Research groups within the theme

Jan Kreft (Lecturer)

Dr. Kreft’s group is broadly interested in the dynamics of interaction between 'parts' (e.g. individual organisms) and how these interactions give rise to emergent behaviour on the next higher level of organisation (e.g. the population). My specific research interests are basically any fascinating interactions between microbes and the environment, such as syntrophy, plasmid transfer, cooperation, and communication (quorum sensing).

My main tool is Individual-based Modelling (IbM), but we also use other models (ODE, PDE) where more appropriate, or in combination with IbM. Our new open-access software platform is called iDynoMiCS.

Peter Winn (Roberts RCUK Fellow)

The group is interested in the physical and chemical processes important for biological organization. In particular, how does this influence protein evolution? Cellular function comes from organized processes of events, often in response to external stimuli. The aim of the group is to use mathematical models of molecular structure and organisation to understand these biological processes better.

Current biological systems being investigated include the protein interactions involved in the biosynthesis of the antibiotics thiomarinol and mupirocin (with the group of Prof Thomas, University of Birmingham), the structure and function of the signalling protein EvgS, which is part of a two component regulatory system (with Dr Lund, University of Birmingham), and plant signalling proteins (with Dr Coates, University of Birmingham). There is also work to interpret protein and peptide structural information from mass-spectrometry data (collaboration with Dr Helen Cooper).

Recent work has investigated ubiquitin and the molecular machinery of ubiquitination and similar pathways including co-developing the ubiquitin resource (www.ubiquitin-resource.org). Controlled ubiquitination is critical for the correct functioning of eukaryotic cells. We have also been involved in modelling the structure of the beta globin gene locus ( Wong,et al, 2009). and how it might regulate the changes in the type of hemoglobin produced during mammalian development (from embryo to adult) and in studying the function of cytochromes P450, which are important proteins for many biosynthetic pathways and for the disposal of foreign compounds, including poisons and medicines.

Neil Hotchin

The group is interested in understanding the mechanisms that the Rho family of small GTP-binding proteins use to regulate both cell adhesion and growth factor mediated signal transduction. The main focus of our research is directed towards understanding how Rho family proteins regulate adhesion-mediated signal transduction events. Normal epithelial cell function is dependent on both cell-cell interactions mediated by cadherin adhesion receptors and interaction with extracellular matrix proteins via integrin adhesion receptors. We are particularly interested in the role played by Rho-family members in regulating adhesion-dependent signaling events in human epidermal keratinocytes. Glioblastoma is a common and aggressive brain tumor, which is generally resistant to currently used therapies. In collaboration with Francesco Falciani we are using a combination of bioinformatics and cell biology to analyze the role of Rho family GTPases in the development and spread of this tumor.

Pete Lund

We are interested in understanding all aspects of bacterial stress responses from molecular mechanisms of the individual components to the organisation of stress response networks at the level of the whole organism.  While the mechanistic level is approached using molecular biology, genetics and biochemistry, the network level analysis requires gathering high throughput data with a view to building, testing, and refining models of network structure.  We collaborate closely with the Falciani group on this aspect of our work.  The routes through which stresses are detected, and how that information is passed on and integrated to produce an adaptive response, are particular current interests

Francesco Falciani (Honoraray Professor)

Our group is primarily interested in deciphering the complex biological processes underlying Cancer and Chronic Inflammation. Although apparently different, these two pathological processes share many characteristics and in many scenarios coexist in a pathological situation.

We predominantly use a systems biology approach, which starts from the identification of important molecular components and aims to infer the underlying structure of the molecular networks connecting these components. For this reason we are highly interdisciplinary group which develop and apply a wide range of computational and experimental approaches.

The group includes people with a theoretical physics, computer science, Bioinformatics and Biology backgrounds. We also have a strong interest in Environmental Biology where we have pioneered the application of advanced statistical modeling and network inference techniques for the development of mechanistic biomarkers of environmental pollution.