Vacancy The Netherlands Institute for Systems Biology (NISB) and Centrum Wiskunde & Informatica (CWI) invite applications for the position of a Postdoc (two years, with possibility for extension): Computational modeling of structural genomic variation in hierarchically-regulated gene networks The opening is a research position within the field of computational biology Research background Structural variation of the genome, including translocation of DNA chunks across chromosomes, inversions, and deletions can have enormous impact on gene expression and consequently on cell function. Hierarchical regulation mechanisms, including conditional DNA folding and nuclear lamina interactions, can switch gene clusters between a state rendering the genes inaccessible to transcription and a “permissive” state in which gene transcription is possible. The consequences of hierarchical network organization for the dynamics and evolution of gene networks are poorly understood. The project will develop computational and mathematical modeling approaches to explore the effects that structural genomic variation can have on gene expression in hierarchically-structured gene networks at single-organism and evolutionary time scales. Job description The postdoc will develop and analyze theoretical, evolutionary models of hierarchical gene network regulation using discrete and/or continuous modeling approaches. Model insights and predictions based on artificial and actual regulatory networks will be interpreted in close collaboration with two functional genomics groups that participate in the NCSB: the Edwin Cuppen group at the Hubrecht laboratory, Utrecht and the Lodewyk Wessels group at the Netherlands Cancer Institute in Amsterdam. Location The work will be embedded in the Biomodeling and Biosystems Analysis group of the Netherlands Institute for Systems Biology (NISB; www.sysbio.nl) and within the Life Sciences group of the Center for Mathematics and Computer Science (CWI) in Amsterdam. As the “core modeling group” of the Netherlands Consortium for Systems Biology, the Biomodeling and Biosystems Analysis group develops quantitative and predictive models and multiscale computer simulations in collaboration with systems biology groups at participating institutes. Profile Candidates ideally fulfill the following criteria: - Ph.D. theoretical biology, computer science, mathematics or a related discipline - able to communicate with scientists in biology and mathematics - good programming skills in C++ or equivalent Conditions of employment The vacancy concerns a temporary research position for two years, with possibility of extension. The salary and terms of employment are in accordance with the "CAO-onderzoekinstellingen" and are based on qualifications. Besides the salary and excellent working conditions, CWI offers attractive and flexible terms of employment, like a collective health insurance, pension-fund, and initial help with housing for foreigners. The position is at postdoc level for 38 hrs/week. Websites http://www.sysbio.nl and http://www.cwi.nl Applications and requests for information Direct requests for information or applications before 1 December 2008 to: Dr. Roeland Merks, Roeland.Merks@sysbio.nl phone +31 20 592 4117, skype: roelandmerks Centrum Wiskunde & Informatica (CWI) and Netherlands Institute for Systems Biology (NISB) Kruislaan 413, 1098SJ Amsterdam, The Netherlands ----- Vacancy The Netherlands Institute for Systems Biology (NISB) and Centrum Wiskunde & Informatica (CWI) invite applications for the position of a: PhD student (OIO): Cell-based modeling of in vitro angiogenesis: role of tip cell selection, cross-talk between diffusive and contact-dependent signaling, and endothelial cell-matrix interactions. The opening is a research position within the field of computational biology Research background Angiogenesis, the outgrowth of sprouts from existing blood vessels, is essential for many biomedical phenomena, including tumor growth and tissue engineering. A detailed understanding of its mechanisms will help identify specific targets for therapeutical intervention. The key players of angiogenesis are endothelial cells (ECs), the cells lining the inner walls of mature blood vessels, and the surrounding matrix proteins. We have previously built simple models of the ECs’ self-organization into angiogenic sprouts. In this project we aim to refine our understanding of angiogenic sprouting, by including the selection of “tip cells”—the leading cells of blood vessel sprouts—and the interactions between the ECs and the protein matrix they live in. The final goal of this project is to develop a multiscale, explanatory model of angiogenesis. Job description The PhD student will further develop and analyze cell-based models of angiogenesis and, depending on interest, validate the cell-based models using mean-field approaches. Techniques include ordinary differential equations (ECs’ regulatory networks), the Cellular Potts Model (cell behavior) and PDEs (protein matrix). Model insights and predictions will be interpreted and validated in close collaboration with our experimental collaborators. Location The work will be embedded in the Biomodeling and Biosystems Analysis group of the Netherlands Institute for Systems Biology (NISB) and within the Life Sciences group of the Center for Mathematics and Computer Science (CWI) in Amsterdam. As the “core modeling group” of the Netherlands Consortium for Systems Biology, the Biomodeling and Biosystems Analysis group develops quantitative and predictive models and multiscale computer simulations in collaboration with systems biology groups at participating institutes. Profile Candidates ideally fulfill the following criteria: - M.Sc. in theoretical biology, computer science, mathematics or a related discipline - able to communicate with scientists in biology and mathematics - good programming skills in C++ and Python or equivalent Conditions of employment The vacancy concerns a temporary research position for four years. The salary and terms of employment are in accordance with the "CAO-onderzoekinstellingen". Besides the salary, CWI offers attractive and flexible terms of employment, like a collective health insurance, pension-fund, and initial help with housing for foreigners. Websites http://www.sysbio.nl and http://www.cwi.nl Applications and requests for information Direct requests for information or applications before 1 December 2008 to: Dr. Roeland Merks, Roeland.Merks@sysbio.nl phone +31 20 592 4117, skype: roelandmerks Centrum Wiskunde & Informatica (CWI) and Netherlands Institute for Systems Biology (NISB) Kruislaan 413, 1098SJ Amsterdam, The Netherlands Applications should include a motivation letter, a curriculum vitae, list of publications, and the names and addresses of at least two persons that can be approached to obtain further information. Closing time 1 December 2008 Literature Roeland M. H. Merks, Sergey V. Brodsky, Michael S. Goligorksy, Stuart A. Newman, James A. Glazier (2006). Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling. Developmental Biology 289, 44-54. doi:10.1016/j.ydbio.2005.10.003 Roeland M. H. Merks, Erica D Perryn, Abbas Shirinifard, James A Glazier (2008). Contact-inhibited chemotaxis in de novo and sprouting blood-vessel growth. PloS Computational Biology 4 (9), e1000163. doi: 10.1371/journal.pcbi.1000163 -- ==================================================================== Note: from September 1st 2008 I will move to the Netherlands Institute for systems biology (www.sysbio.nl) and to CWI, the National Center for Mathematics and Computer Science (www.cwi.nl) in Amsterdam. However, I will be in Ghent until September 5th 2008 for our plant modeling summer school: www.psb.ugent.be/plantmodels. My current e-mail address will still be operational for a while, but it will soon change to: Roeland.Merks@cwi.nl and Roeland.Merks@sysbio.nl. If any of these addresses does not (yet) work, please use my personal e-mail address: post@roelandmerks.nl. ================================================================= Roeland Merks Group Leader "Plant Systems Modeling" Tel:32 (0)9 3313823 Fax:32 (0)9 3313809 VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent Technologiepark 927, 9052 Gent, BELGIUM roeland.merks@psb.ugent.be http://www.psb.ugent.be ==================================================================