his expert knowledge in bioinformatics and its applications to genomics research. In 2012, he started building up a Bioinformatics Core Facility within the Cluster of Excellence „Cellular Stress Responses in Aging-Associated Diseases (CECAD)“ in Cologne. 

Research interests

  • Applications of high-dimensional statistics in molecular biology.
  • Next-generation sequencing.
  • Data integration and systems biology. 

Previous scientific achievements

Dr. Peter Frommolt contributed to the installation of the infrastructure and initiated the data management and analysis solutions for the next-generation sequencing platform at the University of Cologne. The analysis systems he developed have been used in national and international collaborative projects giving rise to several high-impact publications. He developed various tools for in-depth analysis of next-generation sequencing data, e.g. the NGSrich software for evaluation of the target enrichment performance in whole-exome resequencing studies. In cooperation with a CECAD lab, Dr. Peter Frommolt recently developed an innovative approach to molecular pathway analysis in C. elegans implemented as a web-based software called Wormpath.

Current projects

As a Core Facility, the group of Dr. Peter Frommolt provides support and is actively involved in many collaborative projects within SyBACol and CECAD Cologne. In particular, the facility is developing and continuously refining appropriate analysis pipelines and tools to handle huge amounts of next-generation sequencing data, e.g. from RNA-Seq, ChIP-Seq, or whole-exome resequencing studies. Within CECAD Cologne, these analysis pipelines are mainly applied to model organisms such as mouse, C. elegans or D. melanogaster . An active area of further development is the integration of data sets from different applications of next-generation sequencing and other technologies using relational structures of a tailor-made database.

Within the SyBACol consortium, the Core Facility is involved in projects on the transcriptomics and functional characterisation of renal aging as well as contributing expertise in molecular data analysis to projects on mathematical pathway modelling.

 

Selected Publications

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 AJL, Metherell LA (2012): Mutations in NNT  encoding nicotinamide nucleotide transhydrogenase cause familial glucocorticoid deficiency. Nat  Genet. (2012);  44(7): 740-742. 

Frommolt P, Abdallah AT, Altmüller J, Motameny S, Thiele H, Becker C, Stemshorn K, Fischer M,  Freilinger T, Nürnberg P: Assessing the enrichment performance in targeted resequencing  experiments. Hum Mutat.  (2012); 00(0): 1-7.

Huebner AK, Gandia M, Frommolt P, Maak A, Wicklein EM, Thiele H, Altmüller J,  Wagner F,  Vinuela A, Aguirre LA, Moreno F, Maier H, Rau I, Gießelmann S, Nürnberg G, Gal A, Nürnberg P,  Hübner CA, del Castillo I, Kurth I:  Nonsense mutations in SMPX, encoding a protein  responsive to physical force, result in X-chromosomal hearing loss. Am J Hum Genet. (2011); 88: 621-625.  

Frommolt P, Hellmich M: Resampling in multiple-dose factorial designs. Biometr J: (2009); 51(6):  915-931.

Frommolt P, Thomas RK: Standardized high-throughput evaluation of cell-based compound screens. BMC Bioinformatics.  (2008); 9: 475. 

 

Organisation / Institute
Cluster of Excellence: Cellular Stress Responses in Ageing-Associated Diseases (CECAD)
University of Cologne

Address
Dr. Peter Frommolt
CECAD Building
Joseph-Stelzmann-Str. 26
50931 Köln, Germany

peter.frommolt@uni-koeln.de


Scheme of data evaluation for next-generation sequencing at the CECAD Bioinformatics Core Facility. A database stores meta-information for analysis control and results, while the actual data processing is carried out on a compute cluster at the University Computing Center (RRZK). The exported data can then be retrieved via a web server. The system is constantly undergoing further development. 


In conjunction with a CECAD research group, the CECAD Bioinformatics Core Facility is developing the software program Wormpath for the analysis of genetic networks in the nematode C. elegans. The figure shows a diagram of a signalling pathway in the worm which is upregulated in response to stress. The software tool is organized as a web service and can be accessed via the link bifacility.uni-koeln.de/wormpath