Stacy I. Chamberlin, Ph.D. - Related publications

Affiliations: 
2001 University of North Carolina, Chapel Hill, Chapel Hill, NC 
Area:
Structural and Chemical Biology of the Transcriptome
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Chan D, Feng C, England WE, Wyman D, Flynn RA, Wang X, Shi Y, Mortazavi A, Spitale RC. Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing. Nucleic Acids Research. PMID 34634799 DOI: 10.1093/nar/gkab885   
2021 Hong X, Zheng J, Xie J, Tong X, Liu X, Song Q, Liu S, Liu S. RR3DD: an RNA global structure-based RNA three-dimensional structural classification database. Rna Biology. 1-9. PMID 34663179 DOI: 10.1080/15476286.2021.1989200   
2021 Jang B, Jang H, Kim H, Kim M, Jeong M, Lee GS, Lee K, Lee H. Protein-RNA interaction guided chemical modification of Dicer substrate RNA nanostructures for superior in vivo gene silencing. Journal of Controlled Release : Official Journal of the Controlled Release Society. PMID 34763005 DOI: 10.1016/j.jconrel.2021.11.009   
2021 Guo X, Tariq M, Lai Y, Kanwal S, Lv Y, Wang X, Li N, Jiang M, Meng J, Hu J, Yuan J, Luo Z, Ward C, Volpe G, Wang D, et al. Capture of the newly transcribed RNA interactome using click chemistry. Nature Protocols. PMID 34697467 DOI: 10.1038/s41596-021-00609-y   
2021 Hohmann KF, Blümler A, Heckel A, Fürtig B. The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements. Nucleic Acids Research. PMID 34614185 DOI: 10.1093/nar/gkab876   
2021 Bevilacqua PC, Williams AM, Chou HL, Assmann S. RNA Multimerization as an Organizing Force for Liquid-Liquid Phase Separation. Rna (New York, N.Y.). PMID 34706977 DOI: 10.1261/rna.078999.121   
2021 Soszynska-Jozwiak M, Pszczola M, Piasecka J, Peterson JM, Moss WN, Taras-Goslinska K, Kierzek R, Kierzek E. Universal and strain specific structure features of segment 8 genomic RNA of influenza A virus - application of 4-thiouridine photocrosslinking. The Journal of Biological Chemistry. 101245. PMID 34688660 DOI: 10.1016/j.jbc.2021.101245   
2021 Sutanto K, Turcotte M. Assessing Global-Local Secondary Structure Fingerprints to Classify RNA Sequences with Deep Learning. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34633933 DOI: 10.1109/TCBB.2021.3118358   
2021 Chen B, Shi H, Zhang J, Zhou C, Han M, Jiang W, Lai Y, Tu X, Li H. CRISPR-based RNA-binding protein mapping in live cells. Biochemical and Biophysical Research Communications. 583: 79-85. PMID 34735883 DOI: 10.1016/j.bbrc.2021.10.059   
2021 Choi MH, Nguyen VT, Ravi Kumara GS, Seo YJ. RNA Polymerase-Mediated Stepwise RNA-Primed RNA Polymerization for Site-Specific Multiple Labeling into RNA: A Fluorescence Resonance Energy Transfer Probe Detects the Structural Change of an RNA G-Quadruplex. Acs Synthetic Biology. PMID 34762391 DOI: 10.1021/acssynbio.1c00418   
2021 Endo M, Kim JI, Shioi NA, Iwai S, Kuraoka I. endonuclease V is a ribonuclease specific for inosine-containing single-stranded RNA. Open Biology. 11: 210148. PMID 34665969 DOI: 10.1098/rsob.210148   
2021 Zhao J, Hu H, Wang S, Wang L, Wang R. Regulation and Site-Specific Covalent Labeling of via Genetic Encoding Expansion. Genes. 12. PMID 34680884 DOI: 10.3390/genes12101488   
2021 Shatoff E, Bundschuh R. dsRBPBind: Modeling the effect of RNA secondary structure on double stranded RNA-protein binding. Bioinformatics (Oxford, England). PMID 34668517 DOI: 10.1093/bioinformatics/btab724   
2021 Radecki P, Uppuluri R, Deshpande K, Aviran S. Accurate detection of RNA stem-loops in structurome data reveals widespread association with protein binding sites. Rna Biology. 1-16. PMID 34606413 DOI: 10.1080/15476286.2021.1971382   
2021 Wang Y, Yang Y, Ma Z, Wong KC, Li X. EDCNN: Identification of Genome-Wide RNA-binding Proteins Using Evolutionary Deep Convolutional Neural Network. Bioinformatics (Oxford, England). PMID 34694393 DOI: 10.1093/bioinformatics/btab739   
2021 Ageely EA, Chilamkurthy R, Jana S, Abdullahu L, O'Reilly D, Jensik PJ, Damha MJ, Gagnon KT. Gene editing with CRISPR-Cas12a guides possessing ribose-modified pseudoknot handles. Nature Communications. 12: 6591. PMID 34782635 DOI: 10.1038/s41467-021-26989-z   
2021 Mulroney L, Wulf M, Schildkraut I, Tzertzinis G, Buswell J, Jain M, Olsen HE, Diekhans M, Corrêa IR, Akeson M, Ettwiller L. Identification of high confidence human poly(A) RNA isoform scaffolds using nanopore sequencing. Rna (New York, N.Y.). PMID 34728536 DOI: 10.1261/rna.078703.121   
2021 Mulroney L, Wulf M, Schildkraut I, Tzertzinis G, Buswell J, Jain M, Olsen HE, Diekhans M, Corrêa IR, Akeson M, Ettwiller L. Identification of high confidence human poly(A) RNA isoform scaffolds using nanopore sequencing. Rna (New York, N.Y.). PMID 34728536 DOI: 10.1261/rna.078703.121   
2021 Deng X, Wang S, Han Z, Gong W, Liu Y, Li C. Dynamics of binding interactions of TDP-43 and RNA:an equally weighted multiscale elastic network model study. Proteins. PMID 34599611 DOI: 10.1002/prot.26255   
2021 Zhang Z, Chen T, Chen HX, Xie YY, Chen LQ, Zhao YL, Liu BD, Jin L, Zhang W, Liu C, Ma DZ, Chai GS, Zhang Y, Zhao WS, Ng WH, et al. Systematic calibration of epitranscriptomic maps using a synthetic modification-free RNA library. Nature Methods. PMID 34594034 DOI: 10.1038/s41592-021-01280-7   
2021 Murthy AC, Tang WS, Jovic N, Janke AM, Seo DH, Perdikari TM, Mittal J, Fawzi NL. Molecular interactions contributing to FUS SYGQ LC-RGG phase separation and co-partitioning with RNA polymerase II heptads. Nature Structural & Molecular Biology. 28: 923-935. PMID 34759379 DOI: 10.1038/s41594-021-00677-4   
2021 Zhang S, Sun J, Gu M, Wang G, Wang X. Circular RNA: A promising new star for the diagnosis and treatment of colorectal cancer. Cancer Medicine. PMID 34796685 DOI: 10.1002/cam4.4398   
2021 Xiao L, Jun YW, Kool ET. DNA tiling enables precise acylation-based labeling and control of mRNA. Angewandte Chemie (International Ed. in English). PMID 34624169 DOI: 10.1002/anie.202112106   
2021 Zhou M, Wang DO, Li W, Zheng J. RNA adduction derived from electrophilic species in vitro and in vivo. Chemico-Biological Interactions. 351: 109748. PMID 34801539 DOI: 10.1016/j.cbi.2021.109748   
2021 Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, et al. Noncoding RNAs: biology and applications-a Keystone Symposia report. Annals of the New York Academy of Sciences. PMID 34791665 DOI: 10.1111/nyas.14713   
2021 Zhang D, Chen SJ, Zhou R. Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model. The Journal of Physical Chemistry. B. PMID 34694128 DOI: 10.1021/acs.jpcb.1c07288   
2021 Malone B, Campbell EA, Darst SA. CoV-er all the bases: Structural perspectives of SARS-CoV-2 RNA synthesis. The Enzymes. 49: 1-37. PMID 34696829 DOI: 10.1016/bs.enz.2021.06.004   
2021 Peng H, Latifi B, Müller S, Lupták A, Chen IA. Self-cleaving ribozymes: substrate specificity and synthetic biology applications. Rsc Chemical Biology. 2: 1370-1383. PMID 34704043 DOI: 10.1039/d0cb00207k   
2021 Chatterjee B, Shen CJ, Majumder P. RNA Modifications and RNA Metabolism in Neurological Disease Pathogenesis. International Journal of Molecular Sciences. 22. PMID 34769301 DOI: 10.3390/ijms222111870   
2021 Roden CA, Gladfelter AS. Design considerations for analyzing protein translation regulation by condensates. Rna (New York, N.Y.). PMID 34670845 DOI: 10.1261/rna.079002.121   
2021 Su L, Chen F, Yu H, Yan H, Zhao F, Fan C, Zhao Y. Addition-Elimination Mechanism-Activated Nucleotide Transition Sequencing for RNA Dynamics Profiling. Analytical Chemistry. PMID 34612623 DOI: 10.1021/acs.analchem.1c03361   
2021 Luige O, Bose PP, Stulz R, Steunenberg P, Brun O, Andersson S, Murtola M, Strömberg R. Zn-Dependent peptide nucleic acid-based artificial ribonucleases with unprecedented efficiency and specificity. Chemical Communications (Cambridge, England). PMID 34590632 DOI: 10.1039/d1cc04383h   
2021 Quinodoz SA, Jachowicz JW, Bhat P, Ollikainen N, Banerjee AK, Goronzy IN, Blanco MR, Chovanec P, Chow A, Markaki Y, Thai J, Plath K, Guttman M. RNA promotes the formation of spatial compartments in the nucleus. Cell. 184: 5775-5790.e30. PMID 34739832 DOI: 10.1016/j.cell.2021.10.014   
2021 Chen X, Rechavi O. Plant and animal small RNA communications between cells and organisms. Nature Reviews. Molecular Cell Biology. PMID 34707241 DOI: 10.1038/s41580-021-00425-y   
2021 Das AS, Alfonzo JD, Accornero F. The importance of RNA modifications: From cells to muscle physiology. Wiley Interdisciplinary Reviews. Rna. e1700. PMID 34664402 DOI: 10.1002/wrna.1700   
2021 Fu L, Cao Y, Wu J, Peng Q, Nie Q, Xie X. UFold: fast and accurate RNA secondary structure prediction with deep learning. Nucleic Acids Research. PMID 34792173 DOI: 10.1093/nar/gkab1074   
2021 Li X, Peng J, Yi C. The epitranscriptome of small non-coding RNAs. Non-Coding Rna Research. 6: 167-173. PMID 34820590 DOI: 10.1016/j.ncrna.2021.10.002   
2021 Ojha N, Diaz Quiroz JF, Rosenthal JJC. In vitro and in cellula site-directed RNA editing using the λNDD-BoxB system. Methods in Enzymology. 658: 335-358. PMID 34517953 DOI: 10.1016/bs.mie.2021.06.009   
2021 Roy S, Boral S, Maiti S, Kushwaha T, Basak AJ, Lee W, Basak A, Gholap SL, Inampudi KK, De S. Structural and dynamic studies of the human RNA binding protein RBM3 reveals the molecular basis of its oligomerization and RNA recognition. The Febs Journal. PMID 34837346 DOI: 10.1111/febs.16301   
2021 Chauhan A, Avti PK, Shekhar N, Prajapat M, Sarma P, Sangwan N, Singh J, Bhattacharyya A, Kumar S, Kaur H, Sharma S, Prakash A, Medhi B. An insight into the simulation directed understanding of the mechanism in SARS CoV-2 N-CTD, dimer integrity, and RNA-binding: Identifying potential antiviral inhibitors. Journal of Biomolecular Structure & Dynamics. 1-13. PMID 34751101 DOI: 10.1080/07391102.2021.1996463   
2021 Kang J, Tang Q, He J, Li L, Yang N, Yu S, Wang M, Zhang Y, Lin J, Cui T, Hu Y, Tan P, Cheng J, Zheng H, Wang D, et al. RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility. Nucleic Acids Research. PMID 34718726 DOI: 10.1093/nar/gkab997   
2021 Zhu H, Fu H, Cui T, Ning L, Shao H, Guo Y, Ke Y, Zheng J, Lin H, Wu X, Liu G, He J, Han X, Li W, Zhao X, et al. RNAPhaSep: a resource of RNAs undergoing phase separation. Nucleic Acids Research. PMID 34718740 DOI: 10.1093/nar/gkab985   
2021 Mańka R, Janas P, Sapoń K, Janas T, Janas T. Role of RNA Motifs in RNA Interaction with Membrane Lipid Rafts: Implications for Therapeutic Applications of Exosomal RNAs. International Journal of Molecular Sciences. 22. PMID 34502324 DOI: 10.3390/ijms22179416   
2021 Johnson KA, Dangerfield T. Mechanisms of inhibition of viral RNA replication by nucleotide analogs. The Enzymes. 49: 39-62. PMID 34696838 DOI: 10.1016/bs.enz.2021.07.001   
2021 Biswal JK, Ranjan R, Dahiya SS, Mallick S, Mohapatra JK. Regenerated silica-based RNA purification columns to address the short supply of RNA purification kits for COVID-19 diagnosis. Molecular Biology Reports. 48: 6871-6877. PMID 34510319 DOI: 10.1007/s11033-021-06688-0   
2021 Liu C, Cao J, Zhang H, Yin J. The RNA modification in Echinococcus granulosus cysts revealed by mass spectrometry. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 105124. PMID 34710588 DOI: 10.1016/j.meegid.2021.105124   
2021 Li L, Luo H, Lim DH, Han L, Li Y, Fu XD, Qi Y. Global profiling of RNA-chromatin interactions reveals co-regulatory gene expression networks in Arabidopsis. Nature Plants. 7: 1364-1378. PMID 34650265 DOI: 10.1038/s41477-021-01004-x   
2021 Zhao Y, Shu R, Liu J. The development and improvement of ribonucleic acid therapy strategies. Molecular Therapy. Nucleic Acids. PMID 34540356 DOI: 10.1016/j.omtn.2021.09.002   
2021 Wang X, Hu C, Ye W, Wang J, Dong X, Xu J, Li X, Zhang M, Lu H, Zhang F, Wu W, Dai S, Wang HW, Chen Z. Structure of Rift Valley fever virus RNA-dependent RNA polymerase. Journal of Virology. JVI0171321. PMID 34787453 DOI: 10.1128/JVI.01713-21   
2021 Chandler M, Johnson B, Khisamutdinov E, Dobrovolskaia MA, Sztuba-Solinska J, Salem AK, Breyne K, Chammas R, Walter NG, Contreras LM, Guo P, Afonin KA. The International Society of RNA Nanotechnology and Nanomedicine (ISRNN): The Present and Future of the Burgeoning Field. Acs Nano. PMID 34677049 DOI: 10.1021/acsnano.0c10240