Structural basis of archaeal FttA-dependent transcription termination
You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH. Structural basis of archaeal FttA-dependent transcription termination. Nature. 2024. doi: 10.1038/s41586-024-07979-9.

Structural basis of RfaH-mediated transcription-translation coupling
Molodtsov V, Wang C, Zhang J, Kaelber JT, Blaha G, Ebright RH. Structural basis of RfaH-mediated transcription-translation coupling. Nature Structl. Mol. Biol. 2024. doi: 10.1038/s41594-024-01372-w.

Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase
Nova, I., Craig, J., Mazumder, A., Laszlo, A., Derrington, I., Noakes, M., Brinkerhoff, H., Yang, S., Vahedian-Movahed, H., Li, L., Zhang, Y., Bowman, J., Huang, J., Mount, J., Ebright, R.H., and Jens H Gundlach, J., (2024) Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase. Proc. Natl. Acad. Sci. USA 121, e2321017121.

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

Redesign of rifamycin antibiotics to overcome ADP‑ribosylation-mediated resistance
Lan, T., Ganapathy, U., Sharma, S., Ahn, Y.-M.,  Zimmerman, M., Molodtsov, V., Hegde, P., Gengenbacher, M., Ebright, R.H., Dartois, V., Freundlich, J., Dick, T., and Aldrich, C. (2022) Angew. Chem. Intl. Ed. 61, e202211498.

In transcription antitermination by Qlambda, NusA induces refolding of Qlambda to form a nozzle that extends the RNA polymerase RNA-exit channel
Yin, Z., Bird, J., Kaelber, J., Nickels, B., and Ebright, R.H. In transcription antitermination by Qlambda, NusA induces refolding of Qlambda to form a nozzle that extends the RNA polymerase RNA-exit channel. Proc. Natl. Acad. Sci. USA 119, 2205278119, 2022.

Design, synthesis, and characterization of TNP-2198, a dual-targeted rifamycin-nitroimidazole conjugate with potent activity against microaerophilic and anaerobic bacterial pathogens
Ma, Z., He, S., Yuan, Y., Zhuang, Z., Liu, Y., Wang, H., Chen, J., Xu, X., Ding, C., Molodtsov, V., Lin, W., Robertson, G., Weiss, W., Pulse, M., Nguyen, P., Duncan, L., Doyle, T., Ebright, R.H., and Lynch, A. (2022) J. Med Chem. 65, 4481-4495.

Structural and mechanistic basis of sigma-dependent transcriptional pausing
Pukhrambam, C., Molodtsov, V., Kooshkbagh, M., Tareen, A., Vu, H., Skalenko, K., Su, M., Zhou, Y., Winkelman, J., Kinney, J., Ebright, R.H., and Nickels, B. Structural and mechanistic basis of sigma‑dependent transcriptional pausing. Proc. Natl. Acad. Sci. USA 119, e2201301119, 2022

Structural and mechanistic basis of reiterative transcription initiation
Liu, Y., Winkelman, J., Yu, L., Pukhrambam, C., Zhang, Y., Nickels, B., and Ebright, R.H. Structural and mechanistic basis of reiterative transcription initiation. Proc. Natl. Acad. Sci. USA 119, e2115746119, 2022.

Transcription initiation at a consensus bacterial promoter proceeds via a "bind-unwind-load-and-lock" mechanism
Mazumder, A., Ebright, R.H., and Kapanidis, A., Transcription initiation at a consensus bacterial promoter proceeds via a "bind-unwind-load-and-lock" mechanism. eLife 10, e70090, 2021.

Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli
Skalenko, K., Li, L., Zhang, Y., Vvedenskaya, I., Winkelman, J., Cope, A., Taylor, D., Shah, P., Ebright, R.H., Kinney, J., Zhang, Y., and Nickels, B., Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli. Proc. Natl. Acad. Sci. USA 118, e2106388118, 2021.

Structural basis of transcription-translation coupling
Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G, Su M, and Ebright RH, Science 369, 1359-1365, 2020.

XACT-Seq comprehensively defines the promoter-position and promoter-sequence determinants for initial-transcription pausing
Winkelman JT, Pukhrambam C, Vvedenskaya IO, Zhang Y, Taylor DM, Shah P, Ebright RH, and Nickels BE, Molecular Cell 79, 797-811, 2020.

Closing and opening of the RNA polymerase trigger loop
Mazumder A, Lin M, Kapanidis A, and Ebright RH, Proc. Natl. Acad. Sci. USA 117, 15642–15649, 2020

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Li L, Molodtsov V, Lin W, Ebright RH, and Zhang Y, Proc. Natl. Acad. Sci USA 117, 5801-5809, 2020

Structural basis of Q-dependent antitermination
Yin, Z., Kaelber, J., and Ebright, R.H., Proc. Natl. Acad. Sci. USA 116, 18384-18390, 2019

Structural basis of ECF-σ-factor-dependent transcription initiation
Lin, W., Mandal, S., Degen, D., Cho, M., Feng, Y., Das, K., and Ebright, R.H., Nature Commun. 10, 710, 2019

Structural basis of transcription inhibition by fidaxomicin (lipiarmycin A3)
Lin W, Das K, Degen D, Mazumder A, Duchi D, Wang D, Ebright YW, Ebright RY, Sineva E, Gigliotti M, Srivastava A, Mandal S, Jiang Y, Liu Y, Yin R, Zhang Z, Eng ET, Thomas D, Donadio S, Zhang H, Zhang C, Kapanidis AN, Ebright RH, Molecular Cell 7:60-71, 2018

Antibacterial nucleoside-analog inhibitor of bacterial RNA polymerase
Maffioli S, Zhang Y, Degen D, Carzaniga T, Del Gatto G, Serina S, Monciardini P, Mazzetti C, Guglierame P, Candiani G, Chiriac AI, Facchetti G, Kaltofen P, Sahl HG, Dehò G, Donadio S, Ebright RH, Cell 169:1240-1248, 2017 

Structural basis of Mycobacterium tuberculosis transcription and transcription inhibition
Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M, Talaue M, Connell N, Das K, Arnold E, Ebright RH, Molecular Cell 66, 169-179, 2017

Affinity selection-mass spectrometry identifies a novel antibacterial RNA polymerase inhibitor
Walker, SS, Degen D, Nickbarg E, Carr D, Soriano A, Mandal M B, Painter RE, Sheth PR, Xiao L, Sher X, Murgolo N, Su J, Olsen DB, Ebright RH, Young K., ACS Chemical Biology 2, 1346-1352, 2017

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

Structural basis of transcription activation
Feng Y, Zhang Y, Ebright RH, Science 352, 1330-1333, 2016

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