Research Summary:

A fundamental problem in biology is to understand gene regulation on a genome wide scale. The main focus of my research involves studying transcription factors and the regulatory regions in the non-coding portion of the genomes of multiple species in collaborative interdisciplinary projects with life scientists to understand the complex regulation of genes. To further our knowledge of transcriptional regulation, I work on integrating genome wide maps of transcriptional binding sites with other datasets including SNPs, genes, Go terms, and PPI networks.

• Bioinformatics (Genomics, Regulatory Interactions and Networks)
• Data integration
• Data mining
• Machine learning
• Cheminformatics (Ranking and searching small molecules)

Research projects:

Current:

• Analysis of Transcriptional Regulation in Skin Cells Related to Wounding (2011)
• Transcriptional Regulatory Control of Neural Stem Cell Development (2011)
• Analysis of High-Throughput Sequencing Data for Ty3 Transposon Insertion Events in Yeast (2009)
• Building Resources for Analysis of Genome Wide Transcriptional Regulation (2008)

Past:

• Data Structures and Compression Algorithms for High-Throughput Sequencing, 2009
• Similarity Measures for Chemical Searching and Retrieval, 2006
• Prediction of posttranslational protein modifications, (with Predrag Radivojac), 2004-2006
• Analysis of size of duplicated gene families, (with Dennis Groth and Mike Wade), 2003-2004