Bertil Schmidt

Yongchao Liu, Jan Schröder, Bertil Schmidt: Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. Bioinformatics 29(3): 308-315 (2013)

Yupeng Chen, Bertil Schmidt, Douglas L. Maskell: A hybrid short read mapping accelerator. BMC Bioinformatics 14: 67 (2013)

Yongchao Liu, Adrianto Wirawan, Bertil Schmidt: CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions. BMC Bioinformatics 14: 117 (2013)

Bertil Schmidt, Hans Aribowo, Hoang-Vu Dang: 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 25(4): 586-603 (2013)

Yupeng Chen, Bertil Schmidt, Douglas L. Maskell: Reconfigurable Accelerator for the Word-Matching Stage of BLASTN. IEEE Trans. VLSI Syst. 21(4): 659-669 (2013)

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell: CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform. Bioinformatics 28(14): 1830-1837 (2012)

Zejun Zheng, Stefan Kramer, Bertil Schmidt: DySC: software for greedy clustering of 16S rRNA reads. Bioinformatics 28(16): 2182-2183 (2012)

Yongchao Liu, Bertil Schmidt: Long read alignment based on maximal exact match seeds. Bioinformatics 28(18): 318-324 (2012)

Hoang-Vu Dang, Bertil Schmidt: The Sliced COO Format for Sparse Matrix-Vector Multiplication on CUDA-enabled GPUs. Procedia CS 9: 57-66 (2012)

Bertil Schmidt, Douglas L. Maskell: Fourth Workshop on using Emerging Parallel Architectures. Procedia CS 9: 1867-1869 (2012)

Yupeng Chen, Bertil Schmidt, Douglas L. Maskell: Accelerating short read mapping on an FPGA (abstract only). FPGA 2012: 265

Yupeng Chen, Bertil Schmidt, Douglas L. Maskell: An FPGA aligner for short read mapping. FPL 2012: 511-514

Yongchao Liu, Bertil Schmidt: Evaluation of GPU-based Seed Generation for Computational Genomics Using Burrows-Wheeler Transform. IPDPS Workshops 2012: 684-690

Lakshmi Kuttippurathu, Michael Hsing, Yongchao Liu, Bertil Schmidt, Douglas L. Maskell, Kyungjoon Lee, Aibin He, William T. Pu, Sek Won Kong: CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. Bioinformatics 27(5): 715-717 (2011)

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell: DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI. BMC Bioinformatics 12: 85 (2011)

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell: Parallelized short read assembly of large genomes using de Bruijn graphs. BMC Bioinformatics 12: 354 (2011)

Bertil Schmidt, Douglas L. Maskell: Third Workshop on using Emerging Parallel Architectures. Procedia CS 4: 1964-1966 (2011)

Weiguo Liu, Bertil Schmidt, Wolfgang Müller-Wittig: CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware. IEEE/ACM Trans. Comput. Biology Bioinform. 8(6): 1678-1684 (2011)

Bertil Schmidt, Hans Aribowo, Hoang-Vu Dang: Iterative Sparse Matrix-Vector Multiplication for Integer Factorization on GPUs. Euro-Par (2) 2011: 413-424

Weiguo Liu, Bertil Schmidt, Yongchao Liu, Gerrit Voss, Wolfgang Müller-Wittig: Mapping of BLASTP Algorithm onto GPU Clusters. ICPADS 2011: 236-243

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell: An Ultrafast Scalable Many-Core Motif Discovery Algorithm for Multiple GPUs. IPDPS Workshops 2011: 428-434

Zejun Zheng, Thuy-Diem Nguyen, Bertil Schmidt: CRiSPy-CUDA: Computing Species Richness in 16S rRNA Pyrosequencing Datasets with CUDA. PRIB 2011: 37-49

Srinivas Aluru, Sanghamitra Bandyopadhyay, Ümit V. Çatalyürek, Devdatt P. Dubhashi, Phillip H. Jones, Manish Parashar, Bertil Schmidt (Eds.): 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

Adrianto Wirawan, Chee Keong Kwoh, Bertil Schmidt: Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures. Bioinformatics 26(10): 1368-1369 (2010)

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell: MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities. Bioinformatics 26(16): 1958-1964 (2010)

Haixiang Shi, Bertil Schmidt, Weiguo Liu, Wolfgang Müller-Wittig: A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware. Journal of Computational Biology 17(4): 603-615 (2010)

Shandar Ahmad, Madhu Chetty, Bertil Schmidt: Pattern Recognition in Bioinformatics. Pattern Recognition Letters 31(14): 2071-2072 (2010)

Yongchao Liu, Bertil Schmidt, Weiguo Liu, Douglas L. Maskell: CUDA-MEME: Accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units. Pattern Recognition Letters 31(14): 2170-2177 (2010)

Bertil Schmidt, Douglas L. Maskell: Second Workshop on using Emerging Parallel Architectures. Procedia CS 1(1): 1015-1017 (2010)

Haixiang Shi, Bertil Schmidt, Weiguo Liu, Wolfgang Müller-Wittig: Quality-score guided error correction for short-read sequencing data using CUDA. Procedia CS 1(1): 1129-1138 (2010)

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

Jan Schröder, Heiko Schröder, Simon J. Puglisi, Ranjan Sinha, Bertil Schmidt: SHREC: a short-read error correction method. Bioinformatics 25(17): 2157-2163 (2009)

Bertil Schmidt, Ranjan Sinha, Bryan Beresford-Smith, Simon J. Puglisi: A fast hybrid short read fragment assembly algorithm. Bioinformatics 25(17): 2279-2280 (2009)

Adrianto Wirawan, Bertil Schmidt, Huiliang Zhang, Chee Keong Kwoh: High performance protein sequence database scanning on the Cell Broadband Engine. Scientific Programming 17(1-2): 97-111 (2009)

Timothy F. Oliver, Bertil Schmidt, Yanto Jakop, Douglas L. Maskell: High Speed Biological Sequence Analysis With Hidden Markov Models on Reconfigurable Platforms. IEEE Transactions on Information Technology in Biomedicine 13(5): 740-746 (2009)

Yupeng Chen, Bertil Schmidt, Douglas L. Maskell: A Reconfigurable Bloom Filter Architecture for BLASTN. ARCS 2009: 40-49

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell: MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA. ASAP 2009: 121-128

Bertil Schmidt, Douglas L. Maskell: Workshop on Using Emerging Parallel Architectures for Computational Science. ICCS (1) 2009: 861-863

Adrianto Wirawan, Bertil Schmidt, Chee Keong Kwoh: Pairwise Distance Matrix Computation for Multiple Sequence Alignment on the Cell Broadband Engine. ICCS (1) 2009: 954-963

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell: Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA. IPDPS 2009: 1-8

Haixiang Shi, Bertil Schmidt, Weiguo Liu, Wolfgang Müller-Wittig: Accelerating error correction in high-throughput short-read DNA sequencing data with CUDA. IPDPS 2009: 1-8

Dadabhai T. Singh, Rahul Trehan, Bertil Schmidt, Timo Bretschneider: Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment. BMC Bioinformatics 9(S-1) (2008)

Adrianto Wirawan, Chee Keong Kwoh, Nim Tri Hieu, Bertil Schmidt: CBESW: Sequence Alignment on the Playstation 3. BMC Bioinformatics 9 (2008)

Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Müller-Wittig: Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA. Computer Physics Communications 179(9): 634-641 (2008)

Timothy F. Oliver, Leow Yuan Yeow, Bertil Schmidt: Integrating FPGA acceleration into HMMer. Parallel Computing 34(11): 681-691 (2008)

A. Singh, Chen Chen, Weiguo Liu, W. Mitchell, Bertil Schmidt: A Hybrid Computational Grid Architecture for Comparative Genomics. IEEE Transactions on Information Technology in Biomedicine 12(2): 218-225 (2008)

Chen Chen, Bertil Schmidt, Weiguo Liu, Wolfgang Müller-Wittig: GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences. PRIB 2008: 448-459

Huiliang Zhang, Bertil Schmidt, Wolfgang Müller-Wittig: Accelerating BLASTP on the Cell Broadband Engine. PRIB 2008: 460-470

Menaka Rajapakse, Bertil Schmidt, Lin Feng, Vladimir Brusic: Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms. BMC Bioinformatics 8 (2007)

Bertil Schmidt: A survey of desktop grid applications for e-science. IJWGS 3(3): 354-368 (2007)

Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Müller-Wittig: Streaming Algorithms for Biological Sequence Alignment on GPUs. IEEE Trans. Parallel Distrib. Syst. 18(9): 1270-1281 (2007)

Feng Lin, Heiko Schröder, Bertil Schmidt: Solving the Bottleneck Problem in Bioinformatics Computing: An Architectural Perspective. VLSI Signal Processing 48(3): 185-188 (2007)

Weiguo Liu, Bertil Schmidt, Wolfgang Müller-Wittig: Performance Analysis of General-Purpose Computation on Commodity Graphics Hardware: A Case Study Using Bioinformatics. VLSI Signal Processing 48(3): 209-221 (2007)

John Paul Walters, Xiandong Meng, Vipin Chaudhary, Timothy F. Oliver, Leow Yuan Yeow, Bertil Schmidt, Darran Nathan, Joseph I. Landman: MPI-HMMER-Boost: Distributed FPGA Acceleration. VLSI Signal Processing 48(3): 223-238 (2007)

Malcolm Yoke-Hean Low, Weiguo Liu, Bertil Schmidt: A Parallel BSP Algorithm for Irregular Dynamic Programming. APPT 2007: 151-160

Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Müller-Wittig: Molecular Dynamics Simulations on Commodity GPUs with CUDA. HiPC 2007: 185-196

Weiguo Liu, Wolfgang Müller-Wittig, Bertil Schmidt: Performance Predictions for General-Purpose Computation on GPUs. ICPP 2007: 50

Timothy F. Oliver, Leow Yuan Yeow, Bertil Schmidt: High Performance Database Searching with HMMer on FPGAs. IPDPS 2007: 1-7

Adrianto Wirawan, Chee Keong Kwoh, Bertil Schmidt: Parallel DNA Sequence Alignment on the Cell Broadband Engine. PPAM 2007: 1249-1256

Yan Lin Aung, Douglas L. Maskell, Timothy F. Oliver, Bertil Schmidt, William Bong: C-Based Design Methodology for FPGA Implementation of ClustalW MSA. PRIB 2007: 11-18

Jimin Feng, Samarjit Chakraborty, Bertil Schmidt, Weiguo Liu, Unmesh D. Bordoloi: Fast Schedulability Analysis Using Commodity Graphics Hardware. RTCSA 2007: 400-408

Jagath C. Rajapakse, Bertil Schmidt, L. Gwenn Volkert (Eds.): 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

Weiguo Liu, Bertil Schmidt: Mapping of Hierarchical Parallel Genetic Algorithms for Protein Folding onto Computational Grids. IEICE Transactions 89-D(2): 589-596 (2006)

Timothy F. Oliver, Bertil Schmidt, Douglas L. Maskell, Darran Nathan, Ralf Clemens: High-speed Multiple Sequence Alignment on a reconfigurable platform. IJBRA 2(4): 394-406 (2006)

Chunxi Chen, Bertil Schmidt: Constructing large suffix trees on a computational grid. J. Parallel Distrib. Comput. 66(12): 1512-1523 (2006)

Weiguo Liu, Bertil Schmidt: Parallel Pattern-Based Systems for Computational Biology: A Case Study. IEEE Trans. Parallel Distrib. Syst. 17(8): 750-763 (2006)

Menaka Rajapakse, Bertil Schmidt, Vladimir Brusic: Multi-Objective Evolutionary Algorithm for Discovering Peptide Binding Motifs. EvoWorkshops 2006: 149-158

Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Müller-Wittig: GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment. HiPC 2006: 363-374

Timothy F. Oliver, Bertil Schmidt, Yanto Jakop, Douglas L. Maskell: Accelerating the Viterbi Algorithm for Profile Hidden Markov Models Using Reconfigurable Hardware. International Conference on Computational Science (1) 2006: 522-529

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

Timothy F. Oliver, Bertil Schmidt, Darran Nathan, Ralf Clemens, Douglas L. Maskell: Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW. Bioinformatics 21(16): 3431-3432 (2005)

Tong Liu, Bertil Schmidt: Parallel RNA secondary structure prediction using stochastic context-free grammars. Concurrency and Computation: Practice and Experience 17(14): 1669-1685 (2005)

Chunxi Chen, Bertil Schmidt: An adaptive grid implementation of DNA sequence alignment. Future Generation Comp. Syst. 21(7): 988-1003 (2005)

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

Chunxi Chen, Bertil Schmidt: Parallel Construction of Large Suffix Trees on a PC Cluster. Euro-Par 2005: 1227-1236

Timothy F. Oliver, Bertil Schmidt, Douglas L. Maskell: Hyper customized processors for bio-sequence database scanning on FPGAs. FPGA 2005: 229-237

Timothy F. Oliver, Bertil Schmidt, Douglas L. Maskell, Darran Nathan, Ralf Clemens: Multiple Sequence Alignment on an FPGA. ICPADS (2) 2005: 326-330

Menaka Rajapakse, Lonce L. Wyse, Bertil Schmidt, Vladimir Brusic: Deriving Matrix of Peptide-MHC Interactions in Diabetic Mouse by Genetic Algorithm. IDEAL 2005: 440-447

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

Timothy F. Oliver, Bertil Schmidt, Douglas L. Maskell, Achutavarrier Prasad Vinod: A reconfigurable architecture for scanning biosequence databases. ISCAS (5) 2005: 4799-4802

Bertil Schmidt, Lin Feng, Amey V. Laud, Yusdi Santoso: Development of distributed bioinformatics applications with GMP. Concurrency - Practice and Experience 16(9): 945-959 (2004)

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)

Chunxi Chen, Bertil Schmidt: Performance analysis of computational biology applications on hierarchical Grid systems. CCGRID 2004: 426-433

Weiguo Liu, Bertil Schmidt: A Generic Parallel Pattern-Based System for Bioinformatics. Euro-Par 2004: 989-996

Weiguo Liu, Bertil Schmidt: A Tunable Coarse-Grained Parallel Algorithm for Irregular Dynamic Programming Applications. HiPC 2004: 91-100

Chunxi Chen, Bertil Schmidt: Load Balancing for Hierarchical Grid Computing: A Case Study. HiPC 2004: 353-362

Tong Liu, Bertil Schmidt: Parallel RNA Sequence-Structure Alignment. IPDPS 2004

Timothy F. Oliver, Bertil Schmidt: High Performance Biosequence Database Scanning on Reconfigurable Platforms. IPDPS 2004

Chunxi Chen, Bertil Schmidt: Computing Large-Scale Alignments on a Multi-Cluster. CLUSTER 2003: 38-45

Weiguo Liu, Bertil Schmidt: Parallel Design Pattern for Computational Biology and Scientific Computing Applications. CLUSTER 2003: 456-459

Ishfaq Ahmad, Pieter Jonker, Bertil Schmidt, Andreas Uhl: Topic Introduction. Euro-Par 2003: 850

Bertil Schmidt, Lin Feng, Amey V. Laud, Yusdi Santoso: Parallel Detection of Regulatory Elements with gMP. IPDPS 2003: 156

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

Manfred Schimmler, Bertil Schmidt, Hans-Werner Lang, Sven Heithecker: An Area-Efficient Bit-Serial Integer Multiplier. VLSI 2003: 131-137

Bertil Schmidt, Heiko Schröder, Manfred Schimmler: A hybrid architecture for bioinformatics. Future Generation Comp. Syst. 18(6): 855-862 (2002)

Bertil Schmidt, Heiko Schröder, Manfred Schimmler: Massively Parallel Solutions for Molecular Sequence Analysis. IPDPS 2002

Bertil Schmidt, Heiko Schröder, Manfred Schimmler: Tomographic Image Reconstruction on the Instruction Systolic Array. Computers and Artificial Intelligence 20(1) (2001)

Bertil Schmidt, Heiko Schröder: A Hybrid Architecture for Multimedia Processors. Computers and Artificial Intelligence 20(3) (2001)

Bertil Schmidt, Heiko Schröder, Manfred Schimmler: Scanning Biosequence Databases on a Hybrid Parallel Architecture. Euro-Par 2001: 360-370

Bertil Schmidt, Heiko Schröder, Manfred Schimmler: Protein Sequence Comparison on the Instruction Systolic Array. PaCT 2001: 498-509

Bertil Schmidt, Manfred Schimmler: KPROC - An Instruction Systolic Architecture for Parallel Prefix Applications. Scalable Computing: Practice and Experience 3(2) (2000)

Bertil Schmidt: Design of a Parallel Accelerator for Volume Rendering. Euro-Par 2000: 1095-1104

Bertil Schmidt, Manfred Schimmler, Heiko Schröder: A Morphological Approach to Hough Transform on an Instruction Systolic Array. Computers and Artificial Intelligence 18(6) (1999)

Bertil Schmidt, Manfred Schimmler: A Parallel Accelerator Architecture for Multimedia Video Compression. Euro-Par 1999: 950-960

Bertil Schmidt, Manfred Schimmler, Heiko Schröder: Long Operand Arithmetic on Instruction Systolic Computer Architectures and Its Application in RSA Cryptography. Euro-Par 1998: 916-922

Bertil Schmidt, Manfred Schimmler, Heiko Schröder: Morphological Hough Transform on the Instruction Systolic Array. Euro-Par 1997: 798-806

Udo Mahlmeister, Bertil Schmidt, Gerald Sommer: Preattentive Colour Features by Steerable Filters. DAGM-Symposium 1995: 464-472