Neva C. Durand, Muhammad S. Shamim, Ido Machol, Suhas S. P. Rao, Miriam H. Huntley, Eric S. Lander, and Erez Lieberman Aiden. "Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments." Cell Systems 3(1), 2016.
Dudchenko, O., Batra, S.S., Omer, A.D., Nyquist, S.K., Hoeger, M., Durand, N.C., Shamim, M.S., Machol, I., Lander, E.S., Aiden, A.P., et al. (2017). De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science. Apr 7; 356(6333):92-95. doi: https://doi.org/10.1126/science.aal3327. Epub 2017 Mar 23.
Neva C. Durand, James T. Robinson, Muhammad S. Shamim, Ido Machol, Jill P. Mesirov, Eric S. Lander, and Erez Lieberman Aiden. "Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom." Cell Systems 3(1), 2016.
Dudchenko, O., Shamim, M. S., Batra, S. S., Durand, N. C., Musial, N. T., Mostofa, R., Pham, M., Glenn St Hilaire, B., Yao, W., Stamenova, E., Hoeger, M., Nyquist, S. K., Korchina, V., Pletch, K., Flanagan, J. P., Tomaszewicz, A., McAloose, D., Pérez Estrada, C., Novak, B. J., … Aiden, E. L. (2018). The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. https://doi.org/10.1101/254797
Rao, S. S., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., & Aiden, E. L. (2014). A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell, 159(7), 1665–1680. https://doi.org/10.1016/j.cell.2014.11.021