Peer-reviewed papers

  • Eddie Cai, Roman Sarrazin-Gendron, Renata Mutalova, Parham Ghamsemloo Gheidari, Mathieu Blanchette, S ́ebastien Caisse, Rob Knight, Attila Szantner, Jérôme Waldispühl. Learning the Game: Decoding the Differences Between Novice and Expert Players in a Citizen Science Game With Millions of Players. Accepted at Foundations of Digitial Games, February 2024.

  • Roman Sarrazin-Gendron, Parham Ghasemloo, Alexander Butyaev, Timothy Keding, Eddie Cai, Jiayue Zheng, Renata Mutalova, Julien Mounthanyvong, Yuxue Zhu, Elena Nazarova, Chrisostomos Drogaris, Kornel Erhart, Gearbox Software Borderlands Science consortium, Borderlands Science players, Amélie Brouillette, Gabriel Richard, Randy Pitchford, Sébastien Caisse, Mathieu Blanchette, Daniel McDonald, Rob Knight, Attila Szantner, Jérôme Waldispühl. Improving microbial phylogeny with citizen science within a mass-market video game. Accepted to Nature Biotechnology, February 2024.

  • Arnaud Chol, Roman Sarrazin-Gendron, Eric Lecuyer, Mathieu Blanchette, Jérôme Waldispühl. PERFUMES: Pipeline to Extract RNA FUnctional Motifs and Exposed Structures. Application note in Bioinformatics, 2024. full text

  • Chrisostomos Drogaris, Alexander Butyaev, Elena Nazarova, Roman Sarrazin-Gendron, Harsh Patel, Akash Singh, Brenden Kadota, Jérôme Waldispühl. When Online Citizen Science meets Teaching: Storyfication of a science discovery game to teach, learn, and contribute to genomic data analysis, Biochemistry and Molecular Biology Education, 2023, full text

  • Renata Mutalova, Roman Sarrazin-Gendron, Parham Ghasemloo Gheidari, Eddie Cai, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jérôme Waldispühl. Player-Guided AI outperforms standard AI in Sequence Alignment Puzzles, Collective Intelligence Proceedings, 2023. full text

  • Renata Mutalova, Roman Sarrazin-Gendron, Eddie Cai, Gabriel Richard, Parham Ghasemloo Gheidari, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, and Jérôme Waldispühl. Playing the System: Can Puzzle Players Teach us How to Solve Hard Problems?, In Proceedings of the 2023 CHI Conference on Human Factors in Computing Systems (CHI ‘23). full text

  • A. Soulé, V. Reinharz, R. Sarrazin-Gendron, A. Denise, J. Waldispühl. Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs, PLOS Computational Biology (2021) full text

  • C.G. Oliver, V. Mallet, R. Sarrazin-Gendron, V. Reinharz, W.L. Hamilton, N. Moitessier, J. Waldispühl. Augmented base pairing networks encode RNA-small molecule binding preferences. Nucleic acids research (2020) full text

  • R. Sarrazin-Gendron, H. Yao, V. Reinharz, C. Oliver, Y. Ponty and J. Waldispühl. Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification, RECOMB Proceedings (2020) full text.

  • R. Sarrazin-Gendron, V. Reinharz, C. G. Oliver, N. Moitessier and J. Waldispühl. Automated, customizable and efficient identification of 3D base pair modules with BayesPairing. Nucleic acids research (2019) full text.

  • K. Kenyon-Dean, E. Ahmed, S. Fujimoto, …, R. Sarrazin-Gendron et al. Sentiment Analysis: It’s Complicated!. NAACL 2018 full text

Textbook Chapters

Modeling and Predicting RNA Three-Dimensional Structures, RNA Bioinformatics, Springer (2021). preprint full text.

Software and web-servers

Automatic identification of 3D structural modules in RNA sequences.


  • M.Sc. Thesis (full text)
  • Ph.D. Comprehensive Exam Literature Review (PDF)