Alignment of RNA base pairing probability matrices. - Ivo L. Hofacker; Stephan H. Bernhart; Peter F. Stadler (Bioinform., 2004)

Partition function and base pairing probabilities of RNA heterodimers. - Stephan H. Bernhart; Hakim Tafer; Ulrike Mückstein; Christoph Flamm; Peter F. Stadler; Ivo L. Hofacker (Algorithms Mol. Biol., 2006)

Local RNA base pairing probabilities in large sequences. - Stephan H. Bernhart; Ivo L. Hofacker; Peter F. Stadler (Bioinform., 2006)

Thermodynamics of RNA-RNA binding. - Ulrike Mückstein; Hakim Tafer; Jörg Hackermüller; Stephan H. Bernhart; Peter F. Stadler; Ivo L. Hofacker (Bioinform., 2006)

Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics. - Ulrike Mückstein; Hakim Tafer; Stephan H. Bernhart; Maribel Hernandez-Rosales; Jörg Vogel 002; Peter F. Stadler; Ivo L. Hofacker (BIRD, 2008)

RNAalifold: improved consensus structure prediction for RNA alignments. - Stephan H. Bernhart; Ivo L. Hofacker; Sebastian Will; Andreas R. Gruber; Peter F. Stadler (BMC Bioinform., 2008)

Strategies for measuring evolutionary conservation of RNA secondary structures. - Andreas R. Gruber; Stephan H. Bernhart; Ivo L. Hofacker; Stefan Washietl (BMC Bioinform., 2008)

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

RNALfoldz: Efficient Prediction of Thermodynamically Stable, Local Secondary Structures. - Andreas R. Gruber; Stephan H. Bernhart; You Zhou; Ivo L. Hofacker (GCB, 2010)

RNA Accessibility in cubic time. - Stephan H. Bernhart; Ulrike Mückstein; Ivo L. Hofacker (Algorithms Mol. Biol., 2011)

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)

A folding algorithm for extended RNA secondary structures. - Christian Höner zu Siederdissen; Stephan H. Bernhart; Peter F. Stadler; Ivo L. Hofacker (Bioinform., 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)

The Trouble with Long-Range Base Pairs in RNA Folding. - Fabian Amman; Stephan H. Bernhart; Gero Doose; Ivo L. Hofacker; Jing Qin 006; Peter F. Stadler; Sebastian Will (BSB, 2013)

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)

DIEGO: detection of differential alternative splicing using Aitchison's geometry. - Gero Doose; Stephan H. Bernhart; Rabea Wagener; Steve Hoffmann (Bioinform., 2018)

A probabilistic version of Sankoff's maximum parsimony algorithm. - Gábor Balogh; Stephan H. Bernhart; Peter F. Stadler; Jana Schor (J. Bioinform. Comput. Biol., 2020)

TREMSUCS-TCGA - an integrated workflow for the identification of biomarkers for treatment success. - Gábor Balogh; Natasha Jorge; Célia Dupain; Maud Kamal; Nicolas Servant; Christophe Le Tourneau; Peter F. Stadler; Stephan H. Bernhart (J. Integr. Bioinform., 2024)