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Bertil Schmidt
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- affiliation: Johannes Gutenberg University Mainz, Germany
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2020 – today
- 2025
- [j106]Lifeng Yan, Zekun Yin, Tong Zhang, Fangjin Zhu, Xiaohui Duan, Bertil Schmidt, Weiguo Liu:
SWQC: Efficient sequencing data quality control on the next-generation sunway platform. Future Gener. Comput. Syst. 164: 107577 (2025) - 2024
- [j105]Felix Kallenborn
, Bertil Schmidt
CAREx: context-aware read extension of paired-end sequencing data. BMC Bioinform. 25(1): 186 (2024) - [j104]Bertil Schmidt, Felix Kallenborn, Alejandro Chacón, Christian Hundt:
CUDASW++4.0: ultra-fast GPU-based Smith-Waterman protein sequence database search. BMC Bioinform. 25(1): 342 (2024) - [j103]Henrik Järleblad
A framework for synthetic diagnostics using energetic-particle orbits in tokamaks. Comput. Phys. Commun. 294: 108930 (2024) - [c111]Xenia Heilmann, Daan Apeldoorn, Konstantin Strauch, Bertil Schmidt, Timm Lilienthal, Torsten Panholzer:
Studying Privacy Aspects of Learned Knowledge Bases in the Context of Synthetic and Medical Data. GMDS 2024: 261-269 - [c110]André Weißenberger
Massively Parallel Inverse Block-sorting Transforms for bzip2 Decompression on GPUs. ICPP 2024: 856-865 - [c109]Mingkai Wang, Zekun Yin, Lifeng Yan, Yang Yang, Fangjin Zhu, Xiaohui Duan, Xin Li, Bertil Schmidt
RabbitTrim: Highly Optimized Trimming of Illumina Sequencing Data on Multi-core Platforms. ISBRA (2) 2024: 26-37 - [c108]Lifeng Yan, Zekun Yin, Jinjin Li, Yang Yang, Tong Zhang, Fangjin Zhu, Xiaohui Duan, Bertil Schmidt
RabbitSAlign: Accelerating Short-Read Alignment for CPU-GPU Heterogeneous Platforms. ISBRA (2) 2024: 83-94 - [c107]Stefan Niebler
Scalable GPU-Enabled Creation of Three Dimensional Weather Fronts. PASC 2024: 2:1-2:12 - 2023
- [j102]Xiaoming Xu
RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures. Bioinform. 39(10) (2023) - [j101]Thomas Kemmer
CUDA-accelerated protein electrostatics in linear space. J. Comput. Sci. 70: 102022 (2023) - [j100]Hao Zhang
RabbitFX: Efficient Framework for FASTA/Q File Parsing on Modern Multi-Core Platforms. IEEE ACM Trans. Comput. Biol. Bioinform. 20(3): 2341-2348 (2023) - [j99]Xiaohui Duan
Bio-ESMD: A Data Centric Implementation for Large-Scale Biological System Simulation on Sunway TaihuLight Supercomputer. IEEE Trans. Parallel Distributed Syst. 34(3): 881-893 (2023) - [j98]Ping Gao
Redesign and Accelerate the AIREBO Bond-Order Potential on the New Sunway Supercomputer. IEEE Trans. Parallel Distributed Syst. 34(12): 3117-3132 (2023) - [c106]Robin Kobus
Faster Segmented Sort on GPUs. Euro-Par 2023: 664-678 - [c105]Stefan Niebler, Bertil Schmidt
Automated Identification and Location of Three Dimensional Atmospheric Frontal Systems. ICCS (2) 2023: 3-17 - 2022
- [j97]Hao Zhang
RabbitV: fast detection of viruses and microorganisms in sequencing data on multi-core architectures. Bioinform. 38(10): 2932-2933 (2022) - [j96]Felix Kallenborn
CARE 2.0: reducing false-positive sequencing error corrections using machine learning. BMC Bioinform. 23(1): 227 (2022) - [j95]Konstantin Bob
Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data. BMC Bioinform. 23(1): 287 (2022) - [j94]Julian Cascitti, Stefan Niebler, André Müller
RNACache: A scalable approach to rapid transcriptomic read mapping using locality sensitive hashing. J. Comput. Sci. 60: 101572 (2022) - [j93]Kai Xu, Xiaohui Duan, André Müller
FMapper: Scalable read mapper based on succinct hash index on SunWay TaihuLight. J. Parallel Distributed Comput. 161: 72-82 (2022) - [j92]Daniel Jünger
General-purpose GPU hashing data structures and their application in accelerated genomics. J. Parallel Distributed Comput. 163: 256-268 (2022) - [j91]Ping Gao
Optimization of Reactive Force Field Simulation: Refactor, Parallelization, and Vectorization for Interactions. IEEE Trans. Parallel Distributed Syst. 33(2): 359-373 (2022) - [j90]Kai Xu
Redesigning and Optimizing UCSF DOCK3.7 on Sunway TaihuLight. IEEE Trans. Parallel Distributed Syst. 33(10): 4458-4471 (2022) - [j89]Jintao Meng
Automatic Generation of High-Performance Convolution Kernels on ARM CPUs for Deep Learning. IEEE Trans. Parallel Distributed Syst. 33(11): 2885-2899 (2022) - [c104]Lifeng Yan, Zekun Yin, Hao Zhang, Zhan Zhao, Mingkai Wang, André Müller, Robin Kobus, Yanjie Wei, Beifang Niu, Bertil Schmidt
RabbitQCPlus: More Efficient Quality Control for Sequencing Data. BIBM 2022: 619-626 - [c103]André Müller, Bertil Schmidt, Richard Membarth, Roland Leißa
AnySeq/GPU: a novel approach for faster sequence alignment on GPUs. ICS 2022: 20:1-20:11 - [c102]Valentin Henkys
Online Event Selection for Mu3e using GPUs. ISPDC 2022: 17-24 - [i8]André Müller, Bertil Schmidt, Richard Membarth, Roland Leißa, Sebastian Hack:
AnySeq/GPU: A Novel Approach for Faster Sequence Alignment on GPUs. CoRR abs/2205.07610 (2022) - [i7]Valentin Henkys, Bertil Schmidt, Niklaus Berger:
Online Event Selection for Mu3e using GPUs. CoRR abs/2206.11535 (2022) - 2021
- [j88]Zekun Yin
RabbitQC: high-speed scalable quality control for sequencing data. Bioinform. 37(4): 573-574 (2021) - [j87]Zekun Yin
RabbitMash: accelerating hash-based genome analysis on modern multi-core architectures. Bioinform. 37(6): 873-875 (2021) - [j86]Felix Kallenborn
CARE: context-aware sequencing read error correction. Bioinform. 37(7): 889-895 (2021) - [c101]André Weißenberger, Bertil Schmidt
Accelerating JPEG Decompression on GPUs. HiPC 2021: 121-130 - [c100]Julian Cascitti, Stefan Niebler, André Müller, Bertil Schmidt
RNACache: Fast Mapping of RNA-Seq Reads to Transcriptomes Using MinHashing. ICCS (1) 2021: 367-381 - [c99]Robin Kobus, André Müller
MetaCache-GPU: Ultra-Fast Metagenomic Classification. ICPP 2021: 25:1-25:11 - [i6]Robin Kobus, André Müller, Daniel Jünger, Christian Hundt, Bertil Schmidt:
MetaCache-GPU: Ultra-Fast Metagenomic Classification. CoRR abs/2106.08150 (2021) - [i5]André Weißenberger, Bertil Schmidt:
Accelerating JPEG Decompression on GPUs. CoRR abs/2111.09219 (2021) - 2020
- [j85]Robin Kobus, José Manuel Abuín
A big data approach to metagenomics for all-food-sequencing. BMC Bioinform. 21(1): 102 (2020) - [j84]Stefan Niebler, André Müller
RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads. BMC Bioinform. 21(1): 274 (2020) - [j83]Haidong Lan, Jintao Meng
FeatherCNN: Fast Inference Computation with TensorGEMM on ARM Architectures. IEEE Trans. Parallel Distributed Syst. 31(3): 580-594 (2020) - [j82]Ping Gao
Millimeter-Scale and Billion-Atom Reactive Force Field Simulation on Sunway Taihulight. IEEE Trans. Parallel Distributed Syst. 31(12): 2954-2967 (2020) - [c98]Bertil Schmidt
cuDTW++: Ultra-Fast Dynamic Time Warping on CUDA-Enabled GPUs. Euro-Par 2020: 597-612 - [c97]Daniel Jünger, Robin Kobus, André Müller
WarpCore: A Library for fast Hash Tables on GPUs. HiPC 2020: 11-20 - [c96]Maicon Hieronymus, Bertil Schmidt
Reconstruction of Low Energy Neutrino Events with GPUs at IceCube. ICCS (1) 2020: 118-131 - [c95]Kai Xu, Xiaohui Duan, Xiangxu Meng, Xin Li, Bertil Schmidt
SWMapper: Scalable Read Mapper on SunWay TaihuLight. ICPP 2020: 28:1-28:10 - [c94]André Müller
AnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation. IPDPS 2020: 1030-1040 - [c93]Xiaohui Duan, Ping Gao, Meng Zhang, Tingjian Zhang, Hongsong Meng, Yuxuan Li, Bertil Schmidt
Neighbor-list-free molecular dynamics on sunway TaihuLight supercomputer. PPoPP 2020: 413-414 - [c92]Xiaohui Duan, Ping Gao, Meng Zhang, Tingjian Zhang, Hongsong Meng, Yuxuan Li, Bertil Schmidt
Cell-list based molecular dynamics on many-core processors: a case study on sunway TaihuLight supercomputer. SC 2020: 22 - [i4]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 abs/2002.04561 (2020) - [i3]Daniel Jünger, Robin Kobus, André Müller, Christian Hundt, Kai Xu, Weiguo Liu, Bertil Schmidt:
WarpCore: A Library for fast Hash Tables on GPUs. CoRR abs/2009.07914 (2020)
2010 – 2019
- 2019
- [j81]Jikai Zhang, Haidong Lan, Yuandong Chan, Yuan Shang, Bertil Schmidt
BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures. Bioinform. 35(13): 2306-2308 (2019) - [j80]Peng Jiang, Jie Luo, Yiqi Wang, Pingji Deng, Bertil Schmidt
kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers. Bioinform. 35(23): 4871-4878 (2019) - [j79]Felix Kallenborn
Massively parallel computation of atmospheric neutrino oscillations on CUDA-enabled accelerators. Comput. Phys. Commun. 234: 235-244 (2019) - [c91]Zekun Yin, Tianyu Zhang, André Müller, Hui Liu, Yanjie Wei, Bertil Schmidt
Efficient Parallel Sort on AVX-512-Based Multi-Core and Many-Core Architectures. HPCC/SmartCity/DSS 2019: 168-176 - [c90]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: 1477-1483 - [c89]Florian Büren, Daniel Jünger, Robin Kobus, Christian Hundt, Bertil Schmidt
Suffix Array Construction on Multi-GPU Systems. HPDC 2019: 183-194 - [c88]Robin Kobus, Daniel Jünger, Christian Hundt, Bertil Schmidt
Gossip: Efficient Communication Primitives for Multi-GPU Systems. ICPP 2019: 63:1-63:10 - [c87]André Weißenberger, Bertil Schmidt
Massively Parallel ANS Decoding on GPUs. ICPP 2019: 100:1-100:10 - [r1]Bertil Schmidt, Andreas Hildebrandt:
Dedicated Bioinformatics Analysis Hardware. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 1142-1150 - 2018
- [j78]Haowen Zhang
Fast and efficient short read mapping based on a succinct hash index. BMC Bioinform. 19(1): 92:1-92:14 (2018) - [j77]Jorge González-Domínguez
parSRA: A framework for the parallel execution of short read aligners on compute clusters. J. Comput. Sci. 25: 134-139 (2018) - [j76]Roland Leißa
AnyDSL: a partial evaluation framework for programming high-performance libraries. Proc. ACM Program. Lang. 2(OOPSLA): 119:1-119:30 (2018) - [j75]Yongchao Liu
LightSpMV: Faster CUDA-Compatible Sparse Matrix-Vector Multiplication Using Compressed Sparse Rows. J. Signal Process. Syst. 90(1): 69-86 (2018) - [c86]Robin Kobus, Adrian Lamoth, André Müller
cuBool: Bit-Parallel Boolean Matrix Factorization on CUDA-Enabled Accelerators. ICPADS 2018: 465-472 - [c85]André Weißenberger, Bertil Schmidt
Massively Parallel Huffman Decoding on GPUs. ICPP 2018: 27:1-27:10 - [c84]Kai Xu, Robin Kobus, Yuandong Chan, Ping Gao, Xiangxu Meng, Yanjie Wei, Bertil Schmidt
SPECTR: Scalable Parallel Short Read Error Correction on Multi-core and Many-core Architectures. ICPP 2018: 39:1-39:10 - [c83]Daniel Jünger
WarpDrive: Massively Parallel Hashing on Multi-GPU Nodes. IPDPS 2018: 441-450 - 2017
- [j74]Yongchao Liu
AFS: identification and quantification of species composition by metagenomic sequencing. Bioinform. 33(9): 1396-1398 (2017) - [j73]André Müller
MetaCache: context-aware classification of metagenomic reads using minhashing. Bioinform. 33(23): 3740-3748 (2017) - [j72]Robin Kobus, Christian Hundt, André Müller
Accelerating metagenomic read classification on CUDA-enabled GPUs. BMC Bioinform. 18(1): 11:1-11:10 (2017) - [j71]Jan Schröder
CLOVE: classification of genomic fusions into structural variation events. BMC Bioinform. 18(1): 346 (2017) - [j70]Daniel Jünger, Christian Hundt, Jorge González-Domínguez
Speed and accuracy improvement of higher-order epistasis detection on CUDA-enabled GPUs. Clust. Comput. 20(3): 1899-1908 (2017) - [j69]Christian Hundt, Moritz Schlarb
SAUCE: A web application for interactive teaching and learning of parallel programming. J. Parallel Distributed Comput. 105: 163-173 (2017) - [j68]Shuai Zhang, Zhao Wang, Ying Peng, Bertil Schmidt
Mapping of option pricing algorithms onto heterogeneous many-core architectures. J. Supercomput. 73(9): 3715-3737 (2017) - [c82]Shaoliang Peng
mD3DOCKxb: An Ultra-Scalable CPU-MIC Coordinated Virtual Screening Framework. CCGrid 2017: 671-676 - [c81]Xiaohui Duan, Kai Xu, Yuandong Chan, Christian Hundt, Bertil Schmidt
S-Aligner: Ultrascalable Read Mapping on Sunway Taihu Light. CLUSTER 2017: 36-46 - [c80]Haidong Lan, Weiguo Liu, Yongchao Liu, Bertil Schmidt
SWhybrid: A Hybrid-Parallel Framework for Large-Scale Protein Sequence Database Search. IPDPS 2017: 42-51 - [c79]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: 52-61 - [p2]Yongchao Liu
CUSHAW Suite: Parallel and Efficient Algorithms for NGS Read Alignment. Algorithms for Next-Generation Sequencing Data 2017: 203-233 - [i2]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 abs/1706.04397 (2017) - 2016
- [j67]Jorge González-Domínguez
ParDRe: faster parallel duplicated reads removal tool for sequencing studies. Bioinform. 32(10): 1562-1564 (2016) - [j66]Jorge González-Domínguez
MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems. Bioinform. 32(24): 3826-3828 (2016) - [j65]Haidong Lan, Yuandong Chan, Kai Xu, Bertil Schmidt
Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters. BMC Bioinform. 17(S-9): 267 (2016) - [j64]Christian Hundt
rapidGSEA: Speeding up gene set enrichment analysis on multi-core CPUs and CUDA-enabled GPUs. BMC Bioinform. 17: 394 (2016) - [j63]Yongchao Liu
SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations. BMC Syst. Biol. 10(S-2): 47 (2016) - [j62]Hoang-Vu Dang, Bertil Schmidt
CUDA-enabled hierarchical ward clustering of protein structures based on the nearest neighbour chain algorithm. Int. J. High Perform. Comput. Appl. 30(2): 200-211 (2016) - [j61]Tuan Tu Tran, Yongchao Liu
Bit-parallel approximate pattern matching: Kepler GPU versus Xeon Phi. Parallel Comput. 54: 128-138 (2016) - [j60]Yongchao Liu
Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data. IEEE ACM Trans. Comput. Biol. Bioinform. 13(3): 592-598 (2016) - [j59]Junming Shao, Qinli Yang, Hoang-Vu Dang, Bertil Schmidt
Scalable Clustering by Iterative Partitioning and Point Attractor Representation. ACM Trans. Knowl. Discov. Data 11(1): 5:1-5:23 (2016) - [j58]Jorge González-Domínguez
Parallel Pairwise Epistasis Detection on Heterogeneous Computing Architectures. IEEE Trans. Parallel Distributed Syst. 27(8): 2329-2340 (2016) - [c78]Jan Christian Kässens
Combining GPU and FPGA technology for efficient exhaustive interaction analysis in GWAS. ASAP 2016: 170-175 - [c77]Daniel Jünger
Ultra-Fast Detection of Higher-Order Epistatic Interactions on GPUs. Euro-Par Workshops 2016: 421-432 - 2015
- [j57]Yongchao Liu
GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences. Concurr. Comput. Pract. Exp. 27(4): 958-972 (2015) - [j56]Jorge González-Domínguez
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): 506-510 (2015) - [j55]Jorge González-Domínguez
GPU-accelerated exhaustive search for third-order epistatic interactions in case-control studies. J. Comput. Sci. 8: 93-100 (2015) - [j54]Jan Christian Kässens
High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs. J. Comput. Sci. 9: 131-136 (2015) - [j53]Juan Antonio Gómez Pulido
Accelerating Bioinformatics Applications via Emerging Parallel Computing Systems. IEEE ACM Trans. Comput. Biol. Bioinform. 12(5): 971-972 (2015) - [j52]Jorge González-Domínguez
Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems. IEEE ACM Trans. Comput. Biol. Bioinform. 12(5): 982-994 (2015) - [j51]Thuy-Diem Nguyen, Bertil Schmidt
Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting. IEEE ACM Trans. Comput. Biol. Bioinform. 12(5): 1060-1073 (2015) - [c76]Yongchao Liu
LightSpMV: Faster CSR-based sparse matrix-vector multiplication on CUDA-enabled GPUs. ASAP 2015: 82-89 - [c75]Yongchao Liu, Martin Loewer, Srinivas Aluru, Bertil Schmidt:
SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models. BIBM 2015: 83-90 - [c74]Haidong Lan, Weiguo Liu, Bertil Schmidt
Accelerating large-scale biological database search on Xeon Phi-based neo-heterogeneous architectures. BIBM 2015: 503-510 - [c73]Moritz Schlarb
SAUCE: A Web-Based Automated Assessment Tool for Teaching Parallel Programming. Euro-Par Workshops 2015: 54-65 - 2014
- [j50]Adrianto Wirawan, Robert S. Harris, Yongchao Liu
HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. BMC Bioinform. 15: 131 (2014) - [j49]Yongchao Liu
CUSHAW2-GPU: Empowering Faster Gapped Short-Read Alignment Using GPU Computing. IEEE Des. Test 31(1): 31-39 (2014) - [c72]Yongchao Liu
SWAPHI: Smith-waterman protein database search on Xeon Phi coprocessors. ASAP 2014: 184-185 - [c71]Thuy-Diem Nguyen, Bertil Schmidt
Fast dendrogram-based OTU clustering using sequence embedding. BCB 2014: 63-72 - [c70]Jan Christian Kässens
UPC++ for bioinformatics: A case study using genome-wide association studies. CLUSTER 2014: 248-256 - [c69]Yongchao Liu
SWAPHI-LS: Smith-Waterman Algorithm on Xeon Phi coprocessors for Long DNA Sequences. CLUSTER 2014: 257-265 - [c68]Jorge González-Domínguez
Hybrid CPU/GPU Acceleration of Detection of 2-SNP Epistatic Interactions in GWAS. Euro-Par 2014: 680-691 - [c67]Thuy-Diem Nguyen, Bertil Schmidt
SparseHC: A Memory-efficient Online Hierarchical Clustering Algorithm. ICCS 2014: 8-19 - [c66]Lars Wienbrandt
FPGA-based Acceleration of Detecting Statistical Epistasis in GWAS. ICCS 2014: 220-230 - [c65]Christian Hundt, Bertil Schmidt
CUDA-Accelerated Alignment of Subsequences in Streamed Time Series Data. ICPP 2014: 10-19 - [c64]Hoang-Vu Dang, Bertil Schmidt, Andreas Hildebrandt
Parallelized Clustering of Protein Structures on CUDA-Enabled GPUs. PDP 2014: 1-8 - [c63]Christian Hundt, Bertil Schmidt, Elmar Schömer, Herbert Göttler, Hoang-Vu Dang:
GEM: an elastic and translation-invariant similarity measure with automatic trend adjustment. SAC 2014: 105-112 - [c62]Tuan Tu Tran, Simon Schindel, Yongchao Liu
Bit-Parallel Approximate Pattern Matching on the Xeon Phi Coprocessor. SBAC-PAD 2014: 81-88 - [i1]Yongchao Liu, Bertil Schmidt:
SWAPHI: Smith-Waterman Protein Database Search on Xeon Phi Coprocessors. CoRR abs/1404.4152 (2014) - 2013
- [j48]Yongchao Liu
Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. Bioinform. 29(3): 308-315 (2013) - [j47]Yupeng Chen, Bertil Schmidt
A hybrid short read mapping accelerator. BMC Bioinform. 14: 67 (2013) - [j46]Yongchao Liu
CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions. BMC Bioinform. 14: 117 (2013) - [j45]Bertil Schmidt
Iterative sparse matrix-vector multiplication for accelerating the block Wiedemann algorithm over GF(2) on multi-graphics processing unit systems. Concurr. Comput. Pract. Exp. 25(4): 586-603 (2013) - [j44]Hoang-Vu Dang, Bertil Schmidt
CUDA-enabled Sparse Matrix-Vector Multiplication on GPUs using atomic operations. Parallel Comput. 39(11): 737-750 (2013) - [j43]Yupeng Chen, Bertil Schmidt
Reconfigurable Accelerator for the Word-Matching Stage of BLASTN. IEEE Trans. Very Large Scale Integr. Syst. 21(4): 659-669 (2013) - [c61]Yongchao Liu
Faster GPU-Accelerated Smith-Waterman Algorithm with Alignment Backtracking for Short DNA Sequences. PPAM (2) 2013: 247-257 - 2012
- [j42]Yongchao Liu
CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform. Bioinform. 28(14): 1830-1837 (2012) - [j41]Zejun Zheng, Stefan Kramer, Bertil Schmidt
DySC: software for greedy clustering of 16S rRNA reads. Bioinform. 28(16): 2182-2183 (2012) - [j40]Yongchao Liu
Long read alignment based on maximal exact match seeds. Bioinform. 28(18): 318-324 (2012) - [c60]Yupeng Chen, Bertil Schmidt
Accelerating short read mapping on an FPGA (abstract only). FPGA 2012: 265 - [c59]Yupeng Chen, Bertil Schmidt
An FPGA aligner for short read mapping. FPL 2012: 511-514 - [c58]Yongchao Liu
Evaluation of GPU-based Seed Generation for Computational Genomics Using Burrows-Wheeler Transform. IPDPS Workshops 2012: 684-690 - [c57]Hoang-Vu Dang, Bertil Schmidt
The Sliced COO Format for Sparse Matrix-Vector Multiplication on CUDA-enabled GPUs. ICCS 2012: 57-66 - [c56]Bertil Schmidt, Douglas L. Maskell:
Fourth Workshop on using Emerging Parallel Architectures. ICCS 2012: 1867-1869 - 2011
- [j39]Lakshmi Kuttippurathu
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. Bioinform. 27(5): 715-717 (2011) - [j38]Yongchao Liu
DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI. BMC Bioinform. 12: 85 (2011) - [j37]Yongchao Liu
Parallelized short read assembly of large genomes using de Bruijn graphs. BMC Bioinform. 12: 354 (2011) - [j36]Weiguo Liu, Bertil Schmidt
CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware. IEEE ACM Trans. Comput. Biol. Bioinform. 8(6): 1678-1684 (2011) - [c55]Bertil Schmidt
Iterative Sparse Matrix-Vector Multiplication for Integer Factorization on GPUs. Euro-Par (2) 2011: 413-424 - [c54]Weiguo Liu, Bertil Schmidt
Mapping of BLASTP Algorithm onto GPU Clusters. ICPADS 2011: 236-243 - [c53]Yongchao Liu
An Ultrafast Scalable Many-Core Motif Discovery Algorithm for Multiple GPUs. IPDPS Workshops 2011: 428-434 - [c52]Zejun Zheng, Thuy-Diem Nguyen, Bertil Schmidt
CRiSPy-CUDA: Computing Species Richness in 16S rRNA Pyrosequencing Datasets with CUDA. PRIB 2011: 37-49 - [c51]Bertil Schmidt, Douglas L. Maskell:
Third Workshop on using Emerging Parallel Architectures. ICCS 2011: 1964-1966 - [e2]Srinivas Aluru, Sanghamitra Bandyopadhyay, Ümit V. Çatalyürek, Devdatt P. Dubhashi, Phillip H. Jones, Manish Parashar, Bertil Schmidt:
Contemporary Computing - 4th International Conference, IC3 2011, Noida, India, August 8-10, 2011. Proceedings. Communications in Computer and Information Science 168, Springer 2011, ISBN 978-3-642-22605-2 [contents] - 2010
- [j35]Adrianto Wirawan, Chee Keong Kwoh, Bertil Schmidt
Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures. Bioinform. 26(10): 1368-1369 (2010) - [j34]Yongchao Liu
MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities. Bioinform. 26(16): 1958-1964 (2010) - [j33]Haixiang Shi, Bertil Schmidt
A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware. J. Comput. Biol. 17(4): 603-615 (2010) - [j32]Shandar Ahmad
Pattern Recognition in Bioinformatics. Pattern Recognit. Lett. 31(14): 2071-2072 (2010) - [j31]Yongchao Liu
CUDA-MEME: Accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units. Pattern Recognit. Lett. 31(14): 2170-2177 (2010) - [c50]Zejun Zheng, Bertil Schmidt, Guillaume Bourque:
Prediction of low coverage prone regions for Illumina sequencing projects using a support vector machine. BIBM 2010: 13-16 - [c49]Bertil Schmidt, Douglas L. Maskell:
Second Workshop on using Emerging Parallel Architectures. ICCS 2010: 1015-1017 - [c48]Haixiang Shi, Bertil Schmidt
Quality-score guided error correction for short-read sequencing data using CUDA. ICCS 2010: 1129-1138
2000 – 2009
- 2009
- [j30]Jan Schröder
SHREC: a short-read error correction method. Bioinform. 25(17): 2157-2163 (2009) - [j29]Bertil Schmidt
A fast hybrid short read fragment assembly algorithm. Bioinform. 25(17): 2279-2280 (2009) - [j28]Adrianto Wirawan, Bertil Schmidt, Huiliang Zhang, Chee Keong Kwoh:
High performance protein sequence database scanning on the Cell Broadband Engine. Sci. Program. 17(1-2): 97-111 (2009) - [j27]Timothy F. Oliver, Bertil Schmidt
High Speed Biological Sequence Analysis With Hidden Markov Models on Reconfigurable Platforms. IEEE Trans. Inf. Technol. Biomed. 13(5): 740-746 (2009) - [c47]Yupeng Chen, Bertil Schmidt
A Reconfigurable Bloom Filter Architecture for BLASTN. ARCS 2009: 40-49 - [c46]Yongchao Liu
MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA. ASAP 2009: 121-128 - [c45]Bertil Schmidt, Douglas L. Maskell:
Workshop on Using Emerging Parallel Architectures for Computational Science. ICCS (1) 2009: 861-863 - [c44]Adrianto Wirawan, Bertil Schmidt
Pairwise Distance Matrix Computation for Multiple Sequence Alignment on the Cell Broadband Engine. ICCS (1) 2009: 954-963 - [c43]Yongchao Liu
Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA. IPDPS 2009: 1-8 - [c42]Haixiang Shi, Bertil Schmidt
Accelerating error correction in high-throughput short-read DNA sequencing data with CUDA. IPDPS 2009: 1-8 - 2008
- [j26]Dadabhai T. Singh, Rahul Trehan, Bertil Schmidt
Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment. BMC Bioinform. 9(S-1) (2008) - [j25]Adrianto Wirawan, Chee Keong Kwoh, Nim Tri Hieu, Bertil Schmidt
CBESW: Sequence Alignment on the Playstation 3. BMC Bioinform. 9 (2008) - [j24]Weiguo Liu, Bertil Schmidt
Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA. Comput. Phys. Commun. 179(9): 634-641 (2008) - [j23]Timothy F. Oliver, Leow Yuan Yeow, Bertil Schmidt
Integrating FPGA acceleration into HMMer. Parallel Comput. 34(11): 681-691 (2008) - [j22]Aarti Singh, Chen Chen, Weiguo Liu, Wayne P. Mitchell, Bertil Schmidt
A Hybrid Computational Grid Architecture for Comparative Genomics. IEEE Trans. Inf. Technol. Biomed. 12(2): 218-225 (2008) - [c41]Chen Chen, Bertil Schmidt
GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences. PRIB 2008: 448-459 - [c40]Huiliang Zhang, Bertil Schmidt
Accelerating BLASTP on the Cell Broadband Engine. PRIB 2008: 460-470 - 2007
- [j21]Menaka Rajapakse, Bertil Schmidt
Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms. BMC Bioinform. 8 (2007) - [j20]Bertil Schmidt:
A survey of desktop grid applications for e-science. Int. J. Web Grid Serv. 3(3): 354-368 (2007) - [j19]Weiguo Liu, Bertil Schmidt
Streaming Algorithms for Biological Sequence Alignment on GPUs. IEEE Trans. Parallel Distributed Syst. 18(9): 1270-1281 (2007) - [j18]Feng Lin, Heiko Schröder, Bertil Schmidt:
Solving the Bottleneck Problem in Bioinformatics Computing: An Architectural Perspective. J. VLSI Signal Process. 48(3): 185-188 (2007) - [j17]Weiguo Liu, Bertil Schmidt
Performance Analysis of General-Purpose Computation on Commodity Graphics Hardware: A Case Study Using Bioinformatics. J. VLSI Signal Process. 48(3): 209-221 (2007) - [j16]John Paul Walters, Xiandong Meng, Vipin Chaudhary
MPI-HMMER-Boost: Distributed FPGA Acceleration. J. VLSI Signal Process. 48(3): 223-238 (2007) - [c39]Malcolm Yoke Hean Low, Weiguo Liu, Bertil Schmidt
A Parallel BSP Algorithm for Irregular Dynamic Programming. APPT 2007: 151-160 - [c38]Weiguo Liu, Bertil Schmidt
Molecular Dynamics Simulations on Commodity GPUs with CUDA. HiPC 2007: 185-196 - [c37]Weiguo Liu, Wolfgang Müller-Wittig, Bertil Schmidt
Performance Predictions for General-Purpose Computation on GPUs. ICPP 2007: 50 - [c36]Timothy F. Oliver, Leow Yuan Yeow, Bertil Schmidt
High Performance Database Searching with HMMer on FPGAs. IPDPS 2007: 1-7 - [c35]Adrianto Wirawan, Chee Keong Kwoh, Bertil Schmidt
Parallel DNA Sequence Alignment on the Cell Broadband Engine. PPAM 2007: 1249-1256 - [c34]Yan Lin Aung, Douglas L. Maskell, Timothy F. Oliver, Bertil Schmidt
C-Based Design Methodology for FPGA Implementation of ClustalW MSA. PRIB 2007: 11-18 - [c33]Jimin Feng, Samarjit Chakraborty
Fast Schedulability Analysis Using Commodity Graphics Hardware. RTCSA 2007: 400-408 - [p1]Bertil Schmidt, Chunxi Chen, Weiguo Liu:
Hierarchical Grid Computing for High-Performance Bioinformatics. Grid Computing for Bioinformatics and Computational Biology 2007: 87-121 - [e1]Jagath C. Rajapakse, Bertil Schmidt, L. Gwenn Volkert:
Pattern Recognition in Bioinformatics, Second IAPR International Workshop, PRIB 2007, Singapore, October 1-2, 2007, Proceedings. Lecture Notes in Computer Science 4774, Springer 2007, ISBN 978-3-540-75285-1 [contents] - 2006
- [j15]Weiguo Liu, Bertil Schmidt:
Mapping of Hierarchical Parallel Genetic Algorithms for Protein Folding onto Computational Grids. IEICE Trans. Inf. Syst. 89-D(2): 589-596 (2006) - [j14]Timothy F. Oliver, Bertil Schmidt
High-speed Multiple Sequence Alignment on a reconfigurable platform. Int. J. Bioinform. Res. Appl. 2(4): 394-406 (2006) - [j13]Chunxi Chen, Bertil Schmidt
Constructing large suffix trees on a computational grid. J. Parallel Distributed Comput. 66(12): 1512-1523 (2006) - [j12]Weiguo Liu, Bertil Schmidt
Parallel Pattern-Based Systems for Computational Biology: A Case Study. IEEE Trans. Parallel Distributed Syst. 17(8): 750-763 (2006) - [c32]Adrianto Wirawan, Bertil Schmidt:
Parallel Discovery of Transcription Factor Binding Sites. APCCAS 2006: 700-703 - [c31]Menaka Rajapakse, Bertil Schmidt
Multi-Objective Evolutionary Algorithm for Discovering Peptide Binding Motifs. EvoWorkshops 2006: 149-158 - [c30]Weiguo Liu, Bertil Schmidt
GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment. HiPC 2006: 363-374 - [c29]Timothy F. Oliver, Bertil Schmidt
Accelerating the Viterbi Algorithm for Profile Hidden Markov Models Using Reconfigurable Hardware. International Conference on Computational Science (1) 2006: 522-529 - [c28]Weiguo Liu, Bertil Schmidt
Bio-sequence database scanning on a GPU. IPDPS 2006 - 2005
- [j11]Timothy F. Oliver, Bertil Schmidt
Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW. Bioinform. 21(16): 3431-3432 (2005) - [j10]Tong Liu, Bertil Schmidt
Parallel RNA secondary structure prediction using stochastic context-free grammars. Concurr. Comput. Pract. Exp. 17(14): 1669-1685 (2005) - [j9]Chunxi Chen, Bertil Schmidt
An adaptive grid implementation of DNA sequence alignment. Future Gener. Comput. Syst. 21(7): 988-1003 (2005) - [j8]Timothy F. Oliver, Bertil Schmidt
Reconfigurable architectures for bio-sequence database scanning on FPGAs. IEEE Trans. Circuits Syst. II Express Briefs 52-II(12): 851-855 (2005) - [c27]Jacop Yanto, Timothy F. Oliver, Bertil Schmidt, Douglas L. Maskell:
Biological Sequence Analysis with Hidden Markov Models on an FPGA. Asia-Pacific Computer Systems Architecture Conference 2005: 429-439 - [c26]Chunxi Chen, Bertil Schmidt:
Parallel Construction of Large Suffix Trees on a PC Cluster. Euro-Par 2005: 1227-1236 - [c25]Timothy F. Oliver, Bertil Schmidt
Hyper customized processors for bio-sequence database scanning on FPGAs. FPGA 2005: 229-237 - [c24]Timothy F. Oliver, Bertil Schmidt
Multiple Sequence Alignment on an FPGA. ICPADS (2) 2005: 326-330 - [c23]Menaka Rajapakse, Lonce L. Wyse, Bertil Schmidt
Deriving Matrix of Peptide-MHC Interactions in Diabetic Mouse by Genetic Algorithm. IDEAL 2005: 440-447 - [c22]Weiguo Liu, Bertil Schmidt:
A Case Study on Pattern-Based Systems for High Performance Computational Biology. IPDPS 2005 - [c21]Timothy F. Oliver, Bertil Schmidt, Douglas L. Maskell, Achutavarrier Prasad Vinod
A reconfigurable architecture for scanning biosequence databases. ISCAS (5) 2005: 4799-4802 - 2004
- [j7]Bertil Schmidt
Development of distributed bioinformatics applications with GMP. Concurr. Pract. Exp. 16(9): 945-959 (2004) - [j6]Manfred Schimmler, Bertil Schmidt, Hans-Werner Lang:
A bit-serial floating-point unit for a massively parallel system on a chip. Parallel Algorithms Appl. 19(2-3): 79-95 (2004) - [c20]Chunxi Chen, Bertil Schmidt
Performance analysis of computational biology applications on hierarchical Grid systems. CCGRID 2004: 426-433 - [c19]Weiguo Liu, Bertil Schmidt
A Generic Parallel Pattern-Based System for Bioinformatics. Euro-Par 2004: 989-996 - [c18]Weiguo Liu, Bertil Schmidt:
A Tunable Coarse-Grained Parallel Algorithm for Irregular Dynamic Programming Applications. HiPC 2004: 91-100 - [c17]Chunxi Chen, Bertil Schmidt:
Load Balancing for Hierarchical Grid Computing: A Case Study. HiPC 2004: 353-362 - [c16]Tong Liu, Bertil Schmidt:
Parallel RNA Sequence-Structure Alignment. IPDPS 2004 - [c15]Timothy F. Oliver, Bertil Schmidt
High Performance Biosequence Database Scanning on Reconfigurable Platforms. IPDPS 2004 - 2003
- [c14]Chunxi Chen, Bertil Schmidt
Computing Large-Scale Alignments on a Multi-Cluster. CLUSTER 2003: 38-45 - [c13]Weiguo Liu, Bertil Schmidt
Parallel Design Pattern for Computational Biology and Scientific Computing Applications. CLUSTER 2003: 456-459 - [c12]Ishfaq Ahmad, Pieter Jonker, Bertil Schmidt, Andreas Uhl:
Topic Introduction. Euro-Par 2003: 850 - [c11]Bertil Schmidt
Parallel Detection of Regulatory Elements with gMP. IPDPS 2003: 156 - [c10]Manfred Schimmler, Bertil Schmidt, Hans-Werner Lang:
Design of a Bit-Serial Floating Point Unit for a Fine Grained Parallel Processor Array. PDPTA 2003: 255-261 - [c9]Manfred Schimmler, Bertil Schmidt, Hans-Werner Lang, Sven Heithecker:
An Area-Efficient Bit-Serial Integer Multiplier. VLSI 2003: 131-137 - 2002
- [j5]Bertil Schmidt
A hybrid architecture for bioinformatics. Future Gener. Comput. Syst. 18(6): 855-862 (2002) - [c8]Bertil Schmidt
Massively Parallel Solutions for Molecular Sequence Analysis. IPDPS 2002 - 2001
- [j4]Bertil Schmidt, Heiko Schröder, Manfred Schimmler:
Tomographic Image Reconstruction on the Instruction Systolic Array. Comput. Artif. Intell. 20(1): 27-42 (2001) - [j3]Bertil Schmidt, Heiko Schröder:
A Hybrid Architecture for Multimedia Processors. Comput. Artif. Intell. 20(3): 225-244 (2001) - [c7]Bertil Schmidt, Heiko Schröder, Manfred Schimmler:
Scanning Biosequence Databases on a Hybrid Parallel Architecture. Euro-Par 2001: 360-370 - [c6]Bertil Schmidt, Heiko Schröder, Manfred Schimmler:
Protein Sequence Comparison on the Instruction Systolic Array. PaCT 2001: 498-509 - 2000
- [j2]Bertil Schmidt, Manfred Schimmler:
KPROC - An Instruction Systolic Architecture for Parallel Prefix Applications. Parallel Distributed Comput. Pract. 3(2) (2000) - [c5]Bertil Schmidt
Design of a Parallel Accelerator for Volume Rendering. Euro-Par 2000: 1095-1104
1990 – 1999
- 1999
- [j1]Bertil Schmidt, Manfred Schimmler, Heiko Schröder:
A Morphological Approach to Hough Transform on an Instruction Systolic Array. Comput. Artif. Intell. 18(6): 541-557 (1999) - [c4]Bertil Schmidt
A Parallel Accelerator Architecture for Multimedia Video Compression. Euro-Par 1999: 950-960 - 1998
- [c3]Bertil Schmidt
Long Operand Arithmetic on Instruction Systolic Computer Architectures and Its Application in RSA Cryptography. Euro-Par 1998: 916-922 - 1997
- [c2]Bertil Schmidt
Morphological Hough Transform on the Instruction Systolic Array. Euro-Par 1997: 798-806 - 1995
- [c1]Udo Mahlmeister, Bertil Schmidt, Gerald Sommer:
Preattentive Colour Features by Steerable Filters. DAGM-Symposium 1995: 464-472
Coauthor Index
[j106] [c109] [c108] [j102] [j100] [j99] [j98] [j97] [j93] [j92] [j91] [j90] [c104] [j88] [j87] [j83] [j82] [c97] [c95] [c93] [c92] [i3] [j81] [c91] [c90] [j78] [c84] [j68] [c81] [c80] [c79] [j65] [c74] [j36] [c54] [j33] [j31] [c48] [c42] [j24] [j22] [c41] [j19] [j17] [c39] [c38] [c37] [c33] [p1] [j15] [j12] [c30] [c28] [c22] [c19] [c18] [c13]
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