FR3D: finding local and composite recurrent structural motifs in RNA 3D structures M Sarver, CL Zirbel, J Stombaugh, A Mokdad, NB Leontis Journal of mathematical biology 56, 215-252, 2008 | 335 | 2008 |
Frequency and isostericity of RNA base pairs J Stombaugh, CL Zirbel, E Westhof, NB Leontis Nucleic acids research 37 (7), 2294-2312, 2009 | 258 | 2009 |
The Nucleic Acid Database: new features and capabilities B Coimbatore Narayanan, J Westbrook, S Ghosh, AI Petrov, B Sweeney, ... Nucleic acids research 42 (D1), D114-D122, 2014 | 240 | 2014 |
Classification and energetics of the base-phosphate interactions in RNA CL Zirbel, JE Šponer, J Šponer, J Stombaugh, NB Leontis Nucleic acids research 37 (15), 4898-4918, 2009 | 189 | 2009 |
Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas AI Petrov, CL Zirbel, NB Leontis Rna 19 (10), 1327-1340, 2013 | 179 | 2013 |
Nonredundant 3D structure datasets for RNA knowledge extraction and benchmarking NB Leontis, CL Zirbel RNA 3D structure analysis and prediction, 281-298, 2012 | 136 | 2012 |
Comprehensive survey and geometric classification of base triples in RNA structures AS Abu Almakarem, AI Petrov, J Stombaugh, CL Zirbel, NB Leontis Nucleic Acids Research 40 (4), 1407-1423, 2012 | 111 | 2012 |
WebFR3D—a server for finding, aligning and analyzing recurrent RNA 3D motifs AI Petrov, CL Zirbel, NB Leontis Nucleic acids research 39 (suppl_2), W50-W55, 2011 | 82 | 2011 |
R3D Align: global pairwise alignment of RNA 3D structures using local superpositions RR Rahrig, NB Leontis, CL Zirbel Bioinformatics 26 (21), 2689-2697, 2010 | 72 | 2010 |
Identifying novel sequence variants of RNA 3D motifs CL Zirbel, J Roll, BA Sweeney, AI Petrov, M Pirrung, NB Leontis Nucleic acids research 43 (15), 7504-7520, 2015 | 51 | 2015 |
A mean-field statistical theory for the nonlinear Schrödinger equation R Jordan, B Turkington, CL Zirbel Physica D: Nonlinear Phenomena 137 (3-4), 353-378, 2000 | 51 | 2000 |
The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data R Hoehndorf, C Batchelor, T Bittner, M Dumontier, K Eilbeck, R Knight, ... Applied Ontology 6 (1), 53-89, 2011 | 49 | 2011 |
The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs LG Parlea, BA Sweeney, M Hosseini-Asanjan, CL Zirbel, NB Leontis Methods 103, 99-119, 2016 | 44 | 2016 |
RNA 3D structural motifs: definition, identification, annotation, and database searching L Nasalean, J Stombaugh, CL Zirbel, NB Leontis Non-protein coding RNAs, 1-26, 2009 | 38 | 2009 |
Sharing and archiving nucleic acid structure mapping data P Rocca-Serra, S Bellaousov, A Birmingham, C Chen, P Cordero, R Das, ... Rna 17 (7), 1204-1212, 2011 | 36 | 2011 |
RNA 3-dimensional structural motifs as a critical constraint of viroid RNA evolution Y Wang, CL Zirbel, NB Leontis, B Ding PLoS Pathogens 14 (2), e1006801, 2018 | 34 | 2018 |
Isosteric and nonisosteric base pairs in RNA motifs: Molecular dynamics and bioinformatics study of the sarcin–ricin internal loop M Havrila, K Réblová, CL Zirbel, NB Leontis, J Šponer The journal of physical chemistry B 117 (46), 14302-14319, 2013 | 34 | 2013 |
Lagrangian observations of homogeneous random environments CL Zirbel Advances in Applied Probability 33 (4), 810-835, 2001 | 34 | 2001 |
Dispersion of particle systems in Brownian flows CL Zirbel, E Cinlar Advances in applied probability 28 (1), 53-74, 1996 | 33 | 1996 |
A three-dimensional RNA motif mediates directional trafficking of Potato spindle tuber viroid from epidermal to palisade mesophyll cells in Nicotiana benthamiana J Wu, NB Leontis, CL Zirbel, DM Bisaro, B Ding PLoS Pathogens 15 (10), e1008147, 2019 | 32 | 2019 |