| 2022 | DCC | x3: Lossless Data Compressor. | David Barina, Ondrej Klma |
| 2022 | DLT | Well Quasi-Orders Arising from Finite Ordered Semigroups. | Ondrej Klma, Jonatan Kolegar |
| 2020 | LATA | Geometrically Closed Positive Varieties of Star-Free Languages. | Ondrej Klma, Peter Kostolnyi |
| 2019 | LATA | On Varieties of Ordered Automata. | Ondrej Klma, Libor Polk |
| 2019 | LATA | Deterministic Biautomata and Subclasses of Deterministic Linear Languages. | Galina Jirskov, Ondrej Klma |
| 2018 | MICCAI | Virtual 2D-3D Fracture Reduction with Bone Length Recovery Using Statistical Shape Models. | Ondrej Klma, Roman Madeja, Michal Spanel, Martin Cuta, Pavel Zemck, Pavel Stoklsek, Ales Mizera |
| 2018 | MICCAI | Morphometric Sex Estimation from the Hip Bone by Means of the HIP 1.1 Software. | Miroslav Krlk, Ondrej Klma, Petra Urbanov, Lenka Polcerov, Martin Cuta |
| 2016 | DCC | Single-Loop Software Architecture for JPEG 2000. | David Barina, Ondrej Klma, Pavel Zemck |
| 2016 | ICISP | Single-Loop Architecture for JPEG 2000. | David Barina, Ondrej Klma, Pavel Zemck |
| 2015 | DLT | On Decidability of Intermediate Levels of Concatenation Hierarchies. | Jorge Almeida, Jana Bartonov, Ondrej Klma, Michal Kunc |
| 2013 | DLT | Alternative Automata Characterization of Piecewise Testable Languages. | Ondrej Klma, Libor Polk |
| 2012 | DLT | Biautomata for k-Piecewise Testable Languages. | Ondrej Klma, Libor Polk |
| 2010 | DLT | On Schtzenberger Products of Semirings. | Ondrej Klma, Libor Polk |
| 2008 | DLT | Hierarchies of Piecewise Testable Languages. | Ondrej Klma, Libor Polk |
| 2008 | LATA | Literal Varieties of Languages Induced by Homomorphisms onto Nilpotent Groups. | Ondrej Klma, Libor Polk |
| 2006 | MFCS | Systems of Equations over Finite Semigroups and the #CSP Dichotomy Conjecture. | Ondrej Klma, Benot Larose, Pascal Tesson |
| 2002 | MFCS | Unification Modulo Associativity and Idempotency Is NP-complete. | Ondrej Klma |
| 2000 | MFCS | Matching Modulo Associativity and Idempotency Is NP-Complete. | Ondrej Klma, Jir Srba |
| 1999 | SOFSEM | Pattern Equations and Equations with Stuttering. | Ivana Cern, Ondrej Klma, Jir Srba |