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Mukhopadhyay, J., Kapanidis, A., Mekler, V., Kortkhonjia, E., Ebright, Y., and Ebright, R. (2001) Translocation of sigma⁷⁰ with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA.  Cell 106, 453-463.

Mekler, V., Kortkhonjia, E., Mukhopadhyay, J., Knight, J., Revyakin, A., Kapanidis, A., Niu, W., Ebright, Y., Levy, R., and Ebright, R. (2002) Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex.  Cell 108, 599-614.

Benoff, B., Yang, H., Lawson, C., Parkinson, G., Liu, J., Blatter, E., Ebright, Y., Berman, H., and Ebright, R. (2002) Structural basis of transcription activation: the CAP-alphaCTD-DNA complex.  Science  297, 1562-1566.

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Revyakin, A., Liu, C., Ebright, R.H. and Strick, T. (2006) Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science 314, 1139-1143.

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Mukhopadhyay, J., Das, K., Ismail, S., Koppstein, D., Jang, M., Hudson, B., Sarafianos, S., Tuske, S., Patel, J., Jansen, R., Irschik, H., Arnold, E., and Ebright, R. (2008) The RNA polymerase "switch region" is a target of inhibitors  Cell 135, 295-307.

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Chakraborty, A., Wang, D., Ebright, Y., Korlann, Y., Kortkhonjia, E., Kim, T., Chowdhury, S., Wigneshweraraj, S., Irschik, H., Jansen, R., Nixon, B.T., Knight, J., Weiss, S., and Ebright, R. (2012) Opening and closing of the bacterial RNA polymerase clamp.  Science 337, 591-595.

Zhang, Y., Feng, Y., Chatterjee, S., Tuske, S., Ho, M., Arnold, E., and Ebright, R. (2012)  Structural basis of transcription initiation.  Science 338, 1076-1080.

Vvedenskaya, I., Vahedian-Movahed, H., Bird, J., Knoblauch, J., Goldman, S., Zhang, Y., Ebright, R., and Nickels, B. (2014) Interactions between RNA polymerase and the "core recognition element" counteract pausing.  Science 344, 1285-1289.

Winkelman, J., Vvedenskaya, I., Zhang, Y., Zhang, Y., Bird, J., Taylor, D., Gourse, R., Ebright, R., and Nickels, B. (2016) Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection.  Science 351, 1090-1093.

Feng, Y., Zhang, Y., and Ebright, R. (2016) Structural basis of transcription activation. Science 352, 1330‑1333.

Bird, J., Zhang, Y., Tian, Y., Panova, N., Barvík, I., Greene, L., Liu, M., Buckley, B., Krásný, L., Lee, J.K., Kaplan, C., Ebright, R., and Nickels, B. (2016) The mechanism of RNA 5′ capping with NAD+, NADH, and desphospho-CoA.  Nature 535, 444-447. 

Maffioli, S., Zhang, Y., Degen, D., Carzaniga, T., Del Gatto, G., Serina, S., Monciardini, P., Mazzetti, C., Guglierame, P., Candiani, G., Chiriac, A.I., Facchetti, G., Kaltofen, P., Sahl, H.-G., Dehò, G., Donadio, S., and Ebright, R.H. (2017) Antibacterial nucleoside-analog inhibitor of bacterial RNA polymerase. Cell 169, 1240-1248.

Wang, C., Molodtsov, V., Firlar, E., Kaelber, J., Blaha, G., Su, M., and Ebright, R.H. (2020) Structural basis of transcription-translation coupling. Science 369, 1359-1365.

Molodtsov, V., Wang, C., Firlar, E., Kaelber, H., and Ebright, R.H. (2023) Structural basis of Rho‑dependent transcription termination. Nature 614, 367–374.