Raphael Gottardo

Summary

Affiliation: Fred Hutchinson Cancer Research Center
Country: USA

Publications

  1. pmc Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments
    Andrew McDavid
    Department of Statistics, University of Washington, Seattle, WA 98195, USA
    Bioinformatics 29:461-7. 2013
  2. pmc Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data
    Xuekui Zhang
    Statistics Department, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 7:e32095. 2012
  3. pmc An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq
    Eloi Mercier
    Computational Biology Unit, Institut de Recherche Clinique de Montreal, Montreal, Canada
    PLoS ONE 6:e16432. 2011
  4. pmc Comparability and reproducibility of biomedical data
    Yunda Huang
    Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop M2 C200, Seattle, WA 98109 1024, USA
    Brief Bioinform 14:391-401. 2013
  5. pmc Critical assessment of automated flow cytometry data analysis techniques
    Nima Aghaeepour
    Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
    Nat Methods 10:228-38. 2013
  6. ncbi request reprint A flexible and powerful bayesian hierarchical model for ChIP-Chip experiments
    Raphael Gottardo
    Department of Statistics, University of British Columbia, Vancouver, Canada
    Biometrics 64:468-78. 2008
  7. pmc MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis
    Vu T Chu
    Department of Microbiology, University of Washington, Seattle, WA 98195, USA
    Genome Biol 9:R118. 2008
  8. pmc Global panel of HIV-1 Env reference strains for standardized assessments of vaccine-elicited neutralizing antibodies
    Allan DeCamp
    Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    J Virol 88:2489-507. 2014
  9. doi request reprint PICS: probabilistic inference for ChIP-seq
    Xuekui Zhang
    Department of Statistics, University of British Columbia, Vancouver, BC, Canada
    Biometrics 67:151-63. 2011
  10. doi request reprint rMAT--an R/Bioconductor package for analyzing ChIP-chip experiments
    Arnaud Droit
    Institut de Recherches Cliniques de Montreal, 110, avenue des Pins Ouest, Montreal, QC H2W 1R7, Canada
    Bioinformatics 26:678-9. 2010

Collaborators

Detail Information

Publications28

  1. pmc Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments
    Andrew McDavid
    Department of Statistics, University of Washington, Seattle, WA 98195, USA
    Bioinformatics 29:461-7. 2013
    ..However, few analytic tools have been developed specifically for the statistical and analytical challenges of single-cell quantitative polymerase chain reactions data...
  2. pmc Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data
    Xuekui Zhang
    Statistics Department, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 7:e32095. 2012
    ....
  3. pmc An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq
    Eloi Mercier
    Computational Biology Unit, Institut de Recherche Clinique de Montreal, Montreal, Canada
    PLoS ONE 6:e16432. 2011
    ..Our pipeline provides the first complete set of Bioconductor tools for sequence and motif analysis of ChIP-Seq and ChIP-chip data...
  4. pmc Comparability and reproducibility of biomedical data
    Yunda Huang
    Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop M2 C200, Seattle, WA 98109 1024, USA
    Brief Bioinform 14:391-401. 2013
    ..In this article, we review some of the recent developments regarding biomedical reproducibility and comparability and discuss some of the areas where the overall field could be improved. ..
  5. pmc Critical assessment of automated flow cytometry data analysis techniques
    Nima Aghaeepour
    Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
    Nat Methods 10:228-38. 2013
    ....
  6. ncbi request reprint A flexible and powerful bayesian hierarchical model for ChIP-Chip experiments
    Raphael Gottardo
    Department of Statistics, University of British Columbia, Vancouver, Canada
    Biometrics 64:468-78. 2008
    ..In addition, we present a simulation study, which shows that BAC is more powerful than the other four techniques under various simulation scenarios while being robust to model misspecification...
  7. pmc MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis
    Vu T Chu
    Department of Microbiology, University of Washington, Seattle, WA 98195, USA
    Genome Biol 9:R118. 2008
    ..We demonstrate the ability to use MultiExperiment Viewer as a graphical user interface for Bioconductor applications in microarray data analysis by incorporating three Bioconductor packages, RAMA, BRIDGE and iterativeBMA...
  8. pmc Global panel of HIV-1 Env reference strains for standardized assessments of vaccine-elicited neutralizing antibodies
    Allan DeCamp
    Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    J Virol 88:2489-507. 2014
    ..IMC.LucR viruses). This global panel should facilitate highly standardized assessments of vaccine-elicited neutralizing antibodies across multiple HIV-1 vaccine platforms in different parts of the world...
  9. doi request reprint PICS: probabilistic inference for ChIP-seq
    Xuekui Zhang
    Department of Statistics, University of British Columbia, Vancouver, BC, Canada
    Biometrics 67:151-63. 2011
    ..We then use a simulation study to confirm that PICS compares favorably to these methods and is robust to model misspecification...
  10. doi request reprint rMAT--an R/Bioconductor package for analyzing ChIP-chip experiments
    Arnaud Droit
    Institut de Recherches Cliniques de Montreal, 110, avenue des Pins Ouest, Montreal, QC H2W 1R7, Canada
    Bioinformatics 26:678-9. 2010
    ..However, the raw microarray intensities generate a massive amount of data, creating a need for efficient analysis algorithms and statistical methods to identify enriched regions...
  11. ncbi request reprint Flexible empirical Bayes models for differential gene expression
    Kenneth Lo
    Department of Statistics, University of British Columbia, 333 6356 Agricultural Road, Vancouver, BC, Canada V6T 1Z2
    Bioinformatics 23:328-35. 2007
    ..However, to facilitate inference, some unrealistic assumptions have been made. One such assumption is that of a common coefficient of variation across genes, which can adversely affect the resulting inference...
  12. pmc flowClust: a Bioconductor package for automated gating of flow cytometry data
    Kenneth Lo
    Department of Statistics, University of British Columbia, 333 6356 Agricultural Road, Vancouver, BC, V6T1Z2, Canada
    BMC Bioinformatics 10:145. 2009
    ..This is a time-consuming task that ignores the high-dimensionality of FCM data...
  13. doi request reprint Automated gating of flow cytometry data via robust model-based clustering
    Kenneth Lo
    Department of Statistics, University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada
    Cytometry A 73:321-32. 2008
    ..It tends to give more reproducible results, and helps reduce the significant subjectivity and human time cost encountered in manual gating analysis...
  14. ncbi request reprint Bayesian robust inference for differential gene expression in microarrays with multiple samples
    Raphael Gottardo
    Department of Statistics, University of Washington, Box 354322, Seattle, Washington 98195, USA
    Biometrics 62:10-8. 2006
    ..In an experiment with HIV data, our method performed better than these alternatives, on the basis of between-replicate agreement and disagreement...
  15. pmc iBMQ: a R/Bioconductor package for integrated Bayesian modeling of eQTL data
    Greg C Imholte
    Department of Statistics, University of Washington, Seattle, WA 98195, USA, Institut de Recherches Cliniques de Montréal and Université de Montréal, Montreal, Quebec, Canada H2W 1R7, Faculty of Medicine, Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada H3A 1A2 and Vaccine and Infections Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Bioinformatics 29:2797-8. 2013
    ..Bayesian approaches tend to be computationally demanding and require specialized software. As a result, most eQTL studies use univariate methods treating each gene independently, leading to suboptimal results...
  16. pmc Mixture models for single-cell assays with applications to vaccine studies
    Greg Finak
    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center FHCRC, Seattle, WA 98109, USA
    Biostatistics 15:87-101. 2014
    ....
  17. pmc High-throughput flow cytometry data normalization for clinical trials
    Greg Finak
    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109
    Cytometry A 85:277-86. 2014
    ..The normalization framework allows the use of template gates even in the presence of sample-to-sample staining variability, mitigates the subjectivity and bias of manual gating, and decreases the time necessary to analyze large datasets...
  18. pmc Optimizing transformations for automated, high throughput analysis of flow cytometry data
    Greg Finak
    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fariview Ave N, Seattle, WA 98109, USA
    BMC Bioinformatics 11:546. 2010
    ..By making some modelling assumptions about the transformed data, we develop maximum likelihood criteria to optimize parameter choice for these different transformations...
  19. pmc PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data
    Sangsoon Woo
    Vaccine and Infectious Diseases and Public Health Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA
    Bioinformatics 29:2049-50. 2013
    ..We illustrate PING using two paired-end datasets from Saccharomyces cerevisiae and compare its performance with nucleR and ChIPseqR...
  20. doi request reprint Modeling and analysis of ChIP-chip experiments
    Raphael Gottardo
    Department of Statistics, University of British Columbia, Vancouver, BC, Canada
    Methods Mol Biol 567:133-43. 2009
    ..In this chapter, we review some of the issues involved in the analysis of ChIP-chip data and present a few statistical methods that can be used to overcome these issues and improve the detection of DNA-protein binding sites...
  21. ncbi request reprint Probabilistic segmentation and intensity estimation for microarray images
    Raphael Gottardo
    Department of Statistics, University of Washington, Box 354322, Seattle, 98195 4322, USA
    Biostatistics 7:85-99. 2006
    ..These approaches produce comparable results, and both appear to offer some advantages over other methods. We use an HIV experiment to compare our approach to two commercial software products: Spot and Arrayvision...
  22. pmc QUAliFiER: an automated pipeline for quality assessment of gated flow cytometry data
    Greg Finak
    Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    BMC Bioinformatics 13:252. 2012
    ..Gated cell populations and their statistics must be monitored within the context of the experimental run, assay, and the overall study...
  23. pmc B cells with high side scatter parameter by flow cytometry correlate with inferior survival in diffuse large B-cell lymphoma
    Ali Bashashati
    Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada
    Am J Clin Pathol 137:805-14. 2012
    ..This is of particular interest because this biomarker is readily available in most clinical laboratories without significant alteration to existing routine diagnostic strategies or incurring additional costs...
  24. pmc Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial
    Raphael Gottardo
    Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS ONE 8:e75665. 2013
    ..They also generate the hypothesis that IgG to linear epitopes in the V2 and V3 regions of gp120 are part of a complex interplay of immune responses that contributed to protection in RV144. ..
  25. ncbi request reprint A pipeline for automated analysis of flow cytometry data: preliminary results on lymphoma sub-type diagnosis
    Ali Bashashati
    British Columbia Cancer Research Center, Vancouver, Canada
    Conf Proc IEEE Eng Med Biol Soc 2009:4945-8. 2009
    ..Preliminary results show more than 90% accuracy in differentiating between some sub-types of lymphoma. The proposed pipeline also finds biologically meaningful biomarkers that differ between lymphoma subtypes...
  26. pmc A computational framework for the analysis of peptide microarray antibody binding data with application to HIV vaccine profiling
    Greg C Imholte
    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, M2 C200, PO Box 19024, Seattle, WA 98109 1024, United States
    J Immunol Methods 395:1-13. 2013
    ..Data sets from two human clinical trials of candidate HIV-1 vaccines were used to validate the effectiveness of our overall computational framework. ..
  27. ncbi request reprint Statistical analysis of microarray data: a Bayesian approach
    Raphael Gottardo
    University of Washington, Department of Statistics, Box 354322, Seattle, WA 98195 4322, USA
    Biostatistics 4:597-620. 2003
    ..The methods are illustrated using experimental data with prior knowledge. In addition, we present the result of a simulation comparing our methods to well-known statistics and multiple testing adjustments...
  28. pmc Exosomes in human semen carry a distinctive repertoire of small non-coding RNAs with potential regulatory functions
    Lucia Vojtech
    Department of Obstetrics and Gynecology, University of Washington, Seattle, USA
    Nucleic Acids Res 42:7290-304. 2014
    ..Thus, SE could potentially deliver regulatory signals to the recipient mucosa via transfer of small RNA molecules. ..

Research Grants2

  1. The Statistical and Computational Analysis of Flow Cytometry Data
    Raphael Gottardo; Fiscal Year: 2010
    ..The impact of these tools will be to provide better, more reliable, tools for the analysis of flow cytometry data. The domain of application spans all diseases, but current applications are focused on HIV disease and cancer. ..
  2. The Statistical and Computational Analysis of Flow Cytometry Data
    Raphael Gottardo; Fiscal Year: 2010
    ..The impact of these tools will be to provide better, more reliable, tools for the analysis of flow cytometry data. The domain of application spans all diseases, but current applications are focused on HIV disease and cancer. ..