Bertil Schmidt

Summary

Affiliation: Nanyang Technological University
Country: Singapore

Publications

  1. ncbi A fast hybrid short read fragment assembly algorithm
    Bertil Schmidt
    School of Computer Engineering, Nanyang Technological University, Singapore
    Bioinformatics 25:2279-80. 2009
  2. ncbi 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. ncbi 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
  4. ncbi 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
  5. ncbi 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
  6. ncbi 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
  7. ncbi 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
  8. ncbi 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
  9. ncbi CBESW: sequence alignment on the Playstation 3
    Adrianto Wirawan
    School of Computer Engineering, Nanyang Technological University, Singapore
    BMC Bioinformatics 9:377. 2008
  10. ncbi 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

Collaborators

Detail Information

Publications16

  1. ncbi 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. ncbi 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. ncbi 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/ CONTACT: adri0004@ntu.edu.sg..
  4. ncbi 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 ...
  5. ncbi 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...
  6. ncbi 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...
  7. ncbi 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)...
  8. ncbi 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...
  9. ncbi 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...
  10. ncbi 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:..
  11. ncbi 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...
  12. ncbi 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...
  13. ncbi 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...
  14. ncbi 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...
  15. ncbi 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...
  16. ncbi 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...