The Vienna RNA Websuite. - Andreas R. Gruber; Ronny Lorenz; Stephan H. Bernhart; Richard Neuböck; Ivo L. Hofacker (Nucleic Acids Res., 2008)

2D Projections of RNA Folding Landscapes. - Ronny Lorenz; Christoph Flamm; Ivo L. Hofacker (GCB, 2009)

ViennaRNA Package 2.0. - Ronny Lorenz; Stephan H. Bernhart; Christian Höner zu Siederdissen; Hakim Tafer; Christoph Flamm; Peter F. Stadler; Ivo L. Hofacker (Algorithms Mol. Biol., 2011)

RNA Folding Algorithms with G-Quadruplexes. - Ronny Lorenz; Stephan H. Bernhart; Fabian Externbrink; Jing Qin 006; Christian Höner zu Siederdissen; Fabian Amman; Ivo L. Hofacker; Peter F. Stadler (BSB, 2012)

Folding RNA/DNA hybrid duplexes. - Ronny Lorenz; Ivo L. Hofacker; Stephan H. Bernhart (Bioinform., 2012)

2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction. - Ronny Lorenz; Stephan H. Bernhart; Jing Qin 006; Christian Höner zu Siederdissen; Andrea Tanzer; Fabian Amman; Ivo L. Hofacker; Peter F. Stadler (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

TSSAR: TSS annotation regime for dRNA-seq data. - Fabian Amman; Michael T. Wolfinger; Ronny Lorenz; Ivo L. Hofacker; Peter F. Stadler; Sven Findeiß (BMC Bioinform., 2014)

Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA. - Christopher A. Lavender; Ronny Lorenz; Ge Zhang; Rita Tamayo; Ivo L. Hofacker; Kevin M. Weeks (PLoS Comput. Biol., 2015)

RNA folding with hard and soft constraints. - Ronny Lorenz; Ivo L. Hofacker; Peter F. Stadler (Algorithms Mol. Biol., 2016)

SHAPE directed RNA folding. - Ronny Lorenz; Dominik Luntzer; Ivo L. Hofacker; Peter F. Stadler; Michael T. Wolfinger (Bioinform., 2016)

Improving SSE parallel code with grow and graft genetic programming. - William B. Langdon; Ronny Lorenz (GECCO (Companion), 2017)

Evolving Better RNAfold Structure Prediction. - William B. Langdon; Justyna Petke; Ronny Lorenz (EuroGP, 2018)

Evolving AVX512 Parallel C Code Using GP. - William B. Langdon; Ronny Lorenz (EuroGP, 2019)

Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding. - Ronny Lorenz; Christoph Flamm; Ivo L. Hofacker; Peter F. Stadler (BIOINFORMATICS, 2020)

Efficient Algorithms for Co-folding of Multiple RNAs. - Ronny Lorenz; Christoph Flamm; Ivo L. Hofacker; Peter F. Stadler (BIOSTEC (Selected Papers), 2020)

RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes. - Gregor Entzian; Ivo L. Hofacker; Yann Ponty; Ronny Lorenz; Andrea Tanzer (Bioinform., 2021)

Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction. - Christoph Flamm; Julia Wielach; Michael T. Wolfinger; Stefan Badelt; Ronny Lorenz; Ivo L. Hofacker (Frontiers Bioinform., 2022)

Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction. - Sarah von Löhneysen; Thomas Spicher; Yuliia Varenyk; Hua-Ting Yao; Ronny Lorenz; Ivo L. Hofacker; Peter F. Stadler (ISBRA, 2023)

DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model. - Stefan Badelt; Ronny Lorenz; Ivo L. Hofacker (Bioinform., 2023)

Local RNA folding revisited. - Maria Waldl; Thomas Spicher; Ronny Lorenz; Irene K. Beckmann; Ivo L. Hofacker; Sarah von Löhneysen; Peter F. Stadler (J. Bioinform. Comput. Biol., 2023)

Modified RNAs and predictions with the ViennaRNA Package. - Yuliia Varenyk; Thomas Spicher; Ivo L. Hofacker; Ronny Lorenz (Bioinform., 2023)

Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package. - Hua-Ting Yao; Ronny Lorenz; Ivo L. Hofacker; Peter F. Stadler (Algorithms Mol. Biol., 2023)

Squares in Cycles: Prediction of G-Quadruplexes in Circular RNA Secondary Stuctures. - Ronny Lorenz; Peter F. Stadler (BSB, 2024)

Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction. - Sarah von Löhneysen; Thomas Spicher; Yuliia Varenyk; Hua-Ting Yao; Ronny Lorenz; Ivo L. Hofacker; Peter F. Stadler (J. Comput. Biol., 2024)

Integrating High-Throughput RNA-RNA Interaction Data Into RNA Secondary Structure Prediction. - Denis Skibinski; Thomas Spicher; Leonhard Sidl; Paulína Holotová; Yingjie Pan; Maximilian Faissner; Cristian A. Velandia-Huerto; Ronny Lorenz; Maria Waldl; Hua-Ting Yao; Peter F. Stadler (ISBRA (2), 2025)