S. Joseph. 2015. Modification interference analysis of the ribosome. Methods Mol Biol. 1240: 113-123.
E. Chen, M. R. Sharma, X. Shi, R. K. Agrawal and S. Joseph. 2014. Fragile X mental retardation protein regulates translation by binding directly to the ribosome. Molecular Cell 54: 407-417.
V. Alverdi, B. Hetrick, S. Joseph and E. A. Komives. 2014. Direct observation of a transient ternary complex during IkBa-mediated dissociation of NF-kB from DNA. Proc Natl Acad Sci USA 111: 225-230.
K. Trappl, M. A. Mathew and S. Joseph. 2014. Thermodynamic and kinetic insights into stop codon recognition by release factor 1. PLoS One 9: e94058.
P. K. Khade, X. Shi and S. Joseph. 2013. Steric complementarity in the decoding center is important for tRNA selection by the ribosome. J. Mol. Biol. 425: 3778-3789.
B. Sahu, P. K. Khade and S. Joseph. 2013. Highly conserved base A55 of 16S ribosomal RNA is important for the elongation cycle of protein synthesis. Biochemistry 52: 6695-6701.
B. Sahu, P. K. Khade and S. Joseph. 2012. Functional replacement of two highly conserved tetraloops in the bacterial ribosome. Biochemistry 51: 7618-7626.
X. Shi, P. K. Khade, K. Y. Sanbonmatsu and S. Joseph. 2012. Functional role of the sarcin-ricin loop of the 23S rRNA in the elongation cycle of protein synthesis. J. Mol. Biol. 419: 125-138.
P. K. Khade and S. Joseph. 2011. Messenger RNA interactions in the decoding center control the rate of translocation. Nature Structural & Molecular Biology 18: 1300-1302.
A. Field, B. Hetrick, M. Mathew and S. Joseph. 2010. Histidine 197 in release factor 1 is essential for A site binding and peptide release. Biochemistry 49: 9385-9390.
B. Hetrick, P. K. Khade, K. Lee, J. Stephen, A. Thomas and S. Joseph. 2010. Polyamines accelerate codon recognition by transfer RNAs on the ribosome. Biochemistry 49: 7179-7189.
L. Garcia-Ortega, E. Alvarez-Garcia, J. G. Gavilanes, A. Martinez-del-Pozo and S. Joseph. 2010. Cleavage of the sarcin-ricin loop of 23S rRNA differentially affects EF-G and EF-Tu binding. Nucleic Acids Research 38: 4108-4119.
P. K. Khade and S. Joseph. 2010. Functional interactions by transfer RNAs in the ribosome. FEBS Letter 584: 420-426.
B. Hetrick, K. Lee and S. Joseph. 2009. Kinetics of stop codon recognition by release factor 1. Biochemistry 48: 11178-11184.
X. Shi, K. Chiu, S. Ghosh and S. Joseph. 2009. Bases in 16S rRNA important for subunit association, tRNA binding, and translocation. Biochemistry 48: 6772-6782.
L. Garcia-Ortega, J. Stephen and S. Joseph. 2008. Precise alignment of peptidyl tRNA by the decoding center is essential for EF-G-dependent translocation. Molecular Cell 32: 292-299.
S. M. Studer and S. Joseph. 2007. Binding of mRNA to the bacterial translation initiation complex. Methods in Enzymology 430: 31-44.
M. Grunberg-Manago, S. M. Studer and S. Joseph. 2007. Protein synthesis initiation in bacteria. Encyclopedia of Life Sciences 1-10.
C. M. Dunham, M. Selmer, S. S. Phelps, A. C. Kelly, T. Suzuki, S. Joseph and V. Ramakrishnan. 2007. Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit. RNA 13: 817-823.
J. S. Feinberg and S. Joseph. 2006. A conserved base pair between tRNA and 23S rRNA in the peptidyl transferase center is important for peptide release. J. Mol. Biol. 364: 1010-1020.
I. K. Ali, L. Lancaster, J. S. Feinberg, S. Joseph and H. F. Noller. 2006. Deletion of a conserved, central ribosomal intersubunit RNA bridge. Molecular Cell 23: 865-874.
T. Komoda, N. S. Sato, S. S. Phelps, N. Namba, S. Joseph and T. Suzuki. 2006. The A-site finger in 23S rRNA acts as a functional attenuator for translocation. J. Biol. Chem. 281: 32303-32309.
S. S. Phelps, C. Gaudin, S. Yoshizawa, C. Benitez, D. Fourmy and S. Joseph. 2006. Translocation of a tRNA with an extended anticodon through the ribosome. J. Mol. Biol. 360: 610-622.
S. M. Studer and S. Joseph. 2006. Unfolding of mRNA secondary structure by the bacterial translation initiation complex. Molecular Cell 22: 105-115.
J. S. Feinberg and S. Joseph. 2006. Ribose 2'-hydroxyl groups in the 5' strand of the acceptor arm of P-site tRNA are not essential for EF-G catalyzed translocation. RNA 12: 580-588.
K. Y. Sanbonmatsu, S. Joseph and C. S. Tung. 2005. Simulating movement of tRNA into the ribosome during decoding. Proc. Natl. Acad. Sci. USA. 102: 15854-15859.
S. S. Phelps and S. Joseph. 2005. Non-bridging phosphate oxygen atoms within the tRNA anticodon stem-loop are essential for ribosomal A site binding and translocation. J. Mol. Biol. 349: 288-301.
S. Ghosh and S. Joseph. 2005. Nonbridging phosphate oxygens in 16S rRNA important for 30S subunit assembly and association with the 50S ribosomal subunit. RNA 11: 657-667.
S. S. Phelps, A. Malkiewicz, P. F. Agris and S. Joseph. 2004. Modified nucleotides in tRNA-Lys and tRNA-Val are important for translocation. J. Mol. Biol. 338: 439-444.
K. Y. Sanbonmatsu and S. Joseph. 2003. Understanding discrimination by the ribosome: Stability testing and groove measurement of codon-anticodon pairs. J. Mol. Biol. 328: 33-47.
S. M. Studer, J. S. Feinberg and S. Joseph. 2003. Rapid kinetic analysis of EF-G-dependent mRNA translocation in the ribosome. J. Mol. Biol. 327: 369-381.
S. Joseph. 2003. After the ribosome structure: How does translocation work? RNA 9: 160-164.
S. S. Phelps, O. Jerinic and S. Joseph. 2002. Universally conserved interactions between the ribosome and the anticodon stem-loop of A site tRNA important for translocation. Molecular Cell 10: 799-807.
C. Tung, S. Joseph and K. Y. Sanbonmatsu. 2002. All-atom homology model of the Escherichia coli 30S ribosomal subunit. Nature Structural Biology 9: 750-755.
C. Ma, N. A. Baker, S. Joseph and J. A. McCammon. 2002. Binding of aminoglycoside antibiotics to the small ribosomal subunit: a continuum electrostatics investigation. J. Am. Chem. Soc. 124: 1438-1442.
J. S. Feinberg and S. Joseph. 2001. Identification of molecular interactions between P-site tRNA and the ribosome essential for translocation. Proc. Natl. Acad. Sci. USA. 98: 11120-11125.
N. A. Baker, D. Sept, S. Joseph, M. J. Holst, J. A. McCammon. 2001. Electrostatics of cellular components: Application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA. 98: 10037-10041.
O. Jerinic and S. Joseph. 2000. Conformational changes in the ribosome induced by translational miscoding agents. J. Mol. Biol. 304: 707-713.
S. Joseph, M. L. Whirl, D. Kondo, H. F. Noller and R. B. Altman. 2000. Calculation of the relative geometry of tRNAs in the ribosome from directed hydroxyl radical probing data. RNA 6: 220-232.
S. Joseph and H. F. Noller. 2000. Directed hydroxyl radical probing using Fe(II) tethered to RNA. Methods Enzymol. Vol 318: 175-190.
R. R. Samaha, S. Joseph, B. O'Brien, T. W. O'Brien and H. F. Noller. 1999. Site-directed hydroxyl radical probing of 30S ribosomal subunits by using Fe(II) tethered.to an interruption in the 16S rRNA chain. Proc. Natl. Acad. Sci. USA. 96: 366-370.
S. Joseph and H. F. Noller. 1998. EF-G-catalyzed translocation of anticodon stem-loop analogs of transfer RNA in the ribosome. EMBO J. 17: 3478-3483.
S. Joseph, B. Weiser and H. F. Noller. 1997. Mapping the inside of the ribosome with an RNA helical ruler. Science 278: 1093-1098.
S. Joseph and H. F. Noller. 1996. Mapping the rRNA neighborhood of the acceptor end of tRNA in the ribosome. EMBO J. 15: 910-916.
H. F. Noller, R. Green, G. Heilek, V. Hoffarth, A. Huttenhofer, S. Joseph, I. Lee, K. Lieberman, A. Mankin, C. Merryman, T. Powers, E. V. Puglisi, R. R. Samaha, and B. Weiser. 1995. "Structure and function of ribosomal RNA" in A. Matheson, J. Davies, P. Dennis and W. Hill (editors). Proceedings of frontiers in translation, an international ribosome conference, Victoria, B.C., Biochem. Cell Biol. 73: 997-1009.
S. Joseph and J. M. Burke. 1993. Optimization of an anti-HIV hairpin ribozyme by in vitro selection. J. Biol. Chem. 268: 24515-24518.
A. Berzal-Herranz, S. Joseph, B. M. Chowrira, S. E. Butcher and J. M. Burke. 1993. Essential nucleotide sequences and secondary structure elements of the hairpin ribozyme. EMBO J. 12: 2567-2574.
S. Joseph, A. Berzal-Herranz, B. M. Chowrira, S. E. Butcher and J. M. Burke. 1993. Substrate selection rules for the hairpin ribozyme determined by in vitro selection, mutation, and analysis of mismatched substrates. Genes & Dev. 7: 130-138.
A. Berzal-Herranz, S. Joseph and J. M. Burke. 1992. In vitro selection of active hairpin ribozymes by sequential RNA-catalyzed cleavage and ligation reactions. Genes & Dev. 6: 129-134.