Sean P. Ryder, Ph.D. - Publications

2001 Yale University, New Haven, CT 
RNA, Ribosome

45 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Kaymak E, Farley BM, Hay SA, Li C, Ho S, Hartman DJ, Ryder SP. Efficient generation of transgenic reporter strains and analysis of expression patterns in Caenorhabditis elegans using Library MosSCI. Developmental Dynamics : An Official Publication of the American Association of Anatomists. PMID 27294288 DOI: 10.1002/dvdy.24426  1
2015 Elewa A, Shirayama M, Kaymak E, Harrison PF, Powell DR, Du Z, Chute CD, Woolf H, Yi D, Ishidate T, Srinivasan J, Bao Z, Beilharz TH, Ryder SP, Mello CC. POS-1 Promotes Endo-mesoderm Development by Inhibiting the Cytoplasmic Polyadenylation of neg-1 mRNA. Developmental Cell. 34: 108-18. PMID 26096734 DOI: 10.1016/j.devcel.2015.05.024  1
2015 Bohn MF, Shandilya SM, Silvas TV, Nalivaika EA, Kouno T, Kelch BA, Ryder SP, Kurt-Yilmaz N, Somasundaran M, Schiffer CA. The ssDNA Mutator APOBEC3A Is Regulated by Cooperative Dimerization. Structure (London, England : 1993). 23: 903-11. PMID 25914058 DOI: 10.1016/j.str.2015.03.016  1
2015 Ryder SP. Personal reflection (RNA journal 20th anniversary). Rna (New York, N.Y.). 21: 725-6. PMID 25780210 DOI: 10.1261/rna.050005.115  1
2014 Zearfoss NR, Deveau LM, Clingman CC, Schmidt E, Johnson ES, Massi F, Ryder SP. A conserved three-nucleotide core motif defines Musashi RNA binding specificity. The Journal of Biological Chemistry. 289: 35530-41. PMID 25368328 DOI: 10.1074/jbc.M114.597112  1
2014 Clingman CC, Deveau LM, Hay SA, Genga RM, Shandilya SM, Massi F, Ryder SP. Allosteric inhibition of a stem cell RNA-binding protein by an intermediary metabolite. Elife. 3. PMID 24935936 DOI: 10.7554/eLife.02848  1
2013 Kaymak E, Ryder SP. RNA recognition by the Caenorhabditis elegans oocyte maturation determinant OMA-1. The Journal of Biological Chemistry. 288: 30463-72. PMID 24014033 DOI: 10.1074/jbc.M113.496547  1
2013 Zearfoss NR, Johnson ES, Ryder SP. hnRNP A1 and secondary structure coordinate alternative splicing of Mag. Rna (New York, N.Y.). 19: 948-57. PMID 23704325 DOI: 10.1261/rna.036780.112  1
2013 Clingman CC, Ryder SP. Metabolite sensing in eukaryotic mRNA biology. Wiley Interdisciplinary Reviews. Rna. 4: 387-96. PMID 23653333 DOI: 10.1002/wrna.1167  1
2013 Tamburino AM, Ryder SP, Walhout AJ. A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels. G3 (Bethesda, Md.). 3: 297-304. PMID 23390605 DOI: 10.1534/g3.112.004390  1
2012 Zearfoss NR, Ryder SP. End-labeling oligonucleotides with chemical tags after synthesis. Methods in Molecular Biology (Clifton, N.J.). 941: 181-93. PMID 23065562 DOI: 10.1007/978-1-62703-113-4_14  1
2012 Farley BM, Ryder SP. POS-1 and GLD-1 repress glp-1 translation through a conserved binding-site cluster. Molecular Biology of the Cell. 23: 4473-83. PMID 23034181 DOI: 10.1091/mbc.E12-03-0216  1
2011 Broderick JA, Salomon WE, Ryder SP, Aronin N, Zamore PD. Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing. Rna (New York, N.Y.). 17: 1858-69. PMID 21878547 DOI: 10.1261/rna.2778911  1
2011 Kalchhauser I, Farley BM, Pauli S, Ryder SP, Ciosk R. FBF represses the Cip/Kip cell-cycle inhibitor CKI-2 to promote self-renewal of germline stem cells in C. elegans. The Embo Journal. 30: 3823-9. PMID 21822213 DOI: 10.1038/emboj.2011.263  1
2011 Ryder SP. Pumilio RNA recognition: the consequence of promiscuity. Structure (London, England : 1993). 19: 277-9. PMID 21397178 DOI: 10.1016/j.str.2011.02.006  1
2011 Zearfoss NR, Clingman CC, Farley BM, McCoig LM, Ryder SP. Quaking regulates Hnrnpa1 expression through its 3' UTR in oligodendrocyte precursor cells. Plos Genetics. 7: e1001269. PMID 21253564 DOI: 10.1371/journal.pgen.1001269  1
2011 Wright JE, Gaidatzis D, Senften M, Farley BM, Westhof E, Ryder SP, Ciosk R. A quantitative RNA code for mRNA target selection by the germline fate determinant GLD-1. The Embo Journal. 30: 533-45. PMID 21169991 DOI: 10.1038/emboj.2010.334  1
2011 Pagano JM, Clingman CC, Ryder SP. Quantitative approaches to monitor protein-nucleic acid interactions using fluorescent probes. Rna (New York, N.Y.). 17: 14-20. PMID 21098142 DOI: 10.1261/rna.2428111  1
2010 Ryder SP, Massi F. Insights into the structural basis of RNA recognition by STAR domain proteins. Advances in Experimental Medicine and Biology. 693: 37-53. PMID 21189684 DOI: 10.1007/978-1-4419-7005-3_3  1
2010 Ryder SP. Hidden ribozymes in eukaryotic genome sequence. F1000 Biology Reports. 2. PMID 20948783 DOI: 10.3410/B2-50  1
2010 Swamidass SJ, Bittker JA, Bodycombe NE, Ryder SP, Clemons PA. An economic framework to prioritize confirmatory tests after a high-throughput screen. Journal of Biomolecular Screening. 15: 680-6. PMID 20547534 DOI: 10.1177/1087057110372803  1
2010 Kaymak E, Wee LM, Ryder SP. Structure and function of nematode RNA-binding proteins. Current Opinion in Structural Biology. 20: 305-12. PMID 20418095 DOI: 10.1016/  1
2010 Ryder SP. Catalyzing RNA: Finding hidden ribozymes in eukaryotic genomes Scientist. 24.  1
2009 Pagano JM, Farley BM, Essien KI, Ryder SP. RNA recognition by the embryonic cell fate determinant and germline totipotency factor MEX-3. Proceedings of the National Academy of Sciences of the United States of America. 106: 20252-7. PMID 19915141 DOI: 10.1073/pnas.0907916106  1
2009 Furgason ML, MacDonald C, Shanks SG, Ryder SP, Bryant NJ, Munson M. The N-terminal peptide of the syntaxin Tlg2p modulates binding of its closed conformation to Vps45p. Proceedings of the National Academy of Sciences of the United States of America. 106: 14303-8. PMID 19667197 DOI: 10.1073/pnas.0902976106  1
2008 Recht MI, Ryder SP, Williamson JR. Monitoring assembly of ribonucleoprotein complexes by isothermal titration calorimetry. Methods in Molecular Biology (Clifton, N.J.). 488: 117-27. PMID 18982287 DOI: 10.1007/978-1-60327-475-3_8  1
2008 Ryder SP, Recht MI, Williamson JR. Quantitative analysis of protein-RNA interactions by gel mobility shift. Methods in Molecular Biology (Clifton, N.J.). 488: 99-115. PMID 18982286 DOI: 10.1007/978-1-60327-475-3_7  1
2008 Farley BM, Pagano JM, Ryder SP. RNA target specificity of the embryonic cell fate determinant POS-1. Rna (New York, N.Y.). 14: 2685-97. PMID 18952820 DOI: 10.1261/rna.1256708  1
2008 Zearfoss NR, Farley BM, Ryder SP. Post-transcriptional regulation of myelin formation. Biochimica Et Biophysica Acta. 1779: 486-94. PMID 18590840 DOI: 10.1016/j.bbagrm.2008.06.003  1
2008 Farley BM, Ryder SP. Regulation of maternal mRNAs in early development. Critical Reviews in Biochemistry and Molecular Biology. 43: 135-62. PMID 18365862 DOI: 10.1080/10409230801921338  1
2007 Pagano JM, Farley BM, McCoig LM, Ryder SP. Molecular basis of RNA recognition by the embryonic polarity determinant MEX-5. The Journal of Biological Chemistry. 282: 8883-94. PMID 17264081 DOI: 10.1074/jbc.M700079200  1
2006 Ryder SP. Oskar gains weight. Nature Structural & Molecular Biology. 13: 297-9. PMID 16715044 DOI: 10.1038/nsmb0406-297  1
2004 Ryder SP, Williamson JR. Specificity of the STAR/GSG domain protein Qk1: implications for the regulation of myelination. Rna (New York, N.Y.). 10: 1449-58. PMID 15273320 DOI: 10.1261/rna.7780504  1
2004 Ryder SP, Frater LA, Abramovitz DL, Goodwin EB, Williamson JR. RNA target specificity of the STAR/GSG domain post-transcriptional regulatory protein GLD-1. Nature Structural & Molecular Biology. 11: 20-8. PMID 14718919 DOI: 10.1038/nsmb706  1
2003 Strobel SA, Jones FD, Oyelere AK, Ryder SP. Biochemical detection of adenosine and cytidine ionization within RNA by interference analysis. Nucleic Acids Research. Supplement (2001). 229-30. PMID 14510464  1
2002 Mohan M, Ryder S, Claypool PL, Geisert RD, Malayer JR. Analysis of gene expression in the bovine blastocyst produced in vitro using suppression-subtractive hybridization Biology of Reproduction. 67: 447-453. PMID 12135880  1
2002 Ryder SP, Strobel SA. Comparative analysis of hairpin ribozyme structures and interference data. Nucleic Acids Research. 30: 1287-91. PMID 11884625  1
2001 Jones FD, Ryder SP, Strobel SA. An efficient ligation reaction promoted by a Varkud Satellite ribozyme with extended 5'- and 3'-termini. Nucleic Acids Research. 29: 5115-20. PMID 11812844  1
2001 Ryder SP, Oyelere AK, Padilla JL, Klostermeier D, Millar DP, Strobel SA. Investigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping. Rna (New York, N.Y.). 7: 1454-63. PMID 11680850  1
2001 Strobel SA, Ryder SP. Biological catalysis. The hairpin's turn. Nature. 410: 761-3. PMID 11298426 DOI: 10.1038/35071209  1
2000 Ryder SP, Ortoleva-Donnelly L, Kosek AB, Strobel SA. Chemical probing of RNA by nucleotide analog interference mapping. Methods in Enzymology. 317: 92-109. PMID 10829274  1
1999 Ryder SP, Strobel SA. Nucleotide analog interference mapping of the hairpin ribozyme: implications for secondary and tertiary structure formation. Journal of Molecular Biology. 291: 295-311. PMID 10438622 DOI: 10.1006/jmbi.1999.2959  1
1999 Ryder SP, Strobel SA. Nucleotide analog interference mapping. Methods (San Diego, Calif.). 18: 38-50. PMID 10208815 DOI: 10.1006/meth.1999.0755  1
1998 Szewczak AA, Ortoleva-Donnelly L, Ryder SP, Moncoeur E, Strobel SA. A minor groove RNA triple helix within the catalytic core of a group I intron. Nature Structural Biology. 5: 1037-42. PMID 9846872 DOI: 10.1038/4146  1
1998 Strobel SA, Ortoleva-Donnelly L, Ryder SP, Cate JH, Moncoeur E. Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site. Nature Structural Biology. 5: 60-6. PMID 9437431 DOI: 10.1038/nsb0198-60  1
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