Recent Publications

All Ryder Lab publications can be viewed on myNCBI

Mennatallah M Y Albarqi, Sean P Ryder.
The endogenous mex-3 3´UTR is required for germline repression and contributes to optimal fecundity in C. elegans
PLoS Genet . 2021 Aug 23;17(8):e1009775. doi: 10.1371/journal.pgen.1009775. eCollection 2021 Aug.
PMID: 34424904

Sean P Ryder, Brittany R Morgan, Peren Coskun, Katianna Antkowiak, Francesca Massi.
Analysis of Emerging Variants in Structured Regions of the SARS-CoV-2 Genome.
Evol Bioinform Online. 2021 May 5;17:11769343211014167. doi: 10.1177/11769343211014167.
PMID: 34017166

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.
PMID: 32294479

Hu S, Ryan 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.
PMID: 30599151

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. No abstract available.
PMID: 30687814 PMCID: PMC6345105

Han B, Antkowiak KA, Rutigliano M, Ryder SP, Griffn EE.
Polo-like Kinase Couples Cytoplasmic Protein Gradients in the C. elegans Zygote.
Current Biology. 2018; 28(1):60-69.
PMID: 29276126, PMCID: PMC5763555

Dowdle ME, Imboden SB, Park S, Ryder SP, Sheets MD.
Horizontal Gel Electrophoresis for Enhanced Detection of Protein-RNA Complexes.
Journal of visualized experiments : JoVE. 2017; (125).
NIHMSID: NIHMS909022, PMID: 28784977, PMCID: PMC5613780

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. 2017; 5(1):e1295130.
PMID: 28702278, PMCID: PMC5501385

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. 2016; 245(9):925-36.
NIHMSID: NIHMS794597, PMID: 27294288, PMCID: PMC4981527

Ryder SP.
Protein-mRNA interactome capture: cartography of the mRNP landscape.
F1000Research. 2016; 5:2627.
PMID: 29098073, PMCID: PMC5642310

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. 2015; 34(1):108-18.
NIHMSID: NIHMS705200, PMID: 26096734, PMCID: PMC4507413

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; 23(5):903-911.
NIHMSID: NIHMS679858, PMID: 25914058, PMCID: PMC4874493

Ryder SP.
Personal reflection (RNA journal 20th anniversary).
RNA. 2015; 21(4):725-6.
PMID: 25780210, PMCID: PMC4371352

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. 2014; 289(51):35530-41.
PMID: 25368328, PMCID: PMC4271237

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; 3.
PMID: 24935936, PMCID: PMC4094780

Kaymak E, Ryder SP.
RNA recognition by the Caenorhabditis elegans oocyte maturation determinant OMA-1.
The Journal of biological chemistry. 2013; 288(42):30463-72.
PMID: 24014033, PMCID: PMC3798510

Zearfoss NR, Johnson ES, Ryder SP.
hnRNP A1 and secondary structure coordinate alternative splicing of Mag.
RNA. 2013; 19(7):948-57.
PMID: 23704325, PMCID: PMC3683929

Clingman CC, Ryder SP.
Metabolite sensing in eukaryotic mRNA biology.
Wiley interdisciplinary reviews. RNA. 2013; 4(4):387-96.
NIHMSID: NIHMS816492, PMID: 23653333, PMCID: PMC5026232

Tamburino AM, Ryder SP, Walhout AJ.
A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels.
G3 (Bethesda, Md.). 2013; 3(2):297-304.
PMID: 23390605, PMCID: PMC3564989

Farley BM, Ryder SP.
POS-1 and GLD-1 repress glp-1 translation through a conserved binding-site cluster.
Molecular biology of the cell. 2012; 23(23):4473-83.
PMID: 23034181, PMCID: PMC3510010

Zearfoss NR, Ryder SP.
End-labeling oligonucleotides with chemical tags after synthesis.
Methods in molecular biology (Clifton, N.J.). 2012; 941:181-93.
NIHMSID: NIHMS816497, PMID: 23065562, PMCID: PMC5026237