Superfund Research Program
Research Support Core: Bioinformatics and Molecular Modeling
Project Summary (2012-2017)
The Bioinformatics and Molecular Modeling Research Support Core will offer computational tools, expertise, and services in two areas: (1) the analysis of data obtained by high throughput genomic technologies (e.g. microarray experiments and next generation sequencing), including the reconstruction and visualization of regulatory pathways; and (2) modeling the interactions between xenobiotics and protein receptors, primarily nuclear receptors and cytochrome P450s, using methods of structural bioinformatics and computational biology, including some tools originally developed for structure-based drug design. Five of seven research projects ofthis proposal employ oligonucleotide arrays, cDNA microarrays, or next generation sequencing (NGS) methods to determine the genomic and epigenomic effects of xenoestrogens, as well as molecular modeling and structural bioinformatics methods to study interactions between environmental pollutants and protein receptors.
The Core will be a full-service bioinformatics and molecular modeling research support center for the statistical analysis and interpretation of genomic data and for the design of receptor-ligand interactions studies, providing the computational infrastructure to deal with large amounts of data and manage a large variety of bioinformatics, statistical, and molecular modeling software tools. The Core Director has a decadelong experience in the design and development of computational methods for the analysis and integration of genomic data, and will direct a full-time research faculty member with similar training. They will analyze microamay and NGS data, working together with graduate students and post-doctoral fellows from the individual projects, who will gain direct, first hand training in these techniques and methods through their interaction with the Core. The Core Co-Project Leader is an expert in molecular modeling, and will work with a postdoctoral associate on modeling interactions between environmental pollutants and protein receptors as required by the BUSRP projects.