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Qbio Seminar Series-Devesh Bhimsaria

Event Details

When: March 9, 2016, 2:00 PM

Location: 3rd Floor Orchard View Room , Discovery Building

Contact: 608-316-4401, hstampfli@wisc.edu

Devesh Bhimsaria

Devesh Bhimsaria
Department of Biochemistry
Ph.D. Candidate, Electrical Engineering UW-Madison

Protein-DNA Recognition Using Compressed Sensing Approach

Transcription factors are proteins that regulate gene expression by binding to specific DNA sequences. Thus, it is important to identify DNA binding preferences of protein. Different high-throughput methods have been developed to measure in vitro DNA binding to entire sequence spaces. Examples of such methods include Cognate Site Identification (CSI) array and Protein Binding Microarray (PBM).
Importantly, transcription factors with high homology have vital, but difficult to identify differences in their DNA binding preferences. Identifying such differences is critical for discerning biological functions of highly homologous factors. Such differences permit related transcription factors with nearly identical DNA binding domains to regulate different gene networks and manifest different cellular functions. However, computational methods for extracting DNA binding characteristics currently do not have the fidelity to identify these differences. We developed a novel way of representing the data into set of variables called MinSeqs using Compressed Sensing based motif extraction, which enables the detection of subtle differences between related proteins. These differences further can be tested experimentally. We successfully applied our method to micro array based in-vitro binding data and found novel differences between homologous proteins of the homeodomain family of transcription factors.

All QBio sponsored talks take place on Wednesdays at 2:00 p.m. in the 3rd floor Orchard View room of the Discovery Building. Talks are open to the public. Access to the room is via the elevator behind Aldo’s Cafe in the Northeast corner of the building.