Stefan Badelt
Overview
Explore the profile of Stefan Badelt including associated specialties, affiliations and a list of published articles.
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Articles
12
Citations
85
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Recent Articles
1.
Badelt S, Lorenz R
Methods Mol Biol
. 2024 May;
2726:315-346.
PMID: 38780737
Although RNA molecules are synthesized via transcription, little is known about the general impact of cotranscriptional folding in vivo. We present different computational approaches for the simulation of changing structure...
2.
Tanasie A, Kerpedjiev P, Hammer S, Badelt S
Bioinformatics
. 2023 Sep;
39(9).
PMID: 37682108
Motivation: Understanding RNA folding at the level of secondary structures can give important insights concerning the function of a molecule. We are interested to learn how secondary structures change dynamically...
3.
Badelt S, Lorenz R, Hofacker I
Bioinformatics
. 2023 Jan;
39(1).
PMID: 36655786
Motivation: Folding during transcription can have an important influence on the structure and function of RNA molecules, as regions closer to the 5' end can fold into metastable structures before...
4.
Flamm C, Wielach J, Wolfinger M, Badelt S, Lorenz R, Hofacker I
Front Bioinform
. 2022 Oct;
2:835422.
PMID: 36304289
Machine learning (ML) and in particular deep learning techniques have gained popularity for predicting structures from biopolymer sequences. An interesting case is the prediction of RNA secondary structures, where well...
5.
Badelt S, Grun C, Sarma K, Wolfe B, Shin S, Winfree E
J R Soc Interface
. 2020 Jun;
17(167):20190866.
PMID: 32486951
Information technologies enable programmers and engineers to design and synthesize systems of startling complexity that nonetheless behave as intended. This mastery of complexity is made possible by a hierarchy of...
6.
Berleant J, Berlind C, Badelt S, Dannenberg F, Schaeffer J, Winfree E
J R Soc Interface
. 2019 Apr;
15(149):20180107.
PMID: 30958232
As an engineering material, DNA is well suited for the construction of biochemical circuits and systems, because it is simple enough that its interactions can be rationally designed using Watson-Crick...
7.
Tajaddod M, Tanzer A, Licht K, Wolfinger M, Badelt S, Huber F, et al.
Genome Biol
. 2016 Oct;
17(1):220.
PMID: 27782844
Background: Short interspersed elements (SINEs) represent the most abundant group of non-long-terminal repeat transposable elements in mammalian genomes. In primates, Alu elements are the most prominent and homogenous representatives of...
8.
Badelt S, Flamm C, Hofacker I
Artif Life
. 2016 Mar;
22(2):172-84.
PMID: 26934089
RNA molecules engineered to fold into predefined conformations have enabled the design of a multitude of functional RNA devices in the field of synthetic biology and nanotechnology. More complex designs...
9.
Petkovic S, Badelt S, Block S, Flamm C, Delcea M, Hofacker I, et al.
RNA
. 2015 May;
21(7):1249-60.
PMID: 25999318
Reversible chemistry allowing for assembly and disassembly of molecular entities is important for biological self-organization. Thus, ribozymes that support both cleavage and formation of phosphodiester bonds may have contributed to...
10.
Badelt S, Hammer S, Flamm C, Hofacker I
Methods Enzymol
. 2015 Mar;
553:193-213.
PMID: 25726466
Riboswitches are structured RNA regulatory elements located in the 5'-UTRs of mRNAs. Ligand-binding induces a structural rearrangement in these RNA elements, effecting events in downstream located coding sequences. Since they...