Current Grants
My group is currently involved in a number of different grants and collaborations, here’s a quick list.
Rat Genome Database - Established almost 10 years ago, the Rat Genome Database (RGD) is the model organism database for the laboratory rat. I’m one of the co-investigators on the RGD grant along with Howard Jacob, Mindy Dwinell and Diane Munzenmaier. RGD provides a single place for researchers using the rat as a model system to find information for their research. This includes rat genes (where they are in the rat genome, what they do, associations with known genetic diseases), genetic markers, rat strains and much more.
Gene Ontology Consortium - The Gene Ontology Consortium (or GO) has also been going over 10 years and is leading the way in the development and widespread use of controlled vocabularies in the biological sciences. Why does this matter? Its really hard to find and compare data when its all called something different. GO provides a controlled vocabulary that allows us to consistently describe what a gene does, where it lives in the cell and what processes its involved in. When this is being done for many of the model organisms being used for research it provides a common framework for data analysis. I’m a Co-investigator on this grant and we’re funded to support the GO annotation of rat genes.
Ontological Annotation of large scale data repositories - In a collaboration with the National Center for Biomedical Ontology (NCBO) at Stanford we are exploring the use of biomedical ontologies as a way to get more information out of the Gene Expression Omnibus (GEO) expression database. We are a ‘driving biological project’ for the NCBO and we’re making extensive use of their webservices as a framework upon which we can build tools and datasets that tackle a number of issues related to finding and using the data stored in the GEO database. Our project website has more information on this grant and its progress. We’re also creating a series of educational videos introducing the basic
NHLBI National Proteomics Center - Housed within MCW’s Biotechnology and Bioengineering Center the goals of the proteomics project are to push technology development in the area of mass spec proteomics. This is a collaboration between MCW (Andy Greene, Mike Olivier, Simon Twigger), UW Madison (Lloyd Smith, mass spec technology development) and UNC (Mike Ramsey, Microfluidics). As the bioinformatics component of the grant we’ve been building a variety of analytical tools, data pipelines and compute resources to accelerate the analysis and interpretation of mass spec data. These tools include ZoomQuant (perl/Tk application for quantitation of stable isotope labelled proteins), Apropos (web application for annotation of protein/gene lists), ViPDAC (Virtual proteomics data analysis cluster, built using the Amazon EC2 and S3 cloud computing platform) and others (see proteomics website for more complete list, links to downloads, etc.)
Bioinformatics core for Stem Cell proteomics - Building from our work with Lloyd Smith’s group as part of the NHLBI proteomics center, we are collaborating with Lloyd’s group on another proteomics project. This is an exciting collaboration with Drs Jamie Thomson and Josh Coon at UW Madison investigating human stem cell development. We are bringing our bioinformatics tools to help analyze and interpret the proteomics and expression data being generated as the UW researchers explore the molecular pathways that determine the processes involved in stem cell differentiation.
Intermine Data Warehouse and Data Mining for the Rat - In a collaboration with Gos Micklem (U. Cambridge, UK), Mike Cherry (Saccharomyces Genome Databse, Stanford, CA) and Monte Westerfield (Zfin database, Eugene, OR) we are building an Intermine data mining environments for Rat, Yeast and Zebrafish. Gos’s group developed Intermine as a data warehouse to allow rapid access to complex genomic datasets. Intermine was initially used to develop Flymine (Drosophila/Fruit Fly data) and is now in use for the modEncode project to provide access to these complex datasets as they emerge from the labs. We are being funded by the National Human Genome Research Institute (NHGRI) to develop Intermines for the Rat, Yeast and Zebrafish communities. You can use Ratmine as it develops during the course of this grant.
Wisconsin Center of Excellence in Genomic Science - Funded in autumn 2009, the WisconsinCEGS is a collaboration between the Medical College of Wisconsin, University of Wisconsin-Madison and Marquette University to focus on identifying regulatory mechanisms that turn genes on and off and determine how they may be altered by critical biological processes, diseases or environmental factors. We will be developing novel technologies to identify the proteins that bind to particular DNA regions. Our ultimate goal is to develop a toolbox that can be used to better understand the relationship between changes in protein-DNA interactions and the underlying complex machinery controlling genes. My group is applying our proteomics informatics tools, platforms such as Intermine plus building custom software as needed to help analyze and interpret our protein-DNA data.
