Superfund Research Program
Bioinformatics and Molecular Modeling Core
Project Summary (2017-2020)
The Boston University Superfund Research Program (BU SRP) Center Bioinformatics and Molecular Modeling Research Support Core (BMMC) offers computational tools, expertise, and services in three areas:
- Analysis of data obtained by high throughput genomic technologies (microarray and RNA-sequencing experiments), and integration with public data repositories. Three of the five BU SRP Center research projects employ oligonucleotide arrays or high-throughput sequencing (HTS) methods to determine the genomic and epigenomic effects of Superfund chemicals.
- High-throughput in vitro screening of chemicals, and modeling of the association of their transcriptional responses with adverse phenotypes and with other perturbations.
- Modeling the interactions between xenobiotics and protein receptors using methods of structural bioinformatics and computational toxicology, including some tools originally developed by the BMMC for structure-based drug design. The analyses focus on aryl hydrocarbon receptor (AHR) and AHR-interacting protein (AIP) and on nuclear receptors peroxisome proliferator activated receptor γ (PPARγ) and retinoid X receptor (RXR), as well as cytochrome P450 enzymes in fish.
While the projects generate information on the effects of various chemicals on cells and whole organisms, computational studies of receptor-ligand interactions help to develop hypotheses on the mechanisms at the molecular level and to design specific binding and activity experiments for validation.
The Core is 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 interaction 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. Core researchers analyze microarray and HTS 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. Trainee involvement in the Core also is facilitated through the BU SRP Training Core.