Bertil Schmidt

According to our database1, Bertil Schmidt
  • authored at least 159 papers between 1995 and 2018.
  • has a "Dijkstra number"2 of four.

Timeline

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Bibliography

2018
LightSpMV: Faster CUDA-Compatible Sparse Matrix-Vector Multiplication Using Compressed Sparse Rows.
Signal Processing Systems, 2018

2017
Mapping of option pricing algorithms onto heterogeneous many-core architectures.
The Journal of Supercomputing, 2017

SAUCE: A web application for interactive teaching and learning of parallel programming.
J. Parallel Distrib. Comput., 2017

$ν$-net: Deep Learning for Generalized Biventricular Cardiac Mass and Function Parameters.
CoRR, 2017

Speed and accuracy improvement of higher-order epistasis detection on CUDA-enabled GPUs.
Cluster Computing, 2017

CLOVE: classification of genomic fusions into structural variation events.
BMC Bioinformatics, 2017

Accelerating metagenomic read classification on CUDA-enabled GPUs.
BMC Bioinformatics, 2017

MetaCache: context-aware classification of metagenomic reads using minhashing.
Bioinformatics, 2017

AFS: identification and quantification of species composition by metagenomic sequencing.
Bioinformatics, 2017

SWhybrid: A Hybrid-Parallel Framework for Large-Scale Protein Sequence Database Search.
Proceedings of the 2017 IEEE International Parallel and Distributed Processing Symposium, 2017

PUNAS: A Parallel Ungapped-Alignment-Featured Seed Verification Algorithm for Next-Generation Sequencing Read Alignment.
Proceedings of the 2017 IEEE International Parallel and Distributed Processing Symposium, 2017

S-Aligner: Ultrascalable Read Mapping on Sunway Taihu Light.
Proceedings of the 2017 IEEE International Conference on Cluster Computing, 2017

mD3DOCKxb: An Ultra-Scalable CPU-MIC Coordinated Virtual Screening Framework.
Proceedings of the 17th IEEE/ACM International Symposium on Cluster, 2017

2016
Parallel Pairwise Epistasis Detection on Heterogeneous Computing Architectures.
IEEE Trans. Parallel Distrib. Syst., 2016

Scalable Clustering by Iterative Partitioning and Point Attractor Representation.
TKDD, 2016

Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data.
IEEE/ACM Trans. Comput. Biology Bioinform., 2016

Bit-parallel approximate pattern matching: Kepler GPU versus Xeon Phi.
Parallel Computing, 2016

CUDA-enabled hierarchical ward clustering of protein structures based on the nearest neighbour chain algorithm.
IJHPCA, 2016

SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations.
BMC Systems Biology, 2016

Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters.
BMC Bioinformatics, 2016

rapidGSEA: Speeding up gene set enrichment analysis on multi-core CPUs and CUDA-enabled GPUs.
BMC Bioinformatics, 2016

MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems.
Bioinformatics, 2016

ParDRe: faster parallel duplicated reads removal tool for sequencing studies.
Bioinformatics, 2016

Ultra-Fast Detection of Higher-Order Epistatic Interactions on GPUs.
Proceedings of the Euro-Par 2016: Parallel Processing Workshops, 2016

Combining GPU and FPGA technology for efficient exhaustive interaction analysis in GWAS.
Proceedings of the 27th IEEE International Conference on Application-specific Systems, 2016

2015
Accelerating Bioinformatics Applications via Emerging Parallel Computing Systems.
IEEE/ACM Trans. Comput. Biology Bioinform., 2015

Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting.
IEEE/ACM Trans. Comput. Biology Bioinform., 2015

Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems.
IEEE/ACM Trans. Comput. Biology Bioinform., 2015

High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs.
J. Comput. Science, 2015

GPU-accelerated exhaustive search for third-order epistatic interactions in case-control studies.
J. Comput. Science, 2015

Large-scale genome-wide association studies on a GPU cluster using a CUDA-accelerated PGAS programming model.
IJHPCA, 2015

GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences.
Concurrency and Computation: Practice and Experience, 2015

SAUCE: A Web-Based Automated Assessment Tool for Teaching Parallel Programming.
Proceedings of the Euro-Par 2015: Parallel Processing Workshops, 2015

SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

Accelerating large-scale biological database search on Xeon Phi-based neo-heterogeneous architectures.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

LightSpMV: Faster CSR-based sparse matrix-vector multiplication on CUDA-enabled GPUs.
Proceedings of the 26th IEEE International Conference on Application-specific Systems, 2015

2014
CUSHAW2-GPU: Empowering Faster Gapped Short-Read Alignment Using GPU Computing.
IEEE Design & Test, 2014

SWAPHI: Smith-Waterman Protein Database Search on Xeon Phi Coprocessors.
CoRR, 2014

HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data.
BMC Bioinformatics, 2014

Bit-Parallel Approximate Pattern Matching on the Xeon Phi Coprocessor.
Proceedings of the 26th IEEE International Symposium on Computer Architecture and High Performance Computing, 2014

GEM: an elastic and translation-invariant similarity measure with automatic trend adjustment.
Proceedings of the Symposium on Applied Computing, 2014

Parallelized Clustering of Protein Structures on CUDA-Enabled GPUs.
Proceedings of the 22nd Euromicro International Conference on Parallel, 2014

CUDA-Accelerated Alignment of Subsequences in Streamed Time Series Data.
Proceedings of the 43rd International Conference on Parallel Processing, 2014

FPGA-based Acceleration of Detecting Statistical Epistasis in GWAS.
Proceedings of the International Conference on Computational Science, 2014

SparseHC: A Memory-efficient Online Hierarchical Clustering Algorithm.
Proceedings of the International Conference on Computational Science, 2014

Hybrid CPU/GPU Acceleration of Detection of 2-SNP Epistatic Interactions in GWAS.
Proceedings of the Euro-Par 2014 Parallel Processing, 2014

SWAPHI-LS: Smith-Waterman Algorithm on Xeon Phi coprocessors for Long DNA Sequences.
Proceedings of the 2014 IEEE International Conference on Cluster Computing, 2014

UPC++ for bioinformatics: A case study using genome-wide association studies.
Proceedings of the 2014 IEEE International Conference on Cluster Computing, 2014

Fast dendrogram-based OTU clustering using sequence embedding.
Proceedings of the 5th ACM Conference on Bioinformatics, 2014

SWAPHI: Smith-waterman protein database search on Xeon Phi coprocessors.
Proceedings of the IEEE 25th International Conference on Application-Specific Systems, 2014

2013
Reconfigurable Accelerator for the Word-Matching Stage of BLASTN.
IEEE Trans. VLSI Syst., 2013

CUDA-enabled Sparse Matrix-Vector Multiplication on GPUs using atomic operations.
Parallel Computing, 2013

Iterative sparse matrix-vector multiplication for accelerating the block Wiedemann algorithm over GF(2) on multi-graphics processing unit systems.
Concurrency and Computation: Practice and Experience, 2013

CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions.
BMC Bioinformatics, 2013

A hybrid short read mapping accelerator.
BMC Bioinformatics, 2013

Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data.
Bioinformatics, 2013

Faster GPU-Accelerated Smith-Waterman Algorithm with Alignment Backtracking for Short DNA Sequences.
Proceedings of the Parallel Processing and Applied Mathematics, 2013

2012
Fourth Workshop on using Emerging Parallel Architectures.
Proceedings of the International Conference on Computational Science, 2012

The Sliced COO Format for Sparse Matrix-Vector Multiplication on CUDA-enabled GPUs.
Proceedings of the International Conference on Computational Science, 2012

DySC: software for greedy clustering of 16S rRNA reads.
Bioinformatics, 2012

CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform.
Bioinformatics, 2012

Long read alignment based on maximal exact match seeds.
Bioinformatics, 2012

Evaluation of GPU-based Seed Generation for Computational Genomics Using Burrows-Wheeler Transform.
Proceedings of the 26th IEEE International Parallel and Distributed Processing Symposium Workshops & PhD Forum, 2012

An FPGA aligner for short read mapping.
Proceedings of the 22nd International Conference on Field Programmable Logic and Applications (FPL), 2012

Accelerating short read mapping on an FPGA (abstract only).
Proceedings of the ACM/SIGDA 20th International Symposium on Field Programmable Gate Arrays, 2012

2011
CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware.
IEEE/ACM Trans. Comput. Biology Bioinform., 2011

Third Workshop on using Emerging Parallel Architectures.
Proceedings of the International Conference on Computational Science, 2011

Parallelized short read assembly of large genomes using de Bruijn graphs.
BMC Bioinformatics, 2011

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI.
BMC Bioinformatics, 2011

CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments.
Bioinformatics, 2011

CRiSPy-CUDA: Computing Species Richness in 16S rRNA Pyrosequencing Datasets with CUDA.
Proceedings of the Pattern Recognition in Bioinformatics, 2011

An Ultrafast Scalable Many-Core Motif Discovery Algorithm for Multiple GPUs.
Proceedings of the 25th IEEE International Symposium on Parallel and Distributed Processing, 2011

Mapping of BLASTP Algorithm onto GPU Clusters.
Proceedings of the 17th IEEE International Conference on Parallel and Distributed Systems, 2011

Iterative Sparse Matrix-Vector Multiplication for Integer Factorization on GPUs.
Proceedings of the Euro-Par 2011 Parallel Processing - 17th International Conference, 2011

2010
Quality-score guided error correction for short-read sequencing data using CUDA.
Proceedings of the International Conference on Computational Science, 2010

Second Workshop on using Emerging Parallel Architectures.
Proceedings of the International Conference on Computational Science, 2010

CUDA-MEME: Accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units.
Pattern Recognition Letters, 2010

Pattern Recognition in Bioinformatics.
Pattern Recognition Letters, 2010

A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware.
Journal of Computational Biology, 2010

Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures.
Bioinformatics, 2010

MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities.
Bioinformatics, 2010

Prediction of low coverage prone regions for Illumina sequencing projects using a support vector machine.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010

2009
High Speed Biological Sequence Analysis With Hidden Markov Models on Reconfigurable Platforms.
IEEE Trans. Information Technology in Biomedicine, 2009

High performance protein sequence database scanning on the Cell Broadband Engine.
Scientific Programming, 2009

SHREC: a short-read error correction method.
Bioinformatics, 2009

A fast hybrid short read fragment assembly algorithm.
Bioinformatics, 2009

Accelerating error correction in high-throughput short-read DNA sequencing data with CUDA.
Proceedings of the 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009

Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA.
Proceedings of the 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009

Pairwise Distance Matrix Computation for Multiple Sequence Alignment on the Cell Broadband Engine.
Proceedings of the Computational Science, 2009

Workshop on Using Emerging Parallel Architectures for Computational Science.
Proceedings of the Computational Science, 2009

MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA.
Proceedings of the 20th IEEE International Conference on Application-Specific Systems, 2009

A Reconfigurable Bloom Filter Architecture for BLASTN.
Proceedings of the Architecture of Computing Systems, 2009

2008
A Hybrid Computational Grid Architecture for Comparative Genomics.
IEEE Trans. Information Technology in Biomedicine, 2008

Integrating FPGA acceleration into HMMer.
Parallel Computing, 2008

Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA.
Computer Physics Communications, 2008

CBESW: Sequence Alignment on the Playstation 3.
BMC Bioinformatics, 2008

Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment.
BMC Bioinformatics, 2008

Accelerating BLASTP on the Cell Broadband Engine.
Proceedings of the Pattern Recognition in Bioinformatics, 2008

GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences.
Proceedings of the Pattern Recognition in Bioinformatics, 2008

2007
MPI-HMMER-Boost: Distributed FPGA Acceleration.
VLSI Signal Processing, 2007

Performance Analysis of General-Purpose Computation on Commodity Graphics Hardware: A Case Study Using Bioinformatics.
VLSI Signal Processing, 2007

Solving the Bottleneck Problem in Bioinformatics Computing: An Architectural Perspective.
VLSI Signal Processing, 2007

Streaming Algorithms for Biological Sequence Alignment on GPUs.
IEEE Trans. Parallel Distrib. Syst., 2007

A survey of desktop grid applications for e-science.
IJWGS, 2007

Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms.
BMC Bioinformatics, 2007

Fast Schedulability Analysis Using Commodity Graphics Hardware.
Proceedings of the 13th IEEE International Conference on Embedded and Real-Time Computing Systems and Applications (RTCSA 2007), 2007

C-Based Design Methodology for FPGA Implementation of ClustalW MSA.
Proceedings of the Pattern Recognition in Bioinformatics, 2007

Parallel DNA Sequence Alignment on the Cell Broadband Engine.
Proceedings of the Parallel Processing and Applied Mathematics, 2007

High Performance Database Searching with HMMer on FPGAs.
Proceedings of the 21th International Parallel and Distributed Processing Symposium (IPDPS 2007), 2007

Performance Predictions for General-Purpose Computation on GPUs.
Proceedings of the 2007 International Conference on Parallel Processing (ICPP 2007), 2007

Molecular Dynamics Simulations on Commodity GPUs with CUDA.
Proceedings of the High Performance Computing, 2007

A Parallel BSP Algorithm for Irregular Dynamic Programming.
Proceedings of the Advanced Parallel Processing Technologies, 7th International Symposium, 2007

2006
Parallel Pattern-Based Systems for Computational Biology: A Case Study.
IEEE Trans. Parallel Distrib. Syst., 2006

Constructing large suffix trees on a computational grid.
J. Parallel Distrib. Comput., 2006

High-speed Multiple Sequence Alignment on a reconfigurable platform.
IJBRA, 2006

Mapping of Hierarchical Parallel Genetic Algorithms for Protein Folding onto Computational Grids.
IEICE Transactions, 2006

Bio-sequence database scanning on a GPU.
Proceedings of the 20th International Parallel and Distributed Processing Symposium (IPDPS 2006), 2006

Accelerating the Viterbi Algorithm for Profile Hidden Markov Models Using Reconfigurable Hardware.
Proceedings of the Computational Science, 2006

GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment.
Proceedings of the High Performance Computing, 2006

Multi-Objective Evolutionary Algorithm for Discovering Peptide Binding Motifs.
Proceedings of the Applications of Evolutionary Computing, 2006

Parallel Discovery of Transcription Factor Binding Sites.
Proceedings of the IEEE Asia Pacific Conference on Circuits and Systems 2006, 2006

2005
Reconfigurable architectures for bio-sequence database scanning on FPGAs.
IEEE Trans. on Circuits and Systems, 2005

An adaptive grid implementation of DNA sequence alignment.
Future Generation Comp. Syst., 2005

Parallel RNA secondary structure prediction using stochastic context-free grammars.
Concurrency and Computation: Practice and Experience, 2005

Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW.
Bioinformatics, 2005

A reconfigurable architecture for scanning biosequence databases.
Proceedings of the International Symposium on Circuits and Systems (ISCAS 2005), 2005

A Case Study on Pattern-Based Systems for High Performance Computational Biology.
Proceedings of the 19th International Parallel and Distributed Processing Symposium (IPDPS 2005), 2005

Deriving Matrix of Peptide-MHC Interactions in Diabetic Mouse by Genetic Algorithm.
Proceedings of the Intelligent Data Engineering and Automated Learning, 2005

Multiple Sequence Alignment on an FPGA.
Proceedings of the 11th International Conference on Parallel and Distributed Systems, 2005

Hyper customized processors for bio-sequence database scanning on FPGAs.
Proceedings of the ACM/SIGDA 13th International Symposium on Field Programmable Gate Arrays, 2005

Parallel Construction of Large Suffix Trees on a PC Cluster.
Proceedings of the Euro-Par 2005, Parallel Processing, 11th International Euro-Par Conference, Lisbon, Portugal, August 30, 2005

Biological Sequence Analysis with Hidden Markov Models on an FPGA.
Proceedings of the Advances in Computer Systems Architecture, 10th Asia-Pacific Conference, 2005

2004
A bit-serial floating-point unit for a massively parallel system on a chip.
Parallel Algorithms Appl., 2004

Development of distributed bioinformatics applications with GMP.
Concurrency - Practice and Experience, 2004

High Performance Biosequence Database Scanning on Reconfigurable Platforms.
Proceedings of the 18th International Parallel and Distributed Processing Symposium (IPDPS 2004), 2004

Parallel RNA Sequence-Structure Alignment.
Proceedings of the 18th International Parallel and Distributed Processing Symposium (IPDPS 2004), 2004

A Tunable Coarse-Grained Parallel Algorithm for Irregular Dynamic Programming Applications.
Proceedings of the High Performance Computing, 2004

Load Balancing for Hierarchical Grid Computing: A Case Study.
Proceedings of the High Performance Computing, 2004

A Generic Parallel Pattern-Based System for Bioinformatics.
Proceedings of the Euro-Par 2004 Parallel Processing, 2004

Performance analysis of computational biology applications on hierarchical Grid systems.
Proceedings of the 4th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid 2004), 2004

2003
An Area-Efficient Bit-Serial Integer Multiplier.
Proceedings of the International Conference on VLSI, 2003

Design of a Bit-Serial Floating Point Unit for a Fine Grained Parallel Processor Array.
Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, 2003

Parallel Detection of Regulatory Elements with gMP.
Proceedings of the 17th International Parallel and Distributed Processing Symposium (IPDPS 2003), 2003

Topic Introduction.
Proceedings of the Euro-Par 2003. Parallel Processing, 2003

Parallel Design Pattern for Computational Biology and Scientific Computing Applications.
Proceedings of the 2003 IEEE International Conference on Cluster Computing (CLUSTER 2003), 2003

Computing Large-Scale Alignments on a Multi-Cluster.
Proceedings of the 2003 IEEE International Conference on Cluster Computing (CLUSTER 2003), 2003

2002
A hybrid architecture for bioinformatics.
Future Generation Comp. Syst., 2002

Massively Parallel Solutions for Molecular Sequence Analysis.
Proceedings of the 16th International Parallel and Distributed Processing Symposium (IPDPS 2002), 2002

2001
Tomographic Image Reconstruction on the Instruction Systolic Array.
Computers and Artificial Intelligence, 2001

A Hybrid Architecture for Multimedia Processors.
Computers and Artificial Intelligence, 2001

Protein Sequence Comparison on the Instruction Systolic Array.
Proceedings of the Parallel Computing Technologies, 2001

Scanning Biosequence Databases on a Hybrid Parallel Architecture.
Proceedings of the Euro-Par 2001: Parallel Processing, 2001

2000
KPROC - An Instruction Systolic Architecture for Parallel Prefix Applications.
Scalable Computing: Practice and Experience, 2000

Design of a Parallel Accelerator for Volume Rendering.
Proceedings of the Euro-Par 2000, Parallel Processing, 6th International Euro-Par Conference, Munich, Germany, August 29, 2000

1999
A Morphological Approach to Hough Transform on an Instruction Systolic Array.
Computers and Artificial Intelligence, 1999

A Parallel Accelerator Architecture for Multimedia Video Compression.
Proceedings of the Euro-Par '99 Parallel Processing, 5th International Euro-Par Conference, Toulouse, France, August 31, 1999

1998
Long Operand Arithmetic on Instruction Systolic Computer Architectures and Its Application in RSA Cryptography.
Proceedings of the Euro-Par '98 Parallel Processing, 1998

1997
Morphological Hough Transform on the Instruction Systolic Array.
Proceedings of the Euro-Par '97 Parallel Processing, 1997

1995
Preattentive Colour Features by Steerable Filters.
Proceedings of the Mustererkennung 1995, 1995


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