| In vitro assembly of cubic RNA-based scaffolds designed in silico KA Afonin, E Bindewald, AJ Yaghoubian, N Voss, E Jacovetty, BA Shapiro, ... Nature nanotechnology 5 (9), 676-682, 2010 | 413 | 2010 |
| Bridging the gap in RNA structure prediction BA Shapiro, YG Yingling, W Kasprzak, E Bindewald Current opinion in structural biology 17 (2), 157-165, 2007 | 250 | 2007 |
| Design and self-assembly of siRNA-functionalized RNA nanoparticles for use in automated nanomedicine KA Afonin, WW Grabow, FM Walker, E Bindewald, MA Dobrovolskaia, ... Therapeutic RNA Nanotechnology, 249-284, 2021 | 222 | 2021 |
| RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign E Bindewald, R Hayes, YG Yingling, W Kasprzak, BA Shapiro Nucleic acids research 36 (suppl_1), D392-D397, 2008 | 196 | 2008 |
| The favorable IFNL3 genotype escapes mRNA decay mediated by AU-rich elements and hepatitis C virus–induced microRNAs AP McFarland, SM Horner, A Jarret, RC Joslyn, E Bindewald, BA Shapiro, ... Nature immunology 15 (1), 72-79, 2014 | 158 | 2014 |
| RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers E Bindewald, BA Shapiro Rna 12 (3), 342-352, 2006 | 129 | 2006 |
| Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler E Bindewald, C Grunewald, B Boyle, M O’Connor, BA Shapiro Journal of Molecular Graphics and Modelling 27 (3), 299-308, 2008 | 108 | 2008 |
| In Silico Design and Enzymatic Synthesis of Functional RNA Nanoparticles KA Afonin, WK Kasprzak, E Bindewald, M Kireeva, M Viard, M Kashlev, ... Accounts of chemical research 47 (6), 1731-1741, 2014 | 106 | 2014 |
| Functionally-interdependent shape-switching nanoparticles with controllable properties JR Halman, E Satterwhite, B Roark, M Chandler, M Viard, A Ivanina, ... Nucleic acids research 45 (4), 2210-2220, 2017 | 104 | 2017 |
| Multistrand RNA secondary structure prediction and nanostructure design including pseudoknots E Bindewald, K Afonin, L Jaeger, BA Shapiro Therapeutic RNA Nanotechnology, 95-120, 2021 | 98 | 2021 |
| A divide and conquer approach to fast loop modeling SCE Tosatto, E Bindewald, J Hesser, R Männer Protein engineering 15 (4), 279-286, 2002 | 96 | 2002 |
| Computational and experimental characterization of RNA cubic nanoscaffolds KA Afonin, W Kasprzak, E Bindewald, PS Puppala, AR Diehl, KT Hall, ... Therapeutic RNA Nanotechnology, 121-149, 2021 | 76 | 2021 |
| Co-transcriptional production of RNA–DNA hybrids for simultaneous release of multiple split functionalities KA Afonin, R Desai, M Viard, ML Kireeva, E Bindewald, CL Case, ... Nucleic acids research 42 (3), 2085-2097, 2014 | 72 | 2014 |
| CyloFold: secondary structure prediction including pseudoknots E Bindewald, T Kluth, BA Shapiro Nucleic acids research 38 (suppl_2), W368-W372, 2010 | 71 | 2010 |
| Multistrand structure prediction of nucleic acid assemblies and design of RNA switches E Bindewald, KA Afonin, M Viard, P Zakrevsky, T Kim, BA Shapiro Nano letters 16 (3), 1726-1735, 2016 | 70 | 2016 |
| Cellular delivery of RNA nanoparticles L Parlea, A Puri, W Kasprzak, E Bindewald, P Zakrevsky, E Satterwhite, ... Therapeutic RNA Nanotechnology, 477-538, 2021 | 66 | 2021 |
| Genomic analyses reveal broad impact of miR-137 on genes associated with malignant transformation and neuronal differentiation in glioblastoma cells S Tamim, DT Vo, PJ Uren, M Qiao, E Bindewald, WK Kasprzak, ... PloS one 9 (1), e85591, 2014 | 57 | 2014 |
| The SSEA server for protein secondary structure alignment P Fontana, E Bindewald, S Toppo, R Velasco, G Valle, SCE Tosatto Bioinformatics 21 (3), 393-395, 2005 | 57 | 2005 |
| Correlating SHAPE signatures with three-dimensional RNA structures E Bindewald, M Wendeler, M Legiewicz, MK Bona, Y Wang, MJ Pritt, ... Rna 17 (9), 1688-1696, 2011 | 51 | 2011 |
| Protocols for the In Silico Design of RNA Nanostructures BA Shapiro, E Bindewald, W Kasprzak, Y Yingling Nanostructure Design: Methods and Protocols, 93-115, 2008 | 50 | 2008 |
