Centrum Wiskunde & Informatica, The Netherlands

Description of organization

Founded in 1946, Centrum Wiskunde & Informatica (CWI) is the national research center for mathematics and computer science in the Netherlands. CWI's mission is twofold: to perform frontier research in mathematics and computer science, and to transfer new knowledge in these fields to society in general and trade and industry in particular. CWI research groups Interactive Information Access and Life Sciences bring in their expertise and experience in computer science, computational science, and algorithmic mathematics to handle the large amount of data and the complexity of models needed within ITFoM. The Interactive Information Access research group investigates how access to information in rich heterogeneous collections can be improved with humans ‘in the loop’, maximizing the support of the end user's task while minimizing the assumptions about the (structure of) the heterogeneous data. The Life Sciences group performs fundamental interdisciplinary research on algorithms, theory, models and simulations and has a strong focus on mathematical and computational contributions to medical bioinformatics and systems biology.

Previous experience

The Life Sciences group has made core contributions in high-throughput sequencing analysis, integration and analysis of biological networks and experimental data, network-based biomarkers, and systems biology modeling, simulation and prediction. The group maintains strong links to cooperation partners from medicine, including the Netherlands Cancer Institute (NKI) and many university hospitals. CWI is also founding partner of the Netherlands Institute for Systems Biology (NISB), hosts the modeling core group of the Netherlands Consortium for Systems Biology (NCSB) and is a partner within the Netherlands Bioinformatics Centre (NBIC). The Interactive Information Access group has the relevant experience for handling large amounts of heterogeneous data – that in ITFoM vary from patient information to genomic and medical imaging data. Their research agenda focuses on how an information system’s internal representations should evolve given observed user interactions, manually provided annotations (from traditional metadata to mentions in social media), and automatic analysis using computer vision and natural language processing. In the TREC Medical Records track for example, they explore how full-text and ICD taxonomy descriptors interact in the ad-hoc searches carried out for the clinical task of finding cohorts for comparative effectiveness research. The flexible and scalable retrieval technology developed in the group provides the basis for spin-off company Spinque, with a focus on search in professional contexts. Spinque has kindly agreed to allow academic use of their scalable information retrieval platform for research in ITFoM.

Profile of staff members

Arjen de Vries is a computer scientist specialized in information access to dataspaces through the integration of information retrieval and databases. He leads the Interactive Information Access (INS2) research group and holds the part-time full professorship Multimedia Data Spaces at Delft University of Technology. Gunnar Klau is leader of the group Life Sciences. His research focuses on combinatorial algorithms and mathematical models for the analysis of biological and biomedical data, amongst others, for cancer research. Alexander Schönhuth has a unique expertise on hidden Markov processes and related stochastic concepts, and, their application to biological sequence analysis. His research interests comprise personalized medicine, in particular cancer biology as well as comparative and evolutionary (epi-)genomics. A special current focus of his are mathematical and computational approaches in high-throughput genomics, in particular as enabled by next-generation sequencing technology. Frank Bruggeman works on systems biology of molecular regulatory networks, studying eukaryotic gene expression, bursty transcription, epigenetic regulation, nuclear receptor signaling, nucleocytoplasmic shuttling of signaling proteins, stochiometric analysis for microbial ecosystems, GPCR signaling, and metabolic network modeling. Joke Blom is an expert in scientific computing, focusing on the mathematical problems in the life sciences, in particular systems biology and medicine. She focuses on problems including multiscale modelling, analytical and numerical topics (diffusion-reaction systems at the macroscopic and mesoscopic level, hybrid ODE/PDE systems), and parameter estimation (parameter identification, model discrimination and optimal experimental design). Roeland Merks' research focuses on cell-based modeling of plant development and angiogenesis. He heads the “core modeling” group of the Netherlands Consortium for Systems Biology (NCSB) that investigates plant development, angiogenesis, gut microbiota metabolism, epigenetics, and lignin polymerization.

Webpage

The Life Sciences and the Interactive Information Access research groups.

Five recent publications relevant to the project

1) R Cornacchia, S Heman, M Zukowski, AP de Vries, and PA Boncz, Flexible and efficient IR using Array Databases, in VLDB Journal, special issue on IR and DB integration, 17(1):151-168, 2008.

2) AN Kolodkin, FJ Bruggeman, N Plant, MJ Moné, BM Bakker, MJ Campbell, JPTM van Leeuwen, et al. Design principles of nuclear receptor signaling: how complex networking improves signal transduction. Molecular Systems Biology, 6, 446. 2010

3) R Merks, E Perryn, A Shirinifard, J Glazier, J.A. Contact inhibited chemotaxis in de novo and sprouting blood-vessel growth. PLoS Computational Biology, 4, 2008

4) P Dao, R Colak, R Salari, F Moser, A Schönhuth, M Ester. Inferring cancer subnetwork markers using density-constrained biclustering. Bioinformatics, 26(18), i625-631, 2010

5) MT Dittrich, GW Klau, A Rosenwald, T Dandekar, T Müller. Identifying functional modules in protein-protein interaction networks: an integrated exact approach, Bioinformatics(24):i223-i231, 2008