Arbeitsgruppe Technische Informatik

Publikationen

  • Michael Forster, Silke Szymczak, David Ellinghaus, Georg Hemmrich-Stanisak, Malte Rühlemann, Lars Kraemer, Sören Mucha, Lars Wienbrandt, Martin Stanulla, UFO Sequencing Consortium within I-BFM Study Group and Andre Franke, Vy-PER: eliminating false positive detection of virus integration events in next generation sequencing data, Scientific Reports 5:11534, 2015.

  • Jorge González-Domínguez, Jan Christian Kässens, Lars Wienbrandt, and Bertil Schmidt, Large-Scale Genome-Wide Association Studies on a GPU Cluster Using a CUDA-Accelerated PGAS Programming Model, International Journal of High-Performance Computing Applications, vol. 29(4), pp. 506–510, 2015.

  • Jan Christian Kässens, Lars Wienbrandt, Jorge González-Domínguez, Bertil Schmidt, and Manfred Schimmler, High-Speed Exhaustive 3-locus Interaction Epistasis Analysis on FPGAs, Journal of Computational Science 9:131–136, 2015.

  • Jorge González-Domínguez, Lars Wienbrandt, Jan Christian Kässens, David Ellinghaus, Manfred Schimmler, and Bertil Schmidt, Parallelizing Epistasis Detection in GWAS on FPGA and GPU-accelerated Computing Systems, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 12(5), pp. 982–994,  DOI 10.1109/TCBB.2015.2389958, 2015.

  • Ayman Abbas, Rian Voß, Lars Wienbrandt, and Manfred Schimmler, An Efficient Implementation of PBKDF2 with RIPEMD-160 on Multiple FPGAs, 2014 IEEE 20th International Conference on Parallel and Distributed Systems (ICPADS), pp. 454–461, Dec 2014.

  • Jan Christian Kässens, Jorge González-Domínguez, Lars Wienbrandt, and Bertil Schmidt, UPC++ for Bioinformatics: A Case Study Using Gnome-Wide Association Studies, 15th IEEE International Conference on Cluster Computing, Sep 2014.

  • Jorge González-Domínguez, Bertil Schmidt, Jan Christian Kässens, and Lars Wienbrandt, Hybrid CPU/GPU Acceleration of Detection of 2-SNP Epistatic Interactions in GWAS, 20th International European Conference on Parallel and Distributed Computing (Euro-Par 2014), ed. by Lecture Notes on Computer Science, vol. 8632, pp. 680-691, 2014.

  • Lars Wienbrandt, The FPGA-based High-Performance Computer RIVYERA for Applications in Bioinformatics, Invited talk: 10th Conference on Computability in Europe (CiE) 2014, Special Session on Bio-inspired Computation, Jun 2014, Budapest.

  • Lars Wienbrandt, The FPGA-based High-Performance Computer RIVYERA for Applications in Bioinformatics, Language, Life, Limits - Proceedings of the 10th Conference on Computability in Europe (CiE) 2014, Springer, 2014, pp. 383-392.

  • Lars Wienbrandt, Jan Christian Kässens, Jorge González-Domínguez, Bertil Schmidt, David Ellinghaus, and Manfred Schimmler, FPGA-based acceleration of detecting statistical epistasis in GWAS, Procedia Computer Science, vol. 29, 2014, pp. 220-230.

  • Lars Wienbrandt, Bioinformatics Applications on the FPGA-based High-Performance Computer RIVYERA, in "High Performance Computing Using FPGAs" edited by Wim Vanderbauwhede, Khaled Benkrid, Springer, 2013, ISBN 978-1-4614-1790-3.

  • Tim Güneysu, Timo Kasper, Martin Novotný, Christof Paar, Lars Wienbrandt, and Ralf Zimmermann, High-Performance Cryptanalysis on RIVYERA and COPACOBANA Computing Systems, in "High Performance Computing Using FPGAs" edited by Wim Vanderbauwhede, Khaled Benkrid, Springer, 2013, ISBN 978-1-4614-1790-3.

  • Ayman Abbas, Claas Anders Rathje, Lars Wienbrandt, and Manfred Schimmler, Dictionary Attack on TrueCrypt with RIVYERA S3-5000, 2012 IEEE 18th International Conference on Parallel and Distributed Systems (ICPADS), Dec 2012, pp. 93-100. 

  • Florian Schatz, Lars Wienbrandt, and Manfred Schimmler, Probability model for boundaries of short-read sequencing, 2012 International Conference on Advances in Computing and Communications (ICACC), Aug 2012, pp. 223-228. (best paper award)

  • Christoph Starke, Vasco Grossmann, Lars Wienbrandt, and Manfred Schimmler, An FPGA implementation of an Investment Strategy Processor, Procedia Computer Science, vol. 9, 2012, pp. 1880-1889. 

  • Lars Wienbrandt, Daniel Siebert, and Manfred Schimmler, Improvement of BLASTp on the FPGA-Based High-Performance Computer RIVYERA, Lecture Notes in Computer Science, vol. 7292, 2012, pp. 275-286. 

  • Christoph Starke, Vasco Grossmann, Lars Wienbrandt, Sven Koschnicke, John Carstens, and Manfred Schimmler, Optimizing Investment Strategies with the Recongurable Hardware Platform RIVYERA, International Journal of Reconfigurable Computing, vol. 2012, 10 pages. 

  • Lars Wienbrandt, Stefan Baumgart, Jost Bissel, Florian Schatz, and Manfred Schimmler, Massively parallel FPGA-based implementation of BLASTp with the two-hit method, Procedia Computer Science, vol. 4, 2011, pp. 1967-1976

  • Lars Wienbrandt, Hardware implementation and massive parallelization of BLAST, Invited talk: Workshop on Theoretical Biology, Max-Planck-Institute for Evolutionary Biology, Plön 2011. 

  • Lars Wienbrandt, and Manfred Schimmler, Collecting Statistical Information in DNA Sequences for the Detection of Special Motifs, Proceedings of BIOCOMP2010, 2010, pp. 274-278.

  • Manfred Schimmler, Lars Wienbrandt, Tim Güneysu, and Jost Bissel, COPACOBANA: A Massively Parallel FPGA-Based Computer Architecture, in "Bioinformatics: High Performance Parallel Computer Architectures" edited by Bertil Schmidt, CRC Press, 2010, ISBN 978-1-4398-1488-8. 

  • Lars Wienbrandt, Stefan Baumgart, Jost Bissel, Carol May Yen Yeo, and Manfred Schimmler, Using the reconfigurable massively parallel architecture COPACOBANA 5000 for applications in bioinformatics, Procedia Computer Science, vol. 1 (1), 2010, pp. 1027-1034.

  • Jan Schröder, Lars Wienbrandt, Gerd Pfeiffer, and Manfred Schimmler, Massively Parrallelized DNA Motif Search on the Reconfigurable Hardware Platform COPACOBANA, Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB2008), 2008, pp. 436-447.