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RESEARCH PROJECTS

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Analysis of condensate specificity by coevolution and Artificial Intelligence | Dr. Qian Cong

Methods to model interactions between IDRs are currently lacking. We use evolutionary analyses and AI to determine how weak and non-stereospecific interactions between IDRs promote LLPS and encode specificity.

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High-throughput microfluidic platforms to study condensate specificity | Dr. Michael Rosen

We are developing microfluidic technologies to quantify partitioning of large IDR/CCR libraries (~7,500 proteins of 100 residues) into condensates  to learn sequence rules that dictate partitioning.

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Dissection of inter-IDR interactions driving condensation of licensing factors | Dr. Matthew Parker

The IDRs of fly Orc1, Cdc6, and Cdt1—essential factors for DNA replication licensing—drive DNA-dependent phase separation, manifesting as a chromosome-coating protein layer in vivo. The molecular rules governing the specificity of licensing factor co- condensation are unknown. 

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High-resolution mapping of condensate interactions using chemical crosslinking with mass spectrometry (XL-MS) |Dr. Jeff Woodruff

Condensates contain large, disordered proteins that are difficult to analyze by traditional structural methods. To probe condensate structure, we have developed an XL-MS approach that captures physiological contacts between oppositely charged residues (K and D/E).
 

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Identification of proteins that co-partition into transcriptional condensates in extracts and cells | Dr. Ben Sabari

Activating DNA transcription is a multi-step process requiring the coordination of dozens of proteins. How these proteins assemble with each other at the correct locus and at the right time is unclear. We use two methods to characterize the natural composition of condensates: 1) reconstituting condensates in vitro in the presence of a nuclear extract and 2) proximity biotinylation to capture condensate-mediated interactions in situ.

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