| 2025 | CADE | Anti-pattern Templates. | Jan Otop |
| 2025 | ECAI | Active Automata Learning with Advice. | Michal Fica, Jan Otop |
| 2025 | MFCS | Minimization of Deterministic Finite Automata Modulo the Edit Distance. | Jakub Michaliszyn, Jan Otop |
| 2023 | CONCUR | Reachability and Bounded Emptiness Problems of Constraint Automata with Prefix, Suffix and Infix. | Jakub Michaliszyn, Jan Otop, Piotr Wieczorek |
| 2023 | JELIA | Deterministic Weighted Automata Under Partial Observability. | Jakub Michaliszyn, Jan Otop |
| 2022 | MFCS | Learning Deterministic Visibly Pushdown Automata Under Accessible Stack. | Jakub Michaliszyn, Jan Otop |
| 2021 | IJCAI | Minimization of Limit-Average Automata. | Jakub Michaliszyn, Jan Otop |
| 2020 | CONCUR | Multi-Dimensional Long-Run Average Problems for Vector Addition Systems with States. | Krishnendu Chatterjee, Thomas A. Henzinger, Jan Otop |
| 2020 | ECAI | Learning Deterministic Automata on Infinite Words. | Jakub Michaliszyn, Jan Otop |
| 2019 | CONCUR | Long-Run Average Behavior of Vector Addition Systems with States. | Krishnendu Chatterjee, Thomas A. Henzinger, Jan Otop |
| 2019 | CONCUR | Approximate Learning of Limit-Average Automata. | Jakub Michaliszyn, Jan Otop |
| 2018 | CONCUR | Non-deterministic Weighted Automata on Random Words. | Jakub Michaliszyn, Jan Otop |
| 2017 | CONCUR | Bidirectional Nested Weighted Automata. | Krishnendu Chatterjee, Thomas A. Henzinger, Jan Otop |
| 2016 | IJCAI | Querying Data Graphs with Arithmetical Regular Expressions. | Maciej Grabon, Jakub Michaliszyn, Jan Otop, Piotr Wieczorek |
| 2016 | LICS | Quantitative Automata under Probabilistic Semantics. | Krishnendu Chatterjee, Thomas A. Henzinger, Jan Otop |
| 2016 | MFCS | Nested Weighted Limit-Average Automata of Bounded Width. | Krishnendu Chatterjee, Thomas A. Henzinger, Jan Otop |
| 2016 | SAS | Quantitative Monitor Automata. | Krishnendu Chatterjee, Thomas A. Henzinger, Jan Otop |
| 2016 | VMCAI | Lipschitz Robustness of Timed I/O Systems. | Thomas A. Henzinger, Jan Otop, Roopsha Samanta |
| 2015 | ICALP | Edit Distance for Pushdown Automata. | Krishnendu Chatterjee, Thomas A. Henzinger, Rasmus Ibsen-Jensen, Jan Otop |
| 2015 | LICS | The Target Discounted-Sum Problem. | Udi Boker, Thomas A. Henzinger, Jan Otop |
| 2015 | LICS | Nested Weighted Automata. | Krishnendu Chatterjee, Thomas A. Henzinger, Jan Otop |
| 2013 | CONCUR | From Model Checking to Model Measuring. | Thomas A. Henzinger, Jan Otop |
| 2013 | CSL | Elementary Modal Logics over Transitive Structures. | Jakub Michaliszyn, Jan Otop |
| 2013 | FMCAD | Distributed synthesis for LTL fragments. | Krishnendu Chatterjee, Thomas A. Henzinger, Jan Otop, Andreas Pavlogiannis |
| 2012 | LICS | Decidable Elementary Modal Logics. | Jakub Michaliszyn, Jan Otop |
| 2004 | LPAR | On a Semantic Subsumption Test. | Jerzy Marcinkowski, Jan Otop, Grzegorz Stelmaszek |