- 1. AKR Gene Superfamily DatabaseEBIC staff have worked closely with Drs. David Hyndman and Trevor Penning to develop a AKR gene community resource on aldo-keto reductase genes and enzymes. This is a superfamily of important environmental response genes.
2. Environmental Database Mining and Discovery
EBIC staff are working with CEET investigators to interpret public hydraulic fracturing, cheminformatics, and toxicity databases. we developed a web-based graphical tool which provides an overview of mining activities involving known toxins.
3. Gene-Environment Interactions in Lung Cancer
EBIC staff have worked closely with Drs. Penning, Vachani, and Whitehead to store, clean, manage, and analyze more than 11,000 SNPs in 1918 human subjects with and without lung cancer. A central goal of this study is to identify gene-environment interactions that are predictive of lung cancer susceptibility.
4. In-utero Environment Effect Study with IUGR Rat
EBIC works with Dr. Rebecca Simmons lab to study the mechanism of IUGR on the development of newborn rats by analyzing various NGS data (RNA-seq, Chip-seq, HELP-tag and methylation array data).
- 5. GIS mapping of Community Exposomes
We worked with a group of CEET investigators (Drs. Penning, Wang, Vachani) to conduct GIS mapping of Community Exposomes in the Catchment Area of the Cancer Center which is comprised of 421 zip-codes that are in PA and NJ.
- Epigenetic Signatures of Exposure
The goal of this study is to identify cross-generational epigenetic signatures of environmental exposure in an experimental study of iron-deficient rats. EBIC staff are working with Drs. Simmons and Bartolomei to process and analyze genome-wide methylation data.
- UV Genotoxicity in Caenorhabditis elegans
EBIC staff have assisted Dr. David Raizen in gene expression analysis using C. elegans microarray data. Our goal is to profile gene regulation and study the interaction of environment, sleep and germline.
- Transcriptome Change by BPA and Diabetes
This projects aims to seek changes of transcript expression and methylation levels of rats caused by two conditions (BPA, Diabetes). The gender effect is also considered in this study.
Nanoscale Detection of Hazardous Chemicals
EBIC is actively developing electronic sensors of environmental toxins. These devices integrate aptamer functionalist graphene field effect transistors into microfluid channels and promise to allow inexpensive detection of ultra-low quantities of endocrine disrupting chemicals. Our efforts support circuit design, and signal analysis and device fabrication.
- Methylation Analysis of Diabetes
- Geographic Genetic Variation
We assisted Dr. Sarah Tishkoff with her pilot project by visualizing frequencies of genetic variation across geographic regions using the Flask web framework for Python. This allows us to provide up to date visual images of her data via the web and the core wiki.
6. Gene Environment Interaction Software
EBIC provides scientific programming support focused on the epistatic interaction between genes and environmental factors. Our staff develop and support software to perform gene expression analysis as required to model biological responses to exposure in animal models. EBIC also develops interactive software tools with an aim at making advanced machine learning algorithms available to non-experts.
7. Infrastructure Support
EBIC assists investigators with laboratory related IT program planning, including data capture, backup and security. Our staff engage available IT resources to ensure efficient lab process workflows.
8. Informatics Support to CEET Cores and Pilot projects
EBIC provides IT and data analysis support to other CEET cores and pilot projcts. For example, our staff has been working with CEET Translational Biomarker Core and several pilot projects to provide expert assistance with the detection and characterization of meaningful patterns in complex exposure biology data. To this end technologies ranging from computer programming, database development, data management, artificial intelligence, machine learning and network science and data visualization were utilized.
Completed Projects (selected)
We worked with Dr. Pinney to study transcriptome and methylation profiles in amniocytes exposed to Bisphenol A (BPA) and maternal diabetes.