Matthew D. Daugherty, Ph.D. - Related publications

2009 Chemistry and Chemical Biology University of California, San Francisco, San Francisco, CA 
Molecular Biology, General Biophysics
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 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 Martin SR, Ramos A, Masino L. Biolayer Interferometry: Protein-RNA Interactions. Methods in Molecular Biology (Clifton, N.J.). 2263: 351-368. PMID 33877607 DOI: 10.1007/978-1-0716-1197-5_16   
2021 Flynn RA, Belk JA, Qi Y, Yasumoto Y, Wei J, Alfajaro MM, Shi Q, Mumbach MR, Limaye A, DeWeirdt PC, Schmitz CO, Parker KR, Woo E, Chang HY, Horvath TL, et al. Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions. Cell. PMID 33743211 DOI: 10.1016/j.cell.2021.03.012   
2021 Rosenblum SL, Lorenz DA, Garner AL. A live-cell assay for the detection of pre-microRNA-protein interactions. Rsc Chemical Biology. 2: 241-247. PMID 33817642 DOI: 10.1039/d0cb00055h   
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 Bhatnagar P, Sreekanth GP, Murali-Krishna K, Chandele A, Sitaraman R. Dengue Virus Non-Structural Protein 5 as a Versatile, Multi-Functional Effector in Host-Pathogen Interactions. Frontiers in Cellular and Infection Microbiology. 11: 574067. PMID 33816326 DOI: 10.3389/fcimb.2021.574067   
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 F Dudás E, Puglisi R, Korn SM, Alfano C, Bellone ML, Piaz FD, Kelly G, Monaca E, Schlundt A, Schwalbe H, Pastore A. Backbone chemical shift spectral assignments of SARS coronavirus-2 non-structural protein nsp9. Biomolecular Nmr Assignments. PMID 33755914 DOI: 10.1007/s12104-021-10011-0   
2021 Cubuk J, Alston JJ, Incicco JJ, Singh S, Stuchell-Brereton MD, Ward MD, Zimmerman MI, Vithani N, Griffith D, Wagoner JA, Bowman GR, Hall KB, Soranno A, Holehouse AS. The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. Nature Communications. 12: 1936. PMID 33782395 DOI: 10.1038/s41467-021-21953-3   
2021 Winston DS, Boehr DD. The Picornavirus Precursor 3CD Has Different Conformational Dynamics Compared to 3C and 3D in Functionally Relevant Regions. Viruses. 13. PMID 33803479 DOI: 10.3390/v13030442   
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 Liu J, Carino E, Bera S, Gao F, May JP, Simon AE. Structural Analysis and Whole Genome Mapping of a New Type of Plant Virus Subviral RNA: Umbravirus-Like Associated RNAs. Viruses. 13. PMID 33918656 DOI: 10.3390/v13040646   
2021 Fu S, Zhang J, Yuan Q, Wang Q, Deng Q, Li J, Xia N, Wang Y, Wen Y, Tong S. Lost small envelope protein expression from naturally occurring preS1 deletion mutants of hepatitis B virus is often accompanied by increased HBx and core protein expression as well as genome replication. Journal of Virology. PMID 33910956 DOI: 10.1128/JVI.00660-21   
2021 Wierzbicki AT, Blevins T, Swiezewski S. Long Noncoding RNAs in Plants. Annual Review of Plant Biology. PMID 33752440 DOI: 10.1146/annurev-arplant-093020-035446   
2021 Kim GW, Siddiqui A. The role of N6-methyladenosine modification in the life cycle and disease pathogenesis of hepatitis B and C viruses. Experimental & Molecular Medicine. PMID 33742132 DOI: 10.1038/s12276-021-00581-3   
2021 Jing Ru C, Qinqin F, Jianwei L, Ying C, Machida S, Wei C, Yuan YA, Jobichen C. Structural and mechanistic insight into stem-loop RNA processing by yeast Pichia stipitis Dicer. Protein Science : a Publication of the Protein Society. PMID 33884665 DOI: 10.1002/pro.4086   
2021 Shim JS, Park SH, Lee DK, Kim YS, Park SC, Redillas MCFR, Seo JS, Kim JK. The Rice GLYCINE-RICH PROTEIN 3 Confers Drought Tolerance by Regulating mRNA Stability of ROS Scavenging-Related Genes. Rice (New York, N.Y.). 14: 31. PMID 33742286 DOI: 10.1186/s12284-021-00473-0   
2021 Burjoski V, Reddy ASN. The Landscape of RNA-Protein Interactions in Plants: Approaches and Current Status. International Journal of Molecular Sciences. 22. PMID 33799602 DOI: 10.3390/ijms22062845   
2021 Immarigeon C, Frei Y, Delbare SYN, Gligorov D, Machado Almeida P, Grey J, Fabbro L, Nagoshi E, Billeter JC, Wolfner MF, Karch F, Maeda RK. Identification of a micropeptide and multiple secondary cell genes that modulate male reproductive success. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33876742 DOI: 10.1073/pnas.2001897118   
2021 Weis K. Dead or alive: DEAD-box ATPases as regulators of ribonucleoprotein complex condensation. Biological Chemistry. 402: 653-661. PMID 33818025 DOI: 10.1515/hsz-2020-0381   
2021 Zafferani M, Hargrove AE. Small molecule targeting of biologically relevant RNA tertiary and quaternary structures. Cell Chemical Biology. PMID 33823146 DOI: 10.1016/j.chembiol.2021.03.003   
2021 Melidis L, Hill H, Coltman N, Davies S, Winczura K, Chauhan T, Craig J, Garai A, Hooper C, Egan R, McKeating J, Hodges N, Stamataki Z, Grzechnik P, Hannon M. Supramolecular cylinders target bulge structures in the 5' UTR of the RNA genome of SARS-CoV-2 and inhibit viral replication. Angewandte Chemie (International Ed. in English). PMID 33915014 DOI: 10.1002/anie.202104179   
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 Pfaller CK, George CX, Samuel CE. Adenosine Deaminases Acting on RNA (ADARs) and Viral Infections. Annual Review of Virology. PMID 33882257 DOI: 10.1146/annurev-virology-091919-065320   
2021 Zhang M, Li K, Bai J, Velema WA, Yu C, van Damme R, Lee WH, Corpuz ML, Chen JF, Lu Z. Optimized photochemistry enables efficient analysis of dynamic RNA structuromes and interactomes in genetic and infectious diseases. Nature Communications. 12: 2344. PMID 33879794 DOI: 10.1038/s41467-021-22552-y   
2021 Prussia AJ, Chennamadhavuni S. Biostructural Models for the Binding of Nucleoside Analogs to SARS-CoV-2 RNA-Dependent RNA Polymerase. Journal of Chemical Information and Modeling. 61: 1402-1411. PMID 33655751 DOI: 10.1021/acs.jcim.0c01277   
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 Lee HJ, Jhang ST, Jin HJ. Potential Target Site for Inhibitors in MLS Antibiotic Resistance. Antibiotics (Basel, Switzerland). 10. PMID 33807634 DOI: 10.3390/antibiotics10030264   
2021 Biagioni A, Tavakol S, Ahmadirad N, Zahmatkeshan M, Magnelli L, Mandegary A, Fekri HS, Asadi MH, Mohammadinejad R, Ahn KS. Small nucleolar RNA host genes promoting epithelial-mesenchymal transition lead cancer progression and metastasis. Iubmb Life. PMID 33938625 DOI: 10.1002/iub.2501   
2021 Müller M, Schauer T, Becker PB. Identification of Intrinsic RNA Binding Specificity of Purified Proteins by RNA Immunoprecipitation (vitRIP). Bio-Protocol. 11: e3946. PMID 33796620 DOI: 10.21769/BioProtoc.3946   
2021 Krepl M, Dendooven T, Luisi BF, Sponer J. MD simulations reveal the basis for dynamic assembly of Hfq-RNA complexes. The Journal of Biological Chemistry. 100656. PMID 33857481 DOI: 10.1016/j.jbc.2021.100656   
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 Zhang XY, Shu T, Wang X, Xu J, Qiu Y, Zhou X. Guaico Culex virus NSP2 has RNA helicase and chaperoning activities. The Journal of General Virology. 102. PMID 33891535 DOI: 10.1099/jgv.0.001589   
2021 Royan S, Gutmann B, Colas des Francs-Small C, Honkanen S, Schmidberger J, Soet A, Sun YK, Vincis Pereira Sanglard L, Bond CS, Small I. A synthetic RNA editing factor edits its target site in chloroplasts and bacteria. Communications Biology. 4: 545. PMID 33972654 DOI: 10.1038/s42003-021-02062-9   
2021 Wang Y, Kirkpatrick J, Zur Lage S, Korn SM, Neißner K, Schwalbe H, Schlundt A, Carlomagno T. H, C, and N backbone chemical-shift assignments of SARS-CoV-2 non-structural protein 1 (leader protein). Biomolecular Nmr Assignments. PMID 33770349 DOI: 10.1007/s12104-021-10019-6   
2021 Van Vu B, Nguyen Q, Kondo-Takeoka Y, Murata T, Kadotani N, Thi Nguyen G, Arazoe T, Ohsato S, Nakayashiki H. Copy number-dependent DNA methylation of the Pyricularia oryzae MAGGY retrotransposon is triggered by DNA damage. Communications Biology. 4: 351. PMID 33742058 DOI: 10.1038/s42003-021-01836-5   
2021 Sanan-Mishra N, Abdul Kader Jailani A, Mandal B, Mukherjee SK. Secondary siRNAs in Plants: Biosynthesis, Various Functions, and Applications in Virology. Frontiers in Plant Science. 12: 610283. PMID 33737942 DOI: 10.3389/fpls.2021.610283   
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 Riediger M, Spät P, Bilger R, Voigt K, Maček B, Hess WR. Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq). The Plant Cell. 33: 248-269. PMID 33793824 DOI: 10.1093/plcell/koaa017   
2021 Alvarez DR, Ospina A, Barwell T, Zheng B, Dey A, Li C, Basu S, Shi X, Kadri S, Chakrabarti K. The RNA Structurome in the Asexual Blood Stages of Malaria Pathogen . Rna Biology. PMID 33960872 DOI: 10.1080/15476286.2021.1926747   
2021 Satpathi S, Endoh T, Podbevšek P, Plavec J, Sugimoto N. Transcriptome screening followed by integrated physicochemical and structural analyses for investigating RNA-mediated berberine activity. Nucleic Acids Research. PMID 33784402 DOI: 10.1093/nar/gkab189   
2021 Sosic A, Olivato G, Carraro C, Göttlich R, Fabris D, Gatto B. Bis-3-Chloropiperidines Targeting TAR RNA as A Novel Strategy to Impair the HIV-1 Nucleocapsid Protein. Molecules (Basel, Switzerland). 26. PMID 33810333 DOI: 10.3390/molecules26071874   
2021 Hillen HS, Markov DA, Wojtas ID, Hofmann KB, Lidschreiber M, Cowan AT, Jones JL, Temiakov D, Cramer P, Anikin M. The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3'-UTRs of yeast mitochondrial mRNAs. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33876744 DOI: 10.1073/pnas.2009329118   
2021 Ivashuta S, Iandolino A, Watson G. Exogenous RNA as a Regulatory Signal during a Plant's Interaction with the Biotic Environment: An Evolutionary Perspective and Future Applications in Agriculture. Plants (Basel, Switzerland). 10. PMID 33808982 DOI: 10.3390/plants10030532   
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 Li HC, Yang CH, Lo SY. Hepatitis C Viral Replication Complex. Viruses. 13. PMID 33809897 DOI: 10.3390/v13030520   
2021 Schmidt CM, Smolke CD. A convolutional neural network for the prediction and forward design of ribozyme-based gene-control elements. Elife. 10. PMID 33860764 DOI: 10.7554/eLife.59697   
2021 Li H, Zhang K, Binzel DW, Shlyakhtenko LS, Lyubchenko Y, Chiu W, Guo P. RNA Nanotechnology to Build a Dodecahedral Genome of Single-Stranded RNA Virus. Rna Biology. PMID 33845711 DOI: 10.1080/15476286.2021.1915620   
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 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