[Slaam] SLAAM Seminar Monday, Sep 26: Guang Shi (UIUC)

[SLAAM Distribution List]

Dear enthusiasts of the SLAAM seminars,

We invite you to join us for the next Soft Living Active and Adaptive Matter (SLAAM) seminar, to be given by Dr. Guang Shi (University of Illinois at Urbana-Champaign) on Monday, Sep 26 at 9 am Pacific/12 noon Eastern/11am Central time.

Title: Data-driven reconstruction of 3D genome from experimental data
[flyer<https://physics.ucmerced.edu/sites/physics.ucmerced.edu/files/page/documents/guang_shi_slaam.pdf>]

The Zoom information for this talk is:
https://ucmerced.zoom.us/j/92693607475?pwd=TnI5dDhRRnYvejNZK2xNN0s4M0R5UT09
Meeting ID: 926 9360 7475
Passcode: 223642

As usual, there will be a 15 min informal Q&A at the end of the hour. Graduate students will have an opportunity to interact with the speaker in an informal setting during the "Meet the speaker" timeslot just after the talk. Please join if the time works for you. Please sign up here<https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_forms_d_e_1FAIpQLScTyzEuuE7TfrrapgP4tzN-5FoPSqbBhURUxa9-2Dzc8USnY1IPzA_viewform&d=DwMFAw&c=WO-RGvefibhHBZq3fL85hQ&r=6T170XR90Za4-nl9r1e8-WfEJbvH5g5hJbA9UumqfWQ&m=NK4EGo1VvrDiYSxdvOUJXgCkEAzTrQzNpQi-P59LZiKL_lMA3briJm9KQh9Y3suN&s=3hc1lEhiJwBLtMEr12Z9K5XtZaVlEfOZKYXGtXCjRDg&e=> to register your interest to give a talk (postdocs only) and to receive these notifications.

Abstract:
The principles that govern the organization of genomes, which are needed for a deeper understanding of how chromosomes are packaged and function in eukaryotic cells, could be deciphered if the three-dimensional (3D) structures are known. Recently, single-cell imaging experiments have determined the 3D coordinates of a number of loci in a chromosome. Here, we introduce a computational method, based on the maximum entropy principle, with experimental pair-wise distances between loci as constraints, to generate a unique ensemble of 3D chromatin structures. Using the ensemble of structures, we quantitatively account for the distribution of pair- wise distances, three-body co-localization and higher-order interactions. We demonstrate that our method can be applied to both small length-scale and chromosome-scale imaging data to quantify the extent of heterogeneity and fluctuations in the shapes on various length scales. Furthermore, we show that our method can be extended to predict the changes in 3D structures from structural variations. Our method also reveals quantitative differences between the 3D structures inferred from Hi-C and the ones measured in imaging experiments. Finally, the physical interpretation of the parameters extracted from our method provides insights into the origin of phase separation between euchromatin and heterochromatin domains.

About the speaker:
Dr. Guang Shi is a postdoctoral research associate at the University of Illinois at Urbana-Champaign. He is broadly interested in the physical principles that underlie genome organization and biomolecular condensates and their biological functions. He is currently working with Prof. Kenneth S. Schweizer on the phase behavior and rheology of biomolecular condensates using theoretical approaches. Dr. Shi earned his Ph.D. in Biophysics from the University of Maryland at College Park, under the supervision of Prof. Devarajan (Dave) Thirumalai, where he studied the structures and dynamics of the genome using both coarse-grained modeling and data-driven approaches.

Best regards,
Dan Beller
on behalf of the SLAAM organizing team


Daniel Beller
Assistant Professor
Department of Physics and Astronomy
Johns Hopkins University
pages.jh.edu/dbeller3
(he/him/his)

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