| 2024 | FDG | Learning the Game: Decoding the Differences between Novice and Expert Players in a Citizen Science Game with Millions of Players. | Eddie Cai, Roman Sarrazin-Gendron, Renata Mutalova, Parham Ghasemloo Gheidari, Alexander Butyaev, Gabriel Richard, Sbastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jrme Waldisphl |
| 2023 | CHI | Playing the System: Can Puzzle Players Teach us How to Solve Hard Problems? | Renata Mutalova, Roman Sarrazin-Gendron, Eddie Cai, Gabriel Richard, Parham Ghasemloo Gheidari, Sbastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jrme Waldisphl |
| 2022 | HCI | Adaptive Instructional System for Complex Equipment Trainings in the Post-covid Era: Breaking the Ice of Time-Consuming Tasks. | Elena Nazarova, Alexander Butyaev, Mohamed Youssef Bouaouina, Dominic Filion, Jrme Waldisphl |
| 2020 | RECOMB | 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, Jrme Waldisphl |
| 2018 | RECOMB | A Nested 2-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces Cerevisae. | Antoine Soul, Jean-Marc Steyaert, Jrme Waldisphl |
| 2017 | HCOMP | Lessons from an Online Massive Genomics Computer Game. | Akash Singh, Faizy Ahsan, Mathieu Blanchette, Jrme Waldisphl |
| 2015 | PSB | Crowdsourcing RNA Structural Alignments with an Online Computer Game. | Jrme Waldisphl, Arthur Kam, Paul P. Gardner |
| 2014 | HCOMP | Phylo and Open-Phylo: A Human-Computing Platform for Comparative Genomics. | Jrme Waldisphl, Mathieu Blanchette |
| 2013 | RECOMB | A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs. | Vladimir Reinharz, Yann Ponty, Jrme Waldisphl |
| 2011 | RECOMB | Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models. | Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, Jrme Waldisphl |
| 2011 | RECOMB | An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary Pressure. | Jrme Waldisphl, Yann Ponty |
| 2009 | RECOMB | Simultaneous Alignment and Folding of Protein Sequences. | Jrme Waldisphl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger |
| 2002 | ECCB | An approximate matching algorithm for finding (sub-)optimal sequences in S-attributed grammars. | Jrme Waldisphl, Behshad Behzadi, Jean-Marc Steyaert |