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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Dear enthusiasts of the SLAAM seminars,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">We invite you to join us for the next Soft Living Active and Adaptive Matter (SLAAM) seminar, to be given by <b>Dr. Guang Shi
</b>(University of Illinois at Urbana-Champaign) on <b>Monday, Sep 26</b> at <b>9 am Pacific/12 noon Eastern/11am Central time</b>.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">Title: <b>Data-driven reconstruction of 3D genome from experimental data<o:p></o:p></b></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">[<a href="https://physics.ucmerced.edu/sites/physics.ucmerced.edu/files/page/documents/guang_shi_slaam.pdf">flyer</a>]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">The Zoom information for this talk is:<o:p></o:p></span></p>
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<span style="font-size:12.0pt;color:black"><a href="https://ucmerced.zoom.us/j/92693607475?pwd=TnI5dDhRRnYvejNZK2xNN0s4M0R5UT09" title="https://ucmerced.zoom.us/j/92693607475?pwd=TnI5dDhRRnYvejNZK2xNN0s4M0R5UT09"><span style="color:#0563C1">https://ucmerced.zoom.us/j/92693607475?pwd=TnI5dDhRRnYvejNZK2xNN0s4M0R5UT09</span></a><o:p></o:p></span></p>
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<span style="font-size:12.0pt;color:black">Meeting ID: 926 9360 7475<o:p></o:p></span></p>
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<span style="font-size:12.0pt;color:black">Passcode: 223642<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">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 <a href="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=" title="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=NK4EGo1VvrDiYSxdvOUJXgCk">here</a> to
register your interest to give a talk (postdocs only) and to receive these notifications.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt">Abstract:<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:12.0pt">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:12.0pt">About the speaker:</span></b><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">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.</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal">Best regards,<o:p></o:p></p>
<p class="MsoNormal">Dan Beller<o:p></o:p></p>
<p class="MsoNormal">on behalf of the SLAAM organizing team<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> <span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica;color:black">Daniel Beller<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica;color:black">Assistant Professor<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica;color:black">Department of Physics and Astronomy<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica;color:black">Johns Hopkins University<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica;color:black">pages.jh.edu/dbeller3<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica;color:black">(he/him/his)</span><span style="font-size:12.0pt"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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