Stefan Badelt
Stefan Badelt
Institute for Theoretical Chemistry, University of Vienna
Verified email at - Homepage
Cited by
Cited by
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
DNA Computing and Molecular Programming: 23rd International Conference, DNA …, 2017
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
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
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), 1-16, 2016
Thermodynamic and kinetic folding of riboswitches
S Badelt, S Hammer, C Flamm, IL Hofacker
Methods in Enzymology 553, 193-213, 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
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
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
Computational Design of a Circular RNA with Prionlike Behavior
S Badelt, C Flamm, IL Hofacker
Artificial Life 22, 1-13, 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
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), 1-17, 2014
DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model
S Badelt, R Lorenz, IL Hofacker
Bioinformatics 39 (1), btad034, 2023
A guide to computational cotranscriptional folding featuring the SRP RNA
S Badelt, R Lorenz
bioRxiv, 2023.06. 01.543211, 2023
DrForna: visualization of cotranscriptional folding
AR Tănasie, P Kerpedjiev, S Hammer, S Badelt
Bioinformatics, btad555, 2023
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
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