Genome Organization & Subnuclear Phenomena I: Organizational Principles

Presentations

• The three-dimensional architecture of the human genome: understanding the physical mechanisms controlling gene expression

  ORAL · Invited

  March 6, 2024, 4:00 PM – March 6, 2024, 4:36 PM

  Publication: "Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense
  mechanical cues," Nat. Commun. 14, art. no. 326 (2023), V.G. Contessoto, O. Dudchenko, E.L.
  Aiden, P.G. Wolynes, J.N. Onuchic and M. Di Pierro.
  
  "Uncovering the Statistical Physics of 3D Chromosomal Organization Using Data-Driven Modeling,"
  Curr. Opin. Struct. Biol. 75 , art. no. 102418 (2022), V.G. Contessoto, R. Cheng and J.N.
  Onuchic.
  
  "Exploring Chromosomal Structural Heterogeneity Across Multiple Cell Lines,"
  eLife 9, art. no. e60312 (2020), R.R. Cheng, V. Contessoto, E. Lieberman Aiden, P.G. Wolynes,
  M. Di Pierro and J.N. Onuchic.

  Presenters

  • Jose N Onuchic

    Rice University

  Authors

  • Jose N Onuchic

    Rice University

  View abstract →

• Machine learning-based parametrization of a chromatin polymer model

  ORAL

  March 6, 2024, 4:36 PM – March 6, 2024, 4:48 PM

  Publication: Machine learning-based parametrization of a chromatin polymer model (in preparation)

  Presenters

  • Eric Schultz

    University of Chicago

  Authors

  • Eric Schultz

    University of Chicago

  • Soren C Kyhl

    University of Chicago

  • Rebecca Willett

    University of Chicago

  • Juan J De Pablo

    University of Chicago

  View abstract →

• From Effective Interactions Extracted Using Hi-C Data to Chromosome Structures in Conventional and Inverted Nuclei

  ORAL

  March 6, 2024, 4:48 PM – March 6, 2024, 5:00 PM

  Publication: PRX Life 1, 013010 (2023)

  Presenters

  • Sucheol Shin

    University of Texas at Austin

  Authors

  • Sucheol Shin

    University of Texas at Austin

  • Guang Shi

    University of Texas at Austin, University of Illinois at Urbana-Champaign

  • Devarajan Thirumalai

    University of Texas at Austin, Department of Chemistry and Physics, The University of Texas at Austin, Austin 78712, UT Austin

  View abstract →

• Illuminating the link between nuclear geometry and chromatin structure dynamics through 4D nucleus modeling

  ORAL

  March 6, 2024, 5:00 PM – March 6, 2024, 5:12 PM

  Publication: 4D Mesoscale liquid model of nucleus resolves chromatin's radial organization, https://doi.org/10.1101/2023.09.21.558819

  Presenters

  • Rabia Laghmach

    Iowa State University

  Authors

  • Rabia Laghmach

    Iowa State University

  • Michele Di Pierro

    Northeastern University

  • Davit Potoyan

    Iowa State University

  View abstract →

• Data-Driven Simulation of Chromatin Structure and the Epigenetic Code

  ORAL

  March 6, 2024, 5:12 PM – March 6, 2024, 5:24 PM

  Presenters

  • Soren C Kyhl

    University of Chicago

  Authors

  • Soren C Kyhl

    University of Chicago

  • Juan J De Pablo

    University of Chicago

  View abstract →

• A wave pinning model for spread of chromosomal inactivation

  ORAL

  March 6, 2024, 5:24 PM – March 6, 2024, 5:36 PM

  Presenters

  • Shibashis Paul

    University of Tennessee

  Authors

  • Shibashis Paul

    University of Tennessee

  • Tian Hong

    University of Tennessee, Knoxville

  View abstract →

• Activity-driven chromatin organization during interphase: compaction, segregation, and overlap suppression

  ORAL

  March 6, 2024, 5:36 PM – March 6, 2024, 5:48 PM

  Publication: Manuscript in preparation

  Presenters

  • Brian Chan

    Duke University

  Authors

  • Brian Chan

    Duke University

  • Michael Rubinstein

    Duke University

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• Cohesin distribution encodes chromatin 3D organization via conserved-current loop extrusion

  ORAL

  March 6, 2024, 5:48 PM – March 6, 2024, 6:00 PM

  Publication: Tianyu Yuan, Hao Yan, Kevin C. Li, Ivan Surovtsev, Megan C. King, Simon G. J. Mochrie. Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion. bioRxiv 2023.10.05.560890; doi: https://doi.org/10.1101/2023.10.05.560890

  Presenters

  • Tianyu Yuan

    Yale University

  Authors

  • Tianyu Yuan

    Yale University

  • Hao Yan

    Yale University

  • Kevin C Li

    Yale University

  • Ivan Surovtsev

    Yale University

  • Megan C King

    Yale University

  • Simon G Mochrie

    Yale University

  View abstract →

• Loop extrusion with dynamic barriers explains genome folding for long-lived cohesin mutants

  ORAL

  March 6, 2024, 6:00 PM – March 6, 2024, 6:12 PM

  Presenters

  • Hadi Rahmaninejad

    Virginia Tech, University of Southern California

  Authors

  • Hadi Rahmaninejad

    Virginia Tech, University of Southern California

  • Maxime Tortora

    University of Southern California

  • Geoffrey Fudenberg

    University of Southern California

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• Polymer loop extrusion with motor-motor bypassing can explain mitotic chromosome elasticity

  ORAL

  March 6, 2024, 6:12 PM – March 6, 2024, 6:24 PM

  Presenters

  • Edward J Banigan

    Massachusetts Institute of Technology

  Authors

  • Edward J Banigan

    Massachusetts Institute of Technology

  • John F Marko

    Northwestern University

  • Leonid A Mirny

    Massachusetts Institute of Technology MIT

  View abstract →