Bertil Schmidt

ORCID

Publication Activity (10 Years)

Years Active: 1995-2024
Publications (10 Years): 88

Top Venues

Publications

Felix Kallenborn, Bertil Schmidt
CAREx: context-aware read extension of paired-end sequencing data. BMC Bioinform. 25 (1) (2024)
André Weißenberger, Bertil Schmidt
Massively Parallel Inverse Block-sorting Transforms for bzip2 Decompression on GPUs. ICPP (2024)
Mingkai Wang, Zekun Yin, Lifeng Yan, Yang Yang, Fangjin Zhu, Xiaohui Duan, Xin Li, Bertil Schmidt, Weiguo Liu
RabbitTrim: Highly Optimized Trimming of Illumina Sequencing Data on Multi-core Platforms. ISBRA (2) (2024)
Henrik Järleblad, Luke Stagner, Mirko Salewski, J. Eriksson, M. Nocente, Bertil Schmidt, M. Rud Larsen
A framework for synthetic diagnostics using energetic-particle orbits in tokamaks. Comput. Phys. Commun. 294 (2024)
Stefan Niebler, Bertil Schmidt, Peter Spichtinger, Holger Tost
Scalable GPU-Enabled Creation of Three Dimensional Weather Fronts. PASC (2024)
Lifeng Yan, Zekun Yin, Jinjin Li, Yang Yang, Tong Zhang, Fangjin Zhu, Xiaohui Duan, Bertil Schmidt, Weiguo Liu
RabbitSAlign: Accelerating Short-Read Alignment for CPU-GPU Heterogeneous Platforms. ISBRA (2) (2024)
Xiaohui Duan, Qi Shao, Junben Weng, Bertil Schmidt, Lin Gan, Guohui Li, Haohuan Fu, Wei Xue, Weiguo Liu, Guangwen Yang
Bio-ESMD: A Data Centric Implementation for Large-Scale Biological System Simulation on Sunway TaihuLight Supercomputer. IEEE Trans. Parallel Distributed Syst. 34 (3) (2023)
Stefan Niebler, Bertil Schmidt, Holger Tost, Peter Spichtinger
Automated Identification and Location of Three Dimensional Atmospheric Frontal Systems. ICCS (2) (2023)
Xiaoming Xu, Zekun Yin, Lifeng Yan, Huiguang Yi, Hua Wang, Bertil Schmidt, Weiguo Liu
RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures. Bioinform. 39 (10) (2023)
Hao Zhang, Honglei Song, Xiaoming Xu, Qixin Chang, Mingkai Wang, Yanjie Wei, Zekun Yin, Bertil Schmidt, Weiguo Liu
RabbitFX: Efficient Framework for FASTA/Q File Parsing on Modern Multi-Core Platforms. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (3) (2023)
Robin Kobus, Johannes Nelgen, Valentin Henkys, Bertil Schmidt
Faster Segmented Sort on GPUs. Euro-Par (2023)
Ping Gao, Xiaohui Duan, Bertil Schmidt, Wubing Wan, Jiaxu Guo, Wusheng Zhang, Lin Gan, Haohuan Fu, Wei Xue, Weiguo Liu, Guangwen Yang
Redesign and Accelerate the AIREBO Bond-Order Potential on the New Sunway Supercomputer. IEEE Trans. Parallel Distributed Syst. 34 (12) (2023)
Thomas Kemmer, Sebastian Hack, Bertil Schmidt, Andreas Hildebrandt
CUDA-accelerated protein electrostatics in linear space. J. Comput. Sci. 70 (2023)
Daniel Jünger, Robin Kobus, André Müller, Christian Hundt, Kai Xu, Weiguo Liu, Bertil Schmidt
General-purpose GPU hashing data structures and their application in accelerated genomics. J. Parallel Distributed Comput. 163 (2022)
Ping Gao, Xiaohui Duan, Bertil Schmidt, Wusheng Zhang, Lin Gan, Haohuan Fu, Wei Xue, Weiguo Liu, Guangwen Yang
Optimization of Reactive Force Field Simulation: Refactor, Parallelization, and Vectorization for Interactions. IEEE Trans. Parallel Distributed Syst. 33 (2) (2022)
André Müller, Bertil Schmidt, Richard Membarth, Roland Leißa, Sebastian Hack
AnySeq/GPU: A Novel Approach for Faster Sequence Alignment on GPUs. CoRR (2022)
Lifeng Yan, Zekun Yin, Hao Zhang, Zhan Zhao, Mingkai Wang, André Müller, Robin Kobus, Yanjie Wei, Beifang Niu, Bertil Schmidt, Weiguo Liu
RabbitQCPlus: More Efficient Quality Control for Sequencing Data. BIBM (2022)
Kai Xu, Xiaohui Duan, André Müller, Robin Kobus, Bertil Schmidt, Weiguo Liu
FMapper: Scalable read mapper based on succinct hash index on SunWay TaihuLight. J. Parallel Distributed Comput. 161 (2022)
Konstantin Bob, David Teschner, Thomas Kemmer, David Gomez-Zepeda, Stefan Tenzer, Bertil Schmidt, Andreas Hildebrandt
Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data. BMC Bioinform. 23 (1) (2022)
Felix Kallenborn, Julian Cascitti, Bertil Schmidt
CARE 2.0: reducing false-positive sequencing error corrections using machine learning. BMC Bioinform. 23 (1) (2022)
Julian Cascitti, Stefan Niebler, André Müller, Bertil Schmidt
RNACache: A scalable approach to rapid transcriptomic read mapping using locality sensitive hashing. J. Comput. Sci. 60 (2022)
Kai Xu, Jinxiao Zhang, Xiaohui Duan, Xiaobo Wan, Niu Huang, Bertil Schmidt, Weiguo Liu, Guangwen Yang
Redesigning and Optimizing UCSF DOCK3.7 on Sunway TaihuLight. IEEE Trans. Parallel Distributed Syst. 33 (10) (2022)
Hao Zhang, Qixin Chang, Zekun Yin, Xiaoming Xu, Yanjie Wei, Bertil Schmidt, Weiguo Liu
RabbitV: fast detection of viruses and microorganisms in sequencing data on multi-core architectures. Bioinform. 38 (10) (2022)
Valentin Henkys, Bertil Schmidt, Niklaus Berger
Online Event Selection for Mu3e using GPUs. ISPDC (2022)
André Müller, Bertil Schmidt, Richard Membarth, Roland Leißa, Sebastian Hack
AnySeq/GPU: a novel approach for faster sequence alignment on GPUs. ICS (2022)
Valentin Henkys, Bertil Schmidt, Niklaus Berger
Online Event Selection for Mu3e using GPUs. CoRR (2022)
Jintao Meng, Chen Zhuang, Peng Chen, Mohamed Wahib, Bertil Schmidt, Xiao Wang, Haidong Lan, Dou Wu, Minwen Deng, Yanjie Wei, Shengzhong Feng
Automatic Generation of High-Performance Convolution Kernels on ARM CPUs for Deep Learning. IEEE Trans. Parallel Distributed Syst. 33 (11) (2022)
André Weißenberger, Bertil Schmidt
Accelerating JPEG Decompression on GPUs. CoRR (2021)
Felix Kallenborn, Andreas Hildebrandt, Bertil Schmidt
CARE: context-aware sequencing read error correction. Bioinform. 37 (7) (2021)
Zekun Yin, Hao Zhang, Meiyang Liu, Wen Zhang, Honglei Song, Haidong Lan, Yanjie Wei, Beifang Niu, Bertil Schmidt, Weiguo Liu
RabbitQC: high-speed scalable quality control for sequencing data. Bioinform. 37 (4) (2021)
Zekun Yin, Xiaoming Xu, Jinxiao Zhang, Yanjie Wei, Bertil Schmidt, Weiguo Liu
RabbitMash: accelerating hash-based genome analysis on modern multi-core architectures. Bioinform. 37 (6) (2021)
Julian Cascitti, Stefan Niebler, André Müller, Bertil Schmidt
RNACache: Fast Mapping of RNA-Seq Reads to Transcriptomes Using MinHashing. ICCS (1) (2021)
Robin Kobus, André Müller, Daniel Jünger, Christian Hundt, Bertil Schmidt
MetaCache-GPU: Ultra-Fast Metagenomic Classification. ICPP (2021)
André Weißenberger, Bertil Schmidt
Accelerating JPEG Decompression on GPUs. HiPC (2021)
Robin Kobus, André Müller, Daniel Jünger, Christian Hundt, Bertil Schmidt
MetaCache-GPU: Ultra-Fast Metagenomic Classification. CoRR (2021)
Daniel Jünger, Robin Kobus, André Müller, Christian Hundt, Kai Xu, Weiguo Liu, Bertil Schmidt
WarpCore: A Library for fast Hash Tables on GPUs. CoRR (2020)
Stefan Niebler, André Müller, Thomas Hankeln, Bertil Schmidt
RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads. BMC Bioinform. 21 (1) (2020)
André Müller, Bertil Schmidt, Andreas Hildebrandt, Richard Membarth, Roland Leißa, Matthis Kruse, Sebastian Hack
AnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation. IPDPS (2020)
Kai Xu, Xiaohui Duan, Xiangxu Meng, Xin Li, Bertil Schmidt, Weiguo Liu
SWMapper: Scalable Read Mapper on SunWay TaihuLight. ICPP (2020)
Bertil Schmidt, Christian Hundt
cuDTW++: Ultra-Fast Dynamic Time Warping on CUDA-Enabled GPUs. Euro-Par (2020)
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
Millimeter-Scale and Billion-Atom Reactive Force Field Simulation on Sunway Taihulight. IEEE Trans. Parallel Distributed Syst. 31 (12) (2020)
André Müller, Bertil Schmidt, Andreas Hildebrandt, Richard Membarth, Roland Leißa, Matthis Kruse, Sebastian Hack
AnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation. CoRR (2020)
Xiaohui Duan, Ping Gao, Meng Zhang, Tingjian Zhang, Hongsong Meng, Yuxuan Li, Bertil Schmidt, Haohuan Fu, Lin Gan, Wei Xue, Guangwen Yang, Weiguo Liu
Neighbor-list-free molecular dynamics on sunway TaihuLight supercomputer. PPoPP (2020)
Daniel Jünger, Robin Kobus, André Müller, Christian Hundt, Kai Xu, Weiguo Liu, Bertil Schmidt
WarpCore: A Library for fast Hash Tables on GPUs. HiPC (2020)
Robin Kobus, José Manuel Abuín, André Müller, Sören Lukas Hellmann, Juan Carlos Pichel, Tomás F. Pena, Andreas Hildebrandt, Thomas Hankeln, Bertil Schmidt
A big data approach to metagenomics for all-food-sequencing. BMC Bioinform. 21 (1) (2020)
Maicon Hieronymus, Bertil Schmidt, Sebastian Böser
Reconstruction of Low Energy Neutrino Events with GPUs at IceCube. ICCS (1) (2020)
Haidong Lan, Jintao Meng, Christian Hundt, Bertil Schmidt, Minwen Deng, Xiaoning Wang, Weiguo Liu, Yu Qiao, Shengzhong Feng
FeatherCNN: Fast Inference Computation with TensorGEMM on ARM Architectures. IEEE Trans. Parallel Distributed Syst. 31 (3) (2020)
Xiaohui Duan, Ping Gao, Meng Zhang, Tingjian Zhang, Hongsong Meng, Yuxuan Li, Bertil Schmidt, Haohuan Fu, Lin Gan, Wei Xue, Weiguo Liu, Guangwen Yang
Cell-list based molecular dynamics on many-core processors: a case study on sunway TaihuLight supercomputer. SC (2020)
Jikai Zhang, Haidong Lan, Yuandong Chan, Yuan Shang, Bertil Schmidt, Weiguo Liu
BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures. Bioinform. 35 (13) (2019)
Florian Büren, Daniel Jünger, Robin Kobus, Christian Hundt, Bertil Schmidt
Suffix Array Construction on Multi-GPU Systems. HPDC (2019)
Zekun Yin, Tianyu Zhang, André Müller, Hui Liu, Yanjie Wei, Bertil Schmidt, Weiguo Liu
Efficient Parallel Sort on AVX-512-Based Multi-Core and Many-Core Architectures. HPCC/SmartCity/DSS (2019)
André Weißenberger, Bertil Schmidt
Massively Parallel ANS Decoding on GPUs. ICPP (2019)
Zekun Yin, Hao Zhang, Kai Xu, Yuandong Chan, Shaoliang Peng, Xiaoning Wang, Bertil Schmidt, Weiguo Liu
XLCS: A New Bit-Parallel Longest Common Subsequence Algorithm on Xeon Phi Clusters. HPCC/SmartCity/DSS (2019)
Robin Kobus, Daniel Jünger, Christian Hundt, Bertil Schmidt
Gossip: Efficient Communication Primitives for Multi-GPU Systems. ICPP (2019)
Felix Kallenborn, Christian Hundt, Sebastian Böser, Bertil Schmidt
Massively parallel computation of atmospheric neutrino oscillations on CUDA-enabled accelerators. Comput. Phys. Commun. 234 (2019)
Peng Jiang, Jie Luo, Yiqi Wang, Pingji Deng, Bertil Schmidt, Xiangjun Tang, Ningjiang Chen, Limsoon Wong, Liang Zhao
kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers. Bioinform. 35 (23) (2019)
André Weißenberger, Bertil Schmidt
Massively Parallel Huffman Decoding on GPUs. ICPP (2018)
Roland Leißa, Klaas Boesche, Sebastian Hack, Arsène Pérard-Gayot, Richard Membarth, Philipp Slusallek, André Müller, Bertil Schmidt
AnyDSL: a partial evaluation framework for programming high-performance libraries. Proc. ACM Program. Lang. 2 (OOPSLA) (2018)
Jorge González-Domínguez, Christian Hundt, Bertil Schmidt
parSRA: A framework for the parallel execution of short read aligners on compute clusters. J. Comput. Sci. 25 (2018)
Robin Kobus, Adrian Lamoth, André Müller, Christian Hundt, Stefan Kramer, Bertil Schmidt
cuBool: Bit-Parallel Boolean Matrix Factorization on CUDA-Enabled Accelerators. ICPADS (2018)
Haowen Zhang, Yuandong Chan, Kaichao Fan, Bertil Schmidt, Weiguo Liu
Fast and efficient short read mapping based on a succinct hash index. BMC Bioinform. 19 (1) (2018)
Yongchao Liu, Bertil Schmidt
LightSpMV: Faster CUDA-Compatible Sparse Matrix-Vector Multiplication Using Compressed Sparse Rows. J. Signal Process. Syst. 90 (1) (2018)
Daniel Jünger, Christian Hundt, Bertil Schmidt
WarpDrive: Massively Parallel Hashing on Multi-GPU Nodes. IPDPS (2018)
Kai Xu, Robin Kobus, Yuandong Chan, Ping Gao, Xiangxu Meng, Yanjie Wei, Bertil Schmidt, Weiguo Liu
SPECTR: Scalable Parallel Short Read Error Correction on Multi-core and Many-core Architectures. ICPP (2018)
Haidong Lan, Weiguo Liu, Yongchao Liu, Bertil Schmidt
SWhybrid: A Hybrid-Parallel Framework for Large-Scale Protein Sequence Database Search. IPDPS (2017)
André Müller, Christian Hundt, Andreas Hildebrandt, Thomas Hankeln, Bertil Schmidt
MetaCache: context-aware classification of metagenomic reads using minhashing. Bioinform. 33 (23) (2017)
Daniel Jünger, Christian Hundt, Jorge González-Domínguez, Bertil Schmidt
Speed and accuracy improvement of higher-order epistasis detection on CUDA-enabled GPUs. Clust. Comput. 20 (3) (2017)
Christian Hundt, Moritz Schlarb, Bertil Schmidt
SAUCE: A web application for interactive teaching and learning of parallel programming. J. Parallel Distributed Comput. 105 (2017)
Jan Schröder, Adrianto Wirawan, Bertil Schmidt, Anthony T. Papenfuss
CLOVE: classification of genomic fusions into structural variation events. BMC Bioinform. 18 (1) (2017)
Shuai Zhang, Zhao Wang, Ying Peng, Bertil Schmidt, Weiguo Liu
Mapping of option pricing algorithms onto heterogeneous many-core architectures. J. Supercomput. 73 (9) (2017)
Yuandong Chan, Kai Xu, Haidong Lan, Weiguo Liu, Yongchao Liu, Bertil Schmidt
PUNAS: A Parallel Ungapped-Alignment-Featured Seed Verification Algorithm for Next-Generation Sequencing Read Alignment. IPDPS (2017)
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
mD3DOCKxb: An Ultra-Scalable CPU-MIC Coordinated Virtual Screening Framework. CCGrid (2017)
Robin Kobus, Christian Hundt, André Müller, Bertil Schmidt
Accelerating metagenomic read classification on CUDA-enabled GPUs. BMC Bioinform. 18 (1) (2017)
Hinrich B. Winther, Christian Hundt, Bertil Schmidt, Christoph Czerner, Johann Bauersachs, Frank K. Wacker, Jens Vogel-Claussen
$ν$-net: Deep Learning for Generalized Biventricular Cardiac Mass and Function Parameters. CoRR (2017)
Xiaohui Duan, Kai Xu, Yuandong Chan, Christian Hundt, Bertil Schmidt, Pavan Balaji, Weiguo Liu
S-Aligner: Ultrascalable Read Mapping on Sunway Taihu Light. CLUSTER (2017)
Yongchao Liu, Fabian Ripp, Rene Koeppel, Hanno Schmidt, Sören Lukas Hellmann, Mathias Weber, Christopher Felix Krombholz, Bertil Schmidt, Thomas Hankeln
AFS: identification and quantification of species composition by metagenomic sequencing. Bioinform. 33 (9) (2017)
Jorge González-Domínguez, Yongchao Liu, Juan Touriño, Bertil Schmidt
MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems. Bioinform. 32 (24) (2016)
Yongchao Liu, Martin Loewer, Srinivas Aluru, Bertil Schmidt
SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations. BMC Syst. Biol. 10 (S-2) (2016)
Christian Hundt, Andreas Hildebrandt, Bertil Schmidt
rapidGSEA: Speeding up gene set enrichment analysis on multi-core CPUs and CUDA-enabled GPUs. BMC Bioinform. 17 (2016)
Jorge González-Domínguez, Bertil Schmidt
ParDRe: faster parallel duplicated reads removal tool for sequencing studies. Bioinform. 32 (10) (2016)
Junming Shao, Qinli Yang, Hoang-Vu Dang, Bertil Schmidt, Stefan Kramer
Scalable Clustering by Iterative Partitioning and Point Attractor Representation. ACM Trans. Knowl. Discov. Data 11 (1) (2016)
Hoang-Vu Dang, Bertil Schmidt, Andreas Hildebrandt, Tuan Tu Tran, Anna Katharina Hildebrandt
CUDA-enabled hierarchical ward clustering of protein structures based on the nearest neighbour chain algorithm. Int. J. High Perform. Comput. Appl. 30 (2) (2016)
Yongchao Liu, Thomas Hankeln, Bertil Schmidt
Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data. IEEE ACM Trans. Comput. Biol. Bioinform. 13 (3) (2016)
Daniel Jünger, Christian Hundt, Jorge González-Domínguez, Bertil Schmidt
Ultra-Fast Detection of Higher-Order Epistatic Interactions on GPUs. Euro-Par Workshops (2016)
Tuan Tu Tran, Yongchao Liu, Bertil Schmidt
Bit-parallel approximate pattern matching: Kepler GPU versus Xeon Phi. Parallel Comput. 54 (2016)
Jorge González-Domínguez, Sabela Ramos, Juan Touriño, Bertil Schmidt
Parallel Pairwise Epistasis Detection on Heterogeneous Computing Architectures. IEEE Trans. Parallel Distributed Syst. 27 (8) (2016)
Haidong Lan, Yuandong Chan, Kai Xu, Bertil Schmidt, Shaoliang Peng, Weiguo Liu
Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters. BMC Bioinform. 17 (S-9) (2016)
Jan Christian Kässens, Lars Wienbrandt, Manfred Schimmler, Jorge González-Domínguez, Bertil Schmidt
Combining GPU and FPGA technology for efficient exhaustive interaction analysis in GWAS. ASAP (2016)
Juan Antonio Gómez Pulido, Bertil Schmidt, Wu-chun Feng
Accelerating Bioinformatics Applications via Emerging Parallel Computing Systems. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (5) (2015)
Yongchao Liu, Bertil Schmidt
LightSpMV: Faster CSR-based sparse matrix-vector multiplication on CUDA-enabled GPUs. ASAP (2015)
Yongchao Liu, Martin Loewer, Srinivas Aluru, Bertil Schmidt
SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models. BIBM (2015)
Jorge González-Domínguez, Bertil Schmidt
GPU-accelerated exhaustive search for third-order epistatic interactions in case-control studies. J. Comput. Sci. 8 (2015)
Jan Christian Kässens, Lars Wienbrandt, Jorge González-Domínguez, Bertil Schmidt, Manfred Schimmler
High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs. J. Comput. Sci. 9 (2015)
Moritz Schlarb, Christian Hundt, Bertil Schmidt
SAUCE: A Web-Based Automated Assessment Tool for Teaching Parallel Programming. Euro-Par Workshops (2015)
Yongchao Liu, Bertil Schmidt
GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences. Concurr. Comput. Pract. Exp. 27 (4) (2015)
Jorge González-Domínguez, Lars Wienbrandt, Jan Christian Kässens, David Ellinghaus, Manfred Schimmler, Bertil Schmidt
Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (5) (2015)
Jorge González-Domínguez, Jan Christian Kässens, Lars Wienbrandt, Bertil Schmidt
Large-scale genome-wide association studies on a GPU cluster using a CUDA-accelerated PGAS programming model. Int. J. High Perform. Comput. Appl. 29 (4) (2015)
Haidong Lan, Weiguo Liu, Bertil Schmidt, Bingqiang Wang
Accelerating large-scale biological database search on Xeon Phi-based neo-heterogeneous architectures. BIBM (2015)
Thuy-Diem Nguyen, Bertil Schmidt, Zejun Zheng, Chee-Keong Kwoh
Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (5) (2015)
Thuy-Diem Nguyen, Bertil Schmidt, Chee-Keong Kwoh
Fast dendrogram-based OTU clustering using sequence embedding. BCB (2014)

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Publication Activity (10 Years)

Top Topics

Top Venues

Bertil Schmidt