Genome Organization and Subnuclear Phenomena II: Novel Experiments and Computational Methods

Presentations

• Dissecting human gene regulation principles using single-cell measurements and statistical mechanics

  ORAL · Invited

  March 20, 2025, 11:00 AM – March 20, 2025, 11:36 AM

  Publication: Doughty BR*, Hinks MM*, Schaepe* JM, Marinov GK, Thurm AR, Rios-Martinez C, Parks BE, Tan Y, Marklund E, Dubocanin D, Bintu L^, Greenleaf WJ^. Single-molecule states link transcription factor binding to gene expression. Nature. 2024 Nov 20:1-0.<br>https://pubmed.ncbi.nlm.nih.gov/39567683/

  Presenters

  • Lacramioara Bintu

    Stanford University

  Authors

  • Lacramioara Bintu

    Stanford University

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• In Situ Observation of Compressive Forces Experienced by DNA Loci in the Nucleus of Living HeLa Cell

  ORAL

  March 20, 2025, 11:36 AM – March 20, 2025, 11:48 AM

  Presenters

  • Masha Mukhina

    University of Maryland College Park

  Authors

  • Masha Mukhina

    University of Maryland College Park

  • Vincent Tsai

    University of Maryland, College Park

  • Yulia Gromova

    Harvard University

  • Nancy Kleckner

    Harvard University

  View abstract →

• Long-range genomic loci cooperatively form hierarchal chromosome skeleton

  ORAL

  March 20, 2025, 11:48 AM – March 20, 2025, 12:00 PM

  Publication: no

  Presenters

  • Jianhua Xing

    University of Pittsburgh

  Authors

  • Jianhua Xing

    University of Pittsburgh

  • Jingyu Zhang

    University of Pittsburgh

  • Simon C Watkins

    University of Pittsburgh

  • Siyuan Wang

    Yale University

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• Permutation Enhances the Rigor of Single-cell Genomics Data Analysis

  ORAL · Invited

  March 20, 2025, 12:00 PM – March 20, 2025, 12:36 PM

  Publication: Xia, L., Lee, C. & Li, J.J. Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters. Nat Commun 15, 1753 (2024). https://doi.org/10.1038/s41467-024-45891-y<br>​​​​​​​<br>Liu, P. & Li, J.J. mcRigor: a statistical method to enhance the rigor of metacell partitioning in single-cell data analysis. bioRxiv (2024). https://doi.org/10.1101/2024.10.30.621093

  Presenters

  • Jingyi Jessica Li

    UCLA

  Authors

  • Jingyi Jessica Li

    UCLA

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• A machine learning model for CUT&amp;Tag bias correction

  ORAL

  March 20, 2025, 12:36 PM – March 20, 2025, 12:48 PM

  Presenters

  • Chongzhi Zang

    University of Virginia

  Authors

  • Chongzhi Zang

    University of Virginia

  • Shengen Shawn Hu

    University of Virginia

  View abstract →

• Abstract Withdrawn

  ORAL Withdrawn

  March 20, 2025, 12:48 PM – March 20, 2025, 1:00 PM

  View abstract →

• Deciphering regulatory architectures of microbial genomes from synthetic expression patterns

  ORAL

  March 20, 2025, 1:00 PM – March 20, 2025, 1:12 PM

  Publication: Pan RW, Roeschinger T, Faizi K, Garcia H, Phillips R. Deciphering regulatory architectures from synthetic single-cell expression patterns. bioRxiv. 2024. p. 2024.01.28.577658. doi:10.1101/2024.01.28.577658

  Presenters

  • Rosalind Pan

    Caltech

  Authors

  • Rosalind Pan

    Caltech

  • Tom Röschinger

    Caltech

  • Kian Faizi

    Caltech

  • Hernan G. Garcia

    University of California, Berkeley

  • Rob Phillips

    Caltech

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• A biophysically inspired model of transcriptional regulation in hormone signalling

  ORAL

  March 20, 2025, 1:12 PM – March 20, 2025, 1:24 PM

  Presenters

  • Hoda Taeb

    Simon Fraser University

  Authors

  • Hoda Taeb

    Simon Fraser University

  • Tahsin Emirhan Tekoğlu

    Koç University

  • Amin Safaeesirat

    Simon Fraser University

  • Nathan A Lack

    Koç University

  • Eldon Emberly

    Simon Fraser University

  View abstract →

• Deep Learning Framework for G-Quadruplex Stability Prediction

  ORAL

  March 20, 2025, 1:24 PM – March 20, 2025, 1:36 PM

  Publication: This is unpublished work. We are targeting a top tier journal like nature communications.

  Presenters

  • Ee Hou Yong

    Nanyang Technological University

  Authors

  • Ee Hou Yong

    Nanyang Technological University

  • Donn Liew

    Nanyang Technological University

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• Computational modelling of RNA-protein binding interactions under an external force

  ORAL

  March 20, 2025, 1:36 PM – March 20, 2025, 1:48 PM

  Presenters

  • Danielle Wampler

    Ohio State University

  Authors

  • Danielle Wampler

    Ohio State University

  • Ralf Bundschuh

    Ohio State University

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• Optimizing a CRISPR-Cas13d Gene Circuit for Tunable Target RNA Downregulation with Minimal Collateral RNA Cutting

  ORAL

  March 20, 2025, 1:48 PM – March 20, 2025, 2:00 PM

  Publication: Wan, Y., Helenek, C., Coraci, D., & Balázsi, G. (2024). Optimizing a CRISPR-Cas13d gene circuit for tunable target RNA downregulation with minimal collateral RNA cutting. ACS Synthetic Biology.

  Presenters

  • Christopher Helenek

    Stony Brook University (SUNY)

  Authors

  • Christopher Helenek

    Stony Brook University (SUNY)

  • Yiming Wan

    Stony Brook University (SUNY)

  • Damiano Coraci

    Stony Brook University (SUNY)

  • Gabor Balazsi

    Stony Brook University (SUNY)

  View abstract →