| 2025 | FPL | DMA Calypte: Open-Source Ultra-Low Latency DMA Engine for FPGAs. | Vladislav Vlek, Martin Spinler, Jakub Cabal, Toms Martnek |
| 2024 | FCCM | LGBM2VHDL: Mapping of LightGBM Models to FPGA. | Toms Martnek, Jan Korenek, Toms Cejka |
| 2010 | FCCM | Hardware Acceleration of Approximate Tandem Repeat Detection. | Toms Martnek, Matej Lexa |
| 2009 | DDECS | Architecture model for approximate palindrome detection. | Toms Martnek, Jan Vozenilek, Matej Lexa |
| 2008 | DDECS | NetCOPE: Platform for Rapid Development of Network Applications. | Toms Martnek, Martin Kosek |
| 2008 | FPL | GICS: Generic interconnection system. | Tamas Malek, Toms Martnek, Jan Korenek |
| 2007 | DDECS | Automatic Generation of Circuits for Approximate String Matching. | Toms Martnek, Otto Fuck, Patrik Beck, Matej Lexa |
| 2007 | DSD | Online Protocol Testing for FPGA Based Fault Tolerant Systems. | Jiri Tobola, Zdenek Kotsek, Jan Korenek, Toms Martnek, Martin Straka |
| 2007 | FPL | High Level Abstraction Language as an Alternative to Embedded Processors for Internet Packet Processing in FPGA. | Tomas Dedek, Tomas Marek, Toms Martnek |
| 2006 | CEC | Extrinsic and Intrinsic Evolution of Multifunctional Combinational Modules. | Luks Sekanina, Toms Martnek, Zbysek Gajda |
| 2006 | DDECS | A Flexible Technique for the Automatic Design of Approximate String Matching Architectures. | Toms Martnek, Jan Korenek, Otto Fuck, Matej Lexa |