Research
Structural Bioinformatics
Predict the structures of proteins from gene-encoded sequences and investigate the interactions between proteins and ligands such as DNA, peptides, small molecules and other proteins for drug discovery.
Data Integration & Mining
The Biofacets project is a data integration system for biological databases that presents researchers with a uniform interface towards accessing biological databases, and promotes the use of biological facets or categories to help researchers explore the wealth of data available. In addition to addressing the popular data integration issues, Biofacets proposes a unique approach to providing on the fly categorization of query results returned by remote data sources. Biofacets presents researchers with a great opportunity to facilitate and guide routine data search queries of both literature and scientific databases; using query expansion and refinement supported by its unique biological facet-based browsing capabilities.
BioMap
The biomedical literature databases continue to grow rapidly with vital information that is important for conducting sound biomedical research. BioMap is an attempt to create a scalable knowledgebase of biological relationships from vast amount of literature data. The development of BioMap system addresses several innovative research issues related to knowledge discovery from literature documents and real-time, interactive access of this knowledge.
Gene Regulation & Networks
Regulation of genes is a fundamental phenomenon that provides temporal and spatial specificity of gene expression. Immune system is a good model for studying gene regulation due to its prominent role in development and inherent, complex gene expression paradigms. Computational approaches to explore immune system genes and developmental stages include pattern discovery, network inference and ontology mapping tools, and database management methodologies. We employ these and other bioinformatic methods to analyze the critical role of transcriptional regulation in the immune system.
Metabolomics
Studying the structural basis for protein function helps in the rational design of drugs that attack specific biological pathways. Metabolomics allows for the focused study of cell phenotypes with regards to disease and drug treatment, and the discovery of novel metabolic pathways.
Intrinsically Disordered Proteins
The standard view is that a protein must first fold into a 3D structure to create an active site, and then this active site carrys out molecular recognition via the lock and key or via the induced fit mechanism. While the lock and key or induced fit mechanisms are true for enzymes, these mechanisms are not true for many proteins and protein regions involved in signaling and regulation. For many of the latter proteins and regions, the amino acid sequence codes for intrinsically disordered ensembles that display dynamic, rapidly interconverting conformations. We are using bioinformatics to gain a comprehensive view of the roles of intrinsically disordered proteins in living cells.
Systems Biology & Personalized Medicine
Systems Biology is one of the core technologies that can be developed to bridge the gap between information acquired in the post-genome era and new products for tailored clinical care—Personalized medicine. For Systems Biology, we refer to the simultaneous experimental measurement of global changes in perturbed biological systems at multiple scales, particularly at the molecular interaction network level, to understand and predict how biological systems behave. For Personalized Medicine, we refer to the application of cost-effective and individualized strategies for diagnosing, monitoring, and treating diseases.
Dow AgroSciences
Our capacity as scientists to generate data in pursuit of new chemical and biological solutions has never been greater. Integrating that information and translating it into knowledge is a major hurdle in many organisations, particularly in light of new and emergent technologies. Our goal as a group is to work with scientists to demystify the many systems and tools they encounter in their daily work and help them make better decisions more rapidly.
Discovery Target Assessment Tool
The amount of scientific knowledge and information continues to rapidly increase. It is becoming increasingly difficult for scientists to make good, timely decisions based on all the relevant information as these data are scattered in many different locations, of various quality, possibly out of date, and simply not known to the scientist. My interests are in identifying and driving the key scientific questions that need to be answered and being able to integrate the information from the appropriate sources in a way that is intuitive to the scientist. One way that this is done is by using the Life Sciences Grid http://sourceforge.net/projects/lsg/ in the Discovery Target Assessment Tool, which asynchronously fires many plugins providing a myriad of content, yet lets a scientist click on a question of interest and the answering plugin is surfaced.
