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Citing the Nucleome Data Bank:
NDB
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The Nucleome Data Bank: Web-based Resources to Simulate and Analyze the Three-Dimensional Genome.
Vinícius de Godoi Contessoto, Ryan R. Cheng, Arya Hajitaheri, Esteban Dodero-Rojas, Matheus Faria Mello, Erez Lieberman Aiden, Peter Guy Wolynes, Michele Di Pierro, José Nelson Onuchic Nucleic Acids Research, Oct 2020; DOI: 10.1093/nar/gkaa818
MiChroM
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Transferable model for chromosome architecture.
Michele Di Pierro, Bin Zhang, Erez Lieberman Aiden, Peter G. Wolynes, José N. Onuchic Proceedings of the National Academy of Sciences Oct 2016, 113 (43) 12168-12173; DOI: 10.1073/pnas.1613607113
MEGABASE
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De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture.
Michele Di Pierro, Ryan R. Cheng, Erez Lieberman Aiden, Peter G. Wolynes, José N. Onuchic Proceedings of the National Academy of Sciences Nov 2017, 114 (46) 12126-12131; DOI: 10.1073/pnas.1714980114