My Bibliography

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Albarqi MMY, Ryder SP. The endogenous mex-3 3´UTR is required for germline repression and contributes to optimal fecundity in C. elegans. PLoS Genet. 2021 Aug;17(8):e1009775. doi: 10.1371/journal.pgen.1009775. eCollection 2021 Aug. PubMed PMID: 34424904; PubMed Central PMCID: PMC8412283.

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Albarqi MMY, Ryder SP. The role of RNA-binding proteins in orchestrating germline development in Caenorhabditis elegans. Front Cell Dev Biol. 2022;10:1094295. doi: 10.3389/fcell.2022.1094295. eCollection 2022. Review. PubMed PMID: 36684428; PubMed Central PMCID: PMC9846511.

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Albarqi MM, Ryder SP. Multiple RNA regulatory pathways coordinate the activity and expression pattern of a conserved germline RNA-binding protein. [preprint]. 2021 January. Available from: https://www.biorxiv.org/content/10.1101/2021.01.15.426877v1. doi: https://doi.org/10.1101/2021.01.15.426877.

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Antkowiak KR, Coskun P, Noronha ST, Tavella D, Massi F, Ryder SP. A nematode model to evaluate microdeletion phenotype expression. G3 (Bethesda). 2024 Feb 7;14(2). doi: 10.1093/g3journal/jkad258. PubMed PMID: 37956108; PubMed Central PMCID: PMC10849325.

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Antkowiak KR, Coskun P, Noronha ST, Tavella D, Massi F, Ryder SP. A nematode model to evaluate microdeletion phenotype expression. [preprint]. 2022 November. [20 pages]. Available from: https://www.biorxiv.org/content/10.1101/2022.11.09.515676v1. doi: doi: https://doi.org/10.1101/2022.11.09.515676.

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Bohn MF, Shandilya SMD, 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. 2015 May 5;23(5):903-911. doi: 10.1016/j.str.2015.03.016. Epub 2015 Apr 23. PubMed PMID: 25914058; PubMed Central PMCID: PMC4874493.

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Broderick JA, Salomon WE, Ryder SP, Aronin N, Zamore PD. Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing. RNA. 2011 Oct;17(10):1858-69. doi: 10.1261/rna.2778911. Epub 2011 Aug 30. PubMed PMID: 21878547; PubMed Central PMCID: PMC3185918.

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Clingman CC, Ryder SP. Metabolite sensing in eukaryotic mRNA biology. Wiley Interdiscip Rev RNA. 2013 Jul-Aug;4(4):387-96. doi: 10.1002/wrna.1167. Epub 2013 May 7. Review. PubMed PMID: 23653333; PubMed Central PMCID: PMC5026232.

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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. 2014 Jun 16;3. doi: 10.7554/eLife.02848. PubMed PMID: 24935936; PubMed Central PMCID: PMC4094780.

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Dowdle ME, Imboden SB, Park S, Ryder SP, Sheets MD. Horizontal Gel Electrophoresis for Enhanced Detection of Protein-RNA Complexes. J Vis Exp. 2017 Jul 28;(125). doi: 10.3791/56031. PubMed PMID: 28784977; PubMed Central PMCID: PMC5613780.

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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. Dev Cell. 2015 Jul 6;34(1):108-18. doi: 10.1016/j.devcel.2015.05.024. Epub 2015 Jun 18. PubMed PMID: 26096734; PubMed Central PMCID: PMC4507413.

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Farley BM, Ryder SP. Regulation of maternal mRNAs in early development. Crit Rev Biochem Mol Biol. 2008 Mar-Apr;43(2):135-62. doi: 10.1080/10409230801921338. Review. PubMed PMID: 18365862.

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Farley BM, Ryder SP. POS-1 and GLD-1 repress glp-1 translation through a conserved binding-site cluster. Mol Biol Cell. 2012 Dec;23(23):4473-83. doi: 10.1091/mbc.E12-03-0216. Epub 2012 Oct 3. PubMed PMID: 23034181; PubMed Central PMCID: PMC3510010.

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Farley BM, Pagano JM, Ryder SP. RNA target specificity of the embryonic cell fate determinant POS-1. RNA. 2008 Dec;14(12):2685-97. doi: 10.1261/rna.1256708. Epub 2008 Oct 24. PubMed PMID: 18952820; PubMed Central PMCID: PMC2590972.

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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. Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14303-8. doi: 10.1073/pnas.0902976106. Epub 2009 Aug 10. PubMed PMID: 19667197; PubMed Central PMCID: PMC2732825.

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Han B, Antkowiak KR, Fan X, Rutigliano M, Ryder SP, Griffin EE. Polo-like Kinase Couples Cytoplasmic Protein Gradients in the C. elegans Zygote. Curr Biol. 2018 Jan 8;28(1):60-69.e8. doi: 10.1016/j.cub.2017.11.048. Epub 2017 Dec 21. PubMed PMID: 29276126; PubMed Central PMCID: PMC5763555.

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Hu S, Skelly LE, Kaymak E, Freeberg L, Lo TW, Kuersten S, Ryder SP, Haag ES. Multi-modal regulation of C. elegans hermaphrodite spermatogenesis by the GLD-1-FOG-2 complex. Dev Biol. 2019 Feb 15;446(2):193-205. doi: 10.1016/j.ydbio.2018.11.024. Epub 2018 Dec 30. PubMed PMID: 30599151; PubMed Central PMCID: PMC9200065.

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Jones FD, Ryder SP, Strobel SA. An efficient ligation reaction promoted by a Varkud Satellite ribozyme with extended 5'- and 3'-termini. Nucleic Acids Res. 2001 Dec 15;29(24):5115-20. doi: 10.1093/nar/29.24.5115. PubMed PMID: 11812844; PubMed Central PMCID: PMC97611.

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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. EMBO J. 2011 Aug 5;30(18):3823-9. doi: 10.1038/emboj.2011.263. PubMed PMID: 21822213; PubMed Central PMCID: PMC3173791.

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Kaymak E, Ryder SP. RNA recognition by the Caenorhabditis elegans oocyte maturation determinant OMA-1. J Biol Chem. 2013 Oct 18;288(42):30463-30472. doi: 10.1074/jbc.M113.496547. Epub 2013 Sep 6. PubMed PMID: 24014033; PubMed Central PMCID: PMC3798510.

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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. Dev Dyn. 2016 Sep;245(9):925-36. doi: 10.1002/dvdy.24426. Epub 2016 Jul 25. PubMed PMID: 27294288; PubMed Central PMCID: PMC4981527.

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Kaymak E, Wee LM, Ryder SP. Structure and function of nematode RNA-binding proteins. Curr Opin Struct Biol. 2010 Jun;20(3):305-12. doi: 10.1016/j.sbi.2010.03.010. Epub 2010 Apr 24. Review. PubMed PMID: 20418095; PubMed Central PMCID: PMC2916969.

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Pagano JM, Clingman CC, Ryder SP. Quantitative approaches to monitor protein-nucleic acid interactions using fluorescent probes. RNA. 2011 Jan;17(1):14-20. doi: 10.1261/rna.2428111. Epub 2010 Nov 22. Review. PubMed PMID: 21098142; PubMed Central PMCID: PMC3004055.

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Pagano JM, Farley BM, McCoig LM, Ryder SP. Molecular basis of RNA recognition by the embryonic polarity determinant MEX-5. J Biol Chem. 2007 Mar 23;282(12):8883-94. doi: 10.1074/jbc.M700079200. Epub 2007 Jan 30. PubMed PMID: 17264081.

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Pagano JM, Farley BM, Essien KI, Ryder SP. RNA recognition by the embryonic cell fate determinant and germline totipotency factor MEX-3. Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20252-7. doi: 10.1073/pnas.0907916106. Epub 2009 Nov 13. PubMed PMID: 19915141; PubMed Central PMCID: PMC2787150.

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Recht MI, Ryder SP, Williamson JR. Monitoring assembly of ribonucleoprotein complexes by isothermal titration calorimetry. Methods Mol Biol. 2008;488:117-27. doi: 10.1007/978-1-60327-475-3_8. PubMed PMID: 18982287; PubMed Central PMCID: PMC2922068.

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Ryder SP, Williamson JR. Specificity of the STAR/GSG domain protein Qk1: implications for the regulation of myelination. RNA. 2004 Sep;10(9):1449-58. doi: 10.1261/rna.7780504. Epub 2004 Jul 23. PubMed PMID: 15273320; PubMed Central PMCID: PMC1370631.

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Ryder SP. Personal reflection (RNA journal 20th anniversary). RNA. 2015 Apr;21(4):725-6. doi: 10.1261/rna.050005.115. PubMed PMID: 25780210; PubMed Central PMCID: PMC4371352.

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Ryder SP, Massi F. Insights into the structural basis of RNA recognition by STAR domain proteins. Adv Exp Med Biol. 2010;693:37-53. doi: 10.1007/978-1-4419-7005-3_3. Review. PubMed PMID: 21189684; PubMed Central PMCID: PMC5034770.

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Ryder SP. Pumilio RNA recognition: the consequence of promiscuity. Structure. 2011 Mar 9;19(3):277-9. doi: 10.1016/j.str.2011.02.006. PubMed PMID: 21397178.

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Ryder SP. Oskar gains weight. Nat Struct Mol Biol. 2006 Apr;13(4):297-9. doi: 10.1038/nsmb0406-297. PubMed PMID: 16715044.

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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. 2001 Oct;7(10):1454-63. PubMed PMID: 11680850; PubMed Central PMCID: PMC1370189.

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Ryder SP, Strobel SA. Nucleotide analog interference mapping. Methods. 1999 May;18(1):38-50. doi: 10.1006/meth.1999.0755. PubMed PMID: 10208815.

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Ryder SP, Recht MI, Williamson JR. Quantitative analysis of protein-RNA interactions by gel mobility shift. Methods Mol Biol. 2008;488:99-115. doi: 10.1007/978-1-60327-475-3_7. PubMed PMID: 18982286; PubMed Central PMCID: PMC2928675.

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Ryder SP, Ortoleva-Donnelly L, Kosek AB, Strobel SA. Chemical probing of RNA by nucleotide analog interference mapping. Methods Enzymol. 2000;317:92-109. doi: 10.1016/s0076-6879(00)17008-9. PubMed PMID: 10829274.

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Ryder SP, Frater LA, Abramovitz DL, Goodwin EB, Williamson JR. RNA target specificity of the STAR/GSG domain post-transcriptional regulatory protein GLD-1. Nat Struct Mol Biol. 2004 Jan;11(1):20-8. doi: 10.1038/nsmb706. Epub 2003 Dec 29. PubMed PMID: 14718919.

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Ryder SP, Strobel SA. Comparative analysis of hairpin ribozyme structures and interference data. Nucleic Acids Res. 2002 Mar 15;30(6):1287-91. doi: 10.1093/nar/30.6.1287. PubMed PMID: 11884625; PubMed Central PMCID: PMC101345.

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Ryder SP. Protein-mRNA interactome capture: cartography of the mRNP landscape. F1000Res. 2016;5:2627. doi: 10.12688/f1000research.9404.1. eCollection 2016. Review. PubMed PMID: 29098073; PubMed Central PMCID: PMC5642310.

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Ryder SP. Hidden ribozymes in eukaryotic genome sequence. F1000 Biol Rep. 2010 Jul 14;2. doi: 10.3410/B2-50. PubMed PMID: 20948783; PubMed Central PMCID: PMC2950038.

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Ryder SP, Strobel SA. Nucleotide analog interference mapping of the hairpin ribozyme: implications for secondary and tertiary structure formation. J Mol Biol. 1999 Aug 13;291(2):295-311. doi: 10.1006/jmbi.1999.2959. PubMed PMID: 10438622.

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Ryder SP. #CRISPRbabies: Notes on a Scandal. CRISPR J. 2018 Dec 1;1(6):355-357. doi: 10.1089/crispr.2018.29039.spr. Epub 2018 Dec 20. PubMed PMID: 30687814; PubMed Central PMCID: PMC6345105.

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Ryder SP, Morgan BR, Coskun P, Antkowiak K, Massi F. Analysis of Emerging Variants in Structured Regions of the SARS-CoV-2 Genome. Evol Bioinform Online. 2021;17:11769343211014167. doi: 10.1177/11769343211014167. eCollection 2021. PubMed PMID: 34017166; PubMed Central PMCID: PMC8114311.

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Strobel SA, Jones FD, Oyelere AK, Ryder SP. Biochemical detection of adenosine and cytidine ionization within RNA by interference analysis. Nucleic Acids Res Suppl. 2003;(3):229-30. doi: 10.1093/nass/3.1.229. PubMed PMID: 14510464.

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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. Nat Struct Biol. 1998 Jan;5(1):60-6. doi: 10.1038/nsb0198-60. PubMed PMID: 9437431.

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Strobel SA, Ryder SP. Biological catalysis. The hairpin's turn. Nature. 2001 Apr 12;410(6830):761-3. doi: 10.1038/35071209. PubMed PMID: 11298426.

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Swamidass SJ, Bittker JA, Bodycombe NE, Ryder SP, Clemons PA. An economic framework to prioritize confirmatory tests after a high-throughput screen. J Biomol Screen. 2010 Jul;15(6):680-6. doi: 10.1177/1087057110372803. Epub 2010 Jun 14. PubMed PMID: 20547534; PubMed Central PMCID: PMC3069998.

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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. Nat Struct Biol. 1998 Dec;5(12):1037-42. doi: 10.1038/4146. PubMed PMID: 9846872.

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Tamburino AM, Ryder SP, Walhout AJ. A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels. G3 (Bethesda). 2013 Feb;3(2):297-304. doi: 10.1534/g3.112.004390. Epub 2013 Feb 1. PubMed PMID: 23390605; PubMed Central PMCID: PMC3564989.

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Tamburino AM, Kaymak E, Shrestha S, Holdorf AD, Ryder SP, Walhout AJM. PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions. Translation (Austin). 2017;5(1):e1295130. doi: 10.1080/21690731.2017.1295130. eCollection 2017. PubMed PMID: 28702278; PubMed Central PMCID: PMC5501385.

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Tavella D, Ertekin A, Schaal H, Ryder SP, Massi F. A Disorder-to-Order Transition Mediates RNA Binding of the Caenorhabditis elegans Protein MEX-5. Biophys J. 2020 Apr 21;118(8):2001-2014. doi: 10.1016/j.bpj.2020.02.032. Epub 2020 Mar 19. PubMed PMID: 32294479; PubMed Central PMCID: PMC7175634.