===========================
How to cite **OpenMiChroM**
===========================

Please acknowledge the use of this software within the body of your publication for example by copying or adapting the following formulation:

*The chromatin dynamics simulations were performed using Open-MiChroM package[1].*

  Open-MiChroM - [1] Oliveira Jr, A. B., Contessoto, V. G., Mello, M. F., & Onuchic, J. N. (2020). A scalable computational approach for simulating complexes of multiple chromosomes. Journal of Molecular Biology, 433(6), 166700.

  Optimization - [2] Oliveira Jr, A. B., et al. “Chromosome Modeling on Downsampled Hi-C Maps Enhances the Compartmentalization Signal.” The Journal of Physical Chemistry B, vol. 125, no. 31, Aug. 2021, pp. 8757–67.

  CNDB file format - [3] Contessoto, Vinícius G, et al. “The Nucleome Data Bank: Web-Based Resources to Simulate and Analyze the Three-Dimensional Genome.” Nucleic Acids Research, vol. 49, no. D1, Jan. 2021, pp. D172–82.  

  Pulling Simulations - [4] Ruben, Benjamin S., et al. “Structural Reorganization and Relaxation Dynamics of Axially Stressed Chromosomes.” Biophysical Journal, Mar. 2023.


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>

The paper are available online at:

[1] `Journal of Molecular Biology (JMB) <https://www.sciencedirect.com/science/article/pii/S0022283620306185>`_.

[2] `Journal of Physical Chemistry B (JPCB) <https://pubs.acs.org/doi/full/10.1021/acs.jpcb.1c04174>`_.

[3] `Nucleic Acids Research (NAR) <https://academic.oup.com/nar/article/49/D1/D172/5918320>`_.

[4] `Biophysical Journal (BJ) <https://www.sciencedirect.com/science/article/pii/S0006349523002023?via%3Dihub>`_.




To cite these references, you can use the following BibTeX entry:

.. code-block:: bibtex

    @article{OpenMiChroM_2020,
      title={A scalable computational approach for simulating complexes of multiple chromosomes},
      author={Oliveira Jr, Antonio B  and 
      Contessoto, Vinicius G and 
      Mello, Matheus F and 
      Onuchic, Jose N},
      journal={Journal of Molecular Biology},
      volume={433},
      number={6},
      pages={166700},
      year={2020},
      publisher={Elsevier}
      doi = {https://doi.org/10.1016/j.jmb.2020.10.034},
    }

    @article{OpenMiChroM_Opt_2021,
    title = {Chromosome {{Modeling}} on {{Downsampled Hi-C Maps Enhances}} the {{Compartmentalization Signal}}},
    author = {Oliveira Junior, Antonio B. and Estrada, Cynthia Perez and Aiden, Erez Lieberman and Contessoto, Vin{\'i}cius G. and Onuchic, Jos{\'e} N.},
    year = {2021},
    month = aug,
    journal = {The Journal of Physical Chemistry B},
    volume = {125},
    number = {31},
    pages = {8757--8767},
    publisher = {{American Chemical Society}},
    issn = {1520-6106},
    doi = {10.1021/acs.jpcb.1c04174},
    }

    @article{NucleomeDataBank_2021,
      title = {The {{Nucleome Data Bank}}: Web-Based Resources to Simulate and Analyze the Three-Dimensional Genome},
      shorttitle = {The {{Nucleome Data Bank}}},
      author = {Contessoto, Vin{\'i}cius G and Cheng, Ryan R and Hajitaheri, Arya and {Dodero-Rojas}, Esteban and Mello, Matheus F and {Lieberman-Aiden}, Erez and Wolynes, Peter~G and Di~Pierro, Michele and Onuchic, Jos{\'e} N},
      year = {2021},
      month = jan,
      journal = {Nucleic Acids Research},
      volume = {49},
      number = {D1},
      pages = {D172-D182},
      issn = {0305-1048},
      doi = {10.1093/nar/gkaa818},
    }

    @article{Pulling_2023,
      title = {Structural Reorganization and Relaxation Dynamics of Axially Stressed Chromosomes},
      author = {Ruben, Benjamin S. and Brahmachari, Sumitabha and Contessoto, Vin{\'i}cius G. and Cheng, Ryan R. and Oliveira Junior, Antonio B. and Di Pierro, Michele and Onuchic, Jos{\'e} N.},
      year = {2023},
      month = mar,
      journal = {Biophysical Journal},
      issn = {0006-3495},
      doi = {10.1016/j.bpj.2023.03.029},
      urldate = {2023-04-05},
      langid = {english}
    }