I am interested in\u00a0computational modelling and analysis of complex systems, with a special focus on systems biomedicine. My research methods are based on\u00a0network modelling, systems biology, bioinformatics, and data science.<\/span><\/p>\n The Computational Biomodeling Laboratory<\/a><\/p>\n We develop a novel bioinformatics data analysis pipeline called NetControl4BioMed<\/i>based on the concept of target structural control of linear networks. Our pipeline generates novel molecular interaction networks by combining pathway data from various public databases starting from the user\u2019s query. The pipeline then identifies a set of nodes that is enough to control a given, user-defined set of disease-specific essential proteins<\/i> in the network, i.e., it is able to induce a change in their configuration from any initial state to any final state.\u00a0The pipeline can be used by researchers for controlling and better understanding of molecular interaction networks through combinatorial multi-drug therapies, for more efficient therapeutic approaches and personalised medicine.<\/p>\n The article is available here<\/a>.<\/p>\n Bionetgen Implementation of the Heat Shock Response Bogdan Iancu has implemented the Bionetgen source code of the Heat Shock Response. It can also be downloaded as a zip-file.<\/p>\n<\/div>\n<\/div>\n<\/div>\n Download: GeneAssemblySimulator.jar_.zip GeneAssemblySimulator.jar_.tar.gz<\/p>\n Demo: https:\/\/webswing.combio.org\/gas\/<\/p>\n User: demo, password: demo<\/p>\n Tutorial: Creating a new drawing area<\/p>\n To be able to draw a new graph you have to create a new drawing area. By clicking on the icon \ufffdin the toolbar or choosing \ufffdNew Graph\ufffd in file menu, a new internal window will popup where it is.<\/p>\n<\/div>\n<\/div>\n<\/div>\n Petri Net Implementation of the Heat Shock Response Diana-Elena Gratie has built several Petri net models of the heat shock response. The latest standard and coloured Petri net models are available for download.<\/p>\n<\/div>\n<\/div>\n<\/div>\n PRISM Implementation of the Heat Shock Response implemented by Sepinoud Azimi.<\/p>\n<\/div>\n<\/div>\n<\/div>\nMy research group<\/h4>\n
Recent projects<\/h4>\n
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Active projects<\/h4>\n
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Software and models<\/h4>\n
Network controllability for biomedicine<\/a><\/h5>\n
BioNetGen<\/a><\/h5>\n
Gene Assembly Simulator<\/a><\/h5>\n
Heat Shock Response \u2013 Petri Net<\/a><\/h5>\n
Heat Shock Response \u2013 PRISM<\/a><\/h5>\n