King S, Singh M. Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers. PLoS Comput Biol. 2023;19(3):e1010966. PMCID: PMC10035887

Wang D, Shalamberidze A, Arguello E, Purse B, Kleiner R. Live-Cell RNA Imaging with Metabolically Incorporated Fluorescent Nucleosides. J Am Chem Soc. 2022;144(32):14647–14656. PMCID: PMC9940818

Arguello E, Li A, Sun X, Eggert T, Mairhofer E, Kleiner R. Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases. Nat Commun. 2022;13(1):4176. PMCID: PMC9296451

Li A, Sun X, Arguello E, Kleiner R. Chemical Method to Sequence 5-Formylcytosine on RNA. ACS Chem Biol. 2022;17(3):503–508. PMCID: PMC9357364

Kleiner R. Interrogating the transcriptome with metabolically incorporated ribonucleosides. Mol Omics. 2021;17(6):833–841. PMCID: PMC8648987

Chen P, Hussmann J, Yan J, Knipping F, Ravisankar P, Chen P-F, Chen C, Nelson J, Newby G, Sahin M, Osborn M, Weissman J, Adamson B, Liu D. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell. 2021;184(22):5635–5652.e29. PMCID: PMC8584034

Dai W, Li A, Yu N, Nguyen T, Leach R, Wühr M, Kleiner R. Activity-based RNA-modifying enzyme probing reveals DUS3L-mediated dihydrouridylation. Nat Chem Biol. 2021;17(11):1178–1187. PMCID: PMC8551019

Etzion-Fuchs A, Todd D, Singh M. dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains. Nucleic Acids Res. 2021;49(13):e78. PMCID: PMC8287948

Moore R, Kaletsky R, Lesnik C, Cota V, Blackman E, Parsons L, Gitai Z, Murphy C. The role of the Cer1 transposon in horizontal transfer of transgenerational memory. Cell. 2021;184(18):4697–4712.e18. PMCID: PMC8812995

Moore R, Kaletsky R, Murphy C. Protocol for transgenerational learned pathogen avoidance behavior assays in . STAR Protoc. 2021;2(1):100384. PMCID: PMC7960678

Seo K, Kleiner R. Mechanisms of epitranscriptomic gene regulation. Biopolymers. 2021;112(1):e23403. PMCID: PMC7855325

Wang D, Zhang Y, Kleiner R. Cell- and Polymerase-Selective Metabolic Labeling of Cellular RNA with 2’-Azidocytidine. J Am Chem Soc. 2020;142(34):14417–14421. PMCID: PMC7720414

Chen H, Gregor T. Using RNA Tags for Multicolor Live Imaging of Chromatin Loci and Transcription in Drosophila Embryos. Methods Mol Biol. 2020;2166:373–384. PMCID: PMC8130451

Trcek T, Douglas T, Grosch M, Yin Y, Eagle W, Gavis E, Shroff H, Rothenberg E, Lehmann R. Sequence-Independent Self-Assembly of Germ Granule mRNAs into Homotypic Clusters. Mol Cell. 2020;78(5):941–950.e12. PMCID: PMC7325742

Garcia D, Leach R, Wadsworth G, Choudhary K, Li H, Aviran S, Kim H, Zakian V. Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP. Nat Commun. 2020;11(1):2173. PMCID: PMC7195438

Sanders D, Kedersha N, Lee D, Strom A, Drake V, Riback J, Bracha D, Eeftens J, Iwanicki A, Wang A, Wei M-T, Whitney G, Lyons S, Anderson P, Jacobs W, Ivanov P, Brangwynne C. Competing Protein-RNA Interaction Networks Control Multiphase Intracellular Organization. Cell. 2020;181(2):306–324.e28. PMCID: PMC7816278

Nechay M, Kleiner R. High-throughput approaches to profile RNA-protein interactions. Curr Opin Chem Biol. 2020;54:37–44. PMCID: PMC7131871

Kobren S, Singh M. Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions. Nucleic Acids Res. 2019;47(2):582–593. PMCID: PMC6344845

Nogalski M, Solovyov A, Kulkarni A, Desai N, Oberstein A, Levine A, Ting D, Shenk T, Greenbaum B. A tumor-specific endogenous repetitive element is induced by herpesviruses. Nat Commun. 2019;10(1):90. PMCID: PMC6327058

Arguello E, Srikumar T, Kleiner R. A Photocrosslinking-Based RNA Chemical Proteomics Approach to Profile m A-Regulated Protein-RNA Interactions. Curr Protoc Nucleic Acid Chem. 2018;75(1):e69. PMID: 30408339

Dine E, Gil A, Uribe G, Brangwynne C, Toettcher J. Protein Phase Separation Provides Long-Term Memory of Transient Spatial Stimuli. Cell Syst. 2018;6(6):655–663.e5. PMCID: PMC6023754

Kleiner R. Reading the RNA Code. Biochemistry. 2018;57(1):11–12. PMID: 28937209

Arguello E, DeLiberto A, Kleiner R. RNA Chemical Proteomics Reveals the N-Methyladenosine (mA)-Regulated Protein-RNA Interactome. J Am Chem Soc. 2017;139(48):17249–17252. PMID: 29140688

Dine E, Toettcher J. Optogenetic Reconstitution for Determining the Form and Function of Membraneless Organelles. Biochemistry. 2018;57(17):2432–2436. PMCID: PMC5972035

Yin P, Deng D, Yan C, Pan X, Xi J, Yan N, Shi Y. Specific DNA-RNA hybrid recognition by TAL effectors. Cell Rep. 2012;2(4):707–13. PMID: 23022487

Yin P, Li Q, Yan C, Liu Y, Liu J, Yu F, Wang Z, Long J, He J, Wang H-W, Wang J, Zhu J-K, Shi Y, Yan N. Structural basis for the modular recognition of single-stranded RNA by PPR proteins. Nature. 2013;504(7478):168–71. PMID: 24162847

Wang X, Paucek R, Gooding A, Brown Z, Ge E, Muir T, Cech T. Molecular analysis of PRC2 recruitment to DNA in chromatin and its inhibition by RNA. Nat Struct Mol Biol. 2017;24(12):1028–1038. PMCID: PMC5771497

Webb C, Zakian V. Telomerase RNA is more than a DNA template. RNA Biol. 2016;13(8):683–9. PMCID: PMC4993324

Tamayo J, Teramoto T, Chatterjee S, Hall T, Gavis E. The Drosophila hnRNP F/H Homolog Glorund Uses Two Distinct RNA-Binding Modes to Diversify Target Recognition. Cell Rep. 2017;19(1):150–161. PMCID: PMC5392723

Sanders D, Brangwynne C. Neurodegenerative disease: RNA repeats put a freeze on cells. Nature. 2017;546(7657):215–216. PMID: 28562583

Son H, Seo M, Ham S, Hwang W, Lee D, An S, Artan M, Seo K, Kaletsky R, Arey R, Ryu Y, Ha C, Kim Y, Murphy C, Roh T-Y, Nam H, Lee S-J. RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans. Nat Commun. 2017;8:14749. PMCID: PMC5347137

Taylor N, Elbaum-Garfinkle S, Vaidya N, Zhang H, Stone H, Brangwynne C. Biophysical characterization of organelle-based RNA/protein liquid phases using microfluidics. Soft Matter. 2016;12(45):9142–9150. PMCID: PMC6724727

López-Panadès E, Gavis E, Casacuberta E. Specific Localization of the Drosophila Telomere Transposon Proteins and RNAs, Give Insight in Their Behavior, Control and Telomere Biology in This Organism. PLoS One. 2015;10(6):e0128573. PMCID: PMC4467039

Webb C, Zakian V. Telomerase RNA stem terminus element affects template boundary element function, telomere sequence, and shelterin binding. Proc Natl Acad Sci U S A. 2015;112(36):11312–7. PMCID: PMC4568702

Webb C, Zakian V. Telomere les(i/s)ons from a telomerase RNA mutant. Cell Cycle. 2015;14(24):3769–70. PMCID: PMC4825745

Svenningsen S, Tu K, Bassler B. Gene dosage compensation calibrates four regulatory RNAs to control Vibrio cholerae quorum sensing. EMBO J. 2009;28(4):429–39. PMCID: PMC2632942