Exponentially Few RNA Structures are Designable. - Hua-Ting Yao; Cédric Chauve; Mireille Régnier; Yann Ponty (BCB, 2019)

Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification. - Roman Sarrazin-Gendron; Hua-Ting Yao; Vladimir Reinharz; Carlos G. Oliver; Yann Ponty; Jérôme Waldispühl (RECOMB, 2020)

Local Decomposition in RNA Structural Design. (Décomposition Locale dans le Design Structural de l'ARN). - Hua-Ting Yao (2021)

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)

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)

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)

Infrared: a declarative tree decomposition-powered framework for bioinformatics. - Hua-Ting Yao; Bertrand Marchand; Sarah J. Berkemer; Yann Ponty; Sebastian Will (Algorithms Mol. 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)

Old Dog, New Tricks: Exact Seeding Strategy Improves RNA Design Performances. - Théo Boury; Leonhard Sidl; Ivo L. Hofacker; Yann Ponty; Hua-Ting Yao (RECOMB, 2025)