| 2018 | BIBE | Comparative Analysis of System-Level Acceleration Techniques in Bioinformatics: A Case Study of Accelerating the Smith-Waterman Algorithm for BWA-MEM. | Ernst Joachim Houtgast, Vlad Mihai Sima, Koen Bertels, Zaid Al-Ars |
| 2017 | BIBE | High Performance Streaming Smith-Waterman Implementation with Implicit Synchronization on Intel FPGA using OpenCL. | Ernst Houtgast, Vlad Mihai Sima, Zaid Al-Ars |
| 2016 | FCCM | Power-Efficient Accelerated Genomic Short Read Mapping on Heterogeneous Computing Platforms. | Ernst Joachim Houtgast, Vlad Mihai Sima, Giacomo Marchiori, Koen Bertels, Zaid Al-Ars |
| 2015 | ICCAD | Heterogeneous Hardware/Software Acceleration of the BWA-MEM DNA Alignment Algorithm. | Nauman Ahmed, Vlad Mihai Sima, Ernst Houtgast, Koen Bertels, Zaid Al-Ars |
| 2014 | ASPDAC | DRuiD: Designing reconfigurable architectures with decision-making support. | Giovanni Mariani, Gianluca Palermo, Roel Meeuws, Vlad Mihai Sima, Cristina Silvano, Koen Bertels |
| 2014 | EUC | High-Level Synthesis in the Delft Workbench Hardware/Software Co-design Tool-Chain. | Razvan Nane, Vlad Mihai Sima, Cuong Pham-Quoc, Fernando M. Gonalves, Koen Bertels |
| 2013 | FPL | Run-time optimization of a dynamically reconfigurable embedded system through performance prediction. | Giovanni Mariani, Vlad Mihai Sima, Gianluca Palermo, Vittorio Zaccaria, Giacomo Marchiori, Cristina Silvano, Koen Bertels |
| 2012 | DATE | Using multi-objective design space exploration to enable run-time resource management for reconfigurable architectures. | Giovanni Mariani, Vlad Mihai Sima, Gianluca Palermo, Vittorio Zaccaria, Cristina Silvano, Koen Bertels |
| 2012 | FPL | DWARV 2.0: A CoSy-based C-to-VHDL hardware compiler. | Razvan Nane, Vlad Mihai Sima, Bryan Olivier, Roel Meeuws, Yana Yankova, Koen Bertels |
| 2009 | FPL | Compiler assisted runtime task scheduling on a reconfigurable computer. | Mojtaba Sabeghi, Vlad Mihai Sima, Koen Bertels |
| 2008 | FPL | Resource allocation algorithm and OpenMP extensions for parallel execution on a heterogeneous reconfigurable platform. | Vlad Mihai Sima, Elena Moscu Panainte, Koen Bertels |
| 2007 | FPL | HARTES Toolchain Early Evaluation: Profiling, Compilation and HDL Generation. | Koen Bertels, Georgi Kuzmanov, Elena Moscu Panainte, Georgi Gaydadjiev, Yana Yankova, Vlad Mihai Sima, Kamana Sigdel, Roel Meeuws, Stamatis Vassiliadis |