Bertil Schmidt

BMC Bioinform., 2022

Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data.

[BibT_eX]

[DOI]

BMC Bioinform., 2022

RabbitV: fast detection of viruses and microorganisms in sequencing data on multi-core architectures.

[BibT_eX]

[DOI]

Bioinform., 2022

Online Event Selection for Mu3e using GPUs.

[BibT_eX]

[DOI]

Valentin Henkys

Niklaus Berger

Proceedings of the 21st International Symposium on Parallel and Distributed Computing, 2022

AnySeq/GPU: a novel approach for faster sequence alignment on GPUs.

[BibT_eX]

[DOI]

Proceedings of the ICS '22: 2022 International Conference on Supercomputing, Virtual Event, June 28, 2022

RabbitQCPlus: More Efficient Quality Control for Sequencing Data.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

2021

RabbitQC: high-speed scalable quality control for sequencing data.

[BibT_eX]

[DOI]

Bioinform., 2021

RabbitMash: accelerating hash-based genome analysis on modern multi-core architectures.

[BibT_eX]

[DOI]

Bioinform., 2021

CARE: context-aware sequencing read error correction.

[BibT_eX]

[DOI]

Felix Kallenborn

Bioinform., 2021

MetaCache-GPU: Ultra-Fast Metagenomic Classification.

[BibT_eX]

[DOI]

Proceedings of the ICPP 2021: 50th International Conference on Parallel Processing, Lemont, IL, USA, August 9, 2021

RNACache: Fast Mapping of RNA-Seq Reads to Transcriptomes Using MinHashing.

[BibT_eX]

[DOI]

Proceedings of the Computational Science - ICCS 2021, 2021

Accelerating JPEG Decompression on GPUs.

[BibT_eX]

[DOI]

André Weißenberger

Proceedings of the 28th IEEE International Conference on High Performance Computing, 2021

2020

FeatherCNN: Fast Inference Computation with TensorGEMM on ARM Architectures.

[BibT_eX]

[DOI]

IEEE Trans. Parallel Distributed Syst., 2020

Millimeter-Scale and Billion-Atom Reactive Force Field Simulation on Sunway Taihulight.

[BibT_eX]

[DOI]

IEEE Trans. Parallel Distributed Syst., 2020

RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads.

[BibT_eX]

[DOI]

BMC Bioinform., 2020

A big data approach to metagenomics for all-food-sequencing.

[BibT_eX]

[DOI]

BMC Bioinform., 2020

Cell-list based molecular dynamics on many-core processors: a case study on sunway TaihuLight supercomputer.

[BibT_eX]

[DOI]

Proceedings of the International Conference for High Performance Computing, 2020

Neighbor-list-free molecular dynamics on sunway TaihuLight supercomputer.

[BibT_eX]

[DOI]

Proceedings of the PPoPP '20: 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 2020

AnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation.

[BibT_eX]

[DOI]

Proceedings of the 2020 IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2020

SWMapper: Scalable Read Mapper on SunWay TaihuLight.

[BibT_eX]

[DOI]

Proceedings of the ICPP 2020: 49th International Conference on Parallel Processing, 2020

Reconstruction of Low Energy Neutrino Events with GPUs at IceCube.

[BibT_eX]

[DOI]

Maicon Hieronymus

Sebastian Böser

Proceedings of the Computational Science - ICCS 2020, 2020

WarpCore: A Library for fast Hash Tables on GPUs.

[BibT_eX]

[DOI]

Proceedings of the 27th IEEE International Conference on High Performance Computing, 2020

cuDTW++: Ultra-Fast Dynamic Time Warping on CUDA-Enabled GPUs.

[BibT_eX]

[DOI]

Proceedings of the Euro-Par 2020: Parallel Processing, 2020

2019

Dedicated Bioinformatics Analysis Hardware.

[BibT_eX]

[DOI]

Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 2, 2019

Massively parallel computation of atmospheric neutrino oscillations on CUDA-enabled accelerators.

[BibT_eX]

[DOI]

Comput. Phys. Commun., 2019

BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures.

[BibT_eX]

[DOI]

Bioinform., 2019

kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers.

[BibT_eX]

[DOI]

Bioinform., 2019

Massively Parallel ANS Decoding on GPUs.

[BibT_eX]

[DOI]

André Weißenberger

Proceedings of the 48th International Conference on Parallel Processing, 2019

Gossip: Efficient Communication Primitives for Multi-GPU Systems.

[BibT_eX]

[DOI]

Proceedings of the 48th International Conference on Parallel Processing, 2019

Suffix Array Construction on Multi-GPU Systems.

[BibT_eX]

[DOI]

Proceedings of the 28th International Symposium on High-Performance Parallel and Distributed Computing, 2019

XLCS: A New Bit-Parallel Longest Common Subsequence Algorithm on Xeon Phi Clusters.

[BibT_eX]

[DOI]

Proceedings of the 21st IEEE International Conference on High Performance Computing and Communications; 17th IEEE International Conference on Smart City; 5th IEEE International Conference on Data Science and Systems, 2019

Efficient Parallel Sort on AVX-512-Based Multi-Core and Many-Core Architectures.

[BibT_eX]

[DOI]

2018

LightSpMV: Faster CUDA-Compatible Sparse Matrix-Vector Multiplication Using Compressed Sparse Rows.

[BibT_eX]

[DOI]

J. Signal Process. Syst., 2018

AnyDSL: a partial evaluation framework for programming high-performance libraries.

[BibT_eX]

[DOI]

Proc. ACM Program. Lang., 2018

parSRA: A framework for the parallel execution of short read aligners on compute clusters.

[BibT_eX]

[DOI]

J. Comput. Sci., 2018

Fast and efficient short read mapping based on a succinct hash index.

[BibT_eX]

[DOI]

BMC Bioinform., 2018

WarpDrive: Massively Parallel Hashing on Multi-GPU Nodes.

[BibT_eX]

[DOI]

Daniel Jünger

Proceedings of the 2018 IEEE International Parallel and Distributed Processing Symposium, 2018

SPECTR: Scalable Parallel Short Read Error Correction on Multi-core and Many-core Architectures.

[BibT_eX]

[DOI]

Proceedings of the 47th International Conference on Parallel Processing, 2018

Massively Parallel Huffman Decoding on GPUs.

[BibT_eX]

[DOI]

André Weißenberger

Proceedings of the 47th International Conference on Parallel Processing, 2018

cuBool: Bit-Parallel Boolean Matrix Factorization on CUDA-Enabled Accelerators.

[BibT_eX]

[DOI]

Proceedings of the 24th IEEE International Conference on Parallel and Distributed Systems, 2018

2017

Mapping of option pricing algorithms onto heterogeneous many-core architectures.

[BibT_eX]

[DOI]

J. Supercomput., 2017

SAUCE: A web application for interactive teaching and learning of parallel programming.

[BibT_eX]

[DOI]

Moritz Schlarb

J. Parallel Distributed Comput., 2017

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

[BibT_eX]

[DOI]

CoRR, 2017

Speed and accuracy improvement of higher-order epistasis detection on CUDA-enabled GPUs.

[BibT_eX]

[DOI]

Daniel Jünger

Christopher Felix Krombholz

Clust. Comput., 2017

CLOVE: classification of genomic fusions into structural variation events.

[BibT_eX]

[DOI]

BMC Bioinform., 2017

Accelerating metagenomic read classification on CUDA-enabled GPUs.

[BibT_eX]

[DOI]

BMC Bioinform., 2017

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

[BibT_eX]

[DOI]

Bioinform., 2017

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

[BibT_eX]

[DOI]

Thomas Hankeln

Bioinform., 2017

SWhybrid: A Hybrid-Parallel Framework for Large-Scale Protein Sequence Database Search.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

Proceedings of the 2017 IEEE International Parallel and Distributed Processing Symposium, 2017

S-Aligner: Ultrascalable Read Mapping on Sunway Taihu Light.

[BibT_eX]

[DOI]

Proceedings of the 2017 IEEE International Conference on Cluster Computing, 2017

mD3DOCKxb: An Ultra-Scalable CPU-MIC Coordinated Virtual Screening Framework.

[BibT_eX]

[DOI]

Proceedings of the 17th IEEE/ACM International Symposium on Cluster, 2017

CUSHAW Suite: Parallel and Efficient Algorithms for NGS Read Alignment.

[BibT_eX]

[DOI]

Proceedings of the Algorithms for Next-Generation Sequencing Data, Techniques, 2017

2016

Parallel Pairwise Epistasis Detection on Heterogeneous Computing Architectures.

[BibT_eX]

[DOI]

Sabela Ramos

Juan Touriño

IEEE Trans. Parallel Distributed Syst., 2016

Scalable Clustering by Iterative Partitioning and Point Attractor Representation.

[BibT_eX]

[DOI]

ACM Trans. Knowl. Discov. Data, 2016

Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data.

[BibT_eX]

[DOI]

Thomas Hankeln

IEEE ACM Trans. Comput. Biol. Bioinform., 2016

Bit-parallel approximate pattern matching: Kepler GPU versus Xeon Phi.

[BibT_eX]

[DOI]

Tuan Tu Tran

Anna Katharina Hildebrandt

Parallel Comput., 2016

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

[BibT_eX]

[DOI]

Int. J. High Perform. Comput. Appl., 2016

SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations.

[BibT_eX]

[DOI]

BMC Syst. Biol., 2016

Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters.

[BibT_eX]

[DOI]

BMC Bioinform., 2016

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

[BibT_eX]

[DOI]

BMC Bioinform., 2016

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

[BibT_eX]

[DOI]

Juan Touriño

Bioinform., 2016

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

[BibT_eX]

[DOI]

Bioinform., 2016

Ultra-Fast Detection of Higher-Order Epistatic Interactions on GPUs.

[BibT_eX]

[DOI]

Daniel Jünger

Proceedings of the Euro-Par 2016: Parallel Processing Workshops, 2016

Combining GPU and FPGA technology for efficient exhaustive interaction analysis in GWAS.

[BibT_eX]

[DOI]

Juan Antonio Gómez Pulido

Proceedings of the 27th IEEE International Conference on Application-specific Systems, 2016

2015

Accelerating Bioinformatics Applications via Emerging Parallel Computing Systems.

[BibT_eX]

[DOI]

Wu-chun Feng

IEEE ACM Trans. Comput. Biol. Bioinform., 2015

Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2015

Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems.

[BibT_eX]

[DOI]

David Ellinghaus

IEEE ACM Trans. Comput. Biol. Bioinform., 2015

High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs.

[BibT_eX]

[DOI]

J. Comput. Sci., 2015

GPU-accelerated exhaustive search for third-order epistatic interactions in case-control studies.

[BibT_eX]

[DOI]

J. Comput. Sci., 2015

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

[BibT_eX]

[DOI]

Int. J. High Perform. Comput. Appl., 2015

GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences.

[BibT_eX]

[DOI]

Concurr. Comput. Pract. Exp., 2015

SAUCE: A Web-Based Automated Assessment Tool for Teaching Parallel Programming.

[BibT_eX]

[DOI]

Moritz Schlarb

Proceedings of the Euro-Par 2015: Parallel Processing Workshops, 2015

SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

LightSpMV: Faster CSR-based sparse matrix-vector multiplication on CUDA-enabled GPUs.

[BibT_eX]

[DOI]

Proceedings of the 26th IEEE International Conference on Application-specific Systems, 2015

2014

CUSHAW2-GPU: Empowering Faster Gapped Short-Read Alignment Using GPU Computing.

[BibT_eX]

[DOI]

IEEE Des. Test, 2014

HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data.

[BibT_eX]

[DOI]

BMC Bioinform., 2014

Bit-Parallel Approximate Pattern Matching on the Xeon Phi Coprocessor.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

Proceedings of the Symposium on Applied Computing, 2014

Parallelized Clustering of Protein Structures on CUDA-Enabled GPUs.

[BibT_eX]

[DOI]

Anna Katharina Hildebrandt

Proceedings of the 22nd Euromicro International Conference on Parallel, 2014

CUDA-Accelerated Alignment of Subsequences in Streamed Time Series Data.

[BibT_eX]

[DOI]

Elmar Schömer

Proceedings of the 43rd International Conference on Parallel Processing, 2014

FPGA-based Acceleration of Detecting Statistical Epistasis in GWAS.

[BibT_eX]

[DOI]

David Ellinghaus

Proceedings of the International Conference on Computational Science, 2014

SparseHC: A Memory-efficient Online Hierarchical Clustering Algorithm.

[BibT_eX]

[DOI]

Thuy-Diem Nguyen

Proceedings of the International Conference on Computational Science, 2014

Hybrid CPU/GPU Acceleration of Detection of 2-SNP Epistatic Interactions in GWAS.

[BibT_eX]

[DOI]

Proceedings of the Euro-Par 2014 Parallel Processing, 2014

SWAPHI-LS: Smith-Waterman Algorithm on Xeon Phi coprocessors for Long DNA Sequences.

[BibT_eX]

[DOI]

Proceedings of the 2014 IEEE International Conference on Cluster Computing, 2014

UPC++ for bioinformatics: A case study using genome-wide association studies.

[BibT_eX]

[DOI]

Proceedings of the 2014 IEEE International Conference on Cluster Computing, 2014

Fast dendrogram-based OTU clustering using sequence embedding.

[BibT_eX]

[DOI]

Thuy-Diem Nguyen

Chee-Keong Kwoh

Proceedings of the 5th ACM Conference on Bioinformatics, 2014

SWAPHI: Smith-waterman protein database search on Xeon Phi coprocessors.

[BibT_eX]

[DOI]

Proceedings of the IEEE 25th International Conference on Application-Specific Systems, 2014

2013

Reconfigurable Accelerator for the Word-Matching Stage of BLASTN.

[BibT_eX]

[DOI]

IEEE Trans. Very Large Scale Integr. Syst., 2013

CUDA-enabled Sparse Matrix-Vector Multiplication on GPUs using atomic operations.

[BibT_eX]

[DOI]

Parallel Comput., 2013

Iterative sparse matrix-vector multiplication for accelerating the block Wiedemann algorithm over GF(2) on multi-graphics processing unit systems.

[BibT_eX]

[DOI]

Hans Aribowo

Concurr. Comput. Pract. Exp., 2013

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

[BibT_eX]

[DOI]

BMC Bioinform., 2013

A hybrid short read mapping accelerator.

[BibT_eX]

[DOI]

BMC Bioinform., 2013

Musket: a multistage <i>k-</i>mer spectrum-based error corrector for Illumina sequence data.

[BibT_eX]

[DOI]

Jan Schröder

Bioinform., 2013

Faster GPU-Accelerated Smith-Waterman Algorithm with Alignment Backtracking for Short DNA Sequences.

[BibT_eX]

[DOI]

Proceedings of the Parallel Processing and Applied Mathematics, 2013

2012

Fourth Workshop on using Emerging Parallel Architectures.

[BibT_eX]

[DOI]

Proceedings of the International Conference on Computational Science, 2012

The Sliced COO Format for Sparse Matrix-Vector Multiplication on CUDA-enabled GPUs.

[BibT_eX]

[DOI]

Proceedings of the International Conference on Computational Science, 2012

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

[BibT_eX]

[DOI]

Zejun Zheng

Stefan Kramer

Bioinform., 2012

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

[BibT_eX]

[DOI]

Bioinform., 2012

Long read alignment based on maximal exact match seeds.

[BibT_eX]

[DOI]

Bioinform., 2012

Evaluation of GPU-based Seed Generation for Computational Genomics Using Burrows-Wheeler Transform.

[BibT_eX]

[DOI]

Proceedings of the 26th IEEE International Parallel and Distributed Processing Symposium Workshops & PhD Forum, 2012

An FPGA aligner for short read mapping.

[BibT_eX]

[DOI]

Proceedings of the 22nd International Conference on Field Programmable Logic and Applications (FPL), 2012

Accelerating short read mapping on an FPGA (abstract only).

[BibT_eX]

[DOI]

Proceedings of the ACM/SIGDA 20th International Symposium on Field Programmable Gate Arrays, 2012

2011

CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2011

Third Workshop on using Emerging Parallel Architectures.

[BibT_eX]

[DOI]

Proceedings of the International Conference on Computational Science, 2011

Parallelized short read assembly of large genomes using de Bruijn graphs.

[BibT_eX]

[DOI]

BMC Bioinform., 2011

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

[BibT_eX]

[DOI]

BMC Bioinform., 2011

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

[BibT_eX]

[DOI]

Lakshmi Kuttippurathu

Bioinform., 2011

CRiSPy-CUDA: Computing Species Richness in 16S rRNA Pyrosequencing Datasets with CUDA.

[BibT_eX]

[DOI]

Zejun Zheng

Thuy-Diem Nguyen

Proceedings of the Pattern Recognition in Bioinformatics, 2011

An Ultrafast Scalable Many-Core Motif Discovery Algorithm for Multiple GPUs.

[BibT_eX]

[DOI]

Proceedings of the 25th IEEE International Symposium on Parallel and Distributed Processing, 2011

Mapping of BLASTP Algorithm onto GPU Clusters.

[BibT_eX]

[DOI]

Proceedings of the 17th IEEE International Conference on Parallel and Distributed Systems, 2011

Iterative Sparse Matrix-Vector Multiplication for Integer Factorization on GPUs.

[BibT_eX]

[DOI]

Hans Aribowo

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.

[BibT_eX]

[DOI]

Haixiang Shi

Proceedings of the International Conference on Computational Science, 2010

Second Workshop on using Emerging Parallel Architectures.

[BibT_eX]

[DOI]

Proceedings of the International Conference on Computational Science, 2010

CUDA-MEME: Accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units.

[BibT_eX]

[DOI]

Pattern Recognit. Lett., 2010

Pattern Recognition in Bioinformatics.

[BibT_eX]

[DOI]

Shandar Ahmad

Madhu Chetty

Pattern Recognit. Lett., 2010

A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware.

[BibT_eX]

[DOI]

Haixiang Shi

J. Comput. Biol., 2010

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

[BibT_eX]

[DOI]

Bioinform., 2010

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

[BibT_eX]

[DOI]

Bioinform., 2010

Prediction of low coverage prone regions for Illumina sequencing projects using a support vector machine.

[BibT_eX]

[DOI]

Zejun Zheng

Guillaume Bourque

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.

[BibT_eX]

[DOI]

IEEE Trans. Inf. Technol. Biomed., 2009

High performance protein sequence database scanning on the Cell Broadband Engine.

[BibT_eX]

[DOI]

Sci. Program., 2009

SHREC: a short-read error correction method.

[BibT_eX]

[DOI]

Bioinform., 2009

A fast hybrid short read fragment assembly algorithm.

[BibT_eX]

[DOI]

Ranjan Sinha

Bryan Beresford-Smith

Simon J. Puglisi

Bioinform., 2009

Accelerating error correction in high-throughput short-read DNA sequencing data with CUDA.

[BibT_eX]

[DOI]

Haixiang Shi

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.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

Proceedings of the Computational Science, 2009

Workshop on Using Emerging Parallel Architectures for Computational Science.

[BibT_eX]

[DOI]

Proceedings of the Computational Science, 2009

MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA.

[BibT_eX]

[DOI]

Proceedings of the 20th IEEE International Conference on Application-Specific Systems, 2009

A Reconfigurable Bloom Filter Architecture for BLASTN.

[BibT_eX]

[DOI]

Proceedings of the Architecture of Computing Systems, 2009

2008

A Hybrid Computational Grid Architecture for Comparative Genomics.

[BibT_eX]

[DOI]

IEEE Trans. Inf. Technol. Biomed., 2008

Integrating FPGA acceleration into HMMer.

[BibT_eX]

[DOI]

Leow Yuan Yeow

Parallel Comput., 2008

Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA.

[BibT_eX]

[DOI]

Comput. Phys. Commun., 2008

CBESW: Sequence Alignment on the Playstation 3.

[BibT_eX]

[DOI]

BMC Bioinform., 2008

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

[BibT_eX]

[DOI]

BMC Bioinform., 2008

Accelerating BLASTP on the Cell Broadband Engine.

[BibT_eX]

[DOI]

Huiliang Zhang

Proceedings of the Pattern Recognition in Bioinformatics, 2008

GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences.

[BibT_eX]

[DOI]

Chen Chen

Proceedings of the Pattern Recognition in Bioinformatics, 2008

2007

MPI-HMMER-Boost: Distributed FPGA Acceleration.

[BibT_eX]

[DOI]

J. VLSI Signal Process., 2007

Performance Analysis of General-Purpose Computation on Commodity Graphics Hardware: A Case Study Using Bioinformatics.

[BibT_eX]

[DOI]

J. VLSI Signal Process., 2007

Solving the Bottleneck Problem in Bioinformatics Computing: An Architectural Perspective.

[BibT_eX]

[DOI]

Feng Lin

J. VLSI Signal Process., 2007

Streaming Algorithms for Biological Sequence Alignment on GPUs.

[BibT_eX]

[DOI]

IEEE Trans. Parallel Distributed Syst., 2007

A survey of desktop grid applications for e-science.

[BibT_eX]

[DOI]

Int. J. Web Grid Serv., 2007

Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms.

[BibT_eX]

[DOI]

BMC Bioinform., 2007

Fast Schedulability Analysis Using Commodity Graphics Hardware.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

Proceedings of the Pattern Recognition in Bioinformatics, 2007

Parallel DNA Sequence Alignment on the Cell Broadband Engine.

[BibT_eX]

[DOI]

Proceedings of the Parallel Processing and Applied Mathematics, 2007

High Performance Database Searching with HMMer on FPGAs.

[BibT_eX]

[DOI]

Leow Yuan Yeow

Proceedings of the 21th International Parallel and Distributed Processing Symposium (IPDPS 2007), 2007

Performance Predictions for General-Purpose Computation on GPUs.

[BibT_eX]

[DOI]

Proceedings of the 2007 International Conference on Parallel Processing (ICPP 2007), 2007

Molecular Dynamics Simulations on Commodity GPUs with CUDA.

[BibT_eX]

[DOI]

Proceedings of the High Performance Computing, 2007

A Parallel BSP Algorithm for Irregular Dynamic Programming.

[BibT_eX]

[DOI]

Malcolm Yoke Hean Low

Proceedings of the Advanced Parallel Processing Technologies, 7th International Symposium, 2007

Hierarchical Grid Computing for High-Performance Bioinformatics.

[BibT_eX]

[DOI]

Proceedings of the Grid Computing for Bioinformatics and Computational Biology, 2007

2006

Parallel Pattern-Based Systems for Computational Biology: A Case Study.

[BibT_eX]

[DOI]

IEEE Trans. Parallel Distributed Syst., 2006

Constructing large suffix trees on a computational grid.

[BibT_eX]

[DOI]

J. Parallel Distributed Comput., 2006

High-speed Multiple Sequence Alignment on a reconfigurable platform.

[BibT_eX]

[DOI]

Int. J. Bioinform. Res. Appl., 2006

Mapping of Hierarchical Parallel Genetic Algorithms for Protein Folding onto Computational Grids.

[BibT_eX]

[DOI]

IEICE Trans. Inf. Syst., 2006

Bio-sequence database scanning on a GPU.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

Proceedings of the Computational Science, 2006

GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment.

[BibT_eX]

[DOI]

Proceedings of the High Performance Computing, 2006

Multi-Objective Evolutionary Algorithm for Discovering Peptide Binding Motifs.

[BibT_eX]

[DOI]

Menaka Rajapakse

Vladimir Brusic

Proceedings of the Applications of Evolutionary Computing, 2006

Parallel Discovery of Transcription Factor Binding Sites.

[BibT_eX]

[DOI]

Proceedings of the IEEE Asia Pacific Conference on Circuits and Systems 2006, 2006

2005

Reconfigurable architectures for bio-sequence database scanning on FPGAs.

[BibT_eX]

[DOI]

IEEE Trans. Circuits Syst. II Express Briefs, 2005

An adaptive grid implementation of DNA sequence alignment.

[BibT_eX]

[DOI]

Future Gener. Comput. Syst., 2005

Parallel RNA secondary structure prediction using stochastic context-free grammars.

[BibT_eX]

[DOI]

Tong Liu

Concurr. Comput. Pract. Exp., 2005

Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW.

[BibT_eX]

[DOI]

Bioinform., 2005

A reconfigurable architecture for scanning biosequence databases.

[BibT_eX]

[DOI]

Achutavarrier Prasad Vinod

Proceedings of the International Symposium on Circuits and Systems (ISCAS 2005), 2005

A Case Study on Pattern-Based Systems for High Performance Computational Biology.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

Proceedings of the Intelligent Data Engineering and Automated Learning, 2005

Multiple Sequence Alignment on an FPGA.

[BibT_eX]

[DOI]

Proceedings of the 11th International Conference on Parallel and Distributed Systems, 2005

Hyper customized processors for bio-sequence database scanning on FPGAs.

[BibT_eX]

[DOI]

Proceedings of the ACM/SIGDA 13th International Symposium on Field Programmable Gate Arrays, 2005

Parallel Construction of Large Suffix Trees on a PC Cluster.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

Hans-Werner Lang

Parallel Algorithms Appl., 2004

Development of distributed bioinformatics applications with GMP.

[BibT_eX]

[DOI]

Concurr. Pract. Exp., 2004

High Performance Biosequence Database Scanning on Reconfigurable Platforms.

[BibT_eX]

[DOI]

Proceedings of the 18th International Parallel and Distributed Processing Symposium (IPDPS 2004), 2004

Parallel RNA Sequence-Structure Alignment.

[BibT_eX]

[DOI]

Tong Liu

Proceedings of the 18th International Parallel and Distributed Processing Symposium (IPDPS 2004), 2004

A Tunable Coarse-Grained Parallel Algorithm for Irregular Dynamic Programming Applications.

[BibT_eX]

[DOI]

Proceedings of the High Performance Computing, 2004

Load Balancing for Hierarchical Grid Computing: A Case Study.

[BibT_eX]

[DOI]

Proceedings of the High Performance Computing, 2004

A Generic Parallel Pattern-Based System for Bioinformatics.

[BibT_eX]

[DOI]

Proceedings of the Euro-Par 2004 Parallel Processing, 2004

Performance analysis of computational biology applications on hierarchical Grid systems.

[BibT_eX]

[DOI]

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.

[BibT_eX]

Proceedings of the International Conference on VLSI, 2003

Design of a Bit-Serial Floating Point Unit for a Fine Grained Parallel Processor Array.

[BibT_eX]

Hans-Werner Lang

Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, 2003

Parallel Detection of Regulatory Elements with gMP.

[BibT_eX]

[DOI]

Proceedings of the 17th International Parallel and Distributed Processing Symposium (IPDPS 2003), 2003

Topic Introduction.

[BibT_eX]

[DOI]

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

Parallel Design Pattern for Computational Biology and Scientific Computing Applications.

[BibT_eX]

[DOI]

Proceedings of the 2003 IEEE International Conference on Cluster Computing (CLUSTER 2003), 2003

Computing Large-Scale Alignments on a Multi-Cluster.

[BibT_eX]

[DOI]

Proceedings of the 2003 IEEE International Conference on Cluster Computing (CLUSTER 2003), 2003

2002

A hybrid architecture for bioinformatics.

[BibT_eX]

[DOI]

Future Gener. Comput. Syst., 2002

Massively Parallel Solutions for Molecular Sequence Analysis.

[BibT_eX]

[DOI]

Proceedings of the 16th International Parallel and Distributed Processing Symposium (IPDPS 2002), 2002

2001

Tomographic Image Reconstruction on the Instruction Systolic Array.

[BibT_eX]

[DOI]

Comput. Artif. Intell., 2001

A Hybrid Architecture for Multimedia Processors.

[BibT_eX]

[DOI]

Comput. Artif. Intell., 2001

Protein Sequence Comparison on the Instruction Systolic Array.

[BibT_eX]

[DOI]

Proceedings of the Parallel Computing Technologies, 2001

Scanning Biosequence Databases on a Hybrid Parallel Architecture.

[BibT_eX]

[DOI]

Proceedings of the Euro-Par 2001: Parallel Processing, 2001

2000

KPROC - An Instruction Systolic Architecture for Parallel Prefix Applications.

[BibT_eX]

[DOI]

Parallel Distributed Comput. Pract., 2000

Design of a Parallel Accelerator for Volume Rendering.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

Comput. Artif. Intell., 1999

A Parallel Accelerator Architecture for Multimedia Video Compression.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

Proceedings of the Euro-Par '98 Parallel Processing, 1998

1997

Morphological Hough Transform on the Instruction Systolic Array.

[BibT_eX]

[DOI]

Proceedings of the Euro-Par '97 Parallel Processing, 1997

1995

Preattentive Colour Features by Steerable Filters.

[BibT_eX]

[DOI]

Udo Mahlmeister