Research Topics

Ryan Brinkman

Summary

Affiliation: British Columbia
Country: Canada

Publications

  1. ncbi OntoFox: web-based support for ontology reuse
    Zuoshuang Xiang
    Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    BMC Res Notes 3:175. 2010
  2. ncbi flowCore: a Bioconductor package for high throughput flow cytometry
    Florian Hahne
    Life Sciences Department, Computational Biology Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 1024, USA
    BMC Bioinformatics 10:106. 2009
  3. ncbi 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
  4. ncbi FuGEFlow: data model and markup language for flow cytometry
    Yu Qian
    Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
    BMC Bioinformatics 10:184. 2009
  5. ncbi Data reduction for spectral clustering to analyze high throughput flow cytometry data
    Habil Zare
    Terry Fox Laboratory, BC Cancer Agency, 675 W 10th Ave, Vancouver, BC, Canada
    BMC Bioinformatics 11:403. 2010
  6. ncbi Modeling biomedical experimental processes with OBI
    Ryan R Brinkman
    British Columbia Cancer Agency, Vancouver, Canada
    J Biomed Semantics 1:S7. 2010
  7. ncbi Flow cytometry data standards
    Josef Spidlen
    Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada
    BMC Res Notes 4:50. 2011
  8. ncbi 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

Research Grants

  1. Bioinformatics Standards for Flow Cytometry
    Ryan Brinkman; Fiscal Year: 2007

Collaborators

  • Kenneth Lo
  • Ali Bashashati
  • Josef Spidlen
  • Parisa Shooshtari
  • Zuoshuang Xiang
  • Habil Zare
  • Yu Qian
  • Florian Hahne
  • Tobias R Kollmann
  • Yongqun He
  • Melanie Courtot
  • Alan Ruttenberg
  • Arvind Gupta
  • Perry Haaland
  • Errol Strain
  • Robert Gentleman
  • Frank J Manion
  • Byron Ellis
  • Richard H Scheuermann
  • Peter Wilkinson
  • Olga Tchuvatkina
  • Andrew R Jones
  • RAFICK PIERRE SEKALY
  • Nolwenn LeMeur
  • Deepayan Sarkar
  • Maura Gasparetto

Detail Information

Publications8

  1. ncbi OntoFox: web-based support for ontology reuse
    Zuoshuang Xiang
    Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    BMC Res Notes 3:175. 2010
    ..abstract:..
  2. ncbi flowCore: a Bioconductor package for high throughput flow cytometry
    Florian Hahne
    Life Sciences Department, Computational Biology Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 1024, USA
    BMC Bioinformatics 10:106. 2009
    ..However, data management and data analysis methods have not advanced sufficiently far from the initial small-scale studies to support modeling in the presence of multiple covariates...
  3. ncbi 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...
  4. ncbi FuGEFlow: data model and markup language for flow cytometry
    Yu Qian
    Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
    BMC Bioinformatics 10:184. 2009
    ..We have extended FuGE object model to accommodate flow cytometry data and metadata...
  5. ncbi Data reduction for spectral clustering to analyze high throughput flow cytometry data
    Habil Zare
    Terry Fox Laboratory, BC Cancer Agency, 675 W 10th Ave, Vancouver, BC, Canada
    BMC Bioinformatics 11:403. 2010
    ..To address this issue, we have modified spectral clustering by adding an information preserving sampling procedure and applying a post-processing stage. We call this entire algorithm SamSPECTRAL...
  6. ncbi Modeling biomedical experimental processes with OBI
    Ryan R Brinkman
    British Columbia Cancer Agency, Vancouver, Canada
    J Biomed Semantics 1:S7. 2010
    ..AVAILABILITY : OBI is available at http://purl.obolibrary.org/obo/obi/2009-11-02/obi.owl...
  7. ncbi Flow cytometry data standards
    Josef Spidlen
    Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada
    BMC Res Notes 4:50. 2011
    ..abstract:..
  8. ncbi 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...

Research Grants4

  1. Bioinformatics Standards for Flow Cytometry
    Ryan Brinkman; Fiscal Year: 2007
    ..We anticipate that this work will also stimulate the development of further commercial and academic implementations. ..