Primary literature
Flores et al. 2026 — STRS paper (ChromSimPipe use case). Data: GEO GSE310051 (Hi-C), GSE310047 (CUT&Tag).
Fudenberg G, Imakaev M, Lu C, Goloborodko A, Abdennur N, Mirny LA. Formation of Chromosomal Domains by Loop Extrusion. Cell Reports 15(9):2038–2049 (2016). https://doi.org/10.1016/j.celrep.2016.04.085
Banigan EJ, Tang L, van den Berg AA, Stocsits RR, Wutz G, Brandao HB, Busslinger GA, Peters J-M, Mirny LA. Chromosome organization by one-sided and two-sided loop extrusion. eLife 9:e53558 (2020). https://doi.org/10.7554/eLife.53558
Gabriele M, Brandão HB, Grosse-Holz S, Jha A, Dailey GM, Cattoglio C, Hsieh T-HS, Mirny L, Zechner C, Hansen AS. Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging. Science 376(6593):496–501 (2022). https://doi.org/10.1126/science.abn6583
Yang T, Zhang F, Yardımcı GG, Song F, Hardison RC, Noble WS, Yue F, Li Q. HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Genome Research (2017). https://doi.org/10.1101/gr.220640.117
Yang M et al. Polymer simulations reveal a robust chromatin compaction mechanism that enables rapid genome exploration by CTCF and cohesin. Nature Communications 14:1913 (2023). https://doi.org/10.1038/s41467-023-37530-3 (Source of the tiling trick for contact statistics.)