Associate Professor of Bioinformatics and Computational Biology
Normal and abnormal development: Simplifying and understanding its Complexity
My group works on discovery of genes, pathways and processes that cause diseases, and in the more effective provision of suitable therapies to address them. We develop and apply standards, computational systems, methods, and collaborative infrastructures to deliver discoveries and solutions. We make it possible to more broadly compare and integrate experimental data. We standardize the way experiments are named, and the way that the molecular data within them is represented. We make these standardized experimental resources available and searchable – resulting in discoveries by ourselves, collaborators and the community. We apply these integrative approaches to understand stem cell development, cancers and complex disease systems.
We need to figure out what the overall functional state of the cell is at the developmental snapshot we are taking. If we can do that then its possible to compare functional states – which are made up of the sum of the assay activities we are performing already, and draw the conclusions accordingly.
Standardizing experimental descriptions to enable discovery
My group has helped develop and has applied a new standard for experimental description, ISA-Commons at the Harvard Stem Cell Institute (HSCI) to yield understanding of stem cell experimental relationships. The approach has been adopted by more than 20 institutions world wide, and is rapidly becoming embedded into the standards for use across genomics – read the publication. The HSCI Stem Cell Commons, a project that I lead, uses this system to share experimental information between its 221 laboratories at Harvard. The Stem Cell Commons provides a new set of tools to group experiments based upon shared phenotypic and molecular attributes. The commons provides a sharing environment for data, and this sharing environment results in the ability to search and find novel relationships. The ability to share information about experiments, and the molecular profiles they contain, is a goal of major disease and genomics projects.
My group works at the School of Public Health and at the SA National Bioinformatics Insitute, University of Western Cape near Cape Town, South Africa.