Simpson Joseph • UCSD Profiles (original) (raw)

  1. Mapping RNA-Binding Proteins on the Ribosome by Tethered Micrococcal Nuclease. Biochemistry. 2026 Feb 17; 65(4):385-398. Yao CY, Joseph S. PMID: 41582668.
    View in: PubMed Mentions: Fields:
    Translation:AnimalsCells
  2. Capturing Translation in Action with Protein Synthesis Profiling. bioRxiv. 2025 Nov 17. Matta CA, Ten ZQ, Joseph S. PMID: 41332707; PMCID: PMC12667909.
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  3. Structural evidence for metal ion catalysis in the ribosome. bioRxiv. 2025 May 17. Hingey JM, Rudolfs B, Haack DB, Murphy FV, Joseph S, Toor N. PMID: 40463213; PMCID: PMC12132363.
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  4. Validating the EMCV IRES Secondary Structure with Structure-Function Analysis. Biochemistry. 2024 01 02; 63(1):107-115. Maloney A, Joseph S. PMID: 38081770; PMCID: PMC10896073.
    View in: PubMed Mentions: 3 Fields:
    Translation:Cells
  5. Interaction of the Influenza A Virus NS1 Protein with the 5'-m7G-mRNA·eIF4E·eIF4G1 Complex. Biochemistry. 2022 07 19; 61(14):1485-1494. Cruz A, Joseph S. PMID: 35797022; PMCID: PMC10164398.
    View in: PubMed Mentions: 6 Fields:
    Translation:Cells
  6. The Fragile X Protein Disordered Regions Bind a Novel RNA Target. Biochemistry. 2022 06 21; 61(12):1199-1212. Edwards M, Huang M, Joseph S. PMID: 35653700; PMCID: PMC12068066.
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    Translation:AnimalsCells
  7. PABP1 Drives the Selective Translation of Influenza A Virus mRNA. J Mol Biol. 2022 03 15; 434(5):167460. de Rozières CM, Pequeno A, Shahabi S, Lucas TM, Godula K, Ghosh G, Joseph S. PMID: 35074482; PMCID: PMC8897273.
    View in: PubMed Mentions: 10 Fields:
    Translation:HumansCells
  8. Controlling Protein Enrichment in Lipid Sponge Phase Droplets using SNAP-Tag Bioconjugation. Chembiochem. 2022 03 04; 23(5):e202100624. Moinpour M, Fracassi A, Brea RJ, Salvador-Castell M, Pandey S, Edwards MM, Seifert S, Joseph S, Sinha SK, Devaraj NK. PMID: 34936727.
    View in: PubMed Mentions: 3 Fields:
    Translation:Cells
  9. The Fragile X Proteins Differentially Regulate Translation of Reporter mRNAs with G-quadruplex Structures. J Mol Biol. 2022 01 30; 434(2):167396. Edwards M, Joseph S. PMID: 34896112; PMCID: PMC8892671.
    View in: PubMed Mentions: 4 Fields:
    Translation:HumansCells
  10. Discovery of a pre-mRNA structural scaffold as a contributor to the mammalian splicing code. Nucleic Acids Res. 2021 07 09; 49(12):7103-7121. Saha K, Fernandez MM, Biswas T, Joseph S, Ghosh G. PMID: 34161584; PMCID: PMC8266590.
    View in: PubMed Mentions: 8 Fields:
    Translation:HumansCells
  11. Influenza A Virus NS1 Protein Binds as a Dimer to RNA-Free PABP1 but Not to the PABP1·Poly(A) RNA Complex. Biochemistry. 2020 11 24; 59(46):4439-4448. de Rozières CM, Joseph S. PMID: 33172261; PMCID: PMC8034803.
    View in: PubMed Mentions: 6 Fields:
    Translation:Cells
  12. The Human Fragile X Mental Retardation Protein Inhibits the Elongation Step of Translation through Its RGG and C-Terminal Domains. Biochemistry. 2020 10 13; 59(40):3813-3822. Athar YM, Joseph S. PMID: 32945655; PMCID: PMC8034582.
    View in: PubMed Mentions: 8 Fields:
    Translation:HumansCells
  13. A simple procedure for bacterial expression and purification of the fragile X protein family. Sci Rep. 2020 09 28; 10(1):15858. Edwards M, Xu M, Joseph S. PMID: 32985615; PMCID: PMC7522082.
    View in: PubMed Mentions: 2 Fields:
    Translation:HumansCells
  14. RNA-Binding Specificity of the Human Fragile X Mental Retardation Protein. J Mol Biol. 2020 06 12; 432(13):3851-3868. Athar YM, Joseph S. PMID: 32343993; PMCID: PMC7306444.
    View in: PubMed Mentions: 20 Fields:
    Translation:HumansCells
  15. Translation of non-standard codon nucleotides reveals minimal requirements for codon-anticodon interactions. Nat Commun. 2018 11 19; 9(1):4865. Hoernes TP, Faserl K, Juen MA, Kremser J, Gasser C, Fuchs E, Shi X, Siewert A, Lindner H, Kreutz C, Micura R, Joseph S, Höbartner C, Westhof E, Hüttenhofer A, Erlacher MD. PMID: 30451861; PMCID: PMC6242847.
    View in: PubMed Mentions: 23 Fields:
    Translation:HumansCells
  16. RNA Modulates the Interaction between Influenza A Virus NS1 and Human PABP1. Biochemistry. 2018 07 03; 57(26):3590-3598. Arias-Mireles BH, de Rozieres CM, Ly K, Joseph S. PMID: 29782795; PMCID: PMC6205234.
    View in: PubMed Mentions: 8 Fields:
    Translation:HumansCells
  17. Optimization of ClpXP activity and protein synthesis in an E. coli extract-based cell-free expression system. Sci Rep. 2018 02 22; 8(1):3488. Shi X, Wu T, M Cole C, K Devaraj N, Joseph S. PMID: 29472573; PMCID: PMC5823941.
    View in: PubMed Mentions: 8 Fields:
    Translation:Cells
  18. Atomic mutagenesis of stop codon nucleotides reveals the chemical prerequisites for release factor-mediated peptide release. Proc Natl Acad Sci U S A. 2018 01 16; 115(3):E382-E389. Hoernes TP, Clementi N, Juen MA, Shi X, Faserl K, Willi J, Gasser C, Kreutz C, Joseph S, Lindner H, Hüttenhofer A, Erlacher MD. PMID: 29298914; PMCID: PMC5776981.
    View in: PubMed Mentions: 17 Fields:
    Translation:Cells
  19. Determination of nucleoside triphosphatase activities from measurement of true inorganic phosphate in the presence of labile phosphate compounds. Anal Biochem. 2017 03 01; 520:62-67. Katz FEH, Shi X, Owens CP, Joseph S, Tezcan FA. PMID: 28017740; PMCID: PMC5291744.
    View in: PubMed Mentions: 2 Fields:
    Translation:Cells
  20. Mechanism of Translation Termination: RF1 Dissociation Follows Dissociation of RF3 from the Ribosome. Biochemistry. 2016 Nov 15; 55(45):6344-6354. Shi X, Joseph S. PMID: 27779391.
    View in: PubMed Mentions: 12 Fields:
    Translation:Cells
  21. Translocation: lights, camera, and action. Nat Struct Mol Biol. 2016 05 04; 23(5):367-8. Shi X, Joseph S. PMID: 27142323.
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    Translation:Cells
  22. Ribosome Induces a Closed to Open Conformational Change in Release Factor 1. J Mol Biol. 2016 Mar 27; 428(6):1333-1344. Trappl K, Joseph S. PMID: 26827724.
    View in: PubMed Mentions: 13 Fields:
    Translation:Cells
  23. Fragile X mental retardation protein: A paradigm for translational control by RNA-binding proteins. Biochimie. 2015 Jul; 114:147-54. Chen E, Joseph S. PMID: 25701550; PMCID: PMC4458461.
    View in: PubMed Mentions: 38 Fields:
    Translation:HumansAnimalsCells
  24. Modification interference analysis of the ribosome. Methods Mol Biol. 2015; 1240:113-23. Joseph S. PMID: 25352140.
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    Translation:Cells
  25. Fragile X mental retardation protein regulates translation by binding directly to the ribosome. Mol Cell. 2014 May 08; 54(3):407-417. Chen E, Sharma MR, Shi X, Agrawal RK, Joseph S. PMID: 24746697; PMCID: PMC4019695.
    View in: PubMed Mentions: 153 Fields:
    Translation:HumansAnimalsCells
  26. Thermodynamic and kinetic insights into stop codon recognition by release factor 1. PLoS One. 2014; 9(4):e94058. Trappl K, Mathew MA, Joseph S. PMID: 24699820; PMCID: PMC3974865.
    View in: PubMed Mentions: 3 Fields:
    Translation:Cells
  27. Direct observation of a transient ternary complex during IκBα-mediated dissociation of NF-κB from DNA. Proc Natl Acad Sci U S A. 2014 Jan 07; 111(1):225-30. Alverdi V, Hetrick B, Joseph S, Komives EA. PMID: 24367071; PMCID: PMC3890772.
    View in: PubMed Mentions: 32 Fields:
    Translation:HumansCells
  28. Highly conserved base A55 of 16S ribosomal RNA is important for the elongation cycle of protein synthesis. Biochemistry. 2013 Sep 24; 52(38):6695-701. Sahu B, Khade PK, Joseph S. PMID: 24025161; PMCID: PMC11849674.
    View in: PubMed Mentions: 3 Fields:
    Translation:Cells
  29. Steric complementarity in the decoding center is important for tRNA selection by the ribosome. J Mol Biol. 2013 Oct 23; 425(20):3778-89. Khade PK, Shi X, Joseph S. PMID: 23542008; PMCID: PMC3744617.
    View in: PubMed Mentions: 21 Fields:
    Translation:Cells
  30. Functional replacement of two highly conserved tetraloops in the bacterial ribosome. Biochemistry. 2012 Sep 25; 51(38):7618-26. Sahu B, Khade PK, Joseph S. PMID: 22938718; PMCID: PMC3786584.
    View in: PubMed Mentions: 6 Fields:
    Translation:Cells
  31. Functional role of the sarcin-ricin loop of the 23S rRNA in the elongation cycle of protein synthesis. J Mol Biol. 2012 Jun 08; 419(3-4):125-38. Shi X, Khade PK, Sanbonmatsu KY, Joseph S. PMID: 22459262; PMCID: PMC3348345.
    View in: PubMed Mentions: 48 Fields:
    Translation:Cells
  32. Messenger RNA interactions in the decoding center control the rate of translocation. Nat Struct Mol Biol. 2011 Oct 23; 18(11):1300-2. Khade PK, Joseph S. PMID: 22020300; PMCID: PMC11855187.
    View in: PubMed Mentions: 32 Fields:
    Translation:Cells
  33. Histidine 197 in release factor 1 is essential for a site binding and peptide release. Biochemistry. 2010 Nov 02; 49(43):9385-90. Field A, Hetrick B, Mathew M, Joseph S. PMID: 20873815; PMCID: PMC2967428.
    View in: PubMed Mentions: 4 Fields:
    Translation:Cells
  34. Polyamines accelerate codon recognition by transfer RNAs on the ribosome. Biochemistry. 2010 Aug 24; 49(33):7179-89. Hetrick B, Khade PK, Lee K, Stephen J, Thomas A, Joseph S. PMID: 20666453; PMCID: PMC2952548.
    View in: PubMed Mentions: 12 Fields:
    Translation:Cells
  35. Cleavage of the sarcin-ricin loop of 23S rRNA differentially affects EF-G and EF-Tu binding. Nucleic Acids Res. 2010 Jul; 38(12):4108-19. García-Ortega L, Alvarez-García E, Gavilanes JG, Martínez-del-Pozo A, Joseph S. PMID: 20215430; PMCID: PMC2896532.
    View in: PubMed Mentions: 24 Fields:
    Translation:Cells
  36. Functional interactions by transfer RNAs in the ribosome. FEBS Lett. 2010 Jan 21; 584(2):420-6. Khade P, Joseph S. PMID: 19914248; PMCID: PMC2795042.
    View in: PubMed Mentions: 10 Fields:
    Translation:Cells
  37. Kinetics of stop codon recognition by release factor 1. Biochemistry. 2009 Dec 01; 48(47):11178-84. Hetrick B, Lee K, Joseph S. PMID: 19874047; PMCID: PMC2789991.
    View in: PubMed Mentions: 15 Fields:
    Translation:Cells
  38. Bases in 16S rRNA important for subunit association, tRNA binding, and translocation. Biochemistry. 2009 Jul 28; 48(29):6772-82. Shi X, Chiu K, Ghosh S, Joseph S. PMID: 19545171; PMCID: PMC2782751.
    View in: PubMed Mentions: 13 Fields:
    Translation:Cells
  39. Precise alignment of peptidyl tRNA by the decoding center is essential for EF-G-dependent translocation. Mol Cell. 2008 Oct 24; 32(2):292-9. Garcia-Ortega L, Stephen J, Joseph S. PMID: 18951096; PMCID: PMC11849654.
    View in: PubMed Mentions: 13 Fields:
    Translation:Cells
  40. Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit. RNA. 2007 Jun; 13(6):817-23. Dunham CM, Selmer M, Phelps SS, Kelley AC, Suzuki T, Joseph S, Ramakrishnan V. PMID: 17416634; PMCID: PMC1869038.
    View in: PubMed Mentions: 28 Fields:
    Translation:Cells
  41. Binding of mRNA to the bacterial translation initiation complex. Methods Enzymol. 2007; 430:31-44. Studer SM, Joseph S. PMID: 17913633.
    View in: PubMed Mentions: 6 Fields:
    Translation:Cells
  42. A conserved base-pair between tRNA and 23 S rRNA in the peptidyl transferase center is important for peptide release. J Mol Biol. 2006 Dec 15; 364(5):1010-20. Feinberg JS, Joseph S. PMID: 17045291.
    View in: PubMed Mentions: 12 Fields:
    Translation:Cells
  43. Deletion of a conserved, central ribosomal intersubunit RNA bridge. Mol Cell. 2006 Sep 15; 23(6):865-74. Ali IK, Lancaster L, Feinberg J, Joseph S, Noller HF. PMID: 16973438.
    View in: PubMed Mentions: 68 Fields:
    Translation:Cells
  44. The A-site finger in 23 S rRNA acts as a functional attenuator for translocation. J Biol Chem. 2006 Oct 27; 281(43):32303-9. Komoda T, Sato NS, Phelps SS, Namba N, Joseph S, Suzuki T. PMID: 16950778.
    View in: PubMed Mentions: 48 Fields:
    Translation:Cells
  45. Translocation of a tRNA with an extended anticodon through the ribosome. J Mol Biol. 2006 Jul 14; 360(3):610-22. Phelps SS, Gaudin C, Yoshizawa S, Benitez C, Fourmy D, Joseph S. PMID: 16787653.
    View in: PubMed Mentions: 17 Fields:
    Translation:Cells
  46. Unfolding of mRNA secondary structure by the bacterial translation initiation complex. Mol Cell. 2006 Apr 07; 22(1):105-15. Studer SM, Joseph S. PMID: 16600874.
    View in: PubMed Mentions: 79 Fields:
    Translation:Cells
  47. 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. 2006 Apr; 12(4):580-8. Feinberg JS, Joseph S. PMID: 16489185; PMCID: PMC1421097.
    View in: PubMed Mentions: 9 Fields:
    Translation:Cells
  48. Simulating movement of tRNA into the ribosome during decoding. Proc Natl Acad Sci U S A. 2005 Nov 01; 102(44):15854-9. Sanbonmatsu KY, Joseph S, Tung CS. PMID: 16249344; PMCID: PMC1266076.
    View in: PubMed Mentions: 131 Fields:
    Translation:Cells
  49. Non-bridging phosphate oxygen atoms within the tRNA anticodon stem-loop are essential for ribosomal A site binding and translocation. J Mol Biol. 2005 Jun 03; 349(2):288-301. Phelps SS, Joseph S. PMID: 15890196.
    View in: PubMed Mentions: 5 Fields:
    Translation:Cells
  50. Nonbridging phosphate oxygens in 16S rRNA important for 30S subunit assembly and association with the 50S ribosomal subunit. RNA. 2005 May; 11(5):657-67. Ghosh S, Joseph S. PMID: 15811917; PMCID: PMC1370752.
    View in: PubMed Mentions: 10 Fields:
    Translation:Cells
  51. Modified nucleotides in tRNA(Lys) and tRNA(Val) are important for translocation. J Mol Biol. 2004 Apr 30; 338(3):439-44. Phelps SS, Malkiewicz A, Agris PF, Joseph S. PMID: 15081802.
    View in: PubMed Mentions: 38 Fields:
    Translation:Cells
  52. Rapid kinetic analysis of EF-G-dependent mRNA translocation in the ribosome. J Mol Biol. 2003 Mar 21; 327(2):369-81. Studer SM, Feinberg JS, Joseph S. PMID: 12628244.
    View in: PubMed Mentions: 76 Fields:
    Translation:Cells
  53. After the ribosome structure: how does translocation work? RNA. 2003 Feb; 9(2):160-4. Joseph S. PMID: 12554856; PMCID: PMC1370379.
    View in: PubMed Mentions: 15 Fields:
    Translation:Cells
  54. All-atom homology model of the Escherichia coli 30S ribosomal subunit. Nat Struct Biol. 2002 Oct; 9(10):750-5. Tung CS, Joseph S, Sanbonmatsu KY. PMID: 12244297.
    View in: PubMed Mentions: 24 Fields:
    Translation:Cells
  55. Universally conserved interactions between the ribosome and the anticodon stem-loop of A site tRNA important for translocation. Mol Cell. 2002 Oct; 10(4):799-807. Phelps SS, Jerinic O, Joseph S. PMID: 12419224.
    View in: PubMed Mentions: 27 Fields:
    Translation:Cells

This graph shows the number and percent of publications by field. Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications. Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written. To see the data as text, click here.

This graph shows the number and percent of publications by field. Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications. Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written. To see the data as text, click here.

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