Shayan Bordbar

PhD, University of Illinois at Urbana–Champaign

Title

Applying Sequence to expression modeling to experiment design and analysis

Abstract

DNA sequence consists of coding and non-coding region. Coding regions are transcribed to mRNA and later translated to proteins, but the role of non-coding region which forms nearly 98% of the total DNA is not clear. Parts of non-coding region that contain binding sites for proteins called transcription factors (TFs) are known as enhancers. Enhancers are known to regulate the expression of nearby genes. We use Thermodynamic models to explain the expression of one gene based on the sequence of its enhancer, the relative concentration of its relevant TFs and known binding sites for each TF. Modeling approach leads to an ensemble of models in agreement with current data. In order to constrain the ensemble, we choose variants that distinguish our models the most and test them experimentally using massively parallel reporter assays. Refining the models using the experimental results helps us to unravel the complex regulatory network governing the expression of gene of interest.

Bio

I earned my Bachelors and Masters in biotechnology at university of Tehran (2007-2013). I continued my education at university of Illinois in the field of computational neuroscience and earned a master’s degree in molecular and integrative physiology (2013-2015). Afterwards I started my current program in bioinformatics computer science department and University of Illinois in professor Sinha’s group.

Video

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