Dawn A. Defenbaugh, Ph.D. - Related publications

2009 Microbiology & Immunology Georgetown University, Washington, DC 
Virology, Biochemistry
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50 most relevant papers in past 60 days:
Year Citation  Score
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 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 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 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 Brown RS, Kim L, Kielian M. Specific Recognition of a Stem-Loop RNA Structure by the Alphavirus Capsid Protein. Viruses. 13. PMID 34452382 DOI: 10.3390/v13081517   
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 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 Duan N, Arroyo M, Deng W, Cardoso MC, Leonhardt H. Visualization and characterization of RNA-protein interactions in living cells. Nucleic Acids Research. PMID 34313753 DOI: 10.1093/nar/gkab614   
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 Shan M, Ji X, Janssen K, Silverman IM, Humenik J, Garcia BA, Liebhaber SA, Gregory BD. Dynamic changes in RNA-protein interactions and RNA secondary structure in mammalian erythropoiesis. Life Science Alliance. 4. PMID 34315813 DOI: 10.26508/lsa.202000659   
2021 Hallegger M, Chakrabarti AM, Lee FCY, Lee BL, Amalietti AG, Odeh HM, Copley KE, Rubien JD, Portz B, Kuret K, Huppertz I, Rau F, Patani R, Fawzi NL, Shorter J, et al. TDP-43 condensation properties specify its RNA-binding and regulatory repertoire. Cell. PMID 34380047 DOI: 10.1016/j.cell.2021.07.018   
2021 Das B, Murata A, Nakatani K. A small-molecule fluorescence probe ANP77 for sensing RNA internal loop of C, U and A/CC motifs and their binding molecules. Nucleic Acids Research. PMID 34358308 DOI: 10.1093/nar/gkab650   
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   
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 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 Rachez C, Legendre R, Costallat M, Varet H, Yi J, Kornobis E, Muchardt C. HP1γ binding pre-mRNA intronic repeats modulates RNA splicing decisions. Embo Reports. e52320. PMID 34312949 DOI: 10.15252/embr.202052320   
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 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 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 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 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 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 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 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 Lanjanian H, Nematzadeh S, Hosseini S, Torkamanian-Afshar M, Kiani F, Moazzam-Jazi M, Aydin N, Masoudi-Nejad A. High-throughput analysis of the interactions between viral proteins and host cell RNAs. Computers in Biology and Medicine. 135: 104611. PMID 34246161 DOI: 10.1016/j.compbiomed.2021.104611   
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 Wu T, Nance J, Chu F, Fazzio TG. Characterization of R-loop-interacting proteins in embryonic stem cells reveals roles in ribosomal RNA processing and gene expression. Molecular & Cellular Proteomics : McP. 100142. PMID 34478875 DOI: 10.1016/j.mcpro.2021.100142   
2021 Ding P, Kharytonchyk S, Kuo N, Cannistraci E, Flores H, Chaudhary R, Sarkar M, Dong X, Telesnitsky A, Summers MF. 5'-Cap sequestration is an essential determinant of HIV-1 genome packaging. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34493679 DOI: 10.1073/pnas.2112475118   
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 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 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 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 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 Wang Y, Li G, Li X, Wang Y, Huang X, Hu X, Gao J. ecRESCUE: a novel ecDHFR-regulated RESCUE system with reduced RNA off-targeting activity. Cell Communication and Signaling : Ccs. 19: 81. PMID 34332602 DOI: 10.1186/s12964-021-00759-2   
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 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 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 Höfler S, Lukat P, Blankenfeldt W, Carlomagno T. Eukaryotic Box C/D methylation machinery has two non-symmetric protein assembly sites. Scientific Reports. 11: 17561. PMID 34475498 DOI: 10.1038/s41598-021-97030-y   
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 English AM, Green KM, Moon SL. A (dis)integrated stress response: Genetic diseases of eIF2α regulators. Wiley Interdisciplinary Reviews. Rna. e1689. PMID 34463036 DOI: 10.1002/wrna.1689   
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 Pyle JD, Whelan SPJ. Isolation of reconstructed functional ribonucleoprotein complexes of Machupo virus. Journal of Virology. JVI0105421. PMID 34432522 DOI: 10.1128/JVI.01054-21   
2021 Floro J, Dai A, Metzger A, Mora-Martin A, Ganem NJ, Cifuentes D, Wu CS, Dalal J, Lyons SM, Labadorf A, Flynn RL. SDE2 is an essential gene required for ribosome biogenesis and the regulation of alternative splicing. Nucleic Acids Research. PMID 34365507 DOI: 10.1093/nar/gkab647   
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 Shivalingappa PKM, Sharma V, Shiras A, Bapat SA. RNA binding motif 47 (RBM47): emerging roles in vertebrate development, RNA editing and cancer. Molecular and Cellular Biochemistry. PMID 34499322 DOI: 10.1007/s11010-021-04256-5   
2021 Aoyama JJ, Raina M, Storz G. Synthetic dual-function RNA reveals features necessary for target regulation. Journal of Bacteriology. JB0034521. PMID 34460309 DOI: 10.1128/JB.00345-21   
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 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 Du Pont KE, McCullagh M, Geiss BJ. Conserved motifs in the flavivirus NS3 RNA helicase enzyme. Wiley Interdisciplinary Reviews. Rna. e1688. PMID 34472205 DOI: 10.1002/wrna.1688   
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