Rafal Kustra

Summary

Affiliation: University of Toronto
Country: Canada

Publications

  1. ncbi Predictive modeling in case-control single-nucleotide polymorphism studies in the presence of population stratification: a case study using Genetic Analysis Workshop 16 Problem 1 dataset
    Niloofar Arshadi
    Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, M5T 3M7, Canada
    BMC Proc 3:S60. 2009
  2. ncbi A factor analysis model for functional genomics
    Rafal Kustra
    Public Health Sciences, University of Toronto, Toronto, ON, Canada
    BMC Bioinformatics 7:216. 2006
  3. ncbi Efficient p-value estimation in massively parallel testing problems
    Rafal Kustra
    Department of Public Health Sciences, University of Toronto, Toronto, ON, Canada
    Biostatistics 9:601-12. 2008
  4. ncbi Data-fusion in clustering microarray data: balancing discovery and interpretability
    Rafal Kustra
    Department of Public Health Sciences, University of Toronto, Health Sciences Building, Toronto, Ontario, Canada
    IEEE/ACM Trans Comput Biol Bioinform 7:50-63. 2010
  5. ncbi EM-random forest and new measures of variable importance for multi-locus quantitative trait linkage analysis
    Sophia S F Lee
    Department of Public Health Sciences, University of Toronto, Toronto M5T3M7, Canada
    Bioinformatics 24:1603-10. 2008
  6. ncbi Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24
    Brent W Zanke
    Cancer Care Ontario, 620 University Avenue, Toronto, Ontario M5G 1L7, Canada
    Nat Genet 39:989-94. 2007
  7. ncbi The utility and predictive value of combinations of low penetrance genes for screening and risk prediction of colorectal cancer
    Steven J Hawken
    Department of Epidemiology and Community Medicine, University of Ottawa, Ottawa, ON, Canada
    Hum Genet 128:89-101. 2010
  8. ncbi The quantitative evaluation of functional neuroimaging experiments: the NPAIRS data analysis framework
    Stephen C Strother
    Department of Radiology, University of Minnesota, Minneapolis, Minnesota 55455, USA
    Neuroimage 15:747-71. 2002

Collaborators

Detail Information

Publications8

  1. ncbi Predictive modeling in case-control single-nucleotide polymorphism studies in the presence of population stratification: a case study using Genetic Analysis Workshop 16 Problem 1 dataset
    Niloofar Arshadi
    Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, M5T 3M7, Canada
    BMC Proc 3:S60. 2009
    ..The highest accuracy is achieved with the model adjusted for population stratification, when the genetic axes of variation are included among the set of predictors, although this may be misleading given the confounding effects...
  2. ncbi A factor analysis model for functional genomics
    Rafal Kustra
    Public Health Sciences, University of Toronto, Toronto, ON, Canada
    BMC Bioinformatics 7:216. 2006
    ..While biologically plausible, this is both statistically and computationally challenging. Typical approaches are computationally expensive and ignore correlations among expression profiles and functional categories...
  3. ncbi Efficient p-value estimation in massively parallel testing problems
    Rafal Kustra
    Department of Public Health Sciences, University of Toronto, Toronto, ON, Canada
    Biostatistics 9:601-12. 2008
    ..The results show enormous computational savings as compared to evaluating a full set of permutations, with little decrease in accuracy...
  4. ncbi Data-fusion in clustering microarray data: balancing discovery and interpretability
    Rafal Kustra
    Department of Public Health Sciences, University of Toronto, Health Sciences Building, Toronto, Ontario, Canada
    IEEE/ACM Trans Comput Biol Bioinform 7:50-63. 2010
    ..Our results indicate that a data-fusion clustering leads to more stable, biologically relevant clusters that are still representative of the experimental data...
  5. ncbi EM-random forest and new measures of variable importance for multi-locus quantitative trait linkage analysis
    Sophia S F Lee
    Department of Public Health Sciences, University of Toronto, Toronto M5T3M7, Canada
    Bioinformatics 24:1603-10. 2008
    ..We define new VI indices that borrow information from linked markers using the correlation structure inherent in IBD linkage data...
  6. ncbi Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24
    Brent W Zanke
    Cancer Care Ontario, 620 University Avenue, Toronto, Ontario M5G 1L7, Canada
    Nat Genet 39:989-94. 2007
    ..i.): 1.07-1.26; P = 5.05 x 10(-4)). A summary across all seven studies at the 8q24 locus was highly significant (OR = 1.17, c.i.: 1.12-1.23; P = 3.16 x 10(-11)). This locus has also been implicated in prostate cancer...
  7. ncbi The utility and predictive value of combinations of low penetrance genes for screening and risk prediction of colorectal cancer
    Steven J Hawken
    Department of Epidemiology and Community Medicine, University of Ottawa, Ottawa, ON, Canada
    Hum Genet 128:89-101. 2010
    ..Further genotyping and many more samples will be required, and indeed the discovery of many more risk loci associated with CRC before the question of the potential utility of germline genomic profiling can be definitively answered...
  8. ncbi The quantitative evaluation of functional neuroimaging experiments: the NPAIRS data analysis framework
    Stephen C Strother
    Department of Radiology, University of Minnesota, Minneapolis, Minnesota 55455, USA
    Neuroimage 15:747-71. 2002
    ..We propose the NPAIRS framework as a validation tool for testing and optimizing methodological choices and tools in functional neuroimaging...