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Statistical Analysis

TCAG Facilities

Biobanking
Cytogenomics and Genome Resources
DNA Sequencing/Synthesis
Genetic Analysis
Informatics
Microarray Analysis
Statistical Analysis

Selected methodology publications by Statistical Facility staff

  1. RNA-Seq analysis of parietal cortex in Alzheimer's disease reveals alternatively spliced isoforms related to lipid metabolism. JD Mills, T Nalpathamkalam, HIL Jacobs, C Janitz, D Merico, P Hu, M Janitz Neuroscience Letters
    http://dx.doi.org/10.1016/j.neulet.2012.12.042.
  2. Metaphyseal dysplasia with maxillary hypoplasia and brachydactyly is caused by a duplication in RUNX2. P Moffatt, M Ben-Amor, FH Glorieux, P Roschger, K Klaushofer, JA Schwartzentruber, AD Paterson, P Hu, C Marshall, FORGE Canada Consortium, S Fahiminiya, J Majewski, CL Beaulieu, KM Boycott, F Rauch.
    American Journal of Human Genetics doi:10.1016/j.ajhg.2012.12.001
  3. Microarray meta-analysis identifies acute lung injury biomarkers in donor lungs that predict development of primary graft failure in recipients. P Hu*, X Wang*, JJ Haitsma, S Furmli, H Masoom, M Liu, AS Slutsky, J Beyene, CM Greenwood, CC dos Santos.
    Plos One 7, e45506, 2012
  4. SNVerGUI: A desktop tool for variant analysis of next-generation sequencing data. W Wang, W Hu, F Hou, P Hu, Z Wei.
    Journal of Medical Genetics. 0:1-3. doi:10.1136/jmedgenet-2012-101001.
  5. Dynamic pathway analysis of genes associated with blood pressure using whole genome sequence data. P Hu, AD Paterson.
    Proceedings of Genetic Analysis Workshop (GAW18), Stevenson, WA, USA. October 2012.
  6. Association analysis with sequence data using publicly available controls. NM Roslin, A Derkach, LJ Strug.
    Proceedings of Genetic Analysis Workshop (GAW18), Stevenson, WA, USA. October 2012.
  7. Gene network modular-based classification of microarray samples. P Hu, S Bull, H Jiang.
    BMC Bioinformatics13 (Suppl 10), S17, 2012.
  8. Predicting protein functions by relaxation labeling protein interaction network. P Hu, H Jiang, A Emili.
    BMC Bioinformatics 11(Suppl), S64, 2010.
  9. Pathway-based joint effects analysis of rare genetic variants using Genetic Analysis Workshop 17 exon sequence data. P Hu, W Xu, L Chen, X Xing, AD Paterson
    (2011) BMC Proceedings 5(Suppl 9), S45, 2011.
  10. SNVer: a statistical tool for variant calling in analysis of pooling or individual next-generation sequencing data. Nucleic Acids Research, oi:10.1093/nar/gkr599, Z Wei, W Wang, P Hu, GJ Lyon, H Hakonarson
    First published online: August 3, 2011.
  11. Serum Diagnosis of Chronic Fatigue Syndrome Using Array-based Proteomics. Methods of Microarray Data Analysis VI, edited by McConnell, P, Lim, S., and A.J. Cuticchia. P Hu, W Le, S Lim, B Xing, CMT Greenwood, J Beyene
    Scotts Valley, California: Create Space Publishing, 2009
  12. Pathway-based analysis of a genome-wide case-control association study of rheumatoid arthritis. J Beyene, P Hu, JS Hamid, E Parkhomenko, AD Paterson, D Tritchler.
    BMC Proc.2009,Suppl 7:S128.
  13. Scoring of ChIP-seq experiments by modeling large-scale correlated tests. Pingzhao Hu, Zhi Wei, Zhouzhi Wang, Andrew D Paterson, Joseph Beyene, Steve W Scherer
    Proceedings of Critical Assessment of Massive Data Analysis (CAMDA), October, 2009, Chicago, USA.
  14. Using the ratio of means as the effect size measure in combining results of microarray experiments. Pingzhao Hu, Celia MT Greenwood and Joseph Beyene
    BMC Systems Biology 2009, 3:106
  15. A flexible approximate likelihood ratio test for detecting differential expression in microarray data. Ahmed Hossain, Joseph Beyene, Andrew R. Willana, and Pingzhao Hu
    Computational Statistics & Data Analysis 2009, 53:3685-3695.
  16. Chromosomal clustering of periodically expressed genes in plasmodium falciparum. Methods of Microarray Data Analysis V, edited by P McConell, SM Lin and P Hurban. P Hu, CMT Greenwood, CE M'lan, J Beyene
    Springer-Verlag Press, 2007
  17. Identifying cis- and trans-acting single-nucleotide polymorphisms controlling lymphocyte gene expression in humans. Pingzhao Hu, Hui Lan, Wei Xu, Joseph Beyene, Celia MT Greenwood
    BMC Proc. 2007; 1 Suppl 1:S7.
  18. Integrative analysis of gene expression data including an assessment of pathway enrichment for predicting prostate cancer. Pingzhao Hu, Celia MT Greenwood and Joseph Beyene
    Cancer Informatics. 2007; 2:289-300.
  19. Optimal selection of markers for validation or replication from genome-wide association studies. Greenwood CM, Rangrej J, Sun L.
    Genet Epidemiol. 2007;31:396-407.
  20. A hierarchical clustering method for estimating copy number variation. Xing B, Greenwood CM, Bull SB.
    Biostatistics. 2007;8:632-53.
  21. Tests for differential gene expression using weights in oligonucleotide microarray experiments. Pingzhao Hu, Joseph Beyene and Celia MT Greenwood
    BMC Genomics. 2006; 7:33.
  22. Statistical methods for meta-analysis of microarray data: a comparative study. Pingzhao Hu, Celia MT Greenwood and Joseph Beyene
    Information Systems Frontiers 2006; 8:9-20.
  23. Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models. Pingzhao Hu, Celia MT Greenwood and Joseph Beyene
    BMC Bioinformatics. 2005; 6:128.