Preattentive Colour Features by Steerable Filters. - Udo Mahlmeister; Bertil Schmidt; Gerald Sommer (DAGM-Symposium, 1995)

Morphological Hough Transform on the Instruction Systolic Array. - Bertil Schmidt; Manfred Schimmler; Heiko Schröder 001 (Euro-Par, 1997)

Long Operand Arithmetic on Instruction Systolic Computer Architectures and Its Application in RSA Cryptography. - Bertil Schmidt; Manfred Schimmler; Heiko Schröder 001 (Euro-Par, 1998)

A Parallel Accelerator Architecture for Multimedia Video Compression. - Bertil Schmidt; Manfred Schimmler (Euro-Par, 1999)

A Morphological Approach to Hough Transform on an Instruction Systolic Array. - Bertil Schmidt; Manfred Schimmler; Heiko Schröder 001 (Comput. Artif. Intell., 1999)

Design of a Parallel Accelerator for Volume Rendering. - Bertil Schmidt (Euro-Par, 2000)

KPROC - An Instruction Systolic Architecture for Parallel Prefix Applications. - Bertil Schmidt; Manfred Schimmler (Parallel Distributed Comput. Pract., 2000)

Scanning Biosequence Databases on a Hybrid Parallel Architecture. - Bertil Schmidt; Heiko Schröder 001; Manfred Schimmler (Euro-Par, 2001)

Protein Sequence Comparison on the Instruction Systolic Array. - Bertil Schmidt; Heiko Schröder 001; Manfred Schimmler (PaCT, 2001)

A Hybrid Architecture for Multimedia Processors. - Bertil Schmidt; Heiko Schröder 001 (Comput. Artif. Intell., 2001)

Tomographic Image Reconstruction on the Instruction Systolic Array. - Bertil Schmidt; Heiko Schröder 001; Manfred Schimmler (Comput. Artif. Intell., 2001)

Massively Parallel Solutions for Molecular Sequence Analysis. - Bertil Schmidt; Heiko Schröder 001; Manfred Schimmler (IPDPS, 2002)

A hybrid architecture for bioinformatics. - Bertil Schmidt; Heiko Schröder 001; Manfred Schimmler (Future Gener. Comput. Syst., 2002)

Computing Large-Scale Alignments on a Multi-Cluster. - Chunxi Chen; Bertil Schmidt (CLUSTER, 2003)

Parallel Design Pattern for Computational Biology and Scientific Computing Applications. - Weiguo Liu; Bertil Schmidt (CLUSTER, 2003)

Topic Introduction. - Ishfaq Ahmad 001; Pieter Jonker; Bertil Schmidt; Andreas Uhl (Euro-Par, 2003)

Parallel Detection of Regulatory Elements with gMP. - Bertil Schmidt; Lin Feng; Amey V. Laud; Yusdi Santoso (IPDPS, 2003)

Design of a Bit-Serial Floating Point Unit for a Fine Grained Parallel Processor Array. - Manfred Schimmler; Bertil Schmidt; Hans-Werner Lang (PDPTA, 2003)

An Area-Efficient Bit-Serial Integer Multiplier. - Manfred Schimmler; Bertil Schmidt; Hans-Werner Lang; Sven Heithecker (VLSI, 2003)

Performance analysis of computational biology applications on hierarchical Grid systems. - Chunxi Chen; Bertil Schmidt (CCGRID, 2004)

A Generic Parallel Pattern-Based System for Bioinformatics. - Weiguo Liu; Bertil Schmidt (Euro-Par, 2004)

Load Balancing for Hierarchical Grid Computing: A Case Study. - Chunxi Chen; Bertil Schmidt (HiPC, 2004)

A Tunable Coarse-Grained Parallel Algorithm for Irregular Dynamic Programming Applications. - Weiguo Liu; Bertil Schmidt (HiPC, 2004)

Parallel RNA Sequence-Structure Alignment. - Tong Liu; Bertil Schmidt (IPDPS, 2004)

High Performance Biosequence Database Scanning on Reconfigurable Platforms. - Timothy F. Oliver; Bertil Schmidt (IPDPS, 2004)

Development of distributed bioinformatics applications with GMP. - Bertil Schmidt; Lin Feng; Amey V. Laud; Yusdi Santoso (Concurr. Pract. Exp., 2004)

A bit-serial floating-point unit for a massively parallel system on a chip. - Manfred Schimmler; Bertil Schmidt; Hans-Werner Lang (Parallel Algorithms Appl., 2004)

Biological Sequence Analysis with Hidden Markov Models on an FPGA. - Jacop Yanto; Timothy F. Oliver; Bertil Schmidt; Douglas L. Maskell (Asia-Pacific Computer Systems Architecture Conference, 2005)

Parallel Construction of Large Suffix Trees on a PC Cluster. - Chunxi Chen; Bertil Schmidt (Euro-Par, 2005)

Hyper customized processors for bio-sequence database scanning on FPGAs. - Timothy F. Oliver; Bertil Schmidt; Douglas L. Maskell (FPGA, 2005)

Multiple Sequence Alignment on an FPGA. - Timothy F. Oliver; Bertil Schmidt; Douglas L. Maskell; Darran Nathan; Ralf Clemens (ICPADS (2), 2005)

Deriving Matrix of Peptide-MHC Interactions in Diabetic Mouse by Genetic Algorithm. - Menaka Rajapakse; Lonce L. Wyse; Bertil Schmidt; Vladimir Brusic (IDEAL, 2005)

A Case Study on Pattern-Based Systems for High Performance Computational Biology. - Weiguo Liu; Bertil Schmidt (IPDPS, 2005)

A reconfigurable architecture for scanning biosequence databases. - Timothy F. Oliver; Bertil Schmidt; Douglas L. Maskell; Achutavarrier Prasad Vinod (ISCAS (5), 2005)

Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW. - Timothy F. Oliver; Bertil Schmidt; Darran Nathan; Ralf Clemens; Douglas L. Maskell (Bioinform., 2005)

Parallel RNA secondary structure prediction using stochastic context-free grammars. - Tong Liu; Bertil Schmidt (Concurr. Comput. Pract. Exp., 2005)

An adaptive grid implementation of DNA sequence alignment. - Chunxi Chen; Bertil Schmidt (Future Gener. Comput. Syst., 2005)

Reconfigurable architectures for bio-sequence database scanning on FPGAs. - Timothy F. Oliver; Bertil Schmidt; Douglas L. Maskell (IEEE Trans. Circuits Syst. II Express Briefs, 2005)

Parallel Discovery of Transcription Factor Binding Sites. - Adrianto Wirawan; Bertil Schmidt (APCCAS, 2006)

Multi-Objective Evolutionary Algorithm for Discovering Peptide Binding Motifs. - Menaka Rajapakse; Bertil Schmidt; Vladimir Brusic (EvoWorkshops, 2006)

GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment. - Weiguo Liu; Bertil Schmidt; Gerrit Voss; Wolfgang Müller-Wittig (HiPC, 2006)

Accelerating the Viterbi Algorithm for Profile Hidden Markov Models Using Reconfigurable Hardware. - Timothy F. Oliver; Bertil Schmidt; Yanto Jakop; Douglas L. Maskell (International Conference on Computational Science (1), 2006)

Bio-sequence database scanning on a GPU. - Weiguo Liu; Bertil Schmidt; Gerrit Voss; Adrian Schröder; Wolfgang Müller-Wittig (IPDPS, 2006)

Mapping of Hierarchical Parallel Genetic Algorithms for Protein Folding onto Computational Grids. - Weiguo Liu; Bertil Schmidt (IEICE Trans. Inf. Syst., 2006)

High-speed Multiple Sequence Alignment on a reconfigurable platform. - Timothy F. Oliver; Bertil Schmidt; Douglas L. Maskell; Darran Nathan; Ralf Clemens (Int. J. Bioinform. Res. Appl., 2006)

Constructing large suffix trees on a computational grid. - Chunxi Chen; Bertil Schmidt (J. Parallel Distributed Comput., 2006)

Parallel Pattern-Based Systems for Computational Biology: A Case Study. - Weiguo Liu; Bertil Schmidt (IEEE Trans. Parallel Distributed Syst., 2006)

Hierarchical Grid Computing for High-Performance Bioinformatics. - Bertil Schmidt; Chunxi Chen; Weiguo Liu (Grid Computing for Bioinformatics and Computational Biology, 2007)

A Parallel BSP Algorithm for Irregular Dynamic Programming. - Malcolm Yoke Hean Low; Weiguo Liu; Bertil Schmidt (APPT, 2007)

Molecular Dynamics Simulations on Commodity GPUs with CUDA. - Weiguo Liu; Bertil Schmidt; Gerrit Voss; Wolfgang Müller-Wittig (HiPC, 2007)

Performance Predictions for General-Purpose Computation on GPUs. - Weiguo Liu; Wolfgang Müller-Wittig; Bertil Schmidt (ICPP, 2007)

High Performance Database Searching with HMMer on FPGAs. - Timothy F. Oliver; Leow Yuan Yeow; Bertil Schmidt (IPDPS, 2007)

Parallel DNA Sequence Alignment on the Cell Broadband Engine. - Adrianto Wirawan; Chee Keong Kwoh 001; Bertil Schmidt (PPAM, 2007)

C-Based Design Methodology for FPGA Implementation of ClustalW MSA. - Yan Lin Aung; Douglas L. Maskell; Timothy F. Oliver; Bertil Schmidt; William Bong (PRIB, 2007)

Fast Schedulability Analysis Using Commodity Graphics Hardware. - Jimin Feng; Samarjit Chakraborty; Bertil Schmidt; Weiguo Liu; Unmesh D. Bordoloi (RTCSA, 2007)

Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms. - Menaka Rajapakse; Bertil Schmidt; Feng Lin 002; Vladimir Brusic (BMC Bioinform., 2007)

A survey of desktop grid applications for e-science. - Bertil Schmidt (Int. J. Web Grid Serv., 2007)

Streaming Algorithms for Biological Sequence Alignment on GPUs. - Weiguo Liu; Bertil Schmidt; Gerrit Voss; Wolfgang Müller-Wittig (IEEE Trans. Parallel Distributed Syst., 2007)

Solving the Bottleneck Problem in Bioinformatics Computing: An Architectural Perspective. - Feng Lin 002; Heiko Schröder 001; Bertil Schmidt (J. VLSI Signal Process., 2007)

Performance Analysis of General-Purpose Computation on Commodity Graphics Hardware: A Case Study Using Bioinformatics. - Weiguo Liu; Bertil Schmidt; Wolfgang Müller-Wittig (J. VLSI Signal Process., 2007)

MPI-HMMER-Boost: Distributed FPGA Acceleration. - John Paul Walters; Xiandong Meng; Vipin Chaudhary; Timothy F. Oliver; Leow Yuan Yeow; Bertil Schmidt; Darran Nathan; Joseph I. Landman (J. VLSI Signal Process., 2007)

GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences. - Chen Chen; Bertil Schmidt; Weiguo Liu; Wolfgang Müller-Wittig (PRIB, 2008)

Accelerating BLASTP on the Cell Broadband Engine. - Huiliang Zhang; Bertil Schmidt; Wolfgang Müller-Wittig (PRIB, 2008)

Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment. - Dadabhai T. Singh; Rahul Trehan; Bertil Schmidt; Timo Bretschneider (BMC Bioinform., 2008)

CBESW: Sequence Alignment on the Playstation 3. - Adrianto Wirawan; Chee Keong Kwoh 001; Nim Tri Hieu; Bertil Schmidt (BMC Bioinform., 2008)

Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA. - Weiguo Liu; Bertil Schmidt; Gerrit Voss; Wolfgang Müller-Wittig (Comput. Phys. Commun., 2008)

Integrating FPGA acceleration into HMMer. - Timothy F. Oliver; Leow Yuan Yeow; Bertil Schmidt (Parallel Comput., 2008)

A Hybrid Computational Grid Architecture for Comparative Genomics. - Aarti Singh; Chen Chen; Weiguo Liu; Wayne P. Mitchell; Bertil Schmidt (IEEE Trans. Inf. Technol. Biomed., 2008)

A Reconfigurable Bloom Filter Architecture for BLASTN. - Yupeng Chen; Bertil Schmidt; Douglas L. Maskell (ARCS, 2009)

MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA. - Yongchao Liu; Bertil Schmidt; Douglas L. Maskell (ASAP, 2009)

Workshop on Using Emerging Parallel Architectures for Computational Science. - Bertil Schmidt; Douglas L. Maskell (ICCS (1), 2009)

Pairwise Distance Matrix Computation for Multiple Sequence Alignment on the Cell Broadband Engine. - Adrianto Wirawan; Bertil Schmidt; Chee Keong Kwoh 001 (ICCS (1), 2009)

Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA. - Yongchao Liu; Bertil Schmidt; Douglas L. Maskell (IPDPS, 2009)

Accelerating error correction in high-throughput short-read DNA sequencing data with CUDA. - Haixiang Shi; Bertil Schmidt; Weiguo Liu; Wolfgang Müller-Wittig (IPDPS, 2009)

A fast hybrid short read fragment assembly algorithm. - Bertil Schmidt; Ranjan Sinha; Bryan Beresford-Smith; Simon J. Puglisi (Bioinform., 2009)

SHREC: a short-read error correction method. - Jan Schröder; Heiko Schröder 001; Simon J. Puglisi; Ranjan Sinha; Bertil Schmidt (Bioinform., 2009)

High performance protein sequence database scanning on the Cell Broadband Engine. - Adrianto Wirawan; Bertil Schmidt; Huiliang Zhang; Chee Keong Kwoh 001 (Sci. Program., 2009)

High Speed Biological Sequence Analysis With Hidden Markov Models on Reconfigurable Platforms. - Timothy F. Oliver; Bertil Schmidt; Yanto Jakop; Douglas L. Maskell (IEEE Trans. Inf. Technol. Biomed., 2009)

Prediction of low coverage prone regions for Illumina sequencing projects using a support vector machine. - Zejun Zheng; Bertil Schmidt; Guillaume Bourque (BIBM, 2010)

MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities. - Yongchao Liu; Bertil Schmidt; Douglas L. Maskell (Bioinform., 2010)

Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures. - Adrianto Wirawan; Chee Keong Kwoh 001; Bertil Schmidt (Bioinform., 2010)

A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware. - Haixiang Shi; Bertil Schmidt; Weiguo Liu; Wolfgang Müller-Wittig (J. Comput. Biol., 2010)

Pattern Recognition in Bioinformatics. - Shandar Ahmad; Madhu Chetty; Bertil Schmidt (Pattern Recognit. Lett., 2010)

CUDA-MEME: Accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units. - Yongchao Liu; Bertil Schmidt; Weiguo Liu; Douglas L. Maskell (Pattern Recognit. Lett., 2010)

Second Workshop on using Emerging Parallel Architectures. - Bertil Schmidt; Douglas L. Maskell (ICCS, 2010)

Quality-score guided error correction for short-read sequencing data using CUDA. - Haixiang Shi; Bertil Schmidt; Weiguo Liu; Wolfgang Müller-Wittig (ICCS, 2010)

Iterative Sparse Matrix-Vector Multiplication for Integer Factorization on GPUs. - Bertil Schmidt; Hans Aribowo; Hoang-Vu Dang (Euro-Par (2), 2011)

Mapping of BLASTP Algorithm onto GPU Clusters. - Weiguo Liu; Bertil Schmidt; Yongchao Liu; Gerrit Voss; Wolfgang Müller-Wittig (ICPADS, 2011)

An Ultrafast Scalable Many-Core Motif Discovery Algorithm for Multiple GPUs. - Yongchao Liu; Bertil Schmidt; Douglas L. Maskell (IPDPS Workshops, 2011)

CRiSPy-CUDA: Computing Species Richness in 16S rRNA Pyrosequencing Datasets with CUDA. - Zejun Zheng; Thuy-Diem Nguyen; Bertil Schmidt (PRIB, 2011)

CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. - Lakshmi Kuttippurathu; Michael Hsing; Yongchao Liu; Bertil Schmidt; Douglas L. Maskell; Kyungjoon Lee; Aibin He; William T. Pu; Sek Won Kong (Bioinform., 2011)

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI. - Yongchao Liu; Bertil Schmidt; Douglas L. Maskell (BMC Bioinform., 2011)

Parallelized short read assembly of large genomes using de Bruijn graphs. - Yongchao Liu; Bertil Schmidt; Douglas L. Maskell (BMC Bioinform., 2011)

Third Workshop on using Emerging Parallel Architectures. - Bertil Schmidt; Douglas L. Maskell (ICCS, 2011)

CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware. - Weiguo Liu; Bertil Schmidt; Wolfgang Müller-Wittig (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Accelerating short read mapping on an FPGA (abstract only). - Yupeng Chen; Bertil Schmidt; Douglas L. Maskell (FPGA, 2012)

An FPGA aligner for short read mapping. - Yupeng Chen; Bertil Schmidt; Douglas L. Maskell (FPL, 2012)

Evaluation of GPU-based Seed Generation for Computational Genomics Using Burrows-Wheeler Transform. - Yongchao Liu; Bertil Schmidt (IPDPS Workshops, 2012)

Long read alignment based on maximal exact match seeds. - Yongchao Liu; Bertil Schmidt (Bioinform., 2012)

CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform. - Yongchao Liu; Bertil Schmidt; Douglas L. Maskell (Bioinform., 2012)

DySC: software for greedy clustering of 16S rRNA reads. - Zejun Zheng; Stefan Kramer 001; Bertil Schmidt (Bioinform., 2012)

The Sliced COO Format for Sparse Matrix-Vector Multiplication on CUDA-enabled GPUs. - Hoang-Vu Dang; Bertil Schmidt (ICCS, 2012)

Fourth Workshop on using Emerging Parallel Architectures. - Bertil Schmidt; Douglas L. Maskell (ICCS, 2012)

Faster GPU-Accelerated Smith-Waterman Algorithm with Alignment Backtracking for Short DNA Sequences. - Yongchao Liu; Bertil Schmidt (PPAM (2), 2013)

Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. - Yongchao Liu; Jan Schröder; Bertil Schmidt (Bioinform., 2013)

A hybrid short read mapping accelerator. - Yupeng Chen; Bertil Schmidt; Douglas L. Maskell (BMC Bioinform., 2013)

CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions. - Yongchao Liu; Adrianto Wirawan; Bertil Schmidt (BMC Bioinform., 2013)

Iterative sparse matrix-vector multiplication for accelerating the block Wiedemann algorithm over GF(2) on multi-graphics processing unit systems. - Bertil Schmidt; Hans Aribowo; Hoang-Vu Dang (Concurr. Comput. Pract. Exp., 2013)

CUDA-enabled Sparse Matrix-Vector Multiplication on GPUs using atomic operations. - Hoang-Vu Dang; Bertil Schmidt (Parallel Comput., 2013)

Reconfigurable Accelerator for the Word-Matching Stage of BLASTN. - Yupeng Chen; Bertil Schmidt; Douglas L. Maskell (IEEE Trans. Very Large Scale Integr. Syst., 2013)

SWAPHI: Smith-waterman protein database search on Xeon Phi coprocessors. - Yongchao Liu; Bertil Schmidt (ASAP, 2014)

Fast dendrogram-based OTU clustering using sequence embedding. - Thuy-Diem Nguyen; Bertil Schmidt; Chee-Keong Kwoh 001 (BCB, 2014)

UPC++ for bioinformatics: A case study using genome-wide association studies. - Jan Christian Kässens; Jorge González-Domínguez; Lars Wienbrandt; Bertil Schmidt (CLUSTER, 2014)

SWAPHI-LS: Smith-Waterman Algorithm on Xeon Phi coprocessors for Long DNA Sequences. - Yongchao Liu; Tuan Tu Tran; Felix Lauenroth; Bertil Schmidt (CLUSTER, 2014)

Hybrid CPU/GPU Acceleration of Detection of 2-SNP Epistatic Interactions in GWAS. - Jorge González-Domínguez; Bertil Schmidt; Jan Christian Kässens; Lars Wienbrandt (Euro-Par, 2014)

SparseHC: A Memory-efficient Online Hierarchical Clustering Algorithm. - Thuy-Diem Nguyen; Bertil Schmidt; Chee Keong Kwoh 001 (ICCS, 2014)

FPGA-based Acceleration of Detecting Statistical Epistasis in GWAS. - Lars Wienbrandt; Jan Christian Kässens; Jorge González-Domínguez; Bertil Schmidt; David Ellinghaus; Manfred Schimmler (ICCS, 2014)

CUDA-Accelerated Alignment of Subsequences in Streamed Time Series Data. - Christian Hundt 002; Bertil Schmidt; Elmar Schömer (ICPP, 2014)

Parallelized Clustering of Protein Structures on CUDA-Enabled GPUs. - Hoang-Vu Dang; Bertil Schmidt; Andreas Hildebrandt 001; Anna Katharina Hildebrandt (PDP, 2014)

GEM: an elastic and translation-invariant similarity measure with automatic trend adjustment. - Christian Hundt 002; Bertil Schmidt; Elmar Schömer; Herbert Göttler; Hoang-Vu Dang (SAC, 2014)

Bit-Parallel Approximate Pattern Matching on the Xeon Phi Coprocessor. - Tuan Tu Tran; Simon Schindel; Yongchao Liu; Bertil Schmidt (SBAC-PAD, 2014)

HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. - Adrianto Wirawan; Robert S. Harris; Yongchao Liu; Bertil Schmidt; Jan Schröder (BMC Bioinform., 2014)

CUSHAW2-GPU: Empowering Faster Gapped Short-Read Alignment Using GPU Computing. - Yongchao Liu; Bertil Schmidt (IEEE Des. Test, 2014)

LightSpMV: Faster CSR-based sparse matrix-vector multiplication on CUDA-enabled GPUs. - Yongchao Liu; Bertil Schmidt (ASAP, 2015)

Accelerating large-scale biological database search on Xeon Phi-based neo-heterogeneous architectures. - Haidong Lan; Weiguo Liu; Bertil Schmidt; Bingqiang Wang (BIBM, 2015)

SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models. - Yongchao Liu; Martin Loewer; Srinivas Aluru; Bertil Schmidt (BIBM, 2015)

SAUCE: A Web-Based Automated Assessment Tool for Teaching Parallel Programming. - Moritz Schlarb; Christian Hundt 002; Bertil Schmidt (Euro-Par Workshops, 2015)

GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences. - Yongchao Liu; Bertil Schmidt (Concurr. Comput. Pract. Exp., 2015)

Large-scale genome-wide association studies on a GPU cluster using a CUDA-accelerated PGAS programming model. - Jorge González-Domínguez; Jan Christian Kässens; Lars Wienbrandt; Bertil Schmidt (Int. J. High Perform. Comput. Appl., 2015)

GPU-accelerated exhaustive search for third-order epistatic interactions in case-control studies. - Jorge González-Domínguez; Bertil Schmidt (J. Comput. Sci., 2015)

High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs. - Jan Christian Kässens; Lars Wienbrandt; Jorge González-Domínguez; Bertil Schmidt; Manfred Schimmler (J. Comput. Sci., 2015)

Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems. - Jorge González-Domínguez; Lars Wienbrandt; Jan Christian Kässens; David Ellinghaus; Manfred Schimmler; Bertil Schmidt (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting. - Thuy-Diem Nguyen; Bertil Schmidt; Zejun Zheng; Chee-Keong Kwoh 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Accelerating Bioinformatics Applications via Emerging Parallel Computing Systems. - Juan Antonio Gómez Pulido; Bertil Schmidt; Wu-chun Feng (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Combining GPU and FPGA technology for efficient exhaustive interaction analysis in GWAS. - Jan Christian Kässens; Lars Wienbrandt; Manfred Schimmler; Jorge González-Domínguez; Bertil Schmidt (ASAP, 2016)

Ultra-Fast Detection of Higher-Order Epistatic Interactions on GPUs. - Daniel Jünger; Christian Hundt 002; Jorge González-Domínguez; Bertil Schmidt (Euro-Par Workshops, 2016)

ParDRe: faster parallel duplicated reads removal tool for sequencing studies. - Jorge González-Domínguez; Bertil Schmidt (Bioinform., 2016)

MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems. - Jorge González-Domínguez; Yongchao Liu; Juan Touriño; Bertil Schmidt (Bioinform., 2016)

rapidGSEA: Speeding up gene set enrichment analysis on multi-core CPUs and CUDA-enabled GPUs. - Christian Hundt 002; Andreas Hildebrandt 001; Bertil Schmidt (BMC Bioinform., 2016)

Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters. - Haidong Lan; Yuandong Chan; Kai Xu; Bertil Schmidt; Shaoliang Peng; Weiguo Liu (BMC Bioinform., 2016)

SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations. - Yongchao Liu; Martin Loewer; Srinivas Aluru; Bertil Schmidt (BMC Syst. Biol., 2016)

CUDA-enabled hierarchical ward clustering of protein structures based on the nearest neighbour chain algorithm. - Hoang-Vu Dang; Bertil Schmidt; Andreas Hildebrandt 001; Tuan Tu Tran; Anna Katharina Hildebrandt (Int. J. High Perform. Comput. Appl., 2016)

Bit-parallel approximate pattern matching: Kepler GPU versus Xeon Phi. - Tuan Tu Tran; Yongchao Liu; Bertil Schmidt (Parallel Comput., 2016)

Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data. - Yongchao Liu; Thomas Hankeln; Bertil Schmidt (IEEE ACM Trans. Comput. Biol. Bioinform., 2016)

Scalable Clustering by Iterative Partitioning and Point Attractor Representation. - Junming Shao; Qinli Yang; Hoang-Vu Dang; Bertil Schmidt; Stefan Kramer 001 (ACM Trans. Knowl. Discov. Data, 2016)

Parallel Pairwise Epistasis Detection on Heterogeneous Computing Architectures. - Jorge González-Domínguez; Sabela Ramos; Juan Touriño; Bertil Schmidt (IEEE Trans. Parallel Distributed Syst., 2016)

CUSHAW Suite: Parallel and Efficient Algorithms for NGS Read Alignment. - Yongchao Liu; Bertil Schmidt (Algorithms for Next-Generation Sequencing Data, 2017)

mD3DOCKxb: An Ultra-Scalable CPU-MIC Coordinated Virtual Screening Framework. - Shaoliang Peng; Xiaoyu Zhang 008; Shunyun Yang; Wenhe Su; Zhiqiang Zhang; Dong Dong; Kai Lu 001; Yutong Lu; Xiangke Liao; Bertil Schmidt; Weiliang Zhu; Kuan-Ching Li (CCGrid, 2017)

S-Aligner: Ultrascalable Read Mapping on Sunway Taihu Light. - Xiaohui Duan; Kai Xu; Yuandong Chan; Christian Hundt 002; Bertil Schmidt; Pavan Balaji; Weiguo Liu (CLUSTER, 2017)

PUNAS: A Parallel Ungapped-Alignment-Featured Seed Verification Algorithm for Next-Generation Sequencing Read Alignment. - Yuandong Chan; Kai Xu; Haidong Lan; Weiguo Liu; Yongchao Liu; Bertil Schmidt (IPDPS, 2017)

SWhybrid: A Hybrid-Parallel Framework for Large-Scale Protein Sequence Database Search. - Haidong Lan; Weiguo Liu; Yongchao Liu; Bertil Schmidt (IPDPS, 2017)

AFS: identification and quantification of species composition by metagenomic sequencing. - Yongchao Liu; Fabian Ripp; Rene Koeppel; Hanno Schmidt; Sören Lukas Hellmann; Mathias Weber; Christopher Felix Krombholz; Bertil Schmidt; Thomas Hankeln (Bioinform., 2017)

MetaCache: context-aware classification of metagenomic reads using minhashing. - André Müller; Christian Hundt 002; Andreas Hildebrandt 001; Thomas Hankeln; Bertil Schmidt (Bioinform., 2017)

Accelerating metagenomic read classification on CUDA-enabled GPUs. - Robin Kobus; Christian Hundt 002; André Müller; Bertil Schmidt (BMC Bioinform., 2017)

CLOVE: classification of genomic fusions into structural variation events. - Jan Schröder; Adrianto Wirawan; Bertil Schmidt; Anthony T. Papenfuss (BMC Bioinform., 2017)

Speed and accuracy improvement of higher-order epistasis detection on CUDA-enabled GPUs. - Daniel Jünger; Christian Hundt 002; Jorge González-Domínguez; Bertil Schmidt (Clust. Comput., 2017)

$ν$-net: Deep Learning for Generalized Biventricular Cardiac Mass and Function Parameters. - Hinrich B. Winther; Christian Hundt 002; Bertil Schmidt; Christoph Czerner; Johann Bauersachs; Frank K. Wacker; Jens Vogel-Claussen (CoRR, 2017)

SAUCE: A web application for interactive teaching and learning of parallel programming. - Christian Hundt 002; Moritz Schlarb; Bertil Schmidt (J. Parallel Distributed Comput., 2017)

Mapping of option pricing algorithms onto heterogeneous many-core architectures. - Shuai Zhang; Zhao Wang; Ying Peng; Bertil Schmidt; Weiguo Liu (J. Supercomput., 2017)

cuBool: Bit-Parallel Boolean Matrix Factorization on CUDA-Enabled Accelerators. - Robin Kobus; Adrian Lamoth; André Müller; Christian Hundt 002; Stefan Kramer 001; Bertil Schmidt (ICPADS, 2018)

Massively Parallel Huffman Decoding on GPUs. - André Weißenberger; Bertil Schmidt (ICPP, 2018)

SPECTR: Scalable Parallel Short Read Error Correction on Multi-core and Many-core Architectures. - Kai Xu; Robin Kobus; Yuandong Chan; Ping Gao 005; Xiangxu Meng; Yanjie Wei; Bertil Schmidt; Weiguo Liu (ICPP, 2018)

WarpDrive: Massively Parallel Hashing on Multi-GPU Nodes. - Daniel Jünger; Christian Hundt 002; Bertil Schmidt (IPDPS, 2018)

Fast and efficient short read mapping based on a succinct hash index. - Haowen Zhang; Yuandong Chan; Kaichao Fan; Bertil Schmidt; Weiguo Liu (BMC Bioinform., 2018)

parSRA: A framework for the parallel execution of short read aligners on compute clusters. - Jorge González-Domínguez; Christian Hundt 002; Bertil Schmidt (J. Comput. Sci., 2018)

AnyDSL: a partial evaluation framework for programming high-performance libraries. - Roland Leißa; Klaas Boesche; Sebastian Hack; Arsène Pérard-Gayot; Richard Membarth; Philipp Slusallek; André Müller; Bertil Schmidt (Proc. ACM Program. Lang., 2018)

LightSpMV: Faster CUDA-Compatible Sparse Matrix-Vector Multiplication Using Compressed Sparse Rows. - Yongchao Liu; Bertil Schmidt (J. Signal Process. Syst., 2018)

Efficient Parallel Sort on AVX-512-Based Multi-Core and Many-Core Architectures. - Zekun Yin; Tianyu Zhang; André Müller; Hui Liu; Yanjie Wei; Bertil Schmidt; Weiguo Liu (HPCC/SmartCity/DSS, 2019)

XLCS: A New Bit-Parallel Longest Common Subsequence Algorithm on Xeon Phi Clusters. - Zekun Yin; Hao Zhang 142; Kai Xu; Yuandong Chan; Shaoliang Peng; Xiaoning Wang; Bertil Schmidt; Weiguo Liu (HPCC/SmartCity/DSS, 2019)

Suffix Array Construction on Multi-GPU Systems. - Florian Büren; Daniel Jünger; Robin Kobus; Christian Hundt 002; Bertil Schmidt (HPDC, 2019)

Gossip: Efficient Communication Primitives for Multi-GPU Systems. - Robin Kobus; Daniel Jünger; Christian Hundt 002; Bertil Schmidt (ICPP, 2019)

Massively Parallel ANS Decoding on GPUs. - André Weißenberger; Bertil Schmidt (ICPP, 2019)

kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers. - Peng Jiang; Jie Luo; Yiqi Wang 009; Pingji Deng; Bertil Schmidt; Xiangjun Tang; Ningjiang Chen; Limsoon Wong; Liang Zhao (Bioinform., 2019)

BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures. - Jikai Zhang; Haidong Lan; Yuandong Chan; Yuan Shang; Bertil Schmidt; Weiguo Liu (Bioinform., 2019)

Massively parallel computation of atmospheric neutrino oscillations on CUDA-enabled accelerators. - Felix Kallenborn; Christian Hundt 002; Sebastian Böser; Bertil Schmidt (Comput. Phys. Commun., 2019)

Dedicated Bioinformatics Analysis Hardware. - Bertil Schmidt; Andreas Hildebrandt 001 (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

cuDTW++: Ultra-Fast Dynamic Time Warping on CUDA-Enabled GPUs. - Bertil Schmidt; Christian Hundt 002 (Euro-Par, 2020)

WarpCore: A Library for fast Hash Tables on GPUs. - Daniel Jünger; Robin Kobus; André Müller; Christian Hundt 002; Kai Xu; Weiguo Liu; Bertil Schmidt (HiPC, 2020)

Reconstruction of Low Energy Neutrino Events with GPUs at IceCube. - Maicon Hieronymus; Bertil Schmidt; Sebastian Böser (ICCS (1), 2020)

SWMapper: Scalable Read Mapper on SunWay TaihuLight. - Kai Xu; Xiaohui Duan; Xiangxu Meng; Xin Li; Bertil Schmidt; Weiguo Liu (ICPP, 2020)

AnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation. - André Müller; Bertil Schmidt; Andreas Hildebrandt 001; Richard Membarth; Roland Leißa; Matthis Kruse; Sebastian Hack (IPDPS, 2020)

Neighbor-list-free molecular dynamics on sunway TaihuLight supercomputer. - Xiaohui Duan; Ping Gao 005; Meng Zhang; Tingjian Zhang; Hongsong Meng; Yuxuan Li; Bertil Schmidt; Haohuan Fu; Lin Gan; Wei Xue 003; Guangwen Yang; Weiguo Liu (PPoPP, 2020)

Cell-list based molecular dynamics on many-core processors: a case study on sunway TaihuLight supercomputer. - Xiaohui Duan; Ping Gao 005; Meng Zhang; Tingjian Zhang; Hongsong Meng; Yuxuan Li; Bertil Schmidt; Haohuan Fu; Lin Gan; Wei Xue 003; Weiguo Liu; Guangwen Yang (SC, 2020)

A big data approach to metagenomics for all-food-sequencing. - Robin Kobus; José Manuel Abuín; André Müller; Sören Lukas Hellmann; Juan Carlos Pichel; Tomás F. Pena; Andreas Hildebrandt 001; Thomas Hankeln; Bertil Schmidt (BMC Bioinform., 2020)

RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads. - Stefan Niebler; André Müller; Thomas Hankeln; Bertil Schmidt (BMC Bioinform., 2020)

Millimeter-Scale and Billion-Atom Reactive Force Field Simulation on Sunway Taihulight. - Ping Gao 005; Xiaohui Duan; Tingjian Zhang; Meng Zhang; Bertil Schmidt; Xun Zhang; Hongliang Sun; Wusheng Zhang; Lin Gan; Wei Xue 003; Haohuan Fu; Weiguo Liu; et al. (IEEE Trans. Parallel Distributed Syst., 2020)

FeatherCNN: Fast Inference Computation with TensorGEMM on ARM Architectures. - Haidong Lan; Jintao Meng 001; Christian Hundt 002; Bertil Schmidt; Minwen Deng; Xiaoning Wang; Weiguo Liu; Yu Qiao 001; Shengzhong Feng (IEEE Trans. Parallel Distributed Syst., 2020)

Accelerating JPEG Decompression on GPUs. - André Weißenberger; Bertil Schmidt (HiPC, 2021)

RNACache: Fast Mapping of RNA-Seq Reads to Transcriptomes Using MinHashing. - Julian Cascitti; Stefan Niebler; André Müller; Bertil Schmidt (ICCS (1), 2021)

MetaCache-GPU: Ultra-Fast Metagenomic Classification. - Robin Kobus; André Müller; Daniel Jünger; Christian Hundt 002; Bertil Schmidt (ICPP, 2021)

CARE: context-aware sequencing read error correction. - Felix Kallenborn; Andreas Hildebrandt 001; Bertil Schmidt (Bioinform., 2021)

RabbitMash: accelerating hash-based genome analysis on modern multi-core architectures. - Zekun Yin; Xiaoming Xu 004; Jinxiao Zhang; Yanjie Wei; Bertil Schmidt; Weiguo Liu (Bioinform., 2021)

RabbitQC: high-speed scalable quality control for sequencing data. - Zekun Yin; Hao Zhang 142; Meiyang Liu; Wen Zhang; Honglei Song; Haidong Lan; Yanjie Wei; Beifang Niu; Bertil Schmidt; Weiguo Liu (Bioinform., 2021)

RabbitQCPlus: More Efficient Quality Control for Sequencing Data. - Lifeng Yan; Zekun Yin; Hao Zhang 142; Zhan Zhao; Mingkai Wang; André Müller; Robin Kobus; Yanjie Wei; Beifang Niu; Bertil Schmidt; Weiguo Liu (BIBM, 2022)

AnySeq/GPU: a novel approach for faster sequence alignment on GPUs. - André Müller; Bertil Schmidt; Richard Membarth; Roland Leißa; Sebastian Hack (ICS, 2022)

Online Event Selection for Mu3e using GPUs. - Valentin Henkys; Bertil Schmidt; Niklaus Berger (ISPDC, 2022)

RabbitV: fast detection of viruses and microorganisms in sequencing data on multi-core architectures. - Hao Zhang 142; Qixin Chang; Zekun Yin; Xiaoming Xu 004; Yanjie Wei; Bertil Schmidt; Weiguo Liu (Bioinform., 2022)

Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data. - Konstantin Bob; David Teschner; Thomas Kemmer; David Gomez-Zepeda; Stefan Tenzer; Bertil Schmidt; Andreas Hildebrandt 001 (BMC Bioinform., 2022)

CARE 2.0: reducing false-positive sequencing error corrections using machine learning. - Felix Kallenborn; Julian Cascitti; Bertil Schmidt (BMC Bioinform., 2022)

RNACache: A scalable approach to rapid transcriptomic read mapping using locality sensitive hashing. - Julian Cascitti; Stefan Niebler; André Müller; Bertil Schmidt (J. Comput. Sci., 2022)

General-purpose GPU hashing data structures and their application in accelerated genomics. - Daniel Jünger; Robin Kobus; André Müller; Christian Hundt 002; Kai Xu; Weiguo Liu; Bertil Schmidt (J. Parallel Distributed Comput., 2022)

FMapper: Scalable read mapper based on succinct hash index on SunWay TaihuLight. - Kai Xu; Xiaohui Duan; André Müller; Robin Kobus; Bertil Schmidt; Weiguo Liu (J. Parallel Distributed Comput., 2022)

Optimization of Reactive Force Field Simulation: Refactor, Parallelization, and Vectorization for Interactions. - Ping Gao 005; Xiaohui Duan; Bertil Schmidt; Wusheng Zhang; Lin Gan; Haohuan Fu; Wei Xue 003; Weiguo Liu; Guangwen Yang (IEEE Trans. Parallel Distributed Syst., 2022)

Automatic Generation of High-Performance Convolution Kernels on ARM CPUs for Deep Learning. - Jintao Meng 001; Chen Zhuang; Peng Chen 035; Mohamed Wahib; Bertil Schmidt; Xiao Wang 004; Haidong Lan; Dou Wu; Minwen Deng; Yanjie Wei; Shengzhong Feng (IEEE Trans. Parallel Distributed Syst., 2022)

Redesigning and Optimizing UCSF DOCK3.7 on Sunway TaihuLight. - Kai Xu; Jinxiao Zhang; Xiaohui Duan; Xiaobo Wan; Niu Huang; Bertil Schmidt; Weiguo Liu; Guangwen Yang (IEEE Trans. Parallel Distributed Syst., 2022)

Faster Segmented Sort on GPUs. - Robin Kobus; Johannes Nelgen; Valentin Henkys; Bertil Schmidt (Euro-Par, 2023)

Automated Identification and Location of Three Dimensional Atmospheric Frontal Systems. - Stefan Niebler; Bertil Schmidt; Holger Tost; Peter Spichtinger (ICCS (2), 2023)

RabbitFX: Efficient Framework for FASTA/Q File Parsing on Modern Multi-Core Platforms. - Hao Zhang 142; Honglei Song; Xiaoming Xu 004; Qixin Chang; Mingkai Wang; Yanjie Wei; Zekun Yin; Bertil Schmidt; Weiguo Liu (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Bio-ESMD: A Data Centric Implementation for Large-Scale Biological System Simulation on Sunway TaihuLight Supercomputer. - Xiaohui Duan; Qi Shao; Junben Weng; Bertil Schmidt; Lin Gan; Guohui Li; Haohuan Fu; Wei Xue 003; Weiguo Liu; Guangwen Yang (IEEE Trans. Parallel Distributed Syst., 2023)

CUDA-accelerated protein electrostatics in linear space. - Thomas Kemmer; Sebastian Hack; Bertil Schmidt; Andreas Hildebrandt 001 (J. Comput. Sci., 2023)

RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures. - Xiaoming Xu 004; Zekun Yin; Lifeng Yan; Huiguang Yi; Hua Wang; Bertil Schmidt; Weiguo Liu (Bioinform., 2023)

Redesign and Accelerate the AIREBO Bond-Order Potential on the New Sunway Supercomputer. - Ping Gao 005; Xiaohui Duan; Bertil Schmidt; Wubing Wan; Jiaxu Guo; Wusheng Zhang; Lin Gan; Haohuan Fu; Wei Xue 003; Weiguo Liu; Guangwen Yang (IEEE Trans. Parallel Distributed Syst., 2023)

Studying Privacy Aspects of Learned Knowledge Bases in the Context of Synthetic and Medical Data. - Xenia Heilmann; Daan Apeldoorn; Konstantin Strauch; Bertil Schmidt; Timm Lilienthal; Torsten Panholzer (GMDS, 2024)

Massively Parallel Inverse Block-sorting Transforms for bzip2 Decompression on GPUs. - André Weißenberger; Bertil Schmidt (ICPP, 2024)

RabbitTrim: Highly Optimized Trimming of Illumina Sequencing Data on Multi-core Platforms. - Mingkai Wang; Zekun Yin; Lifeng Yan; Yang Yang; Fangjin Zhu; Xiaohui Duan; Xin Li; Bertil Schmidt; Weiguo Liu (ISBRA (2), 2024)

RabbitSAlign: Accelerating Short-Read Alignment for CPU-GPU Heterogeneous Platforms. - Lifeng Yan; Zekun Yin; Jinjin Li; Yang Yang; Tong Zhang; Fangjin Zhu; Xiaohui Duan; Bertil Schmidt; Weiguo Liu (ISBRA (2), 2024)

Scalable GPU-Enabled Creation of Three Dimensional Weather Fronts. - Stefan Niebler; Bertil Schmidt; Peter Spichtinger; Holger Tost (PASC, 2024)

gpuPairHMM: High-speed Pair-HMM Forward Algorithm for DNA Variant Calling on GPUs. - Bertil Schmidt; Felix Kallenborn; Alexander Wichmann; Alejandro Chacón; Christian Hundt 002 (CoRR, 2024)

A framework for synthetic diagnostics using energetic-particle orbits in tokamaks. - Henrik Järleblad; Luke Stagner; Mirko Salewski; J. Eriksson; M. Nocente; Bertil Schmidt; M. Rud Larsen (Comput. Phys. Commun., 2024)

CAREx: context-aware read extension of paired-end sequencing data. - Felix Kallenborn; Bertil Schmidt (BMC Bioinform., 2024)

CUDASW++4.0: ultra-fast GPU-based Smith-Waterman protein sequence database search. - Bertil Schmidt; Felix Kallenborn; Alejandro Chacón; Christian Hundt 002 (BMC Bioinform., 2024)

SWBWA: A Highly Efficient NGS Aligner on the New Sunway Architecture. - Lifeng Yan; Zekun Yin; Qixin Chang; Tong Zhang; Zhisong Wang; Xiaohui Duan; Bertil Schmidt; Weiguo Liu (Euro-Par (3), 2025)

cuTeBool: Fast and Scalable Boolean Matrix Factorization on GPUs Using Tensor Cores. - Andrea Beyer; Valentin Henkys; Robin Kobus; Stefan Kramer 001; Bertil Schmidt (ICCS (2), 2025)

SWQC: Efficient sequencing data quality control on the next-generation sunway platform. - Lifeng Yan; Zekun Yin; Tong Zhang; Fangjin Zhu; Xiaohui Duan; Bertil Schmidt; Weiguo Liu (Future Gener. Comput. Syst., 2025)