Selected Member Publications
How RNA Unfolds and Refolds (2008), P. T. X. Li, J. Vieregg and I. Tinoco, Annu. Rev. Biochem., 77, 77-100 (more ...)
The take and give between retrotransposable elements and their hosts (2008), A. Beauregard, M. J. Curcio and M. Belfort, Annu. Rev. Genet., 42, 587-617 (more ...)
Retrosequence formation restructures the yeast genome (2007), P. H. Maxwell and M. J. Curcio, Genes Dev., 21, 3308-3318 (more ...)
Progression of the Ribosome Recycling Factor Through the Ribosome Dissociates the Two Ribosomal Subunits (2007) C. Barat, P. P. Datta, V. S. Raj, M. R. Sharma, H. Kaji, A. Kaji, and R. K. Agrawal, Mol. Cell, 27, 250-261 (more ...)
Potent effect of target structure on microRNA function (2007), D. Long, R. Lee, P. Williams, C. Y. Chan, V. Ambros, and Y. Ding, Nat. Str. Mol. Biol., 14, 287-294 (highlighted in Nature, recommended in Faculty of 1000) (more ...)
Real-time control of the energy landscape by force directs the folding of RNA molecules (2007), P. T. X. Li, C. Bustamante, and I. Tinoco Jr., Proc. Natl. Acad. Sci. U.S.A., 104, 15847-15852 (more ...)
The beginning of the end: links between ancient retroelements and modern telomerases (2007), M. J. Curcio and M. Belfort, Proc. Natl. Acad. Sci. U.S.A., 100, 9107-9108 (more ...)
RNA aptamers directed to discrete functional sites on a single protein structural domain (2007), H. Shi, X. Fan, A. Sevilimedu, and J. T. Lis, Proc. Natl. Acad. Sci. U.S.A., 104, 3742-3746 (more ...)
Structural and functional characterization of human telomerase RNA processing and Cajal body localization signals (2007), C. A. Theimer, B. E. Jady, N. Chim, P. Richard, K. E. Breece, T. Kiss, and J. Feigon, Mol. Cell, 27, 869-881 (more ...)
RNA-Editing-Associated Protein 1 Null Mutant Reveals Link to Mitochondrial RNA Stability (2007), J. Hans, S. L. Hajduk, and S. Madison-Antenucci, RNA, 13, 881-889 (more ...)
Self-Organization and Branching Morphogenesis of Primary Salivary Epithelial Cells (2007), C. H. Wei, M. Larsen, M. P. Hoffman, and K. M. Yamada, Tissue Engineering, 13, 721-735 (more ...)
RNAi Applications in Target Validation (2007), A. Kourtidis, C. Eiffert, and D. S. Conklin, Ernst Schering Res Found Workshop Systems Biology, 61, 1-21 (more ...)
Visualization of a group II intron in the 23S rRNA of a stable ribosome (2006), J. G. Slagter-Jaeger, G. S. Allen, D. Smith, I. A. Hahn, J. Frank, and M. Belfort, Proc. Natl. Acad. Sci. U.S.A., 103, 9838-9843 (more ...)
Biochemical and pre-steady-state kinetic characterization of the Hepatitis C virus RNA polymerase (2006), J. Cramer, J. Jaeger, and T. Restle, Biochemistry, 45, 3610-3619 (more ...)
Unusual mechanical stability of a minimal RNA kissing complex (2006), P. T. X. Li, C. Bustamante, and I. Tinoco Jr., Proc. Natl. Acad. Sci. U.S.A., 103, 7039-44 (more ...)
Recent advances in the structural and functional characterization of telomerase RNA (2006), C. A. Theimer and J. Feigon, Curr. Op. Struct. Biol., 16, 307-318 (more ...)
Probing the mechanical folding of TAR RNA by hopping, force-jump and force-clamp methods (2006), P. T. X. Li, S. B. Smith, C. Bustamante, and I. Tinoco Jr., Biophys. J., 90, 1-11 (more ...)
One-step, regioselective synthesis of up to 50 mers of RNA oligomers by montmorillonite catalysis (2006), W. Huang and J. P. Ferris, J. Am. Chem. Soc., 128, 8914-8919 (more ...)
Clustering of RNA secondary structures with application to messenger RNAs (2006), Y. Ding, C. Y. Chan, and C. E. Lawrence, J. Mol. Biol., 359, 554-571 (more ...)
Recruitment of host functions suggests a repair pathway for late steps in group II intron retrohoming (2005), D. Smith, J. Zhong, M. Matsuura, and A. M. Lambowitz, and M. Belfort, Genes Dev., 19, 2477-2487 (more ...)
Interaction of the G' domain of elongation factor G and the C-terminal domain of ribosomal protein L7/L12 during translocation as revealed by cryo-EM (2005), P. P. Datta, M. R. Sharma, L. Qi, J. Frank, and R. K. Agrawal, Mol. Cell., 20, 723-731 (more ...)
Distinct transcriptional responses of RNA polymerases I, II, and III to aptamers that bind TBP (2005), X. Fan, H. Shi, and J. T. Lis, Nucleic Acids Research, 33, 838-845 (more ...)
Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function (2005), C. A. Theimer, C. A. Blois, and J. Feigon, Mol. Cell, 17, 671-682 (more ...)
Inhibition of a yeast LTR-retrotransposon by human APOBEC3 cytidine deaminases (2005), J. A. Dutko, A. Schafer, A. E. Kenny, B. R. Cullen, and M.J. Curcio, Curr. Biol., 15, 661-666 (more ...)
Morphogenesis and Branching of Salivary Glands: Characterization of New Matrix and Signaling Regulators (2005), T. Sakai, M. Larsen, and K. M. Yamada, Oral Biosci. Med., 213, 105-113 (more ...)
Free energy landscape of A-DNA to B-DNA conversion in aqueous solution (2005), N. Banavali and B. Roux, J. Am. Chem. Soc., 127, 6866-6876 (more ...)
RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble (2005), Y. Ding, C. Y. Chan, and C. E. Lawrence, RNA, 11, 1157-1166. (more ...)
Cryo-EM visualization of a viral internal ribosome entry site (IRES) bound to human 40S and 80S ribosomes: the IRES functions as an RNA-based translation factor (2004), M. T. Spahn, E. Jan, A. Mulder, R. A. Grassucci, P. Sarnow, and J. Frank, Cell, 118, 465-475 (more ...)
Characterization of a trp RNA-binding attenuation protein (TRAP) mutant with tryptophan independent RNA binding activity (2004), P. T. X. Li and P. Gollnick, J. Mol. Biol., 335, 707-722 (more ...)
Ty1 mobilizes subtelomeric Y elements in telomerase-negative Saccharomyces cerevisiae survivors (2004), P. H. Maxwell, C. Coombes, A. E. Kenny, J. L. Lawler, J. D. Boeke, and M. J. Curcio, Mol. Cell. Biol., 24, 9887-9898 (more ...)
Probing TBP interactions in transcription initiation and reinitiation with RNA aptamers that act in distinct modes (2004), X. Fan, H. Shi, K. Adelman, and J. T. Lis, Proc. Natl. Acad. Sci. U.S.A., 101, 6934-6939 (more ...)
A resource for large-scale RNAi based screens in mammals (2004), P. J. Paddison, J. M. Silva, D. S. Conklin, M. Schlabach, M. Li, S. Aruleba, V. Balija, A. O'Shaughnessy, L. Gnoj, K. Scobie, K. Chang, T. Westbrook, M. Cleary, R. Sachidanandam, W. R. McCombie, S. J. Elledge and G. J. Hannon, Nature, 428, 427-431 (more ...)
Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-EM (2003), M. Valle, A. Zavialov, W. Li, S. M. Stagg, J. Sengupta, R. C. Nielsen, P. Nissen, S. C. Harvey, M. Ehrenberg, and J. Frank. Nat. Str. Biol., 10, 899-906 (more ...)
A bacterial group II intron favors retrotransposition into plasmid targets (2003), K. Ichiyanagi, A. Beauregard, and M. Belfort, Proc. Natl. Acad. Sci. U.S.A., 100, 15742-15747 (more ...)
Substrate Complexes of Hepatitis C Virus RNA Polymerase (HC-J4): Structural Evidence for Nucleotide Import and De-novo Initiation (2003), D. O'Farrell, R. Trowbridge, D. Rowlands, and J. Jaeger, J. Mol. Biol., 326, 1025-1035 (more ...)
Sequence- and regio-selectivity in the montmorillonite-catalyzed synthesis of RNA (2003), S. Miyakawa and J. P. Ferris, J. Am. Chem. Soc., 125, 8202-8208 (more ...)
Mutations linked to dyskeratosis congenita cause changes in the structural equilibrium in telomerase RNA (2003), C. A. Theimer, L. D. Finger, L. Trantirek, and J. Feigon, Proc. Natl. Acad. Sci. U.S.A., 100, 449-454 (more ...)
Structure of the mammalian mitochondrial ribosomes reveals an expanded role for its component proteins (2003), M. R. Sharma, E. C. Koc, P. P. Datta, T. M. Booth, L. L. Spremulli, and R. K. Agrawal, Cell, 115, 97-108. (commentaries in "The Scientist" and "Creation-Evolution Headlines") (more ...)
Activation of an LTR-retrotransposon in response to telomere erosion (2003), D. T. Scholes, A. E. Kenny, E. R. Gamache, Z. Mou, and M. J. Curcio, Proc. Natl. Acad. Sci. U.S.A., 100, 15736-15741 (more ...)
Fibronectin Requirement in Branching Morphogenesis (2003), T. Sakai, M. Larsen, and K. M. Yamada, Nature, 423, 876-881 (Featured in Journal of Cell Biology Research Roundup and Nature Reviews Molecular Cell Biology Research Highlights) (more ...)
Germline transmission of RNAi in mice (2003), M. A. Carmell, L. Zhang, D. S. Conklin, G. J. Hannon and T. A. Rosenquist, Nat. Struct. Biol., 10, 91-92 (more ...)
A statistical sampling algorithm for RNA secondary structure prediction (2003), Y. Ding and C. E. Lawrence, Nucleic Acids Res., 31, 7280-7301. (more ...)
Viral RNA-directed polymerases. Structure-function Relationships of Human Pathogenic Viruses (2002), J. Jaeger and J. D. Pata, E.Bogner/A.Holzenburg ed., Kluwer Academic/Plenum Publishers (more ...)
Mobile introns: pathways and proteins (2002), M. Belfort, V. Derbyshire, M. M. Parker, B. Cousineau, and A. M. Lambowitz, In Mobile DNA II., N. Craig, R. Craigie, M. Gellert, and A. Lambowitz eds., ASM Press, 761-783 (more ...)
Evolutionary dynamics and population control during in vitro selection and amplification with multiple targets (2002), H. Shi, X. Fan, Z. Ni, and J. T. Lis, RNA, 8, 1461-1470 (more ...)
Editing Machines: The Complexities of Trypanosome Editing (2002), S. Madison-Antenucci, J. G. Grams, and S. L. Hajduk, Cell, 108, 435-438 (more ...)
Gene Expression Profiles of Mouse Submandibular Gland Development: FGFR1 Regulates Branching Morphogenesis in Vitro Through BMP- and FGF-Dependent Mechanisms (2002), M. P. Hoffman, B. Kidder, Z. Steinberg, S. Lakhani, S. Ho, H. K. Kleinman, and Melinda Larsen, Development, 129, 5767-5778 (more ...)
RNA interference in adult mice (2002), A. P. McCaffrey, L. Meuse, T. T. Pham, D. S. Conklin, G. J. Hannon and M. A. Kay, Nature, 418, 38-39 (more ...)
Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells (2002), P. J. Paddison, A. A. Caudy, E. Bernstein, G. J. Hannon and D. S. Conklin, Genes Dev., 16, 948-958 (more ...)
Hepatitis C virus IRES RNA induced changes in the conformation of the 40S ribosomal subunit (2001), C. M. T. Spahn, J. S. Kieft, R. A. Grassucci, P. Penczek, K. Zhou, J. A. Doudna, and J. Frank, Science, 291, 1959-1962 (more ...)
RNA-Editing Associated Protein 1 (REAP-1) Is An RNA Binding Protein with Specificity for Pre-Edited mRNA (2001), S. Madison-Antenucci and S. L. Hajduk, Mol. Cell, 7, 879-886 (more ...)
Reevaluation of stereoelectronic contributions to the conformational properties of the phosphodiester and N3'-phosphoramidate moieties of nucleic acids (2001), N. Banavali and A. D. MacKerell Jr., J. Am. Chem. Soc., 123, 6747-6755 (more ...)
Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond (2001), Y. Ding and C. E. Lawrence, Nucleic Acids Res., 29, 1034-1046. (more ...)
Development and current status of the CHARMM force field for nucleic acids (2000-2001), A. D. MacKerell Jr., N. Banavali, and N. Foloppe, Biopolymers, 56, 257-265 (more ...)
Solution structure of the E. coli ribosome at 11.5 Ang. resolution (2000), I. S. Gabashvili, R. K. Agrawal, C. M. T. Spahn, R. A. Grassucci, D. I. Svergun, J. Frank and P. Penczek, Cell, 100, 51-63 (more ...)
A ratchet-like inter-subunit reorganization of the ribosome during translocation (2000), J. Frank and R. K. Agrawal, Nature, 406, 318-322 (more ...)
A trans-acting RNA as a control switch in E. coli: DsrA RNA modulates function by forming alternative structures (2000), R. Lease and M. Belfort, Proc. Natl. Acad. Sci. U.S.A., 97, 9919-9924 (more ...)
Diverse splicing mechanisms fuse the evolutionarily conserved bicistronic MOCS1A and MOCS1B open reading frames (2000), T. A. Gray and R. D. Nicholls, RNA, 6, 928-936 (more ...)
Structure, stability, and function of RNA pseudoknots involved in stimulating ribosomal frameshifting (2000), D. P. Giedroc, C. A. Theimer, and P. L. Nixon, J. Mol. Biol., 298, 167-185 (more ...)
An imprinted, mammalian bicistronic transcript encodes two independent proteins (1999), T. A. Gray, S. Saitoh, and R. D. Nicholls, Proc. Natl. Acad. Sci. U.S.A., 96, 5616-5621 (more ...)
RNA aptamers as effective protein antagonists in a multicellular organism (1999), H. Shi, B. E. Hoffman, and J. T. Lis, Proc. Natl. Acad. Sci. U.S.A., 96, 10033-10038 (more ...)
The Structure of HIV-1 reverse tanscriptase complexed with a RNA pseudoknot inhibitor (1998), J. Jaeger, T. Restle, and T. A. Steitz, EMBO. J., 17, 4535-4542 (more ...)
Kinetoplastid RNA-Editing Associated Protein 1 (REAP 1): A Novel Editing Complex Protein with Repetitive Domains (1998), S. Madison-Antenucci, R. S. Sabatini, V. W. Pollard, and S. L. Hajduk, EMBO J., 17, 6368-6376 (more ...)
Direct visualization of A, P and E site tRNAs in the E. coli ribosome (1996), R. K. Agrawal, P. Penczek, R. Grassucci, Y. Li, A. Leith, K. H. Nierhaus, and J. Frank, Science, 271, 1000-1002 (more ...)
Synthesis of RNA Oligomers on Heterogeneous Templates (1996), G. Ertem and J. P. Ferris, Nature, 379, 238-240 (more ...)
Synthesis of Long Prebiotic Oligomers on Mineral Surfaces (1996), J. P. Ferris, A. R. Hill Jr., R. Liu, and L. E. Orgel, Nature, 381, 59-61 (more ...)
Montmorillonite Catalysis of RNA Oligomer Formation in Aqueous Solution: A Model for the Prebiotic Formation of RNA (1993), J. P. Ferris and G. Ertem, J. Am. Chem. Soc., 115, 12270-12275 (more ...)