Bertil Schmidt

Summary

Affiliation: Nanyang Technological University
Country: Singapore

Publications

  1. doi request reprint A fast hybrid short read fragment assembly algorithm
    Bertil Schmidt
    School of Computer Engineering, Nanyang Technological University, Singapore
    Bioinformatics 25:2279-80. 2009
  2. doi request reprint MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities
    Yongchao Liu
    School of Computer Engineering, Nanyang Technological University, Singapore
    Bioinformatics 26:1958-64. 2010
  3. doi request reprint CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform
    Yongchao Liu
    School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore
    Bioinformatics 28:1830-7. 2012
  4. pmc A hybrid short read mapping accelerator
    Yupeng Chen
    School of Computer Engineering, Nanyang Technological University, Singapore, Singapore
    BMC Bioinformatics 14:67. 2013
  5. doi request reprint A parallel algorithm for error correction in high-throughput short-read data on CUDA-enabled graphics hardware
    Haixiang Shi
    School of Computer Engineering, Nanyang Technological University, Singapore
    J Comput Biol 17:603-15. 2010
  6. doi request reprint Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures
    Adrianto Wirawan
    School of Computer Engineering, Nanyang Technological University, Singapore
    Bioinformatics 26:1368-9. 2010
  7. pmc DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI
    Yongchao Liu
    School of Computer Engineering, Nanyang Technological University, 639798, Singapore
    BMC Bioinformatics 12:85. 2011
  8. doi request reprint High speed biological sequence analysis with hidden Markov models on reconfigurable platforms
    Timothy F Oliver
    School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore
    IEEE Trans Inf Technol Biomed 13:740-6. 2009
  9. pmc Parallelized short read assembly of large genomes using de Bruijn graphs
    Yongchao Liu
    School of Computer Engineering, Nanyang Technological University, Singapore
    BMC Bioinformatics 12:354. 2011
  10. ncbi request reprint Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW
    Tim Oliver
    School of Computer Engineering, Nanyang Technological University, Singapore
    Bioinformatics 21:3431-2. 2005

Collaborators

Detail Information

Publications17

  1. doi request reprint A fast hybrid short read fragment assembly algorithm
    Bertil Schmidt
    School of Computer Engineering, Nanyang Technological University, Singapore
    Bioinformatics 25:2279-80. 2009
    ..We show that this approach can achieve an assembly quality at least as good as the graph-based approaches used in the popular Edena and Velvet assembly tools using a moderate amount of computing resources...
  2. doi request reprint MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities
    Yongchao Liu
    School of Computer Engineering, Nanyang Technological University, Singapore
    Bioinformatics 26:1958-64. 2010
    ..Although a large number of algorithms for computing a multiple sequence alignment have been designed, the efficient computation of highly accurate multiple alignments is still a challenge...
  3. doi request reprint CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform
    Yongchao Liu
    School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore
    Bioinformatics 28:1830-7. 2012
    ..The explosive growth of short read datasets poses a challenge to the mapping of short reads to reference genomes, such as the human genome, in terms of alignment quality and execution speed...
  4. pmc A hybrid short read mapping accelerator
    Yupeng Chen
    School of Computer Engineering, Nanyang Technological University, Singapore, Singapore
    BMC Bioinformatics 14:67. 2013
    ....
  5. doi request reprint A parallel algorithm for error correction in high-throughput short-read data on CUDA-enabled graphics hardware
    Haixiang Shi
    School of Computer Engineering, Nanyang Technological University, Singapore
    J Comput Biol 17:603-15. 2010
    ..Our implementation is freely available for download from http://cuda-ec.sourceforge.net ...
  6. doi request reprint Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures
    Adrianto Wirawan
    School of Computer Engineering, Nanyang Technological University, Singapore
    Bioinformatics 26:1368-9. 2010
    ..Availability and Implementation: Source codes in C are publicly available at https://sourceforge.net/projects/distmatcomp/..
  7. pmc DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI
    Yongchao Liu
    School of Computer Engineering, Nanyang Technological University, 639798, Singapore
    BMC Bioinformatics 12:85. 2011
    ..However, these reads are significantly shorter and more error-prone than conventional Sanger shotgun reads. This poses a challenge for the de novo assembly in terms of assembly quality and scalability for large-scale short read datasets...
  8. doi request reprint High speed biological sequence analysis with hidden Markov models on reconfigurable platforms
    Timothy F Oliver
    School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore
    IEEE Trans Inf Technol Biomed 13:740-6. 2009
    ..We describe how this technique leads to significant runtime savings for HMM database scanning on a standard off-the-shelf field-programmable gate array (FPGA)...
  9. pmc Parallelized short read assembly of large genomes using de Bruijn graphs
    Yongchao Liu
    School of Computer Engineering, Nanyang Technological University, Singapore
    BMC Bioinformatics 12:354. 2011
    ..However, existing assemblers require high execution times and a large amount of compute resources to assemble large genomes from quantities of short reads...
  10. ncbi request reprint Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW
    Tim Oliver
    School of Computer Engineering, Nanyang Technological University, Singapore
    Bioinformatics 21:3431-2. 2005
    ..We present a new approach to compute multiple sequence alignments in far shorter time using reconfigurable hardware. This results in an implementation of ClustalW with significant runtime savings on a standard off-the-shelf FPGA...
  11. pmc CBESW: sequence alignment on the Playstation 3
    Adrianto Wirawan
    School of Computer Engineering, Nanyang Technological University, Singapore
    BMC Bioinformatics 9:377. 2008
    ..In this paper, we demonstrate how the PlayStation 3, powered by the Cell Broadband Engine, can be used as a computational platform to accelerate the Smith-Waterman algorithm...
  12. pmc Parallel mutual information estimation for inferring gene regulatory networks on GPUs
    Haixiang Shi
    School of Computer Engineering, Nanyang Technological University, Singapore
    BMC Res Notes 4:189. 2011
    ..abstract:..
  13. doi request reprint A hybrid computational grid architecture for comparative genomics
    Aarti Singh
    School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore
    IEEE Trans Inf Technol Biomed 12:218-25. 2008
    ..The results of this comparison are then used by phenotype--genotype explorer (PheGee). PheGee is a new tool that nominates candidate genes responsible for a given phenotype...
  14. pmc CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions
    Yongchao Liu
    School of Computer Engineering, Nanyang Technological University, Singapore
    BMC Res Notes 3:93. 2010
    ..To accelerate this algorithm, many efforts have been made to develop techniques in high performance architectures, especially the recently emerging many-core architectures and their associated programming models...
  15. pmc CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units
    Yongchao Liu
    School of Computer Engineering, Nanyang Technological University, Singapore
    BMC Res Notes 2:73. 2009
    ..It provides a significant performance improvement for Smith-Waterman-based protein sequence database searches by fully exploiting the compute capability of commonly used CUDA-enabled low-cost GPUs...
  16. ncbi request reprint High-speed multiple sequence alignment on a reconfigurable platform
    Tim Oliver
    School of Computer Engineering, Nanyang Technological University, Singapore
    Int J Bioinform Res Appl 2:394-406. 2006
    ..We have constructed a linear systolic array to perform pairwise sequence distance computations using dynamic programming. This results in an implementation with significant runtime savings on a standard FPGA...
  17. ncbi request reprint PREDNOD, a prediction server for peptide binding to the H-2g7 haplotype of the non-obese diabetic mouse
    Menaka Rajapakse
    Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore, Singapore, 119613
    Autoimmunity 39:645-50. 2006
    ..We have developed a prediction system, PREDNOD, for accurate identification of peptides that bind the MHC molecules constituting the H-2g7 haplotype. PREDNOD is accessible at http://antigen.i2r.a-star.edu.sg/Ag7...