Affiliation: University of Toronto
- 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 datasetNiloofar 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...
- A factor analysis model for functional genomicsRafal 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...
- Efficient p-value estimation in massively parallel testing problemsRafal 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...
- Data-fusion in clustering microarray data: balancing discovery and interpretabilityRafal 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...
- EM-random forest and new measures of variable importance for multi-locus quantitative trait linkage analysisSophia 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...
- Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24Brent 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...
- The utility and predictive value of combinations of low penetrance genes for screening and risk prediction of colorectal cancerSteven 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...
- The quantitative evaluation of functional neuroimaging experiments: the NPAIRS data analysis frameworkStephen 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...