Irene A. Chen, Ph.D. - Related publications

Affiliations: 
Chemistry University of California, Santa Barbara, Santa Barbara, CA, United States 
 2005 Harvard University, Cambridge, MA, United States 
Area:
Synthetic biology, Systems Biology, Biophysics, Origin of Life, Molecular Evolution, Phage-based Applications, Human Microbiome
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Smith SC, Gribble J, Diller JR, Wiebe MA, Thoner TW, Denison MR, Ogden KM. Reovirus RNA recombination is sequence directed and generates internally deleted defective genome segments during passage. Journal of Virology. PMID 33472930 DOI: 10.1128/JVI.02181-20   
2021 Andrzejewska A, Zawadzka M, Gumna J, Garfinkel DJ, Pachulska-Wieczorek K. In vivo structure of the Ty1 retrotransposon RNA genome. Nucleic Acids Research. PMID 33621339 DOI: 10.1093/nar/gkab090   
2021 Wang B, Zhang T, Yin J, Yu Y, Xu W, Ding J, Patel DJ, Yang H. Structural basis for self-cleavage prevention by tag:anti-tag pairing complementarity in type VI Cas13 CRISPR systems. Molecular Cell. PMID 33472057 DOI: 10.1016/j.molcel.2020.12.033   
2021 Blumberg A, Zhao Y, Huang YF, Dukler N, Rice EJ, Chivu AG, Krumholz K, Danko CG, Siepel A. Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data. Bmc Biology. 19: 30. PMID 33588838 DOI: 10.1186/s12915-021-00949-x   
2021 Goldman AD, Kacar B. Cofactors are Remnants of Life's Origin and Early Evolution. Journal of Molecular Evolution. PMID 33547911 DOI: 10.1007/s00239-020-09988-4   
2021 Yong XE, Raghuvamsi PV, Anand GS, Wohland T, Sharma KK. Dengue virus strain 2 capsid protein switches the annealing pathway and reduces intrinsic dynamics of the conserved 5' untranslated region. Rna Biology. 1-14. PMID 33406991 DOI: 10.1080/15476286.2020.1860581   
2021 Yu AM, Gasper PM, Cheng L, Lai LB, Kaur S, Gopalan V, Chen AA, Lucks JB. Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates. Molecular Cell. PMID 33453165 DOI: 10.1016/j.molcel.2020.12.017   
2021 Lee N. The many ways Epstein-Barr virus takes advantage of the RNA tool kit. Rna Biology. 1-8. PMID 33517840 DOI: 10.1080/15476286.2021.1875184   
2021 Torkamanian-Afshar M, Nematzadeh S, Tabarzad M, Najafi A, Lanjanian H, Masoudi-Nejad A. In silico design of novel aptamers utilizing a hybrid method of machine learning and genetic algorithm. Molecular Diversity. PMID 33554306 DOI: 10.1007/s11030-021-10192-9   
2021 Yépez VA, Mertes C, Müller MF, Klaproth-Andrade D, Wachutka L, Frésard L, Gusic M, Scheller IF, Goldberg PF, Prokisch H, Gagneur J. Detection of aberrant gene expression events in RNA sequencing data. Nature Protocols. PMID 33462443 DOI: 10.1038/s41596-020-00462-5   
2021 Chakraborty P, Chattopadhyay D, Roy S. N-protein-RNA interaction is a drug target in a negative strand RNA virus. Virus Research. 198298. PMID 33508356 DOI: 10.1016/j.virusres.2021.198298   
2021 Galindo-Murillo R, Cohen JS, Akabayov B. Molecular dynamics simulations of acyclic analogs of nucleic acids for antisense inhibition. Molecular Therapy. Nucleic Acids. 23: 527-535. PMID 33510941 DOI: 10.1016/j.omtn.2020.11.023   
2021 Ross CJ, Rom A, Spinrad A, Gelbard-Solodkin D, Degani N, Ulitsky I. Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences. Genome Biology. 22: 29. PMID 33430943 DOI: 10.1186/s13059-020-02247-1   
2021 Marinus T, Fessler AB, Ogle CA, Incarnato D. A novel SHAPE reagent enables the analysis of RNA structure in living cells with unprecedented accuracy. Nucleic Acids Research. PMID 33398343 DOI: 10.1093/nar/gkaa1255   
2021 Tian T, Shu B, Jiang Y, Ye M, Liu L, Guo Z, Han Z, Wang Z, Zhou X. An Ultralocalized Cas13a Assay Enables Universal and Nucleic Acid Amplification-Free Single-Molecule RNA Diagnostics. Acs Nano. 15: 1167-1178. PMID 33498106 DOI: 10.1021/acsnano.0c08165   
2021 Kjellin J, Avesson L, Reimegård J, Liao Z, Eichinger L, Noegel A, Glöckner G, Schaap P, Söderbom F. Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebae. Genome Research. PMID 33479022 DOI: 10.1101/gr.272856.120   
2021 Guo SK, Nan F, Liu CX, Yang L, Chen LL. Mapping circular RNA structures in living cells by SHAPE-MaP. Methods (San Diego, Calif.). PMID 33571668 DOI: 10.1016/j.ymeth.2021.01.011   
2021 Liu Y, Li W, Jiang X, Wang Y, Zhang Z, Liu Q, He R, Chen Q, Yang J, Wang L, Wang F, Ma L. A programmable omnipotent Argonaute nuclease from mesophilic bacteria Kurthia massiliensis. Nucleic Acids Research. PMID 33444443 DOI: 10.1093/nar/gkaa1278   
2021 Videm P, Kumar A, Zharkov O, Grüning BA, Backofen R. ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data. Gigascience. 10. PMID 33511995 DOI: 10.1093/gigascience/giaa158   
2021 Choi HY, Jo H, Zhao X, Hoadley KA, Newman S, Holt J, Hayward MC, Love MI, Marron JS, Hayes DN. SCISSOR: a framework for identifying structural changes in RNA transcripts. Nature Communications. 12: 286. PMID 33436599 DOI: 10.1038/s41467-020-20593-3   
2021 Yu G, Zhu H, Chen X, Yang JR. Specificity of RNA Folding and Its Association with Evolutionarily Adaptive mRNA Secondary Structures. Genomics, Proteomics & Bioinformatics. PMID 33607297 DOI: 10.1016/j.gpb.2019.11.013   
2021 Ortolá B, Cordero T, Hu X, Daròs JA. Intron-assisted, viroid-based production of insecticidal circular double-stranded RNA in . Rna Biology. 1-12. PMID 33472518 DOI: 10.1080/15476286.2021.1872962   
2021 Zhu J, Li C, Peng X, Zhang X. Architecture of RNA influences plant biology. Journal of Experimental Botany. PMID 33484251 DOI: 10.1093/jxb/erab030   
2021 Anastasakis DG, Jacob A, Konstantinidou P, Meguro K, Claypool D, Cekan P, Haase AD, Hafner M. A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol. Nucleic Acids Research. PMID 33503264 DOI: 10.1093/nar/gkab011   
2021 Athapattu US, Amarasekara CA, Immel JR, Bloom S, Barany F, Nagel AC, Soper SA. Solid-phase XRN1 reactions for RNA cleavage: application in single-molecule sequencing. Nucleic Acids Research. PMID 33511416 DOI: 10.1093/nar/gkab001   
2021 Kokic G, Hillen HS, Tegunov D, Dienemann C, Seitz F, Schmitzova J, Farnung L, Siewert A, Höbartner C, Cramer P. Mechanism of SARS-CoV-2 polymerase stalling by remdesivir. Nature Communications. 12: 279. PMID 33436624 DOI: 10.1038/s41467-020-20542-0   
2021 Panchapakesan SSS, Breaker RR. The case of the missing allosteric ribozymes. Nature Chemical Biology. PMID 33495645 DOI: 10.1038/s41589-020-00713-2   
2021 Ramirez P, Crouch RJ, Cheung VG, Grunseich C. R-Loop Analysis by Dot-Blot. Journal of Visualized Experiments : Jove. PMID 33554969 DOI: 10.3791/62069   
2021 Feng Q, Li Y, Zhao ZX, Wang WM. Contribution of Small RNA Pathway to Interactions of Rice with Pathogens and Insect Pests. Rice (New York, N.Y.). 14: 15. PMID 33547972 DOI: 10.1186/s12284-021-00458-z   
2021 Wei H, Chen Q, Lin L, Sha C, Li T, Liu Y, Yin X, Xu Y, Chen L, Gao W, Li Y, Zhu X. Regulation of exosome production and cargo sorting. International Journal of Biological Sciences. 17: 163-177. PMID 33390841 DOI: 10.7150/ijbs.53671   
2021 Dupas SJ, Gussakovsky D, Wai A, Brown MJF, Hausner G, McKenna SA. Predicting human RNA quadruplex helicases through comparative sequence approaches and helicase mRNA interactome analyses. Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire. PMID 33587669 DOI: 10.1139/bcb-2020-0590   
2021 Drexler HL, Choquet K, Merens HE, Tang PS, Simpson JT, Churchman LS. Revealing nascent RNA processing dynamics with nano-COP. Nature Protocols. PMID 33514943 DOI: 10.1038/s41596-020-00469-y   
2021 Radakovic A, Wright TH, Lelyveld VS, Szostak JW. A Potential Role for Aminoacylation in Primordial RNA Copying Chemistry. Biochemistry. PMID 33523633 DOI: 10.1021/acs.biochem.0c00943   
2021 Moon S, Kim H, Kim D, Lee JB. Viscosity-Regulated Control of RNA Microstructure Fabrication. Polymers. 13. PMID 33572561 DOI: 10.3390/polym13030454   
2021 Huston NC, Wan H, Strine MS, de Cesaris Araujo Tavares R, Wilen CB, Pyle AM. Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms. Molecular Cell. PMID 33444546 DOI: 10.1016/j.molcel.2020.12.041   
2021 Soneson C, Srivastava A, Patro R, Stadler MB. Preprocessing choices affect RNA velocity results for droplet scRNA-seq data. Plos Computational Biology. 17: e1008585. PMID 33428615 DOI: 10.1371/journal.pcbi.1008585   
2021 Lu M, Xue M, Wang HT, Kairis EL, Ahmad S, Wei J, Zhang Z, Zhang Y, Gao Y, Garcin D, Peeples ME, Sharma A, Hur S, He C, Li J. Non-segmented negative-sense RNA viruses utilize -methyladenosine (mA) as a common strategy to evade host innate immunity. Journal of Virology. PMID 33536170 DOI: 10.1128/JVI.01939-20   
2021 Murphy DE, de Jong OG, Evers MJW, Nurazizah M, Schiffelers RM, Vader P. Natural or Synthetic RNA Delivery: A Stoichiometric Comparison of Extracellular Vesicles and Synthetic Nanoparticles. Nano Letters. PMID 33570966 DOI: 10.1021/acs.nanolett.1c00094   
2021 Dangerfield TL, Huang NZ, Johnson KA. Expression and Purification of Tag-Free SARS-CoV-2 RNA-Dependent RNA Polymerase in . Star Protocols. 100357. PMID 33558863 DOI: 10.1016/j.xpro.2021.100357   
2021 Kurkowiak M, Arcimowicz Ł, Chruściel E, Urban-Wójciuk Z, Papak I, Keegan L, O'Connell M, Kowalski J, Hupp T, Marek-Trzonkowska N. The effects of RNA editing in cancer tissue at different stages in carcinogenesis. Rna Biology. 1-16. PMID 33593231 DOI: 10.1080/15476286.2021.1877024   
2021 Gerovac M, Wicke L, Chihara K, Schneider C, Lavigne R, Vogel J. A Grad-seq View of RNA and Protein Complexes in Pseudomonas aeruginosa under Standard and Bacteriophage Predation Conditions. Mbio. 12. PMID 33563827 DOI: 10.1128/mBio.03454-20   
2021 Mojarro A, Jin L, Szostak JW, Head JW, Zuber MT. In search of the RNA world on Mars. Geobiology. PMID 33565260 DOI: 10.1111/gbi.12433   
2021 Knutson SD, Heemstra JM. Protein-based molecular recognition tools for detecting and profiling RNA modifications. Current Opinion in Structural Biology. 69: 1-10. PMID 33445115 DOI: 10.1016/j.sbi.2020.12.006   
2021 Mondal M, Peter J, Scarbrough O, Flynt A. Environmental RNAi pathways in the two-spotted spider mite. Bmc Genomics. 22: 42. PMID 33421998 DOI: 10.1186/s12864-020-07322-2   
2021 Bonning BC, Saleh MC. The Interplay Between Viruses and RNAi Pathways in Insects. Annual Review of Entomology. 66: 61-79. PMID 33417818 DOI: 10.1146/annurev-ento-033020-090410   
2021 Han S, Ko O, Lee G, Jeong SW, Choi YJ, Lee JB. Rapid Diagnosis of Coronavirus by RNA-Directed RNA Transcription Using an Engineered RNA-based Platform. Nano Letters. PMID 33395304 DOI: 10.1021/acs.nanolett.0c03917   
2021 Huang J, Zhao R, Mo J, Wang F, Weng X, Zhou X. N3-kethoxal Based Bioorthogonal Intracellular RNA Labeling. Chembiochem : a European Journal of Chemical Biology. PMID 33393712 DOI: 10.1002/cbic.202000755   
2021 Zheng Y, Zhong Y, Hu J, Shang X. SCC: an accurate imputation method for scRNA-seq dropouts based on a mixture model. Bmc Bioinformatics. 22: 5. PMID 33407064 DOI: 10.1186/s12859-020-03878-8   
2021 Zheng Y, Zhong Y, Hu J, Shang X. SCC: an accurate imputation method for scRNA-seq dropouts based on a mixture model. Bmc Bioinformatics. 22: 5. PMID 33407064 DOI: 10.1186/s12859-020-03878-8   
2021 Wood S, Willbanks A, Cheng JX. The Role of RNA Modifications and RNA-modifying Proteins in Cancer Therapy and Drug Resistance. Current Cancer Drug Targets. PMID 33504307 DOI: 10.2174/1568009621666210127092828