Pingzhao Hu

Summary

Affiliation: The Hospital for Sick Children
Country: Canada

Publications

  1. pmc Obesity and prostate cancer: gene expression signature of human periprostatic adipose tissue
    Ricardo Ribeiro
    Molecular Oncology Group, Portuguese Institute of Oncology, ED, Laboratórios Piso 4, Rua Dr, António Bernardino de Almeida 4200 072, Porto, Portugal
    BMC Med 10:108. 2012
  2. pmc Transcriptomic analysis of dystrophin RNAi knockdown reveals a central role for dystrophin in muscle differentiation and contractile apparatus organization
    Mohammad M Ghahramani Seno
    School of Biological Sciences, Royal Holloway University of London, Egham, UK
    BMC Genomics 11:345. 2010
  3. pmc Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models
    Pingzhao Hu
    The Hospital for Sick Children Research Institute, 555 University Ave, Toronto, ON, M5G 1X8, Canada
    BMC Bioinformatics 6:128. 2005
  4. pmc Using the ratio of means as the effect size measure in combining results of microarray experiments
    Pingzhao Hu
    The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
    BMC Syst Biol 3:106. 2009
  5. pmc Identifying cis- and trans-acting single-nucleotide polymorphisms controlling lymphocyte gene expression in humans
    Pingzhao Hu
    Program in Genetics and Genome Biology, The Hospital for Sick Children Research Institute, 15 706 TMDT, 101 College Street, Toronto, Ontario, M5G 1L7, Canada
    BMC Proc 1:S7. 2007
  6. pmc Tests for differential gene expression using weights in oligonucleotide microarray experiments
    Pingzhao Hu
    Program in Genetics and Genomic Biology, The Hospital for Sick Children Research Institute, 15 706 TMDT, Toronto, ON, M5G 1L7, Canada
    BMC Genomics 7:33. 2006
  7. doi request reprint Network analysis of transcriptional responses induced by mesenchymal stem cell treatment of experimental sepsis
    Claudia C dos Santos
    Interdepartmental Division of Critical Care, The Keenan Research Centre of the Li Ka Shing Knowledge Institute of St Michael s Hospital, University of Toronto, Ontario, Canada
    Am J Pathol 181:1681-92. 2012
  8. pmc Microarray meta-analysis identifies acute lung injury biomarkers in donor lungs that predict development of primary graft failure in recipients
    Pingzhao Hu
    The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario, Canada
    PLoS ONE 7:e45506. 2012
  9. pmc Gene network modular-based classification of microarray samples
    Pingzhao Hu
    Department of Computer Science and Engineering, York University, Toronto, M3J 1P3, Canada
    BMC Bioinformatics 13:S17. 2012
  10. doi request reprint The genetic diversity of Epstein-Barr virus in the setting of transplantation relative to non-transplant settings: A feasibility study
    Upton D Allen
    Division of Infectious Diseases, Department of Paediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
    Pediatr Transplant 20:124-9. 2016

Detail Information

Publications40

  1. pmc Obesity and prostate cancer: gene expression signature of human periprostatic adipose tissue
    Ricardo Ribeiro
    Molecular Oncology Group, Portuguese Institute of Oncology, ED, Laboratórios Piso 4, Rua Dr, António Bernardino de Almeida 4200 072, Porto, Portugal
    BMC Med 10:108. 2012
    ..This study aimed to determine the genome-wide expression of genes in PP adipose tissue in obesity/overweight (OB/OW) and prostate cancer patients...
  2. pmc Transcriptomic analysis of dystrophin RNAi knockdown reveals a central role for dystrophin in muscle differentiation and contractile apparatus organization
    Mohammad M Ghahramani Seno
    School of Biological Sciences, Royal Holloway University of London, Egham, UK
    BMC Genomics 11:345. 2010
    ..A study design in which a perfectly matched control cell population is used as reference for transcriptomic studies will give a much more specific insight into the effects of dystrophin deficiency and DMD pathophysiology...
  3. pmc Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models
    Pingzhao Hu
    The Hospital for Sick Children Research Institute, 555 University Ave, Toronto, ON, M5G 1X8, Canada
    BMC Bioinformatics 6:128. 2005
    ..The challenge, however, is in designing and implementing efficient analytic methodologies for combination of data generated by different research groups...
  4. pmc Using the ratio of means as the effect size measure in combining results of microarray experiments
    Pingzhao Hu
    The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
    BMC Syst Biol 3:106. 2009
    ..Moreover, it is widely known that the estimated standard deviations are probably unstable in the commonly used effect size measures (such as standardized mean difference) when sample sizes in each group are small...
  5. pmc Identifying cis- and trans-acting single-nucleotide polymorphisms controlling lymphocyte gene expression in humans
    Pingzhao Hu
    Program in Genetics and Genome Biology, The Hospital for Sick Children Research Institute, 15 706 TMDT, 101 College Street, Toronto, Ontario, M5G 1L7, Canada
    BMC Proc 1:S7. 2007
    ....
  6. pmc Tests for differential gene expression using weights in oligonucleotide microarray experiments
    Pingzhao Hu
    Program in Genetics and Genomic Biology, The Hospital for Sick Children Research Institute, 15 706 TMDT, Toronto, ON, M5G 1L7, Canada
    BMC Genomics 7:33. 2006
    ....
  7. doi request reprint Network analysis of transcriptional responses induced by mesenchymal stem cell treatment of experimental sepsis
    Claudia C dos Santos
    Interdepartmental Division of Critical Care, The Keenan Research Centre of the Li Ka Shing Knowledge Institute of St Michael s Hospital, University of Toronto, Ontario, Canada
    Am J Pathol 181:1681-92. 2012
    ....
  8. pmc Microarray meta-analysis identifies acute lung injury biomarkers in donor lungs that predict development of primary graft failure in recipients
    Pingzhao Hu
    The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario, Canada
    PLoS ONE 7:e45506. 2012
    ..To perform a meta-analysis of gene expression microarray data from animal studies of lung injury, and to identify an injury-specific gene expression signature capable of predicting the development of lung injury in humans...
  9. pmc Gene network modular-based classification of microarray samples
    Pingzhao Hu
    Department of Computer Science and Engineering, York University, Toronto, M3J 1P3, Canada
    BMC Bioinformatics 13:S17. 2012
    ..The statistical challenge for constructing such a predictor is that there are thousands of genes to predict for the disease categories, but only a small number of samples are available...
  10. doi request reprint The genetic diversity of Epstein-Barr virus in the setting of transplantation relative to non-transplant settings: A feasibility study
    Upton D Allen
    Division of Infectious Diseases, Department of Paediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
    Pediatr Transplant 20:124-9. 2016
    ..The results provide the framework for further characterization of EBV strains and related outcomes after organ transplantation. ..
  11. doi request reprint Neuregulin 1-alpha regulates phosphorylation, acetylation, and alternative splicing in lymphoblastoid cells
    Mohammad M Ghahramani Seno
    a The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
    Genome 56:619-25. 2013
    ..Moreover, RPN2, a gene already shown to be dysregulated in breast cancer cells, is also differentially regulated by NRG1-alpha treatment...
  12. ncbi request reprint Computational prediction of cancer-gene function
    Pingzhao Hu
    Program in Proteomics and Bioinformatics, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
    Nat Rev Cancer 7:23-34. 2007
    ....
  13. pmc A high-resolution copy-number variation resource for clinical and population genetics
    Mohammed Uddin
    The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
    Genet Med 17:747-52. 2015
    ..Our aim was to develop a copy-number variation resource from a new population sample that would enable more accurate interpretation of clinical genetics data on this microarray platform and others...
  14. pmc Pathway-based analysis of a genome-wide case-control association study of rheumatoid arthritis
    Joseph Beyene
    Biostatistics Methodology Unit, Research Institute, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
    BMC Proc 3:S128. 2009
    ....
  15. pmc A genotype resource for postmortem brain samples from the Autism Tissue Program
    Richard F Wintle
    Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
    Autism Res 4:89-97. 2011
    ..The genotype and CNV data are provided via the ATP informatics portal as a resource for the autism research community...
  16. pmc Predicting protein functions by relaxation labelling protein interaction network
    Pingzhao Hu
    Department of Computer Science and Engineering, York University, ON, Toronto, Canada
    BMC Bioinformatics 11:S64. 2010
    ..Although many approaches have been developed for this purpose, one of main limitations in most of these methods is that the dependence among functional terms has not been taken into account...
  17. pmc Transcriptomic analysis reveals abnormal muscle repair and remodeling in survivors of critical illness with sustained weakness
    Christopher J Walsh
    Keenan and Li Ka Shing Knowledge Institute of Saint Michael s Hospital, Toronto, Ontario, Canada
    Sci Rep 6:29334. 2016
    ..Our findings provide a pathomolecular basis for sustained ICUAW, implicating aberrant expression of distinct skeletal muscle structural and regenerative genes in early and persistent ICUAW. ..
  18. pmc Association between a multi-locus genetic risk score and inflammatory bowel disease
    Pingzhao Hu
    The Centre for Applied Genomics, The Hospital for Sick Children, 101 College Street, Toronto, ON, Canada
    Bioinform Biol Insights 7:143-52. 2013
    ..015). Our results show that the multi-locus GRS association model can improve the genetic risk assessment on IBD by taking into account both confirmed and as yet unconfirmed disease susceptibility variants...
  19. pmc Using a higher criticism statistic to detect modest effects in a genome-wide study of rheumatoid arthritis
    Elena Parkhomenko
    Biostatistics Methodology Unit, Research Institute, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
    BMC Proc 3:S40. 2009
    ..The goal of higher criticism is to alert the researcher that genetic effects remain to be discovered and to promote the use of more targeted and powerful studies to detect the remaining effects...
  20. pmc Evidence of linkage to chromosome 1 for early age of onset of rheumatoid arthritis and HLA marker DRB1 genotype in NARAC data
    Wei Xu
    Department of Biostatistics, Princess Margaret Hospital, Toronto, Ontario, 610 University Avenue, Room 15 507, Toronto, Ontario, Canada M5G 2M9
    BMC Proc 1:S78. 2007
    ..These results suggest possible gene x gene and gene x environment interactions at chromosome 1 loci and provide directions for further gene mapping...
  21. doi request reprint Gene expression using microarrays in transplant recipients at risk of EBV lymphoproliferation after organ transplantation: preliminary proof-of-concept
    Upton Allen
    Division of Infectious Diseases, The Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
    Pediatr Transplant 13:990-8. 2009
    ..In summary, we demonstrated varying degrees of alignment between levels of VL and gene clusters. Analyses for differential expression of genes showed genes that could be implicated in the pathogenesis of EBV-PTLD...
  22. pmc Genome-wide association study of bipolar disorder in Canadian and UK populations corroborates disease loci including SYNE1 and CSMD1
    Wei Xu
    Neurogenetics Section, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health CAMH, R 32, 250 College Street, Toronto, ON M5T 1R8, Canada
    BMC Med Genet 15:2. 2014
    ..Recently, genome-wide association studies (GWAS) for cases versus controls using single nucleotide polymorphism microarray data have shown promising findings for complex neuropsychiatric disorders, including bipolar disorder (BD)...
  23. doi request reprint Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder
    Mohammed Uddin
    The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
    Nat Genet 46:742-7. 2014
    ..91 × 10(-157); OR = 9.52). Our results suggest that brain-expressed exons under purifying selection should be prioritized in genotype-phenotype studies for ASD and related neurodevelopmental conditions. ..
  24. pmc Pathway-based joint effects analysis of rare genetic variants using Genetic Analysis Workshop 17 exon sequence data
    Pingzhao Hu
    The Centre for Applied Genomics TCAG and Program in Genetics and Genome Biology, The Hospital for Sick Children, 101 College Street, Toronto, ON M5G 1L7, Canada
    BMC Proc 5:S45. 2011
    ..We demonstrate that this approach may be better than studying single rare variants or a gene risk score for identifying individuals with significantly greater risk...
  25. pmc A census of human soluble protein complexes
    Pierre C Havugimana
    Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
    Cell 150:1068-81. 2012
    ....
  26. pmc Markers of survival and metastatic potential in childhood CNS primitive neuro-ectodermal brain tumours: an integrative genomic analysis
    Daniel Picard
    Division of Hematology Oncology, Arthur and Sonia Labatt Brain Tumour Research Centre, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
    Lancet Oncol 13:838-48. 2012
    ..We assessed a large cohort of these rare tumours to identify molecular markers to enhance clinical management of this disease...
  27. pmc A pathway-based association analysis model using common and rare variants
    Lu Cheng
    Department of Biostatistics, Princess Margaret Hospital, 610 University Ave, Toronto, ON M5G 2M9, Canada
    BMC Proc 5:S85. 2011
    ..In this simulated example, we were able to identify several pathways that were potentially associated with the disease status and found that common variants showed stronger genetic effect than rare variants...
  28. pmc Integrative analysis of gene expression data including an assessment of pathway enrichment for predicting prostate cancer
    Pingzhao Hu
    Program in Genetics and Genomic Biology, The Hospital for Sick Children Research Institute, 15 706 TMDT, 101 College Street, Toronto, ON, M5G 1L7, Canada
    Cancer Inform 2:289-300. 2007
    ..This targeted approach can be helpful for revealing information that is not easily visible from the changes in the individual genes...
  29. ncbi request reprint Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling
    Thomas Kislinger
    Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada
    Cell 125:173-86. 2006
    ..This molecular compendium, fully accessible via a searchable web-browser interface, serves as a reliable reference of the expressed tissue and organelle proteomes of a leading model mammal...
  30. doi request reprint Differential gene profiling in acute lung injury identifies injury-specific gene expression
    Claudia C dos Santos
    Thoracic Surgery Research Laboratory, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
    Crit Care Med 36:855-65. 2008
    ..Physiologic and morphologic manifestations of disparate forms of injury are often indistinguishable. We sought to demonstrate that acute lung injury resulting from distinct insults may lead to different gene expression profiles...
  31. pmc Discovering MicroRNA-Regulatory Modules in Multi-Dimensional Cancer Genomic Data: A Survey of Computational Methods
    Christopher J Walsh
    Keenan and Li Ka Shing Knowledge Institute of Saint Michael s Hospital, Toronto, ON, Canada Institute of Medical Sciences and Department of Medicine, University of Toronto, Toronto, ON, Canada
    Cancer Inform 15:25-42. 2016
    ..We highlight strengths and limitations of each of these tools as a practical guide for the computational biologists...
  32. pmc The Histone Methyltransferase Enzyme Enhancer of Zeste Homolog 2 Protects against Podocyte Oxidative Stress and Renal Injury in Diabetes
    Ferhan S Siddiqi
    Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St Michael s Hospital, Toronto, Ontario, Canada
    J Am Soc Nephrol 27:2021-34. 2016
    ..These findings expand the extent to which epigenetic processes affect the diabetic kidney to include antioxidant repair. ..
  33. ncbi request reprint DJ-1/PARK7 Impairs Bacterial Clearance in Sepsis
    Hajera Amatullah
    The Keenan Research Centre for Biomedical Science of the Li Ka Shing Knowledge Institute of St Michael s Hospital, The Keenan Research Centre for Biomedical Science of the Li Ka Shing Knowledge Institute of St Michael s Hospital, Toronto, Ontario, Canada
    Am J Respir Crit Care Med . 2016
    ..DJ-1 is a well-established reactive oxygen species (ROS) scavenger. As cellular ROS status is pivotal to inflammation and bacterial killing, we determined the role of DJ-1 in bacterial sepsis...
  34. pmc Gene expression changes associated with resistance to intravenous corticosteroid therapy in children with severe ulcerative colitis
    Boyko Kabakchiev
    Mount Sinai Hospital, Toronto, Ontario, Canada
    PLoS ONE 5:. 2010
    ..We aimed to determine whether genes expressed in whole blood early following initiation of intravenous corticosteroid treatment can be associated with response...
  35. doi request reprint Salutary effect of resveratrol on sepsis-induced myocardial depression
    Lonneke Smeding
    Department of Medicine and Interdepartmental Division of Critical Care Medicine, The Keenan Research Centre at the Li Ka Shing Knowledge Institute of St Michael s Hospital, University of Toronto, Toronto, Ontario, Canada
    Crit Care Med 40:1896-907. 2012
    ....
  36. pmc NADPH oxidase complex and IBD candidate gene studies: identification of a rare variant in NCF2 that results in reduced binding to RAC2
    Aleixo M Muise
    Division of Gastroenterology, Hepatology, and Nutrition, Department of Paediatrics, Hospital for Sick Children, Toronto, Ontario, Canada
    Gut 61:1028-35. 2012
    ..The aim of this study is to determine if polymorphisms in NOX2 NADPH oxidase complex genes that do not cause CGD are associated with the development of inflammatory bowel disease (IBD)...
  37. pmc Sex, age and generation effects on genome-wide linkage analysis of gene expression in transformed lymphoblasts
    Jagadish Rangrej
    Programs in Genetics and Genome Biology, The Hospital for Sick Children, 101 College Street, TMDT East Tower, Toronto, Ontario M5G 1X8 Canada
    BMC Proc 1:S92. 2007
    ..Many traits differ by age and sex in humans, but genetic analysis of gene expression has typically not included them in the analysis...
  38. pmc Impact of normalization and filtering on linkage analysis of gene expression data
    Joseph Beyene
    Department of Public Health Sciences, University of Toronto, Health Sciences Building 155 College Street, Toronto, Ontario, M5T 3M7, Canada
    BMC Proc 1:S150. 2007
    ..Our results showed that the normalization and filtering algorithms can have a profound influence on genetic analysis of gene expression data...
  39. doi request reprint Gene and miRNA expression profiles in autism spectrum disorders
    Mohammad M Ghahramani Seno
    The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
    Brain Res 1380:85-97. 2011
    ..Our data will provide a valuable resource for discovery purposes and for comparison to other gene expression-based, genome-wide DNA studies and other functional data...
  40. ncbi request reprint Genome-wide association analyses of expression phenotypes
    Gary K Chen
    Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California at San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
    Genet Epidemiol 31:S7-S11. 2007
    ..Finally, for datasets with small sample sizes but a large number of features like the Genetic Analysis Workshop 15 dataset, machine learning approaches may be more practical than traditional parametric approaches...