Systems biology research projects
Research in the Almaas lab is mostly centered on applying network analysis to microbial systems: the variety of interactions between genes, proteins and metabolites in a cell are best represented by networks. Thus, network approaches offer a uniform approach to categorize and analyze very different cellular systems and their associated features. In recent years, we have used Flux Balance Analysis (FBA) and related approaches to model genome-scale metabolism; we have studied large-scale gene-expression and protein interaction networks; we have designed and analyzed synthetic gene circuits. We are also involved in collaborations with experimental groups to test our model predictions. More information at Almaas lab's web page
The Bar's group is mainly focused on Systems modeling and analysis. We view processes in biology as any other process in nature, albeit complex, and thus we can apply the well-developed systems tools. We develop models primarily using Ordinary Differential Equations (ODEs), or state space form, written in Matlab in order to investigate phenomenons such as bi-stability, bifurcations and oscillations in biological processes. We are using simulations to predict outcome or response of stimuli in biology. Currently running projects are 1) dynamic model of fish growth, in which body mass and composition (response) are calculated and predicted given feeding regime and composition (stimuli). 2) Initiation control in Eukaryatic Cells, where we investigate nature' strategies to regulate the translation in the protein synthesis process and finding ways to manipulate it, and 3) developing algorithms and models to predict expression levels in bacteria, focusing on the 5'UTR, 4) Gastrin project (joint with Kuiper's and Almaas's groups): developing dynamical models the describe the cellular response to the hormone Gastrin, and analysing them.
The Kuiper lab focuses on Knowledge Management for the Life Sciences. We have developed the application ontology Cell Cycle Ontology, and the RDF triple store BioGateway. These tools are further matured to enable Semantic Systems Biology , a systems biology approach that uses semantic description of knowledge about biological systems to facilitate integrated data analysis. We are also engaged in collaborations applying common tools like Bioconductor, Cytoscape and CellDesigner on functional genomics data for data analysis, mining, network-based analysis and modelling.