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Items: 49

1.

#CRISPRbabies: Notes on a Scandal.

Ryder SP.

CRISPR J. 2018 Dec 1;1(6):355-357. doi: 10.1089/crispr.2018.29039.spr. Epub 2018 Dec 20. No abstract available.

2.

Multi-modal regulation of C. elegans hermaphrodite spermatogenesis by the GLD-1-FOG-2 complex.

Hu S, Skelly LE, Kaymak E, Freeberg L, Lo TW, Kuersten S, Ryder SP, Haag ES.

Dev Biol. 2019 Feb 15;446(2):193-205. doi: 10.1016/j.ydbio.2018.11.024. Epub 2018 Dec 30.

PMID:
30599151
3.

Polo-like Kinase Couples Cytoplasmic Protein Gradients in the C. elegans Zygote.

Han B, Antkowiak KR, Fan X, Rutigliano M, Ryder SP, Griffin EE.

Curr Biol. 2018 Jan 8;28(1):60-69.e8. doi: 10.1016/j.cub.2017.11.048. Epub 2017 Dec 21.

4.

Protein-mRNA interactome capture: cartography of the mRNP landscape.

Ryder SP.

F1000Res. 2016 Nov 3;5:2627. doi: 10.12688/f1000research.9404.1. eCollection 2016. Review.

5.

Horizontal Gel Electrophoresis for Enhanced Detection of Protein-RNA Complexes.

Dowdle ME, Imboden SB, Park S, Ryder SP, Sheets MD.

J Vis Exp. 2017 Jul 28;(125). doi: 10.3791/56031.

6.

PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions.

Tamburino AM, Kaymak E, Shrestha S, Holdorf AD, Ryder SP, Walhout AJM.

Translation (Austin). 2017 Feb 28;5(1):e1295130. doi: 10.1080/21690731.2017.1295130. eCollection 2017.

7.

Efficient generation of transgenic reporter strains and analysis of expression patterns in Caenorhabditis elegans using library MosSCI.

Kaymak E, Farley BM, Hay SA, Li C, Ho S, Hartman DJ, Ryder SP.

Dev Dyn. 2016 Sep;245(9):925-36. doi: 10.1002/dvdy.24426. Epub 2016 Jul 25.

8.

POS-1 Promotes Endo-mesoderm Development by Inhibiting the Cytoplasmic Polyadenylation of neg-1 mRNA.

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.

Dev Cell. 2015 Jul 6;34(1):108-18. doi: 10.1016/j.devcel.2015.05.024. Epub 2015 Jun 18.

9.

The ssDNA Mutator APOBEC3A Is Regulated by Cooperative Dimerization.

Bohn MF, Shandilya SMD, Silvas TV, Nalivaika EA, Kouno T, Kelch BA, Ryder SP, Kurt-Yilmaz N, Somasundaran M, Schiffer CA.

Structure. 2015 May 5;23(5):903-911. doi: 10.1016/j.str.2015.03.016. Epub 2015 Apr 23.

10.

Personal reflection (RNA journal 20th anniversary).

Ryder SP.

RNA. 2015 Apr;21(4):725-6. doi: 10.1261/rna.050005.115. No abstract available.

11.

A conserved three-nucleotide core motif defines Musashi RNA binding specificity.

Zearfoss NR, Deveau LM, Clingman CC, Schmidt E, Johnson ES, Massi F, Ryder SP.

J Biol Chem. 2014 Dec 19;289(51):35530-41. doi: 10.1074/jbc.M114.597112. Epub 2014 Nov 3.

12.

Allosteric inhibition of a stem cell RNA-binding protein by an intermediary metabolite.

Clingman CC, Deveau LM, Hay SA, Genga RM, Shandilya SM, Massi F, Ryder SP.

Elife. 2014 Jun 16;3. doi: 10.7554/eLife.02848.

13.

RNA recognition by the Caenorhabditis elegans oocyte maturation determinant OMA-1.

Kaymak E, Ryder SP.

J Biol Chem. 2013 Oct 18;288(42):30463-72. doi: 10.1074/jbc.M113.496547. Epub 2013 Sep 6.

14.

hnRNP A1 and secondary structure coordinate alternative splicing of Mag.

Zearfoss NR, Johnson ES, Ryder SP.

RNA. 2013 Jul;19(7):948-57. doi: 10.1261/rna.036780.112. Epub 2013 May 23.

15.

Metabolite sensing in eukaryotic mRNA biology.

Clingman CC, Ryder SP.

Wiley Interdiscip Rev RNA. 2013 Jul-Aug;4(4):387-96. doi: 10.1002/wrna.1167. Epub 2013 May 7. Review.

16.

A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels.

Tamburino AM, Ryder SP, Walhout AJ.

G3 (Bethesda). 2013 Feb;3(2):297-304. doi: 10.1534/g3.112.004390. Epub 2013 Feb 1.

17.

End-labeling oligonucleotides with chemical tags after synthesis.

Zearfoss NR, Ryder SP.

Methods Mol Biol. 2012;941:181-93. doi: 10.1007/978-1-62703-113-4_14.

18.

POS-1 and GLD-1 repress glp-1 translation through a conserved binding-site cluster.

Farley BM, Ryder SP.

Mol Biol Cell. 2012 Dec;23(23):4473-83. doi: 10.1091/mbc.E12-03-0216. Epub 2012 Oct 3.

19.

Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing.

Broderick JA, Salomon WE, Ryder SP, Aronin N, Zamore PD.

RNA. 2011 Oct;17(10):1858-69. doi: 10.1261/rna.2778911. Epub 2011 Aug 30.

20.

FBF represses the Cip/Kip cell-cycle inhibitor CKI-2 to promote self-renewal of germline stem cells in C. elegans.

Kalchhauser I, Farley BM, Pauli S, Ryder SP, Ciosk R.

EMBO J. 2011 Aug 5;30(18):3823-9. doi: 10.1038/emboj.2011.263.

21.

Pumilio RNA recognition: the consequence of promiscuity.

Ryder SP.

Structure. 2011 Mar 9;19(3):277-9. doi: 10.1016/j.str.2011.02.006.

22.

Quaking regulates Hnrnpa1 expression through its 3' UTR in oligodendrocyte precursor cells.

Zearfoss NR, Clingman CC, Farley BM, McCoig LM, Ryder SP.

PLoS Genet. 2011 Jan 6;7(1):e1001269. doi: 10.1371/journal.pgen.1001269.

23.

Insights into the structural basis of RNA recognition by STAR domain proteins.

Ryder SP, Massi F.

Adv Exp Med Biol. 2010;693:37-53. Review.

24.

A quantitative RNA code for mRNA target selection by the germline fate determinant GLD-1.

Wright JE, Gaidatzis D, Senften M, Farley BM, Westhof E, Ryder SP, Ciosk R.

EMBO J. 2011 Feb 2;30(3):533-45. doi: 10.1038/emboj.2010.334. Epub 2010 Dec 17.

25.

Quantitative approaches to monitor protein-nucleic acid interactions using fluorescent probes.

Pagano JM, Clingman CC, Ryder SP.

RNA. 2011 Jan;17(1):14-20. doi: 10.1261/rna.2428111. Epub 2010 Nov 22. Review.

26.

Hidden ribozymes in eukaryotic genome sequence.

Ryder SP.

F1000 Biol Rep. 2010 Jul 14;2. pii: 50. doi: 10.3410/B2-50.

27.

An economic framework to prioritize confirmatory tests after a high-throughput screen.

Swamidass SJ, Bittker JA, Bodycombe NE, Ryder SP, Clemons PA.

J Biomol Screen. 2010 Jul;15(6):680-6. doi: 10.1177/1087057110372803. Epub 2010 Jun 14.

28.

Structure and function of nematode RNA-binding proteins.

Kaymak E, Wee LM, Ryder SP.

Curr Opin Struct Biol. 2010 Jun;20(3):305-12. doi: 10.1016/j.sbi.2010.03.010. Epub 2010 Apr 24. Review.

29.

RNA recognition by the embryonic cell fate determinant and germline totipotency factor MEX-3.

Pagano JM, Farley BM, Essien KI, Ryder SP.

Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20252-7. doi: 10.1073/pnas.0907916106. Epub 2009 Nov 13.

30.

The N-terminal peptide of the syntaxin Tlg2p modulates binding of its closed conformation to Vps45p.

Furgason ML, MacDonald C, Shanks SG, Ryder SP, Bryant NJ, Munson M.

Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14303-8. doi: 10.1073/pnas.0902976106. Epub 2009 Aug 10.

31.

Monitoring assembly of ribonucleoprotein complexes by isothermal titration calorimetry.

Recht MI, Ryder SP, Williamson JR.

Methods Mol Biol. 2008;488:117-27. doi: 10.1007/978-1-60327-475-3_8.

32.

Quantitative analysis of protein-RNA interactions by gel mobility shift.

Ryder SP, Recht MI, Williamson JR.

Methods Mol Biol. 2008;488:99-115. doi: 10.1007/978-1-60327-475-3_7.

33.

RNA target specificity of the embryonic cell fate determinant POS-1.

Farley BM, Pagano JM, Ryder SP.

RNA. 2008 Dec;14(12):2685-97. doi: 10.1261/rna.1256708. Epub 2008 Oct 24.

34.

Post-transcriptional regulation of myelin formation.

Zearfoss NR, Farley BM, Ryder SP.

Biochim Biophys Acta. 2008 Aug;1779(8):486-94. doi: 10.1016/j.bbagrm.2008.06.003. Epub 2008 Jun 11. Review.

PMID:
18590840
35.

Regulation of maternal mRNAs in early development.

Farley BM, Ryder SP.

Crit Rev Biochem Mol Biol. 2008 Mar-Apr;43(2):135-62. doi: 10.1080/10409230801921338 . Review.

PMID:
18365862
36.

Molecular basis of RNA recognition by the embryonic polarity determinant MEX-5.

Pagano JM, Farley BM, McCoig LM, Ryder SP.

J Biol Chem. 2007 Mar 23;282(12):8883-94. Epub 2007 Jan 30.

37.

Oskar gains weight.

Ryder SP.

Nat Struct Mol Biol. 2006 Apr;13(4):297-9. No abstract available.

PMID:
16715044
38.

Specificity of the STAR/GSG domain protein Qk1: implications for the regulation of myelination.

Ryder SP, Williamson JR.

RNA. 2004 Sep;10(9):1449-58. Epub 2004 Jul 23.

39.

RNA target specificity of the STAR/GSG domain post-transcriptional regulatory protein GLD-1.

Ryder SP, Frater LA, Abramovitz DL, Goodwin EB, Williamson JR.

Nat Struct Mol Biol. 2004 Jan;11(1):20-8. Epub 2003 Dec 29.

PMID:
14718919
40.

Biochemical detection of adenosine and cytidine ionization within RNA by interference analysis.

Strobel SA, Jones FD, Oyelere AK, Ryder SP.

Nucleic Acids Res Suppl. 2003;(3):229-30.

PMID:
14510464
41.

Comparative analysis of hairpin ribozyme structures and interference data.

Ryder SP, Strobel SA.

Nucleic Acids Res. 2002 Mar 15;30(6):1287-91.

42.

An efficient ligation reaction promoted by a Varkud Satellite ribozyme with extended 5'- and 3'-termini.

Jones FD, Ryder SP, Strobel SA.

Nucleic Acids Res. 2001 Dec 15;29(24):5115-20.

43.

Investigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping.

Ryder SP, Oyelere AK, Padilla JL, Klostermeier D, Millar DP, Strobel SA.

RNA. 2001 Oct;7(10):1454-63.

44.

Biological catalysis. The hairpin's turn.

Strobel SA, Ryder SP.

Nature. 2001 Apr 12;410(6830):761-3. No abstract available.

PMID:
11298426
45.

Chemical probing of RNA by nucleotide analog interference mapping.

Ryder SP, Ortoleva-Donnelly L, Kosek AB, Strobel SA.

Methods Enzymol. 2000;317:92-109. No abstract available.

PMID:
10829274
46.
47.

Nucleotide analog interference mapping.

Ryder SP, Strobel SA.

Methods. 1999 May;18(1):38-50.

PMID:
10208815
48.

A minor groove RNA triple helix within the catalytic core of a group I intron.

Szewczak AA, Ortoleva-Donnelly L, Ryder SP, Moncoeur E, Strobel SA.

Nat Struct Biol. 1998 Dec;5(12):1037-42.

PMID:
9846872
49.

Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site.

Strobel SA, Ortoleva-Donnelly L, Ryder SP, Cate JH, Moncoeur E.

Nat Struct Biol. 1998 Jan;5(1):60-6.

PMID:
9437431

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