Christopher Schröder, Christoph Stahl, Felix Mölder, André Janowicz, Jasmin Beygo, Marcel Martin, Sven Rahmann
The Exome Analysis GraphicaL Environment (EAGLE) combines a best practices variant calling workflow, with a web frontend. By storing the called information in speficially structerd hdf5 files, EAGLE allows filtering and parameter tuning in almost real time. This enables iterative tuning of thresholds, or the selection of different samples for filtering by non computer scientists via the web interface.
Toll‐like receptor (TLR) 13 and TLR2 are the major sensors of Gram‐positive bacteria in mice. TLR13 recognizes Sa19, a specific 23S ribosomal (r) RNA‐derived fragment and bacterial modification of Sa19 ablates binding to TLR13, and to antibiotics such as erythromycin. Similarly, RNase A‐treated Staphylococcus aureus activate human peripheral blood mononuclear cells (PBMCs) only via TLR2, implying single‐stranded (ss) RNA as major stimulant. Continue reading →
Bioinformatics Analysis of Heterogenous Data Reveals Characteristic Mutational Landscapes of Neuroblastoma Relapses, GCB 2015 in Dortmund
Marc Schulte, Johannes Köster, Daniela Beisser, Corinna Ernst, Christopher Schröder, Alexander Schramm and Sven Rahmann
Neuroblastoma is a malignancy of the developing sympathic nervous system that causes 15% of childhood cancer-related mortality. However, in the vast majority of cases death results not from the initial disease manifestation but rather from metastasis or recurrence.
Systematic search for genomic alterations in primary neuroblastomas has shown low genetic complexity, with significant mutations in only a very few genes. This study explored the genomic landscape of relapsing neuroblastoma in order to evaluate ‘driver’ mutations to be exploited as therapeutic targets.
A. Schramm, J. Köster, Y. Assenov, K. Althoff, M. Peifer, E. Mahlow, A. Odersky, D. Beisser, C. Ernst, A. G. Henssen, H. Stephan, C. Schröder, L. Heukamp, A. Engesser, Y. Kahlert, J. Theissen, B. Hero, F. Roels, J. Altmüller, P. Nürnberg, K. Astrahantseff, C. Gloeckner, K. De Preter, C. Plass, S. Lee, H. N. Lode, K. Henrich, M. Gartlgruber, F. Speleman, P. Schmezer, F. Westermann, S. Rahmann, M. Fischer, A. Eggert, J. H Schulte
Neuroblastoma is a malignancy of the developing sympathetic nervous system that is often lethal when relapse occurs. We here used whole-exome sequencing, mRNA expression profiling, array CGH and DNA methylation analysis to characterize 16 paired samples at diagnosis and relapse from individuals with neuroblastoma. Continue reading →
The German Conference on Bioinformatics (GCB) is an annual, international conference devoted to all areas of bioinformatics. Recent meetings attracted a multinational audience with 250 – 300 participants each year. The meeting is open to all fields of bioinformatics. Continue reading →