| 2026 | MFCS | A Congestion Parameter for Depth-First Graph Traversals. | Codaline Bourotte, Gwendal Ducloz, Pekka Orponen, Shinnosuke Seki |
| 2025 | DNA | Secondary Structure Design for Cotranscriptional 3D RNA Origami Wireframes. | Pekka Orponen, Shinnosuke Seki, Antti Elonen |
| 2024 | DNA | Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops. | Antti Elonen, Pekka Orponen |
| 2024 | UC | A General Design Method for Scaffold-Free DNA Wireframe Nanostructures. | Antti Elonen, Abdulmelik Mohammed, Pekka Orponen |
| 2024 | UC | Automated Rendering of Multi-stranded DNA Complexes with Pseudoknots. | Malgorzata Nowicka, Vinay Kumar Gautam, Pekka Orponen |
| 2018 | UC | Algorithmic Design of Cotranscriptionally Folding 2D RNA Origami Structures. | Abdulmelik Mohammed, Pekka Orponen, Sachith Pai |
| 2012 | MFCS | Unordered Constraint Satisfaction Games. | Lauri Ahlroth, Pekka Orponen |
| 2011 | DNA | Synthesizing Small and Reliable Tile Sets for Patterned DNA Self-assembly. | Tuomo Lempiinen, Eugen Czeizler, Pekka Orponen |
| 2010 | DNA | Synthesizing Minimal Tile Sets for Patterned DNA Self-assembly. | Mika Gs, Pekka Orponen |
| 2008 | EWSN | Lifetime Maximization in Wireless Sensor Networks by Distributed Binary Search. | Andr Schumacher, Pekka Orponen, Thorn Thaler, Harri Haanp |
| 2005 | SAT | Threshold Behaviour of WalkSAT and Focused Metropolis Search on Random 3-Satisfiability. | Sakari Seitz, Mikko Alava, Pekka Orponen |
| 2004 | Algosensors | Balanced Data Gathering in Energy-Constrained Sensor Networks. | Emil Falck, Patrik Floren, Petteri Kaski, Jukka Kohonen, Pekka Orponen |
| 2001 | ICANN | Exponential Transients in Continuous-Time Symmetric Hopfield Nets. | Jir Sma, Pekka Orponen |
| 2001 | STOC | Computing with continuous-time Liapunov systems. | Jir Sma, Pekka Orponen |
| 1999 | SOFSEM | Some Afterthoughts on Hopfield Networks. | Jir Sma, Pekka Orponen, Teemu Antti-Poika |
| 1997 | SOFSEM | The Computational Power of Continuous Time Neural Networks. | Pekka Orponen |
| 1993 | ICALP | On the Computational Power of Discrete Hopfield Nets. | Pekka Orponen |
| 1992 | MFCS | Neural Networks and Complexity Theory. | Pekka Orponen |
| 1991 | KR | Probably Approximately Optimal Derivation Strategies. | Russell Greiner, Pekka Orponen |
| 1990 | COLT | On the Sample Complexity of Finding Good Search Strategies. | Pekka Orponen, Russell Greiner |
| 1990 | IJCNN | A neural implementation of conceptual hierarchies with Bayesian reasoning. | Pekka Orponen, Patrik Floren, Petri Myllymki, Henry Tirri |
| 1986 | ICALP | On Exponential Lowness. | Ronald V. Book, Pekka Orponen, David A. Russo, Osamu Watanabe |
| 1985 | ICALP | Polynomial Levelability and Maximal Complexity Cores. | Pekka Orponen, David A. Russo, Uwe Schning |
| 1984 | MFCS | The Structure of Polynomial Complexity Cores (Extended Abstract). | Pekka Orponen, Uwe Schning |
| 1983 | ICALP | Complexity Classes of Alternating Machines with Oracles. | Pekka Orponen |