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.
The paper are available online at:
[1] Journal of Molecular Biology (JMB).
[2] Journal of Physical Chemistry B (JPCB).
[3] Nucleic Acids Research (NAR).
To cite these references, you can use the following BibTeX entry:
@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}
}