E.J. Houtgast, V.M. Sima, K.L.M. Bertels, Z. Al-Ars, Comparative Analysis of System-Level Acceleration Techniques in Bioinformatics: A Case Study of Accelerating the Smith-Waterman Algorithm for BWA-MEM (October 2018), 18th IEEE International Conference on BioInformatics and BioEngineering (BIBE 2018), 29-31 October 2018, Taichung, Taiwan [Conference Paper]

E.J. Houtgast, V.M. Sima, K.L.M. Bertels, Z. Al-Ars, Hardware Acceleration of BWA-MEM Genomic Short Read Mapping for Longer Read Lengths (August 2018), Computational Biology and Chemistry (Comput. Biol. Chem), volume 75 [Journal Paper]

E.J. Houtgast, V.M. Sima, Z. Al-Ars, High Performance Streaming Smith-Waterman Implementation with Implicit Synchronization on Intel FPGA using OpenCL (October 2017), 17th annual IEEE International Conference on BioInformatics and BioEngineering (BIBE 2017), 23-25 October 2017, Washington DC, USA , full paper [Conference Paper]

E.J. Houtgast, V.M. Sima, G. Marchiori, K.L.M. Bertels, Z. Al-Ars, Power-Efficiency Analysis of Accelerated BWA-MEM Implementations on Heterogeneous Computing Platforms (December 2016), International Conference on Reconfigurable Computing and FPGAs (ReConFig 2016), 30 November - 2 December 2016, Cancun, Mexico , full paper [Conference Paper]

E.J. Houtgast, V.M. Sima, K.L.M. Bertels, Z. Al-Ars, An Efficient GPU-Accelerated Implementation of Genomic Short Read Mapping with BWA-MEM (July 2016), International Symposium on Highly-Efficient Accelerators and Reconfigurable Technologies (HEART 2016), 25-27 July 2016, Hong Kong, China , Proceedings published in ACM SIGARCH Computer Architecture News (journal) [Conference Paper]

E.J. Houtgast, V.M. Sima, K.L.M. Bertels, Z. Al-Ars, Computational Challenges of Next Generation Sequencing Pipelines Using Heterogeneous Systems (July 2016), 12th International Summer School on Advanced Computer Architecture and Compilation for High-Performance and Embedded Systems (ACACES 2016), 10-16 July 2016, Fiuggi, Italy , abstract only [Conference Proceedings]

E.J. Houtgast, V.M. Sima, G. Marchiori, K.L.M. Bertels, Z. Al-Ars, Power-Efficient Accelerated Genomic Short Read Mapping on Heterogeneous Computing Platforms (May 2016), 24th IEEE International Symposium on Field-Programmable Custom Computing Machines (FCCM 2016), 1-3 May 2016, Washington DC, USA , abstract only [Conference Paper]

E.J. Houtgast, V.M. Sima, K.L.M. Bertels, Z. Al-Ars, GPU-Accelerated BWA-MEM Genomic Mapping Algorithm Using Adaptive Load Balancing (April 2016), 29th International Conference on Architecture of Computing Systems (ARCS 2016), 4-7 April 2016, Nuremberg, Germany [Conference Paper]

N. Ahmed, V.M. Sima, E.J. Houtgast, K.L.M. Bertels, Z. Al-Ars, Heterogeneous Hardware/Software Acceleration of the BWA-MEM DNA Alignment Algorithm (November 2015), International Conference On Computer Aided Design (ICCAD 2015), 2-6 November 2015, Austin, USA [Conference Paper]

E.J. Houtgast, V.M. Sima, K.L.M. Bertels, Z. Al-Ars, An FPGA-Based Systolic Array to Accelerate the BWA-MEM Genomic Mapping Algorithm (September 2015), International Conference On Embedded Computer Systems: Architectures, Modeling, And Simulation (SAMOS XV (2015)), 20-23 July 2015, Samos, Greece [Conference Paper]

S. Isaza Ramirez, E.J. Houtgast, G.N. Gaydadjiev, HMMER Performance Model for Multicore Architectures (September 2011), 14th Euromicro Conference On Digital System Design (DSD 2011), 31 August - 2 September 2011, Oulu, Finland [Conference Paper]

S. Isaza Ramirez, E.J. Houtgast, G.N. Gaydadjiev, Sequence Alignment Application Model for Multi- and Manycore Architectures (September 2011), International Journal of Information and Computer Security (IJICS), volume 4, issue 3 [Journal Paper]

S. Isaza Ramirez, E.J. Houtgast, F. Sanchez, A. Ramirez, G.N. Gaydadjiev, Scaling HMMER Performance on Multicore Architectures (July 2011), IEEE International Workshop on Multicore Computing Systems (MuCoCoS 2011), 1 July 2011, Seoul, Korea [Conference Paper]

E.J. Houtgast, Scalability of Bioinformatics Applications for Multicore Architectures (November 2009), [Msc Thesis]