Anne M. Baranger - Related publications

Affiliations: 
University of California, Berkeley, Berkeley, CA 
Area:
RNA Recognition By Proteins and Small Molecules
Website:
http://chemistry.berkeley.edu/faculty/chem/baranger
NOTE: We are testing a new system for identifying relevant work based on semantic analysis that identifies similarities between recently published papers and the current author's publications. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches.
50 most relevant papers in past 60 days:
Year Citation  Score
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 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 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 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 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 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 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 Kordyś M, Sen R, Warkocki Z. Applications of the versatile CRISPR-Cas13 RNA targeting system. Wiley Interdisciplinary Reviews. Rna. e1694. PMID 34553495 DOI: 10.1002/wrna.1694   
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 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 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 Zhan X, Deng L, Chen G. Mechanisms and applications of peptide nucleic acids selectively binding to double-stranded RNA. Biopolymers. e23476. PMID 34581432 DOI: 10.1002/bip.23476   
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 Poudyal RR, Sieg JP, Portz B, Keating CD, Bevilacqua PC. RNA sequence and structure control assembly and function of RNA condensates. Rna (New York, N.Y.). PMID 34551999 DOI: 10.1261/rna.078875.121   
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 Nakamura K, Nakao T, Mori T, Ohno S, Fujita Y, Masaoka K, Sakabayashi K, Mori K, Tobimatsu T, Sera T. Necessity of Flanking Repeats R1' and R8' of Human Pumilio1 Protein for RNA Binding. Biochemistry. PMID 34541851 DOI: 10.1021/acs.biochem.1c00445   
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 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, 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 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 Das R, Russell R. How to Kinetically Dissect an RNA Machine. Biochemistry. PMID 34492193 DOI: 10.1021/acs.biochem.1c00392   
2021 Kim JM, Chun H. TAR RNA Mediated Folding of a Single-Arginine-Mutant HIV-1 Tat Protein within HeLa Cells Experiencing Intracellular Crowding. International Journal of Molecular Sciences. 22. PMID 34576162 DOI: 10.3390/ijms22189998   
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 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 Lemak S, Serbanescu MA, Khusnutdinova AN, Ruszkowski M, Beloglazova N, Xu X, Brown G, Cui H, Tan K, Joachimiak A, Cvitkovitch DG, Savchenko A, Yakunin AF. Structural and biochemical insights into CRISPR RNA processing by the Cas5c ribonuclease SMU1763 from Streptococcus mutans. The Journal of Biological Chemistry. 101251. PMID 34592310 DOI: 10.1016/j.jbc.2021.101251   
2021 Le Vay KK, Song EY, Ghosh B, Tang TD, Mutschler H. Enhanced ribozyme-catalyzed recombination and oligonucleotide assembly in peptide-RNA condensates. Angewandte Chemie (International Ed. in English). PMID 34569680 DOI: 10.1002/anie.202109267   
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 Alonso D, Mondragón A. Mechanisms of catalytic RNA molecules. Biochemical Society Transactions. 49: 1529-1535. PMID 34415304 DOI: 10.1042/BST20200465   
2021 Feng X, Yang S, Zhang Y, Zhiyuan C, Tang K, Li G, Yu H, Leng J, Wang Q. , Encoding a Pentatricopeptide Repeat Protein, Is Essential for Chloroplast RNA Editing and Biogenesis in Soybean. Frontiers in Plant Science. 12: 690973. PMID 34567023 DOI: 10.3389/fpls.2021.690973   
2021 Nandy A, Shekhar S, Paul BK, Mukherjee S. Exploring the Nucleobase-Specific Hydrophobic Interaction of Cryptolepine Hydrate with RNA and Its Subsequent Sequestration. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 34499515 DOI: 10.1021/acs.langmuir.1c02123   
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 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 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 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 Savita BK, Dalal V, Choudhary S, Gupta DN, Das N, Tomar S, Kumar P, Roy P, Sharma AK. Characterization of recombinant pumpkin 2S albumin and mutation studies to unravel potential DNA/RNA binding site. Biochemical and Biophysical Research Communications. 580: 28-34. PMID 34610489 DOI: 10.1016/j.bbrc.2021.09.076   
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 Rapisarda A, Bargiela A, Llamusi B, Pont I, Estrada-Tejedor R, Garcia-España E, Artero R, Perez-Alonso M. Defined D-hexapeptides bind CUG repeats and rescue phenotypes of myotonic dystrophy myotubes in a Drosophila model of the disease. Scientific Reports. 11: 19417. PMID 34593893 DOI: 10.1038/s41598-021-98866-0   
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 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 Asadzadeh H, Moosavi A, Alexandrakis G, Mofrad MRK. Atomic Scale Interactions between RNA and DNA Aptamers with the TNF- Protein. Biomed Research International. 2021: 9926128. PMID 34327241 DOI: 10.1155/2021/9926128   
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 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 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 Wei Y, Yang Z, Zong C, Wang B, Ge X, Tan X, Liu X, Tao Z, Wang P, Ma C, Wan Y, Li J. Trans  Single-Stranded DNA Cleavage Via CRISPR/Cas14a1 Activated by Target RNA without Destruction. Angewandte Chemie (International Ed. in English). PMID 34553468 DOI: 10.1002/anie.202110384   
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 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 Dai W, Li A, Yu NJ, Nguyen T, Leach RW, Wühr M, Kleiner RE. Activity-based RNA-modifying enzyme probing reveals DUS3L-mediated dihydrouridylation. Nature Chemical Biology. PMID 34556860 DOI: 10.1038/s41589-021-00874-8   
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 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 Aphasizheva I, Suematsu T, Vacas A, Wang H, Fan C, Zhao X, Zhang L, Aphasizhev R. CTS tag-based methods for investigating mitochondrial RNA modification factors in Trypanosoma brucei. Methods in Enzymology. 658: 83-109. PMID 34517961 DOI: 10.1016/bs.mie.2021.06.004