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Nucleic Acids Research|November 28, 2023
Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamicsZilong Li, Tamar SchlickBiophysical Journal|September 18, 2022
Brownian dynamics simulations of mesoscale chromatin fibersZilong Li, Stephanie Portillo-Ledesma, Tamar SchlickCurrent Opinion in Cell Biology|July 28, 2023
Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture dataZilong Li, Stephanie Portillo-Ledesma, Tamar SchlickCurrent Opinion in Structural Biology|September 20, 2025
Chromatin higher-order folding as influenced by preferred values of linker DNAZilong Li, Stephanie Portillo-Ledesma, Tamar SchlickCurrent Opinion in Structural Biology|December 28, 2022
Genome modeling: From chromatin fibers to genesStephanie Portillo-Ledesma, Zilong Li, Tamar SchlickBiophysical Journal|August 8, 2025
Molecular dynamics simulations reveal subtle consequences of H3K9 and H3K27 tri-methylation on chromatin constituentsStephanie Portillo-Ledesma, Zilong Li, Tamar SchlickThe Journal of Chemical Physics|March 6, 2025
Incorporating multiscale methylation effects into nucleosome-resolution chromatin models for simulating mesoscale fibersZilong Li, Stephanie Portillo-Ledesma, Moshe Janani, et al.Biophysical Journal|September 3, 2025
What are chromatin fiber topologies for regular nucleosome linker spacing? The influence of 10n and 10n+5 linker lengths explored by mesoscale modelingZilong Li, Stephanie Portillo-Ledesma, Moshe Janani, et al.F1000 Biology Reports|October 16, 2010
Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structureTamar SchlickPageof 47