Bertil Schmidt

243 papers A 18B 17C 9Misc 17Journal 123Unranked 54

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Accelerating Molecular Dynamics Simulations on ARM Multi-Core Processors. IEEE Trans. Parallel Distributed Syst. Ran Chen, Huihai An, Zhihua Sa, Ping Gao, Xiaohui Duan, Bertil Schmidt, Yang Yang, Yizhen Chen, Lin Gan, Guangwen Yang, Weiguo Liu
2026	J	`jnl`	Cuckoo-GPU: Accelerating Cuckoo Filters on Modern GPUs. CoRR Tim Dortmann, Markus Vieth, Bertil Schmidt
2026	J	`jnl`	RabbitVar: Ultra-fast and accurate somatic small-variant calling on multi-core architectures. Future Gener. Comput. Syst. Hao Zhang, Lin Gan, Zekun Yin, Lifeng Yan, Honglei Song, Qixin Chang, Tong Zhang, Yanjie Wei, Beifang Niu, Bertil Schmidt, Weiguo Liu
2026	J	`jnl`	gpuPairHMM: High-Speed Pair-HMM Forward Algorithm for DNA Variant Calling on GPUs. IEEE Trans. Comput. Biol. Bioinform. Bertil Schmidt, Felix Kallenborn, Alexander Wichmann, Alejandro Chacón, Christian Hundt
2025	—	`conf`	Corrigendum to Studying Privacy Aspects of Learned Knowledge Bases in the Context of Synthetic and Medical Data. GMDS Xenia Heilmann, Valentin Henkys, Daan Apeldoorn, Konstantin Strauch, Bertil Schmidt, Timm Lilienthal, Torsten Panholzer
2025	J	`jnl`	Optimizing Bloom Filters for Modern GPU Architectures. CoRR Daniel Jünger, Kevin Kristensen, Yunsong Wang, Xiangyao Yu, Bertil Schmidt
2025	J	`jnl`	RabbitBAM: Accelerating BAM File Manipulation on Multi-Core Platforms. IEEE Trans. Comput. Biol. Bioinform. Lifeng Yan, Zhan Zhao, Zekun Yin, Tong Zhang, Yang Yang, Fangjin Zhu, Xiaohui Duan, Bertil Schmidt, Weiguo Liu
2025	J	`jnl`	RabbitSketch: a high-performance sketching library for genome analysis. Bioinform. Tong Zhang, Zekun Yin, Xiaoming Xu, Lifeng Yan, Fangjin Zhu, Xiaohui Duan, Bertil Schmidt, Weiguo Liu
2025	—	`conf`	RabbitTClust2: Fast, Scalable, and Versatile Clustering for Massive Genomic Datasets. BIBM Tong Zhang, Xiaoming Xu, Zekun Yin, Lifeng Yan, Yang Yang, Yijie Gao, Xiaohui Duan, Bertil Schmidt, Weiguo Liu
2025	J	`jnl`	RabbitTrim: An Efficient and Versatile Trimmer on Multi-Core Platforms. IEEE Trans. Comput. Biol. Bioinform. Mingkai Wang, Yang Yang, Zekun Yin, Lifeng Yan, Tong Zhang, Fangjin Zhu, Xin Li, Xiaohui Duan, Bertil Schmidt, Weiguo Liu
2025	—	`conf`	SWBWA: A Highly Efficient NGS Aligner on the New Sunway Architecture. Euro-Par (3) Lifeng Yan, Zekun Yin, Qixin Chang, Tong Zhang, Zhisong Wang, Xiaohui Duan, Bertil Schmidt, Weiguo Liu
2025	J	`jnl`	SWQC: Efficient sequencing data quality control on the next-generation sunway platform. Future Gener. Comput. Syst. Lifeng Yan, Zekun Yin, Tong Zhang, Fangjin Zhu, Xiaohui Duan, Bertil Schmidt, Weiguo Liu
2025	—	`conf`	cuTeBool: Fast and Scalable Boolean Matrix Factorization on GPUs Using Tensor Cores. ICCS (2) Andrea Beyer, Valentin Henkys, Robin Kobus, Stefan Kramer, Bertil Schmidt
2024	J	`jnl`	A framework for synthetic diagnostics using energetic-particle orbits in tokamaks. Comput. Phys. Commun. Henrik Järleblad, Luke Stagner, Mirko Salewski, J. Eriksson, M. Nocente, Bertil Schmidt, M. Rud Larsen
2024	J	`jnl`	CAREx: context-aware read extension of paired-end sequencing data. BMC Bioinform. Felix Kallenborn, Bertil Schmidt
2024	J	`jnl`	CUDASW++4.0: ultra-fast GPU-based Smith-Waterman protein sequence database search. BMC Bioinform. Bertil Schmidt, Felix Kallenborn, Alejandro Chacón, Christian Hundt
2024	B	`conf`	Massively Parallel Inverse Block-sorting Transforms for bzip2 Decompression on GPUs. ICPP André Weißenberger, Bertil Schmidt
2024	—	`conf`	RabbitSAlign: Accelerating Short-Read Alignment for CPU-GPU Heterogeneous Platforms. ISBRA (2) Lifeng Yan, Zekun Yin, Jinjin Li, Yang Yang, Tong Zhang, Fangjin Zhu, Xiaohui Duan, Bertil Schmidt, Weiguo Liu
2024	—	`conf`	RabbitTrim: Highly Optimized Trimming of Illumina Sequencing Data on Multi-core Platforms. ISBRA (2) Mingkai Wang, Zekun Yin, Lifeng Yan, Yang Yang, Fangjin Zhu, Xiaohui Duan, Xin Li, Bertil Schmidt, Weiguo Liu
2024	—	`conf`	Scalable GPU-Enabled Creation of Three Dimensional Weather Fronts. PASC Stefan Niebler, Bertil Schmidt, Peter Spichtinger, Holger Tost
2024	—	`conf`	Studying Privacy Aspects of Learned Knowledge Bases in the Context of Synthetic and Medical Data. GMDS Xenia Heilmann, Daan Apeldoorn, Konstantin Strauch, Bertil Schmidt, Timm Lilienthal, Torsten Panholzer
2024	J	`jnl`	gpuPairHMM: High-speed Pair-HMM Forward Algorithm for DNA Variant Calling on GPUs. CoRR Bertil Schmidt, Felix Kallenborn, Alexander Wichmann, Alejandro Chacón, Christian Hundt
2023	—	`conf`	Automated Identification and Location of Three Dimensional Atmospheric Frontal Systems. ICCS (2) Stefan Niebler, Bertil Schmidt, Holger Tost, Peter Spichtinger
2023	J	`jnl`	Bio-ESMD: A Data Centric Implementation for Large-Scale Biological System Simulation on Sunway TaihuLight Supercomputer. IEEE Trans. Parallel Distributed Syst. Xiaohui Duan, Qi Shao, Junben Weng, Bertil Schmidt, Lin Gan, Guohui Li, Haohuan Fu, Wei Xue, Weiguo Liu, Guangwen Yang
2023	J	`jnl`	CUDA-accelerated protein electrostatics in linear space. J. Comput. Sci. Thomas Kemmer, Sebastian Hack, Bertil Schmidt, Andreas Hildebrandt
2023	—	`conf`	Faster Segmented Sort on GPUs. Euro-Par Robin Kobus, Johannes Nelgen, Valentin Henkys, Bertil Schmidt
2023	J	`jnl`	RabbitFX: Efficient Framework for FASTA/Q File Parsing on Modern Multi-Core Platforms. IEEE ACM Trans. Comput. Biol. Bioinform. Hao Zhang, Honglei Song, Xiaoming Xu, Qixin Chang, Mingkai Wang, Yanjie Wei, Zekun Yin, Bertil Schmidt, Weiguo Liu
2023	J	`jnl`	RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures. Bioinform. Xiaoming Xu, Zekun Yin, Lifeng Yan, Huiguang Yi, Hua Wang, Bertil Schmidt, Weiguo Liu
2023	J	`jnl`	Redesign and Accelerate the AIREBO Bond-Order Potential on the New Sunway Supercomputer. IEEE Trans. Parallel Distributed Syst. Ping Gao, Xiaohui Duan, Bertil Schmidt, Wubing Wan, Jiaxu Guo, Wusheng Zhang, Lin Gan, Haohuan Fu, Wei Xue, Weiguo Liu, Guangwen Yang
2022	J	`jnl`	AnySeq/GPU: A Novel Approach for Faster Sequence Alignment on GPUs. CoRR André Müller, Bertil Schmidt, Richard Membarth, Roland Leißa, Sebastian Hack
2022	A	`conf`	AnySeq/GPU: a novel approach for faster sequence alignment on GPUs. ICS André Müller, Bertil Schmidt, Richard Membarth, Roland Leißa, Sebastian Hack
2022	J	`jnl`	Automatic Generation of High-Performance Convolution Kernels on ARM CPUs for Deep Learning. IEEE Trans. Parallel Distributed Syst. Jintao Meng, Chen Zhuang, Peng Chen, Mohamed Wahib, Bertil Schmidt, Xiao Wang, Haidong Lan, Dou Wu, Minwen Deng, Yanjie Wei, Shengzhong Feng
2022	J	`jnl`	CARE 2.0: reducing false-positive sequencing error corrections using machine learning. BMC Bioinform. Felix Kallenborn, Julian Cascitti, Bertil Schmidt
2022	J	`jnl`	FMapper: Scalable read mapper based on succinct hash index on SunWay TaihuLight. J. Parallel Distributed Comput. Kai Xu, Xiaohui Duan, André Müller, Robin Kobus, Bertil Schmidt, Weiguo Liu
2022	J	`jnl`	General-purpose GPU hashing data structures and their application in accelerated genomics. J. Parallel Distributed Comput. Daniel Jünger, Robin Kobus, André Müller, Christian Hundt, Kai Xu, Weiguo Liu, Bertil Schmidt
2022	J	`jnl`	Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data. BMC Bioinform. Konstantin Bob, David Teschner, Thomas Kemmer, David Gomez-Zepeda, Stefan Tenzer, Bertil Schmidt, Andreas Hildebrandt
2022	C	`conf`	Online Event Selection for Mu3e using GPUs. ISPDC Valentin Henkys, Bertil Schmidt, Niklaus Berger
2022	J	`jnl`	Online Event Selection for Mu3e using GPUs. CoRR Valentin Henkys, Bertil Schmidt, Niklaus Berger
2022	J	`jnl`	Optimization of Reactive Force Field Simulation: Refactor, Parallelization, and Vectorization for Interactions. IEEE Trans. Parallel Distributed Syst. Ping Gao, Xiaohui Duan, Bertil Schmidt, Wusheng Zhang, Lin Gan, Haohuan Fu, Wei Xue, Weiguo Liu, Guangwen Yang
2022	J	`jnl`	RNACache: A scalable approach to rapid transcriptomic read mapping using locality sensitive hashing. J. Comput. Sci. Julian Cascitti, Stefan Niebler, André Müller, Bertil Schmidt
2022	—	`conf`	RabbitQCPlus: More Efficient Quality Control for Sequencing Data. BIBM Lifeng Yan, Zekun Yin, Hao Zhang, Zhan Zhao, Mingkai Wang, André Müller, Robin Kobus, Yanjie Wei, Beifang Niu, Bertil Schmidt, Weiguo Liu
2022	J	`jnl`	RabbitV: fast detection of viruses and microorganisms in sequencing data on multi-core architectures. Bioinform. Hao Zhang, Qixin Chang, Zekun Yin, Xiaoming Xu, Yanjie Wei, Bertil Schmidt, Weiguo Liu
2022	J	`jnl`	Redesigning and Optimizing UCSF DOCK3.7 on Sunway TaihuLight. IEEE Trans. Parallel Distributed Syst. Kai Xu, Jinxiao Zhang, Xiaohui Duan, Xiaobo Wan, Niu Huang, Bertil Schmidt, Weiguo Liu, Guangwen Yang
2021	Misc	`conf`	Accelerating JPEG Decompression on GPUs. HiPC André Weißenberger, Bertil Schmidt
2021	J	`jnl`	Accelerating JPEG Decompression on GPUs. CoRR André Weißenberger, Bertil Schmidt
2021	J	`jnl`	CARE: context-aware sequencing read error correction. Bioinform. Felix Kallenborn, Andreas Hildebrandt, Bertil Schmidt
2021	B	`conf`	MetaCache-GPU: Ultra-Fast Metagenomic Classification. ICPP Robin Kobus, André Müller, Daniel Jünger, Christian Hundt, Bertil Schmidt
2021	J	`jnl`	MetaCache-GPU: Ultra-Fast Metagenomic Classification. CoRR Robin Kobus, André Müller, Daniel Jünger, Christian Hundt, Bertil Schmidt
2021	—	`conf`	RNACache: Fast Mapping of RNA-Seq Reads to Transcriptomes Using MinHashing. ICCS (1) Julian Cascitti, Stefan Niebler, André Müller, Bertil Schmidt
2021	J	`jnl`	RabbitMash: accelerating hash-based genome analysis on modern multi-core architectures. Bioinform. Zekun Yin, Xiaoming Xu, Jinxiao Zhang, Yanjie Wei, Bertil Schmidt, Weiguo Liu
2021	J	`jnl`	RabbitQC: high-speed scalable quality control for sequencing data. Bioinform. Zekun Yin, Hao Zhang, Meiyang Liu, Wen Zhang, Honglei Song, Haidong Lan, Yanjie Wei, Beifang Niu, Bertil Schmidt, Weiguo Liu
2020	J	`jnl`	A big data approach to metagenomics for all-food-sequencing. BMC Bioinform. Robin Kobus, José Manuel Abuín, André Müller, Sören Lukas Hellmann, Juan Carlos Pichel, Tomás F. Pena, Andreas Hildebrandt, Thomas Hankeln, Bertil Schmidt
2020	A	`conf`	AnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation. IPDPS André Müller, Bertil Schmidt, Andreas Hildebrandt, Richard Membarth, Roland Leißa, Matthis Kruse, Sebastian Hack
2020	J	`jnl`	AnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation. CoRR André Müller, Bertil Schmidt, Andreas Hildebrandt, Richard Membarth, Roland Leißa, Matthis Kruse, Sebastian Hack
2020	A	`conf`	Cell-list based molecular dynamics on many-core processors: a case study on sunway TaihuLight supercomputer. SC Xiaohui Duan, Ping Gao, Meng Zhang, Tingjian Zhang, Hongsong Meng, Yuxuan Li, Bertil Schmidt, Haohuan Fu, Lin Gan, Wei Xue, Weiguo Liu, Guangwen Yang
2020	J	`jnl`	FeatherCNN: Fast Inference Computation with TensorGEMM on ARM Architectures. IEEE Trans. Parallel Distributed Syst. Haidong Lan, Jintao Meng, Christian Hundt, Bertil Schmidt, Minwen Deng, Xiaoning Wang, Weiguo Liu, Yu Qiao, Shengzhong Feng
2020	J	`jnl`	Millimeter-Scale and Billion-Atom Reactive Force Field Simulation on Sunway Taihulight. IEEE Trans. Parallel Distributed Syst. Ping Gao, Xiaohui Duan, Tingjian Zhang, Meng Zhang, Bertil Schmidt, Xun Zhang, Hongliang Sun, Wusheng Zhang, Lin Gan, Wei Xue, Haohuan Fu, Weiguo Liu, Guangwen Yang
2020	B	`conf`	Neighbor-list-free molecular dynamics on sunway TaihuLight supercomputer. PPoPP Xiaohui Duan, Ping Gao, Meng Zhang, Tingjian Zhang, Hongsong Meng, Yuxuan Li, Bertil Schmidt, Haohuan Fu, Lin Gan, Wei Xue, Guangwen Yang, Weiguo Liu
2020	J	`jnl`	RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads. BMC Bioinform. Stefan Niebler, André Müller, Thomas Hankeln, Bertil Schmidt
2020	—	`conf`	Reconstruction of Low Energy Neutrino Events with GPUs at IceCube. ICCS (1) Maicon Hieronymus, Bertil Schmidt, Sebastian Böser
2020	B	`conf`	SWMapper: Scalable Read Mapper on SunWay TaihuLight. ICPP Kai Xu, Xiaohui Duan, Xiangxu Meng, Xin Li, Bertil Schmidt, Weiguo Liu
2020	Misc	`conf`	WarpCore: A Library for fast Hash Tables on GPUs. HiPC Daniel Jünger, Robin Kobus, André Müller, Christian Hundt, Kai Xu, Weiguo Liu, Bertil Schmidt
2020	J	`jnl`	WarpCore: A Library for fast Hash Tables on GPUs. CoRR Daniel Jünger, Robin Kobus, André Müller, Christian Hundt, Kai Xu, Weiguo Liu, Bertil Schmidt
2020	—	`conf`	cuDTW++: Ultra-Fast Dynamic Time Warping on CUDA-Enabled GPUs. Euro-Par Bertil Schmidt, Christian Hundt
2019	J	`jnl`	BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures. Bioinform. Jikai Zhang, Haidong Lan, Yuandong Chan, Yuan Shang, Bertil Schmidt, Weiguo Liu
2019	—	`ch.`	Dedicated Bioinformatics Analysis Hardware. Encyclopedia of Bioinformatics and Computational Biology (2) Bertil Schmidt, Andreas Hildebrandt
2019	—	`conf`	Efficient Parallel Sort on AVX-512-Based Multi-Core and Many-Core Architectures. HPCC/SmartCity/DSS Zekun Yin, Tianyu Zhang, André Müller, Hui Liu, Yanjie Wei, Bertil Schmidt, Weiguo Liu
2019	B	`conf`	Gossip: Efficient Communication Primitives for Multi-GPU Systems. ICPP Robin Kobus, Daniel Jünger, Christian Hundt, Bertil Schmidt
2019	B	`conf`	Massively Parallel ANS Decoding on GPUs. ICPP André Weißenberger, Bertil Schmidt
2019	J	`jnl`	Massively parallel computation of atmospheric neutrino oscillations on CUDA-enabled accelerators. Comput. Phys. Commun. Felix Kallenborn, Christian Hundt, Sebastian Böser, Bertil Schmidt
2019	A	`conf`	Suffix Array Construction on Multi-GPU Systems. HPDC Florian Büren, Daniel Jünger, Robin Kobus, Christian Hundt, Bertil Schmidt
2019	—	`conf`	XLCS: A New Bit-Parallel Longest Common Subsequence Algorithm on Xeon Phi Clusters. HPCC/SmartCity/DSS Zekun Yin, Hao Zhang, Kai Xu, Yuandong Chan, Shaoliang Peng, Xiaoning Wang, Bertil Schmidt, Weiguo Liu
2019	J	`jnl`	kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers. Bioinform. Peng Jiang, Jie Luo, Yiqi Wang, Pingji Deng, Bertil Schmidt, Xiangjun Tang, Ningjiang Chen, Limsoon Wong, Liang Zhao
2018	J	`jnl`	AnyDSL: a partial evaluation framework for programming high-performance libraries. Proc. ACM Program. Lang. Roland Leißa, Klaas Boesche, Sebastian Hack, Arsène Pérard-Gayot, Richard Membarth, Philipp Slusallek, André Müller, Bertil Schmidt
2018	J	`jnl`	Fast and efficient short read mapping based on a succinct hash index. BMC Bioinform. Haowen Zhang, Yuandong Chan, Kaichao Fan, Bertil Schmidt, Weiguo Liu
2018	J	`jnl`	LightSpMV: Faster CUDA-Compatible Sparse Matrix-Vector Multiplication Using Compressed Sparse Rows. J. Signal Process. Syst. Yongchao Liu, Bertil Schmidt
2018	B	`conf`	Massively Parallel Huffman Decoding on GPUs. ICPP André Weißenberger, Bertil Schmidt
2018	B	`conf`	SPECTR: Scalable Parallel Short Read Error Correction on Multi-core and Many-core Architectures. ICPP Kai Xu, Robin Kobus, Yuandong Chan, Ping Gao, Xiangxu Meng, Yanjie Wei, Bertil Schmidt, Weiguo Liu
2018	A	`conf`	WarpDrive: Massively Parallel Hashing on Multi-GPU Nodes. IPDPS Daniel Jünger, Christian Hundt, Bertil Schmidt
2018	B	`conf`	cuBool: Bit-Parallel Boolean Matrix Factorization on CUDA-Enabled Accelerators. ICPADS Robin Kobus, Adrian Lamoth, André Müller, Christian Hundt, Stefan Kramer, Bertil Schmidt
2018	J	`jnl`	parSRA: A framework for the parallel execution of short read aligners on compute clusters. J. Comput. Sci. Jorge González-Domínguez, Christian Hundt, Bertil Schmidt
2017	J	`jnl`	$ν$-net: Deep Learning for Generalized Biventricular Cardiac Mass and Function Parameters. CoRR Hinrich B. Winther, Christian Hundt, Bertil Schmidt, Christoph Czerner, Johann Bauersachs, Frank K. Wacker, Jens Vogel-Claussen
2017	J	`jnl`	AFS: identification and quantification of species composition by metagenomic sequencing. Bioinform. Yongchao Liu, Fabian Ripp, Rene Koeppel, Hanno Schmidt, Sören Lukas Hellmann, Mathias Weber, Christopher Felix Krombholz, Bertil Schmidt, Thomas Hankeln
2017	J	`jnl`	Accelerating metagenomic read classification on CUDA-enabled GPUs. BMC Bioinform. Robin Kobus, Christian Hundt, André Müller, Bertil Schmidt
2017	J	`jnl`	CLOVE: classification of genomic fusions into structural variation events. BMC Bioinform. Jan Schröder, Adrianto Wirawan, Bertil Schmidt, Anthony T. Papenfuss
2017	—	`ch.`	CUSHAW Suite: Parallel and Efficient Algorithms for NGS Read Alignment. Algorithms for Next-Generation Sequencing Data Yongchao Liu, Bertil Schmidt
2017	J	`jnl`	Mapping of option pricing algorithms onto heterogeneous many-core architectures. J. Supercomput. Shuai Zhang, Zhao Wang, Ying Peng, Bertil Schmidt, Weiguo Liu
2017	J	`jnl`	MetaCache: context-aware classification of metagenomic reads using minhashing. Bioinform. André Müller, Christian Hundt, Andreas Hildebrandt, Thomas Hankeln, Bertil Schmidt
2017	A	`conf`	PUNAS: A Parallel Ungapped-Alignment-Featured Seed Verification Algorithm for Next-Generation Sequencing Read Alignment. IPDPS Yuandong Chan, Kai Xu, Haidong Lan, Weiguo Liu, Yongchao Liu, Bertil Schmidt
2017	C	`conf`	S-Aligner: Ultrascalable Read Mapping on Sunway Taihu Light. CLUSTER Xiaohui Duan, Kai Xu, Yuandong Chan, Christian Hundt, Bertil Schmidt, Pavan Balaji, Weiguo Liu
2017	J	`jnl`	SAUCE: A web application for interactive teaching and learning of parallel programming. J. Parallel Distributed Comput. Christian Hundt, Moritz Schlarb, Bertil Schmidt
2017	A	`conf`	SWhybrid: A Hybrid-Parallel Framework for Large-Scale Protein Sequence Database Search. IPDPS Haidong Lan, Weiguo Liu, Yongchao Liu, Bertil Schmidt
2017	J	`jnl`	Speed and accuracy improvement of higher-order epistasis detection on CUDA-enabled GPUs. Clust. Comput. Daniel Jünger, Christian Hundt, Jorge González-Domínguez, Bertil Schmidt
2017	B	`conf`	mD3DOCKxb: An Ultra-Scalable CPU-MIC Coordinated Virtual Screening Framework. CCGrid Shaoliang Peng, Xiaoyu Zhang, Shunyun Yang, Wenhe Su, Zhiqiang Zhang, Dong Dong, Kai Lu, Yutong Lu, Xiangke Liao, Bertil Schmidt, Weiliang Zhu, Kuan-Ching Li
2016	J	`jnl`	Bit-parallel approximate pattern matching: Kepler GPU versus Xeon Phi. Parallel Comput. Tuan Tu Tran, Yongchao Liu, Bertil Schmidt
2016	J	`jnl`	CUDA-enabled hierarchical ward clustering of protein structures based on the nearest neighbour chain algorithm. Int. J. High Perform. Comput. Appl. Hoang-Vu Dang, Bertil Schmidt, Andreas Hildebrandt, Tuan Tu Tran, Anna Katharina Hildebrandt
2016	—	`conf`	Combining GPU and FPGA technology for efficient exhaustive interaction analysis in GWAS. ASAP Jan Christian Kässens, Lars Wienbrandt, Manfred Schimmler, Jorge González-Domínguez, Bertil Schmidt
2016	J	`jnl`	MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems. Bioinform. Jorge González-Domínguez, Yongchao Liu, Juan Touriño, Bertil Schmidt
2016	J	`jnl`	ParDRe: faster parallel duplicated reads removal tool for sequencing studies. Bioinform. Jorge González-Domínguez, Bertil Schmidt
2016	J	`jnl`	Parallel Pairwise Epistasis Detection on Heterogeneous Computing Architectures. IEEE Trans. Parallel Distributed Syst. Jorge González-Domínguez, Sabela Ramos, Juan Touriño, Bertil Schmidt
2016	J	`jnl`	Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters. BMC Bioinform. Haidong Lan, Yuandong Chan, Kai Xu, Bertil Schmidt, Shaoliang Peng, Weiguo Liu
2016	J	`jnl`	Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data. IEEE ACM Trans. Comput. Biol. Bioinform. Yongchao Liu, Thomas Hankeln, Bertil Schmidt
2016	J	`jnl`	SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations. BMC Syst. Biol. Yongchao Liu, Martin Loewer, Srinivas Aluru, Bertil Schmidt
2016	J	`jnl`	Scalable Clustering by Iterative Partitioning and Point Attractor Representation. ACM Trans. Knowl. Discov. Data Junming Shao, Qinli Yang, Hoang-Vu Dang, Bertil Schmidt, Stefan Kramer
2016	—	`conf`	Ultra-Fast Detection of Higher-Order Epistatic Interactions on GPUs. Euro-Par Workshops Daniel Jünger, Christian Hundt, Jorge González-Domínguez, Bertil Schmidt
2016	J	`jnl`	rapidGSEA: Speeding up gene set enrichment analysis on multi-core CPUs and CUDA-enabled GPUs. BMC Bioinform. Christian Hundt, Andreas Hildebrandt, Bertil Schmidt
2015	J	`jnl`	Accelerating Bioinformatics Applications via Emerging Parallel Computing Systems. IEEE ACM Trans. Comput. Biol. Bioinform. Juan Antonio Gómez Pulido, Bertil Schmidt, Wu-chun Feng
2015	—	`conf`	Accelerating large-scale biological database search on Xeon Phi-based neo-heterogeneous architectures. BIBM Haidong Lan, Weiguo Liu, Bertil Schmidt, Bingqiang Wang
2015	J	`jnl`	Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting. IEEE ACM Trans. Comput. Biol. Bioinform. Thuy-Diem Nguyen, Bertil Schmidt, Zejun Zheng, Chee-Keong Kwoh
2015	J	`jnl`	GPU-accelerated exhaustive search for third-order epistatic interactions in case-control studies. J. Comput. Sci. Jorge González-Domínguez, Bertil Schmidt
2015	J	`jnl`	GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences. Concurr. Comput. Pract. Exp. Yongchao Liu, Bertil Schmidt
2015	J	`jnl`	High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs. J. Comput. Sci. Jan Christian Kässens, Lars Wienbrandt, Jorge González-Domínguez, Bertil Schmidt, Manfred Schimmler
2015	J	`jnl`	Large-scale genome-wide association studies on a GPU cluster using a CUDA-accelerated PGAS programming model. Int. J. High Perform. Comput. Appl. Jorge González-Domínguez, Jan Christian Kässens, Lars Wienbrandt, Bertil Schmidt
2015	—	`conf`	LightSpMV: Faster CSR-based sparse matrix-vector multiplication on CUDA-enabled GPUs. ASAP Yongchao Liu, Bertil Schmidt
2015	J	`jnl`	Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems. IEEE ACM Trans. Comput. Biol. Bioinform. Jorge González-Domínguez, Lars Wienbrandt, Jan Christian Kässens, David Ellinghaus, Manfred Schimmler, Bertil Schmidt
2015	—	`conf`	SAUCE: A Web-Based Automated Assessment Tool for Teaching Parallel Programming. Euro-Par Workshops Moritz Schlarb, Christian Hundt, Bertil Schmidt
2015	—	`conf`	SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models. BIBM Yongchao Liu, Martin Loewer, Srinivas Aluru, Bertil Schmidt
2014	C	`conf`	Bit-Parallel Approximate Pattern Matching on the Xeon Phi Coprocessor. SBAC-PAD Tuan Tu Tran, Simon Schindel, Yongchao Liu, Bertil Schmidt
2014	B	`conf`	CUDA-Accelerated Alignment of Subsequences in Streamed Time Series Data. ICPP Christian Hundt, Bertil Schmidt, Elmar Schömer
2014	J	`jnl`	CUSHAW2-GPU: Empowering Faster Gapped Short-Read Alignment Using GPU Computing. IEEE Des. Test Yongchao Liu, Bertil Schmidt
2014	Misc	`conf`	FPGA-based Acceleration of Detecting Statistical Epistasis in GWAS. ICCS Lars Wienbrandt, Jan Christian Kässens, Jorge González-Domínguez, Bertil Schmidt, David Ellinghaus, Manfred Schimmler
2014	—	`conf`	Fast dendrogram-based OTU clustering using sequence embedding. BCB Thuy-Diem Nguyen, Bertil Schmidt, Chee-Keong Kwoh
2014	Misc	`conf`	GEM: an elastic and translation-invariant similarity measure with automatic trend adjustment. SAC Christian Hundt, Bertil Schmidt, Elmar Schömer, Herbert Göttler, Hoang-Vu Dang
2014	J	`jnl`	HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. BMC Bioinform. Adrianto Wirawan, Robert S. Harris, Yongchao Liu, Bertil Schmidt, Jan Schröder
2014	—	`conf`	Hybrid CPU/GPU Acceleration of Detection of 2-SNP Epistatic Interactions in GWAS. Euro-Par Jorge González-Domínguez, Bertil Schmidt, Jan Christian Kässens, Lars Wienbrandt
2014	C	`conf`	Parallelized Clustering of Protein Structures on CUDA-Enabled GPUs. PDP Hoang-Vu Dang, Bertil Schmidt, Andreas Hildebrandt, Anna Katharina Hildebrandt
2014	C	`conf`	SWAPHI-LS: Smith-Waterman Algorithm on Xeon Phi coprocessors for Long DNA Sequences. CLUSTER Yongchao Liu, Tuan Tu Tran, Felix Lauenroth, Bertil Schmidt
2014	J	`jnl`	SWAPHI: Smith-Waterman Protein Database Search on Xeon Phi Coprocessors. CoRR Yongchao Liu, Bertil Schmidt
2014	—	`conf`	SWAPHI: Smith-waterman protein database search on Xeon Phi coprocessors. ASAP Yongchao Liu, Bertil Schmidt
2014	Misc	`conf`	SparseHC: A Memory-efficient Online Hierarchical Clustering Algorithm. ICCS Thuy-Diem Nguyen, Bertil Schmidt, Chee Keong Kwoh
2014	C	`conf`	UPC++ for bioinformatics: A case study using genome-wide association studies. CLUSTER Jan Christian Kässens, Jorge González-Domínguez, Lars Wienbrandt, Bertil Schmidt
2013	J	`jnl`	A hybrid short read mapping accelerator. BMC Bioinform. Yupeng Chen, Bertil Schmidt, Douglas L. Maskell
2013	J	`jnl`	CUDA-enabled Sparse Matrix-Vector Multiplication on GPUs using atomic operations. Parallel Comput. Hoang-Vu Dang, Bertil Schmidt
2013	J	`jnl`	CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions. BMC Bioinform. Yongchao Liu, Adrianto Wirawan, Bertil Schmidt
2013	—	`conf`	Faster GPU-Accelerated Smith-Waterman Algorithm with Alignment Backtracking for Short DNA Sequences. PPAM (2) Yongchao Liu, Bertil Schmidt
2013	J	`jnl`	Iterative sparse matrix-vector multiplication for accelerating the block Wiedemann algorithm over GF(2) on multi-graphics processing unit systems. Concurr. Comput. Pract. Exp. Bertil Schmidt, Hans Aribowo, Hoang-Vu Dang
2013	J	`jnl`	Musket: a multistage Bioinform. Yongchao Liu, Jan Schröder, Bertil Schmidt
2013	J	`jnl`	Reconfigurable Accelerator for the Word-Matching Stage of BLASTN. IEEE Trans. Very Large Scale Integr. Syst. Yupeng Chen, Bertil Schmidt, Douglas L. Maskell
2012	A	`conf`	Accelerating short read mapping on an FPGA (abstract only). FPGA Yupeng Chen, Bertil Schmidt, Douglas L. Maskell
2012	B	`conf`	An FPGA aligner for short read mapping. FPL Yupeng Chen, Bertil Schmidt, Douglas L. Maskell
2012	J	`jnl`	CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform. Bioinform. Yongchao Liu, Bertil Schmidt, Douglas L. Maskell
2012	J	`jnl`	DySC: software for greedy clustering of 16S rRNA reads. Bioinform. Zejun Zheng, Stefan Kramer, Bertil Schmidt
2012	—	`conf`	Evaluation of GPU-based Seed Generation for Computational Genomics Using Burrows-Wheeler Transform. IPDPS Workshops Yongchao Liu, Bertil Schmidt
2012	Misc	`conf`	Fourth Workshop on using Emerging Parallel Architectures. ICCS Bertil Schmidt, Douglas L. Maskell
2012	J	`jnl`	Long read alignment based on maximal exact match seeds. Bioinform. Yongchao Liu, Bertil Schmidt
2012	Misc	`conf`	The Sliced COO Format for Sparse Matrix-Vector Multiplication on CUDA-enabled GPUs. ICCS Hoang-Vu Dang, Bertil Schmidt
2011	—	`conf`	An Ultrafast Scalable Many-Core Motif Discovery Algorithm for Multiple GPUs. IPDPS Workshops Yongchao Liu, Bertil Schmidt, Douglas L. Maskell
2011	—	`conf`	CRiSPy-CUDA: Computing Species Richness in 16S rRNA Pyrosequencing Datasets with CUDA. PRIB Zejun Zheng, Thuy-Diem Nguyen, Bertil Schmidt
2011	J	`jnl`	CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware. IEEE ACM Trans. Comput. Biol. Bioinform. Weiguo Liu, Bertil Schmidt, Wolfgang Müller-Wittig
2011	J	`jnl`	CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. Bioinform. Lakshmi Kuttippurathu, Michael Hsing, Yongchao Liu, Bertil Schmidt, Douglas L. Maskell, Kyungjoon Lee, Aibin He, William T. Pu, Sek Won Kong
2011	—	`ed.`	Contemporary Computing - 4th International Conference, IC3 2011, Noida, India, August 8-10, 2011. Proceedings IC3 Srinivas Aluru, Sanghamitra Bandyopadhyay, Ümit V. Çatalyürek, Devdatt P. Dubhashi, Phillip H. Jones, Manish Parashar, Bertil Schmidt
2011	J	`jnl`	DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI. BMC Bioinform. Yongchao Liu, Bertil Schmidt, Douglas L. Maskell
2011	—	`conf`	Iterative Sparse Matrix-Vector Multiplication for Integer Factorization on GPUs. Euro-Par (2) Bertil Schmidt, Hans Aribowo, Hoang-Vu Dang
2011	B	`conf`	Mapping of BLASTP Algorithm onto GPU Clusters. ICPADS Weiguo Liu, Bertil Schmidt, Yongchao Liu, Gerrit Voss, Wolfgang Müller-Wittig
2011	J	`jnl`	Parallelized short read assembly of large genomes using de Bruijn graphs. BMC Bioinform. Yongchao Liu, Bertil Schmidt, Douglas L. Maskell
2011	Misc	`conf`	Third Workshop on using Emerging Parallel Architectures. ICCS Bertil Schmidt, Douglas L. Maskell
2010	J	`jnl`	A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware. J. Comput. Biol. Haixiang Shi, Bertil Schmidt, Weiguo Liu, Wolfgang Müller-Wittig
2010	J	`jnl`	CUDA-MEME: Accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units. Pattern Recognit. Lett. Yongchao Liu, Bertil Schmidt, Weiguo Liu, Douglas L. Maskell
2010	J	`jnl`	MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities. Bioinform. Yongchao Liu, Bertil Schmidt, Douglas L. Maskell
2010	J	`jnl`	Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures. Bioinform. Adrianto Wirawan, Chee Keong Kwoh, Bertil Schmidt
2010	J	`jnl`	Pattern Recognition in Bioinformatics. Pattern Recognit. Lett. Shandar Ahmad, Madhu Chetty, Bertil Schmidt
2010	—	`conf`	Prediction of low coverage prone regions for Illumina sequencing projects using a support vector machine. BIBM Zejun Zheng, Bertil Schmidt, Guillaume Bourque
2010	Misc	`conf`	Quality-score guided error correction for short-read sequencing data using CUDA. ICCS Haixiang Shi, Bertil Schmidt, Weiguo Liu, Wolfgang Müller-Wittig
2010	Misc	`conf`	Second Workshop on using Emerging Parallel Architectures. ICCS Bertil Schmidt, Douglas L. Maskell
2009	—	`conf`	A Reconfigurable Bloom Filter Architecture for BLASTN. ARCS Yupeng Chen, Bertil Schmidt, Douglas L. Maskell
2009	J	`jnl`	A fast hybrid short read fragment assembly algorithm. Bioinform. Bertil Schmidt, Ranjan Sinha, Bryan Beresford-Smith, Simon J. Puglisi
2009	A	`conf`	Accelerating error correction in high-throughput short-read DNA sequencing data with CUDA. IPDPS Haixiang Shi, Bertil Schmidt, Weiguo Liu, Wolfgang Müller-Wittig
2009	J	`jnl`	High Speed Biological Sequence Analysis With Hidden Markov Models on Reconfigurable Platforms. IEEE Trans. Inf. Technol. Biomed. Timothy F. Oliver, Bertil Schmidt, Yanto Jakop, Douglas L. Maskell
2009	J	`jnl`	High performance protein sequence database scanning on the Cell Broadband Engine. Sci. Program. Adrianto Wirawan, Bertil Schmidt, Huiliang Zhang, Chee Keong Kwoh
2009	—	`conf`	MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA. ASAP Yongchao Liu, Bertil Schmidt, Douglas L. Maskell
2009	—	`conf`	Pairwise Distance Matrix Computation for Multiple Sequence Alignment on the Cell Broadband Engine. ICCS (1) Adrianto Wirawan, Bertil Schmidt, Chee Keong Kwoh
2009	A	`conf`	Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA. IPDPS Yongchao Liu, Bertil Schmidt, Douglas L. Maskell
2009	J	`jnl`	SHREC: a short-read error correction method. Bioinform. Jan Schröder, Heiko Schröder, Simon J. Puglisi, Ranjan Sinha, Bertil Schmidt
2009	—	`conf`	Workshop on Using Emerging Parallel Architectures for Computational Science. ICCS (1) Bertil Schmidt, Douglas L. Maskell
2008	J	`jnl`	A Hybrid Computational Grid Architecture for Comparative Genomics. IEEE Trans. Inf. Technol. Biomed. Aarti Singh, Chen Chen, Weiguo Liu, Wayne P. Mitchell, Bertil Schmidt
2008	—	`conf`	Accelerating BLASTP on the Cell Broadband Engine. PRIB Huiliang Zhang, Bertil Schmidt, Wolfgang Müller-Wittig
2008	J	`jnl`	Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA. Comput. Phys. Commun. Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Müller-Wittig
2008	J	`jnl`	CBESW: Sequence Alignment on the Playstation 3. BMC Bioinform. Adrianto Wirawan, Chee Keong Kwoh, Nim Tri Hieu, Bertil Schmidt
2008	J	`jnl`	Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment. BMC Bioinform. Dadabhai T. Singh, Rahul Trehan, Bertil Schmidt, Timo Bretschneider
2008	—	`conf`	GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences. PRIB Chen Chen, Bertil Schmidt, Weiguo Liu, Wolfgang Müller-Wittig
2008	J	`jnl`	Integrating FPGA acceleration into HMMer. Parallel Comput. Timothy F. Oliver, Leow Yuan Yeow, Bertil Schmidt
2007	—	`conf`	A Parallel BSP Algorithm for Irregular Dynamic Programming. APPT Malcolm Yoke Hean Low, Weiguo Liu, Bertil Schmidt
2007	J	`jnl`	A survey of desktop grid applications for e-science. Int. J. Web Grid Serv. Bertil Schmidt
2007	—	`conf`	C-Based Design Methodology for FPGA Implementation of ClustalW MSA. PRIB Yan Lin Aung, Douglas L. Maskell, Timothy F. Oliver, Bertil Schmidt, William Bong
2007	B	`conf`	Fast Schedulability Analysis Using Commodity Graphics Hardware. RTCSA Jimin Feng, Samarjit Chakraborty, Bertil Schmidt, Weiguo Liu, Unmesh D. Bordoloi
2007	—	`ch.`	Hierarchical Grid Computing for High-Performance Bioinformatics. Grid Computing for Bioinformatics and Computational Biology Bertil Schmidt, Chunxi Chen, Weiguo Liu
2007	A	`conf`	High Performance Database Searching with HMMer on FPGAs. IPDPS Timothy F. Oliver, Leow Yuan Yeow, Bertil Schmidt
2007	J	`jnl`	MPI-HMMER-Boost: Distributed FPGA Acceleration. J. VLSI Signal Process. John Paul Walters, Xiandong Meng, Vipin Chaudhary, Timothy F. Oliver, Leow Yuan Yeow, Bertil Schmidt, Darran Nathan, Joseph I. Landman
2007	Misc	`conf`	Molecular Dynamics Simulations on Commodity GPUs with CUDA. HiPC Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Müller-Wittig
2007	Misc	`conf`	Parallel DNA Sequence Alignment on the Cell Broadband Engine. PPAM Adrianto Wirawan, Chee Keong Kwoh, Bertil Schmidt
2007	—	`ed.`	Pattern Recognition in Bioinformatics, Second IAPR International Workshop, PRIB 2007, Singapore, October 1-2, 2007, Proceedings PRIB Jagath C. Rajapakse, Bertil Schmidt, L. Gwenn Volkert
2007	J	`jnl`	Performance Analysis of General-Purpose Computation on Commodity Graphics Hardware: A Case Study Using Bioinformatics. J. VLSI Signal Process. Weiguo Liu, Bertil Schmidt, Wolfgang Müller-Wittig
2007	B	`conf`	Performance Predictions for General-Purpose Computation on GPUs. ICPP Weiguo Liu, Wolfgang Müller-Wittig, Bertil Schmidt
2007	J	`jnl`	Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms. BMC Bioinform. Menaka Rajapakse, Bertil Schmidt, Feng Lin, Vladimir Brusic
2007	J	`jnl`	Solving the Bottleneck Problem in Bioinformatics Computing: An Architectural Perspective. J. VLSI Signal Process. Feng Lin, Heiko Schröder, Bertil Schmidt
2007	J	`jnl`	Streaming Algorithms for Biological Sequence Alignment on GPUs. IEEE Trans. Parallel Distributed Syst. Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Müller-Wittig
2006	Misc	`conf`	Accelerating the Viterbi Algorithm for Profile Hidden Markov Models Using Reconfigurable Hardware. International Conference on Computational Science (1) Timothy F. Oliver, Bertil Schmidt, Yanto Jakop, Douglas L. Maskell
2006	A	`conf`	Bio-sequence database scanning on a GPU. IPDPS Weiguo Liu, Bertil Schmidt, Gerrit Voss, Adrian Schröder, Wolfgang Müller-Wittig
2006	J	`jnl`	Constructing large suffix trees on a computational grid. J. Parallel Distributed Comput. Chunxi Chen, Bertil Schmidt
2006	Misc	`conf`	GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment. HiPC Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Müller-Wittig
2006	J	`jnl`	High-speed Multiple Sequence Alignment on a reconfigurable platform. Int. J. Bioinform. Res. Appl. Timothy F. Oliver, Bertil Schmidt, Douglas L. Maskell, Darran Nathan, Ralf Clemens
2006	J	`jnl`	Mapping of Hierarchical Parallel Genetic Algorithms for Protein Folding onto Computational Grids. IEICE Trans. Inf. Syst. Weiguo Liu, Bertil Schmidt
2006	—	`conf`	Multi-Objective Evolutionary Algorithm for Discovering Peptide Binding Motifs. EvoWorkshops Menaka Rajapakse, Bertil Schmidt, Vladimir Brusic
2006	—	`conf`	Parallel Discovery of Transcription Factor Binding Sites. APCCAS Adrianto Wirawan, Bertil Schmidt
2006	J	`jnl`	Parallel Pattern-Based Systems for Computational Biology: A Case Study. IEEE Trans. Parallel Distributed Syst. Weiguo Liu, Bertil Schmidt
2005	A	`conf`	A Case Study on Pattern-Based Systems for High Performance Computational Biology. IPDPS Weiguo Liu, Bertil Schmidt
2005	—	`conf`	A reconfigurable architecture for scanning biosequence databases. ISCAS (5) Timothy F. Oliver, Bertil Schmidt, Douglas L. Maskell, Achutavarrier Prasad Vinod
2005	J	`jnl`	An adaptive grid implementation of DNA sequence alignment. Future Gener. Comput. Syst. Chunxi Chen, Bertil Schmidt
2005	—	`conf`	Biological Sequence Analysis with Hidden Markov Models on an FPGA. Asia-Pacific Computer Systems Architecture Conference Jacop Yanto, Timothy F. Oliver, Bertil Schmidt, Douglas L. Maskell
2005	C	`conf`	Deriving Matrix of Peptide-MHC Interactions in Diabetic Mouse by Genetic Algorithm. IDEAL Menaka Rajapakse, Lonce L. Wyse, Bertil Schmidt, Vladimir Brusic
2005	A	`conf`	Hyper customized processors for bio-sequence database scanning on FPGAs. FPGA Timothy F. Oliver, Bertil Schmidt, Douglas L. Maskell
2005	—	`conf`	Multiple Sequence Alignment on an FPGA. ICPADS (2) Timothy F. Oliver, Bertil Schmidt, Douglas L. Maskell, Darran Nathan, Ralf Clemens
2005	—	`conf`	Parallel Construction of Large Suffix Trees on a PC Cluster. Euro-Par Chunxi Chen, Bertil Schmidt
2005	J	`jnl`	Parallel RNA secondary structure prediction using stochastic context-free grammars. Concurr. Comput. Pract. Exp. Tong Liu, Bertil Schmidt
2005	J	`jnl`	Reconfigurable architectures for bio-sequence database scanning on FPGAs. IEEE Trans. Circuits Syst. II Express Briefs Timothy F. Oliver, Bertil Schmidt, Douglas L. Maskell
2005	J	`jnl`	Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW. Bioinform. Timothy F. Oliver, Bertil Schmidt, Darran Nathan, Ralf Clemens, Douglas L. Maskell
2004	—	`conf`	A Generic Parallel Pattern-Based System for Bioinformatics. Euro-Par Weiguo Liu, Bertil Schmidt
2004	Misc	`conf`	A Tunable Coarse-Grained Parallel Algorithm for Irregular Dynamic Programming Applications. HiPC Weiguo Liu, Bertil Schmidt
2004	J	`jnl`	A bit-serial floating-point unit for a massively parallel system on a chip. Parallel Algorithms Appl. Manfred Schimmler, Bertil Schmidt, Hans-Werner Lang
2004	J	`jnl`	Development of distributed bioinformatics applications with GMP. Concurr. Pract. Exp. Bertil Schmidt, Lin Feng, Amey V. Laud, Yusdi Santoso
2004	A	`conf`	High Performance Biosequence Database Scanning on Reconfigurable Platforms. IPDPS Timothy F. Oliver, Bertil Schmidt
2004	Misc	`conf`	Load Balancing for Hierarchical Grid Computing: A Case Study. HiPC Chunxi Chen, Bertil Schmidt
2004	A	`conf`	Parallel RNA Sequence-Structure Alignment. IPDPS Tong Liu, Bertil Schmidt
2004	B	`conf`	Performance analysis of computational biology applications on hierarchical Grid systems. CCGRID Chunxi Chen, Bertil Schmidt
2003	—	`conf`	An Area-Efficient Bit-Serial Integer Multiplier. VLSI Manfred Schimmler, Bertil Schmidt, Hans-Werner Lang, Sven Heithecker
2003	C	`conf`	Computing Large-Scale Alignments on a Multi-Cluster. CLUSTER Chunxi Chen, Bertil Schmidt
2003	Misc	`conf`	Design of a Bit-Serial Floating Point Unit for a Fine Grained Parallel Processor Array. PDPTA Manfred Schimmler, Bertil Schmidt, Hans-Werner Lang
2003	C	`conf`	Parallel Design Pattern for Computational Biology and Scientific Computing Applications. CLUSTER Weiguo Liu, Bertil Schmidt
2003	A	`conf`	Parallel Detection of Regulatory Elements with gMP. IPDPS Bertil Schmidt, Lin Feng, Amey V. Laud, Yusdi Santoso
2003	—	`conf`	Topic Introduction. Euro-Par Ishfaq Ahmad, Pieter Jonker, Bertil Schmidt, Andreas Uhl
2002	J	`jnl`	A hybrid architecture for bioinformatics. Future Gener. Comput. Syst. Bertil Schmidt, Heiko Schröder, Manfred Schimmler
2002	A	`conf`	Massively Parallel Solutions for Molecular Sequence Analysis. IPDPS Bertil Schmidt, Heiko Schröder, Manfred Schimmler
2001	J	`jnl`	A Hybrid Architecture for Multimedia Processors. Comput. Artif. Intell. Bertil Schmidt, Heiko Schröder
2001	B	`conf`	Protein Sequence Comparison on the Instruction Systolic Array. PaCT Bertil Schmidt, Heiko Schröder, Manfred Schimmler
2001	—	`conf`	Scanning Biosequence Databases on a Hybrid Parallel Architecture. Euro-Par Bertil Schmidt, Heiko Schröder, Manfred Schimmler
2001	J	`jnl`	Tomographic Image Reconstruction on the Instruction Systolic Array. Comput. Artif. Intell. Bertil Schmidt, Heiko Schröder, Manfred Schimmler
2000	—	`conf`	Design of a Parallel Accelerator for Volume Rendering. Euro-Par Bertil Schmidt
2000	J	`jnl`	KPROC - An Instruction Systolic Architecture for Parallel Prefix Applications. Parallel Distributed Comput. Pract. Bertil Schmidt, Manfred Schimmler
1999	J	`jnl`	A Morphological Approach to Hough Transform on an Instruction Systolic Array. Comput. Artif. Intell. Bertil Schmidt, Manfred Schimmler, Heiko Schröder
1999	—	`conf`	A Parallel Accelerator Architecture for Multimedia Video Compression. Euro-Par Bertil Schmidt, Manfred Schimmler
1998	—	`conf`	Long Operand Arithmetic on Instruction Systolic Computer Architectures and Its Application in RSA Cryptography. Euro-Par Bertil Schmidt, Manfred Schimmler, Heiko Schröder
1997	—	`conf`	Morphological Hough Transform on the Instruction Systolic Array. Euro-Par Bertil Schmidt, Manfred Schimmler, Heiko Schröder
1995	—	`conf`	Preattentive Colour Features by Steerable Filters. DAGM-Symposium Udo Mahlmeister, Bertil Schmidt, Gerald Sommer