Ronny Lorenz
Overview
Explore the profile of Ronny Lorenz including associated specialties, affiliations and a list of published articles.
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Articles
28
Citations
4088
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Recent Articles
1.
von Lohneysen S, Spicher T, Varenyk Y, Yao H, Lorenz R, Hofacker I, et al.
J Comput Biol
. 2024 Jun;
31(6):549-563.
PMID: 38935442
Extrinsic, experimental information can be incorporated into thermodynamics-based RNA folding algorithms in the form of pseudo-energies. Evolutionary conservation of RNA secondary structure elements is detectable in alignments of phylogenetically related...
2.
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...
3.
Varenyk Y, Lorenz R
Methods Mol Biol
. 2024 May;
2726:169-207.
PMID: 38780732
Nucleotide modifications are occurrent in all types of RNA and play an important role in RNA structure formation and stability. Modified bases not only possess the ability to shift the...
4.
Lorenz R
Methods Mol Biol
. 2024 May;
2726:45-83.
PMID: 38780727
Several different ways to predict RNA secondary structures have been suggested in the literature. Statistical methods, such as those that utilize stochastic context-free grammars (SCFGs), or approaches based on machine...
5.
Varenyk Y, Spicher T, Hofacker I, Lorenz R
Bioinformatics
. 2023 Nov;
39(11).
PMID: 37971965
Motivation: In living organisms, many RNA molecules are modified post-transcriptionally. This turns the widely known four-letter RNA alphabet ACGU into a much larger one with currently more than 300 known...
6.
Waldl M, Spicher T, Lorenz R, Beckmann I, Hofacker I, von Lohneysen S, et al.
J Bioinform Comput Biol
. 2023 Jul;
21(4):2350016.
PMID: 37522173
Most of the functional RNA elements located within large transcripts are local. Local folding therefore serves a practically useful approximation to global structure prediction. Due to the sensitivity of RNA...
7.
Yao H, Lorenz R, Hofacker I, Stadler P
Algorithms Mol Biol
. 2023 Jul;
18(1):8.
PMID: 37516881
Background: RNA features a highly negatively charged phosphate backbone that attracts a cloud of counter-ions that reduce the electrostatic repulsion in a concentration dependent manner. Ion concentrations thus have a...
8.
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...
9.
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...
10.
Entzian G, Hofacker I, Ponty Y, Lorenz R, Tanzer A
Bioinformatics
. 2021 Feb;
37(15):2126-2133.
PMID: 33538792
Motivation: Predicting the folding dynamics of RNAs is a computationally difficult problem, first and foremost due to the combinatorial explosion of alternative structures in the folding space. Abstractions are therefore...