Barbara L. Golden - Related publications

Purdue University, West Lafayette, IN, United States 
RNA structure and function
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Su Z, Zhang K, Kappel K, Li S, Palo MZ, Pintilie GD, Rangan R, Luo B, Wei Y, Das R, Chiu W. Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution. Nature. PMID 34381213 DOI: 10.1038/s41586-021-03803-w   
2021 Yamagami R, Sieg JP, Bevilacqua PC. Functional Roles of Chelated Magnesium Ions in RNA Folding and Function. Biochemistry. 60: 2374-2386. PMID 34319696 DOI: 10.1021/acs.biochem.1c00012   
2021 Carlomagno T, Aguion P, Kirkpatrick J, Marchanka A. Identification of RNA base pairs and complete assignment of nucleobase resonances by 1H-detected solid-state NMR spectroscopy at 100 kHz MAS. Angewandte Chemie (International Ed. in English). PMID 34379871 DOI: 10.1002/anie.202107263   
2021 Stoute J, Liu KF. CLIP-Seq to identify targets and interactions of RNA binding proteins and RNA modifying enzymes. Methods in Enzymology. 658: 419-434. PMID 34517957 DOI: 10.1016/bs.mie.2021.08.001   
2021 Alonso D, Mondragón A. Mechanisms of catalytic RNA molecules. Biochemical Society Transactions. 49: 1529-1535. PMID 34415304 DOI: 10.1042/BST20200465   
2021 Zhou T, Wang H, Zeng C, Zhao Y. RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources. Bmc Bioinformatics. 22: 428. PMID 34496744 DOI: 10.1186/s12859-021-04349-4   
2021 Tang T, Han Y, Wang Y, Huang H, Qian P. Programmable System of Cas13-Mediated RNA Modification and Its Biological and Biomedical Applications. Frontiers in Cell and Developmental Biology. 9: 677587. PMID 34386490 DOI: 10.3389/fcell.2021.677587   
2021 Zhou W, Melamed D, Banyai G, Meyer C, Tuschl T, Wickens M, Cao J, Fields S. Expanding the binding specificity for RNA recognition by a PUF domain. Nature Communications. 12: 5107. PMID 34429425 DOI: 10.1038/s41467-021-25433-6   
2021 Cheng Y, Zhang S, Xu X, Chen SJ. Vfold2D-MC: A Physics-Based Hybrid Model for Predicting RNA Secondary Structure Folding. The Journal of Physical Chemistry. B. PMID 34473508 DOI: 10.1021/acs.jpcb.1c04731   
2021 Sakurai Y, Baeg K, Lam AYW, Shoji K, Tomari Y, Iwakawa HO. Cell-free reconstitution reveals the molecular mechanisms for the initiation of secondary siRNA biogenesis in plants. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34330830 DOI: 10.1073/pnas.2102889118   
2021 Bonilla SL, Denny SK, Shin JH, Alvarez-Buylla A, Greenleaf WJ, Herschlag D. High-throughput dissection of the thermodynamic and conformational properties of a ubiquitous class of RNA tertiary contact motifs. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34373334 DOI: 10.1073/pnas.2109085118   
2021 Phan HD, Lai LB, Zahurancik WJ, Gopalan V. The many faces of RNA-based RNase P, an RNA-world relic. Trends in Biochemical Sciences. PMID 34511335 DOI: 10.1016/j.tibs.2021.07.005   
2021 Furuzono T, Murata A, Okuda S, Mizutani K, Adachi T, Nakatani K. Speeding drug discovery targeting RNAs: An iterative "RNA selection-compounds screening cycle" for exploring RNA-small molecule pairs. Bioorganic & Medicinal Chemistry. 36: 116070. PMID 33773376 DOI: 10.1016/j.bmc.2021.116070   
2021 Zhao Y, Dukler N, Barshad G, Toneyan S, Danko CG, Siepel A. Deconvolution of Expression for Nascent RNA sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. Bioinformatics (Oxford, England). PMID 34382072 DOI: 10.1093/bioinformatics/btab582   
2021 Yu AM, Tu MJ. Deliver the promise: RNAs as a new class of molecular entities for therapy and vaccination. Pharmacology & Therapeutics. 107967. PMID 34403681 DOI: 10.1016/j.pharmthera.2021.107967   
2021 Zhang Y, Yang L, Chen LL. Characterization of Circular RNAs. Methods in Molecular Biology (Clifton, N.J.). 2372: 179-192. PMID 34417752 DOI: 10.1007/978-1-0716-1697-0_16   
2021 Hong S, Jeong D, Ryan J, Foo M, Tang X, Kim J. Design and Evaluation of Synthetic RNA-Based Incoherent Feed-Forward Loop Circuits. Biomolecules. 11. PMID 34439849 DOI: 10.3390/biom11081182   
2021 Gunawardene CD, Im JSH, White KA. RNA Structure Protects the 5'-end of an Uncapped Tombusvirus RNA Genome from Xrn Digestion. Journal of Virology. JVI0103421. PMID 34346764 DOI: 10.1128/JVI.01034-21   
2021 Zaepfel BL, Rothstein JD. RNA Is a Double-Edged Sword in ALS Pathogenesis. Frontiers in Cellular Neuroscience. 15: 708181. PMID 34349625 DOI: 10.3389/fncel.2021.708181   
2021 Thakur P, Abernathy S, Limbach PA, Addepalli B. Locating chemical modifications in RNA sequences through ribonucleases and LC-MS based analysis. Methods in Enzymology. 658: 1-24. PMID 34517943 DOI: 10.1016/bs.mie.2021.06.023   
2021 Deryusheva S, Talross GJ, Gall JG. SnoRNA guide activities - real and ambiguous. Rna (New York, N.Y.). PMID 34385348 DOI: 10.1261/rna.078916.121   
2021 Zhang H, Ding Y. Novel insights into the pervasive role of RNA structure in post-transcriptional regulation of gene expression in plants. Biochemical Society Transactions. PMID 34436520 DOI: 10.1042/BST20210318   
2021 Zhao X, Li Y, Duan Y, Amin A, Xie Y, Shi C, Ma C. A simple methodology for RNA isolation from bacteria by integration of formamide extraction and chitosan-modified silica purification. Analytical and Bioanalytical Chemistry. PMID 34505946 DOI: 10.1007/s00216-021-03644-6   
2021 Zhao Q, Zhao Z, Fan X, Yuan Z, Mao Q, Yao Y. Review of machine learning methods for RNA secondary structure prediction. Plos Computational Biology. 17: e1009291. PMID 34437528 DOI: 10.1371/journal.pcbi.1009291   
2021 Jiang J, Zhang T, Pan Y, Hu Z, Yuan J, Hu X, Zhang L, Zhang Y. Characterization of Long Non-coding RNA Associated Proteins by RNA-Immunoprecipitation. Methods in Molecular Biology (Clifton, N.J.). 2372: 19-26. PMID 34417739 DOI: 10.1007/978-1-0716-1697-0_3   
2021 Yang R, Zou Z, He L, Deng X, Wang H, Huang Z, Xue Q, Qing Z, Lei Y, Liu J. Zn2+-Coordination-Driven RNA Assembly with Retained Integrity and Biological Functions. Angewandte Chemie (International Ed. in English). PMID 34405498 DOI: 10.1002/anie.202110404   
2021 Lin TY, Mehta R, Glatt S. Pseudouridines in RNAs - switching atoms means shifting paradigms. Febs Letters. PMID 34468991 DOI: 10.1002/1873-3468.14188   
2021 Pusic P, Sonnleitner E, Bläsi U. Specific and Global RNA Regulators in . International Journal of Molecular Sciences. 22. PMID 34445336 DOI: 10.3390/ijms22168632   
2021 Mao K, Xiao Y. Learning the Fastest RNA Folding Path Based on Reinforcement Learning and Monte Carlo Tree Search. Molecules (Basel, Switzerland). 26. PMID 34361572 DOI: 10.3390/molecules26154420   
2021 Mollocana-Lara EC, Ni M, Agathos SN, Gonzales-Zubiate FA. The infinite possibilities of RNA therapeutics. Journal of Industrial Microbiology & Biotechnology. PMID 34463324 DOI: 10.1093/jimb/kuab063   
2021 Townshend RJL, Eismann S, Watkins AM, Rangan R, Karelina M, Das R, Dror RO. Geometric deep learning of RNA structure. Science (New York, N.Y.). 373: 1047-1051. PMID 34446608 DOI: 10.1126/science.abe5650   
2021 Wang Y, Fan J, Wang J, Zhu Y, Xu L, Tong D, Cheng H. ZFC3H1 prevents RNA trafficking into nuclear speckles through condensation. Nucleic Acids Research. PMID 34530450 DOI: 10.1093/nar/gkab774   
2021 Zhao B, Katuwawala A, Oldfield CJ, Hu G, Wu Z, Uversky VN, Kurgan L. Intrinsic Disorder in Human RNA-binding Proteins. Journal of Molecular Biology. 167229. PMID 34487791 DOI: 10.1016/j.jmb.2021.167229   
2021 Cavac E, Ramírez-Tapia LE, Martin CT. High salt transcription of DNA co-tethered with T7 RNA polymerase to beads generates increased yields of highly pure RNA. The Journal of Biological Chemistry. 100999. PMID 34303704 DOI: 10.1016/j.jbc.2021.100999   
2021 Islam MS, Bandyra KJ, Chao Y, Vogel J, Luisi BF. Impact of pseudo-uridylation, substrate fold and degradosome organization on the endonuclease activity of RNase E. Rna (New York, N.Y.). PMID 34341070 DOI: 10.1261/rna.078840.121   
2021 Mukherjee P, Raghava Kurup R, Hundley HA. RNA immunoprecipitation to identify in vivo targets of RNA editing and modifying enzymes. Methods in Enzymology. 658: 137-160. PMID 34517945 DOI: 10.1016/bs.mie.2021.06.005   
2021 Pandey M, Ojha D, Bansal S, Rode AB, Chawla G. From bench side to clinic: Potential and challenges of RNA vaccines and therapeutics in infectious diseases. Molecular Aspects of Medicine. 101003. PMID 34332771 DOI: 10.1016/j.mam.2021.101003   
2021 Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, Díaz de León Derby M, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, ... , et al. Accelerated RNA detection using tandem CRISPR nucleases. Nature Chemical Biology. PMID 34354262 DOI: 10.1038/s41589-021-00842-2   
2021 Giurgiu C, Fang Z, Aitken HRM, Kim SC, Pazienza L, Mittal S, Szostak JW. Structure-activity relationships in nonenzymatic template-directed RNA synthesis. Angewandte Chemie (International Ed. in English). PMID 34428345 DOI: 10.1002/anie.202109714   
2021 Jahns H, Degaonkar R, Podbevsek P, Gupta S, Bisbe A, Aluri K, Szeto J, Kumar P, LeBlanc S, Racie T, Brown CR, Castoreno A, Guenther DC, Jadhav V, Maier MA, et al. Small circular interfering RNAs (sciRNAs) as a potent therapeutic platform for gene-silencing. Nucleic Acids Research. PMID 34508350 DOI: 10.1093/nar/gkab724   
2021 Wei G, Almeida M, Pintacuda G, Coker H, Bowness JS, Ule J, Brockdorff N. Acute depletion of METTL3 implicates -methyladenosine in alternative intron/exon inclusion in the nascent transcriptome. Genome Research. 31: 1395-1408. PMID 34131006 DOI: 10.1101/gr.271635.120   
2021 Haack AJ, Lim FY, Kennedy DS, Day JH, Adams KN, Lee JJ, Berthier E, Theberge AB. RNA: A Self-Sampling Kit for the Collection of Peripheral Blood and Stabilization of RNA. Analytical Chemistry. PMID 34546711 DOI: 10.1021/acs.analchem.1c02008   
2021 Kabinger F, Stiller C, Schmitzová J, Dienemann C, Kokic G, Hillen HS, Höbartner C, Cramer P. Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis. Nature Structural & Molecular Biology. PMID 34381216 DOI: 10.1038/s41594-021-00651-0   
2021 Telzrow CL, Zwack PJ, Esher Righi S, Dietrich FS, Chan C, Owzar K, Alspaugh JA, Granek JA. Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries. G3 (Bethesda, Md.). PMID 34518880 DOI: 10.1093/g3journal/jkab301   
2021 Cui T, Dou Y, Tan P, Ni Z, Liu T, Wang D, Huang Y, Cai K, Zhao X, Xu D, Lin H, Wang D. RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation. Nucleic Acids Research. PMID 34551440 DOI: 10.1093/nar/gkab825   
2021 Marichal L, Gargowitsch L, Rubim RL, Sizun C, Kra K, Bressanelli S, Dong Y, Panahandeh S, Zandi R, Tresset G. Relationships between RNA Topology and Nucleocapsid Structure in a Model Icosahedral Virus. Biophysical Journal. PMID 34418368 DOI: 10.1016/j.bpj.2021.08.021   
2021 Tac HA, Koroglu M, Sezerman U. RDDSVM: accurate prediction of A-to-I RNA editing sites from sequence using support vector machines. Functional & Integrative Genomics. PMID 34529170 DOI: 10.1007/s10142-021-00805-9   
2021 Thind AS, Monga I, Thakur PK, Kumari P, Dindhoria K, Krzak M, Ranson M, Ashford B. Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology. Briefings in Bioinformatics. PMID 34329375 DOI: 10.1093/bib/bbab259   
2021 Oechslin N, Da Silva N, Szkolnicka D, Cantrelle FX, Hanoulle X, Moradpour D, Gouttenoire J. Hepatitis E Virus RNA-Dependent RNA Polymerase is Involved in RNA Replication and Infectious Particle Production. Hepatology (Baltimore, Md.). PMID 34387882 DOI: 10.1002/hep.32100   
2021 Gao Y, Ogilvie C, Raghavan A, Von Hoffmann C, Liang B. Generation and Assembly of Virus-Specific Nucleocapsids of the Respiratory Syncytial Virus. Journal of Visualized Experiments : Jove. PMID 34398139 DOI: 10.3791/62010