Publications

Publications by categories in reversed chronological order, generated by jekyll-scholar.
† Shared Firsts

2025

  1. Journal
    Computational complexity, algorithmic scope, and evolution
    Leonhard Sidl, Maximilian Faissner, Manuel Uhlir, Cristian A Velandia-Huerto, and 4 more authors
    Journal of Physics: Complexity, Mar 2025
  2. Conference
    Old dog, new tricks: Exact seeding strategy improves RNA design performances
    Théo Boury, Leonhard Sidl, Ivo L. Hofacker, Yann Ponty, and 1 more author
    In RECOMB 2025 - 29th International Conference of Research in Computational Molecular Biology, Mar 2025
  3. Preprint
    Undesignable motifs in structural RNAs and combinatorial consequences
    Hua-Ting Yao, Cedric Chauve, Mireille Regnier, and Yann Ponty
    May 2025
    working paper or preprint
  4. Conference
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    Integrating High-Throughput RNA-RNA Interaction Data into RNA Secondary Structure Prediction
    Denis Skibinski, Thomas Spicher, Leonhard Sidl, Paulína Holotová, and 7 more authors
    In International Symposium on Bioinformatics Research and Applications (ISBRA) 2025, Apr 2025

2024

  1. Book Chapter
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    Developing Complex RNA Design Applications in the Infrared Framework
    Hua-Ting Yao, Yann Ponty, and Sebastian Will
    In RNA Folding: Methods and Protocols, Apr 2024
  2. Journal
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    Infrared: a declarative tree decomposition-powered framework for bioinformatics
    Hua-Ting Yao, Bertrand Marchand, Sarah J. Berkemer, Yann Ponty, and 1 more author
    Algorithms for Molecular Biology, Apr 2024
  3. Book Chapter
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    Sequence design for RNA-RNA interactions
    Maria Waldl, Hua-Ting Yao, and Ivo Hofacker
    In RNA Design: Methods and Protocols, Mar 2024
  4. Journal
    Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction
    Sarah Löhneysen, Thomas Spicher, Yuliia Varenyk, Hua-Ting Yao, and 3 more authors
    Journal of Computational Biology, Jun 2024

2023

  1. Journal
    Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package
    Hua-Ting Yao, Ronny Lorenz, Ivo L Hofacker, and Peter F Stadler
    Algorithms for Molecular Biology, Jul 2023
  2. Conference
    Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction
    Sarah Löhneysen, Thomas Spicher, Yuliia Varenyk, Hua-Ting Yao, and 3 more authors
    In Bioinformatics Research and Applications, Jul 2023

2021

  1. Conference
    Taming Disruptive Base Pairs to Reconcile Positive and Negative Structural Design of RNA
    In RECOMB 2021 - 25th international conference on research in computational molecular biology, Apr 2021
  2. Thesis
    Local Decomposition in RNA Structural Design
    Hua-Ting Yao
    Ecole Polytechnique (Palaiseau, France) ; Université McGill [Montréal], Dec 2021

2020

  1. Conference
    Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Modules Identification
    Roman Sarrazin-Gendron, Hua-Ting Yao, Vladimir Reinharz, Carlos G Oliver, and 2 more authors
    In RECOMB 2020 - 24th Annual International Conference on Research in Computational Molecular Biology, May 2020
  2. Book Chapter
    Advanced design of structural RNAs using RNARedPrint
    Yann Ponty, Stefan Hammer, Hua-Ting Yao, and Sebastian Will
    In RNA Bioinformatics, May 2020

2019

  1. Conference
    Exponentially few RNA structures are designable
    Hua-Ting Yao, Cedric Chauve, Mireille Regnier, and Yann Ponty
    In ACM-BCB 2019 - 10th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, Sep 2019

2018

  1. Journal
    MentaLiST – A fast MLST caller for large MLST schemes
    Pedro Feijao, Hua-Ting Yao, Dan Fornika, Jennifer Gardy, and 3 more authors
    Microbial Genomics, Feb 2018