| 2026 | ICS | Addressing Key Challenges in Accelerated Computing for Omics Pipelines. | Bertil Schmidt |
| 2025 | EuroPar | SWBWA: A Highly Efficient NGS Aligner on the New Sunway Architecture. | Lifeng Yan, Zekun Yin, Qixin Chang, Tong Zhang, Zhisong Wang, Xiaohui Duan, Bertil Schmidt, Weiguo Liu |
| 2025 | ICCS | cuTeBool: Fast and Scalable Boolean Matrix Factorization on GPUs Using Tensor Cores. | Andrea Beyer, Valentin Henkys, Robin Kobus, Stefan Kramer, Bertil Schmidt |
| 2024 | ICPP | Massively Parallel Inverse Block-sorting Transforms for bzip2 Decompression on GPUs. | Andr Weienberger, Bertil Schmidt |
| 2023 | EuroPar | Faster Segmented Sort on GPUs. | Robin Kobus, Johannes Nelgen, Valentin Henkys, Bertil Schmidt |
| 2023 | ICCS | Automated Identification and Location of Three Dimensional Atmospheric Frontal Systems. | Stefan Niebler, Bertil Schmidt, Holger Tost, Peter Spichtinger |
| 2022 | ICS | AnySeq/GPU: a novel approach for faster sequence alignment on GPUs. | Andr Mller, Bertil Schmidt, Richard Membarth, Roland Leia, Sebastian Hack |
| 2022 | ISPDC | Online Event Selection for Mu3e using GPUs. | Valentin Henkys, Bertil Schmidt, Niklaus Berger |
| 2021 | HiPC | Accelerating JPEG Decompression on GPUs. | Andr Weienberger, Bertil Schmidt |
| 2021 | ICCS | RNACache: Fast Mapping of RNA-Seq Reads to Transcriptomes Using MinHashing. | Julian Cascitti, Stefan Niebler, Andr Mller, Bertil Schmidt |
| 2021 | ICPP | MetaCache-GPU: Ultra-Fast Metagenomic Classification. | Robin Kobus, Andr Mller, Daniel Jnger, Christian Hundt, Bertil Schmidt |
| 2020 | EuroPar | cuDTW++: Ultra-Fast Dynamic Time Warping on CUDA-Enabled GPUs. | Bertil Schmidt, Christian Hundt |
| 2020 | HiPC | WarpCore: A Library for fast Hash Tables on GPUs. | Daniel Jnger, Robin Kobus, Andr Mller, Christian Hundt, Kai Xu, Weiguo Liu, Bertil Schmidt |
| 2020 | ICCS | Reconstruction of Low Energy Neutrino Events with GPUs at IceCube. | Maicon Hieronymus, Bertil Schmidt, Sebastian Bser |
| 2020 | ICPP | SWMapper: Scalable Read Mapper on SunWay TaihuLight. | Kai Xu, Xiaohui Duan, Xiangxu Meng, Xin Li, Bertil Schmidt, Weiguo Liu |
| 2020 | PPoPP | Neighbor-list-free molecular dynamics on sunway TaihuLight supercomputer. | 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 | SC | Cell-list based molecular dynamics on many-core processors: a case study on sunway TaihuLight supercomputer. | Xiaohui Duan, Ping Gao, Meng Zhang, Tingjian Zhang, Hongsong Meng, Yuxuan Li, Bertil Schmidt, Haohuan Fu, Lin Gan, Wei Xue, Weiguo Liu, Guangwen Yang |
| 2019 | HPCC | Efficient Parallel Sort on AVX-512-Based Multi-Core and Many-Core Architectures. | Zekun Yin, Tianyu Zhang, Andr Mller, Hui Liu, Yanjie Wei, Bertil Schmidt, Weiguo Liu |
| 2019 | HPCC | XLCS: A New Bit-Parallel Longest Common Subsequence Algorithm on Xeon Phi Clusters. | Zekun Yin, Hao Zhang, Kai Xu, Yuandong Chan, Shaoliang Peng, Xiaoning Wang, Bertil Schmidt, Weiguo Liu |
| 2019 | HPDC | Suffix Array Construction on Multi-GPU Systems. | Florian Bren, Daniel Jnger, Robin Kobus, Christian Hundt, Bertil Schmidt |
| 2019 | ICPP | Gossip: Efficient Communication Primitives for Multi-GPU Systems. | Robin Kobus, Daniel Jnger, Christian Hundt, Bertil Schmidt |
| 2019 | ICPP | Massively Parallel ANS Decoding on GPUs. | Andr Weienberger, Bertil Schmidt |
| 2018 | ICPADS | cuBool: Bit-Parallel Boolean Matrix Factorization on CUDA-Enabled Accelerators. | Robin Kobus, Adrian Lamoth, Andr Mller, Christian Hundt, Stefan Kramer, Bertil Schmidt |
| 2018 | ICPP | Massively Parallel Huffman Decoding on GPUs. | Andr Weienberger, Bertil Schmidt |
| 2018 | ICPP | SPECTR: Scalable Parallel Short Read Error Correction on Multi-core and Many-core Architectures. | Kai Xu, Robin Kobus, Yuandong Chan, Ping Gao, Xiangxu Meng, Yanjie Wei, Bertil Schmidt, Weiguo Liu |
| 2017 | CCGRID | mD3DOCKxb: An Ultra-Scalable CPU-MIC Coordinated Virtual Screening Framework. | 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 |
| 2017 | CLUSTER | S-Aligner: Ultrascalable Read Mapping on Sunway Taihu Light. | Xiaohui Duan, Kai Xu, Yuandong Chan, Christian Hundt, Bertil Schmidt, Pavan Balaji, Weiguo Liu |
| 2016 | EuroPar | Ultra-Fast Detection of Higher-Order Epistatic Interactions on GPUs. | Daniel Jnger, Christian Hundt, Jorge Gonzlez-Domnguez, Bertil Schmidt |
| 2015 | EuroPar | SAUCE: A Web-Based Automated Assessment Tool for Teaching Parallel Programming. | Moritz Schlarb, Christian Hundt, Bertil Schmidt |
| 2014 | CLUSTER | UPC++ for bioinformatics: A case study using genome-wide association studies. | Jan Christian Kssens, Jorge Gonzlez-Domnguez, Lars Wienbrandt, Bertil Schmidt |
| 2014 | CLUSTER | SWAPHI-LS: Smith-Waterman Algorithm on Xeon Phi coprocessors for Long DNA Sequences. | Yongchao Liu, Tuan Tu Tran, Felix Lauenroth, Bertil Schmidt |
| 2014 | EuroPar | Hybrid CPU/GPU Acceleration of Detection of 2-SNP Epistatic Interactions in GWAS. | Jorge Gonzlez-Domnguez, Bertil Schmidt, Jan Christian Kssens, Lars Wienbrandt |
| 2014 | ICCS | SparseHC: A Memory-efficient Online Hierarchical Clustering Algorithm. | Thuy-Diem Nguyen, Bertil Schmidt, Chee Keong Kwoh |
| 2014 | ICCS | FPGA-based Acceleration of Detecting Statistical Epistasis in GWAS. | Lars Wienbrandt, Jan Christian Kssens, Jorge Gonzlez-Domnguez, Bertil Schmidt, David Ellinghaus, Manfred Schimmler |
| 2014 | ICPP | CUDA-Accelerated Alignment of Subsequences in Streamed Time Series Data. | Christian Hundt, Bertil Schmidt, Elmar Schmer |
| 2014 | PDP | Parallelized Clustering of Protein Structures on CUDA-Enabled GPUs. | Hoang-Vu Dang, Bertil Schmidt, Andreas Hildebrandt, Anna Katharina Hildebrandt |
| 2014 | SAC | GEM: an elastic and translation-invariant similarity measure with automatic trend adjustment. | Christian Hundt, Bertil Schmidt, Elmar Schmer, Herbert Gttler, Hoang-Vu Dang |
| 2014 | SBAC-PAD | Bit-Parallel Approximate Pattern Matching on the Xeon Phi Coprocessor. | Tuan Tu Tran, Simon Schindel, Yongchao Liu, Bertil Schmidt |
| 2013 | PPAM | Faster GPU-Accelerated Smith-Waterman Algorithm with Alignment Backtracking for Short DNA Sequences. | Yongchao Liu, Bertil Schmidt |
| 2012 | FPGA | Accelerating short read mapping on an FPGA (abstract only). | Yupeng Chen, Bertil Schmidt, Douglas L. Maskell |
| 2012 | FPL | An FPGA aligner for short read mapping. | Yupeng Chen, Bertil Schmidt, Douglas L. Maskell |
| 2011 | EuroPar | Iterative Sparse Matrix-Vector Multiplication for Integer Factorization on GPUs. | Bertil Schmidt, Hans Aribowo, Hoang-Vu Dang |
| 2011 | ICPADS | Mapping of BLASTP Algorithm onto GPU Clusters. | Weiguo Liu, Bertil Schmidt, Yongchao Liu, Gerrit Voss, Wolfgang Mller-Wittig |
| 2009 | ICCS | Workshop on Using Emerging Parallel Architectures for Computational Science. | Bertil Schmidt, Douglas L. Maskell |
| 2009 | ICCS | Pairwise Distance Matrix Computation for Multiple Sequence Alignment on the Cell Broadband Engine. | Adrianto Wirawan, Bertil Schmidt, Chee Keong Kwoh |
| 2007 | HiPC | Molecular Dynamics Simulations on Commodity GPUs with CUDA. | Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Mller-Wittig |
| 2007 | ICPP | Performance Predictions for General-Purpose Computation on GPUs. | Weiguo Liu, Wolfgang Mller-Wittig, Bertil Schmidt |
| 2007 | PPAM | Parallel DNA Sequence Alignment on the Cell Broadband Engine. | Adrianto Wirawan, Chee Keong Kwoh, Bertil Schmidt |
| 2007 | RTCSA | Fast Schedulability Analysis Using Commodity Graphics Hardware. | Jimin Feng, Samarjit Chakraborty, Bertil Schmidt, Weiguo Liu, Unmesh D. Bordoloi |
| 2006 | HiPC | GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment. | Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Mller-Wittig |
| 2006 | ICCS | Accelerating the Viterbi Algorithm for Profile Hidden Markov Models Using Reconfigurable Hardware. | Timothy F. Oliver, Bertil Schmidt, Yanto Jakop, Douglas L. Maskell |
| 2005 | EuroPar | Parallel Construction of Large Suffix Trees on a PC Cluster. | Chunxi Chen, Bertil Schmidt |
| 2005 | FPGA | Hyper customized processors for bio-sequence database scanning on FPGAs. | Timothy F. Oliver, Bertil Schmidt, Douglas L. Maskell |
| 2005 | ICPADS | Multiple Sequence Alignment on an FPGA. | Timothy F. Oliver, Bertil Schmidt, Douglas L. Maskell, Darran Nathan, Ralf Clemens |
| 2005 | ISCAS | A reconfigurable architecture for scanning biosequence databases. | Timothy F. Oliver, Bertil Schmidt, Douglas L. Maskell, Achutavarrier Prasad Vinod |
| 2005 | IDEAL | Deriving Matrix of Peptide-MHC Interactions in Diabetic Mouse by Genetic Algorithm. | Menaka Rajapakse, Lonce L. Wyse, Bertil Schmidt, Vladimir Brusic |
| 2004 | CCGRID | Performance analysis of computational biology applications on hierarchical Grid systems. | Chunxi Chen, Bertil Schmidt |
| 2004 | EuroPar | A Generic Parallel Pattern-Based System for Bioinformatics. | Weiguo Liu, Bertil Schmidt |
| 2004 | HiPC | Load Balancing for Hierarchical Grid Computing: A Case Study. | Chunxi Chen, Bertil Schmidt |
| 2004 | HiPC | A Tunable Coarse-Grained Parallel Algorithm for Irregular Dynamic Programming Applications. | Weiguo Liu, Bertil Schmidt |
| 2003 | CLUSTER | Computing Large-Scale Alignments on a Multi-Cluster. | Chunxi Chen, Bertil Schmidt |
| 2003 | CLUSTER | Parallel Design Pattern for Computational Biology and Scientific Computing Applications. | Weiguo Liu, Bertil Schmidt |
| 2003 | EuroPar | Topic Introduction. | Ishfaq Ahmad, Pieter Jonker, Bertil Schmidt, Andreas Uhl |
| 2003 | PDPTA | Design of a Bit-Serial Floating Point Unit for a Fine Grained Parallel Processor Array. | Manfred Schimmler, Bertil Schmidt, Hans-Werner Lang |
| 2001 | EuroPar | Scanning Biosequence Databases on a Hybrid Parallel Architecture. | Bertil Schmidt, Heiko Schrder, Manfred Schimmler |
| 2001 | PACT | Protein Sequence Comparison on the Instruction Systolic Array. | Bertil Schmidt, Heiko Schrder, Manfred Schimmler |
| 2000 | EuroPar | Design of a Parallel Accelerator for Volume Rendering. | Bertil Schmidt |
| 1999 | EuroPar | A Parallel Accelerator Architecture for Multimedia Video Compression. | Bertil Schmidt, Manfred Schimmler |
| 1998 | EuroPar | Long Operand Arithmetic on Instruction Systolic Computer Architectures and Its Application in RSA Cryptography. | Bertil Schmidt, Manfred Schimmler, Heiko Schrder |
| 1997 | EuroPar | Morphological Hough Transform on the Instruction Systolic Array. | Bertil Schmidt, Manfred Schimmler, Heiko Schrder |