Technical University of Delft
 
The Delft Bioinformatics Lab performs research and educates students in the fields of bioinformatics for health and disease and bioinformatics for microbiology. The lab stands out in design of data-driven algorithms that are based on the latest developments in the field of Pattern Recognition. The group applies their algorithms to advance the state-of-the-art in health care and industry. To this end, the Bioinformatics Lab closely collaborates with researchers and educators in molecular and cell biology, medicine and biotechnology. Algorithms are created to infer and exploit simple models of complex interactions, by coupling biological insights and available prior knowledge to high-throughput measurements. The core expertise is in machine learning and pattern recognition. Major application areas are in medicine, trying to understand the biology underlying genetic diseases such as cancer and aging; and in biotechnology, engineering industrially relevant microorganisms.


Staff Expertise
  • The group of Prof. Reinders is one of the leading bioinformatics groups in the Netherlands. His background is within pattern recognition. Besides studying fundamental issues, he applies pattern recognition techniques to the areas of bioinformatics, computer vision and context-aware recommender systems. His special interest goes towards understanding complex systems (such as biological systems). His role will be to supervise the bioinformatics aspects of the project.
  • Prof. Lelieveldt has a main research interest is the integration of a-priori knowledge into segmentation and registration algorithms, with main applications to cardiac imaging, multi-modal pre-clinical imaging and fluorescence-guided surgery. Prof. Lelieveldt will concentrate on the image analysis components of the proposal.
  • TUD's PSs and CSs as well as the mentors that will be assigned to the ITN are all fully committed to spend their time on the project. Their respective postdocs and scientists will also be involved during the SECs that are hosted by the TUD. All assigned staff members will support the SECs utilizing their respective skills to integrate and map out the immune regulatory pathways derived from MSI.

Key facilities and infrastructure
  • The Delft Bionformatics lab has access to a state-of-the-art local compute infrastructure for bioininformatics analysis.
  • In addition, access to national supercomputing facilities is secured.
  • Apart from high-performance computing and networking resources, the group has access to top-level expertise on data visualization, machine learning and image analysis.

Previous involvement in Research and Training Programmes
  • 2001 - 2005 Coordination of a Marie Curie Industry fellowshop (Prof. Lelieveldt)
  • 2008 - 2012: FP7 ENCITE project for cell imaging and tracking
  • 2009 - 2014: CTMM (Dutch) funded program ‘MUSIS’ for and intra-operative image guided surgery

Current Involvement in Research and Training Programmes
  • 2012 - 2015: FP7 CARIOCA Project
  • 2013 - 2017: EU Marie Curie IAPP project, BRAINPATH
  • 2013 - 2018: Human Brain Project
  • 2014 - 2018: EU Marie Curie RISE project, PRISAR

Publications
  • Schaafsma BE et al. Clin. Cancer Res 2014; in press
  • Mahfouz A et al. Methods 2014, in press
  • Abdelmoula WM et al. Anal Chem 2014; 86:9204-9211
  • Abdelmoula WM et al. Anal Chem 2014; 86:3947-3954
  • Van den Akker et al. J Integr Bioinform 2011; 8-188


Overview of all participants ...