Research Interests Overview
ROCK Breast Cancer Knowledge Base
The clinical and pathological heterogeneity of breast cancer has instigated efforts to stratify breast cancer sub-types according to molecular profiles. These profiling efforts are now being augmented by large-scale functional screening of breast tumour cell lines, using approaches such as RNA interference.
ROCKScape and Network/Pathway Analysis
As ROCK expands so must the user interface. We are in the process of creating a robust and intuitive web interface for data searching, submission and analysis.This will include statistical data analysis and meta-analysis workflows, pathway analysis tools, and interactive network visualisation tools: ROCKScape.
Next Generation Sequencing Pipelines and Meta Analysis
Together with the integration of the basic free software analysis pipeline, Cancer Informatics has developed and integrated a range of data analysis solutions. The NGS technology is versatile and can be applied to a range of applications.
Mutex
Systematic integration of related datasets from different sources can be used to generate novel datasets or provide novel perspectives of data. We will use data integration to provide a new level of detail in protein interaction networks by describing the binding interfaces of interacting proteins at residue level, based on high resolution three dimensional structures in the MSD database
Mathematical modelling of specific networks (TANKs and WNT)
The Wnt family of proteins plays a major role in controlling cell proliferation, cell-fate determination and differentiation during embryonic development and adult homeostasis. It has also been suggested that the Wnts activate a number of different signalling pathways.
Molecular Modelling and Drug Docking
The structural modelling of proteins implicated in breast cancer, such as the PI-3 Kinase family is vitally important for the precise understanding of ligand specificity and therefore drug analysis and design. Already a number of successful collaborations have been carried out at Breakthrough.
Sequencing Pipelines and Meta Analysis
Together with the integration of the basic free software analysis pipeline, Cancer Informatics has developed and integrated a range of data analysis solutions.
Integration of Data
We have recently developed a data integration platform, The ROCK database to facilitate mapping and analysis of networks from breast cancer functional and molecular profiling datasets.
