CBio – Computational Biology / Biomedical Engineering, Eindhoven University of Technology
Delegates: Natal van Riel, Peter Hilbers
Researchers at the department of Biomedical Engineering combine basic science (how) with engineering (how to). They investigate, develop and apply engineering principles and tools to unravel the pathophysiology of diseases and enhance diagnostics, intervention and treatment.
Interdisciplinary research has been realised in the three thematic programmes: Regenerative Medicine, Molecular Imaging and Systems Biology.
The Systems Biology theme aims to enhance the shift from ‘describing’ life’s processes to ‘understanding’ them and ‘capturing’ them in validated predictive models, and even ‘managing’ or ‘controlling’ them. The scope of this theme covers all levels from molecules to organs and humans, such as described by the transcriptome, proteome, metabolome and the physiome.
CMSB – Centre for Medical Systems Biology
Delegates: Ko Willems van Dijk, Gert-Jan van Ommen
Common diseases, such as Alzheimer, arthritis, diabetes, migraine and depression pose major healthcare problems. Such diseases are caused by a complex network of factors: age, gender and lifestyle play a role in addition to a patient’s genes. The complexity of common diseases is further increased by the fact that they often interact. At first glance there seems to be no relationship between depression and migraine, diabetes and cancer, or high cholesterol and Alzheimer. Yet we increasingly find hidden connections between these diseases, suggesting the existence of common pathways or biological master switches that underlie multiple clinical outcomes. The main aim of the Centre for Medical Systems Biology (CMSB) is to elucidate this connectivity. In addition, rare forms of these diseases, often with more clear-cut genetic causes, are studied as model systems to develop mechanistic insights, better prognostics and targeted therapies. By combining these approaches, CMSB optimises its mission to improve the diagnosis, treatment and prevention of common and rare diseases.
CSBB – Centre for Systems Biology and Bioenergetics
Delegates: Richard Notebaart, Gert Vriend
CSBB will model mammalian energy production, distribution, expenditure and energy stress responses in the context of human disease.
CSBB focuses its experimental and modelling efforts on the energy stress response network in mouse and human patient cells, tissues and at the whole organism level. Multidisciplinairy approaches with state-of-the-art technologies will be used for modelling of the direct relationship between processes for ATP production and distribution and ATP expenditure, both under physiological conditions and following disease-related environmental or genetic pertubations. The developed physiological and energy stress response models will be used to improve the energy status of man in health and disease via pharmacological and nutritional interventions.
CSBC – Cancer Systems Biology Centre
Delegate: Lodewyk Wessels
From targeted therapeutics to personalised medicine.
The Cancer Systems Biology Center (CSBC) is a center of excellence within the Netherlands Cancer Institute-Antoni van Leeuwenhoek hospital. The CSBC will employ computational modeling and experimental validation cycles spanning multiple levels of complexity including cell lines, mouse models and patients. Within the CSBC several research groups from the NKI-AVL work together to develop a strategy to tackle the complexity of molecular networks that govern breast tumorigenesis with the goal to deliver improved diagnostic tools to enable tailored cancer therapy.
DCMSB – Delft Centre for Microbial Systems Biology
Delegates: Marcel Reinders, Jack Pronk
The Delft Centre for Microbial Systems Biology (DCMSB) harbours scientists in molecular biology, physiology, enzymology, and bionanoscience, as well as engineers in biotechnology, bioinformatics and control theory. The DCMSB performs fundamental research on microorganisms and microbial populations, inspired by current and future industrial applications. Over the past decade, DCMSB participants have fruitfully co-operated in quantitative modelling of (populations of) microorganisms within (a) the Delft Research Centre for Life Science&Technology, (b) substantial national research programmes such as B-Basic, and (c) the Kluyver Centre for Genomics of Industrial Fermentation. Involvement in these large programmes stimulates efficient dissemination and valorisation of DCMSB research. Note that the DCMSB is complementary to these efforts, as it uniquely offers its members an environment dedicated to the study of basic biological phenomena unencumbered by commercial or competitive considerations. Without the DCMSB, this research cannot be performed at the scale and level of collaboration between experts in biology, measurement technology and modelling we believe is required to obtain success.
MaCSBio – Maastricht Centre for Systems Biology
Delegate: Ilja Arts
Maastricht University and Maastricht University Medical Centre have recently decided to strengthen their systems biology research. With support of the Province of Limburg, the Maastricht Centre for Systems Biology (MaCSBio) was founded. The centre will combine modelling expertise and biological research including behavioural research from the Faculty of Health Medicine and Life Sciences, the Faculty of Psychology and Neurosciences, and the Faculty of Humanities and Sciences. The primary aim of MaCSBio is to facilitate the integration of relevant biological data coming from different empirical domains using mathematical multi-scale modelling approaches. This will take shape in two research lines, which will be established within the centre. The focus of the research lines will be determined at the end of 2013 and research will start in 2014.
NISB – Netherlands Institute for Systems Biology
Delegates: Bas Teusink, Roeland Merks, Age Smilde
Within the Netherlands Institute for Systems Biology (NISB), researchers from the University of Amsterdam, VU University Amsterdam and Centrum Wiskunde&Informatica collaborate to develop and exploit systems biology tools to investigate complex biological systems and unravel their underlying principles. NISB researchers approach biological systems as networks of molecules, cells, tissues and organisms that interact in time and space. This is achieved by amalgamating biological and biomedical sciences with chemistry, physics, mathematics, informatics and engineering.
SBC-EMA – Systems Biology Centre of Energy Metabolism and Ageing
Delegates: Matthias Heinemann, Barbara Bakker
The goal of SBC-EMA is to unravel the intricate relationship between metabolism and the biology of ageing. This relationship, which has been conserved throughout evolution, is bidirectional: metabolism affects the ageing of an organism, while the metabolic system itself declines under the influence of ageing. Both metabolism and ageing are systems properties that are affected by a large number of processes at the molecular, cellular and organ level. Hence a full understanding of metabolism, ageing and their interaction necessitates a systems-biology approach.
We use the budding yeast Saccharomyces cerevisiae and the mouse as model organisms. With an interdisciplinary team of scientists,we will use various approaches of systems biology.
MSB-TNO – Microbiology & Systems Biology (TNO)
Delegate: Suzan Wopereis
Microbiology & Systems Biology (MSB) is internationally acclaimed for finding innovative solutions for diverse challenges in nutrition, health and biotechnology. MSB uses its broadly applicable expertise to create tailor-made innovations for companies in agro&food, personal care, chemicals, biotechnology and pharma. We use systems biology to understand relationships in complex biological processes. We are particularly successful in developing indicators of biological and pathogenic processes (inflammation, food spoilage). In collaboration with other TNO groups we have access to a broad collection of state of the art analytical platforms which we apply to an extensive collection of in vitro and in vivo models of health and disease. We use this to solve complex problems for industrial partners. For example, we determine whether food ingredients have healthy effects on gut and mouth microbiota or have health-promoting activity in animals or humans or mouse models for cardiovascular diseases. We also use systems biology to find natural food ingredients that can suppress food spoilage or prevent food poisoning. In addition, we use systems biology to optimise industrial bioprocesses and develop methods to convert biomass into commodity molecules (building blocks and biofuels).
WCSB – Wageningen Centre for Systems Biology
Delegates: Vitor Martins dos Santos, Jaap Molenaar
Wageningen UR has chosen Systems Biology as one of its focal points and invests considerably in this emerging research field. The Wageningen Centre for Systems Biology (WCSB) for Food, Feed, and Health is the condensation point of all Systems Biology developments at Wageningen UR.
WCSB’s research focuses on the entire spectrum of biological systems, from DNA to ecosystem, and involves topics relevant to plants, digestion and microbes.
With the establishment of the WCSB and the financing of 14 systems biology research projects under its auspices, Wageningen UR aims to become a strategic partner in the field of research in systems biology. The projects fall apart into three categories:
a. Learning and predicting how plants respond to stress and the consequences this has for yield and productivity (Virtual Plant)
b. Understanding the functioning of the intestinal tract of mammals in relation to their diet to anticipate or remedy obesity (Virtual Gut)
c.Developing models that can help in the modification of microorganisms for the production of fine chemicals, commodity compounds and energy (Virtual Microbe).
SMEs – Small and Medium Enterprises
SB@NL recognises the importance of valorisation of systems biology knowledge and its effective translation into solutions which benefit the society and economy. SMEs play a crucial role in valorisation being the key drivers of innovation. Hence, SB@NL involves the SME-world in its partnership through representative(s) of SMEs that are active in the systems biology field.
Delegate: Marijana Radonjic (EdgeLeap BV)
EdgeLeap B.V. is an Utrecht-based company providing cutting edge bioinformatics solutions for the life sciences industry. EdgeLeap applies network-based technology for data integration, mining and visualisation to uncover how multiple layers of biological complexity relate, influence each other, and organise themselves into complex systems. This knowledge helps making decisions based on best-evidence for designing strategies to cure disease or improve health. EdgeLeap reinforces the competitive edge of its clients through extracting actionable knowledge out of their complex data.
Founders of EdgeLeap are scientists with years-long involvement in national systems biology platforms (e.g. NgC, NBIC, NTC, NGI). The startup of EdgeLeap has been boosted by the Venture Challenge programme of the Netherlands Genomics Initiative (NGI), fostering the combination of excellent science with entrepreneurship (www.lifesciencesatwork.nl). In parallel with running a business, the EdgeLeap team remains to be active in the academic network through co-supervision of PhD students, editing scientific journals, co-organisation of symposia and workshops, providing training and education, and, acting as co-developers in open source communities.