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Craig Zirbel - Publications

Affiliations: 
Bowling Green State University, Bowling Green, OH, United States 
Area:
Mathematics
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29 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Lawson CL, Berman HM, Chen L, Vallat B, Zirbel CL. The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids. Nucleic Acids Research. PMID 37953312 DOI: 10.1093/nar/gkad957  0.387
2023 Westhof E, Watson ZL, Zirbel CL, Cate JHD. Anionic G•U pairs in bacterial ribosomal rRNAs. Rna (New York, N.Y.). PMID 37068913 DOI: 10.1261/rna.079583.123  0.446
2022 Zirbel CL, Auffinger P. Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey. Molecules (Basel, Switzerland). 27. PMID 35889236 DOI: 10.3390/molecules27144365  0.361
2022 Wu J, Leontis NB, Zirbel CL, Bisaro DM, Ding B. Correction: A three-dimensional RNA motif mediates directional trafficking of Potato spindle tuber viroid from epidermal to palisade mesophyll cells in Nicotiana benthamiana. Plos Pathogens. 18: e1010421. PMID 35316309 DOI: 10.1371/journal.ppat.1010421  0.506
2020 Wu J, Zhou C, Li J, Li C, Tao X, Leontis NB, Zirbel CL, Bisaro DM, Ding B. Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA. Nucleic Acids Research. PMID 33313761 DOI: 10.1093/nar/gkaa1211  0.453
2020 Wu J, Zhou C, Li J, Li C, Tao X, Leontis NB, Zirbel CL, Bisaro DM, Ding B. Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA. Nucleic Acids Research. PMID 32083649 DOI: 10.1093/Nar/Gkaa100  0.519
2019 Wu J, Leontis NB, Zirbel CL, Bisaro DM, Ding B. A three-dimensional RNA motif mediates directional trafficking of Potato spindle tuber viroid from epidermal to palisade mesophyll cells in Nicotiana benthamiana. Plos Pathogens. 15: e1008147. PMID 31644572 DOI: 10.1371/Journal.Ppat.1008147  0.712
2018 Hosseini M, Roy P, Sissler M, Zirbel CL, Westhof E, Leontis N. How to fold and protect mitochondrial ribosomal RNA with fewer guanines. Nucleic Acids Research. PMID 30215760 DOI: 10.1093/Nar/Gky762  0.662
2018 Takeda R, Zirbel CL, Leontis NB, Wang Y, Ding B. Allelic RNA Motifs in Regulating Systemic Trafficking of Potato Spindle Tuber Viroid. Viruses. 10. PMID 29601476 DOI: 10.3390/V10040160  0.68
2018 Wang Y, Zirbel CL, Leontis NB, Ding B. RNA 3-dimensional structural motifs as a critical constraint of viroid RNA evolution. Plos Pathogens. 14: e1006801. PMID 29470541 DOI: 10.1371/Journal.Ppat.1006801  0.707
2016 Roll J, Zirbel CL, Sweeney B, Petrov AI, Leontis N. JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs. Nucleic Acids Research. PMID 27235417 DOI: 10.1093/Nar/Gkw453  0.782
2016 Parlea L, Sweeney BA, Zirbel CL, Leontis NB. The RNA 3D Motif Atlas: Computational Methods for Extraction, Organization and Evaluation of RNA Motifs. Methods (San Diego, Calif.). PMID 27125735 DOI: 10.1016/J.Ymeth.2016.04.025  0.779
2015 Rahrig RR, Zirbel CL. DETECTING CONFORMATIONAL DIFFERENCES BETWEEN RNA 3D STRUCTURES. Jp Journal of Biostatistics. 12: 99-115. PMID 27330250 DOI: 10.17654/JPJBDec2015_099_115  0.716
2015 Theis C, Zirbel CL, Zu Siederdissen CH, Anthon C, Hofacker IL, Nielsen H, Gorodkin J. RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure. Plos One. 10: e0139900. PMID 26509713 DOI: 10.1371/journal.pone.0139900  0.683
2015 Zirbel CL, Roll J, Sweeney BA, Petrov AI, Pirrung M, Leontis NB. Identifying novel sequence variants of RNA 3D motifs. Nucleic Acids Research. 43: 7504-20. PMID 26130723 DOI: 10.1093/Nar/Gkv651  0.767
2015 Cannone JJ, Sweeney BA, Petrov AI, Gutell RR, Zirbel CL, Leontis N. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server. Nucleic Acids Research. 43: W15-23. PMID 26048960 DOI: 10.1093/Nar/Gkv543  0.775
2014 Coimbatore Narayanan B, Westbrook J, Ghosh S, Petrov AI, Sweeney B, Zirbel CL, Leontis NB, Berman HM. The Nucleic Acid Database: new features and capabilities. Nucleic Acids Research. 42: D114-22. PMID 24185695 DOI: 10.1093/Nar/Gkt980  0.431
2013 Havrila M, Réblová K, Zirbel CL, Leontis NB, Šponer J. Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop. The Journal of Physical Chemistry. B. 117: 14302-19. PMID 24144333 DOI: 10.1021/Jp408530W  0.69
2013 Petrov AI, Zirbel CL, Leontis NB. Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas. Rna (New York, N.Y.). 19: 1327-40. PMID 23970545 DOI: 10.1261/Rna.039438.113  0.855
2013 Rahrig RR, Petrov AI, Leontis NB, Zirbel CL. R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures. Nucleic Acids Research. 41: W15-21. PMID 23716643 DOI: 10.1093/Nar/Gkt417  0.815
2012 Abu Almakarem AS, Petrov AI, Stombaugh J, Zirbel CL, Leontis NB. Comprehensive survey and geometric classification of base triples in RNA structures. Nucleic Acids Research. 40: 1407-23. PMID 22053086 DOI: 10.1093/Nar/Gkr810  0.74
2011 Zgarbová M, Jurečka P, Banáš P, Otyepka M, Sponer JE, Leontis NB, Zirbel CL, Sponer J. Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations. The Journal of Physical Chemistry. A. 115: 11277-92. PMID 21910417 DOI: 10.1021/Jp204820B  0.513
2011 Birmingham A, Clemente JC, Desai N, Gilbert J, Gonzalez A, Kyrpides N, Meyer F, Nawrocki E, Sterk P, Stombaugh J, Weinberg Z, Wendel D, Leontis NB, Zirbel C, Knight R, et al. Meeting report of the RNA Ontology Consortium January 8-9, 2011. Standards in Genomic Sciences. 4: 252-6. PMID 21677862 DOI: 10.4056/Sigs.1724282  0.627
2011 Rocca-Serra P, Bellaousov S, Birmingham A, Chen C, Cordero P, Das R, Davis-Neulander L, Duncan CD, Halvorsen M, Knight R, Leontis NB, Mathews DH, Ritz J, Stombaugh J, Weeks KM, ... Zirbel CL, et al. Sharing and archiving nucleic acid structure mapping data. Rna (New York, N.Y.). 17: 1204-12. PMID 21610212 DOI: 10.1261/Rna.2753211  0.322
2011 Petrov AI, Zirbel CL, Leontis NB. WebFR3D--a server for finding, aligning and analyzing recurrent RNA 3D motifs. Nucleic Acids Research. 39: W50-5. PMID 21515634 DOI: 10.1093/Nar/Gkr249  0.836
2011 Hoehndorf R, Batchelor C, Bittner T, Dumontier M, Eilbeck K, Knight R, Mungall CJ, Richardson JS, Stombaugh J, Westhof E, Zirbel CL, Leontis NB. The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data Applied Ontology. 6: 53-89. DOI: 10.1038/Npre.2009.3561.1  0.732
2010 Rahrig RR, Leontis NB, Zirbel CL. R3D Align: global pairwise alignment of RNA 3D structures using local superpositions. Bioinformatics (Oxford, England). 26: 2689-97. PMID 20929913 DOI: 10.1093/Bioinformatics/Btq506  0.795
2009 Zirbel CL, Sponer JE, Sponer J, Stombaugh J, Leontis NB. Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Research. 37: 4898-918. PMID 19528080 DOI: 10.1093/Nar/Gkp468  0.726
2009 Stombaugh J, Zirbel CL, Westhof E, Leontis NB. Frequency and isostericity of RNA base pairs. Nucleic Acids Research. 37: 2294-312. PMID 19240142 DOI: 10.1093/Nar/Gkp011  0.746
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