- AKR Gene Superfamily Database
EBIC 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.
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.
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.
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.
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.
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).
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.
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.
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. One example of such support is the deployment of a data archive system to transfer HDD stored genetic data to tape for Dr. Sara Tishkoff’s lab.
Informatics Support to CEET Cores
EBIC provides IT and data analysis support to other CEET cores. Our staff has been working with CEET Translational Biomarker Core with experiment data management.