Research

Protein-DNA Interaction

My lab’s research interest is in the broad area of structural bioinformatics with a major focus on protein-DNA interactions. Protein-DNA interactions play a crucial role in the regulation of gene expression. Knowledge of protein-DNA interactions at the structural-level can provide insights into the mechanisms of gene regulation and can guide the design of novel therapeutic molecules. We aim to address several important questions regarding specific protein-DNA interaction: 1) what are the structural features for specific protein-DNA interaction? 2) can we model specific protein-DNA interactions based on knowledge learned from existing protein-DNA complex models? 3) can we accurately predict transcription factor (TF) binding sites with protein-DNA interaction models (also called structure-based approach)?

Research Funding

NSF Charlotte Research Institute

1. UNC Charlotte Startup fund, 8/2007-6/2010

2. CMC-UNC Charlotte Collaborative Grants Program
“An Integrative Approach to Study the Transcriptional Regulation of ALAS1 by Heme”, Role: Co-PI, 5/2009-5/2010

3. National Science Foundation (NSF), Division of Biological Infrastructure (DBI)
NSF CAREER Award: “CAREER: A Structure-Based Approach to Transcription Factor-binding Site Prediction via Protein-DNA Docking”, Role: PI, 7/2009-9/2015

4. National Science Foundation (NSF), Division of Biological Infrastructure (DBI)
“Collaborative Research: ABI Innovation: Towards high performance flexible transcription factor-DNA docking”, Role: PI, 8/2014-7/2019

5. National Science Foundation (NSF), Division of Graduate Education (DGE)
“EDU: Collaborative: enhancing education in genetic privacy with integration of research in computer science and bioinformatics”, Role: Co-PI (PI-Mindy Shi), 9/2015-8/2019

6. National Institutes of Health (NIH)
“Structural Features of Specificity in Protein-DNA Recognition”, Role: PI, 9/2015-5/2020

7. National Science Foundation (NSF), Division of Biological Infrastructure (DBI)
“IIBR Informatics: Accurate assessment of protein-DNA complex models and applications”, Role: PI, 5/2021-4/2024

8. National Institutes of Health (NIH)
“Investigation of ssDNA binding proteins and protein-ssDNA interactions”, Role:PI, 4/2021-3/2024

9. National Institutes of Health (NIH)
“Synergistic DNA repair genes and sensitivity to radiation therapy in prostate cancer”, Role:Co-PI (PI: Tomida), 7/2021-6/2024