| Year |
Citation |
Score |
| 2023 |
Xu L, Liu T, Chung K, Pyle AM. Structural insights into intron catalysis and dynamics during splicing. Nature. PMID 37993708 DOI: 10.1038/s41586-023-06746-6 |
0.43 |
|
| 2023 |
Wang W, Götte B, Guo R, Pyle AM. The E3 ligase Riplet promotes RIG-I signaling independent of RIG-I oligomerization. Nature Communications. 14: 7308. PMID 37951994 DOI: 10.1038/s41467-023-42982-0 |
0.335 |
|
| 2023 |
Guo LT, Pyle AM. End-to-end RT-PCR of long RNA and highly structured RNA. Methods in Enzymology. 691: 3-15. PMID 37914451 DOI: 10.1016/bs.mie.2023.07.002 |
0.472 |
|
| 2023 |
Liu T, Patel S, Pyle AM. Making RNA: Using T7 RNA polymerase to produce high yields of RNA from DNA templates. Methods in Enzymology. 691: 185-207. PMID 37914446 DOI: 10.1016/bs.mie.2023.06.002 |
0.446 |
|
| 2023 |
Guo LT, Pyle AM. RT-based Sanger sequencing of RNAs containing complex RNA repetitive elements. Methods in Enzymology. 691: 17-27. PMID 37914445 DOI: 10.1016/bs.mie.2023.07.003 |
0.399 |
|
| 2023 |
Araujo Tavares RC, Mahadeshwar G, Wan H, Pyle AM. MRT-ModSeq - Rapid Detection of RNA Modifications with MarathonRT. Journal of Molecular Biology. 435: 168299. PMID 37802215 DOI: 10.1016/j.jmb.2023.168299 |
0.418 |
|
| 2023 |
Fedorova O, Arhin G, Pyle AM, Frank AT. Discovery of Group II Intron RNA Splicing Inhibitors. Acs Chemical Biology. PMID 37602469 DOI: 10.1021/acschembio.3c00160 |
0.388 |
|
| 2023 |
Zhang C, Zhang Y, Pyle AM. rMSA: A Sequence Search and Alignment Algorithm to Improve RNA Structure Modeling. Journal of Molecular Biology. 435: 167904. PMID 37356900 DOI: 10.1016/j.jmb.2022.167904 |
0.442 |
|
| 2023 |
Patel S, Sexton AN, Strine MS, Wilen CB, Simon MD, Pyle AM. Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq. Nature Communications. 14: 3426. PMID 37296103 DOI: 10.1038/s41467-023-38623-1 |
0.455 |
|
| 2023 |
Araujo Tavares RC, Mahadeshwar G, Wan H, Pyle AM. MRT-ModSeq - Rapid detection of RNA modifications with MarathonRT. Biorxiv : the Preprint Server For Biology. PMID 37292902 DOI: 10.1101/2023.05.25.542276 |
0.418 |
|
| 2023 |
Mahadeshwar G, Tavares RCA, Wan H, Perry ZR, Pyle AM. RSCanner: rapid assessment and visualization of RNA structure content. Bioinformatics (Oxford, England). 39. PMID 36857576 DOI: 10.1093/bioinformatics/btad111 |
0.384 |
|
| 2022 |
Chung K, Xu L, Chai P, Peng J, Devarkar SC, Pyle AM. Structures of a mobile intron retroelement poised to attack its structured DNA target. Science (New York, N.Y.). 378: 627-634. PMID 36356138 DOI: 10.1126/science.abq2844 |
0.305 |
|
| 2022 |
Wang W, Pyle AM. The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands. Molecular Cell. 82: 4131-4144.e6. PMID 36272408 DOI: 10.1016/j.molcel.2022.09.029 |
0.454 |
|
| 2022 |
Zhang C, Pyle AM. A unified approach to sequential and non-sequential structure alignment of proteins, RNAs, and DNAs. Iscience. 25: 105218. PMID 36248743 DOI: 10.1016/j.isci.2022.105218 |
0.32 |
|
| 2022 |
Zhang C, Shine M, Pyle AM, Zhang Y. US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes. Nature Methods. PMID 36038728 DOI: 10.1038/s41592-022-01585-1 |
0.318 |
|
| 2022 |
Guo R, Pyle AM. Monitoring functional RNA binding of RNA-dependent ATPase enzymes such as SF2 helicases using RNA dependent ATPase assays: A RIG-I case study. Methods in Enzymology. 673: 39-52. PMID 35965013 DOI: 10.1016/bs.mie.2022.03.064 |
0.422 |
|
| 2022 |
Guo LT, Olson S, Patel S, Graveley BR, Pyle AM. Direct tracking of reverse-transcriptase speed and template sensitivity: implications for sequencing and analysis of long RNA molecules. Nucleic Acids Research. PMID 35713547 DOI: 10.1093/nar/gkac518 |
0.453 |
|
| 2022 |
Omran QQ, Fedorova O, Liu T, Pyle AM. A molecular beacon assay for monitoring RNA splicing. Nucleic Acids Research. PMID 35438748 DOI: 10.1093/nar/gkac242 |
0.388 |
|
| 2022 |
Zhang C, Pyle AM. CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures. Acta Crystallographica. Section D, Structural Biology. 78: 466-471. PMID 35362469 DOI: 10.1107/S2059798322001292 |
0.422 |
|
| 2022 |
Wan H, Adams RL, Lindenbach BD, Pyle AM. The and Architecture of the Hepatitis C Virus RNA Genome Uncovers Functional RNA Secondary and Tertiary Structures. Journal of Virology. e0194621. PMID 35353000 DOI: 10.1128/jvi.01946-21 |
0.737 |
|
| 2021 |
Liu T, Pyle AM. Discovery of highly reactive self-splicing group II introns within the mitochondrial genomes of human pathogenic fungi. Nucleic Acids Research. 49: 12422-12432. PMID 34850132 DOI: 10.1093/nar/gkab1077 |
0.315 |
|
| 2021 |
Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, ... ... Pyle AM, et al. Noncoding RNAs: biology and applications-a Keystone Symposia report. Annals of the New York Academy of Sciences. PMID 34791665 DOI: 10.1111/nyas.14713 |
0.438 |
|
| 2021 |
Thoresen D, Wang W, Galls D, Guo R, Xu L, Pyle AM. The molecular mechanism of RIG-I activation and signaling. Immunological Reviews. PMID 34514601 DOI: 10.1111/imr.13022 |
0.409 |
|
| 2021 |
Li K, Zheng J, Wirawan M, Trinh NM, Fedorova O, Griffin PR, Pyle AM, Luo D. Insights into the structure and RNA-binding specificity of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3). Nucleic Acids Research. PMID 34403472 DOI: 10.1093/nar/gkab712 |
0.467 |
|
| 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 |
0.419 |
|
| 2020 |
Tavares RCA, Mahadeshwar G, Wan H, Huston NC, Pyle AM. The global and local distribution of RNA structure throughout the SARS-CoV-2 genome. Journal of Virology. PMID 33268519 DOI: 10.1128/JVI.02190-20 |
0.433 |
|
| 2020 |
Huston NC, Wan H, Araujo Tavares RC, Wilen C, Pyle AM. Comprehensive in-vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms. Biorxiv : the Preprint Server For Biology. PMID 32676598 DOI: 10.1101/2020.07.10.197079 |
0.426 |
|
| 2020 |
Manigrasso J, Chillón I, Genna V, Vidossich P, Somarowthu S, Pyle AM, De Vivo M, Marcia M. Visualizing group II intron dynamics between the first and second steps of splicing. Nature Communications. 11: 2837. PMID 32503992 DOI: 10.1038/S41467-020-16741-4 |
0.46 |
|
| 2020 |
Guo LT, Adams RL, Wan H, Huston NC, Potapova O, Olson S, Gallardo CM, Graveley BR, Torbett BE, Pyle AM. Sequencing and structure probing of long RNAs using MarathonRT: a next-generation reverse transcriptase. Journal of Molecular Biology. PMID 32259542 DOI: 10.1016/J.Jmb.2020.03.022 |
0.787 |
|
| 2020 |
Rawling DC, Jagdmann GE, Potapova O, Pyle AM. Small-Molecule Antagonists of the RIG-I Innate Immune Receptor. Acs Chemical Biology. 15: 311-317. PMID 31944652 DOI: 10.1021/Acschembio.9B00810 |
0.302 |
|
| 2019 |
Ren X, Linehan MM, Iwasaki A, Pyle AM. RIG-I Recognition of RNA Targets: The Influence of Terminal Base Pair Sequence and Overhangs on Affinity and Signaling. Cell Reports. 29: 3807-3815.e3. PMID 31851914 DOI: 10.1016/J.Celrep.2019.11.052 |
0.535 |
|
| 2019 |
Dickey TH, Song B, Pyle AM. RNA binding activates RIG-I by releasing an autorepressed signaling domain. Science Advances. 5: eaax3641. PMID 31616790 DOI: 10.1126/Sciadv.Aax3641 |
0.396 |
|
| 2019 |
Adams RL, Huston NC, Tavares RCA, Pyle AM. Sensitive detection of structural features and rearrangements in long, structured RNA molecules. Methods in Enzymology. 623: 249-289. PMID 31239050 DOI: 10.1016/Bs.Mie.2019.04.002 |
0.778 |
|
| 2019 |
Tavares RCA, Pyle AM, Somarowthu S. Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures. Journal of Molecular Biology. PMID 30890332 DOI: 10.1016/J.Jmb.2019.03.012 |
0.499 |
|
| 2019 |
Ren X, Linehan MM, Iwasaki A, Pyle AM. RIG-I Selectively Discriminates against 5'-Monophosphate RNA. Cell Reports. 26: 2019-2027.e4. PMID 30784585 DOI: 10.1016/J.Celrep.2019.01.107 |
0.543 |
|
| 2018 |
Fedorova O, Jagdmann GE, Adams RL, Yuan L, Van Zandt MC, Pyle AM. Small molecules that target group II introns are potent antifungal agents. Nature Chemical Biology. PMID 30323219 DOI: 10.1038/S41589-018-0142-0 |
0.773 |
|
| 2018 |
Schult P, Roth H, Adams RL, Mas C, Imbert L, Orlik C, Ruggieri A, Pyle AM, Lohmann V. microRNA-122 amplifies hepatitis C virus translation by shaping the structure of the internal ribosomal entry site. Nature Communications. 9: 2613. PMID 29973597 DOI: 10.1038/S41467-018-05053-3 |
0.71 |
|
| 2018 |
Linehan MM, Dickey TH, Molinari ES, Fitzgerald ME, Potapova O, Iwasaki A, Pyle AM. A minimal RNA ligand for potent RIG-I activation in living mice. Science Advances. 4: e1701854. PMID 29492454 DOI: 10.1126/Sciadv.1701854 |
0.488 |
|
| 2018 |
Palmer CR, Jacobson ME, Fedorova O, Pyle AM, Wilson JT. Environmentally Triggerable Retinoic Acid-Inducible Gene I Agonists Using Synthetic Polymer Overhangs. Bioconjugate Chemistry. PMID 29350913 DOI: 10.1021/acs.bioconjchem.7b00697 |
0.305 |
|
| 2017 |
Zhao C, Liu F, Pyle AM. An ultra-processive, accurate reverse transcriptase encoded by a metazoan group II intron. Rna (New York, N.Y.). PMID 29109157 DOI: 10.1261/Rna.063479.117 |
0.43 |
|
| 2017 |
Zhou T, Ren X, Adams RL, Pyle AM. NS3 from HCV strain JFH-1 is an unusually robust helicase that is primed to bind and unwind viral RNA. Journal of Virology. PMID 29070684 DOI: 10.1128/Jvi.01253-17 |
0.724 |
|
| 2017 |
Dickey TH, Pyle AM. The SMAD3 transcription factor binds complex RNA structures with high affinity. Nucleic Acids Research. PMID 29036649 DOI: 10.1093/Nar/Gkx846 |
0.515 |
|
| 2017 |
Schlick T, Pyle A. RNA Structural Variability and Functional Versatility Challenges RNA Structural Modeling and Design. Biophysical Journal. PMID 28669406 DOI: 10.1016/J.Bpj.2017.06.040 |
0.563 |
|
| 2017 |
Zhao C, Pyle AM. The group II intron maturase: a reverse transcriptase and splicing factor go hand in hand. Current Opinion in Structural Biology. 47: 30-39. PMID 28528306 DOI: 10.1016/J.Sbi.2017.05.002 |
0.471 |
|
| 2017 |
Adams RL, Pirakitikulr N, Pyle AM. Functional RNA structures throughout the Hepatitis C Virus genome. Current Opinion in Virology. 24: 79-86. PMID 28511116 DOI: 10.1016/J.Coviro.2017.04.007 |
0.764 |
|
| 2017 |
Zhao C, Pyle AM. Structural Insights into the Mechanism of Group II Intron Splicing. Trends in Biochemical Sciences. PMID 28438387 DOI: 10.1016/J.Tibs.2017.03.007 |
0.502 |
|
| 2017 |
Fitzgerald ME, Rawling DC, Potapova O, Ren X, Kohlway A, Pyle AM. Selective RNA targeting and regulated signaling by RIG-I is controlled by coordination of RNA and ATP binding. Nucleic Acids Research. 45: 1442-1454. PMID 28180316 DOI: 10.1093/Nar/Gkw816 |
0.536 |
|
| 2017 |
Schlick T, Pyle AM. Opportunities and Challenges in RNA Structural Modeling and Design. Biophysical Journal. PMID 28162235 DOI: 10.1016/J.Bpj.2016.12.037 |
0.539 |
|
| 2017 |
Liu F, Somarowthu S, Pyle AM. Visualizing the secondary and tertiary architectural domains of lncRNA RepA. Nature Chemical Biology. PMID 28068310 DOI: 10.1038/Nchembio.2272 |
0.507 |
|
| 2017 |
Pyle AM. Group II Intron Self-Splicing. Annual Review of Biophysics. 45: 183-205. PMID 27391926 DOI: 10.1146/Annurev-Biophys-062215-011149 |
0.536 |
|
| 2016 |
Fitzgerald ME, Rawling DC, Potapova O, Ren X, Kohlway A, Pyle AM. Selective RNA targeting and regulated signaling by RIG-I is controlled by coordination of RNA and ATP binding. Nucleic Acids Research. PMID 27625396 DOI: 10.1093/nar/gkw816 |
0.445 |
|
| 2016 |
Chillón I, Pyle AM. Inverted repeat Alu elements in the human lincRNA-p21 adopt a conserved secondary structure that regulates RNA function. Nucleic Acids Research. PMID 27378782 DOI: 10.1093/Nar/Gkw599 |
0.351 |
|
| 2016 |
Molinari E, Bar H, Pyle AM, Patrizio P. Transcriptome analysis of human cumulus cells reveals hypoxia as the main determinant of follicular senescence. Molecular Human Reproduction. PMID 27268410 DOI: 10.1093/Molehr/Gaw038 |
0.374 |
|
| 2016 |
Zhao C, Pyle AM. Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution. Nature Structural & Molecular Biology. PMID 27136328 DOI: 10.1038/Nsmb.3224 |
0.546 |
|
| 2016 |
Pirakitikulr N, Kohlway A, Lindenbach BD, Pyle AM. The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures. Molecular Cell. PMID 26924328 DOI: 10.1016/J.Molcel.2016.01.024 |
0.472 |
|
| 2016 |
Pyle AM, Schlick T. Challenges in RNA Structural Modeling and Design. Journal of Molecular Biology. PMID 26876599 DOI: 10.1016/J.Jmb.2016.02.012 |
0.482 |
|
| 2016 |
Chillon I, Somarowthu S, Liu F, Pyle AM. Abstract IA25: Regulatory control of lincRNA function through formation of complex RNA structural motifs Cancer Research. 76. DOI: 10.1158/1538-7445.Nonrna15-Ia25 |
0.532 |
|
| 2015 |
Zhao C, Rajashankar KR, Marcia M, Pyle AM. Crystal structure of group II intron domain 1 reveals a template for RNA assembly. Nature Chemical Biology. PMID 26502156 DOI: 10.1038/Nchembio.1949 |
0.586 |
|
| 2015 |
Chillón I, Marcia M, Legiewicz M, Liu F, Somarowthu S, Pyle AM. Native Purification and Analysis of Long RNAs. Methods in Enzymology. 558: 3-37. PMID 26068736 DOI: 10.1016/Bs.Mie.2015.01.008 |
0.528 |
|
| 2015 |
Somarowthu S, Legiewicz M, Chillón I, Marcia M, Liu F, Pyle AM. HOTAIR forms an intricate and modular secondary structure. Molecular Cell. 58: 353-61. PMID 25866246 DOI: 10.1016/J.Molcel.2015.03.006 |
0.519 |
|
| 2015 |
Pyle AM. Rediscovering RNA. Rna (New York, N.Y.). 21: 714-5. PMID 25780205 DOI: 10.1261/rna.050807.115 |
0.431 |
|
| 2015 |
Molinari E, Pyle A, Bar H, Patrizio P. RNA sequencing and immuno-fluorescence staining of cumulus cells associated with human oocyte senescence pathways Fertility and Sterility. 104: e200-e201. DOI: 10.1016/J.Fertnstert.2015.07.623 |
0.41 |
|
| 2014 |
Pyle AM. Looking at LncRNAs with the ribozyme toolkit. Molecular Cell. 56: 13-7. PMID 25280101 DOI: 10.1016/J.Molcel.2014.08.025 |
0.514 |
|
| 2014 |
Rawling DC, Kohlway AS, Luo D, Ding SC, Pyle AM. The RIG-I ATPase core has evolved a functional requirement for allosteric stabilization by the Pincer domain. Nucleic Acids Research. 42: 11601-11. PMID 25217590 DOI: 10.1093/Nar/Gku817 |
0.388 |
|
| 2014 |
Kohlway A, Pirakitikulr N, Ding SC, Yang F, Luo D, Lindenbach BD, Pyle AM. The linker region of NS3 plays a critical role in the replication and infectivity of hepatitis C virus. Journal of Virology. 88: 10970-4. PMID 24965468 DOI: 10.1128/Jvi.00745-14 |
0.338 |
|
| 2014 |
Fitzgerald ME, Rawling DC, Vela A, Pyle AM. An evolving arsenal: viral RNA detection by RIG-I-like receptors. Current Opinion in Microbiology. 20: 76-81. PMID 24912143 DOI: 10.1016/J.Mib.2014.05.004 |
0.513 |
|
| 2014 |
Rawling DC, Pyle AM. Parts, assembly and operation of the RIG-I family of motors. Current Opinion in Structural Biology. 25: 25-33. PMID 24878341 DOI: 10.1016/J.Sbi.2013.11.011 |
0.497 |
|
| 2014 |
Marcia M, Pyle AM. Principles of ion recognition in RNA: insights from the group II intron structures. Rna (New York, N.Y.). 20: 516-27. PMID 24570483 DOI: 10.1261/Rna.043414.113 |
0.466 |
|
| 2014 |
Fitzgerald ME, Vela A, Pyle AM. Dicer-related helicase 3 forms an obligate dimer for recognizing 22G-RNA. Nucleic Acids Research. 42: 3919-30. PMID 24435798 DOI: 10.1093/Nar/Gkt1383 |
0.541 |
|
| 2014 |
Somarowthu S, Legiewicz M, Keating KS, Pyle AM. Visualizing the ai5γ group IIB intron. Nucleic Acids Research. 42: 1947-58. PMID 24203709 DOI: 10.1093/Nar/Gkt1051 |
0.54 |
|
| 2014 |
Kohlway A, Pirakitikulr N, Barrera FN, Potapova O, Engelman DM, Pyle AM, Lindenbach BD. Hepatitis C virus RNA replication and virus particle assembly require specific dimerization of the NS4A protein transmembrane domain. Journal of Virology. 88: 628-42. PMID 24173222 DOI: 10.1128/Jvi.02052-13 |
0.357 |
|
| 2014 |
Molinari E, Patrizio P, Pyle A. Rna high throughput sequencing of cumulus cells reveals new pathways involved in human oocyte aging Fertility and Sterility. 102: e331. DOI: 10.1016/J.Fertnstert.2014.07.1121 |
0.426 |
|
| 2013 |
Pyle AM. Coordinating the party: assembly factors and ribogenesis. Molecular Cell. 52: 469-70. PMID 24267447 DOI: 10.1016/J.Molcel.2013.11.007 |
0.379 |
|
| 2013 |
Marcia M, Humphris-Narayanan E, Keating KS, Somarowthu S, Rajashankar K, Pyle AM. Solving nucleic acid structures by molecular replacement: examples from group II intron studies. Acta Crystallographica. Section D, Biological Crystallography. 69: 2174-85. PMID 24189228 DOI: 10.1107/S0907444913013218 |
0.404 |
|
| 2013 |
Ostankovitch M, Pyle AM. Noncoding RNAs: A story of networks and long-distance relationships. Journal of Molecular Biology. 425: 3577-81. PMID 23911549 DOI: 10.1016/J.Jmb.2013.07.032 |
0.431 |
|
| 2013 |
Kohlway A, Luo D, Rawling DC, Ding SC, Pyle AM. Defining the functional determinants for RNA surveillance by RIG-I. Embo Reports. 14: 772-9. PMID 23897087 DOI: 10.1038/Embor.2013.108 |
0.546 |
|
| 2013 |
Nagy V, Pirakitikulr N, Zhou KI, Chillón I, Luo J, Pyle AM. Predicted group II intron lineages E and F comprise catalytically active ribozymes. Rna (New York, N.Y.). 19: 1266-78. PMID 23882113 DOI: 10.1261/Rna.039123.113 |
0.459 |
|
| 2013 |
Marcia M, Somarowthu S, Pyle AM. Now on display: a gallery of group II intron structures at different stages of catalysis. Mobile Dna. 4: 14. PMID 23634971 DOI: 10.1186/1759-8753-4-14 |
0.479 |
|
| 2013 |
Luo D, Kohlway A, Pyle AM. Duplex RNA activated ATPases (DRAs): platforms for RNA sensing, signaling and processing. Rna Biology. 10: 111-20. PMID 23228901 DOI: 10.4161/Rna.22706 |
0.561 |
|
| 2012 |
Marcia M, Pyle AM. Visualizing group II intron catalysis through the stages of splicing. Cell. 151: 497-507. PMID 23101623 DOI: 10.1016/J.Cell.2012.09.033 |
0.454 |
|
| 2012 |
Vela A, Fedorova O, Ding SC, Pyle AM. The thermodynamic basis for viral RNA detection by the RIG-I innate immune sensor. The Journal of Biological Chemistry. 287: 42564-73. PMID 23055530 DOI: 10.1074/Jbc.M112.385146 |
0.503 |
|
| 2012 |
Luo D, Kohlway A, Vela A, Pyle AM. Visualizing the determinants of viral RNA recognition by innate immune sensor RIG-I. Structure (London, England : 1993). 20: 1983-8. PMID 23022350 DOI: 10.1016/J.Str.2012.08.029 |
0.533 |
|
| 2012 |
Keating KS, Pyle AM. RCrane: semi-automated RNA model building. Acta Crystallographica. Section D, Biological Crystallography. 68: 985-95. PMID 22868764 DOI: 10.1107/S0907444912018549 |
0.447 |
|
| 2012 |
Ding SC, Pyle AM. Molecular mechanics of RNA translocases. Methods in Enzymology. 511: 131-47. PMID 22713318 DOI: 10.1016/B978-0-12-396546-2.00006-1 |
0.516 |
|
| 2012 |
Fedorova O, Pyle AM. The brace for a growing scaffold: Mss116 protein promotes RNA folding by stabilizing an early assembly intermediate. Journal of Molecular Biology. 422: 347-65. PMID 22705286 DOI: 10.1016/J.Jmb.2012.05.037 |
0.461 |
|
| 2012 |
Chan RT, Robart AR, Rajashankar KR, Pyle AM, Toor N. Crystal structure of a group II intron in the pre-catalytic state. Nature Structural & Molecular Biology. 19: 555-7. PMID 22484319 DOI: 10.1038/Nsmb.2270 |
0.502 |
|
| 2012 |
Humphris-Narayanan E, Pyle AM. Discrete RNA libraries from pseudo-torsional space. Journal of Molecular Biology. 421: 6-26. PMID 22425640 DOI: 10.1016/J.Jmb.2012.03.002 |
0.546 |
|
| 2011 |
Luo D, Ding SC, Vela A, Kohlway A, Lindenbach BD, Pyle AM. Structural insights into RNA recognition by RIG-I. Cell. 147: 409-22. PMID 22000018 DOI: 10.1016/J.Cell.2011.09.023 |
0.498 |
|
| 2011 |
Butcher SE, Pyle AM. The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks. Accounts of Chemical Research. 44: 1302-11. PMID 21899297 DOI: 10.1021/Ar200098T |
0.579 |
|
| 2011 |
Pyle AM. RNA helicases and remodeling proteins. Current Opinion in Chemical Biology. 15: 636-42. PMID 21862383 DOI: 10.1016/J.Cbpa.2011.07.019 |
0.522 |
|
| 2011 |
Keating KS, Humphris EL, Pyle AM. A new way to see RNA. Quarterly Reviews of Biophysics. 44: 433-66. PMID 21729350 DOI: 10.1017/S0033583511000059 |
0.559 |
|
| 2011 |
Pyle AM, Shakked Z. The ever-growing complexity of nucleic acids: from small DNA and RNA motifs to large molecular assemblies and machines. Current Opinion in Structural Biology. 21: 293-5. PMID 21565486 DOI: 10.1016/J.Sbi.2011.04.003 |
0.433 |
|
| 2011 |
Cao W, Coman MM, Ding S, Henn A, Middleton ER, Bradley MJ, Rhoades E, Hackney DD, Pyle AM, De La Cruz EM. Mechanism of Mss116 ATPase reveals functional diversity of DEAD-Box proteins. Journal of Molecular Biology. 409: 399-414. PMID 21501623 DOI: 10.1016/J.Jmb.2011.04.004 |
0.554 |
|
| 2011 |
Ding SC, Kohlway AS, Pyle AM. Unmasking the active helicase conformation of nonstructural protein 3 from hepatitis C virus. Journal of Virology. 85: 4343-53. PMID 21325413 DOI: 10.1128/Jvi.02130-10 |
0.374 |
|
| 2011 |
Appleby TC, Anderson R, Fedorova O, Pyle AM, Wang R, Liu X, Brendza KM, Somoza JR. Visualizing ATP-dependent RNA translocation by the NS3 helicase from HCV. Journal of Molecular Biology. 405: 1139-53. PMID 21145896 DOI: 10.1016/J.Jmb.2010.11.034 |
0.461 |
|
| 2011 |
Phan T, Kohlway A, Dimberu P, Pyle AM, Lindenbach BD. The acidic domain of hepatitis C virus NS4A contributes to RNA replication and virus particle assembly. Journal of Virology. 85: 1193-204. PMID 21047963 DOI: 10.1128/Jvi.01889-10 |
0.37 |
|
| 2011 |
Luo D, Pyle AM. Structural basis of double-stranded RNA recognition by RIG-I Acta Crystallographica Section a Foundations of Crystallography. 67: C160-C160. DOI: 10.1107/S0108767311096073 |
0.46 |
|
| 2010 |
Karunatilaka KS, Solem A, Pyle AM, Rueda D. Single-molecule analysis of Mss116-mediated group II intron folding. Nature. 467: 935-9. PMID 20944626 DOI: 10.1016/J.Bpj.2009.12.2568 |
0.537 |
|
| 2010 |
Zingler N, Solem A, Pyle AM. Dual roles for the Mss116 cofactor during splicing of the ai5γ group II intron. Nucleic Acids Research. 38: 6602-9. PMID 20554854 DOI: 10.1093/Nar/Gkq530 |
0.508 |
|
| 2010 |
Matranga C, Pyle AM. Double-stranded RNA-dependent ATPase DRH-3: insight into its role in RNAsilencing in Caenorhabditis elegans. The Journal of Biological Chemistry. 285: 25363-71. PMID 20529861 DOI: 10.1074/Jbc.M110.117010 |
0.558 |
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| 2010 |
Pyle AM. The tertiary structure of group II introns: implications for biological function and evolution. Critical Reviews in Biochemistry and Molecular Biology. 45: 215-32. PMID 20446804 DOI: 10.3109/10409231003796523 |
0.536 |
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| 2010 |
Keating KS, Pyle AM. Semiautomated model building for RNA crystallography using a directed rotameric approach. Proceedings of the National Academy of Sciences of the United States of America. 107: 8177-82. PMID 20404211 DOI: 10.1073/Pnas.0911888107 |
0.517 |
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| 2010 |
Fedorova O, Solem A, Pyle AM. Protein-facilitated folding of group II intron ribozymes. Journal of Molecular Biology. 397: 799-813. PMID 20138894 DOI: 10.1016/J.Jmb.2010.02.001 |
0.497 |
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| 2010 |
Roitzsch M, Fedorova O, Pyle AM. The 2'-OH group at the group II intron terminus acts as a proton shuttle. Nature Chemical Biology. 6: 218-224. PMID 20118939 DOI: 10.1038/Nchembio.312 |
0.56 |
|
| 2010 |
Taylor SD, Solem A, Kawaoka J, Pyle AM. The NPH-II helicase displays efficient DNA x RNA helicase activity and a pronounced purine sequence bias. The Journal of Biological Chemistry. 285: 11692-703. PMID 20110368 DOI: 10.1074/Jbc.M109.088559 |
0.816 |
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| 2010 |
Toor N, Keating KS, Fedorova O, Rajashankar K, Wang J, Pyle AM. Tertiary architecture of the Oceanobacillus iheyensis group II intron. Rna (New York, N.Y.). 16: 57-69. PMID 19952115 DOI: 10.1261/Rna.1844010 |
0.511 |
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| 2010 |
Keating KS, Toor N, Perlman PS, Pyle AM. A structural analysis of the group II intron active site and implications for the spliceosome. Rna (New York, N.Y.). 16: 1-9. PMID 19948765 DOI: 10.1261/Rna.1791310 |
0.498 |
|
| 2010 |
Pyle A. Principles of RNA Tertiary Structural Organization Revealed by Group II Intron Crystal Structures Biophysical Journal. 98: 198a. DOI: 10.1016/J.Bpj.2009.12.1052 |
0.506 |
|
| 2010 |
Pyle AM. Touching RNA: RNA can bind and sense the shapes of other molecules by feeling them with its backbone- and not just its bases. What gives RNA molecules this remarkable versatility? Scientist. 24. |
0.429 |
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| 2009 |
Pyle AM. How to drive your helicase in a straight line. Cell. 139: 458-9. PMID 19879832 DOI: 10.1016/J.Cell.2009.10.016 |
0.509 |
|
| 2009 |
Toor N, Keating KS, Pyle AM. Structural insights into RNA splicing. Current Opinion in Structural Biology. 19: 260-6. PMID 19443210 DOI: 10.1016/J.Sbi.2009.04.002 |
0.561 |
|
| 2009 |
Roitzsch M, Pyle AM. The linear form of a group II intron catalyzes efficient autocatalytic reverse splicing, establishing a potential for mobility. Rna (New York, N.Y.). 15: 473-82. PMID 19168748 DOI: 10.1261/Rna.1392009 |
0.463 |
|
| 2009 |
Beran RK, Lindenbach BD, Pyle AM. The NS4A protein of hepatitis C virus promotes RNA-coupled ATP hydrolysis by the NS3 helicase. Journal of Virology. 83: 3268-75. PMID 19153239 DOI: 10.1128/Jvi.01849-08 |
0.468 |
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| 2009 |
Serebrov V, Beran RK, Pyle AM. Establishing a mechanistic basis for the large kinetic steps of the NS3 helicase. The Journal of Biological Chemistry. 284: 2512-21. PMID 19010782 DOI: 10.1074/Jbc.M805460200 |
0.486 |
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| 2008 |
Toor N, Rajashankar K, Keating KS, Pyle AM. Structural basis for exon recognition by a group II intron. Nature Structural & Molecular Biology. 15: 1221-2. PMID 18953333 DOI: 10.1038/Nsmb.1509 |
0.523 |
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| 2008 |
Zingler N, Solem A, Pyle AM. Protein-facilitated ribozyme folding and catalysis. Nucleic Acids Symposium Series (2004). 67-8. PMID 18776256 DOI: 10.1093/nass/nrn034 |
0.363 |
|
| 2008 |
Keating KS, Toor N, Pyle AM. The GANC tetraloop: a novel motif in the group IIC intron structure. Journal of Molecular Biology. 383: 475-81. PMID 18773908 DOI: 10.1016/J.Jmb.2008.08.043 |
0.47 |
|
| 2008 |
Beran RK, Pyle AM. Hepatitis C viral NS3-4A protease activity is enhanced by the NS3 helicase. The Journal of Biological Chemistry. 283: 29929-37. PMID 18723512 DOI: 10.1074/Jbc.M804065200 |
0.386 |
|
| 2008 |
Pyle AM. Translocation and unwinding mechanisms of RNA and DNA helicases. Annual Review of Biophysics. 37: 317-36. PMID 18573084 DOI: 10.1146/Annurev.Biophys.37.032807.125908 |
0.549 |
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| 2008 |
Fedorova O, Pyle AM. A conserved element that stabilizes the group II intron active site. Rna (New York, N.Y.). 14: 1048-56. PMID 18441048 DOI: 10.1261/Rna.942308 |
0.385 |
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| 2008 |
Toor N, Keating KS, Taylor SD, Pyle AM. Crystal structure of a self-spliced group II intron. Science (New York, N.Y.). 320: 77-82. PMID 18388288 DOI: 10.1126/Science.1153803 |
0.433 |
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| 2008 |
Richardson JS, Schneider B, Murray LW, Kapral GJ, Immormino RM, Headd JJ, Richardson DC, Ham D, Hershkovits E, Williams LD, Keating KS, Pyle AM, Micallef D, Westbrook J, Berman HM, et al. RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). Rna (New York, N.Y.). 14: 465-81. PMID 18192612 DOI: 10.1261/Rna.657708 |
0.468 |
|
| 2008 |
de Lencastre A, Pyle AM. Three essential and conserved regions of the group II intron are proximal to the 5'-splice site. Rna (New York, N.Y.). 14: 11-24. PMID 18039742 DOI: 10.1261/Rna.774008 |
0.8 |
|
| 2008 |
Waldsich C, Pyle AM. A kinetic intermediate that regulates proper folding of a group II intron RNA. Journal of Molecular Biology. 375: 572-80. PMID 18022197 DOI: 10.1016/J.Jmb.2007.10.052 |
0.423 |
|
| 2008 |
Fedorova O, Boudvillain M, Kawaoka J, Pyle AM. Nucleotide Analog Interference Mapping and Suppression: Specific Applications in Studies of RNA Tertiary Structure, Dynamic Helicase Mechanism and RNA-Protein Interactions Handbook of Rna Biochemistry. 259-293. DOI: 10.1002/9783527619504.ch17 |
0.436 |
|
| 2008 |
Beran RKF, Serebrov V, Pyle AM. The serine protease domain of hepatitis C viral NS3 activates RNA helicase activity by promoting the binding of RNA substrate (Journal of Biological Chemistry (2007) 282, (34913-34920)) Journal of Biological Chemistry. 283: 5971. |
0.424 |
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| 2007 |
Beran RK, Serebrov V, Pyle AM. The serine protease domain of hepatitis C viral NS3 activates RNA helicase activity by promoting the binding of RNA substrate. The Journal of Biological Chemistry. 282: 34913-20. PMID 17921146 DOI: 10.1074/Jbc.M707165200 |
0.483 |
|
| 2007 |
Wadley LM, Keating KS, Duarte CM, Pyle AM. Evaluating and learning from RNA pseudotorsional space: quantitative validation of a reduced representation for RNA structure. Journal of Molecular Biology. 372: 942-57. PMID 17707400 DOI: 10.1016/J.Jmb.2007.06.058 |
0.825 |
|
| 2007 |
Myong S, Bruno MM, Pyle AM, Ha T. Spring-loaded mechanism of DNA unwinding by hepatitis C virus NS3 helicase. Science (New York, N.Y.). 317: 513-6. PMID 17656723 DOI: 10.1126/Science.1144130 |
0.354 |
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| 2007 |
Lindenbach BD, Prágai BM, Montserret R, Beran RK, Pyle AM, Penin F, Rice CM. The C terminus of hepatitis C virus NS4A encodes an electrostatic switch that regulates NS5A hyperphosphorylation and viral replication. Journal of Virology. 81: 8905-18. PMID 17581983 DOI: 10.1128/Jvi.00937-07 |
0.336 |
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| 2007 |
Pyle AM, Fedorova O, Waldsich C. Folding of group II introns: a model system for large, multidomain RNAs? Trends in Biochemical Sciences. 32: 138-45. PMID 17289393 DOI: 10.1016/J.Tibs.2007.01.005 |
0.571 |
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| 2007 |
Tang CL, Alexov E, Pyle AM, Honig B. Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides. Journal of Molecular Biology. 366: 1475-96. PMID 17223134 DOI: 10.1016/J.Jmb.2006.12.001 |
0.532 |
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| 2007 |
Fedorova O, Waldsich C, Pyle AM. Group II intron folding under near-physiological conditions: collapsing to the near-native state. Journal of Molecular Biology. 366: 1099-114. PMID 17196976 DOI: 10.1016/J.Jmb.2006.12.003 |
0.394 |
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| 2007 |
Waldsich C, Pyle AM. A folding control element for tertiary collapse of a group II intron ribozyme. Nature Structural & Molecular Biology. 14: 37-44. PMID 17143279 DOI: 10.1038/Nsmb1181 |
0.456 |
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| 2007 |
Pyle AM. Group II intron ribozymes: RNA machines that shape eukaryotic evolution The Faseb Journal. 21. DOI: 10.1096/fasebj.21.5.a41-b |
0.425 |
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| 2007 |
Pyle AM, Barton JK. Probing Nucleic Acids with Transition Metal Complexes Progress in Inorganic Chemistry. 38: 413-475. DOI: 10.1002/9780470166390.Ch7 |
0.428 |
|
| 2006 |
Solem A, Zingler N, Pyle AM. A DEAD protein that activates intron self-splicing without unwinding RNA. Molecular Cell. 24: 611-7. PMID 17188036 DOI: 10.1016/J.Molcel.2006.10.032 |
0.499 |
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| 2006 |
Hamill S, Pyle AM. The receptor for branch-site docking within a group II intron active site. Molecular Cell. 23: 831-40. PMID 16973435 DOI: 10.1016/J.Molcel.2006.07.017 |
0.671 |
|
| 2006 |
Beran RK, Bruno MM, Bowers HA, Jankowsky E, Pyle AM. Robust translocation along a molecular monorail: the NS3 helicase from hepatitis C virus traverses unusually large disruptions in its track. Journal of Molecular Biology. 358: 974-82. PMID 16569413 DOI: 10.1016/J.Jmb.2006.02.078 |
0.495 |
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| 2006 |
Dumont S, Cheng W, Serebrov V, Beran RK, Tinoco I, Pyle AM, Bustamante C. RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP. Nature. 439: 105-8. PMID 16397502 DOI: 10.1038/Nature04331 |
0.452 |
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| 2006 |
Pyle AM, Lambowitz AM. 17 Group II Introns: Ribozymes That Splice RNA and Invade DNA Cold Spring Harbor Monograph Archive. 43: 469-505. DOI: 10.1101/087969739.43.469 |
0.548 |
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| 2005 |
Su LJ, Waldsich C, Pyle AM. An obligate intermediate along the slow folding pathway of a group II intron ribozyme. Nucleic Acids Research. 33: 6674-87. PMID 16314300 DOI: 10.1093/Nar/Gki973 |
0.501 |
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| 2005 |
Fedorova O, Pyle AM. Linking the group II intron catalytic domains: tertiary contacts and structural features of domain 3. The Embo Journal. 24: 3906-16. PMID 16252007 DOI: 10.1038/Sj.Emboj.7600852 |
0.413 |
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| 2005 |
Pyle AM. Capping by branching: a new ribozyme makes tiny lariats. Science (New York, N.Y.). 309: 1530-1. PMID 16141065 DOI: 10.1126/Science.1117957 |
0.481 |
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| 2005 |
de Lencastre A, Hamill S, Pyle AM. A single active-site region for a group II intron. Nature Structural & Molecular Biology. 12: 626-7. PMID 15980867 DOI: 10.1038/Nsmb957 |
0.808 |
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| 2005 |
Kawaoka J, Pyle AM. Choosing between DNA and RNA: the polymer specificity of RNA helicase NPH-II. Nucleic Acids Research. 33: 644-9. PMID 15681616 DOI: 10.1093/Nar/Gki208 |
0.816 |
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| 2005 |
Pang PS, Jankowsky E, Wadley LM, Pyle AM. Prediction of functional tertiary interactions and intermolecular interfaces from primary sequence data. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 304: 50-63. PMID 15595717 DOI: 10.1002/Jez.B.21024 |
0.793 |
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| 2004 |
Wadley LM, Pyle AM. The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery. Nucleic Acids Research. 32: 6650-9. PMID 15608296 DOI: 10.1093/Nar/Gkh1002 |
0.831 |
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| 2004 |
Serebrov V, Pyle AM. Periodic cycles of RNA unwinding and pausing by hepatitis C virus NS3 helicase. Nature. 430: 476-80. PMID 15269774 DOI: 10.1038/Nature02704 |
0.535 |
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| 2004 |
Kawaoka J, Jankowsky E, Pyle AM. Backbone tracking by the SF2 helicase NPH-II. Nature Structural & Molecular Biology. 11: 526-30. PMID 15146171 DOI: 10.1038/Nsmb771 |
0.799 |
|
| 2004 |
Sigel RK, Sashital DG, Abramovitz DL, Palmer AG, Butcher SE, Pyle AM. Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif. Nature Structural & Molecular Biology. 11: 187-92. PMID 14745440 DOI: 10.1038/Nsmb717 |
0.425 |
|
| 2004 |
Sigel R, Sashital D, Abramowitz D, Palmer A, Butcher S, Pyle AM. Chemical shifts assignments of domain 5 of the ai5gamma group II intron Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr5962 |
0.36 |
|
| 2003 |
Su LJ, Brenowitz M, Pyle AM. An alternative route for the folding of large RNAs: apparent two-state folding by a group II intron ribozyme. Journal of Molecular Biology. 334: 639-52. PMID 14636593 DOI: 10.1016/J.Jmb.2003.09.071 |
0.554 |
|
| 2003 |
Duarte CM, Wadley LM, Pyle AM. RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. Nucleic Acids Research. 31: 4755-61. PMID 12907716 DOI: 10.1093/Nar/Gkg682 |
0.832 |
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| 2003 |
Fedorova O, Mitros T, Pyle AM. Domains 2 and 3 interact to form critical elements of the group II intron active site. Journal of Molecular Biology. 330: 197-209. PMID 12823961 DOI: 10.1016/S0022-2836(03)00594-1 |
0.427 |
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| 2003 |
Aizawa Y, Xiang Q, Lambowitz AM, Pyle AM. The pathway for DNA recognition and RNA integration by a group II intron retrotransposon. Molecular Cell. 11: 795-805. PMID 12667460 DOI: 10.1016/S1097-2765(03)00069-8 |
0.449 |
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| 2003 |
Adamidi C, Fedorova O, Pyle AM. A group II intron inserted into a bacterial heat-shock operon shows autocatalytic activity and unusual thermostability. Biochemistry. 42: 3409-18. PMID 12653544 DOI: 10.1021/Bi027330B |
0.465 |
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| 2002 |
Fedorova O, Su LJ, Pyle AM. Group II introns: highly specific endonucleases with modular structures and diverse catalytic functions. Methods (San Diego, Calif.). 28: 323-35. PMID 12431436 DOI: 10.1016/S1046-2023(02)00239-6 |
0.49 |
|
| 2002 |
Pyle AM. Metal ions in the structure and function of RNA. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 7: 679-90. PMID 12203005 DOI: 10.1007/S00775-002-0387-6 |
0.508 |
|
| 2002 |
Pang PS, Jankowsky E, Planet PJ, Pyle AM. The hepatitis C viral NS3 protein is a processive DNA helicase with cofactor enhanced RNA unwinding. The Embo Journal. 21: 1168-76. PMID 11867545 DOI: 10.1093/Emboj/21.5.1168 |
0.676 |
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| 2002 |
Kang DC, Gopalkrishnan RV, Wu Q, Jankowsky E, Pyle AM, Fisher PB. mda-5: An interferon-inducible putative RNA helicase with double-stranded RNA-dependent ATPase activity and melanoma growth-suppressive properties. Proceedings of the National Academy of Sciences of the United States of America. 99: 637-42. PMID 11805321 DOI: 10.1073/Pnas.022637199 |
0.44 |
|
| 2002 |
Swisher JF, Su LJ, Brenowitz M, Anderson VE, Pyle AM. Productive folding to the native state by a group II intron ribozyme. Journal of Molecular Biology. 315: 297-310. PMID 11786013 DOI: 10.1006/Jmbi.2001.5233 |
0.814 |
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| 2001 |
Aizawa Y, Xiang Q, Pyle AM. Kinetic dissection of the multistep process in L1.ltrB intron mobility. Nucleic Acids Research. Supplement (2001). 249-50. PMID 12836358 |
0.432 |
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| 2001 |
Chu VT, Adamidi C, Liu Q, Perlman PS, Pyle AM. Control of branch-site choice by a group II intron. The Embo Journal. 20: 6866-76. PMID 11726522 DOI: 10.1093/Emboj/20.23.6866 |
0.73 |
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| 2001 |
Swisher J, Duarte CM, Su LJ, Pyle AM. Visualizing the solvent-inaccessible core of a group II intron ribozyme. The Embo Journal. 20: 2051-61. PMID 11296237 DOI: 10.1093/Emboj/20.8.2051 |
0.805 |
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| 2001 |
Su LJ, Qin PZ, Michels WJ, Pyle AM. Guiding ribozyme cleavage through motif recognition: the mechanism of cleavage site selection by a group ii intron ribozyme. Journal of Molecular Biology. 306: 655-68. PMID 11243778 DOI: 10.1006/Jmbi.2000.4323 |
0.446 |
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| 2001 |
Jankowsky E, Gross CH, Shuman S, Pyle AM. Active disruption of an RNA-protein interaction by a DExH/D RNA helicase. Science (New York, N.Y.). 291: 121-5. PMID 11141562 DOI: 10.1126/Science.291.5501.121 |
0.528 |
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| 2000 |
Sigel RK, Vaidya A, Pyle AM. Metal ion binding sites in a group II intron core. Nature Structural Biology. 7: 1111-6. PMID 11101891 DOI: 10.1038/81958 |
0.422 |
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| 2000 |
Boudvillain M, de Lencastre A, Pyle AM. A tertiary interaction that links active-site domains to the 5' splice site of a group II intron. Nature. 406: 315-8. PMID 10917534 DOI: 10.1038/35018589 |
0.795 |
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| 2000 |
Pyle AM, Chu VT, Jankowsky E, Boudvillain M. Using DNAzymes to cut, process, and map RNA molecules for structural studies or modification. Methods in Enzymology. 317: 140-6. PMID 10829278 DOI: 10.1016/S0076-6879(00)17012-0 |
0.807 |
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| 2000 |
Pyle AM. New tricks from an itinerant intron. Nature Structural Biology. 7: 352-4. PMID 10802726 DOI: 10.1038/75111 |
0.34 |
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| 2000 |
Jankowsky E, Gross CH, Shuman S, Pyle AM. The DExH protein NPH-II is a processive and directional motor for unwinding RNA. Nature. 403: 447-51. PMID 10667799 DOI: 10.1038/35000239 |
0.536 |
|
| 1999 |
Chin K, Sharp KA, Honig B, Pyle AM. Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function. Nature Structural Biology. 6: 1055-61. PMID 10542099 DOI: 10.1038/14940 |
0.47 |
|
| 1999 |
Qin PZ, Pyle AM. Antagonistic substrate binding by a group II intron ribozyme. Journal of Molecular Biology. 291: 15-27. PMID 10438603 DOI: 10.1006/Jmbi.1999.2922 |
0.417 |
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| 1999 |
Qin PZ, Pyle AM. Site-specific labeling of RNA with fluorophores and other structural probes Methods: a Companion to Methods in Enzymology. 18: 60-70. PMID 10208817 DOI: 10.1006/Meth.1999.0757 |
0.51 |
|
| 1998 |
Duarte CM, Pyle AM. Stepping through an RNA structure: A novel approach to conformational analysis Journal of Molecular Biology. 284: 1465-1478. PMID 9878364 DOI: 10.1006/Jmbi.1998.2233 |
0.522 |
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| 1998 |
Konforti BB, Liu Q, Pyle AM. A map of the binding site for catalytic domain 5 in the core of a group II intron ribozyme Embo Journal. 17: 7105-7117. PMID 9843514 DOI: 10.1093/Emboj/17.23.7105 |
0.373 |
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| 1998 |
Boudvillain M, Pyle AM. Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: A NAIM analysis Embo Journal. 17: 7091-7104. PMID 9843513 DOI: 10.1093/Emboj/17.23.7091 |
0.476 |
|
| 1998 |
Chu VT, Liu Q, Podar M, Perlman PS, Pyle AM. More than one way to splice an RNA: branching without a bulge and splicing without branching in group II introns. Rna (New York, N.Y.). 4: 1186-202. PMID 9769094 DOI: 10.1017/S1355838298980724 |
0.786 |
|
| 1998 |
Qin PZ, Pyle AM. The architectural organization and mechanistic function of group II intron structural elements Current Opinion in Structural Biology. 8: 301-308. PMID 9666325 DOI: 10.1016/S0959-440X(98)80062-6 |
0.529 |
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| 1998 |
Konforti BB, Abramovitz DL, Duarte CM, Karpeisky A, Beigelman L, Pyle AM. Ribozyme catalysis from the major groove of group II intron domain 5 Molecular Cell. 1: 433-441. PMID 9660927 DOI: 10.1016/S1097-2765(00)80043-X |
0.405 |
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| 1998 |
Wagner JDO, Jankowsky E, Company M, Pyle AM, Abelson JN. The DEAH-box protein PRP22 is an ATPase that mediates ATP-dependent mRNA release from the spliceosome and unwinds RNA duplexes Embo Journal. 17: 2926-2937. PMID 9582286 DOI: 10.1093/Emboj/17.10.2926 |
0.492 |
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| 1998 |
Xiang Q, Qin PZ, Michels WJ, Freeland K, Pyle AM. Sequence specificity of a group II intron ribozyme: Multiple mechanisms for promoting unusually high discrimination against mismatched targets Biochemistry. 37: 3839-3849. PMID 9521704 DOI: 10.1021/Bi972661N |
0.464 |
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| 1998 |
Podar M, Chu VT, Pyle AM, Perlman PS. Group II intron splicing in vivo by first-step hydrolysis. Nature. 391: 915-8. PMID 9495347 DOI: 10.1038/36142 |
0.761 |
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| 1997 |
Qin PZ, Pyle AM. Stopped-flow fluorescence spectroscopy of a group II intron ribozyme reveals that domain I is an independent folding unit with a requirement for specific Mg2+ ions in the tertiary structure Biochemistry. 36: 4718-4730. PMID 9125492 DOI: 10.1021/Bi962665C |
0.389 |
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| 1997 |
Liu Q, Green JB, Khodadadi A, Haeberli P, Beigelman L, Pyle AM. Branch-site selection in a group II intron mediated by active recognition of the adenine amino group and steric exclusion of non-adenine functionalities. Journal of Molecular Biology. 267: 163-71. PMID 9096215 DOI: 10.1006/Jmbi.1996.0845 |
0.415 |
|
| 1997 |
Abramovitz DL, Pyle AM. Remarkable morphologlical variability of a common RNA folding motif: The GNRA tetraloop-receptor interaction Journal of Molecular Biology. 266: 493-506. PMID 9067606 DOI: 10.1006/Jmbi.1996.0810 |
0.478 |
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| 1997 |
Pyle AM, Konforti BB, Abramovitz DL, Liu Q. Rna folding and catalysis by group ii intron ribozymes Faseb Journal. 11: A1446. DOI: 10.1016/0959-440X(95)80091-3 |
0.492 |
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| 1997 |
Quarte CM, Pyle AM. A pseudotorsional descriptor of rna conformation can quantify secondary Structure Faseb Journal. 11: A1407. |
0.433 |
|
| 1996 |
Daniels DL, Michels WJ, Pyle AM. Two competing pathways for self-splicing by group II introns: A quantitative analysis of in vitro reaction rates and products Journal of Molecular Biology. 256: 31-49. PMID 8609612 DOI: 10.1006/Jmbi.1996.0066 |
0.404 |
|
| 1996 |
Abramovitz DL, Friedman RA, Pyle AM. Catalytic Role of 2′-Hydroxyl Groups Within a Group II Intron Active Site Science. 271: 1410-1413. PMID 8596912 DOI: 10.1126/Science.271.5254.1410 |
0.409 |
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| 1995 |
Griffiin EA, Qin Z, Michels WJ, Pyle AM. Group II intron ribozymes that cleave DNA and RNA linkages with similar efficiency, and lack contacts with substrate 2′-hydroxyl groups Chemistry and Biology. 2: 761-770. PMID 9383483 DOI: 10.1016/1074-5521(95)90104-3 |
0.581 |
|
| 1995 |
Michels WJ, Pyle AM. Conversion of a group II intron into a new multiple-turnover ribozyme that selectively cleaves oligonucleotides: Elucidation of reaction mechanism and structure/function relationships Biochemistry. 34: 2965-2977. PMID 7893710 DOI: 10.1021/Bi00009A028 |
0.508 |
|
| 1995 |
Chin K, Pyle AM. Branch-point attack in group II introns is a highly reversible transesterification, providing a potential proofreading mechanism for 5′-splice site selection Rna. 1: 391-406. PMID 7493317 |
0.326 |
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| 1994 |
Pyle AM, Green JB. Building a kinetic framework for group II intron ribozyme activity: Quantitation of interdomain binding and reaction rate Biochemistry. 33: 2716-2725. PMID 8117737 DOI: 10.1021/Bi00175A047 |
0.479 |
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| 1994 |
Pyle AM, Moran S, Strobel SA, Chapman T, Turner DH, Cech TR. Replacement of the conserved G.U with a G-C pair at the cleavage site of the Tetrahymena ribozyme decreases binding, reactivity, and fidelity. Biochemistry. 33: 13856-63. PMID 7947794 DOI: 10.1021/Bi00250A040 |
0.652 |
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| 1993 |
Pyle AM. Ribozymes: A distinct class of metalloenzymes Science. 261: 709-714. PMID 7688142 DOI: 10.1126/Science.7688142 |
0.388 |
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| 1992 |
Cech TR, Herschlag D, Piccirilli JA, Pyle AM. RNA catalysis by a group I ribozyme. Developing a model for transition state stabilization. The Journal of Biological Chemistry. 267: 17479-82. PMID 1381347 |
0.751 |
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| 1992 |
Pyle AM, Murphy FL, Cech TR. RNA substrate binding site in the catalytic core of the Tetrahymena ribozyme. Nature. 358: 123-8. PMID 1377367 DOI: 10.1038/358123A0 |
0.659 |
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| 1992 |
Sitlani A, Long EC, Pyle AM, Barton JK. DNA photocleavage by phenanthrenequinone diimine complexes of rhodium(III): Shape-selective recognition and reaction Journal of the American Chemical Society. 114: 2303-2312. DOI: 10.1021/Ja00033A003 |
0.68 |
|
| 1991 |
Pyle AM, Cech TR. Ribozyme recognition of RNA by tertiary interactions with specific ribose 2'-OH groups. Nature. 350: 628-31. PMID 1708111 DOI: 10.1038/350628A0 |
0.689 |
|
| 1990 |
Pyle AM, McSwiggen JA, Cech TR. Direct measurement of oligonucleotide substrate binding to wild-type and mutant ribozymes from Tetrahymena. Proceedings of the National Academy of Sciences of the United States of America. 87: 8187-91. PMID 2236030 DOI: 10.1073/Pnas.87.21.8187 |
0.598 |
|
| 1990 |
Pyle AM, Morii T, Barton JK. Probing microstructures in double-helical DNA with chiral metal complexes: Recognition of changes in base-pair propeller twisting in solution Journal of the American Chemical Society. 112: 9432-9434. DOI: 10.1021/Ja00181A077 |
0.495 |
|
| 1990 |
Pyle AM, Chiang MY, Barton JK. Synthesis and characterization of physical, electronic, and photochemical aspects of 9,10-phenanthrenequinone diimine complexes of ruthenium(II) and rhodium(III) Inorganic Chemistry. 29: 4487-4495. DOI: 10.1021/Ic00347A031 |
0.475 |
|
| 1989 |
Uchida K, Pyle AM, Morii T, Barton JK. High resolution footprinting of EcoRI and distamycin with Rh(phi)2(bpy)3+, a new photofootprinting reagent. Nucleic Acids Research. 17: 10259-79. PMID 2602152 DOI: 10.1093/Nar/17.24.10259 |
0.512 |
|
| 1989 |
Pyle AM, Long EC, Barton JK. Shape-selective targeting of DNA by (phenanthrenequinone diimine)rhodium(III) photocleaving agents Journal of the American Chemical Society. 111: 4520-4522. DOI: 10.1021/Ja00194A070 |
0.65 |
|
| 1989 |
Pyle AM, Rehmann JP, Meshoyrer R, Kumar CV, Turro NJ, Barton JK. Mixed-ligand complexes of ruthenium(II): Factors governing binding to DNA Journal of the American Chemical Society. 111: 3051-3058. DOI: 10.1021/Ja00190A046 |
0.632 |
|
| 1989 |
Uchida K, Pyle A, Morii T, Barton J. Photofootprinting of EcoRi endonuclease and distamycin by a phenanthrenequinonediimine rhodium(III) complex Journal of Inorganic Biochemistry. 36: 276. DOI: 10.1016/0162-0134(89)84382-X |
0.39 |
|
| 1987 |
Pyle AM, Barton JK. Synthesis and spectroscopic characterization of the purple tris(phenanthrenequinone diimine)ruthenium(II) ion Inorganic Chemistry. 26: 3820-3823. DOI: 10.1021/Ic00269A041 |
0.492 |
|
| 1987 |
Pyle AM, Barton JK. Synthesis and spectroscopic characterization of the purple tris(phenanthrenequinone diimine)ruthenium(II) ion Inorganic Chemistry. 26: 3820-3823. |
0.407 |
|
| Low-probability matches (unlikely to be authored by this person) |
| 2004 |
Pyle AM. DNA repair: big engine finds small breaks. Nature. 432: 157-8. PMID 15538349 DOI: 10.1038/432157A |
0.291 |
|
| 2019 |
Van Zandt MC, Jagdmann GE, Whitehouse D, Ji MK, Savoy J, Potapova O, Cousido-Siah A, Mitschler A, Howard EI, Pyle AM, Podjarny AD. Discovery of N-substituted 3-amino-4-(3-boronopropyl)pyrrolidine-3-carboxylic acids as highly potent third generation inhibitors of human arginase I and II. Journal of Medicinal Chemistry. PMID 31408339 DOI: 10.1021/Acs.Jmedchem.9B00931 |
0.288 |
|
| 2007 |
Wagner GP, Pyle AM. Tinkering with transcription factor proteins: the role of transcription factor adaptation in developmental evolution. Novartis Foundation Symposium. 284: 116-25; discussion 1. PMID 17710850 DOI: 10.1002/9780470319390.Ch8 |
0.283 |
|
| 2022 |
Shine M, Zhang C, Pyle AM. AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids. Bioinformatics (Oxford, England). 38: 2937-2939. PMID 35561202 DOI: 10.1093/bioinformatics/btac207 |
0.282 |
|
| 2022 |
Shine M, Zhang C, Pyle AM. AMIGOS III: Pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids. Bioinformatics (Oxford, England). PMID 35385068 DOI: 10.1093/bioinformatics/btac207 |
0.282 |
|
| 2023 |
Wang W, Liu F, Pyle AM. A compact regulatory RNA element in human Hsp70 mRNA. Biorxiv : the Preprint Server For Biology. PMID 36865185 DOI: 10.1101/2023.02.22.529618 |
0.271 |
|
| 2022 |
Thoresen DT, Galls D, Götte B, Wang W, Pyle AM. A rapid RIG-I signaling relay mediates efficient antiviral response. Molecular Cell. 83: 90-104.e4. PMID 36521492 DOI: 10.1016/j.molcel.2022.11.018 |
0.27 |
|
| 1996 |
Abramovitz DL, Friedman RA, Pyle AM. Catalytic pole of 2'-hydroxyl groups within a group II intron active site Science. 271: 1410-1413. |
0.261 |
|
| 2023 |
Pánek J, Roithová A, Radivojević N, Sýkora M, Prusty AB, Huston N, Wan H, Pyle AM, Fischer U, Staněk D. The SMN complex drives structural changes in human snRNAs to enable snRNP assembly. Nature Communications. 14: 6580. PMID 37852981 DOI: 10.1038/s41467-023-42324-0 |
0.256 |
|
| 2017 |
Ren X, Gelinas AD, von Carlowitz I, Janjic N, Pyle AM. Structural basis for IL-1α recognition by a modified DNA aptamer that specifically inhibits IL-1α signaling. Nature Communications. 8: 810. PMID 28993621 DOI: 10.1038/S41467-017-00864-2 |
0.244 |
|
| 2007 |
Sigel RK, Pyle AM. Alternative roles for metal ions in enzyme catalysis and the implications for ribozyme chemistry. Chemical Reviews. 107: 97-113. PMID 17212472 DOI: 10.1021/Cr0502605 |
0.242 |
|
| 2019 |
Jiang X, Muthusamy V, Fedorova O, Kong Y, Kim DJ, Bosenberg M, Pyle AM, Iwasaki A. Intratumoral delivery of RIG-I agonist SLR14 induces robust antitumor responses. The Journal of Experimental Medicine. PMID 31601678 DOI: 10.1084/Jem.20190801 |
0.242 |
|
| 2020 |
Jacobson ME, Becker KW, Palmer CR, Pastora LE, Fletcher RB, Collins KA, Fedorova O, Duvall CL, Pyle AM, Wilson JT. Structural Optimization of Polymeric Carriers to Enhance the Immunostimulatory Activity of Molecularly Defined RIG-I Agonists. Acs Central Science. 6: 2008-2022. PMID 33274278 DOI: 10.1021/acscentsci.0c00568 |
0.24 |
|
| 2007 |
Toor N, Keating K, Taylor S, Pyle A. Crystal structure of self-spliced group II intron Chemtracts. 20: 437-439. |
0.239 |
|
| 2016 |
Lilley DM, Pyle AM. Editorial overview: Nucleic acids and their protein complexes. Current Opinion in Structural Biology. 36: vii-viii. PMID 26948825 DOI: 10.1016/J.Sbi.2016.02.002 |
0.238 |
|
| 2017 |
Ren X, Gelinas AD, Carlowitz Iv, Janjic N, Pyle AM. Structural basis for IL-1 alpha recognition by a modified DNA aptamer that specifically inhibits IL-1 alpha signaling. Nature Communications. 8: 810-810. DOI: 10.2210/Pdb5Uc6/Pdb |
0.233 |
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| 2015 |
Foxman EF, Storer JA, Fitzgerald ME, Wasik BR, Hou L, Zhao H, Turner PE, Pyle AM, Iwasaki A. Temperature-dependent innate defense against the common cold virus limits viral replication at warm temperature in mouse airway cells. Proceedings of the National Academy of Sciences of the United States of America. 112: 827-32. PMID 25561542 DOI: 10.1073/Pnas.1411030112 |
0.217 |
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| 2023 |
Wang W, Fedorova O, Pyle AM. A protocol for capturing RNA-sensing innate immune receptors in multiple conformations by single-particle cryo-EM. Star Protocols. 4: 102166. PMID 36920909 DOI: 10.1016/j.xpro.2023.102166 |
0.216 |
|
| 2022 |
Manigrasso J, Chillón I, Genna V, Vidossich P, Somarowthu S, Pyle AM, De Vivo M, Marcia M. Author Correction: Visualizing group II intron dynamics between the first and second steps of splicing. Nature Communications. 13: 1. PMID 34983933 DOI: 10.1038/s41467-021-27699-2 |
0.211 |
|
| 2019 |
Elion DL, Jacobson ME, Hicks DJ, Rahman B, Sanchez V, Gonzales-Ericsson PI, Fedorova O, Pyle AM, Wilson JT, Cook RS. Abstract A187: RIG-I agonists reinforce antitumor adaptive immunity and decrease Treg activity in breast cancer Cancer Immunology Research. 7. DOI: 10.1158/2326-6074.Cricimteatiaacr18-A187 |
0.21 |
|
| 2018 |
Elion DL, Jacobson ME, Hicks DJ, Rahman B, Sanchez V, Gonzalez-Ericsson PI, Fedorova O, Pyle AM, Wilson JT, Cook RS. Therapeutically active RIG-I agonist induces immunogenic tumor cell killing in breast cancers. Cancer Research. PMID 30224377 DOI: 10.1158/0008-5472.Can-18-0730 |
0.209 |
|
| 2006 |
Pyle AM, Widom J. Nucleic acids Current Opinion in Structural Biology. 16: 267-269. DOI: 10.1016/J.Sbi.2006.05.013 |
0.206 |
|
| 2018 |
Mihaylova VT, Kong Y, Fedorova O, Sharma L, Dela Cruz CS, Pyle AM, Iwasaki A, Foxman EF. Regional Differences in Airway Epithelial Cells Reveal Tradeoff between Defense against Oxidative Stress and Defense against Rhinovirus. Cell Reports. 24: 3000-3007.e3. PMID 30208323 DOI: 10.1016/J.Celrep.2018.08.033 |
0.206 |
|
| 1996 |
Pyle AM. Inside an intron invasion Nature. 381: 280-281. PMID 8692263 DOI: 10.1038/381280A0 |
0.205 |
|
| 2015 |
Rawling DC, Fitzgerald ME, Pyle AM. Establishing the role of ATP for the function of the RIG-I innate immune sensor. Elife. 4. PMID 26371557 DOI: 10.7554/Elife.09391 |
0.201 |
|
| 1994 |
Pyle AM. Replacement of the conserved g·u with a g·c pair at the cleavage site of the tetrahymena ribozyme decreases binding, reactivity, and fidelity Biochemistry. 33: 13856-13863. |
0.199 |
|
| 2015 |
Rawling DC, Fitzgerald ME, Pyle AM. Author response: Establishing the role of ATP for the function of the RIG-I innate immune sensor Elife. DOI: 10.7554/Elife.09391.017 |
0.198 |
|
| 2022 |
Gandhi S, Klein J, Robertson AJ, Peña-Hernández MA, Lin MJ, Roychoudhury P, Lu P, Fournier J, Ferguson D, Mohamed Bakhash SAK, Catherine Muenker M, Srivathsan A, Wunder EA, Kerantzas N, Wang W, ... ... Pyle A, et al. De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Nature Communications. 13: 1547. PMID 35301314 DOI: 10.1038/s41467-022-29104-y |
0.181 |
|
| 2021 |
Gandhi S, Klein J, Robertson A, Peña-Hernández MA, Lin MJ, Roychoudhury P, Lu P, Fournier J, Ferguson D, Mohamed Bakhash SA, Catherine Muenker M, Srivathsan A, Wunder EA, Kerantzas N, Wang W, ... ... Pyle A, et al. emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: A case report. Medrxiv : the Preprint Server For Health Sciences. PMID 34909781 DOI: 10.1101/2021.11.08.21266069 |
0.177 |
|
| 2021 |
Mao T, Israelow B, Lucas C, Vogels CBF, Fedorova O, Breban MI, Menasche BL, Dong H, Linehan M, Wilen CB, Landry ML, Grubaugh ND, Pyle AM, Iwasaki A. A stem-loop RNA RIG-I agonist confers prophylactic and therapeutic protection against acute and chronic SARS-CoV-2 infection in mice. Biorxiv : the Preprint Server For Biology. PMID 34159330 DOI: 10.1101/2021.06.16.448754 |
0.147 |
|
| 2023 |
Zhang C, Pyle AM. PDC: a highly compact file format to store protein 3D coordinates. Database : the Journal of Biological Databases and Curation. 2023. PMID 37010520 DOI: 10.1093/database/baad018 |
0.145 |
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| 2021 |
Ravindra NG, Alfajaro MM, Gasque V, Huston NC, Wan H, Szigeti-Buck K, Yasumoto Y, Greaney AM, Habet V, Chow RD, Chen JS, Wei J, Filler RB, Wang B, Wang G, ... ... Pyle AM, et al. Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes. Plos Biology. 19: e3001143. PMID 33730024 DOI: 10.1371/journal.pbio.3001143 |
0.139 |
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| 2022 |
Mao T, Israelow B, Lucas C, Vogels CBF, Gomez-Calvo ML, Fedorova O, Breban MI, Menasche BL, Dong H, Linehan M, Wilen CB, Landry ML, Grubaugh ND, Pyle AM, et al. A stem-loop RNA RIG-I agonist protects against acute and chronic SARS-CoV-2 infection in mice. The Journal of Experimental Medicine. 219. PMID 34757384 DOI: 10.1084/jem.20211818 |
0.136 |
|
| 2024 |
Wang W, Liu F, Ugalde MV, Pyle AM. A compact regulatory RNA element in mouse Hsp70 mRNA. Nar Molecular Medicine. 1: ugae002. PMID 38318492 DOI: 10.1093/narmme/ugae002 |
0.12 |
|
| 2020 |
Ravindra NG, Alfajaro MM, Gasque V, Wei J, Filler RB, Huston NC, Wan H, Szigeti-Buck K, Wang B, Montgomery RR, Eisenbarth SC, Williams A, Pyle AM, Iwasaki A, Horvath TL, et al. Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells. Biorxiv : the Preprint Server For Biology. PMID 32511382 DOI: 10.1101/2020.05.06.081695 |
0.098 |
|
| 2003 |
Sigel RK, Pyle AM. Lanthanide ions as probes for metal ions in the structure and catalytic mechanism of ribozymes. Metal Ions in Biological Systems. 40: 477-512. PMID 12723158 |
0.09 |
|
| 1986 |
Pyle AM, Jens KJ. H/D exchange in methane and other saturated hydrocarbons catalyzed by a supported zirconium complex Journal of Molecular Catalysis. 38: 337-339. DOI: 10.1016/0304-5102(86)85042-8 |
0.08 |
|
| 2010 |
PYLE AM, BARTON JK. ChemInform Abstract: Probing Nucleic Acids with Transition Metal Complexes Cheminform. 22: no-no. DOI: 10.1002/chin.199143288 |
0.074 |
|
| 1996 |
Pyle AM. Role of metal ions in ribozymes Metal Ions in Biological Systems. 32: 479-520. PMID 8640529 |
0.052 |
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| Hide low-probability matches. |
