Sapkota K., Li, S. & Zhang, J. (2022) Co-transcriptional assembly and native purification of large RNA-RNA complexes for structural analyses, Methods in Molecular Biology, 2568, 1-12 (abstract)

Zhang, J. (2022) Probing RNA structure and interactions using fluorescence lifetime analyses, Methods in Molecular Biology, 2568, 13-23 (abstract)

Giarimoglou, N., Kouvela, A., Maniatis, A., Papakyriakou, A., Zhang, J., Stamatopoulou, V., Stathopoulos, C. (2022) A riboswitch-driven era of new antibacterials, Antibiotics, 11, 1243 (abstract)

Giarimoglou, N., Patsi, I., Kouvela, A., Zhang, J., Stamatopoulou, V. & Stathopoulos C. (2022) Lineage-specific insertions in T-box riboswitches modulate antibiotics binding and action, Nucleic Acids Research, 50, 5834. (abstract)

Tu, T., Wang, S., Song, Z., He, X., Liu, X., Lv, X., Lv, J., Xi, H., Zhou, Y., Zhao, J., #Gao, C, #Zhang, J., & #Gu, F. (2022) A precise and efficient adenine base editor, Molecular Therapy, 7, 2933. (abstract)
       #co-corresponding authors

Bou-Nader C., Ankur B., Garboczi D.N., #Leppla S.H., & #Zhang, J. (2022) Structural basis of R-loop recognition by the S9.6 monoclonal antibody, Nature Communications, 13, 1641. (abstract)
       #co-corresponding authors

#Bou-Nader C., & #Zhang, J. (2021) Rational engineering enables co-crystallization and structural determination of the HIV-1 matrix-tRNA complex, STAR Protocols, 3, 101056. (abstract)
       #co-corresponding authors

Skeparnias, I. & Zhang, J. (2021) Cooperativity and interdependency between RNA structure and RNA-RNA interactions, Non-Coding RNA, 7:81. (Review) (abstract)

Fu, J., Li, Q., Liu, X., Tu, T., Lv, X., Yin, X., Song, Z., Zhang, J., Li, J., & Gu, F. (2021) Human cells based directed evolution of adenine base editors with improved efficiency, Nature Communications, 12, 5897. (abstract)

Zhang, J., (2021) Interplay between host tRNAs and HIV-1: a structural perspective, Viruses, 13, 1819. (abstract)

Zhang, J. (2021) The long and short of it: long noncoding RNAs in neural development and diseases, Frontiers in Bioscience-Landmark, 8, 258-261 (Editorial) (abstract)

Suddala K.C & Zhang, J. (2019). An evolving tale of two interacting RNAs — themes and variations of the T-box riboswitch mechanism, IUBMB Life 71, 1167-1180. (Review)(abstract)

Bou-Nader, C., Gordon, J. M., Henderson, F. E. & Zhang, J. (2019). The search for a PKR code - Differential regulation of Protein Kinase R activity by diverse RNA and protein regulators. RNA 25, 539-556. (Review)(abstract)

Stamatopoulou V., Apostolidi M., Li S., Lamprinou K., Papakyriakou A., Zhang J. and Stathopoulos C. (2017). Direct modulation of T-box riboswitch-controlled transcription by protein synthesis inhibitors. Nucleic Acids Research, 45, 10242.

Zhang, J. Brothers in arms: emerging roles of RNA epigenetics in DNA damage repair. Cell & Bioscience 7, 24 (2017). (abstract)

Stagno, J.R., Liu, Y., Bhandari, Y.R., Conrad, C.E., Panja, S., Swain, M., Fan, L., Nelson, G., Li, C., Wendel, D.R., White, T.A. Coe, J.D., Wiedom, M.O., Knoska, J., Oberthuer, D., Tuckey, R.A., Yu, P., Dyba, M., Tarasov, S.G., Weierstall, U., Grant, T.D. Schwieters, C.D., Zhang, J., Ferré-D'Amaré, A.R., Fromme, P., Draper, D.E. Liang. M., Hunter, M.S., Boutet, S., Tan, K., Zuo, X., Ji, X., Barty, A., Zatsepin, N.A., Chapman, H.N., Spence, J.C., Woodson, S.A. & Wang, Y.X. (2017) Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography. Nature 541, 242-246. (abstract)

#Zhang, J. & #Ferré-D'Amaré, A.R. (2016) Trying on tRNA for Size: RNase P and the T-box Riboswitch as Molecular Rulers. Biomolecules, 6, 18. (abstract)
       # corresponding authors.

#Zhang, J. & #Ferré-D'Amaré, A.R. (2016) The tRNA Elbow in Structure, Recognition and Evolution. Life, 6(1), 3.(abstract)
       # corresponding authors

#Zhang, J. & #Landick, R. (2016) A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure. Trends in Biochemical Sciences, doi: 10.1016/j.tibs.2015.12.009 (abstract)
       # corresponding authors

Zhang, J. & Ferré-D'Amaré, A.R. (2015) Structure and mechanism of the T-box riboswitch. WIREs RNA published online May 08, 2015. (abstract)

Liu, Y., Holm, E., Zhang, J., Yu, P., Wang, J., Dyba, M.A., Chen, D., Lockett, S., Nesbit, D., Ferré-D'Amaré, A.R., Sousa, R., Stagno, J.R., & Wang, Y.-X. (2015) Synthesis and applications of RNAs with position-selective labeling and mosaic composition, Nature, published online May 04, 2015.(abstract)
       Highlighted by Faculty of 1000:F1000prime
       Highlighted by ScienceDaily, “Revolutionary method of making RNAs”, May 04, 2015.

Miao, Z., Adamiak, R.W., Blanchet, M.F., Boniecki, M., Bujnicki, J.M., Chen, S.J., Cheng, C., Chojnowski, G., Chou, F.C., Cordero, P., Cruz, J.A., Ferre-D'Amare, A.R., Das, R., Ding, F., Dokholyan, N.V., Dunin-Horkawicz, S., Kladwang, W., Krokhotin, A., Lach, G., Magnus, M., Major, F., Mann, T.H., Masquida, B., Matelska, D., Meyer, M., Peselis, A., Popenda, M., Purzycka, K.J., Serganov, A., Stasiewicz, J., Szachniuk, M., Tandon, A., Tian, S., Wang, J., Xiao, Y., Xu, X., Zhang, J., Zhao, P., Zok, T., Westhof, E. (2015) RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. RNA 21, 1066-1084.(abstract)

Lageix, S., Zhang, J., Rothenberg, S., and Hinnebusch, A.G. (2015) Interaction between the tRNA-binding and C-terminal domains of yeast Gcn2 regulates kinase activity in vivo, PLoS Genetics published online Feb 19, 2015.(abstract)

Zhang, J. & Ferré-D'Amaré, A.R. (2015) Post-crystallization improvement of RNA crystal diffraction quality. Methods in Molecular Biology 1316, 13-24 (abstract)

Zhang, J. & Ferré-D'Amaré, A.R. (2014) A flexible, scalable method for preparation of homogeneous aminoacylated tRNAs.  Methods in Enzymology 549, 105-113. (abstract)

Windgassen, T, Mooney, R.A., Nayak D., Palangat M., Zhang, J., and Landick, R. (2014) Trigger-helix folding pathway and SI3 mediate catalysis and hairpin-stabilized pausing by Escherichia coli RNA polymerase, Nucleic Acids Research 42, 12707-12721. (abstract)

*Zhang, J., *Jones, C.P., Ferré-D'Amaré, A.R. (2014) Global analysis of riboswitches by small-angle X-ray scattering and calorimetry. Biochimica et Biophysica Acta -Gene Regulatory Mechanisms 1839, 1020-1029. (abstract)
       *equal contribution

Zhang, J. & Ferré-D'Amaré, A.R. (2014) Dramatic improvement of crystals of large RNA by cation replacement and dehydration. Structure 22, 1363-1371. (abstract)

Zhang, J. & Ferré-D'Amaré, A.R. (2014) Direct evaluation of tRNA aminoacylation status by the T-box riboswitch using tRNA-mRNA stacking and steric readout. Molecular Cell 55, 148-155. (abstract)

Zhang, J. & Ferré-D'Amaré, A.R. (2014) New molecular engineering approaches for crystallographic studies of large RNAs. Current Opinion in Structural Biology 26, 9-15. (abstract)

Zhang, J. & Ferré-D'Amaré, A.R. (2013) Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA. Nature 500, 363-7. (abstract)
       Highlighted by News and Views article:
            Chetnani, B., & Mondragón, A. (2013) Structural biology: RNA exerts self-control. Nature 500, 279–280.
       Selected for Cover of Abstract Book, The 18th RNA Society Annual Meeting, Davos, Switzerland

*Baird, N.J., *Zhang, J., Hamma, T., Ferré-D'Amaré, A.R. (2012) YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops. RNA18, 759-70 (abstract)
       *equal contribution; Selected as Cover Image.

Zhang, J., Lau M, & Ferré-D'Amaré A.R. (2010) Ribozymes and Riboswitches: Modulation of RNA Function by Small Molecules. Biochemistry 49, 9123-31 (abstract)

Zhang, J., Palangat, M., & Landick, R. (2010) Role of the RNA polymerase trigger loop in catalysis and pausing. Nature Structural & Molecular Biology 17, 99-104 (abstract)

Zhang, J., & Landick, R. (2009) Substrate loading, nucleotide addition, and translocation by RNA polymerase. In RNA Polymerases as Molecular Machines (Buc H., and Strick T., eds) pp 206-235. Royal Society of Chemistry, Cambridge, UK.

*Toulokhonov, I.,*Zhang, J., Palangat, M., & Landick, R. (2007) A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing. Molecular Cell 27, 406-419. (abstract)
       *equal contribution; Selected as Cover Article.

Vassylyev,D.,Vassylyeva,M., Zhang, J., Palangat, M., Artsimovitch, I., & Landick, R. (2007) Structural basis for substrate loading in bacterial RNA polymerase. Nature 448, 163-168. (abstract)
       Highlighted by News and Views article:
            Cramer P. (2007) Gene transcription: Extending the message. Nature 448, 142–3.
       Selected by 2007 “This Year In Nature” feature. Nature 450, 1131.

Kyzer, S., Zhang, J. & Landick, R. (2005) Inhibition of RNA polymerase by streptolydigin: no cycling allowed. Cell122, 494-496. (Preview) (abstract)