Project Summary (2017-2021)

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:

1. 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.
2. High-throughput in vitro screening of chemicals, and modeling of the association of their transcriptional responses with adverse phenotypes and with other perturbations.
3. 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.