Holger H Hoos

Summary

Affiliation: University of British Columbia
Country: Canada

Publications

  1. pmc Ensemble-based prediction of RNA secondary structures
    Nima Aghaeepour
    Department of Computer Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
    BMC Bioinformatics 14:139. 2013
  2. pmc An adaptive bin framework search method for a beta-sheet protein homopolymer model
    Alena Shmygelska
    Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
    BMC Bioinformatics 8:136. 2007
  3. pmc RchyOptimyx: cellular hierarchy optimization for flow cytometry
    Nima Aghaeepour
    Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
    Cytometry A 81:1022-30. 2012
  4. pmc RNA STRAND: the RNA secondary structure and statistical analysis database
    Mirela Andronescu
    Department of Computer Science, University of British Columbia, 2366 Main Mall, Vancouver, BC, Canada
    BMC Bioinformatics 9:340. 2008
  5. ncbi request reprint Efficient parameter estimation for RNA secondary structure prediction
    Mirela Andronescu
    Department of Computer Science, University of British Columbia, Vancouver BC V6T 1Z4, Canada
    Bioinformatics 23:i19-28. 2007
  6. pmc Computational RNA secondary structure design: empirical complexity and improved methods
    Rosalia Aguirre-Hernandez
    Institute of Applied Mathematics, University of British Columbia, Vancouver, BC, Canada
    BMC Bioinformatics 8:34. 2007
  7. pmc A replica exchange Monte Carlo algorithm for protein folding in the HP model
    Chris Thachuk
    Department of Computer Science, University of British Columbia, BC, V6T 1Z4, Canada
    BMC Bioinformatics 8:342. 2007
  8. pmc HotKnots: heuristic prediction of RNA secondary structures including pseudoknots
    Jihong Ren
    Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
    RNA 11:1494-504. 2005
  9. pmc Analysis of energy-based algorithms for RNA secondary structure prediction
    Monir Hajiaghayi
    Computer Science Department, University of British Columbia, Vancouver, BC, Canada
    BMC Bioinformatics 13:22. 2012
  10. pmc Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays
    Nima Aghaeepour
    Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
    Bioinformatics 28:1009-16. 2012

Detail Information

Publications16

  1. pmc Ensemble-based prediction of RNA secondary structures
    Nima Aghaeepour
    Department of Computer Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
    BMC Bioinformatics 14:139. 2013
    ..Furthermore, while there is increasing evidence that no prediction algorithm consistently outperforms all others, no work has been done to exploit the complementary strengths of multiple approaches...
  2. pmc An adaptive bin framework search method for a beta-sheet protein homopolymer model
    Alena Shmygelska
    Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
    BMC Bioinformatics 8:136. 2007
    ..This problem plays an important role in the analysis of systems with complex search landscapes, and particularly in the context of ab initio protein structure prediction...
  3. pmc RchyOptimyx: cellular hierarchy optimization for flow cytometry
    Nima Aghaeepour
    Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
    Cytometry A 81:1022-30. 2012
    ....
  4. pmc RNA STRAND: the RNA secondary structure and statistical analysis database
    Mirela Andronescu
    Department of Computer Science, University of British Columbia, 2366 Main Mall, Vancouver, BC, Canada
    BMC Bioinformatics 9:340. 2008
    ..Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures...
  5. ncbi request reprint Efficient parameter estimation for RNA secondary structure prediction
    Mirela Andronescu
    Department of Computer Science, University of British Columbia, Vancouver BC V6T 1Z4, Canada
    Bioinformatics 23:i19-28. 2007
    ..Moreover, the estimation scheme should also be trained using available experimental free energy data in addition to structural data...
  6. pmc Computational RNA secondary structure design: empirical complexity and improved methods
    Rosalia Aguirre-Hernandez
    Institute of Applied Mathematics, University of British Columbia, Vancouver, BC, Canada
    BMC Bioinformatics 8:34. 2007
    ..Such understanding provides the basis for improving the performance of one of the best algorithms for this problem, RNA-SSD, and for characterising its limitations...
  7. pmc A replica exchange Monte Carlo algorithm for protein folding in the HP model
    Chris Thachuk
    Department of Computer Science, University of British Columbia, BC, V6T 1Z4, Canada
    BMC Bioinformatics 8:342. 2007
    ....
  8. pmc HotKnots: heuristic prediction of RNA secondary structures including pseudoknots
    Jihong Ren
    Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
    RNA 11:1494-504. 2005
    ..The HotKnots algorithm has been implemented in C/C++ and is available from http://www.cs.ubc.ca/labs/beta/Software/HotKnots...
  9. pmc Analysis of energy-based algorithms for RNA secondary structure prediction
    Monir Hajiaghayi
    Computer Science Department, University of British Columbia, Vancouver, BC, Canada
    BMC Bioinformatics 13:22. 2012
    ..Our work advances such understanding for the MFE and (pseudo-)MEA-based methods, with respect to the latest datasets and energy parameters...
  10. pmc Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays
    Nima Aghaeepour
    Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada
    Bioinformatics 28:1009-16. 2012
    ..Thus, the value of PFC as a discovery tool is largely wasted...
  11. ncbi request reprint A new algorithm for RNA secondary structure design
    Mirela Andronescu
    Department of Computer Science, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
    J Mol Biol 336:607-24. 2004
    ..The RNA-SSD software is publically available under the name of RNA Designer at the RNASoft website (www.rnasoft.ca)...
  12. pmc Thermodynamically based DNA strand design
    Dan Tulpan
    Department of Computer Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
    Nucleic Acids Res 33:4951-64. 2005
    ..With respect to these measures of quality, our algorithm consistently finds, within reasonable time, sets that are significantly better than previously published sets in the literature...
  13. pmc Correlation between the secondary structure of pre-mRNA introns and the efficiency of splicing in Saccharomyces cerevisiae
    Sanja Rogic
    Department of Computer Science, University of British Columbia, Vancouver, Canada
    BMC Genomics 9:355. 2008
    ..However, no attempts were made to compute a shortened, 'structural' branchpoint distance and thus the functional relationship between this distance and the splicing efficiency remains unknown...
  14. pmc An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem
    Alena Shmygelska
    Department of Computer Science, University of British Columbia, Vancouver, Canada
    BMC Bioinformatics 6:30. 2005
    ....
  15. pmc Rapid cell population identification in flow cytometry data
    Nima Aghaeepour
    Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
    Cytometry A 79:6-13. 2011
    ..Our approach compares favorably to manual analysis by human experts and current state-of-the-art automated gating algorithms. flowMeans is freely available as an open source R package through Bioconductor...
  16. pmc RNAsoft: A suite of RNA secondary structure prediction and design software tools
    Mirela Andronescu
    Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
    Nucleic Acids Res 31:3416-22. 2003
    ..The tools are based on standard thermodynamic models of RNA secondary structure formation. RNAsoft can be found online at http://www.RNAsoft.ca...