APS Logo

Genome Organization and Subnuclear Phenomena III: Measuring and Manipulating Genome Organization

FOCUS · Z06 · ID: 1067822

Presentations

  • Chromosome Modeling on Downsampled Hi-C Enhances Compartmentalization Signal

    ORAL

    –

    Publication: Oliveira Junior, A. B., Contessoto, V. G., Mello, M. F., & Onuchic, J. N. (2021). A Scalable Computational Approach for Simulating Complexes of Multiple Chromosomes. J. Mol. Biol., 433(6), 166700. doi: 10.1016/j.jmb.2020.10.034<br>Oliveira Junior, A. B., Estrada, C. P., Aiden, E. L., Contessoto, V. G., & Onuchic, J. N. (2021). Chromosome Modeling on Downsampled Hi-C Maps Enhances the Compartmentalization Signal. J. Phys. Chem. B, 125(31), 8757–8767. doi: 10.1021/acs.jpcb.1c04174

    Presenters

    • Antonio B Oliveira Jr

      Rice University

    Authors

    • Antonio B Oliveira Jr

      Rice University

    View abstract →

  • A computational model for correcting intrinsic enzymatic biases in chromatin accessibility profiling data

    ORAL

    –

    Publication: Hu, S.S. et al. Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA. Nature Communications 13, 5533 (2022).

    Presenters

    • Chongzhi Zang

      University of Virginia

    Authors

    • Chongzhi Zang

      University of Virginia

    • Shengen Shawn Hu

      University of Virginia

    View abstract →

  • Live-cell magnetic micromanipulation of a genomic locus reveals interphase chromatin mechanics

    ORAL

    –

    Publication: Keizer et al., Science 377, 489–495 (2022)

    Presenters

    • Simon B Grosse-Holz

      Massachusetts Institute of Technology

    Authors

    • Simon B Grosse-Holz

      Massachusetts Institute of Technology

    • Veer Keizer

      National Cancer Institute, NIH

    • Maxime Woringer

      Institut Curie, Paris, FR

    • Laura Zambon

      Institut Curie, Paris, FR, ESPCI Paris

    • Laura Zambon

      Institut Curie, Paris, FR, ESPCI Paris

    • Laura Zambon

      Institut Curie, Paris, FR, ESPCI Paris

    • Laura Zambon

      Institut Curie, Paris, FR, ESPCI Paris

    • Laura Zambon

      Institut Curie, Paris, FR, ESPCI Paris

    • Vittore Scolari

      Institut Curie, Paris, FR

    • Laura Zambon

      Institut Curie, Paris, FR, ESPCI Paris

    • Edward J Banigan

      Massachusetts Institute of Technology, Department of Physics and Institute of Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139

    • Leonid A Mirny

      Massachusetts Institute of Technology MIT

    • Laura Zambon

      Institut Curie, Paris, FR, ESPCI Paris

    • Daniele Fachinetti

      Institut Curie, Paris, FR

    • Antoine Coulon

      Institut Curie, Paris, FR

    View abstract →

  • Bridging nano- and mesoscale nuclear organization with single-molecule microscopy

    ORAL

    –

    Presenters

    • Yu Shi

      University of North Carolina at Chapel Hill, Department of Biomedical Engineering

    Authors

    • Yu Shi

      University of North Carolina at Chapel Hill, Department of Biomedical Engineering

    • Timothy A Daugird

      University of North Carolina at Chapel Hill, Department of Pharmacology

    • Wesley R Legant

      University of North Carolina at Chapel Hill, Department of Biomedical Engineering

    View abstract →

  • Single-molecule tracking reveals two low-mobility states for chromatin and transcriptional regulators within the nucleus

    ORAL

    –

    Publication: Wagh, K., Stavreva, D.A., Jensen, R.A., Paakinaho, V., Fettweis, G., Schiltz, R.L., Wüstner, D., Mandrup, S., Presman, D.M., Upadhyaya, A. and Hager, G.L., 2022. Single-molecule tracking reveals two low-mobility states for chromatin and transcriptional regulators within the nucleus. bioRxiv.

    Presenters

    • Kaustubh Wagh

      University of Maryland, College Park/NIH

    Authors

    • Kaustubh Wagh

      University of Maryland, College Park/NIH

    • Diana A Stavreva

      NCI, NIH

    • Rikke AM Jensen

      NCI, NIH/University of Southern Denmark

    • Ville Paakinaho

      NCI, NIH/University of Eastern Finland

    • Gregory Fettweis

      NCI, NIH

    • R Louis Schiltz

      NCI, NIH

    • Daniel Wüstner

      University of Southern Denmark

    • Susanne Mandrup

      University of Southern Denmark

    • Diego M Presman

      NCI, NIH/Universidad de Buenos Aires

    • Arpita Upadhyaya

      University of Maryland, College Park

    • Gordon L Hager

      NCI, NIH

    View abstract →

  • Modeling pairing dynamics of homologous chromosomes during Prophase I in Saccharomyces cerivisae using polymer physics

    ORAL

    –

    Publication: Newman, T. A., Beltran, B., McGehee, J. M., Elnatan, D., Cahoon, C. K., Paddy, M. R., ... & Burgess, S. M. (2022). Diffusion and distal linkages govern interchromosomal dynamics during meiotic prophase. Proceedings of the National Academy of Sciences, 119(12), e2115883119.

    Presenters

    • Ariana Tse

      Department of Materials Science, Stanford University

    Authors

    • Ariana Tse

      Department of Materials Science, Stanford University

    • Trent A Newman

      Department of Molecular and Cellular Biology, University of California, Davis

    • Bruno Beltran

      Biophysics Program, Stanford University

    • Sean M Burgess

      Department of Molecular and Cellular Biology, University of California, Davis

    • Andrew J Spakowitz

      Department of Chemical Engineering, Stanford University, Stanford University

    View abstract →

  • Interpretable and tractable probabilistic models for single-cell RNA sequencing

    ORAL

    –

    Publication: Gorin G, Yoshida SR, Pachter L. Transient and delay chemical master equations. bioRxiv; 2022 Oct.<br>Gorin G, Fang M, Chari T, Pachter L. RNA velocity unraveled. PLOS Computational Biology; 2022 Sep.<br>Gorin G, Pachter L. Monod: mechanistic analysis of single-cell RNA sequencing count data. bioRxiv; 2022 Feb.<br>Gorin G, Pachter L. Modeling bursty transcription and splicing with the chemical master equation. Biophysical Journal; 2022 Feb.<br>Gorin G*, Vastola JJ*, Fang M, Pachter L. Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments. bioRxiv; 2021 Sep. <br>Gorin G, Pachter L. Length Biases in Single-Cell RNA Sequencing of pre-mRNA. bioRxiv; 2021 Jul. <br>Gorin G, Pachter L. Intrinsic and extrinsic noise are distinguishable in a synthesis–export–degradation model of mRNA production. bioRxiv; 2020 Sep. <br><br>Planned: <br>Gorin G, Fang M, Pachter L. Modeling RNA dynamics by occupation measures.

    Presenters

    • Gennady Gorin

      California Institute of Technology

    Authors

    • Gennady Gorin

      California Institute of Technology

    • Lior Pachter

      California Institute of Technology, Caltech

    • Meichen Fang

      California Institute of Technology

    • John J Vastola

      Harvard Medical School

    View abstract →