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John Andrew Berglund, Ph.D. - Related publications

Biology University of Oregon, Eugene, OR, United States 
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Rabani M. Massively Parallel Analysis of Regulatory RNA Sequences. Methods in Molecular Biology (Clifton, N.J.). 2218: 355-365. PMID 33606245 DOI: 10.1007/978-1-0716-0970-5_28   
2021 Wang Y, Yu Y, Pang Y, Yu H, Zhang W, Zhao X, Yu J. The Distinct Roles of Zinc Finger CCHC-type (ZCCHC) Superfamily Proteins in the Regulation of RNA Metabolism. Rna Biology. PMID 33787465 DOI: 10.1080/15476286.2021.1909320   
2021 Xu Y, Zhang W, Shen F, Yang X, Liu H, Dai S, Sun X, Huang J, Guo Q. YTH Domain Proteins: A Family of mA Readers in Cancer Progression. Frontiers in Oncology. 11: 629560. PMID 33692959 DOI: 10.3389/fonc.2021.629560   
2021 Srivastava A, Yesudhas D, Ahmad S, Gromiha MM. Understanding disorder-to-order transitions in protein-RNA complexes using molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics. 1-11. PMID 33779503 DOI: 10.1080/07391102.2021.1904005   
2021 Li Z, Tang J, Bassham DC, Howell SH. Daily temperature cycles promote alternative splicing of RNAs encoding SR45a, a splicing regulator in maize. Plant Physiology. PMID 33705553 DOI: 10.1093/plphys/kiab110   
2021 Back S, Manfredi JJ. Knockdown of Target Genes by siRNA In Vitro. Methods in Molecular Biology (Clifton, N.J.). 2267: 159-163. PMID 33786790 DOI: 10.1007/978-1-0716-1217-0_10   
2021 Tong C, Yin Y. Localization of RNAs in the nucleus: - and - regulation. Rna Biology. 1-14. PMID 33682620 DOI: 10.1080/15476286.2021.1894025   
2021 Bailey TL. STREME: Accurate and versatile sequence motif discovery. Bioinformatics (Oxford, England). PMID 33760053 DOI: 10.1093/bioinformatics/btab203   
2021 Ho JJD, Man JHS, Schatz JH, Marsden PA. Translational remodeling by RNA-binding proteins and noncoding RNAs. Wiley Interdisciplinary Reviews. Rna. e1647. PMID 33694288 DOI: 10.1002/wrna.1647   
2021 Yang J, Cao Y, Ma L. Co-Transcriptional RNA Processing in Plants: Exploring from the Perspective of Polyadenylation. International Journal of Molecular Sciences. 22. PMID 33804866 DOI: 10.3390/ijms22073300   
2021 Yeom KH, Pan Z, Lin CH, Lim HY, Xiao W, Xing Y, Black DL. Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring. Genome Research. PMID 33832989 DOI: 10.1101/gr.273904.120   
2021 Dodbele S, Mutlu N, Wilusz JE. Best practices to ensure robust investigation of circular RNAs: pitfalls and tips. Embo Reports. 22: e52072. PMID 33629517 DOI: 10.15252/embr.202052072   
2021 Richards J, Belasco JG. Riboswitch control of bacterial RNA stability. Molecular Microbiology. PMID 33797153 DOI: 10.1111/mmi.14723   
2021 Lusk R, Stene E, Banaei-Kashani F, Tabakoff B, Kechris K, Saba LM. Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence. Nature Communications. 12: 1652. PMID 33712618 DOI: 10.1038/s41467-021-21894-x   
2021 Katz N, Tripto E, Granik N, Goldberg S, Atar O, Yakhini Z, Orenstein Y, Amit R. Overcoming the design, build, test bottleneck for synthesis of nonrepetitive protein-RNA cassettes. Nature Communications. 12: 1576. PMID 33707432 DOI: 10.1038/s41467-021-21578-6   
2021 Chowdhary V, Biswas P, Ghoshal K. Role of Non-coding RNA in Acetaminophen-induced Liver Injury. Gene Expression. PMID 33757622 DOI: 10.3727/105221621X16165282414118   
2021 Saldi T, Riemondy K, Erickson B, Bentley DL. Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing. Molecular Cell. PMID 33631106 DOI: 10.1016/j.molcel.2021.01.040   
2021 Sousa-Luís R, Dujardin G, Zukher I, Kimura H, Weldon C, Carmo-Fonseca M, Proudfoot NJ, Nojima T. POINT technology illuminates the processing of polymerase-associated intact nascent transcripts. Molecular Cell. PMID 33735606 DOI: 10.1016/j.molcel.2021.02.034   
2021 Strittmatter LM, Capitanchik C, Newman AJ, Hallegger M, Norman CM, Fica SM, Oubridge C, Luscombe NM, Ule J, Nagai K. psiCLIP reveals dynamic RNA binding by DEAH-box helicases before and after exon ligation. Nature Communications. 12: 1488. PMID 33674615 DOI: 10.1038/s41467-021-21745-9   
2021 Gamini R, Nakashima R, He W, Huang Y, Zhang Y, Zhao S. QuickIsoSeq for Isoform Quantification in Large-Scale RNA Sequencing. Methods in Molecular Biology (Clifton, N.J.). 2284: 135-145. PMID 33835441 DOI: 10.1007/978-1-0716-1307-8_8   
2021 Torma G, Tombácz D, Csabai Z, Göbhardter D, Deim Z, Snyder M, Boldogkői Z. An Integrated Sequencing Approach for Updating the Pseudorabies Virus Transcriptome. Pathogens (Basel, Switzerland). 10. PMID 33672563 DOI: 10.3390/pathogens10020242   
2021 Wu P, Zhang M, Webster NJG. Alternative RNA Splicing in Fatty Liver Disease. Frontiers in Endocrinology. 12: 613213. PMID 33716968 DOI: 10.3389/fendo.2021.613213   
2021 Huertas-Rosales Ó, Romero M, Chan KG, Hong KW, Cámara M, Heeb S, Barrientos-Moreno L, Molina-Henares MA, Travieso ML, Ramos-González MI, Espinosa-Urgel M. Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in . Frontiers in Molecular Biosciences. 8: 624061. PMID 33693029 DOI: 10.3389/fmolb.2021.624061   
2021 Ariel FD, Manavella PA. When junk DNA turns functional: transposon-derived noncoding RNAs in plants. Journal of Experimental Botany. PMID 33606874 DOI: 10.1093/jxb/erab073   
2021 Sanchez A, Maenner S. Purification of RiboNucleoProtein Particles by MS2-MBP Affinity Chromatography. Methods in Molecular Biology (Clifton, N.J.). 2300: 99-106. PMID 33792875 DOI: 10.1007/978-1-0716-1386-3_10   
2021 Verosloff MS, Corcoran WK, Dolberg TB, Bushhouse DZ, Leonard JN, Lucks JB. RNA sequence and structure determinants of Pol III transcriptional termination in human cells. Journal of Molecular Biology. 166978. PMID 33811918 DOI: 10.1016/j.jmb.2021.166978   
2021 Shi J, Zhang Y, Tan D, Zhang X, Yan M, Zhang Y, Franklin R, Shahbazi M, Mackinlay K, Liu S, Kuhle B, James ER, Zhang L, Qu Y, Zhai Q, et al. PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications. Nature Cell Biology. PMID 33820973 DOI: 10.1038/s41556-021-00652-7   
2021 Niazi AM, Krause M, Valen E. Transcript Isoform-Specific Estimation of Poly(A) Tail Length by Nanopore Sequencing of Native RNA. Methods in Molecular Biology (Clifton, N.J.). 2284: 543-567. PMID 33835463 DOI: 10.1007/978-1-0716-1307-8_30   
2021 Goldfarb CN, Waxman DJ. Global analysis of expression, maturation and subcellular localization of mouse liver transcriptome identifies novel sex-biased and TCPOBOP-responsive long non-coding RNAs. Bmc Genomics. 22: 212. PMID 33761883 DOI: 10.1186/s12864-021-07478-5   
2021 Zhou S, Hill CS, Clark MU, Sheahan TP, Baric R, Swanstrom R. Primer ID Next-Generation Sequencing for the Analysis of a Broad Spectrum Antiviral Induced Transition Mutations and Errors Rates in a Coronavirus Genome. Bio-Protocol. 11: e3938. PMID 33796612 DOI: 10.21769/BioProtoc.3938   
2021 Alam T, Lipovich L. miRCOVID-19: Potential Targets of Human miRNAs in SARS-CoV-2 for RNA-Based Drug Discovery. Non-Coding Rna. 7. PMID 33801496 DOI: 10.3390/ncrna7010018   
2021 Tang YS, Xu S, Chen YW, Wang JH, Shaw PC. Crystal structures of influenza nucleoprotein complexed with nucleic acid provide insights into the mechanism of RNA interaction. Nucleic Acids Research. PMID 33784403 DOI: 10.1093/nar/gkab203   
2021 Seki M, Oka M, Xu L, Suzuki A, Suzuki Y. Transcript Identification Through Long-Read Sequencing. Methods in Molecular Biology (Clifton, N.J.). 2284: 531-541. PMID 33835462 DOI: 10.1007/978-1-0716-1307-8_29   
2021 Kropocheva E, Kuzmenko A, Aravin AA, Esyunina D, Kulbachinskiy A. A programmable pAgo nuclease with universal guide and target specificity from the mesophilic bacterium Kurthia massiliensis. Nucleic Acids Research. PMID 33744962 DOI: 10.1093/nar/gkab182   
2021 Zhang Z, Liu T, Dong H, Li J, Sun H, Qian X, Qin W. An RNA tagging approach for system-wide RNA-binding proteome profiling and dynamics investigation upon transcription inhibition. Nucleic Acids Research. PMID 33693821 DOI: 10.1093/nar/gkab156   
2021 Chen J, Liu Y, Min J, Wang H, Li F, Xu C, Gong A, Xu M. Alternative splicing of lncRNAs in human diseases. American Journal of Cancer Research. 11: 624-639. PMID 33791145   
2021 Ma J, Zhang L, Chen S, Liu H. A brief review of RNA modification related database resources. Methods (San Diego, Calif.). PMID 33705860 DOI: 10.1016/j.ymeth.2021.03.003   
2021 Nuzra Nagoor Pitchai F, Chameettachal A, Vivet-Boudou V, Mohamed Ali L, Pillai VN, Krishnan A, Bernacchi S, Mustafa F, Marquet R, Rizvi TA. Identification of Pr78 binding sites on the Mason-Pfizer monkey virus genomic RNA packaging determinants. Journal of Molecular Biology. 166923. PMID 33713677 DOI: 10.1016/j.jmb.2021.166923   
2021 Porter DF, Miao W, Yang X, Goda GA, Ji AL, Donohue LKH, Aleman MM, Dominguez D, Khavari PA. easyCLIP analysis of RNA-protein interactions incorporating absolute quantification. Nature Communications. 12: 1569. PMID 33692367 DOI: 10.1038/s41467-021-21623-4   
2021 Forsythe HM, Galvan JR, Yu Z, Pinckney S, Reardon P, Cooley RB, Zhu P, Rolland AD, Prell JS, Barbar E. Multivalent binding of the partially disordered SARS-CoV-2 nucleocapsid phosphoprotein dimer to RNA. Biophysical Journal. PMID 33794152 DOI: 10.1016/j.bpj.2021.03.023   
2021 Thalalla Gamage S, Sas-Chen A, Schwartz S, Meier JL. Quantitative nucleotide resolution profiling of RNA cytidine acetylation by ac4C-seq. Nature Protocols. PMID 33772246 DOI: 10.1038/s41596-021-00501-9   
2021 Wang Y, Chong TH, Unarta IC, Xu X, Suarez GD, Wang J, Lis JT, Huang X, Cheung PP. EmPC-seq: Accurate RNA-sequencing and Bioinformatics Platform to Map RNA Polymerases and Remove Background Error. Bio-Protocol. 11: e3921. PMID 33732808 DOI: 10.21769/BioProtoc.3921   
2021 Dubey AP, Tylec BL, McAdams NM, Sortino K, Read LK. Trypanosome RNAEditing Substrate Binding Complex integrity and function depends on the upstream action of RESC10. Nucleic Acids Research. PMID 33677542 DOI: 10.1093/nar/gkab129   
2021 Mattay J, Dittmar M, Rentmeister A. Chemoenzymatic strategies for RNA modification and labeling. Current Opinion in Chemical Biology. 63: 46-56. PMID 33690011 DOI: 10.1016/j.cbpa.2021.01.008   
2021 Li L, Miao H, Chang Y, Yao H, Zhao Y, Wu F, Song X. Multidimensional crosstalk between RNA-binding proteins and noncoding RNAs in cancer biology. Seminars in Cancer Biology. PMID 33722631 DOI: 10.1016/j.semcancer.2021.03.007   
2021 Moeller NH, Shi K, Demir Ö, Banerjee S, Yin L, Belica C, Durfee C, Amaro RE, Aihara H. Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN. Biorxiv : the Preprint Server For Biology. PMID 33821277 DOI: 10.1101/2021.04.02.438274   
2021 Guan L, Grigoriev A. Computational meta-analysis of ribosomal RNA fragments: potential targets and interaction mechanisms. Nucleic Acids Research. PMID 33772581 DOI: 10.1093/nar/gkab190   
2021 Zhang H, Zhong H, Wang X, Zhang S, Shao X, Hu H, Yu Z, Cai Z, Chen X, Xia Y. Use of NAD tagSeq II to identify growth phase-dependent alterations in RNA NAD capping. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33782135 DOI: 10.1073/pnas.2026183118   
2021 Fitzpatrick AH, Rupnik A, O'Shea H, Crispie F, Keaveney S, Cotter P. High Throughput Sequencing for the Detection and Characterization of RNA Viruses. Frontiers in Microbiology. 12: 621719. PMID 33692767 DOI: 10.3389/fmicb.2021.621719   
2021 Malik TN, Doherty EE, Gaded VM, Hill TM, Beal PA, Emeson RB. Regulation of RNA editing by intracellular acidification. Nucleic Acids Research. PMID 33721028 DOI: 10.1093/nar/gkab157