References¶
Antonio B. Oliveira Junior, Vinícius G. Contessoto, Matheus F. Mello, and José N. Onuchic. A Scalable Computational Approach for Simulating Complexes of Multiple Chromosomes. Journal of Molecular Biology, 433(6):166700, March 2021. URL: https://linkinghub.elsevier.com/retrieve/pii/S0022283620306185 (visited on 2021-05-15), doi:10.1016/j.jmb.2020.10.034.
Michele Di Pierro, Bin Zhang, Erez Lieberman Aiden, Peter G. Wolynes, and José N. Onuchic. Transferable model for chromosome architecture. Proceedings of the National Academy of Sciences, 113(43):12168–12173, October 2016. URL: http://www.pnas.org/lookup/doi/10.1073/pnas.1613607113, doi:10.1073/pnas.1613607113.
Vinícius G Contessoto, Ryan R Cheng, Arya Hajitaheri, Esteban Dodero-Rojas, Matheus F Mello, Erez Lieberman-Aiden, Peter G Wolynes, Michele Di Pierro, and José N Onuchic. The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome. Nucleic Acids Research, 49(D1):D172–D182, January 2021. URL: https://academic.oup.com/nar/article/49/D1/D172/5918320, doi:10.1093/nar/gkaa818.
Ryan R Cheng, Vinicius G Contessoto, Erez Lieberman Aiden, Peter G Wolynes, Michele Di Pierro, and Jose N Onuchic. Exploring chromosomal structural heterogeneity across multiple cell lines. eLife, 9:e60312, October 2020. URL: https://elifesciences.org/articles/60312, doi:10.7554/eLife.60312.
Bin Zhang and Peter G. Wolynes. Topology, structures, and energy landscapes of human chromosomes. Proceedings of the National Academy of Sciences, 112(19):6062–6067, May 2015. URL: http://www.pnas.org/lookup/doi/10.1073/pnas.1506257112, doi:10.1073/pnas.1506257112.
We also thank the polychrom <https://github.com/open2c/polychrom>, where part of this code was inspired. You can use this citation <https://zenodo.org/records/3579473>