All Stories

  1. Chromatin higher-order folding as influenced by preferred values of linker DNA

    Article • Current Opinion in Structural Biology, December 2025, Elsevier

    Zilong Li

  2. Compromised two-start zigzag chromatin folding in immature mouse retina cells driven by irregularly spaced nucleosomes with short DNA linkers

    Article • Nucleic Acids Research, May 2025, Oxford University Press (OUP)

    Zilong Li

  3. Incorporating multiscale methylation effects into nucleosome-resolution chromatin models for simulating mesoscale fibers

    Article • The Journal of Chemical Physics, March 2025, American Institute of Physics

    Tamar Schlick, Zilong Li

  4. Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics

    Article • Nucleic Acids Research, November 2023, Oxford University Press (OUP)

    Zilong Li

  5. Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data

    Article • Current Opinion in Cell Biology, August 2023, Elsevier

    Zilong Li

  6. Brownian dynamics simulations of mesoscale chromatin fibers

    Article • Biophysical Journal, July 2023, Elsevier

    Zilong Li

  7. Genome modeling: From chromatin fibers to genes

    Article • Current Opinion in Structural Biology, February 2023, Elsevier

    Zilong Li

  8. Some Mathematical Problems Related to the Rubik’s Snake

    Article • Journal of Mechanisms and Robotics, October 2020, ASME International

    Zilong Li

  9. Genome Dashboards: Framework and Examples

    Article • Biophysical Journal, May 2020, Elsevier

    Zilong Li

  10. Computational Design and Analysis of a Magic Snake

    Article • Journal of Mechanisms and Robotics, March 2020, ASME International

    Zilong Li

  11. Genome Dashboards: A Framework for Unifying Informatics and Structure

    Article • Biophysical Journal, February 2020, Elsevier

    Zilong Li

  12. ANERGY TO SYNERGY-THE ENERGY FUELING THE RXCOVEA FRAMEWORK

    Article • International Journal for Multiscale Computational Engineering, January 2020, Begell House

    Zilong Li

  13. Genome dashboards: Framework and Examples

    Article • October 2019, Cold Spring Harbor Laboratory Press

    Zilong Li

  14. TMB Library of Nucleosome Simulations

    Article • Journal of Chemical Information and Modeling, September 2019, American Chemical Society (ACS)

    Zilong Li

  15. TMB-iBIOMES: An iBIOMES-Lite Database of Nucleosome Trajectories and Meta-Analysis

    Article • March 2019, American Chemical Society (ACS)

    Zilong Li

  16. GDash: A Genomics Dashboard Integrating Modeling and Informatics

    Article • Biophysical Journal, February 2019, Elsevier

    Zilong Li

  17. TMB-iBIOMES: A Database of All Atom Simulation and Analysis for Nucleosomes

    Article • Biophysical Journal, February 2019, Elsevier

    Zilong Li

  18. G-Dash: A Genome Dashboard Integrating Modeling and Informatics

    Article • December 2018, Cold Spring Harbor Laboratory Press

    Zilong Li

  19. Interactive Chromatin Modeling with Genome Browser

    Article • Biophysical Journal, February 2017, Elsevier

    Zilong Li

  20. Molecular Dynamics Simulation Workflow for Nucleosome Studies

    Article • Biophysical Journal, February 2017, Elsevier

    Zilong Li