| A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures S Badelt, C Grun, KV Sarma, B Wolfe, SW Shin, E Winfree Journal of the Royal Society Interface 17 (167), 20190866, 2020 | 55 | 2020 |
| A general-purpose CRN-to-DSD compiler with formal verification, optimization, and simulation capabilities S Badelt, SW Shin, RF Johnson, Q Dong, C Thachuk, E Winfree International conference on DNA-based computers, 232-248, 2017 | 52 | 2017 |
| Animal snoRNAs and scaRNAs with exceptional structures M Marz, AR Gruber, C Höner zu Siederdissen, F Amman, S Badelt, ... RNA biology 8 (6), 938-946, 2011 | 48 | 2011 |
| Caveats to deep learning approaches to RNA secondary structure prediction C Flamm, J Wielach, MT Wolfinger, S Badelt, R Lorenz, IL Hofacker Frontiers in Bioinformatics 2, 835422, 2022 | 36 | 2022 |
| Thermodynamic and kinetic folding of riboswitches S Badelt, S Hammer, C Flamm, IL Hofacker Methods in Enzymology 553, 193-213, 2015 | 23 | 2015 |
| Automated sequence-level analysis of kinetics and thermodynamics for domain-level DNA strand-displacement systems J Berleant, C Berlind, S Badelt, F Dannenberg, J Schaeffer, E Winfree Journal of the Royal Society Interface 15 (149), 20180107, 2018 | 22 | 2018 |
| Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by AFM S Petkovic, S Badelt, S Block, C Flamm, M Delcea, I Hofacker, S Müller RNA 21 (7), 1249-1260, 2015 | 21 | 2015 |
| Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity M Tajaddod, A Tanzer, K Licht, MT Wolfinger, S Badelt, F Huber, O Pusch, ... Genome Biology 17 (1), 220, 2016 | 20 | 2016 |
| DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model S Badelt, R Lorenz, IL Hofacker Bioinformatics 39 (1), btad034, 2023 | 12 | 2023 |
| Computational Design of a Circular RNA with Prionlike Behavior S Badelt, C Flamm, IL Hofacker Artificial Life 22, 1-13, 2016 | 12 | 2016 |
| Computational design of a circular RNA with prion-like behaviour S Badelt, C Flamm, IL Hofacker ALIFE 14: The Fourteenth Conference on the Synthesis and Simulation of …, 2014 | 12 | 2014 |
| Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7 G Ebert, A Steininger, R Weißmann, V Boldt, A Lind-Thomsen, J Grune, ... BMC genomics 15 (1), 537, 2014 | 8 | 2014 |
| DrForna: visualization of cotranscriptional folding AR Tănasie, P Kerpedjiev, S Hammer, S Badelt Bioinformatics 39 (9), btad555, 2023 | 3 | 2023 |
| A guide to computational cotranscriptional folding featuring the SRP RNA S Badelt, R Lorenz RNA Folding: Methods and Protocols, 315-346, 2012 | 2 | 2012 |
| DrTransformer: Heuristic cotranscriptional RNA folding using the nearest neighbor energy model.-Supplementary Material S Badelt, R Lorenz, IL Hofacker | | 2023 |
| Automated Sequence-Level Analysis of Kinetics and Thermodynamics for Domain-Level DNA Strand-Displacement Systems: Supplementary Information (Technical Appendix) J Berleant, C Berlind, S Badelt, F Dannenberg, J Schaeffer, E Winfree | | |
| Supplemental material for: DrForna: visualization of cotranscriptional folding AR Tanasie, P Kerpedjiev, S Hammer, S Badelt | | |
| Supplemental Online Material S Badelt, C Grun, KV Sarma, B Wolfe, SW Shin, E Winfree | | |
| Equivalence of chemical reaction networks in a CRN-to-DNA compiler framework. S Badelt, E Winfree | | |
Ivo HofackerUniversity of ViennaVerified email at tbi.univie.ac.at
