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ORCIDBibTeX records: Bertil Schmidt
@article{DBLP:journals/cphysics/JarlebladSSENSL24,
author = {Henrik J{\"{a}}rleblad and
Luke Stagner and
Mirko Salewski and
J. Eriksson and
M. Nocente and
Bertil Schmidt and
M. Rud Larsen},
title = {A framework for synthetic diagnostics using energetic-particle orbits
in tokamaks},
journal = {Comput. Phys. Commun.},
volume = {294},
pages = {108930},
year = {2024},
url = {https://doi.org/10.1016/j.cpc.2023.108930},
doi = {10.1016/J.CPC.2023.108930},
timestamp = {Sun, 17 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/cphysics/JarlebladSSENSL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XuYYYWSL23,
author = {Xiaoming Xu and
Zekun Yin and
Lifeng Yan and
Huiguang Yi and
Hua Wang and
Bertil Schmidt and
Weiguo Liu},
title = {RabbitKSSD: accelerating genome distance estimation on modern multi-core
architectures},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad695},
doi = {10.1093/BIOINFORMATICS/BTAD695},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/XuYYYWSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jocs/KemmerHSH23,
author = {Thomas Kemmer and
Sebastian Hack and
Bertil Schmidt and
Andreas Hildebrandt},
title = {CUDA-accelerated protein electrostatics in linear space},
journal = {J. Comput. Sci.},
volume = {70},
pages = {102022},
year = {2023},
url = {https://doi.org/10.1016/j.jocs.2023.102022},
doi = {10.1016/J.JOCS.2023.102022},
timestamp = {Thu, 15 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jocs/KemmerHSH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/ZhangSXCWWYSL23,
author = {Hao Zhang and
Honglei Song and
Xiaoming Xu and
Qixin Chang and
Mingkai Wang and
Yanjie Wei and
Zekun Yin and
Bertil Schmidt and
Weiguo Liu},
title = {RabbitFX: Efficient Framework for {FASTA/Q} File Parsing on Modern
Multi-Core Platforms},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {20},
number = {3},
pages = {2341--2348},
year = {2023},
url = {https://doi.org/10.1109/TCBB.2022.3219114},
doi = {10.1109/TCBB.2022.3219114},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/ZhangSXCWWYSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tpds/DuanSWSGLFXLY23,
author = {Xiaohui Duan and
Qi Shao and
Junben Weng and
Bertil Schmidt and
Lin Gan and
Guohui Li and
Haohuan Fu and
Wei Xue and
Weiguo Liu and
Guangwen Yang},
title = {Bio-ESMD: {A} Data Centric Implementation for Large-Scale Biological
System Simulation on Sunway TaihuLight Supercomputer},
journal = {{IEEE} Trans. Parallel Distributed Syst.},
volume = {34},
number = {3},
pages = {881--893},
year = {2023},
url = {https://doi.org/10.1109/TPDS.2022.3220559},
doi = {10.1109/TPDS.2022.3220559},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tpds/DuanSWSGLFXLY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tpds/GaoDSWGZGFXLY23,
author = {Ping Gao and
Xiaohui Duan and
Bertil Schmidt and
Wubing Wan and
Jiaxu Guo and
Wusheng Zhang and
Lin Gan and
Haohuan Fu and
Wei Xue and
Weiguo Liu and
Guangwen Yang},
title = {Redesign and Accelerate the {AIREBO} Bond-Order Potential on the New
Sunway Supercomputer},
journal = {{IEEE} Trans. Parallel Distributed Syst.},
volume = {34},
number = {12},
pages = {3117--3132},
year = {2023},
url = {https://doi.org/10.1109/TPDS.2023.3321927},
doi = {10.1109/TPDS.2023.3321927},
timestamp = {Sun, 10 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tpds/GaoDSWGZGFXLY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/europar/KobusNHS23,
author = {Robin Kobus and
Johannes Nelgen and
Valentin Henkys and
Bertil Schmidt},
editor = {Jos{\'{e}} Cano and
Marios D. Dikaiakos and
George A. Papadopoulos and
Miquel Peric{\`{a}}s and
Rizos Sakellariou},
title = {Faster Segmented Sort on GPUs},
booktitle = {Euro-Par 2023: Parallel Processing - 29th International Conference
on Parallel and Distributed Computing, Limassol, Cyprus, August 28
- September 1, 2023, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {14100},
pages = {664--678},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-3-031-39698-4\_45},
doi = {10.1007/978-3-031-39698-4\_45},
timestamp = {Thu, 14 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/europar/KobusNHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccS/NieblerSTS23,
author = {Stefan Niebler and
Bertil Schmidt and
Holger Tost and
Peter Spichtinger},
editor = {Jir{\'{\i}} Mikyska and
Cl{\'{e}}lia de Mulatier and
Maciej Paszynski and
Valeria V. Krzhizhanovskaya and
Jack J. Dongarra and
Peter M. A. Sloot},
title = {Automated Identification and Location of Three Dimensional Atmospheric
Frontal Systems},
booktitle = {Computational Science - {ICCS} 2023 - 23rd International Conference,
Prague, Czech Republic, July 3-5, 2023, Proceedings, Part {II}},
series = {Lecture Notes in Computer Science},
volume = {14074},
pages = {3--17},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-3-031-36021-3\_1},
doi = {10.1007/978-3-031-36021-3\_1},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iccS/NieblerSTS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangCYXWSL22,
author = {Hao Zhang and
Qixin Chang and
Zekun Yin and
Xiaoming Xu and
Yanjie Wei and
Bertil Schmidt and
Weiguo Liu},
title = {RabbitV: fast detection of viruses and microorganisms in sequencing
data on multi-core architectures},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2932--2933},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac187},
doi = {10.1093/BIOINFORMATICS/BTAC187},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangCYXWSL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KallenbornCS22,
author = {Felix Kallenborn and
Julian Cascitti and
Bertil Schmidt},
title = {{CARE} 2.0: reducing false-positive sequencing error corrections using
machine learning},
journal = {{BMC} Bioinform.},
volume = {23},
number = {1},
pages = {227},
year = {2022},
url = {https://doi.org/10.1186/s12859-022-04754-3},
doi = {10.1186/S12859-022-04754-3},
timestamp = {Tue, 28 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KallenbornCS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BobTKGTSH22,
author = {Konstantin Bob and
David Teschner and
Thomas Kemmer and
David Gomez{-}Zepeda and
Stefan Tenzer and
Bertil Schmidt and
Andreas Hildebrandt},
title = {Locality-sensitive hashing enables efficient and scalable signal classification
in high-throughput mass spectrometry raw data},
journal = {{BMC} Bioinform.},
volume = {23},
number = {1},
pages = {287},
year = {2022},
url = {https://doi.org/10.1186/s12859-022-04833-5},
doi = {10.1186/S12859-022-04833-5},
timestamp = {Mon, 08 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BobTKGTSH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jocs/CascittiNMS22,
author = {Julian Cascitti and
Stefan Niebler and
Andr{\'{e}} M{\"{u}}ller and
Bertil Schmidt},
title = {RNACache: {A} scalable approach to rapid transcriptomic read mapping
using locality sensitive hashing},
journal = {J. Comput. Sci.},
volume = {60},
pages = {101572},
year = {2022},
url = {https://doi.org/10.1016/j.jocs.2022.101572},
doi = {10.1016/J.JOCS.2022.101572},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jocs/CascittiNMS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jpdc/XuDMKSL22,
author = {Kai Xu and
Xiaohui Duan and
Andr{\'{e}} M{\"{u}}ller and
Robin Kobus and
Bertil Schmidt and
Weiguo Liu},
title = {FMapper: Scalable read mapper based on succinct hash index on SunWay
TaihuLight},
journal = {J. Parallel Distributed Comput.},
volume = {161},
pages = {72--82},
year = {2022},
url = {https://doi.org/10.1016/j.jpdc.2021.11.004},
doi = {10.1016/J.JPDC.2021.11.004},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jpdc/XuDMKSL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jpdc/JungerKMHXLS22,
author = {Daniel J{\"{u}}nger and
Robin Kobus and
Andr{\'{e}} M{\"{u}}ller and
Christian Hundt and
Kai Xu and
Weiguo Liu and
Bertil Schmidt},
title = {General-purpose {GPU} hashing data structures and their application
in accelerated genomics},
journal = {J. Parallel Distributed Comput.},
volume = {163},
pages = {256--268},
year = {2022},
url = {https://doi.org/10.1016/j.jpdc.2022.01.006},
doi = {10.1016/J.JPDC.2022.01.006},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jpdc/JungerKMHXLS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tpds/GaoDSZGFXLY22,
author = {Ping Gao and
Xiaohui Duan and
Bertil Schmidt and
Wusheng Zhang and
Lin Gan and
Haohuan Fu and
Wei Xue and
Weiguo Liu and
Guangwen Yang},
title = {Optimization of Reactive Force Field Simulation: Refactor, Parallelization,
and Vectorization for Interactions},
journal = {{IEEE} Trans. Parallel Distributed Syst.},
volume = {33},
number = {2},
pages = {359--373},
year = {2022},
url = {https://doi.org/10.1109/TPDS.2021.3091408},
doi = {10.1109/TPDS.2021.3091408},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tpds/GaoDSZGFXLY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tpds/XuZDWHSLY22,
author = {Kai Xu and
Jinxiao Zhang and
Xiaohui Duan and
Xiaobo Wan and
Niu Huang and
Bertil Schmidt and
Weiguo Liu and
Guangwen Yang},
title = {Redesigning and Optimizing {UCSF} {DOCK3.7} on Sunway TaihuLight},
journal = {{IEEE} Trans. Parallel Distributed Syst.},
volume = {33},
number = {10},
pages = {4458--4471},
year = {2022},
url = {https://doi.org/10.1109/TPDS.2022.3194916},
doi = {10.1109/TPDS.2022.3194916},
timestamp = {Sun, 15 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tpds/XuZDWHSLY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tpds/MengZCWSWLWDWF22,
author = {Jintao Meng and
Chen Zhuang and
Peng Chen and
Mohamed Wahib and
Bertil Schmidt and
Xiao Wang and
Haidong Lan and
Dou Wu and
Minwen Deng and
Yanjie Wei and
Shengzhong Feng},
title = {Automatic Generation of High-Performance Convolution Kernels on {ARM}
CPUs for Deep Learning},
journal = {{IEEE} Trans. Parallel Distributed Syst.},
volume = {33},
number = {11},
pages = {2885--2899},
year = {2022},
url = {https://doi.org/10.1109/TPDS.2022.3146257},
doi = {10.1109/TPDS.2022.3146257},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tpds/MengZCWSWLWDWF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/YanYZZWMKWNSL22,
author = {Lifeng Yan and
Zekun Yin and
Hao Zhang and
Zhan Zhao and
Mingkai Wang and
Andr{\'{e}} M{\"{u}}ller and
Robin Kobus and
Yanjie Wei and
Beifang Niu and
Bertil Schmidt and
Weiguo Liu},
editor = {Donald A. Adjeroh and
Qi Long and
Xinghua Mindy Shi and
Fei Guo and
Xiaohua Hu and
Srinivas Aluru and
Giri Narasimhan and
Jianxin Wang and
Mingon Kang and
Ananda Mondal and
Jin Liu},
title = {RabbitQCPlus: More Efficient Quality Control for Sequencing Data},
booktitle = {{IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2022, Las Vegas, NV, USA, December 6-8, 2022},
pages = {619--626},
publisher = {{IEEE}},
year = {2022},
url = {https://doi.org/10.1109/BIBM55620.2022.9995332},
doi = {10.1109/BIBM55620.2022.9995332},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bibm/YanYZZWMKWNSL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ics/MullerSMLH22,
author = {Andr{\'{e}} M{\"{u}}ller and
Bertil Schmidt and
Richard Membarth and
Roland Lei{\ss}a and
Sebastian Hack},
editor = {Lawrence Rauchwerger and
Kirk W. Cameron and
Dimitrios S. Nikolopoulos and
Dionisios N. Pnevmatikatos},
title = {AnySeq/GPU: a novel approach for faster sequence alignment on GPUs},
booktitle = {{ICS} '22: 2022 International Conference on Supercomputing, Virtual
Event, June 28 - 30, 2022},
pages = {20:1--20:11},
publisher = {{ACM}},
year = {2022},
url = {https://doi.org/10.1145/3524059.3532376},
doi = {10.1145/3524059.3532376},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ics/MullerSMLH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ispdc/HenkysSB22,
author = {Valentin Henkys and
Bertil Schmidt and
Niklaus Berger},
title = {Online Event Selection for Mu3e using GPUs},
booktitle = {21st International Symposium on Parallel and Distributed Computing,
{ISPDC} 2022, Basel, Switzerland, July 11-13, 2022},
pages = {17--24},
publisher = {{IEEE}},
year = {2022},
url = {https://doi.org/10.1109/ISPDC55340.2022.00012},
doi = {10.1109/ISPDC55340.2022.00012},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ispdc/HenkysSB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2205-07610,
author = {Andr{\'{e}} M{\"{u}}ller and
Bertil Schmidt and
Richard Membarth and
Roland Lei{\ss}a and
Sebastian Hack},
title = {AnySeq/GPU: {A} Novel Approach for Faster Sequence Alignment on GPUs},
journal = {CoRR},
volume = {abs/2205.07610},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2205.07610},
doi = {10.48550/ARXIV.2205.07610},
eprinttype = {arXiv},
eprint = {2205.07610},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2205-07610.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2206-11535,
author = {Valentin Henkys and
Bertil Schmidt and
Niklaus Berger},
title = {Online Event Selection for Mu3e using GPUs},
journal = {CoRR},
volume = {abs/2206.11535},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2206.11535},
doi = {10.48550/ARXIV.2206.11535},
eprinttype = {arXiv},
eprint = {2206.11535},
timestamp = {Mon, 27 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2206-11535.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YinZLZSLWNSL21,
author = {Zekun Yin and
Hao Zhang and
Meiyang Liu and
Wen Zhang and
Honglei Song and
Haidong Lan and
Yanjie Wei and
Beifang Niu and
Bertil Schmidt and
Weiguo Liu},
title = {RabbitQC: high-speed scalable quality control for sequencing data},
journal = {Bioinform.},
volume = {37},
number = {4},
pages = {573--574},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btaa719},
doi = {10.1093/BIOINFORMATICS/BTAA719},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YinZLZSLWNSL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YinXZWSL21,
author = {Zekun Yin and
Xiaoming Xu and
Jinxiao Zhang and
Yanjie Wei and
Bertil Schmidt and
Weiguo Liu},
title = {RabbitMash: accelerating hash-based genome analysis on modern multi-core
architectures},
journal = {Bioinform.},
volume = {37},
number = {6},
pages = {873--875},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btaa754},
doi = {10.1093/BIOINFORMATICS/BTAA754},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YinXZWSL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KallenbornHS21,
author = {Felix Kallenborn and
Andreas Hildebrandt and
Bertil Schmidt},
title = {{CARE:} context-aware sequencing read error correction},
journal = {Bioinform.},
volume = {37},
number = {7},
pages = {889--895},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btaa738},
doi = {10.1093/BIOINFORMATICS/BTAA738},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KallenbornHS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hipc/WeissenbergerS21,
author = {Andr{\'{e}} Wei{\ss}enberger and
Bertil Schmidt},
title = {Accelerating {JPEG} Decompression on GPUs},
booktitle = {28th {IEEE} International Conference on High Performance Computing,
Data, and Analytics, HiPC 2021, Bengaluru, India, December 17-20,
2021},
pages = {121--130},
publisher = {{IEEE}},
year = {2021},
url = {https://doi.org/10.1109/HiPC53243.2021.00026},
doi = {10.1109/HIPC53243.2021.00026},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/hipc/WeissenbergerS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccS/CascittiNMS21,
author = {Julian Cascitti and
Stefan Niebler and
Andr{\'{e}} M{\"{u}}ller and
Bertil Schmidt},
editor = {Maciej Paszynski and
Dieter Kranzlm{\"{u}}ller and
Valeria V. Krzhizhanovskaya and
Jack J. Dongarra and
Peter M. A. Sloot},
title = {RNACache: Fast Mapping of RNA-Seq Reads to Transcriptomes Using MinHashing},
booktitle = {Computational Science - {ICCS} 2021 - 21st International Conference,
Krakow, Poland, June 16-18, 2021, Proceedings, Part {I}},
series = {Lecture Notes in Computer Science},
volume = {12742},
pages = {367--381},
publisher = {Springer},
year = {2021},
url = {https://doi.org/10.1007/978-3-030-77961-0\_31},
doi = {10.1007/978-3-030-77961-0\_31},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iccS/CascittiNMS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icpp/KobusMJ0S21,
author = {Robin Kobus and
Andr{\'{e}} M{\"{u}}ller and
Daniel J{\"{u}}nger and
Christian Hundt and
Bertil Schmidt},
editor = {Xian{-}He Sun and
Sameer Shende and
Laxmikant V. Kal{\'{e}} and
Yong Chen},
title = {MetaCache-GPU: Ultra-Fast Metagenomic Classification},
booktitle = {{ICPP} 2021: 50th International Conference on Parallel Processing,
Lemont, IL, USA, August 9 - 12, 2021},
pages = {25:1--25:11},
publisher = {{ACM}},
year = {2021},
url = {https://doi.org/10.1145/3472456.3472460},
doi = {10.1145/3472456.3472460},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icpp/KobusMJ0S21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2106-08150,
author = {Robin Kobus and
Andr{\'{e}} M{\"{u}}ller and
Daniel J{\"{u}}nger and
Christian Hundt and
Bertil Schmidt},
title = {MetaCache-GPU: Ultra-Fast Metagenomic Classification},
journal = {CoRR},
volume = {abs/2106.08150},
year = {2021},
url = {https://arxiv.org/abs/2106.08150},
eprinttype = {arXiv},
eprint = {2106.08150},
timestamp = {Thu, 01 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2106-08150.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2111-09219,
author = {Andr{\'{e}} Wei{\ss}enberger and
Bertil Schmidt},
title = {Accelerating {JPEG} Decompression on GPUs},
journal = {CoRR},
volume = {abs/2111.09219},
year = {2021},
url = {https://arxiv.org/abs/2111.09219},
eprinttype = {arXiv},
eprint = {2111.09219},
timestamp = {Mon, 22 Nov 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2111-09219.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KobusAMHPPHHS20,
author = {Robin Kobus and
Jos{\'{e}} Manuel Abu{\'{\i}}n and
Andr{\'{e}} M{\"{u}}ller and
S{\"{o}}ren Lukas Hellmann and
Juan Carlos Pichel and
Tom{\'{a}}s F. Pena and
Andreas Hildebrandt and
Thomas Hankeln and
Bertil Schmidt},
title = {A big data approach to metagenomics for all-food-sequencing},
journal = {{BMC} Bioinform.},
volume = {21},
number = {1},
pages = {102},
year = {2020},
url = {https://doi.org/10.1186/s12859-020-3429-6},
doi = {10.1186/S12859-020-3429-6},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KobusAMHPPHHS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NieblerMHS20,
author = {Stefan Niebler and
Andr{\'{e}} M{\"{u}}ller and
Thomas Hankeln and
Bertil Schmidt},
title = {RainDrop: Rapid activation matrix computation for droplet-based single-cell
RNA-seq reads},
journal = {{BMC} Bioinform.},
volume = {21},
number = {1},
pages = {274},
year = {2020},
url = {https://doi.org/10.1186/s12859-020-03593-4},
doi = {10.1186/S12859-020-03593-4},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/NieblerMHS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tpds/LanMHSDWLQF20,
author = {Haidong Lan and
Jintao Meng and
Christian Hundt and
Bertil Schmidt and
Minwen Deng and
Xiaoning Wang and
Weiguo Liu and
Yu Qiao and
Shengzhong Feng},
title = {FeatherCNN: Fast Inference Computation with TensorGEMM on {ARM} Architectures},
journal = {{IEEE} Trans. Parallel Distributed Syst.},
volume = {31},
number = {3},
pages = {580--594},
year = {2020},
url = {https://doi.org/10.1109/TPDS.2019.2939785},
doi = {10.1109/TPDS.2019.2939785},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tpds/LanMHSDWLQF20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tpds/GaoDZZSZSZGXFLY20,
author = {Ping Gao and
Xiaohui Duan and
Tingjian Zhang and
Meng Zhang and
Bertil Schmidt and
Xun Zhang and
Hongliang Sun and
Wusheng Zhang and
Lin Gan and
Wei Xue and
Haohuan Fu and
Weiguo Liu and
Guangwen Yang},
title = {Millimeter-Scale and Billion-Atom Reactive Force Field Simulation
on Sunway Taihulight},
journal = {{IEEE} Trans. Parallel Distributed Syst.},
volume = {31},
number = {12},
pages = {2954--2967},
year = {2020},
url = {https://doi.org/10.1109/TPDS.2020.3008499},
doi = {10.1109/TPDS.2020.3008499},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tpds/GaoDZZSZSZGXFLY20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/europar/Schmidt020,
author = {Bertil Schmidt and
Christian Hundt},
editor = {Maciej Malawski and
Krzysztof Rzadca},
title = {cuDTW++: Ultra-Fast Dynamic Time Warping on CUDA-Enabled GPUs},
booktitle = {Euro-Par 2020: Parallel Processing - 26th International Conference
on Parallel and Distributed Computing, Warsaw, Poland, August 24-28,
2020, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12247},
pages = {597--612},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-3-030-57675-2\_37},
doi = {10.1007/978-3-030-57675-2\_37},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/europar/Schmidt020.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hipc/JungerKM0XLS20,
author = {Daniel J{\"{u}}nger and
Robin Kobus and
Andr{\'{e}} M{\"{u}}ller and
Christian Hundt and
Kai Xu and
Weiguo Liu and
Bertil Schmidt},
title = {WarpCore: {A} Library for fast Hash Tables on GPUs},
booktitle = {27th {IEEE} International Conference on High Performance Computing,
Data, and Analytics, HiPC 2020, Pune, India, December 16-19, 2020},
pages = {11--20},
publisher = {{IEEE}},
year = {2020},
url = {https://doi.org/10.1109/HiPC50609.2020.00015},
doi = {10.1109/HIPC50609.2020.00015},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/hipc/JungerKM0XLS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccS/HieronymusSB20,
author = {Maicon Hieronymus and
Bertil Schmidt and
Sebastian B{\"{o}}ser},
editor = {Valeria V. Krzhizhanovskaya and
G{\'{a}}bor Z{\'{a}}vodszky and
Michael Harold Lees and
Jack J. Dongarra and
Peter M. A. Sloot and
S{\'{e}}rgio Brissos and
Jo{\~{a}}o Teixeira},
title = {Reconstruction of Low Energy Neutrino Events with GPUs at IceCube},
booktitle = {Computational Science - {ICCS} 2020 - 20th International Conference,
Amsterdam, The Netherlands, June 3-5, 2020, Proceedings, Part {I}},
series = {Lecture Notes in Computer Science},
volume = {12137},
pages = {118--131},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-3-030-50371-0\_9},
doi = {10.1007/978-3-030-50371-0\_9},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iccS/HieronymusSB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icpp/XuDMLSL20,
author = {Kai Xu and
Xiaohui Duan and
Xiangxu Meng and
Xin Li and
Bertil Schmidt and
Weiguo Liu},
editor = {Jos{\'{e}} Nelson Amaral and
Lizy Kurian John and
Xipeng Shen},
title = {SWMapper: Scalable Read Mapper on SunWay TaihuLight},
booktitle = {{ICPP} 2020: 49th International Conference on Parallel Processing,
Edmonton, AB, Canada, August 17-20, 2020},
pages = {28:1--28:10},
publisher = {{ACM}},
year = {2020},
url = {https://doi.org/10.1145/3404397.3404445},
doi = {10.1145/3404397.3404445},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icpp/XuDMLSL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/MullerS0MLKH20,
author = {Andr{\'{e}} M{\"{u}}ller and
Bertil Schmidt and
Andreas Hildebrandt and
Richard Membarth and
Roland Lei{\ss}a and
Matthis Kruse and
Sebastian Hack},
title = {AnySeq: {A} High Performance Sequence Alignment Library based on Partial
Evaluation},
booktitle = {2020 {IEEE} International Parallel and Distributed Processing Symposium
(IPDPS), New Orleans, LA, USA, May 18-22, 2020},
pages = {1030--1040},
publisher = {{IEEE}},
year = {2020},
url = {https://doi.org/10.1109/IPDPS47924.2020.00109},
doi = {10.1109/IPDPS47924.2020.00109},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ipps/MullerS0MLKH20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ppopp/Duan0ZZMLSFGXYL20,
author = {Xiaohui Duan and
Ping Gao and
Meng Zhang and
Tingjian Zhang and
Hongsong Meng and
Yuxuan Li and
Bertil Schmidt and
Haohuan Fu and
Lin Gan and
Wei Xue and
Guangwen Yang and
Weiguo Liu},
editor = {Rajiv Gupta and
Xipeng Shen},
title = {Neighbor-list-free molecular dynamics on sunway TaihuLight supercomputer},
booktitle = {PPoPP '20: 25th {ACM} {SIGPLAN} Symposium on Principles and Practice
of Parallel Programming, San Diego, California, USA, February 22-26,
2020},
pages = {413--414},
publisher = {{ACM}},
year = {2020},
url = {https://doi.org/10.1145/3332466.3374532},
doi = {10.1145/3332466.3374532},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ppopp/Duan0ZZMLSFGXYL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sc/Duan0ZZMLSFGXLY20,
author = {Xiaohui Duan and
Ping Gao and
Meng Zhang and
Tingjian Zhang and
Hongsong Meng and
Yuxuan Li and
Bertil Schmidt and
Haohuan Fu and
Lin Gan and
Wei Xue and
Weiguo Liu and
Guangwen Yang},
editor = {Christine Cuicchi and
Irene Qualters and
William T. Kramer},
title = {Cell-list based molecular dynamics on many-core processors: a case
study on sunway TaihuLight supercomputer},
booktitle = {Proceedings of the International Conference for High Performance Computing,
Networking, Storage and Analysis, {SC} 2020, Virtual Event / Atlanta,
Georgia, USA, November 9-19, 2020},
pages = {22},
publisher = {{IEEE/ACM}},
year = {2020},
url = {https://doi.org/10.1109/SC41405.2020.00026},
doi = {10.1109/SC41405.2020.00026},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/sc/Duan0ZZMLSFGXLY20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2002-04561,
author = {Andr{\'{e}} M{\"{u}}ller and
Bertil Schmidt and
Andreas Hildebrandt and
Richard Membarth and
Roland Lei{\ss}a and
Matthis Kruse and
Sebastian Hack},
title = {AnySeq: {A} High Performance Sequence Alignment Library based on Partial
Evaluation},
journal = {CoRR},
volume = {abs/2002.04561},
year = {2020},
url = {https://arxiv.org/abs/2002.04561},
eprinttype = {arXiv},
eprint = {2002.04561},
timestamp = {Wed, 12 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2002-04561.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2009-07914,
author = {Daniel J{\"{u}}nger and
Robin Kobus and
Andr{\'{e}} M{\"{u}}ller and
Christian Hundt and
Kai Xu and
Weiguo Liu and
Bertil Schmidt},
title = {WarpCore: {A} Library for fast Hash Tables on GPUs},
journal = {CoRR},
volume = {abs/2009.07914},
year = {2020},
url = {https://arxiv.org/abs/2009.07914},
eprinttype = {arXiv},
eprint = {2009.07914},
timestamp = {Wed, 23 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2009-07914.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangLCSSL19,
author = {Jikai Zhang and
Haidong Lan and
Yuandong Chan and
Yuan Shang and
Bertil Schmidt and
Weiguo Liu},
title = {{BGSA:} a bit-parallel global sequence alignment toolkit for multi-core
and many-core architectures},
journal = {Bioinform.},
volume = {35},
number = {13},
pages = {2306--2308},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty930},
doi = {10.1093/BIOINFORMATICS/BTY930},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangLCSSL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JiangLWDSTCWZ19,
author = {Peng Jiang and
Jie Luo and
Yiqi Wang and
Pingji Deng and
Bertil Schmidt and
Xiangjun Tang and
Ningjiang Chen and
Limsoon Wong and
Liang Zhao},
title = {kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers},
journal = {Bioinform.},
volume = {35},
number = {23},
pages = {4871--4878},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/btz299},
doi = {10.1093/BIOINFORMATICS/BTZ299},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/JiangLWDSTCWZ19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cphysics/KallenbornHBS19,
author = {Felix Kallenborn and
Christian Hundt and
Sebastian B{\"{o}}ser and
Bertil Schmidt},
title = {Massively parallel computation of atmospheric neutrino oscillations
on CUDA-enabled accelerators},
journal = {Comput. Phys. Commun.},
volume = {234},
pages = {235--244},
year = {2019},
url = {https://doi.org/10.1016/j.cpc.2018.07.022},
doi = {10.1016/J.CPC.2018.07.022},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cphysics/KallenbornHBS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hpcc/YinZMLWSL19,
author = {Zekun Yin and
Tianyu Zhang and
Andr{\'{e}} M{\"{u}}ller and
Hui Liu and
Yanjie Wei and
Bertil Schmidt and
Weiguo Liu},
editor = {Zheng Xiao and
Laurence T. Yang and
Pavan Balaji and
Tao Li and
Keqin Li and
Albert Y. Zomaya},
title = {Efficient Parallel Sort on AVX-512-Based Multi-Core and Many-Core
Architectures},
booktitle = {21st {IEEE} International Conference on High Performance Computing
and Communications; 17th {IEEE} International Conference on Smart
City; 5th {IEEE} International Conference on Data Science and Systems,
HPCC/SmartCity/DSS 2019, Zhangjiajie, China, August 10-12, 2019},
pages = {168--176},
publisher = {{IEEE}},
year = {2019},
url = {https://doi.org/10.1109/HPCC/SmartCity/DSS.2019.00038},
doi = {10.1109/HPCC/SMARTCITY/DSS.2019.00038},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/hpcc/YinZMLWSL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hpcc/YinZXCPLSL19,
author = {Zekun Yin and
Hao Zhang and
Kai Xu and
Yuandong Chan and
Shaoliang Peng and
Xiaoning Wang and
Bertil Schmidt and
Weiguo Liu},
editor = {Zheng Xiao and
Laurence T. Yang and
Pavan Balaji and
Tao Li and
Keqin Li and
Albert Y. Zomaya},
title = {{XLCS:} {A} New Bit-Parallel Longest Common Subsequence Algorithm
on Xeon Phi Clusters},
booktitle = {21st {IEEE} International Conference on High Performance Computing
and Communications; 17th {IEEE} International Conference on Smart
City; 5th {IEEE} International Conference on Data Science and Systems,
HPCC/SmartCity/DSS 2019, Zhangjiajie, China, August 10-12, 2019},
pages = {1477--1483},
publisher = {{IEEE}},
year = {2019},
url = {https://doi.org/10.1109/HPCC/SmartCity/DSS.2019.00204},
doi = {10.1109/HPCC/SMARTCITY/DSS.2019.00204},
timestamp = {Wed, 09 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/hpcc/YinZXCPLSL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hpdc/BurenJK0S19,
author = {Florian B{\"{u}}ren and
Daniel J{\"{u}}nger and
Robin Kobus and
Christian Hundt and
Bertil Schmidt},
editor = {Jon B. Weissman and
Ali Raza Butt and
Evgenia Smirni},
title = {Suffix Array Construction on Multi-GPU Systems},
booktitle = {Proceedings of the 28th International Symposium on High-Performance
Parallel and Distributed Computing, {HPDC} 2019, Phoenix, AZ, USA,
June 22-29, 2019},
pages = {183--194},
publisher = {{ACM}},
year = {2019},
url = {https://doi.org/10.1145/3307681.3325961},
doi = {10.1145/3307681.3325961},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/hpdc/BurenJK0S19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icpp/KobusJ0S19,
author = {Robin Kobus and
Daniel J{\"{u}}nger and
Christian Hundt and
Bertil Schmidt},
title = {Gossip: Efficient Communication Primitives for Multi-GPU Systems},
booktitle = {Proceedings of the 48th International Conference on Parallel Processing,
{ICPP} 2019, Kyoto, Japan, August 05-08, 2019},
pages = {63:1--63:10},
publisher = {{ACM}},
year = {2019},
url = {https://doi.org/10.1145/3337821.3337889},
doi = {10.1145/3337821.3337889},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icpp/KobusJ0S19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icpp/WeissenbergerS19,
author = {Andr{\'{e}} Wei{\ss}enberger and
Bertil Schmidt},
title = {Massively Parallel {ANS} Decoding on GPUs},
booktitle = {Proceedings of the 48th International Conference on Parallel Processing,
{ICPP} 2019, Kyoto, Japan, August 05-08, 2019},
pages = {100:1--100:10},
publisher = {{ACM}},
year = {2019},
url = {https://doi.org/10.1145/3337821.3337888},
doi = {10.1145/3337821.3337888},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icpp/WeissenbergerS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/bioinf/Schmidt019,
author = {Bertil Schmidt and
Andreas Hildebrandt},
editor = {Shoba Ranganathan and
Michael Gribskov and
Kenta Nakai and
Christian Sch{\"{o}}nbach},
title = {Dedicated Bioinformatics Analysis Hardware},
booktitle = {Encyclopedia of Bioinformatics and Computational Biology - Volume
2},
pages = {1142--1150},
publisher = {Elsevier},
year = {2019},
url = {https://doi.org/10.1016/b978-0-12-809633-8.20186-6},
doi = {10.1016/B978-0-12-809633-8.20186-6},
timestamp = {Thu, 05 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/reference/bioinf/Schmidt019.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangCFSL18,
author = {Haowen Zhang and
Yuandong Chan and
Kaichao Fan and
Bertil Schmidt and
Weiguo Liu},
title = {Fast and efficient short read mapping based on a succinct hash index},
journal = {{BMC} Bioinform.},
volume = {19},
number = {1},
pages = {92:1--92:14},
year = {2018},
url = {https://doi.org/10.1186/s12859-018-2094-5},
doi = {10.1186/S12859-018-2094-5},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangCFSL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jocs/Gonzalez-Dominguez18,
author = {Jorge Gonz{\'{a}}lez{-}Dom{\'{\i}}nguez and
Christian Hundt and
Bertil Schmidt},
title = {parSRA: {A} framework for the parallel execution of short read aligners
on compute clusters},
journal = {J. Comput. Sci.},
volume = {25},
pages = {134--139},
year = {2018},
url = {https://doi.org/10.1016/j.jocs.2017.01.008},
doi = {10.1016/J.JOCS.2017.01.008},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jocs/Gonzalez-Dominguez18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pacmpl/LeissaBHPMSMS18,
author = {Roland Lei{\ss}a and
Klaas Boesche and
Sebastian Hack and
Ars{\`{e}}ne P{\'{e}}rard{-}Gayot and
Richard Membarth and
Philipp Slusallek and
Andr{\'{e}} M{\"{u}}ller and
Bertil Schmidt},
title = {AnyDSL: a partial evaluation framework for programming high-performance
libraries},
journal = {Proc. {ACM} Program. Lang.},
volume = {2},
number = {{OOPSLA}},
pages = {119:1--119:30},
year = {2018},
url = {https://doi.org/10.1145/3276489},
doi = {10.1145/3276489},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/pacmpl/LeissaBHPMSMS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/vlsisp/LiuS18,
author = {Yongchao Liu and
Bertil Schmidt},
title = {LightSpMV: Faster CUDA-Compatible Sparse Matrix-Vector Multiplication
Using Compressed Sparse Rows},
journal = {J. Signal Process. Syst.},
volume = {90},
number = {1},
pages = {69--86},
year = {2018},
url = {https://doi.org/10.1007/s11265-016-1216-4},
doi = {10.1007/S11265-016-1216-4},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/vlsisp/LiuS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icpads/KobusLMHKS18,
author = {Robin Kobus and
Adrian Lamoth and
Andr{\'{e}} M{\"{u}}ller and
Christian Hundt and
Stefan Kramer and
Bertil Schmidt},
title = {cuBool: Bit-Parallel Boolean Matrix Factorization on CUDA-Enabled
Accelerators},
booktitle = {24th {IEEE} International Conference on Parallel and Distributed Systems,
{ICPADS} 2018, Singapore, December 11-13, 2018},
pages = {465--472},
publisher = {{IEEE}},
year = {2018},
url = {https://doi.org/10.1109/PADSW.2018.8644574},
doi = {10.1109/PADSW.2018.8644574},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icpads/KobusLMHKS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icpp/WeissenbergerS18,
author = {Andr{\'{e}} Wei{\ss}enberger and
Bertil Schmidt},
title = {Massively Parallel Huffman Decoding on GPUs},
booktitle = {Proceedings of the 47th International Conference on Parallel Processing,
{ICPP} 2018, Eugene, OR, USA, August 13-16, 2018},
pages = {27:1--27:10},
publisher = {{ACM}},
year = {2018},
url = {https://doi.org/10.1145/3225058.3225076},
doi = {10.1145/3225058.3225076},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icpp/WeissenbergerS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icpp/XuKCGMWSL18,
author = {Kai Xu and
Robin Kobus and
Yuandong Chan and
Ping Gao and
Xiangxu Meng and
Yanjie Wei and
Bertil Schmidt and
Weiguo Liu},
title = {{SPECTR:} Scalable Parallel Short Read Error Correction on Multi-core
and Many-core Architectures},
booktitle = {Proceedings of the 47th International Conference on Parallel Processing,
{ICPP} 2018, Eugene, OR, USA, August 13-16, 2018},
pages = {39:1--39:10},
publisher = {{ACM}},
year = {2018},
url = {https://doi.org/10.1145/3225058.3225060},
doi = {10.1145/3225058.3225060},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icpp/XuKCGMWSL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/Junger0S18,
author = {Daniel J{\"{u}}nger and
Christian Hundt and
Bertil Schmidt},
title = {WarpDrive: Massively Parallel Hashing on Multi-GPU Nodes},
booktitle = {2018 {IEEE} International Parallel and Distributed Processing Symposium,
{IPDPS} 2018, Vancouver, BC, Canada, May 21-25, 2018},
pages = {441--450},
publisher = {{IEEE} Computer Society},
year = {2018},
url = {https://doi.org/10.1109/IPDPS.2018.00054},
doi = {10.1109/IPDPS.2018.00054},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ipps/Junger0S18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuRKSHWKSH17,
author = {Yongchao Liu and
Fabian Ripp and
Rene Koeppel and
Hanno Schmidt and
S{\"{o}}ren Lukas Hellmann and
Mathias Weber and
Christopher Felix Krombholz and
Bertil Schmidt and
Thomas Hankeln},
title = {{AFS:} identification and quantification of species composition by
metagenomic sequencing},
journal = {Bioinform.},
volume = {33},
number = {9},
pages = {1396--1398},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btw822},
doi = {10.1093/BIOINFORMATICS/BTW822},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuRKSHWKSH17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MullerHHHS17,
author = {Andr{\'{e}} M{\"{u}}ller and
Christian Hundt and
Andreas Hildebrandt and
Thomas Hankeln and
Bertil Schmidt},
title = {MetaCache: context-aware classification of metagenomic reads using
minhashing},
journal = {Bioinform.},
volume = {33},
number = {23},
pages = {3740--3748},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx520},
doi = {10.1093/BIOINFORMATICS/BTX520},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MullerHHHS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KobusHMS17,
author = {Robin Kobus and
Christian Hundt and
Andr{\'{e}} M{\"{u}}ller and
Bertil Schmidt},
title = {Accelerating metagenomic read classification on CUDA-enabled GPUs},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {11:1--11:10},
year = {2017},
url = {https://doi.org/10.1186/s12859-016-1434-6},
doi = {10.1186/S12859-016-1434-6},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KobusHMS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SchroderWSP17,
author = {Jan Schr{\"{o}}der and
Adrianto Wirawan and
Bertil Schmidt and
Anthony T. Papenfuss},
title = {{CLOVE:} classification of genomic fusions into structural variation
events},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {346},
year = {2017},
url = {https://doi.org/10.1186/s12859-017-1760-3},
doi = {10.1186/S12859-017-1760-3},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SchroderWSP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cluster/JungerHGS17,
author = {Daniel J{\"{u}}nger and
Christian Hundt and
Jorge Gonz{\'{a}}lez{-}Dom{\'{\i}}nguez and
Bertil Schmidt},
title = {Speed and accuracy improvement of higher-order epistasis detection
on CUDA-enabled GPUs},
journal = {Clust. Comput.},
volume = {20},
number = {3},
pages = {1899--1908},
year = {2017},
url = {https://doi.org/10.1007/s10586-017-0938-9},
doi = {10.1007/S10586-017-0938-9},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cluster/JungerHGS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jpdc/HundtSS17,
author = {Christian Hundt and
Moritz Schlarb and
Bertil Schmidt},
title = {{SAUCE:} {A} web application for interactive teaching and learning
of parallel programming},
journal = {J. Parallel Distributed Comput.},
volume = {105},
pages = {163--173},
year = {2017},
url = {https://doi.org/10.1016/j.jpdc.2016.12.028},
doi = {10.1016/J.JPDC.2016.12.028},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jpdc/HundtSS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tjs/ZhangWPSL17,
author = {Shuai Zhang and
Zhao Wang and
Ying Peng and
Bertil Schmidt and
Weiguo Liu},
title = {Mapping of option pricing algorithms onto heterogeneous many-core
architectures},
journal = {J. Supercomput.},
volume = {73},
number = {9},
pages = {3715--3737},
year = {2017},
url = {https://doi.org/10.1007/s11227-017-1968-z},
doi = {10.1007/S11227-017-1968-Z},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tjs/ZhangWPSL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ccgrid/PengZYSZDLLLSZL17,
author = {Shaoliang Peng and
Xiaoyu Zhang and
Shunyun Yang and
Wenhe Su and
Zhiqiang Zhang and
Dong Dong and
Kai Lu and
Yutong Lu and
Xiangke Liao and
Bertil Schmidt and
Weiliang Zhu and
Kuan{-}Ching Li},
title = {mD3DOCKxb: An Ultra-Scalable {CPU-MIC} Coordinated Virtual Screening
Framework},
booktitle = {Proceedings of the 17th {IEEE/ACM} International Symposium on Cluster,
Cloud and Grid Computing, {CCGRID} 2017, Madrid, Spain, May 14-17,
2017},
pages = {671--676},
publisher = {{IEEE} Computer Society / {ACM}},
year = {2017},
url = {https://doi.org/10.1109/CCGRID.2017.131},
doi = {10.1109/CCGRID.2017.131},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ccgrid/PengZYSZDLLLSZL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cluster/DuanXC0SBL17,
author = {Xiaohui Duan and
Kai Xu and
Yuandong Chan and
Christian Hundt and
Bertil Schmidt and
Pavan Balaji and
Weiguo Liu},
title = {S-Aligner: Ultrascalable Read Mapping on Sunway Taihu Light},
booktitle = {2017 {IEEE} International Conference on Cluster Computing, {CLUSTER}
2017, Honolulu, HI, USA, September 5-8, 2017},
pages = {36--46},
publisher = {{IEEE} Computer Society},
year = {2017},
url = {https://doi.org/10.1109/CLUSTER.2017.16},
doi = {10.1109/CLUSTER.2017.16},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cluster/DuanXC0SBL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/LanLLS17,
author = {Haidong Lan and
Weiguo Liu and
Yongchao Liu and
Bertil Schmidt},
title = {SWhybrid: {A} Hybrid-Parallel Framework for Large-Scale Protein Sequence
Database Search},
booktitle = {2017 {IEEE} International Parallel and Distributed Processing Symposium,
{IPDPS} 2017, Orlando, FL, USA, May 29 - June 2, 2017},
pages = {42--51},
publisher = {{IEEE} Computer Society},
year = {2017},
url = {https://doi.org/10.1109/IPDPS.2017.42},
doi = {10.1109/IPDPS.2017.42},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ipps/LanLLS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/ChanXLLLS17,
author = {Yuandong Chan and
Kai Xu and
Haidong Lan and
Weiguo Liu and
Yongchao Liu and
Bertil Schmidt},
title = {{PUNAS:} {A} Parallel Ungapped-Alignment-Featured Seed Verification
Algorithm for Next-Generation Sequencing Read Alignment},
booktitle = {2017 {IEEE} International Parallel and Distributed Processing Symposium,
{IPDPS} 2017, Orlando, FL, USA, May 29 - June 2, 2017},
pages = {52--61},
publisher = {{IEEE} Computer Society},
year = {2017},
url = {https://doi.org/10.1109/IPDPS.2017.35},
doi = {10.1109/IPDPS.2017.35},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ipps/ChanXLLLS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/sp/17/LiuS17,
author = {Yongchao Liu and
Bertil Schmidt},
editor = {Mourad Elloumi},
title = {{CUSHAW} Suite: Parallel and Efficient Algorithms for {NGS} Read Alignment},
booktitle = {Algorithms for Next-Generation Sequencing Data, Techniques, Approaches,
and Applications},
pages = {203--233},
publisher = {Springer},
year = {2017},
url = {https://doi.org/10.1007/978-3-319-59826-0\_10},
doi = {10.1007/978-3-319-59826-0\_10},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/books/sp/17/LiuS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/Winther0SCBWV17,
author = {Hinrich B. Winther and
Christian Hundt and
Bertil Schmidt and
Christoph Czerner and
Johann Bauersachs and
Frank K. Wacker and
Jens Vogel{-}Claussen},
title = {{\textdollar}{\(\nu\)}{\textdollar}-net: Deep Learning for Generalized
Biventricular Cardiac Mass and Function Parameters},
journal = {CoRR},
volume = {abs/1706.04397},
year = {2017},
url = {http://arxiv.org/abs/1706.04397},
eprinttype = {arXiv},
eprint = {1706.04397},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/Winther0SCBWV17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Gonzalez-Dominguez16,
author = {Jorge Gonz{\'{a}}lez{-}Dom{\'{\i}}nguez and
Bertil Schmidt},
title = {ParDRe: faster parallel duplicated reads removal tool for sequencing
studies},
journal = {Bioinform.},
volume = {32},
number = {10},
pages = {1562--1564},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw038},
doi = {10.1093/BIOINFORMATICS/BTW038},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Gonzalez-Dominguez16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Gonzalez-Dominguez16a,
author = {Jorge Gonz{\'{a}}lez{-}Dom{\'{\i}}nguez and
Yongchao Liu and
Juan Touri{\~{n}}o and
Bertil Schmidt},
title = {MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory
systems},
journal = {Bioinform.},
volume = {32},
number = {24},
pages = {3826--3828},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw558},
doi = {10.1093/BIOINFORMATICS/BTW558},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Gonzalez-Dominguez16a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LanCXSPL16,
author = {Haidong Lan and
Yuandong Chan and
Kai Xu and
Bertil Schmidt and
Shaoliang Peng and
Weiguo Liu},
title = {Parallel algorithms for large-scale biological sequence alignment
on Xeon-Phi based clusters},
journal = {{BMC} Bioinform.},
volume = {17},
number = {{S-9}},
pages = {267},
year = {2016},
url = {https://doi.org/10.1186/s12859-016-1128-0},
doi = {10.1186/S12859-016-1128-0},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LanCXSPL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HundtHS16,
author = {Christian Hundt and
Andreas Hildebrandt and
Bertil Schmidt},
title = {rapidGSEA: Speeding up gene set enrichment analysis on multi-core
CPUs and CUDA-enabled GPUs},
journal = {{BMC} Bioinform.},
volume = {17},
pages = {394},
year = {2016},
url = {https://doi.org/10.1186/s12859-016-1244-x},
doi = {10.1186/S12859-016-1244-X},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HundtHS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/LiuLAS16,
author = {Yongchao Liu and
Martin Loewer and
Srinivas Aluru and
Bertil Schmidt},
title = {SNVSniffer: an integrated caller for germline and somatic single-nucleotide
and indel mutations},
journal = {{BMC} Syst. Biol.},
volume = {10},
number = {{S-2}},
pages = {47},
year = {2016},
url = {https://doi.org/10.1186/s12918-016-0300-5},
doi = {10.1186/S12918-016-0300-5},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/LiuLAS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijhpca/DangSHTH16,
author = {Hoang{-}Vu Dang and
Bertil Schmidt and
Andreas Hildebrandt and
Tuan Tu Tran and
Anna Katharina Hildebrandt},
title = {CUDA-enabled hierarchical ward clustering of protein structures based
on the nearest neighbour chain algorithm},
journal = {Int. J. High Perform. Comput. Appl.},
volume = {30},
number = {2},
pages = {200--211},
year = {2016},
url = {https://doi.org/10.1177/1094342015597988},
doi = {10.1177/1094342015597988},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijhpca/DangSHTH16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pc/TranLS16,
author = {Tuan Tu Tran and
Yongchao Liu and
Bertil Schmidt},
title = {Bit-parallel approximate pattern matching: Kepler {GPU} versus Xeon
Phi},
journal = {Parallel Comput.},
volume = {54},
pages = {128--138},
year = {2016},
url = {https://doi.org/10.1016/j.parco.2015.11.001},
doi = {10.1016/J.PARCO.2015.11.001},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/pc/TranLS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/LiuHS16,
author = {Yongchao Liu and
Thomas Hankeln and
Bertil Schmidt},
title = {Parallel and Space-Efficient Construction of Burrows-Wheeler Transform
and Suffix Array for Big Genome Data},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {13},
number = {3},
pages = {592--598},
year = {2016},
url = {https://doi.org/10.1109/TCBB.2015.2430314},
doi = {10.1109/TCBB.2015.2430314},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/LiuHS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tkdd/ShaoYDS016,
author = {Junming Shao and
Qinli Yang and
Hoang{-}Vu Dang and
Bertil Schmidt and
Stefan Kramer},
title = {Scalable Clustering by Iterative Partitioning and Point Attractor
Representation},
journal = {{ACM} Trans. Knowl. Discov. Data},
volume = {11},
number = {1},
pages = {5:1--5:23},
year = {2016},
url = {https://doi.org/10.1145/2934688},
doi = {10.1145/2934688},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tkdd/ShaoYDS016.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tpds/Gonzalez-Dominguez16,
author = {Jorge Gonz{\'{a}}lez{-}Dom{\'{\i}}nguez and
Sabela Ramos and
Juan Touri{\~{n}}o and
Bertil Schmidt},
title = {Parallel Pairwise Epistasis Detection on Heterogeneous Computing Architectures},
journal = {{IEEE} Trans. Parallel Distributed Syst.},
volume = {27},
number = {8},
pages = {2329--2340},
year = {2016},
url = {https://doi.org/10.1109/TPDS.2015.2460247},
doi = {10.1109/TPDS.2015.2460247},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tpds/Gonzalez-Dominguez16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/asap/KassensWSGS16,
author = {Jan Christian K{\"{a}}ssens and
Lars Wienbrandt and
Manfred Schimmler and
Jorge Gonz{\'{a}}lez{-}Dom{\'{\i}}nguez and
Bertil Schmidt},
title = {Combining {GPU} and {FPGA} technology for efficient exhaustive interaction
analysis in {GWAS}},
booktitle = {27th {IEEE} International Conference on Application-specific Systems,
Architectures and Processors, {ASAP} 2016, London, United Kingdom,
July 6-8, 2016},
pages = {170--175},
publisher = {{IEEE} Computer Society},
year = {2016},
url = {https://doi.org/10.1109/ASAP.2016.7760788},
doi = {10.1109/ASAP.2016.7760788},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/asap/KassensWSGS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/europar/Junger0GS16,
author = {Daniel J{\"{u}}nger and
Christian Hundt and
Jorge Gonz{\'{a}}lez{-}Dom{\'{\i}}nguez and
Bertil Schmidt},
editor = {Fr{\'{e}}d{\'{e}}ric Desprez and
Pierre{-}Fran{\c{c}}ois Dutot and
Christos Kaklamanis and
Loris Marchal and
Korbinian Molitorisz and
Laura Ricci and
Vittorio Scarano and
Miguel A. Vega{-}Rodr{\'{\i}}guez and
Ana Lucia Varbanescu and
Sascha Hunold and
Stephen L. Scott and
Stefan Lankes and
Josef Weidendorfer},
title = {Ultra-Fast Detection of Higher-Order Epistatic Interactions on GPUs},
booktitle = {Euro-Par 2016: Parallel Processing Workshops - Euro-Par 2016 International
Workshops, Grenoble, France, August 24-26, 2016, Revised Selected
Papers},
series = {Lecture Notes in Computer Science},
volume = {10104},
pages = {421--432},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-58943-5\_34},
doi = {10.1007/978-3-319-58943-5\_34},
timestamp = {Sun, 12 Nov 2023 02:07:45 +0100},
biburl = {https://dblp.org/rec/conf/europar/Junger0GS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/concurrency/LiuS15,
author = {Yongchao Liu and
Bertil Schmidt},
title = {{GSWABE:} faster GPU-accelerated sequence alignment with optimal alignment
retrieval for short {DNA} sequences},
journal = {Concurr. Comput. Pract. Exp.},
volume = {27},
number = {4},
pages = {958--972},
year = {2015},
url = {https://doi.org/10.1002/cpe.3371},
doi = {10.1002/CPE.3371},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/concurrency/LiuS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijhpca/Gonzalez-Dominguez15,
author = {Jorge Gonz{\'{a}}lez{-}Dom{\'{\i}}nguez and
Jan Christian K{\"{a}}ssens and
Lars Wienbrandt and
Bertil Schmidt},
title = {Large-scale genome-wide association studies on a {GPU} cluster using
a CUDA-accelerated {PGAS} programming model},
journal = {Int. J. High Perform. Comput. Appl.},
volume = {29},
number = {4},
pages = {506--510},
year = {2015},
url = {https://doi.org/10.1177/1094342015585846},
doi = {10.1177/1094342015585846},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijhpca/Gonzalez-Dominguez15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jocs/Gonzalez-Dominguez15,
author = {Jorge Gonz{\'{a}}lez{-}Dom{\'{\i}}nguez and
Bertil Schmidt},
title = {GPU-accelerated exhaustive search for third-order epistatic interactions
in case-control studies},
journal = {J. Comput. Sci.},
volume = {8},
pages = {93--100},
year = {2015},
url = {https://doi.org/10.1016/j.jocs.2015.04.001},
doi = {10.1016/J.JOCS.2015.04.001},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jocs/Gonzalez-Dominguez15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jocs/KassensWGSS15,
author = {Jan Christian K{\"{a}}ssens and
Lars Wienbrandt and
Jorge Gonz{\'{a}}lez{-}Dom{\'{\i}}nguez and
Bertil Schmidt and
Manfred Schimmler},
title = {High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs},
journal = {J. Comput. Sci.},
volume = {9},
pages = {131--136},
year = {2015},
url = {https://doi.org/10.1016/j.jocs.2015.04.030},
doi = {10.1016/J.JOCS.2015.04.030},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jocs/KassensWGSS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/PulidoSF15,
author = {Juan Antonio G{\'{o}}mez Pulido and
Bertil Schmidt and
Wu{-}chun Feng},
title = {Accelerating Bioinformatics Applications via Emerging Parallel Computing
Systems},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {12},
number = {5},
pages = {971--972},
year = {2015},
url = {https://doi.org/10.1109/TCBB.2015.2457736},
doi = {10.1109/TCBB.2015.2457736},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/PulidoSF15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/Gonzalez-Dominguez15,
author = {Jorge Gonz{\'{a}}lez{-}Dom{\'{\i}}nguez and
Lars Wienbrandt and
Jan Christian K{\"{a}}ssens and
David Ellinghaus and
Manfred Schimmler and
Bertil Schmidt},
title = {Parallelizing Epistasis Detection in {GWAS} on {FPGA} and GPU-Accelerated
Computing Systems},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {12},
number = {5},
pages = {982--994},
year = {2015},
url = {https://doi.org/10.1109/TCBB.2015.2389958},
doi = {10.1109/TCBB.2015.2389958},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/Gonzalez-Dominguez15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/NguyenSZK15,
author = {Thuy{-}Diem Nguyen and
Bertil Schmidt and
Zejun Zheng and
Chee{-}Keong Kwoh},
title = {Efficient and Accurate {OTU} Clustering with GPU-Based Sequence Alignment
and Dynamic Dendrogram Cutting},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {12},
number = {5},
pages = {1060--1073},
year = {2015},
url = {https://doi.org/10.1109/TCBB.2015.2407574},
doi = {10.1109/TCBB.2015.2407574},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/NguyenSZK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/asap/LiuS15,
author = {Yongchao Liu and
Bertil Schmidt},
title = {LightSpMV: Faster CSR-based sparse matrix-vector multiplication on
CUDA-enabled GPUs},
booktitle = {26th {IEEE} International Conference on Application-specific Systems,
Architectures and Processors, {ASAP} 2015, Toronto, ON, Canada, July
27-29, 2015},
pages = {82--89},
publisher = {{IEEE} Computer Society},
year = {2015},
url = {https://doi.org/10.1109/ASAP.2015.7245713},
doi = {10.1109/ASAP.2015.7245713},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/asap/LiuS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/LiuLAS15,
author = {Yongchao Liu and
Martin Loewer and
Srinivas Aluru and
Bertil Schmidt},
editor = {Jun Huan and
Satoru Miyano and
Amarda Shehu and
Xiaohua Tony Hu and
Bin Ma and
Sanguthevar Rajasekaran and
Vijay K. Gombar and
Matthieu{-}P. Schapranow and
Illhoi Yoo and
Jiayu Zhou and
Brian Chen and
Vinay Pai and
Brian G. Pierce},
title = {SNVSniffer: An integrated caller for germline and somatic SNVs based
on Bayesian models},
booktitle = {2015 {IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2015, Washington, DC, USA, November 9-12, 2015},
pages = {83--90},
publisher = {{IEEE} Computer Society},
year = {2015},
url = {https://doi.org/10.1109/BIBM.2015.7359659},
doi = {10.1109/BIBM.2015.7359659},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibm/LiuLAS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/LanLSW15,
author = {Haidong Lan and
Weiguo Liu and
Bertil Schmidt and
Bingqiang Wang},
editor = {Jun Huan and
Satoru Miyano and
Amarda Shehu and
Xiaohua Tony Hu and
Bin Ma and
Sanguthevar Rajasekaran and
Vijay K. Gombar and
Matthieu{-}P. Schapranow and
Illhoi Yoo and
Jiayu Zhou and
Brian Chen and
Vinay Pai and
Brian G. Pierce},
title = {Accelerating large-scale biological database search on Xeon Phi-based
neo-heterogeneous architectures},
booktitle = {2015 {IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2015, Washington, DC, USA, November 9-12, 2015},
pages = {503--510},
publisher = {{IEEE} Computer Society},
year = {2015},
url = {https://doi.org/10.1109/BIBM.2015.7359735},
doi = {10.1109/BIBM.2015.7359735},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bibm/LanLSW15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/europar/Schlarb0S15,
author = {Moritz Schlarb and
Christian Hundt and
Bertil Schmidt},
editor = {Sascha Hunold and
Alexandru Costan and
Domingo Gim{\'{e}}nez and
Alexandru Iosup and
Laura Ricci and
Mar{\'{\i}}a Engracia G{\'{o}}mez Requena and
Vittorio Scarano and
Ana Lucia Varbanescu and
Stephen L. Scott and
Stefan Lankes and
Josef Weidendorfer and
Michael Alexander},
title = {{SAUCE:} {A} Web-Based Automated Assessment Tool for Teaching Parallel
Programming},
booktitle = {Euro-Par 2015: Parallel Processing Workshops - Euro-Par 2015 International
Workshops, Vienna, Austria, August 24-25, 2015, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {9523},
pages = {54--65},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-319-27308-2\_5},
doi = {10.1007/978-3-319-27308-2\_5},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/europar/Schlarb0S15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WirawanHLSS14,
author = {Adrianto Wirawan and
Robert S. Harris and
Yongchao Liu and
Bertil Schmidt and
Jan Schr{\"{o}}der},
title = {{HECTOR:} a parallel multistage homopolymer spectrum based error corrector
for 454 sequencing data},
journal = {{BMC} Bioinform.},
volume = {15},
pages = {131},
year = {2014},
url = {https://doi.org/10.1186/1471-2105-15-131},
doi = {10.1186/1471-2105-15-131},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WirawanHLSS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dt/LiuS14,
author = {Yongchao Liu and
Bertil Schmidt},
title = {{CUSHAW2-GPU:} Empowering Faster Gapped Short-Read Alignment Using
{GPU} Computing},
journal = {{IEEE} Des. Test},
volume = {31},
number = {1},
pages = {31--39},
year = {2014},
url = {https://doi.org/10.1109/MDAT.2013.2284198},
doi = {10.1109/MDAT.2013.2284198},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dt/LiuS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/asap/LiuS14,
author = {Yongchao Liu and
Bertil Schmidt},
title = {{SWAPHI:} Smith-waterman protein database search on Xeon Phi coprocessors},
booktitle = {{IEEE} 25th International Conference on Application-Specific Systems,
Architectures and Processors, {ASAP} 2014, Zurich, Switzerland, June
18-20, 2014},
pages = {184--185},
publisher = {{IEEE} Computer Society},
year = {2014},
url = {https://doi.org/10.1109/ASAP.2014.6868657},
doi = {10.1109/ASAP.2014.6868657},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/asap/LiuS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/NguyenSK14,
author = {Thuy{-}Diem Nguyen and
Bertil Schmidt and
Chee{-}Keong Kwoh},
editor = {Pierre Baldi and
Wei Wang},
title = {Fast dendrogram-based {OTU} clustering using sequence embedding},
booktitle = {Proceedings of the 5th {ACM} Conference on Bioinformatics, Computational
Biology, and Health Informatics, {BCB} '14, Newport Beach, California,
USA, September 20-23, 2014},
pages = {63--72},
publisher = {{ACM}},
year = {2014},
url = {https://doi.org/10.1145/2649387.2649402},
doi = {10.1145/2649387.2649402},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bcb/NguyenSK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cluster/KassensGWS14,
author = {Jan Christian K{\"{a}}ssens and
Jorge Gonz{\'{a}}lez{-}Dom{\'{\i}}nguez and
Lars Wienbrandt and
Bertil Schmidt},
title = {{UPC++} for bioinformatics: {A} case study using genome-wide association
studies},
booktitle = {2014 {IEEE} International Conference on Cluster Computing, {CLUSTER}
2014, Madrid, Spain, September 22-26, 2014},
pages = {248--256},
publisher = {{IEEE} Computer Society},
year = {2014},
url = {https://doi.org/10.1109/CLUSTER.2014.6968770},
doi = {10.1109/CLUSTER.2014.6968770},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cluster/KassensGWS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cluster/LiuTLS14,
author = {Yongchao Liu and
Tuan Tu Tran and
Felix Lauenroth and
Bertil Schmidt},
title = {{SWAPHI-LS:} Smith-Waterman Algorithm on Xeon Phi coprocessors for
Long {DNA} Sequences},
booktitle = {2014 {IEEE} International Conference on Cluster Computing, {CLUSTER}
2014, Madrid, Spain, September 22-26, 2014},
pages = {257--265},
publisher = {{IEEE} Computer Society},
year = {2014},
url = {https://doi.org/10.1109/CLUSTER.2014.6968772},
doi = {10.1109/CLUSTER.2014.6968772},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cluster/LiuTLS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/europar/Gonzalez-DominguezSKW14,
author = {Jorge Gonz{\'{a}}lez{-}Dom{\'{\i}}nguez and
Bertil Schmidt and
Jan Christian K{\"{a}}ssens and
Lars Wienbrandt},
editor = {Fernando M. A. Silva and
In{\^{e}}s de Castro Dutra and
V{\'{\i}}tor Santos Costa},
title = {Hybrid {CPU/GPU} Acceleration of Detection of 2-SNP Epistatic Interactions
in {GWAS}},
booktitle = {Euro-Par 2014 Parallel Processing - 20th International Conference,
Porto, Portugal, August 25-29, 2014. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8632},
pages = {680--691},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-09873-9\_57},
doi = {10.1007/978-3-319-09873-9\_57},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/europar/Gonzalez-DominguezSKW14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccS/NguyenSK14,
author = {Thuy{-}Diem Nguyen and
Bertil Schmidt and
Chee Keong Kwoh},
editor = {David Abramson and
Michael Lees and
Valeria V. Krzhizhanovskaya and
Jack J. Dongarra and
Peter M. A. Sloot},
title = {SparseHC: {A} Memory-efficient Online Hierarchical Clustering Algorithm},
booktitle = {Proceedings of the International Conference on Computational Science,
{ICCS} 2014, Cairns, Queensland, Australia, 10-12 June, 2014},
series = {Procedia Computer Science},
volume = {29},
pages = {8--19},
publisher = {Elsevier},
year = {2014},
url = {https://doi.org/10.1016/j.procs.2014.05.001},
doi = {10.1016/J.PROCS.2014.05.001},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iccS/NguyenSK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccS/WienbrandtKGSES14,
author = {Lars Wienbrandt and
Jan Christian K{\"{a}}ssens and
Jorge Gonz{\'{a}}lez{-}Dom{\'{\i}}nguez and
Bertil Schmidt and
David Ellinghaus and
Manfred Schimmler},
editor = {David Abramson and
Michael Lees and
Valeria V. Krzhizhanovskaya and
Jack J. Dongarra and
Peter M. A. Sloot},
title = {FPGA-based Acceleration of Detecting Statistical Epistasis in {GWAS}},
booktitle = {Proceedings of the International Conference on Computational Science,
{ICCS} 2014, Cairns, Queensland, Australia, 10-12 June, 2014},
series = {Procedia Computer Science},
volume = {29},
pages = {220--230},
publisher = {Elsevier},
year = {2014},
url = {https://doi.org/10.1016/j.procs.2014.05.020},
doi = {10.1016/J.PROCS.2014.05.020},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iccS/WienbrandtKGSES14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icpp/HundtSS14,
author = {Christian Hundt and
Bertil Schmidt and
Elmar Sch{\"{o}}mer},
title = {CUDA-Accelerated Alignment of Subsequences in Streamed Time Series
Data},
booktitle = {43rd International Conference on Parallel Processing, {ICPP} 2014,
Minneapolis, MN, USA, September 9-12, 2014},
pages = {10--19},
publisher = {{IEEE} Computer Society},
year = {2014},
url = {https://doi.org/10.1109/ICPP.2014.10},
doi = {10.1109/ICPP.2014.10},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icpp/HundtSS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pdp/DangSHH14,
author = {Hoang{-}Vu Dang and
Bertil Schmidt and
Andreas Hildebrandt and
Anna Katharina Hildebrandt},
title = {Parallelized Clustering of Protein Structures on CUDA-Enabled GPUs},
booktitle = {22nd Euromicro International Conference on Parallel, Distributed,
and Network-Based Processing, {PDP} 2014, Torino, Italy, February
12-14, 2014},
pages = {1--8},
publisher = {{IEEE} Computer Society},
year = {2014},
url = {https://doi.org/10.1109/PDP.2014.9},
doi = {10.1109/PDP.2014.9},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/pdp/DangSHH14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sac/HundtSSGD14,
author = {Christian Hundt and
Bertil Schmidt and
Elmar Sch{\"{o}}mer and
Herbert G{\"{o}}ttler and
Hoang{-}Vu Dang},
editor = {Yookun Cho and
Sung Y. Shin and
Sang{-}Wook Kim and
Chih{-}Cheng Hung and
Jiman Hong},
title = {{GEM:} an elastic and translation-invariant similarity measure with
automatic trend adjustment},
booktitle = {Symposium on Applied Computing, {SAC} 2014, Gyeongju, Republic of
Korea - March 24 - 28, 2014},
pages = {105--112},
publisher = {{ACM}},
year = {2014},
url = {https://doi.org/10.1145/2554850.2555041},
doi = {10.1145/2554850.2555041},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/sac/HundtSSGD14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sbac-pad/TranSLS14,
author = {Tuan Tu Tran and
Simon Schindel and
Yongchao Liu and
Bertil Schmidt},
title = {Bit-Parallel Approximate Pattern Matching on the Xeon Phi Coprocessor},
booktitle = {26th {IEEE} International Symposium on Computer Architecture and High
Performance Computing, {SBAC-PAD} 2014, Paris, France, October 22-24,
2014},
pages = {81--88},
publisher = {{IEEE} Computer Society},
year = {2014},
url = {https://doi.org/10.1109/SBAC-PAD.2014.37},
doi = {10.1109/SBAC-PAD.2014.37},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/sbac-pad/TranSLS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/LiuS14a,
author = {Yongchao Liu and
Bertil Schmidt},
title = {{SWAPHI:} Smith-Waterman Protein Database Search on Xeon Phi Coprocessors},
journal = {CoRR},
volume = {abs/1404.4152},
year = {2014},
url = {http://arxiv.org/abs/1404.4152},
eprinttype = {arXiv},
eprint = {1404.4152},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/LiuS14a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuSS13,
author = {Yongchao Liu and
Jan Schr{\"{o}}der and
Bertil Schmidt},
title = {Musket: a multistage \emph{k-}mer spectrum-based error corrector for
Illumina sequence data},
journal = {Bioinform.},
volume = {29},
number = {3},
pages = {308--315},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/bts690},
doi = {10.1093/BIOINFORMATICS/BTS690},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuSS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenSM13,
author = {Yupeng Chen and
Bertil Schmidt and
Douglas L. Maskell},
title = {A hybrid short read mapping accelerator},
journal = {{BMC} Bioinform.},
volume = {14},
pages = {67},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-67},
doi = {10.1186/1471-2105-14-67},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenSM13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuWS13,
author = {Yongchao Liu and
Adrianto Wirawan and
Bertil Schmidt},
title = {{CUDASW++} 3.0: accelerating Smith-Waterman protein database search
by coupling {CPU} and {GPU} {SIMD} instructions},
journal = {{BMC} Bioinform.},
volume = {14},
pages = {117},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-117},
doi = {10.1186/1471-2105-14-117},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuWS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/concurrency/SchmidtAD13,
author = {Bertil Schmidt and
Hans Aribowo and
Hoang{-}Vu Dang},
title = {Iterative sparse matrix-vector multiplication for accelerating the
block Wiedemann algorithm over {GF(2)} on multi-graphics processing
unit systems},
journal = {Concurr. Comput. Pract. Exp.},
volume = {25},
number = {4},
pages = {586--603},
year = {2013},
url = {https://doi.org/10.1002/cpe.2896},
doi = {10.1002/CPE.2896},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/concurrency/SchmidtAD13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pc/DangS13,
author = {Hoang{-}Vu Dang and
Bertil Schmidt},
title = {CUDA-enabled Sparse Matrix-Vector Multiplication on GPUs using atomic
operations},
journal = {Parallel Comput.},
volume = {39},
number = {11},
pages = {737--750},
year = {2013},
url = {https://doi.org/10.1016/j.parco.2013.09.005},
doi = {10.1016/J.PARCO.2013.09.005},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/pc/DangS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tvlsi/ChenSM13,
author = {Yupeng Chen and
Bertil Schmidt and
Douglas L. Maskell},
title = {Reconfigurable Accelerator for the Word-Matching Stage of {BLASTN}},
journal = {{IEEE} Trans. Very Large Scale Integr. Syst.},
volume = {21},
number = {4},
pages = {659--669},
year = {2013},
url = {https://doi.org/10.1109/TVLSI.2012.2196060},
doi = {10.1109/TVLSI.2012.2196060},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tvlsi/ChenSM13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ppam/LiuS13,
author = {Yongchao Liu and
Bertil Schmidt},
editor = {Roman Wyrzykowski and
Jack J. Dongarra and
Konrad Karczewski and
Jerzy Wasniewski},
title = {Faster GPU-Accelerated Smith-Waterman Algorithm with Alignment Backtracking
for Short {DNA} Sequences},
booktitle = {Parallel Processing and Applied Mathematics - 10th International Conference,
{PPAM} 2013, Warsaw, Poland, September 8-11, 2013, Revised Selected
Papers, Part {II}},
series = {Lecture Notes in Computer Science},
volume = {8385},
pages = {247--257},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-642-55195-6\_23},
doi = {10.1007/978-3-642-55195-6\_23},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ppam/LiuS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuSM12,
author = {Yongchao Liu and
Bertil Schmidt and
Douglas L. Maskell},
title = {{CUSHAW:} a {CUDA} compatible short read aligner to large genomes
based on the Burrows-Wheeler transform},
journal = {Bioinform.},
volume = {28},
number = {14},
pages = {1830--1837},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts276},
doi = {10.1093/BIOINFORMATICS/BTS276},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuSM12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhengKS12,
author = {Zejun Zheng and
Stefan Kramer and
Bertil Schmidt},
title = {DySC: software for greedy clustering of 16S rRNA reads},
journal = {Bioinform.},
volume = {28},
number = {16},
pages = {2182--2183},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts355},
doi = {10.1093/BIOINFORMATICS/BTS355},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhengKS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuS12,
author = {Yongchao Liu and
Bertil Schmidt},
title = {Long read alignment based on maximal exact match seeds},
journal = {Bioinform.},
volume = {28},
number = {18},
pages = {318--324},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts414},
doi = {10.1093/BIOINFORMATICS/BTS414},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fpga/ChenSM12,
author = {Yupeng Chen and
Bertil Schmidt and
Douglas L. Maskell},
editor = {Katherine Compton and
Brad L. Hutchings},
title = {Accelerating short read mapping on an {FPGA} (abstract only)},
booktitle = {Proceedings of the {ACM/SIGDA} 20th International Symposium on Field
Programmable Gate Arrays, {FPGA} 2012, Monterey, California, USA,
February 22-24, 2012},
pages = {265},
publisher = {{ACM}},
year = {2012},
url = {https://doi.org/10.1145/2145694.2145740},
doi = {10.1145/2145694.2145740},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/fpga/ChenSM12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fpl/ChenSM12,
author = {Yupeng Chen and
Bertil Schmidt and
Douglas L. Maskell},
editor = {Dirk Koch and
Satnam Singh and
Jim T{\o}rresen},
title = {An {FPGA} aligner for short read mapping},
booktitle = {22nd International Conference on Field Programmable Logic and Applications
(FPL), Oslo, Norway, August 29-31, 2012},
pages = {511--514},
publisher = {{IEEE}},
year = {2012},
url = {https://doi.org/10.1109/FPL.2012.6339267},
doi = {10.1109/FPL.2012.6339267},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/fpl/ChenSM12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/LiuS12,
author = {Yongchao Liu and
Bertil Schmidt},
title = {Evaluation of GPU-based Seed Generation for Computational Genomics
Using Burrows-Wheeler Transform},
booktitle = {26th {IEEE} International Parallel and Distributed Processing Symposium
Workshops {\&} PhD Forum, {IPDPS} 2012, Shanghai, China, May 21-25,
2012},
pages = {684--690},
publisher = {{IEEE} Computer Society},
year = {2012},
url = {https://doi.org/10.1109/IPDPSW.2012.85},
doi = {10.1109/IPDPSW.2012.85},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ipps/LiuS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:journals/procedia/DangS12,
author = {Hoang{-}Vu Dang and
Bertil Schmidt},
editor = {Hesham H. Ali and
Yong Shi and
Deepak Khazanchi and
Michael Lees and
G. Dick van Albada and
Jack J. Dongarra and
Peter M. A. Sloot},
title = {The Sliced {COO} Format for Sparse Matrix-Vector Multiplication on
CUDA-enabled GPUs},
booktitle = {Proceedings of the International Conference on Computational Science,
{ICCS} 2012, Omaha, Nebraska, USA, 4-6 June, 2012},
series = {Procedia Computer Science},
volume = {9},
pages = {57--66},
publisher = {Elsevier},
year = {2012},
url = {https://doi.org/10.1016/j.procs.2012.04.007},
doi = {10.1016/J.PROCS.2012.04.007},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/procedia/DangS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:journals/procedia/SchmidtM12,
author = {Bertil Schmidt and
Douglas L. Maskell},
editor = {Hesham H. Ali and
Yong Shi and
Deepak Khazanchi and
Michael Lees and
G. Dick van Albada and
Jack J. Dongarra and
Peter M. A. Sloot},
title = {Fourth Workshop on using Emerging Parallel Architectures},
booktitle = {Proceedings of the International Conference on Computational Science,
{ICCS} 2012, Omaha, Nebraska, USA, 4-6 June, 2012},
series = {Procedia Computer Science},
volume = {9},
pages = {1867--1869},
publisher = {Elsevier},
year = {2012},
url = {https://doi.org/10.1016/j.procs.2012.05.001},
doi = {10.1016/J.PROCS.2012.05.001},
timestamp = {Sun, 28 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/procedia/SchmidtM12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KuttippurathuHLSMLHPK11,
author = {Lakshmi Kuttippurathu and
Michael Hsing and
Yongchao Liu and
Bertil Schmidt and
Douglas L. Maskell and
Kyungjoon Lee and
Aibin He and
William T. Pu and
Sek Won Kong},
title = {CompleteMOTIFs: {DNA} motif discovery platform for transcription factor
binding experiments},
journal = {Bioinform.},
volume = {27},
number = {5},
pages = {715--717},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btq707},
doi = {10.1093/BIOINFORMATICS/BTQ707},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KuttippurathuHLSMLHPK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuSM11,
author = {Yongchao Liu and
Bertil Schmidt and
Douglas L. Maskell},
title = {DecGPU: distributed error correction on massively parallel graphics
processing units using {CUDA} and {MPI}},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {85},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-85},
doi = {10.1186/1471-2105-12-85},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuSM11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuSM11a,
author = {Yongchao Liu and
Bertil Schmidt and
Douglas L. Maskell},
title = {Parallelized short read assembly of large genomes using de Bruijn
graphs},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {354},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-354},
doi = {10.1186/1471-2105-12-354},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuSM11a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/LiuSM11,
author = {Weiguo Liu and
Bertil Schmidt and
Wolfgang M{\"{u}}ller{-}Wittig},
title = {{CUDA-BLASTP:} Accelerating {BLASTP} on CUDA-Enabled Graphics Hardware},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {8},
number = {6},
pages = {1678--1684},
year = {2011},
url = {https://doi.org/10.1109/TCBB.2011.33},
doi = {10.1109/TCBB.2011.33},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/LiuSM11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/europar/SchmidtAD11,
author = {Bertil Schmidt and
Hans Aribowo and
Hoang{-}Vu Dang},
editor = {Emmanuel Jeannot and
Raymond Namyst and
Jean Roman},
title = {Iterative Sparse Matrix-Vector Multiplication for Integer Factorization
on GPUs},
booktitle = {Euro-Par 2011 Parallel Processing - 17th International Conference,
Euro-Par 2011, Bordeaux, France, August 29 - September 2, 2011, Proceedings,
Part {II}},
series = {Lecture Notes in Computer Science},
volume = {6853},
pages = {413--424},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-23397-5\_41},
doi = {10.1007/978-3-642-23397-5\_41},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/europar/SchmidtAD11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icpads/LiuSLVM11,
author = {Weiguo Liu and
Bertil Schmidt and
Yongchao Liu and
Gerrit Voss and
Wolfgang M{\"{u}}ller{-}Wittig},
title = {Mapping of {BLASTP} Algorithm onto {GPU} Clusters},
booktitle = {17th {IEEE} International Conference on Parallel and Distributed Systems,
{ICPADS} 2011, Tainan, Taiwan, December 7-9, 2011},
pages = {236--243},
publisher = {{IEEE} Computer Society},
year = {2011},
url = {https://doi.org/10.1109/ICPADS.2011.79},
doi = {10.1109/ICPADS.2011.79},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icpads/LiuSLVM11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/LiuSM11,
author = {Yongchao Liu and
Bertil Schmidt and
Douglas L. Maskell},
title = {An Ultrafast Scalable Many-Core Motif Discovery Algorithm for Multiple
GPUs},
booktitle = {25th {IEEE} International Symposium on Parallel and Distributed Processing,
{IPDPS} 2011, Anchorage, Alaska, USA, 16-20 May 2011 - Workshop Proceedings},
pages = {428--434},
publisher = {{IEEE}},
year = {2011},
url = {https://doi.org/10.1109/IPDPS.2011.183},
doi = {10.1109/IPDPS.2011.183},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ipps/LiuSM11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/prib/ZhengNS11,
author = {Zejun Zheng and
Thuy{-}Diem Nguyen and
Bertil Schmidt},
editor = {Marco Loog and
Lodewyk F. A. Wessels and
Marcel J. T. Reinders and
Dick de Ridder},
title = {CRiSPy-CUDA: Computing Species Richness in 16S rRNA Pyrosequencing
Datasets with {CUDA}},
booktitle = {Pattern Recognition in Bioinformatics - 6th {IAPR} International Conference,
{PRIB} 2011, Delft, The Netherlands, November 2-4, 2011. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7036},
pages = {37--49},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-24855-9\_4},
doi = {10.1007/978-3-642-24855-9\_4},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/prib/ZhengNS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:journals/procedia/SchmidtM11,
author = {Bertil Schmidt and
Douglas L. Maskell},
editor = {Mitsuhisa Sato and
Satoshi Matsuoka and
Peter M. A. Sloot and
G. Dick van Albada and
Jack J. Dongarra},
title = {Third Workshop on using Emerging Parallel Architectures},
booktitle = {Proceedings of the International Conference on Computational Science,
{ICCS} 2011, Nanyang Technological University, Singapore, 1-3 June,
2011},
series = {Procedia Computer Science},
volume = {4},
pages = {1964--1966},
publisher = {Elsevier},
year = {2011},
url = {https://doi.org/10.1016/j.procs.2011.04.214},
doi = {10.1016/J.PROCS.2011.04.214},
timestamp = {Thu, 08 Jul 2021 16:04:01 +0200},
biburl = {https://dblp.org/rec/journals/procedia/SchmidtM11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/ic3/2011,
editor = {Srinivas Aluru and
Sanghamitra Bandyopadhyay and
{\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and
Devdatt P. Dubhashi and
Phillip H. Jones and
Manish Parashar and
Bertil Schmidt},
title = {Contemporary Computing - 4th International Conference, {IC3} 2011,
Noida, India, August 8-10, 2011. Proceedings},
series = {Communications in Computer and Information Science},
volume = {168},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-22606-9},
doi = {10.1007/978-3-642-22606-9},
isbn = {978-3-642-22605-2},
timestamp = {Wed, 24 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ic3/2011.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WirawanKS10,
author = {Adrianto Wirawan and
Chee Keong Kwoh and
Bertil Schmidt},
title = {Multi-threaded vectorized distance matrix computation on the {CELL/BE}
and x86/SSE2 architectures},
journal = {Bioinform.},
volume = {26},
number = {10},
pages = {1368--1369},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq135},
doi = {10.1093/BIOINFORMATICS/BTQ135},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WirawanKS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LiuSM10,
author = {Yongchao Liu and
Bertil Schmidt and
Douglas L. Maskell},
title = {MSAProbs: multiple sequence alignment based on pair hidden Markov
models and partition function posterior probabilities},
journal = {Bioinform.},
volume = {26},
number = {16},
pages = {1958--1964},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq338},
doi = {10.1093/BIOINFORMATICS/BTQ338},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuSM10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ShiSLM10,
author = {Haixiang Shi and
Bertil Schmidt and
Weiguo Liu and
Wolfgang M{\"{u}}ller{-}Wittig},
title = {A Parallel Algorithm for Error Correction in High-Throughput Short-Read
Data on CUDA-Enabled Graphics Hardware},
journal = {J. Comput. Biol.},
volume = {17},
number = {4},
pages = {603--615},
year = {2010},
url = {https://doi.org/10.1089/cmb.2009.0062},
doi = {10.1089/CMB.2009.0062},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/ShiSLM10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/prl/AhmadCS10,
author = {Shandar Ahmad and
Madhu Chetty and
Bertil Schmidt},
title = {Pattern Recognition in Bioinformatics},
journal = {Pattern Recognit. Lett.},
volume = {31},
number = {14},
pages = {2071--2072},
year = {2010},
url = {https://doi.org/10.1016/j.patrec.2010.06.001},
doi = {10.1016/J.PATREC.2010.06.001},
timestamp = {Sat, 22 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/prl/AhmadCS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/prl/LiuSLM10,
author = {Yongchao Liu and
Bertil Schmidt and
Weiguo Liu and
Douglas L. Maskell},
title = {{CUDA-MEME:} Accelerating motif discovery in biological sequences
using CUDA-enabled graphics processing units},
journal = {Pattern Recognit. Lett.},
volume = {31},
number = {14},
pages = {2170--2177},
year = {2010},
url = {https://doi.org/10.1016/j.patrec.2009.10.009},
doi = {10.1016/J.PATREC.2009.10.009},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/prl/LiuSLM10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/ZhengSB10,
author = {Zejun Zheng and
Bertil Schmidt and
Guillaume Bourque},
editor = {Taesung Park and
Stephen Kwok{-}Wing Tsui and
Luonan Chen and
Michael K. Ng and
Limsoon Wong and
Xiaohua Hu},
title = {Prediction of low coverage prone regions for Illumina sequencing projects
using a support vector machine},
booktitle = {2010 {IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2010, Hong Kong, China, December 18-21, 2010, Proceedings},
pages = {13--16},
publisher = {{IEEE} Computer Society},
year = {2010},
url = {https://doi.org/10.1109/BIBM.2010.5706527},
doi = {10.1109/BIBM.2010.5706527},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibm/ZhengSB10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:journals/procedia/SchmidtM10,
author = {Bertil Schmidt and
Douglas L. Maskell},
editor = {Peter M. A. Sloot and
G. Dick van Albada and
Jack J. Dongarra},
title = {Second Workshop on using Emerging Parallel Architectures},
booktitle = {Proceedings of the International Conference on Computational Science,
{ICCS} 2010, University of Amsterdam, The Netherlands, May 31 - June
2, 2010},
series = {Procedia Computer Science},
volume = {1},
number = {1},
pages = {1015--1017},
publisher = {Elsevier},
year = {2010},
url = {https://doi.org/10.1016/j.procs.2010.04.112},
doi = {10.1016/J.PROCS.2010.04.112},
timestamp = {Thu, 08 Jul 2021 14:29:22 +0200},
biburl = {https://dblp.org/rec/journals/procedia/SchmidtM10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:journals/procedia/ShiSLM10,
author = {Haixiang Shi and
Bertil Schmidt and
Weiguo Liu and
Wolfgang M{\"{u}}ller{-}Wittig},
editor = {Peter M. A. Sloot and
G. Dick van Albada and
Jack J. Dongarra},
title = {Quality-score guided error correction for short-read sequencing data
using {CUDA}},
booktitle = {Proceedings of the International Conference on Computational Science,
{ICCS} 2010, University of Amsterdam, The Netherlands, May 31 - June
2, 2010},
series = {Procedia Computer Science},
volume = {1},
number = {1},
pages = {1129--1138},
publisher = {Elsevier},
year = {2010},
url = {https://doi.org/10.1016/j.procs.2010.04.125},
doi = {10.1016/J.PROCS.2010.04.125},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/procedia/ShiSLM10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchroderSPSS09,
author = {Jan Schr{\"{o}}der and
Heiko Schr{\"{o}}der and
Simon J. Puglisi and
Ranjan Sinha and
Bertil Schmidt},
title = {{SHREC:} a short-read error correction method},
journal = {Bioinform.},
volume = {25},
number = {17},
pages = {2157--2163},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp379},
doi = {10.1093/BIOINFORMATICS/BTP379},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchroderSPSS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchmidtSBP09,
author = {Bertil Schmidt and
Ranjan Sinha and
Bryan Beresford{-}Smith and
Simon J. Puglisi},
title = {A fast hybrid short read fragment assembly algorithm},
journal = {Bioinform.},
volume = {25},
number = {17},
pages = {2279--2280},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp374},
doi = {10.1093/BIOINFORMATICS/BTP374},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchmidtSBP09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/sp/WirawanSZK09,
author = {Adrianto Wirawan and
Bertil Schmidt and
Huiliang Zhang and
Chee Keong Kwoh},
title = {High performance protein sequence database scanning on the Cell Broadband
Engine},
journal = {Sci. Program.},
volume = {17},
number = {1-2},
pages = {97--111},
year = {2009},
url = {https://doi.org/10.3233/SPR-2009-0274},
doi = {10.3233/SPR-2009-0274},
timestamp = {Wed, 06 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/sp/WirawanSZK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/titb/OliverSJM09,
author = {Timothy F. Oliver and
Bertil Schmidt and
Yanto Jakop and
Douglas L. Maskell},
title = {High Speed Biological Sequence Analysis With Hidden Markov Models
on Reconfigurable Platforms},
journal = {{IEEE} Trans. Inf. Technol. Biomed.},
volume = {13},
number = {5},
pages = {740--746},
year = {2009},
url = {https://doi.org/10.1109/TITB.2007.904632},
doi = {10.1109/TITB.2007.904632},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/titb/OliverSJM09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/arcs/ChenSM09,
author = {Yupeng Chen and
Bertil Schmidt and
Douglas L. Maskell},
editor = {Mladen Berekovic and
Christian M{\"{u}}ller{-}Schloer and
Christian Hochberger and
Stephan Wong},
title = {A Reconfigurable Bloom Filter Architecture for {BLASTN}},
booktitle = {Architecture of Computing Systems - {ARCS} 2009, 22nd International
Conference, Delft, The Netherlands, March 10-13, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5455},
pages = {40--49},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-00454-4\_7},
doi = {10.1007/978-3-642-00454-4\_7},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/arcs/ChenSM09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/asap/LiuSM09,
author = {Yongchao Liu and
Bertil Schmidt and
Douglas L. Maskell},
title = {{MSA-CUDA:} Multiple Sequence Alignment on Graphics Processing Units
with {CUDA}},
booktitle = {20th {IEEE} International Conference on Application-Specific Systems,
Architectures and Processors, {ASAP} 2009, July 7-9, 2009, Boston,
MA, {USA}},
pages = {121--128},
publisher = {{IEEE} Computer Society},
year = {2009},
url = {https://doi.org/10.1109/ASAP.2009.14},
doi = {10.1109/ASAP.2009.14},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/asap/LiuSM09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccS/SchmidtM09,
author = {Bertil Schmidt and
Douglas L. Maskell},
editor = {Gabrielle Allen and
Jaroslaw Nabrzyski and
Edward Seidel and
G. Dick van Albada and
Jack J. Dongarra and
Peter M. A. Sloot},
title = {Workshop on Using Emerging Parallel Architectures for Computational
Science},
booktitle = {Computational Science - {ICCS} 2009, 9th International Conference,
Baton Rouge, LA, USA, May 25-27, 2009, Proceedings, Part {I}},
series = {Lecture Notes in Computer Science},
volume = {5544},
pages = {861--863},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-01970-8\_86},
doi = {10.1007/978-3-642-01970-8\_86},
timestamp = {Tue, 14 May 2019 10:00:48 +0200},
biburl = {https://dblp.org/rec/conf/iccS/SchmidtM09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccS/WirawanSK09,
author = {Adrianto Wirawan and
Bertil Schmidt and
Chee Keong Kwoh},
editor = {Gabrielle Allen and
Jaroslaw Nabrzyski and
Edward Seidel and
G. Dick van Albada and
Jack J. Dongarra and
Peter M. A. Sloot},
title = {Pairwise Distance Matrix Computation for Multiple Sequence Alignment
on the Cell Broadband Engine},
booktitle = {Computational Science - {ICCS} 2009, 9th International Conference,
Baton Rouge, LA, USA, May 25-27, 2009, Proceedings, Part {I}},
series = {Lecture Notes in Computer Science},
volume = {5544},
pages = {954--963},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-01970-8\_96},
doi = {10.1007/978-3-642-01970-8\_96},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iccS/WirawanSK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/LiuSM09,
author = {Yongchao Liu and
Bertil Schmidt and
Douglas L. Maskell},
title = {Parallel reconstruction of neighbor-joining trees for large multiple
sequence alignments using {CUDA}},
booktitle = {23rd {IEEE} International Symposium on Parallel and Distributed Processing,
{IPDPS} 2009, Rome, Italy, May 23-29, 2009},
pages = {1--8},
publisher = {{IEEE}},
year = {2009},
url = {https://doi.org/10.1109/IPDPS.2009.5160923},
doi = {10.1109/IPDPS.2009.5160923},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ipps/LiuSM09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/ShiSLM09,
author = {Haixiang Shi and
Bertil Schmidt and
Weiguo Liu and
Wolfgang M{\"{u}}ller{-}Wittig},
title = {Accelerating error correction in high-throughput short-read {DNA}
sequencing data with {CUDA}},
booktitle = {23rd {IEEE} International Symposium on Parallel and Distributed Processing,
{IPDPS} 2009, Rome, Italy, May 23-29, 2009},
pages = {1--8},
publisher = {{IEEE}},
year = {2009},
url = {https://doi.org/10.1109/IPDPS.2009.5160924},
doi = {10.1109/IPDPS.2009.5160924},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ipps/ShiSLM09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SinghTSB08,
author = {Dadabhai T. Singh and
Rahul Trehan and
Bertil Schmidt and
Timo Bretschneider},
title = {Comparative phyloinformatics of virus genes at micro and macro levels
in a distributed computing environment},
journal = {{BMC} Bioinform.},
volume = {9},
number = {{S-1}},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-S1-S23},
doi = {10.1186/1471-2105-9-S1-S23},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SinghTSB08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WirawanKHS08,
author = {Adrianto Wirawan and
Chee Keong Kwoh and
Nim Tri Hieu and
Bertil Schmidt},
title = {{CBESW:} Sequence Alignment on the Playstation 3},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-377},
doi = {10.1186/1471-2105-9-377},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WirawanKHS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cphysics/LiuSVM08,
author = {Weiguo Liu and
Bertil Schmidt and
Gerrit Voss and
Wolfgang M{\"{u}}ller{-}Wittig},
title = {Accelerating molecular dynamics simulations using Graphics Processing
Units with {CUDA}},
journal = {Comput. Phys. Commun.},
volume = {179},
number = {9},
pages = {634--641},
year = {2008},
url = {https://doi.org/10.1016/j.cpc.2008.05.008},
doi = {10.1016/J.CPC.2008.05.008},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cphysics/LiuSVM08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pc/OliverYS08,
author = {Timothy F. Oliver and
Leow Yuan Yeow and
Bertil Schmidt},
title = {Integrating {FPGA} acceleration into HMMer},
journal = {Parallel Comput.},
volume = {34},
number = {11},
pages = {681--691},
year = {2008},
url = {https://doi.org/10.1016/j.parco.2008.08.003},
doi = {10.1016/J.PARCO.2008.08.003},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/pc/OliverYS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/titb/SinghCLMS08,
author = {Aarti Singh and
Chen Chen and
Weiguo Liu and
Wayne P. Mitchell and
Bertil Schmidt},
title = {A Hybrid Computational Grid Architecture for Comparative Genomics},
journal = {{IEEE} Trans. Inf. Technol. Biomed.},
volume = {12},
number = {2},
pages = {218--225},
year = {2008},
url = {https://doi.org/10.1109/TITB.2007.908462},
doi = {10.1109/TITB.2007.908462},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/titb/SinghCLMS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/prib/ChenSWM08,
author = {Chen Chen and
Bertil Schmidt and
Weiguo Liu and
Wolfgang M{\"{u}}ller{-}Wittig},
editor = {Madhu Chetty and
Alioune Ngom and
Shandar Ahmad},
title = {{GPU-MEME:} Using Graphics Hardware to Accelerate Motif Finding in
{DNA} Sequences},
booktitle = {Pattern Recognition in Bioinformatics, Third {IAPR} International
Conference, {PRIB} 2008, Melbourne, Australia, October 15-17, 2008.
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5265},
pages = {448--459},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-88436-1\_38},
doi = {10.1007/978-3-540-88436-1\_38},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/prib/ChenSWM08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/prib/ZhangSM08,
author = {Huiliang Zhang and
Bertil Schmidt and
Wolfgang M{\"{u}}ller{-}Wittig},
editor = {Madhu Chetty and
Alioune Ngom and
Shandar Ahmad},
title = {Accelerating {BLASTP} on the Cell Broadband Engine},
booktitle = {Pattern Recognition in Bioinformatics, Third {IAPR} International
Conference, {PRIB} 2008, Melbourne, Australia, October 15-17, 2008.
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5265},
pages = {460--470},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-88436-1\_39},
doi = {10.1007/978-3-540-88436-1\_39},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/prib/ZhangSM08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RajapakseSFB07,
author = {Menaka Rajapakse and
Bertil Schmidt and
Feng Lin and
Vladimir Brusic},
title = {Predicting peptides binding to {MHC} class {II} molecules using multi-objective
evolutionary algorithms},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-459},
doi = {10.1186/1471-2105-8-459},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/RajapakseSFB07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijwgs/Schmidt07,
author = {Bertil Schmidt},
title = {A survey of desktop grid applications for e-science},
journal = {Int. J. Web Grid Serv.},
volume = {3},
number = {3},
pages = {354--368},
year = {2007},
url = {https://doi.org/10.1504/IJWGS.2007.014957},
doi = {10.1504/IJWGS.2007.014957},
timestamp = {Tue, 25 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijwgs/Schmidt07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tpds/LiuSVM07,
author = {Weiguo Liu and
Bertil Schmidt and
Gerrit Voss and
Wolfgang M{\"{u}}ller{-}Wittig},
title = {Streaming Algorithms for Biological Sequence Alignment on GPUs},
journal = {{IEEE} Trans. Parallel Distributed Syst.},
volume = {18},
number = {9},
pages = {1270--1281},
year = {2007},
url = {https://doi.org/10.1109/TPDS.2007.1069},
doi = {10.1109/TPDS.2007.1069},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tpds/LiuSVM07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/vlsisp/LinSS07,
author = {Feng Lin and
Heiko Schr{\"{o}}der and
Bertil Schmidt},
title = {Solving the Bottleneck Problem in Bioinformatics Computing: An Architectural
Perspective},
journal = {J. {VLSI} Signal Process.},
volume = {48},
number = {3},
pages = {185--188},
year = {2007},
url = {https://doi.org/10.1007/s11265-007-0088-z},
doi = {10.1007/S11265-007-0088-Z},
timestamp = {Wed, 15 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/vlsisp/LinSS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/vlsisp/LiuSM07,
author = {Weiguo Liu and
Bertil Schmidt and
Wolfgang M{\"{u}}ller{-}Wittig},
title = {Performance Analysis of General-Purpose Computation on Commodity Graphics
Hardware: {A} Case Study Using Bioinformatics},
journal = {J. {VLSI} Signal Process.},
volume = {48},
number = {3},
pages = {209--221},
year = {2007},
url = {https://doi.org/10.1007/s11265-007-0064-7},
doi = {10.1007/S11265-007-0064-7},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/vlsisp/LiuSM07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/vlsisp/WaltersMCOYSNL07,
author = {John Paul Walters and
Xiandong Meng and
Vipin Chaudhary and
Timothy F. Oliver and
Leow Yuan Yeow and
Bertil Schmidt and
Darran Nathan and
Joseph I. Landman},
title = {MPI-HMMER-Boost: Distributed {FPGA} Acceleration},
journal = {J. {VLSI} Signal Process.},
volume = {48},
number = {3},
pages = {223--238},
year = {2007},
url = {https://doi.org/10.1007/s11265-007-0062-9},
doi = {10.1007/S11265-007-0062-9},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/vlsisp/WaltersMCOYSNL07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/appt/LowLS07,
author = {Malcolm Yoke Hean Low and
Weiguo Liu and
Bertil Schmidt},
editor = {Ming Xu and
Yinwei Zhan and
Jiannong Cao and
Yijun Liu},
title = {A Parallel {BSP} Algorithm for Irregular Dynamic Programming},
booktitle = {Advanced Parallel Processing Technologies, 7th International Symposium,
{APPT} 2007, Guangzhou, China, November 22-23, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4847},
pages = {151--160},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-76837-1\_19},
doi = {10.1007/978-3-540-76837-1\_19},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/appt/LowLS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hipc/LiuSVM07,
author = {Weiguo Liu and
Bertil Schmidt and
Gerrit Voss and
Wolfgang M{\"{u}}ller{-}Wittig},
editor = {Srinivas Aluru and
Manish Parashar and
Ramamurthy Badrinath and
Viktor K. Prasanna},
title = {Molecular Dynamics Simulations on Commodity GPUs with {CUDA}},
booktitle = {High Performance Computing - HiPC 2007, 14th International Conference,
Goa, India, December 18-21, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4873},
pages = {185--196},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-77220-0\_20},
doi = {10.1007/978-3-540-77220-0\_20},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/hipc/LiuSVM07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icpp/LiuMS07,
author = {Weiguo Liu and
Wolfgang M{\"{u}}ller{-}Wittig and
Bertil Schmidt},
title = {Performance Predictions for General-Purpose Computation on GPUs},
booktitle = {2007 International Conference on Parallel Processing {(ICPP} 2007),
September 10-14, 2007, Xi-An, China},
pages = {50},
publisher = {{IEEE} Computer Society},
year = {2007},
url = {https://doi.org/10.1109/ICPP.2007.67},
doi = {10.1109/ICPP.2007.67},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icpp/LiuMS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/OliverYS07,
author = {Timothy F. Oliver and
Leow Yuan Yeow and
Bertil Schmidt},
title = {High Performance Database Searching with HMMer on FPGAs},
booktitle = {21th International Parallel and Distributed Processing Symposium {(IPDPS}
2007), Proceedings, 26-30 March 2007, Long Beach, California, {USA}},
pages = {1--7},
publisher = {{IEEE}},
year = {2007},
url = {https://doi.org/10.1109/IPDPS.2007.370448},
doi = {10.1109/IPDPS.2007.370448},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ipps/OliverYS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ppam/WirawanKS07,
author = {Adrianto Wirawan and
Chee Keong Kwoh and
Bertil Schmidt},
editor = {Roman Wyrzykowski and
Jack J. Dongarra and
Konrad Karczewski and
Jerzy Wasniewski},
title = {Parallel {DNA} Sequence Alignment on the Cell Broadband Engine},
booktitle = {Parallel Processing and Applied Mathematics, 7th International Conference,
{PPAM} 2007, Gdansk, Poland, September 9-12, 2007, Revised Selected
Papers},
series = {Lecture Notes in Computer Science},
volume = {4967},
pages = {1249--1256},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-68111-3\_132},
doi = {10.1007/978-3-540-68111-3\_132},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ppam/WirawanKS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/prib/AungMOSB07,
author = {Yan Lin Aung and
Douglas L. Maskell and
Timothy F. Oliver and
Bertil Schmidt and
William Bong},
editor = {Jagath C. Rajapakse and
Bertil Schmidt and
L. Gwenn Volkert},
title = {C-Based Design Methodology for {FPGA} Implementation of ClustalW {MSA}},
booktitle = {Pattern Recognition in Bioinformatics, Second {IAPR} International
Workshop, {PRIB} 2007, Singapore, October 1-2, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4774},
pages = {11--18},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-75286-8\_2},
doi = {10.1007/978-3-540-75286-8\_2},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/prib/AungMOSB07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/rtcsa/FengCSLB07,
author = {Jimin Feng and
Samarjit Chakraborty and
Bertil Schmidt and
Weiguo Liu and
Unmesh D. Bordoloi},
title = {Fast Schedulability Analysis Using Commodity Graphics Hardware},
booktitle = {13th {IEEE} International Conference on Embedded and Real-Time Computing
Systems and Applications {(RTCSA} 2007), 21-24 August 2007, Daegu,
Korea},
pages = {400--408},
publisher = {{IEEE} Computer Society},
year = {2007},
url = {https://doi.org/10.1109/RTCSA.2007.40},
doi = {10.1109/RTCSA.2007.40},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/rtcsa/FengCSLB07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/wi/07/SchmidtCL07,
author = {Bertil Schmidt and
Chunxi Chen and
Weiguo Liu},
editor = {El{-}Ghazali Talbi and
Albert Y. Zomaya},
title = {Hierarchical Grid Computing for High-Performance Bioinformatics},
booktitle = {Grid Computing for Bioinformatics and Computational Biology},
series = {Wiley series on bioinformatics},
pages = {87--121},
publisher = {Wiley},
year = {2007},
url = {https://doi.org/10.1002/9780470191637.ch5},
doi = {10.1002/9780470191637.CH5},
timestamp = {Mon, 16 Sep 2019 14:43:16 +0200},
biburl = {https://dblp.org/rec/books/wi/07/SchmidtCL07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/prib/2007,
editor = {Jagath C. Rajapakse and
Bertil Schmidt and
L. Gwenn Volkert},
title = {Pattern Recognition in Bioinformatics, Second {IAPR} International
Workshop, {PRIB} 2007, Singapore, October 1-2, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4774},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-75286-8},
doi = {10.1007/978-3-540-75286-8},
isbn = {978-3-540-75285-1},
timestamp = {Tue, 14 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/prib/2007.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ieicet/LiuS06,
author = {Weiguo Liu and
Bertil Schmidt},
title = {Mapping of Hierarchical Parallel Genetic Algorithms for Protein Folding
onto Computational Grids},
journal = {{IEICE} Trans. Inf. Syst.},
volume = {89-D},
number = {2},
pages = {589--596},
year = {2006},
url = {https://doi.org/10.1093/ietisy/e89-d.2.589},
doi = {10.1093/IETISY/E89-D.2.589},
timestamp = {Sat, 11 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ieicet/LiuS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijbra/OliverSMNC06,
author = {Timothy F. Oliver and
Bertil Schmidt and
Douglas L. Maskell and
Darran Nathan and
Ralf Clemens},
title = {High-speed Multiple Sequence Alignment on a reconfigurable platform},
journal = {Int. J. Bioinform. Res. Appl.},
volume = {2},
number = {4},
pages = {394--406},
year = {2006},
url = {https://doi.org/10.1504/IJBRA.2006.011038},
doi = {10.1504/IJBRA.2006.011038},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijbra/OliverSMNC06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jpdc/ChenS06a,
author = {Chunxi Chen and
Bertil Schmidt},
title = {Constructing large suffix trees on a computational grid},
journal = {J. Parallel Distributed Comput.},
volume = {66},
number = {12},
pages = {1512--1523},
year = {2006},
url = {https://doi.org/10.1016/j.jpdc.2006.08.004},
doi = {10.1016/J.JPDC.2006.08.004},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jpdc/ChenS06a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tpds/LiuS06,
author = {Weiguo Liu and
Bertil Schmidt},
title = {Parallel Pattern-Based Systems for Computational Biology: {A} Case
Study},
journal = {{IEEE} Trans. Parallel Distributed Syst.},
volume = {17},
number = {8},
pages = {750--763},
year = {2006},
url = {https://doi.org/10.1109/TPDS.2006.109},
doi = {10.1109/TPDS.2006.109},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tpds/LiuS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/apccas/WirawanS06,
author = {Adrianto Wirawan and
Bertil Schmidt},
title = {Parallel Discovery of Transcription Factor Binding Sites},
booktitle = {{IEEE} Asia Pacific Conference on Circuits and Systems 2006, {APCCAS}
2006, Singapore, 4-7 December 2006},
pages = {700--703},
publisher = {{IEEE}},
year = {2006},
url = {https://doi.org/10.1109/APCCAS.2006.342103},
doi = {10.1109/APCCAS.2006.342103},
timestamp = {Wed, 16 Oct 2019 14:14:50 +0200},
biburl = {https://dblp.org/rec/conf/apccas/WirawanS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/evoW/RajapakseSB06,
author = {Menaka Rajapakse and
Bertil Schmidt and
Vladimir Brusic},
editor = {Franz Rothlauf and
J{\"{u}}rgen Branke and
Stefano Cagnoni and
Ernesto Costa and
Carlos Cotta and
Rolf Drechsler and
Evelyne Lutton and
Penousal Machado and
Jason H. Moore and
Juan Romero and
George D. Smith and
Giovanni Squillero and
Hideyuki Takagi},
title = {Multi-Objective Evolutionary Algorithm for Discovering Peptide Binding
Motifs},
booktitle = {Applications of Evolutionary Computing, EvoWorkshops 2006: EvoBIO,
EvoCOMNET, EvoHOT, EvoIASP, EvoINTERACTION, EvoMUSART, and EvoSTOC,
Budapest, Hungary, April 10-12, 2006, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3907},
pages = {149--158},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11732242\_14},
doi = {10.1007/11732242\_14},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/evoW/RajapakseSB06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hipc/LiuSVM06,
author = {Weiguo Liu and
Bertil Schmidt and
Gerrit Voss and
Wolfgang M{\"{u}}ller{-}Wittig},
editor = {Yves Robert and
Manish Parashar and
Ramamurthy Badrinath and
Viktor K. Prasanna},
title = {GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence
Alignment},
booktitle = {High Performance Computing - HiPC 2006, 13th International Conference,
Bangalore, India, December 18-21, 2006, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4297},
pages = {363--374},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11945918\_37},
doi = {10.1007/11945918\_37},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/hipc/LiuSVM06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccS/OliverSJM06,
author = {Timothy F. Oliver and
Bertil Schmidt and
Yanto Jakop and
Douglas L. Maskell},
editor = {Vassil N. Alexandrov and
G. Dick van Albada and
Peter M. A. Sloot and
Jack J. Dongarra},
title = {Accelerating the Viterbi Algorithm for Profile Hidden Markov Models
Using Reconfigurable Hardware},
booktitle = {Computational Science - {ICCS} 2006, 6th International Conference,
Reading, UK, May 28-31, 2006, Proceedings, Part {I}},
series = {Lecture Notes in Computer Science},
volume = {3991},
pages = {522--529},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11758501\_71},
doi = {10.1007/11758501\_71},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iccS/OliverSJM06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/LiuSVSM06,
author = {Weiguo Liu and
Bertil Schmidt and
Gerrit Voss and
Adrian Schr{\"{o}}der and
Wolfgang M{\"{u}}ller{-}Wittig},
title = {Bio-sequence database scanning on a {GPU}},
booktitle = {20th International Parallel and Distributed Processing Symposium {(IPDPS}
2006), Proceedings, 25-29 April 2006, Rhodes Island, Greece},
publisher = {{IEEE}},
year = {2006},
url = {https://doi.org/10.1109/IPDPS.2006.1639531},
doi = {10.1109/IPDPS.2006.1639531},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ipps/LiuSVSM06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OliverSNCM05,
author = {Timothy F. Oliver and
Bertil Schmidt and
Darran Nathan and
Ralf Clemens and
Douglas L. Maskell},
title = {Using reconfigurable hardware to accelerate multiple sequence alignment
with ClustalW},
journal = {Bioinform.},
volume = {21},
number = {16},
pages = {3431--3432},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti508},
doi = {10.1093/BIOINFORMATICS/BTI508},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/OliverSNCM05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/concurrency/LiuS05,
author = {Tong Liu and
Bertil Schmidt},
title = {Parallel {RNA} secondary structure prediction using stochastic context-free
grammars},
journal = {Concurr. Comput. Pract. Exp.},
volume = {17},
number = {14},
pages = {1669--1685},
year = {2005},
url = {https://doi.org/10.1002/cpe.952},
doi = {10.1002/CPE.952},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/concurrency/LiuS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fgcs/ChenS05,
author = {Chunxi Chen and
Bertil Schmidt},
title = {An adaptive grid implementation of {DNA} sequence alignment},
journal = {Future Gener. Comput. Syst.},
volume = {21},
number = {7},
pages = {988--1003},
year = {2005},
url = {https://doi.org/10.1016/j.future.2005.03.001},
doi = {10.1016/J.FUTURE.2005.03.001},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fgcs/ChenS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcas/OliverSM05,
author = {Timothy F. Oliver and
Bertil Schmidt and
Douglas L. Maskell},
title = {Reconfigurable architectures for bio-sequence database scanning on
FPGAs},
journal = {{IEEE} Trans. Circuits Syst. {II} Express Briefs},
volume = {52-II},
number = {12},
pages = {851--855},
year = {2005},
url = {https://doi.org/10.1109/TCSII.2005.853340},
doi = {10.1109/TCSII.2005.853340},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcas/OliverSM05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/aPcsac/YantoOSM05,
author = {Jacop Yanto and
Timothy F. Oliver and
Bertil Schmidt and
Douglas L. Maskell},
editor = {Thambipillai Srikanthan and
Jingling Xue and
Chip{-}Hong Chang},
title = {Biological Sequence Analysis with Hidden Markov Models on an {FPGA}},
booktitle = {Advances in Computer Systems Architecture, 10th Asia-Pacific Conference,
{ACSAC} 2005, Singapore, October 24-26, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3740},
pages = {429--439},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11572961\_34},
doi = {10.1007/11572961\_34},
timestamp = {Tue, 14 May 2019 10:00:42 +0200},
biburl = {https://dblp.org/rec/conf/aPcsac/YantoOSM05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/europar/ChenS05,
author = {Chunxi Chen and
Bertil Schmidt},
editor = {Jos{\'{e}} C. Cunha and
Pedro D. Medeiros},
title = {Parallel Construction of Large Suffix Trees on a {PC} Cluster},
booktitle = {Euro-Par 2005, Parallel Processing, 11th International Euro-Par Conference,
Lisbon, Portugal, August 30 - September 2, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3648},
pages = {1227--1236},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11549468\_134},
doi = {10.1007/11549468\_134},
timestamp = {Tue, 14 May 2019 10:00:46 +0200},
biburl = {https://dblp.org/rec/conf/europar/ChenS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fpga/OliverSM05,
author = {Timothy F. Oliver and
Bertil Schmidt and
Douglas L. Maskell},
editor = {Herman Schmit and
Steven J. E. Wilton},
title = {Hyper customized processors for bio-sequence database scanning on
FPGAs},
booktitle = {Proceedings of the {ACM/SIGDA} 13th International Symposium on Field
Programmable Gate Arrays, {FPGA} 2005, Monterey, California, USA,
February 20-22, 2005},
pages = {229--237},
publisher = {{ACM}},
year = {2005},
url = {https://doi.org/10.1145/1046192.1046222},
doi = {10.1145/1046192.1046222},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/fpga/OliverSM05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icpads/OliverSMNC05,
author = {Timothy F. Oliver and
Bertil Schmidt and
Douglas L. Maskell and
Darran Nathan and
Ralf Clemens},
title = {Multiple Sequence Alignment on an {FPGA}},
booktitle = {11th International Conference on Parallel and Distributed Systems,
{ICPADS} 2005, Fuduoka, Japan, July 20-22, 2005},
pages = {326--330},
publisher = {{IEEE} Computer Society},
year = {2005},
url = {https://doi.org/10.1109/ICPADS.2005.202},
doi = {10.1109/ICPADS.2005.202},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icpads/OliverSMNC05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ideal/RajapakseWSB05,
author = {Menaka Rajapakse and
Lonce L. Wyse and
Bertil Schmidt and
Vladimir Brusic},
editor = {Marcus Gallagher and
James M. Hogan and
Fr{\'{e}}d{\'{e}}ric Maire},
title = {Deriving Matrix of Peptide-MHC Interactions in Diabetic Mouse by Genetic
Algorithm},
booktitle = {Intelligent Data Engineering and Automated Learning - {IDEAL} 2005,
6th International Conference, Brisbane, Australia, July 6-8, 2005,
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3578},
pages = {440--447},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11508069\_57},
doi = {10.1007/11508069\_57},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ideal/RajapakseWSB05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/LiuS05,
author = {Weiguo Liu and
Bertil Schmidt},
title = {A Case Study on Pattern-Based Systems for High Performance Computational
Biology},
booktitle = {19th International Parallel and Distributed Processing Symposium {(IPDPS}
2005), {CD-ROM} / Abstracts Proceedings, 4-8 April 2005, Denver, CO,
{USA}},
publisher = {{IEEE} Computer Society},
year = {2005},
url = {https://doi.org/10.1109/IPDPS.2005.2},
doi = {10.1109/IPDPS.2005.2},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/LiuS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iscas/OliverSMV05,
author = {Timothy F. Oliver and
Bertil Schmidt and
Douglas L. Maskell and
Achutavarrier Prasad Vinod},
title = {A reconfigurable architecture for scanning biosequence databases},
booktitle = {International Symposium on Circuits and Systems {(ISCAS} 2005), 23-26
May 2005, Kobe, Japan},
pages = {4799--4802},
publisher = {{IEEE}},
year = {2005},
url = {https://doi.org/10.1109/ISCAS.2005.1465706},
doi = {10.1109/ISCAS.2005.1465706},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/iscas/OliverSMV05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/concurrency/SchmidtFLS04,
author = {Bertil Schmidt and
Lin Feng and
Amey V. Laud and
Yusdi Santoso},
title = {Development of distributed bioinformatics applications with {GMP}},
journal = {Concurr. Pract. Exp.},
volume = {16},
number = {9},
pages = {945--959},
year = {2004},
url = {https://doi.org/10.1002/cpe.815},
doi = {10.1002/CPE.815},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/concurrency/SchmidtFLS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/paapp/SchimmlerSL04,
author = {Manfred Schimmler and
Bertil Schmidt and
Hans{-}Werner Lang},
title = {A bit-serial floating-point unit for a massively parallel system on
a chip},
journal = {Parallel Algorithms Appl.},
volume = {19},
number = {2-3},
pages = {79--95},
year = {2004},
url = {https://doi.org/10.1080/10637190410001725454},
doi = {10.1080/10637190410001725454},
timestamp = {Sat, 20 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/paapp/SchimmlerSL04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ccgrid/ChenS04,
author = {Chunxi Chen and
Bertil Schmidt},
title = {Performance analysis of computational biology applications on hierarchical
Grid systems},
booktitle = {4th {IEEE/ACM} International Symposium on Cluster Computing and the
Grid (CCGrid 2004), April 19-22, 2004, Chicago, Illinois, {USA}},
pages = {426--433},
publisher = {{IEEE} Computer Society},
year = {2004},
url = {https://doi.org/10.1109/CCGrid.2004.1336597},
doi = {10.1109/CCGRID.2004.1336597},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ccgrid/ChenS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/europar/LiuS04,
author = {Weiguo Liu and
Bertil Schmidt},
editor = {Marco Danelutto and
Marco Vanneschi and
Domenico Laforenza},
title = {A Generic Parallel Pattern-Based System for Bioinformatics},
booktitle = {Euro-Par 2004 Parallel Processing, 10th International Euro-Par Conference,
Pisa, Italy, August 31-September 3, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3149},
pages = {989--996},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-27866-5\_133},
doi = {10.1007/978-3-540-27866-5\_133},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/europar/LiuS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hipc/LiuS04,
author = {Weiguo Liu and
Bertil Schmidt},
editor = {Luc Boug{\'{e}} and
Viktor K. Prasanna},
title = {A Tunable Coarse-Grained Parallel Algorithm for Irregular Dynamic
Programming Applications},
booktitle = {High Performance Computing - HiPC 2004, 11th International Conference,
Bangalore, India, December 19-22, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3296},
pages = {91--100},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-30474-6\_15},
doi = {10.1007/978-3-540-30474-6\_15},
timestamp = {Tue, 14 May 2019 10:00:50 +0200},
biburl = {https://dblp.org/rec/conf/hipc/LiuS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hipc/ChenS04,
author = {Chunxi Chen and
Bertil Schmidt},
editor = {Luc Boug{\'{e}} and
Viktor K. Prasanna},
title = {Load Balancing for Hierarchical Grid Computing: {A} Case Study},
booktitle = {High Performance Computing - HiPC 2004, 11th International Conference,
Bangalore, India, December 19-22, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3296},
pages = {353--362},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-30474-6\_39},
doi = {10.1007/978-3-540-30474-6\_39},
timestamp = {Fri, 26 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/hipc/ChenS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/LiuS04,
author = {Tong Liu and
Bertil Schmidt},
title = {Parallel {RNA} Sequence-Structure Alignment},
booktitle = {18th International Parallel and Distributed Processing Symposium {(IPDPS}
2004), {CD-ROM} / Abstracts Proceedings, 26-30 April 2004, Santa Fe,
New Mexico, {USA}},
publisher = {{IEEE} Computer Society},
year = {2004},
url = {https://doi.org/10.1109/IPDPS.2004.1303207},
doi = {10.1109/IPDPS.2004.1303207},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ipps/LiuS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/OliverS04,
author = {Timothy F. Oliver and
Bertil Schmidt},
title = {High Performance Biosequence Database Scanning on Reconfigurable Platforms},
booktitle = {18th International Parallel and Distributed Processing Symposium {(IPDPS}
2004), {CD-ROM} / Abstracts Proceedings, 26-30 April 2004, Santa Fe,
New Mexico, {USA}},
publisher = {{IEEE} Computer Society},
year = {2004},
url = {https://doi.org/10.1109/IPDPS.2004.1303211},
doi = {10.1109/IPDPS.2004.1303211},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ipps/OliverS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cluster/ChenS03,
author = {Chunxi Chen and
Bertil Schmidt},
title = {Computing Large-Scale Alignments on a Multi-Cluster},
booktitle = {2003 {IEEE} International Conference on Cluster Computing {(CLUSTER}
2003), 1-4 December 2003, Kowloon, Hong Kong, China},
pages = {38--45},
publisher = {{IEEE} Computer Society},
year = {2003},
url = {https://doi.org/10.1109/CLUSTR.2003.1253297},
doi = {10.1109/CLUSTR.2003.1253297},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cluster/ChenS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cluster/LiuS03,
author = {Weiguo Liu and
Bertil Schmidt},
title = {Parallel Design Pattern for Computational Biology and Scientific Computing
Applications},
booktitle = {2003 {IEEE} International Conference on Cluster Computing {(CLUSTER}
2003), 1-4 December 2003, Kowloon, Hong Kong, China},
pages = {456--459},
publisher = {{IEEE} Computer Society},
year = {2003},
url = {https://doi.org/10.1109/CLUSTR.2003.1253348},
doi = {10.1109/CLUSTR.2003.1253348},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cluster/LiuS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/europar/AhmadJSU03,
author = {Ishfaq Ahmad and
Pieter Jonker and
Bertil Schmidt and
Andreas Uhl},
editor = {Harald Kosch and
L{\'{a}}szl{\'{o}} B{\"{o}}sz{\"{o}}rm{\'{e}}nyi and
Hermann Hellwagner},
title = {Topic Introduction},
booktitle = {Euro-Par 2003. Parallel Processing, 9th International Euro-Par Conference,
Klagenfurt, Austria, August 26-29, 2003. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2790},
pages = {850},
publisher = {Springer},
year = {2003},
url = {https://doi.org/10.1007/978-3-540-45209-6\_116},
doi = {10.1007/978-3-540-45209-6\_116},
timestamp = {Tue, 14 May 2019 10:00:46 +0200},
biburl = {https://dblp.org/rec/conf/europar/AhmadJSU03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/SchmidtFLS03,
author = {Bertil Schmidt and
Lin Feng and
Amey V. Laud and
Yusdi Santoso},
title = {Parallel Detection of Regulatory Elements with gMP},
booktitle = {17th International Parallel and Distributed Processing Symposium {(IPDPS}
2003), 22-26 April 2003, Nice, France, CD-ROM/Abstracts Proceedings},
pages = {156},
publisher = {{IEEE} Computer Society},
year = {2003},
url = {https://doi.org/10.1109/IPDPS.2003.1213294},
doi = {10.1109/IPDPS.2003.1213294},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ipps/SchmidtFLS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pdpta/SchimmlerSL03,
author = {Manfred Schimmler and
Bertil Schmidt and
Hans{-}Werner Lang},
editor = {Hamid R. Arabnia and
Youngsong Mun},
title = {Design of a Bit-Serial Floating Point Unit for a Fine Grained Parallel
Processor Array},
booktitle = {Proceedings of the International Conference on Parallel and Distributed
Processing Techniques and Applications, {PDPTA} '03, June 23 - 26,
2003, Las Vegas, Nevada, USA, Volume 1},
pages = {255--261},
publisher = {{CSREA} Press},
year = {2003},
timestamp = {Fri, 05 Dec 2003 09:24:11 +0100},
biburl = {https://dblp.org/rec/conf/pdpta/SchimmlerSL03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/vlsi/SchimmlerSLH03,
author = {Manfred Schimmler and
Bertil Schmidt and
Hans{-}Werner Lang and
Sven Heithecker},
editor = {Hamid R. Arabnia and
Laurence Tianruo Yang},
title = {An Area-Efficient Bit-Serial Integer Multiplier},
booktitle = {Proceedings of the International Conference on VLSI, {VLSI} '03, June
23 - 26, 2003, Las Vegas, Nevada, {USA}},
pages = {131--137},
publisher = {{CSREA} Press},
year = {2003},
timestamp = {Fri, 17 Oct 2003 11:18:22 +0200},
biburl = {https://dblp.org/rec/conf/vlsi/SchimmlerSLH03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fgcs/SchmidtSS02,
author = {Bertil Schmidt and
Heiko Schr{\"{o}}der and
Manfred Schimmler},
title = {A hybrid architecture for bioinformatics},
journal = {Future Gener. Comput. Syst.},
volume = {18},
number = {6},
pages = {855--862},
year = {2002},
url = {https://doi.org/10.1016/S0167-739X(02)00058-4},
doi = {10.1016/S0167-739X(02)00058-4},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fgcs/SchmidtSS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/SchmidtSS02,
author = {Bertil Schmidt and
Heiko Schr{\"{o}}der and
Manfred Schimmler},
title = {Massively Parallel Solutions for Molecular Sequence Analysis},
booktitle = {16th International Parallel and Distributed Processing Symposium {(IPDPS}
2002), 15-19 April 2002, Fort Lauderdale, FL, USA, CD-ROM/Abstracts
Proceedings},
publisher = {{IEEE} Computer Society},
year = {2002},
url = {https://doi.org/10.1109/IPDPS.2002.1016589},
doi = {10.1109/IPDPS.2002.1016589},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ipps/SchmidtSS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cai/SchmidtSS01,
author = {Bertil Schmidt and
Heiko Schr{\"{o}}der and
Manfred Schimmler},
title = {Tomographic Image Reconstruction on the Instruction Systolic Array},
journal = {Comput. Artif. Intell.},
volume = {20},
number = {1},
pages = {27--42},
year = {2001},
url = {http://www.cai.sk/ojs/index.php/cai/article/view/509},
timestamp = {Mon, 14 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/cai/SchmidtSS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cai/SchmidtS01,
author = {Bertil Schmidt and
Heiko Schr{\"{o}}der},
title = {A Hybrid Architecture for Multimedia Processors},
journal = {Comput. Artif. Intell.},
volume = {20},
number = {3},
pages = {225--244},
year = {2001},
url = {http://www.cai.sk/ojs/index.php/cai/article/view/518},
timestamp = {Mon, 14 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/cai/SchmidtS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/europar/SchmidtSS01,
author = {Bertil Schmidt and
Heiko Schr{\"{o}}der and
Manfred Schimmler},
editor = {Rizos Sakellariou and
John A. Keane and
John R. Gurd and
Len Freeman},
title = {Scanning Biosequence Databases on a Hybrid Parallel Architecture},
booktitle = {Euro-Par 2001: Parallel Processing, 7th International Euro-Par Conference
Manchester, {UK} August 28-31, 2001, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2150},
pages = {360--370},
publisher = {Springer},
year = {2001},
url = {https://doi.org/10.1007/3-540-44681-8\_52},
doi = {10.1007/3-540-44681-8\_52},
timestamp = {Wed, 15 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/europar/SchmidtSS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pact/SchmidtSS01,
author = {Bertil Schmidt and
Heiko Schr{\"{o}}der and
Manfred Schimmler},
editor = {Victor E. Malyshkin},
title = {Protein Sequence Comparison on the Instruction Systolic Array},
booktitle = {Parallel Computing Technologies, 6th International Conference, PaCT
2001, Novosibirsk, Russia, September 3-7, 2001, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2127},
pages = {498--509},
publisher = {Springer},
year = {2001},
url = {https://doi.org/10.1007/3-540-44743-1\_52},
doi = {10.1007/3-540-44743-1\_52},
timestamp = {Wed, 15 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/pact/SchmidtSS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/scpe/SchmidtS00,
author = {Bertil Schmidt and
Manfred Schimmler},
title = {{KPROC} - An Instruction Systolic Architecture for Parallel Prefix
Applications},
journal = {Scalable Comput. Pract. Exp.},
volume = {3},
number = {2},
year = {2000},
url = {http://www.scpe.org/index.php/scpe/article/view/189},
timestamp = {Thu, 09 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/scpe/SchmidtS00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/europar/Schmidt00,
author = {Bertil Schmidt},
editor = {Arndt Bode and
Thomas Ludwig and
Wolfgang Karl and
Roland Wism{\"{u}}ller},
title = {Design of a Parallel Accelerator for Volume Rendering},
booktitle = {Euro-Par 2000, Parallel Processing, 6th International Euro-Par Conference,
Munich, Germany, August 29 - September 1, 2000, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1900},
pages = {1095--1104},
publisher = {Springer},
year = {2000},
url = {https://doi.org/10.1007/3-540-44520-X\_155},
doi = {10.1007/3-540-44520-X\_155},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/europar/Schmidt00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cai/SchmidtSS99,
author = {Bertil Schmidt and
Manfred Schimmler and
Heiko Schr{\"{o}}der},
title = {A Morphological Approach to Hough Transform on an Instruction Systolic
Array},
journal = {Comput. Artif. Intell.},
volume = {18},
number = {6},
pages = {541--557},
year = {1999},
url = {http://www.cai.sk/ojs/index.php/cai/article/view/580},
timestamp = {Mon, 14 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/cai/SchmidtSS99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/europar/SchmidtS99,
author = {Bertil Schmidt and
Manfred Schimmler},
editor = {Patrick Amestoy and
Philippe Berger and
Michel J. Dayd{\'{e}} and
Iain S. Duff and
Val{\'{e}}rie Frayss{\'{e}} and
Luc Giraud and
Daniel Ruiz},
title = {A Parallel Accelerator Architecture for Multimedia Video Compression},
booktitle = {Euro-Par '99 Parallel Processing, 5th International Euro-Par Conference,
Toulouse, France, August 31 - September 3, 1999, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1685},
pages = {950--960},
publisher = {Springer},
year = {1999},
url = {https://doi.org/10.1007/3-540-48311-X\_133},
doi = {10.1007/3-540-48311-X\_133},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/europar/SchmidtS99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/europar/SchmidtSS98,
author = {Bertil Schmidt and
Manfred Schimmler and
Heiko Schr{\"{o}}der},
editor = {David J. Pritchard and
Jeff Reeve},
title = {Long Operand Arithmetic on Instruction Systolic Computer Architectures
and Its Application in {RSA} Cryptography},
booktitle = {Euro-Par '98 Parallel Processing, 4th International Euro-Par Conference,
Southampton, UK, September 1-4, 1998, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1470},
pages = {916--922},
publisher = {Springer},
year = {1998},
url = {https://doi.org/10.1007/BFb0057948},
doi = {10.1007/BFB0057948},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/europar/SchmidtSS98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/europar/SchmidtSS97,
author = {Bertil Schmidt and
Manfred Schimmler and
Heiko Schr{\"{o}}der},
editor = {Christian Lengauer and
Martin Griebl and
Sergei Gorlatch},
title = {Morphological Hough Transform on the Instruction Systolic Array},
booktitle = {Euro-Par '97 Parallel Processing, Third International Euro-Par Conference,
Passau, Germany, August 26-29, 1997, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1300},
pages = {798--806},
publisher = {Springer},
year = {1997},
url = {https://doi.org/10.1007/BFb0002816},
doi = {10.1007/BFB0002816},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/europar/SchmidtSS97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dagm/MahlmeisterSS95,
author = {Udo Mahlmeister and
Bertil Schmidt and
Gerald Sommer},
editor = {Gerhard Sagerer and
Stefan Posch and
Franz Kummert},
title = {Preattentive Colour Features by Steerable Filters},
booktitle = {Mustererkennung 1995, 17. DAGM-Symposium, Bielefeld, 13.-15. September
1995, Proceedings},
series = {Informatik Aktuell},
pages = {464--472},
publisher = {Springer},
year = {1995},
url = {https://doi.org/10.1007/978-3-642-79980-8\_55},
doi = {10.1007/978-3-642-79980-8\_55},
timestamp = {Mon, 24 Jun 2019 15:47:45 +0200},
biburl = {https://dblp.org/rec/conf/dagm/MahlmeisterSS95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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