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Zepeda-Mendoza, C. J., Mukhopadhyay, S., Wong, E. S., Harder, N., Splinter, E., de Wit, E., Eckersley-Maslin, M. A., Ried, T., Eils, R., Rohr, K., Mills, A., de Laat, W., Flicek, P., Sengupta, A. M., Spector, D. L. (November 2015) Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2. BMC Genomics, 16 (1). p. 982. ISSN 1471-2164 (Electronic)1471-2164 (Linking)

Mukhopadhyay, Swagatam, Wigler, Michael, Levy, Dan (March 2015) Simple genetic models for autism spectrum disorder. bioRxiv. 017301.

Nagaraj, V. H., Mukhopadhyay, S., Dayarian, A., Sengupta, A. M. (December 2014) Breaking an Epigenetic Chromatin Switch: Curious Features of Hysteresis in Saccharomyces cerevisiae Telomeric Silencing. PLoS One, 9 (12). e113516. ISSN 1932-6203

Mukhopadhyay, S., Sengupta, A. M. (July 2013) The role of multiple marks in epigenetic silencing and the emergence of a stable bivalent chromatin state. PLoS Computational Biology, 9 (7). e1003121. ISSN 1553-7358 (Electronic)1553-734X (Linking)

Mukhopadhyay, S., Schedl, P., Studitsky, V. M., Sengupta, A. M. (December 2011) Theoretical analysis of the role of chromatin interactions in long-range action of enhancers and insulators. Proceedings of the National Academy of Sciences of the United States of America, 108 (50). pp. 19919-19924. ISSN 0027-8424