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Joseph A. Piccirilli - Related publications

Chemistry University of Chicago, Chicago, IL 
chemistry and biochemistryof nucleic acids
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36 most relevant papers in past 60 days:
Year Citation  Score
2022 Goh BC, Xiang X, Lescar J, Dedon PC. Crystal structure and functional analysis of mycobacterial erythromycin resistance methyltransferase Erm38 reveals its RNA binding site. The Journal of Biological Chemistry. 101571. PMID 35007529 DOI: 10.1016/j.jbc.2022.101571   
2022 Ross CJ, Ulitsky I. Discovering functional motifs in long noncoding RNAs. Wiley Interdisciplinary Reviews. Rna. e1708. PMID 34981665 DOI: 10.1002/wrna.1708   
2022 Yoo HB, Park SR, Hong KS, Yang I. Precise RNA Quantification by Counting Individual RNA Molecules Using High-Sensitivity Capillary Flow Cytometry. Analytical Chemistry. 94: 1752-1759. PMID 35026944 DOI: 10.1021/acs.analchem.1c04355   
2022 Danan C, Manickavel S, Hafner M. PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites. Methods in Molecular Biology (Clifton, N.J.). 2404: 167-188. PMID 34694609 DOI: 10.1007/978-1-0716-1851-6_9   
2022 Smith HN, Ma J, Wang Y. Analysis on RNA Motif-Based RNA Trafficking in Plants. Methods in Molecular Biology (Clifton, N.J.). 2316: 29-37. PMID 34845682 DOI: 10.1007/978-1-0716-1464-8_3   
2022 Chen L, Li Z, Zhang S, Zhang YH, Huang T, Cai YD. Predicting RNA 5-Methylcytosine Sites by Using Essential Sequence Features and Distributions. Biomed Research International. 2022: 4035462. PMID 35071593 DOI: 10.1155/2022/4035462   
2022 Su L, Zhao F, Yu H, Bai M, Xue J, Cao X, Chen F, Zhao Y. A bifunctional chemical signature enabling RNA 4-thiouridine enrichment sequencing with single-base resolution. Chemical Communications (Cambridge, England). PMID 34985087 DOI: 10.1039/d1cc06080e   
2022 Mudiyanselage SDD, Wang Y. Fluorescein-Based Electrophoretic Mobility Shift Assay. Methods in Molecular Biology (Clifton, N.J.). 2316: 133-140. PMID 34845691 DOI: 10.1007/978-1-0716-1464-8_12   
2022 Wandera KG, Beisel CL. Rapidly Characterizing CRISPR-Cas13 Nucleases Using Cell-Free Transcription-Translation Systems. Methods in Molecular Biology (Clifton, N.J.). 2404: 135-153. PMID 34694607 DOI: 10.1007/978-1-0716-1851-6_7   
2022 Niu M, Zou Q, Lin C. CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach. Plos Computational Biology. 18: e1009798. PMID 35051187 DOI: 10.1371/journal.pcbi.1009798   
2022 Qi S, Mota J, Chan SH, Villarreal J, Dai N, Arya S, Hromas RA, Rao MK, Corrêa IR, Gupta YK. RNA binding to human METTL3-METTL14 restricts -deoxyadenosine methylation of DNA . Elife. 11. PMID 35060905 DOI: 10.7554/eLife.67150   
2022 Gao F, Zheng K, Li YB, Jiang F, Han CY. A Cas6-based RNA tracking platform functioning in a fluorescence-activation mode. Nucleic Acids Research. PMID 35061906 DOI: 10.1093/nar/gkac014   
2022 Lee MJ, Lee I, Wang K. Recent Advances in RNA Therapy and Its Carriers to Treat the Single-Gene Neurological Disorders. Biomedicines. 10. PMID 35052837 DOI: 10.3390/biomedicines10010158   
2022 Ding D, Zhou L, Giurgiu C, Szostak JW. Kinetic explanations for the sequence biases observed in the nonenzymatic copying of RNA templates. Nucleic Acids Research. 50: 35-45. PMID 34893864 DOI: 10.1093/nar/gkab1202   
2022 Henke KB, Miller RM, Knoener RA, Scalf M, Spiniello M, Smith LM. Identifying Protein Interactomes of Target RNAs Using HyPR-MS. Methods in Molecular Biology (Clifton, N.J.). 2404: 219-244. PMID 34694612 DOI: 10.1007/978-1-0716-1851-6_12   
2022 Dong H, Xu B, Guo P, Zhang J, Yang X, Li L, Fu Y, Shi J, Zhang S, Zhu Y, Shi Y, Zhou F, Bian L, You W, Shi F, et al. Hidden RNA pairings counteract the "first-come, first-served" splicing principle to drive stochastic choice in splice variants. Science Advances. 8: eabm1763. PMID 35080968 DOI: 10.1126/sciadv.abm1763   
2022 Liu R, Yang J, Yao J, Zhao Z, He W, Su N, Zhang Z, Zhang C, Zhang Z, Cai H, Zhu L, Zhao Y, Quan S, Chen X, Yang Y. Optogenetic control of RNA function and metabolism using engineered light-switchable RNA-binding proteins. Nature Biotechnology. PMID 34980910 DOI: 10.1038/s41587-021-01112-1   
2022 Wu X, Ayalew W, Chu M, Pei J, Liang C, Bao P, Guo X, Yan P. Characterization of RNA Editome in the Mammary Gland of Yaks during the Lactation and Dry Periods. Animals : An Open Access Journal From Mdpi. 12. PMID 35049829 DOI: 10.3390/ani12020207   
2022 Jung JK, Alam KK, Lucks JB. ROSALIND: Rapid Detection of Chemical Contaminants with In Vitro Transcription Factor-Based Biosensors. Methods in Molecular Biology (Clifton, N.J.). 2433: 325-342. PMID 34985754 DOI: 10.1007/978-1-0716-1998-8_20   
2022 Zhang J, Eteleeb AM, Rozycki EB, Inkman MJ, Ly A, Scharf RE, Jayachandran K, Krasnick BA, Mazur T, White NM, Fields RC, Maher CA. : A Tool for the Detection of Annotated and Novel Small RNAs. Non-Coding Rna. 8. PMID 35076605 DOI: 10.3390/ncrna8010009   
2022 Chan CP, Jin DY. Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: Theme and variations. Rna (New York, N.Y.). PMID 35031583 DOI: 10.1261/rna.079016.121   
2022 Monaco AP. The selfish environment meets the selfish gene: Coevolution and inheritance of RNA and DNA pools: A model for organismal life incorporating coevolution, horizontal transfer, and inheritance of internal and external RNA and DNA pools.: A model for organismal life incorporating coevolution, horizontal transfer, and inheritance of internal and external RNA and DNA pools. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 44: e2100239. PMID 34985131 DOI: 10.1002/bies.202100239   
2022 Birot A, Kus K, Priest E, Al Alwash A, Castello A, Mohammed S, Vasiljeva L, Kilchert C. RNA-binding protein Mub1 and the nuclear RNA exosome act to fine-tune environmental stress response. Life Science Alliance. 5. PMID 34848435 DOI: 10.26508/lsa.202101111   
2022 Bhattarai DP, Aguilo F. mA RNA Immunoprecipitation Followed by High-Throughput Sequencing to Map N-Methyladenosine. Methods in Molecular Biology (Clifton, N.J.). 2404: 355-362. PMID 34694619 DOI: 10.1007/978-1-0716-1851-6_19   
2022 Fasching N, Petržílek J, Popitsch N, Herzog VA, Ameres SL. Transcriptome-Wide Profiling of RNA Stability. Methods in Molecular Biology (Clifton, N.J.). 2404: 311-330. PMID 34694617 DOI: 10.1007/978-1-0716-1851-6_17   
2022 Suthapot P, Xiao T, Felsenfeld G, Hongeng S, Wongtrakoongate P. The RNA helicases DDX5 and DDX17 facilitate neural differentiation of human pluripotent stem cells NTERA2. Life Sciences. 120298. PMID 35007564 DOI: 10.1016/j.lfs.2021.120298   
2022 Wu WS, Brown JS, Chen PH, Shiue SC, Lee DE, Lee HC. CLASH Analyst: A Web Server to Identify In Vivo RNA-RNA Interactions from CLASH Data. Non-Coding Rna. 8. PMID 35076587 DOI: 10.3390/ncrna8010006   
2022 Das A, Das D, Panda AC. Validation of Circular RNAs by PCR. Methods in Molecular Biology (Clifton, N.J.). 2392: 103-114. PMID 34773618 DOI: 10.1007/978-1-0716-1799-1_8   
2022 Wulf MG, Maguire S, Dai N, Blondel A, Posfai D, Krishnan K, Sun Z, Guan S, Corrêa IR. Chemical capping improves template switching and enhances sequencing of small RNAs. Nucleic Acids Research. 50: e2. PMID 34581823 DOI: 10.1093/nar/gkab861   
2022 Li F, Wang A. Transient Expression-Mediated Gene Silencing in Plants and Suppression of Gene Silencing with Viral Suppressors. Methods in Molecular Biology (Clifton, N.J.). 2400: 33-41. PMID 34905188 DOI: 10.1007/978-1-0716-1835-6_4   
2022 Schroeder GM, Cavender CE, Blau ME, Jenkins JL, Mathews DH, Wedekind JE. A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control. Nature Communications. 13: 199. PMID 35017488 DOI: 10.1038/s41467-021-27790-8   
2022 Xie J, Wen M, Zhang J, Wang Z, Wang M, Qiu Y, Zhao W, Zhu F, Yao M, Rong ZX, Hu W, Pei Q, Sun X, Li J, Mao Z, et al. The roles of RNA helicases in DNA damage repair and tumorigenesis reveal precision therapeutic strategies. Cancer Research. PMID 34987058 DOI: 10.1158/0008-5472.CAN-21-2187   
2022 Cawte AD, Iino H, Unrau PJ, Rueda DS. Single-Molecule RNA Imaging Using Mango II Arrays. Methods in Molecular Biology (Clifton, N.J.). 2404: 267-280. PMID 34694614 DOI: 10.1007/978-1-0716-1851-6_14   
2022 Pretorius LS, Chandra KA, Jooste AEC, Motaung LC, Parkinson LE, Geering ADW. Adaptation of a filter paper method for RNA template preparation for the detection of avocado sunblotch viroid by reverse transcription qPCR. Journal of Virological Methods. 114455. PMID 34998829 DOI: 10.1016/j.jviromet.2022.114455   
2022 Reautschnig P, Wahn N, Wettengel J, Schulz AE, Latifi N, Vogel P, Kang TW, Pfeiffer LS, Zarges C, Naumann U, Zender L, Li JB, Stafforst T. CLUSTER guide RNAs enable precise and efficient RNA editing with endogenous ADAR enzymes in vivo. Nature Biotechnology. PMID 34980913 DOI: 10.1038/s41587-021-01105-0   
2022 Bryll AR, Peterson CL. Functional interaction between the RNA exosome and the sirtuin deacetylase Hst3 maintains transcriptional homeostasis. Genes & Development. 36: 17-22. PMID 34916303 DOI: 10.1101/gad.348923.121