Jesse C. Cochrane, Ph.D. - Related publications

2007 Yale University, New Haven, CT 
RNA, Ribosome
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Weeks KM. SHAPE Directed Discovery of New Functions in Large RNAs. Accounts of Chemical Research. 54: 2502-2517. PMID 33960770 DOI: 10.1021/acs.accounts.1c00118   
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 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 Wilson TJ, Lilley DMJ. The potential versatility of RNA catalysis. Wiley Interdisciplinary Reviews. Rna. e1651. PMID 33949113 DOI: 10.1002/wrna.1651   
2021 Chorostecki U, Willis JR, Saus E, Gabaldon T. Profiling of RNA Structure at Single-Nucleotide Resolution Using nextPARS. Methods in Molecular Biology (Clifton, N.J.). 2284: 51-61. PMID 33835437 DOI: 10.1007/978-1-0716-1307-8_4   
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 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 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 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 Ohashi S, Hashiya F, Abe H. Variety of Nucleotide Polymerase Mutants Aiming to Synthesize Modified RNA. Chembiochem : a European Journal of Chemical Biology. PMID 33822453 DOI: 10.1002/cbic.202100004   
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 Balas MM, Hartwick EW, Barrington C, Roberts JT, Wu SK, Bettcher R, Griffin AM, Kieft JS, Johnson AM. Establishing RNA-RNA interactions remodels lncRNA structure and promotes PRC2 activity. Science Advances. 7. PMID 33853770 DOI: 10.1126/sciadv.abc9191   
2021 Wang T, Li X, Zhang X, Wang Q, Liu W, Lu X, Gao S, Liu Z, Liu M, Gao L, Zhang W. RNA Motifs and Modification Involve in RNA Long-Distance Transport in Plants. Frontiers in Cell and Developmental Biology. 9: 651278. PMID 33869208 DOI: 10.3389/fcell.2021.651278   
2021 Zhu J, Zhao H, Kong F, Liu B, Liu M, Dong Z. Cotranscriptional and Posttranscriptional Features of the Transcriptome in Soybean Shoot Apex and Leaf. Frontiers in Plant Science. 12: 649634. PMID 33897737 DOI: 10.3389/fpls.2021.649634   
2021 Willbanks A, Wood S, Cheng JX. RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases. Genes. 12. PMID 33922187 DOI: 10.3390/genes12050627   
2021 DasGupta S, Piccirilli JA. The Varkud Satellite Ribozyme: A Thirty-Year Journey through Biochemistry, Crystallography, and Computation. Accounts of Chemical Research. PMID 33974386 DOI: 10.1021/acs.accounts.1c00052   
2021 Goldman CH, Neiswender H, Baker F, Veeranan-Karmegam R, Misra S, Gonsalvez GB. Optimal RNA binding by Egalitarian, a Dynein cargo adaptor, is critical for maintaining oocyte fate in . Rna Biology. 1-14. PMID 33904382 DOI: 10.1080/15476286.2021.1914422   
2021 Chao Y, Li HB, Zhou J. Multiple Functions of RNA Methylation in T Cells: A Review. Frontiers in Immunology. 12: 627455. PMID 33912158 DOI: 10.3389/fimmu.2021.627455   
2021 Doherty EE, Wilcox XE, van Sint Fiet L, Kemmel C, Turunen JJ, Klein B, Tantillo DJ, Fisher AJ, Beal PA. Rational Design of RNA Editing Guide Strands: Cytidine Analogs at the Orphan Position. Journal of the American Chemical Society. PMID 33939417 DOI: 10.1021/jacs.0c13319   
2021 Chiba T, Kihara SY, Sato M, Xingkui K, Goto S, Suzumura T, Kawai G, Himeno H, Ushida C. Identification of a short form of a Caenorhabditis elegans Y RNA homolog Cel7 RNA. Biochemical and Biophysical Research Communications. 557: 104-109. PMID 33862452 DOI: 10.1016/j.bbrc.2021.03.143   
2021 Cooperman BS. Site-Specific Fluorescent Labeling of RNA Interior Positions. Molecules (Basel, Switzerland). 26. PMID 33802273 DOI: 10.3390/molecules26051341   
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 Lin X, Fonseca MAS, Breunig JJ, Corona RI, Lawrenson K. discovery of RNA proximal proteins via proximity-dependent biotinylation. Rna Biology. 1-15. PMID 34006179 DOI: 10.1080/15476286.2021.1917215   
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 Staroseletz Y, Gaponova S, Patutina O, Bichenkova E, Amirloo B, Heyman T, Chiglintseva D, Zenkova M. Site-Selective Artificial Ribonucleases: Renaissance of Oligonucleotide Conjugates for Irreversible Cleavage of RNA Sequences. Molecules (Basel, Switzerland). 26. PMID 33808835 DOI: 10.3390/molecules26061732   
2021 Dai Y, Qi CB, Feng Y, Cheng QY, Liu FL, Cheng MY, Yuan BF, Feng YQ. Sensitive and Simultaneous Determination of Uridine Thiolation and Hydroxylation Modifications in Eukaryotic RNA by Derivatization Coupled with Mass Spectrometry Analysis. Analytical Chemistry. PMID 33908769 DOI: 10.1021/acs.analchem.0c04630   
2021 Schellinger IN, Dannert AR, Mattern K, Raaz U, Tsao PS. Unresolved Issues in RNA Therapeutics in Vascular Diseases With a Focus on Aneurysm Disease. Frontiers in Cardiovascular Medicine. 8: 571076. PMID 33937351 DOI: 10.3389/fcvm.2021.571076   
2021 Taneda A, Sato K. A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs. International Journal of Molecular Sciences. 22. PMID 33800268 DOI: 10.3390/ijms22052720   
2021 Liang D, Tatomer DC, Wilusz JE. Use of circular RNAs as markers of readthrough transcription to identify factors regulating cleavage/polyadenylation events. Methods (San Diego, Calif.). PMID 33882363 DOI: 10.1016/j.ymeth.2021.04.012   
2021 Montañés JC, Rojano C, Ylla G, Piulachs MD, Maestro JL. siRNA enrichment in Argonaute 2-depleted Blattella germanica. Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms. 1864: 194704. PMID 33895310 DOI: 10.1016/j.bbagrm.2021.194704   
2021 Balcerowicz M, Di Antonio M, Chung BYW. Monitoring Real-time Temperature Dynamics of a Short RNA Hairpin Using Förster Resonance Energy Transfer and Circular Dichroism. Bio-Protocol. 11: e3950. PMID 33855112 DOI: 10.21769/BioProtoc.3950   
2021 Blatt P, Wong-Deyrup SW, McCarthy A, Breznak S, Hurton MD, Upadhyay M, Bennink B, Camacho J, Lee MT, Rangan P. RNA degradation is required for the germ-cell to maternal transition in Drosophila. Current Biology : Cb. PMID 33989522 DOI: 10.1016/j.cub.2021.04.052   
2021 Bohnsack KE, Ficner R, Bohnsack MT, Jonas S. Regulation of DEAH-box RNA helicases by G-patch proteins. Biological Chemistry. 402: 561-579. PMID 33857358 DOI: 10.1515/hsz-2020-0338   
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 Choudhary C, Sharma S, Meghwanshi KK, Patel S, Mehta P, Shukla N, Do DN, Rajpurohit S, Suravajhala P, Shukla JN. Long Non-Coding RNAs in Insects. Animals : An Open Access Journal From Mdpi. 11. PMID 33919662 DOI: 10.3390/ani11041118   
2021 Wang Z, Gu J, Han T, Li K. High-throughput sequencing profile of laryngeal cancers: analysis of co-expression and competing endogenous RNA networks of circular RNAs, long non-coding RNAs, and messenger RNAs. Annals of Translational Medicine. 9: 483. PMID 33850880 DOI: 10.21037/atm-21-584   
2021 Xu L, Qi J, Wen Y, Liang W, Wang L, Yang Z, Yang X, Qi Y, Duan M, Zhao K, Gu J, Shen Y, Rao P, Ding M, Ren S, et al. A polyA DNA probe-based ultra-sensitive and structure-distinguishable electrochemical biosensor for the analysis of RNAi transgenic maize. The Analyst. PMID 33881427 DOI: 10.1039/d1an00313e   
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 Yang TH. An aggregation method to identify the RNA meta-stable secondary structure and its functionally interpretable structure ensemble. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34014829 DOI: 10.1109/TCBB.2021.3082396   
2021 Liu X, Sun T, Shcherbina A, Li Q, Jarmoskaite I, Kappel K, Ramaswami G, Das R, Kundaje A, Li JB. Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis. Nature Communications. 12: 2165. PMID 33846332 DOI: 10.1038/s41467-021-22489-2   
2021 Begik O, Lucas MC, Pryszcz LP, Ramirez JM, Medina R, Milenkovic I, Cruciani S, Liu H, Vieira HGS, Sas-Chen A, Mattick JS, Schwartz S, Novoa EM. Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing. Nature Biotechnology. PMID 33986546 DOI: 10.1038/s41587-021-00915-6   
2021 Mori Y, Oi H, Suzuki Y, Hidaka K, Sugiyama H, Endo M, Matsumura S, Ikawa Y. Flexible assembly of engineered Tetrahymena ribozymes forming polygonal RNA nanostructures with catalytic ability. Chembiochem : a European Journal of Chemical Biology. PMID 33876531 DOI: 10.1002/cbic.202100109   
2021 Sarkar A, Gasperi W, Begley U, Nevins S, Huber SM, Dedon PC, Begley TJ. Detecting the epitranscriptome. Wiley Interdisciplinary Reviews. Rna. e1663. PMID 33987958 DOI: 10.1002/wrna.1663   
2021 Hulstaert E, Decock A, Morlion A, Everaert C, Verniers K, Nuytens J, Nijs N, Schroth GP, Kuersten S, Gross SM, Mestdagh P, Vandesompele J. Messenger RNA capture sequencing of extracellular RNA from human biofluids using a comprehensive set of spike-in controls. Star Protocols. 2: 100475. PMID 33937877 DOI: 10.1016/j.xpro.2021.100475   
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 Shi H, Zhou Y, Jia E, Pan M, Bai Y, Ge Q. Bias in RNA-seq Library Preparation: Current Challenges and Solutions. Biomed Research International. 2021: 6647597. PMID 33987443 DOI: 10.1155/2021/6647597   
2021 Krissanaprasit A, Key CM, Froehlich K, Pontula S, Mihalko E, Dupont DM, Andersen ES, Kjems J, Brown AC, LaBean TH. Multivalent Aptamer-Functionalized Single-Strand RNA Origami as Effective, Target-Specific Anticoagulants with Corresponding Reversal Agents. Advanced Healthcare Materials. e2001826. PMID 33882195 DOI: 10.1002/adhm.202001826   
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 Tang G, Xie B, Hong X, Qin H, Wang J, Huang H, Hao P, Li X. Creating RNA Specific C-to-U Editase from APOBEC3A by Separation of Its Activities on DNA and RNA Substrates. Acs Synthetic Biology. PMID 33938211 DOI: 10.1021/acssynbio.0c00627   
2021 Moon JD, Wu J, Dey SK, Litke JL, Li X, Kim H, Jaffrey SR. Naturally occurring three-way junctions can be repurposed as genetically encoded RNA-based sensors. Cell Chemical Biology. PMID 34010626 DOI: 10.1016/j.chembiol.2021.04.022