Achillefs Kapanidis - Related publications

1999 Rutgers University, New Brunswick, New Brunswick, NJ, United States 
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Landick R. Transcriptional Pausing as a Mediator of Bacterial Gene Regulation. Annual Review of Microbiology. PMID 34348029 DOI: 10.1146/annurev-micro-051721-043826   
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 Tzerpos P, Daniel B, Nagy L. Global Run-on Sequencing (GRO-Seq). Methods in Molecular Biology (Clifton, N.J.). 2351: 25-39. PMID 34382182 DOI: 10.1007/978-1-0716-1597-3_2   
2021 Trotter M, Harris C, Cloutier M, Samanta M, Kalantry S. Highly Resolved Detection of Long Non-coding RNAs In Situ. Methods in Molecular Biology (Clifton, N.J.). 2372: 123-144. PMID 34417748 DOI: 10.1007/978-1-0716-1697-0_12   
2021 Ibrahim F, Oppelt J, Maragkakis M, Mourelatos Z. TERA-Seq: true end-to-end sequencing of native RNA molecules for transcriptome characterization. Nucleic Acids Research. PMID 34428294 DOI: 10.1093/nar/gkab713   
2021 Bera SC, Seifert M, Kirchdoerfer RN, van Nies P, Wubulikasimu Y, Quack S, Papini FS, Arnold JJ, Canard B, Cameron CE, Depken M, Dulin D. The nucleotide addition cycle of the SARS-CoV-2 polymerase. Cell Reports. 109650. PMID 34433083 DOI: 10.1016/j.celrep.2021.109650   
2021 Lukas O, Simmel FC. Controlling gene expression in mammalian cells using multiplexed conditional guide RNAs for Cas12a. Angewandte Chemie (International Ed. in English). PMID 34533878 DOI: 10.1002/anie.202107258   
2021 Mahas A, Wang Q, Marsic T, Mahfouz MM. A Novel Miniature CRISPR-Cas13 System for SARS-CoV-2 Diagnostics. Acs Synthetic Biology. PMID 34546709 DOI: 10.1021/acssynbio.1c00181   
2021 Yu H, Pu Q, Weng Z, Zhou X, Li J, Yang Y, Luo W, Guo Y, Chen H, Wang D, Xie G. DNAzyme based three-way junction assay for antibody-free detection of locus-specific N-methyladenosine modifications. Biosensors & Bioelectronics. 194: 113625. PMID 34534950 DOI: 10.1016/j.bios.2021.113625   
2021 Feng W, Peng H, Xu J, Liu Y, Pabbaraju K, Tipples G, Joyce MA, Saffran HA, Tyrrell DL, Babiuk S, Zhang H, Le XC. Integrating Reverse Transcription Recombinase Polymerase Amplification with CRISPR Technology for the One-Tube Assay of RNA. Analytical Chemistry. PMID 34506127 DOI: 10.1021/acs.analchem.1c03456   
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 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 Bergen V, Soldatov RA, Kharchenko PV, Theis FJ. RNA velocity-current challenges and future perspectives. Molecular Systems Biology. 17: e10282. PMID 34435732 DOI: 10.15252/msb.202110282   
2021 Tian T, Qiu Z, Jiang Y, Zhu D, Zhou X. Exploiting the orthogonal CRISPR-Cas12a/Cas13a trans-cleavage for dual-gene virus detection using a handheld device. Biosensors & Bioelectronics. 196: 113701. PMID 34653714 DOI: 10.1016/j.bios.2021.113701   
2021 Wang S, Shanthan G, Bouzga MM, Thi Dinh HM, Haas C, Fonneløp AE. Evaluating the performance of five up-to-date DNA/RNA co-extraction methods for forensic application. Forensic Science International. 328: 110996. PMID 34592582 DOI: 10.1016/j.forsciint.2021.110996   
2021 Bai X, Li F, Zhang Z. A hypothetical model of trans-acting R-loops-mediated promoter-enhancer interactions by Alu elements. Journal of Genetics and Genomics = Yi Chuan Xue Bao. PMID 34531149 DOI: 10.1016/j.jgg.2021.07.005   
2021 Takahashi H, Nishiyori-Sueki H, Ramilowski JA, Itoh M, Carninci P. Low Quantity Single Strand CAGE (LQ-ssCAGE) Maps Regulatory Enhancers and Promoters. Methods in Molecular Biology (Clifton, N.J.). 2351: 67-90. PMID 34382184 DOI: 10.1007/978-1-0716-1597-3_4   
2021 Huang Y, Xiao S, Yuan Z. Comparison and Evaluation of Real-Time Taqman PCR for Detection and Quantification of Ebolavirus. Viruses. 13. PMID 34452440 DOI: 10.3390/v13081575   
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 Jimeno S, Prados-Carvajal R, Fernández-Ávila MJ, Silva S, Silvestris DA, Endara-Coll M, Rodríguez-Real G, Domingo-Prim J, Mejías-Navarro F, Romero-Franco A, Jimeno-González S, Barroso S, Cesarini V, Aguilera A, Gallo A, et al. ADAR-mediated RNA editing of DNA:RNA hybrids is required for DNA double strand break repair. Nature Communications. 12: 5512. PMID 34535666 DOI: 10.1038/s41467-021-25790-2   
2021 Zachary M, Bauer S, Klepsch M, Wagler K, Hüttel B, Rudel T, Beier D. Identification and initial characterization of a new pair of sibling sRNAs of involved in type IV pilus biogenesis. Microbiology (Reading, England). 167. PMID 34515630 DOI: 10.1099/mic.0.001080   
2021 Zhao H, Zhang Y, Chen Y, Ho NRY, Sundah NR, Natalia A, Liu Y, Miow QH, Wang Y, Tambyah PA, Ong CWM, Shao H. Accessible detection of SARS-CoV-2 through molecular nanostructures and automated microfluidics. Biosensors & Bioelectronics. 194: 113629. PMID 34534949 DOI: 10.1016/j.bios.2021.113629   
2021 Matsui H. [Molecular mechanisms of myeloid malignancies]. [Rinsho Ketsueki] the Japanese Journal of Clinical Hematology. 62: 883-891. PMID 34497227 DOI: 10.11406/rinketsu.62.883   
2021 Mai L, Qiu Y, Lian Z, Chen C, Wang L, Yin Y, Wang S, Yang X, Li Y, Peng W, Luo C, Pan X. MustSeq, an alternative approach for multiplexible strand-specific 3' end sequencing of mRNA transcriptome confers high efficiency and practicality. Rna Biology. 1-12. PMID 34586036 DOI: 10.1080/15476286.2021.1974208   
2021 Zimmer JT, Rosa-Mercado NA, Canzio D, Steitz JA, Simon MD. STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts. Molecular Cell. PMID 34520723 DOI: 10.1016/j.molcel.2021.08.019   
2021 Ghimire S, Stewart CG, Thurman AL, Pezzulo AA. Performance of a scalable RNA extraction-free transcriptome profiling method for adherent cultured human cells. Scientific Reports. 11: 19438. PMID 34593905 DOI: 10.1038/s41598-021-98912-x   
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 Roth M, Seitz O. A Self-immolative Molecular Beacon for Amplified Nucleic Acid Detection*. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 34516006 DOI: 10.1002/chem.202102600   
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 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 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 Wen G, Vanheusden M, Leen V, Rohand T, Vandereyken K, Voet T, Hofkens J. A Universal Labeling Strategy for Nucleic Acids in Expansion Microscopy. Journal of the American Chemical Society. PMID 34424689 DOI: 10.1021/jacs.1c05931   
2021 Pilotto S, Fouqueau T, Lukoyanova N, Sheppard C, Lucas-Staat S, Díaz-Santín LM, Matelska D, Prangishvili D, Cheung ACM, Werner F. Structural basis of RNA polymerase inhibition by viral and host factors. Nature Communications. 12: 5523. PMID 34535646 DOI: 10.1038/s41467-021-25666-5   
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 Chen S, Xing L, Zhang D, Monferrer A, Hermann T. Nano-sandwich composite by kinetic trapping assembly from protein and nucleic acid. Nucleic Acids Research. PMID 34500473 DOI: 10.1093/nar/gkab797   
2021 Gudanis D, Zielińska K, Baranowski D, Kierzek R, Kozłowski P, Gdaniec Z. Impact of a Single Nucleotide Change or Non-Nucleoside Modifications in G-Rich Region on the Quadruplex-Duplex Hybrid Formation. Biomolecules. 11. PMID 34439902 DOI: 10.3390/biom11081236   
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 Kannan S, Altae-Tran H, Jin X, Madigan VJ, Oshiro R, Makarova KS, Koonin EV, Zhang F. Compact RNA editors with small Cas13 proteins. Nature Biotechnology. PMID 34462587 DOI: 10.1038/s41587-021-01030-2   
2021 Morozov D, Mironov V, Moryachkov RV, Shchugoreva IA, Artyushenko PV, Zamay GS, Kolovskaya OS, Zamay TN, Krat AV, Molodenskiy DS, Zabluda VN, Veprintsev DV, Sokolov AE, Zukov RA, Berezovski MV, et al. The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer. Molecular Therapy. Nucleic Acids. 25: 316-327. PMID 34458013 DOI: 10.1016/j.omtn.2021.07.015   
2021 Nalefski EA, Patel N, Leung PJY, Islam Z, Kooistra RM, Parikh I, Marion E, Knott GJ, Doudna JA, Le Ny AM, Madan D. Kinetic analysis of Cas12a and Cas13a RNA-Guided nucleases for development of improved CRISPR-Based diagnostics. Iscience. 24: 102996. PMID 34505008 DOI: 10.1016/j.isci.2021.102996   
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 Yankey A, Clark SC, Owens MC, Somarowthu S. Purification and Structural Characterization of the Long Noncoding RNAs. Methods in Molecular Biology (Clifton, N.J.). 2372: 93-110. PMID 34417746 DOI: 10.1007/978-1-0716-1697-0_10   
2021 Wu X, Liu Q, Liu F, Wu T, Shang Y, Liu J, Ding B. An RNA/DNA hybrid origami-based nanoplatform for efficient gene therapy. Nanoscale. 13: 12848-12853. PMID 34477769 DOI: 10.1039/d1nr00517k   
2021 Pu Q, Yu H, Zhou X, Li J, Yang Y, Wang T, Li F, Sheng S, Xie G. Xeno nucleic acid probes mediated methylation-specific PCR for single-base resolution analysis of N-methyladenosine in RNAs. The Analyst. PMID 34550117 DOI: 10.1039/d1an01291f   
2021 Zheng YY, Wu Y, Begley TJ, Sheng J. Sulfur modification in natural RNA and therapeutic oligonucleotides. Rsc Chemical Biology. 2: 990-1003. PMID 34458821 DOI: 10.1039/d1cb00038a   
2021 Vong JSL, Ji L, Heung MMS, Cheng SH, Wong J, Lai PBS, Wong VWS, Chan SL, Chan HLY, Jiang P, Chan KCA, Chiu RWK, Lo YMD. Single Cell and Plasma RNA Sequencing for RNA Liquid Biopsy for Hepatocellular Carcinoma. Clinical Chemistry. PMID 34463757 DOI: 10.1093/clinchem/hvab116   
2021 Astatke M, Tiburzi O, Connolly A. A novel RNA detection technique for point-of-care identification of pathogens. Journal of Immunoassay & Immunochemistry. 1955380. PMID 34355634 DOI: 10.1080/15321819.2021.1955380   
2021 Balaratnam S, Rhodes C, Bume DD, Connelly C, Lai CC, Kelley JA, Yazdani K, Homan PJ, Incarnato D, Numata T, Schneekloth JS. A chemical probe based on the PreQ metabolite enables transcriptome-wide mapping of binding sites. Nature Communications. 12: 5856. PMID 34615874 DOI: 10.1038/s41467-021-25973-x   
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 Mohammadniaei M, Zhang M, Ashley J, Christensen UB, Friis-Hansen LJ, Gregersen R, Lisby JG, Benfield TL, Nielsen FE, Henning Rasmussen J, Pedersen EB, Olinger ACR, Kolding LT, Naseri M, Zheng T, et al. A non-enzymatic, isothermal strand displacement and amplification assay for rapid detection of SARS-CoV-2 RNA. Nature Communications. 12: 5089. PMID 34429424 DOI: 10.1038/s41467-021-25387-9